Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimal decision-making with time-varying evidence reliability

Previous theoretical and experimental work on optimal decision-making was restricted to the artificial setting of a reliability of the momentary sensory evidence that remained constant within single trials. The work presented here describes the computation and characterization of optimal decision-making in the more realistic case of an evidence reliability that varies across time even within a trial. It shows that, in this case, the optimal behavior is determined by a bound in the decision maker's belief that depends only on the current, but not the past, reliability. We furthermore demonstrate that simpler heuristics fail to match the optimal performance for certain characteristics of the process that determines the time-course of this reliability, causing a drop in reward rate by more than 50%.
Circularly polarized implanted antenna with conical bio-metallic ground plane

A circularly polarized implanted antenna is designed and numerically analyzed for in-body communication. The turn-style like antenna consists of two orthogonal conformal dipoles located on the bone which contains a conical implant made up by a bio-metallic alloy. The return losses at the central frequency of the Industrial, Scientific and Medical (ISM) band (i.e., ƒ=2.45 GHz) of the two dipoles in stand-alone configurations are −46.1 dB and −57.9 dB, respectively. When both radiators are present to generate a circular polarized radiated field, the dimensions of the dipoles have been redesigned to get resonance close to 2.45 GHz. Numerical results show that circular polarization can be achieved in an angular range of 163° × 23°.
Autoaggregation of Lactobacillus reuteri is mediated by a putative DEAD‐box helicase

We have cloned and sequenced a gene from Lactobacillus reuteri that encodes a 56 kDa protein, which mediates autoaggregation of the bacteria. Using an antiserum raised against extracellular proteins from the pig intestinal isolate L. reuteri 1063, we screened a genomic λ library derived from the same strain. Affinity purification of recombinant protein from the isolated λ clones showed that one type of clone expressed a protein that efficiently aggregated the parental strain when added to the bacteria. Subcloning and introduction of the corresponding gene, here denoted aggHinto the L. reuteri type strain markedly enhanced aggregation. Furthermore, insertional inactivation of aggH in strain 1063 resulted in an autoaggregation‐deficient phenotype. Finally, an affinity‐purified and cleaved fusion of AggH protein and the maltose‐binding protein, MBP, strongly promoted aggregation of L. reuteri 1063, whereas the uncleaved fusion protein was inactive. Sequencing of aggH revealed that the corresponding protein has extensive sequence homology to the large family of ATP‐dependent DEAD‐box helicases. These results are intriguing in view of earlier data on the promotion of genetic exchange in Lactobacillus by aggregation.
Helicobacter pylori eradication for Parkinson's disease.

BACKGROUND Levodopa is the mainstay of treatment for alleviating the motor symptoms associated with Parkinson's disease. However, patients often experience fluctuations in their symptoms over time and 'wearing off' which may be partly related to variable absorption of the drug. There is some evidence that treatment of the common gastrointestinal infection Helicobacter pylori (H pylori) with antibiotics may improve levodopa absorption in the gut and hence improve symptoms. OBJECTIVES 1) What is the prevalence of H pylori in Parkinson's disease patients? 2) Does treatment of H pylori infection with antibiotics improve symptoms in Parkinson's disease patients? Is this effect dependent on improvements in the absorption of levodopa? SEARCH METHODS We searched electronic databases (including CENTRAL, MEDLINE, EMBASE, PsycINFO and CINAHL) and trial registers, handsearched conference proceedings and carried out citation searching on key articles. All searching was updated in August 2009. We contacted authors to provide additional information where necessary. SELECTION CRITERIA Clinical trials in patients with a well-defined definition of Parkinson's disease and who were H pylori-positive. Two people independently selected studies for inclusion using predetermined criteria. We used recruitment figures from clinical trials and other studies identified from the searching to determine the prevalence of H pylori in Parkinson's disease. DATA COLLECTION AND ANALYSIS Two authors abstracted data from the source papers and assessed methodological quality independently. We presented results descriptively. MAIN RESULTS Two completed and one ongoing clinical trial met the inclusion criteria. One trial (34 patients randomised) examined the effects of H pylori eradication on levodopa absorption and motor symptoms and found significant improvements in both. The ongoing trial has similar objectives and aims to recruit 100 patients. The other completed trial (20 patients analysed) sought to find a causal link between infection with H pylori and Parkinsonism and was non-contributory. A worsening of symptoms was noted with eradication failure.The prevalence of H pylori in Parkinson's disease was reported in four studies and ranged from 37% to 59% which is similar to that of the general population. AUTHORS' CONCLUSIONS There is currently a lack of evidence on the effects of screening and treating H pylori in patients with Parkinson's disease. There is limited evidence to suggest that H Pylori eradication improves the absorption of levodopa and improves motor symptoms. Results from an ongoing trial will inform the evidence base and will be incorporated in an update of this review. There is a need for well-conducted randomised controlled trials with standard outcome measures for motor symptoms and incorporating the costs of screening and treatment.
Dendritic development of hippocampal CA1 pyramidal cells in a neonatal hypoxia–ischemia injury model

It is believed that neonatal hypoxia–ischemia (HI) brain injury causes neuron loss and brain functional defects. However, the effect of HI brain injury on dendritic development of the remaining pyramidal cells of the hippocampus and the reaction of contralateral hippocampal neurons require further studies. The Morris water maze and Golgi–Cox staining were used to evaluate the learning and memory and dendritic morphology of pyramidal cells. The results of Golgi–Cox staining showed CA1 pyramidal neurons of HI injury models with fewer bifurcations and shorter dendrite length than the naive control group. The density of dendritic spines of hippocampal CA1 pyramidal neurons was significantly lower in the HI brain injury group than in controls. With respect to hippocampal function, the HI brain injury group presented cognitive deficits in the reference memory task and probe trail. In the HI group, the pyramidal cells of left hippocampus that did not experienced ischemia but did experience hypoxia had more complex dendrites and higher density of spine than the HI injury side and control. The functional implementation of injured hippocampus might depend mainly on the hypertrophy of contralateral hippocampus after HI brain injury. Corticosterone can partially prevent the hippocampal pyramidal cells from HI injury and reduce the difference of the bilateral hippocampus pyramidal cells, but there was no improvement in learning and memory. © 2013 Wiley Periodicals, Inc.
Global nutrient profiling by Phenotype MicroArrays: a tool complementing genomic and proteomic studies in conidial fungi

Conidial fungi or molds and mildews are widely used in modern biotechnology as producers of antibiotics and other secondary metabolites, industrially important enzymes, chemicals and food. They are also important pathogens of animals including humans and agricultural crops. These various applications and extremely versatile natural phenotypes have led to the constantly growing list of complete genomes which are now available. Functional genomics and proteomics widely exploit the genomic information to study the cell-wide impact of altered genes on the phenotype of an organism and its function. This allows for global analysis of the information flow from DNA to RNA to protein, but it is usually not sufficient for the description of the global phenotype of an organism. More recently, Phenotype MicroArray (PM) technology has been introduced as a tool to characterize the metabolism of a (wild) fungal strain or a mutant. In this article, we review the background of PM applications for fungi and the methodic requirements to obtain reliable results. We also report examples of the versatility of this tool.
Interfirm IT Capability Profiles and Communications for Cocreating Relational Value: Evidence from the Logistics Industry

This study seeks to identify the means by which information technology helps cocreate relational value in the context of interfirm relationships in the logistics industry--a large and information-intensive industry. We identify a set of IT functionalities--single-location shipping, multilocation shipping, supply chain visibility, and financial settlement--that can be used to manage the flows of physical goods, information, and finances across locations in interfirm logistics processes. Progressively more advanced sets of IT functionalities, when implemented and used in the interfirm relationship to execute logistics processes, are proposed to form four distinct IT capability profiles of increased sophistication. Interfirm IT capability profiles of higher sophistication are proposed to help cocreate greater relational value by facilitating the flows of physical goods, information, and finances across locations in the interfirm logistics process. Besides their direct role in helping cocreate relational value, these interfirm IT capability profiles are proposed to further enhance relational value cocreation when complemented by interfirm communications for business development and IT development. Our empirical study was situated in one of the world's largest logistics suppliers and over 2,000 of its interfirm relationships with buyers across industries. Integrated data from four archival sources on the IT functionalities implemented and used in interfirm logistics relationships, interfirm communications, relational value (share of wallet and loyalty), and multiple control variables were collected. The results show that the proposed interfirm IT capability profiles and interfirm communications have both a direct and an interaction effect on relational value. Implications for cocreating relational value in interfirm relationships with the aid of IT are discussed.
Ectoparasites of Rodents Captured in Bandar Abbas, Southern Iran

Background: Rodents play important role as host of ectoparasites and reservoir of different zoonotic diseases. The aim of this study was to asses the infestation of commensal rodents with ectoparasites in Bandar Abbas, a port city located in the northern part of the Persian Gulf in Iran. Methods: Rodents were captured using live traps during the study period in year 2007. After transferring the rodents to the laboratory, they were identified and then their ectoparasites were collected and mounted for species identification using appropriate systematic keys. Results: A total of 77 rodents were identified including Rattus norvegicus (74%), R. rattus (16.9%), Mus musculus (7.8%) and one hamster. Among all rodents, 40.3% were found infested with ectoparasites. A total of 69 ectoparasites were collected comprising flea, lice, mite and tick. Two species of fleas; Xenopsylla cheopis and X. astia were identified with higher index of X. astia. Two genera of ticks including Hyalomma sp. and Rhipicephalus sp. were identified. Laelaps nuttalli was the only mite found. The Polyplax spinulosa was considered as lice ectoparasite. Conclusion: Among all arthropods collected, flea and lice had the most and the least frequency, respectively. Nearly all rodent species were infested with Xenopsylla. These fleas are important due to their role in plague and murine typhus transmission. Ticks are important due to their role in CCHF (Crimean-Congo Hemorrhagic Fever), theileriosis, babesiosis, anaplasmosis and ehrlichiosis transmission . Monitoring of ectoparaiste infestation is important for preparedness and early warning preparation for possible control of arthropod-borne diseases.
Comparative Proteomic Analysis Reveals Proteins Putatively Involved in Toxin Biosynthesis in the Marine Dinoflagellate Alexandrium catenella

Alexandrium is a neurotoxin-producing dinoflagellate genus resulting in paralytic shellfish poisonings around the world. However, little is known about the toxin biosynthesis mechanism in Alexandrium. This study compared protein profiles of A. catenella collected at different toxin biosynthesis stages (non-toxin synthesis, initial toxin synthesis and toxin synthesizing) coupled with the cell cycle, and identified differentially expressed proteins using 2-DE and MALDI-TOF-TOF mass spectrometry. The results showed that toxin biosynthesis of A. catenella occurred within a defined time frame in the G1 phase of the cell cycle. Proteomic analysis indicated that 102 protein spots altered significantly in abundance (P < 0.05), and 53 proteins were identified using database searching. These proteins were involved in a variety of biological processes, i.e., protein modification and biosynthesis, metabolism, cell division, oxidative stress, transport, signal transduction, and translation. Among them, nine proteins with known functions in paralytic shellfish toxin-producing cyanobacteria, i.e., methionine S-adenosyltransferase, chloroplast ferredoxin-NADP+ reductase, S-adenosylhomocysteinase, adenosylhomocysteinase, ornithine carbamoyltransferase, inorganic pyrophosphatase, sulfotransferase (similar to), alcohol dehydrogenase and arginine deiminase, varied significantly at different toxin biosynthesis stages and formed an interaction network, indicating that they might be involved in toxin biosynthesis in A. catenella. This study is the first step in the dissection of the behavior of the A. catenella proteome during different toxin biosynthesis stages and provides new insights into toxin biosynthesis in dinoflagellates.
Less is More: Selecting Sources Wisely for Integration

We are often thrilled by the abundance of information surrounding us and wish to integrate data from as many sources as possible. However, understanding, analyzing, and using these data are often hard. Too much data can introduce a huge integration cost, such as expenses for purchasing data and resources for integration and cleaning. Furthermore, including low-quality data can even deteriorate the quality of integration results instead of bringing the desired quality gain. Thus, "the more the better" does not always hold for data integration and often "less is more". In this paper, we study how to select a subset of sources before integration such that we can balance the quality of integrated data and integration cost. Inspired by the Marginalism principle in economic theory, we wish to integrate a new source only if its marginal gain, often a function of improved integration quality, is higher than the marginal cost, associated with data-purchase expense and integration resources. As a first step towards this goal, we focus on data fusion tasks, where the goal is to resolve conflicts from different sources. We propose a randomized solution for selecting sources for fusion and show empirically its effectiveness and scalability on both real-world data and synthetic data.
On the Driven Inverted Pendulum

We explore the solutions of the driven inverted pendulum system l\#0308\=gsinφ-al(t)cosτ where al(·) is a bounded lateral acceleration. We show that, for lateral accelerations that are constant before some initial time, an inverted trajectory always exists and remains within a diamond shaped region in the state space. Functional analytic techniques are also developed to provide further insight into the nature of the inverted pendulum trajectories. Associated to the driven inverted pendulum is a time varying linear system. We show that this system always possesses an exponential dichotomy, allowing for the development of a successive approximation algorithm for finding the desired inverted pendulum trajectory. We show that the curve obtained from one iteration of this algorithm is a very good estimate of the required inverted trajectory. As that curve is obtained by filtering the quasi-static angle trajectory by a noncausal time varying low pass filter with weighting function with a shape similar to h(t) = exp−α0|t|, we find that the current pendulum angle is influenced by the values of the lateral acceleration within only a few seconds of the current time. These results are important as the driven inverted pendulum is a common susbsystem in systems ranging from motorcycles and bicycles to rockets and aircaft.
Approximating functions using rough sets

Approximating of functions that are specified using imperfect knowledge is one of the central issues of many areas such as machine learning, pattern recognition, data mining, or qualitative reasoning. However, we do not have yet satisfactory methods for approximation of functions and developed calculi on function approximations. In the paper we discuss a function approximation using the rough set approach. The main difference with the existing approaches in rough set theory is based on modification of the inclusion measure. This makes it possible to overcome some drawbacks of the previously used definitions. For applications it is important to develop rough measures on approximated objects, in particular on function approximations. The modified inclusion measure is also used to define an exemplary measure, i.e., the rough integral.
Quantitative Detection of Chlamydia psittaci and C. pecorum by High-Sensitivity Real-Time PCR Reveals High Prevalence of Vaginal Infection in Cattle

ABSTRACT Bovine vaginal cytobrush specimens were analyzed for the presence of Chlamydia spp. by a high-sensitivity, high-specificity quantitative PCR. The 53% prevalence of low-level Chlamydia psittaci and C. pecorum genital infection detected in virgin heifers suggests predominantely extragenital transmission of Chlamydia in cattle and conforms to the high seroprevalence of anti-Chlamydia antibodies.
Brain metabolic alterations in medication-free patients with bipolar disorder.

BACKGROUND Bipolar disorder (BD) has substantial morbidity and incompletely understood neurobiological underpinnings. OBJECTIVE To investigate brain chemistry in medication-free individuals with BD. DESIGN Two-dimensional proton echo-planar spectroscopic imaging (PEPSI) (32 x 32, 1-cm(3) voxel matrix) acquired axially through the cingulate gyrus was used to quantify regional brain chemistry. SETTING The Center for Anxiety and Depression at the University of Washington in Seattle and the Bipolar Research Programs at McLean Hospital and the Massachusetts General Hospital in Boston. PARTICIPANTS Thirty-two medication-free outpatients with a diagnosis of BD type I (BDI) or BD type II (BDII), predominantly in a depressed or mixed-mood state, were compared with 26 age- and sex-matched healthy controls. MAIN OUTCOME MEASURES Tissue type (white and gray) and regional analyses were performed to evaluate distribution of lactate; glutamate, glutamine, and gamma-aminobutyric acid (Glx); creatine and phosphocreatine (Cre); choline-containing compounds (Cho); N-acetyl aspartate; and myo-inositol. Chemical relationships for diagnosis and mood state were evaluated. RESULTS Patients with BD exhibited elevated gray matter lactate (P =.005) and Glx (P =.007) levels; other gray and white matter chemical measures were not significantly different between diagnostic groups. Isolated regional chemical alterations were found. An inverse correlation between 17-item Hamilton Depression Rating Scale scores and white matter Cre levels was observed for BD patients. CONCLUSIONS Gray matter lactate and Glx elevations in medication-free BD patients suggest a shift in energy redox state from oxidative phosphorylation toward glycolysis. The possibility of mitochondrial alterations underlying these findings is discussed and may provide a theoretical framework for future targeted treatment interventions.
Decoding of emotional components in complex communicative situations (irony) and its relation to empathic abilities in male chronic alcoholics: an issue for treatment.

BACKGROUND Previous research has shown that deficits in the domain of emotions strongly characterize alcoholism. Patients diagnosed with alcoholism show impairments in emotional mimic recognition, as well as in the domain of emotional prosody. These data suggest that male alcoholics might suffer from a generalized emotional impairment associated with dysfunctions in empathy. Taken altogether, those deficits might influence alcoholics' relational domain and their performance in complex communicative situations such as ironic interactions. The present study investigates the ability of chronic male alcoholics to recognize the emotional component of ironic contexts and its relation to the comprehension of ironic meaning as a function of their empathic abilities. METHODS Forty-four male subjects participated in a story comprehension task. They were asked to read stories with either an ironic or a nonironic ending. Participants were asked to fill in a questionnaire about communicative intentions and the emotional states of the stories' characters. Moreover, the correct comprehension of the ironic meaning was assessed through a self-reported questionnaire and related to the empathy quotient (EQ) which was measured in a preexperimental phase. RESULTS Alcoholic subjects showed a lower EQ in comparison to healthy subjects and recognized significant fewer ironic endings. Social skills results were particularly impaired. The correlation between EQ and ironic endings recognition was significant. Moreover, alcoholics showed a tendency to attribute positive emotions to both ironic and nonironic contexts, showing an opposite pattern in comparison with control subjects who tended to associate negative emotions to ironic contexts. CONCLUSIONS The present study indicates that emotional recognition deficits that have been previously observed in chronic alcoholics extend to complex interactive contexts. This deficit is associated with a more general impairment of empathy, especially in its social skill component. Clinical implications of the present results are discussed.
ProbFuse: a probabilistic approach to data fusion

Data fusion is the combination of the results of independent searches on a document collection into one single output result set. It has been shown in the past that this can greatly improve retrieval effectiveness over that of the individual results.This paper presents probFuse, a probabilistic approach to data fusion. ProbFuse assumes that the performance of the individual input systems on a number of training queries is indicative of their future performance. The fused result set is based on probabilities of relevance calculated during this training process. Retrieval experiments using data from the TREC ad hoc collection demonstrate that probFuse achieves results superior to that of the popular CombMNZ fusion algorithm.