gebhart/patrepeval huggingface dataset:
Seasonal Freeze Resistance of Rainbow Smelt (Osmerus mordax) Is Generated by Differential Expression of Glycerol‐3‐Phosphate Dehydrogenase, Phosphoenolpyruvate Carboxykinase, and Antifreeze Protein Genes (2006)

In winter, rainbow smelt (Osmerus mordax) accumulate glycerol and produce an antifreeze protein (AFP), which both contribute to freeze resistance. The role of differential gene expression in the seasonal pattern of these adaptations was investigated. First, cDNAs encoding smelt and Atlantic salmon (Salmo salar) phosphoenolpyruvate carboxykinase (PEPCK) and smelt glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were cloned so that all sequences required for expression analysis would be available. Using quantitative PCR, expression of beta actin in rainbow smelt liver was compared with that of GAPDH in order to determine its validity as a reference gene. Then, levels of glycerol-3-phosphate dehydrogenase (GPDH), PEPCK, and AFP relative to beta actin were measured in smelt liver over a fall-winter-spring interval. Levels of GPDH mRNA increased in the fall just before plasma glycerol accumulation, implying a driving role in glycerol synthesis. GPDH mRNA levels then declined during winter, well in advance of serum glycerol, suggesting the possibility of GPDH enzyme or glycerol conservation in smelt during the winter months. PEPCK mRNA levels rose in parallel with serum glycerol in the fall, consistent with an increasing requirement for amino acids as metabolic precursors, remained elevated for much of the winter, and then declined in advance of the decline in plasma glycerol. AFP mRNA was elevated at the onset of fall sampling in October and remained elevated until April, implying separate regulation from GPDH and PEPCK. Thus, winter freezing point depression in smelt appears to result from a seasonal cycle of GPDH gene expression, with an ensuing increase in the expression of PEPCK, and a similar but independent cycle of AFP gene expression.
Strategies to overcome trastuzumab resistance in HER2-overexpressing breast cancers: focus on new data from clinical trials (2014)

Breast cancers over-express the human epidermal growth factor receptor 2 (HER2) in about 15% of patients. This transmembrane tyrosine kinase receptor activates downstream signaling pathways and leads to proliferation of cancer cells. Trastuzumab, an anti-HER2 monoclonal antibody, improves outcome in women with early and metastatic breast cancer. Resistance to trastuzumab involves the phosphoinositide 3-kinase/mammalian target of rapamycin (PI3K/mTOR) pathway, truncation of the Her2 receptor or lack of immune response. The last decade has seen major advances in strategies to overcome resistance to trastuzumab. This includes the development of antibody-drug conjugates, dual HER2 inhibition strategies, inhibition of PI3K/mTOR pathway and development of modulators of immune checkpoints.
Proteomics of early zebrafish embryos (2006)

The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis.
Abstract LB-C16: Safety and tumor responses of the anti-Trop-2 antibody drug conjugate, sacituzumab govitecan (IMMU-132), in refractory, metastatic, triple-negative breast cancer (TNBC): An ongoing Phase II trial (2015)

Abstract This abstract has been withheld from publication due to its inclusion in the AACR-NCI-EORTC Molecular Targets Conference 2015 Official Press Program. It will be posted online at the time of its presentation in a press conference or in a session: 12:30 PM ET Sunday, November 8. Citation Format: Aditya Bardia, Ingrid Mayer, Jennifer Diamond, Alexander Starodub, Rebecca Moroose, Steven Isakoff, Allyson Ocean, Michael Guarino, Kevin Kalinsky, Joyce O'Shaugnessy, Francois Wilhelm, Pius Maliakal, Robert Sharkey, David Goldenberg, Linda Vahdat. Safety and tumor responses of the anti-Trop-2 antibody drug conjugate, sacituzumab govitecan (IMMU-132), in refractory, metastatic, triple-negative breast cancer (TNBC): An ongoing Phase II trial. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr LB-C16.
Therapies in Parkinsonʼs disease (2012)

Numerous clinical trials have provided evidence that health-related quality of life can be substantially improved with early diagnosis and institution of exercise and other physical measures, appropriate timing of dopaminergic therapy, and strategies to delay and treat levodopa-related motor complications and nonmotor Parkinson's disease-related symptoms.
DNA Binding: a Novel Function of Pseudomonas aeruginosa Type IV Pili (2005)

The opportunistic pathogen Pseudomonas aeruginosa produces multifunctional, polar, filamentous appendages termed type IV pili. Type IV pili are involved in colonization during infection, twitching motility, biofilm formation, bacteriophage infection, and natural transformation. Electrostatic surface analysis of modeled pilus fibers generated from P. aeruginosa strain PAK, K122-4, and KB-7 pilin monomers suggested that a solvent-exposed band of positive charge may be a common feature of all type IV pili. Several functions of type IV pili, including natural transformation and biofilm formation, involve DNA. We investigated the ability of P. aeruginosa type IV pili to bind DNA. Purified PAK, K122-4, and KB-7 pili were observed to bind both bacterial plasmid and salmon sperm DNA in a concentration-dependent and saturable manner. PAK pili had the highest affinity for DNA, followed by K122-4 and KB-7 pili. DNA binding involved backbone interactions and preferential binding to pyrimidine residues even though there was no evidence of sequence-specific binding. Pilus-mediated DNA binding was a function of the intact pilus and thus required elements present in the quaternary structure. However, binding also involved the pilus tip as tip-specific, but not base-specific, antibodies inhibited DNA binding. The conservation of a Thr residue in all type IV pilin monomers examined to date, along with the electrostatic data, implies that DNA binding is a conserved function of type IV pili. Pilus-mediated DNA binding could be important for biofilm formation both in vivo during an infection and ex vivo on abiotic surfaces.
Impaired production of proinflammatory cytokines in response to lipopolysaccharide (LPS) stimulation in elderly humans (1999)

Ageing is associated with decreased resistance to bacterial infections and concomitant increased circulating levels of inflammatory cytokines. The purpose of the present study was to research age-related changes in levels of early mediators of the acute-phase response in whole blood supernatants following LPS stimulation, representing an ex vivo model of sepsis. Levels of tumour necrosis factor-alpha (TNF-alpha), IL-1beta and IL-6 in whole blood supernatants were measured after in vitro LPS stimulation for 24 h in 168 elderly humans aged 81 years from the 1914 cohort in Glostrup, Denmark and in 91 young controls aged 19-31 years. Levels of TNF-alpha and IL-1beta were significantly lower in elderly humans compared with young controls, whereas no difference was detected with regard to IL-6. Elderly humans with low body mass index had the lowest levels of IL-1beta. Young women had lower levels of proinflammatory cytokines compared with young men, but this difference was blurred by ageing. No relation was found between circulating plasma levels of TNF-alpha and levels after in vitro LPS stimulation. In conclusion, decreased production of TNF-alpha and IL-1beta after exposure to LPS may reflect impaired host defence against infections in the elderly and be of importance in elderly humans with underlying health disorders. However, the clinical relevance is questionable in healthy elderly people because decreased levels were found compared with young men but not compared with young women.
Universally composable security: a new paradigm for cryptographic protocols (2001)

We propose a novel paradigm for defining security of cryptographic protocols, called universally composable security. The salient property of universally composable definitions of security is that they guarantee security even when a secure protocol is composed of an arbitrary set of protocols, or more generally when the protocol is used as a component of an arbitrary system. This is an essential property for maintaining security of cryptographic protocols in complex and unpredictable environments such as the Internet. In particular, universally composable definitions guarantee security even when an unbounded number of protocol instances are executed concurrently in an adversarially controlled manner, they guarantee non-malleability with respect to arbitrary protocols, and more. We show how to formulate universally composable definitions of security for practically any cryptographic task. Furthermore, we demonstrate that practically any such definition can be realized using known techniques, as long as only a minority of the participants are corrupted. We then proceed to formulate universally composable definitions of a wide array of cryptographic tasks, including authenticated and secure communication, key-exchange, public-key encryption, signature, commitment, oblivious transfer, zero knowledge and more. We also make initial steps towards studying the realizability of the proposed definitions in various settings.
Structural Basis for Norovirus Inhibition by Human Milk Oligosaccharides (2016)

Histo-blood group antigens (HBGAs) are important binding factors for norovirus infections. We show that two human milk oligosaccharides, 2'-fucosyllactose (2'FL) and 3-fucosyllactose (3FL), could block norovirus from binding to surrogate HBGA samples. We found that 2'FL and 3FL bound at the equivalent HBGA pockets on the norovirus capsid using X-ray crystallography. Our data revealed that 2'FL and 3FL structurally mimic HBGAs. These results suggest that 2'FL and 3FL might act as naturally occurring decoys in humans.
Inhibition of cell proliferation by chronic wound fluid (1993)

It has been proposed that occlusive wound dressings may enhance chronic wound repair by the stimulatory action of the fluid accumulating beneath the dressings. In this report, we investigated the in vitro proliferative effects of chronic wound fluid obtained from under a polyurethane membrane applied for 24 hours to venous ulcers in the ambulatory setting. By measuring cell counts and DNA synthesis, we found that chronic wound fluid inhibited the proliferation of human dermal fibroblasts (p = 0.008) and failed to stimulate the proliferation of microvascular endothelial cells (p = 0.03) and keratinocytes (p = 0.03). The inhibitory activity of chronic wound fluid on fibroblast proliferation was blocked after the fluid was heated to 100 degrees C, but not 56 degrees C, and was mainly restricted to a fraction of chronic wound fluid enriched in components less than 30 kd in molecular weight (p = 0.028). At concentrations ranging from 1% to 4% and in the presence of serum, chronic wound fluid decreased the viability of fibroblasts, as shown by a decreased ability of the cells to exclude trypan blue (p = 0.02), and the viability of endothelial cells, as shown by an increased release of tritiated adenine (p = 0.03). We conclude that the wound fluid obtained from beneath occlusive dressings applied to chronic wounds inhibits cell proliferation.
Learning Graph Matching (2009)

As a fundamental problem in pattern recognition, graph matching has applications in a variety of fields, from computer vision to computational biology. In graph matching, patterns are modeled as graphs and pattern recognition amounts to finding a correspondence between the nodes of different graphs. Many formulations of this problem can be cast in general as a quadratic assignment problem, where a linear term in the objective function encodes node compatibility and a quadratic term encodes edge compatibility. The main research focus in this theme is about designing efficient algorithms for approximately solving the quadratic assignment problem, since it is NP-hard. In this paper we turn our attention to a different question: how to estimate compatibility functions such that the solution of the resulting graph matching problem best matches the expected solution that a human would manually provide. We present a method for learning graph matching: the training examples are pairs of graphs and the 'labels' are matches between them. Our experimental results reveal that learning can substantially improve the performance of standard graph matching algorithms. In particular, we find that simple linear assignment with such a learning scheme outperforms Graduated Assignment with bistochastic normalisation, a state-of-the-art quadratic assignment relaxation algorithm.
Versatile protein microarray based on carbohydrate‐binding modules (2005)

Non-DNA microarrays, such as protein, peptide and small molecule microarrays, can potentially revolutionize the high-throughput screening tools currently used in basic and pharmaceutical research. However, fundamental obstacles remain that limit their rapid and widespread implementation as an alternative bioanalytical approach. These include the prerequisite for numerous proteins in active and purified form, ineffectual immobilization strategies and inadequate means for quality control of the considerable numbers of multiple reagents. This study describes a simple yet efficient strategy for the production of non-DNA microarrays, based on the tenacious affinity of a carbohydrate-binding module (CBM) for its three-dimensional substrate, i.e., cellulose. Various microarray formats are described, e.g., conventional and single-chain antibody microarrays and peptide microarrays for serodiagnosis of human immunodeficiency virus patients. CBM-based microarray technology overcomes many of the previous obstacles that have hindered fabrication of non-DNA microarrays and provides a technically simple but effective alternative to conventional microarray technology.
Wall-following controllers for sonar-based mobile robots (2002)

For mobile robots equipped with incremental encoders and one sonar sensor this paper presents wall-following controllers that achieve global convergence, as well as the fulfillment of constraints on the orientation of the sonar and the velocities of the wheels. A sensor fusion approach for the estimation of the robot's coordinates is adopted by designing an extended Kalman filter that combines ultrasonic and odometric data.
Correlation of film density and wet etch rate in hydrofluoric acid of plasma enhanced atomic layer deposited silicon nitride (2016)

The continued scaling in transistors and memory elements has necessitated the development of atomic layer deposition (ALD) of silicon nitride (SiNx), particularly for use a low k dielectric spacer. One of the key material properties needed for SiNx films is a low wet etch rate (WER) in hydrofluoric (HF) acid. In this work, we report on the evaluation of multiple precursors for plasma enhanced atomic layer deposition (PEALD) of SiNx and evaluate the film’s WER in 100:1 dilutions of HF in H2O. The remote plasma capability available in PEALD, enabled controlling the density of the SiNx film. Namely, prolonged plasma exposure made films denser which corresponded to lower WER in a systematic fashion. We determined that there is a strong correlation between WER and the density of the film that extends across multiple precursors, PEALD reactors, and a variety of process conditions. Limiting all steps in the deposition to a maximum temperature of 350 °C, it was shown to be possible to achieve a WER in PEALD SiNx of 6.1 Å/min, which is similar to WER of SiNx from LPCVD reactions at 850 °C.
Purging in Bone Marrow Transplantation (1993)

This book discusses the rationale for the use of haematopoietic stem cell transplantation after high dose cytotoxic therapy. Gulatis describes methods for ex-vivo elimination (purging) of stem cells, with emphasis on preclinical investigations and how to evaluate the clinical benefit. He also presents methods for eliminating T-cells in patients undergoing allogeneic BMT. Information related to complication of purging haematopoietic stem cell transplantations and unresolved issues that need further study are discussed.
Genetic engineering of the pseudorabies virus genome to construct live vaccines. (1990)

Pseudorabies virus (PRV) is a herpesvirus of pigs. Homologous recombination with plasmids offers a method to engineer precise changes in the PRV genome to produce advantageous live vaccines. Safety can be ensured by using a non-reverting deletion to inactivate the thymidine kinase gene. One particularly important feature of new PRV vaccines is deletion of an antigen, so that vaccinated pigs are serologically distinguishable from infected pigs. We have constructed a live vaccine strain with deletions in the thymidine kinase gene and in the gene for a glycoprotein, gX. Molecular engineering techniques made it possible to choose deletion of gX, which has no known immunological significance, over deletion of other glycoproteins that contribute to protective immunity. Extensive experiments in pigs with isogenic virus pairs show that deletion of gX does not compromise efficacy of a vaccine as gI deletions do. Deletion of gX also suggests a site for replacement with antigens from other pathogens. In addition to molecular engineering of a live vaccine strain, research on PRV glycoproteins has led to the discovery that expression of the glycoprotein gp50 makes cells resistant to PRV infection. Perhaps this observation could be extrapolated to the level of a whole animal to allow engineering of pigs to become an alternative to engineered vaccines.
Pediatric premedication: a double-blind randomized trial of dexmedetomidine or ketamine alone versus a combination of dexmedetomidine and ketamine (2017)

Chinese Clinical Trial Register (Unique identifier: ChiCTR-TRC-14004475 , Date of registration: 2 April 2014).
Vasopressin and its copilot copeptin in sepsis and septic shock* (2009)

James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research; St. Paul's Hospital; Vancouver, BC, Canada The author has not disclosed any potential conflicts of interest.
Regulation of estrogen receptor alpha by the tumor suppressor p53 in breast cancer cells (2008)

Estrogen receptor (ER) and the tumor suppressor p53 are key prognostic indicators in breast cancer. Estrogen signaling through its receptor (ER) controls proliferation of normal as well as transformed mammary epithelial cells, and the presence of ER is established as a marker of good prognosis and response to therapy. The p53 tumor suppressor gene is often referred to as the "cellular gatekeeper" due to its extensive control of cell proliferation and apoptosis. Loss of functional p53 is a negative prognostic indicator and is correlated with lack of response to antiestrogens, reduced disease-free interval and increased chance of disease recurrence. Clinical studies have demonstrated that tumors with mutated p53 tend to be ER negative, while ER positive tumors tend to have wild type p53. Recent studies from our lab indicate that p53 genotype correlates with estrogen receptor expression in mammary tumors in vivo. We therefore hypothesized that p53 regulates ER expression in mammary cancer cells by recruitment of specific cofactors to the ER promoter. To test this, MCF-7 cells were treated with doxorubicin or ionizing radiation, both of which stimulated significant increases in p53 expression, as expected, but also increased ER expression in a p53-dependent manner. Furthermore, in cells treated with siRNA targeting p53, both p53 and ER protein levels were significantly reduced. P53 was also demonstrated to transcriptionally regulate the ER promoter in luciferase assays and chromatin immunoprecipitation assays showed that p53 was recruited to the ER promoter along with CARM1, CBP, c-Jun and Sp1 and that this multifactor complex was formed in a p53-dependent manner. The regulation of ER by p53 has therapeutic implications, as the treatment of breast cancer cells with doxorubicin sensitized these cells to tamoxifen treatment. Furthermore, response to tamoxifen as well as to estrogen was dependent on p53 expression in ER positive human breast cancer cells. Taken together, these data demonstrate that p53 regulates ER expression through transcriptional control of the ER promoter, accounting for their concordant expression in human breast cancer and identifying potentially beneficial therapeutic strategies for the treatment of ER positive breast cancers.
Coded excitation for diagnostic ultrasound: a system developer's perspective (2004)

Resolution and penetration are primary criteria for clinical image quality. Conventionally, high bandwidth for resolution was achieved with a short pulse, which results in a tradeoff between resolution and penetration. Coded excitation extends the bounds of this tradeoff by increasing SNR through appropriate coding on transmit and decoding on receive. Although used for about 50 years in radar, coded excitation was successfully introduced into commercial ultrasound scanners only within the last 5 years. This delay is at least partly due to practical implementation issues particular to diagnostic ultrasound, which are the focus of this paper. After reviewing the basics of bi-phase and chirp coding, we present simulation results to quantify tradeoffs between penetration and resolution under frequency-dependent attenuation, dynamic focusing, and nonlinear propagation. Next we compare chirp and Golay code performance with respect to image quality and system requirements, and finally show clinical images that illustrate the current applications of coded excitation in B-mode, harmonic, and flow imaging.
Small regulatory RNAs in mammals (2005)

Mammalian cells harbor numerous small non-protein-coding RNAs, including small nucleolar RNAs (snoRNAs), microRNAs (miRNAs), short interfering RNAs (siRNAs) and small double-stranded RNAs, which regulate gene expression at many levels including chromatin architecture, RNA editing, RNA stability, translation, and quite possibly transcription and splicing. These RNAs are processed by multistep pathways from the introns and exons of longer primary transcripts, including protein-coding transcripts. Most show distinctive temporal- and tissue-specific expression patterns in different tissues, including embryonal stem cells and the brain, and some are imprinted. Small RNAs control a wide range of developmental and physiological pathways in animals, including hematopoietic differentiation, adipocyte differentiation and insulin secretion in mammals, and have been shown to be perturbed in cancer and other diseases. The extent of transcription of non-coding sequences and the abundance of small RNAs suggests the existence of an extensive regulatory network on the basis of RNA signaling which may underpin the development and much of the phenotypic variation in mammals and other complex organisms and which may have different genetic signatures from sequences encoding proteins.