gebhart/patrepeval huggingface dataset:
100 nm wide copper lines made by selective electroless deposition (1991)

Copper lines with a minimum width of 100 nm were fabricated by selective electroless copper deposition (SED). The deposition reaction is based on the neutralization of positive copper ions in a basic solution by electrons which are the result of the reaction between formaldehyde and the hydroxyl ions. The reduction reaction requires a high pH typically in the range of 11.5-13 at the deposition temperature which is between 55 degrees C and 70 degrees C. The high pH required for the deposition reaction is achieved either by using alkaline bases, like sodium-hydroxide, or alkaline-free bases, like tetramethylammonium hydroxide (TMAH). Experimental data show similar results for both alkaline and alkaline-free deposition solutions. The copper nanolines were produced using electron beam lithography and polymethylmethacrylate (PMMA) e-beam resist due to its compatibility with the high pH of the deposition solution. The first approach, which is described here for making copper nanolines, produced 100 nm wide lines with vertical side walls and aspect ratio (height/width) as high as 4:1. The lines were uniform over both small and large areas and the deposition was only on the pre-designated regions (i.e. full selectivity). A second fabrication technique, which is also described, formed a fully-planar topography in which the copper is buried in an interlevel dielectric. 150 nm wide copper lines buried in 250 nm deep trenches in chemically-vapor-deposited (CVD) silicon-dioxide were made using that technique. Both techniques are described in detail and experimental results are presented in the form of SEM pictures. Selective copper deposition introduces some new problems in general and there are also some particular problems that are associated with the techniques described. Specific problems, such as step coverage and copper line shapes are discussed as well as more general problems like the compatibility with integrated circuit manufacturing technology.
Characterization of reflectivity inversion, α- and β-phase transitions and nanostructure formation in hydrogen activated thin Pd films on silicon based substrates (2002)

Optically thin palladium metal films evaporated on different silicon based substrates are investigated following exposure to different concentrations of hydrogen gas in air. Laser modulated reflectance off the palladium surface of silicon oxide and silicon nitride substrates is used to recover information regarding the reflectivity inversion and α/β-phases of the palladium complex after both first and multiple gas cycling. Atomic force microscopy confirms the formation of metal nanostructures following exposure to hydrogen of the optically thin palladium films.
Interpreting reservoir talk (2003)

The talk in the seismic business these days is all about the reservoir. But, as OE seismics editor Andrew McBarnet reports, reservoir in this context is a term open to wide interpretation.
Highly Z- and Enantioselective Ring-Opening/Cross-Metathesis Reactions Catalyzed by Stereogenic-at-Mo Adamantylimido Complexes (2009)

The first highly Z- and enantioselective class of ring-opening/cross-metathesis reactions is presented. Transformations are promoted in the presence of <2 mol % of chiral stereogenic-at-Mo monoaryloxide complexes bearing an adamantylimido ligand that are prepared and used in situ. Reactions involve meso oxabicyclic substrates and afford the desired pyrans in 50-85% yield and up to >98:<2 enantiomer ratio. Importantly, the desired chiral pyrans thus obtained bear a Z olefin either exclusively (>98:<2 Z/E) or predominantly (>or=87:13 Z/E).
A Micropower Interface ASIC for a Capacitive 3-Axis Micro-Accelerometer (2007)

In this paper, a micropower interface IC for a capacitive 3-axis micro-accelerometer implemented in a 0.13- BiCMOS process is presented. The sensor interface consists of a front-end that converts the acceleration signal to voltage, two algorithmic ADCs, two frequency references, and a voltage, current, and temperature reference circuit. Die area and power dissipation are reduced by using time-multiplexed sampling and varying duty cycles down to 0.3%. The chip with a 0.51 active area draws 62 from a 1.8 V supply while sampling temperature at 100 Hz, and four proof masses, each at 1.04 kHz. With a 4-g capacitive 3-axis accelerometer, the measured noise floors in the x-, y-, and z-directions are 482 , 639 , and 662 , respectively.
Estimation of Oxygen Distribution in RIF-1 Tumors by Diffusion Model-Based Interpretation of Pimonidazole Hypoxia and Eppendorf Measurements (2001)

Numerical simulations of oxygen diffusion from the capillaries in tumor tissue were used to predict the capillary oxygen supply within and near hypoxic regions of the RIF-1 tumor. A finite element method to simulate the oxygen distribution from a histology section is presented, along with a method to iteratively estimate capillary oxygen concentrations. Pathological structural data for these simulations came from sections of the tumor stained with hematoxylin and eosin and were used to define the capillary positions and shapes, while overlapping regions of low oxygen concentration were defined by the hypoxia marker pimonidazole. These simulations were used to calculate spatial maps of the oxygen concentration and were tested for their ability to reproduce Eppendorf pO(2) histograms from the same tumor line. This simulation study predicted that capillary oxygen concentrations ranged from zero to above 20 microM, with a dominant peak in the hypoxic regions showing 78% of capillaries with less than 1 microM oxygen concentration, compared to only 12% in the non-hypoxic regions. The results were not highly sensitive to the metabolic oxygen consumption rate, within the range of 2 to 16 microM/s. This numerical method for oxygen capillary simulation is readily adaptable to histology sections and provides a method to examine the heterogeneity of oxygen within the capillaries and throughout the tumor tissue section being examined.
Ascorbate Autoxidation in the Presence of Iron and Copper Chelates (1986)

Chelates can inhibit the iron- and copper-catalyzed autoxidation of ascorbate at pH 7.0. Diethylenetriaminepentaacetic acid (DTPA or DETAPAC) and Desferal (deferoximane mesylate) slow the iron-catalyzed oxidation of ascorbate as effectively as reducing the trace levels of contaminating iron in buffers with Chelex resin. DETAPAC, EDTA and HEDTA (N-(2-hydroxyethyl)-ethylenediaminetriacetic acid) are effective at slowing the copper-catalyzed autoxidation of ascorbate while Desferal is ineffective. The ability to inhibit ascorbate autoxidation appears to parallel the rate of the reaction of superoxide with the iron chelate.
Semi-supervised learning of compact document representations with deep networks (2008)

Finding good representations of text documents is crucial in information retrieval and classification systems. Today the most popular document representation is based on a vector of word counts in the document. This representation neither captures dependencies between related words, nor handles synonyms or polysemous words. In this paper, we propose an algorithm to learn text document representations based on semi-supervised autoencoders that are stacked to form a deep network. The model can be trained efficiently on partially labeled corpora, producing very compact representations of documents, while retaining as much class information and joint word statistics as possible. We show that it is advantageous to exploit even a few labeled samples during training.
Constitutive activation of STAT3 and STAT5 is present in the majority of nasopharyngeal carcinoma and correlates with better prognosis (2003)

Constitutively activated signal transducers and activators of transcription (STAT) factors, in particular STAT1, STAT3 and STAT5, have been demonstrated in a variety of human tumours and cancer cell lines. However, data on the expression of these STATs in nasopharyngeal carcinoma (NPC) are limited. In this study, the expression patterns of STAT1, STAT3 and STAT5 were immunohistochemically examined on the archival specimens from 61 patients with NPC. Staining results of each STATs were then correlated with the clinical parameters and prognosis of these patients. The results showed that constitutive activation of STAT3 and STAT5 was detected in the majority, 70.5 and 62.3%, respectively, of the 61 tumour specimens. Furthermore, coexpression of activated STAT3 and STAT5 was found in 54.1% of the specimens. In contrast, constitutive activated STAT1 could only be detected in 8 (13.1%) cases. Surprisingly, following radiotherapy, patients with constitutive STAT5 activation, or activation of both STAT3 and STAT5, had better disease-free survival and overall survival than those without activated STAT5. To our knowledge, this is the first report providing the overall expression patterns and prognostic significance of specific STATs in NPC.
Riboswitch Control of Gene Expression in Plants by Splicing and Alternative 3′ End Processing of mRNAs (2007)

The most widespread riboswitch class, found in organisms from all three domains of life, is responsive to the vitamin B(1) derivative thiamin pyrophosphate (TPP). We have established that a TPP-sensing riboswitch is present in the 3' untranslated region (UTR) of the thiamin biosynthetic gene THIC of all plant species examined. The THIC TPP riboswitch controls the formation of transcripts with alternative 3' UTR lengths, which affect mRNA accumulation and protein production. We demonstrate that riboswitch-mediated regulation of alternative 3' end processing is critical for TPP-dependent feedback control of THIC expression. Our data reveal a mechanism whereby metabolite-dependent alteration of RNA folding controls splicing and alternative 3' end processing of mRNAs. These findings highlight the importance of metabolite sensing by riboswitches in plants and further reveal the significance of alternative 3' end processing as a mechanism of gene control in eukaryotes.
Surface chemistry of HF passivated silicon: X-ray photoelectron and ion scattering spectroscopy results (1986)

X-ray photoelectron spectroscopy and ion scattering spectroscopy studies of HF-treated silicon surfaces are described in an effort to understand the chemical termination leading to the near ideal electrical passivation of such surfaces. Results suggest a fluorine surface density of order a monolayer chemically bonded to silicon with a partial oxygen contamination due to exposure of the HF-treated wafer to air, and a physisorbed hydrocarbon layer on top.
[Sacral nerve stimulation in fecal incontinence; efficacy and safety]. (2004)

Fecal incontinence is common due to various reasons. Conservative therapy of fecal incontinence may sometimes be effective in improving function, but usually many patients require surgery. Sacral nerve stimulation is another treatment modality which gained interest, and appears to be an alternative method that is successful with low morbidity. With the approval of the local ethical committee a total of 14 patients with rectal incontinence had undergone trial stimulation of sacral neuromodulation after failure of conservative treatment modalities. The implantations were performed under surgical sterile conditions with fluoroscopic guidance through the S3 foramen. After correct placement 0.5-2 V, 15 /min, pulse width 210 micro s stimulus was given. The patients had trial period longer than 6 weeks; 9 of 14 patients responded positively to the trial period. Of these 1 had permanent implantation, 3 were booked for permanent implantation, and 2 of the patients had complete incontinence relief from the trial period. Evaluating the data and the results of our study we may conclude that sacral nerve stimulation is an emerging surgical technique to produce a clinically beneficial physiological effect on the lower bowel, pelvic floor and anal canal.
Investigation, treatment and monitoring of late-onset hypogonadism in males (2008)

C. Wang, E. Nieschlag, R. Swerdloff, H. M. Behre, W. J. Hellstrom, L. J. Gooren, J. M. Kaufman, J.-J. Legros, B. Lunenfeld, A. Morales, J. E. Morley, C. Schulman, I. M. Thompson, W. Weidner, and F. C. W. Wu
Study Design Affects Participant Expectations (2009)

These results support the hypothesis that clinical trial design influences participant expectations of improvement. Study design may affect clinical outcomes and should be kept in mind when interpreting the results of antidepressant clinical trials.
Role of Bile Acids and Bile Acid Receptors in Metabolic Regulation (2009)

The incidence of the metabolic syndrome has taken epidemic proportions in the past decades, contributing to an increased risk of cardiovascular disease and diabetes. The metabolic syndrome can be defined as a cluster of cardiovascular disease risk factors including visceral obesity, insulin resistance, dyslipidemia, increased blood pressure, and hypercoagulability. The farnesoid X receptor (FXR) belongs to the superfamily of ligand-activated nuclear receptor transcription factors. FXR is activated by bile acids, and FXR-deficient (FXR(-/-)) mice display elevated serum levels of triglycerides and high-density lipoprotein cholesterol, demonstrating a critical role of FXR in lipid metabolism. In an opposite manner, activation of FXR by bile acids (BAs) or nonsteroidal synthetic FXR agonists lowers plasma triglycerides by a mechanism that may involve the repression of hepatic SREBP-1c expression and/or the modulation of glucose-induced lipogenic genes. A cross-talk between BA and glucose metabolism was recently identified, implicating both FXR-dependent and FXR-independent pathways. The first indication for a potential role of FXR in diabetes came from the observation that hepatic FXR expression is reduced in animal models of diabetes. While FXR(-/-) mice display both impaired glucose tolerance and decreased insulin sensitivity, activation of FXR improves hyperglycemia and dyslipidemia in vivo in diabetic mice. Finally, a recent report also indicates that BA may regulate energy expenditure in a FXR-independent manner in mice, via activation of the G protein-coupled receptor TGR5. Taken together, these findings suggest that modulation of FXR activity and BA metabolism may open new attractive pharmacological approaches for the treatment of the metabolic syndrome and type 2 diabetes.
Proximity effect at the superconductor–topological insulator interface (2010)

We study the excitation spectrum of a topological insulator in contact with an $s$-wave superconductor, starting from a microscopic model, and develop an effective low-energy model for the proximity effect. In the vicinity of the Dirac cone vertex, the effective model describing the states localized at the interface is well approximated by a model of Dirac electrons experiencing superconducting $s$-wave pairing. Away from the cone vertex, the induced pairing potential develops a $p$-wave component with a magnitude sensitive to the structure of the interface. Observing the induced $s$-wave superconductivity may require tuning the chemical potential close to the Dirac point. Furthermore, we find that the proximity of the superconductor leads to a significant renormalization of the original parameters of the effective model describing the surface states of a topological insulator.
<title>Application of advanced cytometric and molecular technologies to minimal residual disease monitoring</title> (2000)

Minimal residual disease monitoring presents a number of theoretical and practical challenges. Recently it has been possible to meet some of these challenges by combining a number of new advanced biotechnologies. To monitor the number of residual tumor cells requires complex cocktails of molecular probes that collectively provide sensitivities of detection on the order of one residual tumor cell per million total cells. Ultra-high-speed, multi parameter flow cytometry is capable of analyzing cells at rates in excess of 100,000 cells/sec. Residual tumor selection marker cocktails can be optimized by use of receiver operating characteristic analysis. New data minimizing techniques when combined with multi variate statistical or neural network classifications of tumor cells can more accurately predict residual tumor cell frequencies. The combination of these techniques can, under at least some circumstances, detect frequencies of tumor cells as low as one cell in a million with an accuracy of over 98 percent correct classification. Detection of mutations in tumor suppressor genes requires insolation of these rare tumor cells and single-cell DNA sequencing. Rare residual tumor cells can be isolated at single cell level by high-resolution single-cell cell sorting. Molecular characterization of tumor suppressor gene mutations can be accomplished using a combination of single- cell polymerase chain reaction amplification of specific gene sequences followed by TA cloning techniques and DNA sequencing. Mutations as small as a single base pair in a tumor suppressor gene of a single sorted tumor cell have been detected using these methods. Using new amplification procedures and DNA micro arrays it should be possible to extend the capabilities shown in this paper to screening of multiple DNA mutations in tumor suppressor and other genes on small numbers of sorted metastatic tumor cells.
Effective Wavelength Scaling for Optical Antennas (2007)

In antenna theory, antenna parameters are directly related to the wavelength lambda of incident radiation, but this scaling fails at optical frequencies where metals behave as strongly coupled plasmas. In this Letter we show that antenna designs can be transferred to the optical frequency regime by replacing lambda by a linearly scaled effective wavelength lambda(eff)=n(1)+n(2)lambda/lambda(p), with lambda(p) being the plasma wavelength and n(1), n(2) being coefficients that depend on geometry and material properties. It is assumed that the antenna is made of linear segments with radii R << lambda. Optical antennas hold great promise for increasing the efficiency of photovoltaics, light-emitting devices, and optical sensors.
Outline for discrete part manufacturing engineering (2002)

It is argued that within the framework of computer integrated manufacturing and engineering reference modeling, manufacturing system models may be and must be verified by prototyping supported by computer-aided methodology rather than by paper-aided methodology. Both synchronic and diachronic life-cycles as employed in integration engineering are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Conjoint pathologic cascades mediated by ALS/FTLD-U linked RNA-binding proteins TDP-43 and FUS (2011)

The RNA-binding proteins TAR DNA-binding protein (TDP-43) and fused in sarcoma (FUS) play central roles in neurodegeneration associated with familial amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U). Normally localized in the nucleus, in sites affected by ALS and FTLD-U they are mislocalized to the cytoplasm and form cytoplasmic inclusions. TDP-43 and FUS are transported to the nucleus in a Ran-GTPase-dependent manner via nuclear import receptors, but they also contribute to the formation of stress granules (SGs), which are intracytoplasmic structures incorporating RNA. C-terminal truncations of TDP-43 eliminate the nuclear transport signal and cause mislocalization of the protein to the cytoplasm, where it accumulates and forms SGs. ALS-associated FUS mutations impair nuclear transport and cause mislocalization of FUS to the cytoplasm, where it also contributes to assembly of SGs. Furthermore, the ALS susceptibility factor ataxin-2, recently identified as a potent modifier of TDP-43 toxicity, is also a predicted cytoplasmic RNA-binding protein and a constituent protein of SGs, suggesting that it is a part of the common pathologic cascade formed by TDP-43 and FUS. Thus, we propose that excessive mislocalization of the RNA-binding proteins TDP-43, FUS, and ataxin-2 into the cytoplasm leads to impairment of the RNA quality control system, forming the core of the ALS/FTLD-U degenerative cascade. In this review, we discuss the molecular basis of the novel disease spectrum of ALS/FTLD-U, including the neurodegenerative mechanism of the cytoplasmic RNA-binding proteins TDP-43 and FUS and the possibility of a novel therapeutic strategy.
The Treatment of Dry Eyes with Na Hyaluronate (Healon??) (1982)

Sodium hyaluronate is a viscoelastic substance used for vitreous replacement and as a protective device for the corneal endothelium. Its structure resembles that of a sponge of mucopolysaccharide chains with water trapped between its molecules. A 0.1% dilution of this preparation was used as tear replacement in 20 patients with severe keratitis sicca. Pain and photophobia improved rapidly in all cases following the application of Na hyaluronate. Relief of symptoms and improvement in vision has been maintained in most patients for a period of over 1 year.
Shape Control of II–VI Semiconductor Nanomaterials (2006)

Anisotropic II-VI semiconductor nanocrystals and nanoparticles have become important building blocks for (potential) nanotechnological applications. Even though a wide variety of differently shaped nanoparticles of this class can be prepared, the underlying mechanisms are mostly not fully understood. This Review article provides a brief overview of the currently studied shape-evolution mechanisms and the most prominent synthesis methods for such particles, with an aim to provide a fundamental understanding on how different morphologies evolve, and to function as a tool to aid in the preparation of specific nanocrystals.
Development of Targeted Near-Infrared Imaging Agents for Prostate Cancer (2014)

Prostate cancer is the most common noncutaneous malignancy affecting men in North America. Radical prostatectomy remains a definitive treatment for prostate cancer. However, prostate surgeries are still performed "blindly" with the extent of tumor infiltration past the margins of the surgery only being determined postoperatively. An imaging modality that can be used during surgery is needed to help define the tumor margins. With its abundant expression in prostate cancer, prostate-specific membrane antigen (PSMA) is an ideal target for detection of prostate cancer. The purpose of this study was to develop PSMA-targeted near-infrared (NIR) optical imaging probes for intraoperative visualization of prostate cancer. We synthesized a high-affinity PSMA ligand (PSMA-1) with low molecular weight and further labeled it with commercially available NIR dyes IRDy800 and Cy5.5. PSMA-1 and PSMA-1-NIR conjugates had binding affinities better than the parent ligand Cys-CO-Glu. Selective binding was measured for each of the probes in both in vitro and in vivo studies using competitive binding and uptake studies. Interestingly, the results indicated that the pharmacokinetics of the probes was dependent of the fluorophore conjugated to the PSMA-1 ligand and varied widely. These data suggest that PSMA-targeted probes have the potential to be further developed as contrast agents for clinical intraoperative fluorescence-guided surgery.
Stress-Inducible Regulation of Heat Shock Factor 1 by the Deacetylase SIRT1 (2009)

Heat shock factor 1 (HSF1) is essential for protecting cells from protein-damaging stress associated with misfolded proteins and regulates the insulin-signaling pathway and aging. Here, we show that human HSF1 is inducibly acetylated at a critical residue that negatively regulates DNA binding activity. Activation of the deacetylase and longevity factor SIRT1 prolonged HSF1 binding to the heat shock promoter Hsp70 by maintaining HSF1 in a deacetylated, DNA-binding competent state. Conversely, down-regulation of SIRT1 accelerated the attenuation of the heat shock response (HSR) and release of HSF1 from its cognate promoter elements. These results provide a mechanistic basis for the requirement of HSF1 in the regulation of life span and establish a role for SIRT1 in protein homeostasis and the HSR.