bluuebunny/crossref_metadata_2025_split huggingface dataset:
Caregiver Accounts of Lucid Episodes in Persons With Advanced Dementia
Authors: Karlawish Jason , Peterson Andrew , Kleid Melanie , Harkins Kristin , Largent Emily A , Stites Shana D , Coykendall Cameron , Clapp Justin T 
Published: December 2023

Abstract

Background and Objectives
Paradoxical lucidity is defined as an instance of unexpected lucid behavior in a person who is assumed to be noncommunicative due to a progressive and pathophysiologic dementing process. To inform studies of the prevalence, characteristics, and impact of these behaviors, this interview study examined caregivers’ experiences of witnessing paradoxical lucidity.

Research Design and Methods
Participants were family caregivers of persons living with advanced dementia caused by a neurodegenerative disease producing significant impairments in communication. Semistructured interviews elicited the caregivers’ experiences of plausible lucid episodes. Data analysis used a thematic analysis approach.

Results
Most caregivers reported at least 1 episode of lucidity. Episodes were typically brief. Most involved utterances, but nonverbal behaviors were also common. The mental capacities associated with these behaviors included recognition, awareness of surroundings, recognizing others’ emotions, and goal-directed behavior. Most caregivers’ reactions were positive. Episodes did not lead to changes in major medical decisions but instead to efforts to either modify or reinforce daily caregiving efforts.

Discussion and Implications
Episodes of lucidity were common, a finding seen in other studies. If prevalence studies confirm this, the qualifier “paradoxical” should be eliminated. The caregivers’ familiarity with the person living with dementia allowed them to attribute meaning to subtle behaviors that might not otherwise be detected or considered lucid. Clinicians who care for persons with advanced-stage dementia should routinely ask caregivers about episodes of lucid communication and their emotional reactions.
Seismotectonic aspects of the Ms 7.3 1948 October 5 Aşgabat (Ashgabat) earthquake, Türkmenistan: right-lateral rupture across multiple fault segments, and continuing urban hazard
Authors: Marshall N , Ou Q , Begenjev G , Bergman E , Bezmenov Y , Dodds N , Gruetzner C , Hudson T , Pierce I , Mirzin R , Rhodes E , Walker R T , Wordsworth P 
Published: December 2023

SUMMARY
The Ms 7.3 1948 Aşgabat earthquake was one of the most devastating earthquakes of the 20th century, yet little is known about its location, style and causative fault. In this study, we bring together new seismic and geomorphic observations with previously published descriptions of surface rupture and damage distributions to determine the likely source of the earthquake. We determine the epicentre and focal mechanism of this earthquake from digitized historical seismograms and the relocation of regional seismicity to show that the earthquake most likely nucleated close to the city of Aşgabat. The earthquake ruptured a right-lateral strike-slip fault to the southeast of the city, which has a clear long-term expression in the landscape, and also likely reactivated a subparallel concealed thrust along the Gyaursdag anticline east of the city. The earthquake potentially also ruptured a right-lateral segment northwest of Aşgabat, which does not have an identifiable expression in the landscape. Using high-resolution satellite imagery and digital elevation models we investigate the geomorphology of active faulting around Aşgabat and adjacent parts of the Köpetdag (Kopeh Dagh) mountain range front, showing that there are significant strike-slip and oblique strike-slip segments adjacent to the city that apparently did not rupture in 1948, and yet show clear geomorphic expression and potential right-lateral displacement of Parthian-era (∼2000 yr) and post-Sassanian era (∼1500 yr) archaeological remains. Luminescence dating of displaced fluvial terraces west of Aşgabat yields a vertical displacement rate of 0.6 mm yr−1, though the strike-slip rate remains undetermined.
The impact of COVID-19 on health literacy among Chinese rural residents
Authors: Du Yawen , Wang Xiaokang , Cheng Luyue , Wang Yao , Bu Xiaoou , Wang Yanjiao , Wang Pei 
Published: December 2023

Abstract
The outbreak of the Coronavirus disease 2019 (COVID-19) pandemic is an opportunity to improve the health literacy of rural residents. This study aims to explore the levels of health literacy among rural residents during the COVID-19 pandemic and investigate the effects of COVID-19-related variables on the health literacy of rural residents. A total of 882 rural residents aged 15–69 years in Shaanxi province participated in this study and completed the questionnaires about health literacy and COVID-19-related variables. These results showed that although overall health literacy and three aspects of health literacy among rural residents were low and lower than those of Chinese national residents, there was no significant difference in health literacy about safety and emergency between rural residents and Chinese national residents. Additionally, COVID-19-related variables significantly predicted health literacy (i.e. scientific health, safety and emergency and infectious disease prevention). Importantly, unlike other types of health literacy, the effect of a COVID-19-related variable (i.e. the frequency of exposure to news about the COVID-19 pandemic) on infectious disease prevention was only slightly smaller than the effect of high education on infectious disease prevention, and low education was no longer a significant predictor of infectious disease prevention. To conclude, rural residents in Shaanxi province have low health literacy. Education is a major factor affecting the health literacy of rural residents, and the frequency of exposure to news about the pandemic may compensate for the negative impact of low education on health literacy.
SUMMIT-FA: a new resource for improved transcriptome imputation using functional annotations
Authors: Melton Hunter J , Zhang Zichen , Wu Chong 
Published: December 2023

AbstractTranscriptome-wide association studies (TWAS) integrate gene expression prediction models and genome-wide association studies (GWAS) to identify gene-trait associations. The power of TWAS is determined by the sample size of GWAS and the accuracy of the expression prediction model. Here, we present a new method, the Summary-level Unified Method for Modeling Integrated Transcriptome using Functional Annotations (SUMMIT-FA), which improves gene expression prediction accuracy by leveraging functional annotation resources and a large expression quantitative trait loci (eQTL) summary-level dataset. We build gene expression prediction models in whole blood using SUMMIT-FA with the comprehensive functional database MACIE and eQTL summary-level data from the eQTLGen consortium. We apply these models to GWAS for 24 complex traits and show that SUMMIT-FA identifies significantly more gene-trait associations and improves predictive power for identifying “silver standard” genes compared to several benchmark methods. We further conduct a simulation study to demonstrate the effectiveness of SUMMIT-FA.
Overadjustment bias in systematic reviews and meta-analyses of socio-economic inequalities in health: a meta-research scoping review
Authors: van Zwieten Anita , Dai Jiahui , Blyth Fiona M , Wong Germaine , Khalatbari-Soltani Saman 
Published: December 2023

Abstract

Background
Overadjustment bias occurs when researchers adjust for an explanatory variable on the causal pathway from exposure to outcome, which leads to biased estimates of the causal effect of the exposure. This meta-research review aimed to examine how previous systematic reviews and meta-analyses of socio-economic inequalities in health have managed overadjustment bias.

Methods
We searched Medline and Embase until 16 April 2021 for systematic reviews and meta-analyses of observational studies on associations between individual-level socio-economic position and health outcomes in any population. A set of criteria were developed to examine methodological approaches to overadjustment bias adopted by included reviews (rated Yes/No/Somewhat/Unclear).

Results
Eighty-four reviews were eligible (47 systematic reviews, 37 meta-analyses). Regarding approaches to overadjustment, whereas 73% of the 84 reviews were rated as Yes for clearly defining exposures and outcomes, all other approaches were rated as Yes for &lt;55% of reviews; for instance, 5% clearly defined confounders and mediators, 2% constructed causal diagrams and 35% reported adjusted variables for included studies. Whereas only 2% included overadjustment in risk of bias assessment, 54% included confounding. Of the 37 meta-analyses, 16% conducted sensitivity analyses related to overadjustment.

Conclusions
Our findings suggest that overadjustment bias has received insufficient consideration in systematic reviews and meta-analyses of socio-economic inequalities in health. This is a critical issue given that overadjustment bias is likely to result in biased estimates of health inequalities and accurate estimates are needed to inform public health interventions. There is a need to highlight overadjustment bias in review guidelines.
Immunologic and Virologic Parameters Associated With Human Immunodeficiency Virus (HIV) DNA Reservoir Size in People With HIV Receiving Antiretroviral Therapy
Authors: Blazkova Jana , Whitehead Emily J , Schneck Rachel , Shi Victoria , Justement J Shawn , Rai M Ali , Kennedy Brooke D , Manning Maegan R , Praiss Lauren , Gittens Kathleen , Wender Paul A , Oguz Cihan , Lack Justin , Moir Susan , Chun Tae-Wook 
Published: December 2023

Abstract

Background
A better understanding of the dynamics of human immunodeficiency virus (HIV) reservoirs in CD4+ T cells of people with HIV (PWH) receiving antiretroviral therapy (ART) is crucial for developing therapies to eradicate the virus.

Methods
We conducted a study involving 28 aviremic PWH receiving ART with high and low levels of HIV DNA. We analyzed immunologic and virologic parameters and their association with the HIV reservoir size.

Results
The frequency of CD4+ T cells carrying HIV DNA was associated with higher pre-ART plasma viremia, lower pre-ART CD4+ T-cell counts, and lower pre-ART CD4/CD8 ratios. During ART, the High group maintained elevated levels of intact HIV proviral DNA, cell-associated HIV RNA, and inducible virion-associated HIV RNA. HIV sequence analysis showed no evidence for preferential accumulation of defective proviruses nor higher frequencies of clonal expansion in the High versus Low group. Phenotypic and functional T-cell analyses did not show enhanced immune-mediated virologic control in the Low versus High group. Of considerable interest, pre-ART innate immunity was significantly higher in the Low versus High group.

Conclusions
Our data suggest that innate immunity at the time of ART initiation may play an important role in modulating the dynamics and persistence of viral reservoirs in PWH.
Epidemiology of the 2022 Mpox Outbreak in the US Veterans Health Administration
Authors: Lucero-Obusan Cynthia , Oda Gina , Schirmer Patricia , Edson Connor , Trevino Christina , Elbeik Tarek , Holodniy Mark 
Published: December 2023

Abstract

Background
In May 2022, mpox cases were reported in nonendemic countries, including the United States. We examined mpox infections in the Veterans Health Administration (VHA).

Methods
Mpox diagnostic and whole genome sequencing (WGS) results, demographics, risk factors, hospitalizations, exposures, deaths, and pharmacy and immunization data were obtained from VHA data sources (23 May 2022–31 May 2023).

Results
Of 1144 Veterans tested, 251 (21.9%) were presumptive positive for nonvariola orthopoxvirus (NVO) or confirmed positive for NVO and Monkeypox virus (MPXV). Incidence rate was 7.5 per 100 000 Veterans in care, with the highest rate observed in Veterans aged 25–34 years (13.83 cases per 100 000). Higher odds of NVO or NVO/MPXV positivity was associated with male sex; non-Hispanic Black race/ethnicity; syphilis or human immunodeficiency virus (HIV) positivity; or genital/rectal sample site, whereas older age and vaccination with JYNNEOS or vaccinia (smallpox) had lower odds. Among 209 with confirmatory testing, 90.4% reported intimate contact and/or an epidemiological link, 84.5% were men who have sex with men (MSM), 24.2% received tecovirimat, and 8.1% were hospitalized with 1 death. Eighty-six sequenced samples had evaluable WGS results. All were clade IIb, representing 10 different lineages from 20 states and the District of Columbia.

Conclusions
Mpox affected younger, MSM, non-Hispanic Black, and HIV/syphilis-positive men among US Veterans. Viral diversity was noted across geographic regions. At-risk Veterans would benefit from vaccination and risk reduction strategies for mpox and other sexually transmitted infections.
Bedaquiline for treatment of non-tuberculous mycobacteria (NTM): a systematic review and meta-analysis
Authors: Omar Shatha , Whitfield Michael G , Nolan Margaret B , Ngom Justice T , Ismail Nabila , Warren Rob M , Klopper Marisa 
Published: December 2023

Abstract

Background
Non-tuberculous mycobacteria (NTM) infections are increasing in incidence and associated mortality. NTM are naturally resistant to a variety of antibiotics, complicating treatment. We conducted a literature assessment on the efficacy of bedaquiline in treating NTM species in vitro and in vivo (animal models and humans); meta-analyses were performed where possible.

Method
Four databases were searched using specific terms. Publications were included according to predefined criteria. Bedaquiline’s impact on NTM in vitro, MICs and epidemiological cut-off (ECOFF) values were evaluated. A meta-analysis of bedaquiline efficacy against NTM infections in animal models was performed. Culture conversion, cure and/or relapse-free cure were used to evaluate the efficacy of bedaquiline in treating NTM infection in humans.

Results
Fifty studies met the inclusion criteria: 33 assessed bedaquiline’s impact on NTM in vitro, 9 in animal models and 8 in humans. Three studies assessed bedaquiline’s efficacy both in vitro and in vivo. Due to data paucity, an ECOFF value of 0.5 mg/mL was estimated for Mycobacterium abscessus only. Meta-analysis of animal studies showed a 1.86× reduction in bacterial load in bedaquiline-treated versus no treatment within 30 days. In humans, bedaquiline-including regimens were effective in treating NTM extrapulmonary infection but not pulmonary infection.

Conclusions
Bedaquiline demonstrated strong antibacterial activity against various NTM species and is a promising drug to treat NTM infections. However, data on the genomic mutations associated with bedaquiline resistance were scarce, preventing statistical analyses for most mutations and NTM species. Further studies are urgently needed to better inform treatment strategies.
A network suspected infectious disease model for the development of syphilis transmission from 2015 to 2021 in Hubei province, China
Authors: Zhang Yue , Wang Kai , Zhu Junjie , Wu Jinyi 
Published: December 2023

Abstract

Aims
Understanding the transmission mode of syphilis is essential to prevent and predict its future prevalence and to develop effective control measures. This study aimed to develop a network suspected infectious disease model to simulate the syphilis transmission.

Methods and results
The number of syphilis cases in Wuhan’s Fourth Hospital, Hubei province, China, from October 2015 to July 2021 was collected. The simulation was carried out by interpersonal network-SI (suspected infectious) model based on temporal exponential family random graph models. Late latent syphilis and tertiary syphilis are predicted by December 2025. The validity of simulated value and real data was tested, including determination coefficient (R2), root means square error (RMSE), and means relative error (MRE). Moreover, we developed an online app that can more easily predict the number of syphilis infections in different scenarios by setting different parameters. Results showed that R2, RMSE, and MRE were 0.995, 36.19, and 6.31, respectively. Speed from latent infection to primary syphilis, primary syphilis to secondary syphilis, and susceptible group to latent infection decreased rapidly. The speed of transformation from secondary syphilis to early incubation period and early latent to late latent experienced a process from increase to decreased. Late latent to tertiary syphilis patients increased steadily. The number of late latent patients, early latent, invisible infection, primary syphilis, and secondary syphilis all increased at first and turn to decreased. However, tertiary syphilis continuously kept rising in the whole process. To better make use of the transmission model, an online application was developed (https://alanwu.shinyapps.io/MD-shiny/).

Conclusions
Based on the simulation that late latent and tertiary syphilis were steadily increasing, the prevention and treatment for syphilis were imperative.
Nudges Increase Choosing but Decrease Consuming: Longitudinal Studies of the Decoy, Default, and Compromise Effects
Authors: Polman Evan , Maglio Sam J 
Published: December 2023

Abstract
Research in marketing, psychology, economics, and decision making has long examined what people choose, when people choose, and why people choose. But almost no research has examined how long people consume their choices. Here, we examined an asymmetry between choosing an option and consuming it. Under the aegis of nudges, we conducted two randomized longitudinal experiments on how long people consumed a choice that was incentivized vis-à-vis a decoy effect, default effect, and compromise effect. We found that these nudges influenced choosing and consuming in opposite directions: Participants were more likely to choose the nudged option; however, they consumed it less compared to participants who chose an identical non-nudged option. Our research thus demonstrates that nudges could lead people to consume a nudged option less after choosing it, illuminating the potential for future research to examine the unexplored area of longitudinal, post-acquisition, post-nudge effects.
Is perioperative chemotherapy effective in patients with localized myxoid liposarcoma?
Authors: Masunaga Tomoya , Tsukamoto Shinji , Nitta Yuji , Honoki Kanya , Fujii Hiromasa , Akahane Manabu , Takeda Masayuki , Tanaka Yasuhito , Mavrogenis Andreas F , Errani Costantino , Kawai Akira 
Published: December 2023

Abstract

Background
This study aimed to compare the local recurrence, distant metastasis and disease-specific survival rates of patients with localized myxoid liposarcoma in the surgery and adjuvant chemotherapy group versus the surgery alone group.

Methods
A total of 456 patients in the Japanese National Bone and Soft Tissue Tumour Registry database who had localized myxoid liposarcoma and underwent surgery and adjuvant chemotherapy or surgery alone between 2001 and 2019 were included in this retrospective study. The study adjusted for background differences between patients who underwent surgery and adjuvant chemotherapy (n = 228) or surgery alone (n = 228) using propensity score matching.

Results
Univariate analysis showed no significant difference in local recurrence rate between the two groups (5-year local recurrence-free survival: 98.6% [95% confidence interval: 95.9–99.6] vs. 94.0% [95% confidence interval: 89.7–96.6], P = 0.052). Univariate analysis showed no difference in the incidence of distant metastases between the two groups (5-year distant metastasis-free survival: 80.5% [95% confidence interval: 73.9–85.8] vs. 75.1% [95% confidence interval: 67.7–81.2], P = 0.508). Univariate analysis showed no difference in disease-specific survival between the two groups (5-year disease-specific survival: 92.6% [95% confidence interval: 86.1–96.2] vs. 93.2% [95% confidence interval: 87.6–96.4], P = 0.804). In the high-risk group (n = 203) with high-grade tumours and tumour size ≥10 cm, there were no significant differences in the local recurrence, distant metastasis and disease-specific survival rates between the surgery and adjuvant chemotherapy group and the surgery alone group.

Conclusion
The effect of adjuvant chemotherapy on localized myxoid liposarcoma appears to be limited.
Measuring cosmic bulk flow with Pantheon catalogue in perturbed f(R) gravity
Authors: Yarahmadi M , Salehi A , Farajollahi H 
Published: December 2023

ABSTRACT
This study investigates the cosmic bulk flow through an analysis of luminosity distance variations in a perturbed Friedmann universe governed by f(R) gravity. The Hubble parameter, derived from perturbed Friedmann equations capturing intrinsic temporal fluctuations, is crucial. Redshift tomography is used to analyse observational data from the Pantheon catalogue from 0.015 to z &lt; 2.3. Our objective is to constrain the cosmic bulk flow’s direction and magnitude within this redshift range. At low redshifts (z &lt; 0.06), the predominant bulk flow aligns with the dominating supercluster in the corresponding range, maintaining a relatively constant magnitude, consistent with Lambda cold dark matter (ΛCDM) model predictions. A shift towards (l, b) = (290 ± 21, 15 ± 20) with $v_{\mathrm{bulk}} = 774 \pm 83 \, \mathrm{km\, s}^{-1}$ occurs between 0.06 &lt; z &lt; 0.1, coinciding with the cosmic microwave background dipole. For 0.1 &lt; z &lt; 0.2, the bulk flow shifts to (l, b) = (270 ± 21, 25 ± 20) with $v_{\mathrm{bulk}} = 903 \pm 102 \, \mathrm{km\, s}^{-1}$, supporting Kashlinsky et al.’s result. Beyond z &gt; 0.2, the bulk flow’s magnitude exceeds $1000 \, \mathrm{km\, s}^{-1}$, deviating from ΛCDM model expectations. Our findings suggest that matter density oscillations under f(R) gravity exhibit ΛCDM model properties at low redshifts. However, the microwave background anisotropy shows noticeable fluctuations at higher redshifts, validating prior findings of strong cosmic bulk flows at these scales.
Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs
Authors: Goldberg Emma E , Lundgren Erik J , Romero-Severson Ethan O , Leitner Thomas 
Published: December 2023

Abstract
When the time of an HIV transmission event is unknown, methods to identify it from virus genetic data can reveal the circumstances that enable transmission. We developed a single-parameter Markov model to infer transmission time from an HIV phylogeny constructed of multiple virus sequences from people in a transmission pair. Our method finds the statistical support for transmission occurring in different possible time slices. We compared our time-slice model results to previously described methods: a tree-based logical transmission interval, a simple parsimony-like rules-based method, and a more complex coalescent model. Across simulations with multiple transmitted lineages, different transmission times relative to the source’s infection, and different sampling times relative to transmission, we found that overall our time-slice model provided accurate and narrower estimates of the time of transmission. We also identified situations when transmission time or direction was difficult to estimate by any method, particularly when transmission occurred long after the source was infected and when sampling occurred long after transmission. Applying our model to real HIV transmission pairs showed some agreement with facts known from the case investigations. We also found, however, that uncertainty on the inferred transmission time was driven more by uncertainty from time calibration of the phylogeny than from the model inference itself. Encouragingly, comparable performance of the Markov time-slice model and the coalescent model—which make use of different information within a tree—suggests that a new method remains to be described that will make full use of the topology and node times for improved transmission time inference.