gebhart/patrepeval huggingface dataset:
Statistical Issues in the Analysis of Neuronal Data (2005)

Analysis of data from neurophysiological investigations can be challenging. Particularly when experiments involve dynamics of neuronal response, scientific inference can become subtle and some statistical methods may make much more efficient use of the data than others. This article reviews well-established statistical principles, which provide useful guidance, and argues that good statistical practice can substantially enhance results. Recent work on estimation of firing rate, population coding, and time-varying correlation provides improvements in experimental sensitivity equivalent to large increases in the number of neurons examined. Modern nonparametric methods are applicable to data from repeated trials. Many within-trial analyses based on a Poisson assumption can be extended to non-Poisson data. New methods have made it possible to track changes in receptive fields, and to study trial-to-trial variation, with modest amounts of data.
The world of the complex Ginzburg-Landau equation (2002)

The cubic complex Ginzburg-Landau equation is one of the most-studied nonlinear equations in the physics community. It describes a vast variety of phenomena from nonlinear waves to second-order phase transitions, from superconductivity, superfluidity, and Bose-Einstein condensation to liquid crystals and strings in field theory. The authors give an overview of various phenomena described by the complex Ginzburg-Landau equation in one, two, and three dimensions from the point of view of condensed-matter physicists. Their aim is to study the relevant solutions in order to gain insight into nonequilibrium phenomena in spatially extended systems.
Magnetic Resonance Classification of Lumbar Intervertebral Disc Degeneration (2001)

Disc degeneration can be graded reliably on routine T2-weighted magnetic resonance images using the grading system and algorithm presented in this investigation.
Adherent Self-Renewable Human Embryonic Stem Cell-Derived Neural Stem Cell Line: Functional Engraftment in Experimental Stroke Model (2008)

The SD56 human neural stem cells derived under the reported conditions are stable, do not form tumors in vivo and enable functional recovery after stroke. These properties indicate that this hNSC line may offer a renewable, homogenous source of neural cells that will be valuable for basic and translational research.
Comorbid depression and anxiety spectrum disorders (1996)

The relationship between depression and anxiety disorders has long been a matter of controversy. The overlap of symptoms associated with these disorders makes diagnosis, research, and treatment particularly difficult. Recent evidence suggests genetic and neurobiologic similarities between depressive and anxiety disorders. Comorbid depression and anxiety are highly prevalent conditions. Patients with panic disorder, generalized anxiety disorder, social phobia, and other anxiety disorders are also frequently clinically depressed. Approximately 85% of patients with depression also experience significant symptoms of anxiety. Similarly, comorbid depression occurs in up to 90% of patients with anxiety disorders. Patients with comorbid disorders do not respond as well to therapy, have a more protracted course of illness, and experience less positive treatment outcomes. One key to successful treatment of patients with mixed depressive and anxiety disorders is early recognition of comorbid conditions. Antidepressant medications, including the selective serotonin reuptake inhibitors, tricyclic antidepressants, and monoamine oxidase inhibitors, are highly effective in the management of comorbid depression and anxiety. The high rates of comorbid depression and anxiety argue for well-designed treatment studies in these populations.
Differentiating benign from malignant solid breast masses: value of shear wave elastography according to lesion stiffness combined with greyscale ultrasound according to BI-RADS classification (2012)

Together, BI-RADS assessment of greyscale ultrasound images and shear wave ultrasound elastography are extremely sensitive for detection of malignancy.
Down-regulation of the KAI1 metastasis suppressor gene during the progression of human prostatic cancer infrequently involves gene mutation or allelic loss. (1996)

The KAI1 gene, located on human chromosome 11p11.2, suppresses tumor metastasis when expressed in certain cancer cells. To evaluate whether dysregulation of KAI1 occurs during the progression of human prostatic cancer, protein expression, mutation, and allelic loss of KAI1 were analyzed using a tissue bank of 98 primary cancers and 32 metastases. By immunohistochemical staining, high levels of KAI1 protein are detected in the epithelial but not stromal compartment of normal prostatic and benign prostatic hyperplasia tissue. In epithelial cells, KAI1 protein is expressed on the plasma membrane. KAI1 protein expression is downregulated in more than 70% of the 49 primary prostatic cancers from untreated patients. In 10 such untreated patients, down-regulation of KAI1 protein occurred in all of the lymph node metastases examined. In 15 patients with metastatic disease who had failed androgen ablation therapy, more than 90% of the primary prostatic cancers had downregulation, with 60% having no KAI1 protein expression. Primers derived from the sequences flanking each exon of KAI1 were used to analyze KAI1 mutation and allelic loss by the method of PLR-single-strand conformational polymorphism. Using this method, no point mutation or allelic loss was detected in metastases from 10 patients. No allelic loss was detected in an additional 34 primary and 12 lymph node metastases via microsatellite analysis using the marker D11S1344, which is located in the region of KAI1. These results demonstrate that KAI1 protein expression is consistently down-regulated during the progression of human prostatic cancer and that this down-regulation does not commonly involve either mutation or allelic loss of the KAI1 gene.
Synthesis and mechanical evaluation of micro-scale truss structures formed from self-propagating polymer waveguides (2015)

Materials with significant porosity, generally termed cellular materials, have considerably lower bulk density than their solid counterparts. However, at the cost of reducing the mass of a material by introducing porosity, mechanical properties such as the strength and elastic modulus are significantly diminished. Ordered cellular structures generally exhibit an increase in modulus and peak strength relative to random cellular configurations by changing the mode of deformation from bending-dominated to stretch/compression-dominated within the microstructure during elastic loading. Nevertheless, techniques to fabricate three-dimensional ordered open-cellular materials, particularly with feature sizes ranging from tens to hundred of microns, are limited. Presented in this dissertation, is a new technique to create cellular materials with a truss architecture from a three-dimensional interconnected pattern of self-propagating polymer waveguides. The self-propagating effect enables the rapid formation (< 1 min) of thick (> 5 mm) three-dimensional open-cellular micro-truss structures from a single two-dimensional exposure surface. The process also affords significant flexibility and control of the resulting truss microstructure.
Morphological and Immunohistochemical Characteristics of the Heterogeneous Prostate-Like Glands (Paraurethral Gland) Seen in Female Brown-Norway Rats (2001)

Morphological and immunohistochemical characteristics of the prostate-like glands (paraurethral gland) seen spontaneously in female Brown-Norway (BN) rats were investigated by gross, and light and electron microscopic examination. At 9- to 10-weeks-old, the paraurethral gland was detected in 50 out of 52 female animals examined (96.2%), and it was observed as single or paired structures located ventrolaterally in the urethra just caudal to neck of the urinary bladder. Microscopically, the glandular acini consisted of flat to cuboidal secretory epithelium surrounded by the smooth muscle. The glands displayed modest secreting activity, and a few secreting materials were observed in the acinar lumens. The main peripheral ducts were located in the urethral wall, and drained into the urethra on both sides. Ultrastructurally, abundant rough endoplasmic reticulum (RER), numerous mitochondria and lysosomes, and secretory granules in the apical portion of the epithelial cells were noted, and basal cells were also observed. These gland epithelial cells showed positive reactions when stained for androgen receptor (AR), prostate specific antigen (PSA), or prostate specific acid phosphatase (PSAP). The nature of this paraurethral gland resembled that of the prostate gland in male rats. Thus, the paraurethral glands seen in the females were considered homologous to the prostate gland in males.
High-Pressure Pyrolysis of Green River Oil Shale (1983)

Oil yields, compositions and rates of evolution are reported for heating rates from 1 to 100°C/h and pressures of 1.5 and 27 atm. Pyrolysis occurred in an autogenous atmosphere and volatile products were allowed to escape the pyrolysis region continuously. Higher pressures and lower heating rates during pyrolysis cause a decrease in oil yield, although the effects are not additive. The lowest oil yield was approximately 72 wt% or 79 vol% of Fischer assay. Lower oil yield is generally accompanied by lower boiling point distribution, nitrogen content and density and higher H/C ratios. Oils produced at high pressure and slow heating rates are a clear amber color instead of the usual opaque brown. The effect of pyrolysis conditions on biological markers and other diagnostic hydrocarbons is also discussed. Existing kinetic expressions for oil evolution slightly overestimate the shift in the oil evolution rate vs temperature with a decrease in heating rate. Finally, the rate of oil evolution is retarded by pressure, a factor not taken into account by current kinetic expressions.
The Structure and Function of P55 PIK Reveal a New Regulatory Subunit for Phosphatidylinositol 3-Kinase (1995)

Phosphatidylinositol 3-kinase (PI-3 kinase) is implicated in the regulation of diverse cellular processes, including insulin-stimulated glucose transport. PI-3 kinase is composed of a 110-kDa catalytic subunit and an 85-kDa regulatory subunit. Here, we describe p55PIK, a new regulatory subunit that was isolated by screening expression libraries with tyrosine-phosphorylated insulin receptor substrate 1 (IRS-1). p55PIK is composed of a unique 30-residue NH2 terminus followed by a proline-rich motif and two Src homology 2 (SH2) domains with significant sequence identify to those in p85. p55PIK mRNA is expressed early during development, remains abundant in adult mouse brain and testis tissue, and is detectable in adult adipocytes and heart and kidney tissues. p55PIK forms a stable complex with p110, and it associates with IRS-1 during insulin stimulation. Moreover, the activated insulin receptor phosphorylates p55PIK in Sf9 cells, and insulin stimulates p55PIK phosphorylation in CHOIR/p55PIK cells. The unique features of p55PIK suggest that it is important in receptor signaling.
MethyLight: a high-throughput assay to measure DNA methylation (2000)

Cytosine-5 DNA methylation occurs in the context of CpG dinucleotides in vertebrates. Aberrant methylation of CpG islands in human tumors has been shown to cause transcriptional silencing of tumor-suppressor genes. Most methods used to analyze cytosine-5 methylation patterns require cumbersome manual techniques that employ gel electrophoresis, restriction enzyme digestion, radiolabeled dNTPs or hybridization probes. The development of high-throughput technology for the analysis of DNA methylation would significantly expand our ability to derive molecular information from clinical specimens. This study describes a high-throughput quantitative methylation assay that utilizes fluorescence-based real-time PCR (TaqMan) technology that requires no further manipulations after the PCR step. MethyLight is a highly sensitive assay, capable of detecting methylated alleles in the presence of a 10,000-fold excess of unmethylated alleles. The assay is also highly quantitative and can very accurately determine the relative prevalence of a particular pattern of DNA methylation. We show that MethyLight can distinguish between mono-allelic and bi-allelic methylation of the MLH1 mismatch repair gene in human colorectal tumor specimens. The development of this technique should considerably enhance our ability to rapidly and accurately generate epigenetic profiles of tumor samples.
Time-based transactional memory with scalable time bases (2007)

Time-based transactional memories use time to reason about the consistency of data accessed by transactions and about the order in which transactions commit. They avoid the large read overhead of transactional memories that always check consistency when a new object is accessed, while still guaranteeing consistency at all times--in contrast to transactional memories that only check consistency on transaction commit.Current implementations of time-based transactional memories use a single global clock that is incremented by the commit operation for each update transaction that commits. In large systems with frequent commits, the contention on this global counter can thus become a major bottleneck.We present a scalable replacement for this global counter and describe how the Lazy Snapshot Algorithm (LSA), which forms the basis for our LSA-STM time-based software transactional memory, has to be changed to support these new time bases. In particular, we show how the global counter can be replaced (1) by an external or physical clock that can be accessed efficiently, and (2) by multiple synchronized physical clocks.
The Cytokine Release Inhibitory Drug CRID3 Targets ASC Oligomerisation in the NLRP3 and AIM2 Inflammasomes (2011)

These results identify CRID3 as a novel inhibitor of the NLRP3 and AIM2 inflammasomes and provide an insight into the mechanism of action of this small molecule. In addition GSTO1 may be a component of the inflammasome that is required for ASC complex formation.
Localization of Trinucleotide Repeat Sequences in Myotonic Dystrophy Cells Using a Single Fluorochrome-Labeled PNA Probe (1998)

A labeled peptide nucleic acid (PNA) antisense probe was used to study the spatial distribution of triplet repeats (CTG) in human myotonic dystrophy (DM) cells by high-resolution fluorescence in situ hybridization (FISH). It was found that transcripts containing triplet repeats were present as a number of discrete foci in the DM nuclei. Greater numbers of foci were visible with the PNA probe than a comparable DNA probe. The PNA probe was also used to visualize the triplet-repeat expansion within the DM gene located on chromosome 19. Using the intensity of the expanded triplet-repeat on the chromosomes as a reference, it was estimated there were between 15-230 RNA molecules in each focus observed in DM nuclei.
Crohnʼs disease-associated Escherichia coli LF82 aggravates colitis in injured mouse colon via signaling by flagellin (2008)

Crohn's disease-associated virulent AIEC LF82 bacteria, via expression of flagella, are able to potentiate an inflammatory mucosal immune response involving increased expression of TLR5 and IPAF flagellin receptors.
Macrophages eat cancer cells using their own calreticulin as a guide: Roles of TLR and Btk (2015)

Macrophage-mediated programmed cell removal (PrCR) is an important mechanism of eliminating diseased and damaged cells before programmed cell death. The induction of PrCR by eat-me signals on tumor cells is countered by don't-eat-me signals such as CD47, which binds macrophage signal-regulatory protein α to inhibit phagocytosis. Blockade of CD47 on tumor cells leads to phagocytosis by macrophages. Here we demonstrate that the activation of Toll-like receptor (TLR) signaling pathways in macrophages synergizes with blocking CD47 on tumor cells to enhance PrCR. Bruton's tyrosine kinase (Btk) mediates TLR signaling in macrophages. Calreticulin, previously shown to be an eat-me signal on cancer cells, is activated in macrophages for secretion and cell-surface exposure by TLR and Btk to target cancer cells for phagocytosis, even if the cancer cells themselves do not express calreticulin.
Solution Structure of the Human pp60c-src SH2 Domain Complexed with a Phosphorylated Tyrosine Pentapeptide (1995)

Human pp60c-src is a cellular nonreceptor tyrosine kinase that participates in cytosolic signal transduction and has been implicated in the development of malignant tumors in the human breast and colon. Signal transduction is mediated by highly specific interactions between the SH2 domain and receptor phosphorylated tyrosine binding motifs. To elucidate the molecular conformation and interactions in solution, a family of highly resolved nuclear magnetic resonance (NMR) structures was determined for the src SH2 domain complexed with a high-affinity phosphorylated pentapeptide, acetyl-p YEEIE-OH. The 23 structures, generated with a distance geometry (DG) and a dynamical simulated annealing (SA) procedure, satisfied 2072 experimental restraints derived from a variety of multifrequency/multidimensional and isotope-filtered NMR data. Superimposition of residues 143-245 upon the mean coordinate set yielded an atomic rmsd of 0.58 +/- 0.09 A for the N, C alpha, C' atoms and 1.04 +/- 0.08 for all the non-hydrogen atoms. Residues in the ordered secondary structure regions superimpose to 0.29 +/- 0.04 A for the N, C alpha, C' and 0.73 +/- 0.08 A for all the non-hydrogen atoms. The angular order parameter calculated for the phi, psi angles was > 0.9 for 81 of the 106 protein residues. The main protein conformational features are three antiparallel beta-strands that traverse a compact core with an alpha-helix on each side of the core near the N- and C-termini. The observed intermolecular nuclear Overhauser effects (NOE) from the pY, +1E, and +3I residues positioned the ligand in an extended conformation across the SH2 domain surface with the pY and +3I side chains inserted into the protein binding pockets. In general, the protein conformation is consistent with previously reported structures of different SH2 domain complexes determined by X-ray crystallography. However, inter- or intramolecular interactions involving the guanidinium side chains of the solvated R alpha A2 or the buried R beta B5 were not observed at pH = 5.5 or 7.0. If such interactions exist in solution, the absence of any confirming data probably arises from rapid exchange with solvent and/or undetermined dynamic components. Thus, the unrestrained R alpha A2 side chain did not show an amino-aromatic interaction or a hydrogen bond to the -1 carbonyl oxygen as observed in the crystal structures. This result is consistent with the solution structure of a different SH2 domain complex. A more detailed comparison between the crystal structure and the NMR-derived solution structures of the same src SH2 domain complex is presented.(ABSTRACT TRUNCATED AT 400 WORDS)
Differential effect of anti-TNF-alpha antibody on proinflammatory cytokine release by Kupffer cells following liver ischemia and reperfusion. (1999)

To study the role of tumor necrosis factor-alpha (TNF-alpha) for induction of the proinflammatory cytokine cascade after liver ischemia and reperfusion (I/R), rats were injected intraperitoneally with anti-TNF-alpha monoclonal antibodies (mAb) or placebo (IgG1) 30 min prior to global hepatic ischemia. Blood levels of TNF-alpha, interleukin (IL)-1alpha and -6 were determined. In addition, Kupffer cells (KC) were harvested after 60 min of reperfusion and spontaneous cytokine release was measured. Sham-operated animals were used as controls. Levels of proinflammatory cytokines in serum and KC supernatants were detected using specific bioassays and ELISA. Liver I/R resulted in increased (p < .01) serum levels of TNF-alpha, IL-1alpha, and IL-6, which was associated with an enhanced (p < .05) release of these cytokines by KC. In vivo pretreatment with anti-TNF-alpha mAb led to complete neutralization of TNF-alpha serum levels and decreased (p < .01) IL-6 levels (-62%). Moreover, anti-TNF-alpha mAb markedly (p < .05) decreased the release of TNF-alpha (-69%) and IL-6 (-56%) by KC, while IL-1alpha was not affected. These data indicate that TNF-alpha produced early after liver I/R triggers both its own secretion as well as IL-6 release by KC during reperfusion while the release of IL-1alpha occurs independent from TNF-alpha.
Content based photograph slide show with incidental music (2003)

In this paper, we proposed a new scheme to generate photograph slide show with incidental music based on the content of the photographs and music. Unlike existing photograph slide show software, which show the photographs one by one (perhaps with some fancy transition effects) with music in the background, our algorithm utilizes content analysis of the photographs and the incidental music. Firstly, low-quality photographs, such as blurred or under exposed, are filtered out by a photograph quality detector; and the rest of the photographs are grouped into a three-layer construction, namely, day, scene, and group of similar photographs (GoS). Incidental music is segmented based on its beats, and then aligned with photographs, which makes the photograph transitions occur at the beat position of the music. Various transition effects and transformation effects are applied based on the structure and content of the photographs. According to different users' preferences, several editing styles are also supported in our algorithm. The experimental results are very impressive according to the user study.
Calcium and lipid regulation of an Arabidopsis protein kinase expressed in Escherichia coli (1993)

Calcium-dependent protein kinases (CDPKs) represent a new family of protein kinases which are proposed to contain, in a single polypeptide, both a kinase domain and an adjoining calmodulin-like domain with four calcium-binding EF-hand motifs [Harper, J.F., Sussman, M.R., Schaller, G.E., Putnam-Evans, C., Charbonneau, H., & Harmon, A.C. (1991) Science 252, 951-954]. DNA cloning and Western blot analysis indicate that multiple CDPK isoforms are present in the model plant system Arabidopsis thaliana. One CDPK gene called AK1 was isolated from Arabidopsis as a full-length cDNA. The predicted AK1 protein has a M(r) of 72,645 and is 116 amino acid residues longer at the amino terminus than the prototype CDPK alpha gene previously identified in soybean. The most highly conserved region between these two CDPKs is a region of 31 amino acids that joins the kinase and calmodulin-like domains. To verify the kinase activity of the enzyme encoded by AK1, a fusion of an amino-terminally truncated AK1 to the C-terminus of glutathione S-transferase was expressed in Escherichia coli. The fusion protein was purified and displayed a maximum kinase activity of 40 nmol of phosphate/(min.mg), using histone IIIs as a substrate. The enzyme activity was stimulated 3-6-fold by calcium and 2-5-fold by crude lipid. However, a synergistic stimulation of 16-30-fold was observed by the addition of both calcium and crude lipid. Lipid stimulation was specific for lysophosphatidylcholine and phosphatidylinositol and did not occur with the addition of phosphatidylserine or phosphatidylcholine.(ABSTRACT TRUNCATED AT 250 WORDS)