bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emerging threat of artemisinin partial resistance markers (pfk13 mutations) in Plasmodium falciparum parasite populations in multiple geographical locations in high transmission regions of Uganda
Authors: Agaba Bosco B. , Travis Jye , Smith David , Rugera Simon P. , Zalwango Maria G. , Opigo Jimmy , Katureebe Charles , Mpirirwe Ruth , Bakary Dembo , Antonio Martin , Khalid Beshir , Ngonzi Joseph , Kamya Moses R. , Kaleebu Pontiano , Piot Peter , Cheng Qin 
Published: November 2024

Abstract
Background
Artemisinin-based combination therapy (ACT) is currently recommended for treatment of uncomplicated malaria. However, the emergence and spread of partial artemisinin resistance threatens their effectiveness for malaria treatment in sub-Saharan Africa where the burden of malaria is highest. Early detection and reporting of validated molecular markers (pfk13 mutations) in Plasmodium falciparum is useful for tracking the emergence and spread of partial artemisinin resistance to inform containment efforts.

Methods
Genomic surveillance was conducted at 50 surveillance sites across four regions of Uganda in Karamoja, Lango, Acholi and West Nile from June 2021 to August 2023. Symptomatic malaria suspected patients were recruited and screened for presence of parasites. In addition, dried blood spots (DBS) were collected for parasite genomic analysis with PCR and sequencing. Out of 563 available dried blood spots (DBS), a random subset of 240 P. falciparum mono-infections, confirmed by a multiplex PCR were selected and used for detecting the pfk13 mutations by Sanger sequencing using Big Dye Terminator method. Regional variations in the proportions of pfk13 mutations were assessed using the chi square or Fisher’s exact tests while Kruskal–Wallis test was used to compare absolute parasite DNA levels between wild type and mutant parasites.

Results
Overall, 238/240 samples (99.2%) contained sufficient DNA and were successfully sequenced. Three mutations were identified within the sequenced samples; pfk13 C469Y in 32/238 (13.5%) samples, pfk13 A675V in 14/238 (5.9%) and pfk13 S522C in (1/238 (0.42%) samples across the four surveyed regions. The prevalence of pfk13 C469Y mutation was significantly higher in Karamoja region (23.3%) compared to other regions, P = 0.007. The majority of parasite isolates circulating in West Nile are of wild type (98.3), P = 0.002. Relative parasite DNA quantity did not differ in samples carrying the wild type, C469Y and A675V alleles (Kruskal–Wallis test, P = 0.6373).

Conclusion
Detection of validated molecular markers of artemisinin partial resistance in multiple geographical locations in this setting provides additional evidence of emerging threat of artemisinin partial resistance in Uganda. In view of these findings, periodic genomic surveillance is recommended to detect and monitor levels of pfk13 mutations in other regions in parallel with TES to assess potential implication on delayed parasite clearance and associated treatment failure in this setting. Future studies should consider identification of potential drivers of artemisinin partial resistance in the different malaria transmission settings in Uganda.
Comparative study of neutralizing antibodies titers in response to different types of COVID-19 vaccines among a group of egyptian healthcare workers
Authors: Maher Sara , Assaly Nihal M. El , Aly Doaa Mamdouh , Atta Shimaa , Fteah Asmaa Mohamed , Badawi Hala , Zahran Manal Youssef , Kamel Manal 
Published: November 2024

Abstract
Background
Defining the protective thresholds against the severe-acute-respiratory-syndrome-related corona virus-2 pandemic is a crucial challenge. To reduce the risks of severe disease, hospitalization, and death, various COVID-19 vaccines have been rapidly developed.

Aim of the work
This study aimed to assess the impact of three common COVID-19 vaccine types; two mRNA COVID-19 vaccines: (Pfizer/BioNTech’s BNT162b2 and Moderna’s mRNA-1273), one adenoviral vector vaccine: Oxford/AstraZeneca’s ChAdOx1, and one inactivated vaccine (Sinovac Biotech/China’s Sinovac) on the level of neutralizing antibodies, considering factors such as vaccine type, demographic characteristics, and hybrid immunity. We conducted a direct comparative analysis involving 300 healthcare workers, both with and without prior SARS-CoV-2 infection (B.1, C.36.3, and AY.32 (Delta) variants). Neutralizing antibodies levels were measured at baseline (before vaccination), before the second dose, and six months after the second dose.

Results
The results showed a significant increase in neutralizing antibodies levels after complete vaccination with all vaccine types. Among healthcare workers, those vaccinated with mRNA vaccines (Moderna or Pfizer) exhibited the highest neutralizing antibodies titers, followed by AstraZeneca, and finally Sinovac with the lowest titer. On studying the effect of previous COVID-19 infection after vaccination, no significant difference in neutralizing antibodies levels was observed between healthcare workers vaccinated with mRNA or AstraZeneca vaccines, both with prior COVID-19 infection, following the first and six months after the second dose.

Conclusion
These findings suggest that individuals with prior COVID-19 may only require a single dose of mRNA or AstraZeneca vaccines to achieve a similar level of immunization as those without prior COVID-19 who completed the vaccination program.

Highlights

There is a significant increase in neutralizing antibodies levels after complete vaccination against COVID-19

Vaccination with mRNA vaccines exhibits the highest neutralizing antibodies titers.

Vaccination with Sinovac exhibits the lowest neutralizing antibodies titers.

Graphical abstract
Pasteurella multocida from deep nasal swabs and tracheobronchial lavage in bovine calves from Sweden
Authors: Myrenås Mattias , Pringle Märit , Harbom Boel , Bengtsson Björn 
Published: November 2024

Abstract
Background
Bovine respiratory disease (BRD) is common in intensively raised cattle and is often treated with antibiotics. For practitioners, knowledge of the bacteria involved in an outbreak and their antibiotic susceptibility is warranted. To this end, samples from the upper or lower respiratory tract of calves can be submitted for bacteriological culture and susceptibility testing of relevant isolates. However, it is debated whether isolates from the upper respiratory tract are representative of bacteria causing infections in the lower respiratory tract. In this study, we used MALDI-TOF MS, multilocus sequence typing (MLST) and core-genome multilocus sequence typing (cgMLST) to compare culture results of 219 paired samples (sample pairs) of deep nasal swabs (DNS) and tracheobronchial lavage (TBL). The sample pairs came from 171 calves in 30 calf groups across 25 farms with 48 calves sampled twice.

Results
The predominant bacterial pathogen was Pasteurella multocida, which was isolated from 37.4% of DNS and 22.4% of TBL. There was no statistically significant difference in isolation frequency of P. multocida between calves considered healthy and those suspected for BRD for DNS (P = 0.778) or TBL (P = 0.410). Among the 49 sample pairs where P. multocida was isolated from TBL, the same species was isolated from DNS in 29 sample pairs (59.2%). Isolates from 28 of these sample pairs were evaluated by MLST, and in 24 pairs (86.0%) P. multocida from DNS and TBL were of the same sequence type (ST). Moreover, cgMLST showed that the genetic distance between isolates within 21 of the 28 sample pairs (75.0%), was less than two alleles, and DNS and TBL isolates were considered identical. In seven sample pairs (25%), the genetic distance was greater, and DNS and TBL isolates were considered nonidentical.

Conclusions
Pasteurella multocida was readily isolated from DNS and in calves where this species was isolated also from TBL, DNS and TBL isolates were identical in 75% of the sample pairs. This suggests that during an outbreak of BRD, submission of DNS samples from 4 to 6 calves could be a convenient approach for practitioners seeking guidance on P. multocida present in the lower respiratory tract and their antibiotic susceptibility.
Assessing the contributions of gender, clinical symptoms, and psychometric traits to non-suicidal self-injury behaviors in Chinese adolescents: a nomogram approach
Authors: Shen Guanghui , Li Cheng-Han , Ruan Qian-Nan , Xu Su , Yan Wen-Jing 
Published: November 2024

Abstract
Background
Non-suicidal self-injury (NSSI) behaviors among adolescents with mood disorders represent a significant global public health concern. This study aimed to assess the prevalence and identify key predictors of NSSI behaviors in Chinese adolescents diagnosed with depressive or bipolar disorders, addressing a critical gap in the literature.

Method
Data from 2343 participants in the Chinese Adolescent Depression Cohort (CADC) were analyzed. The study employed a comprehensive approach, utilizing medical records, clinical assessments, and validated psychometric instruments. Statistical analyses included chi-square tests, logistic regression, and ROC curve analyses, culminating in the development of a predictive nomogram.

Results
The prevalence of NSSI behaviors was strikingly high at 73.32%. Significant predictors included female gender (AOR = 2.14, 95% CI [1.70, 2.68]), presence of hallucinations (AOR = 1.52, 95% CI [1.18, 1.97]), borderline personality features (AOR = 1.03, 95% CI [1.01, 1.08]), and childhood trauma (AOR = 1.02, 95% CI [1.01, 1.03]). The study’s key contribution is a predictive nomogram with an AUC of 0.74, demonstrating good efficacy in predicting NSSI behaviors.

Conclusion
This research reveals an alarmingly high prevalence of NSSI behaviors in Chinese adolescents with mood disorders and identifies critical predictors spanning demographic, clinical, and psychometric domains. The developed nomogram offers a novel approach for risk assessment, highlighting the importance of comprehensive evaluations in adolescent mental healthcare. These findings have significant implications for developing targeted interventions and improving risk assessment strategies in clinical practice.
Two distinct clinical progressions of P67phox-deficient CGD, both commencing with cervical lymphadenitis
Authors: Dong Lili , Zhang Lei , Xu Chunna , Guo Mingfa , Tang Yu , Shen Yuelin 
Published: November 2024

AbstractWe present two rare cases of p67phox-deficient chronic granulomatous disease (CGD) caused by compound heterozygous mutations in the NCF2 gene. They developed cervical lymphadenitis as the initial manifestation of CGD but had distinct clinical progressions. Patient 1 presented with aspergillous meningitis, an extremely rare manifestation of neurological involvement in CGD, which has not been reported before. Patient 2 presented with non-infectious inflammatory lymphadenitis is also very rare and has not been reported previously. These cases emphasize the importance of considering p67phox-deficient CGD in children with late-onset invasive fungal infections and non-infectious inflammatory lesions. Additionally, we also reviewed previous reports of Chinese patients with P67phox-Deficient CGD. Our objective is to raise awareness about the clinical, diagnostic, and genetic characteristics of P67phox-deficient CGD in China, to reduce misdiagnosis and improve the management and prognosis of the disease.
StreaMD: the toolkit for high-throughput molecular dynamics simulations
Authors: Ivanova Aleksandra , Mokshyna Olena , Polishchuk Pavel 
Published: November 2024

AbstractMolecular dynamics simulations serve as a prevalent approach for investigating the dynamic behaviour of proteins and protein–ligand complexes. Due to its versatility and speed, GROMACS stands out as a commonly utilized software platform for executing molecular dynamics simulations. However, its effective utilization requires substantial expertise in configuring, executing, and interpreting molecular dynamics trajectories. Existing automation tools are constrained in their capability to conduct simulations for large sets of compounds with minimal user intervention, or in their ability to distribute simulations across multiple servers. To address these challenges, we developed a Python-based tool that streamlines all phases of molecular dynamics simulations, encompassing preparation, execution, and analysis. This tool minimizes the required knowledge for users engaging in molecular dynamics simulations and can efficiently operate across multiple servers within a network or a cluster. Notably, the tool not only automates trajectory simulation but also facilitates the computation of free binding energies for protein–ligand complexes and generates interaction fingerprints across the trajectory. Our study demonstrated the applicability of this tool on several benchmark datasets. Additionally, we provided recommendations for end-users to effectively utilize the tool.Scientific contributionThe developed tool, StreaMD, is applicable to different systems (proteins, ligands and their complexes including co-factors) and requires a little user knowledge to setup and run molecular dynamics simulations. Other features of StreaMD are seamless integration with calculation of MM-GBSA/PBSA binding free energies and protein-ligand interaction fingerprints, and running of simulations within distributed environments. All these will facilitate routine and massive molecular dynamics simulations.
Machine learning models including patient-reported outcome data in oncology: a systematic literature review and analysis of their reporting quality
Authors: Krepper Daniela , Cesari Matteo , Hubel Niclas J. , Zelger Philipp , Sztankay Monika J. 
Published: November 2024

Abstract
Purpose
To critically examine the current state of machine learning (ML) models including patient-reported outcome measure (PROM) scores in cancer research, by investigating the reporting quality of currently available studies and proposing areas of improvement for future use of ML in the field.

Methods
PubMed and Web of Science were systematically searched for publications of studies on patients with cancer applying ML models with PROM scores as either predictors or outcomes. The reporting quality of applied ML models was assessed utilizing an adapted version of the MI-CLAIM (Minimum Information about CLinical Artificial Intelligence Modelling) checklist. The key variables of the checklist are study design, data preparation, model development, optimization, performance, and examination. Reproducibility and transparency complement the reporting quality criteria.

Results
The literature search yielded 1634 hits, of which 52 (3.2%) were eligible. Thirty-six (69.2%) publications included PROM scores as a predictor and 32 (61.5%) as an outcome. Results of the reporting quality appraisal indicate a potential for improvement, especially in the areas of model examination. According to the standards of the MI-CLAIM checklist, the reporting quality of ML models in included studies proved to be low. Only nine (17.3%) publications present a discussion about the clinical applicability of the developed model and reproducibility and only three (5.8%) provide a code to reproduce the model and the results.

Conclusion
The herein performed critical examination of the status quo of the application of ML models including PROM scores in published oncological studies allowed the identification of areas of improvement for reporting and future use of ML in the field.
Role of copeptin as biomarker of volume overload in children with end-stage renal disease
Authors: Abdelhamid Nehal , Abdelmawla Mohamed A. , El-Sherbini Inji G. , Wahby Aliaa A. , Aboafya Zahraa I. , Abdelkader Mona 
Published: November 2024

Abstract
Background
Children who undergo dialysis may develop hypertension and cardiovascular morbidity as a result of fluid overload. The intravascular parameter is clinically relevant in children because it directly influences systemic blood pressure, cardiac output, and cardiovascular squeals. Optimum fluid management is still a chronic clinical challenge, despite recent advances in the care of children with end-stage renal disease (ESRD). The paraventricular and supraoptic nuclei of the hypothalamus emit arginine vasopressin (AVP), a nonapeptide. It is secreted into the bloodstream by the pituitary gland in response to both osmotic and nonosmotic stimuli. Copeptin and AVP are released at equimolar concentrations. The aim of the study is to determine if copeptin, a surrogate marker of AVP, may be used to predict unfavorable outcomes, including chronic volume overload and its impact on hypertension and cardiovascular diseases in children undergoing dialysis.

Results
A cross-sectional study including 65 children: The mean age of the investigated patients was 10.79 ± 2.857 years, with 53% being male. The patient group had significantly greater mean blood levels of AVP and copeptin compared to the control group (P value = 0.0001). 45% of patients experienced cardiac issues, specifically left ventricular hypertrophy. Hypertensive patients accounted for 57%. The mean blood levels of AVP and copeptin were considerably greater in individuals with cardiac problems and hypertension.

Conclusions
Hemodynamics have a significant influence on cardiac function and hypertension in children receiving hemodialysis. Copeptin is a more appropriate biomarker for evaluating the effects of AVP on hypertension and cardiac problems in children with ESRD.
Does the placement of acetabular cups differ between right and left sides for a right-handed surgeon operating through a direct lateral approach? A comparative study
Authors: Khalifa Ahmed A. , Abdelaal Ahmed M. 
Published: November 2024

Abstract
Purpose
Although many factors were suggested to affect acetabular cup positioning during primary total hip arthroplasty, the effect of surgeon handedness was rarely evaluated. We aimed primarily to assess the difference in cup positioning (inclination and anteversion) between the right and left sides during primary THA. Secondly, to check the difference in the percentages of cups positioned in the safe zone for inclination and anteversion and if there will be a difference in cup positioning according to the type of cup fixation (cemented vs. cementless).

Methods
Cup inclination and anteversion of 420 THAs were radiographically evaluated retrospectively. THAs were performed by a senior right-handed surgeon, who operated through a direct lateral approach in a lateral decubitus position using manual instruments and freehand technique for cup placement. Patients were assigned to two groups: Group A (right, or dominant side), and Group B (left, or non-dominant side), with equal cases of THAs (n = 210) in each group.

Results
No difference was found in patients’ basic characteristics, preoperative diagnosis, and cup fixation (54.3% cemented and 45.7% cementless) between the two groups. There was a significant difference in cup inclination between Groups A and Group B (40.1° ± 6.3° vs. 38.2° ± 6.1°) (P = 0.002). No significant difference was revealed in anteversion between the two groups (11.7° ± 4.4° vs. 11.8° ± 4.7°) (P = 0.95). The percentage of cups located within the safe zone in terms of both inclination and anteversion was 85.2% vs. 83.8% and 69% vs. 73.3% for Group A and Group B, according to Lewinnek and Callahan’s safe zones, respectively. There existed a significant difference in the cemented cup inclination between Group A and Group B (40.8° ± 6.4° vs. 38.3° ± 6.3°) (P = 0.004).

Conclusion
Cup inclination is affected by the surgeon’s handedness when operating through a direct lateral approach and using a freehand technique, while anteversion is less affected. Furthermore, the difference is greater with cemented cups.
Functional and sensory evaluation of bread made from wheat flour fortified with wine byproducts
Authors: Muñoz-Bernal Óscar Adrián , Coria-Oliveros Alma Janeth , Vazquez-Flores Alma Angelica , Subiria-Cueto Carlos Rodrigo , De La Rosa Laura A. , de la Luz Reyes-Vega Maria , Rodrigo-García Joaquín , del Rocio Martinez-Ruiz Nina , Alvarez-Parrilla Emilio 
Published: November 2024

AbstractGrape pomace is the main byproduct of the wine industry and an important source of dietary fiber and phenolic compounds. Grape pomace powder (GPP) partially substituted 8, 10, 12, 15, and 25% of the wheat flour in bread formulations. The proximate composition, total dietary fiber content, phenolic compounds, texture profile, color, and bioaccessibility of phenolic compounds in vitro were measured in the bread. Bread sensory acceptance by consumers was determined using a 9-point hedonic scale. Compared with the control bread (CB), the 8% GPB-substituted bread presented the best results and exhibited an increase in total protein content (7.5%) and total dietary fiber content (6.1%). The total phenolic content was greater in GPB (5.1 mg GAE/g) than in CB (2.1 mg GAE/g). Adding GPP to the bread affected the color, and the color of the GPB-treated bread was darker than that of the CB-treated bread. Still, no significant differences were detected regarding the texture profile or consumer sensory acceptance between the GPB-treated and CB-treated bread. The in vitro analysis of phenolic compound bioaccessibility revealed no differences between the two samples during gastrointestinal digestion. GPP is an interesting byproduct that can be used in bakery. The replacement of 8% of the bread with GPP increased the nutritional content of the bread, particularly the protein, total dietary fiber, and total phenolic content, without affecting the texture or sensory acceptance of the bread. To understand the possible beneficial effect of GPB on consumers, further research on the bioavailability of phenolic compounds and the impact of dietary fiber increment needs to be assessed.
Graphical Abstract