Miracle-dz/UniFAR-FTUs huggingface dataset:
Run-Time Cohesion Metrics: An Empirical Investigation

Cohesion is one of the fundamental measures of the 'goodness' of a software design. The most accepted and widely studied object-oriented cohesion metric is Chi- damber and Kemerer's Lack of Cohesion in Methods mea- sure. However due to the nature of object-oriented pro- grams, static design metrics fail to quantify all the under- lying dimensions of cohesion, as program behaviour is a function of it operational environment as well as the com- plexity of the source code. For these reasons two run-time object-oriented cohesion metrics are described in this pa- per, and applied to Java programs from the SPECjvm98 benchmark suite. A statistical analysis is conducted to as- sess the fundamental properties of the measures and inves- tigate whether they are redundant with respect to the static cohesion metric. Results to date indicate that run-time co- hesion metrics can provide an interesting and informative qualitative analysis of a program and complement existing static cohesion metrics.
Factors predicting survival in patients with proximal gastric carcinoma involving the esophagus.

AIM To investigate the clinicopathologic features which predict surgical overall survival in patients with proximal gastric carcinoma involving the esophagus (PGCE). METHODS Electronic pathology database established in the Department of Pathology of the Nanjing Drum Tower Hospital was searched for consecutive resection cases of proximal gastric carcinoma over the period from May 2004 through July 2009. Each retrieved pathology report was reviewed and the cases with tumors crossing the gastroesophageal junction line were selected as PGCE. Each tumor was re-staged, following the guidelines on esophageal adenocarcinoma, according to the 7th edition of the American Joint Commission on Cancer Staging Manual. All histology slides were studied along with the pathology report for a retrospective analysis of 13 clinicopathologic features, i.e., age, gender, Helicobacter pylori (H. pylori) infection, surgical modality, Siewert type, tumor Bormann's type, size, differentiation, histology type, surgical margin, lymphovascular and perineural invasion, and pathologic stage in relation to survival after surgical resection. Prognostic factors for overall survival were assessed with uni- and multi-variate analyses. RESULTS Patients' mean age was 65 years (range: 47-90 years). The male: female ratio was 3.3. The 1-, 3- and 5-year overall survival rates were 87%, 61% and 32%, respectively. By univariate analysis, age, male gender, H. pylori, tumor Bormann's type, size, histology type, surgical modality, positive surgical margin, lymphovascular invasion, and pT stage were not predictive for overall survival; in contrast, perineural invasion (P = 0.003), poor differentiation (P = 0.0003), > 15 total lymph nodes retrieved (P = 0.008), positive lymph nodes (P = 0.001), and distant metastasis (P = 0.005) predicted poor post-operative overall survival. Celiac axis nodal metastasis was associated with significantly worse overall survival (P = 0.007). By multivariate analysis, ≥ 16 positive nodes (P = 0.018), lymph node ratio > 0.2 (P = 0.003), and overall pathologic stage (P = 0.002) were independent predictors for poor overall survival after resection. CONCLUSION Patients with PGCE showed worse overall survival in elderly, high nodal burden and advanced pathologic stage. This cancer may be more accurately staged as gastric, than esophageal, cancer.
ObamaNet: Photo-realistic lip-sync from text

We present ObamaNet, the first architecture that generates both audio and synchronized photo-realistic lip-sync videos from any new text. Contrary to other published lip-sync approaches, ours is only composed of fully trainable neural modules and does not rely on any traditional computer graphics methods. More precisely, we use three main modules: a text-to-speech network based on Char2Wav, a time-delayed LSTM to generate mouth-keypoints synced to the audio, and a network based on Pix2Pix to generate the video frames conditioned on the keypoints.
The use of heparan sulfate to augment fracture repair in a rat fracture model

Fracture healing is a complex process regulated by numerous growth and adhesive factors expressed at specific stages during healing. The naturally occurring, cell surface‐expressed sugar, heparan sulfate (HS), is known to bind to and potentiate the effects of many classes of growth factors, and as such, may be a potential candidate therapy for enhancing bone repair. This study investigated the local application of bone‐derived HS in the repair of rat femoral fractures. After 2 weeks, there was a significant increase in the callus size of rats administered with 5 µg HS compared to the control and 50 µg HS groups, presumably due to increased trabecular bone volume rather than increased cartilage production. In addition, 5 µg HS increased the expression of ALP, Runx2, FGF‐1, IGF‐II, TGF‐β1, and VEGF. It is hypothesized that these increases resulted from changes in HS‐mediated receptor/ligand interactions that increase local growth factor production to augment bone formation. The findings of this study demonstrate the anabolic potential of HS in bone repair by recruiting and enhancing the production of endogenous growth factors at the site of injury. © 2006 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res
On-the-fly Composition of FPGA-Based SQL Query Accelerators Using a Partially Reconfigurable Module Library

In this paper, we introduce a novel FPGA-based methodology for accelerating SQL queries using dynamic partial reconfiguration. Query acceleration is of utmost importance in large database systems to achieve a very high throughput. Although common FPGA-based accelerators are suitable to achieve such a high throughput, their design is hard to extend for new operations. Using partial dynamic reconfiguration, we are able to build more flexible architectures which can be extended to new operations or SQL constructs with a very low area overhead on the FPGA. Furthermore, the reconfiguration of a few FPGA frames can be used to switch very fast from one query to the next. In our approach, an SQL query is transformed into a hardware pipeline consisting of partially reconfigurable modules. The assembly of the (FPGA) data path is done at run-time using a static system providing the stream-based communication interfaces to the partial modules and the database management system. More specifically, each incoming SQL query is analyzed and divided into single operations which are subsequently mapped onto library modules and the composed data path loaded on the FPGA. We show that our approach is able to achieve a substantially higher throughput compared to a software-only solution.
Divergent Outcomes of Reinforcement Speciation: The Relative Importance of Assortative Mating and Migration Modification

Most studies of reinforcement speciation focus on the evolution of assortative mating, but R. A. Fisher argued that migration modification is likely to be a common alternative mechanism. Despite previous models showing that assortative mating and migration modification may both be involved in reinforcement, no one has determined their relative evolutionary importance. This is surprising because understanding the biological conditions favoring these mechanisms may explain why certain pairs of species exhibit abutting, nonoverlapping geographical ranges with habitat fidelity while other pairs coexist in sympatry with sexual isolation. In this article, we explicitly model the evolution of both mechanisms simultaneously. First, we explore how these mechanisms differ in their evolutionary dynamics. Second, we ask how they affect each other’s evolution and whether the interaction alters their relative importance in reinforcement. Our results reveal that assortative mating may evolve faster and under a broader range of biological conditions than migration modification. However, direct evolutionary interactions favor migration modification when populations experience strong divergent selection. Depending on the nature of postmating isolation, these mechanisms may either interfere with each other’s evolution or coevolve in the same system. These results illustrate the importance of studying multiple mechanisms of speciation simultaneously in future speciation models.
Immunomodulation by blockade of the TRANCE co‐stimulatory pathway in murine allogeneic islet transplantation

We explore herein the effect of TNF‐related activation‐induced cytokine (TRANCE) co‐stimulatory pathway blockade on islet survival after allograft transplantation. Expression of TRANCE on murine C57Bl/6 (B6) CD4+ T cells after allogeneic activation was analyzed by fluorescence‐activated cell sorter (FACS). The effect of a TRANCE receptor fusion protein (TR‐Fc) and anti‐CD154 antibody (MR1) on B6 spleen cell proliferation after allogeneic activation was assessed by mixed lymphocyte reaction (MLR). Three groups of B6 mice were transplanted with allogeneic islets (DBA2): Control; short‐term TR‐Fc‐treatment (days 0–4); and prolonged TR‐Fc‐treatment (days −1 to 13). Donor‐specific transfusion (DST) was performed at the time of islet transplantation in one independent experiment. Transplantectomy samples were analyzed by immunohistochemistry. TRANCE expression was upregulated in stimulated CD4+ T cells in vitro. In MLR experiments, TR‐Fc and MR1 both reduced spleen cell proliferation, but less than the combination of both molecules. Short‐course TR‐Fc treatment did not prolong islet graft survival when compared with controls (10.6 ± 1.9 vs. 10.7 ± 1.5 days) in contrast to prolonged treatment (20.7 ± 3.2 days; P < 0.05). After DST, primary non function (PNF) was observed in half of control mice, but never in TR‐Fc‐treated mice. Immunofluorescence staining for Mac‐1 showed a clear decrease in macrophage recruitment in the treated groups. TRANCE‐targeting may be an effective strategy for the prolongation of allogeneic islet graft survival, thanks to its inhibitory effects on co‐stimulatory signals and macrophage recruitment.
Gingival Crevicular Fluid as a Novel Potential Source of Biomarkers Distinguishes Pubertal from Post-Pubertal Subjects

Detection of pubertal growth peak is vital in orthodontic treatment timing and planning. Gingival crevicular fluid (GCF) contains abundant proteins from different sources and has been proven to be an ideal source of biomarkers. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) is an advanced technique that can detect low-molecular-weight peptides with high sensitivity and resolution. The aim of this research was to identify novel candidate biomarkers in GCF to help the diagnosis of pubertal growth peak by MALDI-TOF/MS. Results showed that the peak intensities of six peptides were significantly different between two groups: 1660.2 Da, 1783.0 Da, 2912.5 Da, 4178.6 Da, 5064.9 Da, and 6108.9 Da and are considered to be potential candidate biomarkers to identify pubertal growth peak. Further studies are needed to identify sequence information of these candidate biomarkers.
Enterobacter spp. Infections Complicating the Course of HIV Disease

Abstract Through a retrospective review of clinical and laboratory data of 2517 consecutive patients with HIV disease hospitalized since 1991, 13 patients were identified (0.52%), who suffered from a confirmed Enterobacter spp. infection (urinary tract disease in 7 cases, sepsis in 4 patients, and pneumonia in 2 cases). A severe immunodeficiency was recognized in all cases, as expressed by a mean CD4+ lymphocyte count <60 cells/μL, and frequently, a prior diagnosis of AIDS. Bloodstream infection proved linked to a lower mean CD4+ cell count, a more frequent occurrence of leukopenia-neutropenia, and nosocomial origin of the infecting pathogen. Hospital-acquired Enterobacter spp. disease was more frequent than community-acquired, and was significantly associated with leukopenia-neutropenia, and a diagnosis of AIDS. Antibiotic susceptibility assays showed a resistance rate to ampicillin and cephalothin involving >90% of tested strains, and a higher (but varied) sensitivity to other ß-lactams, aminoglycosides, fluoroquinolones, and cotrimoxazole. Adequate chemotherapy provided clinical and bacteriological success in all evaluated patients, in the absence of mortality or relapses. Only 34 episodes of HIV-associated Enterobacter spp. infection have been reported to date in 11 different literature studies. Our data point out that also Enterobacter spp. organisms may have an appreciable pathogenic potential in patients with HIV disease, especially in those with a low CD4+ lymphocyte count, leukopenia-neutropenia, who are hospitalized. Despite the unpredictable antibiotic susceptibility profile of these organisms, HIV-related Enterobacter spp. disease may be properly managed through rapid identification and timely and appropriate antimicrobial treatment.
Communication, Marital Satisfaction, and Religious Orientation in Interfaith Marriages

On the assumption that differences in faith traditions may prompt difficulties for married couples, this descriptive study examined interfaith couples’ reports of intrinsic and extrinsic religious orientation, communication during a religious disagreement, social network composition, and social support (N = 87). Spousal intrinsic religious orientation (a strong commitment to faith) is associated with reports of marital satisfaction and constructive communication and inversely associated with demand–withdrawal communication. In contrast, spousal extrinsic religious orientation (religion as a means to another end) is inversely associated with marital satisfaction and constructive communication and directly associated with demand–withdrawal communication and social support satisfaction. Regression analysis suggests spousal intrinsic religious orientation and social support from social network members explain significant unique variance on marital satisfaction, but constructive communication during a religious disagreement is the strongest predictor of marital satisfaction among interfaith couples. An agenda for future research about communication and interfaith couples is suggested.
Oxygen sensitivity of mitochondrial function in rat arterial chemoreceptor cells

• Arterial chemoreceptors measure blood oxygen and are involved in the control of both breathing and the cardiovascular system. • Oxygen is mostly used by cells in their mitochondria to generate energy. • In this study we have investigated the effects of oxygen starvation (hypoxia) on the mitochondria of specialised oxygen sensing cells from arterial chemoreceptors. • Our data confirm that the mitochondria of these oxygen sensing cells are unusually sensitive to modest hypoxia. This effect seems to stem from a reduced affinity of the oxygen utilising enzyme cytochrome oxidase for oxygen. • These results are consistent with a functional adaptation of the mitochondria of oxygen sensing cells that may enable them to play a direct role in the oxygen sensing process itself.
Biclustered Independent Component Analysis for Complex Biomarker and Subtype Identification from Structural Magnetic Resonance Images in Schizophrenia

Clinical and cognitive symptoms domain-based subtyping in schizophrenia (Sz) has been critiqued due to the lack of neurobiological correlates and heterogeneity in symptom scores. We, therefore, present a novel data-driven framework using biclustered independent component analysis to detect subtypes from the reliable and stable gray matter concentration (GMC) of patients with Sz. The developed methodology consists of the following steps: source-based morphometry (SBM) decomposition, selection and sorting of two component loadings, subtype component reconstruction using group information-guided ICA (GIG-ICA). This framework was applied to the top two group discriminative components namely the insula/superior temporal gyrus/inferior frontal gyrus (I-STG-IFG component) and the superior frontal gyrus/middle frontal gyrus/medial frontal gyrus (SFG-MiFG-MFG component) from our previous SBM study, which showed diagnostic group difference and had the highest effect sizes. The aggregated multisite dataset consisted of 382 patients with Sz regressed of age, gender, and site voxelwise. We observed two subtypes (i.e., two different subsets of subjects) each heavily weighted on these two components, respectively. These subsets of subjects were characterized by significant differences in positive and negative syndrome scale (PANSS) positive clinical symptoms (p = 0.005). We also observed an overlapping subtype weighing heavily on both of these components. The PANSS general clinical symptom of this subtype was trend level correlated with the loading coefficients of the SFG-MiFG-MFG component (r = 0.25; p = 0.07). The reconstructed subtype-specific component using GIG-ICA showed variations in voxel regions, when compared to the group component. We observed deviations from mean GMC along with conjunction of features from two components characterizing each deciphered subtype. These inherent variations in GMC among patients with Sz could possibly indicate the need for personalized treatment and targeted drug development.
ecology and evolution Toward a synthetic understanding of the role of phenology in

References http://rstb.royalsocietypublishing. org/content/365/1555/3101.full. html#ref-list-1 This article cites 160 articles, 33 of which can be accessed free Rapid response http://rstb.royalsocietypublishing. org/letters/submit/royptb;365/1555/3101 Respond to this article Subject collections (1963 articles) evolution  (1709 articles) ecology  Articles on similar topics can be found in the following collections
Exploring the factors related to acceptance of evolutionary theory among Turkish preservice biology teachers: Toward a more informative conceptual ecology for biological evolution

In this study, using multiple regression analysis, we aimed to explore the factors related to acceptance of evolutionary theory among preservice Turkish biology teachers using conceptual ecology for biological evolution as a theoretical lens. We aimed to determine the extent to which we can account for the variance in acceptance of evolutionary theory by using understanding of evolutionary theory, epistemological beliefs, thinking dispositions, and parents' educational level as independent variables. Preservice biology teachers' thinking dispositions, their understanding of evolutionary theory, and their parents' educational level are positively correlated with acceptance of evolutionary theory. We did not find any significant positive correlation between epistemological beliefs and acceptance of evolution because of low reliability coefficients of subscales of the epistemological beliefs instrument. Together they explained 10.5% of the variance. These results suggest that studying the relationship between acceptance of evolutionary theory and other related factors in a multivariate context is more informative than examining the relationship between acceptance of evolutionary theory and other factors in isolation. Our findings indicate that studying a controversial issue such as acceptance of evolutionary theory in a multivariate fashion, using conceptual ecology as a theoretical lens to interpret the findings, is informative. Our results suggest the inclusion of thinking dispositions in conceptual ecology for biological evolution. © 2007 Wiley Periodicals, Inc. J Res Sci Teach 45: 420–443, 2008
Bullying, depressive symptoms and suicidal thoughts

Bullies, victims and pupils neutral to bullyingwere compared on depressive symptoms and suicidal thoughts.The sample included 2,088 Norwegian boys and girls in grade 8. The results revealed that both bullies and victims had significantly higher mean scores than neutral pupils on both depressive symptoms and suicidal thoughts. Victims had a significantly higher mean score on depressive thoughts than the bullies. On suicidal thoughts, the mean score for bullies was above that of the victims, but this differencewas not significant. Girls had significantly higher mean scores than boys on both depressive symptoms and suicidal thoughts. This was the case for all pupils, and for victims, bullies and the neutral pupils. Questions of causality between depressive symptoms, suicidal thoughts and involvement in bullying are discussed and research on this issue is suggested.
Principles of protein targeting to the nucleolus

The nucleolus is the hallmark of nuclear compartmentalization and has been shown to exert multiple roles in cellular metabolism besides its main function as the place of rRNA synthesis and assembly of ribosomes. Nucleolar proteins dynamically localize and accumulate in this nuclear compartment relative to the surrounding nucleoplasm. In this study, we have assessed the molecular requirements that are necessary and sufficient for the localization and accumulation of peptides and proteins inside the nucleoli of living cells. The data showed that positively charged peptide entities composed of arginines alone and with an isoelectric point at and above 12.6 are necessary and sufficient for mediating significant nucleolar accumulation. A threshold of 6 arginines is necessary for peptides to accumulate in nucleoli, but already 4 arginines are sufficient when fused within 15 amino acid residues of a nuclear localization signal of a protein. Using a pH sensitive dye, we found that the nucleolar compartment is particularly acidic when compared to the surrounding nucleoplasm and, hence, provides the ideal electrochemical environment to bind poly-arginine containing proteins. In fact, we found that oligo-arginine peptides and GFP fusions bind RNA in vitro. Consistent with RNA being the main binding partner for arginines in the nucleolus, we found that the same principles apply to cells from insects to man, indicating that this mechanism is highly conserved throughout evolution.
Serum IL-33 Levels Are Associated with Liver Damage in Patients with Chronic Hepatitis C

Interleukin-33 (IL-33) is associated with the development of Th2 responses. This study examined the potential role of IL-33 in the pathogenic process of chronic hepatitis C (CHC) in Chinese patients. The levels of serum IL-33 and sST2 in 154 patients with CHC, 24 with spontaneously resolved HCV (SR-HCV) infection and 20 healthy controls (HC), were analyzed by ELISA. The concentrations of serum IL-2, IFN-γ, TNF-α, IL-4, IL-6, and IL-10, HCV loads, ALT, AST, and HCV-Ab were measured. We found that the levels of serum IL-33 in CHC patients were significantly higher than those of SR-HCV and HC but decreased after treatment with interferon for 12 weeks. More importantly, the levels of serum IL-33 were correlated with the concentrations of ALT and AST in CHC patients. The levels of serum sST2, as a decoy receptor of IL-33, were significantly higher in CHC and SR-CHC patients than those in HC, and there was no correlation between the levels of serum sST2 and IL-33. The concentrations of serum IFN-γ and IL-6 in CHC patients were significantly lower than those of SR-HCV. These data suggest that IL-33 may be a pathogenic factor contributing to CHC-related liver injury.
The Influence of Peer Relationships and Maternal Socialization on Kindergartners' Developing Emotion Knowledge

We examined the influence of children's peer relationships and maternal emotional socialization on children's development of emotion knowledge. Children's emotion knowledge was assessed at the beginning (time 1) and end (time 2) of their first semester of kindergarten. Children's peer interactions were measured through observations and teacher ratings. Mothers' beliefs about teaching emotion language and emotional expressive styles were assessed through questionnaires. Children with more stable friendships demonstrated greater increases in emotion label knowledge between time 1 and 2. More popular children had greater increases in emotion script knowledge between time 1 and 2, as did children whose mothers believed in teaching emotion language. Results have implications for future research regarding parents' and teachers' beliefs about socializing children's emotional development.