gebhart/patrepeval huggingface dataset:
Protein Side-Chain Translocation Mutagenesis via Incorporation of Peptoid Residues (2011)

For the last few decades, chemistry has played an important role in protein engineering by providing a variety of synthetic tools such as chemoselective side-chain modifications, chemical conjugation, incorporation of non-natural amino acids, and the development of protein-mimetic heteropolymers. Here we study protein backbone engineering in order to better understand the molecular mechanism of protein function and to introduce protease stable, non-natural residues into a protein structure. Using a combination of genetic engineering and chemical synthesis, we were able to introduce peptoid residues (N-substituted glycine residues) at defined positions into bovine pancreatic ribonuclease A. This results in a side-chain translocation from the Cα carbon to the neighboring backbone nitrogen atom. To generate these peptoid substitutions, we removed the N-terminal S-peptide of the protein by proteolysis and chemically conjugated synthetic peptide-peptoid hybrids to the new N-terminus. A triple peptoid mutant containing a catalytic His12 peptoid mutation was active with a k(cat)/K(m) value of 1.0 × 10(4) M(-1) s(-1). This k(cat)/K(m) value is only 10-fold lower than the control wild-type conjugate and comparable in magnitude to many other natural enzymes. The peptoid mutations increased the chain flexibility at the site of peptoid substitution and at its C-terminal neighboring residue. Our ability to translocate side chains by one atom along the proten backbone advances a synthetic mutagenesis tool and opens up a new level of protein engineering.
Combined live measles-mumps virus vaccine. (1973)

Combined live measles-mumps virus vaccine.Four lots of combined bivalent live Moraten measles-Jeryl Lynn mumps virus vaccine were administered to a total of 334 children 10 months to 6 years of age, who were initially without antibody against either virus.Overall, 99 % of the children responded serologically to the measles virus and 96 % to mumps.The geometric mean titres were of the same general height as those obtained when the individual vaccines were given alone, and there was no indication of immunological suppression.There was no increase in clinical reaction beyond the mild fever and other reactions that follow the administration of Moraten measles vaccine given alone.The combined measles-mumps vaccine provides a simple means for immunization against both these viruses with no apparent alteration in the immunological or clinical responses.The need to simplify administration, reduce costs, and minimize the number of contacts of patient with physician has prompted the development of combined single dose formulations of vaccines.Reports from our laboratories have described the development and clinical evaluation of combined measles-mumps-rubella (M-M-R) (Stokes et al., 1971), measles-rubella (M-R-Vax) (Villarejos et al., 1971), and mumps-rubella (Biavax) (Weibel et al., 1971) vaccines.All gave antibody responses equivalent to those obtained when the vaccines were given individually and there was no increase in clinical reaction.All are being used extensively in the U.S.A. and elsewhere.This report presents the findings in tests to evaluate clinically a new combined live measles-mumps vaccine called M-M-Vax. MethodsDesign of the clinical studies.Three clinical studies were carried out.The first was a pilot study of a laboratory-prepared lot of measles-mumps vaccine (lot 284) tested in 53 children who had no antibody initially either to measles or to mumps virus.Similar groups of children were given either monovalent measles (27 children) (Attenuvax) or mumps virus vaccine (42
Modeling the Early Events of Severe Acute Respiratory Syndrome Coronavirus Infection In Vitro (2006)

The clinical picture of severe acute respiratory syndrome (SARS) is characterized by pulmonary inflammation and respiratory failure, resembling that of acute respiratory distress syndrome. However, the events that lead to the recruitment of leukocytes are poorly understood. To study the cellular response in the acute phase of SARS coronavirus (SARS-CoV)-host cell interaction, we investigated the induction of chemokines, adhesion molecules, and DC-SIGN (dendritic cell-specific ICAM-3-grabbing nonintegrin) by SARS-CoV. Immunohistochemistry revealed neutrophil, macrophage, and CD8 T-cell infiltration in the lung autopsy of a SARS patient who died during the acute phase of illness. Additionally, pneumocytes and macrophages in the patient's lung expressed P-selectin and DC-SIGN. In in vitro study, we showed that the A549 and THP-1 cell lines were susceptible to SARS-CoV. A549 cells produced CCL2/monocyte chemoattractant protein 1 (MCP-1) and CXCL8/interleukin-8 (IL-8) after interaction with SARS-CoV and expressed P-selectin and VCAM-1. Moreover, SARS-CoV induced THP-1 cells to express CCL2/MCP-1, CXCL8/IL-8, CCL3/MIP-1alpha, CXCL10/IP-10, CCL4/MIP-1beta, and CCL5/RANTES, which attracted neutrophils, monocytes, and activated T cells in a chemotaxis assay. We also demonstrated that DC-SIGN was inducible in THP-1 as well as A549 cells after SARS-CoV infection. Our in vitro experiments modeling infection in humans together with the study of a lung biopsy of a patient who died during the early phase of infection demonstrated that SARS-CoV, through a dynamic interaction with lung epithelial cells and monocytic cells, creates an environment conducive for immune cell migration and accumulation that eventually leads to lung injury.
Lymph draining from foot joints in rheumatoid arthritis provides insight into local cytokine and chemokine production and transport to lymph nodes (2001)

High lymph concentrations of cyto kines and chemokines, exceeding those in serum, were found in RA patients. The L:S concentration ratios of > 1 indicate the local production of these cytokines and chemokines in the inflamed tissues. High flow rates of lymph containing high cytokine concentrations through the regional lymph nodes are likely to affect node lymphocytes and dendritic cells. Analysis of cytokines in lymph should provide insight into events in inflamed tissues in RA and in regional lymph nodes.
Two-dimensional numerical simulation of radio frequency sputter amorphous In–Ga–Zn–O thin-film transistors (2009)

We reported on a two-dimensional simulation of electrical properties of the radio frequency (rf) sputter amorphous In–Ga–Zn–O (a-IGZO) thin-film transistors (TFTs). The a-IGZO TFT used in this work has the following performance: field-effect mobility (μeff) of ∼12 cm2/V s, threshold voltage (Vth) of ∼1.15 V, subthreshold swing (S) of ∼0.13 V/dec, and on/off ratio over 1010. To accurately simulate the measured transistor electrical properties, the density-of-states model is developed. The donorlike states are also proposed to be associated with the oxygen vacancy in a-IGZO. The experimental and calculated results show that the rf sputter a-IGZO TFT has a very sharp conduction band-tail slope distribution (Ea=13 meV) and Ti ohmic-like source/drain contacts with a specific contact resistance lower than 2.7×10−3 Ω cm2.
Nonpolar III-nitride vertical-cavity surface emitting lasers with a polarization ratio of 100% fabricated using photoelectrochemical etching (2014)

Photoelectrochemical (PEC) band gap selective undercut etching is discussed as an alternative technique to chemical-mechanical polishing and laser-lift off for substrate removal for III-nitride vertical-cavity surface-emitting lasers (VCSELs). A top-down PEC etch is also described, which offers the ability to epitaxially define an etch-stop layer, thereby achieving a high degree of cavity length control. The temperature-dependent lasing characteristics of m-plane VCSELs fabricated using PEC etching techniques are analyzed. Measurements of multiple VCSELs from the same wafer yielded lasing emission polarized along the a-direction with a polarization ratio of 100%, indicating that the entire array was uniformly polarized.
Modulation of experimental autoimmunity: treatment of adjuvant arthritis by immunization with a recombinant vaccinia virus (1991)

Live recombinant vaccinia viruses, expressing antigens from pathogenic microorganisms, are studied for their use as vaccines designed for the protection against infectious diseases. Infections with these vaccinia virus recombinants, expressing proteins or epitopes from viruses, parasites, or bacteria, have resulted in the development of specific neutralizing antibodies or cytotoxic T lymphocytes. Here, we describe the generation of a recombinant vaccinia virus expressing the mycobacterial 65-kDa heat shock protein (HSP65). A vaccinia recombinant virus was constructed by placing the gene for the Mycobacterium bovis BCG HSP65 under control of a vaccinia virus promoter and inserting this mycobacterial gene in the thymidine kinase locus of the vaccinia virus genome. Mycobacterial HSP65 is a critical antigen in the autoimmune model of adjuvant arthritis induced in Lewis rats by the immunization with Mycobacterium tuberculosis. We report the induction of immunity directed to this mycobacterial HSP65 by testing for the presence of specific antibodies and T-cell proliferation. Furthermore, induction of such immunity resulted in a reduction of arthritis severity when given to rats before or, even more interestingly, during development of arthritis. Disease reduction was not found after administration of HSP65 in the absence of vaccinia virus as a vector when given during arthritis development. Therefore, recombinant vaccinia virus may offer new prospectives for specific intervention in autoimmunity.
Molecular cloning of a candidate tumor suppressor gene, DLC1, from chromosome 3p21.3. (1999)

The short arm of chromosome 3 is thought to contain multiple tumor suppressor genes, because one copy of this chromosomal arm frequently is missing in carcinomas that have arisen in a variety of tissues. We have isolated a novel gene encoding a 1755-amino acid polypeptide, through large-scale sequencing of genomic DNA at 3p21.3. Mutational analysis of this gene by reverse transcription-PCR revealed the lack of functional transcripts and an increase of nonfunctional RNA transcripts in a significant proportion (33%) of cancer cell lines and primary cancers (4 of 14 esophageal cancer cell lines, 2 of 2 renal cancer cell lines, 11 of 30 primary non-small cell lung cancers, and 3 of 10 primary squamous cell carcinomas of the esophagus). However, no alterations of the gene itself were detected in any of the cancers examined. Introduction of the cDNA significantly suppressed the growth of four different cancer cell lines, two of which produced no normal transcript on their own. No such effect occurred when antisense cDNA, cDNA corresponding to an aberrant transcript, or the vector DNA alone were transfected. These data suggest that aberrant transcription of this gene, designated DLC1 (deleted in lung cancer 1), may be involved in carcinogenesis of the lung, esophagus, and kidney.
Playout buffer and rate optimization for streaming over IEEE 802.11 wireless networks (2009)

Most streaming rate selection and buffer optimization algorithms are developed for wired networks and can perform poorly over wireless networks. Wireless MAC layer behavior, such as rate adaptation, retransmissions, and medium sharing, can significantly degrade the effectiveness of current streaming algorithms. This article presents the Buffer and Rate Optimization for Streaming (BROS) algorithm to improve streaming performance. BROS uses a bandwidth estimation tool designed specifically for wireless networks and models the relationship between buffer size, streaming data rate, and available bandwidth distribution. BROS optimizes the streaming data rate and initial buffer size, resulting in a high data rate but with few frame losses and buffer underflow events, while still keeping a small initial buffer delay. BROS is implemented in the Emulated Streaming (EmuS) client-server system and evaluated on an IEEE 802.11 wireless testbed with various wireless conditions. The evaluation shows that BROS can effectively optimize the streaming rate and initial buffer size based on wireless network bandwidth conditions, thus achieving better performance than static rate or buffer selection and jitter removal buffers.
Prolonged Occurrence of Cocaine In Human Saliva and Urine after Chronic Use (1989)

Cocaine was detected by immunoassay in saliva and urine of chronic cocaine addicts for 5-10 days during abstinence. Confirmation by a less sensitive but highly specific GC/MS assay of unmetabolized cocaine was successful in saliva through the first 24 h of collection and for the initial 4-5 days in urine. Cocaine saliva concentrations and subject scores for cocaine craving and depression declined during this time and correlated significantly. The presence of unmetabolized cocaine in these biofluids long after the last drug administration suggests that multiple dosing and high exposure to cocaine in man leads to accumulation in deep body compartments and subsequent slow release back into circulation and eventual excretion. The prolonged presence of cocaine in saliva and urine may have implications in testing for cocaine use and in treatment of cocaine withdrawal.
Carboxypeptidase U, a plasma carboxypeptidase with high affinity for plasminogen. (1994)

A novel basic carboxypeptidase clearly different from carboxypeptidase N has been isolated from human plasma. It circulates as an enzymatically inactive precursor enzyme bound to plasminogen. During fibrinolysis, it can be converted to its active form, carboxypeptidase U, through the action of plasmin. The active enzyme has an apparent molecular weight of 53,000 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. It hydrolyzes the synthetic peptides hippuryl-L-arginine and hippuryl-L-lysine but, in contrast to other human basic carboxypeptidases, has only a limited esterase activity. After its activation, carboxypeptidase U tends to be very unstable.
Neuronal activity recorded extracellularly in chronically decentralized in situ canine middle cervical ganglia (1986)

In chronically decentralized in situ middle cervical ganglia of 10 dogs, 279 spontaneously active neurons were identified. One hundred and ten (39%) of these were spontaneously active during specific phases of the cardiac cycle, primarily during systole, and the activity of nearly half of these cardiovascular-related neurons was modified by gentle mechanical distortion of the vena cavae, heart, or thoracic aorta. Another 60 (22%) of the identified neurons had respiratory--related activity, but the activity of only 2 of them was modified by gentle mechanical distortion of pulmonary tissue. Twenty-nine of the other 109 identified neurons were activated by gentle mechanical distortion of localized regions of the neck, ventral thoracic wall, or ventral abdominal wall. Because of the presence of activity in the chronically decentralized middle cervical ganglion, these data infer that some afferent neurons are located in the thoracic autonomic nervous system. Some middle cervical ganglion neurons were activated by single 1-4 ms stimuli delivered to a nerve connected to the ganglion. During repetitive stimuli delivered at 0.5 Hz none were activated after a fixed latency following the stimuli. Many more neurons were activated by 10- to 200-ms trains of 1-4 ms stimuli delivered with interstimulus intervals of 1-10 ms. The majority of these neurons could still be activated electrically after the administration of cholinergic and adrenergic pharmacological blocking agents.(ABSTRACT TRUNCATED AT 250 WORDS)
High-performance liquid chromatographic analysis of anticarcinogenic indoles in Brassica oleracea (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHigh-performance liquid chromatographic analysis of anticarcinogenic indoles in Brassica oleraceaChristopher A. Bradfield and Leonard F. BjeldanesCite this: J. Agric. Food Chem. 1987, 35, 1, 46–49Publication Date (Print):January 1, 1987Publication History Published online1 May 2002Published inissue 1 January 1987https://pubs.acs.org/doi/10.1021/jf00073a010https://doi.org/10.1021/jf00073a010research-articleACS PublicationsRequest reuse permissionsArticle Views259Altmetric-Citations68LEARN 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-Alertsclose Get e-Alerts
Ultrafast near edge X-ray absorption measurement of the insulator-to-metal transition in VO2 (2004)

We measure the insulator-to-metal transition in VO2 using time-resolved Near-Edge X-ray Absorption. Picosecond pulses of synchrotron radiation are used to detect the red-shift in the Vanadium L3 edge at 516 eV, associated with bandgap collapse.
New Pediatric Model of Ischemic Stroke in Infant Piglets by Photothrombosis (2007)

Ischemic stroke can be produced in infant piglets by middle cerebral artery photothrombosis. The stroke involved both gray and white matter and exhibited a robust inflammatory component. The mean infarct volume determined histopathologically amounted to 9.6+/-2.4% of the affected (ipsilateral) hemisphere, which was correlated well with the mass equivalent of tissue (12.0+/-3.5%), in which severe declines in regional cerebral blood flow were observed at 4 hours.
Performance of honey bee (Apis mellifera) queens reared in beeswax cells impregnated with coumaphos (2004)

SUMMARYThe sublethal effects of coumaphos on developing queens were investigated. Young honey bee larvae were transferred into beeswax cups containing known concentrations (0 to 1000 mg/kg) of coumaphos. The cups with larvae were placed in queenless colonies for rearing and 10 days later acceptance was determined by recording mature queen cells. The queen cells were placed in small mating colonies for 21 days, when the queens were collected after being rated for commercial acceptability. The queens were then either introduced to production colonies and monitored for six months or dissected to determine mating success. All but one queen failed to develop at 1000 mg/kg of coumaphos, and greater than 50% of cells were rejected at 100 mg/kg coumaphos. The queens that were reared were lighter in weight as pre-emergence pupae. The effects on other characters related to queen performance are discussed. The presence of coumaphos in queen rearing cells can reduce the number of queens still functioning in colonies at six months by as much as 75%.Keywords: mating successsperm concentrationsupercedurecoumaphosresiduesqueen rearingmiticide
Fabrication of piezoresistive nanocantilevers for ultra-sensitive force detection (2008)

This paper presents the design, fabrication and characterization method of piezoresistive nanocantilevers for ultra-sensitive force detection application. A shallow boron-doped layer as thin as 40 nm is achieved using spin-on diffusion. The piezoresistive nanocantilevers are patterned by electron beam (EB) lithography and fast atom beam (FAB) etching. The resonance response of the nanocantilevers is characterized by both optical readout using a laser Doppler vibrometer and piezoresistive self-detection. A soft spring effect is detected in the nanocantilevers.
Synthesis of Urea-Based Inhibitors as Active Site Probes of Glutamate Carboxypeptidase II:  Efficacy as Analgesic Agents (2004)

The neuropeptidase glutamate carboxypeptidase II (GCPII) hydrolyzes N-acetyl-L-aspartyl-L-glutamate (NAAG) to liberate N-acetylaspartate and glutamate. GCPII was originally cloned as PSMA, an M(r) 100,000 type II transmembrane glycoprotein highly expressed in prostate tissues. PSMA/GCPII is located on the short arm of chromosome 11 and functions as both a folate hydrolase and a neuropeptidase. Inhibition of brain GCPII may have therapeutic potential in the treatment of certain disease states arising from pathologically overactivated glutamate receptors. Recently, we reported that certain urea-based structures act as potent inhibitors of GCPII (J. Med. Chem. 2001, 44, 298). However, many of the potent GCPII inhibitors prepared to date are highly polar compounds and therefore do not readily penetrate the blood-brain barrier. Herein, we elaborate on the synthesis of a series of potent, urea-based GCPII inhibitors from the lead compound 3 and provide assay data for these ligands against human GCPII. Moreover, we provide data revealing the ability of one of these compounds, namely, 8d, to reduce the perception of inflammatory pain. Within the present series, the gamma-tetrazole bearing glutamate isostere 7d is the most potent inhibitor with a K(i) of 0.9 nM. The biological evaluation of these compounds revealed that the active site of GCPII likely comprises two regions, namely, the pharmacophore subpocket and the nonpharmacophore subpocket. The pharmacophore subpocket is very sensitive to structural changes, and thus, it appears important to keep one of the glutamic acid moieties intact to maintain the potency of the GCPII inhibitors. The site encompassing the nonpharmacophore subpocket that binds to glutamate's alpha-carboxyl group is sensitive to structural change, as shown by compounds 6b and 7b. However, the other region of the nonpharmacophore subpocket can accommodate both hydrophobic and hydrophilic groups. Thus, an aromatic ring can be introduced to the inhibitor, as in 8b and 8d, thereby increasing its hydrophobicity and thus potentially its ability to cross the blood-brain barrier. Intrathecally administered 8d significantly reduced pain perception in the formalin model of rat sensory nerve injury. A maximal dose of morphine (10 mg) applied in the same experimental paradigm provided no significant increase in analgesia in comparison to 8d during phase 1 of this pain study and modestly greater analgesia than 8d in phase 2. These urea-based inhibitors of GCPII thus offer a novel approach to pain management.
Variable time-scale modification of speech using transient information (2002)

Conventional time-scale modification methods have the problem that as the modification rate gets higher the time-scale modified speech signal becomes less intelligible, because they ignore the effect of articulation rate on speech characteristics. We propose a variable time-scale modification method based on the knowledge that the timing information of transient portions of a speech signal plays an important role in speech perception. After identifying transient and steady portions of a speech signal, the proposed method gets the target rate by modifying steady portions only. The result of subjective preference test indicates that the proposed method produces performance superior to that of the conventional SOLA method.