gebhart/patrepeval huggingface dataset:
Optoacoustic micro-tomography at 100 volumes per second (2017)

Optical microscopy remains a fundamental tool for modern biological discovery owing to its excellent spatial resolution and versatile contrast in visualizing cellular and sub-cellular structures. Yet, the time domain is paramount for the observation of biological dynamics in living systems. Commonly, acquisition of microscopy data involves scanning of a spherically- or cylindrically-focused light beam across the imaged volume, which significantly limits temporal resolution in 3D. Additional complications arise from intense light scattering of biological tissues, further restraining the effective penetration depth and field of view of optical microscopy techniques. To overcome these limitations, we devised a fast optoacoustic micro-tomography (OMT) approach based on simultaneous acquisition of 3D image data with a high-density hemispherical ultrasound array having effective detection bandwidth beyond 25 MHz. We demonstrate fast three-dimensional imaging of freely-swimming zebrafish larvae, achieving 3D imaging speed of 100 volumes per second with isotropic spatial resolution approaching the dimensions of large cells across a field of view exceeding 50mm<sup>3</sup>. As opposed to other microscopy techniques based on optical contrast, OMT resolves optical absorption acoustically using unfocused light excitation. Thus, no penetration barriers are imposed by light scattering in deep tissues, suggesting it as a powerful approach for multi-scale functional and molecular imaging applications.
Novel and Unique Diagnostic Biomarkers for<i>Bacillus anthracis</i>Infection (2009)

A search for bacterium-specific biomarkers in peripheral blood following infection with Bacillus anthracis was carried out with rabbits, using a battery of specific antibodies generated by DNA vaccination against 10 preselected highly immunogenic bacterial antigens which were identified previously by a genomic/proteomic/serologic screen of the B. anthracis secretome. Detection of infection biomarkers in the circulation of infected rabbits could be achieved only after removal of highly abundant serum proteins by chromatography using a random-ligand affinity column. Besides the toxin component protective antigen, the following three secreted proteins were detected in the circulation of infected animals: the chaperone and protease HtrA (BA3660), an NlpC/P60 endopeptidase (BA1952), and a protein of unknown function harboring two SH3 (Src homology 3) domains (BA0796). The three proteins could be detected in plasma samples from infected animals exhibiting 10(3) to 10(5) CFU/ml blood and also in standard blood cultures at 3 to 6 h post-bacterial inoculation at a bacteremic level as low as 10(3) CFU/ml. Furthermore, the three biomarkers appear to be present only in the secretome of B. anthracis, not in those of the related pathogens B. thuringiensis and B. cereus. To the best of our knowledge, this is the first report of direct detection of B. anthracis-specific proteins, other than the toxin components, in the circulation of infected animals.
A GPU based high‐resolution multilevel biomechanical head and neck model for validating deformable image registration (2014)

Documenting dose delivery for HN radiotherapy is essential accounting for posture and physiological changes. The biomechanical model discussed in this paper was able to deform in real-time, allowing interactive simulations and visualization of such changes. The model would allow patient specific validations of the dir method and has the potential to be a significant aid in adaptive radiotherapy techniques.
High Energy Density Lithium–Sulfur Batteries: Challenges of Thick Sulfur Cathodes (2015)

High energy and cost‐effective lithium sulfur (Li–S) battery technology has been vigorously revisited in recent years due to the urgent need of advanced energy storage technologies for green transportation and large‐scale energy storage applications. However, the market penetration of Li–S batteries has been plagued due to the gap in scientific knowledge between the fundamental research and the real application need. Here, a facile and effective approach to integrate commercial carbon nanoparticles into microsized secondary ones for application in high loading sulfur electrodes is proposed The slurry with the integrated particles is easily cast into electrode laminates with practically usable mass loadings. Uniform and crack‐free coating with high loading of 2–8 mg cm −2 sulfur are successfully achieved. Based on the obtained thick electrodes, the dependence of areal specific capacity on mass loading, factors influencing electrode performance, and measures used to address the existing issues are studied and discussed.
Semantically-Aware Attentive Neural Embeddings for Image-based Visual Localization (2018)

We present an approach that combines appearance and semantic information for 2D image-based localization (2D-VL) across large perceptual changes and time lags. Compared to appearance features, the semantic layout of a scene is generally more invariant to appearance variations. We use this intuition and propose a novel end-to-end deep attention-based framework that utilizes multimodal cues to generate robust embeddings for 2D-VL. The proposed attention module predicts a shared channel attention and modality-specific spatial attentions to guide the embeddings to focus on more reliable image regions. We evaluate our model against state-of-the-art (SOTA) methods on three challenging localization datasets. We report an average (absolute) improvement of $19\%$ over current SOTA for 2D-VL. Furthermore, we present an extensive study demonstrating the contribution of each component of our model, showing $8$--$15\%$ and $4\%$ improvement from adding semantic information and our proposed attention module. We finally show the predicted attention maps to offer useful insights into our model.
Malware Task Identification: A Data Driven Approach (2015)

Identifying the tasks a given piece of malware was designed to perform (e.g. logging keystrokes, recording video, establishing remote access, etc.) is a difficult and time-consuming operation that is largely human-driven in practice. In this paper, we present an automated method to identify malware tasks. Using two different malware collections, we explore various circumstances for each - including cases where the training data differs significantly from test; where the malware being evaluated employs packing to thwart analytical techniques; and conditions with sparse training data. We find that this approach consistently out-performs the current state-of-the art software for malware task identification as well as standard machine learning approaches - often achieving an unbiased F1 score of over 0.9. In the near future, we look to deploy our approach for use by analysts in an operational cyber-security environment.
Human SULT1A1 gene: copy number differences and functional implications (2006)

SULT1A1, which catalyzes the sulfate conjugation of a wide variety of natural and synthetic compounds, is genetically polymorphic. Biochemical and pharmacogenetic studies have demonstrated that individual variation in the level of enzyme activity is inherited. Common single-nucleotide polymorphisms (SNPs) located in the open reading frame and in the 5'-flanking region (5'-FR) may account for a portion of this individual variation. In this study, we demonstrate the presence of SULT1A1 gene deletions and duplications, representing an additional source of variability in the metabolic activity of this enzyme. A quantitative multiplex PCR assay was used to measure the extent of copy number differences and the frequency of these events in different populations. An analysis of DNA from 362 Caucasian-American and 99 African-American showed the presence of 1 to approximately 5 copies of SULT1A1 in individual samples: 5% of Caucasian subjects contained a single copy of the gene and 26% had three or more copies, while 63% of African-American subjects had three or more copies. Analysis of the genomic region surrounding the SULT1A1 gene in three separate cases with a deletion demonstrated that the entire SULT1A1 gene was affected. Reporter assays, constructed for each of the various 5'-FR SNP haplotypes, suggest that these may also play a role in SULT1A1 activity. However, the variability in the level of enzyme activity among 23 human platelet and 267 human liver samples was best explained by gene copy number differences when all sources of genetic variability were considered (P < 0.0001). Overall, these observations have obvious implications for the effectiveness of SULT1A1 as a drug and hormone metabolizing enzyme and its potential role as a risk factor for disease.
Identification of an animal ω-3 fatty acid desaturase by heterologous expression in  <i>Arabidopsis</i> (1997)

In animals, fatty acid desaturases catalyze key reactions in the synthesis of arachidonic acid and other polyunsaturated fatty acids. A search of the Caenorhabditis elegans DNA databases, using the sequences of Arabidopsis genes, identified several putative desaturases. Here we describe the characterization of the first of these genes, fat-1. The predicted protein encoded by a fat-1 cDNA showed 32-35% identity with both FAD2 and FAD3 of Arabidopsis. When expressed in transgenic plants, fat-1 resulted in a 90% increase in the proportion of alpha-linolenic acid in root lipids. Wild-type Arabidopsis incorporated omega-6 fatty acids (delta8,11,14-20:3 and delta5,8,11,14-20:4) into membrane lipids but did not desaturate them. By contrast, fat-1 transgenic plants efficiently desaturated both of these fatty acids to the corresponding omega-3 products. These findings indicate that the C. elegans fat-1 gene encodes the first animal representative of a class of glycerolipid desaturases that have previously been characterized in plants and cyanobacteria. The FAT-1 protein is an omega-3 fatty acyl desaturase that recognizes a range of 18- and 20-carbon omega-6 substrates.
SwitchReduce: Reducing switch state and controller involvement in OpenFlow networks (2013)

OpenFlow is a popular network architecture where a logically centralized controller (the control plane) is physically decoupled from all forwarding switches (the data plane). Through this controller, the OpenFlow framework enables flow level granularity in switches thereby providing monitoring and control over each individual flow. Among other things, this architecture comes at the cost of placing significant stress on switch state size and overburdening the controller in various traffic engineering scenarios such as dynamic re-routing of flows. Storing a flow match rule and flow counter at every switch along a flow's path results in many thousands of entries per switch. Dynamic rerouting of a flow, either in an attempt to utilize less congested paths, or as a consequence of virtual machine migration, results in controller intervention at every switch along the old and new paths. In the absence of careful orchestration of flow storage and controller involvement, OpenFlow will be unable to scale to anticipated production data center sizes. In this context, we present SwitchReduce - a system to reduce switch state and controller involvement in OpenFlow networks. SwitchReduce is founded on the observation that the number of flow match rules at any switch should be no more than the set of unique processing actions it has to take on incoming flows. Additionally, the flow counters for every unique flow may be maintained at only one switch in the network. We have implemented SwitchReduce as a NOX controller application. Simulation results with real data center traffic traces reveal that SwitchReduce can reduce flow entries by up to approximately 49% on first hop switches, and up to 99.9% on interior switches, while reducing flow counters by 75% on average.
Targeting Notch in cancer with gamma-secretase inhibitors (2007)

C236 Gamma-secretase inhibitors are being evaluated for the treatment of cancers in which the Notch pathway has been activated. Inhibition of gamma-secretase activity prevents cleavage of the Notch receptor and release of the Notch Intracellular Domain, which regulates Notch-dependent gene expression. In vitro and in vivo models of T-ALL and other solid tumors have been developed to explore the mechanism of action of gamma-secretase inhibitors and to study the correlation pathway inhibition and anti-tumor efficacy.
High early strength calcium phosphate bone cement: Effects of dicalcium phosphate dihydrate and absorbable fibers (2005)

Calcium phosphate cement (CPC) sets in situ to form resorbable hydroxyapatite with chemical and crystallographic similarity to the apatite in human bones, hence it is highly promising for clinical applications. The objective of the present study was to develop a CPC that is fast setting and has high strength in the early stages of implantation. Two approaches were combined to impart high early strength to the cement: the use of dicalcium phosphate dihydrate with a high solubility (which formed the cement CPC(D)) instead of anhydrous dicalcium phosphate (which formed the conventional cement CPC(A)), and the incorporation of absorbable fibers. A 2 x 8 design was tested with two materials (CPC(A) and CPC(D)) and eight levels of cement reaction time: 15 min, 30 min, 1 h, 1.5 h, 2 h, 4 h, 8 h, and 24 h. An absorbable suture fiber was incorporated into cements at 25% volume fraction. The Gilmore needle method measured a hardening time of 15.8 min for CPC(D), five-fold faster than 81.5 min for CPC(A), at a powder:liquid ratio of 3:1. Scanning electron microscopy revealed the formation of nanosized rod-like hydroxyapatite crystals and platelet crystals in the cements. At 30 min, the flexural strength (mean +/- standard deviation; n = 5) was 0 MPa for CPC(A) (the paste did not set), (4.2 +/- 0.3) MPa for CPC(D), and (10.7 +/- 2.4) MPa for CPC(D)-fiber specimens, significantly different from each other (Tukey's at 0.95). The work of fracture (toughness) was increased by two orders of magnitude for the CPC(D)-fiber cement. The high early strength matched the reported strength for cancellous bone and sintered porous hydroxyapatite implants. The composite strength S(c) was correlated to the matrix strength S(m): S(c) = 2.16S(m). In summary, substantial early strength was imparted to a moldable, self-hardening and resorbable hydroxyapatite via two synergistic approaches: dicalcium phosphate dihydrate, and absorbable fibers. The new fast-setting and strong cement may help prevent catastrophic fracture or disintegration in moderate stress-bearing bone repairs.
Fully self-aligned tri-layer a-Si:H thin-film transistors with deposited doped contact layer (1998)

We demonstrate a new self-aligned TFT process for hydrogenated amorphous silicon thin-film transistors (a-Si:H TFTs). Two backside exposure photolithography steps are used to fabricate fully self-aligned tri-layer TFTs with deposited n/sup +/ contacts. Since no critical data alignment is required, this simple process is well suited to fabrication of short channel TFTs. We have fabricated fully self-aligned tri-layer a-Si:H TFTs with excellent device performance, and contact overlaps <1 μm. For a 20-μm channel length TFT with an a-Si:H thickness of 13 nm, the linear region (V/sub DS/=0.1 V) and saturation region (V/sub DS/=25 V) extrinsic mobility values are both 1.2 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /V-s, the off currents are <1 pA, and the on/off current ratio is >10/sup 7/.
Toward Flexible Microwave Ablation Antennas With a Balun-Free Helical Dipole Design (2020)

We present a balun-free dipole antenna for generating localized heating patterns in microwave ablation. The dipole antenna is created by extending the outer and inner conductors of the coaxial cable. One dipole arm is a helical outer conductor encompassing the other arm that is the extended inner conductor. The overall lengths of the helix and the extended inner conductor are three quarters and one quarter of a wavelength, respectively. The helix's current direction reverses a quarter of a wavelength away from the feed point, becoming aligned with the extended inner conductor's current. This creates a relatively low-input impedance, choking the current on the outer surface of the outer conductor. The fields produced by the currents flowing on the dipole arms destructively interfere closer to the feed point, while constructively interfering further from it. This helps the antenna produce nearly spherical ablation zones. A 1.9 GHz prototype of the antenna was fabricated and its ablation performance was experimentally verified in egg white. Measurement results showed good agreement with the simulations and confirmed the antenna's effectiveness in generating localized ablation zones. Our proposed design can serve as a promising candidate for performing minimally invasive ablation therapy within flexible and maneuverable embodiments.
Quantum cryptography: uncertainty in the service of privacy (1993)

a cryptographic key, enabling Alice to scramble her messages in a way only Bob, knowing the same key, could unscramble. Privacy thus appeared to be generally unavailable to users lacking the means and foresight by which diplomats and spies share secret keys with their intended correspondents. Classical cryptography offered no purely mathematical solution to this &quot;key distribution problem &quot;. Meanwhile the only solution to the discreet communications problem appeared to be for Alice and Bob to confide their secrets in a trusted intermediary, who might later choose to blackmail them. All this was changed by PKC. The idea of PKC is for each user (eg Alice) to randomly choose a pair of mutually inverse transformations---a scrambling transformation and an unscrambling transformation---and to publish the directions for performing the former but not the latter. Anyone, including Bob, can then use Alice&apos;s public scrambling algorithm to prepare a message that only she can unscramble. Si
Capillary Foams: Stabilization and Functionalization of Porous Liquids and Solids (2015)

Liquid foams are two-phase systems in which a large volume of gas is dispersed as bubbles in a continuous liquid phase. These foams are ubiquitous in nature. In addition, they are found in industrial applications, such as pharmaceutical formulation, food processing, wastewater treatment, construction, and cosmetics. Recently, we reported a new type of foam material, capillary foam, which is stabilized by the synergistic action of particles and a small amount of an immiscible secondary liquid. In this study, we explore in more detail the foam preparation routes. To illustrate some of the potential applications, we create vividly colored wet and dried foams, which are difficult to prepare using traditional methods, and load-bearing porous solids. The combined action of particles and immiscible secondary fluid confers exceptional stability to capillary foams and many options for functionalization, suggesting a wide range of possible applications.
Guaranteeing synchronous message deadlines with the timed token medium access control protocol (1994)

We study the problem of guaranteeing synchronous message deadlines in token ring networks where the timed token medium access control protocol is employed. Synchronous bandwidth, defined as the maximum time for which a node can transmit its synchronous messages every time it receives the token, is a key parameter in the control of synchronous message transmission. To ensure the transmission of synchronous messages before their deadlines, synchronous capacities must be properly allocated to individual nodes. We address the issue of appropriate allocation of the synchronous capacities. Several synchronous bandwidth allocation schemes are analyzed in terms of their ability to satisfy deadline constraints of synchronous messages. We show that an inappropriate allocation of the synchronous capacities could cause message deadlines to be missed, even if the synchronous traffic is extremely low. We propose a scheme, called the normalized proportional allocation scheme, which can guarantee the synchronous message deadlines for synchronous traffic of up to 33% of available utilization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The life cycle of a T cell after vaccination – where does immune ageing strike? (2016)

Vaccination is the optimal intervention to prevent the increased morbidity and mortality from infection in older individuals and to maintain immune health during ageing. To optimize benefits from vaccination, strategies have to be developed that overcome the defects in an adaptive immune response that occur with immune ageing. Most current approaches are concentrated on activating the innate immune system by adjuvants to improve the induction of a T cell response. This review will focus upon T cell-intrinsic mechanisms that control how a T cell is activated, expands rapidly to differentiate into short-lived effector cells and into memory precursor cells, with short-lived effector T cells then mainly undergoing apoptosis and memory precursor cells surviving as long-lived memory T cells. Insights into each step of this longitudinal course of a T cell response that takes place over a period of several weeks is beginning to allow identifying interventions that can improve this process of T cell memory generation and specifically target defects that occur with ageing.
Triangle order optimization for graphics hardware computation culling (2006)

In Nehab et al. [2006], we describe an automatic preprocessing algorithm that reorders triangles in a mesh so as to enable the graphics hardware to efficiently cull both vertex and pixel processing at rendering time. Our method brings the overdraw rates of a wide range of models close to that of front-to-back order, while preserving state-of-the-art vertex cache performance. This results in higher frame rates for pixel-bound applications with no penalty to vertex-bound applications.
Insights into the Organotemplate-Free Synthesis of Zeolite Catalysts (2017)

As the most important nanoporous material, zeolites, which have intricate micropores, are essential heterogeneous catalysts in industrial processes. Zeolites are generally synthesized with organic templates under hydrothermal conditions; however, this method is environmentally unfriendly and costly due to the formation of harmful gases and polluted water. This article briefly summarizes the role of organic templates and describes designed routes for the organotemplate-free synthesis of zeolites, aided by zeolite seeds and zeolite seeds solution. Furthermore, this review explicates that the micropore volume decreases with an increase of the Si/Al ratios in the organotemplate-free synthesis of zeolite products, where Na+ exists as an alkali cation. This feature is very important in directing the synthesis of zeolite catalysts with controllable Si/Al ratios under organotemplate-free conditions, and is thus important for the efficient design of zeolites.
Chemoselective Tertiary C−H Hydroxylation for Late‐Stage Functionalization with Mn(PDP)/Chloroacetic Acid Catalysis (2019)

Aromatic and heterocyclic functionality are ubiquitous in pharmaceuticals. Herein, we disclose a new Mn(PDP)catalyst system using chloroacetic acid additive capable of chemoselectively oxidizing remote tertiary C(<i>sp</i> <sup>3</sup>)-H bonds in the presence of a broad range of aromatic and heterocyclic moieties. Although catalyst loadings can be lowered to 0.1 mol% under a Mn(PDP)/acetic acid system for aromatic and non-basic nitrogen heterocycle substrates, the Mn(PDP)/chloroacetic acid system generally affords 10-15% higher isolated yields on these substrates and is uniquely effective for remote C(<i>sp</i> <sup>3</sup>)-H hydroxylations in substrates housing basic nitrogen heterocycles. The demonstrated ability to perform Mn(PDP)/chloroacetic acid C(<i>sp</i> <sup>3</sup>)-H oxidations in pharmaceutically relevant complex molecules on multi-gram scales will facilitate drug discovery processes via late-stage functionalization.