bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diurnal oscillations of epigenetic modifications are associated with variation in rhythmic expression of homoeologous genes in Brassica napus
Authors: Xue Zhifei , Gao Baibai , Chen Guoting , Liu Jie , Ouyang Weizhi , Foda Mohamed Frahat , Zhang Qing , Zhang Xiwen , Zhang Wei , Guo Mingyue , Li Xingwang , Yi Bin 
Published: October 2023

AbstractBackgroundEpigenetic modifications that exhibit circadian oscillations also promote circadian oscillations of gene expression.Brassica napusis a heterozygous polyploid species that has undergone distant hybridization and genome doubling events and has a young and distinct species origin. Studies incorporating circadian rhythm analysis of epigenetic modifications can offer new insights into differences in diurnal oscillation behavior among subgenomes and the regulation of diverse expressions of homologous gene rhythms in biological clocks.ResultsIn this study, we created a high-resolution and multioscillatory gene expression dataset, active histone modification (H3K4me3, H3K9ac), and RNAPII recruitment inBrassica napus. We also conducted the pioneering characterization of the diurnal rhythm of transcription and epigenetic modifications in an allopolyploid species. We compared the evolution of diurnal rhythms between subgenomes and observed that the Cn subgenome had higher diurnal oscillation activity in both transcription and active histone modifications than the An subgenome. Compared to the A subgenome inBrassica rapa, the An subgenome ofBrassica napusdisplayed significant changes in diurnal oscillation characteristics of transcription. Homologous gene pairs exhibited a higher proportion of diurnal oscillation in transcription than subgenome-specific genes, attributed to higher chromatin accessibility and abundance of active epigenetic modification types. We found that the diurnal expression of homologous genes displayed diversity, and the redundancy of the circadian system resulted in extensive changes in the diurnal rhythm characteristics of clock genes after distant hybridization and genome duplication events. Epigenetic modifications influenced the differences in the diurnal rhythm of homologous gene expression, and the diurnal oscillation of homologous gene expression was affected by the combination of multiple histone modifications.ConclusionsHerein, we presented, for the first time, a characterization of the diurnal rhythm characteristics of gene expression and its epigenetic modifications in an allopolyploid species. Our discoveries shed light on the epigenetic factors responsible for the diurnal oscillation activity imbalance between subgenomes and homologous genes’ rhythmic expression differences. The comprehensive time-series dataset we generated for gene expression and epigenetic modifications provides a valuable resource for future investigations into the regulatory mechanisms of protein-coding genes inBrassica napus.
TPpred-LE: therapeutic peptide function prediction based on label embedding
Authors: Lv Hongwu , Yan Ke , Liu Bin 
Published: October 2023

Abstract
Background
Therapeutic peptides play an essential role in human physiology, treatment paradigms and bio-pharmacy. Several computational methods have been developed to identify the functions of therapeutic peptides based on binary classification and multi-label classification. However, these methods fail to explicitly exploit the relationship information among different functions, preventing the further improvement of the prediction performance. Besides, with the development of peptide detection technology, peptide functions will be more comprehensively discovered. Therefore, it is necessary to explore computational methods for detecting therapeutic peptide functions with limited labeled data.

Results
In this study, a novel method called TPpred-LE based on Transformer framework was proposed for predicting therapeutic peptide multiple functions, which can explicitly extract the function correlation information by using label embedding methodology and exploit the specificity information based on function-specific classifiers. Besides, we incorporated the multi-label classifier retraining approach (MCRT) into TPpred-LE to detect the new therapeutic functions with limited labeled data. Experimental results demonstrate that TPpred-LE outperforms the other state-of-the-art methods, and TPpred-LE with MCRT is robust for the limited labeled data.

Conclusions
In summary, TPpred-LE is a function-specific classifier for accurate therapeutic peptide function prediction, demonstrating the importance of the relationship information for therapeutic peptide function prediction. MCRT is a simple but effective strategy to detect functions with limited labeled data.
Association between antenatal corticosteroid treatment and severe adverse events in pregnant women
Authors: Tsai Hui-Ju , Wallace Beth I. , Waljee Akbar K. , Hong Xiumei , Chang Sheng-Mao , Tsai Yi-Fen , Cheong Mei-Leng , Wu Ann Chen , Yao Tsung-Chieh 
Published: October 2023

Abstract
Background
Antenatal corticosteroids are considered the standard of care for pregnant women at risk for preterm birth, but studies examining their potential risks are scarce. We aimed to estimate the associations of antenatal corticosteroids with three severe adverse events: sepsis, heart failure, and gastrointestinal bleeding, in pregnant women.

Methods
Of 2,157,321 pregnant women, 52,119 at 24 weeks 0/7 days to 36 weeks 6/7 days of gestation were included in this self-controlled case series study during the study period of 2009–2018. We estimated incidence rates of three severe adverse events: sepsis, heart failure, and gastrointestinal bleeding. Conditional Poisson regression was used to calculate incidence rate ratios (IRRs) for comparing incidence rates of the adverse events in each post-treatment period compared to those during the baseline period among pregnant women exposed to a single course of antenatal corticosteroid treatment.

Results
Among 52,119 eligible participants who received antenatal corticosteroid treatment, the estimated incidence rates per 1000 person-years were 0.76 (95% confidence interval (CI): 0.69–0.83) for sepsis, 0.31 (95% CI: 0.27–0.36) for heart failure, and 11.57 (95% CI: 11.27–11.87) for gastrointestinal bleeding. The IRRs at 5 ~ 60 days after administration of antenatal corticosteroids were 5.91 (95% CI: 3.10–11.30) for sepsis and 4.45 (95% CI: 2.63–7.55) for heart failure, and 1.26 (95% CI: 1.02–1.55) for gastrointestinal bleeding; and the IRRs for days 61 ~ 180 were 2.00 (95% CI: 1.01–3.96) for sepsis, 3.65 (95% CI: 2.14–6.22) for heart failure, and 1.81 (95% CI: 1.56–2.10) for gastrointestinal bleeding.

Conclusions
This nationwide population-based study suggests that a single course of antenatal corticosteroids is significantly associated with a 1.3- to 5.9-fold increased risk of sepsis, heart failure, and gastrointestinal bleeding in pregnant women. Maternal health considerations, including recommendations for adverse event monitoring, should be included in future guidelines for antenatal corticosteroid treatment.
Coordinated modulation of long non-coding RNA ASBEL and curcumin co-delivery through multicomponent nanocomplexes for synchronous triple-negative breast cancer theranostics
Authors: He Xuesong , Lin Fengjuan , Jia Runqing , Xia Yang , Liang Zhaoyuan , Xiao Xiangqian , Hu Qin , Deng Xiongwei , Li Qun , Sheng Wang 
Published: October 2023

Abstract
Background
Abnormally regulated long non-coding RNAs (lncRNAs) functions in cancer emphasize their potential to serve as potential targets for cancer therapeutic intervention. LncRNA ASBEL has been identified as oncogene and an anti-sense transcript of tumor-suppressor gene of BTG3 in triple-negative breast cancer (TNBC).

Results
Herein, multicomponent self-assembled polyelectrolyte nanocomplexes (CANPs) based on the polyelectrolytes of bioactive hyaluronic acid (HA) and chitosan hydrochloride (CS) were designed and prepared for the collaborative modulation of oncogenic lncRNA ASBEL with antago3, an oligonucleotide antagonist targeting lncRNA ASBEL and hydrophobic curcumin (Cur) co-delivery for synergetic TNBC therapy. Antago3 and Cur co-incorporated CANPs were achieved via a one-step assembling strategy with the cooperation of noncovalent electrostatic interactions, hydrogen-bonding, and hydrophobic interactions. Moreover, the multicomponent assembled CANPs were ulteriorly decorated with a near-infrared fluorescence (NIRF) Cy-5.5 dye (FCANPs) for synchronous NIRF imaging and therapy monitoring performance. Resultantly, MDA-MB-231 cells proliferation, migration, and invasion were efficiently inhibited, and the highest apoptosis ratio was induced by FCANPs with coordination patterns. At the molecular level, effective regulation of lncRNA ASBEL/BTG3 and synchronous regulation of Bcl-2 and c-Met pathways could be observed.

Conclusion
As expected, systemic administration of FCANPs resulted in targeted and preferential accumulation of near-infrared fluorescence signal and Cur in the tumor tissue. More attractively, systemic FCANPs-mediated collaborative modulating lncRNA ASBEL/BTG3 and Cur co-delivery significantly suppressed the MDA-MB-231 xenograft tumor growth, inhibited metastasis and extended survival rate with negligible systemic toxicity. Our present study represented an effective approach to developing a promising theranostic platform for combating TNBC in a combined therapy pattern.
Combining public health evidence, policy experience and communications expertise to inform preventive health: reflections on a novel method of knowledge synthesis
Authors: Heenan Maddie , Chung Alexandra , Howse Elly , Signy Helen , Rychetnik Lucie 
Published: October 2023

AbstractKnowledge synthesis methods help summarize evidence and utilize content expertise to draw out key messages to aid knowledge mobilization and translation. Systems thinking and coproduction can support this by facilitating a multiperspective view and ensuring that knowledge is mobilized and translated in a useful and meaningful way for policy-makers and practitioners. In this paper, we describe the development of a knowledge synthesis approach that utilizes coproduction with policy-makers to combine the findings of a programme of research with policy knowledge to support decision-makers working in chronic disease prevention. The process developed by The Australian Prevention Partnership Centre combined the expertise of research, policy and science communications experts. We reflect on how we used coproduction processes to embed policy-makers as partners in the evidence synthesis process via research-policy dialogues, and embedded science communication into the development and presentation of the findings. This differs from a more common approach of researchers generating evidence for policy with limited input from policy-makers themselves. By collaborating with policy-makers and using coproduction, we can better inform policy-relevant research and generate policy-relevant knowledge. We describe the development of our knowledge synthesis approach using two case studies: the first drawing on a body of work in public health law, and the second on a body of work focused on the first 2000 days of life. We consider how these case studies demonstrate the value of working with policy partners as part of a knowledge synthesis process, and discuss how this process could be adapted and used in future.
Lycium barbarum glycopeptide alleviates neuroinflammation in spinal cord injury via modulating docosahexaenoic acid to inhibiting MAPKs/NF-kB and pyroptosis pathways
Authors: Jiang Zhanfeng , Zeng Zhong , He He , Li Mei , Lan Yuanxiang , Hui Jianwen , Bie Pengfei , Chen Yanjun , Liu Hao , Fan Heng , Xia Hechun 
Published: October 2023

Abstract
Background
Lycium barbarum polysaccharide (LBP) is an active ingredient extracted from Lycium barbarum that inhibits neuroinflammation, and Lycium barbarum glycopeptide (LbGp) is a glycoprotein with immunological activity that was purified and isolated from LBP. Previous studies have shown that LbGp can regulate the immune microenvironment, but its specific mechanism of action remains unclear.

Aims
In this study, we aimed to explore the mechanism of action of LbGp in the treatment of spinal cord injury through metabolomics and molecular experiments.

Methods
SD male rats were randomly assigned to three experimental groups, and after establishing the spinal cord hemisection model, LbGp was administered orally. Spinal cord tissue was sampled on the seventh day after surgery for molecular and metabolomic experiments. In vitro, LbGp was administered to mimic the inflammatory microenvironment by activating microglia, and its mechanism of action in suppressing neuroinflammation was further elaborated using metabolomics and molecular biology techniques such as western blotting and q-PCR.

Results
In vivo and in vitro experiments found that LbGp can improve the inflammatory microenvironment by inhibiting the NF-kB and pyroptosis pathways. Furthermore, LbGp induced the secretion of docosahexaenoic acid (DHA) by microglia, and DHA inhibited neuroinflammation through the MAPK/NF-κB and pyroptosis pathways.

Conclusions
In summary, we hypothesize that LbGp improves the inflammatory microenvironment by regulating the secretion of DHA by microglia and thereby inhibiting the MAPK/NF-κB and pyroptosis pathways and promoting nerve repair and motor function recovery. This study provides a new direction for the treatment of spinal cord injury and elucidates the potential mechanism of action of LbGp.
Comparative efficacy of unilateral biportal endoscopy and micro-endoscopic discectomy in the treatment of degenerative lumbar spinal stenosis: a systematic review and meta-analysis
Authors: Meng Hai , Su Nan , Lin Jisheng , Fei Qi 
Published: October 2023

Abstract
Background
Given the inconclusive literature on operative time, pain relief, functional outcomes, and complications, this meta-analysis aims to compare the efficacy of Unilateral Biportal Endoscopy (UBE) and Micro-Endoscopic Discectomy (MED) in treating Degenerative Lumbar Spinal Stenosis (DLSS).

Methods
A thorough literature search was conducted in accordance with the PRISMA guidelines and based on the PICO framework. The study interrogated four primary databases—PubMed, Embase, Web of Science, and the Cochrane Library—on August 16, 2023, without time restrictions. The search employed a strategic selection of keywords and was devoid of language barriers. Studies were included based on strict criteria, such as the diagnosis, surgical intervention types, and specific outcome measures. Quality assessment was performed using the Newcastle–Ottawa Scale, and statistical analysis was executed through Stata version 17.

Results
The meta-analysis incorporated 9 articles out of an initial yield of 1,136 potential studies. Considerable heterogeneity was observed in surgical duration, but no statistically significant difference was identified (MD = − 2.11, P = 0.56). For VAS scores assessing lumbar and leg pain, UBE was statistically superior to MED (MD = − 0.18, P = 0.013; MD = − 0.15, P = 0.006, respectively). ODI scores demonstrated no significant difference between the two surgical methods (MD = − 0.57, P = 0.26). UBE had a lower incidence of complications compared to those receiving MED (OR = 0.54, P = 0.036).

Conclusions
UBE and MED exhibited comparable surgical durations and disability outcomes as measured by ODI. However, UBE demonstrated superior efficacy in alleviating lumbar and leg pain based on VAS scores. The findings present an intricate evaluation of the two surgical interventions for DLSS, lending valuable insights for clinical decision-making.
Utilization of spontaneous breathing trial, objective cough test, and diaphragmatic ultrasound results to predict extubation success: COBRE-US trial
Authors: Varón-Vega Fabio , Giraldo-Cadavid Luis F. , Uribe Ana María , Rincón Adriana , Palacios Jonathan , Crevoisier Stephanie , Tuta-Quintero Eduardo , Ordoñez Lina , Boada Natalia , Rincón Paola , Poveda Marcela , Monedero Pablo 
Published: October 2023

Abstract
Background
The results of clinical and weaning readiness tests and the spontaneous breathing trial (SBT) are used to predict the success of the weaning process and extubation.

Methods
We evaluated the capacity of the cuff leak test, rate of rapid and shallow breathing, cough intensity, and diaphragmatic contraction velocity (DCV) to predict the success of the SBT and extubation in a prospective, multicenter observational study with consecutive adult patients admitted to four intensive care units. We used receiver operating characteristic (ROC) curves to assess the tests’ predictive capacity and built predictive models using logistic regression.

Results
We recruited 367 subjects who were receiving invasive mechanical ventilation and on whom 456 SBTs were performed, with a success rate of 76.5%. To predict the success of the SBT, we derived the following equation: (0.56 × Cough) − (0.13 × DCV) + 0.25. When the cutoff point was ≥ 0.83, the sensitivity was 91.5%, the specificity was 22.1%, and the overall accuracy was 76.2%. The area under the ROC curve (AUC-ROC) was 0.63. To predict extubation success, we derived the following equation: (5.7 × SBT) + (0.75 × Cough) − (0.25 × DCV) − 4.5. When the cutoff point was ≥ 1.25, the sensitivity was 96.8%, the specificity was 78.4%, and the overall accuracy was 91.5%. The AUC-ROC of this model was 0.91.

Conclusion
Objective measurement of cough and diaphragmatic contraction velocity could be used to predict SBT success. The equation for predicting successful extubation, which includes SBT, cough, and diaphragmatic contraction velocity values, showed excellent discriminative capacity.
Second-order optimality conditions for interval-valued functions
Authors: Ruiz-Garzón Gabriel , Osuna-Gómez Rafaela , Rufián-Lizana Antonio , Beato-Moreno Antonio 
Published: October 2023

AbstractThis work is included in the search of optimality conditions for solutions to the scalar interval optimization problem, both constrained and unconstrained, by means of second-order optimality conditions. As it is known, these conditions allow us to reject some candidates to minima that arise from the first-order conditions. We will define new concepts such as second-order gH-derivative for interval-valued functions, 2-critical points, and 2-KKT-critical points. We obtain and present new types of interval-valued functions, such as 2-pseudoinvex, characterized by the property that all their second-order stationary points are global minima. We extend the optimality criteria to the semi-infinite programming problem and obtain duality theorems. These results represent an improvement in the treatment of optimization problems with interval-valued functions.
A case of sacrococcygeal teratoma associated with antenatally acquired urethrovaginal fistula and hydrocolpos
Authors: Shibui Yuichi , Obata Satoshi , Hirose Ryuichiro , Nakano Ryo , Setoue Takashi , Miyazaki Takeshi , Matsuoka Hirofumi , Sato Toshihiko 
Published: October 2023

Abstract
Background
Sacrococcygeal teratomas (SCTs) are known to cause urological complications, but urethrovaginal (UV) fistula as a complication of SCT is rare. We herein report a case of SCT with UV fistula and hydrocolpos.

Case presentation
A 1-day-old female neonate presented to our department with prominent swelling in the sacrococcygeal region. She was born at 37 gestational weeks via spontaneous vaginal delivery from a 39-year-old woman. The weight of the baby was 2965 g, and her Apgar scores were 4/10 (at 1 and 5 min). An MRI examination confirmed an 11 × 11 cm Altman classification typeII SCT associated with hydrocolpos, a dilated urinary bladder, and bilateral hydronephrosis. When she was 5 days, the SCT was excised totally and a coccygectomy was performed. After the operation, as her urinary output appeared unstable, a cystoscopic examination was performed on the third postoperative day. This revealed that the UV fistula was located approximately 1 cm from the urethral opening. In addition, the proximal urethra was unobstructed and connected to the bladder. The cystoscope allowed for the passage of a urinary catheter through the urethra. After 1 month of catheter placement, she was discharged from the hospital at 57 days of age. Follow-up was uneventful, with neither urinary infection nor retention.

Conclusions
SCTs are associated with not only trouble with rectal function and lower extremity movement but also urinary complications. The pathogenesis of this UV fistula is thought to be the rapid growth of the SCT that developed in the fetal period, resulting in obstruction of the urethra by the tumor and the pubic bone, which in turn caused urinary retention and the formation of a fistula as an escape route for the pressure. Because SCTs can cause a variety of complications depending on the course of the disease, careful examination and follow-up are necessary.
Nanoarchitectonics of tannic acid based injectable hydrogel regulate the microglial phenotype to enhance neuroplasticity for poststroke rehabilitation
Authors: Liu Zongjian , Zhang Shulei , Ran Yuanyuan , Geng Huimin , Gao Fuhai , Tian Guiqin , Feng Zengguo , Xi Jianing , Ye Lin , Su Wei 
Published: October 2023

AbstractBackgroundStroke is the second leading cause of mortality and disability worldwide. Poststroke rehabilitation is still unsatisfactory in clinics, which brings great pain and economic burdens to stroke patients. In this study, an injectable hydrogel in which tannic acid (TA) acts as not only a building block but also a therapeutic drug, was developed for poststroke rehabilitation.MethodsTA is used as a building block to form an injectable hydrogel (TA gel) with carboxymethyl chitosan (CMCS) by multivalent hydrogen bonds. The morphology, rheological properties, and TA release behavior of the hydrogel were characterized. The abilities of the TA gel to modulate microglial (BV2 cells) polarization and subsequently enhance the neuroplasticity of neuro cells (N2a cells) were assessed in vitro. The TA gel was injected into the cavity of stroke mice to evaluate motor function recovery, microglial polarization, and neuroplasticity in vivo. The molecular pathway through which TA modulates microglial polarization was also explored both in vitro and in vivo.ResultsThe TA gel exhibited sustainable release behavior of TA. The TA gel can suppress the expression of CD16 and IL-1β, and upregulate the expression of CD206 and TGF-β in oxygen and glucose-deprived (OGD) BV2 cells, indicating the regulation of OGD BV2 cells to an anti-inflammatory phenotype in vitro. This finding further shows that the decrease in synaptophysin and PSD95 in OGD N2a cells is effectively recovered by anti-inflammatory BV2 cells. Furthermore, the TA gel decreased CD16/iNOS expression and increased CD206 expression in the peri-infarct area of stroke mice, implying anti-inflammatory polarization of microglia in vivo. The colocalization of PSD95 and Vglut1 stains, as well as Golgi staining, showed the enhancement of neuroplasticity by the TA gel. Spontaneously, the TA gel successfully recovered the motor function of stroke mice. The western blot results in vitro and in vivo suggested that the TA gel regulated microglial polarization via the NF-κB pathway.ConclusionThe TA gel serves as an effective brain injectable implant to treat stroke and shows promising potential to promote poststroke rehabilitation in the clinic.Graphical Abstract