bluuebunny/crossref_metadata_2025_split huggingface dataset:
A seventeenth-centuryMycobacterium tuberculosisgenome supports a Neolithic emergence of theMycobacterium tuberculosiscomplex
Authors: Sabin Susanna , Herbig Alexander , Vågene Åshild J. , Ahlström Torbjörn , Bozovic Gracijela , Arcini Caroline , Kühnert Denise , Bos Kirsten I. 
Published: March 2019

ABSTRACTBackgroundAlthough tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modernMycobacterium tuberculosiscomplex (MTBC) genomes suggests their most recent common ancestor (MRCA) followed human migrations out of Africa ~70,000 years before present (BP). However, studies using ancient genomes as calibration points have yielded much younger MRCA dates of less than 6,000 years. Here we aim to address this discrepancy through the analysis of the highest-coverage and highest quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Peder Winstrup of Lund (b. 1605 – d. 1697).ResultsA metagenomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Subsequent genomic enrichment enabled the reconstruction of a 141-fold coverageM. tuberculosisgenome. In utilizing this high-quality, high-coverage 17thcenturyM. tuberculosisgenome as a calibration point for dating the MTBC, we employed multiple Bayesian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategies more realistically than those based on the coalescent.ConclusionsThe results of our metagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, we estimate an MRCA date for the MTBC of 3683 BP (2253-5821 BP) and for Lineage 4 of 1651 BP (946-2575 BP) using multiple models, confirming a Neolithic emergence for the MTBC.
Cytosolic termini of the FurE transporter regulate endocytosis, pH-dependent gating and specificity
Authors: Papadaki Georgia F. , Lambrinidis George , Zamanos Andreas , Mikros Emmanuel , Diallinas George 
Published: March 2019

AbstractFurE, a member of the NCS1 family, is anAspergillus nidulanstransporter specific for uracil, allantoin and uric acid. Recently we showed that C- or N-terminally truncated FurE versions are blocked for endocytosis and, surprisingly, show modified substrate specifities. Bifluorescence complementation assays and genetic analyses supported that the C- and N-termini interact dynamically and through this interaction regulate selective substrate translocation. Here we functionally dissect and delimit distinct motifs crucial for endocytosis, transport activity, substrate specificity and folding, in both cytosolic termini of FurE. Subsequently, we obtain novel genetic andin silicoevidence supporting that the molecular dynamics of specific N- and C-terminal regions affect allosterically the gating mechanism responsible for substrate selection, via pH-dependent interactions with other internal cytosolic loops and membrane lipids. Our work shows that elongated cytoplasmic termini, acquired through evolution mostly in eukaryotic transporters, provide novel specific functional roles.
De novo transcriptome assembly of the African bullfrog Pyxicephalus adspersus for molecular analysis of aestivation
Authors: Yoshida Naoki , Kaito Chikara 
Published: March 2019

AbstractThe molecular mechanisms of aestivation, a state of dormancy that occurs under dry conditions at ordinary temperature, are not yet clarified. Here, we report the first de novo transcriptome assembly of the African bullfrog Pyxicephalus adspersus, which aestivates for 6-10 months during the hot and dry season. Polyadenylated RNA from tissues was sequenced to 75,320,390 paired-end reads, and the de novo assembly generated 101,682 transcripts. Of these, 100,093 transcripts had open reading frames encoding more than 25 amino acids. BLASTx analysis against the Uniprot Xenopus tropicalis protein database revealed 64,963 transcripts having little homology with an E value higher than 1E-5 and 8,147 transcripts having no homology, indicating that the African bullfrog has many novel genes that are absent in X. tropicalis. The other 28,570 transcripts had homology with an E value lower than 1E-5 for which molecular functions were estimated by gene ontology (GO) analysis and found to contain the aestivation-related genes conserved among other aestivating organisms, including the African lungfish. This study is the first to identify a comprehensive set of genes expressed in the African bullfrog, thus providing basic information for molecular level analysis of aestivation.
Taxonomic and functional anuran beta diversity of a subtropical metacommunity respond differentially to environmental and spatial predictors
Authors: Dalmolin Diego Anderson , Tozetti Alexandro Marques , Ramos Pereira Maria João 
Published: March 2019

AbstractThe relative contributions of environmental and spatial predictors in the patterns of taxonomic and functional anuran beta diversity were examined in 33 ponds of a metacommunity along the coast of south Brazil. Anurans exhibit limited dispersion ability and have physiological and behavioural characteristics that narrow their relationships with both environmental and spatial predictors. So, we expected that neutral processes and, in particular, niche-based processes could have similar influence on the taxonomic and functional beta diversity patterns. Variation partitioning and distance-based methods (db-RDA) were conducted with presence/absence and abundance data to examine taxonomic and functional facets and components (total, turnover and nestedness-resultant) in relation to environmental and spatial predictors. Processes determining metacommunity structure were similar between the components of beta diversity but differed among taxonomic and functional diversity. While taxonomic beta diversity was further accounted by environmental predictors, functional beta diversity responded more strongly to spatial predictors. These patterns were more evident when assessed through abundance data. These opposing patterns were contrary to what we had predicted, suggesting that while there is a taxonomic turnover mediated by environmental filters, the spatial distance promotes the trait dissimilarity between sites. Our results reinforce the idea that studies aiming to evaluate the patterns of structure in metacommunities should include different facets of diversity so that better interpretations can be achieved.
Research on body‐worn cameras
Authors: Lum Cynthia , Stoltz Megan , Koper Christopher S. , Scherer J. Amber 
Published: March 2019

Research SummaryIn this article, we provide the most comprehensive narrative review to date of the research evidence base for body‐worn cameras (BWCs). Seventy empirical studies of BWCs were examined covering the impact of cameras on officer behavior, officer perceptions, citizen behavior, citizen perceptions, police investigations, and police organizations. Although officers and citizens are generally supportive of BWC use, BWCs have not had statistically significant or consistent effects on most measures of officer and citizen behavior or citizens’ views of police. Expectations and concerns surrounding BWCs among police leaders and citizens have not yet been realized by and large in the ways anticipated by each. Additionally, despite the large growth in BWC research, there continues to be a lacuna of knowledge on the impact that BWCs have on police organizations and police–citizen relationships more generally.Policy ImplicationsRegardless of the evidence‐base, BWCs have already rapidly diffused into law enforcement, and many agencies will continue to adopt them. Policy implications from available evidence are not clear‐cut, but most likely BWCs will not be an easy panacea for improving police performance, accountability, and relationships with citizens. To maximize the positive impacts of BWCs, police and researchers will need to give more attention to the ways and contexts (organizational and community) in which BWCs are most beneficial or harmful. They will also need to address how BWCs can be used in police training, management, and internal investigations to achieve more fundamental organizational changes with the long‐term potential to improve police performance, accountability, and legitimacy in the community.
Did de‐policing cause the increase in homicide rates?
Authors: Rosenfeld Richard , Wallman Joel 
Published: March 2019

Research SummaryWidespread protests and demands for accountability in the wake of broadly publicized police killings of unarmed civilians coincided with the marked upturn in homicide levels, especially in large U.S. cities, in 2015. Many observers, including prominent political figures, claimed that de‐policing caused the homicide rate to rise: Fearing increased legal liability and publicity, the police employed less proactive enforcement and made fewer arrests, producing an increase in homicide levels. We use structural equation modeling to estimate the simultaneous relationship between arrest and homicide rates between 2010 and 2015 in 53 large cities. We find no evidence of an effect of arrest rates on city homicide rates for any offense category for any year in this period, including 2015, the year of the spike in homicide levels.Policy ImplicationsThe results of our analysis reveal that declining rates of arrest did not produce the rise in homicide levels. But arrests, the chief formal reaction to crime, can play an important supporting role in crime prevention. Ample research findings have demonstrated the effectiveness of proactive policing practices, such as targeted patrol, in reducing crime rates. The success of such tactics depends, in turn, on citizens’ belief that criminal offenders face an appreciable risk of arrest. It is equally important, however, that residents of communities that have experienced unwarranted police violence believe that law enforcement is fairly applied. Lack of trust and confidence in the police militates against crime prevention as a co‐production of police and community and may promote violence as a form of self‐help.
European Landscapes in Transition: Implications for Policy Integration and Landscape Governance
Authors: Primdahl Jørgen , Pinto‐Correia Teresa , Pedroli Bas 
Published: March 2019

SummaryEuropean rural landscapes are in transition due to macro changes in climate, agriculture and public policy, combined with various forms of urbanisation. These changes are affecting the resource basis of agriculture, the socio‐cultural identity of rural communities, and are challenging the policy regimes affecting European landscapes. Therefore, they demand new forms of landscape governance if the diversity and quality of the landscapes are to be protected and further developed in the future. New analytical tools supported by revised conceptual frameworks are needed to assist identification and assessment of future development options. This article is based on a book published earlier this year. It presents and discusses the current patterns of change and their implications for policy. Three major policy challenges are identified: integration of agricultural and environmental policies; pro‐active approaches to landscape change to cope with non‐agricultural demands including recreation and nature conservation; and stakeholder involvement in policy design and implementation including farmers and other primary managers, public agencies at all levels and local communities in various forms. Key points are illustrated in a case study involving the development of a landscape strategy in the Karby parish in northwest Denmark.
High kinesin family member 18A expression correlates with poor prognosis in primary lung adenocarcinoma
Authors: Li Xiaoqing , Liu Meirong , Zhang Zheng , Zhang Linlin , Liang Xingmei , Sun Linlin , Zhong Diansheng 
Published: March 2019

BackgroundLung adenocarcinoma (LUAD) is the most prevalent pathological subtype of lung cancer. Kinesin family member 18A (KIF18A) plays an important role in tumorigenesis. Its roles in breast cancer, colorectal cancer, and other tumors have been demonstrated; however, studies of KIF18A in LUAD are limited. This study aimed to determine the role of KIF18A in LUAD progression and prognostic prediction.MethodsKIF18A expression was examined in LUAD cells and tissues by immunohistochemistry and Western blotting. Cell proliferation assay was performed to study the role of KIF18A in LUAD cells. Correlations between KIF18A expression and clinicopathological features were analyzed. The role of KIF18A in LUAD prognosis was evaluated using data from The Cancer Genome Atlas (TCGA).ResultsKIF18A expression was increased in tumor cells and tissues. Downregulation of KIF18A expression resulted in the suppression of cancer cell proliferation in in vitro assays, and was particularly related to poor tumor differentiation, big tumor size, lymph node metastasis, and more advanced tumor stage. In the TCGA dataset, high KIF18A messenger RNA expression was associated with poor disease‐free and overall survival in patients with LUAD. In addition, multivariate analysis indicated that KIF18A is an independent prognostic factor of disease‐free and overall survival in LUAD.ConclusionsCollectively, our results demonstrate that KIFl8A is highly expressed in LUAD. KIFl8A plays an important role in LUAD cell proliferation, but is a poor prognostic factor.
NMNAT2‐mediated NAD+ generation is essential for quality control of aged oocytes
Authors: Wu Xinghan , Hu Feifei , Zeng Juan , Han Longsen , Qiu Danhong , Wang Haichao , Ge Juan , Ying Xiaoyan , Wang Qiang 
Published: March 2019

AbstractAdvanced maternal age has been reported to impair oocyte quality; however, the underlying mechanisms remain to be explored. In the present study, we identified the lowered NAD+ content and decreased expression of NMNAT2 protein in oocytes from old mice. Specific depletion of NMNAT2 in mouse oocytes disturbs the meiotic apparatus assembly and metabolic activity. Of note, nicotinic acid supplementation during in vitro culture or forced expression of NMNAT2 in aged oocytes was capable of reducing the reactive oxygen species (ROS) production and incidence of spindle/chromosome defects. Moreover, we revealed that activation or overexpression of SIRT1 not only partly prevents the deficient phenotypes of aged oocytes but also ameliorates the meiotic anomalies and oxidative stress in NMNAT2‐depleted oocytes. To sum up, our data indicate a role for NMNAT2 in controlling redox homeostasis during oocyte maturation and uncover that NMNAT2‐ NAD+‐SIRT1 is an important pathway mediating the effects of maternal age on oocyte developmental competence.
Changes in Drinking Patterns, and Attitudes Toward and Knowledge About Alcohol Consumption During Pregnancy in a Population of Pregnant Danish Women
Authors: Kesmodel Ulrik Schiøler , Urbute Aivara 
Published: March 2019

BackgroundIn 1997, The Danish Health Authority recommended that “it is safest not to drink alcohol when you are pregnant,” and in 1999 expanded recommendations. There are only a few studies evaluating the possible change of average alcohol consumption following changes in national recommendations, and no studies have been found comparing the changes in pregnant women's attitudes toward alcohol consumption during pregnancy. We aimed to evaluate the changes in drinking pattern, and knowledge about and attitudes toward alcohol consumption during pregnancy before and after the change of national recommendations.MethodsThis is a cross‐sectional interview study with a representative sample of 1,418 woman attending antenatal care at the beginning of their second trimester in Aarhus, Denmark, in the year 2000, and a comparable sample of 439 pregnant women from 1998 in Aarhus. Participants were interviewed about their average alcohol consumption, binge drinking, and attitudes toward and knowledge about alcohol consumption during pregnancy. Data collection procedures and questions were identical for both samples.ResultsThere were no differences between the 2 samples in terms of average alcohol consumption before (p = 0.19) and during (p = 0.45) pregnancy, and binge drinking in early pregnancy (p = 0.47). Attitudes toward and knowledge about alcohol in pregnancy did not change either (p > 0.5). Women's knowledge about guidelines was less precise in 2000 (p < 0.001). Worse knowledge was associated with younger age considering both samples (OR = 2.63, 95% CI: 1.63 to 4.26). Most pregnant women reported that they had not been informed or advised about alcohol consumption during pregnancy, but they would like to be advised by their healthcare professionals.ConclusionsAfter the changes in the national guidelines about alcohol consumption during pregnancy, there were no changes in behavior, attitudes, and knowledge of pregnant women. This would indicate that healthcare specialists should be encouraged to initiate a conversation about alcohol consumption during the first antenatal visit.
Incidence of microcracks after preparation of straight and curved root canals with three different NiTi instrumentation techniques assessed by micro‐CT
Authors: Rödig Tina , Krämer Juliane , Müller Christine , Wiegand Annette , Haupt Franziska , Rizk Marta 
Published: March 2019

AbstractThis study evaluated the effect of three different NiTi instrumentation techniques on the incidence of microcracks after the preparation of straight and curved root canals using micro‐CT. Roots from mandibular premolars and maxillary molars (n = 66) with the same mean canal curvatures were assigned to three groups of straight and three groups of curved roots (n = 11). After preoperative micro‐CT scans, root canals were prepared with Reciproc, OneShape and ProTaper Next to size 25. Specimens were scanned again, and pre‐ and post‐operative cross‐sectional images (n = 75 263) were screened to identify the presence of dentinal microcracks. Overall, microcracks were detected in 2.97% (n = 2236) of the cross‐sectional images. No new dentinal microcracks were observed after root canal instrumentation of straight and curved canals with the tested NiTi systems. Instrumentation with Reciproc, OneShape and ProTaper Next did not induce the formation of dentinal microcracks irrespective of canal curvature.
Eye Injuries across history and the evolution of eye protection
Authors: Hoskin Annette K. , Mackey David A. , Keay Lisa , Agrawal Rupesh , Watson Stephanie 
Published: March 2019

AbstractPurposeTo describe the history of eye injuries and the consequent evolution of eye protection.MethodsA comprehensive search of Medline and the grey literature using the terms ‘ocular trauma’ and ‘eye protection’ or ‘injury prevention’ and ‘history’. References were used to identify other relevant publications. Publications were classified according to the setting of eye injury: occupational, recreational or combat‐related.ResultsEye protection has been described in a wide range of sources, including in literature and art. With advances in eye protection material and design, as well as government and societal promotion of appropriate eye protection usage in the workplace, the epidemiology of ocular trauma has changed over time. In developed countries, the use of eye protection in the workplace has reduced the proportion of occupation‐related eye injuries over the last century, with a higher proportion occurring during sports or at home. New protection devices and policies have evolved to meet this change.ConclusionVision loss has broad implications for the individual and for society and despite available prevention strategies, ocular trauma is a significant cause of preventable monocular and bilateral vision loss. The use of appropriate eye protection has reduced the burden of ocular trauma. History provides lessons for informing current eye protection and eye injury prevention strategies.
Characterization of CRISPR‐Cas systems in Leptospira reveals potential application of CRISPR in genotyping of Leptospira interrogans
Authors: Xiao Guohui , Yi Yusi , Che Rongbo , Zhang Qinchao , Imran Muhammad , Khan Abidullah , Yan Jie , Lin Xu'ai 
Published: March 2019

Leptospirosis is a zoonotic disease caused by pathogenic Leptospira. However, understanding of the pathogenic mechanism of Leptospira is still elusive due to the limited number of genetic tools available for this microorganism. Currently, the reason for the genetic inaccessibility of Leptospira is still unknown. It is well known that as an acquired immunity of bacteria, Clustered Regularly Interspaced Short Palindromic Repeat‐CRISPR‐associated gene (CRISPR‐Cas) systems can help bacteria against invading mobile genetic elements. In this study, the occurrence and diversity of CRISPR‐Cas systems in 41 genomes of Leptospira strains were investigated. Three subtypes (subtype I‐B, subtype I‐C and subtype I‐E) of CRISPR‐Cas systems were identified in both pathogenic and intermediate Leptospira species but not in saprophytic species. Noteworthy, the majority of pathogenic species harbor two different types of CRISPR‐Cas systems (subtype I‐B and subtype I‐E). Furthermore, Cas2 protein of subtype I‐C in L. interrogans exhibited a metal‐dependent DNase activity in a nonspecific manner. CRISPR spacers in subtype I‐B are highly conserved within the same serovars and hypervariable across different serovars of L. interrogans. Based on the subtype I‐B CRISPR arrays, the serotypes of different L. interrogans strains were easily identified. Investigation of the origin of CRISPR spacers showed that 192 spacers (23.5%) matched to mobile genetic elements, indicating CRISPR‐Cas systems may play an important role in the defense of foreign invading DNA.
Technology‐enhanced learning: Rethinking the term, the concept and its theoretical background
Authors: Passey Don 
Published: March 2019

AbstractThis theoretical paper is concerned with problematising the rethinking of theoretical backgrounds associated with one of the commonly used educational technology terms (fields)—technology‐enhanced learning—in the wider context of scholarship. Examples will show that the term itself is now used beyond its apparent, stated scope, that it is used in a number of varied ways, and that this is in itself problematic. The ways in which the term is used will be identified, and from these a strategic categorisation to rethink the use of the single term in areas of scholarship (particularly research and teaching) will be proposed, offering terms specifically encompassing the realms in which technologies are being used. From this categorisation, it will be shown that each specific category is based on different conceptions related to or arising from practice. Consequently, ways that theoretical backgrounds should be considered will be explored in each case. While existing theoretical backgrounds enable conceptual underpinnings in some of those cases, in other cases it will be shown that there are currently no fully developed theories or limited theoretical frameworks available. The paper will conclude by identifying key research areas needed if we are to develop and take pertinent aspects of scholarship further forward.