Miracle-dz/UniFAR-FTUs huggingface dataset:
Graph Grammars with Negative Application Conditions

In each graph-grammar approach it is defined how and under which conditions graph productions can be applied to a given graph in order to obtain a derived graph. The conditions under which productions can be applied are called application conditions. Although the generative power of most of the known general graph-grammar approaches is sufficient to generate any recursively enumerable set of graphs, it is often convenient to have specific application conditions for each production. Such application conditions, on the one hand, include context conditions like the existence or non-existence of nodes, edges, or certain subgraphs in the given graph as well as embedding restrictions concerning the morphisms from the left-hand side of the production to the given graph. In this paper, the concept of application conditions introduced by Ehrig and Habel is restricted to contextual conditions, especially negative ones. In addition to the general concept, we state local confluence and the Parallelism Theorem for derivations with application conditions. Finally we study context-free graph grammars with application conditions with respect to their generative power.
Sulforaphane-induced apoptosis involves the type 1 IP3 receptor

In this study we show that anti-tumor effect of sulforaphane (SFN) is partially realized through the type 1 inositol 1,4,5-trisphosphate receptor (IP3R1). This effect was verified in vitro on three different stable cell lines and also in vivo on the model of nude mice with developed tumors. Early response (6 hours) of A2780 ovarian carcinoma cells to SFN treatment involves generation of mitochondrial ROS and increased transcription of NRF2 and its downstream regulated genes including heme oxygenase 1, NAD(P)H:quinine oxidoreductase 1, and KLF9. Prolonged SFN treatment (24 hours) upregulated expression of NRF2 and IP3R1. SFN induces a time-dependent phosphorylation wave of HSP27. Use of IP3R inhibitor Xestospongin C (Xest) attenuates both SFN-induced apoptosis and the level of NRF2 protein expression. In addition, Xest partially attenuates anti-tumor effect of SFN in vivo. SFN-induced apoptosis is completely inhibited by silencing of IP3R1 gene but only partially blocked by silencing of NRF2; silencing of IP3R2 and IP3R3 had no effect on these cells. Xest inhibitor does not significantly modify SFN-induced increase in the rapid activity of ARE and AP1 responsive elements. We found that Xest effectively reverses the SFN-dependent increase of nuclear content and decrease of reticular calcium content. In addition, immunofluorescent staining with IP3R1 antibody revealed that SFN treatment induces translocation of IP3R1 to the nucleus. Our results clearly show that IP3R1 is involved in SFN-induced apoptosis through the depletion of reticular calcium and modulation of transcription factors through nuclear calcium up-regulation.
Omni-word Feature and Soft Constraint for Chinese Relation Extraction

Chinese is an ancient hieroglyphic. It is inattentive to structure. Therefore, segmenting and parsing Chinese are more difficult and less accurate. In this paper, we propose an Omniword feature and a soft constraint method for Chinese relation extraction. The Omni-word feature uses every potential word in a sentence as lexicon feature, reducing errors caused by word segmentation. In order to utilize the structure information of a relation instance, we discuss how soft constraint can be used to capture the local dependency. Both Omni-word feature and soft constraint make a better use of sentence information and minimize the influences caused by Chinese word segmentation and parsing. We test these methods on the ACE 2005 RDC Chinese corpus. The results show a significant improvement in Chinese relation extraction, outperforming other methods in F-score by 10% in 6 relation types and 15% in 18 relation subtypes.
Mortality associated with anxiolytic and hypnotic drugs—A systematic review and meta-analysis

Background: Use of hypnotics or anxiolytic drugs is common and various studies have reported increased mortality with hypnotics or anxiolytic use. Objective: To consolidate the evidence on mortality risk associated with hypnotics or anxiolytic use Methods: Major databases were searched through April 2014 for studies reporting mortality risk associated with hypnotics or anxiolytics use. A pooled hazard ratio with 95% confidence interval was estimated using random-effects model. Results: After screening 2188 articles, 25 studies (24 cohort, 1 case-control) enrolling 2,350,093 patients with 59% females (age 18–102 years) were included in the meta-analysis. Hypnotics or anxiolytic users had 43% higher risk of mortality than non-users (hazard ratio, 1.43; 95% confidence interval, [1.12, 1.84]). Eight studies reported risk estimates for each gender category and pooled results from these studies showed increased risk of mortality among men (hazard ratio = 1.60, 95% confidence interval = [1.29,1.99]) and women (hazard ratio = 1.68, 95% confidence interval = [1.38, 2.04]). Pooled results from 10 studies showed higher mortality among benzodiazepine users compared to non-users (hazard ratio = 1.60, 95% confidence interval = [1.03, 2.49]), while pooled results from five studies showed an increased risk of mortality with Z-drugs use although the effect could not reach statistical significance (hazard ratio = 1.73, 95% confidence interval = [0.95, 3.16]). Significant heterogeneity was observed in the analyses and the quality of included studies was good. Conclusion: This meta-analysis suggests that hypnotics or anxiolytics drugs use is associated with increased mortality and hence should be used with caution. Future studies focused on underlying mechanism of increased mortality with hypnotics or anxiolytics use are required.
Identification of a Male-Specific RNA Binding Protein That Regulates Sex-Specific Splicing of Bmdsx by Increasing RNA Binding Activity of BmPSI

ABSTRACT Bmdsx is a sex-determining gene in the silkworm and is alternatively spliced in males and females. CE1 is a splicing silencer element responsible for the sex-specific splicing of Bmdsx. To identify sex-specific factors implicated in the sex-specific splicing of Bmdsx, we performed RNA affinity chromatography using CE1 RNA as a ligand. We have identified BmIMP, a Bombyx homolog of IGF-II mRNA binding protein (IMP), as a male-specific factor that specifically binds to CE1. The gene encoding BmIMP is localized on the Z chromosome and is male-specifically expressed in various tissues. Antisense inhibition of BmIMP expression increased female-specific splicing of Bmdsx pre-mRNA. Coimmunoprecipitation and glutathione S-transferase (GST) pulldown analyses demonstrated that BmIMP physically interacts with BmPSI, which has been identified as a factor implicated in the sex-specific splicing of Bmdsx, through the KH domains of BmIMP. The functional consequence of this interaction was examined using RNA mobility shift analysis. BmIMP increased BmPSI-CE1 RNA binding activity by decreasing the rate of BmPSI dissociation from CE1 RNA. Truncation analysis of BmIMP suggested that the KH domains are responsible for enhancing BmPSI-CE1 RNA binding activity. These results suggest that BmIMP may enhance the male-specific splicing of Bmdsx pre-mRNA by increasing RNA binding activity of BmPSI.
Searching for People through Textual and Visual Attributes

Searching for people through their personal traits has been largely required for several areas and, consequently, has become the center of attention in the scientific community. Locating a suspect or finding missing people in a public space are some of the practical applications which take advantage of research conducted in this topic. In this paper, we propose the use of describable visual attributes (e.g., male, wear glasses, has beard), as labels that can be assigned to an image to describe its appearance. The approach is based on visual dictionaries to generate an intermediate representation for the face images. We train binary classifiers for the attributes which give to each image a score used to obtain its ranking. However, there are some attributes that have no immediate antagonistic (e.g., asian people). Then, we evaluate unary classifiers for such attributes. The method is easily extensible to new attributes. For queries consisting of more than one attribute, we use two approaches of the state-of-the-art to combine the rankings: product of probabilities and rank aggregation. Experimental results show that incorporating visual dictionaries improves the accuracy for some attributes. Furthermore, for many attributes, rank aggregation achieves better results than traditional methods of rank fusion. The proposed solution might be of interest in a forensic scenario for searching suspects in a database by means of textual descriptions provided by a victim.
Reactivity of Gliadin and Lectins with Celiac Intestinal Mucosa1

ABSTRACT: The binding patterns of gliadin and selected lectins to jejunal biopsy specimens obtained from children with total villous atrophy during active celiac disease (CD; 19 patients) and in remission (16 patients) were examined by light microscopy. Three categories of carbohydrate-specific lectins were chosen for the study: those recognizing mannose/glucose residues, those recognizing N-acetyl-glucosamine/glucose (glcNAc/glc) residues, and those recognizing N-acetylgalactosamine/galactose (galNAc/gal) residues. The galNAc/gal lectins, with the exception of phaseolus vulgaris agglutinin variants, presented a typical staining of the luminal surface of the jejunal mucosa obtained from CD patients. However, these lectins displayed no reactivity to jejunal sections of CD patients in remission or control biopsies that included healthy children (25 children) and patients suffering from cow milk protein allergy (10 children). The glcNAc/glc lectin showed a strong preferential recognition of CD jejunal tissue but also bound with less intensity to specimens from patients with cow milk allergies and healthy children. Unlike other galNAc/gal lectins, phaseolus vulgaris agglutinin variants were indistinguishable in their binding patterns to the mucosa of control groups and CD patients in remission and failed to react to CD biopsies. The mannose/glc lectins were not distinctive in their binding patterns. In all cases, lectin binding was specifically inhibited by the lectins' competitive saccharides. Atypical of lectin binding patterns, gliadin reactivity was restricted to intracellular areas of enterocytes and was unique to active CD mucosa. The distinctive binding patterns of lectins and gliadin provide a diagnostic tool to distinguish patients with active CD from those in remission or patients with other intestinal disorders. These findings raise interesting questions about the role of gliadin and lectins in CD. It is speculated that the presence of new luminal sites may act to manifest lectin susceptibility and exacerbate CD pathology.
Overexpression of the myelin proteolipid protein leads to accumulation of cholesterol and proteolipid protein in endosomes/lysosomes

Duplications and overexpression of the proteolipid protein (PLP) gene are known to cause the dysmyelinating disorder Pelizaeus-Merzbacher disease (PMD). To understand the cellular response to overexpressed PLP in PMD, we have overexpressed PLP in BHK cells and primary cultures of oligodendrocytes with the Semliki Forest virus expression system. Overexpressed PLP was routed to late endosomes/lysosomes and caused a sequestration of cholesterol in these compartments. Similar results were seen in transgenic mice overexpressing PLP. With time, the endosomal/lysosomal accumulation of cholesterol and PLP led to an increase in the amount of detergent-insoluble cellular cholesterol and PLP. In addition, two fluorescent sphingolipids, BODIPY–lactosylceramide and –galactosylceramide, which under normal conditions are sorted to the Golgi apparatus, were missorted to perinuclear structures. This was also the case for the lipid raft marker glucosylphosphatidylinositol–yellow fluorescence protein, which under normal steady-state conditions is localized on the plasma membrane and to the Golgi complex. Taken together, we show that overexpression of PLP leads to the formation of endosomal/lysosomal accumulations of cholesterol and PLP, accompanied by the mistrafficking of raft components. We propose that these accumulations perturb the process of myelination and impair the viability of oligodendrocytes.
A Pilot Genome-Wide Association Study in Postmenopausal Mexican-Mestizo Women Implicates the RMND1/CCDC170 Locus Is Associated with Bone Mineral Density

To identify genetic variants influencing bone mineral density (BMD) in the Mexican-Mestizo population, we performed a GWAS for femoral neck (FN) and lumbar spine (LS) in Mexican-Mestizo postmenopausal women. In the discovery sample, 300,000 SNPs were genotyped in a cohort of 411 postmenopausal women and seven SNPs were analyzed in the replication cohort (n = 420). The combined results of a meta-analysis from the discovery and replication samples identified two loci, RMND1 (rs6904364, P = 2.77 × 10−4) and CCDC170 (rs17081341, P = 1.62 × 10−5), associated with FN BMD. We also compared our results with those of the Genetic Factors for Osteoporosis (GEFOS) Consortium meta-analysis. The comparison revealed two loci previously reported in the GEFOS meta-analysis: SOX6 (rs7128738) and PKDCC (rs11887431) associated with FN and LS BMD, respectively, in our study population. Interestingly, rs17081341 rare in Caucasians (minor allele frequency < 0.03) was found in high frequency in our population, which suggests that this association could be specific to non-Caucasian populations. In conclusion, the first pilot Mexican GWA study of BMD confirmed previously identified loci and also demonstrated the importance of studying variability in diverse populations and/or specific populations.
IL-13 Stimulates Proliferation and Expression of Mucin and Immunomodulatory Genes in Cultured Conjunctival Goblet Cells.

PURPOSE To investigate the effects of IL-13 on goblet cell proliferation, differentiation, and expression of mucin and immunomodulatory genes. METHODS Explants were excised from the conjunctiva of young C57BL/6 mice. Cultures received 200 μL per week of either Keratinocyte media (KSFM) or KSFM supplemented with 10 ng/mL IL-13 and were incubated for 3 (D3), 7 (D7), or 14 (D14) days. Subsequently, cell proliferation was assessed or cultures were immunostained, collected for dot blot, or for reverse transcription (RT) and quantitative real-time PCR (qPCR) or for RT-PCR gene array. RESULTS The cultured conjunctival epithelium expressed goblet cell associated keratin 7 and mucins MUC5AC and MUC2 and when stimulated with IL-13 showed increased proliferation at D3 and D7 (P < 0.05) compared with control. MUC5AC expression was increased in the IL-13-treated group at D3 and D14 (P < 0.05). IL-13-treated cultures showed increased chemokine ligand 26 (CCL26), chloride channel calcium activated channel 3 (CLCA3), fas ligand (FasL), and Relm-β at D7. All conjunctival cultures expressed MUC2, and its expression was decreased at D3 (P < 0.05) and increased at D14 (P < 0.05) with IL-13 treatment. CONCLUSIONS This study demonstrated that conjunctival goblet cells are IL-13 responsive cells that produce factors known to maintain epithelial barrier, stimulate mucin production, and modulate immune response in nonocular mucosa when treated with IL-13. The functional significance of IL-13-stimulated factors remains to be determined.
Psychological and Social Factors Affecting Internet Searches on Suicide in Korea: A Big Data Analysis of Google Search Trends

Purpose The average mortality rate for death by suicide among OECD countries is 12.8 per 100000, and 33.5 for Korea. The present study analyzed big data extracted from Google to identify factors related to searches on suicide in Korea. Materials and Methods Google search trends for the search words of suicide, stress, exercise, and drinking were obtained for 2004-2010. Analyzing data by month, the relationship between the actual number of suicides and search words per year was examined using multi-level models. Results Both suicide rates and Google searches on suicide in Korea increased since 2007. An unconditional slope model indicated stress and suicide-related searches were positively related. A conditional model showed that factors associated with suicide by year directly affected suicide-related searches. The interaction between stress-related searches and the actual number of suicides was significant. Conclusion A positive relationship between stress- and suicide-related searches further confirmed that stress affects suicide. Taken together and viewed in context of the big data analysis, our results point to the need for a tailored prevention program. Real-time big data can be of use in indicating increases in suicidality when search words such as stress and suicide generate greater numbers of hits on portals and social network sites.
Version 3-30-2009 Effect of Conditioning Regimen Intensity on CMV Infection in Allogeneic Hematopoietic Cell Transplantation

Nonmyeloablative conditioning is less toxic and results in initial establishment of mixed hematopoietic T cell chimerism for up to half a year with prolonged presence of host T cell immunity. In this study, we examined whether this translates into differences in the risks and/or severity of cytomegalovirus (CMV) infection and disease. We analyzed data from 537 nonmyeloablative (NM-HCT) and contemporaneous 2489 myeloablative hematopoietic cell transplant (M-HCT) recipients. In CMV seropositive recipients, no difference in the overall hazards of CMV infection at any level [adjusted hazard ratio (adj. HR) 0.9, 95% confidence interval (95%CI): 0.7-1.0, P=0.14] was noted; however, NM-HCT was associated with a lower risk of high-grade CMV infection (adj. HR 0.7, 95%CI: 0.5-0.9, P=0.02). CMV disease rates were similar between the groups during the first 100 days after HCT but NM-HCT recipients had an increased risk of late CMV disease (adj. HR 2.0, 95% CI 1.2-3.4). The increased risk of late CMV disease after NM-HCT was pronounced during the earlier years of the study period but not detectable in more recent years. Contrary to earlier reports, survival following CMV disease was not reduced after NM-HCT when compared to M-HCT recipients. These results suggest that residual host cells after NM-HCT reduce progression to higher CMV viral load in NM-HCT recipients; however, this effect does not appear to protect against serious complications of CMV. Therefore, CMV prevention strategies in NM-HCT recipients should be similar to those used in M-HCT recipients.
Focal dysplasia of the cerebral cortex in epilepsy

An unusual microscopic abnormality has been identified in the lobectomy specimens removed surgically from the brains of 10 epileptic patients. The abnormality could seldom be identified by palpation or with the naked eye. Histologically, it consisted of congregations of large, bizarre neurones which were littered through all but the first cortical layer. In most, but not in all cases, grotesque cells, probably of glial origin, were also present in the depths of the affected cortex and in the subjacent white matter. This kind of abnormality appears to be a malformation. The picture is reminiscent of tuberous sclerosis but too many distinguishing features, both in the clinical and in the pathological aspects, make this diagnosis untenable. The cases are therefore looked on provisionally (since all but one are still alive) as comprising a distinct form of cortical dysplasia in which localized, exotic populations of nerve cells underlie the electrical and clinical manifestations of certain focal forms of epilepsy.
Facial Attractiveness Biases the Perception of Eye Contact

Attractive faces are appealing: We like to look at them, and we like to be looked at by them. We presented attractive and unattractive smiling and neutral faces containing identical eye regions with different gaze directions. Participants judged whether or not a face looked directly at them. Overall, attractive faces increased participants' tendency to perceive eye contact, consistent with a self-referential positivity bias. However, attractiveness effects were modulated by facial expression and gender: For female faces, observers more likely perceived eye contact in attractive than unattractive faces, independent of expression. For male faces, attractiveness effects were limited to neutral expressions and were absent in smiling faces. A signal detection analysis elucidated a systematic pattern in which (a) smiling faces, but not highly attractive faces, reduced sensitivity in gaze perception overall, and (b) attractiveness had a more consistent impact on bias than sensitivity measures. We conclude that combined influences of attractiveness, expression, and gender determine the formation of an overall impression when deciding which individual's interest in oneself may be beneficial and should be reciprocated.
On compression and damage evolution in two thermoplastics

The well-known Taylor cylinder impact test, which follows the impact of a flat-ended cylindrical rod onto a rigid stationary anvil, is conducted over a range of impact speeds for two polymers, polytetrafluoroethylene (PTFE) and polyetheretherketone (PEEK). In previous work, experiments and a model were developed to capture the deformation behaviour of the cylinder after impact. These works showed a region in which spatial and temporal variation of both longitudinal and radial deformation provided evidence of changes in phase within the material. In this further series of experiments, this region is imaged in a range of impacted targets at the Diamond synchrotron. Further techniques were fielded to resolve compressed regions within the recovered polymer cylinders that showed a fracture zone in the impact region. The combination of macroscopic high-speed photography and three-dimensional X-ray imaging has identified the development of failure with these polymers and shown that there is no abrupt transition in behaviours but rather a continuous range of responses to competing operating mechanisms. The behaviours noted in PEEK in these polymers show critical gaps in understanding of polymer high strain-rate response.
Effects of selective wood resin adsorption on paper properties

This paper reports on a study of the effects of adsorption of dissolved hemicelluloses and colloidal wood resin to different fractions of TMP fines on sheet properties. Sheet trials were done at varying ionic strength, resin concentration and hemicellullose concentration. TMP fine material fractions enriched in flakes and fibrils were added separately to bleached kraft pulp (30:70). The colloidal wood resin was adsorbed to the TMP fines prior to the mixing with kraft pulp. Sheets were made immediately after mixing of TMP fines with kraft pulp. Strength and optical properties as well as resin retention and composition of the sheets were determined. As expected, the fibrillar fines gave significantly stronger sheets than the flakelike fines. However, the colloidal wood resin reduced the paper strength of flake-containing sheets somewhat more than the strength of fibril-containing sheets. This effect was enhanced when dissolved hemicellulose from unbleached TMP was added to the colloidal dispersion prior to adsorption. The retention of colloidal wood resin was significantly smaller for sheets containing fibrillar fines. These results conform to the adsorption behaviour of colloidal wood resin indicated by earlier QCM-D and turbidity measurements. Hemicelluloses are more likely to adsorb to the surface of fibrils than to flakes, creating a steric hindrance for adsorption of colloidal wood resin. Thus, the negative effect of wood resin on paper strength is lower for the fibrillar fines than the flake-like fines.