gebhart/patrepeval huggingface dataset:
Genetic differences detected by comparative genomic hybridization in head and neck squamous cell carcinomas from different tumor sites: construction of oncogenetic trees for tumor progression (2002)

For a better understanding of genetic alterations in head and neck squamous cell carcinoma (HNSCC), we applied comparative genomic hybridization (CGH) in the analysis of 75 HNSCCs, comprised of 18 pharyngeal squamous cell carcinomas (PSCCs), 23 laryngeal squamous cell carcinomas (LSCCs), and 34 oral squamous cell carcinomas (OSCCs). The three subgroups of HNSCC showed significant differences in genetic alteration patterns. Overall, PSCC and LSCC had more copy number aberrations (CNAs) per tumor than did OSCC. Apparent differing patterns of high-level amplification were also observed. The smallest recurrent chromosomal regions of high-level amplification (> or = 15% of cases) were 7q22, 8q24.1, and 11q12-13 in PSCC and 3q26.1-29 in OSCC. According to single frequency and combined frequencies of CNAs, we concluded that the most important chromosomal events for progression of head and neck cancer were +3q, +5p, +8q, and -3p for all subgroups of HNSCC; additionally, +7q, +17q, -9p, and -13q for PSCC; +7p, +9q, +11q12-13, +14q, and +17q for LSCC; and +1p and +11q12-13 for OSCC. To identify further important genetic alterations and the relationships among the alterations, we constructed oncogenetic tree models for tumor progression of HNSCC from CGH data using branching and distance-based tree models. The tree models predicted that: (1) +3q21-29 was the most important early chromosomal event, and -3p, which occurred after +3q21-29, was also an important chromosomal event for all subsites of HNSCC; (2) +8q is the second most important early chromosomal event; (3) there may be at least three subgroups of HNSCC: one characterized by -3p, -9p, +7p, and -13q; another by +5p, +9qter, and +17p; and the other by +8q and +18p. These results suggest that different chromosomal aberrations may play a role in the initiation and/or progression of different subgroups of HNSCC.
Point-of-Care Assay Platform for Quantifying Active Enzymes to Femtomolar Levels Using Measurements of Time as the Readout (2013)

This Article describes a strategy for quantifying active enzyme analytes in a paper-based device by measuring the time for a reference region in the paper to turn green relative to an assay region. The assay requires a single step by the user, yet accounts for variations in sample volume, assay temperature, humidity, and contaminants in a sample that would otherwise prevent a quantitative measurement. The assay is capable of measuring enzymes in the low to mid femtomolar range with measurement times that range from ~30 s to ~15 min (lower measurement times correspond to lower quantities of the analyte). Different targets can be selected in the assay by changing a small molecule reagent within the paper-based device, and the sensitivity and dynamic range of the assays can be tuned easily by changing the composition and quantity of a signal amplification reagent or by modifying the configuration of the paper-based microfluidic device. By tuning these parameters, limits-of-detection for assays can be adjusted over an analyte concentration range of low femtomolar to low nanomolar, with dynamic ranges for the assays of at least 1 order of magnitude. Furthermore, the assay strategy is compatible with complex fluids such as serum.
Antitumor Activity from the Combined Application of Poly(I:C) and Chemotherapeutics in Human Metastatic Pharyngeal Cell Lines (2011)

Our study showed that a combined application of the two agents already being used in tumor therapy could lower the necessary dosage of chemotherapeutics, leading to fewer side effects.
Brain-directed gene therapy for lysosomal storage disease: Going well beyond the blood– brain barrier (2002)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Beyond Necrotizing Enterocolitis Prevention: Improving Outcomes with an Exclusive Human Milk–Based Diet (2016)

Extremely premature infants who received an exclusive HUM diet had a significantly lower incidence of NEC and mortality. The HUM group also had a reduction in late-onset sepsis, BPD, and ROP. This multicenter study further emphasizes the many benefits of an exclusive HUM diet, and demonstrates multiple improved outcomes after implementation of such a feeding protocol.
“Photonic lantern” spectral filters in multi-core fibre (2012)

Fiber Bragg gratings are written across all 120 single-mode cores of a multi-core optical Fiber. The Fiber is interfaced to multimode ports by tapering it within a depressed-index glass jacket. The result is a compact multimode "photonic lantern" filter with astrophotonic applications. The tapered structure is also an effective mode scrambler.
The 2‐Aminogluconate Isomer of Rhizobium sin‐1 Lipid A Can Antagonize TNF‐α Production Induced by Enteric LPS (2005)

The naturally occurring lipopolysaccharide (LPS) from Rhizobium sin-1, a nitrogen-fixing bacterial species, can prevent the induction of the tumor necrosis factor TNF-alpha induced by enteric LPS. The proximal saccharide moiety of R. sin-1 lipid A can exist in two forms, namely as a 2-aminogluconolactone or 2-aminogluconate. As it is unknown which of these forms is responsible for the antagonistic properties of R. sin-1 lipid A, compound 4 was prepared, and its inflammatory properties were studied. This compound contains a methyl ether at the C-5 hydroxyl, which prevents lactonization and therefore is ideally suited to determine whether the 2-aminogluconate possesses antagonistic properties. Compound 4 was synthesized by a highly convergent approach with a key disaccharide building block functionalized with a set of orthogonal protecting groups. The novel synthetic compound lacks proinflammatory properties, as indicated by an absence of TNF-alpha protein production. This compound was, however, able to antagonize the production of TNF-alpha induced by enteric LPS; this indicates that the 2-aminogluconate form of R. sin-1 lipid A is responsible for its biological properties.
Affinity precipitation of enzymes (1979)

This paper describes the preparation of a bifunctional NAD compound (Bis-NAD) and its properties as a complexing/precipitating agent for the tetrameric enzyme lactate dehydrogenase (LDH).
Testosterone Pharmacokinetics after Application of an Investigational Transdermal System in Hypogonadal Men (1997)

This open-label, randomized, placebo lead-in, three-treatment crossover study in 19 hypogonadal men (27-82 years of age) evaluated dose proportionality of serum testosterone concentrations with application of one or two investigational transdermal testosterone systems for application to the arm or torso. Testosterone in vivo kinetics profiles were determined using DeMonS, a recently developed numerical deconvolution method that estimates drug absorption at different time intervals and/or drug disposition model parameters. After application of the investigational transdermal systems, the mean serum testosterone, dihydrotestosterone, estradiol, and free testosterone concentrations were elevated to normal levels. Treatment allowed approximation of the normal circadian pattern of endogenous testosterone secretion, and the increase in serum testosterone concentrations was proportional to the surface area of systems applied. The investigational transdermal system provided effective testosterone replacement therapy as judged by pharmacokinetic parameters.
Role of the major homology region of human immunodeficiency virus type 1 in virion morphogenesis (1994)

Retroviral capsid (CA) proteins contain a uniquely conserved stretch of 20 amino acids which has been named the major homology region (MHR). To examine the role of this region in human immunodeficiency virus type 1 morphogenesis and replication, four highly conserved positions in the MHR were individually altered by site-directed mutagenesis. Conservative substitution of two invariant residues (glutamine 155 and glutamic acid 159) abolished viral replication and significantly reduced the particle-forming ability of the mutant gag gene products. Conservative substitution of the third invariant residue in the MHR (arginine 167) or of an invariably aromatic residue (tyrosine 164) had only a moderate effect. However, removal of the extended side chains of these amino acids by substitution with alanine prevented viral replication and affected virion morphogenesis. The replacement of tyrosine 164 with alanine substantially impaired viral particle production. By contrast, the substitution of arginine 167 with alanine had only a two- to threefold effect on particle yield but led to the formation of aberrant core structures. The MHR mutant which were severely defective for particle production had a dominant negative effect on particle formation by the wild-type Gag product. The role of the MHR in the incorporation of the Gag-Pol precursor was examined by expressing the Gag and Gag-Pol polyproteins individually from separate plasmids. Only when the two precursor polyproteins were coexpressed did processed Gag and Pol products appear in the external medium. The appearance of these products was unaffected or only moderately affected by substitutions in the MHR of the Gag-Pol precursor, suggesting that the mutant Gag-Pol precursors were efficiently incorporated into viral particles. The results of this study indicate that specific residues within the MHR are required both for human immunodeficiency virus type 1 particle assembly and for the correct assembly of the viral core. However, mutant Gag and Gag-Pol polyproteins with substitutions in the MHR retained the ability to interact with wild-type Gag protein.
A Survey of Background Levels of Explosives and Related Compounds in the Environment* (2008)

In this paper, swabbings from various public areas in 28 different cities throughout the United States were collected. A wide variety of objects were tested, ranging from park benches and telephones to sign posts and mailboxes. Inorganic anions and cations common in low explosives were detected simultaneously using capillary zone electrophoresis. Organic high explosives including nitroaromatics, nitramines, and nitrate esters were detected using gas chromatography with a pulsed-discharge electron capture detector. Confirmation of selected results was performed by ion chromatography and negative ion chemical ionization GC/MS. In general the results provide two major conclusions: (i) with the exception of nitrate, most low explosive oxidizers are rare in the environment; (ii) no organic explosives or significant interferences to these explosives were detected.
A novel human protein of the maternal centriole is required for the final stages of cytokinesis and entry into S phase (2003)

Centrosomes nucleate microtubules and contribute to mitotic spindle organization and function. They also participate in cytokinesis and cell cycle progression in ways that are poorly understood. Here we describe a novel human protein called centriolin that localizes to the maternal centriole and functions in both cytokinesis and cell cycle progression. Centriolin silencing induces cytokinesis failure by a novel mechanism whereby cells remain interconnected by long intercellular bridges. Most cells continue to cycle, reenter mitosis, and form multicellular syncytia. Some ultimately divide or undergo apoptosis specifically during the protracted period of cytokinesis. At later times, viable cells arrest in G1/G0. The cytokinesis activity is localized to a centriolin domain that shares homology with Nud1p and Cdc11p, budding and fission yeast proteins that anchor regulatory pathways involved in progression through the late stages of mitosis. The Nud1p-like domain of centriolin binds Bub2p, another component of the budding yeast pathway. We conclude that centriolin is required for a late stage of vertebrate cytokinesis, perhaps the final cell cleavage event, and plays a role in progression into S phase.
Robust speech recognition using singular value decomposition based speech enhancement (1996)

Speech recognition systems work reasonably well in laboratory conditions, but their performance deteriorates drastically when they are deployed in practical situations where the speech is corrupted by additive noise distortion. One way to improve the performance of a speech recognition system in the presence of noise is to enhance the speech signal (and remove noise) prior to its recognition. Recently, a singular value decomposition based technique has been proposed for speech enhancement [Dendrinos et al., Speech Commun. 10, 45–57 (1991)]. In this technique, singular value decomposition was applied to an overdetermined, overextended data matrix formed from the noisy speech signal and a noise-free, low-rank approximation was obtained by retaining a specific number of singular values. This technique was applied here as a preprocessor for recognizing speech in the presence of noise and was found to improve the recognition performance significantly, especially at lower signal-to-noise ratios. [Work supported by the Australian Research Council.]
Protection of cattle and swine against foot-and-mouth disease, using biosynthetic peptide vaccines (1990)

A single dose of foot-and-mouth disease (FMD) virus protein 1 (VP1) peptide, expressed in Escherichia coli as a fusion protein with 190 amino acids (AA) of the LE' protein of the tryptophan operon of E coli, elicited an immune response in steers sufficient to withstand the challenge of exposure to animals with acute FMD. The 58-micrograms dose of viral peptide, composed of a segment of the VP1 from the A12 strain (A12) of FMD virus (FMDV; A12-32dimer) in a tandem repeat configuration of AA137 through 168 and emulsified with oil adjuvant, elicited a serologic response in cattle equivalent to that obtained using conventional whole virus vaccines. Two groups of swine were vaccinated, 1 with the A12-32dimer as used in cattle and 1 with AA131 through 157 from VP1 of the A24 strain (A24) of FMDV (A24-peptide), expressed in the same system as A12-32dimer, but as a single copy per molecule. In swine, the 58-micrograms dose of the A12-32dimer repeated at 28 days was an effective immunogen; all swine were protected against A12 and, in addition, the vaccine protected 50% of the swine against A24. The 29-micrograms dose of A24-peptide, administered according to the same schedule, elicited protection against A24 in 50% of the vaccinates and, in addition, protected 25% of those vaccinates against A12. The serologic response elicited by A12-32dimer against A24 virus was considerably greater than the response elicited by A24-peptide against A12 virus. The evidence of multiple immunogenic epitopes between AA131 and AA168 was evaluated.
Persistence of Porcine Reproductive and Respiratory Syndrome Virus in Serum and Semen of Adult Boars (1995)

Four seronegative adult boars were intranasally inoculated with porcine reproductive and respiratory syndrome virus (PRRSV) isolate VR-2332. Serum and semen were collected 2-3 times weekly for over 100 days postinoculation (DPI). Serum samples were assayed for PRRSV by virus isolation (VI) and a polymerase chain reaction (PCR) and screened for antibodies to PRRSV using the indirect fluorescent antibody (IFA) and virus neutralization (VN) tests. Semen was assayed for PRRSV RNA by PCR. Virus and viral RNA was detected in the serum of all boars within 1 DPI by Vi and/or PCR. However, VI results indicated that viremia was transient and occurred from 1 to 9 DPI. Viral RNA was detected in serum from 1 to 31 DPI. In the acute stage of the infection, PRRSV RNA was detected in serum by PCR prior to the presence of viral RNA in semen. The PRRSV RNA was detected in semen as early as 3 DPI and persisted for 25 DPI in 2 of the boars and 56 and 92 DPI in the remaining 2 boars. Detection of PRRSV RNA in semen occurred 2-8 and 28-35 days prior to the detection of antibodies by IFA and VN, respectively. PRRSV was isolated from the bulbourethral gland of the boar that shed viral RNA in semen for 92 DPI. These results suggest that PRRSV RNA can be detected by PCR in boar serum and semen, and may persist for variable periods of time. Viremia and the serologic status of the boar are not adequate indicators of when PRRSV or PRRSV RNA is being shed in the semen. Preliminary findings also indicated that neither shipping stress nor reinoculation with homologous PRRSV resulted in viremia or viral RNA shedding in semen.
The clinical significance of epidermal growth factor receptor (EGF-R) in human breast cancer: a review on 5232 patients (1992)

I. Introduction II.Analytical Review Method III.Results A. EGF-R measurement and positivity B. Relationship with other prognostic factors 1. Relationship with steroid receptor status 2. Relationship with age or menopausal status 3. Relationship with tumor size 4. Relationship with lymph node status and recurrences 5. Relationship with histology 6. Relationship with tumor differentiation and grade 7. Relationship with tumor ploidy 8. Relationship with parameters for cellular proliferation 9. Relationship with oncogenes 10.Relationship with other growth factor or peptide hormone receptors 11.Relationship with membrane-bound tissue plasminogen activator C. Relationship with prognosis and survival 1. Relationship with relapse-free and overall survival 2. Relationship with response to endocrine and chemotherapy IV.Summary V.
Nine digital filters for decimation and interpolation (1977)

Filtering is necessary in decimation (decreasing the sampling rate of) or interpolation (increasing the sampling rate of a digital signal. If the rate change is substantial, the process is more efficient when the decimation or interpolation occurs in stages rather than in one step. Half-band filters are particularly efficient for effecting octave changes in sampling rate and nine digital filters are presented, eight of them half-band filters, to be used as components of multistage interpolators and decimators. Also presented is a procedure for combining the filters to produce multistage designs that meet a very wide range of accuracy requirements (stopband attenuation to 77 dB, passband ripple as low as 0.00014). The nine filters admit changes between sampling rates above 4W, where W is the nominal bandwidth of the signal. Established design techniques may be used to obtain efficient filters for conversion between 4W Hz sampling and 2W Hz, the "baseband sampling rate." With these multistage filters, the possible interpolation and decimation ratios are all integer multiples of powers of two. To overcome this restriction we present a simple resampling technique that extends the range of designs to conversions between any two rates. The interpolation or decimation ratio need not be an integer or even rational. In fact, it can vary slightly as in a practical situation where the input signal and output signal are under the control of autonomous clocks. We demonstrate the approach by means of several design examples and compare its results with those obtained from the optimization scheme of Crochiere and Rabiner.
Antibacterial activity of human natural killer cells. (1989)

The in vitro effects of human NK cells on viability of Gram-negative and Gram-positive bacteria was investigated. PBLs depleted of glass-adherent cells showed a significant antibacterial activity that was increased as the concentration of NK cells became higher. Leu-11-enriched cells exhibited the most efficient bactericidal activity. Stimulation of NK cells with staphylococcal enterotoxin B for 16 h produced a significant increase in the antibacterial activity of all NK cells tested. The antibacterial activity of monocyte-depleted cells and Leu-11-enriched cells was also enhanced after culturing in vitro for 16-24 h without exogenous cytokines. Dependence of the antibacterial activity on the presence of serum in the culture medium was not found. Ultrastructural studies revealed close contact between NK cell membranes and bacteria, no evidence of phagocytosis, and extracellular bacterial ghosts, after incubation at 37 degrees C. Supernatants from purified NK cells exhibited potent bactericidal activity with kinetics and target specificity similar to that of effector cells. These results document the potent antibacterial activity of purified NK cells and suggest an extracellular mechanism of killing.
TETRACYCLINE1 (1953)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTETRACYCLINE1J. H. Boothe, J. Morton II, J. P. Petisi, R. G. Wilkinson, and J. H. WilliamsCite this: J. Am. Chem. Soc. 1953, 75, 18, 4621Publication Date (Print):September 1, 1953Publication History Published online1 May 2002Published inissue 1 September 1953https://pubs.acs.org/doi/10.1021/ja01114a535https://doi.org/10.1021/ja01114a535research-articleACS PublicationsRequest reuse permissionsArticle Views297Altmetric-Citations70LEARN 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
A randomized, double‐blind, placebo‐controlled trial of tegaserod in female patients suffering from irritable bowel syndrome with constipation (2002)

Tegaserod, 6 mg b.d., produced rapid and sustained improvement of symptoms in female irritable bowel syndrome patients and was well tolerated.
Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 (2016)

By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at large computational costs, which has introduced a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow. Both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated well over two orders-of-magnitude on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hardware, and we show that the use of single precision arithmetic does not adversely affect results. This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation.
Unordered error-correcting codes and their applications (2003)

The authors give efficient constructions for error correcting unordered codes, i.e., codes such that any two codewords are at a certain minimal distance apart and at the same time they are unordered. They present three constructions together with tables that compare their efficiencies. These codes are used for detecting a predetermined number of symmetric errors and for detecting all unidirectional errors. An application to parallel asynchronous communications is included.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>