bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dispersal and local persistence shape the genetic structure of a widespread Neotropical plant species with a patchy distribution
Authors: Leal Bárbara Simões Santos , Graciano Vanessa Araujo , Chaves Cleber Juliano Neves , Huacre Luis Alberto Pillaca , Heuertz Myriam , Palma-Silva Clarisse 
Published: June 2019

Abstract

Background and Aims
Isolated populations constitute an ideal laboratory to study the consequences of intraspecific divergence, because intrinsic incompatibilities are more likely to accumulate under reduced gene flow. Here, we use a widespread bromeliad with a patchy distribution, Pitcairnia lanuginosa, as a model to infer processes driving Neotropical diversification and, thus, to improve our understanding of the origin and evolutionary dynamics of biodiversity in this highly speciose region.

Methods
We assessed the timing of lineage divergence, genetic structural patterns and historical demography of P. lanuginosa, based on microsatellites, and plastid and nuclear sequence data sets using coalescent analyses and an Approximate Bayesian Computation framework. Additionally, we used species distribution models (SDMs) to independently estimate potential changes in habitat suitability.

Key Results
Despite morphological uniformity, plastid and nuclear DNA data revealed two distinct P. lanuginosa lineages that probably diverged through dispersal from the Cerrado to the Central Andean Yungas, following the final uplift of the Andes, and passed through long-term isolation with no evidence of migration. Microsatellite data indicate low genetic diversity and high levels of inbreeding within populations, and restricted gene flow among populations, which are likely to be a consequence of bottlenecks (or founder events), and high selfing rates promoting population persistence in isolation. SDMs showed a slight expansion of the suitable range for P. lanuginosa lineages during the Last Glacial Maximum, although molecular data revealed a signature of older divergence. Pleistocene climatic oscillations thus seem to have played only a minor role in the diversification of P. lanuginosa, which probably persisted through adverse conditions in riparian forests.

Conclusions
Our results imply drift as a major force shaping the evolution of P. lanuginosa, and suggest that dispersal events have a prominent role in connecting Neotropical open and forest biomes.
A fully computational and reasonable representation for karyotypes
Authors: Warrender Jennifer D , Moorman Anthony V , Lord Phillip 
Published: June 2019

Abstract

Summary
The human karyotype has been used as a mechanism for describing and detecting gross abnormalities in the genome for many decades. It is used both for routine diagnostic purposes and for research to further our understanding of the causes of disease. Despite these important applications there has been no rigorous computational representation of the karyotype; rather an informal, string-based representation is used, making it hard to check, organize and search data of this form. In this article, we describe our use of OWL, the Ontology Web Language, to generate a fully computational representation of the karyotype; the development of this ontology represents a significant advance from the traditional bioinformatics use for tagging and navigation and has necessitated the development of a new ontology development environment called Tawny-OWL.

Availability and implementation
The Karyotype Ontology and associated Tawny-OWL source code is available on GitHub at https://github.com/jaydchan/tawny-karyotype, under a LGPL License, Version 3.0.
KinomeX: a web application for predicting kinome-wide polypharmacology effect of small molecules
Authors: Li Zhaojun , Li Xutong , Liu Xiaohong , Fu Zunyun , Xiong Zhaoping , Wu Xiaolong , Tan Xiaoqin , Zhao Jihui , Zhong Feisheng , Wan Xiaozhe , Luo Xiaomin , Chen Kaixian , Jiang Hualiang , Zheng Mingyue 
Published: June 2019

Abstract

Motivation
The large-scale kinome-wide virtual profiling for small molecules is a daunting task by experimental and traditional in silico drug design approaches. Recent advances in deep learning algorithms have brought about new opportunities in promoting this process.

Results
KinomeX is an online platform to predict kinome-wide polypharmacology effect of small molecules based solely on their chemical structures. The prediction is made by a multi-task deep neural network model trained with over 140 000 bioactivity data points for 391 kinases. Extensive computational and experimental validations have been performed. Overall, KinomeX enables users to create a comprehensive kinome interaction network for designing novel chemical modulators, and is of practical value on exploring the previously less studied or untargeted kinases.

Availability and implementation
KinomeX is available at: https://kinome.dddc.ac.cn.

Supplementary information
Supplementary data are available at Bioinformatics online.
Personalized Ertapenem Prophylaxis for Carriers of Extended-spectrum β-Lactamase–producing Enterobacteriaceae Undergoing Colorectal Surgery
Authors: Nutman Amir , Temkin Elizabeth , Harbarth Stephan , Carevic Biljana , Ris Frederic , Fankhauser-Rodriguez Carolina , Radovanovic Ivana , Dubinsky-Pertzov Biana , Cohen-Percia Shimrit , Kariv Yehuda , Buchs Nicolas , Schiffer Eduardo , Fallach Noga , Klausner Joseph , Carmeli Yehuda 
Published: June 2019

Abstract

Background
Carriers of extended-spectrum β-lactamase–producing Enterobacteriaceae (ESBL-PE) who receive cephalosporin-based prophylaxis have twice the risk of surgical site infection (SSI) following colorectal surgery as noncarriers. We tested whether ESBL-PE screening and personalized prophylaxis with ertapenem reduces SSI risk among carriers.

Methods
We conducted a prospective nonrandomized, nonblinded, interventional study in 3 hospitals in Israel, Switzerland, and Serbia. Patients were screened for ESBL-PE carriage before elective colorectal surgery. During the baseline phase, departmental guidelines advised prophylaxis with a cephalosporin plus metronidazole. In the intervention phase, guidelines were changed for ESBL-PE carriers to receive ertapenem. The primary outcome was any type of SSI within 30 days. We calculated adjusted risk differences (ARDs) following logistic regression.

Results
The intention-to-treat analysis compared 209 ESBL-PE carriers in the baseline phase to 269 in the intervention phase. SSI rates were 21.5% and 17.5%, respectively (ARD, –4.7% [95% confidence interval {CI}, –11.8% to 2.4%]). Unplanned crossover was high (15%), so to assess efficacy we performed an as-treated analysis comparing 247 patients who received cephalosporin-based prophylaxis with 221 who received ertapenem. SSI rates were 22.7% and 15.8%, respectively (ARD, –7.7% [95% CI, –14.6% to –.8%]), and rates of SSI caused by ESBL-PE were 6.5% and 0.9%, respectively (ARD, –5.6% [95% CI, –8.9% to –2.3%]). There was no significant difference in the rate of deep SSI. The number needed to treat to prevent 1 SSI in ESBL-PE carriers was 13.

Conclusions
Screening for ESBL-PE carriage before colorectal surgery and personalizing prophylaxis for carriers is efficacious in reducing SSI.
The Pitt Bacteremia Score Predicts Mortality in Nonbacteremic Infections
Authors: Henderson Heather , Luterbach Courtney L , Cober Eric , Richter Sandra S , Salata Robert A , Kalayjian Robert C , Watkins Richard R , Doi Yohei , Kaye Keith S , Evans Scott , Fowler Vance G , Bonomo Robert A , Harris Anthony , Napravnik Sonia , Van Duin David 
Published: June 2019

AbstractBackgroundPredicting mortality risk in patients is important in research settings. The Pitt bacteremia score (PBS) is commonly used as a predictor of early mortality risk in patients with bloodstream infections (BSIs). We determined whether the PBS predicts 14-day inpatient mortality in nonbacteremia carbapenem-resistant Enterobacteriaceae (CRE) infections.MethodsPatients were selected from the Consortium on Resistance Against Carbapenems in Klebsiella and Other Enterobacteriaceae, a prospective, multicenter, observational study. We estimated risk ratios to analyze the predictive ability of the PBS overall and each of its components individually. We analyzed each component of the PBS in the prediction of mortality, assessed the appropriate cutoff value for the dichotomized score, and compared the predictive ability of the qPitt score to that of the PBS.ResultsIn a cohort of 475 patients with CRE infections, a PBS ≥4 was associated with mortality in patients with nonbacteremia infections (risk ratio [RR], 21.9; 95% confidence interval [CI], 7.0, 68.8) and with BSIs (RR, 6.0; 95% CI, 2.5, 14.4). In multivariable analysis, the hypotension, mechanical ventilation, mental status, and cardiac arrest parameters of the PBS were independent risk factors for 14-day all-cause inpatient mortality. The temperature parameter as originally calculated for the PBS was not independently associated with mortality. However, a temperature &lt;36.0°C vs ≥36°C was independently associated with mortality. A qPitt score ≥2 had similar discrimination as a PBS ≥4 in nonbacteremia infections.ConclusionsHere, we validated that the PBS and qPitt score can be used as reliable predictors of mortality in nonbacteremia CRE infections.
Levosimendan prevents doxorubicin-induced cardiotoxicity in time- and dose-dependent manner: implications for inotropy
Authors: Efentakis Panagiotis , Varela Aimilia , Chavdoula Evangelia , Sigala Fragiska , Sanoudou Despina , Tenta Roxane , Gioti Katerina , Kostomitsopoulos Nikolaos , Papapetropoulos Andreas , Tasouli Androniki , Farmakis Dimitrios , Davos Costantinos H , Klinakis Apostolos , Suter Thomas , Cokkinos Dennis V , Iliodromitis Efstathios K , Wenzel Philip , Andreadou Ioanna 
Published: June 2019

Abstract

Aims
Levosimendan (LEVO) a clinically-used inodilator, exerts multifaceted cardioprotective effects. Case-studies indicate protection against doxorubicin (DXR)-induced cardiotoxicity, but this effect remains obscure. We investigated the effect and mechanism of different regimens of levosimendan on sub-chronic and chronic doxorubicin cardiotoxicity.

Methods and results
Based on preliminary in vivo experiments, rats serving as a sub-chronic model of doxorubicin-cardiotoxicity and were divided into: Control (N/S-0.9%), DXR (18 mg/kg-cumulative), DXR+LEVO (LEVO, 24 μg/kg-cumulative), and DXR+LEVO (acute) (LEVO, 24 μg/kg-bolus) for 14 days. Protein kinase-B (Akt), endothelial nitric oxide synthase (eNOS), and protein kinase-A and G (PKA/PKG) pathways emerged as contributors to the cardioprotection, converging onto phospholamban (PLN). To verify the contribution of PLN, phospholamban knockout (PLN−/−) mice were assigned to PLN−/−/Control (N/S-0.9%), PLN−/−/DXR (18 mg/kg), and PLN−/−/DXR+LEVO (ac) for 14 days. Furthermore, female breast cancer-bearing (BC) mice were divided into: Control (normal saline 0.9%, N/S 0.9%), DXR (18 mg/kg), LEVO, and DXR+LEVO (LEVO, 24 μg/kg-bolus) for 28 days. Echocardiography was performed in all protocols. To elucidate levosimendan’s cardioprotective mechanism, primary cardiomyocytes were treated with doxorubicin or/and levosimendan and with N omega-nitro-L-arginine methyl ester (L-NAME), DT-2, and H-89 (eNOS, PKG, and PKA inhibitors, respectively); cardiomyocyte-toxicity was assessed. Single bolus administration of levosimendan abrogated DXR-induced cardiotoxicity and activated Akt/eNOS and cAMP-PKA/cGMP-PKG/PLN pathways but failed to exert cardioprotection in PLN−/− mice. Levosimendan’s cardioprotection was also evident in the BC model. Finally, in vitro PKA inhibition abrogated levosimendan-mediated cardioprotection, indicating that its cardioprotection is cAMP-PKA dependent, while levosimendan preponderated over milrinone and dobutamine, by ameliorating calcium overload.

Conclusion
Single dose levosimendan prevented doxorubicin cardiotoxicity through a cAMP-PKA-PLN pathway, highlighting the role of inotropy in doxorubicin cardiotoxicity.
Prevention of chronic diseases in middle-age women: a cross-sectional study on an Italian large sample
Authors: Colombo Alessandra , Voglino Gianluca , Sessa Aurelio , Bert Fabrizio , Maestroni Anna Maria , Lo Moro Giuseppina , Caielli Rosita , Siliquini Roberta , Della Rosa Maria Cristina 
Published: June 2019

Abstract

Background
The age around 50 years represents a crucial point for women: menopause leads to biological changes and it begins breast and colon-rectal cancer screening. This study aimed at assessing frequencies of cardiovascular risk factors and analyzing participation in screening and vaccination.

Methods
In 2017, a cross-sectional study was performed in Northern Italy. Totally, 12 249 women, aged between 50 and 54 years, were enrolled by General Practitioners (GPs). It was used a 21-item form, with information about: socio-demographic, anamnestic and clinical data, execution of a booster shot of tetanus-diphtheria-acellular pertussis (Tdap) vaccine in the last decade and of PAP-test, mammography and faecal occult blood test in the last 2 years. Descriptive and crosstab χ2 analyses were performed with STATA MP13. The significance level was P ≤ 0.05.

Results
Our findings showed the presence of cardiovascular risk factors, such as obesity (10.95%), hypertension (13.76%), hyperlipidaemia (11.57%), glycaemia ≥ 100 mg dl−1 (16.97%), poor physical activity (73.49%), smoking (18.28%), cardiovascular family history (FH) (51.70%). There were a lower participation in colo-rectal cancer screening (45.09%) compared with breast (85.06%) and cervical (77.16%) cancer screening and an insufficient Tdap booster dose compliance (17.56%). Chi-square analyses showed correlations between cardiovascular FH and body mass index, hypertension, hyperlipidaemia, glycaemia and smoking, and between cancer FH and participation in breast and colo-rectal cancer screening (P < 0.05).

Conclusions
Women with cardiovascular disease FH represent a priority target of educational interventions considering the prevalence of concomitant risk factors. Programmes aimed at increasing screening and vaccination participation should be implemented.
Laurel (Litsea glaucescens Kunth) Regeneration in the Presence of Disturbance Events: A Case Study
Authors: Razo-Zárate Ramón , Retama-Cázares Laura Berenice , Rodríguez-Laguna Rodrigo , Palacios-Romero Abraham , Meza-Rangel Joel , Capulín-Grande Juan , Fragoso-López Pablo Irving , Jesús Cortés-Blobaum Hermann 
Published: June 2019

Abstract
A study was carried out in an Abies religiosa Kunth Schltdl. et Cham forest of the community of San Antonio Tecocomulco Tres Cabezas, Municipality of Singuilucan, Hidalgo, to evaluate the resprouting ability of laurel (Litsea glaucescens Kunth) in response to controlled burning treatments and removal of entire stems. The number of laurel bushes, shoots, and mean plant height were evaluated, and three treatments were applied: controlled surface burn; all sprouts cut from the base; and control treatment. Nine weeks after the treatments were applied, the plants in the stem removal treatment remained alive (100 percent), and the appearance of shoots with a mean height of 4.8 cm increased by 18 percent, whereas in the controlled burning treatment, the number of live plants and shoots decreased by 38.2 and 71.5 percent, respectively, with a mean height of 1.1 cm. In the control, the number of bushes remained at 100 percent, and shoots increased by 9.9 percent with a mean bush height of 7.6 cm. This indicates that although surface forest fires tend to affect laurel, surviving plants tend to emit more vigorous shoots, whereas stem removal in laurel bushes generates more shoots
A mutation inactivating the distal SF1 binding site on the human anti-Müllerian hormone promoter causes persistent Müllerian duct syndrome
Authors: Schteingart Helena F , Picard Jean-Yves , Valeri Clara , Marshall Ian , Treton Dominique , di Clemente Nathalie , Rey Rodolfo A , Josso Nathalie 
Published: June 2019

AbstractThe persistent Müllerian duct syndrome (PMDS) is a 46,XY disorder of sexual development characterized by the persistence of Müllerian duct derivatives, uterus and tubes, in otherwise normally masculinized males. The condition, transmitted as a recessive autosomal trait, is usually due to mutations in either the anti-Müllerian hormone (AMH) gene or its main receptor. Many variants of these genes have been described, all targeting the coding sequences. We report the first case of PMDS due to a regulatory mutation. The AMH promoter contains two binding sites for steroidogenic factor 1 (SF1), one at −102 and the other at −228. Our patient carries a single base deletion at −225, significantly decreasing its capacity for binding SF1, as measured by the electrophoresis mobility shift assay. Furthermore, by linking the AMH promoter to the luciferase gene, we show that the transactivation capacity of the promoter is significantly decreased by the mutation, in contrast to the disruption of the −102 binding site. To explain the difference in impact we hypothesize that SF1 could partially overcome the lack of binding to the −102 binding site by interacting with a GATA4 molecule linked to a nearby response element. We show that disruption of both the −102 SF1 and the −84 GATA response elements significantly decreases the transactivation capacity of the promoter. In conclusion, we suggest that the distance between mutated SF1 sites and potentially rescuing GATA binding motifs might play a role in the development of PMDS.
Back to the Future: Democratic Responsiveness and the Estimation of Future Public Opinion
Authors: Merkley Eric , Owen Andrew 
Published: June 2019

AbstractResearch on the responsiveness of policy to public opinion has infrequently confronted the possibility that re-election seeking politicians’ policy choices may reflect their expectations about future public opinion. This article reports observational and experimental findings from a survey of senior Canadian policy-makers. Results from vignette-based experiments that manipulate the characteristics of current and estimates of future opinion show that policy-makers are responsive to the estimated direction of future opinion, but this relationship is conditional on high estimated future salience. Survey results shed additional light on the role that estimates of future opinion play in policy-making. Combined, these experimental and observational results suggest existing empirical work on policy responsiveness is incomplete.
Pediatric clinician perspectives on communicating diagnostic uncertainty
Authors: Meyer Ashley N D , Giardina Traber D , Khanna Arushi , Bhise Viraj , Singhal Geeta R , Street Richard L , Singh Hardeep 
Published: June 2019

Abstract

Objective
Diagnosis often evolves over time, involves uncertainty, and is vulnerable to errors. We examined pediatric clinicians’ perspectives on communicating diagnostic uncertainty to patients’ parents and how this occurs.

Design
We conducted semi-structured interviews, which were audiotaped, transcribed, and analyzed using content analysis. Two researchers independently coded transcripts and then discussed discrepancies to reach consensus.

Setting
A purposive sample of pediatric clinicians at two large academic medical institutions in Texas.

Participants
Twenty pediatric clinicians participated: 18 physicians, 2 nurse practitioners; 7 males, 13 females; 7 inpatient, 11 outpatient, and 2 practicing in mixed settings; with 0–16 years’ experience post-residency.

Intervention(s)
None.

Main outcome measure(s)
Pediatric clinician perspectives on communication of diagnostic uncertainty.

Results
Pediatric clinicians commonly experienced diagnostic uncertainty and most were comfortable seeking help and discussing with colleagues. However, when communicating uncertainty to parents, clinicians used multiple considerations to adjust the degree to which they communicated. Considerations included parent characteristics (education, socioeconomic status, emotional response, and culture) and strength of parent–clinician relationships. Communication content included setting expectations, explaining the diagnostic process, discussing most relevant differentials, and providing reassurance. Responses to certain parent characteristics, however, were variable. For example, some clinicians were more open to discussing diagnostic uncertainty with more educated parents- others were less.

Conclusions
While pediatric clinicians are comfortable discussing diagnostic uncertainty with colleagues, how they communicate uncertainty to parents appears variable. Parent characteristics and parent–clinician relationships affect extent of communication and content discussed. Development and implementation of optimal strategies for managing and communicating diagnostic uncertainty can improve the diagnostic process.
Overlapping Regionalism and Security Cooperation: Power-Based Explanations of Nigeria's Forum-Shopping in the Fight against Boko Haram
Authors: Henneberg Ingo , Plank Friedrich 
Published: June 2019

AbstractRegional conflicts increasingly require multilevel efforts by regional, subregional, and international actors. When states are confronted with a cooperation problem, often there are several institutions available to address this issue. Drawing on the literature of overlapping regionalism and forum-shopping, we argue that existing explanatory models benefit from adding power-based explanations. By conceptualizing an issue-specific dimension and factors specific to the national environment as additional power-based criteria for forum-shopping, we expand the existing literature. Applying our framework to the response to the Boko Haram uprising, our study examines why Nigeria preferred specific regional entities to others. We find that Nigerian resistance toward external intervention and hegemonic interests inherent in national elites as power-based aspects of forum-shopping explain the counterintuitive creation of the Multinational Joint Task Force (MNJTF) under the umbrella of the rather unknown Lake Chad Bassin Commission (LCBC) instead of reliance on the Economic Community of West African States (ECOWAS) or the African Union (AU) as important security providers in Africa.