bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hierarchical annotation of eQTLs by H-eQTL enables identification of genes with cell type-divergent regulation
Authors: Przytycki Pawel F. , Pollard Katherine S. 
Published: November 2024

AbstractWhile context-type-specific regulation of genes is largely determined by cis-regulatory regions, attempts to identify cell type-specific eQTLs are complicated by the nested nature of cell types. We present hierarchical eQTL (H-eQTL), a network-based model for hierarchical annotation of bulk-derived eQTLs to levels of a cell type tree using single-cell chromatin accessibility data and no clustering of cells into discrete cell types. Using our model, we annotate bulk-derived eQTLs from the developing brain with high specificity to levels of a cell type hierarchy, which allows sensitive detection of genes with multiple distinct non-coding elements regulating their expression in different cell types.
Reconsidering tools for measuring gender dimensions in biomedical research
Authors: Morgan Rosemary , Yin Anna , Kalbarczyk Anna , Shapiro Janna R. , Shea Patrick J. , Kuo Helen , Rodriguez Carmen H. , Rosser Erica N. , Pekosz Andrew , Leng Sean X. , Klein Sabra L. 
Published: November 2024

AbstractSex and gender play important roles in contributing to disease and health outcomes and represent essential, but often overlooked, measures in biomedical research. The context-specific, multifaceted, and relational nature of gender norms, roles, and relations (i.e., gender dimensions) make their incorporation into biomedical research challenging. Gender scores—measures of gender dimensions—can help researchers incorporate gender into quantitative methodologies. These measures enable researchers to quantify the gendered dimensions of interest using data collected from survey respondents. To highlight the complexities of using gender scores within biomedical research, we used the application of the Bem Sex Role Inventory (BSRI) scale, a commonly used gender score, to explore gender differences in adverse events to the influenza vaccine among older adults (75+). Within this paper, we focus on the findings from our longitudinal gender score data collected over three influenza seasons (2019-20, 2020-21, and 2021-22), irrespective of adverse event data, to provide commentary on the reliability of gender scores, such as the BSRI, and the complexities of their application. Of the 162 total study participants included within the study, 69 were enrolled in all three consecutive seasons and 35 participants were enrolled in two consecutive seasons. The majority of participants had a different gender score in at least one of the years, demonstrating the nuances and fluidity of gender identity. Interpretations of BSRI data (or other gender score data) when measured against outcome data must, therefore, be time and context specific, as results are unlikely to be replicated across years.
Elevated core temperature in addition to mental fatigue impairs aerobic exercise capacity in highly trained athletes in the heat
Authors: Naito Takashi , Saito Tatsuya , Morinaga Hirotsugu , Eda Nobuhiko , Takai Yohei 
Published: November 2024

AbstractThe purpose of this study was to investigate the effects of elevated core temperature by exposure to heat stress vs. heat exposure without elevated core temperature (mean skin temperature only) in addition to mental fatigue on aerobic exercise capacity in the heat. Seven highly trained athletes completed two experimental conditions: elevation in core and skin temperatures (hyperthermia: HYP), and skin temperatures (SKIN). Participants performed the AX-Continuous Performance Task and Stroop Task to induce mental fatigue during a warm water immersion at 40 °C (HYP) and a passive seated heat exposure in a climatic chamber at 35 °C and 60% relative humidity (SKIN) for 45 min before exercise. Thereafter, participants performed running trial at 80% maximal oxygen uptake until voluntary exhaustion in the same chamber as the SKIN. Exercise time to exhaustion was significantly shorter in the HYP trial (538 ± 200 s) than in the SKIN trial (757 ± 324 s). Rectal temperature at the end of tasks in the HYP trial increased by 0.86 ± 0.26℃ and was significantly higher (37.69 ± 0.18℃) than that of the SKIN trial (36.96 ± 0.13℃), albeit no significant differences in mean skin temperature. Self-reported mental fatigue using visual analog scale was significantly higher after tasks in both trials, but no significant difference between trials was found. Throughout the trial, salivary cortisol concentration and perceptual responses were not affected by hyperthermia. This study demonstrated that a combination of high core temperature and mean skin temperature, and mental fatigue limit aerobic exercise capacity in highly trained athletes in hot environments compared with heat exposure without an elevation of core temperature.
GDF15 propeptide promotes bone metastasis of castration-resistant prostate cancer by augmenting the bone microenvironment
Authors: Yamamichi Gaku , Kato Taigo , Arakawa Noriaki , Ino Yoko , Ujike Takeshi , Nakano Kosuke , Koh Yoko , Motoyama Yuichi , Outani Hidetatsu , Myoba Shohei , Ishizuya Yu , Yamamoto Yoshiyuki , Hatano Koji , Kawashima Atsunari , Fukuhara Shinichiro , Uemura Hiroji , Okada Seiji , Morii Eiichi , Nonomura Norio , Uemura Motohide 
Published: November 2024

Abstract
Background
Bone metastasis (BM) is a common and fatal condition in patients with castration-resistant prostate cancer (CRPC). However, there are no useful blood biomarkers for CRPC with BM, and the mechanism underlying BM is unclear. In this study, we investigated precise blood biomarkers for evaluating BM that can improve the prognosis of patients with CRPC.

Methods
We comprehensively examined culture supernatants from four prostate cancer (PCa) cell lines using Orbitrap mass spectrometry to identify specific proteins secreted abundantly by PCa cells. The effects of this protein to PCa cells, osteoblasts, osteoclasts were examined, and BM mouse model. In addition, we measured the plasma concentration of this protein in CRPC patients for whom bone scan index (BSI) by bone scintigraphy was performed.

Results
A total of 2,787 proteins were identified by secretome analysis. We focused on GDF15 propeptide (GDPP), which is secreted by osteoblasts, osteoclasts, and PCa cells. GDPP promoted the proliferation, invasion, and migration of PC3 and DU145 CRPC cells, and GDPP aggravated BM in a mouse model. Importantly, GDPP accelerated bone formation and absorption in the bone microenvironment by enhancing the proliferation of osteoblasts and osteoclasts by upregulating individual transcription factors such as RUNX2, OSX, ATF4, NFATc1, and DC-STAMP. In clinical settings, including a total of 416 patients, GDPP was more diagnostic of BM than prostate-specific antigen (PSA) (AUC = 0.92 and 0.78) and the seven other blood biomarkers (alkaline phosphatase, lactate dehydrogenase, bone alkaline phosphatase, tartrate-resistant acid phosphatase 5b, osteocalcin, procollagen I N-terminal propeptide and mature GDF15) in patients with CRPC. The changes in BSI over time with systemic treatment were correlated with that of GDPP (r = 0.63) but not with that of PSA (r = -0.16).

Conclusions
GDPP augments the tumor microenvironment of BM and is a novel blood biomarker of BM in CRPC, which could lead to early treatment interventions in patients with CRPC.
Effect of anti-sclerostin antibody on orthodontic tooth movement in ovariectomized rats
Authors: Ahn Hyunna , Park Wonse , Choi Sung-Hwan , Hong Namki , Huh Jisun , Jung Seoyeon 
Published: November 2024

Abstract
Background
This study aimed to evaluate the effect of systemically administered anti-sclerostin antibodies (Anti-Scl Ab) on orthodontic tooth movements (OTM) in an ovariectomized rat.

Methods
Twenty-four 12-week-old female Sprague-Dawley rats were randomly divided into two groups: (1) ovariectomy (OVX) group, (2) ovariectomy + romosozumab (ROMO) group. OTM was performed 8 weeks after OVX. The ROMO group received subcutaneous injections of romosozumab twice a week, starting two weeks after OVX. Eight weeks after the OVX, an orthodontic force of 50 g was measured and applied by connecting orthodontic elastic bands between the maxillary first molar and a mini-screw to facilitate tooth movement (orthodontic treatment). Subsequently, the three rats were sacrificed on days 5, 7, 10, and 14. The plaster models were scanned to measure the amount of tooth movement. The effects on alveolar bone and periodontal tissues were evaluated through micro-computed tomography (micro-CT) analysis, tartrate-resistant acid phosphatase (TRAP) staining, and immunohistochemistry (IHC) analysis.

Results
The ROMO group showed more tooth movement on day 7 of orthodontic treatment. Conversely, on days 10 and 14, relatively less movement was observed. Analysis of the root furcation area of the maxillary first molars revealed that from the 7th day, BV/TV, Tb.N., Tb.Th. increased, while Tb.Sp. decreased in the ROMO group. More TRAP-positive cells were observed in the compression side of the OVX group, the ROMO group exhibited a marked decrease in the positive expression of the RANKL, OPG, and sclerostin. The OPG/RANKL ratio showed significant differences in expression between the two groups. The ROMO group exhibited a higher OPG/RANKL ratio than the OVX group, and the tension side exhibited a higher OPG/RANKL ratio demonstrating significant differences.

Conclusion
Romosozumab initially accelerated tooth movements, but later decreased tooth movement. As new alveolar bone is formed, the micro-CT parameters are also improved. Osteoclasts, RANKL, OPG, and sclerostin decreased, while the OPG/RANKL ratio became higher.
Comprehensive assessment of COVID-19 case fatality rate and influential factors in Khuzestan Province, Iran: a two-year study
Authors: Bastani Mohammad-Navid , Makvandi Manoochehr , Moradi Maryam , Haghighi Somayeh Biparva , Rostami Maryam , Nasimzadeh Sepideh , Amiri Homayoun , Alavi Seyed Mohammad , Rashno Mohammad , Mohtadi Ahmadreza , Yousefi Farid , Fayezi Abbas , Mirkarimi Mohammadreza , Shoushtari Maryam Haddadzadeh , Zadkarami Masoud , Balar Negin , Sameii Siamak Mirab , Torabizadeh Mehdi 
Published: November 2024

Abstract
Background
The emergence of a new pandemic SARS-CoV-2 (COVID-19) resulted in a high mortality rate across the world. This study sought to comprehensively analyze the Case Fatality Rate (CFR) associated with COVID-19 in the Khuzestan province of Iran”. The primary objective was to discern patterns and determinants influencing CFR, shedding light on the evolving impact of the pandemic on morbidity and mortality.

Methods
A retrospective examination was performed on a dataset encompassing confirmed COVID-19 cases and related fatalities in Khuzestan. Data, spanning from December 2020 to April 2022, underwent rigorous statistical analysis. Demographic variables, comorbidities, and temporal trends were scrutinized to identify key factors influencing CFR.

Results
Preliminary findings revealed dynamic shifts in CFR, capturing the nuanced nature of the pandemic over time. Demographic nuances, particularly age and gender, emerged as significant determinants impacting CFR, the reported CFR of COVID-19 in Khuzestan province was 1.79%.

Conclusion
This study contributes critical insights into the CFR landscape of COVID-19 in Khuzestan, providing a foundation for evidence-based decision-making in public health. The identified factors influencing mortality rates offer valuable information for tailoring interventions and optimizing resource allocation. Continuous monitoring and further investigations are recommended to adapt strategies to the evolving nature of the pandemic.
Exploring the potential of curcumin-loaded PLGA nanoparticles for angiogenesis and antioxidant proficiency in zebrafish embryo (Danio rerio)
Authors: Singha Achinta , Harshitha Mave , Kalladka Krithika , Chakraborty Gunimala , Maiti Biswajit , Satyaprasad Akshath Uchangi , Chakraborty Anirban , Sil Samir Kumar 
Published: November 2024

Abstract
Background
Curcumin is an age old traditional medicine. Although curcumin has several advantages, its water solubility and bioavailability limit its use as a natural therapeutic agent. Polymeric nano curcumin could be an excellent option to overcome these challenges to augment its therapeutic efficacy. This work aimed to synthesize curcumin-loaded PLGA nanoparticles and assess their angiogenic and antioxidant potential in the zebrafish model.

Results
The double emulsion solvent evaporation process was employed to make curcumin-loaded PLGA nanoparticles. Curcumin showed ~ 28.23 (± 2.49) encapsulation efficacy with an average diameter of PLGA nanoparticles 168.5 (± 2.5) nm and curcumin nanoparticles about 281.6 (± 17.2) nm, respectively. The curcumin nanoparticles showed no developmental toxicity to the zebrafish embryos while reduced toxicity compared to the native curcumin. Further, the curcumin nanoparticles reduced the generation of reactive oxygen species and improved angiogenesis in the model system. All these results confirmed that the nanoparticle has had higher bio-efficacy than that of native curcumin.

Conclusion
This study shows that PLGA curcumin nanoparticles hold an excellent therapeutic promise for wound healing, tissue regeneration and other biomedical applications where angiogenesis and ROS play critical role.
Anatomical variations and their impact on chronic rhinosinusitis: a retrospective analysis from an Indonesian tertiary hospital
Authors: Maharani Iriana , Putri Giovani I. G. 
Published: November 2024

Abstract
Background
Chronic rhinosinusitis (CRS) is an inflammation of the paranasal sinus mucosa lasting over 12 weeks. Its etiology includes infections, allergies, immune system failures, anatomical abnormalities, and mucociliary transport disorders. The complex anatomy of the sinonasal region can hinder mucociliary drainage; necessitating CT scans to evaluate predisposing factors and minimize surgical risks. This study aimed to understand the anatomical variations in the paranasal sinuses and their correlation with CRS.

Results
The study included 128 CRS patients aged 20 to 75, averaging 36.2 years. The most common symptoms were nasal congestion (98%), runny nose (85%), facial pressure (57%), reduced sense of smell (53%), and posterior nasal discharge (43%). Maxillary rhinosinusitis was the most prevalent (88%), followed by ethmoid (84%), frontal (58%), and sphenoid (48%) rhinosinusitis. Anatomical variations were present in 96% of patients, with deviated nasal septum (81.3%), agger nasi pneumatization (73.4%), and frontoethmoidal cells (60.2%) being the most common. Logistic regression indicated a significant association between concha bullosa and maxillary rhinosinusitis (p < 0.05). No significant correlation was found between anatomical variations number and SNOT-22 scores (r = − 0.177, p > 0.05).

Conclusion
This study found a high prevalence of anatomical variations in CRS patients, with deviated nasal septum, agger nasi pneumatization, and frontoethmoidal cells being the most common. A significant association was identified between concha bullosa and maxillary rhinosinusitis.
Of Simple Cells and Visual Associations in Photobook Editing
Authors: van der Heijden Teun 
Published: November 2024

Abstract
The first thing one does when one looks at a photograph is try to understand what it means. One immediately starts looking for clues. This might be connected to how people learn to read. Each letter in a semiotic alphabet has a specific meaning. Although letters have been derived from a logographic origin, over time they have lost their original connotation. Letters became parts of a code. In order to be fluent in the usage of the code it is important to understand the meaning of its parts. As a photobook designer and visual storyteller, the author of this article has always felt limited by this tendency of looking for meaning—an activity that distracts from quietly looking at a photograph and enjoying its mood, lighting, texture, or color. This essay explores the author's process of editing photographs into photobooks through the lens of neuroscience and the concept of simple cells. It provides several case studies, with a focus on Poulomi Basu's Centralia.
Dynamic remodelling of the endoplasmic reticulum for mitosis
Authors: Kors Suzan , Schlaitz Anne-Lore 
Published: November 2024

ABSTRACT
The endoplasmic reticulum (ER) is a dynamic and continuous membrane network with roles in many cellular processes. The importance and maintenance of ER structure and function have been extensively studied in interphase cells, yet recent findings also indicate crucial roles of the ER in mitosis. During mitosis, the ER is remodelled significantly with respect to composition and morphology but persists as a continuous network. The ER interacts with microtubules, actin and intermediate filaments, and concomitant with the mitotic restructuring of all cytoskeletal systems, ER dynamics and distribution change. The ER is a metabolic hub and several examples of altered ER functions during mitosis have been described. However, we lack an overall understanding of the ER metabolic pathways and functions that are active during mitosis. In this Review, we will discuss mitotic changes to the ER at different organizational levels to explore how the mitotic ER, with its distinct properties, might support cell division.
ANALYSIS OF THE APPLICATION OF CODE-LOCATION POSITIONING IN THE EASTERN DIRECTION OF THE WEST SIBERIAN RAILWAY
Authors: Shugaev Oleg V. , Pokrovskaya Oksana D. , Pochetukha Vasily V. , Lemikhov Sergey V. 
Published: November 2024

The presented research paper with a scientific bias is devoted to the analysis of the application of the system of code-location positioning of rolling stock on the stretch of the Eastern direction of the West Siberian Railway. The article describes the subject and object of research, includes the sequence of individual stages of research with justification and data processing. The publication is conditionally divided into 2 parts, the first is devoted to the methodology of research, the description of the research process, input data and a structural description of individual elements of the interval control system. The mathematical apparatus includes statistical methods for processing data adjusted for the current conditions of the experiment. The determination of throughput and processing capacity was carried out using a foreign method and the author's methodology for evaluating the efficiency of the distillation. The conclusion of the first section of the article indicates the need to use the presented mathematical apparatus. The second part of this publication contains the results of research with conclusions. The uniqueness of the experiment consists in dividing the research part into several separate stages and conducting them for several months on the current stretch of the main line. The first stage of research is devoted to the accuracy of determining the location of rolling stock using a code-location positioning system. The second stage contains an assessment of changes in throughput and carrying capacity on a separate loaded stretch of the Eastern direction of the West Siberian Railway. The final stage of the experiment contains an assessment of the study of the response rate of the proposed motion control system. The results of the research and the summary of the entire work are located in the final part of the publication, which includes analysis and analysis of the experiment. The final section describes recommendations for improving operating conditions using the data obtained and the author's assessment of the effectiveness of the rolling stock code-location positioning system on a separate stretch of the main line section of the Eastern direction of the West Siberian Railway.
Incorporating Promotional Effects in Sales Planning of the Retail Industry Using Geometric Programming
Authors: Khandan Melika , Hoseinpour Pooya 
Published: November 2024

This paper addresses the challenge faced by managers in the fast-moving consumer goods industry: the joint optimization of promotion prices and the scheduling of promotion vehicles for multiple items to boost total profit. We first propose a general multiplicative demand function that encompasses all crossperiod effects, crossitem effects, promotion vehicle effects, and crossterm effects of promotion vehicles. Then, we formulate the problem of planning sales promotions, simultaneously using price reductions and promotion vehicles, considering several business rules as constraints. To efficiently solve this mixed-integer nonlinear program, we reformulate it as a convex optimization form by using the demand function’s multiplicative structure and the concept of geometric programming. Furthermore, to reduce the running time of the large-scale instances, we develop a Lagrangian decomposition algorithm, dividing the original model into a geometric program and an integer program. The algorithm significantly improves computational efficiency as evidenced by a reduction in running time from 8,125 to 78 seconds for large-scale instances. Finally, utilizing real sales data from a meal delivery company, we demonstrate that applying the convex promotion optimization model allows the company to increase its profits by roughly 21% compared with scenarios where neither price reductions nor promotion vehicles are utilized. History: Accepted by Andrea Lodi, Area Editor for Design & Analysis of Algorithms–Discrete. Supplemental Material: The software that supports the findings of this study is available within the paper and its Supplemental Information ( https://pubsonline.informs.org/doi/suppl/10.1287/ijoc.2023.0275 ) as well as from the IJOC GitHub software repository ( https://github.com/INFORMSJoC/2023.0275 ). The complete IJOC Software and Data Repository is available at https://informsjoc.github.io/ .
Self-Regulation for Reputation-Sensitive Buyers: SA8000 in China
Authors: Distelhorst Greg , Stroehle Judith C. , Yang Duanyi 
Published: November 2024

Industries and firms have diverse motives for adopting self-regulatory institutions. This research develops and tests propositions about one motive—exploiting opportunities to do business with reputation-sensitive buyers—as distinct from self-regulation to defend against regulatory or activist threats. To study the adoption and effects of self-regulation for reputation-sensitive buyers, we study the SA8000 socially responsible employment certification among large firms in China in the early 2000s. Using official longitudinal industrial microdata, we test hypotheses generated by this assumed motive for self-regulation and find that (a) despite concerns about the corruptibility of certification bodies, SA8000 adopters in China exhibited higher precertification worker wages than comparable nonadopters, (b) self-regulation led to increased employment and sales to foreign markets, where reputation-sensitive buyers are concentrated, (c) the positive effect on exports was greater than the (insignificant, negatively signed) effect on domestic sales, and (d) there is no evidence that self-regulation increased worker wages beyond the initial high start. Contrasting these findings with prior research on industry self-regulation for other motives, this study highlights how both adoption patterns and downstream effects differ according to the audience for self-regulation. This paper was accepted by Olav Sorenson, organizations. Supplemental Material: The online appendix and data files are available at https://doi.org/10.1287/mnsc.2020.01306 .