gebhart/patrepeval huggingface dataset:
Tumor genomic landscape in younger compared to older patients (pts) with metastatic clear cell renal cell carcinoma (mccRCC). (2022)

373 Background: Renal cell carcinoma is predominant in 6th to 8th decade of life. Younger pts are more likely to have symptomatic tumors on presentation but with favorable pathological features and disease specific survival (PMID: 17092632). Herein, we hypothesized that the genomic landscape for pts with onset of renal cell cancer at a younger age is distinct from those with late age of onset. Methods: In this IRB-approved retrospective study, pts with mccRCC and tumor comprehensive genomic profiling (CGP) available from a CLIA-certified laboratory were evaluated. Among these, the pts in the first and fourth quartiles of age were included in this study. Variants of unknown significance and gene with alterations (GA) present in less than 5% of pts were excluded from the analysis. A chi-square test was used to compare gene aberration frequency and p-values were adjusted for false discovery rate (FDR) using Benjamini-Hochberg (BH) correction. The median number of genomic aberrations per pt was compared using Wilcoxon rank-sum test. Results: 78 pts were eligible and included: first quartile (Range: 25-53 years; n=54) and fourth quartile (Range: 68-77 years; n=38); male vs female: 30/13 vs 20/15. The genomic aberrations observed in both groups is listed in the table. GA in VHL and PBRM1 were the most commonly observed in both groups . Most commonly observed genomic alterations in first quartile was TP53, BAP1, CDKN2B and TSC1; and fourth quartile of age was SETD2, TSC1, KDM5C and TP53. Tumor mutation burden and the frequency of gene aberrations was similar across both the cohorts. Conclusions: In these hypothesis generating data, there was no significant difference in prevalence of targetable genomic aberrations, tumor mutational burden and frequency of genomic alterations in younger vs older pts with mccRCC. The numerically higher GA in KDM5C and SETD2 (both of which contribute to epigenetic dysregulation) in older pts warrant interrogation in a larger data set. Future directions may include the investigation of epigenomic changes and transcriptomic profiling. Detailed genomic landscape of these pts will be presented in the meeting.[Table: see text]
Protein sequence comparison and protein evolution (1995)

This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. This tutorial examines how the information conserved during the evolution of a protein molecule can be used to infer reliably homology, and thus a shared proteinfold and possibly a shared active site or function. The authors start by reviewing a geological/evolutionary time scale. Next they look at the evolution of several protein families. During the tutorial, these families will be used to demonstrate that homologous protein ancestry can be inferred with confidence. They also examine different modes of protein evolution and consider some hypotheses that have been presented to explain the very earliest events in protein evolution. The next part of the tutorial will examine the technical aspects of protein sequence comparison. Both optimal and heuristic algorithms and their associated parameters that are used to characterize protein sequence similarities are discussed. Perhaps more importantly, they survey the statistics of local similarity scores, and how these statistics can both be used to improve the selectivity of a search and to evaluate the significance of a match. They them examine distantly related members of three protein families, the serine proteases, the glutathione transferases, and the G-protein-coupled receptors (GCRs). Finally, the discuss how sequence similarity can be used to examine internal repeated or mosaic structures in proteins.
Update propagation protocols for replicated databates (1999)

Replication is often used in many distributed systems to provide a higher level of performance, reliability and availability. Lazy replica update protocols, which propagate updates to replicas through independent transactions after the original transaction commits, have become popular with database vendors due to their superior performance characteristics. However, if lazy protocols are used indiscriminately, they can result in non-serializable executions. In this paper, we propose two new lazy update protocols that guarantee serializability but impose a much weaker requirement on data placement than earlier protocols. Further, many naturally occurring distributed systems, like distributed data warehouses, satisfy this requirement. We also extend our lazy update protocols to eliminate all requirements on data placement. The extension is a hybrid protocol that propagates as many updates as possible in a lazy fashion. We implemented our protocols on the Datablitz database system product developed at Bell Labs. We also conducted an extensive performance study which shows that our protocols outperform existing protocols over a wide range of workloads.
A Subharmonically Pumped HFET Grid Mixer (1993)

In this work, we report the demonstration of a quasi-optical subharmonically pumped grid mixer. The grid consists of a 4x4 array of dual gate Heterojunction Field Effect Transistors (1IFET's) which are connected in a crossed dipole configuration. Both the drains and sources of the devices are grounded, thus eliminating possible instabilities. The LO and RF signals are applied to the grid quasioptically and with orthogonal polarizations. This enhances the isolation between the LO and RF as well as allowing for the possibility of independent impedance tuning for both signals. The IF signal is removed from the bias lines with an SMA connector. The grid was designed for and tested in the K-band (18-26.5 Gllz), where a minimum conversion loss of 16 dB was obtained at an RF frequency of 19 GHz and an LO power of 3 dBm per device. This is comparable to conventional dual gate HFET mixers which typically have a conversion loss between 10 dB and 15 dB for the same LO power.
Thermal and rheological properties of poly(phenylene sulfide) and poly(ether etherketone) resins and composites (1987)

Abstract Poly(phenylene sulfide) (PPS) and poly(ether etherketone) (PEEK) are high performance engineering thermoplastics with a unique combination of excellent environmental, mechanical, and thermal properties. Research on the thermal and rheological properties of PPS and PEEK resins and carbon fiber reinforced prepregs are described. Experimental studies of the dynamic viscoelasticity and thermal properties of these materials are summarized. The effects of processing cycles and environment on the thermal and rheological properties are discussed. The effects of the processing environment and the addition of carbon fiber on the thermal stability are reported. Crosslinking of poly(phenylene sulfide) in air, enhancing thermal stability, is also investigated.
Field Evaluation of Human Anthrax Vaccine (1962)

Brachman, P S; Gold, H; Plotkin, S A; Fekety, R; Werrin, M; Ingraham, N R Author Information
Draft Genome Sequence of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Isolated from a Patient in Lebanon (2014)

We present the draft genome sequence of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae isolated from a stool sample collected from a patient admitted for a gastrointestinal procedure. The draft genome sequence consists of 86 contigs, including a combined 5,632,663 bases with 57% G+C content.
Ethanol Stress Corrosion Cracking of Carbon Steels (2011)

This chapter contains sections titled: Introduction Contributing factors in ethanol SCC Mitigation of ethanol SCC References
Detection of False Data Injection Attack in Connected and Automated Vehicles via Cloud-Based Sandboxing (2021)

In recent years, developments in vehicle-to-everything communication (V2X) have steadily increased in applications such as platooning and collision avoidance. V2X provides vehicles with long-range information regarding traffic congestion and routing, but also short and mid-range information allowing cooperative adaptive cruise control, automatic collision warnings, and others. Despite being potentially beneficial in several aspects, such interdependence poses a set of specific challenges from safety and reliability standpoint due to the possibility of cyber-attacks aimed at influencing the behavior of the vehicles. In this paper, a Cloud-based approach, a sandboxing framework is presented to detect the false data injection attack on connected and automated vehicles (CAVs). The sandboxing concept comes from computer security and it is adopted in a control framework as a way to isolate and evaluate the data exchanged by the CAVs affecting the vehicle control system. Numerical experiments are conducted to show the effectiveness of the approach using microscopic traffic simulation. Simulation results show that our proposed methodology is able to detect the false data injection attack existing in the V2X communication and identify the attacker in real-time less than 0.2 s.
The Dexter hypertext reference model (1994)

article Free Access Share on The Dexter hypertext reference model Authors: Frank Halasz Xerox, Palo Alto, CA Xerox, Palo Alto, CAView Profile , Mayer Schwartz Tektronix, Inc., Beaverton, OR Tektronix, Inc., Beaverton, ORView Profile , Editors: Kaj Grønbæk View Profile , Randall H. Trigg View Profile Authors Info & Claims Communications of the ACMVolume 37Issue 2Feb. 1994pp 30–39https://doi.org/10.1145/175235.175237Published:01 February 1994Publication History 524citation2,414DownloadsMetricsTotal Citations524Total Downloads2,414Last 12 Months82Last 6 weeks11 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Estimating the costs of potentially preventable hospital acquired complications. (2009)

California and Maryland hospital data are used to estimate the incremental cost associated with 64 categories of hospital acquired complications. The reason for admission, severity of illness at admission and the presence of hospital acquired complications are used in a linear regression model to predict incremental per patient cost yielding an adjusted R2 of 0.58 for Maryland data and 0.60 for California data. The estimated incremental cost due to each of the 64 categories of complications was consistent across both databases and accounted for an increase in total short term acute inpatient hospital cost of 9.39 percent in the California data and 9.63 percent in the Maryland data.
Low Field Conduction of Nematic Liquid Crystals Studied by Means of Electrodialysis (1973)

Abstract An elementary theory of electrodialytic purification in insulating liquid crystals is developed by considering both the degree of ionic dissociation and the kinetic rates of dissolved impurities. It is shown that, on application of a uniform electric field with open electrodes, the only species which exhibit strong dissociation, or fast kinetic rates, can be eliminated from the solution; the molecular concentrations of other species remain unaffected by every ionic depletion process. Distinction is made between an irreversible molecular purification, which takes place when electrolytic impurities are definitively removed, and a reversible displacement of the ionic equilibrium by electrodialysis. The ionic concentrations of species having slow kinetic rates are lowered by the electric field, but they grow back to their initial values when the voltage is switched off. These conclusions lead to propose a model for the interpretation of transient and stationary electrical characteristics of several nematic compounds, when no injection phenomena occur. The temperature dependance of the residual conductivity is studied for several nematic liquid crystals. An exponential-like behaviour is observed in both isotropic and nematic phase and a singularity appears near the transition. The conductivity variations are discussed in terms of number and drift mobility of ionic charge carriers and liquid crystal viscosity.
Tuning the hydrophobic cores of self-immolative polyglyoxylate assemblies (2018)

Amphiphilic block copolymers containing different self-immolative polyglyoxylates were synthesized and self-assembled to provide drug carriers with variable celecoxib loading capacities and release rates, as well as different <italic>in vitro</italic> toxicities.
Affinity and dose of TCR engagement yield proportional enhancer and gene activity in CD4+ T cells (2016)

Affinity and dose of T cell receptor (TCR) interaction with antigens govern the magnitude of CD4+ T cell responses, but questions remain regarding the quantitative translation of TCR engagement into downstream signals. We find that while the response of mouse CD4+ T cells to antigenic stimulation is bimodal, activated cells exhibit analog responses proportional to signal strength. Gene expression output reflects TCR signal strength, providing a signature of T cell activation. Expression changes rely on a pre-established enhancer landscape and quantitative acetylation at AP-1 binding sites. Finally, we show that graded expression of activation genes depends on ERK pathway activation, suggesting that an ERK-AP-1 axis plays an important role in translating TCR signal strength into proportional activation of enhancers and genes essential for T cell function.
Heterogeneous integrated quantum photonic devices with single, deterministically positioned InAs quantum dots (2019)

We demonstrate integrated Si3N4 waveguides containing single-photon emitters based on single InAs quantum dots that were deterministically positioned in a GaAs nanowaveguide via a low-temperature in-situ electron-beam lithography.
Insulin-like Growth Factor-I Induces Renal Cell Hypertrophy via a Calcineurin-dependent Mechanism (2001)

Insulin-like growth factor-I (IGF-I) may play an important role in the development of renal hypertrophy. In this study we determined the effect of IGF-I on cultured mesangial cells (MCs) and examined activation of key signaling pathways. IGF-I induced hypertrophy as determined by an increase in cell size and an increase in protein to DNA ratio and increased accumulation of extracellular matrix (ECM) proteins. IGF-I also activated both Erk1/Erk2 MAPK and phosphatidylinositol 3-kinase (PI3K) in MCs. Inhibition of either MAPK or PI3K, however, had no effect on IGF-I-induced hypertrophy or ECM production. Next, we examined the effect of IGF-I on activation of the calcium-dependent phosphatase calcineurin. IGF-I treatment stimulated calcineurin activity and increased the protein levels of calcineurin and the calcineurin binding protein, calmodulin. Cyclosporin A, an inhibitor of calcineurin, blocked both IGF-I-mediated hypertrophy and up-regulation of ECM. In addition, calcineurin resulted in sustained Akt activation, indicating possible cross-talk with other signaling pathways. Finally, IGF-I treatment resulted in the calcineurindependent nuclear localization of NFATc1. Therefore, IGF-I induces hypertrophy and increases ECM accumulation in MCs. IGF-I-mediated hypertrophy is associated with activation of Erk1/Erk2 MAPK and PI3K but does not require either of these pathways. Instead, IGF-I mediates hypertrophy via a calcineurin-dependent pathway.
Endotoxin-pretreated neutrophils increase pulmonary vascular permeability in dogs (1989)

Endotoxin causes pulmonary vascular neutrophil sequestration and injures the lung. Whether this is primarily due to a direct effect of endotoxin on the endothelium or is mediated by an action on the neutrophil is unclear. Canine neutrophils, isolated on plasma-Percoll gradients in vitro, were incubated with Salmonella enteriditis endotoxin, washed, and injected via wedged pulmonary arterial catheters into discrete lung zones of anesthetized dogs, whereas untreated neutrophils were administered into contralateral control lung zones. 113mIn-transferrin was administered intravenously 2 h before the animals were killed. Morphometry and extravascular protein accumulation were assessed at 4 h. Endotoxin treatment of neutrophils ex vivo induced a two- to three-fold increase in neutrophils in these lung zones (0.096 +/- 0.012 vs. 0.05 +/- 0.002 neutrophils/alveolar septal intercept, P less than 0.05). Extravascular-to-intravascular protein ratios in zones receiving endotoxin-treated neutrophils were significantly increased compared with control zones (0.146 +/- 0.02 vs. 0.079 +/- 0.02, P less than 0.05). Because complement fragments increase injury to endothelium in vitro, exogenous C5 fragments were administered to other dogs before administration of neutrophils but failed to significantly increase the extravascular protein signal (0.154 +/- 0.03 vs. 0.124 +/- 0.04). In summary, endotoxin treatment of neutrophils leads to neutrophil sequestration and increased pulmonary extravascular protein accumulation. C5 fragments failed to further enhance the protein accumulation. These data are consistent with an effect of endotoxin on the neutrophil to initiate neutrophil-endothelial interaction and subsequent lung injury.
Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62 (2022)

The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. Here, we develop a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and use positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which has also been transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines show high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance.
Limitations of the Murine Nose in the Development of Nonviral Airway Gene Transfer (2009)

A clinical program to assess whether lipid GL67A-mediated gene transfer can ameliorate cystic fibrosis (CF) lung disease is currently being undertaken by the UK CF Gene Therapy Consortium. We have evaluated GL67A gene transfer to the murine nasal epithelium of wild-type and CF knockout mice to assess this tissue as a test site for gene transfer agents. The plasmids used were regulated by either (1) the commonly used short-acting cytomegalovirus promoter/enhancer or (2) the ubiquitin C promoter. In a study of approximately 400 mice with CF, vector-specific CF transmembrane conductance regulator (CFTR) mRNA was detected in nasal epithelial cells of 82% of mice treated with a cytomegalovirus-plasmid (pCF1-CFTR), and 62% of mice treated with an ubiquitin C-plasmid. We then assessed whether CFTR gene transfer corrected a panel of CFTR-specific endpoint assays in the murine nose, including ion transport, periciliary liquid height, and ex vivo bacterial adherence. Importantly, even with the comparatively large number of animals assessed, the CFTR function studies were only powered to detect changes of more than 50% toward wild-type values. Within this limitation, no significant correction of the CF phenotype was detected. At the current levels of gene transfer efficiency achievable with nonviral vectors, the murine nose is of limited value as a stepping stone to human trials.
"On-Card" User Authentication for Contactless Smart Cards based on Gesture Recognition. (2012)

www.h-brs.de Abstract: Smart cards are widely used for security purposes. To protect smart cards against misuse an authentication process (e.g. entering a pin or password) is necessary. Due to missing input interfaces “on-card”, an external terminal is required to input the password. Unfortunately the required external hardware (e.g. keypads, etc.) opens up new security issues by being vulnerable against attacks like side channel, forgery &amp;amp; tampering, man in the middle, eavesdropping and others. An elegant solution for such problems is an authentication process “on-card ” without the need for external devices. This paper presents a new class of contactless, ISO 14443 compliant smart cards which are equipped with a multipurpose user input interface as 2D gesture recognition sensor together with an optical feedback component. This offers new “on-card ” authentica-tion, card configuration and even front end interface capabilities. We will describe the basics of the general hardware design and discuss the gesture recognition process. 1
The All-Rounder Sodalis: A New Bacteriome-Associated Endosymbiont of the Lygaeoid Bug Henestaris halophilus (Heteroptera: Henestarinae) and a Critical Examination of Its Evolution (2017)

Hemipteran insects are well-known in their ability to establish symbiotic relationships with bacteria. Among them, heteropteran insects present an array of symbiotic systems, ranging from the most common gut crypt symbiosis to the more restricted bacteriome-associated endosymbiosis, which have only been detected in members of the superfamily Lygaeoidea and the family Cimicidae so far. Genomic data of heteropteran endosymbionts are scarce and have merely been analyzed from the Wolbachia endosymbiont in bed bug and a few gut crypt-associated symbionts in pentatomoid bugs. In this study, we present the first detailed genomic analysis of a bacteriome-associated endosymbiont of a phytophagous heteropteran, present in the seed bug Henestaris halophilus (Hemiptera: Heteroptera: Lygaeoidea). Using phylogenomics and genomics approaches, we have assigned the newly characterized endosymbiont to the Sodalis genus, named as Candidatus Sodalis baculum sp. nov. strain kilmister. In addition, our findings support the reunification of the Sodalis genus, currently divided into six different genera. We have also conducted comparative analyses between 15 Sodalis species that present different genome sizes and symbiotic relationships. These analyses suggest that Ca. Sodalis baculum is a mutualistic endosymbiont capable of supplying the amino acids tyrosine, lysine, and some cofactors to its host. It has a small genome with pseudogenes but no mobile elements, which indicates middle-stage reductive evolution. Most of the genes in Ca. Sodalis baculum are likely to be evolving under purifying selection with several signals pointing to the retention of the lysine/tyrosine biosynthetic pathways compared with other Sodalis.
Estimating ground state multiplet splitting, based on the masses of nuclei (2015)

The pairing interaction between nucleons has a strong effect on the structure of an atomic nucleus. The most precise estimate of the magnitude of pairing forces is obtained by determining it for every isotope, based on the masses of the nuclei. The quality of this estimate is characterized by the degree of reconstruction for levels of the nucleus ground state multiplet (GSM). In this work, GSMs for even-even nuclei with pairs of identical nucleons over a filled core are considered on the basis of the delta interaction. Calculations of the GSM structure for isobar nuclei A = 42 and A = 134 show that analyzing GSM in the case of np pairing yields additional information on the correlation between isoscalar and isovector components in the structure of pairing forces.