gebhart/patrepeval huggingface dataset:
Protein volumes and hydration effects. The calculations of partial specific volumes, neutron scattering matchpoints and 280-nm absorption coefficients for proteins and glycoproteins from amino acid sequences (1986)

Amino acid sequences, carbohydrate compositions and residue volumes are used to compare critically calculations of partial specific volumes v, neutron scattering matchpoints and 280-nm absorption coefficients with experimental v values for proteins and glycoproteins. The v values that are obtained from amino acid densitometry underestimate experimental v values by 0.01-0.02 ml/g while the v values from crystallographic volumes overestimate the experimental v values by 0.04-0.05 ml/g. An intermediate consensus volume set of amino-acid-residue volumes is proposed in order to predict experimental v values using sequence information. The method is extended to carbohydrates and glycoproteins. Neutron scattering matchpoints can be calculated from crystallographic residue volumes on the basis of the non-exchange of 10% of the main-chain NH protons. Crystallographic results on protein-bound water are used to account for the experimental values of v and matchpoints. Finally, 280-nm absorption coefficients, A1%, 1 cm 280, of 5-27 are found to be well predicted by the Wetlaufer procedure based on the totals of Trp, Tyr and Cys residues. Average errors are +/- 0.7, and the experimental A(1%,1cm)280 values can be larger than the predicted values by 3%.
The Conformation of Thermolysin (1974)

Abstract An improved electron density map has been obtained for the thermostable protease thermolysin. The map, calculated at a nominal resolution of 2.3 A, was based on the three heavy atom isomorphs described previously and on data for the zinc-free and europium-substituted enzyme. The zinc-free and native enzymes are closely isomorphous, and the difference in electron density between them shows that the only structural changes which occur on the removal of the zinc ion are slight adjustments in residues in the immediate vicinity of the metal ion. The approximate conformation of most of the thermolysin molecule is revealed without ambiguity, and preliminary atomic coordinates are presented. Some aspects of the molecular stereochemistry are discussed, including tertiary folding, helices, turns, and calcium binding sites. The peptide dihedral angles for most of the residues lie within or near the allowed regions for an empirical hard sphere model, but the conformations of a few residues lie in disallowed regions. There are several indications that the angle τ at the α carbon atom must be significantly greater than the tetrahedral for a number of residues. With the possible exception of the four calcium binding sites, there is nothing particularly unusual in the thermolysin conformation to which one might attribute the thermostability of the molecule. It is suggested that the enhanced stability of thermostable proteins relative to thermolabile ones cannot be attributed to a common determinant such as metal ion or hydrophobic stabilization, but in a given instance may be due to rather subtle differences in hydrophobic character, metal binding, hydrogen bonding, ionic interactions, or a combination of all of these.
ALPHA‐2‐ADRENERGIC PATHWAYS RELEASE GROWTH HORMONE VIA A NON‐GRF‐DEPENDENT MECHANISM IN NORMAL HUMAN SUBJECTS (1988)

Administration of a supramaximal dose of GRF 1-44 (200 micrograms, i.v.) to normal human volunteers increased GH levels while a further bolus of GRF (200 micrograms i.v.) given 2 hours later failed to increase plasma GH levels. In contrast, alpha-adrenergic receptor agonism with either propranolol-adrenaline infusion or clonidine increased plasma GH levels at a time when GH responses to this supramaximal dose of GRF were absent. This indicates that alpha-adrenergic pathways stimulate GH secretion through a non-GRF-dependent mechanism in normal human subjects.
Dendrons/dendrimers: quantized, nano-element like building blocks for soft-soft and soft-hard nano-compound synthesis (2009)

It was A. Lavoisier's original thinking in Traite Elementaire de Chemie (1789) followed by J. Dalton's seminal “atom/molecular hypothesis” (i.e., New System of Chemical Philosophy, 1808) that defined “first principles” for much of our contemporary small molecule chemistry. Dalton's concept, advocating atom-based (elemental) building blocks (0.1–0.6 nm) for the synthesis of well defined small molecules, has emerged as a fundamental theme over the past 200 years. It initiated fundamental concepts such as well defined mass combining ratios, stoichiometries, valency and compound formation which have defined the “central dogma” and underpinned the traditional fields of both organic/polymer and inorganic sciences. As such, these historical examples portend the significant role that similar well defined, quantized soft nano-matter, modules such as dendrons and dendrimers (1.0–20 nm) might be expected to play in the emerging science of nano-syntheses. Dendrimers are well defined collections of atoms that may be viewed as core-shell type atom mimics (i.e., soft nano-element like modules). More than 12,000 published references in the dendrimer field have clearly demonstrated the ability to structure control important Critical Nanoscale Design Parameters (CNDPs) such as: (a) size, (b) shape, (c) surface chemistry, (d) flexibility and (e) architecture over a wide range of structures and compositions. These are features shared with elemental atoms and account for unique atom-like combining properties exhibited by dendrimers to yield well defined nano-module stoichiometries. We report first steps, including many literature examples that demonstrate the construction of well defined soft-soft and soft-hard matter nano-compounds. A variety of dendrimer surface reactions or guest-host assemblies have been shown to produce stoichiometric nano-compounds such as: (a) dendrimer-dendrimer, (b) dendrimer-protein (c) dendrimer-fullerene and dendrimer-metal nanocluster structures, to mention a few. These literature examples provide compelling evidence for the emergence of an active dendron and dendrimer module based synthetic nano-chemistry platform.
Treatment of acute myeloid leukemia cells in vitro with a monoclonal antibody recognizing a myeloid differentiation antigen allows normal progenitor cells to be expressed. (1987)

Monoclonal antibody L4F3 reacts with most acute myeloid leukemia (AML) cells and virtually all normal granulocyte/monocyte colony-forming cells (CFU-GM). Our objective was to determine whether lysis of AML cells with L4F3 and complement allowed expression of normal myeloid progenitors. The five glucose-6-phosphate dehydrogenase (G6PD) heterozygous patients with AML studied manifested only a single G6PD type in blast cells and in most or all granulocyte colony-forming cells, indicating that the leukemias developed clonally. The cells remaining after L4F3 treatment from two of the patients gave rise to granulocytic colonies that expressed the G6PD type not seen in the leukemic clone, indicating that they were derived from normal progenitors (CFU-GM). L4F3-treated cells from these two patients cultured over an irradiated adherent cell layer from normal long-term marrow cultures also gave rise to CFU-GM, which were shown by G6PD analysis to be predominantly nonleukemic. In the other three patients, the progenitor cells remaining after L4F3 treatment were derived mainly from the leukemic clone. The data suggest that in vitro cytolytic treatment with L4F3 of cells from certain patients with AML can enable normal, presumably highly immature progenitors to be expressed.
The Session Initiation Protocol (SIP) and Session Description Protocol (SDP) Static Dictionary for Signaling Compression (SigComp) (2003)

community, and requests discussion and suggestions for improvements.
Distal Protection Improved Reperfusion and Reduced Left Ventricular Dysfunction in Patients With Acute Myocardial Infarction Who Had Angioscopically Defined Ruptured Plaque (2005)

Distal protection reduced microcirculation damage and left ventricular dysfunction in patients with AMI who had angioscopically defined ruptured plaque. Distal embolization of plaque debris was detected more frequently in patients with ruptured plaque. These results suggest that microcirculation damage and left ventricular dysfunction are increased mainly by distal embolization of plaque debris rather than of thrombus.
Pneumatic Carbon Nanotube Actuators (2002)

A new giant actuation mechanism is demonstrated for sheets of carbon single-wall nanotubes that produces a 3 % actuator stroke in the in-plane direction, and amplification to over 300 % in the thickness direction. Electrochemically generated gas bubbles form in the internal pores of the nanotube sheets (see Figure), producing a pneumatic-type actuation at low application voltages.
Notes from the State-Of-The-Technology: DNSSEC (2001)

A meeting of groups involved in the development of the DNS Security
Extensions (DNSSEC) was held in conjunction with the 49th IETF. The
discussion covered the extent of current efforts, a discussion of what
questions are being asked of DNSSEC, and what is needed by the IETF to
progress the definition to the Draft Standard level. In short, this
was a status meeting. 1.0 Introduction [RFC 2535] has
been under consideration for quite a few years, with RFC 2535 being
the core of the most recent definition. is part of the charter
of two working groups, DNSEXT and DNSOP. ISC's BIND v8.2
implemented part of the specification, BIND v9 represents the first
full implementation. In 1999 and 2000, more than a half dozen
workshops have been held to test the concepts and the earliest
versions of implementations. But to date, is not in common use.
The current collective wisdom is that is 1) important, 2) a
buzzword, 3) hard, 4) immature. To capture the true state of the
technology and identify where work is needed, an informal gathering of
groups known to be involved in was held in conjunction with the
49th IETF. The attendees represented NLnet Labs, The Foundation for
Internet Infrastructure, RIPE NCC, ARIN, CAIRN (ISI and NAI Labs),
NIST, DISA, RSSAC, Network Associates and Verisign (COM/NET/ORG TLDs).
The agenda of the meeting consisted of three items. Reports from each
group on their current research goals were followed by a discussion of
questions being asked of DNSSEC. Finally, with reaching Draft standard
status as a goal, what was needed to make this happen was considered.
This report is not simply a transcript of the meeting, it is a
summary. Some of the information presented here was obtained in direct
contact with participants after the meeting. If other groups that are
doing research want to be represented in this document, contact
the editor for inclusion. 1.1 What does the term DNSSEC mean? One
of the comments made during di ...
Expression of metabotropic glutamate receptors in nodose ganglia and the nucleus of the solitary tract (2001)

The purpose of this study was to identify the complement of metabotropic glutamate receptors (mGluRs) expressed in nodose ganglia and the nucleus tractus solitarius (NTS). mRNA from these tissues was isolated and amplified with standard RT-PCR with primers specific for each mGluR subtype. The results of this analysis showed that the NTS expresses all eight mGluR subtypes, whereas nodose ganglia express only group III mGluRs: mGluR4, mGluR6, mGluR7, and mGluR8. Application of the group III-specific mGluR agonist L-(+)-2-amino-4-phosphonobutyric acid (100 microM) reversibly inhibited voltage-gated calcium currents isolated from DiI-labeled aortic baroreceptor neurons and unlabeled nodose neurons. The results of this study suggest that group III mGluRs are the primary mGluR subtype expressed in visceral afferent neurons and that these receptors may be involved in afferent central transmission.
1alpha,25-(OH)(2)-D(3) and its synthetic analogue decrease tumor load in the Apc(min) Mouse. (2002)

Both calcium and vitamin D are thought to be able to inhibit colon carcinogenesis. To better define the effects of vitamin D, we studied 1alpha,25-(OH)(2)-D(3) and a noncalcemic synthetic analogue of vitamin D(3) (VD(3)) in the Apc(min) mouse. Female Apc(min) mice 4-5 weeks old were randomized to four groups: a VD(3)-treated group (n = 11) were given injections of 0.01 microg of 1alpha,25-(OH)(2)-D(3) i.p. three times per week; an analogue-treated group (n = 10) received 5 microg of 1alpha,25-(OH)(2)-16-ene-19-nor-24-oxo-D(3) i.p. three times per week; and a control group (n = 12) received sham injections of PBS. A sulindac-treated group (n = 10) was used as a positive control. Doses of these compounds were chosen based on previous toxicity studies in mice and rats. After 10 weeks of treatment, mice were killed and two observers (S. H., R. W. I.), blinded to treatment, scored polyp number and size. Tumor number was not affected with 1alpha,25-(OH)(2)-D(3) or vitamin D analogue administration. A significant decrease in total tumor load (sum of all polyp areas) over the entire gastrointestinal tract was seen in the analogue (36% decrease; P < 0.05) and the VD(3) groups (46%; P < 0.001). There was a significant decrease in polyp number (49%; P < 0.001) and polyp area (70%; P < 0.001) in the sulindac group. Reverse transcription-PCR of the total RNA derived from intestinal tissue revealed expression of the vitamin D receptor throughout the small intestine and the colon. Serum calcium levels in the analogue group were not elevated at week 4 of treatment and only moderately elevated (22%) by week 8 (P < or =0.001). In contrast, serum calcium in the VD(3) group was significantly elevated (P < or =0.001) at weeks 4 (23%) and 8 (45%). Food intake and growth rate were significantly lower in the VD(3) group (26%, P < 0.001, and 27%, P < 0.001, respectively) at week 10. In contrast, food intake and growth rate were similar for the control, sulindac, and analogue groups. Our results indicate that a noncalcemic analogue of vitamin D can significantly decrease intestinal tumor load in Apc(min) mice without severe toxic side effects and suggest that these compounds may have utility as chemopreventive agents in groups at high-risk for colon cancer.
A method for detecting epistasis in genome-wide studies using case-control multi-locus association analysis (2008)

With the current availability of genetic studies with large numbers of individuals and genetic markers, HFCC can have a great impact in the identification of epistatic effects that escape the standard single-locus association analyses.
Relationship between Nasopharyngeal Colonization and the Development of Otitis Media in Children (1997)

Streptococcus pneumoniae, nontypeable Haemophilus influenzae, and Moraxella catarrhalis are the predominant bacteria associated with otitis media. A cohort of 306 infants was followed from birth through 12 months to determine frequency and duration of colonization and risk of acute otitis media (AOM) and otitis media with effusion (OME). M. catarrhalis was the most common bacterium isolated. Infants colonized at < or = 3 months of age were at increased risk of AOM and OME. Early colonization with M. catarrhalis revealed the greatest risk (relative risk [RR] = 1.24), especially for OME (RR = 1.57). There was a strong relationship between the frequency of colonization and OM (r = .37, P < .001,) for each pathogen. Although S. pneumoniae, nontypeable H. influenzae, and M. catarrhalis are part of the normal nasopharyngeal flora during infancy, an increased rate of colonization may identify a subpopulation of children that is at increased risk of OM.
The yeast Ty virus-like particles (2000)

Virus-like particle (VLP) assembly is a crucial step of the life cycle of retrotransposons. The S. cerevisiae Ty elements represent an interesting model for the analysis of these particles and thus have been studied extensively. Our current knowledge of the organisation and assembly of Ty1 and Ty3 VLPs is reviewed here. This includes the mechanism of assembly, the role of the Tya core protein during VLP formation and the RNA packaging process. The physical properties of Ty1 VLPs are also described and the latest three-dimensional Ty1 VLP reconstructions are shown. In addition, the relevance of these studies is discussed in the context of retro-element biology.
Prolonged Hypoxia Concomitant with Serum Deprivation Induces Massive Human Mesenchymal Stem Cell Death (2007)

Mesenchymal stem cells (MSCs) have been proposed for the repair of damaged tissue including bone, cartilage, and heart tissue. Upon in vivo transplantation, the MSCs encounter an ischemic microenvironment characterized by reduced oxygen (O2) tension and nutrient deprivation that may jeopardize viability of the tissue construct. The aim of this study was to assess the effects of serum deprivation and hypoxia on the MSC survival rates in vitro. As expanded MSCs are transferred from plastic to a scaffold in most tissue engineering approaches, possibly inducing loss of survival signals from matrix attachments, the effects of a scaffold shift on the MSC survival rates were also assessed. Human MSCs were exposed for 48 hours to (i) a scaffold substrate shift, (ii) serum deprivation, and (iii) O2 deprivation. MSCs were also exposed to prolonged (up to 120 hours) hypoxia associated with serum deprivation. Cell death was assessed by Live/Dead staining and image analysis. The MSC death rates were not affected by the shift to scaffold or 48-hour hypoxia, but increased with fetal bovine serum (FBS) starvation, suggesting that between the two components of ischemia, nutrient deprivation is the stronger factor. Long-term hypoxia combined with serum deprivation resulted in the complete death of MSCs (99 +/- 1%), but this rate was reduced by half when MSCs were exposed to hypoxia in the presence of 10% FBS (51 +/- 31%). These results show that MSCs are sensitive to the concurrent serum and O2 deprivation to which they are exposed when transplanted in vivo, and call for the development of new transplantation methods.
Global analysis of metastasis‐associated gene expression in primary cultures from clinical specimens of clear‐cell renal‐cell carcinoma (2008)

Metastatic clear-cell renal-cell carcinoma (ccRCC) has a poor prognosis and unpredictable course, and there are no molecular markers that reliably predict ccRCC metastasis. In this study, ccRCC specimens from 84 patients were directly cultured in vitro. Primary cultures from 38 of 94 specimens contained more than 90% tumor cells at the fourth passage. After identification by immunostaining, the primary cultures of metastatic and nonmetastatic ccRCC specimens from the age- and gender-matched patients were subjected to cDNA microarray assays. A total of 842 differentially expressed genes with a FDR (false discovery rate) of 4.79% were identified. Pathway analysis and co-occurrence with "cancer", "metastasis" and "invasion" in the literature annotations functionally enriched the 842 genes and provided an indication of the reliability of our microarray assays. Novel genes associated with metastasis were selected based on protein-protein interactions between 205 differentially expressed genes that co-occurred with "metastasis" and those that did not co-occur with "metastasis" on Medline, and the results of co-expression analysis between the co-occurred genes and unpublished genes. FSTL1, AV722783, SLC15A1, DDX17, ORC2L and PKMYT1 were found to be potential ccRCC metastasis-associated novel genes, according to expression patterns in cultures and tumor tissues. Interestingly, the upregulated genes (CAV1, PKMYT1 and ORC2L) were also upregulated and the downregulated genes (FSTL1, GSTM3, CYR61, SLC15A1 and AV722783) were also downregulated in the primary ccRCC specimens compared with expression in adjacent renal tissues in 37 patients. This study has identified new candidate biomarkers and targets for the early diagnosis and treatment of ccRCC metastasis.
A 1 V CMOS digital circuits with double-gate-driven MOSFET (2002)

The double gate driven MOSFET (DGMOS) described here is built with standard CMOS technology without the use of low V/sub th/ transistors. The body of the MOSFET is dynamically connected to the gate by a capacitor. This adjusts its effective threshold voltage during operation automatically. It offers faster switching speed while having a lower static power dissipation, and is ideal for high-speed low-voltage systems. In conventional CMOS design, the body (or bulk) of the transistor is connected to the appropriate supply rail. In DGMOS, the potential of the body is determined by its operating state. This allows transistors to have a much higher drain current when turned on (effective low V/sub th/) and much lower leakage current when turned off (effective high V/sub th/) compared with the conventional fixed back gate bias configuration. This mode has the potential for high-speed operation and minimum static power dissipation.
Widely tunable femtosecond neodymium fiber laser (1995)

Continuous tuning of a mode-locked Nd3+ fiber laser over 75 nm is reported. This wide tuning range, which extends over more than twice the FWHM gain bandwidth of Nd:glass, is achieved by optimization of the reflection characteristics and the band-gap energy of the multiple-quantum-well semiconductor saturable absorber. The pulse duration achieved is 300–400 fs over the entire tuning range.
Stimulating Unconventional Reservoirs: Maximizing Network Growth while Optimizing Fracture Conductivity (2008)

Abstract Unconventional reservoirs such as gas shales and tight gas sands require technology-based solutions for optimum development. The successful exploitation of these reservoirs has relied on some combination of horizontal drilling, multi-stage completions, innovative fracturing, and fracture mapping to engineer economic completions. However, the requirements for economic production all hinge on the matrix permeability of these reservoirs, supplemented by the conductivity that can be generated in hydraulic fractures and network fracture systems. Simulations demonstrate that ultra-low shale permeabilities require an interconnected fracture network of moderate conductivity with a relatively small spacing between fractures to obtain reasonable recovery factors. Microseismic mapping demonstrates that such networks are achievable and the subsequent production from these reservoirs support both the modeling and the mapping. Tight gas sands, having orders of magnitude greater permeability than the gas shales, may be successfully depleted without inducing complex fracture networks, but other issues of damage and zonal coverage complicate recovery in these reservoirs. As with the shales, mapping has proved itself to be valuable in assessing the fracturing results.
Post-translational arginylation and intracellular proteolysis. (1991)

Cellular proteins may be designated to fast degradation by their N-terminal amino acids, and especially a N-terminal arginine residue should have an extremely destabilizing effect on cytosol proteins. We investigated the post-translational arginylation of cytosol proteins and especially of ornithine decarboxylase (ODC) by the cytosolic enzyme arginyl transferase by incubation with radioactive L-arginyl-tRNA and isolation of ODC with our monoclonal antibody. Arginylated ODC had a specific radioactivity 8600 times that of the bulk of cytosolic proteins and Edman-degradation of this ODC showed that the post-translational arginylation occurred only at the L-amino-end of the enzyme. The inhibitor of arginyltransferase, L-Glutamyl-L-Valyl-L-Phenylalanine, increased the half-life of ODC in cultured hepatocytes from 39 min to more than 90 min. This post-translational arginylation of ODC and also of other cytosol proteins is reversible. At least 25 different cytosol proteins in addition to ODC can be arginylated in hepatocytes, and at least 15 different proteins can be arginylated in Dictyostelium discoideum. The arginylated proteins are much more rapidly degraded by cellular proteinases, especially by calpains, than those cytosolic proteins which are not arginylated.