Miracle-dz/UniFAR-FTUs huggingface dataset:
Correlated Component Analysis for Enhancing the Performance of SSVEP-Based Brain-Computer Interface

A new method for steady-state visual evoked potentials (SSVEPs) frequency recognition is proposed to enhance the performance of SSVEP-based brain-computer interface (BCI). Correlated component analysis (CORCA) is introduced, which originally was designed to find linear combinations of electrodes that are consistent across subjects and maximally correlated between them. We propose a CORCA algorithm to learn spatial filters with multiple blocks of individual training data for SSVEP-based BCI scenario. The spatial filters are used to remove background noises by combining the multichannel electroencephalogram signals. We conduct a comparison between the proposed CORCA-based and the task-related component analysis (TRCA) based methods using a 40-class SSVEP benchmark data set recorded from 35 subjects. Our experimental study validates the efficiency of the CORCA-based method, and the extensive comparison results indicate that the CORCA-based method significantly outperforms the TRCA-based method. Superior performance demonstrates that the proposed method holds the promising potential to achieve satisfactory performance for SSVEP-based BCI with a large number of targets.
Contemporary Associative Learning Theory Predicts Failures to Obtain Blocking: Comment on Maes et al. (2016)

In a recent article, Maes et al. (2016) report the results from 15 experiments in the blocking effect, all of which failed to replicate the basic phenomenon. Whereas Maes et al. did not dispute the reality of the blocking effect, they concluded that the effect is more difficult to obtain than what could be assumed from the literature and that we lack insight into its boundary conditions. This conclusion is incorrect, because contemporary associative learning theory both agrees with the authors’ conclusion that blocking is parameter-dependent and it makes specific predictions about the experimental parameters likely to produce a small or no blocking effect. Ten of the 15 experiments presented by Maes et al. use exactly those parameters (same-modality stimuli for the compound AX), making their results completely unsurprising in the light of contemporary associative learning theory. The results from 3 other experiments are difficult to interpret because of a floor effect. A failure to replicate blocking in only 2 experiments is unsurprising and can be explained as the result of statistical variability or changes in experimental procedure.
Where are my fingers? Assessing multi-digit proprioceptive localization

The proprioceptive sense is an important component in the sensory system, providing position estimates for the parts of our body that are needed in order to guide behavior. While prior work has characterized proprioceptive localization of the upper limb as a whole, few studies have investigated the proprioceptive localization of individual digits, despite their central role in tactile exploration and fine manipulation. In this study, we asked subjects to report the perceived positions of the endpoints of each finger by means of a virtual reality and multi-finger tracking system, and we investigated the magnitude and variability of the proprioceptive localization errors that ensued. We found the errors to be large, averaging 4.3 cm per digit, even when the location of the wrist was disclosed to participants. This error magnitude is comparable to those that have been reported for whole limb localization, and represents a significant fraction of the length of an entire digit. Localization accuracy is greatest for the thumb and smallest for the little finger, reflecting in all cases, significant biases in perceived locations. The precision of localization was similar for each finger, with uncertainties on the order of several centimeters. The posture of the hand and specific location of the finger both affected errors. The specific error patterns for each subject were idiosyncratic, and the results suggest an underlying proprioceptive hand representation in which the fingers are distorted from the true shape of the hand. These results may have implications for understanding the role of position sensing in tactile exploration and fine manipulation, and suggest that an improved understanding of sensorimotor integration of proprioceptive information from the fingers is needed.
Stability of Programmable Shunt Valve Settings with Simultaneous Use of the Optune Transducer Array: A Case Report

The Optune® transducer array (Novocure Ltd., Haifa, Israel) is an FDA-approved noninvasive regional therapy that aims to inhibit the growth of glioblastoma multiforme (GBM) cells via utilization of alternating electric fields. Some patients with GBM may develop hydrocephalus and benefit from subsequent shunt placement, but special attention must be paid to patients in whom programmable valves are utilized, given the potential effect of the magnetic fields on valve settings. We present the first case report illustrating the stability of programmable shunt valve settings in a neurosurgical patient undergoing therapy with the Optune device. In this study, shunt valve settings were stable over a period of five days despite Optune therapy. This is reassuring for patients with GBM who require simultaneous treatment with both the Optune device and a programmable shunt system.
One-Shot Private Classical Capacity of Quantum Wiretap Channel: Based on one-shot quantum covering lemma

In this work we study the problem of communication over the quantum wiretap channel. For this channel there are three parties Alice (sender), Bob (legitimate receiver) and Eve (eavesdropper). We obtain upper and lower bounds on the amount of information Alice can communicate to Bob such that Eve gets to know as little information as possible about the transmitted messages. Our bounds are in terms of quantum hypothesis testing divergence and smooth max quantum relative entropy. To obtain our result we prove a one-shot version of the quantum covering lemma along with operator Chernoff bound for non-square matrices.
Multi-Context Integrated Deep Neural Network Model for Next Location Prediction

The prediction of next location for users in location-based social networks has become an increasing significant requirement since it can benefit both users and business. However, existing methods lack an integrated analysis of sequence context, input contexts, and user preferences in a unified way, and result in an unsatisfactory prediction. Moreover, the interaction between different kinds of input contexts has not been investigated. In this paper, we propose a multi-context integrated deep neural network model (MCI-DNN) to improve the accuracy of the next location prediction. In this model, we integrate sequence context, input contexts, and user preferences into a cohesive framework. First, we model sequence context and interaction of different kinds of input contexts jointly by extending the recurrent neural network to capture the semantic pattern of user behaviors from check-in records. After that, we design a feedforward neural network to capture high-level user preferences from check-in data and incorporate that into MCI-DNN. To deal with different kinds of input contexts in the form of multi-field categorical, we adopt embedding representation technology to automatically learn dense feature representations of input contexts. Experimental results on two typical real-world data sets show that the proposed model outperforms the current state-of-the-art approaches by about 57.12% for Foursquare and 76.4% for Gowalla on average regarding F1-score@5.
Twenty-Four Hour Total and Dietary Fat Oxidation in Lean, Obese and Reduced-Obese Adults with and without a Bout of Exercise

Background It has been hypothesized that obese and reduced-obese individuals have decreased oxidative capacity, which contributes to weight gain and regain. Recent data have challenged this concept. Objective To determine (1) whether total and dietary fat oxidation are decreased in obese and reduced-obese adults compared to lean but increase in response to an acute exercise bout and (2) whether regular physical activity attenuates these metabolic alterations. Design We measured 24-hr total (whole-room calorimetry) and dietary fat (14C-oleate) oxidation in Sedentary Lean (BMI = 21.5±1.6; n = 10), Sedentary Obese (BMI = 33.6±2.5; n = 9), Sedentary Reduced-Obese (RED-SED; BMI = 26.9±3.7; n = 7) and in Physically Active Reduced-Obese (RED-EX; BMI = 27.3±2.8; n = 12) men and women with or without an acute exercise bout where energy expended during exercise was not replaced. Results Although Red-SED and Red-EX had a similar level of fatness, aerobic capacity and metabolic profiles were better in Red-EX only compared to Obese subjects. No significant between-group differences were seen in 24-hr respiratory quotient (RQ, Lean: 0.831±0.044, Obese: 0.852±0.023, Red-SED: 0.864±0.037, Red-EX: 0.842±0.039), total and dietary fat oxidation. A single bout of exercise increased total (+27.8%, p<0.0001) and dietary (+6.6%, p = 0.048) fat oxidation across groups. Although exercise did not impact RQ during the day, it decreased RQ during sleep (p = 0.01) in all groups. Red-EX oxidized more fat overnight than Red-SED subjects under both resting (p = 0.036) and negative energy balance (p = 0.003) conditions, even after adjustment for fat-free mass. Conclusion Obese and reduced-obese individuals oxidize as much fat as lean both under eucaloric and negative energy balance conditions, which does not support the hypothesis of reduced oxidative capacity in these groups. Reduced-obese individuals who exercise regularly have markers of metabolic health similar to those seen in lean adults. Both the acute and chronic effects of exercise were primarily observed at night suggesting an important role of sleep in the regulation of lipid metabolism.
Apparent Diffusion Coefficient and Cerebrospinal Fluid Flow Measurements in Patients With Hydrocephalus

Objective: To evaluate the efficacy of diffusion magnetic resonance imaging and compare with cerebrospinal fluid (CSF) flow imaging in patients with hydrocephalus before and after treatment. Methods: Twenty patients with hydrocephalus (group 1, pediatric, with primary aqueductal stenosis, n = 10; group 2, adult, with normal-pressure hydrocephalus, n = 10) and 20 age-matched healthy subjects that served as controls were examined. Cerebrospinal fluid flow velocity interval was calculated as the mean absolute values of the peak craniocaudal velocity and caudocranial velocity on CSF flow measurements. On diffusion magnetic resonance imaging, apparent diffusion coefficient (ADC) values from 8 regions were evaluated. Results: The decrease in ADC values after treatment was significant in both groups (P < 0.001 for both). Preoperative mean CSF flow velocity interval value was significantly lower in group 1 and significantly higher than postoperative and control group values in group 2 (P < 0.001 for all). Conclusion: The ADC values increase in hydrocephalus and decrease significantly after treatment. Preoperative ADC value may serve as baseline, and the change in ADC may be an indicator of response to treatment and CSF flow measurements.
Micronutrient Intake among Children in Puerto Rico: Dietary and Multivitamin-Multimineral Supplement Sources.

BACKGROUND Micronutrients are critical for healthy growth and development of children. Micronutrient intake from dietary sources is inadequate among some children and may be improved by use of multivitamin and multimineral (MVMM) supplements. OBJECTIVE To assess micronutrient intake from dietary and MVMM supplement sources among 12-year-old children in Puerto Rico. METHODS A representative sample of 732 children enrolled in an oral health study in Puerto Rico, who completed dietary and MVMM assessments through one 24-h recall, were included in this analysis. Micronutrient intake sources were described and compared to the Dietary Reference Intakes (DRIs) using the Estimated Average Requirement when available (used Adequate Intake for vitamin K and pantothenic acid). Micronutrient profiles of MVMM users and non-users were compared using t-tests. RESULTS Mean intakes of vitamins A, D, E, and K, pantothenic acid, calcium, and magnesium from food and beverage sources were below the DRIs. From food and beverage sources, MVMM users had higher intakes of riboflavin and folate compared to non-users (p < 0.05). When MVMM supplements were taken into account, users had higher intakes of all nutrients except vitamin K. With the help of MVMM, users increased intake of vitamins E, A, D, and pantothenic acid to IOM-recommended levels but calcium, magnesium, and vitamin K remained below guidelines. CONCLUSION Micronutrient intake from diet was below the IOM-recommended levels in the total sample. MVMM use improved intake of selected micronutrients and facilitated meeting recommendations for some nutrients. Public health measures to improve micronutrient intake among children in Puerto Rico are needed.
Host and Viral Determinants of Mx2 Antiretroviral Activity

ABSTRACT Myxovirus resistance 2 (Mx2/MxB) has recently been uncovered as an effector of the anti-HIV-1 activity of type I interferons (IFNs) that inhibits HIV-1 at an early stage postinfection, after reverse transcription but prior to proviral integration into host DNA. The mechanistic details of Mx2 antiviral activity are not yet understood, but a few substitutions in the HIV-1 capsid have been shown to confer resistance to Mx2. Through a combination of in vitro evolution and unbiased mutagenesis, we further map the determinants of sensitivity to Mx2 and reveal that multiple capsid (CA) surfaces define sensitivity to Mx2. Intriguingly, we reveal an unanticipated sensitivity determinant within the C-terminal domain of capsid. We also report that Mx2s derived from multiple primate species share the capacity to potently inhibit HIV-1, whereas selected nonprimate orthologs have no such activity. Like TRIM5α, another CA targeting antiretroviral protein, primate Mx2s exhibit species-dependent variation in antiviral specificity against at least one extant virus and multiple HIV-1 capsid mutants. Using a combination of chimeric Mx2 proteins and evolution-guided approaches, we reveal that a single residue close to the N terminus that has evolved under positive selection can determine antiviral specificity. Thus, the variable N-terminal region can define the spectrum of viruses inhibited by Mx2. IMPORTANCE Type I interferons (IFNs) inhibit the replication of most mammalian viruses. IFN stimulation upregulates hundreds of different IFN-stimulated genes (ISGs), but it is often unclear which ISGs are responsible for inhibition of a given virus. Recently, Mx2 was identified as an ISG that contributes to the inhibition of HIV-1 replication by type I IFN. Thus, Mx2 might inhibit HIV-1 replication in patients, and this inhibitory action might have therapeutic potential. The mechanistic details of how Mx2 inhibits HIV-1 are currently unclear, but the HIV-1 capsid protein is the likely viral target. Here, we determine the regions of capsid that specify sensitivity to Mx2. We demonstrate that Mx2 from multiple primates can inhibit HIV-1, whereas Mx2 from other mammals (dogs and sheep) cannot. We also show that primate variants of Mx2 differ in the spectrum of lentiviruses they inhibit and that a single residue in Mx2 can determine this antiviral specificity.
Encoding contributions to mnemonic discrimination and its age-related decline

iii Table of contents . v Glossary . xiii List of tables . xvi List of figures . xix Chapter 1: Introduction . 1 1.1 Overview . 1 Part 1 – Mnemonic discrimination . 2 1.2 Context . 2 1.2. 1 Episodic memory . 2 1.2. 2 Mnemonic discrimination . 2 1.2. 3 Behavioural investigations of mnemonic discrimination . 3 1.2. 4 Neural basis of encoding . 5 1.3 Gist vs. item-specific memory . 6 1.3. 1 Fuzzy-Trace Theory (FTT) . 6 1.3. 2 Encoding-related predictions of FTT . 8 1.3. 3 Gist accounts incorporating perceptual gist . 10 1.3. 4 Activation-monitoring . 11 1.4 Pattern separation and pattern completion . 13 1.4. 1. Definitions . 13 1.4. 2 Models of pattern separation and completion . 14 1.4. 3 Human fMRI investigations of hippocampal pattern separation . 16 1.4. 4 Contribution of pattern separation to mnemonic discrimination . 20 1.4. 5 Pattern separation and completion outside the hippocampus. 24
Use of chimeric type IV secretion systems to define contributions of outer membrane subassemblies for contact‐dependent translocation

Recent studies have shown that conjugation systems of Gram‐negative bacteria are composed of distinct inner and outer membrane core complexes (IMCs and OMCCs, respectively). Here, we characterized the OMCC by focusing first on a cap domain that forms a channel across the outer membrane. Strikingly, the OMCC caps of the Escherichia coli pKM101 Tra and Agrobacterium tumefaciens VirB/VirD4 systems are completely dispensable for substrate transfer, but required for formation of conjugative pili. The pKM101 OMCC cap and extended pilus also are dispensable for activation of a Pseudomonas aeruginosa type VI secretion system (T6SS). Chimeric conjugation systems composed of the IMCpKM101 joined to OMCCs from the A. tumefaciens VirB/VirD4, E. coli R388 Trw, and Bordetella pertussis Ptl systems support conjugative DNA transfer in E. coli and trigger P. aeruginosa T6SS killing, but not pilus production. The A. tumefaciens VirB/VirD4 OMCC, solved by transmission electron microscopy, adopts a cage structure similar to the pKM101 OMCC. The findings establish that OMCCs are highly structurally and functionally conserved – but also intrinsically conformationally flexible – scaffolds for translocation channels. Furthermore, the OMCC cap and a pilus tip protein coregulate pilus extension but are not required for channel assembly or function.
Green Tea Consumption and Risk of Pancreatic Cancer: A Meta-analysis

Emerging laboratory and animal studies indicate that green tea inhibits development and progression of pancreatic cancer, but evidence from epidemiologic studies appears inconsistent and inconclusive. A meta-analysis summarizing published case-control and cohort studies was performed to evaluate the association of green tea consumption with risk of pancreatic cancer. Pertinent studies were identified by a search of PubMed and EMBASE up to April 2014. A random-effects model was assigned to compute summary risk estimates. A total of three case-control studies and five prospective studies were included, comprising 2317 incident cases and 288209 subjects. Of them, three studies were from China and the reminders were conducted in Japan. Overall, neither high vs. low green consumption (odds ratio (OR) = 0.99, 95% confidence interval [CI] = 0.78–1.25), nor an increase in green tea consumption of two cups/day (OR = 0.95, 95% CI = 0.85–1.06) was associated with risk of pancreatic cancer. The null association persisted when the analysis was stratified by sex or restricted to non-smokers. In the stratification by study location, the summary OR for the studies from China and for those from Japan was 0.77 (95% CI = 0.60–0.99) and 1.21 (95% CI = 0.94–1.54), respectively (P for differences = 0.04). Cumulative epidemiologic evidence suggests that green tea consumption is not associated with pancreatic cancer.
No evidence that rare coding variants in ZNF804A confer risk of schizophrenia

Strong evidence that rare variants of relatively high penetrance are involved in the etiology of schizophrenia is currently restricted to the data from studies investigating copy number variants and major structural re‐arrangements in that disorder. Global tests of the hypothesis of the involvement of fairly high penetrance rare single nucleotide changes or small insertion deletion events await the genesis of data from large‐scale sequencing studies, meanwhile, a pragmatic approach to trying to detect such alleles is to target sequencing efforts on genes for which there is compelling evidence from other sources for their involvement in this disorder. We have undertaken a study, which aimed to identify whether rare (frequency ∼0.001%) coding variants in the schizophrenia susceptibility gene ZNF804A are involved in this disorder. We screened the coding regions of the gene in 517 schizophrenic cases and 501 controls, and genotyped rare non‐synonymous variants in a case–control sample powered to detect association to rare alleles with an effect size (odds ratio) of 5. No single rare variant was associated with schizophrenia, nor was the burden of rare, or even fairly common, non‐synonymous variants. Our results do not support the hypothesis that moderately rare non‐synonymous variants at the ZNF804A locus are involved in schizophrenia susceptibility. © 2010 Wiley‐Liss, Inc.
Consensus paper of the WFSBP Task Force on Genetics: Genetics, epigenetics and gene expression markers of major depressive disorder and antidepressant response

Abstract Major depressive disorder (MDD) is a heritable disease with a heavy personal and socio-economic burden. Antidepressants of different classes are prescribed to treat MDD, but reliable and reproducible markers of efficacy are not available for clinical use. Further complicating treatment, the diagnosis of MDD is not guided by objective criteria, resulting in the risk of under- or overtreatment. A number of markers of MDD and antidepressant response have been investigated at the genetic, epigenetic, gene expression and protein levels. Polymorphisms in genes involved in antidepressant metabolism (cytochrome P450 isoenzymes), antidepressant transport (ABCB1), glucocorticoid signalling (FKBP5) and serotonin neurotransmission (SLC6A4 and HTR2A) were among those included in the first pharmacogenetic assays that have been tested for clinical applicability. The results of these investigations were encouraging when examining patient-outcome improvement. Furthermore, a nine-serum biomarker panel (including BDNF, cortisol and soluble TNF-α receptor type II) showed good sensitivity and specificity in differentiating between MDD and healthy controls. These first diagnostic and response-predictive tests for MDD provided a source of optimism for future clinical applications. However, such findings should be considered very carefully because their benefit/cost ratio and clinical indications were not clearly demonstrated. Future tests may include combinations of different types of biomarkers and be specific for MDD subtypes or pathological dimensions.
MTHFR functional genetic variation and methotrexate treatment response in rheumatoid arthritis: a meta-analysis.

AIM To date, functional MTHFR SNPs have been tested for their impact on low-dose methotrexate (MTX) response in small rheumatoid arthritis (RA) cohorts. We sought to test their effect in the single largest cohort studied to date, and undertook a meta-analysis utilizing stringent study inclusion criteria. MATERIALS & METHODS RA patients treated with MTX monotherapy from the Yorkshire Early Arthritis Register (YEAR) were genotyped using RFLP assays, and tested for association with treatment efficacy. Studies for meta-analysis were screened by a set of stringent inclusion criteria. RESULTS & CONCLUSION rs1801131 and rs1801133 were not associated with response to MTX in the YEAR cohort, nor did they affect the probability of achieving a low disease activity state. A meta-analysis of comparable studies found no association with these SNPs. MTHFR SNPs rs1801131 and rs1801133 are unlikely to have a clinically meaningful effect on the first 6 months of MTX treatment in early RA.