Search results for: okazaki fragments

Authors: Christian Fercher, Jiaul Islam, Simon R. Corrie

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Fluorescence-based immunodiagnostics are an emerging field in biosensor development and exhibit several advantages over traditional detection methods. While various affinity biosensors have been developed to generate a fluorescence signal upon sensing varying concentrations of analytes, reagentless, reversible, and continuous monitoring of complex biological samples remains challenging. Here, we aimed to genetically engineer biosensors based on single-chain antibody fragments (scFv) that are site-specifically labeled with environmentally sensitive fluorescent unnatural amino acids (UAA). A rational design approach resulted in quantifiable analyte-dependent changes in peak fluorescence emission wavelength and enabled antigen detection in vitro. Incorporation of a polarity indicator within the topological neighborhood of the antigen-binding interface generated a titratable wavelength blueshift with nanomolar detection limits. In order to ensure continuous analyte monitoring, scFv candidates with fast binding and dissociation kinetics were selected from a genetic library employing a high-throughput phage display and affinity screening approach. Initial rankings were further refined towards rapid dissociation kinetics using bio-layer interferometry (BLI) and surface plasmon resonance (SPR). The most promising candidates were expressed, purified to homogeneity, and tested for their potential to detect biomarkers in a continuous microfluidic-based assay. Variations of dissociation kinetics within an order of magnitude were achieved without compromising the specificity of the antibody fragments. This approach is generally applicable to numerous antibody/antigen combinations and currently awaits integration in a wide range of assay platforms for one-step protein quantification.

Keywords: antibody engineering, biosensor, phage display, unnatural amino acids

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Authors: Ravindra N. Singh, Dheerendra P. Singh

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Recent discoveries of Bronze Age artefacts, tin slag, furnaces and crucibles, together with new geological evidence on tin deposits in Tosham area of Bhiwani district in Haryana (India) provide the opportunity to survey the evidence for possible sources of tin and the use of bronze in the Harappan sites of north western India. Earlier, Afghanistan emerged as the most promising eastern source of tin utilized by Indus Civilization copper-smiths. Our excavations conducted at Khanak near Tosham mining area during 2014 and 2016 revealed ample evidence of metallurgical activities as attested by the occurrence of slag, ores and evidences of ashes and fragments of furnaces in addition to the bronze objects. We have conducted petrological, XRD, EDAX, TEM, SEM and metallography on the slag, ores, crucible fragments and bronze objects samples recovered from Khanak excavations. This has given positive indication of mining and metallurgy of poly-mettalic Tin at the site; however, it can only be ascertained after the detailed scientific examination of the materials which is underway. In view of the importance of site, we intend to excavate the site horizontally in future so as to obtain more samples for scientific studies.

Keywords: archaeometallurgy, problem of tin, metallography, indus civilization

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Authors: Jesse Rafeiro

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This paper discusses worldbuilding as a pedagogical approach to the first-year architectural design studio. The studio ran for three consecutive terms between 2016-2018. Taking its departure from the fifty-five city narratives in Italo Calvino’s Invisible Cities, students collectively designed in a “nowhere” space where intersecting and diverging narratives could be played out. Along with Calvino, students navigated between three main exercises and their imposed limits to develop architectural insight at three scales simulating the considerations of architectural practice: detail, building, and city. The first exercise asked each student to design and model a ruin based on randomly assigned incongruent fragments. Each student was given one plan fragment and two section fragments from different Renaissance Treatises. The students were asked to translate these in alternating axonometric projection and model-making explorations. Although the fragments themselves were imposed, students were free to interpret how the drawings fit together by imagining new details and atypical placements. An undulating terrain model was introduced in the second exercise to ground the worldbuilding exercises. Here, students were required to negotiate with one another to design a city of ruins. Free to place their models anywhere on the site, the students were restricted by the negotiation of territories marked by other students and the requirement to provide thresholds, open spaces, and corridors. The third exercise introduced new life into the ruined city through a series of design interventions. Each student was assigned an atypical building program suggesting a place for an activity, human or nonhuman. The atypical nature of the programs challenged the triviality of functional planning through explorations in spatial narratives free from preconceived assumptions. By contesting, playing out, or dreaming responses to realities taught in other coursework, this third exercise actualized learnings that are too often self-contained in the silos of differing course agendas. As such, the studio fostered an initial worldbuilding space within which to sharpen sensibility and criticality for subsequent years of education.

Keywords: architectural pedagogy, critical pedagogy, Italo Calvino, worldbuilding

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Authors: Sachil Kumar, Anoop K.Verma, Uma Shankar Singh

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It’s extremely important to study postmortem interval in different causes of death since it assists in a great way in making an opinion on the exact cause of death following such incident often times. With diligent knowledge of the interval one could really say as an expert that the cause of death is not feigned hence there is a great need in evaluating such death to have been at the CRIME SCENE before performing an autopsy on such body. The approach described here is based on analyzing the degradation or proteolysis of a cardiac protein in cases of deaths due to burn as a marker of time since death. Cardiac tissue samples were collected from (n=6) medico-legal autopsies, (Department of Forensic Medicine and Toxicology), King George’s Medical University, Lucknow India, after informed consent from the relatives and studied post-mortem degradation by incubation of the cardiac tissue at room temperature (20±2 OC) for different time periods (~7.30, 18.20, 30.30, 41.20, 41.40, 54.30, 65.20, and 88.40 Hours). The cases included were the subjects of burn without any prior history of disease who died in the hospital and their exact time of death was known. The analysis involved extraction of the protein, separation by denaturing gel electrophoresis (SDS-PAGE) and visualization by Western blot using cTnT specific monoclonal antibodies. The area of the bands within a lane was quantified by scanning and digitizing the image using Gel Doc. As time postmortem progresses the intact cTnT band degrades to fragments that are easily detected by the monoclonal antibodies. A decreasing trend in the level of cTnT (% of intact) was found as the PM hours increased. A significant difference was observed between <15 h and other PM hours (p<0.01). Significant difference in cTnT level (% of intact) was also observed between 16-25 h and 56-65 h & >75 h (p<0.01). Western blot data clearly showed the intact protein at 42 kDa, three major (28 kDa, 30kDa, 10kDa) fragments, three additional minor fragments (12 kDa, 14kDa, and 15 kDa) and formation of low molecular weight fragments. Overall, both PMI and cardiac tissue of burned corpse had a statistically significant effect where the greatest amount of protein breakdown was observed within the first 41.40 Hrs and after it intact protein slowly disappears. If the percent intact cTnT is calculated from the total area integrated within a Western blot lane, then the percent intact cTnT shows a pseudo-first order relationship when plotted against the time postmortem. A strong significant positive correlation was found between cTnT and PM hours (r=0.87, p=0.0001). The regression analysis showed a good variability explained (R2=0.768) The post-mortem Troponin-T fragmentation observed in this study reveals a sequential, time-dependent process with the potential for use as a predictor of PMI in cases of burning.

Keywords: burn, degradation, postmortem interval, troponin-T

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Authors: Ismael Zamora, Elisabeth Ortega, Tatiana Radchenko, Guillem Plasencia

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The structure elucidation based on Mass Spectra (MS) data of unknown substances is an unresolved problem that affects many different fields of application. The recent overview of software available for structure elucidation of small molecules has shown the demand for efficient computational tool that will be able to perform structure elucidation of unknown small molecules and peptides. We developed an algorithm for De-Novo fragment analysis based on MS data that proposes a set of scored and ranked structures that are compatible with the MS and MSMS spectra. Several different algorithms were developed depending on the initial set of fragments and the structure building processes. Also, in all cases, several scores for the final molecule ranking were computed. They were validated with small and middle databases (DB) with the eleven test set compounds. Similar results were obtained from any of the databases that contained the fragments of the expected compound. We presented an algorithm. Or De-Novo fragment analysis based on only mass spectrometry (MS) data only that proposed a set of scored/ranked structures that was validated on different types of databases and showed good results as proof of concept. Moreover, the solutions proposed by Mass Spectrometry were submitted to the prediction of NMR spectra in order to elucidate which of the proposed structures was compatible with the NMR spectra collected.

Keywords: De Novo, structure elucidation, mass spectrometry, NMR

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Authors: Michael A. Kraus, Navid Pourmoghaddam, Martin Botz, Jens Schneider, Geralt Siebert

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Fragmentation analysis of tempered glass gives insight into the quality of the tempering process and defines a certain degree of safety as well. Different standard such as the European EN 12150-1 or the American ASTM C 1048/CPSC 16 CFR 1201 define a minimum number of fragments required for soda-lime safety glass on the basis of fragmentation test results for classification. This work presents an approach for the glass breakage pattern prediction using a Voronoi Tesselation over Random Fields. The random Voronoi tessellation is trained with and validated against data from several breakage patterns. The fragments in observation areas of 50 mm x 50 mm were used for training and validation. All glass specimen used in this study were commercially available soda-lime glasses at three different thicknesses levels of 4 mm, 8 mm and 12 mm. The results of this work form a Bayesian framework for the training and prediction of breakage patterns of tempered soda-lime glass using a Voronoi Random Field Tesselation. Uncertainties occurring in this process can be well quantified, and several statistical measures of the pattern can be preservation with this method. Within this work it was found, that different Random Fields as basis for the Voronoi Tesselation lead to differently well fitted statistical properties of the glass breakage patterns. As the methodology is derived and kept general, the framework could be also applied to other random tesselations and crack pattern modelling purposes.

Keywords: glass breakage predicition, Voronoi Random Field Tessellation, fragmentation analysis, Bayesian parameter identification

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Authors: Ogbonnaya O. Iroanya, Samson T. Fakorede, Osamudiamen J. Edosa, Hadiat A. Azeez

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The human mitochondrial DNA (mtDNA) is about 17 kbp circular DNA fragments found within the mitochondria together with smaller fragments of 1200 bp known as the control region. Knowledge of variation within populations has been employed in forensic and molecular anthropology studies. The study was aimed at investigating the polymorphic nature of the two hypervariable segments (HVS) of the mtDNA, i.e., HVS1 and HVS2, and to determine the haplogroup distribution among individuals resident in Lagos, Southwestern Nigeria. Peripheral blood samples were obtained from sixty individuals who are not related maternally, followed by DNA extraction and amplification of the extracted DNA using primers specific for the regions under investigation. DNA amplicons were sequenced, and sequenced data were aligned and compared to the revised Cambridge Reference Sequence (rCRS) GenBank Accession number: NC_012920.1) using BioEdit software. Results obtained showed 61 and 52 polymorphic nucleotide positions for HVS1 and HVS2, respectively. While a total of three indels mutation were recorded for HVS1, there were seven for HVS2. Also, transition mutations predominate nucleotide change observed in the study. Genetic diversity (GD) values for HVS1 and HVS2 were estimated to be 84.21 and 90.4%, respectively, while random match probability was 0.17% for HVS1 and 0.89% for HVS2. The study also revealed mixed haplogroups specific to the African (L1-L3) and the Eurasians (U and H) lineages. New polymorphic sites obtained from the study are promising for human identification purposes.

Keywords: hypervariable region, indels, mitochondrial DNA, polymorphism, random match probability

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Authors: Huajuan Shi

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Background: The biopsy of the preimplantation embryo may increase the potential risk and concern of embryo viability. Clinically discarded spent embryo medium (SEM) has entered the view of researchers, sparking an interest in noninvasive embryo screening. However, one of the major restrictions is the extremelty low quantity of cf-RNA, which is difficult to efficiently and unbiased amplify cf-RNA using traditional methods. Hence, there is urgently need to an efficient and low bias amplification method which can comprehensively and accurately obtain cf-RNA information to truly reveal the state of SEM cf-RNA. Result: In this present study, we established an agarose PCR amplification system, and has significantly improved the amplification sensitivity and efficiency by ~90 fold and 9.29 %, respectively. We applied agarose to sequencing library preparation (named AG-seq) to quantify and characterize cf-RNA in SEM. The number of detected cf-RNAs (3533 vs 598) and coverage of 3' end were significantly increased, and the noise of low abundance gene detection was reduced. The increasing percentage 5' end adenine and alternative splicing (AS) events of short fragments (< 400 bp) were discovered by AG-seq. Further, the profiles and characterizations of cf-RNA in spent cleavage medium (SCM) and spent blastocyst medium (SBM) indicated that 4‐mer end motifs of cf-RNA fragments could remarkably differentiate different embryo development stages. Significance: This study established an efficient and low-cost SEM amplification and library preparation method. Not only that, we successfully described the characterizations of SEM cf-RNA of preimplantation embryo by using AG-seq, including abundance features fragment lengths. AG-seq facilitates the study of cf-RNA as a noninvasive embryo screening biomarker and opens up potential clinical utilities of trace samples.

Keywords: cell-free RNA, agarose, spent embryo medium, RNA sequencing, non-invasive detection

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Authors: Adel M. Zakri, Mohammed A. Al-Saleh, Judith. K. Brown, Ali M. Idris

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Betasatellites are small circular single stranded DNA molecules found associated with begomoviruses on field symptomatic plants. Their genome size is about half that of the helper begomovirus, ranging between 1.3 and 1.4 kb. The helper begomoviruses are usually members of the family Geminiviridae. Okra leaves showing vein thickening were collected from okra plants growing in Jazan, Saudi Arabia. Total DNA was extracted from leaves and used as a template to amplify circular DNA using rolling circle amplification (RCA) technology. Products were digested with PstI to linearize the helper viral genome(s), and associated DNA satellite(s), yielding a 2.8kbp and 1.4kbp fragment, respectively. The linearized fragments were cloned into the pGEM-5Zf (+) vector and subjected to DNA sequencing. The 2.8 kb fragment was identified as Cotton leaf curl Gezira virus genome, at 2780bp, an isolate closely related to strains reported previously from Saudi Arabia. A clone obtained from the 1.4 kb fragments he 1.4kb was blasted to GeneBank database found to be a betasatellite. The genome of betasatellite was 1357-bp in size. It was found to be a recombinant containing one fragment (877-bp) that shared 91% nt identity with Cotton leaf curl Gezira betasatellite [KM279620], and a smaller fragment [133--bp) that shared 86% nt identity with Tomato leaf curl Sudan virus [JX483708]. This satellite is thus a recombinant between a malvaceous-infecting satellite and a solanaceous-infecting begomovirus.

Keywords: begomovirus, betasatellites, cotton leaf curl Gezira virus, okra plants

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Authors: Huajuan Shi

Abstract:

Background: The biopsy of the preimplantation embryo may increase the potential risk and concern of embryo viability. Clinically discarded spent embryo medium (SEM) has entered the view of researchers, sparking an interest in noninvasive embryo screening. However, one of the major restrictions is the extremelty low quantity of cf-RNA, which is difficult to efficiently and unbiased amplify cf-RNA using traditional methods. Hence, there is urgently need to an efficient and low bias amplification method which can comprehensively and accurately obtain cf-RNA information to truly reveal the state of SEM cf-RNA. Result: In this present study, we established an agarose PCR amplification system, and has significantly improved the amplification sensitivity and efficiency by ~90 fold and 9.29 %, respectively. We applied agarose to sequencing library preparation (named AG-seq) to quantify and characterize cf-RNA in SEM. The number of detected cf-RNAs (3533 vs 598) and coverage of 3' end were significantly increased, and the noise of low abundance gene detection was reduced. The increasing percentage 5' end adenine and alternative splicing (AS) events of short fragments (< 400 bp) were discovered by AG-seq. Further, the profiles and characterizations of cf-RNA in spent cleavage medium (SCM) and spent blastocyst medium (SBM) indicated that 4‐mer end motifs of cf-RNA fragments could remarkably differentiate different embryo development stages. Significance: This study established an efficient and low-cost SEM amplification and library preparation method. Not only that, we successfully described the characterizations of SEM cf-RNA of preimplantation embryo by using AG-seq, including abundance features fragment lengths. AG-seq facilitates the study of cf-RNA as a noninvasive embryo screening biomarker and opens up potential clinical utilities of trace samples.

Keywords: cell-free RNA, agarose, spent embryo medium, RNA sequencing, non-invasive detection

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Authors: Juliana C. Alencar, Monica Ferreira do Amaral Porto

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The blue-green infrastructure in recent years has been pointed out as a possibility to increase the environmental quality of watersheds. The regulation ecosystem services brought by these areas are many, such as the improvement of the air quality of the air, water, soil, microclimate, besides helping to control the peak flows and to promote the quality of life of the population. This study proposes a blue-green infrastructure scenario for the Jaguaré watershed, located in the western zone of the São Paulo city in Brazil. Based on the proposed scenario, it was verified the impact of the adoption of the blue and green infrastructure in the control of the peak flow of the basin, the benefits for the avifauna that are also reflected in the flora and finally, the quantification of the regulation ecosystem services brought by the adoption of the scenario proposed. A survey of existing green areas and potential areas for expansion and connection of these areas to form a network in the watershed was carried out. Based on this proposed new network of green areas, the peak flow for the proposed scenario was calculated with the help of software, ABC6. Finally, a survey of the ecosystem services contemplated in the proposed scenario was made. It was possible to conclude that the blue and green infrastructure would provide several regulation ecosystem services for the watershed, such as the control of the peak flow, the connection frame between the forest fragments that promoted the environmental enrichment of these fragments, improvement of the microclimate and the provision of leisure areas for the population.

Keywords: green and blue infrastructure, sustainable drainage, urban waters, ecosystem services

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Authors: E. C. Mattos, V. S. M. G. Daros, R. Dal Col, A. L. Nascimento

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The aim of this study is to present the results of a retrospective survey on the foreign matter found in foods analyzed at the Adolfo Lutz Institute, from July 2001 to July 2015. All the analyses were conducted according to the official methods described on Association of Official Agricultural Chemists (AOAC) for the micro analytical procedures and Food and Drug Administration (FDA) for the macro analytical procedures. The results showed flours, cereals and derivatives such as baking and pasta products were the types of food where foreign matters were found more frequently followed by condiments and teas. Fragments of stored grains insects, its larvae, nets, excrement, dead mites and rodent excrement were the most foreign matter found in food. Besides, foreign matters that can cause a physical risk to the consumer’s health such as metal, stones, glass, wood were found but rarely. Miscellaneous (shell, sand, dirt and seeds) were also reported. There are a lot of extraneous materials that are considered unavoidable since are something inherent to the product itself, such as insect fragments in grains. In contrast, there are avoidable extraneous materials that are less tolerated because it is preventable with the Good Manufacturing Practice. The conclusion of this work is that although most extraneous materials found in food are considered unavoidable it is necessary to keep the Good Manufacturing Practice throughout the food processing as well as maintaining a constant surveillance of the production process in order to avoid accidents that may lead to occurrence of these extraneous materials in food.

Keywords: extraneous materials, food contamination, foreign matter, surveillance

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Authors: Maxime Merheb, Rachel Matar

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Retrieving ancient DNA sequences which in return permit the entire genome sequencing from fossils have extraordinarily improved in recent years, thanks to sequencing technology and other methodological advances. In any case, the quest to search for ancient DNA is still obstructed by the damage inflicted on DNA which accumulates after the death of a living organism. We can characterize this damage into three main categories: (i) Physical abnormalities such as strand breaks which lead to the presence of short DNA fragments. (ii) Modified bases (mainly cytosine deamination) which cause errors in the sequence due to an incorporation of a false nucleotide during DNA amplification. (iii) DNA modifications referred to as blocking lesions, will halt the PCR extension which in return will also affect the amplification and sequencing process. We can clearly see that the issues arising from breakage and coding errors were significantly decreased in recent years. Fast sequencing of short DNA fragments was empowered by platforms for high-throughput sequencing, most of the coding errors were uncovered to be the consequences of cytosine deamination which can be easily removed from the DNA using enzymatic treatment. The methodology to repair DNA sequences is still in development, it can be basically explained by the process of reintroducing cytosine rather than uracil. This technique is thus restricted to amplified DNA molecules. To eliminate any type of damage (particularly those that block PCR) is a process still pending the complete repair methodologies; DNA detection right after extraction is highly needed. Before using any resources into extensive, unreasonable and uncertain repair techniques, it is vital to distinguish between two possible hypotheses; (i) DNA is none existent to be amplified to begin with therefore completely un-repairable, (ii) the DNA is refractory to PCR and it is worth to be repaired and amplified. Hence, it is extremely important to develop a non-enzymatic technique to detect the most degraded DNA.

Keywords: ancient DNA, DNA barcodong, enzymatic repair, PCR

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Authors: Saut Samuel Simamora

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PURPOSE: Nucleus drop is one of the most feared and severe complications of modern cataract surgery. The lens material may drop through iatrogenic breaks of the posterior capsule. The incidence of the nucleus as the complication of phacoemulsification increases concomitant to the increased frequency of phacoemulsification. Pars plana vitrectomy (PPV) followed by endofragmentation and secondary intraocular lens (IOL) implantation is the choice of management procedure. This case report aims to present the outcome of PPV for the treatment dropped nucleus after cataract surgery METHODS: A 65 year old female patient came to Vitreoretina department with chief complaints blurry vision in her left eye after phacoemulsification one month before. Ophthalmological examination revealed visual acuity of the right eye (VA RE) was 6/15, and the left eye (VA LE) was hand movement. The intraocular pressure (IOP) on the right eye was 18 mmHg, and on the left eye was 59 mmHg. On her left eye, there were aphakic, dropped lens nucleus and secondary glaucoma.RESULTS: The patient got antiglaucoma agent until her IOP was decreased. She underwent pars plana vitrectomy to remove dropped nucleus and iris fixated IOL. One week post operative evaluation revealed VA LE was 6/7.5 and iris fixated IOL in proper position. CONCLUSIONS: Nucleus drop generally occurs in phacoemulsification cataract surgery techniques. Retained lens nucleus or fragments in the vitreous may cause severe intraocular inflammation leading to secondary glaucoma. The proper and good management for retained lens fragments in nucleus drop give excellent outcome to patient.

Keywords: secondary glaucoma, complication of phacoemulsification, nucleus drop, pars plana vitrectomy

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Authors: Sergei Aleinik, Yuri Matveev

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In this paper a novel method for the detection of clipping in speech signals is described. It is shown that the new method has better performance than known clipping detection methods, is easy to implement, and is robust to changes in signal amplitude, size of data, etc. Statistical simulation results are presented.

Keywords: clipping, clipped signal, speech signal processing, digital signal processing

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Authors: Irene Alevizos, Jessica Lewis, Marina Harper, John Boyce

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Acinetobacter baumannii causes a range of severe nosocomial-acquired infections, and many strains are multi-drug resistant. A. baumannii possesses survival mechanisms allowing it to thrive in competitive polymicrobial environments, including a Type VI Secretion System (T6SS) that injects effector proteins into other bacteria to give a competitive advantage. The effects of T6SS firing are broad and depend entirely on the effector that is delivered. Effects can include toxicity against prokaryotic or eukaryotic cells and the acquisition of essential nutrients. The T6SS of some species can deliver ‘specialised effectors’ that are fused directly to T6SS components, such as PAAR proteins. PAAR proteins are predicted to form the piercing tip of the T6SS and are essential for T6SS function. Although no specialised effectors have been identified in A. baumannii, many strains encode multiple PAAR proteins. Analysis of PAAR proteins across the species identified 12 families of PAAR proteins with distinct C-terminal extensions. A. baumannii AB307-0294 encodes two PAAR proteins, one of which has a C-terminal extension. Mutation of one or both of the PAAR-encoding genes in this strain showed that expression of either PAAR protein was sufficient for T6SS function. We employed a heterologous expression approach and determined that PAAR proteins from different A. baumannii strains, as well as the closely related A. baylyi species, could complement the A. baumannii ∆paar mutant and restore T6SS function. Furthermore, we showed that PAAR fusions could be used to deliver artificially cloned protein fragments by generating Histidine- and Streptavidin- tagged PAAR specialised effectors, which restored T6SS activity. This provides evidence that the fusion of protein fragments onto PAAR proteins in A. baumannii is compatible with a functional T6SS. Successful delivery by this mechanism extends the scope of what the T6SS can deliver, including user designed proteins.

Keywords: A. baumannii, effectors, PAAR, T6SS

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Authors: Gholamreza Hashemitabr, Reza Valadan, Alireza Rafiei, Mohammad Reza Bassami

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Breast cancer is the most common malignancy among women worldwide. Cancer cells use a complex multilayer network of epidermal growth factor receptors (EGFRs) signaling pathways to support their survival and growth. The overlapping networks of EGFRs signaling pathways account for the failure of most ErbB-targeted therapies. The aim of this study was to enrich a pool of recombinant antibody fragments against common epitopes of ErbB1 and ErbB2 in order to simultaneous blockade of ErbBs signaling pathways. ErbB1 and ErbB2 were expressed stably in VERO cells. Selection of recombinant antibodies was performed on live cells expressing either of ErbB1 and ErbB2 receptors using subtractive phage display approach. The results of PCR and DNA fingerprinting in the last round of panning showed that most clones contained insert (80% and 85% for ErbB1 and ErbB2 respectively) with an identical restriction pattern. The selected clones showed positive reaction to both ErbB1 and ErbB2 receptors in phage-ELISA test. Furthermore, the resulting soluble antibody fragments recognized common epitopes of both immunoprecipitated ErbB1 and ErbB2 in western blot. Additionally, the antibodies directed against the dimerization domain of ErbB1 demonstrated a significant absorbance in EGF-stimulated VERO/ErbB1 cells than non-stimulated cells (1.91 and 1.09 respectively). Moreover, the results of dimerization inhibition test showed that these antibodies blocked ErbB1 and ErbB2 dimerization on the surface of ErbB1 and ErbB2 expressing VERO cells. Regarding the importance of pan-ErbB approach to cancer therapy, the antibodies developed here might provide novel therapeutics for simultaneous blockade of ErbBs signaling pathways.

Keywords: breast cancer, single-chain antibody, ErbB1, ErbB2, epitope

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Authors: Amr A. El Hanafy, Muhammad I. Qureshi, Jamal Sabir, Mohamed Mutawakil, Mohamed M. Ahmed, Hassan El Ashmaoui, Hassan Ramadan, Mohamed Abou-Alsoud, Mahmoud Abdel Sadek

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β-Lactoglobulin (β-LG) is the dominant non-casein whey protein found in bovine milk and of most ruminants. The amino acid sequence of β-LG along with its 3-dimensional structure illustrates linkage with the lipocalin superfamily. Preliminary studies in goats indicated that milk yield can be influenced by polymorphism in genes coding for whey proteins. The aim of this study is to identify and evaluate the incidence of functional polymorphisms in the exonic and intronic portions of β-LG gene in native Saudi goat breeds (Ardi, Habsi, and Harri). Blood samples were collected from 300 animals (100 for each breed) and genomic DNA was extracted using QIAamp DNA extraction Kit. A fragment of the β-LG gene from exon 7 to 3’ flanking region was amplified with pairs of specific primers. Subsequent digestion with Sac II restriction endonuclease revealed two alleles (A and B) and three different banding patterns or genotypes i.e. AA, AB and BB. The statistical analysis showed that β-LG AA genotype had higher milk yield than β-LG AB and β-LG BB genotypes. Nucleotide sequencing of the selected β-LG fragments was done and submitted to GenBank NCBI (Accession No. KJ544248, KJ588275, KJ588276, KJ783455, KJ783456 and KJ874959). Two already established SNPs in exon 7 (+4601 and +4603) and one fresh SNP in the 3’ UTR region were detected in the β-LG fragments with designated AA genotype. The polymorphisms in exon 7 did not produce any amino acid change. Phylogenetic analysis on the basis of nucleotide sequences of native Saudi goats indicated evolutional similarity with the GenBank reference sequences of goat, Bubalus bubalis and Bos taurus.

Keywords: β-Lactoglobulin, Saudi goats, PCR-RFLP, functional polymorphism, nucleotide sequencing, phylogenetic analysis

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Authors: Mohammed H. Karim, Bestoon M. Faraj

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Introduction: This study aimed to compare the effectiveness of a Dynamic Navigation System (DNS) and a three-dimensional microscope in retrieving broken rotary NiTi files when using trepan burs and the extractor system. Materials and Methods: Thirty maxillary first bicuspids with sixty separate roots were split into two comparable groups based on a comprehensive Cone-Beam Computed Tomography (CBCT) analysis of the root length and curvature. After standardized access opening, glide paths, and patency attainment with the K file (sizes 10 and 15), the teeth were arranged on 3D models (three per quadrant, six per model). Subsequently, controlled-memory heat-treated NiTi rotary files (#25/0.04) were notched 4 mm from the tips and fractured at the apical third of the roots. The C-FR1 Endo file removal system was employed under both guidance to retrieve the fragments, and the success rate, canal aberration, treatment time and volumetric changes were measured. The statistical analysis was performed using IBM SPSS software at a significance level of 0.05. Results: The microscope-guided group had a higher success rate than the DNS guidance, but the difference was insignificant (p > 0.05). In addition, the microscope-guided drills resulted in a substantially lower proportion of canal aberration, required less time to retrieve the fragments and caused minimal change in the root canal volume (p < 0.05). Conclusion: Although dynamically guided trephining with the extractor can retrieve separated instruments, it is inferior to three-dimensional microscope guidance regarding treatment time, procedural errors, and volume change.

Keywords: separated instruments retrieval, dynamic navigation system, 3D video microscope, trephine burs, extractor

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Authors: D. Leibman, D. Wolf, A. Gal-On

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Viral diseases of tomato crops result in heavy yield losses and may even jeopardize the production of these crops. Classical tomato breeding for disease resistance against Tomato yellow leaf curl virus (TYLCV), leads to partial resistance associated with a number of recessive genes. To author’s best knowledge Pepino mosaic virus (PepMV) genetic resistance is not yet available. The generation of viral resistance by means of genetic engineering was reported and implemented for many crops, including tomato. Transgenic resistance against viruses is based, in most cases, on Post Transcriptional Gene Silencing (PTGS), an endogenous mechanism which destroys the virus genome. In this work, we developed immunity against PepMV and TYLCV in a tomato based on a PTGS mechanism. Tomato plants were transformed with a hairpin-construct-expressed transgene-derived double-strand-RNA (tr-dsRNA). In the case of PepMV, the binary construct harbored three consecutive fragments of the replicase gene from three different PepMV strains (Italian, Spanish and American), to provide resistance against a range of virus strains. In the case of TYLCV, the binary vector included three consecutive fragments of the IR, V2 and C2 viral genes constructed in a hairpin configuration. Selected transgenic lines (T0) showed a high accumulation of transgene siRNA of 21-24 bases, and T1 transgenic lines showed complete immunity to PepMV and TYLCV. Graft inoculation displayed immunity of the transgenic scion against PepMV and TYLCV. The study presents the engineering of resistance in tomato against two serious diseases, which will help in the production of high-quality tomato. However, unfortunately, these resistant plants have not been implemented due to public ignorance and opposition against breeding by genetic engineering.

Keywords: PepMV, PTGS, TYLCV, tr-dsRNA

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Authors: Ali S. Gargoum

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Graphical modeling plays an important role in providing efficient probability calculations in high dimensional problems (computational efficiency). In this paper, we address one of such problems where we discuss fragmenting puff models and some distributional assumptions concerning models for the instantaneous, emission readings and for the fragmenting process. A graphical representation in terms of a junction tree of the conditional probability breakdown of puffs and puff fragments is proposed.

Keywords: graphical models, influence diagrams, junction trees, Bayesian nets

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Authors: Galina Portnova, Kseniya Gladun

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In our EEG experiment participated 27 children with ASD with the average age of 6.13 years and the average score for CARS 32.41 and 25 healthy children (of 6.35 years). Six types of musical stimulation were presented, included Gluck, Javier-Naida, Kenny G, Chopin and other classic musical compositions. Children with autism showed orientation reaction to the music and give behavioral responses to different types of music, some of them might assess stimulation by scales. The participants were instructed to remain calm. Brain electrical activity was recorded using a 19-channel EEG recording device, 'Encephalan' (Russia, Taganrog). EEG epochs lasting 150 s were analyzed using EEGLab plugin for MatLab (Mathwork Inc.). For EEG analysis we used Fast Fourier Transform (FFT), analyzed Peak alpha frequency (PAF), correlation dimension D2 and Stability of rhythms. To express the dynamics of desynchronizing of different rhythms we've calculated the envelope of the EEG signal, using the whole frequency range and a set of small narrowband filters using Hilbert transformation. Our data showed that healthy children showed similar EEG spectral changes during musical stimulation as well as described the feelings induced by musical fragments. The exception was the ‘Chopin. Prelude’ fragment (no.6). This musical fragment induced different subjective feeling, behavioral reactions and EEG spectral changes in children with ASD and healthy children. The correlation dimension D2 was significantly lower in autists compared to healthy children during musical stimulation. Hilbert envelope frequency was reduced in all group of subjects during musical compositions 1,3,5,6 compositions compared to the background. During musical fragments 2 and 4 (terrible) lower Hilbert envelope frequency was observed only in children with ASD and correlated with the severity of the disease. Alfa peak frequency was lower compared to the background during this musical composition in healthy children and conversely higher in children with ASD.

Keywords: electroencephalogram (EEG), emotional perception, ASD, musical perception, childhood Autism rating scale (CARS)

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Authors: Sachil Kumar, Anoop Kumar Verma, Wahid Ali, Uma Shankar Singh

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Globally approximately 55.3 million people die each year. In the India there were 95 lakh annual deaths in 2013. The number of deaths resulted from homicides, suicides and unintentional injuries in the same period was about 5.7 lakh. The ever-increasing crime rate necessitated the development of methods for determining time since death. An erroneous time of death window can lead investigators down the wrong path or possibly focus a case on an innocent suspect. In this regard a research was carried out by analyzing the temperature dependent degradation of a Cardiac Troponin-T protein (cTnT) in the myocardium postmortem as a marker for time since death. Cardiac tissue samples were collected from (n=6) medico-legal autopsies, (in the Department of Forensic Medicine and Toxicology, King George’s Medical University, Lucknow India) after informed consent from the relatives and studied post-mortem degradation by incubation of the cardiac tissue at room temperature (20±2 OC), 12 0C, 25 0C and 37 0C for different time periods ((~5, 26, 50, 84, 132, 157, 180, 205, and 230 hours). The cases included were the subjects of road traffic accidents (RTA) without any prior history of disease who died in the hospital and their exact time of death was known. The analysis involved extraction of the protein, separation by denaturing gel electrophoresis (SDS-PAGE) and visualization by Western blot using cTnT specific monoclonal antibodies. The area of the bands within a lane was quantified by scanning and digitizing the image using Gel Doc. The data shows a distinct temporal profile corresponding to the degradation of cTnT by proteases found in cardiac muscle. The disappearance of intact cTnT and the appearance of lower molecular weight bands are easily observed. Western blot data clearly showed the intact protein at 42 kDa, two major (27 kDa, 10kDa) fragments, two additional minor fragments (32 kDa) and formation of low molecular weight fragments as time increases. At 12 0C the intensity of band (intact cTnT) decreased steadily as compared to RT, 25 0C and 37 0C. Overall, both PMI and temperature had a statistically significant effect where the greatest amount of protein breakdown was observed within the first 38 h and at the highest temperature, 37 0C. The combination of high temperature (37 0C) and long Postmortem interval (105.15 hrs) had the most drastic effect on the breakdown of cTnT. If the percent intact cTnT is calculated from the total area integrated within a Western blot lane, then the percent intact cTnT shows a pseudo-first order relationship when plotted against the log of the time postmortem. These plots show a good coefficient of correlation of r = 0.95 (p=0.003) for the regression of the human heart at different temperature conditions. The data presented demonstrates that this technique can provide an extended time range during which Postmortem interval can be more accurately estimated.

Keywords: degradation, postmortem interval, proteolysis, temperature, troponin

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Authors: Edite Kulmane, Mara Pilmane, Romans Lacis

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Introduction: Acquired heart diseases remain one of the leading health care problems in the world. Changes in myocardium of the diseased hearts are complex and pathogenesis is still not fully clear. The aim of this study was to identify appearance and distribution of apoptosis, homeostasis regulating factors, and innervation and ischemia markers in right atrial tissue in different acquired heart diseases. Methods: During elective open heart surgery were taken right atrial tissue fragments from 12 patients. All patients were operated because of acquired heart diseases- aortic valve stenosis (5 patients), coronary heart disease (5 patients), coronary heart disease and secondary mitral insufficiency (1 patient) and mitral disease (1 patient). The mean age was (mean±SD) 70,2±7,0 years (range 58-83 years). The tissues were stained with haematoxylin and eosin methods for routine light-microscopical examination and for immunohistochemical detection of protein gene peptide 9.5 (PGP 9.5), human atrial natriuretic peptide (hANUP), vascular endothelial growth factor (VEGF), chromogranin A and endothelin. Apoptosis was detected by TUNEL method. Results: All specimens showed degeneration of cardiomyocytes with lysis of myofibrils, diffuse vacuolization especially in perinuclear region, different size of cells and their nuclei. The severe invasion of connective tissue was observed in main part of all fragments. The apoptotic index ranged from 24 to 91%. One specimen showed region of newly performed microvessels with cube shaped endotheliocytes that were positive for PGP 9.5, endothelin, chromogranin A and VEGF. From all fragments, taken from patients with coronary heart disease, there were observed numerous PGP 9.5-containing nerve fibres, except in patient with secondary mitral insufficiency, who showed just few PGP 9.5 positive nerves. In majority of specimens there were regions observed with cube shaped mixed -VEGF immunoreactive endocardial and epicardial cells. Only VEGF positive endothelial cells were observed just in few specimens. There was no significant difference of hANUP secreting cells among all specimens. All patients operated due to the coronary heart disease moderate to numerous number of chromogranin A positive cells were seen while in patients with aortic valve stenosis tissue demonstrated just few factor positive cells. Conclusions: Complex detection of different factors may indicate selectively disordered morphopathogenetical event of heart disease: decrease of PGP 9.5 nerves suggests the decreased innervation of organ; increased apoptosis indicates the cell death without ingrowth of connective tissue; persistent presence of hANUP proves the unchanged homeostasis of cardiomyocytes probably supported by expression of chromogranins. Finally, decrease of VEGF detects the regions of affected blood vessels in heart affected by acquired heart disease.

Keywords: heart, apoptosis, protein-gene peptide 9.5, atrial natriuretic peptide, vascular endothelial growth factor, chromogranin A, endothelin

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Authors: Cristina Opris, Bogdan Cojocaru, Madalina Tudorache, Simona M. Coman, Vasile I. Parvulescu, Camelia Bala, Bahir Duraki, Jeroen A. Van Bokhoven

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The tremendous achievements in the development of the society concretized by more sophisticated materials and systems are merely based on non-renewable resources. Consequently, after more than two centuries of intensive development, among others, we are faced with the decrease of the fossil fuel reserves, an increased impact of the greenhouse gases on the environment, and economic effects caused by the fluctuations in oil and mineral resource prices. The use of biomass may solve part of these problems, and recent analyses demonstrated that from the perspective of the reduction of the emissions of carbon dioxide, its valorization may bring important advantages conditioned by the usage of genetic modified fast growing trees or wastes, as primary sources. In this context, the abundance and complex structure of lignin may offer various possibilities of exploitation. However, its transformation in fuels or chemicals supposes a complex chemistry involving the cleavage of C-O and C-C bonds and altering of the functional groups. Chemistry offered various solutions in this sense. However, despite the intense work, there are still many drawbacks limiting the industrial application. Thus, the proposed technologies considered mainly homogeneous catalysts meaning expensive noble metals based systems that are hard to be recovered at the end of the reaction. Also, the reactions were carried out in organic solvents that are not acceptable today from the environmental point of view. To avoid these problems, the concept of this work was to investigate the synthesis of superparamagnetic core shell catalysts for the fragmentation of lignin directly in the aqueous phase. The magnetic nanoparticles were covered with a nanoshell of an oxide (niobia) with a double role: to protect the magnetic nanoparticles and to generate a proper (acidic) catalytic function and, on this composite, cobalt nanoparticles were deposed in order to catalyze the C-C bond splitting. With this purpose, we developed a protocol to prepare multifunctional and magnetic separable nano-composite Co@Nb2O5@Fe3O4 catalysts. We have also established an analytic protocol for the identification and quantification of the fragments resulted from lignin depolymerization in both liquid and solid phase. The fragmentation of various lignins occurred on the prepared materials in high yields and with very good selectivity in the desired fragments. The optimization of the catalyst composition indicated a cobalt loading of 4wt% as optimal. Working at 180 oC and 10 atm H2 this catalyst allowed a conversion of lignin up to 60% leading to a mixture containing over 96% in C20-C28 and C29-C37 fragments that were then completely fragmented to C12-C16 in a second stage. The investigated catalysts were completely recyclable, and no leaching of the elements included in the composition was determined by inductively coupled plasma optical emission spectrometry (ICP-OES).

Keywords: superparamagnetic core-shell catalysts, environmental production of fuels, renewable lignin, recyclable catalysts

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Authors: N. Singh, G. K. Darbha

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Since the last decade, a wave of research has begun to study the prevalence and impact of ever-increasing plastic pollution in the environment. The wide application and ubiquitous distribution of plastic have become a global concern due to its persistent nature. The disposal of plastics has emerged as one of the major challenges for waste management landfills. Microplastics (MPs) have found its existence in almost every environment, from the high altitude mountain lake to the deep sea sediments, polar icebergs, coral reefs, estuaries, beaches, and river, etc. Microplastics are fragments of plastics with size less than 5 mm. Microplastics can be classified as primary microplastics and secondary microplastics. Primary microplastics includes purposefully introduced microplastics into the end products for consumers (microbeads used in facial cleansers, personal care product, etc.), pellets (used in manufacturing industries) or fibres (from textile industries) which finally enters into the environment. Secondary microplastics are formed by disintegration of larger fragments under the exposure of sunlight, mechanical abrasive forces by rain, waves, wind and/or water. A number of factors affect the quantity of microplastic present in freshwater environments. In addition to physical forces, human population density proximal to the water body, proximity to urban centres, water residence time, and size of the water body also affects plastic properties. With time, other complex processes in nature such as physical, chemical and biological break down plastics by interfering with its structural integrity. Several studies demonstrate that microplastics found in wastewater sludge being used as manure for agricultural fields, thus having the tendency to alter the soil environment condition influencing the microbial population as well. Inadequate data are available on the fate and transport of microplastics under varying environmental conditions that are required to supplement important information for further research. In addition, microplastics have the tendency to absorb heavy metals and hydrophobic organic contaminants such as PAHs and PCBs from its surroundings and thus acting as carriers for these contaminants in the environment system. In this study, three kinds of microplastics (polyethylene, polypropylene and expanded polystyrene) of different densities were chosen. Plastic samples were placed in sand with different aqueous media (distilled water, surface water, groundwater and marine water). It was incubated at varying temperatures (25, 35 and 40 °C) and agitation levels (rpm). The results show that the number of plastic fragments enhanced with increase in temperature and agitation speed. Moreover, the rate of disintegration of expanded polystyrene is high compared to other plastics. These results demonstrate that temperature, salinity, and mechanical abrasion plays a major role in degradation of plastics. Since weathered microplastics are more harmful as compared to the virgin microplastics, long-term studies involving other environmental factors are needed to have a better understanding of degradation of plastics.

Keywords: environmental contamination, fragmentation, microplastics, temperature, weathering

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Authors: Mohammed H. Karim, Bestoon M. Faraj

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Introduction: instrument separation is a common challenge in the endodontic field. Various techniques and technologies have been developed to improve the retrieval success rate. This study aimed to compare the effectiveness of a Dynamic Navigation System (DNS) and a three-dimensional microscope in retrieving broken rotary NiTi files when using trepan burs and the extractor system. Materials and Methods: Thirty maxillary first bicuspids with sixty separate roots were split into two comparable groups based on a comprehensive Cone-Beam Computed Tomography (CBCT) analysis of the root length and curvature. After standardised access opening, glide paths, and patency attainment with the K file (sizes 10 and 15), the teeth were arranged on 3D models (three per quadrant, six per model). Subsequently, controlled-memory heat-treated NiTi rotary files (#25/0.04) were notched 4 mm from the tips and fractured at the apical third of the roots. The C-FR1 Endo file removal system was employed under both guidance to retrieve the fragments, and the success rate, canal aberration, treatment time and volumetric changes were measured. The statistical analysis was performed using IBM SPSS software at a significance level of 0.05. Results: The microscope-guided group had a higher success rate than the DNS guidance, but the difference was insignificant (p > 0.05). In addition, the microscope-guided drills resulted in a substantially lower proportion of canal aberration, required less time to retrieve the fragments and caused a minor change in the root canal volume (p < 0.05). Conclusion: Although dynamically guided trephining with the extractor can retrieve separated instruments, it is inferior to three-dimensional microscope guidance regarding treatment time, procedural errors, and volume change.

Keywords: dynamic navigation system, separated instruments retrieval, trephine burs and extractor system, three-dimensional video microscope

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Authors: Caspar S. Carson, Gabriel W. Prather, Nicholas E. Wong, Jeffery R. Anton, William H. McCoy

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Cutibacterium acnes is a commensal bacterium found on human skin that has been linked to acne. C. acnes can also be an opportunistic pathogen when it infiltrates the body during surgery. This pathogen can cause dangerous infections of medical implants, such as shoulder replacements, leading to life-threatening blood infections. Compounding this issue, C. acnes resistance to many antibiotics has become an increasing problem worldwide, creating a need for special forms of treatment. C. acnes expresses the protein RoxP, and it requires this protein to colonize human skin. Though this protein is required for C. acnes skin colonization, its function is not yet understood. Inhibition of RoxP function might be an effective treatment for C. acnes infections. To develop such reagents, the McCoy Laboratory generated four unique anti-RoxP antibodies. Preliminary studies in the McCoy Lab have established that each antibody binds a distinct site on RoxP. To assess the potential of these antibodies as therapeutics, it is necessary to specifically characterize these antibody epitopes and evaluate them in assays that assess their ability to inhibit RoxP-dependent C. acnes growth. To provide material for these studies, an antibody expression construct, Fv-clasp(v2), was adapted to encode anti-RoxP antibody sequences. The author hypothesizes that this expression strategy can produce sufficient amounts of >95% pure antibody fragments for further characterization of these antibodies. Four anti-RoxP Fv-clasp(v2) expression constructs (pET vector-based) were transformed into E. coli BL21-Gold(DE3) cells and a small-scale expression and purification trial was performed for each construct to evaluate anti-RoxP Fv-clasp(v2) yield and purity. Successful expression and purification of these antibody constructs will allow for their use in structural studies, such as protein crystallography and cryogenic electron microscopy. Such studies would help to define the antibody binding sites on RoxP, which could then be leveraged in the development of certain methods to treat C. acnes infection through RoxP inhibition.

Keywords: structural biology, protein expression, infectious disease, antibody, therapeutics, E. coli

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Authors: J. Mona, R. R. da Silva, C.-L.Cheng, Y. Kopelevich

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We report on a possible occurrence of superconductivity in 5 nm particle size diamond powders treated with sulfur (S) at 500 o C for 10 hours in ~10-2 Torr vacuum. Superconducting-like magnetization hysteresis loops M(H) have been measured up to ~ 50 K by means of the SQUID magnetometer (Quantum Design). Both X-ray (Θ-2Θ geometry) and Raman spectroscopy analyses revealed no impurity or additional phases. Nevertheless, the measured Raman spectra are characteristic to the diamond with embedded disordered carbon and/or graphitic fragments suggesting a link to the previous reports of the local or surface superconductivity in graphite- and amorphous carbon–sulfur composites.

Keywords: nanodiamond, sulfur, superconductivity, Raman spectroscopy

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Authors: Sokkhey Phauk, Takeo Okazaki

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The challenging task in educational institutions is to maximize the high performance of students and minimize the failure rate of poor-performing students. An effective method to leverage this task is to know student learning patterns with highly influencing factors and get an early prediction of student learning outcomes at the timely stage for setting up policies for improvement. Educational data mining (EDM) is an emerging disciplinary field of data mining, statistics, and machine learning concerned with extracting useful knowledge and information for the sake of improvement and development in the education environment. The study is of this work is to propose techniques in EDM and integrate it into a web-based system for predicting poor-performing students. A comparative study of prediction models is conducted. Subsequently, high performing models are developed to get higher performance. The hybrid random forest (Hybrid RF) produces the most successful classification. For the context of intervention and improving the learning outcomes, a feature selection method MICHI, which is the combination of mutual information (MI) and chi-square (CHI) algorithms based on the ranked feature scores, is introduced to select a dominant feature set that improves the performance of prediction and uses the obtained dominant set as information for intervention. By using the proposed techniques of EDM, an academic performance prediction system (APPS) is subsequently developed for educational stockholders to get an early prediction of student learning outcomes for timely intervention. Experimental outcomes and evaluation surveys report the effectiveness and usefulness of the developed system. The system is used to help educational stakeholders and related individuals for intervening and improving student performance.

Keywords: academic performance prediction system, educational data mining, dominant factors, feature selection method, prediction model, student performance

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