Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Pre-Spike Network in Patients with Mesial Temporal Lobe Epilepsy

Background: Seizures and interictal spikes in mesial temporal lobe epilepsy (MTLE) affect a network of brain regions rather than a single epileptic focus. Simultaneous electroencephalography and functional magnetic resonance imaging (EEG-fMRI) studies have demonstrated a functional network in which hemodynamic changes are time-locked to spikes. However, whether this reflects the propagation of neuronal activity from a focus, or conversely the activation of a network linked to spike generation remains unknown. The functional connectivity (FC) changes prior to spikes may provide information about the connectivity changes that lead to the generation of spikes. We used EEG-fMRI to investigate FC changes immediately prior to the appearance of interictal spikes on EEG in patients with MTLE. Methods/principal findings: Fifteen patients with MTLE underwent continuous EEG-fMRI during rest. Spikes were identified on EEG and three 10 s epochs were defined relative to spike onset: spike (0–10 s), pre-spike (−10 to 0 s), and rest (−20 to −10 s, with no previous spikes in the preceding 45s). Significant spike-related activation in the hippocampus ipsilateral to the seizure focus was found compared to the pre-spike and rest epochs. The peak voxel within the hippocampus ipsilateral to the seizure focus was used as a seed region for FC analysis in the three conditions. A significant change in FC patterns was observed before the appearance of electrographic spikes. Specifically, there was significant loss of coherence between both hippocampi during the pre-spike period compared to spike and rest states. Conclusion/significance: In keeping with previous findings of abnormal inter-hemispheric hippocampal connectivity in MTLE, our findings specifically link reduced connectivity to the period immediately before spikes. This brief decoupling is consistent with a deficit in mutual (inter-hemispheric) hippocampal inhibition that may predispose to spike generation.
The Molecular Subtype Classification Is a Determinant of Sentinel Node Positivity in Early Breast Carcinoma

Introduction Several authors have underscored a strong relation between the molecular subtypes and the axillary status of breast cancer patients. The aim of our work was to decipher the interaction between this classification and the probability of a positive sentinel node biopsy. Materials and Methods Our dataset consisted of a total number of 2654 early-stage breast cancer patients. Patients treated at first by conservative breast surgery plus sentinel node biopsies were selected. A multivariate logistic regression model was trained and validated. Interaction covariate between ER and HER2 markers was a forced input of this model. The performance of the multivariate model in the training and the two validation sets was analyzed in terms of discrimination and calibration. Probability of axillary metastasis was detailed for each molecular subtype. Results The interaction covariate between ER and HER2 status was a stronger predictor (p = 0.0031) of positive sentinel node biopsy than the ER status by itself (p = 0.016). A multivariate model to determine the probability of sentinel node positivity was defined with the following variables; tumour size, lympho-vascular invasion, molecular subtypes and age at diagnosis. This model showed similar results in terms of discrimination (AUC = 0.72/0.73/0.72) and calibration (HL p = 0.28/0.05/0.11) in the training and validation sets. The interaction between molecular subtypes, tumour size and sentinel nodes status was approximated. Discussion We showed that biologically-driven analyses are able to build new models with higher performance in terms of breast cancer axillary status prediction. The molecular subtype classification strongly interacts with the axillary and distant metastasis process.
Protein array–based profiling of CSF identifies RBPJ as an autoantigen in multiple sclerosis

Objective: To profile the reactivity of CSF-derived immunoglobulin from patients with multiple sclerosis (MS) against a large panel of antigens, to identify disease-specific reactivities. Methods: CSF from subjects with MS with elevated immunoglobulin G and CSF from control subjects presenting with other inflammatory neurologic disease were screened against a protein array consisting of 9,393 proteins. Reactivity to a candidate protein identified using these arrays was confirmed with ELISA and immunocytochemistry. Results: Autoantibodies against one protein on the array, recombination signal binding protein for immunoglobulin kappa J region (RBPJ), discriminated between patients with MS and controls (p = 0.0052). Using a large validation cohort, we found a higher prevalence of autoantibodies against RBPJ in the CSF of patients with MS (12.5%) compared with the CSF of patients with other neurologic diseases (1.6%; p = 0.02) by ELISA. This difference in reactivity was restricted to the CSF as serum reactivity against RBPJ did not differ between patients and controls. The presence of CSF autoantibodies against RBPJ was further confirmed by immunocytochemistry. Conclusions: These data indicate that RBPJ, a ubiquitous protein of the Notch signaling pathway that plays an important role in Epstein-Barr virus infection, is a novel MS autoantigen candidate that is recognized by CSF-derived immunoglobulin G in a subset of patients with MS.
Incidence and Predictors of First Line Antiretroviral Regimen Modification in Western Kenya

Background Limited antiretroviral treatment regimens in resource-limited settings require long-term sustainability of patients on the few available options. We evaluated the incidence and predictors of combined antiretroviral treatment (cART) modifications, in an outpatient cohort of 955 patients who initiated cART between January 2009 and January 2011 in western Kenya. Methods cART modification was defined as either first time single drug substitution or switch. Incidence rates were determined by Poisson regression and risk factor analysis assessed using multivariate Cox regression modeling. Results Over a median follow-up period of 10.7 months, 178 (18.7%) patients modified regimens (incidence rate (IR); 18.6 per 100 person years [95% CI: 16.2–21.8]). Toxicity was the most common cited reason (66.3%). In adjusted multivariate Cox piecewise regression model, WHO disease stage III/IV (aHR; 1.82, 95%CI: 1.25–2.66), stavudine (d4T) use (aHR; 2.21 95%CI: 1.49–3.30) and increase in age (aHR; 1.02, 95%CI: 1.0–1.04) were associated with increased risk of treatment modification within the first year post-cART. Zidovudine (AZT) and tenofovir (TDF) use had a reduced risk for modification (aHR; 0.60 95%CI: 0.38–0.96 and aHR; 0.51 95%CI: 0.29–0.91 respectively). Beyond one year of treatment, d4T use (aHR; 2.75, 95% CI: 1.25–6.05), baseline CD4 counts ≤350 cells/mm3 (aHR; 2.45, 95%CI: 1.14–5.26), increase in age (aHR; 1.05 95%CI: 1.02–1.07) and high baseline weight >60kg aHR; 2.69 95% CI: 1.58–4.59) were associated with risk of cART modification. Conclusions Early treatment initiation at higher CD4 counts and avoiding d4T use may reduce treatment modification and subsequently improve sustainability of patients on the available limited options.
K-band observations of boxy bulges – I. Morphology and surface brightness profiles

Kn-band images, unsharp-masked images, as well as major-axis and vertically- summed surface brightness profiles are presented for 30 edge-on spiral galaxies, most with a boxy or peanut-shaped (B/PS) bulge. Such galaxies have more complex morphologies than galaxies of other bulge types, more often showing (off-)centered X structures, secondary major-axis maxima and spiral-like structures. Those features are also observed in N-body simulations of barred discs and may trace the main bar orbit families. The surface brightness profiles of galaxies with a B/PS bulge are also more complex, with typically 3 or more clearly separated regions, including a flat intermediate region (Freeman Type II profiles). Those radial breaks offer evidence for bar-driven transfer of angular momentum and radial redistribution of material. The profiles also suggest a rapid variation of the scaleheight of the disc material, contrary to conventional wisdom but again as expected from vertical resonances and instabilities in barred discs. The steep inner region of the surface brightness profiles is often shorter than the isophotally thick part of the galaxies, itself always shorter than the flat region of the profiles. Contrary to the standard `bulge + disc' model, we thus propose that galaxies with a B/PS bulge are composed of a thin concentrated disc (a disc-like bulge) contained within a partially thick bar (the B/PS bulge) and a thin outer disc. The inner disc likely formed secularly through bar-driven processes and is responsible for the steep inner region of the surface brightness profiles, while the bar is responsible for the flat region and the thick complex morphological structures observed. Those components are strongly coupled dynamically and are formed mostly of the same (disc) material. [Abridged]
PKD1 Mediates Negative Feedback of PI3K/Akt Activation in Response to G Protein-Coupled Receptors

We examined whether protein kinase D1 (PKD1) mediates negative feeback of PI3K/Akt signaling in intestinal epithelial cells stimulated with G protein-coupled receptor (GPCR) agonists. Exposure of intestinal epithelial IEC-18 cells to increasing concentrations of the PKD family inhibitor kb NB 14270, at concentrations that inhibited PKD1 activation, strikingly potentiated Akt phosphorylation at Thr308 and Ser473 in response to the mitogenic GPCR agonist angiotensin II (ANG II). Enhancement of Akt activation by kb NB 142-70 was also evident in cells with other GPCR agonists, including vasopressin and lysophosphatidic acid. Cell treatment rovincial Hospital Affiliated to Shandong University, Jinan, China with the structurally unrelated PKD family inhibitor CRT0066101 increased Akt phosphorylation as potently as kb NB 142–70. Knockdown of PKD1 with two different siRNAs strikingly enhanced Akt phosphorylation in response to ANG II stimulation in IEC-18 cells. To determine whether treatment with kb NB 142–70 enhances accumulation of phosphatidylinositol (3,4,5)-trisphosphate (PIP3) in the plasma membrane, we monitored the redistribution of Akt-pleckstrin homology domain-green fluorescent protein (Akt-PH-GFP) in single IEC-18 cells. Exposure to kb NB 142–70 strikingly increased membrane accumulation of Akt-PH-GFP in response to ANG II. The translocation of the PIP3 sensor to the plasma membrane and the phosphorylation of Akt was completed prevented by prior exposure to the class I p110α specific inhibitor A66. ANG II markedly increased the phosphorylation of p85α detected by a PKD motif-specific antibody and enhanced the association of p85α with PTEN. Transgenic mice overexpressing PKD1 showed a reduced phosphorylation of Akt at Ser473 in intestinal epithelial cells compared to wild type littermates. Collectively these results indicate that PKD1 activation mediates feedback inhibition of PI3K/Akt signaling in intestinal epithelial cells in vitro and in vivo.
A Goal Based Approach for QFD Refinement in Systematizing and Identifying Business Process Requirements

The traditional Quality Function Deployment (QFD) methodology has successfully been used in many organizations in order to increase the productivity and the quality of service. However, this methodology has many limitations such as the ambiguous and unsystematic identification of customer requirements. In this paper, based on a goal oriented approach for the definition of business process requirement model, we define a model that overcomes the defined limits.
Essays on infrastructure, female labor force participation and economic development

A central question in economics is why some countries are substantially richer than others. The income per capita of the five richest countries in the world is 30 times the income of the five poorest. It is a fundamental quantitative question for which growth and development economists still have no definite answer. The first chapter of this dissertation contributes to this literature. The chapter offers new evidence on the sources of cross-country income differences by investigating the role public capital in development accounting. I explicitly measure private and public capital stocks, and I find large differences in both types of capital across countries. Moreover, differences in private capital are larger than the ones I find for total capital for the richest and poorest countries. The methodology I use implies a share of public capital in output of at most 10%. My findings indicate that differences in capital stocks can not account for a substantial part of the observed dispersion in income across countries. Other macroeconomic facts of underdeveloped and developing economies may also explain their low income per capita. These facts may be related to economic policies that could distort the allocation of resources in these economies. In the second chapter of this dissertation I document differences in labor supply between a set of Latin American countries and the U.S. in the period 1990-2005. In the U.S. the female labor force participation was 69% by 1990, while in Brazil and Mexico was 39% and 37%, respectively. Females began to participate more in the labor market of these countries after more households acquired access to basic infrastructure and when distortive policies affecting the price of household appliances were partially removed. I
Matching Markets : Design and Analysis Thesis Proposal

A market consists of buyers and sellers of some commodity, say a DVD movie. In this thesis, we assume the role of market operator. Our goal is to ensure that the market has certain desirable properties, which may include fairness, revenue maximization, and so on. We achieve these properties by designing rules for how buyers and sellers can perform transactions. Our main focus will be on matching markets. An example of a matching market is Netflix [31], the mail-based DVD rental business. Each day, Netflix allocates DVDs from its warehouses to customers entitled to rent a DVD on this day. Typically, there are not enough DVDs to give all customers their first choice, so Netflix must decide on an allocation that somehow takes into account the preferences of customers over DVDs. This is an example of a bipartite market, since there are two disjoint sets of participants, namely the customers and the DVDs/Netflix, and each set of participants only interacts with the other set. Other bipartite matching markets include the allocation of doctors to internships, children to public schools, and midshipman to naval jobs. More generally, a matching market can be non-bipartite, in which case participants can interact with any other participant. One type of non-bipartite matching market is a barter-exchange market. An example of a such a market is Swaptree [36], the mail-based DVD swapping business. (Swaptree also allows swapping of CDs, games, books, and so on.) Customers give Swaptree a list of DVDs they want to own, and a list of DVDs they want to trade. Whenever Swaptree finds an exchange (possibly involving three or more customers), it organizes for the customers to swap their DVDs by mail. In this market, the buyers and sellers coincide, and no money is exchanged. There are many other examples of barter-exchange markets. For example, there is a currently a move in the United States to establish a national kidney-exchange market [38]. Many kidney-disease patients have a willing but blood-type incompatible donor amongst their family. In the past, these potential donors have been sent home, leaving the patients to wait for cadaver kidneys, which are in very limited supply. However, more and more, doctors are performing exchanges in which patients swap their incompatible donors in order
Characterization of Light Lesion Paradigms and Optical Coherence Tomography as Tools to Study Adult Retina Regeneration in Zebrafish

Light-induced lesions are a powerful tool to study the amazing ability of photoreceptors to regenerate in the adult zebrafish retina. However, the specificity of the lesion towards photoreceptors or regional differences within the retina are still incompletely understood. We therefore characterized the process of degeneration and regeneration in an established paradigm, using intense white light from a fluorescence lamp on swimming fish (diffuse light lesion). We also designed a new light lesion paradigm where light is focused through a microscope onto the retina of an immobilized fish (focused light lesion). Focused light lesion has the advantage of creating a locally restricted area of damage, with the additional benefit of an untreated control eye in the same animal. In both paradigms, cell death is observed as an immediate early response, and proliferation is initiated around 2 days post lesion (dpl), peaking at 3 dpl. We furthermore find that two photoreceptor subtypes (UV and blue sensitive cones) are more susceptible towards intense white light than red/green double cones and rods. We also observed specific differences within light lesioned areas with respect to the process of photoreceptor degeneration: UV cone debris is removed later than any other type of photoreceptor in light lesions. Unspecific damage to retinal neurons occurs at the center of a focused light lesion territory, but not in the diffuse light lesion areas. We simulated the fish eye optical properties using software simulation, and show that the optical properties may explain the light lesion patterns that we observe. Furthermore, as a new tool to study retinal degeneration and regeneration in individual fish in vivo, we use spectral domain optical coherence tomography. Collectively, the light lesion and imaging assays described here represent powerful tools for studying degeneration and regeneration processes in the adult zebrafish retina.
The Relative Impacts of Federal Capital and Recurrent Expenditures on Nigeria’s Economy (1980-2011)

The paper explores the relative impacts of federal capital and recurrent expenditures on Nigeria’s economy in the 1980–2011 period. The empirical analysis begins with an investigation of the effect of total government expenditure (GOVEXP) on gross domestic product (GDP) using multiple linear regression analysis. The estimation result provides evidence that strongly supports Ram’s growth accounting model. GOVEXP was thereafter disaggregated into capital expenditure (CAPEXP) and recurrent expenditure (RECEXP) and the impacts of these on GDP were investigated by exploiting the cointegration and error correction mechanism. Unit root test results indicate that the variables which were non-stationary in levels became stationary after first differencing. The cointegration test result indicates the existence of a long-run relationship between the variables. The estimated ECM model reveals that the short-run impact of each explanatory variable on GDP was statistically insignificant contemporaneously, but significant with a lag, with RECEXP exerting greater impact than CAPEXP, though the impact of the former was negative while that of the latter was positive. The variance decomposition results indicate that the proportion of forecast error variance of GDP explained by innovations in RECEXP dominates the proportion explained by innovations in CAPEXP in all the periods. The paper recommends, inter alia that larger share of government expenditure should go into provision of infrastructure and other capital projects.
FSM based Manchester encoder for UHF RFID tag emulator

The radio frequency identification system (RFID) is becoming one of the most popular system in wireless technologies. The UHF RFID tag emulator is a part of RFID testing tools. The UHF RFID tag emulator would be imitating the behavior of RFID Tag. The UHF RFID tag emulator (860 MHz to 960 MHz) is aimed for testing the RFID systems and also acts as a general-purpose data transport device for other RFID systems. The tag emulator belongs to the EPC class-III (semi-passive) tags, but it implements the Class-1Generation II (C1G2) air interface protocol for communicating with the reader. In this work, we have presented RTL design of Manchester encoder. As motivated by Finite State Machine (FSM) and RTL implementations of encoder are discussed with particular focus to use the RFID Emulator as data transport device and debugging tool. The synthesis result shows that FSM design is efficient (less area and high speed) and it operates at a maximum frequency of 256.54 MHz.
Solving three-dimensional (3D) Laplace equations by successive over-relaxation method

Motivated by the assertion that all physical systems exist in three space dimensions, and that representation in one or two space dimensions entails a large degree of approximations. The main objective of this paper is to extend the successive over-relaxation (SOR) method which is one of the widely used numerical methods in solving the Laplace equation, the most often encountered of the Elliptic partial differential equations (PDEs) in two dimensions to solving it in three dimensions. This is done by providing an easier procedure to obtain proper estimates to the SOR parameter and the stability criterion which are the two determinant elements used in facilitating convergence to the solution when solving PDEs by the SOR method. The hope is that, with the emergence of this finding, the representation of physical and environmental science problem will be closer to reality by representing them in three dimensions. Key words: Stability criterion, over relaxation parameter, Laplace equation, finite differencing, successive over-relaxation.
LeakProber: a framework for profiling sensitive data leakage paths

In this paper, we present the design, implementation, and evaluation of LeakProber, a framework that leverages the whole system dynamic instrumentation and the inter-procedural analysis to enable data propagation path profiling in production system. We integrate both the static analysis and runtime tracking to establish a holistic and practical approach to generating the sensitive data propagation graph (sDPG) with minimum runtime overhead. We evaluate our system on several data stealing attacks scenario for generating sDPG. The sDPG generated by our system captures multiple aspects of data accessing patterns and provides clear insights into the data leakage path. We also measure the performance of our system and find that it degrades the production system about 6% in the trace-on mode. When our prototype works in the trace-off mode, the runtime overhead is even lower, on an average of 1.5% across each benchmark we run. We believe that it is feasible to directly apply our prototype into production system environment.