gebhart/patrepeval huggingface dataset:
Mechanical strength and interfacial failure analysis of cantilevered SU-8 microposts (2003)

This paper reports the study of both the mechanical strength and interfacial failure of cantilevered SU-8 microposts fabricated on silicon substrates. An ultra-precision instrument was developed to simultaneously measure both the displacement and resultant force of specially designed SU-8 microposts under a static bending load increasing up to an interfacial fracture. Experimental results were presented for two sets of SU-8 microposts with different geometry, one with a circular cross-section and the other with a square cross-section, both having an aspect ratio larger than 1. Shear failure stresses of both circular and square microposts were estimated to be approximately 6.53 MPa ± 4.2% and 6.83 MPa ± 9.7%, respectively. The failure regions were characterized by a scanning electron microscope to determine the failure mechanism. Our experiments showed that the hardness and Young's modulus of SU-8 decreased with increasing penetration depth, and both quantities are sensitive to loading/unloading speeds.
Separation of Recombination and SOS Response in Escherichia coli RecA Suggests LexA Interaction Sites (2011)

RecA plays a key role in homologous recombination, the induction of the DNA damage response through LexA cleavage and the activity of error-prone polymerase in Escherichia coli. RecA interacts with multiple partners to achieve this pleiotropic role, but the structural location and sequence determinants involved in these multiple interactions remain mostly unknown. Here, in a first application to prokaryotes, Evolutionary Trace (ET) analysis identifies clusters of evolutionarily important surface amino acids involved in RecA functions. Some of these clusters match the known ATP binding, DNA binding, and RecA-RecA homo-dimerization sites, but others are novel. Mutation analysis at these sites disrupted either recombination or LexA cleavage. This highlights distinct functional sites specific for recombination and DNA damage response induction. Finally, our analysis reveals a composite site for LexA binding and cleavage, which is formed only on the active RecA filament. These new sites can provide new drug targets to modulate one or more RecA functions, with the potential to address the problem of evolution of antibiotic resistance at its root.
Gut feelings about the endocannabinoid system (2011)

Stemming from the centuries-old and well known effects of Cannabis on intestinal motility and secretion, research on the role of the endocannabinoid system in gut function and dysfunction has received ever increasing attention since the discovery of the cannabinoid receptors and their endogenous ligands, the endocannabinoids. In this article, some of the most recent developments in this field are discussed, with particular emphasis on new data, most of which are published in Neurogastroenterology & Motility, on the potential tonic endocannabinoid control of intestinal motility, the function of cannabinoid type-1 (CB1) receptors in gastric function, visceral pain, inflammation and sepsis, the emerging role of cannabinoid type-2 (CB2) receptors in the gut, and the pharmacology of endocannabinoid-related molecules and plant cannabinoids not necessarily acting via cannabinoid CB1 and CB2 receptors. These novel data highlight the multi-faceted aspects of endocannabinoid function in the GI tract, support the feasibility of the future therapeutic exploitation of this signaling system for the treatment of GI disorders, and leave space for some intriguing new hypotheses on the role of endocannabinoids in the gut.
Monte Carlo simulations on primitive models of water and methanol (1987)

The recently introduced primitive model of associated liquids which accounts for both short-ranged repulsions due to excluded volume effects and strongly directional hydrogen bonding has been extended to water and methanol. Hard spheres and homonuclear dumbbells have been considered to mimic the cores of water and methanol molecules, respectively, while the H-bonding has been mimicked by localized square-well attractions. For a number of temperatures and densities thermodynamic and structural properties as well as parameters characterizing association in the system have been evaluated by Monte Carlo simulations; low density properties have been determined analytically. Special attention has also been paid to the effectiveness of the simulation and error analysis.
Optical Absorption Spectra of the Alkali Halides at 10°K (1967)

The absorption spectra of all the alkali halides except LiF and LiI, measured in the range 5.0 to 12.0 eV at 10\ifmmode^\circ\else\textdegree\fi{}K, are presented. These data complement earlier measurements made at 80\ifmmode^\circ\else\textdegree\fi{}K. Identification of excition lines involving $d$-like electrons is made by a comparison of the crystal absorption and the absorption spectra of rare-gas atoms. From the positions of exciton states with $d$-like electrons, the energy of the second conduction band at $\ensuremath{\Gamma}$ is deduced for some of the alkali halides. The results of these deductions are compared with recent calculations of the conduction-band structure of KI and KCl.
<i>Pseudomonas</i> Lipopolysaccharide Accelerates Wound Repair via Activation of a Novel Epithelial Cell Signaling Cascade (2006)

Abstract The surface of the airway epithelium represents a battleground in which the host intercepts signals from pathogens and activates epithelial defenses to combat infection. Wound repair is an essential function of the airway epithelium in response to injury in chronic airway diseases, and inhaled pathogens such as Pseudomonas bacteria are implicated in the pathobiology of several of these diseases. Because epidermal growth factor receptor (EGFR) activation stimulates wound repair and because LPS activates EGFR, we hypothesized that LPS accelerates wound repair via a surface signaling cascade that causes EGFR phosphorylation. In scrape wounds of NCI-H292 human airway epithelial cells, high concentrations of LPS were toxic and decreased wound repair. However, lower concentrations of LPS accelerated wound repair. This effect was inhibited by treatment with a selective inhibitor of EGFR phosphorylation (AG 1478) and by an EGFR neutralizing Ab. Metalloprotease inhibitors and TNF-α-converting enzyme (TACE) small interfering RNA inhibited wound repair, implicating TACE. Additional studies implicated TGF-α as the active EGFR ligand cleaved by TACE during wound repair. Reactive oxygen species scavengers, NADPH oxidase inhibitors, and importantly small interfering RNA of dual oxidase 1 inhibited LPS-induced wound repair. Inhibitors of protein kinase C isoforms αβ and a TLR-4 neutralizing Ab also inhibited LPS-induced wound repair. Normal human bronchial epithelial cells responded similarly. Thus, LPS accelerates wound repair in airway epithelial cells via a novel TLR-4→protein kinase C αβ→dual oxidase 1→reactive oxygen species→TACE→TGF-α→EGFR phosphorylation pathway.
ULTRASONIC DRY COUPLING THROUGH TISSUE (2015)

Ultrasonic transcutaneous energy transmission (UTET) is a promising new technology for delivering electrical power to active biomedical implants.  A key piece of technology required to make UTET devices viable is a “dry” acoustic coupling that can be worn daily for long periods of time by a patient.  The dry coupling must provide a low-reflectance, low-loss, transmission pathway for acoustic energy. For other ultrasound applications such as diagnostic imaging, a coupling gel is typically used to acoustically interface a transducer with the patient. However, in a more permanent application like UTET coupling gel is likely dry out or wash away over time and so a solid-state solution is needed.  The solid coupling must be comfortable, must not lead to skin irritation or other skin problems and must provide good acoustic coupling without requiring large and uncomfortable contact force with the skin. We report on our investigations into the use of soft silicones for this application.  Silicones are highly biocompatible, and at less than 2 MHz they exhibit low acoustic losses.  Soft silicones have a “sticky” quality to them that provides good acoustic coupling to skin (<20% loss) with very low contact force (<0.5 N).  We present the results of studies into the relationship between contact force and acoustic reflectance for soft silicone couplings in a dry ex vivo porcine skin model. Silicone can be made with a wide array of mechanical properties. As a result, the acoustic impedance of the coupling material can be matched to skin, reducing losses due to reflection. We present two methods used to impedance match to skin; one by increasing the material’s speed of sound, the other by increasing its density. Material property effects on the UTET link efficiency are simulated using a KLM model and the simulation is compared to empirical measurements of the efficiency.
Evaluation of remedial options for treatment of heavy metal and petroleum hydrocarbon contaminated soil (1993)

Abstract This article describes remedial options for the treatment of heavy metal and petroleum hydrocarbon contaminated soil. Treatment of these soils with traditional methods often requires a combination of techniques, resulting in treatment costs that are unacceptable in today's financial climate. A detailed review of relevant remedial technologies is presented, as well as treatability studies for hybrid immobilization, petroleum hydrocarbon reduction, extraction, and soil washing technologies. Our studies and review demonstrate that hybrid immobilization may be suitable for sites where only soluble chemical levels exceed federal or state guidelines; soil washing may provide a viable alternative for sites with appropriate soil characteristics; petroleum hydrocarbon bioremediation can potentially reduce soluble lead levels; and extraction processes, though promising, still require some development. Descriptions of the chemical and physical properties of heavy metals and petroleum hydrocarbons in soil and residual levels of these chemicals in soil following treatment are also given.
Design, Synthesis, X-ray Analysis, and Dopamine Receptor-Modulating Activity of Mimics of the "C5" Hydrogen-Bonded Conformation in the Peptidomimetic 2-Oxo-3(R)-[(2(S)-pyrrolidinylcarbonyl)amino]-1-pyrrolidineacetamide (1994)

3(R)-(7a(S)-Hexahydro-1-oxo-3,3-dimethyl-1H-pyrrolo[1,2-c]imidazol-2-yl) - oxo-1-pyrrolidine-acetamide (2) and 3(R)-[1-(2,5-dioxopyrrolidino[3,4-c]piperazino)]-2-oxo-1- pyrrolidineacetamide (3) were designed and prepared as mimics of the "C5" hydrogen-bonded structure found in the crystal structure of 2-oxo-3(R)-[(2(S)-pyrrolidinylcarbonyl)amino]-1- pyrrolidineacetamide (1). Both compounds effectively restrict the psi 1 torsional angle to very near the value found in the X-ray structure of 1 as seen in the X-ray crystallographic determination of 2 and methyl 3(R)-[1-(2,5-dioxopyrrolidino[3,4-c]piperazino)]-2-oxo-1- pyrrolidineacetate (11), a diketopiperazine intermediate in the synthesis of 3. These analogs were tested for their ability to enhance the binding of the dopamine D2 receptor agonist N-propylnorapomorphine (NPA) in the absence and presence of 5'-guanylylimidodiphosphate (Gpp(NH)p). Both compounds enhanced [3H]-NPA binding in a dose-dependent manner by increasing both the binding affinity of the agonist and the number of high-affinity sites available for binding. Both 2 and 3 also attenuated the Gpp(NH)p-induced conversion of D2 receptor high-affinity states to the low-affinity states.
Proviruses of mouse mammary tumor virus in normal and neoplastic tissues from GR and C3Hf mouse strains (1980)

We analyzed two experimental situations to assess the role of endogenous mouse mammary tumor virus (MMTV) DNA in the genesis of mammary carcinomas. (i) GR mice carry in their germ line one or more proviruses indistinguishable by limited restriction mapping from the proviruses introduced into cells by experimental infection with the highly tumorigenic virus isolated from GR mouse milk, MMTV(GR). Most tumors arising in GR mice contain one or more proviruses at various sites in tumor DNA in addition to those present endogenously. Detection of these new proviruses is possible as a consequence of the clonal or quasiclonal character of the tumors. (ii) C3H/He mice carry three units of endogenous viral DNA, none of which resembles the DNA of the commonly encountered strains of milk-borne MMTV. Nevertheless, MMTV-associated tumors arise late in life when these animals are removed from the influence of milk-borne virus; the responsible agent, MMTV(C3Hf), can also produce tumors in BALB/c mice. We found that tumors arising in both C3Hf/He mice and BALB/c mice infected with MMTV(C3Hf) were clonal or quasiclonal and contained one or more new copies of proviral DNA at various sites in the host genome. These new proviruses were readily distinguished from the proviruses of the common milk-borne virus strains and closely resembled unit II of endogenous MMTV DNA (Cohen et al., J. Virol., 32:483-496). Thus, in both experimental systems, we found evidence for new proviruses in mammary tumors, despite the preexistence of similar or identical proviruses in the germ line. The results suggest that the repositioning of MMTV proviruses may be required for the full expression of the oncogenic potential of endogenous MMTV DNA.
Expression of c-met Proto-oncogene in Primary Colorectal Cancer and Liver Metastases (1997)

We have examined the expression of c-met mRNA in tissue from 27 colorectal cancers and ten liver metastases using the reverse transcriptase-polymerase chain reaction method. The expression of c-met mRNA in these tissues was quantified and the copy number of c-met mRNA to 10(8.0) copies of beta-actin mRNA was calculated. Mean copy numbers of c-met mRNA in cancer tissue and normal mucosa were 10(5.5) and 10(4.5) respectively. The c-met expression of cancer was significantly higher than that of normal mucosa (P < 0.0001). In 20 of 22 samples in which c-met expression of both tumor and corresponding normal tissue were examined, c-met was overexpressed in the cancer tissue. No correlation was found between c-met expression and the clinicopathologic background. The mean copy numbers of c-met mRNA in the tissue from the ten liver metastases and normal liver were 10(6.1) and 10(6.2) respectively. Although c-met expression in metastatic tissue was higher than that in the primary cancer tissue, the increase was not statistically significant. In three of four patients with synchronous liver metastases, c-met was overexpressed in the metastatic tissue compared with that in the corresponding primary cancer tissue. These results show that c-met is overexpressed in both primary colorectal cancer and liver metastases and suggest that c-met plays a role in the development of colorectal cancer liver metastases.
Digraphs Theory Algorithms And Applications (2002)

Graph theory is a very popular area of discrete mathematics with not only numerous theoretical developments, but also countless applications to practical problems. As a research area, graph theory is still relatively young, but it is maturing rapidly with many deep results having been discovered over the last couple of decades. The theory of graphs can be roughly partitioned into two branches: the areas of undirected graphs and directed graphs (digraphs). Even though both areas have numerous important applications, for various reasons, undirected graphs have been studied much more extensively than directed graphs. One of the reasons is that undirected graphs form in a sense a special class of directed graphs (symmetric digraphs) and hence problems that can be formulated
Inverted Index based Modified Version of K-Means Algorithm for Text Clustering (2008)

This research proposes a new strategy where documents are encoded into string vectors and modified version of k means algorithm to be adaptable to string vectors for text clustering. Traditionally, when k means algorithm is used for pattern classification, raw data should be encoded into numerical vectors. This encoding may be difficult, depending on a given application area of pattern classification. For example, in text clustering, encoding full texts given as raw data into numerical vectors leads to two main problems: huge dimensionality and sparse distribution. In this research, we encode full texts into string vectors, and modify the k means algorithm adaptable to string vectors for text clustering.
The map method for synthesis of combinational logic circuits (1953)

THE SEARCH for simple abstract techniques to be applied to the design of switching systems is still, despite some recent advances, in its early stages. The problem in this area which has been attacked most energetically is that of the synthesis of efficient combinational that is, nonsequential, logic circuits.
The Therapeutic Effect of Human Adult Stem Cells Derived from Adipose Tissue in Endotoxemic Rat Model (2013)

Excessive systemic inflammation following sepsis, trauma or burn could lead to multi-organ damage and death. Bone marrow stromal cells (BMSCs), commonly referred to as mesenchymal stem cells (MSCs), has been studied in several immune-associated diseases in human and animal by modulating the inflammatory response. Adipose tissue derived mesenchymal stem cells (ATSCs), which can be obtained more easily, compared with BMSCs, has emerged as an attractive alternative MSCs source for cell therapy. We investigated the therapeutic effects of human ATSCs (hATSCs) in endotoxemic rat model and their capacity to modulate the inflammatory response. Endotoxemia was induced with Lipopolysaccaride intravenously injection (LPS, 10mg/kg). Animals were divided into the following three groups: (1) saline + saline (n=5), (2) LPS + saline (n=5) and (3) LPS + hATSCs (2x10(6)) (n=5). The administration of LPS caused a consistent systemic inflammatory responses, increased concentrations of the pro-inflammatory cytokines that have an important role in sepsis. Treatment of endotoxemia with hATSCs decreased the level of inflammatory cytokines both in serum and in the lung, reduced inflammatory changes in the lung, prevented apoptosis in the kidney and improved multi-organ injury. In conclusion, our data demonstrates that hATSCs regulate the immue/inflammatory responses and improve multi-organ injury and they could be attractive candidates for cell therapy to treat endotoxemia.
Maximally flat low-pass FIR filters with reduced delay (1998)

This paper describes a new class of nonsymmetric maximally flat low-pass finite impulse response (FIR) filters. By subjecting the magnitude and group delay responses (individually) to differing numbers of flatness constraints, the new filters are obtained. It is found that these filters achieve a smaller delay than symmetric filters while maintaining relatively constant group delay around /spl omega/=0, with no degradation of the frequency response magnitude. The design of these filters is initially investigated using Grubner bases. An analytic design technique, applicable to a subset of the forgoing filters, is provided that does not depend on Grubner basis computations.
Uncoupling of T-cell effector functions by inhibitory killer immunoglobulin–like receptors (2006)

Killer immunoglobulin-like receptors (KIRs) are a family of regulatory cell-surface molecules expressed on natural killer (NK) cells and memory T-cell subsets. Their ability to prevent the formation of an activation platform and to inhibit NK cell activation is the basis of the missing self model of NK cell function. The benefits of KIR expression for T-cell biology are unclear. We studied how KIR2DL2 regulates T-cell function. Engagement of KIR2DL2 by the ligand human leukocyte antigen (HLA)-Cw3 did not affect conjugate formation between CD4(+)KIR2DL2(+) T cells and superantigen-pulsed target cells or the development of mature immune synapses with lipid rafts. KIR2DL2 and the corresponding HLA-C ligand were initially recruited to the peripheral supramolecular activation cluster (pSMAC). Consequently, KIR2DL2 engagement did not inhibit the phosphorylation of early signaling proteins and T-cell-receptor (TCR)-mediated cytotoxicity or granule exocytosis. After 15-30 minutes, KIR2DL2 moved to the central supramolecular activation cluster (cSMAC), colocalizing with CD3. TCR synapses dissociated, and phosphorylated phospholipase C (PLC)-gamma1, Vav1, and extracellular signal-regulated kinase 1/2 (ERK1/2) were reduced 90 minutes after stimulation. Gene array studies documented that the inhibition of late signaling events by KIR2DL2 affected transcriptional gene activation. We propose that KIRs on memory T cells operate to uncouple effector functions by modifying the transcriptional profile while leaving granule exocytosis unabated.
Purification and Characterization of a Nuclear SS‐B Antigen (1982)

A nuclear SS-B antigen was isolated from a saline extract of acetone powder of rabbit thymus by precipitation with ammonium sulphate, affinity chromatography with Blue Sepharose CL-6B, and preparative agarose gel electrophoresis. The mol. wt of the antigen was 68,000. Its electrophoretic mobility was similar to that of pre-albumin, and the iso-electric point was around pH 4.0. The main amino acids of the antigen were glutamic acid, leucine, lysine and alanine. Both histidine and tyrosine were also found. The purified antigen precipitated with anti-SS-B sera but not with any other reference antisera. It resembled La and Ha antigens in susceptibility to proteolytic and nucleolytic enzymes and to heat. The purified SS-B antigen, however, had a higher molecular weight than did the Ha and La antigens. The molecule could not be split into subunits with mercaptoethanol or acid. Counter-electrophoresis showed antibodies to the SS-B antigen in sera from patients with rheumatic diseases, including rheumatoid arthritis, systemic lupus erythematosus and Sjögren's syndrome, but not in amy of the control sera.
Novel bacteriocins from lactic acid bacteria (LAB): various structures and applications (2014)

Bacteriocins are heat-stable ribosomally synthesized antimicrobial peptides produced by various bacteria, including food-grade lactic acid bacteria (LAB). These antimicrobial peptides have huge potential as both food preservatives, and as next-generation antibiotics targeting the multiple-drug resistant pathogens. The increasing number of reports of new bacteriocins with unique properties indicates that there is still a lot to learn about this family of peptide antibiotics. In this review, we highlight our system of fast tracking the discovery of novel bacteriocins, belonging to different classes, and isolated from various sources. This system employs molecular mass analysis of supernatant from the candidate strain, coupled with a statistical analysis of their antimicrobial spectra that can even discriminate novel variants of known bacteriocins. This review also discusses current updates regarding the structural characterization, mode of antimicrobial action, and biosynthetic mechanisms of various novel bacteriocins. Future perspectives and potential applications of these novel bacteriocins are also discussed.