bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discrete SARS-CoV-2 antibody titers track with functional humoral stability
Authors: Bartsch Yannic C. , Fischinger Stephanie , Siddiqui Sameed M. , Chen Zhilin , Yu Jingyou , Gebre Makda , Atyeo Caroline , Gorman Matthew J. , Zhu Alex Lee , Kang Jaewon , Burke John S. , Slein Matthew , Gluck Matthew J. , Beger Samuel , Hu Yiyuan , Rhee Justin , Petersen Eric , Mormann Benjamin , Aubin Michael de St , Hasdianda Mohammad A. , Jambaulikar Guruprasad , Boyer Edward W. , Sabeti Pardis C. , Barouch Dan H. , Julg Boris D. , Musk Elon R. , Menon Anil S. , Lauffenburger Douglas A. , Nilles Eric J. , Alter Galit 
Published: February 2021

AbstractAntibodies serve as biomarkers of infection, but if sustained can confer long-term immunity. Yet, for most clinically approved vaccines, binding antibody titers only serve as a surrogate of protection. Instead, the ability of vaccine induced antibodies to neutralize or mediate Fc-effector functions is mechanistically linked to protection. While evidence has begun to point to persisting antibody responses among SARS-CoV-2 infected individuals, cases of re-infection have begun to emerge, calling the protective nature of humoral immunity against this highly infectious pathogen into question. Using a community-based surveillance study, we aimed to define the relationship between titers and functional antibody activity to SARS-CoV-2 over time. Here we report significant heterogeneity, but limited decay, across antibody titers amongst 120 identified seroconverters, most of whom had asymptomatic infection. Notably, neutralization, Fc-function, and SARS-CoV-2 specific T cell responses were only observed in subjects that elicited RBD-specific antibody titers above a threshold. The findings point to a switch-like relationship between observed antibody titer and function, where a distinct threshold of activity—defined by the level of antibodies—is required to elicit vigorous humoral and cellular response. This response activity level may be essential for durable protection, potentially explaining why re-infections occur with SARS-CoV-2 and other common coronaviruses.
PrimeDesign software for rapid and simplified design of prime editing guide RNAs
Authors: Hsu Jonathan Y. , Grünewald Julian , Szalay Regan , Shih Justine , Anzalone Andrew V. , Lam Kin Chung , Shen Max W. , Petri Karl , Liu David R. , Joung J. Keith , Pinello Luca 
Published: February 2021

AbstractPrime editing (PE) is a versatile genome editing technology, but design of the required guide RNAs is more complex than for standard CRISPR-based nucleases or base editors. Here we describe PrimeDesign, a user-friendly, end-to-end web application and command-line tool for the design of PE experiments. PrimeDesign can be used for single and combination editing applications, as well as genome-wide and saturation mutagenesis screens. Using PrimeDesign, we construct PrimeVar, a comprehensive and searchable database that includes candidate prime editing guide RNA (pegRNA) and nicking sgRNA (ngRNA) combinations for installing or correcting >68,500 pathogenic human genetic variants from the ClinVar database. Finally, we use PrimeDesign to design pegRNAs/ngRNAs to install a variety of human pathogenic variants in human cells.
Asymmetric introgression reveals the genetic architecture of a plumage trait
Authors: Semenov Georgy A. , Linck Ethan , Enbody Erik D. , Harris Rebecca B. , Khaydarov David R. , Alström Per , Andersson Leif , Taylor Scott A. 
Published: February 2021

AbstractGenome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration from personata to alba subspecies of the white wagtail. A previous study of their hybrid zone in Siberia revealed that the geographic transition in this sexual signal that mediates assortative mating was offset from other traits and genetic markers. Here we show that head plumage is associated with two small genetic regions. Despite having a simple genetic architecture, head plumage inheritance is consistent with partial dominance and epistasis, which could contribute to its asymmetric introgression.
Maternal aryl hydrocarbon receptor activation protects newborns against necrotizing enterocolitis
Authors: Lu Peng , Yamaguchi Yukihiro , Fulton William B. , Wang Sanxia , Zhou Qinjie , Jia Hongpeng , Kovler Mark L. , Salazar Andres Gonzalez , Sampah Maame , Prindle Thomas , Wipf Peter , Sodhi Chhinder P. , Hackam David J. 
Published: February 2021

AbstractNecrotizing enterocolitis (NEC) is a disease of premature infants characterized by acute intestinal necrosis. Current dogma suggests that NEC develops in response to post-natal dietary and bacterial factors, and so a potential role for in utero factors in NEC remains unexplored. We now show that during pregnancy, administration of a diet rich in the aryl hydrocarbon receptor (AHR) ligand indole-3-carbinole (I3C), or of breast milk, activates AHR and prevents NEC in newborn mice by reducing Toll-like receptor 4 (TLR4) signaling in the newborn gut. Protection from NEC requires activation of AHR in the intestinal epithelium which is reduced in mouse and human NEC, and is independent of leukocyte activation. Finally, we identify an AHR ligand (“A18”) that limits TLR4 signaling in mouse and human intestine, and prevents NEC in mice when administered during pregnancy. In summary, AHR signaling is critical in NEC development, and maternally-delivered, AHR-based therapies may alleviate NEC.
Loop competition and extrusion model predicts CTCF interaction specificity
Authors: Xi Wang , Beer Michael A. 
Published: February 2021

AbstractThree-dimensional chromatin looping interactions play an important role in constraining enhancer–promoter interactions and mediating transcriptional gene regulation. CTCF is thought to play a critical role in the formation of these loops, but the specificity of which CTCF binding events form loops and which do not is difficult to predict. Loops often have convergent CTCF binding site motif orientation, but this constraint alone is only weakly predictive of genome-wide interaction data. Here we present an easily interpretable and simple mathematical model of CTCF mediated loop formation which is consistent with Cohesin extrusion and can predict ChIA-PET CTCF looping interaction measurements with high accuracy. Competition between overlapping loops is a critical determinant of loop specificity. We show that this model is consistent with observed chromatin interaction frequency changes induced by CTCF binding site deletion, inversion, and mutation, and is also consistent with observed constraints on validated enhancer–promoter interactions.
Whole exome sequencing uncovered highly penetrant recessive mutations for a spectrum of rare genetic pediatric diseases in Bangladesh
Authors: Akter Hosneara , Hossain Mohammad Shahnoor , Dity Nushrat Jahan , Rahaman Md. Atikur , Furkan Uddin K. M. , Nassir Nasna , Begum Ghausia , Hameid Reem Abdel , Islam Muhammad Sougatul , Tusty Tahrima Arman , Basiruzzaman Mohammad , Sarkar Shaoli , Islam Mazharul , Jahan Sharmin , Lim Elaine T. , Woodbury-Smith Marc , Stavropoulos Dimitri James , O’Rielly Darren D. , Berdeiv Bakhrom K. , Nurun Nabi A. H. M. , Ahsan Mohammed Nazmul , Scherer Stephen W. , Uddin Mohammed 
Published: February 2021

AbstractCollectively, rare genetic diseases affect a significant number of individuals worldwide. In this study, we have conducted whole-exome sequencing (WES) and identified underlying pathogenic or likely pathogenic variants in five children with rare genetic diseases. We present evidence for disease-causing autosomal recessive variants in a range of disease-associated genes such as DHH-associated 46,XY gonadal dysgenesis (GD) or 46,XY sex reversal 7, GNPTAB-associated mucolipidosis II alpha/beta (ML II), BBS1-associated Bardet–Biedl Syndrome (BBS), SURF1-associated Leigh Syndrome (LS) and AP4B1-associated spastic paraplegia-47 (SPG47) in unrelated affected members from Bangladesh. Our analysis pipeline detected three homozygous mutations, including a novel c. 863 G > C (p.Pro288Arg) variant in DHH, and two compound heterozygous variants, including two novel variants: c.2972dupT (p.Met991Ilefs*) in GNPTAB and c.229 G > C (p.Gly77Arg) in SURF1. All mutations were validated by Sanger sequencing. Collectively, this study adds to the genetic heterogeneity of rare genetic diseases and is the first report elucidating the genetic profile of (consanguineous and nonconsanguineous) rare genetic diseases in the Bangladesh population.
Work absence in patients with asthma and/or COPD: a population-based study
Authors: Dierick Boudewijn J. H. , Flokstra-de Blok Bertine M. J. , van der Molen Thys , Toledo-Pons Núria , Román-Rodríguez Miguel , Cosío Borja G. , Soriano Joan B. , Kocks Janwillem W. H. , van Boven Job F. M. 
Published: February 2021

AbstractChronic obstructive pulmonary disease (COPD) and asthma impact on work productivity, but their population-based burden and clinical predictors are understudied. In this observational, real-life study, work absence of 14,383 asthma and/or COPD patients present in the MAJORICA cohort (Spain) was compared with the general population. Using multivariable regression, we studied the association of work absence with demographic and clinical characteristics. Patients with asthma and/or COPD had more work absence than the general population (15.2% vs 8.9%, p < 0.0001). Patients with asthma had more often periods of work absence compared to patients with COPD (16.0% vs 12.8%, p < 0.0001). The number of days absent were, however, less in asthma than in COPD (median: 15 days [IQR: 5–51] vs 39 days [IQR: 13–134], p < 0.001). Patients with asthma–COPD overlap were in between (14.5% with absence; median: 27 days [IQR: 10–82]). Comorbid anxiety, allergic rhinitis, and sleep apnoea were independently associated with more work absence.
Characterizing decoherence rates of a superconducting qubit by direct microwave scattering
Authors: Lu Yong , Bengtsson Andreas , Burnett Jonathan J. , Wiegand Emely , Suri Baladitya , Krantz Philip , Roudsari Anita Fadavi , Kockum Anton Frisk , Gasparinetti Simone , Johansson Göran , Delsing Per 
Published: February 2021

AbstractWe experimentally investigate a superconducting qubit coupled to the end of an open transmission line, in a regime where the qubit decay rates to the transmission line and to its own environment are comparable. We perform measurements of coherent and incoherent scattering, on- and off-resonant fluorescence, and time-resolved dynamics to determine the decay and decoherence rates of the qubit. In particular, these measurements let us discriminate between non-radiative decay and pure dephasing. We combine and contrast results across all methods and find consistent values for the extracted rates. The results show that the pure dephasing rate is one order of magnitude smaller than the non-radiative decay rate for our qubit. Our results indicate a pathway to benchmark decoherence rates of superconducting qubits in a resonator-free setting.
Entanglement formation in continuous-variable random quantum networks
Authors: Zhang Bingzhi , Zhuang Quntao 
Published: February 2021

AbstractEntanglement is not only important for understanding the fundamental properties of many-body systems, but also the crucial resource enabling quantum advantages in practical information processing tasks. Although previous works on quantum networks focus on discrete-variable systems, light—as the only traveling carrier of quantum information in a network—is bosonic and thus requires a continuous-variable description. We extend the study to continuous-variable quantum networks. By mapping the ensemble-averaged entanglement dynamics on an arbitrary network to a random-walk process on a graph, we are able to exactly solve the entanglement dynamics. We identify squeezing as the source of entanglement generation, which triggers a diffusive spread of entanglement with a "parabolic light cone”. A surprising linear superposition law in the entanglement growth is predicted by the theory and numerically verified, despite the nonlinear nature of the entanglement dynamics. The equilibrium entanglement distribution (Page curves) is exactly solved and has various shapes depending on the average squeezing density and strength.
Immunomodulation for optimal cardiac regeneration: insights from comparative analyses
Authors: Farache Trajano Luiza , Smart Nicola 
Published: February 2021

AbstractDespite decades of research, regeneration of the infarcted human heart remains an unmet ambition. A significant obstacle facing experimental regenerative therapies is the hostile immune response which arises following a myocardial infarction (MI). Upon cardiac damage, sterile inflammation commences via the release of pro-inflammatory meditators, leading to the migration of neutrophils, eosinophils and monocytes, as well as the activation of local vascular cells and fibroblasts. This response is amplified by components of the adaptive immune system. Moreover, the physical trauma of the infarction and immune-mediated tissue injury provides a supply of autoantigens, perpetuating a cycle of autoreactivity, which further contributes to adverse remodelling. A gradual shift towards an immune-resolving environment follows, culminating in the formation of a collagenous scar, which compromises cardiac function, ultimately driving the development of heart failure. Comparing the human heart with those of animal models that are capable of cardiac regeneration reveals key differences in the innate and adaptive immune responses to MI. By modulating key immune components to better resemble those of regenerative species, a cardiac environment may be established which would, either independently or via the synergistic application of emerging regenerative therapies, improve functional recovery post-MI.
Adaptation of the small intestine to microbial enteropathogens in Zambian children with stunting
Authors: Amadi Beatrice , Zyambo Kanekwa , Chandwe Kanta , Besa Ellen , Mulenga Chola , Mwakamui Simutanyi , Siyumbwa Stepfanie , Croft Sophie , Banda Rose , Chipunza Miyoba , Chifunda Kapula , Kazhila Lydia , VanBuskirk Kelley , Kelly Paul 
Published: February 2021

AbstractEnvironmental enteropathy is a major contributor to growth faltering in millions of children in Africa and South Asia. We carried out a longitudinal, observational and interventional study in Lusaka, Zambia, of 297 children with stunting (aged 2–17 months at recruitment) and 46 control children who had good growth (aged 1–5 months at recruitment). Control children contributed data only at baseline. Children were provided with nutritional supplementation of daily cornmeal-soy blend, an egg and a micronutrient sprinkle, and were followed up to 24 months of age. Children whose growth did not improve over 4–6 months of nutritional supplementation were classified as having non-responsive stunting. We monitored microbial translocation from the gut lumen to the bloodstream in the cohort with non-responsive stunting (n = 108) by measuring circulating lipopolysaccharide (LPS), LPS-binding protein and soluble CD14 at baseline and when non-response was declared. We found that microbial translocation decreased with increasing age, such that LPS declined in 81 (75%) of 108 children with non-responsive stunting, despite sustained pathogen pressure and ongoing intestinal epithelial damage. We used confocal laser endomicroscopy and found that mucosal leakiness also declined with age. However, expression of brush border enzyme, nutrient transporter and mucosal barrier genes in intestinal biopsies did not change with age or correlate with biomarkers of microbial translocation. We propose that environmental enteropathy arises through adaptation to pathogen-mediated epithelial damage. Although environmental enteropathy reduces microbial translocation, it does so at the cost of impaired growth. The reduced epithelial surface area imposed by villus blunting may explain these findings.
GDIS, a global dataset of geocoded disaster locations
Authors: Rosvold Elisabeth L. , Buhaug Halvard 
Published: February 2021

AbstractThis article presents a new open source extension to the Emergency Events Database (EM-DAT) that allows researchers, for the first time, to explore and make use of subnational, geocoded data on major disasters triggered by natural hazards. The Geocoded Disasters (GDIS) dataset provides spatial geometry in the form of GIS polygons and centroid latitude and longitude coordinates for each administrative entity listed as a disaster location in the EM-DAT database. In total, GDIS contains spatial information on 39,953 locations for 9,924 unique disasters occurring worldwide between 1960 and 2018. The dataset facilitates connecting the EM-DAT database to other geographic data sources on the subnational level to enable rigorous empirical analyses of disaster determinants and impacts.
The quality of life of children with neurodevelopmental disorders and their parents during the Coronavirus disease 19 emergency in Japan
Authors: Ueda Riyo , Okada Takashi , Kita Yosuke , Ozawa Yuri , Inoue Hisami , Shioda Mutsuki , Kono Yoshimi , Kono Chika , Nakamura Yukiko , Amemiya Kaoru , Ito Ai , Sugiura Nobuko , Matsuoka Yuichiro , Kaiga Chinami , Kubota Masaya , Ozawa Hiroshi 
Published: February 2021

AbstractThis study aimed to reveal how the COVID-19 stay-at-home period has affected the quality of life (QOL) of children with neurodevelopmental disorders and their parents and to identify possible factors that enabled them to maintain their QOL. We enrolled 136 school-aged children (intellectual quotient ≥ 50) and their parents and administered QOL questionnaires to assess the maladaptive behavior of the children; depression, anxiety, and stress of the parents; and activities of their daily lives. The relationship between their QOL and clinical features was examined. The decrease in QOL of children and parents was associated with the mother’s limited job flexibility. Decreased QOL was also associated with changes in the sleep rhythms of the children. Maladaptive behaviors in children were associated with parental stress. However, maintained QOL of some families who faced these same conditions of job stress and sleep disorders was associated with less parental stress, less parental depression and anxiety, and milder maladaptive behavior in children. Both mothers with limited job flexibility and changes in the sleep rhythm of children were associated with reduced QOL of children and their parents. Low parental stress was associated with decreased maladaptive behavior in children and with maintained QOL of the family.
Optimal fishing effort benefits fisheries and conservation
Authors: Rees Adam , Sheehan Emma V. , Attrill Martin J. 
Published: February 2021

AbstractThe ecosystem effects of all commercial fishing methods need to be fully understood in order to manage our marine environments more effectively. The impacts associated with the most damaging mobile fishing methods are well documented leading to such methods being removed from some partially protected areas. In contrast, the impacts on the ecosystem from static fishing methods, such as pot fishing, are less well understood. Despite commercial pot fishing increasing within the UK, there are very few long term studies (> 1 year) that consider the effects of commercial pot fishing on temperate marine ecosystems. Here we present the results from a controlled field experiment where areas of temperate reef were exposed to a pot fishing density gradient over 4 years within a Marine Protected Area (MPA), simulating scenarios both above and below current levels of pot fishing effort. After 4 years we demonstrate for the first time negative effects associated with high levels of pot fishing effort both on reef building epibiota and commercially targeted species, contrary to existing evidence. Based on this new evidence we quantify a threshold for sustainable pot fishing demonstrating a significant step towards developing well-managed pot fisheries within partially protected temperate MPAs.
A rapid screening model for early predicting novel coronavirus pneumonia in Zhejiang Province of China: a multicenter study
Authors: Dai Yi-Ning , Zheng Wei , Wu Qing-Qing , Hui Tian-Chen , Sun Nan-Nan , Chen Guo-Bo , Tong Yong-Xi , Bao Su-Xia , Wu Wen-Hao , Huang Yi-Cheng , Yin Qiao-Qiao , Wu Li-Juan , Yu Li-Xia , Shi Ji-Chan , Fang Nian , Shen Yue-Fei , Xie Xin-Sheng , Ma Chun-Lian , Yu Wan-Jun , Tu Wen-Hui , Yan Rong , Wang Ming-Shan , Chen Mei-Juan , Zhang Jia-Jie , Ju Bin , Gao Hai-Nv , Huang Hai-Jun , Li Lan-Juan , Pan Hong-Ying 
Published: February 2021

AbstractNovel coronavirus pneumonia (NCP) has been widely spread in China and several other countries. Early finding of this pneumonia from huge numbers of suspects gives clinicians a big challenge. The aim of the study was to develop a rapid screening model for early predicting NCP in a Zhejiang population, as well as its utility in other areas. A total of 880 participants who were initially suspected of NCP from January 17 to February 19 were included. Potential predictors were selected via stepwise logistic regression analysis. The model was established based on epidemiological features, clinical manifestations, white blood cell count, and pulmonary imaging changes, with the area under receiver operating characteristic (AUROC) curve of 0.920. At a cut-off value of 1.0, the model could determine NCP with a sensitivity of 85% and a specificity of 82.3%. We further developed a simplified model by combining the geographical regions and rounding the coefficients, with the AUROC of 0.909, as well as a model without epidemiological factors with the AUROC of 0.859. The study demonstrated that the screening model was a helpful and cost-effective tool for early predicting NCP and had great clinical significance given the high activity of NCP.