gebhart/patrepeval huggingface dataset:
The role of PSA and percent free PSA for staging and prognosis prediction in clinically localized prostate cancer. (1998)

Prostate-specific antigen (PSA) is the most important tumor marker for early detection, staging, and monitoring of men with prostatic cancer today. However, its sensitivity and specificity are not sufficient to use it as a single tool for screening for men with clinically localized prostate cancer. Recently, assays have become available that selectively detect several of the various molecular forms of PSA, especially the unbound or free PSA. Several studies have shown the clinical usefulness of percent free PSA (free PSA/total PSA) for the early detection of men with clinically localized prostate cancer. However, the use of percent free PSA for staging of prostate cancer remains controversial. Based on the case scenario presented, the value of total PSA and percent free PSA for the staging of men with clinically localized prostate cancer is reviewed.
Comparative analysis of the complete genome sequence of the plant growth–promoting bacterium Bacillus amyloliquefaciens FZB42 (2007)

Bacillus amyloliquefaciens FZB42 is a Gram-positive, plant-associated bacterium, which stimulates plant growth and produces secondary metabolites that suppress soil-borne plant pathogens. Its 3,918-kb genome, containing an estimated 3,693 protein-coding sequences, lacks extended phage insertions, which occur ubiquitously in the closely related Bacillus subtilis 168 genome. The B. amyloliquefaciens FZB42 genome reveals an unexpected potential to produce secondary metabolites, including the polyketides bacillaene and difficidin. More than 8.5% of the genome is devoted to synthesizing antibiotics and siderophores by pathways not involving ribosomes. Besides five gene clusters, known from B. subtilis to mediate nonribosomal synthesis of secondary metabolites, we identified four giant gene clusters absent in B. subtilis 168. The pks2 gene cluster encodes the components to synthesize the macrolactin core skeleton.
Effects of light on development of mammalian zygotes (2007)

It is generally assumed that light has no effect on the physiology of oocytes, zygotes, or early embryos. Therefore, little or no attention has been paid to lighting conditions during the handling of these cells in vitro. Here we show that cool white fluorescent light, rich in short-wavelength visible light and commonly used in research and clinical laboratories, produces more reactive oxygen species in mouse and hamster zygotes than does warm white fluorescent light. Mouse blastocysts that developed from zygotes shielded from light best developed to term fetuses followed by those exposed to warm white fluorescent light and then by those exposed to cool white fluorescent light. We hypothesized that light is one of the physical factors affecting embryonic environment and that its effects on cultured mammalian zygotes and embryos should not be overlooked.
A phase 3 study of gemtuzumab ozogamicin during induction and postconsolidation therapy in younger patients with acute myeloid leukemia (2013)

This randomized phase 3 clinical trial evaluated the potential benefit of the addition of gemtuzumab ozogamicin (GO) to standard induction and postconsolidation therapy in patients with acute myeloid leukemia. Patients were randomly assigned to receive daunorubicin (45 mg/m(2) per day on days 1, 2, and 3), cytarabine (100 mg/m(2) per day by continuous infusion on days 1-7), and GO (6 mg/m(2) on day 4; DA+GO) vs standard induction therapy with daunorubicin (60 mg/m(2) per day on days 1, 2, and 3) and cytarabine alone (DA). Patients who achieved complete remission (CR) received 3 courses of high-dose cytarabine. Those remaining in CR after consolidation were randomly assigned to receive either no additional therapy or 3 doses of GO (5 mg/m(2) every 28 days). From August 2004 until August 2009, 637 patients were registered for induction. The CR rate was 69% for DA+GO and 70% for DA (P = .59). Among those who achieved a CR, the 5-year relapse-free survival rate was 43% in the DA+GO group and 42% in the DA group (P = .40). The 5-year overall survival rate was 46% in the DA+GO group and 50% in the DA group (P = .85). One hundred seventy-four patients in CR after consolidation underwent the postconsolidation randomization. Disease-free survival was not improved with postconsolidation GO (HR, 1.48; P = .97). In this study, the addition of GO to induction or postconsolidation therapy failed to show improvement in CR rate, disease-free survival, or overall survival.
Pharmacologic Modulation of Acute Ocular Inflammation with Quercetin (1989)

Anti-inflammatory potentials of a safe, common dietary component, quercetin, were investigated in suppression of intraocular inflammation induced by retinal S antigen. Lewis rats sensitized to S antigen were treated daily with intraperitoneal injections of quercetin. Control rats with S-antigen-induced uveitis were similarly treated with diluent. When compared with controls the treated group showed marked reduction in uveal and retinal inflammation and in vasculitis and perivasculitis. Morphometric analysis revealed a significant reduction (p less than 0.005) in choroidal thickness when compared with that of control animals. These results clearly show the antiphlogistic effects of quercetin in experimental uveitis.
High frequency ofTARDBPgene mutations in Italian patients with amyotrophic lateral sclerosis (2009)

Recent studies identified rare missense mutations in amyotrophic lateral sclerosis (ALS) patients in the TARDBP gene encoding TAR DNA binding protein (TDP)-43, the major protein of the ubiquitinated inclusions (UBIs) found in affected motor neurons (MNs). The aim of this study was to further define the spectrum of TARDBP mutations in a large cohort of 666 Italian ALS patients (125 familial and 541 sporadic cases). The entire coding region was sequenced in 281 patients, while in the remaining 385 cases only exon 6 was sequenced. In 18 patients, of which six are familial, we identified 12 different heterozygous missense mutations (nine novel) all locating to exon 6, which were absent in 771 matched controls. The c.1144G>A (p.A382T) variation was observed in seven patients, thus representing the most frequent TARDBP mutation in ALS. Analysis of microsatellites surrounding the TARDBP gene indicated that p.A382T was inherited from a common ancestor in 5 of the 7 patients. Altogether, the frequency of TARDBP gene mutations appears to be particularly high in Italian ALS patients compared to individuals of mainly Northern European origin (2.7% vs. 1%). Western blot analysis of lymphocyte extracts from two patients carrying the p.A382T and p.S393L TARDBP mutations showed the presence of lower molecular weight TDP-43 bands, which were more abundant than observed in healthy controls and patients negative for TARDBP mutations. In conclusion, this report contributes to the demonstration of the causative role of the TARDBP gene in ALS pathogenesis and indicates that mutations may affect the stability of the protein even in nonneuronal tissues.
Vascular disrupting agents (2012)

VDAs represent a unique class of anticancer compounds. Their clinical development is hampered by cardiovascular, neurological toxicities as single agent and by hematological toxicity in combination with chemotherapy. Molecular predictors of their efficacy are crucial for further development. As single agent, only few objective responses have been observed in a variety of solid tumors. However, VDAs have failed to demonstrate a survival advantage in several phase II/III trials especially in combination with chemotherapy.
Quantitative DNA slot blot analysis: inhibition of DNA binding to membranes by magnesium ions (1997)

Titers of wild-type and recombinant adeno-associated viruses are routinely determined by DNA slot blot analysis. The binding of viral DNA to nylon membranes was found to be inhibited by magnesium ions, which are critical components of the DNase I digestion carried out prior to slot blot analysis. Mg2+ions also interfered with the adsorption of plasmid DNA to nylon and nitrocellulose membranes. These observations yield practical insights into the poorly understood mechanisms by which DNA molecules are retained on solid supports.
Syntheses of .DELTA.1-tetrahydrocannabinol and related cannabinoids (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSyntheses of .DELTA.1-tetrahydrocannabinol and related cannabinoidsRaphael Mechoulam, Paul Braun, and Yehiel GaoniCite this: J. Am. Chem. Soc. 1972, 94, 17, 6159–6165Publication Date (Print):August 1, 1972Publication History Published online1 May 2002Published inissue 1 August 1972https://pubs.acs.org/doi/10.1021/ja00772a038https://doi.org/10.1021/ja00772a038research-articleACS PublicationsRequest reuse permissionsArticle Views1308Altmetric-Citations89LEARN 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
Mechanisms of room temperature metastable tetragonal phase stabilisation in zirconia (2005)

Mechanisms of tetragonal phase stabilisation, at room temperature, in nanocrystalline (<100 nm), submicrometre-sized (100 nm-1 μm), and bulk zirconia (ZrO2) (>1 μm) are reviewed in detail. The merits, demerits and scope of each individual model are outlined. The analysis of the literature shows that, although the mechanism of tetragonal phase stabilisation in bulk ZrO2 is well understood, the room temperature tetragonal phase stabilisation mechanism in undoped, nanocrystalline ZrO2 is controversial. Various proposed models, based on surface energy (nanocrystallite size), strain energy, internal and external hydrostatic pressure, structural similarities, foreign surface oxides, anionic impurities, water vapour and lattice defects (oxygen ion vacancies), are discussed in detail. It is proposed that generation of excess oxygen ion vacancies within the nanocrystalline ZrO2 is primarily responsible for the room temperature tetragonal phase stabilisation, below a critical size, Hence, the mechanism of tetragonal phase stabilisation in nanocrystalline ZrO2 appears to be the same as that in doped ZrO2 (at room temperature) and undoped ZrO2 (at higher temperature). © 2005 Institute of Materials, Minerals and Mining and ASM International.
Cows' milk protein intolerance: a possible association with gastroenteritis, lactose intolerance, and IgA deficiency. (1976)

Twenty-five children with cows' milk protein intolerance were studied. Twenty had presented with an illness clinically indistinguishable from infantile gastroenteritis; an enteropathogenic Escherichia coli was isolated from the stools in two children, and in six another member of the family simultaneously developed acute diarrhoea and vomiting. Twenty-three children had lactose intolerance secondary to cows' milk protein intolerance. Eight out of 20 children were found to be partially IgA deficient. An acute attack of gastroenteritis, in damaging the small mucosa, may act as a triggering mechanism in cows' milk protein intolerance, and a deficiency in IgA may be a predisposing factor in so far as it allows the patient to become sensitised to foreign protein.
TL1A Synergizes with IL-12 and IL-18 to Enhance IFN-γ Production in Human T Cells and NK Cells (2004)

TL1A, a recently described TNF-like cytokine that interacts with DR3, costimulates T cells and augments anti-CD3 plus anti-CD28 IFN-gamma production. In the current study we show that TL1A or an agonistic anti-DR3 mAb synergize with IL-12/IL-18 to augment IFN-gamma production in human peripheral blood T cells and NK cells. TL1A also enhanced IFN-gamma production by IL-12/IL-18 stimulated CD56(+) T cells. When expressed as fold change, the synergistic effect of TL1A on cytokine-induced IFN-gamma production was more pronounced on CD4(+) and CD8(+) T cells than on CD56(+) T cells or NK cells. Intracellular cytokine staining showed that TL1A significantly enhanced both the percentage and the mean fluorescence intensity of IFN-gamma-producing T cells in response to IL-12/IL-18. The combination of IL-12 and IL-18 markedly up-regulated DR3 expression in NK cells, whereas it had minimal effect in T cells. Our data suggest that TL1A/DR3 pathway plays an important role in the augmentation of cytokine-induced IFN-gamma production in T cells and that DR3 expression is differentially regulated by IL-12/IL-18 in T cells and NK cells.
An inter-reference gap model for temporal locality in program behavior (1995)

The property of locality in program behavior has been studied and modelled extensively because of its application to memory design, code optimization, multiprogramming etc. We propose a k order Markov chain based scheme to model the sequence of time intervals between successive references to the same address in memory during program execution. Each unique address in a program is modelled separately. To validate our model, which we call the Inter-Reference Gap (IRG) model, we show substantial improvements in three different areas where it is applied. (1) We improve upon the miss ratio for the Least Recently Used (LRU) memory replacement algorithm by up to 37%. (2) We achieve up to 22% space-time product improvement over the Working Set (WS) algorithm for dynamic memory management. (3) A new trace compression technique is proposed which compresses up to 2.5% with zero error in WS simulations and up to 3.7% error in the LRU simulations. All these results are obtained experimentally, via trace driven simulations over a wide range of cache traces, page reference traces, object traces and database traces.
Blue-green (450-nm) upconversion Tm^3+:YLF laser (1989)

We report an upconversion laser that is pumped by two colors-one red and one near infrared-and emits in the blue-green region.
Mass spectrometric detection of tyrosine sulfation in human pancreatic trypsinogens, but not in tumor‐associated trypsinogen (2007)

Trypsinogen-1 and -2 are well-characterized enzymes that are expressed in the pancreas and also in several other tissues. Many cancers produce trypsinogen isoenzymes that differ from the pancreatic ones with respect to substrate specificity and isoelectric point. These tumor-associated trypsinogens play a pivotal role in cancer progression and metastasis. The differences between these and the pancreatic isoenzymes have been suggested to be caused by post-translational modification, either sulfation or phosphorylation of a tyrosine residue. We aimed to elucidate the cause of these differences. We isolated trypsinogens from pancreatic juice and conditioned medium from a colon carcinoma cell line. Intact proteins, and tryptic and chymotryptic peptides were characterized by electrospray ionization mass spectrometry. We also used immunoblotting with antibody against phosphotyrosine and N-terminal sequencing. The results show that pancreatic trypsinogen-1 and -2 are sulfated at Tyr154, whereas tumor-associated trypsinogen-2 is not. Detachment of a labile sulfogroup could be demonstrated by both in-source dissociation and low-energy collision-induced dissociation in a tandem mass spectrometer. Tyrosine sulfation is an ubiquitous protein modification occurring in the secretory pathway, but its significance is often underestimated due to difficulties in its analysis. Sulfation is an almost irreversible modification that is thought to regulate protein-protein interactions and the activity of proteolytic enzymes. We conclude that the previously known differences in charge, substrate specificity and inhibitor binding between pancreatic and tumor-associated trypsinogens are probably caused by sulfation of Tyr154 in pancreatic trypsinogens.
High-field NMR of adsorbed xenon polarized by laser pumping (1991)

Optical pumping has been used to enhance the pulsed NMR signal of $^{129}\mathrm{Xe}$, allowing the detecting of low-pressure xenon gas and of xenon adsorbed on powdered solids. We observe an increase in sensitivity of more than 2 orders of magnitude over conventional NMR, the current limitation being the laser power. Adsorbed xenon is observed at 298 K on graphitized carbon (about 10 ${\mathrm{m}}^{2}$g and on powdered benzanthracene (\ensuremath{\sim}0.5 ${\mathrm{m}}^{2}$g) below 170 K. The increased sensitivity of this technique allows the study of a large class of amorphous materials with surface areas below 10 ${\mathrm{m}}^{2}$/g including semiconductors, polymers, metal oxides, and catalysts.
A Modular Approach toward Block Copolymers (2005)

A novel methodology for the formation of block copolymers has been developed that combines ring-opening metathesis polymerization (ROMP) with functional chain-transfer agents (CTAs) and self-assembly. Telechelic homopolymers of cyclooctene derivatives end-functionalized with hydrogen-bonding or metal-coordination sites are formed through the combination of ROMP with a corresponding functional CTA. These telechelic homopolymers are fashioned with a high control over molecular weight and without the need for post-polymerization procedures. The homopolymers undergo fast and efficient self-assembly with their complement homopolymer or small molecule analogue to form block-copolymer architectures. The block copolymers show equivalent association constants as their small molecule analogues described in the literature, regardless of size or nature of the complementary unit or the polymer side chain.
Wasserstein GAN and Waveform Loss-Based Acoustic Model Training for Multi-Speaker Text-to-Speech Synthesis Systems Using a WaveNet Vocoder (2018)

WaveNet, which learns directly from speech waveform samples, has been used as an alternative to vocoders and achieved very high-quality synthetic speech in terms of both naturalness and speaker similarity even in multi-speaker text-to-speech synthesis systems. However, the WaveNet vocoder uses acoustic features as local condition parameters, and these parameters need to be accurately predicted by another acoustic model. So far, it is not yet clear how to train this acoustic model, which is problematic because the final quality of synthetic speech is significantly affected by the performance of the acoustic model. Significant degradation occurs, especially when predicted acoustic features have mismatched characteristics compared to natural ones. In order to reduce the mismatched characteristics between natural and generated acoustic features, we propose new frameworks that incorporate either a conditional generative adversarial network (GAN) or its variant, Wasserstein GAN with gradient penalty (WGAN-GP), into multi-speaker speech synthesis that uses the WaveNet vocoder. The GAN generator performs as an acoustic model and its outputs are used as the local condition parameters of the WaveNet. We also extend the GAN frameworks and use the discretized-mixture-of-logistics (DML) loss of a well-trained WaveNet in addition to mean squared error and adversarial losses as parts of objective functions. Experimental results show that acoustic models trained using the WGAN-GP framework using back-propagated DML loss achieves the highest subjective evaluation scores in terms of both quality and speaker similarity.
Systematic Identification of Selective Essential Genes in Helicobacter pylori by Genome Prioritization and Allelic Replacement Mutagenesis (2001)

A comparative genomic approach was used to identify Helicobacter pylori 26695 open reading frames (ORFs) which are conserved in H. pylori J99 but highly diverged in other eubacteria. A survey of selected pathways of central intermediary metabolism was also carried out, and genes with a potentially selective role in H. pylori were identified. Forty-five ORFs identified in these two analyses were screened using a rapid vector-free allelic replacement mutagenesis technique, and 33 were shown to be essential in vitro. Notably, 13 ORFs gave essentiality results which are unexpected in view of their known or proposed functions, and phylogenetic analysis was used to investigate the annotation of 7 such ORFs which are highly diverged. We propose that the products of a number of these H. pylori-specific essential genes may be suitable targets for novel anti-H. pylori therapies.
Vaccines againstCampylobacter jejuni (1997)

Campylobacter jejuni is one of the most common causes of diarrhea worldwide. The gastrointestinal manifestations of Campylobacter infection range from watery diarrhea to severe dysentery. Campylobacter infection has also been linked to the postinfectious sequelae of reactive arthritis and Guillain-Barré syndrome. Evidence from epidemiologic and volunteer studies suggests that development of a vaccine to prevent gastrointestinal disease and limit colonization is possible. Efforts to develop live attenuated or subunit vaccines are limited by the finite knowledge of Campylobacter pathogenesis and lack of a conserved protective antigen, respectively. An oral killed, whole-cell vaccine has been shown to be safe and effective in animal models and is currently being tested in phase I volunteer studies.
Symbol-Level Stochastic Chase Decoding of Reed-Solomon and BCH Codes (2019)

This paper proposes the symbol-level-stochastic Chase decoding algorithm (S-SCA) for the Reed-Solomon (RS) and Bose-Chaudhuri-Hocquenghem (BCH) codes, which is a soft-input soft-output (SISO) decoder. By the efficient usage of void space between constellation points for q-ary modulations and using soft information at the input of the decoder, the S-SCA is capable of outperforming conventional symbol-levelChase algorithm (S-CA) with a less computational cost. Since the S-SCA starts with the randomized generation of likely testvectors, it reduces the complexity to polynomial order and also it does not need to find the least reliable symbols to generate testvectors. The symbol-level-search bitwise-transmission stochastic Chase algorithm (SSBT-SCA) is also introduced for RS codes over binary phase shift keying (BPSK) transmission that is capable of generating symbol-level test-vectors with reduced complexity and to better mitigate burst errors. Simulation results show that by increasing the number of test-vectors, the performance of the algorithm can asymptotically approach the maximum-likelihood (ML) bound. The S-SCA provides near 2 dB decoding gain in comparison with S-CA for a (31, 25) RS code using 32-QAM, when 1024 test-vectors are used. Furthermore, the algorithm provides near 3 dB additional gain with 1024 test-vectors compared with S-CA that uses 65536 iterations when a (255, 239) RS code is used in an additive white Gaussian noise (AWGN) channel. For the Rayleigh fading channel and the same code, the algorithm provides more than 5 dB gain. Furthermore, for (63, 57) BCH codes and 8-PSK modulation, the proposed algorithm provides 3 dB gain with less complexity.