Miracle-dz/UniFAR-FTUs huggingface dataset:
Complexes between Activated Protein C and Protein C Inhibitor Measured with a New Method

Summary A first clinical evaluation has been made of the performance of a newly devised immunofluorometric assay for measuring plasma concentrations of activated protein C (APC) in complex with protein C inhibitor (PCI). The method was compared with testing for other markers of hypercoagulability in a case-control study comprising 123 patients with clinical suspicion of deep vein thrombosis (DVT). The diagnosis was confirmed by ascending phlebography, and the thrombotic burden estimated with a newly developed scoring system. Receiver operating characteristics (ROC) curves calculated to demonstrate the discriminatory capacity of the methods, showed the area under the curves (AUCs) to be similar for the APC-PCI and D-dimer methods. However, in contrast to the D-dimer method, the APC-PCI method measures a well-defined analyte, a prerequisite for reliable comparisons of future clinical studies. The APC-PCI method appears to be particularly useful as a marker for detection of recently developed proximal thrombi.
Kinetics of Myeloid Dendritic Cell Trafficking and Activation: Impact on Progressive, Nonprogressive and Controlled SIV Infections

We assessed the role of myeloid dendritic cells (mDCs) in the outcome of SIV infection by comparing and contrasting their frequency, mobilization, phenotype, cytokine production and apoptosis in pathogenic (pigtailed macaques, PTMs), nonpathogenic (African green monkeys, AGMs) and controlled (rhesus macaques, RMs) SIVagmSab infection. Through the identification of recently replicating cells, we demonstrated that mDC mobilization from the bone marrow occurred in all species postinfection, being most prominent in RMs. Circulating mDCs were depleted with disease progression in PTMs, recovered to baseline values after the viral peak in AGMs, and significantly increased at the time of virus control in RMs. Rapid disease progression in PTMs was associated with low baseline levels and incomplete recovery of circulating mDCs during chronic infection. mDC recruitment to the intestine occurred in all pathogenic scenarios, but loss of mucosal mDCs was associated only with progressive infection. Sustained mDC immune activation occurred throughout infection in PTMs and was associated with increased bystander apoptosis in blood and intestine. Conversely, mDC activation occurred only during acute infection in nonprogressive and controlled infections. Postinfection, circulating mDCs rapidly became unresponsive to TLR7/8 stimulation in all species. Yet, stimulation with LPS, a bacterial product translocated in circulation only in SIV-infected PTMs, induced mDC hyperactivation, apoptosis and excessive production of proinflammatory cytokines. After infection, spontaneous production of proinflammatory cytokines by mucosal mDCs increased only in progressor PTMs. We thus propose that mDCs promote tolerance to SIV in the biological systems that lack intestinal dysfunction. In progressive infections, mDC loss and excessive activation of residual mDCs by SIV and additional stimuli, such as translocated microbial products, enhance generalized immune activation and inflammation. Our results thus provide a mechanistic basis for the role of mDCs in the pathogenesis of AIDS and elucidate the causes of mDC loss during progressive HIV/SIV infections.
NK3 receptors mediate an increase in firing rate of midbrain dopamine neurons of the rat and the guinea pig

This in vitro study investigates and compares the effects of NK3 receptor ligands on the firing rate of rat and guinea pig midbrain dopamine neurons. The findings are discussed in the light of choosing suitable animal models for investigating pharmacological properties of NK3 receptor antagonists, which have been proposed to possess therapeutic activity in neuropsychiatric diseases like e.g. schizophrenia. In vitro midbrain slice preparations of both species were used to record (extracellularly) the firing rates of dopamine neurons located in the substantia nigra (SN) and ventral tegmental area (VTA). Furthermore, the effect of the D2 receptor agonist quinpirole on guinea pig SN and VTA dopamine neurons was investigated. The efficacy of quinpirole in inhibiting guinea pig dopamine neuron firing activity was much less as compared to that of rat dopamine neurons, suggesting a lower dopamine D2 autoreceptor density on the guinea pig neurons. The NK3 receptor agonist senktide induced in subpopulations of rat SN (55%) and VTA (79%) and guinea pig SN (50%) and VTA (21%) dopamine neurons an increase in firing rate. In responsive neurons this effect was concentration‐dependent with EC50 values of 3–5 nM (for both species). The selective NK3 receptor antagonist osanetant (100 nM) was able to partly block the senktide‐induced increase in firing rates of dopamine neurons and shifted the concentration‐response relation curves for senktide to the right (pA2 values were ∼7.5). The fractional block of the senktide responses by osanetant appeared to be larger in guinea pig dopamine neurons, indicating that osanetant is a more potent blocker of NK3 receptor‐mediated responses with noncompetitive properties in the guinea pig. Synapse 2011. © 2011 Wiley‐Liss, Inc.
Mood and Cognitive Performance Effects of "Energy" Drink Constituents: Caffeine, Glucose and Carbonation

Abstract Three studies using healthy volunteers ( n =271) investigated the effects of caffeine, carbohydrates and carbonation in functional "energy" drinks (EDs) with the aim of determining their benefit in every-day life. The results showed caffeine to be the main ED constituent responsible for the effects found, with possible minor, relatively weak effects of carbohydrates. EDs were found to improve and/or maintain mood and performance during fatiguing and cognitively demanding tasks relative to placebo. In terms of absolute values, EDs maintained levels of arousal compared to a deterioration in arousal where placebo was consumed. These effects were found in caffeine-deprived participants, and so may be largely due to "withdrawal reversal". There were only minor differences in the effects of water vs. "sensory-matched" placebo, supporting previous findings indicating that the type of placebo does not alter the conclusions drawn about the effects of the full ED. Finally, carbonation had various effects on mood, some of which were present immediately following consumption, others were consistent with slower absorption of caffeine (and possibly carbohydrates) from carbonated drinks.
Proximity relevance model for query expansion

Query expansion (QE) aims at improving information retrieval effectiveness by enhancing the query formulation. Because users' queries are generally short and because of the language ambiguity, some information needs are difficult to satisfy. Query reformulation and QE methods have been developed to face this issue. Pseudo relevance feedback (PRF) considers the top retrieved documents as relevant and uses their content in order to expand the initial query. Rather than considering feedback documents as a bag of words, it is possible to exploit term proximity information. Although there are some researches in this direction, the majority of them is empirical. The lack of theoretical works in this area motivated us to introduce a novel method integrated into the language model formalism that takes advantage of the remoteness of candidate terms for QE from query terms within feedback documents. In contrast to previous works, our approach captures the proximity directly and in terms of sentences rather than tokens. We show that the method significantly improves the retrieval performance on TREC collections especially for difficult queries.
Statistical Approach to Basis Function Truncation in Digital Interpolation Filters

In this paper an alternative analysis in the time domain is described and the results of the interpolation process are presented by means of functions that are based on the rule of conditional mathematical expectation and the covariance function. A comparison between the interpolation error caused by low order filters and the classic sinc(t) truncated function is also presented. When fewer samples are used, low-order filters have less error. If the number of samples increases, the sinc(t) type functions are a better alternative. Generally speaking there is an optimal filter for each input signal which depends on the filter length and covariance function of the signal. A novel scheme of work for adaptive interpolation filters is also presented. Keywords—Interpolation, basis function, over-sampling.
Chromosome 6 abnormalities in ovarian surface epithelial tumors of borderline malignancy suggest a genetic continuum in the progression model of ovarian neoplasms.

PURPOSE We used conventional cytogenetics, molecular cytogenetics, and molecular genetic analyses to study the pattern of allelic loss on chromosome 6q in a cohort of borderline epithelial ovarian tumors. EXPERIMENTAL DESIGN Fifteen tumor samples were collected from patients undergoing surgery for ovarian tumors. The tumors of borderline malignancy, classified according to the standard criteria, included 4 mucinous and 11 serous tumors. Cytogenetic and molecular cytogenetic (with yeast artificial chromosome clones from 6q26-27) studies were performed on tumor areas contiguous to those used for histological examination ensuring the appropriate sampling. Moreover loss of heterozygosity analysis was performed using PCR amplification of eight microsatellite markers mapping on 6q27 (D6S193, D6S297), 6q26 (D6S305, D6S415, D6S441), 6q21 (D6S287), 6q16 (D6S311), and 6q14 (D6S300). RESULTS Deletions of this chromosome arm, in particular of 6q24-27, were the most frequent lesions found in this set of tumors. In a tumor with a normal karyotype the only detectable alteration was a deletion of approximately 300 kb within the D6S149-D6S193 interval at band 6q27. This is, to date, the smallest deletion described for borderline tumors. CONCLUSION Alterations in the above-mentioned interval are a common finding in advanced ovarian carcinomas but also in benign ovarian cysts, implying that some tumors of borderline malignancy may arise from benign tumors and that malignant ones may evolve from tumors of borderline malignancy. Genes located in 6q27 seem to be crucial for this mechanism of early events in ovarian tumorigenesis.
Translating Institutional Change to Local Communities: The Role of Linking Organizations

We examine the processes and mechanisms of translating broader field-level change to the local community, drawing on insights from the inhabited institutions perspective and community-based institutionalism. In particular, we develop the concept of linking organizations as key actors in institutional change that connect the broader field and community levels. We use multiple forms of qualitative data, collected over a two-year time frame, to study the processes of a community foundation, the ‘Rainbow Wellness Foundation’, as a linking organization that engaged five community coalitions to embed a new wellness approach, locally. Our findings suggest that linking organizations interpret the central tenets of the approach, define them locally around relevant aims, and regulate community organizations’ adherence, to ensure legitimacy with the field. In addition, by engaging and negotiating with the community and helping manage ambiguity, linking organizations enable local ‘filling-in’ of these models with practices that meet community needs and interests. This study contributes to the literature on institutional change by identifying the activities of linking organizations as agents that translate broader field change, locally.
X-Ray Properties of Pre-Main-Sequence Stars in the Orion Nebula Cluster with Known Rotation Periods

We reanalyze all archival Chandra/ACIS observations of the Orion Nebula Cluster (ONC) to study the X-ray properties of a large sample of pre–main-sequence (PMS) stars with optically determined rotation periods. Our goal is to elucidate the origins of X-rays in PMS stars by seeking out connections between the X-rays and the mechanisms most likely driving their production—rotation and accretion. Stars in our sample have LX/Lbol near, but below, the "saturation" value of 10-3. In addition, in this sample X-ray luminosity is significantly correlated with stellar rotation, in the sense of decreasing LX/Lbol with more rapid rotation. These findings suggest that stars with optical rotation periods are in the "super-saturated" regime of the rotation-activity relationship, consistent with their Rossby numbers. However, we also find that stars with optical rotation periods are significantly biased to high LX. This is not the result of magnitude bias in the optical rotation–period sample, but rather of the diminishingly small amplitude of optical variations in stars with low LX. Evidently, there exists in the ONC a population of stars whose rotation periods are unknown and that possess lower average X-ray luminosities than those of stars with known rotation periods. These stars may sample the linear regime of the rotation-activity relationship. Accretion also manifests itself in X-rays, though in a somewhat counterintuitive fashion: while stars with spectroscopic signatures of accretion show harder X-ray spectra than nonaccretors, they show lower X-ray luminosities and no enhancement of X-ray variability. We interpret these findings in terms of a common origin for the X-ray emission observed from both accreting and nonaccreting stars, with the X-rays from accreting stars simply being attenuated by magnetospheric accretion columns. This suggests that X-rays from PMS stars have their origins primarily in chromospheres, not accretion.
O R I G I N a L I N V E S T I G a T I O N Open Access

Inflammatory biomarkers in type 2 diabetic patients: effect of glycemic control and impact of ldl subfraction phenotype Abstract Background: Type 2 diabetes mellitus (T2D) is associated with higher cardiovascular risk partly related to an increase in inflammatory parameters. The aim of this study was to determine the association of inflammatory biomarkers with low-density lipoprotein (LDL) subfraction phenotype and glycemic control in subjects with T2D and poor glycemic control.
The Effectiveness of Reading Interventions for English Learners

This article reviews published experimental studies from 2000 to 2012 that evaluated the effects of providing reading interventions to English learners who were at risk for experiencing academic difficulties, including students with learning disabilities. Criteria included: (a) the study was published in a peer-referred journal, (b) the study was an intervention for English learners at risk or with a learning disability in Grades K–12, (c) data were disaggregated by English learner status if all participants were not English learners, and (d) information about fidelity of implementation was reported. Twelve studies met these criteria. Results of seven studies conducted in kindergarten and first grade indicated significant moderate-to-large effect sizes (ES range, 0.58–0.91) for interventions targeting beginning reading skills. Findings in five of the 12 studies suggested significant moderate-to-large effects in reading or listening comprehension (ES range, 0.47–2.34). The interventions in these studies included explicit instruction, and 10 used published intervention programs. Moderator variables, such as group size, minutes of intervention, and type of personnel delivering the intervention, were not significant predictors of outcomes.
Chemokine Profile of Human Serum from Whole Blood: Migratory Effects of CXCL-10 and CXCL-11 on Human Mesenchymal Stem Cells

Autologous human serum is used in cartilage repair and may exert its effect by the recruitment of mesenchymal stem and progenitor cells (MSC). Aim of our study was to analyze the chemokine profile of human serum and to verify chemotactic activity of selected chemokines on MSC. Human MSC were isolated from iliac crest bone marrow aspirates. Chemotactic activity of human serum made from whole blood and pharma grade serum was tested in 96-well chemotaxis assays and chemokine levels were analyzed using human chemokine antibody membrane arrays. The chemotactic potential of selected chemokines on MSC was tested dose dependently using chemotaxis assays. Human serum derived from whole blood significantly attracted human MSC, while pharma grade serum did not recruit MSC. Human chemokine antibody array analysis showed that the level of chemokines CXCL-3, 5, 7-8, 10-12, 16; CCL- 2, 5, 11, 13, 16-20, 24-25, 27; as well as XCL-1 was elevated (fold change >1.5) in serum derived from whole blood compared to nonrecruiting pharma grade serum. Chemotaxis assays showed that the chemokines IP-10/CXCL-10 and I-TAC/CXCL-11 significantly recruit human MSC. PARC/CCL-18, HCC-4/CCL-16, CTACK/CCL-27, and Lymphotactin/XCL-1 showed no chemotactic effect on MSC. Therefore, human serum derived from whole blood contains chemokines that may contribute to serum-mediated recruitment of human mesenchymal progenitors from bone marrow.
Regime Switching Model with Endogenous Autoregressive Latent Factor∗

This paper introduces a model with regime switching, which is driven by an autoregressive latent factor correlated with the innovation to the observed time series. In our model, the mean or volatility process is switched between two regimes, depending upon whether the underlying autoregressive latent factor takes values above or below some threshold level. If the latent factor becomes exogenous, our model reduces to the conventional markov switching model, and therefore, our model may be regarded as an extended markov switching model allowing for endogeneity in regime switching. Our model is estimated by the maximum likelihood method using a newly developed modified markov switching filter. For both mean and volatility models that are frequently analyzed in markov switching framework, we demonstrate that the presence of endogeneity in regime switching is indeed strong and ubiquitous. This version: April 8, 2015 JEL Classification: C13, C32
Image Comparative Assessment Using Iterative Reconstructions: Clinical Comparison of Low-Dose Abdominal/Pelvic Computed Tomography Between Adaptive Statistical, Model-Based Iterative Reconstructions and Traditional Filtered Back Projection in 65 Patients

ObjectivesThe objective of this study was to compare image quality (objective and subjective parameters) and confidence in lesion detection between 3 image reconstruction algorithms in computed tomographic (CT) examinations of the abdomen/pelvis. Materials and MethodsThis prospective institutional review board–approved study included 65 patients (mean [SD] age, 71.3 ± 9 years; mean [SD] body mass index, 24.4 [4.8] kg) who underwent routine CT examinations of the abdomen/pelvis followed immediately by 2 low-dose scans. Raw data sets were reconstructed by using filtered back projection (FBP), adaptive statistical iterative reconstruction (ASIR), and a model-based iterative reconstruction (MBIR). Measurements of objective noise and CT numbers were compared using repeated-measures analysis of variance. Six subjective image quality parameters were scored. Diagnostic confidence and accuracy in detection of various elementary lesions were performed. ResultsObjectively, mean image noise for MBIR was significantly superior at all dose levels (P < 0.001). Subjectively, standard-dose ASIR and low-dose MBIR scans were better than standard-dose FBP scan in all parameters assessed (P < 0.05). Low-dose MBIR scans were comparable with standard-dose ASIR scans in all parameters except at noise index of 70 (approximately 85% dose reduction), where, in this case, the detection of liver lesions less than 5 mm were rated inferior (P < 0.05) with diagnostic accuracy reducing to 77.4%. ConclusionsLow-dose MBIR scan shows superior objective noise reduction compared with standard-dose FBP and ASIR. Subjectively, low-dose MBIR scans at 76% dose reduction were also superior compared with standard-dose FBP and ASIR. However, at dose reductions of 85%, small liver lesions may be missed.
A New Fluctuating Asymmetry Index, or the Solution for the Scaling Effect?

Two principal methods are commonly employed for the estimation of developmental instability at the population level. Some studies use variances of morphological traits (σ2p), while others use fluctuating asymmetry (FA). In both cases, differences in the degree of developmental instability can be tested with an F-test, which is the most common way to compare variances. However, the variance is expected to scale proportionally to the square of the mean as there is a tendency in biological data for σ2p to scale proportionally to the square of the mean ( ): σ2p = Z ξ, where ξ is the scaling exponent, which is expected to be two for pure statistical reasons, is the mean of the trait and Z is a measure of individual-level variability. Because of this scaling effect, the fluctuating asymmetry will be affected, FA is estimated as the variance between the right and the left sides of a trait (σ2r − l = σ2r + σ2l − 2rσrσl), where σ2r and σ2l are the variances of the right and the left trait values, respectively. In this paper, we propose a novel method that allows an exact correction of the scaling effect, which will enable a proper comparison of the degree of fluctuating asymmetry for a trait. The problem of the scaling of the FA with the trait size is quite crucial if FA is to be considered an indicator of fitness or an indicator of environmental or genetic stress, as different stresses or fitness levels are typically accompanied by a change of the traits’ .
The Synaptic Representation of Sound Source Location in Auditory Cortex

A key function of the auditory system is to provide reliable information about the location of sound sources. Here, we describe how sound location is represented by synaptic input arriving onto pyramidal cells within auditory cortex by combining free-field acoustic stimulation in the frontal azimuthal plane with in vivo whole-cell recordings. We found that subthreshold activity was panoramic in that EPSPs could be evoked from all locations in all cells. Regardless of the sound location that evoked the largest EPSP, we observed a slowing in the EPSP slope along the contralateral–ipsilateral plane that was reflected in a temporal sequence of peak EPSP times. Contralateral sounds evoked EPSPs with earlier peak times and consequently generated action potential firing with shorter latencies than ipsilateral sounds. Thus, whereas spiking probability reflected the region of space evoking the largest EPSP, across the population, synaptic inputs enforced a gradient of spike latency and precision along the horizontal axis. Therefore, within auditory cortex and regardless of preferred location, the time window of synaptic integration reflects sound source location and ensures that spatial acoustic information is represented by relative timings of pyramidal cell output.
Individual Differences in Sensitivity to Transient Electrocutaneous Stimulation

124 subjects were tested in a procedure designed to measure sensitivity to transient currents applied cutaneously, and to assess individual characteristics accounting for sensitivity differences. College students (one male and one female group), female office workers, and male maintenance workers (electricians, carpenters, plumbers, and sheet metal workers) were tested. Perception and annoyance thresholds were determined for capacitive discharge stimuli to the fingertip and forearm. Nonsensory data were taken for each individual in an attempt to account for individual sensitivity differences (occupation, sex, age, height, weight, skin temperature, finger and forearm diameter, skin hardness, customary physical activity level, and prior degree of experience with electric shock). Of these, body size was the only significant correlate of electrical sensitivity. Apparent correlations with sex and occupation were found to be artifacts of the body size relationship. A regression equation relating sensitivity to body weight is presented.