Miracle-dz/UniFAR-FTUs huggingface dataset:
The impact of fibromyalgia syndrome and the role of comorbidity with mood and post-traumatic stress disorder in worsening the quality of life

Background: The aim is to measure the association between fibromyalgia syndrome (FMS) and post-traumatic stress disorder (PTSD), mood and anxiety disorders using reliable psychiatric diagnoses according to Diagnostic and Statistical Manual of Mental Disorders (4th ed.; DSM-IV) and with a case–control design. Methods: Case–control study with cases (71 consecutive female patients with FMS) and controls (284 subjects without FMS), randomly drawn after a gender- and age-matching technique from the database of an epidemiological survey. Psychiatric diagnoses were conducted according to DSM-IV and carried out by clinical staff using a structured interview (Advanced Neuropsychiatric Tools and Assessment Schedule). QoL was measured by Short Form Health Survey (SF-12). Results: The lifetime prevalence of major depressive disorder (MDD; 43.7% vs 8.1%, p < .0001), bipolar disorder (BD; 21.1% vs 0.7%, p < .0001), PTSD (8.4% vs 1.4%, p < .0001) and panic disorder (28.2% vs 5.6%, p < .001) was higher in people with FMS than in controls. People with FMS showed a poorer QoL than controls on the SF-12 (26.43 ± 6.04 vs 37.45 ± 5.80, p < .0001). Those with comorbidity with MDD and BD showed a mean SF-12 score of 24.75 ± 6.31 versus 29.52 ± 4.84 (N = 25) of people with FMS without any mood disorder (p = .002). The attributable burden of FMS in worsening QoL was found comparable to that of serious chronic diseases such as multiple sclerosis. Conclusion: FMS is a disorder that ‘in itself’ can have a devastating impact on an individual’s life. The frequency of the association with major depressive and bipolar disorders increases the impact on the QoL of people with FMS. One of the causes of this association appears to be the extreme vulnerability to chronic stress that this disorder involves. The findings have important clinical significance: the physician must interpret in the right dimension and with dignity the suffering of the people with FMS.
Cirrhotic stiffness affects the migration of hepatocellular carcinoma cells and induces sorafenib resistance through YAP

A majority of hepatocellular carcinomas (HCCs) combine with liver cirrhosis. The cirrhotic liver has been implicated in interfering with the effects of HCC‐targeted drugs, including sorafenib. Alterations in the tumor microenvironment of the cirrhotic liver include both biochemical and biomechanical factors. In this study, we induced sorafenib resistance in HCC cells. We observed changes in cell morphology, cytoskeletal architecture, and cellular stiffness in these sorafenib‐resistant cells, resembling those adapted to stiffer substrates. To examine the contribution of mechanical factors in HCC cell growth and drug resistance, we used an in vitro cell culture system with adjustable stiffness mimicking the normal or cirrhotic liver tissues. We identified that mechanical adaptation conferred HCC cells with increased motility and sorafenib resistance. We further reported the mechanism underlying the involvement of the transcription coactivator YAP. Our results underline the important role of mechanical factors in the interaction between tumor cells and their microenvironment.
A comprehensive analysis of SNCA‐related genetic risk in sporadic parkinson disease

The goal of this study was to refine our understanding of disease risk attributable to common genetic variation in SNCA, a major locus in Parkinson disease, with potential implications for clinical trials targeting α‐synuclein. We aimed to dissect the multiple independent association signals, stratify individuals by SNCA‐specific risk profiles, and explore expression quantitative trait loci.
Transient microstructural brain anomalies and epileptiform discharges in mice defective for epilepsy and language‐related NMDA receptor subunit gene Grin2a

The epilepsy‐aphasia spectrum (EAS) is a heterogeneous group of age‐dependent childhood disorders characterized by sleep‐activated discharges associated with infrequent seizures and language, cognitive, and behavioral deficits. Defects in the GRIN2A gene, encoding a subunit of glutamate‐gated N‐methyl‐d‐aspartate (NMDA) receptors, represent the most important cause of EAS identified so far. Neocortical or thalamic lesions were detected in a subset of severe EAS disorders, and more subtle anomalies were reported in patients with so‐called “benign” phenotypes. However, whether brain structural alterations exist in the context of GRIN2A defects is unknown.
Features of word similarity

In this theoretical note we compare different types of computational models of word similarity and association in their ability to predict a set of about 900 rating data. Using regression and predictive modeling tools (neural net, decision tree) the performance of a total of 28 models using different combinations of both surface and semantic word features is evaluated. The results present evidence for the hypothesis that word similarity ratings are based on more than only semantic relatedness. The limited cross-validated performance of the models asks for the development of psychological process models of the word similarity rating task.
Is Nighttime Really Not the Right Time for a Laparoscopic Cholecystectomy?

Purpose The impact of an out-of-hours laparoscopic cholecystectomy on outcome is controversial. We sought to determine the association between an out-of-hours procedure and postoperative complications within 90 days. Methods Between 2014 and 2016, 1553 laparoscopic cholecystectomies were performed. Therapeutic, operative, and outcome data were prospectively collected and analyzed. We defined out of hours as during weekends, national holidays, and daily between 5PM and 8AM. Results Most patients operated on were female (n=988; 63.6%) and the majority of procedures were electives (n=1341; 86.3%). Although all procedures were performed with a laparoscopic intent, 42 (2.7%) were converted to open procedure. In total, 145 (9.3%) procedures were out of hours, all nonelective, and in most cases for acute cholecystitis (n=111; 7.1%). Overall, there were 212 complications in 191 patients (12.3%), most (n=153; 9.9%) classified as minor. The conversion rate in the out-of-hours group was significantly higher (9.7% vs 2.0%; p<0.001). While univariate analyses revealed out-of-hours procedure (OR=1.83; p=0.008) to be associated with an increased risk of complications, when controlling for confounding factors by multivariate analysis, this association was not found. However, operation by surgical staff (OR=1.71) and conversion to laparotomy (OR=3.74) were found to be independently associated with an increased risk of complications (both p<0.05), while an emergency procedure tended to be associated with postoperative morbidity (OR=1.82; p=0.069). Conclusion An out-of-hours laparoscopic cholecystectomy was not found to be an independent risk factor for developing postoperative morbidity and time of day should therefore only be a relative contraindication.
The role of education in the association between race/ethnicity/nativity, cognitive impairment, and dementia among older adults in the United States

BACKGROUND Older Black and Hispanic adults are more likely to be cognitively impaired than older White adults. Disadvantages in educational achievement for minority and immigrant populations may contribute to disparities in cognitive impairment. OBJECTIVE Examine the role of education in racial/ethnic and nativity differences in cognitive impairment/no dementia (CIND) and dementia among older US adults. METHODS Data comes from the 2012 Health and Retirement Study. A total of 19,099 participants aged ≥50 were included in the analysis. Participants were categorized as having normal cognition, CIND, or dementia based on the Telephone Interview for Cognitive Status (TICS) or questions from a proxy interview. We document age and educational differences in cognitive status among White, Black, US-born Hispanic, and foreign-born Hispanic adults by sex. Logistic regression is used to quantify the association between race/ethnicity/nativity, education, and cognitive status by sex. RESULTS Among women, foreign-born Hispanics have higher odds of CIND and dementia than Whites. For men, Blacks have higher odds for CIND and dementia compared to Whites. The higher odds for CIND and dementia across race/ethnic and nativity groups was reduced after controlling for years of education but remained statistically significant for older Black and US-born Hispanic adults. Controlling for education reduces the odds for CIND (women and men) and dementia (men) among foreign-born Hispanics to nonsignificance. CONTRIBUTION These results highlight the importance of education in CIND and dementia, particularly among foreign-born Hispanics. Addressing inequalities in education can contribute to reducing racial/ethnic/nativity disparities in CIND and dementia for older adults.
The Barnacle Balanus improvisus as a Marine Model - Culturing and Gene Expression

Barnacles are marine crustaceans with a sessile adult and free-swimming, planktonic larvae. The barnacle Balanus (Amphibalanus) improvisus is particularly relevant as a model for the studies of osmoregulatory mechanisms because of its extreme tolerance to low salinity. It is also widely used as a model of settling biology, in particular in relation to antifouling research. However, natural seasonal spawning yields an unpredictable supply of cyprid larvae for studies. A protocol for the all-year-round culturing of B. improvisus has been developed and a detailed description of all steps in the production line is outlined (i.e., the establishment of adult cultures on panels, the collection and rearing of barnacle larvae, and the administration of feed for adults and larvae). The description also provides guidance on troubleshooting and discusses critical parameters (e.g., the removal of contamination, the production of high-quality feed, the manpower needed, and the importance of high-quality seawater). Each batch from the culturing system maximally yields roughly 12,000 nauplii and can deliver four batches in a week, so up to almost 50,000 larvae per week can be produced. The method used to culture B. improvisus is, probably, to a large extent also applicable to other marine invertebrates with free-swimminglarvae. Protocols are presented for the dissection of various tissues from adults as well as the production of high-quality RNA for studies on gene expression. It is also described how cultured adults and reared cyprids can be utilized in a wide array of experimental designs for examining gene expression in relation to external factors. The use of cultured barnacles in gene expression is illustrated with studies of possible osmoregulatory roles of Na+/K+ ATPase and aquaporins.
Validation of the Oswestry Risk of Knee Arthroplasty Index (ORKA-1) for Patients Undergoing Autologous Chondrocyte Implantation

Objective The purpose of this study was first to externally validate the Oswestry Risk of Knee Arthroplasty index (ORKA-1) by applying it to an autologous chondrocyte implantation (ACI) patient cohort in the United States with a broader definition of failure than only arthroplasty, and second, to determine predictive factors for the risk of ACI failure as defined by the senior author. Design A total of 171 patients that underwent ACI were included to validate the ORKA-1 as all factors needed for calculation and outcomes were recorded. For Cox regression analysis, 154 patients were included as they completed preoperative Knee Injury and Osteoarthritis Outcome Score (KOOS), Tegner, Lysholm, International Knee Documentation Committee (IKDC), and 12-item Shor Form (SF-12) scores. Patient- and lesion-associated parameters were recorded for each patient. Results At final follow-up (maximum of 10 years post-ACI), a total of 27 patients (15.8%) were considered a failure by senior author’s definition. With ACI failure as endpoint, the mean survival was 7.96 years in risk group 1 and 5.4 years in risk group 5. Cox regression analysis identified preoperative KOOS Sport/Recreation as the only significant predictive factor for ACI failure (P = 0.007). Conclusion The ORKA-1 is a helpful tool for surgeons to estimate an individual patient’s likelihood of ACI survival. Further studies with larger patient cohorts as well as a consensus definition of failure are needed to further refine predictors of ACI failure.
In Their Voices: Client and Staff Perceptions of the Physical and Social Environments of Adult Day Services Centers in Taiwan

Studies have examined the impact of environments on long-term care residents' quality of life; however, environment gets little attention in adult day services (ADS). The current study gives voice to clients and staff by capturing their perceptions of the physical and social environments of their ADS centers. Data were collected from 23 interviews with staff and clients and 270 hours of participant observations at two ADS centers in Taiwan. The authors triangulated field notes with interview transcriptions and analyzed them with the Grounded Theory coding procedure method. Findings reveal clients' and staff members' perceptions of appropriate and inappropriate physical and social environmental features affecting quality of life at the center and reflecting Taiwanese culture. We address how perceived appropriate features can be sustained or replicated and how perceived inappropriate influences can be remedied. Results can be translated into action research by implementing supportive environments for both staff and clients at ADS centers.
Evidence for intragenic recombination and selective sweep in an effector gene of Phytophthora infestans

Effectors, a group of small proteins secreted by pathogens, play a critical role in the antagonistic interaction between plant hosts and pathogens through their dual functions in regulating host immune systems and pathogen infection capability. In this study, evolution in effector genes was investigated through population genetic analysis of Avr3a sequences generated from 96 Phytophthora infestans isolates collected from six locations representing a range of thermal variation and cropping systems in China. We found high genetic variation in the Avr3a gene resulting from diverse mechanisms extending beyond point mutations, frameshift, and defeated start and stop codons to intragenic recombination. A total of 51 nucleotide haplotypes encoding 38 amino acid isoforms were detected in the 96 full sequences with nucleotide diversity in the pathogen populations ranging from 0.007 to 0.023 (mean = 0.017). Although haplotype and nucleotide diversity were high, the effector gene was dominated by only three haplotypes. Evidence for a selective sweep was provided by (i) the population genetic differentiation (GST) of haplotypes being lower than the population differentiation (FST) of SSR marker loci; and (ii) negative values of Tajima's D and Fu's FS. Annual mean temperature in the collection sites was negatively correlated with the frequency of the virulent form (Avr3aEM), indicating Avr3a may be regulated by temperature. These results suggest that elevated air temperature due to global warming may hamper the development of pathogenicity traits in P. infestans and further study under confined thermal regimes may be required to confirm the hypothesis.
Identification of compound CA-5f as a novel late-stage autophagy inhibitor with potent anti-tumor effect against non-small cell lung cancer

ABSTRACT Currently, particular focus is placed on the implication of autophagy in a variety of human diseases, including cancer. Discovery of small-molecule modulators of autophagy as well as their potential use as anti-cancer therapeutic agents would be of great significance. To this end, a series of curcumin analogs previously synthesized in our laboratory were screened. Among these compounds, (3E,5E)-3-(3,4-dimethoxybenzylidene)-5-[(1H-indol-3-yl)methylene]-1-methylpiperidin-4-one (CA-5f) was identified as a potent late-stage macroautophagy/autophagy inhibitor via inhibiting autophagosome-lysosome fusion. We found that CA-5f neither impaired the hydrolytic function nor the quantity of lysosomes. Use of an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic screen in combination with bioinformatics analysis suggested that treatment of human umbilical vein endothelial cells (HUVECs) with CA-5f for 1 h suppressed the levels of cytoskeletal proteins and membrane traffic proteins. Subsequent studies showed that CA-5f exhibited strong cytotoxicity against A549 non-small cell lung cancer (NSCLC) cells, but low cytotoxicity to normal human umbilical vein endothelial cells (HUVECs), by increasing mitochondrial-derived reactive oxygen species (ROS) production. Moreover, CA-5f effectively suppressed the growth of A549 lung cancer xenograft as a single agent with an excellent tolerance in vivo. Results from western blot, immunofluorescence, and TdT-mediated dUTP nick end labeling (TUNEL) assays showed that CA-5f inhibited autophagic flux, induced apoptosis, and did not affect the level of CTSB (cathepsin B) and CTSD (cathepsin D) in vivo, which were consistent with the in vitro data. Collectively, these results demonstrated that CA-5f is a novel late-stage autophagy inhibitor with potential clinical application for NSCLC therapy. Abbreviations: 3-MA, 3-methyladenine; ANXA5, annexin A5; ATG, autophagy related; CA-5f, (3E,5E)-3-(3,4-dimethoxybenzylidene)-5-[(1H-indol-3-yl)methylene]-1-methylpiperidin-4-one; CQ, chloroquine; CTSB, cathepsin B; CTSD, cathepsin D; DMSO, dimethyl sulfoxide; DNM2, dynamin 2; EBSS, Earle’s balanced salt solution; GFP, green fluorescent protein; HCQ, hydroxyl CQ; HEK293, human embryonic kidney 293; HUVEC, human umbilical vein endothelial cells; LAMP1, lysosomal associated membrane protein 1; LC-MS/MS, liquid chromatography coupled to tandem mass spectrometry; LDH, lactic acid dehydrogenase; LMO7, LIM domain 7; MAP1LC3B/LC3B, microtubule associated protein 1 light chain 3 beta; NAC, N-acetyl cysteine; MYO1E, myosin IE; NSCLC, non-small cell lung cancer; PARP1, poly(ADP-ribose) polymerase 1; PI, propidium iodide; RFP, red fluorescent protein; ROS, reactive oxygen species; SQSTM1, sequestosome 1; TUNEL, terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling.
A Comparison of Ki67, Syndecan-1 (CD138), and Molecular RANK, RANKL, and OPG Triad Expression in Odontogenic Keratocyts, Unicystic Ameloblastoma, and Dentigerous Cysts

Background and Objective Reduced expression of syndecan-1 (CD138), increased proliferation index, and modifications in the expression of the molecular RANK/RANKL/OPG triad are related to an intensified potential of aggressiveness and invasion of diverse tumors and cysts. The aim was to compare the expression of Ki-67, CD138, and the molecular triad RANK, RANKL, and OPG in odontogenic keratocysts (OKC), unicystic ameloblastomas (UA), and dentigerous cysts (DC). Methods Immunohistochemistry for Ki-67, CD138, RANK, RANKL, and OPG was performed in 58 odontogenic cystic lesions (22 OKC, 17 DC, and 19 UA). Results A higher expression of Ki-67 was identified in OKC as compared to UA (p < 0.0001). UA exhibited a greater loss of CD138 expression versus OKCs (p > 0.0034). RANKL was expressed higher in the epithelium (p = 0.0002) and in the stroma (p = 0.0004) of UA. DC had a lower expression of these markers. Conclusion Higher RANKL expression together with the reduction on CD138 expression in UA could be linked to a greater invasive and destructive potential, while the increased proliferation rate observed in OKC could be related to its continuous intrabony growth. The expansion of DC does not seem to be related to such factors, justifying the different therapeutic approaches proposed for each of these entities.
Pathway Network Analysis of Complex Diseases Based on Multiple Biological Networks

Biological pathways play important roles in the development of complex diseases, such as cancers, which are multifactorial complex diseases that are usually caused by multiple disorders gene mutations or pathway. It has become one of the most important issues to analyze pathways combining multiple types of high-throughput data, such as genomics and proteomics, to understand the mechanisms of complex diseases. In this paper, we propose a method for constructing the pathway network of gene phenotype and find out disease pathogenesis pathways through the analysis of the constructed network. The specific process of constructing the network includes, firstly, similarity calculation between genes expressing data combined with phenotypic mutual information and GO ontology information, secondly, calculating the correlation between pathways based on the similarity between differential genes and constructing the pathway network, and, finally, mining critical pathways to identify diseases. Experimental results on Breast Cancer Dataset using this method show that our method is better. In addition, testing on an alternative dataset proved that the key pathways we found were more accurate and reliable as biological markers of disease. These results show that our proposed method is effective.
Future Automation Engineering using Structural Graph Convolutional Neural Networks

The digitalization of automation engineering generates large quantities of engineering data that is interlinked in knowledge graphs. Classifying and clustering subgraphs according to their functionality is useful to discover functionally equivalent engineering artifacts that exhibit different graph structures. This paper presents a new graph learning algorithm designed to classify engineering data artifacts -- represented in the form of graphs -- according to their structure and neighborhood features. Our Structural Graph Convolutional Neural Network (SGCNN) is capable of learning graphs and subgraphs with a novel graph invariant convolution kernel and downsampling/pooling algorithm. On a realistic engineering-related dataset, we show that SGCNN is capable of achieving ~91% classification accuracy.
Knockdown of A‐kinase anchor protein 4 inhibits hypoxia‐induced epithelial‐to‐mesenchymal transition via suppression of the Wnt/β‐catenin pathway in human gastric cancer cells

Hypoxia induces epithelial‐mesenchymal transition (EMT) in tumorigenesis. A‐kinase anchor protein 4 (AKAP4) is a member of AKAPs family and plays a critical role in tumorigenesis. However, the biological role of AKAP4 in gastric cancer remains unknown. Thus, we investigated the effect of AKAP4 on EMT in human gastric cancer cells under hypoxic conditions. Our results showed that AKAP4 expression was significantly upregulated in human gastric cancer cell lines. In addition, silenced expression of hypoxia‐inducible factor‐1α markedly suppressed AKAP4 expression in gastric cancer cells under hypoxia. Furthermore, knockdown of AKAP4 significantly prevented hypoxia‐induced migration, invasion, and EMT process in gastric cancer cells. Mechanistically, knockdown of AKAP4 prevented the activation of the Wnt/β‐catenin pathway in gastric cancer cells under hypoxia condition. These findings indicate that knockdown of AKAP4 inhibits hypoxia‐induced EMT in human gastric cancer cells, at least in part, via inactivation of the Wnt/β‐catenin signaling pathway. It is, therefore, AKAP4 may be a potential therapeutic target for the treatment of gastric cancer.