bluuebunny/crossref_metadata_2025_split huggingface dataset:
FADD as a key molecular player in cancer progression
Authors: Liu Ying , Li Xiaoge , Zhou Xuehao , Wang Jianxun , Ao Xiang 
Published: November 2022

AbstractCancer is a leading disease-related cause of death worldwide. Despite advances in therapeutic interventions, cancer remains a major global public health problem. Cancer pathogenesis is extremely intricate and largely unknown. Fas-associated protein with death domain (FADD) was initially identified as an adaptor protein for death receptor-mediated extrinsic apoptosis. Recent evidence suggests that FADD plays a vital role in non-apoptotic cellular processes, such as proliferation, autophagy, and necroptosis. FADD expression and activity of are modulated by a complicated network of processes, such as DNA methylation, non-coding RNA, and post-translational modification. FADD dysregulation has been shown to be closely associated with the pathogenesis of numerous types of cancer. However, the detailed mechanisms of FADD dysregulation involved in cancer progression are still not fully understood. This review mainly summarizes recent findings on the structure, functions, and regulatory mechanisms of FADD and focuses on its role in cancer progression. The clinical implications of FADD as a biomarker and therapeutic target for cancer patients are also discussed. The information reviewed herein may expand researchers’ understanding of FADD and contribute to the development of FADD-based therapeutic strategies for cancer patients.
Fat storage-inducing transmembrane proteins: beyond mediating lipid droplet formation
Authors: Wang Gaiping , Chen Anqi , Wu Yu , Wang Danlin , Chang Cuifang , Yu Guoying 
Published: November 2022

AbstractFat storage-inducing transmembrane proteins (FITMs) were initially identified in 2007 as members of a conserved endoplasmic reticulum (ER) resident transmembrane protein gene family, and were found to be involved in lipid droplet (LD) formation. Recently, several studies have further demonstrated that the ability of FITMs to directly bind to triglyceride and diacylglycerol, and the diphosphatase activity of hydrolyzing fatty acyl-CoA, might enable FITMs to maintain the formation of lipid droplets, engage in lipid metabolism, and protect against cellular stress. Based on the distribution of FITMs in tissues and their important roles in lipid droplet biology and lipid metabolism, it was discovered that FITMs were closely related to muscle development, adipocyte differentiation, and energy metabolism. Accordingly, the abnormal expression of FITMs was not only associated with type 2 diabetes and lipodystrophy, but also with cardiac disease and several types of cancer. This study reviews the structure, distribution, expression regulation, and functionality of FITMs and their potential relationships with various metabolic diseases, hoping to provide inspiration for fruitful research directions and applications of FITM proteins. Moreover, this review will provide an important theoretical basis for the application of FITMs in the diagnosis and treatment of related diseases.
An interpretable DIC risk prediction model based on convolutional neural networks with time series data
Authors: Yang Hao , Li Jiaxi , Liu Siru , Zhang Mengjiao , Liu Jialin 
Published: November 2022

AbstractDisseminated intravascular coagulation (DIC) is a complex, life-threatening syndrome associated with the end-stage of different coagulation disorders. Early prediction of the risk of DIC development is an urgent clinical need to reduce adverse outcomes. However, effective approaches and models to identify early DIC are still lacking. In this study, a novel interpretable deep learning based time series is used to predict the risk of DIC. The study cohort included ICU patients from a 4300-bed academic hospital between January 1, 2019, and January 1, 2022. Experimental results show that our model achieves excellent performance (AUC: 0.986, Accuracy: 95.7%, and F1:0.935). Gradient-weighted Class Activation Mapping (Grad-CAM) was used to explain how predictive models identified patients with DIC. The decision basis of the model was displayed in the form of a heat map. The model can be used to identify high-risk patients with DIC early, which will help in the early intervention of DIC patients and improve the treatment effect.
C3NA: correlation and consensus-based cross-taxonomy network analysis for compositional microbial data
Authors: Song Kuncheng , Zhou Yi-Hui 
Published: November 2022

Abstract
Background
Studying the co-occurrence network structure of microbial samples is one of the critical approaches to understanding the perplexing and delicate relationship between the microbe, host, and diseases. It is also critical to develop a tool for investigating co-occurrence networks and differential abundance analyses to reveal the disease-related taxa–taxa relationship. In addition, it is also necessary to tighten the co-occurrence network into smaller modules to increase the ability for functional annotation and interpretability of these taxa-taxa relationships. Also, it is critical to retain the phylogenetic relationship among the taxa to identify differential abundance patterns, which can be used to resolve contradicting functions reported by different studies.

Results
In this article, we present Correlation and Consensus-based Cross-taxonomy Network Analysis (C3NA), a user-friendly R package for investigating compositional microbial sequencing data to identify and compare co-occurrence patterns across different taxonomic levels. C3NA contains two interactive graphic user interfaces (Shiny applications), one of them dedicated to the comparison between two diagnoses, e.g., disease versus control. We used C3NA to analyze two well-studied diseases, colorectal cancer, and Crohn’s disease. We discovered clusters of study and disease-dependent taxa that overlap with known functional taxa studied by other discovery studies and differential abundance analyses.

Conclusion
C3NA offers a new microbial data analyses pipeline for refined and enriched taxa–taxa co-occurrence network analyses, and the usability was further expanded via the built-in Shiny applications for interactive investigation.
Collectively encoding protein properties enriches protein language models
Authors: An Jingmin , Weng Xiaogang 
Published: November 2022

AbstractPre-trained natural language processing models on a large natural language corpus can naturally transfer learned knowledge to protein domains by fine-tuning specific in-domain tasks. However, few studies focused on enriching such protein language models by jointly learning protein properties from strongly-correlated protein tasks. Here we elaborately designed a multi-task learning (MTL) architecture, aiming to decipher implicit structural and evolutionary information from three sequence-level classification tasks for protein family, superfamily and fold. Considering the co-existing contextual relevance between human words and protein language, we employed BERT, pre-trained on a large natural language corpus, as our backbone to handle protein sequences. More importantly, the encoded knowledge obtained in the MTL stage can be well transferred to more fine-grained downstream tasks of TAPE. Experiments on structure- or evolution-related applications demonstrate that our approach outperforms many state-of-the-art Transformer-based protein models, especially in remote homology detection.
Genome-wide identification and analysis of bZIP gene family reveal their roles during development and drought stress in Wheel Wingnut (Cyclocarya paliurus)
Authors: Tao Yu-Tian , Chen Lu-Xi , Jin Jie , Du Zhao-Kui , Li Jun-Min 
Published: November 2022

AbstractBackgroundThebZIPgene family has important roles in various biological processes, including development and stress responses. However, little information about this gene family is available for Wheel Wingnut (Cyclocarya paliurus). ResultsIn this study, we identified 58bZIPgenes in theC. paliurusgenome and analyzed phylogenetic relationships, chromosomal locations, gene structure, collinearity, and gene expression profiles. The 58bZIPgenes could be divided into 11 groups and were unevenly distributed among 16C. paliuruschromosomes. An analysis of cis-regulatory elements indicated thatbZIPpromoters were associated with phytohormones and stress responses. The expression patterns ofbZIPgenes in leaves differed among developmental stages. In addition, severalbZIPmembers were differentially expressed under drought stress. These expression patterns were verified by RT-qPCR.ConclusionsOur results provide insights into the evolutionary history of thebZIPgene family inC. paliurusand the function of these genes during leaf development and in the response to drought stress. In addition to basic genomic information, our results provide a theoretical basis for further studies aimed at improving growth and stress resistance inC. paliurus,an important medicinal plant.
Prediction of SYNTAX score II improvement by adding temporal heart rate changes between discharge and first outpatient visit in patients with acute myocardial infarction
Authors: Li Chuang , Zhang Wanjing , Yang Yixing , Zhang Qian , Li Kuibao , Chen Mulei , Wang Lefeng , Xia Kun 
Published: November 2022

Abstract
Background
The prognostic ability of the temporal changes in resting heart rate (ΔHR) in patients with acute myocardial infarction (AMI) for cardiovascular (CV) mortality and clinical outcomes is rarely examined. This study investigated the predictive value of ΔHR using models with SYNTAX score II (SxS-II) for the long-term prognosis of patients with AMI.

Methods
Six hundred five AMI patients with vital signs recorded at the first outpatient visit (2–4 weeks after discharge) were retrospectively recruited into this study. The changes between discharge and outpatient resting heart rate (D-O ΔHR) were calculated by subtracting the HR at the first post-discharge visit from the value recorded at discharge. The major adverse cardiovascular and cerebrovascular events (MACCE) include cardiovascular death, recurrent myocardial infarction, revascularization, and nonfatal stroke. The predictive values and reclassification ability of the different models were assessed using a likelihood ratio test, Akaike’s information criteria (AIC), receiver operating characteristic (ROC) curves, net reclassification improvement (NRI), and integrated discrimination improvement (IDI).

Results
During the follow-up period, a drop-in resting heart rate (RHR) from discharge to first outpatient visit was independently associated with less risk of CV mortality [D-O ΔHR: hazards ratio (HR) = 0.97, 95% CI = 0.96–0.99, P < 0.001] and MACCE (HR = 0.98, 95% CI = 0.97–0.99, p = 0.001). The likelihood test indicated that the combined model of SxS-II and D-O ΔHR yielded the lowest AIC for CV mortality and MACCE (P < 0.001). Moreover, D-O ΔHR alone significantly improved the net reclassification and integrated discrimination of the models containing SxS-II for CV mortality and MACCE (CV mortality: NRI = 0.5600, P = 0.001 and IDI = 0.0759, P = 0.03; MACCE: NRI = 0.2231, P < 0.05 and IDI = 0.0107, P < 0.05).

Conclusions
The change in D-O ΔHR was an independent predictor of long-term CV mortality and MACCE. The D-O ΔHR combined with SxS-II could significantly improve its predictive probability.
Effect of an increase in Lp(a) following statin therapy on cardiovascular prognosis in secondary prevention population of coronary artery disease
Authors: Zhu Lijun , Fang Yangliang , Gao Beibei , Jin Xiangbo , Zheng Jiamin , He Ying , Huang Jinyu 
Published: November 2022

Abstract
Background
Lipoprotein (a) [Lp(a)] is an independent risk factor for coronary artery disease (CAD). Recent studies have indicated that statins tend to increase Lp(a) levels by 10–20%. However, the association of statin-mediated increases in Lp(a) levels with CAD has not been determined.

Methods
This study included 488 patients with acute coronary syndrome (ACS) who underwent percutaneous coronary intervention (PCI). Lp(a) levels were measured at baseline and 1 month after statin therapy. The study endpoints were major adverse cardiovascular events (MACE). Hazard ratios for the MACE were adjusted for potential confounder using Cox regression.

Results
After statin therapy, the mean level of Lp(a) increased by 19.3% from baseline. Lp(a) levels increased in 307 patients (62.9%) with a median elevation of 4.1 mg/dL. Patients with an increase in Lp(a) were at higher risk for MACE than those without an increase in Lp(a) (p = 0.044). Subgroup analyses revealed that a mild-to-moderate increase in Lp(a) was not associated with MACE, whereas there was a strong correlation between the highest quartile increase in Lp(a) (≥ 10.1 mg/dL) and MACE (HR = 2.29, 95%CI = 1.36–3.84, p = 0.002). This correlation was independent of baseline Lp(a) levels but not independent of on-statin Lp(a) levels.

Conclusions
Severe increases in Lp(a) following statin therapy raise the risk of MACE, but a mild-to-moderate increase in Lp(a) may not affect the cardiovascular prognosis of CAD patients. Even if the baseline Lp(a) levels are low, it is necessary to continue testing for Lp(a) concentration at least once after statin.
Association between living arrangements and cognitive decline in older adults: A nationally representative longitudinal study in China
Authors: Yu Yifan , Lv Junqi , Liu Jing , Chen Yueqiao , Chen Kejin , Yang Yanfang 
Published: November 2022

Abstract
Background
Living arrangements are critical to the survival and well-being of older people, especially in China where the filial piety culture demands adult children care for and serve their parents. The study aimed to explore the association between living arrangements and cognitive decline among older people in China.

Methods
Participants included 6,074 older adults over 60 years old (49.65% male, mean age 67.2 years [range 60–98]) from four waves (2011–2018) of the China Health and Retirement Longitudinal Study. Two to four assessments were conducted over a follow-up of an average of 5.3 years (range, 2–7). Cognitive function was assessed using an adapted Chinese version of Mini-Mental State Examination (MMSE). Living arrangements were classified as follows: living alone, living with spouse, living with adult children, living with spouse and adult children and living with others. Multilevel models were used to investigate the relationship between living arrangements and cognitive decline, as well as the gender difference.

Results
As the main type of living arrangements of the study participants (44.91%), living with spouse was taken as the reference group. Compared to the reference group, living alone (β=-0.126, P < 0.001), living with adult children (β=-0.136, P < 0.001), living with spouse and adult children (β=-0.040, P < 0.05) and living with others (β=-0.155, P < 0.05) were all related to a faster rate of cognitive decline. Further, the association between living arrangements and cognitive decline varied by gender. Living alone (β=-0.192, P < 0.001) was associated with a faster cognitive decline only in older men. Living with spouse and adult children (β=-0.053, P < 0.05) and living with others (β=-0.179, P < 0.05) were associated with faster cognitive decline only in older women.

Conclusion
This study suggests that living arrangements in older people in China were associated with cognitive decline, and these associations varied by gender. Greater attention to living arrangements might yield practical implications for preserving the cognitive function of the older population.
mir-145-5p is a suppressor of colorectal cancer at early stage, while promotes colorectal cancer metastasis at late stage through regulating AKT signaling evoked EMT-mediated anoikis
Authors: Cheng Xianshuo , Shen Tao , Liu Ping , Fang Shaojun , Yang Zhibin , Li Yunfeng , Dong Jian 
Published: November 2022

Abstract
Background:
miR-145-5P is generally considered as a tumor suppressor at early stage of colorectal cancer, but up-regulation occurs in the progressive and later stages which is associated with metastasis, indicating miR-145-5p may play dual role in colorectal cancer (CRC). To explore the detailed mechanism of miR-145-5p in carcinogenic is of importance.

Methods:
The expression pattern of miR-145-5p in CRC patients was downloaded from TCGA database, and the probable mechanism involved in the carcinogenic effect of miR-145-5p was predicted by bioinformatics analysis. Then, interference of miR-145-5p on SW480 and SW620 cells was conducted, and the influences on tumor cell viability, invasion ability, epithelial-mesenchymal transition (EMT), anoikis, and relative protein expression were examined respectively.

Results:
A total of 522 CRC patients’ data indicated that miR-145-5p expression was significantly higher in metastatic CRC than that in non-metastatic CRC, and higher expression of miR-145-5p was correlate with worse prognosis. Overexpression of miR-145-5P-5p enhanced the proliferation and invasion ability of SW620, but inhibited them in SW480. EMT was induced in SW620 after miR-145-5p overexpression and mesenchymal–epithelial transition (MET) was induced in SW480, resulted in the decreased apoptotic rate in SW620 and elevated apoptotic rate in SW480 respectively. Western blot results showed that AKT signaling pathway was involved in the miR-145-5p evoked EMT-mediated anoikis process in SW620 and SW480 cells.

Conclusion:
miR-145-5p is a tumor suppressor at early stage of CRC, and an oncogene at advanced stage of CRC. AKT signaling evoked EMT-mediated anoikis might be the pathway by which miR-145-5P regulates CRC cell invasion and metastasis.
Rucaparib in recurrent ovarian cancer: real-world experience from the rucaparib early access programme in Spain – A GEICO study
Authors: Yubero Alfonso , Barquín Aranzazu , Estévez Purificación , Pajares Bella , Sánchez Luisa , Reche Piedad , Alarcón Jesús , Calzas Julia , Gaba Lydia , Fuentes José , Santaballa Ana , Salvador Carmen , Manso Luis , Herrero Ana , Taus Álvaro , Márquez Raúl , Madani Julia , Merino María , Marquina Gloria , Casado Victoria , Constenla Manuel , Gutiérrez María , Dosil Alba , González-Martín Antonio 
Published: November 2022

AbstractBackground:Rucaparib is a poly(ADP-ribose) polymerase inhibitor approved in Europe as maintenance therapy for recurrent platinum-sensitive (Pt-S) ovarian cancer (OC). The Rucaparib Access Programme (RAP) was designed to provide early access to rucaparib for the above-mentioned indication, as well as for patients withBRCA-mutated Pt-S or platinum-resistant (Pt-R) OC and no therapeutic alternatives.Methods:In this observational, retrospective study we analysed the efficacy and safety of rucaparib within the RAP in Spain. Hospitals associated with the Spanish Ovarian Cancer Research Group (GEICO) recruited patients with high-grade epithelial ovarian, fallopian tube, or primary peritoneal cancer treated with rucaparib 600 mg twice daily as maintenance or treatment (Pt-S/Pt-R) in the RAP. Baseline characteristics, efficacy, and safety data were collected.Results:Between July 2020 and February 2021, 51 patients treated in 22 hospitals in the RAP were included in the study. Eighteen patients with a median of 3 (range, 1–6) prior treatment lines received rucaparib as maintenance; median progression-free survival (PFS) for this group was 9.1 months (95% confidence interval [CI], 4.2–11.6 months). Among 33 patients (median 5 [range, 1–9] prior treatment lines) who received rucaparib as treatment, 7 and 26 patients had Pt-S and Pt-R disease, respectively. Median PFS was 10.6 months (95% CI, 2.5 months-not reached) in the Pt-S group and 2.2 months (95% CI, 1.1–3.2 months) in the Pt-R group. Grade ≥ 3 treatment-emergent adverse events were reported in 39% of all patients, the most common being anaemia (12% and 15% in the maintenance and treatment groups, respectively). At data cut-off, 5 patients remained on treatment.ConclusionEfficacy results in these heavily pre-treated patients were similar to those from previous trials. The safety profile of rucaparib in real life was predictable and manageable.
The effect of behavioral therapy based counseling with anxious mothers on their infants' colic: a randomized controlled clinical trial
Authors: Montazeri Reihaneh , Hasanpour Shirin , Mirghafourvand Mojgan. , Gharehbaghi Manizheh Mostafa , Tehrani Mohammad Mehdi Ghods , Rezaei Shiva Mohajjel 
Published: November 2022

Abstract
Background
Given the possible effect of maternal anxiety on the severity of colic pain in infants, this study aimed to investigate the effects of behavioral therapy counseling on infantile colic (primary outcome), maternal anxiety, and mother-infant attachment (secondary outcomes) in anxious mothers with colicky infants.

Method
This randomized controlled clinical trial was conducted on 46 anxious mothers of 2–6-weeks-old exclusively breastfed colicky infants who had a score of 112 and above according to the Postpartum Specific Anxiety Scale (PSAS), reffered to the pediatric clinics of Al-Zahra, Taleghani and Children Hospitals of Tabriz, Iran. The participants were randomly assigned to the intervention (n = 23) and control (n = 23) groups using randomized block design. Mothers in the intervention group attended 8 systematic desensitization counseling sessions (2–3 sessions per week). Those in the control group received routine care. The researcher completed the Postpartum Specific Anxiety Scale (PSAS), Mother-Infant Attachment Questionnaire (MIAQ), and Infant Colic Scale (ICS) by interviewing the participants before and two weeks after the intervention.

Results
There was no significant difference between the intervention and control groups in the socio-demographic profile of participants. After the intervention, the mean postpartum anxiety score of women in the intervention group was significantly lower than that of those in the control group (Mean Difference (MD) = 22.5, 95% Confidence Interval (CI) = 2.3 to 42.7; p = 0.029). The mean infant colic score of the infants of mothers in the intervention group was insignificantly lower than that of those in the control group (MD = -2.9, 95% CI = -8.3 to 2.4; p = 0.271). In addition, no significant difference was observed between the two groups in terms of their mean mother-infant attachment scores (MD = -0.04, 95% CI = -3.1 to 0.3; p = 0.976).

Conclusion
Behavioral therapy counseling effectively reduced postpartum anxiety in women with colicky infants; however, this reduction did not lead to a significant decrease in the infants’ colic pain. Therefore, health care providers are recommended to use this counseling method in combination with other effective counseling approaches to promote mental health of these mothers.

Trial Registration
IRCT Registration Number: IRCT20111219008459N14, registered on 08/10/2020. https://irct.ir/user/trial/45949/view