gebhart/patrepeval huggingface dataset:
Analysis of the Hand1 cell lineage reveals novel contributions to cardiovascular, neural crest, extra‐embryonic, and lateral mesoderm derivatives (2010)

The basic Helix-Loop-Helix (bHLH) transcription factors Hand1 and Hand2 play critical roles in the development of multiple organ systems during embryogenesis. The dynamic expression patterns of these two factors within developing tissues obfuscate their respective unique and redundant organogenic functions. To define cell lineages potentially dependent upon Hand gene expression, we generated a mutant allele in which the coding region of Hand1 is replaced by Cre recombinase. Subsequent Cre-mediated activation of β-galactosidase or eYFP reporter alleles enabled lineage trace analyses that clearly define the fate of Hand1-expressing cells. Hand1-driven Cre marks specific lineages within the extra embryonic tissues, placenta, sympathetic nervous system, limbs, jaw, and several cell types within the cardiovascular system. Comparisons between Hand1 expression and Hand1-lineage greatly refine our understanding of its dynamic spatial-temporal expression domains and raise the possibility of novel Hand1 functions in structures not thought to be Hand1-dependent.
Secondary Structure and Interfacial Aggregation of Amyloid-β(1−40) on Sodium Dodecyl Sulfate Micelles (2006)

Alzheimer's disease (AD) is characterized by the presence of large numbers of fibrillar amyloid deposits in the form of senile plaques in the brain. The fibrils in senile plaques are composed of 40- and 42-residue amyloid-beta (Abeta) peptides. Several lines of evidence indicate that fibrillar Abeta and especially soluble Abeta aggregates are important in the pathogenesis of AD, and many laboratories have investigated soluble Abeta aggregates generated from monomeric Abeta in vitro. Of these in vitro aggregates, the best characterized are called protofibrils. They are composed of globules and short rods, show primarily beta-structure by circular dichroism (CD), enhance the fluorescence of bound thioflavin T, and readily seed the growth of long fibrils. However, one difficulty in correlating soluble Abeta aggregates formed in vitro with those in vivo is the high probability that cellular interfaces affect the aggregation rates and even the aggregate structures. Reports that focus on the features of interfaces that are important in Abeta aggregation have found that amphiphilic interactions and micellar-like Abeta structures may play a role. We previously described the formation of Abeta(1-40) aggregates at polar-nonpolar interfaces, including those generated at microdroplets formed in dilute hexafluoro-2-propanol (HFIP). Here we compared the Abeta(1-40) aggregates produced on sodium dodecyl sulfate (SDS) micelles, which may be a better model of biological membranes with phospholipids that have anionic headgroups. At both HFIP and SDS interfaces, changes in peptide secondary structure were observed by CD immediately when Abeta(1-40) was introduced. With HFIP, the change involved an increase in predominant beta-structure content and in fluorescence with thioflavin T, while with SDS, a partial alpha-helical conformation was adopted that gave no fluorescence. However, in both systems, initial amorphous clustered aggregates progressed to soluble fibers rich in beta-structure over a roughly 2 day period. Fiber formation was much faster than in the absence of an interface, presumably because of the close intermolecular proximity of peptides at the interfaces. While these fibers resembled protofibrils, they failed to seed the aggregation of Abeta(1-40) monomers effectively.
Refractory silicides of titanium and tantalum for low-resistivity gates and interconnects (1980)

A study of the refractory-gate metallization schemes had been undertaken to provide a low-resistivity metallization for LSI and VLSI. In this paper, we describe an overview of the efforts made in this direction and present two different metallization schemes which lead to a resistivity of ≤20 and 40 µΩ.cm at the gate level. These schemes involve formation of titanium and tantalum silicides on polysilicon gates, respectively. The recommended structure is a metal or a cosputtered alloy/polysilicon/gate oxide/substrate which, when sintered, gives the desired structure silicide/polysilicon/gate oxide substrate. By the use of 1000-Å Ti or Ta, the sheet resistance of nearly 1 or 2 Ω/□, respectively, can be routinely obtained. The silicides are mechanically strong and can be dry etched using radial-flow or barrel-type plasma reactors. The Ta silicide structure is found to be very stable throughout standard processing and can be retrofitted in the present processing sequence. Ti silicide structures are similarly stable except for the reactivity of the silicide with HF-containing reagents. The Ti silicide metallization scheme can therefore be employed in processing with changes incorporated to avoid HF-silicide contact.
Efficacy and Safety of the Neuraminidase Inhibitor Zanamivirin the Treatment of Influenza A and B Virus Infections (1999)

The efficacy and safety of zanamivir, administered 2x or 4x daily over 5 days, was evaluated in the treatment of influenza infections. A total of 1256 patients entered the study; 57% of those randomized had laboratory-confirmed influenza infection. The primary end point, "alleviation of major symptoms," was created to evaluate differences in clinical impact. In the overall population with or without influenza infection, zanamivir reduced the median number of days to reach this end point by 1 day (P=.012 2x daily vs. placebo; P=.014 4x daily vs. placebo). The reduction was greater in patients treated within 30 h of symptom onset, febrile at study entry, and in defined high-risk groups. Zanamivir reduced nights of disturbed sleep, time to resumption of normal activities, and use of symptom relief medications. It was well tolerated. These results suggest that zanamivir can significantly reduce the duration and overall symptomatic effect of influenza.
Trypsin Action on the Growth of Sendai Virus in Tissue Culture Cells III. Structural Difference of Sendai Viruses Grown in Eggs and Tissue Culture Cells (1973)

Polypeptides of egg-borne Sendai virus (egg Sendai), which is biologically active on the basis of criteria of the infectivity for L cells and of hemolytic and cell fusion activities, were compared by polyacrylamide gel electrophoresis with those of L cell-borne (L Sendai) and HeLa cell-borne Sendai (HeLa Sendai) viruses, which are judged biologically inactive by the above criteria. Densitometer profiles on the stained gels of egg Sendai resolved six polypeptides (virion protein [VP] 1 to VP6), in which VP2 and VP4 were identified as glycoproteins by PAS stain. Comparative electropherograms of both L Sendai and HeLa Sendai revealed that there were significantly larger amounts in the VP2 region of these viruses but VP4 was present only in greatly reduced amounts as compared to egg Sendai. It was also found that VP2 of L Sendai and HeLa Sendai consisted of two components, VP2a and VP2b, but the one of egg Sendai consisted of only VP2a. A mild trypsin treatment which converts both L Sendai and HeLa Sendai to a biologically active form selectively removed VP2b from these viruses and increased concomitantly the amounts of materials in the VP4 region. The same treatment of egg Sendai affected neither its biological activities nor its electropherogram. Consequently, gross polypeptide profiles on the stained gels of L Sendai and HeLa Sendai after trypsin treatment became favorably comparable to that of egg Sendai. Electrophoresis of labeled L Sendai and HeLa Sendai with a (3)H-amino acids mixture and (14)C-glucosamine resolved at least three glycoproteins, GP1, GP2, and GP3, each corresponding to VP2a, VP2b, and VP4, respectively. The trypsin treatment of these viruses removed almost all the radioactivity of GP2 and simultaneously increased the radioactive counts of GP3 and raised small amounts of rapidly moving heterogeneous glycoprotein, GP4. A possible relationship between the biological modification and the above characteristic polypeptide patterns of Sendai virus was discussed.
Mucosal Vaccination against Serogroup B Meningococci: Induction of Bactericidal Antibodies and Cellular Immunity following Intranasal Immunization with NadA of Neisseria meningitidis and Mutants of Escherichia coli Heat-Labile Enterotoxin (2004)

Conjugated polysaccharide vaccines protect against serogroup C meningococci. However, this approach cannot be applied to serogroup B, which is still a major cause of meningitis. We evaluated the immunogenicity of three surface-exposed proteins from serogroup B Neisseria meningitidis (App, NhhA, and NadA) identified during whole-genome sequencing. Mice were immunized intranasally with individual proteins in the presence of wild-type Escherichia coli heat-labile enterotoxin (LTwt), LTR72, a partially inactivated mutant, or LTK63, a completely nontoxic mutant, as the adjuvant. Each of the meningococcal proteins induced significant cellular responses; NhhA and NadA induced strong antibody responses, but only NadA induced bactericidal antibody when administered intranasally with mucosal adjuvants. In addition, immunoglobulin A and bactericidal antibodies were detected in the respiratory tract following intranasal delivery of NadA. Analysis of antigen-specific cytokine production by T cells from immunized mice revealed that intranasal immunization with NadA alone failed to generate detectable cellular immune responses. In contrast, LTK63, LTR72, and LTwt significantly augmented NadA-specific gamma interferon, interleukin-4 (IL-4), IL-5, and IL-10 production by spleen and lymph node cells, suggesting that both Th1 and Th2 cells were induced in vivo. The strongest cellular responses and highest bactericidal antibody titers were generated with LTR72 as the adjuvant. These findings demonstrate that the quality and magnitude of the immune responses generated by mucosal vaccines are influenced by the antigen as well as the adjuvant and suggest that nasal delivery of NadA with mucosal adjuvants has considerable potential in the development of a mucosal vaccine against serogroup B meningococci.
Th1 and Th2 cytokine profile in patients with early onset periodontitis and their healthy siblings (2000)

Early onset periodontitis (EOP) is a chronic inflammatory periodontal disease with a strong genetic link affecting individuals aged 17 to 25. In the familial studies we tested the hypothesis about the role of Th1 and Th2 cytokines in the pathogenesis of EOP disease. The study involved 6 individuals with EOP disease and their 6 siblings with healthy periodontium. Actinobacillus actinomycetemcomitans (A. a), a bacterium typical for EOP, was detected in all people studied. Th1 and Th2 cytokine production was measured after in vitro stimulation. Peripheral blood mononuclear cells (PBMC) were isolated and cultivated for 24 h and 7 days with PWM, A. a. or Escherichia coli. The levels of IL-4, IFN-gamma, IgA, IgG and IgM were measured by ELISA methods. After in vitro stimulation of PBMC, a significantly higher production of IL-4 and significantly lower production of IFN-gamma were found in the group of patients compared with their healthy siblings. The increased level of IL-4 in patients was in good agreement with an increased level of IgM after stimulation of lymphocytes with E. coli. These results support Seymour's hypothesis according to which patients with progressive disease primarily activate Th2 lymphocytes while non-susceptible individuals activate Th1 lymphocytes.
Measurements and Performance Evaluation of Novel Interdigital Sensors for Different Chemicals Related to Food Poisoning (2011)

New types of planar interdigital sensors, were fabricated using three different methods. These sensors were used to assess different chemicals related to food poisoning. The sensors were designed to have different configurations and were constructed on different substrates. The substrate variation was used to investigate the effect of substrate properties on sensing performance. The first design was fabricated on a Printed Circuit Board (PCB) material made from a FR4 fiberglass; the second sensor design was fabricated using thick film on alumina. The third sensor was designed using thin-film [microelectromechanical systems (MEMS)] technology and was fabricated on a glass substrate. The performances of the sensors were evaluated for different configurations of the electrode structures as well as dielectric materials. Initial experiments have been conducted to analyze the sensor's performance with two peptide derivatives, namely, Sarcosine and Proline. These peptides are closely related to the target molecule of domoic acid, a natural toxin in seafood. Experiments with endotoxin have been presented and the possibility of extending the sensors for detection of chemicals responsible for food poisoning has been discussed. Initial investigation on the sensors' performance based on Impedance Spectroscopy method is reported in this paper.
Properties of high κ gate dielectrics Gd2O3 and Y2O3 for Si (2001)

We present the materials growth and properties of both epitaxial and amorphous films of Gd2O3 (κ=14) and Y2O3 (κ=18) as the alternative gate dielectrics for Si. The rare earth oxide films were prepared by ultrahigh vacuum vapor deposition from an oxide source. The use of vicinal Si (100) substrates is key to the growth of (110) oriented, single domain films in the Mn2O3 structure. Compared to SiO2 gate oxide, the crystalline Gd2O3 and Y2O3 oxide films show a reduction of electrical leakage at 1 V by four orders of magnitude over an equivalent oxide thickness range of 10–20 Å. The leakage of amorphous Y2O3 films is about six orders of magnitude better than SiO2 due to a smooth morphology and abrupt interface with Si. The absence of SiO2 segregation at the dielectric/Si interface is established from infrared absorption spectroscopy and scanning transmission electron microscopy. The amorphous Gd2O3 and Y2O3 films withstand the high temperature anneals to 850 °C and remain electrically and chemically intact.
The structure of octapeptin D. Studies on antibiotics from the genus Bacillus. XXVIII. (1980)

Amino acid analysis of the acid hydrolyzate of octapeptin D revealed the amino acid composition. These amino acids were converted to L-leucyl-derivatives and analyzed by high performance liquid chromatography to clarify their chiralities. These were determined to be: 2,4-diaminobutyric acid (4L), Ser (D), Leu (2L, 1D). Deacylation with polymyxin acylase afforded deacyl octapeptin D. EDMAN degradation on deacyl octapeptin D revealed the N-terminal amino acid. Application of the chemical cleavage reaction for fragmentation of seryl peptides on tri (DNP)-octapeptin D afforded a DNP-heptapeptide, whose sequence was clarified by EDMAN degradation. Octapeptin D was separated into four components (D1,D2,D3 and D4) by high performance liquid chromatography. All the components were examined for their amino acid and fatty acid compositions. From the results, the structures of octapeptins D1, D2, D3 and D4 were determined.
Hereditary complete deficiency of lactate dehydrogenase H-subunit. (1989)

We report the second known case of a patient, a 45-year-old Japanese woman, with hereditary complete deficiency of lactate dehydrogenase (LDH; EC 1.1.1.27) H-subunit. Total LDH activity in her serum was abnormally low (35 U/L, normal reference interval 195-360). LDH activity in her erythrocytes was also low, but all the other glycolytic enzyme activities in her erythrocytes were within normal limits. Electrophoresis of her serum, erythrocytes, lymphocytes, thrombocytes, and saliva showed only one band, the LDH M4 isoenzyme. LDH activities in her saliva and lymphocytes exceeded the reference interval. Her erythrocytes contained fructose 1,6-diphosphate 26 mumol/L (normal range 4-13), dihydroxyacetone phosphate 75 mumol/L (normal range 8-22), glyceraldehyde 3-phosphate 57 mumol/L (normal range 4-14), and pyruvate 45 mumol/L (normal range 31-63). The family study of three generations showed that this deficiency was inherited in an autosomal recessive mode.
An ultraprocessive, accurate reverse transcriptase encoded by a metazoan group II intron (2017)

Group II introns and non-LTR retrotransposons encode a phylogenetically related family of highly processive reverse transcriptases (RTs) that are essential for mobility and persistence of these retroelements. Recent crystallographic studies on members of this RT family have revealed that they are structurally distinct from the retroviral RTs that are typically used in biotechnology. However, quantitative, structure-guided analysis of processivity, efficiency, and accuracy of this alternate RT family has been lacking. Here, we characterize the processivity of a group II intron maturase RT from <i>Eubacterium rectale</i> (<i>E.r</i>), for which high-resolution structural information is available. We find that the <i>E.r.</i> maturase RT (MarathonRT) efficiently copies transcripts at least 10 kb in length and displays superior intrinsic RT processivity compared to commercial enzymes such as Superscript IV (SSIV). The elevated processivity of MarathonRT is at least partly mediated by a loop structure in the finger subdomain that acts as a steric guard (the α-loop). Additionally, we find that a positively charged secondary RNA binding site on the surface of the RT diminishes the primer utilization efficiency of the enzyme, and that reengineering of this surface enhances capabilities of the MarathonRT. Finally, using single-molecule sequencing, we show that the error frequency of MarathonRT is comparable to that of other high-performance RTs, such as SSIV, which were tested in parallel. Our results provide a structural framework for understanding the enhanced processivity of retroelement RTs, and they demonstrate the potential for engineering a powerful new generation of RT tools for application in biotechnology and research.
Single-Wall Carbon Nanotube Films for Photocurrent Generation. A Prompt Response to Visible-Light Irradiation (2004)

Electrophoretically deposited single-wall carbon nanotube (SWCNT) films on optically transparent electrodes are photoelctrochemically active and generate photocurrent upon visible excitation. A low photon-to-current conversion efficiency of 0.15% suggests that most of the photogenerated charge carriers are lost in the recombination process. Time-resolved transient absorption experiments confirm the charge separation following the laser-pulse excitation of SWCNTs. Relaxation of photogenerated charge carriers in the SWCNT to the lowest energy gap occurs in ∼1 ps.
Somatosensory evoked potentials in rat cerebral cortex before and after middle cerebral artery occlusion. (1990)

We recorded somatosensory evoked potentials in pentobarbital-anesthetized rats before and after middle cerebral artery occlusion. Trigeminal (vibrissae), median (forelimb), and sciatic (hind limb) nerve stimuli produced consistent, robust, and sharply localized responses in the trigeminal, forelimb, and hind limb regions of the somatosensory cortex of 18 rats. These regions are situated at sequentially greater distances from the center of infarcts produced by middle cerebral artery occlusion. In eight rats, occlusion 1-2 mm below the rhinal fissure abolished somatosensory evoked potentials in all three cortical region within minutes. Positive wavelets preceding the primary cortical response were also diminished by the occlusion, suggesting that ischemia affected the thalamocortical white matter. Four of these eight rats did not show histologically apparent ischemic involvement of the hind limb cortical region at 3 hours after occlusion; sciatic nerve evoked potentials recovered substantially in all four rats, and the amplitudes exceeded baseline (129 +/- 30% at 1 hour, 173 +/- 33% at 3 hours) in three of the four rats. Three of the eight rats did not have gross ischemic involvement of the forelimb cortical region; median nerve evoked potentials recovered fully in all eight rats, but the amplitudes did not exceed baseline. All eight rats had evidence of ischemic damage in the trigeminal cortex; no rat showed full recovery in this region, and all but one had trigeminal evoked potentials that were less than 20% of baseline amplitudes by 3 hours after occlusion.(ABSTRACT TRUNCATED AT 250 WORDS)
The CEA/CD3-Bispecific Antibody MEDI-565 (MT111) Binds a Nonlinear Epitope in the Full-Length but Not a Short Splice Variant of CEA (2012)

MEDI-565 (also known as MT111) is a bispecific T-cell engager (BiTE®) antibody in development for the treatment of patients with cancers expressing carcinoembryonic antigen (CEA). MEDI-565 binds CEA on cancer cells and CD3 on T cells to induce T-cell mediated killing of cancer cells. To understand the molecular basis of human CEA recognition by MEDI-565 and how polymorphisms and spliced forms of CEA may affect MEDI-565 activity, we mapped the epitope of MEDI-565 on CEA using mutagenesis and homology modeling approaches. We found that MEDI-565 recognized a conformational epitope in the A2 domain comprised of amino acids 326-349 and 388-410, with critical residues F(326), T(328), N(333), V(388), G(389), P(390), E(392), I(408), and N(410). Two non-synonymous single-nucleotide polymorphisms (SNPs) (rs10407503, rs7249230) were identified in the epitope region, but they are found at low homozygosity rates. Searching the National Center for Biotechnology Information GenBank® database, we further identified a single, previously uncharacterized mRNA splice variant of CEA that lacks a portion of the N-terminal domain, the A1 and B1 domains, and a large portion of the A2 domain. Real-time quantitative polymerase chain reaction analysis of multiple cancers showed widespread expression of full-length CEA in these tumors, with less frequent but concordant expression of the CEA splice variant. Because the epitope was largely absent from the CEA splice variant, MEDI-565 did not bind or mediate T-cell killing of cells solely expressing this form of CEA. In addition, the splice variant did not interfere with MEDI-565 binding or activity when co-expressed with full-length CEA. Thus MEDI-565 may broadly target CEA-positive tumors without regard for expression of the short splice variant of CEA. Together our data suggest that MEDI-565 activity will neither be impacted by SNPs nor by a splice variant of CEA.
A Bead-Based Method for Multiplexed Identification and Quantitation of DNA Sequences Using Flow Cytometry (2000)

A new multiplexed, bead-based method which utilizes nucleic acid hybridizations on the surface of microscopic polystyrene spheres to identify specific sequences in heterogeneous mixtures of DNA sequences is described. The method consists of three elements: beads (5.6-microm diameter) with oligomer capture probes attached to the surface, three fluorophores for multiplexed detection, and flow cytometry instrumentation. Two fluorophores are impregnated within each bead in varying amounts to create different bead types, each associated with a unique probe. The third fluorophore is a reporter. Following capture of fluorescent cDNA sequences from environmental samples, the beads are analyzed by flow cytometric techniques which yield a signal intensity for each capture probe proportional to the amount of target sequences in the analyte. In this study, a direct hybrid capture assay was developed and evaluated with regard to sequence discrimination and quantitation of abundances. The target sequences (628 to 728 bp in length) were obtained from the 16S/23S intergenic spacer region of microorganisms collected from polluted groundwater at the nuclear waste site in Hanford, Wash. A fluorescence standard consisting of beads with a known number of fluorescent DNA molecules on the surface was developed, and the resolution, sensitivity, and lower detection limit for measuring abundances were determined. The results were compared with those of a DNA microarray using the same sequences. The bead method exhibited far superior sequence discrimination and possesses features which facilitate accurate quantitation.