bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constraining PBH mass distributions from 21cm brightness temperature results and an analytical mapping between probability distribution of 21cm signal and PBH masses
Authors: Mukhopadhyay Upala , Majumdar Debasish , Halder Ashadul 
Published: October 2022

Abstract
The evaporation of primordial black hole (PBH) via Hawking radiation influences the evolution of Inter Galactic Medium by heating up the latter and consequently affects the 21cm signal originated from the neutral Hydrogen atoms. In this work, we have considered EDGES observational data of 21cm line corresponding to cosmic dawn era to constrain the mass and the abundance of PBHs. In this context, two different PBH mass distributions namely, power law and lognormal mass distributions are considered to estimate the effects of PBH evaporation on the 21cm brightness temperature T
21. In addition to these two mass distributions, different monochromatic masses are also considered. The impacts of dark matter-baryon interactions on T
21 are also considered in this work along with the influences of PBH evaporation. Furthermore, adopting different monochromatic masses for PBHs, an attempt has been made to formulate a distribution for PBH masses by associating a probability weightage of the T
21 values (at z ∼ 17.2), within the range given by EDGES experiment, with the calculated T
21 values for each of the PBH mass values. The distribution best suited for the present purpose is found to be a combination of an error function and Owen function. Allowed contours in the parameter space of (initial PBH mass-dark matter mass) are obtained.
Association between changes in diet quality from mid-life to late-life and healthy ageing: the Singapore Chinese Health Study
Authors: Zhou Yan-Feng , Lai Jun S , Chong Mary Foong-Fong , Tong Eunice Huiying , Neelakantan Nithya , Pan An , Koh Woon-Puay 
Published: October 2022

Abstract

Background
Few studies have evaluated the association between changes in diet quality from mid-life to late-life and healthy ageing.

Methods
We included 12,316 Chinese adults aged 45–74 years at baseline (1993–1998) from the Singapore Chinese Health Study. Diet quality was measured using the Dietary Approaches to Stop Hypertension (DASH) scores at baseline and follow-up 3 interviews (2014–2016). Healthy ageing was assessed at follow-up 3 interviews, and was defined as absence of specific chronic diseases, good mental and overall self-perceived health, good physical functioning and absence of cognitive impairment, limitations in instrumental activities of daily living or function-limiting pain. Multivariable-adjusted logistic regression models were applied to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for the association between changes in DASH scores and healthy ageing.

Results
Compared with participants who maintained relatively stable DASH scores, a &gt;10% decrease in DASH score was associated with a 16% (95% CI, 4–26%) lower likelihood of healthy ageing, whereas a &gt;10% increase in DASH score was associated with a 19% (95% CI, 3–37%) higher likelihood of healthy ageing. Compared with participants who were in the low-score group consistently, participants who increased their DASH scores from moderate-score at baseline to high-score at follow-up 3 had a 53% (95% CI, 21–92%) higher likelihood of healthy ageing, whereas those who were in the high-score group consistently had 108% (95% CI, 71–152%) higher likelihood of healthy ageing.

Conclusions
Improving diet quality from mid- to late-life was associated with a higher likelihood of healthy ageing.
k
mdiff, large-scale and user-friendly differential k-mer analyses
Authors: Lemane Téo , Chikhi Rayan , Peterlongo Pierre 
Published: October 2022

Abstract

Summary
Genome wide association studies elucidate links between genotypes and phenotypes. Recent studies point out the interest of conducting such experiments using k-mers as the base signal instead of single-nucleotide polymorphisms. We propose a tool, kmdiff, that performs differential k-mer analyses on large sequencing cohorts in an order of magnitude less time and memory than previously possible.

Availabilityand implementation
https://github.com/tlemane/kmdiff

Supplementary information
Supplementary data are available at Bioinformatics online.
Altered synaptic connectivity in anin vitrohuman model of STXBP1 encephalopathy
Authors: McLeod Faye , Dimtsi Anna , Marshall Amy C , Lewis-Smith David , Thomas Rhys , Clowry Gavin J , Trevelyan Andrew J 
Published: October 2022

AbstractEarly infantile developmental and epileptic encephalopathies are devastating conditions, generally of genetic origin, but the pathological mechanisms often remain obscure. A major obstacle in this field of research is the difficulty of studying cortical brain development in humans, at the relevant time period in utero. To address this, we established an in vitro assay to study the impact of gene variants on the developing human brain by using living organotypic cultures of the human subplate and neighbouring cortical regions, prepared from ethically sourced, 14–17 post-conception week brain tissue (www.hdbr.org). We were able to maintain cultures for several months, during which time the gross anatomical structures of the cortical plate, subplate and marginal zone persisted, while neurons continued to develop morphologically and form new synaptic networks. This preparation thus permits the study of genetic manipulations and their downstream effects on an intact developing human cortical network. We focused on STXBP1 haploinsufficiency, which is among the most common genetic causes of developmental and epileptic encephalopathy. This was induced using shRNA interference, leading to impaired synaptic function and a reduced density of glutamatergic synapses. We thereby provide a critical proof-of-principle for how to study the impact of any gene of interest on the development of the human cortex.
Lesions to both somatic and affective pain pathways lead to decreased salience network connectivity
Authors: Jalon Itamar , Berger Assaf , Shofty Ben , Goldway Noam , Artzi Moran , Gurevitch Guy , Hochberg Uri , Tellem Rotem , Hendler Talma , Gonen Tal , Strauss Ido 
Published: October 2022

Abstract
Human pain is a salient stimulus composed of two main components: a sensory/somatic component, carrying peripheral nociceptive sensation via the spinothalamic tract and brainstem nuclei to the thalamus and then to sensory cortical regions, and an affective (suffering) component, where information from central thalamic nuclei is carried to the anterior insula, dorsal anterior cingulate cortex and other regions. While the sensory component processes information about stimulus location and intensity, the affective component processes information regarding pain-related expectations, motivation to reduce pain and pain unpleasantness. Unlike investigations of acute pain that are based on the introduction of real-time stimulus during brain recordings, chronic pain investigations are usually based on longitudinal and case-control studies, which are limited in their ability to infer the functional network topology of chronic pain.
In the current study, we utilized the unique opportunity to target the CNS’s pain pathways in two different hierarchical locations to establish causality between pain relief and specific connectivity changes seen within the salience and sensorimotor networks. We examined how lesions to the affective and somatic pain pathways affect resting-state network topology in cancer patients suffering from severe intractable pain. Two procedures have been employed: percutaneous cervical cordotomy (n = 15), hypothesized to disrupt the transmission of the sensory component of pain along the spinothalamic tract, or stereotactic cingulotomy (n = 7), which refers to bilateral intracranial ablation of an area in the dorsal anterior cingulate cortex and is known to ameliorate the affective component of pain. Both procedures led to immediate significant alleviation of experienced pain and decreased functional connectivity within the salience network. However, only the sensory procedure (cordotomy) led to decreased connectivity within the sensorimotor network. Thus, our results support the existence of two converging systems relaying experienced pain, showing that pain-related suffering can be either directly influenced by interfering with the affective pathway or indirectly influenced by interfering with the ascending spinothalamic tract.
Structural hyperconnectivity of the subthalamic area with limbic cortices underpins anxiety and impulsivity in Tourette syndrome
Authors: Temiz Gizem , Atkinson-Clement Cyril , Lau Brian , Czernecki Virginie , Bardinet Eric , Francois Chantal , Worbe Yulia , Karachi Carine 
Published: October 2022

AbstractTourette syndrome (TS) is a neurodevelopmental disorder characterized by motor and vocal tics, which is often associated with psychiatric comorbidities. Dysfunction of basal ganglia pathways might account for the wide spectrum of symptoms in TS patients. Although psychiatric symptoms may be related to limbic networks, the specific contribution of different limbic structures remains unclear. We used tractography to investigate cortical connectivity with the striatal area (caudate, putamen, core and shell of the nucleus accumbens), the subthalamic nucleus (STN), and the adjacent medial subthalamic region (MSR) in 58 TS patients and 35 healthy volunteers. 82% of TS patients showed psychiatric comorbidities, with significantly higher levels of anxiety and impulsivity compared to controls. Tractography analysis revealed significantly increased limbic cortical connectivity of the left MSR with the entorhinal (BA34), insular (BA48), and temporal (BA38) cortices in TS patients compared to controls. Furthermore, we found that left insular-STN connectivity was positively correlated with impulsivity scores for all subjects and with anxiety scores for all subjects, particularly for TS. Our study highlights a heterogenous modification of limbic structure connectivity in TS, with specific abnormalities found for the subthalamic area. Abnormal connectivity with the insular cortex might underpin the higher level of impulsivity and anxiety observed in TS.
Adverse Events Following Immunization With mRNA and Viral Vector Vaccines in Individuals With Previous Severe Acute Respiratory Syndrome Coronavirus 2 Infection From the Canadian National Vaccine Safety Network
Authors: Bettinger Julie A , Irvine Michael A , Shulha Hennady P , Valiquette Louis , Muller Matthew P , Vanderkooi Otto G , Kellner James D , Top Karina A , Sadarangani Manish , McGeer Allison , Isenor Jennifer E , Marty Kimberly , Soe Phyumar , De Serres Gaston ,   for the Canadian Immunization Research Network
Published: October 2022

AbstractBackgroundAdults previously infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop short-term immunity and may have increased reactogenicity to coronavirus disease 2019 (COVID-19) vaccines. This prospective, multicenter, active-surveillance cohort study examined the short-term safety of COVID-19 vaccines in adults with a prior history of SARS-CoV-2.MethodsCanadian adults vaccinated between 22 December 2020 and 27 November 2021 were sent an electronic questionnaire 7 days post–dose 1, dose 2, and dose 3 vaccination. The main outcome was health events occurring in the first 7 days after each vaccination that prevented daily activities, resulted in work absenteeism, or required a medical consultation, including hospitalization.ResultsAmong 684 998 vaccinated individuals, 2.6% (18 127/684 998) reported a prior history of SARS-CoV-2 infection a median of 4 (interquartile range: 2–6) months previously. After dose 1, individuals with moderate (bedridden) to severe (hospitalized) COVID-19 who received BNT162b2, mRNA-1273, or ChAdox1-S vaccines had higher odds of a health event preventing daily activities, resulting in work absenteeism or requiring medical consultation (adjusted odds ratio [95% confidence interval]: 3.96 [3.67–4.28] for BNT162b2, 5.01 [4.57–5.50] for mRNA-1273, and 1.84 [1.54–2.20] for ChAdox1-S compared with no infection). Following dose 2 and 3, the greater risk associated with previous infection was also present but was attenuated compared with dose 1. For all doses, the association was lower or absent after mild or asymptomatic infection.ConclusionsAdults with moderate or severe previous SARS-CoV-2 infection were more likely to have a health event sufficient to impact routine activities or require medical assessment in the week following each vaccine dose.
Sapovirus Infections in an Australian Community-Based Healthy Birth Cohort During the First 2 Years of Life
Authors: El-Heneidy Asmaa , Ware Robert S , Lambert Stephen B , Grimwood Keith 
Published: October 2022

AbstractBackgroundSapovirus is an important cause of acute gastroenteritis (AGE) in young children. However, knowledge gaps remain in community settings. We investigated the epidemiology, disease characteristics, and healthcare use associated with sapovirus infections in Australian children during their first 2 years of life.MethodsChildren in the Brisbane-based Observational Research in Childhood Infectious Diseases birth cohort provided daily gastrointestinal symptoms (vomiting/loose stools), weekly stool swabs, and healthcare data until age 2 years. Swabs were batch-tested for sapovirus using real-time polymerase chain reaction assays. Incidence rates and estimates of associations were calculated.ResultsOverall, 158 children returned 11 124 swabs. There were 192 sapovirus infection episodes. The incidence rate in the first 2 years of life was 0.89 infections per child-year (95% confidence interval [CI], .76–1.05), and the symptomatic incidence rate was 0.26 episodes per child-year (95% CI, .17–.37). Age ≥6 months, the fall season, and childcare attendance increased disease incidence significantly. Fifty-four of the 180 (30%) infections with linked symptom diaries were symptomatic, with 72% recording vomiting and 48% diarrhea. Prior infection reduced risk of further infections (adjusted hazard ratio, 0.70 [95% CI, .54–.81]) in the study period. Viral loads were higher and viral shedding duration was longer in symptomatic than asymptomatic children. Twenty-three (43%) symptomatic episodes required healthcare, including 6 emergency department presentations and 2 hospitalizations.ConclusionsSapovirus infections are common in Australian children aged 6–23 months. Efforts to reduce childhood AGE after the global rollout of rotavirus vaccines should include sapovirus where estimates of its incidence in communities will be crucial.
Racial Differences in the Diagnosis of Lyme Disease in Children
Authors: Hunt Kathryn M , Michelson Kenneth A , Balamuth Fran , Thompson Amy D , Levas Michael N , Neville Desiree N , Kharbanda Anupam B , Chapman Laura , Nigrovic Lise E ,   for Pedi Lyme Net
Published: October 2022

AbstractBlack children with Lyme disease compared with children of other races were less likely to have an erythema migrans lesion diagnosed (adjusted odds ratio, 0.34; 95% confidence interval, .14-.79) but more likely to have a swollen joint (adjusted odds ratio, 3.68; 95% confidence interval, 2.13-6.36) after adjustment for age and local Lyme incidence.
Increased Risk of Cancer and Mortality in a Large French Population-Based Paediatric-Onset Inflammatory Bowel Disease Retrospective Cohort
Authors: Dupont-Lucas Claire , Leroyer Ariane , Ley Delphine , Spyckerelle Claire , Bertrand Valérie , Turck Dominique , Savoye Guillaume , Maunoury Vincent , Guillon Nathalie , Fumery Mathurin , Sarter Hélène , Gower-Rousseau Corinne ,   EPIMAD Study Group
Published: October 2022

Abstract

Background and Aims
Paediatric-onset IBD [pIBD] is associated with an increased risk of cancer and mortality in adulthood. The aims of this study were to measure the incidence of cancer and mortality in patients with pIBD and identify factors associated with mortality and cancer.

Methods
All patients diagnosed with Crohn’s disease [CD] or ulcerative colitis [UC] before the age of 17 years between 1988 and 2011 in the EPIMAD registry were retrospectively followed until 2013 for cancer and 2015 for mortality. Standardized incidence [SIR] and mortality ratios [SMR] were estimated compared to the general population. Cox regression was used to compare the effect of exposures on cancer and mortality among IBD patients.

Results
We included 1344 patients [52% males, 75% CD], totalling 12 957 patient-years for cancer incidence and 18 817 patient-years for mortality. There were 14 cases of cancer [median age 27.8 years] and 15 deaths [median age 28.8 years]. The incidence of cancer and of mortality were increased compared to the general population: all-cancer SIR = 2.7 (95% confidence interval [CI]: 1.5–4.8), SMR = 1.7 [95% CI: 1.0–2.8]. Colorectal cancer had the highest SIR and SMR: SIR = 41.2 [95% CI: 17.2–99.0], SMR = 70.4 [95% CI 22.7–218.2]. Cancer was associated with (hazard ratio [HR], 95% CI): active smoking at diagnosis [5.5, 1.8–16.5], p = 0.002; any exposure to anti-tumour necrosis factor [6.1, 1.7–22.3], p = 0.0065; and exposure to combination therapy [7.4, 1.8–29.7], p = 0.0047. Mortality was associated with extraintestinal manifestations (HR 4.9 [95% CI: 1.7–13.8], p = 0.003).

Conclusions
In this large population-based cohort, patients with pIBD had an increased risk of both cancer [2.7-fold] and mortality [1.7-fold], particularly for colorectal cancer.
Trends in the teaching of sexual and reproductive health topics and skills in required courses in secondary schools, in 38 US states between 2008 and 2018
Authors: Szucs Leigh E , Demissie Zewditu , Steiner Riley J , Brener Nancy D , Lindberg Laura , Young Emily , Rasberry Catherine N 
Published: October 2022

Abstract
Information about state and local education policies regarding sexually transmitted infections, including human immunodeficiency virus, and unintended pregnancy prevention is available, yet less is known about school-level implementation of such policies. We examine trends in the percentage of US secondary schools teaching sexual and reproductive health (SRH) topics in a required course in Grades 6–8 and 9–12, including healthy relationships, sexual abstinence, condoms and condoms with other contraceptive methods. We analyze representative data from 38 states across six cycles of School Health Profiles (2008–18) assessed through self-administered questionnaires completed by lead health teachers. Logistic regression models examined linear trends in the percentages of schools teaching topics for Grades 6–8 and 9–12, separately. Trends were calculated for states having representative data for at least three cycles, including 2018. During 2008–18, it was more common to have increases in teaching how to obtain condoms, correct condom use and use condoms with other contraceptive methods in Grades 6–12 than decreases. More states showed decreases in teaching abstinence in Grades 6–12 than increases. Most states had no change in teaching SRH topics across grades. Findings suggest some improvement in school-based SRH education, yet efforts are needed to improve comprehensive, developmentally appropriate content.
Effect of Human Immunodeficiency Virus Infection on Human Papillomavirus Clearance Among Women in Senegal, West Africa
Authors: Li Zhuochen , Winer Rachel L , Ba Selly , Sy Marie Pierre , Lin John , Feng Qinghua , Gottlieb Geoffrey S , Salif Sow Papa , Kiviat Nancy B , Hawes Stephen E 
Published: October 2022

Abstract

Background
Persistent infection with high-risk human papillomavirus (HPV) is associated with development of invasive cervical cancer.

Methods
Longitudinal data was collected from 174 Senegalese women. We employed marginal Cox proportional hazards models to examine the effect of human immunodeficiency virus (HIV) status (HIV positive vs HIV negative) and HIV type (HIV-1 vs HIV-2 vs dual HIV-1/HIV-2) on clearance of type-specific HPV infection. Analyses were stratified by incident versus prevalent HPV infection.

Results
Incident HPV infections in HIV-positive women were less likely to clear than those in HIV-negative women (adjusted hazard ratio [HR] = 0.60; 95% confidence interval [CI], .38–.94). Among HIV-positive women, HIV-2–infected women and HIV-1/2 dually infected women were more likely to clear HPV incident infections than HIV-1–infected women (HR = 1.66; 95% CI, .95–2.92 and HR = 2.17; 95% CI, 1.12–4.22, respectively). Incident HPV infections in HIV-positive women with CD4 cell count ≤500 cells/μL were less likely to clear than those in HIV-positive women with CD4 cell count &gt;500 cells/μL (HR = 0.65; 95% CI, .42–1.01). No significant associations were observed for prevalent HPV infections.

Conclusions
HIV infection reduced the likelihood of clearance of incident HPV infection. Furthermore, among HIV-positive women, low CD4 cell count and dual HIV infection were each associated with reduced likelihood of clearance.
Serum Neutralization Against SARS-CoV-2 Variants Is Heterogenic and Depends on Vaccination Regimen
Authors: Jäger Michael , Dichtl Stefanie , Bellmann-Weiler Rosa , Reindl Markus , Lass-Flörl Cornelia , Wilflingseder Doris , Posch Wilfried 
Published: October 2022

Abstract
Omicron variants are still the dominant SARS-CoV-2 viruses worldwide, therefore determination of the level of protection from infection and severe disease is essential. Here, we investigated humoral and cellular immunity of individuals immunized by ChAdOx1, BNT162b2, and mRNA-1273 and our results show that IgG and neutralization titers wane over time. However, strongest neutralization against Omicron BA.1 and T-cell responses were detected in ChAdOx1 vaccinees 6 months after the second dose, while no long-lasting neutralization was shown against BA.2 in any cohort. Crucially, our investigation revealed that immunity against variants of concern is heterogenic and dependent on the immunization status.
Development and validation of a resazurin assay for in vitro susceptibility testing of Actinomadura madurae: a common causative agent of actinomycetoma
Authors: Abd Algaffar S O , Verbon A , Khalid S A , van de Sande W W J 
Published: October 2022

Abstract

Objectives
Actinomycetoma is a chronic granulomatous disease affecting skin, subcutaneous tissue, fascia, muscle and bones. With increasing resistance against commonly used treatment regimens, susceptibility testing is urgently needed.

Methods
We developed an in vitro susceptibility assay for Actinomadura madurae, one of the common causative agents of actinomycetoma, employing resazurin for endpoint reading. Using this assay, reproducible MICs were determined for the most commonly used antibacterial agents for actinomycetoma treatment. The tested antibacterial agents included trimethoprim/sulfamethoxazole, amikacin, streptomycin, amoxicillin, ceftriaxone, gentamicin, ciprofloxacin, doxycycline, imipenem, linezolid, penicillin G and rifampicin.

Results
Following the clinical breakpoints as stated by CLSI, 100% of the tested strains were susceptible to trimethoprim/sulfamethoxazole (MIC 0.03/0.59–1/19 mg/L), amikacin (MIC 0.0078–0.25 mg/L), doxycycline (MIC &lt;0.25–1 mg/L) and linezolid (MIC &lt;0.25–2 mg/L), 90% to ciprofloxacin (MIC &lt;0.25–2 mg/L), 80% to ceftriaxone (MIC &lt;0.5 to &gt;64 mg/L) and imipenem (MIC &lt;0.25–32 mg/L) and only 20% to amoxicillin (MIC &lt;0.5 to &gt;64 mg/L) and rifampicin (MIC 0.5 to &gt;32 mg/L).

Conclusions
Determinations of MICs by visual readings of colour changes versus spectrophotometric readings were comparable. This convenient visual reading has the advantage of feasible implementation in endemic settings.