bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of Daily Alcohol Intake, Volumetric Breast Density, and Breast Cancer Risk
Authors: Rustagi Alison S , Scott Christopher G , Winham Stacey J , Brandt Kathleen R , Norman Aaron D , Jensen Matthew R , Shepherd John A , Hruska Carrie , Heine John J , Pankratz Vernon S , Kerlikowske Karla , Vachon Celine M 
Published: January 2021

Abstract
High alcohol intake and breast density increase breast cancer (BC) risk, but their interrelationship is unknown. We examined whether volumetric density modifies and/or mediates the alcohol-BC association. BC cases (n = 2233) diagnosed from 2006 to 2013 in the San Francisco Bay area had screening mammograms 6 or more months before diagnosis; controls (n = 4562) were matched on age, mammogram date, race or ethnicity, facility, and mammography machine. Logistic regression was used to estimate alcohol-BC associations adjusted for age, body mass index, and menopause; interaction terms assessed modification. Percent mediation was quantified as the ratio of log (odds ratios [ORs]) from models with and without density measures. Alcohol consumption was associated with increased BC risk (2-sided Ptrend = .004), as were volumetric percent density (OR = 1.45 per SD, 95% confidence interval [CI] = 1.36 to 1.56) and dense volume (OR = 1.30, 95% CI = 1.24 to 1.37). Breast density did not modify the alcohol-BC association (2-sided P &gt; .10 for all). Dense volume mediated 25.0% (95% CI = 5.5% to 44.4%) of the alcohol-BC association (2-sided P = .01), suggesting alcohol may partially increase BC risk by increasing fibroglandular tissue.
Global optimization-based reference star differential imaging for high-contrast exoplanet imaging survey
Authors: Ren Deqing , Chen Yili 
Published: January 2021

ABSTRACT
We propose a data reduction approach called global optimization-based reference star differential imaging (G-RDI), which can be used for exoplanet imaging survey, where large numbers of target stars from the same young stellar association are imaged and where no field rotation is needed. One of the unique features of our G-RDI is that we select reference stars from other scientific target stars in the same stellar association to optimize for high-contrast imaging with a target star, which maximizes the observational efficiency and also delivers good performance to remove the speckle noise so that high contrast is achievable even at a small inner working angle (IWA) to the host star of being imaged. We proposed the G-RDI that is optimized for high-contrast exoplanet imaging at a small IWA and to provide a contrast that is significantly better than the current reference star differential imaging (RDI) method. In addition, we also propose the use of multiple reference stars and found that our G-RDI can further deliver better performance in that case. The result was compared with other exoplanet data reduction techniques, including the traditional RDI, and it indicated that our G-RDI with two reference stars can significantly improve the contrast performance at a small IWA with a high observational efficiency – two critical features that current data reduction techniques cannot offer. This approach could be used with both equatorial and alt-azimuth mount telescopes, and provides a new option for future exoplanet imaging surveys with high observational efficiency at a small IWA.
An excess of globular clusters in Ultra-Diffuse Galaxies formed through tidal heating
Authors: Carleton Timothy , Guo Yicheng , Munshi Ferah , Tremmel Michael , Wright Anna 
Published: January 2021

ABSTRACT
To investigate the origin of elevated globular cluster (GC) abundances observed around Ultra-Diffuse Galaxies (UDGs), we simulate GC populations hosted by UDGs formed through tidal heating. Specifically, GC formation is modelled as occurring in regions of dense star formation. Because star formation-rate densities are higher at high redshift, dwarf galaxies in massive galaxy clusters, which formed most of their stars at high redshift, form a large fraction of their stars in GCs. Given that UDGs formed through environmental processes are more likely to be accreted at high redshift, these systems have more GCs than non-UDGs. In particular, our model predicts that massive UDGs have twice the GC mass of non-UDGs of similar stellar mass, in rough agreement with observations. Although this effect is somewhat diminished by GC disruption, we find that the relationship between GC mass fraction and cluster-centric distance, and the relationship between GC mass fraction and galaxy half-light radius are remarkably similar to observations. Among our model objects, both UDGs and non-UDGs present a correlation between halo mass and GC mass, although UDGs have lower dynamical masses at a given GC mass. Furthermore, because of the effectiveness of GC disruption, we predict that GCs around UDGs should have a more top heavy mass function than GCs around non-UDGs. This analysis suggests that dwarfs with older stellar populations, such as UDGs, should have higher GC mass fractions than objects with young stellar populations, such as isolated dwarfs.
A morphological appraisal of the new subfamily Epidesmiinae (Lepidoptera: Geometridae) with an overview of all geometrid subfamilies
Authors: Murillo-Ramos Leidys , Friedrich Egbert , Williams Steve , Wahlberg Niklas , Brehm Gunnar , Sihvonen Pasi 
Published: January 2021

AbstractOur study revises Epidesmiinae, the first new Geometridae subfamily that has been described in 127 years. We studied the morphological characters of representatives from all genera currently classified into Epidesmiinae, and compared those with all other geometrid subfamilies. Epidesmiinae were found to have an Australasian distribution, with one species occurring in the Indo-Malayan realm. They compose a lineage diagnosable by a combination of the following morphological characters: male antennae unipectinate; labial palps elongated (particularly the second segment), vom Raths’s organ with an elliptical invagination; forewing with two areoles; hindwing with one anal vein; gnathos arms fused, granulate or dentate apically; female genitalia with two signa, one stellate, another an elongated and spinose plate. We also present a summary of diagnostic characters of all geometrid subfamilies, which confirm the lack of single unique morphological characters. The limited information on the biology and ecology of Epidesmiinae species are summarized, indicating that some species fly during the day, most adult records are from the Southern Hemisphere summer months and larvae are found on Myrtaceae. We transfer Arcina Walker, 1863 from Oenochrominae s.l. to Epidesmiinae. Epidesmiinae includes 102 species that are now classified into nine genera: Abraxaphantes, Adeixis, Arcina, Dichromodes, Ecphyas, Epidesmia, Phrataria, Phrixocomes and Systatica.
Development of a saliva-optimized RT-LAMP assay for SARS-CoV-2
Authors: Yu Albert Dayuan , Galatsis Kristina , Zheng Jian , Le Jasmine Quynh , Ma Dingbang , Perlman Stanley , Rosbash Michael 
Published: January 2021

AbstractConventional reverse transcription quantitative polymerase chain reaction (RT-qPCR) technology has struggled to fulfill the unprecedented need for diagnostic testing created by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Complexity and cost hinder access to testing, and long turnaround-time decreases its utility. To ameliorate these issues, we focus on saliva and introduce several advances to colorimetric reverse-transcription loop-mediated isothermal amplification (RT-LAMP) technology; RT-LAMP offers a minimal equipment alternative to RT-qPCR. First, we validated the use of the novel dye LAMPShade Violet (LSV), which improves the visual clarity and contrast of the colorimetric readout. Second, we compared different inactivation conditions on infectivity and RNA yield from saliva. Third, we developed a ten-minute RNA purification protocol from saliva. We call this magnetic bead protocol SalivaBeads. Finally, we developed a magnetic stick, StickLAMP, which provides reliable bead-based RNA purification as well as simple and low-cost access to scalable testing from saliva.
The evaluation of a newly developed antigen test (QuickNavi™-COVID19 Ag) for SARS-CoV-2: A prospective observational study in Japan
Authors: Takeuchi Yuto , Akashi Yusaku , Kato Daisuke , Kuwahara Miwa , Muramatsu Shino , Ueda Atsuo , Notake Shigeyuki , Nakamura Koji , Ishikawa Hiroichi , Suzuki Hiromichi 
Published: January 2021

AbstractIntroductionSeveral antigen tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed worldwide, but their clinical utility has not been well established. In this study, we evaluated the analytical and clinical performance of QuickNavi™-COVID19 Ag, a newly developed antigen test in Japan.MethodsThis prospective observational study was conducted at a PCR center between October 7 and December 5, 2020. The included patients were referred from a local public health center and 89 primary care facilities. We simultaneously obtained two nasopharyngeal samples with flocked swabs; one was used for the antigen test and the other for real-time reverse transcription PCR (RT-PCR). Using the results of real-time RT-PCR as a reference, the performance of the antigen test was evaluated.ResultsA total of 1186 patients were included in this study, and the real-time RT-PCR detected SARS-CoV-2 in 105 (8.9%). Of these 105 patients, 33 (31.4%) were asymptomatic. The antigen test provided a 98.8% (95% confident interval [CI]: 98.0%-99.4%) concordance rate with real-time RT-PCR, along with a sensitivity of 86.7% (95% CI: 78.6%-92.5%) and a specificity of 100% (95% CI: 99.7%-100%). False-negatives were observed in 14 patients, 8 of whom were asymptomatic and had a low viral load (cycle threshold (Ct) >30). In symptomatic patients, the sensitivity was 91.7% (95% CI: 82.7%-96.9%).ConclusionQuickNavi™-COVID19 Ag showed high specificity and sufficient sensitivity for the detection of SARS-CoV-2. This test is a promising potential diagnostic modality especially in symptomatic patients.
Long-term neurological manifestations of COVID-19: prevalence and predictive factors
Authors: Pilotto Andrea , Cristillo Viviana , Piccinelli Stefano Cotti , Zoppi Nicola , Bonzi Giulio , Sattin Davide , Schiavolin Silvia , Raggi Alberto , Canale Antonio , Gipponi Stefano , Libri Ilenia , Frigerio Martina , Bezzi Michela , Leonardi Matilde , Padovani Alessandro 
Published: January 2021

ABSTRACTBackgroundClinical investigations have argued for long-term neurological manifestations in both hospitalized and non-hospitalized COVID-19 patients. It is unclear whether long-term neurological symptoms and features depend on COVID-19 severity.Methodsfrom a sample of 208 consecutive non-neurological patients hospitalized for COVID-19 disease, 165 survivors were re-assessed at 6 months according to a structured standardized clinical protocol. Prevalence and predictors of long-term neurological manifestations were evaluated using multivariate logistic regression analyses.ResultsAt 6-month follow-up after hospitalisation due to COVID-19 disease, patients displayed a wide array of symptoms; fatigue (34%), memory/attention (31%), and sleep disorders (30%) were the most frequent. At neurological examination, 40% of patients exhibited neurological abnormalities, such as hyposmia (18.0%), cognitive deficits (17.5%), postural tremor (13.8%) and subtle motor/sensory deficits (7.6%). Older age, premorbid comorbidities and severity of COVID-19 were independent predictors of neurological manifestations in logistic regression analyses.Conclusionspremorbid vulnerability and severity of SARS-CoV-2 infection impact on prevalence and severity of long-term neurological manifestations.
A study of metabolic syndrome in patients of HIV on ART in India
Authors: Sashindran V K , Singh Anchit Raj 
Published: January 2021

AbstractMetabolic syndrome is a risk factor for cardiovascular disease. With improvement in therapy for HIV, morbidity related to metabolic syndrome becomes a focus of interest. Change in nutritional status and introduction of newer regimens of ART are changing the impact of metabolic syndrome on patients of HIV. Few studies in recent times from developing countries have addressed this question. This is a cross sectional study to study the prevalence of Metabolic Syndrome in patients of HIV on ART from clinics in a tertiary care hospital in India. Data from 1208 patients of HIV on ART was analyzed and metabolic syndrome was seen in 257(21.3%) patients.The high prevalence of metabolic syndrome in patients of HIV in India found in this study gives an insight on the morbidity of noncommunicable diseases in patients with HIV in India in recent times.
Simulating the Impacts of Interregional Mobility Restriction on the Spatial Spread of COVID-19 in Japan
Authors: Kondo Keisuke 
Published: January 2021

AbstractThis study develops a spatial Susceptible–Exposed–Infectious–Recovered (SEIR) model that analyzes the effect of interregional mobility on the spatial spread of the coronavirus disease 2019 (COVID-19) outbreak in Japan. National and local governments have requested that residents refrain from traveling between 47 prefectures during the state of emergency. However, the extent to which restricting the interregional mobility prevents infection expansion has not been elucidated. Our spatial SEIR model describes the spatial spread pattern of COVID-19 when people commute to a prefecture where they work or study during the daytime and return to their residential prefecture at night. We assume that people are exposed to infection risk during their daytime activities. According to our simulation results, interregional mobility restriction can prevent geographical expansion of the infection. However, in prefectures with many infectious individuals, residents are exposed to higher infection risk when their mobility is restricted. Our simulation results also show that interregional mobility restriction plays a limited role in reducing the national total number of infected individuals.
Animal-to-Animal Variability in Hippocampal Remapping
Authors: Nilchian Parsa , Wilson Matthew A. , Sanders Honi 
Published: January 2021

AbstractHippocampal place cells form a map of an animal’s environment. When the animal moves to a new environment, place field locations and firing rates change, a phenomenon known as remapping. Different animals can have different remapping responses to the same environments. This variability across animals in remapping behavior is not well understood. In this work, we analyzed electrophysiological recordings from Alme et al. (2014), in which five male rats were exposed to 11 different environments. To compare the hippocampal maps in two rooms, we computed average rate map correlation coefficients. We discovered that the heterogeneity in animals’ remapping behavior is structured: animals’ remapping behavior is consistent across a range of independent comparisons. Our findings highlight that remapping behavior between repeated environments depends on animal-specific factors.
An amiRNA screen uncovers redundant CBF & ERF34/35 transcription factors that differentially regulate arsenite and cadmium responses
Authors: Xie Qingqing , Yu Qi , Jobe Timothy O. , Pham Allis , Ge Chennan , Guo Qianqian , Liu Jianxiu , Liu Honghong , Zhang Huijie , Zhao Yunde , Xue Shaowu , Hauser Felix , Schroeder Julian I. 
Published: January 2021

AbstractArsenic stress causes rapid transcriptional responses in plants. However, transcriptional regulators of arsenic-induced gene expression in plants remain less well known. To date, forward genetic screens have proven limited for dissecting arsenic response mechanisms. We hypothesized that this may be due to the extensive genetic redundancy present in plant genomes. To overcome this limitation, we pursued a forward genetics screen for arsenite tolerance using a randomized library of plants expressing >2,000 artificial microRNAs (amiRNAs). This library was designed to knock-down diverse combinations of homologous gene family members within sub-clades of transcription factor and transporter gene families. We identified six transformant lines showing an altered response to arsenite in root growth assays. Further characterization of an amiRNA line targeting closely homologous CBF and ERF transcription factors show that the CBF1,2 and 3 transcription factors negatively regulate arsenite sensitivity. Furthermore, the ERF34 and ERF35 transcription factors are required for cadmium resistance. Generation of CRISPR lines, higher-order T-DNA mutants, and gene expression analyses, further support our findings. These ERF transcription factors differentially regulate arsenite sensitivity and cadmium tolerance.
Single-cell and single-variant resolution analysis of clonal evolution in human liver cancer
Authors: Su Xianbin , Zhao Linan , Shi Yi , Zhang Rui , Long Qi , Bai Shihao , Luo Qing , Lin Yingxin , Zou Xin , Ghazanfar Shila , Tao Kun , Yang Guoliang , Wang Lan , He Kun-Yan , Cui Xiaofang , He Jian , Wu Jiao-Xiang , Han Bo , Wang Na , Li Xiaolin , Yang Pengyi , Hou Shangwei , Sun Jielin , Yang Jean Y. H. , Chen Jinhong , Han Ze-Guang 
Published: January 2021

AbstractGenetic heterogeneity of tumor is closely related to clonal evolution, phenotypic diversity and treatment resistance. Such heterogeneity has been characterized in liver cancer at single-cell sub-chromosomal scale, and a more precise single-variant resolution analysis is lacking. Here we employed a strategy to analyze both the single-cell genomic mutations and transcriptomic changes in 5 patients with liver cancer. Target sequencing was done for a total of 480 single cells in a patient-specific manner. DNA copy number status of point mutations was obtained from single-cell mutational profiling. The clonal structures of liver cancers were then uncovered at single-variant resolution, and mutation combinations in single cells enabled reconstruction of their evolutionary history. A common origin but independent evolutionary fate was revealed for primary liver tumor and intrahepatic metastatic portal vein tumor thrombus. The mutational signature suggested early evolutionary process may be related to specific etiology like aristolochic acids. By parallel single-cell RNA-Seq, the transcriptomic phenotype was found to be related with genetic heterogeneity in liver cancer. We reconstructed the single-cell and single-variant resolution clonal evolutionary history of liver cancer, and dissection of both genetic and phenotypic heterogeneity provides knowledge for mechanistic understanding of liver cancer initiation and progression.
Retroviral Infection of Human Neurospheres and Use of Stem Cell EVs to Repair Cellular Damage
Authors: Branscome Heather , Khatkar Pooja , Sharif Sarah Al , Yin Dezhong , Jacob Sheela , Cowen Maria , Kim Yuriy , Erickson James , Brantner Christine A. , El-Hage Nazira , Liotta Lance A. , Kashanchi Fatah 
Published: January 2021

AbstractHIV-1 remains an incurable infection that is associated with substantial economic and epidemiologic impacts. HIV-associated neurocognitive disorders (HAND) are commonly linked with HIV-1 infection; despite the development of combination antiretroviral therapy (cART), HAND is still reported to affect at least 50% of HIV-1 infected individuals. It is believed that the over-amplification of inflammatory pathways, along with release of toxic viral proteins from infected cells, are primarily responsible for the neurological damage that is observed in HAND; however, the underlying mechanisms are not well-defined. Therefore, there is an unmet need to develop more physiologically relevant and reliable platforms for studying these pathologies. In recent years, neurospheres derived from induced pluripotent stem cells (iPSCs) have been utilized to model the effects of different neurotropic viruses. Here, we report the generation of neurospheres from iPSC-derived neural progenitor cells (NPCs) and we show that these cultures are permissive to retroviral (e.g. HIV-1, HTLV-1) replication. In addition, we also examine the potential effects of stem cell derived extracellular vesicles (EVs) on HIV-1 damaged cells as there is abundant literature supporting the reparative and regenerative properties of stem cell EVs in the context of various CNS pathologies. Consistent with the literature, our data suggests that stem cell EVs may modulate neuroprotective and anti-inflammatory properties in damaged cells. Collectively, this study demonstrates the feasibility of NPC-derived neurospheres for modeling HIV-1 infection and, subsequently, highlights the potential of stem cell EVs for rescuing cellular damage induced by HIV-1 infection.
Allosteric communication in DNA polymerase clamp loaders relies on a critical hydrogen-bonded junction
Authors: Subramanian Subu , Gorday Kent , Marcus Kendra , Orellana Matthew R. , Ren Peter , Luo Xiao Ran , O’Donnell Mike , Kuriyan John 
Published: January 2021

ABSTRACTClamp loaders are AAA+ ATPases that load sliding clamps onto DNA. We mapped the mutational sensitivity of the T4 bacteriophage sliding clamp and clamp loader by deep mutagenesis, and found that residues not involved in catalysis or binding display remarkable tolerance to mutation. An exception is a glutamine residue in the AAA+ module (Gln 118) that is not located at a catalytic or interfacial site. Gln 118 forms a hydrogen-bonded junction in a helical unit that we term the central coupler, because it connects the catalytic centers to DNA and the sliding clamp. A suppressor mutation indicates that hydrogen bonding in the junction is important, and molecular dynamics simulations reveal that it maintains rigidity in the central coupler. The glutamine-mediated junction is preserved in diverse AAA+ ATPases, suggesting that a connected network of hydrogen bonds that links ATP molecules is an essential aspect of allosteric communication in these proteins.
Structural and molecular basis for foot-and-mouth disease virus neutralization by two potent protective antibodies
Authors: Dong Hu , Liu Pan , Bai Manyuan , Wang Kang , Feng Rui , Zhu Dandan , Sun Yao , Mu Suyu , Li Haozhou , Harmsen Michiel , Sun Shiqi , Wang Xiangxi , Guo Huichen 
Published: January 2021

AbstractOutbreaks of Foot-and-mouth disease (FMD) caused by FMD virus result in significant economic losses. Vaccination is helpful, but the benefits are diminished with antigenic diversity within serotypes, instability of the immunogen and inability to confer protection for long durations. Here we have further dissected the mechanisms underpinning the protective efficacy of two previously reported neutralizing antibodies (NAbs), M8 and M170. The atomic details of the epitopes of M8 and M170 unveiled suggest that protection is conferred by disrupting the virus-receptor interactions. Consequently, administration of these NAbs conferred prophylactic and therapeutic benefit in guinea pigs, raising the possibility of administering NAbs before or during vaccination to confer immediate protection; well before the bolstering of the immune response by the vaccine. Differences in the residues and the conformation of elements making up the epitopes explain the differences in specificities of M8 and M170. An ability to bind 146S viral particles specifically, but not 12S degraded components, highlights a likely role for M170 in the quality control of vaccines.