bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mineralogical attributes to the distribution of trace and rare earth elements in alteration zones and copper‐gold veins in the Lepanto copper‐gold deposit, Luzon, Philippines
Authors: Claveria Rene Juna R. 
Published: April 2024

AbstractIn high sulfidation systems, acidic hydrothermal fluids can produce wide alteration zones with specific mineral assemblages/associations as well as identifiable and elemental distribution patterns. The Lepanto Cu‐Au deposit exhibits a consistent zonation pattern of silicic alteration near the Cu‐Au veins evolving outwards to advanced argillic and argillic alteration with chloritic alteration farthest from the vein. Recent exploration of high sulfidation Cu‐Au veins indicated the usefulness of mineralogical assemblages/associations and the complementing information provided by the elemental distribution patterns in the identification and characterization of the different alteration zones. In this study, I characterize the mineral assemblages/associations and interpret their occurrences in the different alteration zones of the Lepanto Cu‐Au deposit. An assemblage that is composed predominantly of chlorite‐epidote/clinozoisite‐calcite‐quartz‐pyrite represents the propylitic/chloritic alteration zone. The argillic alteration has a mineral association of smectite‐sericite‐chlorite‐epidote‐kaolinite‐quartz‐pyrite. The advanced argillic alteration zone has alunite‐kaolinite‐pyrophyllite‐diaspore‐sericite‐quartz‐pyrite as mineral association. In the silicic alteration zone, the mineral association is composed of quartz‐alunite‐diaspore‐anhydrite‐pyrite. Also presented are the distributions of trace and rare earth elements. In the distribution of trace and REEs across alteration zones, there is an observed increase of Te, Au, Mo, Cu, Sn, and Bi values from the chloritic to silicic alteration zones. A corresponding decrease of REE, LILE (Ba, Pb, Rb, K), HFSE (Ti, Nb, U, Th), Al, Na, Ca, Zn, Mn, Co and Cd values are observed. This study also characterizes the ore mineral assemblages/associations of the Cu‐Au veins as well as the distribution patterns of trace and rare earth elements. The Northwest‐NOA, hanging wall branch veins (HWBV), main ore body (MOB), foot wall branch veins (FWBV), and Easterlies are generally made up of enargite‐luzonite‐pyrite‐chalcopyrite‐tennantite‐tetrahedrite‐tellurides‐covellite. The associated gangue minerals are anhydrite‐gypsum‐alunite‐barite‐quartz. In the distribution of elements across the different Cu‐Au veins, there is an observed decrease of Cu, As, and Sb values from the Easterlies towards the Northwest‐NOA Cu‐Au veins. The observed variations in the alteration and ore mineral assemblages/associations have strongly influenced the distribution of elemental values in both alteration zones and Cu‐Au veins. The identification of mineralogical assemblages/associations and elemental distribution patterns may provide possible guides and reference tools in the exploration of Lepanto type Cu‐Au deposits.
Knowledge is not power: Learning in polycentric governance systems
Authors: Rittelmeyer Pamela , Lubell Mark , Hovis Meredith , Heikkila Tanya , Gerlak Andrea , Pozzi Tara 
Published: April 2024

AbstractThe link between knowledge and decision‐making in polycentric systems is shaped by the process of collective learning, where policy actors participate in multiple policy forums to acquire, translate, and disseminate knowledge. This article argues that the relationship between learning and participation in polycentric systems differs for actors with executive responsibilities versus specialized staff. Using a mix of quantitative and qualitative data, we show that executive staff are less likely to learn because of their incentives, resources, and position in the system. In contrast, specialized staff are more likely to learn as they form epistemic communities focused on specific policy issues. The different learning experiences of executive versus technical staff contributes to the disjunction between knowledge and power that is a feature of all polycentric systems. Bridging this gap requires institutional arrangements and training to enable the development of trust‐based relationships between decision‐makers, scientists, and other types of specialized knowledge communities.
Consideration for alpha‐gal syndrome in two critically ill persons with group O blood who received group B plasma
Authors: Miller Maureen J. , Lee Patricia , Lee Brian G. , Flegel Willy A. , West‐Mitchell Kamille , Conry‐Cantilena Kathleen , De Giorgi Valeria 
Published: April 2024

AbstractBackgroundThe U.S. Centers for Disease Control and Prevention (CDC) has reported increasing rates of alpha‐gal syndrome, an allergic response after meat ingestion (AGS). AGS has been associated with prior exposure to tick bites or other biologics characterized by a life‐threatening immunoglobulin E (IgE)–mediated hypersensitivity to galactose‐alpha‐1,3‐galactose (alpha‐gal) an oligosaccharide structurally similar to the group B antigen on red blood cells (RBC) found in most non‐primate mammalian meat and products derived from these mammals. In 2023, Transfusion reported 3 group O recipients of group B plasma in the Washington, D.C. metropolitan area with no history of meat allergy who had anaphylactic transfusion reactions compatible with AGS.AimsWe investigated allergic reactions in 2 additional patients who received ABO minor‐incompatible blood products at 2 hospitals in the D.C. area during fall 2023.MethodsFor both patients, a medical chart review was performed and IgE levels to alpha‐gal were measured.ResultsThe first patient, a 64‐year‐old, O‐positive patient status post heart transplant with no known allergies, was admitted with acute COVID‐19 induced antibody‐mediated transplant rejection and placed on extracorporeal membrane oxygenation (ECMO). While undergoing plasma exchange (PLEX) (50% albumin/50% fresh frozen plasma (FFP)), the patient tolerated 2 units of group O FFP and 1 unit of group A FFP before becoming hemodynamically unstable during transfusion of 1 unit of B‐positive FFP. PLEX was stopped. The patient later died of sepsis from underlying causes. The second patient, a 57‐year‐old O‐positive man with a history of melanoma and neuro fibromatosis type 1, was undergoing an abdominal resection including transfusion of 3 units of O‐positive RBC when he suffered hypotension and ventricular tachycardia requiring intraoperative code after receiving 2 units of group B FFP. Hiveswere noted after resuscitation. The patient had a history of tick bites but no known allergies. He is alive 5 months after the possible allergic event. Both patients had full transfusion reaction evaluations and immunology testing results above the positive cutoff for anti‐alpha‐gal IgE.Discussion and conclusionTwo patients with O‐positive blood and no known allergies experience danaphyl axis after transfusion with group B FFP. The symptoms cannot definitively be imputed to an allergic transfusion reaction, but the presence of IgE against alpha‐gal supports an association. Medicating patients with antihistamines and IV steroids pre‐transfusion may prevent allergic reactions. Restricting group B plasma‐containing products (plasma, platelets, cryoprecipitate) for patients who experience AGS‐like symptoms may be considered.
Update of biomarkers to diagnose diabetic foot osteomyelitis: A meta‐analysis and systematic review
Authors: Ansert Elizabeth A. , Tarricone Arthur N. , Coye Tyler L. , Crisologo Peter A. , Truong David , Suludere Mehmet A. , Lavery Lawrence A. 
Published: April 2024

AbstractThe aim of this study was to evaluate the diagnostic characteristics of biomarker for diabetic foot osteomyelitis (DFO). We searched PubMed, Scopus, Embase and Medline for studies who report serological markers and DFO before December 2022. Studies must include at least one of the following diagnostic parameters for biomarkers: area under the curve, sensitivities, specificities, positive predictive value, negative predictive value. Two authors evaluated quality using the Quality Assessment of Diagnostic Accuracy Studies tool. We included 19 papers. In this systematic review, there were 2854 subjects with 2134 (74.8%) of those patients being included in the meta‐analysis. The most common biomarkers were erythrocyte sedimentation rate (ESR), C‐reactive protein (CRP) and procalcitonin (PCT). A meta‐analysis was then performed where data were evaluated with Forrest plots and receiver operating characteristic curves. The pooled sensitivity and specificity were 0.72 and 0.75 for PCT, 0.72 and 0.76 for CRP and 0.70 and 0.77 for ESR. Pooled area under the curves for ESR, CRP and PCT were 0.83, 0.77 and 0.71, respectfully. Average diagnostic odds ratios were 16.1 (range 3.6–55.4), 14.3 (range 2.7–48.7) and 6.7 (range 3.6–10.4) for ESR, CRP and PCT, respectfully. None of the biomarkers we evaluated could be rated as ‘outstanding’ to diagnose osteomyelitis. Based on the areas under the curve, ESR is an ‘excellent’ biomarker to detect osteomyelitis, and CRP and PCT are ‘acceptable’ biomarkers to diagnose osteomyelitis. Diagnostic odds ratios indicate that ESR, CRP and PCT are ‘good’ or ‘very good’ tools to identify osteomyelitis.
Pulmonary Nodule Segmentation Network Based on Res Select Kernel Contextual U-Net
Authors: Luo Yi , Cao Miao , Chang Xu 
Published: April 2024

Abstract
U-Net network is widely used in the field of medical image segmentation. The automatic segmentation and detection of lung nodules can help in the early detection of lung cancer. Therefore, in this paper, to solve the problems of small proportion of nodules in computer tomography (CT) images, complex features, and insufficient segmentation accuracy, an improved U-Net network based on residual network and attention mechanism was proposed. The feature extraction part of Res select Kernel Contextual U-Net (RkcU-Net) network is based on Res2net, a variant of Resnet, and on which a feature extraction module with automatic selection of convolution kernel size is designed to perform multiscale convolution inside the feature layer to form perceptual fields of different sizes. This module selects the appropriate convolution kernel size to extract lung nodule features in the face of different fine-grained lung nodules. Second, the contextual supplementary (CS) block is designed to use the information of adjacent upper and lower layers to correct for the upper layer features, eliminating the discrepancy in the fusion of features at different levels. In this paper, the LUNA16 dataset was selected as the basis for lung nodule segmentation experiments. The method used in this dataset can achieve an intersection ratio (IoU) of 80.59% and a dice similarity coefficient (DSC) score of 89.25%. The network effectively improves the accuracy of lung nodule segmentation compared with other models. The results show that the method enhances the feature extraction ability of the network and improves the segmentation effect. In addition, the contribution of jump connections to information recovery should be noted.
A Fuzzy Ontology-Based Decision Tool for Concept Selection to Maintain Consistency Throughout Design Iterations
Authors: Liu Yan , Chen Xinru , Eckert Claudia , Zhang Xin 
Published: April 2024

Abstract
Concept selection is one of the most important activities in new product development processes in that it greatly influences the direction of subsequent design activities. As a complex multiple-criteria decision-making problem, it often requires iterations before reaching the final decision where each selection is based on previous selection results. Reusing key decision elements ensures decision consistency between iterations and improves decision efficiency. To support this reuse, this article proposes a fuzzy ontology-based decision tool for concept selection. It models the key decision elements and their relations in an ontological way and scores the concepts using weighted fuzzy TOPSIS (Technique for Order Preference by Similarity to an Ideal Solution). By applying the tool to an example, this article demonstrates how the concepts, criteria, weights, and results generated for one decision can be reused in the next iteration.
Single-cell analysis reveals an antiviral network that controls Zika virus infection in human dendritic cells
Authors: Moore Kathryn M. , Pelletier Adam-Nicolas , Lapp Stacey , Metz Amanda , Tharp Gregory K. , Lee Michelle , Bhasin Swati Sharma , Bhasin Manoj , Sékaly Rafick-Pierre , Bosinger Steven E. , Suthar Mehul S. 
Published: April 2024

ABSTRACT

Zika virus (ZIKV) is a mosquito-borne flavivirus that caused an epidemic in the Americas in 2016 and is linked to severe neonatal birth defects, including microcephaly and spontaneous abortion. To better understand the host response to ZIKV infection, we adapted the 10× Genomics Chromium single-cell RNA sequencing (scRNA-seq) assay to simultaneously capture viral RNA and host mRNA. Using this assay, we profiled the antiviral landscape in a population of human monocyte-derived dendritic cells infected with ZIKV at the single-cell level. The bystander cells, which lacked detectable viral RNA, expressed an antiviral state that was enriched for genes coinciding predominantly with a type I interferon (IFN) response. Within the infected cells, viral RNA negatively correlated with type I IFN-dependent and -independent genes (the antiviral module). We modeled the ZIKV-specific antiviral state at the protein level, leveraging experimentally derived protein interaction data. We identified a highly interconnected network between the antiviral module and other host proteins. In this work, we propose a new paradigm for evaluating the antiviral response to a specific virus, combining an unbiased list of genes that highly correlate with viral RNA on a per-cell basis with experimental protein interaction data.

IMPORTANCE
Zika virus (ZIKV) remains a public health threat given its potential for re-emergence and the detrimental fetal outcomes associated with infection during pregnancy. Understanding the dynamics between ZIKV and its host is critical to understanding ZIKV pathogenesis. Through ZIKV-inclusive single-cell RNA sequencing (scRNA-seq), we demonstrate on the single-cell level the dynamic interplay between ZIKV and the host: the transcriptional program that restricts viral infection and ZIKV-mediated inhibition of that response. Our ZIKV-inclusive scRNA-seq assay will serve as a useful tool for gaining greater insight into the host response to ZIKV and can be applied more broadly to the flavivirus field.
mSphere of Influence: Deciphering purine auxotrophy in protozoan parasites
Authors: Martorelli Di Genova Bruno 
Published: April 2024

ABSTRACT

Bruno Martorelli Di Genova works in parasitology, focusing on
Toxoplasma gondii
metabolism. In this mSphere of Influence article, he reflects on how the articles “Metabolic Reprogramming during Purine Stress in the Protozoan Pathogen
Leishmania donovani
” and “Yeast-Based High-Throughput Screen Identifies
Plasmodium falciparum
Equilibrative Nucleoside Transporter 1 Inhibitors That Kill Malaria Parasites” impacted him, informing his research strategies and understanding of metabolic flexibility in
Toxoplasma gondii
.
Soil prokaryotic and fungal biome structures associated with crop disease status across the Japan Archipelago
Authors: Fujita Hiroaki , Yoshida Shigenobu , Suzuki Kenta , Toju Hirokazu 
Published: April 2024

ABSTRACT

Archaea, bacteria, and fungi in the soil are increasingly recognized as determinants of agricultural productivity and sustainability. A crucial step for exploring soil microbiomes with important ecosystem functions is to perform statistical analyses on the potential relationship between microbiome structure and functions based on comparisons of hundreds or thousands of environmental samples collected across broad geographic ranges. In this study, we integrated agricultural field metadata with microbial community analyses by targeting 2,903 bulk soil samples collected along a latitudinal gradient from cool-temperate to subtropical regions in Japan (26.1–42.8 °N). The data involving 632 archaeal, 26,868 bacterial, and 4,889 fungal operational taxonomic units detected across the fields of 19 crop plant species allowed us to conduct statistical analyses (permutational analyses of variance, generalized linear mixed models, randomization analyses, and network analyses) on the relationship among edaphic factors, microbiome compositions, and crop disease prevalence. We then examined whether the diverse microbes form species sets varying in potential ecological impacts on crop plants. A network analysis suggested that the observed prokaryotes and fungi were classified into several species sets (network modules), which differed substantially in association with crop disease prevalence. Within the network of microbe-to-microbe coexistence, ecologically diverse microbes, such as an ammonium-oxidizing archaeon, an antibiotics-producing bacterium, and a potentially mycoparasitic fungus, were inferred to play key roles in shifts between crop-disease-promotive and crop-disease-suppressive states of soil microbiomes. The bird’s-eye view of soil microbiome structure will provide a basis for designing and managing agroecosystems with high disease-suppressive functions.

IMPORTANCE
Understanding how microbiome structure and functions are organized in soil ecosystems is one of the major challenges in both basic ecology and applied microbiology. Given the ongoing worldwide degradation of agroecosystems, building frameworks for exploring structural diversity and functional profiles of soil microbiomes is an essential task. Our study provides an overview of cropland microbiome states in light of potential crop-disease-suppressive functions. The large data set allowed us to explore highly functional species sets that may be stably managed in agroecosystems. Furthermore, an analysis of network architecture highlighted species that are potentially used to cause shifts from disease-prevalent states of agroecosystems to disease-suppressive states. By extending the approach of comparative analyses toward broader geographic ranges and diverse agricultural practices, agroecosystem with maximized biological functions will be further explored.
Interventions to address antimicrobial resistance: an ethical analysis of key tensions and how they apply in low- income and middle-income countries
Authors: Pokharel Sunil , Adhikari Bipin , Johnson Tess , Cheah Phaik Yeong 
Published: April 2024

AbstractAntimicrobial resistance (AMR) is a global health and one health problem. Efforts to mitigate the problem of AMR are challenging to implement due to unresolved ethical tensions. We present an in-depth ethical analysis of tensions that might hinder efforts to address AMR. First, there is a tension between access and excess in the current population: addressing lack of access requires facilitating use of antimicrobials for some populations, while addressing excessive use for other populations. Second, there is a tension between personal interests and a wider, shared interest in curbing AMR. These personal interests can be viewed from the perspective of individuals seeking care and healthcare providers whose livelihoods depend on using or selling antimicrobials and who profit from the sales and use of antimicrobials. Third, there is a tension between the interests of current populations and the interests of future generations. Last, there is a tension between addressing immediate health threats such as pandemics, and AMR as a ‘silent’, chronic threat. For each of these tensions, we apply ‘descriptive ethics’ methods that draw from existing evidence and our experiences living and working in low-income and middle-income countries to highlight how these ethical tensions apply in such settings.
Descriptive study of causes of death and COVID-19-associated morbidities from the New York City electronic death record: first wave of the pandemic March–July 2020
Authors: Maduro Gil , Li Wenhui , Huynh Mary , Bernard-Davila Blanca , Gould L Hannah , Van Wye Gretchen 
Published: April 2024

ObjectiveAssessing excess deaths from benchmarks across causes of death during the first wave of the COVID-19 pandemic and identifying morbidities most frequently mentioned alongside COVID-19 deaths in the death record.MethodsDescriptive study of death records between 11 March 2020 and 27 July 2020, from the New York City Bureau of Vital Statistics. Mortality counts and percentages were compared with the average for the same calendar period of the previous 2 years. Distributions of morbidities from among forty categories of conditions were generated citywide and by sex, race/ethnicity and four age groups. Causes of death were assumed to follow Poisson processes for Z-score construction.ResultsWithin the study period, 46 563 all-cause deaths were reported; 132.9% higher than the average for the same period of the previous 2 years (19 989). Of those 46 563 records, 19 789 (42.5%) report COVID-19 as underlying cause of death. COVID-19 was the most prevalent cause across all demographics, with respiratory conditions (prominently pneumonia), hypertension and diabetes frequently mentioned morbidities. Black non-Hispanics had greater proportions of mentions of pneumonia, hypertension, and diabetes. Hispanics had the largest proportion of COVID-19 deaths (52.9%). Non-COVID-19 excess deaths relative to the previous 2-year averages were widely reported.ConclusionMortality directly due to COVID-19 was accompanied by significant increases across most other causes from their reference averages, potentially suggesting a sizable COVID-19 death undercount. Indirect effects due to COVID-19 may partially account for some increases, but findings are hardly dispositive. Unavailability of vaccines for the time period precludes any impact over excess deaths. Respiratory and cardiometabolic-related conditions were most frequently reported among COVID-19 deaths across demographic characteristics.