gebhart/patrepeval huggingface dataset:
Modification of Silicon Surfaces with  H 2 SO 4 :  H 2 O 2 :  HF  and  HNO 3 :  HF  for Wafer Bonding Applications (1996)

Two combinations of oxidizing and etching agents, and , have been used to modify silicon surfaces prior to wafer bonding. The chemical oxide thickness can be adjusted between 0 and 10 Å by tuning the HF content of the mixtures. Using x‐ray photoelectron spectroscopy it was found that the chemical composition of the surfaces can also be affected. Hydroxyl groups, fluorine, and hydrogen are terminating species that can be obtained by the described procedures. Both the described cleaning procedures permit hydrophilic bonding, giving a high room temperature bond strength with a minimum of interfacial oxide. The bond between a mainly fluorine‐terminated or a mainly OH terminated surface and a hydrogen‐terminated surface is no stronger than the bond between two hydrogen‐terminated surfaces.
Site-Specific Recombination Between Homologous Chromosomes in Drosophila (1991)

The ability to mark a cell and its descendants genetically so that the resulting cell clone can be distinguished from neighboring cells facilitates studies in animal biology and development. A method of generating clones by inducing homologous mitotic recombination in Drosophila with a site-specific yeast recombinase is described. This method allows for frequent mosaicism after mitotic exchange is induced at predefined sites in the genome.
2,3,7,8-Tetrachlorodibenzo-p-Dioxin and Related Halogenated Aromatic Hydrocarbons: Examination of the Mechanism of Toxicity (1982)

In this review, we have examined the biochemical and toxic responses produced by halogenated aromatic hydrocarbons and have tried to develop a model for their mechanism of action. These compounds bind to a cellular receptor and evoke a sustained pleiotropic response. In many tissues this response consists of the expression of a battery of enzymes which are, for the most part, involved in drug metabolism, but in other tissues, those which develop toxicity, an additional set of genes is expressed which effects cellular involution, division, and/or differentiation. The toxicity of these compounds appears to be due to the sustained expression of a normal cellular regulatory system, of which we were previously unaware. In future investigations it is hoped that we will learn the nature and physiologic role of this regulatory system. Only then can we hope to understand the mechanism of toxicity of these compounds.
BEC++: a software tool for increased flexibility in algorithm development (2003)

Sometimes, there is little interest by algorithm developers in creating a fixed-point simulation from a floating-point algorithm. However, often it is vital that high levels of speech quality be maintained in a fixed-point application. The process of converting floating-point simulations to fixed-point is time consuming, expensive, and if not done well, a state-of-the-art algorithm may never see product implementation. There is a critical need for software tools that reduce the time and effort that algorithm developers spend on floating-point to fixed-point software conversion. Bit-Exact C++ (BEC++) is just such a tool. This paper discusses a fixed-point software implementation tool, BEC++, with syntax similar in look and feel to that of floating-point C. Based on the ETSI Bit-Exact C (BEC) software now commonly used in industry, BEC++ extends the capabilities of BEC through the introduction of C++ language features and object-oriented techniques. This paper also details how to use the software, providing comparisons between BEC++ and BEC implementations.
Impaired functional activity of alveolar macrophages from GM-CSF-deficient mice (2001)

We hypothesized that pulmonary granulocyte-macrophage colony-stimulating factor (GM-CSF) is critically involved in determining the functional capabilities of alveolar macrophages (AM) for host defense. To test this hypothesis, cells were collected by lung lavage from GM-CSF mutant mice [GM(-/-)] and C57BL/6 wild-type mice. GM(-/-) mice yielded almost 4-fold more AM than wild-type mice. The percentage of cells positive for the beta(2)-integrins CD11a and CD11c was reduced significantly in GM(-/-) AM compared with wild-type cells, whereas expression of CD11b was similar in the two groups. The phagocytic activity of GM(-/-) AM for FITC-labeled microspheres was impaired significantly compared with that of wild-type AM both in vitro and in vivo (after intratracheal inoculation with FITC-labeled beads). Stimulated secretion of tumor necrosis factor-alpha (TNF-alpha) and leukotrienes by AM from the GM(-/-) mice was greatly reduced compared with wild-type AM, whereas secretion of monocyte chemoattractant protein-1 was increased. Transgenic expression of GM-CSF exclusively in the lungs of GM(-/-) mice resulted in AM with normal or supranormal expression of CD11a and CD11c, phagocytic activity, and TNF-alpha secretion. Thus, in the absence of GM-CSF, AM functional capabilities for host defense were significantly impaired but were restored by lung-specific expression of GM-CSF.
3D Nonlinear Super-Resolution Microwave Inversion Technique Using Time-Domain Data (2010)

A nonlinear three-dimensional full-wave inverse scattering method using time-domain data and models is presented. It successfully reconstructs 3D images of various unknown objects using time-domain data. The method uses Born-type iterations and a constrained minimization to reconstruct successively improved images. The use of time-domain data allows very few transmitters and receivers to be used. It is shown that this technique achieves super-resolution, namely 0.1 wavelength. The method is able to recover contrasts of over 2:1. It can also recover objects with minute contrasts of as low as 10%, thus taking a step towards addressing recent findings in the breast cancer imaging community, for example, that some breast tumors have only a 10% contrast with respect to the glandular tissues. This method could present a promising tool for the early-stage breast cancer detection as well as other medical and subsurface imaging applications.
Carbohydrate-remodelled acid α-glucosidase with higher affinity for the cation-independent mannose 6-phosphate receptor demonstrates improved delivery to muscles of Pompe mice (2005)

To enhance the delivery of rhGAA (recombinant GAA, where GAA stands for acid alpha-glucosidase) to the affected muscles in Pompe disease, the carbohydrate moieties on the enzyme were remodelled to exhibit a high affinity ligand for the CI-MPR (cation-independent M6P receptor, where M6P stands for mannose 6-phosphate). This was achieved by chemically conjugating on to rhGAA, a synthetic oligosaccharide ligand bearing M6P residues in the optimal configuration for binding the receptor. The carbonyl chemistry used resulted in the conjugation of approx. six synthetic ligands on to each enzyme. The resulting modified enzyme [neo-rhGAA (modified recombinant human GAA harbouring synthetic oligosaccharide ligands)] displayed near-normal specific activity and significantly increased affinity for the CI-MPR. However, binding to the mannose receptor was unaffected despite the introduction of additional mannose residues in neo-rhGAA. Uptake studies using L6 myoblasts showed neo-rhGAA was internalized approx. 20-fold more efficiently than the unmodified enzyme. Administration of neo-rhGAA into Pompe mice also resulted in greater clearance of glycogen from all the affected muscles when compared with the unmodified rhGAA. Comparable reductions in tissue glycogen levels in the Pompe mice were realized using an approx. 8-fold lower dose of neo-rhGAA in the heart and diaphragm and an approx. 4-fold lower dose in the skeletal muscles. Treatment of older Pompe mice, which are more refractory to enzyme therapy, with 40 mg/kg neo-rhGAA resulted in near-complete clearance of glycogen from all the affected muscles as opposed to only partial correction with the unmodified rhGAA. These results demonstrate that remodelling the carbohydrate of rhGAA to improve its affinity for the CI-MPR represents a feasible approach to enhance the efficacy of enzyme replacement therapy for Pompe disease.
Modeling familial Danish dementia in mice supports the concept of the amyloid hypothesis of Alzheimer's disease (2010)

Familial Danish dementia (FDD) is a progressive neurodegenerative disease with cerebral deposition of Dan-amyloid (ADan), neuroinflammation, and neurofibrillary tangles, hallmark characteristics remarkably similar to those in Alzheimer's disease (AD). We have generated transgenic (tg) mouse models of familial Danish dementia that exhibit the age-dependent deposition of ADan throughout the brain with associated amyloid angiopathy, microhemorrhage, neuritic dystrophy, and neuroinflammation. Tg mice are impaired in the Morris water maze and exhibit increased anxiety in the open field. When crossed with TauP301S tg mice, ADan accumulation promotes neurofibrillary lesions, in all aspects similar to the Tau lesions observed in crosses between beta-amyloid (Abeta)-depositing tg mice and TauP301S tg mice. Although these observations argue for shared mechanisms of downstream pathophysiology for the sequence-unrelated ADan and Abeta peptides, the lack of codeposition of the two peptides in crosses between ADan- and Abeta-depositing mice points also to distinguishing properties of the peptides. Our results support the concept of the amyloid hypothesis for AD and related dementias, and suggest that different proteins prone to amyloid formation can drive strikingly similar pathogenic pathways in the brain.
Organic Nanoparticles in the Aqueous Phase—Theory, Experiment, and Use (2001)

Many active organic compounds and organic effect materials are poorly soluble in water, or even insoluble. Aqueous forms of application thus require special formulation techniques to utilize or optimize the physiological (pharmaceuticals, cosmetics, plant protection, nutrition) or technical (varnishes, printing inks, toners) action. The most interesting properties of nanodispersions of active organic compounds and effect materials include the impressive increase in solubility, the improvement in biological resorption, and the modification of optical, electrooptical, and other physical properties which are achievable only with particle sizes in the middle or lower nanometer range (50-500 nm). Hence in addition to economic and ecological constraints there are also technical demands which appear to urgently require the development of new processes for the production of organic nanoparticles as alternatives to the established mechanical milling processes. In this context attention is drawn to the recent increase in research activities which have as their objective the continuous, automatic preparation of nanodispersed systems by precipitation from molecular solution. In this review the current state of knowledge of the fundamentals of particle formation from homogeneous solution and the effect of solvent and polymer additives on the morphology and supramolecular structure of the nanoparticle will be discussed. The practical implementation of this new formulation technology will be explored in detail for the carotenoids, a class of compounds of both physiological and technical interest.
Phosphodiesterase 1B Knock-Out Mice Exhibit Exaggerated Locomotor Hyperactivity and DARPP-32 Phosphorylation in Response to Dopamine Agonists and Display Impaired Spatial Learning (2002)

Using homologous recombination, we generated mice lacking phosphodiesterase-mediated (PDE1B) cyclic nucleotide-hydrolyzing activity. PDE1B(-/-) mice showed exaggerated hyperactivity after acute D-methamphetamine administration. Striatal slices from PDE1B(-/-) mice exhibited increased levels of phospho-Thr34 DARPP-32 and phospho-Ser845 GluR1 after dopamine D1 receptor agonist or forskolin stimulation. PDE1B(-/-) and PDE1B(+/-) mice demonstrated Morris maze spatial-learning deficits. These results indicate that enhancement of cyclic nucleotide signaling by inactivation of PDE1B-mediated cyclic nucleotide hydrolysis plays a significant role in dopaminergic function through the DARPP-32 and related transduction pathways.
Mechanisms of action of aminoglycoside antibiotics in eucaryotic protein synthesis (1984)

Tetrahymena thermophila is a eucaryotic organism that is highly susceptible to growth inhibition by aminoglycoside antibiotics. Concentrations of paromomycin, gentamicin G418, and hygromycin B at 22, 10, and 17 microM, respectively, inhibited growth by 50%. A combination of in vitro and in vivo methods was used to determine the mechanisms of action of these aminoglycoside antibiotics on protein synthesis in T. thermophila. Analysis of polysome profiles from paromomycin- and gentamicin G418-treated cells showed clear, progressive depletions of polysomes concomitant with an inhibition of in vivo [14C] lysine incorporation. In vitro, paromomycin and gentamicin G418, which are disubstituted 2-deoxystreptamine-containing molecules, were not very effective inhibitors of either the translocation of peptidyl-tRNA or the elongation of nascent polypeptide chains on polysomes. In contrast, we found that the translocation of phe-tRNA on polyuridylate programmed ribosomes was susceptible to inhibition by paromomycin. We conclude that the primary inhibitory action of paromomycin and gentamicin G418 was at (i) an early stage of elongation after initiation, (ii) the initiation stage of translation, or (iii) a stage of translation before initiation. Hygromycin B, which is a monosubstituted 2-deoxystreptamine-containing aminoglycoside, potently inhibited the elongation of nascent chains during the translation of polysomes. In addition, the in vitro translation of polysomes from two hygromycin B-resistant mutants was resistant to the inhibition of elongation caused by hygromycin B.
Catalytic Pauson−Khand-Type Reaction Using Aldehydes as a CO Source (2002)

[reaction: see text]. Rhodium complex-catalyzed carbonylative alkene-alkyne coupling proceeds using aldehydes as a CO source. Cinnamaldehyde is the best CO donor, and various cyclopentenones were provided in high isolated yields by a solvent-free system.
Postgraduate Diploma in Management (1990)

In response to the de-engineering of senior management posts in engineering organisations, the Association of Professional Engineers, Australia, decided that the most effective way to combat the de-engineering phenomenon was to encourage Professional Engineers to acquire skills in a range of non-technical disciplines as a means of enhancing their managerial capabilities. After extensive market research, the Association launched a distance education Postgraduate Diploma in Management in February 1989. The Postgraduate Diploma in Management currently has in excess of 1200 enrolments from over 400 separate organisations in Australia and overseas. The program is now fully accredited and is expected to be a major factor in the resurgence of Professional Engineers in leadership positions in their organisations.
CLP-36 PDZ-LIM Protein Associates with Nonmuscle α-Actinin-1 and α-Actinin-4 (2000)

The PDZ-LIM family of proteins (Enigma/LMP-1, ENH, ZASP/Cypher, RIL, ALP, and CLP-36) has been suggested to act as adapters that direct LIM-binding proteins to the cytoskeleton. Most interactions of PDZ-LIM proteins with the cytoskeleton have been identified in striated muscle, where several PDZ-LIM proteins are predominantly expressed. By contrast, CLP-36 mRNA is expressed in several nonmuscle tissues, and here we demonstrate high expression of CLP-36 in epithelial cells by in situ hybridization analysis. Our subcellular localization studies indicate that in nonmuscle cells, CLP-36 protein localizes to actin stress fibers. This localization is mediated via the PDZ domain of CLP-36 that associates with the spectrin-like repeats of alpha-actinin. Interestingly, immunoprecipitation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis indicate that both nonmuscle alpha-actinin-1 and alpha-actinin-4 form complexes with CLP-36. The high expression of alpha-actinin-4 in the colon, together with these results, suggests a specific function for the alpha-actinin-4-CLP-36 complex in the colonic epithelium. More generally, results presented here demonstrate that the association of PDZ-LIM proteins with the cytoskeleton extends to the actin stress fibers of nonmuscle cells.
DNN Dataflow Choice Is Overrated. (2018)

Many DNN accelerators have been proposed and built using different microarchitectures and program mappings. To fairly compare these different approaches, we modified the Halide compiler to produce hardware as well as CPU and GPU code, and show that Halide's existing scheduling language has enough power to represent all existing dense DNN accelerators. Using this system we can show that the specific dataflow chosen for the accelerator is not critical to achieve good efficiency: many different dataflows yield similar energy efficiency with good performance. However, finding the best blocking and resource allocation is critical, and we achieve a 2.6X energy savings over Eyeriss system by reducing the size of the local register file. Adding an additional level in the memory hierarchy saves an additional 25%. Based on these observations, we develop an optimizer that automatically finds the optimal blocking and storage hierarchy. Compared with Eyeriss system, it achieves up to 4.2X energy improvement for Convolutional Neural Networks (CNNs), 1.6X and 1.8X improvement for Long Short-Term Memories (LSTMs) and multi-layer perceptrons (MLPs) respectively.
Diagnosis and Management of the Metabolic Syndrome (2005)

The metabolic syndrome has received increased attention in the past few years. This statement from the American Heart Association (AHA) and the National Heart, Lung, and Blood Institute (NHLBI) is intended to provide up-to-date guidance for professionals on the diagnosis and management of the metabolic syndrome in adults.

The metabolic syndrome is a constellation of interrelated risk factors of metabolic origin— metabolic risk factors —that appear to directly promote the development of atherosclerotic cardiovascular disease (ASCVD).1 Patients with the metabolic syndrome also are at increased risk for developing type 2 diabetes mellitus. Another set of conditions, the underlying risk factors , give rise to the metabolic risk factors. In the past few years, several expert groups have attempted to set forth simple diagnostic criteria to be used in clinical practice to identify patients who manifest the multiple components of the metabolic syndrome. These criteria have varied somewhat in specific elements, but in general they include a combination of both underlying and metabolic risk factors.

The most widely recognized of the metabolic risk factors are atherogenic dyslipidemia, elevated blood pressure, and elevated plasma glucose. Individuals with these characteristics commonly manifest a prothrombotic state and a pro-inflammatory state as well. Atherogenic dyslipidemia consists of an aggregation of lipoprotein abnormalities including elevated serum triglyceride and apolipoprotein B (apoB), increased small LDL particles, and a reduced level of HDL cholesterol (HDL-C). The metabolic syndrome is often referred to as if it were a discrete entity with a single cause. Available data suggest that it truly is a syndrome, ie, a grouping of ASCVD risk factors, but one that probably has more than one cause. Regardless of cause, the syndrome identifies individuals at an elevated risk for ASCVD. The magnitude of the increased risk can vary according to which components of the syndrome are …
A randomized controlled trial of the efficacy of orally administered fluralaner (Bravecto™) against induced Ixodes holocyclus (Australian paralysis tick) infestations on dogs (2015)

Oral fluralaner treatment can prevent Australian paralysis tick infestations for at least 115 days.
Infection of honey bees with acute bee paralysis virus does not trigger humoral or cellular immune responses (2012)

We have studied the responses of honey bees at different life stages (Apis mellifera) to controlled infection with acute bee paralysis virus and have identified the haemolymph of infected larvae and adult worker bees as the compartment where massive propagation of ABPV occurs. Insects respond with a broad spectrum of induced innate immune reactions to bacterial infections, whereas defence mechanisms based on RNA interference play a major role in antiviral immunity. In this study, we have determined that honey bee larvae and adult workers do not produce a humoral immune reaction upon artificial infection with ABPV, in contrast to control individuals challenged with Escherichia coli. ABPV-infected bees produced neither elevated levels of specific antimicrobial peptides (AMPs), such as hymenoptaecin and defensin, nor any general antimicrobial activity, as revealed by inhibition-zone assays. Additionally, adult bees did not generate melanised nodules upon ABPV infection, an important cellular immune function activated by bacteria and viruses in some insects. Challenge of bees with both ABPV and E. coli showed that innate humoral and cellular immune reactions are induced in mixed infections, albeit at a reduced level.
Targeting Bruton tyrosine kinase with ibrutinib in relapsed/refractory marginal zone lymphoma (2017)

Marginal zone lymphoma (MZL) is a heterogeneous B-cell malignancy for which no standard treatment exists. MZL is frequently linked to chronic infection, which may induce B-cell receptor (BCR) signaling, resulting in aberrant B-cell survival and proliferation. We conducted a multicenter, open-label, phase 2 study to evaluate the efficacy and safety of ibrutinib in previously treated MZL. Patients with histologically confirmed MZL of all subtypes who received ≥1 prior therapy with an anti-CD20 antibody-containing regimen were treated with 560 mg ibrutinib orally once daily until progression or unacceptable toxicity. The primary end point was independent review committee-assessed overall response rate (ORR) by 2007 International Working Group criteria. Among 63 enrolled patients, median age was 66 years (range, 30-92). Median number of prior systemic therapies was 2 (range, 1-9), and 63% received ≥1 prior chemoimmunotherapy. In 60 evaluable patients, ORR was 48% (95% confidence interval [CI], 35-62). With median follow-up of 19.4 months, median duration of response was not reached (95% CI, 16.7 to not estimable), and median progression-free survival was 14.2 months (95% CI, 8.3 to not estimable). Grade ≥3 adverse events (AEs; >5%) included anemia, pneumonia, and fatigue. Serious AEs of any grade occurred in 44%, with grade 3-4 pneumonia being the most common (8%). Rates of discontinuation and dose reductions due to AEs were 17% and 10%, respectively. Single-agent ibrutinib induced durable responses with a favorable benefit-risk profile in patients with previously treated MZL, confirming the role of BCR signaling in this malignancy. As the only approved therapy, ibrutinib provides a treatment option without chemotherapy for MZL. This study is registered at www.clinicaltrials.gov as #NCT01980628.