bluuebunny/crossref_metadata_2025_split huggingface dataset:
CONTRAST SENSITIVITY IS IMPAIRED IN SUSPECTED PRIMARY OPEN-ANGLE GLAUCOMA PATIENTS
Authors: Tripolone María Constanza , Issolio Luis Alberto , Perez Daniel , Barrionuevo Pablo Alejandro 
Published: March 2024

ABSTRACTPurposeTo assess contrast sensitivity (CS) for detecting visual changes in suspected POAG patients.MethodsCS was measured foveally at photopic conditions and peripherally at mesopic conditions using sinusoidal gratings of 4 cycles/degree. In experiment 1, foveal and peripheral CS were assessed in suspected POAG patients and age-matched healthy control subjects. In experiment 2, foveal CS was assessed in early POAG patients age-matched with suspected POAG group. Analysis was done considering two age ranges (Under and Over 50 years of age). Correlations between CS and clinical parameters were evaluated.ResultsPeripheral CS was decreased only for older POAG suspect patients from the control group (Over 50: p = 0.008. Under 50: p = 0.566). Foveal CS was reduced in POAG suspect participants for both age ranges (Over 50: p = 0.028. Under 50: p < 0.001) and in early POAG patients (Under 50: p = 0.001; Over 50: p < 0.001), both compared to the control group. Foveal CS was lower in early POAG compared to POAG suspect for older patients (Over 50: p = 0.019. Under 50: p = 0.824). Foveal CS was correlated with cup-disc ratio in early POAG patients (Early: p < 0.001. Suspect: p = 0.766) and with age in both patient groups (Early: p = 0.001. Suspect: p = 0.002).ConclusionCS is affected in patients with a high risk of developing POAG and recently diagnosed. Our results suggest that CS could serve as a screening tool, detecting early damage even before structural changes occur.
Solicited Cough Sound Analysis for Tuberculosis Triage Testing: The CODA TB DREAM Challenge Dataset
Authors: Huddart Sophie , Yadav Vijay , Sieberts Solveig K. , Omberg Larson , Raberahona Mihaja , Rakotoarivelo Rivo , Lyimo Issa N. , Lweno Omar , Christopher Devasahayam J , Viet Nhung Nguyen , Theron Grant , Worodria William , Yu Charles Y. , Bachman Christine M , Burkot Stephen , Dewan Puneet , Kulhare Sourabh , Small Peter M , Cattamanchi Adithya , Jaganath Devan , Grandjean Lapierre Simon 
Published: March 2024

ABSTRACTCough is a common and commonly ignored symptom of lung disease. Cough is often perceived as difficult to quantify, frequently self-limiting, and non-specific. However, cough has a central role in the clinical detection of many lung diseases including tuberculosis (TB), which remains the leading infectious disease killer worldwide. TB screening currently relies on self-reported cough which fails to meet the World Health Organization (WHO) accuracy targets for a TB triage test. Artificial intelligence (AI) models based on cough sound have been developed for several respiratory conditions, with limited work being done in TB. To support the development of an accurate, point-of-care cough-based triage tool for TB, we have compiled a large multi-country database of cough sounds from individuals being evaluated for TB. The dataset includes more than 700,000 cough sounds from 2,143 individuals with detailed demographic, clinical and microbiologic diagnostic information. We aim to empower researchers in the development of cough sound analysis models to improve TB diagnosis, where innovative approaches are critically needed to end this long-standing pandemic.
Protocol: Trust Your Gut: An Analysis of Dermatologic Diagnostic Accuracy
Authors: Jolley Dana , Korman Abraham M. 
Published: March 2024

AbstractBackgroundThe current clinical misdiagnosis rate among all medical specialties is approximately 10-15%, but diagnostic error within the field of dermatology has not been studied thoroughly1,2. As a field that relies heavily on visual perception, many physicians consider clinical intuition to be advantageous in diagnosing skin diseases and consider it to be a rapid and unconscious phenomenon7. Therefore, too much contemplation may lead to more incorrect diagnoses4. However, while clinical intuition is a valuable clinical tool, it is widely considered to be developed throughout medical training and only successfully employed by experienced attending physicians, perhaps due to experiential knowledge and associated confidence1,2,5. One may expect that self-reported confidence in diagnosis would correlate with diagnostic accuracy, but this is not supported in the literature9. The focus of our study is to examine the development and reliability of clinical intuition as well as associated self-reported confidence levels in diagnoses at different levels of medical training among dermatologists.MethodsApproximately 20 dermatologists who are PGY-2 or higher will be recruited for study participation via email. Participants will be sent a Qualtrics survey at two separate time points with a month waiting period in between. The survey will contain demographics questions, photos of 10 different dermatologic conditions for dermatologists to diagnose, and a self-reported confidence level for each diagnosis. The first survey will allow 5 seconds to evaluate a clinical photo prior to diagnosis, and this timeframe will be extended to 15 seconds in the second survey. The second survey will contain the same diagnoses, but with different pictures to avoid recall of specific photos. Following completion of all surveys, descriptive statistics will be completed with goal of publication.DiscussionThis study has the potential to provide invaluable information regarding the development of clinical intuition among dermatologic physicians while also examining their confidence levels and likelihood of changing correct diagnoses when given more time to ruminate. It is possible that physicians are more likely to second guess original diagnoses based off of certain demographic factors, as one systematic review found that women in medicine perceive their clinical performance as deficient more often than men10. Therefore, this study may give insight to the ways that complicated societal factors contribute to clinical decision making. Data from this study may be used to aid dermatologists in understanding their thought processes when diagnosing patients, and may be useful in developing education curriculum. The protocol will hopefully serve as a blueprint for creation of studies in a multitude of fields, ultimately leading to better understanding of clinical decision making and, thus, improved patient care.
Sulfated N-glycans Upregulation in Sera Predicts Early-Stage Breast Cancer in Patients
Authors: Feleke Dereje G. , Montalban Bryan M. , Gizaw Solomon T. , Hinou Hiroshi 
Published: March 2024

AbstractAlterations in sulfated glycans are associated with several pathological conditions, including cancer. However, analysis of sulfated glycans poses challenges, making the investigation of sulfated glycan profiles a topic of significant interest in the search for novel biomarkers for early BC detection. We used a glycoblotting-based sulphoglycomics workflow to examine sulfated N-glycans present in the serum of Ethiopian patients with BC. Seven mono-sulfated glycans were significantly upregulated in the sera of BC patients compared to the control group. Each identified glycan showed significant abundance with AUC ≥ 0.8 and demonstrated high diagnostic accuracy in predicting early stage BC patients. Importantly, the sulfated glycans were analyzed without removing the sialic group, allowing for comprehensive evaluation of the sialylation status of the identified sulfated glycans. This study represents the first quantitative analysis of sulfated N-glycans in patients with BC and identifies novel biomarkers with discriminatory potential in the early stages of BC.Statement of significanceThis study presents a quantitative analysis of sulfated N-glycans in BC, aiming to identify novel glyco-biomarkers that demonstrate high diagnostic accuracy for early stage BC. Analyzing sulfated glycans without removing sialic acids offers comprehensive insights. These findings advance the understanding of BC, potentially enhance early detection, and improve patient outcomes.
Development and Organization of the Retinal Orientation Selectivity Map
Authors: Vita Dominic J. , Orsi Fernanda S. , Stanko Nathan G. , Clark Natalie A. , Tiriac Alexandre 
Published: March 2024

AbstractOrientation or axial selectivity, the property of neurons in the visual system to respond preferentially to certain angles of a visual stimuli, plays a pivotal role in our understanding of visual perception and information processing. This computation is performed as early as the retina, and although much work has established the cellular mechanisms of retinal orientation selectivity, how this computation is organized across the retina is unknown. Using a large dataset collected across the mouse retina, we demonstrate functional organization rules of retinal orientation selectivity. First, we identify three major functional classes of retinal cells that are orientation selective and match previous descriptions. Second, we show that one orientation is predominantly represented in the retina and that this predominant orientation changes as a function of retinal location. Third, we demonstrate that neural activity plays little role on the organization of retinal orientation selectivity. Lastly, we usein silicomodeling followed by validation experiments to demonstrate that the overrepresented orientation aligns along concentric axes. These results demonstrate that, similar to direction selectivity, orientation selectivity is organized in a functional map as early as the retina.One Sentence SummaryDevelopment and organization of retinal orientation selectivity
Loss of LasR function leads to decreased repression ofPseudomonas aeruginosaPhoB activity at physiological phosphate concentrations
Authors: Conaway Amy , Todorovic Igor , Mould Dallas L. , Hogan Deborah A. 
Published: March 2024

AbstractWhile thePseudomonas aeruginosaLasR transcription factor plays a role in quorum sensing (QS) across phylogenetically-distinct lineages, isolates with loss-of-function mutations inlasR(LasR– strains) are commonly found in diverse settings including infections where they are associated with worse clinical outcomes. In LasR– strains, the transcription factor RhlR, which is controlled by LasR, can be alternately activated in low inorganic phosphate (Pi) concentrations via the two-component system PhoR-PhoB. Here, we demonstrate a new link between LasR and PhoB in which the absence of LasR increases PhoB activity at physiological Pi concentrations and raises the Pi concentration necessary for PhoB inhibition. PhoB activity was also less repressed by Pi in mutants lacking different QS regulators (RhlR and PqsR) and in mutants lacking genes required for the production of QS-regulated phenazines suggesting that decreased phenazine production was one reason for decreased PhoB repression by Pi in LasR– strains. In addition, the CbrA-CbrB two-component system, which is elevated in LasR– strains, was necessary for reduced PhoB repression by Pi and a Δcrcmutant, which lacks the CbrA-CbrB-controlled translational repressor, activated PhoB at higher Pi concentrations than the wild type. The ΔlasRmutant had a PhoB-dependent growth advantage in a medium with no added Pi and increased virulence-determinant gene expression in a medium with physiological Pi, in part through reactivation of QS. This work suggests PhoB activity may contribute to the virulence of LasR–P. aeruginosaand subsequent clinical outcomes.ImportanceLoss-of-function mutations in the gene encoding thePseudomonas aeruginosaquorum sensing (QS) regulator LasR occur frequently and are associated with worse clinical outcomes. We have found that LasR–P. aeruginosahave elevated PhoB activity at physiological concentrations of inorganic phosphate (Pi). PhoB activity promotes Pi acquisition as well as the expression of QS and virulence-associated genes. Previous work has shown that PhoB induce RhlR, another QS regulator, in a LasR-mutant in low Pi conditions. Here, we demonstrate a novel relationship wherein LasR represses PhoB activity, in part through the production of phenazines and Crc-mediated translational repression. This work suggests PhoB activity may contribute to the increased virulence of LasR–P. aeruginosa.
The inflammatory microenvironment of the lung at the time of infection governs innate control of SARS-CoV-2 replication
Authors: Baker Paul J. , Bohrer Andrea C. , Castro Ehydel , Amaral Eduardo P. , Snow-Smith Maryonne , Torres-Juárez Flor , Gould Sydnee T. , Queiroz Artur T. L. , Fukutani Eduardo R. , Jordan Cassandra M. , Khillan Jaspal S. , Cho Kyoungin , Barber Daniel L. , Andrade Bruno B. , Johnson Reed F. , Hilligan Kerry L. , Mayer-Barber Katrin D. 
Published: March 2024

ABSTRACTSARS-CoV-2 infection leads to vastly divergent clinical outcomes ranging from asymptomatic infection to fatal disease. Co-morbidities, sex, age, host genetics and vaccine status are known to affect disease severity. Yet, how the inflammatory milieu of the lung at the time of SARS-CoV-2 exposure impacts the control of viral replication remains poorly understood. We demonstrate here that immune events in the mouse lung closely preceding SARS-CoV-2 infection significantly impact viral control and we identify key innate immune pathways required to limit viral replication. A diverse set of pulmonary inflammatory stimuli, including resolved antecedent respiratory infections withS. aureusor influenza, ongoing pulmonaryM. tuberculosisinfection, ovalbumin/alum-induced asthma or airway administration of defined TLR ligands and recombinant cytokines, all establish an antiviral state in the lung that restricts SARS-CoV-2 replication upon infection. In addition to antiviral type I interferons, the broadly inducible inflammatory cytokines TNFα and IL-1 precondition the lung for enhanced viral control. Collectively, our work shows that SARS-CoV-2 may benefit from an immunologically quiescent lung microenvironment and suggests that heterogeneity in pulmonary inflammation that precedes or accompanies SARS-CoV-2 exposure may be a significant factor contributing to the population-wide variability in COVID-19 disease outcomes.
TCR transgenic clone selection guided by immune receptor analysis and single cell RNA expression of polyclonal responders
Authors: Debeuf Nincy , Lameire Sahine , Vanheerswynghels Manon , Deckers Julie , De Wolf Caroline , Toussaint Wendy , Verbeke Rein , Verstaen Kevin , Hammad Hamida , Vanhee Stijn , Lambrecht Bart N. 
Published: March 2024

ABSTRACTSince the precursor frequency of naïve T cells is extremely low, investigating the early steps of antigen-specific T cell activation is challenging. To overcome this detection problem, adoptive transfer of a cohort of T cells purified from T cell receptor (TCR) transgenic donors has been extensively used but is not readily available for emerging pathogens. Constructing TCR transgenic mice from T cell hybridomas is a labor-intensive and sometimes erratic process, since the best clones are selected based on antigen-induced CD69 upregulation or IL-2 productionin vitro, and TCR chains are PCR-cloned into expression vectors. Here, we exploited the rapid advances in single cell sequencing and TCR repertoire analysis to select the best clones without hybridoma selection, and generated CORSET8 mice (CORonaSpikeEpitope specific CD8Tcell), carrying a TCR specific for the Spike protein of SARS-CoV-2. Implementing newly created DALI software for TCR repertoire analysis in single cell analysis enabled the rapid selection of the ideal responder CD8 T cell clone, based on antigen reactivity, proliferation and immunophenotypein vivo.Identified TCR sequences were inserted as synthetic DNA into an expression vector and transgenic CORSET8 donor mice were created. After immunization with Spike/CpG-motifs, mRNA vaccination or SARS-CoV2 infection, CORSET8 T cells strongly proliferated and showed signs of T cell activation. Thus, a combination of TCR repertoire analysis and scRNA immunophenotyping allowed rapid selection of antigen-specific TCR sequences that can be used to generate TCR transgenic mice.
Absolute quantification of rare gene targets in limited samples using crude lysate and ddPCR
Authors: Kaur Charandeep , Adams Stuart , Kibirige Catherine N , Asquith Becca 
Published: March 2024

AbstractBackgroundAccurate quantification of rare genes from limited clinical samples is crucial for research purposes but is technically challenging. In particular, nucleic acid extraction for quantification of gene targets may lead to target loss. Here, we report the development and validation of a novel crude lysate ddPCR assay for the absolute quantification of rare genes, TRECs in our case, from infrequent cells, that removes the need for DNA extraction, hence minimizing the target loss.MethodsThe analytical validation was performed on PBMCs extracted from the blood of healthy donors. Standard ddPCR was first optimized to detect TREC copies/cell and then applied to a crude lysate ddPCR assay. The assay was optimized by varying several steps. The optimised assay was directly compared to standard ddPCR and the performance of the assay quantified.ResultsThe newly developed assay showed good agreement with the standard ddPCR assay in the range from 0.0003 to 0.01 TRECs/cell. The assay had a limit of quantification of <0.0003 TRECs/cell and a limit of detection of <0.0001 TRECs/cell; this performance is favourable compared to standard ddPCR. The intra-assay variation was low. This method can also be applied to fixed and permeabilized cells.ConclusionsThe newly developed crude lysate ddPCR assay for quantifying rare targets from limited samples has high accuracy, specificity, and reproducibility; additionally, it eliminates the need for DNA extraction for absolute quantification. The assay has the potential to be used for quantification of other trace targets from small samples.
Genome-wide association study elucidates the genetic architecture of manganese tolerance inBrassica napus
Authors: Raman Harsh , Bai Zetao , McVittie Brett , Mukherjee Sourav , Goold Hugh D , Zhang Yuanyuan , Khin Nay Chi , Qiu Yu , Liu Shengyi , Delourme Regine , Pogson Barry , Balasubramanian Sureshkumar , Raman Rosy 
Published: March 2024

AbstractBrassica napus(canola) is a significant contributor to the world’s oil production and is cultivated across continents, yet acidic soils with Al3+and Mn2+toxicities limit its production. The genetic determinants underlying acidic soil tolerance in canola are unknown and require to be uncovered for canola breeding and production. Here, through comprehensive phenotyping, whole genome resequencing, and genome-wide association analysis, we identified three QTLs for tolerance to Mn2+toxicity on chromosomes A09, C03, and C09. Allelism tests between four tolerance sources confirmed that at least one locus on A09 controls Mn2+tolerance inB. napus. Integrated analysis of genomic and expression QTL and Mn2+tolerance data reveals thatBnMTP8.A09,in conjunction withBnMATE.C03,BnMTP8.C04andBnMTP8.C08, play a central role in conferring Mn2+tolerance inB. napus. Gene expression analysis revealed a high correlation (R2= 0.74) between Mn2+tolerance and theBnMTP8.A09expression. Yeast complementation assays show thatBnMTP8.A09can complement manganese-hypersensitive yeast mutant strainPMR1Δ and restore Mn2+tolerance to wild-type levels. Inductively coupled plasma mass spectrometry revealed that Mn2+tolerant accessions accumulate less Mn in the shoots compared to Mn2+sensitives, suggesting that theBnMTP8.A09transporter likely sequesters Mn2+into the tonoplast. Taken together, our research unveils the genetic architecture of Mn2+tolerance and identifiesBnMTP8.A09as a major gene imparting tolerance to Mn2+toxicity inB. napus.
Targeted proteomics addresses selectivity and complexity of protein degradation by autophagy
Authors: Leytens Alexandre , Benítez-Fernández Rocío , Jiménez-García Carlos , Roubaty Carole , Stumpe Michael , Boya Patricia , Dengjel Jörn 
Published: March 2024

AbstractAutophagy is a constitutively active catabolic lysosomal degradation pathway, often found dysregulated in human diseases. It is often considered to act in a cytoprotective manner and is commonly upregulated in cells undergoing stress. Its initiation is regulated at the protein level and does not requirede novoprotein synthesis. Historically, autophagy has been regarded as non-selective; however, it is now clear that different stimuli can lead to the selective degradation of cellular components via selective autophagy receptors (SARs). Due to its selective nature and the existence of multiple degradation pathways potentially acting in concert, monitoring of autophagy flux,i.e.selective autophagy-dependent protein degradation, should address this complexity. Here, we introduce a targeted proteomics approach monitoring abundance changes of 37 autophagy-relevant proteins covering process-relevant proteins such as the initiation complex and the ATG8 lipidation machinery, as well as most known SARs. We show that proteins involved in autophagosome biogenesis are upregulated and spared from degradation under autophagy inducing conditions in contrast to SARs. Classical bulk stimuli such as nutrient starvation mainly induce degradation of ubiquitin-dependent soluble SARs and not of ubiquitin-independent, membrane-bound SARs. In contrast, treatment with the iron chelator deferiprone leads to the degradation of ubiquitin-dependent and - independent SARs linked to mitophagy and reticulophagy/ER-phagy. Our approach is automatable and supports large-scale screening assays paving the way to (pre)clinical applications and monitoring of specific autophagy fluxes.
A Novel Dual Probe-based Method for Mutation Detection using Isothermal Amplification
Authors: Nandu Nidhi , Miller Michael , Tong Yanhong , Lu Zhi-xiang 
Published: March 2024

ABSTRACTCost efficient and rapid detection tools to detect mutations especially those linked to drug-resistance are important to address concerns of the rising multi-drug resistance infections. Here we integrated dual probes, namely a calibrator probe and an indicator probe, into isothermal amplification detection system. These two probes are designed to bind distinct regions on the same amplicon to determine the presence or absence of mutation. The calibrator probe signal is used as an internal signal calibrator for indicator probe which detects the presence or absence of the mutation. As an illustrative example, we evaluated the applicability of this dual probe method for detecting mutations associated with rifampicin (RIF) drug resistance at codons 516, 526 and 531 of the rpoB gene inMycobacterium tuberculosis. In this assessment, we examined 127 artificial samples comprising wild type and mutant target sequences with single or multiple mutations. Our results demonstrated 100% accuracy of both wild type and mutant samples for mutations at codons 526 and 531. As regards to mutations at codon 516, the wild type was identified with 100% accuracy, while the mutant type was identified with 95% accuracy. Moreover, when we extended our evaluation using the Zeptometrix MTB Verification panel, our dual probe method correctly differentiated between the wild type and mutant, and identified the RIF-mutant strain which harbors mutations at codon 531 of the rpoB gene. Our isothermal mutation detection system, relying on dual probes exhibits a versatile approach. With the capability to identify mutations without prior knowledge of their specific mutation direction, our dual-probe method shows significant promise for applications in drug resistance nucleic acid testing, particularly in resource-limited settings.