gebhart/patrepeval huggingface dataset:
Structural Requirements for PAK Activation by Rac GTPases (1998)

The Rho family GTPases, Rac1 and Rac2, regulate a variety of cellular functions including cytoskeletal reorganization, the generation of reactive oxygen species, G1 cell cycle progression and, in concert with Ras, oncogenic transformation. Among the many putative protein targets identified for Rac (and/or Cdc42), the Ser/Thr kinase p21-activated kinase (PAK) is a prime candidate for mediating some of Rac's cellular effects. This report shows that Rac1 binds to and stimulates the kinase activity of PAK1 approximately 2- and 4-5-fold, respectively, better than Rac2. Mutational analysis was employed to determine the structural elements on Rac and PAK that are important for optimal binding and activation. The most notable difference between the highly homologous Rac isomers is the composition of their C-terminal polybasic domains. Mutation of these six basic residues in Rac1 to neutral amino acids dramatically decreased the ability of Rac1 to bind PAK1 and almost completely abolished its ability to stimulate PAK activity. Moreover, replacing the highly charged polybasic domain of Rac1 with the less charged domain of Rac2 (and vice versa) completely reversed the PAK binding/activation properties of the two Rac isomers. Thus, polybasic domain differences account for the disparate abilities of Rac1 and Rac2 to activate PAK. PAK proteins also contain a basic region, consisting of three contiguous lysine residues (Lys66-Lys67-Lys68), which lies outside of the previously identified Cdc42/Rac-binding domain. Mutation of these Lys residues to neutral residues decreased PAK binding to activated Rac1 and Rac2 (but not Cdc42) and greatly reduced PAK1 activation by Rac1, Rac2, and Cdc42 proteins in vivo. In contrast, mutation of lysines 66-68 to basic Arg residues did not decrease (and in some cases enhanced) the ability of Rac1, Rac2, and Cdc42 to bind and activate PAK1. Our studies suggest that the polybasic domain of Rac is a novel effector domain that may allow the two Rac isomers to activate different effector proteins. In addition, our results indicate that a basic region in PAK is required for PAK activation and that binding of Rac/Cdc42 to PAK is not sufficient for kinase activation.
Gly-Pro-Arg Confers Stability Similar to Gly-Pro-Hyp in the Collagen Triple-helix of Host-Guest Peptides (1997)

A set of host-guest peptides of the form Ac(Gly-Pro-Hyp)3-Gly-X-Y-(Gly-Pro-Hyp)4-Gly-Gly-NH2 has been designed to evaluate the propensity of different Gly-X-Y triplets for the triple-helix conformation (Shah, N. K., Ramshaw, J. A. M., Kirkpatrick, A., Shah, C., and Brodsky, B. (1996) Biochemistry 35, 10262-10268). All Gly-X-Y guest triplets led to a decrease in melting temperature from the host (Gly-Pro-Hyp)8 peptide except for Gly-Pro-Arg. In this Gly-Pro-Hyp-rich environment, Gly-Pro-Arg was found to be as stabilizing as Gly-Pro-Hyp. Decreased stability of host-guest peptides containing Gly-Pro-Lys, Gly-Pro-homo-Arg, and Gly-Arg-Hyp compared with Gly-Pro-Arg indicated a stabilization that is optimal for Arg and specific to the Y-position. Arg was found to have a similar stabilizing effect when residues other than Pro are in the X-position. Both Arg and Hyp stabilize the triple-helix preferentially in the Y-position in a stereospecific manner and occupy largely Y-positions in collagen. However, contiguous Gly-Pro-Hyp units are highly stable and promote triple-helix folding, whereas incorporation of multiple Gly-Pro-Arg triplets was destabilizing and folded slowly due to charge repulsion. In collagen, Gly-Pro-Arg may contribute maximally to local triple-helix stability while also having the potential for electrostatic interactions in fibril formation and binding.
Is There a Path Forward for mGlu2 Positive Allosteric Modulators for the Treatment of Schizophrenia? (2013)

Two recent Phase II results show opposing outcomes for the potential of activators of mGlu2 in the treatment of schizophrenia. The first outcome revealed that Eli Lilly's mGlu2/3 agonist, pomaglumetad methionil (LY2140023), failed to meet the primary efficacy end point. The second report showed the mGlu2 positive allosteric modulator (PAM) from Addex (ADX71149) in conjunction with Janssen Research & Development met the primary objectives of safety, tolerability and demonstrated an effect on negative symptoms in patients.
The Anti- Candida Vaccine Based on the Recombinant N-Terminal Domain of Als1p Is Broadly Active against Disseminated Candidiasis (2006)

We have previously shown that vaccination with a vaccine based on the recombinant N-terminal domain of Als1p (rAls1p-N) protected BALB/c mice against disseminated infection caused by a single strain of Candida albicans (A. S. Ibrahim, B. J. Spellberg, V. Avenissian, Y. Fu, S. G. Filler, and J. E. Edwards, Jr., Infect. Immun. 73:999-1005, 2005, and B. J. Spellberg, A. S. Ibrahim, V. Avenissian, S. G. Filler, C. Myers, Y. Fu, and J. E. Edwards, Jr., Infect. Immun. 73:6191-6193, 2005). Here we show that the rAls1p-N vaccine also improves survival of outbred mice from disseminated candidiasis and that it is active against multiple virulent strains of C. albicans and non-C. albicans spp.
Vascular endothelial growth factor. Expression in human vulvar neoplastic and nonneoplastic tissues. (1996)

To investigate the expression of vascular endothelial growth factor (VEGF) in human vulvar neoplastic and nonneoplastic tissues.Specimens were collected at the Vulvovaginal Clinic, Department of Obstetrics and Gynecology, University of Milan. Human vulvar neoplastic and nonneoplastic tissues were dissected and frozen immediately at -80 degrees C until RNA extraction. Five micrograms of total RNA from each sample was denatured and transferred to nitrocellulose and nylon membranes for dot blot hybridization with labeled [alpha-32P]dCTP cDNA probe for VEGF.Messenger RNA encoding VEGF was detected in all tissues studied. VEGF mRNA was highly expressed in vulvar epithelial neoplasia (VIN) associated with human papillomavirus infection and minimally expressed in invasive squamous cells carcinoma of the vulva. Nonneoplastic lesions, such as chronic inflammation, lichen sclerosus, lichen planus, squamous hyperplasia and squamous papilloma, were also assessed, and none had a significant difference in VEGF mRNA expression.The prominence of VEGF mRNA levels in particular cases of VIN demonstrated that VEGF may be involved in promoting a new vascular network as a basic condition for the progression or at least self-maintenance of those lesions.
The effect of NAG?thiazoline on morphology and surface hydrophobicity of Escherichia coli (2004)

The beta-hexosaminidase inhibitor and structural analog of the putative oxazolium reaction intermediate of lytic transglycosylases, N-acetylglucosamine thiazoline (NAG-thiazoline), was synthesized in 46% overall yield and tested as an inhibitor of Escherichia coli growth. NAG-thiazoline, at concentrations up to 1 mg/ml, was not found to affect the viability of E. coli DH5alpha. However, the compound did induce morphological changes to the cells. Growth of cells in the presence of NAG-thiazoline caused an apparent inhibition of the biosynthesis of the cylindrical regions of the cells such that they became much shorter in length. The surface of these shorter cells was found to be much less hydrophobic compared to untreated cells as determined by the bacterial adhesion to hydrocarbon (BATH) assay. In addition, the co-administration of NAG-thiazoline with 1.7 x MIC concentrations of ampicillin prevented cell lysis suggesting that the compound inhibited autolytic enzymes, in particular the lytic transglycosylases.
Coronavirus Replication Complex Formation Utilizes Components of Cellular Autophagy (2004)

The coronavirus mouse hepatitis virus (MHV) performs RNA replication on double membrane vesicles (DMVs) in the cytoplasm of the host cell. However, the mechanism by which these DMVs form has not been determined. Using genetic, biochemical, and cell imaging approaches, the role of autophagy in DMV formation and MHV replication was investigated. The results demonstrated that replication complexes co-localize with the autophagy proteins, microtubule-associated protein light-chain 3 and Apg12. MHV infection induces autophagy by a mechanism that is resistant to 3-methyladenine inhibition. MHV replication is impaired in autophagy knockout, APG5-/-, embryonic stem cell lines, but wild-type levels of MHV replication are restored by expression of Apg5 in the APG5-/-cells. In MHV-infected APG5-/-cells, DMVs were not detected; rather, the rough endoplasmic reticulum was dramatically swollen. The results of this study suggest that autophagy is required for formation of double membrane-bound MHV replication complexes and that DMV formation significantly enhances the efficiency of replication. Furthermore, the rough endoplasmic reticulum is implicated as the possible source of membranes for replication complexes.
Identification of a receptor for gamma melanotropin and other proopiomelanocortin peptides in the hypothalamus and limbic system. (1993)

Corticotropin (ACTH) and melanotropin (MSH) peptides (melanocortins) are produced not only in the pituitary but also in the brain, with highest concentrations in the arcuate nucleus of the hypothalamus and the commisural nucleus of the solitary tract. We have identified a receptor for MSH and ACTH peptides that is specifically expressed in regions of the hypothalamus and limbic system. This melanocortin receptor (MC3-R) is found in neurons of the arcuate nucleus known to express proopiomelanocortin (POMC) and in a subset of the nuclei to which these neurons send projections. The MC3-R is 43% identical to the MSH receptor present in melanocytes and is strongly coupled to adenylyl cyclase. Unlike the MSH or ACTH receptors, MC3-R is potently activated by gamma-MSH peptides, POMC products that were named for their amino acid homology with alpha- and beta-MSH, but lack melanotropic activity. The primary biological role of the gamma-MSH peptides is not yet understood. The location and properties of this receptor provide a pharmacological basis for the action of POMC peptides produced in the brain and possibly a specific physiological role for gamma-MSH.
Phytomedicinal Flora and their Folk claim of Visakha Patnam District Agency, Andhra Pradesh, India. (2014)

The phytomedicinal plants study was carried out in adjoining tribal areas of Visakha patnam District, Andhra Pradesh during the month of November - December 2011. The information related to medicinal species which are used to cure common ailments and diseases were collected by the local people of study area. A total of 100 plants belonging to 53 families are listed in this paper.
Common transplantation antigens on methylcholanthrene-induced murine sarcomas detected by three assays of tumor rejection. (1977)

Advances in sensing technology enable the emotional state of car drivers to be captured and interfaces to be built that respond to these emotions. To evaluate such emotion-aware interfaces, researchers need to evoke certain emotional states within participants. Emotion elicitation in driving studies poses a challenge as the driving task can interfere with the elicitation task. Induced emotions also lose intensity with time and through secondary tasks. This is why we have analyzed different emotion elicitation techniques for their suitability in automotive research and compared the most promising approaches in a user study. We recommend using autobiographical recollection to induce emotions in driving studies, and suggest a way to prolong emotional states with music playback. We discuss experiences from a a driving simulator study, including solutions for addressing potential privacy issues.
Implementation of flying, scaling and grabbing in virtual worlds (1992)

In a virtual world viewed with a head-mounted display, the user may wish to perform certain actions under the control of a manual input device. The most important of these actions are flying through the world, scaling the world, and grabbing objects. This paper shows how these actions can be precisely specified with Frame-to-frame invariants, and how the code to implement the actions can bc dcrivcd from the invariants by algebraic manipulation.
Phase I study of sorafenib in Japanese patients with hepatocellular carcinoma (2007)

Sorafenib is an orally active multikinase inhibitor that targets serine and threonine, and tyrosine kinases that are involved in tumor-cell signal transduction and tumor angiogenesis. This phase I trial was conducted to evaluate the pharmacokinetics (PK), safety, and preliminary efficacy of sorafenib in Japanese patients with hepatocellular carcinoma (HCC) with underlying liver dysfunction. Patients with unresectable HCC, Child-Pugh status A or B, and adequate organ functions were treated. A single dose of sorafenib was administered, followed by a 7-day wash-out period, after which patients received either sorafenib 200 mg (cohort 1) or 400 mg (cohort 2) twice daily. The PK were investigated after a single dose and during steady state. The efficacy was evaluated using the Response Evaluation Criteria in Solid Tumors. A total of 27 patients were evaluated for PK, safety, and efficacy. Although both area under the concentration-time curve for 0-12 h and maximal concentration at steady state were slightly lower in Child-Pugh B patients than in Child-Pugh A patients, the difference was not considered to be clinically relevant. Common adverse drug events included elevated lipase, amylase, rash or desquamation, diarrhea, and hand-foot skin reaction. A dose-limiting toxicity of hand-foot skin reaction was observed in one patient (cohort 2). Among the 24 patients evaluable for tumor response, one patient (4%) achieved a partial response, 20 (83%) had stable disease, and three (13%) had progressive disease. Sorafenib demonstrated a favorable tolerability and safety profile in Japanese HCC patients. Moreover, promising preliminary antitumor activity has been observed. Finally, there were no clinically relevant differences in PK between Child-Pugh A and B patients.
Differences in Antibodies to the Surface Components of Mumps Virus after Immunization with Formalin-Inactivated and Live Virus Vaccines (1978)

Military recruits with or without antibodies to mumps virus were immunized with live or formalin-inactivated mumps virus vaccines. Antibodies to the two major surface components of the virus, the hemagglutinin and the hemolysin, were identified separately. Immunization with the live vaccine did not change the humoral immunity in individuals with detectable antibodies. In seronegative recruits immunization with the live vaccine induced an antibody response against both the hemagglutinin and the hemolysin corresponding to the quality of the immune response after natural infection. In contrast, the formalin-inactivated vaccine only induced an antibody response against the hemagglutinin. This effect was found after immunization of both seronegative and seropositive individuals. The latter displayed a selective boosting of titers of hemagglutination-inhibiting antibody. These findings may have relevance for the interpretation of the short-lived immunity after the use of formalin-inactivated mumps vaccine without repeated boosting.
Controlled release, biodegradable cytokine depots: a new approach in cancer vaccine design. (1993)

Experimental studies using murine tumor models have demonstrated that potent systemic immunity can be generated using tumor vaccines engineered by gene transfer to secrete certain cytokines. The underlying physiological principle behind these strategies involves the sustained release of high doses of cytokine at the site of the tumor. In some cases, this paracrine approach appears to enhance tumor antigen presentation and avoids systemic cytokine toxicity. The widespread clinical use of autologous cytokine gene transduced tumor vaccines may be limited by the technical difficulty and labor intensity of individualized gene transfer. We have therefore explored an alternate approach to generating sustained release of cytokines local to the tumor cells. High doses of granulocyte-macrophage colony-stimulating factor encapsulated in cell-sized gelatin-chondroitin sulfate microspheres were mixed with irradiated tumor cells prior to s.c. injection. This vaccination scheme resulted in systemic anti-tumor immune responses comparable to granulocyte-macrophage colony-stimulating factor gene transduced tumor vaccines.
Placental and/or Umbilical Cord Blood: An Alternative Source of Hematopoietic Stem Cells for Transplantation (1997)

HLA-MATCHED RELATED allogeneic stem cell transplantation has been successfully used as the treatment of choice in selected high-risk or recurrent hematologic malignancies, marrow failure syndromes, severe congenital immunodeficiency states, and selected metabolic disorders.[1][1] Recently, the use
HEC, a Novel Nuclear Protein Rich in Leucine Heptad Repeats Specifically Involved in Mitosis (1997)

The protein encoded by the human gene HEC (highly expressed in cancer) contains 642 amino acids and a long series of leucine heptad repeats at its C-terminal region. HEC protein is expressed most abundantly in the S and M phases of rapidly dividing cells but not in terminal differentiated cells. It localizes to the nuclei of interphase cells, and a portion distributes to centromeres during M phase. Inactivation of HEC by microinjection of specific monoclonal antibodies into cells during interphase severely disturbs the subsequent mitoses. Disordered sister chromatid alignment and separation, as well as the formation of nonviable cells with multiple, fragmented micronuclei, are common features observed. These results suggest that the HEC protein may play an important role in chromosome segregation during M phase.
In vivo post‐translational modifications of recombinant mussel adhesive protein in insect cells (2011)

Mussel adhesive proteins (MAPs) have been suggested as promising bioadhesives for diverse application fields, including medical uses. Previously, we successfully constructed and produced a new type of functional recombinant MAP, fp-151, in a prokaryotic Escherichia coli expression system. Even though the E. coli-derived MAP showed several excellent features, such as high production yield and efficient purification, in vitro enzymatic modification is required to convert tyrosine residues to l-3,4-dihydroxyphenyl alanine (dopa) molecules for its adhesive ability, due to the intrinsic inability of E. coli to undergo post-translational modification. In this work, we produced a soluble recombinant MAP in insect Sf9 cells, which are widely used as an effective and convenient eukaryotic expression system for eukaryotic foreign proteins. Importantly, we found that insect-derived MAP contained converted dopa residues by in vivo post-translational modification. In addition, insect-derived MAP also had other post-translational modifications including phosphorylation of serine and hydroxylation of proline that originally occurred in some natural MAPs. To our knowledge, this is the first report on in vivo post-translational modifications of MAP containing dopa and other modified amino acid residues.
Theory of Pseudorandomness (2010)

Pseudorandomness is the theory of eciently generating objects that \look random despite being constructed with little or no randomness. One of the achievements of this research area has been the realization that a number of fundamental and widely studied \pseudorandom objects are all almost equivalent when viewed appropriately. These objects include pseudorandom generators, expander graphs, list-decodable error- correcting codes, averaging samplers, and hardness ampliers. In this survey, we describe the connections between all of these objects, showing how they can all be cast within a single \list-decoding framework that brings out both their similarities and dierences.
Nanostructured electroactive polymeric composites for energy storage and separation applications (2018)

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2018
Engineering the thermostability of Bacillus licheniformis alpha-amylase (2002)

Bacillus licheniformis a-amylase (BLA) is a highly thermostable enzyme which is widely used in biotechnological processes. Although it is produced by a non-thermophilic bacterium, it remains active for several hours at temperatures over 90degreesC under conditions of industrial starch hydrolysis. It is also far more thermostable than the alpha-amylases from B. stearothermophilus and B. amyloliquefaciens despite the strong sequence similarities between these three proteins. BLA provides therefore an interesting model for protein engineers investigating enzyme thermostability and thermostabilization. Over the last decade, we have performed an extensive mutational and structural analysis on BLA in order to elucidate the origin of its unusual thermal properties and, if possible, increase its thermostability even further. Before the three-dimensional structure was known, we had used "blind" mutagenesis and identified two critical positions where amino-acid substitutions could either increase or decrease significantly the rate of irreversible thermoinactivation. Once a detailed X- ray structure of BLA was solved, structure-based mutagenesis was used to probe the role of residues involved in salt- bridges, calcium-binding or potential deamidation processes. Our results revealed the key role of domain B and its interface with domain A in determining the overall thermostability of BLA. Most of the mutations we introduced in this region modify the stability in one way or another by influencing the network of electrostatic interactions entrapping a Ca-Na-Ca metal triad at the domain A/B interface. In the course of this mutational study we have constructed over 500 BLA variants bearing single or multiple mutations, among which many were found to be either highly detrimental or slightly beneficial to the stability. The cumulative effect of the mutations enabled us to modulate the enzyme stability over a 50degreesC temperature range without perturbing significantly the amylolytic function. Although a full understanding of the origin of BLA natural thermoresistance has not yet been reached, our study demonstrated that it is not optimized and that it can be increased or decreased artificially by several means.
Copper-catalyzed decarboxylative cross-coupling of alkynyl carboxylic acids with aryl halides (2010)

The copper-catalyzed decarboxylative reactions of alkynyl carboxylic acids with aryl halides were performed under relatively mild reaction conditions. Benzofurans could be further prepared smoothly by a one-pot domino protocol on the basis of decarboxylative cross-coupling of 2-iodophenol.
Cell-Based Therapeutics from an Economic Perspective: Primed for a Commercial Success or a Research Sinkhole? (2008)

Despite widespread hype and significant investment through the late 1980s and 1990s, cell-based therapeutics have largely failed from both a clinical and financial perspective. While the early pioneers were able to create clinically efficacious products, small margins coupled with small initial indications made it impossible to produce a reasonable return on the huge initial investments that had been made to support widespread research activities. Even as US FDA clearance opened up larger markets, investor interest waned, and the crown jewels of cell-based therapeutics went bankrupt or were rescued by corporate bailout. Despite the hard lessons learned from these pioneering companies, many of today's regenerative medicine companies are supporting nearly identical strategies. It remains to be seen whether or not our proposed tenets for investment and commercialization strategy yield an economic success or whether the original model can produce a return on investment sufficient to justify the large up-front investments. Irrespective of which approach yields a success, it is critically important that more of the second-generation products establish profitability if the field is to enjoy continued investment from both public and private sectors.