bluuebunny/crossref_metadata_2025_split huggingface dataset:
A rare presentation of dengue fever: bilateral psoas muscle hematoma, intrahepatic cholestatic hepatitis, pancreatitis and pancytopenia
Authors: Islam Jemima , Mondal Karimulla , Ghosh Sumit Kumar , Datta Anup Kumar , Ghosh Soumitra 
Published: September 2023

AbstractDengue is the foremost cause of arthropod-borne viral disease in the world. It is and commonly found in tropical and subtropical parts of the world. Dengue fever is caused by one of the four distinct serotypes (DENV 1–4) of single-stranded RNA Flavivirus genus and transmitted through Aedes mosquito. Infection caused by one serotype develops lifelong immunity to that serotype, but not to others. Dengue fever (DF) presents with high fever, headache, myalgia, and arthralgia, and rash. Severe dengue, dengue haemorrhagic fever (DHF), and dengue shock syndrome (DSS) are accompanied by thrombocytopenia, vascular leakage, and hypotension. DSS is characterized by shock, which can be fatal with case fatality high as 12% to 44%. There are few atypical manifestations of dengue fever growing with rising disease burden, often missed and sometimes difficult to diagnosis. In this case report, we will discuss atypical manifestations of bilateral psoas muscle hematoma, intrahepatic cholestatic hepatitis, pancreatitis and pancytopenia observed in dengue fever patient.
Construction of a Diagnostic Model for Small Cell Lung Cancer Combining Metabolomics and Integrated Machine Learning
Authors: Shang Xiaoling , Zhang Chenyue , Kong Ronghua , Zhao Chenglong , Wang Haiyong 
Published: September 2023

Abstract

Background
To date, no study has systematically explored the potential role of serum metabolites and lipids in the diagnosis of small cell lung cancer (SCLC). Therefore, we aimed to conduct a case-cohort study that included 191 cases of SCLC, 91 patients with lung adenocarcinoma, 82 patients with squamous cell carcinoma, and 97 healthy controls.

Methods
Metabolomics and lipidomics were applied to analyze different metabolites and lipids in the serum of these patients. The SCLC diagnosis model (d-model) was constructed using an integrated machine learning technology and a training cohort (n = 323) and was validated in a testing cohort (n=138).

Results
Eight metabolites, including 1-mristoyl-sn-glycero-3-phosphocholine, 16b-hydroxyestradiol, 3-phosphoserine, cholesteryl sulfate, D-lyxose, dioctyl phthalate, DL-lactate and Leu-Phe, were successfully selected to distinguish SCLC from controls. The d-model was constructed based on these 8 metabolites and showed improved diagnostic performance for SCLC, with the area under curve (AUC) of 0.933 in the training cohort and 0.922 in the testing cohort. Importantly, the d-model still had an excellent diagnostic performance after adjusting the stage and related clinical variables and, combined with the progastrin-releasing peptide (ProGRP), showed the best diagnostic performance with 0.975 of AUC for limited-stage patients.

Conclusion
This study is the first to analyze the difference between metabolomics and lipidomics and to construct a d-model to detect SCLC using integrated machine learning. This study may be of great significance for the screening and early diagnosis of SCLC patients.
Metabolomic Analysis of the Desert Moss Syntrichia caninervis Provides Insights into Plant Dehydration and Rehydration Response
Authors: Yang Qilin , Yang Ruirui , Gao Bei , Liang Yuqing , Liu Xiujin , Li Xiaoshuang , Zhang Daoyuan 
Published: September 2023

Abstract
Desiccation-tolerant (DT) plants can survive extreme dehydration and tolerate the loss of up to 95% of their water content, making them ideal systems to determine the mechanism behind extreme drought stress and identify potential approaches for developing drought-tolerant crops. The desert moss Syntrichia caninervis is an emerging model for extreme desiccation tolerance that has benefited from high-throughput sequencing analyses, allowing identification of stress-tolerant genes; however, its metabolic response to desiccation is unknown. A liquid chromatography–mass spectrometry analysis of S. caninervis at six dehydration–rehydration stages revealed 912 differentially abundant compounds, belonging to 93 metabolic classes. Many (256) metabolites accumulated during rehydration in S. caninervis, whereas only 71 accumulated during the dehydration period, in contrast to the pattern observed in vascular DT plants. During dehydration, nitrogenous amino acids (l-glutamic acid and cysteinylglycine), alkaloids (vinleurosine) and steroids (physalin D) accumulated, whereas glucose 6-phosphate decreased. During rehydration, γ-aminobutyric acid, glucose 6-phosphate and flavonoids (karanjin and aromadendrin) accumulated, as did the plant hormones 12-oxo phytodienoic acid (12-OPDA) and trans-zeatin riboside. The contents ofl-arginine, maltose, turanose, lactulose and sucrose remained high throughout dehydration–rehydration. Syntrichia caninervis thus accumulates antioxidants to scavenge reactive oxygen species, accumulating nitrogenous amino acids and cytoprotective metabolites and decreasing energy metabolism to enter a protective state from dehydration-induced damage. During subsequent rehydration, many metabolites rapidly accumulated to prevent oxidative stress and restore physiological activities while repairing cells, representing a more elaborate rehydration repair mechanism than vascular DT plants, with a faster and greater accumulation of metabolites. This metabolic kinetics analysis in S. caninervis deepens our understanding of its dehydration mechanisms and provides new insights into the different strategies of plant responses to dehydration and rehydration.
The limits of human mobility traces to predict the spread of COVID-19: A transfer entropy approach
Authors: Delussu Federico , Tizzoni Michele , Gauvin Laetitia 
Published: September 2023

Abstract
Mobile phone data have been widely used to model the spread of COVID-19; however, quantifying and comparing their predictive value across different settings is challenging. Their quality is affected by various factors and their relationship with epidemiological indicators varies over time. Here, we adopt a model-free approach based on transfer entropy to quantify the relationship between mobile phone-derived mobility metrics and COVID-19 cases and deaths in more than 200 European subnational regions. Using multiple data sources over a one-year period, we found that past knowledge of mobility does not systematically provide statistically significant information on COVID-19 spread. Our approach allows us to determine the best metric for predicting disease incidence in a particular location, at different spatial scales. Additionally, we identify geographic and demographic factors, such as users’ coverage and commuting patterns, that explain the (non)observed relationship between mobility and epidemic patterns. Our work provides epidemiologists and public health officials with a general—not limited to COVID-19—framework to evaluate the usefulness of human mobility data in responding to epidemics.
Physics-based approach to extend a de novo TIM barrel with rationally designed helix-loop-helix motifs
Authors: Kordes Sina , Beck Julian , Shanmugaratnam Sooruban , Flecks Merle , Höcker Birte 
Published: September 2023

Abstract
Computational protein design promises the ability to build tailor-made proteins de novo. While a range of de novo proteins have been constructed so far, the majority of these designs have idealized topologies that lack larger cavities which are necessary for the incorporation of small molecule binding sites or enzymatic functions. One attractive target for enzyme design is the TIM-barrel fold, due to its ubiquity in nature and capability to host versatile functions. With the successful de novo design of a 4-fold symmetric TIM barrel, sTIM11, an idealized, minimalistic scaffold was created. In this work, we attempted to extend this de novo TIM barrel by incorporating a helix-loop-helix motif into its βα-loops by applying a physics-based modular design approach using Rosetta. Further diversification was performed by exploiting the symmetry of the scaffold to integrate two helix-loop-helix motifs into the scaffold. Analysis with AlphaFold2 and biochemical characterization demonstrate the formation of additional α-helical secondary structure elements supporting the successful extension as intended.
Micro-porous PLGA/β-TCP/TPU scaffolds prepared by solvent-based 3D printing for bone tissue engineering purposes
Authors: Hatt Luan P , Wirth Sylvie , Ristaniemi Aapo , Ciric Daniel J , Thompson Keith , Eglin David , Stoddart Martin J , Armiento Angela R 
Published: September 2023

Abstract
The 3D printing process of fused deposition modelling is an attractive fabrication approach to create tissue-engineered bone substitutes to regenerate large mandibular bone defects, but often lacks desired surface porosity for enhanced protein adsorption and cell adhesion. Solvent-based printing leads to the spontaneous formation of micropores on the scaffold’s surface upon solvent removal, without the need for further post processing. Our aim is to create and characterize porous scaffolds using a new formulation composed of mechanically stable poly(lactic-co-glycol acid) and osteoconductive β-tricalcium phosphate with and without the addition of elastic thermoplastic polyurethane prepared by solvent-based 3D-printing technique. Large-scale regenerative scaffolds can be 3D-printed with adequate fidelity and show porosity at multiple levels analysed via micro-computer tomography, scanning electron microscopy and N2 sorption. Superior mechanical properties compared to a commercially available calcium phosphate ink are demonstrated in compression and screw pull out tests. Biological assessments including cell activity assay and live-dead staining prove the scaffold’s cytocompatibility. Osteoconductive properties are demonstrated by performing an osteogenic differentiation assay with primary human bone marrow mesenchymal stromal cells. We propose a versatile fabrication process to create porous 3D-printed scaffolds with adequate mechanical stability and osteoconductivity, both important characteristics for segmental mandibular bone reconstruction.
Female sexual medicine: an assessment of medical school curricula in a major United States city
Authors: Codispoti Nicolette , Negris Olivia , Myers Monica C , Petersen Anna , Nico Elsa , Romanello Jennifer P , Rubin Rachel S 
Published: September 2023

Abstract

Background
Although approximately 41% of women experience sexual dysfunction, limited education on female sexual medicine (FSM) in medical school results in underpreparedness among physicians when addressing these bothersome conditions.

Aim
This study aims to evaluate the extent to which FSM is represented in medical education by examining current preclinical and clinical curricula.

Methods
Preclinical curriculum materials on female sexual anatomy, physiology, and pathology, as well as obstetrics and gynecology clinical materials (syllabi, lecture materials, and supplemental resources), were collected from medical schools in the Chicago area. We utilized previous literature to identify specific components of medical school content to evaluate.

Outcomes
Upon reviewing each institution’s curricula, we evaluated materials for topic saturation and assessed goals of each syllabus in terms of required content.

Results
Curriculum materials were collected from 7 medical schools. In the preclinical assessment, 1 institution identified all anatomic components of the clitoris in our review, 4 discussed the physiology of the female orgasm, 3 highlighted the prevalence and epidemiology of female sexual dysfunction (FSD), 3 addressed treatments for FSD, and 1 instructed a genitourinary physical exam specific to assessing FSD. When assessing obstetrics and gynecology clinical materials, 5 institutions included topics related to FSM. Of these, only 1 institution had corresponding required synchronous clerkship time dedicated to these topics as a 1-hour lecture, in addition to an optional online training to third-year clinical students in comprehensive sexual history–taking practices, including screening for FSD. One other institution offered supplemental case-based gynecology modules including vulvovaginal diseases and chronic pelvic pain, though sexual pleasure, arousal, and libido were not included.

Clinical Implications
The results of this study highlight the need for the inclusion of standardized curricula related to FSM in medical education to equip future physicians to treat patients with sexual dysfunction.

Strengths and Limitations
The strengths of this study include that it is the first of its kind to complete a comprehensive review of FSM curricula at a cohort of undergraduate medical institutions. Its limitations include a small sample size of 7 medical schools limited to 1 geographical area.

Conclusion
Our focused needs assessment of medical schools in the Chicago area reveals inconsistencies in outlined institution-specific course goals related to FSM and thus highlights the need for restructuring the curricula to prepare future physicians to recognize and treat patients with sexual dysfunction.
Phase-amplitude coupling of Go/Nogo task-related neuronal oscillation decreases for humans with insufficient sleep
Authors: Zhang Peng , Sun Chuancai , Liu Zhongqi , Zhou Qianxiang 
Published: September 2023

Abstract
Phase-amplitude coupling (PAC) across frequency might be associated with the long-range synchronization of brain networks, facilitating the spatiotemporal integration of multiple cell assemblies for information transmission during inhibitory control. However, sleep problems may affect these cortical information transmissions based on cross-frequency PAC, especially when humans work in environments of social isolation. This study aimed to evaluate changes in the theta–beta/gamma PAC of task-related electroencephalography (EEG) for humans with insufficient sleep. Here, we monitored the EEG signals of 60 healthy volunteers and 18 soldiers in the normal environment, performing a Go/Nogo task. Soldiers also participated in the same test in isolated cabins. These measures demonstrated theta–beta PACs between the frontal and central-parietal, and robust theta–gamma PACs between the frontal and occipital cortex. Unfortunately, these PACs significantly decreased when humans experienced insufficient sleep, which was positively correlated with the behavioral performance of inhibitory control. The evaluation of theta–beta/gamma PAC of Go/Nogo task-related EEG is necessary to help understand the different influences of sleep problems in humans.
Sleep disturbances and change in multiple cognitive domains among older adults: a multicenter study of five Nordic cohorts
Authors: Overton Marieclaire , Skoog Johan , Laukka Erika J , Bodin Timothy Hadarsson , Mattsson Alexander Darin , Sjöberg Linnea , Hofer Scott M , Johansson Lena , Kulmala Jenni , Kivipelto Miia , Solomon Alina , Skoog Ingmar , Kåreholt Ingemar , Sindi Shireen 
Published: September 2023

Abstract

Study Objectives
We examined and compared cross-sectional and longitudinal associations between self-reported sleep disturbances and various cognitive domains in five separate Nordic European longitudinal aging studies (baseline N = 5631, mean age = 77.7, mean follow-up = 4.16 years).

Methods
Comparable sleep parameters across studies included reduced sleep duration/quality, insomnia symptoms (sleep latency, waking up at night, and early awakenings), short and long sleep duration, and daytime napping. The cognitive domains were episodic memory, verbal fluency, perceptual speed, executive functioning, and global cognition (aggregated measure). A series of mixed linear models were run separately in each study and then compared to assess the level and rate of change in cognitive functioning across each sleep disturbance parameter. Models were adjusted for age, sex, education, hypnotic usage, depressive symptoms, lifestyle factors, cardiovascular, and metabolic conditions. By using a coordinated analytic approach, comparable construct-level measurements were generated, and results from identical statistical models were qualitatively compared across studies.

Results
While the pattern of statistically significant results varied across studies, subjective sleep disturbances were consistently associated with worse cognition and steeper cognitive decline. Insomnia symptoms were associated with poorer episodic memory and participants sleeping less or more than 7–8 hours had a steeper decline in perceptual speed. In addition, daytime napping (&gt;2 hours) was cross-sectionally and longitudinally associated with all examined cognitive domains. Most observed associations were study-specific (except for daytime napping), and a majority of association estimates remained significant after adjusting for covariates.

Conclusion
This rigorous multicenter investigation further supports the importance of sleep disturbance, including insomnia, long and short sleep duration, and daytime napping on baseline cognitive functioning and rate of change among older adults. These sleep factors may be targeted in future lifestyle interventions to reduce cognitive decline.
Evaluation of protected benzoic acid on growth performance, nutrient digestibility, and gut health indices in starter pigs
Authors: Outlaw Alex , Gachman Alexandra , Kim Haejin , Xu Xiangyi , Tan Zhigang , Qin Zhonghua , Peng Xianfeng , Rudar Marko 
Published: September 2023

Abstract
Benzoic acid is a common alternative for antibiotic and zinc oxide use in nursery diets. Free benzoic acid (BZA) is often supplied, but this form is absorbed before it can exert any effect on distal segments of the gut. The study aimed to evaluate the effects of protected benzoic acid on growth performance, nutrient digestibility, plasma metabolites, and gut health indices in starter pigs. A total of 192 pigs were weaned at 28 ± 1 d age (initial body weight, 8.72 ± 1.13 kg). Pens were assigned to one of four treatment diets (n = 8 pens per treatment): (1) no additive (NC), (2) free benzoic acid (BZA; 0.6%), (3) protected benzoic acid (BC50; 0.2%, supplied at a ratio of one to three equivalents of BZA), and (4) antibiotic growth promoter (AGP; Carbadox, 50 ppm). Diets were fed for three weeks over two periods (period 1, 7 d; period 2, 14 d). Body weight and feed intake were measured for each period. Feces were collected at the end of each period to determine apparent total tract digestibility (ATTD) of organic matter (OM), gross energy (GE), and crude protein (CP). One pig per pen was euthanized per period to determine plasma metabolites; jejunum and ileum morphology; jejunum, ileum, and colon cytokine abundance; and jejunum, ileum, and colon tight junction protein expression. The AGP group had increased average daily gain (ADG) and average daily feed intake (ADFI) compared to other groups in period 1 and overall (P &lt; 0.05); however, ADG and ADFI of the BC50 group was intermediate between the NC and BZA groups and the AGP group in period 2. The ATTD of OM, GE, and CP were greater in the AGP group compared to the NC and BC50 groups (P &lt; 0.05), whereas the BZA group was intermediate. Jejunum and ileum villus height and crypt depth increased from period 1 to period 2 (P &lt; 0.01) but were similar across groups. Ileum and colon tumor necrosis factor-α (TNF-α) abundances were greater, whereas colon interleukin (IL)-1β and colon and ileum IL-8 abundances were less, in the AGP group compared to the BZA group (P &lt; 0.05); the NC and BC50 groups exhibited intermediate TNF-α, IL-1β, and IL-8 abundance in the ileum and colon. Jejunum cytokine abundance did not vary among groups but declined from period 1 to period 2 (P &lt; 0.05). Tight junction protein expression also did not vary among groups. In summary, protected BZA supported a slight increase in growth performance in starter pigs, suggesting its potential as an alternative feed additive in nursery diets.
Serum inflammation and oxidative DNA damage amelioration in cocks-fed supplemental Vernonia amygdalina and zinc in aflatoxin B1 contaminated diets
Authors: Olarotimi Olumuyiwa J , Gbore Francis A , Oloruntola Olugbenga D , Jimoh Olatunji A 
Published: September 2023

Abstract
The objective of the study was to assess the comparative effects of Vernonia amygdalina leaf meal (VALM) and zinc (Zn) on the serum proinflammatory and anti-inflammatory cytokines as well as DNA damage of cocks-fed aflatoxin B1 (AFB1) contaminated diets. A total of 250 sexually mature Isa White cocks of 24 weeks old were randomly distributed into five groups (treatments) with each containing 50 birds, which was replicated five times with 10 birds per replicate. Cocks in group A were fed basal diet only, group B was fed basal diet contaminated with 1 mg AFB1/kg diet, group C received diet B (basal + 1 mg/kg AFB1) with 50 mg/kg Zn, group D was fed diet B with 2.5 g/kg VALM, and group E received diet B with 5.0 g/kg VALM, respectively. Feed and water were supplied ad libitum with fresh feed added to the feed troughs at 6:00 a.m. and 6:00 p.m., respectively. While serum tumor necrosis factor-alpha (TNF-α), interleukin 1 beta (IL-1β), 8-hydroxy-2ʹ-deoxyguanosine (8-OHdG), and nuclear factor kappa B (NF-κB) were significantly (P &lt; 0.05) elevated among the cocks on diet B, significant (P &lt; 0.05) reductions were recorded among cocks on diets C, D, and E. Conversely, birds in group B had significant (P &lt; 0.05) depression in serum interleukin 4 (IL-4) and interleukin 10 (IL-10) while improvements (P &lt; 0.05) were recorded among cocks in groups C, D, and E, respectively. Therefore, the inclusion of VALM offset the adverse physiological effects of AFB1 observed among group B birds. The effects were comparable with the results presented by the cocksfed diet containing Zn.
Interpretable predictive models of genome-wide aryl hydrocarbon receptor-DNA binding reveal tissue-specific binding determinants
Authors: Filipovic David , Qi Wenjie , Kana Omar , Marri Daniel , LeCluyse Edward L , Andersen Melvin E , Cuddapah Suresh , Bhattacharya Sudin 
Published: September 2023

Abstract
The aryl hydrocarbon receptor (AhR) is an inducible transcription factor whose ligands include the potent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Ligand-activated AhR binds to DNA at dioxin response elements (DREs) containing the core motif 5′-GCGTG-3′. However, AhR binding is highly tissue specific. Most DREs in accessible chromatin are not bound by TCDD-activated AhR, and DREs accessible in multiple tissues can be bound in some and unbound in others. As such, AhR functions similarly to many nuclear receptors. Given that AhR possesses a strong core motif, it is suited for a motif-centered analysis of its binding. We developed interpretable machine learning models predicting the AhR binding status of DREs in MCF-7, GM17212, and HepG2 cells, as well as primary human hepatocytes. Cross-tissue models predicting transcription factor (TF)-DNA binding generally perform poorly. However, reasons for the low performance remain unexplored. By interpreting the results of individual within-tissue models and by examining the features leading to low cross-tissue performance, we identified sequence and chromatin context patterns correlated with AhR binding. We conclude that AhR binding is driven by a complex interplay of tissue-agnostic DRE flanking DNA sequence and tissue-specific local chromatin context. Additionally, we demonstrate that interpretable machine learning models can provide novel and experimentally testable mechanistic insights into DNA binding by inducible TFs.