gebhart/patrepeval huggingface dataset:
Metallic Twin Grain Boundaries Embedded in MoSe2 Monolayers Grown by Molecular Beam Epitaxy (2017)

Twin grain boundaries in MoSe<sub>2</sub> are metallic and undergo a metal to insulator Peierls transition at low temperature. Growth of MoSe<sub>2</sub> by molecular beam epitaxy results in the spontaneous formation of a high density of these twin grain boundaries, likely as a mechanism to incorporate Se deficiency in the film. Using scanning tunneling microscopy, we study the grain boundary network that is formed in homoepitaxially grown MoSe<sub>2</sub> and for MoSe<sub>2</sub> grown heteroepitaxially on MoS<sub>2</sub> and HOPG substrates. No statistically relevant variation of the grain boundary concentration has been found for the different substrates, indicating that the grain boundary formation is substrate independent and depends mainly on the growth conditions. Twin grain boundaries exhibit three crystallographically identical orientations, and thus they form an intersecting network. Different intersection geometries are identified that imply varying defect configurations. These intersection points act as preferential nucleation sites for vapor-deposited metal atoms, which we demonstrate on the example of selective gold cluster formation at grain boundary intersections. Scanning tunneling spectroscopy shows a band gap narrowing of MoSe<sub>2</sub> in the immediate vicinity of the metallic grain boundary, which may be associated with lattice strain induced at the grain boundary. Tunneling noise spectra taken over the grain boundaries indicate random telegraphic noise, suggestive of pinning/depinning behavior of conductive channels in the metallic grain boundaries or their intersection points. Finally, indications for incommensurate and commensurate Peierls-driven charge density wave formation were observed in microprobe transport measurements at 205 and 227 K, respectively.
Electrical Impedance Response of a Thick-Thin film Hybrid Anodic Nanoporous Alumina Sensor to Methanol Vapors. (2008)

Abstract The response of an anodic aluminum oxide (AAO) nanoporous humidity sensor to an organic vapor such as methanol is presented in this paper. Sensors constructed at Northern Illinois University were exposed to various organic vapors. The characteristic response of the sensor to various vapor dilutions was analyzed using real and complex impedance parameters.
Detection and quantification of degradative genes in soils contaminated by toluene (1996)

A method based on the polymerase chain reaction (PCR) was developed for a rapid and specific detection of toluene degradative genes in soil. The xylE gene coding for catechol 2,3-dioxygenase was chosen as a target gene. The detection threshold was evaluated in microcosms using a sterilized standard soil inoculated with various amounts of a degradative strain of Pseudomonas putida (mX). The extracted DNA was used as a template to amplify the xylE gene. PCR followed by hybridization with an internal probe allowed us to detect 102 bacteria per g of soil. In polluted soils, quantification of target DNA by competitive PCR was compared with enumeration of degradative microflora. This molecular method appeared to be rapid, sensitive and more suitable than the microbiological approach to estimate the biodegradative potential of a polluted soil.
Recent advancements in sputter-type heavy negative ion sources (2003)

Significant advancements have been made in sputter-type negative ion sources which utilize (1) direct surface ionization or (2) a plasma to form the positive ion beam used to effect sputtering of samples containing the material of interest. Typically, such sources can be used to generate unstable beam intensities of a few microamperes to several milliamperes from all chemically active elements, depending on the particular source and the electron affinity of the element in question. An introduction to the fundamental processes underlying negative ion formation by sputtering from a low-work-function surface is presented. Several sources which reflect the progress made in this technology are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
NORTH CAROLINA MARINE ALGAE. VIII. THE REPRODUCTIVE MORPHOLOGY OF CALLITHAMNION CORDATUM BØRGENSEN (RHODOPHYTA, CERAMIACEAE) (1980)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Exosomes from uninfected cells activate transcription of latent HIV-1 (2017)

HIV-1 infection causes AIDS, infecting millions worldwide. The virus can persist in a state of chronic infection due to its ability to become latent. We have previously shown a link between HIV-1 infection and exosome production. Specifically, we have reported that exosomes transport viral proteins and RNA from infected cells to neighboring uninfected cells. These viral products could then elicit an innate immune response, leading to activation of the Toll-like receptor and NF-κB pathways. In this study, we asked whether exosomes from uninfected cells could activate latent HIV-1 in infected cells. We observed that irrespective of combination antiretroviral therapy, both short- and long-length viral transcripts were increased in wild-type HIV-1-infected cells exposed to purified exosomes from uninfected cells. A search for a possible mechanism for this finding revealed that the exosomes increase RNA polymerase II loading onto the HIV-1 promoter in the infected cells. These viral transcripts, which include trans-activation response (TAR) RNA and a novel RNA that we termed TAR-<i>gag</i>, can then be packaged into exosomes and potentially be exported to neighboring uninfected cells, leading to increased cellular activation. To better decipher the exosome release pathways involved, we used siRNA to suppress expression of ESCRT (endosomal sorting complex required for transport) proteins and found that ESCRT II and IV significantly control exosome release. Collectively, these results imply that exosomes from uninfected cells activate latent HIV-1 in infected cells and that true transcriptional latency may not be possible <i>in vivo</i>, especially in the presence of combination antiretroviral therapy.
Measuring Autonomic Symptoms with the Body Perception Questionnaire Short Form (BPQ-SF): Factor Analysis, Derivation of U.S. Adult Normative Values, and Association with Sensor-Based Physiological Measures (2022)

Abstract Objective Autonomic regulation of organ and tissues may give rise to disruptions of typical functions. The Body Perception Questionnaire Short Form (BPQ-SF) includes items that were developed to assess autonomic symptoms in daily life. This pair of studies aimed to establish previously unexplored psychometric properties of the BPQ-SF, develop normative values for clinical and research use, and validate the self-reports with sensor-based measures. Methods Study 1 reports exploratory and confirmatory factor analysis (CFA) on BPQ-SF autonomic reactivity items from a large U.S. population-based online study (n = 2048). In study 2, BPQ-SF scores were examined for associations with heart period, respiratory sinus arrhythmia (RSA), and skin conductance (SC) during seated leg lifts in a community sample (n = 62). Results Study 1 results supported a 2-factor supra- and sub-diaphragmatic autonomic symptom solution (CFA: RMSEA = .040, CFI = .99, TLI = .99), though a 1-factor solution also fit the data well ( RMSEA = .080, CFI = .99, TLI = .99). In study 2, flexible HP responses to lifts and rests were demonstrated at all autonomic symptom levels. However, low self-reported autonomic symptoms were associated with flexible dynamic RSA and SC, moderate symptoms with prolonged SC responses during rest periods, and high symptoms with little systematic changes in RSA and SC during leg lifts. Conclusion Results support the validity of self-reports of autonomic symptoms in research and clinical applications, with higher symptoms likely indicating impairment in autonomic flexibility.
CXCR4 Sequences Involved in Coreceptor Determination of Human Immunodeficiency Virus Type-1 Tropism (1998)

The interaction of human immunodeficiency virus type 1 (HIV-1) with CD4 and one of a cadre of chemokine receptors triggers conformational changes in the HIV-1 envelope (Env) glycoprotein that lead to membrane fusion. The coreceptor activity of the second extracellular loop of CXCR4, which is restricted to dual tropic and T-tropic strains, was insensitive to the removal of charged residues either singly or in combinations by alanine scanning mutagenesis or to the conversion of acidic residues to lysine. Conversion of Asp-187 to a neutral residue exclusively unmasked activity with M-tropic Env in fusion and infection experiments. Insertion of the D187V mutation into chimeras containing extracellular loop 2 of CXCR4 in a CXCR2 framework also resulted in the acquisition of M-tropic coreceptor activity. The independence of CXCR4 coreceptor activity from charged residues and the extension of its repertoire by removing Asp-187 suggest that this interaction is not electrostatic and that coreceptors have the potential to be utilized by a spectrum of Env, which may be masked by charged amino acids in extracellular domains. These findings indicate that the primary structural determinants of coreceptors that program reactivity with M-, dual, and T-tropic Env are surprisingly subtle and that relatively insignificant changes in CXCR4 can dramatically alter utilization by Env of varying tropism.
Synthesis and Properties of Gramicidin S Analogs Consisting of Eight Amino Acid Residues (1991)

Abstract Three cyclic octapeptides (des-Val1,1′-gramicidin S, des-Leu3,3′-gramicidin S and des-Val1, Leu3′-gramicidin S), showed no antibiotic activity. Although their CD spectra resembled each other, they differed from that of gramicidin S. These results indicate that the removal of two of the Val and/ or Leu residues at positions 1, 1′, 3, and 3′ of gramicidin S greately affects both the antibiotic activity and conformation.
Abstract 16536: Characterizing the PKA and PKG Phosphoproteomes of the Cardiac Myocyte (2012)

Protein phosphorylation is an important post translational modification involved in cellular signaling. Disruption of this balance alters cellular phenotype and in some cases can lead to adverse ef...
Thirteen novel canine dog leukocyte antigen‐88 alleles identified by sequence‐based typing (2017)

Major histocompatibility complex (MHC) genes in mammals include highly polymorphic class I and class II genes that are critical for donor-recipient matching for transplantation. Dogs have served as an effective, directly translatable model for stem/progenitor cell transplantation. Previous analyses of MHC class I genes in dogs point to a single highly polymorphic gene, dog leukocyte antigen (DLA)-88, as an important factor in the success or failure of hematopoietic stem cell transplants. Fifty-nine DLA-88 alleles have been identified and reported so far. Here, we extend this list by presenting 13 novel DLA-88 alleles found in domestic dogs.
A test-bed for user interface designs (1982)

Most presently available interactive computer interfaces treat their users in an unfriendly, uncooperative, and inflexible way, resulting in feelings of frustration and a conseqeuent loss of productivity for the users. These problems have led to attempts (e.g. [6, 8, 12, 13]) to make interfaces appear more friendly and cooperative through the addition of advanced interface features such as spelling correction, on-line help, personalized defaults, etc.. While common-sense suggests such features may be helpful, there is little hard evidence about how helpful they are or whether they are worth the overheads they entail. A primary reason for this lack of information is the practical difficulty of experimentation. Many of these features are time-consuming to implement, are usually implemented without adequate instrumentation, and are implemented in different and difficult to compare ways from system to system (see [10], for example). These problems in evaluation suggest the need for a test-bed interface in which various advanced features could be tried out in a consistent and adequately instrumented way with a variety of application systems. In this paper, we present a detailed rationale and a partially implemented design for a test-bed of this kind.
Peri-Procedural Management of Direct-Acting Oral Anticoagulants (DOACs) in Transcatheter Miniaturized Leadless Pacemaker Implantation (2023)

Standardized peri-procedural DOAC management was more often implemented for elective TPS procedures and did not seem to increase bleeding or thromboembolic adverse events.
Elections in a Distributed Computing System (1982)

After a failure occurs in a distributed computing system, it is often necessary to reorganize the active nodes so that they can continue to perform a useful task. The first step in such a reorganization or reconfiguration is to elect a coordinator node to manage the operation. This paper discusses such elections and reorganizations. Two types of reasonable failure environments are studied. For each environment assertions which define the meaning of an election are presented. An election algorithm which satisfies the assertions is presented for each environment.
Photo-crystallography meets optoelectronic structures and reaction energetics (2010)

This presentation features a combined photo-crystallography and Density Functional Theory study on two Ru-based complexes that have potential application in optical data storage Solid-state linkage photo-isomerism is the transformative process, that yields a binary structural signature from 0 (ground-state) to 1 (the photo-isomer) The compounds are based on the general series of materials, [Ru(SO 2 )(NH 3 ) 4 X]Y, where X is trans to the SO 2 ligand. In this particular study, X = isonicotinamide, Y = tosylate 2 ; X = H 2 O and Y = camphorsulfonate. The SO 2 is the photoactive ligand, converting from S-end bound ( 1 ) to side-bound ( 2 ) coordination with the Ru metal centre [3]. Photo-crystallography experiments reveal the 3-D geometry of these light-activated molecular species [4], with up to 27% photoconversion efficiency. Complementary DFT calculations quantify a relationship between the photoconversion fraction and the size of the reaction cavity, i.e. the void surrounding the SO 2 ligand within the crystal lattice. The associated energetics of the ligand photoisomerism are presented in tandem with these findings. The relevance of these findings to the optical data storage industry are discussed; in particular, their role in helping to solve the current challenges in securing suitable materials for industrial application. This leads to the ultimate goal of being able to tailor an optoelectronic material for a given device application.
P‐69: A Weighted Masking Model for Colorimetric Characterization of LCDs (2009)

Abstract Accurate colorimetric characterization is an important step in establishing the color management system (CMS) for liquid crystal displays (LCDs). The difficulty in achieving accurate characterization of LCDs is mainly due to cross talks among color channels. In this paper, a model based on the concept of under color removal (UCR) and utilizing the correlations among color components is proposed to accurately estimate the XYZ values of the colors displayed on LCDs. Experimental results indicate that the proposed model outperforms many existing models in terms of the CIEDE2000 color difference between the XYZ values of the measured color samples and the estimated XYZ values.
ThrR, a DNA‐binding transcription factor involved in controlling threonine biosynthesis in Bacillus subtilis (2016)

The threonine dehydratase IlvA is part of the isoleucine biosynthesis pathway in the Gram-positive model bacterium Bacillus subtilis. Consequently, deletion of ilvA causes isoleucine auxotrophy. It has been reported that ilvA pseudo-revertants having a derepressed hom-thrCB operon appear in the presence of threonine. Here we have characterized two classes of ilvA pseudo-revertants. In the first class the hom-thrCB operon was derepressed unmasking the threonine dehydratase activity of the threonine synthase ThrC. In the second class of mutants, threonine biosynthesis was more broadly affected. The first class of ilvA pseudo-revertants had a mutation in the Phom promoter (P*hom ), resulting in constitutive expression of the hom-thrCB operon. In the second class of ilvA pseudo-revertants, the thrR gene encoding a putative DNA-binding protein was inactivated, also resulting in constitutive expression of the hom-thrCB operon. Here we demonstrate that ThrR is indeed a DNA-binding transcription factor that regulates the hom-thrCB operon and the thrD aspartokinase gene. DNA binding assays uncovered the DNA-binding site of ThrR and revealed that the repressor competes with the RNA polymerase for DNA binding. This study also revealed that ThrR orthologs are ubiquitous in genomes from the Gram-positive phylum Firmicutes and in some Gram-negative bacteria.
Techniques for software quality analysis of binaries (2009)

In this paper we present our efforts to measure different quality aspects of large-scale, binary software. We apply four well established metrics to binary versions of Windows and Debian Linux, analyze our results and discuss our observations. It is surprising to see that our metrics, which search for well known bad coding habits, result with so many violations. It appears that although bad and insecure software development practices are well understood and documented, in practice, recommended coding styles are not followed. Our work evaluates binary versions of software, allowing us to inspect software quality without the need of source code. We believe that this approach, if successful, could lead in the future to better priced software. This is because the quality of software bought today is not transparent to its users.
Enhanced self-injection locking of semiconductor laser to high-Q microresonator (2021)

In this work we theoretically study a scheme of a self-injection locking to a high-Q microresonator with drop-port coupled mirror, in which optical feedback level is optimally adjusted by tuning the drop-port mirror coupling.
Supplementary Figures 1 and 2 from Antagonism of IAPs Enhances CAR T-cell Efficacy (2023)

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509 Dynamic Simulation of Flexible Multibody System with the Electronic-Hydraulic Drive (2008)

A simulation model of a hybrid excavator has been developed for the estimation of the fuel consumption and the optimum design of the hybrid system dynamics in the practical operation of the hybrid excavator. The hybrid excavator consists of a hybrid power train system with power electronics devices such as converter, an actuator system driven by electro-hydraulic system, and linkage system of a front attachment with the boom, the arm, and bucket. The simulation model enables us to analyze these systems totally. In this paper, the power electronics system is modeled to second order differential equations of motion, and the total system equations are established with considering the coupling with the power electronic system, the hydraulic system, and linkage system. The boom system is picked up for the operability design for the residual vibration, and the energy saving effect is estimated for the practical operations.
Translational Research In Glioblastoma Multiforme: Molecular Criteria For Patient Selection (2008)

In spite of the dismal outcome of glioblastoma multiforme (GBM), we are in a position to provide a ray of hope to patients and families. Methylation of MGMT in tumor occurs in approximately a third of patients and predicts meaningful response and survival to adjuvant radiotherapy plus temozolomide. Limited access to tumor tissue in some patients could be circumvented by examining MGMT methylation in circulating serum DNA, although this approach needs to be validated. Molecular signatures are also promising prognostic and predictive markers, and clinical trials should be carried out to validate their use in the selection of patients for specific targeted therapies. Gene expression by quantitative PCR of key components of these molecular signatures could pave the way for easy identification of different subgroups of patients. Translational clinical trials are warranted in order to detect the subgroups of patients resistant to radiotherapy who may derive benefit from novel therapies, including antiangiogenic drugs.
Network Coding for Wireless Mesh Networks: A Case Study (2006)

Network coding is a new transmission paradigm that proved its strength in optimizing the usage of network resources. In this paper, we evaluate the gain from using network coding for file sharing applications running on top of wireless mesh networks. With extensive simulations carried out on a simulator we developed specifically for this study, we confirm that network coding can improve the performance of the file sharing application, but not as in wired networks. The main reason is that nodes over wireless cannot listen to different neighbors simultaneously. Nevertheless, one can get more from network coding if the information transmission is made more diverse inside the network. We support this argument by varying the loss rate over wireless links and adding more sources.
A checklist for suitability of biomarkers as surrogate endpoints in chemoprevention of breast cancer. (1994)

By reference to a "checklist" of requirements for substances or processes to qualify as surrogate endpoint biomarkers, both malignin and antimalignin antibody are found to be suitable for use in breast cancer chemoprevention trials. Antimalignin has been shown to be highly specific and sensitive, modulatable and reversible, detectable early in appearance of malignancy and upon recovery therefrom, and differentially expressed in high-risk individuals as compared with the general population.
Nonpigtail optical coupling to embedded fiber Bragg grating sensors (2010)

In recent decades, optical fiber has proven useful for many sensor applications. Specifically, fiber Bragg grating (FBG) sensors have shown great utility for integrity management and environmental sensing of composite structures. One major drawback of FBG sensors, however, is the lack of a robust, nonpigtail technique for coupling to the embedded FBG sensor. In this paper, a novel method of free-space passive coupling of light into FBG sensors is described. An angled 45-deg mirror integrated directly into the fiber was used as an input coupling technique. We investigated the application of this approach to both single- and multimode glass fibers containing FBGs. For multimode FBGs, we studied the grating's uniformity across the fiber diameter and its effect on normal free-space coupling. In single-mode investigations, a novel method of coupling to the sensor via splicing a multimode fiber to a single-mode FBG (SMFBG) was developed. Finally, free-space coupling to an embedded SMFBG was employed to measure the tensile strain. Excellent agreement was found between the FBG and conventional electrical resistance strain gauges. We conclude that this coupling method might eliminate the need for pigtailing by providing a more robust coupling method for FBG sensors.