bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of PICK1 and BDNF variations with increased risk of methamphetamine dependence among Iranian population; a case-control study
Authors: Tajbakhsh Amir , Alimardani Maliheh , Asghari Mahla , Abedini Soheila , Khadem Sohrab Saghafi , Bajestani Abolfazl Nesaei , Alipoor Forough , Alidoust Maryam , Savardashtaki Amir , Hashemian Peyman , Pasdar Alireza 
Published: December 2020

Abstract
Background: Genetic factors play an important role in susceptibility to methamphetamine dependency. In this line, protein that interact with C-kinase-1 (PICK1) and brain-derived neurotrophic factor (BDNF) genes are linked to methamphetamine dependence (substance use disorder). Thus, in a case-control study, we investigated the association between polymorphisms of PICK1 and BDNF genes and methamphetamine dependence in an Iranian population.Methods: Total of 235 cases and 204 controls were recruited in a period between 2015 to 2018. The PICK1-rs713729, -rs2076369 and BDNF-rs6265 genotypes were determined via ARMS-PCR assay. Statistical analysis was performed, using SPSS 20.0, PHASE 2.1.1 program as well as SNP Analyzer 2.0.Results: In the present study, two polymorphisms including PICK1-rs713729 (OR: 1.38 (CI: 1.08-1.52; P-value: 0.004) in multiplicative and dominant models, and PICK1-rs2076369 (OR: 1.31 (CI: 1.10-1.56; P-value: 0.002) in multiplicative, dominant and co-dominant models were associated with the risk of methamphetamine abuse. Moreover, haplotype analysis showed a significant association of haplotype AG (OR: 2.50 (CI: 1.50-4.16; P-value: 0.0002) in dominant, recessive and co-dominant models, and haplotype TT (OR: 0.67 (CI: 0.50-0.91; P-value: 0.009) in dominant and co-dominant models with the risk of methamphetamine abuse. None of the polymorphisms in this study had a high level of linkage disequilibrium. Conclusion: Our findings indicate that the PICK1 gene polymorphism might affect the risk of methamphetamine dependency in our population.
Identification of globin switching-related genes and RNAs via transcriptomic profiling of nucleated red blood cells isolated from the cord blood of preterm and full-term newborns&nbsp;
Authors: Han Yuanyuan , Huang Ling , Zhou Man , Tan Xiaoyu , Gong Shangjin , Zhang Zhaojun , Jin Tingting , Liu Juan , Hu Li , Zhang Wenqiu , Fang Xiangdong , Jia Yankai , Huang Shengwen 
Published: December 2020

Abstract
Background: β-thalassemia and sickle cell disease (SCD) are chronic hemolytic anemias caused by mutation or deletion of the β-globin gene. Reactivation of fetal γ-globin gene (HBG) expression can ameliorate the clinical course of β-hemoglobinopathies. Our current understanding of the globin switching mechanism is not comprehensive, and research into the roles of long non-coding RNAs (lncRNAs) in this process remains limited. Results: We collected umbilical cord blood samples from preterm and full-term infants, from which we enriched and isolated nucleated red blood cells (NRBCs) for transcriptome sequencing. We identified mRNAs, lncRNAs, and microRNAs that were differentially expressed in the preterm and full-term samples, and constructed hub gene network of differentially expressed transcription factors. Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis revealed the biological significance of differentially expressed mRNAs and the targets of differentially expressed lncRNAs and microRNAs. Our analyses revealed that the Fanconi anemia pathway may be involved in the regulation of globin switching at birth. Using quantitative polymerase chain reaction, we confirm that BCL11A is more highly expressed in full-term samples than in preterm samples and is statistically differentially expressed based on biological sex. Results of RNA sequencing and quantitative polymerase chain reaction demonstrated that the lncRNA H19 was expressed at a statistically lower level in full-term samples than in preterm samples. Furthermore, we established the H19‑related lncRNA/miRNA/mRNA network to reveal the potential regulatory mechanisms of H19.Conclusions: Our results suggest that the Fanconi anemia pathway and the H19/let-7/LIN28B axis may be involved in globin switching in umbilical cord blood. The differentially expressed transcripts and related pathways may constitute novel therapeutic targets for β-thalassemia.
Metabolic Bone Disease in Chronic Kidney Disease Patients (CKD-MBD) and its Associated Factors at Muhimbili National Hospital in Dar es salaam, Tanzania: A Cross-Sectional Study
Authors: Mungulluh Felix Faustin , Ruggajo Paschal , Furia Francis Fredrick 
Published: December 2020

Abstract
Background: Metabolic bone disease in chronic kidney disease patients is associated with high morbidity and mortality, and it has been reported to start early in the course of the disease and worsen as the kidney damage progresses. However, the prevalence and factors associated with metabolic bone disease in chronic kidney disease patients in our setting has not been established, so we aimed to determine the prevalence and factors associated with metabolic bone disease among patients with chronic kidney disease at a tertiary Muhimbili National Hospital in Dar es salaam, Tanzania so as to help physicians recognize the patients at risk, diagnose the problem and prevent complications sooner. Methods: This was a hospital based cross-sectional study involving adult patients with chronic kidney disease attending renal unit Muhimbili National Hospital, a tertiary referral center in Dar es Salaam, Tanzania. Systematic sampling technique was employed to get study participants after being given informed consent. In this study, CKD-MBD was defined basing on the abnormality of serum calcium, phosphate or parathyroid hormone level. Data analysis was done using the SPSS version 23.0 software. Results: A total of 300 participants with chronic kidney disease stage 3 and above were included in this study. Majority were male, 198 (66.0%), with a mean age of 53 years. The prevalence of metabolic bone disease was found to be 75.0%. The most common form of metabolic bone disease was hyperparathyroidism 196 (87.1%), followed by hypocalcemia 174 (77.3%) and hyperphosphatemia 82 (36.4%), which was the least common. Factors which were found to be significantly associated with CKD-MBD were the use of calcium supplements, use of phosphate binders, being on dialysis, a calcium rich diet and a low phosphate diet. Conclusion: Metabolic bone diseases are common in patients with CKD at Muhimbili National Hospital. Patients with CKD should undergo serial assessment of phosphate, calcium and parathyroid hormone level, considered together, so as to diagnose metabolic bone disease early and treat those patients who will be found to have persistently or prolonged abnormalities in these bone mineral biomarkers.
Improving CLIP-seq data analysis by incorporating transcript information
Authors: Uhl Michael , Tran Van Dinh , Backofen Rolf 
Published: December 2020

Abstract
Background: Current peak callers for identifying RNA-binding protein (RBP) binding sites from CLIP-seq data take into account genomic read profiles, but they ignore the underlying transcript information, that is information regarding splicing events. So far, there are no studies available that closer observe this issue. Results: Here we show that current peak callers are susceptible to false peak calling near exon borders. We quantify its extent in publicly available datasets, which turns out to be substantial. By providing a tool called CLIPcontext for automatic transcript and genomic context sequence extraction, we further demonstrate that context choice affects the performances of RBP binding site prediction tools. Moreover, we show that known motifs of exon-binding RBPs are often enriched in transcript context sites, which should enable the recovery of more authentic binding sites. Finally, we discuss possible strategies on how to integrate transcript information into future workflows. Conclusions: Our results demonstrate the importance of incorporating transcript information in CLIP-seq data analysis. Taking advantage of the underlying transcript information should therefore become an integral part of future peak calling and downstream analysis tools.
What interferes with conducting free lists? A comparative ethnobotanical experiment
Authors: Meireles Melise Pessôa Araujo , de Albuquerque Ulysses Paulino , de Medeiros Patrícia Muniz 
Published: December 2020

Abstract
Background: The free list, also written “freelist”, or “free recall”, is an ethnographic method that characterizes the local knowledge of a population about a given cultural domain. However, there is still much to elucidate about the variables that can influence the number of items that participants cite using this technique. This study applied a casual-comparative experiemental design to analyze whether three months’ time, age and external stimuli influence the similarity of plant free lists applied at different times.Methods: Data was collected from 103 farmers from the rural community Alto dos Canutos, in the municipality of Picos, Piauí state, Brazil.Two free lists were conducted at two different times, with an interval of three months between them. Subsequently, the similarity between the first and second free lists of each participant was calculated using the Jaccard Similarity Index. The Generalized Linear Model (GLM) with binomial errors and stepwise approach was used to analyze the effects of age and external stimuli on information collection when comparing free lists applied at different times.Results: Participants’ age influenced the information that the free lists collected, demonstrating that the older the participants, the lower the similarity among the free lists. Among the external stimuli analyzed, only the presence of third parties influenced the content of the free lists at the time of the interview. However, contrary to expectations, third-party presence positively influenced the similarity of the lists. Conclusion: The results show that the studied variables age and third-party presence can influence the capture of knowledge. These findings warrant future research into the influences' causes and their potential mitigation, e.g., by isolation or by breaking the medicinal plant domain into focused sub-domains and conducting simpler, successive free-lists, which can mitigate memory issues.
“Stroke-Stop” Formula: A Tool for Risk Index Determination in Development of Acute Cerebrovascular Disease in Patients with Asymptomatic Internal Carotid Artery Stenosis
Authors: Kopolovets Ivan , Berek Peter , Stefanic Peter , Lotnyk Dmytro , Mucha Rastislav , Hertelyova Zdenka , Toth Stefan , Boyko Nadiya , Sihotsky Vladimir 
Published: December 2020

Abstract
Background: Extracranial carotid artery disease is considered a risk factor for developing acute cerebrovascular diseases. The paper presents the “Stroke-Stop” formula proposed for the determination of the risk of developing stroke in patients with asymptomatic internal carotid artery (ICA) stenosis. The formula is based on a mathematical calculation of the major risk factors for stroke: the degree of ICA stenosis, the morphological structure of the atherosclerotic plaque and the level of lipoprotein-associated phospholipase A2 (Lp-PLA2) concentration.Methods: The study included 70 patients with atherosclerotic ICA stenosis. Among vascular inflammatory markers, Lp-PLA2 was determined with concentration 252.7-328.6 mg/l. The obtained results were evaluated using descriptive statistics (the frequency, percentage ratio) as well as the one-way analysis of variance (ANOVA) and chi-square test. Results: The risk of stroke development is eminently increasing with the progression of ICA stenosis and elevation of Lp-PLA2 levels. In patients with soft atherosclerotic plaque, the risk of stroke development was significantly higher in correlation with patients with hard atherosclerotic plaque. Based on calculations using “Stroke-Stop” formula, three main groups were generated: low (<70 points), medium (70 – 100 points) and high (>100 points) risk of stroke development. Conclusions: The “Stroke-Stop” formula may serve as an additional criterion for individual selection of patients with asymptomatic ICA stenosis for carotid endarterectomy. This model could be used as a diagnostic and prognostic tool to identify patients with potentially high risk development of ischemic stroke in clinical praxis.
Chronic pain after breast surgery: incidence, associated factors and impact on quality of life, an observational prospective study
Authors: Villa Gianluca , Mandarano Raffaele , Calabrisotto Caterina Scirè , Rizzelli Valeria , Duca Martina Del , Montin Diego Pomarè , Paparella Laura , De Gaudio A. Raffaele , Romagnoli Stefano 
Published: December 2020

Abstract
Background. Chronic pain after breast surgery (CPBS) has a disabling impact on postoperative health status. Mainly because of the lack of a clear definition, inconsistency does exist in the literature concerning both the actual incidence and the risk factors associated to CPBS. The aim of this prospective, observational study is to describe the incidence of and risk factors for CPBS, according to the definition provided by the IASP taskforce. The impact of CPBS on patients’ function and quality of life is also described. Methods. Adult female patients scheduled for oncological or reconstructive breast surgery at the Breast Unit of Careggi Hospital (Florence, Italy) were prospectively observed. Postoperative pain was evaluated at 3 months (CPBS) after surgery. Preoperative, intraoperative, and postoperative factors were compared in CPBS and No-CPBS groups through multivariate logistic regression analysis. Results. Among the 307 patients considered in this study, the incidence of CPBS was 28% [95%CI 23.1%-33.4%]. Results from the logistic regression analysis suggest that axillary surgery (OR [95%CI], 2.99 [1.13-7.87], p=0.03), preoperative use of pain medications (OR [95%CI], 2.04 [1.20-3.46], p=0.01), and higher dynamic NRS values at 6 hours postoperatively (OR [95%CI], 1.28 [1.05-1.55], p=0.01) were all independent predictors for CPBS. Conclusions. Chronic pain after breast surgery is a frequent complication. In our cohort, long-term use of analgesics for preexisting chronic pain, axillary surgery, and higher dynamic NRS values at 6 hours postoperatively were all factors associated with increased risk of developing CPBS. The possibility to early detect persistent pain, particularly in those patients at high risk for CPBS, might help physicians to more effectively prevent pain chronicisation.Trial registration: clinicalTrials.gov registration NCT04309929
A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs.
Authors: Flossmann Gabriele , Wurmser Christine , Pausch Hubert , Tenghe Amabel , Dodenhoff Jörg , Dahinten Günther , Götz Kay-Uwe , Russ Ingolf , Fries Ruedi 
Published: December 2020

Abstract
Background Atypical external genitalia are often a sign of reproductive organ pathologies and infertility with both environmental or genetic causes, including karyotypic abnormalities. Genome-wide association studies (GWAS) provide a means for identifying chromosomal regions harboring deleterious DNA-variants causing such phenotypes. We performed a GWAS to unravel the causes of incidental cases of atypically small vulvae in German Landrace gilts.Results A case-control GWAS involving Illumina porcine SNP60 BeadChip-called genotypes of 17 gilts with atypically small vulvae and 1,818 control animals (fertile German Landrace sows) identified a significantly associated region on the X-chromosome (P = 8.81 × 10-43). Inspection of whole-genome sequencing data in the critical area allowed us to pinpoint a likely causal variant in the form of a nonsense mutation of bone morphogenetic protein-15 (BMP15; Sscrofa11.1_X:g.44618787C>T, BMP15:p.R212X). The mutant allele occurs at a frequency of 6.2% in the German Landrace breeding population. Homozygous gilts exhibit underdeveloped, most likely not functional ovaries and are not fertile. Male carriers do not seem to manifest defects. Heterozygous sows produce 0.41±0.02 (P=4.5 × 10-83) piglets more than wildtype animals. However, the mutant allele’s positive effect on litter size accompanies a negative impact on lean meat growth.Conclusion Our results provide an example for the power of GWAS in identifying the genetic causes of a fuzzy phenotype and add to the list of natural deleterious BMP15 mutations that affect fertility in a dosage-dependent manner, the first time in a poly-ovulatory species. We advise eradicating the mutant allele from the German Landrace breeding population since the adverse effects on the lean meat growth outweigh the larger litter size in heterozygous sows.
Examining Supports and Barriers to Breastfeeding through a Socio-Ecological Lens: A Qualitative Study
Authors: Snyder Kailey , Hulse Emily , Dingman Holly , Cantrell Angie , Hanson Corrine , Dinkel Danae 
Published: December 2020

Abstract
BACKGROUND: Early breastfeeding cessation is a societal concern given the massive benefits associated with breastfeeding for mother and child. More effective interventions are needed to increase breastfeeding duration. Prior to developing such interventions more research is needed to examine breastfeeding supports and barriers from the perspective of breastfeeding stakeholders. One such framework that can be utilized is the Socio-Ecological Model which stems from Urie Broffenbrenner’s early theoretical frameworks (1973-1979). The purpose of this study was to examine supports and barriers to breastfeeding across environmental systems. METHODS: A total of 49 representatives participated in a telephonic interview. Interviewees represented various levels of the model based on their current breastfeeding experience (i.e., mother or significant other) or occupation. A direct content analysis was performed as well as a constant comparative analysis to determine differences between level representatives. RESULTS: Common supports identified by all interviewees were in-hospital breastfeeding education (organizational level) and the existence of breastfeeding protection legislation (policy level). Barriers identified by all interviewees included a lack of support (interpersonal level), lack of hospital resources (organizational level) and lack of specificity within the existing breastfeeding protection legislation (policy level). Other identified supports and barriers varied by representatives for each level of the model. CONCLUSION: Future efforts should target multiple levels of the SEM to eliminate the disparities between breastfeeding mothers’ perceptions and the stakeholders working to increase breastfeeding initiation and duration rate.
Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaﬃi
Authors: Alva Troy R , Riera Melanie , Chartron Justin 
Published: December 2020

Abstract
Background: Eukaryotes use distinct networks of biogenesis factors to synthesize, fold, monitor, traffic, and secrete proteins. During heterologous expression, saturation of any of these networks may bottleneck titer and yield. To understand the flux through various routes into the early secretory pathway, we quantified the global and membrane-associated translatomes of Komagataella phaffii . Results: By coupling Ribo-seq with long-read mRNA sequencing, we generated a new annotation of protein-encoding genes. By using Ribo-seq with subcellular fractionation, we quantified demands on co- and posttranslational translocation pathways. During exponential growth in rich media, protein components of the cell-wall represent the greatest number of nascent chains entering the ER. Transcripts encoding the transmembrane protein PMA1 sequester more ribosomes at the ER membrane than any others. Comparison to Saccharomyces cerevisiae reveals conservation in the resources allocated by gene ontology, but variation in the diversity of gene products entering the secretory pathway. Conclusion: A subset of host proteins, particularly cell-wall components, impose the greatest biosynthetic demands in the early secretory pathway. These proteins are potential targets in strain engineering aimed at alleviating bottlenecks during heterologous protein production.
Maternal Folic Acid Impacts DNA Methylation Profile in Male Rat Offspring implicated in Neurodevelopment and Learning/Memory Abilities
Authors: Wang Xinyan , Li Zhenshu , Zhu Yun , Yan Jing , Liu Huan , Huang Guowei , Li Wen 
Published: December 2020

Abstract
Background: Periconceptional folic acid (FA) supplementation not only reduces the incidence of neural tube defects, but also improves cognitive performances in offspring. However, the genes or pathways that are epigenetically regulated by FA in neurodevelopment were rarely reported. Methods: To elucidate the underlying mechanism, the effect of FA on the methylation profiles in brain tissue of male rat offspring was assessed by methylated DNA immunoprecipitation chip. Differentially methylated genes (DMGs) and gene network analysis were identified using DAVID and KEGG pathway analysis. Results: Compared with the folate-normal diet group, 1939 DMGs were identified in the folate-deficient diet group, and 1498 DMGs were identified in the folate-supplemented diet group, among which 298 DMGs were overlapped. The pathways associated with neurodevelopment and learning/memory abilities were differentially methylated in response to maternal FA intake during pregnancy, and there were some identical and distinctive potential mechanisms under FA deficiency or supplemented conditions. Conclusions: In conclusion, genes and pathways associated with neurodevelopment and learning/memory abilities were differentially methylated in male rat offspring in response to maternal FA deficiency or supplementation during pregnancy.
"Running myself ragged": Stressors Faced by Peer Workers in Overdose Response Settings
Authors: Mamdani Zahra , McKenzie Sophie , Pauly Bernadette , Cameron Fred , Conway-Brown Jennifer , Edwards Denice , Howell Amy , Scott Tracy , Seguin Ryan , Woodrow Peter , Buxton Jane 
Published: December 2020

Abstract
Background: Peer workers or ‘peers’ (workers with past or present drug use experience) are at the forefront of overdose response initiatives and their role is essential in creating safe spaces for people who use drugs (PWUD). Working in overdose response settings has benefits for peer workers but is also stressful, with lasting emotional and mental health effects. Yet, little is known about the stressors peer workers face and what interventions can be implemented to support them in their roles. Methods: This project used a community-based sequential mixed methods research design. Eight peer researcher-led focus groups (n=31) were conducted between November 2018 and March 2019 to assess needs of peer workers. The transcripts were thematically coded and analyzed using interpretative description. These results informed a survey which was conducted (n=50) in September 2019 to acquire quantitative data on peer workers’ perception of health, quality of life, working conditions and stressors. Frequency distributions were used to describe characteristics of participants. X 2 distribution values with Yates correction were conducted to check for association between variables. Results: Five themes emerged from the focus groups that point to stressors felt by peer workers: (1) Financial insecurity; (2) lack of respect and recognition at work; (3) housing challenges; (4) inability to access and/or refer individuals to resources; and (5) constant exposure to death and trauma. Consistent with this, the factors that survey participants picked as one of their “top three stressors” included financial situation, work situation, and housing challenges. Conclusion: Peer workers are faced with a diversity of stressors in their lives which often reflect societal stigmatization of drug use. Recognition of these systemic stressors is critical in designing interventions to ease the emotional, physical and financial burden faced by peer workers.