bluuebunny/crossref_metadata_2025_split huggingface dataset:
RADON IN DRINKING WATER FROM ALTERNATIVE SOURCES OF WATER SUPPLY IN THE NORTH OF KOSOVO
Authors: Vučković Biljana , Kurilić Sanja Mrazovac , Nikolić-Bujanović Ljiljana , Todorović Nataša , Nikolov Jovana , Radovanović Jelena Živković , Milošević Rade , Jokić Anja 
Published: November 2022

Abstract
In this study, the results of research on radon activity concentrations in natural mineral waters, traditionally used for drinking but also for other needs, in rural and urban households in northern Kosovo are presented. Radon activity concentration in water was measured by the alpha spectrometric method with a RAD7 device. Radon activity concentrations in the 24 waters studied ranged from 1.6 ± 0.5 to 46.3 ± 6.3 Bq l−1, with an average activity concentration of 12.4 ± 2.0 Bq l−1, which was somewhat higher than the EPA recommended maximum activity concentration, but below the WHO recommended maximum. The contribution of radon activity concentrations in water was determined in relation to the total radon activity in air and enclosed space. The estimated annual effective doses of inhalation and ingestion radon from water were 109.4 ± 16.7 and 2.6 ± 0.4 μSv y−1, respectively.
Repurposing Spinal Distractor to Reduce Pediatric Wrist Fractures
Authors: Uppal Harjot S. , Biama Richard A. 
Published: November 2022

Fracture geometry, particularly a jagged bone spike, can present a physical barrier in closed reduction of pediatric distal radius-ulna fractures. When closed reduction of the fracture is not possible, accepting an incomplete reduction and hoping for remodeling, or open reduction, which poses a greater risk for infection and potential physeal injury, are alternative treatment options. The objective of this study was to describe a technique, coined as Percutaneous Skeletal Traction Aided Reduction (P_STAR), for reducing these fractures, thereby eliminating the acceptance of an incomplete reduction and the risks associated with open reduction. In P_STAR, 2 distraction pins are placed 1.5 cm proximal and distal to the fracture site in clearance of the distal radial physis. A shadow-line spinal distractor is then used to distract the pins, reducing the fracture over the irregular impeding fracture geometry. After distraction is released, 1 or 2 K-wires can be percutaneously inserted to transfix the fracture. A video of the technique was also included as Supplemental Digital Content, http://links.lww.com/BTH/A188. When performed on 18 children with distal radius-ulna fractures, P_STAR achieved near anatomic fracture alignment with no nerve or tendon injury, infection, or refracture.
Comprehensive Understanding of Hydrogeochemical evaluation of seasonal variability in groundwater quality Dynamics in the Gold Mining Areas of Osun State, Nigeria
Authors: Olalekan Awogbami Stephen , Adewoye Solomon Olayinka , Henry Sawyerr Olawale , Olaniyi Opasola Afolabi , Raimi Morufu Olalekan 
Published: November 2022

BackgroundA crucial issue directly affecting the wellbeing of the human race is water quality. Within a few decades, a greater reliance on groundwater was needed to supply water for drinking, agriculture, and other uses due to the scarcity and contamination of surface water. To forecast its long-term use and increase output, irrigated agriculture requires high-quality water, which must be measured.ObjectiveThe goals of the current study are to comprehend the hydro-geochemistry, drinking water appropriateness, and occurrence of hydro-geochemistry concepts in the groundwater of the gold mining regions of Osun State, South-West Nigeria.MethodStandardized analytical methods were used in the research. All sampling, conservation, transportation, and analysis were carried out in accordance with APHA guidelines (2012). To prevent deterioration of the organic compounds, all acquired samples were sent to research laboratory, while maintaining in an icebox.ResultsThe study also identifies critical pollutants, affecting the ground water quality within its course through the gold mining areas of Osun State. Finally, Colour, pH, DO, EC, TDS, TSS, TS, Hardness, Magnesium, Nitrate, Phosphate, Lead, Cadmium, Chromium, Manganese, Mercury and Arsenic have been found to be critical parameters for the stretch in each season of this research.ConclusionThe authors advise developing ongoing systems for monitoring water quality as well as efficient management techniques to prevent excessive groundwater pollution. These findings will therefore aid decision-makers in managing pollution in Osun State’s gold mining zones and better understanding the impact of different seasons on water quality. The findings of this study can serve as a foundation for the future monitoring of the effects of anthropogenic activities on local watercourses when mining companies are developed. This requires consideration in terms of both regulatory measures and proactive initiatives for addressing the ensuing issues in the future. In order to maintain sustainability, a long-term monitoring plan is suggested in this study to be implemented into the groundwater bodies to restore their quality.
FHIR-DHP: A Standardized Clinical Data Harmonisation Pipeline for scalable AI application deployment
Authors: Williams Elena , Kienast Manuel , Medawar Evelyn , Reinelt Janis , Merola Alberto , Ines Klopfenstein Sophie Anne , Flint Anne Rike , Heeren Patrick , Poncette Akira-Sebastian , Balzer Felix , Beimes Julian , Bünau Paul von , Chromik Jonas , Arnrich Bert , Scherf Nico , Niehaus Sebastian 
Published: November 2022

BackgroundIncreasing digitalisation in the medical domain gives rise to large amounts of healthcare data which has the potential to expand clinical knowledge and transform patient care if leveraged through artificial intelligence (AI). Yet, big data and AI oftentimes cannot unlock their full potential at scale, owing to non-standardised data formats, lack of technical and semantic data interoperability, and limited cooperation between stakeholders in the healthcare system. Despite the existence of standardised data formats for the medical domain, such as Fast Healthcare Interoperability Resources (FHIR), their prevalence and usability for AI remains limited.ObjectiveWe developed a data harmonisation pipeline (DHP) for clinical data sets relying on the common FHIR data standard.MethodsWe validated the performance and usability of our FHIR-DHP with data from the MIMIC IV database including > 40,000 patients admitted to an intensive care unit.ResultsWe present the FHIR-DHP workflow in respect of transformation of “raw” hospital records into a harmonised, AI-friendly data representation. The pipeline consists of five key preprocessing steps: querying of data from hospital database, FHIR mapping, syntactic validation, transfer of harmonised data into the patient-model database and export of data in an AI-friendly format for further medical applications. A detailed example of FHIR-DHP execution was presented for clinical diagnoses records.ConclusionsOur approach enables scalable and needs-driven data modelling of large and heterogenous clinical data sets. The FHIR-DHP is a pivotal step towards increasing cooperation, interoperability and quality of patient care in the clinical routine and for medical research.
Requirements to minimize airborne infections related to virus aerosol contamination at indoor cultural events
Authors: Salthammer Tunga , Moriske Heinz-Jörn 
Published: November 2022

AbstractThe SARS-CoV-2 pandemic has resulted in many live events being canceled or held without spectator participation. It is therefore necessary to develop strategies to determine the conditions under which cultural activities can be maintained. In this study the results from available literature were combined with findings, guidelines and regulations for other indoor environments and recommendations were derived. In the cultural sector, the number of experimental investigations, surveys and simulations is comparatively small. This is probably due to the complexity of the events in terms of location and visitor flow, so the respective conditions under which they take place can be very different. It is therefore practically impossible to predict the risk of infection for a specific situation with potential virus spreaders attending or to derive general rules that go beyond the known measures of vaccination, testing, masks and distance. Cultural events can be held under pandemic conditions, provided certain conditions are met. Most study results agree on this. However, any recommendations for hygiene, safety and ventilation measures in cultural institutions can only minimize the risk of infection, but cannot completely rule it out. It is also of considerable importance that visitors protect themselves individually and act responsibly.Graphical Abstract
Efficacy of a Filtered Far-UVC Handheld Disinfection Device on Reducing Microbial Bioburden of Hospital Surfaces
Authors: Navarathna Thanuri , Jinadatha Chetan , Corona Brandon A. , Coppin John David , Choi Hosoon , Bennett Morgan R. , Ghamande Gautam S. , Williams Marjory D. , Keene Robin E. , Chatterjee Piyali 
Published: November 2022

AbstractObjectivesThe Filtered Far-UVC (FFUV) handheld disinfection device is a small portable device that emits far UVC at 222nm. The objective of this study was to evaluate the device’s ability to kill microbial pathogens on hospital surfaces and compare it to manual disinfection using germicidal sodium hypochlorite wipes.MethodsA total of 344 observations (4 observations from 86 objects’ surfaces) were sampled with 2 paired samples per surface: a pre- and a post-sodium hypochlorite, and a pre- and a post-FFUV samples. The results were analyzed via a Bayesian multilevel negative binomial regression model. Additionally, the bacterial flora recovered were identified using mass spectrometry.ResultsThe estimated mean colony counts for the sodium hypochlorite control and treatment groups were 20.5 (11.7 – 36.0) and 0.1 (0.0 – 0.2) colony forming units (CFUs) respectively. The FFUV control and treatment groups had mean colony counts of 22.2 (12.5 – 40.1) and 4.1 (2.3 – 7.2) CFUs. The sodium hypochlorite samples had an estimated 99.4% (99.0% – 99.7%) reduction in colony counts, while those from the FFUV group had an 81.4% (76.2% − 85.7%) reduction.ConclusionsOur study demonstrated that FFUV handheld device effectively reduced microbial bioburden on surfaces in the healthcare setting. Several healthcare-associated infections (HAIs) causing pathogens (gram positive and negative bacteria) were retrieved from the pre-clean surfaces. The major benefit of FFUV is likely seen when manual disinfection is not possible or when supplementing cleaners or disinfectants with the low-level disinfection properties.
A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling
Authors: Hackney Jason A. , Shivram Haridha , Heiden Jason Vander , Overall Chris , Orozco Luz , Gao Xia , West Nathan , Qamra Aditi , Chang Diana , Chakrabarti Arindam , Choy David F. , Combes Alexis J. , Courau Tristan , Fragiadakis Gabriela K. , Rao Arjun Arkal , Ray Arja , Tsui Jessica , Hu Kenneth , Kuhn Nicholas F. , Krummel Matthew F. , Erle David J. , Kangelaris Kirsten , Sarma Aartik , Lyon Zoe , Calfee Carolyn S. , Woodruff Prescott G. , Ghale Rajani , Mick Eran , Byrne Ashley , Zha Beth Shoshana , Langelier Charles , Hendrickson Carolyn M. , van der Wijst Monique G.P. , Hartoularos George C. , Grant Tianna , Bueno Raymund , Lee David S. , Greenland John R. , Sun Yang , Perez Richard , Ogorodnikov Anton , Ward Alyssa , Ye Chun Jimmie ,   UCSF COMET Consortium, Ramalingam Thiru , McBride Jacqueline M. , Cai Fang , Teterina Anastasia , Bao Min , Tsai Larry , Rosas Ivan O. , Regev Aviv , Kapadia Sharookh B. , Bauer Rebecca N. , Rosenberger Carrie M. 
Published: November 2022

SummaryAltered myeloid inflammation and lymphopenia are hallmarks of severe infections, including SARS-CoV-2. Here, we identified a gene program, defined by correlation with EN-RAGE (S100A12) gene expression, which was up-regulated in patient airway and blood myeloid cells. The EN-RAGE program was expressed in 7 cohorts and observed in patients with both COVID-19 and acute respiratory distress syndrome (ARDS) from other causes. This program was associated with greater clinical severity and predicted future mechanical ventilation and death. EN-RAGE+myeloid cells express features consistent with suppressor cell functionality, with low HLA-DR and high PD-L1 surface expression and higher expression of T cell-suppressive genes. Sustained EN-RAGE signature expression in airway and blood myeloid cells correlated with clinical severity and increasing expression of T cell dysfunction markers, such as PD-1. IL-6 upregulated many of the severity-associated genes in the EN-RAGE gene programin vitro, along with potential mediators of T cell suppression, such as IL-10. Blockade of IL-6 signaling by tocilizumab in a placebo-controlled clinical trial led to rapid normalization of ENRAGE and T cell gene expression. This identifies IL-6 as a key driver of myeloid dysregulation associated with worse clinical outcomes in COVID-19 patients and provides insights into shared pathophysiological mechanisms in non-COVID-19 ARDS.
Antiviral innate immunity is diminished in the upper respiratory tract of severe COVID-19 patients
Authors: Ramos-Benitez Marcos J. , Strich Jeffrey R. , Alehashemi Sara , Stein Sydney , Rastegar Andre , de Jesus Adriana Almeida , Bhuyan Farzana , Ramelli Sabrina , Babyak Ashley , Perez-Valencia Luis , Vannella Kevin M. , Grubbs Gabrielle , Khurana Surender , Gross Robin , Hadley Kyra , Liang Janie , Mazur Steven , Postnikova Elena , Warner Seth , Holbrook Michael R. , Busch Lindsay M. , Warner Blake , Applefeld Willard , Warner Sarah , Kadri Sameer S , Davey Richard T , Goldbach-Mansky Raphaela , Chertow Daniel S. 
Published: November 2022

AbstractUnderstanding early innate immune responses to coronavirus disease 2019 (COVID–19) is crucial to developing targeted therapies to mitigate disease severity. Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection elicits interferon expression leading to transcription of IFN-stimulated genes (ISGs) to control viral replication and spread. SARS-CoV-2 infection also elicits NF-κB signaling which regulates inflammatory cytokine expression contributing to viral control and likely disease severity. Few studies have simultaneously characterized these two components of innate immunity to COVID-19. We designed a study to characterize the expression of interferon alpha-2 (IFNA2) and interferon beta-1 (IFNB1), both type-1 interferons (IFN-1), interferongamma (IFNG), a type-2 interferon (IFN-2), ISGs, and NF-κB response genes in the upper respiratory tract (URT) of patients with mild (outpatient) versus severe (hospitalized) COVID-19. Further, we characterized the weekly dynamics of these responses in the upper and lower respiratory tracts (LRTs) and blood of severe patients to evaluate for compartmental differences. We observed significantly increased ISG and NF-κB responses in the URT of mild compared with severe patients early during illness. This pattern was associated with increasedIFNA2andIFNGexpression in the URT of mild patients, a trend toward increasedIFNB1-expression and significantly increasedSTING/IRF3/cGAS expression in the URT of severe patients. Our by-week across-compartment analysis in severe patients revealed significantly higher ISG responses in the blood compared with the URT and LRT of these patients during the first week of illness, despite significantly lower expression ofIFNA2, IFNB1, andIFNGin blood. NF-κB responses, however, were significantly elevated in the LRT compared with the URT and blood of severe patients during peak illness (week 2). Our data support that severe COVID-19 is associated with impaired interferon signaling in the URT during early illness and robust pro-inflammatory responses in the LRT during peak illness.
Bioinformatic approaches to draft the viral genome sequence of Canary Islands cases related to the multi-country Monkeypox virus 2022-outbreak
Authors: Muñoz-Barrera Adrián , Ciuffreda Laura , Alcoba-Florez Julia , Rubio-Rodríguez Luis A. , Rodríguez-Pérez Héctor , Gil-Campesino Helena , de Artola Diego García-Martínez , Salas-Hernández Josmar , Rodríguez-Núñez Julia , Íñigo-Campos Antonio , Díez-Gil Oscar , González-Montelongo Rafaela , Valenzuela-Fernández Agustín , Lorenzo-Salazar José M. , Flores Carlos 
Published: November 2022

AbstractDuring May 2022, the World Health Organization declared community transmission of monkeypox (MPXV) due to a multi-country outbreak. In Europe, several cases of this outbreak were detected in the Canary Islands (Spain). Here we describe the combination of DNA sequencing and bioinformatic approaches, including methods forde novogenome assembly and short- and long-read technologies, used to reconstruct the first MPXV genome isolated in the Canary Islands on the 31stof May 2022 from a male adult patient with mild symptoms. We obtained the best results using a reference-based approach with short reads, evidencing 46-67 nucleotide variants against sequences from the 2018-2019 outbreak, and placing the sequence in the B.1 clade. This study demonstrates the potential of metagenomics sequencing for rapid and precise pathogen identification.
Arrayed Imaging Reflectometry monitoring of anti-viral antibody production throughout vaccination and breakthrough Covid-19
Authors: Klose Alanna M. , Kosoy Gabrielle , Miller Benjamin L. 
Published: November 2022

AbstractImmune responses to COVID-19 infection and vaccination are individual and varied. There is a need to understand the timeline of vaccination efficacy against current and yet to be discovered viral mutations. Assessing immunity to SARS-CoV-2 in the context of immunity to other respiratory viruses is also valuable. Here we demonstrate the capability of a fully automated prototype Arrayed Imaging Reflectometry (AIR) system to perform reliable longitudinal serology against a 34-plex respiratory array. The array contains antigens for respiratory syncytial virus, seasonal influenza, common human coronaviruses, MERS, SARS-CoV-1, and SARS-CoV-2. AIR measures a change in reflectivity due to the binding of serum antibodies to the antigens on the array. Samples were collected from convalescent COVID-19 donors and individuals vaccinated with a two-dose mRNA vaccine regimen. Vaccinated samples were collected prior to the first dose, one week after the first dose, one week after the second dose, and monthly thereafter. Information following booster dose and/or breakthrough infection is included for a subset of subjects. Longitudinal samples of vaccinated individuals demonstrate a rise and fall of SARS-CoV-2 spike antibodies in agreement with general knowledge of the adaptive immune response and other studies. Linear Regression analysis was performed to understand the relationship between antibodies binding to different antigens on the array. Our analysis identified strong correlations between closely related influenza virus strains as well as correlations between SARS-CoV-2, SARS-CoV-1, and human coronavirus 229E. A small test of using diluted whole blood from a fingerstick provided clean arrays with antibody binding comparable to serum. Potential applications include assessing immunity in the context of exposure to multiple respiratory viruses, clinical serology, population monitoring to facilitate public health recommendations, and vaccine development against new viruses and virus mutations.
Identification of multi-omic biomarkers from Fecal DNA for improved Detection of Colorectal Cancer and precancerous lesions
Authors: Fang Yujing , Peng Jiaxi , Li Zhilong , Jiang Ruijingfang , Lin Yuxiang , Shi Ying , Sun Jianlong , Zhuo Duan , Ou Qingjian , Chen Jiali , Wang Xiaohan , Cai Jielun , Zhu Shida , Wan Desen , Wang Yuying , Lu Zhenhai 
Published: November 2022

AbstractBackgroundTimely diagnosis and intervention of colorectal cancer (CRC) at curable stages is essential for improving patient survival. Stool samples carry exfoliation of intestinal epithelium, therefore providing excellent opportunity for non-invasive diagnosis of CRC as well as precancerous lesions. In this study, we aimed to conduct multi-dimensional analysis of fecal DNA and investigate the utility of different types of biomarkers for CRC detection.MethodIn this case-control study, we performed comprehensive analyses of the genomic, epigenomic, and metagenomic features of fecal DNA from CRC patients, individuals with advanced precancerous lesions (APLs) and controls. DNA methylation markers were identified by whole genome bisulfite sequencing of paired colorectal cancer and normal tissues. A multi-gene fecal DNA methylation test was then developed based on three marker genes (SDC2, ADHFE1andPPP2R5C) using quantitative methylation-specific PCR (qMSP), and validated on fecal DNA samples. Genomic mutation profiles as well as microbiome signatures of fecal DNA were analyzed using high-throughput sequencing.ResultsThe methylation-based fecal DNA test demonstrated an overall sensitivity of 88% for CRC and 46.2% for APL respectively, and a specificity of 91.8% for controls. On the other hand, the mutation-based diagnostic model yielded limited sensitivity, and combined detection of methylation markers and mutation in fecal DNA did not improve the assay performance. Meanwhile, a diagnostic model based on the relative abundance of bacterial species showed inferior performance than the methylation-based model. Finally, integrated diagnostic model combining both methylation and microbial markers showed an enhanced performance (AUC= 0.95) compared to methylation markers alone.ConclusionsThe multi-gene fecal DNA methylation test provided remarkable diagnostic performance for CRCs and APLs. Furthermore, multi-target assay integrating both methylation and microbial markers may further improve the diagnostic performance. Our findings may aid in the development of novel diagnostic tools for CRC.
Exposure profiles in pregnant women from a birth cohort in a highly contaminated area of southern Italy
Authors: Drago Gaspare , Ruggieri Silvia , Sprovieri Mario , Rizzo Giulia , Colombo Paolo , Giosuè Cristina , Quinci Enza , Traina Anna , Gastaldelli Amalia , Cibella Fabio , Panunzi Simona 
Published: November 2022

AbstractProtecting the health of pregnant women from environmental stressors is crucial for reducing the burden of non-communicable diseases. In industrially contaminated sites, this action is particularly challenging due to the heterogeneous pollutant mixtures in environmental matrices. Aim of this study was to evaluate distribution patterns of mercury, hexacholobenzene and polychlorobyfenils in the serum of 161 pregnant women recruited in the framework of the NEHO cohort and living both inside and outside the National Priority Contaminated Site (NPCS) of Priolo. Food macro-categories were determined, and serum levels of contaminants were used to perform k-means cluster analysis and identify the role of food in pollutant transfer from the environment. Two groups of mothers with high and low measured pollutant levels were distinguished. Concentrations in mothers in the high-exposure cluster were at least twofold for all the evaluated pollutants (p<0.0001) and includes mothers living inside and outside NPCS, with predominance of individuals from the NPCS (p=0.045). Fish and vegetable consumption was higher in the high-exposure cluster (p=0.02). These findings suggest a direct link between marine sediments and soil contaminations, which in turn drives maternal exposure through the food chain. Such consideration appears poorly investigated in the context of contaminated sites.Highlights- HCB, PCBs and Hg were measured in pregnant women from a highly contaminated area- Pregnant women’s exposure profiles were obtained through k-means cluster analysis- Distance of residence from emission sources only partially explains exposure levels- Maternal age and food consumption appear to primarily drive contaminant levelsAbstract Figure