bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Gamma Index Analysis for Detecting Errors in Patient-specific Quality Assurance in Intensity Modulated Radiotherapy
Authors: Tuğrul Taylan 
Published: January 2025

Abstract
Quality assurance practices performed before treatment are believed to identify various potential errors. In this study, 2-dimensional (2D) dosimetric results were analyzed by making some intentional mistakes in six different treatment plans. In this way, the detectability of errors was investigated. In all segments of all treatment plans, one of the multileaf collimators was kept fixed at different positions on the central axis. In addition to multileaf collimators error, gantry error was also examined in the study. The dose distribution results obtained by Treatment Planning System (TPS) were compared with those obtained by the 2D array device, both as local calculation and global calculation methods, using the gamma analysis method. When the results are examined in the case where the Multi-leaf collimators (MLC) is fixed at the 1 cm position, the gamma analysis pass rate of the other plans, except two plans in the MD criterion, are calculated above the 95% limit. When the dose distributions obtained as a result of irradiation with 0.5-degree erroneous gantry angle were analyzed, it was found that all plans were at an acceptable rate in the maximum dose criterion. In case of incorrect irradiation, dose reduction or overdose may occur in the irradiated target area, even if gamma analysis pass rates are sufficient. Quality control procedures performed before treatment may be less effective. It is suggested that it would be better to examine the gamma analysis criteria applied for error detection with different values and local calculation method, and that device-based quality controls should be performed frequently.
“Central retinal artery occlusion following scleral buckling surgery with gas insertion in a patient with sickle cell disease”
Authors: Jalil Assad , Lippera Myrta , Ivanova Tsveta 
Published: January 2025

Purpose-
To describe a case of central retinal artery occlusion following scleral buckling procedure combined with pneumoretinopexy in a patient with sickle cell (HbSC) retinopathy (SCR).

Methods-
Scleral buckling procedure, combined with injection of 0.3 ml of 100% perfluoropropane (C3F8) gas in the vitreous, was performed without intra-operative complications under general anaesthesia as treatment of two separate macula-sparing rhegmatogenous retinal detachments secondary to round holes, involving superior and inferior retina respectively, in the right eye of a 26-year-old Afro-Caribbean female with sickle cell disease.

Results-
On day one post-operatively, central retinal artery occlusion (CRAO) was detected in the operated eye. We hypothesize that the expansion of the gas in the postoperative period combined with the presence of a retinal explant might have caused a moderate elevation of the IOP that caused extensive retinal arteriolar shutdown in the backdrop of SCR.

Conclusion-
CRAO can be a devastating complication following scleral buckling procedure combined with gas insertion in SCR, caution is required when performing scleral explant combined with expansile gas in a patient with sickle cell vasculopathy.
Medication Withdrawal With Normal or Near-normal Histology in Ulcerative Colitis is Associated With Clinical Relapse
Authors: Shaffer Seth R. , Chu Jenny , Algarni Amal , Nugent Zoann , Schaeffer David F. , Bernstein Charles N. 
Published: January 2025

Goals:
We sought to understand the clinical course and risk of dysplasia in persons with UC who achieve near or complete normalization of histology.

Background:
Histologic remission and normalization in ulcerative colitis (UC) is associated with improved clinical outcomes. We sought to understand the clinical course and risk of dysplasia in persons with UC who achieve near or complete normalization of histology.

Study:
We performed a retrospective single-centred study of persons with UC who were in endoscopic remission with normal histology. Pathology slides were reread by a gastrointestinal-expert pathologist and both right and left colon were scored using the Geboes score. The primary outcome was time to clinical relapse, with secondary outcomes including episodes of dysplasia and colectomy.

Results:
Seventy-eight persons had normal histology reported, although only 2 had completely normal histology on expert review. Approximately one-fifth of persons developed a clinical relapse at a mean of 4.7 years. Neither right nor left-sided colon histology was predictive of future clinical relapse. Forty-three percent of those who withdrew their IBD-therapy had a future clinical relapse, and were more likely to relapse than those who did not withdraw therapy (HR: 4.89, 95% CI: 1.32-18.08). There were zero episodes of dysplasia in follow-up, and 2 persons who relapsed ended up receiving a colectomy.

Conclusions:
Persons with UC who achieve normal or near-normal histology have moderate rates of clinical relapse. Physicians should be cautious when considering withdrawing IBD-therapy as this was associated with an increased risk of clinical relapse.
Gut-brain Axis and Irritable Bowel Syndrome During the Lockdown due to the SARS-CoV-2 Pandemic
Authors: Piskorz María Marta , Stefanolo Juan Pablo , Ibañez Agustin , Eugenia Hesse , Bravo Velez Gladys , Tevez Adriana , Gutierrez Cielo , Uehara Tatiana , Hashimoto Harumi , Puga-Tejada Miguel , Gonzalez Ballerga Esteban , Olmos Jorge Atilio 
Published: January 2025

Background:
Irritable bowel syndrome (IBS) is influenced by various factors, including socioemotional stressors. The COVID-19 lockdown created a unique environment characterized by reduced social interactions, potentially impacting IBS symptoms.

Aim:
To assess how lockdown measures affected symptoms related to the gut-brain axis in IBS patients in Buenos Aires, Argentina.

Methods:
Patients with IBS-diarrhea subtype who previously participated in surveys were re-surveyed during the lockdown. Surveys included symptom severity scales and assessments for anxiety, depression, and somatization.

Findings:
One hundred twenty-nine patients (median age 57 y, 78% female) were surveyed. Severe IBS decreased (40.4% vs. 25%; P<0.001), along with abdominal discomfort (72.4% vs. 43%; P<0.001), bloating (72.4% vs. 51.5%; P<0.001), and Bristol scale (6 vs. 4; P<0.001) during-lockdown. Headache and dyspepsia increased, whereas anxiety (45.8% vs. 34.9%; P=0.014) and severe somatization (29.6% vs. 23.3%; P=0.081) decreased.

Conclusion:
Lockdown was associated with improved clinical status in IBS-D patients, reflected in reduced somatization, anxiety, and symptom intensity. This may be attributed to decreased exposure to external stressors on the gut-brain axis.
Increased Risk of Stroke in Constipation Patients
Authors: Suenghataiphorn Thanathip , Yanpiset Panat , Xanthavanij Nutchapon , Srikulmontri Thitiphan , Thiravetyan Ben , Tribuddharat Narisara , Prasitsumrit Vitchapong , Danpanichkul Pojsakorn , Sodsri Tulaton , Kulthamrongsri Narathorn , Wattanachayaku Phuuwadith 
Published: January 2025

Objective:
Constipation is commonly seen among patients with cardiovascular diseases and is linked to adverse outcomes. However, the association between constipation and the risk of stroke remains conflicting. Therefore, we aim to conduct a systematic review and meta-analysis to summarize the available data on this topic.

Methods:
We identified potentially eligible studies from the MEDLINE and EMBASE databases, searching from inception to May 2024, to investigate the association between constipation and stroke. To be included, studies needed to compare the incidence of stroke between groups with and without constipation. Effect size and 95% CIs were combined using the generic inverse variance method.

Results:
Our meta-analysis included 8 studies that met the eligibility criteria. There were 5,360,573 participants, with a mean age of 53.9 years and 69% are males. We found that patients with constipation have a 41% increased risk of stroke with a pooled risk ratio of 1.41 (95% CI: 1.13-1.75; P < 0.01, I
2 = 99%) compared with those without constipation. Subgroup analysis revealed that patients with constipation have a 50% increased risk of ischemic stroke with a pooled risk ratio of 1.50 (95% CI: 1.15-1.96; P < 0.01, I
2 = 99%), but no statistical significance was found for mixed-type stroke outcome.

Conclusions:
Our study revealed that constipation is associated with a higher risk of stroke. These findings could influence future strategies for cardiovascular disease prevention and management in patients with chronic constipation
Insights into proliferative glomerulonephritis with monoclonal immunoglobulin deposits – is it really monoclonal or not?
Authors: Nasr Samih H. , Javaugue Vincent 
Published: January 2025

Purpose of review
Proliferative glomerulonephritis with monoclonal immunoglobulin deposits (PGNMID), is a disease defined by the presence of glomerulonephritis with nonorganized mono-isotypic immunoglobulin (Ig) deposits. This review will discuss the pathogenesis of PGNMID and address novel techniques for detection of monoclonal Ig and pathologic B-cell clones and for distinguishing monoclonal from oligoclonal Ig deposits.

Recent findings
Because of low detection rate of circulating monoclonal Ig and nephritogenic B-cell clones and emerging reports of PGNMID-IgG in children, it has been recently argued that many PGNMID-IgG3 cases may not be monoclonal lesions. A mass spectrometry-based method, serum matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry, has been shown to have superior sensitivity than immunofixation for detection of monoclonal Ig in PGNMID and other monoclonal gammopathy of renal significance (MGRS) lesions. Two novel sequencing techniques, RNA-based immunoglobulin repertoire sequencing and single-molecule real-time sequencing of monoclonal immunoglobulin, enable identification of the full-length variable sequence of monoclonal Ig, even in MGRS patients with low tumor burden and undetectable monoclonal Ig by conventional methods. Finally, staining of kidney biopsy for Ig light chain variable domain subgroups may allow for separation of true monoclonal from oligoclonal PGNMID.

Summary
Novel sequencing, mass spectrometry, and immunofluorescence techniques have the potential to increase the detection rate of nephritogenic monoclonal Ig/B-cell clone and distinguish monoclonal from oligoclonal deposits in PGNMID.
Identification of a distinctive gene signature in granulomatous myositis
Authors: Pinal-Fernandez Iago , Ruffer Nikolas , Casal-Dominguez Maria , Pak Katherine , Kleefeld Felix , Preusse Corinna , Kirou Raphael , Kinder Travis B. , Orso Stefania Del , Naz Faiza , Islam Shamima , Gutierrez-Cruz Gustavo , Milone Margherita , Selva-O’Callaghan Albert , Milisenda Jose C. , Schneider Udo , Liewluck Teerin , Stenzel Werner , Mammen Andrew L. 
Published: January 2025

SUMMARYObjectivesGranulomatous myositis (GM) is defined by focal collections of activated macrophages that fuse to form multinucleated cells that aggregate into granulomas within skeletal muscle. This study aimed to elucidate the pathophysiology of GM by defining its specific transcriptomic profile.MethodsBulk RNA sequencing was performed on 722 muscle biopsies, including 38 from patients with GM, other myopathies, and healthy comparators. Spatial transcriptomics and immunohistochemistry assays were used to identify the location of specific transcripts and proteins within the tissue.ResultsThe transcriptomic signature of GM muscle biopsies was characterized by high levels of IFNγ, IFNγ-inducible genes, and proinflammatory cytokine genes including IL1B, TNF, and TGFB1. The expression levels of 1293 specifically upregulated and 256 specifically downregulated genes were highly correlated with transcriptomic markers of disease activity. Support vector machine models using this gene set identified GM with an AUC of 99.6% (99.0%-99.9%) and an accuracy of 98.6% (98.2%-98.9%). Expression of CHIT1, the most significantly upregulated gene, strongly correlated with disease severity and was detected at the RNA and protein level in granulomas and giant cells.ConclusionsGM is transcriptomically characterized by a strong IFNγ signature and overexpression of proinflammatory cytokines, including IL1B, TNF, and TGFB1. Additionally, it exhibits a unique transcriptomic profile, including CHIT1, which correlates with disease activity.
Theory of non-dilute binding and surface phase separation applied to membrane-binding proteins
Authors: Zhao Xueping , Sun Daxiao , Bartolucci Giacomo , Hyman Anthony A. , Honigmann Alf , Weber Christoph A. 
Published: January 2025

AbstractSurface binding and surface phase separation of cytosolic scaffold proteins on lipid membranes are involved in many cellular processes, such as cell signaling, cell adhesion, and cortex regulation. However, the interplay between surface binding and surface phase separation is poorly understood. In this work, we study this interplay by deriving a general thermodynamic model and applying it to in vitro reconstitution experiments of membrane-binding proteins involved in tight junction initiation. Our theory extends the classical surface binding isotherm to account for non-dilute and heterogeneous conditions where components can phase separate. We use our theory to demonstrate how surface phase separation is governed by the interaction strength among membrane-bound scaffold proteins and their binding affinity to the membrane surface. Comparing the theory to reconstitution experiments, we show that tuning the oligomerization state of the adhesion receptors in the membrane controls surface phase transition and patterning of the scaffold protein ZO1. These findings suggest a fundamental role of the interplay between non-dilute surface binding and surface phase separation in forming the tight junction. More broadly, our work highlights non-dilute surface binding and surface phase separation as a common organizational principle for membrane-associated structures in living cells.
Optimal Inference of Asynchronous Boolean Network Models
Authors: Karlebach Guy 
Published: January 2025

AbstractAssociations between phenotype and genomic and epigenomic markers are often derived by correlation. Systems Biology aims to make more robust connections and uncover broader insights by modeling the cellular mechanisms that produce a phenotype. The question of choosing the modeling methodology is of central importance. A model that does not capture biological reality closely enough will not explain the system’s behavior. At the same time, highly detailed models suffer from computational limitations and are likely to overfit the data. Boolean networks strike a balance between complexity and descriptiveness and thus have received increasing interest. We previously described an algorithm for fitting Boolean networks to high-throughout experimental data that finds the optimal network with respect to the information in a given dataset. In this work, we describe a simple extension that enables the modeling of asynchronous dynamics, i.e. different reaction times for different network nodes. Our approach greatly simplifies the construction of Boolean network models for time-series datasets, where asynchronicty often occurs. We demonstrate our methodology by integrating real data from transcriptomics experiments, and provide an implementation that can be used by the community for network reconstruction using any high-throughout dataset. Our approach significantly expands the applicability of the Boolean network model to experimental data.
Trust in physicians as a mediator of the relationship between person-centered care and medication adherence in patients undergoing hemodialysis: A cross-sectional study
Authors: Kanakubo Yusuke , Inanaga Ryohei , Toida Tatsunori , Aita Tetsuro , Ukai Mamiko , Kawaji Atsuro , Toishi Takumi , Matsunami Masatoshi , Munakata Yu , Suzuki Tomo , Okada Tadao , Kurita Noriaki 
Published: January 2025

AbstractRationale & ObjectivePerson-centered care (PCC) and trust in physicians influence medication adherence (MA) among patients undergoing dialysis. However, the mechanisms linking PCC to MA, particularly the mediating effect of trust in physicians, remain unclear. This study aimed to investigate the interrelationships between PCC, trust in physicians, and MA.Study DesignMulticenter cross-sectional study.Setting & ParticipantsJapanese adults receiving outpatient hemodialysis at six dialysis centers.ExposuresPCC was assessed using the 13-item Japanese Primary Care Assessment Tool-Short Form, which included longitudinality and coordination of care. Trust in physicians was measured using the five-item Wake Forest Physician Trust Scale.OutcomeMA was measured using the 12-item Adherence Starts Knowledge (ASK-12) scale.Analytical ApproachGeneral linear models were used to examine the relationships between PCC, trust in physicians, and MA. Mediation analysis determined the extent to which trust in physicians mediated the PCC-MA relationship.ResultsIn total, 483 patients were analyzed. High-quality PCC was associated with lower barriers to MA in a dose-response manner across JPCAT-SF quartiles compared to no usual source of care (Q1: −3.90 (95% CI: −5.95 to −1.75); Q2: −4.78 (95% confidence interval [CI]: −7.02 to −2.69); Q3: −4.69 (95% CI: −6.96 to −2.58); Q4: −4.95 (95% CI: −7.21 to −2.62). Trust in physicians partially mediated this relationship in a dose-response pattern, with the proportion of the indirect effect increasing from 16.1% (95% CI: 4.5 to 33.8%) in Q2 to 33.3% (95% CI: 17.4 to 65.5%) in Q4. Similar findings were observed for PCC subdomains.LimitationPossible reverse causation.ConclusionsHigh-quality PCC was associated with MA, with trust in physicians playing a key mediating role. Strategies to enhance MA in patients undergoing hemodialysis should incorporate multidimensional PCC approaches, focusing on building trust and strengthening continuity and coordination of care.
Transcriptomic analyses of human brains with Alzheimer’s disease identified dysregulated epilepsy-causing genes
Authors: Eteleeb Abdallah M. , Santos Alves Suélen , Buss Stephanie , Shafi Mouhsin , Press Daniel , Garcia-Cairasco Norberto , Benitez Bruno A. 
Published: January 2025

AbstractBackground & ObjectiveAlzheimer’s Disease (AD) patients at multiple stages of disease progression have a high prevalence of seizures. However, whether AD and epilepsy share pathophysiological changes remains poorly defined. In this study, we leveraged high-throughput transcriptomic data from sporadic AD cases at different stages of cognitive impairment across multiple independent cohorts and brain regions to examine the role of epilepsy-causing genes.MethodsEpilepsy-causing genes were manually curated, and their expression levels were analyzed across bulk transcriptomic data from three AD cohorts and three brain regions. RNA-seq data from sporadic AD and control cases from the Knight ADRC, MSBB, and ROSMAP cohorts were processed and analyzed under the same analytical pipeline. An integrative clustering approach employing machine learning and multi-omics data was employed to identify molecularly defined profiles with different cognitive scores.ResultsWe found several epilepsy-associated genes/pathways significantly dysregulated in a group of AD patients with more severe cognitive impairment. We observed 15 genes consistently downregulated across the three cohorts, including sodium and potassium channels, suggesting that these genes play fundamental roles in cognitive function or AD progression. Notably, we found 25 of these genes dysregulated in earlier stages of AD and become worse with AD progression.ConclusionOur findings showed that epilepsy-causing genes showed changes in the early and late stages of AD progression, suggesting that they might be playing a role in AD progression. We can not establish directionality or cause-effect with our findings. However, changes in the epilepsy-causing genes might underlie the presence of seizures in AD patients, which might be present before or concurrently with the initial stages of AD.
Looking for the optimal pathway to stimulate hippocampus in human participants using transcranial ultrasound stimulation (TUS): a simulation study
Authors: Lu Hanna , Li Zeyan , Ni Xi , Guo Liwei , Qiu Zhihai , Meng Lin , Yuan Yi 
Published: January 2025

AbstractAt present, very limited methods can directly modulate the neural activities in deep brain structures in human participants. Low-intensity transcranial ultrasound stimulation (TUS), as an emerging and advanced modality of non-invasive brain stimulation (NIBS), has great potential for focally stimulating the subcortical structures that are related to sleep, emotion and the functions of motor of cognition. Due to the focality, the integration of various methods, including magnetic resonance imaging and possible pathways, is important to perform TUS intervention for precise targeting and dosing. Based on structural MRI scans, we constructed a simulation model of low-intensity TUS, with a particular focus on the optimal pathways of targeting hippocampus in human participants. Finally, we outlooked the future perspectives of TUS in clinical applications in neurological and psychiatric fields.
Melatonin attenuates kidney injury by alleviating lysosomal damage in diabetic kidney disease
Authors: Chen Jiaqi , Zhang Shuting , Ma Xiaoqin , Chen Aomiao , Wu Yichuan , Wang Geningyue , Zhang Qian , Xue Yaoming , Jia Yijie , Zheng Zongji 
Published: January 2025

ABSTRACTProteinuria-induced damage to renal tubular epithelial cells is one of the main causes of diabetic kidney disease (DKD), and the clearance of overloaded albumin by lysosomes is crucial for maintaining the homeostasis of renal tubular epithelial cells. Therefore, lysosomal damage is closely related to the pathogenesis of DKD, but effective prevention and treatment measures are still lacking. Melatonin (MLT) is secreted by the pineal gland and can not only regulate circadian rhythms but also maintain lysosomal homeostasis. In this study, we demonstrate the presence of significant lysosomal damage in renal tubules of DKD patients, which causes autophagy impairment and a concomitant oxidative stress imbalance; however, MLT can upregulate transcription factor EB (TFEB) to improve lysosomal damage and restore the biosynthesis in this organelle. Mechanistically, MLT may protect lysosomes via the upregulation of TFEB and the miR-205-5p‒LRP-1 pathway in renal tubules, thus improving autophagy dysfunction and oxidative imbalance in DKD.