Search results for: irish dairy cattle

Authors: L. A. Bosnea, T. Moschakis, C. Biliaderis

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Two probiotic strains of Lactobacillus paracasei subsp. paracasei (E6) and Lactobacillus paraplantarum (B1), isolated from traditional Greek dairy products, were microencapsulated by complex coacervation using whey protein isolate (WPI, 3% w/v) and gum arabic (GA, 3% w/v) solutions mixed at different polymer ratio (1:1, 2:1 and 4:1). The effect of total biopolymer concentration on cell viability was assessed using WPI and GA solutions of 1, 3 and 6% w/v at a constant ratio of 2:1. Also, several parameters were examined for optimization of the microcapsule formation, such as inoculum concentration and the effect of ionic strength. The viability of the bacterial cells during heat treatment and under simulated gut conditions was also evaluated. Among the different WPI/GA weight ratios tested (1:1, 2:1, and 4:1), the highest survival rate was observed for the coacervate structures made with the ratio of 2:1. The protection efficiency at low pH values is influenced by both concentration and the ratio of the added biopolymers. Moreover, the inoculum concentration seems to affect the efficiency of microcapsules to entrap the bacterial cells since an optimum level was noted at less than 8 log cfu/ml. Generally, entrapment of lactobacilli in the complex coacervate structure enhanced the viability of the microorganisms when exposed to a low pH environment (pH 2.0). Both encapsulated strains retained high viability in simulated gastric juice (>73%), especially in comparison with non-encapsulated (free) cells (<19%). The encapsulated lactobacilli also exhibited enhanced viability after 10–30 min of heat treatment (65oC) as well as at different NaCl concentrations (pH 4.0). Overall, the results of this study suggest that complex coacervation with WPI/GA has a potential to deliver live probiotics in low pH food systems and fermented dairy products; the complexes can dissolve at pH 7.0 (gut environment), releasing the microbial cells.

Keywords: probiotic, complex coacervation, whey, encapsulation

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Authors: Aliasghar Golmohammadian, Sona Rostampour Yasouri

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One of the most important intestinal pathogenic strains is E. coli O₁₅₇:H₇. This pathogenic bacterium is transmitted to humans through water and food. E. coli O₁₅₇:H₇ is the main cause of Hemorrhagic colitis (HC), Hemolytic Uremic Syndrome (HUS), Thrombotic Thrombocytopenic Purpura (TTP) and in some cases death. Since E. coli O₁₅₇:H₇ can be transmitted through the consumption of different foods, including vegetables, agricultural products, and fresh dairy products, this study aims to identify and isolate E. coli O₁₅₇:H₇ from wastewater by PCR technique. One hundred twenty samples of water and wastewater were collected by Falcom Sterile from Shahrood and Neka cities. The samples were checked for colony formation after appropriate centrifugation and cultivation in the specific medium of Sorbitol MacConkey Agar (SMAC) and other diagnostic media of E. coli O₁₅₇:H₇. Also, the plates were observed macroscopically and microscopically. Then, the necessary phenotypic tests were performed on the colonies, and finally, after DNA extraction, the PCR technique was performed with specific primers related to rfbE and stx2 genes. The number of 5 samples (6%) out of all the samples examined were determined positive by PCR technique with observing the bands related to the mentioned genes on the agarose gel electrophoresis. PCR is a fast and accurate method to identify the bacteria E. coli O₁₅₇:H₇. Considering that E. coli bacteria is a resistant bacteria and survives in water and food for weeks and months, the PCR technique can provide the possibility of quick detection of contaminated water. Moreover, it helps people in the community control and prevent the transfer of bacteria to healthy and underground water and agricultural and even dairy products.

Keywords: E. coli O₁₅₇:H₇, PCR, water, wastewater

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Authors: Farideh Tabatabei-Yazdi, Fereshteh Falah, Alireza Vasiee

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Nowadays, production of functional foods has become very essential. Inulin is one of the most functional hydrocolloid compounds used in such products. In the present study, the production of a synbiotic yogurt containing 1, 2.5, and 5% (w/v) inulin has been investigated. The yogurt was fermented with Lactobacillus brevis PML1 derived from Tarkhineh, an Iranian cereal-dairy fermented food. Furthermore, the physicochemical properties, antioxidant activity, sensory attributes, and microbial viability properties were investigated on the 0th, 7th, and 14th days of storage after fermentation. The viable cells of L. brevis PML1 reached 108 CFU/g, and the product resisted to simulated digestive juices. Moreover, the synbiotic yogurt impressively increased the production of antimicrobial compounds and had the most profound antimicrobial effect on S. typhimurium. The physiochemical properties were in the normal range, and the fat content of the synbiotic yogurt was reduced remarkably. The antioxidant capacity of the fermented yogurt was significantly increased (p<0:05), which was equal to those of DPPH (69:18±1:00%) and BHA (89:16±2:00%). The viability of L. brevis PML1 was increased during storage. Sensory analysis showed that there were significant differences in terms of the impressive parameters between the samples and the control (p<0:05). Addition of 2.5% inulin not only improved the physical properties but also retained the viability of the probiotic after 14 days of storage, in addition to the viability of L. brevis with a viability count above 6 log CFU/g in the yogurt. Therefore, a novel synbiotic product containing L. brevis PML1, which can exert the desired properties, can be used as a suitable carrier for the delivery of the probiotic strain, exerting its beneficial health effects.

Keywords: functional food, lactobacillus brevis, symbiotic yogurt, physiochemical properties

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Authors: Alazar Nebyou, Sujata Pandit

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Lactic acid bacteria (LAB) are essential ingredients in probiotic foods, intestinal microflora, and dairy products that are capable of coping up with harsh gastrointestinal tract conditions and are available in a variety of environments. The objective of this study is to evaluate the probiotic property of LAB isolated from bovine milk. Milk samples were collected from local dairy farms. Samples were obtained using sterile test tubes and transported to a laboratory in the icebox for further biochemical characterization. Preliminary physiological and biochemical identification of LAB isolates was conducted by growing on MRS agar after ten-fold serial dilution. Seven of the best isolates were selected for the evaluation of the probiotic property. The LAB isolates were checked for resistance to antibiotics and their antimicrobial activity by disc diffusion assay and agar well diffusion assay respectively. Bile salt hydrolase activity of isolates was studied by growing isolates in a BSH medium with bile salt. Cell surface property of isolates was assayed by studying their autoaggregation and coaggregation percentage with S. aerues. All isolates were found BSH positive. In addition, BCM2 and BGM1 were susceptible to all antibiotic disks except BBM1 which was resistant to all antibiotic disks. BCM1 and BGM1 had the highest autoaggregation and coaggregation potential respectively. Since all LAB isolates showed gastrointestinal tolerance and good cell surface property they could be considered as good potential probiotic candidates for treatment and probiotic starter culture preparation.

Keywords: probiotic, aggregation, lactic acid bacteria, antimicrobial activity

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Authors: Omnia M.Kandil, Noha M. F. Hassan, Doaa Sedky, Hatem A. Shalaby, Heba M. Ashry, Nadia M. T. Abu El Ezz, Sahar M. Kandeel, Mohamed S. Abdelfattah Ying L, Ebtesam M. Al-Olayan

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The cestode, Taenia saginata is a zoonotic tapeworm that it’s larval stage which known as Cysticercus bovis cause cyst formation in cattle’s organs such as heart, lung, liver, tongue, esophagus and diaphragm muscle, despite the infected cattle may show no clinical signs. In view of considerable interest in developing cysticidal drugs including those from medicinal plants, because of their consideration as eco-friendly and biodegradable as well as having multiple bioactive compounds that may translate to multiple mechanisms in killing the parasites. This study was achieved to evaluate, for the first time, the efficacy of methanolic extract of Balanites aegyptiaca fruits and Moringa oleifera seeds against metacestode larval stage of the cestode Taenia saginata in BALB/c mice compared with commonly used anthelmintic albendazole and assigning the level of tumor necrosis factor (TNF-α) to monitor immune and inflammatory response of experimentally infected animals. The results revealed a marked decrease in the numbers of cysticerci found in all treated mice groups and up to 88% reduction was achieved in the B. aegyptiaca treated group; higher than that was recorded in both M. oleifera (72.23%) and albendazole treated ones (80.56%). The cysts of the treated groups were smaller of the control one. Besides, the mean concentration of TNF-α following treatment with Balanites and Moringa extracts, was higher but not significant difference than that in the untreated infected control one (P<0.05), evidence for inflammation and cyst damage. It can be concluded that the in vivo efficacy of M. oleifera extract was comparable to a commercial anthelmintic, and the B. aegyptiaca extract was superior in the reduction of cysticerci numbers.

Keywords: Balanites aeggyptica, Moringa oleifera, cysticercosis, BALB/C mice

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Authors: Amir Saber Gharamaleki, Beitollah Alipour, Zeinab Faghfoori, Ahmad YariKhosroushahi

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Colorectal cancer (CRC) is one of the most prevalent cancers and intestinal microbial community plays an important role in colorectal tumorigenesis. Probiotics have recently been assessed as effective anti-proliferative agents and thus this study was performed to examine whether CRC undergo apoptosis by treating with isolated Iranian native dairy yeast, Kluyveromyces marxianus YAS, secretion metabolites. The cytotoxicity assessments on cells (HT-29, Caco-2) were accomplished through 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay as well as qualitative DAPI (4',6-diamidino-2-phenylindole staining) and quantitative (flow cytometry assessments) evaluations of apoptosis. To evaluate the main mechanism of apoptosis, Real time PCR method was applied. Kluyveromyces marxianus YAS secretions (IC50) showed significant cytotoxicity against HT-29 and Caco-2 cancer cell lines (66.57 % and 66.34 % apoptosis) similar to 5-Fluorouracil (5-FU) while apoptosis only was developed in 27.57 % of KDR normal cells. The prophylactic effects of Kluyveromyces marxianus (PTCC 5195), as a reference yeast, was not similar to Kluyveromyces marxianus YAS indicating strain dependency of bioactivities on CRC disease prevention. Based on real time PCR results, the main cytotoxicity is related to apoptosis phenomenon and the core related mechanism is depended on the overexpression of BAX, CASP 9, CASP 8 and CASP 3 inducing apoptosis genes. However, several investigations should be conducted to precisely determine the effective compounds to be used as anticancer therapeutics in the future.

Keywords: anticancer, anti-proliferative, apoptosis, cytotoxicity, yeast

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Authors: Alok Kumar, Hari Ram, Lebin Thomas, Ved Pal Singh

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Organic solvent tolerant amylases and proteases of microbial origin are in great demand for their application in transglycosylation of water-insoluble flavanoids and in peptide synthesizing reaction in organic media. Most of the amylases and proteases are unstable in presence of organic solvent. In the present work two different bacterial strains M-11 and VP-07 were isolated from the soil sample of a dairy farm in Delhi, India, for the efficient production of extracellular amylase and protease through their screening on starch agar (SA) and skimmed milk agar (SMA) plates, respectively. Both the strains (M-11 and VP-07) were identified based on morphological, biochemical and 16S rRNA gene sequencing methods. After analysis through Ez-Taxon software, the strains M-11 and VP-07 were found to have maximum pairwise similarity of 98.63% and 100% with Bacillus subtilis subsp. inaquosorum BGSC 3A28 and Bacillus anthracis ATCC 14578 and were therefore identified as Bacillus sp. UKS1 and Bacillus sp. UKS2, respectively. Time course study of enzyme activity and bacterial growth has shown that both strains exhibited typical sigmoid growth behavior and maximum production of amylase (180 U/ml) and protease (78 U/ml) by these strains (UKS1 and UKS2) was commenced during stationary phase of growth at 24 and 20 h, respectively. Thereafter, both amylase and protease were tested for their tolerance towards organic solvents and were found to be active as well stable in p-xylene (130% and 115%), chloroform (110% and 112%), isooctane (119% and 107%), benzene (121% and 104%), n-hexane (116% and 103%) and toluene (112% and 101%, respectively). Owing to such properties, these enzymes can be exploited for their potential application in industries for organic synthesis.

Keywords: amylase, enzyme activity, industrial applications, organic solvent tolerant, protease

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Authors: Ramūnas Antanaitis, Lina Anskienė, Robertas Stoškus

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This study was conducted during 2021.05.01 – 2021.08.31 at the Lithuanian University of health sciences and one Lithuanian dairy farm with 500 dairy cows (55.911381565736, 21.881321760608195). Average calving – 50 cows per month. Cows (n=20) in the treatment group (TG) were fed with feed supplement Optipartum C+ 200 (Enzymes: Alfa- Amylase 57 Units; Beta-Glucanase 107 Units) from 21 days before calving till 30 days after calving with feeding rate 200g/cow/day. Cows in the control group (CG) were fed a feed ration without feed supplement. Measurements started from 6 days before calving and continued till 21 days after calving. The following indicators were registered: with the RumiWatch System: Rumination time; Eating time; Drinking time; Rumination chews; Eating chews; Drinking gulps; Bolus; Chews per minute; Chews per bolus. With SmaXtec system - the temperature, pH of the contents of cows' reticulorumens and cows' activity. According to our results, we found that feeding of cows, from 21 days before calving to 30 days after calving, with a feed supplement with alfa- amylase and beta-glucanase (Optipartum C+ 200) (with dose 200g/cow/day) can produce an increase in: 9% rumination time and eating time, 19% drinking time, 11% rumination chews, 16% eating chews,13% number of boluses per rumination, 5% chews per minute and 16% chews per bolus. We found 1.28 % lower reiticulorumen pH and 0.64% lower reticulorumen temperature in cows fed with the supplement compared with control group cows. Also, cows feeding with enzymes were 8.80% more active.

Keywords: Alfa-Amylase, Beta-Glucanase, cows, in-line, sensors

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Authors: F. O’Dowd, G. Murphy, M. Roche, E. Shudell, F. Keane, M. O’Kane

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Intoduction: Apremilast (Otezla®) is an oral phosphodiesterase-4 (PDE4) inhibitor indicated for treatment of adult patients with moderate to severe plaque psoriasis who have contraindications to have failed or intolerant of standard systemic therapy and/or phototherapy; and adult patients with active psoriatic arthritis. Apremilast influences intracellular regulation of inflammatory mediators. Two randomized, placebo-controlled trials evaluating apremilast in 1426 patients with moderate to severe plague psoriasis (ESTEEM 1 and 2) demonstrated that the commonest adverse reactions (AE’s) leading to discontinuation were nausea (1.6%), diarrhoea (1.0%), and headaches (0.8%). The overall proportion of subjects discontinuing due to adverse reactions was 6.1%. At week 16 these trials demonstrated significant more apremilast-treated patients (33.1%) achieved the primary end point PASI-75 than placebo (5.3%). We began prescribing apremilast in July 2015. Aim: To evaluate efficacy and tolerability of apremilast in an Irish teaching hospital psoriasis population. Methods: A proforma documenting clinical evaluation parameters, prior treatment experience and AE’s; was completed prospectively on all patients commenced on apremilast since July 2015 – July 2017. Data was collected at week 0,6,12,24,36 and week 52 with 20/71 patients having passed week 52. Efficacy was assessed using Psoriasis Area and Severity Index (PASI) and Dermatology Life Quality Index (DLQI). AE’s documented included GI effects, infections, changes in weight and mood. Retrospective chart review and telephone review was utilised for missing data. Results: A total of 71 adult subjects (38 male, 33 female; age range 23-57), with moderate to severe psoriasis, were evaluated. Prior treatment: 37/71 (52%) were systemic/biologic/phototherapy naïve; 14/71 (20%) has prior phototherapy alone;20/71 (28%) had previous systemic/biologic exposure; 12/71 (17%) had both psoriasis and psoriatic arthritis. PASI responses: mean baseline PASI was 10.1 and DLQI was 15.Week 6: N=71, n=15 (21%) achieved PASI 75. Week 12: N= 48, n=6 (13%) achieved a PASI 100%; n=16 (34.5%) achieved a PASI 75. Week 24: N=40, n=10 (25%) achieved a PASI 100; n=15 (37.5%) achieved a PASI 75. Week 52: N= 20, n=4 (20%) achieved a PASI 100; n= 16 (80%) achieved a PASI 75. (N= number of pts having passed the time point indicated, n= number of pts (out of N) achieving PASI or DLQI responses at that time). DLQI responses: week 24: N= 40, n=30 (75%) achieved a DLQI score of 0; n=5 (12.5%) achieved a DLQI score of 1; n=1 (2.5%) achieved a DLQI score of 10 (due to lack of efficacy). Adverse Events: The proportion of patients that discontinued treatment due to AE’s was n=7 (9.8%). One patient experienced nausea alleviated by dose reduction; another developed significant dysgeusia for certain foods, both continued therapy. Two patients lost 2-3 kg. Conclusion: Initial Irish patient experience of Apremilast appears comparable to that observed in trials with good efficacy and tolerability.

Keywords: Apremilast, introduction, Ireland, clinical audit

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Authors: Karima Oldyerou, B. Meddah, A. Tirtouil

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The food borne infections have a significant impact on public health. Salmonella is the first bacterial cause, especially because of its general availability in the intestinal tract of poultry, pigs and cattle. This bacteria and essential oil of Laurus nobilis subject in this article. In vitro evaluation of the antibacterial activity shows a sensitivity of Salmonella spp. with a MIC of 2.5 mg.ml -1 in vivo after infection of wistar rats and administered orally this essential oil, microbiological results fecal material shows the antibacterial effect of this oil on Salmonella spp.

Keywords: Laurus nobilis, essential oil, salmonella, antibacterial activity, fecal matte

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Authors: Adeline Meriaux, Claire Gaiani, Jennifer Burgain, Frantz Fournier, Lionel Muniglia, Jérémy Petit

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Spray-drying process is widely used for the production of dairy powders for food and pharmaceuticals industries. It involves the atomization of a liquid feed into fine droplets, which are subsequently dried through contact with a hot air flow. The resulting powders permit transportation cost reduction and shelf life increase but can also exhibit various interesting functionalities (flowability, solubility, protein modification or acid gelation), depending on operating conditions and milk composition. Indeed, particles porosity, surface composition, lactose crystallization, protein denaturation, protein association or crust formation may change. Links between spray-drying conditions and physicochemical and functional properties of powders were investigated by a design of experiment methodology and analyzed by principal component analysis. Quadratic models were developed, and multicriteria optimization was carried out by the use of genetic algorithm. At the time of abstract submission, verification spray-drying trials are ongoing. To perform experiments, milk from dairy farm was collected, skimmed, froze and spray-dried at different air pressure (between 1 and 3 bars) and outlet temperature (between 75 and 95 °C). Dry matter, minerals content and proteins content were determined by standard method. Solubility index, absorption index and hygroscopicity were determined by method found in literature. Particle size distribution were obtained by laser diffraction granulometry. Location of the powder color in the Cielab color space and water activity were characterized by a colorimeter and an aw-value meter, respectively. Flow properties were characterized with FT4 powder rheometer; in particular, compressibility and shearing test were performed. Air pressure and outlet temperature are key factors that directly impact the drying kinetics and powder characteristics during spray-drying process. It was shown that the air pressure affects the particle size distribution by impacting the size of droplet exiting the nozzle. Moreover, small particles lead to more cohesive powder and less saturated color of powders. Higher outlet temperature results in lower moisture level particles which are less sticky and can explain a spray-drying yield increase and the higher cohesiveness; it also leads to particle with low water activity because of the intense evaporation rate. However, it induces a high hygroscopicity, thus, powders tend to get wet rapidly if they are not well stored. On the other hand, high temperature provokes a decrease of native serum proteins, which is positively correlated to gelation properties (gel point and firmness). Partial denaturation of serum proteins can improve functional properties of powder. The control of air pressure and outlet temperature during the spray-drying process significantly affects the physicochemical and functional properties of powder. This study permitted to better understand the links between physicochemical and functional properties of powder to identify correlations between air pressure and outlet temperature. Therefore, mathematical models have been developed, and the use of genetic algorithm will allow the optimization of powder functionalities.

Keywords: dairy powders, spray-drying, powders functionalities, design of experiment

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Authors: Gulmira Zhakupova, Tamara Tultabayeva, Aknur Muldasheva, Assem Sagandyk

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The development of technology and production of products with increased biological value based on the use of natural food raw materials are important tasks in the policy of the food market of the Republic of Kazakhstan. For Kazakhstan, livestock farming, in particular sheep farming, is the most ancient and developed industry and way of life. The history of the Kazakh people is largely connected with this type of agricultural production, with established traditions using dairy products from sheep's milk. Therefore, the development of new technologies from sheep’s milk remains relevant. In addition, one of the most promising areas for the development of food technology for therapeutic and prophylactic purposes is sheep milk products as a source of protein, immunoglobulins, minerals, vitamins, and other biologically active compounds. This article presents the results of research on the study of milk processing technology. The objective of the study is to study the possibilities of processing sheep milk and its role in human nutrition, as well as the results of research to improve the technology of sheep milk products. The studies were carried out on the basis of sanitary and hygienic requirements for dairy products in accordance with the following test methods. To perform microbiological analysis, we used the method for identifying Salmonella bacteria (Horizontal method for identifying, counting, and serotyping Salmonella) in a certain mass or volume of product. Nutritional value is a complex of properties of food products that meet human physiological needs for energy and basic nutrients. The protein mass fraction was determined by the Kjeldahl method. This method is based on the mineralization of a milk sample with concentrated sulfuric acid in the presence of an oxidizing agent, an inert salt - potassium sulfate, and a catalyst - copper sulfate. In this case, the amino groups of the protein are converted into ammonium sulfate dissolved in sulfuric acid. The vitamin composition was determined by HPLC. To determine the content of mineral substances in the studied samples, the method of atomic absorption spectrophotometry was used. The study identified the technological parameters of sheep milk products and determined the prospects for researching sheep milk products. Microbiological studies were used to determine the safety of the study product. According to the results of the microbiological analysis, no deviations from the norm were identified. This means high safety of the products under study. In terms of nutritional value, the resulting products are high in protein. Data on the positive content of amino acids were also obtained. The results obtained will be used in the food industry and will serve as recommendations for manufacturers.

Keywords: dairy, milk processing, nutrition, colostrum

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Authors: Samaneh Yavari, Christiane Pferrer, Elisabeth Engelke, Alexander Starke, Juergen Rehage

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Background: Three nociceptive thresholds of thermal, electrical, and mechanical thresholds commonly use to evaluate the local anesthesia in many species, for instance, cow, horse, cat, dog, rabbit, and so on. Due to the lack of investigations to evaluate and/or validate such those nociceptive thresholds, our plan was the comparison of two-foot local anesthesia methods of Intravenous Regional Anesthesia (IVRA) and our modified four-point Nerve Block Anesthesia (NBA). Materials and Methods: Eight healthy nonpregnant nondairy Holstein Frisian cows in a cross-over study design were selected for this study. All cows divided into two different groups to receive two local anesthesia techniques of IVRA and our modified four-point NBA. Three thermal, electrical, and mechanical force and pinpricks were applied to evaluate the quality of local anesthesia methods before and after local anesthesia application. Results: The statistical evaluation demonstrated that our four-point NBA has a qualification to select as a standard foot local anesthesia. However, the recorded results of our study revealed no significant difference between two groups of local anesthesia techniques of IVRA and modified four-point NBA related to quality and duration of anesthesia stimulated by electrical, mechanical and thermal nociceptive stimuli. Conclusion and discussion: All three nociceptive threshold stimuli of electrical, mechanical and heat nociceptive thresholds can be applied to measure and evaluate the efficacy of foot local anesthesia of dairy cows. However, our study revealed no superiority of those three nociceptive methods to evaluate the duration and quality of bovine foot local anesthesia methods. Veterinarians to investigate the duration and quality of their selected anesthesia method can use any of those heat, mechanical, and electrical methods.

Keywords: mechanical, thermal, electrical threshold, IVRA, NBA, hind limb, dairy cow

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Authors: Jemma McGourty, Brid Delahunt, Fiona Hackett, Sharon Courtney, Richard English, Graham Russell, Sinéad O’Connor

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Fundamental Movement Skills (FMS) mastery is considered essential for children’s ongoing, meaningful engagement in Physical Activity (PA). There has been a dearth of Irish research on baseline FMS and their development by means of intervention in young primary school children. In addition, as children’s participation in PA is heavily influenced by both parents and teachers, it is imperative to understand their attitudes and perceptions towards PA participation and its’ promotion in children. The ‘Fun, Move, Play’ Project investigated the effect of a 6-week play based PA intervention on primary school children’s (aged 6-8 years) FMS while also exploring the attitudes and perceptions of their parents and teachers towards PA participation. The FMS intervention utilised a pre-post quasi-experimental design to determine the effect of a 6-week play based PA intervention (devised from the iCoach Kids Programme) on 176 primary school children’s FMS (N = 176: 90 girls and 86 boys; M = 7.2 years; SD = 0.48). Objective measures of 7 FMS (run, skip, vertical jump, static balance, stationary dribble, catch, kick) were made using a combination of the TGMD2 and Get Skilled, Get Active resources. One hundred parents (87 mothers; 13 fathers; M=36 years; SD=5.45) and 90 teachers (67 females; 23 males) completed surveys investigating their attitudes and perceptions towards PA participation. In addition, 19 of these parents and 9 of these teachers participated in semi-structured qualitative interviews to explore, in more depth, their views and perceptions of PA participation. Both the FMS data set and survey responses were analysed using SPSS version 23, using appropriate statistical analysis. A thematic analysis framework was used to analyse the qualitative findings. A significant improvement was observed in the children’s overall FMS score pre-post intervention (t = 16.67; df = 175; p < 0.001), while there were also significant improvements in each of the seven individual FMS measured in the children, pre-post intervention. Findings from the parent surveys and interviews indicated that parents had positive attitudes towards PA, viewed it as important and supported their child’s PA participation. However, a lack of knowledge regarding the amount and intensity of PA that children should participate in emerged as a recurrent finding. Also, there was a significant positive correlation between the PA levels of parents’ and their children (r = .41; n = 100; p < .001). Arising from the teachers’ surveys and interviews was a positive attitude towards PA and the impact that it has on a child’s health and well-being. They also reported feeling more confident teaching certain aspects of the PE curriculum (games and sports) compared to others (gymnastics, dance), where they appreciate working with specialist practitioners. Conclusion: A short-term PA intervention has a positive effect on children’s FMS. While parents are supportive of their child’s PA participation, there is a knowledge gap regarding National PA guidelines for children. Teachers appreciate the importance of PA in children, but face a number of challenges in its implementation and promotion.

Keywords: fundamental movement skills, parents attitudes to physical activity, short-term intervention, teachers attitudes to physical activity

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Authors: Yassir Adam Shuaib, Stefan Niemann, Eltahir Awad Khalil, Ulrich Schaible, Lothar Heinz Wieler, Mohammed Ahmed Bakhiet, Abbashar Osman Mohammed, Mohamed Abdelsalam Abdalla, Elvira Richter

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Tuberculosis (TB) is a chronic bacterial disease of humans and animals and it is characterized by the progressive development of specific granulomatous tubercle lesions in affected tissues. In a six-month study, from June to November 2014, a total of 2,304 carcasses of cattle, camel, sheep, and goats slaughtered at East and West Gaash slaughterhouses, Kassala, were investigated during postmortem, in parallel, 101 sputum samples from TB suspected patients at Kassala and El-Gadarif Teaching Hospitals were collected in order to investigate tuberculosis in animals and humans. Only 0.1% carcasses were found with suspected TB lesions in the liver and lung and peritoneal cavity of two sheep and no tuberculous lesions were found in the carcasses of cattle, goats or camels. All samples, tissue lesions and sputum, were decontaminated by the NALC-NaOH method and cultured for mycobacterial growth at the NRZ for Mycobacteria, Research Center Borstel, Germany. Genotyping and molecular characterization of the grown strains were done by line probe assay (GenoType CM and MTBC) and 16S rDNA, rpoB gene, and ITS sequencing, spoligotyping, MIRU-VNTR typing and next generation sequencing (NGS). Culture of the specimens revealed growth of organisms from 81.6% of all samples. Mycobacterium tuberculosis (76.2%), M. intracellulare (14.2%), mixed infection with M. tuberculosis and M. intracellulare (6.0%) and mixed infection with M. tuberculosis and M. fortuitum and with M. intracellulare and unknown species (1.2%) were detected in the sputum samples and unknown species (1.2%) were detected in the samples of one of the animals tissues. From the 69 M. tuberculosis strains, 25 (36.2%) were showing either mono-drug-resistant or multi-drug-resistant or poly-drug-resistant but none was extensively drug-resistant. In conclusion, the prevalence of TB in animals was very low while in humans M. tuberculosis-Delhi/CAS lineage was responsible for most cases and there was an evidence of MDR transmission and acquisition.

Keywords: animal, human, slaughterhouse, Sudan, tuberculosis

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Authors: Cha-ah C. N., Awah N. J., Mouiche M. M. M.

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Brucellosis is a neglected zoonotic disease of animals and man caused by bacteria of genus Brucella. Though eradicated in some parts of the world, it remains endemic in sub-Saharan Africa including Cameroon. The aim of this study was to contribute to the epidemiology of brucellosis in the North-West region of Cameroon by detecting the presence of anti-Brucella antibodies in bovine bulk milk as this serves as a route of transmission from animals to man. A cross sectional study was conducted to determine the prevalence of Brucella abortus antibodies in bovine bulk milk in the peri-urban zones of Bamenda. One hundred bulk milk samples were collected from 100 herds and tested by milk I-ELISA test. The conducted study revealed the presence of anti-Brucella abortus antibodies in bovine bulk milk. The study revealed that bovine brucellosis is widespread in animal production systems in this area. The animal infection pressure in these systems has remained strong due to movement of livestock in search of pasture, co-existence of animal husbandry, communal sharing of grazing land, concentration of animals around water points, abortions in production systems, locality of production systems and failure to quarantine upon introduction of new animals. The circulation of Brucella abortus antibodies in cattle farms recorded in the study revealed potential public health implication and suggest economic importance of brucellosis to the cattle industry in the Northwest region of Cameroon. The risk for re-emergence and transmission of brucellosis is evident as a result of the co-existence of animal husbandry activities and social-cultural activities that promote brucellosis transmission. Well-designed countrywide, evidence-based studies of brucellosis are needed. These could help to generate reliable frequency and potential impact estimates, to identify Brucella reservoirs, and to propose control strategies of proven efficacy.

Keywords: brucellosis, bulk milk, northwest region Cameroon, prevalence

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Authors: Prem Bahadur Giri, MathineeYucharoen

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Community forest user groups (CFUGs) have been the core stone of forest management efforts in Nepal. Due to the lack of a smooth transition into the local governance structure in 2017, policy instruments have not been effectively cascaded to the local level, creating ambiguity and inconsistency in forest governance. Descriptive mixed-method research was performed with community users and stakeholders of the Tarpakha community forest, Siranchowk Rural Municipality, to understand the role of the political economy in CFUG management. The household survey was conducted among 100 households (who also are existing members of the Tarpakha CFUG) to understand and document their energy consumption preferences and practices. Likewise, ten key informant interviews and five focus group discussions with the municipality and forest management officials were also conducted to have a wider overview of the factors and political, socio-economic, and religious contexts behind the utilization of renewable energy for sustainable development. Findings from our study suggest that only 3% of households use biogas as their main source of energy. The rest of the households mention liquid petroleum gas (LPG), electricity, and firewood as major sources of energy for domestic purposes. Community members highlighted the difficulty in accessing firewood due to strict regulations from the CFUG, lack of cattle and manpower to rear cattle to produce cow dung (for biogas), and lack of technical expertise at the community level for the operation and maintenance of solar energy, among others as challenges of the resource. Likewise, key informants have mentioned policy loopholes at both the federal and local levels, especially with regard to the promotion of alternative or renewable energy, as there are no clear mandates and provisions to regulate the renewable energy industry. The study recommends doing an in-depth study on the feasibility of renewable energy sources, especially in the context of CFUGs, where biodiversity conservation aspects need to be equally taken into consideration while thinking of the promotion and expansion of renewable energy sources.

Keywords: community forest, renewable energy, sustainable development, Nepal

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Authors: Patrick Ahern, David Collery

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The implementation of lean thinking in the manufacturing industry revolutionized the traditional approach to large-scale production through the process of identifying the waste in each task and putting in place mitigation measures to eliminate the waste in all its forms. The Irish construction industry, however, has been much slower to adopt the principles of lean, opting instead to stick with the traditional approach to construction project delivery which is inherently wasteful. Lean thinking holds the potential to revolutionize the construction industry in a similar manner to the adoption of lean manufacturing. Lean principles present opportunities for reduced project duration, reduced project cost, improved quality, and elimination of re-works and non-value-added activities. The following research has been designed to accumulate research data through available literature, electronic surveys, and interviews. The results show an industry reluctant to accept change and an undefined path to successful lean construction implementation.

Keywords: barriers, lean construction, lean implementation, lean manufacturing, lean philosophy

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Authors: Emmanuel C. Ngerem

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The ever-increasing depletion of the dominant global form of energy (fossil fuels) calls for the development of sustainable and green alternative energy sources such as bioethanol, biohydrogen, and biodiesel. The production of the major biofuels relies on biomass feedstocks that are mainly derived from edible food crops and some inedible plants. One suitable feedstock with great potential as raw material for biofuel production is microalgal biomass. Despite the tremendous attributes of microalgae as a source of biofuel, their cultivation requires huge volumes of freshwater, thus posing a serious threat to commercial-scale production and utilization of algal biomass. In this study, a multi-media wastewater mixture for microalgae growth was formulated and optimized. Moreover, the obtained microalgae biomass was pre-treated to reduce sugar recovery and was compared with previous studies on microalgae biomass pre-treatment. The formulated and optimized mixed wastewater media for biomass and lipid accumulation was established using the simplex lattice mixture design. Based on the superposition approach of the potential results, numerical optimization was conducted, followed by the analysis of biomass concentration and lipid accumulation. The coefficients of regression (R²) of 0.91 and 0.98 were obtained for biomass concentration and lipid accumulation models, respectively. The developed optimization model predicted optimal biomass concentration and lipid accumulation of 1.17 g/L and 0.39 g/g, respectively. It suggested 64.69% dairy wastewater (DWW) and 35.31% paper and pulp wastewater (PWW) mixture for biomass concentration, 34.21% DWW, and 65.79% PWW for lipid accumulation. Experimental validation generated 0.94 g/L and 0.39 g/g of biomass concentration and lipid accumulation, respectively. The obtained microalgae biomass was pre-treated, enzymatically hydrolysed, and subsequently assessed for reducing sugars. The optimization of microwave pre-treatment of Chlorococcum sp. was achieved using response surface methodology (RSM). Microwave power (100 – 700 W), pre-treatment time (1 – 7 min), and acid-liquid ratio (1 – 5%) were selected as independent variables for RSM optimization. The optimum conditions were achieved at microwave power, pre-treatment time, and acid-liquid ratio of 700 W, 7 min, and 32.33:1, respectively. These conditions provided the highest amount of reducing sugars at 10.73 g/L. Process optimization predicted reducing sugar yields of 11.14 g/L on microwave-assisted pre-treatment of 2.52% HCl for 4.06 min at 700 watts. Experimental validation yielded reducing sugars of 15.67 g/L. These findings demonstrate that dairy wastewater and paper and pulp wastewater that could pose a serious environmental nuisance. They could be blended to form a suitable microalgae growth media, consolidating the potency of microalgae as a viable feedstock for fermentable sugars. Also, the outcome of this study supports the microalgal wastewater biorefinery concept, where wastewater remediation is coupled with bioenergy production.

Keywords: wastewater cultivation, mixture design, lipid, biomass, nutrient removal, microwave, Chlorococcum, raceway pond, fermentable sugar, modelling, optimization

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Authors: Henri El Zakhem, Anthony Dahdah, Lara Frangieh, Jessica Koura

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Nowadays, the removal of whey produced in the dairy processes has been the most important problem in the dairy industry. Every year, about 47% of the 115 million tons of whey produced world-wide are disposed in the environment. Whey is a nutritious liquid, containing whey proteins (β-lactoglobulin, α-lactalbumin, immunoglobulin-G, proteose pepton), lactose, vitamins (B5, B2, C, and B6), minerals (Calcium, Magnesium, Phosphorous, Potassium, Chloride, and Sodium), and trace elements (Zinc, Iron, Iodine, and Copper). The first objective was to increase the economical and commercial value of whey which is considered as by-product. The second objective of this study was to formulate a new baby food with good nutritional, sensory and storage properties and acceptable to consumers using the cheese whey. The creation of the new product must pass through the following stages: idea stage, development stage which includes the business planning and the product development prototype, packaging stage, production stage, test marketing stage, quality control/sanitation. Three types of whey-based food were selected and prepared by mixing whey and apple, whey and banana as well as whey, apple, and banana.To compile with the recommended dietary allowances (RDA) and adequate intakes (AI) for vitamins and minerals, each sample is formed from 114g of sliced and smashed fruits mixed with 8 mL of whey. Mixtures are heated to 72oC for 15 seconds, and filled in pasteurized jars. Jars were conserved at 4oC. Following the experimental part, sensory evaluation made by an experienced panel took place. Hedonic tests results show that the mixture of whey, apple, and banana has the most delicious and sweetness taste followed by the mixture of whey and banana, and finally the mixture of whey and apple. This study was concluded with a managerial and engineering study that reveals that the project is economically profitable to be executed in Lebanon.

Keywords: baby food, by-product, cheese whey, formulation

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Authors: Marianna Ciaccia, Gennaro Agrimi, Isabella Pisano, Maurizio Bettiga, Silvia Rapacioli, Giulia Mensa, Monica Marzagalli

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Objective: Untargeted metabolomic analysis of extracellular metabolites is a powerful approach that focuses on comprehensively profiling in the extracellular space. In this study, we applied extracellular metabolomic analysis to investigate the metabolism of two probiotic microorganisms with health benefits that extend far beyond the digestive tract and the immune system. Methods: Analytical techniques employed in extracellular metabolomic analysis encompass various technologies, including mass spectrometry (MS), which enables the identification of metabolites present in the fermentation media, as well as the comparison of metabolic profiles under different experimental conditions. Multivariate statistical analysis techniques like principal component analysis (PCA) or partial least squares-discriminant analysis (PLS-DA) play a crucial role in uncovering metabolic signatures and understanding the dynamics of metabolic networks. Results: Different types of supernatants from fermentation processes, such as dairy-free, not dairy-free media and media with no cells or pasteurized, were subjected to metabolite profiling, which contained a complex mixture of metabolites, including substrates, intermediates, and end-products. This profiling provided insights into the metabolic activity of the microorganisms. The integration of advanced software tools has facilitated the identification and characterization of metabolites in different fermentation conditions and microorganism strains. Conclusions: In conclusion, untargeted extracellular metabolomic analysis, combined with software tools, allowed the study of the metabolites consumed and produced during the fermentation processes of probiotic microorganisms. Ongoing advancements in data analysis methods will further enhance the application of extracellular metabolomic analysis in fermentation research, leading to improved bioproduction and the advancement of sustainable manufacturing processes.

Keywords: biotechnology, metabolomics, lactic bacteria, probiotics, postbiotics

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Authors: Nejib Turki, Karima Kouki Khalfallah

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The effect of six treatments of organic amendments were evaluated on a sandy soil in the region of Soukra in Tunisia. T1: cattle manure 55 t.ha-1, T2: commercial compost from Germany to 1 t.ha-1, T3: a mixture of 27.5 t.ha-1 of T1 with 0.5 t. ha-1 of T2, T4: commercial compost from France 2 t.ha-1, T5: a Tunisian commercial compost to 10 t.ha-1 and T0: control without treatment. The nitrogen in the soil increase to 0.029 g.kg-1 of soil treatment for the T1 and 0.021 g. kg-1 of soil treatment for the T3. The highest content of P2O5 has been registered by the T3 treatment that 0.44 g kg-1 soil with respect to the control (T0), which shows a content of 0.36 g.kg-1 soil. The soil was initially characterized by a potassium content of 0.8 g kg-1 soil, K2O exchangeable rate varied between 0.63 g.Kg-1 and 0.71 g.kg-1 soil respectively T2 and T1.

Keywords: compost, organic amendement, Ntot, P2O5, K2O

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Authors: Lorenzo Cocola, Massimo Fedel, Dragiša Savić, Bojana Danilović, Luca Poletto

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An instrument for the detection and evaluation of gaseous carbon dioxide in the headspace of closed containers has been developed in the context of Packsensor Italian-Serbian joint project. The device is based on Tunable Diode Laser Absorption Spectroscopy (TDLAS) with a Wavelength Modulation Spectroscopy (WMS) technique in order to accomplish a non-invasive measurement inside closed containers of fermented dairy products (yogurts and fermented cheese in cups and bottles). The purpose of this instrument is the continuous monitoring of carbon dioxide concentration during incubation and storage of products over a time span of the whole shelf life of the product, in the presence of different microorganisms. The instrument’s optical front end has been designed to be integrated in a thermally stabilized incubator. An embedded computer provides processing of spectral artifacts and storage of an arbitrary set of calibration data allowing a properly calibrated measurement on many samples (cups and bottles) of different shapes and sizes commonly found in the retail distribution. A calibration protocol has been developed in order to be able to calibrate the instrument on the field also on containers which are notoriously difficult to seal properly. This calibration protocol is described and evaluated against reference measurements obtained through an industry standard (sampling) carbon dioxide metering technique. Some sets of validation test measurements on different containers are reported. Two test recordings of carbon dioxide concentration evolution are shown as an example of instrument operation. The first demonstrates the ability to monitor a rapid yeast growth in a contaminated sample through the increase of headspace carbon dioxide. Another experiment shows the dissolution transient with a non-saturated liquid medium in presence of a carbon dioxide rich headspace atmosphere.

Keywords: TDLAS, carbon dioxide, cups, headspace, measurement

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Authors: Igbakura I. Luga, Alex A. Adikwu

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A comparison of resistance to quinolones was carried out on isolates of Shiga toxin-producing Escherichia coliO157:H7 from cattle and mecA and nuc genes harbouring Staphylococcus aureus from pigs. The isolates were separately tested in the first and current decades of the 21^st century. The objective was to demonstrate the dissemination of resistance to this frontline class of antibiotic by bacteria from food animals and bring to the limelight the spread of antibiotic resistance in Nigeria. A total of 10 isolates of the E. coli O157:H7 and 9 of mecA and nuc genes harbouring S. aureus were obtained following isolation, biochemical testing, and serological identification using the Remel Wellcolex E. coli O157:H7 test. Shiga toxin-production screening in the E. coli O157:H7 using the verotoxin E. coli reverse passive latex agglutination (VTEC-RPLA) test; and molecular identification of the mecA and nuc genes in S. aureus. Detection of the mecA and nuc genes were carried out using the protocol by the Danish Technical University (DTU) using the following primers mecA-1:5'-GGGATCATAGCGTCATTATTC-3', mecA-2: 5'-AACGATTGTGACACGATAGCC-3', nuc-1: 5'-TCAGCAAATGCATCACAAACAG-3', nuc-2: 5'-CGTAAATGCACTTGCTTCAGG-3' for the mecA and nuc genes, respectively. The nuc genes confirm the S. aureus isolates and the mecA genes as being methicillin-resistant and so pathogenic to man. The fluoroquinolones used in the antibiotic resistance testing were norfloxacin (10 µg) and ciprofloxacin (5 µg) in the E. coli O157:H7 isolates and ciprofloxacin (5 µg) in the S. aureus isolates. Susceptibility was tested using the disk diffusion method on Muller-Hinton agar. Fluoroquinolone resistance was not detected from isolates of E. coli O157:H7 from cattle. However, 44% (4/9) of the S. aureus were resistant to ciprofloxacin. Resistance of up to 44% in isolates of mecA and nuc genes harbouring S. aureus is a compelling evidence for the rapid spread of antibiotic resistance from bacteria in food animals from Nigeria. Ciprofloxacin is the drug of choice for the treatment of Typhoid fever, therefore widespread resistance to it in pathogenic bacteria is of great public health significance. The study concludes that antibiotic resistance in bacteria from food animals is on the increase in Nigeria. The National Food and Drug Administration and Control (NAFDAC) agency in Nigeria should implement the World Health Organization (WHO) global action plan on antimicrobial resistance. A good starting point can be coordinating the WHO, Office of International Epizootics (OIE), Food and Agricultural Organization (FAO) tripartite draft antimicrobial resistance monitoring and evaluation (M&E) framework in Nigeria.

Keywords: Fluoroquinolone, Nigeria, resistance, Staphylococcus aureus

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Authors: Ashraf M. Ward, Ruban S. Yu

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Data consisting of 2757 records from tow Holstein herds made between 2000 and 2010 were used to examine environmental factors affecting age at first calving (AFC) and calving intervals (CI) and consequently estimate genetic and phenotypic parameters and trends. The overall means and standard errors for AFC and CI were 39.4 ± 7.2 months and 487.5 ± 151.6 days respectively. The respective heritability estimates were 0.091 ± 0.05 and 0.044 ± 0.032, while the repeatability estimate for CI was 0.096 ± 0.001. The genetic trends for CI and AFC were -0.6 d/yr and -0.01 mo/yr respectively and were both significant (P < 0.001), indicating a decrease in mean breeding value over the study period. Phenotypic trends were -0.31 mo/yr and -0.35 d/yr for AFC and CI respectively though non-significant (P > 0.05). The low heritability for CI and AFC indicated that temporary environmental influences were much greater than genetic influences or permanent environmental influences on these traits.

Keywords: Holstein, reproductive, genetic parameters, heritability

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Authors: Yusuke Sugaya

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Our research conducts a cross-linguistic experimental investigation into the cognitive processes involved in distance judgment necessary for selecting demonstratives in deictic usage. Speakers may consider the addressee's judgment or apply certain criteria for distance judgment when they produce demonstratives. While it can be assumed that there are language and cultural differences, it remains unclear how these differences manifest across languages. This research conducted online experiments involving speakers of six languages—Japanese, Spanish, Irish, English, Italian, and French—in which a wide variety of drawings were presented on a screen, varying conditions from three perspectives: addressee, comparisons, and standard. The results of the experiments revealed various distinct features associated with demonstratives in each language, highlighting differences from a comparative standpoint. For one thing, there was an influence of a specific reference point (i.e., Standard) on the selection in Japanese and Spanish, whereas there was relatively an influence of competitors in English and Italian.

Keywords: demonstratives, cross-linguistic experiment, distance judgment, social cognition

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Authors: Sohyoung Won, Heebal Kim, Dajeong Lim

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Genomic prediction is an effective way to measure the abilities of livestock for breeding based on genomic estimated breeding values, statistically predicted values from genotype data using best linear unbiased prediction (BLUP). Using haplotypes, clusters of linked single nucleotide polymorphisms (SNPs), as markers instead of individual SNPs can improve the reliability of genomic prediction since the probability of a quantitative trait loci to be in strong linkage disequilibrium (LD) with markers is higher. To efficiently use haplotypes in genomic prediction, finding optimal ways to define haplotypes is needed. In this study, 770K SNP chip data was collected from Hanwoo (Korean cattle) population consisted of 2506 cattle. Haplotypes were first defined in three different ways using 770K SNP chip data: haplotypes were defined based on 1) length of haplotypes (bp), 2) the number of SNPs, and 3) k-medoids clustering by LD. To compare the methods in parallel, haplotypes defined by all methods were set to have comparable sizes; in each method, haplotypes defined to have an average number of 5, 10, 20 or 50 SNPs were tested respectively. A modified GBLUP method using haplotype alleles as predictor variables was implemented for testing the prediction reliability of each haplotype set. Also, conventional genomic BLUP (GBLUP) method, which uses individual SNPs were tested to evaluate the performance of the haplotype sets on genomic prediction. Carcass weight was used as the phenotype for testing. As a result, using haplotypes defined by all three methods showed increased reliability compared to conventional GBLUP. There were not many differences in the reliability between different haplotype defining methods. The reliability of genomic prediction was highest when the average number of SNPs per haplotype was 20 in all three methods, implying that haplotypes including around 20 SNPs can be optimal to use as markers for genomic prediction. When the number of alleles generated by each haplotype defining methods was compared, clustering by LD generated the least number of alleles. Using haplotype alleles for genomic prediction showed better performance, suggesting improved accuracy in genomic selection. The number of predictor variables was decreased when the LD-based method was used while all three haplotype defining methods showed similar performances. This suggests that defining haplotypes based on LD can reduce computational costs and allows efficient prediction. Finding optimal ways to define haplotypes and using the haplotype alleles as markers can provide improved performance and efficiency in genomic prediction.

Keywords: best linear unbiased predictor, genomic prediction, haplotype, linkage disequilibrium

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Authors: L. Lindsay, S. A. Coleman, D. Kerr, B. J. Taylor, A. Moorhead

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Cognitive decline and frailty is apparent in older adults leading to an increased likelihood of the risk of falling. Currently health care professionals have to make professional decisions regarding such risks, and hence make difficult decisions regarding the future welfare of the ageing population. This study uses health data from The Irish Longitudinal Study on Ageing (TILDA), focusing on adults over the age of 50 years, in order to analyse health risk factors and predict the likelihood of falls. This prediction is based on the use of machine learning algorithms whereby health risk factors are used as inputs to predict the likelihood of falling. Initial results show that health risk factors such as long-term health issues contribute to the number of falls. The identification of such health risk factors has the potential to inform health and social care professionals, older people and their family members in order to mitigate daily living risks.

Keywords: classification, falls, health risk factors, machine learning, older adults

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Authors: Priscila A. Bernardes, Marcos E. Buzanskas, Luciana C. A. Regitano, Ricardo V. Ventura, Danisio P. Munari

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The best linear unbiased predictor (BLUP) is a method commonly used in genetic evaluations of breeding programs. However, this approach can lead to higher inbreeding coefficients in the population due to the intensive use of few bulls with higher genetic potential, usually presenting some degree of relatedness. High levels of inbreeding are associated to low genetic viability, fertility, and performance for some economically important traits and therefore, should be constantly monitored. Unreliable pedigree data can also lead to misleading results. Genomic information (i.e., single nucleotide polymorphism – SNP) is a useful tool to estimate the inbreeding coefficient. Runs of homozygosity have been used to evaluate homozygous segments inherited due to direct or collateral inbreeding and allows inferring population selection history. This study aimed to evaluate runs of homozygosity (ROH) and inbreeding in a population of Nelore beef cattle. A total of 814 animals were genotyped with the Illumina BovineHD BeadChip and the quality control was carried out excluding SNPs located in non-autosomal regions, with unknown position, with a p-value in the Hardy-Weinberg equilibrium lower than 10⁻⁵, call rate lower than 0.98 and samples with the call rate lower than 0.90. After the quality control, 809 animals and 509,107 SNPs remained for analyses. For the ROH analysis, PLINK software was used considering segments with at least 50 SNPs with a minimum length of 1Mb in each animal. The inbreeding coefficient was calculated using the ratio between the sum of all ROH sizes and the size of the whole genome (2,548,724kb). A total of 25.711 ROH were observed, presenting mean, median, minimum, and maximum length of 3.34Mb, 2Mb, 1Mb, and 80.8Mb, respectively. The number of SNPs present in ROH segments varied from 50 to 14.954. The longest ROH length was observed in one animal, which presented a length of 634Mb (24.88% of the genome). Four bulls were among the 10 animals with the longest extension of ROH, presenting 11% of ROH with length higher than 10Mb. Segments longer than 10Mb indicate recent inbreeding. Therefore, the results indicate an intensive use of few sires in the studied data. The distribution of ROH along the chromosomes showed that chromosomes 5 and 6 presented a large number of segments when compared to other chromosomes. The mean, median, minimum, and maximum inbreeding coefficients were 5.84%, 5.40%, 0.00%, and 24.88%, respectively. Although the mean inbreeding was considered low, the ROH indicates a recent and intensive use of few sires, which should be avoided for the genetic progress of breed.

Keywords: autozygosity, Bos taurus indicus, genomic information, single nucleotide polymorphism

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Authors: Priscila A. Bernardes, Marcos E. Buzanskas, Luciana C. A. Regitano, Ricardo V. Ventura, Danisio P. Munari

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Genotype imputation has been used to reduce genomic selections costs. In order to increase haplotype detection accuracy in methods that considers the linkage disequilibrium, another approach could be used, such as combined genotype data from different panels. Therefore, this study aimed to evaluate the linkage disequilibrium and haplotype blocks in two high-density panels before and after the imputation to a combined panel in Nelore beef cattle. A total of 814 animals were genotyped with the Illumina BovineHD BeadChip (IHD), wherein 93 animals (23 bulls and 70 progenies) were also genotyped with the Affymetrix Axion Genome-Wide BOS 1 Array Plate (AHD). After the quality control, 809 IHD animals (509,107 SNPs) and 93 AHD (427,875 SNPs) remained for analyses. The combined genotype panel (CP) was constructed by merging both panels after quality control, resulting in 880,336 SNPs. Imputation analysis was conducted using software FImpute v.2.2b. The reference (CP) and target (IHD) populations consisted of 23 bulls and 786 animals, respectively. The linkage disequilibrium and haplotype blocks studies were carried out for IHD, AHD, and imputed CP. Two linkage disequilibrium measures were considered; the correlation coefficient between alleles from two loci (r²) and the |D’|. Both measures were calculated using the software PLINK. The haplotypes' blocks were estimated using the software Haploview. The r² measurement presented different decay when compared to |D’|, wherein AHD and IHD had almost the same decay. For r², even with possible overestimation by the sample size for AHD (93 animals), the IHD presented higher values when compared to AHD for shorter distances, but with the increase of distance, both panels presented similar values. The r² measurement is influenced by the minor allele frequency of the pair of SNPs, which can cause the observed difference comparing the r² decay and |D’| decay. As a sum of the combinations between Illumina and Affymetrix panels, the CP presented a decay equivalent to a mean of these combinations. The estimated haplotype blocks detected for IHD, AHD, and CP were 84,529, 63,967, and 140,336, respectively. The IHD were composed by haplotype blocks with mean of 137.70 ± 219.05kb, the AHD with mean of 102.10kb ± 155.47, and the CP with mean of 107.10kb ± 169.14. The majority of the haplotype blocks of these three panels were composed by less than 10 SNPs, with only 3,882 (IHD), 193 (AHD) and 8,462 (CP) haplotype blocks composed by 10 SNPs or more. There was an increase in the number of chromosomes covered with long haplotypes when CP was used as well as an increase in haplotype coverage for short chromosomes (23-29), which can contribute for studies that explore haplotype blocks. In general, using CP could be an alternative to increase density and number of haplotype blocks, increasing the probability to obtain a marker close to a quantitative trait loci of interest.

Keywords: Bos taurus indicus, decay, genotype imputation, single nucleotide polymorphism

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