bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights from genomes and genetic epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh
Authors: Roja Rani Pallavali , Imran Mohamed , Lakshmi J. Vijaya , Jolly Bani , Afsar S. , Jain Abhinav , Divakar Mohit Kumar , Suresh Panyam , Sharma Disha , Rajesh Nambi , Bhoyar Rahul C. , Ankaiah Dasari , Shanthi Kumari Sanaga , Ranjan Gyan , Anitha Lavanya Valluri , Rophina Mercy , Umadevi S. , Sehgal Paras , Renuka Devi Avula , Surekha A. , Chandra Sekhar Pulala , Hymavathy Rajamadugu , Vanaja P.R. , Scaria Vinod , Sivasubbu Sridhar 
Published: August 2021

Abstract
Coronavirus disease 2019 (COVID-19) emerged from a city in China and has now spread as a global pandemic affecting millions of individuals. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is being extensively studied in terms of its genetic epidemiology using genomic approaches. Andhra Pradesh is one of the major states of India with the third-largest number of COVID-19 cases with a limited understanding of its genetic epidemiology. In this study, we have sequenced 293 SARS-CoV-2 genome isolates from Andhra Pradesh with a mean coverage of 13324X. We identified 564 high-quality SARS-CoV-2 variants. A total of 18 variants mapped to reverse transcription polymerase chain reaction primer/probe sites, and four variants are known to be associated with an increase in infectivity. Phylogenetic analysis of the genomes revealed the circulating SARS-CoV-2 in Andhra Pradesh majorly clustered under the clade A2a (20A, 20B and 20C) (94%), whereas 6% fall under the I/A3i clade, a clade previously defined to be present in large numbers in India. To the best of our knowledge, this is the most comprehensive genetic epidemiological analysis performed for the state of Andhra Pradesh.
Sorting out the aid–corruption nexus
Authors: Pavlik Jamie Bologna , Young Andrew T. 
Published: August 2021

AbstractWe employ matching methods to explore the relationships between foreign aid flows and corruption in recipient countries. Data are drawn from recipients of foreign aid for the 1996–2013 period. We find no compelling evidence of an effect running from corruption to aid flows. Furthermore, point estimates imply that corruption reforms lead countries to receive less aid. Alternatively, we generally find that, over a 10-year horizon, a sustained increase in aid leads to more corruption in a recipient. It is the sustained nature of an aid increase that seems to be important for this effect. (We generally do not report significant results for large changes in aid that are not sustained over time.)
Genetic Susceptibility to Pneumonia: A GWAS Meta-Analysis Between the UK Biobank and FinnGen
Authors: Campos Adrian I. , Kho Pik , Vazquez-Prada Karla X. , García-Marín Luis M. , Martin Nicholas G. , Cuéllar-Partida Gabriel , Rentería Miguel E. 
Published: August 2021

AbstractPneumonia is a respiratory condition with complex etiology. Host genetic variation is thought to contribute to individual differences in susceptibility and symptom manifestation. Here, we analyze pneumonia data from the UK Biobank (14,780 cases and 439,096 controls) and FinnGen (9980 cases and 86,519 controls) and perform a genomewide association study meta-analysis. We use gene-based tests, colocalization, genetic correlation, latent causal variable (LCV) and polygenic prediction in an independent Australian sample (N = 5595) to draw insights into the etiology of pneumonia risk. We identify two independent loci on chromosome 15 (lead single-nucleotide polymorphisms rs2009746 and rs76474922) to be associated with pneumonia (p < 5e−8). Gene-based tests revealed 18 genes in chromosomes 15, 16 and 9, including IL127, PBX3, ApoB receptor (APOBR) and smoking related genes CHRNA3/5, statistically associated with pneumonia. We observed genetic correlations between pneumonia and cardiorespiratory, psychiatric and inflammatory related traits. LCV analysis suggests a strong genetic causal relationship with cardiovascular health phenotypes. Polygenic risk scores for pneumonia significantly predicted self-reported pneumonia in an independent sample, albeit with a small effect size (OR = 1.11 95% CI [1.04, 1.19], p < .05). Sensitivity analyses suggested the associations in chromosome 15 are mediated by smoking history, but the associations in chromosomes 16 and 9, and polygenic prediction were robust to adjustment for smoking. Altogether, our results highlight common genetic variants, genes and potential pathways that contribute to individual differences in susceptibility to pneumonia, and advance our understanding of the genetic factors underlying heterogeneity in respiratory medical outcomes.
Geometry of the Décollement Below Eastern Bangladesh and Implications for Seismic Hazard
Authors: Bürgi Paula , Hubbard Judith , Akhter Syed Humayun , Peterson Dana E. 
Published: August 2021

AbstractEastern Bangladesh sits on the seismically active Chittagong‐Myanmar fold and thrust belt (CMFB), a north‐trending accretionary wedge on the eastern side of the India‐Eurasia collision. Earthquakes on the basal décollement and associated thrusts within the CMFB present a hazard to this densely populated region. In this study, we interpret 28 seismic reflection profiles from both published and unpublished sources to constrain the depth of the basal décollement. To convert profiles from the time domain to the depth domain, we integrate sonic log and seismic stacking velocity data to generate time‐velocity relationships for different parts of the CMFB. Our analysis reveals that the décollement is ∼9 km deep in northeast and southeast Bangladesh, but shallows to ∼5 km in east‐central Bangladesh. The décollement has an area of 7.25 × 104 km2 (∼150 × 450 km), making it capable of an Mw 8.5 earthquake. However, the warped geometry of this fault might act as a rupture barrier were a large earthquake to occur on the décollement. Our combined velocity and fault model lay the groundwork for future studies to address seismic segmentation, ground shaking, and rupture modeling in the CMFB. Finally, we use our compiled data set to analyze the evolution of fold kinematics in the CMFB. We observe that folding style and failure mode varies, from mainly ductile deformation in the foreland to mainly brittle in the hinterland. The dual‐failure modes within the CMFB support the hypothesis that a region with ductile deformation may still be capable of seismic behavior.
Interannual Variations of Vegetation Optical Depth are Due to Both Water Stress and Biomass Changes
Authors: Konings Alexandra G. , Holtzman Nataniel M. , Rao Krishna , Xu Liang , Saatchi Sassan S. 
Published: August 2021

AbstractMicrowave radiometry can be used to measure vegetation water content through vegetation optical depth (VOD). VOD can vary due to changes in water stress alone, but also scales with aboveground biomass. Several studies have therefore interpreted VOD temporal anomalies as linearly proportional to biomass anomalies, neglecting the influence of water stress. Here, we explicitly test this assumption using a new annual‐resolution data set of biomass derived from optical, radar, and lidar remote sensing. Both L‐band and X‐band VOD datasets are tested. Although VOD and biomass variations are highly correlated in space, their temporal anomalies are almost uncorrelated. At regional scale, it is as common for VOD anomalies to be more correlated to root‐zone soil moisture anomalies (a proxy for water stress) than to biomass anomalies as for the opposite to occur. Care should therefore be taken when deriving biomass anomalies from VOD, especially in the absence of any large‐scale biomass disturbances.
Assessment of pregnancy dietary intake and association with maternal and neonatal outcomes
Authors: Costanza Jole , Camanni Margherita , Ferrari Maria Maddalena , De Cosmi Valentina , Tabano Silvia , Fontana Laura , Radaelli Tatjana , Privitera Giulia , Alberico Daniela , Colapietro Patrizia , Motta Silvia , Sirchia Silvia , Stampalija Tamara , Tabasso Chiara , Roggero Paola , Parazzini Fabio , Mosca Fabio , Ferrazzi Enrico , Bosari Silvano , Miozzo Monica , Agostoni Carlo 
Published: August 2021

Abstract
Background
Maternal dietary habits are contributors of maternal and fetal health; however, available data are heterogeneous and not conclusive.

Methods
Nutrient intake during pregnancy was assessed in 503 women with uncomplicated pregnancies, using the validated Food Frequency Questionnaire developed by the European Prospective Investigation into Cancer and Nutrition (EPIC-FFQ).

Results
In all, 68% of women had a normal body mass index at the beginning of pregnancy, and 83% of newborns had an appropriate weight for gestational age. Maternal pre-pregnancy body mass index (BMI), gestational weight gain (GWG), and placental weight were independently correlated with birth weight. GWG was not related to the pre-pregnancy BMI. EPIC-FFQ evaluation showed that 30% of women adhered to the European Food Safety Authority (EFSA) ranges for macronutrient intake. In most pregnant women (98.1%), consumption of water was below recommendations. Comparing women with intakes within EFSA ranges for macronutrients with those who did not, no differences were found in BMI, GWG, and neonatal or placental weight. Neither maternal nor neonatal parameters were associated with the maternal dietary profiles.

Conclusions
In our population, maternal pre-pregnancy BMI, GWG, and placental weight are determinants of birth weight percentile, while no association was found with maternal nutrition. Future studies should explore associations through all infancy.

Impact

Maternal anthropometrics and nutrition status may affect offspring birth weight.

In 503 healthy women, maternal pre-pregnancy body mass index (BMI), gestational weight gain (GWG), and placental weight were independently correlated to neonatal birth weight. GWG was not related to the pre-pregnancy BMI. In all, 30% of women respected the EFSA ranges for macronutrients. Neither maternal nor neonatal parameters were associated with maternal dietary profiles considered in this study.

Maternal pre-pregnancy BMI, GWG, and placental weight are determinants of neonatal birth weight percentile, while a connection with maternal nutrition profiles was not found.
Alternatively spliced ANLN isoforms synergistically contribute to the progression of head and neck squamous cell carcinoma
Authors: Guo Erliang , Mao Xionghui , Wang Xueying , Guo Lunhua , An Changming , Zhang Cong , Song Kaibin , Wang Guohui , Duan Chunbin , Zhang Xiwei , Yang Xianguang , Yuan Zhennan , Sun Ji , Li Xiaomei , Yang Weiwei , Meng Hongxue , Miao Susheng 
Published: August 2021

AbstractHead and neck squamous cell carcinoma (HNSCC) is a common cancer with high mortality. Anilin actin-binding protein (ANLN) has been reported to be associated with carcinogenesis in multiple tumors. However, the expression pattern and functional effects of ANLN in HNSCC remain to be unclear. Clinical data and online databases were used to analyze the expression of ANLN and its relationship with HNSCC patient survival. Expression of two major splice variants of ANLN was assessed in HNSCC tissues and cell lines. The functional effects and related mechanisms of ANLN isoforms were investigated in HNSCC in vitro and in vivo. Our study showed that patients with high expression of ANLN had a poor prognosis. The two primary isoforms of ANLN transcripts ANLN-201 and ANLN-210 were highly expressed in HNSCC tissues and cell lines. Knockout of ANLN restrained cell proliferation, migration, and invasion of SCC-9 cells. Mechanically, ANLN-201 could interact with c-Myc to keep its protein stability, thereby playing a oncogenic role in HNSCC. ANLN-210 could be transferred to macrophages via exosomes by binding to RNA-binding protein hnRNPC. Exosomal ANLN-210 promoted macrophage polarization via PTEN/PI3K/Akt signaling pathway, thus stimulating tumor growth of HNSCC. ANLN was an independent prognostic factor in patients with HNSCC. Alternatively spliced ANLN isoforms collaboratively promote HNSCC tumorigenesis in vitro and in vivo, which might provide the in-depth role and mechanism of ANLN in HNSCC development.
Interleukin-17A regulates ependymal cell proliferation and functional recovery after spinal cord injury in mice
Authors: Miyajima Hisao , Itokazu Takahide , Tanabe Shogo , Yamashita Toshihide 
Published: August 2021

AbstractEpendymal cells have been suggested to act as neural stem cells and exert beneficial effects after spinal cord injury (SCI). However, the molecular mechanism underlying ependymal cell regulation after SCI remains unknown. To examine the possible effect of IL-17A on ependymal cell proliferation after SCI, we locally administrated IL-17A neutralizing antibody to the injured spinal cord of a contusion SCI mouse model, and revealed that IL-17A neutralization promoted ependymal cell proliferation, which was paralleled by functional recovery and axonal reorganization of both the corticospinal tract and the raphespinal tract. Further, to test whether ependymal cell-specific manipulation of IL-17A signaling is enough to affect the outcomes of SCI, we generated ependymal cell-specific conditional IL-17RA-knockout mice and analyzed their anatomical and functional response to SCI. As a result, conditional knockout of IL-17RA in ependymal cells enhanced both axonal growth and functional recovery, accompanied by an increase in mRNA expression of neurotrophic factors. Thus, Ependymal cells may enhance the regenerative process partially by secreting neurotrophic factors, and IL-17A stimulation negatively regulates this beneficial effect. Molecular manipulation of ependymal cells might be a viable strategy for improving functional recovery.
Splicing modulators: on the way from nature to clinic
Authors: Schneider-Poetsch Tilman , Chhipi-Shrestha Jagat Krishna , Yoshida Minoru 
Published: August 2021

AbstractOver the course of more than two decades, natural products isolated from various microorganisms and plants have built the foundation for chemical biology research into the mechanism of pre-mRNA splicing. Hand in hand with advances in scientific methodology small molecule splicing modulators have become powerful tools for investigating, not just the splicing mechanism, but also the cellular effect of altered mRNA processing. Based on thorough structure-activity studies, synthetic analogues have moved on from scientific tool compounds to experimental drugs. With current advances in drug discovery methodology and new means of attacking targets previously thought undruggable, we can expect further advances in both research and therapeutics based on small molecule splicing modulators.
The search for lunar mantle rocks exposed on the surface of the Moon
Authors: Moriarty Daniel P. , Dygert Nick , Valencia Sarah N. , Watkins Ryan N. , Petro Noah E. 
Published: August 2021

AbstractThe lunar surface is ancient and well-preserved, recording Solar System history and planetary evolution processes. Ancient basin-scale impacts excavated lunar mantle rocks, which are expected to remain present on the surface. Sampling these rocks would provide insight into fundamental planetary processes, including differentiation and magmatic evolution. There is contention among lunar scientists as to what lithologies make up the upper lunar mantle, and where they may have been exposed on the surface. We review dynamical models of lunar differentiation in the context of recent experiments and spacecraft data, assessing candidate lithologies, their distribution, and implications for lunar evolution.
Chemical tools for epichaperome-mediated interactome dysfunctions of the central nervous system
Authors: Bolaender Alexander , Zatorska Danuta , He Huazhong , Joshi Suhasini , Sharma Sahil , Digwal Chander S. , Patel Hardik J. , Sun Weilin , Imber Brandon S. , Ochiana Stefan O. , Patel Maulik R. , Shrestha Liza , Shah Smit. K. , Wang Shuo , Karimov Rashad , Tao Hui , Patel Pallav D. , Martin Ananda Rodilla , Yan Pengrong , Panchal Palak , Almodovar Justina , Corben Adriana , Rimner Andreas , Ginsberg Stephen D. , Lyashchenko Serge , Burnazi Eva , Ku Anson , Kalidindi Teja , Lee Sang Gyu , Grkovski Milan , Beattie Bradley J. , Zanzonico Pat , Lewis Jason S. , Larson Steve , Rodina Anna , Pillarsetty Nagavarakishore , Tabar Viviane , Dunphy Mark P. , Taldone Tony , Shimizu Fumiko , Chiosis Gabriela 
Published: August 2021

AbstractDiseases are a manifestation of how thousands of proteins interact. In several diseases, such as cancer and Alzheimer’s disease, proteome-wide disturbances in protein-protein interactions are caused by alterations to chaperome scaffolds termed epichaperomes. Epichaperome-directed chemical probes may be useful for detecting and reversing defective chaperomes. Here we provide structural, biochemical, and functional insights into the discovery of epichaperome probes, with a focus on their use in central nervous system diseases. We demonstrate on-target activity and kinetic selectivity of a radiolabeled epichaperome probe in both cells and mice, together with a proof-of-principle in human patients in an exploratory single group assignment diagnostic study (ClinicalTrials.gov Identifier: NCT03371420). The clinical study is designed to determine the pharmacokinetic parameters and the incidence of adverse events in patients receiving a single microdose of the radiolabeled probe administered by intravenous injection. In sum, we introduce a discovery platform for brain-directed chemical probes that specifically modulate epichaperomes and provide proof-of-principle applications in their use in the detection, quantification, and modulation of the target in complex biological systems.
Time-varying optimization of COVID-19 vaccine prioritization in the context of limited vaccination capacity
Authors: Han Shasha , Cai Jun , Yang Juan , Zhang Juanjuan , Wu Qianhui , Zheng Wen , Shi Huilin , Ajelli Marco , Zhou Xiao-Hua , Yu Hongjie 
Published: August 2021

AbstractDynamically adapting the allocation of COVID-19 vaccines to the evolving epidemiological situation could be key to reduce COVID-19 burden. Here we developed a data-driven mechanistic model of SARS-CoV-2 transmission to explore optimal vaccine prioritization strategies in China. We found that a time-varying vaccination program (i.e., allocating vaccines to different target groups as the epidemic evolves) can be highly beneficial as it is capable of simultaneously achieving different objectives (e.g., minimizing the number of deaths and of infections). Our findings suggest that boosting the vaccination capacity up to 2.5 million first doses per day (0.17% rollout speed) or higher could greatly reduce COVID-19 burden, should a new wave start to unfold in China with reproduction number ≤1.5. The highest priority categories are consistent under a broad range of assumptions. Finally, a high vaccination capacity in the early phase of the vaccination campaign is key to achieve large gains of strategic prioritizations.
Cognitive functions and underlying parameters of human brain physiology are associated with chronotype
Authors: Salehinejad Mohammad Ali , Wischnewski Miles , Ghanavati Elham , Mosayebi-Samani Mohsen , Kuo Min-Fang , Nitsche Michael A. 
Published: August 2021

AbstractCircadian rhythms have natural relative variations among humans known as chronotype. Chronotype or being a morning or evening person, has a specific physiological, behavioural, and also genetic manifestation. Whether and how chronotype modulates human brain physiology and cognition is, however, not well understood. Here we examine how cortical excitability, neuroplasticity, and cognition are associated with chronotype in early and late chronotype individuals. We monitor motor cortical excitability, brain stimulation-induced neuroplasticity, and examine motor learning and cognitive functions at circadian-preferred and non-preferred times of day in 32 individuals. Motor learning and cognitive performance (working memory, and attention) along with their electrophysiological components are significantly enhanced at the circadian-preferred, compared to the non-preferred time. This outperformance is associated with enhanced cortical excitability (prominent cortical facilitation, diminished cortical inhibition), and long-term potentiation/depression-like plasticity. Our data show convergent findings of how chronotype can modulate human brain functions from basic physiological mechanisms to behaviour and higher-order cognition.
Cerebral malaria: insight into pathology from optical coherence tomography
Authors: Tu Zhanhan , Gormley Jack , Sheth Viral , Seydel Karl B. , Taylor Terrie , Beare Nicholas , Barrera Valentina , Proudlock Frank A. , Manda Chatonda , Harding Simon , Gottlob Irene 
Published: August 2021

AbstractWe aimed to investigate structural retinal changes in malarial retinopathy (MR) using hand-held optical coherence tomography (HH-OCT) to assess its diagnostic potential. Children with MR (n = 43) underwent ophthalmoscopy, fluorescein angiography and HH-OCT during admission, 1-month (n = 31) and 1-year (n = 8) post-discharge. Controls were comatose patients without malaria (n = 6) and age/sex-matched healthy children (n = 43). OCT changes and retinal layer thicknesses were compared. On HH-OCT, hyper-reflective areas (HRAs) were seen in the inner retina of 81% of MR patients, corresponding to ischaemic retinal whitening on fundus photography. Cotton wool spots were present in 37% and abnormal hyper-reflective dots, co-localized to capillary plexus, in 93%. Hyper-reflective vessel walls were present in 84%, and intra-retinal cysts in 9%. Vascular changes and cysts resolved within 48 h. HRAs developed into retinal thinning at 1 month (p = 0.027) which was more pronounced after 1 year (p = 0.009). Ischaemic retinal whitening is located within inner retinal layers, distinguishing it from cotton wool spots. Vascular hyper-reflectivity may represent the sequestration of parasitized erythrocytes in vessels, a key CM feature. The mechanisms of post-ischemic retinal atrophy and cerebral atrophy with cognitive impairment may be similar in CM survivors. HH-OCT has the potential for monitoring patients, treatment response and predicting neurological deficits.
Hazardous base surges of Taal’s 2020 eruption
Authors: Lagmay A. M. F. , Balangue-Tarriela M. I. R. , Aurelio M. , Ybanez R. , Bonus-Ybanez A. , Sulapas J. , Baldago C. , Sarmiento D. M. , Cabria H. , Rodolfo R. , Rafael D. J. , Trinidad J. R. , Obille E. , Rosell N. 
Published: August 2021

AbstractAfter 43 years of repose, Taal Volcano erupted on 12 January 2020 forming hazardous base surges. Using field, remote sensing (i.e. UAV and LiDAR), and numerical methods, we gathered primary data to generate well-constrained observed information on dune bedform characteristics, impact dynamic pressures and velocities of base surges. This is to advance our knowledge on this type of hazard to understand and evaluate its consequences and risks. The dilute and wet surges traveled at 50-60 ms−1 near the crater rim and decelerated before making impact on coastal communities with dynamic pressures of at least 1.7 kPa. The base surges killed more than a thousand livestock in the southeast of Taal Volcano Island, and then traveled another ~ 600 m offshore. This work is a rare document of a complete, fresh, and practically undisturbed base surge deposit, important in the study of dune deposits formed by volcanic and other processes on Earth and other planets.