bluuebunny/crossref_metadata_2025_split huggingface dataset:
FunlncModel: integrating multi-omic features from upstream and downstream regulatory networks into a machine learning framework to identify functional lncRNAs
Authors: Li Yan-Yu , Qian Feng-Cui , Zhang Guo-Rui , Li Xue-Cang , Zhou Li-Wei , Yu Zheng-Min , Liu Wei , Wang Qiu-Yu , Li Chun-Quan 
Published: November 2024

Abstract
Accumulating evidence indicates that long noncoding RNAs (lncRNAs) play important roles in molecular and cellular biology. Although many algorithms have been developed to reveal their associations with complex diseases by using downstream targets, the upstream (epi)genetic regulatory information has not been sufficiently leveraged to predict the function of lncRNAs in various biological processes. Therefore, we present FunlncModel, a machine learning–based interpretable computational framework, which aims to screen out functional lncRNAs by integrating a large number of (epi)genetic features and functional genomic features from their upstream/downstream multi-omic regulatory networks. We adopted the random forest method to mine nearly 60 features in three categories from &gt;2000 datasets across 11 data types, including transcription factors (TFs), histone modifications, typical enhancers, super-enhancers, methylation sites, and mRNAs. FunlncModel outperformed alternative methods for classification performance in human embryonic stem cell (hESC) (0.95 Area Under Curve (AUROC) and 0.97 Area Under the Precision-Recall Curve (AUPRC)). It could not only infer the most known lncRNAs that influence the states of stem cells, but also discover novel high-confidence functional lncRNAs. We extensively validated FunlncModel’s efficacy by up to 27 cancer-related functional prediction tasks, which involved multiple cancer cell growth processes and cancer hallmarks. Meanwhile, we have also found that (epi)genetic regulatory features, such as TFs and histone modifications, serve as strong predictors for revealing the function of lncRNAs. Overall, FunlncModel is a strong and stable prediction model for identifying functional lncRNAs in specific cellular contexts. FunlncModel is available as a web server at https://bio.liclab.net/FunlncModel/.
Clinical Course of Isolated Recurrent, Persistent Complex Perianal Fistulas Without Luminal Crohn’s Disease: A Multicenter Case Series of 24 Patients
Authors: Fiske Hannah W , Tse Chung Sang , Al-Bawardy Badr , Magavi Pooja , Konijeti Gauree Gupta , Mao Eric , Fine Sean , Parian Alyssa , Lazarev Mark , Shah Samir A 
Published: November 2024

Abstract

Background
Isolated complex perianal fistulas, without luminal evidence of inflammatory bowel disease in the gastrointestinal tract, pose diagnostic and treatment dilemmas for gastroenterologists and colorectal surgeons. For patients who develop recurrent complex fistulas, a presumptive diagnosis of Crohn’s disease may be made. It is unclear whether these cases of isolated perianal disease in the absence of luminal inflammation truly represent isolated severe cryptoglandular fistulas or rather an early presentation of Crohn’s disease. We aimed to investigate the clinical course and outcomes of patients with isolated complex perianal fistulas.

Methods
In this retrospective multicenter case series across 6 institutions in the United States, we report the clinical course of patients with isolated recurrent complex perianal fistulas, including their diagnostic evaluation, medical and surgical therapies, and clinical outcomes.

Results
All patients (n = 24) required incision and drainage of perirectal abscesses. The majority received setons (n = 19, 79%), more intensive surgical interventions (n = 15, 62.5%, including fistulotomy/sphincterotomy, advancement flap, and ligation of the intersphincteric fistula tract), antibiotics (n = 17, 71%), and biologic therapy (n = 16, 67%). Nine patients (37.5%) underwent a combined medical-surgical approach with biologics and intensive surgical intervention. Despite surgical and/or medical management, active symptomatic complex perianal fistulas persisted in 58% (n = 14) of patients at follow-up (median 5.5 years, interquartile range 2.5-10 years); symptom remission was achieved in 21% (n = 5), and fistula closure in 21% (n = 5).

Conclusions
These cases highlight a multidisciplinary and multimodal approach when treating isolated complex perianal fistulas and their propensity to persist despite the incorporation of advanced therapies.
Evaluation of temporomandibular joint disc displacement with MRI-based radiomics analysis
Authors: Duyan Yüksel Hazal , Orhan Kaan , Evlice Burcu , Kaya Ömer 
Published: November 2024

Abstract

Objectives
The purpose of this study was to propose a machine learning model and assess its ability to classify temporomandibular joint (TMJ) disc displacements on MR T1-weighted and proton density-weighted images.

Methods
This retrospective cohort study included 180 TMJs from 90 patients with TMJ signs and symptoms. A radiomics platform was used to extract imaging features of disc displacements. Thereafter, different machine learning algorithms and logistic regression were implemented on radiomics features for feature selection, classification, and prediction. The radiomics features included first-order statistics, size- and shape-based features, and texture features. Six classifiers, including logistic regression, random forest, decision tree, k-nearest neighbours (KNN), XGBoost, and support vector machine were used for a model building which could predict the TMJ disc displacements. The performance of models was evaluated by sensitivity, specificity, and ROC curve.

Results
KNN classifier was found to be the most optimal machine learning model for prediction of TMJ disc displacements. The AUC, sensitivity, and specificity for the training set were 0.944, 0.771, 0.918 for normal, anterior disc displacement with reduction (ADDwR) and anterior disc displacement without reduction (ADDwoR) while testing set were 0.913, 0.716, and 1 for normal, ADDwR, and ADDwoR. For TMJ disc displacements, skewness, root mean squared, kurtosis, minimum, large area low grey level emphasis, grey level non-uniformity, and long-run high grey level emphasis, were selected as optimal features.

Conclusions
This study has proposed a machine learning model by KNN analysis on TMJ MR images, which can be used for TMJ disc displacements.
Based proteomics analyses reveal response mechanisms of Apis mellifera (Hymenoptera: Apidae) against the heat stress
Authors: Li Xinyu 
Published: November 2024

Abstract
Heat stress can significantly affect the survival, metabolism, and reproduction of honeybees. It is important to understand the proteomic changes of honeybees under heat stress to understand the molecular mechanism behind heat resistance. However, the proteomic changes of honeybees under heat stress are poorly understood. We analyzed the proteomic changes of Apis mellifera Ligustica (Hymenoptera: Apidae) under heat stress using mass spectrometry-based proteomics with TMT (Tandem mass tags) stable isotope labeling. A total of 3,799 proteins were identified, 85 of which differentially abundance between experimental groups. The most significant categories affected by heat stress were associated with transcription and translation processes, metabolism, and stress-resistant pathways. We found that heat stress altered the protein profiles in A. mellifera, with momentous resist proteins being upregulated in heat groups. These results show a proof of molecular details that A. mellifera can respond to heat stress by increasing resist proteins. Our findings add research basis for studying the molecular mechanisms of honeybees’ resistance to heat stress. The differentially expressed proteins identified in this study can be used as biomarkers of heat stress in bees, and provide a foundation for future research on honeybees under heat stress. Our in-depth proteomic analysis provides new insights into how bees cope with heat stress.
Young and naïve B cells are a diagnostic pitfall in pediatric tonsillectomies
Authors: Tillotson Sophie , Shi Ping , Ray Elizabeth , Seifert Robert P 
Published: November 2024

Abstract
Tonsillar marginal zone hyperplasia may mimic mucosa-associated lymphoid tissue lymphoma, a rare diagnosis in children. Histologically, both entities can demonstrate expansion of the marginal zone with disruption of follicular architecture. However, marginal zone hyperplasia may appear polyclonal by flow cytometry. We present two pediatric tonsillectomy cases with tonsillar marginal zone hyperplasia and discuss the diagnostic challenges this poses in the pediatric population. Both tonsillectomies demonstrated expansion of marginal zones with partial architectural effacement, and flow cytometric analysis of both cases detected lambda light chain restricted, CD20(bright) B cells without CD38. Authors have suggested that the lambda restricted B cells in this setting represent naïve, unmutated B cells with preferential, but polyclonal, lambda expression. Our cases are in line with this thought. While robust, BIOMED-2 primer PCR can show dominant IgK peaks, which may be misinterpreted. This presents a diagnostic pitfall in the workup of pediatric tonsils that community pathologists must consider.
Multiwavelength investigations of PKS 2300–18: S-shaped radio quasar with precessing jets and double-peaked broad emission-line spectrum
Authors: Misra Arpita , Jamrozy Marek , Weżgowiec Marek , Kozieł-Wierzbowska Dorota 
Published: November 2024

ABSTRACT
S-shaped radio galaxy jets are prime sources for investigating the dynamic interplay between the central active galactic nucleus (AGN), the jets, and the ambient intergalactic medium. These sources are excellent candidates for studying jet precession, as their S-shaped inversion symmetry strongly indicates underlying precession. We present a multiwavelength analysis of the giant inversion-symmetric S-shaped radio galaxy PKS 2300$-$18, which spans 0.76 Mpc. The host is a quasar at a redshift of 0.128, displaying disturbed optical morphology due to an ongoing merger with a companion galaxy. We conducted a broad-band radio spectral study using multifrequency data ranging from 183 MHz to 6 GHz, incorporating dedicated observations with the upgraded Giant Metrewave Radio Telescope (uGMRT) and Karl G. Jansky Very Large Array (JVLA) alongside archival radio data. A particle injection model was fitted to the spectra of different regions of the source to perform ageing analysis, which was supplemented with a kinematic jet precession model. The ageing analysis revealed a maximum plasma age of $\sim$ 40 Myr, while the jet precession model indicated a precession period of $\sim$ 12 Myr. ROentgen SATellite (ROSAT) data revealed an X-ray halo of Mpc size, and from Chandra the AGN X-ray spectrum was modelled using thermal and power-law components. The optical spectrum displaying double-peaked broad emission lines was modelled, indicating complex broad-line region kinematics at the centre with the possibility of a binary SMBH. We present the results of our multiwavelength analysis of the source, spanning scales from a few light-days to a few Mpc, and discuss its potential evolutionary path.
A natural variant of NON-RIPENING promotes fruit ripening in watermelon
Authors: Wang Jinfang , Yu Yongtao , Guo Shaogui , Zhang Jie , Ren Yi , Tian Shouwei , Li Maoying , Liao Shengjin , Gong Guoyi , Zhang Haiying , Xu Yong 
Published: November 2024

Abstract
The regulation of non-climacteric fruit ripening by the transcription factor NON-RIPENING (NOR) is poorly understood. Here, we identified that the NOR homolog in the non-climacteric fruit watermelon (Citrullus lanatus) was located within the selective sweep and sweetness quantitative trait locus that was selected during domestication from landraces to cultivars. ClNOR knockout substantially delayed fruit ripening, and the fruits of the knockout plants had lower abscisic acid (ABA) levels, lighter colored flesh, and were less sweet compared to wild type. Transcriptome analysis and DNA affinity purification sequencing revealed that ClNOR targeted the Basic Leucine Zipper gene ClbZIP1, which links ClNOR to genes that do not have a ClNOR-binding motif in their promoters, such as the ABA biosynthesis gene, 9-cis-epoxycarotenoid dioxygenase ClNCED1 and the chromoplast phosphate transporter gene ClPHT4;2. The double mutant Clnor Clbzip1 exhibited delayed fruit ripening, lower ABA level, and lighter colored flesh. Its delayed ripening phenotype was stronger than that of the Clbzip1 single mutant. Additionally, the ClNORT,T haplotype in cultivated watermelon resulted in higher ClbZIP1 expression, but ClNORC,T from landraces and ClNORC,G from ancestral watermelon did not. Heterologous ClNORT,T expression rescued the delayed ripening phenotype of the Slnor knockout in tomato (Solanum lycopersicum). This natural variant (564T/C) of ClNOR promoted fruit ripening by enhancing target genes transcription. Overall, these findings will help elucidate the evolutionary mechanisms of nonclimacteric fruit ripening.
Role of vitamin D3 in mitigating sodium arsenite-induced neurotoxicity in male rats
Authors: Abdou Heba Mohamed , Saad Alaa Mohamed , Abd Elkader Heba-Tallah Abd Elrahim , Essawy Amina E 
Published: November 2024

Abstract
Arsenic is associated with various neurological disorders, notably affecting memory and cognitive functions. The current study examined the protective effects of vitamin D3 (Vit. D3) in countering oxidative stress, neuroinflammation and apoptosis induced by sodium arsenite (SA) in the cerebral cortex of rats. Male Wistar rats were subjected to a daily oral administration of sodium arsenite (NaAsO2, SA) at a dosage of 5 mg/kg, along with 500 IU/kg of Vit. D3, and a combination of both substances for four weeks. The results indicated that Vit. D3 effectively mitigated the SA-induced increase in oxidative stress markers, thiobarbituric acid reactive substances (TBARS) and nitric oxide (NO), the decrease in antioxidants (reduced glutathione; GSH, superoxide dismutase; SOD, catalase; CAT, and glutathione peroxidase; GPx), as well as the increase in pro-inflammatory markers including, tumor necrosis factor-alpha (TNF-α), interleukin-1 beta (IL-1β), and amyloid-beta (Aβ)1–42. Furthermore, Vit. D3 reversed the alterations in the neurochemicals acetylcholinesterase (AchE), monoamine oxidase (MAO), dopamine (DA), and acetylcholine (Ach) and ameliorated the histopathological changes in the cerebral cortex. Moreover, immunohistochemical analyses revealed that Vit. D3 reduced the SA-induced overexpression of cerebral cysteine aspartate-specific protease-3 (caspase-3) and glial fibrillary acidic protein (GFAP) in the cerebral cortex of male rats. Consequently, the co-administration of Vit. D3 can protect the cerebral cortex against SA-induced neurotoxicity, primarily through its antioxidant, anti-inflammatory, anti-apoptotic, and anti-astrogliosis effects.
Lower Incidence of ASP Requiring Surgery With Minimally Invasive TLIF Than With Open PLIF
Authors: Roh Young-Ho , Soh Jaewan , Lee Jae Chul , Jang Hae-Dong , Choi Sung-Woo , Shin Byung-Joon 
Published: November 2024

Study Design:
Retrospective analysis.

Objective:
To assess the incidence of and risk factors for adjacent segment pathology (ASP) requiring surgery among patients previously treated with spinal fusion. Survival of the adjacent segment was compared in patients undergoing open posterior lumbar interbody fusion (O-PLIF) versus minimally invasive transforaminal interbody fusion (MI-TLIF).

Summary of Background Data:
Compared with O-PLIF, MI-TLIF may reduce ASP in the long term by preserving more of the paraspinal muscle and ligamentous structures connected to adjacent segments.

Methods:
The study population consisted of 740 consecutive patients who had undergone lumbar spinal fusion of 3 or fewer segments. O-PLIF was performed in 564 patients, and MI-TLIF in 176 patients. The incidence and prevalence of revision surgery for ASP were calculated using the Kaplan-Meier method. A risk factor analysis was performed using the log-rank test and a Cox regression analysis.

Results:
After index spinal fusion, 26 patients (3.5%) underwent additional surgery for ASP. Kaplan-Meier analysis predicted a disease-free survival rate of adjacent segments in 87.2% at 10 years after the index operation. The incidence of ASP requiring surgery within 10 years was 16.4% after O-PLIF and 6.1% after MI-TLIF (P=0.045). This result was supported by the Cox regression analysis, which showed a significant difference between MI-TLIF and O-PLIF (P=0.034). The hazard ratio of revision surgery was about 3 times higher with O-PLIF than with MI-TLIF. Patients 65 years or older at the time of the index operation were 2.9 times more likely to undergo revision surgery than those younger than 65 years (P=0.015).

Conclusions:
MI-TLIF results in less ASP requiring surgery than O-PLIF. 65 years or older is an independent risk factor for ASP. By preserving the soft tissues, MI-TLIF may result in a lower incidence of ASP than the open technique.

Level of Evidence:
Level 3.
FOUR-YEAR OUTCOMES AFTER INTRAVITREAL AFLIBERCEPT FOR MACULAR NEOVASCULARIZATION IN PATIENTS WITH PATHOLOGIC MYOPIA
Authors: Mizuno-Onishi Yuka , Igarashi Tae , Uramoto Kengo , Kaneko Yuichiro , Nagaoka Natsuko , Yoshida Takeshi , Ohno-Matsui Kyoko 
Published: November 2024

Purpose:
The natural course of the visual acuity in eyes with myopic macular neovascularization is poor. Intravitreal injections of anti-vascular endothelial growth factor agents have demonstrated safety and efficacy in the short term for managing myopic macular neovascularization. The purpose of this study was to determine the 4-year outcomes of intravitreal aflibercept injections.

Methods:
A retrospective monocentric study including 49 eyes of 48 patients diagnosed with myopic macular neovascularization. These patients underwent treatment with intravitreal aflibercept using the pro re nata regimen after the first injection. The minimum follow-up duration was 4 years.

Results:
The patients had an average age of 63.8 years and an average axial length of 29.7 mm. The mean number of intravitreal aflibercept injections was 1.6, and 30 eyes (61.2%) had a single injection. At the baseline and at 1, 2, 3, and 4 years, the mean best-corrected visual acuities were 20/45, 20/41, 20/43, 20/51, and 20/53, respectively. The differences in the best-corrected visual acuity at the different times from that at the baseline were not significant.

Conclusion:
Intravitreal aflibercept therapy with the pro re nata regimen provides a 4-year visual benefit in eyes with myopic macular neovascularization, and it is better than the reported natural course in maintaining the best-corrected visual acuity.
Comparison of Cochet–Bonnet, Dental Floss, and Cotton Wisp With Applications to Corneal Sensation Testing
Authors: Schultheis William Grant , Hampton Thomas , Gensheimer William 
Published: November 2024

Purpose:
The measurement of corneal sensation can be useful in the diagnosis of corneal neuropathies. Although the Cochet–Bonnet esthesiometer (CB) is the gold standard, cotton wisp (CW) and dental floss are commonly used in clinical practice.

Methods:
We assessed the steady-state force of thick dental floss (tkDF), thin dental floss (tnDF), and CW compared with that of CB. We surveyed cornea/refractive specialists (CRS) and noncornea/refractive specialists (NCRS) for frequency and method by which corneal sensation was checked.

Results:
Compared with CB, the maximum force applied by tkDF was 0.92 grams more (P << 0.05), 0.15 grams more for tnDF (P < 0.05), and 0.23 grams less for CW (P < 0.05). Compared with CB, force per unit length was 0.13 g/mm higher for tkDF (P << 0.05), 0.001 g/mm higher for tnDF (P = 0.44), and 0.008 g/mm lower for CW (P = 0.10). We collected responses from 182/284 CRS and 102/284 NCRS. 12/182 CRS checked cornea sensation 0x/month compared with 42/102 NCRS. A total of 103/182 CRS and 54/102 NCRS checked cornea sensation 1-5x/month. CW was the most common tool used for CRS (115/170) and NCRS (53/60).

Conclusions:
tnDF provides the best analog for the CB. CW provides a small amount of force over a large range of lengths and may be a useful screening tool. tkDF is less suitable for screening. CRS check corneal sensation at a higher rate than NCRS. CW was the most common method used in both groups.
The effect of cataract surgery on lowering intraocular pressure
Authors: Shah Yesha S. , Garg Anupam K. , Ramulu Pradeep Y. 
Published: November 2024

Purpose of review
To review the literature evaluating the effectiveness of cataract surgery alone and cataract surgery in combination with other procedures and surgeries on intraocular pressure (IOP) in patients with ocular hypertension and glaucoma.

Recent findings
Recent studies of large trials have shown the IOP-lowering effect of cataract surgery and the beneficial effect of minimally invasive glaucoma surgery (MIGS). More studies are being published on when to use cataract surgery alone, with MIGS, or with traditional glaucoma surgeries for both primary open angle glaucoma and primary angle closure glaucoma.

Summary
Patients with ocular hypertension and visually significant cataracts would benefit from cataract surgery alone to lower intraocular pressure. Patients with mild to moderate glaucoma would likely benefit from cataract surgery and MIGS to achieve a lower IOP. Patients with more advanced glaucoma would benefit from cataract surgery combined with a traditional incisional glaucoma surgery. Clear lens extraction can be used in patients with primary angle closure and early primary angle closure glaucoma. In patients with more advanced disease, phacoemulsification and another glaucoma surgery is likely to be required to achieve IOP control. MIGS are starting to be used in angle closure glaucoma, although more research needs to be done to define its role.
Women Physicians and Nurses in Treatment for Substance Use Disorders
Authors: González-Irizar Olga , Nieva Gemma , Gómez-Duran Esperanza Luisa , Heredia Meritxell , Llavayol Enric , Pujol Tania , Valero Sergi , Grau-López Lara , Bruguera Eugeni , Braquehais Maria Dolores 
Published: November 2024

Abstract
Women physicians and nurses are health professionals with significant differences in their role, but they share common social and occupational stressors. This study compares the outcomes of female physicians and nurses in treatment in a highly specialized program for health professionals with substance use disorders. This was a 9-year, survival, observational, cohort study, conducted with data from medical e-records of female nurses (n = 58) and physicians (n = 50) in treatment for addictions. The most common drug of abuse was alcohol (62% of physicians and 75.9% of nurses) followed by sedatives (16% vs. 12.1%). The median time in treatment was similar (49.1 and 46.4 months for physicians and nurses, respectively). Abstinence rates of physicians (76%) were higher than those of nurses (61.4%) as well as their median time to first lapse (15.5 and 7.6 months, respectively). However, after multivariate analyses, differences did not remain statistically significant neither for their abstinence rates nor for their survival time. To have an alcohol use disorder emerged as a risk factor of relapse for all (Hazard Ratio = 3.41, p = .03). More knowledge is needed to ascertain the common and differential factors related to the treatment response of women physicians and nurses with addictions and particularly to improve alcohol use disorder outcomes in these populations.