Miracle-dz/UniFAR-FTUs huggingface dataset:
Tumor recurrence and survival in patients treated for thymomas and thymic squamous cell carcinomas: a retrospective analysis.

PURPOSE Thymic epithelial tumors (TET) are rare epithelial neoplasms of the thymus with considerable histologic heterogeneity. This retrospective study focused on the correlation of WHO-defined TET histotypes with survival and tumor recurrence in a large cohort of patients receiving different modes of treatment. PATIENTS AND METHODS Two hundred twenty-eight patients were followed for up to 21 years (median, 60 months; range, 1 to 252 months) after primary surgery. Forty-two patients received adjuvant radiotherapy (mean dose, 53 Gy), and 33 patients received adjuvant chemotherapy. RESULTS Seventy-six (88%) of 86 patients with WHO type A, AB, and B1 thymomas were treated by surgery alone, with three tumor relapses after 3 to 10 years (median, 3.4 years). Twelve of 67 patients with WHO type B2 and B3 thymomas in Masaoka stages I and II were treated by adjuvant radiotherapy without evidence of tumor recurrence after 1 to 12 years (median, 4 years). Among 75 patients with B2 and B3 thymomas with incomplete resection or a tumor stage III or higher, the recurrence rate was 34% (n = 23) after 0.5 to 17 years (median, 5 years) in patients receiving adjuvant radiochemotherapy, compared to 78% (seven of nine patients) in patients without adjuvant radiochemotherapy. Incomplete tumor resection was associated with a high recurrence rate (65%) and a poor prognosis (P <.01). CONCLUSION The long-term outcome of TET patients is related to tumor stage, WHO histotype, completeness of surgical removal, and type of treatment. Prospective trials are warranted to formally address the efficacy of adjuvant therapy in the treatment of localized and advanced malignant TETs.
The Synaptic Basis of GABAA,slow

Although two kinetically distinct evoked GABAAresponses (GABAA,fast and GABAA,slow) have been observed in CA1 pyramidal neurons, studies of spontaneous IPSCs (sIPSCs) in these neurons have reported only a single population of events that resemble GABAA,fast in their rise and decay kinetics. The absence of slow sIPSCs calls into question the synaptic basis of GABAA,slow. We present evidence here that both evoked responses are synaptic in origin, because two classes of minimally evoked, spontaneous and miniature IPSCs exist that correspond to GABAA,fast and GABAA,slow. Slow sIPSCs occur infrequently, suggesting that the cells underlying these events have a low spontaneous firing rate, unlike the cells giving rise to fast sIPSCs. Like evoked GABAA,fast and GABAA,slow, fast and slow sIPSCs are modulated differentially by furosemide, a subtype-specific GABAAantagonist. Furosemide blocks fast IPSCs by acting directly on the postsynaptic receptors, because it reduces the amplitude of both miniature IPSCs and the responses of excised patches to applied GABA. Thus, in the hippocampus, parallel inhibitory circuits are composed of separate populations of interneurons that contact anatomically segregated and pharmacologically distinct postsynaptic receptors.
Trail following with omnidirectional vision

We describe a system which follows “trails” for autonomous outdoor robot navigation. Through a combination of visual cues provided by stereo omnidirectional color cameras and ladar-based structural information, the algorithm is able to detect and track rough paths despite widely varying tread material, border vegetation, and illumination conditions. The approaching trail region is simply modeled as a circular arc of constant width. Using an adaptive measure of color and brightness contrast between a hypothetical region and flanking areas, the tracker performs a robust randomized search for the most likely trail region and robot pose relative to it with no a priori appearance model. Stereo visual odometry improves tracker dynamics on uneven terrain and permits local obstacle map maintenance. A motion planner is also described which takes the trail shape estimate and local map to plan smooth trajectories around in-trail and near-trail hazards. Our system's performance is analyzed on several long sequences with diverse appearance and structural characteristics using ground-truth segmentations.
Cdc37 has distinct roles in protein kinase quality control that protect nascent chains from degradation and promote posttranslational maturation

Cdc37 is a molecular chaperone that functions with Hsp90 to promote protein kinase folding. Analysis of 65 Saccharomyces cerevisiae protein kinases (∼50% of the kinome) in a cdc37 mutant strain showed that 51 had decreased abundance compared with levels in the wild-type strain. Several lipid kinases also accumulated in reduced amounts in the cdc37 mutant strain. Results from our pulse-labeling studies showed that Cdc37 protects nascent kinase chains from rapid degradation shortly after synthesis. This degradation phenotype was suppressed when cdc37 mutant cells were grown at reduced temperatures, although this did not lead to a full restoration of kinase activity. We propose that Cdc37 functions at distinct steps in kinase biogenesis that involves protecting nascent chains from rapid degradation followed by its folding function in association with Hsp90. Our studies demonstrate that Cdc37 has a general role in kinome biogenesis.
The Myxovirus‐Resistance Protein, MX1, is a Component of Exosomes Secreted by Uterine Epithelial Cells

Dairy cattle suffer from high percentages of early embryonic loss, and therefore, it is critical to study the function of the uterus at this time. We hypothesize that the antiviral protein, myxovirus resistance (MX)1, regulates secretion in uterine glandular cells during early pregnancy.
Prolonged auditory brainstem responses in infants with autism

Numerous studies have attempted to identify early physiological abnormalities in infants and toddlers who later develop autism spectrum disorder (ASD). One potential measure of early neurophysiology is the auditory brainstem response (ABR), which has been reported to exhibit prolonged latencies in children with ASD. We examined whether prolonged ABR latencies appear in infancy, before the onset of ASD symptoms, and irrespective of hearing thresholds. To determine how early in development these differences appear, we retrospectively examined clinical ABR recordings of infants who were later diagnosed with ASD. Of the 118 children in the participant pool, 48 were excluded due to elevated ABR thresholds, genetic aberrations, or old testing age, leaving a sample of 70 children: 30 of which were tested at 0–3 months, and 40 were tested at toddlerhood (1.5–3.5 years). In the infant group, the ABR wave‐V was significantly prolonged in those who later developed ASD as compared with case‐matched controls (n = 30). Classification of infants who later developed ASD and case‐matched controls using this measure enabled accurate identification of ASD infants with 80% specificity and 70% sensitivity. In the group of toddlers with ASD, absolute and interpeak latencies were prolonged compared to clinical norms. Findings indicate that ABR latencies are significantly prolonged in infants who are later diagnosed with ASD irrespective of their hearing thresholds; suggesting that abnormal responses might be detected soon after birth. Further research is needed to determine if ABR might be a valid marker for ASD risk. Autism Res 2016, 9: 689–695. © 2015 The Authors Autism Research published by Wiley Periodicals, Inc. on behalf of International Society for Autism Research
How systemic inflammation modulates adenosine metabolism and adenosine receptor expression in humans in vivo

Objective:Adenosine modulates inflammation and prevents associated organ injury by activation of its receptors. During sepsis, the extracellular adenosine concentration increases rapidly, but the underlying mechanism in humans is unknown. We aimed to determine the changes in adenosine metabolism and signaling both in vivo during experimental human endotoxemia and in vitro. Design:We studied subjects participating in three different randomized double-blind placebo-controlled trials. In order to prevent confounding by the different pharmacological interventions in these trials, analyses were performed on data of placebo-treated subjects only. Setting:Intensive care research unit at the Radboud University Nijmegen Medical Center. Subjects:In total, we used material of 24 healthy male subjects. Interventions:Subjects received 2 ng/kg Escherichia coli endotoxin (lipopolysaccharide) intravenously. Measurements and Main Results:Following experimental endotoxemia, endogenous adenosine concentrations increased. Expression of 5’ectonucleotidase messenger RNA was upregulated (p = .01), whereas adenosine deaminase messenger RNA was downregulated (p = .02). Furthermore, both adenosine deaminase and adenosine kinase activity was significantly diminished (both p ⩽ .0001). A2a and A2b receptor messenger RNA expression was elevated (p = .02 and p = .04, respectively), whereas messenger RNA expression of A1 and A3 receptors was reduced (both, p = .03). In vitro, lipopolysaccharide dose-dependently attenuated the activity of both adenosine deaminase and adenosine kinase (both p ⩽ .0001). Conclusions:Adenosine metabolism and signaling undergo adaptive changes during human experimental endotoxemia promoting higher levels of adenosine thereby facilitating its inflammatory signaling.
An analytical approach to assess sentiment of text

Sentiment (i.e., bad or good opinion) described in texts has been studied widely, and at three different levels: word, sentence, and document level. This paper describes a well-founded approach for the task of sentence level sentiment analysis by studying the relationship between sentiments conveyed through texts and structure of natural language by a method of numerical analysis. Different approaches have been employed to ldquosenserdquo sentiment, especially from the texts, but none of those ever considered the valence based appraisal structure of sentiments which we have employed. Therefore the paper describes an approach to sense sentiments contained in a sentence by applying a numerical-valence based analysis. To meet this objective a linguistic tool, SenseNet, has been developed that provides lexical-units on the basis of each semantic verb frame obtained from the input sentence; assigns a numerical value to those based on their sense affinity; assesses the values using rules; and finally outputs sense-valence for each input sentence. Several experiments with a variety of datasets containing data from different domains have been conducted. The obtained results indicate significant performance gains over existing state-of-the-art approaches.
A Two-Choice Preference Assessment With Five Cotton-Top Tamarins (Saguinus oedipus)

A study selected 5 cotton-top tamarins (Saguinus oedipus) located at the Frank Buck Zoo in Gainesville, Texas, for a food preference assessment. The study used a paired-choice procedure across 7 different food items for all 5 tamarins. Preferences for the food items across all the tamarins varied, although general trends were noted as well. This article discusses the benefits of using paired-choice preference assessments in zoo settings.
A new incremental algorithm for computing Groebner bases

In this paper, we present a new algorithm for computing Gröbner bases. Our algorithm is incremental in the same fashion as F5 and F5C. At a typical step, one is given a Gröbner basis G for an ideal I and any polynomial g, and it is desired to compute a Gröbner basis for the new ideal , obtained from I by joining g. Let (I: g) denote the colon ideal of I divided by g. Our algorithm computes Gröbner bases for and (I: g) simultaneously. In previous algorithms, S-polynomials that reduce to zero are useless, in fact, F5 tries to avoid such reductions as much as possible. In our algorithm, however, these "useless" S-polynomials give elements in (I: g) and are useful in speeding up the subsequent computations. Computer experiments on some benchmark examples indicate that our algorithm is much more efficient (two to ten times faster) than F5 and F5C.
Contributions of Prosodic and Distributional Features of Caregivers' Speech in Early Word Learning

How do characteristics of caregiver speech contribute to a child’s early word learning? We explore the relationship between a single child’s vocabulary growth and the distributional and prosodic characteristics of the speech he hears using data collected for the Human Speechome Project, an ecologically valid corpus collected from the home of a family with a young child. We measured F0, intensity, phoneme duration, usage frequency, recurrence, and MLU for caregivers’ production of each word that the child learned during the period of recording. When all variables are considered, we obtain a model of word acquisition as a function of caregiver input speech. Coefficient estimates in the model help to illuminate which factors are relevant to learning classes of words. In addition, words that deviate from the model’s prediction are of interest as they may suggest important social, contextual and other cues relevant to word learning.
Extensively Drug-Resistant Pseudomonas aeruginosa Isolates Containing blaVIM-2 and Elements of Salmonella Genomic Island 2: a New Genetic Resistance Determinant in Northeast Ohio

ABSTRACT Carbapenems are a mainstay of treatment for infections caused by Pseudomonas aeruginosa. Carbapenem resistance mediated by metallo-β-lactamases (MBLs) remains uncommon in the United States, despite the worldwide emergence of this group of enzymes. Between March 2012 and May 2013, we detected MBL-producing P. aeruginosa in a university-affiliated health care system in northeast Ohio. We examined the clinical characteristics and outcomes of patients, defined the resistance determinants and structure of the genetic element harboring the blaMBL gene through genome sequencing, and typed MBL-producing P. aeruginosa isolates using pulsed-field gel electrophoresis (PFGE), repetitive sequence-based PCR (rep-PCR), and multilocus sequence typing (MLST). Seven patients were affected that were hospitalized at three community hospitals, a long-term-care facility, and a tertiary care center; one of the patients died as a result of infection. Isolates belonged to sequence type 233 (ST233) and were extensively drug resistant (XDR), including resistance to all fluoroquinolones, aminoglycosides, and β-lactams; two isolates were nonsusceptible to colistin. The blaMBL gene was identified as blaVIM-2 contained within a class 1 integron (In559), similar to the cassette array previously detected in isolates from Norway, Russia, Taiwan, and Chicago, IL. Genomic sequencing and assembly revealed that In559 was part of a novel 35-kb region that also included a Tn501-like transposon and Salmonella genomic island 2 (SGI2)-homologous sequences. This analysis of XDR strains producing VIM-2 from northeast Ohio revealed a novel recombination event between Salmonella and P. aeruginosa, heralding a new antibiotic resistance threat in this region's health care system.
Brief Report: Intestinal Dysbiosis in Ankylosing Spondylitis

Ankylosing spondylitis (AS) is a common, highly heritable immune‐mediated arthropathy that occurs in genetically susceptible individuals exposed to an unknown but likely ubiquitous environmental trigger. There is a close relationship between the gut and spondyloarthritis, as exemplified in patients with reactive arthritis, in whom a typically self‐limiting arthropathy follows either a gastrointestinal or urogenital infection. Microbial involvement in AS has been suggested; however, no definitive link has been established. The aim of this study was to determine whether the gut in patients with AS carries a distinct microbial signature compared with that in the gut of healthy control subjects.
Decreased Phytohemagglutinin-Induced Aggregation and C5a-Induced Chemotaxis of Human Newborn Neutrophils

Summary: Phytohemagglutinin (PHA)-induced lectin aggregation, chemotactic response to C5a, and random migration were measured on paired samples of neutrophils obtained from human peripheral blood and cord blood of normal newborn infants. The mean aggregation rate (± 1 SD) of adult neutrophils with PHA was 16.8 ± 4.4 vs. 12.0 ± 3.6 for newborn neutrophils (P < 0.005), and the mean percent aggregation of adult neutrophils was 56.2 ± 9.2 vs. 45.6 ± 8.3 for newborn neutrophils (P < 0.005). Exposure to newborn plasma had no affect on adult neutrophil aggregation. Whereas vinblastine (VBL) decreased both the percent and rate of PHA-induced adult neutrophil aggregation, only the rate of newborn neutrophil aggregation was reduced by VBL. Newborn neutrophil chemotactic response to C5a, was reduced by 80% (P < 0.0025), and showed a positive correlation with percent PHA-induced aggregation (r = 0.6037, P < 0.05). On the other hand, random migration was not significantly reduced and did not correlate with PHA-induced aggregation. These observations suggest that the decreased chemotactic responsiveness of newborn neutrophils may be due to developmental membrane differences which adversely affect the number and/or availability of C5a receptors. Lectin-induced aggregation studies of other chemotactic defects may identify similar differences.Speculation: Although the precise nature of decreased newborn neutrophil chemotactic responsiveness remains unknown, these studies demonstrating decreased PHA-induced aggregation and decreased chemotactic response of newborn neutrophils suggest that developmental membrane differences in newborn neutrophil may adversely affect requisite premigratory membrane events. Persistence of these developmental membrane differences or their reappearance may be the basis of other chemotactic defects.
Comparative Study Regarding the Effect of Different Remineralizing Products on Primary and Permanent Teeth Enamel Caries Lesions

The aims of this study were to investigate the surface topography and to compare the remineralization potential of four commercial remineralizing products on deciduous and permanent teeth enamel. After artificial caries lesion formation, the enamel samples were divided into five experimental groups for permanent teeth, respectively deciduous teeth. In group 1 the samples have been stored in distilled water (control group). In group 2 each enamel sample was brushed two times a day for fourteen days with a commercial fluoride gel (Colgate® 6+ ), in group 3 each enamel sample was brushed two times a day for fourteen days with a commercial fluoride gel (CarrefourKids® +6). In group 4 a water-based cream with fluoride and hydroxyapatite (Remin Pro®, Voco) was applied for 5 minutes two times a day for fourteen days. In group 5 the enamel samples were rinsed with 20 mL antibacterial mouthwash with alcohol free natrium fluoride (Colgate® Plax) for 30 s two times a day for fourteen days. Between the remineralizing cycles, the samples have been stored in artificial saliva. The samples were analyzed using a scanning electron microscopeand an EDX detector.For primary and permanent teeth samples, lower values of calcium and phosphorus ion concentrations were recorded in groups 2-5 when compared to group 1. For groups 2 and 3 the values of calcium and phosphorus ion concentrations were nearly the same. In group 4 the concentration of both ions recorded the highest level from all study groups (groups 2-5). The lowest values of calcium and phosphorus ion concentrations were observed in group 5.All the products tested in this study had the capacity to remineralize dental enamel of primary and permanent teeth, but the remineralization was not complete. The products containing fluoride and hydroxyapatite showed a higher remineralization potential when compared to fluoride products.
Automatically Linking News Articles to Blog Entries

People often write in their blogs about news articles or events in news articles. In this case, however, the details of the news articles or events are often poorly described in such blog entries. Therefore, the readers of blogs need to find the original articles, which contain more details of the news articles, when they want to know about them. In this paper, we propose a method for linking news articles to blog entries that refer to them. Since blog entries and news articles are considered to be rather different, the common model for linking is not applicable. Therefore, we similarly used a vector space model for finding similar documents, but we tried to devise a new weighting method and a distance metric to improve the performance, by taking into account the properties of blog entries and news articles document sets.
Two new species of Neozoanthus (Cnidaria, Hexacorallia, Zoantharia) from the Pacific

Abstract The zoanthid genus Neozoanthus was originally described in 1972 from a single species in Madagascar. This monotypic genus was placed within its own family, Neozoanthidae, given its unusual characters of only partial sand encrustation, and an endodermal sphincter muscle combined with a brachycnemic mesenterial arrangement. Recently, undescribed specimens of Neozoanthus were discovered thousands of kilometers away in both Australia and Japan. While the phylogenetic and evolutionary aspects of Neozoanthus spp. are now somewhat well understood, the new specimens remained undescribed. Here we describe the specimens as two new species, Neozoanthus uchina sp. n. from the Middle Ryukyu Islands of southern Japan, and Neozoanthus caleyi sp. n. from the waters around Heron Island, on the Great Barrier Reef in Australia. Both species can be distinguished from each other and the type species, Neozoanthus tulearensis, by their distributions, oral disk colors, and average numbers of tentacles. Additionally, each species appears to have subtle differences in their cnidae. The division of Japanese and Australian specimens into two species is strongly supported by recently reported phylogenetic data. The discovery and description of these two species highlights how little is known of zoanthid species diversity in the Indo-Pacific.
Altered topological properties of the cortical motor‐related network in patients with subcortical stroke revealed by graph theoretical analysis

Cerebral neuroplasticity after stroke has been elucidated by functional neuroimaging. However, little is known concerning how topological properties of the cortical motor‐related network evolved following subcortical stroke. In the present study, we investigated 24 subcortical stroke patients with only left motor pathway damaged and 24 matched healthy controls. A cortical motor‐related network consisting of 20 brain regions remote from the primary lesion was constructed using resting‐state functional MRI datasets. We subsequently used graph theoretical approaches to analyze the topological properties of this network in both stroke patients and healthy controls. In addition, we divided the stroke patients into two subgroups according to their outcomes in hand function to explore relationships between topological properties of this network and outcomes in hand function. Although we observed that the cortical motor‐related network in both healthy controls and stroke patients exhibited small‐world topology, the local efficiency of this network in stroke patients is higher than and global efficiency is lower than those in healthy controls. In addition, striking alterations in the betweenness centrality of regions were found in stroke patients, including the contralesional supplementary motor area, dorsolateral premotor cortex, and anterior inferior cerebellum. Moreover, we observed significant correlations between betweenness centrality of regions and Fugl‐Meyer assessment scores. A tendency for the cortical motor‐related network to be close to a regular configuration and altered betweenness centrality of regions were demonstrated in patients with subcortical stroke. This study provided insight into functional organization after subcortical stroke from the viewpoint of network topology. Hum Brain Mapp 35:3343–3359, 2014. © 2013 Wiley Periodicals, Inc.