bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus
Authors: Azam Sarwar , Sahu Abhisek , Pandey Naveen Kumar , Neupane Mahesh , Van Tassell Curtis P , Rosen Benjamin D , Gandham Ravi Kumar , Rath Subha Narayan , Majumdar Subeer S 
Published: February 2025

Abstract

Background
India harbors the world’s largest cattle population, encompassing over 50 distinct Bos indicus breeds. This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle. To comprehensively characterize the genomic variation within Bos indicus and, specifically, dairy breeds, we aim to identify non-reference sequences and construct a comprehensive pangenome.

Results
Five representative genomes of prominent dairy breeds, including Gir, Kankrej, Tharparkar, Sahiwal, and Red Sindhi, were sequenced using 10X Genomics ‘linked-read’ technology. Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb, comparable to the Bos indicus Brahman reference genome. A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods, revealing 8 Mb and 17.7 Mb of novel sequence respectively. A confident set of 6,844 Non-reference Unique Insertions (NUIs) spanning 7.57 Mb was identified through both methods, representing the pangenome of Indian Bos indicus breeds. Comparative analysis with previously published pangenomes unveiled 2.8 Mb (37%) commonality with the Chinese indicine pangenome and only 1% commonality with the Bos taurus pangenome. Among these, 2,312 NUIs encompassing ~ 2 Mb, were commonly found in 98 samples of the 5 breeds and designated as Bos indicus Common Insertions (BICIs) in the population. Furthermore, 926 BICIs were identified within 682 protein-coding genes, 54 long non-coding RNAs (lncRNA), and 18 pseudogenes. These protein-coding genes were enriched for functions such as chemical synaptic transmission, cell junction organization, cell-cell adhesion, and cell morphogenesis. The protein-coding genes were found in various prominent quantitative trait locus (QTL) regions, suggesting potential roles of BICIs in traits related to milk production, reproduction, exterior, health, meat, and carcass. Notably, 63.21% of the bases within the BICIs call set contained interspersed repeats, predominantly Long Interspersed Nuclear Elements (LINEs). Additionally, 70.28% of BICIs are shared with other domesticated and wild species, highlighting their evolutionary significance.

Conclusions
This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India. The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.
Systematic analysis of the pharmacogenomics landscape towards clinical implementation of precision therapeutics in Greece
Authors: Patrinos George P. , Karamperis Kariofyllis , Koufaki Margarita-Ioanna , Skokou Maria , Kordou Zoe , Sparaki Eirini , Skaraki Margarita , Mitropoulou Christina 
Published: February 2025

Abstract
Pharmacogenomics (PGx) aims to delineate a patient’s genetic profile with differences in drug efficacy and/or toxicity, particularly focusing on genes encoding for drug-metabolizing enzymes and transporters. Clinical implementation of PGx is a complex undertaking involving a multidisciplinary approach that includes, among others, a thorough understanding of a country’s preparedness to adopt this modern discipline and a detailed knowledge of PGx biomarkers allelic spectrum at a population level. In several European populations, particularly in countries with lower income, clinical implementation of PGx is still in its infancy. We have previously performed a pilot study to determine the prevalence of PGx biomarkers in 18 European populations, as the first step towards population PGx at the European level. Here, we provide a comprehensive analysis of the current state of PGx in Greece, including a detailed allelic frequency spectrum of clinically actionable PGx biomarkers, the level of PGx education in academia, the provision of PGx testing services from public and private laboratories, and the aspects of the regulatory PGx environment, especially with respect to the discrepancies between the Greek National Organization of Medicines and the European Medicine Agency and health technology assessment. This study would not only provide the foundations for expediting the adoption of PGx in clinical reality in Greece but can also serve as a paradigm for replicating future studies in other European countries, to expand on previously available pilot studies.
Environmental, socioeconomic, and sociocultural drivers of monkeypox transmission in the Democratic Republic of the Congo: a One Health perspective
Authors: Lu Guangyu , Chong Zeyin , Xu Enyu , Na Ce , Liu Kaixuan , Chai Liying , Xia Pengpeng , Yang Kai , Zhu Guoqiang , Zhao Jinkou , Müller Olaf 
Published: February 2025

Abstract

Background
Monkeypox (mpox) is an emerging zoonotic disease that has persistently impacted public health in endemic regions of West and Central Africa for over half a century. The Democratic Republic of the Congo (DRC) remains one of the countries most affected. Understanding the risk factors for disease transmission from a One Health perspective is of great importance in the risk assessment, prevention, and control of zoonotic diseases. Therefore, this study aimed to investigate the risk factors for human mpox transmission at the human–animal–environment interface in the DRC.

Methods
Epidemiological, environmental, socioeconomic, and sociocultural data from the DRC from 2000 to 2015 were obtained from publicly available dataset. Using these data, we applied negative binomial regression model, least absolute shrinkage and selection operator regression model, and principal component analysis (PCA) to identify key environmental, socioeconomic, and sociocultural factors contributing to mpox transmission. Moreover, a grey prediction model GM (1, n) was constructed to predict the epidemic trend of mpox post-2015 and validated using suspected mpox case data in the DRC from 2016 to 2021, sourced from the United States Centers for Disease Control and Prevention.

Results
Between 2000 and 2021, a total of 43,628 suspected mpox cases were reported in the DRC, with a peak of 6216 cases in 2020. From 2016 to 2021, suspected cases accounted for over half (24,379/43,628, 55.9%) of the total reported during the 2000–2021 period. The proportion of primary forest [incidence rate ratio (IRR): 1.023, 95% confidence interval (CI): 1.018–1.027], index of economic well-being (IRR: 1.046, 95% CI: 1.039–1.052), and mean annual precipitation (IRR 1.040, 95% CI: 1.031–1.049) were positively associated with mpox incidence. PCA identified five principal components, explaining 69% of the variance in the environmental, socioeconomic, and sociocultural variables. The first component was characterized by socioeconomic factors. The GM (1, n) model, based on the proportion of primary forest, index of economic well-being, and mean annual precipitation, predicted the epidemic trend (revealed relative error: 2.69).

Conclusions
Both socioeconomic and environmental factors play important roles in mpox transmission. Our study further highlighted the importance of considering the interconnectedness among humans, animals, and the environment, and treating these factors as a whole to explain the transmission and emergence of mpox outbreaks in the DRC according to the One Health concept.
Using the alternative model of personality disorders for DSM-5 traits to identify personality types, and the relationship with disordered eating, depression, anxiety and stress
Authors: Gilmartin Tanya , Gurvich Caroline , Dipnall Joanna F. , Sharp Gemma 
Published: February 2025

Abstract

Background
There is a substantial and growing evidence base that has identified three distinct personality types (Overcontrol, Undercontrol and Resilient) among samples of individuals with eating disorders, as well as non-clinical samples. Even in studies where up to six personality types have been identified, the three core types representing Overcontrol, Undercontrol and Resilient consistently emerge. The aim of the research was to explore whether latent Overcontrol and Undercontrol personality types could be identified using pathological personality types as part of the Alternative Model for Personality Disorders published in DSM-5. We further aimed to understand how these personality types were associated with eating pathology, depressed mood and anxiety.

Methods
A total of 391 women, 167 men and 10 gender-diverse individuals aged 16 to 31 years completed measures of the alternative model of personality disorder traits, disordered eating behaviours, eating pathology, depression, anxiety and stress. A systematic four-step process using hierarchical, k-means, and random forest cluster analyses were used to identify the best fitting cluster solution in the data.

Results
The results revealed a four-cluster solution that represented overcontrol, undercontrol, resilient and an antisocial/psychoticism cluster. The overcontrol, undercontrol, and antisocial/psychoticism types were all associated with increased disordered eating, eating pathology, depression, anxiety and stress compared to the resilient types, with the undercontrol cluster scoring significantly higher than the other three clusters on all measures of clinical pathology.

Conclusions
Pathological personality traits, as conceptualised within the DSM-5 alternative model of personality disorders may have merit for identifying overcontrol and undercontrol personality types. Our findings provide additional evidence that both overcontrol and undercontrol personality types are associated with increased eating pathology, depression, anxiety and stress.
Patient experiences and discomfort associated with mid-palatal temporary skeletal anchorage devices
Authors: Barry Aoife P. , Knode Vanessa , Fleming Padhraig S. , Ludwig Björn 
Published: February 2025

Abstract

Background
Mid-palatal placement of temporary skeletal anchorage devices (TSADs) has become increasingly popular among clinicians due to high success rates, low associated risk and streamlining and enhanced customization of associated supra-structures. There is however limited patient data in relation to associated experiences and impacts.

Methods
A survey of patients undergoing mid-palatal TSAD insertion was undertaken using a 27-item bespoke questionnaire. Questionnaires were sent using both electronic and surface mail with a 3-month period allowed for response. Pain experience; the use of analgesia; requirement for additional visits; impacts on hygiene, speech, eating, and hobbies; and social impacts were assessed. Reponses involved the use of a Visual Analogue Scale as well as binary information.

Results
Overall, 152 responses were obtained with 87.5% describing experience of TSAD insertion either “as expected” or “better”. Procedural pain was reported as mild in 62.5%. Local post-operative pain was scored as moderate in 21.1%. Some functional impairment was reported with 63.2% attributing difficulty with speech and 67.8% difficulty with eating due to the implant. However, these functional impairments were generally considered mild (by 68.1% and 60.2%, respectively) and most were very likely to recommend this treatment to others, with 65.1% (n = 99) scoring 8 or above out of 10.

Conclusions
Appreciable levels of pain, discomfort and functional impairment were noted with the use of mid-palatal TSADs. However, any unpleasant experiences were generally regarded as mild with most highly likely to recommend mid-palatal TSADs to prospective patients.
Freestanding VO2 membranes on epidermal nanomesh for ultra-sensitive correlated breathable sensors
Authors: Kim Dongha , Lee Dongju , Park Jiseok , Bae Jihoon , Chen Aiping , MacManus-Driscoll Judith L. , Lee Sungwon , Lee Shinbuhm 
Published: February 2025

Abstract
The interest in highly sensitive sensors is rapidly increasing for detecting very tiny signals for Internet of Things devices. Here, we achieve ultra-sensitive correlated breathable sensors based on freestanding VO2 membranes. We fabricate the membranes by growing VO2 films onto sacrificial Sr3Al2O6 layer grown on SrTiO3, selectively dissolving the Sr3Al2O6 in water, and then rendering freestanding VO2 membrane on nanomesh. The nanomeshes are extremely flexible, sweat permeable, and readily skin-adhesive. The resistance of the VO2 membranes is reversibly tuned by human’s tiny mechanical stimuli and breath stimuli. The stimuli modulate the Peierls dimerization of one-dimensional V−V chains in the VO2 lattice which concomitantly controls the electron correlation and hence resistivity. Since our breathable sensors operate based on quantum-mechanical correlation effects, their sensitivity is 1−2 orders of magnitude higher than conventional tactile and respiratory sensors based on other materials. Thus, the freestanding membranes of correlated oxides on epidermal nanomeshes are multifunctional platforms for developing ultra-sensitive correlated breathable sensors.

Graphical Abstract
Shortening duration of untreated illness in young people with first episode eating disorders: protocol of a randomised controlled feasibility trial of a smartphone friendly multi-modal decision-making tool (FREED-M) to improve help-seeking
Authors: Grycuk Luiza , Monssen Dina , Davies Molly R. , Sharpe Helen , Allen Karina L. , Prasad Vibhore , Potterton Rachel , Popat Priya , Mountford Victoria A. , McNeil Sheryllin , Lawrence Vanessa , Grant Nina , Goldsmith Kimberley A. , Glennon Danielle , Byford Sarah , Brown Amy , Schmidt Ulrike 
Published: February 2025

Abstract

Background
Early intervention gives young people the best chance to recover from eating disorders (EDs). An important focus of early intervention is shortening the time between a person first developing symptoms and starting treatment (duration of untreated eating disorder; DUED). Patient-related factors (e.g. poor mental health literacy and help-seeking difficulties) are strongly associated with DUED. The aims of our study are to co-design and test the feasibility of FREED-Mobile (FREED-M), an online intervention tool for young people with early-stage EDs. This tool aims to improve knowledge about EDs, increase motivation to seek treatment and teach early steps towards change or recovery, thus reducing DUED.

Methods
We will carry out a randomised controlled feasibility trial comparing the FREED-M tool with a control intervention where individuals are sign-posted to an ED charity website. The objectives of the proposed trial are to establish/estimate: (a) attrition rates at follow-up (primary feasibility outcome); (b) participant recruitment; (c) intervention uptake, completion rates and acceptability; (d) intervention effect sizes and standard deviations for outcomes to inform the sample size calculation for a large-scale randomised controlled trial (RCT); (e) stakeholder views on the intervention.
We aim to recruit 116 participants (young people, aged 16–25, with first episode ED) from primary care, schools and universities, ED services and social media. Online assessments will be carried out at baseline, end of intervention and follow-up (weeks 0, 4 and 12 post-randomisation, respectively). Outcomes will include motivation and readiness to change, attitudes and intentions towards help-seeking, ED symptoms, mood and social functioning, and health-related quality of life. Additionally, we will carry out a qualitative evaluation of participants’ views of the intervention and study design.

Discussion
The results of this feasibility trial will inform adaptations to the intervention as needed, as well as the study design (e.g. sample size, primary outcomes) of a future large-scale RCT to assess the effectiveness of the FREED-M intervention. If effective, this novel, online intervention has the potential for wide dissemination and for substantially reducing DUED to improve long-term patient outcomes.

Trial registration
ISRCTN, ISRCTN15662055. Registered 27 July 2022, https://www.isrctn.com/ISRCTN15662055.
Context-dependent modulation of spatial attention: prioritizing behaviourally relevant stimuli
Authors: Britt Noah , Chau Jackie , Sun Hong-jin 
Published: February 2025

Abstract
Human attention can be guided by semantic information conveyed by individual objects in the environment. Over time, we learn to allocate attention resources towards stimuli that are behaviourally relevant to ongoing action, leading to attention capture by meaningful peripheral stimuli. A common example includes, while driving, stimuli that imply a possibly hazardous scenario (e.g. a pedestrian about to cross the road) warrant attentional prioritization to ensure safe proceedings. In the current study, we report a novel phenomenon in which the guidance of attention is dependent on the stimuli appearing in a behaviourally relevant context. Using a driving simulator, we simulated a real-world driving task representing an overlearned behaviour for licensed drivers. While driving, participants underwent a peripheral cue-target paradigm where a roadside pedestrian avatar (target) appeared following a cylinder cue. Results revealed that, during simulated driving conditions, participants (all with driver’s licenses) showed greater attentional facilitation when pedestrians were oriented towards the road compared to away. This orientation-specific selectivity was not seen if the 3-D context was removed (Experiment 1) or the same visual scene was presented, but participants’ viewpoints remained stationary (Experiment 2), or an inanimate object served as a target during simulated driving (Experiment 3). This context-specific attention modulation likely reflects drivers’ expertise in automatically attending to behaviourally relevant information in a context-dependent manner.
Prospective evaluation of the diagnostic accuracy of FDG-PET/CT for the detection of sternal wound infection post-sternotomy
Authors: Cai Angela , Bakhshi Mehrshad , Lamarche Yoan , Harel Francois , Pelletier-Galarneau Matthieu 
Published: February 2025

Abstract

Purpose
Sternal wound infections (SWI) are complications of sternotomy and can be divided into deep SWI (DSWI) and superficial SWI (SSWI). In recent years, the use of 18F-Fluorodeoxyglucose (FDG)-positron emission tomography (PET)/computed tomography (CT) in diagnosing infections and inflammation has expanded significantly, with a growing number of clinical indications. This study assesses FDG-PET/CT diagnostic role in DSWI detection, the evolution of FDG uptake intensity in patients without DSWI and the potential biomarkers for DSWIs prediction.

Methods
We conducted a single center prospective study of consecutive patients referred for suspected SWI post-median sternotomy. Gold standard diagnosis was established by chart review of clinical follow-up, surgical findings, and cultures. To characterize the time between sternotomy and imaging, participants were subsequently subdivided into recent (< 3 months) or remote surgery (≥ 3 months) groups.

Results
44 FDG-PET/CT scans, 12 (27%) of which had DSWI according to the gold standard, were collected and analyzed. 20 studies were assigned to the recent group, and 24 studies to the remote surgery group. Sensitivity and specificity of FDG-PET/CT for detection of DSWI were 67% and 66%, respectively and an accuracy of 66% was obtained. Positive and negative predictive values were 42% and 84%, respectively. The NPV was higher in the remote surgery group (100%) compared to the recent surgery group (73%). SUVmax of the median sternal wound was significantly higher in the DSWI (9.3 ± 2.3) than the non-DSWI group (7.1 ± 3.0) (p = 0.025). There was however significant overlap of SUVmax between the two groups. CRP, WBC counts, and PCT levels were not significantly different between the DSWI and non-DSWI groups (p ≥ 0.34).

Conclusion
FDG-PET/CT has modest sensitivity and specificity for the detection of DSWI post-sternotomy. FDG-PET/CT results must take into account time since surgery; when PET/CT is performed more than 3 months following surgery, a negative scan can exclude DSWI with a high level of certainty.
Benign mature teratoma of the conus medullaris in a 57-year-old-female: case report and literature review
Authors: Yamba Yamba Daniel , Cissé Dramane , Hmamouche Oualid Mohammed , Lakhdar Faycal , Benzagmout Mohammed , Chakour Khalid , Chaoui Mohammed El Faiz 
Published: February 2025

Abstract

Background
The diagnosis of a mature teratoma in the conus medullaris is extremely rare, and few cases are reported in the literature.

Case presentation
We present a case of a 57-year-old woman who was referred from the neurology department for sudden weakness of the lower limbs. The patient has a medical history of chronic low back pain. She has normal bowel and bladder function. The neurological examination found reduced lower limb power, where the right and left proximal power were 0/5 and 2/5, respectively. Spinal cord MRI was performed, showing a well-delineated intramedullary mass at the level of the conus medullaris. Emergent surgery was performed using a surgical microscope, and the patient underwent a total resection of the tumor after T12–L2 bilateral laminectomy. The histological results were consistent with a benign mature teratoma and no additional postoperative neurological deficits were reported by the patient.

Conclusion
Adult’s cases of mature teratoma of the conus medullaris are extremely rare. The tumor present various symptoms primarily caused by compression, and definitive diagnosis is made by histological examination. Surgical excision is the most effective treatment, and total resection should be the aim. However, the surgical excision should be made under neurophysiological monitoring to avoid some injury to the surrounding neural tissue. Furthermore, the paucity of literature on the Adjuvant therapy for spinal teratoma is a challenge for neurosurgery for aiming of total resection.
Exploring physiological beta-hydroxybutyrate level in children treated with the classical ketogenic diet for drug-resistant epilepsy
Authors: Qiao Xiaoying , Ye Zimeng , Wen Jialun , Lin Sufang , Cao Dezhi , Chen Li , Zou Dongfang , Zou Huafang , Zhang Man , Chen Zhibin , Kwan Patrick , Scheffer Ingrid E. , Qin Jiong , Liao Jianxiang 
Published: February 2025

Abstract

Background
The ketogenic diet (KD) therapy is a primary treatment for drug-resistant epilepsy, and beta-hydroxybutyrate (BHB) is the main ketone produced during KD. However, the pattern of increase in BHB levels is not well understood, and the reference range for BHB need to be defined. The aim of this study was to evaluate the BHB levels in the first three months, especially one week, after KD initiation, and to explore the physiological reference range for BHB.

Methods
In our study, a fasting initiation strategy was used for the majority of patients (252/300, 84%) who underwent fasting for 24–48 h, the rest fasted for at least 12 h. The concentration of blood BHB was measured four times a day during the first week, at one month and three months. Seizure frequency was recorded at one week, one month and three months. Responders were defined as those with a seizure reduction 50% or more compared to baseline. BHB levels were compared between responders and non-responders. The BHB levels of responders were used to calculate the reference range.

Results
A total of 300 patients were recruited, of whom 172 (57%) had accessible BHB data. BHB levels rapidly rose to 2.0 mmol/L at 19 h, peaked at 4.2 mmol/L at 43 h of therapy, and stabilized by three months. The reference range for BHB was 1.1 to 4.9 mmol/L.

Conclusions
BHB levels increased rapidly following fasting, reaching the peak at day 2, stabilizing from the end of the first week through three months. The lower reference limit for BHB to ensure KD efficacy should be set at 1.1 mmol/L.