Miracle-dz/UniFAR-FTUs huggingface dataset:
Microarray‐assisted fine mapping of quantitative trait loci on chromosome 15 for susceptibility to seizure‐induced cell death in mice

Prior studies with crosses of the FVB/NJ (FVB; seizure‐induced cell death‐susceptible) mouse and the C57BL/6J (B6; seizure‐induced cell death‐resistant) mouse revealed the presence of a quantitative trait locus (QTL) on chromosome 15 that influenced susceptibility to kainic acid‐induced cell death (Sicd2). In an earlier study, we confirmed that the Sicd2 interval harbors gene(s) conferring strong protection against seizure‐induced cell death through the creation of the FVB.B6‐Sicd2 congenic strain, and created three interval‐specific congenic lines (ISCLs) that encompass Sicd2 on chromosome 15 to fine‐map this locus. To further localise this Sicd2 QTL, an additional congenic line carrying overlapping intervals of the B6 segment was created (ISCL‐4), and compared with the previously created ISCL‐1–ISCL‐3 and assessed for seizure‐induced cell death phenotype. Whereas all of the ISCLs showed reduced cell death associated with the B6 phenotype, ISCL‐4, showed the most extensive reduction in seizure‐induced cell death throughout all hippocampal subfields. In order to characterise the susceptibility loci on Sicd2 by use of this ISCL and identify compelling candidate genes, we undertook an integrative genomic strategy of comparing exon transcript abundance in the hippocampus of this newly developed chromosome 15 subcongenic line (ISCL‐4) and FVB‐like littermates. We identified 10 putative candidate genes that are alternatively spliced between the strains and may govern strain‐dependent differences in susceptibility to seizure‐induced excitotoxic cell death. These results illustrate the importance of identifying transcriptomics variants in expression studies, and implicate novel candidate genes conferring susceptibility to seizure‐induced cell death.
Interaction of SH‐SY5Y Cells with Nanogratings During Neuronal Differentiation: Comparison with Primary Neurons

Controlling neuronal cell adhesion, migration, and axonal outgrowth via contact interactions with biomaterials is a critical element for tissue engineering applications and for developing artificial neuronal interfaces. One promising approach relies on the exploitation of nanostructured surfaces. Here, the human neuroblastoma cell line SH‐SY5Y is interfaced with plastic nanogratings (NGs; anisotropic topographies composed by alternating lines of grooves and ridges with sub‐micrometer lateral dimension). The SH‐SY5Y cells' (SHs) contact guidance is investigated under proliferating conditions and upon differentiation after treatment with retinoic acid (RA) and brain‐derived neurotrophin factor (BDNF), and compared with mouse primary hippocampal neurons (HNs). Quantitative readouts are obtained by measuring changes in tubulin cytoskeleton organization and cell morphology induced by mechanotransduction. Results demonstrate that SHs effectively retrieve substrate topographical signals, in particular during differentiation. Remarkably, RA/BDNF improves SH responsiveness to NG directional cues, and significantly enhances the alignment to the NG lines. HNs behave similarly, showing a marked change in network organization if cultured on NGs. These results might help the rational engineering of neuro‐regenerative scaffolds to improve peripheral nerve wound healing, as well as to investigate the basic mechanisms of neuronal wiring.
The welfare use of immigrants and natives in Germany: the case of Turkish immigrants

Purpose - This paper aims to analyze the welfare use of Turkish immigrants and natives in Germany. The authors ask whether the immigrant-native gap in welfare use can be explained by observable characteristics, whether the mechanisms behind welfare dependence differ for Turkish immigrants and natives, and, finally, they compare the situation before and after the 2005 reform of the German welfare system. Design/methodology/approach - Using data from the German Socio-Economic Panel Study, the authors estimate linear probability models with random effects to investigate the correlates of transfer receipt for Turkish immigrants and natives. Findings - Turkish immigrants have a higher propensity to use welfare benefits than natives. After controlling for general individual and household level characteristics, the difference in welfare receipt is statistically significant only for the group of second generation immigrants. The correlation of observable characteristics with welfare dependence differs significantly for the native and immigrant sample. The share of benefit recipients increased after the policy reform in 2005 for both immigrants and natives. Practical implications - First, as human capital and particularly labor market status are important determinants of welfare use, training programs designed for the special needs of immigrants might support their labor market integration. Second, measures to ameliorate the integration of older people into the labor market might be particularly useful because the need for welfare benefits arises particularly at the 50-60 age range. Originality/value - This is the first study to investigate welfare use of Turkish immigrants after the German 2005 labor market policy reform.
Assessment of English Letters' Legibility Using Image Descriptors

The study derived seven descriptors from the pixel matrices of both the uppercase and lowercase forms of the 26 letters in the English alphabet in the regular and italic versions of the most commonly used font. Times New Roman. A factor analysis of the seven descriptors showed that a two-factor solution of letter width and height explained 76.6% of the variance. Legibility threshold of the 26 letters in the regular and italic Times Roman font and in two-case forms were collected to specify effects of letter width and height. 20 university students, 10 women and 10 men, with a mean age of 24.1 yr, (SD = 1.6) participated. They identified letters displayed initially on a PC screen at a minimum font size and enlarged gradually until the participant correctly recognized the letter. Analysis showed letters of greater width or height were more legible than those of smaller width or height. Given an oblique effect, letters in the italic Times Roman font had significantly greater width but were less legible than those in the regular font.
Fungal negative-stranded RNA virus that is related to bornaviruses and nyaviruses

Significance Mycoviruses are viruses that infect fungi and replicate in fungi. Previously, no mycoviruses had been discovered with negative-stranded (−)ssRNA genomes. Here, we characterize a (−)ssRNA mycovirus that infects a fungal plant pathogen. Although its genome and organization are significantly different from those of current mononegaviruses, this virus is closely related to viruses in families Nyamiviridae and Bornaviridae that infect animals. This discovery may provide insights into the global ecology and evolution of (−)ssRNA viruses. Furthermore, since many (−)ssRNA viruses are serious human pathogens, this system is likely to provide a less hazardous way to study replication of a (−)ssRNA virus and could be useful in establishing a system to screen antiviral compounds against (−)ssRNA viruses. Mycoviruses are widespread in nature and often occur with dsRNA and positive-stranded RNA genomes. Recently, strong evidence from RNA sequencing analysis suggested that negative-stranded (−)ssRNA viruses could infect fungi. Here we describe a (−)ssRNA virus, Sclerotinia sclerotiorum negative-stranded RNA virus 1 (SsNSRV-1), isolated from a hypovirulent strain of Sclerotinia sclerotiorum. The complete genome of SsNSRV-1 is 10,002 nt with six ORFs that are nonoverlapping and linearly arranged. Conserved gene-junction sequences that occur widely in mononegaviruses, (A/U)(U/A/C)UAUU(U/A)AA(U/G)AAAACUUAGG(A/U)(G/U), were identified between these ORFs. The analyses 5′ and 3′ rapid amplification of cDNA ends showed that all genes can be transcribed independently. ORF V encodes the largest protein that contains a conserved mononegaviral RNA-dependent RNA polymerase (RdRp) domain. Putative enveloped virion-like structures with filamentous morphology similar to members of Filoviridae were observed both in virion preparation samples and in ultrathin hyphal sections. The nucleocapsids are long, flexible, and helical; and are 22 nm in diameter and 200–2,000 nm in length. SDS/PAGE showed that the nucleocapsid possibly contains two nucleoproteins with different molecular masses, ∼43 kDa (p43) and ∼41 kDa (p41), and both are translated from ORF II. Purified SsNSRV-1 virions successfully transfected a virus-free strain of S. sclerotiorum and conferred hypovirulence. Phylogenetic analysis based on RdRp showed that SsNSRV-1 is clustered with viruses of Nyamiviridae and Bornaviridae. Moreover, SsNSRV-1 is widely distributed, as it has been detected in different regions of China. Our findings demonstrate that a (−)ssRNA virus can occur naturally in fungi and enhance our understanding of the ecology and evolution of (−)ssRNA viruses.
Thermal Soaring Compared in Three Dissimilar Tropical Bird Species, Fregata Magnificens, Pelecanus Occidentals and Coragyps Atratus

1.All three species were observed in straight flight, and circling in thermals, from Flamenco Island, Panama. Measurements were made by ornithodolite, an instrument which records a series of timed, three-dimensional position estimates, from which speeds, circle diameters and rates of climb can be calculated. 2.Mean lift coefficients in straight glides ranged from 0.72 to 0.84, except in slope soaring, where a mean of 1.6 was recorded for both the frigatebird and black vulture. 3.Mean circling radii were proportional to wing loading, and varied from 12.0m for the frigatebird to 18.0 m for the pelican. Mean rates of climb ranged from 0.40 ms −1 for the black vulture to 0.57 ms −1 for the pelican. All species showed mean circling lift coefficients between 1.33 and 1.45, and angles of bank between 22.9° and 24.7°. 4.It is argued that the frigatebird is adapted to stay airborne continuously, day and night, for extended periods, by exploiting thermals over the sea under trade wind cumulus clouds. The low wing loading is seen as an adaptation to circling in narrow thermals, and the low disc loading as an adaptation giving low minimum power, when flapping cannot be avoided. Take-off appears to be possible only by dropping from an elevated perch, not from the ground or water surface. 5.The low aspect-ratio, tip-slotted wings of the black vulture are certainly less efficient for soaring, but appear to be better for upward take-off from the ground. The pelican also has tip-slotted wings. Although its aspect ratio is higher, it is still capable of taking off from a level water surface.
Prognostic factors for survival in patients with colorectal liver metastases: experience of a single brazilian cancer center.

CONTEXT Liver metastases are a common event in the clinical outcome of patients with colorectal cancer and account for 2/3 of deaths from this disease. There is considerable controversy among the data in the literature regarding the results of surgical treatment and prognostic factors of survival, and no analysis have been done in a large cohort of patients in Brazil. OBJECTIVES To characterize the results of surgical treatment of patients with colorectal liver metastases, and to establish prognostic factors of survival in a Brazilian population. METHOD This was a retrospective study of patients undergoing liver resection for colorectal metastases in a tertiary cancer hospital from 1998 to 2009. We analyzed epidemiologic variables and the clinical characteristics of primary tumors, metastatic disease and its treatment, surgical procedures and follow-up, and survival results. Survival analyzes were done by the Kaplan-Meier method and the log-rank test was applied to determine the influence of variables on overall and disease-free survival. All variables associated with survival with P<0.20 in univariate analysis, were included in multivariate analysis using a Cox proportional hazard regression model. RESULTS During the period analyzed, 209 procedures were performed on 170 patients. Postope-rative mortality in 90 days was 2.9% and 5-year overall survival was 64.9%. Its independent prognostic factors were the presence of extrahepatic disease at diagnosis of liver metastases, bilateral nodules and the occurrence of major complications after liver surgery. The estimated 5-year disease-free survival was 39.1% and its prognostic factors included R1 resection, extrahepatic disease, bilateral nodules, lymph node involvement in the primary tumor and primary tumors located in the rectum. CONCLUSION Liver resection for colorectal metastases is safe and effective and the analysis of prognostic factors of survival in a large cohort of Brazilian patients showed similar results to those pointed in international series. The occurrence of major postoperative complications appears to be able to compromise overall survival and further investigation in needed in this topic.
SU6656, a Selective Src Family Kinase Inhibitor, Used To Probe Growth Factor Signaling

ABSTRACT The use of small-molecule inhibitors to study molecular components of cellular signal transduction pathways provides a means of analysis complementary to currently used techniques, such as antisense, dominant-negative (interfering) mutants and constitutively activated mutants. We have identified and characterized a small-molecule inhibitor, SU6656, which exhibits selectivity for Src and other members of the Src family. A related inhibitor, SU6657, inhibits many kinases, including Src and the platelet-derived growth factor (PDGF) receptor. The use of SU6656 confirmed our previous findings that Src family kinases are required for both Myc induction and DNA synthesis in response to PDGF stimulation of NIH 3T3 fibroblasts. By comparing PDGF-stimulated tyrosine phosphorylation events in untreated and SU6656-treated cells, we found that some substrates (for example, c-Cbl, and protein kinase C δ) were Src family substrates whereas others (for example, phospholipase C-γ) were not. One protein, the adaptor Shc, was a substrate for both Src family kinases (on tyrosines 239 and 240) and a distinct tyrosine kinase (on tyrosine 317, which is perhaps phosphorylated by the PDGF receptor itself). Microinjection experiments demonstrated that a Shc molecule carrying mutations of tyrosines 239 and 240, in conjunction with an SH2 domain mutation, interfered with PDGF-stimulated DNA synthesis. Deletion of the phosphotyrosine-binding domain also inhibited synthesis. These inhibitions were overcome by heterologous expression of Myc, supporting the hypothesis that Shc functions in the Src pathway. SU6656 should prove a useful additional tool for further dissecting the role of Src kinases in this and other signal transduction pathways.
ReCoM: A new Reconfigurable Compute Fabric Architecture for Computation-Intensive Applications

Reconfigurable mixed grain (ReCoM) is a novel reconfigurable compute fabric (RCF) architecture based on a mixed-grain reconfigurable array which combines a RISC microprocessor and a reconfigurable hardware for computation-intensive applications. ReCoM comprises a modified RISC microprocessor, a dynamically reconfigurable processing array including reconfigurable cells formed by a 64-bits ALU, look up tables (LUTs), word-level arithmetic units, and an efficient configuration and data memory architecture. This paper describes the ReCoM architecture and presents its effectiveness for a digital signal processing benchmark application
Interocular symmetry analysis of bilateral eyes

Abstract The purpose of this study was to evaluate the interocular symmetry of several biometric parameters between both eyes. The symmetry between the right and left eye of 397 subjects in 14 biometric parameters, spherical equivalent of refractive error (SE), Jackson crossed cylinder power of refractive error astigmatism with axes at 90° and 180° (RJ0) and at 45° and 135° (RJ45), best-corrected visual acuity (BCVA), average corneal curvature (CC), Jackson crossed cylinder power of corneal astigmatism (CJ0 and CJ45), corneal asphericity coefficient (Q), intraocular pressure (IOP), central corneal thickness (CCT), axial length (AL), anterior chamber depth (ACD), lens thickness (LT) and vitreous chamber depth (VCD), was assessed by comparative data analysis. Aside from RJ0 (p = 0.00), RJ45 (p = 0.02) and Q (p = 0.00), the overall interocular differences of other biometric parameters between fellow eyes were not significant (p > 0.05). The interocular correlation and Bland-Altman plots showed a good agreement between fellow eyes in 14 biometric parameters. Correlations between interocular differences in SE and that in RJ0 (p = 0.03), CC (p = 0.00), AL (p = 0.00) and VCD (p = 0.00) were statistically significant. There were similar strong linear relationships between refractive error astigmatism vectors and corneal astigmatism vectors in bilateral eyes. There were negative correlations of RJ45 and CJ45 between bilateral eyes. A potentially clinically important interocular symmetry in SE, BCVA, CC, CJ0, CJ45, IOP, CCT, AL, ACD, LT and VCD is found in this research, while the differences of RJ0, RJ45 and Q between left and right eyes seem a bit large. The negative interocular relationships of RJ45 and CJ45 demonstrate moderate mirror symmetry exists among fellow eyes. High interocular symmetry in bilateral eyes may be helpful in intraocular lens power calculation, intraocular pressure evaluation, post-operative visual acuity and refraction prediction at the time the fellow eye is undergoing refractive surgery.
Six-Fold Acceleration of High-Spatial Resolution 3D SPACE MRI of the Knee Through Incoherent k-Space Undersampling and Iterative Reconstruction—First Experience

PurposeThe aim of this study was to prospectively test the hypothesis that 6-fold acceleration of a 3-dimensional (3D) turbo spin echo (TSE) magnetic resonance imaging (MRI) pulse sequence with k-space undersampling and iterative reconstruction is feasible for fast high spatial resolution MRI of the knee, while yielding similar image quality and diagnostic performance when compared with a conventional 2-dimensional (2D) TSE MRI standard. Materials and MethodsThe study was approved by the institutional review board. A 10-minute isotropic 3D TSE knee protocol consisting of accelerated intermediate-weighted (repetition time, 900 milliseconds; echo time, 29 milliseconds; voxel size, 0.5 × 0.5 × 0.5 mm3; acquisition time, 4:45 minutes) and fat-saturated T2-weighted (repetition time, 900 milliseconds; echo time, 92 milliseconds; voxel size, 0.5 × 0.5 × 0.5 mm3; acquisition time, 5:10 minutes) SPACE (sampling perfection with application optimized contrast using different flip angle evolutions) sequence prototypes was compared against a 20-minute 2D TSE standard protocol. The accelerated SPACE sequences were equipped with an optional variable-density poisson-disc pattern as an undersampling mask. An undersampling factor of 0.17 was chosen (6-fold acceleration compared with an acquisition with full sampling). An iterative, sensitivity encoding-type reconstruction with L1 norm-based regularization term was used. The study was performed on a 3 T MRI system using a 15-channel transmit/receive knee coil. The study groups included 15 asymptomatic volunteers and 15 patient volunteers. Quantitative and qualitative assessments were performed by 2 observers. Outcome variables included signal and contrast-to-noise ratio, image quality, and diagnostic accuracy. Qualitative and quantitative measurements were statistically analyzed using nonparametric tests. P values of less than 0.01 were considered significant. ResultsThe signal-to-noise ratios of 2D and 3D MRI were similar with the exception of fluid, which was brighter on 2D MRI. Relevant contrast-to-noise ratios of 2D MRI were higher than 3D MRI; however, observer ratings for satisfaction, image quality, and visibility of anatomic structures were similar for 2D and 3D MRI. There was moderate to excellent interobserver (&kgr; = 0.54–1.00) and intermethod (&kgr; = 0.54–1.00) agreement for assessing menisci, cartilage, ligaments, cartilage, and bone. Two-dimensional and 3D MRI had similar sensitivity (100%/100%, respectively) and specificity (87%/75%, respectively) for detecting 9 meniscal tears (P = 1.00). ConclusionsWe demonstrate the successful clinical implementation of 3D TSE MRI with incoherent k-space undersampling and iterative reconstruction for 6-fold accelerated high spatial resolution isotropic 3D MRI data acquisition. Our preliminary assessments suggest similar image quality and diagnostic performance of a comprehensive 10-minute 3D TSE MRI prototype protocol and 20-minute TSE MRI standard protocol.
Signal‐to‐noise ratio and absorbed power as functions of main magnetic field strength, and definition of “90°” RF pulse for the head in the birdcage coil

Calculations of the RF magnetic (B1) field as a function of frequency between 64 and 345 MHz were performed for a head model in an idealized birdcage coil. Absorbed power (Pabs) and SNR were calculated at each frequency with three different methods of defining excitation pulse amplitude: maintaining 90° flip angle at the coil center (center α = π/2), maximizing FID amplitude (Max. AFID), and maximizing total signal amplitude in a reconstructed image (Max. Aimage). For center α = π/2 and Max. Aimage, SNR increases linearly with increasing field strength until 260 MHz, where it begins to increase at a greater rate. For these two methods, Pabs increases continually, but at a lower rate at higher field strengths. Above 215 MHz in MRI of the human head, the use of FID amplitude to set B1 excitation pulses may result in apparent decreases in SNR and power requirements with increasing static field strength. Magn Reson Med 45:684–691, 2001. © 2001 Wiley‐Liss, Inc.
Validation of digital spiral analysis as outcome parameter for clinical trials in essential tremor

Essential tremor, one of the most prevalent movement disorders, is characterized by kinetic and postural tremor affecting activities of daily living. Spiral drawing is commonly used to visually rate tremor intensity, as part of the routine clinical assessment of tremor and as a tool in clinical trials. We present a strategy to quantify tremor severity from spirals drawn on a digitizing tablet. We validate our method against a well‐established visual spiral rating method and compare both methods on their capacity to capture a therapeutic effect, as defined by the change in clinical essential tremor rating scale after an ethanol challenge. Fifty‐four Archimedes spirals were drawn using a digitizing tablet by nine ethanol‐responsive patients with essential tremor before and at five consecutive time points after the administration of ethanol in a standardized treatment intervention. Quantitative spiral tremor severity was estimated from the velocity tremor peak amplitude after numerical derivation and Fourier transformation of pen‐tip positions. In randomly ordered sets, spirals were scored by seven trained raters, using Bain and Findley's 0 to 10 rating scale. Computerized scores correlated with visual ratings (P < 0.0001). The correlation was significant at each time point before and after ethanol (P < 0.005). Quantitative ratings provided better sensitivity than visual rating to capture the effects of an ethanol challenge (P < 0.05). Using a standardized treatment approach, we were able to demonstrate that spirography time‐series analysis is a valid, reliable method to document tremor intensity and a more sensitive measure for small effects than currently available visual spiral rating methods. © 2011 Movement Disorder Society