bluuebunny/crossref_metadata_2025 huggingface dataset:
Shortened SARS-CoV-2 shedding in saliva during early Omicron compared to wild-type pandemic phase
Authors: Kozanli Eva , Winkel Angelique M.A.M. , Han Alvin X. , van den Brink Sharon , van den Brandt Annemarie , Haverkort Milly E. , Euser Sjoerd , Russell Colin A. , de Jong Menno D. , van Houten Marlies A. , van Lelyveld Steven F.L. , Eggink Dirk
Published: September 2024

This study compared the dynamics of SARS-CoV-2 viral shedding in saliva between wild-type virus-infected and Omicron-infected household cohorts. Pre-existing immunity in participants likely shortens duration of viral shedding and lowers viral load peaks. Dense saliva sampling can be a convenient tool to study viral load dynamics.
Association between plausible genetic factors and weight loss from GLP1-RA and bariatric surgery: a multi-ancestry study in 10 960 individuals from 9 biobanks
Authors: German Jakob , Cordioli Mattia , Tozzo Veronica , Urbut Sarah , Arumäe Kadri , Smit Roelof A.J. , Lee Jiwoo , Li Josephine H. , Janucik Adrian , Ding Yi , Akinkuolie Akintunde , Heyne Henrike , Eoli Andrea , Saad Chadi , Al-Sarraj Yasser , Abdel-latif Rania , Mohammed Shaban , Al Hail Moza , Barry Alexandra , Wang Zhe ,   Estonian Biobank research team, Cajuso Tatiana , Corbetta Andrea , Natarajan Pradeep , Ripatti Samuli , Philippakis Anthony , Szczerbinski Lukasz , Pasaniuc Bogdan , Kutalik Zoltan , Mbarek Hamdi , Loos Ruth J.F. , Vainik Uku , Ganna Andrea
Published: September 2024

Obesity is a significant public health concern. GLP-1 receptor agonists (GLP1-RA), predominantly in use as a type 2 diabetes treatment, are a promising pharmacological approach for weight loss, while bariatric surgery (BS) remains a durable, but invasive, intervention. Despite observed heterogeneity in weight loss effects, the genetic effects on weight loss from GLP1-RA and BS have not been extensively explored in large sample sizes, and most studies have focused on differences in race and ethnicity, rather than genetic ancestry. We studied whether genetic factors, previously shown to affect body weight, impact weight loss due to GLP1-RA therapy or BS in 10,960 individuals from 9 multi-ancestry biobank studies in 6 countries. The average weight change between 6 and 12 months from therapy initiation was -3.93% for GLP1-RA users, with marginal differences across genetic ancestries. For BS patients the weight change between 6 and 48 months from the operation was -21.17%. There were no significant associations between weight loss due to GLP1-RA and polygenic scores for BMI or type 2 diabetes or specific missense variants in theGLP1R, PCSK1 and APOEgenes, after multiple-testing correction. A higher polygenic score for BMI was significantly linked to lower weight loss after BS (+0.7% for 1 standard deviation change in the polygenic score, P = 1.24×10-4), but the effect was modest and further reduced in sensitivity analyses. Our findings suggest that existing polygenic scores related to weight and type 2 diabetes and missense variants in the drug target gene do not have a large impact on GLP1-RA effectiveness. Our results also confirm the effectiveness of these treatments across all major continental ancestry groups considered.
Cross-EHR validation of antidepressant response algorithm and links with genetics of psychiatric traits
Authors: Sealock Julia M. , Tubbs Justin D. , Lake Allison M. , Straub Peter , Smoller Jordan W. , Davis Lea K.
Published: September 2024

Objective

Antidepressants are commonly prescribed medications in the United States, however, factors underlying response are poorly understood. Electronic health records (EHRs) provide a cost-effective way to create and test response algorithms on large, longitudinal cohorts. We describe a new antidepressant response algorithm, validation in two independent EHR databases, and genetic associations with antidepressant response.

Method

We deployed the algorithm in EHRs at Vanderbilt University Medical Center (VUMC), the All of Us Research Program, and the Mass General Brigham Healthcare System (MGB) and validated response outcomes with patient health questionnaire (PHQ) scores. In a meta-analysis across all sites, worse antidepressant response associated with higher PHQ-8 scores (beta = 0.20, p-value = 1.09 x 10−18).

Results

We used polygenic scores to investigate the relationship between genetic liability of psychiatric disorders and response to first antidepressant trial across VUMC and MGB. After controlling for depression diagnosis, higher polygenic scores for depression, schizophrenia, bipolar, and cross-disorders associated with poorer response to the first antidepressant trial (depression: p-value = 2.84 x 10−8, OR = 1.07; schizophrenia: p-value = 5.93 x 10−4, OR = 1.05; bipolar: p-value = 1.99 x 10−3, OR = 1.04; cross-disorders: p-value = 1.03 x 10−3, OR = 1.05).

Conclusions

Overall, we demonstrate our antidepressant response algorithm can be deployed across multiple EHR systems to increase sample size of genetic and epidemiologic studies of antidepressant response.
Comparison of visual function analysis of people with low vision using three different models of augmented reality devices
Authors: Gopalakrishnan Sarika , Kartha Arathy , Schuchard Ronald , Fletcher Donald
Published: September 2024

We compared visual function in individuals with low vision (>20/60) using three different models of augmented reality (AR) devices: Ziru, IrisVision, and NuEyes-Pro3. The distance visual acuity (VA) was measured in high luminance high contrast (HLHC), high luminance low contrast (HLLC), low luminance high contrast (LLHC), and low luminance low contrast (LLLC) settings. The other tests were near VA, distance and near contrast sensitivity (CS), color vision, depth perception and indoor navigation. The change in visual function without and with AR devices was analyzed. Out of 27 participants, 17 were female. The mean age was 66.7±18.2 years. The median baseline VA was 0.66 (0.49) logMAR in HLHC, 0.87 (0.54) logMAR in HLLC, 0.84 (0.67) logMAR in LLHC and 1.04 (0.34) logMAR in LLLC. The median baseline near VA was 0.55(0.4) logMAR, distance and near CS was 1.10(0.26) logCS, and 1.20(0.30) logCS respectively. Distance and near vision showed significant differences with both Ziru and IrisVision (p<0.01), but not with NuEyes. There was a significant change in CS using Ziru and IrisVision for both distance and near (p<0.05) but both reduced significantly with NuEyes (p<0.01). The baseline functional vision score (FVS) was 45.76 (44.47) which improved to 79.04 (33.98) with Ziru and 76.14 (33.76) with IrisVision significantly, whereas it significantly reduced to 35.00 (33.97) with NuEyes (p<0.01). During the objective identification task on the indoor mobility course using AR devices, head-level objects were missed more compared to waist or floor-level objects across all three models. Majority of the visual functions improved with Ziru and IrisVision, with limited improvement in certain lighting condition of distance visual acuity with NuEyes.
Proteogenomic signature of risk of Alzheimer’s disease and related dementia risk in individuals with a history of major depression disorder
Authors: Diniz Breno Satler , Chen Zhiduo , Steffens David C. , Pilling Luke , Fortinsky Richard H. , Kuchel George A. , Kuo Chia-Ling
Published: September 2024

The mechanisms linking a history of major depressive disorder (MDD) to an increased risk of Alzheimer’s disease and related dementia (ADRD) are not fully understood. Using the UK Biobank available proteomic and genomic data, we evaluated the biological mechanisms linking both conditions. In participants with a history of MDD at baseline (n=3,615), we found that plasma levels of NfL, GFAP, PSG1 were associated with higher risk (HR=1.38; 1.37; 1.34, respectively; all adjusted p-values<0.05), while VGF, GET3, and HPGDS were associated with lower risk of incident ADRD (n=150) (HR=0.73; 0.71; 0.66, respectively; all adjusted p-values<0.05) during a mean follow-up of 13.7 years (SD=2.2). Two-sample Mendelian randomization analysis using cis-pQTLs genetic instruments revealed that a lower protein expression of apolipoprotein E and higher IL-10 receptor subunit B were causally linked to incident ADRD. Finally, we developed a Proteomic Risk Score (PrRSMDD-ADRD), which showed strong discriminative power (C-statistic = 0.84) to identify participants with MDD that developed ADRD upon follow-up. In addition to demonstrating an association between plasma proteins associated with inflammation and future ADRD risk in individuals with MDD, our findings include an element of causality using Mendelian Randomization (MR) and PrRSMDD-ADRDcan be useful to identify individuals with the highest risk to develop ADRD in a highly vulnerable population.
Machine learning for the prediction of spontaneous preterm birth using early second and third trimester maternal blood gene expression: A Cautionary Tale
Authors: Hornaday Kylie K , Werbicki Ty , Tough Suzanne C , Wood Stephen L , Anderson David W , Slater Donna M
Published: September 2024

Preterm birth (PTB) remains a significant global health challenge and a leading cause of neonatal mortality and morbidity. Despite advancements in neonatal care, the prediction of PTB remains elusive, in part due to complex etiologies and heterogeneous patient populations. This study aimed to validate and extend information on gene expression biomarkers previously described for predicting spontaneous PTB (sPTB) using maternal whole blood from the All Our Families pregnancy cohort study based in Calgary, Canada. The results of this study are two-fold: first, using additional replicates of maternal blood samples from the All Our Families cohort, we were unable to repeat the findings of a 2016 study which identified top maternal gene expression predictors for sPTB. Second, we conducted a secondary analysis of the original gene expression dataset from the 2016 study, including external validation using a pregnancy cohort based in Detroit, USA. While initial results of our machine learning model suggested promising performance (area under the receiver operating curve, AUC 0.90 in the training set), performance was significantly degraded on the test set (AUC 0.54), and further degraded in external validation (AUC 0.51), suggesting poor generalizability, likely due to overfitting exacerbated by a low feature-to-noise ratio. Prediction was not improved when using machine learning approaches over traditional statistical learning. These findings underscore the challenges in translating biomarker discovery into clinically useful predictive models for sPTB. This study highlights the critical need for rigorous methodological safeguards and external validation in biomarker research. It also emphasizes the impact of data noise and overfitting on model performance, particularly in high-dimensional omics datasets. Future research should prioritize robust validation strategies and explore mechanistic insights to improve our understanding and prediction of PTB.
Malaria prevalence and its associated factors amongst rural adults: Cross-sectional study in East Nusa Tenggara Province Indonesia
Authors: Guntur Robertus Dole , Pahnael Jusrry Rosalina , Ginting Keristina Br , Bria Yulianti Paula , Kusumaningrum Damai , Islam Fakir M Amirul
Published: September 2024

Introduction

Malaria is a global health issue including in Indonesia. Currently, most of the cases was in the rural of eastern part of the country. However, malaria risk factors amongst rural adult were less documented. This study investigated malaria risk factors amongst rural adults in East Nusa Tenggara Province (ENTP).

Methods

A community based cross-sectional study was conducted to interview 1495 rural adults in ENTP. A multi-stage cluster random sampling technique was applied to collect data on malaria history, demographic, behavioural and environmental factors of malaria of participants. Logistic regression model was applied to decide significant factors associated with malaria.

Results

The prevalence of malaria was 13.4%. The prevalence of malaria was significantly higher for adults with low level of malaria knowledge (Adjusted odd ratio (AOR): 2.43, 95% confidence interval (CI): 1.38 – 4.27) compared to those with high malaria knowledge level, having moderate malaria knowledge level (AOR: 1.99, 95% CI: 1.11 – 3.57) compared to those high malaria knowledge level, having no education (AOR: 2.18, 95% CI: 1.37 – 3.45) compared to those junior high school or above education level, outdoor occupation (AOR: 1.81, 95% CI: 1.22 – 2.68) compared to indoor occupation, having family size > 4 (AOR 2.08, 95% CI: 1.52 –2.87) compared to those ≤ 4

Conclusion

The study revealed the prevalence of malaria amongst rural adults in this province was high. The study highlights the power of malaria knowledge level on the prediction of malaria prevalence amongst rural adults. Health education intervention is critical for vulnerable groups to reduce malaria prevalence in the province.
Proteostasis and metabolic dysfunction in a distinct subset of storage-induced senescent erythrocytes targeted for clearance
Authors: Peltier Sandy , Marin Mickaël , Dzieciatkowska Monika , Dussiot Michaël , Roy Micaela Kalani , Bruce Johanna , Leblanc Louise , Hadjou Youcef , Georgeault Sonia , Fricot Aurélie , Roussel Camille , Stephenson Daniel , Casimir Madeleine , Sissoko Abdoulaye , Paye François , Dokmak Safi , Ndour Papa Alioune , Roingeard Philippe , Gautier Emilie-Fleur , Spitalnik Steven L , Hermine Olivier , Buffet Pierre A , D’Alessandro Angelo , Amireault Pascal
Published: September 2024

Although refrigerated storage slows the metabolism of volunteer donor RBCs, cellular aging still occurs throughout thisin vitroprocess, which is essential in transfusion medicine. Storage-induced microerythrocytes (SMEs) are morphologically-altered senescent RBCs that accumulate during storage and which are cleared from circulation following transfusion. However, the molecular and cellular alterations that trigger clearance of this RBC subset remain to be identified. Using a staining protocol that sorts long-stored SMEs (i.e., CFSEhigh) and morphologically-normal RBCs (CFSElow), thesein vitroaged cells were characterized.

Metabolomics analysis identified depletion of energy, lipid-repair, and antioxidant metabolites in CFSEhighRBCs. By redox proteomics, irreversible protein oxidation primarily affected CFSEhighRBCs. By proteomics, 96 proteins, mostly in the proteostasis family, had relocated to CFSEhighRBC membranes. CFSEhighRBCs exhibited decreased proteasome activity and deformability; increased phosphatidylserine exposure, osmotic fragility, and endothelial cell adherence; and were cleared from the circulation during human spleenex vivoperfusion. Conversely, molecular, cellular, and circulatory properties of long-stored CFSElowRBCs resembled those of short-stored RBCs.

CFSEhighRBCs are morphologically and metabolically altered, have irreversibly oxidized and membrane-relocated proteins, and exhibit decreased proteasome activity.In vitroaging during storage selectively alters metabolism and proteostasis in SMEs, targeting these senescent cells for clearance.
IGF1R is protective in pneumococcal pneumonia
Authors: Felten Matthias , Alves Luiz-Gustavo Teixeira , Letsiou Eleftheria , Arnedo Elvira Alfaro , Piñeiro-Hermida Sergio , López Icíar P. , Dietert Kristina , Firsching Theresa , Gruber Achim D. , Fatykhova Diana , Hocke Andreas , Lingscheid Tilmann , Lienau Jasmin , Rohde Gernot ,   Capnetz Study Group, Pichel Jose G. , Witzenrath Martin
Published: September 2024

Background

Streptococcus pneumoniae(S.pn) is the most prevalent causal bacterial pathogen in community-acquired pneumonia. Despite appropriate antimicrobial therapy, pneumococcal pneumonia can progress to acute respiratory distress syndrome where actual therapies are mainly supportive, and the discovery of new molecular targets is needed.

Objective

To investigate the role of IGF1R (Insulin-like Growth Factor 1 Receptor) in pneumococcal pneumonia.

Methods

Igf1r-deficient (UBC-CreERT2; Igf1rfl/fl) and control (Igf1rfl/fl) mice were infected with 5×106S.pn(PN36) or PBS (sham infected). Mice were sacrificed 48 h after infection. Pulmonary permeability, local inflammatory response, and pulmonary and extra-pulmonary bacterial loads were analyzed. Further, IGF1R protein expression was determined in human lung tissue afterS.pninfection and IGF1 and IGF1R levels were determined serum of pneumonia patients.

Results

In patients and mice infected withS.pn, IGF1 signaling was significantly altered.Igf1r-deficient mice had significantly increased pulmonary permeability after infection with increased pulmonary inflammatory cytokine levels, while inflammatory cell recruitment was not altered compared to infectedIgf1rfl/flcontrol animals. Pulmonary bacterial load was significantly higher inIgf1r-deficient mice, and histological analysis confirmed increased alveolar edema and necrosis compared to infectedIgf1rfl/flcontrol and sham-infected mice.Ex vivo,S.pncaused a decrease in IGF1R protein expression in human lung tissue.

Conclusion

Our results demonstrate a significant regulation of IGF1R in ex-vivo infected human lung tissue and in serum ofS.pnpneumonia patients. Moreover, pneumonia severity was increased inIgf1r-deficient mice uponS.pninfection compared toIgf1rfl/flcontrol mice, suggesting that IGF1R plays a protective role in pneumococcal pneumonia.
A critical affinity window for IgSF proteins DIP-α and Dpr10 is required for proper motor neuron arborization
Authors: Lopez Davys H. , Rostam Kevin D. , Zamurrad Sumaira , Xu Shuwa , Mann Richard S.
Published: September 2024

For flies to walk properly, motor neurons (MNs) from the ventral nerve cord (VNC) need to reach the correct muscle, and arborize appropriately during development. The canonical view of how this is achieved is that cell surface proteins are expressed pre- and post-synaptically that bind to each other like molecular “lock-and-keys” that guide neurons to their targets. The binding affinities of these molecules can vary by more than 100-fold. In the fly leg neuromuscular system, three MNs expressDIP-αand their target muscles express its cognate partner,dpr10, both of which encode members of the Immunoglobulin superfamily (IgSF). Although, both of these molecules are necessary for the maintenance of MN-muscle contacts, the role that specific affinities play in this process has not been examined. Here we use knock-in mutations intoDIP-αanddpr10that either decrease or increase the affinity between these two proteins. Compared to control animals, decreasing the affinity results in phenotypes similar toDIP-αordpr10 null animals, where MN axons fail to maintain contacts with their muscle targets and retract their filopodia, resulting in stunted and/or branchless axons. We also find that the threeDIP-α-expressing motor neurons behave differently to the loss of affinity. Surprisingly, if the affinity increases past a certain threshold, a similar branchless phenotype is observed in adult legs. Live imaging during pupal development shows that MN filopodia are unable to productively engage their muscle targets and behavioral assays suggest that these defects lead to locomotor deficits. These data suggest that CAM affinities are tuned to a specific range to achieve proper neuronal morphology.
SRY-Box Transcription Factor 9 regulates 3’-Phosphoadenosine 5’-Phosphosulfate Synthase 2 mRNA expression through derepression of the transcriptional repressor, CCAAT/enhancer-binding protein beta
Authors: Liu Cunren , Serra Rosa
Published: September 2024

Previously, we showed thatPapss2expression is regulated through a Sox9-dependent pathway. Here we explore molecular mechanisms whereby Sox9 regulates mousePapss2. A 509bp Sox9-responsive DNA element (Region C) was identified upstream of thePapss2second start site using co-transfection and luciferase reporter assays. A Sox9 responsive element was narrowed down to 32bps within Region C (Sox9RE). Putative SoxE and C/EBPβ binding sites were identified within S9RE. C/EBPβ was identified as a repressor for Sox9-mediated activity. In cells transfected with expression vectors for C/EBPβ and Sox9, increasing amounts of C/EBPβ resulted in attenuation of Sox9-mediated activation of Region C while increasing amounts of Sox9 activated transcription in the presence of C/EBPβ. Using electromobility shift assays, three protein complexes were identified on S9RE after incubation with nuclear extracts from ATDC5 cells. Super shift assays indicated that under basal conditions C/EBPβ was present in the DNA-protein complexes observed. Unlabeled S9RE with point mutations in the predicted SoxE binding site competed with protein complex formation on the S9RE while excess oligo corresponding to the predicted SoxE binding site did not, suggesting that proteins do not bind to SoxE motiff under basal conditions. Under conditions of high Sox9 expression, the formation of protein-DNA complexes on S9RE was inhibited. We then showed by western blot that increasing Sox9 protein resulted in reduced C/EBPβ protein levels. Co-immunoprecipitation indicated interaction of Sox9 and C/EBPβ proteins. We propose that Sox9 acts to derepress C/EBPβ-inhibited transcription of Papss2 by first interacting with C/EBPβ to prevent it from binding DNA, then reducing C/EBPβ expression.
HIV Vpr activates a nucleolar-specific ATR pathway to degrade the nucleolar stress sensor CCDC137
Authors: Nisson Karly A , Patel Rishi S , Delgado Yennifer , Bouhaddou Mehdi , Etienne Lucie , Fregoso Oliver I
Published: September 2024

The lentiviral accessory protein Vpr engages an extensive network of cellular pathways to drive diverse host consequences. Of its many phenotypes, CRL4A-E3 ubiquitin ligase complex co-option, DNA damage response (DDR) engagement, and G2/M arrest are conserved and thus proposed to be functionally important. How Vpr effects these functions and whether they explain how Vpr dysregulates additional cellular pathways remain unclear. Here we leverage the ability of Vpr to deplete the nucleolar protein CCDC137 to understand how Vpr-induced DDR activation impacts nucleolar processes. We characterize CCDC137 as an indirect Vpr target whose degradation does not correlate with Vpr-induced G2/M arrest. Yet, degradation is conserved among Vpr from the pandemic HIV-1 and related SIVcpz/SIVgor, and it is triggered by genomic insults that activate a nucleolar ATR pathway in a manner similar to camptothecin. We determine that Vpr causes ATR-dependent features of nucleolar stress that correlate with CCDC137 degradation, including redistribution of nucleolar proteins, altered nucleolar morphology, and repressed ribosome biogenesis. Together, this data distinguishes CCDC137 as a non-canonical Vpr target that may serve as a sensor of nucleolar disruption, and in doing so, identifies a novel role for Vpr in nucleolar stress.

GRAPHICAL ABSTRACT
Autism and Intellectual Disability-AssociatedMYT1LMutation Alters Human Cortical Interneuron Differentiation, Maturation, and Physiology
Authors: Prakasam Ramachandran , Determan Julianna , Narasimhan Mishka , Shen Renata , Saleh Maamoon , Chapman Gareth , Kaushik Komal , Gontarz Paul , Meganathan Kesavan , Hakim Bilal , Zhang Bo , Huettner James E. , Kroll Kristen L.
Published: September 2024

MYT1L is a neuronal transcription factor highly expressed in the developing and adult brain. While pathogenicMYT1Lmutation causes neurodevelopmental disorders, these have not been characterized in human models of neurodevelopment. Here, we defined the consequences of pathogenicMYT1Lmutation in human pluripotent stem cell-derived cortical interneurons. During differentiation, mutation reduced MYT1L expression and increased progenitor cell cycle exit and neuronal differentiation and synapse-related gene expression, morphological complexity, and synaptic puncta formation. Conversely, interneuron maturation was compromised, while variant neurons exhibited altered sodium and potassium channel activity and reduced function in electrophysiological analyses. CRISPRi-based knockdown similarly impaired interneuron differentiation and maturation, supporting loss of function-based effects. We further defined MYT1L genome-wide occupancy in interneurons and related this to the transcriptomic dysregulation resulting fromMYT1Lmutation, to identify direct targets that could mediate these phenotypic consequences. Together, this work delineates contributors to the etiology of neurodevelopmental disorders resulting fromMYT1Lmutation.
Time on Task in Psychotherapeutic/Psychoeducational Intervention with Intermittent Explosive Disorder
Authors: Strayhorn Joseph , Faraone Stephen V. , Zhang-James Yanli
Published: September 2024

Objective

Anger control has been seen as a set of learnable skills. How much time is necessary for such learning? Comparisons with time requirements for other skills make it plausible that for many people, learning anger control may require well over 100 hours of time on task. Research interventions have been shorter -- a mean of 9 sessions was reported in one meta-analysis. In this study, our goal was to examine how much psychotherapeutic intervention is being delivered in the “real world” to patients with Intermittent Explosive Disorder.

Method

We studied a de-identified electronic health record data from TriNetX, collected from 87 medical institutions. We studied 32,322 individuals with Intermittent Explosive Disorder. We examined the distribution of the number of individuals across numbers of sessions received.

Results

The distribution for the numbers of sessions is highly skewed, resembling a curve of inverse proportion, or a Pareto function. The mode and the median were zero. Only about 25% of patients received any psychotherapy. For that subset, the median was 5 sessions, and the mean was 16. Approximately 10% received 9 visits or more; 5% 30 or more; 2% 50 or more. A large fraction of the psychotherapeutic labor was devoted to a small fraction of the patients: 80% of the sessions went to 7.5% of the patients.

Conclusions

The ability of health care systems to reduce the societal problem of aggression, at least by psychotherapeutic intervention, appears limited by the factors leading to low, or no, time on task.
The Healthy Human Global Project - Hong Kong : a community-based cross-sectional study of a healthy Asian population
Authors: Hung Rex L , Ng Wilson W , Chung Peter K , Li Ashley B S , Luk Theodora H Y , Fong Rosanna , Lee Anna , Mok Raina , Yung Hebronson , Tse Vera , Cheng Raven , Schneider Amandine , Telford Rachel L , Dubois Florian , Bourayou Elsa ,   Milieu Interieur, De Andrade Moral Rafael , Doisne Jean Marc , Hasan Milena , Leung Gabriel M , Ni Michael Y , Tse Michael , Peiris Malik , Di Santo James , Bruzzone Roberto , Rouilly Vincent , Duffy Darragh
Published: September 2024

Immune responses are highly variable from one individual to another, with this variability determined by factors such as age, sex, genetics and environment, which also affect physical and mental well-being. Systems immunology studies have been applied to human cohort studies to better understand these effects, but most are performed in Western populations of mostly European ancestry, neglecting the vast majority of human global diversity. To overcome this limitation, we established the Healthy Human Global Project Hong Kong (HHGP-HK) cohort to allow the study of immune variability in a healthy Asian population. Taking inspiration from the established French Milieu Interieur study we adapted inclusion and exclusion criteria to identify healthy donors, and to facilitate cross comparison between the two cohorts we collected similar demographic, medical and lifestyle information. To study the effects of age and sex, donors were stratified for both ranging from 20-79 years. We report here significant age and sex effects on multiple clinical laboratory measures, many of which were consistently observed in the Milieu Interieur cohort. C-reactive protein and liver enzymes were two exceptions perhaps reflecting different environmental effects between the two cohorts. We applied biological aging, physiological, and mental health scores to our cohort which highlights the need to develop and adapt such scores for application to populations of non-European descent. We also included wearable fitness trackers from which we observed significant age and sex differences for sleep, physical activity, and heart rate variability. This unique cohort will enable the better understanding of factors that determine immune variability within Asian populations.
Prevalence of Chikungunya, Dengue, and West Nile arboviruses in Iran based on enzyme-linked immunosorbent assay (ELISA): A systematic review and meta-analysis
Authors: Abbasi Ebrahim , Moemenbellah-Fard Mohammad Djaefar
Published: September 2024

Introduction

Arboviruses, including Chikungunya (CHIKV), Dengue (DENV), and West Nile (WNV) viruses, are significant viral threats that affect numerous people globally each year. This report explore the prevalence of these viruses in Iran through a systematic review and meta-analysis.

Methods

The present survey was performed with a systematic review and meta-analysis method on the seroprevalence of WNV, CHIKV, and DENV using the ELISA test. Based on this, by search in Web of Science, PubMed, Scopus, Cochrane Library, Science Direct, and Google Scholar scientific databases, all relevant published papers were sorted out and reviewed. Power ratification of data was carried out with a random effects model in meta-analysis, meta-regression,I2index, and Egger test.

Results

Twelve published papers between 2000 and 2024 were embodied in this meta-analysis report. The seroprevalence of positive ELISA test for WNV in Iran was estimated at 12.9% (CI=95%: 7.4-18.4), and for CHIKV at 6.2% (CI=95%: 0.6-11.8). Regarding DENV, only two studies were conducted with a zero prevalence in one study, and a seroprevalence of 5.6% in another study.

Conclusion

According to these data, WNV, CHIKV, and DENV fevers have been detected in Iran using ELISA test. Considering the seropositivity of WNV and CHIKV, and the finding of these viruses from several provinces, it could be for granted that these two viruses are ubiquitous and DENV fever is sporadic in Iran.

Author Summary

Arboviruses, including Chikungunya (CHIKV), Dengue (DENV), and West Nile (WNV), pose significant health threats globally, with increasing infections reported, including in Iran. This report conducts a systematic review and meta-analysis of the seroprevalence of these viruses in Iran through ELISA testing. A total of twelve studies published from 2000 to 2024 were analyzed, revealing a seroprevalence of 12.9% for WNV and 6.2% for CHIKV, while DENV showed a mixed prevalence of 0% in one study and 5.6% in another. The results suggest that WNV and CHIKV are widespread in Iran, whereas DENV appears to be sporadic.
Mapping the Psychopathic Brain: Divergent Neuroimaging Findings converge onto a Common Brain Network
Authors: Dugré Jules R. , De Brito Stéphane A.
Published: September 2024

Psychopathy is a personality disorder characterized by a constellation of interpersonal, affective, lifestyle, and antisocial features. However, its neural underpinnings remain poorly understood because functional neuroimaging studies have produced disparate findings. Here, we tackled this lack of replication by investigating whether peak coordinates of studies on psychopathy could in fact map onto a common functional connectivity network. An updated meta-analysis of 23 functional neuroimaging studies (534 cases vs 594 controls) first revealed no significant regional spatial convergence. However, using functional connectomes of 1,000 healthy participants, we demonstrated that the heterogeneous study findings do indeed converge onto a common brain network with a replicability reaching up to 85.2% across studies. We subsequently showed strong associations between this Psychopathy Network and a lesion network of 17 lesion sites causally linked to antisocial behaviors, as well as its association with neurotransmission systems and genetic markers previously implicated in the pathophysiology of psychopathy. Taken together, our study highlights the importance of examining the neural correlates of psychopathy from a network perspective, which can be validated using a multilevel approach, encompassing neural, genetic and neurochemical data. Ultimately, this approach may pave the way for novel and more personalised treatments.
Coherent-synchrotron-radiation-free longitudinal shaping of a high-charge electron bunch based on velocity modulation
Authors: Song Zhi , Zhou Shiyu , Hua Jianfei , Du Yingchao , Li Fei , Peng Bo , Lu Wei , Wang Zhen
Published: September 2024

Beam-driven plasma wakefield acceleration (PWFA) is a promising technique to generate high-energy electron bunches for future electron-positron colliders. Longitudinal shaping of high-charge drive beam is highly desired for achieving high-transformer ratio and loading high-charge witness beam. However, the existing shaping schemes either focused on relatively low-charge bunch shaping or accompanied with significant charge-loss rate (typically over 50%). In this paper, a coherent-synchrotron-radiation-free shaping scheme based on velocity modulation is proposed to generate a high-charge beam with a linearly ramped profile. A >10  kA-peak-current shaped beam containing >50  nC charge with a low charge-loss rate is demonstrated by a start-to-end simulation, and the tunabilities of the beam charge and the peak current, and the robustness of the proposed shaping scheme are also discussed. When loaded by a 3 nC witness beam, a >GV/m accelerating electric field with a transformer ratio larger than 4 can be achieved in a uniform plasma for the shaped drive beam, providing the possibility of high-transformer-ratio PWFA for a high-charge beam.

Published by the American Physical Society
2024
Microscale fiber-integrated vector magnetometer with on-tip field biasing using
N
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V
ensembles in diamond microcrystals
Authors: Homrighausen Jonas , Hoffmann Frederik , Pogorzelski Jens , Glösekötter Peter , Gregor Markus
Published: September 2024

In quantum sensing of magnetic fields, ensembles of nitrogen-vacancy centers in diamond offer high sensitivity, high bandwidth and outstanding spatial resolution while operating in harsh environments. Moreover, the orientation of defect centers along four crystal axes forms an intrinsic coordinate system, enabling vector magnetometry within a single diamond crystal. While most vector magnetometers rely on a known bias magnetic field for full recovery of three-dimensional (3D) field information, employing external 3D Helmholtz coils or permanent magnets results in bulky, laboratory-bound setups, impeding miniaturization of the device. Here, a novel approach is presented that utilizes a fiber-integrated microscale coil at the fiber tip to generate a localized uniaxial magnetic field. The same fiber-tip coil is used in parallel for spin control by combining dc and microwave signals in a bias tee. To implement vector magnetometry using a uniaxial bias field, the orientation of the diamond crystal is preselected and then fully characterized by rotating a static magnetic field in three planes of rotation. The measurement of vector magnetic fields in the full solid angle is demonstrated with a shot-noise-limited sensitivity of 19.4nT/Hz1/2 and microscale spatial resolution while achieving a fiber sensor head cross section of less than 1mm2.

Published by the American Physical Society
2024
Laser-frequency stabilization using light shift in compact atomic clocks
Authors: Calosso Claudio E. , Gozzelino Michele , Levi Filippo , Micalizio Salvatore
Published: September 2024

This paper describes the light-shift laser-lock (LSLL) technique, an alternative method intended for laser-based compact atomic clocks. The technique greatly simplifies the laser setup by stabilizing the pumping-laser frequency to the same atoms involved in the clock operation, without the need of an external reference. By alternating two clock sequences, the method estimates and cancels out a controlled amount of induced light shift, acting on the laser frequency. The LSLL technique is compatible with state-of-the-art three-level clocks and was demonstrated with field-programmable-gate-array-based electronics on a pulsed-optically-pumped vapor-cell clock developed at INRIM. The results have shown that the LSLL technique operates robustly, having a capture range of gigahertz without significantly compromising clock stability. In our tests, the clock exhibited a white frequency noise of 3.2×10−13τ−1/2 for averaging times τ up to 4000 s, reaching a floor below 1×10−14 up to 100 000 s. This level of performance meets the requirements of future global navigation satellite systems on-board clocks, adding the benefits of a reduced clock footprint, as well as increased reliability and robustness.

Published by the American Physical Society
2024
Band terminations and maximum spin values with up to 18 aligned particles (and holes) in the
Z,N=50
to 82 shells
Authors: Ragnarsson I. , Kardan A. , Carlsson B. G. , Paul E. S. , Petrache C. M. , Riley M. A. , Sharpey-Schafer J. F. , Simpson J.
Published: September 2024

Observed rotational bands that terminate or appear to terminate at very high spin are analyzed within the configuration constrained cranked Nilsson-Strutinsky (unpaired CNS or CNSB with pairing) formalism. Spin values for the nuclei discussed reach or come close to the maximum spin that can be built within the Z,N=50–82 shells. Configurations are distinguished not only by the number of particles in high-j and low-j shells within each N shell but, in some cases, also by the number of particles in pseudospin partners like d5/2g7/2 and s1/2d3/2. Configurations in Dy156 and Hf164, which terminate at I≈60, are well understood in terms of their occupation of open j shells or groups of j shells. The bands in Dy156 are tentatively observed up to termination while the bands in Hf164 are still a few spin units away. These terminating states are built with up to 18 aligned particles or 18 particles+holes outside a core. The core is built from nucleons in filled

j

shells, which gives no contribution to the spin. Analysis of the high-spin bands in Xe125,126 and Ce131,132 suggests that bands in Xe126 and Ce132 are observed to terminate at similar spin values, where terminating bands in Xe126 are observed high above yrast. It is remarkable that the deformed mean field, plus single-particle configurations, is able to provide such a comprehensive description of known experimental levels in nuclei up to spin 60ℏ and beyond. It is also impressive that the model can relate alignments of single-particle spin vectors to changes in shape with the nuclear spin.

Published by the American Physical Society
2024
CP
-odd window into long distance dynamics in rare semileptonic
B
decays
Authors: Kamenik Jernej F. , Košnik Nejc , Novoa-Brunet Martín
Published: September 2024

We consider the combined measurements of CP-averaged decay rates and direct CP asymmetries of B±→K±ℓ+ℓ− and B±→π±ℓ+ℓ− to probe (nonlocal) four-quark operator matrix element contributions to rare semileptonic B meson decays. We also explore how their effects could be in principle disentangled from possible local new physics effects using U-spin relations. To this end, we construct a ratio of CP-odd decay rate differences which are exactly predicted within the standard model in the U-spin limit, while the leading U-spin breaking effects can also be systematically calculated. Our results motivate binned measurements of the direct CP asymmetry in B±→π±ℓ+ℓ− as well as dedicated theoretical estimates of U-spin breaking both in local form factors as well as in four-quark matrix elements.

Published by the American Physical Society
2024
One-loop QCD amplitudes in the Feynman-diagram gauge
Authors: Hagiwara Kaoru , Mawatari Kentarou , Yamada Youichi , Zheng Ya-Juan
Published: September 2024

Scattering amplitudes for the massless QCD process, qq¯→q′q¯′, are calculated in the one-loop order in the Feynman-Diagram (FD) gauge, where gluons are quantized on the light cone with opposite direction of the three-momenta. We find non-decoupling of the Faddeev-Popov ghosts and nonconventional UV singularities in dimensional regularization. The known QCD amplitudes with asymptotic freedom are reproduced only after summing propagator and vertex corrections. By quantizing gluons in the Feynman gauge on the FD gauge background, we obtain the one-loop improved FD gauge amplitudes.

Published by the American Physical Society
2024
Amplitude factorization in the electroweak standard model
Authors: Plätzer Simon , Sjödahl Malin
Published: September 2024

We provide tools to analyze factorization at the amplitude level for processes involving the entire standard model. We focus in particular on a momentum region, in which the factorization of real and certain virtual corrections appears in a generalized eikonal approximation in which we expand around a quasisoft limit for massive gauge bosons, fermions, and scalars. We use the chirality-flow formalism to express loop exchanges or emissions as operators on chiral structures. This provides key tools for amplitude evolution with parton exchange and branching in the full Standard Model, including the electroweak sector.

Published by the American Physical Society
2024
Excited Abelian-Higgs vortices: Decay rate and radiation emission
Authors: Alonso-Izquierdo A. , Blanco-Pillado J. J. , Miguélez-Caballero D. , Navarro-Obregón S. , Queiruga J.
Published: September 2024

The evolution of 1 vortices when their massive bound mode is excited is investigated in detail (both analytically and numerically) in the Abelian-Higgs model for different ranges of the self-coupling constant. The dependence of the spectrum of the 1 vortex fluctuation operator on the model parameter is discussed initially. A perturbative approach is employed to study the radiation emission in both the scalar and the vector channels. Our findings reveal that the oscillating initial configuration of the 1 vortex radiates at a frequency twice that of the internal mode. Through energy conservation considerations, we derive the decay law of the massive mode. Finally, these analytical results are compared with numerical simulations in field theory.

Published by the American Physical Society
2024
Laser-driven electron source suitable for single-shot Gy-scale irradiation of biological cells at dose rates exceeding
1010
Gy/s
Authors: McAnespie C. A. , Chaudhary P. , Calvin L. , Streeter M. J. V. , Nersysian G. , McMahon S. J. , Prise K. M. , Sarri G.
Published: September 2024

We report on the first systematic characterization of a tuneable laser-driven electron source capable of delivering Gy-scale doses in a duration of 10–20 ps in a single irradiation, thus reaching unprecedented dose rates in the range of 1010–1012 Gy/s. Detailed characterization of the source indicates, in agreement with Monte Carlo simulations, dose delivery over cm-scale areas with a high degree of spatial uniformity. The results reported here confirm that a laser-driven source of this kind can be used for systematic studies of the response of biological cells to picosecond-scale radiation at ultrahigh dose rates.

Published by the American Physical Society
2024
Thermal hysteresis in wettability and the Leidenfrost phenomenon
Authors: Kita Yutaku , Kida Kensuke , Ariyoshi Takaaki , Hidaka Sumitomo , Kohno Masamichi , Takata Yasuyuki
Published: September 2024

The Leidenfrost temperature (TL), at which the liquid drop lifetime peaks on a superheated surface, is believed to be wettability dependent. Here, we show that the wettability effect on TL is subject to the history of the surface temperature. Observing a water drop evaporating on a polished stainless-steel surface heated from 100 to 400∘C in argon gas, we find TL≈265∘C. We then repeat the experiment along decreasing temperature and find a TL increase by 10 K, i.e., TL≈275∘C. This thermal hysteresis is due to a reduced contact angle during heating. Once hydrophilized, the hysteresis disappears until the contact angle recovers. Similar observations are made in the air where oxidation is possible.

Published by the American Physical Society
2024
Power-law-exponential interaction induced quantum spiral phases
Authors: Tian Guoqing , Wu Ying , Lü Xin-You
Published: September 2024

We theoretically predict a kind of power-law-exponential (PLE) dipole-dipole interaction between quantum emitters in a 1D waveguide QED system. This unconventional long-range interaction is the combination of power-law growth and exponential decay couplings. Applying the PLE interaction to a spin model, we uncover the rich many-body phases. Most remarkably, we find that the PLE interaction can induce the ordered and critical spiral phases. These spiral phases emerge from the strong frustration generated by the power-law factor of the PLE interaction; hence they are absent for other types of long-range interaction, e.g., pure exponential and power-law decay interactions. Our work is also applicable for the higher-dimensional systems. It fundamentally broadens the realm of many-body physics and has significant applications in quantum simulation of strongly correlated matter.

Published by the American Physical Society
2024
Signal Crosstalk in a Flip-Chip Quantum Processor
Authors: Kosen Sandoko , Li Hang-Xi , Rommel Marcus , Rehammar Robert , Caputo Marco , Grönberg Leif , Fernández-Pendás Jorge , Kockum Anton Frisk , Biznárová Janka , Chen Liangyu , Križan Christian , Nylander Andreas , Osman Amr , Roudsari Anita Fadavi , Shiri Daryoush , Tancredi Giovanna , Govenius Joonas , Bylander Jonas
Published: September 2024

Quantum processors require a signal-delivery architecture with high addressability (low crosstalk) to ensure high performance already at the scale of dozens of qubits. Signal crosstalk causes inadvertent driving of quantum gates, which will adversely affect quantum gate fidelities in scaled-up devices. Here, we demonstrate packaged flip-chip superconducting quantum processors with signal-crosstalk performance competitive with those reported in other platforms. For capacitively coupled qubit-drive lines, we find on-resonant crosstalk better than −27 dB (average −37 dB). For inductively coupled magnetic-flux-drive lines, we find less than 0.13% direct-current flux crosstalk (average 0.05%). These observed crosstalk levels are adequately small and indicate a decreasing trend with increasing distance, which is promising for further scaling up to larger numbers of qubits. We discuss the implications of our results for the design of a low-crosstalk on-chip signal-delivery architecture, including the influence of a shielding tunnel structure, potential sources of crosstalk, and estimation of crosstalk-induced qubit-gate error in scaled-up quantum processors.

Published by the American Physical Society
2024