bluuebunny/crossref_metadata_2025 huggingface dataset:
Lymphatic Mapping for LVA with Noncontrast Lymphatic Ultrasound: How We Do It
Authors: Hara Hisako , Ichinose Michiru , Shimomura Fumika , Kawahara Mari , Mihara Makoto
Published: April 2024

Recently, lymphatic ultrasonography has received increasing attention. Although there are several reports on contrast-enhanced lymphatic ultrasound as a preoperative examination for lymphaticovenous anastomosis (LVA), we have been reporting the usefulness of preoperative noncontrast lymphatic ultrasound. In this article, the detailed procedure for conducting lymphatic ultrasound during the preoperative examination of LVA is thoroughly described. The only items required for lymphatic ultrasound are an ultrasound device, an echo jelly, a straw for marking, and a marker. We use an ordinary ultrasound device with an 18-MHz linear probe. We apply the Doppler, Crossing, Uncollapsible, Parallel, and Superficial fascia index to identify the lymphatic vessels. While imagining the course of the lymph vessels, we position the probe perpendicular to the long axis of the lymphatic vessels. When a vessel is found under the superficial fascia, the probe is moved proximally to trace the vessel’s path. If the vessel transverses a nearby vein without connecting to it, it is most likely a lymphatic vessel. To confirm, we ensure that the vessel does not exhibit coloration in the Doppler mode. As LVA is most effective when the dilated lymph vessels are anastomosed, we use lymphatic ultrasound to identify the most dilated lymphatic vessels in each lymphosome, and mark incision lines where suitable veins are in close proximity. No contrast agent is required; therefore, medical staff such as nurses and ultrasound technicians can autonomously conduct the test.
Management of Superficial and Deep Peroneal Nerve Neuromas with Targeted Muscle Reinnervation in Nonamputees: Operative Technique and Early Outcomes
Authors: Moradian Simon , Taritsa Iulianna C. , Sharma Sripadh , Mioton Lauren , Dumanian Gregory A. , Ko Jason H.
Published: April 2024

Background:

Targeted muscle reinnervation (TMR), a surgical technique developed by the senior authors that coapts proximal ends of nerves to distal motor nerves of adjacent muscles, has demonstrated efficacy in the treatment and prevention of neuroma pain. The objective of this study is to describe the surgical technique for TMR of the superficial peroneal nerve (SPN) and deep peroneal nerve (DPN) in nonamputee patients and provide data on postoperative functional outcomes.

Methods:

A single-institution retrospective chart review was performed between March 2018 and April 2021. Patients were de-identified and included if they were nonamputees receiving TMR for pain in the peroneal nerve distribution. Data extracted included demographic information, symptoms before operation, relevant nerve coaptation, peri-, and postoperative complications, and long-term functional outcomes.

Results:

Of the 19 patients reviewed, 11 patients underwent TMR of the SPN alone: eight had complete resolution of their symptoms; two indicated partial improvement in pain; and one patient had no improvement. Four patients underwent TMR of the DPN alone: two patients had complete resolution of their pain, and two patients had partial improvement with pain. Four patients underwent TMR of both the SPN/DPN: two patients had complete resolution of their symptoms, and two patients were noted to have significant improvement but had persistent pain from prior foot operations. Average follow-up time was 260 days.

Conclusions:

TMR is a successful technique in the management of SPN and DPN neuroma pain. Our technique revealed excellent clinical outcomes, no procedure-specific complications, and improved subjective pain reports.
mARC1 in MASLD: Modulation of lipid accumulation in human hepatocytes and adipocytes
Authors: Jones Amanda K. , Bajrami Besnik , Campbell Morgan K. , Erzurumluoglu Abdullah Mesut , Guo Qiusha , Chen Hongxing , Zhang Xiaomei , Zeveleva Svetlana , Kvaskoff David , Brunner Andreas-David , Muller Stefanie , Gathey Vasudha , Dave Rajvee M. , Tanner James W. , Rixen Sophia , Struwe Michel A. , Phoenix Kathryn , Klumph Kaitlyn J. , Robinson Heather , Veyel Daniel , Muller Annkatrin , Noyvert Boris , Bartholdy Boris Alexander , Steixner-Kumar Agnes A. , Stutzki Jan , Drichel Dmitriy , Omland Steffen , Sheehan Ryan , Hill Jon , Bretschneider Tom , Gottschling Dirk , Scheidig Axel J. , Clement Bernd , Giera Martin , Ding Zhihao , Broadwater John , Warren Curtis R.
Published: April 2024

Background:

Mutations in the gene MTARC1 (mitochondrial amidoxime–reducing component 1) protect carriers from metabolic dysfunction–associated steatohepatitis (MASH) and cirrhosis. MTARC1 encodes the mARC1 enzyme, which is localized to the mitochondria and has no known MASH-relevant molecular function. Our studies aimed to expand on the published human genetic mARC1 data and to observe the molecular effects of mARC1 modulation in preclinical MASH models.

Methods and Results:

We identified a novel human structural variant deletion in MTARC1, which is associated with various biomarkers of liver health, including alanine aminotransferase levels. Phenome-wide Mendelian Randomization analyses additionally identified novel putatively causal associations between MTARC1 expression, and esophageal varices and cardiorespiratory traits. We observed that protective MTARC1 variants decreased protein accumulation in in vitro overexpression systems and used genetic tools to study mARC1 depletion in relevant human and mouse systems. Hepatocyte mARC1 knockdown in murine MASH models reduced body weight, liver steatosis, oxidative stress, cell death, and fibrogenesis markers. mARC1 siRNA treatment and overexpression modulated lipid accumulation and cell death consistently in primary human hepatocytes, hepatocyte cell lines, and primary human adipocytes. mARC1 depletion affected the accumulation of distinct lipid species and the expression of inflammatory and mitochondrial pathway genes/proteins in both in vitro and in vivo models.

Conclusions:

Depleting hepatocyte mARC1 improved metabolic dysfunction–associated steatotic liver disease–related outcomes. Given the functional role of mARC1 in human adipocyte lipid accumulation, systemic targeting of mARC1 should be considered when designing mARC1 therapies. Our data point to plasma lipid biomarkers predictive of mARC1 abundance, such as Ceramide 22:1. We propose future areas of study to describe the precise molecular function of mARC1, including lipid trafficking and subcellular location within or around the mitochondria and endoplasmic reticulum.
Hepatitis delta testing trends in a US national cohort: An analysis of patient and provider-level predictive factors
Authors: John Binu V. , Amoli Mahmoud Manouchehri , Evon Donna M. , Wong Robert , Dahman Bassam
Published: April 2024

Background:

The low prevalence of HDV infection in the United States could be attributed to insufficient testing rate, which can result in an underestimation of the true burden of HDV. The primary objective of this study is to quantify the prevalence of and factors associated with HDV antibody (anti-HDV) or RNA testing, among participants with positive HBsAg in the Veterans Health Administration (VHA).

Methods:

We conducted a retrospective cohort study of participants who tested positive for HBsAg between January 2000 and December 2022 within the VHA. We identified those who were tested for HDV, and patient and provider-level factors associated with HDV testing.

Results:

Of 41,658 participants with positive HBsAg who had follow-up, 4438 (10.7%) were tested at least once for HDV, of which 135 (3.0%) were positive. Participants in the Northeast (adjusted odds ratio [aOR]: 1.30, 95% CI: 1.17–1.44, p<0.001), and receiving hepatology care (aOR: 1.38, 95% CI: 1.24–1.54, p<0.001) were more likely, while those in the Midwest (aOR: 0.69, 95% CI: 0.60–0.79, p<0.001), under the care of a primary care provider (aOR: 0.61, 95% CI: 0.50–0.74, p<0.001), Blacks (aOR: 0.85, 95% CI: 0.77–0.94, p=0.001), participants who were HCV antibody–positive (aOR: 0.89, 95% CI: 0.81–0.99, p=0.03), and participants who were HIV-positive (aOR: 0.80, 95% CI: 0.71–0.90, p<0.001) were less likely to be tested for HDV.

Conclusions:

HDV screening rates in the VHA remain low overall. Participants who are Black, living in the Midwest, patients who are HIV-positive, and patients who are HCV-positive are less likely to be tested for HDV. These results suggest that risk-based screening strategies are ineffective in the VHA and highlight the need for refining testing strategies to increase HDV screening rates.
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.
Bacillus subtilis comparative genomics
Authors: Jain Priyanshi Mahendrakumar , Cheruvari Athira , Jenifer Helga Maria Tamilselvan , Kammara Rajagopal
Published: April 2024

As a producer of industrial enzymes and secondary metabolites, Bacillus subtilis is generally considered to be more beneficial for humans, animals, and notably industry. Consequently, it is imperative to investigate various Bacillus spp at the genome level. The comparative genomics of Bacillus spp is the subject of this manuscript. Wherein various Bacillus spp genomes were collected and examined. The sources of the bacteria included fermented foods, soil, and liquid wastes. A wide range of bioinformatics resources and tools were used in the study for genome annotation, assembly, and comparison. The isolate B. subtilis S2 is closely linked to the B. subtilis SRCM103571 and B. subtilis SRCM104005 species cluster, according to the phylogenetic tree analysis. The WGS is also unique in that it produces two bacteriocins, Sublancin and Subtilosin A, according to antiSMASH & BAGEL-4 analysis. Subsequent investigation revealed that it has the fewest rRNA -just nine-and tRNA -72. However, at 4438, it has the highest number of genes, which makes the S2 strain distinct at the genome level. We conclude by noting the different nature of B. subtilis S2.
Massilia luteola sp. nov., a novel indole-producing and cellulose-degrading bacterium isolated from soil
Authors: Huang Xinbing , Qi Shengtao , Song Wenshuai , Yu Xiaoxin , Zhang Haifeng , Xiang Wensheng , Zhao Junwei , Wang Xiangjing
Published: April 2024

A Gram-stain-negative, rod-shaped, indole-producing, and cellulose-degrading bacterial strain, designated NEAU-G-C5T, was isolated from soil collected from a forest in Dali city, Yunnan province, south China. 16S rRNA gene sequence analysis showed that strain NEAU-G-C5T was assigned to the genus Massilia and showed high sequence similarities to Massilia phosphatilytica 12-OD1T (98.32 %) and Massilia putida 6 NM-7T (98.41 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-G-C5T formed a lineage related to M. phosphatilytica 12-OD1T and M. putida 6 NM-7T. The major fatty acids of the strain were C16 : 0, C16 : 1 ω7c, and C17 : 0 cyclo. The respiratory quinone was Q-8. The polar lipid profile of the strain showed the presence of diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. In addition, the average nucleotide identity values between strain NEAU-G-C5T and its reference strains M. phosphatilytica 12-OD1T, M. putida 6 NM-7T, M. norwichensis NS9T, and M. kyonggiensis TSA1T were 89.7, 88.2, 81.3, and 88.0 %, respectively, and the levels of digital DNA–DNA hybridization between them were found to be 58.5 % (54.9–62.0 %), 53.2 % (49.8–56.7 %), 31.9 % (28.6–35.5 %), and 57.7 % (54.1–61.2 %), respectively, which were lower than the accepted threshold values of 95–96 % and 70 %, respectively. The DNA G+C content of strain NEAU-G-C5T was 66.5 mol%. The strain could produce indoleacetic acid and cellulase. On the basis of the phenotypic, genotypic, and chemotaxonomic characteristics, we conclude that strain NEAU-G-C5T represents a novel species of the genus Massilia, for which the name Massilia luteola sp. nov. is proposed. The type strain is NEAU-G-C5T (=MCCC 1K08668T=KCTC 8080T).
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

Objective

Sexually 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.

Method

The 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.

Results

Our proposed model surpassed Teixeira’s models exhibiting higher specificity (94.74%) and a slight increase in sensitivity (70.37%).

Conclusions

Our 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

Predation 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

Phenotypic 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 Statement

Environments 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

Bluetongue (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

Aim: 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: France

Time period: 1978-2022

Major taxa studied: 146 tree species

Methods: 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

Energy 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 STATEMENT

Optimization 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

Scalable 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

BACKGROUND

Chronic systemic inflammation links to type 2 diabetes mellitus (T2DM) onset, and the potential role of interleukins in this pathogenic process is increasingly recognized.

PURPOSE

To quantitatively evaluate circulating interleukin concentrations data available for T2DM patients.

DATA SOURCES

We performed a systematic review using PubMed, Web of Science, and the Cochrane Library.

STUDY SELECTION

Original 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 SYNTHESIS

Data 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.

LIMITATIONS

Of 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.

CONCLUSIONS

Meta-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 HIGHLIGHTS

Why 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.
HOP/STIP1 is required for KSHV lytic replication
Authors: Kirigin Elisa , Matandirotya Lorraine , Ruck Jamie-Lee , Weaver Frederick , Jackson Zoe , Chakraborty Abir , Veale Clinton Gareth Lancaster , Whitehouse Adrian , Edkins Adrienne Lesley
Published: April 2024

Kaposi sarcoma associated herpesvirus (KSHV) is a DNA virus that causes Kaposi sarcoma, a cancer of endothelial origin. KSHV uses the activity of host molecular chaperones like Hsp70 and Hsp90 for the folding of host and viral proteins required for productive infection. Hsp70 and Hsp90 chaperones form proteostasis networks with several regulatory proteins known as co-chaperones. Of these, Hsp90-Hsp70 organising protein (HOP) is an early-stage co-chaperone that regulates transfer of folding substrate proteins between the Hsp70 and Hsp90 chaperone systems. While roles for Hsp90 and Hsp70 in KSHV biology have been described, HOP has not previously been studied in this context despite its prominent interaction with both chaperones. Here we demonstrate a novel function for HOP as a new host factor required for effective lytic replication of KSHV in primary effusion cell lines.

Data summary

The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
The immune checkpoint pathophysiology of depression and chronic fatigue syndrome due to preeclampsia: focus on sCD80 and sCTLA-4
Authors: Omar Jangir Sami , Albarzinji Niaz , Niu Mengqi , Taher Naz Hawree , Aram Bayar , Sulaiman Mohammed Salam , Moustafa Shatha Rouf , Al-Hakeim Hussein Kadhem , Maes Michael
Published: April 2024

Background

Neuropsychiatric disorders in preeclampsia (PE) women are prevalent and worsen PE outcome. Immune-related biomarkers including soluble sCD80 and cytotoxic T-lymphocyte antigen-4 (sCTLA-4) are not well studied in relation to depression, anxiety, and chronic fatigue due to PE.

Aims

To study serum immune-inflammatory biomarkers of PE and delineate their associations with the Hamilton Depression (HAMD), Anxiety (HAMA), and Fibro-Fatigue (FF) rating Scale scores.

Methods

sCD80, sCTLA-4, vitamin D, granulocyte-macrophage colony-stimulating factor, zinc, copper, magnesium, and calcium were measured in 90 PE compared with 60 non-PE pregnant women.

Results

PE women show higher depression, anxiety and FF rating scale scores as compared with control women. sCTLA-4, sCD80, and copper were significantly higher and zinc, magnesium, and calcium significantly lower in PE women than in controls. Multiple regression analysis showed that around 55.8%-58.0% of the variance in the HAMD, HAMA and FF scores was explained by the regression on biomarkers; the top 3 most important biomarkers were sCTLA-4, sCD80, and vitamin D. The sCTLA-4/sCD80 ratio was significantly and inversely associated with the HAMD/HAMA/FF scores. We found that around 70% of the variance in systolic blood pressure could be explained by sCTLA-4, vitamin D, calcium, and copper.

Conclusions

The findings underscore that PE and depression, anxiety, and chronic fatigue symptoms due to PE are accompanied by activation of the immune-inflammatory response system. More specifically, disbalances among soluble checkpoint molecules seem to be involved in the pathophysiology of hypertension and neuropsychiatric symptoms due to PE.
Towards a Dataset for State of the Art Protein Toxin Classification
Authors: Challacombe Chance A. , Haas Nikhil S.
Published: April 2024

In-silicotoxin classification assists in industry and academic endeavors and is critical for biosecurity. For instance, proteins and peptides hold promise as therapeutics for a myriad of conditions, and screening these biomolecules for toxicity is a necessary component of synthesis. Additionally, with the expanding scope of biological design tools, improved toxin classification is essential for mitigating dual-use risks. Here, a general toxin classifier that is capable of addressing these demands is developed. Applications forin-silicotoxin classification are discussed, conventional and contemporary methods are reviewed, and criteria defining current needs for general toxin classification are introduced. As contemporary methods and their datasets only partially satisfy these criteria, a comprehensive approach to toxin classification is proposed that consists of training and validating a single sequence classifier, BioLMTox, on an improved dataset that unifies current datasets to align with the criteria. The resulting benchmark dataset eliminates ambiguously labeled sequences and allows for direct comparison against nine previous methods. Using this comprehensive dataset, a simple fine-tuning approach with ESM-2 was employed to train BioLMTox, resulting in accuracy and recall validation metrics of 0.964 and 0.984, respectively. This LLM-based model does not use traditional alignment methods and is capable of identifying toxins of various sequence lengths from multiple domains of life in sub-second time frames.
Piezoaxionic effect
Authors: Arvanitaki Asimina , Madden Amalia , Van Tilburg Ken
Published: April 2024

Axion dark matter (DM) constitutes an oscillating background that violates parity and time-reversal symmtries. Inside piezoelectric crystals, where parity is broken spontaneously, this axion background can result in a stress. We call this new phenomenon “the piezoaxionic effect.” When the frequency of axion DM matches the natural frequency of a bulk acoustic normal mode of the piezoelectric crystal, the piezoaxionic effect is resonantly enhanced and can be read out electrically via the piezoelectric effect. We explore all axion couplings that can give rise to the piezoaxionic effect—the most promising one is the defining coupling of the QCD axion, through the anomaly of the strong sector. We also point our another, subdominant phenomenon present in all dielectrics, namely the “electroaxionic effect.” An axion background can produce an electric displacement field in a crystal which in turn will give rise to a voltage across the crystal. The electroaxionic effect is again largest for the axion coupling to gluons. We find that this model-independent coupling of the QCD axion may be probed through the combination of the piezoaxionic and electroaxionic effects in piezoelectric crystals with aligned nuclear spins, with near-future experimental setups applicable for axion masses between 10−11  eV and 10−7  eV, a challenging range for most other detection concepts.

Published by the American Physical Society
2024
Study on the mixing of
Ξc
and
Ξc′
by the transition
Ξb→Ξc(′)
Authors: Ke Hong-Wei , Fang Gang-Yang , Shi Yan-Liang
Published: April 2024

Recently, the LHCb Collaboration has observed the decays Ξb0→Ξc+Ds− and Ξb−→Ξc0Ds−. They measured the relative branching fractions times the ratio of beauty-baryon production cross sections R(Ξb0Λb)≡σ(Ξb0)σ(Λb0)×B(Ξb0→Ξc+Ds−)B(Λb0→Λc+Ds−) and R(Ξb−Λb)≡σ(Ξb−)σ(Λb0)×B(Ξb−→Ξc0Ds−)B(Λb0→Λc+Ds−). Once the ratio σ(Ξb0)σ(Λb0) or σ(Ξb−)σ(Λb0) is known, one can determine the relative branching fractions which can be used to exam the mixing of Ξc and Ξc′. In previous literature, Ξc and Ξc′ were assumed to belong to SU(3)F antitriple and sextet, respectively. However, recent experimental measurements, such as the ratio Γ(Ξcc→Ξcπ+)/Γ(Ξcc→Ξc′π+), indicate the spin-flavor structures of Ξc and Ξc′ are a mixture of Ξc3¯ and Ξc6. The exact value of mixing angle θ is still under debate. In theoretical models, the mixing angle was fitted to be about 16.27°±2.30° or 85.54°±2.30° based on decay channels Ξcc→Ξc(′). While in lattice calculation, a small angle (1.2°±0.1°) is preferred. To address such discrepancy and test the mixing of Ξc and Ξc′, here we propose the analysis of semileptonic and nonleptonic decays of Ξb→Ξc and Ξb→Ξc′. We calculate the decay rate of Ξb→Ξc and Ξb→Ξc′ based on the light-front quark model and study the effect of the mixing angle on the ratios of weak decays Ξb→Ξc and Ξb→Ξc′. In particular, we find the transition Ξb→Ξc′ can be an ideal channel to verify the mixing and extract the mixing angle because in theory, the decay rate would be extremely tiny without mixing. Our calculation suggests a measurement of Ξb→Ξc′ can be feasible in the near future, which will help to test flavor mixing angle θ and elucidate the mechanism of decay of heavy baryons.

Published by the American Physical Society
2024
Magnetic field dependence of the neutral pion longitudinal screening mass in the linear sigma model with quarks
Authors: Ayala Alejandro , Farias Ricardo L. S. , Hernández L. A. , Mizher Ana Julia , Rendón Javier , Villavicencio Cristian , Zamora R.
Published: April 2024

We use the linear sigma model with quarks to study the magnetic-field-induced modifications on the longitudinal screening mass for the neutral pion at one-loop level. The effects of the magnetic field are introduced into the self-energy, which contains the contributions from all the model particles. We find that, to obtain a reasonable description for the behavior with the field strength, we need to account for the magnetic field dependence of the particle masses. We also find that the couplings need to decrease fast enough with the field strength to then reach constant and smaller values as compared to their vacuum ones. The results illustrate the need to treat the magnetic corrections to the particle masses and couplings in a self-consistent manner, accounting for the backreaction of the field effects for the magnetic field dependence of the rest of the particle species and couplings in the model.

Published by the American Physical Society
2024
Electroweak baryogenesis, dark matter, and dark
CP
symmetry
Authors: Ma Jinghong , Wang Jie , Wang Lei
Published: April 2024

With the motivation of explaining the dark matter and achieving the electroweak baryogenesis via the spontaneous CP violation at high temperature, we propose a complex singlet scalar (S=χ+iηs2) extension of the two-Higgs-doublet model respecting a discrete dark CP symmetry: S→−S*. The dark CP symmetry guarantees χ to be a dark matter candidate on one hand and on the other hand allows ηs to have mixings with the pseudoscalars of the Higgs doublet fields, which play key roles in generating the CP violation sources needed by the electroweak baryogenesis at high temperature. The Universe undergoes multistep phase transitions, including a strongly first-order electroweak phase transition during which the baryon number is produced. At the present temperature, the observed vacuum is produced and the CP symmetry is restored so that the stringent electric dipole moment experimental bounds are satisfied. Considering relevant constraints, we study the simple scenario of mχ around the Higgs resonance region, and find that the dark matter relic abundance and the baryon asymmetry can be simultaneously explained. Finally, we briefly discuss the gravitational wave signatures at future space-based detectors and the LHC signatures.

Published by the American Physical Society
2024
Probing for chiral
Z′
gauge boson through scattering measurement experiments
Authors: Asai Kento , Das Arindam , Li Jinmian , Nomura Takaaki , Seto Osamu
Published: April 2024

Motivated by the observation that tiny neutrino mass cannot be explained within the framework of the Standard Model, we consider extra gauge extended scenarios in which tiny neutrino masses are generated through the seesaw mechanism. These scenarios are equipped with a beyond the Standard Model neutral gauge boson called Z′ in the general U(1)X symmetry, which is a linear combination of U(1)Y and U(1)B−L. In this case, left- and right-handed fermions interact differently with the Z′. The Z′ gives rise to different processes involving neutrino-nucleon, neutrino-electron, electron-nucleus, and electron-muon scattering processes. By comparing with proton and electron beam-dump experiment data, recast data from searches for the long-lived and dark photon at , LHCb, and CMS experiments, the electron and muon g−2 data, and the data of the dilepton and dijet searches at the LEP experiment, we derive bounds on the gauge coupling and the corresponding gauge boson mass for different U(1)X charges and evaluate the prospective limits from the future beam-dump scenarios at DUNE, FASER (2), and ILC. We conclude that large parameter regions could be probed by scattering, beam-dump, and collider experiments in the future.

Published by the American Physical Society
2024