bluuebunny/crossref_metadata_2025_split huggingface dataset:
Social factors, not anthropogenic noise or artificial light, influence onset of dawn singing in a common songbird
Authors: Stuart Carley J , Grabarczyk Erin E , Vonhof Maarten J , Gill Sharon A 
Published: August 2019

AbstractWith worldwide increases in artificial light and anthropogenic noise, understanding how these pollutants influence animals allows us to better mitigate potential negative effects. Both light and noise affect the timing of daily activities, including the onset of dawn song in birds, yet the influence of these pollutants compared with social factors that also influence song onset remains unknown. We investigated the onset of dawn song, testing hypotheses aimed at understanding the influences of light and noise pollution as well as male competition, pairing status, and breeding stage on timing of dawn singing by male House Wrens (Troglodytes aedon). Overall, models with social factors fit song onset data better than models with abiotic factors of noise and sky glow, and the highest ranking model included nesting stage, number of male neighbors, and temperature. Males began singing earlier when they were building nests and when mates were fertile than during later nesting stages. Males also sang earlier as the number of male neighbors increased. The timing of dawn song by male House Wrens appeared unaffected by day-to-day variation in light and noise pollution, with social factors having larger effects on the onset of daily behavior in this species.
RICOPILI: Rapid Imputation for COnsortias PIpeLIne
Authors: Lam Max , Awasthi Swapnil , Watson Hunna J , Goldstein Jackie , Panagiotaropoulou Georgia , Trubetskoy Vassily , Karlsson Robert , Frei Oleksander , Fan Chun-Chieh , De Witte Ward , Mota Nina R , Mullins Niamh , Brügger Kim , Lee S Hong , Wray Naomi R , Skarabis Nora , Huang Hailiang , Neale Benjamin , Daly Mark J , Mattheisen Manuel , Walters Raymond , Ripke Stephan 
Published: August 2019

Abstract

Summary
Genome-wide association study (GWAS) analyses, at sufficient sample sizes and power, have successfully revealed biological insights for several complex traits. RICOPILI, an open-sourced Perl-based pipeline was developed to address the challenges of rapidly processing large-scale multi-cohort GWAS studies including quality control (QC), imputation and downstream analyses. The pipeline is computationally efficient with portability to a wide range of high-performance computing environments. RICOPILI was created as the Psychiatric Genomics Consortium pipeline for GWAS and adopted by other users. The pipeline features (i) technical and genomic QC in case-control and trio cohorts, (ii) genome-wide phasing and imputation, (iv) association analysis, (v) meta-analysis, (vi) polygenic risk scoring and (vii) replication analysis. Notably, a major differentiator from other GWAS pipelines, RICOPILI leverages on automated parallelization and cluster job management approaches for rapid production of imputed genome-wide data. A comprehensive meta-analysis of simulated GWAS data has been incorporated demonstrating each step of the pipeline. This includes all the associated visualization plots, to allow ease of data interpretation and manuscript preparation. Simulated GWAS datasets are also packaged with the pipeline for user training tutorials and developer work.

Availability and implementation
RICOPILI has a flexible architecture to allow for ongoing development and incorporation of newer available algorithms and is adaptable to various HPC environments (QSUB, BSUB, SLURM and others). Specific links for genomic resources are either directly provided in this paper or via tutorials and external links. The central location hosting scripts and tutorials is found at this URL: https://sites.google.com/a/broadinstitute.org/RICOPILI/home

Supplementary information
Supplementary data are available at Bioinformatics online.
Mitochondrial DNA copy number in peripheral blood leukocytes is associated with biochemical recurrence in prostate cancer patients in African Americans
Authors: Xu Junfeng , Chang Wen-Shin , Tsai Chia-Wen , Bau Da-Tian , Davis John W , Thompson Timothy C , Logothetis Christopher J , Gu Jian 
Published: August 2019

Abstract
Mitochondria play multiple important cellular functions. The purpose of this study was to evaluate whether leukocyte mitochondrial DNA copy number (mtDNAcn) is associated with aggressive prostate cancer (PCa) in African American (AA) men. We measured the mtDNAcn in peripheral blood leukocytes from 317 localized AA PCa patients and evaluated its associations with aggressive disease features at diagnosis and biochemical recurrence (BCR) after treatments. There was no significant difference in mtDNAcn among the clinical features at diagnosis, including age, prostate-specific antigen level, Gleason score and clinical stage under analysis of variance test. However, mtDNAcn was significantly associated with BCR in multivariate Cox analysis. Dichotomized into low and high mtDNAcn groups by the median value of mtDNAcn, patients with low mtDNAcn exhibited a significantly lower risk of BCR (hazard ratio = 0.32, 95% confidence interval: 0.13–0.79) compared to those with high mtDNAcn. There was a significant dose–response in tertile and quartile analyses (P for trend = 0.012 and 0.002, respectively). In Kaplan–Meier survival analyses, patients with higher mtDNAcn exhibited significantly shorter BCR-free survival time than those with lower mtDNAcn in dichotomous, tertile and quartile analyses, with long-rank P values of 0.017, 0.024 and 0.019, respectively. Our results showed for the first time that high leukocyte mtDNAcn was associated with worse prognosis in AA PCa patients.
Inhibitory Theta Burst Stimulation Highlights the Role of Left aIPS and Right TPJ during Complementary and Imitative Human–Avatar Interactions in Cooperative and Competitive Scenarios
Authors: Era Vanessa , Aglioti Salvatore Maria , Candidi Matteo 
Published: August 2019

Abstract
Competitive and cooperative interactions are based on anticipation or synchronization with the partner’s actions. Both forms of interaction may either require performing imitative or complementary movements with respect to those performed by our partner. We explored how parietal regions involved in the control of imitative behavior (temporo-parietal junction, TPJ), goal coding and visuo-motor integration (anterior intraparietal sulcus, aIPS) contribute to the execution of imitative and complementary movements during cooperative and competitive interactions. To this aim, we delivered off-line non-invasive inhibitory brain stimulation to healthy individuals’ left aIPS and right TPJ before they were asked to reach and grasp an object together with a virtual partner by either performing imitative or complementary interactions. In different blocks, participants were asked to compete or cooperate with the virtual partner that varied its behavior according to cooperative or competitive contexts. Left aIPS and right TPJ inhibition impaired individuals’ performance (i.e., synchrony in cooperative task and anticipation in competition) during complementary and imitative interactions, respectively, in both cooperative and competitive contexts, indicating that aIPS and TPJ inhibition affects own-other action integration and action imitation (that are different in complementary vs imitative interactions) more than action synchronization or anticipation (that are different in cooperative vs competitive contexts).
Declining Trends of Pneumococcal Meningitis in Gambian Children After the Introduction of Pneumococcal Conjugate Vaccines
Authors: Sanneh Bakary , Okoi Catherine , Grey-Johnson Mary , Bah-Camara Haddy , Kunta Fofana Baba , Baldeh Ignatius , Papa Sey Alhagie , Labbo Bah Mahamadou , Cham Mamadi , Samateh Amadou , Usuf Effua , Ndow Peter Sylvanus , Senghore Madikay , Worwui Archibald , Mwenda Jason M , Kwambana-Adams Brenda , Antonio Martin 
Published: August 2019

Abstract

Background
Acute bacterial meningitis remains a major cause of childhood mortality in sub-Saharan Africa. We document findings from hospital-based sentinel surveillance of bacterial meningitis among children <5 years of age in The Gambia, from 2010 to 2016.

Methods
Cerebrospinal fluid (CSF) was collected from children admitted to the Edward Francis Small Teaching Hospital with suspected meningitis. Identification of Streptococcus pneumoniae (pneumococcus), Neisseria meningitidis (meningococcus), and Haemophilus influenzae was performed by microbiological culture and/or polymerase chain reaction where possible. Whole genome sequencing was performed on pneumococcal isolates.

Results
A total of 438 children were admitted with suspected meningitis during the surveillance period. The median age of the patients was 13 (interquartile range, 3–30) months. Bacterial meningitis was confirmed in 21.4% (69/323) of all CSF samples analyzed. Pneumococcus, meningococcus, and H. influenzae accounted for 52.2%, 31.9%, and 16.0% of confirmed cases, respectively. There was a significant reduction of pneumococcal conjugate vaccine (PCV) serotypes, from 44.4% in 2011 to 0.0% in 2014, 5 years after PCV implementation. The majority of serotyped meningococcus and H. influenzae belonged to meningococcus serogroup W (45.5%) and H. influenzae type b (54.5%), respectively. Meningitis pathogens were more frequently isolated during the dry dusty season of the year. Reduced susceptibility to tetracycline, trimethoprim-sulfamethoxazole, and chloramphenicol was observed. No resistance to penicillin was found.

Conclusions
The proportion of meningitis cases due to pneumococcus declined in the post-PCV era. However, the persistence of vaccine-preventable meningitis in children aged <5 years is a major concern and demonstrates the need for sustained high-quality surveillance.
Therapeutic inhibition of microRNA-34a ameliorates aortic valve calcification via modulation of Notch1-Runx2 signalling
Authors: Toshima Taku , Watanabe Tetsu , Narumi Taro , Otaki Yoichiro , Shishido Tetsuro , Aono Tomonori , Goto Jun , Watanabe Ken , Sugai Takayuki , Takahashi Tetsuya , Yokoyama Miyuki , Kinoshita Daisuke , Tamura Harutoshi , Kato Shigehiko , Nishiyama Satoshi , Arimoto Takanori , Takahashi Hiroki , Miyamoto Takuya , Sadahiro Mitsuaki , Watanabe Masafumi 
Published: August 2019

AbstractAimsCalcific aortic valve stenosis (CAVS) is the most common valvular heart disease and is increased with elderly population. However, effective drug therapy has not been established yet. This study aimed to investigate the role of microRNAs (miRs) in the development of CAVS.Methods and resultsWe measured the expression of 10 miRs, which were reportedly involved in calcification by using human aortic valve tissue from patients who underwent aortic valve replacement with CAVS or aortic regurgitation (AR) and porcine aortic valve interstitial cells (AVICs) after treatment with osteogenic induction medium. We investigated whether a specific miR-inhibitor can suppress aortic valve calcification in wire injury CAVS mice model. Expression of miR-23a, miR-34a, miR-34c, miR-133a, miR-146a, and miR-155 was increased, and expression of miR-27a and miR-204 was decreased in valve tissues from CAVS compared with those from AR. Expression of Notch1 was decreased, and expression of Runt-related transcription factor 2 (Runx2) was increased in patients with CAVS compared with those with AR. We selected miR-34a among increased miRs in porcine AVICs after osteogenic treatment, which was consistent with results from patients with CAVS. MiR-34a increased calcium deposition in AVICs compared with miR-control. Notch1 expression was decreased, and Runx2 expression was increased in miR-34a transfected AVICs compared with that in miR-control. Conversely, inhibition of miR-34a significantly attenuated these calcification signals in AVICs compared with miR-control. RNA pull-down assay revealed that miR-34a directly targeted Notch1 expression by binding to Notch1 mRNA 3′ untranslated region. In wire injury CAVS mice, locked nucleic acid miR-34a inhibitor suppressed aortic velocity, calcium deposition of aortic valves, and cardiac hypertrophy, which were involved in decreased Runx2 and increased Notch1 expressions.ConclusionmiR-34a plays an important role in the development of CAVS via Notch1–Runx2 signalling pathway. Inhibition of miR-34a may be the therapeutic target for CAVS.
Lazarus in asystole: a case report of autoresuscitation after prolonged cardiac arrest
Authors: Sprenkeler David J , van Hout Gerardus P J , Chamuleau Steven A J 
Published: August 2019

Abstract

Background
Third-degree atrioventricular (AV) block can result in sudden cardiac death if no reliable escape rhythm is present. Here, we report a case of an 86-year-old female patient who developed a third-degree AV block leading to cardiac arrest. Surprisingly, sinus rhythm returned after 4 min of asystole, and she showed complete neurological recovery.

Case summary
Emergency services were contacted by the husband of an 86-year-old woman after she was found unconscious. Ambulance personnel diagnosed a third-degree AV block without an escape rhythm and transcutaneous pacing was started. At arrival on the emergency ward, pacing was inadequate, resulting in absence of circulation for ∼10 min. After consultation with the family, the patient turned out to have signed a ‘do not resuscitate’ order. Given the impression that the considerable delay deemed favourable neurological recovery unlikely, it was decided together with the family to stop the resuscitation. Subsequently, she had an intermittent junctional escape rhythm but eventually developed a documented asystole of more than 4 min. Against all expectations, she regained sinus rhythm and fully recovered. Eventually, a pacemaker was implanted and she was discharged home without neurological sequalae of the cardiac arrest.

Discussion
Autoresuscitation, also known as the Lazarus syndrome, is the spontaneous return of circulation after cardiac arrest and is incidentally seen after failed cardiopulmonary resuscitation (CPR). Autoresuscitation in the absence of CPR is highly unusual, but could, in this case, be due to the total AV block as the cause of the cardiac arrest.
Intestinal Clostridium species lower host susceptibility to enterohemorrhagic Escherichia coli O157:H7 infection
Authors: Koyanagi Yukako , Suzuki Rie , Ihara Kohei , Miyagi Hikaru , Isogai Hiroshi , Yoneyama Hiroshi , Isogai Emiko 
Published: August 2019

ABSTRACT
Susceptibility to enterohemorrhagic Escherichia coli (EHEC) infection varies among humans. The intestinal microbiota seems to play an essential role in host defense against EHEC; thus, we hypothesized that indigenous bacteria, such as Clostridium ramosum and Clostridium perfringens, could influence the susceptibility to EHEC infection. To evaluate the effect of indigenous bacteria on EHEC infection, germ-free mice were precolonized with each indigenous bacterium, and then infected with EHEC O157:H7. Precolonization with C. ramosum or C. perfringens completely prevented death from EHEC infection througout a test period. Precolonization with C. ramosum also reduced the level of secreted Shiga toxin (Stx) 2 and prevented histopathological changes in the kidneys in a similar way to precolonization with Bifidobacterium longum, which is used as a model for preventing EHEC infection. In contrast, the mice precolonized with C. perfringens showed mild renal injuries. When evaluated using an in vitro co-culturing system, again C. ramosum inhibited the growth and Stx production of EHEC more potently than C. perfringens. These results indicate that C. ramosum and C. perfringens suppressed EHEC infection; however, the extent of their preventive effects differed. Therefore, the susceptibility to EHEC infection and its severity can depend on the functional bacteria present in the intestinal microbiota of individuals.
Major Depressive Disorder (MDD) and Schizophrenia– Addressing Unmet Needs With Partial Agonists at the D2 Receptor: A Review
Authors: Mallet Jasmina , Gorwood Philip , Le Strat Yann , Dubertret Caroline 
Published: August 2019

AbstractSecond-generation antipsychotics are common candidates for the adjunctive treatment of major depressive disorder and for the treatment of schizophrenia. However, unmet needs remain in the treatment of both disorders. Considering schizophrenia, antipsychotics are the most common treatment and have demonstrated good efficacy. Still, side effects of these treatments are commonly reported and may impact adherence to the medication and functioning in patients with schizophrenia. Regarding major depressive disorder, despite the availability of several classes of antidepressants, many patients do not achieve remission. Adjunctive treatment with antipsychotics may improve clinical and functional outcomes. Compared with dopamine D2 receptor antagonism that is exhibited by most antipsychotics, partial agonism may result in improved outcomes in major depressive disorder and in schizophrenia. Aripiprazole, cariprazine, and brexpiprazole have partial agonism at the dopamine D2 receptor and could potentially overcome limitations associated with D2 antagonism. The objectives of this review were (1) to discuss the goal of treatment with second-generation antipsychotics in major depressive disorder and schizophrenia, and the clinical factors that should be considered, and (2) to examine the short- and long-term existing data on the efficacy and safety of D2 receptor partial agonists (aripiprazole, cariprazine, and brexpiprazole) in the adjunctive treatment of major depressive disorder and in the treatment of schizophrenia.
Emergence of NDM-producing Klebsiella pneumoniae and Escherichia coli in Spain: phylogeny, resistome, virulence and plasmids encoding blaNDM-like genes as determined by WGS
Authors: Pérez-Vázquez María , Sola Campoy Pedro J , Ortega Adriana , Bautista Verónica , Monzón Sara , Ruiz-Carrascoso Guillermo , Mingorance Jesus , González-Barberá Eva M , Gimeno Concepción , Aracil Belén , Sáez David , Lara Noelia , Fernández Sara , González-López Juan José , Campos José , Kingsley Robert A , Dougan Gordon , Oteo-Iglesias Jesús ,   Spanish NDM Study Group, Rodrigo Cristina Herrera , Aznar Esteban , García-Picazo Luisa , Martínez Beatriz Orden , Mansilla Emilia Cercenado , Álvarez-García Patricia , Carretero Julia María Pita , Rodríguez-Conde Irene , Cao Sonia María Rey , Gimeno Adelina , Moreno Mar Olga Pérez , Rodríguez Ma Luz Cordón , Cavero Teresa Alarcón , Gil Yolanda , Esteras Ma Antonia Remacha , Andrés José Luis Barrios , Trujillo Gloria , Almaraz José Luis Hernández , José Luis del Pozo José Leiva León y , Salas Carmen Martín , Adán Fernando Buñuel , Bertomeu Frederic Gómez , Cascales Paloma , Dorado José Cobos , Suarez Concepción Balado 
Published: August 2019

Abstract

Objectives
NDM carbapenemases have spread worldwide. However, little information exists about the impact of NDM-producing Enterobacteriaceae in Spain. By WGS, we sought to elucidate the population structure of NDM-like-producing Klebsiella pneumoniae and Escherichia coli in Spain and to determine the plasmids harbouring blaNDM-like genes.

Methods
High-resolution SNP typing, core-genome MLST and plasmid reconstruction (PlasmidID) were performed on 59 NDM-like-producing K. pneumoniae and 8 NDM-like-producing E. coli isolated over an 8 year period in Spain.

Results
Five major epidemic clones of NDM-producing K. pneumoniae caused five important nationwide outbreaks: ST437/NDM-7, ST437/NDM-1, ST147/NDM-1, ST11/NDM-1 and ST101/NDM-1; in contrast, the spread of NDM-producing E. coli was polyclonal. Three blaNDM types were identified: blaNDM-1, 61.2%; blaNDM-7, 32.8%; and blaNDM-5, 6%. Five K. pneumoniae isolates co-produced other carbapenemases (three blaOXA-48 and two blaVIM-1). The average number of acquired resistance genes was higher in K. pneumoniae than in E. coli. The plasmids encoding blaNDM-like genes belonged to IncFII, IncFIB, IncX3, IncR, IncN and IncC types, of which IncF, IncR and IncC were associated with MDR. The genetic surroundings of blaNDM-like genes showed a highly variable region upstream of ISAba125.

Conclusions
In recent years NDM-producing K. pneumoniae and E. coli have emerged in Spain; the spread of a few high-risk K. pneumoniae clones such as ST437/NDM-7, ST437/NDM-1, ST147/NDM-1, ST11/NDM-1 and ST101/NDM-1 have caused several interregional outbreaks. In contrast, the spread of NDM-producing E. coli has been polyclonal. Plasmid types IncFII, IncFIB, IncX3, IncR, IncN and IncC carried blaNDM, and the same IncX3 plasmid was detected in K. pneumoniae and E. coli.
miR-211-5p contributes to chondrocyte differentiation by suppressing Fibulin-4 expression to play a role in osteoarthritis
Authors: Liu Hao , Luo Jun 
Published: August 2019

Abstract
MicroRNAs (miRNAs) serve as key regulators in human disorders. Previous research reported that miR-211-5p is down-regulated in osteoarthritis (OA) and that Fibulin-4 inhibits chondrocyte differentiation. However, the role of miR-211-5p in the development of OA has not been clarified, and its downstream target has not been studied. This study aimed to explore the effect of miR-211-5p on chondrocyte differentiation and its influence on OA pathogenesis, as well as the interaction between miR-211-5p and Fibulin-4. In this study, we found that miR-211-5p is significantly down-regulated in articular cartilage tissues in an OA rat model, whereas it is clearly up-regulated during chondrocyte differentiation of ATDC5 cells. Silencing miR-211-5p in ATDC5 cells had an adverse effect on chondrocyte differentiation. Fibulin-4 was identified as a target of miR-211-5p, and miR-211-5p participated in chondrocyte differentiation by negatively regulating Fibulin-4 expression. In the OA rat model, miR-211-5p overexpression facilitated chondrocyte differentiation, along with the reduced pro-inflammatory cytokines level and the level of proteinases responsible for cartilage matrix degradation. In summary, miR-211-5p promotes chondrocyte differentiation by negatively regulating Fibulin-4 expression, and represses the expression of pro-inflammatory cytokines and proteinases responsible for cartilage matrix degradation in OA. miR-211-5p may serve as a promising target for OA treatment.