bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Formation of Chromite Chains and Clusters in Igneous Rocks
Authors: Holness Marian B , Vukmanovic Zoja , O’Driscoll Brian 
Published: December 2022

Abstract
Crystal clusters are common in both extrusive and plutonic rocks, but the mechanisms by which they form are not well-constrained. Following a consideration of the physics of nucleation, we outline the expected microstructural characteristics of clusters formed by heterogeneous nucleation and those formed by synneusis, together with the ways they might evolve during subsequent grain growth and textural equilibration. By combining analysis of the microstructures in experimental chromite-basalt charges with a detailed microstructural analysis of the UG2 chromitite of the Bushveld layered intrusion using EBSD, we argue that the UG2 chromitite formed by settling and accumulation of single grains and clusters comprising randomly oriented grains produced by the aggregation of previously isolated chromite crystals. Although there is no evidence of epitaxy, at least some of the lowermost chromite grains of the main UG2 chromitite may have nucleated heterogeneously on the silicate grains forming the floor, with subsequent accumulation and sintering of individual grains or clusters. The reduced thickness of chromitites on the steep and overhanging parts of the floor is thus due to the relative difficulty of sticking more grains to the existing layer in these orientations. The absence of any fining-upwards of grains in either the main UG2 chromitite or the associated stringer can be accounted for if both layers were formed by the settling and accumulation of clusters as well as single grains. Comparison with examples of clustered chromite grains in extrusive rocks suggests that aggregation by synneusis is a widespread magmatic process. The ‘chicken-wire’ texture formed by clustered chromite grains commonly found in olivine-rich cumulates is argued to also be formed by gravitational settling, with the possible exception of clusters of chromite grains in relatively thin seams argued to be the result of metasomatism, which may instead have formed by impingement during in situ growth.
CorrelatingCoffea canephora3D architecture to plant photosynthesis at a daily scale and vegetative biomass allocation
Authors: Rakocevic Miroslava , Baroni Danilo Força , de Souza Guilherme Augusto Rodrigues , Bernado Wallace de Paula , de Almeida Claudio Martins , Matsunaga Fabio Takeshi , Rodrigues Weverton Pereira , Ramalho José Cochicho , Campostrini Eliemar 
Published: December 2022

AbstractCoffea canephora (C. canephora) has two botanical varieties, Robusta and Conilon. Intraspecific variability was hypothesized and projected for the selection of C. canephora plants able to maintain production in the context of global climate changes. For that, architectural, C-assimilation and biomass analyses were performed on 17-month-old Robusta (clones ‘A1’ and ‘3 V’) and Conilon (clones ‘14’ and ‘19’) varieties grown in non-limiting soil, water and mineral nutrient conditions. Nondestructive coffee plant architecture coding, reconstruction and plant photosynthesis estimations were performed using a functional-structural plant modeling platform OpenAlea. 3D reconstructions and inclusion of parameters calculated and estimated from light response curves, such as dark respiration (Rd), maximum rate of carboxylation of RuBisCO and photosynthetic electron transport allowed the estimation of instantaneous and daily plant photosynthesis. The virtual orchard leaf area index was low, and light was not a limiting factor in early C. canephora development stages. Under such conditions, Robusta assimilated more CO2 at the plant and orchard scale and produced higher total biomass than Conilon. Lower plant daily photosynthesis and total biomass were correlated to higher Rd in Conilon than in Robusta. Among the architectural traits, leaf inclination, size and allometry were most highly correlated with plant assimilation and biomass. Relative allocation in leaf biomass was higher in ‘19’ Conilon than in young Robusta plants, indicating intraspecific biomass partitioning. Similarly, variation in relative distribution of the root biomass and the root volume reflected clonal variation in soil occupation, indicating intraspecific variability in space occupation competitiveness. Coffea canephora denoted high root allocation in both Conilon and Robusta clones. However, relevant differences at subspecific levels were found, indicating the high potential of C. canephora to cope with drought events, which are expected to occur more frequently in the future, because of climate changes. The methodology developed here has the potential to be used for other crops and tree species.Highlights Functional-structural plant model was used to estimate photosynthesis on a plant and daily scales in Coffea canephora (C. canephora). Among the architectural traits, leaf shape and inclination had the most impact on photosynthesis and biomass. Under non-limiting conditions, Robusta had higher plant photosynthesis and biomass than Conilon. A higher leaf biomass allocation in Conilon clone ‘19’ than in Robusta suggested variety-specific partitioning. Variation in the relative distribution of the root biomass indicated C. canephora intraspecific soil occupation variability.
Advancing considerations of context in the evaluation and implementation of evidence-based biomedical HIV prevention interventions: a review of recent research
Authors: Velloza Jennifer , Roche Stephanie , Concepcion Tessa , Ortblad Katrina F. 
Published: December 2022

Purpose of review
A paradigm shift is needed in how we think about biomedical HIV prevention product effectiveness. Often, we expect randomized trial findings to be generalizable across populations and settings where products will be delivered, without consideration of key contextual drivers that could impact effectiveness. Moreover, researchers and policy-makers generally discount products with varied effect sizes across contexts, rather than explicating the drivers of these differences and using them to inform equitable product choice and delivery. We conducted a review of the recent HIV prevention research to advance considerations of context in choices of when, why, and how to implement biomedical HIV prevention products, with a particular focus on daily oral preexposure prophylaxis (PrEP) and the dapivirine vaginal ring (DPV).

Recent findings
Findings across recent studies of PrEP and DPV emphasize that products that do not work well in one context might be highly desirable in another. Key contextual drivers of PrEP and DPV effectiveness, use, and implementation include population, health system, cultural, and historical factors. We recommend conceptualization, measurement, and analysis approaches to fully understand the potential impact of context on prevention product delivery. Execution of these approaches has real-world implications for HIV prevention product choice and could prevent the field from dismissing biomedical HIV prevention products based on trial findings alone.

Summary
Ending the HIV epidemic will require tailored, person-centered, and equitable approaches to design, implement, and evaluate HIV prevention products which necessitates considerations of context in ongoing research and implementation.
Promoting patient-centered care within HIV care settings in sub-Saharan Africa
Authors: Wachira Juddy , Genberg Becky L. , Wilson Ira B. 
Published: December 2022

Purpose of review
Patient centered care (PCC) in human immunodeficiency virus (HIV) care systems in sub-Saharan Africa (SSA) may improve outcomes for persons with HIV (PWH). We review the progress the region has made in promoting PCC and highlight some of the implementation challenges and potential areas of research.

Recent findings
Studies show growing interest in promoting PCC across HIV care programs in SSA. Effective implementation of PCC, however, is hampered by: (1) lack of consensus on the conceptualization of PCC, including definition, frameworks, measures, and implementation strategies; (2) limited regional studies on the adoption and sustainability of PCC interventions; and (3) healthcare structural challenges including limited capital and human resources, poor provider-patient dynamics, high provider turnover, and lack of continuity in care. Recent studies in the region have focused on identifying key PCC domains addressable in resource limited settings, understanding the PCC experiences and expectations of PWH and their providers, and testing innovative interventions. We highlight the need for additional studies to address the existing gaps.

Summary
We discuss the progress and challenges of implementing PCC in HIV care settings in SSA as well as the need for additional research to ensure that proposed PCC interventions have optimal impact.
Point of care diagnostics for Cryptosporidium: new and emerging technologies
Authors: Hijjawi Nawal , Zahedi Alizera , Ryan Una 
Published: December 2022

Purpose of review
Although Cryptosporidium detection and typing techniques have improved dramatically in recent years, relatively little research has been conducted on point of care (POC) detection and typing tools. Therefore, the main purpose of the present review is to summarize and evaluate recent and emerging POC diagnostic methods for Cryptosporidium spp.

Recent findings
Microscopy techniques such as light-emitting diode fluorescence microscopy with auramine-phenol staining (LED-AP), still have utility for (POC) diagnostics but require fluorescent microscopes and along with immunological-based techniques, suffer from lack of specificity and sensitivity. Molecular detection and typing tools offer higher sensitivity, specificity and speciation, but are currently too expensive for routine POC diagnostics. Isothermal amplification methods such as loop-mediated isothermal amplification (LAMP) or recombinase polymerase amplification (RPA) including a commercially available LAMP kit have been developed for Cryptosporidium but are prone to false positives. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas diagnostic technologies (CRISPRDx) have recently been combined with isothermal amplification to increase its specificity and sensitivity for detection and typing. Other emerging technologies including amplification-free CRISPR detection methods are currently being developed for Cryptosporidium using a smartphone to read the results.

Summary
Many challenges are still exist in the development of POC diagnostics for Cryptosporidium. The ideal POC tool would be able to concentrate the pathogen prior to detection and typing, which is complicated and research in this area is still very limited. In the short-term, CRISPR-powered isothermal amplification lateral flow tools offer the best opportunity for POC Cryptosporidium species and subtype detection, with a fully integrated autonomous biosensor for the long-term goal.
Hemophagocytic Lymphohistiocytosis: A Practical Review for Liver Pathologists
Authors: Xiong Yuqing , Del Portillo Armando , Fazlollahi Ladan , Remotti Helen E. , Lee Michael , Lagana Stephen M. 
Published: December 2022

Abstract
Hemophagocytic lymphohistiocytosis (HLH) is a rare disease with a high mortality. Liver involvement is common, with most patients demonstrating acute hepatitis. Therefore, liver biopsies are frequently obtained in the setting of suspected HLH. Several studies have described the clinicopathologic manifestations of liver involvement by HLH. The histology is highly variable, as are rates of demonstrated hemophagocytosis. This review summarizes the clinical characteristics of HLH, with particular emphasis on hepatic manifestations thereof. We then describe the histologic patterns that have been commonly and uncommonly reported. Finally, we address difficulties faced by liver pathologists when considering this entity and offer our opinions regarding the worst “pain points.”
Analysis of Body Contouring and Sustained Weight Loss in a Diverse, Urban Population: A Seven-Year Retrospective Review
Authors: Greige Nicolas , Kamel George N. , Leibl Kayla , Jacobson Joshua , Garfein Evan S. , Weichman Katie E. , Benacquista Teresa 
Published: December 2022

Background:
Studies demonstrating the positive impact of body contouring on sustained weight loss in bariatric patients describe a narrow cohort. We sought to evaluate the impact of post bariatric body contouring procedures on sustained weight loss in minority race patients.

Methods:
A retrospective review of bariatric surgery patients at a single institution was performed. Patients were grouped by: (1) those that underwent body contouring, (2) those that had consultation but did not undergo body contouring, and (3) those without consultation. Body mass index (BMI) and excess body weight loss (EBWL) over 7 years were the primary outcomes.

Results:
2531 patients were analyzed, 350 in Group 1, 364 in Group 2, and 1817 in Group 3. At postoperative year 7, Groups 1 and 2 had average BMIs 4.71 and 2.31 kg/m2 lower than Group 3, respectively, while adjusting for covariates. After exclusion of 105 patients in Group 2 that were not offered body contouring due to inadequate weight loss, however, Group 2 had an average BMI 4.07 kg/m2 lower than Group 3 at postoperative year 7. During postoperative year 1, Group 1 had an average EBWL of 74.38%, which declined 1.51% yearly, and Group 2 had an average EBWL of 70.12%, which declined 1.86% yearly. After exclusion of the aforementioned patients, Group 2 had an average EBWL of 74.9% at postoperative year 1, which declined 1.88% yearly.

Conclusions:
Body contouring after bariatric surgery did not impart a clinically significant, long-term sustained weight loss benefit in our cohort. In our study population, we found that patients identifying as Black had significantly worse sustained weight loss.
Adipocyte differentiation of 3T3-L1 cells under tenofovir alafenamide, tenofovir disoproxil fumarate, and integrase strand transfer inhibitors selective challenge: an in-vitro model
Authors: Perna Angelica , Carleo Maria A. , Mascolo Silvia , Guida Alessandra , Contieri Marcella , Sellitto Carmine , Hay Eleonora , De Blasiis Paolo , Lucariello Angela , Guerra Germano , Baldi Alfonso , De Luca Antonio , Maggi Paolo , Esposito Vincenzo 
Published: December 2022

Objective:
Integrase strand transfer inhibitors (INSTIs) are a class of antiretroviral therapy (ART) medications with a good tolerability profile and a high genetic barrier to HIV drug resistance. However, several studies report significant weight gain among persons receiving INSTI-based ART regimens compared with other regimens.

Design:
In-vitro model of adipogenesis.

Methods:
We used 3T3-L1 cells to investigate the effects of the nucleoside reverse transcriptase inhibitors (NRTIs) tenofovir disoproxil fumarate (TDF) and tenofovir alafenamide (TAF), alone or in combination with INSTIs: raltegravir (RAL), elvitegravir (ELV), dolutegravir (DTG), and bictegravir (BIC) on adipose differentiation. To monitor adipocyte differentiation, expression levels of PPARɣ and C/EBPα and the intracellular lipid accumulation by Red Oil staining were used. Furthermore, we evaluated the immunohistochemical expression of ER-TR7, a fibroblastic marker, after INSTIs treatment.

Results:
Compared with control, INSTIs were able to increase adipogenesis, especially RAL and ELV. TAF and TDF inhibited adipogenesis alone and in combination with INSTIs. This ability was more evident when TAF was used in combination with DTG and BIC. Finally, INSTIs increased the expression of ER-TR7 compared with control and cells treated with TAF or TDF.

Conclusion:
Our data support the evidence that in-vitro challenge of 3T3-L1 cells with INSTIs is able to increase adipocytic differentiation and to drive a number of these cells toward the expression of fibroblastic features, with a different degree according to the various drugs used whereas TAF and TDF have an antagonistic role on this phenomenon.
A cell-and-plasma numerical model reveals hemodynamic stress and flow adaptation in zebrafish microvessels after morphological alteration
Authors: Maung Ye Swe Soe , Phng Li-Kun 
Published: December 2022

AbstractThe development of a functional cardiovascular system ensures successful embryonic development and a sustainable oxygen, nutrient and hormones delivery system for homeostasis in adulthood. While early vessels are formed by biochemical signaling and genetic programming, the onset of blood flow provides mechanical cues that participate in the vascular remodeling of the embryonic cardiovascular system. The zebrafish is a prolific animal model for studying the quantitative relationship between blood flow and vascular morphogenesis due to a combination of favorable factors including blood flow visualization in optically transparent larvae. While imaging techniques can be employed for measuring flow velocity and blood perfusion levels, hemodynamic forces such as the lumen wall shear stress (WSS) and lumen blood pressure cannot be measured directly. In this study, we have developed a cell and plasma blood transport model using CFD to understand how red blood cell (RBC) partitioning asymmetries affect WSS in a network. Furthermore, we employed the CFD model on rheological and morphological alterations of a wildtype network. We discuss how careful consideration of boundary conditions and acquisition of systemic parameters of blood flow are required to understand the intimate relationship between flow physiology and compensatory responses to hemorheological or morphological alterations.
Population divergence in maternal investment and embryo energy use and allocation reveals adaptive responses to cool climates
Authors: Pettersen A.K. , Ruuskanen S. , Nord Andreas , Nilsson J. F. , Miñano M.R. , Fitzpatrick L. J. , While G.M. , Uller T. 
Published: December 2022

AbstractThe thermal sensitivity of early life stages can play a fundamental role in constraining species distribution. For egg-laying ectotherms, cool temperatures often extend development time and exacerbate developmental energy cost. Despite these costs, egg laying is still observed at high latitudes and altitudes. How embryos overcome the developmental constraints posed by cool climates is crucial knowledge for explaining the persistence of oviparous species in such environments and for understanding thermal adaptation more broadly. Here, we studied maternal investment, and embryo energy use and allocation in wall lizards spanning altitudinal regions, as potential mechanisms of local adaptation to development in cool climates. Specifically, we compared population-level differences in (1) investment from mothers (egg mass, embryo retention and thyroid yolk hormone concentration), (2) embryo energy expenditure during development, and (3) embryo energy allocation from yolk towards tissue. We found evidence that energy expenditure was greater under cool compared with warm incubation temperatures. Females from relatively cool regions did not compensate for this energetic cost of development by producing larger eggs or increasing thyroid hormone concentration in yolk. Instead, embryos from the high-altitude region used less energy to complete development, i.e., they developed faster without a concomitant increase in metabolic rate, compared with those from the low-altitude region. Embryos from high altitudes also allocated relatively more energy towards tissue production, hatching with lower residual yolk:tissue ratios than low-altitude region embryos. These results suggest that local adaptation to cool climate in wall lizards involves mechanisms that regulate embryonic utilisation of yolk reserves and its allocation towards tissue, rather than shifts in maternal investment of yolk content or composition.
Graph neural networks learn emergent tissue properties from spatial molecular profiles
Authors: Fischer David S. , Ali Mayar , Richter Sabrina , Ertürk Ali , Theis Fabian 
Published: December 2022

AbstractTissue phenotypes such as metabolic states, inflammation, and tumor properties are functions of molecular states of cells that constitute the tissue. Recent spatial molecular profiling assays measure tissue architecture motifs in a molecular and often unbiased way and thus can explain some aspects of emergence of these phenotypes. Here, we characterize the ability of graph neural networks to model tissue-level emergent phenotypes based on spatial data by evaluating phenotype prediction across model complexities. First, we show that immune cell dispersion in colorectal tumors, which is known to be predictive of disease outcome, can be captured by graph neural networks. Second, we show that breast cancer tumor classes can be predicted from gene expression alone without spatial information and are thus too simplistic a phenotype to require a complex model of emergence. Third, we show that representation learning approaches for spatial graphs of molecular profiles are limited by overfitting in the prevalent regime of up to 100s of images per study. We address overfitting with within-graph self-supervision and illustrate its promise for tissue representation learning as a constraint for node representations.
Differential Expression Analysis for Metatranscriptomics with Sample-Paired Metagenomics Data
Authors: Yan Binghao , Wu Di 
Published: December 2022

1AbstractMotivationLarge microbial communities have contributed to essential ecosystems and multiple health and disease processes. Metatranscriptomics (MTX) is becoming increasingly important for profiling the gene expression pattern and functional activities of microbial communities. A fundamental task for analyzing the high-throughput sequencing data is the Differential Expression (DE) analysis, which aims to identify up/down-regulated genes/pathways across multiple conditions. However, DE analysis is complicated by the variation of underlying DNA copies, which is caused by the highly dynamic nature of microbial communities. The non-independent change between MTX and MGX may lead to false discoveries about which genes are biologically differentially expressed. Nevertheless, We can settle this problem by using the information from paired metagenomics (MGX) data.ResultsWe proposed the MetaDePair, a statistical model for DE analysis in MTX with paired MGX data. It relied on a conditional Negative-Binomial distribution to model the count data. We showed that the adjustment of underlying DNA copies could significantly eliminate the variations of RNA data, thus improving the power of statistical inference. Also, we found that appropriate pre-filtering of zeros can also improve the sensitivity and precision of the model. Moreover, we proposed a method to simulate the paired MTX and MGX data. Using simulated data and real microbial data sets, we demonstrated that our method has a high statistical power while controlling the false discovery rate (FDR). We applied the tool to oral microbiome data and identified significant genes that are associated with Early Childhood Caries (ECC). Our tool enabled a more accurate and effective DE analysis based on MTX with paired MGX data and helped us improve the understanding of the functional characterization of microbial communities.