Miracle-dz/UniFAR-FTUs huggingface dataset:
Kriya - An end-to-end Hierarchical Phrase-based MT System

Kriya - An end-to-end Hierarchical Phrase-based MT System This paper describes Kriya - a new statistical machine translation (SMT) system that uses hierarchical phrases, which were first introduced in the Hiero machine translation system (Chiang, 2007). Kriya supports both a grammar extraction module for synchronous context-free grammars (SCFGs) and a CKY-based decoder. There are several re-implementations of Hiero in the machine translation community, but Kriya offers the following novel contributions: (a) Grammar extraction in Kriya supports extraction of the full set of Hiero-style SCFG rules but also supports the extraction of several types of compact rule sets which leads to faster decoding for different language pairs without compromising the BLEU scores. Kriya currently supports extraction of compact SCFGs such as grammars with one non-terminal and grammar pruning based on certain rule patterns, and (b) The Kriya decoder offers some unique improvements in the implementation of cube-pruning, such as increasing diversity in the target language n-best output and novel methods for language model (LM) integration. The Kriya decoder can take advantage of parallelization using a networked cluster. Kriya supports both KENLM and SRILM for language model queries. This paper also provides several experimental results which demonstrate that the translation quality of Kriya compares favourably to the Moses (Koehn et al., 2007) phrase-based system in several language pairs while showing a substantial improvement for Chinese-English similar to Chiang (2007). We also quantify the model sizes for phrase-based and Hiero-style systems and also present experiments comparing variants of Hiero models.
Comparative Study of the Effects of Different Fibers on the Processing and Properties of Polypropylene Matrix Composites

The effects of different types of fibers on the physical and mechanical behavior of isotactic polypropylene (iPP) are reported. In particular, the flow behavior, mechanical properties (tensile, flexural and impact resistance) and morphology are examined. It has been found that all the fibers studied behave as effective reinforcing agents for the polypropylene matrix. In fact, a notable increase of the mechanical properties is observed in presence of the fibers, the aramid ones being the most effective. Moreover, dynamic-mechanical measurements provide a further confirmation of the reinforcement effect of the fibers, where a sensible increment of the storage modulus in presence of the fibers is obtained. The morphology of the composites is analyzed by scanning electron microscopy (SEM). A good fiber-matrix interfacial adhesion is observed, in particular, for aramid and glass fiber-reinforced composites. As expected, a good adhesion at the fiber-matrix interface gives rise to a sensible increment of composites properties.
INDOCYANINE GREEN VIDEOANGIOGRAPHY OF IDIOPATHIC POLYPOIDAL CHOROIDAL VASCULOPATHY

Purpose: To identify the precise choroidal abnormalities associated with idiopathic polypoidal choroidal vasculopathy (IPCV), patients with IPCV were examined with indocyanine green (ICG) videoangiography. Methods: Twelve patients with IPCV were examined using standard clinical, fluorescein, and ICG videoangiographic techniques. Results: Indocyanine green videoangiography showed two basic choroidal vascular changes: a branching network of vessels in the inner choroid, and vascular dilations at the border of the network of vessels. The vascular dilations appeared to be associated with the exudative and hemorrhagic manifestations of IPCV. Conclusion: The choroidal vasculopathy seen in IPCV is distinct from the changes seen in other choroidal abnormalities. Recognition of these changes aids in diagnosis and patient management, since the clinical implications of IPCV differ from those of other similar entities.
Extreme deconvolution: Inferring complete distribution functions from noisy, heterogeneous and incomplete observations

We generalize the well-known mixtures of Gaussians approach to density estimation and the accompanying Expectation-Maximization technique for finding the maximum likelihood parameters of the mixture to the case where each data point carries an individual d-dimensional uncertainty covariance and has unique missing data properties. This algorithm reconstructs the error-deconvolved or “underlying” distribution function common to all samples, even when the individual data points are samples from different distributions, obtained by convolving the underlying distribution with the unique uncertainty distribution of the data point and projecting out the missing data directions. We show how this basic algorithm can be extended with Bayesian priors on all of the model parameters and a “split-and-merge” procedure designed to avoid local maxima of the likelihood. We apply this technique to a few typical astrophysical applications.
The Spectrum of Thrombotic Thrombocytopenic Purpura: A Clinicopathologic Demonstration of Tacrolimus-Induced Thrombotic Thrombocytopenic Purpura in a Lung Transplant Patient

Immunosuppressive drugs used post-transplantation are among the most common causes of thrombotic thrombocytopenic purpura (TTP). Diagnosis is often confounded not only by its myriad presentations, but also because these manifestations may be explained by the comorbidities or complications of transplantation. A 61-year-old female who had a single lung transplant for severe chronic obstructive pulmonary disease maintained on corticosteroids, tacrolimus and mycophenolate mofetil, was admitted for fever, headache with confusion and lethargy. She was mildly anemic and thrombocytopenic. Peripheral smear showed rare fragmented red cells. Muddy brown casts were present on urinalysis. She was diagnosed with TTP. Tacrolimus was discontinued and the mental status of the patient, anemia and thrombocytopenia improved significantly.
The effect of parental age and egg weight on fertility , hatchability and day-old chick weight of Japanese quail ( Cortunix cortunix japonica )

The study was carried out to determine the effects of the parental age and egg weight of Japanese quail on the weight of one day old chick, fertility and hatchability of incubated eggs. Three hundred and sixty Japanese quail eggs were obtained from 22 and 36 weeks old quails. The eggs were weighed and grouped into 2 categories: Light (7.5-9.5g) and Heavy (9.6 – 12g). The weight of the chicks were recorded, percent fertility and hatchability were also calculated. The data was analyzed with SAS (2003) and means were separated with Duncan’s Multiple Range Test. The parental age was found to have a significant effect on hatchability and fertility of incubated eggs (P<0.001) and the effect of egg weight groups on the weight of day old chick was found to be significant (P<0.05). Results obtained from this study reveal that the parental age of quail had a significant effect on the egg weight, fertility and hatchability of incubated eggs. It was also observed that with increasing egg weight, chick weight increased.
Protein Coding Gene Nucleotide Substitution Pattern in the Apicomplexan Protozoa Cryptosporidium parvum and Cryptosporidium hominis

Cryptosporidium parvum and C. hominis are related protozoan pathogens which infect the intestinal epithelium of humans and other vertebrates. To explore the evolution of these parasites, and identify genes under positive selection, we performed a pairwise whole-genome comparison between all orthologous protein coding genes in C. parvum and C. hominis. Genome-wide calculation of the ratio of nonsynonymous versus synonymous nucleotide substitutions (d N/d S) was performed to detect the impact of positive and purifying selection. Of 2465 pairs of orthologous genes, a total of 27 (1.1%) showed a high ratio of nonsynonymous substitutions, consistent with positive selection. A majority of these genes were annotated as hypothetical proteins. In addition, proteins with transmembrane and signal peptide domains are significantly more frequent in the high d N/d S group.
Comparison of the Luminex xTAG Respiratory Viral Panel with xTAG Respiratory Viral Panel Fast for Diagnosis of Respiratory Virus Infections

ABSTRACT Nucleic acid tests are sensitive and specific and provide a rapid diagnosis, making them invaluable for patient and outbreak management. Multiplex PCR assays have additional advantages in providing an economical and comprehensive panel for many common respiratory viruses. Previous reports have shown the utility of the xTAG respiratory viral panel (RVP) assay manufactured by Luminex Molecular Diagnostics for this purpose. A newer generation of this kit, released in Canada in early 2010, is designed to simplify the procedure and reduce the turnaround time by about 24 h. The assay methodology and targets included in this version of the kit are different; consequently, the objective of this study was to compare the detection of a panel of respiratory viral targets using the older Luminex xTAG RVP (RVP Classic) assay with that using the newer xTAG RVP Fast assay. This study included 334 respiratory specimens that had been characterized for a variety of respiratory viral targets; all samples were tested by both versions of the RVP assay in parallel. Overall, the RVP Classic assay was more sensitive than the RVP Fast assay (88.6% and 77.5% sensitivities, respectively) for all the viral targets combined. Targets not detected by the RVP Fast assay included primarily influenza B virus, parainfluenza virus type 2, and human coronavirus 229E. A small number of samples positive for influenza A virus, respiratory syncytial virus B, human metapneumovirus, and parainfluenza virus type 1 were not detected by the RVP Classic assay and in general had low viral loads.
Cellular Response of Shewanella oneidensis to Strontium Stress

ABSTRACT The physiology and transcriptome dynamics of the metal ion-reducing bacterium Shewanella oneidensis strain MR-1 in response to nonradioactive strontium (Sr) exposure were investigated. Studies indicated that MR-1 was able to grow aerobically in complex medium in the presence of 180 mM SrCl2 but showed severe growth inhibition at levels above that concentration. Temporal gene expression profiles were generated from aerobically grown, mid-exponential-phase MR-1 cells shocked with 180 mM SrCl2 and analyzed for significant differences in mRNA abundance with reference to data for nonstressed MR-1 cells. Genes with annotated functions in siderophore biosynthesis and iron transport were among the most highly induced (>100-fold [P < 0.05]) open reading frames in response to acute Sr stress, and a mutant (SO3032::pKNOCK) defective in siderophore production was found to be hypersensitive to SrCl2 exposure, compared to parental and wild-type strains. Transcripts encoding multidrug and heavy metal efflux pumps, proteins involved in osmotic adaptation, sulfate ABC transporters, and assimilative sulfur metabolism enzymes also were differentially expressed following Sr exposure but at levels that were several orders of magnitude lower than those for iron transport genes. Precipitate formation was observed during aerobic growth of MR-1 in broth cultures amended with 50, 100, or 150 mM SrCl2 but not in cultures of the SO3032::pKNOCK mutant or in the abiotic control. Chemical analysis of this precipitate using laser-induced breakdown spectroscopy and static secondary ion mass spectrometry indicated extracellular solid-phase sequestration of Sr, with at least a portion of the heavy metal associated with carbonate phases.
Small intestinal CD 103 + dendritic cells display unique functional properties that are conserved between mice and humans

The Rockefeller University Press $30.00 J. Exp. Med. www.jem. org/cgi/doi/10.1084/jem.20080414 Cite by DOI: 10.1084/jem.20080414 1 of 11 DCs are well recognized for their role in the priming and diff erentiation of naive T cells ( 1, 2 ). Murine conventional DCs have been extensively studied and have traditionally been divided into fi ve distinct subsets based on their expression of CD11b, CD4, CD8 , and Langerin. The spleen contains three of these subsets (CD11b + CD4 + , CD11b + CD4 CD8 , and CD11b CD8 + ), whereas LNs contain two additional populations (CD4 Langerin + and CD4 CD8  CD11b lo ) that display a more mature phenotype and appear to represent tissue-derived migratory DCs ( 3, 4 ). Although the developmental relationships between these populations remains unclear, several of these subsets have been described to have distinct functional properties ( 5, 6 ). Nevertheless, surprisingly few studies have attempted to characterize DC subsets in human LN ( 4, 7 – 10 ) and, thus, the possibility of targeting distinct conventional DC subsets for regulating human immune responses remains unclear. Indeed, to our knowledge functionally distinct conventional DC subsets in human LN have yet to be described. Recent evidence suggests that the tissue environment in which DCs reside has a major impact on their phenotypic and functional properties. This is particularly apparent in the intestinal mucosa. Intestinal DCs are located throughout the villus lamina propria (LP) and in intestinal lymphoid tissue (Peyers Patches CORRESPONDENCE William Agace: William.Agace@med.lu. se
Effect of Cocoa and Its Flavonoids on Biomarkers of Inflammation: Studies of Cell Culture, Animals and Humans

Chronic inflammation has been identified as a necessary step to mediate atherosclerosis and cardiovascular disease and as a relevant stage in the onset and progression of several types of cancer. Considerable attention has recently been focused on the identification of dietary bioactive compounds with anti-inflammatory activities as an alternative natural source for prevention of inflammation-associated diseases. The remarkable capacity of cocoa flavanols as antioxidants, as well as to modulate signaling pathways involved in cellular processes, such as inflammation, metabolism and proliferation, has encouraged research on this type of polyphenols as useful bioactive compounds for nutritional prevention of cardiovascular disease and cancer. Data from numerous studies suggest that cocoa and cocoa-derived flavanols can effectively modify the inflammatory process, and thus potentially provide a benefit to individuals with elevated risk factors for atherosclerosis/cardiovascular pathology and cancer. The present overview will focus on the most recent findings about the effects of cocoa, its main constituents and cocoa derivatives on selected biomarkers of the inflammatory process in cell culture, animal models and human cohorts.
Cumulative trauma and midlife well-being in American women who served in Vietnam: effects of combat exposure and postdeployment social support

Background and Objectives: Research increasingly demonstrates that trauma exposure can have cumulative effects, yet much remains to be learned about effects of cumulative trauma, particularly regarding longer term adjustment. One such trauma, combat exposure, is insufficiently understood, especially for women, who are increasingly engaged in professional combat activities. Design: The study comprised a cross-sectional survey assessing multiple aspects of current well-being in women approximately 25 years after their service in Vietnam during the Vietnam War. Methods: Participants were 1374 women (78% military and 22% nonmilitary; mean age = 59.7). This study investigated the relations between three separate categories of trauma exposure (childhood, adulthood, and combat) and well-being and examined whether perceived social support at return from Vietnam moderated the association between combat exposure and well-being. Results: While both childhood and adulthood trauma exposure related to midlife well-being, combat exposure still uniquely predicted outcomes. Further, postdeployment perceived social support moderated the association of combat and well-being: recollected higher perceived social support at homecoming buffered participants from the links between combat exposure and well-being. Conclusions: These results may have important implications for interventions to reduce the impact of traumatic experiences, particularly in light of the increasing exposure of women to direct combat events.
Continuous Renal Replacement Therapy in Patients following Traumatic Injury

In critically injured patients, the incidence of acute renal failure has been reported to occur in as many as 31% of patients. The use of CRRT modalities for patients following traumatic injuries is becoming more common, albeit slowly, and this therapy may impact upon long-term recovery of renal function and mortality. Historical studies investigating the early use of intermittent dialysis reported significant improvement in survival in patients who were dialyzed earlier and more vigorously than in control subjects. Early trauma patients also showed improved survival following war injuries when dialyzed prophylactically. Although there is a growing acceptance in favor of earlier renal replacement therapy, the published consensus and the practice in many centers has been to dialyze/filter relatively ill rather than relatively healthy patients. The R Adams Cowley Shock Trauma Center (STC) in Baltimore, Maryland, USA, admits over 8,000 trauma patients each year. Within the STC, a program of continuous renal replacement therapy was established in the early 1980's. We review both historical and current literature on the use of renal replacement therapies after traumatic injury, and suggest some future areas of investigation and indications for these modalities.
Development and measurement properties of the Orthotics and Prosthetics Users’ Survey (OPUS): A comprehensive set of clinical outcome instruments

The need to measure and evaluate orthotics and prosthetics (O&P) practice has received growing recognition in the past several years. Reliable and valid self-report instruments are needed that can help facilities evaluate patient outcomes. The objective of this project was to develop a set of self-report instruments that assess functional status, quality of life, and satisfaction with devices and services that can be used in an orthotics and prosthetics clinic. Selecting items from a variety of existing instruments, the authors developed and revised four instruments that differentiate patients with varying levels of lower limb function, quality of life, and satisfaction with devices and services. Evidence of construct validity is provided by hierarchies of item difficulty that are consistent with clinical experience. For example, with the lower limb function instrument, running one block was much more difficult than walking indoors. The instruments demonstrate adequate internal consistency (0.88 for lower limb function, 0.88 for quality of life, 0.74 for service satisfaction, 0.78 for device satisfaction). The next steps in their research programme are to evaluate sensitivity and construct validity. The Orthotics and Prosthetics Users’ Survey (OPUS) is a promising self-report instrument which may, with further development, allow orthotic and prosthetic practitioners to evaluate the quality and effectiveness of their services as required by accreditation standards such as those of the American Board for Certification in Orthotics and Prosthetics that mandate quality assessment.
Linear Latent Force Models Using Gaussian Processes

Purely data-driven approaches for machine learning present difficulties when data are scarce relative to the complexity of the model or when the model is forced to extrapolate. On the other hand, purely mechanistic approaches need to identify and specify all the interactions in the problem at hand (which may not be feasible) and still leave the issue of how to parameterize the system. In this paper, we present a hybrid approach using Gaussian processes and differential equations to combine data-driven modeling with a physical model of the system. We show how different, physically inspired, kernel functions can be developed through sensible, simple, mechanistic assumptions about the underlying system. The versatility of our approach is illustrated with three case studies from motion capture, computational biology, and geostatistics.
PG13 Packaging Cells Produce Recombinant Retroviruses Carrying a Diphtheria Toxin Mutant Which Kills Cancer Cells

ABSTRACT The development of suicide gene therapy with gene products that are directly toxic to cells, such as the A subunit of diphtheria toxin (DT-A), has been hampered by the difficulty of engineering recombinant viruses. DT-A is a strong inhibitor of protein synthesis that acts by ADP-ribosylating elongation factor 2, and a low level of DT-A expression in virus producer cells prevents the production of recombinant virus. We analyzed here the natural resistance of packaging cells to DT-A toxicity, and we report that PG13 and PA317 packaging cell lines are resistant to H21G, a DT-A mutant. PG13 cells produce recombinant H21G virus that efficiently kills a variety of human tumor cells. Our finding indicates that PG13 packaging cells provide a new potential for the development of DT-A-based suicide gene therapy.
Discovering object categories in image collections

Given a set of images containing multiple object categories, we seek to discover those categories and their image locations without supervision. We achieve this using generative models from the statistical text literature: probabilistic Latent Semantic Analysis (pLSA), and Latent Dirichlet Allocation (LDA). In text analysis these are used to discover topics in a corpus using the bag-of-words document representation. Here we discover topics as object categories, so that an image containing instances of several categories is modelled as a mixture of topics. The models are applied to images by using a visual analogue of a word, formed by vector quantizing SIFT like region descriptors. We investigate a set of increasingly demanding scenarios, starting with image sets containing only two object categories through to sets containing multiple categories (including airplanes, cars, faces, motorbikes, spotted cats) and background clutter. The object categories sample both intra-class and scale variation, and both the categories and their approximate spatial layout are found without supervision. We also demonstrate classification of unseen images and images containing multiple objects. Performance of the proposed unsupervised method is compared to the semi-supervised approach of [7]. 1 1This work was sponsored in part by the EU Project CogViSys, the University of Oxford, Shell Oil, and the National Geospatial-Intelligence Agency.
Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655

ABSTRACT Defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. We used a genetic footprinting technique for a genome-wide assessment of genes required for robust aerobic growth of Escherichia coli in rich media. We identified 620 genes as essential and 3,126 genes as dispensable for growth under these conditions. Functional context analysis of these data allows individual functional assignments to be refined. Evolutionary context analysis demonstrates a significant tendency of essential E. coli genes to be preserved throughout the bacterial kingdom. Projection of these data over metabolic subsystems reveals topologic modules with essential and evolutionarily preserved enzymes with reduced capacity for error tolerance.