gebhart/patrepeval huggingface dataset:
Plasma Low-Molecular-Weight Proteome Profiling Identified Neuropeptide-Y as a Prostate Cancer Biomarker Polypeptide (2013)

In prostate cancer diagnosis, PSA test has greatly contributed to the early detection of prostate cancer; however, expanding overdiagnosis and unnecessary biopsies have emerged as serious issues. To explore plasma biomarkers complementing the specificity of PSA test, we developed a unique proteomic technology QUEST-MS (Quick Enrichment of Small Targets for Mass Spectrometry). The QUEST-MS method based on 96-well formatted sequential reversed-phase chromatography allowing efficient enrichment of <20 kDa proteins quickly and reproducibly. Plasma from 24 healthy controls, 19 benign prostate hypertrophy patients, and 73 prostate cancer patients were purified with QUEST-MS and analyzed by LC/MS/MS. Among 153 057 nonredundant peptides, 189 peptides showed prostate cancer specific detection pattern, which included a neurotransmitter polypeptide neuropeptide-Y (NPY). We further validated the screening results by targeted multiple reaction monitoring technology using independent sample set (n = 110). The ROC curve analysis revealed that logistic regression-based combination of NPY, and PSA showed 81.5% sensitivity and 82.2% specificity for prostate cancer diagnosis. Thus QUEST-MS technology allowed comprehensive and high-throughput profiling of plasma polypeptides and had potential to effectively uncover very low abundant tumor-derived small molecules, such as neurotransmitters, peptide hormones, or cytokines.
ChemInform Abstract: Alkyloxy‐Substituted CTTV Derivatives that Exhibit Columnar Mesophases. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Determination of Acid Site Location in Dealuminated MCM-68 by 27Al MQMAS NMR and FT-IR Spectroscopy with Probe Molecules (2017)

A series of MCM-68 zeolites with different Si/Al ratios were prepared by treatment with nitric acid and compared with beta zeolites. Speciation of aluminum and location of acid sites changed depending on the Si/Al ratio. The location of Brønsted acid sites in MCM-68 samples was able to be classified by FT-IR measurements with pyridine and 2,6-di-tert-butylpyridine as probe molecules, and the number of Brønsted acid sites was quantified according to the locations. For high-aluminum MCM-68, Brønsted acid sites were broadly distributed in both the 12-ring channel and 10-ring windows as well as inside the supercage. The Brønsted acid sites in the 12-ring channel were easily removed by the acid treatment, and consequently, high-silica MCM-68 had Brønsted acid sites predominantly in the 10-ring windows and inside the supercage. 27Al MQMAS NMR spectra of high-silica MCM-68 showed two specific peaks assignable to T6 and T7 sites, which did not face the 12-ring channel, forming the Brønsted acid sites highly tolerant to the acid treatment. MCM-68 catalysts showed better catalytic performance in dehydration of sorbitol than beta, mordenite, and ZSM-5. Large void spaces at the intersection of 12- and 10-ring channels and inside the supercage for MCM-68 made it easy to take bulky transition states in the dehydration of sorbitol, resulting in its high catalytic performance.
Single cell whole transcriptome analysis of disease cells to generate a targeted RNA-sequencing gene panel for the simultaneous analysis of targeted mRNA and protein (2019)

Abstract Single cell RNA-sequencing (scRNA-seq) is a powerful tool for understanding the sample heterogeneity of individual cells. Many methods rely on whole transcriptome analysis (WTA) to get a snapshot of the entire cellular landscape. Although WTA analysis can be used to discover novel biomarkers, this technique can be expensive. To enable scaling of experiments, WTA data can be mined to design targeted gene panels. To showcase this, we used single cell sequencing to examine thousands of B cells isolated from the bone marrow and peripheral blood of chronic lymphocytic leukemia (CLL) and healthy donors. B cells that had been sorted using the BD FACSMelody™ cell sorter were multiplexed using the BD™ Human Single-Cell Multiplexing Kit and pooled before being processed on the BD Rhapsody™ system, thereby minimizing batch effects. The resulting data was mined to design a panel of differentially expressed genes between CLL and healthy B cells that could be used for subsequent CLL phenotyping. By combining this panel with the BD Rhapsody™ Immune Response Panel (together comprising ~500 mRNAs), along with 36 DNA-barcoded BD™ AbSeq antibodies, we were able to simultaneously analyze mRNA and protein targets from a new subset of CLL and healthy B cells for additional high-resolution analysis. This study showcases the power of using WTA data to design specific gene panels that can be used alone or in combination with existing targeted panels for routine and cost-effective transcriptional profiling at a single cell level. For Research Use Only. Not for use in diagnostic or therapeutic procedures. BD, the BD Logo, FACSMelody, and Rhapsody are trademarks of Becton, Dickinson and Company. © 2019 BD and its subsidiaries. All rights reserved.
Impact of Winding Layer Number and Slot/Pole Combination on AC Armature Losses of Synchronous Surface PM Machines Designed for Wide Constant-Power Speed Range Operation (2008)

This paper examines the impact of the winding layer number (single- and double-layer), and magnet type (sintered and bonded), as well as slot/pole combinations on AC stator losses in surface permanent magnet (SPM) synchronous machines equipped with fractional-slot concentrated windings that are designed for wide speed ranges of constant-power operation. It is shown that the use of bonded magnets instead of sintered magnets tends to increase the AC losses, while magnetic saturation of the tooth-tips tends to reduce these losses. The effect of terminal conditions, i.e. series and parallel connections, on AC losses is also investigated. The effect of leakage flux on AC losses is studied for the various slot/pole combinations within the same slot/pole/phase (spp) family as well as for different spp values, indicating that high numbers of stator poles tend to increase the AC losses. An AC loss index has been defined incorporating these effects to serve as a quick screening tool for the various slot/pole combinations under consideration.
GPflowOpt: A Bayesian Optimization Library using TensorFlow (2017)

A novel Python framework for Bayesian optimization known as GPflowOpt is introduced. The package is based on the popular GPflow library for Gaussian processes, leveraging the benefits of TensorFlow including automatic differentiation, parallelization and GPU computations for Bayesian optimization. Design goals focus on a framework that is easy to extend with custom acquisition functions and models. The framework is thoroughly tested and well documented, and provides scalability. The current released version of GPflowOpt includes some standard single-objective acquisition functions, the state-of-the-art max-value entropy search, as well as a Bayesian multi-objective approach. Finally, it permits easy use of custom modeling strategies implemented in GPflow.
Synthesis and reactions of some optically active epoxides formally derived from tertiary allylic alcohols (2001)

The epoxyketones 2, 3 and 7–9 reacted with Grignard reagents in a highly stereocontrolled manner to give the epoxyalcohols 20, 4–6 and 11-13 in high yields. The epoxyalcohol 12 underwent a Payne rearrangement on base treatment to give the isomer 15 while epoxyalcohols 4, 5, 12 and 20 suffered ring-opening (with retention of configuration) using tin(IV) chloride to afford chlorodiols 18, 17, 19 and 21 respectively. On the other hand, the alcohols 4, 5 and 12 reacted with trialkylsilyl chlorides to furnish the chlorodiols 22, 24 and 23 respectively with inversion of configuration.
Fabrication of Electroless CoWP/NiB Diffusion Barrier Layer on SiO[sub 2] for ULSI Devices (2009)

We investigated the electroless CoWP/NiB diffusion barrier layer for ultralarge-scale integration (ULSI) interconnection by forming the immobilizing Pd catalyst on an organosilane layer. When the electroless CoWP film was formed directly on a Pd-activated organosilane layer, it became islandlike and did not form a continuous layer. When it was formed on an electroless NiB deposited on a Pd-activated organosilane layer, the electroless CoWP film was uniform and formed a continuous layer 10 nm thick. The transmission electron microscopy images of the interfaces of showed that, at an annealing temperature up to for 30 min, the interfaces remained unchanged and clear, showing no trace of Cu diffusion into the substrate. In-plane X-ray diffraction patterns indicated that the CoWP/NiB film had an amorphous structure and was stable against heat-treatment up to for 30 min. An evaluation of sheet resistance measurements suggested that the CoWP/NiB film shows appropriate barrier properties for Cu diffusion up to . The CoWP/NiB film was used as a seed for electroless Cu plating. Trenches 100 nm wide were coated with a 10 nm CoWP/NiB barrier followed by successful trench filling by electroless Cu plating.
In situ thin-film texture determination (1999)

A kinematic theory of reflection high energy electron diffraction (RHEED) is presented for textured polycrystalline thin films. RHEED patterns are calculated for arbitrary texture situations and for any general crystallographic orientation that may be encountered in thin-film growth. It is shown that the RHEED pattern can be used as a fast and convenient tool for in situ texture characterization. The approach also permits quantitative extraction of angular dispersion parameters which are useful for optimizing thin-film growth conditions.
Powerful Analytical Tools for Citrus Characterization: LC/MS and LC/NMR Characterization of Polymethoxylated Flavones (2006)

Citrus fruits are well known for their unique flavor and their health benefits. Volatile compounds such as terpenes are formed as secondary metabolites in the plant. These volatile compounds mainly contribute to the flavor and scent of the plant. However, other non-volatile metabolites are formed via biosynthesis in citrus. These non-volatile compounds contribute to certain health benefits like anticarcinogenic, antitumor, antiviral or antimicrobial activities. Our goal is to establish efficient analytical technologies to identify and characterize the volatile and non-volatile compounds from citrus plants. For a fast and reliable screening of volatile compounds in citrus flavors, solid phase micro-extraction (SPME) and solid phase dynamic extraction (SPDE) are well known techniques for flavor analysis. Residues obtained from molecular distillation of cold pressed peel oils of oranges and clementines were analyzed using LC/MS and LC/NMR to characterize non-volatile compounds.
Macrophage diversity in renal injury and repair (2008)

Monocyte-derived macrophages can determine the outcome of the immune response and whether this response contributes to tissue repair or mediates tissue destruction. In addition to their important role in immune-mediated renal disease and host defense, macrophages play a fundamental role in tissue remodeling during embryonic development, acquired kidney disease, and renal allograft responses. This review summarizes macrophage phenotype and function in the orchestration of kidney repair and replacement of specialized renal cells following injury. Recent advances in our understanding of macrophage heterogeneity in response to their microenvironment raise new and exciting therapeutic possibilities to attenuate or conceivably reverse progressive renal disease in the context of fibrosis. Furthermore, parallels with pathological processes in many other organs also exist.
A Constructive Approach To Software Evolution (2007)

Abstract — In many software design and evaluation techniques, either the software evolution problem is not systematically elaborated, or only the impact of evolution is considered. Thus, most of the time software is changed by editing the components of the software system, i.e. breaking down the software system. The software engineering discipline provides many mechanisms that allow evolution without breaking down the system; however, the contexts where these mechanisms are applicable are not taken into account. Furthermore, the software design and evaluation techniques do not support identifying these contexts. In this paper, we provide a taxonomy of software evolution that can be used to identify the context of the evolution problem. The identified contexts are used to retrieve, from the software engineering discipline, the mechanisms, which can evolve the software software without breaking it down. To build such a taxonomy, we build a model for software evolution and use this model to identify the factors that effect the selection of software evolution mechanisms.
Carbohydrates great and small, from dietary fiber to sialic acids: How glycans influence the gut microbiome and affect human health (2021)

Gut microbiome composition depends heavily upon diet and has strong ties to human health. Dietary carbohydrates shape the gut microbiome by providing a potent nutrient source for particular microbes. This review explores how dietary carbohydrates in general, including individual monosaccharides and complex polysaccharides, influence the gut microbiome with subsequent effects on host health and disease. In particular, the effects of sialic acids, a prominent and influential class of monosaccharides, are discussed. Complex plant carbohydrates, such as dietary fiber, generally promote microbial production of compounds beneficial to the host while preventing degradation of host carbohydrates from colonic mucus. In contrast, simple and easily digestible sugars such as glucose are often associated with adverse effects on health and the microbiome. The monosaccharide class of sialic acids exerts a powerful but nuanced effect on gut microbiota. Sialic acid consumption (in monosaccharide form, or as part of human milk oligosaccharides or certain animal-based foods) drives the growth of organisms with sialic acid metabolism capabilities. Minor chemical modifications of Neu5Ac, the most common form of sialic acid, can alter these effects. All aspects of carbohydrate composition are therefore relevant to consider when designing dietary therapeutic strategies to alter the gut microbiome.
Evolution of the ribosome at atomic resolution (2014)

Significance Ribosomes exist in every cell and are responsible for translation from mRNA to protein. The structure of the ribosomal common core is highly conserved in all living species, while the outer regions of the ribosome are variable. Ribosomal RNA of eukaryotes contains expansion segments accreted onto the surface of the core, which is nearly identical in structure to that in prokaryotic ribosomes. Comparing eukaryotic and prokaryotic ribosomes allows us to identify 3D insertion fingerprints of the expansion segments. Similar fingerprints allow us to analyze the common core and detect ancestral expansion segments within it. We construct a molecular model of ribosomal evolution starting from primordial biological systems near the dawn of life, culminating with relatively recent changes specific to metazoans.
Preparation and properties of polyaniline doped with poly(thiophenylenesulfonic acid) (1999)

A novel polyaromatic acid, poly(thiophenylenesulfonic acid) (PTPSA), prepared from a soluble precursor of poly(arylenesulfonium salt) was employed as a dopant for polyaniline (PAn). The electro-oxidative polymerization of aniline in PTPSA aqueous solution gives an electroactive PAn/PTPSA composite with three redox couples at 0.16, 0.53, and 0.71V (vs. SCE). Composites of different molar ratio ([SO3H]/[An] = 0.10, 0.21, 0.42, 0.50, 0.83, 1.67) was prepared in order to confirm the transformation from the emeraldine base to its PTPSA salt, where a quantitative doping reaction was observed by means of UV-VIS and IR measurements. The thermogravimetric analysis revealed that the composites do not decompose up to 200°C in nitrogen atmosphere. The composite ([SO3H]/[An] = 0.50) shows an electrical conductivity of 1.5 S·cm–1 at 30°C and 3.0×10–1 S·cm–1 at 170°C. The composite retains its conductivity after heating at 150°C for 24 h.
A specific inhibitor of ALDH1A3 regulates retinoic acid biosynthesis in glioma stem cells (2021)

Elevated aldehyde dehydrogenase (ALDH) activity correlates with poor outcome for many solid tumors as ALDHs may regulate cell proliferation and chemoresistance of cancer stem cells (CSCs). Accordingly, potent, and selective inhibitors of key ALDH enzymes may represent a novel CSC-directed treatment paradigm for ALDH<sup>+</sup> cancer types. Of the many ALDH isoforms, we and others have implicated the elevated expression of ALDH1A3 in mesenchymal glioma stem cells (MES GSCs) as a target for the development of novel therapeutics. To this end, our structure of human ALDH1A3 combined with in silico modeling identifies a selective, active-site inhibitor of ALDH1A3. The lead compound, MCI-INI-3, is a selective competitive inhibitor of human ALDH1A3 and shows poor inhibitory effect on the structurally related isoform ALDH1A1. Mass spectrometry-based cellular thermal shift analysis reveals that ALDH1A3 is the primary binding protein for MCI-INI-3 in MES GSC lysates. The inhibitory effect of MCI-INI-3 on retinoic acid biosynthesis is comparable with that of ALDH1A3 knockout, suggesting that effective inhibition of ALDH1A3 is achieved with MCI-INI-3. Further development is warranted to characterize the role of ALDH1A3 and retinoic acid biosynthesis in glioma stem cell growth and differentiation.
Role of antibiotics in treatment of diarrhea in school going children (2020)

To assess the efficacy of different antibiotic regime in treatment of diarrhoea of paediatric patients. Total of 40 paediatric patients with present of diarrhoea were included in the present study. All the patients were divided into two study groups with 20 patients in each group. Group 1 included subjects who were treated with ceftriaxone therapy while group2 included subjects who were treated with ciprofloxacin therapy. Microbial stool cultures were used as a standard for assessing the efficacy of both the antibiotic regimens. All the results were recorded in Microsoft excel sheet and were analyzed by SPSS software. Results: Mean age of the patients of group 1 and group 2 was 15.8 years and 14.9 years respectively. There were 12 males and 8 females in group 1 while there were 11 males and 9 females in group 2. Success rate among both the study groups was found to be 95 percent. Non- significant results were obtained while comparing the success rate of both the antibiotic treatment therapies. Conclusion: Both ceftriaxone and ciprofloxacin therapy are equally effective in treating diarrhoea in paediatric patients.
ChemInform Abstract: Diels—Alder Reactions of a Styrene‐Isocyanate: Unexpected Formation of a Pyridinone and Uracil. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Development of 1H-Pyrazolo[3,4-b]pyridines as Metabotropic Glutamate Receptor 5 Positive Allosteric Modulators (2016)

The metabotropic glutamate receptor 5 (mGluR5) is an attractive target for the treatment of schizophrenia due to its role in regulating glutamatergic signaling in association with the <i>N</i>-methyl-d-aspartate receptor (NMDAR). We describe the synthesis of 1<i>H</i>-pyrazolo[3,4-<i>b</i>]pyridines and their utility as mGluR5 positive allosteric modulators (PAMs) without inherent agonist activity. A facile and convergent synthetic route provided access to a structurally diverse set of analogues that contain neither the aryl-acetylene-aryl nor aryl-methyleneoxy-aryl elements, the predominant structural motifs described in the literature. Binding studies suggest that members of our new chemotype do not engage the receptor at the MPEP and CPPHA mGluR5 allosteric sites. SAR studies culminated in the first non-MPEP site PAM, 1<i>H</i>-pyrazolo[3,4-<i>b</i>]pyridine <b>31</b> (BMT-145027), to improve cognition in a preclinical rodent model of learning and memory.
The effect of the immunomodulatory peptide gamma-D-glutamyl-L-tryptophan in leukemia, lymphoma, and head and neck cancer xenograft models. (2011)

5592 Background: Gamma-D-glutamyl-L-tryptophan (SCV-07) is being studied for attenuation of oral mucositis in head and neck cancer patients receiving chemoradiation therapy. A challenge for agents which target regimen-related toxicities is to provide clinical benefit without detracting from the anti-tumor effects of the cancer therapy. Results of animal studies showed that SCV-07 decreased tumor growth in various xenograft models and did not alter the tumoricidal effect of radiation. Here we further describe SCV-07’s anti-tumor efficacy. Methods: Mice were inoculated with cell lines from the ATCC: EL-4 murine T cell lymphoma in C57/B6 mice; MOLT-4 human acute lymphoblastic leukemia, HL-60 human acute promyelocytic leukemia, and FADU human HNC in nude mice. When tumors reached 100 mm3, animals were treated daily with saline or various doses of SCV-07. Tumor size was measured every two days with micro-calipers; animals were weighed every day to assess possible toxicity. Any animal exhibiting a loss of >20% of starting weight or whose tumor grew to 1500 mm3 was euthanized. Statistical differences between treatment groups were determined using Mann-Whitney Rank Sum or ANOVA tests with a critical value of 0.05. Results: No animal deaths occurred as a direct result of SCV-07 treatment and no statistically significant differences in weight gain were seen between the SCV-07 and control groups. Tumors in SCV-07-treated animals grew more slowly than those in control animals; the reduction was dose-dependent and statistically significant. For EL-4 differences were seen in the groups treated with SCV-07 at 20 mg/kg (p=0.001) and 40 mg/kg (p<0.001); for MOLT-4 at10 mg/kg (p=0.003), 20 mg/kg (p=0.002) and 40 mg/kg (p<0.001); for HL-60 at 20 mg/kg (p=0.025) and 40 mg/kg (p=0.005); and for FADU at 20 mg/kg (p=0.004) and 40 mg/kg (p=0.004). Conclusions: The immune modulating peptide SCV-07 is able to inhibit growth of a variety of tumor cell line types, including a human head and neck tumor line in nude mice. These results suggest that the use of SCV-07 as an intervention for mucositis should not interfere with therapy, but may enhance the tumor response to conventional therapy.
Development of fine grained structures using severe plastic deformation (2000)

Severe plastic deformation provides a processing tool for introducing fine grain sizes into polycrystalline materials. This paper describes the principles of equal channel angular pressing (ECAP) in which a material is pressed through a die where two channels form an L shaped configuration. The process of ECAP imposes a severe strain on the sample but there is no concomitant change in the cross-sectional dimensions so that repetitive pressings may be undertaken to achieve very high total strains. Several factors influence the nature of the microstructures attained in ECAP including the processing route by which the sample is rotated between consecutive pressings, the angle subtended by the two channels within the die, and the speed and temperature associated with the pressing. These various factors are described for a series of experiments conducted on samples of pure aluminium.