bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of concurrency on the performance of a whole exome sequencing pipeline
Authors: Dall’Olio Daniele , Curti Nico , Fonzi Eugenio , Sala Claudia , Remondini Daniel , Castellani Gastone , Giampieri Enrico 
Published: February 2021

Abstract
Background
Current high-throughput technologies—i.e. whole genome sequencing, RNA-Seq, ChIP-Seq, etc.—generate huge amounts of data and their usage gets more widespread with each passing year. Complex analysis pipelines involving several computationally-intensive steps have to be applied on an increasing number of samples. Workflow management systems allow parallelization and a more efficient usage of computational power. Nevertheless, this mostly happens by assigning the available cores to a single or few samples’ pipeline at a time. We refer to this approach as naive parallel strategy (NPS). Here, we discuss an alternative approach, which we refer to as concurrent execution strategy (CES), which equally distributes the available processors across every sample’s pipeline.

Results
Theoretically, we show that the CES results, under loose conditions, in a substantial speedup, with an ideal gain range spanning from 1 to the number of samples. Also, we observe that the CES yields even faster executions since parallelly computable tasks scale sub-linearly. Practically, we tested both strategies on a whole exome sequencing pipeline applied to three publicly available matched tumour-normal sample pairs of gastrointestinal stromal tumour. The CES achieved speedups in latency up to 2–2.4 compared to the NPS.

Conclusions
Our results hint that if resources distribution is further tailored to fit specific situations, an even greater gain in performance of multiple samples pipelines execution could be achieved. For this to be feasible, a benchmarking of the tools included in the pipeline would be necessary. It is our opinion these benchmarks should be consistently performed by the tools’ developers. Finally, these results suggest that concurrent strategies might also lead to energy and cost savings by making feasible the usage of low power machine clusters.
lncEvo: automated identification and conservation study of long noncoding RNAs
Authors: Bryzghalov Oleksii , Makałowska Izabela , Szcześniak Michał Wojciech 
Published: February 2021

AbstractBackgroundLong noncoding RNAs represent a large class of transcripts with two common features: they exceed an arbitrary length threshold of 200 nt and are assumed to not encode proteins. Although a growing body of evidence indicates that the vast majority of lncRNAs are potentially nonfunctional, hundreds of them have already been revealed to perform essential gene regulatory functions or to be linked to a number of cellular processes, including those associated with the etiology of human diseases. To better understand the biology of lncRNAs, it is essential to perform a more in-depth study of their evolution. In contrast to protein-encoding transcripts, however, they do not show the strong sequence conservation that usually results from purifying selection; therefore, software that is typically used to resolve the evolutionary relationships of protein-encoding genes and transcripts is not applicable to the study of lncRNAs.ResultsTo tackle this issue, we developed lncEvo, a computational pipeline that consists of three modules: (1) transcriptome assembly from RNA-Seq data, (2) prediction of lncRNAs, and (3) conservation study—a genome-wide comparison of lncRNA transcriptomes between two species of interest, including search for orthologs. Importantly, one can choose to apply lncEvo solely for transcriptome assembly or lncRNA prediction, without calling the conservation-related part.ConclusionslncEvo is an all-in-one tool built with the Nextflow framework, utilizing state-of-the-art software and algorithms with customizable trade-offs between speed and sensitivity, ease of use and built-in reporting functionalities. The source code of the pipeline is freely available for academic and nonacademic use under the MIT license athttps://gitlab.com/spirit678/lncrna_conservation_nf.
High genetic diversity and strong genetic structure of Strongyllodes variegatus populations in oilseed rape production areas of China
Authors: Zhan Hai-Xia , Hao Zhong-Ping , Tang Rui , Zhu Li-Ni , Zhou Jing-Jiang , Hou Shu-Min 
Published: February 2021

Abstract
Background
Strongyllodes variegatus (Fairmaire) is a major insect pest of oilseed rape in China. Despite its economic importance, the contribution of its population genetics in the development of any suitable protection control strategy for the management of oilseed rape crops is poorly studied. It is a much urgent need to prevent its spread to the rest of the world.

Results
Using the sequences of mitochondrial DNA cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) as genetic markers, we analyzed the population genetic diversity and structure of 437 individuals collected from 15 S. variegatus populations located in different oilseed rape production areas in China. In addition, we estimated the demographic history using neutrality test and mismatch distribution analysis. The high level of genetic diversity was detected among the COI and Cytb sequences of S. variegatus. The population structure analyses strongly suggested three distinct genetic and geographical regions in China with limited gene flow. The Mantel test showed that the genetic distance was greatly influenced by the geographical distance. The demographic analyses showed that S. variegatus had experienced population fluctuation during the Pleistocene Epoch, which was likely to be related to the climatic changes.

Conclusion
Overall, these results demonstrate that the strong genetic structure of S. variegatus populations in China, which is attributed by the isolation through the geographical distance among populations, their weak flight capacity and subsequent adaptation to the regional ecological conditions.
Adaptive evolution driving the young duplications in six Rosaceae species
Authors: Zhong Yan , Zhang Xiaohui , Shi Qinglong , Cheng Zong-Ming 
Published: February 2021

Abstract
Background
In plant genomes, high proportions of duplicate copies reveals that gene duplications play an important role in the evolutionary processes of plant species. A series of gene families under positive selection after recent duplication events in plant genomes indicated the evolution of duplicates driven by adaptive evolution. However, the genome-wide evolutionary features of young duplicate genes among closely related species are rarely reported.

Results
In this study, we conducted a systematic survey of young duplicate genes at genome-wide levels among six Rosaceae species, whose whole-genome sequencing data were successively released in recent years. A total of 35,936 gene families were detected among the six species, in which 60.25% were generated by young duplications. The 21,650 young duplicate gene families could be divided into two expansion types based on their duplication patterns, species-specific and lineage-specific expansions. Our results showed the species-specific expansions advantaging over the lineage-specific expansions. In the two types of expansions, high-frequency duplicate domains exhibited functional preference in response to environmental stresses.

Conclusions
The functional preference of the young duplicate genes in both the expansion types showed that they were inclined to respond to abiotic or biotic stimuli. Moreover, young duplicate genes under positive selection in both species-specific and lineage-specific expansions suggested that they were generated to adapt to the environmental factors in Rosaceae species.
Left ventricular deformation mechanics over time in patients with thalassemia major with and without iron overload
Authors: Bonios Michael J. , Fountas Epameinontas , Delaporta Polyxeni , Kyrzopoulos Stamatis , Kattamis Antonis , Adamopoulos Stamatis N. , Tsiapras Dimitris 
Published: February 2021

Abstract
Background
Myocardial iron overload in patients with thalassemia major (TM) is one of the most important complications. The purpose of the study was to identify advanced echocardiography parameters for early identification of myocardial dysfunction during follow-up of patients with TM.

Methods
Forty TM patients who were 41 ± 5 years old were included in the study and divided into two groups according to cardiac magnetic resonance T2* results (Group 1: Τ2* > 25 ms, Group 2: Τ2* ≤ 25 ms). Liver T2* parameters were also measured. Conventional and deformational echocardiographic parameters were measured at baseline and approximately 2 years later.

Results
Thirty-two patients had Τ2* = 34 ± 4 ms (Group 1), and 8 had Τ2* = 17 ± 9 ms (Group 2). Blood consumption was 185 ± 60 and 199 ± 37 ml/kg/yr (p = 0.64), and liver T2* was 4 ± 5 and 17 ± 21 ms (p = 0.01) in Groups 1 and 2, respectively. At baseline, Group 1 had better left ventricular global longitudinal strain (GLS) (− 22 ± 3 vs. − 18 ± 5, p = 0.01) and similar left ventricular ejection fraction (LVEF) (62 ± 5% vs. 58 ± 10%, p = 0.086) than Group 2. At the 28 ± 11-month follow-up, LVEF, GLS, and T2* values in Group 1 (63 ± 3%, − 21 ± 3%, 34 ± 4 ms) and Group 2 (56 ± 11%, − 17 ± 4%, 17 ± 9 ms) did not change significantly compared to their corresponding baseline values. In 8 patients from Group 1, a worsening (> 15%) in LS (p = 0.001) was detected during follow-up, with a marginal reduction in LVEF.

Conclusions
GLS seems to be an efficient echocardiographic parameter for detecting hemochromatosis-related cardiac dysfunction earlier than LVEF. It also seems to be affected by other factors (free radical oxygen, immunogenetic mechanisms or viral infections) in a minority of patients, underscoring the multifactorial etiology of cardiomyopathy.
Cervical lymph node enlargement as the initial manifestation of rectal cancer
Authors: Xie Tong-Hui , Su Peng , Hong Jian-Guo , Zhang Hui 
Published: February 2021

Abstract
Background
Colorectal cancer is a very common malignant tumor worldwide. The clinical manifestations of advanced colorectal cancer include the changes in bowel habits, hematochezia, diarrhea, local abdominal pain and other symptoms. However, the colorectal cancer with an initial symptom of cervical lymph node enlargement is extremely rare. In this article, we report a case of rectal cancer presenting with cervical lymph nodes enlargement as the initial symptom.

Case presentation
A 57-year-old woman was admitted to our hospital for cervical lymph node enlargement which was accidentally detected during physical examination. Computed tomography scan revealed multiple enlarged lymph nodes in the neck. Cervical ultrasound showed normal thyroid gland and multiple left supraclavicular lymph nodes enlargement. The patient underwent lymph nodes biopsy and pathologic results showed metastatic adenocarcinoma. The subsequent lower gastrointestinal endoscopy revealed a mucosal bulge lesion located at rectus and biopsy revealed adenocarcinoma. The patient underwent rectal cancer resection. She is alive with no evidence of recurrence or new tumors 2 years after surgery.

Conclusions
Cervical lymph node metastasis is a rare metastatic way in colorectal cancer. This is the first case of rectal cancer presenting with cervical lymph nodes metastases as the initial symptom. Surgical resection combined with postoperative chemotherapy improved long-term prognosis of the patient. This rare metastatic way of rectal cancer should be paid attention for clinicians.
Repetitive transcranial magnetic stimulation treatment for peripartum depression: systematic review & meta-analysis
Authors: Lee Hyune June , Kim Sung Min , Kwon Ji Yean 
Published: February 2021

Abstract
Background
Peripartum depression is a common disorder with very high potential hazards for both the patients and their babies. The typical treatment options include antidepressants and electroconvulsive therapy. However, these treatments do not ensure the safety of the fetus. Recently, repetitive transcranial magnetic stimulation has emerged as a promising treatment for neuropathies as well as depression. Nevertheless, many studies excluded pregnant women. This systematic review was conducted to confirm whether repetitive transcranial magnetic stimulation was a suitable treatment option for peripartum depression.

Methods
We performed a systematic review that followed the PRISMA guidelines. We searched for studies in the MEDLINE, PsycINFO, EMBASE, and Cochrane library databases published until the end of September 2020. Eleven studies were selected for the systematic review, and five studies were selected for quantitative synthesis. Data analysis was conducted using Comprehensive Meta-Analysis 3 software. The effect size was analyzed using the standardized mean difference, and the 95% confidence interval (CI) was determined by the generic inverse variance estimation method.

Results
The therapeutic effect size of repetitive transcranial magnetic stimulation for peripartum depression was 1.394 (95% CI: 0.944–1.843), and the sensitivity analysis effect size was 1.074 (95% CI: 0.689–1.459), indicating a significant effect. The side effect size of repetitive transcranial magnetic stimulation for peripartum depression was 0.346 (95% CI: 0.214–0.506), a meaningful result. There were no severe side effects to the mothers or fetuses.

Conclusions
From various perspectives, repetitive transcranial magnetic stimulation can be considered an alternative treatment to treat peripartum depression to avoid exposure of fetuses to drugs and the severe side effects of electroconvulsive therapy. Further research is required to increase confidence in the results.
Association of term isolated microcephaly with mode of delivery and perinatal outcome - a retrospective case-control analysis
Authors: Bardin Ron , Krispin Eyal , Salman Lina , Navon Inbal , Shmueli Anat , Perlman Sharon , Gilboa Yinon , Hadar Eran 
Published: February 2021

Abstract
Background
We aimed to evaluate the association of isolated fetal microcephaly measured by ultrasound prior to delivery at term with mode of delivery and perinatal outcome.

Methods
A single-center retrospective study was conducted in 2012–2016. Fetal microcephaly was defined as head circumference > 2 standard deviations of the mean for gestational age and sex. We compared the obstetric, delivery, and outcome parameters of women in whom ultrasound performed up to 10 days prior to term delivery showed isolated fetal microcephaly (study group) or normal head circumference (reference group). Exclusion criteria were intrauterine fetal death, birthweight below the 10th percentile, and antepartum cesarean delivery for any indication.

Results
Of 3677 women included in the study, 26 (0.7%) had a late ultrasound finding of isolated fetal microcephaly. Baseline characteristics were similar in the two groups except for estimated fetal weight based on abdominal circumference and biparietal diameter, which was lower in the microcephaly group (3209.8 ± 557.6 vs. 2685.8 ± 420.8 g, p < .001). There was no significant between-group difference in rate of vaginal operative deliveries (11.7% vs 14.8%, respectively, p = 0.372). The study group had no intrapartum cesarean deliveries compared to 6.3% of the reference group (NS). Compared to controls, neonates in the study group were smaller (3323.2 ± 432.2 vs. 2957.0 ± 330.4 g, p < .001), with lower birthweight percentile (60.5 ± 26.5 vs. 33.6 ± 21.5%, p < .001) and were more often males (48.2 vs. 90.0%, p < .001). No significant differences were noted in perinatal outcomes between the groups, including admission to neonatal intensive care unit, intraventricular hemorrhage, 5-min Apgar score < 7, asphyxia, seizures, and sepsis.

Conclusions
Isolated microcephaly in term fetuses is not advantageous for a vaginal delivery, nor does it does not pose a greater than normal risk of adverse perinatal outcome.
Working memory deficits in schizophrenia are associated with the rs34884856 variant and expression levels of the NR4A2 gene in a sample Mexican population: a case control study
Authors: Ruiz-Sánchez Elizabeth , Jiménez-Genchi Janet , Alcántara-Flores Yessica M. , Castañeda-González Carlos J. , Aviña-Cervantes Carlos L. , Yescas Petra , del Socorro González-Valadez María , Martínez-Rodríguez Nancy , Ríos-Ortiz Antonio , González-González Martha , López-Navarro María E. , Rojas Patricia 
Published: February 2021

Abstract
Background
Cognitive functions represent useful endophenotypes to identify the association between genetic variants and schizophrenia. In this sense, the NR4A2 gene has been implicated in schizophrenia and cognition in different animal models and clinical trials. We hypothesized that the NR4A2 gene is associated with working memory performance in schizophrenia. This study aimed to analyze two variants and the expression levels of the NR4A2 gene with susceptibility to schizophrenia, as well as to evaluate whether possession of NR4A2 variants influence the possible correlation between gene expression and working memory performance in schizophrenia.

Methods
The current study included 187 schizophrenia patients and 227 controls genotyped for two of the most studied NR4A2 genetic variants in neurological and neuropsychiatric diseases. Genotyping was performed using High Resolution Melt and sequencing techniques. In addition, mRNA expression of NR4A2 was performed in peripheral mononuclear cells of 112 patients and 118 controls. A group of these participants, 54 patients and 87 controls, performed the working memory index of the WAIS III test.

Results
Both genotypic frequencies of the two variants and expression levels of the NR4A2 gene showed no significant difference when in patients versus controls. However, patients homozygous for the rs34884856 promoter variant showed a positive correlation between expression levels and auditory working memory.

Conclusions
Our finding suggested that changes in expression levels of the NR4A2 gene could be associated with working memory in schizophrenia depending on patients’ genotype in a sample from a Mexican population.
Shared decision making from reintegration professionals’ perspectives to support return to work: a qualitative study
Authors: Vooijs Marloes , van Kesteren Nicole M. C. , Hazelzet Astrid M. , Otten Wilma 
Published: February 2021

Abstract
Background
Work participation is an important determinant of public health; being unemployed leads to a decrease in an individual’s health. In the Netherlands, people with a work disability can apply for disability benefits, in which people also receive support to return to work (RTW). A method, currently used in the medical sector, that can include both the perspective of the reintegration professional and of the individual in the process of RTW, is shared decision making (SDM). In this article we explore to what extent reintegration professionals currently use SDM, and to what extent they prefer to use SDM in their ideal interaction with clients.

Methods
We performed semi-structured interviews with fourteen reintegration professionals from four different municipalities. The transcripts were coded according to content analysis, applying open and axial coding.

Results
Reintegration professionals emphasised the importance of having a good relationship with clients, of building trust and collaborating as a team. They did not inform their clients that they could be part of the decision-making process, or discussed a shared goal. Although professionals did emphasise the importance of aligning their approach with the preferences of the client and though they tried to offer some choice options, they did not mention available options, discussed the pros and cons of these options or evaluated decisions with their clients. Furthermore, they did not mention any of these aspects in their ideal interaction with clients.

Conclusions
SDM has a potential value, because all professionals underline the importance of having an alliance with clients, collaborating as a team, and striving to align their approach with the preferences of the client. However, professionals currently perform a limited set of SDM steps. Additional knowledge and skills are needed for both reintegration professionals and municipalities so that professionals can consider and reflect on the value of using SDM, or SDM steps, in supporting RTW. Providing clients with knowledge and skills seems necessary to facilitate both self-management and SDM.
Prematurity and body composition at 6, 18, and 30 years of age: Pelotas (Brazil) 2004, 1993, and 1982 birth cohorts
Authors: Bortolotto Caroline Cardozo , Santos Iná S. , dos Santos Vaz Juliana , Matijasevich Alicia , Barros Aluísio J. D. , Barros Fernando C. , Santos Leonardo Pozza , Munhoz Tiago Neuenfeld 
Published: February 2021

Abstract
Background
We aimed to investigate the association between preterm birth and body composition at 6, 18, and 30 years of age using data from three population-based birth cohort studies.

Methods
Gestational age (GA), defined by the date of the last menstrual period (categorized in ≤33, 34–36, and ≥ 37 weeks), was gathered in the first 24-h after delivery for all live births occurring in the city of Pelotas, Brazil, in 2004, 1993 and 1982. Body composition was assessed by air-displacement plethysmography. Outcomes included fat mass (FM, kg), percent FM (%FM), FM index (FMI, kg/m2), fat-free mass (FFM, kg); percent FFM (%FFM), FFM index (FFMI, kg/m2), body mass index (BMI, kg/m2 at 18 years in the 1993 cohort and 30 years in the 1982 cohort), and BMI Z-score (at 6 years in the 2004 cohort). We further explored the association of birth weight for GA with body composition indicators and BMI. Crude and adjusted linear regressions provided beta coefficients with 95% confidence intervals (95%CI).

Results
A total of 3036, 3027, and 3369 participants, respectively, from the 2004, 1993, and 1982 cohorts were analyzed. At 6 years, preterm boys (born at 34–36 weeks) presented lower adjusted mean of FM (β = − 0.80 kg, − 1.45;-0.16, p = 0.046), %FM (β = − 2.39%, − 3.90;-0.88, p = 0.008), FMI (β = − 0.70 kg/m2, − 1.13;-0.27, p = 0.004) as well as lower FFM (β = − 0.4 kg, − 0.77; − 0.12, p = 0.010) and FFMI (β = − 0.3 kg/m2, − 0.46;-0.10, p < 0.001), and BMI Z-score (β = − 0.69,; − 0.99;-0.40, p < 0.001); but higher %FFM (β = 2.4%, 0.87;-3.90, p = 0.008), when compared to boys born at term (≥37). At 30 years, FM (15.7 kg, 0.25;31.1, p = 0.102) was higher among males born at ≤33 weeks. No association was observed for females from the three cohorts and for 18-year-old males. The association of birth weight for GA with body composition and BMI was not significant in any cohort. At 6 years, SGA boys had lower FFMI than boys AGA.

Conclusions
Our results suggest that preterm birth is associated with decreased body fat and fat-free mass in childhood but higher fat mass in adulthood. Nevertheless, results were only significant for males. SGA boys also showed lower FFMI.