bluuebunny/crossref_metadata_2025_split huggingface dataset:
Famished for Freedom: Pellagra and Medical Clemency at the Mississippi State Penitentiary
Authors: Landress Dana 
Published: January 2025

Abstract
This paper provides a case study of one medical experiment conducted in 1915 by the United States Public Health Service in collaboration with the Mississippi State Penitentiary. The experiment was non-therapeutic and its objective was to induce pellagra (a vitamin deficiency disease) in twelve healthy White male prisoners to confirm its etiology. Extant archival records produced by the convict participants, state politicians, and health researchers underscore that the men selected for the pellagra experiment were unique among incarcerated people in Mississippi at the time: they were White, wealthy, and politically well-connected. This paper contends that the convict participants leveraged a wide range of social and political connections to secure their participation in the pellagra experiment as an expeditious pathway to pre-arranged executive pardon, a phenomenon that I term medical clemency. By situating the 1915 pellagra prison experiment amid the broader landscape of incarceration, public health research, and systems of political patronage in Mississippi, this paper highlights the ways in which penal systems are embedded in broader social and political contexts. Not only did the experiment exacerbate pre-existing social inequalities behind bars, it also had lasting consequences for those involved in prison medical research – namely, the power to determine which kinds of convicts could ultimately re-enter the social order.
Efficient data sampling scheme to reduce acquisition time in statistical ALCHEMI
Authors: Ishizuka Akimitsu , Ohtsuka Masahiro , Muto Shunsuke 
Published: January 2025

Abstract
The distribution of dopants in host crystals significantly influences the chemical and electronic properties of materials. Therefore, determining this distribution is crucial for optimizing material performance. The previously developed statistical ALCHEMI (St-ALCHEMI), an extension of the atom-location by channeling-enhanced microanalysis (ALCHEMI) technique, utilizes variations in electron channeling based on the beam direction relative to the crystal orientation. It statistically analyzes spectra collected across multiple beam directions. However, the total experimental time can be extensive, particularly for low dopant concentrations, where typical experiments can span several hours. In this study, we propose a scheme based on efficient sampling point selection that reduces the experimental time required while maintaining accuracy. Guidelines for selecting beam directions were derived from theoretical and experimental analyses of data redundancy. The strategies include choosing directions that exhibit greater variances in the host ionization channeling patterns and lower correlation coefficients between them. Additionally, an edge detection scheme using the dual tree complex wavelet transform, applied to electron channeling patterns, is proposed to significantly reduce measurement time. Our findings suggest that effective sampling can reduce experimental duration by at least two orders of magnitude without compromising accuracy. Implementing the proposed guidelines shortens total measurement times, minimizes electron irradiation damage and improves S/N ratio through extended data acquisition per tilt.
Nonlinear response of soil organic carbon sequestration to deadwood decomposition in a subtropical–temperate ecotonal forest
Authors: Hu Mengjun , Wang Jiali , Zhou Zhenxing , Zhang Min , Xu Xinchuang , Wang Lingxuan , Zhong Mingxing , Chen Jixun , Liu Xuehao , Fu Shenglei 
Published: January 2025

Abstract
The decomposition of deadwood is a crucial process for the accumulation and sequestration of soil organic carbon (SOC) in forest ecosystems. Yet, the response of SOC to various classes of deadwood decay and the underlying mechanisms remain unclear. Here, we investigated the dynamics of SOC, soil properties, extracellular enzyme activities, and phospholipid fatty acid biomarkers across five decay classes (defined from 1 to 5) of Masson pine (Pinus massoniana Lamb.) downed deadwood in a subtropical-temperate ecotone forest in Central China. Results showed a nonlinear response pattern of SOC along the deadwood decomposition gradient, with the maximum value at the decay class 4. Soil available nitrogen content, bacterial biomass, fungal biomass, the ratio of fungal to bacterial biomass, cellulase, and ligninase all increased, whereas soil pH decreased along with the intensification of deadwood decay. Increases in SOC content were associated with a direct positive effect of bacteria, and direct and indirect positive effects of fungi via cellulase, but ligninase showed no significant relationship with SOC content. These findings suggest that cellulose and microbial biomass determine soil C formation and sequestration during deadwood decomposition. This study highlights the importance of the nonlinear response of SOC to deadwood decay intensification, thus helping to predict future C–climate feedbacks.
The influence of pectins and cellulose in the mechanical and adhesive properties of seed mucilage
Authors: Gorges Helen , Serbe Elena , Kovalev Alexander , Gorb Stanislav N 
Published: January 2025

Abstract
Several plant seeds release a mucilaginous envelope through hydration, rich in pectins and stabilized by cellulose fibers. This mucilage aids in seed protection, development, and adhesion for dispersal. This study aimed to separate the effects of pectins and cellulose fibers by using pectinase to remove mucilage pectins, leaving cellulose arrays, and performing wet and dry pull-off force measurements on seeds of three plant species: Salvia hispanica (Chia), Collomia grandiflora (Collomia) and Linum usitatissimum (Flax). We used light and scanning electron microscopy to confirm partial pectin removal and intact cellulose fibers. Pull-off force measurements revealed similar wet adhesive properties and E-moduli in S. hispanica and C. grandiflora seeds before and after pectin removal. L. usitatissimum seeds, lacking cellulose fibers, exhibited significantly lower wet and dry adhesion forces post-pectin removal. Desiccation dynamics showed shorter desiccation times after pectin removal in all three species. Results indicated that adhesion forces in seed mucilage with cellulose fibers did not change significantly after pectin removal, suggesting that cellulose fibers contribute to the adhesive properties of seed mucilage, while pectins might not play an exclusive role in adhering to surfaces.
Direct Evidence of Anomalous Peierls Transition-Induced Charge Density Wave Order at Room Temperature in Metallic NaRu2O4
Authors: Scheid Anna , Isha  , Yogi Arvind Kumar , Isobe Masahiko , Bußmann Birgit , Heil Tobias , van Aken Peter A 
Published: January 2025

Abstract
In the field of quantum materials, understanding anomalous behavior under charge degrees of freedom through bond formation is of fundamental importance, with two key concepts: Dimerization and charge order at different cation sites. The coexistence of both dimerization and charge ordering is unusually found in NaRu2O4, even in its metallic state at room temperature. Our work unveils the origin of the interplay of these effects within metallic single-crystalline NaRu2O4. Employing advanced transmission electron microscopy techniques, we probe the lattice order of NaRu2O4 as a function of temperature and provide direct microscopic evidence of a Peierls-type transition. This transition is accompanied by a pronounced dimerization of the ruthenium chains, resulting in a distinctive twofold superstructure along the b axis below the critical transition temperature of ∼535 K, coinciding with a charge order. In situ heating experiments confirm the reversibility of this first-order phase transition, and periodic lattice displacement maps depict atomic-scale displacements linked to dimerization.
TIPPo: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with High-Fidelity Data
Authors: Xian Wenfei , Bezrukov Ilja , Bao Zhigui , Vorbrugg Sebastian , Gautam Anupam , Weigel Detlef 
Published: January 2025

Abstract
Plant cells have two major organelles with their own genomes: chloroplasts and mitochondria. While chloroplast genomes tend to be structurally conserved, the mitochondrial genomes of plants, which are much larger than those of animals, are characterized by complex structural variation. We introduce TIPPo, a user-friendly, reference-free assembly tool that uses PacBio high-fidelity long-read data and that does not rely on genomes from related species or nuclear genome information for the assembly of organellar genomes. TIPPo employs a deep learning model for initial read classification and leverages k-mer counting for further refinement, significantly reducing the impact of nuclear insertions of organellar DNA on the assembly process. We used TIPPo to completely assemble a set of 54 complete chloroplast genomes. No other tool was able to completely assemble this set. TIPPo is comparable with PMAT in assembling mitochondrial genomes from most species but does achieve even higher completeness for several species. We also used the assembled organelle genomes to identify instances of nuclear plastid DNA (NUPTs) and nuclear mitochondrial DNA (NUMTs) insertions. The cumulative length of NUPTs/NUMTs positively correlates with the size of the nuclear genome, suggesting that insertions occur stochastically. NUPTs/NUMTs show predominantly C:G to T:A changes, with the mutated cytosines typically found in CG and CHG contexts, suggesting that degradation of NUPT and NUMT sequences is driven by the known elevated mutation rate of methylated cytosines. Small interfering RNA loci are enriched in NUPTs and NUMTs, consistent with the RdDM pathway mediating DNA methylation in these sequences.
Occupational exposure and sarcoidosis: a case-control study in three countries
Authors: Vinnikov D , Strizhakov L , Rybina T , Babanov S , Brovko M , Sholomova V , Lebedeva M , Mukatova I , Lavrenteva N , Manavitskaya N , Hinko I , Мakhnach S , Rybina A , Vasileuski S , Savich L 
Published: January 2025

Abstract

Background
Preceding studies of environmental and occupational risk factors of sarcoidosis yielded inconsistent findings.

Aims
We aimed to ascertain the occupational risk factors for sarcoidosis in a case-control study.

Methods
A total of 237 sarcoidosis patients with a histologically confirmed diagnosis were matched with 474 controls for sex and age (median 49, interquartile range 37; 60 years) recruited from the university hospitals and outpatient centres in Belarus, Kazakhstan and the Russian Federation. Ever and cumulative (considering years and hours per week) exposure to 24 occupational factors were analysed using logistic regression.

Results
In the overall sample of 711 subjects, 50% were females and any occupational exposure was more prevalent in cases compared to controls (60% versus 40%, P &lt; 0.001). Current daily smoking as opposed to ex-smoking was associated with the lower risk of the outcome. Adjusted for smoking, age, sex and a few other exposures, ever-exposure to hay in agriculture (odds ratio (OR) 3.64 (95% confidence interval (CI) 1.26; 10.50)), engine exhausts (OR 2.94 (95% CI 1.14; 7.54)) and printing equipment (OR 1.66 (95% 1.03; 2.68)) was associated with sarcoidosis. The effect was also positive for cumulative exposure to hay in agriculture (OR 2.02 (95% CI 1.00; 4.07)), stone dust (OR 1.07 (95% CI 1.01; 1.14)) and engine exhausts (OR 1.18 (95% CI 1.03; 1.38)) and was stronger in never-smokers and subjects 40 years and older.

Conclusions
Widespread occupational exposures may increase the risk of sarcoidosis, but further research is needed to elucidate the complex interplay of environmental and occupational factors in the epidemiology of sarcoidosis.
Chromatin landscape alteration uncovers multiple transcriptional circuits during memory CD8+ T cell differentiation
Authors: Liu Qiao , Dong Wei , Liu Rong , Xu Luming , Ran Ling , Xie Ziying , Lei Shun , Su Xingxing , Yue Zhengliang , Xiong Dan , Wang Lisha , Wen Shuqiong , Zhang Yan , Hu Jianjun , Qin Chenxi , Chen Yongchang , Zhu Bo , Chen Xiangyu , Wu Xia , Xu Lifan , Huang Qizhao , Cao Yingjiao , Ye Lilin , Tang Zhonghui 
Published: January 2025

Abstract
Extensive epigenetic reprogramming involves in memory CD8+ T-cell differentiation. The elaborate epigenetic rewiring underlying the heterogeneous functional states of CD8+ T cells remains hidden. Here, we profile single-cell chromatin accessibility and map enhancer-promoter interactomes to characterize the differentiation trajectory of memory CD8+ T cells. We reveal that under distinct epigenetic regulations, the early activated CD8+ T cells divergently originated for short-lived effector and memory precursor effector cells. We also uncover a defined epigenetic rewiring leading to the conversion from effector memory to central memory cells during memory formation. Additionally, we illustrate chromatin regulatory mechanisms underlying long-lasting versus transient transcription regulation during memory differentiation. Finally, we confirm the essential roles of Sox4 and Nrf2 in developing memory precursor effector and effector memory cells, respectively, and validate cell state-specific enhancers in regulating Il7r using CRISPR-Cas9. Our data pave the way for understanding the mechanism underlying epigenetic memory formation in CD8+ T-cell differentiation.
Elite embeddedness: the rise of financiers on university boards as parallel social organizations
Authors: Eaton Charlie , Gibadullina Albina 
Published: January 2025

Abstract
We develop a theory of elite embeddedness in which social organizations parallel to the economy can provide advantages via private information and reciprocity from other elites. The growing representation of private equity and hedge fund managers on university boards of trustees is analyzed to show how this increasingly wealthy sub-group of financiers gained elite social ties despite the decline of bank-based interlocks between corporate boards. We find evidence that financiers secured trustee positions both because of their high rates of elite degree holding and their attraction to trustee appointments at the most selective schools. We also find that private equity firms attained higher investment returns when their general partners held more trustee positions. The results suggest that benefits accrue to elite intermediaries from social closure in parallel social organizations such as universities.
Sensitivity of driving simulation to sleep deprivation: effect of task duration
Authors: Meyer Morgane , Lejeune Laure , Giot Claire , Hay Marion , Bessot Nicolas 
Published: January 2025

Abstract

Study Objectives
The Psychomotor Vigilance Task (PVT) is widely recognized as the gold standard for measuring vigilance, providing a rapid and objective measure of this state. While driving simulations are also used, they typically require longer administration times. This study examines the sensitivity of driving simulation variables to sleep deprivation throughout the task. The aim is to determine the shorter duration at which performance declines can be observed. A secondary goal is to compare driving simulation and PVT variables’ sensitivity in detecting sleep deprivation.

Methods
Forty-three participants (22 males; aged 46.7 ± 17.8 years) completed a 90-minute driving simulation and a 10-minute PVT under two conditions (normal sleep and partial sleep deprivation of 3.5 hours). Signed-rank Wilcoxon tests and effect sizes were computed for variables from both tasks. Effect sizes were calculated for each 10-minute interval to assess sensitivity over time.

Results
All the variables showed sensitivity to sleep deprivation. The largest effect sizes were observed in the driving simulation and specifically for the standard deviation of lateral position (SDLP) (r = 0.73) and the standard deviation of steering wheel movement (r = 0.73). A large effect size for the SDLP (r = 0.71) was observed after only 20 minutes of driving. For the 10-minute PVT, the highest effect size was observed for the number of lapses (r = 0.52).

Conclusion
Driving-related variables are highly sensitive to sleep deprivation while providing continuous performance measurements. The SDLP is a particularly sensitive variable even with a reduced driving time of 20 minutes, suggesting that driving simulation tasks can be effectively shortened to 20 minutes.
Investigating outcomes of female genital schistosomiasis in communities in Ogun State, Nigeria: a pilot cross-sectional study
Authors: Gyang Vincent P , Abdulssalam Hameedat O , Ahmed Aminat O , Tokun Oluwatomilola V , Ejike Timothy N , Jonathan Joseph , Bayegun Adedotun A , Adubi Taiwo O , Patrobas Maryam N , Ajayi Jacob B , Akinwale Pheabian O 
Published: January 2025

Abstract

Background
Female genital schistosomiasis (FGS) is still a relatively new area of study in Nigeria, although the knowledge has improved since the Female Genital Schistosomiasis Society of Nigeria was launched in 2022, but gaps exist in evaluating the consequences of this disease. This pilot study investigated outcomes of FGS in two communities in Ogun State, Nigeria.

Methods
Women &lt;65 y of age from two communities in Ogun State were investigated. Of 126 women screened by urine microscopy, only 47 participants further consented for colposcopy to investigate FGS, guided by the World Health Organization FGS pocket atlas. Samples from the cervix and vagina were also subjected to a Pap test. Questionnaires were also used.

Results
Among the 47 participants, 23.4% had egg-patent urogenital schistosomiasis, with younger women being significantly more infected (p&lt;0.05): age group 16–25 y (30.8%) and 26–35 y (35.7%). Investigation by colposcopy showed that 18 (38.3%) women had signs that could be considered as FGS, including grainy sandy patches (12.8%), yellow sandy patches (38.3%), abnormal blood vessels (17%) and rubbery papules (4.3%). Pap smear results showed cervical atypia in all samples, with two having Schistosoma ova.

Conclusions
The results of this pilot study reaffirm the reason why more attention to FGS from the Federal Ministry of Health is required, and we strongly recommend the need for more studies with larger sample sizes to gather more information.
TAK-925 (danavorexton), an Orexin Receptor 2 Agonist, Reduces Opioid-Induced Respiratory Depression and Sedation Without Affecting Analgesia in Healthy Adult Males
Authors: van Lemmen Maarten , Dahan Albert , Hang Yaming , Jansen Simone C. , Lu Hong , Naylor Melissa , Olsson Tina , Sheikh Sarah , Sullivan Danielle , Tolkoff Max , van der Schrier Rutger , van Velzen Monique , von Rosenstiel Philipp , Wu Rebecca L. , Meyer Seetha 
Published: January 2025

Background:
Orexin neuropeptides help regulate sleep/wake states, respiration, and pain. However, their potential role in regulating breathing, particularly in perioperative settings, is not well understood. TAK-925 (danavorexton), a novel, orexin receptor 2-selective agonist, directly activates neurons associated with respiratory control in the brain and improves respiratory parameters in rodents undergoing fentanyl-induced sedation. This study assessed the safety and effect of danavorexton on ventilation in healthy men in an established remifentanil-induced respiratory depression model.

Methods:
This single-center, double-blind, placebo-controlled, two-way crossover, phase 1 trial randomized (1:1) 13 healthy men to danavorexton (11mg [low-dose] then 19mg [high-dose]) or placebo, under remifentanil infusion, on two occasions separated by a ≥36-hour washout period. Remifentanil infusion was titrated under isohypercapnic conditions to achieve ~30% to 40% decrease in minute ventilation (from ~20 to ~14 L/minute) before danavorexton/placebo administration. Assessments included safety, ventilation measurements, sedation, and pain tolerance.

Results:
4 (30.8%) danavorexton-treated participants and 1 (8.3%) placebo-treated participant experienced treatment-emergent adverse events (all mild in severity). Insomnia, lasting 1 day, occurred in 1 participant, and was considered related to danavorexton. Compared with placebo, low- and high-dose danavorexton significantly increased ventilation variables (observed mean [95% confidence interval] change, sensitivity analysis model-based p-values) including minute volume (8.2[5.0, 11.4] and 13.0[9.4, 16.5] L/min), tidal volume (312[180, 443] and 483[309, 657] mL), and respiratory rate (3.8[1.9, 5.7] and 5.2[2.7, 7.7] breaths/min) (all P<0.001). High-dose danavorexton significantly decreased sedation on visual analog scale (–29.7[–54.1, –5.3] mm, P<0.001) and Richmond Agitation Sedation Scale (0.4[0.0, 0.7], P<0.001), compared with placebo. Improvements in respiratory variables continued beyond completion of danavorexton infusion. No significant differences in pain tolerance were observed between danavorexton doses or between danavorexton and placebo (~13% increase from baseline; low-dose:P=0.491; high-dose:P=0.140).

Conclusions:
Danavorexton has effects on respiration and wakefulness in an opioid-induced respiratory depression setting without reversing opioid analgesia.
The Psychometric Properties of the EuroQol 5D Five Level in Survivors of Critical Illness
Authors: De Silva Sheraya , Neto Ary Serpa , Sathe Aditya , Higgins Alisa M. , Hodgson Carol L. 
Published: January 2025

OBJECTIVES:
The EuroQol 5D five level (EQ-5D-5L) instrument is a standardized measure of health-related quality of life and is routinely used in survivors of critical illness. However, information on its psychometric properties and minimal clinically important difference (MCID) in this patient group is lacking.

DESIGN:
Secondary analysis of data from the previously published PREDICT (a registry in critically ill patients to determine predictors of disability-free survival) study, a prospective, multicenter cohort study.

SETTING:
Six ICUs in the state of Victoria, Australia.

PATIENTS:
Four hundred fifty adult patients admitted to the ICU and ventilated for over 24 hours.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
The EQ-5D-5L was administered by telephone at 6 months following ICU admission. Internal consistency (inter-item correlations, Cronbach’s α, and split-half reliability coefficients), construct validity (against age, body mass index, and other outcome measures), responsiveness (observing change over time and effect sizes), percentage of participants presenting no change, and MCID (triangulation of distribution-based and anchor-based estimates) were evaluated. The EQ-5D-5L showed high internal consistency, Cronbach α coefficients of 0.82 (between dimensions) and 0.79 (between the EuroQol-Visual Analogue Scale [EQ-VAS] and utility score), and average split-half coefficients of 0.79 each (between dimensions and between EQ-VAS and utility score). Construct validity was confirmed with a strong correlation between the EQ-5D-5L and the World Health Organization Disability Assessment Schedule 2.0 (EQ-VAS: r = 0.72; p < 0.001 and utility score: r = 0.81; p < 0.001). Effect sizes for change over time for EQ-VAS and utility score were low. The final MCID estimates were 10 (EQ-VAS) and 0.11 (utility score).

CONCLUSIONS:
The EQ-5D-5L, using the Australian value set, demonstrated evidence of good internal consistency and validity, but poor responsiveness in a critically ill population.