gebhart/patrepeval huggingface dataset:
Increasing gene expression in yeast by fusion to ubiquitin (1989)

Heterologous gene expression in yeast can be increased up to several hundred-fold by expressing a foreign gene as a fusion to the ubiquitin gene. An endogenous yeast endoprotease (Ub-Xase) removes the ubiquitin from the fusion product to produce the authentic protein. The utility of this technique has been demonstrated by expression of three different proteins in yeast as both unfused and ubiquitin-fused forms: 1) the alpha subunit of the mammalian stimulating G-protein of the adenylate cyclase complex (Gs alpha); 2) a soluble fragment of the T cell receptor protein (sCD4); and 3) the protease domain of human urokinase (UKP). The sequence specificity of the Ub-Xase was demonstrated by mutagenesis of the carboxyl-terminal glycine of ubiquitin to an alanine, which inhibited ubiquitin removal in vivo. Processing of the ubiquitin-Gs alpha fusion protein (ub-Gs alpha) in vivo resulted in Gs alpha which could be reconstituted in mammalian membrane preparations and had the same specific activity as the authentic Gs alpha expressed in yeast. The yeast Ub-Xase has also been shown to work in vitro by the processing of a ub-sCD4 fusion protein synthesized in Escherichia coli. This technology should greatly enhance the utility of yeast for heterologous protein production.
Acceptance of oral chemotherapy in breast cancer patients - a survey study (2011)

P.o. chemotherapy shows a high acceptance in MBC patients under palliative therapy. Compliance can be achieved in particular through a differentiated indication, patient education and competent support along a p.o. treatment.
Anomalous Proximity Effect in UnderdopedYBa2Cu3O6+xJosephson Junctions (2000)

Josephson junctions were photogenerated in underdoped thin films of the YBa2Cu3O6+x family using a near-field scanning optical microscope. The observation of the Josephson effect for separations as large as 100 nm between two wires indicates the existence of an anomalously large proximity effect and shows that the underdoped insulating material in the gap of the junction is readily perturbed into the superconducting state. The critical current of the junctions was found to be consistent with the conventional Josephson relationship. This result appears to constrain the applicability of SO(5) theory to explain the phase diagram of high critical temperature superconductors.
A role for ATR in the DNA damage-induced phosphorylation of p53 (1999)

Phosphorylation at Ser-15 may be a critical event in the up-regulation and functional activation of p53 during cellular stress. In this report we provide evidence that the ATM-Rad3-related protein ATR regulates phosphorylation of Ser-15 in DNA-damaged cells. Overexpression of catalytically inactive ATR (ATRki) in human fibroblasts inhibited Ser-15 phosphorylation in response to gamma-irradiation and UV light. In gamma-irradiated cells, ATRki expression selectively interfered with late-phase Ser-15 phosphorylation, whereas ATRki blocked UV-induced Ser-15 phosphorylation in a time-independent manner. ATR phosphorylated p53 at Ser-15 and Ser-37 in vitro, suggesting that p53 is a target for phosphorylation by ATR in DNA-damaged cells.
Role of Constitutive Isoflavone Conjugates in the Accumulation of Glyceollin in Soybean Infected withPhytophthora megasperma (1990)

These results suggest that 1) glyceollin biosynthesis may not be solely dependent on the induction of enzymes of early phenylpropanoid and flavonoid metabolism in this organ and 2) resistance to P. m. f. sp. glycinea race 1, as defined by the Rps 1 c gene in this organ, may reside partly in the rapid release of the isoflavone aglycones from their conjugates and/or in the later steps of glyceollin biosynthesis
Extrapancreatic incretin receptors modulate glucose homeostasis, body weight, and energy expenditure (2006)

The incretin hormones glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP) control glucose homeostasis through well-defined actions on the islet beta cell via stimulation of insulin secretion and preservation and expansion of beta cell mass. We examined the importance of endogenous incretin receptors for control of glucose homeostasis through analysis of Glp1r(-/-), Gipr(-/-), and double incretin receptor knockout (DIRKO) mice fed a high-fat (HF) diet. DIRKO mice failed to upregulate levels of plasma insulin, pancreatic insulin mRNA transcripts, and insulin content following several months of HF feeding. Both single incretin receptor knockout and DIRKO mice exhibited resistance to diet-induced obesity, preservation of insulin sensitivity, and increased energy expenditure associated with increased locomotor activity. Moreover, plasma levels of plasminogen activator inhibitor-1 and resistin failed to increase significantly in DIRKO mice after HF feeding, and the GIP receptor agonist [D-Ala(2)]GIP, but not the GLP-1 receptor agonist exendin-4, increased the levels of plasma resistin in studies of both acute and chronic administration. These findings extend our understanding of how endogenous incretin circuits regulate glucose homeostasis independent of the beta cell via control of adipokine secretion and energy expenditure.
Thermodynamics of Hydrogen Atom Transfer to a High-Valent Iron Imido Complex (2008)

Thermodynamic investigations relevant to hydrogen atom transfer by the high-valent iron imido complex [LMesFe[triple bond]NAd]OTf have been undertaken. The complex is found to be weakly oxidizing by cyclic voltammetry (E1/2 = -0.98 V vs Cp2Fe+/Cp2Fe in MeCN). A combination of experimental and computational studies has been used to determine the acidity of LMesFe-N(H)Ad+ (pKa = 37 in MeCN), allowing the N-H BDFE (88(5) kcal/mol) to be calculated from a thermodynamic cycle. Consistent with this value, [LMesFe[triple bond]NAd]OTf reacts with 9,10-dihydroanthracene (C-H BDE = 78(1) kcal/mol) to form anthracene.
Recombinant Toluene-4-monooxygenase:  Catalytic and Mössbauer Studies of the Purified Diiron and Rieske Components of a Four-Protein Complex (1996)

Expression of the tmoA-F gene cluster from Pseudomonas mendocina KRI in Escherichia coli BL21(DE3) produces a catalytically active form of the toluene-4-monooxygenase (T4MO) complex. Here we report the purification and characterization of four soluble proteins required for the in vitro reconstitution of T4MO catalytic activity. These proteins are a diiron hydroxylase (T4MOH), a Riesketype ferredoxin (T4MOC), an effector protein (T4MOD), and an NADH oxidoreductase (T4MOF). The T4MOH component is composed of the tmoA, tmoB, and tmoE gene products [quaternary structure (alpha beta epsilon)2, Mr approximately 220 kDa]. The T4MOA polypeptide contains two copies of the amino acid sequence motif (D/E)X(28-37)DEXRH; the same motif provides all of the protein-derived ligands to the diiron centers of ribonucleotide reductase, the soluble methane monooxygenase, and the stearoyl-ACP delta 9 desaturase. Mössbauer, optical, and EPR measurements show that the T4MOH contains diiron centers and suggest that the diiron center contains hydroxo bridge(s) in the diferric state, as observed for methane monooxygenase. Mössbauer and EPR measurements also show that the T4MOC contains a Rieske-type iron-sulfur center. This assignment is in accord with the presence of the amino acid sequence motif CPHX(15-17)CX2H, which has also been found in the bacterial, chloroplastic, and mitochondrial Rieske proteins as well as the bacterial NADH-dependent cis-dihydrodiol-forming aromatic dioxygenases. While single-turnover catalytic studies confirm the function of the T4MOH as the hydroxylase, the NADH-dependent multiple-turnover hydroxylation activity is increased by more than 100-fold in the presence of the T4MOC, which mediates highly specific electron transfer between the T4MOF and the T4MOH. The T4MOD can be purified as an 11.6 kDa monomeric protein devoid of cofactors or redox-active metal ions; this component is also detected as a substoichiometric consitutent of the purified T4MOH. The rate of the hydroxylation reaction can be mildly stimulated by the further addition of separately purified T4MOD to the T4MOH, implying the formation of a high affinity, catalytically competent complex between these two components. These characterizations define a novel, four-component oxygenase combining elements from the soluble methane oxidation complex of the methanotrophic bacteria and the aromatic hydroxylation complexes of the soil pseudomonads.
Partially Modified Retro-Inverso-Enkephalinamides: Topochemical Long-Acting Analogs in Vitro and in Vivo (1979)

The synthesis of four enkephalinamide analogs is described in which the peptide bond between residues 4 and 5 is reversed with or without simultaneous reversal of the carboxyl-terminal amide bond. These so-called partially modified retro-inverso-isomers are new, potent, topochemical analogs of the enkephalins. Tests, both in vitro and in vivo, have shown that these analogs are considerably longer acting than any previously studied enkephalins. Thus, partial reversal of the peptide bonds of the backbone can result in peptides with enhanced activity compared to a parent compound, provide that the structural complementarity of both the side chains and end groups are conserved.
What, where and who? Classifying events by scene and object recognition (2007)

We propose a first attempt to classify events in static images by integrating scene and object categorizations. We define an event in a static image as a human activity taking place in a specific environment. In this paper, we use a number of sport games such as snow boarding, rock climbing or badminton to demonstrate event classification. Our goal is to classify the event in the image as well as to provide a number of semantic labels to the objects and scene environment within the image. For example, given a rowing scene, our algorithm recognizes the event as rowing by classifying the environment as a lake and recognizing the critical objects in the image as athletes, rowing boat, water, etc. We achieve this integrative and holistic recognition through a generative graphical model. We have assembled a highly challenging database of 8 widely varied sport events. We show that our system is capable of classifying these event classes at 73.4% accuracy. While each component of the model contributes to the final recognition, using scene or objects alone cannot achieve this performance.
Gastrointestinal leiomyosarcoma metastatic to the liver. Durable tumor regression by hepatic chemoembolization infusion with cisplatin and vinblastine (1995)

Hepatic chemoembolization infusion appears to induce a high rate of durable tumor response in patients with notoriously chemoresistant gastrointestinal leiomyosarcoma metastatic to the liver.
Loss of conserved Gsdma3 self-regulation causes autophagy and cell death (2015)

Gasdermin A3 (Gsdma3) was originally identified in association with hair-loss phenotype in mouse mutants. Our previous study found that AE mutant mice, with a Y344H substitution at the C-terminal domain of Gsdma3, display inflammation-dependent alopecia and excoriation [Zhou et al. (2012) Am. J. Pathol. 180, 763-774]. Interestingly, we found that the newly-generated null mutant of Gsdma3 mice did not display the skin dysmorphology, indicating that Gsdma3 is not essential for differentiation of epidermal cells and maintenance of the hair cycle in normal physiological conditions. Consistently, human embryonic kidney (HEK)293 and HaCaT cells transfected with wild-type (WT) Gsdma3 did not show abnormal morphology. However, Gsdma3 Y344H mutation induced autophagy. Gsdma3 N-terminal domain, but not the C-terminal domain, also displayed the similar pro-autophagic activity. The Gsdma3 Y344H mutant protein and N-terminal domain-induced autophagy was associated with mitochondria and ROS generation. Co-expression of C-terminal domain reversed the cell autophagy induced by N-terminal domain. Moreover, C-terminal domain could be co-precipitated with N-terminal domain. These data indicated that the potential pro-autophagic activity of WT Gsdma3 protein is suppressed through an intramolecular inhibition mechanism. Studies on other members of the GSDM family suggested this mechanism is conserved in several sub-families.
Antibodies of predetermined specificity detect two retroviral oncogene products and inhibit their kinase activities (1983)

Oligopeptides predicted from the nucleotide sequence of the oncogene v-fes of feline sarcoma virus (FeSV) were synthesized chemically and used to generate specific antibodies. Antisera against a 12-amino-acid-long oligopeptide (12-mer) located 42 residues from the carboxyl terminus of the v-fes coding sequence efficiently recognized the transforming proteins encoded by Snyder-Theilen (ST) and Gardner-Arnstein (GA) strains of FeSV. This 12-mer also contains 10 amino acid residues homologous in order and position to those predicted from the nucleotide sequence of the oncogene v-fps of avian Fujinami sarcoma virus (FSV). The anti-12-mer immunoprecipitated the FSV-specific transforming protein molecules from FSV-transformed cells. Binding of these antipeptide antibody molecules to the v-fes and the v-fps gene products inhibited their associated tyrosine-specific protein kinase (EC 2.7.1.37) activities. The ability to generate such site-specific antisera to the products of related oncogenes will be valuable in the molecular characterization of retroviral transforming proteins and their normal cellular homologs.
Nitroxide chemistry. Part IV. Reaction of bistrifluoromethyl nitroxide with aldehydes (1973)

Bistrifluoromethyl nitroxide abstracts aldehydic hydrogen atoms from acetaldehyde, propionaldehyde, pivalaldehyde, benzaldehyde, m- and p-tolualdehyde, terephthalaldehyde, and pentafluorobenzaldehyde with great ease, to give NN-bistrifluoromethylhydroxylamine and the corresponding (bistrifluoromethylamino-oxy)carbonyl-alkane or -arene in almost quantitative yields. Basic hydrolysis of the carbonyl compounds ArCO2·N(CF3)2(Ar = Ph or C6F5) yields the corresponding arenecarboxylic acids, and attack of bistrifluoromethyl nitroxide on the phenyl compound at elevated temperature leads to nuclear substitution with the formation of (bistrifluoromethylamino-oxy)[(bistrifluoromethylamino-oxy)carbonyl]benzenes.
Interaction of Cody, a novel Bacillus subtillis DNA‐binding protein, with the dpp promoter region (1996)

The product of the codY gene is required for nutritional repression of the Bacillus subtillis dipeptide permease operon (dpp), an operon expressed at early stationary phase in nutrient-rich medium. Though unrelated to any known DNA-binding protein, CodY was shown to bind specifically to the dpp promoter region. DNase I footprinting experiments revealed that the CodY-protected region encompasses the dpp transcription start site and overlaps with the region protected by another regulatory protein, AbrB. CodY and AbrB were found to compete, in vitro, for binding to the dpp promoter region. Binding of CodY was altered in mutants defective in nutritional regulation.
조선 시대 김해 도자기로 본 한일 관계 (2018)

김해는 고대부터 일본과 밀접한 교류를 맺어왔던 지역이다. 본 논문에서는 그동안 연구가 부족하였던 고려, 조선 시대의 김해를 통한 한일 교류를 도자사의 관점에서 살펴보고자 한다. 11세기 후반부터 김해는 일본으로 도자기가 건너간 경유지가 되었다. 조선 시대에 들어 1423년에는 김해도호부가 제포왜관에 배치된 그릇을 담당하였다. 김해부는 제포에 머물었던 일본인 대접용으로 다수의 그릇을 마련해야 했었다. 이 그릇들이 바로 김해 대감리 가마터에서 제작된 인화 분청사기이었을 가능성이 높다. 임진왜란과 정유왜란 당시 연행된 조선 사람 중에는 큐슈(九州) 지역의 요업 시조(開祖)가 된 사기장들도 포함되어 있었다. 사가현(佐賀縣) 우치노야마(內野山) 가마에서는 신카이(深海)라는 사기장이 시작하였다고 하는데, 이것은 김해를 잘 못 들었을 가능성이 있다고 한다. 아울러 가고시마현(鹿兒島縣)　사쓰마(薩摩)에서도 김해라는 사기장이 기록이 남아 있다. 이와 같은 사기장들의 김해란 이름을 왜 썼는가에 대해서는 검토가 필요하겠으나 17세기에 들어 김해가 도자기와 밀접한 관계가 있는 지역으로 인식된 것으로 생각된다. 끝으로 긴카이(金海)라 불린 다완에 대해 언급한다. 문헌에서는 1611년에 김해 장인에게 대마도 사람이 주문한 다완을 굽게 하던 기록이 나타났는데, 긴카이 다완의 굽, 형태, 장식을 살펴볼 때, 대체로 1610-1620년대에 제작된 것으로 추정된다. 이상과 같이 김해는 고려와 조선 시대에도 일본과 밀접한 관계에 있었으며 일본인들 사이에서 김해＝도자기라는 인식으로도 이어진 것으로 생각된다.
Explaining the Escalation of Drug Use in Substance Dependence: Models and Appropriate Animal Laboratory Tests (2007)

Escalation of drug use, a hallmark of drug dependence, has traditionally been interpreted as reflecting the development of tolerance to the drug's effects. However, on the basis of animal behavioral data, several groups have recently proposed alternative explanations, i.e. that such an escalation of drug use might not be based on (1) tolerance, but rather be indicative of (2) sensitization to the drug's reinforcing effect, (3) reward allostasis, (4) an increase in the incentive salience of drug-associated stimuli, (5) an increase in the reinforcing strength of the drug reinforcer relative to alternative reinforcers, or (6) habit formation. From the pharmacological perspective, models 1-3 allow predictions about the change in the shape of drug dose-effect curves that are based on mathematically defined models governing receptor-ligand interaction and signal transduction. These predictions are tested in the present review, which also describes the other currently championed models for drug use escalation and other components of apparent 'reinforcement' (in its original meaning, like 'tolerance' or 'sensitization', a purely descriptive term). It evaluates the animal experimental approaches employed to support or prove the existence of each of the models and reinforcement components, and recapitulates the clinical evidence, which strongly suggests that escalation of drug use is predominantly based on an increase in the frequency of intoxication events rather than an increase in the dose taken at each intoxication event. Two apparent discrepancies in animal experiments are that (a) sensitization to overall reinforcement has been found more often for psychostimulants than for opioids, and that (b) tolerance to the reinforcing and other effects has been observed more often for opioids than for cocaine. These discrepancies are resolved by the finding that cocaine levels seem to be more tightly regulated at submaximum reinforcing levels than opioid levels are. Consequently, animals self-administering opioids are more likely to expose themselves to higher above-threshold doses than animals self-administering psychostimulants, rendering the development of tolerance to opioids more likely than tolerance to psychostimulants. The review concludes by making suggestions on how to improve the current behavioral experimental approaches.
Evidence that absence of endometrial gland secretions in uterine gland knockout ewes compromises conceptus survival and elongation (2002)

Endometrial glands are necessary for conceptus implantation and growth. In the ovine uterine gland knockout (UGKO) model, blastocysts hatch normally but fail to survive or elongate. This peri-implantation defect in UGKO ewes may be due to the absence of endometrial glands or, alternatively, to the lack of certain epithelial adhesion molecules or the inability of the endometrium to respond to signals from the conceptus. Two studies were performed to examine these hypotheses. In study one, normal (n = 8) and UGKO (n = 12) ewes were mated at oestrus (day 0) with intact rams and their uteri were flushed 14 days after oestrus. Normal ewes (n = 4) were also flushed on 14 days after oestrus. Uterine flushes from bred normal ewes contained filamentous conceptuses (n = 7 of 8), whereas those from UGKO ewes contained no conceptus (n = 5 of 12), a growth-retarded, tubular conceptus (n = 6 of 12), or a fragmented, filamentous conceptus (n = 1 of 12). In all groups, expression of mucin 1 and integrin alpha(v), alpha(5), beta(3) and beta(5) was localized at the apical surface of the endometrial luminal epithelium with no detectable differences between normal and UGKO ewes. Uterine flushes from pregnant ewes, but not cyclic or UGKO ewes, contained abundant immunoreactive interferon tau and the cell adhesion proteins, osteopontin and glycosylation-dependent cell adhesion molecule one. In study two, UGKO ewes were fitted with uterine catheters 5 days after oestrus, infused with recombinant ovine interferon tau or control proteins from 11 to 15 days after oestrus, and underwent hysterectomy 16 days after oestrus. Expression of several interferon tau-stimulated genes (ISG17, STAT1, STAT2 and IRF-1) was increased in the endometrium from interferon tau-infused UGKO ewes. These results support the hypothesis that the defects in conceptus elongation and survival in UGKO ewes are due to the absence of endometrial glands and their secretions rather than to alterations in expression of anti-adhesive or adhesive molecules on the endometrial luminal epithelium or to the responsiveness of the endometrium to the conceptus pregnancy recognition signal.
Detection and evaluation of intron retention events in the human transcriptome (2004)

Alternative splicing is a very frequent phenomenon in the human transcriptome. There are four major types of alternative splicing: exon skipping, alternative 3' splice site, alternative 5' splice site, and intron retention. Here we present a large-scale analysis of intron retention in a set of 21,106 known human genes. We observed that 14.8% of these genes showed evidence of at least one intron retention event. Most of the events are located within the untranslated regions (UTRs) of human transcripts. For those retained introns interrupting the coding region, the GC content, codon usage, and the frequency of stop codons suggest that these sequences are under selection for coding potential. Furthermore, 26% of the introns within the coding region participate in the coding of a protein domain. A comparison with mouse shows that at least 22% of all informative examples of retained introns in human are also present in the mouse transcriptome. We discuss that the data we present suggest that a significant fraction of the observed events is not spurious and might reflect biological significance. The analyses also allowed us to generate a reliable set of intron retention events that can be used for the identification of splicing regulatory elements.
Layered Nanoprobe for Long‐Lasting Fluorescent Cell Label (2012)

A long-lasting particle-based fluorescent label is designed for extended cell imaging studies. This onion-like nanoprobe is constructed through layer-by-layer fabrication technology. The nanoprobes are assembled with multiple layers of optically quenched polyelectrolytes, the fluorescence signal of which can be released later by intracellular proteolysis. Upon incubation with cells, the assembled nanoprobes are taken up efficiently. The tight packing and layered assembly of the quenched polyelectrolytes slow subsequent intracellular degradation, and then result in a prolonged intracellular fluorescence signal for up to 3 weeks with no noticeable toxicity.
Enhancement of Clinicians' Diagnostic Reasoning by Computer-Based Consultation (1999)

Our study supports the idea that "hands-on" use of diagnostic DSSs can influence diagnostic reasoning of clinicians. The larger effect for students suggests a possible educational role for these systems.
Insertion of a New Gene of Viral Origin into Bone Marrow Cells of Mice (1980)

DNA containing the herpes simplex virus thymidine kinase (HSVtk) gene was used to transform wild-type tk+ mouse L cells to a tk++ status in vitro using methotrexate as a selective agent. HSVtk DNA was also used to transform mouse bone marrow cells in vitro. Transformed marrow cells injected into irradiated and methotrexate-treated recipient mice gave rise to proliferating cells which in some cases dominated the marrow population and which contained HSVtk gene sequences.