gebhart/patrepeval huggingface dataset:
HIV-1 envelope, integrins and co-receptor use in mucosal transmission of HIV (2011)

It is well established that HIV-1 infection typically involves an interaction between the viral envelope protein gp120/41 and the CD4 molecule followed by a second interaction with a chemokine receptor, usually CCR5 or CXCR4. In the early stages of an HIV-1 infection CCR5 using viruses (R5 viruses) predominate. In some viral subtypes there is a propensity to switch to CXCR4 usage (X4 viruses). The receptor switch occurs in ~ 40% of the infected individuals and is associated with faster disease progression. This holds for subtypes B and D, but occurs less frequently in subtypes A and C. There are several hypotheses to explain the preferential transmission of R5 viruses and the mechanisms that lead to switching of co-receptor usage; however, there is no definitive explanation for either. One important consideration regarding transmission is that signaling by R5 gp120 may facilitate transmission of R5 viruses by inducing a permissive environment for HIV replication. In the case of sexual transmission, infection by HIV requires the virus to breach the mucosal barrier to gain access to the immune cell targets that it infects; however, the immediate events that follow HIV exposure at genital mucosal sites are not well understood. Upon transmission, the HIV quasispecies that is replicating in an infected donor contracts through a "genetic bottleneck", and often infection results from a single infectious event. Many details surrounding this initial infection remain unresolved. In mucosal tissues, CD4(+) T cells express high levels of CCR5, and a subset of these CD4(+)/CCR5(high) cells express the integrin α₄β₇, the gut homing receptor. CD4(+)/CCR5(high)/ α4β7(high) T cells are highly susceptible to infection by HIV-1 and are ideal targets for an efficient productive infection at the point of transmission. In this context we have demonstrated that the HIV-1 envelope protein gp120 binds to α₄β₇ on CD4(+) T cells. On CD4(+)/CCR5(high)/ α4β7(high) T cells, α₄β₇ is closely associated with CD4 and CCR5. Furthermore, α₄β₇ is ~3 times the size of CD4 on the cell surface, that makes it a prominent receptor for an efficient virus capture. gp120-α₄β₇ interactions mediate the activation of the adhesion-associated integrin LFA-1. LFA-1 facilitates the formation of virological synapses and cell-to-cell spread of HIV-1. gp120 binding to α₄β₇ is mediated by a tripeptide located in the V1/V2 domain of gp120. Of note, the V1/V2 domain of gp120 has been linked to variations in transmission fitness among viral isolates raising the intriguing possibility that gp120-α₄β₇ interactions may be linked to transmission fitness. Although many details remain unresolved, we hypothesize that gp120-α₄β₇ interactions play an important role in the very early events following sexual transmission of HIV and may have important implication in the design of vaccine strategies for the prevention of acquisition of HIV infection.
Adam Induces Implicit Weight Sparsity in Rectifier Neural Networks (2018)

In recent years, deep neural networks (DNNs) have been applied to various machine leaning tasks, including image recognition, speech recognition, and machine translation. However, large DNN models are needed to achieve state-of-the-art performance, exceeding the capabilities of edge devices. Model reduction is thus needed for practical use. In this paper, we point out that deep learning automatically induces group sparsity of weights, in which all weights connected to an output channel (node) are zero, when training DNNs under the following three conditions: (1) rectified-linear-unit (ReLU) activations, (2) an L2-regularized objective function, and (3) the Adam optimizer. Next, we analyze this behavior both theoretically and experimentally, and propose a simple model reduction method: eliminate the zero weights after training the DNN. In experiments on MNIST and CIFAR-10 datasets, we demonstrate the sparsity with various training setups. Finally, we show that our method can efficiently reduce the model size and performs well relative to methods that use a sparsity-inducing regularizer.
Ultrafast Charge Transfer in Amino-Substituted Boron Dipyrromethene Dyes and Its Inhibition by Cation Complexation:  A New Design Concept for Highly Sensitive Fluorescent Probes (1998)

The photophysical behavior of a newly synthesized aza crown-substituted boron−dipyrromethene (BDP) dye and its dimethylamino analogue were investigated with steady-state and time-resolved fluorometry and compared to a reference compound. In solvents more polar than hexane, excitation of the dyes leads to a fast charge transfer from the locally excited (LE) state to a weakly emissive charge-transfer (CT) state. The donor-substituted compounds show dual emission from the LE and CT state, both fluorescence quantum yields being low. The rate constant of excited-state charge separation, calculated from the global analysis of time-resolved emission data, was determined to 1.6 × 1011 s-1 in 1,4-dioxane. The crowned compound forms 1:1-complexes with various alkali and alkaline-earth metal ions, which exist as two conformers in solution. In these complexes, coordination of the cation to the nitrogen donor atom of the crown inhibits the charge-transfer process, leading to a cation-dependent enhancement of the LE emission and the fluorescence lifetimes by factors >103. This efficient “switching on” of the fluorescence renders the crowned BDP dye an extremely sensitive fluorescent probe for metal ions.
REPRESENTAÇÕES GRÁFICAS ESPACIAIS EM GEOCIÊNCIAS AUXILIADAS POR COMPUTADOR (1988)

This paper presents a revision of the current methodology for computer aided graphical displaying of geological data. The main techniques and mathematical concepts of computer graphics,i.e., interpolation, determination of convex hull, determination of the position of a point relative to convex hull, automatic contouring, and hidden line elimination are presented and discussed. Aplications over real topographical and chemical data from the Anitápolis Alkaline Complex, State of Santa Catarina, are also discussed.
Characterization of <i>Bacillus cereus</i> Isolates Associated with Fatal Pneumonias: Strains Are Closely Related to <i>Bacillus anthracis</i> and Harbor <i>B. anthracis</i> Virulence Genes (2006)

Bacillus cereus is ubiquitous in nature, and while most isolates appear to be harmless, some are associated with food-borne illnesses, periodontal diseases, and other more serious infections. In one such infection, B. cereus G9241 was identified as the causative agent of a severe pneumonia in a Louisiana welder in 1994. This isolate was found to harbor most of the B. anthracis virulence plasmid pXO1 (13). Here we report the characterization of two clinical and one environmental B. cereus isolate collected during an investigation of two fatal pneumonia cases in Texas metal workers. Molecular subtyping revealed that the two cases were not caused by the same strain. However, one of the three isolates was indistinguishable from B. cereus G9241. PCR analysis demonstrated that both clinical isolates contained B. anthracis pXO1 toxin genes. One clinical isolate and the environmental isolate collected from that victim's worksite contained the cap A, B, and C genes required for capsule biosynthesis in B. anthracis. Both clinical isolates expressed a capsule; however, neither was composed of poly-D-glutamic acid. Although most B. cereus isolates are not opportunistic pathogens and only a limited number cause food-borne illnesses, these results demonstrate that some B. cereus strains can cause severe and even fatal infections in patients who appear to be otherwise healthy.
Bi-scale appearance fabrication (2013)

Surfaces in the real world exhibit complex appearance due to spatial variations in both their reflectance and local shading frames (i.e. the local coordinate system defined by the normal and tangent direction). For opaque surfaces, existing fabrication solutions can reproduce well only the spatial variations of isotropic reflectance. In this paper, we present a system for fabricating surfaces with desired spatially-varying reflectance, including anisotropic ones, and local shading frames. We approximate each input reflectance, rotated by its local frame, as a small patch of oriented facets coated with isotropic glossy inks. By assigning different ink combinations to facets with different orientations, this bi-scale material can reproduce a wider variety of reflectance than the printer gamut, including anisotropic materials. By orienting the facets appropriately, we control the local shading frame. We propose an algorithm to automatically determine the optimal facets orientations and ink combinations that best approximate a given input appearance, while obeying manufacturing constraints on both geometry and ink gamut. We fabricate the resulting surface with commercially available hardware, a 3D printer to fabricate the facets and a flatbed UV printer to coat them with inks. We validate our method by fabricating a variety of isotropic and anisotropic materials with rich variations in normals and tangents.
Imputation for the analysis of missing values and prediction of time series data (2011)

Data preprocessing plays an important and critical role in the data mining process. Data preprocessing is required in order to improve the efficiency of an algorithm. This paper focuses on missing value estimation and prediction of time series data based on the historical values. A number of algorithms have been developed to solve this problem, but they have several limitations. Most existing algorithms like KNNimpute (K-Nearest Neighbours imputation), BPCA (Bayesian Principal Component Analysis) and SVDimpute (Singular Value Decomposition imputation) are not able to deal with the situation where a particular time point (column) of the data is missing entirely. This paper focuses on autoregressive-model-based missing value estimation method (ARLSimpute) which is effective for the situation where a particular time point contains many missing values or where the entire time point is missing. Data preprocessing output is given to the input of the prediction techniques namely linear prediction and quadratic prediction. These techniques are used to predict the future values based on the historical values. The performance of the algorithm is measured by performance metrics like precision and recall. Experimental results on real-life datasets demonstrate that the proposed algorithm is effective and efficient to reveal future time series data.
Kangaroo care for the preterm infant and family (2012)

Kangaroo care (KC) is the practice of skin-to-skin contact between infant and parent. In developing countries, KC for low-birthweight infants has been shown to reduce mortality, severe illness, infection and length of hospital stay. KC is also beneficial for preterm infants in high-income countries. Cardiorespiratory and temperature stability, sleep organization and duration of quiet sleep, neurodevelopmental outcomes, breastfeeding and modulation of pain responses appear to be improved for preterm infants who have received KC during their hospital stay. No detrimental effects on physiological stability have been demonstrated for infants as young as 26 weeks’ gestational age, including those on assisted ventilation. Mothers show enhanced attachment behaviours and describe an increased sense of their role as a mother. The practice of KC should be encouraged in nurseries that care for preterm infants. Information is available to assist in developing guidelines and protocols.
On the role of the cAMP and cGMP-dependent protein kinases in cell function. (1978)

Cyclic AMP and cGMP-dependent protein kinases have many similarities in physical and kinetic properties. Thus, the two enzymes appear to be homologous proteins, even though the subunit compositions of the two enzymes differ. Of several possible evolutionary schemes, two likely ones are proposed: (i) the ancestral protein kinase was composed of a single type of subunit which evolved into separate regulatory and catalytic subunits by gene splitting; or (ii) the ancestral protein kinase was composed of separate regulatory and catalytic subunits which evolved into a single type of subunit by gene fusion. The evolutionary parallelism poses interesting questions on the functional relatwonships between the two enzymes. Although, there is overlapping substrate specificity between the two kinases, the cAMP kinase is generally a more efficient and versatile catalyst than the cGMP kinase. This difference in catalytic versatility could have offered an evolutionary advantage to the cAMP kinase, and could explain the more widespread distribution of this enzyme in mammalian tissues. The cGMP kinase is proposed to be a more specific enzyme than the cAMP kinase. This implies a less diverse role for cGMP in the regulation of cell function.
Skew and slant correction for document images using gradient direction (2002)

A fast algorithm is presented for skew and slant correction in printed document images. The algorithm employs only the gradient information. The skew angle is obtained by searching for a peak in the histogram of the gradient orientation of the input grey-level image. The skewness of the document is corrected by a rotation at such an angle. The slant of characters can also be detected using the same technique, and can be corrected by a shear operation. A second method for character slant correction by fitting parallelograms to the connected components is also described. Document images with different contents (tables, figures, and photos) have been tested for skew correction and the algorithm gives accurate results on all the test images, and the algorithm is very easy to implement.
Three-dimensional size and orientation of the precipitates in AZ91 magnesium alloys measured by TEM techniques (2009)

Knowledge of the microscopic structure, including three-dimensional (3-D) size and orientation of the precipitates, is essential to fully understand the mechanical properties of the magnesium alloys and designing the alloys with better performance. Analytical TEM with high spatial resolution offers the simultaneous measurements of 3-D size, structure, orientation, composition of the precipitates from one typical sample along an established crystallographic axis. Besides popular Burgers orientation relationship (OR), other ORs such as Pitsch?Schrader OR, Crawley OR, Potter OR and a new OR with the form of [0001]? 1.0? from [311]? and (110)? 2.0?? from (03)? between the magnesium matrix and the precipitate ?-Mg17Al12 are identified by TEM imaging and diffraction techniques. As a case study, the thicknesses of the individual precipitates with Burgers OR are further measured to be 100?200 nm through both electron energy-loss spectroscopy and x-ray energy dispersive spectroscopy combining differential x-ray absorption and extrapolation, which are in agreement with the overall 3-D size statistic distribution results obtained through analysing various samples along various directions. Furthermore, the fabricated wedge-shape structure provides a platform on which to study the dependence of the interfacial strain on the variation of the thickness.
Scan time reduction in snapshot flash MRI (1992)

We describe the speeding up of snapshot FLASH MRI by placing a slice selection experiment before the whole imaging sequence. In conventional snapshot FLASH slice selection is made in every projection, thus consuming a great deal of experimental time. This problem can be overcome by applying only one slice-selective procedure before starting the imaging. The idea is to make a selective saturation of the outer volume and to interrogate the unaffected slice by a train of rapid, hard, low-angle pulses. By this new method the measuring times of snapshot FLASH can be further reduced.
Some condition for strictly positive real and almost strictly positive real structures (2002)

The requirement for an almost strictly positive real system is part of the stability analysis of the simplified adaptive controller. The relation between this property and strict positive realness is examined for structures with collocated position/velocity sensors and actuators. A numerical procedure is developed to determine whether a given system is almost strictly positive real, and its application is illustrated with an example
Effect of Aminoglycoside and β‐Lactam Combination Therapy versus β‐Lactam Monotherapy on the Emergence of Antimicrobial Resistance: A Meta‐analysis of Randomized, Controlled Trials (2005)

Compared with beta-lactam monotherapy, the aminoglycoside/ beta-lactam combination was not associated with a beneficial effect on the development of antimicrobial resistance among initially antimicrobial-susceptible isolates.
Vapor deposition of organic-inorganic hybrid perovskite thin-films for photovoltaic applications (2014)

In this work, we developed CH <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> NH <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> PbI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> perovskite films using sequential vapor deposition technique for photovoltaic applications. For thin PbI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> films vacuum-deposited on different substrates (e. g. Si, PEDOT/PSS/ITO/ glass), the complete conversion to perovskite on exposure to the CH <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> NH <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> I vapor was confirmed based on X-ray diffraction data. For perovskite films prepared under these vapor deposition conditions, planar heterojunction solar cells were fabricated using PEDOT:PSS and PCBM as the hole and electron transport layer, respectively (glass/ITO/ PEDOT:PSS/CH <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> NH <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> PbI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> /PCBM/Ag). Under simulated one sun illumination, a high open-circuit voltage of 970 mV with an average efficiency of 4.5% was obtained. While the efficiency of the device with sequential vapor deposited perovskite films needs to be further improved through process optimization, we demonstrated that sequential vapor deposition has a potential to produce high-quality perovskite absorbers for efficient planar heterojunction solar cells.
Gender-related differences in cocaine toxicity in the rat. (1993)

To test our hypotheses that gender-related differences in cocaine toxicity exist in the rat, cocaine (2 mg/kg/min) was infused intravenously in chronically catheterized male and ovariectomized or intact female rats until the onset of circulatory collapse. Sequential manifestations of cocaine toxicity from mild central nervous stimulation to fatal cardiovascular collapse were observed. Arterial blood was withdrawn at the onset of the toxic signs or symptoms for determination of cocaine concentrations. Dosages and plasma concentrations of cocaine required to produce cardiovascular toxic manifestations were significantly lower in male and ovariectomized rats than in intact females. Plasma cholinesterase activity was lowest in the male animals and highest in intact females. These data suggest that systemic toxicity of cocaine is enhanced in male rats, because lower doses and plasma concentrations are required to induce toxic signs and symptoms.
Low resistive and highly reliable Cu dual-damascene interconnect technology using self-formed MnSi/sub x/O/sub y/ barrier layer (2005)

Copper (Cu) dual-damascene interconnects with self-formed MnSi/sub x/O/sub y/ barrier layer using a copper-manganese (Cu-Mn) alloy seed layer is successfully fabricated for the first time. No delamination is found in the chemical mechanical polishing process, probably because of better adhesion strength between the MnSi/sub x/O/sub y/ barrier and dielectric. More than 90% yield is obtained for a 1 million via chain. Microstructure analysis by transmission electron microscopy shows that an approximately 2 nm thick and continuous MnSi/sub x/O/sub y/ layer is formed at the interface between Cu and dielectric of the via and trench and there is no barrier at the via bottom. This via structure without the bottom barrier provides these essential advantages: reduced via resistance; significant via-electromigration lifetime improvement due to there being no flux divergence site at the via; excellent stress-induced voiding performance.
VOICE: A Framework for Speech-Based Mobile Systems (2007)

The advent of mobile phones and the Internet opened the doors for an emerging class of applications that connect mobile users to online resources and information services available anytime and anywhere. VoiceXML is an enabling technology for creating a streamlined speech-based interface for Web-based information services. In this paper, we describe VOICE, a framework used to develop mobile context-aware speech-enabled systems powered by VoiceXML. Restaurant search guide, a simple context-aware recommender system has been built using VOICE to test the feasibility of the proposed framework.
Performance evaluation of high performance switches on parallel and distributed computers (2002)

The performance of switching fabrics is crucial to the global quality of service offered by an interconnection networks. It is shown that highly detailed simulations can be accelerated by using a parallel (high performance) computer as the computational platform. The simulation model is represented totally independently of the specific computer: hence validation has to be performed only once and the acceleration and optimization of a given implementation are strictly orthogonal to the problem description.
Cloning and neuronal expression of a type III newt neuregulin and rescue of denervated, nerve-dependent newt limb blastemas by rhGGF2 (2000)

Urodele amphibians are the only vertebrates that can regenerate their limbs throughout their life. The critical feature of limb regeneration is the formation of a blastema, a process that requires an intact nerve supply. Nerves appear to provide an unidentified factor, known as the neurotrophic factor (NTF), which stimulates cycling of blastema cells. One candidate NTF is glial growth factor (GGF), a member of the neuregulin (NRG) growth factor family. NRGs are both survival factors and mitogens to glial cells, including Schwann cells. All forms of NRGs contain an EGF-like domain that is sufficient to activate NRG receptors erbB2, erbB3, and erbB4. To investigate the involvement of neuregulin in newt limb regeneration, we cloned and characterized one neuregulin isoform, a neuregulin with a cysteine-rich domain (CRD-NRG), from newt (Notophthalmus viridescens) spinal cord. Results of in situ hybridization showed that the newt CRD-NRG is highly expressed in dorsal root ganglia and spinal cord neurons that innervate the limbs. We also demonstrated the biological activity of recombinant human GGF2 (rhGGF2) in urodele limb regeneration. When rhGGF2 was injected into denervated, nerve-dependent axolotl blastemas, the labeling index (LI) of blastema cells was maintained at a level near to that of control, innervated blastemas, whereas without rhGGF2 the LI decreased significantly. In another experiment, rhGGF2 was delivered into denervated, nerve-dependent blastemas either by direct infusion into blastemas or by injection into the intraperitoneal cavity. The denervated blastemas were rescued into a regeneration response.