bluuebunny/crossref_metadata_2025_split huggingface dataset:
HAT: haplotype assembly tool using short and error-prone long reads
Authors: Shirali Hossein Zade Ramin , Urhan Aysun , Assis de Souza Alvaro , Singh Akash , Abeel Thomas 
Published: October 2022

Abstract

Motivation
Haplotypes are the set of alleles co-occurring on a single chromosome and inherited together to the next generation. Because a monoploid reference genome loses this co-occurrence information, it has limited use in associating phenotypes with allelic combinations of genotypes. Therefore, methods to reconstruct the complete haplotypes from DNA sequencing data are crucial. Recently, several attempts have been made at haplotype reconstructions, but significant limitations remain. High-quality continuous haplotypes cannot be created reliably, particularly when there are few differences between the homologous chromosomes.

Results
Here, we introduce HAT, a haplotype assembly tool that exploits short and long reads along with a reference genome to reconstruct haplotypes. HAT tries to take advantage of the accuracy of short reads and the length of the long reads to reconstruct haplotypes. We tested HAT on the aneuploid yeast strain Saccharomyces pastorianus CBS1483 and multiple simulated polyploid datasets of the same strain, showing that it outperforms existing tools.

Availability and implementation
https://github.com/AbeelLab/hat/.

Supplementary information
Supplementary data are available at Bioinformatics online.
EcoTransLearn: an R-package to easily use transfer learning for ecological studies—a plankton case study
Authors: Wacquet Guillaume , Lefebvre Alain 
Published: October 2022

Abstract

Summary
In recent years, Deep Learning (DL) has been increasingly used in many fields, in particular in image recognition, due to its ability to solve problems where traditional machine learning algorithms fail. However, building an appropriate DL model from scratch, especially in the context of ecological studies, is a difficult task due to the dynamic nature and morphological variability of living organisms, as well as the high cost in terms of time, human resources and skills required to label a large number of training images. To overcome this problem, Transfer Learning (TL) can be used to improve a classifier by transferring information learnt from many domains thanks to a very large training set composed of various images, to another domain with a smaller amount of training data. To compensate the lack of ‘easy-to-use’ software optimized for ecological studies, we propose the EcoTransLearn R-package, which allows greater automation in the classification of images acquired with various devices (FlowCam, ZooScan, photographs, etc.), thanks to different TL methods pre-trained on the generic ImageNet dataset.

Availability and implementation
EcoTransLearn is an open-source package. It is implemented in R and calls Python scripts for image classification step (using reticulate and tensorflow libraries). The source code, instruction manual and examples can be found at https://github.com/IFREMER-LERBL/EcoTransLearn.

Supplementary information
Supplementary data are available at Bioinformatics online.
‘Have They Talked About Us At All?’ The Moral Distress of Healthcare Social Workers during the COVID-19 Pandemic: A Qualitative Investigation in the State of Texas
Authors: Fantus Sophia , Cole Rebecca , Hawkins Lataya , Chakraborty Priyanjali 
Published: October 2022

Abstract
Amid the ongoing pandemic, as overburdened and underfunded health systems are requiring health care social workers (HSWs) to assume responsibilities beyond their scope of practice, institutional constraints have undoubtedly heightened encounters of moral distress (MD). MD is the psychological disequilibrium that arises when institutional factors obligate an individual to carry out a task that violates their professional and/or personal ethics. Our qualitative study investigated HSWs’ (n = 43) MD in Texas during the 2019 COVID-19 pandemic. Findings from our study indicate that MD occurs across five levels: (i) patient care decisions; (ii) personal care decisions; (iii) team/unit decisions; (iv) organisational decisions; and (v) social justice decisions. MD is rooted in systems that disproportionately impact historically excluded populations, including social inequities such as financial instability, homelessness and substance use. Organisations need to explicitly consider social justice initiatives that seek to identify growing disparities in care that have been at the forefront of the pandemic; macro-level perspectives that expand MD must address social and health inequities that impede daily tasks of all health care workers. MD encounters that are rooted in social determinants of health can inform supervision, education and practice to ameliorate HSWs’ value conflict.
Precuneus magnetic stimulation for Alzheimer’s disease: a randomized, sham-controlled trial
Authors: Koch Giacomo , Casula Elias Paolo , Bonnì Sonia , Borghi Ilaria , Assogna Martina , Minei Marilena , Pellicciari Maria Concetta , Motta Caterina , D’Acunto Alessia , Porrazzini Francesco , Maiella Michele , Ferrari Clarissa , Caltagirone Carlo , Santarnecchi Emiliano , Bozzali Marco , Martorana Alessandro 
Published: October 2022

AbstractRepetitive transcranial magnetic stimulation (rTMS) is emerging as a non-invasive therapeutic strategy in the battle against Alzheimer’s disease. Alzheimer’s disease patients primarily show alterations of the default mode network for which the precuneus is a key node. Here, we hypothesized that targeting the precuneus with TMS represents a promising strategy to slow down cognitive and functional decline in Alzheimer’s disease patients.We performed a randomized, double-blind, sham-controlled, phase 2, 24-week trial to determine the safety and efficacy of precuneus stimulation in patients with mild-to-moderate Alzheimer’s disease. Fifty Alzheimer’s disease patients were randomly assigned in a 1:1 ratio to either receive precuneus or sham rTMS (mean age 73.7 years; 52% female). The trial included a 24-week treatment, with a 2-week intensive course in which rTMS (or sham) was applied daily five times per week, followed by a 22-week maintenance phase in which stimulation was applied once weekly. The Clinical Dementia Rating Scale–Sum of Boxes was selected as the primary outcome measure, in which post-treatment scores were compared to baseline. Secondary outcomes included score changes in the Alzheimer’s Disease Assessment Scale–Cognitive Subscale, Mini-Mental State Examination and Alzheimer’s Disease Cooperative Study–Activities of Daily Living scale. Moreover, single-pulse TMS in combination with EEG was used to assess neurophysiological changes in precuneus cortical excitability and oscillatory activity.Our findings show that patients that received precuneus repetitive magnetic stimulation presented a stable performance of the Clinical Dementia Rating Scale–Sum of Boxes score, whereas patients treated with sham showed a worsening of their score. Compared with the sham stimulation, patients in the precuneus stimulation group also showed also significantly better performances for the secondary outcome measures, including the Alzheimer’s Disease Assessment Scale–Cognitive Subscale, Mini-Mental State Examination and Alzheimer’s Disease Cooperative Study–Activities of Daily Living scale. Neurophysiological results showed that precuneus cortical excitability remained unchanged after 24 weeks in the precuneus stimulation group, whereas it was significantly reduced in the sham group. Finally, we found an enhancement of local gamma oscillations in the group treated with precuneus stimulation but not in patients treated with sham.We conclude that 24 weeks of precuneus rTMS may slow down cognitive and functional decline in Alzheimer’s disease. Repetitive TMS targeting the default mode network could represent a novel therapeutic approach in Alzheimer’s disease patients.
Striatal resting-state connectivity after long-term diacetylmorphine treatment in opioid-dependent patients
Authors: Schaub Anna-Chiara , Vogel Marc , Baumgartner Sophie , Lang Undine E , Borgwardt Stefan , Schmidt André , Walter Marc 
Published: October 2022

Abstract
New treatment approaches for opioid-dependent patients include injectable opioid agonist treatment with diacetylmorphine. While evidence has shown beneficial clinical effects of diacetylmorphine, it is still not clear how long-term diacetylmorphine treatment affects the brain and whether functional brain changes are accompanied by clinical improvements. Therefore, this prospective case-control study focuses on long-term effects of diacetylmorphine on resting-state functional connectivity.
We included opioid-dependent patients (N = 22, age range 33–58, 16 males) treated with diacetylmorphine and healthy controls (N = 9, age range 27–55, 5 males) that underwent two MRI assessments approximately nine years apart. For the patients, the assessments took part shortly after the diacetylmorphine intake to be able to explore changes in resting-state functional connectivity in brain regions related to the stage of binge and intoxication (caudate, putamen, nucleus accumbens).
A cluster in the right superior frontal gyrus was detected, showing over nine years an increase in functional connectivity originating from the left caudate and the left accumbens in patients but not in healthy controls. These connectivity changes in patients were related to the duration of the diacetylmorphine treatment at the follow-up, indicating smaller increases in functional connectivity with longer treatment duration (r = 0.63, P &lt; 0.01).
These results suggest that long-term diacetylmorphine treatment in opioid-dependent patients increases fronto-striatal connections, an effect that is linked to the duration of the treatment duration. Future research needs to further address the wide-ranging effects of diacetylmorphine on brain functioning and deepen the understanding of their clinical relevance.
Reproductive biology ofGazella arabica: Predictors of offspring weight and short- and long-term offspring survival
Authors: Martin Ryan A , Riesch Rüdiger , Plath Martin , Al Hanoosh Naif A , Wronski Torsten 
Published: October 2022

AbstractReproductive traits are central to organismal fitness, and so the factors influencing patterns of reproduction and offspring survival are at the heart of biology. Making use of breeding data collected over 16 years at the King Khalid Wildlife Research Centre in Saudi Arabia, we investigated the reproductive biology of Arabian gazelles Gazella arabica. Offspring survival was mainly a function of birth weight, with heavier offspring having higher survival rates than lighter offspring. However, while sons were heavier than daughters, daughters had higher survival rates. We could not find evidence that giving birth to sons negatively impacts offspring weight in the following year. We uncovered large narrow-sense heritability (h2) in offspring weight at birth, while maternal effects (m2) on birth weight were of lesser importance. However, maternal effects on offspring survival were strong until weaning age, while paternal effects dominated survival to sexual maturity and first reproduction. We propose that variation in maternal postnatal care might overshadow the effects of maternal inheritance of birth weights, while the overall strong heritability of weight at birth and the paternal effects on survival illustrates strong variance in sire fitness based on genetic quality, suggesting a role for sexual selection by female mate choice in wild populations.
Systematic lung ultrasound in Omicron-type vs. wild-type COVID-19
Authors: Banai Ariel , Lupu Lior , Shetrit Aviel , Hochstadt Aviram , Lichter Yael , Levi Erez , Szekely Yishay , Schellekes Nadav , Jacoby Tammy , Zahler David , Itach Tamar , Taieb Philippe , Gefen Sheizaf , Viskin Dana , Shidlansik Lia , Adler Amos , Levitsky Ekaterina , Havakuk Ofer , Banai Shmuel , Ghantous Eihab , Topilsky Yan 
Published: October 2022

Abstract

Aims
Preliminary data suggested that patients with Omicron-type-Coronavirus-disease-2019 (COVID-19) have less severe lung disease compared with the wild-type-variant. We aimed to compare lung ultrasound (LUS) parameters in Omicron vs. wild-type COVID-19 and evaluate their prognostic implications.

Methods and results
One hundred and sixty-two consecutive patients with Omicron-type-COVID-19 underwent LUS within 48 h of admission and were compared with propensity-matched wild-type patients (148 pairs). In the Omicron patients median, first and third quartiles of the LUS-score was 5 [2–12], and only 9% had normal LUS. The majority had either mild (≤5; 37%) or moderate (6–15; 39%), and 15% (≥15) had severe LUS-score. Thirty-six percent of patients had patchy pleural thickening (PPT). Factors associated with LUS-score in the Omicron patients included ischaemic-heart-disease, heart failure, renal-dysfunction, and C-reactive protein. Elevated left-filling pressure or right-sided pressures were associated with the LUS-score. Lung ultrasound-score was associated with mortality [odds ratio (OR): 1.09, 95% confidence interval (CI): 1.01–1.18; P = 0.03] and with the combined endpoint of mortality and respiratory failure (OR: 1.14, 95% CI: 1.07–1.22; P &lt; 0.0001). Patients with the wild-type variant had worse LUS characteristics than the matched Omicron-type patients (PPT: 90 vs. 34%; P &lt; 0.0001 and LUS-score: 8 [5, 12] vs. 5 [2, 10], P = 0.004), irrespective of disease severity. When matched only to the 31 non-vaccinated Omicron patients, these differences were attenuated.

Conclusion
Lung ultrasound-score is abnormal in the majority of hospitalized Omicron-type patients. Patchy pleural thickening is less common than in matched wild-type patients, but the difference is diminished in the non-vaccinated Omicron patients. Nevertheless, even in this milder form of the disease, the LUS-score is associated with poor in-hospital outcomes.
Comparison of low-density lipoprotein cholesterol equations in patients with dyslipidaemia receiving cholesterol ester transfer protein inhibition
Authors: Martin Seth S , Ditmarsch Marc , Simmons Mark , Alp Nicholas , Turner Traci , Davidson Michael H , Kastelein John J P 
Published: October 2022

Abstract

Aims
Low-density lipoprotein (LDL-C) lowering is imperative in cardiovascular disease prevention. We aimed to compare accuracy of three clinically-implemented LDL-C equations in a clinical trial of cholesterol ester transfer protein (CETP) inhibition.

Methods and results
Men and women aged 18–75 years with dyslipidaemia were recruited from 17 sites in the Netherlands and Denmark. Patients were randomly assigned to one of nine groups using various combinations of the CETP inhibitor TA-8995 (obicetrapib), statin therapy, and placebo. In pooled measurements over 12 weeks, we calculated LDL-C by the Friedewald, Martin/Hopkins, and Sampson equations, and compared values with preparative ultracentrifugation (PUC) LDL-C overall and with a special interest in the low LDL-C/high triglycerides subgroup. There were 242 patients contributing 921 observations. Overall median LDL-C differences between estimates and PUC were small: Friedewald, 0.00 (25th, 75th: −0.10, 0.08) mmol/L [0 (−4, 3) mg/dL]; Martin/Hopkins, 0.02 (−0.08, 0.10) mmol/L [1 (−3, 4) mg/dL]; and Sampson, 0.05 (−0.03, 0.15) mmol/L [2 (−1, 6) mg/dL]. In the subgroup with estimated LDL-C &lt;1.8 mmol/L (&lt;70 mg/dL) and triglycerides 1.7–4.5 mmol/L (150−399 mg/dL), the Friedewald equation underestimated LDL-C with a median difference versus PUC of −0.25 (−0.33, −0.10) mmol/L [−10 (−13, −4) mg/dL], whereas the median difference by Martin/Hopkins was 0.00 (−0.08, 0.10) mmol/L [0 (−3, 4) mg/dL] and by Sampson was −0.06 (−0.13, 0.00) mmol/L [−2 (−5, 0) mg/dL]. In this subgroup, the proportion of LDL-C observations &lt;1.8 mmol/L (&lt;70 mg/dL) that were correctly classified compared with PUC was 71.4% by Friedewald vs. 100.0% by Martin/Hopkins and 93.1% by Sampson.

Conclusion
In European patients with dyslipidaemia receiving a CETP inhibitor, we found improved LDL-C accuracy using contemporary equations vs. the Friedewald equation, and the greatest accuracy was observed with the Martin/Hopkins equation.

Registration
ClinicalTrials.gov, NCT01970215
Early anticoagulation after aortic valve replacement with porcine bioprosthesis randomized control trial (ANTIPRO)
Authors: Fernandez Amparo , Loza Gimena , Parma Gabriel , Florio Lucia , Estigarribia Jorge , Soca Gerardo , Robaina Ricardo , Duran Ariel , Brusich Daniel , Dayan Victor 
Published: October 2022

Abstract

OBJECTIVES
Most evidence for anticoagulation (AC) in aortic bioprosthesis is centred on embolic events, bleeding and reintervention risk. The effect of AC on haemodynamics has not been previously assessed. Our hypothesis was that patients with early AC after aortic valve replacement (AVR) with porcine bioprosthesis have better haemodynamics at 1 year of follow-up.

METHODS
Prospective, randomized, open-label trial conducted at 2 cardiac surgery centres. All patients undergoing AVR with porcine bioprosthesis were consecutively recruited. The anticoagulated group received warfarin + aspirin and the non-anticoagulated (control) only aspirin. The primary outcome was mean gradient after 1 year of AVR and change in New York Heart Association class. Secondary outcomes were major and minor bleeding, embolic events and prosthetic leak.

RESULTS
Of 140 participants in the study, 71 were assigned to the anticoagulated group and 69 to the control group. The mean age of the overall population was 72.4 (SD: 7.1) years. Global EuroSCORE was 7.65 (SD: 5.73). At 1 year, the mean gradient was similar between both groups [18.6 (SD: 1.1 mmHg) and 18.1 (SD: 1.0 mmHg) in the control and anticoagulated groups, respectively, P = 0.701]. No differences in functional class at 3 months or 1 year were found among groups. No differences were found among groups in the secondary outcomes.

CONCLUSIONS
The addition of 3 months of oral AC to anti-aggregation treatment was not detected to affect bioprosthetic haemodynamics nor functional class at 1 year after AVR. Likewise, AC does not lead to the higher incidence of complications.
Social and cultural mobility: rising to the middle class and cultural practices in contemporary Finland
Authors: Kallunki Jarmo 
Published: October 2022

Abstract
How does social mobility influence cultural taste and participation? Cultural reproduction theory predicts little change, while cultural mobility theory suggests more substantial makeover. This article explores the influence of upward educational and occupational mobility in reading literature, participation in highbrow activities, television watching, and music and food tastes, focusing on mobility from the secondary-level education and the working class to the higher education and the middle class. By analysing survey data (N = 2,813) collected in Finland in 2007 and 2018 with ordinary least squares regression, we show that educational mobility and occupational mobility are mostly differently related to tastes and participation. Both educationally and occupationally upwardly mobile people tend to participate more in highbrow activities, watch less television and dislike meat-heavy food, as is more typical to their social destination than to their social origins. Conversely, the educationally upwardly mobile, again more typical to their destination, tend to read more books, like light-ethnic food and classical music, and dislike popular folk, but occupational mobility is not associated with reading or liking light-ethnic food, and the occupationally mobile retain their original tastes in classical and popular folk music when education is controlled for. We discuss the implications of our results.
Interventions to improve teamwork and wellbeing in primary care settings: a mixed method review
Authors: Panagioti M , Tyler N , Hodkinson A 
Published: October 2022

Abstract

Background
General practices are experiencing increasing pressures due to rising demand, declining staff numbers, and knock-on impacts on patient care. The COVID-19 pandemic has added further challenges and reinforced the importance of teamwork and organisational settings. We undertook a mixed-method systematic review to explore which interventions can improve teamwork within primary care and improve inter-sector partnerships with other health and social care services.

Methods
Five major bibliographic databases were systematically searched for relevant studies from inception to February 2022. We included controlled intervention study designs and linked qualitative studies. For amenable data, meta-analysis is being undertaken using random effects models taking into account the between study heterogeneity (quantified using the I2 statistic) and potential publication bias (funnel plots and Egger's test). The qualitative studies are analysed using thematic analyses.

Results
The original search yield of 3012 studies, of which 14 studies with 1,534 participants were include in our analyses. Most of the evaluated interventions focused on improving non-technical skills and provided evidence of improvements in the quality of teamwork in primary care. Meta-analysis and narrative synthesis is undertaken to examine the impact of the teamwork interventions on staff outcomes (team attitudes, knowledge, and functioning; wellbeing), and patient outcomes (e.g. quality of patient care, patient satisfaction/experience).

Conclusions
The findings provide information of immediate importance for the mental health and wellbeing and teamwork support of professionals entering primary care and for the organisation of primary care services.
Do preventive child examinations in general practice reduce the risk of overweight and obesity?
Authors: Heuckendorff S , Eggertsen C , Thomsen JL , Fonager K 
Published: October 2022

Abstract

Background
The prevalence of children with overweight and obesity is increasing. General practitioners in Denmark follow children throughout early childhood via the preventive child health examinations. These examinations are offered to all children from birth to the age of five. Thus, the general practitioners have a unique opportunity for early tracing and identification of overweight and obesity, but the impact of the examinations are not examined. Therefore, the aim of this study was to examine the association between attending preventive child health examinations and the risk of overweight and obesity at the age of six both for the total pediatric population and within groups of vulnerable children such as children of parents with low educational level or low household income.

Methods
A population-based birth cohort study was conducted including all Danish children born from 2000-2012 using the Danish nationwide registers. Data included information on child participation in preventive health examinations at general practice, height and weight at the age of six, and parental information on socioeconomic factors.

Results
The analyses included 801,444 children. Attending preventive child health examinations were not associated with a lower risk of overweight at the age of six. A lower risk of obesity was seen in children attending the examinations, both in the general population (RR 0.71, 95% CI 0.66-0.76) and within vulnerable groups (low level of maternal education: RR 0.80, 95% CI 0.72-0.89), low household income (RR 0.79, 95% CI 0.72-0.87). The risk of obesity was greater in the vulnerable groups than in the not-vulnerable groups.

Conclusions
Attending preventive child health examinations were associated with a lower risk of obesity at the age of six, but not overweight. This was seen for both the general pediatric population and within vulnerable groups. The lowest risk of obesity was seen in the not-vulnerable groups.

Key messages
• The results indicated that attending preventive child health examinations in general practice reduced the risk of obesity at the age of six, but not the risk of overweight.
• The lowest risk of obesity was seen in the not-vulnerable groups attending the preventive child health examinations in general practice.