gebhart/patrepeval huggingface dataset:
Identification of Tethering Domains for Protein Kinase A Type Iα Regulatory Subunits on Sperm Fibrous Sheath Protein FSC1 (1998)

The fibrous sheath is a unique cytoskeletal structure in the sperm flagellum believed to modulate sperm motility. FSC1 is the major structural protein of the fibrous sheath. The yeast two-hybrid system was used to identify other proteins that contribute to the structure of the fibrous sheath or participate in sperm motility. When FSC1 was used as the bait to screen a mouse testis cDNA library, two clones were isolated encoding the type Ialpha regulatory subunit (RIalpha) of cAMP-dependent protein kinase. Deletion analysis using the yeast two-hybrid system and in vitro binding assays with glutathione S-transferase-FSC1 fusion proteins identified two RIalpha tethering domains on FSC1. A domain located at residues 219-232 (termed domain A) corresponds to the reported tethering domain for a type II regulatory subunit (RII) of cAMP-dependent protein kinase, indicating that this binding domain has dual specificity to RI and RII. Another RIalpha tethering site (termed domain B) at residues 335-344 shows specific binding of RIalpha and had no significant sequence homology with known RII tethering domains. However, helical wheel projection analysis indicates that domain B is likely to form an amphipathic helix, the secondary structure of RII tethering domains of protein kinase A anchoring proteins. This was supported by the finding that site-directed mutagenesis to disrupt the amphipathic helix eliminated RIalpha binding. This is apparently the first report of an RIalpha-specific protein kinase A anchoring protein tethering domain.
Imperfect Oriented Attachment: Dislocation Generation in Defect-Free Nanocrystals (1998)

Dislocations are common defects in solids, yet all crystals begin as dislocation-free nuclei. The mechanisms by which dislocations form during early growth are poorly understood. When nanocrystalline materials grow by oriented attachment at crystallographically specific surfaces and there is a small misorientation at the interface, dislocations result. Spiral growth at two or more closely spaced screw dislocations provides a mechanism for generating complex polytypic and polymorphic structures. These results are of fundamental importance to understanding crystal growth.
Mutated p53 in tumors, mutant p53 and p53-specific antibodies in the circulation in patients with gastric cancer. (2000)

The accumulation of mutated p53 in tumor cells results in the presence in the circulation of mutant p53 (p53m) and the production of p53-specific antibodies (p53Ab). We examined the relationships among these phenomena and analyzed their clinical implications in 62 patients with gastric cancer at various stages. Expression of p53 in tumors was studied by an immunohistochemical method and circulating p53m and p53Ab were quantitated with commercially available enzyme-linked immunosorbent assay kits. The detectable expression of p53 in tumors and circulating p53Ab was recognized in 28 (45.2%) and 7 (11.3%) of the 62 patients, respectively. The number of patients with higher levels of circulating p53m increased with the progression of the depth of cancer invasion. Patients with any positive findings for the three p53-related parameters had a poorer prognosis, and the difference was statistically significant in patients with p53Ab. When survival was analyzed in terms of the combination of the three p53-related parameters (detectable expression of p53 in tumor cells, high levels of p53m and p53Ab in the circulation), a significantly poorer prognosis was associated with an increase in the number of positive parameters. Analysis of p53 in tumor cells, together with analysis of circulating p53m and p53Ab, could improve the accuracy of prognosis in patients with gastric cancer.
Functional analysis of the Shigella flexneri IpaC invasin by insertional mutagenesis (1997)

The ability of Shigella to enter epithelial cells, to escape from the phagocytic vacuole, and to induce apoptosis in macrophages requires the IpaB, IpaC, and IpaD proteins. An extracellular complex containing IpaB and IpaC can promote the uptake of inert particles by epithelial cells. To determine whether the function of IpaC is to act as an extracellular chaperone for IpaB in the Ipa complex or as an effector of entry involved in a direct interaction with the cell surface, we have constructed eight IpaC recombinant proteins by inserting the coding sequence for a 12- to 14-amino-acid fragment into restriction sites scattered within the ipaC gene. We have investigated the ability of recombinant proteins to bind IpgC in the bacterial cytoplasm and IpaB in the extracellular medium and to complement an ipaC null mutant for entry into HeLa cells, lysis of erythrocytes, and escape from the phagocytic vacuole in infected macrophages. Most recombinant proteins were produced and secreted at a level similar to that of wild-type IpaC and did not exhibit altered susceptibility to proteolysis by trypsin, and all were able to bind IpgC and IpaB. Some recombinant proteins did not complement the ipaC mutant for entry into HeLa cells, lysis of erythrocytes, or escape from the phagocytic vacuole, which indicates that IpaC plays an active role in these processes and does not act solely as a chaperone for IpaB. In addition, some insertions which were located outside of the hydrophobic region of IpaC differentially affected the abilities of Shigella to enter epithelial cells and to lyse cell membranes.
Anti–Interleukin-9 Antibody Treatment Inhibits Airway Inflammation and Hyperreactivity in Mouse Asthma Model (2002)

Numerous in vitro and in vivo studies in both animals and patients with asthma have shown that interleukin (IL)-9 is an important inflammatory mediator in asthma. To examine the effects of IL-9 antagonism on airway inflammation, ovalbumin-sensitized BALB/c mice were intravenously given anti-IL-9 antibody or an isotype-matched control antibody 30 minutes before challenge with aerosolized ovalbumin. Airway response to methacholine was measured, and samples of bronchoalveolar lavage fluid (BALF) were obtained 24 hours after the last antigen challenge. Lung tissue was harvested and examined histopathologically. After ovalbumin challenge, there were significant increases in airway hyperreactivity, the numbers of inflammatory cells in lung, and IL-4, IL-5, and IL-13 production in BALF. Treatment with anti-IL-9 antibody significantly prevented airway hyperreactivity in response to methacholine inhalation. Blockade of IL-9 reduced the numbers of eosinophils (0.3 +/- 0.1 x 10(5) and 23.6 +/- 0.5 x 10(5)/ml, anti-IL-9 antibody/control immunoglobulin G) and lymphocytes (0.2 +/- 0.2 x 10(5) and 0.8 +/- 0.1 x 10(5)/ml) in BALF. Anti-IL-9 antibody treatment also reduced the concentrations of IL-4 (from 70.6 +/- 4.6 to 30.8 +/- 5.2 pg/ml), IL-5 (from 106.4 +/- 12 to 54.4 +/- 6.6 pg/ml), and IL-13 (from 44.2 +/- 7.6 to 30.1 +/- 5.5 pg/ml) in BALF. Macrophage-derived cytokine expression in the airways was also decreased by IL-9 blockade. Taken together, our findings emphasize the importance of IL-9 in the pathogenesis of asthma and suggest that blockade of IL-9 may be a new therapeutic strategy for bronchial asthma.
Regulation of p53 levels by the E1B 55-kilodalton protein and E4orf6 in adenovirus-infected cells (1997)

The adenovirus type 5 243R E1A protein induces p53-dependent apoptosis in the absence of the 19- and 55-kDa E1B polypeptides. This effect appears to result from an accumulation of p53 protein and is unrelated to expression of E1B products. We now report that in the presence of the E1B 55-kDa polypeptide, the 289R E1A protein does not induce such p53 accumulation and, in fact, is able to block that induced by E1A 243R. This inhibition also requires the 289R-dependent transactivation of E4orf6 expression. E4orf6 is known to form complexes with the E1B 55-kDa protein and to function both in the transport and stabilization of viral mRNA and in shutoff of host cell protein synthesis. We demonstrated that the block in p53 accumulation is not due to the generalized shutoff of host cell metabolism. Rather, it appears to result from a mechanism targeted specifically to p53, most likely involving a decrease in the stability of p53 protein. The E1B 55-kDa protein is known to interact with both E4orf6 and p53, and as demonstrated recently by others, we showed that E4orf6 also binds directly to p53. Thus, multiple interactions between all three proteins may regulate p53 stability, resulting in the maintenance of low levels of p53 following virus infection.
Total Synthesis of Aigialomycin D (2004)

[reaction: see text] The first total synthesis of resorcinylic macrolide aigialomycin D was described. The resorcinylic moiety was constructed by a highly efficient Diels-Alder reaction using a disiloxydiene and a 14-membered "ynolide" as the dienophile synthesized by ring-forming olefin metathesis.
Prospective, Randomized, Double-Blind Study Comparing Single-Agent Antibiotic Therapy, Ciprofloxacin, to Combination Antibiotic Therapy in Open Fracture Wounds (2000)

Single-agent antibiotic therapy with ciprofloxacin is effective in treatment of Type I and Type II open fracture wounds. However, on the basis of our results, we cannot recommend ciprofloxacin alone for Type III wounds. Possibly one can use fluoroquinolones in combination therapy, specifically as an alternate to an aminoglycoside.
Restoring Light Sensitivity in Blind Retinae Using a Photochromic AMPA Receptor Agonist (2015)

Retinal degenerative diseases can have many possible causes and are currently difficult to treat. As an alternative to therapies that require genetic manipulation or the implantation of electronic devices, photopharmacology has emerged as a viable approach to restore visual responses. Here, we present a new photopharmacological strategy that relies on a photoswitchable excitatory amino acid, ATA. This freely diffusible molecule selectively activates AMPA receptors in a light-dependent fashion. It primarily acts on amacrine and retinal ganglion cells, although a minor effect on bipolar cells has been observed. As such, it complements previous pharmacological approaches based on photochromic channel blockers and increases the potential of photopharmacology in vision restoration.
Modeling IT operations to derive provider-accepted management tools (2003)

In this paper a process-oriented approach to derive requirements on IT management tools is presented. The starting point is given by the processes that have to be carried out to run a distributed system. The better a management tool supports these processes the more useful it is from the viewpoint of the provider. Hence, the more accepted the tool is by the operators doing their work in the IT organization. The process model describing IT operations of a distributed networked system stems from an industrial project. The project goal was to introduce a process-oriented quality management system into a complex IT environment. One of the operational processes of the model, the process operation of changes is described in detail which demonstrates the method to derive demands on management tools from the process description. The result of this method is a collection of tools supporting request, commitment, performance and evaluation of an IT change. The integrated software architecture and the central software modules of our solution are outlined. The method described in this paper has been successfully applied to various fields of IT management.
Angiotensin II Type 1a Receptor Is Involved in the Occurrence of Reperfusion Arrhythmias (1998)

Ang II may be critically involved in the induction of ventricular arrhythmias but not in the determination of infarct size after IR.
Fast Quantum Nondemolition Readout by Parametric Modulation of Longitudinal Qubit-Oscillator Interaction (2015)

We show how to realize fast and high-fidelity quantum nondemolition qubit readout using longitudinal qubit-oscillator interaction. This is accomplished by modulating the longitudinal coupling at the cavity frequency. The qubit-oscillator interaction then acts as a qubit-state dependent drive on the cavity, a situation that is fundamentally different from the standard dispersive case. Single-mode squeezing can be exploited to exponentially increase the signal-to-noise ratio of this readout protocol. We present an implementation of this longitudinal parametric readout in circuit quantum electrodynamics and a possible multiqubit architecture.
Phosphoamino acid analysis (2001)

Phosphorylation of amino acid residues in proteins plays a major role in biological systems. Often, phosphorylation acts as a molecular switch controlling the protein activity in different pathways as in metabolism, signal transduction, cell division etc. Therefore, identification of phosphoamino acids in proteins is an important task in protein analysis. Since the introduction of high resolution two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) a separation of phosphorylated and dephosphorylated protein species is possible. The identification of phosphorylation sites from preparative 2-D gels need very sensitive mass spectrometry methods and a specific enrichment of the phosphoprotein or -peptide.
From RECIST to PERCIST: Evolving Considerations for PET Response Criteria in Solid Tumors (2009)

Anatomic imaging alone using standard WHO, RECIST, and RECIST 1.1 criteria have limitations, particularly in assessing the activity of newer cancer therapies that stabilize disease, whereas (18)F-FDG PET appears particularly valuable in such cases. The proposed PERCIST 1.0 criteria should serve as a starting point for use in clinical trials and in structured quantitative clinical reporting. Undoubtedly, subsequent revisions and enhancements will be required as validation studies are undertaken in varying diseases and treatments.
Effect of Topically Applied Epithelial Sodium Channel Inhibitors on Tear Production in Normal Mice and in Mice with Induced Aqueous Tear Deficiency (2012)

We conclude that the inhibition of ENaC provides long-lasting increases in ocular surface hydration and that ENaC blockers could provide an effective new therapy for chronic dry eye.
Milk: the new sports drink? A Review (2008)

There has been growing interest in the potential use of bovine milk as an exercise beverage, especially during recovery from resistance training and endurance sports. Based on the limited research, milk appears to be an effective post-resistance exercise beverage that results in favourable acute alterations in protein metabolism. Milk consumption acutely increases muscle protein synthesis, leading to an improved net muscle protein balance. Furthermore, when post-exercise milk consumption is combined with resistance training (12 weeks minimum), greater increases in muscle hypertrophy and lean mass have been observed. Although research with milk is limited, there is some evidence to suggest that milk may be an effective post-exercise beverage for endurance activities. Low-fat milk has been shown to be as effective, if not more effective, than commercially available sports drinks as a rehydration beverage. Milk represents a more nutrient dense beverage choice for individuals who partake in strength and endurance activities, compared to traditional sports drinks. Bovine low-fat fluid milk is a safe and effective post exercise beverage for most individuals, except for those who are lactose intolerant. Further research is warranted to better delineate the possible applications and efficacy of bovine milk in the field of sports nutrition.
Dystrophin Immunity in Duchenne's Muscular Dystrophy (2010)

We report on delivery of a functional dystrophin transgene to skeletal muscle in six patients with Duchenne's muscular dystrophy. Dystrophin-specific T cells were detected after treatment, providing evidence of transgene expression even when the functional protein was not visualized in skeletal muscle. Circulating dystrophin-specific T cells were unexpectedly detected in two patients before vector treatment. Revertant dystrophin fibers, which expressed functional, truncated dystrophin from the deleted endogenous gene after spontaneous in-frame splicing, contained epitopes targeted by the autoreactive T cells. The potential for T-cell immunity to self and nonself dystrophin epitopes should be considered in designing and monitoring experimental therapies for this disease. (Funded by the Muscular Dystrophy Association and others; ClinicalTrials.gov number, NCT00428935.).
Generating Long and Diverse Responses with Neural Conversation Models (2017)

Building general-purpose conversation agents is a very challenging task, but necessary on the road toward intelligent agents that can interact with humans in natural language. Neural conversation models -- purely data-driven systems trained end-to-end on dialogue corpora -- have shown great promise recently, yet they often produce short and generic responses. This work presents new training and decoding methods that improve the quality, coherence, and diversity of long responses generated using sequence-to-sequence models. Our approach adds self-attention to the decoder to maintain coherence in longer responses, and we propose a practical approach, called the glimpse-model, for scaling to large datasets. We introduce a stochastic beam-search algorithm with segment-by-segment reranking which lets us inject diversity earlier in the generation process. We trained on a combined data set of over 2.3B conversation messages mined from the web. In human evaluation studies, our method produces longer responses overall, with a higher proportion rated as acceptable and excellent as length increases, compared to baseline sequence-to-sequence models with explicit length-promotion. A back-off strategy produces better responses overall, in the full spectrum of lengths.
Iterated function systems and the global construction of fractals (1985)

Abstract Iterated function systems (i. f. ss) are introduced as a unified way of generating a broad class of fractals. These fractals are often attractors for i. f. ss and occur as the supports of probability measures associated with functional equations. The existence of certain ‘p-balanced’ measures for i. f. ss is established, and these measures are uniquely characterized for hyperbolic i. f. ss. The Hausdorff—Besicovitch dimension for some attrac­tors of hyperbolic i. f. ss is estimated with the aid of p-balanced measures. What appears to be the broadest framework for the exactly computable moment theory of p-balanced measures — that of linear i. f. ss and of probabilistic mixtures of iterated Riemann surfaces — is presented. This extensively generalizes earlier work on orthogonal polynomials on Julia sets. An example is given of fractal reconstruction with the use of linear i. f. ss and moment theory.
Superior Protection against Malaria and Melanoma Metastases by a C-glycoside Analogue of the Natural Killer T Cell Ligand α-Galactosylceramide (2003)

α-Galactosylceramide (α-GalCer) is a glycolipid that stimulates natural killer T cells to produce both T helper (Th) 1 and Th2 cytokines. This property enables α-GalCer to ameliorate a wide variety of infectious, neoplastic, and autoimmune diseases; however, its effectiveness against any one disease is limited by the opposing activities of the induced Th1 and Th2 cytokines. Here, we report that a synthetic C-glycoside analogue of α-GalCer, α-C-galactosylceramide (α-C-GalCer), acts as natural killer T cell ligand in vivo, and stimulates an enhanced Th1-type response in mice. In two disease models requiring Th1-type responses for control, namely malaria and melanoma metastases, α-C-GalCer exhibited a 1,000-fold more potent antimalaria activity and a 100-fold more potent antimetastatic activity than α-GalCer. Moreover, α-C-GalCer consistently stimulated prolonged production of the Th1 cytokines interferon-γ and interleukin (IL)-12, and decreased production of the Th2 cytokine IL-4 compared with α-GalCer. Finally, α-C-GalCer's enhanced therapeutic activity required the presence of IL-12, which was needed to stimulate natural killer cells for optimal interferon-γ production, but did not affect IL-4. Overall, our results suggest that α-C-GalCer may one day be an excellent therapeutic option for diseases resolved by Th1-type responses.
Molecular events in the processing of recombinant type 1 pre-pro-transforming growth factor beta to the mature polypeptide. (1988)

Recently, the simian type 1 transforming growth factor beta (TGF-beta 1) cDNA was expressed at high levels in Chinese hamster ovary (CHO) cells by dihydrofolate reductase-induced gene amplification (L.E. Gentry, N.R. Webb, G.J. Lim, A.M. Brunner, J.E. Ranchalis, D.R. Twardzik, M.N. Lioubin, H. Marquardt, and A.F. Purchio, Mol. Cell. Biol. 7:3418-3427, 1987). We have now purified and characterized the recombinant proteins released by these cells. Analyses of the precursor proteins by amino acid sequencing identified potentially important proteolytic processing sites. Signal peptide cleavage occurs at the Gly-29-Leu-30 peptide bond of pre-pro-TGF-beta 1, yielding pro-TGF-beta 1 (30 to 390). In addition, proteolytic processing of the precursor to yield mature TGF-beta 1 occurs at the dibasic cleavage site immediately preceding Ala-279, indicating that CHO cells possess the appropriate processing enzyme. Greater than 95% of the biological activity detected in the conditioned medium of the CHO transfectant was due to mature, properly processed growth factor. Highly purified recombinant TGF-beta 1 had the same specific biological activity as natural TGF-beta 1. The concentration of TGF-beta 1 required for half-maximal inhibition of Mv1Lu mink lung epithelial cell growth was approximately 1 to 2 pM. Purified precursor inhibited mink lung cell proliferation at 50 to 60 pM concentrations. The purified precursor preparation was shown to consist of pro-TGF-beta 1 (30 to 390), the pro region of the precursor (30 to 278), and mature TGF-beta 1 (279 to 390) interlinked by at least one disulfide bond with the pro portion of the precursor. These recombinant forms of TGF-beta1 should prove useful for further structural and functional studies.
Development of therapeutic proteins: advances and challenges (2015)

Therapeutic proteins have shown to be effective against a variety of diseases. Pharmaceutical companies are progressively focusing on research using proteins in search of novel effective therapeutics. The significant attention by researchers has resulted in considerable advances in the production and usage of therapeutic proteins in recent years. In the current study we focused on the understanding of therapeutic proteins and their impact on the human health care system. Advancements in the field of biotechnology have increased and facilitated the production of therapeutically significant proteins to combat various fatal diseases. Although protein-based therapeutics have taken center stage in drug discovery and development and enhanced safety for human beings, certain challenges remain, including safety and immunogenicity issues, protein stability, and degradation issues. We made an attempt to discuss all possible factors that are linked with the basis of therapeutic proteins and possible challenges that are currently being faced by scientists during the development of these therapeutic proteins.