bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations of Endometriosis and Hormone Therapy With Risk of Hyperlipidemia
Authors: Chang Cherry Yin-Yi , Muo Chih-Hsin , Yeh Yi-Chun , Lu Chung-Yen , Lin William Wu-Chou , Chen Pei-Chun 
Published: August 2020

Abstract
Using claims data from the universal health insurance program of Taiwan, we conducted a retrospective cohort study to investigate whether endometriosis and hormone therapy are associated with the risk of developing hyperlipidemia. We selected 9,155 women aged 20–55 years with endometriosis diagnosed during the period 2000–2013 and 212,641 women without endometriosis with a median follow-up time of 7 years. Among patients with endometriosis, 86% of cases were identified on the basis of diagnosis codes with an ultrasound claim, and 14% were defined by diagnostic laparoscopy or surgical treatments. In a Cox proportional hazards model, the adjusted hazard ratio was 1.30 (95% confidence interval (CI): 1.19, 1.41) for all women, 1.04 (95% CI: 0.81, 1.32) for women under 35 years of age, 1.17 (95% CI: 1.03, 1.32) for women aged 35–44 years, and 1.34 (95% CI: 1.18, 1.52) for women aged 45–54 years. Hysterectomy and/or bilateral oophorectomy accounted for 46.9% of the association between endometriosis and hyperlipidemia, and hormone therapy accounted for 21.6%. Among women with endometriosis, the marginal structural model approach adjusting for time-varying hysterectomy/bilateral oophorectomy showed no association between use of hormone medications and risk of hyperlipidemia. We concluded that women with endometriosis are at increased risk of hyperlipidemia; use of hormone therapy by these women was not independently associated with the development of hyperlipidemia.
Adjusting Coronavirus Prevalence Estimates for Laboratory Test Kit Error
Authors: Sempos Christopher T , Tian Lu 
Published: August 2020

AbstractTesting representative populations to determine the prevalence or the percentage of the population with active severe acute respiratory syndrome coronavirus 2 infection and/or antibodies to infection is being recommended as essential for making public policy decisions to ease restrictions or to continue enforcing national, state, and local government rules to shelter in place. However, all laboratory tests are imperfect and have estimates of sensitivity and specificity less than 100%—in some cases, considerably less than 100%. That error will lead to biased prevalence estimates. If the true prevalence is low, possibly in the range of 1%–5%, then testing error will lead to a constant background of bias that most likely will be larger, and possibly much larger, than the true prevalence itself. As a result, what is needed is a method for adjusting prevalence estimates for testing error. Methods are outlined in this article for adjusting prevalence estimates for testing error both prospectively in studies being planned and retrospectively in studies that have been conducted. If used, these methods also would help harmonize study results within countries and worldwide. Adjustment can lead to more accurate prevalence estimates and to better policy decisions. However, adjustment will not improve the accuracy of an individual test.
Neurogenic Orthostatic Hypotension. Lessons From Synucleinopathies
Authors: Idiaquez Juan Francisco , Idiaquez Juan , Casar Juan Carlos , Biaggioni Italo 
Published: August 2020

Abstract
Maintenance of upright blood pressure critically depends on the autonomic nervous system and its failure leads to neurogenic orthostatic hypotension (NOH). The most severe cases are seen in neurodegenerative disorders caused by abnormal α-synuclein deposits: multiple system atrophy (MSA), Parkinson’s disease, Lewy body dementia, and pure autonomic failure (PAF). The development of novel treatments for NOH derives from research in these disorders. We provide a brief review of their underlying pathophysiology relevant to understand the rationale behind treatment options for NOH. The goal of treatment is not to normalize blood pressure but rather to improve quality of life and prevent syncope and falls by reducing symptoms of cerebral hypoperfusion. Patients not able to recognize NOH symptoms are at a higher risk for falls. The first step in the management of NOH is to educate patients on how to avoid high-risk situations and providers to identify medications that trigger or worsen NOH. Conservative countermeasures, including diet and compression garments, should always precede pharmacologic therapies. Volume expanders (fludrocortisone and desmopressin) should be used with caution. Drugs that enhance residual sympathetic tone (pyridostigmine and atomoxetine) are more effective in patients with mild disease and in MSA patients with spared postganglionic fibers. Norepinephrine replacement therapy (midodrine and droxidopa) is more effective in patients with neurodegeneration of peripheral noradrenergic fibers like PAF. NOH is often associated with other cardiovascular diseases, most notably supine hypertension, and treatment should be adapted to their presence.
Environmentally driven escalation of host egg rejection decimates success of an avian brood parasite
Authors: Eadie John M , Lyon Bruce E 
Published: August 2020

Abstract
The black-headed duck (Heteronetta atricapilla) of South America is the only known avian obligate brood parasite with precocial offspring. In Argentina, it relies on two species of coots as primary hosts, which typically reject 35–65% of duck eggs. We show that environmentally driven increases in host egg rejection behavior lead to substantial reductions in the reproductive success of the brood parasite. Episodes of flooding and vegetation loss caused dramatic shifts in host egg-rejection behavior, resulting in rejection (85–95%) of almost all duck eggs. Coots respond to fluctuating water levels by building up their nest, raising their own eggs but leaving duck eggs behind. Coots can apparently recognize parasitic duck eggs, but large-scale rejection is triggered only when hosts must actively make a choice. We use a simple population model to illustrate the unique demographic challenges that black-headed ducks face with their parasitic lifestyle and to explore the potential impact of environmentally induced escalation of egg rejection. Using the best available estimates for key vital rates, we show that obligate parasitism may provide a demographically precarious existence for black-headed ducks, even under benign environmental conditions. Environmentally mediated increases in egg rejection rates by hosts could impact significantly the viability of this enigmatic species of brood parasitic duck. Our results demonstrate that egg rejection rates are not fixed properties of host populations or individuals but are strongly influenced by social and ecological factors. Shifts in these environmental drivers could have important and unforeseen demographic consequences for brood parasites.
Potential inhibitors for the novel coronavirus (SARS-CoV-2)
Authors: Han Yanqiang , Wang Zhilong , Ren Jiahao , Wei Zhiyun , Li Jinjin 
Published: August 2020

Abstract
The lack of a vaccine or any effective treatment for the aggressive novel coronavirus disease (COVID-19) has created a sense of urgency for the discovery of effective drugs. Several repurposing pharmaceutical candidates have been reported or envisaged to inhibit the emerging infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but their binding sites, binding affinities and inhibitory mechanisms are still unavailable. In this study, we use the ligand-protein docking program and molecular dynamic simulation to ab initio investigate the binding mechanism and inhibitory ability of seven clinically approved drugs (Chloroquine, Hydroxychloroquine, Remdesivir, Ritonavir, Beclabuvir, Indinavir and Favipiravir) and a recently designed α-ketoamide inhibitor (13b) at the molecular level. The results suggest that Chloroquine has the strongest binding affinity with 3CL hydrolase (Mpro) among clinically approved drugs, indicating its effective inhibitory ability for SARS-CoV-2. However, the newly designed inhibitor 13b shows potentially improved inhibition efficiency with larger binding energy compared with Chloroquine. We further calculate the important binding site residues at the active site and demonstrate that the MET 165 and HIE 163 contribute the most for 13b, while the MET 165 and GLN 189 for Chloroquine, based on residual energy decomposition analysis. The proposed work offers a higher research priority for 13b to treat the infection of SARS-CoV-2 and provides theoretical basis for further design of effective drug molecules with stronger inhibition.
TRTools: a toolkit for genome-wide analysis of tandem repeats
Authors: Mousavi Nima , Margoliash Jonathan , Pusarla Neha , Saini Shubham , Yanicky Richard , Gymrek Melissa 
Published: August 2020

Abstract

Summary
A rich set of tools have recently been developed for performing genome-wide genotyping of tandem repeats (TRs). However, standardized tools for downstream analysis of these results are lacking. To facilitate TR analysis applications, we present TRTools, a Python library and suite of command line tools for filtering, merging and quality control of TR genotype files. TRTools utilizes an internal harmonization module, making it compatible with outputs from a wide range of TR genotypers.

Availability and implementation
TRTools is freely available at https://github.com/gymreklab/TRTools. Detailed documentation is available at https://trtools.readthedocs.io.

Supplementary information
Supplementary data are available at Bioinformatics online.
Diversity in leading and laggard regions: living standards, residual income and regional policy
Authors: Calafati Luca , Froud Julie , Haslam Colin , Johal Sukhdev , Williams Karel 
Published: August 2020

Abstract
This article develops a Foundational Economy contribution to debate about regional inequalities by presenting new calculations of household income after the costs of three essential items (housing, transport and utilities). These residual income measures illustrate the diversity of living standards within and between English and Welsh regions. The analysis shows a mosaic of variation in residual income and wealth accumulation driven by the variability of housing costs in four different tenure groups (outright owners, mortgage payers, private renters and social renters). The article argues that GVA averages and descriptors like “left behind” are a poor guide to differences within and between regions; they also misdirect policy towards “levelling up” the apparently unsuccessful places without directly addressing the quality of and access to essential services. From a foundational point of view, regional policy needs to focus on access to housing at reasonable cost for all income and tenure groups in every region.
Barriers to Psychosocial Support and Quality of Life for Patients With Inflammatory Bowel Disease: A Survey Study
Authors: Lawrence Rebecca , Choudhary Cuckoo 
Published: August 2020

AbstractBackgroundPsychological comorbidities are common among people with inflammatory bowel disease (IBD) and are associated with worse disease outcomes. Evidence-based psychotherapy is an effective means to increase psychosocial support. This study aimed to identify the barriers to attending psychotherapy.MethodsThis electronic survey study included a demographic, quality of life, and barriers to psychotherapy questionnaire. Quality of life was assessed using the Short Inflammatory Bowel Disease Questionnaire (SIBDQ). Barriers were assessed using the Perceived Barriers to Psychological Treatments scale (PBPT). Linear regression was used to identify participant characteristics associated with higher PBPT scores.ResultsOne hundred eighty-seven participants completed the study. Fifty-eight percent of participants had ≥1 significant barrier. Time (28%), knowledge about the availability of services (25%), and cost (19%) were the most common barriers. Least common were stigma (14%), lack of motivation (12%), and emotional concerns (7%). Lower SIBDQ scores, being male, not being full-time employed, having Crohn disease, and being in disease remission were associated with higher PBPT scores.ConclusionsKnowledge about the availability of services, time constraints, and cost are the leading barriers to psychotherapy among people with IBD. Care providers should develop a network of psychotherapists available to those with IBD. Being male and not being full-time employed may be risk factors for greater barriers. Further research is needed on barriers among groups underrepresented in this study and on novel psychotherapy solutions, like telehealth and low-cost options.
Utilization of diagnostic resources and costs in patients with suspected cardiac chest pain
Authors: Vester Marijke P M , Eindhoven Daniëlle C , Bonten Tobias N , Wagenaar Holger , Holthuis Hendrik J , Schalij Martin J , de Grooth Greetje J , van Dijkman Paul R M 
Published: August 2020

Abstract

Aims
Non-acute chest pain is a common complaint and can be caused by various conditions. With the rising healthcare expenditures of today, it is necessary to use our healthcare resources effectively. This study aims to give insight into the diagnostic effort and costs for patients with non-acute chest pain.

Methods and results
Financial data of patients without a cardiac history from four hospitals (January 2012–October 2018), who were registered with the national diagnostic code ‘no cardiac pathology’ (ICD-10 Z13.6), ‘chest wall syndrome’ (ICD-10 R07.4), or ‘stable angina pectoris’ (ICD-10 I20.9) were extracted. In total, 74 091 patients were included for analysis and divided into the following final diagnosis groups: no cardiac pathology: N = 19 688 (age 53 ± 18), 46% male; chest wall syndrome: N = 40 858 (age 56 ± 15), 45% male; and stable angina pectoris (AP): N = 13 545 (age 67 ± 11), 61% male. A total of approximately €142.7 million was spent during diagnostic work-up. The total expenditure during diagnostic effort was €1.97, €8.13, and €10.7 million, respectively for no cardiac pathology, chest wall syndrome, and stable AP per year. After 8 years of follow-up, ≥95% of the patients diagnosed with no cardiac pathology or chest wall syndrome had an (cardiac) ischaemic-free survival.

Conclusion
The diagnostic expenditure and clinical effort to ascertain non-cardiac chest pain are high. We should define what we as society find acceptable as ‘assurance costs’ with an increasing pressure on the healthcare system and costs.
Textbook analysis: the case of the first Nicaraguan ELT series
Authors: Tórrez Nahúm Misael , Lund Ragnhild Elisabeth 
Published: August 2020

AbstractNicaragua published its first series of textbooks for the teaching of English in public secondary schools in 2016. This article reports on an investigation of the first three textbooks belonging to this series. The aim was to see how the textbooks follow up the Nicaraguan national curriculum, which emphasizes the need for learners to develop communication skills. We discuss the approaches with reference to principles of communicative language teaching and Nation’s four strands for a well-balanced language course. We identify significant discrepancies between the three books and, thus, a lack of progression in the course. The investigation is also an example of the affordances of our analytical tool for textbook analysis.
Impact of cardiovascular risk factors and genetics on 10-year absolute risk of dementia: risk charts for targeted prevention
Authors: Juul Rasmussen Ida , Rasmussen Katrine Laura , Nordestgaard Børge G , Tybjærg-Hansen Anne , Frikke-Schmidt Ruth 
Published: August 2020

AbstractAimsDementia is a major global challenge for health and social care in aging populations. A third of all dementia may be preventable due to cardiovascular risk factors. Intensive multi-domain intervention trials targeting primarily cardiovascular risk factors show improved cognitive function in people at risk. Such interventions will, however, be expensive to implement in all individuals at risk and will represent unrealistic economic tasks for most societies. Therefore, a risk score identifying high-risk individuals is warranted.Methods and resultsIn 61 664 individuals from two prospective cohorts of the Danish general population, we generated 10-year absolute risk scores for all-cause dementia from cardiovascular risk factors and genetics. In both sexes, 10-year absolute risk of all-cause dementia increased with increasing age, number of apolipoprotein E (APOE) ɛ4 alleles, number of genome-wide association studies (GWAS) risk alleles, and cardiovascular risk factors. The highest 10-year absolute risks of all-cause dementia seen in smoking women with diabetes, low education, APOE ɛ44 genotype, and 22–31 GWAS risk alleles were 6%, 23%, 48%, and 66% in those aged 50–59, 60–69, 70–79, and 80–100, respectively. Corresponding values for men were 5%, 19%, 42%, and 60%, respectively.ConclusionTen-year absolute risk of all-cause dementia increased with age, APOE ɛ4 alleles, GWAS risk alleles, diabetes, low education, and smoking in both women and men. Ten-year absolute risk charts for dementia will facilitate identification of high-risk individuals, those who likely will benefit the most from an early intervention against cardiovascular risk factors.
Infanticide vs. inherited cardiac arrhythmias
Authors: Brohus Malene , Arsov Todor , Wallace David A , Jensen Helene Halkjær , Nyegaard Mette , Crotti Lia , Adamski Marcin , Zhang Yafei , Field Matt A , Athanasopoulos Vicki , Baró Isabelle , Ribeiro de Oliveira-Mendes Bárbara B , Redon Richard , Charpentier Flavien , Raju Hariharan , DiSilvestre Deborah , Wei Jinhong , Wang Ruiwu , Rafehi Haloom , Kaspi Antony , Bahlo Melanie , Dick Ivy E , Chen Sui Rong Wayne , Cook Matthew C , Vinuesa Carola G , Overgaard Michael Toft , Schwartz Peter J 
Published: August 2020

Abstract

Aims
In 2003, an Australian woman was convicted by a jury of smothering and killing her four children over a 10-year period. Each child died suddenly and unexpectedly during a sleep period, at ages ranging from 19 days to 18 months. In 2019 we were asked to investigate if a genetic cause could explain the children’s deaths as part of an inquiry into the mother’s convictions.

Methods and results
Whole genomes or exomes of the mother and her four children were sequenced. Functional analysis of a novel CALM2 variant was performed by measuring Ca2+-binding affinity, interaction with calcium channels and channel function. We found two children had a novel calmodulin variant (CALM2 G114R) that was inherited maternally. Three genes (CALM1-3) encode identical calmodulin proteins. A variant in the corresponding residue of CALM3 (G114W) was recently reported in a child who died suddenly at age 4 and a sibling who suffered a cardiac arrest at age 5. We show that CALM2 G114R impairs calmodulin's ability to bind calcium and regulate two pivotal calcium channels (CaV1.2 and RyR2) involved in cardiac excitation contraction coupling. The deleterious effects of G114R are similar to those produced by G114W and N98S, which are considered arrhythmogenic and cause sudden cardiac death in children.

Conclusion
A novel functional calmodulin variant (G114R) predicted to cause idiopathic ventricular fibrillation, catecholaminergic polymorphic ventricular tachycardia, or mild long QT syndrome was present in two children. A fatal arrhythmic event may have been triggered by their intercurrent infections. Thus, calmodulinopathy emerges as a reasonable explanation for a natural cause of their deaths.
Early ecological succession patterns of bacterial, fungal and plant communities along a chronosequence in a recently deglaciated area of the Italian Alps
Authors: Franzetti A , Pittino F , Gandolfi I , Azzoni R S , Diolaiuti G , Smiraglia C , Pelfini M , Compostella C , Turchetti B , Buzzini P , Ambrosini R 
Published: August 2020

ABSTRACTIn this study, the early ecological succession patterns of Forni Glacier (Ortles-Cevedale group, Italian Alps) forefield along an 18-year long chronosequence (with a temporal resolution of 1 year) has been reported. Bacterial and fungal community structures were inferred by high-throughput sequencing of 16S rRNA gene and ITS, respectively. In addition, the occurrence of both herbaceous and arboreous plants was also recorded at each plot. A significant decrease of alpha-diversity in more recently deglaciated areas was observed for both bacteria and plants. Time since deglaciation and pH affected the structure of both fungal and bacterial communities. Pioneer plants could be a major source of colonization for both bacterial and fungal communities. Consistently, some of the most abundant bacterial taxa and some of those significantly varying with pH along the chronosequence (Polaromonas, Granulicella, Thiobacillus, Acidiferrobacter) are known to be actively involved in rock-weathering processes due to their chemolithotrophic metabolism, thus suggesting that the early phase of the chronosequence could be mainly shaped by the biologically controlled bioavailability of metals and inorganic compounds. Fungal communities were dominated by ascomycetous filamentous fungi and basidiomycetous yeasts. Their role as cold-adapted organic matter decomposers, due to their heterotrophic metabolism, was suggested.
The hydrogen threshold of obligately methyl-reducing methanogens
Authors: Feldewert Christopher , Lang Kristina , Brune Andreas 
Published: August 2020

ABSTRACT
Methanogenesis is the final step in the anaerobic degradation of organic matter. The most important substrates of methanogens are hydrogen plus carbon dioxide and acetate, but also the use of methanol, methylated amines, and aromatic methoxy groups appears to be more widespread than originally thought. Except for most members of the family Methanosarcinaceae, all methylotrophic methanogens require external hydrogen as reductant and therefore compete with hydrogenotrophic methanogens for this common substrate. Since methanogenesis from carbon dioxide consumes four molecules of hydrogen per molecule of methane, whereas methanogenesis from methanol requires only one, methyl-reducing methanogens should have an energetic advantage over hydrogenotrophic methanogens at low hydrogen partial pressures. However, experimental data on their hydrogen threshold is scarce and suffers from relatively high detection limits. Here, we show that the methyl-reducing methanogens Methanosphaera stadtmanae (Methanobacteriales), Methanimicrococcus blatticola (Methanosarcinales), and Methanomassiliicoccus luminyensis (Methanomassiliicoccales) consume hydrogen to partial pressures &lt; 0.1 Pa, which is almost one order of magnitude lower than the thresholds for M. stadtmanae and M. blatticola reported in the only previous study on this topic. We conclude that methylotrophic methanogens should outcompete hydrogenotrophic methanogens for hydrogen and that their activity is limited by the availability of methyl groups.