bluuebunny/crossref_metadata_2025_split huggingface dataset:
18F-FDG PET imaging for treatment response assessment and management guidance in patients with skull base osteomyelitis
Authors: Saxena Awiral , Subramanyam Padma , Sarma Manjit , Bhad Bhagirath , Bhaskaran Renjitha , Palaniswamy Shanmuga Sundaram 
Published: April 2024

Objective
The objective of this study is to evaluate the role of hybrid 18F-FDG PET for treatment response assessment and management guidance in patients with skull base osteomyelitis.

Materials and methods
Retrospectively, 33 patients, with at least a baseline and follow-up PET (computed tomography/MRI) scan, were included. Parameters like standardized uptake value (SUV) max, erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP) (initial, follow-up, percentage change) were analysed and outcomes based on 18F-FDG PET reports were classified into resolution (a), partial response (b), progression (c) and stable disease (d). The clinical course and response on anatomical imaging were also compared with 18F-FDG PET.

Results
There was mild correlation between initial SUV with ESR (0.338) and CRP (0.384). Moderate correlation was seen between follow-up SUV and CRP (0.619), percentage change in SUV max (PC SUV) with percentage change in ESR (0.456) and CRP (0.668). Mean PC SUV was 70% (a), 35% (b), −40% (c) and −18% (d), respectively. 48% (16/33) (resolution, progression, stable disease) patients had clear management change with 18F-FDG PET with either escalation or stopping of antibiotics/antifungals. Management decision in partial response group (52%, 17/33) was taken clinically. On retrospective PC SUV analysis, treatment continuation group (8 patients) showed 20% decrease, whereas the group that was only monitored further (9 patients) had 48% reduction in SUV.

Conclusion
18F-FDG PET showed a moderate association with clinical markers used in follow-up of patients with skull base osteomyelitis and is a reliable investigation for assessment of disease status. This can be used as a guide along with clinical evaluation for de-escalation of treatment.
Relationship between transient ischemic dilatation and changes in heart rate during gated SPECT acquisition in a low-risk population without perfusion defects
Authors: Mut Fernando , Gaudiano María P. , Kapitán Miguel 
Published: April 2024

Objectives
Transient ischemic dilatation (TID) in myocardial perfusion single photon emission computed tomography (SPECT) is considered a marker of poor prognosis. However, it has been suggested that some cases are due to apparent volumetric changes secondary to differences in heart rate (HR) at the time of acquisition. We assessed the correlation between transient dilatation and HR in low risk patients with no perfusion defects.

Methods
We retrospectively analyzed patients sent for 99mTc-MIBI SPECT using a 2-day protocol. We recorded the median HR during acquisition and the HR difference (HRD) between the rest and post-stress. We obtained the medium ventricular volume, end-diastolic volume (EDV), and end-systolic volume (ESV). We included patients in which TID using medium ventricular volume (TIDMV) was ≥1.2. TID was also calculated for the EDV and ESV (TIDEDV, TIDESV). We excluded patients with known coronary artery disease, perfusion defects, various ECG disorders, positive stress test, or ESV < 10 ml.

Results
From a total of 2006 patients, 63 (50 exercise, 13 dipyridamole) met the criteria for analysis (age 63.8 ± 9.7, 44 men). TIDMV was 1.29 ± 0.09 and HRD 9.8 beats per minute (BPM) (range −10 to 41). There was positive correlation between HRD and TIDMV (r = 0.51, P < 0.001) and TIDEDV (r = 0.5, P < 0.001), but not TIDESV (r = 0.23, P = 0.07). Correlation was stronger when HRD was ≥10 BPM (r = 0.67, P < 0.001).

Conclusion
TID without perfusion defects should be interpreted with caution in the presence of HRD ≥ 10 BPM during post-stress acquisition.
Uptake and persistent use of HIV pre-exposure prophylaxis (PrEP) among key populations: Results from Ukraine’s scaled national PrEP program
Authors: Vitruk Olga , Ihnatiuk Alyona P. , Kazanzhy Anna P. , Shvab Maria , Sharma Monisha , Manhart Lisa E. , Hetman Larisa I. , Shapoval Anna Y. , Puttkammer Nancy H. 
Published: April 2024

Background:
Ukraine has implemented ambitious HIV-prevention programs since 1999 and began offering pre-exposure prophylaxis (PrEP) in 2017. Little is known about PrEP uptake and persistence in this setting.

Setting:
We analyzed data from 40 facilities providing PrEP in 11 oblasts (regions) of Ukraine between October 2020-February 2022.

Methods:
We estimated the time between PrEP visits and conducted Kaplan-Meier analyses to estimate retention on PrEP stratified by sex, age, and key populations (KPs): men who have sex with men (MSM), people who inject drugs (PWID), sex workers (SW), discordant couples and others vulnerable to HIV acquisition (DC/Other). We used Cox regression to estimate risk of PrEP discontinuation by KP group and sex, adjusting for age.

Results:
Overall, 2,033 clients initiated PrEP across regions; the majority (51%) were DC/Other, 22% were MSM, 22% were PWID, and 5% were SW. The overall three-month persistence was 52.3% (95% confidence interval [CI]: 49.9-54.8%) and was lowest among MSM (46.7%; 95% CI: 41.9-52.2%) and SW (25.9%; 95% CI: 18.2-36.9%) (p<0.05 for differences by KP group). After adjusting for age, PrEP discontinuation was not statistically significantly different across groups, although female PWID tended to have the lowest discontinuation risk (adjusted hazard ratio [aHR] 0.59; 95% CI: 0.31-1.11 while male SW tended to have the highest risk (aHR 1.87, 95% CI: 0.57-6.11) compared with females in the DC/Other group).

Conclusion:
Three-month PrEP persistence was low across KP groups, especially in SW. Further research examining the barriers and enablers of persistence by KPs is needed.
Predicting congenital syphilis: Using machine learning to enhance disease management and control
Authors: da Silva Rocha Élisson , de Morais Cleber Matos , Teixeira Igor Vitor , Brandão Neto Waldemar , Lynn Theo , Endo Patricia Takako 
Published: April 2024

AbstractObjectiveSexually Transmitted Infections (STIs) present significant challenges to global public health, affecting physical and mental well-being and straining healthcare systems and economies. This study aims to enhance the predictive performance of models for congenital syphilis prediction by incorporating additional information obtained during gestational follow-up. Building upon the work of Teixeira et al. [1], which utilizes clinical and sociodemographic data, our model was enriched with results from venereal disease research laboratory (VDRL) and rapid tests for congenital syphilis conducted on pregnant women.MethodThe dataset utilized in this study comprised 47,604 records spanning the period from 2013 to 2022, with 27 attributes collected from pregnant women enrolled in the Mãe Coruja Pernambucana Program in Pernambuco, Brazil. Among these attributes, we included clinical and sociodemographic factors, as well as results from venereal disease research laboratory (VDRL) and rapid tests for congenital syphilis.ResultsOur proposed model surpassed Teixeira’s models exhibiting higher specificity (94.74%) and a slight increase in sensitivity (70.37%).ConclusionsOur study highlights the value of incorporating additional information from VDRL and rapid tests into models for predicting congenital syphilis. The combined approach involving both clinical, sociodemographic, and test result data enhances the accuracy of predictions thereby facilitating better informed healthcare decisions at different stages of pregnancy. This approach also holds significant potential in combating and managing congenital syphilis by providing assistance to health system decision makers and public policymakers. As a result, it can ultimately enhance the overall outcomes of maternal and child health and contribute to disease control.
Trace DNA from kill sites identifies predating tigers
Authors: Chhattani Himanshu , Harihar Abishek , Dean Rounak , Yadav Ajay , Patel Kaushal , Rana Divyashree , Pandit Awadhesh , Shukla Sanjay Kumar , Rahim Vincent , Ramakrishnan Uma 
Published: April 2024

AbstractPredation ecology and evidence-based conflict management strategies require reliable and accurate identification of individual predators. Identifying predators is, however, complex, as they are secretive and individual identification is difficult. Trace DNA that predators leave behind at kill sites might provide an effective strategy to identify them but remains poorly evaluated at scale. We use non-invasive genetic samples from kill sites to assess their utility for predator identification. We systematically investigated 198 livestock kills in two critical source tiger populations in central India: Kanha and Bandhavgarh Tiger Reserves. We collected 342 salivary swabs from carcasses, 33 scat and 395 shed hair samples as potential sources of predator DNA, and individual tigers were identified using up to 123 SNP markers. All three sample sources identified predator species with high success (>95%). We identified individuals (with at least one sample per kill site, based on >40 SNPs) at 86% of all kill sites where tigers were detected. Shed hair samples were most effective for individual identification, followed by saliva and scat. Sample source and sampling season were the primary determinants of the number of SNPs typed per sample and the success of individual identification. Based on the site and type of sample collection, we classify species and individuals into three categories: true predator (high confidence as predator), circumstantial predator (medium confidence) and predator uncertain (low confidence). Individuals were classified as a true predator at 72 sites, circumstantial predator at 34 sites and predator uncertain at 49 sites. Our protocol allowed us to differentiate between predators and scavengers, even when multiple tigers were detected at the same kill site. Surprisingly, ∼40% of Bandhavgarh’s tigers were identified at at least one kill site. We suggest that when paired with systematic kill site investigation and sample collection, these methods can be effectively used to understand predation ecology better and facilitate evidence-based conflict management.
Plasticity and environment-specific relationships between gene expression and fitness inSaccharomyces cerevisiae
Authors: Siddiq Mohammad A. , Duveau Fabien , Wittkopp Patricia J. 
Published: April 2024

AbstractPhenotypic evolution is shaped by interactions between organisms and their environments. The environment influences how an organism’s genotype determines its phenotype and how this phenotype affects its fitness. To better understand this dual role of the environment in the production and selection of phenotypic variation, we empirically determined and compared the genotype-phenotype-fitness relationship for mutant strains of the budding yeastSaccharomyces cerevisiaein four environments. Specifically, we measured how mutations in the promoter of the metabolic geneTDH3modified its expression level and affected its growth on media with four different carbon sources. In each environment, we observed a clear relationship betweenTDH3expression level and fitness, but this relationship differed among environments. Genetic variants with similar effects onTDH3expression in different environments often had different effects on fitness and vice versa. Such environment-specific relationships between phenotype and fitness can shape the evolution of phenotypic plasticity. The set of mutants we examined also allowed us to compare the effects of mutations disrupting binding sites for key transcriptional regulators and the TATA box, which is part of the core promoter sequence. Mutations disrupting the binding sites for the transcription factors had more variable effects on expression among environments than mutations disrupting the TATA box, yet mutations with the most environmentally variable effects on fitness were located in the TATA box. This observation suggests that mutations affecting different molecular mechanisms are likely to contribute unequally to regulatory sequence evolution in changing environments.Significance StatementEnvironments can affect the phenotypic traits an organism produces as well as the adaptive value of these traits (i.e. whether those traits will allow the organism to better survive and pass their genes on to the next generation). This study shows how the environment impacts both the production and selection of traits using the expression of a metabolic gene in the baker’s yeast as a model system. This study further shows that some types of genetic changes make gene expression traits more responsive to environmental changes than others, suggesting that genetic changes affecting different molecular mechanisms of gene regulation may contribute differently to genetic evolution.
Unleashing the Immune Arsenal: Development of Broad-spectrum Multiepitope Bluetongue Vaccine Targeting Conserved T Cell Epitopes of Structural Proteins
Authors: Kolla Harish Babu , Kumar Anuj , Dutt Mansi , Nanjunadappa Roopa Hebbandi , Singh Karam Pal , Mertens Peter Paul Clement , Kelvin David , Umeshappa Channakeshava Sokke 
Published: April 2024

AbstractBluetongue (BT) is a severe arboviral disease affecting sheep, cows, and other wild ruminants, caused by the Bluetongue virus (BTV). The virus has evolved into over 32 serotypes, rendering existing vaccines less effective. While the structural proteins of this virus represent promising targets for vaccine development, they unfortunately exhibit high amino acid polymorphism and are laden with numerous inhibitory epitopes. Structural proteins such as VP1 and VP7 are highly conserved and may contain epitopes capable of triggering cross-reactive cell-mediated immunity (CMI). In this study, we identified highly conserved MHC-I and -II-restricted T cell epitopes within VP1, VP5, and VP7 BTV proteins and developed an effectivein silico-immuno-informatics-based broad-spectrum BT multiepitope vaccine for bovine and laboratory mouse systems. The conserved epitopes utilized in the vaccines are highly antigenic, non-allergenic, non-toxic, and capable of inducing IFN-γ(only CD4+ T cell epitopes). Both mouse and bovine vaccines were tethered with Toll-like receptor (TLR)-4-agonist adjuvants, beta-defensin 2, and the 50s ribosomal unit to stimulate innate immunity for CMI development. Protein-protein docking analysis revealed strong binding affinities, while extensive 100-nanosecond molecular dynamics simulations indicated stable complexes between the vaccine structures and TLR4. Vaccination simulation studies demonstrated their ability to trigger proinflammatory responses. Therefore, these novel vaccine designs necessitate further exploration through wet lab experiments to evaluate their immunogenicity, safety, and effectiveness for practical deployment in livestock.
Turning point in forest productivity revealed from 40 years of national forest inventory data
Authors: Hertzog Lionel , Bontemps Jean-Daniel , Piedallu Christian , Lebourgeois Francois , Bouriaud Olivier 
Published: April 2024

AbstractAim: Global changes, such as changing climate or disruption in biogeochemical cycles, are affecting forest productivity worldwide. Trends in productivity are depending on the focal spatial scale and on the considered time window, stable trends at large spatial scale can mask divergence at smaller scale while short time windows limit the capacity to reveal non-linear trends such as turning points. Capitalizing on 40 years of national forest inventory data from more than 100 tree species we explored trends in forest productivity at the regional level across 4 biogeographical regions.Location: FranceTime period: 1978-2022Major taxa studied: 146 tree speciesMethods: We fitted two classes of models, a first one explicitly estimating temporal trends and a second one including no temporal components but climatic variables reflecting changing temperature and water availability.Results: We find a decrease in productivity in 95% of the regions and a high contrast in trend shapes between regions over the period studied: lowland regions with average temperature above 11.9°C showed linear negative trends in productivity since 1985 while colder lowland regions showed hump-shaped trends with turning points between 1985 and 2005, followed by declines in productivity. In mountainous regions, average climate did not appear to be a strong mediator of trend shapes. The temporal trends were reconstituted with high fidelity from the model including only climatic variables implying that changes in temperature and water availability are likely drivers of the reported trends.Main conclusion: These results illustrate the progression during the last decades of the adverse effects of climate change on forest productivity over the European forests. They suggest the expected changes over the 21stcentury that will put further pressure on forest productivity, impacting forest carbon sink potential and reducing sustainable rate of timber extraction.
Improved whole-mount immunofluorescence protocol for consistent and robust labeling of adultDrosophila melanogasteradipose tissue
Authors: Ott Rachael K. , Armstrong Alissa R. 
Published: April 2024

ABSTRACTEnergy storage and endocrine functions of theDrosophilafat body make it an excellent model for elucidating mechanisms that underlie physiological and pathophysiological organismal metabolism. Combined withDrosophila’srobust genetic and immunofluorescence microscopy toolkits, studies ofDrosophilafat body function are ripe for cell biological analysis. Unlike the larval fat body, which is easily removed as a single, cohesive sheet of tissue, isolating intact adult fat body proves to be more challenging, thus hindering consistent immunofluorescence labeling even within a single piece of adipose tissue. Here, we describe an improved approach to handlingDrosophilaabdomens that ensures full access of the adult fat body to solutions generally used in immunofluorescence labeling protocols. In addition, we assess the quality of fluorescence reporter expression and antibody immunoreactivity in response to variations in fixative type, fixation incubation time, and detergent used for cellular permeabilization. Overall, we provide several recommendations for steps in a whole mount staining protocol that results in consistent and robust immunofluorescence labeling of the adultDrosophilafat body.SUMMARY STATEMENTOptimization of adultDrosophilafat body fluorescence microscopy via modifications of tissue handling, fixation, and permeabilization steps in a whole mount immunolabeling protocol.
Precision Phenotyping for Curating Research Cohorts of Patients with Post-Acute Sequelae of COVID-19 (PASC) as a Diagnosis of Exclusion
Authors: Azhir Alaleh , Hügel Jonas , Tian Jiazi , Cheng Jingya , Bassett Ingrid V. , Bell Douglas S. , Bernstam Elmer V. , Farhat Maha R. , Henderson Darren W. , Lau Emily S. , Morris Michele , Semenov Yevgeniy R. , Triant Virginia A. , Visweswaran Shyam , Strasser Zachary H. , Klann Jeffrey G. , Murphy Shawn N. , Estiri Hossein 
Published: April 2024

AbstractScalable identification of patients with the post-acute sequelae of COVID-19 (PASC) is challenging due to a lack of reproducible precision phenotyping algorithms and the suboptimal accuracy, demographic biases, and underestimation of the PASC diagnosis code (ICD-10 U09.9). In a retrospective case-control study, we developed a precision phenotyping algorithm for identifying research cohorts of PASC patients, defined as a diagnosis of exclusion. We used longitudinal electronic health records (EHR) data from over 295 thousand patients from 14 hospitals and 20 community health centers in Massachusetts. The algorithm employs an attention mechanism to exclude sequelae that prior conditions can explain. We performed independent chart reviews to tune and validate our precision phenotyping algorithm. Our PASC phenotyping algorithm improves precision and prevalence estimation and reduces bias in identifying Long COVID patients compared to the U09.9 diagnosis code. Our algorithm identified a PASC research cohort of over 24 thousand patients (compared to about 6 thousand when using the U09.9 diagnosis code), with a 79.9 percent precision (compared to 77.8 percent from the U09.9 diagnosis code). Our estimated prevalence of PASC was 22.8 percent, which is close to the national estimates for the region. We also provide an in-depth analysis outlining the clinical attributes, encompassing identified lingering effects by organ, comorbidity profiles, and temporal differences in the risk of PASC. The PASC phenotyping method presented in this study boasts superior precision, accurately gauges the prevalence of PASC without underestimating it, and exhibits less bias in pinpointing Long COVID patients. The PASC cohort derived from our algorithm will serve as a springboard for delving into Long COVID’s genetic, metabolomic, and clinical intricacies, surmounting the constraints of recent PASC cohort studies, which were hampered by their limited size and available outcome data.
Increased circulating interleukin concentrations in type 2 diabetes mellitus: A systematic review and meta-analysis
Authors: Cao Chang , Yuan Jing , Gilbert Elizabeth R. , Cline Mark A. , Lam Fan , Li King C. , Dilger Ryan N. 
Published: April 2024

BACKGROUNDChronic systemic inflammation links to type 2 diabetes mellitus (T2DM) onset, and the potential role of interleukins in this pathogenic process is increasingly recognized.PURPOSETo quantitatively evaluate circulating interleukin concentrations data available for T2DM patients.DATA SOURCESWe performed a systematic review using PubMed, Web of Science, and the Cochrane Library.STUDY SELECTIONOriginal studies reporting data on circulating interleukin concentrations in at least one group of T2DM patients [obese T2DM, overweight T2DM, or lean T2DM] and healthy weight controls (HWCs) were included.DATA EXTRACTION AND SYNTHESISData were extracted from 43 included studies uniquely encompassing 2,646 T2DM patients and 6,605 HWCs by independent investigators. We used a random-effects model to pool data in the Comprehensive Meta-Analysis Version 2 software. Effect sizes were calculated as the standardized mean difference in interleukin concentrations between groups and then transformed into Hedge’s g statistic.LIMITATIONSOf the ILs included in the analysis (interleukin 2, 4, 6, 8, 10, 12, 17, 18, 22, and 33), 70% were with a high level of between-study heterogeneity and could not be fully accounted for by factors such as BMI, sex, age, and publication year. More studies are warranted to identify more contributing clinical variables.CONCLUSIONSMeta-analysis outcomes demonstrated higher circulating concentrations of IL-4, IL-6, IL-17, and IL-18 in T2DM patients, strengthening the clinical evidence that T2DM is accompanied by a systemic inflammatory response.ARTICLE HIGHLIGHTSWhy did we undertake this study? Possible changes in circulating concentrations for most interleukins (ILs) in type 2 diabetes mellitus (T2DM) patients remains uncertain.What is the specific question(s) we wanted to answer? We wanted to quantitatively assess available data on circulating IL concentrations in T2DM patients and healthy weight control (HWC) subjects.What did we find? Increased circulating concentrations of IL-4, IL-6, IL-17, and IL-18 were found in T2DM patients compared with HWC.What are the implications of our findings? These findings affirm T2DM pathogenesis correlates with systemic inflammation, evidenced by elevated circulating concentrations of both pro- and anti-inflammatory interleukins.