bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of COVID‐19 Pandemic Lockdown in Ambient Concentrations of Aromatic Volatile Organic Compounds in a Metropolitan City of Western India
Authors: Sahu L. K. , Tripathi Nidhi , Gupta Mansi , Singh Vikas , Yadav Ravi , Patel Kashyap 
Published: March 2022

AbstractThe real‐time Benzene, Toluene, Ethylbenzene, and Xylenes (BTEX) concentrations were measured in a metropolitan city of India during January to May of 2020 and 2014‐2015‐2018 to assess the impact of emission reduction during the COVID‐19 lockdown. The total BTEX (∑BTEX) concentrations were 11.5 ± 9.0, 15.7 ± 16, 5.3 ± 5.0, 2.9 ± 2.0, and 0.93 ± 1.2 ppbv in January–May 2020, respectively. The evening rush hour peaks of BTEX during lockdown decreased by 4–5 times from the same period of years 2014‐2015‐2018. A significant decline in background concentrations suggests a regional‐scale reduction in anthropogenic emissions. The contributions of ∑TEX compounds to ∑BTEX increased from 42% to 59% in winter to 64%–75% during the lockdown under hot summer conditions. While emission reductions dominated during the lockdown period, the meteorological and photochemical factors may also have contributed. Meteorological influence on actual observed BTEX data was removed by normalizing with ventilation coefficient (VC). The actual ambient air reductions of 85%–90% and VC‐normalized reductions of 54%–88% of the BTEX concentrations during lockdown were estimated compared to those during the same period of 2014‐2015‐2018. The estimated changes using nighttime data, which take into account BTEX photooxidation removal, are ∼8% lower than the VC‐normalized estimates using all data. These significant reductions in BTEX concentrations are consistent with the change in people's movement as inferred from mobility data during the lockdown. Although enforced, the significant decline in ambient BTEX levels during lockdown was a good change for the air quality. The study suggests a need for more effective science‐based policies that consider local and regional factors.
Preventing autosomal-dominant hearing loss in Bth mice with CRISPR/CasRx-based RNA editing
Authors: Zheng Ziwen , Li Guo , Cui Chong , Wang Fang , Wang Xiaohan , Xu Zhijiao , Guo Huiping , Chen Yuxin , Tang Honghai , Wang Daqi , Huang Mingqian , Chen Zheng-Yi , Huang Xingxu , Li Huawei , Li Geng-Lin , Hu Xiaoxiang , Shu Yilai 
Published: March 2022

AbstractCRISPR/RfxCas13d (CasRx) editing system can specifically and precisely cleave single-strand RNAs, which is a promising treatment for various disorders by downregulation of related gene expression. Here, we tested this RNA-editing approach on Beethoven (Bth) mice, an animal model for human DFNA36 due to a point mutation in Tmc1. We first screened 30 sgRNAs in cell cultures and found that CasRx with sgRNA3 reduced the Tmc1Bth transcript by 90.8%, and the Tmc1 wild type transcript (Tmc1+) by 44.3%. We then injected a newly developed AAV vector (AAV-PHP.eB) based CasRx into the inner ears of neonatal Bth mice, and we found that Tmc1Bth was reduced by 70.2% in 2 weeks with few off-target effects in the whole transcriptome. Consistently, we found improved hair cell survival, rescued hair bundle degeneration, and reduced mechanoelectrical transduction current. Importantly, the hearing performance, measured in both ABR and DPOAE thresholds, was improved significantly in all ages over 8 weeks. We, therefore, have validated the CRISPR/CasRx-based RNA editing strategy in treating autosomal-dominant hearing loss, paving way for its further application in many other hereditary diseases in hearing and beyond.
Plasma proteomic and metabolomic characterization of COVID-19 survivors 6 months after discharge
Authors: Li Hongwei , Li Xue , Wu Qian , Wang Xing , Qin Zhonghua , Wang Yaguo , He Yanbin , Wu Qi , Li Li , Chen Huaiyong 
Published: March 2022

AbstractCoronavirus disease 2019 (COVID-19) has gained prominence as a global pandemic. Studies have suggested that systemic alterations persist in a considerable proportion of COVID-19 patients after hospital discharge. We used proteomic and metabolomic approaches to analyze plasma samples obtained from 30 healthy subjects and 54 COVID-19 survivors 6 months after discharge from the hospital, including 30 non-severe and 24 severe patients. Through this analysis, we identified 1019 proteins and 1091 metabolites. The differentially expressed proteins and metabolites were then subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Among the patients evaluated, 41% of COVID-19 survivors reported at least one clinical symptom and 26.5% showed lung imaging abnormalities at 6 months after discharge. Plasma proteomics and metabolomics analysis showed that COVID-19 survivors differed from healthy control subjects in terms of the extracellular matrix, immune response, and hemostasis pathways. COVID-19 survivors also exhibited abnormal lipid metabolism, disordered immune response, and changes in pulmonary fibrosis-related proteins. COVID-19 survivors show persistent proteomic and metabolomic abnormalities 6 months after discharge from the hospital. Hence, the recovery period for COVID-19 survivors may be longer.
βIV-spectrin as a stalk cell-intrinsic regulator of VEGF signaling
Authors: Kwak Eun-A , Pan Christopher C. , Ramonett Aaron , Kumar Sanjay , Cruz-Flores Paola , Ahmed Tasmia , Ortiz Hannah R. , Lochhead Jeffrey J. , Ellis Nathan A. , Mouneimne Ghassan , Georgieva Teodora G. , Lee Yeon Sun , Vanderah Todd W. , Largent-Milnes Tally , Mohler Peter J. , Hund Thomas J. , Langlais Paul R. , Mythreye Karthikeyan , Lee Nam Y. 
Published: March 2022

AbstractDefective angiogenesis underlies over 50 malignant, ischemic and inflammatory disorders yet long-term therapeutic applications inevitably fail, thus highlighting the need for greater understanding of the vast crosstalk and compensatory mechanisms. Based on proteomic profiling of angiogenic endothelial components, here we report βIV-spectrin, a non-erythrocytic cytoskeletal protein, as a critical regulator of sprouting angiogenesis. Early loss of endothelial-specific βIV-spectrin promotes embryonic lethality in mice due to hypervascularization and hemorrhagic defects whereas neonatal depletion yields higher vascular density and tip cell populations in developing retina. During sprouting, βIV-spectrin expresses in stalk cells to inhibit their tip cell potential by enhancing VEGFR2 turnover in a manner independent of most cell-fate determining mechanisms. Rather, βIV-spectrin recruits CaMKII to the plasma membrane to directly phosphorylate VEGFR2 at Ser984, a previously undefined phosphoregulatory site that strongly induces VEGFR2 internalization and degradation. These findings support a distinct spectrin-based mechanism of tip-stalk cell specification during vascular development.
Alpine permafrost could account for a quarter of thawed carbon based on Plio-Pleistocene paleoclimate analogue
Authors: Cheng Feng , Garzione Carmala , Li Xiangzhong , Salzmann Ulrich , Schwarz Florian , Haywood Alan M. , Tindall Julia , Nie Junsheng , Li Lin , Wang Lin , Abbott Benjamin W. , Elliott Ben , Liu Weiguo , Upadhyay Deepshikha , Arnold Alexandrea , Tripati Aradhna 
Published: March 2022

AbstractEstimates of the permafrost-climate feedback vary in magnitude and sign, partly because permafrost carbon stability in warmer-than-present conditions is not well constrained. Here we use a Plio-Pleistocene lacustrine reconstruction of mean annual air temperature (MAAT) from the Tibetan Plateau, the largest alpine permafrost region on the Earth, to constrain past and future changes in permafrost carbon storage. Clumped isotope-temperatures (Δ47-T) indicate warmer MAAT (~1.2 °C) prior to 2.7 Ma, and support a permafrost-free environment on the northern Tibetan Plateau in a warmer-than-present climate. Δ47-T indicate ~8.1 °C cooling from 2.7 Ma, coincident with Northern Hemisphere glacial intensification. Combined with climate models and global permafrost distribution, these results indicate, under conditions similar to mid-Pliocene Warm period (3.3–3.0 Ma), ~60% of alpine permafrost containing ~85 petagrams of carbon may be vulnerable to thawing compared to ~20% of circumarctic permafrost. This estimate highlights ~25% of permafrost carbon and the permafrost-climate feedback could originate in alpine areas.
Extended topological valley-locked surface acoustic waves
Authors: Wang Ji-Qian , Zhang Zi-Dong , Yu Si-Yuan , Ge Hao , Liu Kang-Fu , Wu Tao , Sun Xiao-Chen , Liu Le , Chen Hua-Yang , He Cheng , Lu Ming-Hui , Chen Yan-Feng 
Published: March 2022

AbstractStable and efficient guided waves are essential for information transmission and processing. Recently, topological valley-contrasting materials in condensed matter systems have been revealed as promising infrastructures for guiding classical waves, for they can provide broadband, non-dispersive and reflection-free electromagnetic/mechanical wave transport with a high degree of freedom. In this work, by designing and manufacturing miniaturized phononic crystals on a semi-infinite substrate, we experimentally realized a valley-locked edge transport for surface acoustic waves (SAWs). Critically, original one-dimensional edge transports could be extended to quasi-two-dimensional ones by doping SAW Dirac “semimetal” layers at the boundaries. We demonstrate that SAWs in the extended topological valley-locked edges are robust against bending and wavelength-scaled defects. Also, this mechanism is configurable and robust depending on the doping, offering various on-chip acoustic manipulation, e.g., SAW routing, focusing, splitting, and converging, all flexible and high-flow. This work may promote future hybrid phononic circuits for acoustic information processing, sensing, and manipulation.
Microfluidic manipulation by spiral hollow-fibre actuators
Authors: Li Sitong , Zhang Rui , Zhang Guanghao , Shuai Luyizheng , Chang Wang , Hu Xiaoyu , Zou Min , Zhou Xiang , An Baigang , Qian Dong , Liu Zunfeng 
Published: March 2022

AbstractA microfluidic manipulation system that can sense a liquid and control its flow is highly desirable. However, conventional sensors and motors have difficulty fitting the limited space in microfluidic devices; moreover, fast sensing and actuation are required because of the fast liquid flow in the hollow fibre. In this study, fast torsional and tensile actuators were developed using hollow fibres employing spiral nonlinear stress, which can sense the fluid temperature and sort the fluid into the desired vessels. The fluid-driven actuation exhibited a highly increased response speed (27 times as fast as that of air-driven actuation) and increased power density (90 times that of an air-driven solid fibre actuator). A 0.5 K fluid temperature fluctuation produced a 20° rotation of the hollow fibre. These high performances originated from increments in both heat transfer and the average bias angle, which was understood through theoretical analysis. This work provides a new design strategy for intelligent microfluidics and inspiration for soft robots and smart devices for biological, optical, or magnetic applications.
PanCancer analysis of somatic mutations in repetitive regions reveals recurrent mutations in snRNA U2
Authors: Bousquets-Muñoz Pablo , Díaz-Navarro Ander , Nadeu Ferran , Sánchez-Pitiot Ana , López-Tamargo Sara , Shuai Shimin , Balbín Milagros , Tubio Jose M. C. , Beà Sílvia , Martin-Subero Jose I. , Gutiérrez-Fernández Ana , Stein Lincoln D. , Campo Elías , Puente Xose S. 
Published: March 2022

AbstractCurrent somatic mutation callers are biased against repetitive regions, preventing the identification of potential driver alterations in these loci. We developed a mutation caller for repetitive regions, and applied it to study repetitive non protein-coding genes in more than 2200 whole-genome cases. We identified a recurrent mutation at position c.28 in the gene encoding the snRNA U2. This mutation is present in B-cell derived tumors, as well as in prostate and pancreatic cancer, suggesting U2 c.28 constitutes a driver candidate associated with worse prognosis. We showed that the GRCh37 reference genome is incomplete, lacking the U2 cluster in chromosome 17, preventing the identification of mutations in this gene. Furthermore, the 5′-flanking region of WDR74, previously described as frequently mutated in cancer, constitutes a functional copy of U2. These data reinforce the relevance of non-coding mutations in cancer, and highlight current challenges of cancer genomic research in characterizing mutations affecting repetitive genes.
Distinctive pattern of neutrophil count change in clozapine-associated, life-threatening agranulocytosis
Authors: Taylor David , Vallianatou Kalliopi , Whiskey Eromona , Dzahini Olubanke , MacCabe James 
Published: March 2022

AbstractThe wider use of clozapine is limited by the risk of agranulocytosis and the associated requirement for monitoring of neutrophil counts. We searched local electronic patient records for cases of agranulocytosis occurring during clozapine treatment during the period 2007–2020. We found 23 episodes recorded as agranulocytosis in clozapine patients. Of these, nine met pre-defined criteria and were considered episodes of life-threatening agranulocytosis (LTA). These episodes of clozapine-induced LTA exhibited a distinct pattern of continuous and rapid neutrophil count decline to zero or near zero. Mean time for neutrophils to fall from ANC > 2 to ANC <0.5 × 109/L was 8.4 days (range 2–15 days). Each event was also characterised by a prolonged nadir and delayed recovery (range 4–16 days). Non-LTA episodes were, in contrast, brief and benign. We conclude that an important proportion of cases of agranulocytosis identified in people prescribed clozapine are not life-threatening and may not even be clozapine-related. Monitoring schemes should aim to identify true clozapine-induced LTA as opposed to threshold-defined nominal agranulocytosis. Genetics studies might benefit from examining associations with clozapine-induced LTA rather than with recorded cases of agranulocytosis or neutropenia.
Intranasal administration of BReC-CoV-2 COVID-19 vaccine protects K18-hACE2 mice against lethal SARS-CoV-2 challenge
Authors: Wong Ting Y. , Lee Katherine S. , Russ Brynnan P. , Horspool Alexander M. , Kang Jason , Winters Michael T. , Allison Wolf M. , Rader Nathaniel A. , Miller Olivia A. , Shiflett Morgane , Izac Jerilyn , Varisco David , Sen-Kilic Emel , Cunningham Casey , Cooper Melissa , Cyphert Holly A. , Barbier Mariette , Martinez Ivan , Bevere Justin R. , Ernst Robert K. , Damron F. Heath 
Published: March 2022

AbstractSARS-CoV-2 is a viral respiratory pathogen responsible for the current global pandemic and the disease that causes COVID-19. All current WHO approved COVID-19 vaccines are administered through the muscular route. We have developed a prototype two-dose vaccine (BReC-CoV-2) by combining the Receptor Binding Domain (RBD) antigen, via conjugation to Diphtheria toxoid (EcoCRM®). The vaccine is adjuvanted with Bacterial Enzymatic Combinatorial Chemistry (BECC), BECC470. Intranasal (IN) administration of BreC-CoV-2 in K18-hACE2 mice induced a strong systemic and localized immune response in the respiratory tissues which provided protection against the Washington strain of SARS-CoV-2. Protection provided after IN administration of BReC-CoV-2 was associated with decreased viral RNA copies in the lung, robust RBD IgA titers in the lung and nasal wash, and induction of broadly neutralizing antibodies in the serum. We also observed that BReC-CoV-2 vaccination administered using an intramuscular (IM) prime and IN boost protected mice from a lethal challenge dose of the Delta variant of SARS-CoV-2. IN administration of BReC-CoV-2 provided better protection than IM only administration to mice against lethal challenge dose of SARS-CoV-2. These data suggest that the IN route of vaccination induces localized immune responses that can better protect against SARS-CoV-2 than the IM route in the upper respiratory tract.
Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape
Authors: Muloi Dishon M. , Wee Bryan A. , McClean Deirdre M. H. , Ward Melissa J. , Pankhurst Louise , Phan Hang , Ivens Alasdair C. , Kivali Velma , Kiyong’a Alice , Ndinda Christine , Gitahi Nduhiu , Ouko Tom , Hassell James M. , Imboma Titus , Akoko James , Murungi Maurice K. , Njoroge Samuel M. , Muinde Patrick , Nakamura Yukiko , Alumasa Lorren , Furmaga Erin , Kaitho Titus , Öhgren Elin M. , Amanya Fredrick , Ogendo Allan , Wilson Daniel J. , Bettridge Judy M. , Kiiru John , Kyobutungi Catherine , Tacoli Cecila , Kang’ethe Erastus K. , Davila Julio D. , Kariuki Samuel , Robinson Timothy P. , Rushton Jonathan , Woolhouse Mark E. J. , Fèvre Eric M. 
Published: March 2022

AbstractQuantitative evidence for the risk of zoonoses and the spread of antimicrobial resistance remains lacking. Here, as part of the UrbanZoo project, we sampledEscherichia colifrom humans, livestock and peri-domestic wildlife in 99 households across Nairobi, Kenya, to investigate its distribution among host species in this rapidly developing urban landscape. We performed whole-genome sequencing of 1,338E. coliisolates and found that the diversity and sharing patterns ofE. coliwere heavily structured by household and strongly shaped by host type. We also found evidence for inter-household and inter-host sharing and, importantly, between humans and animals, although this occurs much less frequently. Resistome similarity was differently distributed across host and household, consistent with being driven by shared exposure to antimicrobials. Our results indicate that a large, epidemiologically structured sampling framework combined with WGS is needed to uncover strain-sharing events among different host populations in complex environments and the major contributing pathways that could ultimately drive the emergence of zoonoses and the spread of antimicrobial resistance.
Dataset of first appearances of the scholarly bibliographic references on Wikipedia articles
Authors: Kikkawa Jiro , Takaku Masao , Yoshikane Fuyuki 
Published: March 2022

AbstractReferencing scholarly documents as information sources on Wikipedia is important because it supports or improves the quality of Wikipedia content. Several studies have been conducted regarding scholarly references on Wikipedia; however, little is known of the editors and their edits contributing to add the scholarly references on Wikipedia. In this study, we develop a methodology to detect the oldest scholarly reference added to Wikipedia articles by which a certain paper is uniquely identifiable as the “first appearance of the scholarly reference.” We identified the first appearances of 923,894 scholarly references (611,119 unique DOIs) in 180,795 unique pages on English Wikipedia as of March 1, 2017 and stored them in the dataset. Moreover, we assessed the precision of the dataset, which was highly precise regardless of the research field. Finally, we demonstrate the potential of our dataset. This dataset is unique and attracts those who are interested in how the scholarly references on Wikipedia grew and which editors added them.
Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9
Authors: Biegler Matthew T. , Fedrigo Olivier , Collier Paul , Mountcastle Jacquelyn , Haase Bettina , Tilgner Hagen U. , Jarvis Erich D. 
Published: March 2022

AbstractThe zebra finch is one of the most commonly studied songbirds in biology, particularly in genomics, neuroscience and vocal communication. However, this species lacks a robust cell line for molecular biology research and reagent optimization. We generated a cell line, designated CFS414, from zebra finch embryonic fibroblasts using the SV40 large and small T antigens. This cell line demonstrates an improvement over previous songbird cell lines through continuous and density-independent growth, allowing for indefinite culture and monoclonal line derivation. Cytogenetic, genomic, and transcriptomic profiling established the provenance of this cell line and identified the expression of genes relevant to ongoing songbird research. Using this cell line, we disrupted endogenous gene sequences using S.aureus Cas9 and confirmed a stress-dependent localization response of a song system specialized gene, SAP30L. The utility of CFS414 cells enhances the comprehensive molecular potential of the zebra finch and validates cell immortalization strategies in a songbird species.
A preliminary study of the diagnostic efficacy and safety of the novel boring biopsy for brain lesions
Authors: Ogiwara Toshihiro , Nitta Junpei , Fujii Yu , Watanabe Gen , Kuwabara Haruki , Agata Masahiro , Kobayashi Hideki , Miyaoka Yoshinari , Kitamura Satoshi , Hanaoka Yoshiki , Goto Tetsuya , Iwaya Mai , Hongo Kazuhiro , Horiuchi Tetsuyoshi 
Published: March 2022

AbstractExisting methods for biopsy of intraparenchymal brain lesions, including stereotactic biopsy and open block biopsy, have advantages and disadvantages. We propose a novel biopsy method, called “boring biopsy,” which aims to overcome the drawbacks of each conventional method. This method is less invasive and allows obtaining continuous specimens of sufficient volume. We aimed to assess the feasibility and efficacy of using boring biopsy for intraparenchymal brain lesions. We included 26 consecutive patients who underwent boring biopsy for intraparenchymal lesions. Columnar continuous specimens from the surface of the normal brain tissue to the tumor margin and the center of the lesion were obtained using the boring biopsy method. We used a catheter introducer with original modifications to create a cylindrical biopsy tool for surgery. Columnar continuous specimens were successfully obtained. Histopathological diagnosis was based on cellular changes and differentiation from normal tissues to the core of the lesion and established in all cases. No permanent deficits, major adverse outcomes, or deaths were observed. This novel technique may improve diagnostic accuracy and reduce invasiveness associated with brain biopsy. This method may become the next standard procedure, particularly in some cases where histological evaluation is paramount, and conventional biopsy methods are not suitable.
Urine autotaxin levels reflect the disease activity of sarcoidosis
Authors: Murakami Koji , Tamada Tsutomu , Saigusa Daisuke , Miyauchi Eisaku , Nara Masayuki , Ichinose Masakazu , Kurano Makoto , Yatomi Yutaka , Sugiura Hisatoshi 
Published: March 2022

AbstractSince the clinical outcome of patients with sarcoidosis is still unpredictable, a good prognostic biomarker is necessary. Autotaxin (ATX) and phosphatidylserine-specific phospholipase A1 (PS-PLA1) function as main enzymes to produce lysophospholipids (LPLs), and these enzymes are attracting attention as useful biomarkers for several chronic inflammatory diseases. Here, we investigated the relationships between LPLs-producing enzymes and the disease activity of sarcoidosis. In total, 157 patients with sarcoidosis (active state, 51%) were consecutively enrolled. Using plasma or urine specimens, we measured the values of LPLs-producing enzymes. Urine ATX (U-ATX) levels were significantly lower in the active state compared to those in the inactive state, while the plasma ATX (P-ATX) and PS-PLA1 levels showed no significant difference between these two states. Concerning the comparison with existing clinical biomarkers for sarcoidosis, U-ATX showed a weak negative correlation to ACE, P-ATX a weak positive correlation to both ACE and sIL-2R, and PS-PLA1 a weak positive one to sIL-2R. Notably, only the U-ATX levels inversely fluctuated depending on the status of disease activity whether OCS had been used or not. These findings suggest that U-ATX is likely to be a novel and useful molecule for assessing the disease activity of sarcoidosis.