Miracle-dz/UniFAR-FTUs huggingface dataset:
A New IgG Immunoblot Kit for Diagnosis of Toxoplasmosis in Pregnant Women

The determination of the accurate immune status of pregnant women is crucial in order to prevent congenital toxoplasmosis. Equivocal results with conventional serological techniques are not uncommon when IgG titers are close to the cut-off value of the test, so that a confirmatory technique is needed. For this purpose, we developed a homemade immunoblot (IB) using soluble extract of Toxoplasma gondii tachyzoites and assessed it by testing 154 positive, 100 negative, and 123 equivocal sera obtained from pregnant women. In order to select the more valuable bands in terms of sensitivity and specificity, we used the Youden Index (YI). The highest YIs were those given by the 32, 36, 98, 21, and 33 bands. The simultaneous presence on the same blot of at least 3 bands showed a much higher YI (0.964) and was adapted as the positivity criterion. The analysis of results showed that our homemade IB correlated well with the commercial LDBIO Toxo II IgG® kit recently recommended as a confirmatory test (96.7% of concordance).
Federal Reserve Bank of Dallas Globalization and Monetary Policy Institute Has Globalization Transformed U.s. Macroeconomic Dynamics?

This paper estimates a structural New Keynesian model to test whether globalization has changed the behavior of U.S. macroeconomic variables. Several key coefficients in the model-such as the slopes of the Phillips and IS curves, the sensitivities of domestic inflation and output to " global " output, and so forth-are allowed in the estimation to depend on the extent of globalization (modeled as the changing degree of openness to trade of the economy), and, therefore, they become time-varying. The empirical results indicate that globalization can explain only a small part of the reduction in the slope of the Phillips curve. The sensitivity of U.S. inflation to global measures of output may have increased over the sample, but it remains very small. The changes in the IS curve caused by globalization are similarly modest. Globalization does not seem to have led to an attenuation in the effects of monetary policy shocks. The nested closed economy specification still appears to provide a substantially better fit of U.S. data than various open economy specifications with time-varying degrees of openness. Some time variation in the model coefficients over the postwar sample exists, particularly in the volatilities of the shocks, but it is unlikely to be related to globalization. The views in this paper are those of the author and do not necessarily reflect the views of the Federal Reserve Bank of Dallas or the Federal Reserve System.
Spotlight on taliglucerase alfa in the treatment of pediatric patients with type 1 Gaucher disease

Gaucher disease (GD) is a heritable storage disorder caused by functional defects of the lysosomal acid β-glucosidase and the accumulation of glucosylceramide within macrophages, resulting in multiple organ dysfunction. There are three commercially available enzyme replacement therapy (ERT) products for the treatment of GD type 1 (GD1): imiglucerase, velaglucerase alfa, and taliglucerase alfa. Imiglucerase and velaglucerase alfa are produced in different mammalian cell systems; imiglucerase requires postproduction deglycosylation to expose terminal α-mannose residues, which are required for mannose receptor-mediated uptake by target macrophages. These steps are critical to the success of ERT for the treatment of visceral and hematologic manifestations of GD. Taliglucerase alfa is the first US Food and Drug Administration-approved plant-cell-expressed recombinant human protein, using carrot root cell cultures. Furthermore, it does not require postproduction glycosidic modifications. It is indicated for treatment of adults with GD1 in the US, Israel, Australia, Canada, Chile, Brazil, and other countries, and it is additionally approved for the treatment of pediatric patients in the US, Australia, and Canada and for the treatment of hematologic manifestations in pediatric patients with Type 3 GD in Canada and other countries. Our review focuses on the role of taliglucerase alfa in the pediatric population. A literature search through PubMed (from 1995 up till November 2016) of English language articles was performed with the following terms: Gaucher disease, lysosomal storage disease, taliglucerase. Secondary and tertiary references were obtained by reviewing related articles as well as the website www.Clinicaltrials. gov. It has been demonstrated that taliglucerase alfa is efficacious, with a well-established safety profile in pediatric, ERT-naïve patients with symptomatic GD1, as well as for those patients previously treated with imiglucerase.
VEGFR1 single nucleotide polymorphisms associated with outcome in patients with metastatic renal cell carcinoma treated with sunitinib – a multicentric retrospective analysis

Abstract Background. There are no validated markers that predict outcome in metastatic renal cell cancer (mRCC) patients treated with sunitinib. Recently, single nucleotide polymorphism (SNP) rs9582036 in VEGFR1 has been proposed as a predictor of progression-free survival (PFS) and overall survival (OS) to bevacizumab in patients with pancreatic cancer and rs7993418 in VEGFR1 as predictor for PFS in mRCC-patients treated with bevacizumab. Here, we aim to study the impact of these SNPs in mRCC patients treated with sunitinib. Methods. We included patients with mRCC treated in 15 institutions in France and Belgium. Patients received sunitinib as first-line targeted therapy. We assessed response, time-to-tumor progression (TTP), OS, and clinical and biochemical parameters associated with outcome. We genotyped rs9582036 and rs7993418 as well as three other surrounding SNPs in VEGFR1: rs9554320, rs9554316 and rs9513070. Association between SNPs and treatment outcome were studied by univariate analysis and by multivariate Cox regression using relevant clinical factors associated with TTP and OS as covariates. Findings. Ninety-one patients were included. We found that mRCC patients with the CC-variant in rs9582036 in VEGFR1 have a poorer response rate (RR) (0% vs. 46%, p = 0.028), a poorer PFS (10 vs. 18 months, p = 0.033 on univariate and 0.06 on multivariate analysis) and a poorer OS (14 vs. 31 months, p = 0.019 on univariate and 0.008 on multivariate analysis) compared to patients with the AC- and AA-genotypes. mRCC patients with the AA-variant in rs9554320 in VEGFR1 have a poorer PFS (12 vs. 21 months, p = 0.0066 on univariate and 0.005 on multivariate analysis) and a poorer OS (22 vs. 34 months, p = 0.019 on univariate and 0.067 on multivariate analysis) compared to patients with the AC- and CC-genotypes. Interpretation. mRCC patients with the CC-genotype in VEGFR1 SNP rs9582036 have a poorer response rate, PFS and OS when treated with sunitinib. These findings are in agreement with the association of rs9582036 and outcome observed in bevacizumab treated pancreatic cancer patients. Prospective validation of this SNP is warranted.
Serine protease mechanism and specificity.

Almost one-third of all proteases can be classified as serine proteases, named for the nucleophilic Ser residue at the active site. This mechanistic class was originally distinguished by the presence of the AspHis-Ser “charge relay” system or “catalytic triad”. 1 The Asp-His-Ser triad can be found in at least four different structural contexts, indicating that this catalytic machinery has evolved on at least four separate occasions.2 These four clans of serine proteases are typified by chymotrypsin, subtilisin, carboxypeptidase Y, and Clp protease (MEROPS nomenclature;3 Table 1). More recently, serine proteases with novel catalytic triads and dyads have been discovered, including Ser-His-Glu, Ser-Lys/His, His-Ser-His, and N-terminal Ser.2 Several of these novel serine proteases are subjects of accompanying articles in this issue. This article will review recent work on the mechanism and specificity of chymotrypsin-like enzymes, with the occasional references to pertinent experiments with subtilisin. Chymotrypsin-like proteases are the most abundant in nature, with over 240 proteases recognized in the MEROPS database.3 * E-mail: hedstrom@brandeis.edu; phone: 781-736-2333; FAX: 781-736-2349. 4501 Chem. Rev. 2002, 102, 4501−4523
Artificial Radionuclides in Squid from northwestern Pacific in 2011followingthe Fukushima accident

Abstract. In order to better understand the impact of Fukushima Nuclear Power Plant (NPP) Accident on commercial marine species, squid (Ommastrephe bartrami) samples, obtained from the northwestern Pacific in November 2011, were analyzed for a range of artificial and natural radionuclides (Cs-134, Cs-137, Ag-110m, U-238, Ra-226 and K-40). Short-lived radionuclides Cs-134 and Ag-110m released from Fukushima NPP Accident were found in the samples, with an extremely high water-to-organism concentration ratio for Ag-110m (> 2.9E + 04). The radiological dose rates for the squid from the radionuclides measured were far lower than the relevant benchmark of 10 µGy h −1 . For human consumers ingesting these squid, the dose contribution from natural radionuclides (> 99.9 %) including Po-210, was far greater than that of Fukushima-accident radionuclides ( 0.1 %). The whole-body to tissue and whole-body to gut concentration ratios were calculated and reported, providing a simple method to estimate the whole-body concentration in the environmental monitoring programs, and filling the data gap of concentration ratios in cephalopods. Our results help fill data gaps on uptake of NPP radionuclides in the commercially important Cephalopoda class and add to scarce data on open-ocean nekton in the northwestern Pacific soon after the Fukushima accident.
Dynamic power management for portable systems

Portable systems require long battery lifetime while still delivering high performance. Dynamic power management (DPM) policies trade off the performance for the power consumption at the system level in portable devices. In this work we present the time-indexed SMDP model (TISMDP) that we use to derive optimal policy for DPM in portable systems. TISMDP model is needed to handle the non-exponential user request interarrival times we observed in practice. We use our policy to control power consumption on three different devices: the SmartBadge portable device [18], the Sony Vaio laptop hard disk and WLAN card. Simulation results show large savings for all three devices when using our algorithm. In addition, we measured the power consumption and performance of our algorithm and compared it with other DPM algorithms for laptop hard disk and WLAN card. The algorithm based on our TISMDP model has 1.7 times less power consumption as compared to the default Windows timeout policy for the hard disk and three times less power consumption as compared to the default algorithm for the WLAN card.
Polyspecific monoclonal lupus autoantibodies reactive with both polynucleotides and phospholipids

Hybridomas the produce anti-DNA autoantibodies were prepared from spleen cells of unimmunized MRL/1 mice, a strain that spontaneously develops severe systemic lupus erythematous (SLE). Reactivities of these monoclonal antibodies with a wide range of polynucleotides prompted tests of their reactions with phospholipids which, like polynucleotides, contain diester-linked phosphate groups in their backbones. In competitive radioimmunoassays, cardiolipin, phosphatidic acid, and phosphatidyl glycerol blocked the binding of these hybridoma antibodies to denatured DNA. These phospholipids also specifically inhibited the reaction between a hybridoma antibody and a site-specific anti-idiotypic antibody. The antinuclear reaction of one of these antibodies was specifically inhibited by cardiolipin. This same antibody prolonged the activated partial thromboplastin time in a manner characteristic of a lupus anticoagulant, presumably by binding to phospholipid in the test system. The polyspecific reactivity of a single molecular species of lupus autoantibody suggests that some of the diverse serological abnormalities of SLE may be a result of the binding of certain autoantibodies to a phosphodiester-containing epitope that is present in diverse biological molecules.
Arm path fragmentation and spatiotemporal features of hand reaching in healthy subjects and stroke patients

Arm motion in healthy humans is characterized by smooth and relatively short paths. The current study focused on 3D reaching in stroke patients. Sixteen right-hemiparetic stroke patients and 8 healthy adults performed 42 reaching movements towards 3 visual targets located at an extended arm distance. Performance was assessed in terms of spatial and temporal features of the movement; i.e., hand path, arm posture and smoothness. Differences between groups and within subjects were hypothesized for spatial and temporal aspects of reaching under the assumption that both are independent. As expected, upper limb motion of patients was characterized by longer and jerkier hand paths and slower speeds. Assessment of the number of sub-movements within each movement did not clearly discriminate between groups. Principal component analyses revealed specific clusters of either spatial or temporal measures, which accounted for a large proportion of the variance in patients but not in healthy controls. These findings support the notion of a separation between spatial and temporal features of movement. Stroke patients may fail to integrate the two aspects when executing reaching movements towards visual targets.
Classifiers with limited connectivity

For many neural network models that are based on perceptrons, the number of activity patterns that can be classified is limited by the number of plastic connections that each neuron receives, even when the total number of neurons is much larger. This poses the problem of how the biological brain can take advantage of its huge number of neurons given that the connectivity is extremely sparse, especially when long range connections are considered. One possible way to overcome this limitation in the case of feed-forward networks is to combine multiple perceptrons together, as in committee machines. The number of classifiable random patterns would then grow linearly with the number of perceptrons, even when each perceptron has limited connectivity. However, the problem is moved to the downstream readout neurons, which would need a number of connections that is as large as the number of perceptrons. Here we propose a different approach in which the readout is implemented by connecting multiple perceptrons in a recurrent attractor neural network. We show with analytical calculations that the number of random classifiable patterns can grow unboundedly with the number of perceptrons, even when the connectivity of each perceptron remains finite. Most importantly both the recurrent connectivity and the connectivity of a downstream readout are also finite. Our study shows that feed-forward neural classifiers with numerous long range connections connecting different layers can be replaced by networks with sparse long range connectivity and local recurrent connectivity without sacrificing the classification performance. Our strategy could be used in the future to design more general scalable network architectures with limited connectivity, which resemble more closely brain neural circuits dominated by recurrent connectivity.
Interaction of drug- and granulocyte-mediated killing of Pseudomonas aeruginosa in a murine pneumonia model.

BACKGROUND Killing of bacterial pathogens by granulocytes is a saturable process, as previously demonstrated. There is virtually no quantitative information about how granulocytes interact with antimicrobial chemotherapy to kill bacterial cells. METHODS We performed a dose-ranging study with the aminoglycoside plazomicin against Pseudomonas aeruginosa ATCC27853 in a granulocyte-replete murine pneumonia model. Plazomicin was administered in a humanized fashion (ie, administration of decrementing doses 5 times over 24 hours, mimicking a human daily administration profile). Pharmacokinetic profiling was performed in plasma and epithelial lining fluid. All samples were simultaneously analyzed with a population model. Mouse cohorts were treated for 24 hours; other cohorts treated with the same therapy were observed for another 24 hours after therapy cessation, allowing delineation of the therapeutic effect necessary to reduce the bacterial burden to a level below the half-saturation point. RESULTS The mean bacterial burden (±SD) at which granulocyte-mediated kill was half saturable was 2.45 × 10(6) ± 6.84 × 10(5) colony-forming units of bacteria per gram of tissue (CFU/g). Higher levels of plazomicin exposure reduced the bacterial burden to <5 log10 CFU/g, allowing granulocytes to kill an additional 1.0-1.5 log CFU/g over the subsequent 24 hours. CONCLUSIONS For patients with large bacterial burdens (eg, individuals with ventilator-requiring hospital-acquired pneumonia), it is imperative to kill ≥2 log10 CFU/g early after treatment initiation, to allow the granulocytes to contribute optimally to bacterial clearance.
Gentamicin fails to increase dystrophin expression in dystrophin‐deficient muscle

A recent report that aminoglycoside antibiotics restored the expression of functional dystrophin to skeletal muscles of mdx mice, a model of Duchenne muscular dystrophy (DMD), raised hopes that DMD may be treatable by a conventional drug. Subsequently, several human trials were initiated for evaluating gentamicin therapy in selected DMD patients. An increase of dystrophin expression was not detected in one human trial that was fully reported. Here, we report that we were unable to replicate previously published beneficial results by gentamicin treatment in the mdx mouse. Therefore, we believe that additional animal experimentation is required to further evaluate the possibility of in vivo aminoglycoside therapy of DMD. Muscle Nerve 27: 624–627, 2003
Cytosolic Glyceraldehyde-3-Phosphate Dehydrogenases Interact with Phospholipase Dδ to Transduce Hydrogen Peroxide Signals in the Arabidopsis Response to Stress[C][W]

Plants produce hydrogen peroxide (H2O2) as a stress signal. This study shows that H2O2 promotes the binding of cytosolic, glycolytic enzymes, GAPCs, to the plasma membrane–associated phospholipase PLDδ. The GAPC–PLDδ interaction mediates the plant response to H2O2 and provides a molecular link between stress signaling and the alteration of cellular metabolism and growth in the plant response to drought. Reactive oxygen species (ROS) are produced in plants under various stress conditions and serve as important mediators in plant responses to stresses. Here, we show that the cytosolic glycolytic enzymes glyceraldehyde-3-phosphate dehydrogenases (GAPCs) interact with the plasma membrane–associated phospholipase D (PLDδ) to transduce the ROS hydrogen peroxide (H2O2) signal in Arabidopsis thaliana. Genetic ablation of PLDδ impeded stomatal response to abscisic acid (ABA) and H2O2, placing PLDδ downstream of H2O2 in mediating ABA-induced stomatal closure. To determine the molecular link between H2O2 and PLDδ, GAPC1 and GAPC2 were identified to bind to PLDδ, and the interaction was demonstrated by coprecipitation using proteins expressed in Escherichia coli and yeast, surface plasmon resonance, and bimolecular fluorescence complementation. H2O2 promoted the GAPC–PLDδ interaction and PLDδ activity. Knockout of GAPCs decreased ABA- and H2O2-induced activation of PLD and stomatal sensitivity to ABA. The loss of GAPCs or PLDδ rendered plants less responsive to water deficits than the wild type. The results indicate that the H2O2-promoted interaction of GAPC and PLDδ may provide a direct connection between membrane lipid–based signaling, energy metabolism and growth control in the plant response to ROS and water stress.
Extracting structured information from Wikipedia articles to populate infoboxes

Roughly every third Wikipedia article contains an infobox - a table that displays important facts about the subject in attribute-value form. The schema of an infobox, i.e., the attributes that can be expressed for a concept, is defined by an infobox template. Often, authors do not specify all template attributes, resulting in incomplete infoboxes. With iPopulator, we introduce a system that automatically populates infoboxes of Wikipedia articles by extracting attribute values from the article's text. In contrast to prior work, iPopulator detects and exploits the structure of attribute values to independently extract value parts. We have tested iPopulator on the entire set of infobox templates and provide a detailed analysis of its effectiveness. For instance, we achieve an average extraction precision of 91% for 1,727 distinct infobox template attributes.
Evidence of a decline in beluga, Delphinapterus leucas, abundance off West Greenland

Aerial surveys of belugas, or white whales,Delphinapterus leucas, were conducted off West Greenland in March 1993 and 1994. These surveys were designed to permit comparisons with similar surveys in 1981, 1982, and 1991. Differences in methods between the surveys in the early 1980s and those in the 1990s should mean that the 1990s surveys were, if anything, more efficient than the 1980s surveys. Weighted linear regressions of strip-census estimates of the relative abundance of belugas showed a significant decline from 1981 to 1994. While annual variability in ice conditions and other unknown factors may have had some local or small-scale effects on the movements and distribution of belugas off West Greenland, it is unlikely that these effects would account for the apparent decline in relative abundance. The most reasonable conclusion is that the stock size has declined considerably during the past 13 years, perhaps by as much as 62%.
Cohere: Towards Web 2.0 Argumentation

Students, researchers and professional analysts lack effective tools to make personal and collective sense of problems while working in distributed teams. Central to this work is the process of sharing---and contesting---interpretations via different forms of argument. How does the “Web 2.0” paradigm challenge us to deliver useful, usable tools for online argumentation? This paper reviews the current state of the art in Web Argumentation, describes key features of the Web 2.0 orientation, and identifies some of the tensions that must be negotiated in bringing these worlds together. It then describes how these design principles are interpreted in Cohere, a web tool for social bookmarking, idea-linking, and argument visualization.
A probabilistic analysis of the biometrics menagerie existence: a case study in fingerprint data

The use of biometrics, until very recently, has been restricted to high-security environments and criminal identification applications, for economic and technological reasons. However, with its popularisation, it has been noted that users within the system may have different degrees of accuracy. Some people may have trouble authenticating, while others may be particularly vulnerable to imitation. Recent studies have investigated and identified these types of users, giving them the names of animals: Sheep, Goats, Lambs, Wolves, Doves, Chameleons, Worms and Phantoms. The aim of this study is to evaluate the existence of these animals in a database of fingerprints by proposing a new way of their identification, based on the performance of verification between subjects samples.