gebhart/patrepeval huggingface dataset:
Design of wireless sensor networks based on ZigBee stack (2012)

First,the basic topological structures of wireless sensor network and the structure of sensor node are introduced.The starting-up process of wireless sensor network based on ZigBee stack is explained in details,including startup and establishing network of coordinator,startup and joining network of sensor node,binding between sensor nodes and coordinator,and the process of terminal nodes sending data to coordinator.The wireless sensor network is designed based on ZigBee stack.Taking sampling temperature information as a example,the coordinator can collect the information from sensor nodes,and send them to PC by using RS232.The temperature information can be displayed in PC.The experiment shows that good communication quality of this system can be obtained,although at the distance of 80 meters.
High-precision Secure Computation of Satellite Collision Probabilities. (2016)

The costs of designing, building, launching and maintaining satellites make satellite operators extremely motivated to protect their on-orbit assets. Unfortunately, privacy concerns present a serious barrier to coordination between different operators. One obstacle to improving safety arises because operators view the trajectories of their satellites as private, and refuse to share this private information with other operators. Without data-sharing, preventing collisions between satellites becomes a challenging task. A 2014 report from the RAND Corporation proposed using cryptographic tools from the domain of secure Multiparty Computation MPC to allow satellite operators to calculate collision probabilities conjunction analyses without sharing private information about the trajectories of their satellites.

In this work, we report on the design and implementation of a new MPC framework for high-precision arithmetic on real-valued variables in a two-party setting where, unlike previous works, there is no honest majority, and where the players are not assumed to be semi-honest. We show how to apply this new solution in the domain of securely computing conjunction analyses. Our solution integrates the integer-based Goldreich-Micali-Wigderson GMW protocol and Garbled Circuits GC. We prove security of our protocol in the two party, semi-honest setting, assuming only the existence of one-way functions and Oblivious Transfer the OT-hybrid model. The protocol allows a pair of satellite operators to compute the probability that their satellites will collide without sharing their underlying private orbital information. Techniques developed in this paper would potentially have a wide impact on general secure numerical analysis computations. We also show how to strengthen our construction with standard arithmetic message-authentication-codes MACs to enforce honest behavior beyond the semi-honest setting.

Computing a conjunction analysis requires numerically estimating a complex triple integral to a high degree of precision. The complexity of the calculation, and the possibility of numeric instability presents many challenges for MPC protocols which typically model calculations as simple integer arithmetic or binary circuits. Our secure numerical integration routines are extremely stable and efficient, and our secure conjunction analysis protocol takes only a few minutes to run on a commodity laptop.

The full version appears ini?ź[HLOW16].
Cutting Edge: The Mucosal Adjuvant Cholera Toxin Redirects Vaccine Proteins into Olfactory Tissues (2000)

We tested the notion that the mucosal adjuvant cholera toxin (CT) could target, in addition to nasal-associated lymphoreticular tissues, the olfactory nerves/epithelium (ON/E) and olfactory bulbs (OBs) when given intranasally. Radiolabeled CT ((125)I-CT) or CT-B subunit ((125)I-CT-B), when given intranasally to mice, entered the ON/E and OB and persisted for 6 days; however, neither molecule was present in nasal-associated lymphoreticular tissues beyond 24 h. This uptake into olfactory regions was monosialoganglioside (GM1) dependent. Intranasal vaccination with (125)I-tetanus toxoid together with unlabeled CT as adjuvant resulted in uptake into the ON/E but not the OB, whereas (125)I-tetanus toxoid alone did not penetrate into the CNS. We conclude that GM1-binding molecules like CT target the ON/E and are retrograde transported to the OB and may promote uptake of vaccine proteins into olfactory neurons. This raises concerns about the role of GM1-binding molecules that target neuronal tissues in mucosal immunity.
CpG Island Methylator Phenotype Associates with Low-Degree Chromosomal Abnormalities in Colorectal Cancer (2008)

CIMP-positive tumors generally possess lower chromosomal aberrations, which may only be revealed using a genome-wide approach. The significant difference in the degree of chromosomal aberrations between CIMP-positive and the remainder of samples suggests that epigenetic (CIMP) and genetic (CIN) abnormalities may arise from independent molecular mechanisms of tumor progression.
PEG-b-AGE polymer coated magnetic nanoparticle probes with facile functionalization and anti-fouling properties for reducing non-specific uptake and improving biomarker targeting (2015)

Non-specific surface adsorption of bio-macromolecules (e.g. proteins) on nanoparticles, known as biofouling, and the uptake of nanoparticles by the mononuclear phagocyte system (MPS) and reticuloendothelial system (RES) lead to substantial reduction in the efficiency of target-directed imaging and delivery in biomedical applications of engineered nanomaterials <i>in vitro</i> and <i>in vivo</i>. In this work, a novel copolymer consisting of blocks of poly ethylene glycol and allyl glycidyl ether (PEG-<i>b</i>-AGE) was developed for coating magnetic iron oxide nanoparticles (IONPs) to reduce non-specific protein adhesion that leads to formation of "protein corona" and uptake by macrophages. The facile surface functionalization was demonstrated by using targeting ligands of a small peptide of RGD or a whole protein of transferrin (Tf). The PEG-<i>b</i>-AGE coated IONPs exhibited anti-biofouling properties with significantly reduced protein corona formation and non-specific uptake by macrophages before and after the surface functionalization, thus improving targeting of RGD-conjugated PEG-<i>b</i>-AGE coated IONPs to integrins in U87MG glioblastoma and MDA-MB-231 breast cancer cells that overexpress α<sub>v</sub>β<sub>3</sub> integrins, and Tf-conjugated PEG-<i>b</i>-AGE coated IONPs to transferrin receptor (TfR) in D556 and Daoy medulloblastoma cancer cells with high overexpression of transferrin receptor, compared to respective control cell lines. Magnetic resonance imaging (MRI) of cancer cells treated with targeted IONPs with or without anti-biofouling PEG-<i>b</i>-AGE coating polymers demonstrated the target specific MRI contrast change using anti-biofouling PEG-<i>b</i>-AGE coated IONP with minimal off-targeted background compared to the IONPs without anti-biofouling coating, promising the highly efficient active targeting of nanoparticle imaging probes and drug delivery systems and potential applications of imaging quantification of targeted biomarkers.
Multiplexed Charge Detection Mass Spectrometry for High-Throughput Single Ion Analysis of Large Molecules (2019)

Applications of charge detection mass spectrometry (CDMS) for measuring the masses of large molecules, macromolecular complexes, and synthetic polymers that are too large or heterogeneous for conventional mass spectrometry measurements are made possible by weighing individual ions in order to avoid interferences between ions. Here, a new multiplexing method that makes it possible to measure the masses of many ions simultaneously in CDMS is demonstrated. Ions with a broad range of kinetic energies are trapped. The energy of each ion is obtained from the ratio of the intensity of the fundamental to the second harmonic frequencies of the periodic trapping motion making it possible to measure both the m/ z and charge of each ion. Because ions with the exact same m/ z but with different energies appear at different frequencies, the probability of ion-ion interference is significantly reduced. We show that the measured mass of a protein complex consisting of 16 protomers, RuBisCO (517 kDa), is not affected by the number of trapped ions with up to 21 ions trapped simultaneously in these experiments. Ion-ion interactions do not affect the ion trapping lifetime up to 1 s, and there is no influence of the number of ions on the measured charge-state distribution of bovine serum albumin (66.5 kDa), indicating that ion-ion interactions do not adversely affect any of these measurements. Over an order of magnitude gain in measurement speed over single ion analysis is demonstrated, and significant additional gains are expected with this multi-ion measurement method.
Discrimination Between Intracellular Uptake and Surface Adhesion of Bacterial Pathogens (1991)

Most bacterial pathogens initiate infectious diseases by adhering to host cells. Bacterial adherence to nonphagocytic cells usually leads to extracellular colonization; however, many invasive microorganisms enter host cells after binding to the host cell surface. It is unclear why bacterial adherence can result in these two different fates for the microorganism. Analyses of model systems, such as the uptake of enteropathogenic Yersinia into cultured cells, indicate that the particular mammalian cell receptors bound and the nature of the binding event dictate whether the bacterium remains extracellular or enters host cells.
Accelerated Ray Traced Animations Exploiting Temporal Coherence (2005)

Ray tracing is a well-know technique for producing realistic graphics. However, the time necessary to generate images is unacceptably long. When producing the many frames that are necessary for animations, the time is magnified. Many methods have been proposed to reduce the calculations necessary in ray tracing. Much of the effort has attempted to reduce the number of rays cast or to reduce the number of intersection calculations. Both of these techniques exploit spatial coherence. These acceleration techniques are expanded not only to exploit spatial coherence but also to exploit temporal coherence in order to reduce calculations by treating animation information as a whole as opposed to isolating calculations to each individual frame. Techniques for exploiting temporal coherence are explored along with associated temporal bounding methods. By first ray tracing a temporally expanded scene, we are able to avoid traversal calculations in associated frames where object intersection is limited. This reduces the rendering times of the associated frames.
The Plight of the Bees (2010)

The loss of biodiversity is a trend that is garnering much concern. As organisms have evolved mutualistic and synergistic relationships, the loss of one or a few species can have a much wider environmental impact. Since much pollination is facilitated by bees, the reported colony collapse disorder has many worried of widespread agricultural fallout and thus deleterious impact on human foodstocks. In this Feature, Spivak et al. review what is known of the present state of bee populations and provide information on how to mitigate and reverse the trend.
Hierarchical optical proximity correction on contact hole layers (2002)

As the size of contact holes shrinks below 0.2 /spl mu/m, optical proximity correction (OPC) on contact hole layers becomes essential. When correcting contact holes, 1-dimensional correction is not applicable, and 2-dimensional correction is required, which needs much more intensive computation. To reduce computation, it is very effective to take advantage of the hierarchy of the input data. In order to further accelerate the OPC calculation, we adopted pattern matching into the OPC system, which can extract the hierarchy implicit in the layout data.
The human papillomavirus E6 and E7 inducible oncogene, hWAPL, exhibits potential as a therapeutic target (2005)

Here we show that human papillomavirus (HPV) E6 and E7 oncoproteins induce hWAPL expression. In addition, small interfering RNA (siRNA) of hWAPL suppressed the growth of tumours derived from SiHa cells in nude mice. Thus, hWAPL may be one of the effective targets of uterine cervical cancer therapy.
[Transobturator tape (Uratape). A new minimally invasive method in the treatment of urinary incontinence in women]. (2003)

Transobturator Uratape is a simple and effective procedure with a follow-up of one year for the treatment of female stress urinary incontinence. The transobturator approach avoids the risks of bladder, intestinal and vascular injuries. Evaluation of the results with a longer follow-up is necessary to validate this technique.
Network Coding Applications for 5G Millimeter-Wave Communications (2015)

The millimeter-wave bands have been attracting significant interest as a means to achieve major improvements in data rates and network efficiencies. One significant limitation for use of the millimeter-wave bands for cellular communication is that the communication suffers from much higher path-loss compared to the microwave bands. Millimeter-wave links have also been shown to change rapidly, causing links between devices and access points to switch among line-of-sight, non-line-of-sight and outage states. We propose using Random Linear Network Coding to overcome the unreliability of individual communication links in such millimeter-wave systems. Our system consists of devices transmitting and receiving network-coded packets through several access points. For downlink communication, network-coded packets are transmitted to a device via multiple access points. For uplink communication, the access points perform network coding of packets of several devices, and then send the network-coded packets to the core network. We compare our approach against a naive approach in which non-network coded packets are transmitted via multiple access points ("Forwarding" approach). We find that the network coding approach significantly outperforms the forwarding approach. In particular, network coding greatly improves the efficiency of the air-interface transmissions and the efficiency of the backhaul transmissions for the downlink and uplink communication, respectively.
Structural Implications for Selective Targeting of PARPs (2013)

Poly(ADP-ribose) polymerases (PARPs) are a family of enzymes that use NAD(+) as a substrate to synthesize polymers of ADP-ribose (PAR) as post-translational modifications of proteins. PARPs have important cellular roles that include preserving genomic integrity, telomere maintenance, transcriptional regulation, and cell fate determination. The diverse biological roles of PARPs have made them attractive therapeutic targets, which have fueled the pursuit of small molecule PARP inhibitors. The design of PARP inhibitors has matured over the past several years resulting in several lead candidates in clinical trials. PARP inhibitors are mainly used in clinical trials to treat cancer, particularly as sensitizing agents in combination with traditional chemotherapy to reduce side effects. An exciting aspect of PARP inhibitors is that they are also used to selectivity kill tumors with deficiencies in DNA repair proteins (e.g., BRCA1/2) through an approach termed "synthetic lethality." In the midst of the tremendous efforts that have brought PARP inhibitors to the forefront of modern chemotherapy, most clinically used PARP inhibitors bind to conserved regions that permits cross-selectivity with other PARPs containing homologous catalytic domains. Thus, the differences between therapeutic effects and adverse effects stemming from pan-PARP inhibition compared to selective inhibition are not well understood. In this review, we discuss current literature that has found ways to gain selectivity for one PARP over another. We furthermore provide insights into targeting other domains that make up PARPs, and how new classes of drugs that target these domains could provide a high degree of selectivity by affecting specific cellular functions. A clear understanding of the inhibition profiles of PARP inhibitors will not only enhance our understanding of the biology of individual PARPs, but may provide improved therapeutic options for patients.
Comparison of autofocus methods for automated microscopy (1991)

Traditional autofocus methods were designed for microscopes driven by single processor computers. As computers are developed that exploit massive parallelism when acquiring and analyzing images, parallel cellular logic techniques became available to focus automatically. This paper introduces the reader to both cellular logic techniques for autofocus and a new spectral moment autofocus measure. It then compares these methods with more traditional autofocus methods. It is shown that traditional methods based on measurements of image power-give the best results when tested on one set of real images and two sets of synthetic images. The next best methods are the cellular logic and spectral moment techniques, while the worst are those based on the image probability density function or histogram.
Improved Pulsed Neutron Capture Logging With Slim Carbon-Oxygen Tools: Methodology (1995)

Abstract Recently, two new slim through-tubing carbon-oxygen tools were introduced and described in the literature. In addition to carbon-oxygen water-saturation capability, these new instruments can provide, during the same trip, pulsed neutron capture (PNC) measurements (formation sigma, porosity, borehole fluid salinity, etc.). The answers have improved accuracy and precision compared to prior logging instruments. This paper describes the Dual-Burst* PNC measurement scheme for the RST* Reservoir Saturation Tool, as well as the algorithm methodology for determining corrected sigma, porosity, borehole fluid salinity, log quality and other associated outputs. Also documented are database measurements on which the algorithms are based, accuracy benchmarks in industry-standard calibration facilities, and precision (repeatability) comparisons. Log examples are presented. Diffusion, borehole and lithology effects must be considered when transforming observed quantities such as decay times or near-to-far ratios to actual physical quantities. However, these effects are difficult to account for in direct analytical approaches over the entire range of oilfield conditions. Therefore, a multidimensional dynamic parameterization technique, based on an extensive set of laboratory measurements, has been developed and refined. This technique keeps the order of parameters low, resulting in a well-behaved response both inside and outside the range spanned by the database. The supporting database for each tool includes over 1000 measured points augmented with approximately 400 modeled points spanning different lithologies, porosities, borehole sizes, casing sizes and weights, formation fluid salinities, and borehole fluid salinities typically encountered in the oilfield. Also reported are the sigma and porosity accuracy benchmark measurements made in the industry-standard calibration facilities (EUROPA facility, Aberdeen, Scotland and API test pits, University of Houston, Houston, Texas, USA). Precision (repeatability) is also compared to prior PNC logging instruments, demonstrating logging speeds typically several times faster for comparable precision.
Mid-infrared field-tunable intersubband electroluminescence at room temperature by photon-assisted tunneling in coupled-quantum wells (1994)

Electroluminescence associated with intersubband transition energies greater than the optical phonon energy and at temperatures as high as 300 K is reported. The mid-infrared (λ∼5 μm) luminescence is generated by electron injection into AlInAs/GaInAs coupled-quantum wells via an AlInAs/GaInAs pseudoquaternary graded gap alloy. Optical powers up to a few nanowatts and linear in the drive current have been measured. The large Stark shift of the luminescence peak demonstrates the photon-assisted tunneling nature of the transition. The temperature independence of the luminescence slope efficiency in the 10–100 K range and the linearity of the optical power versus drive current provide strong evidence of population inversion.
High-throughput computational design of cathode coatings for Li-ion batteries (2016)

Cathode degradation is a key factor that limits the lifetime of Li-ion batteries. To identify functional coatings that can suppress this degradation, we present a high-throughput density functional theory based framework which consists of reaction models that describe thermodynamic and electrochemical stabilities, and acid-scavenging capabilities of materials. Screening more than 130,000 oxygen-bearing materials, we suggest physical and hydrofluoric-acid barrier coatings such as WO<sub>3</sub>, LiAl<sub>5</sub>O<sub>8</sub> and ZrP<sub>2</sub>O<sub>7</sub> and hydrofluoric-acid scavengers such as Sc<sub>2</sub>O<sub>3</sub>, Li<sub>2</sub>CaGeO<sub>4</sub>, LiBO<sub>2</sub>, Li<sub>3</sub>NbO<sub>4</sub>, Mg<sub>3</sub>(BO<sub>3</sub>)<sub>2</sub> and Li<sub>2</sub>MgSiO<sub>4</sub>. Using a design strategy to find the thermodynamically optimal coatings for a cathode, we further present optimal hydrofluoric-acid scavengers such as Li<sub>2</sub>SrSiO<sub>4</sub>, Li<sub>2</sub>CaSiO<sub>4</sub> and CaIn<sub>2</sub>O<sub>4</sub> for the layered LiCoO<sub>2</sub>, and Li<sub>2</sub>GeO<sub>3</sub>, Li<sub>4</sub>NiTeO<sub>6</sub> and Li<sub>2</sub>MnO<sub>3</sub> for the spinel LiMn<sub>2</sub>O<sub>4</sub> cathodes. These coating materials have the potential to prolong the cycle-life of Li-ion batteries and surpass the performance of common coatings based on conventional materials such as Al<sub>2</sub>O<sub>3</sub>, ZnO, MgO or ZrO<sub>2</sub>.
Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale (1997)

DNA microarrays containing virtually every gene of Saccharomyces cerevisiae were used to carry out a comprehensive investigation of the temporal program of gene expression accompanying the metabolic shift from fermentation to respiration. The expression profiles observed for genes with known metabolic functions pointed to features of the metabolic reprogramming that occur during the diauxic shift, and the expression patterns of many previously uncharacterized genes provided clues to their possible functions. The same DNA microarrays were also used to identify genes whose expression was affected by deletion of the transcriptional co-repressor TUP1 or overexpression of the transcriptional activator YAP1. These results demonstrate the feasibility and utility of this approach to genomewide exploration of gene expression patterns.
Easy as ABC? (2008)

Pictorial communication systems convert natural language text into pictures to assist people with limited literacy. We define a novel and challenging problem: picture layout optimization. Given an input sentence, we seek the optimal way to lay out word icons such that the resulting picture best conveys the meaning of the input sentence. To this end, we propose a family of intuitive "ABC" layouts, which organize icons in three groups. We formalize layout optimization as a sequence labeling problem, employing conditional random fields as our machine learning method. Enabled by novel applications of semantic role labeling and syntactic parsing, our trained model makes layout predictions that agree well with human annotators. In addition, we conduct a user study to compare our ABC layout versus the standard linear layout. The study shows that our semantically enhanced layout is preferred by non-native speakers, suggesting it has the potential to be useful for people with other forms of limited literacy, too.