gebhart/patrepeval huggingface dataset:
COD: Database / Operating System Co-Design (2013)

www.systems.ethz.ch Trends in multicore processors and hardware virtualization pose severe structural challenges to system software in general, and databases in particular. On the one hand, machines are becoming increasingly heterogeneous in terms of, i.e., cache hierarchies, processor interconnect, instruction sets, etc., thereby making it increasingly difficult to develop optimal software for all possible platforms. On the other hand, virtualization forces databases to share resources with other applications without the databases having any knowledge about the run-time conditions. As part of a long-term effort in our group to revisit the entire software stack of the data center, in this paper we explore how to enhance the interaction between databases and OS to allow the database better cope with varying hardware characteristics and runtime conditions. The goals is to integrate the database’s extensive internal knowledge of its own resource requirements –including cost models – into the system-wide and run-time view of the hardware configuration and application mix available inside the OS. 1.
Diagnostic accuracy between readers for identifying electrographic seizures in critically ill adults (2016)

Diagnosing electrographic seizures in critically ill adults is highly specific and moderately sensitive. Improved criteria for diagnosing electrographic seizures in the ICU are needed.
Characterization of the Subunits of the Flagella of Proteus vulgaris (1969)

Abstract A procedure is described for the purification of Proteus vulgaris flagellin. The purified protein is homogeneous on acrylamide gel electrophoresis under a variety of conditions and in the ultracentrifuge. The amino acid composition of the unmodified and oxidized flagellin is reported. The protein is totally lacking in half-cystine, histidine, and tryptophan. Molecular weight determinations, by sedimentation equilibrium in the presence of 6 m guanidine, tryptic maps, and the amino acid composition are all consistent with the conclusion that Proteus vulgaris flagellin consists of a polypeptide chain with a molecular weight of approximately 40,000. Alanine, recovered in a yield of 0.5 residue per mole of protein, was the sole amino-terminal residue, as determined by the cyanate method. The results obtained with this flagellin, in conjunction with data available on flagellins of other bacteria, lead to the conclusion that identical subunits, of about 40,000 molecular weight, having a similar number of basic residues, form the fundamental building block of bacterial flagella.
A double‐blind study with a new monodrug Kan Jang: Decrease of symptoms and improvement in the recovery from common colds (1995)

Abstract In a placebo‐controlled double‐blind study, the therapeutic effect of Kan Jang tablets made from Andrographis paniculata (Barm. F.) (Ness) dried extract was tested in patients with common colds. The patients were divided in two groups, in which group 1 ( n = 33) received 1200 mg of Andrographis paniculata and group 2 ( n = 28) a placebo (P). On day 3–4 after treatment the possible effect of Kan Jang tablets on selected symptoms and clinical signs of common cold was evaluated. A significant reduction in clinical symptoms at day 4 of administration of the Kan Jang tablets was observed. A better efficacy against the placebo is discussed. The differences in the total ‘sumscores’ of clinical and symptomatic findings indicate that the Kan Jang treated group did far better than the placebo group. We conclude that Kan Jang in a dose of 1200 mg daily has the capacity to significantly shorten the course/duration of the disease and therefore is indicated for an enhanced resistance to common colds.
Recent advances in PET imaging of folate receptor positive diseases (2014)

Folate receptor (FR) is overexpressed on a variety of cancers (FR-α) and on activated macrophages (FR-β), with limited or no expression on most normal cells.  This restricted distribution of FR to malignant and inflamed cell types has enabled the use of folic acid to deliver attached drugs selectively to associated pathologies, thereby avoiding unwanted the uptake and derived collateral toxicity to normal tissues. Folate-based radiotracers have also been found to serve as versatile agents for the diagnosis, staging, and prediction of response to therapy of patients with FR-expressing cancers and inflammatory/autoimmune diseases. In this review, we summarize the properties of 18 F-labeled folate conjugates that have undergone preclinical evaluation during the past decade.  The advantages and disadvantages of these folate-targeted PET agents, as well as the pros and cons of several emerging 18 F-folate PET imaging agents, are discussed.
Molecular Structure of Nitrogen in Coal from XANES Spectroscopy (1993)

Five major nitrogen chemical structures, present in coals of varying ranks, have been quantitatively determined with the use of nitrogen x-ray absorption near-edge spectroscopy (XANES). Similar studies of the sulfur chemical structures of coals have been performed for the last ten years; nitrogen studies on these fossil-fuel samples have only recently been realized. XANES spectra of coals exhibit several distinguishable resonances which can be correlated with characteristic resonances of particular nitrogen chemical structures, thereby facilitating analysis of these complicated systems. Many model compounds have been examined; for some, the relative peak positions are explained in terms of the orbital description of the lone pair of electrons. All features in the XANES spectra of coals have been accounted for; thus, all the major structural groups of nitrogen present in coals have been determined. A wide variety of aromatic nitrogen compounds is found in the coals; no evidence of saturated amine is found. Pyrroles, pyridines, pyridones, and aromatic amines are found in coal; of these, pyrrolic structures are the most prevalent. Pyridine nitrogen is prevalent in all except low-rank coals. The low pyridine content in low-rank (high-oxygen) coals correlates with a large pyridone content. This observation suggests that, with increasing maturation of coal, the pyridone loses its oxygen and is transformed into pyridine. Aromatic amines are present at low levels in coals of all rank. The spectral effects of aromatic amines are shown by comparing the XANES spectra of coal and petroleum asphaltenes.
Immunology in the clinic review series; focus on type 1 diabetes and viruses: role of antibodies enhancing the infection with Coxsackievirus-B in the pathogenesis of type 1 diabetes (2011)

Type 1 diabetes results from an interaction between genetic and environmental factors. Coxsackieviruses B (CV-B) are major environmental candidates, as suggested by epidemiological and experimental studies. The mechanisms leading to the disease involve interactions between the virus, host target tissue (pancreas) and the immune system. The infection of target cells with viruses can be prevented by antibodies. Conversely, the infection can be enhanced by antibodies. The antibody-dependent enhancement (ADE) of infection has been described with various viruses, especially Picornaviruses. In mice infected with CV-B3 this phenomenon resulted in an extended inflammatory reaction and myocarditis. In the human system non-neutralizing antibodies can increase the infection of monocytes with CV-B4 and stimulate the production of interferon (IFN)-α by these cells in vitro. CV-B4/immunoglobulin (Ig)G immune complexes interacted with a specific viral receptor [Coxsackievirus and adenovirus receptor (CAR)] and with IgG Fc fraction receptors (FcγRII and FcγRIII) at the surface of monocytes. The virus-antibody complexes are internalized (CAR) and receptors for the Fc of IgG (FcγRII and FcγRIII). Such antibodies have been detected in patients with type 1 diabetes and they could be responsible for the presence of enteroviral RNA and IFN-α in peripheral blood mononuclear cells (PBMC) of these individuals. The target of enhancing antibodies has been identified as the VP4 protein, which allowed the detection of these antibodies by enzyme-linked immunosorbent assay (ELISA). It cannot be excluded that antibodies enhancing the infection with CV-B may play a role in the pathogenesis of type 1 diabetes, induced or aggravated by these viruses. They can cause a viral escape from the immune response and may participate in the spreading of viruses to β cells. Whether enhancing antibodies raised against VP4 can play a role in iterative homologous and/or heterologous CV-B infections and in the persistence of viruses within the host deserves further study.
Pairwise detection of site-specific receptor phosphorylations using single-molecule blotting (2016)

Post-translational modifications (PTMs) of receptor tyrosine kinases (RTKs) at the plasma membrane (PM) determine the signal transduction efficacy alone and in combination. However, current approaches to identify PTMs provide ensemble results, inherently overlooking combinatorial PTMs in a single polypeptide molecule. Here, we describe a single-molecule blotting (SiMBlot) assay that combines biotinylation of cell surface receptors with single-molecule fluorescence microscopy. This method enables quantitative measurement of the phosphorylation status of individual membrane receptor molecules and colocalization analysis of multiple immunofluorescence signals to directly visualize pairwise site-specific phosphorylation patterns at the single-molecule level. Strikingly, application of SiMBlot to study ligand-dependent epidermal growth factor receptor (EGFR) phosphorylation, which is widely thought to be multi-phosphorylated, reveals that EGFR on cell membranes is hardly multi-phosphorylated, unlike in vitro autophosphorylated EGFR. Therefore, we expect SiMBlot to aid understanding of vast combinatorial PTM patterns, which are concealed in ensemble methods, and to broaden knowledge of RTK signaling.
Coupling modulation of microrings at rates beyond the linewidth limit (2013)

We demonstrate optical modulation rates exceeding the conventional cavity linewidth limit using a silicon coupling modulated microring. Small-signal measurements show coupling modulation was free of the parasitic cavity linewidth limitations at rates at least 6× the cavity linewidth. Eye diagram measurements show coupling modulation achieved data rates > 2× the rate attainable by conventional intracavity phase modulation. We propose to use DC-balanced encoding to mitigate the inter-symbol interference in coupling modulation. Analysis shows that coupling modulation can be more efficient than intracavity modulation for large output swings and high-Q resonators. Coupling modulation enables very high-Q resonant modulators to be simultaneously low-power and high-speed, features which are mutually incompatible in typical resonant modulators studied to date.
Genome-Wide Disease Screening in Early Human Embryos with Primary Template-Directed Amplification (2021)

Abstract Current preimplantation genetic testing (PGT) enables the selection of embryos based on fetal aneuploidy or the presence a small number of preselected disease-associated variants. Here we present a new approach that takes advantage of the improved genome coverage and uniformity of primary template-directed amplification (PTA) to call most early embryo genetic variants accurately and reproducibly from a preimplantation biopsy. With this approach, we identified clonal and mosaic chromosomal aneuploidy, de novo mitochondrial variants, and variants predicted to cause mendelian and non-mendelian diseases. In addition, we utilized the genome-wide information to compute polygenic risk scores for common diseases. Although numerous computational, interpretive, and ethical challenges remain, this approach establishes the technical feasibility of screening for and preventing numerous debilitating inherited diseases.
Placental Growth Factor Influences Maternal Cardiovascular Adaptation to Pregnancy in Mice1 (2014)

In healthy human pregnancies, placental growth factor (PGF) concentrations rise in maternal plasma during early gestation, peak over Weeks 26-30, then decline. Because PGF in nongravid subjects participates in protection against and recovery from cardiac pathologies, we asked if PGF contributes to pregnancy-induced maternal cardiovascular adaptations. Cardiovascular function and structure were evaluated in virgin, pregnant, and postpartum C56BL/6-Pgf(-) (/) (-) (Pgf(-) (/) (-)) and C57BL/6-Pgf(+/+) (B6) mice using plethysmography, ultrasound, quantitative PCR, and cardiac and renal histology. Pgf(-/-) females had higher systolic blood pressure in early and late pregnancy but an extended, abnormal midpregnancy interval of depressed systolic pressure. Pgf(-/-) cardiac output was lower than gestation day (gd)-matched B6 after midpregnancy. While Pgf(-) (/) (-) left ventricular mass was greater than B6, only B6 showed the expected gestational gain in left ventricular mass. Expression of vasoactive genes in the left ventricle differed at gd8 with elevated Nos expression in Pgf(-) (/) (-) but not at gd14. By gd16, Pgf(-) (/) (-) kidneys were hypertrophic and had glomerular pathology. This study documents for the first time that PGF is associated with the systemic maternal cardiovascular adaptations to pregnancy.
Syntheses and applications of periodic mesoporous organosilica nanoparticles (2015)

Periodic Mesoporous Organosilica (PMO) nanomaterials are envisioned to be one of the most prolific subjects of research in the next decade. Similar to mesoporous silica nanoparticles (MSN), PMO nanoparticles (NPs) prepared from organo-bridged alkoxysilanes have tunable mesopores that could be utilized for many applications such as gas and molecule adsorption, catalysis, drug and gene delivery, electronics, and sensing; but unlike MSN, the diversity in chemical nature of the pore walls of such nanomaterials is theoretically unlimited. Thus, we expect that PMO NPs will attract considerable interest over the next decade. In this review, we will present a comprehensive overview of the synthetic strategies for the preparation of nanoscaled PMO materials, and then describe their applications in catalysis and nanomedicine. The remarkable assets of the PMO structure are also detailed, and insights are provided for the preparation of more complex PMO nanoplatforms.
High-Frequency Ultrasound-Guided Fluorescence Tomography of Protoporphyrin IX in Subcutaneous Tumors (2010)

An automated ultrasound-guided fluorescence tomography system was created to image the Protoporphyrin IX production of subcutaneous tumors in vivo. Negative production and positive production tumors were compared to validate the system capability.
NMR study of the spacial relation of hydrogen to phosphorus and boron in amorphous silicon (1987)

Hydrogen’s role in the doping efficiency and long term stability of hydrogenated amorphous silicon is not well understood. The introduction of dopants has been observed to cause an increase in the deposition rate and in the formation of dangling bonds. The structural arrangement of the dopant and the surrounding amorphous matrix has only been inferred by comparison to crystalline Si and thus the issue of dopants in the presence of hydrogen has not been examined in detail. The relaxation of constraints due to the amorphous matrix along with the addition of hydrogen has allowed many more configurations. To determine the structural units, more experimental evidence on the actual structural units is needed. To this effort, we have performed NMR spin echo double resonance measurements on heavily doped amorphous silicon samples prepared via plasma deposition. The resultant dopant concentrations were 0.5 at. % boron for the p‐type and 0.5 at. at. % phosphorus for n‐type material. The strong distance dependence of this double resonance technique makes it ideally suited to investigate the near‐neighbor environment of the dopants. The resulting dopant‐to‐hydrogen distances indicate that in p‐type material, 40% of the boron atoms are directly bonded to a hydrogen, while in n‐type, the phosphorus to hydrogen distance indicates P and H are not nearest neighbors.
Data from Constitutive Activation of Signal Transducers and Activators of Transcription Predicts Vorinostat Resistance in Cutaneous T-Cell Lymphoma (2023)

&lt;div&gt;Abstract&lt;p&gt;Vorinostat is a histone deacetylase inhibitor that induces differentiation, growth arrest, and/or apoptosis of malignant cells both &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; and has shown clinical responses in ∼30% of patients with advanced mycosis fungoides and Sézary syndrome cutaneous T-cell lymphoma (CTCL). The purpose of this study was to identify biomarkers predictive of vorinostat response in CTCL using preclinical model systems and to assess these biomarkers in clinical samples. The signal transducer and activator of transcription (STAT) signaling pathway was evaluated. The data indicate that persistent activation of STAT1, STAT3, and STAT5 correlate with resistance to vorinostat in lymphoma cell lines. Simultaneous treatment with a pan-Janus-activated kinase inhibitor resulted in synergistic antiproliferative effect and down-regulation of the expression of several antiapoptotic genes. Immunohistochemical analysis of STAT1 and phosphorylated tyrosine STAT3 (pSTAT3) in skin biopsies obtained from CTCL patients enrolled in the vorinostat phase IIb trial showed that nuclear accumulation of STAT1 and high levels of nuclear pSTAT3 in malignant T cells correlate with a lack of clinical response. These results suggest that deregulation of STAT activity plays a role in vorinostat resistance in CTCL, and strategies that block this pathway may improve vorinostat response. Furthermore, these findings may be of prognostic value in predicting the response of CTCL patients to vorinostat. [Cancer Res 2008;68(10):3785–94]&lt;/p&gt;&lt;/div&gt;
Simple Route to Gradient Concentric Metal and Metal Oxide Rings (2006)

Gradient concentric rings with unprecedented regularity, formed by drying a polymer solution from a sphere-on-Si geometry, are utilized as templates for preparing a wide variety of metal or metal oxide rings. This simple yet novel approach affords a cost-effective means to produce metal or metal oxide rings in a concentric fashion.
Lasers Solutions for Annealing (2007)

The application of lasers for annealing of wafer-based and thin-film microelectronic devices is steadily increasing. Excellent control of material characteristics (for example, dopant activation profile) can be achieved through proper selection of laser parameters, such as wavelength, pulse duration and fluence, which directly influence the laser material interaction. In this paper, we present several lasers and optical systems from Coherent that have proven to be useful for annealing in both microelectronic and macroelectronic applications. These laser systems include Excimer Lasers in the ultraviolet and our unique high-power continuous-wave laser system that delivers scalable output power of multiple hundreds of Watts in the visible wavelength range. We will present results from recent work involving dopant activation, and will present several application examples from Flat Panel Display annealing and crystallization, which we propose are directly applicable to wafer-based microelectronics as well.
A chimeric type II/type I interleukin-1 receptor can mediate interleukin-1 induction of gene expression in T cells (1993)

The type I interleukin-1 receptor (IL-1R) is capable of transducing a signal resulting in promoter activation in T cells. This signal transduction is dependent on the cytoplasmic domain, which consists of 213 amino acids. In contrast to the type I receptor, the type II IL-1R has a small cytoplasmic tail, and it is not clear whether this receptor is a signal-transducing or a regulatory molecule. Here we report that the type II IL-1R does not mediate gene activation in Jurkat cells. However, a hybrid receptor composed of the extracellular and transmembrane regions of the human type II interleukin-1 fused to the cytoplasmic domain of the human type I IL-1R was capable of transducing a signal across the membrane resulting in a pattern of gene activation identical to that mediated by the type I IL-1R. Our results indicated that the extracellular domain of the type II IL-1R was capable of functionally interacting with interleukin-1 and transmitting the resulting signal to a heterologous cytoplasmic domain.
Lamellar orientation of block copolymer using polarity switch of nitrophenyl self-assembled monolayer induced by electron beam (2017)

Directed self-assembly (DSA) was investigated on self-assembled monolayers (SAMs) of 6-(4-nitrophenoxy) hexane-1-thiol (NPHT), which were chemically modified by electron beam (EB) irradiation. By irradiating a responsive interfacial surface, the orientation and selective patterning of block copolymer domains could be achieved. We demonstrated that spatially-selective lamellar orientation of polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) could be induced via modification of an underlying SAM; for instance the conversion of an NO<sub>2</sub> group to an NH<sub>2</sub> group, induced by EB. The lamellar orientation of PS-b-PMMA was controlled by the change in the polarity of different regions of the SAM using EB lithography. The reductive treatment of SAM substrates plays a crucial role in the orientation of block copolymer. This method might greatly simplify block copolymer DSA processes as compared to the conventional multi-step chemo-epitaxy DSA process. By examining the lamellae orientation by EB, we found that the vertical orientation persists only for appropriate an irradiation dose and annealing temperature.
Studies of carcino‐fetal proteins. III. Development of a radioimmunoassay for α‐fetoprotein. Demonstration of α‐fetoprotein in serum of healthy human adults (1971)

Abstract A radioimmunoassay (RIA) for human α‐fetoprotein (α‐FP) was developed. The sensitivity threshold of the method is 250 picograms per ml, which means that it is 20,000‐40,000 times more sensitive than immunodiffusion, and covers completely the thousandfold concentration gap between the α‐FP levels in normal human serum and the level detectable by immunodiffusion. Evidence for the presence of α‐FP in serum of healthy human individuals is as follows: (I) Normal serum in 1:5 dilution inhibited the binding of labelled α‐FP by antibody. (2) The activity inhibiting in RIA could be removed from serum by prior treatment with anti‐α‐FP immunoadsorbent. (3) At low pH α‐FP could be eluted from immunoadsorbent that had been previously treated with serum. (4) After fractionation of normal human serum by electrofocusing the activity inhibiting in RIA was present in a fraction whose isoelectric point was that previously shown for fetal α‐FP. The α‐FP present in cancer is currently believed to be a product of an activated fetal gene which is suppressed at the adult stage. Our results show that this suppression is not complete in all cells. Measurement of α‐FP at the radioimmunoassay level is considered to be a contribution to the early diagnosis of cancer.
Perturbed angular correlation studies of uniaxial compressive stressed zinc, titanium, rutile, Ti2AlN, and Nb2AlC (2014)

We use the perturbed angular correlation method with (111)In-(111)Cd probe atoms to in situ study the changes in the electric field gradient at room temperature of polycrystalline Ti(2)AlN and Nb(2)AlC, titanium and zinc, and rutile samples, as a function of cyclic uniaxial compressive loads. The load dependence of the quadrupole coupling constant νQ was found to be large in titanium and zinc but small in Ti(2)AlN, Nb(2)AlC and rutile. Reversible and irreversible increases in the electric field gradient distribution widths were found under load and after releasing the load, respectively. Annihilation of dislocations, as well as elastic deformation, are considered to contribute to the reversible behavior. The irreversible response must be caused by a permanent increase in dislocation and point defect densities. The deformation induced broadening of the electric field gradient can be recovered by post-annealing of the deformed sample.