gebhart/patrepeval huggingface dataset:
Selective Inhibition of NF-κB Activation by a Peptide That Blocks the Interaction of NEMO with the IκB Kinase Complex (2000)

Activation of the transcription factor nuclear factor (NF)-kappaB by proinflammatory stimuli leads to increased expression of genes involved in inflammation. Activation of NF-kappaB requires the activity of an inhibitor of kappaB (IkappaB)-kinase (IKK) complex containing two kinases (IKKalpha and IKKbeta) and the regulatory protein NEMO (NF-kappaB essential modifier). An amino-terminal alpha-helical region of NEMO associated with a carboxyl-terminal segment of IKKalpha and IKKbeta that we term the NEMO-binding domain (NBD). A cell-permeable NBD peptide blocked association of NEMO with the IKK complex and inhibited cytokine-induced NF-kappaB activation and NF-kappaB-dependent gene expression. The peptide also ameliorated inflammatory responses in two experimental mouse models of acute inflammation. The NBD provides a target for the development of drugs that would block proinflammatory activation of the IKK complex without inhibiting basal NF-kappaB activity.
Anastomotic Healing in a Small Bowel Transplantation Model in the Rat (2003)

Anastomotic healing is impaired after intestinal surgery because of ischemia and reperfusion injury (IRI), which can result in intestinal leaks leading to increased mortality. The objective of this study was to determine the effects of transplant IRI and immune mechanisms on intestinal graft anastomotic healing. Orthotopic intestinal transplantations (OIT) were performed in rats. The experimental design consisted of six groups A-F (n=5/group): A, allogeneic OIT treated with tacrolimus (1 mg/kg/day); B, syngeneic OIT treated with tacrolimus; C, syngeneic OIT; D, allogeneic OIT; E, proximal and distal anastomoses performed in nontransplanted animals; F, same as in group E but treated with tacrolimus. Anastomotic bursting pressure (ABP), hydroxyproline content (HPC), and mucosal inflammatory infiltrate (MII) were determined at the anastomotic sites (proximal and distal) and compared between groups. ABP was significantly (p<0.001) reduced in OIT groups A, B, C, and D compared to control groups E and F at both the proximal and distal anastomotic sites. HPC was approximately 1 microg/mg of tissue in groups A, B, C, and D, and approximately 5 microg/mg of tissue in groups E and F. This demonstrates a significant (p<0.001) reduction in HPC after OIT. MII was significantly (p<0.001) increased in OIT groups when compared to nontransplanted control groups. MII was also significantly (p<0.05) increased in allogeneic OIT groups A and D compared to syngeneic OIT groups B and C. Generally, ABP and HPC were inversely proportional to MII in both nontransplanted control and OIT groups. Reduced anastomotic strength was demonstrated in both syngeneic and allogeneic OIT anastomotic sites irrespective of immunosuppressive therapy, and is probably related to IRI.
Causal Entropic Forces (2013)

Recent advances in fields ranging from cosmology to computer science have hinted at a possible deep connection between intelligence and entropy maximization, but no formal physical relationship between them has yet been established. Here, we explicitly propose a first step toward such a relationship in the form of a causal generalization of entropic forces that we find can cause two defining behaviors of the human “cognitive niche”—tool use and social cooperation—to spontaneously emerge in simple physical systems. Our results suggest a potentially general thermodynamic model of adaptive behavior as a nonequilibrium process in open systems.
Optimal insulin infusion resulting from a mathematical model of blood glucose dynamics (1989)

Mathematical optimization techniques are applied to a simplified mathematical model of blood glucose dynamics to derive insulin infusion programs for the control of blood glucose levels in diabetic individuals. Two particular cases are discussed. First, the insulin infusion program which results in an initially high blood glucose level being reduced to acceptable levels. Second, the control of blood glucose levels following a meal, prior to which blood glucose and net blood-glycemic hormone were at their fasting levels.
KIT and Platelet-Derived Growth Factor Receptor Alpha Tyrosine Kinase Gene Mutations and KIT Amplifications in Human Solid Tumors (2004)

Despite frequent KIT protein expression in some tumor types, KIT and PDGFRA gene mutations are uncommon in most human cancers. Cancer KIT expression is frequently associated with multiple copies of the wild-type KIT gene.
Identification of the second major allergen of Japanese cedar pollen (1990)

We isolated and characterized the second major allergen (Cry j II) from Japanese cedar pollen. We found that most patients with this pollinosis had IgE antibody to this protein in addition to IgE antibody to Cry j I; however, some sera reacted only with Cry j I or Cry j II. IgE-ELISA inhibition studies revealed that Cry j I and Cry j II had no cross-allergenicity. Cry j II did not react with anti-Cry j I monoclonal antibodies. In SDS-PAGE under a non-reducing condition, Cry j II showed a band at the 37 kDa position, compared with the 45-50 kDa bands of Cry j I. N-terminal amino acid sequence of Cry j II was completely different from that of Cry j I.
Dynamo (2007)

Reliability at massive scale is one of the biggest challenges we face at Amazon.com, one of the largest e-commerce operations in the world; even the slightest outage has significant financial consequences and impacts customer trust. The Amazon.com platform, which provides services for many web sites worldwide, is implemented on top of an infrastructure of tens of thousands of servers and network components located in many datacenters around the world. At this scale, small and large components fail continuously and the way persistent state is managed in the face of these failures drives the reliability and scalability of the software systems. This paper presents the design and implementation of Dynamo, a highly available key-value storage system that some of Amazon's core services use to provide an "always-on" experience. To achieve this level of availability, Dynamo sacrifices consistency under certain failure scenarios. It makes extensive use of object versioning and application-assisted conflict resolution in a manner that provides a novel interface for developers to use.
Identification of a Novel Transmembrane Semaphorin Expressed on Lymphocytes (1996)

Semaphorin (also known as collapsin) members are thought to be involved in axon guidance during neural network formation. Here, we report the isolation of a novel member, mouse semaphorin G (M-sema G), which encodes a semaphorin domain followed by a single putative immunoglobulin-like domain, a transmembrane domain, and a cytoplasmic domain. M-sema G is most closely related to M-sema F, which we previously reported, and semB and semC. These four members appear to constitute a transmembrane type subfamily in mouse semaphorins. In contrast to the predominant expression of M-sema F mRNAs in the nervous tissues, M-sema G mRNAs are strongly expressed in lymphoid tissues, especially in the thymus, as well as in the nervous tissues. The mRNAs are also detected in various cell lines from hematopoietic cells. By generating specific antibodies, we confirmed the strong expression of M-Sema G proteins on the surface of lymphocytes. These results provide the first evidence that semaphorin is expressed on lymphocytes and suggest that semaphorins may play an important role in the immune system, as well as in the nervous system.
Effect of a Commercial Competitive Exclusion Culture on Reduction of Colonization of an Antibiotic-Resistant Pathogenic Escherichia coli in Day-Old Broiler Chickens (2002)

One-day-of-age broiler chickens were administered a commercial competitive exclusion (CE) product and then challenged by three different methods with an Escherichia coli O78:K80 that was pathogenic for poultry and resistant to six antibiotics. Three challenge methods were used on 2-day-old broilers: direct challenge, precolonized seeder, and instant seeder. Direct challenge was accomplished by administering the challenge E. coli per os. The precolonized seeder challenge had two chicks that had received the challenge E. coli 24 hr previously, whereas the instant seeder challenge had two chicks given the challenge E. coli per os with immediate placement with the experimental birds. One oral dose of the commercial CE product significantly reduced the colonization of the small intestine, large intestine, and ceca by the highly antimicrobial resistant poultry pathogenic E. coli O78:K80 at 7 and 14 days postchallenge by all three challenge methods. The overall mean reductions in colonization were 3.0 log10 for the large intestine, 3.0 log10 for the small intestine, and 4.0 log10 for the cecum. The most severe challenge method, on the basis of the least amount of reduction of colonization of the challenge E. coli by the CE, was by the direct oral gavage at 2 days of age.
LONG-TERM EVALUATION OF REGENERATION ALONG CANINE PERONEAL NERVE USING A POLYGLYCOLIC ACID (PGA) — COLLAGEN NERVE CONDUITS FILLED WITH COLAGEN FIBERS (2003)

Purpose: We have previously reported successful functional peroneal nerve regeneration in dogs through use of a polyglycolic acid (PGA)-collagen tube filled with collagen fibers at 12 months. In the present investigation, nerve regeneration was examined after 4–5 years implantations. Methods: Nerve conduits consisting of a PGA-collagen tube filled with collagen fibers were implanted into an 80-mm gap of the left peroneal nerve of 8 beagle dogs. 4–5 years after implantation, nerve regeneration was evaluated electrophysiologically and histologically, and compared to those after 12 months operation in our previous reports. Results: Partial recovery of motor and sensory systems was demonstrated with restored compound muscle action potentials and somatosensory evoked potential records after 4–5 years implantations. Amplitudes in these records were higher than those at 12 months. Histologically, the mid-portion of the regenerated segments and the non-resected portions of the nerve distal to the conduit consisted of numerous myelinated and unmyelinated nerve fibers at 4–5 years implantation. The regenerated nerve fibers of the latter portion were much more matured in diameter and percentages of neural tissue than those at 12 months operation. Conclusions: Further nerve regenerations were demonstrated at long term periods compared to 12 months implantation. Long-term observation is essential for the evaluation of nerve regeneration after implantation.
Dynamic adaptive streaming over HTTP (2012)

In this tutorial we present dynamic adaptive streaming over HTTP ranging from content creation to consumption. It particular, it provides an overview of the recently ratified MPEG-DASH standard, how to create content to be delivered using DASH, its consumption, and the evaluation thereof with respect to competing industry solutions. The tutorial can be roughly clustered into three parts. In part I we will provide an introduction to DASH, part II covers content creation, delivery, and consumption, and, finally, part III deals with the evaluation of existing (open source) MPEG-DASH implementations compared to state-of-art deployed industry solutions.
Clinical wear of 63 ultrahigh molecular weight polyethylene acetabular components: Effect of starting resin and forming method (1999)

This study compares the clinical wear rates and implant characteristics of 63 surgically retrieved acetabular components. All components were made by the same manufacturer, implanted by the same surgeon, in articulation against the same type of femoral component, and revised for the same reason; 19 were made from directly compression molded, calcium stearate free, ultrahigh molecular weight polyethylene (UHMWPE) and 44 were made from machined, ram extruded, calcium stearate containing UHMWPE. There were significant differences in wear, duration, and wear rate between the molded (type I) and machined (type II and III) components. Most importantly, the wear rates of type I (molded) components were significantly (p < 0.0001) lower than the wear rates of type II, type III, and type II and III components as a group (all machined). The machined components had wear rates 2.3 times greater than the molded components. The wear rates between the two different groups of machined components (type II and III) were not significantly different. The scanning electron microscope observations did not reveal any major differences in wear mechanisms between the three types of components, although the machined components did show more evidence of brittleness. The molded components were better consolidated (or had less fusion defects) than the ram extruded components.
Programming the Assembly of Two- and Three-Dimensional Architectures with DNA and Nanoscale Inorganic Building Blocks, (2000)

The use of biochemical molecular recognition principles for the assembly of nanoscale inorganic building blocks into macroscopic functional materials constitutes a new frontier in science. This article details efforts pertaining to the use of sequence-specific DNA hybridization events and novel inorganic surface coordination chemistry to control the formation of both two- and three-dimensional functional architectures.
GENETICS OF POLIOVIRUS (1993)

Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A ...Read More
Tyrosinase as a multifunctional reporter gene for Photoacoustic/MRI/PET triple modality molecular imaging (2013)

Development of reporter genes for multimodality molecular imaging is highly important. In contrast to the conventional strategies which have focused on fusing several reporter genes together to serve as multimodal reporters, human tyrosinase (TYR)--the key enzyme in melanin production--was evaluated in this study as a stand-alone reporter gene for in vitro and in vivo photoacoustic imaging (PAI), magnetic resonance imaging (MRI) and positron emission tomography (PET). Human breast cancer cells MCF-7 transfected with a plasmid that encodes TYR (named as MCF-7-TYR) and non-transfected MCF-7 cells were used as positive and negative controls, respectively. Melanin targeted N-(2-(diethylamino)ethyl)-18F-5-fluoropicolinamide was used as a PET reporter probe. In vivo PAI/MRI/PET imaging studies showed that MCF-7-TYR tumors achieved significant higher signals and tumor-to-background contrasts than those of MCF-7 tumor. Our study demonstrates that TYR gene can be utilized as a multifunctional reporter gene for PAI/MRI/PET both in vitro and in vivo.
Signaling in the elicitation process is mediated through the octadecanoid pathway leading to jasmonic acid. (1993)

Fungal cell walls and fragments thereof (elicitors) induce the formation of low and high molecular weight defense compounds in plant cell suspension cultures. This induced synthesis requires a signal molecule transmitting the message between the elicitor plant cell wall receptor and gene activation. We demonstrate in this study that cis-jasmonic acid is rapidly synthesized in plant cell cultures of diverse taxonomic origin (gymnosperms and mono- and dicotyledonous plants) after challenge with a fungal elicitor preparation. The rapid decline of cis-jasmonic acid in some of these tissues is attributed to rapid metabolism of this pentacyclic acid. The induction of alkaloids by several different molecules provoking the elicitation process is strictly correlated with the synthesis of jasmonates. Elicitation leads to a rapid release of alpha-linolenic acid from the lipid pool of the plant cell. alpha-Linolenic acid and 12-oxophytodienoic acid, the formation of which is also induced, are known to be distant precursors of jasmonic acid. We assume cis-jasmonic acid and its precursors to be the signaling molecules in the elicitation process.
Subtractive immunization techniques for the production of monoclonal antibodies to rare antigens. (1992)

Traditional techniques for the production of monoclonal antibodies usually result in generation of monoclonal antibodies to immunodominant molecules. To enhance the production of monoclonal antibodies to rare or less immunodominant antigens, subtractive immunization techniques have been employed. This study compared the ability of several subtractive immunization techniques to suppress the immune system to a given antigen. Neonatal tolerization, chemical immunosuppression with cyclophosphamide, a combination of the two and various permutations of these techniques were compared. The results from this study indicated that chemical immunosuppression with cyclophosphamide was the most effective subtractive immunization technique and that the cyclophosphamide regime employed was a critical determinant in the success of chemical immunosuppression.
Molecular Cloning Reveals that the p160 Myb-Binding Protein Is a Novel, Predominantly Nucleolar Protein Which May Play a Role in Transactivation by Myb (1998)

We have previously detected two related murine nuclear proteins, p160 and p67, that can bind to the leucine zipper motif within the negative regulatory domain of the Myb transcription factor. We now describe the molecular cloning of cDNA corresponding to murine p160. The P160 gene is located on mouse chromosome 11, and related sequences are found on chromosomes 1 and 12. The predicted p160 protein is novel, and in agreement with previous studies, we find that the corresponding 4.5-kb mRNA is ubiquitously expressed. We showed that p67 is an N-terminal fragment of p160 which is generated by proteolytic cleavage in certain cell types. The protein encoded by the cloned p160 cDNA and an engineered protein (p67*) comprising the amino-terminal region of p160 exhibit binding specificities for the Myb and Jun leucine zipper regions identical to those of endogenous p160 and p67, respectively. This implies that the Myb-binding site of p160 lies within the N-terminal 580 residues and that the Jun-binding site is C-terminal to this position. Moreover, we show that p67* but not p160 can inhibit transactivation by Myb. Unexpectedly, immunofluorescence studies show that p160 is localized predominantly in the nucleolus. The implications of these results for possible functions of p160 are discussed.
On the calculation of fractal features from images (1993)

Fractal geometry is becoming increasingly more important in the study of image characteristics. There are numerous methods available to estimate parameters from images of fractal surfaces. A very general technique to calculate numerous fractal features involves the estimation of the mass density function by box counting. The authors analyze the box-counting method, establish a lower bound for the box size, and indicate how algorithms can be improved to give better estimates of fractal features of images. This provides a theoretical basis for a heuristic approach used by C.A. Pickover and A.L. Khorasani (1986).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Luminescence of Copper-Activated Orthophosphates of the Type ABPO[sub 4] (A = Ca, Sr, or Ba and B = Li, Na, or K) (1962)

Activation of orthophosphates of the type with copper gives an efficient phosphor in some cases. The brightest phosphors found are and , with an emission peak (with 2537Aå excitation) at 4150 and 4600Aå, respectively. The properties of orthophosphates of the type with two kinds of alkali earth or alkali metal ions, respectively, were also studied. X‐ray diagrams of the compounds investigated are given.
Control Theoretic Models of Pointing (2017)

This article presents an empirical comparison of four models from manual control theory on their ability to model targeting behaviour by human users using a mouse: McRuer’s Crossover, Costello’s Surge, second-order lag (2OL), and the Bang-bang model. Such dynamic models are generative, estimating not only movement time, but also pointer position, velocity, and acceleration on a moment-to-moment basis. We describe an experimental framework for acquiring pointing actions and automatically fitting the parameters of mathematical models to the empirical data. We present the use of time-series, phase space, and Hooke plot visualisations of the experimental data, to gain insight into human pointing dynamics. We find that the identified control models can generate a range of dynamic behaviours that captures aspects of human pointing behaviour to varying degrees. Conditions with a low index of difficulty (ID) showed poorer fit because their unconstrained nature leads naturally to more behavioural variability. We report on characteristics of human surge behaviour (the initial, ballistic sub-movement) in pointing, as well as differences in a number of controller performance measures, including overshoot, settling time, peak time, and rise time . We describe trade-offs among the models. We conclude that control theory offers a promising complement to Fitts’ law based approaches in HCI, with models providing representations and predictions of human pointing dynamics, which can improve our understanding of pointing and inform design.
Genetic Interactions Among Late-Flowering Mutants of Arabidopsis (1998)

Flowering time in Arabidopsis is controlled by a large number of genes, identified by induced mutations. Forty-two double mutants involving 10 of these loci were obtained and analyzed for their flowering behavior under long-day conditions, with and without vernalization, and under short-day conditions. The genetic interactions between the various mutants proved to be complex, although a major epistatic group (called group A) could be identified corresponding to the mutants, which are relatively insensitive to vernalization and daylength. In contrast, the genetic behavior of the mutants much more responsive to these environmental factors (group B) is more complex. The vernalization responsiveness of the group B mutants did not compensate for the lateness of the group A mutants. This indicated that these genes do not control vernalization sensitivity as such, but provide a factor that becomes limiting in short days. The classification of these mutants in different physiological groups is discussed in relation to the detected genetic interactions, and based on these interactions a more detailed model of their role in flowering initiation is proposed.
Targeted Cargo Delivery in Senescent Cells Using Capped Mesoporous Silica Nanoparticles (2012)

Learning to let go with age: Intracellular controlled release of molecules within senescent cells was achieved using mesoporous silica nanoparticles (MSNs) capped with a galacto-oligosaccharide (GOS) to contain the cargo molecules (magenta spheres; see scheme). The GOS is a substrate of the senescent biomarker, senescence-associated β-galactosidase (SA-β-gal), and releases the cargo upon entry into SA-β-gal expressing cells.