gebhart/patrepeval huggingface dataset:
Alpha‐Lactalbumin: Its Production Technologies and Bioactive Peptides (2010)

ABSTRACT: Alpha‐lactalbumin (α‐La), a globular protein found in all mammalian milk, has been used as an ingredient in infant formulas. The protein can be isolated from milk using chromatography/gel filtration, membrane separation, enzyme hydrolysis, and precipitation/aggregation technologies. α‐La is appreciated as a source of peptides with antitumor and apoptosis, antiulcerative, immune modulating, antimicrobial, antiviral, antihypertensive, opioid, mineral binding, and antioxidative bioactivities, which may be utilized in the production of functional foods. Nanotubes formed by the protein could find applications in foods and pharmaceuticals, and understanding its amyloid fibrils is important in drawing strategies for controlling amyloidal diseases. Bioactive peptides in α‐La are released during the fermentation or ripening of dairy products by starter and nonstarter microorganisms and during digestion by gastric enzymes. Bioactive peptides are also produced by deliberate hydrolysis of α‐La using animal, microbial, or plant proteases. The occurrence, structure, and production technologies of α‐La and its bioactive peptides are reviewed.
Detoxification of environmental mutagens and carcinogens: Structure, mechanism, and evolution of liver epoxide hydrolase (1999)

The crystal structure of recombinant murine liver cytosolic epoxide hydrolase (EC 3.3.2.3) has been determined at 2.8-A resolution. The binding of a nanomolar affinity inhibitor confirms the active site location in the C-terminal domain; this domain is similar to that of haloalkane dehalogenase and shares the alpha/beta hydrolase fold. A structure-based mechanism is proposed that illuminates the unique chemical strategy for the activation of endogenous and man-made epoxide substrates for hydrolysis and detoxification. Surprisingly, a vestigial active site is found in the N-terminal domain similar to that of another enzyme of halocarbon metabolism, haloacid dehalogenase. Although the vestigial active site does not participate in epoxide hydrolysis, the vestigial domain plays a critical structural role by stabilizing the dimer in a distinctive domain-swapped architecture. Given the genetic and structural relationships among these enzymes of xenobiotic metabolism, a structure-based evolutionary sequence is postulated.
Hermansky–Pudlak Syndrome and Related Disorders of Organelle Formation (2000)

Hermansky-Pudlak syndrome (HPS) consists of a group of genetically heterogeneous disorders which share the clinical findings of oculocutaneous albinism, a platelet storage pool deficiency, and some degree of ceroid lipofuscinosis. Related diseases share some of these findings and may exhibit other symptoms and signs but the underlying defect in the entire group of disorders involves defective intracellular vesicle formation, transport or fusion. Two HPS-causing genes, HPS1 and ADTB3A, have been isolated but the function of only the latter has been determined. ADTB3A codes for the beta 3A subunit of adaptor complex-3, responsible for vesicle formation from the trans-Golgi network (TGN). The many HPS patients who do not have HPS1 or ADTB3A mutations have their disease because of mutations in other genes. Candidates for these HPS-causing genes include those responsible for mouse models of HPS or for the 'granule' group of eye color genes in Drosophila. Each gene responsible for a subset of HPS or a related disorder codes for a protein which almost certainly plays a pivotal role in vesicular trafficking, inextricably linking clinical and cell biological interests in this group of diseases.
Escherichia coli dnaK null mutants are inviable at high temperature (1987)

DnaK, a major Escherichia coli heat shock protein, is homologous to major heat shock proteins (Hsp70s) of Drosophila melanogaster and humans. Null mutations of the dnaK gene, both insertions and a deletion, were constructed in vitro and substituted for dnaK+ in the E. coli genome by homologous recombination in a recB recC sbcB strain. Cells carrying these dnaK null mutations grew slowly at low temperatures (30 and 37 degrees C) and could not form colonies at a high temperature (42 degrees C); furthermore, they also formed long filaments at 42 degrees C. The shift of the mutants to a high temperature evidently resulted in a loss of cell viability rather than simply an inhibition of growth since cells that had been incubated at 42 degrees C for 2 h were no longer capable of forming colonies at 30 degrees C. The introduction of a plasmid carrying the dnaK+ gene into these mutants restored normal cell growth and cell division at 42 degrees C. These null mutants showed a high basal level of synthesis of heat shock proteins except for DnaK, which was completely absent. In addition, the synthesis of heat shock proteins after induction in these dnaK null mutants was prolonged compared with that in a dnaK+ strain. The well-characterized dnaK756 mutation causes similar phenotypes, suggesting that they are caused by a loss rather than an alteration of DnaK function. The filamentation observed when dnaK mutations were incubated at a high temperature was not suppressed by sulA or sulB mutations, which suppress SOS-induced filamentation.(ABSTRACT TRUNCATED AT 250 WORDS)
B7-1 but not B7-2 efficiently costimulates CD8+ T lymphocytes in the P815 tumor system in vitro (1996)

We recently have developed a method to generate primary P815-specific CTL in vitro from normal syngeneic splenocytes by employing transfection of B7-1 combined with exogenous IL-12 and IL-6. Surprisingly, when the homologous costimulator molecule B7-2 was substituted for B7-1 in this system, no specific CTL activity was obtained. Similarly, B7-1- but not B7-2-transfected P815 cells generated alloantigen-specific CTL activity from C57BL/6, accessory cell- and CD4(+)-depleted splenocytes, and costimulated proliferation of CD8+ lymphocytes in the presence of low doses of anti-CD3 mAb. In all systems, combined expression of both B7-1 and B7-2 costimulated as effectively as B7-1 alone, arguing against delivery of a dominant negative signal by B7-2. Proliferation of allogeneic, CD4(+)-depleted splenocytes in response to P815 cells, which relies on costimulation by normal accessory cells, was inhibited by anti-B7-1 but not anti-B7-2 mAbs. Finally, indirect evidence suggested a higher avidity of B7-1+ cells than B7-2+ cells for CTLA4. Thus, at least in the context of primary stimulation by irradiated P815 transfectants, B7-1 appears to be superior to B7-2 at costimulation of CD8+ T lymphocytes.
Extensible query processing in starburst (1989)

Today's DBMSs are unable to support the increasing demands of the various applications that would like to use a DBMS. Each kind of application poses new requirements for the DBMS. The Starburst project at IBM's Almaden Research Center aims to extend relational DBMS technology to bridge this gap between applications and the DBMS. While providing a full function relational system to enable sharing across applications, Starburst will also allow (sophisticated) programmers to add many kinds of extensions to the base system's capabilities, including language extensions (e.g., new datatypes and operations), data management extensions (e.g., new access and storage methods) and internal processing extensions (e.g., new join methods and new query transformations). To support these features, the database query language processor must be very powerful and highly extensible. Starburst's language processor features a powerful query language, rule-based optimization and query rewrite, and an execution system based on an extended relational algebra. In this paper, we describe the design of Starburst's query language processor and discuss the ways in which the language processor can be extended to achieve Starburst's goals.
DNA-Mediated Fluctuations in Ionic Current through Silicon Oxide Nanopore Channels (2004)

Single molecule sensors in which nanoscale pores within biological or artificial membranes act as mechanical gating elements are very promising devices for the rapid characterization and sequencing of nucleic acid molecules. The two terminal electrical measurements of translocation of polymers through single ion channels and that of ssDNA molecules through protein channels have been demonstrated, and have sparked tremendous interest in such single molecule sensors. The prevailing view regarding the nanopore sensors is that there exists no electrical interaction between the nanopore and the translocating molecule, and that all nanopore sensors reported to-date, whether biological or artificial, operate as a coulter-counter, i.e., the ionic current measured across the pore decreases (is mechanically blocked) when the DNA molecule transverses through the pore. We have fabricated nanopore “channel” sensors with a silicon oxide inner surface, and our results challenge the prevailing view of exclusive mechanical interaction during the translocation of dsDNA molecules through these channels. We demonstrate that the ionic current can actually increase due to electrical gating of surface current in the channel due to the charge on the DNA itself.
Substantial Background Reduction in Ligase-Based Apoptosis Detection Using Newly Designed Hairpin Oligonucleotide Probes (1999)

A method for selective detection of apoptotic cells by ligation of DNA probes to the ends of specific double-stranded DNA breaks in tissue sections was recently reported (1). Unfortunately, this method produces high levels of background staining, due to nonspecific attachment of the probes to the tissue sections, and thereby requires extensive and repeated washing. In the current study we redesigned the oligoprobes in a manner that virtually eliminated background staining. This new design substantially reduces the cost of the probe preparation, making it a convenient and robust methodology to detect apoptosis.
Immunoblot assay using excreted-secreted antigens of Trypanosoma cruzi in serodiagnosis of congenital, acute, and chronic Chagas' disease (1996)

Immunoblotting with trypomastigote excreted-secreted antigens (TESA blot) of Trypanosoma cruzi was evaluated as a method for diagnosis of chronic and acute phases as well as congenital (in newborn children) Chagas' disease. Serum samples from acute-phase and congenital infections were considered to be positive when they reacted with ladder-like bands of 130- to 200-kDa antigens, recognized by immunoglobulin M (IgM) and IgG antibodies, while IgG from chronic-phase sera recognized a broad band antigen of 150 to 160 kDa. Nonchagasic sera were not reactive to these antigens. The study was carried out on 512 patients, 111 of whom were nonchagasic but included cases of leishmaniasis or other pathologies, and 401 chagasic patients. The latter group comprised 361 chronic cases, 36 acute cases, and 4 congenital cases in newborn children. Among the chronic cases, 256 were from areas in which T. cruzi is endemic but which differed widely in the pathogenic expression of T. cruzi infection and in parasitemia levels. These patients at the same time showed a broad range of low, medium, and high reactivity to conventional enzyme-linked immunosorbent assays and indirect immunofluorescence serotests for Chagas' disease. For these reasons they may better represent the universe of chagasic patients than would a sample of highly reactive sera obtained from chagasic patients in a single area endemic for T. cruzi. All acute and congenital cases showed positivity in the IgM and IgG TESA blots, while chronic cases were 100% positive for IgG antibodies. In nonchagasic sera, including 30 cases of visceral and muco-cutaneous leishmaniasis, the specificity index was 1.000, and no cross-reactions were observed. The TESA blot thus seems to be useful as a sensitive and specific diagnostic assay in cases of suspected acute or congenital T. cruzi infection and as a general confirmatory test for conventional Chagas' disease serology.
Mass spectrometry in the development of drugs from traditional medicines (1994)

The mass spectrometer ionizes molecules to separate and weigh the resulting molecular ions and their dissociation products. These product masses indicate directly the sequence of constituents of the original molecule, such as amino acids in proteins or bases in nucleotides. Because single ions can be detected, even subfemtomole sensitivities are possible. In tandem mass spectrometry (MS/MS), molecular ions from a mixture can be separated to isolate ions of a specific component, whose further dissociation can then give structural information on that component. Electrospray ionization and other recently developed methods make possible the ionization of biomolecules even larger than 100 kDa. The Fourier-transfer mass spectrometer has unusual capabilities for measuring ions over a 100 kDa mass range simultaneously at unit resolution for MS/MS applications utilizing subfemtomole sample quantities.
Asymmetric Transition-Metal-Catalyzed Allylic Alkylations:  Applications in Total Synthesis (2003)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAsymmetric Transition-Metal-Catalyzed Allylic Alkylations: Applications in Total SynthesisBarry M. Trost and Matthew L. CrawleyView Author Information Department of Chemistry, Stanford University, Stanford, California 94305-5080 Cite this: Chem. Rev. 2003, 103, 8, 2921–2944Publication Date (Web):June 21, 2003Publication History Received21 January 2003Published online21 June 2003Published inissue 1 August 2003https://pubs.acs.org/doi/10.1021/cr020027whttps://doi.org/10.1021/cr020027wresearch-articleACS PublicationsCopyright © 2003 American Chemical SocietyRequest reuse permissionsArticle Views34612Altmetric-Citations2528LEARN 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 SUBJECTS:Alcohols,Ligands,Organic synthesis,Post-translational modification,Substitution reactions Get e-Alerts
Highly Precise Shape Mimicry by a Difluorotoluene Deoxynucleoside, a Replication‐Competent Substitute for Thymidine (1997)

Large differences in the electrostatic properties of nucleosides can have surprisingly small effects on DNA replication. Size and shape appear to be more important, as structural studies of difluorotoluene deoxynucleoside 1, an isostere of thymidine (2), prove. The two nucleosides have virtually the same aromatic ring, almost identical sugar puckers, and very similar glycosidic angles (see the structural formulas). Hydrogen-bonding capacity is apparently not crucial for templating in DNA replication.
Twin Vivaldi antenna fed by coplanar waveguide (1997)

The authors describe twin Vivaldi antennas directly fed by a coplanar waveguide. They have been designed and measured for various angles between the radiating slots. All the designs show a centred zero in the E plane with a low cross-polarisation. In the H plane they provide zeros for phis = 90° and 270° and are omnidirectional for other values.
Adoptive immunotherapy with tumor-infiltrating lymphocytes and interleukin-2 in patients with metastatic malignant melanoma and renal cell carcinoma: a pilot study. (1995)

Immunotherapy with polyclonally activated TIL and moderate-dose IL-2 could be successfully used for the treatment of immunogenic tumors with less toxicity and lower costs as compared with high-dose IL-2 protocols.
Challenges and Opportunities for Small Molecule Aptamer Development (2012)

Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.
Image-based adaptive optics for two-photon microscopy (2009)

We demonstrate wavefront sensorless aberration correction in a two-photon excited fluorescence microscope. Using analysis of the image-formation process, we have developed an optimized correction scheme permitting image-quality improvement with minimal additional exposure of the sample. We show that, as a result, our correction process induces little photobleaching and significantly improves the quality of images of biological samples. In particular, increased visibility of small structures is demonstrated. Finally, we illustrate the use of this technique on various fresh and fixed biological tissues.
Modeling flexural plate wave devices (2000)

A lumped-parameter model is derived for flexural plate wave (FPW) devices which are rectangular plates or diaphragms with structural layers, a piezoelectric layer, and with interdigitated conducting combs for driving and sensing. This configuration is often used in micromechanical chemical sensors. The model is based an a closed-form solution of a resonating beam; however, the results are applicable to plates supported on four edges. The model gives a voltage or charge output from the sense combs as a function of voltage applied to the drive combs. The analysis predicts the response of the multiple plate modes to axial tensions and to comb finger dimensions and position relative to the diaphragm eigenfunctions. These models are much more detailed than those described in the literature on acoustic chemical sensors and are difficult to obtain by finite-element solutions. Frequency responses of FPW devices constructed from silicon with deposited aluminum nitride as the piezoelectric compared well with analytic results. The effects of boundary conditions on the plate's lateral edges are discussed in both the analysis and testing.
Wavelength stabilization of a DBR laser using an in-fiber Bragg filter (1993)

A control loop that stabilizes the wavelength of a tunable distributed-Bragg-reflector (DBR) laser is discussed. An in-fiber Bragg grating is used as the wavelength reference. Over a 25-hour period, this control loop held the laser wavelength constant to within 0.022 nm. This variation is traced to the temperature dependence of the in-fiber Bragg grating and can be reduced by controlling the grating's temperature.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A random forest-based framework for 3D kidney segmentation from dynamic contrast-enhanced CT images (2016)

A framework for 3D kidney segmentation from abdominal computed tomography (CT) images is proposed. Accurate kidney segmentation from CT images is a challenging task due to the large inhomogeneity of the kidney (e.g., cortex and medulla), inter-patient anatomical differences, etc. To account for these challenges, a novel framework utilizing random forest (RF) classification that has the ability to cluster complex data is proposed. To build a robust classification model, discriminative features are needed for better separation of data classes. In this work, regional features from the CT appearance, a kidney shape prior model, and higher-order spatial interactions are extracted and are used for tissue classification. The shape model is constructed using a set of training images and is updated during segmentation using an appearance-based method taking into account both voxels' locations and appearances. The spatial interactions between CT data voxels are modeled using a higher-order spatial model that adds to the pairwise cliques the families of the triple- and quad cliques. The proposed framework has been tested on CT data that has been collected from 20 subjects and consist of multiple 3D CT scans acquired at the pre-and post-contrast agent administration. Evaluation results, using both volumetric and distance-based metrics, between manually drawn and automatically segmented contours confirm the high accuracy of the proposed technique.
Database searching using mass spectrometry data (1998)

Large-scale DNA sequencing is creating a sequence infrastructure of great benefit to protein biochemistry. Concurrent with the application of large-scale DNA sequencing to whole genome analysis, mass spectrometry has attained the capability to rapidly, and with remarkable sensitivity, determine weights and amino acid sequences of peptides. Computer algorithms have been developed to use the two different types of data generated by mass spectrometers to search sequence databases. When a protein is digested with a site-specific protease, the molecular weights of the resulting collection of peptides, the mass map or fingerprint, can be determined using mass spectrometry. The molecular weights of the set of peptides derived from the digestion of a protein can then be used to identify the protein. Several different approaches have been developed. Protein identification using peptide mass mapping is an effective technique when studying organisms with completed genomes. A second method is based on the use of data created by tandem mass spectrometers. Tandem mass spectra contain highly specific information in the fragmentation pattern as well as sequence information. This information has been used to search databases of translated protein sequences as well as nucleotide databases such as expressed sequence tag (EST) sequences. The ability to search nucleotide databases is an advantage when analyzing data obtained from organisms whose genomes are not yet completed, but a large amount of expressed gene sequence is available (e.g., human and mouse). Furthermore, a strength of using tandem mass spectra to search databases is the ability to identify proteins present in fairly complex mixtures.
The myosin-binding UCS domain but not the Hsp90-binding TPR domain of the UNC-45 chaperone is essential for function in Caenorhabditis elegans (2011)

The UNC-45 family of molecular chaperones is expressed in metazoan organisms from Caenorhabditis elegans to humans. The UNC-45 protein is essential in C. elegans for early body-wall muscle cell development and A-band assembly. We show that the myosin-binding UCS domain of UNC-45 alone is sufficient to rescue lethal unc-45 null mutants arrested in embryonic muscle development and temperature-sensitive loss-of-function unc-45 mutants defective in worm A-band assembly. Removal of the Hsp90-binding TPR domain of UNC-45 does not affect rescue. Similar results were obtained with overexpression of the same fragments in wild-type nematodes when assayed for diminution of myosin accumulation and assembly. Titration experiments show that, on a per molecule basis, UCS has greater activity in C. elegans muscle in vivo than full-length UNC-45 protein, suggesting that UNC-45 is inhibited by either the TPR domain or its interaction with the general chaperone Hsp90. In vitro experiments with purified recombinant C. elegans Hsp90 and UNC-45 proteins show that they compete for binding to C. elegans myosin. Our in vivo genetic and in vitro biochemical experiments are consistent with a novel inhibitory role for Hsp90 with respect to UNC-45 action.