bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prenatal organophosphate pesticide exposure and sex-specific estimated fetal size
Authors: Medley Eleanor A , Trasande Leonardo , Naidu Mrudula , Wang Yuyan , Ghassabian Akhgar , Kahn Linda G , Long Sara , Afanasyeva Yelena , Liu Mengling , Kannan Kurunthachalam , Mehta-Lee Shilpi S , Cowell Whitney 
Published: August 2024

Abstract
Prenatal organophosphate (OP) pesticide exposure may be associated with reduced fetal growth, although studies are limited and have mixed results. We investigated associations between prenatal OP pesticide exposure and fetal size and modification by fetal sex. Maternal urinary concentrations of dialkyl phosphate (DAP) metabolites were measured at 3 time points. Fetal biometrics were obtained from ultrasounds in the second (n = 773) and third (n = 535) trimesters. Associations between pregnancy-averaged ΣDAP and fetal biometry z scores were determined through multiple linear regression. Modification by sex was investigated through stratification and interaction. In the second trimester, one ln-unit increase in ΣDAP was associated with lower estimated fetal weight (–0.15 SD; 95% CI, –0.29 to –0.01), head circumference (–0.11 SD; CI, –0.22 to 0.01), biparietal diameter (–0.14 SD; CI, –0.27 to –0.01), and abdominal circumference (–0.12 SD; CI, –0.26 to 0.01) in females. In the third trimester, one ln-unit increase in ΣDAP was associated with lower head circumference (–0.14 SD; CI, –0.28 to 0.00) and biparietal diameter (–0.12 SD; CI, –0.26 to 0.03) in males. Our results suggest that prenatal OP pesticide exposure is negatively associated with fetal growth in a sex-specific manner, with associations present for females in mid-gestation and males in late gestation.
This article is part of a Special Collection on Environmental Epidemiology.
Strategies of resource sharing in clonal plants: a conceptual model and an example of contrasting strategies in two closely related species
Authors: Duchoslavová Jana , Jansa Jan 
Published: August 2024

Abstract

Background and Aims
Clonal growth is widespread among herbaceous plants, and helps them to cope with environmental heterogeneity through resource integration via connecting clonal organs. Such integration is considered to balance heterogeneity by translocation of resources from rich to poor patches. However, such an ‘equalization’ strategy is only one of several possible strategies. Under certain conditions, a strategy emphasizing acropetal movement and exploration of new areas or a strategy of accumulating resources in older ramets may be preferred. The optimal strategy may be determined by environmental conditions, such as resource availability and level of light competition. We aimed to summarize possible translocation strategies in a conceptual analysis and to examine translocation in two species from different habitats.

Methods
Resource translocation was compared between two closely related species from different habitats with contrasting productivity. The study examined the bidirectional translocation of carbon and nitrogen in pairs of mother and daughter ramets grown under light heterogeneity (one ramet shaded) at two developmental stages using stable-isotope labelling.

Key Results
At the early developmental stage, both species translocated resources towards daughters and the translocation was modified by shading. Later, the species of low-productivity habitats, Fragaria viridis, translocated carbon to shaded ramets (both mother and daughter), according to the ‘equalization’ strategy. In contrast, the species of high-productivity habitats, Potentilla reptans, did not support shaded mother ramets. Nitrogen translocation remained mainly acropetal in both species.

Conclusions
The two studied species exhibited different translocation strategies, which may be linked to the habitat conditions experienced by each species. The results indicate that we need to consider different possible strategies. We emphasize the importance of bidirectional tracing in translocation studies and the need for further studies to investigate the translocation patterns in species from contrasting habitats using a comparative approach.
xSiGra: explainable model for single-cell spatial data elucidation
Authors: Budhkar Aishwarya , Tang Ziyang , Liu Xiang , Zhang Xuhong , Su Jing , Song Qianqian 
Published: August 2024

Abstract
Recent advancements in spatial imaging technologies have revolutionized the acquisition of high-resolution multichannel images, gene expressions, and spatial locations at the single-cell level. Our study introduces xSiGra, an interpretable graph-based AI model, designed to elucidate interpretable features of identified spatial cell types, by harnessing multimodal features from spatial imaging technologies. By constructing a spatial cellular graph with immunohistology images and gene expression as node attributes, xSiGra employs hybrid graph transformer models to delineate spatial cell types. Additionally, xSiGra integrates a novel variant of gradient-weighted class activation mapping component to uncover interpretable features, including pivotal genes and cells for various cell types, thereby facilitating deeper biological insights from spatial data. Through rigorous benchmarking against existing methods, xSiGra demonstrates superior performance across diverse spatial imaging datasets. Application of xSiGra on a lung tumor slice unveils the importance score of cells, illustrating that cellular activity is not solely determined by itself but also impacted by neighboring cells. Moreover, leveraging the identified interpretable genes, xSiGra reveals endothelial cell subset interacting with tumor cells, indicating its heterogeneous underlying mechanisms within complex cellular interactions.
TransTEx: novel tissue-specificity scoring method for grouping human transcriptome into different expression groups
Authors: Surana Pallavi , Dutta Pratik , Davuluri Ramana V 
Published: August 2024

Abstract

Motivation
Although human tissues carry out common molecular processes, gene expression patterns can distinguish different tissues. Traditional informatics methods, primarily at the gene level, overlook the complexity of alternative transcript variants and protein isoforms produced by most genes, changes in which are linked to disease prognosis and drug resistance.

Results
We developed TransTEx (Transcript-level Tissue Expression), a novel tissue-specificity scoring method, for grouping transcripts into four expression groups. TransTEx applies sequential cut-offs to tissue-wise transcript probability estimates, subsampling-based P-values and fold-change estimates. Application of TransTEx on GTEx mRNA-seq data divided 199 166 human transcripts into different groups as 17 999 tissue-specific (TSp), 7436 tissue-enhanced, 36 783 widely expressed (Wide), 79 191 lowly expressed (Low), and 57 757 no expression (Null) transcripts. Testis has the most (13 466) TSp isoforms followed by liver (890), brain (701), pituitary (435), and muscle (420). We found that the tissue specificity of alternative transcripts of a gene is predominantly influenced by alternate promoter usage. By overlapping brain-specific transcripts with the cell-type gene-markers in scBrainMap database, we found that 63% of the brain-specific transcripts were enriched in nonneuronal cell types, predominantly astrocytes followed by endothelial cells and oligodendrocytes. In addition, we found 61 brain cell-type marker genes encoding a total of 176 alternative transcripts as brain-specific and 22 alternative transcripts as testis-specific, highlighting the complex TSp and cell-type specific gene regulation and expression at isoform-level. TransTEx can be adopted to the analysis of bulk RNA-seq or scRNA-seq datasets to find tissue- and/or cell-type specific isoform-level gene markers.

Availability and implementation
TransTEx database: https://bmi.cewit.stonybrook.edu/transtexdb/ and the R package is available via GitHub: https://github.com/pallavisurana1/TransTEx.
‘Seeing Like a Cop’: Police Perception in Spaces of Gender and Racial Criminalization
Authors: Russell Emma K 
Published: August 2024

Abstract
Building on conceptions of policing as a colonial project, this article contributes to spatial and sensory understandings of policing by examining everyday practices of gender and racial criminalization. I argue that criminalization results from ‘seeing like a cop’ (Guenther 2019), and reordering and securing spaces accordingly. I explore the logics, practices and effects of this regime of visuality and spatial governance, drawing upon research on the criminalization of women who experience interpersonal, state and structural violence in Melbourne, Australia. For these women, police visions of danger, disorder and disposability pre-empt their displacement and punishment. The perceptual practices of police forge carceral continuums that connect the gentrifying streetscape and the home, producing both as sites of racial surveillance and gender entrapment. The article highlights the capacity for sensory analysis to deepen understandings of the violence work of policing.
Evaluation of clinical outcome and predictors of mortality in patients undergoing antegrade transvenous variceal embolization in adjunct to salvage transjugular intrahepatic portosystemic shunt for active uncontrolled gastric variceal bleeding
Authors: Patidar Yashwant , Chatterjee Navojit , Mukund Amar , Sarin Shiv Kumar 
Published: August 2024

Abstract

Objectives
Salvage transjugular intrahepatic portosystemic shunt (TIPS) is indicated in patients with active endoscopically uncontrollable variceal bleeding. TIPS alone is not effective in the management of gastric varices, and balloon occluded transvenous obliteration (BRTO) requires favourable variceal anatomy. Concomitant placement of a TIPS stent with antegrade variceal embolization leads to control of gastric variceal bleeding with no significant increase in portal pressure.

Methods
A single-centre retrospective observational study in which patients with active uncontrollable gastric variceal bleeding were included. Technical success of the procedure, 5-day rebleeding, 6-week, and 6-month survival, as well as other additional outcomes, were evaluated.

Results
A total of 18 patients were included in the study. Technical success was 100% and significant non-target embolization was seen in 0% of patients. The 6-week and 6-month survival rates were 66.67%, with an overall survival of 108.786 days (censored at 180 days). The 5-day rebleed rate was 11.1%. A significant difference in Child-Turcotte-Pugh score (P = .03), model for end-stage liver disease-sodium (MELD–Na) score (P = .022), requirement of intubation (P = .038), haemoglobin (Hb) levels (P = .042), haematocrit value (P = .018), packed red blood cell infusion required prior to and after the procedure (P = .045, .044), and presence of refractory shock (P = .013) was observed between the survival and the mortality groups. Post-variceal bleeding Hb levels, mean arterial pressure, and MELD-Na scores were significant predictors of mortality.

Conclusion
TIPS in adjunct to antegrade transvenous embolization is a safe and effective modality for the management of active uncontrolled gastric variceal bleeding in patients with variceal anatomy unfavourable for performing retrograde obliteration.

Advances in knowledge
(1) TIPS alone may not be effective in the management of gastric varices. BRTO requires favourable variceal anatomy and may lead to catastrophic oesophageal variceal haemorrhage. Concomitant placement of a TIPS stent with antegrade variceal embolization leads to control of gastric variceal bleeding with no significant increase in portal pressure. (2) TIPS, in conjunction with antegrade transvenous embolization, requires proper knowledge of variceal anatomy and the embolizing agent. Post-variceal bleeding Hb levels, mean arterial pressure, and MELD-Na scores were significant predictors of mortality.
Anatomical conservatism in the wood and bark of the species-rich Byrsonimoid clade (Malpighiaceae)
Authors: Bueno Luís Henrique , Hernández-Hernández Brenda , Francener Augusto , Amorim André M , Pace Marcelo R 
Published: August 2024

Abstract
The byrsonimoids include approximately 152 species of trees and shrubs native to the Neotropical region. The clade is monophyletic and consists of three genera: Byrsonima, Blepharandra, and Diacidia. Byrsonima woods are among the most well-known within the Malpighiaceae due to their economic importance. Nonetheless, here for the first time we explore the interspecific stem anatomical diversity of Byrsonima, its similarities and differences to Blepharandra and Diacidia, and how the previously proposed taxonomic circumscriptions for the genus Byrsonima are reflected or not in their wood and bark anatomy. Using a newly reconstructed phylogeny for the Malpighiaceae focusing on the clade Byrsonimoid and a broad selection of species, we conducted phylogenetic comparative analyses to determine how wood and bark traits have evolved across evolutionary time. Our results indicate stem anatomical homogeneity within the clade, particularly in wood traits. On one hand, the presence of septate fibres and prismatic crystals in the rays distinguishes Byrsonima from other members of the clade, but on the other hand, wood and bark traits do not support the classical infrageneric classifications for the genus. The bark in byrsonimoids displays the entire range of variation known for sclerenchyma in this tissue, from cells that can be considered true fibres to fibre-sclereids and typical true sclereids. Ancestral character state reconstructions revealed that radial arrangement, septate fibres, thin heterocellular rays, marginal parenchyma, and prismatic crystals are ancestral traits within the clade, with homoplasy common within the group. These observations demonstrate anatomical conservatism within the Byrsonimoid clade, which might be either related to their proposed recent diversification or a highly effective set of positively selected features.
Unexplained fever with consumptive syndrome in the elderly: two cases of VEXAS syndrome with inflammasome dysregulation
Authors: Mendonça Leonardo Oliveira , Leal Vinicius N C , Roa Mariela E G V , Barros Samar Freschi , Kalil Jorge , Pontillo Alessandra 
Published: August 2024

Abstract
The aim of this study is to investigate the inflammasome dysregulation in peripheral blood leukocytes of VEXAS patients. The constitutive and in vitro triggered activation of inflammasome in PBMC and neutrophils was analyzed in two Brazilian patients with typical UBA1 mutations, and compared with healthy donors. Our findings highlight the constitutive activation of caspase-1 in VEXAS leukocytes, accompanied by increased plasma levels of IL-18. Furthermore, upon stimulation of isolated peripheral blood mononuclear cells (PBMC) and neutrophils, we observed not only the exhaustion of NLRP3 and NLRP1/CARD8 pathways in VEXAS PBMC but also a significant increase in NLRP3-mediated NETs release in VEXAS neutrophils. These findings support previous studies on the contribution of the inflammasome to VEXAS pathogenesis, identifying at least two profoundly affected pathways (NLRP3 and NLRP1/CARD8) in VEXAS peripheral blood.
Multi-dimensional analysis of B cells reveals the expansion of memory and regulatory B-cell clusters in humans living in rural tropical areas
Authors: Chayé Mathilde A M , van Hengel Oscar R J , Voskamp Astrid L , Ozir-Fazalalikhan Arifa , König Marion H , Stam Koen A , Manurung Mikhael D , Mouwenda Yoanne D , Aryeetey Yvonne A , Kurniawan Agnes , Kruize Yvonne C M , Sartono Erliyani , Buisman Anne-Marie , Yazdanbakhsh Maria , Tak Tamar , Smits Hermelijn H 
Published: August 2024

Abstract
B-cells play a critical role in the formation of immune responses against pathogens by acting as antigen-presenting cells, by modulating immune responses, and by generating immune memory and antibody responses. Here, we studied B-cell subset distributions between regions with higher and lower microbial exposure, i.e. by comparing peripheral blood B-cells from people living in Indonesia or Ghana to those from healthy Dutch residents using a 36-marker mass cytometry panel. By applying an unbiased multidimensional approach, we observed differences in the balance between the naïve and memory compartments, with higher CD11c+ and double negative (DN-IgDnegCD27neg) memory (M)B-cells in individuals from rural tropical areas, and conversely lower naïve B-cells compared to residents from an area with less pathogen exposure. Furthermore, characterization of total B-cell populations, CD11c+, DN, and Breg cells showed the emergence of specific memory clusters in individuals living in rural tropical areas. Some of these differences were more pronounced in children compared to adults and suggest that a higher microbial exposure accelerates memory B-cell formation, which “normalizes” with age.
Diagnosing Myocardial Injury in an Acute Chest Pain Cohort; Long-Term Prognostic Implications of Cardiac Troponin T and I
Authors: Saeed Nasir , Steiro Ole-Thomas , Langørgen Jørund , Tjora Hilde L , Bjørneklett Rune O , Skadberg Øyvind , Bonarjee Vernon V S , Mjelva Øistein R , Norekvål Tone M , Steinsvik Trude , Vikenes Kjell , Omland Torbjørn , Aakre Kristin M 
Published: August 2024

Abstract

Background
There are limited data regarding the utility of follow-up cardiac troponin (cTn) measurements after admission for acute chest pain and how long-term stability of myocardial injury and prognostic value differ when using cardiac troponin T (cTnT) or I (cTnI).

Methods
We measured high-sensitivity (hs)-cTnT (Roche Diagnostics) and hs-cTnI (Siemens Healthineers) during hospitalization for acute chest pain and after 3 months. Acute myocardial injury was defined as concentrations &gt; sex-specific upper reference limit (URL) during hospitalization and ≤URL at 3-months. Chronic myocardial injury (CMI) was defined as concentrations &gt; URL at both time points. Patients were followed from the 3-month sampling point for a median of 1586 (IQR 1161–1786) days for a primary composite endpoint of all-cause mortality, myocardial infarction (MI), revascularization, and heart failure, and a secondary endpoint of all-cause mortality.

Results
Among 754 patients, 33.8% (hs-cTnT) and 19.2% (hs-cTnI) had myocardial injury during hospitalization. The rate of CMI was 5 times higher by hs-cTnT (20%) assay than hs-cTnI (4%), while acute myocardial injury was equally common; 14% (hs-cTnT) and 15% (hs-cTnI), respectively (6% and 5% when excluding index non-ST-elevation MI (NSTEMI). For hs-cTnT, peak index concentration, 3-month concentration and classification of CMI predicted the primary endpoint; hazard ratios (HRs) 1.38 (95% CI 1.20–1.58), 2.34 (1.70–3.20), and 2.31 (1.30–4.12), respectively. For hs-cTnI, peak index concentration predicted the primary endpoint; HR 1.14 (1.03–1.25). This association was nonsignificant after excluding index NSTEMI.

Conclusions
Acute myocardial injury is equally frequent, whereas CMI is more prevalent using hs-cTnT assay than hs-cTnI. Measuring hs-cTnT 3 months after an acute chest pain episode could assist in further long-term risk assessment.
ClinicalTrials.gov Registration Number: NCT02620202
Right coronary ischaemia caused by a sinus of Valsalva aneurysm improved by releasing mechanical stretch: a case report
Authors: Yamazaki Sachiko , Okawa Kazunari , Shunto Keisuke , Ito Daisuke , Takahashi Akiyuki 
Published: August 2024

Abstract

Background
A sinus of Valsalva aneurysm involving a single cusp is a rare condition, and coronary computed tomography angiography with fractional flow reserve-computed tomography helps evaluate not only the anatomical aspects of the aneurysm and coronary artery but also the physiological details of coronary artery disease.

Case summary
A 71-year-old woman presented with exertional chest pain and dyspnoea. Enhanced computed tomography revealed an aneurysmal change in the right sinus of Valsalva, and coronary computed tomography angiography revealed diffuse narrowing of the proximal segment of right coronary artery due to mechanical stretching by the large Valsalva aneurysm. Fractional flow reserve-computed tomography revealed a significantly low fractional flow reserve (0.50 in the distal right coronary artery). A modified Bentall procedure was performed with a 21 mm bioprosthetic valve and a 24 mm Valsalva graft conduit for the aortic root aneurysm; mitral valve annuloplasty was performed for mitral valve regurgitation. Post-operative coronary computed tomography angiography revealed no significant stenosis in the proximal segment of the right coronary artery. Furthermore, fractional flow reserve-computed tomography revealed a normalized fractional flow reserve in the distal right coronary artery. The patient experienced relief from chest pain and was discharged 19 days after the surgery.

Discussion
A right coronary sinus of Valsalva aneurysm, which caused right coronary artery ischaemia, was successfully treated using a modified Bentall procedure. Coronary computed tomography angiography and fractional flow reserve-computed tomography revealed anatomical and functional improvements in the right coronary artery ischaemia post-operatively.
ST-elevation myocardial infarction from septic embolism secondary to prosthetic aortic valve endocarditis: a case report
Authors: Rohla Miklos , Philip Legate , Wolf Janina , Jaffer Farouc A , Räber Lorenz 
Published: August 2024

Abstract

Background
ST-elevation myocardial infarction (STEMI) is a cardiac emergency that requires prompt diagnosis and treatment. We describe a challenging and complex case of managing acute STEMI in a patient with severe anaemia, deranged clotting profile, and infective prodrome.

Case summary
A 54-year-old Caucasian gentleman was referred by his general practitioner as an emergency after presenting with acute onset of chest pain. His electrocardiogram revealed anterior ST elevation. His past medical history includes a mechanical aortic valve, requiring anticoagulation, and a recent gastrointestinal bleed secondary to type C gastritis. His initial presentation was further complicated by severe anaemia, deranged clotting profile, and elevated infective markers. He required a prompt transfer to the catheterization laboratory to assess and stabilize the situation. We discuss the emerging challenges during treatment, particularly as the diagnosis of septic embolism from infective prosthetic valve endocarditis was unfolding, requiring urgent cardiac surgery.

Discussion
Acute coronary vessel closure leading to STEMI from septic embolism secondary to prosthetic aortic valve endocarditis is very rare. It is essential to consider the whole picture of the presentation for timely diagnosis and tailored treatment.