gebhart/patrepeval huggingface dataset:
Pancreatic Precursors and Differentiated Islet Cell Types From Murine Embryonic Stem Cells (2003)

Embryonic stem (ES) cells differentiating in vitro reproduce many facets of early embryonic development, including the expression of developmentally regulated transcription factors and the differentiation of multipotent precursor cells. ES cells were evaluated for their ability to differentiate into pancreatic and islet lineage-restricted stages including pancreatic duodenal homeobox 1 (PDX1)-positive pancreatic precursor cells, early endocrine cell progenitors, and islet hormone-producing cells. Following growth and differentiation in nonselective medium containing serum, murine ES cells spontaneously differentiated into cells individually expressing each of the four major islet hormones: insulin, glucagon, somatostatin, and pancreatic polypeptide. PDX1 immunostaining cells appeared first, before hormone-positive cells had emerged. Hormone-positive cells appeared within focal clusters of cells coexpressing PDX1 and the nonclassical hormone markers peptide YY (YY) and islet amyloid polypeptide (IAPP) in combination with the definitive hormones, characteristic of endocrine cells appearing during early pancreaticogenesis. This system allows the investigation of many facets of islet development since it promotes the appearance of the complete range of islet phenotypes and reproduces important developmental stages of normal islet cytodifferentiation in differentiating ES cell cultures.
Adsorption Mechanism and Uptake of Methane in Covalent Organic Frameworks: Theory and Experiment (2010)

We determined the methane (CH(4)) uptake (at 298 K and 1 to 100 bar pressure) for a variety of covalent organic frameworks (COFs), including both two-dimensional (COF-1, COF-5, COF-6, COF-8, and COF-10) and three-dimensional (COF-102, COF-103, COF-105, and COF-108) systems. For all COFs, the CH(4) uptake was predicted from grand canonical Monte Carlo (GCMC) simulations based on force fields (FF) developed to fit accurate quantum mechanics (QM) [second order Møller-Plesset (MP2) perturbation theory using doubly polarized quadruple-ζ (QZVPP) basis sets]. This FF was validated by comparison with the equation of state for CH(4) and by comparison with the experimental uptake isotherms at 298 K (reported here for COF-5 and COF-8), which agrees well (within 2% for 1-100 bar) with the GCMC simulations. From our simulations we have been able to observe, for the first time, multilayer formation coexisting with a pore filling mechanism. The best COF in terms of total volume of CH(4) per unit volume COF absorbent is COF-1, which can store 195 v/v at 298 K and 30 bar, exceeding the U.S. Department of Energy target for CH(4) storage of 180 v/v at 298 K and 35 bar. The best COFs on a delivery amount basis (volume adsorbed from 5 to 100 bar) are COF-102 and COF-103 with values of 230 and 234 v(STP: 298 K, 1.01 bar)/v, respectively, making these promising materials for practical methane storage.
Enzymes Utilizing Glutamine as an Amide Donor (1998)

Amide nitrogen from glutamine is a major source of nitrogen atoms incorporated biosynthetically into other amino acids, purine and pyrimidine bases, amino-sugars, and coenzymes. A family comprised of at least sixteen amidotransferases are known to catalyze amide nitrogen transfer from glutamine to their acceptor substrates. Recent fine structural advances, largely as a result of X-ray crystallography, now provide structure-based mechanisms that help to explain fundamental aspects of the catalytic and regulatory interactions of several of these aminotransferases. This chapter provides an overview of this recent progress made on the characterization of amidotransferase structure and mechanism.
Vaccination of Metastatic Melanoma Patients With Autologous Tumor-Derived Heat Shock Protein gp96-Peptide Complexes: Clinical and Immunologic Findings (2002)

Vaccination of metastatic melanoma patients with autologous HSPPC-96 is feasible and devoid of significant toxicity. This vaccine induced clinical and tumor-specific T-cell responses in a significant minority of patients.
Expression of MUC1, MUC2, MUC3 and MUC4 mucin mrnas in human pancreatic and intestinal tumor cell lines (1994)

We examined the steady-state expression levels of mRNA for the MUC1, MUC2, MUC3 and MUC4 gene products in 12 pancreatic tumor cell lines, 6 colon tumor cell lines, and one ileocecal tumor cell line. The results showed that 10 of 12 pancreatic tumor cell lines expressed MUC1 mRNA and that 7 of these 12 lines also expressed relatively high levels of MUC4 mRNA. In contrast, MUC2 mRNA was expressed at only low levels and MUC3 was not detected in the pancreatic tumor cell lines. All 7 intestinal tumor cell lines examined expressed MUC2, and 5 of 7 expressed MUC3; however only one expressed significant levels of MUC1 and 2 expressed low levels of MUC4 mRNA. This report of high levels of MUC4 mRNA expression by pancreatic tumor cells raises the possibility that mucin carbohydrate epitopes defined by antibodies such as DuPan 2 may be expressed on a second mucin core protein produced by pancreatic tumor cells.
Detection of herpes simplex virus type 1 transcripts during latent infection in mice (1987)

A latent infection can be established in the trigeminal ganglia of mice after corneal inoculation of herpes simplex virus type 1 (HSV-1). With a virion DNA probe, three transcripts (2.0, 1.5, and 1.45 kilobases [kb]) were detected by Northern blot (RNA blot) analysis of RNAs isolated from the ganglia of latently infected mice. All three transcripts hybridized to a nick-translated HSV-1 DNA probe from BamHI restriction fragment B (strain F). These RNAs were mapped with subfragments of BamHI-B and with strand-specific probes. They are at least partially colinear with each other, map to a 3.0-kb PstI-MluI subfragment of BamHI-B, and are transcribed from left to right. The latent HSV-1 RNAs partially overlap the 3' end of ICP0 mRNA but are transcribed in the opposite direction. The latent RNAs were not as extensively poly(A)+ as actin mRNA. The HSV-1 transcripts detected in latently infected trigeminal ganglia did not correspond with any that have been previously identified in permissively infected cells in tissue culture. However, the 2.0-kb HSV-1 RNA present during latency was detectable at reduced levels in the trigeminal ganglia of acutely infected mice and in infected tissue culture cells. The data indicate that the pattern of viral gene expression during HSV-1 latency in the trigeminal ganglia of mice does not represent restriction of the genes actively transcribed during the lytic replication cycle in tissue culture.
Evolution of antiviral activity in the ribonuclease A gene superfamily: evidence for a specific interaction between eosinophil-derived neurotoxin (EDN/RNase 2) and respiratory syncytial virus (1998)

We have demonstrated that the human eosinophil-derived neurotoxin (EDN, RNase 2), a rapidly evolving secretory protein derived from eosinophilic leukocytes, mediates the ribonucleolytic destruction of extracellular virions of the single-stranded RNA virus respiratory syncytial virus (RSV). While RNase activity is crucial to antiviral activity, it is clearly not sufficient, as our results suggest that EDN has unique structural features apart from RNase activity that are necessary to promote antiviral activity. We demonstrate here that the interaction between EDN and extracellular virions of RSV is both saturatable and specific. Increasing concentrations of the antivirally inactivated, ribonucleolytically inactivated point mutant form of recombinant human EDN, rhEDNdK38, inhibits rhEDN's antiviral activity, while increasing concentrations of the related RNase, recombinant human RNase k6, have no effect whatsoever. Interestingly, acquisition of antiviral activity parallels the evolutionary development of the primate EDN lineage, having emerged some time after the divergence of the Old World from the New World monkeys. Using this information, we created ribonucleolytically active chimeras of human and New World monkey orthologs of EDN and, by evaluating their antiviral activity, we have identified an N-terminal segment of human EDN that contains one or more of the sequence elements that mediate its specific interaction with RSV.
Internal Ribosome Entry Sites Tests with Circular mRNAs (2003)

It was shown that eukaryotic ribosomes, in contrast to prokaryotic ribosomes, were unable to bind to small circular RNAs (1,2). This finding was a key feature in the scanning model for translational initiation, which postulates that eukaryotic 40S ribosomal subunits enter mRNAs exclusively at their free, capped 5′ ends like beads on a string (3). Subsequently, 40S subunits carrying eukaryotic translation initiation factors and initiator tRNAs are thought to scan the mRNA in a 5′ to 3′ direction until an appropriate AUG codon is encountered that can be used as start site for protein biosynthesis (3). However, this model has been challenged with the discovery of internal ribosome entry site (IRES) elements, present in certain viral and cellular mRNAs, that can mediate translational initiation without prior scanning of the mRNA by 40S sub-units (4–9).
Materials integration for high-performance photovoltaics by wafer bonding (2005)

The fundamental efficiency limit for state of the art triple-junction photovoltaic devices is being approached. By allowing integration of non-lattice-matched materials in monolithic structures, wafer bonding enables novel photovoltaic devices that have a greater number of subcells to improve the discretization of the solar spectrum, thus extending the efficiency limit of the devices. Additionally, wafer bonding enables the integration of non-lattice-matched materials with foreign substrates to confer desirable properties associated with the handle substrate on the solar cell structure, such as reduced mass, increased thermal conductivity, and improved mechanical toughness. This thesis outlines process development and characterization of wafer bonding integration technologies essential for transferring conventional triple-junction solar cell designs to potentially lower cost Ge/Si epitaxial templates. These epitaxial templates consist of a thin film of single-crystal Ge on a Si handle substrate. Additionally, a novel four-junction solar cell design consisting of non-lattice matched subcells of GaInP, GaAs, InGaAsP, and InGaAs based on InP/Si wafer-bonded epitaxial templates is proposed and InP/Si template fabrication and characterization is pursued. In this thesis the detailed-balance theory of the thermodynamic limiting performance of solar cell efficiency is applied to several device designs enabled by wafer bonding and layer exfoliation. The application of the detailed-balance theory to the novel four-junction cell described above shows that operating under 100 suns at 300 K a maximum efficiency of 54.9% is achievable with subcell bandgaps of 1.90, 1.42, 1.02, and 0.60 eV, a material combination achievable by integrating two wide-bandgap subcells lattice matched to GaAs and two narrow-bandgap subcells lattice matched to InP. Wafer bonding and layer transfer processes with sufficient quality to enable subsequent material characterization are demonstrated for both Ge/Si and InP/Si structures. The H-induced exfoliation process in each of these materials is studied using TEM, AFM, and FTIR to elucidate the chemical states of hydrogen leading to exfoliation. Additionally, the electrical properties of wafer-bonded interfaces between bulk-Ge/Si and bulk-InP/Si structures are show Ohmic, low-resistance electrical contact. Further studies of p-p isotype heterojunctions in Ge/Si indicate that significant conduction paths exist through defects at the bonded interface. The first known instance of epitaxy of III-V compound semiconductors on wafer-bonded Ge/Si epitaxial templates is demonstrated. Additionally InGaAs is grown on InP/Si templates that have been improved by removal of damage induced by the ion implantation and exfoliation processes.
Symbol nomenclature for glycan representation (2009)

The glycan symbol nomenclature proposed by Harvey et al. in these pages has relative advantages and disadvantages. The use of symbols to depict glycans originated from Kornfeld in 1978, was systematized in the First Edition of "Essentials of Glycobiology" and updated for the second edition, with input from relevant organizations such as the Consortium for Functional Glycomics. We also note that >200 illustrations in the second edition have already been published using our nomenclature and are available for download at PubMed.
Adhesive Technology: Surface Preparation Techniques on Aluminum (2009)

Chemical surface treatment of aluminum has a significant effect on the bonding characteristics and the applications in which adhesive bonding of aluminum is used. Chromic acid etching is one of the oldest and most widely conducted treatment methods in industry. Henkel Loctite often receives requests to perform the chromic acid etching process on aluminum but it can be hazardous and inefficient. An actual chromic acid etching system for aluminum was designed and compared to other surface treatment methods to determine if this system would be of benefit to the sponsor in the future.
Heterogeneity in the glycosylation pattern of human pancreatic ribonuclease. (1994)

Different molecular forms of ribonuclease were isolated from fresh human pancreas obtained from healthy transplant donors. The purification procedure consists of the preparation of an acetone powder, followed by (NH4)2SO4 precipitation and two chromatography steps (cationic exchange and reversed-phase). Protein bands in gel electrophoresis with RNAase activity were monitored using a negative-staining zymogram technique. Several glycosylated enzyme forms with apparent molecular masses ranging from 14 to 40 kDa were separated. Peptides containing the three Asn-Xaa-Thr/Ser acceptor sites for glycosylation were isolated and analysed. The site with Asn-34 was almost completely glycosylated, while the sites with Asn-76 and Asn-88 had carbohydrate in about half and a minor part of the molecules, respectively. The carbohydrate compositions of the glycopeptides are different from those of the same gene product isolated from human urine. C-Terminal threonine was present in part of the molecules, indicating partial degradation by carboxypeptidase.
Night Myopia (1976)

The relationship between night myopia under simulated night driving conditions and the dark focus accomodation was examined. Over a range of luminance and contrast conditions typical of the night driving situation, college-age subjects accommodated to about one-half the difference between a distant simulated road sign and their individual dark focus. Subsequent laboratory and field experiments demonstrated that: (1) a negative correction equal to one-half the value of the dark focus significantly improved night visual performance as compared with their normal or full dark-focus correction, and (2) greater improvements in performance were obtained for subjects who exhibited a relatively near dark focus.
Study of the role of the htrB gene in Salmonella typhimurium virulence (1997)

We have undertaken a study to investigate the contribution of the htrB gene to the virulence of pathogenic Salmonella typhimurium. An htrB::mini-Tn10 mutation from Escherichia coli was transferred by transduction to the mouse-virulent strain S. typhimurium SL1344 to create an htrB mutant. The S. typhimurium htrB mutant was inoculated into mice and found to be severely limited in its ability to colonize organs of the lymphatic system and to cause systemic disease in mice. A variety of experiments were performed to determine the possible reasons for this loss of virulence. Serum killing assays revealed that the S. typhimurium htrB mutant was as resistant to killing by complement as the wild-type strain. However, macrophage survival assays revealed that the S. typhimurium htrB mutant was more sensitive to the intracellular environment of murine macrophages than the wild-type strain. In addition, the bioactivity of the lipopolysaccharide (LPS) of the htrB mutant was reduced compared to that of the LPS from the parent strain as measured by both a Limulus amoebocyte lysate endotoxin quantitation assay and a tumor necrosis factor alpha bioassay. These results indicate that the htrB gene plays a role in the virulence of S. typhimurium.
Alternative Splicing Variant of Kallikrein-Related Peptidase 8 as an Independent Predictor of Unfavorable Prognosis in Lung Cancer (2010)

The KLK8-T4 alternative splice variant, alone or in combination, may be a new independent marker of unfavorable prognosis in lung cancer.
Synthesis of α,β-Unsaturated Carbonyl Compounds by Titanium Tetraalkoxide-Induced Aldol Condensation under Neutral Conditions (1990)

Aldehydes and ketones, when treated with titanium tetraalkoxides in a hydrocarbon solvent at 20-140°C, undergo aldol condensation to give a, α,β-unsaturated carbonyl compounds. To avoid Meerwein-Ponndorf-Verley type reduction of the carbonyl compounds, titantium tetra-tert-butoxide is used, if the reaction is carried out at higher temperatures. In all other cases titanium tetraisopropoxide can be successfully employed. The outlined procedure offers the possibility of performing aldol condensations under neutral conditions.
Alternatively spliced variants of prostate-specific membrane antigen RNA: ratio of expression as a potential measurement of progression. (1995)

We examined expression of prostate-specific membrane antigen (PSM) mRNA in normal prostate using reverse transcription-PCR and sequencing. An alternatively spliced variant, PSM', along with the previously described PSM form, was found in normal prostate. PSM' cDNA is shorter (2387 nucleotides) than PSM (2653 nucleotides). The cDNAs are identical except for a 266-nucleotide region near the 5' end of PSM cDNA (nucleotide 114-380) that is absent from PSM'. This deleted region includes the translation initiation codon and codons for the putative transmembrane domain of PSM. Thus, PSM' RNA codes for a protein that has no apparent signal sequence. We verified the existence of spliced mRNA variants in human primary tissue specimens by RNase protection assay. In LNCaP human prostatic cancer cells and in primary prostate tumors, PSM is the dominant form. In contrast, normal human prostate expressed more PSM' than PSM. Benign prostatic hypertrophy samples showed about equal expression of both variants. We quantified the relative expression of each variant by densitometry and compiled a tumor index, which is the ratio of PSM:PSM' level. LNCaP has an index ranging from 9-11, carcinoma of the prostate from 3-6, benign prostatic hypertrophy from 0.75-1.6, and normal prostate from 0.075-0.45. The index reflects the increased expression of PSM over PSM' following the progression from normal to tumor state. This tumor index may be a useful indicator for the measurement of tumor progression. PSM and PSM' may be functionally different proteins as a result of differences in structure or cellular location. We are investigating the prevalence of one form over the other and how it may influence tumor progression.
Design, synthesis, characterization and in-vivo activity of a novel salmon calcitonin conjugate containing a novel PEG-lipid moiety (2010)

The resultant novel PEG-lipid has a potential role to optimize protein and peptide delivery.
Fast and low voltage-driven solid-state electrochromics using 3-D conductive FTO nanobead electrodes (2013)

A solid-state electrochromic device using 3-D conducting fluorinated tin oxide nanobeads (roughness factor >500) as electrodes enables fast electron transport and concentrates the voltage drop at the interfaces. This method reduces the driving voltage to 0.9 V and the response time to ∼272 ms, far exceeding the performance of conventional 2-D flat FTO film-based counterparts.
R. H. Smith (1991)

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A two-step hybridization method for chemiluminescent detection of single copy genes. (1992)

We have developed a technique for the chemiluminescent detection of single copy genes that eliminates the high backgrounds and problems with probe labeling associated with existing methods. The procedure employs a primary hybridization of single-stranded probe DNA to immobilized target DNA, a secondary hybridization with a covalently cross-linked oligonucleotide-alkaline phosphatase conjugate, followed by incubation in the chemiluminescent substrate AMPPD and detection on x-ray film. The key to the success of this method is that the primary probe contains a region complementary to the target DNA as well as to the oligonucleotide sequence of the secondary probe-alkaline phosphatase conjugate. Here we report our results using the two-step hybridization procedure to detect single copy genes from genomic Southern blots.
T cell acute lymphoblastic leukemia/lymphoma: a human cancer commonly associated with aberrant NOTCH1 signaling (2004)

These findings support a central role for aberrant NOTCH signaling in the pathogenesis of human T cell acute lymphoblastic leukemia/lymphoma, and they provide a rationale for trials of NOTCH inhibitors, such as gamma-secretase antagonists, in this aggressive human malignancy.
Characterization of the physical interaction between antigen-specific B and T cells. (1986)

It has been assumed that physical interaction between B cells and helper T cells in the presence of specific antigen is an early and essential step in the physiologic antibody response to thymus-dependent antigens. The present studies were designed to examine this physical interaction by employing carrier-specific T hybridoma cells that can provide help to highly enriched hapten-binding B cells. Direct conjugation of the B and T cells can be visualized at both the light and electron microscopic level and the number of conjugates can be directly quantified. Before their effective conjugation with T cells, the B cells must be incubated with specific antigen for 4 to 6 hr. After this time, the T cells form conjugates with the B cells within 5 min. Conjugate formation requires hapten specificity, carrier specificity, covalent linkage between hapten and carrier, and is MHC restricted. Two types of T-B conjugates were observed by electron microscopy: an antigen-independent attachment of B cell microvilli to small portions of the T cell surface and an antigen-dependent, intimate apposition of large areas of the plasma membranes of the T and B cells. The kinetics of development of the two modes of interaction suggest that the second type may be important for signal transduction, since the number of T and B cells showing intimate interactions increases with time. Monoclonal antibodies directed against Thy-1.2, LFA-1 alpha, L3T4, and I-A partially block conjugation of the two cell types, suggesting that these surface molecules are involved in T-B interaction.
Measured capacity of an Ethernet: myths and reality (1988)

Ethernet, a 10 Mbit/sec CSMA/CD network, is one of the most successful LAN technologies. Considerable confusion exists as to the actual capacity of an Ethernet, especially since some theoretical studies have examined operating regimes that are not characteristic of actual networks. Based on measurements of an actual implementation, we show that for a wide class of applications, Ethernet is capable of carrying its nominal bandwidth of useful traffic, and allocates the bandwidth fairly. We discuss how implementations can achieve this performance, describe some problems that have arisen in existing implementations, and suggest ways to avoid future problems.