bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information
Authors: Pang Xiao-Xu , Zhang Da-Yong 
Published: January 2024

Abstract
In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression—the transfer of genetic material from extinct or unsampled lineages to extant species—emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving 3 species with a known phylogenetic tree. Using mathematical analyses and simulations, we evaluated the performance of popular phylogenetic methods, including HyDe and PhyloNet/MPL, and the full-likelihood method, Bayesian Phylogenetics and Phylogeography (BPP), in detecting ghost introgression. Our findings suggest that heuristic approaches relying on site-pattern counts or gene-tree topologies struggle to differentiate ghost introgression from introgression between sampled non-sister species, frequently leading to incorrect identification of donor and recipient species. The full-likelihood method BPP uses multilocus sequence alignments directly—hence taking into account both gene-tree topologies and branch lengths, by contrast, is capable of detecting ghost introgression in phylogenomic datasets. We analyzed a real-world phylogenomic dataset of 14 species of Jaltomata (Solanaceae) to showcase the potential of full-likelihood methods for accurate inference of introgression.
Melatonin alleviates cadmium toxicity by regulating root endophytic bacteria community structure and metabolite composition in apple
Authors: Cao Yang , Zhang Jiran , Du Peihua , Ji Jiahao , Zhang Xue , Xu Jizhong , Ma Changqing , Liang Bowen 
Published: January 2024

Abstract
The level of cadmium (Cd) accumulation in orchard soils is increasing, and excess Cd will cause serious damage to plants. Melatonin is a potent natural antioxidant and has a potential role in alleviating Cd stress. This study aimed to investigate the effects of exogenous melatonin on a root endophyte bacteria community and metabolite composition under Cd stress. The results showed that melatonin significantly scavenged the reactive oxygen species and restored the photosynthetic system (manifested by the improved photosynthetic parameters, total chlorophyll content and the chlorophyll fluorescence parameters (Fv/Fm)), increased the activity of antioxidant enzymes (the activities of catalase, superoxide dismutase, peroxidase and ascorbate oxidase) and reduced the concentration of Cd in the roots and leaves of apple plants. High-throughput sequencing showed that melatonin increased the endophytic bacterial community richness significantly and changed the community structure under Cd stress. The abundance of some potentially beneficial endophytic bacteria (Ohtaekwangia, Streptomyces, Tabrizicola and Azovibrio) increased significantly, indicating that the plants may absorb potentially beneficial microorganisms to resist Cd stress. The metabolomics results showed that melatonin significantly changed the composition of root metabolites, and the relative abundance of some metabolites decreased, suggesting that melatonin may resist Cd stress by depleting root metabolites. In addition, co-occurrence network analysis indicated that some potentially beneficial endophytes may be influenced by specific metabolites. These results provide a theoretical basis for studying the effects of melatonin on the endophytic bacterial community and metabolic composition in apple plants.
Molecular monitoring of treatment efficacy in human visceral leishmaniasis
Authors: Roy Sutopa , Moulik Srija , Chaudhuri Surya Jyati , Ghosh Manab K , Goswami R P , Saha Bibhuti , Chatterjee Mitali 
Published: January 2024

Abstract

Background
Focused efforts of the visceral leishmaniasis elimination program have led to a drastic decline in cases, and the present challenge is disease monitoring, which this study aimed to assess.

Methods
A Leishmania kinetoplastid-targeted qPCR quantified parasite load at disease presentation, and following treatment completion (n=49); an additional 80 cases were monitored after completion of treatment.

Results
The parasite load at disease presentation was 13 461.00 (2560.00–37764.00)/µg gDNA, which upon completion of treatment reduced in 47 of 49 cases to 1(1–1)/µg gDNA, p&lt;0.0001. In 80 cases that presented &gt;2 months post-treatment, their parasite burden similarly decreased to 1(1–1)/µg gDNA except in 6 of 80 cases, which were qPCR positive.

Conclusion
In 129 cases of visceral leishmaniasis, qPCR by quantification of parasite burden proved effective for monitoring treatment.
Assessing Neurological Complications in Thoracic Three-Column Osteotomy
Authors: Lo Yuan-Shun , Shi Ben-Long , Lin Erh-Ti Ernest , Yeh Chen-Wei , Tsai Chun-Hao , Chen Hsien-Te , Zhu Ze-Zhang , Qiu Yong 
Published: January 2024

Study Design.
Retrospective comparative study.

Objective.
To investigate the occurrence of neurological complications in patients undergoing thoracic three-column osteotomy (3CO) utilizing an magnetic resonance imaging (MRI)-based classification that assesses spinal cord shape and the presence of cerebrospinal fluid at the curve apex and evaluate its prognostic capacity for postoperative neurological deficits.

Summary of Background Data.
Recent advancements in correction techniques have improved outcomes for severe spinal deformity patients undergoing 3CO. A novel MRI-based spinal cord classification system was introduced, but its validation and association with postoperative complications remain unexplored.

Materials and Methods.
Between September 2012 and September 2018, a retrospective analysis was conducted on 158 adult patients with spinal deformities undergoing 3CO. Radiographic parameters were measured. T2-weighted axial MRI was used to describe spinal cord morphology at the apex. Intraoperative neurophysiological monitoring alerts were recorded, and preoperative and postoperative neurological functions were assessed using the Frankel score. Categorical data were compared using the χ2 or the Fisher exact test. The paired t test was utilized to assess the mean difference between preoperative and postoperative measurements, while the one-way analysis of variance and independent t test were used for comparative analyses among the different spinal cord types.

Results.
Patients were categorized into three groups: type 1, type 2, and type 3, consisting of 12, 85, and 61 patients. Patients with type 3 morphology exhibited larger Cobb angles of the main curve (P<0.001). This disparity persisted both postoperatively and during follow-up (P<0.05). Intraoperative neurophysiological monitoring alerts were triggered in 32 patients (20.3%), with a distribution of one case in type 1, six cases in type 2, and 22 cases in type 3 morphologies (P<0.001). New neurological deficits were observed in 15 patients (9.5%), with 1, 3, and 11 cases in type 1, 2, and 3 morphologies, respectively.

Conclusions.
Patients with type 3 morphology exhibited greater spinal deformity severity, a higher likelihood of preoperative neurological deficits, and an elevated risk of postoperative neurological complications. This underscores the utility of the classification as a tool for predicting postoperative neurological complications in patients undergoing thoracic 3CO.

Level of Evidence:
4.
Impact of aerobic and resistance training on fatigue, quality of life, and physical activity in prostate cancer patients: a systematic review and meta-analysis
Authors: Nader Simon , Massoud Amr , Al-Obeidat Feras , Mohamed Waleed F. , Hafez Wael , Rashid Asrar , Yousef Omar A. E. , Gador Muneir , Ahmed Sabah , Jose Mohan , Abdelrahman Ahmed , abdelshakour Mahmoud , Fathey Sherihan , Osorio María F. , Robles-Velasco Karla , Cherrez-Ojeda Iván 
Published: January 2024

Background:
Prostate cancer (PCa) is a prevalent cancer with significant morbidity and mortality rates. In most cases, PCa remains asymptomatic until advanced disease manifests with symptoms, such as benign prostate hyperplasia. Timely detection and better management have improved overall survival in patients with PCa, and fatigue, reduced physical activity, and impaired quality of life (QoL) remain major challenges that impact daily life.

Objective:
This study aimed to systematically review and conduct a meta-analysis to evaluate the impact of aerobic and resistance training on fatigue, QoL, and physical activity in PCa patients undergoing treatment.

Material and methods:
A comprehensive literature search was conducted using the PubMed, Cochrane Library, and clinicaltrials.gov databases, adhering to the PRISMA guidelines. Twenty studies, involving 1393 participants, were included in the final analysis. The inclusion criteria were studies that evaluated the effects of exercise interventions relative to passive controls in patients with PCa were included. The primary outcomes of interest were fatigue, QoL, and PA. Data from eligible studies were extracted, and a meta-analysis was performed using RevMan 5.40.

Results:
Twenty studies met our inclusion criteria. Data analysis of the included studies demonstrated a significant improvement in QoL among PCa patients in the exercise group compared to the control group (SMD=0.20, 95% CI=0.07–0.34, P=0.003). However, there was no significant association between exercise and fatigue (SMD=0.07, 95% CI=−0.13–0.26, P=0.51). Sensitivity analysis did not alter these findings. Regarding physical activity outcomes, the control group exhibited superior performance in the 400 m walk test (P<0.05). No significant associations were found between exercise and the 6 m walk test or up-and-go time.

Conclusion:
This systematic review revealed that aerobic and resistance training enhance the QoL of patients with PCa, although it has a limited impact on fatigue and physical activity levels. These findings advocate a shift in clinical practice and the positioning of exercise as a core component of comprehensive cancer care. Tailoring exercise regimens according to individual patient needs and treatment stages should become the norm in treatment planning. This approach goes beyond physical wellness and addresses the psychological and emotional facets of cancer management. Moreover, there is an evident need for further research to develop holistic exercise interventions that effectively address the complex dynamics of fatigue, physical activity, and QoL in this patient group.
Integration of Intraosseous Approach Method in Georgia
Authors: Kikodze Nino , Nemsadze Ketevan 
Published: January 2024

Objective
In pediatric emergencies, as in case of shock, the use of intraosseous (IO) route is recommended to get rapid vascular access as soon as possible, as it revealed better outcome. Nevertheless, the IO approach is not used at all and/or is limited because of lack of demand and lack of training on the issue of medical staff. The aim of the study was to test applicable and/or demand of IO in clinics providing pediatric critical care services and assess the opportunities to integrate IO access use in emergency care in Georgia.

Methods
A quasi-experimental study was conducted, following a training of medical staff to perform IO access procedure. Our study involved 140 children admitted to emergency department, 114 of whom underwent venous access and 26 underwent IO access. Several parameters were monitored and reported. Outcomes were compared between the 2 procedures.

Results
Use of an IO catheter has significantly altered the clinical outcome of the patient's condition; 35% of the total number of patients needed to continue their treatment in the intensive care unit, whereas 65% of the patient's continued treatment in the various general wards (compared with 99% and 1%, respectively, in intravenous access patients). None of IO patients were transferred to other clinics because of the deterioration of their clinical condition. Complications in the form of local infection were not observed in any of the patients using the IO approach (which is interesting in terms of infection control).

Conclusion
With proper training and in certain indications, the internationally approved method can be safely used in pediatric emergency management in Georgian and similar country health system contexts. Several urgent conditions with high rates of requiring hospitalization could benefit from the IO approach.
Mediation analysis of chronic kidney disease risk factors using kidney biomarkers in women living with HIV
Authors: Edrosolan Kristienne A. , Shlipak Michael G. , Scherzer Rebecca , Estrella Michelle M. , Gustafson Deborah , Karim Roksana , Fisher Molly , Cohen Mardge , Kassaye Seble , Dumond Julie , Abraham Alison , McCulloch Charles E. , Ascher Simon B. 
Published: January 2024

Objective:
Novel urinary biomarkers reflecting kidney tubule health are associated with chronic kidney disease (CKD) risk in persons living with HIV. However, it is unknown whether these biomarkers provide mechanistic insight into the associations between clinical risk factors for CKD and subsequent CKD risk.

Methods:
Among 636 women living with HIV in the Women's Interagency HIV Study with estimated glomerular filtration rate (eGFR) >60 ml/min/1.73 m2, we used a counterfactual approach to causal mediation analysis to evaluate the extent to which systolic blood pressure (SBP), diastolic blood pressure (DBP), hemoglobin a1c (Hba1c) and serum albumin associations with incident CKD were mediated by eight urine proteins. These biomarkers reflect proximal tubular reabsorptive dysfunction (α1-microglobulin [a1m], β2-microglobulin, trefoil factor 3); tubular injury (interleukin 18 [IL-18], kidney injury molecule 1 [KIM-1]); kidney repair (epidermal growth factor); tubular reserve (uromodulin); and glomerular injury (urinary albumin). Incident CKD was defined as eGFR <60 ml/min/1.73 m2 measured at two consecutive 6-month visits with an average annual eGFR decline ≥3% per year.

Results:
During a median follow-up of 7 years, 11% developed CKD. Urinary albumin and KIM-1 mediated 32% (95% CI: 13.4%, 76.6%) and 23% (6.9%, 60.7%) of the association between SBP and incident CKD, respectively; and 19% (5.1%, 42.3%) and 22% (8.1%, 45.7%) of the association between DBP and incident CKD, respectively. Urinary albumin, α1m, and IL-18 were significant mediators of the association between Hba1c and incident CKD. None of the eight biomarkers mediated the association between serum albumin and incident CKD.

Conclusions:
Among women living with HIV, several urinary biomarkers reflecting distinct dimensions of kidney health may partially explain the associations between SBP, DBP, and Hba1c and subsequent CKD risk.
Addressing Current Deficits in Patient Education Materials Through Crowdsourcing
Authors: Hung Ya-Ching , Chaker Sara C. , Sigel Matthew , Saad Mariam , Yu-Hsuan Chang Monal , Slater Elizabeth D. 
Published: January 2024

Background
Patient education materials are commonly reported to be difficult to understand.

Objectives
We aimed to use crowdsourcing to improve patient education materials at our institution.

Methods
This was a department-wide quality improvement project to increase organizational health literacy. There are 6 phases of this pilot study: (1) evaluating preexisting patient education materials, (2) evaluating online patient education materials at the society (the American Society of Plastic Surgeon) and government level (Medline Plus), (3) redesigning our patient education material and reevaluating the education material, (4) crowdsourcing to evaluate understandability of the new patient education material, (5) data analysis, and (6) incorporating crowdsourcing suggestions to the patient education material.

Results
Breast-related patient education materials are not easy to read at the institution level, the society level, and the government level. Our new implant-based breast reconstruction patient education material is easy to read as demonstrated by the crowdsourcing evaluation. More than 90% of the participants reported our material is “very easy to understand” or “easy to understand.” The crowdsourcing process took 1.5 days, with 700 workers responding to the survey. The total cost was $9. After incorporating participants' feedback into the finalized material, the readability of the material is at the recommended reading level. The material also had the recommended length (between 400 and 800 words).

Discussion
Our study demonstrated a pathway for clinicians to efficiently obtain a large amount of feedback to improve patient education materials. Crowdsourcing is an effective tool to improve organizational health literacy.
The Kidney Not Taken: Single-Kidney Use in Deceased Donors
Authors: McCracken Emily KE , Jay Colleen L , Garner Matthew , Webb Christopher , Farney Alan C , Orlando Giuseppe , Reeves-Daniel Amber , Mena-Gutierrez Alejandra , Sakhovskaya Natalia , Stratta Robert J 
Published: January 2024

BACKGROUND:The nonuse rate for kidneys recovered from deceased donors is increasing, rising to 27% in 2023. In 10% of these cases, 1 kidney is transplanted but the mate kidney is not.STUDY DESIGN:We conducted a retrospective, single-center cohort study from December 2001 to May 2023 comparing single kidneys transplanted at our center (where the contralateral kidney was not used) to kidneys where both were transplanted separately, at least 1 of which was at our center.RESULTS:We performed 395 single deceased-donor kidney transplants in which the mate kidney was not transplanted. Primary reasons for mate kidney nonuse were as follows: no recipient located or list exhausted (33.4%), kidney trauma or injury or anatomic abnormalities (18.7%), biopsy findings (16.7%), and poor renal function (13.7%). Mean donor and recipient ages were 51.5 ± 14.2 and 60 ± 12.6 years, respectively. Mean kidney donor profile index was 73% ± 22%, and 104 donors (26.3%) had kidney donor profile index >85%. Mean cold ischemia was 25.6 ± 7.4 hours, and 280 kidneys (70.7%) were imported. Compared with 2,303 concurrent control transplants performed at our center, primary nonfunction or thrombosis (5.1% single vs 2.8% control) and delayed graft function (35.4% single vs 30.1% control) were greater with single-kidney use (both p < 0.05). Median patient and death-censored graft survival were shorter in the single group (11.6 vs 13.5 years, p = 0.03 and 11.6 vs 19 years, p = 0.003), although the former was at least double median survival on the waiting list. In patients with functioning grafts in the single-kidney group, 1-year mean serum creatinine was 1.77 ± 0.8 mg/dL and estimated glomerular filtration rate was 44.8 ± 20 mL/min/1.73 m2.CONCLUSIONS:These findings suggest that many mate kidneys are being inappropriately rejected, given the acceptable outcomes that can be achieved by transplanting the single kidney in appropriately selected recipients.
Analytic and conformal scattering in general relativity
Authors: Nicolas Jean-Philippe 
Published: January 2024

This paper is about two important trends of scattering theory in general relativity: time-dependent spectral analytic scattering and conformal scattering. The former was initiated by Jonathan Dimock and Bernard Kay in the mid-1980s and is based on spectral and functional analysis. The latter was proposed by Roger Penrose in 1965 and then constructed for the first time by Gerard Friedlander in 1980 by putting together Penrose’s conformal method and another analytic approach to scattering: the Lax–Phillips theory due to Peter Lax and Ralph Phillips. We shall review the history of the two approaches and explain their general principles. We shall also explore an important question: ‘can the tools of one approach be used to obtain a complete construction in the other?’
This article is part of a discussion meeting issue ‘At the interface of asymptotics, conformal methods and analysis in general relativity’.
Repetitive Learning Control for Body Caudal Undulation with Soft Sensory Feedback
Authors: Schwab Fabian , El Arayshi Mohamed , Rezaei Seyedreza , Sprumont Hadrien , Allione Federico , Mucignat Claudio , Lunati Ivan , Verrelli Cristiano Maria , Jusufi Ardian 
Published: January 2024

ABSTRACTSoft bio-inspired robotics is a growing field of research that seeks to close the gap with animal robustness and adaptability where conventional robots fall short. The embedding of sensors with the capability to discriminate between different body deformation modes is a key technological challenge in soft robotics to enhance robot control – a difficult task for such kinds of systems with high degrees of freedom. The recently conceived Linear Repetitive Learning Estimation Scheme (LRLES) – to be included in the traditional Proportional Integral Derivative (PID) control – is proposed here as a way to compensate for uncertain dynamics on a soft swimming robot, which is actuated with soft pneumatic actuators and equipped with soft sensors providing proprioceptive information pertaining to lateral body caudal bending akin to a goniometer. The proposed controller is derived in detail and experimentally validated, with the experiment consisting of tracking a desired trajectory for bending angle while continuously oscillating with a constant frequency. The results are compared vis a vis those achieved with the traditional PID controller, finding that the PID endowed with the LRLES outperforms the PID controller (though the latter has been separately tuned) and experimentally validating the novel controller’s effectiveness, accuracy, and matching speed.
With the leisure of time, kinetic proofreading can still perform reliable ligand discrimination
Authors: Xiao Fangzhou , Galstyan Vahe 
Published: January 2024

AbstractIn a recent PNAS publication, Kirby and Zilman studied kinetic proofreading for receptor signaling and argued that having more proofreading steps does not generally improve ligand discrimination when stochastic effects are taken into account. In their analysis, however, the authors made an implicit assumption about a fixed discrimination time, which is not always warranted. We show that when the discrimination time is allowed to vary in order to maintain a fixed level of signaling activity, the proofreading performance can, in fact, uniformly improve with the number of steps. We therefore call for a comprehensive study of the interplay between discrimination time, discrimination accuracy, and signaling activity, where the two seemingly contradictory results will be slices of the trade-off surface along different axes.
Decreased sarcomeric mitochondrial creatine kinase 2 impairs skeletal muscle mitochondrial function independently of insulin action in type 2 diabetes
Authors: Rizo-Roca David , Guimarães Dimitrius SPSF. , Pendergrast Logan A. , Di Leo Nicolas , Chibalin Alexander V. , Maqdasy Salwan , Rydén Mikael , Näslund Erik , Zierath Juleen R. , Krook Anna 
Published: January 2024

SUMMARYPlasma creatine levels are associated with risk of type 2 diabetes. Since skeletal muscle is the main disposal site of both creatine and glucose, we investigated the role of intramuscular creatine metabolism in the pathophysiology of insulin resistance in type 2 diabetes. We report in men with type 2 diabetes, plasma creatine levels are increased, while intramuscular phosphocreatine content is reduced. These alterations are coupled to reduced expression of sarcomeric mitochondrial creatine kinase 2 (CKMT2). In C2C12 myotubes,Ckmt2silencing reduced mitochondrial respiration, membrane potential, and glucose oxidation. Electroporation-mediated overexpression ofCkmt2in skeletal muscle of high-fat diet-fed male mice increased mitochondrial respiration, independent of creatine availability. Thus, beyond the canonical role of CKMT2 on creatine phosphorylation, we reveal a previously underappreciated role of CKMT2 on mitochondrial homeostasis, independent of insulin action. Collectively, our data provides functional evidence into how CKMT2 mediates mitochondrial dysfunction associated with type 2 diabetes.