bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using new tools for building construction teaching during the sanitary emergency
Authors: Brioso X , Calderon-Hernandez C , Fuentes-Hurtado D 
Published: February 2022

Abstract
Covid-19 pandemic has originated that a great number of countries’ governments demand universities to teach online classes, presenting a challenge to redesign the courses that had construction site visits included in the curricula. The purpose of this work is to present the successful strategies employed on the teaching of building construction, applied in a third-year civil engineering program of the Pontifical Catholic University of Peru. The methodology was designed so that one can adapt the pandemic and post-pandemic stages proposing a balanced use of virtual platforms and software for video conferences and laboratories, incorporating tools like Building Information Modeling, Lean construction, among other systems. Given the sanitary emergency, the construction site visits were replaced by virtual visits to construction projects generated with scanner laser technology, photogrammetry, and BIM, generating digital twins that were stored in online platforms. Students toured the construction project virtually and in an interactive manner, and along with the description of the professionals in charge of the project they were able to reach a good level of comprehension of the organization and the construction processes. In addition, students developed the layout plans of the temporary works with BIM models. On the other hand, the course taught to generate and analyze the unit prices and quantity surveying of activities using the BIM methodology with 5D software, developing the project budget. The success of this methodology is shown through the notable quality of papers and evaluations taken, through the results of surveys taken on students--which had an effectiveness rate of 96.4 % --, and on the improvement opportunities determined. This paper presents tools relevant that may be adapted by the academia and practitioners related to building constructions, for virtual or face-to-face learning.
Construction and Climate Change; Challenges and Opportunities: A Case Study of the Northeast U.S
Authors: Pourmokhtarian Afshin , Bakhshi Payam , Bannon Zachary , Everett Benjamin 
Published: February 2022

Abstract
The Northeast megalopolis of the United States, which covers a high-density corridor from Washington, D.C., north to Boston, is one of the most developed environments in the world. It contains a gigantic, complicated, and intertwined network of supporting infrastructure with average score of D+, hence requiring substantial rehabilitation and renewal. The 2020 North American Construction report forecasted a CAGR of 8.4% by 2024 despite the pandemic. The pace of growth will recover from 2021 onwards as the ongoing infrastructure investments and smart city projects will add momentum for the region’s construction industry. On the other hand, climate change impacts are underway across the globe and the Northeast of the U.S. is not an exception. Populations and aging infrastructures that they depend on, are highly vulnerable to climate hazards including heat waves, as well as flooding due to a combination of sea level rise, storm surge, and extreme precipitation events.
In this study, future projections of climate change in the Northeast of the U.S. were used to explore their potential impacts on construction industry including but not limited to safety of workforce, selection of building materials and their lifecycle, logistics, scheduling, costs, and insurance. The challenges and opportunities that construction industry faces under climate change were also covered. Later, the feedback loop between the construction and climate change were discussed as well as how sustainable construction practices could mitigate climate change impacts while providing safety for construction workforce. Finally, this paper focuses on resilience, buildings carbon footprint, green infrastructure, sustainability, and a prototype decision-support tool for construction projects to better manage weather risk from contract to project completion, known as Climate-i Construction, and how construction industry can benefit from them under 21st century changing climate.
The Automated Farmlands of Tomorrow: An IoT Integration with Farmlands
Authors: Singh Priyanka , Dixit Saurav , Sammanit Debaroti , Krishnan Paritosh 
Published: February 2022

Abstract
The rapid urbanization and industrialization of the population have resulted in a critical shortage of agricultural land and manpower to meet the growing population’s needs. The future of tomorrow requires impetus through concepts such as IoT Automation in farmlands to meet the increased demand for labour and inspection while maintaining economic efficiency without depleting the environment. Monitoring becomes difficult with a reduced manpower base, which may result in crop failures. The purpose of this paper is to propose how IoT, in conjunction with basic service automation, can be used to influence climate control. Thus, a working model is created using sensors that control the humidity and required temperature conditions, thereby maintaining a suitable growth environment while monitoring and analyzing in real time.
The effect of the fibrocalcific pathological process on aortic valve stenosis in female patients: a finite element study
Authors: Karnibad Maya , Sharabi Mirit , Lavon Karin , Morany Adi , Hamdan Ashraf , Haj-Ali Rami 
Published: February 2022

Abstract
Calcific aortic valve disease (CAVD) is the most common heart valvular disease in the developed world. Most of the relevant research has been sex-blind, ignoring sex-related biological variables and thus under-appreciate sex differences. However, females present pronounced fibrosis for the same aortic stenosis (AS) severity compared with males, who exhibit more calcification. Herein, we present a computational model of fibrocalcific AV, aiming to investigate its effect on AS development. A parametric study was conducted to explore the influence of the total collagen fiber volume and its architecture on the aortic valve area (AVA). Towards that goal, computational models were generated for three females with stenotic AVs and different volumes of calcium. We have tested the influence of fibrosis on various parameters as fiber architecture, fibrosis location, and transvalvular pressure. We found that increased fiber volume with a low calcium volume could actively contribute to AS and reduce the AVA similarly to high calcium volume. Thus, the computed AVAs for our fibrocalcific models were 0.94 and 0.84 cm2 and the clinical (Echo) AVAs were 0.82 and 0.8 cm2. For the heavily calcified model, the computed AVA was 0.8 cm2 and the clinical AVA was 0.73 cm2. The proposed models demonstrated how collagen thickening influence the fibrocalcific-AS process in female patients. These models can assist in the clinical decision-making process and treatment development in valve therapy for female patients.
PACKMAN-Molecule: Python Toolbox for Structural Bioinformatics
Authors: Khade Pranav M , Jernigan Robert L 
Published: February 2022

Abstract

PACKMAN-molecule is a Structural Bioinformatics toolbox in the form of an Application Programming Interface (API) that contains several utilities that can be used for structural bioinformatics applications. It has already been used in several applications, and its added features and unique object hierarchy make it readily extensible, feature-rich, and user-friendly. The tutorial for it is available at: https://py-packman.readthedocs.io/en/latest/tutorials/molecule.html

Availability
PACKMAN-Molecule is freely available with an MIT license on GitHub at https://github.com/Pranavkhade/PACKMAN

Supplementary information
No Supplementary data.
Short-distance gene flow and morphological divergence inEschscholzia parishii(Papaveraceae): implications for speciation in desert winter annuals
Authors: Spalink Daniel , Karimi Nisa , Richards Jeannine H , Eifler Evan , Dinicola Alexa , Thein Thomas , Schomaker Lisa , Drew Bryan T , Mcculloh Katherine A , Givnish Thomas J 
Published: February 2022

AbstractWinter annuals comprise a large fraction of warm-desert plant species, but the drivers of their diversity are little understood. One factor that has generally been overlooked is the lack of obvious means of long-distance seed dispersal in many desert-annual lineages, which could lead to genetic differentiation at small spatial scales and, ultimately, to speciation and narrow endemism. If our gene-flow hypothesis is correct, individual winter-annual species should have populations with genetic spatial structures implying short distances of gene flow. To test this idea, we sampled six populations of Eschscholzia parishii (Papaveraceae) in three pairs of watersheds within a 28-km radius in southern California. We quantified genetic diversity and structure and inferred the distance of gene flow in these populations using single nucleotide polymorphisms derived from genotyping-by-sequencing. Estimated distances of gene flow were quite small (σ = 10.4–14.9 m), with strong genetic structure observed within and between populations. Kinship declined steeply with ln distance (r2 = 0.85). Petal size and shape differed significantly between the northernmost and southernmost populations. These findings support the hypothesis that the high diversity of warm-desert winter annuals might result, in part, from genetic differentiation within species at small spatial scales driven by poor seed dispersal.
Understanding responses to chemical mixtures: looking forward from the past
Authors: Derby Charles D , McClintock Timothy S , Caprio John 
Published: February 2022

AbstractOur goal in this article is to provide a perspective on how to understand the nature of responses to chemical mixtures. In studying responses to mixtures, researchers often identify “mixture interactions”—responses to mixtures that are not accurately predicted from the responses to the mixture’s individual components. Critical in these studies is how to predict responses to mixtures and thus to identify a mixture interaction. We explore this issue with a focus on olfaction and on the first level of neural processing—olfactory sensory neurons—although we use examples from taste systems as well and we consider responses beyond sensory neurons, including behavior and psychophysics. We provide a broadly comparative perspective that includes examples from vertebrates and invertebrates, from genetic and nongenetic animal models, and from literature old and new. In the end, we attempt to recommend how to approach these problems, including possible future research directions.
Qualitative and Quantitative Analyses of Four Active Components in Different Organs ofSalvia DesertaSchang by High-Performance Thin-Layer Chromatography
Authors: Wang Liwa , Wu Wenxia , Tian Shuge 
Published: February 2022

AbstractThis method aims to analyze rosmarinic acid (RA), caffeic acid (CA), ursolic acid (UA) and oleanolic acid (OA) in different organs of Salvia deserta Schang qualitatively and quantitatively by high-performance thin-layer chromatography. Using chloroform–methanol–formic acid (10: 2: 0.5, v/v/v) as mobile phase and silica gel plate as stationary phase to analyze RA and CA at 330 nm. Using cyclohexane–ethyl acetate–methanol (10: 2: 0.5, v/v/v) as mobile phase and silica gel F254 plate as stationary phase to analyze UA and OA at 550 nm. The linearity ranges of RA, CA, UA and OA were 0.1250–0.4375, 0.0145–0.0870, 0.5000–2.5000 and 0.5000–2.5000 mg, respectively, with corresponding correlation coefficients of 0.9938, 0.9981, 0.9971 and 0.9969, respectively. Good precision, stability, accuracy (recovery rates were between 95 and 105%) of the method were determined. The limits of detection and the limits of quantification of RA, CA, UA and OA were determined, respectively, as 50, 58, 25, 33 and 160, 191, 80, 106 ng. The established method is simple, rapid, effective and can be easily used to determine the contents of RA, CA, UA and OA in different parts of S. deserta Schang.
Social Vulnerability and Rurality Associated With Higher Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection–Induced Seroprevalence: A Nationwide Blood Donor Study—United States, July 2020–June 2021
Authors: Li Zheng , Lewis Brian , Berney Kevin , Hallisey Elaine , Williams Austin M , Whiteman Ari , Rivera-González Luis O , Clarke Kristie E N , Clayton Heather B , Tincher Terry , Opsomer Jean D , Busch Michael P , Gundlapalli Adi V , Jones Jefferson M 
Published: February 2022

Abstract

Background
Most studies on health disparities during the coronavirus disease 2019 (COVID-19) pandemic focused on reported cases and deaths, which are influenced by testing availability and access to care. This study aimed to examine severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody seroprevalence in the United States and its associations with race/ethnicity, rurality, and social vulnerability over time.

Methods
This repeated cross-sectional study used data from blood donations in 50 states and Washington, DC, from July 2020 through June 2021. Donor zip codes were matched to counties and linked with Social Vulnerability Index (SVI) and urban-rural classification. SARS-CoV-2 antibody seroprevalences induced by infection and infection-vaccination combined were estimated. Association of infection-induced seropositivity with demographics, rurality, SVI, and its 4 themes were quantified using multivariate regression models.

Results
Weighted seroprevalence differed significantly by race/ethnicity and rurality, and increased with increasing social vulnerability. During the study period, infection-induced seroprevalence increased from 1.6% to 27.2% and 3.7% to 20.0% in rural and urban counties, respectively, while rural counties had lower combined infection- and vaccination-induced seroprevalence (80.0% vs 88.1%) in June 2021. Infection-induced seropositivity was associated with being Hispanic, non-Hispanic Black, and living in rural or more socially vulnerable counties, after adjusting for demographic and geographic covariates.

Conclusions
The findings demonstrated increasing SARS-CoV-2 seroprevalence in the United States across all geographic, demographic, and social sectors. The study illustrated disparities by race-ethnicity, rurality, and social vulnerability. The findings identified areas for targeted vaccination strategies and can inform efforts to reduce inequities and prepare for future outbreaks.
Melioidosis of the Central Nervous System: Impact of the bimA
Bm Allele on Patient Presentation and Outcome
Authors: Gora Hannah , Hasan Tasnim , Smith Simon , Wilson Ian , Mayo Mark , Woerle Celeste , Webb Jessica R , Currie Bart J , Hanson Josh , Meumann Ella M 
Published: February 2022

Abstract

Background
The autotransporter protein Burkholderia intracellular motility A (BimA) facilitates the entry of Burkholderia pseudomallei into the central nervous system (CNS) in mouse models of melioidosis. Its role in the pathogenesis of human cases of CNS melioidosis is incompletely defined.

Methods
Consecutive culture-confirmed cases of melioidosis at 2 sites in tropical Australia after 1989 were reviewed. Demographic, clinical, and radiological data of the patients with CNS melioidosis were recorded. The bimA allele (bimABm or bimABp) of the B. pseudomallei isolated from each patient was determined.

Results
Of the 1587 cases diagnosed at the 2 sites during the study period, 52 (3.3%) had confirmed CNS melioidosis: 20 (38.5%) had a brain abscess, 18 (34.6%) had encephalomyelitis, 4 (7.7%) had isolated meningitis, and 10 (19.2%) had extra-meningeal disease. Among the 52 patients, there were 8 (15.4%) deaths; 17/44 (38.6%) survivors had residual disability. The bimA allele was characterized in 47/52; 17/47 (36.2%) had the bimABm allele and 30 (63.8%) had the bimABp allele. Patients with a bimABm variant were more likely to have a predominantly neurological presentation (odds ratio [OR]: 5.60; 95% confidence interval: 1.52–20.61; P = .01), to have brainstem involvement (OR: 7.33; 1.92–27.95; P = .004), and to have encephalomyelitis (OR: 4.69; 1.30–16.95; P = .02). Patients with a bimABm variant were more likely to die or have residual disability (OR: 4.88; 1.28–18.57; P = .01).

Conclusions
The bimA allele of B. pseudomallei has a significant impact on the clinical presentation and outcome of patients with CNS melioidosis.
Combined large cell neuroendocrine carcinoma: clinical characteristics, prognosis and postoperative management
Authors: Yang Zhengyu , Wang Yanan , Chen Ya , Qian Fangfei , Zhang Yanwei , Hu Minjuan , Zhang Wei , Han Baohui 
Published: February 2022

Abstract

OBJECTIVES
Combined large cell neuroendocrine carcinoma (C-LCNEC) is pulmonary large cell neuroendocrine carcinoma (LCNEC) mixed with other components, such as adenocarcinoma (AD) and squamous cell carcinoma (SCC). This study aimed to describe the distinct features between C-LCNEC with different components and explore the treatment strategy.

METHODS
We retrospectively collected data of 96 C-LCNEC patients who underwent surgical resection. Propensity score matching was used to balance baseline characteristics of LCNEC combined with AD (LCNEC/AD) and LCNEC combined with SCC (LCNEC/SCC).

RESULTS
In our final cohort, 71 (74%) were LCNEC/AD, while 25 (26%) were LCNEC/SCC. LCNEC/AD was more likely to occur in female, younger adults, with visceral pleural invasion and with driver gene expression. However, there was no significant difference in disease-free survival and overall survival between the 2 groups (before matching: P = 0.79 and P = 0.85; after matching: P = 0.87 and P = 0.48), while adjuvant chemotherapy (P = 0.019 and P = 0.043) was an independent predictor. C-LCNEC patients of stage II or III receiving adjuvant chemotherapy had longer disease-free survival and overall survival (P = 0.054 and P = 0.025), and the benefit of etoposide-based chemotherapy was greater than the other regimens (P = 0.010 and P = 0.030). EGFR and ALK mutations were present in 28% (17/60) and 7% (4/60) of C-LCNEC patients, respectively, and they responded well to targeted therapy.

CONCLUSIONS
LCNEC/AD was the most common type of C-LCNEC, and there were many differences between different combined components. Adjuvant chemotherapy, especially etoposide-based chemotherapy, was a beneficial option for resected C-LCNEC.
Subj collection: 152
Serum N-glycomics of a novel CDG-IIb patient reveals aberrant IgG glycosylation
Authors: Beimdiek Julia , Hennig René , Burock Robert , Puk Oliver , Biskup Saskia , Rapp Erdmann , Lesinski-Schiedat Anke , Buettner Falk F R , Das Anibh M 
Published: February 2022

Abstract
Rare genetic mutations of the mannosyl-oligosaccharide glucosidase (MOGS) gene affecting the function of the mannosyl-oligosaccharide glucosidase (glucosidase I) are the cause of the congenital disorder of glycosylation IIb (CDG-IIb). Glucosidase I specifically removes the distal α1,2-linked glucose from the protein bound precursor N-glycan Glc3Man9GlcNAc2, which is the initial step of N-glycan maturation. Here, we comparatively analyzed N-glycosylation of the whole serum proteome, serum-derived immunoglobulin G (IgG), transferrin (TF), and α-1-antitrypsin (AAT) of a female patient who is compound heterozygous for 2 novel missense mutations in the MOGS gene, her heterozygous parents, and a sibling with wildtype genotype by multiplexed capillary gel electrophoresis coupled to laser induced fluorescence detection (xCGE-LIF) at unprecedented depth. Thereby, we detected the CDG-IIb-characteristic non-de-glucosylated N-glycans Glc3Man7-9GlcNAc2 as well as the free tetrasaccharide Glc3-Man in whole serum of the patient but not in the other family members. The N-glycan analysis of the serum proteome further revealed that relative intensities of IgG-specific complex type di-antennary N-glycans with core-fucosylation were considerably reduced in the patient’s serum whereas TF- and AAT-characteristic sialylated di- and tri-antennary N-glycans were increased. This finding reflected the hypogammaglobulinemia diagnosed in the patient. We further detected aberrant oligo-mannose (Glc3Man7GlcNAc2) and hybrid type N-glycans on patient-derived IgGs and we attributed this defective glycosylation to be the reason for an increased IgG clearance. This mechanism can explain the hypogammaglobulinemia that is associated with CDG-IIb.
Non-canonical initiation factors modulate repeat-associated non-AUG translation
Authors: Green Katelyn M , Miller Shannon L , Malik Indranil , Todd Peter K 
Published: February 2022

Abstract
Repeat-associated non-AUG (RAN) translation of expanded repeat-mutation mRNA produces toxic peptides in neurons of patients suffering from neurodegenerative diseases. Recent findings indicate that RAN translation in diverse model systems is not inhibited by cellular stressors that impair global translation through phosphorylation of the alpha subunit of eIF2, the essential eukaryotic translation initiation factor that brings the initiator tRNA to the 40S ribosome. Using in vitro, cell-based and Drosophila models, we examined the role of alternative ternary complex factors that may function in place of eIF2, including eIF2A, eIF2D, DENR and MCTS1. Among these factors, DENR knockdown had the greatest inhibitory effect on RAN translation of expanded GGGGCC and CGG repeat reporters and its reduction improved the survival of Drosophila expressing expanded GGGGCC repeats. Taken together, these data support a role for alternative initiation factors in RAN translation and suggest these may serve as novel therapeutic targets in neurodegenerative disease.
Proteomic profiling identifies novel proteins for genetic risk of severe COVID-19: the Atherosclerosis Risk in Communities Study
Authors: Steffen Brian T , Pankow James S , Lutsey Pamela L , Demmer Ryan T , Misialek Jeffrey R , Guan Weihua , Cowan Logan T , Coresh Josef , Norby Faye L , Tang Weihong 
Published: February 2022

Abstract

Background
Genome-wide association studies have identified six genetic variants associated with severe COVID-19, yet the mechanisms through which they may affect disease remains unclear. We investigated proteomic signatures related to COVID-19 risk variants rs657152 (ABO), rs10735079 (OAS1/OAS2/OAS3), rs2109069 (DPP9), rs74956615 (TYK2), rs2236757 (IFNAR2) and rs11385942 (SLC6A20/LZTFL1/CCR9/FYCO1/CXCR6/XCR1) as well as their corresponding downstream pathways that may promote severe COVID-19 in risk allele carriers and their potential relevancies to other infection outcomes.

Methods
A DNA aptamer-based array measured 4870 plasma proteins among 11 471 participants. Linear regression estimated associations between the COVID-19 risk variants and proteins with correction for multiple comparisons, and canonical pathway analysis was conducted. Cox regression assessed associations between proteins identified in the main analysis and risk of incident hospitalized respiratory infections (2570 events) over a 20.7-year follow-up.

Results
The ABO variant rs657152 was associated with 84 proteins in 7241 white participants with 24 replicated in 1671 Black participants. The TYK2 variant rs74956615 was associated with ICAM-1 and -5 in white participants with ICAM-5 replicated in Black participants. Of the 84 proteins identified in the main analysis, seven were significantly associated with incident hospitalized respiratory infections including Ephrin type-A receptor 4 (hazard ratio (HR): 0.87; P = 2.3 × 10−11) and von Willebrand factor type A (HR: 1.17; P = 1.6x10−13).

Conclusions
Novel proteomics signatures and pathways for COVID-19-related risk variants TYK2 and ABO were identified. A subset of these proteins predicted greater risk of incident hospitalized pneumonia and respiratory infections. Further studies to examine these proteins in COVID-19 patients are warranted.