bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tuberculous pleuritis: clinical presentations and diagnostic challenges
Authors: Chan Ken Ka Pang , Lee Yun Chor Gary 
Published: February 2024

Purpose of review
Tuberculous pleuritis (TBP) is one of the most common types of extrapulmonary tuberculosis. We highlight the latest epidemiology of TBP, the heterogeneity of its presentation and the performance of different diagnostic strategies.

Recent findings
There are differential trends in the incidences of TBP worldwide. Its incidence increased in China but decreased in the United States in the past decade. The presentation of TBP is heterogeneous regarding clinical symptoms, radiological findings and pleural fluid analysis results. Conventional microbiological tests have low sensitivities to diagnose TBP. Recent research focused on various diagnostic tools with better yield. The sensitivity of nucleic acid amplification tests (NAAT) in pleural fluid, including the latest generation of PCR and sequencing-based techniques for detecting tuberculosis, remains suboptimal. Various pleural fluid biomarkers have been explored, but there is a lack of consensus on their clinical utility and cutoff levels.

Summary
The heterogeneity of clinical presentation poses obstacles to diagnosing TBP. Further development of diagnostic tools, including more robust NAAT and biomarkers with additional validation, is needed before incorporation into routine clinical practice.
Postoperative atrial fibrillation following coronary artery bypass grafting surgery: role of IL-6 from structural to electrical remodeling
Authors: Deng Yufeng , Wu Ying 
Published: February 2024

Abstract
Postoperative atrial fibrillation (POAF) is a common complication of coronary artery bypass grafting (CABG) surgery, and contributes significantly to morbidity, mortality, and rising healthcare costs. Although the underlying mechanisms for POAF are not completely understood, surgery-related inflammation, often in the presence of pre-existing factors, renders the atria susceptible to the induction and persistence of POAF. Notably, interleukin-6 (IL-6), a primary cytokine of the inflammatory cascade, has been identified as one of the principal molecular components of POAF pathogenesis. Atrial fibrosis may also be a key mechanistic link by which inflammation contributes to POAF. Recently, it has been shown that atrial fibrosis, in combination with the presence of an electrophysiological substrate capable of maintaining atrial fibrillation (AF), also promotes arrhythmia, suggesting that POAF shares proarrhythmic mechanisms with other types of AF. In this review, the impact of inflammation and the particular role of IL-6, on the structural and electrical changes that promote to the development of POAF is summarized.
Surgical Outcome Reporting. Moving From a Comic to a Tragic Opera?
Authors: Abbassi Fariba , Pfister Matthias , Domenghino Anja , Puhan Milo A. , Clavien Pierre-Alain 
Published: February 2024

Objectives:
To assess the current quality of surgical outcome reporting in the medical literature and to provide recommendations for improvement.

Background:
In 1996, The Lancet labeled surgery as a “comic opera” mostly referring to the poor quality of outcome reporting in the literature impeding improvement in surgical quality and patient care.

Methods:
We screened 3 first-tier and 2 second-tier surgical journals, as well as 3 leading medical journals for original articles reporting on results of surgical procedures published over a recent 18-month period. The quality of outcome reporting was assessed using a prespecified 12-item checklist.

Results:
Six hundred twenty-seven articles reporting surgical outcomes were analyzed, including 125 randomized controlled trials. Only 1 (0.2%) article met all 12 criteria of the checklist, whereas 356 articles (57%) fulfilled less than half of the criteria. The poorest reporting was on cumulative morbidity burden, which was missing in 94% of articles (n=591) as well as patient-reported outcomes missing in 83% of publications (n=518). Comparing journal groups for the individual criterion, we found moderate to very strong statistical evidence for better quality of reporting in high versus lower impact journals for 7 of 12 criteria and strong statistical evidence for better reporting of patient-reported outcomes in medical versus surgical journals (P<0·001).

Conclusions:
The quality of outcomes reporting in the medical literature remains poor, lacking improvement over the past 20 years on most key end points. The implementation of standardized outcome reporting is urgently needed to minimize biased interpretation of data thereby enabling improved patient care and the elaboration of meaningful guidelines.
Geoffrey Eglinton. 1 November 1927—11 March 2016
Authors: Brassell Simon C. , Eglinton FRS Timothy I. 
Published: February 2024

Where have all life's molecules gone?
Recycled to carbon dioxide every one!
Ah! But look—a hardy few remain

As biomarkers imprisoned in the fossil domain (G. Eglinton & R. Pancost,
Immortal molecules
(
47
))

Geoffrey Eglinton trained as an organic chemist at the University of Manchester working on acetylene synthesis, and the Eglinton reaction signifies his discovery of an effective method for their oxidative coupling. At the University of Glasgow, he recognized the potential of analytical advances to open new frontiers for characterization of molecular constituents of complex mixtures and continued to adopt and adapt instrumental techniques throughout his career. Eglinton's exploration of plant leaf waxes, and their taxonomic profiles, prompted forays in organic geochemistry, seeking molecular evidence for ancient life. Thus, his focus shifted to studying ‘chemical fossils’ preserved in the rock record and pioneering identification and interpretation of their compositions. At the University of Bristol, he established the Organic Geochemistry Unit and steered its rise to international prominence as a leading centre for research, a legacy that continues today. He served in planning the Apollo sampling programme and led research that explicated the carbon chemistry of the Moon. Major advances in using molecules as witnesses of the origins and fate of sedimentary organic matter bear the hallmarks of his insightful contributions and commitment to interdisciplinary, collaborative ventures. They include deciphering how environmental controls and thermal transformations govern the composition of petroleum hydrocarbons, and validating the ability for molecules to afford invaluable evidence of past climates. Eglinton's research accomplishments were recognized by many prestigious awards, including a Royal Gold Medal of the Royal Society, the V. M. Goldschmidt Medal of the Geochemical Society, the Wollaston Medal of the Geological Society, and the Dan David Prize.
An image segmentation pipeline optimized for human microglia uncovers sources of morphological diversity in Alzheimer’s disease
Authors: De Jager Robert M. , Lee Annie J. , Sigalov Alina , Taga Mariko 
Published: February 2024

AbstractAlzheimer’s disease (AD) is a neurodegenerative disorder characterized by cognitive decline and the accumulation of beta-amyloid plaques and neurofibrillary tangles. Microglia, the resident immune cells in the brain, play a crucial role in AD pathology, particularly in relation to amyloid plaques. However, the exact role of plaque-associated microglia and their morphological changes in AD progression remains under debate. In this study, we aimed to establish an automated image segmentation and analysis pipeline optimized for the detection of human microglia, and we assessed its utility by systematically investigating topological relationships between microglia morphology and amyloid plaques.We accessed post-mortem brain tissue samples from persons with AD and utilized immunofluorescence staining to label microglia (IBA1) and amyloid plaques (Aβ1-42). The acquired images were processed using CellProfiler, an open-source image analysis software, to automatically segment microglia and measure their morphological features. Specifically, since activated (stage III) microglia have a condensed morphology with retracted processes, we prioritized a morphological parameter called “compactness” in our analyses to capture shape changes in microglial found in proximity to amyloid plaques.Our results revealed that microglia unassociated with plaques (Mip-) were more abundant than microglia associated with plaques (Mip+) in the Dorsolateral Prefrontal Cortex (DLPFC) of both men and women with AD. Furthermore, we observed that Mip+exhibited a significantly more ramified shape and had a higher expression of the IBA1 microglial marker gene compared to Mip. There were no significant differences in microglia morphology between men and women.Our study highlights the utility of automated image analysis in characterizing detailed microglia morphology at the single-cell level and its relationship with AD pathology.
Toward Sustainable Biocultural Tourism: An Integrated Spatial Analysis of Cultural and Biodiversity Richness in Colombia
Authors: Echeverri Alejandra , Batista Natasha M. , Wolny Stacie , Herrera-R Guido A. , Andrade-Rivas Federico , Bailey Allison , Cardenas-Navarrete Anaid , Dávila Arenas Armando , Díaz-Salazar Andres Felipe , Hernandez Katherine Victoria , Langhans Kelley E. , Mateus-Aguilar Bryam E. , Levey Dallas , Neill Andrew , Nguyen Oliver , Suárez-Castro Andres Felipe , Zapata Felipe , Ocampo-Peñuela Natalia 
Published: February 2024

AbstractTourism plays a vital role in both economic development and depending on the scale, it can also aid environmental conservation. Tourism planning often considers culture-based and nature-based tourism separately, failing to recognize the synergies between them, with the potential to market locations as biocultural destinations.Using Colombia as a case study, we created metrics of taxonomic biological diversity as measured by vertebrate species richness (including birds, mammals, freshwater fishes, reptiles, and amphibians) and institutionalized cultural richness (by counting the number of UNESCO world heritage sites, intangible cultural heritage sites, museums, endemic music festivals, Afro-Colombian territories, and Indigenous reserves), and evaluated the spatial correlations between them.To determine biocultural tourism potential, we evaluated whether biocultural richness was accessible, and mapped potential biocultural tourism supply. By mapping areas of sports fisheries, birdwatching destinations, and airport arrivals we also estimated spatial demand. We also analyzed the difference between demand and supply to assess the realized and untapped potential for biocultural destinations.While biocultural richness is high in the Amazon, Pacific, and Caribbean regions, we found that there are no win-win-win locations where culture, species richness, and accessibility are all high. Areas with great potential for biocultural tourism development largely coincide with designated Indigenous reserves and Afro-Colombian territories.This study underscores the power of integrating cultural and biological variables to reshape the tourism sector. Our paper offers practical recommendations for policymakers, conservation organizations, and local communities seeking to create transformative and inclusive tourism experiences.
Towards a Survival Risk Prediction Model for Metastatic NSCLC Patients on Durvalumab Using Whole-Lung CT Radiomics
Authors: Patwardhan Kedar , RaviPrakash Harish , Nikolaou Nikos , Gonzalez-García Ignacio , Salazar José Domingo , Metcalfe Paul , Reischl Joachim 
Published: February 2024

AbstractBackgroundExisting criteria for predicting patient survival from immunotherapy are primarily centered on the PD-L1 status of patients. We tested the hypothesis that noninvasively captured baseline whole-lung radiomics features from CT images, baseline clinical parameters, combined with advanced machine learning approaches, can help to build models of patient survival that compare favorably with PD-L1 status for predicting ‘less-than-median-survival risk’ in the metastatic NSCLC setting for patients on durvalumab. With a total of 1062 patients, inclusive of model training and validation, this is the largest such study yet.MethodsTo ensure a sufficient sample size, we combined data from treatment arms of three metastatic NSCLC studies. About 80% of this data was used for model training, and the remainder was held-out for validation. We first trained two independent models; Model-C trained to predict survival using clinical data; and Model-R trained to predict survival using whole-lung radiomics features. Finally, we created Model-C+R which leveraged both clinical and radiomics features.ResultsThe classification accuracy (for median survival) of Model-C, Model-R, and Model-C+R was 63%, 55%, and 68% respectively. Sensitivity analysis of survival prediction across different training and validation cohorts showed concordance indices ([95 percentile]) of 0.64 ([0.63, 0.65]), 0.60 ([0.59, 0.60]), and 0.66 ([0.65,0.67]), respectively. We additionally evaluated generalization of these models on a comparable cohort of 144 patients from an independent study, demonstrating classification accuracies of 65%, 62%, and 72% respectively.ConclusionMachine Learning models combining baseline whole-lung CT radiomic and clinical features may be a useful tool for patient selection in immunotherapy. Further validation through prospective studies is needed.
OligoFormer: an accurate and robust prediction method for siRNA design
Authors: Bai Yilan , Zhong Haochen , Wang Taiwei , Lu Zhi John 
Published: February 2024

AbstractMotivationRNA interference(RNAi) has become a widely used experimental approach for post-transcriptional regulation and is increasingly showing its potential as future targeted drugs. However, the prediction of highly efficient siRNAs(small interfering RNA) is still hindered by dataset biases, the inadequacy of prediction methods, and the presence of off-target effects. To overcome these limitations, we propose an accurate and robust prediction method, OligoFormer, for siRNA design.ResultsOligoFormer comprises three different modules including thermodynamic calculation, RNA-FM module, and Oligo encoder. Oligo encoder is the core module based on the transformer encoder. Taking siRNA and mRNA sequences as input, OligoFormer can obtain thermodynamic parameters, RNA-FM embedding, and Oligo embedding through these three modules, respectively. We carefully benchmarked OligoFormer against 5 comparable methods on siRNA efficacy datasets. OligoFormer outperforms all the other methods, with an average improvement of 9% in AUC and 10.7% in F1 score in our inter-dataset validation. We also provide a comprehensive pipeline with prediction of siRNA efficacy and off-target effects using PITA score and TargetScan score. The ablation study shows RNA-FM module and thermodynamic parameters improved the performance and accelerated convergence of OligoFormer. The saliency map by gradient backpropagation shows certain base preferences in initial and terminal region of siRNAs.
Characterization Of Bitter Taste Receptor Dependent Autophagy in Oral Epithelial Cells
Authors: Singh Nisha , Ghavami Saeid , Chelikani Prashen 
Published: February 2024

AbstractMicrobial dysbiosis is an important trigger in the development of oral diseases. Oral keratinocytes or gingival epithelial cells (GECs) offer protection against various microbial insults. Recent studies suggest GECs expressed higher level of bitter taste receptor 14 (T2R14) compared to other taste receptors and toll-like receptors and acts as innate immune sentinels. Macroautophagy or autophagy is a cellular conserved process involved in the regulation of host innate immune responses against microbial infection. Here, we describe a robust method for evaluation of T2R14-dependent autophagy flux in GECs. Autophagy flux was detected using western blot analysis in GECs and further was confirmed using Acridine Orange dependent flow cytometry analysis.WorkflowGraphical abstractSchematic showing the methodology (Western blot and flow cytometry) used for assessment of autophagy flux in GEC (created with Biorender). GEC: Gingival epithelial cells, BafA1: Bafilomycin, Rapa: Rapamycin, LC3-II: microtubule associated light chain protein, p62: sequestosome 1
The spread of pESI-mediated extended-spectrum cephalosporin resistance inSalmonellaserovars - Infantis, Senftenberg, and Alachua isolated from food animal sources in the United States
Authors: Li Cong , Tate Heather , Huang Xinyang , Hsu Chih-Hao , Harrison Lucas B. , Zhao Shaohua , Fortenberry Gamola Z. , Dessai Uday , McDermott Patrick F. , Strain Errol A. 
Published: February 2024

AbstractThe goal of this study is to investigate the origin, prevalence, and evolution of the pESI megaplasmid inSalmonellaisolated from animals, foods, and humans. We queried 510,097Salmonellagenomes under the National Center for Biotechnology Information (NCBI) Pathogen Detection (PD) database for the presence of potential sequences containing the pESI plasmid in animal, food, and environmental sources. The presence of the pESI megaplasmid was confirmed by using seven plasmid-specific markers (rdA,pilL,SogS,TrbA,ipf,ipr2 andIncFIB(pN55391)). The plasmid and chromosome phylogeny of these isolates was inferred from single nucleotide polymorphisms (SNPs). Our search resolved sixSalmonellaclusters carrying the pESI plasmid. Four were emergentSalmonellaInfantis clusters, and one each belonged to serovar Senftenberg and Alachua. The Infantis cluster with a pESI plasmid carryingblaCTX-M-65gene was the biggest of the four emergent Infantis clusters, with over 10,000 isolates. This cluster was first detected in South America and has since spread widely in United States. Over time the composition of pESI in United States has changed with the average number of resistance genes showing a decrease from 9 in 2014 to 5 in 2022, resulting from changes in gene content in two integrons present in the plasmid. A recent and emerging cluster of Senftenberg, which carries theblaCTX-M-65gene and is primarily associated with turkey sources, was the second largest in the United States. SNP analysis showed that this cluster likely originated in North Carolina with the recent acquisition of the pESI plasmid. A single Alachua isolate from turkey was also found to carry the pESI plasmid containingblaCTX-M-65gene. The study of the pESI plasmid, its evolution and mechanism of spread can help us in developing appropriate strategies for the prevention and further spread of this multi-drug resistant plasmid inSalmonellain poultry and humans.
Different types of social links contrastingly shape reproductive wellbeing in a multi-level society of wild songbirds
Authors: Gokcekus Samin , Firth Josh A. , Cole Ella F. , Sheldon Ben C. , Albery Gregory F. 
Published: February 2024

AbstractThe social environment has diverse consequences for individuals’ welfare, health, reproductive success, and survival. This environment consists of different kinds of dyadic bonds that exist at different levels; in many social species, smaller social units come together in larger groups, creating multilevel societies. In great tits (Parus major), individuals have four major types of dyadic bonds: pair mates, breeding neighbours, flockmates, and spatial associates, all of which have been previously linked to fitness outcomes. Here, we show that these different types of dyadic bonds are differentially linked with subsequent reproductive success metrics in this wild population and that considering spatial effects provides further insights into these relationships. We provide evidence that more social individuals had a higher number of fledglings, and individuals with more spatial associates had smaller clutch sizes. We also show individuals with stronger bonds with their pair mate had earlier lay dates. Our study highlights the importance of considering different types of dyadic relationships when investigating the relationship between wellbeing and sociality, and the need for future work aimed at experimentally testing these relationships, particularly in spatially structured populations.
TPPB modulates PKC activity to attenuate neuroinflammation and ameliorate experimental multiple sclerosis
Authors: Shanmukha Shruthi , Godfrey Wesley H. , Gharibani Payam , Lee Judy J. , Guo Yu , Deng Xiaojing , Wender Paul A. , Kornberg Michael D. , Kim Paul M. 
Published: February 2024

AbstractProtein kinase C (PKC) plays a key role in modulating the activities of the innate immune cells of the central nervous system (CNS). A delicate balance between pro-inflammatory and regenerative activities by microglia and CNS-associated macrophages is necessary for the proper functioning of the CNS. Thus, a maladaptive activation of these CNS innate immune cells results in neurodegeneration and demyelination associated with various neurologic disorders, such as multiple sclerosis (MS) and Alzheimer’s disease. Prior studies have demonstrated that modulation of PKC activity by bryostatin-1 (bryo-1) and its analogs (bryologs) attenuates the pro-inflammatory processes by microglia/CNS macrophages and alleviates the neurologic symptoms in experimental autoimmune encephalomyelitis (EAE), an MS animal model. Here, we demonstrate that (2S,5S)-(E,E)-8-(5-(4-(trifluoromethyl)phenyl)-2,4-pentadienoylamino)benzolactam (TPPB), a structurally distinct PKC modulator, has a similar effect to bryo-1 on CNS innate immune cells both in vitro and in vivo, attenuating neuroinflammation and resulting in CNS regeneration and repair. This study identifies a new structural class of PKC modulators, which can therapeutically target CNS innate immunity as a strategy to treat neuroinflammatory and neurodegenerative disorders.
Commonly used software tools produce conflicting and overly-optimistic AUPRC values
Authors: Chen Wenyu , Miao Chen , Zhang Zhenghao , Fung Cathy Sin-Hang , Wang Ran , Chen Yizhen , Qian Yan , Cheng Lixin , Yip Kevin Y. , Tsui Stephen Kwok-Wing , Cao Qin 
Published: February 2024

AbstractThe precision-recall curve (PRC) and the area under it (AUPRC) are useful for quantifying classification performance. They are commonly used in situations with imbalanced classes, such as cancer diagnosis and cell type annotation. We evaluated 10 popular tools for plotting PRC and computing AUPRC, which were collectively used in>3,000 published studies. We found the AUPRC values computed by the tools rank classifiers differently and some tools produce overly-optimistic results.
DNA N-gram Analysis Framework (DNAnamer): A generalized N-gram frequency analysis framework for the supervised classification of DNA sequences
Authors: Malamon John S. 
Published: February 2024

AbstractIn 1948, Claude Shannon published a mathematical system describing the probabilistic relationships between the letters of a natural language and their subsequent order or syntax structure. By counting unique, reoccurring sequences of letters called N-grams, this language model was used to generate recognizable English sentences from N-gram frequency probability tables. More recently, N-gram analysis methodologies have been successful in addressing many complex problems in a variety of domains, from language processing to genomics. One such example is the common use of N-gram frequency patterns and supervised classification models to determine authorship and plagiarism. In this methodology, DNA is a language model where nucleotides are analogous to the letters of a word and nucleotide N-grams are analogous to the words of a sentence. Because DNA contains highly conserved and identifiable nucleotide sequence frequency patterns, this approach can be applied to a variety of classification and data reduction problems, such as identifying species based on unknown DNA segments. Other useful applications of this methodology include the identification of functional gene elements, sequence contamination, and sequencing artifacts. To this end, I present DNAnamer, a generalized and extensible methodological framework and analysis toolkit for the supervised classification of DNA sequences based on their N-gram frequency patterns.