Miracle-dz/UniFAR-FTUs huggingface dataset:
Correlation of CT Enteroclysis With Surgical Pathology in Crohn's Disease

BACKGROUND:The response to therapy in Crohn's disease (CD) depends on the inflammatory or fibrostenotic nature of the underlying pathological process. Standard diagnostic tests cannot reliably distinguish between these two entities. Although CT enteroclysis (CTE) has shown promise in the evaluation of small bowel disorders, its accuracy for the differentiation of CD phenotypes is unknown.AIMS:To determine the accuracy of CTE compared with surgical pathology in patients with CD and to assess the association of CTE variables with inflammatory or fibrostenotic pathological lesions.METHODS:CTE studies from patients who underwent resective bowel surgery for CD were reviewed and compared with the pathological specimens using a standardized scoring system. Patients were excluded if they had incomplete studies, nonresective surgeries, or a diagnosis of malignancy. CTE variables, such as mucosal and mural enhancement, wall thickness, engorgement of vasa recta (comb sign), adenopathy, and the presence and severity of strictures were compared with the pathology results using Mantel-Haenszel χ2, Spearman's rank coefficient, and logistic regression analyses.RESULTS:Of the 54 patients enrolled, 10 were excluded. The remaining patients (61% female, 84% white) underwent 44 surgical interventions generating 47 bowel segments that were included in the analysis. The indications for surgery were: bowel obstruction in 21; perforating disease in 13; and refractory, nonobstructive disease in 15. The accuracy of CTE for inflammatory and fibrostenotic lesions was 76.6% and 78.7% using a four- and three-point grading system, respectively. There was good correlation between CTE and pathology in regards to inflammation (Spearman's r = 0.7, P < 0.0001) and fibrostenosis (Spearman's r = 0.6, P < 0.0001) scores. The pathological inflammation score was significantly associated with the CTE variables mucosal enhancement, wall thickness, comb sign, and adenopathy (Mantel-Haenszel χ2 P values 0.04, 0.04, <0.0001, and 0.016, respectively). The pathological fibrostenosis score was significantly associated with the presence and severity of stenosis on CTE (P = 0.001 and 0.007, respectively). By logistic regression analysis, the strongest association was seen with the comb sign (OR 5.52, P < 0.001) for inflammation and the presence of stenosis (OR 5.87, P = 0.006) for fibrostenosis. There was no interaction between the time interval from CTE to surgery and the strength of these associations.CONCLUSIONS:CTE may reliably differentiate between inflammatory and fibrostenotic lesions and may have an important role in the management of CD. Specific CTE variables correlate with each of these phenotypes and deserve further investigations in prospective studies.
Functional role of cell surface integrins on human trophoblast cell migration: regulation by TGF-beta, IGF-II, and IGFBP-1.

Trophoblast invasion of the human uterus is stringently controlled by the microenvironment. Invasive extravillous trophoblast cells in situ as well as in culture express a selective repertoire of cell surface integrins. Since migration is a necessary step in the invasion cascade, we tested whether certain integrins or invasion-regulating molecules, i.e., TGF-beta, IGF-II, and IGFBP-1 produced at the fetomaternal interface had a functional role on trophoblast migration. Flow cytometric analysis of integrin expression and the use of an in vitro cell migration assay revealed that exogenous TGF-beta upregulates integrin expression and reduces migratory ability to the invasive trophoblast, whereas IGF-II has no effect on integrin expression but stimulates migration. Trophoblast migration was inhibited in the presence of alpha 5 and beta 1 integrin blocking antibodies, indicating its dependence on the expression of these subunits. Furthermore, IGFBP-1, which contains an RGD sequence recognizing certain integrins, stimulated migration, an effect that was blocked by pretreatment with anti-alpha 5 or -beta 1 blocking Abs. These studies demonstrate that the migration of first trimester invasive trophoblast in vitro (1) requires the expression of alpha 5 and beta 1 integrin subunits, (2) is inhibited by TGF-beta, possibly due to increased cell adhesiveness to the extracellular matrix, (3) is stimulated by IGF-II by an as yet undetermined mechanism, and (4) is stimulated by IGFBP-1, likely by interaction with the RGD binding site of the alpha 5 beta 1 integrin. The invasion-regulating effects of TGF-beta, IGF-II, and IGFBP-1 may thus, at least in part, be due to their migration-regulating effects on the invasive trophoblast.
Evidence for a conserved CCAP-signaling pathway controlling ecdysis in a hemimetabolous insect, Rhodnius prolixus

A vital feature in the success of Ecdysozoa is their ability to shed their exoskeleton (a process called ecdysis) such that they can grow or change their morphology. In holometabolous insects, these behaviors are orchestrated by the sequential actions of neuropeptides, one of which is crustacean cardioactive peptide (CCAP). Little is known about the control of ecdysis in hemimetabolous insects. Here, we report that CCAP is essential for successful ecdysis in the hemimetabolous insect, Rhodnius prolixus; the vector of Chagas disease. The first indication of CCAP's involvement in ecdysis was the observation of decreased staining intensity of CCAP-containing neurons immediately following ecdysis, indicative of the release of CCAP. The critical importance of the CCAP signaling pathway was further demonstrated by knockdown (as determined by qPCR and immunohistochemistry) of the CCAP and CCAPR transcripts utilizing dsRNA. This technique reduced the staining intensity of CCAP-containing neurons, and knocked down the transcript levels by up to 92%, with lethal consequences to the insect. Insects with these transcripts knocked down had very high mortality (up to 84%), typically at the expected time of the ecdysis sequence, or had ecdysis extremely delayed. This is the first report of the susceptibility of R. prolixus to dsRNA knockdown of neuropeptide and receptor transcripts, and the data clearly demonstrates the conserved nature of the CCAP signaling pathway in ecdysis between holometabolous and hemimetabolous insects.
Training and Scaling Preference Functions for Disambiguation

We present an automatic method for weighting the contributions of preference functions used in disambiguation. Initial scaling factors are derived as the solution to a least squares minimization problem, and improvements are then made by hill climbing. The method is applied to disambiguating sentences in the Air Travel Information System corpus, and the performance of the resulting scaling factors is compared with hand-tuned factors. We then focus on one class of preference function, those based on semantic lexical collocations. Experimental results are presented showing that such functions vary considerably in selecting correct analyses. In particular, we define a function that performs significantly better than ones based on mutual information and likelihood ratios of lexical associations.
Differential Responses of Cecal Microbiota to Fishmeal, Eimeria and Clostridium perfringens in a Necrotic Enteritis Challenge Model in Chickens

Clostridium perfringens causes enteric diseases in animals and humans. In poultry, avian-specific C. perfringens strains cause necrotic enteritis, an economically significant poultry disease that costs the global industry over $2 billion annually in losses and control measures. With removal of antibiotic growth promoters in some countries this disease appears to be on the rise. In experimental conditions used to study disease pathogenesis and potential control measures, reproduction of the disease relies on the use of predisposing factors such as Eimeria infection and the use of high protein diets, indicating complex mechanisms involved in the onset of necrotic enteritis. The mechanisms by which the predisposing factors contribute to disease progression are not well understood but it has been suggested that they may cause perturbations in the microbiota within the gastrointestinal tract. We inspected changes in cecal microbiota and short chain fatty acids (SCFA) induced by Eimeria and fishmeal, in birds challenged or not challenged with C. perfringens. C. perfringens challenge in the absence of predisposing factors did not cause significant changes in either the alpha or beta diversity of the microbiota nor in concentrations of SCFA. Moreover, there was no C. perfringens detected in the cecal microbiota 2 days post-challenge without the presence of predisposing factors. In contrast, both fishmeal and Eimeria caused significant changes in microbiota, seen in both alpha and beta diversity and also enabled C. perfringens to establish itself post challenge. Eimeria had its strongest influence on intestinal microbiota and SCFA when combined with fishmeal. Out of 6 SCFAs measured, including butyric acid, none were significantly influenced by C. perfringens, but their levels were strongly modified following the use of both predisposing factors. There was little overlap in the changes caused following Eimeria and fishmeal treatments, possibly indicating multiple routes for progressing towards clinical symptoms of necrotic enteritis.
Constructing a lexicon of action

This paper describes a Japanese speech dialogue system that enables a user to interact with agents in a virtual world and proposes a design framework for building a lexicon of action. This lexicon is used to realize the behavior of the agents in response to the user’s commands. The lexicon has two levels – a macro and micro level. The system uses the macro-level lexicon, which is similar to a conventional plan library, to translate the user’s goal to a sequence of basic movements. This process is the same as conventional planning with symbol manipulation. The micro-level lexicon is used to translate the basic movements into animation, which is represented by a sequence of avatar postures. We discuss how to define a set of basic movements and how to make these basic movements reusable.
Verification of Evolving Software

We define the substitutability problem in the context of evolving software systems as the verification of the following two criteria: (i) previously established system correctness properties must remain valid for the new version of a system, and (ii) the updated portion of the system must continue to provide all (and possibly more) services offered by its earlier counterpart. We present a completely automated procedure based on learning techniques for regular sets to solve the substitutability problem for component based software. We have implemented and validated our approach in the context of the ComFoRT reasoning framework and report encouraging preliminary results on an industrial benchmark.
The cdk5 homologue, crp, regulates endocytosis and secretion in dictyostelium and is necessary for optimum growth and differentiation.

Dictyostelium Crp is a member of the cyclin-dependent kinase (Cdk) family of proteins. It is most related in sequence to mammalian Cdk5, which unlike other members of the family, has functions that are unrelated to the cell cycle. In order to better understand the function of Crp in Dictyostelium, we overexpressed a dominant negative form, Crp-D144N, under the control of the actin 15 promoter. Cells overexpressing Crp-D144N exhibit a reduced growth rate in suspension culture and reduced rates of fluid-phase endocytosis and phagocytosis. There is no reduction in Cdc2 kinase activity in extracts from cells overexpressing Crp-D144N, suggesting that the growth defect is not due to inhibition of Cdc2. In addition to the growth defect, the act15::crp-D144N transformants aggregate at a slower rate than wild-type cells and form large aggregation streams. These eventually break up to form small aggregates and most of these do not produce mature fruiting bodies. The aggregation defect is fully reversed in the presence of wild-type cells but terminal differentiation is only partially rescued. In act15::crp-D144N transformants, the countin component of the counting factor, a secreted protein complex that regulates the breakup of streams, mostly appears outside the cell as degradation products and the reduced level of the intact protein may at least partially account for the initial formation of the large aggregation streams. Our observations indicate that Crp is important for both endocytosis and efflux and that defects in these functions lead to reduced growth and aberrant development.
NIST Open Machine Translation 2008 Evaluation: Stanford University's System Description

This document describes Stanford University’s first entry into a NIST MT evaluation. Our entry to the 2008 evaluation mainly focused on establishing a competent baseline with a phrase-based system similar to (Och and Ney, 2004; Koehn et al., 2007). In a three-week effort prior to the evaluation, our attention focused on scaling up our system to exploit nearly all Chinese-English parallel data permissible under the constrained track, incorporating competitive language models into the decoder using Gigaword and Google n-grams, evaluating Chinese word segmentation models, and incorporating a document classifier as a pre-processing stage to the decoder.
Using witness generators to support bi-directional update between object-based databases (extended abstract)

‘I’his paper considers the issue of incrementally maintaining materialized replicated information in the context of objectbased databases. Uni-directional update concerns propagating updates in one direction, and is closely related to the materialized view update problem. Bi-directional update arises when two databases hold overlapping information, and users of either database have the authority to make updates to that information. The focus here is on the impact of object identifiers (OIDS). A restricted form of ILOG is used, that corresponds essentially to select-project-join queries extended to include OID invention. If auxiliary information is not maintained, then the uniand hi-directional update problems are shown to be essentially equivalent to the graph isomorphism problem, and thus probably intractable. A form of auxiliary information, called “witnesses”, can be used to bring the uni-directional update problem into LOGSPACE. For the hi-directional case a subtlety arises in connection with incremental maintanence of the witnesses. This paper presents a non-trivial procedure that can be used in a limited context for creating programs that maintain witnesses. If such “witness generator” programs are available, then the hi-directional update problem is also in LOCL5PACE.
Foveal Receptors of the Monkey Retina: Fine Structure

The outer segments of the foveal cones of the rhesus monkey are about 40 microns long and 0.9 microns wide. They consist of stacks of membrane-limited, transverse discs about 140 � thick, surrounded by a plasma membrane. The inner segments are about 30 microns long and 2.5 to 3 microns wide at the base, and they taper gradually to a tip diameter of about 1.5 microns. They contain many long mitochondria which are oriented length-wise and are concentrated in the distal portion of the segment. The terminal pedicles show many synaptic contacts, probably as many as 36 per pedicle.
Developing a decision support system to determine carbohydrate intake of diabetic patients

The use of telecommunication methods for healthcare purposes is nowadays inevitable to provide satisfactory service. This article introduces and investigates the concept of a decision support system using telemedicine solutions, namely supporting the medical staff and the patient to treat diabetes by determining diet plans and monitoring food consumption (focusing on carbohydrate intake). The system's requirements are to support the monitoring of the patient's well-being, making a choice on the right therapy, the identification of deterioration of health and alert before the patient's situation gets worse. After summarizing the currently existing diet planning systems, the current article focuses on the presentation of the preliminary work, an application developed by Healthcare Technologies Knowledge Centre of Budapest University of Technology and Economics and the Dept. of Control Engineering and Information Technology. The article introduces in detail the homecare supporting system which is the base of the application, the next steps of the specification and the existing literature. Along with present tasks the future plans are also presented.
Lutein and zeaxanthin intake and the risk of age-related macular degeneration: a systematic review and meta-analysis

Lutein and zeaxanthin are thought to decrease the incidence of age-related macular degeneration (AMD); however, findings have been inconsistent. We conducted a systematic literature review and meta-analysis to evaluate the relationship between dietary intake of lutein and zeaxanthin and AMD risk. Relevant studies were identified by searching five databases up to April 2010. Reference lists of articles were retrieved, and experts were contacted. Literature search, data extraction and study quality assessment were performed independently by two reviewers and results were pooled quantitatively using meta-analysis methods. The potential sources of heterogeneity and publication bias were also estimated. The search yielded six longitudinal cohort studies. The pooled relative risk (RR) for early AMD, comparing the highest with the lowest category of lutein and zeaxanthin intake, was 0·96 (95 % CI 0·78, 1·17). Dietary intake of these carotenoids was significantly related with a reduction in risk of late AMD (RR 0·74; 95 % CI 0·57, 0·97); and a statistically significant inverse association was observed between lutein and zeaxanthin intake and neovascular AMD risk (RR 0·68; 95 % CI 0·51, 0·92). The results were essentially consistent among subgroups stratified by participant characteristics. The findings of the present meta-analysis indicate that dietary lutein and zeaxanthin is not significantly associated with a reduced risk of early AMD, whereas an increase in the intake of these carotenoids may be protective against late AMD. However, additional studies are needed to confirm these relationships.
Time configuration of combined neuromodulation and motor training after stroke: A proof-of-concept study.

BACKGROUND Intensive motor training is a therapeutic intervention that supports recovery of movement function after stroke by capitalizing on the brain's capacity for neuroplastic change. Peripheral nerve stimulation and transcranial direct current stimulation are neuromodulation techniques that can upregulate neuroplasticity and, in turn, enhance outcomes of motor training after stroke. Few studies have investigated possible adjuvant effects between peripheral nerve stimulation, transcranial direct current stimulation, and intensive motor training. OBJECTIVE This proof-of-concept study investigated whether timing variations in neuromodulation paired with robot-assisted motor training effect differential outcomes for subjects with chronic, moderate-to-severe upper extremity impairment after stroke. METHODS Ten subjects in the chronic phase (>12 months after stroke) of recovery completed the study. Subjects received 10 daily sessions of transcranial direct current stimulation either at the start (n = 4) or at the end (n = 6) of peripheral nerve stimulation preceding intensive motor training. Pre-post changes in motor function (Fugl-Meyer Assessment; Stroke Impact Scale) and neuroplasticity (transcranial magnetic stimulation) were assessed by condition. RESULTS Significant improvement in Stroke Impact Scale (p = 0.02) and no change in Fugl-Meyer Assessment were associated with the start condition. No changes in Stroke Impact Scale and Fugl-Meyer Assessment were associated with the end condition. Only 1 subject in the start group had measurable neuroplastic responses and demonstrated an increase in ipsilesional cortical map volume. Only 1 subject in the end group had measurable neuroplastic responses and demonstrated a decrease in ipsilesional cortical map volume. Opposite shifts in ipsilesional cortical centers of gravity occurred relative to condition. CONCLUSION In cases of moderate-to-severe impairment after stroke, transcranial direct current stimulation at the start, rather than the end, of peripheral nerve stimulation prior to motor training may effect better functional outcomes. Future research with a larger sample size is needed to validate the findings of this proof-of-concept study.
Designing spelling correctors for inflected languages using lexical transducers

This paper describes the components used in the design of the commercial X u x e n I I spelling checker/corrector for Basque. It is a new version of the Xuxen spelling corrector (Aduriz et al., 97) which uses lexical transducers to improve the process. A very important new feature is the use of user dictionaries whose entries can recognise both the original and inflected forms. In languages with a high level of inflection such as Basque spelling checking cannot be resolved without adequate treatment of words from a morphological standpoint. In addition to this, the morphological treatment has other important features: coverage, reusability of tools, orthogonality and security. The tool is based in lexical transducers and is built using the fst library of Inxight 1. A lexical transducer (Karttunen, 94) is a finite-state automaton that maps inflected surface forms to lexical forms, and can be seen as an evolution of twolevel morphology (Koskenniemi, 83) where the use of diacritics and homographs can be avoided and the intersection and composition of transducers is possible. In addition, the process is very fast and the transducer for the whole morphological description can be compacted in less than 1Mbyte. The design of the spelling corrector consists of four main modules:
Modeling of anisotropic magneto-piezoelastic materials

The anisotropic magneto-piezoelastic materials are analyzed. It is shown that Green's function method is applicable to time harmonic magneto-elastic-piezoelectricity problems using the boundary integral technique, and the exact analytical solutions are obtained. As an application, a two-dimensional static plane-strain problem is considered to investigate the effect of magnetic field on piezoelectric materials. The closed-form analytical solutions are obtained for a number of boundary conditions for all components of the magneto-piezoelectric field. As a special case, analytical results are presented for two-dimensional static magneto-electroelastic field of a piezoelectric solid subjected to a concentrated line load and an electric charge.
Modeling Interneuron Dysfunction in Schizophrenia

Schizophrenia is a debilitating neurodevelopmental disorder affecting approximately 1% of the population and imposing a significant burden on society. One of the most replicated and well-established postmortem findings is a deficit in the expression of the gene encoding the 67-kDa isoform of glutamic acid decarboxylase (GAD67), the primary GABA-producing enzyme in the brain. GAD67 is expressed in various classes of interneurons, with vastly different morphological, molecular, and physiological properties. Importantly, GABA system deficits in schizophrenia encompass multiple interneuronal subtypes, raising several important questions. First, do different classes of interneurons regulate different aspects of behavior? Second, can we model cell-type-specific GABAergic deficits in mice, and will the rodent findings translate to human physiology? Finally, will this knowledge open the door to knowledge-based approaches to treat schizophrenia?