gebhart/patrepeval huggingface dataset:
Immune responses to the 18-kDa protein of Mycobacterium leprae. Similar B cell epitopes but different T cell epitopes seen by inbred strains of mice (1991)

Antibody responses to the 18-kDa protein of Mycobacterium leprae have been analyzed in different strains of mice. High, intermediate, and low responder strains have been identified and these response patterns show clear linkage to genes encoded in the H-2 complex. Three peptides, residues 1-50, 51-100, and 101-148 have been synthesized, as well as a series of 20-mer peptides, which span the entire 18-kDa protein. Repeated immunization of different strains of mice with the 18-kDa protein resulted in IgG responses to epitopes found on all three synthetic peptides. Immunization of BALB/cJ and B10.BR mice, two high responder strains, with 18-kDa protein resulted in high levels of IgG antibody to epitopes found on peptides 1-20, 16-35, 31-50, 46-65, and 76-95. B10.BR mice also contained IgG that bound peptide 61-80 and BALB/cJ mice produced IgG that bound peptide 91-110. Although B10.BR mice produced IgG that bound the 50-mer peptide 101-148, this IgG was not detected by binding to peptides 91-110, 106-125, 121-140, and 131-148. Immunization of B10.BR mice with individual overlapping 20-mer peptides as Ag revealed that peptides 1-20, 16-35, 31-50, and 76-95 elicited high titers of IgG that bound both the immunizing peptide as well as 18-kDa protein. As these peptides induce antibody synthesis they must contain both B cell and T cell epitopes. By contrast, immunization of BALB/cJ mice with the same 20-mer peptides, all of which contain B cell epitopes for this strain, failed to elicit IgG responses with one exception. Peptide 91-110 induced IgG that bound peptide 91-110, but not the intact 18-kDa protein. We conclude that peptides 1-20, 16-35, 31-50, and 76-95 either lack T cell epitopes for BALB/cJ mice, or activate different T cell subpopulations in the two strains. We suggest that the induction of IgG responses to small peptide Ag is an in vivo assay of the activity of Th2 cell subpopulations.
Neural Network Prediction of the Solvatochromic Polarity/Polarizability Parameter (1997)

A three-layer feed-forward neural network was used for the prediction of the polarity/polarizability parameter . A simulated annealing algorithm was used to minimize the error at the neural network output. Descriptors related to the structure of the compounds were calculated as the input vector. The Kohonen neural network was used to split the data set into training and testing sets. The results obtained from the neural network were compared with the MLRA results.
Whole Genome Analysis of Human Neural Stem Cells Derived from Embryonic Stem Cells and Stem and Progenitor Cells Isolated from Fetal Tissue (2007)

Multipotent neural stem cells (NSC) have been derived from human embryonic stem cells (hESC) as well as isolated from fetal tissues. However, there have been few exclusive markers of NSC identified to date, and the differences between NSC from various sources are poorly understood. Although cells isolated from these two sources share many important characteristics, it is not clear how closely they are related in terms of gene expression. Here, we compare the gene expression profiles of 11 lines of NSC derived from hESC (ES_NSC), four lines of NSC isolated from fetus (F_NSC), and two lines of restricted progenitors in order to characterize these cell populations and identify differences between NSC derived from these two sources. We showed that ES_NSC were clustered together with high transcriptional similarities but were distinguished from F_NSC, oligodendrocyte precursor cells, and astrocyte precursor cells. There were 17 genes expressed in both ES_NSC and F_NSC whose expression was not identified in restricted neural progenitors. Furthermore, the major differences between ES_NSC and F_NSC were mostly observed in genes related to the key neural differentiation pathways. Here, we show that comparison of global gene expression profiles of ES_NSC, F_NSC, and restricted neural progenitor cells makes it possible to identify some of the common characteristics of NSC and differences between similar stem cell populations derived from hESCs or isolated from fetal tissue. Disclosure of potential conflicts of interest is found at the end of this article.
Axotomy Reduces the Effect of Analgesic Opioids Yet Increases the Effect of Nociceptin on Dorsal Root Ganglion Neurons (1998)

There is some doubt as to the effectiveness of opioids in the management of neuropathic pain. We therefore examined the actions of morphine and the opioid-like peptide nociceptin (both 1 mu) on dorsal root ganglion (DRG) neurons that were isolated from control or from nerve-injured rats. Both substances reduced omega-conotoxin (CTX) GVIA-sensitive, N-type Ca2+ channel current and small persistent nifedipine/ CTX-insensitive (non-N, non-L type) current. Nifedipine-sensitive L-type current was unaffected. The effect of nociceptin was antagonized by naloxone benzoylhydrazone (nalbzoh) but not by naloxone. Sciatic nerve section (axotomy) profoundly reduced the effects of morphine and the mu-receptor agonist D-ala2, N-Me-Phe4,Gly-ol5 enkephalin (DAMGO). The effect of the kappa-agonist [(+)-(5alpha,7alpha, 8beta)-N-methyl-N-(7-(1-pyrrolidinyl)-1-oxaspiro(4, 5)dec-8-yl)-benzeneacetamide] (U69593) was unchanged, whereas the effect of nociceptin was increased. All agonists produced their strongest effects on the small, putative nociceptive cells and their weakest effects on the largest cells. The delta-receptor agonist, enkephalin D-pen2,5 (DPDPE), was without effect on control or on axotomized cells. These and other data suggest that the functional downregulation of mu-opioid receptors on sensory nerves contributes to the poor efficacy of opioids in neuropathic pain. Also, the increased effectiveness of nociceptin after axotomy supports the hypothesis that its actions are mediated via a "non-opioid" receptor. Pronounced suppression of Ca2+ channel current in axotomized DRG neurons by nociceptin led to a reduction in Ca2+-dependent K+ conductance and a marked increase in excitability. Despite this, the spinal administration of nociceptin or agonists that activate ORL1 (opioid-like orphan receptor) may prove to be of clinical interest in the management of neuropathic pain.
Spontaneous Molecular Orientation of Polyimides Induced by Thermal Imidization. 2. In-Plane Orientation (1996)

The degree of in-plane molecular orientation of various polyimides (PIs) and their precursors, poly(amic acid)s (PAAs), were estimated by measuring the visible dichroic absorption at an incidence angle for a rod-like dye (perylenediimide, PEDI) dispersed in the matrices. The effects of PI chain structure, film thickness, heating rate, and residual solvent on a spontaneous in-plane orientation phenomenon were examined to fully understand the mechanism. All PAA films cast on a substrate showed the low degrees of in-plane orientation of the chain axis, nearly independent of the chain structure. Upon thermal imidization of the PAA films adhered on a substrate, a striking spontaneous in-plane orientation behavior was observed for some PI systems with rigid chains; in contrast to that, some flexible PI systems showed no spontaneous behavior. Cure of the PAA films adhered on a substrate induced the spontaneous orientation even if the films were considerably thick (∼50 μm); in contrast to that, the cure of the free-standing thick film did not. However, upon cure of the free-standing thin films (∼10 μm), the spontaneous orientation behavior was observed. For rigid PI systems in which interchain stacking preferentially occurs, thermal cure of the PAA films on a substrate forms liquid-crystal-like highly oriented regions, and simultaneously, apparent stretching (due to constraint of film contraction during imidization) promotes the molecular orientation further. The mechanism is closely associated with a “cooperative effect” in which the neighboring chains enhance the molecular orientation of each other during cure. In addition, structural changes (orientations of the chain axis and a molecular plane and molecular packing) upon stepwise annealing were followed. Polarized infrared absorption spectra measured at an incidence angle demonstrated that the phthalimide molecular plane in the PI film on a silicon wafer aligns somewhat parallel to the film plane, but no significant orientational and conformational changes occurred upon stepwise annealing.
Dynamic queue length thresholds in a shared memory ATM switch (2002)

Buffer management schemes are needed to fairly regulate the sharing of memory among different output port queues in a shared memory ATM switch. Of the conventional schemes, static threshold is simple but does not adapt to changing traffic conditions while pushout is efficient and adaptive but difficult to implement. We propose a novel scheme called dynamic threshold which combines the simplicity of static threshold and the adaptability of pushout. The key idea is that the maximum permissible length, for any individual queue at any instant of time, is proportional to the unused buffering in the switch. A queue whose length equals or exceeds the current threshold value may accept no more new cells. The dynamic threshold procedure presented improves the fairness and switch efficiency by guaranteeing access to the buffer space for all output queues. Computer simulation is used to compare the loss performance of the dynamic threshold technique with that of static threshold and pushout. The dynamic threshold scheme is shown to be a good compromise: while nearly as simple as static threshold control, it offers most of the performance benefits of pushout. Like pushout, the dynamic threshold method is adaptive, so it is more robust to uncertainties and changes in traffic conditions than, static threshold control.
Efficient demultiplexing of incoming TCP packets (1992)

When a transport protocol segment arrives at a receiving system, the receiving system must determine which application is to receive the protocol segment. This decision is typically made by looking up a protocol control block (PCB) for the segment, based on information in the segment's header. PCB lookup (a form of demultiplexing) is typically one of the more expensive operations in handling inbound protocol segment [Fe190]. Many recent protocol optimizations for the Transmission Control Protocol (TCP) [Jac88] assume that a large component of TCP traffic is bulk-data transfers, which result in packet trains [JR86]. If packet trains are prevalent, there is a high likelihood that the next TCP segment is en route to the same application (i.e. uses the same PCB) as the previous TCP segment. In these environments a very simple one-PCB cache like those used in BSD systems yields very high cache hit rates. However, there are classes of applications that do not form packet trains, and these applications do not perform well with a one-PCB cache. Examples of such applications are quite common in the area of heads-down data entry into on-line transaction-processing (OLTP) systems. OLTP systems make heavy use of computer communications networks and have large aggregate-packet-rates but are also characterized by large numbers of connections, low per-connection packet rates, and rather small packets. This combination of characteristics results in a very low incidence of packet trains. This paper uses a simple analytic approach to examine how different PCB lookup schemes perform with OLTP traffic. One scheme is shown to work an order of magnitude better for OLTP traffic than the one-PCB cache approach while still maintaining good performance for packet-train traffic.
Nanoliter-Scale Protein Crystallization and Screening with a Microfluidic Droplet Robot (2014)

Large-scale screening of hundreds or even thousands of crystallization conditions while with low sample consumption is in urgent need, in current structural biology research. Here we describe a fully-automated droplet robot for nanoliter-scale crystallization screening that combines the advantages of both automated robotics technique for protein crystallization screening and the droplet-based microfluidic technique. A semi-contact dispensing method was developed to achieve flexible, programmable and reliable liquid-handling operations for nanoliter-scale protein crystallization experiments. We applied the droplet robot in large-scale screening of crystallization conditions of five soluble proteins and one membrane protein with 35-96 different crystallization conditions, study of volume effects on protein crystallization, and determination of phase diagrams of two proteins. The volume for each droplet reactor is only ca. 4-8 nL. The protein consumption significantly reduces 50-500 fold compared with current crystallization stations.
Approaches to the synthesis of the tetrahydropyran subunit of the polyether nigericin (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTApproaches to the synthesis of the tetrahydropyran subunit of the polyether nigericinChristopher P. Holmes and Paul A. BartlettCite this: J. Org. Chem. 1989, 54, 1, 98–108Publication Date (Print):January 1, 1989Publication History Published online1 May 2002Published inissue 1 January 1989https://pubs.acs.org/doi/10.1021/jo00262a025https://doi.org/10.1021/jo00262a025research-articleACS PublicationsRequest reuse permissionsArticle Views777Altmetric-Citations43LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Expression of galectin-7 during epithelial development coincides with the onset of stratification (1999)

Galectin-7 is a 14 KDa member of the galectin family that we have cloned from human, rat and mouse. Our previous studies have shown that in the adult, galectin-7 is expressed in all cell layers of epidermis and of other stratified epithelia such asthe cornea and the lining of the oesophagus. This suggested that galectin-7 expression might be induced at a particular stage in the embryonic development of stratified epithelia. In the present study we have investigated this hypothesis by in situ hybridization of galectin-7 mRNA in mouse embryos. Starting from E13.5, weak expression of galectin-7 was detected in bilayered ectoderm, and stronger expression was found in areas of embryonic epidermis where stratification was more advanced. Galectin-7 expression was maintained in all living layers after epidermal development was completed. Galectin-7 was also strongly and specifically expressed in stratified regions of ectodermally-derived non-epidermal epithelia such as the lining of the buccal cavity, the oesophagus and the ano-rectal region. In contrast, no expression of galectin-7 was found in epithelia derived from endoderm, such as lining of the intestine, kidney and lung. Our results demonstrate that galectin-7 is expressed in all stratified epithelia examined so far, and that the onset of its expression coincides with the first visible signs of stratification. These results establish galectin-7 as the first region-independent marker of epithelial stratification.
Use of Molecular Probes to Assess Geographic Distribution of Pfiesteria Species (2001)

Parke A. Rublee, Jason W. Kempton, Eric F. Schaefer, Coy Allen, Janera Harris, David W. Oldach, Holly Bowers, Torstein Tengs, JoAnn M. Burkholder, H. B. Glasgow, Use of Molecular Probes to Assess Geographic Distribution of Pfiesteria Species, Environmental Health Perspectives, Vol. 109, Supplement 5: Pfiesteria: From Biology to Public Health (Oct., 2001), pp. 765-767
Influence of Syneresis on Permeability Reduction by Polymer Gels (1996)

Summary Syneresis is commonly believed to be incompatible with the application of polymer gels to reduce the permeability of porous media. In this paper, it is shown that, although the permeability of a geltreated porous medium does increase as syneresis proceeds, the degree of permeability reduction in cores remains technologically useful even when 95% syneresis is observed in bulk samples. Arguments are presented for the preferential shrinking of syneresed gel into pore throats; this model explains why permeability reduction is maintained and accounts for several other experimental results. The absence of performance penalties for syneresis has significant implications for the applicability of gels for water shutoff treatments in matrix formations. For example, it raises the possibility that polymer gels can be applied successfully in situations previously considered unfeasible because of the difficulty of maintaining gel stability, e.g., at high temperatures or in the presence of hard formation brines.
Comparison of the Diversity of the Vaginal Microbiota in HIV‐Infected and HIV‐Uninfected Women with or without Bacterial Vaginosis (2008)

The present study demonstrated that both LH-PCR analysis and pyrosequencing differentiated microbiota in BV(+) women from that in BV(-) women and that pyrosequencing indicated a trend toward increased diversity in BV(+)HIV(+) women, suggesting that HIV infection is associated with changes in the diversity of genital microbiota.
Accelerated phase‐contrast cine MRI using k‐t SPARSE‐SENSE (2011)

Phase-contrast (PC) cine MRI is a promising method for assessment of pathologic hemodynamics, including cardiovascular and hepatoportal vascular dynamics, but its low data acquisition efficiency limits the achievable spatial and temporal resolutions within clinically acceptable breath-hold durations. We propose to accelerate PC cine MRI using an approach which combines compressed sensing and parallel imaging (k-t SPARSE-SENSE). We validated the proposed 6-fold accelerated PC cine MRI against 3-fold accelerated PC cine MRI with parallel imaging (generalized autocalibrating partially parallel acquisitions). With the programmable flow pump, we simulated a time varying waveform emulating hepatic blood flow. Normalized root mean square error between two sets of velocity measurements was 2.59%. In multiple blood vessels of 12 control subjects, two sets of mean velocity measurements were in good agreement (mean difference = -0.29 cm/s; lower and upper 95% limits of agreement = -5.26 and 4.67 cm/s, respectively). The mean phase noise, defined as the standard deviation of the phase in a homogeneous stationary region, was significantly lower for k-t SPARSE-SENSE than for generalized autocalibrating partially parallel acquisitions (0.05 ± 0.01 vs. 0.19 ± 0.06 radians, respectively; P < 0.01). The proposed 6-fold accelerated PC cine MRI pulse sequence with k-t SPARSE-SENSE is a promising investigational method for rapid velocity measurement with relatively high spatial (1.7 mm × 1.7 mm) and temporal (∼35 ms) resolutions.
Interrelations of Cold Work, Microstructure and Mechanical Behaviour of Carbon-Free Cubic Martensites (1985)

Article Interrelations of Cold Work, Microstructure and Mechanical Behaviour of Carbon-Free Cubic Martensites was published on February 1, 1985 in the journal International Journal of Materials Research (volume 76, issue 2).
Synchronous elevation of soluble intercellular adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1) correlates with gastric cancer progression (1998)

Soluble forms of ICAM-1 (sICAM-1) and VCAM-1 (sVCAM-1) have been reported from the supernatant of cytokine-activated endothelial cells, cancer cells and from sera of cancer patients. We measured sICAM-1 and sVCAM-1 from the serum of 20 healthy volunteers and 142 gastric cancer patients by ELISA assay. Ninety-five patients were operable and 47 patients were in-operable at the time of this study. Particularly in the 28 operable patients, we sampled both portal and peripheral blood simultaneously and measured the levels of the soluble forms of cell adhesion molecules (sCAMs). The sCAMs level and sero-positivity rate increased with cancer progression in order of the healthy controls, operable patients, and inoperable patients. In in-operable cancer, the sICAM-1 level increased more with liver metastasis. sICAM-1 and sVCAM-1 did not correlate with each other in either portal or peripheral blood. A total of 58.3% of patients with liver metastasis and 22.9% of patients without liver metastasis showed synchronous expression of both sCAMs (p = 0.03). Synchronous sero-positivity of sCAMs and alpha FP was higher with liver metastasis (p = 0.01). The median overall survival duration which co-expressed both sCAMs was 9 months. This showed a significant difference compared with the sICAMs non-expressing group, where the median survival was not reached until 24 months follow-up (p = 0.002). The synchronous expression of sCAMs was an independent risk factor in gastric cancer patients. We raise the possibility that synchronous sICAM-1 and sVCAM-1 elevation may be a useful monitor to determine tumor burden in gastric cancer.
Jitter and phase noise in ring oscillators (1999)

A companion analysis of clock jitter and phase noise of single-ended and differential ring oscillators is presented. The impulse sensitivity functions are used to derive expressions for the jitter and phase noise of ring oscillators. The effect of the number of stages, power dissipation, frequency of oscillation, and short-channel effects on the jitter and phase noise of ring oscillators is analyzed. Jitter and phase noise due to substrate and supply noise is discussed, and the effect of symmetry on the upconversion of 1/f noise is demonstrated. Several new design insights are given for low jitter/phase-noise design. Good agreement between theory and measurements is observed.
Creation of GPCR-based chemical sensors by directed evolution in yeast (2005)

G protein-coupled receptors (GPCRs) form a class of biological chemical sensors with an enormous diversity in ligand binding and sensitivity. To explore structural aspects of ligand recognition, we subjected the human UDP-glucose receptor (P2Y14) functionally expressed in the yeast Saccharomyces to directed evolution. We sought to generate new receptor subtypes with ligand-binding properties that would be useful in the development of practical biosensors. Mutagenesis of the entire UDP-glucose receptor gene yielded receptors with increased activity but similar ligand specificities, while random mutagenesis of residues in the immediate vicinity of the ligand-binding pocket yielded mutants with altered ligand specificity. By first sensitizing the P2Y14 receptor and then redirecting ligand specificity, we were able to create mutant receptors suitable for a simple biosensor. Our results demonstrate the feasibility of altering receptor ligand-binding properties via a directed evolution strategy, using standard yeast genetic techniques. The novel receptor mutants can be used to detect chemical ligands in complex mixtures and to discriminate among chemically or stereochemically related compounds. Specifically, we demonstrate how engineered receptors can be applied in a pairwise manner to differentiate among several chemical analytes that would be indistinguishable with a single receptor. These experiments demonstrate the feasibility of a combinatorial approach to detector design based on the principles of olfaction.