bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probabilistic identification of bacterial essential genes via insertion density using TraDIS data with Tn5 libraries
Authors: Nlebedim Valentine U , Chaudhuri Roy R , Walters Kevin 
Published: July 2021

AbstractMotivationProbabilistic Identification of bacterial essential genes using transposon-directed insertion-site sequencing (TraDIS) data based on Tn5 libraries has received relatively little attention in the literature; most methods are designed for mariner transposon insertions. Analysis of Tn5 transposon-based genomic data is challenging due to the high insertion density and genomic resolution. We present a novel probabilistic Bayesian approach for classifying bacterial essential genes using transposon insertion density derived from transposon insertion sequencing data. We implement a Markov chain Monte Carlo sampling procedure to estimate the posterior probability that any given gene is essential. We implement a Bayesian decision theory approach to selecting essential genes. We assess the effectiveness of our approach via analysis of both simulated data and three previously published Escherichia coli, Salmonella Typhimurium and Staphylococcus aureus datasets. These three bacteria have relatively well characterized essential genes which allows us to test our classification procedure using receiver operating characteristic curves and area under the curves. We compare the classification performance with that of Bio-Tradis, a standard tool for bacterial gene classification.ResultsOur method is able to classify genes in the three datasets with areas under the curves between 0.967 and 0.983. Our simulated synthetic datasets show that both the number of insertions and the extent to which insertions are tolerated in the distal regions of essential genes are both important in determining classification accuracy. Importantly our method gives the user the option of classifying essential genes based on the user-supplied costs of false discovery and false non-discovery.Availability and implementationAn R package that implements the method presented in this paper is available for download from https://github.com/Kevin-walters/insdens.Supplementary informationSupplementary data are available at Bioinformatics online.
Simulation-based environmental-impact assessment of glycerol-to-hydrogen conversion technologies
Authors: Khalil Yehia F 
Published: July 2021

Abstract
This simulation-based comparative assessment aims to quantify the environmental and human-health impacts of greener hydrogen (H2) production via three glycerol-based technologies, including: supercritical water reforming (SCWR), aqueous-phase reforming (APR) and autothermal reforming (ATR). The GaBi (2018 edition) life-cycle assessment (LCA) platform is used to develop cradle-to-gate product system models for these technologies and the TRACI 2.1 methodology is used to quantify their midpoint impact categories. Aspen HYSYS (v11) process-simulation software is used to generate the life-cycle inventory (LCI) primary data required to produce 1 kg of H2 via each of the indicated glycerol-reforming technologies. Per ISO 14040:2006 reporting requirements for the LCA results interpretation step, three base case (BC) scenarios and four sensitivity scenarios (SS) are developed and quantified to compare the effects of different process electricity sources (US grid mix versus wind power) and thermal energy sources (natural gas versus biogas) on the LCA results. The high operating pressure (viz. 240 bar) of SCWR enabled assessment of the impact of in situ electricity generation to offset some of electricity required for this technology. The major insights from this research are as follows: (i) per 1 kg of produced H2, APR reduces CO2 emissions by ≈95% compared to ATR and by ≈92% compared to SCWR, (ii) for BC scenarios, the primary energy consumption (in MJ/kg of produced H2) is in the following order from highest to lowest: ATR &gt; SCWR &gt; APR and (iii) H2 production via glycerol APR is more environmentally sustainable than SCWR and ATR, and thus offers a promising path for greener H2 production. Future environmental sustainability studies should focus on expanding the scope of this study to include H2 production via water electrolysis using renewable electricity sources and via solar and nuclear-driven thermochemical water splitting.
A software-based approach in designing a rooftop bifacial PV system for the North Hall of Residence, IUT
Authors: Mehadi Abdullah Al , Chowdhury Misbahul Alam , Nishat Mirza Muntasir , Faisal Fahim , Islam Md Minhajul 
Published: July 2021

Abstract
Bifacial rooftop photovoltaic panels appear to be an excellent means of power generation in this era of urbanization, especially for land-limited countries like Bangladesh. This paper presents a software-based approach to design and simulate a bifacial solar-panel-based energy model on the rooftop of the North Hall of Residence of the Islamic University of Technology, Gazipur. This vertically mounted model investigates the feasibility and applicability of such an energy model in a university residence, situated in a load-shedding-prone area. Hence, three prominent software platforms, namely PVSOL, PVsyst and System Advisor Model (SAM), are brought into action and rigorous simulations are performed for three different orientations; promising outcomes are observed in terms of annual energy yield, bifacial gain (BG) and consumption coverage of the grid and PV model. The annual energy demand of the North Hall is ~444 733.5 kWh. The three orientations can generate annually 92 508.62, 94 643.48 and 86 758.94 kWh, respectively. Hence, it is evident that the proposed orientations can supply almost 19–21% of the site’s annual demand. Monthly BG analysis shows an overall increase in energy gain of 13%, 15.6% and 6% for Orientation-1, Orientation-2 and Orientation-3, respectively. A rigorous comparative analysis and deviation analysis among the software results has been accomplished to gain more insight into the feasibility of the proposed system. Thus, we have focused on a detailed software-based estimation of energy production for different orientations of the PV panels, considering several factors, which will provide prior knowledge and assessment before going for hardware implementation in the future.
Novel Approaches Identifying Relevant Patient-Reported Outcomes in Patients With Inflammatory Bowel Diseases—LISTEN 1
Authors: Teich Niels , Schulze Hermann , Knop Jana , Obermeier Michael , Stallmach Andreas 
Published: July 2021

Abstract

Background
Several patient-reported outcomes (PROs) have been established and are widely used in the assessment of patients with inflammatory bowel disease (IBD). However, it has never been investigated which PRO items are experienced by and are considered most relevant for IBD patients.

Methods
A review of IBD-related disease scores by a steering committee led to the identification of relevant PRO questions and assignment to 16 different PRO categories (9 symptoms and 7 impacts) that characterize patient’s disease burden. In a cross-sectional study, a digital patient survey was carried out to determine the self-reported experience by multiple response, the relevance of these PRO categories by pairwise comparison and the suitability of the respective questions and answer possibilities by yes-or-no-question.

Results
Sixty patients with Crohn’s disease (CD) (56.7% women; mean age 40.6 years; mean disease duration 12.4 years) and 60 patients with ulcerative colitis (UC) (51.7% women; mean age 37.3 years; mean disease duration 9.0 years) participated in the patient survey. All predefined symptoms and impacts, with the exception of nausea, were experienced by at least 50% of patients. Stool urgency and pain were rated the 2 most important symptoms in CD patients with similar ratings for relevance. Stool urgency was also the most important symptom in patients with UC, followed by stool frequency. Differences in self-reported experience between CD and UC patients were seen for the symptoms of rectal bleeding, pain, and nausea. Most important impact of symptoms in both patient groups were general wellbeing followed by social activities, while sexual activity was the least relevant impact category.

Conclusions
Stool urgency was the most relevant and most self-reported symptom for both CD and UC. Relevance and self-reported experience of pain and rectal bleeding differed between the 2 diseases. Therefore, the future collection of PROs should take these disease specificities into consideration.
An evaluation of the predictive performance and mapping power of the BayesR model for genomic prediction
Authors: Mollandin Fanny , Rau Andrea , Croiseau Pascal 
Published: July 2021

Abstract
Technological advances and decreasing costs have led to the rise of increasingly dense genotyping data, making feasible the identification of potential causal markers. Custom genotyping chips, which combine medium-density genotypes with a custom genotype panel, can capitalize on these candidates to potentially yield improved accuracy and interpretability in genomic prediction. A particularly promising model to this end is BayesR, which divides markers into four effect size classes. BayesR has been shown to yield accurate predictions and promise for quantitative trait loci (QTL) mapping in real data applications, but an extensive benchmarking in simulated data is currently lacking. Based on a set of real genotypes, we generated simulated data under a variety of genetic architectures and phenotype heritabilities, and we evaluated the impact of excluding or including causal markers among the genotypes. We define several statistical criteria for QTL mapping, including several based on sliding windows to account for linkage disequilibrium (LD). We compare and contrast these statistics and their ability to accurately prioritize known causal markers. Overall, we confirm the strong predictive performance for BayesR in moderately to highly heritable traits, particularly for 50k custom data. In cases of low heritability or weak LD with the causal marker in 50k genotypes, QTL mapping is a challenge, regardless of the criterion used. BayesR is a promising approach to simultaneously obtain accurate predictions and interpretable classifications of SNPs into effect size classes. We illustrated the performance of BayesR in a variety of simulation scenarios, and compared the advantages and limitations of each.
Decision G 1/19 and the Messy Misconception of the COMVIK Approach
Authors: Baldus Oliver 
Published: July 2021

Abstract
Decision G 1/19 of the Enlarged Board of Appeal (EBA) of the European Patent Office (EPO) answers the question whether computer simulations can be protected under the EPC. It was decided that these simulations in principle could solve a technical problem by producing a technical effect going beyond the simulation’s implementation on a computer. The result of the decision is rather non-spectacular and obvious, since it simply states that simulations can be protected under EPC law when they solve a technical problem. Nevertheless, the decision casts an extensive light on the general and established criteria to be used for assessing technicality. In this context a misconception of the COMVIK approach becomes apparent. The COMVIK approach is based on distinguishing technical from non-technical features. All technical features must be considered when assessing inventive step of an invention over prior art, while non-technical features have no significance for this purpose. In this view it is assumed that all information provided by a claim can be either classified as a technical or a non-technical feature. Further it is assumed that features exist that are inherently technical, i.e. technical per se. However, this concept of an inherent technical character is misleading. Basically, all information should first be distinguished as to whether it has a substantial effect on the design of the claimed subject-matter. Information that does not influence its ‘appearance’ must be seen a ‘non-feature’, whereas all other information describing a characteristic of the claimed subject-matter forms a ‘feature’. Secondly the so determined features are to be divided into technical or non-technical features, solely depending on whether they contribute to the solution of the concrete technical problem of the invention. In this way, the non-feature concept avoids many classification problems associated with the former COMVIK approach and constitutes the only admissible way to assess technicality correctly, consistently and non-sophistically.
Comparative Evaluation of the SMARTCHEK Salmonella Species Detection Kit for GENECHECKER UF-300 Real-Time PCR System with Rapi:chipTM and Rapi:DirectTM Lysis Buffer for Select Foods: AOAC Performance Tested MethodSM 032101
Authors: Lee Dobu , Choi Okran , Park Jinhee 
Published: July 2021

Abstract

Background
The candidate method, SMARTCHEK Salmonella spp. Detection Kit assay is designed for rapid detection of Salmonella spp. in select food matrixes, for use in conjunction with the Genesystems Rapi:chipTM and GENECHECKER UF-300 real-time PCR system.

Objective
The independent laboratory evaluation consisted of an inclusivity and exclusivity study, product consistency study, robustness study, stability study, and a matrix study. The paired matrix study tested romaine lettuce, peanut butter, liquid whole egg, chicken carcass rinsate, and raw chicken. The robustness study evaluated the method by changing three method parameters. The accelerated stability and product consistency study was conducted at 8, 16, 24, 32, and 40 days.

Methods
The candidate method was compared to the U.S. Department of Agriculture Food Safety and Inspection Service Microbiology Laboratory Guidebook 4.10 Isolation and Identification of Salmonella from Meat, Poultry, Pasteurized Egg, and Siluriformes (Fish) Products and Carcass and Environmental Sponges and to the U.S. Food and Drug Administration Bacteriological Analytical Manual, Chapter 5: Salmonella following a paired study design.

Results
All 108 Salmonella isolates were detected in all three broths tested for inclusivity, while all 35 non-Salmonella isolates were correctly excluded. In the matrix study, the candidate method showed no significant differences between confirmed candidate method results and reference method results for all food matrixes evaluated.

Conclusion
The candidate method is an effective method for the qualitative detection of Salmonella spp. in select food matrixes.

Highlights
The SMARTCHEK Salmonella spp. Detection Kit assay allows for fast, reliable detection of Salmonella spp. with results obtained after 24 h of incubation and a PCR run time of only 35 min.
Consequences of the Lack of Criminalization of Enforced Disappearance at the Domestic Level
Authors: Citroni Gabriella 
Published: July 2021

Abstract
The obligation to codify enforced disappearance as an autonomous offence under domestic criminal legislation is well established in international law and jurisprudence, and it responds to the need to adequately comprehend and address the extraordinarily complex nature of this crime. Yet very few states abide by such an obligation. When called upon to explain this failure, those lacking a separate offence in their domestic legislation — including Italy — argue that other offences (e.g. kidnapping, abduction, torture, or illegal deprivation of liberty) are adequate. The article analyses the Italian experience with investigations and proceedings conducted in the absence of an autonomous offence of enforced disappearance. They concern enforced disappearances perpetrated in the context of the Operación Cóndor in Latin America where the victims were Italian nationals, requests for extradition concerning cases that amount to enforced disappearance, and enforced disappearances committed in the realm of operations of ‘extraordinary renditions’. The consequences of the lack of criminalization of enforced disappearance include the undue fragmentation of responsibility when pressing charges; challenges concerning the evidentiary criteria, especially with regard to the mental element; the application of tight statutes of limitation; and the failure to adequately implement the aut dedere aut judicare principle, ultimately resulting in an increased rate of impunity.
Are the well-fed less thirsty? Effects of drought and salinity on New Zealand mangroves
Authors: Ravi Sridevi , Bader Martin K-F , Young Tim , Duxbury Mark , Clearwater Michael , Macinnis-Ng Cate , Leuzinger Sebastian 
Published: July 2021

AbstractDespite a large number of studies examining the effects of abiotic stress factors on plants, the mechanistic explanations of drought-induced tree mortality remain inconclusive and even less is known about how multiple stressors interact. The role of non-structural carbohydrates (NSCs) in preventing or postponing drought mortality is gaining attention. Here, we tested the role of NSCs in mitigating the effects of drought and salinity in New Zealand mangroves, Avicennia marina subsp. australasica. We experimentally manipulated plant NSC levels, prior to subjecting them to combinations of drought and salinity. Plant growth and survival rates were 2- and 3-fold higher in the high-NSC (H-NSC) group than in the low-NSC (L-NSC) group under high salinity and drought conditions, respectively. After 12 weeks under high salinity–high drought conditions, the H-NSC group showed higher stem hydraulic conductivity (281 ± 50 mmol cm−1 s−1 MPa−1) compared with the L-NSC group (134 ± 40 mmol cm−1 s−1 MPa−1). Although starch levels remained relatively constant, we found a 20% increase in soluble sugars in the stems of H-NSC group under high drought and high salinity in week 8 compared with week 12. Our results suggest (i) an important role of NSCs in mitigating the effects of low soil water potential caused by drought and salinity, and (ii) sink-limited growth under conditions of combined salinity and drought.
Antegrade revascularization of the three mesenteric vessels to treat chronic mesenteric ischemia
Authors: Chaouch Nazih , Zagzoog Mohammad M 
Published: July 2021

Abstract
Chronic mesenteric ischemia is a serious vascular disease that progresses with acute mesenteric ischemia, along with high mortality. Elective intervention has been shown to prevent this progression and improve symptoms. Controversy remains about whether antegrade or retrograde mesenteric bypass has better outcomes and whether restoration of flow to a single vessel versus multiple mesenteric vessels should be performed. This study reports on our experience using an antegrade prosthetic bypass graft to treat chronic occlusions of the celiac trunk, superior mesenteric artery, and inferior mesenteric artery at their origins, all of which result in visceral ischemia.
Reduced Susceptibility to Metronidazole Is Associated With Initial Clinical Failure in Clostridioides difficile Infection
Authors: Gonzales-Luna Anne J , Olaitan Abiola O , Shen Wan-Jou , Deshpande Aditi , Carlson Travis J , Dotson Kierra M , Lancaster Chris , Begum Khurshida , Alam M Jahangir , Hurdle Julian G , Garey Kevin W 
Published: July 2021

Abstract

Background
Clinical studies have demonstrated inferior cure rates when metronidazole (MTZ) is used to treat Clostridioides difficile infection (CDI). We hypothesized that a newly identified, heme-inducible form of reduced MTZ susceptibility in C. difficile leads to higher odds of initial clinical failure in patients with CDI treated with MTZ.

Methods
This multicenter cohort study included adults diagnosed with CDI between 2017 and 2018. C. difficile isolated from stool samples underwent agar dilution MTZ susceptibility testing with incorporation of fresh heme. Blinded investigators reviewed medical records for initial clinical failure and other relevant clinical variables. Classification and regression tree (CART) analysis was used to identify the MTZ minimum inhibitory concentration (MIC) breakpoint that was predictive of initial clinical failure. Results were confirmed using univariate and multivariable logistic regression analyses to account for potential confounders.

Results
Of the 356 patients included, 72% received MTZ-based therapy and 27% experienced initial clinical failure. CART analysis identified an MTZ MIC ≥1 µg/mL above which patients had a higher rate of initial clinical failure. MTZ MICs ranged from 0.25 to 8 µg/mL (MIC50/90 = 0.25/2 µg/mL), and approximately 18% of isolates had MTZ MICs ≥1 µg/mL. In multivariable analysis, an MTZ MIC ≥1 µg/mL was an independent predictor of initial clinical failure in patients receiving an MTZ-based treatment regimen (odds ratio, 2.27 [95% confidence interval, 1.18–4.34]).

Conclusions
Using a reproducible method to determine C. difficile MICs to MTZ, a breakpoint of ≥1 µg/mL identified patients at higher risk of initial clinical failure.
Addressing digital diversity: Care matters in vulnerable digital relations in a Swedish library context
Authors: Sefyrin Johanna , Gustafsson Mariana , Wihlborg Elin 
Published: July 2021

AbstractAs societies become increasingly digitalized, the requirements for inclusion continuously increase. In a Swedish public, municipal, library context, it is common that individuals who face difficulties related to digital technologies come and ask for help. In this paper, we explore care in relations constituted by individuals and digital technologies and analyze how care matters for digital inclusion. It builds on field studies in a Swedish library context and includes qualitative interviews, focus groups, and observations of employees working to support individuals with digital needs. In order to analyze the material, we apply the concept of care. In the concluding discussion, we argue first for viewing individuals as sociomaterial entanglements of relations constituted by humans and non-humans, second that these sociomaterial entangled relations are vulnerable, shifting, and fluid, rather than stable, and third that these relations are in constant need of care.
The activation of nuclear factor-E2-related factor 2 (Nrf2)/heme oxygenase-1 (HO-1) signaling blunts cholestasis-induced liver and kidney injury
Authors: Mousavi Khadijeh , Niknahad Hossein , Li Huifeng , Jia Zhipeng , Manthari Ram Kumar , Zhao Yangfei , Shi Xiong , Chen Yuanyu , Ahmadi Asrin , Azarpira Negar , Khalvati Bahman , Ommati Mohammad Mehdi , Heidari Reza 
Published: July 2021

Abstract
Cholestasis is a severe clinical complication that severely damages the liver. Kidneys are also the most affected extrahepatic organs in cholestasis. The pivotal role of oxidative stress has been mentioned in the pathogenesis of cholestasis-induced organ injury. The activation of the nuclear factor-E2-related factor 2 (Nrf2) pathway is involved in response to oxidative stress. The current study was designed to evaluate the potential role of Nrf2 signaling activation in preventing bile acids-induced toxicity in the liver and kidney. Dimethyl fumarate was used as a robust activator of Nrf2 signaling. Rats underwent bile duct ligation surgery and were treated with dimethyl fumarate (10 and 40 mg/kg). Severe oxidative stress was evident in the liver and kidney of cholestatic animals (P &lt; 0.05). On the other hand, the expression and activity of Nrf2 and downstream genes were time-dependently decreased (P &lt; 0.05). Moreover, significant mitochondrial depolarization, decreased ATP levels, and mitochondrial permeabilization were detected in bile duct-ligated rats (P &lt; 0.05). Histopathological alterations included liver necrosis, fibrosis, inflammation and kidney interstitial inflammation, and cast formation. It was found that dimethyl fumarate significantly decreased hepatic and renal injury in cholestatic animals (P &lt; 0.05). Based on these data, the activation of the cellular antioxidant response could serve as an efficient therapeutic option for managing cholestasis-induced organ injury.