gebhart/patrepeval huggingface dataset:
HotWire: a visual debugger for C++ (1994)

We argue that visualization is essential in a modern debugger. Instead of inserting debug statements throughout the code, it should be possible to easily define visualizations while running the program under control of the debugger, resulting in what might be called printf's. A visualization of a C++ program can provide exciting insights. Bugs that cannot be found that easily with non-visual techniques are now found, just by watching the visualizations. However, the mechanisms to define the visualizations should be easy to understand, easy to apply and cause only minimal overhead to the programmer (who is the end-user of the visual debugger). HotWire is not only equipped with a couple of standard visualizations, but also with a small declarative script language (using constraints) that can be used to define new custom visualizations. This paper addresses user interface aspects of debugging tools. Specifically, the user interface of HotWire, a debugger for C++ and SmallTalk on AIX and OS/2 is described.
Protein extraction from secondary sludge of paper mill wastewater and its utilization as a wood adhesive (2011)

In this study, secondary sludge (SS) from a kraft paper mill was used as a source of biomass to recover protein and investigate its potential use as a wood adhesive. The process of protein recovery involved disruption of the floc structure in alkaline medium to disintegrate and release intercellular contents into the aqueous phase followed by separation of soluble protein. Finally, the soluble protein was subjected to low pH precipitation and the pelletized sludge protein, referred to as recovered sludge protein (RSP) was tested for crude protein, moisture, and other contents. A significant process yield of 90% in terms of precipitation of soluble protein from disintegrated sludge was estimated through calorimetric studies, whereas an overall material balance confirmed a RSP yield of up to 23% based on total suspended solids of raw sludge. The RSP containing 30% crude protein was used as a wood adhesive and its adhesion performance was compared with soy protein isolate (SPI) and phenol formaldehyde (PF) resin. The testing of plywood lap joints has shown up to 41% shear strength level of RSP adhesive compared to PF. This work demonstrates the technical feasibility and potential of SS as a biomass resource to develop eco-friendly adhesives for wood composite applications.
Contribution of MicroRNA-1275 to Claudin11 Protein Suppression via a Polycomb-mediated Silencing Mechanism in Human Glioma Stem-like Cells (2012)

Glioblastomas show heterogeneous histological features, and tumor cells show distinct phenotypic states that confer different functional attributes and an aggressive character. However, the molecular mechanisms underlying the heterogeneity in this disease are poorly understood. Glioma stem-like cells (GSCs) are considered able to aberrantly differentiate into diverse cell types and may contribute to the establishment of tumor heterogeneity. Using a GSC model, we investigated differentially expressed microRNAs (miRNAs) and associated epigenetic mechanisms that regulate the differentiation of GSCs. miRNA profiling using microarray technology showed that 13 and 34 miRNAs were commonly up-regulated and down-regulated in two independent GSC lines during differentiation, respectively. Among this set of miRNAs, quantitative PCR analysis showed that miRNA-1275 (miR-1275) was consistently down-regulated during GSC differentiation, along with the up-regulation of its target, CLDN11, an important protein during oligodendroglial lineage differentiation. Inhibition of miR-1275 with a specific antisense oligonucleotide (anti-miR-1275) in GSCs increased the expression of CLDN11, together with significant growth suppression. Epigenetic analysis revealed that gain of histone H3 lysine 27 trimethylation (H3K27me3) in the primary microRNA-1275 promoter was closely associated with miR-1275 expression. Treatment with 3-deazaneplanocin A, an inhibitor of H3K27 methyltransferase, attenuated CLDN11 induction by serum stimulation in parallel with sustained miR-1275 expression. Our results have illuminated the epigenetic regulatory pathways of miR-1275 that are closely associated with oligodendroglial differentiation, which may contribute to the tissue heterogeneity seen in the formation of glioblastomas. Given that inhibition of miR-1275 induces expression of oligodendroglial lineage proteins and suppresses tumor cell proliferation, this may be a potential therapeutic target for glioblastomas.
Quantum dot as a resource for teleportation and state swapping (2007)

We studied the use of quantum dots as a resource for teleportation and investigated how entanglement of the resource would affect the average fidelity of such a process. We then identified a suitable magnetic field, interdot distance, and the temperature to be used to achieve an average fidelity beyond the limit of the classical communication channel. We also explored the effects of decoherence on the teleportation process. We then investigated the state transfer or swapping between two quantum dots. We found that perfect quantum swap is possible in this system. A smaller magnetic field and interdot distance shortened the perfect state transfer time. Finally, we report on the performance of the system under different decoherence models.
Hybrid 2D/3D Photonic Integration for Non-Planar Circuit Topologies (2016)

Complex photonic integrated circuits (PIC) may have strongly non-planar topologies that require waveguide crossings (WGX) when realized in single-layer integration platforms. The number of WGX increases rapidly with the complexity of the circuit, in particular when it comes to highly interconnected optical switch topologies. Here, we present a concept for WGX-free PIC that rely on 3D-printed freeform waveguide overpasses (WOP). We experimentally demonstrate the viability of our approach using the example of a $4 \times 4$ switch-and-select (SAS) circuit realized on the silicon photonic platform. We further present a comprehensive graph-theoretical analysis of different $n \times n$ SAS circuit topologies. We find that for increasing port counts $n$ of the SAS circuit, the number of WGX increases with $n^4$, whereas the number of WOP increases only in proportion to $n^2$.
The Double-Sided Floating-Surface Detector: An Enhanced Charge-Detection Architecture for CCD Image Sensors (1995)

A new high speed, low noise, non-destructive charge detector, called the Double-Sided Floating-Surface Detector (DSFSD), which is fabricated in a standard CCD image sensor process, is reported. This detector can be integrated in CCD image sensors and is capable of detecting large charge packets at very low noise levels. Typical values are 5-8 noise electrons (within 5 MHz) for a charge packet size of 100,000 to 250,000 electrons. The detector is used as the first MOS transistor in a three-stage source-follower configuration with a bandwidth of 150 MHz. The performance of the detector is calculated using a new, simple, model and experimentally verified.
Topological spin current (2012)

This chapter discusses another type of equilibrium spin current similar to the exchange spin current – the topological spin current. Topological spin currents are driven by topological band structure and classified into bulk and surface topological spin currents. The former is confined onto electron-band manifolds, sometimes affecting their motions. This confinement is addressed through the standard method of combining the equations of motion and the Boltzmann equation for semi-classical electrons in a band. The latter class, on the other hand, is a surface spin current, which is limited near surfaces of a three-dimensional system and flows along these surfaces. This type is known to appear in topological insulators, where the bulk is insulating but the surface or edge is electrically conducting due to the surface or edge state.
Pretrained Transformers for Text Ranking: BERT and Beyond (2021)

The goal of text ranking is to generate an ordered list of texts retrieved from a corpus in response to a query. Although the most common formulation of text ranking is search, instances of the task can also be found in many natural language processing applications. This tutorial, based on a forthcoming book, provides an overview of text ranking with neural network architectures known as transformers, of which BERT is the best-known example. The combination of transformers and self-supervised pretraining has, without exaggeration, revolutionized the fields of natural language processing (NLP), information retrieval (IR), and beyond. We provide a synthesis of existing work as a single point of entry for both researchers and practitioners. Our coverage is grouped into two categories: transformer models that perform reranking in multi-stage ranking architectures and learned dense representations that perform ranking directly. Two themes pervade our treatment: techniques for handling long documents and techniques for addressing the tradeoff between effectiveness (result quality) and efficiency (query latency). Although transformer architectures and pretraining techniques are recent innovations, many aspects of their application are well understood. Nevertheless, there remain many open research questions, and thus in addition to laying out the foundations of pretrained transformers for text ranking, we also attempt to prognosticate the future.
A framework for distributed workflow systems (2001)

Workflow management systems (WFMS) are being adopted to assist the automation of business processes that involve the exchange of information. As a result of developments in distributed information system technology, it is now possible to extend the WFMS idea to wider spheres of activity in the industrial and commercial world and thereby to encompass the increasingly sprawling nature of modern organisations. This paper describes a framework under development that employs such technology so that software tools and processes may interoperate in a distributed and dynamic environment. The framework employs Petri nets to model the interaction between various sub-processes. CORBA technology is used to enable different participants who are physically disparate to monitor activity in and make resource-level adaptations to their particular subnet.
Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection (2021)

Understanding immune memory to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for improving diagnostics and vaccines and for assessing the likely future course of the COVID-19 pandemic. We analyzed multiple compartments of circulating immune memory to SARS-CoV-2 in 254 samples from 188 COVID-19 cases, including 43 samples at ≥6 months after infection. Immunoglobulin G (IgG) to the spike protein was relatively stable over 6+ months. Spike-specific memory B cells were more abundant at 6 months than at 1 month after symptom onset. SARS-CoV-2-specific CD4<sup>+</sup> T cells and CD8<sup>+</sup> T cells declined with a half-life of 3 to 5 months. By studying antibody, memory B cell, CD4<sup>+</sup> T cell, and CD8<sup>+</sup> T cell memory to SARS-CoV-2 in an integrated manner, we observed that each component of SARS-CoV-2 immune memory exhibited distinct kinetics.
Automatic Discovery and Geotagging of Objects from Street View Imagery (2018)

Many applications, such as autonomous navigation, urban planning, and asset monitoring, rely on the availability of accurate information about objects and their geolocations. In this paper, we propose the automatic detection and computation of the coordinates of recurring stationary objects of interest using street view imagery. Our processing pipeline relies on two fully convolutional neural networks: the first segments objects in the images, while the second estimates their distance from the camera. To geolocate all the detected objects coherently we propose a novel custom Markov random field model to estimate the objects’ geolocation. The novelty of the resulting pipeline is the combined use of monocular depth estimation and triangulation to enable automatic mapping of complex scenes with the simultaneous presence of multiple, visually similar objects of interest. We validate experimentally the effectiveness of our approach on two object classes: traffic lights and telegraph poles. The experiments report high object recall rates and position precision of approximately 2 m, which is approaching the precision of single-frequency GPS receivers.
Self-directed channel memristor for high temperature operation (2016)

Ion-conducting memristors comprised of the layered chalcogenide materials Ge2Se3/SnSe/Ag are described. The memristor, termed a self-directed channel (SDC) device, can be classified as a generic memristor and can tolerate continuous high temperature operation (at least 150 °C). Unlike other chalcogenide-based ion conducting device types, the SDC device does not require complicated fabrication steps, such as photodoping or thermal annealing, making these devices faster and more reliable to fabricate. Device pulsed response shows fast state switching in the 10−9 s range. Device cycling at both room temperature and 140 °C show write endurance of at least 1 billion.
Evaluation of MPEG-4 IPMP Extension (2006)

MPEG-4 IPMPX (intellectual property management and protection extension) is the latest ISO standard which provides a flexible framework for protecting MPEG streams. The message mechanism of IPMPX enables interoperability among IPMPX-compliant devices no matter which protection methods are embedded. This paper highlights several problems in the message syntax of IPMPX: the tool delivery message IPMP/spl I.bar/ToolES/spl I.bar/AU is vulnerable to network attack, the authentication message IMP/spl I.bar/Mutual/spl I.bar/Authentication is incapable of defending against forgery attack, and the configuration message IPMP/spl I.bar/SelectiveDecrptionInit is ambiguous and redundant. We propose a number of remedies to those problems, which can be incorporated into a corrigenda to improve the present ISO MPEG-4 IPMP standard.
Features of rumen and sewage sludge strains of Eubacterium limosum, a methanol- and H2-CO2-utilizing species (1981)

Eubacterium limosum was isolated as the most numerous methanol-utilizing bacterium in the rumen fluid of sheep fed a diet in which molasses was a major component (mean most probable number of 6.3 X 10(8) viable cells per ml). It was also isolated from sewage sludge at 9.5 X 10(4) cells per ml. It was not detected in the rumen fluid of a steer on a normal hay-grain diet, although Methanosarcina, as expected, was found at 9.5 X 10(5) cells per ml. The doubling time of E. limosum in basal medium (5% rumen fluid) with methanol as the energy source (37 degree C) was 7 h. Acetate, cysteine, carbon dioxide, and the vitamins biotin, calcium-D-pantothenate, and lipoic acid were required for growth on a chemically defined methanol medium. Acetate, butyrate, and caproate were produced from methanol. Ammonia or each of several amino acids served as the main nitrogen source. Other energy sources included adonitol, arabitol, erythritol, fructose, glucose, isoleucine, lactate, mannitol, ribose, valine, and H2-CO2. The doubling time for growth on H2-CO2 (5% rumen fluid, 37 degree C) was 14 h as compared with 5.2 h for isoleucine and 3.5 h for glucose. The vitamin requirements for growth on H2-CO2 were the same as those for methanol; however, acetate was not required for growth on H2-CO2, although it was necessary for growth on valine, isoleucine, and lactate and was stimulatory to growth on glucose. Acetate and butyrate were formed during growth on H2-CO2, whereas branched-chain fatty acids and ammonia were fermentation products from the amino acids. Heat tolerance was detected, but spores were not observed. The type strain of E. limosum (ATCC 8486) and strain L34, which was isolated from the rumen of a young calf, grew on methanol, H2-CO2, valine, and isoleucine and showed the same requirements for acetate as the freshly isolated strains.
Classical deterministic complexity of Edmonds' Problem and quantum entanglement (2003)

Generalizing a decision problem for bipartite perfect matching, J. Edmonds introduced in [14] the problem (now known as the Edmonds Problem) of deciding if a given linear subspace of M(N) contains a nonsingular matrix, where M(N) stands for the linear space of complex NxN matrices. This problem led to many fundamental developments in matroid theory etc.Classical matching theory can be defined in terms of matrices with nonnegative entries. The notion of Positive operator, central in Quantum Theory, is a natural generalization of matrices with nonnegative entries. (Here operator refers to maps from matrices to matrices.) First, we reformulate the Edmonds Problem in terms of of completely positive operators, or equivalently, in terms of bipartite density matrices. It turns out that one of the most important cases when Edmonds' problem can be solved in polynomial deterministic time, i.e. an intersection of two geometric matroids, corresponds to unentangled (aka separable) bipartite density matrices. We introduce a very general class (or promise) of linear subspaces of M(N) on which there exists a polynomial deterministic time algorithm to solve Edmonds' problem. The algorithm is a thoroughgoing generalization of algorithms in [23], [26], and its analysis benefits from an operator analog of permanents, so called Quantum Permanents. Finally, we prove that the weak membership problem for the convex set of separable normalized bipartite density matrices is NP-HARD.
Thermal lens and beam properties in multiple longitudinally diode laser pumped Nd:YAG slab lasers (1996)

The focal length of the thermal lens and the beam quality factor (beam propagation factor) M/sup 2/ for a multiple longitudinally diode pumped slab laser is deduced for pump and output powers up to 16 and 4.5 W, respectively. Due to the geometry of the arrangement, a stronger thermal lens is observed in the plane with the larger pump spot radius as predicted by an analytical model for slab geometries. In addition, the second stable zone of an asymmetric resonator is found to be advantageous for improved beam properties at high output powers.
Statistical Qualitative Analysis on Chemical Mechanical Polishing Process and Equipment Characterization (2011)

The characterization of the chemical mechanical polishing (CMP) process for undensified phophosilicate glass (PSG) film is reported using design of experiments (DOE). DOE has been used by experimenters to understand the relationship between the input variables and responses of interest in a simple and efficient way, and it typically is beneficial for determining the appropriatesize of experiments with multiple process variables and making statistical inferences for the responses of interest. The equipment controllable parameters used to operate the machine consist of the down force of the wafer carrier, pressure on the back side wafer, table and spindle speeds (SS), slurry flow (SF) rate, pad condition, etc. None of these are independent ofeach other and, thus, the interaction between the parameters also needs to be understoodfor improved process characterization in CMP. In this study, we selected the five controllable equipment parameters the most recommendedby process engineers, viz. the down force (DF), back pressure (BP), table speed (TS), SS, and SF, for the characterization of the CMP process with respect to the material removal rate and film uniformity in percentage terms. The polished material is undensified PSG which is widely used for the plananization of multi-layered metal interconnects. By statistical modeling and the analysis of the metrology data acquired from a series of <TEX>$2^{5-1}$</TEX> fractional factorial designs with two center points, we showed that the DF, BP and TS have the greatest effect on both the removal rate and film uniformity, as expected. It is revealed that the film uniformity of the polished PSG film contains two and three-way interactions. Therefore, one can easily infer that process control based on a better understanding of the process is the key to success in current semiconductor manufacturing, in which the size of the wafer is approaching 300 mm and is scheduled to continuously increase up to 450 mm in or slightly after 2012.
Suppressor of cytokine signaling-1 mimetic peptides attenuate lymphocyte activation in the MRL/lpr mouse autoimmune model (2021)

Autoimmune diseases are driven largely by a pathogenic cytokine milieu produced by aberrantly activated lymphocytes. Many cytokines, including interferon gamma (IFN-γ), utilize the JAK/STAT pathway for signal propagation. Suppressor of Cytokine Signaling-1 (SOCS1) is an inducible, intracellular protein that regulates IFN-γ signaling by dampening JAK/STAT signaling. Using Fas deficient, MRL/MpJ-Fas<sup>lpr</sup>/J (MRL/lpr) mice, which develop lupus-like disease spontaneously, we tested the hypothesis that a peptide mimic of the SOCS1 kinase inhibitory region (SOCS1-KIR) would inhibit lymphocyte activation and modulate lupus-associated pathologies. Consistent with in vitro studies, SOCS1-KIR intraperitoneal administration reduced the frequency, activation, and cytokine production of memory CD8<sup>+</sup> and CD4<sup>+</sup> T lymphocytes within the peripheral blood, spleen, and lymph nodes. In addition, SOCS1-KIR administration reduced lymphadenopathy, severity of skin lesions, autoantibody production, and modestly reduced kidney pathology. On a cellular level, peritoneal SOCS1-KIR administration enhanced Foxp3 expression in total splenic and follicular regulatory T cells, reduced the effector memory/naïve T lymphocyte ratio for both CD4<sup>+</sup> and CD8<sup>+</sup> cells, and reduced the frequency of GL7<sup>+</sup> germinal center enriched B cells. Together, these data show that SOCS1-KIR treatment reduced auto-reactive lymphocyte effector functions and suggest that therapeutic targeting of the SOCS1 pathway through peptide administration may have efficacy in mitigating autoimmune pathologies.
Adaptation of hybrid human-computer interaction systems using EEG error-related potentials (2010)

Performance improvement in both humans and artificial systems strongly relies in the ability of recognizing erroneous behavior or decisions. This paper, that builds upon previous studies on EEG error-related signals, presents a hybrid approach for human computer interaction that uses human gestures to send commands to a computer and exploits brain activity to provide implicit feedback about the recognition of such commands. Using a simple computer game as a case study, we show that EEG activity evoked by erroneous gesture recognition can be classified in single trials above random levels. Automatic artifact rejection techniques are used, taking into account that subjects are allowed to move during the experiment. Moreover, we present a simple adaptation mechanism that uses the EEG signal to label newly acquired samples and can be used to re-calibrate the gesture recognition system in a supervised manner. Offline analysis show that, although the achieved EEG decoding accuracy is far from being perfect, these signals convey sufficient information to significantly improve the overall system performance.