bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving onchocerciasis elimination surveillance: trials of odour baited Esperanza Window Traps to collect black fly vectors and real-time qPCR detection of Onchocerca volvulus in black fly pools
Authors: Adeleke Monsuru A. , Opara Kenneth N. , Mafuyai Hayward B. , Nwoke Bertram Ekejiuba Bright , Surakat Olabanji A. , Akinde Sunday B. , Nwoke Murphy , Chikezie Friday M. , Yaro Clement A. , Mmaduabuchi Ugagu , Igbe Michael , Makata Emeka , Oyediran Fatai , Anyaike Chukwuma , Tongjura Joseph , Hawkes Frances , Iwalewa Zahra O. 
Published: November 2024

Abstract
Background
Entomological data for onchocerciasis surveillance relies on sampling black flies through human landing collectors in the field and laboratory testing of the flies for infection using pooled screening O-150 PCR-ELISA assay. Both techniques require improvements. This study aimed to optimize the Esperanza Window Trap (EWT) for black fly collection. We tested alternative carbon dioxide (CO2) mimics to attract black flies to the traps. Additionally, we evaluated new quantitative PCR (qPCR) methods that target mitochondrial DNA markers and have been proposed to enhance the sensitivity and specificity for detecting Onchocerca volvulus infections in blackflies.

Methods
Traps baited with low, medium and high release rates of either 2-butanone or cyclopentanone as CO2 mimics were field tested against traps baited with organically generated CO2 in four ecological zones in Nigeria: Guinea savannah, derived savannah, rainforest and montane forest. The performance of EWTs baited with CO2 or in combination with 2-butanone (low release) were subsequently evaluated against the human landing collection (HLC). Trap scaling was also pilot tested by comparing two EWTs to a single HLC team. Collected black flies were used to test detection of O. volvulus in black flies using Ov ND5 real-time PCR (qPCR) compared to the conventional pool screening O-150 PCR.

Results
EWTs baited with 2-butanone caught similar numbers of black flies (Simulium damnosum s.l.) to those baited with CO2, while cyclopentanone collected significantly fewer flies in all locations. The low release of 2-butanone was the most effective overall, although HLCs collected higher numbers of black flies than EWT baited with CO2 either singly or in combination with low-release 2-butanone. The combination of two EWTs baited with CO2 and deployed 100 m apart from each other collected similar numbers of flies as one HLC. More black fly pools were positive for O. volvulus by Ov ND5 qPCR compared with O-150 PCR in derived savannah (31.15 vs. 15.57%), montane forest (11.54 vs. 0%) and rainforest (23.08 vs. 2.56%), with only one positive pool in Guinea savannah detected by both methods.

Conclusions
The 2-butanone has potential to be used in xenomonitoring as a standardized replacement for organically generated CO2. Ov ND5 qPCR detected more positive pools than O-150 PCR. The positive pools found in foci hitherto considered to have interrupted/eliminated onchocerciasis highlight the need for more sensitive and specific methods that support programmatic assessments to identify and combat recrudescence.

Graphical Abstract
Ascorbate peroxidase modulation confirms key role in Leishmania infantum oxidative defence
Authors: Santos Isabella Fernandes Martins , Moreira Douglas de Souza , Costa Karla Ferreira , Ribeiro Juliana Martins , Murta Silvane Maria Fonseca , Santi Ana Maria Murta 
Published: November 2024

Abstract
Background
Ascorbate peroxidase (APX) has emerged as a promising target for chemotherapy because of its absence in humans and crucial role in the antioxidant defence of trypanosomatids. APXs, which are class I haeme-containing enzymes, reduces hydrogen peroxide using ascorbate to produce water and monodehydroascorbate, thereby preventing cell damage caused by H2O2.

Methods
We aimed to create an APX-knockout L. infantum line using CRISPR/Cas9. Despite unsuccessful attempts at full knockouts, we achieved deletion of chromosomal copies post-APX episomal insertion, yielding LiΔchrAPX::LbAPX parasites. We performed phenotypic characterization to assess the impact of these genetic modifications, which included the determination of APX transcript expression levels using quantitative PCR, drug sensitivity, infectivity, and parasite survival in macrophages.

Results
Quantitative polymerase chain reaction (PCR) analysis revealed a 10- to 13-fold reduction in APX transcript expression in LiΔchrAPX::LbAPX compared with wild-type (LiWT) and APX-overexpressing (Li::Cas9::LbAPX) parasites, respectively. The episomes in those knockdown parasites remained stable even after 20 drug-free passages in vitro. Li::Cas9::LbAPX parasites showed increased resistance to trivalent antimony (SbIII) and isoniazid, reduced tolerance to H2O2, and unchanged macrophage infectivity compared with LiWT. In contrast, LiΔchrAPX::LbAPX parasites were more sensitive to SbIII and isoniazid, exhibited greater susceptibility to H2O2-induced oxidative stress, and 72 h post-infection, showed fewer infected macrophages and intracellular amastigotes compared with LiWT parasites.

Conclusions
Our findings hint at the indispensability of APX in L. infantum and raise the possibility of its potential as a therapeutic target for leishmaniasis.

Graphical Abstract
Pre-diagnosis blood DNA methylation profiling of twin pairs discordant for breast cancer points to the importance of environmental risk factors
Authors: Bode Hannes Frederik , He Liang , Hjelmborg Jacob V. B. , Kaprio Jaakko , Ollikainen Miina 
Published: November 2024

Abstract
Background
Assessment of breast cancer (BC) risk generally relies on mammography, family history, reproductive history, and genotyping of major mutations. However, assessing the impact of environmental factors, such as lifestyle, health-related behavior, or external exposures, is still challenging. DNA methylation (DNAm), capturing both genetic and environmental effects, presents a promising opportunity. Previous studies have identified associations and predicted the risk of BC using DNAm in blood; however, these studies did not distinguish between genetic and environmental contributions to these DNAm sites. In this study, associations between DNAm and BC are assessed using paired twin models, which control for shared genetic and environmental effects, allowing testing for associations between DNAm and non-shared environmental exposures and behavior.

Results
Pre-diagnosis blood samples of 32 monozygotic (MZ) and 76 dizygotic (DZ) female twin pairs discordant for BC were collected at the mean age of 56.0 years, with the mean age at diagnosis 66.8 years and censoring 75.2 years. We identified 212 CpGs (p < 6.4*10–8) and 15 DMRs associated with BC risk across all pairs using paired Cox proportional hazard models. All but one of the BC risks associated with CpGs were hypomethylated, and 198/212 CpGs had their DNAm associated with BC risk independent of genetic effects. According to previous literature, at least five of the top CpGs were related to estrogen signaling. Following a comprehensive two-sample Mendelian randomization analysis, we found evidence supporting a dual causal impact of DNAm at cg20145695 (gene body of NXN, rs480351) with increased risk for estrogen receptor positive BC and decreased risk for estrogen receptor negative BC.

Conclusion
While causal effects of DNAm on BC risk are rare, most of the identified CpGs associated with the risk of BC appear to be independent of genetic effects. This suggests that DNAm could serve as a valuable biomarker for environmental risk factors for BC, and may offer potential benefits as a complementary tool to current risk assessment procedures.
CTN-0138: adaptation, implementation, and cluster randomized trial of a Community Pharmacy-Based Prescription Drug Monitoring Program Opioid Risk Assessment Tool—a protocol paper
Authors: Cochran Gerald T. , Brown Jennifer L. , Yu Ziji , Gordon Adam J. , Frede Stacey , Hardy Clinton , Castora-Binkley Melissa , Homsted Felicity , Marsch Lisa A. , Holtyn August F. , Winhusen T. John 
Published: November 2024

Abstract
Background
As the opioid epidemic continues to have a major negative impact across the US, community pharmacies have come under scrutiny from legal systems attempting to hold them accountable for their role in over dispensing and lack of patient intervention. While the most available tool for monitoring patients’ opioid use is Prescription Drug Monitoring Programs (PDMP), these do not provide pharmacists with actionable information and decision support. Our study addresses this gap through three objectives: [1] incorporate validated opioid risk metric thresholds into a PDMP platform to create the Opioid Risk Reduction Clinical Decision Support (ORRCDS) tool; [2] assess ORRCDS’ ability to reduce patient opioid risk; [3] assess ORRCDS’ sustainability and viability for broader dissemination in community pharmacy.

Methods
For objective 1, our team is partnering with leadership from the largest US PDMP organization and a top-five pharmacy chain to implement ORRCDS into the pharmacy chain’s workflow following the Guideline Implementation with Decision Support (GUIDES) framework. For objective 2, our team will conduct a type-1 implementation mixed methods study using a 2-arm parallel group clustered randomized design. We anticipate enrolling ~ 6,600 patients with moderate and high opioid use risk during the 6-month enrollment phase across 80 pharmacies. This sample size will provide 96.3% power to detect a 5% or greater difference in responder rate between the intervention and control arm. Responders are patients with moderate-risk at baseline who reduce to low-risk or those with high-risk at baseline who reduce to moderate or low-risk at 180 days post last intervention. To accomplish objective 3, we will use the Consolidated Framework for Implementation Research (CFIR) to develop and execute cross-sectional qualitative interviews with pharmacists (n = 15), pharmacy leaders (n = 15), and PDMP leaders (n = 15) regarding long term adoption and sustainability of the ORRCDS tool.

Conclusions
A PDMP tool that addresses moderate- and high-risk opioid use is not available in community pharmacy. This study will implement ORRCDS in a large retail pharmacy chain that will include additional screening and guidance to pharmacy staff to address risky opioid medication use. Our results will make critical advancements for protecting patient health and addressing the opioid epidemic.
Roles of posttranslational modifications in lipid metabolism and cancer progression
Authors: Feng Tianyu , Zhang He , Zhou Yanjie , Zhu Yalan , Shi Shiya , Li Kai , Lin Ping , Chen Jie 
Published: November 2024

AbstractLipid metabolism reprogramming has emerged as a hallmark of malignant tumors. Lipids represent a complex group of biomolecules that not only compose the essential components of biological membranes and act as an energy source, but also function as messengers to integrate various signaling pathways. In tumor cells, de novo lipogenesis plays a crucial role in acquiring lipids to meet the demands of rapid growth. Increasing evidence has suggested that dysregulated lipid metabolism serves as a driver of cancer progression. Posttranslational modifications (PTMs), which occurs in most eukaryotic proteins throughout their lifetimes, affect the activity, abundance, function, localization, and interactions of target proteins. PTMs of crucial molecules are potential intervention sites and are emerging as promising strategies for the cancer treatment. However, there is limited information available regarding the PTMs that occur in cancer lipid metabolism and the potential treatment strategies associated with these PTMs. Herein, we summarize current knowledge of the roles and regulatory mechanisms of PTMs in lipid metabolism. Understanding the roles of PTMs in lipid metabolism in cancer could provide valuable insights into tumorigenesis and progression. Moreover, targeting PTMs in cancer lipid metabolism might represent a promising novel therapeutic strategy.
Synthesis and characterization of titanium oxynitride catalyst via direct ammonia nitridation of titanium polyacrylate for oxygen reduction reaction
Authors: Tamaki Yushi , Seino Satoshi , Shinyoshi Naoki , Uetake Yuta , Nagai Takaaki , Monden Ryuji , Ishihara Akimitsu , Nakagawa Takashi 
Published: November 2024

AbstractA titanium oxynitride catalyst for the oxygen reduction reaction (ORR) in polymer electrolyte fuel cells was synthesized through the direct ammonia nitridation of titanium complexes. Titanium polyacrylate was employed as the catalyst precursor, and the effect of the calcination temperature between 600 and 1000 °C on the catalyst structure was studied. The catalysts were characterized via X-ray diffraction, X-ray absorption spectroscopy, transmission electron microscopy, cyclic voltammetry, and powder electrical resistivity measurements. The formation of titanium oxynitride particles and deposited carbon was observed for all the samples; however, significant variations in the catalyst structure and catalytic activity were also observed. With an increase in the calcination temperature, nitridation of titanium oxynitride progressed, and the conductivity of the catalyst powder increased. The highest rest potential and ORR current density were achieved with calcination at 800 °C. Importantly, the results suggest that maintaining an optimal nitrogen doping level within the catalyst particles, along with ensuring the formation of electroconductive deposited carbon, is essential for achieving a high ORR current. This work introduces the direct ammonia nitridation of metal complexes as a promising process for designing metal oxynitride catalysts.
Survey of real-time brainmedia in artistic exploration
Authors: Lin Rem RunGu , Zhang Kang 
Published: November 2024

AbstractThis survey examines the evolution and impact of real-time brainmedia on artistic exploration, contextualizing developments within a historical framework. To enhance knowledge on the entanglement between the brain, mind, and body in an increasingly mediated world, this work defines a clear scope at the intersection of bio art and interactive art, concentrating on real-time brainmedia artworks developed in the 21st century. It proposes a set of criteria and a taxonomy based on historical notions, interaction dynamics, and media art representations. The goal is to provide a comprehensive overview of real-time brainmedia, setting the stage for future explorations of new paradigms in communication between humans, machines, and the environment.
Automatic identification of the endangered hawksbill sea turtle behavior using deep learning and cross-species transfer learning
Authors: Jeantet Lorène , Zondo Kukhanya , Delvenne Cyrielle , Martin Jordan , Chevallier Damien , Dufourq Emmanuel 
Published: November 2024

ABSTRACT
The accelerometer, an onboard sensor, enables remote monitoring of animal posture and movement, allowing researchers to deduce behaviors. Despite the automated analysis capabilities provided by deep learning, data scarcity remains a challenge in ecology. We explored transfer learning to classify behaviors from acceleration data of critically endangered hawksbill sea turtles (Eretmochelys imbricata). Transfer learning reuses a model trained on one task from a large dataset to solve a related task. We applied this method using a model trained on green turtles (Chelonia mydas) and adapted it to identify hawksbill behaviors such as swimming, resting and feeding. We also compared this with a model trained on human activity data. The results showed an 8% and 4% F1-score improvement with transfer learning from green turtle and human datasets, respectively. Transfer learning allows researchers to adapt existing models to their study species, leveraging deep learning and expanding the use of accelerometers for wildlife monitoring.
Demographic, Disease, and Treatment Characteristics of Primary Tracheal Cancers
Authors: Armel Kristen , Stamey Taylor , Maitre Joseph , Cunningham Andrew R. , Ju Andrew W. , Burke Aidan , Speicher James E. , Navaid Musharraf , Bhatt Arjun , Larkins Michael C. 
Published: November 2024

Abstract
Background
Primary tracheal cancers (PTCs) are rare neoplasms underreported in the literature. No consensus guidelines exist for the treatment of these cancers and multimodal management of these cancers has not been adequately explored for cases diagnosed over the past 2 decades.

Methods
The Surveillance, Epidemiology, and End Results (SEER) database was queried to identify patients with PTC. Cox proportional hazards and log-rank testing was used to assess the association between demographic and treatment variables and 5-year cause-specific survival (CSS).

Results
Among the 689 identified patients, age < 65 years at diagnosis (hazard ratio [HR] 0.64, p < 0.001), non-squamous cell carcinoma (SCC) histology (HR 0.22, p < 0.001), and treatment with surgery (HR 0.43, p < 0.001) were all associated with increased 5-year CSS. Regarding disease histology, patients with adenoid cystic carcinomas (ACCs) had increased 5-year CSS compared with those with neither SCC nor ACC histology and those with SCC histology (83.4% [76.0%, 90.8%] versus 50.3% [42.5%, 58.1%] and 28.8% [23.2%, 34.4%]; p < 0.001) based on univariate analysis. Despite the improved CSS associated with surgery, 55% of the identified cohort did not undergo surgery, with only 5.5% of these patients having ACC compared with 58% having SCC (p < 0.001).

Conclusions
Age < 65 years, ACC histology, and treatment with surgery were associated with improved 5-year CSS among patients with PTC, although the significant proportion of this group not receiving surgery represents an opportunity for improved outcomes.
Reassessing the Association of Sedentary Behavior and Physical Activity with Ischemic Stroke: A Mendelian Randomization Study
Authors: Lin Yidie , Li Xuechao , Hu Meijing , Zhao Jian , Zhu Cairong 
Published: November 2024

ABSTRACT

Purpose
Findings from previous Mendelian randomization (MR) studies disagreed with the current scientific consensus regarding the role of physical activity (PA) and sedentary behavior in ischemic stroke (IS). We reassessed these associations with a focus on etiological subtypes of IS and the potential mediating roles of cardiometabolic traits and brain imaging-derived phenotypes (IDPs).

Methods
We performed MR analyses using summary statistics from genome-wide association studies of sedentary behavior and PA (n = 88,411~608,595), cardiometabolic traits (n = 393,193~694,649), brain IDPs (n = 33,224) and the latest IS data (62,100 cases and 1,234,808 controls). Inverse-variance weighted regression was used as the primary method, complemented by several sensitivity analyses. A two-step MR approach was employed to assess the mediating effects of cardiometabolic traits and brain IDPs.

Results
Genetic liability to leisure-time moderate-to-vigorous PA (LTMVPA) and higher overall PA (OPA) were associated with reduced risks of IS and small vessel stroke (Benjamini–Hochberg adjusted P < 0.05). Suggestive associations were observed between longer leisure-screen time and higher IS risk and between higher OPA and lower cardioembolic stroke risk (P < 0.05). The isotropic volume fraction in the anterior limb of the left internal capsule (ALIC), as well as some cardiometabolic metrics, partially mediated these associations. There was no evidence for causal effects of overall MVPA, overall light-intensity PA or overall sedentary duration on IS.

Conclusions
Longer LST, less OPA and not engaging in moderate-to-vigorous PA during leisure time were associated with higher risk of ischemic stroke. The associations between PA and ischemic stroke depended on different subtypes and were mediated by changes in ALIC and cardiometabolic biomarkers.
A Single Night in Hypoxia Either with or without Ketone Ester Ingestion Reduces Sleep Quality Without Impacting Next Day Exercise Performance
Authors: Stalmans Myrthe , Tominec Domen , Robberechts Ruben , Lauriks Wout , Ramaekers Monique , Debevec Tadej , Poffé Chiel 
Published: November 2024

ABSTRACT

Background
Sleeping at altitude is highly common in athletes as an integral part of altitude training camps or sport competitions. However, concerns have been raised due to expected negative effects on sleep quality, thereby potentially hampering exercise recovery and next-day exercise performance. We recently showed that ketone ester (KE) ingestion beneficially impacted sleep following strenuous, late evening exercise in normoxia, and alleviated hypoxemia. Therefore, we hypothesized that KE ingestion may be an effective strategy to attenuate hypox(em)ia-induced sleep dysregulations.

Methods
Eleven healthy, male participants completed three experimental sessions including normoxic training and subsequent sleep in normoxia or at a simulated altitude of 3,000 m while receiving either KE or placebo post-exercise and pre-sleep. Sleep was evaluated using polysomnography, while next-day exercise performance was assessed through a 30-min all-out time trial (TT30’). Physiological measurements included oxygen status, heart rate variability, ventilatory parameters, blood acid-base balance and capillary blood gases.

Results
Hypoxia caused a ~3% drop in sleep efficiency, established through a doubled wakefulness after sleep onset and a ~22% reduction in slow wave sleep. KE ingestion alleviated the gradual drop in SpO2 throughout the first part of the night, but did not alter hypoxia-induced sleep dysregulations. Neither KE, nor nocturnal hypoxia affected TT30’ performance, but nocturnal hypoxia hampered heart rate recovery following TT30’.

Conclusions
We observed that sleeping at 3,000 m altitude impairs sleep efficiency. Although this hypoxia-induced sleep disruption was too subtle to limit exercise performance, we for the first time indicate that sleeping at altitude might impair next-day exercise recovery. KE alleviated nocturnal hypoxemia only when SpO2 values dropped below ~85%, but this did not translate into improved sleep or next-day exercise performance.
Limb Underloading in Walking Transmits Less Dynamic Knee Joint Contact Forces after Anterior Cruciate Ligament Reconstruction
Authors: Munsch Amanda E. , Evans-Pickett Alyssa , Davis-Wilson Hope , Pietrosimone Brian , Rauch Carly M. , Roth Joshua D. , Franz Jason R. 
Published: November 2024

ABSTRACT

Introduction
Individuals with anterior cruciate ligament reconstruction (ACLR) often walk with a less dynamic vertical ground reaction force (vGRF), exemplified by a reduced first peak vGRF and elevated midstance vGRF compared to uninjured controls. However, the mechanism by which altered limb loading affects actual tibial plateau contact forces during walking remains unclear.

Methods
Our purpose was to use musculoskeletal simulation to evaluate the effects of first peak vertical ground reaction force (vGRF) biofeedback on bilateral tibiofemoral contact forces relevant to the development of post-traumatic osteoarthritis (OA) in 20 individuals with ACLR. We hypothesized that reduced first peak vGRF would produce less dynamic tibial plateau contact forces during walking in individuals with ACLR.

Results
As the pivotal outcome from this study, and in support of our hypothesis, we found that less dynamic vGRF profiles in individuals with ACLR – observations that have associated in prior studies with more cartilage breakdown serum biomarkers and reduced proteoglycan density – are accompanied by less dynamic tibiofemoral joint contact forces during walking.

Conclusion
We conclude that more sustained limb-level loading, a phenotype that associates with worse knee joint health outcomes following ACLR and was prescribed herein using biofeedback, alters the loading profile and magnitude of force applied to tibiofemoral cartilage.