Miracle-dz/UniFAR-FTUs huggingface dataset:
Methods for Sentence Compression

Sentence compression is the task of producing a summary of a single sentence. The compressed sentence should be shorter, contain the important content from the original, and itself be grammatical. The three papers discussed here take different approaches to identifying important content, determining which sentences are grammatical, and jointly optimizing these objectives. One family of approaches we will discuss is those that are tree-based, which create a compressed sentence by making edits to the syntactic tree of the original sentence. A second type of approach is sentence-based, which generates strings directly. Orthogonal to either of these two approaches is whether sentences are treated in isolation or if the surrounding discourse affects compressions. We compare a tree-based, a sentence-based, and a discourse-based approach and conclude with ideas for future work in this area. Comments University of Pennsylvania Department of Computer and Information Science Technical Report No. MSCIS-10-20. This technical report is available at ScholarlyCommons: http://repository.upenn. edu/cis_reports/929 Methods for Sentence Compression
Mapping and configuration methods for multi-use-case networks on chips

To provide a scalable communication infrastructure for systems on chips (SoCs), networks on chips (NoCs), a communication centric design paradigm is needed. To be cost effective, SoCs are often programmable and integrate several different applications or use-cases on to the same chip. For the SoC platform to support the different use-cases, the NoC architecture should satisfy the performance constraints of each individual use-case. In this work we motivate the need to consider multiple use-cases during the NoC design process. We present a method to efficiently map the applications on to the NoC architecture, satisfying the design constraints of each individual use-case. We also present novel ways to dynamically reconfigure the network across the different use-cases and explore the possibility of integrating dynamic voltage and frequency scaling (DVS/DFS) techniques with the use-case centric NoC design methodology. We validate the performance of the design methodology on several SoC applications. The dynamic reconfiguration of the NoC integrated with DVS/DFS schemes results in large power savings for the resulting NoC systems
Comparison of exogenous glucose, fructose and galactose oxidation during exercise using 13C-labelling

Six subjects exercised for 120;min on a cycle ergometer (65 (se 3) % V˙O2max) when ingesting a placebo or glucose, fructose or galactose (100g in 1000 ml water) labelled with 13C. The oxidation of energy substrates including exogenous hexoses was compared using indirect respiratory calorimetry and 13CO2 production at the mouth. Total carbohydrate progressively decreased and total fat oxidation increased over the 120min exercise period in the four experimental situations. During the 120min of exercise, the amount of fructose oxidized (38·8 (se 2·6) g; 9·0 (se 0·6)% energy yield) was not significantly (approximately 4%) lower than that of exogenous glucose (40·5 (se 3·4) g; 9·2 (se 0·8)% energy yield), while that of galactose (23·7 (se 3·5) g; 5·5 (se 0·9) % energy yield) was only 59% and 61% that of glucose and fructose, respectively. When compared with the placebo, the ingestion and oxidation of the three hexoses did not significantly modify fat oxidation or total carbohydrate oxidation, but it significantly reduced (9–13%) endogenous carbohydrate oxidation. The present data indicate that fructose and exogenous glucose ingested during exercise could be oxidized at a similar rate, but that the oxidation rate of galactose was only approximately 60% that of the exogenous glucose and fructose, presumably because of a preferential incorporation of galactose into liver glycogen (Leloir pathway). The reduction in endogenous carbohydrate oxidation was, however, similar with the three hexoses.
Three-year route census study on welfare status of free-roaming cats in old-town Onomichi, Japan

ABSTRACT The free-roaming cat population in Japan is increasing, and these cats are regarded as a tourism resource in some areas; however, their welfare status is unknown. Thus, this study assessed the welfare status of free-roaming cats in the old town of Onomichi City, Hiroshima, Japan. Route censuses were conducted 8 times per month for 3 years to estimate cat populations in the uptown and downtown areas of Onomichi. In the 1st year, we found 124 cats and 80 cats in the uptown and downtown areas, respectively. Approximately half the cats in each area were in poor physical condition. By the 3rd year, 99 of the 124 uptown cats and 66 of the 80 downtown cats had disappeared; moreover, uptown cats in poor physical condition disappeared in significantly greater numbers than those in good condition. It was presumed most missing cats died from illness or injury as opposed to having migrated elsewhere. This study suggests the welfare status of free-roaming cats in Onomichi is poor, and organized management of these cats is a matter of great urgency to improve their status.
Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 Protease

Understanding the complex mutation patterns that give rise to drug resistant viral strains provides a foundation for developing more effective treatment strategies for HIV/AIDS. Multiple sequence alignments of drug-experienced HIV-1 protease sequences contain networks of many pair correlations which can be used to build a (Potts) Hamiltonian model of these mutation patterns. Using this Hamiltonian model we translate HIV protease sequence covariation data into quantitative predictions for the probability of observing specific mutation patterns which are in agreement with the observed sequence statistics. We find that the statistical energies of the Potts model are correlated with the fitness of individual proteins containing therapy-associated mutations as estimated by in vitro measurements of protein stability and viral infectivity. We show that the penalty for acquiring primary resistance mutations depends on the epistatic interactions with the sequence background. Primary mutations which lead to drug resistance can become highly advantageous (or entrenched) by the complex mutation patterns which arise in response to drug therapy despite being destabilizing in the wildtype background. Anticipating epistatic effects is important for the design of future protease inhibitor therapies.
Control of Initiation of Sporulation by Replication Initiation Genes in Bacillus subtilis

ABSTRACT Initiation of spore formation in Bacillus subtilisappears to depend on initiation of DNA replication. This regulation was first identified using a temperature-sensitive mutation indnaB. We found that mutations in the replication initiation genes dnaA and dnaD also inhibit sporulation, indicating that inhibition of sporulation is triggered by general defects in the function of replication initiation proteins.
Analysis of PIK3CA Mutations and Activation Pathways in Triple Negative Breast Cancer

Background Triple Negative Breast Cancer (TNBC) accounts for 12–24% of all breast carcinomas, and shows worse prognosis compared to other breast cancer subtypes. Molecular studies demonstrated that TNBCs are a heterogeneous group of tumors with different clinical and pathologic features, prognosis, genetic-molecular alterations and treatment responsivity. The PI3K/AKT is a major pathway involved in the regulation of cell survival and proliferation, and is the most frequently altered pathway in breast cancer, apparently with different biologic impact on specific cancer subtypes. The most common genetic abnormality is represented by PIK3CA gene activating mutations, with an overall frequency of 20–40%. The aims of our study were to investigate PIK3CA gene mutations on a large series of TNBC, to perform a wider analysis on genetic alterations involving PI3K/AKT and BRAF/RAS/MAPK pathways and to correlate the results with clinical-pathologic data. Materials and Methods PIK3CA mutation analysis was performed by using cobas® PIK3CA Mutation Test. EGFR, AKT1, BRAF, and KRAS genes were analyzed by sequencing. Immunohistochemistry was carried out to identify PTEN loss and to investigate for PI3K/AKT pathways components. Results PIK3CA mutations were detected in 23.7% of TNBC, whereas no mutations were identified in EGFR, AKT1, BRAF, and KRAS genes. Moreover, we observed PTEN loss in 11.3% of tumors. Deregulation of PI3K/AKT pathways was revealed by consistent activation of pAKT and p-p44/42 MAPK in all PIK3CA mutated TNBC. Conclusions Our data shows that PIK3CA mutations and PI3K/AKT pathway activation are common events in TNBC. A deeper investigation on specific TNBC genomic abnormalities might be helpful in order to select patients who would benefit from current targeted therapy strategies.
Seeded Region Growing Features Extraction Algorithm; Its Potential Use in Improving Screening for Cervical Cancer

Region growing algorithm has successfully been used as a segmentation technique of digital images. The current study went one step further by utilizing the potential use of thresholding the region growing algorithm as features extraction technique. The proposed features extraction algorithm is called seeded region growing features extraction (SRGFE). This algorithm was used to extract four features of cervical cells; size of nucleus, size of cytoplasm, grey level of nucleus and grey level of cytoplasm. Correlation test was applied between data extracted using the proposed SRGFE algorithm with the data extracted manually by cytotechnologists. The high correlation value obtained in the correlation test show that the SRGFE algorithm is suitable and has high capability to be used as an image extraction technique to extract important features of cervical cells. This would assist cytopathologists and cytotechnologists in the cervical cancer screening by providing accurate value of size and grey level of nuclear and cytoplasmic features.
First Metatarsophalangeal Joint Arthrodesis Technique With Interposition Allograft Bone Block

Background: We present a technique of first metatarsophalangeal joint arthrodesis utilizing an interposition allograft bone block with a bipolar reaming technique that creates congruent fusion surfaces on both ends of the graft-host bone interface. In addition, we examined the union rates, fusion position, patient satisfaction, and functional outcome of this technique. Methods: Fifteen patients underwent first metatarsophalangeal joint arthrodesis with an interposition allograft bone block between September 2004 and October 2013. Charts and radiographs were reviewed. Six measures were compared on preoperative and postoperative radiographs. Clinical outcomes were measured using a telephone questionnaire, pre- and postoperative visual analog scale pain scale, and Foot and Ankle Ability Measure. Average follow-up was 46 weeks (range, 19 to 97). Results: Thirteen of 15 (87%) patients achieved bony union at an average of 21 weeks. One patient underwent revision arthrodesis for their nonunion. Symptomatic hardware was removed in 3 cases. Improvement was noted in visual analog scale pain scores (6 to 2) and functional scores as measured by the Foot and Ankle Ability Measure. There were no postoperative wound complications or infections. Average length of the first ray on anteroposterior radiograph increased from 10.7 to 11.3 cm and from 10.0 to 10.7 cm on the lateral radiograph. Thirteen of 14 patients were very satisfied or satisfied. One patient expressed dissatisfaction with the procedure. One patient was not available for clinical follow-up. Conclusion: First metatarsophalangeal joint allograft bone block arthrodesis using the bipolar reaming technique achieved high bony union rates and satisfactory radiographic and clinical outcomes. This procedure was an effective salvage option for managing bone loss on 1 or both sides of the joint. Level of Evidence: Level IV, retrospective case series.
A Two-Step Mechanism for Cell Fate Decision by Coordination of Nuclear and Mitochondrial p53 Activities

The tumor suppressor p53 has a crucial role in the DNA damage response. Here, we proposed an integrated model of the p53 network and explored how the nuclear and mitochondrial p53 pathways are coordinated to determine cell fates after -irradiation in radiosensitive tissues. Using numerical simulations, we found that depending on the extent of DNA damage, cells may survive, commit apoptosis after cell cycle arrest, or undergo apoptosis soon after irradiation. There exists a large cell-to-cell variability in outcome because of stochasticity in the generation and repair of DNA damage as well as cellular heterogeneity. At the cell population level, there occur two waves of apoptosis: a fast wave mediated by mitochondrial p53 within three hours postirradiation, and a slow wave mediated by nuclear p53 after eight hours postirradiation. Thus, we propose a two-step mechanism for cell fate decision. The first step is to decide whether DNA damage is severe enough to trigger apoptosis directly through the mitochondrial p53 pathway, while the second step is to determine whether the damage is fixed after cell cycle arrest. Such a mechanism may represent an efficient and reliable control mode, avoiding unnecessary death or greatly promoting the execution of apoptosis. It was also demonstrated that nuclear p53 can inhibit the pro-apoptotic activity of mitochondrial p53 by transactivating p21, and Mdm2 can facilitate apoptosis by promoting the mono-ubiquitination of p53. These results are either in good agreement with experimental observations or experimentally testable. Our work suggests that both the transcription-independent and -dependent p53 activities are indispensable for a reliable choice of cell fate and also provides clues to therapeutic manipulation of the p53 pathway in cancer treatment.
Content-based retrieval of medical images: From context to perception

A challenge in Content-Based retrieval of image exams is to provide a timely answer that complies to the specialist's expectation. In many situations, when a specialist gets a new image to analyze, having information and knowledge from similar cases can be very helpful. However, the semantic gap between low-level image features and their high level semantics may impair the system acceptability. In this paper we propose a new method where we gather from the physicians the visual patterns they use to recognize anomalies in images and apply this knowledge not only in the preprocessing of the images, but also on building feature extractors based on these visual patterns. Moreover, our approach generates feature vectors with lower dimensionality diminishing the “dimensionality curse” problem. Experiments using computed tomography lung images show that the proposed method improves the precision of the query results up to 75%, and generates feature vectors up to 94% smaller than traditional feature extraction techniques while keeping the same representative power. This work shows that perception-based feature extraction combined with the image context can be successfully employed to perform similarity queries in medical image databases.
Effect of Different Surface Treatments on Bond Strength of Resin Cement to a CAD/CAM Restorative Material

PURPOSE To investigate the effects of various surface treatment methods on the shear bond strength of self-adhesive resin cement to a novel CAD/CAM hybrid ceramic material. MATERIALS AND METHODS A novel hybrid ceramic restorative material (Vita Enamic) was used in this study. Sixty resin block specimens were prepared and separated into six groups for each surface treatment method (n = 10); group 1: control group, no treatment applied; group 2: sandblasted by 30 μm silicate-coated alumina particles (CoJet Sandblasting); group 3: 50 μm Al2 O3 sandblasting; group 4: 10% hydrofluoric acid; group 5: no surface treatment + universal adhesive (3M Single Bond Universal); group 6: 200 mJ, 10 Hz 2W Er,Cr:YSGG laser treatment. For each specimen, surface roughness measurements in noncontact mode were taken after the surface treatments using a portable surface texture-measuring machine. A self-adhesive resin cement (3M U200) was applied on every surface treated with the help of a cylindrical mold (2 × 4 mm) and was filled gradually. Shear bond strength was measured using a universal test machine, and one-way ANOVA and a Duncan test (p = 0.05) were used to analyze the data. RESULTS Mean values of the shear bond strength varied between 7.75 and 10.73 MPa. Bond strength values were enhanced by all surface treatment methods compared to the control group. The difference between group 5 and the control group (p < 0.05) was statistically significant, whereas there were no considerable differences between other treatment methods. CONCLUSION Surface treatments of hybrid ceramic resin blocks could enhance the bond strength to resin cement; however, using Single Bond Universal without surface treatment showed a higher bond strength value.
S1 gene sequence analysis of new variant isolates of avian infectious bronchitis virus in Tunisia.

Purpose Tissue samples were collected from suspected broiler flocks showing respiratory signs to identify infectious bronchitis virus (IBV), characterize emerging field strains, and study their relationships with the Massachusetts H120 strain, the only IB vaccine used in Tunisia. Samples and methods Several IBV isolates were identified from field samples collected from flocks located in different regions in the northeast of Tunisia. The IBV isolates were characterized and compared to commonly used vaccine strains (including 793B, D274, and H120 types), other reference IBV strains from Europe, and the recently characterized Tunisian field variants TN20/00, TN200/01, and TN335/01. Reverse transcription-polymerase chain reaction and nucleotide sequencing analyses of the hypervariable regions of the S1 gene were carried out. Results Four new IBV variants were isolated during the period 2007-10 and were designated TN295/07, TN296/07, TN556/07, and TN557/07. The amino acid sequence data showed 100% similarity between TN295/07 and TN296/07, suggesting that these two isolates are identical and belong to the same genotype. Similar results were demonstrated for TN556/07 and TN557/07. Sequence identity values indicated that TN296/07 and TN556/07 share 55% amino acid homologies between each other, but are very different from the reference IBV serotypes, in particular the H120 strain. It was also shown that they have 50%-77% similarities with the Tunisian virus isolated between 2000 and 2001. Phylogenetic clustering allowed classification of these Tunisian isolates as new genotypes that are closer to TN200/01, TN335/01 Tunisian field variants, and Italy02 variant than MassH120 vaccine strain. Conclusion S1 sequence analyses confirmed the cocirculation of H120 vaccine strain with novel IBV variants isolated from Tunisian field.
Energy release rate and quasi-static evolution via vanishing viscosity in a fracture model depending on the crack opening

In the setting of planar linearized elasticity, we study a fracture model depending on the crack opening. Assuming that the crack path is known a priori and sufficiently smooth, we prove that the energy release rate is well defined. Then, we consider the problem of quasi-static evolution for our model. Thanks to a vanishing viscosity approach, we show the existence of such an evolution satisfying a weak Griffith’s criterion.
Enumeration and phenotypic assessment of human plasmacytoid and myeloid dendritic cells in whole blood

Traditionally, flow cytometry analysis of dendritic cells (DC) has followed a negative selection procedure, often limiting the characterization of individual DC subsets to enumeration. We demonstrate the development, evaluation, and clinical application of a novel 6 color/8 parameter flow cytometry panel to allow enumeration and monitoring of activation status of circulating human myeloid (MDC1) and plasmacytoid (PDC) dendritic cells in human whole blood. Enumeration showed a trend of greater numbers of MDC1s and PDCs being collected for fresh whole blood than frozen PBMCs, with this difference being statistically significant (P = 0.04) for unstimulated PDC enumeration. Intra‐assay variation had a coefficient of variation <10% and interassay results between operators showed good correlation (r > 0.95). Our results on fresh whole blood showed a significant up regulation of CD83 on both MDC1 and PDC at 4 h post Toll‐like ligand stimulus and this activity was comparable in frozen PBMC samples. Comparison for the late activation marker CCR7 showed a significant difference (P <0.05) in expression between fresh and frozen samples, precluding its use for batch analysis of frozen samples. In addition, the level of activation is dependent on the anticoagulant used for sample collection. For CD83 expression at 4 h both EDTA and lithium heparin samples are comparable for MDC1 and PDC populations. Whereas for CCR7 expression, lithium heparin is preferable as EDTA increases the background expression in PDC, preventing further functional assessments. We demonstrate the importance of establishing the kinetic profile of activation marker expression and the importance of evaluating sample collection tubes and sample type before application of novel cytometry panels to a clinical study. We have shown that this DC enumeration flow cytometry panel is a robust analysis system that allows the flexibility of including activation markers. © 2010 International Society for Advancement of Cytometry
Autologous Bone-Marrow Mononuclear Cell Implantation Improves Endothelium-Dependent Vasodilation in Patients With Limb Ischemia

Background—Patients with limb ischemia were associated with endothelial dysfunction. The purpose of this study was to determine whether autologous bone-marrow mononuclear cell (BM-MNC) implantation improves endothelial dysfunction in patients with limb ischemia. Methods and Results—We evaluated the leg blood flow (LBF) response to acetylcholine (ACh), an endothelium-dependent vasodilator, and sodium nitroprusside (SNP), an endothelium-independent vasodilator, before and after BM-MNC implantation in 7 patients with limb ischemia. LBF was measured with a mercury-filled Silastic strain-gauge plethysmograph. The number of BM-MNCs implanted into ischemic limbs was 1.6×109±0.3×109. The number of CD34+ cells included in the implanted BM-MNCs was 3.8×107±1.6×107. BM-MNC implantation improved the ankle-brachial pressure index (0.33±0.21 to 0.39±0.17, P =0.06), transcutaneous oxygen pressure (28.4±11.5 to 36.6±5.2 mm Hg, P =0.03), and pain-free walking time (0.8±0.6 to 2.9±2.2 minutes, P =0.02). After BM-MNC implantation, LBF response to ACh was enhanced (19.3±6.8 versus 29.6±7.1 mL/min per 100 mL; P =0.002). The vasodilatory effect of SNP was similar before and after BM-MNC implantation. Conclusions—These findings suggest that BM-MNC implantation augments endothelium-dependent vasodilation in patients with limb ischemia.
Examining the Gap between Science and Public Opinion about Genetically Modified Food and Global Warming

There is great uncertainty due to challenges of escalating population growth and climate change. Public perception that diverges from the scientific community may decrease the effectiveness of scientific inquiry and innovation as tools to solve these challenges. The objective of this study was to identify the factors associated with the divergence of public opinion from scientific consensus regarding the safety of genetically modified (GM) foods and human involvement in global warming (GW). Results indicate that the effects of knowledge on public opinion are complex and non-uniform across types of knowledge (i.e., perceived and actual) or issues. Political affiliation affects agreement with science; Democrats were more likely to agree that GM food is safe and human actions cause GW. Respondents who had relatively higher cognitive function or held illusionary correlations about GM food or GW were more likely to have an opinion that differed from the scientific community.