gebhart/patrepeval huggingface dataset:
Acyclic Permutants of Naturally Occurring Cyclic Proteins (2000)

Kalata B1 is a prototypic member of the unique cyclotide family of macrocyclic polypeptides in which the major structural features are a circular peptide backbone, a triple-stranded beta-sheet, and a cystine knot arrangement of three disulfide bonds. The cyclotides are the only naturally occurring family of circular proteins and have prompted us to explore the concept of acyclic permutation, i.e. opening the backbone of a cross-linked circular protein in topologically permuted ways. We have synthesized the complete suite of acyclic permutants of kalata B1 and examined the effect of acyclic permutation on structure and activity. Only two of six topologically distinct backbone loops are critical for folding into the native conformation, and these involve disruption of the embedded ring in the cystine knot. Surprisingly, it is possible to disrupt regions of the beta-sheet and still allow folding into native-like structure, provided the cystine knot is intact. Kalata B1 has mild hemolytic activity, but despite the overall structure of the native peptide being retained in all but two cases, none of the acyclic permutants displayed hemolytic activity. This loss of activity is not localized to one particular region and suggests that cyclization is critical for hemolytic activity.
Wide area information accesses and the information gateways (2002)

The various information access methods will be consolidated into a general and global solution in the future. We propose that the solution should be based on the information gateway model, in which a user can access information by navigating through layers of objects starting from the information brokers represented by the gateways, and by specifying various queries at any level of the navigation layer. This gateway model and its system structure represent a "standard" user and system interface for future information accessing and logical data association.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fisiología del cultivo in vitro (2001)

The culture procedures described up to the eighties, did not made any mention to the environmental control of in vitro plant development. However, growth rate, development and many of the physiologic-morphologic features of the in vitro grown plants are influenced by the culture vessel. The increasing knowledge about the environmental control of culture vessels under sterile conditions, is helping to change micorpropagation procedures. The in vitro environment with lower rate ventilation, brings about low flow rates of matter and energy, with minimum variations of temperature, high relative humidity and large daily changes of the concentration of CO2 inside the culture vessel. The type of culture vessel (size, shape, fabric and closing system) can influence the evolution of the atmosphere along the time of culture. Although submitted to different stresses factors plant can be grown in vitro , but plants can be faulty in their anatomy, morphology and physiology. As a consequence, these plants shown a phenotype unable to survive to ex vitro conditions. Different strategies can be used to control the atmosphere along the different phases of micropropagation, in heterotrophic, mixotrophic or autotrophic cultures. The election of the best strategy will be based on different factors as species, number of transplantes required, or quality-price relationship. enviromental control, tissue culture, micropropagation Keywords: in vitro enviromental , characteristic physiology,
GSPS all-optical ADC for future communication and imaging (2005)

Multi-beam phased array antennas are employed in wireless communications, where RF direct down-conversion, timing synchronization, and analog-to-digital are of important functions. Design of a novel all-optical ADC using spectral technique is presented, where sampling speeds as high as 40 GSPS with 6 bits of resolution is attainable.
Approaching language transfer through text classification : explorations in the detection-based approach (2012)

1 Scott Jarvis: The Detection-Based Approach: An Overview 2 Scott Jarvis, Gabriela Castaneda-Jimenez and Rasmus Nielsen: Detecting L2 Writers' L1s on the Basis of their Lexical Styles 3 Scott Jarvis and Magali Paquot: Exploring the Role of N-Grams in L1 Identification 4 Scott A. Crossley and Danielle S. McNamara: Detecting the First Language of Second Language Writers Using Automated Indices of Cohesion, Lexical Sophistication, Syntactic Complexity, and Conceptual Knowledge 5 Yves Bestgen, Sylviane Granger and Jennifer Thewissen: Error Patterns and Automatic L1 Identification 6 Scott Jarvis, Yves Bestgen, Scott A. Crossley, Sylviane Granger, Magali Paquot, Jennifer Thewissen and Danielle S. McNamara: The Comparative and Combined Contributions of N-grams, Coh-Metrix Indices, and Error Types in the L1 Classification of Learner Texts 7 Scott A. Crossley: Detection-Based Approaches: Methods, Theories and Applications
Structural Identification Using Computer Vision–Based Bridge Health Monitoring (2017)

This paper presents a new structural identification (St-Id) framework along with a damage indicator, displacement unit influence surface using computer vision–based measurements for bridge health monitoring. Unit influence surface (UIS) of a certain response (e.g., displacement, strain) at a measurement location on a beam-type or plate-type structure (e.g., single-span or multispan bridge with its deck) is defined as a response function of the unit load with respect to the any given location of the unit load on that structure. The novel aspect of this paper is a framework integrating vehicle load (input) modeling using computer vision and the development of a new damage indicator, UIS, using image-based structural identification. This framework is demonstrated on the large-scale bridge model in the University of Central Florida Structures Laboratory for verification and validation. The UIS damage indicators successfully identified the simulated damage on the bridge model, including damage detection and damage localization.
Angiotensin-Converting Enzyme Inhibitory Activity of SCH 31846, a New Non-Sulfhydryl Inhibitor (1983)

SCH 31846, 1-(N-[1(S)-(ethoxycarbonyl)-3-phenylpropyl]-(S)-alanyl)-cis, syn-octahydro-(H-indole-2-S)-carboxylic acid; CI-907; PD 109, 763-2, is a new non-sulfhydryl-containing, angiotensin-converting enzyme (ACE) inhibitor. The present investigation describes its ACE inhibitory properties and compares them to those of MK 421. The diacid of SCH 31846 inhibited rabbit pulmonary ACE with an IC50 of 2.2 nM (MK 421 diacid 2.5 nM). The drug behaved as a competitive and specific inhibitor in vitro. SCH 31846 and its diacid effectively inhibited pressor actions of intravenous injection of angiotensin I (AI) in anesthetized rats. ID50 values were 27 and 11 micrograms/kg for SCH 31846 and SCH 31846 diacid, respectively (MK 421 and MK 421 diacid 57 and 15 micrograms/kg, respectively). Oral administration of SCH 31846 (0.03-1 mg/kg) inhibited pressor actions of AI in conscious rats with a duration of over 16 h at 0.3 and 1 mg/kg. SCH 31846 was 2.2 times as potent as MK 421 in this regard. The diacid of SCH 31846 was considerably less potent than the ester, implying poor oral absorption of the former. Effective ACE inhibition, as judged by attenuation of pressor actions of AI, was noted in dogs after both intravenous and oral administrations of SCH 31846. Onset of action was more rapid than that of MK 421. Intravenous administration of SCH 31846 inhibited the renal vascular actions of intrarenal injection of AI, indicating effective blockade of the renal enzyme. Intracerebroventricular administration of SCH 31846 diacid blocked pressor responses to intracerebroventricular AI, whereas oral administration of SCH 31846 (10 mg/kg) did not, implying that SCH 31846 inhibits brain ACE but does not gain access to the cerebral enzyme when administered orally. These data indicate that SCH 31846 is a potent and specific non-sulfhydryl ACE inhibitor. As such, it should be useful in the treatment of hypertension and heart failure.
Identification of Biologically Active Chemokine Isoforms from Ascitic Fluid and Elevated Levels of CCL18/Pulmonary and Activation-regulated Chemokine in Ovarian Carcinoma (2002)

Chemokines are important in leukocyte homeostasis, inflammation, angiogenesis, and metastasis. Here, the molecular diversity of chemokines present in ovarian carcinoma was studied by purifying the proteins to homogeneity from ascitic fluid. Biologically active intact CCL2 and processed CXCL8, CCL3, and CCL18 isoforms were recovered. CCL7 and CCL20 were also purified, but their levels were 10-fold lower compared with CXCL8, CCL2, and CCL3 and even 100-fold lower than the amounts of CCL18 isolated. In ascitic fluids from patients with ovarian carcinoma (n = 12), significantly higher levels of CXCL8 and CCL18 (2.0 versus 0.7 ng/ml (p = 0.01) and 120 versus 44 ng/ml (p = 0.0002), respectively) were detected compared with those in nonovarian carcinoma patients (n = 12). In contrast to CXCL8, CCL18 was not inducible in carcinoma cell lines. Immunostaining showed CCL18 expression in tumor-infiltrating cells with monocyte/macrophage morphology but not in the ovarian carcinoma cells. Our data demonstrate that biochemically heterogenous but biologically active forms of several chemokines are present at different concentrations in ovarian carcinoma ascitic fluid. This points to a delicate balance of chemokines in epithelial ovarian cancer and to a potentially major role for CXCL8 and CCL18 in this tumor.
Role of acid tolerance response genes in Salmonella typhimurium virulence (1993)

The atp and fur genes are involved in the acid tolerance response of Salmonella typhimurium. An atp::Tn10 mutant was avirulent in the mouse typhoid model when assayed by oral and intraperitoneal routes. However, a fur mutant was completely virulent by the intraperitoneal route. No relevant differences in intracellular survival or invasion rates were observed for the two mutants in macrophages and epithelial cells. These data indicate that separate acid tolerance response genes may have different roles in S. typhimurium virulence.
Wave-equation-based seismic illumination analysis (2006)

Abstract We present a wave-equation-based method for seismic illumination analysis. A one-way wave-equation-based, generalized screen propagator is used to extrapolate the wavefields from sources and receivers to the subsurface target. A local plane-wave analysis is used at the target to calculate localized, directional energy fluxes for both source and receiver wavefields. We construct an illumination matrix using these energy fluxes to quantify the target illumination conditions. The target geometry information is used to manipulate the illumination matrix and generate different types of illumination measures. The wave-equation-based approach can properly handle forward multiple-scattering phenomena, including focusing/defocusing, diffraction, and interference effects. It can be directly applied to complex velocity models. Velocity-model smoothing and Fresnel-zone smoothing are not required. Different illumination measurements derived from this method can be applied to target-oriented or volumetric illumination analyses. This new method is flexible and practical for illumination analysis in complex 2D and 3D velocity models with nontrivial acquisition and target geometries.
Perspectives on the Morphology and Biology of CD34-Negative Stem Cells (2000)

The CD34 antigen is the classical indicator molecule of pluripotent hematopoietic stem cells. But there is more and more evidence that progenitors of a yet uncommitted stem cell population do not express this surrogate marker. The bone marrow and other sites of hematopoiesis consist also of fibroblast-like stromal cells, quiescent hematopoietic stem cells, and mesenchymal stem cells. Depending on their stage of differentiation, CD34- stem cells cannot only generate hematopoietic progenitors, but also more specified mesenchymal precursors, such as osteoblasts, chondrocytes, myocytes, adipocyts, and others. The stromal cell compartment produces not only matrix proteins, such as collagens, fibronectin and others, but also the essential growth factors, which initiate and support the differentiation of primary quiescent, but eventually activated CD34- stem cells into CD34+ hematopoietic progenitors. In vivo studies have shown that long-term hematopoietic and mesenchymal reconstitution can be achieved with CD34- stem cell lines, isolated from various sources, although the frequency of CD34- stem cells seams to be quite low among the progenitor population. Some authors deny the reconstitution ability of CD34- cells. The majority of CD34- stem cells are quiescent fibroblast-like cells, which can be identified in the bone marrow biopsy as "bone lining cells". Some of those bone lining cells show protein synthesis and contain secretory vesicles. Recent studies have demonstrated that there is a surprising plasticity of the earliest stem cell population, consisting of cells with stromal cell function as well as hematopoietic and mesenchymal progenitors. The new insights into the biology of totipotent stem cells give us novel perspectives for cell- and gene therapy of various malignant and nonmalignant diseases and the possibility to replace defective organ functions with autologous CD34- stem cells.
The Impact of Multidideoxynucleoside Resistance-Conferring Mutations in Human Immunodeficiency Virus Type 1 Reverse Transcriptase on Polymerase Fidelity and Error Specificity (1998)

Variants of human immunodeficiency virus type 1 (HIV-1) that are highly resistant to a number of nucleoside analog drugs have been shown to develop in some patients receiving 2',3'-dideoxy-3'-azidothymidine therapy in combination with 2',3'-dideoxycytidine or 2',3'-dideoxyinosine. The appearance, in the reverse transcriptase (RT), of the Q151M mutation in such variants precedes the sequential appearance of three or four additional mutations, resulting in a highly resistant virus. Three of the affected residues are proposed to lie in the vicinity of the template-primer in the three-dimensional structure of the HIV-1 RT-double-stranded DNA complex. The amino acid residue Q151 is thought to be very near the templating base. The nucleoside analog resistance mutations in the beta9-beta10 (M184V) and the beta5a (E89G) strands of HIV-1 RT were previously shown to increase the fidelity of deoxynucleoside triphosphate insertion. Therefore, we have examined wild-type HIV-1BH10 RT and two nucleoside analog-resistant variants, the Q151M and A62V/V75I/F77L/F116Y/Q151M (VILYM) RTs, for their overall forward mutation rates in an M13 gapped-duplex assay that utilizes lacZ alpha as a reporter. The overall error rates for the wild-type, the Q151M, and the VILYM RTs were 4.5 x 10(-5), 4.0 x 10(-5), and 2.3 x 10(-5) per nucleotide, respectively. Although the mutant RTs displayed minimal decreases in the overall error rates compared to wild-type RT, the error specificities of both mutant RTs were altered. The Q151M RT mutant generated new hot spots, which were not observed for wild-type HIV-1 RT previously. The VILYM RT showed a marked reduction in error rate at two of the predominant mutational hot spots that have been observed for wild-type HIV-1 RT.
Structure of UDP Complex of UDP-galactose:β-Galactoside-α-1,3-galactosyltransferase at 1.53-Å Resolution Reveals a Conformational Change in the Catalytically Important C Terminus (2001)

UDP-galactose:beta-galactosyl alpha-1,3-galactosyltransferase (alpha3GT) catalyzes the transfer of galactose from UDP-alpha-d-galactose into an alpha-1,3 linkage with beta-galactosyl groups in glycoconjugates. The enzyme is expressed in many mammalian species but is absent from humans, apes, and old world monkeys as a result of the mutational inactivation of the gene; in humans, a large fraction of natural antibodies are directed against its product, the alpha-galactose epitope. alpha3GT is a member of a family of metal-dependent retaining glycosyltransferases including the histo-blood group A and B synthases. A crystal structure of the catalytic domain of alpha3GT was recently reported (Gastinel, L. N., Bignon, C., Misra, A. K., Hindsgaul, O., Shaper, J. H., and Joziasse, D. H. (2001) EMBO J. 20, 638-649). However, because of the limited resolution (2.3 A) and high mobility of the atoms (as indicated by high B-factors) this structure (form I) does not provide a clear depiction of the catalytic site of the enzyme. Here we report a new, highly ordered structure for the catalytic domain of alpha3GT at 1.53-A resolution (form II). This provides a more accurate picture of the details of the catalytic site that includes a bound UDP molecule and a Mn(2+) cofactor. Significantly, in the new structure, the C-terminal segment (residues 358-368) adopts a very different, highly structured conformation and appears to form part of the active site. The properties of an Arg-365 to Lys mutant indicate that this region is important for catalysis, possibly reflecting its role in a donor substrate-induced conformational change.
PPARgamma induces the insulin-dependent glucose transporter GLUT4 in the absence of C/EBPalpha during the conversion of 3T3 fibroblasts into adipocytes. (1998)

To define the molecular mechanisms that control GLUT4 expression during adipogenesis, NIH-3T3 fibroblasts ectopically expressing different adipogenic transcription factors (C/EBPbeta, C/EBPdelta, C/EBPalpha, and PPARgamma) under the control of a tetracycline-responsive inducible (C/EBPs) or a constitutive retroviral (PPARgamma) expression system were used. Enhanced production of C/EBPbeta (beta2 cell line), C/EBPbeta together with C/EBPdelta (beta/delta39 cell line), C/EBPalpha (alpha1 cell line), or PPARgamma (Pgamma2 cell line) in cells exposed to dexamethasone and the PPARgamma ligand ciglitazone (a thiazolidinedione) resulted in expression of GLUT4 mRNA as well as other members of the adipogenic gene program, including aP2 and adipsin. Focusing our studies on the beta/delta39 cells, we have demonstrated that C/EBPbeta along with C/EBPdelta in the presence of dexamethasone induces PPARgamma, adipsin, and aP2 mRNA production; however, GLUT4 mRNA is only expressed in cells exposed to ciglitazone. In addition, enhanced expression of a ligand-activated form of PPARgamma in the beta/delta39 fibroblasts stimulates synthesis of GLUT4 protein and gives rise to a population of adipocytic cells that take up glucose in direct response to insulin. C/EBPalpha is not expressed in the beta/delta39 cells under conditions that stimulate the adipogenic program. This observation suggests that PPARgamma alone or in combination with C/EBPbeta and C/EBPdelta is capable of activating GLUT4 gene expression.
Self-similarity in World Wide Web traffic: evidence and possible causes (1997)

The notion of self-similarity has been shown to apply to wide-area and local-area network traffic. We show evidence that the subset of network traffic that is due to World Wide Web (WWW) transfers can show characteristics that are consistent with self-similarity, and we present a hypothesized explanation for that self-similarity. Using a set of traces of actual user executions of NCSA Mosaic, we examine the dependence structure of WWW traffic. First, we show evidence that WWW traffic exhibits behavior that is consistent with self-similar traffic models. Then we show that the self-similarity in such traffic can be explained based on the underlying distributions of WWW document sizes, the effects of caching and user preference in file transfer, the effect of user "think time", and the superimposition of many such transfers in a local-area network. To do this, we rely on empirically measured distributions both from client traces and from data independently collected at WWW servers.
Generation of microcellular polymeric foams using supercritical carbon dioxide. I: Effect of pressure and temperature on nucleation (1994)

Abstract Supercritical carbon dioxide is known to swell and plasticize poly(methyl methacrylate), PMMA, dramatically. We have employed a pressure quench in a CO 2 ‐swollen PMMA sample to generate a microcellular core structure encased by a nonporous skin. Further, we have demonstrated that classical nucleation theory can be used to model the effects of saturation pressure, temperature, and time on the cell density of the porous materials, provided that the effects of the CO 2 ‐diluent on the surface tension of PMMA are adequately taken into account. This is because our system is in a homogeneous liquid state at our operating conditions because of the plasticization. Both model predictions and data indicate that cell density rises sharply at a saturation pressure of approximately 14 MPa (at 40°C), leveling out above 27 MPa. By contrast, the effect of temperature on cell density in the range 40°C to 80°C is minimal.
Effects of enhanced UV-B radiation on seed growth characteristics and yield components in soybean (2013)

In order to understand the effects of enhanced ultraviolet-B (UV-B) radiation on soybean yield components and seed growth characteristics, three determinate soybean cultivars, Hai339 (H339), Heinong35 (HN35) and Kennong18 (KN18) were grown for 2 years in a field experiment exposed to enhanced UV-B radiation. Enhanced UV-B radiation decreased plant height, dry weight of individual stem and yield per plant of three soybean cultivars on average by 15.5%, 16.9% and 43.7%, respectively. Pod number per plant was the most responsible component for yield change under UV-B radiation in the 2-year study. Seed number per pod was less affected by change in light treatment in our experiment, compared with the pod number per plant. UV-B radiation had no significant effect on effective filling period, however, seed size was negatively impacted by UV-B radiation and it decreased 12.3% for three soybean cultivars. Reduction of seed size was mainly due to the decrease of cotyledon cell number. Enhanced UV-B radiation had no significant effect on cotyledon cell volume, cell growth rate or cell weight. Our results suggested that the reduction of seed ABA concentration was directly responsible for lower cotyledon cell number under enhanced UV-B radiation.
Assembly Pathway of Hepatitis B Core Virus-like Particles from Genetically Fused Dimers (2015)

Macromolecular complexes are responsible for many key biological processes. However, in most cases details of the assembly/disassembly of such complexes are unknown at the molecular level, as the low abundance and transient nature of assembly intermediates make analysis challenging. The assembly of virus capsids is an example of such a process. The hepatitis B virus capsid (core) can be composed of either 90 or 120 dimers of coat protein. Previous studies have proposed a trimer of dimers as an important intermediate species in assembly, acting to nucleate further assembly by dimer addition. Using novel genetically-fused coat protein dimers, we have been able to trap higher-order assembly intermediates and to demonstrate for the first time that both dimeric and trimeric complexes are on pathway to virus-like particle (capsid) formation.