bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pediatric HIV Disclosure Intervention Improves Immunologic Outcome at 48 Weeks: The Sankofa Trial Experience
Authors: Shabanova Veronika , Emuren Leonard , Gan Geliang , Antwi Sampson , Renner Lorna , Amissah Kofi , Kusah Jonas Tettey , Lartey Margaret , Reynolds Nancy R. , Paintsil Elijah ,   on behalf of the Sankofa Study Team
Published: August 2023

Background:
The World Health Organization recommends disclosure of HIV status to children and adolescents living with HIV (CALWH). HIV disclosure improves adherence to antiretroviral therapy and immunologic and virologic outcomes. However, the prevalence of HIV disclosure is low in sub-Saharan Africa. We assessed the longitudinal effect of the Sankofa Pediatric HIV disclosure intervention on immunologic and virologic outcomes among CALWH in Ghana.

Methods:
We conducted a secondary analysis of a two-arm site-randomized clinical trial among CALWH aged 7–18 years. Data were collected at baseline, 24, and 48 weeks. Generalized linear mixed models were used to compare immunologic (CD4) and virologic (viral load) outcomes as both continuous and categorical variables by disclosure status and by intervention group.

Results:
Among participants who had their HIV status disclosed during this study, the proportion with CD4 percent >25% increased from 56.5% at baseline to 75.4% at week 48 (P = 0.03), with a slight increase in the undisclosed group (69.5% vs. 74.3%, P = 0.56). In the intervention arm, there was a steady increase in proportion with CD4 percent >25% from 47.1% at baseline to 67.8% at week 48 (P = 0.01) while it remained unchanged in the control arm (80.5% vs. 81.3% [P = 0.89]). Concurrently, declines in detectable viral load were observed in both disclosed (63.3% vs. 51.5%, P = 0.16) and undisclosed (69.9% vs. 62.0%, P = 0.17) groups while the intervention group experienced a meaningful drop from 72.9% to 57.6% at 24 weeks (P = 0.04), which was maintained at 48 weeks.

Conclusions:
A structured, culturally relevant disclosure intervention can improve clinical outcomes.
Virtual Surgical Planning in Craniosynostosis Reduces Operative Time and Length of Stay for Cranial Vault Remodeling
Authors: Almeida Mariana N. , Alper David P. , Williams Mica C.G. , Ihnat Jacqueline M.H. , Parikh Neil , Diluna Michael , Alperovich Michael 
Published: August 2023

Cranial vault remodeling (CVR) with and without frontal orbital advancement remodels the skull in craniosynostosis. Virtual surgical planning (VSP) for preoperative planning has been previously shown to be effective in CVR. In this study, the authors aimed to evaluate the impact of VSP on operative and perioperative efficiency for craniosynostosis surgery. A retrospective chart review was conducted of patients with craniosynostosis who underwent CVR. Patient demographics, perioperative variables, use of VSP, and complications were obtained. Perioperative variables collected include operative time and length of stay. An independent t test was used to compare variables from patients who had surgery with VSP and patients who did not. Records were available for 126 patients with craniosynostosis who underwent CVR of whom 79 (62.7%) utilized VSP. There was no difference in average age at surgery (9.3±5.7 mo versus 13.2±31.1 mo, P=0.39). Surgeries planned using VSP demonstrated a decreased operative time of 1.3 hours (3.7±1.1 versus 5.0±1.1 h, P<0.001) and a shorter length of stay (3.9±1.3 versus 4.6±1.7 d, P=0.01). There were no differences in complication rates of dehiscence, infection, returns to the operating room, or 30-day readmission. These trends were similar among patients who underwent fronto-orbital advancement in addition to CVR. Virtual surgical planning was associated with decreased operative time and length of stay for patients with craniosynostosis and comparable complication rates. Virtual surgical planning is an effective tool for reducing anesthetic exposure time.
Impact of Community Socioeconomic Distress on Survival Following Heart Transplantation
Authors: Sakowitz Sara , Bakhtiyar Syed Shahyan , Mallick Saad , Curry Joanna , Ascandar Nameer , Benharash Peyman 
Published: August 2023

Objective:To assess the impact of community-level socioeconomic deprivation on survival outcomes following heart transplantation.Background:Despite growing awareness of socioeconomic disparities in the U.S. healthcare system, significant inequities in outcomes remain. While recent literature has increasingly considered the effects of structural socioeconomic deprivation, the impact of community socioeconomic distress on outcomes following heart transplantation has not yet been elucidated.Methods:All adult heart transplant recipients from 2004-2022 were ascertained from the Organ Procurement and Transplantation Network. Community socioeconomic distress was assessed using the previously-validated Distressed Communities Index, a metric that represents education level, housing vacancies, unemployment, poverty rate, median household income, and business growth by zip code. Communities in the highest quintile were considered theDistressedcohort (others:Non-Distressed). Outcomes were considered across two eras (2004-2018 and 2019-2022) to account for the 2018 UNOS Policy Change. 3- and 5-year patient and graft survival were assessed using Kaplan-Meier and Cox proportional hazards models.Results:Of 36,777 heart transplants, 7,450 (20%) were consideredDistressed. Following adjustment,Distressedrecipients demonstrated greater hazard of 5-year mortality from 2004-2018 (Hazard Ratio [HR] 1.10, confidence interval [CI] 1.03-1.18;P=0.005) and 3-year mortality from 2019-2022 (HR 1.29, CI 1.10-1.51;P=0.002), relative toNon-Distressed. Similarly, theDistressedgroup was associated with increased hazard of graft failure at 5-years from 2004-2018 (HR 1.10, CI 1.03-1.18;P=0.003) and at 3-years from 2019-2022 (HR 1.31, CI 1.11-1.53;P=0.001).Conclusions:Community-level socioeconomic deprivation is linked with inferior patient and graft survival following heart transplantation. Future interventions are needed to address pervasive socioeconomic inequities in transplantation outcomes.
Reply to: Contribution of carbon inputs to soil carbon accumulation cannot be neglected
Authors: Tao Feng , Houlton Benjamin Z. , Frey Serita D. , Lehmann Johannes , Manzoni Stefano , Huang Yuanyuan , Jiang Lifen , Mishra Umakant , Hungate Bruce A. , Schmidt Michael W. I. , Reichstein Markus , Carvalhais Nuno , Ciais Philippe , Wang Ying-Ping , Ahrens Bernhard , Hugelius Gustaf , Hocking Toby D. , Lu Xingjie , Shi Zheng , Viatkin Kostiantyn , Vargas Ronald , Yigini Yusuf , Omuto Christian , Malik Ashish A. , Peralta Guillermo , Cuevas-Corona Rosa , Paolo Luciano E. Di , Luotto Isabel , Liao Cuijuan , Liang Yi-Shuang , Saynes Vinisa S. , Huang Xiaomeng , Luo Yiqi 
Published: August 2023

AbstractIn the accompanying Comment1, He et al. argue that the determinant role of microbial carbon use efficiency in global soil organic carbon (SOC) storage shown in Tao et al. (2023)2was overestimated because carbon inputs were neglected in our data analysis while they suggest that our model-based analysis could be biased and model-dependent. Their argument is based on a different choice of independent variables in the data analysis and a sensitivity analysis of two process-based models other than that used in our study. We agree that both carbon inputs and outputs (as mediated by microbial processes) matter when predicting SOC storage – the question is their relative contributions. While we encourage further studies to examine how the evaluation of the relative importance of CUE to global SOC storage may vary with different model structures, He et al.’s claims about Tao et al. (2023) need to be taken as an alternative, unproven hypothesis until empirical data support their specific parameterization. Here we show that an additional literature assessment of global data does not support He et al.’s argument, in contrast to our study, and that further study on this topic is essential.
Bivariate joint modelling for mixed continuous and binary responses in the presence of non-monotone, non-ignorable missingness: The case of prostate cancer
Authors: Liaqat Madiha , Kamal Shahid , Fischer Florian 
Published: August 2023

AbstractJoint modelling for mixed longitudinal responses has played a prominent part in disease decision-making. It is based on a joint strategy of estimating joint likelihood with shared random effects. Non-ignorable missingness in outcomes increases complexity in joint model; a shared parameter model is proposed to incorporate non-ignorable missing data for joint modelling of longitudinal responses and missing data mechanism. Parameters are estimated under the Bayesian paradigm and implemented via Markov chain Monte Carlo (MCMC) methods with Gibbs sampler. To demonstrate the effectiveness of the proposed method, the joint model is applied to analyze a prostate cancer dataset. The objective is to assess whether there is an association between two mixed longitudinal biomarkers, which could have important implications for understanding disease progression and guiding treatment decisions. The dataset contains non-monotone missingness pattern. To evaluate the performance and robustness of the proposed joint model, simulation studies are conducted.
Dissecting MPXV neurotropism and host antiviral signaling using human stem cell-based models
Authors: Bauer Lisa , Giussani Stefania , Palazzi Nicola , Bot Erik , Colombo Elisa , Zare Farnaz , Pinci Francesca , Leijten Lonneke , Lanko Kristina , Benavides Feline F.W. , Smeenk Hilde , Embregts Carmen W.E. , Spoor Jochem K.H. , Dirven Clemens , Gao Zhenyu , Bolleboom Anne , Verstrepen Babs E. , Schuele Leonard , de Vrij Femke M.S. , Kushner Steven A. , Oude Munnink Bas B. , Davila-Velderrain Jose , van Riel Debby , Harschnitz Oliver 
Published: August 2023

AbstractMpox is a zoonotic illness of international concern that can lead to severe disease including neurological sequelae. However, the neurotropism of monkeypox virus (MPXV) and the mechanisms regulating cell-intrinsic antiviral immunity within the central nervous system (CNS) remain poorly understood. Here, we investigated the neurotropism of MPXV using astrocytes, cortical neurons, and microglia derived from human pluripotent stem cells (hPSCs) andex vivohuman brain tissue to demonstrate that MPXV infects and replicates more efficiently in astrocytes and microglia compared to cortical neurons. Upon MPXV exposure, glial cells, in contrast to cortical neurons, inhibit type I IFN antiviral programs potentially conferring differential susceptibility to MPXV. Furthermore, we demonstrate that treatment using either IFN-beta or tecovirimat inhibits MPXV infection. Together, our results suggest that MPXV has a broad tropism within the CNS and that differential type I IFN signaling underpins cell type-specific susceptibility to MPXV infection.
Limited impact of lifting universal masks on SARS-COV-2 transmission in schools: The crucial role of outcome measurements
Authors: Li Mingwei , Yang Bingyi , Cowling Benjamin 
Published: August 2023

ABSTRACTAs the pandemic’s dynamics changed, many municipalities lifted face wearing requirement in school which was initially implemented to mitigate the transmission of COVID-19. This study examines the effects of lifting mask mandates on COVID-19 transmission within Massachusetts school districts. We first replicated previous research by Cowger et al. (2022) utilizing a Difference-in-Difference (DID) model. Then, we back project the case infection and calculate the Rt value to redo the DID analysis. However, when shifting the outcome measurement to the reproductive number (Rt), our findings suggest that lifting mask mandates can only significantly influence the Rt first two weeks post-intervention. This implies that while mask mandate plays a role in mitigation, its lifting does not drastically influence COVID-19 transmissibility in the long term.
Intravenous psilocybin administration attenuates mechanical hypersensitivity in a rat model of chronic pain
Authors: Kolbman Nicholas , Liu Tiecheng , Guzzo Peter , Gilligan Jim P. , Mashour George A. , Vanini Giancarlo , Pal Dinesh 
Published: August 2023

AbstractThere is a renewed interest in the therapeutic potential of psychedelics, including psilocybin, in treating mental health disorders. However, there are no data on the efficacy of psilocybin in alleviating chronic pain. In this study, we investigated the effect of psilocybin on mechanical hypersensitivity and thermal hyperalgesia in a rat model of formalin-induced chronic pain. Adult male and female rats were surgically implanted with a jugular vein catheter for psilocybin or saline administration. After two weeks of post-surgical recovery and conditioning, baseline responses to mechanical (von Frey assay) and thermal (hot plate assay) stimuli were measured. Twenty-four hours after baseline measurements, rats received a subcutaneous injection of formalin (5%, 50µL) into one of the hind paws and 2h later, responses to the mechanical and thermal stimuli were measured. Twenty-four hours after formalin injection, rats received an intravenous bolus of 1 mg/kg psilocybin (n=14) or 10 mg/kg psilocybin (n=12) or saline (n=13), and approximately 3h later, responses to the mechanical and thermal stimuli were measured. Rats were tested every other day during week 1, and then weekly for the next 3 weeks. Formalin injection induced thermal hyperalgesia and bilateral mechanical hypersensitivity in the hind paws of all rats. Intravenous psilocybin produced significant attenuation (p<0.05) of the formalin-induced bilateral mechanical hypersensitivity for 28 days but had limited effect (p<0.05 only on days 1, 3, 5, and 21) on thermal hyperalgesia. These data demonstrate that a single intravenous bolus of psilocybin can attenuate indices of chronic pain in a rat model.
Learning chemical sensitivity reveals mechanisms of cellular response
Authors: Connell William , Garcia Kristle , Goodarzi Hani , Keiser Michael J. 
Published: August 2023

AbstractChemical probes interrogate disease mechanisms at the molecular level by linking genetic changes to observable traits. However, comprehensive chemical screens in diverse biological models are impractical. To address this challenge, we developed ChemProbe, a model that predicts cellular sensitivity to hundreds of molecular probes and drugs by learning to combine transcriptomes and chemical structures. Using ChemProbe, we inferred the chemical sensitivity of cancer cell lines and tumor samples and analyzed how the model makes predictions. We retrospectively evaluated drug response predictions for precision breast cancer treatment and prospectively validated chemical sensitivity predictions in new cellular models, including a genetically modified cell line. Our model interpretation analysis identified transcriptome features reflecting compound targets and protein network modules, identifying genes that drive ferroptosis. ChemProbe is an interpretablein silicoscreening tool that allows researchers to measure cellular response to diverse compounds, facilitating research into molecular mechanisms of chemical sensitivity.
In situstructural insights into the excitation contraction coupling mechanism of skeletal muscle
Authors: Xu Jiashu , Liao Chenyi , Yin Chang-Cheng , Li Guohui , Zhu Yun , Sun Fei 
Published: August 2023

AbstractExcitation–contraction coupling (ECC) is a fundamental mechanism in control of skeletal muscle contraction and occurs at triad junctions, where dihydropyridine receptors (DHPRs) on transverse tubules sense excitation signals and then cause calcium release from the sarcoplasmic reticulum via coupling to type 1 ryanodine receptors (RyR1s), inducing the subsequent contraction of muscle filaments. However, the molecular mechanism remains unclear due to the lack of structural details. Here, we explored the nanometre-resolution architecture of triad junction by cryo-electron tomography, solved thein situstructure of RyR1 in complex with FKBP12 and calmodulin, and discovered the intact RyR1-DHPR supercomplex. RyR1s arrange into two rows on the terminal cisternae membrane by forming right-hand corner-to-corner contacts, and tetrads of DHPRs bind to RyR1s in an alternating manner, forming another two rows on the transverse tubule membrane. Such unique arrangement is important for synergistic calcium release and provides direct evidence of physical coupling in ECC.
The consumption of iceberg lettuce may reduce the adhesion of dietary fat to the mucus surface of the stomach barrier lining decreasing the risk of triggering acute gastroesophageal reflux
Authors: Hurr Thomas J. 
Published: August 2023

AbstractIceberg lettuce (IL) leaves contain surface epicuticular waxes that can adsorb significant quantities of dietary fat per unit weight. Fats such as olive oil, butter, lamb fat and lard readily adsorb onto IL with soft solid fats contained in lamb fat and lard, showing strong adhesion and more resistance to removal on rinsing in a water stream. Dishwashing detergents containing surfactants prevent the adsorption of both liquid and solid fats to the lettuce leaf surface, unless at very low concentrations, highlighting their significant influence on surface properties. Based on the adhesion of fats to the IL leaf surface, it is proposed the consumption of IL could reduce acute gastroesophageal reflux (GER) and the development of gastroesophageal reflux disease (GERD). In diets containing fat, the adhesion to IL reduces the amount of fat available to adhere to the mucus surface of the stomach barrier lining, protecting the lining and reducing access by trigger foods to underlying surfaces that could potentially initiate GER.Graphical abstractIceberg lettuce leaves have approximately twice the surface area of the stomach for a 50g serve and 500cm3meal volume and due to the waxy surface, can adsorb significant amounts of dietary fat. Lettuce may also adsorb on the mucus layer of the stomach barrier lining but is not regarded as a trigger food. Lettuce with its large surface area to adsorb fat, can keep fat suspended in solution, protecting the lining from fat adsorption and reducing the probability that fatty trigger foods can access underlying surfaces and cause acute gastroesophageal reflux.
Reference genome sequence of the solitary beeCamptopoeum frieseiMocsáry, 1894 (Hymenoptera, Andrenidae)
Authors: Stolle Eckart , Guiglielmoni Nadège , Kirangwa Joseph , Kukowka Sandra , Meitzel Tobias , Cartney Ann M. Mc , Heilmann-Heimbach Stefanie , Becker Kerstin , Köhrer Karl , Böhne Astrid 
Published: August 2023

AbstractBees are major pollinators of flowering plants and thus are important ecosystem service providers for natural habitats and crops. Evolution led to a wide range of adaptations in behaviors, morphology and ecological traits. Many plants rely on specialized bee species for pollination events, and so this interdependence can make them increasingly vulnerable to ongoing threats of habitat loss and pesticide exposure. Studying the genomes of bee species across different life histories and ecological specializations can help understand the evolution of these traits more generally, but also inform conservation efforts forCamptopoeum frieseispecifically.Here, we present the reference genome of the solitary beeCamptopoeum friesei(Arthropoda; Insecta; Hymenoptera; Andrenidae).C. frieseiis highly dependent on steppe habitats where it nests in saline soils. Further, it is highly specialized (oligolectic) on a few Asteraceae:CentaureaandCirsium, in particular onCentaurea stoebe. As a consequence of its high specialization level, it is of its ecological niche with an extremely scattered and rare habitat,C. frieseiis highly threatened in central Europe, albeit local aggregations can be rich in individuals.The high-quality genome assembly for the colourful beeCamptopoeum frieseiwas generated using long-read PacBio HiFi in combination with chromatin conformation capture (Hi-C) sequencing. The genome spans 367.7 megabases (Mb), N50 of 25.2 Mb. The majority of the assembly is scaffolded into 10 chromosomes and harbours ∼40% repeats.Species taxonomyEukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Anthophila; Andrenidae; Panurginae; Panurgini;Camptopoeum frieseiMocsáry, 1894 (NCBI:txid2918745)
Comparative Genomics Points to Tandem Duplications ofSADGene Clusters as Drivers of Increased ω-3 Content inS. hispanicaSeeds
Authors: Zare Tannaz , Paril Jeff F. , Barnett Emma M. , Kaur Parwinder , Appels Rudi , Ebert Berit , Roessner Ute , Fournier-Level Alexandre 
Published: August 2023

ABSTRACTA high-quality chromosome-level reference genome ofS. hispanicawas assembled and analysed.Ancestral whole-genome duplication events have not promoted the high α-linolenic acid content inS. hispanicaseedsTandem duplication of six stearoyl-ACP desaturase genes is a plausible cause for high ω-3 content in chia seeds.Salvia hispanicaL. (chia) is an abundant source of ω-3 polyunsaturated fatty acids (PUFAs) that are highly beneficial to human health. The genomic basis for this accrued PUFA content in this emerging crop was investigated through the assembly and comparative analysis of a chromosome-level reference genome forS. hispanica(321.5 Mbp). The highly contiguous 321.5Mbp genome assembly, which covers all six chromosomes enabled the identification of 32,922 protein coding genes. Two whole-genome duplications (WGD) events were identified in theS. hispanicalineage. However, these WGD events could not be linked to the high α-linolenic acid (ALA, ω-3) accumulation inS. hispanicaseeds based on phylogenomics. Instead, our analysis supports the hypothesis that evolutionary expansion through tandem duplications of specific lipid gene families, particularly the stearoyl-acyl carrier protein (ACP) desaturase (ShSAD) gene family, is the main driver of the abundance of ω-3 PUFAs inS. hispanicaseeds. The insights gained from the genomic analysis ofS. hispanicawill help leveraging advanced genome editing techniques and will greatly support breeding efforts for improving ω-3 content in other oil crops.
Social transmission of valence-linked new knowledge without firsthand experience in mice
Authors: Kim Ryang , Bito Haruhiko , Kitamura Takashi 
Published: August 2023

AbstractAnimals can acquire new knowledge by observing others’ contexts and behavior, a process called social learning, which is essential for animals to survive in nature. While the social transmission of food preference (STFP) was previously adopted as a social learning test, several studies pointed out that non-social parameters might influence its food preference. We re-evaluated critical steps in the STFP test and designed an improved social learning test, which we now refer to as social transmission of food finding (STFF). A significant advance in the STFF test is the demonstration that mice learned the odor-food relationship with either positive or negative valence from the demonstrator without prior experience in the observer. Furthermore, a circuit dissection experiment showed that hippocampal function was differentially involved during learning and recall for STFF. Thus, STFF constitutes a highly advantageous social learning model in which valence-linked new knowledge can be socially transmitted without firsthand experience.