bluuebunny/crossref_metadata_2025 huggingface dataset:
The Accuracy of Identifying Constituencies with Geographic Assignment Within State Legislative Districts
Authors: Steelman Tyler , Curiel John A.
Published: February 2023

Identifying the geographic constituencies of representatives is among the most crucial, yet challenging, aspects of state and local politics research. Regularly changing district lines, incomplete data, and computational obstacles can present barriers to matching individuals to their respective districts. Geocoding residential addresses is the ideal method for matching purposes. However, cost constraints can limit its applicability for many researchers, leading to geographic assignment methods that use polygonal units, such as ZIP codes, to estimate constituency membership. In this study, we quantify the trade-offs between three geographic assignment matching methods – centroid, geographic overlap, and population overlap matching – on the assignment of individual voters to state legislative districts. We confirm that population overlap matching produces the highest accuracy in assigning voters to their state legislative districts when polygonal location data are all that is available. We validate this finding by improving model estimates of lobbying influence through a replication analysis of Bishop and Dudley (2017), “The Role of Constituency, Party, and Industry in Pennsylvania’s Act 13,” State Politics and Policy Quarterly 17 (2): 154–79. Our replication suggests that distinguishing between out-of-district and in-district donations reveals a greater impact for in-district lobbying efforts. We make evident that population overlap assignment can confidently be used to identify constituencies when precise location data is not available.
Rock‐Matrix Porosity and Permeability of the Hydrothermally Altered, Upper Oceanic Crust, Oman Ophiolite
Authors: Brett‐Adams Alannah C. , Diamond Larryn W. , Weber Samuel , Gilgen Samuel A.
Published: February 2023

Porosity and permeability are key controls on hydrothermal circulation and alteration in magmatically heated upper oceanic crust. However, the hydraulic properties of basalts altered above 200°C are largely unknown, leaving their role in high‐temperature systems unclear. Here, we assess rock‐matrix porosities and permeabilities of pervasively altered MORB‐like basalts from outcrops in the sheeted dikes and axial lavas of the Semail ophiolite, Oman. The samples represent regional spilite alteration (chlorite–albite–quartz ± actinolite; 150–440°C) and localized epidosite alteration (epidote–quartz; 255–435°C). Porosity and permeability of spilitized rocks vary as follows: interpillow hyaloclastites (14–27 vol.%, 10−17–10−15 m2) > pillow cores (4–12 vol.%; ∼10−19–6 × 10−18 m2) > pillow rims (4–11 vol.%; ∼10−19–2 × 10−18 m2) > massive sheet flows (1–9 vol.%; ∼10−19 m2) ≥ dikes (1–5 vol.%; ∼10−19 m2). Pillow values fall within the ranges of existing data on fresh and low‐temperature altered basalts in in situ crust. However, hyaloclastite permeabilities are 1–4 orders of magnitude higher and are clearly preferred flow paths. Epidosites have elevated porosity and permeability irrespective of rock morphology (18–26 vol.%; ∼10−16–10−14 m2). Pillow stacks have upscaled (∼104 m3) matrix porosities and permeabilities of ∼9 vol.% and ∼10−17–10−16 m2 when spilitized and 16 vol.% and up to ∼10−14 m2 when epidotized. Upscaled permeabilities of spilites meet minimum requirements for observed heat and fluid discharge from high‐temperature seafloor systems even without fracture networks, and reflect strong flow through the rock‐matrix.
Impacts of Agricultural Soil NOx Emissions on O3 Over Mainland China
Authors: Shen Yonglin , Xiao Zemin , Wang Yi , Xiao Wen , Yao Ling , Zhou Chenghu
Published: February 2023

Regional ozone (O3) pollution has currently become an urgent air pollution problem in China. Nitrogen oxides (NOX) are key precursor pollutants for O3 formation. However, pollution control policies have generally neglected or simplified the impacts of soil NOX emissions in rural regions. This study aims to evaluate the effect of soil NOX emissions on O3 in agricultural areas of China based on high‐resolution soil NOX emission inventory and the WRF‐Chem air quality model. We first validate the simulation result of the O3 concentration with surface O3 observations over China using the selected optimal physicochemical scheme. After that, four scenarios are designed to simulate and analyze the regional sensitivity of O3 to soil NOX emissions and to quantify the effect of soil NOX emissions on O3 concentration. The results indicate that as soil NOX emissions increase, the overall spatial pattern does not change notably over mainland China, but the O3 concentration increases remarkably in the northwest and northeast of China. Additionally, we discover that changes of O3 concentration across mainland China differ substantially among regions. Our results highlight the effect of soil NOX emissions on air quality in agricultural areas. The control of O3 pollution in China should take into account the comprehensive consequences of various emission sources, as well as their regional differences.
Anomalous 33S in the Lunar Mantle
Authors: Dottin J. W. , Kim S.‐T. , Wing B. , Farquhar J. , Shearer C.
Published: February 2023

The origin, evolution, and cycling of volatiles on the Moon are established by processes such as the giant moon forming impact, degassing of the lunar magma ocean, degassing during surface eruptions, and lunar surface gardening events. These processes typically induce mass‐dependent stable isotope fractionations. Mass‐independent fractionation of stable isotopes has yet to be demonstrated during events that release large volumes of gas on the moon and establish transient lunar atmospheres. We present quadruple sulfur isotope compositions of orange and black glass beads from drive tube 74002/1. The sulfur isotope and concentration data collected on the orange and black glasses confirm a role for magmatic sulfur loss during eruption. The Δ33S value of the orange glasses is homogenous (Δ33S = −0.029‰ ± 0.004‰, 2SE) and different from the isotopic composition of lunar basalts (Δ33S = 0.002‰ ± 0.004‰, 2SE). We link the negative Δ33S composition of the orange glasses to an anomalous sulfur source in the lunar mantle. The nature of this anomalous sulfur source remains unknown and is either linked to (a) an impactor that delivered anomalous sulfur after late accretion, (b) sulfur that was photochemically processed early during lunar evolution and was transported to the lunar mantle, or (c) a primitive sulfur component that survived mantle mixing. The examined black glass preserves a mass‐dependent Δ33S composition (−0.008‰ ± 0.006‰, 2SE). The orange and black glasses are considered genetically related, but the discrepancy in Δ33S composition among the two samples calls their relationship into question.
A New Approach for Assessing Groundwater Recharge by Combining GRACE and Baseflow With Case Studies in Karst Areas of Southwest China
Authors: Huang Zhiyong , Yeh Pat J.‐F. , Jiao Jiu Jimmy , Luo Xin , Pan Yun , Long Yuannan , Zhang Chong , Zheng Longqun
Published: February 2023

A new approach combining groundwater storage change (GWSC) derived from Gravity Recovery and Climate Experiment (GRACE) satellite data and baseflow was proposed to estimate groundwater recharge at large spatial scales but a short (monthly) time scale. This method was applied in two typical karst basins of southwest China, the Wujiang River basin (WRB, ∼87,900 km2, ∼70% karstification) and Xijiang River Basin (XRB, ∼360,000 km2, ∼44% karstification). The 2006–2012 monthly baseflow was first separated from in situ streamflow through multivariate regression analysis. Groundwater recharge was estimated using separated baseflow and GWSC estimated from GRACE data and observation‐based groundwater‐level data. The comparison between GRACE‐ and observation‐based recharge in the larger XRB shows better consistency, while that in the smaller WRB shows larger discrepancies. Considering the associated uncertainty (60–93 mm/yr), the 2006–2012 mean recharge in two basins, ranging 199–225 mm/yr (17%–19% of precipitation) is comparable to bulletin‐reported estimates (∼145 mm/yr). Both the degree of karstification and aquifer water table depth influence recharge and discharge processes in karst areas of southwest China. The more karstic WRB exhibits more rapid infiltration (due to more developed permeable epikarst zone) and higher discharge capability (due to more developed underground drainage systems), particularly during dry periods (2009, 2011, and winter). Baseflow exhibits a shorter time lag to recharge and GWSC in the XRB than WRB owing to more quick flow, lower storage with more rapid infiltration, and shorter mean groundwater residence time. Observation‐based monthly recharge reflects different rainfall‐infiltration‐runoff processes under different rainfall intensities, particularly in the WRB.
Climate and Human Impacts on Hydrological Processes and Flood Risk in Southern Louisiana
Authors: Getirana Augusto , Kumar Sujay , Konapala Goutam , Nie Wanshu , Locke Kim , Loomis Bryant , Birkett Charon , Ricko Martina , Simard Marc
Published: February 2023

Satellite observations of coastal Louisiana indicate an overall land loss over recent decades, which could be attributed to climate and human‐induced factors, including sea level rise (SLR). Climate‐induced hydrological change (CHC) has impacted the way flood control structures are used, altering the spatiotemporal water distribution. Based on “what‐if” scenarios, we determine relative impacts of SLR and CHC on increased flood risk over southern Louisiana and examine the role of water management, via flood control structures, in mitigating flood risk over the region. Our findings show that CHC has increased flood risk over the past 28 years. The number of affected people increases as extreme hydrological events become more exceptional. Water management reduces flood risk to urban areas and croplands, especially during exceptional hydrological events. For example, currently (i.e., 2016–2020 period), CHC‐induced flooding puts an additional 73 km2 of cropland under flood risk at least half of the time (median flood event) and 65 km2 once a year (annual flood event), when compared to a past period (1993–1997). A 10‐ to 20‐fold increase relative to SLR‐induced flooding. CHC also increases population vulnerability in southern Louisiana to flooding; additional 9,900 residents currently live under flood risk at least half of the time, and that number increases to 27,400 for annual flood events. Residents vulnerable to SLR‐induced flooding is lower (6,000 and 3,300 residents, respectively). Conclusions are that CHC is a major factor that should be accounted for flood resilience and that water management interventions can mitigate risks to human life and activities.
Racial and ethnic disparities in postnatal growth among very low birth weight infants in California
Authors: Lee Soon Min , Sie Lillian , Liu Jessica , Profit Jochen , Main Elliot , Lee Henry C.
Published: February 2023

Objective

To identify racial/ethnic disparities in postnatal growth by year and gestational age among very low birth weight infants.

Study design

Total 37,122 infants, with birth weight 500–1500 g or gestational age 23–34 weeks in the California Perinatal Quality Care Collaborative in 2008–2016. Postnatal growth failure (PGF) was defined as change in weight Z-score from birth to discharge below −1.28. Multivariable regression analysis with birth hospital as random effect was used to estimate odds ratios (OR).

Results

Infants born to Hispanic mothers had highest risk of PGF at 30%, compared to white (24%, OR 1.33), Black (22%, OR 1.50), or Asian/Pacific Islander mothers (23%, OR 1.38). PGF incidence decreased from 2008 (27.4%) to 2016 (22.8%) with differences in trends by race. Each increasing gestational age week was associated with decreasing risk for PGF (OR 0.73, 95% confidence interval 0.72–0.74).

Conclusion

Targeted interventions addressing PGF are needed to address disparities.
circIPO7 dissociates caprin-1 from ribosomes and inhibits gastric cancer cell proliferation by suppressing EGFR and mTOR
Authors: Liu Jing , Niu Liling , Hao Jiaru , Yao Yuan , Yan Meinan , Li Hui
Published: February 2023

Circular RNA (circRNA) is a novel RNA molecule characterized by covalently closed loop structure. Since its discovery, researchers have shown that circRNA is not “splicing noise” but a participant of various pathophysiological processes through unique mechanisms. circIPO7, which was identified as an independent prognostic factor in gastric cancer (GC) patients, was downregulated in GC tissues and cells compared to paracarcinoma tissues and normal epithelial cells. circIPO7 overexpression significantly suppressed GC cell proliferation in vitro and in vivo. Mechanistically, circIPO7 directly binds with caprin-1, an RNA-binding protein involved in mRNA translation, sharing overlapping binding sites with G3BP1. Thus, the complex containing overexpressed circIPO7 blocked the caprin-1-G3BP1 interaction and dissociated caprin-1 and its target mRNAs (EGFR and mTOR) from ribosomes, resulting in their translational inhibition, followed by PI3K/AKT/mTOR pathway inactivation. We uncovered a novel molecular mechanism for circRNAs in GC development, identifying circIPO7 as a potential target for cancer treatment.
Osteoarthritis: pathogenic signaling pathways and therapeutic targets
Authors: Yao Qing , Wu Xiaohao , Tao Chu , Gong Weiyuan , Chen Mingjue , Qu Minghao , Zhong Yiming , He Tailin , Chen Sheng , Xiao Guozhi
Published: February 2023

Osteoarthritis (OA) is a chronic degenerative joint disorder that leads to disability and affects more than 500 million population worldwide. OA was believed to be caused by the wearing and tearing of articular cartilage, but it is now more commonly referred to as a chronic whole-joint disorder that is initiated with biochemical and cellular alterations in the synovial joint tissues, which leads to the histological and structural changes of the joint and ends up with the whole tissue dysfunction. Currently, there is no cure for OA, partly due to a lack of comprehensive understanding of the pathological mechanism of the initiation and progression of the disease. Therefore, a better understanding of pathological signaling pathways and key molecules involved in OA pathogenesis is crucial for therapeutic target design and drug development. In this review, we first summarize the epidemiology of OA, including its prevalence, incidence and burdens, and OA risk factors. We then focus on the roles and regulation of the pathological signaling pathways, such as Wnt/β-catenin, NF-κB, focal adhesion, HIFs, TGFβ/ΒΜP and FGF signaling pathways, and key regulators AMPK, mTOR, and RUNX2 in the onset and development of OA. In addition, the roles of factors associated with OA, including MMPs, ADAMTS/ADAMs, and PRG4, are discussed in detail. Finally, we provide updates on the current clinical therapies and clinical trials of biological treatments and drugs for OA. Research advances in basic knowledge of articular cartilage biology and OA pathogenesis will have a significant impact and translational value in developing OA therapeutic strategies.
Dietary patterns related to biological mechanisms and survival after breast cancer diagnosis: results from a cohort study
Authors: Castro-Espin Carlota , Bonet Catalina , Crous-Bou Marta , Katzke Verena , Le Cornet Charlotte , Jannasch Franziska , Schulze Matthias B. , Olsen Anja , Tjønneland Anne , Dahm Christina C. , Antoniussen Christian S. , Sánchez Maria Jose , Amiano Pilar , Chirlaque María Dolores , Guevara Marcela , Agnoli Claudia , Tumino Rosario , Sacerdote Carlotta , De Magistris Maria Santucci , Sund Malin , Bodén Stina , Jensen Torill Enget , Olsen Karina Standahl , Skeie Guri , Gunter Marc J. , Rinaldi Sabina , Gonzalez-Gil Esther M. , Weiderpass Elisabete , Christakoudi Sofia , Heath Alicia K. , Dossus Laure , Agudo Antonio
Published: February 2023

Background

Inflammatory, insulin and oestrogenic pathways have been linked to breast cancer (BC). We aimed to examine the relationship between pre-diagnostic dietary patterns related to these mechanisms and BC survival.

Methods

The diabetes risk reduction diet (DRRD), inflammatory score of diet (ISD) and oestrogen-related dietary pattern (ERDP) were calculated using dietary data from the European Prospective Investigation into Cancer and Nutrition (EPIC) study. Cox proportional hazards models were used to assess associations between dietary patterns and overall mortality and competing risk models for associations with BC-specific mortality.

Results

We included 13,270 BC cases with a mean follow-up after diagnosis of 8.6 years, representing 2340 total deaths, including 1475 BC deaths. Higher adherence to the DRRD score was associated with lower overall mortality (HR1–SD 0.92; 95%CI 0.87–0.96). Greater adherence to pro-inflammatory diets was borderline associated with 6% higher mortality HR1–SD 1.06; 95%CI 1.00–1.12. No significant association with the oestrogen-related dietary pattern was observed. None of the dietary patterns were associated with BC-specific mortality.

Conclusions

Greater adherence to an anti-diabetic and anti-inflammatory diet prior to diagnosis is associated with lower overall mortality among BC survivors. Long-term adherence to these dietary patterns could be a means to improve the prognosis of BC survivors.
CCN3/NOV promotes metastasis and tumor progression via GPNMB-induced EGFR activation in triple-negative breast cancer
Authors: Son Seogho , Kim Hyungjoo , Lim Hogeun , Lee Joo-hyung , Lee Kyung-min , Shin Incheol
Published: February 2023

Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer. TNBC patients typically exhibit unfavorable outcomes due to its rapid growth and metastatic potential. Here, we found overexpression of CCN3 in TNBC patients. We identified that CCN3 knockdown diminished cancer stem cell formation, metastasis, and tumor growth in vitro and in vivo. Mechanistically, ablation of CCN3 reduced activity of the EGFR/MAPK pathway. Transcriptome profiling revealed that CCN3 induces glycoprotein nonmetastatic melanoma protein B (GPNMB) expression, which in turn activates the EGFR pathway. An interrogation of the TCGA dataset further supported the transcriptional regulation of GPNMB by CCN3. Finally, we showed that CCN3 activates Wnt signaling through a ligand-dependent or -independent mechanism, which increases microphthalmia-associated transcription factor (MITF) protein, a transcription factor inducing GPNMB expression. Together, our findings demonstrate the oncogenic role of CCN3 in TNBC, and we propose CCN3 as a putative therapeutic target for TNBC.
Macromolecular sheets direct the morphology and orientation of plate-like biogenic guanine crystals
Authors: Wagner Avital , Upcher Alexander , Maria Raquel , Magnesen Thorolf , Zelinger Einat , Raposo Graça , Palmer Benjamin A.
Published: February 2023

Animals precisely control the morphology and assembly of guanine crystals to produce diverse optical phenomena in coloration and vision. However, little is known about how organisms regulate crystallization to produce optically useful morphologies which express highly reflective crystal faces. Guanine crystals form inside iridosome vesicles within chromatophore cells called iridophores. By following iridosome formation in developing scallop eyes, we show that pre-assembled, fibrillar sheets provide an interface for nucleation and direct the orientation of the guanine crystals. The macromolecular sheets cap the (100) faces of immature guanine crystals, inhibiting growth along the π-stacking growth direction. Crystal growth then occurs preferentially along the sheets to generate highly reflective plates. Despite their different physical properties, the morphogenesis of iridosomes bears a striking resemblance to melanosome morphogenesis in vertebrates, where amyloid sheets template melanin deposition. The common control mechanisms for melanin and guanine formation inspire new approaches for manipulating the morphologies and properties of molecular materials.
Shark nanobodies with potent SARS-CoV-2 neutralizing activity and broad sarbecovirus reactivity
Authors: Chen Wei-Hung , Hajduczki Agnes , Martinez Elizabeth J. , Bai Hongjun , Matz Hanover , Hill Thomas M. , Lewitus Eric , Chang William C. , Dawit Layla , Peterson Caroline E. , Rees Phyllis A. , Ajayi Adelola B. , Golub Emily S. , Swafford Isabella , Dussupt Vincent , David Sapna , Mayer Sandra V. , Soman Sandrine , Kuklis Caitlin , Corbitt Courtney , King Jocelyn , Choe Misook , Sankhala Rajeshwer S. , Thomas Paul V. , Zemil Michelle , Wieczorek Lindsay , Hart Tricia , Duso Debora , Kummer Larry , Yan Lianying , Sterling Spencer L. , Laing Eric D. , Broder Christopher C. , Williams Jazmean K. , Davidson Edgar , Doranz Benjamin J. , Krebs Shelly J. , Polonis Victoria R. , Paquin-Proulx Dominic , Rolland Morgane , Reiley William W. , Gromowski Gregory D. , Modjarrad Kayvon , Dooley Helen , Joyce M. Gordon
Published: February 2023

Despite rapid and ongoing vaccine and therapeutic development, SARS-CoV-2 continues to evolve and evade, presenting a need for next-generation diverse therapeutic modalities. Here we show that nurse sharks immunized with SARS-CoV-2 recombinant receptor binding domain (RBD), RBD-ferritin (RFN), or spike protein ferritin nanoparticle (SpFN) immunogens elicit a set of new antigen receptor antibody (IgNAR) molecules that target two non-overlapping conserved epitopes on the spike RBD. Representative shark antibody variable NAR-Fc chimeras (ShAbs) targeting either of the two epitopes mediate cell-effector functions, with high affinity to all SARS-CoV-2 viral variants of concern, including the divergent Omicron strains. The ShAbs potently cross-neutralize SARS-CoV-2 WA-1, Alpha, Beta, Delta, Omicron BA.1 and BA.5, and SARS-CoV-1 pseudoviruses, and confer protection against SARS-CoV-2 challenge in the K18-hACE2 transgenic mouse model. Structural definition of the RBD-ShAb01-ShAb02 complex enabled design and production of multi-specific nanobodies with enhanced neutralization capacity, and picomolar affinity to divergent sarbecovirus clade 1a, 1b and 2 RBD molecules. These shark nanobodies represent potent immunotherapeutics both for current use, and future sarbecovirus pandemic preparation.
Origins of Barents-Kara sea-ice interannual variability modulated by the Atlantic pathway of El Niño–Southern Oscillation
Authors: Luo Binhe , Luo Dehai , Ge Yao , Dai Aiguo , Wang Lin , Simmonds Ian , Xiao Cunde , Wu Lixin , Yao Yao
Published: February 2023

Winter Arctic sea-ice concentration (SIC) decline plays an important role in Arctic amplification which, in turn, influences Arctic ecosystems, midlatitude weather and climate. SIC over the Barents-Kara Seas (BKS) shows large interannual variations, whose origin is still unclear. Here we find that interannual variations in winter BKS SIC have significantly strengthened in recent decades likely due to increased amplitudes of the El Niño-Southern Oscillation (ENSO) in a warming climate. La Niña leads to enhanced Atlantic Hadley cell and a positive phase North Atlantic Oscillation-like anomaly pattern, together with concurring Ural blocking, that transports Atlantic ocean heat and atmospheric moisture toward the BKS and promotes sea-ice melting via intensified surface warming. The reverse is seen during El Niño which leads to weakened Atlantic poleward transport and an increase in the BKS SIC. Thus, interannual variability of the BKS SIC partly originates from ENSO via the Atlantic pathway.
Alternative polyadenylation transcriptome-wide association study identifies APA-linked susceptibility genes in brain disorders
Authors: Cui Ya , Arnold Frederick J. , Peng Fanglue , Wang Dan , Li Jason Sheng , Michels Sebastian , Wagner Eric J. , La Spada Albert R. , Li Wei
Published: February 2023

Alternative polyadenylation (APA) plays an essential role in brain development; however, current transcriptome-wide association studies (TWAS) largely overlook APA in nominating susceptibility genes. Here, we performed a 3′ untranslated region (3′UTR) APA TWAS (3′aTWAS) for 11 brain disorders by combining their genome-wide association studies data with 17,300 RNA-seq samples across 2,937 individuals. We identified 354 3′aTWAS-significant genes, including known APA-linked risk genes, such as SNCA in Parkinson’s disease. Among these 354 genes, ~57% are not significant in traditional expression- and splicing-TWAS studies, since APA may regulate the translation, localization and protein-protein interaction of the target genes independent of mRNA level expression or splicing. Furthermore, we discovered ATXN3 as a 3′aTWAS-significant gene for amyotrophic lateral sclerosis, and its modulation substantially impacted pathological hallmarks of amyotrophic lateral sclerosis in vitro. Together, 3′aTWAS is a powerful strategy to nominate important APA-linked brain disorder susceptibility genes, most of which are largely overlooked by conventional expression and splicing analyses.
Learning local equivariant representations for large-scale atomistic dynamics
Authors: Musaelian Albert , Batzner Simon , Johansson Anders , Sun Lixin , Owen Cameron J. , Kornbluth Mordechai , Kozinsky Boris
Published: February 2023

A simultaneously accurate and computationally efficient parametrization of the potential energy surface of molecules and materials is a long-standing goal in the natural sciences. While atom-centered message passing neural networks (MPNNs) have shown remarkable accuracy, their information propagation has limited the accessible length-scales. Local methods, conversely, scale to large simulations but have suffered from inferior accuracy. This work introduces Allegro, a strictly local equivariant deep neural network interatomic potential architecture that simultaneously exhibits excellent accuracy and scalability. Allegro represents a many-body potential using iterated tensor products of learned equivariant representations without atom-centered message passing. Allegro obtains improvements over state-of-the-art methods on QM9 and revMD17. A single tensor product layer outperforms existing deep MPNNs and transformers on QM9. Furthermore, Allegro displays remarkable generalization to out-of-distribution data. Molecular simulations using Allegro recover structural and kinetic properties of an amorphous electrolyte in excellent agreement with ab-initio simulations. Finally, we demonstrate parallelization with a simulation of 100 million atoms.
COVID-Dynamic: A large-scale longitudinal study of socioemotional and behavioral change across the pandemic
Authors: Rusch Tessa , Han Yanting , Liang Dehua , Hopkins Amber R. , Lawrence Caroline V. , Maoz Uri , Paul Lynn K. , Stanley Damian A. ,   the COVID-Dynamic Team, Adolphs Ralph , Alvarez R. Michael , Camplisson Isabella , Harrison Laura , Hien Denise , Lan Tian , Lin Chujusn , Lopez-Castro Teresa , Nizzic Marie-Christine , Golden Allison Rabkin , Wahle Iman , Yaffe Gideon
Published: February 2023

The COVID-19 pandemic has caused enormous societal upheaval globally. In the US, beyond the devastating toll on life and health, it triggered an economic shock unseen since the great depression and laid bare preexisting societal inequities. The full impacts of these personal, social, economic, and public-health challenges will not be known for years. To minimize societal costs and ensure future preparedness, it is critical to record the psychological and social experiences of individuals during such periods of high societal volatility. Here, we introduce, describe, and assess the COVID-Dynamic dataset, a within-participant longitudinal study conducted from April 2020 through January 2021, that captures the COVID-19 pandemic experiences of >1000 US residents. Each of 16 timepoints combines standard psychological assessments with novel surveys of emotion, social/political/moral attitudes, COVID-19-related behaviors, tasks assessing implicit attitudes and social decision-making, and external data to contextualize participants’ responses. This dataset is a resource for researchers interested in COVID-19-specific questions and basic psychological phenomena, as well as clinicians and policy-makers looking to mitigate the effects of future calamities.
Chákṣu: A glaucoma specific fundus image database
Authors: Kumar J. R. Harish , Seelamantula Chandra Sekhar , Gagan J. H. , Kamath Yogish S. , Kuzhuppilly Neetha I. R. , Vivekanand U. , Gupta Preeti , Patil Shilpa
Published: February 2023

We introduce Chákṣu–a retinal fundus image database for the evaluation of computer-assisted glaucoma prescreening techniques. The database contains 1345 color fundus images acquired using three brands of commercially available fundus cameras. Each image is provided with the outlines for the optic disc (OD) and optic cup (OC) using smooth closed contours and a decision of normal versus glaucomatous by five expert ophthalmologists. In addition, segmentation ground-truths of the OD and OC are provided by fusing the expert annotations using the mean, median, majority, and Simultaneous Truth and Performance Level Estimation (STAPLE) algorithm. The performance indices show that the ground-truth agreement with the experts is the best with STAPLE algorithm, followed by majority, median, and mean. The vertical, horizontal, and area cup-to-disc ratios are provided based on the expert annotations. Image-wise glaucoma decisions are also provided based on majority voting among the experts. Chákṣu is the largest Indian-ethnicity-specific fundus image database with expert annotations and would aid in the development of artificial intelligence based glaucoma diagnostics.
Multimodal sensor fusion in the latent representation space
Authors: Piechocki Robert J. , Wang Xiaoyang , Bocus Mohammud J.
Published: February 2023

A new method for multimodal sensor fusion is introduced. The technique relies on a two-stage process. In the first stage, a multimodal generative model is constructed from unlabelled training data. In the second stage, the generative model serves as a reconstruction prior and the search manifold for the sensor fusion tasks. The method also handles cases where observations are accessed only via subsampling i.e. compressed sensing. We demonstrate the effectiveness and excellent performance on a range of multimodal fusion experiments such as multisensory classification, denoising, and recovery from subsampled observations.
Evaluation of the portability of computable phenotypes with natural language processing in the eMERGE network
Authors: Pacheco Jennifer A. , Rasmussen Luke V. , Wiley Ken , Person Thomas Nate , Cronkite David J. , Sohn Sunghwan , Murphy Shawn , Gundelach Justin H. , Gainer Vivian , Castro Victor M. , Liu Cong , Mentch Frank , Lingren Todd , Sundaresan Agnes S. , Eickelberg Garrett , Willis Valerie , Furmanchuk Al’ona , Patel Roshan , Carrell David S. , Deng Yu , Walton Nephi , Satterfield Benjamin A. , Kullo Iftikhar J. , Dikilitas Ozan , Smith Joshua C. , Peterson Josh F. , Shang Ning , Kiryluk Krzysztof , Ni Yizhao , Li Yikuan , Nadkarni Girish N. , Rosenthal Elisabeth A. , Walunas Theresa L. , Williams Marc S. , Karlson Elizabeth W. , Linder Jodell E. , Luo Yuan , Weng Chunhua , Wei WeiQi
Published: February 2023

The electronic Medical Records and Genomics (eMERGE) Network assessed the feasibility of deploying portable phenotype rule-based algorithms with natural language processing (NLP) components added to improve performance of existing algorithms using electronic health records (EHRs). Based on scientific merit and predicted difficulty, eMERGE selected six existing phenotypes to enhance with NLP. We assessed performance, portability, and ease of use. We summarized lessons learned by: (1) challenges; (2) best practices to address challenges based on existing evidence and/or eMERGE experience; and (3) opportunities for future research. Adding NLP resulted in improved, or the same, precision and/or recall for all but one algorithm. Portability, phenotyping workflow/process, and technology were major themes. With NLP, development and validation took longer. Besides portability of NLP technology and algorithm replicability, factors to ensure success include privacy protection, technical infrastructure setup, intellectual property agreement, and efficient communication. Workflow improvements can improve communication and reduce implementation time. NLP performance varied mainly due to clinical document heterogeneity; therefore, we suggest using semi-structured notes, comprehensive documentation, and customization options. NLP portability is possible with improved phenotype algorithm performance, but careful planning and architecture of the algorithms is essential to support local customizations.
Fabrication of biochar derived from different types of feedstocks as an efficient adsorbent for soil heavy metal removal
Authors: Burachevskaya Marina , Minkina Tatiana , Bauer Tatiana , Lobzenko Ilya , Fedorenko Alexey , Mazarji Mahmoud , Sushkova Svetlana , Mandzhieva Saglara , Nazarenko Alexander , Butova Vera , Wong Ming Hung , Rajput Vishnu D.
Published: February 2023

For effective soil remediation, it is vital to apply environmentally friendly and cost-effective technologies following the notion of green sustainable development. In the context of recycling waste and preserving nutrients in the soil, biochar production and utilization have become widespread. There is an urgent need to develop high-efficiency biochar-based sorbents for pollution removal from soil. This research examined the efficacy of soil remediation using biochar made from three distinct sources: wood, and agricultural residues (sunflower and rice husks). The generated biochars were characterized by SEM/SCEM, XRF, XRD, FTIR, BET Specific Surface Area, and elemental compositions. The presence of hydroxyl and phenolic functional groups and esters in wood, sunflower and rice husk biochar were noted. The total volume of pores was in the following descending order: rice husk > wood > sunflower husk. However, wood biochar had more thermally stable, heterogeneous, irregular-shaped pores than other samples. Adsorption of soil-heavy metals into biochars differed depending on the type of adsorbent, according to data derived from distribution coefficients, sorption degree, Freundlich, and Langmuir adsorption models. The input of biochars to Calcaric Fluvic Arenosol increased its adsorption ability under contamination by Cu(II), Zn(II), and Pb(II) in the following order: wood > rice husk > sunflower husk. The addition of sunflower husk, wood, and rice husk biochar to the soil led to an increase in the removal efficiency of metals in all cases (more than 77%). The increase in the percentage adsorption of Cu and Pb was 9–19%, of Zn was 11–21%. The present results indicated that all biochars functioned well as an absorbent for removing heavy metals from soils. The tailor-made surface chemistry properties and the high sorption efficiency of the biochar from sunflower and rice husks could potentially be used for soil remediation.
Plasmodium falciparum infection prevalence among children aged 6–59 months from independent DHS and HIV surveys: Nigeria, 2018
Authors: Oviedo Adan , Abubakar Ado , Uhomoibhi Perpetua , Maire Mark , Inyang Uwem , Audu Bala , Iriemenam Nnaemeka C. , Ogunniyi Abiodun , Ssekitooleko James , Kalambo Jo-Angeline , Greby Stacie M. , Mba Nwando , Swaminathan Mahesh , Ihekweazu Chikwe , Okoye McPaul I. , Rogier Eric , Steinhardt Laura C.
Published: February 2023

Prevalence estimates are critical for malaria programming efforts but generating these from non-malaria surveys is not standard practice. Malaria prevalence estimates for 6–59-month-old Nigerian children were compared between two national household surveys performed simultaneously in 2018: a Demographic and Health Survey (DHS) and the Nigeria HIV/AIDS Indicator and Impact Survey (NAIIS). DHS tested via microscopy (n = 8298) and HRP2-based rapid diagnostic test (RDT, n = 11,351), and NAIIS collected dried blood spots (DBS) which were later tested for histidine-rich protein 2 (HRP2) antigen (n = 8029). National Plasmodium falciparum prevalence was 22.6% (95% CI 21.2– 24.1%) via microscopy and 36.2% (34.6– 37.8%) via RDT according to DHS, and HRP2 antigenemia was 38.3% (36.7–39.9%) by NAIIS DBS. Between the two surveys, significant rank-order correlation occurred for state-level malaria prevalence for RDT (Rho = 0.80, p < 0.001) and microscopy (Rho = 0.75, p < 0.001) versus HRP2. RDT versus HRP2 positivity showed 24 states (64.9%) with overlapping 95% confidence intervals from the two independent surveys. P. falciparum prevalence estimates among 6–59-month-olds in Nigeria were highly concordant from two simultaneous, independently conducted household surveys, regardless of malaria test utilized. This provides evidence for the value of post-hoc laboratory HRP2 detection to leverage non-malaria surveys with similar sampling designs to obtain accurate P. falciparum estimates.
Development of a treatment for water contaminated with Cr (VI) using cellulose xanthogenate from E. crassipes on a pilot scale
Authors: Sayago Uriel Fernando Carreño , Ballesteros Ballesteros Vladimir
Published: February 2023

Water care is an imperative duty in industries with effluents loaded with pollutants such as heavy metals, especially chromium (VI), extremely dangerous for humans and the environment. One way of treating water is possible through a continuous system with dry and crushed vegetable biomass of cellulose xanthogenate because it can adsorb heavy metals, especially due to its low production costs. Through continuous systems and with the waste of PET plastics, it is possible to develop a water treatment process adapting this system and biomass. The objective of this research is the development of a treatment for water contaminated with Cr (VI) using cellulose xanthogenate from E.crassipeson a pilot scale. Where a mass balance conducted to determine the adsorption capacity of this heavy metal, corroborating it through the Thomas model. The treatment process eliminated around 95% of Cr (VI) present in the water, in addition, biomass reuse cycles carried out, which maintained a considerable adsorption capacity in all the cycles conducted through EDTA reagent.
Physical and psychosocial factors associated with sexual satisfaction in long-term cancer survivors 5 and 10 years after diagnosis
Authors: Heyne Svenja , Taubenheim Sabine , Dietz Andreas , Lordick Florian , Götze Heide , Mehnert-Theuerkauf Anja
Published: February 2023

Our study provides data on sexual satisfaction among long-term cancer survivors 5 and 10 years after diagnosis, and identifies factors detrimental (e.g. psychosocial and physical symptom burden) or beneficial (e.g. social support) to survivors’ sexual satisfaction. We measured sexual satisfaction among cancer survivors recruited via the local clinical cancer registry across a wide range of tumor sites 5 years (cohort 1) and 10 years (cohort 2) after diagnosis. We further assessed chronic comorbidity index (CCI) and symptom scales (EORTC QLQ-C30), depression (PHQ-9) and anxiety (GAD-7), satisfaction with partnership (PFB), quality of life (EORTC QLQ-C30), and social support (OSSS). 924 patients (5‐year cohort = 608/10‐year cohort = 316) participated in the study (53% men, 80% cohabiting, mean age 66 years, range 18–85). We found that nearly half of the respondents perceived their sexual life as less satisfying than before cancer. High sexual satisfaction was associated with a low chronic comorbidities index (r = − 0.27, p < .001),  less fatigue (r = − 0.35, p<.001), less nausea/vomiting (r = − 0.13, p<.001) and less pain (r = − 0.23, p<.001), r ; less depression (r = − 0.24, p < .001), less anxiety(r = − 0.23, p < .001); a high level of social support (r = 0.16, p < .001), a high level of satisfaction with their relationship (r = 0.24, p < .001), and high quality of life (r = 0.33, p < .001). Sexual satisfaction may be affected by both psychosocial and physical symptom burden, with the latter having a greater impact on sexual satisfaction. It is essential for health care providers that sexual health issues are understood, evaluated, and treated, including those of long-term cancer survivors.
Integrative pathway and network analysis provide insights on flooding-tolerance genes in soybean
Authors: Jhan Li-Hsin , Yang Chin-Ying , Huang Chih-Min , Lai Mu-Chien , Huang Yen-Hsiang , Baiya Supaporn , Kao Chung-Feng
Published: February 2023

Soybean is highly sensitive to flooding and extreme rainfall. The phenotypic variation of flooding tolerance is a complex quantitative trait controlled by many genes and their interaction with environmental factors. We previously constructed a gene-pool relevant to soybean flooding-tolerant responses from integrated multiple omics and non-omics databases, and selected 144 prioritized flooding tolerance genes (FTgenes). In this study, we proposed a comprehensive framework at the systems level, using competitive (hypergeometric test) and self-contained (sum-statistic, sum-square-statistic) pathway-based approaches to identify biologically enriched pathways through evaluating the joint effects of the FTgenes within annotated pathways. These FTgenes were significantly enriched in 36 pathways in the Gene Ontology database. These pathways were related to plant hormones, defense-related, primary metabolic process, and system development pathways, which plays key roles in soybean flooding-induced responses. We further identified nine key FTgenes from important subnetworks extracted from several gene networks of enriched pathways. The nine key FTgenes were significantly expressed in soybean root under flooding stress in a qRT-PCR analysis. We demonstrated that this systems biology framework is promising to uncover important key genes underlying the molecular mechanisms of flooding-tolerant responses in soybean. This result supplied a good foundation for gene function analysis in further work.
Immature and mature bone marrow-derived dendritic cells exhibit distinct intracellular mechanical properties
Authors: Leblanc-Hotte Antoine , Audiger Cindy , Chabot-Roy Geneviève , Lombard-Vadnais Félix , Delisle Jean-Sébastien , Peter Yves-Alain , Lesage Sylvie
Published: February 2023

Dendritic cells (DCs) patrol the organism at an immature stage to detect the presence of pathogens. Once activated, these mature DCs reach the lymph nodes to activate antigen-specific T lymphocytes and thus initiate an adaptative immune response to control the pathogen. The migration of both immature and mature DCs is a key process for their optimal function. DC migration requires transit through narrow constrictions that is allowed by their high local and global deformation capabilities. In addition to cytoplasmic changes, the nucleus mechanical properties also have a major impact for cellular migration and motility. Yet, nucleus intracellular mobility of dendritic cells or its variation upon maturation have not been investigated. Our study defines the biophysical phenotypic variations of dendritic cells upon maturation using interferometric deformability cytometry. This method characterizes different cellular mechanical properties, such as elongation and nucleus offset, by assessing the refractive index spatial distribution of shear-induced deformed cells. By using these parameters, our data suggest that in vitro bone marrow derived dendritic cell (BMDC) maturation induces cell stiffening and reduces nucleus mobility, allowing to distinguish immature and mature dendritic cells. Overall, our method provides insights on intracellular mechanical properties of two dendritic cell states.
Evaluating the effects of giraffe skin disease and wire snare wounds on the gaits of free-ranging Nubian giraffe
Authors: Bernstein-Kurtycz L. M. , Dunham N. T. , Evenhuis J. , Brown M. B. , Muneza A. B. , Fennessy J. , Dennis P. M. , Lukas K. E.
Published: February 2023

Giraffe skin disease (GSD), a condition that results in superficial lesions in certain giraffe (Giraffaspp.) populations, has emerged as a potential conservation threat. Preliminary findings suggested that individuals with GSD lesions move with greater difficulty which may in turn reduce their foraging efficiency or make them more vulnerable to predation. A current known threat to some giraffe populations is their mortality associated with entrapment in wire snares, and the morbidity and potential locomotor deficiencies associated with wounds acquired from snares. The goal of our study was to quantify the locomotor kinematics of free-ranging Nubian giraffe (G. camelopardalis camelopardalis) in Murchison Falls National Park (MFNP), Uganda, and compare spatiotemporal limb and neck angle kinematics of healthy giraffe to those of giraffe with GSD lesions, snare wounds, and both GSD lesions and snare wounds. The presence of GSD lesions did not significantly affect spatiotemporal limb kinematic parameters. This finding is potentially because lesions were located primarily on the necks of Nubian giraffe in MFNP. The kinematic parameters of individuals with snare wounds differed from those of healthy individuals, resulting in significantly shorter stride lengths, reduced speed, lower limb phase values, and increased gait asymmetry. Neck angle kinematic parameters did not differ among giraffe categories, which suggests that GSD neck lesions do not impair normal neck movements and range of motion during walking. Overall, MFNP giraffe locomotor patterns are largely conservative between healthy individuals and those with GSD, while individuals with snare wounds showed more discernible kinematic adjustments consistent with unilateral limb injuries. Additional studies are recommended to assess spatiotemporal limb kinematics of giraffe at sites where lesions are found predominantly on the limbs to better assess the potential significance of GSD on their locomotion.
Lysine 222 in PPAR γ1 functions as the key site of MuRF2-mediated ubiquitination modification
Authors: Fan Yucheng , Xu Fangjing , Wang Rui , He Jun
Published: February 2023

Peroxisome proliferator-activated receptor gamma (PPAR γ) plays key roles in the development, physiology, reproduction, and homeostasis of organisms. Its expression and activity are regulated by various posttranslational modifications. We previously reported that E3 ubiquitin ligase muscle ring finger protein 2 (MuRF2) inhibits cardiac PPAR γ1 protein level and activity, eventually protects heart from diabetic cardiomyopathy; furthermore, by GST-pulldown assay, we found that MuRF2 modifies PPAR γ1 via poly-ubiquitination and accelerates PPAR γ1 proteasomal degradation. However, the key ubiquitination site on PPAR γ that MuRF2 targets for remains unclear. In the present study, we demonstrate that lysine site 222 is the receptor of MuRF2-mediated PPAR γ1 ubiquitination modification, using prediction of computational models, immunoprecipitation, ubiquitination assays, cycloheximide chasing assay and RT-qPCR. Our findings elucidated the underlying details of MuRF2 prevents heart from diabetic cardiomyopathy through the PPAR γ1 regulatory pathway.