bluuebunny/crossref_metadata_2025_split huggingface dataset:
animalcules: Interactive Microbiome Analytics and Visualization in R
Authors: Zhao Yue , Federico Anthony , Manimaran Solaiappan , Segre Daniel , Monti Stefano , Johnson W. Evan 
Published: November 2020

Abstract
Background: Microbial communities that live in and on the human body play a vital role in health and disease. Recent advances in sequencing technologies have enabled the study of microbial communities at unprecedented resolution. However, these advances in data generation have presented novel challenges to researchers attempting to analyze and visualize these data. Results: To address some of these challenges, we have developed animalcules, an easy-to-use interactive microbiome analysis toolkit for 16S rRNA sequencing data, shotgun DNA metagenomics data, and RNA-based metatranscriptomics profiling data. This toolkit combines novel and existing analytics, visualization methods, and machine learning models. For example, the toolkit features traditional microbiome analyses such as alpha/beta diversity and differential abundance analysis, combined with new methods for biomarker identification are. In addition, animalcules provides interactive and dynamic figures that enable users to understand their data and discover new insights. animalcules can be used as a standalone command-line R package or users can explore their data with the accompanying interactive R Shiny interface. Conclusions: We present animalcules, an R package for interactive microbiome analysis through either an interactive interface facilitated by R Shiny or various command-line functions. It is the first microbiome analysis toolkit that supports the analysis of all 16S rRNA, DNA-based shotgun metagenomics, and RNA-sequencing based metatranscriptomics datasets. animalcules can be freely downloaded from GitHub at https://github.com/compbiomed/animalcules or installed through Bioconductor at https://www.bioconductor.org/packages/release/bioc/html/animalcules.html.
Predictors of young people’s use of sexual and reproductive health services in Nigeria: a mixed-method approach
Authors: Odo Amelia Ngozi , OFUEBE Justina Ifeoma , ANIKE Anthony Ifeanyi , Samuel Efiong S 
Published: November 2020

Abstract
Background: Sexual and Reproductive health Services (SRHS) are essential for prevention and control of SRH problems among young people and the achievement of sustainable development goal 3. These services may be available but certain factors interfere with their access and utilization by the young people. This study sought to determine factors that predict the utilization of SRHS among young people in Enugu State, Nigeria. Methods: The study adopted mixed method research employing cross-sectional research design. The population of the study comprised young people within the ages of 12 and 22 years. Multi-stage sampling procedure was used to select 1,447 young people used for the study. Questionnaire, in-depth interview, and focus group discussion were used for data collection. Percentages, Chi-square, and logistic regression were used to analyse quantitative data, while qualitative data were thematically analysed using NVivo software. Results: Socio-demographic factors of gender, age, education, income and living status ( p = < .05) were significant predictors of utilization of SRHS. Psycho-cultural and health system factors ( p = < .05) were also significant predictors of utilization of SRHS. Conclusion: The study concluded that some socio-demographic factors (of gender, age, level of education, income and living status), psycho-cultural and health system factors can be used to predict young people’s utilization of SRHS. These predictors could be addressed through home sex education, regular training of health care providers on youth-friendly services delivery and policy reforms
Barriers to women's disclosure of Domestic Violence in health services in Palestine: qualitative interview-based study
Authors: Shaheen Amira , ashkar suzy , alkaiyat abdulsalam , bacchus loraine , colombini manuela , feder gene , evans maggie 
Published: November 2020

Abstract
Background: Domestic violence (DV) damages health and requires a global public health response and engagement of clinical services. Recent surveys show that 27% of married Palestinian women experienced some form of violence from their husbands over a 12 month’s period, but only 5% had sought formal help, and rarely from health services. Across the globe, barriers to disclosure of DV have been recorded, including self-blame, fear of the consequences and lack of knowledge of services. This is the first qualitative study to address barriers to disclosure within health services for Palestinian women. Methods: In-depth interviews were carried out with 20 women who had experienced DV. They were recruited from a non-governmental organisation offering social and legal support. Interviews were recorded, transcribed and translated into English and the data were analysed thematically. Results: Women encountered barriers at individual, health care service and societal levels. Lack of knowledge of available services, concern about the health care primary focus on physical issues, lack of privacy in health consultations, lack of trust in confidentiality, fear of being labelled ‘mentally ill’ and losing access to their children were all highlighted. Women wished for health professionals to take the initiative in enquiring about DV. Wider issues concerned women’s social and economic dependency on their husbands which led to fears about transgressing social and cultural norms by speaking out. Women feared being blamed and ostracised by family members and others, or experiencing an escalation of violence.Conclusions: Palestinian women’s agency to be proactive in help-seeking for DV is clearly limited. Our findings can inform training of health professionals in Palestine to address these barriers, to increase awareness of the link between DV and many common presentations such as depression, to ask sensitively about DV in private, reassure women about confidentiality, and increase awareness among women of the role that health services can play in DV.
Genomic imbalances in the placenta are associated with poor fetal growth
Authors: Gobbo Giulia F. Del , Yin Yue , Choufani Sanaa , Butcher Emma A. , Wei John , Rajcan-Separovic Evica , Bos Hayley , von Dadelszen Peter , Weksberg Rosanna , Robinson Wendy P , Yuen Ryan K.C. 
Published: November 2020

Abstract
Background: Fetal growth restriction (FGR) is associated with increased risks for complications before, during, and after birth, in addition to risk of disease through to adulthood. Although placental insufficiency, failure to supply the fetus with adequate nutrients, underlies most cases of FGR, its causes are diverse and not fully understood. One of the few diagnosable causes of placental insufficiency in ongoing pregnancies is the presence of large chromosomal imbalances such as trisomy confined to the placenta; however, the impact of smaller copy number variants (CNVs) has not yet been adequately addressed. In this study, we confirm the importance of placental aneuploidy, and assess the potential contribution of CNVs to fetal growth.Methods: We used molecular-cytogenetic approaches to identify aneuploidy in placentas from N=101 infants born small-for-gestational age (SGA), typically used as a surrogate for FGR, and from N=173 non-SGA controls from uncomplicated pregnancies. We confirmed aneuploidies and assessed mosaicism by microsatellite genotyping. We then profiled CNVs using high-resolution microarrays in a subset of N=53 SGA and N=61 control euploid placentas, and compared the load, impact, gene enrichment and clinical relevance of CNVs between groups. Candidate CNVs were confirmed using quantitative PCR.Results: Aneuploidy was over 10-fold more frequent in SGA-associated placentas compared to controls (11.9% vs. 1.1%; p=0.0002, OR=11.4, 95% CI 2.5-107.4), was confined to the placenta, and typically involved autosomes, whereas only sex chromosome abnormalities were observed in controls. We found no significant difference in CNV load or number of placental-expressed or imprinted genes in CNVs between SGA and controls, however, a rare and likely clinically-relevant germline CNV was identified in 5.7% of SGA cases. These CNVs involved candidate genes INHBB, HSD11B2, CTCF, and CSMD3.Conclusions: We conclude that placental genomic imbalances at the cytogenetic and submicroscopic level may underlie up to ~18% of SGA cases in our population. This work contributes to the understanding of the underlying causes of placental insufficiency and FGR, which is important for counselling and prediction of long term outcomes for affected cases.
Developmental trends in early childhood and their predictors from an Indian birth cohort
Authors: Koshy Beena , Sriniva Manikandan , Bose Anuradha , John Sushil Mathew , Mohan Venkata Raghava , Roshan Reeba , Ramanujam Karthikeyen , Kang Gagandeep 
Published: November 2020

Abstract
Background: Early childhood developmental pattern analyses not only project future cognition potential, but also identify potential risks for possible intervention. The current study evaluates developmental trends in the first three years of life and their predictors in a low and middle income country setting.Methods: Trends of early childhood development at 6, 15, 24 and 36 months of age and their predictors were explored in a longitudinal community-based birth cohort study in an urban slum in Vellore, South India. Development was assessed using the Bayley Scales of Infant and Toddler Development-III (BSID-III).Results: The birth cohort enrolled 251 children with 94%, 91% and 87% follow-up at 6, 24 and 36 months respectively. Child development domains of cognition, language, motor and social skills showed a significant decline in scores between 6 and 36 months of age. Higher socioeconomic position (SEP) and nurturing home environment contributed to increase in cognition scores by 1.9 and 0.9 units respectively. However, stunting resulted in drop of cognition scores by 1.7 units. Higher maternal cognition, higher SEP, and caregiver responsivity positively contributed to language change over time, while higher maternal depression contributed negatively. An enriching home environment, growth parameters and blood iron status had positive association with change in motor skills.Conclusions: A triple intervention plan to enhance home environment and nurturance, early childhood nutrient supplementation, and maternal education and well-being might prevent child developmental decline in high risk settings.
Comparison of oral glucose tolerance test and HbA1c in detection of disorders of glucose metabolism in patients with acute stroke
Authors: Matz Karl , Tuomilehto Jaakko , Teuschl Yvonne , Dachenhausen Alexandra , Brainin Michael 
Published: November 2020

Abstract
Background: Diabetes is an increasingly important risk factor for ischemic stroke and worsens stroke prognosis. Yet a large proportion of stroke patients who are eventually diabetic are undiagnosed. Therefore, it is important to have sensitive assessment of unrecognized hyperglycaemia in stroke patients.Design: Secondary outcome analysis of a randomized controlled trial focussing on parameters of glucose metabolism and detection of diabetes and prediabetes in patients with acute ischemic stroke (AIS).Methods: A total of 130 consecutively admitted patients with AIS without previously known type 2 diabetes mellitus (T2DM) were screened for diabetes or prediabetes as part of secondary outcome analysis of a randomized controlled trial that tested lifestyle intervention to prevent post-stroke cognitive decline. Patients had the oral glucose tolerance test (OGTT) and glycated hemoglobin (HbA1c) measurements in the second week after stroke onset and after one year. The detection rates of diabetes and prediabetes based on the OGTT or HbA1c values were compared.Results: By any of the applied tests at the second week after stroke onset 62 of 130 patients (48%) had prediabetes or T2DM. Seventy-five patients had results from both tests available, the OGTT and HbA1c; according to the OGTT 40 (53.3%) patients had normal glucose metabolism, 33 (44%) had prediabetes, two (2.7%) T2DM. In 50 (66.7%) patients the HbA1c results were normal, 24 (32%) in the prediabetic and one (1.3%) in the diabetic range. The detection rate for disorders of glucose metabolism was 10% higher (absolute difference; relative difference 29%) with the OGTT compared with HbA1c. After one year the detection rate for prediabetes or T2DM was 7% higher with the OGTT (26% relative difference).The study intervention led to a more favourable evolution of glycemic status after one year.Conclusion: The OGTT is a more sensitive screening tool than HbA1c for the detection of previously unrecognized glycemic disorders in patients with acute stroke with an at least a 25% relative difference in detection rate. Therefore, an OGTT should be performed in all patients with stroke with no history of diabetes.
Genomic variation in the American pika: signatures of geographic isolation and implications for conservation
Authors: Klingler Kelly Brie , Jahner Joshua P , Parchman Thomas L , Ray Chris , Peacock Mary 
Published: November 2020

Abstract
Background: Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results: Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (𝜋=0.0006–0.0009; 𝜃W=0.0005–0.0007) relative to populations in California (𝜋=0.0014–0.0019; 𝜃W=0.0011–0.0017) and the Rocky Mountains (𝜋=0.0025–0.0027; 𝜃W=0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D=0.240-0.811), consistent with recent contraction in population sizes range-wide. Conclusions: Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.
Survey study of research integrity officers' perceptions of research practices associated with instances of research misconduct
Authors: Kalichman Michael 
Published: November 2020

Abstract
Background: Research on research integrity has tended to focus on frequency of research misconduct and factors that might induce someone to commit research misconduct. A definitive answer to the first question has been elusive, but it remains clear that any research misconduct is too much. Answers to the second question are so diverse, it might be productive to ask a different question: What about how research is done allows research misconduct to occur?Methods: With that question in mind, research integrity officers (RIOs) of the 62 members of the American Association of Universities were invited to complete a brief survey about their most recent instance of a finding of research misconduct. Respondents were asked whether one or more good practices of research (e.g., openness and transparency, keeping good research records) were present in their case of research misconduct.Results: Twenty-four (24) of the respondents (39% response rate) indicated they had dealt with at least one finding of research misconduct and answered the survey questions. Over half of these RIOs reported that their case of research misconduct had occurred in an environment in which at least nine of the ten listed good practices of research were deficient.Conclusions: These results are not evidence for a causal effect of poor practices, but it is arguable that committing research misconduct would be more difficult if not impossible in research environments adhering to good practices of research.
Extracting Optimal Preparation Parameters of TiO2 Electron Transmission Layer in Perovskite Solar Cell for Increasing Efficiency of the Cell
Authors: Solookinejad Ghahraman , Asadi Mohsen Vaezzadeh , Izadneshan Heydar 
Published: November 2020

Abstract
In this research, a thin film of titanium dioxide was prepared as electron transporting layer to be used in perovskite solar cell simulation. The thin film TiO 2 was prepared under different lab conditions such as changing the chamber pressure from 2.0×10 -2 to 4.0×10 -2 mbar and changing the power of deposition device from 200 to 240 watts for different thickness ranging from 30 to 150 nm. Radio frequency magnetron sputtering method has been used to fabricate the layers under the mentioned laboratory conditions. Then, the band gap energy of the thin films was calculated by Tauc’s plot method. It was shown that the bands gap energy which is one of the contributing factors in solar cell characteristics, such as short-circuit current, open-circuit voltage, fill factor and solar cell efficiency, highly depends on laboratory conditions of preparing the thin film and it changes with changes in deposition parameters of the device. The simulated solar cells were considered as ZnO:Al/TiO 2 compact layer/CH 3 NH 3 SnI 3 /CuI/Au. Investigation on the effects of preparation conditions of TiO 2 on properties of the cell and perovskite soar efficiency was carried out using experimental data related to TiO 2 and extraction of data of other layers from authentic articles using comsol multiphysics software. In comparison with other preparation conditions, the prepared layer with 30 nm thickness under 240 watts device power and 3.5×10 -2 mbar chamber pressure had the best possible results. In this condition, perovskite solar cell characteristics obtained I s c = 22.368mA, V o c = 1.02mV, % FF = 80.522 and % PCE = 18.371.
The Lomagundi-Jatuli Event and Earth’s oxygenation
Authors: Prave Anthony , Kirsimäe Kalle , Lepland Aivo , Fallick Tony , Kreitsmann Timmu , Deines Yulia , Romashkin Alexandr , Rychanchik Dimitri , Medvedev Pavel , Moussavou Mathieu , Mayika Karen Bakakas 
Published: November 2020

Abstract
The Palaeoproterozoic Lomagundi-Jatuli Event (LJE) is the largest positive carbonate C-isotope ( δ13Ccarb) excursion in Earth history. Conventional thinking is that it represents a perturbation of the global C cycle between c. 2.3–2.1 Ga linked directly to the postulated Great Oxidation Event. Here we show that the LJE worldwide is, in fact, entirely facies (i.e. palaeoenvironment) dependent. During the LJE, the C-isotope composition of open and deeper marine settings remained undisturbed, with a mean d13Ccarb value of 1.5‰, whereas nearshore marine and coastal-evaporitic settings have means of 6.2‰ and 8.1‰, respectively. This finding refutes conventional thinking and obliges complete re-evaluation of concepts using the LJE as a means of assessing oxygenation of the atmosphere.
Tracking excited state decay mechanisms of pyrimidine nucleosides in real time
Authors: Cerullo Giulio , Borrego-Varillas Rocio , Nenov Artur , Kabacinski Piotr , Conti Irene , Ganzer Lucia , Oriana Aurelio , Delfino Ines , Weingart Oliver , Manzoni Cristian , Rivalta Ivan , Garavelli Marco 
Published: November 2020

Abstract
DNA owes its remarkable photostability to the ability of its building blocks – the nucleosides – to efficiently dissipate the excess electronic energy acquired upon photoexcitation with ultraviolet light. The exact mechanism occurring on a sub-picosecond time scale has been a matter of intense debate. Here we combine sub-30-fs transient absorption spectroscopy with broad spectral coverage and state-of-the-art quantum dynamics simulations to resolve the early steps of the deactivation mechanisms of uridine (Urd) and 5-methyluridine (5mUrd) in aqueous solution. For both nucleosides we track the wave packet motion from the Franck-Condon region to the conical intersection (CI) with to the ground state and observe a direct spectral signature of an excited-state vibrational mode leading to the CI. We find that 5mUrd exhibits an order of magnitude longer excited state lifetime with respect to Urd and assign it to the larger inertia of the methyl group involved in the ring puckering mode leading to the CI. We argue that this longer lifetime enables the activation of potentially lesion-inducing coordinates such as ring opening, elucidating the origin of the susceptibility of thymine-containing DNA strands to photodamage.
Immunohistochemical Study of VEGF in Placenta of Hypertensive Mothers
Authors: H K Sharath Kumar , N Chaitra , G Nataraju , M Bharathi 
Published: November 2020

Background: Pregnancy is most commonly complicated by Hypertensive disorders. In India, the incidence of gestational hypertension varies from 0.5-1.8%. VEGF is a prime regulator of angiogenesis and overall maintenance of endothelial cell health. This study aims to determine the role of VEGF in placentae of Hypertensive and Normotensive pregnancies by assessing its immunohistochemical expression in Syncytiotrophoblasts.

Methods: The study was conducted in the Department of Pathology in our institute. This is a case-control study which included 50 placentae. Out of which,25 were from Normal mothers and 25 placentae from Hypertensive mothers. Immunohistochemistry for VEGF was performed on tissue section using commercially available monoclonal antibodies. The results were interpreted by evaluating Positivity and Intensity of Immunostaining.

Result: Out of 25 Hypertensive placentae, 22 showed Positivity for VEGF immunostaining. Out of 25 Normotensive placentae, 23 showed Negative results for syncytiotrophoblastic staining of VEGF. The difference in VEGF expression in syncytiotrophoblast of hypertensive and normotensive placentae was statistically significant.

Conclusion: Hypoxia acts as a potent stimulus for induction of VEGF mRNA in an attempt to normalize fetal blood flow and thus VEGF is increased. This results in the notable increase in immunohistochemical expression of VEGF in the syncytiotrophoblasts of hypertensive placenta.