gebhart/patrepeval huggingface dataset:
Cloning, sequencing, and characterization of Escherichia coli thioesterase II (1991)

The gene (tesB) encoding Escherichia coli thioesterase II, a low-abundance enzyme of unknown physiological function which can hydrolyze a broad range of acyl-CoA thioesters, has been localized by transposon mutagenesis, cloned and sequenced. A two-cistron construct containing both the lac and tesB promoters was used successfully to overexpress the 286-residue polypeptide. The recombinant enzyme constituted up to 25% of the soluble proteins of E. coli and was readily purified to homogeneity as a tetramer of approximately 120,000 Da. Amino-terminal sequence analysis and electrospray ionization mass spectrometry confirmed the identity of the thioesterase and revealed that the amino-terminal formyl-methionine had been removed yielding a subunit species of average molecular mass 31,842 Da. The protein does not contain the GXSXG motif found characteristically in animal thioesterases which function as chain-terminating enzymes in fatty acid synthesis and exhibits no sequence similarity with these or any other known proteins. Activity of the recombinant enzyme was inhibited by iodoacetamide and diethylpyrocarbonate. The carboxamidomethylated residue was identified as histidine 58, and a role for this amino acid in catalysis is suggested. E. coli strains having a large deletion within the genomic tesB gene grew normally but retained a low level of thioesterase activity toward decanoyl-CoA. This residual activity indicates the presence of an additional decanoyl-CoA hydrolase in E. coli. Over-expression of the recombinant enzyme, under control of the lac promoter, did not alter the fatty acids synthesized by E. coli at any stage of cell growth and the physiological role of this enzyme remains an enigma.
The Ultrastructure of Mouse Lung: The Alveolar Macrophage (1958)

Free alveolar macrophages of normal mouse lung have been studied in the electron microscope. The tissue was obtained from several young adult white mice. One other animal was instilled intranasally with diluted India ink 1(1/2) hours prior to the removal of the lung. Thin sections of the osmium-fixed, methacrylate-embedded tissue were examined either in an RCA EMU 2 electron microscope or in a Siemens and Halske Elmiskop I b. A few thick sections obtained from the same embeddings were stained for iron. The normal alveolar macrophages, which are usually in contact with the alveolar epithelium, were found to contain a variety of inclusion bodies, along with the usual cytoplasmic components like mitochondria, endoplasmic reticulum, and Palade granules. Another typical component of the cytoplasm of these cells which appears as small ( approximately 6 mmicro) very dense granules of composite fine structure is interpreted as ferritin. It is assumed that this ferritin is formed from red blood cells ingested by the alveolar macrophages. The macrophages in the alveoli were found to phagocytize intranasally instilled India ink particles. Such cells, with engulfed India ink particles, were often of more rounded form and the particles were frequently seen lying inside membrane-bound vacuoles or vesicles of the cytoplasm. The membrane of a few vesicles containing India ink particles was seen as the invaginated portion of the cell plasma membrane, and in one instance these same vesicles were seemingly interconnected with a rough surfaced cisterna of the endoplasmic reticulum. The process of phagocytosis is recognized as related to the "normal" process of pinocytosis.
Treatment of Cerebral Edema (2006)

The therapy for brain edema remains largely empirical. More research aimed at enhancing our understanding of the pathophysiology of cerebral edema is needed to identify new and more effective forms of treatment.
Syntheses of di-heterocyclic compounds; pyrazolylimidazoles and isoxazolylimidazoles (1998)

Fifteen substituted di-heterocyclic imidazoles were prepared. Ten substituted pyrazolylimidazoles were obtained by cyclocondensation of α-oxo-α-imidazolylketene dithioacetal or N, S-acetals with hydrazine and by ring-chain transformation of cyclic α-oxo-α-imidazolylketene N, O-acetals. Five isoxazolylimidazoles were obtained by reaction of α-oxo-α-imidazolylketene dithioacetal with hydroxylamine. © 1998 John Wiley & Sons, Inc. Heteroatom Chem 9:317–320, 1998
High-Dose Antithrombin III in Severe Sepsis (2001)

High-dose antithrombin III therapy had no effect on 28-day all-cause mortality in adult patients with severe sepsis and septic shock when administered within 6 hours after the onset. High-dose antithrombin III was associated with an increased risk of hemorrhage when administered with heparin. There was some evidence to suggest a treatment benefit of antithrombin III in the subgroup of patients not receiving concomitant heparin.
Adenosine A2 receptors on human monocytes modulate C2 production. (1984)

Adenosine inhibits C2 production by human monocytes. The use of synthetic analogues of adenosine suggested that the action was mediated by receptors of A2 type. EHNA which inhibits the enzyme adenosine deaminase and increases the concentration of intracellular adenosine also reduces C2 production. It is therefore possible that endogenous adenosine regulates C2 synthesis.
Efficient Production of a Small Peptide by Expression as a Multimeric Form Fused with the Dihydrofolate Reductase Affinity Handle (1992)

A pentapeptide which potently inhibits primary IgE antibody formation, Asp-Ser-Asp-Gly-Lys (DSDGK), has been efficiently produced with the aid of the dihydrofolate reductase (DHFR) handle [M. Iwakura, et al. (1992) J. Biochem. 111, 37-45]. The genes coding fused proteins comprising DHFR and multimeric forms of DSDGK, namely, DHFR-(DSDGK)3, DHFR-(DSDGK)14, and DHFR-(DSDGK)28, were constructed and expressed in Escherichia coli. The C-terminal peptides attached to DHFR did not affect the expression or the function of the DHFR handle, even when the length of the C-terminal peptide was as long as 160 amino acid residues. The fused proteins were easily purified by methotrexate affinity chromatography, one of the major advantages of the DHFR handle. The fused proteins were digested with trypsin and the monomeric peptide, DSDGK, was purified by HPLC. The yields of the peptide were estimated to be 11, 43, and 99 mg per 1 gram of the total cell proteins from E. coli cells producing DHFR-(DSDGK)3, DHFR-(DSDGK)14, and DHFR-(DSDGK)28, respectively.
Identification of serotype 1-, 3-, and 6-specific antigens of Ureaplasma urealyticum by using monoclonal antibodies (1994)

Little is known about the antigens responsible for serotype specificity in Ureaplasma urealyticum. We produced monoclonal antibodies to U. urealyticum serotypes 1, 3, and 6, the serotypes most commonly found in pregnant women, and analyzed serotype-specific antigens for the three serotypes. Clinical isolates belonging to serotype 1, 3, or 6 were tested in immunoblots with these monoclonal antibodies. The immunoblot patterns of these isolates were, in most cases, different from each other as well as from those of the reference strains, indicating a high rate of antigenic variation among U. urealyticum strains.
Production of Group C Streptococcus Phage-associated Lysin and the Preparation of Streptococcus pyogenes Protoplast Membranes (1980)

Optimum conditions of pH, temperature and multiplicity of bacteriophage infection for the production of phage-associated lysin from Group C streptococci were defined. Lysin obtained by the optimum method was used to make protoplast membranes of Group A type 12 streptococci. These membranes consistently contained very low concentrations of rhamnose, indicating minimal cell wall contamination. The development of such a reproducible technique for the preparation of protoplast membranes will permit more meaningful studies on the involvement of these membranes in the pathogenesis of acute post-streptococcal glomerulonephritis.
A multiple exchange algorithm for constrained design of FIR filters in the complex domain (1999)

We present a fast multiple exchange algorithm that designs FIR filters with magnitude and phase specifications subject to constraints on the error function. We use a constrained least squares criterion which minimizes error energy and imposes bounds on the magnitude of the error. We can trade error energy versus peak error, and complex least squares and complex Chebyshev filters result as special cases. We provide a Matlab program implementing the proposed algorithm. This program has proved to be efficient and reliable.
Slow fiber cluster pattern in pig longissimus thoracis muscle: Implications for myogenesis (2003)

Recent evidence implicates fiber type proportions as playing a role in meat eating quality, and in pigs it has been suggested that the slow oxidative fibers contribute to both juiciness and tenderness. The fiber distribution in pigs is different from that found in most other species, in which the various types of skeletal muscle fiber are distributed in a "checkerboard" pattern, because in pigs the slow oxidative fibers have a clustered distribution. The initial processes leading to fiber clustering are likely to occur during myogenesis, but the precise mechanistic aetiology of this patterning and whether the slow oxidative fiber clusters occur in a random or ordered fashion is unknown. In the present study longissimus thoracis muscle from Large White crossbred pigs was sampled at the 10th rib, 48 h postmortem. Transverse cryo-sections were cut and histochemically stained to allow the identification of the main muscle fiber types: slow oxidative, fast glycolytic, and fast oxidative glycolytic. Images of the sections were captured and analyzed using point processes and Voronoi Tesselations to examine the randomness and spatial distribution of the clusters of slow oxidative fibers found in pig longissimus thoracis muscle. The results showed that an assumption of complete spatial randomness can be rejected and that a mathematical model incorporating a minimum distance of 1.7 to 2.0 microm between cluster centers produced fiber patterns similar to those observed in the original transverse sections of the muscle. In addition, if it assumed that the central fiber in each cluster is derived from primary myoblast progenitors, these results suggest that there may be some degree of repulsion between the primary fibers during the initial stages of cluster formation. The mechanistic basis of such repulsion is not clear, but it is speculated that secreted factors, such as sonic hedgehog or myostatin may play a role.
Microbial growth on substitutable substrates: Characterizing the consumer‐resource relationship (1997)

In this article, we consider the growth of microorganisms on mixtures of carbon sources and characterize the consumer-resource relationship for this system. The characteristic features observed for the growth of a single microorganism on a pair of carbon sources allow a representation of this relationship based on a general paradigm for resource classification. This representation is verified using a comprehensive model for microbial growth on carbon sources. The results show that for the same pair of carbon sources the qualitative nature of the consumer-resource relationship changes with changing specific growth rate, and therefore a change in the identity of the rate-limiting substrate(s). © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 54: 77–90, 1997.
Performance optimization using template mapping for datapath-intensive high-level synthesis (1996)

This paper introduces a new approach to performance-driven template mapping for high-level synthesis. Template mapping, the process of mapping high-level algorithmic descriptions to specialized hardware libraries or instruction sets, involves template matching, template selection, and clock selection. Efficient algorithms for each are presented, and novel issues such as partial matching are addressed. The paper focuses on datapath-intensive ASIC design, though the concepts are also highly applicable to compiler development. Experimental results on examples from real applications show significant improvements in throughput with limited area overhead.
Preparative enzymic synthesis of nucleoside-5'-phosphates. (1975)

1. Wheat shoot phosphotransferase has been employed, with p-nitrophenylphosphate as a phosphate donor, to specifically phosphorylate the 5'-position of a variety of nucleosides and nucleoside analogues. The specificity of the enzyme towards the 5'-position of pentose nucleosides is testified to by the complete resistance to phosphorylation of 5'-O-methylcytidine. 2. With the use of ion-exchange chromatography, the foregoing procedure has been applied to the large-scale preparation of nucleoside-5'-phosphates with overall yields of the order of 80-90%. Quantitative recovery of unreacted nucleoside makes it possible to use this method without risk of losses either on a small or large scale with rare nucleosides. It is also applicable to acid- and alkali-labile nucleosides which cannot readily be phosphorylated by chemical procedures. 3. The wheat shoot phosphotransferase also phosphorylated a galactopyranosyl nucleoside, as well as such derivatives as 1-(beta-hydroxyethyl)cytosine and 5-(beta-hydroxyethyl)uracil, showing that the enzyme does not have an absolute requirement for a 5-membered sugar ring, but rather for the presence of a primary hydroxyl group. 4. The phosphorylated derivatives of galactopyranosyluracil, and of both hydroxyethyl pyrimidines, were resistant to 5'-nucleotidase. E. coli alkaline phosphatase converted all three nucleotides quantitatively to the starting compounds. 5. A synthesis of 1-(beta-hydroxyethyl)cytosine is described.
The Histone Deacetylase HDAC4 Connects Neural Activity to Muscle Transcriptional Reprogramming (2007)

Neural activity actively regulates muscle gene expression. This regulation is crucial for specifying muscle functionality and synaptic protein expression. How neural activity is relayed into nuclei and connected to the muscle transcriptional machinery, however, is not known. Here we identify the histone deacetylase HDAC4 as the critical linker connecting neural activity to muscle transcription. We found that HDAC4 is normally concentrated at the neuromuscular junction (NMJ), where nerve innervates muscle. Remarkably, reduced neural input by surgical denervation or neuromuscular diseases dissociates HDAC4 from the NMJ and dramatically induces its expression, leading to robust HDAC4 nuclear accumulation. We present evidence that nuclear accumulated HDAC4 is responsible for the coordinated induction of synaptic genes upon denervation. Inactivation of HDAC4 prevents denervation-induced synaptic acetyl-choline receptor (nAChR) and MUSK transcription whereas forced expression of HDAC4 mimics denervation and activates ectopic nAChR transcription throughout myofibers. We determined that HDAC4 executes activity-dependent transcription by regulating the Dach2-myogenin transcriptional cascade where inhibition of the repressor Dach2 by HDAC4 permits the induction of the transcription factor myogenin, which in turn activates synaptic gene expression. Our findings establish HDAC4 as a neural activity-regulated deacetylase and a key signaling component that relays neural activity to the muscle transcriptional machinery.
Methanofollis aquaemaris sp. nov., a methanogen isolated from an aquaculture fish pond. (2001)

A novel methanogen, designated strain N2F9704T, was isolated from an aquaculture fish pond near Wang-gong, Taiwan. The cells were irregular cocci, non-motile, 1.2-2.0 microm in diameter and stained gram-negative. Cells of strain N2F9704T lysed easily by SDS treatment (0.1 g l(-1)) and the S-layer protein had an Mr of 137000. The catabolic substrates used included formate and H2+CO2, but not acetate, methanol, trimethylamine or secondary alcohols. The optimal growth parameters for strain N2F9704T were pH 6.5, 37 degrees C with 0.5% NaCl. Trace amounts of tungstate not only promoted growth but also extended the range of growth conditions. Analysis of the 16S rDNA sequence revealed a phylogenetic relationship to Methanofollis species and the name Methanofollis aquaemaris sp. nov. is therefore proposed for strain N2F9704T (= OCM 746T = CCRC 16166T). Additionally, the strain was infected with a novel coccus-shaped, enveloped virus with a diameter of 200 nm.
Standard smart batteries for consumer applications (2002)

Accurately predicting the battery state of charge requires resident intelligence that utilizes cell models of performance along with real time data (current, voltage, temperature). To facilitate the transfer of that information to devices, Duracell and Intel have jointly developed specifications for intelligent battery communication which they are proposing as industry standards. Two main specifications describe the electrical protocol (System Management Bus) and the data content (Smart Battery Data), while secondary specifications describe chargers, software and multiple battery systems. The electronic hardware necessary inside the battery to meet those specifications is anything but standard; it is expected to be an active area of competition, manufacturers will continue to emphasise differences in cell chemistry, algorithms, and innovative charge control.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Viroid RNA systemic spread may depend on the interaction of a 71-nucleotide bulged hairpin with the host protein VirP1 (2003)

Viroids are noncoding circular single-stranded RNAs that are propagated systemically in plants. VirP1 is a protein from tomato, which is an excellent host for potato spindle tuber viroid (PSTVd), and it has been isolated by virtue of its specific in vitro binding to PSTVd RNA. We report on the specific in vivo interaction of VirP1 with full-length viroid RNA as well as with subfragments in the three-hybrid system. The terminal right domain (TR) of PSTVd was identified as a strong interacting partner for VirP1. A weaker partner is provided by a right-hand subfragment of hop stunt viroid (HSVd), a viroid that infects tomato poorly. We present a sequence and structural motif of the VirP1-interacting subfragments. The motif is disturbed in the replicative but nonspreading R+ mutant of the TR. According to our in vivo and in vitro binding assays, the interaction of this mutant with VirP1 is compromised. We propose that the AGG/CCUUC motif bolsters recognition of the TR by VirP1 to achieve access of the viroid to pathways that propagate endogenous RNA systemic signals in plants. Systemic trafficking has been suggested for miRNA precursors, of which the TR, as a stable bulged hairpin 71 nt long, is quite reminiscent.
Harnessing T-lymphocytes for human cancer immunotherapy (1985)

After nearly a decade of controversy, the concept of adoptive immunotherapy in humans is gaining greater acceptance. More recently, investigators have made use immunotherapeutically of T-lymphocytes nonspecifically activated in vitro by a number of agents, including lymphokines, lectins, and autologous and allogeneic tumor cells. The limitations for the investigational use of these highly specialized and "educated" lymphocytes have been the inability to generate sufficient numbers of cells in vitro for adoptive transfer experiments and to sustain their growth over long periods of time. While marked success has been demonstrated over the years in tumor-bearing animal models, the feasibility of such work in humans has been greatly improved by the experimental expansion and maintenance of immune lymphocytes (those exposed to antigenic challenge) in vitro using either highly purified or recombinant, interleukin 2. As a result, large numbers of lymphocytes can successfully be infused into patients, and whole body scans can show migration of these labeled cells to the lung, liver, and spleen. The use of nontoxic, nonspecific activated "killer" lymphocytes is an innovative approach with enormous potential. This report presents discussion of these findings and addresses the issue of an alternative approach to cancer treatment therapy, the in vivo use of cloned cytotoxic T-lymphocytes sensitized to the autologous tumor.
The biosynthetic gene cluster of the maytansinoid antitumor agent ansamitocin from Actinosynnema pretiosum (2002)

Maytansinoids are potent antitumor agents found in plants and microorganisms. To elucidate their biosynthesis at the biochemical and genetic level and to set the stage for their structure modification through genetic engineering, we have cloned two gene clusters required for the biosynthesis of the maytansinoid, ansamitocin, from a cosmid library of Actinosynnema pretiosum ssp. auranticum ATCC 31565. This is a rare case in which the genes involved in the formation of a secondary metabolite are dispersed in separate regions in an Actinomycete. A set of genes, asm22-24, asm43-45, and asm47, was identified for the biosynthesis of the starter unit, 3-amino-5-hydroxybenzoic acid (AHBA). Remarkably, there are two AHBA synthase gene homologues, which may have different functions in AHBA formation. Four type I polyketide synthase genes, asmA-D, followed by the downloading asm9, together encode eight homologous sets of enzyme activities (modules), each catalyzing a specific round of chain initiation, elongation, or termination steps, which assemble the ansamitocin polyketide backbone. Another set of genes, asm13-17, encodes the formation of an unusual "methoxymalonate" polyketide chain extension unit that, notably, seems to be synthesized on a dedicated acyl carrier protein rather than as a CoA thioester. Additional ORFs are involved in postsynthetic modifications of the initial polyketide synthase product, which include methylations, an epoxidation, an aromatic chlorination, and the introduction of acyl and carbamoyl groups. Tentative functions of several asm genes were confirmed by inactivation and heterologous expression.
Pharmacokinetic Properties of 9-Tetrahydrocannabinol in Oral Fluid of Occasional and Chronic Users (2010)

Saliva is of continuing interest in detecting the influence of drugs while driving. Commercial tests are currently available where cannabis detectability is a major challenge. The present study aids in the understanding of tetrahydrocannabinol (THC) pharmacokinetics in oral fluid. The oral fluid analyses exhibited no significant differences between 12 occasional users and 12 chronic users smoking a standardized cannabis joint, except for the maximum concentrations in the first samples (occasional users, 397- 6438 ng/g; chronic users 387-71,747 ng/g). THC was detectable in all samples with medians in the last samples (8 h) of 6.3 and 11.3 ng/g in occasional and chronic users, respectively. The elimination half-life in both groups was 1.6 +/- 0.4 h. A series of samples was obtained over a period of 8 h without actual drug use representing a later elimination phase. Of these oral fluid samples, only 4.3% were negative for THC despite positive serum, and 24.1% of serum samples were negative despite positive oral fluid. This confirms that THC is detectable for longer in oral fluid than in serum. The oral fluid-to-serum ratios were 0.3 to 425 (median 16.5) with no difference between chronic and occasional users. The large inter- and intraindividual variability observed precludes a reliable estimation of THC serum concentrations from oral fluid data using this collection device.
Enol Esters:  Versatile Substrates for Mannich-Type Multicomponent Reactions (2007)

The interaction of cyclic enol esters with diversely substituted anilines and ethyl glyoxalate yields, under Sc(OTf)3 catalysis, disubstituted N-aryl lactams in a multicomponent reaction. The protocol allows access to the trans stereoisomers after an epimerization of the initial mixture in which the cis isomers predominate. Vinyl acetate yields quinoline derivatives, whereas isopropenyl acetate leads to the corresponding Mannich adducts.