gebhart/patrepeval huggingface dataset:
A noninvasive method for measuring the velocity of diffuse hydrothermal flow by tracking moving refractive index anomalies (2010)

Diffuse flow velocimetry (DFV) is introduced as a new, noninvasive, optical technique for measuring the velocity of diffuse hydrothermal flow. The technique uses images of a motionless, random medium (e.g., rocks) obtained through the lens of a moving refraction index anomaly (e.g., a hot upwelling). The method works in two stages. First, the changes in apparent background deformation are calculated using particle image velocimetry (PIV). The deformation vectors are determined by a cross correlation of pixel intensities across consecutive images. Second, the 2‐D velocity field is calculated by cross correlating the deformation vectors between consecutive PIV calculations. The accuracy of the method is tested with laboratory and numerical experiments of a laminar, axisymmetric plume in fluids with both constant and temperature‐dependent viscosity. Results show that average RMS errors are ∼5%–7% and are most accurate in regions of pervasive apparent background deformation which is commonly encountered in regions of diffuse hydrothermal flow. The method is applied to a 25 s video sequence of diffuse flow from a small fracture captured during the Bathyluck'09 cruise to the Lucky Strike hydrothermal field (September 2009). The velocities of the ∼10°C–15°C effluent reach ∼5.5 cm/s, in strong agreement with previous measurements of diffuse flow. DFV is found to be most accurate for approximately 2‐D flows where background objects have a small spatial scale, such as sand or gravel.
Genotype-independent transformation of lettuce usingAgrobacterium tumefaciens (1994)

Journal Article Genotype-independent transformation of lettuce using Agrobacterium tumefaciens Get access I.S. Curtis, I.S. Curtis 1Plant Genetic Manipulation Group, Department of Life Science, University of NottinghamNottingham NG72RD, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar J.B. Power, J.B. Power 1Plant Genetic Manipulation Group, Department of Life Science, University of NottinghamNottingham NG72RD, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar N.W. Blackhall, N.W. Blackhall 1Plant Genetic Manipulation Group, Department of Life Science, University of NottinghamNottingham NG72RD, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar A.M.M. de Laat, A.M.M. de Laat 2Department of Biotechnology, Van der Have ResearchNL-4410 AA Rilland, PO Box 1, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar M.R. Davey M.R. Davey 3 1Plant Genetic Manipulation Group, Department of Life Science, University of NottinghamNottingham NG72RD, UK 1To whom correspondence should be addressed. Fax: +44 602 513251 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Experimental Botany, Volume 45, Issue 10, October 1994, Pages 1441–1449, https://doi.org/10.1093/jxb/45.10.1441 Published: 01 October 1994 Article history Accepted: 20 June 1994 Published: 01 October 1994 Received: 20 December 1994
RELT, a new member of the tumor necrosis factor receptor superfamily, is selectively expressed in hematopoietic tissues and activates transcription factor NF-κB (2001)

The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the "guardians of the immune system" due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis). This study reports the cloning of a new member of the TNFR superfamily, RELT (Receptor Expressed in Lymphoid Tissues). RELT is a type I transmembrane glycoprotein with a cysteine-rich extracellular domain, possessing significant homology to other members of the TNFR superfamily, especially TNFRSF19, DR3, OX40, and LTbeta receptor. The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1. Although the soluble form of RELT fusion protein does not inhibit the one-way mixed lymphocyte reaction, immobilized RELT is capable of costimulating T-cell proliferation in the presence of CD3 signaling. These results define a new member of the TNFR superfamily that may be a potential regulator of immune responses.
Free and Liposome-Encapsulated Double-Stranded RNAs as Inducers of Interferon, Interleukin-6, and Cellular Toxicity (1991)

Poly(rI:rC) and Ampligen were entrapped in liposomes that were covalently coupled to Protein A, permitting binding to antibodies specific for the major histocompatibility complex-encoded H2K molecule of L929 cells, or to control antibodies. Free and encapsulated polynucleotides were compared for their capacity to stimulate secretion of interferon (IFN) and interleukin-6 (IL-6) and to induce cellular toxicity on L929 cells pretreated with IFN-alpha/beta. Free and encapsulated poly(rI:rC) or Ampligen (poly(rI:rC12-rU] induced similar levels of secretion of IFN over a broad dose range. The activity of the liposome-encapsulated polynucleotides was dependent on its binding to an antibody that permitted cell association and internalization; the same liposomes were inactive in the presence of control antibodies. IL-6 secretion was induced by double-stranded (ds) RNA in a dose-dependent manner, with a significantly greater effect seen for targeted, liposome-encapsulated material. The marked toxicity of targeted poly(rI:rC), as compared to free poly(rI:rC), was confirmed. Encapsulated Ampligen was less toxic than encapsulated Poly(rI:rC).
Severe Sepsis and Septic Shock (2013)

epsis is one of the oldest and most elusive syndromes in medicine. Hippocrates claimed that sepsis ( ) was the process by which flesh rots, swamps generate foul airs, and wounds fester. However, with the advent of modern antibiotics, germ theory did not fully explain the pathogenesis of sepsis: many patients with sepsis died despite successful eradication of the inciting pathogen. Thus, researchers suggested that it was the host, not the germ, that drove the pathogenesis of sepsis. n 1992, an international consensus panel defined sepsis as a systemic inflammatory response to infection, noting that sepsis could arise in response to multiple infectious causes and that septicemia was neither a necessary condition nor a helpful term. Instead, the panel proposed the term "severe sepsis" to describe instances in which sepsis is complicated by acute organ dysfunction, and they codified "septic shock" as sepsis complicated by either hypotension that is refractory to fluid resuscitation or by hyperlactatemia. In 2003, a second consensus panel endorsed most of these concepts, with the caveat that signs of a systemic inflammatory response, such as tachycardia or an elevated white-cell count, occur in many infectious and noninfectious conditions and therefore are not helpful in distinguishing sepsis from other conditions. 5 Thus, "severe sepsis" and "sepsis" are sometimes used interchangeably to describe the syndrome of infection complicated by acute organ dysfunction.
Price Discovery and Learning during the Preopening Period in the Paris Bourse (1999)

Before the opening of the Paris Bourse, traders place orders and indicative prices are set. This offers a laboratory to study empirically the tâtonnement process through which markets discover equilibrium prices. Since preopening orders can be revised or canceled before the opening, indicative prices could be noise. We test this against the hypothesis that preopening prices reflect learning.Early in the preopening the noise hypothesis is not rejected. As the opening gets closer, the informational content and efficiency of prices increase and the learning hypothesis is not rejected. We also propose a GMM‐based estimate of the speed of learning.
Functional Replacement of Cytokine Receptor Extracellular Domains by Leucine Zippers (1996)

Granulocyte-macrophage colony-stimulating factor receptor signals by a complex which includes the ligand and two different receptor subunits: a low affinity alpha receptor binding chain (granulocyte-macrophage colony-stimulating factor receptor alpha subunit (GM-Ralpha)) and a signal-transducing beta chain (GM-Rbeta). To investigate two unresolved issues in the initiation of signaling, the role of receptor extracellular domains and receptor stoichiometry, we replaced the mouse GM-Ralpha and GM-Rbeta extracellular domains with the leucine zipper domain of either the Fos or Jun molecule. We co-transfected combinations of chimeric receptors into Ba/F3 cells and found that both simple heterodimers of the GM-Ralpha and GM-Rbeta intracellular domains and homodimers of the GM-Rbeta intracellular domain signaled for proliferation. Surprisingly, homodimers of the GM-Ralpha intracellular domain also signaled for prevention of apoptosis in transfected cells. We similarly engineered dimers of the intracellular domain of the human interferon gamma receptor beta subunit and found that homodimers of the intracellular domain signaled for proliferation. When Fos peptide was added to Ba/F3 cells expressing the human interferon gamma receptor beta subunit construct, thereby preventing homodimer formation, the cells no longer proliferated in the absence of mouse interleukin 3.
A Molecular Screening Approach to Identify and Characterize Inhibitors of Glioblastoma Stem Cells (2011)

Glioblastoma (GBM) is among the most lethal of all cancers. GBM consist of a heterogeneous population of tumor cells among which a tumor-initiating and treatment-resistant subpopulation, here termed GBM stem cells, have been identified as primary therapeutic targets. Here, we describe a high-throughput small molecule screening approach that enables the identification and characterization of chemical compounds that are effective against GBM stem cells. The paradigm uses a tissue culture model to enrich for GBM stem cells derived from human GBM resections and combines a phenotype-based screen with gene target-specific screens for compound identification. We used 31,624 small molecules from 7 chemical libraries that we characterized and ranked based on their effect on a panel of GBM stem cell-enriched cultures and their effect on the expression of a module of genes whose expression negatively correlates with clinical outcome: MELK, ASPM, TOP2A, and FOXM1b. Of the 11 compounds meeting criteria for exerting differential effects across cell types used, 4 compounds showed selectivity by inhibiting multiple GBM stem cells-enriched cultures compared with nonenriched cultures: emetine, n-arachidonoyl dopamine, n-oleoyldopamine (OLDA), and n-palmitoyl dopamine. ChemBridge compounds #5560509 and #5256360 inhibited the expression of the 4 mitotic module genes. OLDA, emetine, and compounds #5560509 and #5256360 were chosen for more detailed study and inhibited GBM stem cells in self-renewal assays in vitro and in a xenograft model in vivo. These studies show that our screening strategy provides potential candidates and a blueprint for lead compound identification in larger scale screens or screens involving other cancer types.
Overactive bladder syndrome - management and treatment options. (2012)

Overactive bladder syndrome can have a significant effect on quality of life, and affects 12-17% of the population. Prevalence increases with age. The management of overactive bladder syndrome involves exclusion of underlying pathology. First line treatment includes lifestyle interventions, pelvic floor exercises, bladder training and antimuscarinic agents. Failure of conservative management necessitates urology referral. Second line therapies are more invasive, and include botulinum toxin, neuromodulation or surgical interventions such as augmentation cystoplasty or urinary diversion.
A Canadian Working Group Report on Fecal Microbial Therapy: Microbial Ecosystems Therapeutics (2012)

A working group from across Canada comprised of clinician and basic scientists, epidemiologists, ethicists, Health Canada regulatory authorities and representatives of major funding agencies (Canadian Institutes of Health Research and the Crohn's and Colitis Foundation of Canada) met to review the current experience with fecal microbial therapy and to identify the key areas of study required to move this field forward. The report highlights the promise of fecal microbial therapy and related synthetic stool therapy (together called 'microbial ecosystems therapeutics') for the treatment of Clostridium difficile colitis and, possibly, other disorders. It identifies pressing clinical issues that need to be addressed as well as social, ethical and regulatory barriers to the use of these important therapies.
Efficient and Selective Gene Transfer into Primary Human Brain Tumors by Using Single-Chain Antibody-Targeted Adenoviral Vectors with Native Tropism Abolished (2002)

The application of adenoviral vectors in cancer gene therapy is hampered by low receptor expression on tumor cells and high receptor expression on normal epithelial cells. Targeting adenoviral vectors toward tumor cells may improve cancer gene therapy procedures by providing augmented tumor transduction and decreased toxicity to normal tissues. Targeting requires both the complete abolition of native tropism and the addition of a new specific binding ligand onto the viral capsid. Here we accomplished this by using doubly ablated adenoviral vectors, lacking coxsackievirus-adenovirus receptor and alpha(v) integrin binding capacities, together with bispecific single-chain antibodies targeted toward human epidermal growth factor receptor (EGFR) or the epithelial cell adhesion molecule. These vectors efficiently and selectively targeted both alternative receptors on the surface of human cancer cells. Targeted doubly ablated adenoviral vectors were also very efficient and specific with primary human tumor specimens. With primary glioma cell cultures, EGFR targeting augmented the median gene transfer efficiency of doubly ablated adenoviral vectors 123-fold. Moreover, EGFR-targeted doubly ablated vectors were selective for human brain tumors versus the surrounding normal brain tissue. They transduced organotypic glioma and meningioma spheroids with efficiencies similar to those of native adenoviral vectors, while exhibiting greater-than-10-fold-reduced background levels on normal brain explants from the same patients. As a result, EGFR-targeted doubly ablated adenoviral vectors had a 5- to 38-fold-improved tumor-to-normal brain targeting index compared to native vectors. Hence, single-chain targeted doubly ablated adenoviral vectors are promising tools for cancer gene therapy. They should provide an improved therapeutic index with efficient tumor transduction and effective protection of normal tissue.
Immobilization of individual cells by local photo-polymerization on a chip (2005)

A novel separation method for random screening of target cells from a large heterogeneous population by using a local photo-polymerization is developed. A photo-crosslinkable resin solution is mixed with the sample liquid and we controlled the state from sol to gel by irradiating the near ultraviolet (UV) light with the mercury lamp and He-Cd laser near the target cell. We applied three types of immobilization methods such as direct immobilization method, caging method, and direct immobilization with position control method. The selected cell is immobilized in the cured resin directly or inside the cage of the cured resin. In the position control method, laser tweezers are employed to manipulate the target cell indirectly by using the droplet of the resin as a microtool. The cell is positioned properly by the laser manipulation system and is immobilized in the polymerized resin. After the selected cells are immobilized we can easily remove the other objects by the cleaning flow in the microchannel since the polymerized resin strongly binds with the cover glass and resists more than 466 mm s(-1) flow speed in the microchannel (microchannel size: width is 500 micron and depth is 100 micron). We tested the mercury lamp as well as the He-Cd laser for UV-light irradiation at the local area and confirmed improvement of resolution of the cured area by using the He-Cd laser (from 7 micron to 5 micron). Based on this method, we succeeded in single cell immobilization and basic experiments such as culture and fluorescent dyeing of immobilized yeast cells.
1109 (2012)

Introduction: To evaluate the relatives perception of a strategy with no sedation. Hypothesis: A strategy with no sedation has been shown to reduce the length of mechanical ventilation, reduce ICU and total hospital length of stay (1). No study has investigated the relatives’ perception of levels of information provided, the relatives’ satisfaction with patient care and personal distress in relation to no sedation compared to a daily wake-up trial. Methods: In our original trial patients in need of mechanical ventilation were randomized to either a strategy with no sedation or standard treatment with sedation and daily interruption of sedatives. As a pilot study a questionnaire was send to the relatives after the patient was discharged from the ICU. The questionnaire consisted of 40 questions graded on a 5 point scale. The questions concerned: the information provided, the level of personal distress, and the overall satisfaction with the ICU. Results: In our pilot study 1/3 of the relatives to the 140 randomized received a questionnaire. 49 questionnaires were sent out and 36 were returned (73 %); 16 from the awake group and 20 from the sedated control group receiving a daily wake-up trial. Overall both groups of relatives graded their satisfaction with the ICU stay as good, and no difference was seen between the groups (p=0.38). Both groups rated the level of information received as rather high (P=0.05) and the treatment of the patient as very good (P=0.29). Relatives from both groups rated the degree of stress from seeing their loved ones in the ICU as moderate to high (p=0.27). Conclusions: In this questionnaire investigation of relatives to patients randomized to either no sedation or sedation, we found no difference between the groups with respect to overall satisfaction with the ICU, levels of information provided, and satisfaction with patient care. Relatives of patients who were awake did not experience a higher level of stress compared to relatives of sedated patients.(1) Strom T, Martinussen T, Toft P. A protocol of no sedation for critically ill patients receiving mechanical ventilation: a randomised trial. Lancet 2010 February 6;375(9713):475-80.
The molecular and cellular basis of olfactory-driven behavior inAnopheles gambiaelarvae (2008)

The mosquito Anopheles gambiae is the principal Afrotropical vector for human malaria. A central component of its vectorial capacity is the ability to maintain sufficient populations of adults. During both adult and preadult (larval) stages, the mosquitoes depend on the ability to recognize and respond to chemical cues that mediate feeding and survival. In this study, we used a behavioral assay to identify a range of odorant-specific responses of An. gambiae larvae that are dependent on the integrity of the larval antennae. Parallel molecular analyses have identified a subset of the An. gambiae odorant receptors (AgOrs) that are localized to discrete neurons within the larval antennae and facilitate odor-evoked responses in Xenopus oocytes that are consistent with the larval behavioral spectrum. These studies shed light on chemosensory-driven behaviors and represent molecular and cellular characterization of olfactory processes in mosquito larvae. These advances may ultimately enhance the development of vector control strategies, targeting olfactory pathways in larval-stage mosquitoes to reduce the catastrophic effects of malaria and other diseases.
Fan-beam and cone-beam image reconstruction via filtering the backprojection image of differentiated projection data (2004)

In this paper, a new image reconstruction scheme is presented based on Tuy's cone-beam inversion scheme and its fan-beam counterpart. It is demonstrated that Tuy's inversion scheme may be used to derive a new framework for fanbeam and cone-beam image reconstruction. In this new framework, images are reconstructed via filtering the backprojection image of differentiated projection data. The new framework is mathematically exact and is applicable to a general source trajectory provided the Tuy data sufficiency condition is satisfied. By choosing a piece-wise constant function for one of the components in the factorized weighting function, the filtering kernel is one dimensional, viz. the filtering process is along a straight line. Thus, the derived image reconstruction algorithm is mathematically exact and efficient. In the cone-beam case, the derived reconstruction algorithm is applicable to a large class of source trajectories where the pi-lines or the generalized pi-lines exist. In addition, the new reconstruction scheme survives the super-short scan mode in both the fan-beam and cone-beam cases provided the data are not transversely truncated. Numerical simulations were conducted to validate the new reconstruction scheme for the fan-beam case.
Stem cell niches in the adult mouse heart (2006)

Cardiac stem cells (CSCs) have been identified in the adult heart, but the microenvironment that protects the slow-cycling, undifferentiated, and self-renewing CSCs remains to be determined. We report that the myocardium possesses interstitial structures with the architectural organization of stem cell niches that harbor long-term BrdU-retaining cells. The recognition of long-term label-retaining cells provides functional evidence of resident CSCs in the myocardium, indicating that the heart is an organ regulated by a stem cell compartment. Cardiac niches contain CSCs and lineage-committed cells, which are connected to supporting cells represented by myocytes and fibroblasts. Connexins and cadherins form gap and adherens junctions at the interface of CSCs-lineage-committed cells and supporting cells. The undifferentiated state of CSCs is coupled with the expression of alpha(4)-integrin, which colocalizes with the alpha(2)-chain of laminin and fibronectin. CSCs divide symmetrically and asymmetrically, but asymmetric division predominates, and the replicating CSC gives rise to one daughter CSC and one daughter committed cell. By this mechanism of growth kinetics, the pool of primitive CSCs is preserved, and a myocyte progeny is generated together with endothelial and smooth muscle cells. Thus, CSCs regulate myocyte turnover that is heterogeneous across the heart, faster at the apex and atria, and slower at the base-midregion of the ventricle.
Tandem time-of-flight mass spectrometer (1993)

A compact, laser desorption tandem time-of-flight mass spectrometer is described. The instrument incorporates two dual-stage reflectron analyzers and a collision region for producing product ions by collision-induced dissociation. Selection of ions of a particular mass is accomplished by deflection of ions from stable trajectory angles entering the second reflectron, while the use of a pulsed valve for introduction of the collision gas obviates the need for differential pumping of the collision region. Initial results are presented, as well as a discussion for optimizing the performance of tandem time-of-flight instruments.