Search results for: J. M. Prins

Authors: Birome Holo Ba, Christian Prins, Caroline Prodhon

Abstract:

Optimization is an important aspect of logistics management. It can reduce significantly logistics costs and also be a good tool for decision support. In this paper, we address a planning problem specific to biomass supply chain. We propose a new mixed integer linear programming (MILP) model dealing with different feed stock production operations such as harvesting, packing, storage, pre-processing and transportation, with the objective of minimizing the total logistic cost of the system on a regional basis. It determines the optimal number of harvesting machine, the fleet size of trucks for transportation and the amount of each type of biomass harvested, stored and pre-processed in each period to satisfy demands of refineries in each period. We illustrate the effectiveness of the proposal model with a numerical example, a case study in Aube (France department), which gives preliminary and interesting, results on a small test case.

Keywords: biomass logistics, supply chain, modelling, optimization, bioenergy, biofuels

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Authors: Elham Jelodari Mamaghani, Christian Prins, Haoxun Chen

Abstract:

In this paper, there is concentration on collaborative transportation planning (CTP) among multiple carriers with pickup and delivery requests and time windows. This problem is a vehicle routing problem with constraints from standard vehicle routing problems and new constraints from a real-world application. In the problem, each carrier has a finite number of vehicles, and each request is a pickup and delivery request with time window. Moreover, each carrier has reserved requests, which must be served by itself, whereas its exchangeable requests can be outsourced to and served by other carriers. This collaboration among carriers can help them to reduce total transportation costs. A mixed integer programming model is proposed to the problem. To solve the model, a hybrid algorithm that combines Genetic Algorithm and Simulated Annealing (GASA) is proposed. This algorithm takes advantages of GASA at the same time. After tuning the parameters of the algorithm with the Taguchi method, the experiments are conducted and experimental results are provided for the hybrid algorithm. The results are compared with those obtained by a commercial solver. The comparison indicates that the GASA significantly outperforms the commercial solver.

Keywords: centralized collaborative transportation, collaborative transportation with pickup and delivery, collaborative transportation with time windows, hybrid algorithm of GA and SA

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Authors: Sintayehu W. Dejene, Ignas M. A. Heitkönig, Herbert H. T. Prins, Zewdu K. Tessema, Willem F. de Boer

Abstract:

Current theories on diversity-disease relationships describe host species diversity and species identity as important factors influencing disease risk, either diluting or amplifying disease prevalence in a community. Whereas the simple term ‘diversity’ embodies a set of animal community characteristics, it is not clear how different measures of species diversity are correlated with disease risk. We, therefore, tested the effects of species richness, Pielou’s evenness and Shannon’s diversity on bTB risk in cattle in the Afar Region and Awash National Park between November 2013 and April 2015. We also analysed the identity effect of a particular species and the effect of host habitat use overlap on bTB risk. We used the comparative intradermal tuberculin test to assess the number of bTB infected cattle. Our results suggested a dilution effect through species evenness. We found that the identity effect of greater kudu - a maintenance host – confounded the dilution effect of species diversity on bTB risk. bTB infection was positively correlated with habitat use overlap between greater kudu and cattle. Different diversity indices have to be considered together for assessing diversity-disease relationships, for understanding the underlying causal mechanisms. We posit that unpacking diversity metrics is also relevant for formulating control strategies to manage cattle in ecosystems characterized by seasonally limited resources and intense wildlife-livestock interactions.

Keywords: evenness, diversity, greater kudu, identity effect, maintenance hosts, multi-host disease ecology, habitat use overlap

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Authors: H. Akhloufi, M. Hulscher, J. M. Prins, I. H. Van Der Sijs, D. Melles, A. Verbon

Abstract:

Background: A timely switch from intravenous to oral antibiotic therapy has many advantages, such as reduced incidence of IV-line related infections, a decreased hospital length of stay and less workload for healthcare professionals with equivalent patient safety. Additionally, numerous studies have demonstrated significant decreases in costs of a timely intravenous to oral antibiotic therapy switch, while maintaining efficacy and safety. However, a considerable variation in iv to oral antibiotic switch therapy criteria has been described in literature. Here, we report the development of a set of iv to oral switch criteria that are generally applicable in all hospitals. Material/methods: A RAND-modified Delphi procedure, which was composed of 3 rounds, was used. This Delphi procedure is a widely used structured process to develop consensus using multiple rounds of questionnaires within a qualified panel of selected experts. The international expert panel was multidisciplinary and composed out of clinical microbiologists, infectious disease consultants and clinical pharmacists. This panel of 19 experts appraised 6 major intravenous to oral antibiotic switch therapy criteria and operationalized these criteria using 41 measurable conditions extracted from the literature. The procedure to select a concise set of iv to oral switch criteria included 2 questionnaire rounds and a face-to-face meeting. Results: The procedure resulted in the selection of 16 measurable conditions, which operationalize 6 major intravenous to oral antibiotic switch therapy criteria. The following 6 major switch therapy criteria were selected: (1) Vital signs should be good or improving when bad. (2) Signs and symptoms related to the infection have to be resolved or improved. (3) The gastrointestinal tract has to be intact and functioning. (4) The oral route should not be compromised. (5) Absence of contra-indicated infections. (6) An oral variant of the antibiotic with good bioavailability has to exist. Conclusions: This systematic stepwise method which combined evidence and expert opinion resulted in a feasible set of 6 major intravenous to oral antibiotic switch therapy criteria operationalized by 16 measurable conditions. This set of early antibiotic iv to oral switch criteria can be used in daily practice in all adult hospital patients. Future use in audits and as rules in computer assisted decision support systems will lead to improvement of antimicrobial steward ship programs.

Keywords: antibiotic resistance, antibiotic stewardship, intravenous to oral, switch therapy

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Authors: Gabriela Prins, Quinette Louw, Dawn Ernstzen

Abstract:

Background: Access to rehabilitation services is a major challenge globally, especially in low-and-middle income countries (LMICs) where resources and infrastructure are extremely limited. Telerehabilitation (TR) has emerged in recent decades as a highly promising method to dramatically expand accessibility to rehabilitation services globally. TR provides rehabilitation care remotely using communication technologies such as video conferencing, smartphones, and internet-connected devices. This boosts accessibility to underprivileged regions and allows for greater flexibility for patients. Despite this, TR is hindered by several factors, including limited technological resources, high costs, lack of digital access, and the unavailability of healthcare systems, which are major barriers to widespread adoption among LMIC patients. These barriers have collectively hindered the potential implementation and adoption of TR services in LMICs healthcare settings. Adoption of TR will also require the buy-in of end users and limited information is known on the perspectives of the SA population. Aim: The study aimed to understand patients' perspectives regarding the use of digital technology as part of their OA rehabilitation at a public community healthcare centre in the Cape Metropole Area. Methods: A qualitative descriptive study design was used on 10 OA patients from a public community rehabilitation centre in South Africa. Data collection included semi-structured interviews and patient-reported outcome measures (PSFS, ASES-8, and EuroQol EQ-5D-5L) on functioning and quality of life. Transcribed interview data were coded in Atlas.ti. 22.2 and analyzed using thematic analysis. The results were narratively documented. Results: Four themes arose from the interviews. The themes were Telerehabilitation awareness (Use of Digital Technology Information Sources and Prior Experience with Technology /TR), Telerehabilitation Benefits (Access to healthcare providers, Access to educational information, Convenience, Time and Resource Efficiency and Facilitating Family Involvement), Telerehabilitation Implementation Considerations (Openness towards TR Implementation, Learning about TR and Technology, Therapeutic relationship, and Privacy) and Future use of Telerehabilitation (Personal Preference and TR for the next generation). The ten participants demonstrated limited awareness and exposure to TR, as well as minimal digital literacy and skills. Skepticism was shown when comparing the effectiveness of TR to in-person rehabilitation and valued physical interactions with health professionals. However, some recognized potential benefits of TR for accessibility, convenience, family involvement and improving community health in the long term. Willingness existed to try TR with sufficient training. Conclusion: With targeted efforts addressing identified barriers around awareness, technological literacy, clinician readiness and resource availability, perspectives on TR may shift positively from uncertainty towards endorsement of this expanding approach for simpler rehabilitation access in LMICs.

Keywords: digital technology, osteoarthritis, primary health care, telerehabilitation

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Authors: Wen-Yang Hu, Ranli Lu, Mark Maienschein-Cline, Danping Hu, Larisa Nonn, Toshi Shioda, Gail S. Prins

Abstract:

Background: Genetic mutations are highly associated with increased prostate cancer risk. In addition to whole genome sequencing, somatic mutations can be identified by aligning transcriptome sequences to the human genome. Here we analyzed bulk RNAseq and single cell RNAseq data of human prostate cancer cells and their matched non-cancer cells in benign regions from 4 individual patients. Methods: Sequencing raw reads were aligned to the reference genome hg38 using STAR. Variants were annotated using Annovar with respect to overlap gene annotation information, effect on gene and protein sequence, and SIFT annotation of nonsynonymous variant effect. We determined cancer-specific novel alleles by comparing variant calls in cancer cells to matched benign cells from the same individual by selecting unique alleles that were only detected in the cancer samples. Results: In bulk RNAseq data from 3 patients, the most common variants were the noncoding mutations at UTR3/UTR5, and the major variant types were single-nucleotide polymorphisms (SNP) including frameshift mutations. C>T transversion is the most frequently presented substitution of SNP. A total of 222 genes carrying unique exonic or UTR variants were revealed in cancer cells across 3 patients but not in benign cells. Among them, transcriptome levels of 7 genes (CITED2, YOD1, MCM4, HNRNPA2B1, KIF20B, DPYSL2, NR4A1) were significantly up or down regulated in cancer stem cells. Out of the 222 commonly mutated genes in cancer, 19 have nonsynonymous variants and 11 are damaged genes with variants including SIFT, frameshifts, stop gain/loss, and insertions/deletions (indels). Two damaged genes, activating transcription factor 6 (ATF6) and histone demethylase KDM3A are of particular interest; the former is a survival factor for certain cancer cells while the later positively activates androgen receptor target genes in prostate cancer. Further, single cell RNAseq data of cancer cells and their matched non-cancer benign cells from both primary 2D and 3D tumoroid cultures were analyzed. Similar to the bulk RNAseq data, single cell RNAseq in cancer demonstrated that the exonic mutations are less common than noncoding variants, with SNPs including frameshift mutations the most frequently presented types in cancer. Compared to cancer stem cell enriched-3D tumoroids, 2D cancer cells carried 3-times higher variants, 8-times more coding mutations and 10-times more nonsynonymous SNP. Finally, in both 2D primary and 3D tumoroid cultures, cancer stem cells exhibited fewer coding mutations and noncoding SNP or insertions/deletions than non-stem cancer cells. Summary: Our study demonstrates the usefulness of bulk and single cell RNAseaq data in identifying somatic mutations in prostate cancer, providing an alternative method in screening candidate genes for prostate cancer diagnosis and potential therapeutic targets. Cancer stem cells carry fewer somatic mutations than non-stem cancer cells due to their inherited immortal stand DNA from parental stem cells that explains their long-lived characteristics.

Keywords: prostate cancer, stem cell, genomic mutation, RNAseq

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