bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and functional characterization of the extremely long allele of the serotonin transporter-linked polymorphic region
Authors: Ikegame Tempei , Hidaka Yosuke , Nakachi Yutaka , Murata Yui , Watanabe Risa , Sugawara Hiroko , Asai Tatsuro , Kiyota Emi , Saito Takeo , Ikeda Masashi , Sasaki Tsukasa , Hashimoto Mamoru , Ishikawa Tomohisa , Takebayashi Minoru , Iwata Nakao , Kakiuchi Chihiro , Kato Tadafumi , Kasai Kiyoto , Bundo Miki , Iwamoto Kazuya 
Published: February 2021

AbstractSLC6A4, which encodes the serotonin transporter, has a functional polymorphism called the serotonin transporter-linked polymorphic region (5-HTTLPR). The 5-HTTLPR consists of short (S) and long (L) alleles, each of which has 14 or 16 tandem repeats. In addition, the extralong (XL) and other rare alleles have been reported in 5-HTTLPR. Although they are more frequent in Asian and African than in other populations, the extent of variations and allele frequencies (AFs) were not addressed in a large population. Here, we report the AFs of the rare alleles in a large number of Japanese subjects (N = 2894) consisting of two cohorts. The first cohort (case-control study set, CCSS) consisted of 1366 subjects, including 485 controls and 881 patients with psychosis (bipolar disorder or schizophrenia). The second cohort (the Arao cohort study set, ACSS) consisted of 1528 elderly subjects. During genotyping, we identified 11 novel 5-HTTLPR alleles, including 3 XL alleles. One novel allele had the longest subunit ever reported, consisting of 28 tandem repeats. We named this XL28-A. An in vitro luciferase assay revealed that XL28-A has no transcriptional activity. XL28-A was found in two unrelated patients with bipolar disorder in the CCSS and one healthy subject in the ACSS who did not show depressive symptoms or a decline in cognitive function. Therefore, it is unlikely that XL28-A is associated with psychiatric disorders, despite its apparent functional deficit. Our results suggest that unraveling the complex genetic variations of 5-HTTLPR will be important for further understanding its role in psychiatric disorders.
Childhood maltreatment history and attention bias variability in healthy adult women: role of inflammation and the BDNF Val66Met genotype
Authors: Hori Hiroaki , Itoh Mariko , Lin Mingming , Yoshida Fuyuko , Niwa Madoka , Hakamata Yuko , Matsui Mie , Kunugi Hiroshi , Kim Yoshiharu 
Published: February 2021

AbstractChildhood maltreatment has been associated with greater attention bias to emotional information, but the findings are controversial. Recently, a novel index of attention bias, i.e., attention bias variability (ABV), has been developed to better capture trauma-related attentional dysfunction. However, ABV in relation to childhood trauma has not been studied. Here, we examined the association of childhood maltreatment history with attention bias/ABV in 128 healthy adult women. Different types of childhood maltreatment were assessed with the Childhood Trauma Questionnaire. Attention bias/ABV was measured by the dot-probe task. Possible mechanisms whereby childhood maltreatment affects attention bias/ABV were also explored, focusing on blood proinflammatory markers and the BDNF Val66Met polymorphism. We observed a significant positive correlation between childhood emotional abuse and ABV (P = 0.002). Serum high-sensitivity tumor necrosis factor-α levels were significantly positively correlated with ABV (P < 0.001), but not with childhood maltreatment. Jonckheere–Terpstra trend test showed a significant tendency toward greater ABV with increasing numbers of the BDNF Met alleles (P = 0.021). A two-way analysis of variance further revealed that the genotype-by-emotional abuse interaction for ABV was significant (P = 0.022); individuals with the Val/Met and Met/Met genotypes exhibited even greater ABV when childhood emotional abuse was present. These results indicate that childhood emotional abuse can have a long-term negative impact on emotional attention control. Increased inflammation may be involved in the mechanism of ABV, possibly independently of childhood maltreatment. The BDNF Met allele may dose-dependently increase ABV by interacting with childhood emotional abuse.
AFLOW-XtalFinder: a reliable choice to identify crystalline prototypes
Authors: Hicks David , Toher Cormac , Ford Denise C. , Rose Frisco , Santo Carlo De , Levy Ohad , Mehl Michael J. , Curtarolo Stefano 
Published: February 2021

AbstractThe accelerated growth rate of repository entries in crystallographic databases makes it arduous to identify and classify their prototype structures. The open-source AFLOW-XtalFinder package was developed to solve this problem. It symbolically maps structures into standard designations following the AFLOW Prototype Encyclopedia and calculates the internal degrees of freedom consistent with the International Tables for Crystallography. To ensure uniqueness, structures are analyzed and compared via symmetry, local atomic geometries, and crystal mapping techniques, simultaneously grouping them by similarity. The software (i) distinguishes distinct crystal prototypes and atom decorations, (ii) determines equivalent spin configurations, (iii) reveals compounds with similar properties, and (iv) guides the discovery of unexplored materials. The operations are accessible through a Python module ready for workflows, and through command line syntax. All the 4+ million compounds in the AFLOW.org repositories are mapped to their ideal prototype, allowing users to search database entries via symbolic structure-type. Furthermore, 15,000 unique structures — sorted by prevalence — are extracted from the AFLOW-ICSD catalog to serve as future prototypes in the Encyclopedia.
Convergence of biomarkers and risk factor trait loci of coronary artery disease at 3p21.31 and HLA region
Authors: Nikpay Majid , McPherson Ruth 
Published: February 2021

AbstractHere we seek to identify molecular biomarkers that mediate the effect of risk factors on coronary artery disease (CAD). We perform a SNP-based multiomics data analysis to find biomarkers (probes) causally associated with the risk of CAD within known genomic loci for its risk factors. We identify 78 biomarkers, the majority (64%) of which are methylation probes. We detect the convergence of several CNS and lifestyle trait loci and their biomarkers at the 3p21.31 and human leukocyte antigen (HLA) regions. The 3p21.31 locus was the most populated region in the convergence of biomarkers and risk factors. In this region, we noted as the BSN gene becomes methylated the level of stomatin (STOM) in blood increases and this contributes to higher risk of CAD. In the HLA locus, we identify several methylation biomarkers associated with various CAD risk factors. SNPs in the CFB gene display a trans-regulatory impact on the GRIA4 protein level. A methylation site upstream of the APOE gene is associated with a higher protein level of S100A13 which in turn leads to higher LDL-C and greater CAD risk. We find UHRF1BP1 and ILRUN mediate the effect of obesity on CAD whereas methylation sites within NOS3 and CKM mediate the effect of their associated-risk factors on CAD. This study provides further insight into the biology of CAD and identifies a list of biomarkers that mediate the impact of risk factors on CAD. A SNP-based initiative can unite data from various fields of omics into a single network of knowledge.
Genetic profiles of 103,106 individuals in the Taiwan Biobank provide insights into the health and history of Han Chinese
Authors: Wei Chun-Yu , Yang Jenn-Hwai , Yeh Erh-Chan , Tsai Ming-Fang , Kao Hsiao-Jung , Lo Chen-Zen , Chang Lung-Pao , Lin Wan-Jia , Hsieh Feng-Jen , Belsare Saurabh , Bhaskar Anand , Su Ming-Wei , Lee Te-Chang , Lin Yi-Ling , Liu Fu-Tong , Shen Chen-Yang , Li Ling-Hui , Chen Chien-Hsiun , Wall Jeffrey D. , Wu Jer-Yuarn , Kwok Pui-Yan 
Published: February 2021

AbstractPersonalized medical care focuses on prediction of disease risk and response to medications. To build the risk models, access to both large-scale genomic resources and human genetic studies is required. The Taiwan Biobank (TWB) has generated high-coverage, whole-genome sequencing data from 1492 individuals and genome-wide SNP data from 103,106 individuals of Han Chinese ancestry using custom SNP arrays. Principal components analysis of the genotyping data showed that the full range of Han Chinese genetic variation was found in the cohort. The arrays also include thousands of known functional variants, allowing for simultaneous ascertainment of Mendelian disease-causing mutations and variants that affect drug metabolism. We found that 21.2% of the population are mutation carriers of autosomal recessive diseases, 3.1% have mutations in cancer-predisposing genes, and 87.3% carry variants that affect drug response. We highlight how TWB data provide insight into both population history and disease burden, while showing how widespread genetic testing can be used to improve clinical care.
State leakage during fast decay and control of a superconducting transmon qubit
Authors: Babu Aravind Plathanam , Tuorila Jani , Ala-Nissila Tapio 
Published: February 2021

AbstractSuperconducting Josephson junction qubits constitute the main current technology for many applications, including scalable quantum computers and thermal devices. Theoretical modeling of such systems is usually done within the two-level approximation. However, accurate theoretical modeling requires taking into account the influence of the higher excited states without limiting the system to the two-level qubit subspace. Here, we study the dynamics and control of a superconducting transmon using the numerically exact stochastic Liouville–von Neumann equation approach. We focus on the role of state leakage from the ideal two-level subspace for bath induced decay and single-qubit gate operations. We find significant short-time state leakage due to the strong coupling to the bath. We quantify the leakage errors in single-qubit gates and demonstrate their suppression with derivative removal adiabatic gates (DRAG) control for a five-level transmon in the presence of decoherence. Our results predict the limits of accuracy of the two-level approximation and possible intrinsic constraints in qubit dynamics and control for an experimentally relevant parameter set.
The Zoltar forecast archive, a tool to standardize and store interdisciplinary prediction research
Authors: Reich Nicholas G. , Cornell Matthew , Ray Evan L. , House Katie , Le Khoa 
Published: February 2021

AbstractForecasting has emerged as an important component of informed, data-driven decision-making in a wide array of fields. We introduce a new data model for probabilistic predictions that encompasses a wide range of forecasting settings. This framework clearly defines the constituent parts of a probabilistic forecast and proposes one approach for representing these data elements. The data model is implemented in Zoltar, a new software application that stores forecasts using the data model and provides standardized API access to the data. In one real-time case study, an instance of the Zoltar web application was used to store, provide access to, and evaluate real-time forecast data on the order of 108rows, provided by over 40 international research teams from academia and industry making forecasts of the COVID-19 outbreak in the US. Tools and data infrastructure for probabilistic forecasts, such as those introduced here, will play an increasingly important role in ensuring that future forecasting research adheres to a strict set of rigorous and reproducible standards.
Decreased activity in the reward network of chronic insomnia patients
Authors: Motomura Yuki , Katsunuma Ruri , Ayabe Naoko , Oba Kentaro , Terasawa Yuri , Kitamura Shingo , Moriguchi Yoshiya , Hida Akiko , Kamei Yuichi , Mishima Kazuo 
Published: February 2021

AbstractIn modern society, many people have insomnia. Chronic insomnia has been noted as a risk factor for depression. However, there are few functional imaging studies of the brain on affective functions in chronic insomnia. This study aimed to investigate brain activities induced by emotional stimuli in chronic insomnia patients. Fifteen patients with primary insomnia and 30 age and gender matched healthy controls participated in this study. Both groups were presented images of fearful, happy, and neutral expressions consciously and non-consciously while undergoing MRI to compare the activity in regions of the brain responsible for emotions. Conscious presentation of the Happy-Neutral contrast showed significantly lower activation in the right orbitofrontal cortex of patients compared to healthy controls. The Happy-Neutral contrast presented in a non-conscious manner resulted in significantly lower activation of the ventral striatum, right insula, putamen, orbitofrontal cortex and ventral tegmental area in patients compared to healthy controls. Our findings revealed that responsiveness to positive emotional stimuli were decreased in insomniac patients. Specifically, brain networks associated with rewards and processing positive emotions showed decreased responsiveness to happy emotions especially for non-conscious image. The magnitude of activity in these areas also correlated with severity of insomnia, even after controlling for depression scale scores. These findings suggest that insomnia induces an affective functional disorder through an underlying mechanism of decreased sensitivity in the regions of the brain responsible for emotions and rewards to positive emotional stimuli.
Long-term movements and activity patterns of platypus on regulated rivers
Authors: Hawke Tahneal , Bino Gilad , Kingsford Richard T. , Iervasi Dion , Iervasi Kylie , Taylor Matthew D. 
Published: February 2021

AbstractThe platypus is a semi-aquatic mammal, endemic to freshwater habitats of eastern Australia. There are gaps in the understanding of platypus movement behaviour within river systems, including spatial and temporal organization of individuals. We tracked movements of 12 platypuses on the regulated Snowy and Mitta Mitta Rivers for up to 12-months, the longest continuous tracking of platypus using acoustic telemetry. Platypuses remained relatively localized, occupying 0.73–8.45 km of river over 12 months, consistent with previous tracking studies over shorter periods. Males moved further than females, and larger males had higher cumulative movements, suggesting a possible relationship to metabolic requirements. Platypuses moved greater distances on the Mitta Mitta River, possibly associated with impacts of altered flow regimes to their macroinvertebrate diet. Increased movements and diurnal activity during winter were primarily driven by males, possibly attributable to breeding behaviours, rather than increased costs of winter foraging. Evidence for relatively small movements has implications for declining populations, given areas of localised declines are unlikely to be supplemented by migrating platypuses, especially when dispersal is restricted by dam walls. Understanding platypus movement behaviour is pertinent for their conservation, as water resource development and habitat modification continue to reduce connectivity between populations across their distribution.
Temperature dependence of molybdenum dialkyl dithiocarbamate (MoDTC) tribofilms via time-resolved Raman spectroscopy
Authors: Garcia Carlos E. , Ueda Mao , Spikes Hugh , Wong Janet S. S. 
Published: February 2021

AbstractMolybdenum dialkyl dithiocarbamate (MoDTC) is a friction reducing additive commonly used in lubricants. MoDTC works by forming a low-friction molybdenum disulphide (MoS2) film (tribofilm) on rubbed surfaces. MoDTC-induced MoS2 tribofilms have been studied extensively ex-situ; however, there is no consensus on the chemical mechanism of its formation process. By combining Raman spectroscopy with a tribometer, effects of temperature and shear stress on MoS2 tribofilm formation in steel-steel contacts were examined. Time-resolved Raman spectra of the tribofilm were acquired, together with the instantaneous friction coefficient. The tribofilm is constantly being formed and removed mechanically during rubbing. Increasing shear stress promotes MoS2 formation. The nature of the tribofilm is temperature-dependent, with high-temperature tribofilms giving a higher friction than lower temperature films. Below a critical temperature Tc, a small amount of MoS2 gives significant friction reduction. Above Tc, a patchy film with more MoS2, together with a substantial amount of amorphous carbon attributed to base oil degradation, forms. The composition of this tribofilm evolves during rubbing and a temporal correlation is found between carbon signal intensity and friction. Our results highlight the mechanochemical nature of tribofilm formation process and the role of oil degradation in the effectiveness of friction modifier MoDTC.
Microsaccades mediate perceptual alternations in Monet’s “Impression, sunrise”
Authors: Alexander Robert G. , Venkatakrishnan Ashwin , Chanovas Jordi , Macknik Stephen L. , Martinez-Conde Susana 
Published: February 2021

AbstractTroxler fading, the perceptual disappearance of stationary images upon sustained fixation, is common for objects with equivalent luminance to that of the background. Previous work showed that variations in microsaccadic rates underlie the perceptual vanishing and intensification of simple stimuli, such as Gabor patches. Here, we demonstrate that microsaccade dynamics also contribute to Troxler fading and intensification during the viewing of representational art. Participants fixated a small spot while viewing either a Gabor patch on a blank background, or Monet’s painting “Impression, Sunrise.” They continuously reported, via button press/release, whether the Gabor patch, or the sun in Monet’s painting, was fading versus intensifying, while their eye movements were recorded with high precision. Microsaccade rates peaked before reports of increased visibility, and dropped before reports of decreased visibility or fading, both when viewing Gabor patches and Monet’s sun. These results reveal that the relationship between microsaccade production and the reversal and prevention of Troxler fading applies not only to the viewing of contrived stimuli, but also to the observation of “Impression, Sunrise.” Whether or not perceptual fading was consciously intended by Monet, our findings indicate that observers’ oculomotor dynamics are a contributor to the cornerstone of Impressionism.
Natron glass beads reveal proto-Silk Road between the Mediterranean and China in the 1st millennium BCE
Authors: Lü Qin-Qin , Henderson Julian , Wang Yongqiang , Wang Binghua 
Published: February 2021

AbstractNatron-based glass was a vital part of material culture in the Mediterranean and Europe for nearly two millennia, but natron glass found elsewhere on the Eurasian Continent has not received adequate discussion, despite its influence on ancient Asian glass. Here we present a new interpretation of natron glass finds from both the West and the East. After establishing the compositional types and technological sequence of Mediterranean natron glass (eighth-second century BCE) using trace elements, we report the analysis of a mid-1st millennium BCE glass bead from Xinjiang, China, which was likely made with Levantine raw glass, and identify common types of stratified eye beads in Eurasia based on a compositional and typological comparison. Combining these findings, we propose that a considerable number of Mediterranean natron glass products had arrived in East Asia at least by the fifth century BCE, which may have been a contributing factor in the development of native Chinese glass-making. The swift diffusion of natron glass across Eurasia in the 1st millennium BCE was likely facilitated by a three-stage process involving maritime and overland networks and multiple forms of trade and exchange, indicating a highly adaptable and increasingly efficient transcontinental connection along the ‘Proto-Silk Road’.
Electroencephalography measures of relative power and coherence as reaching skill emerges in infants born preterm
Authors: Nishiyori Ryota , Xiao Ran , Vanderbilt Douglas , Smith Beth A. 
Published: February 2021

AbstractElectroencephalography (EEG) measures of relative power and coherence are associated with motor experience in infants with typical development, but these relationships have not been assessed in infants born preterm. The goal of our study was to investigate the changing patterns of relative power and coherence in the alpha band during resting state EEG in infants born preterm as they developed the skill of reaching. We collected monthly longitudinal data from fourteen infants born preterm between the adjusted ages of 56 and 295 days for a total of 37 sessions of EEG data. Alpha band power at motor cortices and cross-regional connectivity do not present consistent changing trends at the group level in infants born preterm. Individual level analysis reveals that infants born preterm are a heterogeneous group with subtypes of neural function development, some presenting similar changing trends as observed in the typically developing group while others present atypical patterns. This may be linked to the variability in developmental outcomes in infants born preterm. This study was a critical first step to support EEG as a potential tool for identifying and quantifying the developmental trajectories of neuromotor control in infants born preterm.
The evolutionary history of manatees told by their mitogenomes
Authors: de Souza Érica Martinha Silva , Freitas Lucas , da Silva Ramos Elisa Karen , Selleghin-Veiga Giovanna , Rachid-Ribeiro Michelle Carneiro , Silva Felipe André , Marmontel Miriam , dos Santos Fabrício Rodrigues , Laudisoit Anne , Verheyen Erik , Domning Daryl P. , Nery Mariana Freitas 
Published: February 2021

AbstractThe manatee family encompasses three extant congeneric species: Trichechus senegalensis (African manatee), T. inunguis (Amazonian manatee), and T. manatus (West Indian manatee). The fossil record for manatees is scant, and few phylogenetic studies have focused on their evolutionary history. We use full mitogenomes of all extant manatee species to infer the divergence dates and biogeographical histories of these species and the effect of natural selection on their mitogenomes. The complete mitochondrial genomes of T. inunguis (16,851 bp), T. senegalensis (16,882 bp), and T. manatus (16,882 bp), comprise 13 protein-coding genes, 2 ribosomal RNA genes (rRNA - 12S and 16S), and 22 transfer RNA genes (tRNA), and (D-loop/CR). Our analyses show that the first split within Trichechus occurred during the Late Miocene (posterior mean 6.56 Ma and 95% HPD 3.81–10.66 Ma), followed by a diversification event in the Plio-Pleistocene (posterior mean 1.34 Ma, 95% HPD 0.1–4.23) in the clade composed by T. inunguis and T. manatus; T. senegalensis is the sister group of this clade with higher support values (pp > 0.90). The branch-site test identified positive selection on T. inunguis in the 181st position of the ND4 amino acid gene (LRT = 6.06, p = 0.0069, BEB posterior probability = 0.96). The ND4 gene encodes one subunit of the NADH dehydrogenase complex, part of the oxidative phosphorylation machinery. In conclusion, our results provide novel insight into the evolutionary history of the Trichechidae during the Late Miocene, which was influenced by geological events, such as Amazon Basin formation.