bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations
Authors: Karcher Nicolai , Pasolli Edoardo , Asnicar Francesco , Huang Kun D. , Tett Adrian , Manara Serena , Armanini Federica , Bain Debbie , Duncan Sylvia H. , Louis Petra , Zolfo Moreno , Manghi Paolo , Valles-Colomer Mireia , Raffaetà Roberta , Rota-Stabelli Omar , Collado Maria Carmen , Zeller Georg , Falush Daniel , Maixner Frank , Walker Alan W. , Huttenhower Curtis , Segata Nicola 
Published: June 2020

AbstractBackgroundEubacterium rectaleis one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been carried out.ResultsHere, we leverage metagenomic assembly followed by a reference-based binning strategy to screen over 6500 gut metagenomes spanning geography and lifestyle and reconstruct over 1300E. rectalehigh-quality genomes from metagenomes. We extend previous results of biogeographic stratification, identifying a new subspecies predominantly found in African individuals and showing that closely related non-human primates do not harborE. rectale. Comparison of pairwise genetic and geographic distances between subspecies suggests that isolation by distance and co-dispersal with human populations might have contributed to shaping the contemporary population structure ofE. rectale. We confirm that a relatively recently divergedE. rectalesubspecies specific to Europe consistently lacks motility operons and that it is immotile in vitro, probably due to ancestral genetic loss. The same subspecies exhibits expansion of its carbohydrate metabolism gene repertoire including the acquisition of a genomic island strongly enriched in glycosyltransferase genes involved in exopolysaccharide synthesis.ConclusionsOur study provides new insights into the population structure and ecology ofE. rectaleand shows that shotgun metagenomes can enable population genomics studies of microbiota members at a resolution and scale previously attainable only by extensive isolate sequencing.
Association between variation of circulating 25-OH vitamin D and methylation of secreted frizzled-related protein 2 in colorectal cancer
Authors: Boughanem Hatim , Cabrera-Mulero Amanda , Hernández-Alonso Pablo , Clemente-Postigo Mercedes , Casanueva Felipe F. , Tinahones Francisco José , Morcillo Sonsoles , Crujeiras Ana B. , Macias-Gonzalez Manuel 
Published: June 2020

Abstract
Backgrounds
Colorectal cancer (CRC) results from the accumulation of epigenetic and genetic changes in colon cells during neoplasic transformation, which the activation of Wingless (Wnt) signaling pathway is a common mechanism for CRC initiation. The Wnt pathway is mainly regulated by Wnt antagonists, as secreted frizzled-related protein (SFRP) family. Indeed, SFRP2 is proposed as a noninvasive biomarker for CRC diagnosis. Vitamin D also antagonizes Wnt signaling in colon cancers cells. Several studies showed that vitamin D was able to alter DNA methylation, although this mechanism is not yet clear. Therefore, the aim of this study was to find an association between circulating 25-OH vitamin D (30th percentile of vitamin D) and the SFRP2 methylation.

Methods
A total of 67 CRC patients were included in the study. These patients were subdivided into two groups based on their 30th percentile vitamin D (20 patients were below, and 47 participants were above the 30th percentile of vitamin D). We investigated the SFRP2 methylation in peripheral blood mononuclear cells (PBMCs), visceral adipose tissue (VAT), CRC tumor tissue, and adjacent tumor-free area. We also determined the relationship between SFRP2 methylation and methylation of carcinogenic and adipogenic genes. Finally, we tested the effect of vitamin D on the SFRP2 methylation in human colorectal carcinoma cell lines 116 (HCT116) and studied the association of neoadjuvant therapy under the 30th percentile vitamin D with SFRP2 promoter methylation.

Results
SFRP2 methylation in tumor area was decreased in patients who had higher levels of vitamin D. SFRP2 promoter methylation was positively correlated in tumor area with insulin and homeostasis model assessment of insulin resistance (HOMA-IR) but negatively correlated with HDL-c. SFRP2 methylation was also correlated with T cell lymphoma invasion and metastasis 1 (TIAM1) methylation in tumor area and CCAAT/enhancer-binding protein alpha (C/EBPα) in VAT. Treatment with vitamin D did not affect SFRP2 methylation in HCT116 cell line. Finally, neoadjuvant treatment was correlated with higher circulating 25-OH vitamin D and SFRP2 methylation under linear regression model.

Conclusion
Our results showed that higher circulating vitamin D is associated with low SFRP2 promoter methylation. Therefore, our results could suggest that vitamin D may have an epigenetic effect on DNA methylation. Finally, higher vitamin D could contribute to an improvement response to neoadjuvant treatment.
Absence of parvalbumin increases mitochondria volume and branching of dendrites in inhibitory Pvalb neurons in vivo: a point of convergence of autism spectrum disorder (ASD) risk gene phenotypes
Authors: Janickova Lucia , Rechberger Karin Farah , Wey Lucas , Schwaller Beat 
Published: June 2020

Abstract
Background
In fast firing, parvalbumin (PV)-expressing (Pvalb) interneurons, PV acts as an intracellular Ca2+ signal modulator with slow-onset kinetics. In Purkinje cells of PV−/− mice, adaptive/homeostatic mechanisms lead to an increase in mitochondria, organelles equally capable of delayed Ca2+ sequestering/buffering. An inverse regulation of PV and mitochondria likewise operates in cell model systems in vitro including myotubes, epithelial cells, and oligodendrocyte-like cells overexpressing PV. Whether such opposite regulation pertains to all Pvalb neurons is currently unknown. In oligodendrocyte-like cells, PV additionally decreases growth and branching of processes in a cell-autonomous manner.

Methods
The in vivo effects of absence of PV were investigated in inhibitory Pvalb neurons expressing EGFP, present in the somatosensory and medial prefrontal cortex, striatum, thalamic reticular nucleus, hippocampal regions DG, CA3, and CA1 and cerebellum of mice either wild-type or knockout (PV−/−) for the Pvalb gene. Changes in Pvalb neuron morphology and PV concentrations were determined using immunofluorescence, followed by 3D-reconstruction and quantitative image analyses.

Results
PV deficiency led to an increase in mitochondria volume and density in the soma; the magnitude of the effect was positively correlated with the estimated PV concentrations in the various Pvalb neuron subpopulations in wild-type neurons. The increase in dendrite length and branching, as well as thickness of proximal dendrites of selected PV−/− Pvalb neurons is likely the result of the observed increased density and length of mitochondria in these PV−/− Pvalb neuron dendrites. The increased branching and soma size directly linked to the absence of PV is assumed to contribute to the increased volume of the neocortex present in juvenile PV−/− mice. The extended dendritic branching is in line with the hypothesis of local hyperconnectivity in autism spectrum disorder (ASD) and ASD mouse models including PV−/− mice, which display all ASD core symptoms and several comorbidities including cortical macrocephaly at juvenile age.

Conclusion
PV is involved in most proposed mechanisms implicated in ASD etiology: alterations in Ca2+ signaling affecting E/I balance, changes in mitochondria structure/function, and increased dendritic length and branching, possibly resulting in local hyperconnectivity, all in a likely cell autonomous way.
Bulgarian consumers’ objective understanding of front-of-package nutrition labels: a comparative, randomized study
Authors: Andreeva Valentina A. , Egnell Manon , Handjieva-Darlenska Teodora , Talati Zenobia , Touvier Mathilde , Galan Pilar , Hercberg Serge , Pettigrew Simone , Julia Chantal 
Published: June 2020

Abstract
Background
Bulgaria continues to lag behind other EU Member States with respect to chronic disease morbidity and mortality prevention.

Methods
In line with efforts targeting the improvement of dietary practices, this comparative study assessed objective understanding of five different front-of-package labels (FOPL) (Reference Intakes, Multiple Traffic Lights, Warning label, Nutri-Score, and Health Star Rating) in a sample of 1010 Bulgarian adults. Objective understanding was assessed by comparing the results of two nutritional quality ranking tasks (with and without FOPL) in an online randomized experiment featuring three food categories (pizza, cakes, breakfast cereals). Multivariable ordinal logistic regression models within and across food categories were fit.

Results
Compared with the Reference Intakes group, participants randomized to Nutri-Score exhibited the largest improvement in product ranking ability across food categories (OR = 2.33; 95% CI: 1.55–3.51), followed by those randomized to Health Star Rating (OR = 1.99; 95% CI: 1.32–3.00). Nutri-Score also performed best within two (pizza and breakfast cereals) of the three food categories. The Multiple Traffic Lights and Warning label groups did not display any significant improvement in objective understanding either within or across food categories compared with the Reference Intakes group.

Conclusion
Nutri-Score, which is a summary, interpretive, polychromatic FOPL, emerged as the most effective model in the Bulgarian context, with the potential to help consumers better understand the nutritional quality of food. The findings are of particular interest to public health policymakers in the region and across Europe, as the debate about an EU-wide FOPL model continues to gather momentum.

Trial registration
Registration number ACTRN12618001221246. Trial registered at the Australian New Zealand Clinical Trials Registry.
The sound velocity of wüstite at high pressures: implications for low-velocity anomalies at the base of the lower mantle
Authors: Tanaka Ryosuke , Sakamaki Tatsuya , Ohtani Eiji , Fukui Hiroshi , Kamada Seiji , Suzuki Akio , Tsutsui Satoshi , Uchiyama Hiroshi , Baron Alfred Q. R. 
Published: June 2020

AbstractThe longitudinal sound velocity (VP) and the density (ρ) of wüstite, FeO, were measured at pressures of up to 112.3 GPa and temperatures of up to 1700 K using both inelastic X-ray scattering and X-ray diffraction combined with a laser-heated diamond-anvil cell. The linear relationship between VP and ρ, Birch’s law, for wüstite can be expressed as VP = 1.55 (1) × ρ [g/cm3] − 2.03 (8) [km/s] at 300 K and VP = 1.61 (1) × ρ [kg/m3] − 2.82 (10) [km/s] at 1700 K. The sound velocity of wüstite is significantly lower than that of bridgmanite and ferropericlase under lower mantle conditions. In other words, the existence of wüstite in the lower mantle can efficiently decrease the seismic velocity. Considering its slow velocity and several mechanisms for the formation of FeO-rich regions at the core–mantle boundary, we confirm earlier suggestions indicating that wüstite enrichment at the bottom of the Earth’s mantle may contribute to the formation of denser ultra-low velocity zones.
Perforated duodenal diverticulum successfully treated with a combination of surgical drainage and endoscopic nasobiliary and nasopancreatic drainage: a case report
Authors: Shimada Ayako , Fujita Koji , Kitago Minoru , Ichisaka Shunsuke , Ishikawa Keiichi , Kikunaga Hiroyuki , Kumai Koichiro , Miura Hiroshi 
Published: June 2020

Abstract
Background
Perforation of a duodenal diverticulum is a rare complication that may become fatal with a delay in appropriate treatment. However, the optimal treatment for perforated duodenal diverticulum remains controversial, ranging from conservative therapy to surgery including pancreatoduodenectomy.

Case presentation
The patient was a 60-year-old woman with no particular medical history who visited our hospital with chief complaints of continuous fever and right dorsal pain. Upon arrival, she had tenderness in the right upper quadrant of the abdomen. Laboratory data showed the elevation of inflammatory markers. Computed tomography revealed free air with abscess formation around the duodenum, which was diagnosed as duodenal perforation with abdominal abscess. We decided on emergent surgery, and we identified the perforation site on the dorsal side of the second portion of the duodenum intraoperatively. However, the inflammation around the perforation site was severe, and it was difficult to perform primary closure or dissection of the perforated diverticulum. Therefore, we finished surgery by placing four indwelling intra-abdominal tubes. Since postoperative day (POD) 1, the elevation of inflammation markers appeared to be uncontrollable, owing to the leakage of bile and pancreatic juice. We decided to perform endoscopic retrograde cholangiopancreatography on POD 2, and inserted endoscopic nasobiliary drainage and nasopancreatic drainage tubes. The patient showed a good postoperative course and was discharged on POD 57.

Conclusions
Endoscopic nasobiliary and nasopancreatic drainage in combination with surgical drainage may be an effective treatment for perforated duodenal diverticulum.
Latent organizing for responding to emergencies: foundations for research
Authors: van Fenema Paul C. , Romme A. Georges L. 
Published: June 2020

AbstractTime and again, many organizations and their staff members must respond to unexpected catastrophes like hurricanes (e.g., Katrina), virus pandemics (e.g., COVID-19), or other major emergencies. As a result, some organizations allow their employees to respond to external emergencies by engaging in response actions for a limited time, like in the case of emergency response teams. The latter teams consist of employees that act as emergency response officers who can respond to floods, train crashes, or other emergencies. Emergency response teams constitute an example of so-called latent organizing (LO) in the preparation for and response to any (unpredictable) future emergency. While latent organizing is ubiquitous in a societal and professional sense, it has hardly been studied in the organization design literature. In this paper, we develop a research agenda for studying LO. LO serves to prepare for and respond to emergencies, but otherwise remains largely dormant and inactive. When it is inactive, host organizations use the LO’s human and other resources for their own gainful purposes. Resources for LO are thus organized in a quasi-permanent fashion, one that is rather latent until activated by an emergency. We further develop the construct of latency to explore how effective LO can be designed and facilitated. In addition, we develop a research agenda for future work in this area.
Perceived stress, psychological distress and serum anti-Müllerian hormone levels among infertile and fertile women in North-central Nigeria
Authors: Lawal Oyinkansola Islamiyat , Akinyemi Joshua Odunayo , Yusuff Jameelu-deen Omokunmi , Okunlola Micheal Abiola 
Published: June 2020

AbstractBackgroundPrevious studies reported that self-reported stress, stressful life events, and psychological distress influence ovarian ageing and response. However, there are limited, yet conflicting findings on the effect of stress and psychological distress on serum anti-Müllerian hormone (AMH) as a biomarker of ovarian reserve, response, and ageing. This case-control study aimed to determine if stress and psychological distress levels were associated with serum anti-Müllerian hormone levels among 81 infertile and 109 fertile women of reproductive age attending the gynaecology and immunization clinics of a tertiary hospital in North-central Nigeria, respectively. Stress and psychological distress were measured using the Perceived Stress scale-10 and Kessler Psychological Distress Scale-10, respectively. The serum concentration of AMH was determined using enzyme-linked immunosorbent assays.ResultsThere was a significantly higher stress (p= 0.001) and psychological distress (p= 0.005) levels among infertile women; however, there was no difference in serum anti-Müllerian hormone levels between the two groups (p= 0.409). There was no significant correlation found between perceived stress and serum anti-Müllerian hormone in both infertile (r= 0.041,p= 0.719) and fertile (r= − 0.090,p= 0.353) women. There was also no correlation between psychological distress and serum anti-Müllerian hormone in the infertile (r= − 0.020,p= 0.860) and fertile (r= − 0.049,p= 0.636) groups. Controlling for age and body mass index in multivariate linear regression; stress and psychological distress were not significantly associated with serum anti-Müllerian hormone (B= − 0.005;p= 0.370 andB= − 0.001;p= 0.811).ConclusionSelf-reported stress and psychological distress are not associated with serum anti-Müllerian hormone levels in infertile and fertile women of reproductive age. Also, ovarian ageing was accelerated in infertile women when compared to fertile women; however, this does not appear to be related to stress or psychological distress. More research is needed to understand factors that may contribute to this accelerated decline.
Intermodality agreement between TTE and low kVp ECG-gated MDCTA in diagnosis of complex CHD in pediatrics
Authors: Ali Susan Adil , Amin Darine Helmy , Khattab Rasha Tolba 
Published: June 2020

Abstract
Background
Transthoracic echocardiography (TTE) is considered the primary diagnostic modality in congenital heart disease (CHD). However, it has limited role in evaluation of extra-cardiac major vessels abnormalities. Cardiac catheterization angiography is considered the gold standard investigation, yet, it is invasive. The aim of this study is to evaluate the agreement between TTE and low kVp ECG-gated cardiac multi-detector CT angiography (MDCTA) in detecting cardiac and extra-cardiac findings of complex congenital heart disease in a sample size of 36 patients (19 males and 17 females) with an age ranged between 30 days and 12 years (mean age 25.5 months). All cases were diagnosed to have complex CHD clinically and by TTE then referred to undergo cardiac low kVp ECG-gated MDCTA to confirm diagnosis and for better assessment of extra-cardiac major vessels abnormalities. Data derived from both modalities were then compared to calculate the inter-technique variability by using Cohen’s kappa statistics.

Results
TTE diagnosed 96% of intra-cardiac anomalies and only 54% of extra-cardiac major vessels anomalies detected by MDCTA, with variable degrees of intermodality agreement in detection different anomalies ranging between perfect agreement in diagnosing most of intra-cardiac lesions and very poor agreement in diagnosing extra-cardiac SVC anomalies.

Conclusion
Low kVp ECG-gated cardiac MDCTA is a rapid, non-invasive and reliable diagnostic modality in complex congenital heart diseases. It confirms TTE findings in intra-cardiac anomalies and significantly surpasses TTE reliability in diagnosis of extra-cardiac major vessels anomalies. So, it is indispensable as part of adequate preoperative assessment algorithm in cases of complex CHD and can't be replaced by TTE even with the later providing accurate assessment of intra-cardiac anomalies.
Misdiagnosis and missed diagnosis of adult attention-deficit hyperactivity disorder
Authors: Johnson Joe , Morris Sarah , George Sanju 
Published: June 2020

SUMMARYAttention-deficit hyperactivity disorder (ADHD) is a persistent, pervasive disorder characterised by symptoms of inattention, impulsivity and hyperactivity. Although traditionally considered a disorder of childhood, symptoms and associated impairments persist into adulthood for a significant proportion of individuals. Untreated ADHD can have a number of adverse effects for both the individual and wider society. Despite this, ADHD in adults is often misdiagnosed or its diagnosis is ‘missed’ in general psychiatric settings and this article highlights some reasons for this.
Effect of Cancer on Clinical Outcomes of Patients With COVID-19: A Meta-Analysis of Patient Data
Authors: Giannakoulis Vassilis G. , Papoutsi Eleni , Siempos Ilias I. 
Published: June 2020

PURPOSE Whether cancer is associated with worse prognosis among patients with COVID-19 is unknown. We aimed to quantify the effect (if any) of the presence as opposed to absence of cancer on important clinical outcomes of patients with COVID-19 by carrying out a systematic review and meta-analysis. METHODS We systematically searched PubMed, medRxiv, COVID-19 Open Research Dataset (CORD-19), and references of relevant articles up to April 27, 2020, to identify observational studies comparing patients with versus without cancer infected with COVID-19 and to report on mortality and/or need for admission to the intensive care unit (ICU). We calculated pooled risk ratios (RR) and 95% CIs with a random-effects model. The meta-analysis was registered with PROSPERO (CRD42020181531). RESULTS A total of 32 studies involving 46,499 patients (1,776 patients with cancer) with COVID-19 from Asia, Europe, and the United States were included. All-cause mortality was higher in patients with versus those without cancer (2,034 deaths; RR, 1.66; 95% CI, 1.33 to 2.07; P < .0001; 8 studies with 37,807 patients). The need for ICU admission was also more likely in patients with versus without cancer (3,220 events; RR, 1.56; 95% CI, 1.31 to 1.87; P < .0001; 26 studies with 15,375 patients). However, in a prespecified subgroup analysis of patients > 65 years of age, all-cause mortality was comparable between those with versus without cancer (915 deaths; RR, 1.06; 95% CI, 0.79 to 1.41; P = .71; 8 studies with 5,438 patients). CONCLUSION The synthesized evidence suggests that cancer is associated with worse clinical outcomes among patients with COVID-19. However, elderly patients with cancer may not be at increased risk of death when infected with COVID-19. These findings may inform discussions of clinicians with patients about prognosis and may guide health policies.
Decidual glycodelin-A polarizes human monocytes into a decidual macrophage-like phenotype through Siglec-7
Authors: Vijayan Madhavi , Lee Cheuk-Lun , Wong Vera H. H. , Wang Xia , Bai Kungfeng , Wu Jian , Koistinen Hannu , Seppälä Markku , Lee Kai-Fai , Yeung William S. B. , Ng Ernest H. Y. , Chiu Philip C. N. 
Published: June 2020

ABSTRACT
Decidual macrophages constitute 20–30% of the total leukocytes in the uterus of pregnant women, regulating the maternal immune tolerance and placenta development. Abnormal number or activities of decidual macrophages (dMs) are associated with fetal loss and pregnancy complications, such as preeclampsia. Monocytes differentiate into dMs in a decidua-specific microenvironment. Despite their important roles in pregnancy, the exact factors that regulate the differentiation into dMs remain unclear. Glycodelin-A (PAEP, hereafter referred to as GdA) is a glycoprotein that is abundantly present in the decidua, and plays an important role in fetomaternal defense and placental development. It modulates the differentiation and activity of several immune cell types residing in the decidua. In this study, we demonstrated that GdA induces the differentiation of human monocytes into dM-like phenotypes in terms of transcriptome, cell surface marker expression, secretome, and regulation of trophoblast and endothelial cell functions. We found that Sialic acid-binding Ig-like lectin 7 (Siglec-7) mediates the binding and biological actions of GdA in a sialic acid-dependent manner. We, therefore, suggest that GdA, induces the polarization of monocytes into dMs to regulate fetomaternal tolerance and placental development.