bluuebunny/crossref_metadata_2025_split huggingface dataset:
The adverse inflammatory response of tobacco smoking in COVID-19 patients: biomarkers from proteomics and metabolomics
Authors: Cui Tenglong , Miao Gan , Jin Xiaoting , Yu Haiyi , Zhang Ze , Xu Liting , Wu Yili , Qu Guangbo , Liu Guoliang , Zheng Yuxin , Jiang Guibin 
Published: June 2022

Abstract
Whether tobacco smoking affects the occurrence and development of coronavirus disease 2019 (COVID-19) is still a controversial issue, and potential biomarkers to predict the adverse outcomes of smoking in the progression of COVID-19 patients have not yet been elucidated. To further uncover their linkage and explore the effective biomarkers, three proteomics and metabolomics databases (i.e. smoking status, COVID-19 status, and basic information of population) from human serum proteomic and metabolomic levels were established by literature search. Bioinformatics analysis was then performed to analyze the interactions of proteins or metabolites among the above three databases and their biological effects. Potential confounding factors (age, body mass index (BMI), and gender) were controlled to improve the reliability. The obtained data indicated that smoking may increase the relative risk of conversion from non-severe to severe COVID-19 patients by inducing the dysfunctional immune response. Seven interacting proteins (C8A, LBP, FCN2, CRP, SAA1, SAA2, and VTN) were found to promote the deterioration of COVID-19 by stimulating the complement pathway and macrophage phagocytosis as well as inhibiting the associated negative regulatory pathways, which can be biomarkers to reflect and predict adverse outcomes in smoking COVID-19 patients. Three crucial pathways related to immunity and inflammation, including tryptophan, arginine, and glycerophospholipid metabolism, were considered to affect the effect of smoking on the adverse outcomes of COVID-19 patients. Our study provides novel evidence and corresponding biomarkers as potential predictors of severe disease progression in smoking COVID-19 patients, which is of great significance for preventing further deterioration in these patients.
PolyAtailor: measuring poly(A) tail length from short-read and long-read sequencing data
Authors: Liu Mengfei , Hao Linlin , Yang Sien , Wu Xiaohui 
Published: June 2022

Abstract
The poly(A) tail is a dynamic addition to the eukaryotic mRNA and the change in its length plays an essential role in regulating gene expression through affecting nuclear export, mRNA stability and translation. Only recently high-throughput sequencing strategies began to emerge for transcriptome-wide profiling of poly(A) tail length in diverse developmental stages and organisms. However, there is currently no easy-to-use and universal tool for measuring poly(A) tails in sequencing data from different sequencing protocols. Here we established PolyAtailor, a unified and efficient framework, for identifying and analyzing poly(A) tails from PacBio-based long reads or next generation short reads. PolyAtailor provides two core functions for measuring poly(A) tails, namely Tail_map and Tail_scan, which can be used for profiling tails with or without using a reference genome. Particularly, PolyAtailor can identify all potential tails in a read, providing users with detailed information such as tail position, tail length, tail sequence and tail type. Moreover, PolyAtailor integrates rich functions for poly(A) tail and poly(A) site analyses, such as differential poly(A) length analysis, poly(A) site identification and annotation, and statistics and visualization of base composition in tails. We compared PolyAtailor with three latest methods, FLAMAnalysis, FLEPSeq and PAIsoSeqAnalysis, using data from three sequencing protocols in HeLa samples and Arabidopsis. Results show that PolyAtailor is effective in measuring poly(A) tail length and detecting significance of differential poly(A) length, which achieves much higher sensitivity and accuracy than competing methods. PolyAtailor is available at https://github.com/BMILAB/PolyAtailor.
Reimagining Social Work Placements in the Covid-19 Pandemic
Authors: O’Keeffe Patrick , Haralambous Betty , Egan Ronnie , Heales Emily , Baskarathas Sobika , Thompson Scott , Jerono Caroline 
Published: June 2022

Abstract
The Covid-19 pandemic has fundamentally changed how social work education is provided, and these changes are particularly pronounced in field education. Globally, the introduction of restrictions on mobility and social interaction have contributed to the cancellation, postponement and early termination of social work field placements. Accrediting bodies, social work field education departments and industry partner agencies have needed to rapidly adapt how placements are conceptualised and provided. This article examines the experiences of agencies who have continued to provide student placements throughout the pandemic. Interviews were conducted with placement supervisors employed at twelve human services agencies partnering with a university social work department in Melbourne, Australia. Whilst experiencing challenges, agencies outlined how they adapted to the environment to enable meaningful student placement experiences. This article contributes to an ongoing discussion around the trajectory of social work field education and the significance of agency-based placements in this evolution.
Cell-Free DNA as Biomarker for Sepsis by Integration of Microbial and Host Information
Authors: Jing Qiuyu , Leung Chi Hung Czarina , Wu Angela Ruohao 
Published: June 2022

Abstract

Background
Cell-free DNA (cfDNA) is emerging as a biomarker for sepsis. Previous studies have been focused mainly on identifying blood infections or simply quantifying cfDNA. We propose that by characterizing multifaceted unexplored components, cfDNA could be more informative for assessing this complex syndrome.

Methods
We explored multiple aspects of cfDNA in septic and nonseptic intensive care unit (ICU) patients by metagenomic sequencing, with longitudinal measurement and integrative assessment of plasma cfDNA quantity, human cfDNA fragmentation patterns, infecting pathogens, and overall microbial composition.

Results
Septic patients had significantly increased cfDNA quantity and altered human cfDNA fragmentation pattern. Moreover, human cfDNA fragments appeared to comprise information about cellular oxidative stress and could indicate disease severity. Metagenomic sequencing was more sensitive than blood culture in detecting bacterial infections and allowed for simultaneous detection of viral pathogens. We found differences in microbial composition between septic and nonseptic patients and between survivors and nonsurvivors by 28-day mortality, both on the first day of ICU admission and across the study period. By integrating all the information into a machine learning model, we achieved improved performance in identifying sepsis and prediction of clinical outcome for ICU patients with areas under the curve of 0.992 (95% CI 0.969–1.000) and 0.802 (95% CI 0.605–0.999), respectively.

Conclusions
We were able to diagnose sepsis and predict mortality as soon as the first day of ICU admission by integrating multifaceted cfDNA information obtained in a single metagenomic assay; this approach could provide important advantages for clinical management and for improving outcomes in ICU patients.
Hereditary Colorectal Cancer Syndromes and Inflammatory Bowel Diseases: an ECCO CONFER Multicentre Case Series
Authors: Barberio Brigida , Savarino Edoardo , Verstockt Bram , Fumery Mathurin , Pugliese Daniela , Bertani Lorenzo , Buda Andrea , Dragoni Gabriele , Goren Idan , Laish Ido , Spinelli Antonino , Teich Niels , Truyens Marie , Ellul Pierre 
Published: June 2022

Abstract

Background
Hereditary colorectal cancer syndromes [HCCS] are rare polyposis or nonpolyposis syndromes with a higher risk of developing colorectal cancer [CRC]. Coexisting inflammatory bowel disease [IBD], including ulcerative colitis [UC] and Crohn’s disease [CD], with HCCS is exceedingly rare and presumably increases the risk of early-onset CRC.

Methods
This was a multicentre case series performed as a part of the European Crohn’s and Colitis Organisation [ECCO] Collaborative Network of Exceptionally Rare case reports [CONFER] project.

Results
This report includes 26 patients with IBD (10 UC, 15 CD, and one with IBD unclassified [IBD-U]) and concomitant HCCS. Among these 26 patients([median age 33 years, interquartile range [IQR] 20–44], 15 [57.7%] were males, 24 [92.3%] Caucasians, and two [7.7%] of Arab origin. HCCS was diagnosed before the IBD diagnosis in 11 patients [42.3%], after diagnosis of IBD in 11 patients [42.3%], and concurrently in four patients [15.4%]. Sixteen patients had Lynch syndrome, seven had familial adenomatous polyposis [FAP], two had MYH-associated polyposis [MAP], and one had attenuated FAP [AFAP]. The most frequent genetic mutations were those of APC [n = 7] and MLH1 [n = 7]. Overall, CRC developed in 38.5% of patients [n = 10]: in four patients [40%] after IBD diagnosis, in four [40%] patients before IBD diagnosis, and in two patients the two conditions were diagnosed simultaneously. Eighteen [69.2%] patients underwent colectomy or abdominal surgery: nine patients due to CRC diagnosis, five patients preventively due to the underlying HCCS, three due to the underlying HCCS and concomitant active IBD disease, and one patient because of active IBD disease. One patient died due to CRC.

Conclusions
To date, this is the largest case series of patients with IBD and HCCS. The most frequent diagnosis of HCCS associated with IBD was Lynch syndrome. These data demonstrate the high malignancy rate and surgical intervention rate in this IBD cohort, despite the endoscopic surveillance. The optimal medical approach still needs to be addressed.
Estimating the rates of crossover and gene conversion from individual genomes
Authors: Setter Derek , Ebdon Sam , Jackson Ben , Lohse Konrad 
Published: June 2022

Abstract
Recombination can occur either as a result of crossover or gene conversion events. Population genetic methods for inferring the rate of recombination from patterns of linkage disequilibrium generally assume a simple model of recombination that only involves crossover events and ignore gene conversion. However, distinguishing the 2 processes is not only necessary for a complete description of recombination, but also essential for understanding the evolutionary consequences of inversions and other genomic partitions in which crossover (but not gene conversion) is reduced. We present heRho, a simple composite likelihood scheme for coestimating the rate of crossover and gene conversion from individual diploid genomes. The method is based on analytic results for the distance-dependent probability of heterozygous and homozygous states at 2 loci. We apply heRho to simulations and data from the house mouse Mus musculus castaneus, a well-studied model. Our analyses show (1) that the rates of crossover and gene conversion can be accurately coestimated at the level of individual chromosomes and (2) that previous estimates of the population scaled rate of recombination ρ=4Ner under a pure crossover model are likely biased.
Medication Barriers and Adherence: Experiences of Pediatric Transplant Recipients
Authors: Killian Michael Otis , Triplett Kelli , Mayersohn Gillian , Howry Savarra K , Masood Saba , Desai Dev 
Published: June 2022

Abstract
This study examined associations between scores on the Adolescent Medication Barriers Scale (AMBS) and the Parent Medication Barriers Scale (PMBS), patient and family factors, and medication adherence outcomes. Patients and caregivers from a pediatric solid organ transplantation (SOT) program were recruited for participation. Pediatric SOT recipients ages 10 to 21 years were eligible for participation. Analyses included reliability analyses and regression modeling with posttransplant medication adherence measured by Medication Level Variability Index scores. Seventy-three patients and caregivers completed an AMBS or PMBS questionnaire. Patient–caregiver inter-rater reliability was poor to fair. Greater medication barriers were reported among younger and female patients and families with more children. AMBS scores predicted greater nonadherence, while the PMBS was not predictive of adherence. Results point to the difficulty of assessing barriers to medication adherence and the lack of agreement between adolescent patients and caregivers. AMBS scores were more closely aligned with medication nonadherence, whereas PMBS scores may have been more influenced by family social factors. Adolescent reports of medication barriers may offer multidisciplinary transplant teams greater clinical utility when addressing these challenges with patients. Transplant social workers and psychologists should engage adolescents and caregivers in efforts to address medication nonadherence.
P-355 Association between high serum uric acid level and adverse reproductive outcomes in infertile women with polycystic ovary syndrome
Authors: Mu L , Liu C , Yang H 
Published: June 2022

Abstract

Study question
Does high serum uric acid (SUA) level affect the reproductive outcomes in women with polycystic ovary syndrome (PCOS) undergoing in-vitro fertilization (IVF)?

Summary answer
Elevated SUA is associated with decreased live birth rate, biochemical pregnancy rate and clinical pregnancy rate, and increased miscarriage rate in women with PCOS.

What is known already
SUA levelsand the prevalence of hyperuricemia (25.48%) are both significantly higher in women with PCOS than in women without PCOS (8.74%). SUA levels also can be used as a predictor of pregnancy complications (gestational diabetes mellitus and hypertensive disorders of pregnancy) and adverse foetal outcomes (preterm birth and low birth weight).

Study design, size, duration
This retrospective cohort study was conducted ininfertile women with PCOS between September 2012 and December 2019.

Participants/materials, setting, methods
A total of 1,032 infertile PCOS women undergoing their first IVF/ICSI cycle were observed. Data of reproductive outcomes including live birth rate, biochemical pregnancy rate, clinical pregnancy rate, and miscarriage rate were analyzed according to the quartile groups of SUA levels.

Main results and the role of chance
In quartiles of SUA levels, there was a significant decreasing trend in live birth rate from the lowest quartile (Q1: 34.5%) to the highest (Q4: 19.2%) (Pfor trend &lt;0.001). Notably, the miscarriage rate in Q4 was significantly higher than that in the other 3 quartiles (all P values &lt; 0.05). From Q1 to Q4, the incidence of miscarriage dramatically increased from 15.5% to 31.0% (Pfor trend &lt;0.05). In addition, the biochemical pregnancy rate and clinical pregnancy rate decreased significantly from the lowest quartile to the highest (Pfor trend &lt;0.05). With the first quartile of uric acid as the reference group, the logistic regression analysis showed that in both unadjusted and adjusted models, elevated SUA level was associated with significantly lower probabilities of live birth, biochemical pregnancy, and clinical pregnancy, and a higher risk of miscarriage in a linear fashion (all Pfor trend&lt; 0.05).

Limitations, reasons for caution
This study is limited by its retrospective design. It was difficult to ensure consistency in clinical practice among the physicians.

Wider implications of the findings
Our study suggeststhat clinical physicians need to pay close attention to PCOS women with high SUA levelsbefore IVF treatment. Prospective studies to determine an appropriate range of lower-SUA levels prior to treatment is necessary to support our findings.

Trial registration number
not applicable
P-490 Patient Care Guidance: Development of a unique tool for fertility clinics based on best practice evidence
Authors: Baccino G , Dejewski J 
Published: June 2022

Abstract

Study question
How can fertility clinics be encouraged to implement evidence-based person-centred care?

Summary answer
To help fertility clinics provide holistic care to their patients a multidisciplinary team developed a user-friendly, evidence based practical guidance.

What is known already
Despite wide evidence about the benefits of person-centred care for patients seeking fertility treatment, this is not systematically implemented in most fertility clinics.

Study design, size, duration
The aim was to develop evidence-based practical guidance on person-centred care for fertility clinics. A multidisciplinary team collaborated to developed person-centred care guidance for fertility clinics over a 12-month period.

Participants/materials, setting, methods
A group of 18 stakeholders, including:15 fertility experts, 2 patient associations and 1 quality manager reviewed and summarised evidence relating to the needs of fertility patients to guide the implementation of person-centred care in fertility clinics. It was specially designed to fulfil the needs of different countries’ legislation and cultural contexts.

Main results and the role of chance
This collaboration resulted in a unique and practical evidence-based tool to help fertility clinics implement best practice in person-centred care. It includes a range of topics such as: the importance of a patient care system in ART; benefits of patient-centered care for patients, staff, and the clinic; ways to communicate information to patients; informing about fertility treatment options; fertility awareness; men’s needs; emotional support; benefits of a mentor program; how to support to staff; exit strategies; needs of patients seeking cross-border care; the fertility clinic’ online communication; engaging patients in good and safe choices; and also how to care about patients undergoing a gamete donation treatment.

Limitations, reasons for caution
Despite the large number of topics required to support on fertility clinics, high impact topics were prioritised in the first phase of the guidance document – which will be updated periodically.

Wider implications of the findings
This guidance offers added value to fertility clinics and patients. The authors were able to adapt scientific evidence into a practical and user-friendly guidance that allows all staff to understand the concept of patient-centred care, the roles, responsibilities, actions that can be taken to improve patient experience, outcome and care.

Trial registration number
NO
P-593 Low dose clomiphene citrate does not reduce implantation rates - a cohort study based on modified Natural Cycle IVF
Authors: Grädel F , Mitter V , Kohl Schwartz A , Von Wolff M 
Published: June 2022

Abstract

Study question
Does low dose clomiphene citrate (CC) reduce implantation and eventually pregnancy and live birth rates?

Summary answer
Low dose CC does not reduce implantation rate and pregnancy and live birth rates – based on the model of modified Natural Cycle IVF (NC-IVF).

What is known already
CC is commonly used for ovulation induction in the treatment of anovulation or idiopathic infertility. It is also added to NC-IVF cycles to mildly stimulate follicular growth and to inhibit LH surge. CC reduces endometrial thickness and affects endometrial function. Therefore it is assumed that CC negatively affects implantation and thereby reduced pregnancy and live birth per embryo. However, previous studies have shown inconsistent results as previous studies mainly calculated pregnancy rates per cycle but not implantation rate per embryo.

Study design, size, duration
This cohort study included embryos transferred in NC–IVF and CC-NC-IVF cycles. Women with a maximum age of 42 years were treated at a university hospital between 2011 and 2016. Clinical pregnancy rate and live birth rate per embryo transferred and miscarriage rate per amniotic sac were calculated.

Participants/materials, setting, methods
A daily dose of 25mg of CC starting on day 5-7 of the cycle until the day of ovulation trigger was applied. A modified mixed effect Poisson regression model was used to account for the number of cycles in the same women and the number of embryos in the same cycle to achieve rate ratios (RR). Adjustment for maternal age, parity, type of infertility, duration of subfertility and indication for IVF were made.

Main results and the role of chance
499 couples underwent a total of 1043 IVF cycles, 453 NC-IVF and 590 CC-NC-IVF cycles. Baseline characteristics of both groups were not different. The additional administration of CC did neither decrease clinical pregnancy rate (aRR 1.16; 95% CI: 0.90 – 1.50)[MV1] nor live birth rate per transferred embryo (aRR 1.20; 95% CI: 0.89 – 1.62). Miscarriage rate was also not different in CC-NC-IVF compared to NC-IVF (aRR 1.05; 95%: CI 0.63 – 1.76).

Limitations, reasons for caution
This study does not allow to draw any conclusions regarding the effect of higher CC dosages. As randomization was not performed, some bias regarding the choice of IVF treatment cannot be completely excluded.

Wider implications of the findings
As this study revealed for the first time that low dose CC does not affect implantation, low does CC can be used for many different treatments. However, further studies are required to evaluate if this also applies to higher CC dosages.

Trial registration number
not applicable
Genetic architecture of a composite beef cattle population
Authors: Hay El Hamidi , Toghiani Sajjad , Roberts Andrew J , Paim Tiago , Kuehn Larry Alexander , Blackburn Harvey D 
Published: June 2022

Abstract
Composite breeds are widely used in the beef industry. Composites allow producers to combine desirable traits from the progenitor breeds and simplify herd management, without repeated crossbreeding and maintenance of purebreds. In this study, genomic information was used to evaluate the genetic composition and characteristics of a three-breed beef cattle composite. This composite population referred to as Composite Gene Combination (CGC) consisted of 50% Red Angus, 25% Charolais, and 25% Tarentaise. A total of 248 animals were used in this study: CGC (n = 79), Red Angus (n = 61), Charolais (n = 79), and Tarentaise (n = 29). All animals were genotyped with 777k HD panel. Principal component and ADMIXTURE analyses were carried out to evaluate the genetic structure of CGC animals. The ADMIXTURE revealed the proportion of Tarentaise increased to approximately 57%, whereas Charolais decreased to approximately 5% and Red Angus decreased to 38% across generations. To evaluate these changes in the genomic composition across different breeds and in CGC across generations, runs of homozygosity (ROH) were conducted. This analysis showed Red Angus to have the highest total length of ROH segments per animal with a mean of 349.92 Mb and lowest in CGC with a mean of 141.10 Mb. Furthermore, it showed the formation of new haplotypes in CGC around the sixth generation. Selection signatures were evaluated through Fst and HapFlk analyses. Several selection sweeps in CGC were identified especially in chromosomes 5 and 14 which have previously been reported to be associated with coat color and growth traits. The study supports our previous findings that progenitor combinations are not stable over generations and that either direct or natural selection plays a role in modifying the progenitor proportions. Furthermore, the results showed that Tarentaise contributed useful attributes to the composite in a cool semi-arid environment and suggests a re-exploration of this breed’s role may be warranted.