gebhart/patrepeval huggingface dataset:
Human Ca2+ Receptor Cysteine-rich Domain (2000)

The 612-residue extracellular domain of the human Ca(2+) receptor (hCaR) has been speculated to consist of a Venus's-flytrap domain (VFT) and a cysteine-rich domain. We studied the function of the hCaR Cys-rich domain by using mutagenesis and chimera approaches. A chimeric hCaR with the sequence from residues 540-601 replaced by the corresponding sequence from the Fugu CaR remained fully functional. Another chimeric hCaR with the same region of sequence replaced by the corresponding sequence from metabotropic glutamate receptor subtype 1 (mGluR1) still was activated by extracellular Ca(2+) ([Ca(2+)](o)), but its function was severely compromised. Chimeric receptors with the hCaR VFT and mGluR1 seven-transmembrane domain plus C-tail domain retained good response to [Ca(2+)](o) whether the Cys-rich domain was from hCaR or from mGluR1. Mutant hCaR with the Cys-rich domain deleted failed to respond to [Ca(2+)](o), although it was expressed at the cell surface and capable of dimerization. Our results indicate that the hCaR Cys-rich domain plays a critical role in signal transmission from VFT to seven-transmembrane domain. This domain tolerates a significant degree of amino acid substitution and may not be directly involved in the binding of [Ca(2+)](o).
Metabolic Syndrome and Health‐related Quality of Life in Obese Individuals Seeking Weight Reduction (2008)

Individuals with MetSyn reported lower HRQoL. This appeared to be an effect of increased weight, rather than a unique effect of MetSyn. Larger studies are needed to assess whether MetSyn may have an independent effect on HRQoL.
Single-shot sonogram generation for femtosecond laser pulse diagnostics by use of two-photon absorption in a silicon CCD camera (2002)

We present an experimental technique capable of single-shot recording of an ultrashort laser pulse sonogram by use of two-photon absorption in a conventional silicon CCD camera. The quadratic spectral phase, introduced into a 100-fs pulse by a grating stretcher, was measured and found to be in good agreement with the analytically calculated value. The nonlinear response of silicon allows sonogram characterization in a wavelength range from 1 to 2 mum .
A novel in vivo assay for the analysis of protein-protein interaction (1999)

The Ras Recruitment System (RRS) is a method for identification and isolation of protein-protein interaction.The method is based on translocation of cytoplasmic mammalian Ras protein to the inner leaflet of the plasma membrane through protein-protein interaction.The system is studied in a temperaturesensitive yeast strain where the yeast Ras guanyl nucleotide exchange factor is inactive at 36°°°°C.Protein-protein interaction results in cell growth at the restrictive temperature.We developed a gene reporter assay for the analysis of protein-protein interaction in mammalian cells.Ras activation in mammalian cells induces the mitogen-activated kinase cascade (MAPK), which can be monitored using Ras-dependent reporter genes.This greatly extends the usefulness of the system and provides a novel assay for protein-protein interaction in mammalian cells.
SPLANCHNICECTOMY FOR ESSENTIAL HYPERTENSION (1953)

Hypertensive cardiovascular disease remains one of the foremost problems facing medicine today. It has been estimated that one-fourth of the adult population of this country has high blood pressure1and that the complications of this condition account for more deaths annually than does cancer. Hypertension is of particular importance because it is responsible for many deaths and much premature disability in young and middle-aged persons. It is highly desirable, therefore, to lower the mortality for such a disease. Many forms of therapy have been used in an effort to control hypertension. The principal ones may be classified under three headings: (1) diets low in sodium and fat, (2) drugs with a hypotensive or sedative effect, and (3) surgery. The form of surgical therapy that has been used most extensively is intervention on the sympathetic nervous system. There are many data in the literature concerning the short-term effects of various
Galectin-1: a small protein with major functions (2006)

Galectins are a family of carbohydrate-binding proteins with an affinity for beta-galactosides. Galectin-1 (Gal-1) is differentially expressed by various normal and pathological tissues and appears to be functionally polyvalent, with a wide range of biological activity. The intracellular and extracellular activity of Gal-1 has been described. Evidence points to Gal-1 and its ligands as one of the master regulators of such immune responses as T-cell homeostasis and survival, T-cell immune disorders, inflammation and allergies as well as host-pathogen interactions. Gal-1 expression or overexpression in tumors and/or the tissue surrounding them must be considered as a sign of the malignant tumor progression that is often related to the long-range dissemination of tumoral cells (metastasis), to their dissemination into the surrounding normal tissue, and to tumor immune-escape. Gal-1 in its oxidized form plays a number of important roles in the regeneration of the central nervous system after injury. The targeted overexpression (or delivery) of Gal-1 should be considered as a method of choice for the treatment of some kinds of inflammation-related diseases, neurodegenerative pathologies and muscular dystrophies. In contrast, the targeted inhibition of Gal-1 expression is what should be developed for therapeutic applications against cancer progression. Gal-1 is thus a promising molecular target for the development of new and original therapeutic tools.
Ghrelin (2004)

The discovery of ghrelin has increased our understanding of feeding regulation, nutritional homeostasis, and metabolic processes. Further characterization of ghrelin's functions will likely generate new pharmacological approaches to diagnose and treat different disease entities including those related to the over-nutrition of obesity and the catabolic response to surgical trauma.
A field guide to whole‐genome sequencing, assembly and annotation (2014)

Genome sequencing projects were long confined to biomedical model organisms and required the concerted effort of large consortia. Rapid progress in high-throughput sequencing technology and the simultaneous development of bioinformatic tools have democratized the field. It is now within reach for individual research groups in the eco-evolutionary and conservation community to generate de novo draft genome sequences for any organism of choice. Because of the cost and considerable effort involved in such an endeavour, the important first step is to thoroughly consider whether a genome sequence is necessary for addressing the biological question at hand. Once this decision is taken, a genome project requires careful planning with respect to the organism involved and the intended quality of the genome draft. Here, we briefly review the state of the art within this field and provide a step-by-step introduction to the workflow involved in genome sequencing, assembly and annotation with particular reference to large and complex genomes. This tutorial is targeted at scientists with a background in conservation genetics, but more generally, provides useful practical guidance for researchers engaging in whole-genome sequencing projects.
Functional Significance of NH2- and COOH-Terminal Regions of Staphylokinase in Plasminogen Activation (1996)

Structure/function relationships in the activation of plasminogen with staphylokinase were studied using mutants of recombinant staphylokinase (Sak42D). Deletion of up to 10 NH2-terminal amino acids (Sak42D delta N10) did not affect plasminogen activation, but removal of 11 amino acids completely abolished the ability to activate plasminogen. Elimination of potential plasmin cleavage sites in the NH2-terminal region yielding mutants Sak42D(K8H,K10H,K11H) and Sak42D(K6H,K8H,K11H) did not alter the rate of the exposure of a proteolytically active site (amidolytic activity) in equimolar mixtures with plasminogen, but destroyed the plasminogen activator properties of these muteins. Deleting two residues following the preferred processing site at position 10 (Sak42 delta (K11,G12)) resulted in a mutein also inactive in plasminogen activation. Removal of the COOH-terminal Lys136, yielding Sak42D delta C1, or of Lys135 and Lys136 in Sak42D delta C2 resulted in proteins with strongly reduced plasminogen activation capacity. In contrast, substitution of Lys135 and Lys136 with Ala in Sak42D(K135A,K136A) did not affect activation. Cyanogen bromide cleavage of Sak42D(M26L,E61M,D82E) produced a 61 amino acid NH2-terminal and a 65 amino acid COOH-terminal fragment which did not activate plasminogen, but bound to plasminogen with affinity constants Ka of 4.0 x 10(5) M-1 and 1.4 x 10(7) M-1, respectively (as compared to a Ka of 1.1 x 10(8) M-1 for Sak42D). These results indicate that Lys11 and the COOH-terminal region of staphylokinase play a key role in the activation of plasminogen.
A High Performance and Low Power Banked-Promotion TLB Structure (2002)

There are many methods for improving TLB (translation lookaside buffer) performance, such as increasing the number of entry in TLB, supporting large page or multiple page sizes. The best way is to support multiple page sizes, but any operating system doesn't support multiple page sizes in user mode. So, we propose the new structure of TLB supporting two pages to obtain the effect of multiple page sizes with high performance and at low cost without operating system support. we propose a new TLB structure supporting two page sizes dynamically and selectively for high performance and low cost design without any operating system support. For high performance, a promotion-TLB is designed by supporting two page sizes. Also in order to attain low power consumption, a banked-TLB is constructed by dividing one fully associative TLB space into two sub-fully associative TLBs. These two banked-TLB structures are integrated into a banked-promotion TLB as a low power and high performance TLB structure for embedded processors. According to the results of comparison and analysis, a similar performance can be achieved by using fewer TLB entries and also power consumption can be reduced by around 50% comparing with the fully associative TLB.
Zernike annular polynomials for imaging systems with annular pupils (1981)

The aberrations of imaging systems with uniformly illuminated annular pupils are discussed in terms of a complete set of polynomials that are orthogonal over an annular region. These polynomials, which we call Zernike annular polynomials, are similar to the Zernike circle polynomials and reduce to them as the annulus approaches the full circle. The Zernike-polynomial expansion of an aberration function is compared with its power-series expansion. The orthogonal aberrations given by Zernike annular polynomials describe how a higher-order classical aberration of a power-series expansion is balanced with one or more lower-order classical aberrations to minimize its variance. It is shown that as the obscuration ratio increases, the standard deviation of an orthogonal as well as a classical primary aberration decreases in the case of spherical aberration and field curvature and increases in the case of coma, astigmatism, and distortion. The only exception is the case of orthogonal coma, for which the standard deviation first increases and then decreases. The orthogonal aberrations for nonuniformly illuminated annular pupils are also considered, and, as an example, Gaussian illumination is discussed. It is shown that the standard deviation of an orthogonal primary aberration for a given amount of the corresponding classical aberration is somewhat smaller for a Gaussian pupil than that for a uniformly illuminated pupil.
Th1 and Th2 mediate acute graft-versus-host disease, each with distinct end-organ targets (2000)

STAT4 and STAT6 are transcription factors that play crucial roles in responding to IL-12 and IL-4, respectively. STAT4 gene knockout (STAT4(-/-)) mice have markedly reduced Th1 responses and enhanced Th2 responses. STAT6(-/-) mice show the inverse phenotype. We compared the ability of bone marrow transplantation (BMT) with the inclusion of spleen cells from STAT6(-/-), STAT4(-/-), and wild-type (WT) mice to produce graft-versus-host disease (GVHD) in lethally irradiated MHC-mismatched recipients. Acute GVHD mortality was more rapid when induced by cells from STAT6(-/-) mice than when induced by STAT4(-/-) cells. However, cells from STAT4(-/-) and STAT6(-/-) donors both induced delayed GVHD mortality compared with WT controls, or compared with combined STAT4(-/-) and STAT6(-/-) cells, indicating a contribution of both Th1 cells and Th2 cells to acute GVHD. Recipients of STAT6(-/-) BMT showed evidence of acute GVHD with severe diarrhea and marked weight loss. Recipients of STAT4(-/-) BMT showed signs of GVHD with only initial transient weight loss and later development of severe skin GVHD. Histopathology showed that Th2 responses were required for the induction of both hepatic and severe skin GVHD. In contrast, both Th1 cells and Th2 cells were capable of causing intestinal pathology of GVHD. Our studies demonstrate an additive role for Th1 and Th2 cells in producing acute GVHD, and suggest a cytokine-directed approach to treating end-organ manifestations of GVHD.
Epidemiological and molecular characteristics of HIV infection in Gabon, 1986–1994 (1996)

Our data from 1986 to 1994 show a stable and low HIV prevalence in Gabon, and a high genetic diversity of HIV-1 strains. This, also observed in Cameroon, is in contrast to that found elsewhere in Africa. Differences in rate of spread of HIV infection are probably explained by interplay between numerous factors. The role of different HIV subtypes in the dynamics of the HIV epidemic should be examined further.
An analysis of orthogonal frequency-division multiple access (2002)

We analyze the performance of orthogonal frequency-division multiple access (OFDMA) for the return channel on CATV networks, and compare this technique to the well-known time-division multiple access (TDMA). We examine the basic implementation issues of OFDMA including clock and carrier frequency synchronization, power control and ranging, and point out how these problems can be solved in practice. We also address some additional issues such as frequency hopping and strict bandlimiting of individual carriers. Our analysis indicates that OFDMA is an attractive multiple access technique which offers increased robustness to narrowband interference, impulse noise, and other signal impairments which characterize typical CATV networks.
Rule-Based Generation of Ancient Chinese Architecture from the Song Dynasty (2015)

Ancient Chinese architecture from the Song dynasty is a prominent example of the ancient oriental architectures. The cai-fen system was a module system used for the carpentry of Song architectures, which was specified by the governmental manual, the Yingzao Fashi (State Building Standards) compiled by Li Jie [1103]. We present a rule-based approach for generation of ancient Chinese architectures from the Song dynasty. Based on the special module system and the hierarchical topology of structural patterns in traditional Chinese architectures, the approach parameterizes the wooden elements of buildings and formalizes the construction rules for different architecture styles. In the approach, XML-based description files are generated for displaying the construction process. What the approach generates are standard architectures that strictly follow the ancient Chinese governmental manual. To demonstrate the efficiency of our approach, architectures in different styles have been generated based on their corresponding rules. The fundamental difference between our approach and previous works is that we apply and implement the module system in digitalization of ancient Chinese architecture.
Smooth Continuous Films of Stoichiometric Silicon Carbide from Poly(methylsilyne) (2004)

A new synthesis of the silicon‐network‐backbone polymer poly(methylsilyne) gives a material that is easily converted by pyrolysis to smooth continous films of stoichiometric silicon carbide (see Figure). The films are adherent to the silicon or alumina substrates, and show root mean square roughness of 169 Å over a 500 μm range. Applications in electronics are envisaged.
Identification of Insulin-like Growth Factor-binding Protein-1 as a Potential Physiological Substrate for Human Stromelysin-3 (1997)

To elucidate the physiological role of human stromelysin-3 (hST-3) in tumor progression and/or wound healing, insulin-like growth factor-binding protein-1 (IGFBP-1) was analyzed as a potential physiological substrate. hST-3 proteolysis generates two fragments of 16 and 9 kDa that react with IGFBP-1 monoclonal antibody, although they do not bind insulin-like growth factor-I (IGF-I) in ligand blot. N-terminal sequencing shows that hST-3 cleaves IGFBP-1 at the His140-Val141 bond located in the IGFBP-1 midregion. We show that IGFBP-1 inhibits IGF-I-induced survival and proliferation of BAF/3 cells, as well as IGF-I-mediated activation of phosphatidylinositol 3-kinase (PI 3-K). Co-incubation of the IGF-I. IGFBP-1 complex with hST-3 restores IGF-I-induced proliferation and PI 3-K kinase activity in these cells. BAF/3 proliferation is significantly increased with the hST-3-treated IGF-I.IGFBP-1 complex compared with that obtained using IGF-I alone. To produce this enhanced proliferation, IGF-I must bind to IGFBP-1 before hST-3 proteolysis, demonstrated using an IGF-I variant that does not bind IGFBP. IGFBP-1 also inhibits IGF-I-induced proliferation of the MCF-7 breast adenocarcinoma, and this inhibition was not seen in hST-3-transfected MCF-7 cells. Such proteolysis may thus play a role in in vivo tumor progression. These results indicate that hST-3 may regulate IGF-I bioavailability by proteolyzing IGFBP, thus favoring cell survival and proliferation.
Enhancement of target specificity of CRISPR–Cas12a by using a chimeric DNA–RNA guide (2020)

The CRISPR-Cas9 system is widely used for target-specific genome engineering. CRISPR-Cas12a (Cpf1) is one of the CRISPR effectors that controls target genes by recognizing thymine-rich protospacer adjacent motif (PAM) sequences. Cas12a has a higher sensitivity to mismatches in the guide RNA than does Cas9; therefore, off-target sequence recognition and cleavage are lower. However, it tolerates mismatches in regions distant from the PAM sequence (TTTN or TTN) in the protospacer, and off-target cleavage issues may become more problematic when Cas12a activity is improved for therapeutic purposes. Therefore, we investigated off-target cleavage by Cas12a and modified the Cas12a (cr)RNA to address the off-target cleavage issue. We developed a CRISPR-Cas12a that can induce mutations in target DNA sequences in a highly specific and effective manner by partially substituting the (cr)RNA with DNA to change the energy potential of base pairing to the target DNA. A model to explain how chimeric (cr)RNA guided CRISPR-Cas12a and SpCas9 nickase effectively work in the intracellular genome is suggested. Chimeric guide-based CRISPR- Cas12a genome editing with reduced off-target cleavage, and the resultant, increased safety has potential for therapeutic applications in incurable diseases caused by genetic mutations.
Nanostructuring of tips for scanning probe microscopy by ion sputtering: Control of the apex ratio and the tip radius (2001)

Ion etching under well-defined conditions represents a very powerful tool to fabricate tips in a controlled and reproducible manner for Scanning Probe Microscopy which possess clean, relatively smooth, and oxide-free surfaces. The possibilities and limitations of ion etching are demonstrated thoroughly for tungsten, which is of particular interest for scanning tunneling microscopy. Iterative computer simulations and experimental studies are provided. The simulation of the etching process at the atomic level is based on the Monte Carlo program (Transport of Ions in Matter), which provides reliable values for the key input parameters such as the sputtering yield Y(θ,Eion) and the mean ion range in the material for ion energies between 1 and 6 keV. The simulation program starts with a large tip radius as a crude form and asymptotically approaches a “final form” of a very sharp tip in the course of ion etching. Our experimental results with argon ions in the energy range up to 6 keV and crude electrochemically etched polycrystalline tungsten wire agreed very reasonably with the simulated results. For example, the minimum tip radius obtained experimentally amounts to approximately 5 nm. This value corresponds closely to the ion range, which obviously sets a limit to the smallest achievable tip radius by the effect of transmission sputtering. By variation of the angle between the ion beam and the macroscopic tip, the tip angle can be controlled in the range between 12° and 35°.
In vitro collagen fibril assembly in glycerol solution: evidence for a helical cooperative mechanism involving microfibrils (1986)

Glycerol inhibits the in vitro self-association of monomeric collagen into fibrils and induces the dissociation of fibrils preassembled from NaBH4-reduced collagen. These effects were investigated in an effort to understand the mechanism of fibril assembly of the protein. In PS buffer (0.03 M NaPi and 0.1 M NaCl, pH 7.0) containing 0.1-1.0 M glycerol, the self-association of type I collagen from calf skin took place only if the protein concentration was above a critical value. This critical protein concentration increased with increasing glycerol concentration. Velocity sedimentation studies showed that below the critical protein concentration and under fibril assembly conditions, the collagen was predominantly in a monomeric state. Electron microscopic examinations revealed that the collagen aggregates formed above the critical concentration consisted mostly of microfibrils of 3-5-nm diameter along with some banded fibrils were found. Collagen treated with pepsin to remove its nonhelical telopeptides also self-associated into microfibrils and fibrils in the presence of glycerol, but the reaction did not exhibit any critical concentration. These results are consistent with a mechanism of in vitro collagen fibril assembly which involves the initial formation of microfibrils through a helical cooperative mechanism. They also suggest that contacts of the nonhelical telopeptides of each collagen with its neighboring molecules provide the necessary negative free energy change for the cooperativity and that subsequent lateral association of the microfibrils leads to banded fibrils.
Electron and Optical Phonon Temperatures in Electrically Biased Graphene (2010)

We examine the intrinsic energy dissipation steps in electrically biased graphene channels. By combining in-situ measurements of the spontaneous optical emission with a Raman spectroscopy study of the graphene sample under conditions of current flow, we obtain independent information on the energy distribution of the electrons and phonons. The electrons and holes contributing to light emission are found to obey a thermal distribution, with temperatures in excess of 1500 K in the regime of current saturation. The zone-center optical phonons are also highly excited and are found to be in equilibrium with the electrons. For a given optical phonon temperature, the anharmonic downshift of the Raman G mode is smaller than expected under equilibrium conditions, suggesting that the electrons and high-energy optical phonons are not fully equilibrated with all of the phonon modes.