bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reporting standards in randomized controlled trials involving neuro-oncology caregivers: A systematic review report from the RANO-Cares working group
Authors: Boele Florien W , Hertler Caroline , Sherwood Paula , Cachia David , Dirven Linda , Young Jacob S , Walbert Tobias , Stockdill Macy , Rodriguez Almaraz Eduardo , Piil Karin 
Published: September 2024

Abstract

Background
Family caregivers in neuro-oncology (eg, spouse, family member, friend to a patient) have high unmet support needs, yet intervention trials and effective support options are scarce. The Response Assessment in Neuro-Oncology (RANO)-Cares working group investigated the methodological quality of neuro-oncology caregiver outcomes reporting in randomized controlled trials (RCTs).

Methods
A systematic review was performed to evaluate to what extent RCTs assessing outcomes of caregivers of adult primary brain tumor patients adhere to minimum reporting standards. A 33-item checklist (23 applicable to secondary analysis reports) based on the International Society for Quality of Life Research (ISOQOL) criteria for patient-reported outcome reporting was used. Risk of bias was assessed per RCT.

Results
Fifteen publications from 11 unique RCTs included 676 neuro-oncology caregivers, with low overall risk of bias. Ten publications (66%) reported on caregiver outcomes as a primary aim, of which 8 (80%) satisfied ≥2/3 of the key methodological criteria. Of the 5 secondary analysis reports (33%), 2 (40%) met ≥2/3 of applicable key criteria. Criteria often not reported adequately included sample size calculations (reported adequately in n = 8, 53%), participant flow (n = 9, 60%) window for data collection (n = 1, 6%), and extent of (n = 10, 66%), reasons for (n = 9, 60%), and statistical approaches in dealing with (n = 4, 26%) missing data.

Conclusions
Whilst there are opportunities to enhance reporting standards, RCTs that include neuro-oncology caregiver outcomes generally adhere to high-quality reporting standards and have low risk of bias, indicating good potential to impact clinical practice.
Recent advances in microenvironment regulation for electrocatalysis
Authors: Xu Zhiyuan , Tan Xin , Chen Chang , Wang Xingdong , Sui Rui , Zhuang Zhongbin , Zhang Chao , Chen Chen 
Published: September 2024

ABSTRACT
High-efficiency electrocatalysis could serve as the bridge that connects renewable energy technologies, hydrogen economy and carbon capture/utilization, promising a sustainable future for humankind. It is therefore of paramount significance to explore feasible strategies to modulate the relevant electrocatalytic reactions and optimize device performances so as to promote their large-scale practical applications. Microenvironment regulation at the catalytic interface has been demonstrated to be capable of effectively enhancing the reaction rates and improving the selectivities for specific products. In this review we summarize the latest advances in microenvironment regulation in typical electrocatalytic processes (including water electrolysis, hydrogen–oxygen fuel cells, and carbon dioxide reduction) and the related in situ/operando characterization techniques and theoretical simulation methods. At the end of this article, we present an outlook on development trends and possible future directions.
Effect of Severe Fever With Thrombocytopenia Syndrome Virus Genotype on Disease Severity, Viral Load, and Cytokines in South Korea
Authors: Kwon Ji-Soo , Kim Ji Yeun , Jang Choi Young , Son Ju Yeon , Kim Woori , Kim Taeeun , Park Se Yoon , Kim Min-Chul , Park Seong Yeon , Cha Hye Hee , Jang Hyeon Mu , Kim Min-Jae , Chong Yong Pil , Lee Sang-Oh , Choi Sang-Ho , Kim Yang Soo , Kim Sung-Han 
Published: September 2024

Abstract

Background
Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne disease caused by Bandavirus dabieense (SFTS virus [SFTSV]). Recently, at least 6 different genotypes of SFTSV have been identified, with genotypes A, D, and F dominant in China and B dominant in Japan and Korea. This study investigated the effect of SFTSV genotypes circulating in South Korea on disease severity, viral load, and cytokine profile.

Methods
We prospectively enrolled 70 patients with SFTS from July 2015 to June 2022. Serial plasma samples were obtained during hospitalization and analyzed. Viral load was measured by real-time reverse-transcription polymerase chain reaction. Partial sequences of the viral genome were analyzed for genotyping. Plasma concentrations of 17 cytokines were measured by multiplex-bead immunoassay.

Results
Of 70 samples, 51 could be genotyped. Genotype B was predominant (80.4%) and other genotypes were uncommon. Intensive care unit admission rates (51.2% vs 50.0%) and mortality rates (26.8% vs 40.0%) did not show any significant differences between genotype B and non-B genotypes. The initial viral load did not show any significant differences (3.59 vs 3.64 log copies/μL), whereas viral load measured at hospital day 3–4 tended to be higher in genotype B than non-B genotypes (3.83 vs 1.83 log copies/μL, P = .07). Additionally, the plasma concentrations of interferon-α, interleukin 10, and interferon-γ–induced protein 10, which are closely related to mortality in cases of SFTS, did not show any significant differences.

Conclusions
SFTSV genotype B was the prevalent genotype in South Korea, with no genotype-specific difference in clinical outcomes, initial viral load, or cytokine profiles.
Mortality risk assessment using deep learning-based frequency analysis of electroencephalography and electrooculography in sleep
Authors: Kristjánsson Teitur Óli , Stone Katie L , Sorensen Helge B D , Brink-Kjaer Andreas , Mignot Emmanuel , Jennum Poul 
Published: September 2024

Abstract

Study Objectives
To assess whether the frequency content of electroencephalography (EEG) and electrooculography (EOG) during nocturnal polysomnography (PSG) can predict all-cause mortality.

Methods
Power spectra from PSGs of 8716 participants, including from the MrOS Sleep Study and the Sleep Heart Health Study, were analyzed in deep learning-based survival models. The best-performing model was further examined using SHapley Additive Explanation (SHAP) for data-driven sleep-stage specific definitions of power bands, which were evaluated in predicting mortality using Cox Proportional Hazards models.

Results
Survival analyses, adjusted for known covariates, identified multiple EEG frequency bands across all sleep stages predicting all-cause mortality. For EEG, we found an all-cause mortality hazard ratio (HR) of 0.90 (CI: 95% 0.85 to 0.96) for 12–15 Hz in N2, 0.86 (CI: 95% 0.82 to 0.91) for 0.75–1.5 Hz in N3, and 0.87 (CI: 95% 0.83 to 0.92) for 14.75–33.5 Hz in rapid-eye-movement sleep. For EOG, we found several low-frequency effects including an all-cause mortality HR of 1.19 (CI: 95% 1.11 to 1.28) for 0.25 Hz in N3, 1.11 (CI: 95% 1.03 to 1.21) for 0.75 Hz in N1, and 1.11 (CI: 95% 1.03 to 1.20) for 1.25–1.75 Hz in wake. The gain in the concordance index (C-index) for all-cause mortality is minimal, with only a 0.24% increase: The best single mortality predictor was EEG N3 (0–0.5 Hz) with a C-index of 77.78% compared to 77.54% for confounders alone.

Conclusions
Spectral power features, possibly reflecting abnormal sleep microstructure, are associated with mortality risk. These findings add to a growing literature suggesting that sleep contains incipient predictors of health and mortality.
In vitro transcription-based biosensing of glycolate for prototyping of a complex enzyme cascade
Authors: Barthel Sebastian , Brenker Luca , Diehl Christoph , Bohra Nitin , Giaveri Simone , Paczia Nicole , Erb Tobias J 
Published: September 2024

Abstract
In vitro metabolic systems allow the reconstitution of natural and new-to-nature pathways outside of their cellular context and are of increasing interest in bottom-up synthetic biology, cell-free manufacturing, and metabolic engineering. Yet, the analysis of the activity of such in vitro networks is very often restricted by time- and cost-intensive methods. To overcome these limitations, we sought to develop an in vitro transcription (IVT)-based biosensing workflow that is compatible with the complex conditions of in vitro metabolism, such as the crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle, a 27-component in vitro metabolic system that converts CO2 into glycolate. As proof of concept, we constructed a novel glycolate sensor module that is based on the transcriptional repressor GlcR from Paracoccus denitrificans and established an IVT biosensing workflow that allows us to quantify glycolate from CETCH samples in the micromolar to millimolar range. We investigate the influence of 13 (shared) cofactors between the two in vitro systems to show that Mg2+, adenosine triphosphate , and other phosphorylated metabolites are critical for robust signal output. Our optimized IVT biosensor correlates well with liquid chromatography–mass spectrometry–based glycolate quantification of CETCH samples, with one or multiple components varying (linear correlation 0.94–0.98), but notably at ∼10-fold lowered cost and ∼10 times faster turnover time. Our results demonstrate the potential and challenges of IVT-based systems to quantify and prototype the activity of complex reaction cascades and in vitro metabolic networks.
Innovation in viruses: fitness valley crossing, neutral landscapes, or just duplications?
Authors: Banse Paul , Elena Santiago F , Beslon Guillaume 
Published: September 2024

Abstract
Viruses evolve by periods of relative stasis interleaved with sudden, rapid series of mutation fixations, known as evolutionary bursts. These bursts can be triggered by external factors, such as environmental changes, antiviral therapies, or spill-overs from reservoirs into novel host species. However, it has also been suggested that bursts may result from the intrinsic evolutionary dynamics of viruses. Indeed, bursts could be caused by fitness valley crossing, or a neutral exploration of a fitness plateau until an escape mutant is found. In order to investigate the importance of these intrinsic causes of evolutionary bursts, we used a simulation software package to perform massive evolution experiments of viral-like genomes. We tested two conditions: (i) after an external change and (ii) in a constant environment, with the latter condition guaranteeing the absence of an external triggering factor. As expected, an external change was almost systematically followed by an evolutionary burst. However, we also observed bursts in the constant environment as well, albeit much less frequently. We analyzed how many of these bursts are triggered by deleterious, quasi-neutral, or beneficial mutations and show that, while bursts can occasionally be triggered by valley crossing or traveling along neutral ridges, many of them were triggered by chromosomal rearrangements and, in particular, segmental duplications. Our results suggest that combinatorial differences between the different mutation types lead to punctuated evolutionary dynamics, with long periods of stasis occasionally interrupted by short periods of rapid evolution, akin to what is observed in virus evolution.
Weight, height, waist circumference: association with knee osteoarthritis findings from the osteoarthritis initiative
Authors: Antoine Lisa H. , Watts Kristen Allen , Rumble Deanna D. , Buchanan Taylor , Sims Andrew , Goodin Burel R. 
Published: September 2024

Abstract

Introduction:
Global prevalence of knee osteoarthritis is more than 300 million. Uncontrollable risk factors include age, sex, and height. Controllable risk factors include trauma, weight, and waist circumference.

Objectives:
Our goal was to determine the association between knee osteoarthritis and anthropometric measures that include weight, height, and waist circumference.

Methods:
Using 4,602 participants (45–79 years) from the Osteoarthritis Initiative, we analyzed the association between knee osteoarthritis and anthropometry collectively and by sex. We calculated female and male tertiles (3 groups) for anthropometry.

Results:
Anthropometric measures were correlated with knee osteoarthritis (P ≤ 0.05) except the correlation between height and activities and height and quality of life. When comparing female weight tertiles, there were associations (P's < 0.001) between knee osteoarthritis and weight, but when comparing male weight tertiles, these associations were primarily between the lowest weight and highest weight groups. There were significant associations between knee osteoarthritis and height among female tertiles, with no differences among male tertiles. There were knee osteoarthritis/waist circumference tertile associations (P's < 0.001) for the lowest and highest waist circumference groups.

Conclusion:
Higher weight in female participants was a stronger predictor of increases in knee osteoarthritis discomforts when compared to waist circumference, while weight and waist circumference were almost equivalent in predicting increases in knee osteoarthritis for male participants. Height did not predict increases in knee osteoarthritis with the exception of female symptoms and quality of life. Quality of life for both sexes was the most unfavorable with female participants reporting a more unfavorable quality of life than male participants.
Blood folate level needed for fully effective neural tube defect prevention
Authors: Wald Nicholas J. , Vale Stephen H. , Bestwick Jonathan P. , Morris Joan K. 
Published: September 2024

ABSTRACTIntroductionNeural tube defects (NTDs) are a folate deficiency disorder. NTDs are preventable; increasing folic acid intake through food fortification or use of supplements increases serum and red blood cell folate and reduces the risk of a woman having an NTD pregnancy. There is controversy over whether there is a blood folate level needed to achieve the full preventive effect because of discrepant conclusions from studies investigating the relationship between folate levels and NTD risk. Resolving the controversy is important in determining public health policy.MethodsData from two studies conducted in Ireland and China were used to determine the relationship between serum folate and NTD risk. The relationship from each study was compared with the observed result in a randomised trial of folic acid that increased serum folate from 5 ng/ml to 44 ng/ml among the women who took the daily folic acid supplement before and during early pregnancy.ResultsData from both studies showed a proportional (logarithmic) relationship between serum folate and NTD risk with no evidence of a folate threshold above which there is no further NTD risk reduction. Both studies accurately predicted the observed result from the randomised trial that achieved serum folate levels beyond the average levels found in the general population with an 83% preventive effect. This is higher than can be achieved with current levels of folic acid food fortification or with the recommended peri-conceptional use of 0.4mg supplements. The suggestion of a threshold is not due to discrepant data but the incorrect interpretation of the folate-NTD risk association when plotted on arithmetic scales which conceals the proportional relationship between the two.ConclusionTo achieve fully effective fortification serum folate levels need to be about 44ng/ml.Key MessagesWhat is already known on this topicNeural tube defects (NTDs), among the most common serious birth defects worldwide, are a folate deficiency disorder. Increasing folic acid (vitamin B9) intake increases serum folate and reduces the risk of an NTD pregnancy. There is a difference of opinion on the serum folate level needed for fully effective NTD prevention.What this study addsThere is no threshold above which NTD risk does not decrease and population folate levels need to be substantially increased to have the expected potential achieve effect on the prevention of NTDs.How this study might affect research, practice or policyA serum folate level of about 44ng/ml is a reasonable target to achieve an approximate 83% reduction in the prevalence of NTD pregnancies. This result can be used to help influence folic acid fortification policy.
Towards large-scale museomics projects: a cost-effective and high-throughput extraction method for obtaining historical DNA from museum insect specimens
Authors: Holmquist Anna J. , Tavris Holly , Kim Grace , Esposito Lauren A. , Fisher Brian L. , Lam Athena 
Published: September 2024

AbstractNatural history collections serve as invaluable repositories of biodiversity data. Large-scale genomic analysis would greatly expand the utility and accessibility of museum collections but the high cost and time-intensive nature of genomic methods limit such projects, particularly for invertebrate specimens. This paper presents an innovative, cost-effective and high-throughput approach to extracting genomic DNA from diverse insect specimens using single-phase reverse immobilization (SPRI) beads. We optimized PEG-8000 and NaCl concentrations to balance DNA yield and purity, reducing reagent cost to 6-11 cents per sample. Our method was validated against three widely used extraction protocols, and showed comparable DNA yield and amplification success to the widely used Qiagen DNeasy kit. We successfully applied the protocol in a high-throughput manner, extracting DNA from 3,786 insect specimens across a broad range of ages, taxonomies, and tissue types. A detailed protocol is provided to facilitate the adoption of the method by other researchers. By improving one of the most crucial steps in any molecular project, this SPRI bead-based DNA extraction approach has significant potential for enabling large-scale museomics projects, thereby increasing the utility of historical collections for biodiversity research and conservation efforts.
The diverse diet of southern Alaska resident killer whales changes across spatiotemporally distinct foraging aggregations
Authors: Myers Hannah , Olsen Daniel , Van Cise Amy , Parsons Kim , Wells Abigail , Matkin Craig 
Published: September 2024

AbstractTop predators influence ecological communities in part through the prey they consume, which they often track through cycles of seasonal and geographic abundance. Killer whales are top predators in the marine ecosystem. In the North Pacific, they have diverged into three distinct lineages with different diets, of which the fish-eating type is most abundant. In this study, we examine the diet of the southern Alaska resident killer whale population across three major foraging aggregations. We take advantage of two unique sampling methods to reveal strong spatiotemporal patterns in diet from May through September. Chinook, chum, and coho salmon were each dominant in different locations and times, with substantial dietary contributions from Pacific halibut, arrowtooth flounder, and sablefish. The diverse, location-specific, and seasonal nature of the feeding habits of this marine top predator highlights the importance of diet sampling across broad spatiotemporal and population-level scales.
The H3K4me3 binding ALFIN-LIKE proteins recruit SWR1 for gene-body deposition of H2A.Z
Authors: Xu Linhao , Wang Yafei , Li Xueying , Hu Qin , Adamkova Vanda , Xu Junjie , Harris C. Jake , Ausin Israel 
Published: September 2024

AbstractThe H2A.Z histone variant is highly enriched over gene bodies, playing an essential role in several genome-templated processes, including transcriptional regulation and epigenetic patterning across eukaryotes. The SWR1 chromatin remodeling complex deposits H2A.Z. How SWR1 is directed to gene bodies is largely unknown. Here, we show that ALFIN-LIKE (AL) proteins are responsible for H2A.Z gene body patterning inArabidopsis. AL proteins encode H3K4me3-binding PHD domains, and by ChIP-seq, we confirm preferential binding of AL5 to H3K4me3 over H3K4me1/2in planta. We observe a global reduction in H2A.Z inalseptuple mutants (al7m), especially of over H3K4me3-enriched genic regions. While MBD9 recruits SWR1 to nucleosome-free regions, ALs act non-redundantly with MBD9 for deposition of H2A.Z. Notably,al7mmutants show severe developmental abnormalities and upregulation of H2A.Z gene body-enriched responsive genes. Therefore, we propose a model whereby AL proteins direct gene body enrichment of H2A.Z by recruiting SWR1 to H3K4me3-containing responsive genes.
PEARL: Protein Eluting Alginate with Recombinant Lactobacilli
Authors: Tadimarri Varun Sai , Blanch-Asensio Marc , Deshpande Ketaki , Baumann Jonas , Baumann Carole , Müller Rolf , Trujillo Sara , Sankaran Shrikrishnan 
Published: September 2024

ABSTRACTEngineered living materials (ELMs) made of bacteria in hydrogels have shown considerable promise for therapeutic applications through controlled and sustained release of complex biopharmaceuticals at low costs and with reduced wastage. While most therapeutic ELMs useE. colidue to its large genetic toolbox, most live biotherapeutic bacteria in development are lactic acid bacteria due to native health benefits they offer. Among these, lactobacilli form the largest family of probiotics with therapeutic potential in almost all sites of the body with a microbiome. A major factor limiting the use of lactobacilli in ELMs is their limited genetic toolbox.In this study, we build upon our recent work to expand the genetic programmability of probioticLactiplantibacillus plantarumWCFS1 for protein secretion and encapsulate it in a simple, cost-effective, and biocompatible core-shell alginate bead to develop an ELM. We demonstrate the controlled release of recombinant proteins, even up to 14 days from this ELM, thereby terming it PEARL - Protein Eluting Alginate with Recombinant Lactobacilli. Notably, lactobacillus encapsulation offered benefits like bacterial containment, protein release profile stabilization, and metabolite-induced cytotoxicity prevention. These findings demonstrate the mutual benefits of combining recombinant lactobacilli with alginate for the controlled and sustained release of proteins.
Qing-Luo-Yin-induced SIRT1 inhibition contributes to the immune improvement of adjuvant-induced arthritis rats
Authors: Wang Dan-Dan , Song Meng-Ke , Yin Qin , Chen Wen-Gang , Olatunji Opeyemi Joshua , Yang Kui , Zuo Jian 
Published: September 2024

AbstractThe herbal formula Qing-Luo-Yin (QLY) was proved containing SIRT1 inhibitors. Whether they contribute to the anti-rheumatic effects is to be confirmed. Adjuvant-induced arthritis (AIA) rats were treated by QLY or/and nicotinamide mononucleotide (NMN) for 38 days. After sacrifice, main tissues were collected for histological and western-blot experiments. Levels of rheumatoid arthritis (RA)-related indictors in blood or tissue homogenates were detected by commercial kits. Normal pre-adipocytes were cultured by the relevant rat serums, and the medium was collected for monocytes culture. In replicate experiments, some pre-adipocytes received additional compounds or SIRT1 silencing/overexpression treatments. Due to spontaneous remission of inflammation, QLY didn’t further improve immune milieu in AIA rats, but greatly eased paw edema and joint injuries. Besides, it reversed triglyceride/glucose depletion in liver and adipose tissues, and inhibited the expression and function of SIRT1, causing concomitant changes of related signals and adipkines production. All the effects were weakened by NMN, which activated SIRT1 by increasing NAD production. The serum from QLY-treated rats improved AIA rat serum-induced metabolism and secretion changes of pre-adipocytes, and reduced the secretion of IL-1β, IL-6 and TNF-α in the monocytes cultured with the corresponding medium. A mixture of matrine, sinomenine, sophocarpine, dioscin, berberine showed the similar effects on pre-adipocytes to QLY-containing serum. eNAMPT decrease was especially notable, which was obviously weakened by SIRT1 overexpression but overshadowed SIRT1-silencing. SIRT1 inhibitors in QLY reshaped metabolism and secretion profiles of adipose tissues. It consequently mitigated eNAMPT-mediated inflammation and eased AIA in rats.