bluuebunny/crossref_metadata_2025_split huggingface dataset:
Introducing Fair Work through ‘Soft’ Regulation in Outsourced Public Service Networks: Explaining Unintended Outcomes in the Implementation of the Scottish Living Wage Policy
Authors: Cunningham Ian , James Philip , Baluch Alina , Cullen Anne-Marie 
Published: October 2022

Abstract
Using a regulatory analysis from Martinez Lucio and Mackenzie (2014 and 2016), this study contributes to debates concerning the capacity of ‘soft’ regulation to advance employment conditions and outcomes. This study explores the implementation of a real living wage policy for employees in outsourced Scottish social care. Despite employer compliance in implementing the living wage, it had a mixed impact on the income of workers and did not improve staff recruitment and retention. The theoretical framework challenges recent optimistic views concerning the impact of such regulation by revealing unintended and problematic consequences, such as problems with differentials and providers walking away from contracts. It further reveals how actor roles, interests, power resources and inter-relationships, as well as surrounding structural contextual influences (austerity, marketisation and engrained values and processes in political settlements), interacted to shape these outcomes. Insights from this study include that ‘soft’ regulation was unable to create conditions for actors such as trade unions, employers and non-governmental organisations to colonise or seize the regulatory space to secure the full benefits of the Scottish Living Wage. The political settlement with the Scottish Government allowed local authorities to retain coercive control over other actors in the regulatory space. Employers and trade unions were further hindered by lack of unity and continued isolation from decisions, respectively. Surrounding economic and ideological restrictions imposed by the central UK government’s austerity agenda, and the retention of powers over employment regulation added to the failure of these ‘soft’ measures to increase pay and improve recruitment and retention in social care.
Team is brain: leveraging EHR audit log data for new insights into acute care processes
Authors: Rose Christian , Thombley Robert , Noshad Morteza , Lu Yun , Clancy Heather A , Schlessinger David , Li Ron C , Liu Vincent X , Chen Jonathan H , Adler-Milstein Julia 
Published: October 2022

Abstract

Objective
To determine whether novel measures of contextual factors from multi-site electronic health record (EHR) audit log data can explain variation in clinical process outcomes.

Materials and Methods
We selected one widely-used process outcome: emergency department (ED)-based team time to deliver tissue plasminogen activator (tPA) to patients with acute ischemic stroke (AIS). We evaluated Epic audit log data (that tracks EHR user-interactions) for 3052 AIS patients aged 18+ who received tPA after presenting to an ED at three Northern California health systems (Stanford Health Care, UCSF Health, and Kaiser Permanente Northern California). Our primary outcome was door-to-needle time (DNT) and we assessed bivariate and multivariate relationships with six audit log-derived measures of treatment team busyness and prior team experience.

Results
Prior team experience was consistently associated with shorter DNT; teams with greater prior experience specifically on AIS cases had shorter DNT (minutes) across all sites: (Site 1: −94.73, 95% CI: −129.53 to 59.92; Site 2: −80.93, 95% CI: −130.43 to 31.43; Site 3: −42.95, 95% CI: −62.73 to 23.17). Teams with greater prior experience across all types of cases also had shorter DNT at two sites: (Site 1: −6.96, 95% CI: −14.56 to 0.65; Site 2: −19.16, 95% CI: −36.15 to 2.16; Site 3: −11.07, 95% CI: −17.39 to 4.74). Team busyness was not consistently associated with DNT across study sites.

Conclusions
EHR audit log data offers a novel, scalable approach to measure key contextual factors relevant to clinical process outcomes across multiple sites. Audit log-based measures of team experience were associated with better process outcomes for AIS care, suggesting opportunities to study underlying mechanisms and improve care through deliberate training, team-building, and scheduling to maximize team experience.
New onset delirium prediction using machine learning and long short-term memory (LSTM) in electronic health record
Authors: Liu Siru , Schlesinger Joseph J , McCoy Allison B , Reese Thomas J , Steitz Bryan , Russo Elise , Koh Brian , Wright Adam 
Published: October 2022

Abstract

Objective
To develop and test an accurate deep learning model for predicting new onset delirium in hospitalized adult patients.

Methods
Using electronic health record (EHR) data extracted from a large academic medical center, we developed a model combining long short-term memory (LSTM) and machine learning to predict new onset delirium and compared its performance with machine-learning-only models (logistic regression, random forest, support vector machine, neural network, and LightGBM). The labels of models were confusion assessment method (CAM) assessments. We evaluated models on a hold-out dataset. We calculated Shapley additive explanations (SHAP) measures to gauge the feature impact on the model.

Results
A total of 331 489 CAM assessments with 896 features from 34 035 patients were included. The LightGBM model achieved the best performance (AUC 0.927 [0.924, 0.929] and F1 0.626 [0.618, 0.634]) among the machine learning models. When combined with the LSTM model, the final model’s performance improved significantly (P = .001) with AUC 0.952 [0.950, 0.955] and F1 0.759 [0.755, 0.765]. The precision value of the combined model improved from 0.497 to 0.751 with a fixed recall of 0.8. Using the mean absolute SHAP values, we identified the top 20 features, including age, heart rate, Richmond Agitation-Sedation Scale score, Morse fall risk score, pulse, respiratory rate, and level of care.

Conclusion
Leveraging LSTM to capture temporal trends and combining it with the LightGBM model can significantly improve the prediction of new onset delirium, providing an algorithmic basis for the subsequent development of clinical decision support tools for proactive delirium interventions.
Use of patient portals to support recruitment into clinical trials and health research studies: results from studies using MyChart at one academic institution
Authors: Sherman Scott E , Langford Aisha T , Chodosh Joshua , Hampp Carina , Trachtman Howard 
Published: October 2022

Abstract
Electronic health records (EHRs) are often used for recruitment into research studies, as they efficiently facilitate targeted outreach. While studies increasingly are reaching out to potential participants through the EHR patient portal, there is little available information about which approaches are most effective. We surveyed all investigators at one academic medical center who had used the Epic MyChart patient portal for recruitment. We found that messages were typically adapted for a large group, but not tailored further for individual subgroups. The vast majority of studies sent a message only once. Recruitment costs were modest, averaging $431/study. The results show some promise for recruiting through the patient portal but also identified ways in which messages could be optimized.
A New Ultra-Performance Liquid Chromatographic Method for the Quantification of Vitamin C in Fresh and Dried Goji Berries (Lycium barbarumL.) Cultivated in Turkey
Authors: Dinç Erdal , Üçer Asiye , Ünal Nazangül , Üstündağ Özgür 
Published: October 2022

AbstractBackgroundThe potential background of the study is related to comprehensive detection of the content of vitamin C with an actual chromatographic method.ObjectiveVitamin C is of vital importance in terms of human life and health due to its polyfunctional activity such as antioxidant activity and antiviral effect with other biological functions. In this regard, it may be necessary to update analytical methods or develop up-to-date analytical methods to accurately estimate the amount of vitamin C in natural samples. In this study, a new ultra-performance liquid chromatography with photodiode array detection (UPLC-PDA) method has been developed for the determination of vitamin C content in fresh and dried goji berries (Lycium barbarum L.), which are cultivated in Turkey.MethodThe chromatographic elution of vitamin C in natural fruit samples was achieved on an ACQUITY UPLC BEH C18 (1.7 µm, 2.1 mm × 100 mm) column using methanol and 0.1 M H3PO4 pH 2.15 (20:80, v/v), which are mobile phase. UPLC determination was done at the 242.8 nm. Flow rate was 0.20 mL/min at a column temperature of 30°C. Linearity range of the calibration graph was found to be at 5–30 µg/mL. The validity of the newly developed UPLC method was tested by analyzing individual test samples and added samples.ResultsApplicability of the validated UPLC method was verified by the quantitative analysis of vitamin C content in both fresh and dried goji berries.ConclusionsWe believe that the newly developed and validated UPLC method would be a useful and promising approach for simple quantitative analysis of goji berry samples for vitamin C.HighlightsIn previous studies, no UPLC-PDA method was reported for the analysis of vitamin C in goji berries. The method provided a good repeatability for the analysis of real samples.
Sex-specific Feeding Behavior of Adult House Flies, Musca domestica L. (Diptera: Muscidae)
Authors: Neupane Saraswoti , Hall Brandon , Brooke Grant , Nayduch Dana 
Published: October 2022

Abstract
House flies, Musca domestica L., (Diptera: Muscidae) mechanically vector diverse disease-causing microorganisms while foraging for food in agricultural and urban habitats. Although flies are diverse feeders, nutrient composition of food is important for both fly longevity and reproduction, especially for anautogenous females who require protein for egg production. We investigated whether fly sex and/or mating status influenced their preference for foods with varying macronutrient composition. Presumably mated or unmated male and female flies were separated by sex and offered four food, each in 10% solution offered on cotton wicks: sugar (carbohydrate-rich), fat-free milk (protein-rich, moderate carbohydrate), egg-yolk (protein and lipid-rich), and water (no macronutrients). Foods were colored with nontoxic dyes, which were rotated between replicates. After 4h exposure, flies were dissected to determine the type of food(s) ingested. The interaction of house fly sex and food type significantly influenced food preference, where females preferred milk (protein and carbohydrate-rich food), and males preferred mainly sugar (carbohydrate-rich). Furthermore, 32.8% of females and 10.6% of males foraged on multiple foods. While interaction of sex and mating status had no effect on food preference, milk preference was significantly higher in presumably mated than unmated females. We also tested whether food color influenced fly feeding preference, and found that color was most significant when flies were offered one food type, but negligible when multiple food types were present. This study suggests that bait-based fly control strategies should consider sex-specific preferences for various food attractants if aiming to target and control both male and female house flies.
Phlebotomine Fauna (Diptera: Psychodidae) and Infection by Leishmania spp. in Forest Fragments of a University Campus, Western Amazon
Authors: Carneiro Ana Carolina Gomes , de Souza Eduardo Alcici , Barroso Edmilson Pereira , de Ávila Márcia Moreira , Melchior Leonardo Augusto Kohara , Rocha Ricardo da Costa , Shimabukuro Paloma Helena Fernandes , Galati Eunice Aparecida Bianchi , Brilhante Andréia Fernandes 
Published: October 2022

Abstract
Forest fragments consist of important ecosystems for the maintenance of sand fly populations and Leishmania hosts. This study sought to identify the phlebotomine fauna and its infection by Leishmania spp. in forest fragments on the campus of the Federal University of Acre (UFAC), Western Amazon. Monthly collections with CDC traps were carried out from March 2020 to June 2021, in four forest fragments of UFAC. Male and female insects were processed and identified at species level. A sample of females was subjected to polymerase chain reaction (PCR) analysis to verify the presence Leishmania DNA. In total, 465 specimens were collected, of which 238 were males and 227 were females. The most frequent species were Nyssomyia antunesi (Coutinho, 1939) (47.3%), Trichophoromyia sp. (Mangabeira, 1942) (18.70%), and Ny. whitmani (Antunes & Coutinho, 1939) (8.81%). Molecular analysis detected the presence of Leishmania (Ross, 1903) DNA in a specimen of Ny. antunesi, and another one of Evandromyia walker (Newstead, 1914). The forest fragments of the university campus harbor a diverse sand fly fauna with the presence of Leishmania DNA in these insects, in addition to the presence of other species considered incriminated vectors of Leishmania parasites.
Acceptability and Feasibility of eSCCIP: Results From a Pilot Study of the Electronic Surviving Cancer Competently Intervention Program
Authors: Canter Kimberly S , Vega Gabriela , Perez Ramirez Alejandra , Munoz Osorio Angel , Thomas Courtney , Lewis Amanda M , Arasteh Kamyar , Kazak Anne 
Published: October 2022

AbstractBackgroundProviding high-quality psychosocial care to parents and other primary caregivers of children with cancer (henceforth referred to as caregivers) is important, given the numerous challenges associated with a pediatric cancer diagnosis and the increased risk for negative psychosocial sequelae among caregivers. The Electronic Surviving Cancer Competently Intervention Program (eSCCIP) is a psychosocial eHealth intervention for caregivers, developed using an iterative, user-centered process.MethodeSCCIP was tested in a single-arm pilot trial at Nemours Children’s Hospital, Delaware (NCT05333601). The primary outcomes were intervention acceptability and feasibility, assessed via enrollment and retention targets, and item-level acceptability ratings. Enrollment and retention targets of 45% were set based on previous work, and an item-level acceptability threshold of 80% was set. A secondary exploratory analysis was conducted examining acute distress, anxiety, symptoms of post-traumatic stress, and family functioning.Results44 caregivers enrolled in the study and 31 completed. The intervention was rated favorably by completers, with over 80% of the sample selecting “mostly true” or “very true” for all items of the eSCCIP Evaluation Questionnaire, which was used to assess acceptability and feasibility. Enrollment and retention rates were 54% and 70%, respectively. Exploratory psychosocial outcomes showed statistically significant decreases from pre-intervention to post-intervention for overall symptoms of post-traumatic stress disorder (PTSD), cluster D symptoms of PTSD (negative mood and cognitions), and anxiety. Small-moderate effect sizes were observed for all psychosocial outcomes of interest.ConclusionseSCCIP is an acceptable and feasible intervention for caregivers. Results are promising regarding reductions in symptoms of post-traumatic stress and anxiety.
Alternative splicing in plants: current knowledge and future directions for assessing the biological relevance of splice variants
Authors: Tognacca Rocío S , Rodríguez Florencia S , Aballay Federico E , Cartagena Carla M , Servi Lucas , Petrillo Ezequiel 
Published: October 2022

AbstractAlternative splicing is an important regulatory process that produces multiple transcripts from a single gene, significantly modulating the transcriptome and potentially the proteome, during development and in response to environmental cues. In the first part of this review, we summarize recent advances and highlight the accumulated knowledge on the biological roles of alternative splicing isoforms that are key for different plant responses and during development. Remarkably, we found that many of the studies in this area use similar methodological approaches that need to be improved to gain more accurate conclusions, since they generally presume that stable isoforms undoubtedly have coding capacities. This is mostly done without data indicating that a particular RNA isoform is in fact translated. So, in the latter part of the review, we propose a thorough strategy to analyze, evaluate, and characterize putative functions for alternative splicing isoforms of interest.
Taming the Selection of Optimal Substitution Models in Phylogenomics by Site Subsampling and Upsampling
Authors: Sharma Sudip , Kumar Sudhir 
Published: October 2022

Abstract
The selection of the optimal substitution model of molecular evolution imposes a high computational burden for long sequence alignments in phylogenomics. We discovered that the analysis of multiple tiny subsamples of site patterns from a full sequence alignment recovers the correct optimal substitution model when sites in the subsample are upsampled to match the total number of sites in the full alignment. The computational costs of maximum-likelihood analyses are reduced by orders of magnitude in the subsample–upsample (SU) approach because the upsampled alignment contains only a small fraction of all site patterns. We present an adaptive protocol, ModelTamer, that implements the new SU approach and automatically selects subsamples to estimate optimal models reliably. ModelTamer selects models hundreds to thousands of times faster than the full data analysis while needing megabytes rather than gigabytes of computer memory.
FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations
Authors: Zhou Nan , Yuan Xiaoqing , Du Qingsong , Zhang Zhiyu , Shi Xiaolei , Bao Jinku , Ning Yuping , Peng Li 
Published: October 2022

AbstractFerroptosis is a mode of regulated cell death characterized by iron-dependent accumulation of lipid peroxidation. It is closely linked to the pathophysiological processes in many diseases. Since our publication of the first ferroptosis database in 2020 (FerrDb V1), many new findings have been published. To keep up with the rapid progress in ferroptosis research and to provide timely and high-quality data, here we present the successor, FerrDb V2. It contains 1001 ferroptosis regulators and 143 ferroptosis-disease associations manually curated from 3288 articles. Specifically, there are 621 gene regulators, of which 264 are drivers, 238 are suppressors, 9 are markers, and 110 are unclassified genes; and there are 380 substance regulators, with 201 inducers and 179 inhibitors. Compared to FerrDb V1, curated articles increase by &gt;300%, ferroptosis regulators increase by 175%, and ferroptosis-disease associations increase by 50.5%. Circular RNA and pseudogene are novel regulators in FerrDb V2, and the percentage of non-coding RNA increases from 7.3% to 13.6%. External gene-related data were integrated, enabling thought-provoking and gene-oriented analysis in FerrDb V2. In conclusion, FerrDb V2 will help to acquire deeper insights into ferroptosis. FerrDb V2 is freely accessible at http://www.zhounan.org/ferrdb/.
RiboXYZ: a comprehensive database for visualizing and analyzing ribosome structures
Authors: Kushner Artem , Petrov Anton S , Dao Duc Khanh 
Published: October 2022

Abstract
Recent advances in Cryo-EM led to a surge of ribosome structures deposited over the past years, including structures from different species, conformational states, or bound with different ligands. Yet, multiple conflicts of nomenclature make the identification and comparison of structures and ortholog components challenging. We present RiboXYZ (available at https://ribosome.xyz), a database that provides organized access to ribosome structures, with several tools for visualisation and study. The database is up-to-date with the Protein Data Bank (PDB) but provides a standardized nomenclature that allows for searching and comparing ribosomal components (proteins, RNA, ligands) across all the available structures. In addition to structured and simplified access to the data, the application has several specialized visualization tools, including the identification and prediction of ligand binding sites, and 3D superimposition of ribosomal components. Overall, RiboXYZ provides a useful toolkit that complements the PDB database, by implementing the current conventions and providing a set of auxiliary tools that have been developed explicitly for analyzing ribosome structures. This toolkit can be easily accessed by both experts and non-experts in structural biology so that they can search, visualize and compare structures, with various potential applications in molecular biology, evolution, and biochemistry.
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes
Authors: Dong Mei-Jing , Luo Hao , Gao Feng 
Published: October 2022

Abstract
DoriC was first launched in 2007 as a database of replication origins (oriCs) in bacterial genomes and has since been constantly updated to integrate the latest research progress in this field. The database was subsequently extended to include the oriCs in archaeal genomes as well as those in plasmids. This latest release, DoriC 12.0, includes the oriCs in both draft and complete prokaryotic genomes. At the same time, the number of oriCs in the database has also increased significantly and currently contains over 200 000 bacterial entries distributed in more than 40 phyla. Among them, a large number are from bacteria in new phyla whose oriCs were not explored before. Additionally, new oriC features and improvements have been introduced, especially in the visualization and analysis of oriCs. Currently, DoriC is considered as an important database in the fields of bioinformatics, microbial genomics, and even synthetic biology, providing a valuable resource as well as a comprehensive platform for the research on oriCs. DoriC 12.0 can be accessed at https://tubic.org/doric/ and http://tubic.tju.edu.cn/doric/.
Habit formation and trade unions
Authors: Goerke Laszlo , Hartmann Sven A 
Published: October 2022

Abstract
We analyse how habit formation affects collective bargaining outcomes if a firm-specific trade union determines wages. For a wide variety of alternative analytical settings, such internal reference points induce the union to increase wages over time. A numerical example suggests that the resulting decline in employment can be substantial. Furthermore, policy changes in one period, which are either reversed in the next or anticipated in previous periods, have effects on wage outcomes for multiple periods because they affect the habit stock at times at which they are not yet or no longer in operation.
Liver Disease and Treatment Needs of Asymptomatic Persons Living With Hepatitis B in Senegal
Authors: Ramírez Mena Adrià , Thioubou Mame Aissé , Diallo Kalilou , Tine Judicaël , Ngom Ndeye Fatou , Fortes Louise , Ndiaye Kiné , Karasi Jean-Claude , Seguin-Devaux Carole , Goedertz Henri , Diouf Daouda , Seydi Moussa , Sambou Benjamin Amaye , Arendt Vic , Wandeler Gilles , Manga Noël Magloire ,   for SEN-B and CARES
Published: October 2022

Abstract
The prevalence of active hepatitis B among asymptomatic persons remains unclear in Africa. Of 1206 newly diagnosed persons in Senegal, 12.3% had significant fibrosis and 31.3% had hepatitis B virus (HBV) DNA levels &gt;2000 IU/mL. Overall, 128 (12.9%) were eligible for antiviral therapy. Generalized HBV screening allowed the identification of a large population requiring HBV care.