gebhart/patrepeval huggingface dataset:
Transcriptomic Analysis of Mouse Brain After Traumatic Brain Injury Reveals That the Angiotensin Receptor Blocker Candesartan Acts Through Novel Pathways (2021)

Traumatic brain injury (TBI) results in complex pathological reactions, where the initial lesion is followed by secondary inflammation and edema. Our laboratory and others have reported that angiotensin receptor blockers (ARBs) have efficacy in improving recovery from traumatic brain injury in mice. Treatment of mice with a subhypotensive dose of the ARB candesartan results in improved functional recovery, and reduced pathology (lesion volume, inflammation and gliosis). In order to gain a better understanding of the molecular mechanisms through which candesartan improves recovery after controlled cortical impact injury (CCI), we performed transcriptomic profiling on brain regions after injury and drug treatment. We examined RNA expression in the ipsilateral hippocampus, thalamus and hypothalamus at 3 or 29 days post injury (dpi) treated with either candesartan (0.1 mg/kg) or vehicle. RNA was isolated and analyzed by bulk mRNA-seq. Gene expression in injured and/or candesartan treated brain region was compared to that in sham vehicle treated mice in the same brain region to identify genes that were differentially expressed (DEGs) between groups. The most DEGs were expressed in the hippocampus at 3 dpi, and the number of DEGs reduced with distance and time from the lesion. Among pathways that were differentially expressed at 3 dpi after CCI, candesartan treatment altered genes involved in angiogenesis, interferon signaling, extracellular matrix regulation including integrins and chromosome maintenance and DNA replication. At 29 dpi, candesartan treatment reduced the expression of genes involved in the inflammatory response. Some changes in gene expression were confirmed in a separate cohort of animals by qPCR. Fewer DEGs were found in the thalamus, and only one in the hypothalamus at 3 dpi. Additionally, in the hippocampi of sham injured mice, 3 days of candesartan treatment led to the differential expression of 384 genes showing that candesartan in the absence of injury had a powerful impact on gene expression specifically in the hippocampus. Our results suggest that candesartan has broad actions in the brain after injury and affects different processes at acute and chronic times after injury. These data should assist in elucidating the beneficial effect of candesartan on recovery from TBI.
Inhibition of EGFR signaling in human prostate cancer PC-3 cells by combination treatment with β-phenylethyl isothiocyanate and curcumin (2005)

Many naturally occurring compounds, including beta-phenylethyl isothiocyanate (PEITC) and curcumin, exhibit significant anti-cancer chemopreventive effects. In this study, we investigated the combined effects of PEITC and curcumin in PC-3 human prostate cancer cells and in PC-3 cells that were stably transfected with an NF-kappaB luciferase plasmid (PC-3 C4). We found an additive effect of PEITC and curcumin for the induction of apoptosis. To elucidate the potential mechanisms of this effect, we studied several critical cellular signaling pathways, including the critical NF-kappaB cell survival signal that is hyper-activated in PC-3 cells and many other cancers. PEITC and curcumin additively inhibited NF-kappaB luciferase activity. Furthermore, the combined treatment significantly increased the activity of poly(ADP-Ribose) polymerase and cleavage of caspase-3 in correlation with apoptotic cell death. Studying upstream signaling events, we found that the phosphorylations of IkappaBalpha and Akt (Ser473, Thr308) were significantly attenuated by the combination of PEITC and curcumin. As these events can be downstream of the activation of epidermal growth factor receptor (EGFR), we pretreated PC-3 cells with PEITC and curcumin and then stimulated them with EGF. EGFR phosphorylations (Y845 and Y1068) were dramatically suppressed by PEITC or curcumin, and more so by the combination. Importantly, the degree of Akt and PI3K phosphorylations induced by EGF were also significantly suppressed. We conclude that the simultaneous targeting of EGFR, Akt and NF-kappaB signaling pathways by PEITC and curcumin could be the molecular targets by which PEITC and curcumin exert their additive inhibitory effects on cell proliferation and ultimately lead to programmed cell death of tumor cells.
Antihypertensive Action of Angiotensin-I Converting Enzyme Inhibitors in the Kidney (1987)

In order to elucidate the antihypertensive action of angiotensin-I converting enzyme inhibitors (CEIs) in the kidney, intrarenal (IR) administration of CEIs was performed in norepinephrine (NE) or angiotensin-II (AII) induced acute hypertension in conscious unrestrained rabbits. IR administration of the two kinds of CEIs, captopril (5 mg/kg) and MK-422 (1 mg/kg), dose which caused no significant effect when injected intravenously, elicited a prompt and marked depressor action in NE but not in AII induced hypertension. In addition, IR infusion of the angiotensin-II analogue, saralasin (2 and 10 micrograms/kg/min) showed no depressor effect in NE induced acute hypertension. These results indicate that the kidney plays an important role in the depressor action of CEIs in NE but not in AII induced hypertension and this effect may not be related to the IR renin-angiotensin system.
What are the molecular mechanisms of neural tube defects? (1998)

Neural tube defects (NTDs) are some of the most common human malformations. The vast majority of NTDs can be prevented by the administration of folic acid; however, to date there has been no effective treatment of folic acid-resistant NTDs. A recent paper has confirmed an earlier report that the administration of inositol to the curly tail mutant mouse, which is a model of folate-resistant NTDs, can cure such defects. The molecular pathway by which this is achieved is thought to occur by the up-regulation of the retinoic acid receptor beta in the underlying hindgut endoderm, correcting a proliferation defect. However, alternative explanations also may account for NTDs.
Moving object detection with laser scanners (2012)

The detection and tracking of moving objects is an essential task in robotics. The CMU‐RI Navlab group has developed such a system that uses a laser scanner as its primary sensor. We will describe our algorithm and its use in several applications. Our system worked successfully on indoor and outdoor platforms and with several different kinds and configurations of two‐dimensional and three‐dimensional laser scanners. The applications vary from collision warning systems, people classification, observing human tracks, and input to a dynamic planner. Several of these systems were evaluated in live field tests and shown to be robust and reliable. © 2012 Wiley Periodicals, Inc.
Bi(OTf)3-Catalyzed Multicomponent α-Amidoalkylation Reactions (2015)

A bismuth(III) triflate catalyzed three-component synthesis of α-substituted amides starting from amides, aldehydes, and (hetero)arenes is reported. The reaction has a broad substrate scope, encompassing formaldehyde as well as aryl and alkyl aldehydes. Low catalyst loadings are required, and water is formed as the only side product. The scope and limitation of this method will be discussed.
Superior properties of LaFe11.8Si1.2/La65Co35 magnetocaloric composites processed by spark plasma sintering (2022)

A series of LaFe11.8Si1.2/La65Co35 bulk composites were fabricated by spark plasma sintering (SPS) followed by diffusion annealing. The effect of sintering temperature (1073–1223 K) on the magnetocaloric and other properties of LaFe11.8Si1.2/La65Co35 bulk composites were investigated. The 1:13 phase content in all the annealed samples was ∼90 wt%. The mechanical and magnetocaloric properties of these annealed bulk composites could be improved by tuning the sintering temperature. The Curie temperature (TC) and maximum magnetic entropy change (−ΔSM)max of the annealed samples varied in the range of 211–228 K and 5.56–9.33 J kg−1 K−1, respectively. Selected samples exhibited excellent mechanical and magnetocaloric properties. The (−ΔSM)max value was 9.33 J kg−1 K−1 at TC of 217.8 K. Its maximum compressive strength (σbc)max value was 540 MPa at a strain of 3.48%, which exceeded the mechanical properties of most La–Fe–Si based bulk composites prepared by hot-pressing sintering (HPS). Thus, La–Fe–Si based bulk composites with good comprehensive properties could be obtained by combining SPS and diffusion annealing.
Data from <i>ZFTA</i> Translocations Constitute Ependymoma Chromatin Remodeling and Transcription Factors (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;i&gt;ZFTA&lt;/i&gt; (&lt;i&gt;C11orf95&lt;/i&gt;)—a gene of unknown function—partners with a variety of transcriptional coactivators in translocations that drive supratentorial ependymoma, a frequently lethal brain tumor. Understanding the function of &lt;i&gt;ZFTA&lt;/i&gt; is key to developing therapies that inhibit these fusion proteins. Here, using a combination of transcriptomics, chromatin immunoprecipitation sequencing, and proteomics, we interrogated a series of deletion-mutant genes to identify a tripartite transformation mechanism of ZFTA-containing fusions, including: spontaneous nuclear translocation, extensive chromatin binding, and SWI/SNF, SAGA, and NuA4/Tip60 HAT chromatin modifier complex recruitment. Thereby, ZFTA tethers fusion proteins across the genome, modifying chromatin to an active state and enabling its partner transcriptional coactivators to promote promiscuous expression of a transforming transcriptome. Using mouse models, we validate further those elements of ZFTA-fusion proteins that are critical for transformation—including ZFTA zinc fingers and partner gene transactivation domains—thereby unmasking vulnerabilities for therapeutic targeting.&lt;/p&gt;Significance:&lt;p&gt;Ependymomas are hard-to-treat brain tumors driven by translocations between &lt;i&gt;ZFTA&lt;/i&gt; and a variety of transcriptional coactivators. We dissect the transforming mechanism of these fusion proteins and identify protein domains indispensable for tumorigenesis, thereby providing insights into the molecular basis of ependymoma tumorigenesis and vulnerabilities for therapeutic targeting.&lt;/p&gt;&lt;p&gt;&lt;i&gt;This article is highlighted in the In This Issue feature, p. 2113&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Spin-flavor asymmetry in nucleon structure (1995)

Experiment shows the deep‐inelastic scattering structure function ratio Fn2/Fp2 and the nucleon spin asymmetries to be strongly x‐dependent. In the context of the parton model, the observed inhomogeneities mean that quarks with different isospins and spins carry different fractions of the nucleon momentum. A systematic procedure is presented which permits the structure functions of nucleons to be calculated from a nonrelativistic constituent quark model. This calculation shows that all of these asymmetry effects can be qualitatively understood in terms of the admixtures of excited‐state configurations in the nucleon wave function due to color hyperfine interactions.
Global existence of weak solutions to unsaturated poroelasticity (2021)

We study unsaturated poroelasticity, i.e. , coupled hydro-mechanical processes in variably saturated porous media, here modeled by a non-linear extension of Biot’s well-known quasi-static consolidation model. The coupled elliptic-parabolic system of partial differential equations is a simplified version of the general model for multi-phase flow in deformable porous media, obtained under similar assumptions as usually considered for Richards’ equation. In this work, existence of weak solutions is established in several steps involving a numerical approximation of the problem using a physically-motivated regularization and a finite element/finite volume discretization. Eventually, solvability of the original problem is proved by a combination of the Rothe and Galerkin methods, and further compactness arguments. This approach in particular provides the convergence of the numerical discretization to a regularized model for unsaturated poroelasticity. The final existence result holds under non-degeneracy conditions and natural continuity properties for the constitutive relations. The assumptions are demonstrated to be reasonable in view of geotechnical applications.
Design and Development of a Biaxial Strength Testing Device (1988)

Abstract The apparatus described herein is designed for the performance of biaxial stretching tests on flat cross-shaped specimens. It can be used with a conventional uniaxial tensile testing machine. The device converts the machine from one that exerts a uniaxial force to one that applies a system of forces in two perpendicular directions. A fixed value of the logarithmic strain ratio ρ = ϵ2/ϵ1 can be imposed on the test specimen along these two directions. The fixed ρ-value may be chosen between 0 and 1 according to the geometrical configuration of the device.
On processor allocation in hypercube multiprocessors (2003)

The processor allocation problem in a hypercube system is to find a free subcube for a given request. The subcube recognition capability of existing allocation strategies, e.g. the buddy strategy and the Gray code strategy, is far below the theoretical upper bound due to their incomplete representation of the hypercube interconnection structure. A complete strategy that outperforms the existing ones in subcube recognition capability and average waiting time but incurs a higher overhead is proposed. Efficient implementation of the complete strategy is also studied.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
High spatial resolution diagnostics of optical waveguides using a photon-scanning tunneling microscope (1995)

We propose a high-resolution diagnostics technique for optical waveguides using a photon-scanning tunneling microscope (P-STM). This technique has the advantageous capabilities of nondestructive measurement and informative analysis of guided mode. The capability of this technique was evaluated by measuring the characteristics of an LiTaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> waveguide. Scattered light spot of 500-nm diameter caused by defects was measured, and a normalized width was estimated to be 3.7 μm. Moreover, we obtained the power dispersion in Y-branch waveguides, which were in good agreement with the theoretical plots calculated by the beam propagation method (BPM).
Surface Morphology, Molecular Reorientation, and Liquid Crystal Alignment Properties of Rubbed Nanofilms of a Well-Defined Brush Polyimide with a Fully Rodlike Backbone (2002)

Nanoscaled films of poly{p-phenylene 3,6-bis[4-(n-butoxy)phenyloxy]pyromellitimide} (C4-PMDA-PDA PI), a well-defined brush polyimide (PI) composed of aromatic−aliphatic bristles set into a fully rodlike polymer backbone (two bristles per chemical repeat unit of the polymer backbone), were studied by atomic force microscopy, optical retardation, prism coupling, and linearly polarized IR spectroscopy before and after mechanical rubbing with velvet fabric, and their liquid crystal (LC) aligning abilities were investigated. Uniform, homogeneous LC alignment was achieved at the rubbed film surfaces of PIs with positively birefringent characteristics. Surprisingly, however, the LC alignment director for this PI is perpendicular to the rubbing direction as well as to the reorientation direction of the polymer main chains. This is the first time that LCs on a PI surface have been induced to align in the direction perpendicular to the rubbing direction, a significant departure from the LC alignment observed for all other PI materials reported so far, for which LC alignment is always parallel to the rubbing direction. This unusual LC alignment is attributed to the strength of the anisotropic intermolecular interactions of the LC molecules with the short bristles attached perpendicularly to the polymer chain, which override the interactions with the main polymer chains and with the microgroove lines with fine grooves that are created along the rubbing direction. The LC pretilt angle is expected to be 25−55° with respect to a direction perpendicular to the rubbing direction, although this angle could not be determined due to the limitations of the crystal-rotation apparatus employed. In particular, the n-butyl end group of the bristle was found to play a critical role in the pretilting of LC molecules, as well as in the perpendicular LC alignment. In addition, the surface morphology of the rubbed PI films was investigated in detail, with particular consideration being given to the polymer property characteristics, the structure of the velvet fabric fibers, and the rubbing conditions.
STAT1 and STAT3 do not participate in FGF-mediated growth arrest in chondrocytes (2008)

Activating mutations in fibroblast growth factor receptor 3 (FGFR3) cause several human skeletal dysplasias as a result of attenuation of cartilage growth. It is believed that FGFR3 inhibits chondrocyte proliferation via activation of signal transducers and activators of transcription (STAT) proteins, although the exact mechanism of both STAT activation and STAT-mediated inhibition of chondrocyte growth is unclear. We show that FGFR3 interacts with STAT1 in cells and is capable of activating phosphorylation of STAT1 in a kinase assay, thus potentially serving as a STAT1 kinase in chondrocytes. However, as demonstrated by western blotting with phosphorylation-specific antibodies, imaging of STAT nuclear translocation, STAT transcription factor assays and STAT luciferase reporter assays, FGF does not activate STAT1 or STAT3 in RCS chondrocytes, which nevertheless respond to a FGF stimulus with potent growth arrest. Moreover, addition of active STAT1 and STAT3 to the FGF signal, by means of cytokine treatment, SRC-mediated STAT activation or expression of constitutively active STAT mutants does not sensitize RCS chondrocytes to FGF-mediated growth arrest. Since FGF-mediated growth arrest is rescued by siRNA-mediated downregulation of the MAP kinase ERK1/2 but not STAT1 or STAT3, our data support a model whereby the ERK arm but not STAT arm of FGF signaling in chondrocytes accounts for the growth arrest phenotype.
Functional Antibodies Targeting IsaA of Staphylococcus aureus Augment Host Immune Response and Open New Perspectives for Antibacterial Therapy (2010)

Staphylococcus aureus is the most common cause of nosocomial infections. Multiple antibiotic resistance and severe clinical outcomes provide a strong rationale for development of immunoglobulin-based strategies. Traditionally, novel immunological approaches against bacterial pathogens involve antibodies directed against cell surface-exposed virulence-associated epitopes or toxins. In this study, we generated a monoclonal antibody targeting the housekeeping protein IsaA, a suggested soluble lytic transglycosylase of S. aureus, and tested its therapeutic efficacy in two experimental mouse infection models. A murine anti-IsaA antibody of the IgG1 subclass (UK-66P) showed the highest binding affinity in Biacore analysis. This antibody recognized all S. aureus strains tested, including hospital-acquired and community-acquired methicillin-resistant S. aureus strains. Therapeutic efficacy in vivo in mice was analyzed using a central venous catheter-related infection model and a sepsis survival model. In both models, anti-IsaA IgG1 conferred protection against staphylococcal infection. Ex vivo, UK-66P activates professional phagocytes and induces highly microbicidal reactive oxygen metabolites in a dose-dependent manner, resulting in bacterial killing. The study provides proof of concept that monoclonal IgG1 antibodies with high affinity to the ubiquitously expressed, single-epitope-targeting IsaA are effective in the treatment of staphylococcal infection in different mouse models. Anti-IsaA antibodies might be a useful component in an antibody-based therapeutic for prophylaxis or adjunctive treatment of human cases of S. aureus infections.
Impregnation of Bombax ceiba and Bombax insigne wood with a N-methylol melamine compound (2012)

Methylated N-methylol melamine (NMM) is known for its ability to enhance physico-mechanical properties, anti-fungal ability, and hydrophobicity and was therefore used to impregnate two less used and non-durable wood species from Myanmar, Bombax ceiba and Bombax insigne. Solution uptake, weight percent gain and nitrogen content were increased by increasing melamine concentrations with B. ceiba always achieving higher values compared with B. insigne. According to the leaching results, a higher degree of condensation after curing as well as a better crosslinking of NMM could be obtained at higher temperatures. However, both curing temperatures used (90 and 120 °C) resulted in almost the same amount of nitrogen fixed in the cell wall. UV microspectrophotometry confirmed the penetration of the NMM into different morphological regions of wood tissues, which was again supported by the analysis of point measurement spectra of treated and untreated specimens.
Closure of Atrial and Ventricular Septal Defects Should Be Performed by the Surgeon (2005)

Surgeons look back on 57 years of experience in the closure of atrial septal defects (ASDs) and 46 years in the closure of ventricular septal defects (VSDs). The transcatheter approaches to repair ASDs started first in the 1980s and for VSDs 8 years later. This study sought to reveal the surgical features only given by the surgical therapy and the limitation of interventional ASD and VSD closure. A variety of surgical techniques including the minimal invasive techniques for ASD or VSD closure are well described in recent publication with good results. The surgical trend is to improve the cosmetic outcome by minimizing the size of skin incision. The latest robotically assisted technique requires only four stab wound incisions. New techniques and devices have revolutionized the transcatheter technique but could not achieve the surgical ability to close all types of ASD or VSD, control arrhythmias, and correct additional valve disease or malformation. The mortality for interventional and surgical procedures approaches zero in recent publication. The residual shunting after surgical closure of ASD varies from 2% to 7.8% versus 5% to 33% after interventional closure. General complications caused by the surgical procedure are negligible; however, the shortness of hospital stay and the cosmetic appeal is an advantage of interventional ASD closure. There is no scientific comparison of surgical vs. interventional VSD closure yet.