bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growing research in geriatric medicine: a trainee perspective
Authors: Welch Carly ,   Geriatric Medicine Research Collaborative, McCluskey Lauren , Wilson Daisy , Moorey Hannah , Majid Zeinab , Madden Katy , McNeela Natalie , Richardson Sarah , Burton Jenni , Taylor Joanne , Masoli Jane , Ronan Lindsay , Torsney Kelli , Lochlainn Mary Ni , Cox Natalie , Lim Stephen , Todd Oliver , Hale Matthew , Lunt Eleanor , Willott Ruth , Healy Roisin , Makin Stephen , Gaunt Victoria , Jelley Benjamin , Walesby Katherine , Hernandez Nazaneen , Alsahab Mustafa , Giridharan Kumudhini , Alme Katinka Nordheim , Cedeño Veloz Bernardo Abel , Lal Rajni , Jasper Emily , Subramanian Manicka S , Matchekhina Lubov , Lamloum Mounir , Briggs Robert 
Published: March 2020

Abstract
Growing research in geriatric medicine is a priority area. Currently, involvement of geriatricians in research lags behind other specialties. The reasons for this are multifactorial, but a lack of training infrastructure within geriatric medicine higher specialist training is contributory. This is widespread across European countries and internationally. The Geriatric Medicine Research Collaborative (GeMRC) offers an opportunity to engage trainees in research, regardless of their previous individual research experiences. Utilising national trainee networks, GeMRC is able to conduct large-scale projects within short periods of time that can have real impact upon patient care. We consider that embedding GeMRC within higher specialist training with formal college support will assist to upskill trainee geriatricians in research methodology. Collaboratives are internationally recognised across disciplines. Expansion across European and international countries offers the opportunity for international collaboration in geriatric medicine. International trainee-led networks will enable the conduct of large-scale global projects in geriatric medicine.
Cancer Stage at Diagnosis, Historical Redlining, and Current Neighborhood Characteristics: Breast, Cervical, Lung, and Colorectal Cancers, Massachusetts, 2001–2015
Authors: Krieger Nancy , Wright Emily , Chen Jarvis T , Waterman Pamela D , Huntley Eric R , Arcaya Mariana 
Published: March 2020

Abstract
In the 1930s, maps created by the federal Home Owners’ Loan Corporation (HOLC) nationalized residential racial segregation via “redlining,” whereby HOLC designated and colored in red areas they deemed to be unsuitable for mortgage lending on account of their Black, foreign-born, or low-income residents. We used the recently digitized HOLC redlining maps for 28 municipalities in Massachusetts to analyze Massachusetts Cancer Registry data for late stage at diagnosis for cervical, breast, lung, and colorectal cancer (2001–2015). Multivariable analyses indicated that, net of age, sex/gender, and race/ethnicity, residing in a previously HOLC-redlined area imposed an elevated risk for late stage at diagnosis, even for residents of census tracts with present-day economic and racial privilege, whereas the best historical HOLC grade was not protective for residents of census tracts without such current privilege. For example, a substantially elevated risk of late stage at diagnosis occurred among men with lung cancer residing in currently privileged areas that had been redlined (risk ratio = 1.17, 95% confidence interval: 1.06, 1.29), whereas such risk was attenuated among men residing in census tracts lacking such current privilege (risk ratio = 1.01, 95% confidence interval: 0.94, 1.08). Research on historical redlining as a structural driver of health inequities is warranted.
Clinical Competencies for the Care of Hospitalized Patients with Alcohol Use Disorders
Authors: Phillips Thomas , Porter Amy , Sinclair Julia 
Published: March 2020

Abstract

Aims
The UK government aims to develop alcohol care teams (ACTs) that provide care for alcohol dependence in general hospital settings. Service descriptors have been identified to support the development of ACTs. The aim of this study was to use Delphi panel principles to identify the clinical competencies required to provide these elements of service.

Methods
We formed an expert consensus panel of 24 senior clinical alcohol practitioners, leaders and experts by experience drawn from all regions of England. The study was divided into three distinct phases: (a) a review and synthesis of current literature in this area, (b) a face-to-face meeting of the expert panel and (c) subsequent iterations to refine the competencies until consensus was reached.

Results
Our initial search strategy resulted in 555 competency statements being extracted from a range of national clinical professional and occupational standards and other sources. The research team refined these statements to 98 competencies in advance of the expert meeting. The panel identified 14 additional statements and reduced the number of competencies to 78. Subsequent iterations finalized 72 competencies across the 8 service descriptors.

Conclusions
Drawing on the existing published resources and clinical experience, the expert panel has provided consensus on the core clinical competencies required for alcohol care teams in caring for hospitalized patients with alcohol use disorders. Whilst it is acknowledged that the range of current provision is variable, these competencies provide a template for clinical practice and the development of multidisciplinary ACTs.
The Quaternary evolutionary history of Bristol rock cress (Arabis scabra, Brassicaceae), a Mediterranean element with an outpost in the north-western Atlantic region
Authors: Koch Marcus A , Möbus Johanna , Klöcker Clara A , Lippert Stephanie , Ruppert Laura , Kiefer Christiane 
Published: March 2020

AbstractBackground and AimsBristol rock cress is among the few plant species in the British Isles considered to have a Mediterranean–montane element. Spatiotemporal patterns of colonization of the British Isles since the last interglacial and after the Last Glacial Maximum (LGM) from mainland Europe are underexplored and have not yet included such floristic elements. Here we shed light on the evolutionary history of a relic and outpost metapopulation of Bristol rock cress in the south-western UK.MethodsAmplified fragment length polymorphisms (AFLPs) were used to identify distinct gene pools. Plastome assembly and respective phylogenetic analysis revealed the temporal context. Herbarium material was largely used to exemplify the value of collections to obtain a representative sampling covering the entire distribution range.Key ResultsThe AFLPs recognized two distinct gene pools, with the Iberian Peninsula as the primary centre of genetic diversity and the origin of lineages expanding before and after the LGM towards mountain areas in France and Switzerland. No present-day lineages are older than 51 ky, which is in sharp contrast to the species stem group age of nearly 2 My, indicating severe extinction and bottlenecks throughout the Pleistocene. The British Isles were colonized after the LGM and feature high genetic diversity.ConclusionsThe short-lived perennial herb Arabis scabra, which is restricted to limestone, has expanded its distribution range after the LGM, following corridors within an open landscape, and may have reached the British Isles via the desiccated Celtic Sea at about 16 kya. This study may shed light on the origin of other rare and peculiar species co-occurring in limestone regions in the south-western British Isles.
HiChIP-Peaks: a HiChIP peak calling algorithm
Authors: Shi Chenfu , Rattray Magnus , Orozco Gisela 
Published: March 2020

Abstract

Motivation
HiChIP is a powerful tool to interrogate 3D chromatin organization. Current tools to analyse chromatin looping mechanisms using HiChIP data require the identification of loop anchors to work properly. However, current approaches to discover these anchors from HiChIP data are not satisfactory, having either a very high false discovery rate or strong dependence on sequencing depth. Moreover, these tools do not allow quantitative comparison of peaks across different samples, failing to fully exploit the information available from HiChIP datasets.

Results
We develop a new tool based on a representation of HiChIP data centred on the re-ligation sites to identify peaks from HiChIP datasets, which can subsequently be used in other tools for loop discovery. This increases the reliability of these tools and improves recall rate as sequencing depth is reduced. We also provide a method to count reads mapping to peaks across samples, which can be used for differential peak analysis using HiChIP data.

Availability and implementation
HiChIP-Peaks is freely available at https://github.com/ChenfuShi/HiChIP_peaks.

Supplementary information
Supplementary data are available at Bioinformatics online.
Developmental Regulation of Basket Interneuron Synapses and Behavior through NCAM in Mouse Prefrontal Cortex
Authors: Sullivan Chelsea S , Mohan Vishwa , Manis Paul B , Moy Sheryl S , Truong Young , Duncan Bryce W , Maness Patricia F 
Published: March 2020

AbstractParvalbumin (PV)-expressing basket interneurons in the prefrontal cortex (PFC) regulate pyramidal cell firing, synchrony, and network oscillations. Yet, it is unclear how their perisomatic inputs to pyramidal neurons are integrated into neural circuitry and adjusted postnatally. Neural cell adhesion molecule NCAM is expressed in a variety of cells in the PFC and cooperates with EphrinA/EphAs to regulate inhibitory synapse density. Here, analysis of a novel parvalbumin (PV)-Cre: NCAM F/F mouse mutant revealed that NCAM functions presynaptically in PV+ basket interneurons to regulate postnatal elimination of perisomatic synapses. Mutant mice exhibited an increased density of PV+ perisomatic puncta in PFC layer 2/3, while live imaging in mutant brain slices revealed fewer puncta that were dynamically eliminated. Furthermore, EphrinA5-induced growth cone collapse in PV+ interneurons in culture depended on NCAM expression. Electrophysiological recording from layer 2/3 pyramidal cells in mutant PFC slices showed a slower rise time of inhibitory synaptic currents. PV-Cre: NCAM F/F mice exhibited impairments in working memory and social behavior that may be impacted by altered PFC circuitry. These findings suggest that the density of perisomatic synapses of PV+ basket interneurons is regulated postnatally by NCAM, likely through EphrinA-dependent elimination, which is important for appropriate PFC network function and behavior.
Different Principles Govern Different Scales of Brain Folding
Authors: Mallela Arka N , Deng Hansen , Bush Alan , Goldschmidt Ezequiel 
Published: March 2020

Abstract
The signature folds of the human brain are formed through a complex and developmentally regulated process. In vitro and in silico models of this process demonstrate a random pattern of sulci and gyri, unlike the highly ordered and conserved structure seen in the human cortex. Here, we account for the large-scale pattern of cortical folding by combining advanced fetal magnetic resonance imaging with nonlinear diffeomorphic registration and volumetric analysis. Our analysis demonstrates that in utero brain growth follows a logistic curve, in the absence of an external volume constraint. The Sylvian fissure forms from interlobar folding, where separate lobes overgrow and close an existing subarachnoid space. In contrast, other large sulci, which are the ones represented in existing models, fold through an invagination of a flat surface, a mechanistically different process. Cortical folding is driven by multiple spatially and temporally different mechanisms; therefore regionally distinct biological process may be responsible for the global geometry of the adult brain.
Research on Invasive Nontyphoidal Salmonella Disease and Developments Towards Better Understanding of Epidemiology, Management, and Control Strategies
Authors: Kariuki Samuel , Owusu-Dabo Ellis 
Published: March 2020

AbstractDuring the 11th International Conference on Typhoid and Other Invasive Salmonelloses held in Hanoi, Vietnam, a number of papers were presented on the burden of disease, epidemiology, genomics, management, and control strategies for invasive nontyphoidal Salmonella (iNTS) disease, which is increasingly becoming an important public health threat in low- and middle-income countries, but especially in sub-Saharan Africa (sSA). Although there were minor variations in characteristics of iNTS in different settings (urban vs rural, country to country), it was observed that iNTS has gained greater recognition as a major disease entity in children younger than 5 years. Renewed efforts towards greater understanding of the burden of illness, detection and diagnostic strategies, and management and control of the disease in communities in sSA through the introduction of vaccines will be important.
Serological Evaluation of Onchocerciasis and Lymphatic Filariasis Elimination in the Bakoye and Falémé Foci, Mali
Authors: Dolo Housseini , Coulibaly Yaya I , Sow Moussa , Dembélé Massitan , Doumbia Salif S , Coulibaly Siaka Y , Sangare Moussa B , Dicko Ilo , Diallo Abdallah A , Soumaoro Lamine , Coulibaly Michel E , Diarra Dansine , Colebunders Robert , Nutman Thomas B , Walker Martin , Basáñez Maria-Gloria 
Published: March 2020

Abstract

Background
Ivermectin-based onchocerciasis elimination, reported in 2009–2012, for Bakoye and Falémé, Mali, supported policy-shifting from morbidity control to elimination of transmission (EOT). These foci are coendemic with lymphatic filariasis (LF). In 2007–2016 mass ivermectin plus albendazole administration was implemented. We report Ov16 (onchocerciasis) and Wb123 (LF) seroprevalence after 24–25 years of treatment to determine if onchocerciasis EOT and LF elimination as a public health problem (EPHP) have been achieved.

Methods
The SD Bioline Onchocerciasis/LF Ig[immunoglobulin]G4 biplex rapid diagnostic test (RDT) was used in 2186 children aged 3–10 years in 13 villages (plus 2 hamlets) in Bakoye and in 2270 children in 15 villages (plus 1 hamlet) in Falémé. In Bakoye, all-age serosurveys were conducted in 3 historically hyperendemic villages (1867 individuals aged 3 -78 years).

Results
In Bakoye, IgG4 seropositivity was 0.27% (95% confidence interval [CI] = .13%–.60%) for both Ov16 and Wb123 antigens. In Falémé, Ov16 and Wb123 seroprevalence was 0.04% (95% CI = .01%–.25%) and 0.09% (95% CI = .02%–.32%), respectively. Ov16-seropositive children were from historically meso/hyperendemic villages. Ov16 positivity was &lt;2% in ≤14 year-olds, and 16% in ≥40 year-olds. Wb123 seropositivity was &lt;2% in ≤39 year-olds, reaching 3% in ≥40 year-olds.

Conclusions
Notwithstanding uncertainty in the biplex RDT sensitivity, Ov16 and Wb123 seroprevalence among children in Bakoye and Falémé is consistent with EOT (onchocerciasis) and EPHP (LF) since stopping treatment in 2016. The few Ov16-seropositive children should be skin-snip polymerase chain reaction tested and followed up.
Listening to the Patient: Improving the Design and Conduct of Clinical Trials in Inflammatory Bowel Diseases
Authors: Sharp Dan , Ringer Sara , Park K T , Tole Swati , Rubin David T , Regueiro Miguel 
Published: March 2020

Lay Summary
There is an urgent need for new treatments for inflammatory bowel diseases, but it’s hard to enroll the large number of patients needed for clinical trials. Making trials more patient-friendly by giving patients a voice would help solve this problem.
The Neglected Medium: Postage Stamps as Mass Media
Authors: Limor Yehiel , Tamir Ilan 
Published: March 2020

AbstractThe large number of comprehensive studies on mass media is indicative of the role mass media play in society and societal effects, as a result of which they are instrumental in the analysis, interpretation, and construction of social reality (Shoemaker & Reese, 2014). Mass media themselves—the print press, television, radio, books, as well as the Internet and social media—and especially the contents they produce and widely disseminate, have been the topics of diverse studies anchored in many disciplines. It appears, however, that one such medium has failed to attract the research attention it deserves and has even failed to be recognized as a mass medium. This medium is postage stamps, with billions of copies printed annually and disseminated worldwide. In 2009, 37 billion stamps were printed in the United States alone (Ballentine, 2016). This article proposes to define postage stamps as a mass medium, based on generally accepted definitions and well-known communication theories. Postage stamps constitute official state documents that reflect the values that a country wishes to represent to its citizens and the world. Embracing the definition of postage stamps as a mass medium would, among other things, extend the research horizons of fields such as media, politics, arts, and culture. The article has three aims: First, to define, identify, and explore the features of postage stamps as a mass medium; Second, to gain insight into the reasons for postage stamps' neglect in media research; and third, to propose potential research directions to explore postage stamps' functions as a mass medium.
Inflammatory Bowel Disease Care in the COVID-19 Pandemic Era: The Humanitas, Milan, Experience
Authors: Fiorino Gionata , Allocca Mariangela , Furfaro Federica , Gilardi Daniela , Zilli Alessandra , Radice Simona , Spinelli Antonino , Danese Silvio 
Published: March 2020

AbstractThe outbreak of the COVID-19 caused by coronavirus SARS-CoV2, is rapidly spreading worldwide. This is the first pandemic caused by a coronavirus in history. More than 150 000 confirmed cases worldwide are reported involving the SARS-CoV2, with more than 5000 COVID-19-related deaths on March 14, 2020. Fever, chills, cough, shortness of breath, generalised myalgia, malaise, drowsiness, diarrhoea, confusion, dyspnoea, and bilateral interstitial pneumonia are the common symptoms. No therapies are available, and the only way to contain the virus spread is to regularly and thoroughly clean one’s hands with an alcohol-based hand rub or wash them with soap and water, to maintain at least 1 m [3 feet] distance from anyone who is coughing or sneezing, to avoid touching eyes, nose, and mouth, and to stay home if one feels unwell. No data are available on the risk of COVID-19 and outcomes in inflammatory bowel disease [IBD] patients. Outbreak restrictions can impact on the IBD care. We aim to give a viewpoint on how operationally to manage IBD patients and ensure quality of care in the current pandemic era.
Metastasectomy of left atrial mesenchymal chondrosarcoma
Authors: Talukder Shagorika , Murphy Michael O , Lyon Alexander , Rosendahl and Ulrich 
Published: March 2020

Abstract
Metastasis of chondrosarcoma of skeletal origin to the heart is uncommonly reported in the literature, with the majority of cases involving right atrial metastases. Surgical resection remains the mainstay of treatment, and the literature has shown improved median survival with this form of therapy, possibly by reducing thromboembolic risk in this patient population. We report the case of a patient with metastatic mesenchymal chondrosarcoma of the left atrium who underwent resection, following a lack of response to anticoagulation therapy. This is the first report of surgical resection of left atrial metastatic disease prior to the onset of thromboembolic sequelae.
A framework to bridge scales in distribution modeling of soil microbiota
Authors: Lembrechts Jonas J , Broeders L , De Gruyter J , Radujković D , Ramirez-Rojas I , Lenoir J , Verbruggen E 
Published: March 2020

ABSTRACT
Creating accurate habitat suitability and distribution models (HSDMs) for soil microbiota is far more challenging than for aboveground organism groups. In this perspective paper, we propose a conceptual framework that addresses several of the critical issues holding back further applications. Most importantly, we tackle the mismatch between the broadscale, long-term averages of environmental variables traditionally used, and the environment as experienced by soil microbiota themselves. We suggest using nested sampling designs across environmental gradients and objectively integrating spatially hierarchic heterogeneity as covariates in HSDMs. Second, to incorporate the crucial role of taxa co-occurrence as driver of soil microbial distributions, we promote the use of joint species distribution models, a class of models that jointly analyze multiple species’ distributions, quantifying both species-specific environmental responses (i.e. the environmental niche) and covariance among species (i.e. biotic interactions). Our approach allows incorporating the environmental niche and its associated distribution across multiple spatial scales. The proposed framework facilitates the inclusion of the true relationships between soil organisms and their abiotic and biotic environments in distribution models, which is crucial to improve predictions of soil microbial redistributions as a result of global change.
Density and distribution of lymphocytes in pretherapeutic rectal cancer and response to neoadjuvant therapy
Authors: Lai Sicong , Lou Xiaoying , Fan Xinjuan , Sun Weipeng , Deng Yanhong , Wang Jianping , Huang Yan , Dou Ruoxu 
Published: March 2020

Abstract

Background
Lymphocytic density in rectal cancer has been reported to be associated with therapeutic response, but the role of the lymphocytic distribution pattern remains to be determined. This study aimed to evaluate the association between the distribution and density of lymphocytes in rectal-cancer tissue with tumor response to neoadjuvant therapy.

Methods
We retrospectively analysed 134 patients with rectal cancer receiving neoadjuvant therapy within a prospectively maintained cohort. Pretherapeutic biopsy samples were stained with immunohistochemistry (CD4 and CD8). Densities of intratumoral periglandular lymphocytes (IPLs) and tumor-infiltrating lymphocytes (TILs) were assessed separately. Logistic-regression analysis was used to assess associations of lymphocyte densities with tumor regression grade (TRG), controlling for clinicopathological, molecular, and regimen features.

Results
Compared with cases in the lowest quartile of CD8+ TILs, those in the highest quartile were significantly associated with better TRG (multivariate odds ratio, 0.23; 95% confidence interval, 0.07 to 0.76; P &lt; 0.001). In contrast, CD8+ IPLs, CD4+ IPLs, and CD4+ TILs were not significantly associated with TRG (P = 0.033, 0.156, and 0.170, respectively). Sensitivity analyses detected no interaction between CD8+ TILs and regimen of neoadjuvant radiation (Pinteraction = 0.831) or chemotherapy (Pinteraction = 0.879) on TRG.

Conclusions
Our data suggest that CD8+ TILs, but not IPLs, are independently associated with response to neoadjuvant therapy, regardless of the regimen of radiation or chemotherapy.