gebhart/patrepeval huggingface dataset:
Compile-Time Estimation of Communication Costs in Multicomputers (1991)

An important problem facing numerous research projects on parallelizing compilers for distributed memory machines is that of automatically determining a suitable data partitioning scheme for a pro gram.Any strategy for automatic data partitioning needs a mechanism for estimating the performance of a program under a given partitioning scheme, the most crucial part of which involves determining the communication costs incurred by the program.In this paper, we decribe a methodology for esti mating the communication costs at compile-time as functions of the numbers of processors over which various arrays are distributed.W e also describe a strategy for making program transformations that expose opportunities for combining of messages, leading to considerable savings in the communication costs.For certain loops with constant dependences, the compiler can detect the possibility of pipelining, and thus estimate communication costs more accurately than it could otherwise.These results are of great significance to any parallelization system supporting numeric applications on multicomputers.In particular, they lay down a framework for effective synthesis of communication on multicomputers from sequential program references.
Alfalfa yield response to inoculation with recombinant strains of Rhizobium meliloti with an extra copy of dctABD and/or modified nifA expression (1994)

The construction of rhizobial strains which increase plant biomass under controlled conditions has been previously reported. However, there is no evidence that these newly constructed strains increase legume yield under agricultural conditions. This work tested the hypothesis that carefully manipulating expression of additional copies of nifA and dctABD in strains of Rhizobium meliloti would increase alfalfa yield in the field. The rationale for this hypothesis is based on the positive regulatory role that nifA plays in the expression of the nif regulon and the fact that a supply of dicarboxylic acids from the plant is required as a carbon and energy source for nitrogen fixation by the Rhizobium bacteroids in the nodule. These recombinant strains, as well as the wild-type strains from which they were derived, are ideal tools to examine the effects of modifying or increasing the expression of these genes on alfalfa biomass. The experimental design comprised seven recombinant strains, two wild-type strains, and an uninoculated control. Each treatment was replicated eight times and was conducted at four field sites in Wisconsin. Recombinant strain RMBPC-2, which has an additional copy of both nifA and dctABD, increased alfalfa biomass by 12.9% compared with the yield with the wild-type strain RMBPC and 17.9% over that in the uninoculated control plot at the site where soil nitrogen and organic matter content was lowest. These increases were statistically significant at the 5% confidence interval for each of the three harvests made during the growing season. Strain RMBPC-2 did increase alfalfa biomass at the Hancock site; however, no other significant increases or decreases in alfalfa biomass were observed with the seven other recombinant strains at that site. At three sites where this experiment was conducted, either native rhizobial populations or soil nitrogen concentrations were high. At these sites, none of the recombinant strains affected yield. We conclude that RMBPC -2 can increase alfalfa yields under field conditions of nitrogen limitation, low endogenous rhizobial competitors, and sufficient moisture.
Thermal Modeling of the Lithium/Polymer Battery: I . Discharge Behavior of a Single Cell (1995)

Two models are presented to predict the thermal behavior of the lithium/polymer battery. Part I presents the one‐cell model, a one‐dimensional model for predicting the thermal behavior of the lithium negative electrode/solid polymer separator/insertion positive electrode cell. Part II presents the cell‐stack model, a one‐dimensional model that uses variable heat‐generation rates calculated by the one‐cell model to predict temperature profiles in cell stacks. The one‐cell model, presented in Part I , is based on the model of Doyle et al1. with the addition of an energy balance in the form given by Bernardi et al2. Physical properties are allowed to vary with temperature. The model is general and can be used to simulate a wide range of polymeric separator materials, lithium salts, and composite insertion electrodes. Simulation results for the system are presented for isothermal operation at several temperatures and adiabatic operation at several discharge rates. Heat transfer to the surroundings is considered by defining a position‐dependent heat‐transfer coefficient for various cells in a cell stack.
Cancer Internet Search Activity on a Major Search Engine, United States 2001-2003 (2005)

Media coverage appears to play a powerful role in prompting online searches for cancer information. Internet search activity offers an innovative tool for passive surveillance of health information-seeking behavior.
Large granular lymphocytes: Morphological studies (1982)

Large granular lymphocytes from normal human blood were enriched by centrifugation on discontinuous Percoll density gradients. Their capacity for natural killing, but not for phagocytosis of yeast cells, was demonstrated. Large granular lymphocytes are characterized in electron microscopy by their fine structure, especially by typical granules and by inclusions of tubular structures in a parallel array. Their lymphocyte nature is supported by activity of acid-alpha-naphthyl acetate esterase and by the absence of myelo-peroxidase (POX) and of macrophage POX. The Fc gamma receptor of their cell membrane is marked by soluble POX-anti-POX-complexes; labeled parts of their membrane are not incorporated into the cytoplasm as in monocytes.
Site-Specific Immobilization of Monoclonal Antibodies Using Spacer-Mediated Antibody Attachment (1996)

Site-directed and random coupling of antibodies (Abs) was performed using aminated silica surfaces as substrates. The site-directed coupling linked the Ab, a monoclonal anti-fluorescein IgG1 (9−40), to the surface via 3400 Dalton (Da) poly(ethylene oxide) (PEO) spacers. The hydrazide end groups of these spacers were attached to aldehyde groups in the hinge region of the oxidized Ab to yield surfaces with an Ab concentration of 2.1 pmol/cm2. The random coupling, in turn, linked the Ab via its available primary amines directly to the glutaraldehyde-activated surface with a yield of 3.8 pmol/cm2. Despite a nearly twofold difference in Ab concentration, the two surfaces bound similar amounts of the FL-BSA antigen (0.56 vs 0.55 pmol/cm2), while their nonspecific uptake of protein was 0.11 vs. 0.21 pmol/cm2, respectively, reflecting the protein repellent quality of PEO-coated surfaces. Fab‘ fragments of the 9−40 Ab were also linked to the same tethers. Here, the succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC) difunctional coupling reagent was attached to the PEO−hydrazide via its succinimide end and to the carboxy-terminal thiol of the Fab‘ via its maleimide end. The concentration of reactive groups was varied by mixing difunctionalized PEO (PEO−(HZ)2) with monofunctionalized polymer (CH3O−PEO−HZ) prior to surface attachment. At 100% PEO−(HZ)2 the FL−BSA (Ag) binding was 0.77 pmol/cm2 while the nonspecific binding was 0.058 pmol/cm2. Progressive dilution of the reactive PEO chains to 25% led to the remarkable binding of 0.87 pmol/cm2 of Ag with 0.037 pmol/cm2 of nonspecific binding. Competitive release from these various surfaces showed more favorable kinetics for the Fab‘ surface with 25% active tethers.
Conserved Oncogenic Behavior of the FAM83 Family Regulates MAPK Signaling in Human Cancer (2014)

FAM83 proteins represent a novel family of oncogenes suitable for the development of cancer therapies aimed at suppressing MAPK signaling.
A rational mechanism for combination treatment of Huntington's disease using lithium and rapamycin (2007)

Huntington's disease (HD) is caused by a polyglutamine expansion mutation in the huntingtin protein that confers a toxic gain-of-function and causes the protein to become aggregate-prone. Aggregate-prone proteins are cleared by macroautophagy, and upregulating this process by rapamycin, which inhibits the mammalian target of rapamycin (mTOR), attenuates their toxicity in various HD models. Recently, we demonstrated that lithium induces mTOR-independent autophagy by inhibiting inositol monophosphatase (IMPase) and reducing inositol and IP3 levels. Here we show that glycogen synthase kinase-3beta (GSK-3beta), another enzyme inhibited by lithium, has opposite effects. In contrast to IMPase inhibition that enhances autophagy, GSK3beta inhibition attenuates autophagy and mutant huntingtin clearance by activating mTOR. In order to counteract the autophagy inhibitory effects of mTOR activation resulting from lithium treatment, we have used the mTOR inhibitor rapamycin in combination with lithium. This combination enhances macroautophagy by mTOR-independent (IMPase inhibition by lithium) and mTOR-dependent (mTOR inhibition by rapamycin) pathways. We provide proof-of-principle for this rational combination treatment approach in vivo by showing greater protection against neurodegeneration in an HD fly model with TOR inhibition and lithium, or in HD flies treated with rapamycin and lithium, compared with either pathway alone.
EWS-Fli1 antisense oligodeoxynucleotide inhibits proliferation of human Ewing's sarcoma and primitive neuroectodermal tumor cells. (1997)

The translocation t(11;22) is a common chromosomal abnormality detected both in Ewing's sarcoma and in primitive neuroectodermal tumor cells. The translocation results in an EWS-Fli1 fusion gene, made up of the 5' half of the EWS gene on chromosome 22 fused to the 3' half of the Fli1 gene on chromosome 11. Recent studies have evaluated possible roles of the fusion gene products. However, the biological significance of EWS-Fli1 is still unknown. Using a competitive polymerase chain reaction technique, we show here that there might be a correlation between the expression levels of the EWS-Fli1 fusion gene and the proliferative activities of Ewing's sarcoma and primitive neuroectodermal tumor cells. When the EWS-Fli1 expression is inhibited by antisense oligodeoxynucleotides against the fusion RNA, the growth of the tumor cells is significantly reduced both in vitro and in vivo. The data further indicate the growth inhibition of the cells by the antisense sequence might be mediated by G0/G1 block in the cell cycle progression. These results suggest that EWS-Fli1 may play an important role in the proliferation of the tumor cells, and the EWS-Fli1 fusion RNA could be used as a target to inhibit the growth of Ewing's sarcoma and primitive neuroectodermal tumor with the specific antisense oligonucleotide.
A Comparison of Gentamicin-Impregnated Polymethylmethacrylate Bead Implantation to Conventional Parenteral Antibiotic Therapy in Infected Total Hip and Knee Arthroplasty (1993)

A multicenter study of infected total knee and total hip arthroplasties was conducted from 1985 until 1990. Twenty-eight patients (22 total hip arthroplasties and six total knee arthroplasties) who had periprosthetic infections were treated according to a prospective, randomized protocol. After initial debridement for their infections, patients were randomized into one of the two following groups: Group I, debridement and the implantation of gentamicin-polymethylmethacrylate (PMMA) beads; and Group 2, debridement and conventional parenteral systemic antibiotic therapy. After initial treatment, the patients were then scheduled for a delayed reconstruction total joint arthroplasty. Of the 28 patients, 25 subsequently had delayed total arthroplasty, and if acrylic bone cement was used for fixation at the time of reimplantation, antibiotics were not added to the cement. The average follow-up period was three years (range, six months to 5.6 years). Infection recurred in two patients treated by debridement and the implantation of gentamicin-PMMA beads (15%) and in four patients treated with debridement and conventional systemic antibiotic therapy (30%). All recurrences occurred in patients who had infected total hip arthroplasties; none occurred in patients with total knee arthroplasties. The conditions that were common in patients with recurrent infection were (1) multiple previous surgeries, (2) host compromise and malnutrition, (3) extensive infection, and (4) inadequate debridement. The recurrence of infection was not statistically significantly more common in either treatment group. The outcome of treatment in patients with infected total joint arthroplasties using debridement, gentamicin-PMMA bead implantation,and a two-stage delayed reconstruction was similar to that of patients treated with debridement combined with conventional parenteral systemic arthroplasty and two-stage reconstruction.
Rationally Designed High-Affinity 2-Amino-6-halopurine Heat Shock Protein 90 Inhibitors That Exhibit Potent Antitumor Activity (2007)

Heat shock protein 90 (Hsp90) is a molecular chaperone protein implicated in stabilizing the conformation and maintaining the function of many cell-signaling proteins. Many oncogenic proteins are more dependent on Hsp90 in maintaining their conformation, stability, and maturation than their normal counterparts. Furthermore, recent data show that Hsp90 exists in an activated form in malignant cells but in a latent inactive form in normal tissues, suggesting that inhibitors selective for the activated form could provide a high therapeutic index. Hence, Hsp90 is emerging as an exciting new target for the treatment of cancer. We now report on a novel series of 2-amino-6-halopurine Hsp90 inhibitors exemplified by 2-amino-6-chloro-9-(4-iodo-3,5-dimethylpyridin-2-ylmethyl)purine (30). These highly potent inhibitors (IC50 of 30 = 0.009 microM in a HER-2 degradation assay) also display excellent antiproliferative activity against various tumor cell lines (IC50 of 30 = 0.03 microM in MCF7 cells). Moreover, this class of inhibitors shows higher affinity for the activated form of Hsp90 compared to our earlier 8-sulfanylpurine Hsp90 inhibitor series. When administered orally to mice, these compounds exhibited potent tumor growth inhibition (>80%) in an N87 xenograft model, similar to that observed with 17-allylamino-17-desmethoxygeldanamycin (17-AAG), which is a compound currently in phase I/II clinical trials.
Solid Lipid Nanoparticle Formulations of Docetaxel Prepared with High Melting Point Triglycerides: In Vitro and in Vivo Evaluation (2014)

Docetaxel (DCX) is a second generation taxane. It is approved by the U.S. Food and Drug Administration for the treatment of various types of cancer, including breast, non-small cell lung, and head and neck cancers. However, side effects, including those related to Tween 80, an excipient in current DCX formulations, can be severe. In the present study, we developed a novel solid lipid nanoparticle (SLN) composition of DCX. Trimyristin was selected from a list of high melting point triglycerides as the core lipid component of the SLNs, based on the rate at which the DCX was released from the SLNs and the stability of the SLNs. The trimyristin-based, PEGylated DCX-incorporated SLNs (DCX-SLNs) showed significantly higher cytotoxicity against various human and murine cancer cells in culture, as compared to DCX solubilized in a Tween 80/ethanol solution. Moreover, in a mouse model with pre-established tumors, the new DCX-SLNs were significantly more effective than DCX solubilized in a Tween 80/ethanol solution in inhibiting tumor growth without toxicity, likely because the DCX-SLNs increased the concentration of DCX in tumor tissues, but decreased the levels of DCX in major organs such as liver, spleen, heart, lung, and kidney. DCX-incorporated SLNs prepared with one or more high-melting point triglycerides may represent an improved DCX formulation.
Transmission Characteristics of a Twisted Radio Wave Based on Circular Traveling-Wave Antenna (2015)

A traveling-wave circular loop antenna with its phase distribution along the circle of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\bm{l}\bm{\varphi}$</tex-math></inline-formula> is demonstrated to generate the twisted radio wave. Theoretical formulations of its radiation fields are deduced in the cylindrical coordinate system and used to analyze its transmission characteristics, such as the radiation patterns, the evolution of the polarization states, and the angular momentum modes including the orbital angular momentum (OAM) modes and the spin angular momentum (SAM) modes. The prototype of a practical configuration for such antenna is proposed and conducted to validate the theoretical results. This theoretical analysis is applicable not only to radio waves but also to the whole electromagnetic spectrum.
Cloning of the Gene Encoding the 44-Kilodalton Antigen of the Agent of Human Granulocytic Ehrlichiosis and Characterization of the Humoral Response (1998)

Antibodies in the sera of patients with human granulocytic ehrlichiosis (HGE) commonly recognize a 44-kDa antigen. We cloned the gene encoding the 44-kDa protein of the agent of HGE (aoHGE) by probing an aoHGE lambda ZAP II genomic DNA expression library with sera from aoHGE-infected mice. The gene, hge-44, is part of a multigene family, with sequence similarity to the Anaplasma marginale msp-2 genes. RNA-PCR studies confirmed that hge-44 is expressed by aoHGE cultured in HL-60 cells and by aoHGE during murine infection. Recombinant HGE-44, expressed and purified as a glutathione transferase fusion protein, was used as the substrate in immunoblots to help diagnose HGE. Antibodies in eight sera from eight patients with HGE and in two sera from two aoHGE-infected mice bound recombinant HGE-44. Antibodies in the sera of healthy individuals or patients with Ehrlichia chaffeensis or Borrelia burgdorferi infection did not recognize HGE-44. We conclude that hge-44 is a member of a multigene family and that hge-44 is expressed and elicits specific antibodies during infection.
Effects of a selective phosphodiesterase IV inhibitor (CDP-840) in a leukotriene-dependent non-human primate model of allergic asthma. (1998)

The activity of CDP-840, a novel, selective phosphodiesterase IV inhibitor was determined in a leukotriene-dependent non-human primate model of allergic asthma. Measurements of specific airway resistance (sRaw) were recorded in a dual chamber plethysmograph for 1 h and 3-5 h after challenge of allergic conscious squirrel monkeys with an aerosol of ascaris antigen. Orally administered CDP-840 (10 mg/kg; 1 h before challenge) produced partial inhibition (41 and 45%, respectively) of both the acute (1 h post antigen) response and the late (3-5 h post antigen) response to antigen but failed to alter the response to an aerosol of leukotriene D4. In a second series of experiments, intravenous CDP-840 (5 mg/kg; 30 min before challenge) showed improved potency, producing 82% inhibition of the early and 51% inhibition of the late phase response. CDP-840 was inactive when tested intravenously at 1 mg/kg and was inactive against the 3-5 h response when administered after the early phase response (5 mg/kg; i.v. 60 min post antigen challenge). The novel phosphodiesterase IV inhibitor CDP-840 selectively inhibited antigen-induced bronchoconstriction in conscious squirrel monkeys. This effect appears to be independent of any direct bronchodilator action. It is concluded that the activity of CDP-840 in this model may be due to an inhibitory effect on mediator (e.g., leukotriene) release.
A Phase I clinical study of cisplatin-incorporated polymeric micelles (NC-6004) in patients with solid tumours (2011)

The delayed and sustained release of cisplatin after i.v. administration contributes to the low toxicity of NC-6004.
Partial matching of planar polylines under similarity transformations (1997)

Given two planar polylines T and P with n and m edges, respectively, we present an O(m{sup 2}n{sup 2}) time, O(mn) space algorithm to find portions of the {open_quotes}text{close_quotes} T which are similar in shape to the {open_quotes}pattern{close_quotes} P. In the common case of a simple pattern, such as a line segment or comer, m = O(l) and our algorithm requires O(n{sup 2}) time and O(n) space. We use the well-known arclength versus cumulative turning angle graph to judge how well a scaled, rotated, and translated version of the pattern matches a piece of the text. Our match scoring function balances the length of a match against the mean squared error in the match; given two matches with the same mean squared error (length), the longer (lower mean squared error) match will have a higher score. The match score is a function of the pattern scale, orientation, and position within the text, and our algorithm seeks to find local maxima of the scoring function. An analytic formula for the highest scoring pattern orientation in terms of scale and position leaves us with a search problem in scale-position space. This space is divided by a set of lines into combinatorially distinctmore » regions in each of which we have an analytic formula for the scoring function. Our algorithm discovers local maxima of the scoring function by performing a topological line sweep over this scale-position space line arrangement.« less
Doxycycline inhibits type XI collagenolytic activity of extracts from human osteoarthritic cartilage and of gelatinase. (1991)

Doxycycline was shown to inhibit digestion of exogenous type XI collagen by homogenates of human osteoarthritic cartilage in vitro. On SDS-PAGE, the cleavage products generated by cartilage extracts were larger and less abundant, indicating less complete cleavage, when doxycycline (10 or 30 microM) was added to the samples. The inhibitory effect was concentration dependent. Purified gelatinase from canine kidney epithelial cells, which also digests type XI collagen, was inhibited in a similar manner by doxycycline. If tetracyclines inhibit this metalloproteinase activity in articular cartilage in vivo, they could modify cartilage breakdown in osteoarthritis.
Phosphorylated Peptides Are Naturally Processed and Presented by Major Histocompatibility Complex Class I Molecules in Vivo (2000)

Posttranslational modification of peptide antigens has been shown to alter the ability of T cells to recognize major histocompatibility complex (MHC) class I-restricted peptides. However, the existence and origin of naturally processed phosphorylated peptides presented by MHC class I molecules have not been explored. By using mass spectrometry, significant numbers of naturally processed phosphorylated peptides were detected in association with several human MHC class I molecules. In addition, CD8(+) T cells could be generated that specifically recognized a phosphorylated epitope. Thus, phosphorylated peptides are part of the repertoire of antigens available for recognition by T cells in vivo.