gebhart/patrepeval huggingface dataset:
A Comparison of Fresh Frozen vs. Formalin-Fixed, Paraffin-Embedded Specimens of Canine Mammary Tumors via Branched-DNA Assay (2016)

Mammary neoplasms are the tumors most affecting female dogs and women. Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable source of archived biological material. Fresh frozen (FF) tissue is considered ideal for gene expression analysis. However, strategies based on FFPE material offer several advantages. Branched-DNA assays permit a reliable and fast workflow when analyzing gene expression. The aim of this study was to assess the comparability of the branched-DNA assay when analyzing certain gene expression patterns between FF and FFPE samples in canine mammary tumors. RNA was isolated from 109 FFPE samples and from 93 FF samples of different canine mammary tissues. Sixteen (16) target genes (Tp53; Myc; HMGA1; Pik3ca; Mcl1; MAPK3; FOXO3; PTEN; GATA4; PFDN5; HMGB1; MAPK1; BRCA2; BRCA1; HMGA2; and Her2) were analyzed via branched-DNA assay (b-DNA). ACTB, GAPDH, and HPRT1 were used as data normalizers. Overall, the relative gene expression of the two different origins of samples showed an agreement of 63%. Still, care should be taken, as FFPE specimens showed lower expression of the analyzed targets when compared to FF samples. The fact that the gene expression in FFPE proved to be lower than in FF specimens is likely to have been caused by the effect of storage time. ACTB had the best performance as a data normalizer.
A Framework for Realizing Security on Demand in Cloud Computing (2013)

In this paper we present our vision for Security on Demand in cloud computing: a system where cloud providers can offer customized security for customers' code and data throughout the term of contract. Security on demand enables security-focussed competitive service differentiation and pricing, based on a threat model that matches the customer's security requirements for the virtual machine he is leasing. It also enables a cloud provider to bring in new secure servers to the data center, and derive revenue from these servers, while still using existing servers. We show a framework where customers' security requests can be expressed and enforced by leveraging the capabilities of servers with different security architectures.
Evaluation of a quadrivalent inactivated vaccine for the protection of cattle against diseases due to common viral infections : research report (2004)

Efficacy of an inactivated quadrivalent vaccine containing infectious bovine rhinotracheitis (IBR) virus, parainfluenza type 3 (PI3) virus, bovine virus diarrhoea virus (BVDV) and bovine respiratory syncytial virus (BRSV) was assessed in naive bovine calves to evaluate short-term (4-18 weeks) and long-term (24-38 weeks) protection following the basic intramuscular vaccination regime of 2 inoculations a month apart. Vaccination was staggered between the long-term and the short-term groups by about 5 months so that both groups, along with a matched group of 6 unvaccinated (control) calves, could be challenged at the same time. Sequential challenges at intervals of 3-8 weeks were done in the order: IBR virus (intranasally, IN), PI3 virus (IN and intratracheally, IT), pestiviruses (IN) and BRSV (IN and IT). The IBR virus challenge produced febrile rhinotracheitis (FRT) in control calves but both the severity and the duration of FRT was significantly reduced in both vaccinated groups. The amount and the duration of IBR virus shed by the vaccinated groups was significantly reduced compared to the control group. Although PI3 virus, pooled pestivirus and BRSV challenges did not result in a noteworthy disease, challenge virus shedding (amount and duration) from the upper (all 3 viruses) and the lower (BRSV) respiratory tracts was significantly reduced in vaccinated groups. After pestivirus challenge, sera and leukocytes from all control calves were infectious for 6-9 days whereas virus was recovered only from leukocytes in vaccinated calves and only for 1.6-2.7 days. Thus a standard course of the quadrivalent vaccine afforded a significant protection against IBR virus, PI3 virus, BVDV and BRSV for at least 6 months.
Adenovirus type 5 E1A gene products act as transformation suppressors of the neu oncogene. (1991)

The adenovirus type 5 early region 1A (E1A) gene was introduced into neu-transformed B104-1-1 cells. Cells that expressed E1A possessed reduced transforming activity in vitro and reduced tumorigenicity in nude mice. These results demonstrate that the E1A gene products can act negatively to suppress the transformed phenotype in neu-transformed cells.
Mechanical Oscillation and Cooling Actuated by the Optical Gradient Force (2009)

In this work, we combine the large per-photon optical gradient force with the sensitive feedback of a high quality factor whispering-gallery microcavity. The cavity geometry, consisting of a pair of silica disks separated by a nanoscale gap, shows extremely strong dynamical backaction, powerful enough to excite coherent oscillations even under heavily damped conditions (mechanical Q approximately 4). In vacuum, the threshold for regenerative mechanical oscillation is lowered to an optical input power of only 270 nW, or roughly 1000 stored cavity photons, and efficient cooling of the mechanical motion is obtained with a temperature compression factor of nearly 14 dB with an input optical power of only 11 microW.
Red Autofluorescence of Dental Plaque Bacteria (2006)

Red autofluorescence of plaque and its relation to fluorescence of a single species in the biofilm was studied. Fluorescence images of non-disclosed and disclosed plaque of 28 first-year students were captured. The plaque samples were assessed by culture methods and studied for red autofluorescence. Species capable of producing red autofluorescence were cultivated from subjects with and without red plaque autofluorescence. Red autofluorescence was observed from Actinomyces odontolyticus, Prevotella intermedia and from Porphyromonas gingivalis and Peptostreptococcus micros grown together. The microbial findings indicated that the intrinsic characteristics of the mature biofilm itself are more responsible for the red autofluorescence than the characteristics of the single species.
Crosswell electromagnetic inversion using integral and differential equations (1995)

Abstract The crosswell electromagnetic (EM) inverse problem is solved with an integral-equation (IE) formulation using successive Born approximations in the frequency domain. Because the inverse problem is nonlinear, the predicted fields and Green's functions are continually updated. Updating the fields and Green's functions relates small changes in the predicted data to small changes in the model parameters through Frechet kernels. These fields and Green functions are calculated with an efficient 3-D finite-difference solver. Since the resistivity is invariant along strike, the 3-D fields are integrated along strike so the 2-D kernels can be assembled.At the early stages of the inversion, smoothing of the electrical conductivity stabilizes the inverse solution when it is far from convergence. As the solution converges, this smoothing is relaxed and more effort is made to reduce the data misfit. Bounds on the conductivity are included in the solution to eliminate unrealistic estimates.The robustness of the inversion scheme has been demonstrated with synthetic and field data that are underdetermined from the standpoint of the smooth models being sought. Two synthetic examples with added Gaussian noise were considered, including data arising from an IE solver. This IE solver is different from the one embedded in the inversion algorithm and has provided a stronger check on the scheme. The synthetic examples show it is more difficult to reconstruct a target's conductivity than its geometry at a single frequency. The inversion scheme has been successfully tested using data collected at the Richmond-field site near Berkeley, California, where it has imaged a salt water plume injected into the interwell region. The data in this experiment consisted of two sets of measurements, taken before and after the injection of 50000 gallons of 1 Omega m salt water. Findings show that underdetermined inversion using small amounts of field data can be sufficient to produce useful, but smoothed, maps of the conductivity. The data in this instance need be only single frequency and single component.
Notch signaling in gastrointestinal tract (Review) (2007)

Notch signaling is one of key pathways constituting the stem cell signaling network. DLL1, DLL3, DLL4, JAG1 and JAG2 with DSL domain are typical Notch ligands, while DNER, F3/Contactin and NB-3 without DSL domain are atypical Notch ligands. Notch-ligand binding to NOTCH1, NOTCH2, NOTCH3 or NOTCH4 receptor induces the receptor proteolysis by metalloprotease and gamma-secretase to release Notch intracellular domain (NICD). Typical Notch ligands transduce signals to the CSL-NICD-Mastermind complex for the maintenance of stem or progenitor (transit-amplifying) cells through transcriptional activation of HES1, HES5, HES7, HEY1, HEY2 and HEYL genes, and also to the NF-kappaB-NICD complex for the augmentation of NF-kappaB signaling. Atypical Notch ligands transduce signals to the CSL-NICD-Deltex complex for the differentiation of progenitor cells through MAG transcriptional activation. Notch signals are transduced to the canonical pathway (CSL-NICD-Mastermind signaling cascade) or the non-canonical pathway (NF-kappaB-NICD and CSL-NICD-Deltex signaling cascades) based on the expression profile of Notch ligands, Notch receptors, and Notch signaling modifiers. Canonical Notch signaling is activated in the stem or progenitor domain of gastrointestinal epithelium, such as basal layer in esophagus and lower part of the crypt in colon. Notch signaling to inhibit secretory cell differentiation is oncogenic in gastric cancer and colorectal cancer, while Notch signaling to promote keratinocyte differentiation is anti-oncogenic in esophageal squamous cell carcinoma (SCC). Single nucleotide polymorphism (SNP), epigenetic change, and genetic alteration of genes encoding Notch signaling-associated molecules will be utilized as biomarkers for gastrointestinal cancer. gamma-Secretase inhibitors, functioning as Notch signaling inhibitors, will be applied as anti-cancer drugs for gastric cancer and colorectal cancer.
Scalable selective re-execution for EDGE architectures (2004)

Pipeline flushes are becoming increasingly expensive in modern microprocessors with large instruction windows and deep pipelines. Selective re-execution is a technique that can reduce the penalty of mis-speculations by re-executing only instructions affected by the mis-speculation, instead of all instructions. In this paper we introduce a new selective re-execution mechanism that exploits the properties of a dataflow-like Explicit Data Graph Execution (EDGE) architecture to support efficient mis-speculation recovery, while scaling to window sizes of thousands of instructions with high performance. This distributed selective re-execution (DSRE) protocol permits multiple speculative waves of computation to be traversing a dataflow graph simultaneously, with a commit wave propagating behind them to ensure correct execution. We evaluate one application of this protocol to provide efficient recovery for load-store dependence speculation. Unlike traditional dataflow architectures which resorted to single-assignment memory semantics, the DSRE protocol combines dataflow execution with speculation to enable high performance and conventional sequential memory semantics. Our experiments show that the DSRE protocol results in an average 17% speedup over the best dependence predictor proposed to date, and obtains 82% of the performance possible with a perfect oracle directing the issue of loads.
An architecture for software-controlled data prefetching (1991)

Article An architecture for software-controlled data prefetching Share on Authors: Alexander C. Klaiber University of Washington, Seattle, WA University of Washington, Seattle, WAView Profile , Henry M. Levy University of Washington, Seattle, WA University of Washington, Seattle, WAView Profile Authors Info & Claims ISCA '91: Proceedings of the 18th annual international symposium on Computer architectureApril 1991 Pages 43–53https://doi.org/10.1145/115952.115958Online:01 April 1991Publication History 133citation673DownloadsMetricsTotal Citations133Total Downloads673Last 12 Months17Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Involvement of Abscisic Acid in Potato Cold Acclimation (1983)

Upon exposure to 2 degrees C day/night (D/N), leaves of Solanum commersonii (Sc) began acclimating on the 4th day from a -5 degrees C (killing temperature) hardy level to -12 degrees C by the 15th day. Leaves of S. tuberosum L. (St) cv ;Red Pontiac' typically failed to acclimate and were always killed at -3 degrees C. Leaves of control (20/15 degrees C, D/N) and treated plants (2 degrees C, D/N) of St showed similar levels of free abscisic acid (ABA) during a 15-day sampling period. In treated Sc plants, however, free ABA contents increased 3-fold on the 4th day and then declined to their initial level thereafter. The increase was not observed in leaves of Sc control plants.Treated St plants showed a slightly higher content of leaf soluble protein than controls. In Sc, leaves of controls maintained relatively constant soluble proteins, but leaves of treated plants showed a distinct increase. This significant increase was initiated on the 4th day, peaked on the 5th day, and remained at a high level throughout the 15-day sampling period.Exogenously applied ABA induced frost hardiness in leaves of Sc plants whether plants were grown under a 20 degrees C or 2 degrees C temperature regime. When cycloheximide was added to the medium of stem-cultured plants at the beginning of 2 degrees C acclimation, or at the beginning of the ABA treatment in the 20 degrees C regime, it completely inhibited the development of frost hardiness. However, when cycloheximide was added to plants on the 5th day during 2 degrees C acclimation, the induction of frost hardiness was not inhibited. The role of ABA in triggering protein synthesis needed to induce frost hardiness is discussed.
Hypoxia Inducible Carbonic Anhydrase IX, Marker of Tumour: Hypoxia, Survival Pathway and Therapy Target (2004)

Over 50 genes are inducible by hypoxia, via hypoxia inducible factor 1alpha (HIF-1alpha). Carbonic anhydrase IX (CAIX) is one of the most inducible and most uniformly induced genes and because of its stability and membrane location provides a reliable histochemical marker of hypoxia. Recent studies have shown the importance of pH in cell death under hypoxia, thus mechanisms of pH regulation are likely to be vital pathways for survival. Carbonic anhydrases have a widespread role in normal tissues in regulating pH, with 14 isoforms described, so inhibition may have substantial normal tissue toxicity. Selective nonmembrane permeable inhibitors are available and may synergise with chemotherapy agents more active in acid conditions. CAIX has a major role in regulating hydrogen ion (H+) flux and blockade of CAIX results in increased cell death under hypoxia, indicating that it is one mechanism of hypoxic adaptation. As it is commonly expressed in tumours with the worst prognosis it is a potential target for therapy.
Cloning and sequencing of the pertussis toxin genes: operon structure and gene duplication. (1986)

Pertussis toxin, a protein composed of five different subunits (S1, S2, S3, S4, and S5), is the major virulence factor of Bordetella pertussis. We have cloned and sequenced a DNA fragment of 4.7 kilobases that contains the genes coding for the five subunits. The genes are clustered within 3.2 kilobases in the following order: S1, S2, S4, S5, and S3. A sequence closely resembling Escherichia coli promoters is found only before the S1 gene, and a possible termination signal is present at the end of the S3 gene, which suggests that the pertussis toxin genes are organized in a single operon. A possible Shine-Dalgarno sequence is present before the S1 gene but not before the other four genes that 8-12 nucleotides upstream from the ATG codon show a new consensus sequence, 5'TCC(T)GG3', possibly involved in the regulation of translation. We have also found sequence homology between the S2 and S3 genes and their protein products indicating that gene duplication played a major role in the evolution of pertussis toxin.
Molecular and functional characterization of a novel efflux pump, AmvA, mediating antimicrobial and disinfectant resistance in Acinetobacter baumannii (2010)

This report describes the functions of a novel resistance determinant, a member of the MFS efflux pumps, for the first time in A. baumannii.
Preparation of fluorescently‐labeled amyloid‐beta peptide assemblies: the effect of fluorophore conjugation on structure and function (2009)

Recent research has focused on soluble oligomeric assemblies of the 42 amino acid isoform of the amyloid-beta peptide (A beta 42) as the proximal cause of neuronal injury, synaptic loss, and the eventual dementia associated with Alzheimer's disease (AD). While neurotoxicity, neuroinflammation, and deficits in behavior and memory have all been attributed to oligomeric A beta 42, the specific roles for this assembly in the cellular neuropathology of AD remain poorly understood. In particular, lack of reliable and well-characterized forms of easily detectable A beta 42 oligomers has hindered study of the cellular trafficking of exogenous A beta 42 by neurons in vitro and in vivo. Therefore, the objective of this study is to fluorescently label soluble oligomeric A beta 42 without altering the structure or function of this assembly. Previous studies have demonstrated the advantages of using tapping mode atomic force microscopy (AFM) to characterize the structural assemblies formed by synthetic A beta 42 under specific solution conditions (e.g., oligomers, protofibrils, and fibrils). Here, we extend these methods to establish a strategy for fluorescent labeling of oligomeric A beta 42 assemblies that are structurally comparable to unlabeled oligomeric A beta 42. To compare function, we demonstrate that the uptake of labeled and unlabeled oligomeric A beta 42 by neurons in vitro is similar. AFM-characterized fluorophore-A beta 42 oligomers are an exciting new reagent for use in a variety of studies designed to elucidate critical cellular and molecular mechanisms underlying the functions of this A beta 42 assembly form in AD.
Krüppel-like Factor 4 Mediates p53-dependent G1/S Cell Cycle Arrest in Response to DNA Damage (2003)

The tumor suppressor p53 is required for the maintenance of genomic integrity following DNA damage. One mechanism by which p53 functions is to induce a block in the transition between the G(1) and S phase of the cell cycle. Previous studies indicate that the Krüppel-like factor 4 (KLF4) gene is activated following DNA damage and that such activation depends on p53. In addition, enforced expression of KLF4 causes G(1)/S arrest. The present study examines the requirement of KLF4 in mediating the p53-dependent cell cycle arrest process in response to DNA damage. We show that the G(1) population of a colon cancer cell line, HCT116, that is null for the p53 alleles (-/-) was abolished following gamma irradiation compared with cells with wild-type p53 (+/+). Conditional expression of KLF4 in irradiated HCT116 p53-/- cells restored the G(1) cell population to a level similar to that seen in irradiated HCT116 p53+/+ cells. Conversely, treatment of HCT116 p53+/+ cells with small interfering RNA (siRNA) specific for KLF4 significantly reduced the number of cells in the G(1) phase following gamma irradiation compared with the untreated control or those treated with a nonspecific siRNA. In each case the increase or decrease in KLF4 level because of conditional induction or siRNA inhibition, respectively, was accompanied by an increase or decrease in the level of p21(WAF1/CIP1). Results of our study indicate that KLF4 is an essential mediator of p53 in controlling G(1)/S progression of the cell cycle following DNA damage.
ESR1 mutations are frequent in newly diagnosed metastatic and loco-regional recurrence of endocrine-treated breast cancer and carry worse prognosis (2020)

Clinically relevant ESR1 mutations are prevalent in newly diagnosed metastatic and local recurrence of endocrine-treated breast cancer. Since local recurrences are amenable to curative therapy, these mutations may inform the selection of subsequent endocrine therapies.
Highly Parallel Fast KD‐tree Construction for Interactive Ray Tracing of Dynamic Scenes (2007)

Abstract We present a highly parallel, linearly scalable technique of kd‐tree construction for ray tracing of dynamic geometry. We use conventional kd‐tree compatible with the high performing algorithms such as MLRTA or frustum tracing. Proposed technique offers exceptional construction speed maintaining reasonable kd‐tree quality for rendering stage. The algorithm builds a kd‐tree from scratch each frame, thus prior knowledge of motion /deformation or motion constraints are not required. We achieve nearly real‐time performance of 7‐12 FPS for models with 200K of dynamic triangles at 1024x1024 resolution with shadows and textures.
Antifungal activity of synthetic 15-mer peptides based on the Rs-AFP2 (Raphanus sativus antifungal protein 2) sequence. (1997)

Plant defensins are a class of cysteine-rich peptides of which several members have been shown to be potent inhibitors of fungal growth. A series of overlapping 15-mer peptides based on the amino acid sequence of the radish antifungal protein Rs-AFP2 have been synthesized. Peptides 6, 7, 8 and 9, comprising the region from cysteine 27 to cysteine 47 of Rs-AFP2 showed substantial antifungal activity against several fungal species (minimal inhibitory concentrations of 30-60 micrograms/mL), but no activity towards bacteria (except peptide 6 at 100 micrograms/mL). The active peptides were shown to be sensitive to the presence of cations in the medium and to the composition and pH of the medium. When present at a subinhibitory concentration (20 micrograms/mL), peptides 1, 7, 8 and 10 potentiated the activity of Rs-AFP2 from 2.3-fold to 2.8-fold. By mapping the characteristics of the active peptide on the structure of Rs-AFP2 as determined by nuclear magnetic resonance, the active region of the antifungal protein appears to involve beta-strands 2 and 3 in combination with the loop connecting those strands. A cyclized synthetic mimic of the loop, cysteine 36 to cysteine 45, was shown to have antifungal activity. Substitution of tyrosine 38 by alanine in the cyclic peptide substantially reduced the antifungal activity, indicating the importance of this residue for the activity of Rs-AFP2 as demonstrated carrier by mutational analysis.
Democratizing transactional programming (2014)

Control transactions without compromising their simplicity for the sake of expressiveness, application concurrency, or performance.