Miracle-dz/UniFAR-FTUs huggingface dataset:
Qualitative and Quantitative Detection of Chlamydophila pneumoniae DNA in Cerebrospinal Fluid from Multiple Sclerosis Patients and Controls

A standardized molecular test for the detection of Chlamydophila pneumoniae DNA in cerebrospinal fluid (CSF) would assist the further assessment of the association of C. pneumoniae with multiple sclerosis (MS). We developed and validated a qualitative colorimetric microtiter plate-based PCR assay (PCR-EIA) and a real-time quantitative PCR assay (TaqMan) for detection of C. pneumoniae DNA in CSF specimens from MS patients and controls. Compared to a touchdown nested-PCR assay, the sensitivity, specificity, and concordance of the PCR-EIA assay were 88.5%, 93.2%, and 90.5%, respectively, on a total of 137 CSF specimens. PCR-EIA presented a significantly higher sensitivity in MS patients (p = 0.008) and a higher specificity in other neurological diseases (p = 0.018). Test reproducibility of the PCR-EIA assay was statistically related to the volumes of extract DNA included in the test (p = 0.033); a high volume, which was equivalent to 100 µl of CSF per reaction, yielded a concordance of 96.8% between two medical technologists running the test at different times. The TaqMan quantitative PCR assay detected 26 of 63 (41.3%) of positive CSF specimens that tested positive by both PCR-EIA and nested-PCR qualitative assays. None of the CSF specimens that were negative by the two qualitative PCR methods were detected by the TaqMan quantitative PCR. The PCR-EIA assay detected a minimum of 25 copies/ml C. pneumoniae DNA in plasmid-spiked CSF, which was at least 10 times more sensitive than TaqMan. These data indicated that the PCR-EIA assay possessed a sensitivity that was equal to the nested-PCR procedures for the detection of C. pneumoniae DNA in CSF. The TaqMan system may not be sensitive enough for diagnostic purposes due to the low C. pneumoniae copies existing in the majority of CSF specimens from MS patients.
Speech segmentation is adaptvie even in adulthood: Role of the linguistic environment

In this paper, we show that adult listeners who speak the same native language but live in different linguistic environments differ in their use of prosodic cues that signal word boundaries in the native language. Non-utterance-final word-final syllables have higher fundamental frequency in French. Adult native French listeners living in France or in the US completed an artificial-language segmentation task where fundamental frequency cued word-final boundaries (experimental). Other native French listeners living in France completed the corresponding task without prosodic cues (control). Results showed that France French listeners outperformed US French listeners and control French listeners, but US French listeners did not outperform control French listeners. The poorer performance of US French listeners is attributed to their regular exposure to (and thus interference from) English, a language where fundamental frequency signals wordinitial boundaries. This suggests speech segmentation is adaptive, with listeners tuning in to the prosody of their linguistic environment.
UML as knowledge acquisition frontend for Semantic Web configuration knowledge bases

The trend towards highly specialized solution providers cooperatively offering configurable products and services to their customers requires the extension of current (standalone) configuration technology with capabilities of knowledge sharing and distributed configuration problem solving. On the one hand, a standardized representation language is needed in order to tackle the challenges imposed by heterogeneous representation formalisms of state-of-the-art configuration environments (e.g. description logic or predicate logic based configurators), on the other hand it is important to integrate the development and maintenance of configuration systems into industrial software development processes. We show how to support both goals by demonstrating the applicability of the Unified Modeling Language (UML) for configuration knowledge acquisition and by providing a set of rules for transforming UML models into configuration knowledge bases specified by languages such as OIL or DAML+OIL which represent the foundation for the description of configuration Web services.
Influence of the solvent representation on vibrational entropy calculations: Generalized born versus distance‐dependent dielectric model

The harmonic model is the most popular approximation for estimating the “configurational” entropy of a solute in molecular mechanics/Poisson‐Boltzmann solvent accessible surface area (MM/PBSA)‐type binding free energy calculations. Here, we investigate the influence of the solvent representation in the harmonic model by comparing estimates of changes in the vibrational entropies for 30 trypsin/ligand complexes on ligand binding. Second derivatives of Amber generalized Born (GB) solvation models are available in the nucleic acid builder code. They allow one to use these models for the calculation of vibrational entropies instead of using a simpler solvation model based on a distance‐dependent dielectric (DDD) constant. Estimates of changes in the vibrational entropies obtained with a DDD model are systematically and significantly larger, by on average, 6 kcal mol−1 (at T = 300 K), than estimates obtained with a GB model and so are more favorable for complex formation. The difference becomes larger the more the vibrational entropy contribution disfavors complex formation, that is, the larger the ligand is (for the complexes considered here). A structural decomposition of the estimates into per‐residue contributions reveals polar interactions between the ligand and the surrounding protein, in particular involving charged nitrogens, as a main source of the differences. Snapshots minimized with the DDD model showed a structural deviation from snapshots minimized in explicit water that is larger by, on average, 0.5 Å RMSD compared to snapshots that were minimized with GBHCT. As experimental vibrational entropies of biomacromolecules are elusive, there is no direct way to establish a solvent model's superiority. Thus, we can only recommend using the GB harmonic model for vibrational entropy calculations based on the reasoning that smaller structural deviations should point to the implicit solvent model that closer approximates the energy landscape of the solute in explicit solvent. © 2012 Wiley Periodicals, Inc.
New AC current shunts of MIKES

A new construction principle of AC current shunts has been applied to a set of shunts for AC currents from 1 A to 20 A, 20 Hz-10 kHz. The completed set will also cover current ranges from 20 mA to 1 A. The shunts are stable and do not show excessive AC-DC amplitude or phase differences and can thus be calibrated to work as AC current and resistance reference standards up to 10 kHz.
Neuroanatomical correlates of different vulnerability states for psychosis and their clinical outcomes.

BACKGROUND Structural brain abnormalities have been described in individuals with an at-risk mental state for psychosis. However, the neuroanatomical underpinnings of the early and late at-risk mental state relative to clinical outcome remain unclear. AIMS To investigate grey matter volume abnormalities in participants in a putatively early or late at-risk mental state relative to their prospective clinical outcome. METHOD Voxel-based morphometry of magnetic resonance imaging data from 20 people with a putatively early at-risk mental state (ARMS-E group) and 26 people with a late at-risk mental state (ARMS-L group) as well as from 15 participants with at-risk mental states with subsequent disease transition (ARMS-T group) and 18 participants without subsequent disease transition (ARMS-NT group) were compared with 75 healthy volunteers. RESULTS Compared with healthy controls, ARMS-L participants had grey matter volume losses in frontotemporolimbic structures. Participants in the ARMS-E group showed bilateral temporolimbic alterations and subtle prefrontal abnormalities. Participants in the ARMS-T group had prefrontal alterations relative to those in the ARMS-NT group and in the healthy controls that overlapped with the findings in the ARMS-L group. CONCLUSIONS Brain alterations associated with the early at-risk mental state may relate to an elevated susceptibility to psychosis, whereas alterations underlying the late at-risk mental state may indicate a subsequent transition to psychosis.
Optimal sizing and energy management of hybrid storage systems

This paper targets the development of hybrid energy storage systems (ESS), based on the batteries-supercapacitors blending. In particular, we will develop two methodologies for the combined sizing/energy management of hybrid ESS. The first method assumes that the division of power between the sources is performed through low/high pass filters, which allow us to evaluate, in a simple and rapid way, the trade-offs and economic gains due to the hybridization. The second approach relies on a nonlinear optimization problem, and seeks the minimization of the installation and electrical charging costs of the sources. Simulation results reveal the existence of a threshold in the EV range, from which the introduction of the supercapacitors is less beneficial in economic terms.
Purification and Characterization of a Novel 5-Oxoprolinase (without ATP-Hydrolyzing Activity) fromAlcaligenes faecalis N-38A

ABSTRACT A novel type of 5-oxoprolinase was found in a cell extract of strain N-38A, which was later identified as Alcaligenes faecalis. The enzyme in the cell extract was purified to a homogeneous state with a yield of 16.6%. The molecular weight of the purified enzyme was estimated to be 47,000 by both sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration, suggesting that the enzyme is a monomeric protein. The enzyme specifically catalyzed a decyclization of l-pyroglutamate without hydrolyzing ATP and also without any requirements for metal ions such as Mg2+ and K+. The optimal pH for the decyclization was 7.4. The reaction was reversible. The equilibrium constant of the reaction, Keq = [l-glutamate]/[l-pyroglutamate], was evaluated to be approximately 0.035, which indicates that the reaction tends to form l-pyroglutamate. The amino-terminal amino acid sequence of the enzyme was H-Glu-Pro-Arg-Leu-Asp-Thr-Ser-Gln-Leu-Tyr-Ala-Asp-Val-His-Phe-. No protein with a similar sequence was found in the DNASIS database. Based on these data, it was strongly suggested that the enzyme described here is a novel type of 5-oxoprolinase.
Cellular Mechanisms Underlying Burst Firing in Substantia Nigra Dopamine Neurons

Burst firing of substantia nigra dopamine (SN DA) neurons is believed to represent an important teaching signal that instructs synaptic plasticity and associative learning. However, the mechanisms through which synaptic excitation overcomes the limiting effects of somatic Ca2+-dependent K+ current to generate burst firing are controversial. Modeling studies suggest that synaptic excitation sufficiently amplifies oscillatory dendritic Ca2+ and Na+ channel currents to lead to the initiation of high-frequency firing in SN DA neuron dendrites. To test this model, visually guided compartment-specific patch-clamp recording and ion channel manipulation were applied to rodent SN DA neurons in vitro. As suggested previously, the axon of SN DA neurons was typically found to originate from a large-diameter dendrite that was proximal to the soma. However, in contrast to the predictions of the model, (1) somatic current injection generated firing that was similar in frequency and form to burst firing in vivo, (2) the efficacy of glutamatergic excitation was inversely related to the distance of excitation from the axon, (3) pharmacological blockade or genetic deletion of Ca2+ channels did not prevent high-frequency firing, (4) action potential bursts were invariably detected first at sites that were proximal to the axon, and (5) pharmacological blockade of Na+ channels in the vicinity of the axon/soma but not dendritic excitation impaired burst firing. Together, these data suggest that SN DA neurons integrate their synaptic input in a more conventional manner than was hypothesized previously.
LIVING WITH FIBROMYALGIA (FM): THE SALIENCE OF CLINICAL SUBGROUPS

Fibromyalgia (FM) is an elusive syndrome that affects 2% of the United States population, with health care costs exceeding $20 billion in 1998. FM alters lives with its symptoms and by interfering with everyday life. This dissertation explored the association between subgroups of women with FM and their functional status. The first study examined the effectiveness of an Internet-based health promotion intervention to improve the clinical outcomes for two subgroups of women with FM: those with high Fibromyalgia Impact Questionnaire (FIQ) scores (n = 5) and those with low FIQ scores (n = 5). Single subject design and grouped data revealed that the intervention had mixed results for the two subgroups. The clinical response to the intervention depended on the method of analysis (individual versus group) and the target behavior of interest. The second study examined the associations among objective and subjective measures, and two target outcomes: physical activity and functional status (FIQ total score), and then used the data to classify FM subgroups (n = 72). Using Exhaustive Chi-square Automatic Interaction Detector (Exhaustive CHAID), we developed two models. Model I, with the target outcome of physical activity, yielded 9 distinct subgroups, whose members had characteristics that were significantly associated with very unfavorable to very favorable physical activity outcomes. Model II, with the target outcome of the FIQ total score, yielded 5 distinct subgroups whose members had characteristics that were significantly associated with very unfavorable to very favorable functional status outcomes. The third study used qualitative and quantitative methods to identify clinically relevant triggers of FM flares, experienced by three subgroups women with low (n = 6), average (n = 5), and high (n = 4) FM impact, to explore the effect of triggers on their functional status. Using mixed methods, we were able to substantiate, quantify, and qualify the affects of FM on the lives of persons with FM and the direct consequences of those affects on activities. Overall activity, FM symptoms, and weather were the most prominent triggers. Findings from these studies suggest that the influence of FM on functional status affects women differently based on subgroup membership.
meshmixer: an interface for rapid mesh composition

In recent years a wide variety of mesh editing techniques have been developed for tasks such as smoothing, deformation, and parameterization. Comparatively fewer alternatives are available for composition tasks, such as combining parts of existing meshes. As designs often evolve from a combination of existing ideas and models, rapid composition techniques could significantly improve the workflow of mesh-based modeling tools. In our work we are exploring shape reuse and composition problems in 3D mesh modeling.
A heuristic for morpheme discovery based on string edit distance

This paper derives from work we have been doing on unsupervised learning of the morphology of languages with rich morphologies, that is, with a high average number of morphemes per word. Our focus in this paper is Swahili, a major Bantu language of East Africa, and our goal is the development of a system that can automatically produce a morphological analyzer of a text on the basis of a large corpus. While a certain amount of work in computational linguistics has already been done on Swahili, our specific goal is a system that can quickly and accurately perform a morphological analysis of any of the approximately 500 Bantu languages when presented with data from it, and little or no computational work currently exists for 99% of them. Our work reported here extends Linguistica, an open source system available at http://linguistica.uchicago. edu.
Antioxidant Properties of two Edible Green Seaweeds From Northern Coasts of the Persian Gulf

Background Ulva genus, an edible seaweed, and an important food source in many south-east Asian countries is also recognized by its synonymous name as Enteromorpha. Objectives This study was carried out to evaluate antioxidant activity, contents of total phenolics, and flavonoids of methanolic extracts of edible green seaweeds including Ulva clathrata (Roth) C. Agardh and three samples of Ulva prolifera O.F. Müller grown at different parts of Bushehr Province along the northern coasts of the Persian Gulf. Materials and Methods The seaweeds were collected from Bordekhoun, Northern Ouli, Taheri and Kangan coasts in December 2011. Methanolic extracts of the seaweeds were assessed for their antioxidant activity using DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging assay and was performed in a microplate reader. Total phenolics were determined by Folin-Ciocalteu reagent and flavonoid content was evaluated by colorimetric method. Results All samples showed antioxidant activity to various degrees. Ulva clathrata exhibited a high DPPH radical scavenging activity with a low IC50 (the half-maximal inhibitory concentration) (0.715 ± 0.078 mg. mL-1). The highest phenolic content (4.468 ± 0.379 mg GAE g-1) (gallic acid equivalent) and flavonoid content (45.577 ± 0.949 mg RE g-1) (rutin equivalent) were also observed in U . clathrata. The phenolic and flavonoid contents showed positive correlations with the DPPH radical scavenging activity and negative correlations with IC50 (P < 0.01). Besides, Results showed that there was a positive correlation between total phenolics and flavonoid content of extracts (P < 0.01). Conclusions Strong positive and significant correlations between DPPH radical scavenging and phenolic and flavonoid contents showed that, phenolic compounds, including flavonoids are the main contributors of antioxidant activity in these Ulva species and variations in phenolics and flavonoid contents of the seaweed extracts may be due to the variation in physicochemical parameters such as salinity amongst the selected stations.
FFT Program Generation for Shared Memory: SMP and Multicore

The chip maker's response to the approaching end of CPU frequency scaling are multicore systems, which offer the same programming paradigm as traditional shared memory platforms but have different performance characteristics. This situation considerably increases the burden on library developers and strengthens the case for automatic performance tuning frameworks like Spiral, a program generator and optimizer for linear transforms such as the discrete Fourier transform (DFT). We present a shared memory extension of Spiral. The extension within Spiral consists of a rewriting system that manipulates the structure of transform algorithms to achieve load balancing and avoids false sharing, and of a backend to generate multithreaded code. Application to the DFT produces a novel class of algorithms suitable for multicore systems as validated by experimental results: we demonstrate a parallelization speed-up already for sizes that fit into L1 cache and compare favorably to other DFT libraries across all small and midsize DFTs and considered platforms
Measuring unlinkability revisited

Unlinkability describes the inability of an observer to decide whether certain items of interest are related or not. Privacy aware protocol designers need a consistent and meaningful unlinkability measure to asses protocols in face of different attacks. In this paper we show that entropy measures are not sufficient for measuring unlinkability. We propose an alternative measure that estimates the error made by an attacker. We show by example that our expected distance provides a consistent measure that offers a better estimation of message-unlinkability.
Examining a Ripple Effect: Do Spouses' Behavior Changes Predict Each Other's Weight Loss?

Background. Including spouses in obesity treatment has been found to promote weight loss. We assessed whether spouses' diet and activity changes impacted each other's weight loss when both members attended an active weight loss program (TOGETHER) or only the primary participant attended treatment (ALONE). Methods. Heterosexual couples (N = 132) enrolled in an 18-month randomized controlled weight loss trial were weighed and completed measures of dietary intake and physical activity at baseline and 6 months. We conducted dyadic data analyses using the Actor-Partner Interdependence Model. Results. Participants' weight loss was not predicted by their partners' behavior changes. However, partners' weight loss was predicted by their participants' changes in calorie and fat intake. When partners were coupled with a participant who did not reduce their own calorie and fat intake as much, these partners had higher weight loss when treated in the TOGETHER group but lower weight loss when they were untreated in the ALONE group. There were no reciprocal effects found with physical activity changes. Conclusions. Direct treatment had the greatest impact on participants and partners who were treated. Untreated partners' weight losses were positively impacted by their spouses' dietary changes, suggesting a ripple effect from treated spouses to their untreated partners.
Long-Term Impacts of Foetal Malnutrition Followed by Early Postnatal Obesity on Fat Distribution Pattern and Metabolic Adaptability in Adult Sheep

We aimed to investigate whether over- versus undernutrition in late foetal life combined with obesity development in early postnatal life have differential implications for fat distribution and metabolic adaptability in adulthood. Twin-pregnant ewes were fed NORM (100% of daily energy and protein requirements), LOW (50% of NORM) or HIGH (150%/110% of energy/protein requirements) diets during the last trimester. Postnatally, twin-lambs received obesogenic (HCHF) or moderate (CONV) diets until 6 months of age, and a moderate (obesity correcting) diet thereafter. At 2½ years of age (adulthood), plasma metabolite profiles during fasting, glucose, insulin and propionate (in fed and fasted states) tolerance tests were examined. Organ weights were determined at autopsy. Early obesity development was associated with lack of expansion of perirenal, but not other adipose tissues from adolescence to adulthood, resulting in 10% unit increased proportion of mesenteric of intra-abdominal fat. Prenatal undernutrition had a similar but much less pronounced effect. Across tolerance tests, LOW-HCHF sheep had highest plasma levels of cholesterol, urea-nitrogen, creatinine, and lactate. Sex specific differences were observed, particularly with respect to fat deposition, but direction of responses to early nutrition impacts were similar. However, prenatal undernutrition induced greater metabolic alterations in adult females than males. Foetal undernutrition, but not overnutrition, predisposed for adult hypercholesterolaemia, hyperureaemia, hypercreatinaemia and hyperlactataemia, which became manifested only in combination with early obesity development. Perirenal expandability may play a special role in this context. Differential nutrition recommendations may be advisable for individuals with low versus high birth weights.