gebhart/patrepeval huggingface dataset:
Biology of Prostate-Specific Antigen (2003)

Prostate-specific antigen (PSA) is an androgen-regulated serine protease produced by both prostate epithelial cells and prostate cancer (PCa) and is the most commonly used serum marker for cancer. It is a member of the tissue kallikrein family, some of the members of which are also prostate specific. PSA is a major protein in semen, where its function is to cleave semenogelins in the seminal coagulum. PSA is secreted into prostatic ducts as an inactive 244-amino acid proenzyme (proPSA) that is activated by cleavage of seven N-terminal amino acids. PSA that enters the circulation intact is rapidly bound by protease inhibitors, primarily alpha1-antichymotrypsin, although a fraction is inactivated in the lumen by proteolysis and circulates as free PSA. This proteolytic inactivation, as well as the cleavage of proPSA to PSA, is less efficient in PCa. Serum total PSA levels are increased in PCa, and PSA screening has dramatically altered PCa presentation and management. Unfortunately, although high PSA levels are predictive of advanced PCa, a large fraction of organ-confined cancers present with much lower total PSA values that overlap those levels found in men without PCa. Measurement of free versus total PSA can increase specificity for PCa, and tests under development to measure forms of proPSA may further enhance the ability to detect early-stage PCa. PSA is also widely used to monitor responses to therapy and is under investigation as a therapeutic target. Finally, recent data indicate that there may be additional roles for PSA in the pathogenesis of PCa.
A New Bidirectionally Motion-Compensated Orthogonal Transform for Video Coding (2007)

Motion-compensated lifted wavelets have received much interest for video compression. While they are biorthogonal, they may substantially deviate from orthonormality due to motion compensation, even if based on an orthogonal or near-orthogonal wavelet. A temporal transform for video sequences that maintains orthonormality while permitting flexible motion compensation would be very desirable. We have recently introduced such a transform for unidirectional motion compensation from one previous frame. In this paper, we extend this idea to bidirectional motion compensation. Orthonormality is maintained for arbitrary integer-pixel motion compensation by cascading a sequence of incremental orthogonal 3×3 transforms. The energy of three input pictures is accumulated in two temporal low-bands while the temporal high-band is zero if the input pictures are identical after motion compensation. Further, the motion-compensated orthogonal transforms can be cascaded to build a dyadic wavelet decomposition. The new bidirectionally motion-compensated orthogonal transform compares favorably with the lifted 5/3 wavelet in video coding experiments with integer-pixel motion compensation.
Effect of Warm Compress Therapy From Hard-Boiled Eggs on Corneal Shape (2007)

Because it is difficult to standardize the pressing force, it is recommended to place the hard-boiled egg close to, but not touching, the eyelid during warm compress therapy. The temperature rise from this treatment protocol should be large enough to melt the meibomian gland secretions without distorting the corneal shape.
Novel Blue Electroluminescent Polymers with Well-Defined Conjugation Length (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNovel Blue Electroluminescent Polymers with Well-Defined Conjugation LengthTaehyoung Zyung, Do-Hoon Hwang, In-Nam Kang, Hong-Ku Shim, Wol-Yon Hwang, and Jang-Joo KimCite this: Chem. Mater. 1995, 7, 8, 1499–1503Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://pubs.acs.org/doi/10.1021/cm00056a015https://doi.org/10.1021/cm00056a015research-articleACS PublicationsRequest reuse permissionsArticle Views246Altmetric-Citations96LEARN 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
Prebiotic stimulation of human colonic butyrate-producing bacteria and bifidobacteria,in vitro (2013)

Dietary macronutrients affect the composition of the gut microbiota, and prebiotics are used to improve and maintain a healthy gut. The impact of prebiotics on dominant gut bacteria other than bifidobacteria, however, is under-researched. Here, we report carbohydrate utilisation patterns for representative butyrate-producing anaerobes, belonging to the Gram-positive Firmicutes families Lachnospiraceae and Ruminococcaceae, by comparison with selected Bacteroides and Bifidobacterium species. Growth assessments using anaerobic Hungate tubes and a new rapid microtitre plate assay were generally in good agreement. The Bacteroides strains tested showed some growth on basal medium with no added carbohydrates, utilising peptides in the growth medium. The butyrate-producing strains exhibited different growth profiles on the substrates, which included starch, inulin, fructooligosaccharides (FOS), galactooligosaccharides (GOS) and xylooligosaccharides (XOS). Eleven were able to grow on short-chain FOS, but this number decreased as the chain length of the fructan substrates increased. Long-chain inulin was utilised by Roseburia inulinivorans, but by none of the Bifidobacterium species examined here. XOS was a more selective growth substrate than FOS, with only six of the 11 Firmicutes strains able to use XOS for growth. These results illustrate the selectivity of different prebiotics and help to explain why some are butyrogenic.
Abstract 2384: TAK-169, an exceptionally potent CD38 targeted engineered toxin body, as a novel direct cell kill approach for the treatment of multiple myeloma (2019)

Abstract Advances in the treatment of multiple myeloma have been driven by the development of new modalities, including proteasome inhibitors, immunomodulatory agents and monoclonal antibodies. TAK-169 is an engineered toxin body (ETB) comprising a proprietarily engineered, deimmunized form of the ribosome inactivating Shiga-like toxin A-subunit (SLTA) genetically fused to an antibody fragment that specifically targets the CD38 cell surface receptor. Although CD38 is a poorly internalizing receptor, TAK-169 is able to efficiently internalize and directly kill CD38-expressing cells through the enzymatic and irreversible inhibition of protein synthesis. This novel mechanism of action may be relevant in patients who have progressed after or are unlikely to respond to CD38-targeted antibody therapy. A library of unique CD38-targeting antibodies fused to deimmunized SLTA was screened in a variety of efficacy and safety models to identify TAK-169. TAK-169 demonstrated potent cytotoxicity across a range of myeloma cell lines with a range of CD38 expression in vitro as well as in patient-derived samples including with previous exposure to daratumumab. TAK-169 retains activity in whole blood and PBMCs, indicating that the presence of red blood cells is not restrictive to cytotoxicity. Furthermore, TAK-169 retains activity in the presence of excess approved, CD38 targeted therapeutic daratumumab. TAK-169 is efficacious in several myeloma xenograft models, both subcutaneous and disseminated. Complete regressions were observed using both a once-weekly and bi-weekly schedule. In addition, a syngeneic model cell line expressing human CD38 was shown to be responsive to TAK-169 treatment in an immunocompetent mouse model, suggesting the possibility of immune mediated cell death induced by TAK-169. Tolerability studies in non-human primates demonstrate that repeat administration is tolerated at doses expected to be efficacious. Takeda Pharmaceuticals and Molecular Templates jointly discovered TAK-169 and are co-developing the molecule for the treatment of multiple myeloma. TAK-169 is expected to enter clinical studies in 2019. Citation Format: Erin K. Willert, Garrett L. Robinson, Jack P. Higgins, Jensing Liu, Janice Lee, Sakeena Syed, Yuhong Zhang, Dan Tavares, Anya Lublinsky, Nibedita Chattopadhyay, Haiqing Wang, Laura Packer, Pu Shi, Carole Harbison, Sanjay Patel, John Newcomb. TAK-169, an exceptionally potent CD38 targeted engineered toxin body, as a novel direct cell kill approach for the treatment of multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2384.
Hyaluronic acid combined with mannitol to improve protection against free-radical endothelial damage: Experimental Model (2005)

All of the OVDs tested efficiently reduced endothelial lesions against free radicals compared with the control group in which no OVD was used. The following sequence for the efficacy of endothelial cell protection was established: Visiol>Viscoat>Healon>no OVD.
Chaos theory and first-order ray tracing in ducts (1998)

The author highlights the importance of chaos theory to high frequency electromagnetic scattering problems and provides a novel method for presenting first-order ray theory related to the compound deviation matrix. This is applied to straight ducts of general cross-section and the average rate of reduction of ray intensity is related to the Lyapunov exponent. This allows estimates to be formed on the maximum duct length and incidence angle over which deterministic predictions are possible.
Tolerance of Pseudomonas aeruginosa to killing by ciprofloxatin, gentamicin and imipenem in vitro and in vivo (1988)

In the rat croton oil pouch model, treatment with ciprofloxacin, gentamicin or imipenem caused a sharp reduction in the numbers of Pseudomonas aeruginosa when applied 24 h after infection but treatment had little or no effect when delayed until 48 h after infection. Surviving bacteria from treated animals were fully susceptible on subculture in vitro. Between 24 h and 48 h after infection there was an increase in the concentration of magnesium and a decrease in the concentration of oxygen but no significant change in the pH of the pouch fluid. In-vitro, the MBC of gentamicin was increased four-fold by the addition of magnesium ions and eight-fold under anaerobic conditions whereas these variables had no significant effect upon the MBC of ciprofloxacin and imipenem. However, cells of P. aeruginosa incubated in batch culture for 4, 24 and 48 h became progressively more tolerant to killing by all three drugs. We conclude that the tolerance of P. aeruginosa in vivo was only partly explained by biochemical changes at the site of infection. The stationary growth phase was associated with progressive tolerance to killing by ciprofloxacin, gentamicin and imipenem both in vivo and in vitro.
CRC Desk Reference for Allergy and Asthma (2000)

As the prevalence of allergic diseases and asthma has increased in recent years, scientists have intensified research efforts to understand the pathogenesis of these sometimes debilitating conditions. Indeed, researchers have provided key insights-and new concepts-that have changed therapeutic strategies. Moreover, allergic inflammation has served
Copper-Free Huisgen 1,3-Dipolar Cycloaddition to 3-Benzotriazolo-3-Deoxy-β-D-Galactopyranosides – Cyclization of a Secondary Azide and Benzyne (2010)

Methyl 2-O-acetyl-3-benzotriazolo-4,6-O-benzylidene-3-deoxy- β -D-galactopyranoside was assembled by reacting benzyne, from 2-trimethylsilyl-trifluoromethansulfonylbenzene, and a secondary galactopyranoside azide in a copper-free Huisgen 1,3-dipolar cycloaddition. Following deprotection, the resulting benzotriazoles were evaluated as galectin inhibitors resulting in a 2-4 fold increase in affinity against galectin-1, -2 and -4 N-terminus compared to the parent methyl galactoside.
Structural Studies of Trimethoxysilane Containing R′R″Im<SUP>+</SUP>I<SUP>−</SUP> Ionic Liquid and its Nanocomposite with Tetramethoxysilane (TMOS) (2006)

A dialkylsubstituted imidazolium iodide ionic liquid (1-methyl-3-[3-(trimethoxy-lambda4-silyl)propyl]imida-zolium iodide, MTMSPIm+I-) was prepared with the intention of using it as a quasi-solid-state electrolyte for dye-sensitized photoelectrochemical (DSPEC) cells of Grätzel design, while the analogous electrolyte in a gel state was made by the addition of tetramethoxysilane (TMOS) in the molar ratio MTMSPIm+I-:TMOS = 1:1. The structure of the MTMSPIm+I- in its non-hydrolyzed and hydrolyzed states and in its fully condensed form, obtained after ageing the sols for various times (from a few hours to a few weeks) and heating them at 200 degrees C (fully condensed form), was studied employing time-dependent infrared attenuated total reflection (ATR) and 29Si NMR spectroscopic measurements. The structure of the condensed species was correlated with the viscosity and the specific conductivity measurements of MTMSPIm+I- sols and TMOS/MTMSPIm+I- gels during their ageing. The final product of the condensation of MTMSPIm+I- sols was described as a positively-charged ladder-like polysilsesquioxane with Tn end groups exhibiting a single T3 signal in 29Si NMR spectra and characteristic doublet bands at 1138 and 1049 cm(-1) in IR. This structure was retained to a large extent in TMOS/MTMSPIm+I- gels, confirming their nanocomposite structure. The results of the ATR infrared time-dependent spectroscopic studies showed that in the course of condensation of sols, the refractive index of the modes attributed to the polysilsesquioxane species exhibited strong dispersion, which led to shifts in the vibrational band positions in the experimental ATR spectra. This effect accompanies the sol-to-gel transformations and has not yet been considered as a possible error in analysis of the ATR spectra of sols and gels. The calculation procedure for obtaining the corresponding transmission spectra is briefly outlined and the results applied in this work.
Correlation of enterohemorrhagic Escherichia coli O157 prevalence in feces, hides, and carcasses of beef cattle during processing (2000)

A survey was performed to estimate the frequency of enterohemorrhagic Escherichia coli O157:H7 or O157:nonmotile (EHEC O157) in feces and on hides within groups of fed cattle from single sources (lots) presented for slaughter at meat processing plants in the Midwestern United States, as well as frequency of carcass contamination during processing from cattle within the same lots. Of 29 lots sampled, 72% had at least one EHEC O157-positive fecal sample and 38% had positive hide samples. Overall, EHEC O157 prevalence in feces and on hides was 28% (91 of 327) and 11% (38 of 355), respectively. Carcass samples were taken at three points during processing: preevisceration, postevisceration before antimicrobial intervention, and postprocessing after carcasses entered the cooler. Of 30 lots sampled, 87% had at least one EHEC O157-positive preevisceration sample, 57% of lots were positive postevisceration, and 17% had positive postprocessing samples. Prevalence of EHEC O157 in the three postprocessing samples was 43% (148 of 341), 18% (59 of 332) and 2% (6 of 330), respectively. Reduction in carcass prevalence from preevisceration to postprocessing suggests that sanitary procedures were effective within the processing plants. Fecal and hide prevalence were significantly correlated with carcass contamination (P = 0.001), indicating a role for control of EHEC O157 in live cattle.
Synthesis and secretion of recombinant tick-borne encephalitis virus protein E in soluble and particulate form (1995)

A quantitative study was performed to investigate the requirements for secretion of recombinant soluble and particulate forms of the envelope glycoprotein E of tick-borne encephalitis (TBE) virus. Full-length E and a carboxy terminally truncated anchor-free form were expressed in COS cells in the presence and absence of prM, the precursor of the viral membrane protein M. Formation of a heteromeric complex with prM was found to be necessary for efficient secretion of both forms of E, whereas only low levels of anchor-free E were secreted in the absence of prM. The prM-mediated transport function could also be provided by coexpression of prM and E from separate constructs, but a prM-to-E ratio of greater than 1:1 did not further enhance secretion. Full-length E formed stable intracellular heterodimers with prM and was secreted as a subviral particle, whereas anchor-free E was not associated with particles and formed a less stable complex with prM, suggesting that prM interacts with both the ectodomain and anchor region of E.
Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus (2013)

A novel betacoronavirus associated with lethal respiratory and renal complications was recently identified in patients from several countries in the Middle East. We report the deep genome sequencing of the virus directly from a patient's sputum sample. Our high-throughput sequencing yielded a substantial depth of genome sequence assembly and showed the minority viral variants in the specimen. Detailed phylogenetic analysis of the virus genome (England/Qatar/2012) revealed its close relationship to European bat coronaviruses circulating among the bat species of the Vespertilionidae family. Molecular clock analysis showed that the 2 human infections of this betacoronavirus in June 2012 (EMC/2012) and September 2012 (England/Qatar/2012) share a common virus ancestor most likely considerably before early 2012, suggesting the human diversity is the result of multiple zoonotic events.
Cis,cis-Muconate Lactonizing Enzyme from Trichosporon cutaneum: Evidence for a Novel Class of Cycloisomerases in Eucaryotes (1994)

The absolute stereochemical courses of cis,cis-muconate lactonizing enzyme (MLE;EC 5.5.1.1) from Trichosporon cutaneum (TcMLE) and chloromuconate cycloisomerase (MLE II; EC 5.5.1.7) from Pseudomonas sp B13 have been determined from 1H NMR measurements. Both cycloisomerases convert cis,cis-muconate to (4S)-muconolactone by a syn lactonization, the absolute stereochemical outcome of which is identical to that observed with MLE from Pseudomonas putida. The regiochemical courses of cyclization of 3-halo-cis,cis-muconates by TcMLE and MLE II have been characterized and shown to differ in a halogen substituent dependent manner, suggesting at least a different active site architecture of the two MLEs. Moreover, the regiochemical preferences of MLE II and TcMLE parallel results previously observed for the nonenzymatic lactonization of the 3-halomuconates at pH 1-6 and in concentrated HCl, respectively, in which alternate mechanisms of cyclization were proposed [Pieken, W. A., & Kozarich, J. W. (1990) J. Org. Chem. 55, 3029-3035]. Complementary DNA clones encoding TcMLE have been isolated from phenol induced T. cutaneum cDNA using the polymerase chain reaction. The deduced amino acid sequence does not exhibit any similarity to that of MLE from P. putida. It does however, exhibit moderate sequence similarity (21% residue identity, 14 gaps) with 3-carboxy-cis,cis-muconate lactonizing enzyme (CMLE; EC 5.5.1.5) from Neurospora crassa, which catalyzes a regiochemically analogous and stereochemically identical lactonization reaction with 3-carboxymuconate. The limited data available suggest that the fungal CMLE and yeast MLE are representative of a unique class of eucaryotic cycloisomerases which have evolved convergently with the bacterial MLEs.
Prognostic significance of loss of heterozygosity at loci on chromosome 17p13.3-ter in sporadic breast cancer is evidence for a putative tumour suppressor gene (1999)

Several studies indicate that the short arm of chromosome 17 is one of the most frequently altered regions in sporadic breast carcinomas (45-60%). In the present report the 17p13.3-ter locus in tumour DNA of breast cancer patients, along with their matching normal lymphocyte DNA, have been mapped with four markers (D17S5, D17S379, ABR and D17S34), spanning nearly 3 cM of the telomer. Sixty-five of 143 heterozygous tumours had lost at least one of the markers at the minimum region of loss (45%). High levels of loss of these distal markers on 17p13.3 are independent of TP53 mutations and are associated with tumour cell proliferation. A follow-up period of over 7 years demonstrates that loss of these markers correlates both with disease-free (P = 0.004) and overall survival (P = 0.007). In addition we show that for disease-free survival the prognostic power of this genetic alteration is second only to axillary lymph node involvement (3.1 vs 6.3 relative risk), and is a better predictor than the mutational status of TP53 (1.6 relative risk). Our results are further evidence of the presence, within the region, of at least a second tumour suppressor gene distal to TP53, that might be targeted by deletions.
Left Ventricular Chamber Function During Inhaled Nitric Oxide in Patients with Dilated Cardiomyopathy (1999)

Inhaled nitric oxide is a potent and selective pulmonary vasodilator. However, when used in patients with congestive cardiac failure, the decrease in pulmonary vascular resistance is associated with an increase in pulmonary capillary wedge pressure (PCWP). This study examined load-independent indexes of left ventricular chamber function during inhaled nitric oxide in 10 patients with dilated cardiomyopathy (mean ejection fraction, 30.2+/-7.8%, mean +/- SD). Etiology of cardiomyopathy was idiopathic in six and ischemic in four. Pulmonary hemodynamics in seven patients revealed normal resting pulmonary vascular resistance. Chamber function was defined by recording pressure-volume loops at steady state and during inferior vena caval occlusion during inhalation of 20 ppm nitric oxide for 10 min. We found no effect of inhaled nitric oxide on steady-state left ventricular pressures, volumes, contractility (end-systolic elastance or preload recruitable stroke work), contraction duration, or active (tau, dP/dt(min)) or passive (end-diastolic pressure-volume relation) diastolic function. Right heart filling pressures did not change. We therefore conclude that 20 ppm inhaled nitric oxide does not affect left ventricular chamber function in patients with controlled heart failure. Previously described elevations in PCWP during inhaled nitric oxide are most likely due to altered left ventricular loading conditions related to secondary pulmonary hypertension in severe heart failure.