Miracle-dz/UniFAR-FTUs huggingface dataset:
Decoding Dynamic Brain Patterns from Evoked Responses: A Tutorial on Multivariate Pattern Analysis Applied to Time Series Neuroimaging Data

Multivariate pattern analysis (MVPA) or brain decoding methods have become standard practice in analyzing fMRI data. Although decoding methods have been extensively applied in brain–computer interfaces, these methods have only recently been applied to time series neuroimaging data such as MEG and EEG to address experimental questions in cognitive neuroscience. In a tutorial style review, we describe a broad set of options to inform future time series decoding studies from a cognitive neuroscience perspective. Using example MEG data, we illustrate the effects that different options in the decoding analysis pipeline can have on experimental results where the aim is to “decode” different perceptual stimuli or cognitive states over time from dynamic brain activation patterns. We show that decisions made at both preprocessing (e.g., dimensionality reduction, subsampling, trial averaging) and decoding (e.g., classifier selection, cross-validation design) stages of the analysis can significantly affect the results. In addition to standard decoding, we describe extensions to MVPA for time-varying neuroimaging data including representational similarity analysis, temporal generalization, and the interpretation of classifier weight maps. Finally, we outline important caveats in the design and interpretation of time series decoding experiments.
Differential induction of bidirectional long‐term changes in neurotransmitter release by frequency‐coded patterns at the cerebellar input

Sensory stimulation conveys spike discharges of variable frequency and duration along the mossy fibres of cerebellum raising the question of whether and how these patterns determine plastic changes at the mossy fibre–granule cell synapse. Although various combinations of high‐frequency bursts and membrane depolarization can induce NMDA receptor‐dependent long‐term depression (LTD) and long‐term potentiation (LTP), the effect of different discharge frequencies remained unknown. Here we show that low‐frequency mossy fibre stimulation (100 impulses−1 Hz) induces mGlu receptor‐dependent LTD. For various burst frequencies, the plasticity–[Ca2+]i relationship was U‐shaped resembling the Bienenstok–Cooper–Munro (BCM) learning rule. Moreover, LTD expression was associated with increased paired‐pulse ratio, coefficient of variation and failure rate, and with a decrease in release probability, therefore showing changes opposite to those characterizing LTP. The plasticity–[Ca2+]i relationship and the changes in neurotransmitter release measured by varying induction frequencies were indistinguishable from those obtained by varying high‐frequency burst duration. These results suggest that different glutamate receptors converge onto a final common mechanism translating the frequency and duration of mossy fibre discharges into a regulation of the LTP/LTD balance, which may play an important role in adapting spatio‐temporal signal transformations at the cerebellar input stage.
Src promotes GTPase activity of Ras via tyrosine 32 phosphorylation

Significance Despite the well-established connection between Ras and Src, there currently is no evidence of direct interaction between these two proteins. We show here that Src binds to and phosphorylates GTP-loaded Ras on a conserved Y32 residue within the switch I region. It has been shown that Raf binds to Ras with an affinity 1,000-fold greater than that of GAP. However, it has remained unclear how GAP is able to outcompete Raf for Ras upon Raf displacement. We show here that Y32 phosphorylation inhibits Raf binding to Ras and concomitantly promotes GAP association and GTP hydrolysis, thereby ensuring unidirectionality to the Ras GTPase cycle. These findings reveal new fundamental mechanistic insight into how Src negatively regulates Ras. Mutations in Ras GTPase and various other components of the Ras signaling pathways are among the most common genetic alterations in human cancers and also have been identified in several familial developmental syndromes. Over the past few decades it has become clear that the activity or the oncogenic potential of Ras is dependent on the nonreceptor tyrosine kinase Src to promote the Ras/Raf/MAPK pathway essential for proliferation, differentiation, and survival of eukaryotic cells. However, no direct relationship between Ras and Src has been established. We show here that Src binds to and phosphorylates GTP-, but not GDP-, loaded Ras on a conserved Y32 residue within the switch I region in vitro and that in vivo, Ras-Y32 phosphorylation markedly reduces the binding to effector Raf and concomitantly increases binding to GTPase-activating proteins and the rate of GTP hydrolysis. These results suggest that, in the context of predetermined crystallographic structures, Ras-Y32 serves as an Src-dependent keystone regulatory residue that modulates Ras GTPase activity and ensures unidirectionality to the Ras GTPase cycle.
Translational Control of Host Gene Expression by a Cys-Motif Protein Encoded in a Bracovirus

Translational control is a strategy that various viruses use to manipulate their hosts to suppress acute antiviral response. Polydnaviruses, a group of insect double-stranded DNA viruses symbiotic to some endoparasitoid wasps, are divided into two genera: ichnovirus (IV) and bracovirus (BV). In IV, some Cys-motif genes are known as host translation-inhibitory factors (HTIF). The genome of endoparasitoid wasp Cotesia plutellae contains a Cys-motif gene (Cp-TSP13) homologous to an HTIF known as teratocyte-secretory protein 14 (TSP14) of Microplitis croceipes. Cp-TSP13 consists of 129 amino acid residues with a predicted molecular weight of 13.987 kDa and pI value of 7.928. Genomic DNA region encoding its open reading frame has three introns. Cp-TSP13 possesses six conserved cysteine residues as other Cys-motif genes functioning as HTIF. Cp-TSP13 was expressed in Plutella xylostella larvae parasitized by C. plutellae. C. plutellae bracovirus (CpBV) was purified and injected into non-parasitized P. xylostella that expressed Cp-TSP13. Cp-TSP13 was cloned into a eukaryotic expression vector and used to infect Sf9 cells to transiently express Cp-TSP13. The synthesized Cp-TSP13 protein was detected in culture broth. An overlaying experiment showed that the purified Cp-TSP13 entered hemocytes. It was localized in the cytosol. Recombinant Cp-TSP13 significantly inhibited protein synthesis of secretory proteins when it was added to in vitro cultured fat body. In addition, the recombinant Cp-TSP13 directly inhibited the translation of fat body mRNAs in in vitro translation assay using rabbit reticulocyte lysate. Moreover, the recombinant Cp-TSP13 significantly suppressed cellular immune responses by inhibiting hemocyte-spreading behavior. It also exhibited significant insecticidal activities by both injection and feeding routes. These results indicate that Cp-TSP13 is a viral HTIF.
A Case of Mania following Deep Brain Stimulation for Obsessive Compulsive Disorder

Deep brain stimulation (DBS) of the basal ganglia is an effective treatment for select movement disorders, including Parkinson’s disease, essential tremor and dystonia. Based on these successes, DBS has been explored as an experimental treatment for medication-resistant neuropsychiatric disease. During a multiyear experience employing DBS to treat patients for obsessive compulsive disorder (OCD) we encountered several unanticipated stimulation-induced psychiatric side effects. We present a case of a young woman treated for OCD with DBS of the anterior limb of the internal capsule and nucleus accumbens region, who subsequently manifested a manic episode. We aim to discuss the case details, treatment and potential neuroanatomical underpinnings of this response.
Efficient Inference of CRFs for Large-Scale Natural Language Data

This paper presents an efficient inference algorithm of conditional random fields (CRFs) for large-scale data. Our key idea is to decompose the output label state into an active set and an inactive set in which most unsupported transitions become a constant. Our method unifies two previous methods for efficient inference of CRFs, and also derives a simple but robust special case that performs faster than exact inference when the active sets are sufficiently small. We demonstrate that our method achieves dramatic speedup on six standard natural language processing problems.
Global Built-In Self-Repair for 3D memories with redundancy sharing and parallel testing

3D integration is a promising technology that provides high memory bandwidth, reduced power, shortened latency, and smaller form factor. Among many issues in 3D IC design and production, testing remains one of the major challenges. This paper introduces a new design-for-test technique called 3D-GESP, an efficient Built-In-Self-Repair (BISR) algorithm to fulfill the test and reliability needs for 3D-stacked memories. Instead of the local testing and redundancy allocation method as most current BISR techniques employed, we introduce a global 3D BISR scheme, which not only enables redundancy sharing, but also parallelizes the BISR procedure among all the stacked layers of a 3D memory. Our simulation results show that our proposed technique will significantly increase the memory repair rate and reduce the test time.
Technical note: optimization of unmanned aerial vehicles flight planning in steep terrains

ABSTRACT We present an approach to manage Unmanned Aerial Vehicle (UAV) photogrammetric data acquisition in areas with steep slopes, i.e., typical conditions of high mountain environments prone to slope instabilities and potentially to catastrophic failures. Starting from the Mission Planner from Ardupilot, an open access and widely used UAV flight planning software, we have developed a set of Matlab™ routines to take into account available topographic relief of the area under investigation. We validated our approach in the Swiss Alps, in a steep slope area where very high-resolution digital models and orthophotos are necessary to analyze fracture surface geometries in detail and to better understand the exfoliation fracture processes. Our results provide a best-practice solution to generate very high-resolution photogrammetric products and can be applied in different UAV mapping tasks and/or monitoring scenarios.
Computationally Efficient Speaker Identification for Large Population Tasks using MLLR and Sufficient Statistics

In conventional Speaker-Identification using GMM-UBM framework, the likelihood of the given test utterance is computed with respect to all speaker-models before identifying the speaker, based on the maximum likelihood criterion. The calculation of likelihood score of the test utterance is computationally intensive, especially when there are tens of thousands of speakers in database. In this paper, we propose a computationally efficient (Fast) method to calculate the likelihood of the test utterance using speaker-specific Maximum Likelihood Linear Regression (MLLR) matrices (which are precomputed) and sufficient statistics estimated from the test utterance only once. We show that while this method is an order of magnitude faster, there is some degradation in performance. Therefore, we propose a cascaded system with the Fast MLLR system identifying the top-N most probable speakers, followed by a conventional GMM-UBM to identify the most probable speaker from the topN speakers. Experiments performed on the NIST 2004 database indicate that the cascaded system provides a speed up of 3.16 and 6.08 times for 1-side test (core condition) and 10 sec. test condition respectively, with a marginal degradation in accuracy over the conventional GMM-UBM system.
Highly SpecIfic and Sensitive Pharmacophore Model for Identifying CXCR4 Antagonists. Comparison with Docking and Shape-Matching Virtual Screening Performance

HIV infection is initiated by fusion of the virus with the target cell through binding of the viral gp120 protein with the CD4 cell surface receptor protein and the CXCR4 or CCR5 coreceptors. There is currently considerable interest in developing novel ligands that can modulate the conformations of these coreceptors and, hence, ultimately block virus-cell fusion. Herein, we present a highly specific and sensitive pharmacophore model for identifying CXCR4 antagonists that could potentially serve as HIV entry inhibitors. Its performance was compared with docking and shape-matching virtual screening approaches using 3OE6 CXCR4 crystal structure and high-affinity ligands as query molecules, respectively. The performance of these methods was compared by virtually screening a library assembled by us, consisting of 228 high affinity known CXCR4 inhibitors from 20 different chemotype families and 4696 similar presumed inactive molecules. The area under the ROC plot (AUC), enrichment factors, and diversity of the resulting virtual hit lists was analyzed. Results show that our pharmacophore model achieves the highest VS performance among all the docking and shape-based scoring functions used. Its high selectivity and sensitivity makes our pharmacophore a very good filter for identifying CXCR4 antagonists.
Modeling and stability analysis of an active filter for DC current compensation

The widespread use of power converters and nonlinear loads connected to the grid have caused the emergence of problems regarding the power quality. Among different kind of non-linear distortion, there is the issue of the DC current component. In fact, a DC current component flowing in the grid transformers has various detrimental effects, i.e. increased harmonic distortion, increased power losses, and possible damage due to consequent overheating. This paper proposes a non-linear sensor and a compensator system that act as an active filter to remove the DC current component flowing in the power lines. In the first part, the strategy is outlined and then the stability issue is addressed by means of a simplified model. Simulation results confirmed that the simplified model closely approximates the real system. An approximated analysis of stability is also presented. Finally we present some experimental results that shows the effectiveness of the proposed solution.
A hardware platform for performance evaluation of in-body sensors

Body area network is expected to be the next breakthrough invention with great potential due to miniaturization of wireless communication devices. One of the major challenges for design of sensor devices for wireless communications inside human body is the accessibility of the medium for performance evaluation. It is practically impossible to install a development module for a sensor inside the human body and when the sensor designed we need expensive procedure with physician supervisions to examine the performance of the sensors. In this paper, we introduce an interference controllable, repeatable real-time hardware platform for performance evaluation of a typical in-body sensor chipset used in most implant applications (Zarlink ZL70101 ADK operating at 402-405 MHz) utilizing an existing multipath channel emulator (Elektrobit PROPSim™ C8) to analyze the performance of the communication link between a sensor located inside the human body and a body mounted sensor. We show how link quality is analyzed by observing the packet reception rate under three different transmission alternatives.
Sources of Productivity Growth in Bihar in the Recent Decade A District Level Analysis

This paper applies the non-parametric data envelopment approach (DEA) to estimate Total Factor Productivity (TFP) growth rate for agricultural output comprising the period 2000– 2012 across districts of Bihar. The approach ûnds the shift in the frontier as well as improved efficiency play an important role as a source of productivity growth, suggesting that technological adoption and catching up may be a vitally important source for overall productivity growth. The approach identifies the frontier districts in terms of agricultural production.
Do Foliar, Litter, and Root Nitrogen and Phosphorus Concentrations Reflect Nutrient Limitation in a Lowland Tropical Wet Forest?

Understanding nutrient limitation of net primary productivity (NPP) is critical to predict how plant communities will respond to environmental change. Foliar nutrients, especially nitrogen and phosphorus concentrations ([N] and [P]) and their ratio, have been used widely as indicators of plant nutritional status and have been linked directly to nutrient limitation of NPP. In tropical systems, however, a high number of confounding factors can limit the ability to predict nutrient limitation —as defined mechanistically by NPP responses to fertilization— based on the stoichiometric signal of the plant community. We used a long-term full factorial N and P fertilization experiment in a lowland tropical wet forest in Costa Rica to explore how tissue (foliar, litter and root) [N] and [P] changed with fertilization, how different tree size classes and taxa influenced the community response, and how tissue nutrients related to NPP. Consistent with NPP responses to fertilization, there were no changes in community-wide foliar [N] and [P], two years after fertilization. Nevertheless, litterfall [N] increased with N additions and root [P] increased with P additions. The most common tree species (Pentaclethra macroloba) had 9 % higher mean foliar [N] with NP additions and the most common palm species (Socratea exohrriza) had 15% and 19% higher mean foliar [P] with P and NP additions, respectively. Moreover, N:P ratios were not indicative of NPP responses to fertilization, either at the community or at the taxa level. Our study suggests that in these diverse tropical forests, tissue [N] and [P] are driven by the interaction of multiple factors and are not always indicative of the nutritional status of the plant community.
Explaining trends in UK household spending

In this paper we model the changing distribution of household spending in the UK over the period 1978 to 1999 and explore the interpretation of remaining time trends in spending once changes in other observed covariates have been accounted for. Acknowledgements This research was funded by the Leverhulme Trust research programme into The changing distribution of consumption, economic resources and the welfare of households (project reference F/386/J) and co-funded by the ESRC Centre for the Microeconomic Analysis of Fiscal Policy at the Institute for Fiscal Studies. Special thanks are due to James Banks for his generous help during the writing of this paper. We are grateful to Richard Blundell, Andrew Chesher and Ian Preston for useful discussions, as well seminar participants at UCL. The usual disclaimer applies. JEL ClassiÞcation: D12 ∗Institute for Fiscal Studies
Longitudinal Awareness: A Study of Vulnerability to Flooding in Polk County, Iowa

VI CHAPTER ONE: INTRODUCTION . 1 1.1LITERATURE REVIEW . 4 1.1.1Overview: Hazards Research in Geography . 4 1.1. 2Social Vulnerability . 5 1.1. 3Risk and Temporal Scale . 11 1.1. 4Environmental Justice . 14 1.2RESEARCH QUESTIONS . 16 CHAPTER TWO: METHODOLOGY . 17 2.1STUDY AREA . 17 2.2 DATASETS . 23 2.2. 1Data Exclusions . 24 2.3ANALYSES METHODOLOGIES . 25 2.3. 1Methodology for Creation of the Social Vulnerability Index (SoVI) . 26 2.3. 2Methodology for Exploring the Relationship Between Polk County, IA SoVI and Flood Hazard Areas . 33 2.3.3 -Methodology for Inquiry: Link Between Individual Vulnerability Variables and Flood Hazard Areas: Environmental Justice Approach . 34 CHAPTER THREE: POLK COUNTY, IOWA SOCIAL VULNERABILITY INDEX . 40 3.1SUITABILITY OF THE DATA FOR PCA . 40 3.2EXTRACTION AND NAMING OF THE COMPONENTS. 41 3.3POLK COUNTY, IA SOVI COMPONENTS . 44 3.3. 1Component One . 44 3.3. 2Component Two . 47 3.3.3Component Three . 48 3.3. 4Component Four . 50 3.3. 5Component Five . 51 3.3. 6Component Six . 52 3.3. 7Component Seven . 54 3.3. 8Component Eight . 55 3.3. 9Component Nine . 57 3.4POLK COUNTY, IA SOVI COMPOSITE . 58 3.5CHAPTER 3 CONCLUSIONS. 63
FTIR - An Essential Characterization Technique for Polymeric Materials

The spectrometer may operate in transmission or reflection, but also in attenuated total reflection (ATR) mode, which have been widely used during the last two decades. The transmission mode is very suitable for quantitative analysis, since the main parameters to apply on the Beer-Lambert law are known or easily estimated. The reflection mode is used when polymer is not well dissolved at room temperature, and a film or pellets of the sample is characterized. Such is the case of polyolefins and some engineering polymers like PET.
Selectivity of stop codon recognition in translation termination is modulated by multiple conformations of GTS loop in eRF1

Translation termination in eukaryotes is catalyzed by two release factors eRF1 and eRF3 in a cooperative manner. The precise mechanism of stop codon discrimination by eRF1 remains obscure, hindering drug development targeting aberrations at translation termination. By solving the solution structures of the wild-type N-domain of human eRF1 exhibited omnipotent specificity, i.e. recognition of all three stop codons, and its unipotent mutant with UGA-only specificity, we found the conserved GTS loop adopting alternate conformations. We propose that structural variability in the GTS loop may underline the switching between omnipotency and unipotency of eRF1, implying the direct access of the GTS loop to the stop codon. To explore such feasibility, we positioned N-domain in a pre-termination ribosomal complex using the binding interface between N-domain and model RNA oligonucleotides mimicking Helix 44 of 18S rRNA. NMR analysis revealed that those duplex RNA containing 2-nt internal loops interact specifically with helix α1 of N-domain, and displace C-domain from a non-covalent complex of N-domain and C-domain, suggesting domain rearrangement in eRF1 that accompanies N-domain accommodation into the ribosomal A site.
Evaluation of the potential interaction between methylmercuric chloride and naringenin on pre- and postnatal rat development

The present work aims to examine the potential role of methylmercury (MMC) in inducing developmental toxicity as well as to evaluate the role of naringenin in preventing or alleviating the induced defects. In the present work 80 pregnant rats were divided into four groups (each comprising 20 rats); control group, naringenin (Ng) treated group (50 mg /kg b.wt./day), MMC treated group with 1 mg/ kg bwt and co-treated group with both MMC and Ng at the same dosages. Half of the animals were treated daily from gestational day 7 to 19 th day by gastric intubation, and the other half were treated daily from the 7 th day of gestation to the postnatal day (PN) 29 by gastric intubation. All animals were killed in the day next to the last given dose. The results indicated that oral administration of naringenin to rats treated with MMC improved the fetal and pups growth rate and markedly reduced the fetal morphological and skeletal abnormalities. Naringenin also improved the percentage of fragmented DNA in fetal and neonatal brain as well as the histpathological lesions observed in cortex of both fetuses and pups maternally treated with MMC.