bluuebunny/crossref_metadata_2025_split huggingface dataset:
The evolution of HIV-associated cryptococcal meningitis in Uganda from 2010 to 2022
Authors: Walukaga Stewart , Fieberg Ann , Musubire Abdu , Tugume Lillian , Ssebambulidde Kenneth , Kagimu Enock , Kasibante John , Rutakingirwa Morris K , Mpoza Edward , Gakuru Jane , Akampurira Andrew , Jjunju Samuel , Mwesigye James , Muzoora Conrad , Nuwagira Edwin , Bangdiwala Ananta S , Williams Darlisha A , Rhein Joshua , Meya David B , Boulware David R , Hullsiek Kathy Huppler , Rajasingham Radha ,   the ASTRO team, Ndyetukira Jane Francis , Ahimbisibwe Cynthia , Kugonza Florence , Namuju Carolyne , Sadiq Alisat , Namudde Alice , Mwesigye James , Cresswell Fiona V , Kandole Tadeo Kiiza , Kirumira Paul , Okirwoth Michael , Luggya Tony , Kwizera Richard , Mukaremera Liliane , Lofgren Sarah M , Stadelman Anna , Morawski Bozena , Rolfes Melissa A , Wiesner Darin L , Najjuka Grace , Nanteza Catherine , Mushagara Rhina , Bahr Nathan , Namawejje Mariam , Ssennono Mark , Kiragga Agnes , Taseera Kabanda , Nabeta Henry W 
Published: January 2025

Abstract
Given extensive improvements in access to antiretroviral therapy (ART) over the past 12 years, the HIV and cryptococcal meningitis landscapes have dramatically changed since 2010. We sought to evaluate changes in clinical presentation and clinical outcomes of people presenting with HIV-associated cryptococcal meningitis between 2010 and 2022 in Uganda. We analyzed three prospective cohorts of HIV-infected Ugandans with cryptococcal meningitis during 2010–2012, 2013–2017, and 2018–2022. We summarized baseline demographics, clinical characteristics at presentation, and 2-week and 16-week mortality. Overall, 2022 persons had confirmed cryptococcal meningitis between 2010 and 2022. In the most recent 2018–2022 cohort, 48% presented as ART-naïve, and the median CD4 cell count was 26 cells/µl. Participants in the 2018–2022 cohort had the lowest cerebrospinal fluid (CSF) opening pressure (median 22 cmH2O) and the highest percentage with sterile CSF quantitative cultures (21%) compared with earlier cohorts (P &lt; .001 for both), signifying a less severely ill population presenting with cryptococcal meningitis. Two-week mortality was lowest among participants with cryptococcal meningitis enrolled in a clinical trial in the 2018–2022 cohort at 13% compared to 26% in both 2010–2012 and 2013–2017 (P &lt; .001). While AIDS-related deaths have dramatically declined over the past 12 years, cryptococcosis persists, presenting challenges to HIV program implementation. Two-week mortality has improved in the most recent cohort, likely due to the establishment of cryptococcal screening programs, better supportive care including scheduled lumbar punctures, and the availability of flucytosine—an essential component of antifungal therapy.
Testing disc reprocessing models for AGN optical variability by comparison of X-ray and optical power spectra of NGC 4395
Authors: Beard M W J , MᶜHardy I M , Horne K , Cackett E M , Vincentelli F , Santisteban J V Hernández , Miller J , Dhillon V S , Knapen J H , Littlefair S P , Kynoch D , Breedt E , Shen Y , Gelbord J 
Published: January 2025

ABSTRACT
It is generally thought that active galactic nucleus (AGN) optical variability is produced, at least in part, by reprocessing of central X-rays by a surrounding accretion disc, resulting in wavelength-dependent lags between bands. Any good model of AGN optical variability should explain not only these lags, but also the overall pattern of variability as quantified by the power spectral density (PSD). Here, we present $\sim$daily g′-band monitoring of the low-mass AGN NGC 4395 over 3 yr. Together with previous Transiting Exoplanet Survey Satellite (TESS) and Gran Telescopio Canarias (GTC)/HiPERCAM observations, we produce an optical PSD covering an unprecedented frequency range of ∼seven decades allowing excellent determination of PSD parameters. The PSD is well fitted by a bending power law with low-frequency slope $\alpha _{L} = 1.0 \pm 0.2$, high-frequency slope $2.1^{+0.2}_{-0.4}$, and bend time-scale $3.0^{+6.6}_{-1.7}\,$ d. This time-scale is close to that derived previously from a damped random walk (DRW) model fitted to just the TESS observations, although $\alpha _{L}$ is too steep to be consistent with a DRW. We compare the observed PSD with one made from light curves synthesized assuming reprocessing of X-rays, as observed by XMM–Newton and Swift, in a disc defined by the observed lags. The simulated PSD is also well described by a bending power law but with a bend two decades higher in frequency. We conclude that the large-amplitude optical variations seen on long time-scales are not due to disc reprocessing but require a second source of variability whose origin is unknown but could be propagating disc accretion rate variations.
From Galaxy Zoo DECaLS to BASS/MzLS: detailed galaxy morphology classification with unsupervised domain adaption
Authors: Ye Renhao , Shen Shiyin , de Souza Rafael S , Xu Quanfeng , Chen Mi , Chen Zhu , Ishida Emille E O , Krone-Martins Alberto , Durgesh Rupesh 
Published: January 2025

ABSTRACT
The Dark Energy Spectroscopic Instrument Legacy Imaging Surveys (DESI-LIS) comprise three distinct surveys: the Dark Energy Camera Legacy Survey (DECaLS), the Beijing–Arizona Sky Survey (BASS), and the Mayall z-band Legacy Survey (MzLS). The citizen science project Galaxy Zoo DECaLS 5 (GZD-5) has provided extensive and detailed morphology labels for a sample of 253 287 galaxies within the DECaLS survey. This data set has been foundational for numerous deep learning-based galaxy morphology classification studies. However, due to differences in signal-to-noise ratios and resolutions between the DECaLS images and those from BASS and MzLS (collectively referred to as BMz), a neural network trained on DECaLS images cannot be directly applied to BMz images due to distributional mismatch. In this study, we explore an unsupervised domain adaptation (UDA) method that fine-tunes a source domain model trained on DECaLS images with GZD-5 labels to BMz images, aiming to reduce bias in galaxy morphology classification within the BMz survey. Our source domain model, used as a starting point for UDA, achieves performance on the DECaLS galaxies’ validation set comparable to the results of related works. For BMz galaxies, the fine-tuned target domain model significantly improves performance compared to the direct application of the source domain model, reaching a level comparable to that of the source domain. We also release a catalogue of detailed morphology classifications for 248 088 galaxies within the BMz survey, accompanied by usage recommendations.
Identifying components of care coordination for primary brain tumor: A scoping review
Authors: Jeon Megan S , Banks Hannah , He Sharon , Carlick Thomas , Shaw Joanne M , Kelly Brian , Koh Eng-Siew , Halkett Georgia K B , Ownsworth Tamara , Chan Raymond J , Pinkham Mark B , Sansom-Daly Ursula M , Dhillon Haryana M ,   for the BRAINS Investigator Group
Published: January 2025

Abstract
For people with primary brain tumors (PBT) and their carers, care coordination (CC) offers comprehensive, timely, person-centered care. This review aimed to systematically scope the breadth of literature relevant to approaches to CC for PBT. Four databases were searched (PubMed, PsycINFO, EMBASE, and CINAHL) for empirical research, and gray literature was searched for doctoral theses, clinical guidelines, and education resources for healthcare professionals (HCPs) related to the concept/model of CC in neuro-oncology. Data were systematically evaluated and synthesized following PRISMA-SCR guidelines. From 1163 screened abstracts, 30 eligible reports were reviewed (13 addressed CC interventions, 9 narrative reports, 5 describing CC/navigator positions, and 3 clinical guidelines). Most reports described nurse-led models of care within single tertiary care centers in metropolitan settings: a single HCP acting as primary contact, educator, and liaison, screening patient/carer distress and providing referrals as key components of CC. Clinical guidelines emphasize healthcare system navigation and access to medical care in CC. A CC approach overseeing the whole PBT trajectory was lacking. Facilitators of CC included availability of HCP dedicated to CC; HCPs’ competency in relationship-based and communication skills; and improved access to resources. System-level and resource barriers to CC were identified. Knowledge about CC is largely based on descriptions of nurse-led models of PBT care. Further research is required to refine the framework of CC reflecting factors of known importance in PBT care, and identify training and support needs of HCPs who may play a pivotal role in current models of neuro-oncology CC.
Enhancing the Design of Nutrient Clinical Trials for Disease Prevention—A Focus on Vitamin D: A Systematic Review
Authors: Wimalawansa Sunil J 
Published: January 2025

Abstract

Objectives
This systematic review (SR) highlights principles for nutrient clinical trials and explore the diverse physiological functions of vitamin D beyond its traditional role in the musculoskeletal system related to clinical study designs.

Background
Thousands of published research articles have investigated the benefits of vitamin D (a nutrient example taken in this SR) beyond the musculoskeletal system, including the immune, pulmonary, and cardiovascular systems; pregnancy; autoimmune disorders; and cancer. They illustrated vitamin D's molecular mechanisms, interactions, and genomic and nongenomic actions.

Methods
This SR was designed to identify shortcomings in clinical study designs, statistical methods, and data interpretation that led to inconsistent findings in vitamin D–related publications. SR also highlights examples and insights into avoiding study design errors in future clinical studies, including randomized controlled clinical trials (RCTs). The SR adheres to the latest PRISMA statement, guidelines, and the PICOS process.

Results
Inappropriate or flawed study designs were frequent in clinical trials. Major failures discussed here include too short clinical study duration, inadequate or infrequent doses, insufficient statistical power, failure to measure baseline and achieved levels, and recruiting vitamin D–sufficient participants. These design errors have led to misleading interpretations. Thus, conclusions from such studies should not be generalized or used in guidelines, recommendations, or policymaking.

Conclusion
Adequately powered epidemiological studies and RCTs with sufficient vitamin D and duration in individuals with vitamin D deficiency reported favorable clinical outcomes, enriching the literature, enabling to understand its physiology and mechanisms. Proper study designs with rigorous methodologies and cautious interpretation of outcomes are crucial in advancing the nutrient field. The principles discussed apply not only to vitamin D, but also other micro-nutrients and nutraceutical research. Adhering to them enhances the credibility and reliability of clinical trials, SRs, and meta-analysis outcomes. The study emphasizes the importance of focused, hypothesis-driven, well-designed, statistically powered RCTs to explore the diverse benefits of nutrients, conducted in index nutrient deficient participants, and avoidance of study design errors. Findings from such studies should be incorporated into clinical practice, policymaking, and public health guidelines, improving the health of the nation and reducing healthcare costs.
Branched oligosaccharides cause atypical starch granule initiation in Arabidopsis chloroplasts
Authors: Heutinck Arvid J M , Camenisch Selina , Fischer-Stettler Michaela , Sharma Mayank , Pfister Barbara , Eicke Simona , Liu Chun , Zeeman Samuel C 
Published: January 2025

Abstract
Plant chloroplasts store starch during the day, which acts as a source of carbohydrates and energy at night. Starch granule initiation relies on the elongation of malto-oligosaccharide primers. In Arabidopsis thaliana, PROTEIN TARGETING TO STARCH 2 (PTST2) and STARCH SYNTHASE 4 (SS4) are essential for the selective binding and elongation of malto-oligosaccharide primers, respectively, and very few granules are initiated in their absence. However, the precise origin and metabolism of the primers remain unknown. Potential origins of malto-oligosaccharide primers include de novo biosynthesis or their release from existing starch granules. For example, the endoamylase α-AMYLASE 3 (AMY3) can cleave a range of malto-oligosaccharides from the granule surface during starch degradation at night, some of which are branched. In the Arabidopsis double mutant deficient in the two debranching enzymes ISOAMYLASE 3 (ISA3) and LIMIT DEXTRINASE (LDA), branched malto-oligosaccharides accumulate in the chloroplast stroma. Here, we reveal that the isa3 lda double mutant shows a substantial increase in granule number per chloroplast, caused by these branched malto-oligosaccharides. The amy3 isa3 lda triple mutant, which lacks branched malto-oligosaccharides, has far fewer granules than isa3 lda, and its granule numbers are barely higher than in the wild type. Plants lacking both ISA3 and LDA and either PTST2 or SS4 show granule over-initiation, indicating that this process occurs independently of the recently described granule initiation pathway. Our findings provide insight into how and where starch granules are initiated. This knowledge can be used to alter granule number and morphological characteristics, traits known to affect starch properties.
Recommendations For Mobilization and Manipulation Treatment and Screening for Vascular Complications in Clinical Practice Guidelines for Neck Pain: A Systematic Review
Authors: Peters Renske , Hallegraeff Joannes , Koes Bart , Van Trijffel Emiel 
Published: January 2025

Abstract

Objective
This systematic review aimed to determine the methodological quality of international clinical practice guidelines and the clinical credibility and implementability of recommendations regarding manipulation or mobilization treatment recommendations proposed in clinical practice guidelines for the management of people with neck pain. A secondary aim of this review was to provide an overview of recommendations for manipulation or mobilization in patients with neck pain. Manipulation or mobilization treatment of patients with neck pain is under debate for its potential risk of serious adverse events. Serious adverse events are rare, but it is the clinicians’ responsibility to thoroughly screen patients at risk of vascular complications. A third aim of this review was to describe the extent to which the included guidelines inform clinical practice about screening for the risk of complications due to vascular pathology in the cervical spine.

Methods
A systematic review of 13 electronic databases and 4 repositories was performed for potentially relevant guidelines published between January 1, 2000 and September 22, 2022. Two reviewers independently appraised eligible guidelines using Appraisal of Guidelines for Research and Evaluation II (AGREE II) and Appraisal of Guidelines for Research and Evaluation: Recommendation EXcellence (AGREE-REX) criteria. A best evidence synthesis was performed and screening of risk factors was assessed.

Results
A total of 19 clinical practice guidelines were included, of which 5 were of high quality. All high-quality guidelines recommend the use of manipulation or mobilization, with or without exercise. Eight (42%) guidelines described the screening of risk factors for adverse events. Two (11%) guidelines met the a priori defined criteria for screening and scored present and complete.

Conclusion
International clinical practice guidelines consistently recommend the use of manipulations and mobilizations in the treatment of neck pain. There is a notable absence of recommendations regarding the identification of patients at risk for vascular complications.

Impact
The findings of this study allow guideline developers to improve the quality of future neck pain guidelines, and to consider including vascular screening tools. Furthermore, it proposes recommendations to physical therapists interested in applying manipulations and mobilizations in the treatment of patients with neck pain.
Risk-based screening for the evaluation of atrial fibrillation in general practice (R-BEAT): a randomized cross-over trial
Authors: Murphy Robert , Waters Ruairi , Murphy Andrew , McDermott Suzanne , Reddin Catriona , Hernon Orlaith , Davies Naomi , Alvarez-Iglesias Alberto , Twomey Eamonn , O’Shea Eamon , Sloane Peter , Curran Joseph , Kiely Aoife , Waters Caitriona , Kilraine John , McDonagh Siobhan , Carney Adrian , Devane Declan , O’Donnell Martin 
Published: January 2025

Abstract

Background
The optimal approach to the diagnosis of atrial fibrillation in primary care is unclear.

Aim
To determine if external loop recorder (ELR) screening improves atrial fibrillation detection in community-dwelling adults with a CHA2DS2-VASc score of greater than two.

Design
Randomized cross-over clinical trial.

Methods
Community-dwelling adults ≥55 years with a CHA2DS2-VASc score of greater than two, who were deemed suitable for atrial fibrillation screening and oral anticoagulation by their general practitioner were randomly assigned to immediate or delayed ELR monitoring. The intervention period was ELR cardiac monitoring for 1 week and the usual care period was healthcare professional pulse screening and completion of electrocardiogram (ECG) or cardiac rhythm strip if pulse was identified as irregular.

Results
Of the 488 participants randomized, 244 were assigned to the immediate monitoring period (intervention) and 244 were assigned to the delayed monitoring period. Mean (SD) age was 75.0 (7.0) years and 333 participants were women (68%). Atrial fibrillation was detected in 32 of 488 participants (6.6%) in the intervention period versus five of 488 (1%) in the usual care period (absolute difference, 5.53% (3.2–7.9%), P &lt; 0.001; number needed to screen 15 (11–23)). Twelve cases (37.5%) of ELR-detected atrial fibrillation were greater than 24 h in duration. Oral anticoagulation was initiated in all participants (n = 32).

Conclusions
Among older community-dwelling adults with a CHA2DS2-VASc score of greater than two, screening with ELR for one week was associated with a 5.5% incremental detection of new atrial fibrillation over usual care.

Trial registration
ClinicalTrials.gov Register: NCT03911986
Inference with a Single Treated Cluster
Authors: Hagemann Andreas 
Published: January 2025

Abstract
I introduce a generic method for inference about a scalar parameter in research designs with a finite number of heterogeneous clusters where only a single cluster received treatment. This situation is commonplace in difference-in-differences estimation, but the test developed here applies more broadly. I show that the test controls size and has power under asymptotics where the number of observations within each cluster is large but the number of clusters is fixed. The test combines weighted, approximately Gaussian parameter estimates with a rearrangement procedure to obtain its critical values. The weights needed for most empirically relevant situations are tabulated in the paper. Calculation of the critical values is computationally simple and does not require simulation or resampling. The rearrangement test is highly robust to situations where some clusters are much more variable than others. Examples and an empirical application are provided.
Histone deacetylase 6 inhibition prevents hypercholesterolemia-induced erectile dysfunction independent of changes in markers of autophagy
Authors: Ihrig Colin M , Montgomery McLane M , Nomura Yohei , Nakano Mitsunori , Pandey Deepesh , La Favor Justin D 
Published: January 2025

Abstract

Background
Erectile dysfunction is a condition with a rapidly increasing prevalence globally with a strong correlation to the increase in obesity and cardiovascular disease rates.

Aim
The aim of the current study is to investigate the potential role of tubacin, a histone deacetylase 6 (HDAC6) inhibitor, in restoring erectile function in a hypercholesterolemia-induced endothelial dysfunction model.

Methods
Thirty-nine male C57Bl/6 J mice were divided into 3 groups. Two groups were administered an adeno-associated virus encoding for the gain of function of proprotein convertase subtilisin/kexin type 9 (PCSK9) and placed on a high-fat diet (HFD) with 1.25% cholesterol added for 18 weeks in order to induce a prolonged state of hypercholesterolemia. One of the PCSK9 groups received daily intraperitoneal injections of the HDAC6 inhibitor tubacin, while the other 2 groups received daily vehicle injections. Erectile function was assessed through measurement of intracavernosal pressure and mean arterial pressure during cavernous nerve stimulation, as well as assessment of agonist-stimulated ex vivo relaxation of the corpus cavernosum (CC). Western blotting was performed from CC tissue samples.

Outcomes
Erectile and endothelial functions were assessed, as well as protein markers of mitochondrial dynamics, mitophagy, and autophagy.

Results
Erectile function was impaired in the HFD + PCSK9 group throughout the entire voltage range of stimulation. However, the HFD + PCSK9 mice that were treated with tubacin experienced significant restoration of erectile function at the medium and high voltages of nerve stimulation. Similarly, ex vivo CC relaxation responses to acetylcholine and the cystathionine γ-lyase (CSE) substrate L-cysteine were reduced in the vehicle-treated HFD + PCSK9 mice, both of which were restored in the HFD + PCSK9 mice treated with tubacin. Corpus-cavernosum protein expression of CSE was significantly elevated in the tubacin-treated HFD + PCSK9 mice relative to both other groups. There were no significant differences observed in any of the protein markers of mitochondrial dynamics, mitophagy, or autophagy investigated.

Clinical translation
Histone deacetylase 6 inhibition may protect against erectile and endothelial dysfunction associated with hypercholesterolemia.

Strengths and limitations
This was the first study to investigate HDAC6-specific inhibition for treatment of erectile dysfunction. A study limitation was the exclusive focus on the CC, rather than structure and function of the pre-penile arteries that may develop a substantial atherosclerotic plaque burden under hypercholesterolemic conditions.

Conclusions
Tubacin may prevent hypercholesterolemia-induced erectile dysfunction through a hydrogen sulfide–related mechanism unrelated to regulation of mitophagy or autophagy.
Novel insights into the role of gut microbiota and its metabolites in diabetic chronic wounds
Authors: Huang Yixuan , Tang Ying , Zhao Xiaotong , Xu Murong , Chen Mingwei 
Published: January 2025

AbstractWounds in patients with diabetes present significant physical and economic challenges due to impaired healing and prolonged inflammation, exacerbated by complex interactions between microbes. Especially, the development and healing of diabetic foot ulcers (DFUs) remain an urgent clinical problem. The human gut harbors a vast microbial ecosystem comprising intestinal flora and their metabolic products. Recent advancements in research have illuminated the concept of the “gut‐skin axis,” revealing intricate relationships between gut microbiota, microbiota‐derived metabolites, and various skin diseases, including DFUs. This review aims to unravel the formation and healing process of DFUs in the context of the gut‐skin axis. We reviewed the current research progress worldwide regarding to the gut‐skin axis, compared and discussed significant changes in the microbiota colonizing the skin and gut in patients with DFUs. The roles of microbiota‐derived metabolites such as lipopolysaccharides, short‐chain fatty acids, and trimethylamine‐N‐oxide in the development of DFUs are highlighted. We also reviewed treatment strategies currently employed in clinical practice and identified potential therapeutic targets such as probiotics for treating DFUs. The need for more comprehensive experimental designs to elucidate the intricate relationship between gut microbiota and its metabolites in the context of DFUs are therefore highlighted.