gebhart/patrepeval huggingface dataset:
Isolation of recombinant proteins from milk (1992)

Milk is a complex bio-colloid which presents some unique problems for the protein isolation chemist, but the majority of the processing criteria for purifying recombinant proteins are the same as with any complex biological mixture. The casein micelles and fat globules behave as separate phases; they prevent filtration of the milk and interfere with the usual separation methods. The usual first step is to centrifuge the milk to remove the fat and precipitate the casein micelles with low pH or precipitating agents. Some recombinant proteins may associate to some degree with the micelles which may necessitate solubilizing them with chelating agents. If the majority of the product protein associates with either the fat or micelles, this can be used to advantage. Once the casein micelles have been removed or disrupted, the clarified milk can be processed by the usual separation methods. There also are proteases in milk which can degrade recombinant proteins. The greatest advantage of producing recombinant proteins in milk is the high concentration which can be obtained. The high levels of product protein can alleviate many problems associated with the application of classical purification strategies to transgenic milk proteins.
Assignment of the membrane attachment, DNA binding, and transcriptional activation domains of sterol regulatory element-binding protein-1 (SREBP-1). (1994)

Transcription of the low density lipoprotein receptor gene and other sterol-regulated genes is stimulated by sterol regulatory element-binding protein-1 (SREBP-1), a basic-helix-loop-helix-leucine zipper (bHLH-ZIP) transcription factor. Human SREBP-1 is synthesized as an 1147-amino acid precursor that is attached intrinsically to membranes of the nuclear envelope and endoplasmic reticulum. In sterol-depleted cells the precursor is cleaved to generate an NH2-terminal fragment that enters the nucleus and activates transcription by binding to sterol regulatory element-1 (SRE-1). Sterols prevent transcriptional activation by blocking the proteolytic cleavage. In the current studies, performed with hamster SREBP-1, we used mutational analysis to localize the transcriptional activation domain to an acidic NH2-terminal sequence. Deletion of this sequence converted SREBP-1 from an activator to an inhibitor of transcription. DNA binding was assigned to the basic region of the bHLH-ZIP domain. Binding was abolished by substitution of 3 amino acids that were previously implicated in DNA binding by Max, another bHLH-ZIP protein. The membrane attachment domain was localized to two hydrophobic regions at residues 477-497 and 536-556. Truncation of SREBP-1 prior to these regions gave rise to an NH2-terminal fragment that was soluble and entered the nucleus. This fragment was more than 30-fold more active than full-length SREBP-1 in stimulating transcription of an SRE-1 containing reporter gene in transfected cells. Deletion of the hydrophobic sequences (delta 476-556) yielded a protein that appeared cytosolic by immunofluorescence microscopy but failed to enter the nucleus readily, apparently because of inhibition by sequences in the remaining COOH-terminal domain. This study provides a picture of the domain structure of SREBP-1 and further elucidates the mechanism by which it adjusts gene transcription to maintain cholesterol homeostasis in animal cells.
Effect of the vaccine Ad5 [E1-, E2b-]-CEA(6D) on CEA-directed CMI responses in patients with advanced CEA-expressing malignancies in a phase I/II clinical trial. (2012)

2585 Background: Adenovirus (Ad) vectors are promising platforms for use as cancer vaccines because of their substantial immunogenicity; however, Ad-specific neutralizing antibodies, present due to natural infection, limit their use. We created a new vector containing additional deletions of the E2b gene and observed that this Ad5 [E1-, E2b-] vector, engineered to express carcinoembryonic antigen (CEA(6D)), could induce antitumor immune responses in mice despite pre-existing Ad5 immunity. The purpose of the current translational study was to evaluate the immunologic effect of increasing doses of Ad5 [E1-, E2b-]-CEA(6D) in mice and then to extended these pre-clinical observations into a phase I/II study. Methods: Ad5 naïve female C57Bl/6 mice, 4-6 weeks old, were immunized subcutaneously 3 times at 2 week intervals with doses of 1.4X10 7 viral particles (vp) up to1.4X10 9 vp of Ad5 [E1-, E2b-]-CEA(6D). Two weeks after the last immunization, splenocytes were harvested for immune determinations. Cohorts of patients (n=25 total) with advanced colorectal cancer, refractory to prior therapies, received escalating doses of Ad5 [E1-, E2B-]-CEA(6D) (10 9 to 10 11 vp) subcutaneously every 3 weeks for 3 immunizations.CEA-specific cell mediated immunity was measured by ELISPOT. Results: Increasing doses of Ad5 [E1-, E2b-]-CEA(6D) in mice induced increasing CEA-specifc CMI responses. Similarly, patients who received the highest dose of Ad5 [E1-, E2b-]-CEA(6D) exhibited the highest levels of CEA-specific CMI responses. The induction of CEA-specific CMI responses increased over the course of the 3 injections despite the presence of pre-existing Ad5 immunity in the majority (75%) of patients. There were no drug related grade 3/4 toxicities.Two patients with stable disease remained so during the study. All other patients experienced progressive disease; however, 1-year survival was 54%. Conclusions: Multiple homologous doses of Ad5 [E1-, E2b-]-CEA(6D) could break tolerance and generate CEA-specific CMI responses in the setting of Ad specific immunity in colorectal cancer patients.
Hematopoietic stem cell transplantation in nonmalignant diseases. (1997)

Treatment of patients with nonmalignant hematopoietic diseases by marrow grafts from HLA identical family members has progressed to a point where event free survivals of 75-90% can be expected. For allografts to be successful, conditioning programs have been devised that provide both the immunosuppression and the marrow space required for the incoming grafts to be accepted. Despite graft versus host disease prevention with methotrexate and cyclosporine, the acute and chronic forms of this disease continue to pose problems for a minority of patients after transplant, and they may necessitate prolonged courses of immunosuppressive therapy. The transplant procedures required for patients with these nonmalignant hematopoietic diseases could be directly applied to patients with autoimmune diseases.
ITS Intelligent Transportation System: fleet management with GPS dead reckoning, advanced displays, smartcards, etc (1993)

The ITS Intelligent Transportation System is provided as a modular construction set for enhanced fleet navigation and operational management, as well as passenger service and information. ITS provides fully autonomous vehicle operation through shifting as much intelligence as possible from the control center to the vehicles. ITS utilizes Global Positioning System (GPS) and/or dead reckoning for autonomous vehicle location (AVL) and vehicle navigation and provides the fully autonomous vehicle functions for AVM, including schedule adherence, traffic signal pre-emption, and management of on-board passenger service facilities such as destination display, stop announcement and passenger counting.
Correlation between the induction of a gene for Δ1‐pyrroline‐5‐carboxylate synthetase and the accumulation of proline in Arabidopsis thaliana under osmotic stress (1995)

The isolation and characterization is reported of a cDNA for delta 1-pyrroline-5-carboxylate (P5C) synthetase (cAtP5CS), an enzyme involved in the biosynthesis of proline, from a cDNA library prepared from a dehydrated rosette plant of Arabidopsis thaliana. Southern blot analysis suggested that only one copy of the corresponding gene (AtP5CS) is present in A. thaliana. The deduced amino acid sequence of the P5CS protein (AtP5CS) from A. thaliana exhibited 74% homology to that of the P5CS from Vigna aconitifolia. Northern blot analysis revealed that the gene for P5CS was induced by dehydration, high salt and treatment with ABA, while it was not induced by heat or cold treatment. Moreover, the simultaneous accumulation of proline was observed as a result of the former treatments in A. thaliana. A cDNA for P5C reductase (cAtP5CR) was also isolated from A. thaliana and Northern blot analysis was performed. The AtP5CR gene was not induced to a significant extent by dehydration or high-salt stress. These observations suggest that the AtP5CS gene plays a principal role in the biosynthesis of proline in A. thaliana under osmotic stress.
Glucuronoxylomannan promotes the generation of antigen‐specific T regulatory cell that suppresses the antigen‐specific Th2 response upon activation (2008)

T regulatory cells (Treg) have the capability to suppress the skewed immune response, but the generation of antigen (Ag)-specific Treg for therapeutic purpose is a challenge; the mechanism of Ag-specific Treg activation remains obscure. Here, we report that glucuronoxylomannan (GXM) is capable of promoting the development of human tolerogenic dendritic cells (DC). GXM-pulsed DCs increased the expression of forkhead box P3 (Foxp3) in naïve human CD4(+)CD25(-) T cells via activating Fc gamma receptor IIb and activator protein-1 and promoting the expression of transforming growth factor beta in dendritic cells. Furthermore, the conjugated complex of house dust mite Ag, Dermatophagoides pteronyssinus (Der p) 1, and GXM-pulsed DCs to drive the naïve human CD4(+)CD25(-) T cells to develop into the Der p 1-specific Tregs, which efficiently suppressed the Ag-specific Th2 responses. We conclude that GXM-conjugated specific Ag have the capacity to up-regulate the tolerogenic property of DCs and promote the generation of Ag-specific Tregs; the latter can be activated upon the re-exposure to specific Ag and suppress the skewed Ag-specific T helper (Th)2 responses.
Quantitative Study of Data Caches on a Multistreamed Architecture (1998)

In this paper, we quantify the effect that fine grained multistreamed interaction of threads within a shared cache has on the miss rate. By concentrating on the miss rate, we focus on just the cache performance and separate ourselves from a given system architecture. We show the effects of cache capacity, associativity, and line size on the miss rates of multistreamed workloads of two, three and four streams. We then separate the individual components of the miss rate into misses that are intrinsic to the workload (i.e., misses present in a non-multistreamed processor) and extrinsic (i.e., misses introduced due to the multistreamed nature of the processor). Our preliminary results show that for two streamed workloads the increase in miss rate due to multistreaming is less than 60% for caches with some associativity. We observe that for larger cache capacities, direct mapped caches and caches with larger line sizes exhibit poor performance due to a significant increase in the number of ...
Small-Angle Neutron Scattering from Surfactant-Assisted Aqueous Dispersions of Carbon Nanotubes (2004)

The mechanism of surfactant-assisted dispersion of single-walled carbon nanotubes in water is studied by small-angle neutron scattering. The previously hypothesized formation of cylindrical micelles with the nanotubes forming the core of cylinders is inconsistent with the data presented. The scattering data favor a random structureless adsorption model for the dispersion of the nanotubes.
Mechanical effects of airway humidification devices in difficult to wean patients* (2003)

Objective To evaluate the influence of airway humidification devices on the efficacy of ventilation in difficult to wean patients. Design A prospective, randomized, controlled physiologic study. Setting A 22-bed medical intensive care unit in a university hospital. Patients Chronic respiratory failure patients. Interventions Performances of a heated humidifier and a heat and moisture exchanger were evaluated on diaphragmatic muscle activity, breathing pattern, gas exchange, and respiratory comfort during weaning from mechanical ventilation by using pressure support ventilation. Eleven patients with chronic respiratory failure were submitted to four pressure support ventilation sequences by using the heated humidifier and the heat and moisture exchanger at two different levels of pressure support ventilation (7 and 15 cm H2O). Measurement and Main Results Compared with the heated humidifier and regardless of the pressure support ventilation level used, the heat and moisture exchanger significantly increased all of the inspiratory effort variables (inspiratory work of breathing expressed in J/L and J/min, pressure time product, changes in esophageal pressure, and transdiaphragmatic pressure;p < .05) and dynamic intrinsic positive end-expiratory pressure (p < .05). Similarly, the heat and moisture exchanger produced a significant increase in Paco2 (p < .01) responsible for severe respiratory acidosis (p < .05), which was insufficiently compensated for despite a significant increase in minute ventilation (p < .05). This resulted in respiratory discomfort for all patients with the heat and moisture exchanger (p < .01). Adverse effects were partially counterbalanced by increasing the pressure support ventilation level with the heat and moisture exchanger by ≥8 cm H2O. Conclusions The type of airway humidification device used may negatively influence the mechanical efficacy of ventilation and, unless the pressure support ventilation level is considerably increased, the use of a heat and moisture exchanger should not be recommended in difficult or potentially difficult to wean patients with chronic respiratory failure.
Saporin-S6: A Useful Tool in Cancer Therapy (2013)

Thirty years ago, the type 1 ribosome-inactivating protein (RIP) saporin-S6 (also known as saporin) was isolated from Saponaria officinalis L. seeds. Since then, the properties and mechanisms of action of saporin-S6 have been well characterized, and it has been widely employed in the construction of conjugates and immunotoxins for different purposes. These immunotoxins have shown many interesting results when used in cancer therapy, particularly in hematological tumors. The high enzymatic activity, stability and resistance to conjugation procedures and blood proteases make saporin-S6 a very useful tool in cancer therapy. High efficacy has been reported in clinical trials with saporin-S6-containing immunotoxins, at dosages that induced only mild and transient side effects, which were mainly fever, myalgias, hepatotoxicity, thrombocytopenia and vascular leak syndrome. Moreover, saporin-S6 triggers multiple cell death pathways, rendering impossible the selection of RIP-resistant mutants. In this review, some aspects of saporin-S6, such as the chemico-physical characteristics, the structural properties, its endocytosis, its intracellular routing and the pathogenetic mechanisms of the cell damage, are reported. In addition, the recent progress and developments of saporin-S6-containing immunotoxins in cancer immunotherapy are summarized, including in vitro and in vivo pre-clinical studies and clinical trials.
One Stage Full‐ Versus Partial‐Mouth Disinfection in the Treatment of Chronic Adult or Generalized Early‐Onset Periodontitis. (1999)

These findings support the benefit of a one stage full-mouth disinfection in the treatment of patients with either chronic adult or early-onset periodontitis.
Static analysis of binary code to isolate malicious behaviors (2003)

We address the problem of static slicing on binary executables for the purposes of malicious code detection in COTS components. By operating directly on binary code without any assumption on the availability of source code, our approach is realistic and appropriate for the analysis of COTS software products. To be able to reason on such low-level code, we need a suite of program transformations that aim to get a high level imperative representation of the code. The intention is to significantly improve the analysability while preserving the original semantics. Next we apply slicing techniques to extract those code fragments that are critical from the security standpoint. Finally, these fragments are subjected to verification against behavioral specifications to statically decide whether they exhibit malicious behaviors or not.
Human HPK1, a novel human hematopoietic progenitor kinase that activates the JNK/SAPK kinase cascade. (1996)

The c-Jun amino-terminal kinases (JNKs)/stress-activated protein kinases (SAPKs) play a crucial role in stress responses in mammalian cells. The mechanism underlying this pathway in the hematopoietic system is unclear, but it is a key in understanding the molecular basis of blood cell differentiation. We have cloned a novel protein kinase, termed hematopoietic progenitor kinase 1 (HPK1), that is expressed predominantly in hematopoietic cells, including early progenitor cells. HPK1 is related distantly to the p21(Cdc42/Rac1)-activated kinase (PAK) and yeast STE20 implicated in the mitogen-activated protein kinase (MAPK) cascade. Expression of HPK1 activates JNK1 specifically, and it elevates strongly AP-1-mediated transcriptional activity in vivo. HPK1 binds and phosphorylates MEKK1 directly, whereas JNK1 activation by HPK1 is inhibited by a dominant-negative MEKK1 or MKK4/SEK mutant. Interestingly, unlike PAK65, HPK1 does not contain the small GTPase Rac1/Cdc42-binding domain and does not bind to either Rac1 or Cdc42, suggesting that HPK1. activation is Rac1/Cdc42-independent. These results indicate that HPK1 is a novel functional activator of the JNK/SAPK signaling pathway.
Cultivation of cell–polymer tissue constructs in simulated microgravity (1995)

Tissue-engineered cartilage was cultivated under conditions of simulated microgravity using rotating bioreactors. Rotation randomized the effects of gravity on inoculated cells (chondrocytes) and permitted their attachment to three-dimensional (3D) synthetic, biodegradable polymer scaffolds that were freely suspended within the vessel. After 1 week of cultivation, the cells regenerated a cartilaginous extracellular matrix (ECM) consisting of glycosaminoglycan (GAG) and collagen types I and II. Tissue constructs grown in simulated microgravity had higher GAG contents and thinner outer capsules than control constructs grown in turbulent spinner flasks. Two fluid dynamic regimes of simulated microgravity were identified, depending on the vessel rotation speed: (i) a settling regime in which the constructs were maintained in a state of continuous free-fall close to a stationary point within the vessel and (ii) an orbiting regime in which the constructs orbited around the vessel spin axis. In the settling regime, the numerically calculated relative fluid-construct velocity was comparable to the experimentally measured construct settling velocity (2-3 cm/s). A simple mathematical model was used in conjunction with measured construct physical properties to determine the hydrodynamic drag force and to estimate the hydrodynamic stress at the construct surface (1.5 dyn/cm(2)). Rotating bioreactors thus provide a powerful research tool for cultivating tissue-engineered cartilage and studying 3D tissue morphogenesis under well-defined fluid dynamic conditions. (c) 1995 John Wiley & Sons, Inc.
Inhibition of GFAP synthesis by antisense RNA in astrocytes (1991)

Glial fibrillary acidic protein (GFAP) accumulation is a prominent feature of astrocytic gliosis. The inhibition or delay in GFAP synthesis might delay scar formation resulting from an insult such as spinal cord injury or central nervous system (CNS) demyelination. The delay in the formation of a physical barrier might allow the neurons and oligodendrocytes to reestablish a functional environment. We delivered antisense GFAP RNA complexed with Lipofectin (LF), a cationic liposome, into cerebral astrocytes in culture and tested the feasibility of inhibiting GFAP synthesis. Our results demonstrate that LF facilitated antisense RNA uptake into astrocytes. Astrocytes took up 3H-antisense GFAP RNA alone and reached an equilibrium of 7-8.8 eta g per mg protein after 2.5 hr. When complexed with LF, astrocytes could increase the uptake to 14 eta g per mg protein and the time for reaching this quantity was shortened to 10 min. This uptake level was further enhanced if experiments were carried out in HEPES buffered saline (HBS). All uptake studies were dose- and time-dependent. Dibutyryl cyclic AMP (dBcAMP) is known to induce an increase of GFAP content in cultured astrocytes. We studied the effect of LF/antisense GFAP RNA on the GFAP content in dBcAMP (0.25 mM)-treated astrocytes. Cultures of astrocytes treated with dBcAMP contained almost twice as much GFAP as untreated cultures after 2 days. Similar cultures treated with LF/antisense RNA in HBS did not show an increase but a 30-40% decrease in GFAP content 2 days after treatment.(ABSTRACT TRUNCATED AT 250 WORDS)
Expression of Survivin mRNA in Endometrial Carcinoma and its Significance (2006)

Objective To investigate the expression of Survivin genein endometrial carcinoma and its significance.Methods Survivin mRNA was examined by semi-quantitative PCR in specimens of 26 cases of endometrial carcinoma,17 cases of normal endometrium,3 cases of atypical hyperplasia and 3 cases of simple/complex hyperplasia.Results The expression of Survivin mRNA in malignant endometrial tissue was significantly higher than that in normal endometrial tissue(0.7660±0.0447 vs 0.4577±0.0345,P0.05).In the 26 cases of endometrial carcinoma,the expression of Survivin mRNA was higher in diseases in higher stage.However,the expression of Survivin mRNA was not related to the age,menopause,and myometrial invasion.Conclusion The transcription level of Survivin genes may play an important role in the carcinogenesis and development of endometrial carcinoma.
Production of pure and functional RNA for in vitro reconstitution experiments (2013)

Reconstitution of protein complexes has been a valuable tool to test molecular functions and to interpret in vivo observations. In recent years, a large number of RNA-protein complexes has been identified to regulate gene expression and to be important for a range of cellular functions. In contrast to protein complexes, in vitro analyses of RNA-protein complexes are hampered by the fact that recombinant expression and purification of RNA molecules is more difficult and less well established than for proteins. Here we review the current state of technology available for in vitro experiments with RNAs. We outline the possibilities to produce and purify large amounts of homogenous RNA and to perform the required quality controls. RNA-specific problems such as degradation, 5' and 3' end heterogeneity, co-existence of different folding states, and prerequisites for reconstituting RNAs with recombinantly expressed proteins are discussed. Additionally a number of techniques for the characterization of direct and indirect RNA-protein interactions are explained.