Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploiting Social Annotation for Automatic Resource Discovery

Information integration applications, such as mediators or mashups, that require access to information resources currently rely on users manually discovering and integrating them in the application. Manual resource discovery is a slow process, requiring the user to sift through results obtained via keyword-based search. Although search methods have advanced to include evidence from document contents, its metadata and the contents and link structure of the referring pages, they still do not adequately cover information sources -- often called ``the hidden Web''-- that dynamically generate documents in response to a query. The recently popular social bookmarking sites, which allow users to annotate and share metadata about various information sources, provide rich evidence for resource discovery. In this paper, we describe a probabilistic model of the user annotation process in a social bookmarking system del.icio. us. We then use the model to automatically find resources relevant to a particular information domain. Our experimental results on data obtained from \emph{del.icio. us} show this approach as a promising method for helping automate the resource discovery task.
Proliferating cell nuclear antigen (PCNA): a dancer with many partners

Proliferating cell nuclear antigen (PCNA) was originally characterised as a DNA sliding clamp for replicative DNA polymerases and as an essential component of the eukaryotic chromosomal DNA replisome. Subsequent studies, however, have revealed its striking ability to interact with multiple partners, which are involved in several metabolic pathways, including Okazaki fragment processing, DNA repair, translesion DNA synthesis, DNA methylation, chromatin remodeling and cell cycle regulation. PCNA in mammalian cells thus appears to play a key role in controlling several reactions through the coordination and organisation of different partners. Two major questions have emerged: how do these proteins access PCNA in a coordinated manner, and how does PCNA temporally and spatially organise their functions? Structural and biochemical studies are starting to provide a first glimpse of how both tasks can be achieved.
The Impact of Leadership on Student Outcomes: An Analysis of the Differential Effects of Leadership Types

Purpose: The purpose of this study was to examine the relative impact of different types of leadership on students' academic and nonacademic outcomes. Research Design: The methodology involved an analysis of findings from 27 published studies of the relationship between leadership and student outcomes. The first meta-analysis, including 22 of the 27 studies, involved a comparison of the effects of transformational and instructional leadership on student outcomes. The second meta-analysis involved a comparison of the effects of five inductively derived sets of leadership practices on student outcomes. Twelve of the studies contributed to this second analysis. Findings: The first meta-analysis indicated that the average effect of instructional leadership on student outcomes was three to four times that of transformational leadership. Inspection of the survey items used to measure school leadership revealed five sets of leadership practices or dimensions: establishing goals and expectations; resourcing strategically; planning, coordinating, and evaluating teaching and the curriculum; promoting and participating in teacher learning and development, and ensuring an orderly and supportive environment. The second meta-analysis revealed strong average effects for the leadership dimension involving promoting and participating in teacher learning and development and moderate effects for the dimensions concerned with goal setting and planning, coordinating, and evaluating teaching and the curriculum. Conclusions and Implications for Research and Practice: The comparisons between transformational and instructional leadership and between the five leadership dimensions suggested that the more leaders focus their relationships, their work, and their learning on the core business of teaching and learning, the greater their influence on student outcomes. The article concludes with a discussion of the need for leadership research and practice to be more closely linked to the evidence on effective teaching and effective teacher learning. Such alignment could increase the impact of school leadership on student outcomes even further.
COWLS: hardware-software cosynthesis of wireless low-power distributed embedded client-server systems

In this paper, we present COWLS, a hardware-software cosynthesis algorithm that targets embedded systems composed of servers and low-power clients that communicate with each other through a channel of limited bandwidth, e.g., a wireless link. A novel scheduling algorithm is used to pipeline the execution of tasks that serve multiple clients associated with a given server. COWLS simultaneously optimizes the price of the client-server system, the power consumption of the clients, and the response times of tasks that have only soft deadlines, while meeting all of the hard deadlines. It produces numerous solutions that trade off different architectural features, e.g., price, power consumption, and response time, of an embedded client-server system. As far as we know, this is the first synthesis algorithm of its kind. We present the experimental results for numerous pseudorandom examples, a low-power client-server camera system, as well as the rest of the benchmarks within a publicly released embedded system synthesis benchmark suite.
Rice koji reduced body weight gain, fat accumulation, and blood glucose level in high-fat diet-induced obese mice

Rice koji is considered a readily accessible functional food that may have health-promoting effects. We investigated whether white, yellow, and red koji have the anti-obesity effect in C57BL/6J mice fed a high-fat diet (HFD), which is a model for obesity. Mice were fed HFD containing 10% (w/w) of rice koji powder or steamed rice for 4 weeks. Weight gain, epididymal white adipose tissue, and total adipose tissue weight were significantly lower in all rice koji groups than in the HFD-rice group after 4 weeks. Feed efficiency was significantly reduced in the yellow koji group. Blood glucose levels were significantly lower in the white and red koji groups with HOMA-R and leptin levels being reduced in the white koji group. White and red koji increased glucose uptake and GLUT4 protein expression in L6 myotube cells. These results showed that all rice koji have the anti-obesity or anti-diabetes effects although the mechanisms may differ depending on the type of rice koji consumed.
The follicular variant of papillary thyroid carcinoma: characteristics of preoperative ultrasonography and cytology

Purpose: The goal of this study was to validate the ultrasonography (US) and cytopathological features that are used in the diagnosis of the follicular variant of papillary thyroid carcinoma (FVPTC) and to characterize the role of BRAFV600E mutation analysis in the diagnosis of FVPTC. Methods: From May 2012 to February 2014, 40 thyroid nodules from 40 patients (mean age, 56.2 years; range, 26 to 81 years) diagnosed with FVPTC were included in this study. The US features of the nodules were analyzed and the nodules were classified as probably benign or suspicious for malignancy. Twenty-three thyroid nodules (57.5%) underwent BRAFV600E mutation analysis. Clinical information and histopathologic results were obtained by reviewing the medical records of the patients. Results: Thirty nodules (75.0%) were classified as suspicious for malignancy, while 10 (25.0%) were classified as probably benign. Seven of the eight nodules (87.5%) with atypia of undetermined significance/follicular lesion of undetermined significance (AUS/FLUS) cytology showed suspicious US features, while one of the two nodules (50.0%) with follicular neoplasm cytology presented suspicious US features. Five of the 23 nodules (21.7%) that underwent BRAFV600E mutation analysis had positive results, all of which were diagnosed as suspicious for malignancy or malignant based on cytology. None of the nodules with benign, AUS/FLUS, or follicular neoplasm cytology were positive for the BRAFV600E mutation. Conclusion: US features allow nodules to be classified as suspicious for malignancy, and the presence of suspicious US features in nodules with ambiguous cytology may aid in the diagnosis of FVPTC. BRAFV600E mutation analysis is of limited value in the diagnosis of FVPTC.
Evolving Rule-Based Trading Systems

In this study, a market trading rulebase is optimised using g enetic programming (GP). The rulebase is comprised of simple relation ships between technical indicators, and generates signals to buy, sell short, and remain inactive. The methodology is applied to prediction of the Standard & Poor’ s composite index (02-Jan-1990 to 18-Oct-2001). Two potential market system are inferred: a simple system using few rules and nodes, and a more complex syste m. R sults are compared with a benchmark buy-and-hold strategy. Neither t rading system was found capable of consistently outperforming this benchmar k. More complicated rulebases, in addition to being difficult to understand, are susceptible to overfitting. Simpler rulebases are more robust to changing market c onditions, but cannot take advantage of high-profit-making opportunities. By inc reasing the richness of the available rulebase building-blocks and the variety of t raining data, it is anticipated that subsequent systems will surpass the benchmark s tr tegy.
Modelling of the static and dynamic properties of tho-type silicates

Auxetic materials are materials exhibiting a negative Poisson’s ratio in one of their planes. This phenomenon has been studied in various materials. Zeolites are crystalline substances whose structure is characterised by the framework of linked tetrahedra, each consisting of four oxygen atoms surrounding a cation. The resulting interstitial spaces make them efficient for use as adsorbents and molecular sieves, and many studies have been focused on this aspect. Some of these zeolites may exhibit auxeticity at least in one of their planes. THO (and similar systems, such as NAT and EDI) together with the all-silica equivalent of these have been studied extensively via static simulations for their negative Poisson’s ratio in the (001) plane. In this paper a study of the all-silica equivalent of THO has been carried out via both static and dynamic simulations using the same force-field, where the system was subjected to stress along the x direction. The hypothesised semi-rigid mechanism of deformation, proposed by Grima et al. was then projected over this framework. The results obtained confirmed auxeticity along this plane by means of the COMPASS force-field, in both static and dynamic studies and compared well with the proposed mechanism of semi-rigid rotating polygons. It also showed that as the Young’s modulus of this mechanism increases other mechanisms of deformation increase in importance.
Metallurgical Characterization and Diffusion Studies of Successively Buttered Deposit of Ni–Fe Alloy and Inconel on SA508 Ferritic Steel

The present work aims to investigate the major problem of carbon diffusion in dissimilar metal weld (DMW) between ferritic and austenitic stainless steel used in Nuclear Power Plants. For such DMW joints, Inconel 82 is often deposited on ferritic steel with Gas Tungsten Arc Welding (GTAW) process, but the problems associated with carbon diffusion persist. In the present study, Ni–Fe alloy (ERNiFe-CI) and Inconel 82 (ERNiCr-3) have been successively deposited with Gas Metal Arc Welding (GMAW) process. The substrates of SA508Gr.3Cl. 1 ferritic steel were used for deposition. First buffer layer of Ni–Fe alloy was deposited with GTAW in order to have low heat input initially and the subsequent deposition was carried out using GMAW over the buffer layer. The effect of operating temperature of DMW joints on carbon migration from the ferritic steel to buttering zone was studied by carrying out the thermal ageing 450°C for 240 h. Diffusivity of carbon at different ageing temperatures was quantified. The effectiveness of buttering deposit was addressed with respect to metallurgical properties and carbon diffusion by carrying out the heat flow analysis, Electron Probe Micro Analysis (EPMA), Optical Emission Spectroscopy (OES), martensite formation analysis at fusion interfaces, micro-hardness variation across the fusion interfaces and the microstructure evolution. Significant amount of martensite was observed to be formed at the fusion interface and the subsequent effect of stress relieving was addressed. Momentous reduction in carbon diffusion and favourable metallurgical properties owing to successive buttering deposit could increase the life of DMW joints with cost effective GMAW over the GTAW process at Nuclear Plants.
Bivalent Motif-Ear Interactions Mediate the Association of the Accessory Protein Tepsin with the AP-4 Adaptor Complex*

The heterotetrameric (ϵ-β4-μ4-σ4) complex adaptor protein 4 (AP-4) is a component of a non-clathrin coat involved in protein sorting at the trans-Golgi network (TGN). Considerable interest in this complex has arisen from the recent discovery that mutations in each of its four subunits are the cause of a congenital intellectual disability and movement disorder in humans. Despite its physiological importance, the structure and function of this coat remain poorly understood. To investigate the assembly of the AP-4 coat, we dissected the determinants of interaction of AP-4 with its only known accessory protein, the ENTH/VHS-domain-containing protein tepsin. Using a variety of protein interaction assays, we found that tepsin comprises two phylogenetically conserved peptide motifs, [GS]LFXG[ML]X[LV] and S[AV]F[SA]FLN, within its C-terminal unstructured region, which interact with the C-terminal ear (or appendage) domains of the β4 and ϵ subunits of AP-4, respectively. Structure-based mutational analyses mapped the binding site for the [GS]LFXG[ML]X[LV] motif to a conserved, hydrophobic surface on the β4-ear platform fold. Both peptide-ear interactions are required for efficient association of tepsin with AP-4, and for recruitment of tepsin to the TGN. The bivalency of the interactions increases the avidity of tepsin for AP-4 and may enable cross-linking of multiple AP-4 heterotetramers, thus contributing to the assembly of the AP-4 coat. In addition to revealing critical aspects of this coat, our findings extend the paradigm of peptide-ear interactions, previously established for clathrin-AP-1/AP-2 coats, to a non-clathrin coat.
Breast diseases: a histopathological analysis of 3279 cases at a tertiary care center in Pakistan.

OBJECTIVE To know the frequency of breast diseases in Pakistani females. METHODS A retrospective analysis of 3279 breast specimens received over a period of 4 years (1993-1996) at the department of pathology, the Aga Khan University Hospital. RESULTS Out of a total of 3279 breast specimens, common breast lesions included infiltrating duct carcinoma 37%, followed by fibro adenoma 16.95%, fibrocystic change 13.96%, mastitis 6.83% and duct ectasia 5.33%. Majority of the cases of infiltrating duct carcinoma were encountered in the 5th and 6th decades of life. Tumour size was 2 or >2 cms. in 93% of cases and 40% of them showed 3 or >3 positive lymph nodes. Grade I tumours were 11.38%, grade II 59.17% and grade III tumours 29.47%. Correlation of grade with lymph node metastases (3 or >3+ve nodes) showed 15 cases (1.53%) of grade I, 178 cases (18.25%) of grade II and 68 (6.97%) cases of grade III tumours. CONCLUSION This study shows that in Pakistani females, the most commonly encountered lesion in carcinoma of the breast followed by the benign lesions such as fibro adenoma, fibrocystic disease & others. Breast carcinoma occurs at a younger age group with predominance of high-grade lesions and with frequent lymph node metastasis.
Overview of the gene ontology task at BioCreative IV

Gene Ontology (GO) annotation is a common task among model organism databases (MODs) for capturing gene function data from journal articles. It is a time-consuming and labor-intensive task, and is thus often considered as one of the bottlenecks in literature curation. There is a growing need for semiautomated or fully automated GO curation techniques that will help database curators to rapidly and accurately identify gene function information in full-length articles. Despite multiple attempts in the past, few studies have proven to be useful with regard to assisting real-world GO curation. The shortage of sentence-level training data and opportunities for interaction between text-mining developers and GO curators has limited the advances in algorithm development and corresponding use in practical circumstances. To this end, we organized a text-mining challenge task for literature-based GO annotation in BioCreative IV. More specifically, we developed two subtasks: (i) to automatically locate text passages that contain GO-relevant information (a text retrieval task) and (ii) to automatically identify relevant GO terms for the genes in a given article (a concept-recognition task). With the support from five MODs, we provided teams with >4000 unique text passages that served as the basis for each GO annotation in our task data. Such evidence text information has long been recognized as critical for text-mining algorithm development but was never made available because of the high cost of curation. In total, seven teams participated in the challenge task. From the team results, we conclude that the state of the art in automatically mining GO terms from literature has improved over the past decade while much progress is still needed for computer-assisted GO curation. Future work should focus on addressing remaining technical challenges for improved performance of automatic GO concept recognition and incorporating practical benefits of text-mining tools into real-world GO annotation. Database URL: http://www.biocreative. org/tasks/biocreative-iv/track-4-GO/.
Diagnostic and prognostic value of serum MACC1 in breast cancer patients

Metastasis-associated in colon cancer-1 (MACC1) promotes colorectal cancer progression and predicts prognosis. The aim of our study was to determine the diagnostic and prognostic value of preoperative serum MACC1 levels in breast cancer patients. Serum MACC1 levels were measured in 378 breast cancer patients, 120 patients with benign breast disease, and 40 healthy volunteers using an ELISA. Serum MACC1 levels were higher in breast cancer patients than patients with benign disease or healthy volunteers. Increased serum MACC1 was associated with breast cancer TNM stage (P < 0.001), tumor size (P < 0.001), lymph node metastasis (P < 0.001), and Ki-67 status (P = 0.014). Serum MACC1 measurement successfully discriminated breast cancer patients from normal and healthy controls (AUC = 0.785, 95% CI: 0.746–0.825) with an optimal cut-off value of 38.35 pg/ml (sensitivity = 0.725, specificity = 0.696). Moreover, serum MACC1 exhibited significant prognostic value in breast cancer (AUC = 0.757, 95% CI: 0.700–0.814), and high MACC1 was associated with poor disease-free survival (HR 5.63, 95% CI: 3.51–9.04; P < 0.001). Our findings demonstrated that circulating MACC1 could serve as a reliable diagnostic and prognostic biomarker for breast cancer.
Mixed-mode fracture of ceramics in asymmetric four-point bending: Effect of crack-face grain interlocking/bridging

The mixed-mode fracture of a large-grain-size alumina ceramic and a soda-lime glass is investigated. These ceramics are tested using straight-through precracked or notched specimens. The straight-through precrack is introduced by the single-edge-precracked beam method. Precracked or notched specimens are subjected to combined mode I/II or pure mode II fracture, under asymmetric four-point bending, and pure mode I fracture, under symmetric four-point bending. A pure mode II fracture is never achieved in the precracked polycrystalline alumina by the crack-face friction inevitably induced by grain interlocking/bridging. The crack-face friction in sliding mode reduces the local mode II stress intensity factor in the crack-tip region and produces a sizable amount of mode I deformation. Accounting for the contribution of the crack-face friction to the crack-tip local stress intensity factors, K{sub I} and K{sub II}, in mixed-mode fracture tests, the experimental results of the K{sub I}/K{sub Ic} versus K{sub II}/K{sub Ic} envelope and the initial angle of noncoplanar crack extension are in good agreement with the theoretical predictions of the maximum hoop-stress theory.
ITI implant use in private practice: clinical results with 5,526 implants followed up to 72+ months in function.

PURPOSE To evaluate the success and failure rates over time of ITI implants placed in 3 private practices and used in a variety of clinical situations. MATERIALS AND METHODS ITI solid-screw implants (n = 5,526) were placed in 3 private practices and restored by a variety of clinicians. Numerous clinical scenarios were treated with the implants, which were in function for between 0 and 72+ months. RESULTS After 72+ months the cumulative success rates were 94.8% for maxillary implants and 97.5% for mandibular implants. The overall cumulative implant success rate was 96.1%. Implants that failed to osseointegrate were included in the data as failures in the 0- to 12-month interval. The criteria of Albrektsson and associates were used to assess implant success or failure. DISCUSSION The results, which were achieved in conjunction with numerous restorative clinicians, were comparable to those reported by other authors. The clinical viability of ITI implant use was thus reinforced. CONCLUSION ITI solid-screw implants were a predictable treatment modality in 3 private practices for a variety of clinical applications.
Rapid HCV-RNA decline with once daily TMC435: a phase I study in healthy volunteers and hepatitis C patients.

BACKGROUND & AIMS The search for targeted anti-hepatitis C virus (HCV) drugs is driven by the adverse effect profile and limited efficacy of the current standard of care (pegylated interferon-alpha/ribavirin). In a first-in-human trial, we tested the safety, tolerability, and pharmacokinetics of the macrocyclic HCV NS3/4A protease inhibitor TMC435 in healthy volunteers, followed by HCV genotype 1-infected patients to assess antiviral activity. METHODS The TMC435350-C101 study was a phase I, randomized, double-blind, placebo-controlled trial in 49 healthy volunteers, followed by an open-label, nonplacebo-controlled panel in 6 genotype 1 hepatitis C patients. Healthy volunteers received oral, single, ascending doses (up to 600 mg) or 5-day multiple ascending doses (200 mg twice daily or 100, 200, or 400 mg once daily). Patients received 200 mg once daily for 5 days. Pharmacokinetics and safety were evaluated for all panels, and plasma HCV-RNA levels were determined in patients. RESULTS There were no serious adverse events, no grade 3 reactions, and no treatment-related discontinuations; pharmacokinetics supported a once daily dosing regimen. Plasma HCV-RNA levels dropped rapidly in all patients, with a median maximal reduction of 3.9-log(10) IU/mL and a median of 6 days to maximal reduction. The initial steep reduction of HCV-RNA (median 3.5-log(10) IU/mL at day 3) was followed by a more gradual decline that was maintained over the dosing period. No viral breakthroughs (>1-log(10) IU/mL HCV-RNA increase from nadir) were observed during treatment nor in the 3 days posttreatment; HCV-RNA returned to pretreatment levels by week 4. CONCLUSIONS Once daily TMC435 given orally was generally safe and well tolerated and demonstrated potent antiviral activity.