bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sodium citrate versus sodium bicarbonate for metabolic acidosis in patients with chronic kidney disease: A randomized controlled trial
Authors: Sorohan Bogdan Marian , Obrișcă Bogdan , Jurubiță Roxana , Lupușoru Gabriela , Achim Camelia , Andronesi Andreea , Frățilă Georgiana , Berechet Andreea , Micu Georgia , Ismail Gener 
Published: March 2024

Background:
Metabolic acidosis (MA) is frequently associated with chronic kidney disease (CKD) progression. Our aim was to compare the effect of oral sodium citrate (SC) with that of oral sodium bicarbonate (SB) on renal function and serum bicarbonate correction, as well as to evaluate their safety profile in patients with MA of CKD.

Methods:
We conducted a prospective, single-center, randomized 1:1, parallel, controlled, unblinded clinical trial of 124 patients with MA and CKD stages 3b and 4. The primary outcome was the mean change in estimated glomerular filtration rate (eGFR). The secondary outcomes were mean change in serum bicarbonate level, eGFR decrease by 30%, eGFR decrease by 50%, dialysis, death or prolonged hospitalization, and a combined endpoint.

Results:
No significant difference was found between the groups in terms of mean eGFR change [adjusted mean difference = −0.99 mL/min/1.73 m2 (95% CI: −2.51 to 0.93, P = .20)]. We observed a mean serum bicarbonate change of 6.15 mmol/L [(95% CI: 5.55–6.74), P < .001] in the SC group and of 6.19 mmol/L [(95% CI: 5.54–6.83), P < .001] in the SB group, but no significant difference between the 2 groups [adjusted mean difference = 0.31 mmol/L (−0.22 to 0.85), P = .25]. Cox proportional hazard analysis showed similar risks regarding eGFR decrease by 30% (P = .77), eGFR decrease by 50% (P = .50), dialysis (P = .85), death or prolonged hospitalization (P = .29), and combined endpoint (P = .57). Study drug discontinuation due to adverse events was significantly more common in the SB group (17.7% vs 4.8%, P = .02).

Conclusions:
SC and SB have a similar effect on kidney function decline, both improve serum bicarbonate level, but SB is associated with higher rates of medication discontinuation due to adverse events.
Clinical effects of a novel deep learning-based rehabilitation application on cardiopulmonary function, dynamic and static balance, gait function, and activities of daily living in adolescents with hemiplegic cerebral palsy
Authors: An Yeongsang , Min Seunghwa , Park Chanhee 
Published: March 2024

Background:
Adolescents with hemiplegic cerebral palsy undergo conventional physical therapy (CPT) to improve static and dynamic balance, activities of daily living and cardiopulmonary function. To overcome this problem, we developed an innovative deep learning-based rehabilitation application (DRA) to provide a motivational and chaffed platform for such individuals. DRA evaluates the patients’ functional abilities and diagnosis an appropriate therapeutic intervention like CPT.

Methods:
We compared the effects of DRA and CPT on 6-minute walking test (6 MWT), Borg rating of perceived exertion scale, Berg balance scale, functional ambulation category, and modified Barthel index in adolescents with hemiplegic cerebral palsy. A convenience sample of 30 adolescents with hemiplegic cerebral palsy was randomized into either the DRA or CPT group. DRA and CPT were administered to the participants, with each session lasting 30 minutes and apportioned thrice a week for a total of 4 weeks.

Results:
Analysis of variance was performed and the level of significance was set at P < .05. The analysis indicated that DRA showed therapeutic effects on 6 MWT, Berg balance scale, and modified Barthel index compared to CPT.

Conclusion:
Our results provide evidence that DRA can improve cardiopulmonary function, balance, and activities of daily living more effectively than CPT in adolescents with hemiplegic cerebral palsy.
Rupture of a dermoid cyst in the subarachnoid space a case report
Authors: Jamal Oufaa , Makhchoune Marouane , Laidi Abdelkoudous , Misbahi Tarek , Haouas Mohamed Yassine , Chellaoui Abdelmajid , Bertal Abderrazak , Hilmani Said , Ibahiouine Khadija , Naja Abdesamad , Lakhder Abdelhakim 
Published: March 2024

Introduction and importance
Intracranial dermoid cysts (IDC) are defined as rare, slow-growing cystic congenital neoplasms. Rupture of an intracranial dermoid cyst occurs rarely and most often spontaneously and results in potentially serious symptoms.

Case presentation
A39-year-old female, with mechanical prosthetic heart valve presented with history of headache for 10 months and generalized tonicoclonic seizures. On the admission, the patient had a normal neurological and cranial nerve exam. We performed a CT of the brain, The MRI could not be performed because of the presence of the prosthetic valve, revealed rupture of the dermoid cyst in the bilateral subarachnoid spaces. The patient underwent a large temporal craniotomy and the tumor was well exposed and completely removed without incident, the histopathological exam concludes to dermoid cyst, the patient recovered well from surgery.

Clinical discussion:
Rupture is a very rare phenomenon. there are about 60 cases reported in the literature. the contents of the cyst disseminate into the subarachnoid and ventricular spaces in the event of rupture. A variety of clinical symptoms is usually caused. The mechanism of spontaneous rupture of the dermoid cyst is unclear. Among the proposed mechanisms is a rapid expansion of the cyst. Complete surgical resection of dermoid cysts is the only effective treatment for the prevention of recurrences and/or complications.

Conclusion:
Rupture of an intracranial dermoid cyst is associated with significant morbidity and mortality, although it remains a rare phenomenon. Surgical excision should be considered as soon as the diagnosis is made in order to prevent more severe intracranial complication.
Factors Associated With Delay in Lung Cancer Diagnosis and Surgery in a Lung Cancer Screening Program
Authors: El Alam Raquelle , Hammer Mark M. , Byrne Suzanne C. 
Published: March 2024

Purpose:
Delays to biopsy and surgery after lung nodule detection can impact survival from lung cancer. The aim of this study was to identify factors associated with delay in a lung cancer screening (LCS) program.

Materials and Methods:
We evaluated patients in an LCS program from May 2015 through October 2021 with a malignant lung nodule classified as lung CT screening reporting and data system (Lung-RADS) 4B/4X. A cutoff of more than 30 days between screening computed tomography (CT) and first tissue sampling and a cutoff of more than 60 days between screening CT and surgery were considered delayed. We evaluated the relationship between delays to first tissue sampling and surgery and patient sex, age, race, smoking status, median income by zip code, language, Lung-RADS category, and site of surgery (academic vs community hospital).

Results:
A total of 185 lung cancers met the inclusion criteria, of which 150 underwent surgical resection. The median time from LCS CT to first tissue sampling was 42 days, and the median time from CT to surgery was 52 days. 127 (69%) patients experienced a first tissue sampling delay and 60 (40%) had a surgical delay. In multivariable analysis, active smoking status was associated with delay to first tissue sampling (odds ratio: 3.0, CI: 1.4-6.6, P = 0.005). Only performing enhanced diagnostic CT of the chest before surgery was associated with delayed lung cancer surgery (odds ratio: 30, CI: 3.6-252, P = 0.02). There was no statistically significant difference in delays with patients’ sex, age, race, language, or Lung-RADS category.

Conclusion:
Delays to first tissue sampling and surgery in a LCS program were associated with current smoking and performing diagnostic CT before surgery.
Single-center Outcomes After Liver Transplantation With SARS-CoV-2–Positive Donors: An Argument for Increased Utilization
Authors: Connor Ashton A. , Adelman Max W. , Mobley Constance M. , Moaddab Mozhgon , Erhardt Alexandra J. , Hsu David E. , Brombosz Elizabeth W. , Sanghvi Mansi , Cheah Yee Lee , Simon Caroline J. , Hobeika Mark J. , Saharia Ashish S. , Victor David W. , Kodali Sudha , Basra Tamneet , Graviss Edward A. , Nguyen Duc T. , Elsaiey Ahmed , Moore Linda W. , Nigo Masayuki , Drews Ashley L. , Grimes Kevin A. , Arias Cesar A. , Li Xian C. , Gaber A. Osama , Ghobrial R. Mark 
Published: March 2024

Background.
The COVID-19 pandemic has led to an increase in SARS-CoV-2–test positive potential organ donors. The benefits of life-saving liver transplantation (LT) must be balanced against the potential risk of donor-derived viral transmission. Although emerging evidence suggests that the use of COVID-19–positive donor organs may be safe, granular series thoroughly evaluating safety are still needed. Results of 29 consecutive LTs from COVID-19–positive donors at a single center are presented here.

Methods.
A retrospective cohort study of LT recipients between April 2020 and December 2022 was conducted. Differences between recipients of COVID-19–positive (n = 29 total; 25 index, 4 redo) and COVID-19–negative (n = 472 total; 454 index, 18 redo) deceased donor liver grafts were compared.

Results.
COVID-19–positive donors were significantly younger (P = 0.04) and had lower kidney donor profile indices (P = 0.04) than COVID-19–negative donors. Recipients of COVID-19–positive donor grafts were older (P = 0.04) but otherwise similar to recipients of negative donors. Donor SARS-CoV-2 infection status was not associated with a overall survival of recipients (hazard ratio, 1.11; 95% confidence interval, 0.24-5.04; P = 0.89). There were 3 deaths among recipients of liver grafts from COVID-19–positive donors. No death seemed virally mediated because there was no qualitative association with peri-LT antispike antibody titers, post-LT prophylaxis, or SARS-CoV-2 variants.

Conclusions.
The utilization of liver grafts from COVID-19–positive donors was not associated with a decreased overall survival of recipients. There was no suggestion of viral transmission from donor to recipient. The results from this large single-center study suggest that COVID-19–positive donors may be used safely to expand the deceased donor pool.
Selective Elimination and Rationalization of Cell-based Assays in Deceased Donor Kidney Transplant Crossmatching
Authors: Khalili Myriam , Famure Olusegun , Minkovich Michelle , Tinckam Kathryn J. , Kim Sang Joseph 
Published: March 2024

Background.
While there is increasing reliance on a negative virtual crossmatch to proceed with deceased donor kidney transplantation, a flow cytometry crossmatch (FCXM) is still usually performed after the transplant has already occurred. Our center has eliminated pretransplant physical crossmatches for most patients, and since 2018, we have eliminated the systematic performance of posttransplant FCXMs.

Methods.
We studied all deceased donor kidney transplants in our program between June 1, 2018, and March 31, 2021, to evaluate the impact of eliminating retrospective FCXMs on resource utilization and graft outcomes (ie, the occurrence of antibody-mediated rejection [AMR] in the first 3-mo posttransplant).

Results.
A total of 358 kidney transplants occurred during the study period, and approximately 70% of these transplants proceeded without the performance of any FCXM. Incidence rates of AMR were low (9.63 per 1000 person-months), which compared favorably with the incidence rate of AMR during the 3-y period preceding the policy (4.82 per 1000 person-months, P = 0.21).

Conclusions.
Our results suggest that moving away from retrospective FCXM and relying exclusively on the virtual crossmatch is safe and efficient for kidney allocation.
The Relationship Between Rehabilitation and Frailty in Advanced Heart or Lung Disease
Authors: Dinesh Vaishnavi , Pierce Rachel , Hespe Lauren , Thakkar Sonali , Wong Marko , El Sabbagh Luke , Honeysett Liarna , Brown Peter , Delbaere Kim , Havryk Adrian , Malouf Monique , Macdonald Peter S. 
Published: March 2024

Background.
Frailty increases morbidity and mortality in patients with advanced heart and lung disease. Emerging evidence shows that postoperative cardiac or pulmonary rehabilitation can improve the frailty status of these patients. The aim of this hypothesis-generating study was to test the relationship between prehabilitation and frailty in patients with advanced heart or lung disease referred for heart and lung transplantation.

Methods.
The study was a retrospective audit of consecutive patients with advanced heart or lung disease referred for transplant assessment between January 2021 and December 2022. Frailty scores were recorded using Fried’s frailty phenotype (range, 0–5), and rehabilitation status of patients at the time of frailty assessment was recorded.

Results.
Of 286 patients, 124 patients had advanced heart disease (mean age 53 ± 12 y; 82% men) and 162 patients had advanced lung disease (mean age 55 ± 12 y; 43% men). Sixty-nine (24%) patients were robust (score 0), 156 (55%) were prefrail (score, 1–2), and 61 (21%) were frail (score, 3–5). Eighty-two (29%) patients participated in hospital-based rehabilitation, 72 (25%) in home-based rehabilitation, and 132 (46%) in no rehabilitation. Frailty scores were significantly lower in patients participating in hospital-based or home-based rehabilitation compared with patients not participating in rehabilitation (0.8 ± 1.0 versus 0.8 ± 0.9 versus 2.3±1.2, P < 0.0001).

Conclusions.
This study shows that patients participating in cardiac or pulmonary rehabilitation are less frail compared with patients not participating in rehabilitation. These findings suggest that prehabilitation could be beneficial for patients awaiting heart or lung transplantation.
Ocular Manifestations of Multiple Sclerosis: A Population-Based Study
Authors: Kraker Jessica A. , Xu Sarah Chaoying , Flanagan Eoin P. , Foster Robert , Wang Feng , Chen John J. 
Published: March 2024

Background:
To evaluate the population-based frequency and severity of multiple sclerosis (MS)-related ocular diseases.

Methods:
Retrospective, population-based study examining patients with MS between January 1, 1998 and December 31, 2011. Patients were identified using the Rochester Epidemiology Project, which is a record-linkage system of medical records for all patient–physician encounters among Olmsted County, Minnesota residents. Diagnosis of MS was confirmed based on neuroimaging, cerebrospinal fluid studies, and serum studies for each patient according to the 2017 McDonald criteria. Patient data were obtained using the medical records and followed through April 1, 2018.

Results:
Of the 116 patients with MS, 66% were female and the median age of onset was 36 years (interquartile range 27.5–43.5 years). About half (61/116, 53%) had MS-related neuro-ophthalmic manifestations during their disease course, and about one-fourth (33/116, 28%) had visual symptoms as their presenting symptom of MS, most commonly as optic neuritis (26/116, 22%). Optic neuritis was the leading MS-related ocular condition (37%), followed by internuclear ophthalmoplegia (16%) and nystagmus (13%). Optic neuritis was mostly unilateral (40/43, 93%), with 16% (6/43) having a visual acuity of 20/200 or worse at nadir but ultimately 95% (35/37) improving to a visual acuity of 20/40 or better.

Conclusions:
This study provides the population-based frequency of MS-related ocular disease, which demonstrates a high frequency of ocular manifestations in MS both at disease onset and during the disease course, emphasizing the utility of neuro-ophthalmologists, or collaboration between neurologists and ophthalmologists, in the care of patients with MS.
Should I See You Again Soon? Multispecialty Assessment of Impact and Burden of Preoperative History and Physical Update Visits
Authors: Soegaard Ballester Jacqueline M , Ginzberg Sara P , Finn Caitlin B , Passman Jesse , Miranda Stephen P , Blue Rachel , Stein Jacob , Mahmoud Najjia N , Kelz Rachel R , Wachtel Heather 
Published: March 2024

BACKGROUND:
Federal regulations require a history and physical (H&P) update performed 30 days or less before a planned procedure. We evaluated the use and burdens of H&P update visits by determining impact on operative management, suitability for telehealth, and visit time and travel burden.

STUDY DESIGN:
We identified H&P update visits performed in our health system during 2019 for 8 surgical specialties. As available, up to 50 visits per specialty were randomly selected. Primary outcomes were interval changes in history, examination, or operative plan between the initial and updated H&P notes, and visit suitability for telehealth, as determined by 2 independent physician reviewers. Clinic time was captured, and round-trip driving time and distance between patients’ home and clinic ZIP codes were estimated.

RESULTS:
We identified 8,683 visits and 362 were randomly selected for review. Documented changes were most commonly identified in histories (60.8%), but rarely in physical examinations (11.9%) and operative plans (11.6%). Of 362 visits, 359 (99.2%) visits were considered suitable for telehealth. Median clinic time was 52 minutes (interquartile range 33.8 to 78), driving time was 55.6 minutes (interquartile range 35.5 to 85.5), and driving distance was 20.2 miles (interquartile range 8.5 to 38.4). At the health system level, patients spent an estimated aggregate 7,000 hours (including 4,046 hours of waiting room and travel time) and drove 142,273 miles to attend in-person H&P update visits in 2019.

CONCLUSIONS:
Given their minimal impact on operative management, regulatory requirements for in-person H&P updates should be reconsidered. Flexibility in update timing and modality might help defray the substantial burdens these visits impose on patients.
Cohort-specific Boolean models highlight different regulatory modules during Parkinson’s disease progression
Authors: Hemedan Ahmed Abdelmonem , Satagopam Venkata , Schneider Reinhard , Ostaszewski Marek 
Published: March 2024

1AbstractParkinson’s Disease (PD) is a multifaceted neurodegenerative disorder characterised by complex molecular dysregulations and diverse comorbidities. It is critical to decode the molecular pathophysiology of PD, which involves complex molecular interactions and their changes over time. Systems medicine approaches can help with this by a) encoding knowledge about the mechanisms into computational models b) simulating these models using patient-specific omics data. This study employs the PD map, a detailed repository of PD-related molecular interactions, as a comprehensive knowledge resource. We aim to dissect and understand the intricate molecular pathways implicated in PD by using logical modelling. This approach is essential for capturing the dynamic interplay of molecular components that contribute to the disease. We incorporate cohort-level and real-world patient data to ensure our models accurately reflect PD’s subtype-specific pathway deregulations. This integration is crucial for addressing the heterogeneity observed in PD manifestations and responses to treatment. To combine logical modelling with empirical data, we rely on Probabilistic Boolean Networks (PBNs).These networks provide a robust framework, capturing the stochastic nature of molecular interactions and offering insights into the variable progression of the disease. By combining logical modelling with empirical data through PBNs, we achieve a more refined and realistic representation of PD’s molecular landscape. The findings provide insights into the molecular mechanisms of PD. We identify key regulatory biomolecules and pathways that differ significantly across PD subtypes. These discoveries have substantial implications for the development of precise medical treatments. The study provides hypothesis for targeted therapeutic interventions by linking molecular dysregulation patterns to clinical phenotypes and advancing our understanding of PD progression and patient stratification.
Coordination of cytochromebc1complex assembly at MICOS
Authors: Zerbes Ralf M. , Colina-Tenorio Lilia , Bohnert Maria , Peikert Christian D. , von der Malsburg Karina , Mehnert Carola S. , Perschil Inge , Klar Rhena , van der Klei Ida , Oeljeklaus Silke , Warscheid Bettina , Rampelt Heike , van der Laan Martin 
Published: March 2024

ABSTRACTThe boundary and cristae domains of the mitochondrial inner membrane are connected by crista junctions. Most cristae membrane proteins are nuclear-encoded and inserted by the mitochondrial protein import machinery into the inner boundary membrane. Thus, they must overcome the diffusion barrier imposed by crista junctions to reach their final location. Here, we show that respiratory chain complexes and assembly intermediates are physically connected to the mitochondrial contact site and cristae organizing system (MICOS) that is essential for formation and stability of crista junctions. We identify the inner membrane protein Mar26 (Fmp10) as determinant in the biogenesis of the cytochromebc1complex (complex III). Mar26 couples a Rieske Fe/S protein-containing assembly intermediate to MICOS. Our data indicate that Mar26 maintains an assembly-competent Rip1 pool at crista junctions where complex III maturation likely occurs. MICOS facilitates efficient Rip1 assembly by recruitment of complex III assembly intermediates to crista junctions. We propose that MICOS, via interaction with assembly factors such as Mar26, directly contributes to the spatial and temporal coordination of respiratory chain biogenesis.
Discovery of a pentose as a cytosine nucleobase modification inShewanellaphage Thanatos-1 genomic DNA mediating enhanced resistance towards host restriction systems
Authors: Brandt David , Dörrich Anja K. , Persicke Marcus , Leonhard Tabea , Haak Markus , Nölting Sophia , Ruwe Matthias , Schmid Nicole , Thormann Kai M. , Kalinowski Jörn 
Published: March 2024

ABSTRACTCo-evolution of bacterial defense systems and phage counter defense mechanisms has resulted in an intricate biological interplay between bacteriophages and their prey. To evade nuclease-based mechanisms targeting the DNA, various bacteriophages modify their nucleobases, which impedes or even inhibits recognition by endonucleases. We found thatShewanellaphage Thanatos-1 DNA is insensitive to multiple restriction enzymes and, partially, also to Cas I-Fv and Cas9 cleavage. Furthermore, the phage genome shows strongly impaired basecalling with nanopore sequencing. We characterised the phage adenine methyltransferase TH1_126 in methylase-freeE. coliER3413 and derived and confirmed its recognition motif 5’-ATC-3’. Moreover, the data pointed to an additional, much more substantial nucleobase modification. Using LC-MS, we identified a deoxypentose of unknown configuration attached to cytosine as a yet undiscovered phage DNA modification, which is present in Thanatos-1 genomic DNA, likely mediates the observed resistance to restriction endonucleases, as well as a strong reduction in Cas nuclease activity. To elucidate the underlying enzyme functions, we determined structural homologs of Thanatos-1 proteins among known glycosyltransferase folds and experimentally proved a UDP-xylose pyrophosphorylase function of phage protein TH1_063 byin vitroenzyme assays.