Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of motivation on reward and attentional networks: an fMRI study

Existing evidence suggests that reward and attentional networks function in concert and that activation in one system influences the other in a reciprocal fashion; however, the nature of these influences remains poorly understood. We therefore developed a three‐component task to assess the interaction effects of reward anticipation and conflict resolution on the behavioral performance and the activation of brain reward and attentional systems. Sixteen healthy adult volunteers aged 21–45 years were scanned with functional magnetic resonance imaging (fMRI) while performing the task. A two‐way repeated measures analysis of variance (ANOVA) with cue (reward vs. non‐reward) and target (congruent vs. incongruent) as within‐subjects factors was used to test for main and interaction effects. Neural responses to anticipation, conflict, and reward outcomes were tested. Behaviorally there were main effects of both reward cue and target congruency on reaction time. Neuroimaging results showed that reward anticipation and expected reward outcomes activated components of the attentional networks, including the inferior parietal and occipital cortices, whereas surprising non‐rewards activated the frontoinsular cortex bilaterally and deactivated the ventral striatum. In turn, conflict activated a broad network associated with cognitive control and motor functions. Interaction effects showed decreased activity in the thalamus, anterior cingulated gyrus, and middle frontal gyrus bilaterally when difficult conflict trials (e.g., incongruent targets) were preceded by reward cues; in contrast, the ventral striatum and orbitofrontal cortex showed greater activation during congruent targets preceded by reward cues. These results suggest that reward anticipation is associated with lower activation in attentional networks, possibly due to increased processing efficiency, whereas more difficult, conflict trials are associated with lower activity in regions of the reward system, possibly because such trials are experienced as less rewarding.
Network, Anatomical, and Non-Imaging Measures for the Prediction of ADHD Diagnosis in Individual Subjects

Brain imaging methods have long held promise as diagnostic aids for neuropsychiatric conditions with complex behavioral phenotypes such as Attention-Deficit/Hyperactivity Disorder. This promise has largely been unrealized, at least partly due to the heterogeneity of clinical populations and the small sample size of many studies. A large, multi-center dataset provided by the ADHD-200 Consortium affords new opportunities to test methods for individual diagnosis based on MRI-observable structural brain attributes and functional interactions observable from resting-state fMRI. In this study, we systematically calculated a large set of standard and new quantitative markers from individual subject datasets. These features (>12,000 per subject) consisted of local anatomical attributes such as cortical thickness and structure volumes, and both local and global resting-state network measures. Three methods were used to compute graphs representing interdependencies between activations in different brain areas, and a full set of network features was derived from each. Of these, features derived from the inverse of the time series covariance matrix, under an L1-norm regularization penalty, proved most powerful. Anatomical and network feature sets were used individually, and combined with non-imaging phenotypic features from each subject. Machine learning algorithms were used to rank attributes, and performance was assessed under cross-validation and on a separate test set of 168 subjects for a variety of feature set combinations. While non-imaging features gave highest performance in cross-validation, the addition of imaging features in sufficient numbers led to improved generalization to new data. Stratification by gender also proved to be a fruitful strategy to improve classifier performance. We describe the overall approach used, compare the predictive power of different classes of features, and describe the most impactful features in relation to the current literature.
Enhancement of the Rate of Pyrophosphate Hydrolysis by Nonenzymatic Catalysts and by Inorganic Pyrophosphatase*

To estimate the proficiency of inorganic pyrophosphatase as a catalyst, 31P NMR was used to determine rate constants and thermodynamics of activation for the spontaneous hydrolysis of inorganic pyrophosphate (PPi) in the presence and absence of Mg2+ at elevated temperatures. These values were compared with rate constants and activation parameters determined for the reaction catalyzed by Escherichia coli inorganic pyrophosphatase using isothermal titration calorimetry. At 25 °C and pH 8.5, the hydrolysis of MgPPi2− proceeds with a rate constant of 2.8 × 10−10 s−1, whereas E. coli pyrophosphatase was found to have a turnover number of 570 s−1 under the same conditions. The resulting rate enhancement (2 × 1012-fold) is achieved entirely by reducing the enthalpy of activation (ΔΔH‡ = −16.6 kcal/mol). The presence of Mg2+ ions or the transfer of the substrate from bulk water to dimethyl sulfoxide was found to increase the rate of pyrophosphate hydrolysis by as much as ∼106-fold. Transfer to dimethyl sulfoxide accelerated PPi hydrolysis by reducing the enthalpy of activation. Mg2+ increased the rate of PPi hydrolysis by both increasing the entropy of activation and reducing the enthalpy of activation.
Reference Price and Price Perceptions: A Comparison of Alternative Models

Reference price effects on consumer price perceptions are often explained by Helson's adaptation-level theory, in which the cognitive representation of reference price is the prototype of the relevant category. However, recent conceptualizations and empirical evidence suggest the possibility of an exemplar model, which may be specified using Volkmann's range theory or Parducci's range-frequency theory. In two experiments, these three contextual models of reference price effects are pitted against one another. Based on the MANOVA and model fitting, range-frequency theory accounted for reference price effects that the other theories could not, suggesting that consumers compare the target price against specific members of the category rather than the category prototype. A third experiment demonstrated that range and frequency effects are moderated by the stimulus presentation condition, suggesting that consumers place greater weight on extreme prices anchoring the range for internal reference prices than for external reference prices. Copyright 2001 by the University of Chicago.
Gene expression Improving missing value estimation in microarray data with gene ontology

Motivation: Gene expression microarray experiments produce datasets with frequent missing expression values. Accurate estimation of missing values is an important prerequisite for efficient data analysis as many statistical and machine learning techniques either require a complete dataset or their results are significantly dependent on the quality of suchestimates.A limitationof theexistingestimationmethods for microarray data is that they use no external information but the estimation is based solely on the expression data. We hypothesized that utilizing a priori information on functional similarities available from public databases facilitates the missing value estimation. Results:We investigated whether semantic similarity originating from geneontology (GO) annotations could improve the selection of relevant genes for missing value estimation. The relative contribution of each information source was automatically estimated from the data using an adaptive weight selection procedure. Our experimental results in yeast cDNA microarray datasets indicated that by considering GO information in the k-nearest neighbor algorithm we can enhance its performance considerably, especially when the number of experimental conditions is small and the percentage of missing values is high. The increase of performance was less evident with a more sophisticated estimation method. We conclude that even a small proportion of annotated genes can provide improvements in data quality significant for the eventual interpretation of the microarray experiments. Availability: Java and Matlab codes are available on request from the
Critical Evaluation of the Use of Cell Cultures for Inclusion in Clinical Trials of Patients Affected by Collagen VI Myopathies

Collagen VI myopathies (Ullrich congenital muscular dystrophy (UCMD), Bethlem myopathy (BM), and myosclerosis myopathy) share a common pathogenesis, that is, mitochondrial dysfunction due to deregulation of the permeability transition pore (PTP). This effect was first identified in the Col6a1−/− mouse model and then in muscle cell cultures from UCMD and BM patients; the normalizing effect of cyclosporin A (CsA) confirmed the pathogenic role of PTP opening. In order to determine whether mitochondrial performance can be used as a criterion for inclusion in clinical trials and as an outcome measure of the patient response to therapy, it is mandatory to establish whether mitochondrial dysfunction is conserved in primary cell cultures from UCMD and BM patients. In this study we report evidence that mitochondrial dysfunction and the consequent increase of apoptotic rate can be detected not only, as previously reported, in muscle, but also in fibroblast cell cultures established from muscle biopsies of collagen VI‐related myopathic patients. However, the mitochondrial phenotype is no longer maintained after nine passages in culture. These data demonstrate that the dire consequences of mitochondrial dysfunction are not limited to myogenic cells, and that this parameter can be used as a suitable diagnostic criterion, provided that the cell culture conditions are carefully established. J. Cell. Physiol. 227: 2927–2935, 2012. © 2011 Wiley Periodicals, Inc.
Update of Practice Guidelines for the Management of Community-Acquired Pneumonia in Immunocompetent Adults

The Infectious Diseases Society of America (IDSA) produced guidelines for community-acquired pneumonia (CAP) in immunocompetent adults in 1998 and again in 2000 [1, 2]. Because of evolving resistance to antimicrobials and other advances, it was felt that an update should be provided every few years so that important developments could be highlighted and pressing questions answered. We addressed those issues that the committee believed were important to the practicing physician, including suggestions for initial empiric therapy for CAP. In some cases, only a few paragraphs were needed, whereas, in others, a somewhat more in-depth discussion was provided. Because many physicians focus on the tables rather than on the text of guidelines, it was decided that all of the information dealing with the initial empiric treatment regimens should be in tabular format with footnotes (tables 1–3). The topics selected for updating have been organized according to the headings used in the August 2000 CAP guidelines pub-
FATCAT: a web server for flexible structure comparison and structure similarity searching

Protein structure comparison, an important problem in structural biology, has two main applications: (i) comparing two protein structures in order to identify the similarities and differences between them, and (ii) searching for structures similar to a query structure. Many web-based resources for both applications are available, but all are based on rigid structural alignment algorithms. FATCAT server implements the recently developed flexible protein structure comparison algorithm FATCAT, which automatically identifies hinges and internal rearrangements in two protein structures. The server provides access to two algorithms: FATCAT-pairwise for pairwise flexible structure comparison and FATCAT-search for database searching for structurally similar proteins. Given two protein structures [in the Protein Data Bank (PDB) format], FATCAT-pairwise reports their structural alignment and the corresponding statistical significance of the similarity measured as a P-value. Users can view the superposition of the structures online in web browsers that support the Chime plug-in, or download the superimposed structures in PDB format. In FATCAT-search, users provide one query structure and the server returns a list of protein structures that are similar to the query, ordered by the P-values. In addition, FATCAT server can report the conformational changes of the query structure as compared to other proteins in the structure database. FATCAT server is available at http://fatcat.burnham. org.
Serum Testosterone Levels and Symptom-Based Depression Subtypes in Men

The main objective of this preliminary study was to further clarify the association between testosterone (T) levels and depression by investigating symptom-based depression subtypes in a sample of 64 men. The data were taken from the ZInEP epidemiology survey. Gonadal hormones of a melancholic (n = 25) and an atypical (n = 14) depression subtype, derived from latent class analysis, were compared with those of healthy controls (n = 18). Serum T was assayed using an enzyme-linked immunosorbent assay procedure. Analysis of variance, analysis of covariance, non-parametrical tests, and generalized linear regression models were performed to examine group differences. The atypical depressive subtype showed significantly lower T levels compared with the melancholic depressives. While accumulative evidence indicates that, beyond psychosocial characteristics, the melancholic and atypical depressive subtypes are also distinguishable by biological correlates, the current study expanded this knowledge to include gonadal hormones. Further longitudinal research is warranted to disclose causality by linking the multiple processes in pathogenesis of depression.
In vitro activity of cefoperazone plus sulbactam compared with that of other antimicrobial agents against anaerobic bacteria

The activity of two cefoperazone-sulbactam combinations against anaerobic bacteria was tested and compared both with that of cefoperazone alone and with that of other commonly used antimicrobial agents. Imipenem was the most active of the tested agents, followed by chloramphenicol, metronidazole, and cefoperazone-sulbactam (90 to 100% of bacterial growth inhibited). Clindamycin and cefoxitin inhibited approximately 80%, cefoperazone inhibited 63%, and penicillin G inhibited 47% of the strains tested. The agents were variable in activity against the Bacteroides fragilis group, with percents susceptible as follows: cefoperazone-sulbactam, imipenem, metronidazole, and chloramphenicol, 99 to 100%; cefoxitin and clindamycin, approximately 80%; cefoperazone, 49%; and penicillin G, 15.5%.
Membranes and the setting of energy demand

SUMMARY In his classic 1961 book, The Fire of Life, Max Kleiber presented a critique of the theories advanced to explain the BMR-body size relationship. One of the theories he dismissed was that the chemical composition of animals varies with body size. Since this time, however, much has been learned about the make-up of BMR in different animals as well as the chemical composition of different-sized animals. Specifically, in recent years it has become obvious that mammal species and bird species do vary in chemical composition in a systematic manner associated with the body size of the species. Small mammal and bird species have cellular membranes that are predominantly polyunsaturated, and as mammal and bird species increase in size, their cellular membranes become progressively less polyunsaturated. Since Kleiber's time, it has also become obvious that a substantial amount of the energy turnover of BMR is associated with the activity of membrane processes, specifically the maintenance of trans-membrane gradients, such as the Na+ gradient across the plasmalemmal membrane and the H+ gradient across the mitochondrial inner membrane. The variation in both membrane composition and membrane processes associated with body size variation in metabolic rate has been combined in the `membrane pacemaker' theory of metabolism. This theory proposes that: (1) membrane-associated activities are significant and dominant components of BMR; (2) when BMR varies among species, all the activities that constitute BMR vary in unison; (3) species with high mass-specific BMR have highly polyunsaturated membranes while those with low BMR have less polyunsaturation of their membranes; (4) highly polyunsaturated membranes have distinctive physical properties that cause the proteins in the membranes to have a high molecular activity, and this results in higher rates of metabolism of cells, tissues and, consequently, the whole animal. Evidence supporting this theory is both correlative and experimental. Manipulation of membrane composition changes the molecular activity of membrane proteins. These differences in membrane composition may also represent a link between metabolism and aging. They probably explain the lifespan-body size relationship in mammals and birds and also the mammal-bird difference in lifespan.
Cell-Edge-Aware Precoding for Downlink Massive MIMO Cellular Networks

We propose a <italic>cell-edge-aware</italic> (CEA) zero forcing (ZF) precoder that exploits the excess spatial degrees of freedom provided by a large number of base station (BS) antennas to suppress inter-cell interference at the most vulnerable user equipments (UEs). We evaluate the downlink performance of CEA-ZF, as well as that of a conventional <italic>cell-edge-unaware</italic> (CEU) ZF precoder in a network with a random BS topology. Our analysis and simulations show that the proposed CEA-ZF precoder outperforms CEU-ZF precoding in terms of (i) aggregate per-cell data rate, (ii) coverage probability, and (iii) <inline-formula><tex-math notation="LaTeX">$95\%$</tex-math> </inline-formula>-likely, or edge user, rate. In particular, when both perfect channel state information and a large number of antennas <inline-formula><tex-math notation="LaTeX">$N$</tex-math></inline-formula> are available at the BSs, we demonstrate that the outage probability under CEA-ZF and CEU-ZF decay as <inline-formula> <tex-math notation="LaTeX">${1}/{N^2}$</tex-math></inline-formula> and <inline-formula><tex-math notation="LaTeX"> ${1}/{N}$</tex-math></inline-formula>, respectively. This result identifies CEA-ZF as a more effective precoding scheme for massive multiple-input multiple-output (MIMO) cellular networks. Our framework also reveals the importance of scheduling the optimal number of UEs per BS, and confirms the necessity to control the amount of pilot contamination received during the channel estimation phase.
Joint tensor compression for coupled canonical polyadic decompositions

To deal with large multimodal datasets, coupled canonical polyadic decompositions are used as an approximation model. In this paper, a joint compression scheme is introduced to reduce the dimensions of the dataset. Joint compression allows to solve the approximation problem in a compressed domain using standard coupled decomposition algorithms. Computational complexity required to obtain the coupled decomposition is therefore reduced. Also, we propose to approximate the update of the coupled factor by a simple weighted average of the independent updates of the coupled factors. The proposed approach and its simplified version are tested with synthetic data and we show that both do not incur substantial loss in approximation performance.
Context Effects

This article provides an analysis of the way in which placebo effects could be investigated and taken into account, supported by a description of some of the major articles that have been published on this topic. Based on conceptual, theoretical, and methodological issues, the authors highlight some of the reasons for current controversies regarding the nature of placebo effects. They suggest the use of the term context effects to overcome some of the negative connotations associated with the term placebo and to highlight the therapeutic nature of the health care context, and they present the major findings and limitations from their systematic review of the therapeutic effects of health care interactions. Recommendations for future research are proposed.
X-Ray Absorption Spectroscopy as a Probe of Microbial Sulfur Biochemistry: the Nature of Bacterial Sulfur Globules Revisited

ABSTRACT The chemical nature of the sulfur in bacterial sulfur globules has been the subject of controversy for a number of years. Sulfur K-edge X-ray absorption spectroscopy (XAS) is a powerful technique for probing the chemical forms of sulfur in situ, but two groups have used it with very different conclusions. The root of the controversy lies with the different detection strategies used by the two groups, which result in very different spectra. This paper seeks to resolve the controversy. We experimentally demonstrate that the use of transmittance detection for sulfur K-edge XAS measurements is highly prone to spectroscopic distortions and that much of the published work on sulfur bacteria is very likely based on distorted data. We also demonstrate that all three detection methods used for X-ray absorption experiments yield essentially identical spectra when the measurements are carried out under conditions where no experimental distortions are expected. Finally, we turn to the original question—the chemical nature of bacterial sulfur. We examine isolated sulfur globules of Allochromatium vinosum and intact cells of a strain of magnetotactic coccus and show that XAS indicates the presence of a chemical form of sulfur resembling S8.
Maternal screening and postpartum vaccination for measles infection in Japan: a cohort study

Please cite this paper as: Shoda A, Hayashi M, Takayama N, Oshima K, Nishikawa M, Okazaki T, Negishi M, Hayashida S, Watanabe H, Inaba N. Maternal screening and postpartum vaccination for measles infection in Japan: a cohort study. BJOG 2011;118:88–92.
Histological and histochemical effects of Gly-phosate on testicular tissue and function

Background: In this study we aimed to evaluate the impact of chronic exposure to the Gly-phosate (GP) on rat’s testicular tissue and sperm parameters. Objective: Testicular tissue, morphology of sperms and testosterone level in serum of mature male rats were analyzed. Materials and Methods: Animals were divided into two test and control-sham groups. The test group was subdivided into 4 groups (10, 20, 30 and 40 days GP administrated). Each test group (n=8) received the compound at dose of 125 mg/kg, once a day, orally for 40 days while control-sham group (n=16) received the corn oil (0.2 ml/day). Results: Microscopic analyses revealed increased thickness of tunica albuginea, obvious edema in sub-capsular and interstitial connective tissue, atrophied seminiferous tubules, arrested spermatogenesis, negative tubular differentiation and repopulation indexes, decreased Leydig cells/mm2 of interstitial tissue, hypertrophy and cytoplasmic granulation of Leydig cells, elevated death, immature sperm and increased immotile and abnormal sperm percentage. The carbohydrate ratio was reduced in first three layers of the germinal epithelium (GE) cytoplasm. The upper layers of the GE series were manifested with low rate of lipid accumulation in cytoplasm, while the cells which were located in first layers were revealed with higher amount of lipid foci. Hematological investigations showed significant (p<0.05) decreasing of testosterone level in serum. Conclusion: The current data provide inclusive histological feature of chronic exposure against GP with emphasizing on reproductive disorders including histological adverse effect on the testicular tissue, spermatogenesis, sperm viability and abnormality which potentially can cause infertility.