bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic characteristics and epidemiology of inherited retinal degeneration in Taiwan
Authors: Chen Ta-Ching , Huang Ding-Siang , Lin Chao-Wen , Yang Chang-Hao , Yang Chung-May , Wang Victoria Y. , Lin Jou-Wei , Luo Allen Chilun , Hu Fung-Rong , Chen Pei-Lung 
Published: February 2021

AbstractInherited retinal degenerations (IRDs) are a group of phenotypically and genotypically heterogeneous disorders with substantial socioeconomic impact. In this cohort study, we tried to address the genetic characteristics and epidemiology of IRDs in Taiwan. Totally, 312 families with IRDs were identified and recruited and genetic testing was performed via probe capture-based NGS targeting 212 IRD-related genes. Statistical analysis was based on the proband of each affected family. Disease-causing genotypes were identified in 178 families (57.1%). ABCA4 variants were the most common cause of disease in this cohort (27 families, 15.2%), whereas CYP4V2 variants were the most common cause for the single phenotype—Bietti’s crystalline dystrophy (12 families, 3.8%). Some variants such as ABCA4:c.1804C>T, CYP4V2:c.802-8_810delinsGC, and EYS:c6416G>A were population-specific disease-causing hotspots. Probands affected by ABCA4, RPGR, RP1L1, and CEP290 sought medical help earlier while patients affected by EYS and CYP4V2 visited our clinic at an older age. To evaluate the representativeness of our cohort in the genetic epidemiology of IRDs in Taiwan, our demographic data were compared with that of the total IRD population in Taiwan, obtained from the National Health Insurance Research Database. This is currently the largest-scale, comprehensive study investigating the genetic characteristics and epidemiology of IRD in Taiwan. These data could help patients and caregivers to adopt precision genomic medicine and novel gene therapies in near future.
Single-bubble EHD behavior into water two-phase flow under electric-field stress and gravitational acceleration using PFM
Authors: Mianmahale Maryam Aliakbary , Mehrabani-Zeinabad Arjomand , Zare Masoud Habibi , Ghadiri Mahdi 
Published: February 2021

AbstractIn this study, single-bubble electro-hydrodynamic effects on the two-phase laminar flow of water under electric field stress are investigated using numerical modeling. A 2D axisymmetric model is also developed to study the growth and departure of a single bubble. The phase-field method is applied to track the interphase between liquid and gas. The growth of the attached vapor bubble nucleus to a superheat at 7.0 °C and 8.5 °C are evaluated with 50° and 90° contact angles. The results show that the enhancement of the contact angle changes the velocity and temperature fields around the bubble. It is observed that the growing size and base of the bubble is increased with increasing the wall superheat, but the bubble departure diameter and time are decreased. The electric field results in raising the number of detached bubbles from the superheat at a certain time interval but decreasing the bubbles departure size. Additionally, the formation of stretched bubbles enhances the rate of heat flux and there is a non-linear relationship between the applied voltage and heat flux.
Female fertile phase synchrony, and male mating and reproductive skew, in the crested macaque
Authors: Higham James P. , Heistermann Michael , Agil Muhammad , Perwitasari-Farajallah Dyah , Widdig Anja , Engelhardt Antje 
Published: February 2021

AbstractHigh social status is the primary determinant of reproductive success among group-living male mammals. Primates living in multimale–multifemale groups show the greatest variation in the strength of this link, with marked variation in reproductive skew by male dominance among species, dependent on the degree of female fertile phase synchrony, and the number of competing males. Here, we present data on two groups of wild crested macaques (Macaca nigra), living in the Tangkoko Reserve, Sulawesi, Indonesia. We investigated male monopolization of fertile females in 31 cycles of 19 females, and genetic paternity of 14 offspring conceived during the study period. We show that female fertile phase synchrony was low, that females had few mating partners in their fertile phase, and that dominant males monopolized a high proportion of consortships and matings, resulting in marked and steep mating and reproductive skew. We conclude that female cycle asynchrony provides the opportunity for strong direct male–male competition in crested macaques, resulting in monopolization of females by dominant males, consistent with their marked sexual dimorphism. Our study provides a test of the underlying factors that determine the relative occurrence and strength of different mechanisms of sexual selection, and the phenotypes that evolve as a result.
Convection heat mass transfer and MHD flow over a vertical plate with chemical reaction, arbitrary shear stress and exponential heating
Authors: Sehra  , Haq Sami Ul , Shah Syed Inayat Ali , Nisar Kottakkaran Sooppy , Jan Saeed Ullah , Khan Ilyas 
Published: February 2021

AbstractThe present research article is directed to study the heat and mass transference analysis of an incompressible Newtonian viscous fluid. The unsteady MHD natural convection flow over an infinite vertical plate with time dependent arbitrary shear stresses has been investigated. In heat and mass transfer analysis the chemical molecular diffusivity effects have been studied. Moreover, the infinite vertical plate is subjected to the phenomenon of exponential heating. For this study, we formulated the problem into three governing equations along with their corresponding initial and boundary conditions. The Laplace transform method has been used to gain the exact analytical solutions to the problem. Special cases of the obtained solutions are investigated. It is noticed that some well-known results from the published literature are achieved from these special cases. Finally, different physical parameters’ responses are investigated graphically through Mathcad software.
A high-throughput RNA-Seq approach to elucidate the transcriptional response of Piriformospora indica to high salt stress
Authors: Nivedita  , Rawoof Abdul , Ramchiary Nirala , Abdin Malik Z. 
Published: February 2021

AbstractPiriformospora indica, a root endophytic fungus, augments plant nutrition and productivity as well as protects plants against pathogens and abiotic stresses. High salinity is a major problem faced by plants as well as by microbes. Until now, the precise mechanism of salt stress tolerance in P. indica has remained elusive. In this study, the transcriptomes of control and salt-treated (0.5 M NaCl) P. indica were sequenced via the RNA-seq approach. A total of 30,567 transcripts and 15,410 unigenes for P. indica were obtained from 7.3 Gb clean reads. Overall 661 differentially expressed genes (DEGs) between control and treated samples were retrieved. Gene ontology (GO) and EuKaryotic Orthologous Groups (KOG) enrichments revealed that DEGs were specifically involved in metabolic and molecular processes, such as “response to salt stress”, “oxidoreductase activity”, “ADP binding”, “translation, ribosomal structure and biogenesis”, “cytoskeleton”, and others. The unigenes involved in “cell wall integrity”, “sterol biosynthesis”, and “oxidative stress” such as Rho-type GTPase, hydroxymethylglutaryl-CoA synthase, and thioredoxin peroxidase were up-regulated in P. indica subjected to salt stress. The salt-responsive DEGs have shown that they might have a potential role in salt stress regulation. Our study on the salt-responsive DEGs established a foundation for the elucidation of molecular mechanisms related to P. indica stress adaptation and a future reference for comparative functional genomics studies of biotechnologically important fungal species.
Integrins mediate placental extracellular vesicle trafficking to lung and liver in vivo
Authors: Nguyen Sean L. , Ahn Soo Hyun , Greenberg Jacob W. , Collaer Benjamin W. , Agnew Dalen W. , Arora Ripla , Petroff Margaret G. 
Published: February 2021

AbstractMembrane-bound extracellular vesicles (EVs) mediate intercellular communication in all organisms, and those produced by placental mammals have become increasingly recognized as significant mediators of fetal-maternal communication. Here, we aimed to identify maternal cells targeted by placental EVs and elucidate the mechanisms by which they traffic to these cells. Exogenously administered pregnancy-associated EVs traffic specifically to the lung; further, placental EVs associate with lung interstitial macrophages and liver Kupffer cells in an integrin-dependent manner. Localization of EV to maternal lungs was confirmed in unmanipulated pregnancy using a transgenic reporter mouse model, which also provided in situ and in vitro evidence that fetally-derived EVs, rarely, may cause genetic alteration of maternal cells. These results provide for the first time direct in vivo evidence that placental EVs target maternal immune cells, and further, that EVs can alter cellular phenotype.
Characterization of HIV-1 recombinant and subtype B near full-length genome among men who have sex with men in South Korea
Authors: Ryou Sangmi , Yoo Myeongsu , Kim Kisoon , Kim Sangsoo , Kim Sang Il , Kim Youn Jeong , Park Dae Won , Choi Jun Yong , Kim Hyo Youl , Kim Jung Ho , Song Joon Young , Kim Shin-Woo , Chang Hyun-Ha , Choi Bo Youl , Kee Mee-Kyung 
Published: February 2021

AbstractIn Korea, subtype B is the predominant variant of HIV-1, but full genome sequencing and analysis of its viral variants are lacking. We performed near full-length genome (NFLG) sequencing and phylogenetic and recombination analyses of fifty plasma samples from HIV-positive men who have sex with men (MSM) from a Korea HIV/AIDS cohort study. Viral genomes were amplified and the near-full-length sequences were determined using next-generation sequencing (NGS) and Sanger sequencing. We focused on the HIV-1 subtype classification and identification of HIV recombinants. Twelve HIV-1 NFLGs were determined: ten were subtyped as pure HIV-1 subtype B and two recombinant strains as a common subtype CRF07_BC, and a novel subtype CRF43_02G recombined with CRF02_AG again, or a new CRF02_AG and subtype G recombinant. For the ten NFLGs determined by NGS, “the novel recombinant emerged at approximately 2003 and the other nine subtype B about 2004 or 2005”. This is the first report analyzing HIV-1 NFLG, including recombinants and clinical characteristics, by subtype among MSM in Korea. Our results provide novel insights for understanding the recombinants in the HIV-1 epidemic in Korea.
Antibody mediated activation of natural killer cells in malaria exposed pregnant women
Authors: Damelang Timon , Aitken Elizabeth H. , Hasang Wina , Lopez Ester , Killian Martin , Unger Holger W. , Salanti Ali , Shub Alexis , McCarthy Elizabeth , Kedzierska Katherine , Lappas Martha , Kent Stephen J. , Rogerson Stephen J. , Chung Amy W. 
Published: February 2021

AbstractImmune effector responses against Plasmodium falciparum include antibody-mediated activation of innate immune cells, which can induce Fc effector functions, including antibody-dependent cellular cytotoxicity, and the secretion of cytokines and chemokines. These effector functions are regulated by the composition of immunoglobulin G (IgG) Fc N-linked glycans. However, a role for antibody-mediated natural killer (NK) cells activation or Fc N-linked glycans in pregnant women with malaria has not yet been established. Herein, we studied the capacity of IgG antibodies from pregnant women, with placental malaria or non-placental malaria, to induce NK cell activation in response to placental malaria-associated antigens DBL2 and DBL3. Antibody-mediated NK cell activation was observed in pregnant women with malaria, but no differences were associated with susceptibility to placental malaria. Elevated anti-inflammatory glycosylation patterns of IgG antibodies were observed in pregnant women with or without malaria infection, which were not seen in healthy non-pregnant controls. This suggests that pregnancy-associated anti-inflammatory Fc N-linked glycans may dampen the antibody-mediated activation of NK cells in pregnant women with malaria infection. Overall, although anti-inflammatory glycans and antibody-dependent NK cell activation were detected in pregnant women with malaria, a definitive role for these antibody features in protecting against placental malaria remains to be proven.
Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community
Authors: Lee Hye Kyung , Knabl Ludwig , Pipperger Lisa , Volland Andre , Furth Priscilla A. , Kang Keunsoo , Smith Harold E. , Knabl Ludwig , Bellmann Romuald , Bernhard Christina , Kaiser Norbert , Gänzer Hannes , Ströhle Mathias , Walser Andreas , von Laer Dorothee , Hennighausen Lothar 
Published: February 2021

AbstractSARS-CoV-2 infection ranges from asymptomatic to severe with lingering symptomatology in some. This prompted investigation of whether or not asymptomatic disease results in measurable immune activation post-infection. Immune activation following asymptomatic SARS-CoV-2 infection was characterized through a comparative investigation of the immune cell transcriptomes from 43 asymptomatic seropositive and 52 highly exposed seronegative individuals from the same community 4–6 weeks following a superspreading event. Few of the 95 individuals had underlying health issues. One seropositive individual reported Cystic Fibrosis and one individual reported Incontinentia pigmenti. No evidence of immune activation was found in asymptomatic seropositive individuals with the exception of the Cystic Fibrosis patient. There were no statistically significant differences in immune transcriptomes between asymptomatic seropositive and highly exposed seronegative individuals. Four positive controls, mildly symptomatic seropositive individuals whose blood was examined 3 weeks following infection, showed immune activation. Negative controls were four seronegative individuals from neighboring communities without COVID-19. All individuals remained in their usual state of health through a five-month follow-up after sample collection. In summary, whole blood transcriptomes identified individual immune profiles within a community population and showed that asymptomatic infection within a super-spreading event was not associated with enduring immunological activation.
One-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by chemical ratchet mechanism
Authors: Kinebuchi Takashi , Shimamoto Nobuo 
Published: February 2021

AbstractSeveral DNA-binding proteins show the affinities for their specific DNA sites that positively depend on the length of DNA harboring the sites, i. e. antenna effect. DNA looping can cause the effect for proteins with two or more DNA binding sites, i. e. the looping mechanism. One-dimensional diffusion also has been suggested to cause the effect for proteins with single DNA sites, the diffusion mechanism, which could violate detailed balance. We addressed which mechanism is possible for E. coli TrpR showing 104-fold antenna effect with a single DNA binding site. When a trpO-harboring DNA fragment was connected to a nonspecific DNA with biotin-avidin connection, the otherwise sevenfold antenna effect disappeared. This result denies the looping mechanism with an unknown second DNA binding site. The 3.5-fold repression by TrpR in vivo disappeared when a tight LexA binding site was introduced at various sites near the trpO, suggesting that the binding of LexA blocks one-dimensional diffusion causing the antenna effect. These results are consistent with the chemical ratchet recently proposed for TrpR-trpO binding to solve the deviation from detailed balance, and evidence that the antenna effect due to one-dimensional diffusion exists in cells.
Enabling deeper learning on big data for materials informatics applications
Authors: Jha Dipendra , Gupta Vishu , Ward Logan , Yang Zijiang , Wolverton Christopher , Foster Ian , Liao Wei-keng , Choudhary Alok , Agrawal Ankit 
Published: February 2021

AbstractThe application of machine learning (ML) techniques in materials science has attracted significant attention in recent years, due to their impressive ability to efficiently extract data-driven linkages from various input materials representations to their output properties. While the application of traditional ML techniques has become quite ubiquitous, there have been limited applications of more advanced deep learning (DL) techniques, primarily because big materials datasets are relatively rare. Given the demonstrated potential and advantages of DL and the increasing availability of big materials datasets, it is attractive to go for deeper neural networks in a bid to boost model performance, but in reality, it leads to performance degradation due to the vanishing gradient problem. In this paper, we address the question of how to enable deeper learning for cases where big materials data is available. Here, we present a general deep learning framework based on Individual Residual learning (IRNet) composed of very deep neural networks that can work with any vector-based materials representation as input to build accurate property prediction models. We find that the proposed IRNet models can not only successfully alleviate the vanishing gradient problem and enable deeper learning, but also lead to significantly (up to 47%) better model accuracy as compared to plain deep neural networks and traditional ML techniques for a given input materials representation in the presence of big data.
Avoiding gauge ambiguities in cavity quantum electrodynamics
Authors: Rouse Dominic M. , Lovett Brendon W. , Gauger Erik M. , Westerberg Niclas 
Published: February 2021

AbstractSystems of interacting charges and fields are ubiquitous in physics. Recently, it has been shown that Hamiltonians derived using different gauges can yield different physical results when matter degrees of freedom are truncated to a few low-lying energy eigenstates. This effect is particularly prominent in the ultra-strong coupling regime. Such ambiguities arise because transformations reshuffle the partition between light and matter degrees of freedom and so level truncation is a gauge dependent approximation. To avoid this gauge ambiguity, we redefine the electromagnetic fields in terms of potentials for which the resulting canonical momenta and Hamiltonian are explicitly unchanged by the gauge choice of this theory. Instead the light/matter partition is assigned by the intuitive choice of separating an electric field between displacement and polarisation contributions. This approach is an attractive choice in typical cavity quantum electrodynamics situations.
Brain functional connectivity differs when viewing pictures from natural and built environments using fMRI resting state analysis
Authors: Kühn Simone , Forlim Caroline Garcia , Lender Anja , Wirtz Janina , Gallinat Jürgen 
Published: February 2021

AbstractHuman beings evolved in “natural” environments. Many intervention studies have shown that exposure to natural environments (compared to built/urban environments) reduces stress and increases cognitive functioning. We set out to test differences in fMRI functional connectivity while showing participants photographs from natural versus built environments (matched in terms of scenicness ratings). No differences in self-reported perceived stress, rumination, valence, arousal or dominance were observed. However, functional connectivity was significantly higher when participants saw natural rather than built environmental photographs in circuits consisting of dorsal attention network (DAN) and ventral attention network (VAN), DAN and default mode network (DMN) and DMN and Somatomotor connections. In addition, we observed lower functional connectivity during the natural environment condition correlated with more years that individuals spent in major cities during upbringing. Future studies, linking changes in cognitive functioning due to nature exposure and alterations in functional connectivity, are warranted.
Atorvastatin treatment does not abolish inflammatory mediated cardiovascular risk in subjects with chronic kidney disease
Authors: Hoogeveen Renate M. , Verweij Simone L. , Kaiser Yannick , Kroon Jeffrey , Verberne Hein J. , Vogt Liffert , Moens Sophie J. Bernelot , Stroes Erik S. G. 
Published: February 2021

AbstractIndividuals with chronic kidney disease are at an increased risk for cardiovascular disease. This risk may partially be explained by a chronic inflammatory state in these patients, reflected by increased arterial wall and cellular inflammation. Statin treatment decreases cardiovascular risk and arterial inflammation in non-CKD subjects. In patients with declining kidney function, cardiovascular benefit resulting from statin therapy is attenuated, possibly due to persisting inflammation. In the current study, we assessed the effect of statin treatment on arterial wall and cellular inflammation. Fourteen patients with chronic kidney disease stage 3 or 4, defined by an estimated Glomerular Filtration Rate between 15 and 60 mL/min/1.73 m2, without cardiovascular disease were included in a single center, open label study to assess the effect of atorvastatin 40 mg once daily for 12 weeks (NTR6896). At baseline and at 12 weeks of treatment, we assessed arterial wall inflammation by 18F-fluoro-deoxyglucose positron-emission tomography computed tomography (18F-FDG PET/CT) and the phenotype of circulating monocytes were assessed. Treatment with atorvastatin resulted in a 46% reduction in LDL-cholesterol, but this was not accompanied by an attenuation in arterial wall inflammation in the aorta or carotid arteries, nor with changes in chemokine receptor expression of circulating monocytes. Statin treatment does not abolish arterial wall or cellular inflammation in subjects with mild to moderate chronic kidney disease. These results imply that CKD-associated inflammatory activity is mediated by factors beyond LDL-cholesterol and specific anti-inflammatory interventions might be necessary to further dampen the inflammatory driven CV risk in these subjects.
Population decline in a ground-nesting solitary squash bee (Eucera pruinosa) following exposure to a neonicotinoid insecticide treated crop (Cucurbita pepo)
Authors: Willis Chan D. Susan , Raine Nigel E. 
Published: February 2021

AbstractInsect pollinators are threatened by multiple environmental stressors, including pesticide exposure. Despite being important pollinators, solitary ground-nesting bees are inadequately represented by pesticide risk assessments reliant almost exclusively on honeybee ecotoxicology. Here we evaluate the effects of realistic exposure via squash crops treated with systemic insecticides (Admire-imidacloprid soil application, FarMore FI400-thiamethoxam seed-coating, or Coragen-chlorantraniliprole foliar spray) for a ground-nesting bee species (Hoary squash bee, Eucera pruinosa) in a 3-year semi-field experiment. Hoary squash bees provide essential pollination services to pumpkin and squash crops and commonly nest within cropping areas increasing their risk of pesticide exposure from soil, nectar, and pollen. When exposed to a crop treated at planting with soil-applied imidacloprid, these bees initiated 85% fewer nests, left 5.3 times more pollen unharvested, and produced 89% fewer offspring than untreated controls. No measurable impacts on bees from exposure to squash treated with thiamethoxam as a seed-coating or foliage sprayed with chlorantraniliprole were found. Our results demonstrate important sublethal effects of field-realistic exposure to a soil-applied neonicotinoid (imidacloprid) on bee behaviour and reproductive success. Soil must be considered a potential route of pesticide exposure in risk assessments, and restrictions on soil-applied insecticides may be justified, to mitigate impacts on ground-nesting solitary bee populations and the crop pollination services they provide.