gebhart/patrepeval huggingface dataset:
A high resolution, holographically corrected microscope with a Fresnel lens objective at large working distances (1998)

We present details of a microscope which incorporates an inexpensive, high numerical aperture Fresnel lens objective. The system aberrations are corrected by the use of an image hologram of the lens recorded using a point source of coherent illumination. This device gives high resolution, real time imaging while maintaining a large working distance. The same microscope can be used for micromachining and photolithography in situations where close proximity to the sample is impossible or undesirable.
A novel tri-functional antibody fusion protein with improved pharmacokinetic properties generated by fusing a bispecific single-chain diabody with an albumin-binding domain from streptococcal protein G (2007)

The therapeutic application of small recombinant antibody molecules is often limited by a short serum half-life. In order to improve the pharmacokinetic properties, we have investigated a strategy utilizing fusion with an albumin-binding domain (ABD) from streptococcal protein G. This strategy was applied to a bispecific single-chain diabody (scDb CEACD3) developed for the retargeting of cytotoxic T cells to CEA-expressing tumor cells. This novel tri-functional fusion protein (scDb-ABD) was expressed in mammalian cells and recognized both antigens as well as human and mouse serum albumin. scDb-ABD was capable to retarget T cells to CEA-expressing target cells in vitro and to activate the effector cells as measured by stimulation of IL-2 release. Although activity was reduced 3-fold compared with scDb and further reduced 4-fold in the presences of human serum albumin, this assay demonstrated that scDb-ABD is active when exposed to all three antigens. Compared with scDb, the circulation time of scDb-ABD in mice was prolonged 5- to 6-fold similar to a previously described scDb-HSA fusion protein. This strategy, which adds only a small protein domain (46 amino acids) and which utilizes high-affinity, non-covalent albumin interaction, should be broadly applicable to improve serum half-lives of small recombinant antibody molecules.
Bacteriocins of gram-positive bacteria. (1995)

In recent years, a group of antibacterial proteins produced by gram-positive bacteria have attracted great interest in their potential use as food preservatives and as antibacterial agents to combat certain infections due to gram-positive pathogenic bacteria. They are ribosomally synthesized peptides of 30 to less than 60 amino acids, with a narrow to wide antibacterial spectrum against gram-positive bacteria; the antibacterial property is heat stable, and a producer strain displays a degree of specific self-protection against its own antibacterial peptide. In many respects, these proteins are quite different from the colicins and other bacteriocins produced by gram-negative bacteria, yet customarily they also are grouped as bacteriocins. Although a large number of these bacteriocins (or bacteriocin-like inhibitory substances) have been reported, only a few have been studied in detail for their mode of action, amino acid sequence, genetic characteristics, and biosynthesis mechanisms. Nevertheless, in general, they appear to be translated as inactive prepeptides containing an N-terminal leader sequence and a C-terminal propeptide component. During posttranslational modifications, the leader peptide is removed. In addition, depending on the particular type, some amino acids in the propeptide components may undergo either dehydration and thioether ring formation to produce lanthionine and beta-methyl lanthionine (as in lantibiotics) or thio ester ring formation to form cystine (as in thiolbiotics). Some of these steps, as well as the translocation of the molecules through the cytoplasmic membrane and producer self-protection against the homologous bacteriocin, are mediated through specific proteins (enzymes). Limited genetic studies have shown that the structural gene for such a bacteriocin and the genes encoding proteins associated with immunity, translocation, and processing are present in a cluster in either a plasmid, the chromosome, or a transposon. Following posttranslational modification and depending on the pH, the molecules may either be released into the environment or remain bound to the cell wall. The antibacterial action against a sensitive cell of a gram-positive strain is produced principally by destabilization of membrane functions. Under certain conditions, gram-negative bacterial cells can also be sensitive to some of these molecules. By application of site-specific mutagenesis, bacteriocin variants which may differ in their antimicrobial spectrum and physicochemical characteristics can be produced. Research activity in this field has grown remarkably but sometimes with an undisciplined regard for conformity in the definition, naming, and categorization of these molecules and their genetic effectors. Some suggestions for improved standardization of nomenclature are offered.
Identification of a Transcriptional Enhancer Element Upstream from the Proto-Oncogene fos (1985)

Sequences upstream from the proto-oncogene fos were shown to be essential for its transcription. Transient expression of the chloramphenicol acetyl-transferase (CAT) gene linked to upstream sequences of the fos gene including its promoter reveals that sequences located 64 to 404 base pairs 5' to the fos cap site contain a typical transcriptional enhancer. Moreover, these enhancer sequences, which are strikingly conserved between mouse and human fos genes, coincide with a deoxyribonuclease I-hypersensitive site in the chromatin. The expression of the fos-CAT fusion genes was stimulated only two to three times by the fos inducer 12-0-tetradecanoyl phorbol-13-acetate. The fos enhancer does not appear to be tissue-specific.
Regulation of Longevity and Stress Resistance by Sch9 in Yeast (2001)

The protein kinase Akt/protein kinase B (PKB) is implicated in insulin signaling in mammals and functions in a pathway that regulates longevity and stress resistance in Caenorhabditis elegans. We screened for long-lived mutants in nondividing yeast Saccharomyces cerevisiae and identified mutations in adenylate cyclase and SCH9, which is homologous to Akt/PKB, that increase resistance to oxidants and extend life-span by up to threefold. Stress-resistance transcription factors Msn2/Msn4 and protein kinase Rim15 were required for this life-span extension. These results indicate that longevity is associated with increased investment in maintenance and show that highly conserved genes play similar roles in life-span regulation in S. cerevisiae and higher eukaryotes.
A pulse-radiolysis study of the manganese-containing superoxide dismutase from Bacillus stearothermophilus. A kinetic model for the enzyme action (1977)

The enzymic reaction mechanism of a manganese-containing superoxide dismutase from Bacillus stearothermophilus was studied by using pulse radiolysis. During catalysis (pH 8.9; 25 degrees C), changes occurring in the kinetics of substrate disappearance and in the visible absorption of the enzyme at 480 nm established that the simple two-step mechanism found for copper- and iron-containing superoxide dismutases is not involved. At a low ratio (less than 15) of substrate concentration to enzyme concentration the decay of O2--is close to exponetial, whereas at much higher ratios (greater than 100) the observed decay is predominantly zero-order. The simplest interpretation of the results invokes a rapid one-electron oxidation-reduction cycle ('the fast cycle') and, concurrently, a slower reaction giving a form of the enzyme that is essentially unreactive towards O2-- but which undergoes a first-order decay to yield fully active native enzyme ('the slow cycle'). The fast cycle involves the native enzyme EA and a form of the enzyme EB which can be obtained also by treating the form EA with H2O2. Computer calculations made with such a simple model predict behaviour in excellent agreement with the observed results.
High level transient expression of a chloramphenicol acetyl transferase gene by DEAE-dextran mediated DNA transfection coupled with a dimethyl sulfoxide or glycerol shock treatment (1984)

Using a plasmid containing the bacterial chloramphenicol acetyl transferase gene, we have assayed for transient expression of DNA introduced into mouse L cells by a variety of transfection conditions. High efficiency uptake and expression of this foreign DNA have been achieved by modifying the DEAE dextran mediated transfection procedure of McCutchan and Pagano (1) to include a shock with either dimethyl sulfoxide or glycerol. Inclusion of the shock step can increase expression of the transfected gene a surprising approximately 50 fold. With plasmid constructs that do not replicate after transfection, we can readily detect CAT activity in an overnight autoradiographic exposure from less than 0.1% of an extract from a 60 mm dish of transfected cells. We have determined the amounts of DNA, the amount and time course of DEAE-dextran and dimethyl sulfoxide treatments, the effects of additional DNA, and the time after transfection which yield maximal expression. Overall, this transfection protocol using DEAE-dextran coupled to a shock treatment is simple, straightforward, and gives consistently high levels of expression of the input DNA.
Segmental and chain orientational behavior of spandex fibers (1997)

The internal structure and orientation behavior of two series of spandex fibers, which were made with different spinning methods and different soft and hard segment types, were studied by FTIR (Fourier Transform Infrared Spectroscopy), polarizing light microscopy, and Instron. The orientation behavior of hard and soft segments was studied with FTIR and those of polymeric chains with polarizing miscroscopy while the fibers were being stretched by the mechanical stretcher. The orientation behavior of dry-spun fibers was observed to be very different from that of the melt-spun fibers, which may be explained in terms of the internal structural difference such as the degree of phase separation and mechanical stability of the hard domains between the two types of fibers. In general, the dry-spun fibers showed better elastic recovery property than the melt-spun fibers. Since the polymer for the dry-spun fibers was synthesized with ethylene diamine as a chain extender resulting in the urea groups in the hard segments, it forms more stable hard domain due to the high cohesion energy between the urea groups. The change of the birefringence values during the cyclic deformation was studied with the polarizing light microscopy. The birefringence behaviors of the two dry-spun fibers were similar, whereas there was a noticeable difference between the two melt-spun fibers. The difference was explained in terms of the effect of crosslinking agent in one of the melt-spun fibers, which can stabilize the hard domain structure against the external stress. Mechanical hysteresis values measured gave results consistent with those of FTIR and birefringence measurements. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35: 1821–1832, 1997
Rewriting the rules for end joining via enzymatic splicing of DNA 3′-PO 4 and 5′-OH ends (2013)

There are many biological contexts in which DNA damage generates "dirty" breaks with 3'-PO4 (or cyclic-PO4) and 5'-OH ends that cannot be sealed by DNA ligases. Here we show that the Escherichia coli RNA ligase RtcB can splice these dirty DNA ends via a unique chemical mechanism. RtcB transfers GMP from a covalent RtcB-GMP intermediate to a DNA 3'-PO4 to form a "capped" 3' end structure, DNA3'pp5'G. When a suitable DNA 5'-OH end is available, RtcB catalyzes attack of the 5'-OH on DNA3'pp5'G to form a 3'-5' phosphodiester splice junction. Our findings unveil an enzymatic capacity for DNA 3' capping and the sealing of DNA breaks with 3'-PO4 and 5'-OH termini, with implications for DNA repair and DNA rearrangements.
Triac (3,5,3’Triiodo-Thyroacetic Acid) Induced « Pseudohypothyroidism » (1984)

SummaryTwo cases of chronic 3, 5, 3’-triiodo-thyroacetic acid (Triac) consumption (2.1 mg/day) are reported. Profound alterations of thyroid function were observed: thyroxine and free thyroxine concentrations were low, normal to excessively high triiodothyronine values were detected and thyroid stimulating hormone response to 200 fig thyroid releasing hormone i.v. was abolished.The literature concerning Triac use is reviewed, and the efficiency of the drug in the treatment of obesity is discussed.
Emergence and Apparent Transmission of Rimantadine-Resistant Influenza A Virus in Families (1989)

To determine whether rimantadine can protect family members from acquiring influenza A viral illness and to assess the possible selection of drug-resistant strains of virus, we conducted a randomized, double-blind, placebo-controlled study in three communities during two influenza seasons. When influenza A occurred in a family, the members (including the index patient) were given either rimantadine (adult oral dose, 200 mg per day) or placebo for 10 days. The presence of illness was monitored by daily recording of symptoms and temperature measurements; infection was determined by isolation of the virus and by serologic studies. Among households with documented influenza A infections, symptomatic illness occurred in one or more contacts in 10 of 28 families treated with rimantadine and in 10 of 209 families treated with placebo. Asymptomatic secondary influenza A infections were found in five families assigned to receive rimantadine and in four families assigned to receive placebo. Rimantadine-resistant strains of influenza A virus (H3N2 subtype) with mutations consisting of single amino acid changes in the M2 protein (residue 27, 30, or 31) were recovered from eight index patients and five contacts treated with rimantadine. There was apparent transmission of drug-resistant strains of virus in six contacts with secondary illnesses in five families. We conclude that when index patients are treated concurrently, rimantadine is ineffective in protecting household members from influenza A infection. If rimantadine is used for both treatment and postexposure prophylaxis in families, rapid selection and apparent transmission of drug-resistant influenza A viruses can occur.
The inactivation of thiamin by Bracken (Pteris aquilina) (1949)

Abstract The anti‐thiamin effect of bracken, noted by Weswig, Freed and Haeg, has been confirmed. Rats on a diet containing 40% bracken, and providing adequate amounts of thiamin, lost weig it and died within thirty days. Control groups receiving large supplementary doses of thiamin made continuous increases in bodyweight. The hearts and livers of rats which had succumbed to a bracken‐containing diet were shown to be of abnormally low thiamin content. An incubation technique developed by the authors, showed that bracken had the capacity to inactivate large amounts of vitamin.
Adaptive Cancellation of Floor Vibrations in Standing Ballistocardiogram Measurements Using a Seismic Sensor as a Noise Reference (2009)

An adaptive noise canceller was used to reduce the effect of floor vibrations on ballistocardiogram (BCG) measurements from a modified electronic bathroom scale. A seismic sensor was placed next to the scale on the floor and used as the noise reference input to the noise canceller. BCG recordings were acquired from a healthy subject while another person stomped around the scale, thus causing increased floor vibrations. The noise canceller substantially eliminated the artifacts in the BCG signal due to these vibrations without distorting the morphology of the measured BCG. Additionally, recordings were obtained from another subject standing inside a parked bus while the engine was running. The artifacts due to the vibrations of the engine, and the other vehicles moving on the road next to the bus, were also effectively eliminated by the noise canceller. The system with automatic floor vibration cancellation could be used to increase BCG measurement robustness in home monitoring applications. Additionally, the noise cancellation approach may enable BCG recording in ambulances-or other transport vehicles-where noninvasive hemodynamic monitoring may otherwise not be feasible.
A genetic locus of enteropathogenic Escherichia coli necessary for the production of attaching and effacing lesions on tissue culture cells. (1990)

The ability of enteropathogenic Escherichia coli (EPEC) to form attaching and effacing intestinal lesions is a major characteristic of EPEC pathogenesis. Using TnphoA mutagenesis we have identified a chromosomal gene (eae, for E. coli attaching and effacing) that is necessary for this activity. A DNA probe derived from this gene hybridizes to 100% of E. coli of EPEC serogroups that demonstrate attaching and effacing activity on tissue culture cells as well as other pathogenic E. coli that produce attaching and effacing intestinal lesions, such as RDEC-1 (an EPEC of weanling rabbits) and enterohemorrhagic E. coli. The predicted amino acid sequence derived from the nucleotide sequence of eae shows significant homology to that of the invasin of Yersinia pseudotuberculosis.
Design of Open APIs for Personalized IPTV Service (2007)

With the broadcasting and network convergences, IPTV which is a broadcasting service using IP network, becomes popular as a new business model. The IPTV service supports the user-interactive and personalized broadcasting service. However, it is difficult to serve the IPTV services to the universal user terminals in the heterogeneous network environment. In this paper, we study the service scenarios for the personalized broadcasting services under open network environments and extend the Parlay X Web service structure for the personalized EPG, NDR and target advertisement services from the service scenarios. For these three services, we specify open APIs based on Parlay X for open network environments. Based on these open network environments for the personalized broadcasting services, it is possible to provide new business model to the network operators, to reduce the duplicable investment in new business by defining the roles of each service provider and to develop the various and inventive services through the third party application service. We also implement the prototype system for open APIs based on the extended Parlay X Web service structure which are named personalized EPG, NDR and target advertisement.
A multi-band CELP wideband speech coder (2002)

A novel low-delay wideband speech coder, called multiband CELP (MB-CELP), overcomes the major obstacles usually associated with two traditional CELP approaches to wideband speech coding-namely fullband CELP and split-band CELP. The new MB-CELP coder employs a multi-band bank of off-line filtered excitation codebooks, fullband linear prediction synthesis, and minimization of the error between the original and the synthesized speech signal over the full frequency range. A 16 kbps version of the MB-CELP coder with two equal bands, is described. Subjective comparison test results show that this coder performs better than the G.722 coder at a bit-rate of 48 kbps.
Molecular heterogeneity of the gamma-aminobutyric acid (GABA) transport system. Cloning of two novel high affinity GABA transporters from rat brain. (1992)

cDNA clones encoding two novel gamma-aminobutyric acid (GABA) transporters (designated GAT-2 and GAT-3) have been isolated from rat brain, and their functional properties have been examined in mammalian cells. The transporters display high affinity for GABA (Km approximately 10 microM) and exhibit pharmacological properties distinct from the previously cloned neuronal GABA transporter (GAT-1). Both transporters require sodium and chloride for transport activity. The nucleotide sequences of GAT-2 and GAT-3 predict proteins of 602 and 627 amino acids, respectively, which can be modeled with 12 transmembrane domains, similar to the topology proposed for other cloned neurotransmitter transporters. Localization studies indicate that both transporters are present in brain and retina, while GAT-2 is also present in peripheral tissues. The cloning of these transporter genes from rat brain reveals previously undescribed heterogeneity in GABA transporters.
Electrostatics in Protein Binding and Function (2002)

Protein electrostatic properties stem from the proportion and distribution of polar and charged residues. Polar and charged residues regulate the electrostatic properties by forming short-range interactions, like salt-bridges and hydrogen-bonds, and by defining the over-all electrostatic environment in the protein. Electrostatics play a major role in defining the mechanisms of protein-protein complex formation, molecular recognitions, thermal stabilities, conformational adaptabilities and protein movements. For example:- Functional hinges, or flexible regions of the protein, lack short-range electrostatic interactions; Thermophilic proteins have higher electrostatic interactions than their mesophilic counter parts; Increase in binding specificity and affinity involve optimization of electrostatics; High affinity antibodies have higher, and stronger, electrostatic interactions with their antigens; Rigid parts of proteins have higher and stronger electrostatic interactions. In this review we address the significance of electrostatics in protein folding, binding and function. We discuss that the electrostatic properties are evolutionally selected by a protein to perform an specific function. We also provide bona fide examples to illustrate this. Additionally, using continuum electrostatic and molecular dynamics approaches we show that the "hot-spot" inter-molecular interactions in a very specific antibody-antigen binding are mainly established through charged residues. These "hot-spot" molecular interactions stay intact even during high temperature molecular dynamics simulations, while the other inter-molecular interactions, of lesser functional significance, disappear. This further corroborates the significance of charge-charge interactions in defining binding mechanisms. High affinity binding frequently involves "electrostatic steering". The forces emerge from over-all electrostatic complementarities and by the formation of charged and polar interactions. We demonstrate that although the high affinity binding of barnase-barstar and anti-hen egg white lysozyme (HEL) antibody-HEL complexes involve different molecular mechanisms, it is electrostatically regulated in both the cases. These observations, and several other studies, suggest that a fine tuning of local and global electrostatic properties are essential for protein binding and function.