gebhart/patrepeval huggingface dataset:
Escapes of fishes from Norwegian sea-cage aquaculture: causes, consequences and prevention (2010)

The escape of fish from aquaculture is perceived as a threat to wild fish populations. The escapes problem is largely caused by technical and operational failures of fish farming equipment. In Norway, 3.93 million Atlantic salmon Salmo salar, 0.98 million rainbow trout Oncorhynchus mykiss and 1.05 million Atlantic cod Gadus morhua escaped from 2001 to 2009. Salmonids primarily escape after structural failures of containment equipment, while a far greater percentage of cod than salmon escape through holes in the nets. Correlative evidence suggests that after the Norwegian technical standard (NS 9415) for sea-cage farms took effect in 2004, the total number of escaped Atlantic salmon declined from > 600 000 (2001 to 2006) to < 200 000 fish yr -1 (2007 to 2009), despite the total number of salmon held in sea-cages increasing by 44% during this period. No similar decrease in escaped cod has occurred, suggesting that other measures, such as improved netting materials for sea-cages, are required. In addition to escaping as juveniles or adults, cod may reproduce in seacages, and thus fertilised eggs escape to the environment. The ecological effects of 'escape through spawning' are unclear, and methods to inhibit escape by this mechanism are being explored. To prevent escapes of juvenile and adult fish as sea-cage aquaculture industries develop, we recommend that policy-makers implement a 5 component strategy: (1) establish mandatory reporting of all escape incidents; (2) establish a mechanism to analyse and learn from the mandatory reporting; (3) conduct mandatory, rapid, technical assessments to determine the causes of escape incidents involving more than 10 000 fish; (4) introduce a technical standard for sea-cage aquaculture equipment coupled with an independent mechanism to enforce the standard; and (5) conduct mandatory training of fish farm staff in escape-critical operations and techniques.
Task-Robust Model-Agnostic Meta-Learning (2020)

Meta-learning methods have shown an impressive ability to train models that rapidly learn new tasks. However, these methods only aim to perform well in expectation over tasks coming from some particular distribution that is typically equivalent across meta-training and meta-testing, rather than considering worst-case task performance. In this work we introduce the notion of task-robustness by reformulating the popular Model-Agnostic Meta-Learning (MAML) objective [Finn et al. 2017] such that the goal is to minimize the maximum loss over the observed meta-training tasks. The solution to this novel formulation is task-robust in the sense that it places equal importance on even the most difficult and/or rare tasks. This also means that it performs well over all distributions of the observed tasks, making it robust to shifts in the task distribution between meta-training and meta-testing. We present an algorithm to solve the proposed min-max problem, and show that it converges to an $\epsilon$-accurate point at the optimal rate of $\mathcal{O}(1/\epsilon^2)$ in the convex setting and to an $(\epsilon, \delta)$-stationary point at the rate of $\mathcal{O}(\max\{1/\epsilon^5, 1/\delta^5\})$ in nonconvex settings. We also provide an upper bound on the new task generalization error that captures the advantage of minimizing the worst-case task loss, and demonstrate this advantage in sinusoid regression and image classification experiments.
Near-field photonics: tip-enhanced microscopy and spectroscopy on the nanoscale (2006)

Any detailed study of the interaction of electromagnetic radiation with nanoscale systems is limited by diffraction effects in classical optical systems. Near-field microscopy extends conventional imaging beyond this self-imposed barrier and is used to perform microscopy and spectroscopy with ultra-high spatial resolution. In this article we will discuss the use of the enhanced electric field created at the apex of a sharp laser-irradiated metal tip as a means of producing a truly nanoscale light source. This confined light source can be used to excite locally vibrational modes along carbon nanotubes or to investigate surface charge oscillations in optically resonant nanoparticles. We report the use of such a technique to demonstrate localized photofluorescence and Raman imaging with sub 20 nm spatial resolution.
Next-generation sequencing reveals cryptic Symbiodinium diversity within Orbicella faveolata and Orbicella franksi at the Flower Garden Banks, Gulf of Mexico (2014)

The genetic composition of the resident Symbiodinium endosymbionts appears to strongly modulate the physiological performance of reef-building corals. Here, we used deep amplicon sequencing to quantitatively assess Symbiodinium genetic diversity for the two mountainous star corals, Orbicella franksi and Orbicella faveolata , from two reefs separated by 19 kilometers of deep water. We aimed to determine if symbiont diversity is largely partitioned with respect to coral host species or geographic location. Our results demonstrate that across the two reefs both coral species contained only Symbiodinium identifiable as clade B type B1, represented by five distinct haplotypes. Three of these haplotypes have not been previously described and may be endemic to the Flower Garden Banks. No consistent differences in symbiont composition were detected between the two coral species. However, significant quantitative differences were observed between the east and west banks for two of the five haplotypes. These results highlight the need for consistent molecular genotyping techniques to assess local community assemblages of Symbiodinium -host relationships, which could be largely irrespective of host genetic background. This deep-sequencing approach used to sensitively characterize cryptic genetic diversity of Symbiodinium will potentially contribute to the understanding of physiological variations among coral populations.
Reduction of T Lymphoma Cells and Immunological Invigoration in a Patient Concurrently Affected by Melanoma and Sezary Syndrome Treated With Nivolumab (2020)

Despite the recent availability of several new drugs in hemato-oncology, T-cell lymphomas are still incurable and PD-1 blockade could represent a therapeutic chance for selected patients affected by these malignancies, although further studies are required to understand the biological effects of anti-PD-1 mAbs on neoplastic T-cells and to identify biomarkers for predicting and/or monitoring patients' response to therapy. Sezary Syndrome (SS) represents a rare and aggressive variant of cutaneous T cell lymphoma (CTCL) with a life expectancy of less than 5 years, characterized by the co-presence of neoplastic lymphocytes mainly in the blood, lymph nodes and skin. In this study we analyzed longitudinal blood samples and lesional skin biopsies of a patient concurrently affected by SS and melanoma who underwent 22 nivolumab administrations. In blood, we observed a progressive reduction of SS cell number and a raise in the percentage of normal CD4+ and CD8+ T cells and NK cells over total leukocytes. Eight weeks from the start of nivolumab, these immune cell subsets showed an increase of Ki67 proliferation index that positively correlated with their PD-1 expression. Conversely, SS cells displayed a strong reduction of Ki67 positivity despite their high PD-1 expression. On skin biopsies we observed a marked reduction of SS cells which were no more detectable at the end of therapy. We also found an increase in the percentage of normal CD4+ T cells with a concomitant decrease of that of CD8+ and CD4+ CD8+ T cells, two cell subsets that, however, acquired a cytotoxic phenotype. In summary, our study demonstrated that nivolumab marked reduced SS tumor burden and invigorated immune responses in our patient. Our data also suggest, for the first time, that Ki67 expression in circulating neoplastic and immune cell subsets, as well as an enrichment in T cells with a cytotoxic phenotype in lesional skin could be valuable markers to assess early on treatment SS patients' response to PD-1 blockade, a therapeutic strategy under clinical investigation in CTCL (ClinicalTrials.gov NCT03385226, NCT04118868).
New Saddle Trajectories for CT (2006)

The geometrical properties of saddle-trajectories are studied based on the requirements of possible CT reconstruction algorithms. Besides the standard saddle we introduce the so-called high-frequency saddle. The study focuses on Pi-lines. First, we illustrate the volume, which is covered by Pi-lines. Furthermore, we discuss, how the number of Pi-lines varies over the volume of object-points, and we analyze the detector utilization of a saddle-scan.
Chemistry of 1,6‐diazaphenalene. Reaction with alkylating and acylating agents (1982)

Abstract A study of the reactivity of 1,6‐diazaphenalene ( 1 ) toward alkylating and acylating agents has been carried out in order to investigate the chemistry of this new heterocycle. Attempts to alkylate 1 were successfully completed by stirring the lithium stabilized anion of 1 with either methyl iodide or benzyl bromide to provide N ‐alkyldiazaphenalenes 4 and 5, respectively, whereas, experiments performed to alkylate 1 under conditions employed for alkylation of imidazole were unsuccessful. Studies directed toward acylation of 1 did not lead, in general, to isolable acyldiazaphenalenes; however, in one specific case successful acylation of 2‐chloro‐9‐methoxy‐1,6‐diazaphenalene ( 10 ) did provide a characterisable amide ( 14 ). Where possible the chemistry of 1,6‐diazaphenalene has been compared to that reported for imidazole.
Efficient Hydroxymethylation Reactions of Iodoarenes Using CO and 1,3-Dimethylimidazol-2-ylidene Borane (2013)

A hydroxymethylation reaction of a variety of iodoarenes proceeded effectively in the presence of CO, NHC-borane, diMeImd-BH3 (2) as a radical mediator, and a catalytic amount of AIBN. The reaction took place chemoselectively at the aryl-iodine bond but not at the aryl-bromine and aryl-chlorine bonds. A three-component coupling reaction comprising aryl iodides, CO, and electron-deficient alkenes also proceeded well to give unsymmetrical ketones in good yields. Control experiments show that 2 would act as a hydrogen donor to acyl radicals and iodinated NHC-borane as a reducing agent of aldehydes.
Simple Heat Treatment of Zirconia Ceramic Pre-Treated with Silane Primer to Improve Resin Bonding (2014)

Establishing a strong resin bond to dental zirconia ceramic remains difficult. Previous studies have shown that the conventional application of silane does not work well with zirconia. This paper reports that a silane pre-treatment of dental zirconia ceramic combined with subsequent heat treatment has potential as an adhesive cementation protocol for improving zirconia-resin bonding. Among the various concentrations (0.1 to 16 vol%) of experimental γ-methacryloxypropyltrimethoxysilane (γ-MPTS) primers assessed, the 1% solution was found to be the most effective in terms of the shear bond strength of the resin cement to dental zirconia ceramic. A high shear bond strength (approx. 30 MPa) was obtained when zirconia specimens were pre-treated with this primer and then heat-treated in a furnace for 60 min at 150 degrees C. Heat treatment appeared to remove the hydrophilic constituents from the silane film formed on the zirconia ceramic surface and accelerate the condensation reactions between the silanol groups of the hydrolyzed silane molecules at the zirconia/resin interface, finally making a more desirable surface for bonding with resin. This estimation was supported by Fourier transform infrared spectroscopy of the silanes prepared in this study.
Alkene-Directed, Nickel-Catalyzed Alkyne Coupling Reactions (2004)

In alkene-directed, nickel-catalyzed coupling reactions of 1,3-enynes with aldehydes and epoxides, the conjugated alkene dramatically enhances reactivity and uniformly directs regioselectivity, independent of the nature of the other alkyne substituent (aryl, alkyl (1 degrees , 2 degrees , 3 degrees )) or the degree of alkene substitution (mono-, di-, tri-, and tetrasubstituted). These observations are best explained by a temporary interaction between the alkene and the transition metal center during the regioselectivity-determining step. The highly substituted 1,3-diene products are useful in organic synthesis and, in conjunction with a Rh-catalyzed, site-selective hydrogenation, afford allylic and homoallylic alcohols that previously could not be prepared in high regioselectivity (or at all) with related Ni-catalyzed alkyne coupling reactions.
Imager Evaluation of Diabetic Retinopathy at the Time of Imaging in a Telemedicine Program (2012)

Appropriately trained imagers can accurately identify stDR at the time of imaging.
COLLECTIVE BEHAVIOR OF A COUPLED GYROSCOPE SYSTEM WITH COUPLING ALONG THE DRIVING- AND SENSING-MODES (2013)

A critical component of many Inertial Navigation Systems (INS) is the gyroscope — a device used for detecting rotation rates and orientation. Gyroscopes are subject to material imperfections and manufacturing defects, potentially reducing their ability to detect signals and to minimize phase drift. This manuscript explores the idea of performance enhancement by combining the input–output response of an ensemble of gyroscopes coupled bidirectionally, through the driving- and sensing-modes, in a ring fashion. Numerical simulations and bifurcation analysis via perturbation methods show the existence of a stable synchronization state in which all gyroscopes vibrate with the same phase and amplitude. In this state, the sum output of the sensing modes is significantly larger than any individual sensing mode, which leads to significant reductions in phase drift caused by material imperfections, fabrication variations, and system noise. Similarities and differences with respect to a system of gyroscopes coupled only along the driving-axis are discussed in great detail as well.
Evidence that intrarenal dopamine acts as a paracrine substance at the renal tubule (1989)

Dopamine is synthesized within the kidney and dopamine 1 (DA1) receptors are associated with the proximal tubule. In pharmacological doses, dopamine increases renal blood flow and sodium excretion. It is possible that dopamine formed intrarenally acts locally via renal dopamine receptors to control renal function. We investigated the possible paracrine action of renal dopamine by intrarenal administration of a specific DA1 antagonist, Sch 23390, in doses confined to the kidney in conscious uninephrectomized dogs (n = 5) in metabolic balance at a sodium intake of 40 meq/day. Changes (mean +/- SE) in renal excretory and hemodynamic function in response to cumulative infusions of several doses of Sch 23390 (0.01, 0.1, 1.0, 5.0, and 10.0 pmol.kg-1.min-1) were studied. Sch 23390 at 0.01 pmol.kg-1.min-1 did not cause any changes in urinary flow rate or sodium excretion. Sch 23390 in doses from 0.1 to 10.0 mol.kg-1.min-1 caused a significant dose-dependent antidiuresis (F = 44.9, P less than 0.0001) and antinatriuresis (F = 42.1, P less than 0.0001) and a decrease in fractional sodium excretion (F = 44.2, P less than 0.0001). No changes in estimated renal plasma flow, glomerular filtration rate, plasma aldosterone concentration, plasma renin activity, or systemic arterial pressure occurred with any dose of intrarenal Sch 23390 infused into the renal artery. Rebound diuresis and natriuresis occurred after cessation of the DA1 blockade.(ABSTRACT TRUNCATED AT 250 WORDS)
ASK1 contributes to fibrosis and dysfunction in models of kidney disease (2018)

Oxidative stress is an underlying component of acute and chronic kidney disease. Apoptosis signal-regulating kinase 1 (ASK1) is a widely expressed redox-sensitive serine threonine kinase that activates p38 and c-Jun N-terminal kinase (JNK) mitogen-activated protein kinase kinases, and induces apoptotic, inflammatory, and fibrotic signaling in settings of oxidative stress. We describe the discovery and characterization of a potent and selective small-molecule inhibitor of ASK1, GS-444217, and demonstrate the therapeutic potential of ASK1 inhibition to reduce kidney injury and fibrosis. Activation of the ASK1 pathway in glomerular and tubular compartments was confirmed in renal biopsies from patients with diabetic kidney disease (DKD) and was decreased by GS-444217 in several rodent models of kidney injury and fibrosis that collectively represented the hallmarks of DKD pathology. Treatment with GS-444217 reduced progressive inflammation and fibrosis in the kidney and halted glomerular filtration rate decline. Combination of GS-444217 with enalapril, an angiotensin-converting enzyme inhibitor, led to a greater reduction in proteinuria and regression of glomerulosclerosis. These results identify ASK1 as an important target for renal disease and support the clinical development of an ASK1 inhibitor for the treatment of DKD.
A Hybrid Silicon/InP Integrated Feedback Stabilized Mode-Locked Laser (2014)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text M. L. Davenport, S. Srinivasan, M. J. R. Heck, and J. E. Bowers, "A Hybrid Silicon/InP Integrated Feedback Stabilized Mode-Locked Laser," in Optical Fiber Communication Conference, OSA Technical Digest (online) (Optica Publishing Group, 2014), paper Th3A.5. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
A Dual-Gate Complementary Metal-Oxide-Semiconductor Technology with Novel Self-Aligned Pocket Implantation which Takes Advantage of Elevated Source/Drain Configurations (2001)

A dual-gate complementary metal-oxide-semiconductor technology with novel self-aligned pocket implantation is demonstrated which takes advantage of the elevated source/drain (S/D) configurations. Using the present procedure, S/D junction capacitance and leakage current were significantly suppressed for p-channel metal-oxide-semiconductor field-effect-transistors (MOSFETs) as well as for n-channel MOSFETs without degradation of the short channel characteristics. These results are interpreted in terms of the fact that the pocket impurity profiles shift to the upper positions in the deep S/D regions, though the impurity distribution at the gate edges was hardly varied. Furthermore, the suppression effects were more marked for a higher pocket implantation dosage, which will be required to suppress the short channel effects in future MOSFETs. In addition, improvement of drivability due to the reduction of the parasitic S/D resistance, an original benefit of the elevated S/D engineering, is maintained by the present technique. The present self-aligned pocket procedure is very promising as a key technology beyond the 0.1 µm node.
Design of Effective Primary MicroRNA Mimics With Different Basal Stem Conformations (2016)

Primary microRNA (pri-miRNA) mimics are important mediators of effective gene silencing and are well suited for sustained therapeutic applications. Pri-miRNA mimics are processed in the endogenous miRNA biogenesis pathway, where elements of the secondary RNA structure are crucial for efficient miRNA production. Cleavage of the pri-miRNA to a precursor miRNA (pre-miRNA) by Drosha-DGCR8 typically occurs adjacent to a basal stem of ~11 bp. However, a number of pri-miRNA structures are expected to contain slightly shorter or longer basal stems, which may be further disrupted in predicted folding of the expressed pri-miRNA sequence. We investigated the function and processing of natural and exogenous RNA guides from pri-miRNAs with various basal stems (9-13 bp), where a canonical hairpin was predicted to be well or poorly maintained in predicted structures of the expressed sequence. We have shown that RNA guides can be effectively derived from pri-miRNAs with various basal stem conformations, while predicted guide region stability can explain the function of pri-miRNA mimics, in agreement with previously proposed design principles. This study provides insight for the design of effective mimics based on naturally occurring pri-miRNAs and has identified several novel scaffolds suitable for use in gene silencing applications.
ChemInform Abstract: TRYPSIN INHIBITORS. I. SYNTHESIS OF PROTECTED PEPTIDES RELATED TO SEQUENCE 1‐10 OF PORCINE PANCREATIC SECRETORY TRYPSIN INHIBITOR II (KAZAL) (1976)

Abstract Die generelle Methode zur Synthese von Schweine‐PSTI II wird diskutiert.
The global transcriptional maturation program and stimuli-specific gene expression profiles of human myeloid dendritic cells (2003)

Dendritic cells (DC) are central to the immune response against invading pathogens. How DC translate different signals received from either other components of the immune system or from pathogens into a tailored immune response is not understood in detail. Using oligonucleotide microarray technology we performed a genome-wide analysis to investigate the transcriptional program in immature human monocyte-derived DC induced to mature with either CD40 ligand (CD40L), lipopolysaccharide (LPS) or a cocktail of inflammatory cytokines and prostaglandin (PG) E(2) (CyC). We identified elements of a sustained common response to LPS and CyC, as well as sets of transient and stimulus-specific gene expression changes. Interestingly, the transient LPS response as well as the sustained LPS-specific response included a high number of chemokines, suggesting that LPS stimulation of DC leads to enhanced recruitment of immune cells and potentially prolongs the immune response compared to an inflammatory signal mimicked by CyC. Of note, the core response common to both LPS and CyC comprised a high number of unknown genes as well as genes that have not been previously identified as part of the maturation response in DC. Since some of these genes have down-regulatory functions in other settings, they may have a regulatory role in DC maturation and immune response generation.
Extracellular Histones Trigger Disseminated Intravascular Coagulation by Lytic Cell Death (2022)

Histones are cationic nuclear proteins that are essential for the structure and functions of eukaryotic chromatin. However, extracellular histones trigger inflammatory responses and contribute to death in sepsis by unknown mechanisms. We recently reported that inflammasome activation and pyroptosis trigger coagulation activation through a tissue-factor (TF)-dependent mechanism. We used a combination of various deficient mice to elucidate the molecular mechanism of histone-induced coagulation. We showed that histones trigger coagulation activation in vivo, as evidenced by coagulation parameters and fibrin deposition in tissues. However, histone-induced coagulopathy was neither dependent on intracellular inflammasome pathways involving caspase 1/11 and gasdermin D (GSDMD), nor on cell surface receptor TLR2- and TLR4-mediated host immune response, as the deficiency of these genes in mice did not protect against histone-induced coagulopathy. The incubation of histones with macrophages induced lytic cell death and phosphatidylserine (PS) exposure, which is required for TF activity, a key initiator of coagulation. The neutralization of TF diminished the histone-induced coagulation. Our findings revealed lytic cell death as a novel mechanism of histone-induced coagulation activation and thrombosis.
Mining the pre-diagnostic antibody repertoire of TgMMTV-neu mice to identify autoantibodies useful for the early detection of human breast cancer (2013)

Meeting abstracts Breast cancer has been shown to be immunogenic and can stimulate an antibody immune response. Because of this immunogenicity, identification of early breast tumor antigens could allow identification of autoantibodies for the early detection of breast cancer. In this study, the