bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antagonistic action of GPS2 and KDM1A at enhancers governs alternative macrophage activation by interleukin 4
Authors: Huang Zhiqiang , Efthymiadou Astradeni , Liang Ning , Fan Rongrong , Treuter Eckardt 
Published: January 2023

AbstractThe Th2 cytokine interleukin 4 (IL4) promotes macrophage differentiation into alternative subtypes and plays important roles in physiology, in metabolic and inflammatory diseases, in cancer and in tissue regeneration. While the regulatory transcription factor networks governing IL4 signaling are already well-characterized, it is currently less understood which transcriptional coregulators are involved and how they operate mechanistically. In this study, we discover that G protein pathway suppressor 2 (GPS2), a core subunit of the HDAC3 corepressor complex assembled by SMRT and NCOR, represses IL4-dependent enhancer activation in mouse macrophages. Our genome-wide and gene-specific characterization revealed that, instead of directly repressing STAT6, chromatin-bound GPS2 cooperates with SMRT and NCOR to antagonize enhancer activation by lysine demethylase 1A (KDM1A, LSD1). Mechanistically, corepressor depletion increased KDM1A recruitment to enhancers linked to IL4-induced genes, accompanied by demethylation of the repressive histone marks H3K9me2/3 without affecting H3K4me1/2, the classic KDM1A substrates for demethylation in other cellular contexts. This in turn caused enhancer and gene activation already in the absence of IL4/STAT6 and sensitized the STAT6-dependent IL4 responsiveness of macrophages. Thus, our work identified with the antagonistic action of a GPS2-containing corepressor complex and the lysine demethylase KDM1A a hitherto unknown epigenetic corepressor-coactivator switching mechanism that governs alternative macrophage activation.
Structural basis of Qng1-mediated salvage of the micronutrient queuine from queuosine-5′-monophosphate as the biological substrate
Authors: Hung Shr-Hau , Elliott Gregory I , Ramkumar Thakku R , Burtnyak Lyubomyr , McGrenaghan Callum J , Alkuzweny Sana , Quaiyum Samia , Iwata-Reuyl Dirk , Pan Xiaobei , Green Brian D , Kelly Vincent P , de Crécy-Lagard Valérie , Swairjo Manal A 
Published: January 2023

Abstract
Eukaryotic life benefits from—and ofttimes critically relies upon—the de novo biosynthesis and supply of vitamins and micronutrients from bacteria. The micronutrient queuosine (Q), derived from diet and/or the gut microbiome, is used as a source of the nucleobase queuine, which once incorporated into the anticodon of tRNA contributes to translational efficiency and accuracy. Here, we report high-resolution, substrate-bound crystal structures of the Sphaerobacter thermophilus queuine salvage protein Qng1 (formerly DUF2419) and of its human ortholog QNG1 (C9orf64), which together with biochemical and genetic evidence demonstrate its function as the hydrolase releasing queuine from queuosine-5′-monophosphate as the biological substrate. We also show that QNG1 is highly expressed in the liver, with implications for Q salvage and recycling. The essential role of this family of hydrolases in supplying queuine in eukaryotes places it at the nexus of numerous (patho)physiological processes associated with queuine deficiency, including altered metabolism, proliferation, differentiation and cancer progression.
Hypothalamic-pituitary-gonadal function, pubertal development, and fertility outcomes in male and female medulloblastoma survivors: a single-center experience
Authors: Stern Eve , Ben-Ami Michal , Gruber Noah  , Toren Amos , Caspi Shani , Abebe-Campino Gadi , Lurye Michal , Yalon Michal , Modan-Moses Dalit 
Published: January 2023

Abstract

Background
Endocrine deficiencies, including hypothalamic-pituitary-gonadal axis (HPGA) impairment, are common in survivors of childhood and adolescent medulloblastoma. Still, data regarding pubertal development and fecundity are limited, and few studies assessed HPGA function in males. We aimed to describe HPGA function in a large cohort of patients with medulloblastoma.

Methods
A retrospective study comprising all 62 medulloblastoma patients treated in our center between 1987 and 2021, who were at least 2 years from completion of therapy. HPGA function was assessed based on clinical data, biochemical markers, and questionnaires.

Results
Overall, 76% of female patients had clinical or biochemical evidence of HPGA dysfunction. Biochemical evidence of diminished ovarian reserve was seen in all prepubertal girls (n = 4). Among the males, 34% had clinical or biochemical evidence of gonadal dysfunction, 34% had normal function, and 29% were age-appropriately clinically and biochemically prepubertal. The difference between males and females was significant (P = .003). Cyclophosphamide-equivalent dose was significantly associated with HPGA function in females, but not in males. There was no association between HPGA dysfunction and other endocrine deficiencies, length of follow-up, weight status, and radiation treatment protocol. Two female and 2 male patients achieved successful pregnancies, resulting in 6 live births.

Conclusions
HPGA dysfunction is common after treatment for childhood medulloblastoma. This is seen more in females, likely due to damage to the ovaries from spinal radiotherapy. Our findings may assist in counseling patients and their families regarding risk to future fertility and need for fertility preservation.
Collagen deposition within brain metastases is associated with leptomeningeal failure after &#x2028;cavity-directed radiosurgery
Authors: Abdulhaleem Mohammed , Ruiz Jimmy , O’Neill Stacey , Hughes Ryan T , Qasem Shadi , Strowd Roy E , Furdui Cristina , Watabe Konousuke , Miller Lance D , Debinski Waldemar , Tatter Stephen , Metheny-Barlow Linda , White Jaclyn J , Lee Jingyun , McTyre Emory R , Laxton Adrian , Chan Michael D , Su Jing , Soike Michael H 
Published: January 2023

Abstract

Background
Leptomeningeal failure (LMF) represents a devastating progression of disease following resection of brain metastases (BrM). We sought to identify a biomarker at time of BrM resection that predicts for LMF using mass spectrometry-based proteomic analysis of resected BrM and to translate this finding with histochemical assays.

Methods
We retrospectively reviewed 39 patients with proteomic data available from resected BrM. We performed an unsupervised analysis with false discovery rate adjustment (FDR) to compare proteomic signature of BrM from patients that developed LMF versus those that did not. Based on proteomic analysis, we applied trichrome stain to a total of 55 patients who specifically underwent resection and adjuvant radiosurgery. We used competing risks regression to assess predictors of LMF.

Results
Of 39 patients with proteomic data, FDR revealed type I collagen-alpha-1 (COL1A1, P = .045) was associated with LMF. The degree of trichrome stain in each block correlated with COL1A1 expression (β = 1.849, P = .001). In a cohort of 55 patients, a higher degree of trichrome staining was associated with an increased hazard of LMF in resected BrM (Hazard Ratio 1.58, 95% CI 1.11–2.26, P = .01).

Conclusion
The degree of trichrome staining correlated with COL1A1 and portended a higher risk of LMF in patients with resected brain metastases treated with adjuvant radiosurgery. Collagen deposition and degree of fibrosis may be able to serve as a biomarker for LMF.
Cannabis Use Is Associated With Decreased Antiretroviral Therapy Adherence Among Older Adults With HIV
Authors: Manuzak Jennifer A , Granche Janeway , Tassiopoulos Katherine , Rower Joseph E , Knox Justin R , Williams Dionna W , Ellis Ronald J , Goodkin Karl , Sharma Anjali , Erlandson Kristine M ,   for the AIDS Clinical Trials Group (ACTG) A5322 Study Team
Published: January 2023

Abstract

Background
Conflicting evidence exists on the impact of cannabis use on antiretroviral therapy (ART) adherence among people with human immunodeficiency virus (PWH). We leveraged data collected among older PWH to characterize longitudinal associations between cannabis use and ART adherence.

Methods
AIDS Clinical Trials Group (ACTG) A5322 study participants were categorized as &lt;100% (≥1 missed dose in past 7 days) or 100% (no missed doses) ART adherent. Participants self-reported current (past month), intermittent (past year but not past month), and no cannabis (in past year) use at each study visit. Generalized linear models using generalized estimating equations were fit and inverse probability weighting was used to adjust for time-varying confounders and loss to follow-up.

Results
Among 1011 participants (median age, 51 years), 18% reported current, 6% intermittent, and 76% no cannabis use at baseline; 88% reported 100% ART adherence. Current cannabis users were more likely to be &lt;100% adherent than nonusers (adjusted risk ratio [aRR], 1.53 [95% CI, 1.11–2.10]). There was no association between ART adherence and current versus intermittent (aRR, 1.39 [95% CI, .85–2.28]) or intermittent versus no cannabis use (aRR, 1.04 [95% CI, .62–1.73]).

Conclusions
Among a cohort of older PWH, current cannabis users had a higher risk of &lt;100% ART adherence compared to nonusers. These findings have important clinical implications as suboptimal ART adherence is associated with ART drug resistance, virologic failure, and elevated risk for mortality. Further research is needed to elucidate the mechanisms by which cannabis use decreases ART adherence in older PWH and to advance the development of more efficacious methods to mitigate nonadherence in this vulnerable population.
Laboratory Evaluation Links Some False-Positive COVID-19 Antigen Test Results Observed in a Field Study to a Specific Lot of Test Strips
Authors: Carter Alyssa M , Viloria Winnett Alexander , Romano Anna E , Akana Reid , Shelby Natasha , Ismagilov Rustem F 
Published: January 2023

Abstract
During a household-transmission field study using COVID-19 antigen rapid diagnostic tests (Ag-RDT), a common test strip lot was identified among 3 participants with false-positive results. In blinded laboratory evaluation, this lot exhibited a significantly higher false-positive rate than other lots. Because a positive Ag-RDT result often prompts action, reducing lot-specific false positives can maintain confidence and actionability of true-positive Ag-RDT results.
High Prevalence of Hepatitis B Virus Infection Among People With HIV in Rural and Periurban Communities in Botswana
Authors: Phinius Bonolo B , Anderson Motswedi , Gobe Irene , Mokomane Margaret , Choga Wonderful T , Mutenga Sharon R , Mpebe Gorata , Pretorius-Holme Molly , Musonda Rosemary , Gaolathe Tendani , Mmalane Mompati , Shapiro Roger , Makhema Joseph , Lockman Shahin , Novitsky Vlad , Essex Max , Moyo Sikhulile , Gaseitsiwe Simani 
Published: January 2023

Abstract

Background
We aimed to determine the prevalence of hepatitis B virus (HBV) infection among people with human immunodeficiency virus (PWH) in rural and periurban communities in Botswana.

Methods
PWH from a previous population-based study, the Botswana Prevention Combination Project, which enrolled adults in 30 communities across Botswana (2013–2018), were screened for HBV surface antigen (HBsAg) and HBV core antibody (anti-HBc). HBsAg-positive (HBsAg+) samples were further screened for HBV core immunoglobulin M antibodies (anti-HBc immunoglobulin M [IgM]) and HBV e antigen (HBeAg). We quantified HBV viral load on participants who tested positive (n = 148) and negative for HBsAg (n = 381).

Results
Of 3304 participants tested, 271 (8% [95% confidence interval {CI}, 7%–9%]) were HBsAg+ while 1788 (56% [95% CI, 54%–57%]) of 3218 PWH whom we tested had positive anti-HBc. Approximately 88% of HBsAg+ participants were on antiretroviral therapy (ART), 40% and 56% of whom were receiving lamivudine- and tenofovir-containing ART, respectively. Male sex (relative risk ratio [RRR], 1.8 [95% CI, 1.2–2.7]) and the northern geographic region (RRR, 2.5 [95% CI, 1.4–4.7]) were independent predictors of HBV infection (HBsAg+). Of 381 persons with negative HBsAg who were tested for occult HBV, 126 (33% [95% CI, 29%–38%]) had positive HBV DNA. Eleven participants were highly viremic with high HBV viral load while on a lamivudine- or tenofovir-containing regimen. Ten (91%) of these participants also had positive HBeAg serology, while 4 (36%) had positive anti-HBc IgM serology.

Conclusions
The prevalence of HBV was high among PWH in Botswana while on ART regimens with activity against HBV.
Challenges in Harnessing Shared Within-Host Severe Acute Respiratory Syndrome Coronavirus 2 Variation for Transmission Inference
Authors: Walter Katharine S , Kim Eugene , Verma Renu , Altamirano Jonathan , Leary Sean , Carrington Yuan J , Jagannathan Prasanna , Singh Upinder , Holubar Marisa , Subramanian Aruna , Khosla Chaitan , Maldonado Yvonne , Andrews Jason R 
Published: January 2023

Abstract

Background
The limited variation observed among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) consensus sequences makes it difficult to reconstruct transmission linkages in outbreak settings. Previous studies have recovered variation within individual SARS-CoV-2 infections but have not yet measured the informativeness of within-host variation for transmission inference.

Methods
We performed tiled amplicon sequencing on 307 SARS-CoV-2 samples, including 130 samples from 32 individuals in 14 households and 47 longitudinally sampled individuals, from 4 prospective studies with household membership data, a proxy for transmission linkage.

Results
Consensus sequences from households had limited diversity (mean pairwise distance, 3.06 single-nucleotide polymorphisms [SNPs]; range, 0–40). Most (83.1%, 255 of 307) samples harbored at least 1 intrahost single-nucleotide variant ([iSNV] median, 117; interquartile range [IQR], 17–208), above a minor allele frequency threshold of 0.2%. Pairs in the same household shared significantly more iSNVs (mean, 1.20 iSNVs; 95% confidence interval [CI], 1.02–1.39) than did pairs in different households infected with the same viral clade (mean, 0.31 iSNVs; 95% CI, .28–.34), a signal that decreases with increasingly stringent minor allele frequency thresholds. The number of shared iSNVs was significantly associated with an increased odds of household membership (adjusted odds ratio, 1.35; 95% CI, 1.23–1.49). However, the poor concordance of iSNVs detected across sequencing replicates (24.8% and 35.0% above a 0.2% and 1% threshold) confirms technical concerns that current sequencing and bioinformatic workflows do not consistently recover low-frequency within-host variants.

Conclusions
Shared within-host variation may augment the information in consensus sequences for predicting transmission linkages. Improving sensitivity and specificity of within-host variant identification will improve the informativeness of within-host variation.
Partial-Oral Antibiotic Therapy for Bone and Joint Infections in People With Recent Injection Drug Use
Authors: Yang Wei-Teng , Dombrowski Julia C , Glick Sara N , Kim H Nina , Beieler Alison M , Lan Kristine F , Dhanireddy Shireesha 
Published: January 2023

Abstract

Background
Limited outcome data exist regarding partial-oral antibiotic therapy, defined as oral antibiotics as part of a patient's treatment, for bone and joint infections (BJIs) in people who inject drugs (PWID).

Methods
We conducted a retrospective study of all PWID reporting drug use within 3 months and BJIs requiring ≥6 weeks of antibiotics in an urban safety-net hospital between February 1, 2019, and February 1, 2021. Treatment outcomes were assessed by chart review. Rates of failure, defined as death, symptoms, or signs concerning for worsening or recurrent infections, were assessed 90 and 180 days after completion of antibiotics. Univariate logistic regression was used to explore the association between covariates and failure.

Results
Of 705 patients with BJI, 88 (13%) were PWID. Eighty-six patients were included in the final cohort. Forty-four (51%) were homeless, 50 (58%) had spine infection, 68 (79%) had surgery, and 32 of 68 (47%) had postoperatively retained hardware. Twelve (14%) of 86 patients received exclusively intravenous (IV) antibiotics, and 74 (86%) received partial-oral antibiotics. Twelve (14%) of 86 patients had patient-directed discharge. In those who received partial-oral antibiotics, the failure rate was 20% at 90 days and 21% at 180 days after completion of intended treatment. Discharge to a medical respite and follow-up with infectious diseases (ID) or surgery were negatively associated with odds of failure.

Conclusions
Partial-oral treatment of BJI in PWID was a common practice and often successful when paired with medical respite and follow-up with ID or surgery.
Monkeypox Vaccination Strategy and Missed Opportunities in STI and HIV Prevention: An Urban Sexual Health Clinic's Experience During a Public Health Emergency
Authors: Stewart Jessica , Bartkus Mary , Sperring Heather , Ruiz-Mercado Glorimar , Johnson Samantha , Pierre Cassandra 
Published: January 2023

Abstract
Among individuals presenting for monkeypox vaccination, transition from an opt-out protocol for sexually transmitted infection (STI) and HIV risk assessment and testing to an opt-in protocol was associated with a substantial increase in missed opportunities for HIV pre-exposure prophylaxis and STI testing at an ambulatory sexual health clinic.
Using an online community of practice to explore the informal use of mobile phones by health workers
Authors: Glenton Claire , Nabukenya Josephine , Agarwal Smisha , Meltzer Michele , Mukendi Elisabeth , Lwanga Immaculate Nakityo , Namitala Josephine , Reddy Sunanda , Royston Geoff , Tamrat Tigest , Pakenham-Walsh Neil 
Published: January 2023

Abstract
Health workers are increasingly harnessing mobile phones to develop their own solutions to work challenges. The mHEALTH-INNOVATE project aims to explore this topic further. In 2022, Healthcare Information for All organized an online discussion among health workers and other stakeholders to inform the project. Twenty-five people joined the discussion. Contributors’ descriptions of the varieties of mobile phone use tallied with previous research, including for communication with patients and colleagues. In addition, they described increased mobile phone use in response to the COVID-19 pandemic and the increased need for communication, monitoring and reporting, including during lockdowns. Some solutions were health worker-initiated, including the establishment of WhatsApp groups. The discussion has helped develop a definition of informal mobile phone use.
Determining influences of different stirring methods for encapsulating stearic acid with SiO2 shell for thermal energy storage applications
Authors: Şahan Nurten , Nigon Daniel , Mantell Susan C , Davidson Jane H , Paksoy Halime 
Published: January 2023

ABSTRACTStearic acid was encapsulated successfully with SiO2 shell in nanoscale by in situ emulsion interfacial hydrolysis and poly-condensation techniques. The influence of using different mixing techniques on these techniques was investigated. Morphologic, thermal and crystal structure analysis results show that the ultrasonic mixing technique is suggested for synthesis of SiO2 nanocapsules. Ultrasonic vibrations lead to more homogeneous covering of the oil droplets without residuals by effectively orienting SiO2 molecules during polymerization.
Female and male plumage brightness is positively correlated among populations of the dichromatic Variable Seedeater
Authors: Ocampo Diego , Barrantes Gilbert , Uy J Albert C 
Published: January 2023

AbstractBecause studies of plumage coloration often focus on highly elaborate and conspicuous males, little is known about the factors driving theevolution of drab plumage in females of dichromatic species. We explored variation in the color properties of drab female plumage across subspecies of the Variable Seedeater (Sporophila corvina) and found a correlation between plumage brightness of male and female plumage patches. This correlation is consistent with the hypothesis that differences in plumage brightness among females result, at least partially, from a genetic correlation or shared developmental pathway with the more conspicuous male plumage traits that are shaped by sexual selection. Furthermore, we modeled the perception of female plumage using the avian visual system and found that most of the variation in color among females is undetectable by birds; therefore, it is unlikely for such variation to have evolved via direct sexual selection as a signal for recognition or assortative mating. Together, these results suggest that variation in S. corvina female color result from non-adaptive processes. However, we found a reduced variation on color of dorsal patches compared with that of ventral patches among females, which could be explained by natural selection on crypsis, reducing the variation on dorsal patches. Finally, we found little differences in plumage color between adult females and juveniles, which suggest selection for juveniles to resemble adult females possibly to reduce aggression from adult males. Additional within-population studies and behavioral experiments are needed to discern the evolutionary factors driving variation on S. corvina female color and its function.
Pseudo-observation of spiral galaxies in the radio band to verify depolarization models
Authors: Tashima Yuta , Ohmura Takumi , Machida Mami 
Published: January 2023

AbstractStudies of the three-dimensional structures of galactic magnetic fields are now entering a new era, with broad-band, highly sensitive radio observations and new analysis methods. To reveal the magnetic field configuration from the observed intensities integrated along the line of sight, it is necessary to derive an appropriate model involving various combinations of parameters that can reproduce the same observational characteristics. We aim to clarify the relationship between the radiation field and the spatial distribution of physical quantities through pseudo-observations using global three-dimensional magnetohydrodynamics (MHD) simulation results. In particular, we focus here on using the depolarization effect, which is important in the meter-wave band, to verify the polarization model and to identify the emission region. First, we show that wavelength-independent depolarization, which takes into account anisotropic turbulence, does not work efficiently because the polarized emission is stronger in regions of ordered spiral fields than in regions dominated by isotropic turbulent fields. Beam depolarization, specifically internal depolarization, becomes more effective below 1 GHz. Although in and close to the equatorial plane there will be strong depolarization that increases with observing wavelength, this effect is less in the halo, making halo magnetic fields detectable through their polarized emission at meter-wavelength bands. Although polarized emission from the halo is below the detection limit of current facilities, it will be detectable within the Square Kilometer Array era. In addition, we find that the spiral polarization projected on a screen is produced by overlapping magnetic flux tubes extending to different heights from the equatorial plane. This suggests that the traditional classification of global magnetic fields has difficulty reproducing the global structure of the magnetic fields. Finally, we demonstrate the method to separate magnetic flux tubes at different heights by using peak frequencies that cause the decrease of polarized flux.