gebhart/patrepeval huggingface dataset:
The Hofmeister Anion Effect and the Growth of Polyelectrolyte Multilayers (2004)

The influence of a variety of counteranions on the properties of polyelectrolyte multilayers deposited by layer-by-layer technique is studied by using ellipsometry and AFM. We found out that in thin dry multilayers (20-90 nm) ofpoly(4-styrenesulfonate) (PSS) and poly(diallyldimethylammonium) (PDADMA), the thickness follows reasonably well the position of the counteranion in the Hofmeister series. The polyelectrolyte-counteranion interaction is studied by means of viscosity measurements of semidilute solutions of PDADMA in the presence of different anions. The dynamic viscosities follow the Hofmeister series of anions and correlate with the thickness of multilayers. Two parameters describing the interaction of ions with water, the Jones-Dole viscosity B coefficient and the hydration entropy, are used to explain the anion effect on the developing multilayer thickness. Reasonably smooth and monotonic functional dependence is observed between the layer thickness and these two parameters.
A soluble 60 <i>kilo</i> Dalton antigen of <i>Chlamydia</i> spp. is a homologue of <i>Escherichia coli</i> GroEL (1990)

Two major 60 kD protein species can be separated by differential detergent extraction in Chlamydia spp. A Sarkosyl-soluble 60 kD protein is (i) structurally and antigenically distinct from the previously characterized 60 kD Omp2 outer membrane protein; and (ii) antigenically related to a bacterial common antigen of similar molecular weight which includes a 65 kD mycobacterial antigen and the GroEL heat-shock protein of Escherichia coli. Among GroEL homologues, the chlamydial protein (chl-GroEL) uniquely displays affinity towards immobilized thiol groups. The significance of this property is discussed with respect to the synthesis and assembly of the chlamydial disulphide-rich cell wall late in the growth cycle. Chl-GroEL is identical to the Triton X-100-soluble, ocular delayed-type hypersensitivity agent (Morrison et al., 1989), an essential component in the development of blinding trachoma. An autoimmune mechanism for chronic chlamydial diseases based on chl-GroEL homology to host proteins is hypothesized.
Detection of coliform bacteria in water by polymerase chain reaction and gene probes (1990)

Polymerase chain reaction (PCR) amplification and gene probe detection of regions of two genes, lacZ and lamB, were tested for their abilities to detect coliform bacteria. Amplification of a segment of the coding region of Escherichia coli lacZ by using a PCR primer annealing temperature of 50 degrees C detected E. coli and other coliform bacteria (including Shigella spp.) but not Salmonella spp. and noncoliform bacteria. Amplification of a region of E. coli lamB by using a primer annealing temperature of 50 degrees C selectively detected E. coli and Salmonella and Shigella spp. PCR amplification and radiolabeled gene probes detected as little as 1 to 10 fg of genomic E. coli DNA and as a few as 1 to 5 viable E. coli cells in 100 ml of water. PCR amplification of lacZ and lamB provides a basis for a method to detect indicators of fecal contamination of water, and amplification of lamB in particular permits detection of E. coli and enteric pathogens (Salmonella and Shigella spp.) with the necessary specificity and sensitivity for monitoring the bacteriological quality of water so as to ensure the safety of water supplies.
Roles of silver oxide in the bipolar resistance switching devices with silver electrode (2011)

Three devices, Ag/WO3−x/Pt, Ag/AgOx/Pt, and Ag/AgOx/WO3−x/Pt, were investigated to elucidate the influence of the silver oxide on the bipolar resistive switching behavior. The silver oxide films were obtained by depositing silver at oxygen atmosphere. We find that the resistive switching behavior was determined by the silver oxide layer. Bulk and interface resistive switching were observed in the Ag/AgOx/Pt and Ag/AgOx/WO3−x/Pt devices, respectively. By the micro-x-ray photoemission spectroscopy analysis, it was demonstrated that the electrochemical redox reaction occurred in the AgOx layer is responsible for the resistive switching behavior at silver/oxide interface.
Influence of growth temperature on order within silicon films grown by ultrahigh-vacuum evaporation on silica (2006)

We study the role that the growth temperature plays in determining the amount of order present within silicon films deposited on fused silica substrates through ultrahigh-vacuum evaporation at growth temperatures ranging from 98 to 572°C. Through measurements of the Raman and optical absorption spectra, we quantitatively determine how the growth temperature influences the order present within 11 such films. We employ three disparate measures of order for the purposes of this study: the breadth of the transverse-optic phonon Raman peak, this being related to the amount of short-range order present; the area under the transverse-acoustic Raman peak divided by the area under the corresponding transverse-optic peak, this being related to the amount of intermediate-range order present; and the breadth of the optical absorption tail, which is a general measure of the overall amount of order present. All three measures of order indicate a dramatic increase in the amount of order present for growth temperatures above 400°C.
Skyfire: Data-Driven Seed Generation for Fuzzing (2017)

Programs that take highly-structured files as inputs normally process inputs in stages: syntax parsing, semantic checking, and application execution. Deep bugs are often hidden in the application execution stage, and it is non-trivial to automatically generate test inputs to trigger them. Mutation-based fuzzing generates test inputs by modifying well-formed seed inputs randomly or heuristically. Most inputs are rejected at the early syntax parsing stage. Differently, generation-based fuzzing generates inputs from a specification (e.g., grammar). They can quickly carry the fuzzing beyond the syntax parsing stage. However, most inputs fail to pass the semantic checking (e.g., violating semantic rules), which restricts their capability of discovering deep bugs. In this paper, we propose a novel data-driven seed generation approach, named Skyfire, which leverages the knowledge in the vast amount of existing samples to generate well-distributed seed inputs for fuzzing programs that process highly-structured inputs. Skyfire takes as inputs a corpus and a grammar, and consists of two steps. The first step of Skyfire learns a probabilistic context-sensitive grammar (PCSG) to specify both syntax features and semantic rules, and then the second step leverages the learned PCSG to generate seed inputs. We fed the collected samples and the inputs generated by Skyfire as seeds of AFL to fuzz several open-source XSLT and XML engines (i.e., Sablotron, libxslt, and libxml2). The results have demonstrated that Skyfire can generate well-distributed inputs and thus significantly improve the code coverage (i.e., 20% for line coverage and 15% for function coverage on average) and the bug-finding capability of fuzzers. We also used the inputs generated by Skyfire to fuzz the closed-source JavaScript and rendering engine of Internet Explorer 11. Altogether, we discovered 19 new memory corruption bugs (among which there are 16 new vulnerabilities and received 33.5k USD bug bounty rewards) and 32 denial-of-service bugs.
Transcriptional Activation of egr-1 by Granulocyte-Macrophage Colony-stimulating Factor but Not Interleukin 3 Requires Phosphorylation of cAMP Response Element-binding Protein (CREB) on Serine 133 (1995)

Granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin 3 (IL-3) stimulate the proliferation and maturation of myeloid progenitor cells following interaction with heterodimeric receptors that share a common beta subunit required for signal transduction. Our previous studies have demonstrated that GM-CSF and IL-3 activate signaling pathways which converge upon a cAMP response element-binding protein (CREB)-binding site of the human immediate early response gene (early growth response gene-1, egr-1) promoter. Using electromobility supershift assays and antibodies directed against CREB phosphorylated on serine 133, we show that CREB is phosphorylated on serine 133 in response to GM-CSF or IL-3 stimulation. We demonstrate that phosphorylation of CREB on serine 133 substantially contributes to transcriptional activation of egr-1 in response to GM-CSF but not IL-3. These studies suggest that phosphorylation of CREB may play different roles during signal transduction, resulting in unique and overlapping biological functions in myeloid cells.
Pannexin-1 channel opening is critical for COVID-19 pathogenesis (2021)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rapidly rampaged worldwide, causing a pandemic of coronavirus disease (COVID -19), but the biology of SARS-CoV-2 remains under investigation. We demonstrate that both SARS-CoV-2 spike protein and human coronavirus 229E (hCoV-229E) or its purified S protein, one of the main viruses responsible for the common cold<i>,</i> induce the transient opening of Pannexin-1 (Panx-1) channels in human lung epithelial cells. However, the Panx-1 channel opening induced by SARS-CoV-2 is greater and more prolonged than hCoV-229E/S protein, resulting in an enhanced ATP, PGE<sub>2</sub>, and IL-1β release. Analysis of lung lavages and tissues indicate that Panx-1 mRNA expression is associated with increased ATP, PGE<sub>2</sub>, and IL-1β levels. Panx-1 channel opening induced by SARS-CoV-2 spike protein is angiotensin-converting enzyme 2 (ACE-2), endocytosis, and furin dependent. Overall, we demonstrated that Panx-1 channel is a critical contributor to SARS-CoV-2 infection and should be considered as an alternative therapy.
Pre-Authenticated Fast Handoff in a Public Wireless LAN based on IEEE 802.1x Model (2003)

With the popularity of portable devices, public Internet access service using wireless LAN has started in many countries. In the public wireless LAN network, since re-authentication latency during handoff affects the service quality of multimedia applications, minimizing authentication latency is very important in order to support real-time multimedia applications on the wireless IP network. In this paper, we proposed a fast handoff scheme using the predictive authentication method based on IEEE 802.1x model. In our scheme, a mobile host entering an area of an access point (AP) performs authentication procedures for a set of multiple APs instead of the current AP. Multiple APs are selected using a Frequent Handoff Region (FHR) selection algorithm considering users’ mobility patterns and their service classes. Since a mobile host is authenticated for FHR in advance, the handoff latency due to the re-authentication can be minimized. Simulation results show that the proposed scheme is more efficient than other schemes in terms of delay.
Road Segmentation of Remotely-Sensed Images Using Deep Convolutional Neural Networks with Landscape Metrics and Conditional Random Fields (2017)

Object segmentation of remotely-sensed aerial (or very-high resolution, VHS) images and satellite (or high-resolution, HR) images, has been applied to many application domains, especially in road extraction in which the segmented objects are served as a mandatory layer in geospatial databases. Several attempts at applying the deep convolutional neural network (DCNN) to extract roads from remote sensing images have been made; however, the accuracy is still limited. In this paper, we present an enhanced DCNN framework specifically tailored for road extraction of remote sensing images by applying landscape metrics (LMs) and conditional random fields (CRFs). To improve the DCNN, a modern activation function called the exponential linear unit (ELU), is employed in our network, resulting in a higher number of, and yet more accurate, extracted roads. To further reduce falsely classified road objects, a solution based on an adoption of LMs is proposed. Finally, to sharpen the extracted roads, a CRF method is added to our framework. The experiments were conducted on Massachusetts road aerial imagery as well as the Thailand Earth Observation System (THEOS) satellite imagery data sets. The results showed that our proposed framework outperformed Segnet, a state-of-the-art object segmentation technique, on any kinds of remote sensing imagery, in most of the cases in terms of precision, recall, and F 1 .
Differential insulin response to myo-inositol administration in obese polycystic ovary syndrome patients (2012)

Polycystic ovary syndrome (PCOS) is characterized by hyperandrogenism, chronic anovulation, polycystic ovaries at ultrasound evaluation, and quite frequently by insulin resistance or compensatory hyperinsulinemia. Attention has been given to the role of inositol-phosphoglycan (IPG) mediators of insulin action and growing evidences suggest that a deficiency of D-chiro-inositol (DCI) containing IPG might be at the basis of insulin resistance, frequent in PCOS patients. On such basis, we investigated the efficacy on insulin sensitivity and hormonal parameters of 8 weeks treatment with myo-inositol (MYO) (Inofert, ItalPharmaco, Milano, Italy) at the dosage of 2 g day in a group (n = 42) of obese PCOS patients,. After the treatment interval body mass index (BMI) and insulin resistance decreased together with luteinizing hormone (LH), LH/FSH and insulin. When subdividing the patients according to their fasting insulin levels, Group A (n = 15) insulin below 12 µU/ml and Group B (n = 27) insulin above 12 µU/ml, MYO treatment induced similar changes in both groups but only patients of Group B showed the significant decrease of both fasting insulin plasma levels (from 20.3 ± 1.8 to 12.9 ± 1.8 µU/ml, p < 0.00001) and of area under the curve (AUC) of insulin under oral glucose tolerance test (OGTT). In conclusion, our study supports the hypothesis that MYO administration is more effective in obese patients with high fasting insulin plasma levels.
Comedogenesis: Some Aetiological, Clinical and Therapeutic Strategies (2003)

Hypercornification is an early feature of acne and usually precedes inflammation. It is associated with ductal hyperproliferation, and there are many controlling factors such as androgens, retinoids, sebum composition and cytokines. Cycling of normal follicles and of comedones may explain the natural resolution of comedones and, in the longer term, resolution of the disease itself. There is a need to tailor treatment according to comedonal type. Suboptimal therapy can often result from inappropriate assessments of comedones, especially microcomedones, sandpaper comedones, submarine comedones and macrocomedones. Macrocomedones can produce devastating acne flares, particularly if patients are inappropriately prescribed oral isotretinoin. Gentle cautery under topical local anaesthesia is a useful therapy in the treatment of such lesions. The newer retinoids and new formulations of all-trans-retinoic acid show a better benefit/risk ratio.
Development and testing of AAV-delivered single-chain variable fragments for the treatment of methamphetamine abuse (2018)

Methamphetamine (METH) substance abuse disorders have major impact on society, yet no medications have proven successful at preventing METH relapse or cravings. Anti-METH monoclonal antibodies can reduce METH brain concentrations; however, this therapy has limitations, including the need for repeated dosing throughout the course of addiction recovery. An adeno-associated viral (AAV)-delivered DNA sequence for a single-chain variable fragment could offer long-term, continuous expression of anti-METH antibody fragments. For these studies, we injected mice via tail vein with 1 x 10(12) vector genomes of two AAV8 scFv constructs and measured long-term expression of the antibody fragments. Mice expressed each scFv for at least 212 days, achieving micromolar scFv concentrations in serum. In separate experiments 21 days and 50 days after injecting mice with AAV-scFvs mice were challenged with METH in vivo. The circulating scFvs were capable of decreasing brain METH concentrations by up to 60% and sequestering METH in serum for 2 to 3 hrs. These results suggest that AAV-delivered scFv could be a promising therapy to treat methamphetamine abuse.
Hydrogen absorption by thin Pd/Nb films deposited on glass (1996)

Hydrogen absorption by 200--2000-\AA{}-thick Pd-capped Nb films, between 5 and 110 \ifmmode^\circ\else\textdegree\fi{}C, was studied by simultaneous four-probe resistivity and volumetric measurements. The resistivity as a function of hydrogen concentration was measured while charging the films with hydrogen, and was used to compute the change in hydrogen concentration in the film, during the reaction with oxygen. For the thinnest films (200 \AA{} thick), the hydrogen charging and discharging curves indicate that a first-order gas-liquid-like phase transition with a ${\mathit{T}}_{\mathit{c}}$ of 70--75 \ifmmode^\circ\else\textdegree\fi{}C takes place. The H-Nb phase diagram for the 200-\AA{} film looks like the H/bulk Nb \ensuremath{\alpha}-\ensuremath{\alpha}\ensuremath{'} phase diagram which has a higher ${\mathit{T}}_{\mathit{c}}$ (173 \ifmmode^\circ\else\textdegree\fi{}C). We attribute the substantial modifications of the film's phase diagram to the clamping of the Nb film at its interfaces with glass and Pd and to the nanostructure of the films. \textcopyright{} 1996 The American Physical Society.
The GeoTiff data interchange standard for raster geographic images (1997)

Abstract Abstract The GeoTIFF interchange standard is an extension of the popular TIFF format, to support a geodetically sound raster data georeferencing capability. The geographic content supported in the GeoTIFF tag structure includes its cartographic projection, datum, ground pixel dimension, and other geographic variables, based upon the non-profit Petrotechnical Open Software Company (POSC)'s Epicentre 2.0 geodetic model. This paper is a review of the progress and status of the GeoTIFF initiative, as well as an overview of the main technical characteristics and principles of the GeoTIFF format.
Numerical Approximation of a Two-phase Flow Problem in a Porous Medium with Discontinuous Capillary Forces (2006)

We consider a simplified model of a two-phase flow through a heterogeneous porous medium. Focusing on the capillary forces motion, a nonlinear degenerate parabolic problem is approximated in a domain shared in two homogeneous parts, each of them being characterized by its relative permeability and capillary curves functions of the phase saturations. We first give a weak form of the conservation equations on the whole domain, with a new general expression of the conditions at the interface between the two regions. We then propose a finite volume scheme for the approximation of the solution, which is shown to converge to a weak solution in one-, two-, or three-dimensional domains. We conclude with some numerical tests.
Structural insights into the binding of small ligand molecules to a G-quadruplex DNA located in the HIV-1 promoter (2017)

Targeting guanine (G)-rich DNA sequences, folded into non-canonical G-quadruplex (G4) structures, by small ligand molecules is a promising strategy for gene therapy of various diseases. There is experimental proposal that, among eight studied ligands, nitidine chloride - NC and a benzo phenanthridine derivative - BPD have the highest binding affinity for such a sequence (5'-T<sup>1</sup>G<sup>2</sup>G<sup>3</sup>C<sup>4</sup>C<sup>5</sup>T<sup>6</sup>G<sup>7</sup>G<sup>8</sup>G<sup>9</sup>C<sup>10</sup>G<sup>11</sup>G<sup>12</sup>G<sup>13</sup>A<sup>14</sup>C<sup>15</sup>T<sup>16</sup>G<sup>17</sup>G<sup>18</sup>G<sup>19</sup>-3') in the HIV-1 promoter, indicating that an anti-HIV-1 prodrug may regulate the expression of the promoter. Herein, this experimental indication is elaborated by using molecular docking simulations and by characterizing the modes of binding of the eight natural molecules to the particular G4. Moreover, the configurational entropy, as an upper bound of the true entropy contribution to the free energy in noncovalent binding, is employed to see into the structural changes experienced by the G4-DNA upon ligand binding. For various parts (complete structure, backbone, system of all bases, bases of G-tetrads) of the G4-DNA structure, a subtle molecular dynamics (MD) is exploited to determine the change of asymptotic (for infinitely long MD simulation) configurational entropy, being the thermodynamic consequence of DNA flexibility change upon complex formation. While NC increases rigidity of G4 (mainly through the system of all nucleobases), BPD increases flexibility of G4 (more than 50% stems from the sugar-phosphate backbone). These insights are further dissected and substantiated by considering the configurational entropy contributions at the level of individual base pairs making the two G-tetrads (G<sup>2</sup>G<sup>7</sup>G<sup>13</sup>G<sup>17</sup> and G<sup>3</sup>G<sup>8</sup>G<sup>12</sup>G<sup>18</sup>) and by exploring the estimates of the total intra-base pair and inter-base pair entropies. This work makes the structural origin of enhanced stability of G4-DNA more certain - useful information when attempting to design optimal G4-DNA binders.
Anytime Stereo Image Depth Estimation on Mobile Devices (2019)

Many applications of stereo depth estimation in robotics require the generation of accurate disparity maps in real time under significant computational constraints. Current state-of-the-art algorithms force a choice between either generating accurate mappings at a slow pace, or quickly generating inaccurate ones, and additionally these methods typically require far too many parameters to be usable on power- or memory-constrained devices. Motivated by these shortcomings, we propose a novel approach for disparity prediction in the anytime setting. In contrast to prior work, our end-to-end learned approach can trade off computation and accuracy at inference time. Depth estimation is performed in stages, during which the model can be queried at any time to output its current best estimate. Our final model can process 1242×375 resolution images within a range of 10-35 FPS on an NVIDIA Jetson TX2 module with only marginal increases in error - using two orders of magnitude fewer parameters than the most competitive baseline. The source code is available at https://github.com/mileyan/AnyNet.
3GPP NR Sidelink Transmissions Toward 5G V2X (2020)

Featuring direct communications between two user equipments (UEs) without signal relay through a base station, 3GPP sidelink transmissions have manifested their crucial roles in the Long-Term Evolution (LTE) Advanced (LTE-A) for public safety and vehicle-to-everything (V2X) services. With this successful development in LTE-A, the evolution of sidelink transmissions continues in 3GPP New Radio (NR), which renders sidelink an inevitable component as well as downlink and uplink. Targeting at offering low latency, high reliability and high throughout V2X services for advanced driving use cases, a number of new sidelink functions not provided in the LTE-A are supported in NR, including the feedback channel, grant-free access, enhanced channel sensing procedure, and new control channel design. To fully comprehend these new functions, this paper therefore provides essential knowledge of 3GPP NR sidelink transmissions, including the physical layer structure, resource allocation mechanisms, resource sensing and selection procedures, synchronization, and quality-of-service (QoS) management. Furthermore, this paper also provides performance evaluation to assess the gains brought from the new control channel design. As NR sidelink transmissions have been regarded as a foundation to provide advanced services other than V2X in future releases (e.g., advanced relay), potential enhancements are also discussed to serve the urgent demand in corresponding normative works.