bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leveraging genomic diversity for discovery in an electronic health record linked biobank: the UCLA ATLAS Community Health Initiative
Authors: Johnson Ruth , Ding Yi , Venkateswaran Vidhya , Bhattacharya Arjun , Boulier Kristin , Chiu Alec , Knyazev Sergey , Schwarz Tommer , Freund Malika , Zhan Lingyu , Burch Kathryn S. , Caggiano Christa , Hill Brian , Rakocz Nadav , Balliu Brunilda , Denny Christopher T. , Sul Jae Hoon , Zaitlen Noah , Arboleda Valerie A. , Halperin Eran , Sankararaman Sriram , Butte Manish J. ,   UCLA Precision Health Data Discovery Repository Working Group, UCLA Precision Health ATLAS Working Group, Lajonchere Clara , Geschwind Daniel H. , Pasaniuc Bogdan 
Published: September 2022

Abstract
Background
Large medical centers in urban areas, like Los Angeles, care for a diverse patient population and offer the potential to study the interplay between genetic ancestry and social determinants of health. Here, we explore the implications of genetic ancestry within the University of California, Los Angeles (UCLA) ATLAS Community Health Initiative—an ancestrally diverse biobank of genomic data linked with de-identified electronic health records (EHRs) of UCLA Health patients (N=36,736).

Methods
We quantify the extensive continental and subcontinental genetic diversity within the ATLAS data through principal component analysis, identity-by-descent, and genetic admixture. We assess the relationship between genetically inferred ancestry (GIA) and >1500 EHR-derived phenotypes (phecodes). Finally, we demonstrate the utility of genetic data linked with EHR to perform ancestry-specific and multi-ancestry genome and phenome-wide scans across a broad set of disease phenotypes.

Results
We identify 5 continental-scale GIA clusters including European American (EA), African American (AA), Hispanic Latino American (HL), South Asian American (SAA) and East Asian American (EAA) individuals and 7 subcontinental GIA clusters within the EAA GIA corresponding to Chinese American, Vietnamese American, and Japanese American individuals. Although we broadly find that self-identified race/ethnicity (SIRE) is highly correlated with GIA, we still observe marked differences between the two, emphasizing that the populations defined by these two criteria are not analogous. We find a total of 259 significant associations between continental GIA and phecodes even after accounting for individuals’ SIRE, demonstrating that for some phenotypes, GIA provides information not already captured by SIRE. GWAS identifies significant associations for liver disease in the 22q13.31 locus across the HL and EAA GIA groups (HL p-value=2.32×10−16, EAA p-value=6.73×10−11). A subsequent PheWAS at the top SNP reveals significant associations with neurologic and neoplastic phenotypes specifically within the HL GIA group.

Conclusions
Overall, our results explore the interplay between SIRE and GIA within a disease context and underscore the utility of studying the genomes of diverse individuals through biobank-scale genotyping linked with EHR-based phenotyping.
Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury
Authors: Hinze Christian , Kocks Christine , Leiz Janna , Karaiskos Nikos , Boltengagen Anastasiya , Cao Shuang , Skopnik Christopher Mark , Klocke Jan , Hardenberg Jan-Hendrik , Stockmann Helena , Gotthardt Inka , Obermayer Benedikt , Haghverdi Laleh , Wyler Emanuel , Landthaler Markus , Bachmann Sebastian , Hocke Andreas C. , Corman Victor , Busch Jonas , Schneider Wolfgang , Himmerkus Nina , Bleich Markus , Eckardt Kai-Uwe , Enghard Philipp , Rajewsky Nikolaus , Schmidt-Ott Kai M. 
Published: September 2022

Abstract
Background
Acute kidney injury (AKI) occurs frequently in critically ill patients and is associated with adverse outcomes. Cellular mechanisms underlying AKI and kidney cell responses to injury remain incompletely understood.

Methods
We performed single-nuclei transcriptomics, bulk transcriptomics, molecular imaging studies, and conventional histology on kidney tissues from 8 individuals with severe AKI (stage 2 or 3 according to Kidney Disease: Improving Global Outcomes (KDIGO) criteria). Specimens were obtained within 1–2 h after individuals had succumbed to critical illness associated with respiratory infections, with 4 of 8 individuals diagnosed with COVID-19. Control kidney tissues were obtained post-mortem or after nephrectomy from individuals without AKI.

Results
High-depth single cell-resolved gene expression data of human kidneys affected by AKI revealed enrichment of novel injury-associated cell states within the major cell types of the tubular epithelium, in particular in proximal tubules, thick ascending limbs, and distal convoluted tubules. Four distinct, hierarchically interconnected injured cell states were distinguishable and characterized by transcriptome patterns associated with oxidative stress, hypoxia, interferon response, and epithelial-to-mesenchymal transition, respectively. Transcriptome differences between individuals with AKI were driven primarily by the cell type-specific abundance of these four injury subtypes rather than by private molecular responses. AKI-associated changes in gene expression between individuals with and without COVID-19 were similar.

Conclusions
The study provides an extensive resource of the cell type-specific transcriptomic responses associated with critical illness-associated AKI in humans, highlighting recurrent disease-associated signatures and inter-individual heterogeneity. Personalized molecular disease assessment in human AKI may foster the development of tailored therapies.
Evaluation of dynamic F wave parameters before and after physical activity in normal population
Authors: Khosrawi Saeid , Haghighat Shila , Hamedfar Hadi 
Published: September 2022

Abstract
Objectives
F wave is one of the nerve conduction studies, mainly used to study the proximal pathway of peripheral nerves. One of its applications is dynamic assessment, i.e., before and after physical activity, when symptoms develop in some patients. Best to our knowledge, few studies evaluate normal dynamic F wave values in healthy individuals. This study aims to determine and compare normal values of several parameters of Compound Muscle Action Potential (CMAP) and F waves of tibial nerves dynamically before and after physical activity in the lower extremities of 34 normal subjects. These parameters were recorded before and after 15 min of continuous walking at intervals of 1, 5, and 10 min after the end of physical activity.

Results
Normal values of CMAP onset latency and amplitude, minimum, maximum, and mean latency of 10 F waves, F chronodispersion, and F persistence were dynamically collected before and during 10 min after physical activity in three phases. Some of the parameters showed significant changes (P < 0.05). Although physical activity showed statistically significant effects on some CMAP and F wave parameters (especially F chronodispersion) in normal subjects, none of them exceeded the normal clinical values introduced in the literature.
Lactobacillus rhamnosus GR-1 attenuates foodborne Bacillus cereus-induced NLRP3 inflammasome activity in bovine mammary epithelial cells by protecting intercellular tight junctions
Authors: Shan Qiang , Liu Ning , Wang Xue , Zhu Yaohong , Yin Jinhua , Wang Jiufeng 
Published: September 2022

Abstract
Background
Bacillus cereus is an important pathogen that causes human food poisoning, specifically diarrhea and vomiting. B. cereus can also induce mastitis in dairy cows and has a strong survival ability in milk, as it cannot be inactivated by high-temperature short-time pasteurization. Therefore, B. cereus can enter the market through pasteurized milk and other dairy products, imposing enormous hidden dangers on food safety and human health.

Results
In this study, B. cereus 2101 (BC) was isolated from milk samples of cows with mastitis. BC grew rapidly with strong hemolysis, making it difficult to prevent mastitis and ensure food security. MAC-T cells were treated with BC and/or Lactobacillus rhamnosus GR-1 (LGR-1). Pretreatment with LGR-1 protected the integrity of tight junctions and the expression of zonula occludens-1 (ZO-1) and occludin destroyed by BC. Furthermore, LGR-1 pretreatment reduced the expression of NOD-like receptor family member pyrin domain-containing protein 3 (NLRP3), caspase recruitment and activation domain (ASC), Caspase-1 p20, gasdermin D (GSDMD) p30, inflammatory factors (interleukin (IL)-1β and IL-18), and cell death induced by BC. Moreover, LGR-1 pretreatment reduced NLRP3 inflammasome activity and increased expressions of ZO-1 and occludin induced by lipopolysaccharides (LPS) + ATP stimulation. MAC-T cells were transfected with NLRP3 siRNA or MCC950 and/or treated with BC and/or LGR-1. NLRP3-siRNA transfection and MCC950 attenuated BC-induced NLRP3 inflammasome activity. Expression of inflammatory cytokines and cell death suggested that the inflammatory pathway might play an important role in the induction of the NLRP3 inflammasome by BC and the protection of LGR-1.

Conclusions
These results suggest that LGR-1 might be a probiotic alternative to antibiotics and could be administered to prevent mastitis in dairy cows, thus ensuring food security.
Key characterization efforts to support the graffiti ink removal and care of Mark Rothko’s painting ‘Black on Maroon’ 1958
Authors: Wills Scott T. , Ormsby Bronwyn A. , Keefe Melinda H. , Sammler Robert L. 
Published: September 2022

Abstract
Analytical characterization efforts carried out in support of the conservation treatment of Mark Rothko's painting 'Black on Maroon' 1958 (Tate T01170), involving the removal of graffiti (tag) ink, are summarized. The proprietary ink product, of unfamiliar and unknown composition, was investigated using a suite of analytical techniques (IR spectroscopy, GC–MS, ICP-MS, pyrolysis GC–MS, thin layer chromatography, SEC, MALDI-TOF–MS, and UHPLC-MS) to identify key colorants and other components. The ink solubility properties proved vital to informing the solvent selection process for the ink removal procedure, which helped enable the re-display of the painting at Tate Modern in 2014. The possible impact of ink residues remaining within the cotton duck canvas support of the conserved painting was also explored using mockup canvas mechanical strength data, measured before and after ‘soiling’ at two ink levels to assess whether the ink residues had any immediate and possible longer-term effects on canvas properties. These findings, elucidated using a range of complementary analytical techniques, provide information on this hitherto-unknown graffiti product, contribute to a growing body of knowledge in this area, and offer analytical approaches which may be useful for the characterization of similar unknown materials, whether used to damage, augment, or create works of art.
Associated bacteria of a pine sawyer beetle confer resistance to entomopathogenic fungi via fungal growth inhibition
Authors: Deng Jundan , Xu Weikang , Lv Guochang , Yuan Hang , Zhang Qing-He , Wickham Jacob D. , Xu Letian , Zhang Longwa 
Published: September 2022

AbstractBackgroundThe entomopathogenicBeauveria bassianais a popular fungus used to control the Japanese pine sawyer,Monochamus alternatusHope, the key vector of pine wood nematode (Bursaphelenchus xylophilus) that is the causal agent of pine wilt disease, resulting in devastating losses of pines in China and Portugal. However, recent studies have demonstrated that some insect-associated bacteria might decrease fungal toxicity and further undermine its biological control efficacy againstM. alternatus. Thus, it is of great significance to uncover whether and how associated bacteria ofM. alternatusbecome involved in the infection process ofB. bassiana.ResultsHere, we show that axenicM. alternatuslarvae died significantly faster than non-axenic larvae infected by four increasing concentrations ofB. bassianaspores (Log-rank test,P < 0.001). The infection ofB. bassianasignificantly changed the richness and structure of the beetle-associated bacterial community both on the cuticle and in the guts ofM. alternatus; meanwhile, the abundance ofPseudomonasandSerratiabacteria were significantly enriched as shown by qPCR. Furthermore, these two bacteria genera showed a strong inhibitory activity againstB. bassiana(One-way ANOVA,P < 0.001) by reducing the fungal conidial germination and growth rather than regulating host immunity.ConclusionsThis study highlights the role of insect-associated bacteria in the interaction between pest insects and entomopathogenic fungi, which should be taken into consideration when developing microbial-based pest control strategies.
Water quality index for assessment of drinking groundwater purpose case study: area surrounding Ismailia Canal, Egypt
Authors: Atta Hend Samir , Omar Maha Abdel-Salam , Tawfik Ahmed Mohamed 
Published: September 2022

AbstractThe dramatic increase of different human activities around and along Ismailia Canal threats the groundwater system. The assessment of groundwater suitability for drinking purpose is needed for groundwater sustainability as a main second source for drinking. The Water Quality Index (WQI) is an approach to identify and assess the drinking groundwater quality suitability.The analyses are based on Pearson correlation to build the relationship matrix between 20 variables (electrical conductivity (Ec), pH, total dissolved solids (TDS), sodium (Na), potassium (K), calcium (Ca), magnesium (Mg), chloride (Cl), carbonate (CO3), sulphate (SO4), bicarbonate (HCO3), iron (Fe), manganese (Mn), zinc (Zn), copper (Cu), lead (Pb), cobalt (Co), chromium (Cr), cadmium (Cd), and aluminium (Al). Very strong correlation is found at [Ec with Na, SO4] and [Mg with Cl]; strong correlation is found at [TDS with Na, Cl], [Na with Cl, SO4], [K with SO4], [Mg with SO4] and [Cl with SO4], [Fe with Al], [Pb with Al]. The water type is Na–Cl in the southern area due to salinity of the Miocene aquifer and Mg–HCO3 water type in the northern area due to seepage from Ismailia Canal and excess of irrigation water.The WQI classification for drinking water quality is assigned with excellent and good groundwater classes between km 10 to km 60, km 80 to km 95 and the adjacent areas around Ismailia Canal. While the rest of WQI classification for drinking water quality is assigned with poor, very poor, undesirable and unfit limits which are assigned between km 67 to km 73 and from km 95 to km 128 along Ismailia Canal.
Programmatic Implementation of a Custom Subspecialized Oncologic Imaging Workflow Manager at a Tertiary Cancer Center
Authors: Becker Anton S. , Das Jeeban P. , Woo Sungmin , Elnajjar Pierre , Chaim Joshua , Erinjeri Joseph P. , Hricak Hedvig , Vargas Hebert Alberto 
Published: September 2022

PURPOSE To evaluate whether a custom programmatic workflow manager reduces reporting turnaround times (TATs) from a body oncologic imaging workflow at a tertiary cancer center. METHODS A custom software program was developed and implemented in the programming language R. Other aspects of the workflow were left unchanged. TATs were measured over a 12-month period (June-May). The same prior 12-month period served as a historical control. Median TATs of magnetic resonance imaging (MRI) and computed tomography (CT) examinations were compared with a Wilcoxon test. A chi-square test was used to compare the numbers of examinations reported within 24 hours and after 72 hours as well as the proportions of examinations assigned according to individual radiologist preferences. RESULTS For all MRI and CT examinations (124,507 in 2019/2020 and 138,601 in 2020/2021), the median TAT decreased from 4 (interquartile range: 1-22 hours) to 3 hours (1-17 hours). Reports completed within 24 hours increased from 78% (124,127) to 89% (138,601). For MRI, TAT decreased from 22 (5-49 hours) to 8 hours (2-21 hours), and reports completed within 24 hours increased from 55% (14,211) to 80% (23,744). For CT, TAT decreased from 3 (1-19 hours) to 2 hours (1-13 hours), and reports completed within 24 hours increased from 84% (82,342) to 92% (99,922). Delayed reports (with a TAT > 72 hours) decreased from 17.0% (4,176) to 2.2% (649) for MRI and from 2.5% (2,500) to 0.7% (745) for CT. All differences were statistically significant ( P < .001). CONCLUSION The custom workflow management software program significantly decreased MRI and CT report TATs.
A Bayesian Cohort Component Projection Model to Estimate Women of Reproductive Age at the Subnational Level in Data-Sparse Settings
Authors: Alexander Monica , Alkema Leontine 
Published: September 2022

Abstract
Accurate estimates of subnational populations are important for policy formulation and monitoring population health indicators. For example, estimates of the number of women of reproductive age are important to understand the population at risk of maternal mortality and unmet need for contraception. However, in many low-income countries, data on population counts and components of population change are limited, and so subnational levels and trends are unclear. We present a Bayesian constrained cohort component model for the estimation and projection of subnational populations. The model builds on a cohort component projection framework, incorporates census data and estimates from the United Nation's World Population Prospects, and uses characteristic mortality schedules to obtain estimates of population counts and the components of population change, including internal migration. The data required as inputs to the model are minimal and available across a wide range of countries, including most low-income countries. The model is applied to estimate and project populations by county in Kenya for 1979–2019 and is validated against the 2019 Kenyan census.
“Two Kings” in the Tungkhungia Court?
Authors: Ghosh Samyak 
Published: September 2022

Abstract
This article situates the court of the Tungkhungia kings of Brahmaputra Valley (1680–1830), in present day Assam, in the space of courtly convergence and response in eighteenth-century South Asia. It studies a particular moment in the Tungkhungia royal court (1714–44) when a unique political arrangement (“two kings”) was expressed by courtiers, chroniclers, and poets in the language of a stylized fiction of love. The article tries to make meaning of the “two kings” problem by looking at a set of textual and visual materials and situates them within a context of “multilayered cultural semiotics” at work in borderland courts in eighteenth-century South Asia, loosely held within the crumbling edifice of Mughal Hindustan. Toward this end, the article uses its research findings to add fresh insights on the ongoing discussion on courtly culture in early eighteenth-century South Asia and highlights the importance of studying emotions towards understanding political practice.
Wahhabis without Religion; or, A Genealogy of Jihadis in Colonial Law, 1818 to 1857
Authors: Choudhury Rishad 
Published: September 2022

AbstractThis article offers a new interpretation of the “Indian Wahhabi” beyond an ostensibly religious identity. Examining encounters between a centralizing state and decentralized circulatory regimes, the study thus illuminates an overlooked sociolegal genealogy of the jihadi militant in colonial India. From 1818, the East India Company secured its sovereignty by designating as deviant or permissible a host of itinerant figures in and around South Asia. In police records, court transcripts, and legislative archives, pilgrims with links to Arabia accordingly began appearing as suspected Wahhabis. Yet, in then seeking to distinguish “faqirs” from “fanatics,” colonial law used logics and exceptions with two important implications. First, as the “Wahhabi” came to imply a violent counterclaim to sovereignty, it also became a juridical formulation more political than religious. The faqir pilgrim here supplied the conceit of religion. Second, the complex question of jihad produced a deeper paradox, as grappling with a “religious” problem without “religion” stretched secular jurisprudence to breaking points. Until 1857, around South Asia, states of emergency hence dominated official responses to Wahhabis. Ultimately, colonial law's gestures not only rendered unexceptional its regimes of exception. Ironically, they also reified religion, such that Islam and violence became culturally consubstantial in colonial thought.
Introduction
Authors: Zeleke Elleni Centime , Davari Arash 
Published: September 2022

Abstract
This essay outlines a research agenda the authors call “Third World Historical,” combining reflections from Ethiopia and Iran to query the legacies of revolutionary politics in our present. Third world activists from the 1960s and 1970s engaged revolutionary talk to pose questions about the particularities of their immediate contexts, and they posed new concepts of revolution along the way. Congealed manifestations of the term revolution can preclude our effort to think the event as experience. If revolution signals the disruption of existing categories, can we in turn disrupt congealed categories to rethink revolution? What could it mean to reposition the question of revolution in the specificity of the third world, against the tendency to map revolutions as models, patterns, and stages?
Waiting for Revolution
Authors: Kara Taushif 
Published: September 2022

AbstractThis essay takes as its point of departure the conceptual problem posed by intezar, or waiting, in revolutionary Iran. Kara suggests that this problem mirrors the suspension or deferral of sovereignty implied by the logic of historicism, and thus the wider state of belatedness faced across what was once called the “third world.” Though confronted by the problem of waiting in different ways, the author shows how thinkers from revolutionary Iran and colonial India—namely Ali Shariati (1933–77) and Muhammad Iqbal (1877–1938)—may have arrived at similar conclusions. Rather than reject the principle of waiting, their thought sought to augment it, mainly by discarding the future as the focus of the political in order to render an invisible present visible. But if the conceptual possibilities condensed in colonial India and Iran's revolution reveal a shared genealogy of waiting, the resonance of this problem today is confined neither to the geography nor to the condition of coloniality that produced it. Kara concludes by suggesting that the struggle against anticipation in the twentieth century may have prefigured the planetary condition of waiting that characterizes the political in the twenty-first, a condition accentuated and elevated by the climate crisis.