bluuebunny/crossref_metadata_2025 huggingface dataset:
Masonry Dust Risk Control Practices and the Barriers to the Adoption of Engineering Controls in Reducing Risk due to Dust Exposure in Masonry Work
Authors: Abas N H , Mad Ali M , Abas N A
Published: November 2021

The construction industry is known to be among the most vulnerable industries in terms of occupational safety and health. One of the riskiest activities in construction involves masonry, which reports several cases involving occupational health diseases due to the exposure to silica dust. Thus, this study aims to investigate the perception toward health risks due to exposure to dust in masonry work. A survey research method was adopted for this study, which involved the participation of 25 active construction contractors in Selangor and Kuala Lumpur. The findings reveal that respiratory problems and health diseases are the most perceived risks associated to dust exposure in masonry work. There are various barriers to the adoption of engineering control in masonry work such as high costs, lack of awareness of dust hazards, and workers’ attitudes. The current practical intervention methods used by contractor firms are respiratory protection, wet method, and sweeping compound. This study provides information on the current masonry work environment and the barriers of the adoption of engineering control technologies. Additionally, this study suggests that the key players in the construction industry should take an active part to increase the implementation of engineering controls in a construction project, and not rely solely on the use of PPE.
A Study of The Practical Use of Green Engineering-Based Technology for Building Sustainability: Users’ Perspective
Authors: Hasan Amirul Hakim , Ismail Sushilawati
Published: November 2021

Sustainable construction has been the main priority in the global construction industry. For that reason, Malaysia is moving towards green building approach to promote built environment sustainability. Therefore, it is essential to raise awareness about the environmental-responsible practice among construction players particularly on the implementation of green engineering-based technology. This study aims to explore the existing green engineering-based technology and to investigate the preferred green engineering-based technology to upgrade the sustainability of existing residential buildings. The study focuses on the existing technology to be incorporated in the operation of buildings. A comprehensive literature review was carried out and 384 feedback was collected from questionnaire survey distribution among respondents in Johor Bahru. Various green engineering-based technology includes solar energy, wastewater treatment, rainwater harvesting, window shading, housing landscape, natural ventilation, smart PDLC film glasses, roof thermal insulation, and smart home control panel are discussed in this paper. From this study, it was found that that the housing landscape is the most preferred with the highest mean index value followed by daylighting system and solar panel. The results indicate the preferred green engineering-based technology is because of low cost and familiarity among users. The future study should consider relating the awareness of individuals on sustainability with their preferred green technology. Perhaps, the coverage of this study should be extended by involving respondents from all over Malaysia.
Numerical Modelling Observations of Settlement for Pad Footings Supported on Soft Clay Soil
Authors: Arab O A , Lim A J M S , Sim S Y , Guntor N A A
Published: November 2021

Settlement calculation is an important part in the design of shallow foundations resting on soft soils. The size of the foundation, the depth of the footings, and the rise in ground water level are thought to influence settlement and have been the subject of much research for many years. Thus, this study compared several pad footing sizes using numerical techniques as the basis. The first objective of this study was to analyse soil and pad footing settlement, and to determine the optimal size of footing that withstands excessive settlement due to variation in the water table and the depth of the foundation. Three footing embedment depths of 1.5, 2, and 3m with three water table positions, at the GL (0m), 1.5, and 3m with an applied foundation concentrated load of 440 kN using five footing models of 1.5mx1.5m, 2mx1.5m, 2 m x 2 m, 2.5x1.5m, and 2.5x1.5m pad footing with a uniform thickness of 0.5m were considered. In this study, a 3D Plaxis simulation is used for predicting the settlement of shallow foundations on soft clay soils. Settlement results were discovered at various water table positions and foundation depths. The study found that the 2.5x2m footing was deemed the best among the simulated foundations, and the 3m foundation embedment was considered the best at shallow depths due to less excessive settlement than the other tested foundations. The settlement had a significant impact on the size of the foundation and the depth of the footing. The depth of the water table has a small impact on the settlement. Parametric analysis is also being used to gain a better understanding of the behaviour of the elastic settlement of various shallow foundations. It is found that the footing area increases, settlement decreases and vice versa.
Effects of transglutaminase cross-linking process on printability of gelatin microgel-gelatin solution composite bioink
Authors: Song Kaidong , Ren Bing , Zhai Yingnan , Chai Wenxuan , Huang Yong
Published: November 2021

Three-dimensional (3D) bioprinting has emerged as a powerful engineering approach for various tissue engineering applications, particularly for the development of 3D cellular structures with unique mechanical and/or biological properties. For the jammed gelatin microgel-gelatin solution composite bioink, comprising a discrete phase of microgels (enzymatically gelled gelatin microgels) and a cross-linkable continuous gelatin precursor solution-based phase containing transglutaminase (TG), its rheological properties and printability change gradually due to the TG enzyme-induced cross-linking process. The objective of this study is to establish a direct mapping between the printability of the gelatin microgel-gelatin solution based cross-linkable composite bioink and the TG concentration and cross-linking time, respectively. Due to the inclusion of TG in the composite bioink, the bioink starts cross-linking once prepared and is usually prepared right before a printing process. Herein, the bioink printability is evaluated based on the three metrics: injectability, feature formability, and process-induced cell injury. In this study, the rheological properties such as the storage modulus and viscosity have been first systematically investigated and predicted at different TG concentrations and times during the cross-linking process using the first-order cross-linking kinetics model. The storage modulus and viscosity have been satisfactorily modeled as exponential functions of the TG concentration and time with an experimentally calibrated cross-linking kinetic rate constant. Furthermore, the injectability, feature formability, and process-induced cell injury have been successfully correlated to the TG concentration and cross-linking time via the storage modulus, viscosity, and/or process-induced shear stress. By combing the good injectability, good feature formability, and satisfactory cell viability zones, a good printability zone (1.65, 0.61, and 0.31 h for the composite bioinks with 1.00, 2.00, and 4.00% w/v TG, respectively) has been established during the printing of mouse fibroblast-based 2% gelatin B microgel-3% gelatin B solution composite bioink. This printability zone approach can be extended to the use of other cross-linkable bioinks for bioprinting applications.
Performance analysis of nanowire and nanosheet NCFETs for future technology nodes
Authors: Sakib Fahimul Islam , Hasan Md Azizul , Hossain Mainul
Published: November 2021

Negative capacitance (NC) effect in nanowire (NW) and nanosheet (NS) field effect transistors (FETs) provide the much-needed voltage scaling in future technology nodes. Here, we present a comparative analysis on the performance of NC-NWFETs and NC-NSFETs through fully calibrated, three-dimensional computer aided design (TCAD) simulations. In addition to single channel NC-NSFETs and NC-NWFETs, those, with vertically stacked NSs and NWs, have been examined for the same layout footprint (LF). Results show that NC-NSFETs can achieve lower subthreshold swing (SS) and higher ON-current (I

ON
) than NC-NWFET of comparable device dimensions. However, NC-NWFETs show slightly higher I

ON

/I

OFF
ratio. Negative differential resistance (NDR) is found to be more pronounced in NC-NSFET, enabling these devices to attain a stronger drain-induced-barrier-rising (DIBR) and steeper SS for gate lengths as small as 10 nm. The results presented here can, therefore, provide useful insights for performance optimization of NC-NWFETs and NC-NSFETs, in ultra-scaled and high-density logic applications, for 7 nm and beyond technology nodes.
The Political, the Personal, and “The Function of American Literary Criticism at the Present Time,” 1983–2021
Authors: Gillman Susan
Published: November 2021

Focused on the work of Amy Kaplan and Edward Said, two critics known for their engagements with that longtime hot-button slogan, “the personal = the political,” this essay updates Mathew Arnold’s formula of the function of criticism at the present time. In her 2003 ASA presidential address, Kaplan posed the question, what should be the role of American studies scholars today, in the face of American empire today?—and together with Said, she answered it in a series of experiments with form. The essay, the address, and the book, all three reoriented toward making the personal = the political, become their routes to thinking empire as an ongoing historical subject, anarchic and incoherent rather than monolithic. The work on US empire in the 1980s, when Kaplan’s denial thesis on the absence of empire in American studies took hold and inspired so many scholars, is still present but with new terminology in new disciplinary locations. The larger function of criticism appears when we superimpose the timeline of earlier empire work onto other, current confluences of dates (the centenaries 1992/1998, 9/11, BLM, and COVID-19, 2019–2020) and speculate on the why of these still-open-ended key contexts, textual clusters of empire.
Isoform-level quantification for single-cell RNA sequencing
Authors: Pan Lu , Dinh Huy Q , Pawitan Yudi , Vu Trung Nghia
Published: November 2021

Motivation

RNA expression at isoform level is biologically more informative than at gene level and can potentially reveal cellular subsets and corresponding biomarkers that are not visible at gene level. However, due to the strong 3ʹ bias sequencing protocol, mRNA quantification for high-throughput single-cell RNA sequencing such as Chromium Single Cell 3ʹ 10× Genomics is currently performed at the gene level.

Results

We have developed an isoform-level quantification method for high-throughput single-cell RNA sequencing by exploiting the concepts of transcription clusters and isoform paralogs. The method, called Scasa, compares well in simulations against competing approaches including Alevin, Cellranger, Kallisto, Salmon, Terminus and STARsolo at both isoform- and gene-level expression. The reanalysis of a CITE-Seq dataset with isoform-based Scasa reveals a subgroup of CD14 monocytes missed by gene-based methods.

Availability and implementation

Implementation of Scasa including source code, documentation, tutorials and test data supporting this study is available at Github: https://github.com/eudoraleer/scasa and Zenodo: https://doi.org/10.5281/zenodo.5712503.

Supplementary information

Supplementary data are available at Bioinformatics online.
The impact of coronary revascularization on vessel-specific coronary flow capacity and long-term outcomes: a serial [15O]H2O positron emission tomography perfusion imaging study
Authors: de Winter Ruben W , Jukema Ruurt A , van Diemen Pepijn A , Schumacher Stefan P , Driessen Roel S , Stuijfzand Wynand J , Everaars Henk , Bom Michiel J , van Rossum Albert C , van de Ven Peter M , Verouden Niels J , Nap Alexander , Raijmakers Pieter G , Danad Ibrahim , Knaapen Paul
Published: November 2021

Aims

Coronary flow capacity (CFC) integrates quantitative hyperaemic myocardial blood flow (hMBF) and coronary flow reserve (CFR) to comprehensively assess physiological severity of coronary artery disease (CAD). This study evaluated the effects of revascularization on CFC as assessed by serial [15O]H2O positron emission tomography (PET) perfusion imaging.

Methods and results

A total of 314 patients with stable CAD underwent [15O]H2O PET imaging at baseline and after myocardial revascularization to assess changes in hMBF, CFR, and CFC in 415 revascularized vessels. Using thresholds for ischaemia and normal perfusion, vessels were stratified in five CFC categories: myocardial steal, severely reduced CFC, moderately reduced CFC, minimally reduced CFC, and normal flow. Additionally, the association between CFC increase and the composite endpoint of death and non-fatal myocardial infarction (MI) was studied. Vessel-specific CFC improved after revascularization (P < 0.01). Furthermore, baseline CFC was an independent predictor of CFC increase (P < 0.01). The largest changes in ΔhMBF (0.90 ± 0.74, 0.93 ± 0.65, 0.79 ± 0.74, 0.48 ± 0.61, and 0.29 ± 0.66 mL/min/g) and ΔCFR (1.01 ± 0.88, 0.99 ± 0.69, 0.87 ± 0.88, 0.66 ± 0.91, and −0.01 ± 1.06) were observed in vessels with lower baseline CFC (P < 0.01 for both). During a median follow-up of 3.5 (95% CI 3.1–3.9) years, an increase in CFC was independently associated with lower rates of death and non-fatal MI (HR 0.43, 95% CI 0.19–0.98, P = 0.04).

Conclusion

Successful revascularization results in an increase in CFC. Furthermore, baseline CFC was an independent predictor of change in hMBF, CFR, and subsequently CFC. In addition, an increase in CFC was associated with a favourable outcome in terms of death and non-fatal MI.
Gut microbiome status of urban and rural Filipino adults in relation to diet and metabolic disorders
Authors: Watanabe Mai , Sianoya Abraham , Mishima Riko , Therdtatha Phatthanaphong , Rodriguez Abigail , Ramos Donna Christene , Lee Yuan Kun , Dalmacio Leslie Michelle , Nakayama Jiro
Published: November 2021

Here, we aim to understand the condition of the gut microbiome of Filipino adults in relation to their diet and metabolic status. Compared to rural Albay (n = 67), the gut microbiome of subjects living in urban Manila (n = 25) was more colonized by the order Clostridiales, which was negatively correlated with host carbohydrate consumption. Principal component analysis using the genus composition of the 92 total subjects indicated four microbiome types: one type driven by Prevotella, which was associated with high rice consumption and mainly consisted of healthy Albay subjects, one Clostridiales-driven group containing a number of type 2 diabetes mellitus (T2D) subjects from both Manila and Albay who showed lower butyrate levels in association with a decrease in Mediterraneibacter faecis, and the other two types showing dysbiosis-like microbiomes with Lactobacillus and Bifidobacterium overgrowth, with a high ratio of T2D and obese subjects. Multivariate logistic regression analysis suggested high dietary energy intake, and two Veillonellaeae genera, Dialister and Megasphaera, as T2D risk factors, while Prevotella and M. faecis as anti-T2D factors. In conclusion, low-carbohydrate diets restructured the Prevotella-driven gut microbiome, which may predispose Filipino people with high energy diet to T2D.
A Reference Genome Assembly of Hybrid-Derived California Wild Radish (Raphanus sativus × raphanistrum)
Authors: Alexandre Nicolas M , Haji Diler , Bakhtiari Moe , Chatla Kamalakar , Aguilar Jessica M , Arzumanova Ksenia , Whiteman Noah K
Published: November 2021

For agriculturally important plants, pollination and herbivory are 2 ecological factors that play into the success of crop yields. Each is also important in natural environments where invasive plants and their effect on species interactions may alter the native ecology. The California Wild Radish (Raphanus sativus × raphanistrum), a hybrid derived from an agriculturally important crop and a nonnative cultivar, is common in California. Remarkably, it has recently replaced wild populations of both progenitor species. Experiments on phenotypic variation for petal color and antiherbivore defenses suggest both pairs of polymorphisms are maintained as a result of pollinator- and herbivore-mediated natural selection. This species provides an opportunity to understand how natural selection shapes the evolution of ecologically important traits when traits are constrained by 2 opposing forces. Here we provide the genome assembly of the California Wild Radish displaying improvement to currently existing genomes for agronomically important crucifers. This genome sequence provides the tools to dissect the genomic architecture of traits related to herbivory and pollination using natural variation in the wild as well as the ability to infer demographic and selective history in the context of hybridization. Study systems like these will improve our understanding and predictions of evolutionary change for correlated traits.
Evaluation of Discordant Results Between FilmArray Meningitis/Encephalitis Panel and Conventional Testing in Pediatric Patients: A Multisite Retrospective Cohort Study
Authors: Ekambaram Maheswari , Nabower Aleisha , Rajbhandari Prabi , Eisenberg Jaclyn , Goodrich Nathaniel , Ampofo Krow , Gollehon Nathan S , Martin Kimberly C , Lyden Elizabeth , Snowden Jessica
Published: November 2021

Background

The FilmArray Meningitis/Encephalitis panel (MEP) has an 11% false-positive and 2.2% false-negative rate compared with conventional testing. We describe clinical characteristics, treatment decisions, and outcomes in children with discordant results between MEP and conventional testing.

Methods

We conducted a multisite review of patients ≤ 18 years with suspected central nervous system infection and positive results by MEP or conventional testing (cerebrospinal fluid [CSF] culture, herpes simplex virus [HSV] polymerase chain reaction (PCR), and enterovirus [EV] PCR). Descriptive results are provided for patients with discordant results. Comparison between group 1 (MEP and CSF culture positive) and group 2 (MEP positive, CSF culture negative, or showing a different pathogen) was made by Mann-Whitney test for continuous and Fisher’s test for categorical variables.

Results

A total of 355 patients had at least one pathogen identified. More than half of patients with bacterial pathogens identified that are included in the MEP had discordant results (30/52; 58%). There were 28 samples with bacterial pathogen identified on MEP only, 1 with different bacterial pathogens on MEP and culture, and 1 with Escherichia coli identified on CSF culture only. Patients in group 1 were more likely to have CSF pleocytosis, elevated CSF protein, and decreased CSF glucose than group 2 (P < .05). Two patients were HSV positive by MEP while HSV negative by PCR. Ten patients had discordant results between MEP and EV PCR.

Conclusions

Discordant results between MEP and conventional testing are common. Treatment decisions based on a positive MEP should be made in the appropriate clinical context.
Hiatus hernia with gastric volvulus and duodenum component: a case report
Authors: Gimenez F Y , Takahashi L A R , Oliveira G G , Myaki J Y , Inaba M E , Feitosa F P A , Adão D
Published: November 2021

Gastric volvulus is a rare condition defined as an abnormal stomach rotation around its axis, which usually presents in children under a year or in adults in their fifth decade. Cases over 70-year-old are rare and only 30% of cases of this disease present with mesenteric-axial rotation of the stomach.

In this article, we report a rare case of mesenteroaxial gastric volvulus associated with hiatal hernia, in an 88-year-old woman, who presented to the Emergency Department of our institution with bowel obstruction symptoms.

The diagnosis could be difficult due to the rarity of the pathology, the patient's age outside the expected incidence age range and the less common mesenteroaxial presentation.

This report highlights the importance of the differential diagnosis of gastric volvulus as a cause of intestinal obstruction.
Global survey of alternative splicing and gene modules associated with fertility regulation in a thermosensitive genic male sterile wheat
Authors: Bai Jianfang , Wang Yukun , Liu Zihan , Guo Haoyu , Zhang Fengting , Guo Liping , Yuan Shaohua , Duan Wenjing , Li Yanmei , Tan Zhaoguo , Zhao Changping , Zhang Liping
Published: November 2021

Thermosensitive genic male sterile (TGMS) wheat lines are the core of two-line hybrid systems. Understanding the mechanism that regulates male sterility in TGMS wheat lines is helpful for promoting wheat breeding. Several studies have obtained information regarding the mechanisms associated with male sterility at the transcriptional level, but it is not clear how the post-transcriptional process of alternative splicing might contribute to controlling male sterility. In this study, we performed genome-wide analyses of alternative splicing during the meiosis stage in TGMS line BS366 using PacBio and RNA-Seq hybrid sequencing. Cytological observations indicated that cytoskeleton assembly in pollen cells, calcium deposition in pollen and tapetal cells, and vesicle transport in tapetal cells were deficient in BS366. According to our cytological findings, 49 differentially spliced genes were isolated. Moreover, 25 long non-coding RNA targets and three bHLH transcription factors were identified. Weighted gene co-expression network analysis detected four candidate differentially spliced genes that had strong co-relation with the seed setting percentage, which is the direct representation of male sterility in BS366. In this study, we obtained comprehensive data regarding the alternative splicing-mediated regulation of male sterility in TGMS wheat. The candidates identified may provide the molecular basis for an improved understanding of male sterility.
Investigating the structure of star-forming regions using INDICATE
Authors: Blaylock-Squibbs George A , Parker Richard J , Buckner Anne S M , Güdel Manuel
Published: November 2021

The ability to make meaningful comparisons between theoretical and observational data of star-forming regions is key to understanding the star formation process. In this paper, we test the performance of INDICATE, a new method to quantify the clustering tendencies of individual stars in a region, on synthetic star-forming regions with substructured, and smooth, centrally concentrated distributions. INDICATE quantifies the amount of stellar affiliation of each individual star, and also determines whether this affiliation is above random expectation for the star-forming region in question. We show that INDICATE cannot be used to quantify the overall structure of a region due to a degeneracy when applied to regions with different geometries. We test the ability of INDICATE to detect differences in the local stellar surface density and its ability to detect and quantify mass segregation. We then compare it to other methods such as the mass segregation ratio ΛMSR, the local stellar surface density ratio ΣLDR, and the cumulative distribution of stellar positions. INDICATE detects significant differences in the clustering tendencies of the most massive stars when they are at the centre of a smooth, centrally concentrated distribution, corresponding to areas of greater stellar surface density. When applied to a subset of the 50 most massive stars, we show INDICATE can detect signals of mass segregation. We apply INDICATE to the following nearby star-forming regions: Taurus, ONC, NGC 1333, IC 348, and ρ Ophiuchi and find a diverse range of clustering tendencies in these regions.
Financial Literacy in the Age of Green Investment
Authors: Anderson Anders , Robinson David T
Published: November 2021

We survey a large sample of Swedish households and connect the responses to administrative data to relate pro-environmental attitudes and values to actual investment decisions. Pro-environment households are not more likely to hold pro-environment portfolios. This results from financial disengagement: they are less likely to own stocks, check pension balances, or make green active retirement planning choices. Green financial engagement is stronger in settings where financial literacy is higher or where informational hurdles are lower. Informational barriers appear to prevent financial market prices and returns from fully reflecting household environmental preferences.
Adoption of Best Management Practices for Grapevine Leafroll and Red Blotch Diseases: A Survey of West Coast Growers
Authors: Hobbs Malcolm B. , Vengco Selena M. , Bolton Stephanie L. , Bettiga Larry J. , Moyer Michelle M. , Cooper Monica L.
Published: November 2021

Grapevine leafroll disease (GLD) and red blotch disease (RBD) threaten the sustainability of the U.S. wine grape industry. To understand the factors influencing the adoption of disease management practices, we surveyed wine grape industry professionals in California, Oregon, and Washington ( n = 154). Economic factors were the fundamental cost of implementing management practices and the ability to sell products from diseased vines (salability). Respondents who encountered reduced salability were more likely to adopt virus testing, replace infected vines, and view these practices as economically favorable. Salability was a strong driver for adoption among Californian respondents but less so in Washington, where wineries appeared more willing to accept infected products. Respondents who had acquired technical knowledge of disease ecology were more likely to adopt management practices and to perceive them as economical. Conversely, when there was a lack of knowledge of GLD ecology, notably that mealybugs transmit the pathogen, adoption was reduced, and practices were considered less economical. Factors affecting adoption were broadly generalizable across diseases. However, knowledge of GLD ecology was more strongly associated with adoption, likely reflecting the remaining knowledge gaps in RBD related to vector ecology and field spread. An emphasis on grower knowledge acquisition and the development of economical disease management practices can improve adoption of best management practices for viral diseases of grapevine.

[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Nursing Is No Day at the Beach
Authors: Kennedy Maureen Shawn
Published: November 2021

But more than ever, nurses need one.
Race vs. Racism: The Eligibility of African American Race as a Risk Factor
Authors: Mwilu Jacinta
Published: November 2021

Higher disease susceptibility in populations is too often seen as a nonmodifiable characteristic.
School Nursing During a Pandemic
Authors: Fauteux Nicole
Published: November 2021

School nurses gear up for more COVID-related challenges this fall.
Lamotrigine may Increase Risk of Arrythmias
Authors: Aschenbrenner Diane S.
Published: November 2021

The Food and Drug Administration (FDA) is advising health care practitioners that lamotrigine (Lamictal), used in managing seizures and bipolar disorder, may increase the risk of serious and potentially lethal arrythmias.

The risk is greater if the patient has underlying cardiac disease or is taking medications that affect heart conduction.

The FDA is requiring in vitro studies of other sodium channel blockers to determine if this risk is a class effect or unique to lamotrigine.
A Case of Heart Palpitations and a Rapid Pulse
Authors: Kupchik Nicole , Green Joel
Published: November 2021

Editor's note: This article is one in a series on electrocardiogram (ECG) interpretation. Nurses in all settings should know the basics, as medications and physiological changes can cause cardiac arrhythmias. Each article will start with a brief case scenario and an ECG strip and then take you step by step through analyzing the heart rhythm. To see all the articles in the series, go to http://links.lww.com/AJN/A207.
Intermittent vs. Continuous Pulse Oximetry in Infants Hospitalized with Bronchiolitis
Authors: Rosenberg Karen
Published: November 2021

According to this study:

Clinical outcomes were similar with intermittent and continuous pulse oximetry in infants who had stabilized bronchiolitis, providing support for standard use of intermittent monitoring in this population.
QI Intervention Reduces use of Nonbeneficial ICU Treatments
Authors: Rosenberg Karen
Published: November 2021

According to this study:

A quality improvement intervention that trained physicians to communicate with family members of critically ill patients in the ICU led to an improvement in the quality of family meetings and reduced the use of nonbeneficial treatments.
Similar Clinical Outcomes with Higher and Lower Oxygenation Targets
Authors: Rosenberg Karen
Published: November 2021

According to this study:

Among adults in the ICU who had acute hypoxemic respiratory failure, a lower oxygenation target didn't result in lower mortality rates compared with a higher target.
Protecting Nursing Home Residents and Staff from COVID-19
Authors: Ortelli Tracy A.
Published: November 2021

Two new tools from the AHRQ help facilitate observational audits.
Deep learning to estimate gestational age from blind ultrasound sweeps of the gravid abdomen
Authors: Pokaprakarn Teeranan , Prieto Juan C. , Price Joan T. , Kasaro Margaret P. , Sindano Ntazana , Shah Hina R. , Peterson Marc , Akapelwa Mutinta M. , Kapilya Filson M. , Sebastião Yuri V. , Goodnight William , Stringer Elizabeth M. , Freeman Bethany L. , Montoya Lina M. , Chi Benjamin H. , Rouse Dwight J. , Cole Stephen R. , Vwalika Bellington , Kosorok Michael R. , Stringer Jeffrey S. A.
Published: November 2021

Background

Ultrasound is indispensable to gestational age estimation, and thus to quality obstetric care, yet high equipment cost and need for trained sonographers limit its use in low-resource settings.

Methods

From September 2018 through June 2021, we recruited 4,695 pregnant volunteers in North Carolina and Zambia and obtained blind ultrasound sweeps (cineloops) of the gravid abdomen alongside standard fetal biometry. We trained a neural network to estimate gestational age from the sweeps and, in three test sets, assessed performance of the model and biometry against previously established gestational age.

Results

In our main test set, model mean absolute error (MAE) was 3.9 days (standard error [SE] 0.12) vs. 4.7 days (SE 0.15) for biometry (difference -0.8 days; 95% CI -1.1, -0.5; p<0.001). Results were similar in North Carolina (difference -0.6 days, 95% CI -0.9, -0.2) and Zambia (−1.0 days, 95% CI -1.5, -0.5). Findings were supported in the test set of women who conceived by in vitro fertilization (model MAE 2.8 days [SE 0.28] vs. 3.6 days [SE 0.53] for biometry; difference -0.8 days, 95% CI -1.7, 0.2), and in the set of women from whom sweeps were collected by untrained users with low-cost, battery-powered devices (model MAE 4.9 days [SE 0.29] vs. 5.4 days [SE 0.28] for biometry; difference -0.6, 95% CI -1.3, 0.1).

Conclusions

Our model estimated gestational age more accurately from blindly obtained ultrasound sweeps than did trained sonographers performing fetal biometry. These results presage a future where all pregnant people – not just those in rich countries – can access the diagnostic benefits of sonography.
Modeling on Wastewater Treatment Process in Saudi Arabia: a perspective of Covid-19
Authors: Ahmadini Abdullah , Msmali Ahmed , Mutum Zico , Raghav Yashpal Singh
Published: November 2021

The novel coronavirus disease (COVID-19) pandemic has had devastating effects on healthcare systems and the global economy. Moreover, coronavirus has been found in human feces, sewage, and in wastewater treatment plants. In this paper, we highlight the transmission behavior, occurrence, and persistence of the virus in sewage and wastewater treatment plants. Our approach follows the process of identifying a coronavirus hotspot through existing wastewater plants in major cities of Saudi Arabia. The mathematical distributions, including the log-normal distribution, Gaussian model, and susceptible exposed infected recovery (SEIR) model, are adopted to predict the coronavirus load in wastewater plants. We highlight not only the potential virus removal techniques from wastewater treatment plants, but also methods of tracing SARS-CoV-2 in humans through wastewater treatment plants.
Imaging synaptic microstructure and synaptic loss in vivo in early Alzheimer’s Disease
Authors: Venkataraman Ashwin V , Bishop Courtney , Mansur Ayla , Rizzo Gaia , Lewis Yvonne , Kocagoncu Ece , Lingford-Hughes Anne , Huiban Mickael , Passchier Jan , Rowe James B , Tsukada Hideo , Brooks David J. , Martarello Laurent , Comley Robert A. , Chen Laigao , Hargreaves Richard , Schwarz Adam J. , Gunn Roger N. , Rabiner Eugenii A. , Matthews Paul M
Published: November 2021

1.

Background

Synaptic loss and neurite dystrophy are early events in Alzheimer’s Disease (AD). We aimed to characterise early synaptic microstructural changes in vivo.

Methods

MRI neurite orientation dispersion and density imaging (NODDI) and diffusion tensor imaging (DTI) were used to image cortical microstructure in both sporadic, late onset, amyloid PET positive AD patients and healthy controls (total n = 28). We derived NODDI measures of grey matter extracellular free water (FISO), neurite density (NDI) and orientation dispersion (ODI), which provides an index of neurite branching and orientation, as well as more conventional DTI measures of fractional anisotropy (FA), mean/axial/radial diffusivity (MD, AD, RD, respectively). We also performed [11C]UCB-J PET, which provides a specific measure of the density of pre-synaptic vesicular protein SV2A. Both sets of measures were compared to regional brain volumes.

Results

The AD patients showed expected relative decreases in regional brain volumes (range, -6 to - 23%) and regional [11C]UCB-J densities (range, -2 to -25%). Differences between AD and controls were greatest in the hippocampus. NODDI microstructural measures showed greater FISO (range, +26 to +44%) in AD, with little difference in NDI (range, -1 to +7%) and mild focal changes in ODI (range, -4 to +3%). Regionally greater FISO and lower [11C]UCB-J binding were correlated across grey matter in patients (most strongly in the caudate, r2 = 0.37, p = 0.001). FISO and DTI RD were strongly positively associated, particularly in the hippocampus (r2 = 0.98, p < 7.4 × 10−9). After 12-18 months we found a 5% increase in FISO in the temporal lobe, but little change across all ROIs in NDI and ODI. An exploratory analysis showed higher parietal lobe FISO was associated with lower language scores in people with AD.

Conclusions

We interpreted the increased extracellular free water as a possible consequence of glial activation. The dynamic range of disease-associated differences and the feasibility of measuring FISO on commercially available imaging systems makes it a potential surrogate for pathology related to synapse loss that could be used to support early-stage evaluations of novel therapeutics for AD.
Recurring Spatiotemporal Patterns of COVID-19 in the United States
Authors: Jalal Hawre , Lee Kyueun , Burke Donald S.
Published: November 2021

We analyzed the waxing and waning patterns (“surges”) of reported SARS-CoV-2 cases from January 1, 2020 through Oct 31, 2021 in all states and provinces (n = 93) in the USA, Mexico, and Canada, and across all counties (N = 3142) in the USA. A correlation matrix of the 576 × 576 daily case incidence rates in the 50 US states generates a distinctive “checkerboard” pattern showing that the epidemic has consisted of seven distinct internally coherent spatiotemporal wave patterns, four in the first year of the epidemic, and three thus far in the second year. Geoclustering of state case rate trajectories reveals three dominant co-varying spatial clusters of similar case rate trajectories, in the northeastern, southeastern and central/western regions of the USA. The spatiotemporal patterns of epidemic year 1 have thus far been repeated (p<.001) in epidemic year 2. The “checkerboard” pattern of the correlation matrix of case trajectories can be closely simulated as three sets of interacting sine waves with annual frequencies of 1:1:2 major cycles per year, corresponding to the northeastern, central/western, and southeastern state clusters. Case incidence patterns in Mexico and Canada have been similar to nearby regions in the southern US and the northern US, respectively. Time lapse videos allow visualization of the wave patterns. These highly structured geographical and temporal patterns, coupled with emerging evidence of annual repetition of these same patterns, show that SARS-CoV-2 case rates are driven at least in part by predictable seasonal factors.

Significance Statement

Local COVID-19 rates wax and wane. Often these epidemic changes are attributed to localized human behavioral factors. Our finding of highly structured continental scale spatiotemporal patterns that cross state and national boundaries, coupled with emerging evidence of annual repetition of these same patterns, shows that COVID-19 transmission is driven at least in part by seasonal factors. Other epidemic factors such as vaccine coverage rates, or emergence of new strains like the Delta variant of SARS-CoV-2 appear to modify, but not totally eclipse, these underlying seasonal patterns. COVID-19 seasonal transmission patterns are associated with, and may be driven by, seasonal weather patterns. Predictability of these patterns can provide opportunities for forecasting the epidemic and for guiding public health preparedness and control efforts.
Phylogeny of the ingoid clade (Caesalpinioideae, Fabaceae), based on nuclear and plastid data
Authors: Ferm Julia , Ståhl Bertil , Wikström Niklas , Rydin Catarina
Published: November 2021

We investigated generic relationships in the ingoid clade (Fabaceae) (sensu Koenen & al. 2020a), with main focus on genera with a taxonomic history inCalliandras.l. of the tribe Ingeae (i.e.Afrocalliandra, Calliandras.s.,Sanjappa, Thailentadopsis, Viguieranthus, Zapoteca), and three genera of the tribe Acacieae (i.e.,Acacia, Acaciella, Senegalia). The nuclear ribosomal ETS and ITS, and the plastidmatK, trnL-trnFandycf1DNA-regions were analysed for 246 representatives from 36 genera using maximum likelihood as implemented in IQ-tree. The results show an Ingeae–Acaciaclade within the ingoid clade, resolved in three major clades. Clade 1 (Calliandras.s. andAfrocalliandra) is sister to clades 2 and 3. Clade 2 comprisesFaidherbia, Sanjappa, Thailentadopsis, ViguieranthusandZapoteca. Clade 3 comprises the remaining genera of the Ingeae, plusAcacia. The ingoid genusSenegaliais excluded from the Ingeae–Acaciaclade.Acaciellais sister to the remaining ingoid clade when nuclear ribosomal data is included in the analyses, but included in the Ingeae–Acaciaclade based on plastid data.Acaciaand perhaps alsoAcaciellaare thus nested within Ingeae. Species traditionally referred toCalliandra(Calliandras.l.) are resolved in two clades, and the “Calliandra-pod” has apparently evolved independently several times.
SARS-CoV-2 Delta Spike Protein Enhances the Viral Fusogenicity and Inflammatory Cytokine Production
Authors: Ao Zhujun , Ouyang Maggie Jing , Olukitibi Titus Abiola , Yao Xiaojian
Published: November 2021

The Delta variant is now the most dominant and virulent SARS-CoV-2 variant of concern (VOC). In this study, we investigated several virological features of Delta spike protein (SPDelta), including protein maturation and its impact on viral entry of cell-free pseudotyped virus, cell-cell fusion ability and its induction of inflammatory cytokine production in human macrophages and dendritic cells. The results showed that SPΔCDelta exhibited enhanced S1/S2 cleavage in cells and pseudotyped virus-like particles (PVLPs). We further showed that SPΔCDelta elevated pseudovirus infection in human lung cell lines and mediated significantly enhanced syncytia formation. Furthermore, we revealed that SPΔCDelta-PVLPs had stronger effects on stimulating NF-κB and AP-1 signaling in human monocytic THP1 cells and induced significantly higher levels of pro-inflammatory cytokine, such as TNF-α, IL-1β and IL-6, released from human macrophages and dendritic cells. Overall, these studies provide evidence to support the important role of SPΔCDelta during virus infection, transmission and pathogenesis.
Learning the Rules of Cell Competition without Prior Scientific Knowledge
Authors: Soelistyo Christopher J. , Vallardi Giulia , Charras Guillaume , Lowe Alan R.
Published: November 2021

Abstract

Deep learning is now a powerful tool in microscopy data analysis, and is routinely used for image processing applications such as segmentation and denoising. However, it has rarely been used to directly learn mechanistic models of a biological system, owing to the complexity of the internal representations. Here, we develop an end-to-end machine learning model capable of learning the rules of a complex biological phenomenon, cell competition, directly from a large corpus of time-lapse microscopy data. Cell competition is a quality control mechanism that eliminates unfit cells from a tissue and during which cell fate is thought to be determined by the local cellular neighborhood over time. To investigate this, we developed a new approach (τ-VAE) by coupling a probabilistic encoder to a temporal convolution network to predict the fate of each cell in an epithelium. Using the τ-VAE’s latent representation of the local tissue organization and the flow of information in the network, we decode the physical parameters responsible for correct prediction of fate in cell competition. Remarkably, the model autonomously learns that cell density is the single most important factor in predicting cell fate – a conclusion that is in agreement with our current understanding from over a decade of scientific research. Finally, to test the learned internal representation, we challenge the network with experiments performed in the presence of drugs that block signalling pathways involved in competition. We present a novel discriminator network that, using the predictions of the τ-VAE, can identify conditions which deviate from the normal behaviour, paving the way for automated, mechanism-aware drug screening.
Fluidic Circuit Board with Modular Sensor and Valves Enables Stand-Alone, Tubeless Microfluidic Flow Control in Organs-on-Chips
Authors: Vivas Aisen , van den Berg Albert , Passier Robert , Odijk Mathieu , van der Meer Andries D.
Published: November 2021

Organs-on-chips are a unique class of microfluidic in vitro cell culture models, in which the in vivo tissue microenvironment is mimicked. Unfortunately, its widespread use is hampered by their operation complexity and incompatibility with end-user research settings. To address these issues, many commercial and non-commercial platforms have been developed for semi-automated culture of organs-on-chips. However, these organ-on-chip culture platforms each represent a closed ecosystem, with very little opportunity to interchange and integrate components from different platforms or to develop new ones. The Translational Organ-on-Chip Platform (TOP) is a multi-institutional effort to develop an open platform for automated organ-on-chip culture and integration of components from various developers. Central to TOP is the fluidic circuit board (FCB), a microfluidic plate with the form factor of a typical well plate. The FCB enables microfluidic control of multiple components like sensors or organ-on-chip devices through an interface based on openly available standards. Here, we report an FCB to integrate commercial and in-house developed components forming a stand-alone flow control system for organs-on-chips. The control system is able to achieve constant and pulsatile flow recirculation through a connected organ-on-chip device. We demonstrate that this system is able to automatically perfuse a heart-on-chip device containing co-cultures of cardiac tissues derived from human pluripotent stem cell-derived cardiomyocytes and monolayers of endothelial cells for five days. Altogether, we conclude that open technology platforms allow the integration of components from different sources to form functional and fit-for-purpose organ-on-chip systems. We anticipate that open platforms will play a central role in catalysing and maturing further technological development of organ-on-chip culture systems.
ECLIPSER: identifying causal cell types and genes for complex traits through single cell enrichment of e/sQTL-mapped genes in GWAS loci
Authors: Rouhana John M. , Wang Jiali , Eraslan Gokcen , Anand Shankara , Hamel Andrew R. , Cole Brian , Regev Aviv , Aguet François , Ardlie Kristin G. , Segrè Ayellet V.
Published: November 2021

ECLIPSER was developed to identify pathogenic cell types and cell type-specific genes that may affect complex disease susceptibility and trait variation by integrating single cell data with known GWAS loci. ECLIPSER maps genes to GWAS loci for a given complex trait based on expression and splicing quantitative trait loci (e/sQTLs) and other functional data, and tests whether the mapped genes are enriched for cell type-specific expression in particular cell types using single-cell/nucleus RNA-seq data from one or more tissues of interest. A Bayesian Fisher’s exact test is used to compute fold-enrichment significance. We demonstrate the application of ECLIPSER on various skin diseases and traits using snRNA-seq of healthy human skin samples.

Availability and Implementation

The source code and documentation for ECLIPSER and a Jupyter notebook for generating output tables and figures are available at https://github.com/segrelabgenomics/ECLIPSER. The source code for GWASvar2gene that maps genes to GWAS loci based on e/sQTLs is available at https://github.com/segrelabgenomics/GWASvar2gene. The analysis presented here used data from GTEx (https://gtexportal.org/home/datasets) and Open Targets Genetics (https://genetics-docs.opentargets.org/data-access/graphql-api), but can also be applied to other GWAS variant lists and QTL studies. Data used to reproduce the results of the paper are available in Supplementary data.
Spread of pathological human Tau from neurons to oligodendrocytes and loss of high-firing pyramidal neurons in ageing mice
Authors: Viney Tim J. , Sarkany Barbara , Ozdemir A. Tugrul , Hartwich Katja , Schweimer Judith , Bannerman David , Somogyi Peter
Published: November 2021

Intracellular aggregation of hyperphosphorylated Tau (pTau) in the brain is associated with cognitive and motor impairments, and ultimately neurodegeneration. We investigate how human pTau affects cells and network activity in the hippocampal formation of THY-Tau22 tauopathy model micein vivo. We find that pTau preferentially accumulates in deep-layer pyramidal neurons, leading to neurodegeneration, and we establish that pTau spreads to oligodendrocytes. During goal-directed virtual navigation in aged transgenic mice, we detect fewer high-firing prosubicular pyramidal cells but the firing population retains its coupling to theta oscillations. Analysis of network oscillations and firing patterns of pyramidal and GABAergic neurons recorded in head-fixed and freely-moving mice suggests preserved neuronal coordination. In spatial memory tests, transgenic mice have reduced short-term familiarity but spatial working and reference memory are surprisingly normal. We hypothesize that unimpaired subcortical network mechanisms maintain cortical neuronal coordination, counteracting the widespread pTau aggregation, loss of high-firing cells, and neurodegeneration.