gebhart/patrepeval huggingface dataset:
Proline-Rich Domain and Glycosylation Are Not Essential for the Enzymic Activity of Bile Salt-Activated Lipase. Kinetic Studies of T-BAL, a Truncated Form of the Enzyme, Expressed in Escherichia coli (1994)

We have expressed and purified a truncated recombinant human milk bile salt-activated lipase (T-BAL) from the T7 expression system in Escherichia coli. This T-BAL contains the N-terminal 538 residues of the 722-residue native enzyme. The purified T-BAL, when assayed with PANA (p-nitrophenyl acetate), had a specific activity of 64 +/- 2 units/mg (n = 4), as compared to 52 units/mg for the native enzyme. Because the recombinant T-BAL expressed in E. coli is not glycosylated, these results indicated that the highly glycosylated C-terminal region of BAL is not essential for catalytic function. Heat inactivation patterns of native BAL and T-BAL were found to be similar, further suggesting that the folding of T-BAL is similar to that of the catalytic domain of the native enzyme. With the availability of a sufficient amount of recombinant T-BAL, the specificity and kinetics of T-BAL and native BAL were compared. Fluorescence studies of T-BAL indicated that it has a slightly higher affinity for the monomeric form of taurocholate with a dissociation constant (KA) of 0.32 mM, compared with the reported 0.37 mM for the native enzyme. Further kinetic analysis indicated that there are enzyme specificity changes revealed with the use of PANA and PANB (p-nitrophenyl butyrate) as substrates. When assayed in the presence of taurocholate, T-BAL has a higher turnover rate constant with p-nitrophenyl acetate than with p-nitrophenyl butyrate, which was found to be in contrast to native BAL.(ABSTRACT TRUNCATED AT 250 WORDS)
Bias temperature instability in silicon carbide (2009)

Low mobility and oxide instability have hindered SiC MOSFETs from commercial introduction. A potential reliability problem for such MOS devices is bias-temperature instability (BTI). MOSFET mobility, already low in SiC devices, is further degraded by increased interface trap density. With continued SiC technology development, it is only a question of time until BTI reliability concerns arise. BTI in SiC is especially important as one application is at high temperatures where this effect occurs. Our initial data indicate that BTI is a problem in SiC MOS devices.
Detection of Aneuploidy with Digital Polymerase Chain Reaction (2007)

The widespread use of genetic testing in high-risk pregnancies has created strong interest in rapid and accurate molecular diagnostics for common chromosomal aneuploidies. We show here that digital polymerase chain reaction (dPCR) can be used for accurate measurement of trisomy 21 (Down syndrome), the most common human aneuploidy. dPCR is generally applicable to any aneuploidy, does not depend on allelic distribution or gender, and is able to detect signals in the presence of mosaics or contaminating maternal DNA.
Realization of All-Optical Digital Comparator Using Single Mode Fabry–Pérot Laser Diodes (2011)

A two-bit all-optical digital comparator using single mode Fabry-Pérot laser diodes (SMFP-LDs) at an input data rate of 10 Gbps is proposed and demonstrated. All-optical comparator is demonstrated using cascaded logic units which are based on injection locking, multi-input injection locking and supporting beam principles for suppressing the dominant mode of SMFP-LDs. Digital comparators are the key components for the decision making circuits, the integral part of the arithmetic and logical units of optical data processors. The output performance of the proposed all-optical comparator is verified with output waveform, rising-falling time, output eye diagram, and bit error rate (BER) at 10 Gbps input Non Return to Zero (NRZ) PRBS of 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">31</sup> -1 signal. The rising/falling time of about 47 ps, clear output waveforms, and clear output eye diagram with an extinction ratio of about 12 dB are obtained. A maximum power penalty of 1.3 dB is measured at a BER of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-9</sup> .
Models and molecular approaches to assessing the effects of the microgravity environment on vertebrate development. (1995)

The extent to which gravity, and especially the lack thereof, can affect normal development in higher organisms is poorly understood. Underlying this question is the assumption that normal development depends on the embryo's ability to maintain a programmed temporal and spatial coordination of morphogenetic events. There are several reports documenting the apparently normal development of several vertebrate species, including mammals, under conditions of exposure to space flight during various periods of the development process. Evidence to the contrary also exists and it is therefore likely that some alterations in morphology do occur in a microgravity environment. Although subsequent development may appear overtly normal, more subtle abnormalities result. In all studies, the evaluation is restricted by the few numbers of specimens that can be examined and the relatively insensitive techniques for assessing potentially subtle effects. In the present discussion, we summarize some observations of mammalian development made in microgravity and consider which stages might be expected to be differentially sensitive to altered gravity conditions. While we emphasize mammalian development, we discuss the suitability of another model system for examining such effects in a cross-species context. Furthermore, we consider recent developments in our understanding of the molecular genetic program regulating embryogenesis that could serve as markers for assessing perturbations of development.
GRAVITY GRADIENT TENSORS DUE TO A POLYHEDRON WITH POLYGONAL FACETS1 (1991)

A bstract Using the conjugate complex variables formulation, closed‐form formulae for the gravity gradient tensors of the gravitational potential due to a homogeneous polyhedral body composed of polygonal facets are derived. The treatise considers the cases of the observation point being inside the polyhedron, on the surface of a facet, or outside the polyhedron.
The guinea pig as a transmission model for human influenza viruses (2006)

The severity of epidemic and pandemic influenza outbreaks is dictated in part by the efficiency with which the causative strain transmits between human hosts. The mechanisms underlying influenza virus spread are poorly understood, in part because of the lack of a convenient animal model to study this phenomenon. Indeed, despite extremely efficient transmission among humans and virulence in the mouse model, we have shown that even the 1918 pandemic influenza virus does not transmit between mice. We therefore evaluated the guinea pig as a model mammalian host for influenza virus. Using the recent human isolate A/Panama/2007/99 (Pan/99) (H3N2) virus, we found that guinea pigs were highly susceptible to infection with the unadapted virus (ID(50) = 5 plaque-forming units). Pan/99 virus grew to high titers in the upper respiratory tract and was shed in nasal washings of infected animals. Moreover, influenza virus was transmitted from infected guinea pigs to noninfected guinea pigs housed in the same cage, an adjacent cage, and a cage placed 91 cm away. Our results demonstrate that influenza virus can pass between guinea pigs by means of droplet spread and thereby establish the suitability of the guinea pig as a model host for influenza virus transmission studies.
Acoustic Wave Based Microfluidics and Lab-on-a-Chip (2013)

Microfluidics refers to a set of technologies that control the flow of minute amounts of liquids, typically from a few picolitres (pls) to a few microlitres (μls) in a miniaturized system [1,2]. Lab-on-a-chip (LOC) systems typically consist of a set of microfluidics and sensors with dimensions from a few square millimetres (mm2) to a few square centimetres (cm2). Microfluidics handles liquids through droplet generation, transportation and mixing of liquid samples, chemical reactions etc. Sensors may include biochemical sensors, gas sensors and physical sensors such as humidity and temperature sensors, flow meter and viscometers etc. Therefore, LOCs are microsystems with a much broader meaning, and generally perform single or multiple laboratory processes and functions on a chip-scale.
The Molecular and Genetic Basis of Fibroblast Growth Factor Receptor 3 Disorders: The Achondroplasia Family of Skeletal Dysplasias, Muenke Craniosynostosis, and Crouzon Syndrome with Acanthosis Nigricans* (2000)

Achondroplasia, the most common form of short-limbed dwarfism in humans, occurs between 1 in 15,000 and 40,000 live births. More than 90% of cases are sporadic and there is, on average, an increased paternal age at the time of conception of affected individuals. More then 97% of persons with achondroplasia have a Gly380Arg mutation in the transmembrane domain of the fibroblast growth factor receptor (FGFR) 3 gene. Mutations in the FGFR3 gene also result in hypochondroplasia, the lethal thanatophoric dysplasias, the recently described SADDAN (severe achondroplasia with developmental delay and acanthosis nigricans) dysplasia, and two craniosynostosis disorders: Muenke coronal craniosynostosis and Crouzon syndrome with acanthosis nigricans. Recent evidence suggests that the phenotypic differences may be due to specific alleles with varying degrees of ligand-independent activation, allowing the receptor to be constitutively active. Since the Gly380Arg achondroplasia mutation was recognized, similar observations regarding the conserved nature of FGFR mutations and resulting phenotype have been made regarding other skeletal phenotypes, including hypochondroplasia, thanatophoric dysplasia, and Muenke coronal craniosynostosis. These specific genotype-phenotype correlations in the FGFR disorders seem to be unprecedented in the study of human disease. The explanation for this high degree of mutability at specific bases remains an intriguing question.
Isolation, characterization and amino‐acid sequence of γ‐seminoprotein, a glycoprotein from human seminal plasma (1987)

gamma-Seminoprotein (gamma-SM), a glycoprotein from human seminal plasma, was isolated in highly purified form by ion-exchange chromatography on a Mono Q column. The main form, fraction M, was homogeneous by PAGE at pH 8.3 and by SDS-PAGE. The complete amino acid sequence of gamma-SM was determined with the aid of fragments generated by cleavages with cyanogen bromide, clostripain, chymotrypsin and Staphylococcus aureus V8 protease. The fragments were aligned with overlapping sequences. The single polypeptide chain of gamma-SM contains 237 amino acids with a calculated Mr of 26079. A single N-linked carbohydrate side chain is attached to Asn45. The complex structure of this oligosaccharide has been determined recently [van Halbeek H. et al. (1985) Biochem. Biophys. Res. Commun. 131, 507-514]. Sequence comparison with serine proteases shows a high degree of homology, especially with the kallikrein family. The residues in the vicinity of the active site of serine proteases are also highly conserved in gamma-SM, indicating the participation of His41, Asp96 and Ser189 in its active site. gamma-SM hydrolyzed M-casein with a pH optimum at 8.0, but failed to hydrolyze any of the synthetic substrates tested. This proteolytic activity could be inhibited with diisopropylfluorophosphate, phenylmethylsulfonyl fluoride, Zn2+ or Hg2+ ions.
Supersensitive Time-resolved Immunofluorometric Assay of Free Prostate-specific Antigen with Nanoparticle Label Technology (2001)

The sensitivity of the new assay is equal to that of the ambient-analyte, microspot immunoassay and will be improved by use of optimized, high binding-site density nanoparticle-antibody bioconjugates with reduced nonspecific binding and improved monovalent binding affinity.
A ‘sticky’ interhemispheric switch in bipolar disorder? (1998)

Despite years of research into bipolar disorder (manic depression), its underlying pathophysiology remains elusive. It is widely acknowledged that the disorder is strongly heritable, but the genetics are complex with less than full concordance in monozygotic twins and at least four susceptibility loci identified. We propose that bipolar disorder is the result of a genetic propensity for slow interhemispheric switching mechanisms that become 'stuck' in one or the other state. Because slow switches are also 'sticky' when compared with fast switches, the clinical manifestations of bipolar disorder may be explained by hemispheric activation being 'stuck' on the left (mania) or on the right (depression). Support for this 'sticky' interhemispheric switching hypothesis stems from our recent observation that the rate of perceptual alternation in binocular rivalry is slow in euthymic subjects with bipolar disorder (n = 18, median = 0.27 Hz) compared with normal controls (n = 49, median = 0.60 Hz, p < 0.0005). We have presented evidence elsewhere that binocular rivalry is itself an interhemispheric switching phenomenon. The rivalry alternation rate (putative interhemispheric switch rate) is robust in a given individual, with a test-retest correlation of more than 0.8, making it suitable for genetic studies. The interhemispheric switch rate may provide a trait-dependent biological marker for bipolar disorder.
Neurolysosomal pathology in human prosaposin deficiency suggests essential neurotrophic function of prosaposin (2006)

A neuropathologic study of three cases of prosaposin (pSap) deficiency (ages at death 27, 89 and 119 days), carried out in the standard autopsy tissues, revealed a neurolysosomal pathology different from that in the non-neuronal cells. Non-neuronal storage is represented by massive lysosomal accumulation of glycosphingolipids (glucosyl-, galactosyl-, lactosyl-, globotriaosylceramides, sulphatide, and ceramide). The lysosomes in the central and peripheral neurons were distended by pleomorphic non-lipid aggregates lacking specific staining and autofluorescence. Lipid storage was borderline in case 1, and at a low level in the other cases. Neurolysosomal storage was associated with massive ubiquitination, which was absent in the non-neuronal cells and which did not display any immunohistochemical aggresomal properties. Confocal microscopy and cross-correlation function analyses revealed a positive correlation between the ubiquitin signal and the late endosomal/lysosomal markers. We suppose that the neuropathology most probably reflects excessive influx of non-lipid material (either in bulk or as individual molecules) into the neurolysosomes. The cortical neurons appeared to be uniquely vulnerable to pSap deficiency. Whereas in case 1 they populated the cortex, in cases 2 and 3 they had been replaced by dense populations of both phagocytic microglia and astrocytes. We suggest that this massive neuronal loss reflects a cortical neuronal survival crisis precipitated by the lack of pSap. The results of our study may extend the knowledge of the neurotrophic function of pSap, which should be considered essential for the survival and maintenance of human cortical neurons.
Intravenous Immunoglobulin Therapy Affects T Regulatory Cells by Increasing Their Suppressive Function (2007)

Intravenous Ig therapy (IVIg) is reported to be a useful regimen in treating autoimmune diseases. In this study, we asked whether IVIg (in vitro) could increase the expression of TGF-beta, IL-10, and the transcription factor FoxP3 in T regulatory (Treg) cells, and the idea that IVIg could enhance suppressive properties of these cells. CD4(+) T cells from 12 healthy individuals were cultured in the presence or absence of IVIg vs human control IgG during 16, 24, and 36 h. Using FACS analysis and gating on CD4(+)CD25(high) Treg cells, we assessed the expression of intracellular TGF-beta, IL-10, and FoxP3. In addition, the production of TNF-alpha by stimulated CD4(+) T cells alone or in culture with CD25(+) by itself or together with IVIg was also assessed. The presence of IVIg with Treg cells in culture significantly increased the intracellular expression of TGF-beta (17.7 +/- 8.5% vs 29.8 +/- 13%; p = 0.02), IL-10 (20.7 +/- 4.7% vs 34.2 +/- 5.2%; p = 0.008) and FoxP3 (20.8 +/- 5.2% vs 33.7 +/- 5.9%; p = 0.0006) when compared with cells cultured alone or with control human IgG. The suppressive effect of CD4(+)CD25(+) T cells presented as the decrease of TNF-alpha production by stimulated CD4(+)CD25(-) (effector T cells) was further increased by adding IVIg to cell culture. We hereby demonstrate an additional mechanism by which IVIg could maintain self-tolerance and decrease immune-mediated inflammation.
Optimization of the Central Heterocycle of α-Ketoheterocycle Inhibitors of Fatty Acid Amide Hydrolase (2008)

The synthesis and evaluation of a refined series of alpha-ketoheterocycles based on the oxazole 2 (OL-135) incorporating systematic changes in the central heterocycle bearing a key set of added substituents are described. The nature of the central heterocycle, even within the systematic and minor perturbations explored herein, significantly influenced the inhibitor activity: 1,3,4-oxadiazoles and 1,2,4-oxadiazoles 9 > tetrazoles, the isomeric 1,2,4-oxadiazoles 10, 1,3,4-thiadiazoles > oxazoles including 2 > 1,2-diazines > thiazoles > 1,3,4-triazoles. Most evident in these trends is the observation that introduction of an additional heteroatom at position 4 (oxazole numbering, N > O > CH) substantially increases activity that may be attributed to a reduced destabilizing steric interaction at the FAAH active site. Added heterocycle substituents displaying well-defined trends may be utilized to enhance the inhibitor potency and, more significantly, to enhance the inhibitor selectivity. These trends, exemplified herein, emerge from both enhancements in the FAAH activity and simultaneous disruption of binding affinity for competitive off-target enzymes.
Islet cell autoantigen 69 kD (ICA69). Molecular cloning and characterization of a novel diabetes-associated autoantigen. (1993)

We have identified a novel 69-kD peptide autoantigen (ICA69) associated with insulin-dependent diabetes mellitus (IDDM) by screening a human islet lambda gt11 cDNA expression library with cytoplasmic islet cell antibody positive sera from relatives of IDDM patients who progressed to the overt disease. The deduced open reading frame of the ICA69 cDNA predicts a 483-amino acid protein. ICA69 shows no nucleotide or amino acid sequence relation to any known sequence in GenBank, except for two short regions of similarity with BSA. The ICA69 cDNA probe hybridizes with a 2-kb mRNA in poly(A+) RNA from human pancreas, brain, heart, thyroid, and kidney, but not with skeletal muscle, placenta, spleen, or ovary. Expression of ICA69 was also detected in beta cells and cell lines, as well as in tumoral tissue of islet cell origin. The native ICA69 molecule migrates to 69 kD in SDS-PAGE as detected with specific antibodies. Serum samples from relatives of IDDM patients specifically reacted with affinity-purified recombinant ICA69 on Western blotting. The structural gene for ICA69 was designated ICA1. A homologue in the mouse, designated Ica-1 was mapped to the proximal end of chromosome 6 (within 6 cM of the Met protooncogene). ICA69 adds a novel autoantigen to the family of identified islet target molecules, and by the manner of its identification and characterization large amounts of antigen are available for development of quantitative, convenient predictive assays for autoantibodies and analysis of the role of this molecule in diabetes autoimmunity, as well as its physiologic function.
A Convenient Oxazole C-2 Protecting Group:  The Synthesis of 4- and 5-Substituted Oxazoles via Metalation of 2-Triisopropylsilyloxazoles (2005)

Metalation of oxazoles at the 4 and 5 position was achieved after regioselective C-2 silyl protection. Removal of the protecting group was then accomplished under mild conditions allowing for a straightforward preparation of C-5 monosubstituted and C-4,5 disubstituted oxazoles. The first practical C-2 protecting group of oxazoles has been demonstrated.
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing (2012)

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
A Highly Efficient 24-Condition Matrix for the Crystallization of Nucleic Acid Fragments (1996)

A matrix screen is presented with optimized conditions for the crystallization of nucleic acid fragments. The screen consists of 24 conditions only and utilizes minimal amounts of sample. It has been tested on a series of DNA and RNA oligomers, and yielded diffraction-quality crystals of many specimens including drug-DNA complexes. Preliminary X-ray analysis of the crystals is reported.
ChemInform Abstract: CONDENSATION REACTIONS BETWEEN O‐PHENYLENEDIAMINE AND 2‐SUBSTITUTED 1,3‐BENZOXAZIN‐4‐ONES (1976)

Abstract Die Kondensation des Diamins (II) mit den Benzoxazinonen (I), die nach bekannten Methoden z.B. durch Cyclisierung von 2‐Phenylacetamido‐benzoesäure (Ausbeute 81%) dargestellt werden, wird in Chloroform, m‐Kresol oder in der Schmelze bei 200°C durchgeführt.
Local Microwave Hyperthermia in the Treatment of Benign Prostatic Hypertrophy (1990)

Local deep microwave hyperthermia has been introduced recently for the treatment of benign prostatic hypertrophy (BPH). We report the results of treatment in 114 patients divided into 2 groups. The first group included 83 patients with severe obstructive symptoms. Although some improvement was found in the scoring of both subjective and objective parameters, the number of patients benefiting was small, with only 28% showing improvement in both parameters. Approximately 50% reported subjective improvement but in only 25% was this significant. In 42% there was objective evidence of improvement. Prostatic volumes did not change as a result of treatment. The second group comprised 31 patients with indwelling catheters because of acute urinary retention. After treatment, 19 patients (61%) were able to dispense with the catheter. The difficulties of interpreting an open trial of treatment for BPH and assessing its impact on objective parameters and symptomatology are discussed. Our results should be regarded cautiously in view of these reservations.