Miracle-dz/UniFAR-FTUs huggingface dataset:
The association between copy number aberration, DNA methylation and gene expression in tumor samples

Abstract We systematically studied the association between somatic copy number aberration (SCNA), DNA methylation and gene expression using -omic data from The Cancer Genome Atlas (TCGA) on six cancer types: breast cancer, colon cancer, glioblastoma, leukemia, lower-grade glioma and prostate cancer. A major challenge for such integrated study is that the association between DNA methylation and gene expression is severely confounded by tumor purity and cell type composition, which are often unobserved and difficult to estimate. To overcome this challenge, we developed a method to remove confounding effects by calculating the principal components that span the space of the latent factors. Another intriguing findings of our study is that there could be both positive and negative associations between SCNA and DNA methylation, while the CpGs with negative/positive associations with SCNA are often located around CpG islands/ocean, respectively. A joint study of SCNA, DNA methylation, and gene expression suggest that SCNA often affect DNA methylation and gene expression independently.
Characterization of a PLLA-Collagen I Blend Nanofiber Scaffold with Respect to Growth and Osteogenic Differentiation of Human Mesenchymal Stem Cells

The aim of this study was to enhance synthetic poly(L-lactic acid) (PLLA) nanofibers by blending with collagen I (COLI) in order to improve their ability to promote growth and osteogenic differentiation of stem cells in vitro. Fiber matrices composed of PLLA and COLI in different ratios were characterized with respect to their morphology, as well as their ability to promote growth of human mesenchymal stem cells (hMSC) over a period of 22 days. Furthermore, the course of differentiation was analyzed by gene expression of alkaline phosphatase (ALP), osteocalcin (OC), and COLI. The PLLA-COLI blend nanofibers presented themselves with a relatively smooth surface. They were more hydrophilic as compared to PLLA nanofibers alone and formed a gel-like structure with a stable nanofiber backbone when incubated in aqueous solutions. We examined nanofibers composed of different PLLA and COLI ratios. A composition of 4:1 ratio of PLLA:COLI showed the best results. When hMSC were cultured on the PLLA-COLI nanofiber blend, growth as well as osteoblast differentiation (determined as gene expression of ALP, OC, and COLI) was enhanced when compared to PLLA nanofibers alone. Therefore, the blending of PLLA with COLI might be a suitable tool to enhance PLLA nanofibers with respect to bone tissue engineering.
Polymorphisms of multiple genes involved in NER pathway predict prognosis of gastric cancer

Nucleotide excision repair (NER) is a versatile system that repairs various DNA damage. Polymorphisms of core NER genes could change NER ability and affect gastric cancer (GC) prognosis. We systematically analyzed the association between 43 SNPs of ten key NER pathway genes (ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, ERCC6, ERCC8, XPA, XPC, and DDB2) and overall survival (OS) of 373 GC patients in Chinese. Genotyping was performed by Sequenom MassARRAY platform. We found for the first time that carriers of ERCC2 rs50871 GG genotype demonstrated significantly increased hazards of death than GT/TT individuals (HR=2.55, P=0.002); ERCC6 rs1917799 heterozygote GT were associated with significantly shorter OS than wild-type TT (adjusted HR=1.68, P=0.048); patients with DDB2 rs3781619 GG genotype suffered higher hazards of death compared with AG/AA carriers (adjusted HR=2.30, P=0.003). Patients with ERCC1 rs3212961 AA/AC genotype exhibited longer OS than CC genotype (adjusted HR=0.63, P=0.028); ERCC5 rs2094258 AA/AG genotype revealed significantly favorable OS compared with GG genotype (adjusted HR=0.65, P=0.033); DDB2 rs830083 CG genotype could increase OS compared with GG genotype (adjusted HR=0.61, P=0.042). Furthermore, patients simultaneously carrying two “hazard” genotypes exhibited even significantly worse survival with HR of 3.75, 3.76 and 6.30, respectively. Similarly, combination of “favorable” genotypes predicted better prognosis with HR of 0.56, 0.49 and 0.33, respectively. In conclusion, ERCC2 rs50871 G/T, ERCC6 rs1917799 G/T, DDB2 rs3781619 A/G polymorphisms could predict shorter OS while ERCC1 rs3212961 A/C, ERCC5 rs2094258 A/G, DDB2 rs830083 C/G polymorphisms could predict longer OS of GC, which might serve as promising biomarkers for GC prognosis.
Dependency Parser for Chinese Constituent Parsing

This paper presents our work for participation in the 2010 CIPS-ParsEval shared task on Chinese syntactic constituent tree parsing. We use dependency parsers for this constituent parsing task based on a formal dependency-constituent transformation method which converts dependency to constituent structures us-ing a machine learning approach. A conditional random ﬁelds (CRF) tagger is adopted for head information recognition. Our experiments shows that acceptable parsing and head tagging results are obtained on our approaches.
The Role of the Melanocortin System in Metabolic Disease: New Developments and Advances

Obesity is increasing in prevalence across all sectors of society, and with it a constellation of associated ailments including hypertension, type 2 diabetes, and eating disorders. The melanocortin system is a critical neural system underlying the control of body weight and other functions. Deficits in the melanocortin system may promote or exacerbate the comorbidities of obesity. This system has therefore generated great interest as a potential target for treatment of obesity. However, drugs targeting melanocortin receptors are plagued by problematic side effects, including undesirable increases in sympathetic nervous system activity, heart rate, and blood pressure. Circumnavigating this roadblock will require a clearer picture of the precise neural circuits that mediate the functions of melanocortins. Recent, novel experimental approaches have significantly advanced our understanding of these pathways. We here review the latest advances in our understanding of the role of melanocortins in food intake, reward pathways, blood pressure, glucose control, and energy expenditure. The evidence suggests that downstream melanocortin-responsive circuits responsible for different physiological actions do diverge. Ultimately, a more complete understanding of melanocortin pathways and their myriad roles should allow treatments tailored to the mix of metabolic disorders in the individual patient.
Deep grey matter volume loss drives disability worsening in multiple sclerosis

Objective Grey matter (GM) atrophy occurs in all multiple sclerosis (MS) phenotypes. We investigated whether there is a spatiotemporal pattern of GM atrophy that is associated with faster disability accumulation in MS. Methods We analysed 3,604 brain high-resolution T1-weighted MRI scans from 1,417 participants: 1,214 MS patients (253 clinically-isolated syndrome[CIS], 708 relapsingremitting[RRMS], 128 secondary-progressive[SPMS], 125 primary-progressive[PPMS]), over an average follow-up of 2.41 years (standard deviation[SD]=1.97), and 203 healthy controls (HCs) [average follow-up=1.83 year, SD=1.77], attending 7 European centres. Disability was assessed with the Expanded-Disability Status Scale (EDSS). We obtained volumes of the deep GM (DGM), temporal, frontal, parietal, occipital and cerebellar GM, brainstem and cerebral white matter. Hierarchical mixed-models assessed annual percentage rate of regional tissue loss and identified regional volumes associated with time-to-EDSS progression. Results SPMS showed the lowest baseline volumes of cortical GM and DGM. Of all baseline regional volumes, only that of the DGM predicted time-to-EDSS progression (hazard ratio=0.73, 95% CIs 0.65, 0.82; p<0.001): for every standard deviation decrease in baseline DGM volume, the risk of presenting a shorter time to EDSS worsening during follow-up increased by 27%. Of all longitudinal measures, DGM showed the fastest annual rate of atrophy, which was faster in SPMS (-1.45%), PPMS (-1.66%), and RRMS (-1.34%) than CIS (-0.88%) and HCs (-0.94%)[p<0.01]. The rate of temporal GM atrophy in SPMS (-1.21%) was significantly faster than RRMS (-0.76%), CIS (-0.75%), and HCs (-0.51%). Similarly, the rate of parietal GM atrophy in SPMS (-1.24-%) was faster than CIS (-0.63%) and HCs (-0.23%) (all p values <0.05). Only the atrophy rate in DGM in patients was significantly associated with disability accumulation (beta=0.04, p<0.001). Interpretation This large multi-centre and longitudinal study shows that DGM volume loss drives disability accumulation in MS, and that temporal cortical GM shows accelerated atrophy in SPMS than RRMS. The difference in regional GM atrophy development between phenotypes needs to be taken into account when evaluating treatment effect of therapeutic interventions.
Construction of High-Density Genetic Linkage Maps and Mapping of Growth-Related Quantitative Trail Loci in the Japanese Flounder (Paralichthys olivaceus)

High-density genetic linkage maps were constructed for the Japanese flounder (Paralichthys olivaceus). A total of 1624 microsatellite markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 resulted in the mapping of 1487 markers to 24 linkage groups, a result which was consistent with the 24 chromosomes seen in chromosome spreads. The female map was composed of 1257 markers, covering a total of 1663.8 cM with an average interval 1.35 cM between markers. The male map consisted of 1224 markers, spanning 1726.5 cM, with an average interval of 1.44 cM. The genome length in the Japanese flounder was estimated to be 1730.3 cM for the females and 1798.0 cM for the males, a coverage of 96.2% for the female and 96.0% for the male map. The mean recombination at common intervals throughout the genome revealed a slight difference between sexes, i.e. 1.07 times higher in the male than female. High-density genetic linkage maps are very useful for marker-assisted selection (MAS) programs for economically valuable traits in this species and for further evolutionary studies in flatfish and vertebrate species. Furthermore, four quantiative trait loci (QTL) associated with growth traits were mapped on the genetic map. One QTL was identified for body weight on LG 14 f, which explained 14.85% of the total variation of the body weight. Three QTL were identified for body width on LG14f and LG14m, accounting for 16.75%, 13.62% and 13.65% of the total variation in body width, respectively. The additive effects were evident as negative values. There were four QTL for growth traits clustered on LG14, which should prove to be very useful for improving growth traits using molecular MAS.
Ion induced effects in polymers

Polymer films are finding many applications like microfilters for gas separation, water purification and blood filtration , etc. The effect of irradiation of 85 MeV 0+ ions on polycarbonate, Teflon and Mylar films characterized by Positron Annihilation Lifetime Spectroscopy (PALS) is reported here. The PALS is a non-destructive, non-interfering probe, which has high detection efficiency for vacancy and free/open volume defects. The positron lifetime study shows 7-20% increase in free volume size.
Frequency of folate‐related polymorphisms varies by skin pigmentation

Folate‐mediated 1‐carbon transfer processes are vital in human health but are susceptible to independent and interactive influences of genetic variance and environmental exposures. Evidence suggests folate levels may be impacted by genetic variance and environmental UVR, with the effect of UVR levels influenced in part by degree of skin pigmentation. Folate‐related genes are also influenced by UVR levels; however, the potential relationship between key folate‐related genes and skin pigmentation has not yet been explored. The purpose of this study was to examine potential associations between frequencies of key folate variants and degree of skin pigmentation.
Inhalation exposure during spray application and subsequent sanding of a wood sealant containing zinc oxide nanoparticles

ABSTRACT Nano-enabled construction products have entered into commerce. There are concerns about the safety of manufactured nanomaterials, and exposure assessments are needed for a more complete understanding of risk. This study assessed potential inhalation exposure to ZnO nanoparticles during spray application and power sanding of a commercially available wood sealant and evaluated the effectiveness of local exhaust ventilation in reducing exposure. A tradesperson performed the spraying and sanding inside an environmentally-controlled chamber. Dust control methods during sanding were compared. Filter-based sampling, electron microscopy, and real-time particle counters provided measures of exposure. Airborne nanoparticles above background levels were detected by particle counters for all exposure scenarios. Nanoparticle number concentrations and particle size distributions were similar for sanding of treated versus untreated wood. Very few unbound nanoparticles were detected in aerosol samples via electron microscopy, rather nano-sized ZnO was contained within, or on the surface of larger airborne particles. Whether the presence of nanoscale ZnO in these aerosols affects toxicity merits further investigation. Mass-based exposure measurements were below the NIOSH Recommended Exposure Limit for Zn, although there are no established exposure limits for nanoscale ZnO. Local exhaust ventilation was effective, reducing airborne nanoparticle number concentrations by up to 92% and reducing personal exposure to total dust by at least 80% in terms of mass. Given the discrepancies between the particle count data and electron microscopy observations, the chemical identity of the airborne nanoparticles detected by the particle counters remains uncertain. Prior studies attributed the main source of nanoparticle emissions during sanding to copper nanoparticles generated from electric sander motors. Potentially contrary results are presented suggesting the sander motor may not have been the primary source of nanoparticle emissions in this study. Further research is needed to understand potential risks faced by construction workers exposed to mixed aerosols containing manufactured nanomaterials. Until these risks are better understood, this study demonstrates that engineering controls can reduce exposure to manufactured nanomaterials; doing so may be prudent for protecting worker health.
The Neural Correlates of Identity Faking and Concealment: An fMRI Study

The neural basis of self and identity has received extensive research. However, most of these existing studies have focused on situations where the internal representation of the self is consistent with the external one. The present study used fMRI methodology to examine the neural correlates of two different types of identity conflict: identity faking and concealment. Participants were presented with a sequence of names and asked to either conceal their own identity or fake another one. The results revealed that the right insular cortex and bilaterally inferior frontal gyrus were more active for identity concealment compared to the control condition, whereas identity faking elicited a significantly larger percentage signal increase than the control condition in the right superior frontal gyrus, left calcarine, and right caudate. These results suggest that different neural systems associated with both identity processing and deception were involved in identity concealment and faking.
Mini-Incision Living Donors Nephrectomy Using Anterior Muscle-Splitting Approach with Hybrid Technique

Background: Significant morbidity is associated with standard open flank living donor nephrectomy. Laparoscopic donor nephrectomy is criticized for a steep learning curve and a tendency to avoid the right kidney. The anterior muscle-splitting technique uses principles or advantages of an open extraperitoneal approach with minimal morbidity and the advantageous muscle-splitting (instead of cutting) procedure. Objective: To compare mini-incision laparoscopic instrument-assisted (MILIA) live donor nephrectomy using a muscle-splitting technique to the standard open-flank donor nephrectomy (ODN) approach for efficacy and safety. Methods: MILIA living donor nephrectomies were performed in 119 donors and compared to a cohort of open-flank nephrectomy donors (n=38) from the same center. Both donor groups were matched for body mass index as well as other personal characteristics. Results: The mean donor age was 35 (range: 18–60) years. The right kidney was procured in 28% of cases. The majority of donors were female (58%) and Caucasian (60%). No differences were observed between MILIA and ODN donors for the age, gender and ethnicity. However, MILIA donors experienced a longer mean±SD operative time (234±47 vs. 197±33 min, p<0.0001) but a shorter hospital stay (4±1 vs. 6±3 days for the ODN group, p<0.0001) and less intraoperative blood loss (215±180 vs. 331±397 mL, p<0.02). No difference was found in the number of units of blood transfused (0.13±0.6 vs. 0.34±1.0 units, p=0.13). Right-sided kidneys were almost equally harvested in both groups (29% of MILIA donors vs. 26% of ODN donors). Post-operatively, MILIA donors had a significantly lower mean pain scores at one week and one month after surgery (p<0.001). They showed significant better post-operative recovery—earlier stopping of pain medications and restoration of other preoperative activities. Moreover, they were better satisfied with their scar appearance. Scores on the short form-36 quality of life questionnaire were comparable for both groups. Conclusion: MILIA is a viable option as an alternative for pure laparoscopic donor nephrectomy. MILIA appears to be as safe as open donor nephrectomy and may provide advantages over ODN, such as smaller incision, shorter hospital stay, and less incisional pain. Patient recovery and satisfaction after MILIA are excellent. This technique avoids the possibility of adhesive intestinal obstruction and also improves handling of major complications (e.g., bleeding) of laparoscopic donor nephrectomy. Utilization of this hybrid technique is particularly feasible on smaller (BMI<24 kg/m2) and medium-sized (BMI<28 kg/m2) donors. We believe that this technique should be adopted by centers that have limited advanced laparoscopic surgical experience and also it could be used selectively for the right donor nephrectomies, even in centers performing hand assisted donor nephrectomies by including a small patch of inferior vena cava for a better quality of right donor kidney during transplantation.
Event Time Extraction with a Decision Tree of Neural Classifiers

Extracting the information from text when an event happened is challenging. Documents do not only report on current events, but also on past events as well as on future events. Often, the relevant time information for an event is scattered across the document. In this paper we present a novel method to automatically anchor events in time. To our knowledge it is the first approach that takes temporal information from the complete document into account. We created a decision tree that applies neural network based classifiers at its nodes. We use this tree to incrementally infer, in a stepwise manner, at which time frame an event happened. We evaluate the approach on the TimeBank-EventTime Corpus (Reimers et al., 2016) achieving an accuracy of 42.0% compared to an inter-annotator agreement (IAA) of 56.7%. For events that span over a single day we observe an accuracy improvement of 33.1 points compared to the state-of-the-art CAEVO system (Chambers et al., 2014). Without retraining, we apply this model to the SemEval-2015 Task 4 on automatic timeline generation and achieve an improvement of 4.01 points F1-score compared to the state-of-the-art. Our code is publically available.
Epithelialization of mouse ovarian tumor cells originating in the fallopian tube stroma

Epithelial ovarian carcinoma accounts for 90% of all ovarian cancer and is the most deadly gynecologic malignancy. Recent studies have suggested that fallopian tube fimbriae can be the origin of cells for high-grade serous subtype of epithelial ovarian carcinoma (HGSOC). A mouse HGSOC model with conditional Dicer-Pten double knockout (Dicer-Pten DKO) developed primary tumors, intriguingly, from the fallopian tube stroma. We examined the growth and epithelial phenotypes of the Dicer-Pten DKO mouse tumor cells contributable by each gene knockout. Unlike human ovarian epithelial cancer cells that expressed full-length E-cadherin, the Dicer-Pten DKO stromal tumor cells expressed cleaved E-cadherin fragments and metalloproteinase 2, a mixture of epithelial and mesenchymal markers. Although the Dicer-Pten DKO tumor cells lost the expression of mature microRNAs as expected, they showed high levels of tRNA fragment expression and enhanced AKT activation due to the loss of PTEN function. Introduction of a Dicer1-expressing construct into the DKO mouse tumor cells significantly reduced DNA synthesis and the cell growth rate, with concurrent diminished adhesion and ZO1 epithelial staining. Hence, it is likely that the loss of Dicer promoted mesenchymal-epithelial transition in fallopian tube stromal cells, and in conjunction with Pten loss, further promoted cell proliferation and epithelial-like tumorigenesis.
A New Variant of the Capsule 3 Cluster Occurs in Streptococcus pneumoniae from Deceased Wild Chimpanzees

The presence of new Streptococcus pneumoniae clones in dead wild chimpanzees from the Taï National Park, Côte d'Ivoire, with previous respiratory problems has been demonstrated recently by DNA sequence analysis from samples obtained from the deceased apes. In order to broadenour understanding on the relatedness of these pneumococcal clones to those from humans, the gene locus responsible for biosynthesis of the capsule polysaccharide (CPS) has now been characterized. DNA sequence analysis of PCR fragments identified a cluster named cps3Taï containing the four genes typical for serotype 3 CPS, but lacking a 5′-region of ≥2 kb which is degenerated in other cps3 loci and not required for type 3 biosynthesis. CPS3 is composed of a simple disaccharide repeat unit comprising glucose and glucuronic acid (GlcUA). The two genes ugd responsible for GlcUA synthesis and wchE encoding the type 3 synthase are essential for CPS3 biosynthesis, whereas both, galU and the 3′-truncated gene pgm are not required due to the presence of homologues elsewhere in the genome. The DNA sequence of cps3Taï diverged considerably from those of other cps3 loci. Also, the gene pgm Taï represents a full length version with a nonsense mutation at codon 179. The two genes ugd Taï and wchE Taï including the promoter region were transformed into a nonencapsulated laboratory strain S. pneumoniae R6. Transformants which expressed type 3 capsule polysaccharide were readily obtained, documenting that the gene products are functional. In summary, the data indicate that cps3Taï evolved independent from other cps3 loci, suggesting the presence of specialized serotype 3 S. pneumoniae clones endemic to the Taï National Park area.