gebhart/patrepeval huggingface dataset:
Permutation tests for factorially designed neuroimaging experiments (2004)

Permutation methods for analysis of functional neuroimaging data acquired as factorially designed experiments are described and validated. The F ratio was estimated for main effects and interactions at each voxel in standard space. Critical values corresponding to probability thresholds were derived from a null distribution sampled by appropriate permutation of observations. Spatially informed, cluster-level test statistics were generated by applying a preliminary probability threshold to the voxel F maps and then computing the sum of voxel statistics in each of the resulting three-dimensional clusters, i.e., cluster "mass." Using simulations comprising two between- or within-subject factors each with two or three levels, contaminated by Gaussian and non-normal noise, the voxel-wise permutation test was compared to the standard parametric F test and to the performance of the spatially informed statistic using receiver operating characteristic (ROC) curves. Validity of the permutation-testing algorithm and software is endorsed by almost identical performance of parametric and permutation tests of the voxel-level F statistic. Permutation testing of suprathreshold voxel cluster mass, however, was found to provide consistently superior sensitivity to detect simulated signals than either of the voxel-level tests. The methods are also illustrated by application to an experimental dataset designed to investigate effects of antidepressant drug treatment on brain activation by implicit sad facial affect perception in patients with major depression. Antidepressant drug effects in left amygdala and ventral striatum were detected by this software for an interaction between time (within-subject factor) and group (between-subject factor) in a representative two-way factorial design.
GaAs MESFET characterization using least squares approximation by rational functions (1993)

The authors propose a method of characterizing active devices such as the FET by describing S-parameters with a set of rational functions of angular frequency. The set of rational functions is uniquely determined by only 27 coefficients, while the conventional method using tabulated S-parameters requires eight times the number of sampling points (a typical case might require 404 data points in floating-point notation). This drastically reduces the database size required to give adequate information for circuit design. A method for determining the equivalent circuit is described. Since the equivalent circuit is determined from the set of rational functions, no additional measurements are needed to determine extrinsic elements. In conventional methods, selection of initial values affects the final results. In the present method, reliable initial values are extracted from the rational functions' coefficients. The calculated S-parameters of three GaAs MESFETs having different gate widths agree closely with those measured by wafer-probe.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Translational Repression by Deadenylases (2010)

The CCR4-CAF1-NOT complex is a major cytoplasmic deadenylation complex in yeast and mammals. This complex associates with RNA-binding proteins and microRNAs to repress translation of target mRNAs. We sought to determine how CCR4 and CAF1 participate in repression and control of maternal mRNAs using Xenopus laevis oocytes. We show that Xenopus CCR4 and CAF1 enzymes are active deadenylases and repress translation of an adenylated mRNA. CAF1 also represses translation independent of deadenylation. The deadenylation-independent repression requires a 5' cap structure on the mRNA; however, deadenylation does not. We suggest that mere recruitment of CAF1 is sufficient for repression, independent of deadenylation.
A Multivariate Approach to the Treatment of Peripheral Nerve Transection Injury (1991)

A multivariate approach to the treatment of peripheral nerve transection injury has been used in a rat model. A pilot study (48 animals, 8 groups) examined variables associated with the method and timing of surgical repair, the arrest of wallerian degeneration, and the role of pulsing electromagnetic field therapy (PEMF) in functional recovery. A second phase (90 animals, 6 groups) then studied the timing and duration of pulsing electromagnetic field therapy as the only variable in larger groups of animals. The pilot study revealed that a vein-graft conduit did not improve functional recovery compared with standard epineurial repair. Additionally, delayed repair compared favorably with immediate repair. The use of chlorpromazine to inhibit the toxic effects of calcium influx appeared to enhance early functional recovery, and the combination of delayed nerve repair and pulsing electromagnetic field therapy seemed to consistently improve function. The second phase of the study has demonstrated (for the first time) statistical improvement in ambulation in animals treated with delayed surgical repair and prolonged pulsing electromagnetic field therapy. We postulate that future treatment of nerve transection injuries will involve a combined treatment regimen consisting of the immediate arrest of wallerian degeneration, delayed surgery, and pulsing electromagnetic field therapy.
Incidence of BK Virus and JC Virus Viruria in Human Immunodeficiency Virus-Infected and -Uninfected Subjects (1993)

BK virus (BKV) and JC virus (JCV) are present within the renal system of most adults. Reactivation may be linked to immunodeficiency, since many of the extant virus strains have been isolated from urine or kidney tissue of patients who were receiving immunosuppressive therapy or who had disorders of the immune system. To more critically evaluate the relationship between immunodeficiency and viruria, urine samples from individuals infected with human immunodeficiency virus (HIV) with various degrees of immunodeficiency were screened for the presence of viral DNA. JCV viruria occurred in 24%-27% of immunocompetent control subjects and was not increased with immunodeficiency. By contrast, there were both qualitative and quantitative changes in BKV viruria in immunodeficient subjects. The incidence of BKV viruria was increased, and some immunodeficient subjects shed BKV at levels up to 3000 times greater than levels shed by any of the nonimmunodeficient controls. DNA sequence rearrangements in the viral regulatory region did not appear to be required for shedding of virus, although they were present in approximately 20% of samples.
A unique epidermal mucus lectin identified from catfish (Silurus asotus): first evidence of intelectin in fish skin slime (2011)

The present study reports a new type of skin mucus lectin found in catfish Silurus asotus. The lectin exhibited calcium-dependent mannose-binding activity. When mannose eluate from chromatography with mannose-conjugated agarose was analysed by SDS-PAGE, the lectin appeared as a single 35-kDa band. Gel filtration showed that the lectin forms monomers and dimers. A 1216-bp cDNA sequence obtained by RACE-PCR from the skin encoded a 308 amino acid secretory protein with homology to mammalian and fish intelectins. RT-PCR demonstrated that the lectin gene was expressed in the gill, kidney and skin. Subsequent sequencing revealed the presence of an isoform in the gills. Antiserum detected the intelectin protein in club cells in the skin and gill, renal tubules and blood plasma. Although intelectin gene expression was not induced by in vivo bacterial stimulation, the intelectin showed agglutination activity against the pathogenic bacterium Aeromonas salmonicida, suggesting that the lectin plays an important role in self-defence against bacteria in the skin surface of the catfish. These findings represent one of the few examples of characterization and functional analysis of a fish intelectin protein.
The centrosome–Golgi apparatus nexus (2014)

A shared feature among all microtubule (MT)-dependent processes is the requirement for MTs to be organized in arrays of defined geometry. At a fundamental level, this is achieved by precisely controlling the timing and localization of the nucleation events that give rise to new MTs. To this end, MT nucleation is restricted to specific subcellular sites called MT-organizing centres. The primary MT-organizing centre in proliferating animal cells is the centrosome. However, the discovery of MT nucleation capacity of the Golgi apparatus (GA) has substantially changed our understanding of MT network organization in interphase cells. Interestingly, MT nucleation at the Golgi apparently relies on multiprotein complexes, similar to those present at the centrosome, that assemble at the cis-face of the organelle. In this process, AKAP450 plays a central role, acting as a scaffold to recruit other centrosomal proteins important for MT generation. MT arrays derived from either the centrosome or the GA differ in their geometry, probably reflecting their different, yet complementary, functions. Here, I review our current understanding of the molecular mechanisms involved in MT nucleation at the GA and how Golgi- and centrosome-based MT arrays work in concert to ensure the formation of a pericentrosomal polarized continuous Golgi ribbon structure, a critical feature for cell polarity in mammalian cells. In addition, I comment on the important role of the Golgi-nucleated MTs in organizing specialized MT arrays that serve specific functions in terminally differentiated cells.
Activity of lapatinib is independent of EGFR expression level in HER2-overexpressing breast cancer cells (2008)

Epidermal growth factor receptor (EGFR/ErbB1) and HER2 (ErbB2/neu), members of the ErbB receptor tyrosine kinase family, are frequently overexpressed in breast cancer and are known to drive tumor growth and progression, making them promising targets for cancer therapy. Lapatinib is a selective competitive inhibitor of both the HER2 and EGFR tyrosine kinases. Although lapatinib showed significant activity in patients with HER2-positive breast cancer, the role of EGFR in the response of breast cancer to lapatinib has not been defined. Here, we examined the role of EGFR expression levels in the sensitivity of HER2-overexpressing breast cancer cells to lapatinib. Depletion of EGFR by EGFR small-interfering RNA knockdown did not affect lapatinib sensitivity in these cells, whereas treated HER2 siRNA knockdown cells became more resistant to lapatinib. We conclude that the in vitro activity of lapatinib is not dependent on EGFR expression level in HER2-overexpressing breast cancer cells.
Antihyperglycemic Effect of T-1095 via Inhibition of Renal Na+-Glucose Cotransporters in Streptozotocin-Induced Diabetic Rats. (2000)

T-1095, a derivative of phlorizin, is an orally active inhibitor of Na+-glucose cotransporter (SGLT). We investigated the acute antihyperglycemic effect of T-1095 in streptozotocin-induced diabetic rats (STZ rats). T-1095 and its metabolite T-1095A inhibited the SGLT activity in brush border membranes prepared from kidneys of both normal and STZ rats, but the latter agent was approximately 10 times more potent than the former. Single oral administration of T-1095 (30-100 mg/kg) dose-dependently induced glycosuria in normal rats. The fed glucose levels in STZ rats were dose-dependently suppressed by single oral administration of T-1095 (3-100 mg/kg), whereas there was only marginal hypoglycemic effect in normal rats. Since there was no effect on blood glucose in nephrectomized STZ rats, inhibition of renal glucose reabsorption rather than intestinal glucose absorption mainly contributes to the antihyperglycemic effect of T-1095. In conclusion, T-1095 is the first orally active agent which has an acute antihyperglycemic action in the absence of endogenous insulin secretion with a low risk of hypoglycemia and has therapeutic potential for treatment of diabetes mellitus.
Color sequences for univariate maps: theory, experiments and principles (1988)

Pseudocoloring for presenting univariate map information on a graphic display system is investigated. The kinds of information available in maps are divided into two classes: metric information denotes the quantity stored at each point on the surface, and form information denotes the shape or structure of the surface. Theoretical principles are proposed to predict which color sequences will be effective at conveying value and form information respectively. According to this theory, a scale that approximates the physical spectrum should be good at conveying value information, because of the reduced effects of simultaneous contrast. It should be poor at conveying form information, however, because the brain prefers form information to come through the lightness-processing channel. Conversely, a gray scale should be poor at conveying value information and good at conveying form information, according to the same theory. These predictions are tested in a series of psychophysical experiments that test five color sequences. The results show that simultaneous contrast can be a major source of error when reading maps, but only partially confirm the form hypothesis. Guidelines are given for designing color sequences to be effective in both conveying form and value information. An experimental color sequence is presented to illustrate these guidelines.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Time-lapse gravity: A numerical demonstration using robust inversion and joint interpretation of 4D surface and borehole data (2012)

ABSTRACT There are a number of ongoing developments in the 4D gravity method for time-lapse production and sequestration problems. Complex model construction is an essential component for meaningful feasibility studies and data interpretation in 4D. In the case of oil reservoirs, for example, the 4D gravity method must deal with very small density contrasts at depth, and overly simplistic model representations of a field site may not properly guide monitoring efforts for effective reservoir management decisions. The tracking of injected fluid through inversion can be significantly improved with the joint interpretation of surface and borehole gravity data. This is particularly relevant for time-lapse gravity problems where subtle changes in density contrast at depth may not produce surface data that alone contain the necessary information to recover the boundaries of fluid movement. Complex model construction and robust inversion show that time-lapse gravity surveys may contribute to improved production efficiency and reservoir management in-between the more traditional, and expensive 4D seismic surveys. Results hint that the true value of time-lapse gravity as an additional tool for production efficiency and reservoir management may be greatly undervalued. Data simulated within current and ongoing sensor technologies, combined with advances in computing power and robust inversion, can extract much more meaningful information about fluid movement in reservoirs that are geometrically complex and relatively thin and deep. To illustrate these points, simulations are performed using a representation of the published Jotun Field in the Norwegian North Sea, a well-studied site demonstrating successful application of the time-lapse seismic method, and reconstructed for 4D gravity understanding.
A refined look at Bernstein's AES side-channel analysis (2006)

In a recent manuscript Dan Bernstein claims the successful extraction of an AES key from a network server through another client computer. His side-channel attack was actually the simplest conceivable timing analysis of AES. Although Bernstein gave no thorough analysis of his methodology or the underlying technique the paper contained the full C-source code. This was actually very useful to repeat, analyze and extend his experiments and technique. Our paper improves upon the work done by Bernstein in the following ways:
Towards automated segmentation of cells and cell nuclei in nonlinear optical microscopy (2012)

Nonlinear optical (NLO) imaging techniques based e.g. on coherent anti-Stokes Raman scattering (CARS) or two photon excited fluorescence (TPEF) show great potential for biomedical imaging. In order to facilitate the diagnostic process based on NLO imaging, there is need for an automated calculation of quantitative values such as cell density, nucleus-to-cytoplasm ratio, average nuclear size. Extraction of these parameters is helpful for the histological assessment in general and specifically e.g. for the determination of tumor grades. This requires an accurate image segmentation and detection of locations and boundaries of cells and nuclei. Here we present an image processing approach for the detection of nuclei and cells in co-registered TPEF and CARS images. The algorithm developed utilizes the gray-scale information for the detection of the nuclei locations and the gradient information for the delineation of the nuclear and cellular boundaries. The approach reported is capable for an automated segmentation of cells and nuclei in multimodal TPEF-CARS images of human brain tumor samples. The results are important for the development of NLO microscopy into a clinically relevant diagnostic tool.
Combining Atomic Layer Deposition with a Template-Assisted Approach To Fabricate Size-Reduced Nanowire Arrays on Substrates and Their Electrochemical Characterization (2007)

We report a combinational method to fabricate well-aligned size-reduced gold nanowire (Au NW) arrays on a Si substrate over large areas (>1.5 cm2). In this method, we employ a SiO2 atomic layer deposition (ALD) technique to reduce the pores of a porous anodic alumina (PAA) template which serves as a template for the electrodeposition of Au NW arrays and is directly integrated on the Si substrate. Unlike conventional method that simultaneously reduces the pore size and the interpore spacing by decreasing the applied potential during PAA anodization, our method allows for independently tuning these parameters. By using the ALD-reduced PAA template, we can fabricate the size-reduced Au NW arrays directly on the Si substrate with the average diameter reduced from ∼79 to ∼33 nm while their nanowire density and interwire spacing remain constant. The ALD technique enables the fine-tuning of the pore size or the nanowire diameter at an angstrom scale. Electrochemical characterization of the size-reduced Au NW arrays as nanoelectrodes is performed. The double-layer charging current (noise of the nanoelectrodes) decreases with the reduction of the nanowire diameter. Our method could be used to fabricate nanowire arrays with large spacing and small diameters via high voltage anodization and subsequent ALD reduction on the PAA template. This type of nanowire arrays might have potential applications in electrochemical and field-emission devices.
Neuropathic pain: an updated grading system for research and clinical practice (2016)

The redefinition of neuropathic pain as "pain arising as a direct consequence of a lesion or disease affecting the somatosensory system," which was suggested by the International Association for the Study of Pain (IASP) Special Interest Group on Neuropathic Pain (NeuPSIG) in 2008, has been widely accepted. In contrast, the proposed grading system of possible, probable, and definite neuropathic pain from 2008 has been used to a lesser extent. Here, we report a citation analysis of the original NeuPSIG grading paper of 2008, followed by an analysis of its use by an expert panel and recommendations for an improved grading system. As of February, 2015, 608 eligible articles in Scopus cited the paper, 414 of which cited the neuropathic pain definition. Of 220 clinical studies citing the paper, 56 had used the grading system. The percentage using the grading system increased from 5% in 2009 to 30% in 2014. Obstacles to a wider use of the grading system were identified, including (1) questions about the relative significance of confirmatory tests, (2) the role of screening tools, and (3) uncertainties about what is considered a neuroanatomically plausible pain distribution. Here, we present a revised grading system with an adjusted order, better reflecting clinical practice, improvements in the specifications, and a word of caution that even the "definite" level of neuropathic pain does not always indicate causality. In addition, we add a table illustrating the area of pain and sensory abnormalities in common neuropathic pain conditions and propose areas for further research.
Prognostic Value of Vascular Endothelial Growth Factor Expression in Resected Gastric Cancer (2012)

Positive expression of tissue VEGF, circulating VEGF, VEGF-C and VEGF-D were all associated with poor prognosis in resected gastric cancer. However, VEGF demonstrated no significant prognostic value for non-Asian populations. Circulating VEGF may be better than tissue VEGF in predicting prognosis.
Fabrication of Nanoscale Vias by Offset Patterning (2008)

Patterning of features with photolithography technique by overlying multiple exposure patterns with intentional offset reduces the effective size of the resultant opening when the openings overlap incompletely. The size of resultant opening depends on the size of the parental opening and the degree of overlap. Overlapping via patterns helps to achieve small via size from photolithography. In the present study, two oxide layers with via pattern were involved. The bottom oxide layer was deposited and patterned first. The top oxide layer and the poly-Si sandwich layer were then deposited on the patterned bottom oxide layer and patterned with an offset afterwards. Experimental results show resultant vias with size reduction by more than 50% compared with the parental vias. The equivalent diameter of the resultant vias goes down to as small as 400 nm. It was found that the equivalent diameter decreases with reduction in parental via size. The length-to-width ratio of the resultant vias opening increases as the parental via size becomes larger. The offset distance is also found to contribute significant effect to the size of the resultant via. The large offset distance leads to small but high-aspect ratio resultant vias.
Adherence to Vitamin D Recommendations Among US Infants (2010)

Our findings suggest that most US infants are not consuming adequate amounts of vitamin D according to the 2008 AAP recommendation. Pediatricians and health care providers should encourage parents of infants who are either breastfed or consuming <1 L/day of infant formula to give their infants an oral vitamin D supplement.
A Direct, Efficient Method for the Preparation of siRNAs Containing Ribo-like <i>North</i> Bicyclo[3.1.0]hexane Pseudosugars (2011)

An efficient method for the preparation of siRNAs modified with ribo-like North bicyclo[3.1.0]hexane pseudosugars is described. The combined use of 2'-O-(2-cyanoethoxymethyl) (CEM) and 2'-O-TBDMS protection was successfully employed for RNA synthesis with the added advantage that both groups were efficiently removed in a single step. The resulting North ribo-methanocarba-modified siRNAs are compatible with the intracellular RNAi machinery and can mediate specific degradation of target mRNA.