Miracle-dz/UniFAR-FTUs huggingface dataset:
Kinetics of cyclocreatine and Na+ cotransport in human breast cancer cells: mechanism of activity.

The growth-inhibitory effect of cyclocreatine (CCr) and the kinetics of CCr and Na+ cotransport were investigated in MCF7 human breast cancer cells and its adriamycin-resistant subline with use of 31P- and23Na-NMR spectroscopy. The growth-inhibitory effect in the resistant line occurred at a lower CCr concentration and was more pronounced than in the wild-type line. This correlated with an ∼10-fold higher affinity of CCr to the transporter in the resistant line. The passive diffusion coefficient of CCr was also higher in the resistant line by three- to fourfold. The transport of CCr was accompanied by a rapid increase in intracellular Na+. This increase was found to depend on the rate of CCr transport and varied differently with CCr concentration in the two cell lines. It is proposed that the cotransport of CCr and Na+followed by increased Na+concentration, together with the accumulation of the highly charged phosphocyclocreatine, are responsible for cell swelling and death.
Downregulated in adenoma gene encodes a chloride transporter defective in congenital chloride diarrhea.

Congenital chloride diarrhea (CLD) is a recessively inherited disorder characterized by massive loss of chloride in stool. We previously identified mutations in the downregulated in adenoma ( DRA) gene in patients with CLD and demonstrated that DRA encodes an intestine-specific sulfate transporter. To determine whether DRA is an intestinal chloride transporter and how mutations affect transport, Xenopus oocytes were injected with wild-type and mutagenized DRA cRNA and uptake of Cl- and[Formula: see text] was assayed. Both Cl- and[Formula: see text] were transported by wild-type DRA and an outwardly directed pH gradient stimulated Cl- uptake, consistent with Cl-/OH-exchange. Among three mutants, C307W transported both anions as effectively as wild-type, whereas transport activity was lost in V317del and the double mutant identified in 32 of 32 Finnish CLD patients. We conclude that DRA is a chloride transporter defective in CLD and that V317del is a functional mutation and C307W a silent polymorphism.
Drought Sensitivity of Norway Spruce at the Species’ Warmest Fringe: Quantitative and Molecular Analysis Reveals High Genetic Variation Among and Within Provenances

Norway spruce (Picea abies) is by far the most important timber species in Europe, but its outstanding role in future forests is jeopardized by its high sensitivity to drought. We analyzed drought response of Norway spruce at the warmest fringe of its natural range. Based on a 35-year old provenance experiment we tested for genetic variation among and within seed provenances across consecutively occurring strong drought events using dendroclimatic time series. Moreover, we tested for associations between ≈1,700 variable SNPs and traits related to drought response, wood characteristics and climate-growth relationships. We found significant adaptive genetic variation among provenances originating from the species’ Alpine, Central and Southeastern European range. Genetic variation between individuals varied significantly among provenances explaining up to 44% of the phenotypic variation in drought response. Varying phenotypic correlations between drought response and wood traits confirmed differences in selection intensity among seed provenances. Significant associations were found between 29 SNPs and traits related to drought, climate-growth relationships and wood properties which explained between 11 and 43% of trait variation, though 12 of them were due to single individuals having extreme phenotypes of the respective trait. The majority of these SNPs are located within exons of genes and the most important ones are preferentially expressed in cambium and xylem expansion layers. Phenotype-genotype associations were stronger if only provenances with significant quantitative genetic variation in drought response were considered. The present study confirms the high adaptive variation of Norway spruce in Central and Southeastern Europe and demonstrates how quantitative genetic, dendroclimatic and genomic data can be linked to understand the genetic basis of adaptation to climate extremes in trees.
Physical-virtual tools for spatial augmented reality user interfaces

This paper presents a new user interface methodology for Spatial Augmented Reality systems. The methodology is based on a set of physical tools that are overloaded with logical functions. Visual feedback presents the logical mode of the tool to the user by projecting graphics onto the physical tools. This approach makes the tools malleable in their functionality, with this change conveyed to the user by changing the projected information. Our prototype application implements a two handed technique allowing an industrial designer to digitally airbrush onto an augmented physical model, masking the paint using a virtualized stencil.
Diversity and distribution of culturable lactic acid bacterial species in Indonesian Sayur Asin

Background and Objectives: Lactic acid bacteria (LAB) play important roles in processing of Sayur Asin (spontaneously fermented mustard). Unfortunately, information about LAB in Indonesian Sayur Asin, prepared by traditional manufactures which is important as baseline data for maintenance of food quality and safety, is unclear. The aim of this study was to describe the diversity and distribution of culturable lactic acid bacteria in Sayur Asin of Indonesia. Materials and Methods: Four Sayur Asin samples (fermentation liquor and fermented mustard) were collected at harvesting times (3–7 days after fermentation) from two traditional manufactures in Tulung Agung (TA) and Kediri (KDR), East Java provinces, Indonesia. LAB strains were isolated by using MRS agar method supplemented with 1% CaCO 3 and characterized morphologically. Identification of the strains was performed basedon 16S rDNA analysis and the phylogenetic tree was drawn to understand the phylogenetic relationship of the collected strains. Results: Different profiles were detected in total count of the plates, salinity and pH of fermenting liquor of Sayur Asin in TA and KDR provinces. A total of 172 LAB isolates were successfully isolated and identified based on their 16S rDNA sequences. Phylogenetic analysis of 27 representative LAB strains from Sayur Asin showed that these strains belonged to 5 distinct species namely Lactobacilus farciminis (N=32), L. fermentum (N=4), L. namurensis (N=15), L. plantarum (N=118) and L. parafarraginis (N=1). Strains D5-S-2013 and B4-S-2013 showed a close phylogenetic relationship with L. composti and L. paralimentarius, respectively where as the sequence had slightly lower similarity of lower than 99%, suggesting that they may be classified into novel species and need further investigation due to exhibition of significant differences in their nucleotide sequences. Lactobacillus plantarum was found being dominant in all sayur asin samples. Conclusion: Lactobacilli were recognized as the major group of lactic acid bacteria in Sayur Asin including 5 known and 2 novel candidate species. The distribution of LAB species was associated with the manufactures where Sayur Asin is produced.
Boosting margin based distance functions for clustering

The performance of graph based clustering methods critically depends on the quality of the distance function used to compute similarities between pairs of neighboring nodes. In this paper we learn distance functions by training binary classifiers with margins. The classifiers are defined over the product space of pairs of points and are trained to distinguish whether two points come from the same class or not. The signed margin is used as the distance value. Our main contribution is a distance learning method (DistBoost), which combines boosting hypotheses over the product space with a weak learner based on partitioning the original feature space. Each weak hypothesis is a Gaussian mixture model computed using a semi-supervised constrained EM algorithm, which is trained using both unlabeled and labeled data. We also consider SVM and decision trees boosting as margin based classifiers in the product space. We experimentally compare the margin based distance functions with other existing metric learning methods, and with existing techniques for the direct incorporation of constraints into various clustering algorithms. Clustering performance is measured on some benchmark databases from the UCI repository, a sample from the MNIST database, and a data set of color images of animals. In most cases the DistBoost algorithm significantly and robustly outperformed its competitors.
Alzheimer’s Disease, Oligomers, and Inflammation

The production of soluble amyloid-β oligomers (AβOs) and the activation of inflammation are two important early steps in the pathogenesis of Alzheimer’s disease (AD). The central role of oligomers as responsible for the neuronal dysfunction associated with the clinical features has been extended to the other protein misfolding disorders definable, on this basis, as oligomeropathies. In AD, recent evidence indicates that the mechanism of inflammation as a consequence of neurodegeneration must be assessed in favor of a more direct role of glial activation in the alteration of synaptic function. Our own experimental models demonstrate the efficacy of anti-inflammatory treatments in preventing the cognitive deficits induced acutely by AβOs applied directly in the brain. Moreover, some promising clinical tools are based on immunological activation reducing the presence of cerebral Aβ deposits. However, the strategies based on the control of inflammatory factors as well as the amyloid aggregation show poor or non-therapeutic efficacy. Numerous studies have examined inflammatory factors in biological fluids as possible markers of the neuroinflammation in AD. In some cases, altered levels of cytokines or other inflammatory markers in cerebrospinal fluid correlate with the severity of the disease. Here we propose, according to the precision medicine principles, innovative therapeutic approaches to AD based on the patient’s inflammatory profile/state. The earlier intervention and a multifactor approach are two other elements considered essential to improve the chances of effective therapy in AD.
Transport-domain applications of widely used data sources in the smart transportation: A survey

The rapid growth of population and the permanent increase in the number of vehicles engender several issues in transportation systems, which in turn call for an intelligent and cost-effective approach to resolve the problems in an efficient manner. Smart transportation is a framework that leverages the power of Information and Communication Technology for acquisition, management, and mining of traffic-related data sources, which, in this study, are categorized into: 1) traffic flow sensors, 2) video image processors, 3) probe people and vehicles based on Global Positioning Systems (GPS), mobile phone cellular networks, and Bluetooth, 4) location-based social networks, 5) transit data with the focus on smart cards, and 6) environmental data. For each data source, first, the operational mechanism of the technology for capturing the data is succinctly demonstrated. Secondly, as the most salient feature of this study, the transport-domain applications of each data source that have been conducted by the previous studies are reviewed and classified into the main groups. Thirdly, a number of possible future research directions are provided for all types of data sources. Moreover, in order to alleviate the shortcomings pertaining to each single data source and acquire a better understanding of mobility behavior in transportation systems, the data fusion architectures are introduced to fuse the knowledge learned from a set of heterogeneous but complementary data sources. Finally, we briefly mention the current challenges and their corresponding solutions in the smart transportation.
Heart rate and behavior of fur seals: implications for measurement of field energetics.

Archival data loggers were used to collect information about depth, swimming speed, and heart rate in 23 free-ranging antarctic fur seals. Deployments averaged 9.6 ± 5.6 days (SD) and totaled 191 days of recording. Heart rate averaged 108.7 ± 17.7 beats/min (SD) but varied from 83 to 145 beats/min among animals. Morphometrics explained most variations in heart rate among animals. These interacted with diving activity and swimming speed to produce a complex relationship between heart rate and activity patterns. Heart rate was also correlated with behavior over time lags of several hours. There was significant ( P < 0.05) variation among animals in the degree of diving bradycardia. On average, heart rate declined from 100-130 beats/min before the dive to 70-100 beats/min during submersion. On the basis of the relationship between heart rate and rate of oxygen consumption, the overall metabolic rate was 5.46 ± 1.61 W/kg (SD). Energy expenditure appears to be allocated to different activities within the metabolic scope of individual animals. This highlights the possibility that some activities can be mutually exclusive of one another.
Dose-related effects of GLP-1 on insulin secretion, insulin sensitivity, and glucose effectiveness in mice.

We examined the dose-related net effects of glucagon-like peptide 1 (GLP-1) on insulin secretion, insulin sensitivity, and glucose disposal as derived from the minimal model of glucose disappearance in anesthetized mice. GLP-1 dose dependently potentiated insulin secretion after glucose administration, with the half-maximal effect at 1 nmol/kg. GLP-1 also dose dependently reduced the area under the glucose curve (AUCglucose) and increased the glucose elimination rate (KG) but did not affect the glucose effectiveness (SG). Furthermore, the insulin sensitivity index (SI) was reduced after administration of GLP-1. Because insulin secretion was stimulated to a larger degree than SI was reduced, the peptide increased the global disposition index (GDI = AUCinsulin × SI). Matching plasma insulin levels after GLP-1 by exogenous insulin reproduced the influences of GLP-1 on AUCglucose, KG, SI, and GDI. Finally, the GLP-1 receptor antagonist exendin-3-(9-39) inhibited the actions of GLP-1. We conclude that GLP-1 increases glucose tolerance in the mouse mainly by potently stimulating insulin secretion.
Probabilistic logic learning

The past few years have witnessed an significant interest in probabilistic logic learning, i.e. in research lying at the intersection of probabilistic reasoning, logical representations, and machine learning. A rich variety of different formalisms and learning techniques have been developed. This paper provides an introductory survey and overview of the state-of-the-art in probabilistic logic learning through the identification of a number of important probabilistic, logical and learning concepts.
Effect of a chronic stress on CRF neuronal activity and expression of its type 1 receptor in the rat brain.

The purpose of this study was to compare the effect of an acute versus a chronic immobilization stress on the genetic expression of c- fos and corticotropin-releasing factor type 1 receptor (CRF1receptor) in the paraventricular nucleus (PVN) of the rat hypothalamus. Male Sprague-Dawley rats were exposed to either a single 90-min immobilization stress or the same session for 11 consecutive days. Animals were deeply anesthetized before (control); immediately, 1.5, 3, 6, or 12 h after the acute stress; or after the last session of the repeated exposures to immobilization. Coronal frozen sections (30 μm) of the brains were cut and mRNAs encoding the rat c- fos and CRF1 receptor were assayed by in situ hybridization histochemistry using35S-labeled riboprobes. Localization of these transcripts within PVN CRF-immunoreactive (ir) neurons was also determined. The expression of the mRNA encoding either c- fos or CRF1 receptor was barely detectable to low in the PVN of control animals, but the acute stress session induced a robust signal for both transcripts in this endocrine nucleus. Numerous CRF-ir neurons were positive for the gene encoding either c- fos or CRF1 receptor in the PVN of acutely stressed animals. In contrast, the PVN of chronically stressed animals displayed a significantly lower CRF1 receptor mRNA signal after the last stress session. In these animals, stress-induced transcription of c- fos mRNA occurred in the magnocellular PVN 90 min after the end of the last stress session but only a low signal was detected in the parvocellular division. Moreover, very few CRF-ir neurons of the PVN expressed either the CRF1 receptor or c- fos transcript in chronically stressed rats. These data provide evidence for an adaptive cellular mechanism involving an attenuated action of CRF within the PVN in response to repeated homotypic stress exposures.
Effect of Uniformly Distributed Tangential Follower Force on the Stability of Rotating Cantilever Tube Conveying Fluid

In this paper, the Euler-Bernoulli beam model is used to predict the structural instability of rotating cantilever tubes conveying fluid and subjected to uniform distributed tangential compressive load. The governing equation of motion and boundary conditions of the system are derived using the Hamilton's principle. Then, Galerkin method is applied in order to transform the resulting equation into a general eigenvalue problem. The present analysis is validated by comparing the results with those available in literature. Furthermore, the model is utilized to elucidate the stability characteristics of the system for different conditions.
Effects of sevoflurane pretreatment on the apoptosis of rat H9c2 cardiomyocytes and the expression of GRP78

The protective effect of sevoflurane on apoptosis of rat H9c2 cardiomyocytes induced by H2O2 and the effect on the expression of glucose-regulated protein 78 (GRP78) were investigated. H9c2 cells were routinely cultured and divided into the control, model and sevoflurane groups. Cells in the model group were treated with 400 µM H2O2, and cells in the sevoflurane group were pretreated with sevoflurane prior to treatment with 400 µM H2O2. MTT assay was used to assess cell viability. Annexin V-propidium iodide (AV-PI) double staining flow cytometry was used to detect apoptosis. The intracellular free Ca2+ concentration was measured by the fluorescence-based assay using Fluo-3 AM as a calcium ion fluorescence probe. The mRNA expression level of GRP78 and protein expression levels of GRP78, CHOP and caspase-12 were measured using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and western blot analysis, respectively. The assays showed that after sevoflurane pretreatment the H9c2 cell viability was significantly increased, whereas the H2O2-induced apoptosis, intracellular Ca2+ concentration, mRNA expression of GRP78, and the protein expression of GRP78, CHOP and caspase-12 were all reduced. The results show that pretreatment with sevoflurane inhibited H2O2-induced apoptosis in H9c2 cells. The mechanism may be related to inhibition of the stress-related protein GRP78 expression in endoplasmic reticulum, resulting in decreased intracellular Ca2+ concentration and the downregulation of CHOP and caspase-12 expression levels.
The Ferrety algorithm for the KDD Cup 2005 problem

In this paper, we present a general solution for the KDD Cup 2005 problem. It uses the Internet as source of knowledge and extends it to categorize very short (less than 5 words) documents with reasonable accuracy. Our approach consists of three main parts: i. ) a central knowledge filter ii. ) an on-demand web crawler and iii. ) a very efficient categorizer system. Our solution obtained Creativity and Precision Runner-up Awards at the competition. The main idea of Ferrety Algorithm can be generalized for mapping one taxonomy to another if training documents are available.
Automatic delineation of white matter fascicles by localization based upon anatomical spatial relationships

Delineation of white matter fascicles is generally achieved with tractography by specifying seeding and exclusion regions of interest (ROIs) defined by anatomical landmarks. In practice, the most popular approach has been to manually draw the ROIs for each scan which requires extensive training, is strongly subject to inter- and intra-expert variability and is highly time consuming. Fully automatic localization of the ROIs is of central interest, particularly for white matter investigations involving a large number of subjects. In this work, we propose an original approach in which the ROIs are localized using the fuzzy set theory by discovering stable anatomical spatial relationships in the brain anatomy. Our approach relies on a learning procedure, in which stable relationships are identified from a limited number of training templates supplied with manually delineated ROIs. For a new subject, the spatial relationships are applied and the ROIs localized. We show that our approach enables successful automatic delineation of the ROIs in the individual. Importantly, we show that this localization is robust across subjects age.
SHREC 2010: robust large-scale shape retrieval benchmark

SHREC’10 robust large-scale shape retrieval benchmark simulates a retrieval scenario, in which the queries include multiple modifications and transformations of the same shape. The benchmark allows evaluating how algorithms cope with certain classes of transformations and what is the strength of the transformations that can be dealt with. The present paper is a report of the SHREC’10 robust large-scale shape retrieval benchmark results.
The Association between Intelligence Scores and Family History of Psychiatric Disorder in Schizophrenia Patients, Their Siblings and Healthy Controls

Background The degree of intellectual impairment in schizophrenia patients and their relatives has been suggested to be associated with the degree of familial loading for schizophrenia. Since other psychiatric disorders are also more present in relatives of schizophrenia patients, the definition of family history should be broadened. The association between family history for psychiatric disorder and intelligence scores was investigated in patients with non-affective psychosis, their unaffected siblings and controls. Methods A sample of 712 schizophrenia proband families (696 patients and 766 siblings) and 427 healthy control families (517 subjects) participated in this study. Family history of psychiatric disorder was determined while excluding the data of the participating schizophrenia patient. A dichotomous division was made between families with no first- or second degree relative with psychiatric disorder and families with one or more affected relatives. Total intelligence scores were estimated by admission of the short form of the Wechsler Adult Intelligence Scale III. Results A significant interaction was found between family history of psychiatric disorder and clinical status (F(2,1086.87)= 4.17; p=. 016). Patients with a positive family history of psychiatric disorder obtained higher intelligence scores compared to patients with no family history (mean IQ scores are 95.52 and 92.72) with an opposite effect in controls (mean IQ scores are 108.71 and 111.19). No significant difference was found between siblings of schizophrenia patients with or without a positive family history (mean IQ scores are 102.98 and 103.24). Conclusion In patients with schizophrenia, a negative family history of psychiatric disorder was associated with relatively low IQ suggesting that the etiology in these patients may involve environmental or genetic factors which are unique to the patient and are not observed in other relatives. Possible factors include severe environmental stressors containing premature birth or brain injury and genetic factors (e.g de novo Copy Number Variants).