gebhart/patrepeval huggingface dataset:
Photoresist Removal Using Alternative Chemistries and Pressures (2009)

Approximately 20% of the processing steps in integrated circuit (IC) fabrication involve surface cleaning and removal of photoresist and plasma etch residues. Continuous device minimization requires the use of thin films (<20 nm), closely spaced features, and ultra shallow junctions (<50nm); as a result, the challenges associated with effective surface cleaning are intensified. In addition, to insure high device performance, incorporation of alternate materials such as copper, ruthenium, and molybdenum, porous low dielectric constant SiO2-based insulators, and hafnium or zirconium oxides or silicates into device structures is taking place. Integration of these materials into working devices requires precise control of surface properties. In order to eliminate damage to films or substrates, avoid modification of surfaces, promote contaminant removal rates and enhance process control, approaches such as use of downstream plasmas, liquid cleaning with low concentrations of reactive chemicals, mechanical agitation, and liquid or particle jets have been implemented [1].
Energy distributions of liquid metal alloy ion sources (1988)

The energy distributions of liquid metal ion sources using Au–Si–Be, Pd–Ni–Si–Be–B, Al–Si, and Pt–Si alloys have been measured. Profiles of singly charged ion species which are strongly dependent on alloy systems typically exhibit an abrupt rise at the high-energy position and gradual decay at the low-energy position in the profiles. This gradual decay, which appears rather like a subsidiary shoulder, may be caused by free space field ionization in addition to field evaporation. Profiles also have long tails at both the high- and low-energy positions. These tails can be explained by charge transfer collision between ions and neutral atoms coming from the outer space. The intensity of the tails is discussed on the basis of the charge transfer collision process.
Coordinated checkpointing-rollback error recovery for distributed shared memory multicomputers (2002)

Most recovery schemes that have been proposed for Distributed Shared Memory (DSM) systems require unnecessarily high checkpointing frequency and checkpoint traffic, which are sensitive to the frequency of interprocess communication in the applications. For message-passing systems, low overhead error recovery based on coordinated checkpointing allows the frequency of checkpointing to be determined only by the reliability requirements of the application. Efficient adaptation of this approach to DSM multicomputers is complicated by the absence of explicit messages in DSM systems, the presence of a shared and partially replicated address space, and the presence of a distributed coherency directory. We present solutions to these issues, and propose an error recovery scheme based on coordinated checkpointing and rollback for DSM multicomputers. Our performance evaluation based on trace-driven simulations indicates that this scheme incurs less checkpoint traffic than recovery schemes previously proposed for DSM systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The fabrication of high sensitive spin-valve sensor for magnetic bead detection (2004)

Manipulation and detection of magnetic beads on a chip open up new perspectives for analysis of magnetically labeled specimens in biological and medical applications. This work has studied to achieve the high sensitive spin-valve (SV) sensor detecting the stray field from a spherical-shaped superparamagnetic bead magnetized by external field. First of all, SV structures of Ta(50)/NiFe(45)/CoFe(15)/Cu(26)/ CoFe(40)/IrMn(150)/Ta(50) [unit of ( ) is A] with 8 - 9% magnetoresistive ratio (MR) were deposited on substrate Si/SiO 2 (1500) by UHV magnetron sputter system. SV sensor was fabricated through photolithographic techniques and ion milling processes. The working of sensor was confirmed by obtaining the output signal as a function of sense current under the external field parallel to magnetization direction of pinned layer. The sensitivity of the fabricated SV sensor was about 0.3%/Oe (sense current 10 mA). Sensor signal (AV) output of 2 mV was obtained for 2.8 μm magnetic beads positioned over the SV sensor using an external in-plane field and 10 mA sense current.
Fast reconstruction of off-axis digital holograms based on digital spatial multiplexing (2014)

A method for fast reconstruction of off-axis digital holograms based on digital multiplexing algorithm is proposed. Instead of the existed angular multiplexing (AM), the new method utilizes a spatial multiplexing (SM) algorithm, in which four off-axis holograms recorded in sequence are synthesized into one SM function through multiplying each hologram with a tilted plane wave and then adding them up. In comparison with the conventional methods, the SM algorithm simplifies two-dimensional (2-D) Fourier transforms (FTs) of four N*N arrays into a 1.25-D FTs of one N*N arrays. Experimental results demonstrate that, using the SM algorithm, the computational efficiency can be improved and the reconstructed wavefronts keep the same quality as those retrieved based on the existed AM method. This algorithm may be useful in design of a fast preview system of dynamic wavefront imaging in digital holography.
A Theory and Computational Model of Auditory Selective Attention (2002)

The auditory system must separate an acoustic mixture in order to create a perceptual description of each sound source. It has been proposed that this is achieved by a process of auditory scene analysis (ASA) in which a number of streams are produced, each describing a single sound source. Few computer models of ASA attempt to incorporate attentional effects, since ASA is typically seen as a precursor to attentional mechanisms. This assumption may be flawed: recent work has suggested that attention plays a key role in the formation of streams, as opposed to the conventional view that attention merely selects a pre-constructed stream. This study presents a conceptual framework for auditory selective attention in which the formation of groups and streams is heavily influenced by conscious and subconscious attention. This framework is implemented as a computational model comprising a network of neural oscillators which perform stream segregation on the basis of oscillatory correlation. Within the network, attentional interest is modelled as a gaussian distribution in frequency. This determines the connection weights between oscillators and the attentional process the attentional leaky integrator (ALI). A segment or group of segments are said to be attended to if their oscillatory activity coincides temporally with a peak in the ALI activity. The output of the model is an ‘attentional stream’: a description of which frequencies are being attended at each epoch. The model successfully simulates a range of psychophysical phenomena. Furthermore, a number of predictions are made and a psychophysical experiment is conducted to investigate the time course of attentional allocation in a binaural streaming task. The results support the model prediction that attention is subject to a form of ‘reset’ when the attentional focus is moved in space.
Formalizing Assistive Teleoperation (2012)

In assistive teleoperation, the robot helps the user accomplish the desired task, making teleoperation easier and more seamless. Rather than simply executing the user's input, which is hindered by the inadequacies of the interface, the robot attempts to predict the user's intent, and assists in accomplishing it. In this work, we are interested in the scientific underpinnings of assistance: we formalize assistance under the general framework of policy blending, show how previous work methods instantiate this formalism, and provide a principled analysis of its main components: prediction of user intent and its arbitration with the user input. We define the prediction problem, with foundations in Inverse Reinforcement Learning, discuss simplifying assumptions that make it tractable, and test these on data from users teleoperating a robotic manipulator under various circumstances. We propose that arbitration should be moderated by the confidence in the prediction. Our user study analyzes the effect of the arbitration type, together with the prediction correctness and the task difficulty, on the performance of assistance and the preferences of users.
Preface (2006)

Total sales of software worldwide exceed $200 billion annually, and it has been estimated that software errors cost the United States economy $59.5 billion, or .6 percent of the gross domestic product, each year. Despite this, the practice of mature software engineering is still, in many ways, a goal rather than a current reality.
Id Proteins - Tumor Markers or Oncogenes? (2002)

The Id (Inhibitor of differentiation or Inhibitor of DNA-binding) proteins act as dominant negative inhibitors of differentiation-specific basic Helix-Loop-Helix (bHLH) transcription factors. Id proteins negatively regulate cellular differentiation and they induce proliferation by modulating different cell cycle regulators both by direct and indirect mechanisms. Ectopic expression of Id proteins in tissue culture models can result in cellular immortalization and abrogation of differentiation processes. Recent reports show that Id proteins are overexpressed in various cancer types implying a role of these regulatory proteins in carcinogenesis. This review focuses on the biology of the Id proteins and their role as potential oncogenes.
ALFA: Agglomerative Late Fusion Algorithm for Object Detection (2018)

We propose ALFA - a novel late fusion algorithm for object detection. ALFA is based on agglomerative clustering of object detector predictions taking into consideration both the bounding box locations and the class scores. Each cluster represents a single object hypothesis whose location is a weighted combination of the clustered bounding boxes. ALFA was evaluated using combinations of a pair (SSD and DeNet) and a triplet (SSD, DeNet and Faster R-CNN) of recent object detectors that are close to the state-of-the-art. ALFA achieves state of the art results on PASCAL VOC 2007 and PASCAL VOC 2012, outperforming the individual detectors as well as baseline combination strategies, achieving up to 32% lower error than the best individual detectors and up to 6% lower error than the reference fusion algorithm DBF - Dynamic Belief Fusion.
A rate adaption gateway to the ISDN (2003)

A multistandard rate adapter coprocessor chip, designed for use in integrated services digital network (ISDN) terminal adapters and U-interface modems, is presented. It provides a compact low-power protocol convertor to connect asynchronous (up to 19200 b/s) and synchronous (up to 64 kbit/s) data terminal equipment with any digital 64-kbit/s network. The chip was developed in a 2- mu m CMOS technology using a hierarchical design methodology. The chip provides a compact cost- and power-efficient solution for universal-terminal adapter design. The rate adapter is the cornerstone of a 144-kbit/s U-interface modem and a major breakthrough for the next-generation multistandard terminal adapter.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Cytokines in T-cell development (1991)

The thymus provides a unique environment for the development of T cells, supporting both precursor cell proliferation and differentiation. The control of these processes is unknown but they may be mediated by cytokines, or other soluble factors, or by interactions with specific elements of the thymic stroma. Here, Simon Carding, Adrian Hayday and Kim Bottomly describe cellular, immunochemical and molecular studies of the production and action of cytokines within the human and mouse thymus and demonstrate their essential role in T-cell development.
Preformed Selenoesters Enable Rapid Native Chemical Ligation at Intractable Sites (2011)

Going pro: The first facile Pro–Cys ligation using a preformed prolyl selenoester is reported (see scheme; P=peptide). In a comparative study of peptide selenoesters in native chemical ligation peptide α-selenoesters are shown to be superior acyl donors and result in rate enhancements of at least two orders of magnitude when compared to the well-established peptide α-thioesters. This method permits rapid chemical ligation even at previously intractable sites, such as Pro-Cys. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
COM-1 is over-expressed in human colorectal carcinomas (2007)

21001 Background: COM-1, candidate of metastasis-1, is a primarily nuclear protein thought to play a role in the development and maintenance of metastatic tumours and to have some mitogenic activity. However subsequent investigations have demonstrated a much more diverse role in cancer and cell growth. Here we have investigated the expression and sub-cellular distribution patterns of COM-1 in human colorectal carcinomas. Methods: Carcinoma and normal matched tissues were collected following surgery and frozen for future analysis. Sections of tissue underwent immuno-histochemistry (IHC) staining for COM-1 to determine degree of staining and changes in cellular distribution of the proteins within the tissue. Furthermore, quantitative analysis (quantitative polymerase chain reaction - qPCR) of mRNA levels of COM-1 transcripts was performed to compare levels in normal tissue with those in carcinoma tissues. Statistical analysis was by the Mann-Whitney test. Results: IHC -Normal tissue demonstrated strong nuclear staining for COM-1 protein with little or no cytoplasmic staining. In carcinoma tissue the level of overall staining was found to be much greater, with a greater degree of cytoplasmic staining and little evidence of nuclear staining. qPCR- COM-1 mRNA expression within cells was significantly higher within tumour tissue when compared to normal tissue (Mean 36.7 v 26.5, p=0.003). Moreover, there was a trend in increasing levels of expression and significance of difference between normal tissue and carcinoma tissue with increasing Dukes stage (A p=.52, B p=0.03, C p=0.03) , T-Stage (1 p=1.0, 2 p=0.69, 3 p=0.04, 4 p=0.03), Nodal status (−ve p=0.07, +ve p=0.04 and tumour differentiation (well diff p=0.91, Mod. Diff p= 0.06, Poor. Diff. p= 0.026). Conclusions: COM-1 expression is increased in colorectal tumour tissues when compared to normal mucosa. This is reflected at both the protein and mRNA levels within the cells. In addition there is evidence of dislocated expression and redistribution of COM-1 protein with normal protein expression remaining intra-nuclear however, in tumours COM-1 then becomes cytoplasmic. Aberant over-expression of COM-1 has been identified in other human carcinoma types and has been linked with advanced disease, here we have demonstrated a similar pattern in colorectal carcinomas. No significant financial relationships to disclose.
Phosphofructokinase. I. Mechanism of the pH-dependent inactivation and reactivation of the rabbit muscle enzyme. (1976)

The kinetics of inactivation and reactivation of rabbit skeletal muscle phosphofructokinase have been studied as a function of pH and enzyme concentration at constant temperature in phosphate buffer. From the enzyme concentration dependence, we conclude that the minimal mechanism for inactivation involves a protonation step followed by isomerization to an inactive form and then dissociation to a species of one-half the molecular weight. Other data indicate a subsequent isomerization of the dissociated form. The pH and temperature dependence of the inactivation process shows that it is controlled by ionizable groups, and that the apparent pK for these groups is temperature-dependent in such a way as to make the enzyme show the characteristic of cold lability below pH 7. Reactivation of the inactive enzyme occurs by a kinetically different pathway involving deprotonation of an inactive, dissociated form to a form which may either isomerize to another inactive form, or dimerize to the active enzyme. A general mechanism is postulated in which the inactivation and reactivation processes are different aspects of the same mechanism. This mechanism assumes four species (two containing four subunits and two containing two subunits) each of which can exist in a protonated and unprotonated form. Inactivation or reactivation induced by changes in pH or temperature reflect the kinetic establishment of a new steady state between these forms. How the apparent pK values which control the distribution of the enzyme between protonated and unprotonated forms describe the pH-dependent characteristics of the enzyme is discussed in terms of the proposed mechanism.
Structural and Kinetic Analysis of Schwanniomyces occidentalis Invertase Reveals a New Oligomerization Pattern and the Role of Its Supplementary Domain in Substrate Binding (2010)

Schwanniomyces occidentalis invertase is an extracellular enzyme that hydrolyzes sucrose and releases beta-fructose from various oligosaccharides and essential storage fructan polymers such as inulin. We report here the three-dimensional structure of Sw. occidentalis invertase at 2.9 A resolution and its complex with fructose at 1.9 A resolution. The monomer presents a bimodular arrangement common to other GH32 enzymes, with an N-terminal 5-fold beta-propeller catalytic domain and a C-terminal beta-sandwich domain for which the function has been unknown until now. However, the dimeric nature of Sw. occidentalis invertase reveals a unique active site cleft shaped by both subunits that may be representative of other yeast enzymes reported to be multimeric. Binding of the tetrasaccharide nystose and the polymer inulin was explored by docking analysis, which suggested that medium size and long substrates are recognized by residues from both subunits. The identified residues were mutated, and the enzymatic activity of the mutants against sucrose, nystose, and inulin were investigated by kinetic analysis. The replacements that showed the largest effect on catalytic efficiency were Q228V, a residue putatively involved in nystose and inulin binding, and S281I, involved in a polar link at the dimer interface. Moreover, a significant decrease in catalytic efficiency against inulin was observed in the mutants Q435A and Y462A, both located in the beta-sandwich domain of the second monomer. This highlights the essential function that oligomerization plays in substrate specificity and assigns, for the first time, a direct catalytic role to the supplementary domain of a GH32 enzyme.
Analysis ofin vitro reaction layers formed on Bioglass� using thin-film X-ray diffraction and ATR-FTIR microspectroscopy (1998)

Fourier transform infrared spectroscopy and thin-film X-ray diffraction (TF-XRD) techniques were used to analyze the inorganic carbonate apatite (CA) layer developed on a bioactive glass (45S5 type Bioglass) in an in vitro environment. The C-O and P-O vibrational modes appeared on the bioactive glass surface following immersion in the simulated body fluid solution. Initially, the C-O and P-O peaks increased with immersion time as crystallization of CA phase progressed. The TF-XRD confirmed that the deposited layer was apatite, crystallographically. Furthermore, evidence of preferred orientation in the 001 direction was seen, indicated by very strong 002 reflection. With time, the crystal growth became more random and the intensity of the 002 reflection decreased.
Abdominal drainage following cholecystectomy: high, low, or no suction? (1983)

A prospective trial to assess the effect of suction in an abdominal drain following cholecystectomy was carried out. Three types of closed drainage system were compared: a simple tube drain, a low negative pressure drain, and a high negative pressure drain: 120 consecutive patients undergoing cholecystectomy were randomly allocated to one of the three drainage groups. There was no significant difference in postoperative pyrexia, wound infection, chest infection, or hospital stay. This study failed to demonstrate any clinically useful difference between high negative pressure, low negative pressure, and static drainage system were compared: a simple tube drain, a low negative used, suction is not necessary and a simple tube drain (greater than 6 mm internal diameter) is the most effective form of drainage.
High performing micromachined retroreflector (2003)

This paper reports on the realization of a type of micromachined retroreflecting sheeting material. The geometry presented has high reflection efficiency even at large incident angles, and it can be manufactured through polymer replication techniques. The paper consists of two parts: A theoretical section outlining the design parameters and their impact on the optical performance, and secondly, an experimental part comprising both manufacturing and optical evaluation for a candidate retroreflecting sheet material in traffic control devices. Experimental data show that the retroreflecting properties are promising. The retroreflector consists of a front layer of densely packed spherical microlenses, a back surface of densely packed spherical micromirrors, and a transparent spacer layer. The thickness of the spacer layer determines in part the optical characteristics of the retroreflector.
Multiscale geometric wavelets for the analysis of point clouds (2010)

Data sets are often modeled as point clouds in ¿ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sup> , for D large. It is often assumed that the data has some interesting low-dimensional structure, for example that of a d-dimensional manifold M, with d much smaller than D. When M is simply a linear subspace, one may exploit this assumption for encoding efficiently the data by projecting onto a dictionary of d vectors in ¿ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sup> (for example found by SVD), at a cost (d + n)D for n data points. When M is nonlinear, there are no "explicit" constructions of dictionaries that achieve a similar efficiency: typically one uses either random dictionaries, or dictionaries obtained by black-box optimization. In this paper we construct data-dependent multiscale dictionaries that aim at efficient encoding and manipulating of the data. Their construction is fast, and so are the algorithms to map data points to dictionary coefficients and vice versa. In addition, data points are guaranteed to have a sparse representation in terms of the dictionary. We think of dictionaries as the analogue of wavelets, but for approximating point clouds rather than functions.
Serum Amyloid A as a Surrogate Marker for Mucosal and Histologic Inflammation in Patients with Crohnʼs Disease (2016)

High circulating SAA levels can correlate with lack of MH and may be used as a surrogate marker for disease activity, even in those patients in whom CRP levels do not correlate with disease activity.