Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of bacterial populations of the pig cecum and colon based upon enumeration with specific energy sources

Concentrations of bacteria in the ceca and colons of pigs were measured by determinations of colony counts on rumen fluid-based media in anaerobic roll tubes. With our most complete medium (medium CCA), the mean colony count of cecal samples from 20 pigs was 2.37 X 10(10) +/- 1.0 X 10(10) (+/- standard deviation)/g (wet weight). The mean number of bacteria attached to or associated with cecal epithelial tissues from three pigs on medium CCA was 2.67 X 10(7) +/- 0.81 X 10(7)/cm2 of tissue. The proportions of gut bacterial populations able to use various energy substrates were estimated on the basis of relative colony counts. The following substrates are listed in descending order of their capacity to support growth of cecal bacteria: glucose, starch, cellobiose, xylose, Trypticase, gastric mucin from swine, mannitol, glycerol, and lactate. The effect of diet upon this distribution was not examined. The relative proportions of bacteria from a given population that were able to grow on various selective media were used as population profiles. Comparisons of populations in this way indicated that differences could be detected between (i) populations from the cecum of littermate pigs, (ii) populations from the cecum and colon of the same pig, and (iii) populations in the lumen of the cecum as compared with populations associated with cecal mucosa.
Characteristics of epilepsy and immunological markers in epileptic patients after infl uenza- associated encephalopathy

Objective: This study aimed to elucidate the electro-clinical characteristics of epilepsy and immunological markers in patients with epilepsy after infl uenza-associated encephalopathy/encephalitis (IAE). Methods: Eighteen patients with epilepsy after IAE (8 males, 10 females; mean age of onset 6.4±6.4 years) were studied. Antibodies to glutamate receptor (GluR) e2 (NR2B) were examined by immunoblot and ELISA. Cytokines were measured by BioPlex. Results: Mean interval between IAE and epilepsy onset was 63.2 ± 95.0 days (mean ± SD). In 16 of 18 patients, complex partial seizures were observed. Most complex partial seizures were of short durations and showed few lateralizing signs. Interictal discharges were seen in the frontal area in 7 of 14 patients. Ictal EEG showed rapid propagation to bilateral hemispheres. Patients with higher cerebrospinal fl uid levels of anti-GluRe2 antibodies, higher cerebrospinal fl uid levels of IL-1β, soluble tumor necrosis factor receptor 1 and IFN-γ during chronic stage, had higher frequency of epileptic seizures. Conclusion: This study indicates that the frontal lobes are susceptible to rapid epileptogenesis after IAE, and that epileptic partial seizures after IAE had characteristics resembling generalized seizures. Presence of anti-GluRe2 antibodies and elevated IL-1β, TNFα, and IFN-γ in cerebrospinal fl uid may be associated with intractability of epileptic seizures.
Reproducibility and Relative Validity of a Short Food Frequency Questionnaire in 9–10 Year-Old Children

The aim of this study was to assess the reproducibility and validity of a non-quantitative 28-item food frequency questionnaire (FFQ). Children aged 9–10 years (n = 50) from three schools in Dunedin, New Zealand, completed the FFQ twice and a four-day estimated food diary (4DEFD) over a two-week period. Intraclass correlation coefficients (ICC) and Spearman’s correlation coefficients (SCC) were used to determine reproducibility and validity of the FFQ, respectively. Weekly intakes were estimated for each food item and aggregated into 23 food items/groups. More than half of the food items/groups (52.2%) had an ICC ≥0.5. The median SCC between FFQ administrations was 0.66 (ranging from 0.40 for processed meat to 0.82 for sweets and non-dairy drinks). Cross-classification analysis between the first FFQ and 4DEFD for ranking participants into thirds showed that breakfast cereals had the highest agreement (54.0%) and pasta the lowest (34.0%). In validity analyses, 70% of food items/groups had a SCC ≥0.3. Results indicate that the FFQ is a useful tool for ranking children according to food items/groups intake. The low respondent burden and relative simplicity of the FFQ makes it suitable for use in large cohort studies of 9–10 year-old children in New Zealand.
Wikipedia Page View Reflects Web Search Trend

The frequency of a web search keyword generally reflects the degree of public interest in a particular subject matter. Search logs are therefore useful resources for trend analysis. However, access to search logs is typically restricted to search engine providers. In this paper, we investigate whether search frequency can be estimated from a different resource such as Wikipedia page views of open data. We found frequently searched keywords to have remarkably high correlations with Wikipedia page views. This suggests that Wikipedia page views can be an effective tool for determining popular global web search trends.
Implementation of Two Dimensional Discrete Cosine Transform Using Field Programmable Gate Array PUNYA THITIMAJSHIMA

Abstract : This paper presents an architectural design of two-dimensional discrete cosine transform for implementation using FPGA. The technique consists of separating two-dimension transform into a cascade of one-dimension transform. Then, the number of multiplications is reduced by taking into account the redundancy of calculations. A hardware architecture of such an algorithm is proposed. It requires only 12 multipliers for one dimensional transform. A software simulation of this architecture comparing to the direct transform illustrates the usefulness of the proposed design.
Stress assessment using hair cortisol of kangaroos affected by the lumpy jaw disease

The aim of this study was to objectively assess stress of kangaroos affected by lumpy jaw disease (LJD) using plasma and hair cortisol concentrations. The plasma and hair samples were collected from kangaroos with LJD and healthy controls. Collected hair samples were extracted with methanol after washing with isopropanol, following which they were processed with the cortisol enzyme immunoassay kit. The plasma cortisol concentration of LJD animals tended to be higher than that of the control. Ventral hair cortisol, but not dorsal hair, of LJD animals was significantly higher than that of the control. In conclusion, stress in kangaroos infected with LJD could be assessed by measuring ventral hair cortisol.
Learning Temporal Dynamics of Behavior Propagation in Social Networks

Social influence has been widely accepted to explain people's cascade behaviors and further utilized in many related applications. However, few of existing work studied the direct, microscopic and temporal impact of social influence on people's behaviors in detail. In this paper we concentrate on the behavior modeling and systematically formulate the family of behavior propagation models (BPMs) including the static models (BP and IBP), and their discrete temporal variants (DBP and DIBP). To address the temporal dynamics of behavior propagation over continuous time, we propose a continuous temporal interest-aware behavior propagation model, called CIBP. As a new member of the BPM family, CIBP exploits the continuous-temporal functions (CTFs) to model the fully-continuous dynamic variance of social influence over time. Experiments on real-world datasets evaluated the family of BPMs and demonstrated the effectiveness of our proposed approach.
Simplified Analytical Optimization and Comparison of Torque Densities Between Electrically Excited and Permanent-Magnet Machines

This paper presents the simplified analytical optimization and comparison between electrically excited (EE) and permanent-magnet (PM) machines in terms of torque per volume T/V and torque per weight T/G for low-speed applications when their copper loss and overall size are the same. Analytical torque models for both machines are individually developed and optimized to obtain the optimal flux density ratio, split ratio, and maximum torque densities. Furthermore, the variation of optima with the number of poles and machine size is also investigated. The analytical analyses are validated by both finite-element analyses and experiments. It is concluded that torque densities of PM machines can be more than √2 times higher than those of EE machines. For EE machines, there is an optimal pole number to maximize torque densities, and large volume applications are preferred. In actual applications, EE machines are more likely to compromise the torque density to meet the thermal constraints. It also shows that the optimal T/G designs have significantly higher split ratio and are more cost- and weight-effective than the optimal T/V designs.
Response to acetylcholine and nicotine of the perfused vessels of the rabbit ear

1 The vessels of the isolated rabbit ear were perfused at 23 mbar with Krebs solution with (tonic) and without (atonic) noradrenaline (5.9 × 10−7M) at selected temperatures of 20°–38° C. Peripheral resistance units (PRU) were calculated from the observed peak flow rates and alterations caused by drugs expressed as Δ% PRU. 2 ACh is constrictor in the atonic vessel. 3 ACh is a vasodilator of the tonic vessel perfused with NA. This effect is potentiated by anticholinesterase and by denervation, unaffected by botulinum toxin and antagonized by atropine. ACh also dilates the vessel perfused with vasopressin. 4 Increasing the temperature reduces the responses to ACh but increases the effect of anticholinesterase. 5 Nicotine causes a dose dependent dilatation of the tonic vessels, reduced but not abolished by C6, by atropine, by botulinum toxin and by denervation. 6 Nicotine causes a dose dependent constriction of the atonic vessels, abolished by C6 and by phentolamine, reduced by denervation, but unaffected by botulinum toxin.
Performance Diagnosis Using Bigtable Monitoring for Cloud Computing System

Reduplication services are allocated in individual physical nodes in the cloud. They can be amassed into various types of services, serving large amount of user requests. The existing diagnosis techniques for such distributed systems can't effectively solve. In fine-grained performance abnormality is still lacking. Production cloud systems should be completely unaided. CloudDiag systematically collects the point-to-point tracking data from each physical node in the cloud and classifies into different categories according to call tree. It then employs a customized Map-Reduce algorithm to proactively analyze the tracing data. Specifically, it assembles the tracing data of each user request, and classifies the tracing data into different categories according to call trees of the requests.
Glucose metabolism in patients with schizophrenia treated with olanzapine or quetiapine: a frequently sampled intravenous glucose tolerance test and minimal model analysis.

OBJECTIVE Clozapine and olanzapine treatment has been associated with insulin resistance in non-obese schizophrenia patients. Much less is known regarding other agents such as quetiapine. The objective of this study was to compare matched olanzapine- and quetiapine-treated schizophrenia patients and normal controls on measures of glucose metabolism. METHOD A cross-sectional comparison of quetiapine-treated and olanzapine-treated non-obese (body mass index < 30.0 kg/m2) schizophrenia subjects (DSM-IV) with matched normal controls using a frequently sampled intravenous glucose tolerance test and nutritional assessment was conducted from April 2002 to October 2004. Data from 24 subjects were included in the analysis (7 quetiapine, 8 olanzapine, 9 normal controls). RESULTS There was a significant difference among groups for fasting baseline plasma glucose concentrations (p = .02), with olanzapine greater than normal controls (p = .01). The insulin sensitivity index (SI) differed significantly among groups (p = .039); olanzapine subjects exhibited significant insulin resistance compared to normal controls (p = .01), but there was no significant difference for quetiapine versus olanzapine (p = .1) or quetiapine versus normal controls (p = .40). SI inversely correlated with quetiapine dose (p = .0001) and waist circumference (p = .03) in quetiapine-treated subjects. Insulin resistance calculated by the homeostasis model assessment of insulin resistance (HOMA-IR) also differed significantly among groups (p = .03). The olanzapine group had a higher HOMA-IR level than normal controls (p = .01). There was a significant difference in glucose effectiveness (SG) among the groups (p = .049). SG was lower in the olanzapine group than in the quetiapine group (p = .03) and in the olanzapine group compared to normal controls (p = .049). CONCLUSIONS Our findings are consistent with our previous report that nonobese olanzapine-treated subjects showed insulin resistance, measured by both HOMA-IR and SI, and reduction in SG. Studies that include larger samples, unmedicated patients, and varying durations of antipsychotic exposure are necessary to confirm these results.
A Corpus for Cross-Document Co-reference

This paper describes a newly created text corpus of news articles that has been annotated for cross-document co-reference. Being able to robustly resolve references to entities across document boundaries will provide a useful capability for a variety of tasks, ranging from practical information retrieval applications to challenging research in information extraction and natural language understanding. This annotated corpus is intended to encourage the development of systems that can more accurately address this problem. A manual annotation tool was developed that allowed the complete corpus to be searched for likely co-referring entity mentions. This corpus of 257K words links mentions of co-referent people, locations and organizations (subject to some additional constraints). Each of the documents had already been annotated for within-document co-reference by the LDC as part of the ACE series of evaluations. The annotation process was bootstrapped with a string-matching-based linking procedure, and we report on some of initial experimentation with the data. The cross-document linking information will be made publicly available.
A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes

Motivation Next generation sequencing technologies have provided us with a wealth of information on genetic variation, but predicting the functional significance of this variation is a difficult task. While many comparative genomics studies have focused on gene flux and large scale changes, relatively little attention has been paid to quantifying the effects of single nucleotide polymorphisms and indels on protein function, particularly in bacterial genomics. Results We present a hidden Markov model based approach we call delta-bitscore (DBS) for identifying orthologous proteins that have diverged at the amino acid sequence level in a way that is likely to impact biological function. We benchmark this approach with several widely used datasets and apply it to a proof-of-concept study of orthologous proteomes in an investigation of host adaptation in Salmonella enterica. We highlight the value of the method in identifying functional divergence of genes, and suggest that this tool may be a better approach than the commonly used dN/dS metric for identifying functionally significant genetic changes occurring in recently diverged organisms. Availability A program implementing DBS for pairwise genome comparisons is freely available at: https://github.com/UCanCompBio/deltaBS. Contact nicole.wheeler@pg.canterbury. ac.nz, lars.barquist@uni-wuerzburg.de Supplementary information Supplementary data are available at BioRxiv online.
Correct-by-Construction Concurrency: Using Dependent Types to Verify Implementations of Effectful Resource Usage Protocols

In the modern, multi-threaded, multi-core programming environment, correctly managing system resources, including locks and shared variables, can be especially difficult and errorprone. A simple mistake, such as forgetting to release a lock, can have major consequences on the correct operation of a program, by, for example, inducing deadlock, often at a time and location that is isolated from the original error. In this paper, we propose a new type-based approach to resource management, based on the use of dependent types to construct a Domain-Specific Embedded Language (DSEL) whose typing rules directly enforce the formal program properties that we require. In this way, we ensure strong static guarantees of correctness-by-construction, without requiring the development of a new special-purpose type system or the associated special-purpose soundness proofs. We also reduce the need for “over-serialisation”, the overly-conservative use of locks that often occurs in manually constructed software, where formal guarantees cannot be exploited. We illustrate our approach by implementing a DSEL for concurrent programming and demonstrate its applicability with reference to an example based on simple bank account transactions.
SPEAKERS ARE HONEST BECAUSE HEARERS ARE VIGILANT REPLY TO KOURKEN MICHAELIAN1

Abstract In ‘The Evolution of Testimony: Receiver Vigilance, Speaker Honesty and the Reliability of Communication,’ Kourken Michaelian questions the basic tenets of our article ‘Epistemic Vigilance’ (Sperber et al. 2010). Here I defend against Michaelian's criticisms the view that epistemic vigilance plays a major role in explaining the evolutionary stability of communication and that the honesty of speakers and the reliability of their testimony are, to a large extent, an effect of hearers' vigilance.
Increased Risk of Cutaneous Melanoma Associated with p53 Arg72Pro Polymorphism

Objective The objective of this study was to test the hypothesis that p53 Arg72Pro polymorphism may contribute to an increased risk of cutaneous melanoma (CM). Methods By searching the databases of PubMed, EMBASE, and Web of Science, a total of 8 eligible case-control studies with 1,957 CM cases and 2,887 controls were included in this meta-analysis. Stata software was used to analyze all the statistical data. Results The pooled data by a fixed-effects model suggested an increased risk of CM associated with p53 Arg72Pro polymorphism under the genetic model of Arg/Pro vs. Pro/Pro without heterogeneity (ORArg/Pro vs. Pro/Pro = 1.76, 95% CI = 1.55-1.99, P heterogeneity = 0.075). A similar trend was seen in subgroups of hospital-based studies and population-based studies. Conclusion Our meta-analysis based on all studies shows that the p53 Arg72Pro polymorphism may increase individual susceptibility to CM, particularly in Caucasians and could serve as a biomarker to predict the population at high risk of CM.
Generic, scalable and decentralized fault detection for robot swarms

Robot swarms are large-scale multirobot systems with decentralized control which means that each robot acts based only on local perception and on local coordination with neighboring robots. The decentralized approach to control confers number of potential benefits. In particular, inherent scalability and robustness are often highlighted as key distinguishing features of robot swarms compared with systems that rely on traditional approaches to multirobot coordination. It has, however, been shown that swarm robotics systems are not always fault tolerant. To realize the robustness potential of robot swarms, it is thus essential to give systems the capacity to actively detect and accommodate faults. In this paper, we present a generic fault-detection system for robot swarms. We show how robots with limited and imperfect sensing capabilities are able to observe and classify the behavior of one another. In order to achieve this, the underlying classifier is an immune system-inspired algorithm that learns to distinguish between normal behavior and abnormal behavior online. Through a series of experiments, we systematically assess the performance of our approach in a detailed simulation environment. In particular, we analyze our system’s capacity to correctly detect robots with faults, false positive rates, performance in a foraging task in which each robot exhibits a composite behavior, and performance under perturbations of the task environment. Results show that our generic fault-detection system is robust, that it is able to detect faults in a timely manner, and that it achieves a low false positive rate. The developed fault-detection system has the potential to enable long-term autonomy for robust multirobot systems, thus increasing the usefulness of robots for a diverse repertoire of upcoming applications in the area of distributed intelligent automation.
Influence of testing methodology on the tigecycline activity profile against presumably tigecycline-non-susceptible Acinetobacter spp.

OBJECTIVES To compare the tigecycline activity profile against Acinetobacter spp. by Etest versus broth microdilution in isolates with high Etest MIC. METHODS Acinetobacter spp. isolates with tigecycline MICs of >or=0.5 mg/L determined by commercially developed Etests strips (January 2006 to July 2007) in five Spanish hospitals were considered. Values were rounded to the nearest upper double-dilution. Susceptibility by broth microdilution following CLSI (formerly NCCLS) recommendations, as the reference method, was determined in a central laboratory. BSAC breakpoints were used: susceptible <or=1 mg/L; intermediate = 2 mg/L; and resistant >2 mg/L. RESULTS One hundred and forty-eight isolates were collected: 12 isolates with a tigecycline Etest MIC of 0.5 mg/L, 14 with 1 mg/L, 86 with 2 mg/L, 31 with 4 mg/L and 5 with 8 mg/L. Isolates with Etest MICs of 0.5-1 mg/L showed the same values by broth microdilution. Among isolates with Etest MICs of 2 mg/L, only 5.8% of strains showed the same value by both methods (88.4% showed values that were one or two dilutions lower by microdilution). None of the 36 isolates with Etest MICs of 4-8 mg/L showed the same value by both methods, with values at least two dilutions lower by microdilution. Weak correlation (R = 0.238; P <or= 0.001) was found between both methods. All 26 Etest susceptible isolates, 80/86 (93.0%) Etest intermediate and 32/36 (88.9%) Etest resistant strains were susceptible by microdilution. CONCLUSIONS Caution should be taken in interpreting Etest MICs of >or=2 mg/L for Acinetobacter spp. since strains with Etest MICs of 2-4 mg/L are susceptible when tested by microdilution. False non-susceptibility by Etest may exclude tigecycline as a therapeutic option in a field where multiresistance is the rule.
The Necessary Accord of Word with Deed: Two Experiments and One Questionnaire on Honesty in Eight Societies

In an online survey, the honesty of residents of eight countries was measured in three ways: by the standard coin flip experimental paradigm, by a new experiment designed to resemble a test with the possibility of cheating, and by a questionnaire of integrity. While the coin flip paradigm successfully predicted cheating in the test, the integrity questionnaire was either not correlated with the two experimental measures, or correlated in an unexpected direction. I also report findings on the differences in honesty across societies, and on the accuracy of respondents’ beliefs about different societies’ honesty levels.