gebhart/patrepeval huggingface dataset:
Neurotrophin-3: a neurotrophic factor related to NGF and BDNF (1990)

The development and maintenance of the nervous system depends on proteins known as neurotrophic factors. Although the prototypical neurotrophic factor, nerve growth factor (NGF), has been intensively studied for decades, the discovery and characterization of additional such factors has been impeded by their low abundance. Sequence homologies between NGF and the recently cloned brain-derived neurotrophic factor (BDNF) were used to design a strategy that has now resulted in the cloning of a gene encoding a novel neurotrophic factor, termed neurotrophin-3 (NT-3). The distribution of NT-3 messenger RNA and its biological activity on a variety of neuronal populations clearly distinguish NT-3 from NGF and BDNF, and provide compelling evidence that NT-3 is an authentic neurotrophic factor that has its own characteristic role in vivo.
The identification of an Onchocerca -specific recombinant antigen containing a T cell epitope. (1990)

Recombinant Onchocerca volvulus Ag have been derived from expression libraries and examined for their ability to stimulate PBMC from patients infected with O. volvulus. Ten clones producing recombinant Ag were selected and plaque purified; lysogens were produced and found to express beta-galactosidase fusion proteins ranging in molecular mass from 115 to 138 kDa. When ammonium sulfate-precipitated lysates of these recombinant phage clones were examined for their ability to stimulate PBMC from a patient with onchocerciasis, all 10 recombinants produced stimulation above that to nonrecombinant phage. When individual fusion proteins, affinity purified on anti-beta-galactosidase linked to agarose, were used to stimulate PBMC from patients with onchocerciasis, only one of the recombinant Ag induced PBMC proliferation (stimulation index greater than 4) above that to Ag from nonrecombinant phage. Characterization of the DNA coding for this Ag showed it to be 1.2 kb in length with a small (90 bp) open reading frame; furthermore, it appears to be Onchocerca specific (on genomic dot blots) and single copy. Using overlapping peptides encompassing the entire open reading frame, one T cell epitope has been localized.
Novel dislocation structure and surface morphology effects in relaxed Ge/Si-Ge(graded)/Si structures (1997)

The defect structure in relaxed graded Ge/GexSi1−x/Si structures grown on (001) exact and (001) off-cut substrates using ultra-high vacuum chemical vapor deposition was characterized using transmission electron microscopy (TEM), atomic force microscopy, and electron beam induced current. The samples grown on off-cut (001) substrates showed a remarkable improvement in surface roughness and dislocation pile-up densities. By applying both a dislocation blocking criterion and surface roughness to graded Si-Ge/Si(001) structures, we can predict the formation of dislocation pile-ups in graded structures. Nonparallel misfit dislocation networks in off-cut wafer samples are not as efficient at blocking perpendicular dislocation motion, leading to a large reduction in dislocation pile-up density. The lower pile-up density on layers grown on off-cut wafers results in less stress-induced surface instability during growth, leading to surfaces with much lower roughness. TEM studies revealed that the array of 60° dislocations, that usually forms to relieve the misfit stress, transforms into a lower energy hexagonal dislocation network consisting of edge dislocations with Burgers vectors of the type 1/2〈110〉, 1/2〈1̄10〉, and 〈100〉. Such reactions were found to be more prevalent in the samples grown on off-cut substrates. Favorable intersections of {111} type planes on the off-cut substrates were found to aid such reactions.
Carboxylic acid reductase: a new tungsten enzyme catalyses the reduction of non‐activated carboxylic acids to aldehydes (1989)

An enzyme which we call carboxylic acid reductase (aldehyde dehydrogenase) seems to be the first which is able to reduce non-activated carboxylic acids to aldehydes at the expense of reduced viologens. There is no further reduction of the aldehydes to the corresponding alcohols. In the presence of oxidized viologens aldehydes can be dehydrogenated to carboxylic acids roughly 20 times faster than the latter are reduced. The specific enzyme activity in crude extracts is about 100 times increased if 10 microM tungstate and a sulphur source in addition to sulphate is given to the growth medium of Clostridium thermoaceticum. Carboxylic acid reductase seems to be present in two forms. One has an apparent molecular mass of about 240 kDa and is bound to red-Sepharose, whereas, the other, a form of an apparent molecular mass of about 60 kDa, is not bound. SDS gel electrophoresis shows a higher complexity. The very labile enzyme has been enriched by a factor of about 145 by binding to octyl-Sepharose and further chromatographic separation by red-Sepharose and FPLC using Mono-Q and phenyl-Superose columns. After cell growth in the presence of [185W]tungstate, radioactivity coincides with the two forms of enzyme activity during all purification steps. This is also the case when the enzyme is electrophoretically separated on polyacrylamide slab gels.
An Integrated Framework for the Methodological Assurance of Security and Privacy in the Development and Operation of MultiCloud Applications (2020)

This Thesis studies research questions about how to design multiCloud applications taking into account security and privacy requirements to protect the system from potential risks and about how to decide which security and privacy protections to include in the system. In addition, solutions are needed to overcome the difficulties in assuring security and privacy properties defined at design time still hold all along the system life-cycle, from development to operation.In this Thesis an innovative DevOps integrated methodology and framework are presented, which help to rationalise and systematise security and privacy analyses in multiCloud to enable an informed decision-process for risk-cost balanced selection of the protections of the system components and the protections to request from Cloud Service Providers used. The focus of the work is on the Development phase of the analysis and creation of multiCloud applications.The main contributions of this Thesis for multiCloud applications are four: i) The integrated DevOps methodology for security and privacy assurance; and its integrating parts: ii) a security and privacy requirements modelling language, iii) a continuous risk assessment methodology and its complementary risk-based optimisation of defences, and iv) a Security and Privacy Service Level AgreementComposition method.The integrated DevOps methodology and its integrating Development methods have been validated in the case study of a real multiCloud application in the eHealth domain. The validation confirmed the feasibility and benefits of the solution with regards to the rationalisation and systematisation of security and privacy assurance in multiCloud systems.
Mini-Review of Neural Regeneration Peptides in Brain Development (2016)

During mammalian and especially human ontogenetic brain development, cues of chemoattractive and chemorepulsive character are interacting in a spatial-temporal manner to direct neuroblasts to the dedicated locations in the neocortex. Finally, neuroblasts differentiate to fulfil their respective function in the neural circuit. Most if not all of these important molecules, that direct neuronal migration, display activity profiles in the nanomolar range. In contrast, the novel gene family of Neural Regeneration Peptides (NRPs) has a neuronal survival and chemo attraction profile in the subpicomolar range which makes the NRPs interesting candidates to represent the main constituents for neuronal chemo attraction during ontogenesis as well as injury or disease states of the brain. This review is focusing on early gene expression of the mouse nrp gene within the cortex as well as on the potential for the drug candidate NRP2945 to provide breakthrough treatment options for chronic disease states of the brain in the future.
Inertial migration of rigid spheres in two-dimensional unidirectional flows (1974)

The familiar Segré-Silberberg effect of inertia-induced lateral migration of a neutrally buoyant rigid sphere in a Newtonian fluid is studied theoretically for simple shear flow and for two-dimensional Poiseuille flow. It is shown that the spheres reach a stable lateral equilibrium position independent of the initial position of release. For simple shear flow, this position is midway between the walls, whereas for Poiseuille flow, it is 0·6 of the channel half-width from the centre-line. Particle trajectories are calculated in both cases and compared with available experimental data. Implications for the measurement of the rheological properties of a dilute suspension of spheres are discussed.
Gene therapy: a 2001 perspective (2001)

In the past year, three clinical trials of gene therapy for haemophilia have been initiated. Years of preclinical studies have culminated in translation of research findings into the clinical arena. It is too early to predict which, if any, of these strategies will show efficacy. This paper will review basic aspects of gene therapy for haemophilia and will briefly outline current clinical trials. The three clinical trials all share a dose escalation design. The ongoing trial for haemophilia B involves the intramuscular administration of an adeno-associated virus (AAV) vector expressing human factor IX. In preclinical studies, this strategy has produced therapeutic levels of circulating factor IX in haemophilic mice and dogs.
Cutting Edge: STAT1 and T-bet Play Distinct Roles in Determining Outcome of Visceral Leishmaniasis Caused by Leishmania donovani (2006)

T-bet and STAT1 regulate IFN-gamma gene transcription in CD4+ T cells, which mediate protection against Leishmania. Here we show that T-bet and STAT1 are required for the induction of an efficient Th1 response during Leishmania donovani infection, but they play distinct roles in determining disease outcome. Both STAT1(-/-) and T-bet(-/-) mice failed to mount a Th1 response, but STAT1(-/-) mice were highly resistant to L. donovani and developed less immunopathology, whereas T-bet(-/-) mice were highly susceptible and eventually developed liver inflammation. Adoptive cell transfer studies showed that RAG2(-/-) recipients receiving STAT1(+/+) or STAT1(-/-) T cells developed comparable liver pathology, but those receiving STAT1(-/-) T cells were significantly more susceptible to infection. These unexpected findings reveal distinct roles for T-bet and STAT1 in mediating host immunity and liver pathology during visceral leishmaniasis.
ABC≠A,B,C (2003)

ABC不同于A,B,C, 前者是一个词,后者是三个不同的字母。ABC用作名词,意为“字母”或“字母表”。如:I can say my ABC.我会念字母。ABC用作名词时,还表示“初步、入门、基础”。
Altered acyltransferase activity in Escherichia coli associated with mutations in acyl coenzyme A synthetase. (1983)

Growth of a temperature-sensitive general fatty acid synthesis mutant of Escherichia coli K12 at its restrictive temperature in the presence of exogenous palmitate results in lysis of the bacterium. Under these conditions, palmitate is incorporated into membrane phospholipid to a high level. Mutants of bacteria restricting this incorporation (having a palmitate-resistant phenotype) have been isolated and one such mutant, strain L8-2/3, has been further characterized. This mutant has lowered acyl-CoA synthetase (fadD) activity (25-33% of normal) and consequently is defective in fatty acid uptake. This lowered uptake could explain the palmitate-resistant phenotype of strain L8-2/3. However, both in vivo (fatty acid composition and positional distribution data) and in vitro (acyltransferase activity measurements) experiments suggest that this mutant is also altered in its acyltransferase activities. The mutation(s) of strain L8-2/3 appears to allow increased (approximately 2-fold) incorporation of myristate (and possible unsaturated fatty acids) into position 2 of 1-acyl-sn-glycerol 3-phosphate but normal palmitate incorporation into the same position. The incorporation of palmitate, myristate, and oleate into position 1 of sn-glycerol 3-phosphate by strain L8-2/3 is also higher than that observed with the parent, strain L8-2. Replacing the partially defective fadD gene of strain L8-2/3 with a wild type allele conferred on this strain the palmitate sensitivity and the acyltransferase activity of the parent strain L8-2. This finding, taken together with other data, suggests that acyl-CoA synthetase interacts with the acyltransferase(s) in some manner to influence the fatty acid specificity of the acyltransferase.
Comparison of Formic and Sulfuric Acids as a Glucose Decomposition Catalyst (2010)

Dilute sulfuric acid hydrolysis of cellulose is the oldest and a well-studied technology for converting biomass to ethanol. Despite continuous technology improvements, the process still gives only a moderate selectivity due to glucose decomposition in the cellulose hydrolysis conditions. According to the recent literature, carboxylic acids have been recognized as more selective acid hydrolysis catalysts than sulfuric acid in low hydrogen ion concentrations. In this paper, formic acid was compared to sulfuric acid as a glucose decomposition catalyst at values below pH 2.2 at 180−220 °C. It was found that glucose decomposition depends only on the hydrogen ion concentration in the prevailing reaction conditions and is independent of the hydrogen ion source. Earlier contradictory findings can be the consequence of ignoring the temperature function of the dissociation constants of the acids and setting hydrogen ion concentrations at room temperature.
Sequence changes in the pilus subunit lead to tropism variation of Neisseria gonorrhoeae to human tissue (1994)

Pili of Neisseria gonorrhoeae are correlated with increased bacterial attachment to epithelial cells and undergo both phase and antigenic variation. Phase variation of gonococcal pili can be brought about by recombination events in the pilin structural gene, pilE, or by the on/off switch in expression of PilC, a pilus biogenesis protein for which two loci exist. We have studied the binding to epithelial cell lines and to fixed tissue sections of N. gonorrhoeae MS11 derivatives and mutants carrying structurally defined PilE and PilC proteins. In situ binding studies of N. gonorrhoeae to formalin-fixed tissue sections resulted in a binding pattern similar to that obtained using viable epithelial cell lines of different origin. Piliated gonococcal clones, containing different pilE sequences, varied dramatically from one another in their efficiencies at binding to corneal and conjunctival tissue, but bound equally well to cervical and endometrial tissues. Further, the binding data suggested that PilC expression by itself, i.e. without pili, cannot confer bacterial binding and that expression of either PilC1 or PilC2 does not confer different binding properties to the bacterial cells. Possible receptors for piliated gonococci were expressed in human tissues, such as cervix, endometrium, cornea, intestine, stomach, mid-brain and meninges, but not in human kidney. Pretreatment of the target tissues with Proteinase K decreased the gonococcal binding dramatically, whereas pretreatment with neuraminidase and meta-periodate, which cleave carbon-carbon linkages between vicinal hydroxyl groups in carbohydrates, did not affect attachment of gonococci. These data argue that pilus-dependent attachment of N. gonorrhoeae to human tissue may be mediated by a eukaryotic receptor having protein characteristics, and that the pilus subunit sequence may play an important role in the interaction with human cornea.
Guided-wave optical wavelength demultiplexer using an asymmetric Y junction (1989)

An optical wavelength demultiplexer using an asymmetric Y junction is numerically analyzed and the experimental results are reported. This demultiplexer utilizes both the mode splitting characteristic of an asymmetric Y junction and the waveguide dispersion of channel waveguides. Analysis shows that the device with step-index profile has more than 20 dB isolation for wavelengths with 6.5% separation from the center wavelength. The fabricated device composed of two-step ion exchanged soda-lime glass waveguides coated asymmetrically with Corning 7059 glass thin film separated the lights of 0.63 and 0.84 μm wavelengths.
Antibacterial Activities of Thin Films Containing Ceragenins (2008)

Ceragenins are small molecule mimics of naturally occurring antimicrobial peptides and display potent antimicrobial activities against a range of Gram-negative and positive organisms. When covalently attached to polymers, ceragenins retain antimicrobial activity. Materials, such as medical grade foams, coated with thin films of polymeric ceragenins release the polymers slowly into aqueous solution providing sustained antimicrobial activity in the surrounding solution over periods greater than three weeks.
Identification of Molecular Pathway Aberrations in Uterine Serous Carcinoma by Genome-wide Analyses (2012)

Molecular genetic aberrations involving the p53, cyclin E-FBXW7, and PI3K pathways represent major mechanisms in the development of uterine serous carcinoma.
Suppression of Gene Expression by RNA Interference in Cultured Plant Cells (2001)

Suppression by double-stranded RNA (dsRNA) of the expression of a target gene is known as RNA interference (RNAi). No quantitative analysis of the effects of RNAi on the expression of specific genes in cultured plant cells has been reported. However, as it is possible to produce populations of cultured plant cells that are uniform and divide synchronously for functional analysis of genes of interest, we performed a quantitative study of the effects of RNAi in such cells. We constructed dsRNA expression plasmids for a luciferase gene under the control of the cauliflower mosaic virus (CaMV) 35S promoter by simply connecting sense and antisense sequences in a head-to-head manner. An RNAi effect was observed 24 hours after the introduction of dsRNA expression plasmids into tobacco BY-2 cells by electroporation. The simple system for suppression of specific genes in plant cells should be useful in attempts to elucidate the roles of individual genes in plant cells.
[Effect of different hemopoietic microenvironment on the differentiation of hemopoietic cells from human embryonic stem cells]. (2007)

The inductive efficiency of deriving hematopoietic cells from EBs co-cultured with human fetal liver stromal cells was higher than EBs co-cultured with human yolk sac stromal cells and fetal bone marrow stromal cells.
Structure–activity analysis of buforin II, a histone H2A-derived antimicrobial peptide: The proline hinge is responsible for the cell-penetrating ability of buforin II (2000)

Buforin II is a 21-aa potent antimicrobial peptide that forms, in a hydrophobic medium, an amphipathic structure consisting of an N-terminal random coil region (residues 1-4), an extended helical region (residues 5-10), a hinge (residue 11), and a C-terminal regular alpha-helical region (residues 12-21). To elucidate the structural features of buforin II that are required for its potent antimicrobial activity, we synthesized a series of N- and C-terminally truncated or amino acid-substituted synthetic buforin II analogs and examined their antimicrobial activity and mechanism of action. Deletion of the N-terminal random coil region increased the antibacterial activity approximately 2-fold, but further N-terminal truncation yielded peptide analogs with progressively decreasing activity. Removal of four amino acids from the C-terminal end of buforin II resulted in a complete loss of antimicrobial activity. The substitution of leucine for the proline hinge decreased significantly the antimicrobial activity. Confocal fluorescence microscopic studies showed that buforin II analogs with a proline hinge penetrated the cell membrane without permeabilization and accumulated in the cytoplasm. However, removal of the proline hinge abrogated the ability of the peptide to enter cells, and buforin II analogs without a proline hinge localized on the cell surface, permeabilizing the cell membrane. In addition, the cell-penetrating efficiency of buforin II and its truncated analogs, which depended on the alpha-helical content of the peptides, correlated linearly with their antimicrobial potency. Our results demonstrate clearly that the proline hinge is responsible for the cell-penetrating ability of buforin II, and the cell-penetrating efficiency determines the antimicrobial potency of the peptide.
Effect of plasminogen activator (urokinase), plasmin, and thrombin on glycoprotein and collagenous components of basement membrane. (1981)

Tumor cells traverse basement membranes (BM) during the stages of the metastatic process. Penetration of the BM may involve proteolysis by enzymes directly or indirectly associated with tumor cells. This study evaluated the role of the serine proteases urokinase (plasminogen activator), plasmin, and another regulatory protease, alpha-thrombin, in the degradation of the BM. Homogeneously pure enzyme preparations were incubated with isolated components of BM and with whole human amnion BM. The BM components consisted of acid-extracted type IV collagen, pepsin fragments of collagen type IV, laminin, and fibronectin. Collagen type V (alpha A alpha B) associated with the peri-BM zone was also studied. The purity of the enzymes was verified by gel electrophoresis and inhibitor studies. Digestion of the BM components was performed at 25 degrees using matched activity for the different enzymes. Urokinase failed to significantly degrade fibronectin or any of the other BM components. Under the same 25 degrees (native) conditions, plasmin and thrombin cleaved fibronectin and laminin into multiple specific fragments but did not produce a major cleavage of acid-extracted type IV collagen, pepsinized type IV collagen, or alpha A alpha B (type V) collagade fibronectin or any of the other BM components. Under the same 25 degrees (native) conditions, plasmin and thrombin cleaved fibronectin and laminin into multiple specific fragments but did not produce a major cleavage of acid-extracted type IV collagen, pepsinized type IV collagen, or alpha A alpha B (type V) collagade fibronectin or any of the other BM components. Under the same 25 degrees (native) conditions, plasmin and thrombin cleaved fibronectin and laminin into multiple specific fragments but did not produce a major cleavage of acid-extracted type IV collagen, pepsinized type IV collagen, or alpha A alpha B (type V) collagen. alpha-Thrombn selectively degraded only the m.w. 400,000 chain of laminin, whereas plasmin degraded both the laminin chains. Digestion of laminin by the serine proteases was time and concentration dependent, as verified by a new degradation assay using [14C]laminin. A variety of normal and neoplastic cells were tested for the presence of laminin-degrading proteases. macrophages, polymorphonuclear leukocytes, and metastatic tumor cells contained a significant laminin-degarding activity. The activity was enhanced by the addition of plasminogen. Type V collagen was cleaved by thrombin and plasmin at 35 degrees but not at temperatures below 33 degrees. Following treatment of whole-amnion BM with any of these enzymes, electron microscopy demonstrated preservation of the lamina densa. Immunohistology studies indicated that laminin, but not type IV collagen, was removed from the whole BM by plasmin treatment. The results suggest that these BM components are poor substrates for plasminogen activators and that plasmin alone is not sufficient to completely degrade the whole BM...