gebhart/patrepeval huggingface dataset:
Overlapping Reading Frames at the LYS5 Locus in the Yeast Yarrowia lipolytica (1990)

Mutants affected at the LYS5 locus of Yarrowia lipolytica lack detectable dehydrogenase (SDH) activity. The LYS5 gene has previously been cloned, and we present here the sequence of the 2.5-kilobase-pair (kb) DNA fragment complementing the lys5 mutation. Two large antiparallel open reading frames (ORF1 and ORF2) were observed, flanked by potential transcription signals. Both ORFs appear to be transcribed, but several lines of evidence suggest that only ORF2 is translated and encodes SDH. (i) The global amino acid compositions of Saccharomyces cerevisiae SDH and of the putative ORF2 product are similar and that of ORF1 is dissimilar. (ii) An in-frame translational fusion of ORF2 with the Escherichia coli lacZ gene was introduced into yeast cells and resulted in a beta-galactosidase activity regulated similarly to SDH; no beta-galactosidase activity was obtained with an in-frame fusion of ORF1 with lacZ. (iii) The introduction of a stop codon at the beginning of ORF2 prevented SDH expression in yeast cells, whereas no phenotypic effect was observed when ORF1 translation was blocked.
Detection of human papillomavirus deoxyribonucleic acid by filter in situ hybridization during pregnancy (1989)

Samples taken from 101 healthy pregnant women (49 over and 52 under the 20-week gestational period) and 108 healthy nonpregnant women were tested for human papillomavirus (HPV) types. Using 6, 11, 16, and 18 HPV DNA probes, 3-5 x 10(5) exfoliated cells scraped from the cervix were tested by filter in situ hybridization (FISH). Thirty-five of the pregnant women (34.6%) had evidence of the presence of HPV DNA: with 11.8% (12/101) HPV 6; 7.9% (8/101) HPV 11; 8.9% (9/101) HPV 16; and 5.9% (6/101) HPV 18 positivity. HPV DNA was detected in 20.4% (22/108) of the non-pregnant women. Compared with the healthy, nonpregnant group, the higher level of asymptomatic cervical HPV infection was mainly due to the accumulation of HPV 16 and 18 nucleic acids during the gestational period: with detection of HPV 16 in 8/49 cases (16.3%) and of HPV 18 DNA sequences in 4/49 (7.6%) cases. Screening 6-8 weeks after delivery indicated a decline of HPV positivity. Of the 4/12 HPV type 16 positive mothers, only one retained the presence of HPV 16 DNA, whereas neither of the 2/12 type 18 positive women reacted after birth with the type 18 radioactive probe.
NUCLEOTIDE EXCISION REPAIR (1993)

Nucleotide excision repair is the major DNA repair mechanism in all species tested. This repair system is the sole mechanism for removing bulky adducts from DNA, but it repairs essentially all DNA lesions, and thus, in addition to its main function, it plays a back-up role for other repair systems. In both pro- and eukaryotes nucleotide excision is accomplished by a multisubunit ATP-dependent nuclease. The excision nuclease of prokaryotes incises the eighth phosphodiester bond 5' and the fourth or fifth phosphodiester bond 3' to the modified nucleotide and thus excises a 12-13-mer. The excision nuclease of eukaryotes incises the 22nd, 23rd, or 24th phosphodiester bond 5' and the fifth phosphodiester bond 3' to the lesion and thus removes the adduct in a 27-29-mer. A transcription repair coupling factor encoded by the mfd gene in Escherichia coli and the ERCC6 gene in humans directs the excision nuclease to RNA polymerase stalled at a lesion in the transcribed strand and thus ensures preferential repair of this strand compared to the nontranscribed strand.
Interaction of the two components of leukocidin from Staphylococcus aureus with human polymorphonuclear leukocyte membranes: sequential binding and subsequent activation (1994)

The sequential interaction between the two components S and F of leukocidin from Staphylococcus aureus and the membrane of human polymorphonuclear neutrophils has been investigated in the presence of 1 mM Ca2+. With 125I-labeled components, it has been shown that binding of the F component occurred only after binding of the S component. The kinetic constants of binding of both components were not statistically different (Kd, approximately 5 nM; Bm, approximately 35,000 molecules per cell), and both Hill coefficients were 1. The application of increasing concentrations of leukocidin provoked a dose-dependent secretion of the granule content, as determined by hexosaminidase and lysozyme activity measurements. Furthermore, the separate perfusion of S and F components on human polymorphonuclear neutrophils deposited on a filter induced secretion of the granules content only when the perfusion of the S component preceded that of the F component. We conclude, therefore, that (i) S-component binding is a prerequisite for F-component binding and for subsequent activation of polymorphonuclear neutrophils and (ii) there is a specific binding site for the S component in the plasma membrane.
Brown adipose tissue–specific insulin receptor knockout shows diabetic phenotype without insulin resistance (2001)

Although insulin regulates metabolism in both brown and white adipocytes, the role of these tissues in energy storage and utilization is quite different. Recombination technology using the Cre-loxP approach allows inactivation of the insulin receptor in a tissue-specific manner. Mice lacking insulin receptors in brown adipocytes show an age-dependent loss of interscapular brown fat but increased expression of uncoupling protein-1 and -2. In parallel, these mice develop an insulin-secretion defect resulting in a progressive glucose intolerance, without insulin resistance. This model provides direct evidence for not only a role for the insulin receptors in brown fat adipogenesis, the data also suggest a novel role of brown adipose tissue in the regulation of insulin secretion and glucose homeostasis.
Role of envelope glycoprotein carbohydrate in human immunodeficiency virus (HIV) infectivity and virus-induced cell fusion. (1986)

Human immunodeficiency virus (HIV) envelope glycoprotein interactions with cell surface CD4 are involved in both virion infectivity and virally mediated cell fusion. D-mannose-specific lectins such as Con A specifically blocked virion infectivity and cell fusion. Studies with a recombinant vaccinia virus containing the HIV envelope gene demonstrated that Con A-mediated inhibition of HIV-induced fusion involved lectin binding to the viral envelope glycoprotein. These results indicate the importance of envelope glycosylation in the pathobiology of HIV infection, and suggest potential mechanisms for interfering with HIV infectivity and cytopathology.
Two-dimensional protein crystallization via metal-ion coordination by naturally occurring surface histidines. (1996)

A powerful and potentially general approach to the targeting and crystallization of proteins on lipid interfaces through coordination of surface histidine residues to lipid-chelated divalent metal ions is presented. This approach, which should be applicable to the crystallization of a wide range of naturally occurring or engineered proteins, is illustrated here by the crystallization of streptavidin on a monolayer of an iminodiacetate-Cu(II) lipid spread at the air-water interface. This method allows control of the protein orientation at interfaces, which is significant for the facile production of highly ordered protein arrays and for electron density mapping in structural analysis of two-dimensional crystals. Binding of native streptavidin to the iminodiacetate-Cu lipids occurs via His-87, located on the protein surface near the biotin binding pocket. The two-dimensional streptavidin crystals show a previously undescribed microscopic shape that differs from that of crystals formed beneath biotinylated lipids.
Dextrous telerobotics with force feedback — An overview part 2: control and implementation (1991)

SUMMARY The control stategy for a dextrous masters is different from the general case of bilateral teleoperation since it models the human hand in much more detail. Such a model is discussed together with the selection of actuators used for force feedback control. Existing prototypes of dextrous masters with force feedback are then reviewed. These are the Servo Controlled Manipulator Device, the Portable Dextrous Force Feedback Master (P.D.M.F.F.), the Remote Handler, and the Advanced Multiple DOF Force Reflective Hand/Wrist Master.
27-Hydroxylated Low Density Lipoprotein (LDL) Cholesterol Can Be Converted to 7α,27-Dihydroxy-4-cholesten-3-one (Cytosterone) before Suppressing Cholesterol Production in Normal Human Fibroblasts (1996)

The formation of oxysterols in cultured human fibroblasts and their physiological roles as intracellular regulators of cholesterol production have been investigated. In the presence of low density lipoproteins (LDL), normal fibroblasts converted LDL cholesterol to 27hydroxycholesterol, which was further metabolized to 7alpha, 27-dihydroxycholesterol, 7alpha,27-dihydroxy-4-cholesten-3-one, and 7alpha-hydroxy-3-oxo-4-cholestenoic acid. Autooxidation products of cholesterol contaminating the lipoproteins were also metabolized in the cells. 7alpha-Hydroxycholesterol was converted to 7alpha-hydroxy-4-cholesten-3-one prior to 27-hydroxylation and further oxidation to 7alpha-hydroxy-3-oxo-4-cholestenoic acid. 7beta-Hydroxycholesterol and 7-oxocholesterol were 27-hydroxylated and then oxidized to C27-acids. Oxidation of the 7beta-hydroxy group also occurred. 25-Hydroxycholesterol was 7alpha-hydroxylated and further oxidized to 7alpha,25-dihydroxy-4-cholesten-3-one. 25-Hydroxylation of sterols was observed only under specific conditions. In contrast, only small amounts of oxysterols were formed in virus-transformed human fibroblasts when incubated with lipoproteins. This was due to very low activities of the 27- and 7alpha-hydroxylating enzymes. The rate of oxidation at C-3 was also decreased moderately. A defective suppression of 3-hydroxy-3-methylglutaryl coenzyme A reductase by LDL and autooxidation products of cholesterol observed in the transformed fibroblasts could be caused by the deficiencies of the sterol-metabolizing enzymes, since these cells responded normally to the sterol metabolites 7alpha,27-dihydroxy-4-cholesten-3-one, 7alpha, 25-dihydroxy-4-cholesten-3-one, and 27-hydroxy-7-oxo-cholesterol. These metabolites, which all possessed an oxo group with a conjugated double bond in the steroid nucleus and a hydroxyl group in the side chain, did not seem to require further metabolism in order to be active. An impaired response to LDL was also seen in other human tumor cells, including breast carcinoma, colonic carcinoma, and malignant melanoma cells. Common to all the malignant cells was an intracellular shortage of 7alpha, 27-dihydroxy-4-cholesten-3-one caused by a decreased formation or an increased metabolism.
The Structure of Scientific Literatures II: Toward a Macro- and Microstructure for Science (1974)

Part I of this paperl described the first steps in mapping the scientific literature, using a new technique-co-citation-to measure the degree of similarity among documents. The work developed directly from an earlier paper2 which defined this measure, and explored its relationship to other citation measures for identifying relationships among documents. We now report the outcome of an attempt to create 'maps' of the scientific literature. The scales of these maps have been systematically manipulated so that they present, not only an overview of all highly-cited papers in natural science, but
The formation of erythrocyte membrane proteins during erythropoietin-induced differentiation. (1981)

The effect of erythropoietin on the synthesis of the proteins characteristic of mature erythrocyte membranes was studied in cultures of bone marrow cells from adult, polycythemic rats. Stimulated synthesis of the major glycoprotein, glycophorin, was maximal at 30 h and fell to control level by 66 h. Stimulated synthesis of the major integral membrane protein, band 3, occurred at about 18 h was maximal at 66 h, and fell to control level by 114 h. In contrast, stimulated hemoglobin synthesis did not start until after 24 h, was maximal at 96 h, and was at control level at 114 h. Erythropoietin had, in addition, a transient effect on the synthesis of some membrane proteins found in marrow cells but not in mature red cells.
A new micro-machined millimeter-wave and terahertz snap-together rectangular waveguide technology (1999)

A novel technique for micro-machining millimeter and submillimeter-wave rectangular waveguide components is reported. These are fabricated in two halves which simply snap together, utilizing locating pins and holes, and are physically robust, and cheap, and easy to manufacture. In addition, S-parameter measurements on these structures are reported for the first time and display lower loss than previously reported micro-machined rectangular waveguides.
RNA-mediated interaction of Cajal bodies and U2 snRNA genes (2001)

Cajal bodies (CBs) are nuclear structures involved in RNA metabolism that accumulate high concentrations of small nuclear ribonucleoproteins (snRNPs). Notably, CBs preferentially associate with specific genomic loci in interphase human cells, including several snRNA and histone gene clusters. To uncover functional elements involved in the interaction of genes and CBs, we analyzed the expression and subcellular localization of stably transfected artificial arrays of U2 snRNA genes. Although promoter substitution arrays colocalized with CBs, constructs containing intragenic deletions did not. Additional experiments identified factors within CBs that are important for association with the native U2 genes. Inhibition of nuclear export or targeted degradation of U2 snRNPs caused a marked decrease in the levels of U2 snRNA in CBs and strongly disrupted the interaction with U2 genes. Together, the results illustrate a specific requirement for both the snRNA transcripts as well as the presence of snRNPs (or snRNP proteins) within CBs. Our data thus provide significant insight into the mechanism of CB interaction with snRNA loci, strengthening the putative role for this nuclear suborganelle in snRNP biogenesis.
Compatible Solutes Protect against Chaotrope(Ethanol)-Induced, Nonosmotic WaterStress (2003)

Water stress is one of the major stresses experienced by cellular systems and can take a number of distinct forms. In response to turgor-related osmotic stress, cells produce compatible solutes that are macromolecule protectants and also counteract the outflow of water from stressed cells. In this report we show that the germination of conidia of Aspergillus nidulans, a sensitive indicator of water stress, in the presence of ethanol is correlated with the intracellular concentration of the compatible solutes glycerol and erythritol, which protect against both osmotic and nonturgor forms of water stress.
Applications for the scalable coherent interface (1990)

IEEE P1596, the Scalable Coherent Interface (formerly known as SuperBus) is based on experience gained while developing Fastbus (ANSI/IEEE 960-1986, IEC 935), Futurebus (IEEE P896.x) and other modern high-performance buses. SCI goals include a minimum bandwidth of 1 GByte/sec per processor in multiprocessor systems with thousands of processors; efficient support of a coherent distributed-cache image of distributed shared memory; support for bridges which interface to existing or future buses; and support for inexpensive small rings as well as for general switched interconnections like Banyan, Omega, or crossbar networks. This paper reports the status of the work in progress and suggests some applications in data acquisition and physics. 9 refs.
The gastrointestinal tract (1999)

The choice of imaging modality for optimal demonstration of gastrointestinal anatomy is highly dependent on the clinical symptoms and signs. With the advent of newer technology, the role of plain abdominal radiography has diminished, although characteristic gas and soft tissue patterns can be of great importance in the diagnosis of the ‘acute abdomen’.
The Three-dimensional Structure of Cys-47-modified Mouse Liver Glutathione S-Transferase P1-1 (1998)

The three-dimensional structure of mouse liver glutathione S-transferase P1-1 carboxymethylated at Cys-47 and its complex with S-(p-nitrobenzyl)glutathione have been determined by x-ray diffraction analysis. The structure of the modified enzyme described here is the first structural report for a Pi class glutathione S-transferase with no glutathione, glutathione S-conjugate, or inhibitor bound. It shows that part of the active site area, which includes helix alphaB and helix 310B, is disordered. However, the environment of Tyr-7, an essential residue for the catalytic reaction, remains unchanged. The position of the sulfur atom of glutathione is occupied in the ligand-free enzyme by a water molecule that is at H-bond distance from Tyr-7. We do not find any structural evidence for a tyrosinate form, and therefore our results suggest that Tyr-7 is not acting as a general base abstracting the proton from the thiol group of glutathione. The binding of the inhibitor S-(p-nitrobenzyl)-glutathione to the carboxymethylated enzyme results in a partial restructuring of the disordered area. The modification of Cys-47 sterically hinders structural organization of this region, and although it does not prevent glutathione binding, it significantly reduces the affinity. A detailed kinetic study of the modified enzyme indicates that the carboxymethylation increases the Km for glutathione by 3 orders of magnitude, although the enzyme can function efficiently under saturating conditions.
Cancer Dissemination during Laparoscopic Surgery: Tubes, Gas, and Cells (1998)

Port-site metastasis has been an unexpected finding after laparoscopic surgery in gastrointestinal cancer patients. No clear explanation exists for this phenomenom. The aims of this study were to evaluate the dissemination pattern in an experimental model of hepatocarcinoma in the rat and summarize current knowledge about the risks and the results of experimental studies on cancer dissemination during laparoscopic surgery. NDA-induced hepatocarcinoma was obtained in Sprague-Dawley rats. Tumors were manipulated during laparoscopy (group 1, n = 11) or laparotomy (group 2, n = 12). A Medline review of all experimental studies about the risk of cancer dissemination during laparoscopic surgery was undertaken. Both models were associated with implants in parietal wounds [1/11 in group 1 (9%) vs. 1/12 in group 2 (8%), p = NS]. Analysis of the current literature confirms that laparoscopy is associated with abdominal cell mobilization, and cells can be recovered in trocars, filtered exhaust gas, and instruments. Postoperative immunosuppression, the biologic aggressiveness of the tumor, and the gas used for laparoscopy also influence tumoral growth. Port-site metastases are secondary to multiple factors, including the technical skill of the surgeon, the biologic properties of the tumors, and local environmental aspects. Undoubtedly, laparoscopy can help disseminate aggressive tumors and should be reserved for diagnostic and staging procedures or for treatment of low-grade malignant tumors. Therapeutic resection, especially of colon cancer, should be restricted to prospective and randomized trials until there are enough hard data to rule out the clinical importance of this potentially severe complication.
BLAT—The BLAST-Like Alignment Tool (2002)

Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. BLAT's speed stems from an index of all nonoverlapping K-mers in the genome. This index fits inside the RAM of inexpensive computers, and need only be computed once for each genome assembly. BLAT has several major stages. It uses the index to find regions in the genome likely to be homologous to the query sequence. It performs an alignment between homologous regions. It stitches together these aligned regions (often exons) into larger alignments (typically genes). Finally, BLAT revisits small internal exons possibly missed at the first stage and adjusts large gap boundaries that have canonical splice sites where feasible. This paper describes how BLAT was optimized. Effects on speed and sensitivity are explored for various K-mer sizes, mismatch schemes, and number of required index matches. BLAT is compared with other alignment programs on various test sets and then used in several genome-wide applications. http://genome.ucsc.edu hosts a web-based BLAT server for the human genome.
Condensates Made of Light (2007)

At low temperature, atom wave functions can lock together. Such a state has now been seen in trapped photons and electron-hole pairs.
Transgenic models of amyotrophic lateral sclerosis. (2004)

Amyotrophic lateral sclerosis (ALS), the most frequent paralytic disease of adults, is untreatable and invariably fatal. Up to 20% of ALS cases are inherited (familial, fALS) and associated with mutations, usually of the superoxide dismutase type 1 (SOD-1) gene. This paper shortly reviews the background for and the use of rodent transgenic models of ALS. Silencing the SOD-1 gene does not produce paralytic phenotype, but transgenic rodents expressing human mutated (hm) SOD-1 atop their own enzyme develop relatively selective and fatal degeneration of motoneurons. Many essential neuropathological and biochemical features of the paralytic disease in hmSOD-1 transgenic mice and rats are similar to human fALS, and these animals are currently considered a model of the human disease. Two types of hypotheses put forward to explain pathomechanism of motoneuron degeneration in hmSOD-1 transgenics (hence also in human ALS) are the "gain of function" hypotheses which assume that the mutated enzyme displays new toxic catalytic properties, and the "gain of interaction" hypotheses which assume that the mutated protein molecules are toxic because they became misfolded and undergo oligomerization. Transgenic animal models of ALS are used for preclinical assessments of new therapeutic approaches ranging from mono- and polipharmacotherapy to gene therapy and stem cell therapy.
Darstellung polymerer Steroidacetale und Steroidester (1984)

Abstract Zur Eigenschaftsmodifizierung polymerer Pharmaka wurden 3β‐Hydroxysteroide mit polymeren Trägern bzw. polymerisierbaren Monomeren umgesetzt. Die Acetalisierung erfolgte unter milden Bedingungen und ergab in Abhängigkeit vom eingesetzten 3β‐Hydroxysteroid bzw. vom Lösungsmittel Acetale mit einem Umsetzungsgrad von maximal 15%. Als polymere Träger wurden die auf radikalischem Wege hergestellten Copolymere Vinylacetat/Crotonaldehyd sowie der bei der Oxidation von Dextran mit NaIO 4 erhaltene Dextranaldehyd eingesetzt. Polymere Ester wurden durch Umsetzung von 3β‐Hydroxysteroiden mit Methacrylsäurechlorid und anschließender radikalischer Copolymerisation mit Methacrylsäure erhalten.
Hepatic stem‐like cells in hepatoblastoma: expression of cytokeratin 7, albumin and oval cell associated antigens detected by OV‐1 and OV‐6 (1997)

The results demonstrate that antigens associated with oval cells are found in certain cells in hepatoblastoma. SEC, like oval cells, co-express markers for hepatocytic and biliary differentiation. The findings further support the hypothesis that SEC are closely related to the putative bipotent hepatic stem cell, which, by definition, gives rise to both hepatocytes and biliary epithelial cells.