Miracle-dz/UniFAR-FTUs huggingface dataset:
Pattern classification of brain activation during emotional processing in subclinical depression: psychosis proneness as potential confounding factor

We used Support Vector Machine (SVM) to perform multivariate pattern classification based on brain activation during emotional processing in healthy participants with subclinical depressive symptoms. Six-hundred undergraduate students completed the Beck Depression Inventory II (BDI-II). Two groups were subsequently formed: (i) subclinical (mild) mood disturbance (n = 17) and (ii) no mood disturbance (n = 17). Participants also completed a self-report questionnaire on subclinical psychotic symptoms, the Community Assessment of Psychic Experiences Questionnaire (CAPE) positive subscale. The functional magnetic resonance imaging (fMRI) paradigm entailed passive viewing of negative emotional and neutral scenes. The pattern of brain activity during emotional processing allowed correct group classification with an overall accuracy of 77% (p = 0.002), within a network of regions including the amygdala, insula, anterior cingulate cortex and medial prefrontal cortex. However, further analysis suggested that the classification accuracy could also be explained by subclinical psychotic symptom scores (correlation with SVM weights r = 0.459, p = 0.006). Psychosis proneness may thus be a confounding factor for neuroimaging studies in subclinical depression.
Validity and Reliability of Korean Version of International Physical Activity Questionnaire (IPAQ) Short Form.

Validity and Reliability of Korean Version of International Physical Activity Questionnaire (IPAQ) Short FormJi Yeon Oh, D.D.S., Ph.D., Yun Jun Yang, M.D., PH.D.*†, Byung Sung Kim, M.D., PH.D.**, Jae Hun Kang, M.D., PH.D.*
FPGA Accelerated Online Boosting for Multi-target Tracking

Robust real time tracking of multiple targets is a requisite feature for many applications. Online boosting has become an effective approach for dealing with the variability in object appearance. This approach can adapt its classifier to changes in appearance at the cost of additional runtime computation. In this paper, we address the task of accelerating online boosting for multiple target tracking. We propose a FPGA hardware accelerated architecture to evaluate and train a boosted classifier in real time. A general purpose CPU based software-only implementation can track a single target at 17 frames per second (FPS). The FPGA accelerated design is capable of tracking a single target at 1160 FPS or 57 independent targets at 30 FPS. This represents a 68× speed up over software.
LRP1 is a receptor for Clostridium perfringens TpeL toxin indicating a two-receptor model of clostridial glycosylating toxins

Significance Glycosylating toxins are major virulence factors of pathogenic Clostridia, including Clostridium difficile toxins A and B, which cause antibiotics-associated diarrhea and pseudomembranous colitis. Host cell uptake of these toxins is suggested to be mediated via C-terminal combined repetitive oligopeptides (CROP). Here, we identified LDL receptor-related protein 1 (LRP1) as a host cell receptor of Clostridium perfringens TpeL toxin, a recently identified clostridial glycosylating toxin, which has no CROP domain. TpeL binds to LRP1 with a C-terminal receptor-binding domain, which is conserved in all other clostridial glycosylating toxins and precedes the CROP domain. Thus, our study identifies LRP1 as TpeL receptor and suggests a two-receptor model for clostridial glycosylating toxins, which offers additional perspectives in antitoxin strategies. Large glycosylating toxins are major virulence factors of various species of pathogenic Clostridia. Prototypes are Clostridium difficile toxins A and B, which cause antibiotics-associated diarrhea and pseudomembranous colitis. The current model of the toxins’ action suggests that receptor binding is mediated by a C-terminal domain of combined repetitive oligopeptides (CROP). This model is challenged by the glycosylating Clostridium perfringens large cytotoxin (TpeL toxin) that is devoid of the CROP domain but still intoxicates cells. Using a haploid genetic screen, we identified LDL receptor-related protein 1 (LRP1) as a host cell receptor for the TpeL toxin. LRP1-deficient cells are not able to take up TpeL and are not intoxicated. Expression of cluster IV of LRP1 is sufficient to rescue toxin uptake in these cells. By plasmon resonance spectroscopy, a KD value of 23 nM was determined for binding of TpeL to LRP1 cluster IV. The C terminus of TpeL (residues 1335–1779) represents the receptor-binding domain (RBD) of the toxin. RBD-like regions are conserved in all other clostridial glycosylating toxins preceding their CROP domain. CROP-deficient C. difficile toxin B is toxic to cells, depending on the RBD-like region (residues 1349–1811) but does not interact with LRP1. Our data indicate the presence of a second, CROP-independent receptor-binding domain in clostridial glycosylating toxins and suggest a two-receptor model for the cellular uptake of clostridial glycosylating toxins.
LATERAL NANO-CHANNEL FABRICATED IN FUSED SILICA BY FEMTOSECOND LASER IRRADIATION AND WET ETCHING

We demonstrate a lateral patch-cramp device structure, made of fused silica, whose patch pipettes were fabricated by using femtosecond laser irradiation and wet etching. The pipettes were an oval-shaped cross-section that was 200 nm ×� 4 µm, and the minor axis can be controlled on the nano-scale. It is expected that a Giga-seal resistance and its observation using a high magnification microscope can be simultaneously achieved. We confirmed that fluids such as buffer solutions can flow through the nano-pipettes, and some bacteria (B. Subtilis) were successfully trapped at the inlet of a nano-pipette at a given moment.
Preparing of Barium Titanate Using Chemical Method and Studying of its Structural Properties

Single crystalline BaTiO3 (BT) was prepared using TiCl4, BaCl 2 and oxalic acid. The structure of the prepared nanocrystalline BT powders were a tetragonal perovskite according to XRD and HRTEM analysis. Annealing powder to 750 o C show that pure BT phase was formed according to XRD, TG, and FTIR spectroscopy. The TEM images of the prepared powder reveal spherical morphology of BT, while a finger twin, dendritic and embryo shape are observed of BT powder calcined at 230, 530, and 750 o C respectively. SAED and HRTEM images showed a high crystalline BT powder and a single crystalline BT respectively.
Time variable Tempo Detection and beat Marking

In this paper, we present a novel approach to the automatic estimation of tempo over time. This method aims at detecting tempo for music with and without percussion. An onset-energy function is first proposed based on the reassigned spectral energy flux. A combination of Discrete Fourier Transform and Frequency Mapped AutoCorrelation Function is used to estimate the dominant periodicities at each time. A Viterbi algorithm is then used in order to detect the most likely tempo and meter/beat subdivision paths over time. The performance of the proposed method is evaluated on three databases.
JPEG2000-Based Scalable Interactive Video (JSIV) With Motion Compensation

In a recent work, the authors proposed a novel paradigm for interactive video streaming and coined the term JPEG2000-Based Scalable Interactive Video (JSIV) for it. In this work, we investigate JSIV when motion compensation is employed to improve prediction, something that was intentionally left out in our earlier treatment. JSIV relies on three concepts: storing the video sequence as independent JPEG2000 frames to provide quality and spatial resolution scalability, prediction and conditional replenishment of code-blocks to exploit inter-frame redundancy, and loosely coupled server and client policies in which a server optimally selects the number of quality layers for each code-block transmitted and a client makes the most of the received (distorted) frames. In JSIV, the server transmission problem is optimally solved using Lagrangian-style rate-distortion optimization. The flexibility of JSIV enables us to employ a wide variety of frame prediction arrangements, including hierarchical B-frames. JSIV provides considerably better interactivity compared with existing schemes and can adapt immediately to interactive changes in client interests, such as forward or backward playback and zooming into individual frames. Experimental results show that JSIV's performance is inferior to that of SVC in conventional streaming applications while JSIV performs better in interactive browsing applications.
Adjustment of Kindergarten Children through Play Sessions Facilitated by Fifth Grade Students Trained in Child-Centered Play Therapy Procedures and Skills

This research study investigated the effectiveness of the application of child-centered play therapy procedures and skills by trained fifth grade students in play sessions with kindergarten children who had adjustment difficulties. Specifically, this research determined if play sessions with trained fifth grade students facilitated change in kindergarten children's self concept, internalizing behavior, and externalizing behavior and their parents' stress level.
Optimal Resource Allocation for OFDMA Downlink Systems

This paper proposes efficient rate and power allocation algorithms for OFDMA downlink systems where each tone is taken by at most one user. Weighted sum rate maximization (WSRmax) and weighted sum power minimization (WSPmin) problems are considered. Since these resource allocation problems are non-convex, complexity of finding the optimal solutions is prohibitively high. This paper employs the Lagrange dual decomposition method to efficiently solve both optimization problems. Because of their non-convex nature, there is no guarantee for the solution obtained by the dual decomposition method to be optimal. However, it is shown that with practical number of tones, the duality gap is virtually zero and the optimal solutions can be efficiently obtained
Diffusion Tensor Imaging for Glioma Grading: Analysis of Fiber Density Index

Introduction: The most common primary tumors of brain are gliomas and tumor grading is essential for designing proper treatment strategies. The gold standard choice to determine grade of glial tumor is biopsy which is an invasive method. The purpose of this study was to investigate the role of fiber density index (FDi) by means of diffusion tensor imaging (DTI) (as a noninvasive method) in glial tumor grading. Methods: A group of 20 patients with histologically confirmed diagnosis of gliomas were evaluated in this study. We used a 1.5 Tesla MR system (AVANTO; Siemens, Germany) with a standard head coil for scanning. Multidirectional diffusion weighted imaging (measured in 12 noncollinear directions), and T1 weighted nonenhanced were performed for all patients. We defined two regions of interest (ROIs); 1) White matter fibers near the tumor and 2) Similar fibers in the contralateral hemisphere. Results: FDi of the low-grade gliomas was higher than those of high-grade gliomas, which was significant (P=0.017). FDi ratio (ratio of fiber density in vicinity of the tumor to homologous fiber tracts in the contralateral hemisphere) is higher in low-grade than high-grade tumors, (P=0.05). In addition, we performed ROC (receiver operating characteristic) curve and the area under curve (AUC) was 0.813(P=0.013). Conclusion: Our findings prove significant difference in FDi near by low-grade and high-grade gliomas. Therefore, FDi values and ratios are helpful in glial tumor grading.
SymPLFIED: Symbolic program-level fault injection and error detection framework

This paper introduces SymPLFIED, a program-level framework that allows specification of arbitrary error detectors and the verification of their efficacy against hardware errors. SymPLFIED comprehensively enumerates all transient hardware errors in registers, memory, and computation (expressed as value errors) that potentially evade detection and cause program failure. The framework uses symbolic execution to abstract the state of erroneous values in the program and model checking to comprehensively find all errors that evade detection. We demonstrate the use of SymPLFIED on a widely deployed aircraft collision avoidance application, tcas. Our results show that the SymPLFIED framework can be used to uncover hard-to-detect corner cases caused by transient errors in programs that may not be exposed by random fault-injection based validation.
The earliest memory in individuals raised in either traditional and reformed kibbutz or outside the kibbutz

In two studies we compared the age of traditional kibbutz members' first memories with the first memories of people raised in Israeli cities (Study 1) and of people who were raised in reformed kibbutzim (Study 2). Building on the socio-cultural model of autobiographical memory, we predicted and found that children raised in the traditional kibbutz, not by their parents, but by a metapelet, had a significantly later onset of autobiographical memory than children raised in reformed kibbutzim or outside the kibbutz, who were under the primary care of their parents. We also examined gender differences in reporting the earliest memory. No gender differences were observed within each setting in the age of the earliest memory, but consistent with past research, memories reported by females were more elaborate than those reported by males.
Analysis and quantification of multiple methylation variable positions in CpG islands by Pyrosequencing.

of the technology is the close correlation between the peak heights in a Pyrogram (Pyrosequencing AB), representing the sequence raw data, and the amount of nucleotides incorporated by the DNA polymerase during the Pyrosequencing reaction that allows for precise allele frequency determination for a SNP in pooled DNA samples (10–12). Very recently, an approach to the analysis of the degree of methylation on a single MVP after bisulfite treatment was shown using mixtures of PCR products for calibration (13). Bisulfite treatment converts unmethylated cytosines to uracils, while methylated cytosines remain unchanged under the appropriate reaction conditions. Therefore, after PCR, methylation sites can be treated as C/T SNPs with an allele frequency spectrum spanning the entire range (0%–100%). Here we demonstrate the Pyrosequencing technology to analyze and precisely quantify the degree of DNA methylation. Up to six MVPs were examined simultaneously in a single Pyrosequencing reaction. The method is amenable to the analysis of bisulfite-treated DNA derived from paraffin-embedded tissue samples, highly reproducible, and accurate if calibration is carried out properly (to detect any biased PCR amplification).
Nucleotide Sequence and Temporal Expression of a Baculovirus Regulatory Gene

The nucleotide sequence of a trans-activating regulatory gene (IE-1) of the baculovirus Autographa californica nuclear polyhedrosis virus has been determined. This gene encodes a protein of 581 amino acids with a predicted molecular weight of 66,856. A DNA fragment containing the entire coding sequence of IE-1 was inserted downstream of an RNA promoter. Subsequent cell-free transcription and translation directed the synthesis of a single peptide with an apparent molecular weight of 70,000. Quantitative S1 nuclease analysis indicated that IE-1 was maximally synthesized during a 1-h virus adsorption period and that steady-state levels of IE-1 message were maintained during the first 24 h of infection. Northern blot hybridization indicated that several late transcripts which overlap the IE-1 gene were transcribed from both strands. The precise locations of the 5′ and 3′ ends of these overlapping transcripts were mapped using S1 nuclease. The overlapping transcripts were grouped in two transcriptional units. One unit was composed of IE-1 and overlapping γ transcripts which initiated upstream of IE-1 and terminated downstream of IE-1. The other unit, transcribed from the opposite strand, consisted of γ transcripts with coterminal 5′ ends and extended 3′ ends. The shorter, more abundant transcripts in this unit overlapped 30 to 40 bases of IE-1 at the 3′ end, while the longer transcripts overlapped the entire IE-1 gene. Transcription of several early A. californica nuclear polyhedrosis virus genes, in addition to 39K, was shown to be trans-activated by IE-1, indicating that IE-1 may have a central role in the regulation of β-gene expression.
Moving beyond Common‐Garden and Transplant Designs: Insight into the Causes of Local Adaptation in Species Interactions

Theoretical and empirical studies of local adaptation in species interactions have increased greatly over the past decade, yielding new insights into the conditions that favor local adaptation or maladaptation. Generalizing the results of these studies is difficult, however, because of the different experimental designs that have been used to infer local adaptation. Particularly challenging is comparing results across empirical studies conducted in a common laboratory or garden environment with results of those conducted using transplants in natural environments. Here we develop simple and easily interpretable mathematical expressions for the quantities measured by these two different types of studies. Our results reveal that common‐garden designs measure only a single component of local adaptation—the spatial covariance between the genotype frequencies of the interacting species—and thus provide only a partial description of local adaptation. In contrast, reciprocal‐transplant designs incorporate additional terms that measure the contribution of spatial variability in the ecological environment. Consequently, the two types of studies should yield identical results only when local adaptation is caused by spatial variability in the genotype frequencies of the interacting species alone. In order to unify these disparate approaches, we develop a new methodology that can be used to estimate the individual components of local adaptation. When implemented in an appropriate experimental system, this partitioning allows the examination of fundamental questions such as the relative proportion of local adaptation attributable to interactions between species or to the abiotic environment.
Imaging guided trials of the angiogenesis inhibitor sunitinib in mouse models predict efficacy in pancreatic neuroendocrine but not ductal carcinoma

Preclinical trials in mice represent a critical step in the evaluation of experimental therapeutics. Genetically engineered mouse models (GEMMs) represent a promising platform for the evaluation of drugs, particularly those targeting the tumor microenvironment. We evaluated sunitinib, an angiogenesis inhibitor that targets VEGF and PDGF receptor signaling, in two GEMMs of pancreatic cancer. Sunitinib did not reduce tumor burden in pancreatic ductal adenocarcinoma (PDAC), whereas tumor burden was reduced in the pancreatic neuroendocrine tumor (PNET) model, the latter results confirming and extending previous studies. To explore the basis for the lack of pathologic response in PDAC, we used noninvasive microbubble contrast-enhanced ultrasound imaging, which revealed that sunitinib reduced blood flow both in PDAC and in PNET, concomitant with a reduction in vessel density; nevertheless, PDAC tumors continued to grow, whereas PNET were growth impaired. These results parallel the response in humans, where sunitinib recently garnered FDA and European approval in PNET, whereas two antiangiogenic drugs failed to demonstrate efficacy in PDAC clinical trials. The demonstration of on-target activity but with discordant benefit in the PDAC and PNET GEMMs illustrates the potential value of linked preclinical and clinical trials.
Human Papillomavirus (HPV) in Atypical Squamous Cervical Cytology: the Invader HPV Test as a New Screening Assay

ABSTRACT In surveillance for cervical neoplasia, a diagnosis of cytologically atypical squamous cells of undetermined significance (ASCUS) presents a significant clinical issue, often dependent on testing for high-risk (HR) human papillomavirus (HPV) for the triage of patients. HPV type 16 now appears to be a critical concern in the follow-up of patients with ASCUS. The Invader HPV (Inv2) test, by Third Wave Technologies, Inc., is a recently developed analyte-specific reagent assay that uses probe sets for the detection of 14 HR HPV subtypes. These probe sets are A5/A6 (HPV types 51, 56, and 66), A7 (HPV types 18, 39, 45, 59, and 68), and A9 (HPV types 16, 31, 33, 35, 52, and 58). This report describes the performance characteristics of the Inv2 test in the screening of ASCUS cervical cytology specimens and correlates the results of the Inv2 test with those of the Hybrid Capture II HPV (HC2) test by Digene. The linear array HPV genotyping test (Roche Molecular Systems) was used as a reference method for the testing of samples with discordant results. Ninety-four Pap smear samples with a cytological diagnosis of ASCUS and 39 samples with a negative diagnosis were tested. The results of the Inv2 test demonstrated a good (86.6%) concordance with those of the HC2 test, with an overall sensitivity and specificity of 96% for the Inv2 test. Additionally, the Inv2 assay, which offers high-throughput, semiautomated DNA extraction, allows the subgrouping of HPV types by differential probe sets, could provide a useful test for screening for HPV, and has the potential to provide an improved means of risk stratification and the selection of patients for further HPV subtyping.
Cooperative search with autonomous vehicles in a 3D aquatic testbed

We consider the problem of cooperative search using autonomous aquatic vehicles, giving a proof-of-concept demonstration in an aquatic testbed. We implement a point-to-point controller for remote-controlled submarines with severe control and buoyancy limitations, develop software to track their motion and establish reliable communication and control. We then propose multiple randomized algorithms, based on Lévy flights, for locating sparse targets in a three-dimensional bounded environment. These algorithms are tested in simulation, showing that they are competitive with nonrandom systematic search, while likely also more robust. The simulations are combined with in-tank tests to display performance under real physical conditions.
Constrained Global Design Optimization Using a Multi-fidelity Model

1. Abstract In many engineering optimization problems, the number of function evaluations is severely limited due to time or cost for obtaining the optimal solution when the time for one function evaluation is long. In this study, we present a constrained global optimization method using a multi-fidelity model. A multi-fidelity model employed in this study is a surrogate that combines two models of different fidelities. The multi-fidelity model has been used to obtain unconstrained optimal solution with less number of function evaluations than using just a high fidelity model. The multi-fidelity model we used in this study is that based on Bayesian prediction. For sequential sampling taking the constrained global optimization into account, we formulate an optimization problem to find an infill sampling point that maximizes the generalized expected improvement (GEI), a generalized form of the expected improvement. The GEI balances a local exploitation and a global exploration with a cooling scheme. To solve the formulated optimization problem, we employ the pattern search method to find the constrained global optimal solution. The sequential sampling terminates when stopping criteria are met. In order to demonstrate the effectiveness and usefulness of the proposed method, several mathematical problems are solved and its performance is compared to that of constrained global optimization methods using a high fidelity model only.