bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of a Voluntary Safety Reporting System to a Global Trigger Tool for Identifying Adverse Events in an Oncology Population
Authors: Samal Lipika , Khasnabish Srijesa , Foskett Cathy , Zigmont Katherine , Faxvaag Arild , Chang Frank , Clements Marsha , Rossetti Sarah Collins , Dalal Anuj K. , Leone Kathleen , Lipsitz Stuart , Massaro Anthony , Rozenblum Ronen , Schnock Kumiko O. , Yoon Catherine , Bates David W. , Dykes Patricia C. 
Published: July 2022

Objective
There is a lack of research on adverse event (AE) detection in oncology patients, despite the propensity for iatrogenic harm. Two common methods include voluntary safety reporting (VSR) and chart review tools, such as the Institute for Healthcare Improvement’s Global Trigger Tool (GTT). Our objective was to compare frequency and type of AEs detected by a modified GTT compared with VSR for identifying AEs in oncology patients in a larger clinical trial.

Methods
Patients across 6 oncology units (from July 1, 2013, through May 29, 2015) were randomly selected. Retrospective chart reviews were conducted by a team of nurses and physicians to identify AEs using the GTT. The VSR system was queried by the department of quality and safety of the hospital. Adverse event frequencies, type, and harm code for both methods were compared.

Results
The modified GTT detected 0.90 AEs per patient (79 AEs in 88 patients; 95% [0.71–1.12] AEs per patient) that were predominantly medication AEs (53/79); more than half of the AEs caused harm to the patients (41/79, 52%), but only one quarter were preventable (21/79; 27%). The VSR detected 0.24 AEs per patient (21 AEs in 88 patients; 95% [0.15–0.37] AEs per patient), a large plurality of which were medication/intravenous related (8/21); more than half did not cause harm (70%). Only 2% of the AEs (2/100) were detected by both methods.

Conclusions
Neither the modified GTT nor the VSR system alone is sufficient for detecting AEs in oncology patient populations. Further studies exploring methods such as automated AE detection from electronic health records and leveraging patient-reported AEs are needed.
Obstetrical Outcomes After Implementation of Laborist Model During the COVID-19 Pandemic
Authors: Prasannan Lakha , Gerber Rachel , Gulersen Moti , Shan Weiwei , Blitz Matthew J. , Rochelson Burton 
Published: July 2022

Objective
The COVID-19 pandemic prompted labor and delivery units to establish ways to decrease viral exposure to healthcare workers while continuing to deliver optimal patient care. A laborist model was implemented to improve safety at our tertiary care hospital in Long Island. The aim of the study is to determine whether implementation of a laborist model during the COVID-19 pandemic is associated with a change in the frequency of cesarean birth.

Methods
The retrospective cohort study included patients who delivered at a single tertiary center during March 2019 to May 2019 and March 2020 to May 2020 when our laborist model was initiated. The primary outcome compared the frequency of a cesarean delivery between both models. Secondary outcomes were the frequency of adverse obstetrical complications, which included intensive care unit admission, shoulder dystocia, intra-amniotic infection, hemorrhage, and need for blood transfusion. Statistical analysis included multivariable regression to adjust for potential confounders.

Results
A total of 1506 patients were included. Baseline characteristics were similar between the 2 groups. After adjusting for potential confounders, there was no significant difference in the frequency of cesarean births between both models (37% versus 35%; adjusted odds ratio, 1.003; 95% confidence interval, 0.46–2.89). Similarly, there were no significant differences in adverse outcomes between the study populations (adjusted odds ratio, 1.064; 95% confidence interval, 0.68–1.59).

Conclusions
A change in practice behavior during a pandemic was not associated with an increase in frequency of cesarean births or adverse obstetrical outcomes.
High-dose radiation exposure of cold-stored whole blood does not affect hemostatic function
Authors: Becerra Sandra C. , Darlington Daniel N. , Abaasah Isaac E. , Herzig Maryanne C. , Bynum James A. , Christy Barbara A. 
Published: July 2022

BACKGROUND
Whole blood (WB) transfusion is routinely used to resuscitate severely injured military trauma patients. Blood can be stored refrigerated while still maintaining reasonable function but is susceptible to environmental influences, including radiation exposure. Immune-compromised patients are transfused with irradiated blood to inactivate donor lymphocyte function (25 Gy per Association for the Advancement of Blood and Biotherapies [AARB] standard 5.7.3.2). However, there is limited information on function of WB exposed to high radiation doses.

OBJECTIVE
This study aimed to determine if stored irradiated WB still retains function. This will be important if the stored blood supply is exposed to radiation in a combat situation or mass casualty incident when the need for blood will be high.

METHODS
Whole blood collected from healthy donors was irradiated at 0, 25, or 75 Gy and stored at 4°C. Blood cell count, blood gas chemistry, thromboelastometry, platelet aggregation, and reactive oxygen species were measured before irradiation and at 1, 7, and 14 days of storage. Irradiated WB was compared with nonirradiated WB controls.

RESULTS
Irradiated WB stored for up to 14 days was not significantly different than nonirradiated WB in most of the parameters measured. Stored blood showed expected changes associated with functional decline at longer storage times, but irradiation did not hasten the decline. There was a significant change in potassium and sodium ion concentrations after irradiation, but the functional relevance is not clear.

CONCLUSION
High-dose irradiation had little effect on stored WB. Although there were changes in plasma sodium and potassium levels, there was little to no effect on hemostasis and blood cell viability. This suggests that stored blood subjected to a radiation event generating at least a dose of 75 Gy is still suitable for transfusion, which could be particularly important in the event of a mass casualty event where a large amount of blood is needed.
Historical development and contemporary use of neuromodulation in human spinal cord injury
Authors: Harkema Susan , Angeli Claudia , Gerasimenko Yury 
Published: July 2022

Purpose of review
There is a long history of neuromodulation of the spinal cord after injury in humans with recent momentum of studies showing evidence for therapeutic potential. Nonrandomized, mechanistic, hypothesis-driven, small cohort, epidural stimulation proof of principle studies provide insight into the human spinal circuitry functionality and support the pathway toward clinical treatments.

Recent findings
Individuals living with spinal cord injury can recover motor, cardiovascular, and bladder function even years after injury using neuromodulation. Integration of continuous feedback from sensory information, task-specific training, and optimized excitability state of human spinal circuitry are critical spinal mechanisms. Neuromodulation activates previously undetectable residual supraspinal pathways to allow intentional (voluntary) control of motor movements. Further discovery unveiled the human spinal circuitry integrated regulatory control of motor and autonomic systems indicating the realistic potential of neuromodulation to improve the capacity incrementally, but significantly for recovery after severe spinal cord injury.

Summary
The discovery that both motor and autonomic function recovers with lumbosacral spinal cord placement of the electrode reveals exciting avenues for a synergistic overall improvement in function, health, and quality of life for those who have been living with the consequences of spinal cord injury even for decades.
The mental health of healthcare workers during the COVID-19 pandemic: a narrative review
Authors: De Kock Johannes H. , Latham Helen Ann , Cowden Richard G. 
Published: July 2022

Purpose of review
Mental health (MH) problems among healthcare workers (HCWs) have the potential to impact negatively on the capacity of health systems to respond effectively to COVID-19. A thorough understanding of the factors that degrade or promote the MH of HCWs is needed to design and implement suitable intervention strategies to support the wellbeing of this population.

Recent findings
MH problems among HCWs were elevated prior to the COVID-19 pandemic. Accumulating evidence indicates that this public health crisis has had a disproportionately negative impact on the MH of specialised populations, including HCWs. Literature from prior health pandemics suggests that the adverse effects of the COVID-19 pandemic on the MH of HCWs are likely to persist in the aftermath of the public health crisis. Primary and secondary risk factors for adverse MH outcomes have been identified and should be considered when implementing interventions to protect the MH of HCWs.

Summary
The MH of HCWs has been negatively impacted by the COVID-19 pandemic, which is having a detrimental influence on the public health response to COVID-19. Protecting the MH of HCWs both during and beyond this public health crisis should remain a top priority, with particular emphasis on multifaceted interventions that aim to balance the psychological needs of individual HCWs with organisational-level strategies that could be targeted to promote their wellbeing.
Individual reference intervals in practice: A guide to personalise clinical and omics level data with IRIS
Authors: Pusparum Murih , Thas Olivier , Ertaylan Gökhan 
Published: July 2022

AbstractReference intervals (RI) are the best-established methodology used for the interpretation of numerical clinical level data in healthcare and clinical practice. As the test results are interpreted by comparing with the (population-derived) reference intervals, the quality of the calculation and implementation of reference intervals play a major role in decision-making process at the subject level. Here we describe the IRIS workflow to compute Individual Reference Intervals (IRI) based on multiple “healthy” data points from the same subjects and also utilising peers’ test results. We have improved the IRI models so they allow for covariate adjustments, such as sex and age. The IRI is expected to play pivotal roles in i) early detection of disease transition in chronic diseases by facilitating the detection of small deviations in clinical measurements, ii) monitoring personal disease progression, either using the standard clinical biochemistry test results or the omics level data. We demonstrate the utility of IRI in clinical and omics level data (proteomics and metabolomics) from two different longitudinal studies, including prior data processing and data quality check procedures. We have created an integrated application IRIS incorporating all described steps in an easy-to-use tool in research and/or clinical practice. We compute the IRI estimates in a healthy population to demonstrate its diagnostic utility in chronic diseases and from a diseased cohort to demonstrate its potential in disease monitoring.
Characterizations of enhanced infectivity and antibody evasion of Omicron BA.2.75
Authors: Cao Yunlong , Song Weiliang , Wang Lei , Liu Pan , Yue Can , Jian Fanchong , Yu Yuanling , Yisimayi Ayijiang , Wang Peng , Wang Yao , Zhu Qianhui , Deng Jie , Fu Wangjun , Yu Lingling , Zhang Na , Wang Jing , Xiao Tianhe , An Ran , Wang Jing , Liu Lu , Yang Sijie , Niu Xiao , Gu Qingqing , Shao Fei , Hao Xiaohua , Jin Ronghua , Wang Youchun , Xie Xiaoliang Sunney , Wang Xiangxi 
Published: July 2022

AbstractRecently emerged SARS-CoV-2 Omicron subvariant, BA.2.75, displayed a local growth advantage over BA.2.38, BA.2.76 and BA.5 in India. The underlying mechanism of BA.2.75’s enhanced infectivity, especially compared to BA.5, remains unclear. Here, we show that BA.2.75 exhibits substantially higher ACE2-binding affinity than BA.5. Also, BA.2.75 spike shows decreased thermostability and increased “up” RBD conformation in acidic conditions, suggesting enhanced low-pH-endosomal cell-entry pathway utilization. BA.2.75 is less humoral immune evasive than BA.4/BA.5 in BA.1/BA.2 breakthrough-infection convalescents; however, BA.2.75 shows heavier neutralization evasion in Delta breakthrough-infection convalescents. Importantly, plasma from BA.5 breakthrough infection exhibit significantly weaker neutralization against BA.2.75 than BA.5, mainly due to BA.2.75’s distinct RBD and NTD-targeting antibody escaping pattern from BA.4/BA.5. Additionally, Evusheld and Bebtelovimab remain effective against BA.2.75, and Sotrovimab recovered RBD-binding affinity. Together, our results suggest BA.2.75 may prevail after the global BA.4/BA.5 wave, and its increased receptor-binding capability could allow further incorporation of immune-evasive mutations.
Neurophysiological markers of successful learning in healthy aging
Authors: Strzelczyk Dawid , Popov Tzvetan , Kelly Simon P. , Langer Nicolas 
Published: July 2022

AbstractThe capacity to learn and memorize is a key determinant for the quality of life, but is known to decline to varying degrees with age. Previous ERP research methods had the limitation that their design did not allow to track the gradual memory formation process. Thus, the neural mechanisms underlying memory formation and the critical features that determine the extent to which aging affects learning are still unknown. By using a visual sequence learning task, which consists of the repeated presentation of a simple sequence of tokens, we are able to track the progress of gradual memory formation through both neurophysiological and behavioral markers. On a neurophysiological level, we focused on two learning related centroparietal ERP components: the P300 and broad positivity.Our results revealed that although both age groups showed significant learning progress, young individuals learned faster and remembered more stimuli than older participants. Successful learning was directly linked to a decrease of P300 amplitude. However, young participants showed larger P300 amplitude with a sharper decrease during the memory formation process. The P300 amplitude predicted learning success in both age groups, was associated with increased fronto-parietal brain network activation and showed good test-retest reliability. Highly, similar results were found for the broad positivity component, which raises the questions if the BP is a distinct component or just a prolonged P300. In a series of analyses, including topographic analysis of variance (TANOVA), equivalence testing and source reconstruction analysis, we addressed the unresolved questions. These analyses revealed concordant distributed brain activation patterns within parietal circuits. Thus, there is no evidence (rather evidence for equivalence) for distinct underlying neural generators for the two components.Taken together, the results highlight the importance of the P300 as a neurophysiological marker of learning and may enable the development of preventive measures for age-related impeded learning.
Functional diversity increases the resistance of a tritrophic food web to environmental changes
Authors: Adje George , Wojcik Laurie A. , Gaedke Ursula 
Published: July 2022

AbstractIn the light of global climate change and biodiversity loss, understanding the role of functional diversity in the response of food webs to environmental change is growing ever more important. Using a tritrophic food web model, with a variable degree of functional diversity at each trophic level, we studied the role of functional diversity on the resistance of a system against press perturbations affecting either nutrient availability or the mortality of the species, which can be interpreted as effects of eutrophication and warming respectively. We compared food webs with different levels of functional diversity by investigating the species trait and biomass dynamics, the overall changes in the species’ standing biomass as measured by the warping distance, and the duration of the system transients after the onset of a perturbation (transition time). We found that higher functional diversity increased resistance since it buffered trophic cascading effects and delayed the onset of oscillatory behaviour caused by either bottom-up forcing via perturbations to nutrient concentration or top-down forcing via perturbations to mortality rate. This increased resistance emerged from a higher top-down control of the intermediate species on the basal species. Functional diversity also promoted a higher top biomass, in particular via a higher proportion of top selective species undergoing high mortality rates. Additionally, functional diversity had context-dependent effects on warping distances, and increased transition times. Overall, this study encourages accounting for functional diversity in future investigations about the response of multitrophic systems to global change and in management strategies.
Fasting increases investment in soma upon refeeding at the cost of gamete quality in zebrafish
Authors: Ivimey-Cook Edward R , Murray David S. , de Coriolis Jean-Charles , Edden Nathan , Immler Simone , Maklakov Alexei A. 
Published: July 2022

AbstractFasting increases lifespan in invertebrates, improves biomarkers of health in vertebrates, and is increasingly proposed as a promising route to improve human health. Nevertheless, little is known about how fasted animals use resources upon refeeding, and how such decisions affect putative trade-offs between somatic growth and repair, reproduction, and gamete quality. Such fasting-induced trade-offs are based on strong theoretical foundations and have been recently discovered in invertebrates, but the data on vertebrates is lacking. Here we report that fasted female zebrafish, Danio rerio, increase investment in soma upon refeeding but it comes at a cost of egg quality.Specifically, an increase in fin re-growth was accompanied by a reduction in 24-hours post-fertilization offspring survival. Refed males showed a reduction in sperm velocity and impaired 24-hour post-fertilisation offspring survival. These findings underscore the necessity of considering the impact on eggs and sperm when assessing evolutionary and biomedical implications of lifespan-extending treatments in females and males and call for careful evaluation of the effects of fasting (both during and post) on fertilisation.
Postural sway is not affected by estrogen fluctuations during the menstrual cycle
Authors: Reschechtko Sasha , Nguyen Thuy Ngoc , Tsang Michelle , Giltvedt Kristine , Kern Mark , Hooshmand Shirin 
Published: July 2022

AbstractWhen people stand still, they exhibit a phenomenon called postural sway, or spontaneous movement of the body’s center of pressure, which is related to balance control. In general females show less sway than males, but this difference only begins to appear around puberty, pointing to different levels of sex hormones as one potential mechanism for sway sex differences. In this study, we followed one group of young females using oral contraceptives (n = 32) and one group not using oral contraceptives (n = 19), to investigate associations between estrogen availability and postural sway, both over the course of the menstrual cycle (in the group not using oral contraceptives) and long-term (between the two groups). All participants visited the lab four times over the putative 28-day menstrual cycle. At each visit, we performed blood draws to measure plasma estrogen (estradiol) levels, and tests of postural sway using a force plate. Due to the hormone-stabilizing effects of oral contraceptives, estradiol levels were higher in participants not using oral contraceptives (690.45 pmol/L versus 464.50 pmol/L), reflecting higher estradiol concentrations during the late follicular and luteal phase. Postural sway was similar on average for participants not using oral contraceptives (21.47 cm versus 23.56 cm). Overall, we found no significant effects of the estimated menstrual cycle phase – or absolute levels of estradiol – on postural sway.
RatesTools: a Nextflow pipeline for detecting de novo germline mutations in pedigree sequence data
Authors: Armstrong Ellie E. , Campana Michael G. 
Published: July 2022

AbstractSummaryHere, we introduce RatesTools, an automated pipeline to infer de novo mutation rates from parent-offspring trio data of diploid organisms. By providing a reference genome and high-coverage, whole-genome resequencing data of a minimum of three individuals (sire, dam, offspring), RatesTools provides a list of candidate de novo mutations and calculates a putative mutation rate. RatesTools uses several quality filtering steps, such as discarding sites with low mappability and highly repetitive regions, as well as sites with low genotype and mapping qualities to find potential de novo mutations. In addition, RatesTools implements several optional filters based on post hoc assumptions of the heterozygosity and mutation rate of the organism. Filters are highly customizable to user specifications in order to maximize utility across a wide-range of applications.AvailabilityRatesTools is freely available at https://github.com/campanam/RatesTools under a Creative Commons Zero (CC0) license. The pipeline is implemented in Nextflow (Di Tommaso et al. 2017), Ruby (http://www.ruby-lang.org), Bash (https://www.gnu.org/software/bash/), and R (R Core Team 2020) with reliance upon several other freely available tools. RatesTools is compatible with macOS and Linux operating systems.Supplementary InformationWe document RatesTools’ performance using published datasets in the online Supplementary information.
Predicting the Reprogrammability of Human Cells Based on Transcriptome Data and SGD Classifier with Elastic-Net Regularization
Authors: Saygili Gorkem , Turktas Mine , Gurcan Cansu , Delogu Lucia Gemma , Aktuna Acelya Yilmazer 
Published: July 2022

ABSTRACTCell reprogramming has shown considerable importance in recent years; however, the programmability of cells and efficiency of reprogramming varies across different cell types. Considering several weeks of cell programming process and costly programming agents used through the process, every failure in reprogramming comes with a significant burden. Better planning for reprogramming experiments could be possible if there is a way of predicting the outcome of reprogramming before the experiments using transcriptome data. In this study, we have accessed the transcriptome data of successful or unsuccessful programming studies published in literature and constructed a Stochastic Gradient Descent (SGD) classifier with Elastic-Net regularization for predicting whether the cell lines are reprogrammable. We tested our classifier using 10-fold cross validation over cell lines and on each cell separately. Our results showed that it is possible to predict the outcome of cell reprogramming with accuracies up to 98% and Area Under the Curve (AUC) scores up to 0.98%. Considering the success of our experimental outcomes we conclude that an outcome of a cell reprogramming experiment can be predicted with high accuracy using machine learning on transcriptome data.