gebhart/patrepeval huggingface dataset:
Authentication in Time-Triggered Systems Using Time-Delayed Release of Keys (2011)

This paper investigates on the security of time -- triggered transmission channels, which are used to establish a predictable and timely message transfer in a distributed embedded system with potential safety constraints. Within such a system, safety and security are closely related, because malicious attacks can have an impact on a system's safety and thereby cause severe damage. An attacker could masquerade as an original sender and try to alter some system parameters by injecting malicious messages in the system. In the embedded real-time systems domain particularly the authenticity of data items is of interest, because a lack of integrity can lead to incorrect or erroneous system behavior. In addition, we address the open research question how a common notion of time can contribute to a system's security. Our solution encompasses an authentication protocol to secure time-triggered transmission channels. We illustrate two attack scenarios (insertion and substitution) that aim at injecting fake messages in such a channel thereby corrupting the internal system state of a receiver. We discuss the feasibility of several key management strategies for embedded systems and describe an authentication protocol using time-delayed release of symmetric keys for time-triggered systems. In a case study we implement the protocol for a prototype Time-Triggered Ethernet (TTE) system. The insight gained from the evaluation is that the computation of the cryptographic algorithms consumes most resources. Our solution shows that authentication can be transparently applied to a time-triggered system exploiting the available global time base and without violating its timeliness properties.
Dynamics of Collagen Oxidation and Cross Linking in Regenerating and Irreversibly Infarcted Myocardium (2023)

In mammalian hearts myocardial infarction produces a permanent collagen-rich scar. Conversely, in zebrafish a collagen-rich scar forms but is completely resorbed as the myocardium regenerates. The formation of cross-links in collagen hinders its degradation but cross-linking has not been well characterized in zebrafish hearts. Here, a library of fluorescent probes to quantify collagen oxidation, the first step in collagen cross-link (CCL) formation, was developed. Myocardial injury in mice or zebrafish resulted in similar dynamics of collagen oxidation in the myocardium in the first month after injury. However, during this time, mature CCLs such as pyridinoline and deoxypyridinoline developed in the murine infarcts but not in the zebrafish hearts. High levels of newly oxidized collagen were still seen in murine scars with mature CCLs. These data suggest that fibrogenesis remains dynamic, even in mature scars, and that the absence of mature CCLs in zebrafish hearts may facilitate their ability to regenerate.
A chromosome-length genome assembly and annotation of blackberry ( Rubus argutus , cv. “Hillquist”) (2022)

Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. Here we present a chromosome-length assembly and annotation of the diploid blackberry germplasm accession "Hillquist" (R. argutus). "Hillquist" is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The "Hillquist" assembly, generated using Pacific Biosciences long reads scaffolded with high-throughput chromosome conformation capture sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on 7 chromosome-length scaffolds with an average length of 38.6 Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted, of which 72% were functionally annotated. Eighteen flowering gene homologs within a previously mapped locus aligning to an 11.2 Mb region on chromosome Ra02 were identified as potential candidate genes for primocane-fruiting. The utility of the "Hillquist" genome has been demonstrated here by the development of the first genotyping-by-sequencing-based linkage map of tetraploid blackberry and the identification of possible candidate genes for primocane-fruiting. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.
Antiserum against the conserved nine amino acid N-terminal peptide of influenza A virus matrix protein 2 is not immunoprotective (2010)

The recent emergence and rapid spread of the pandemic H1N1 swine influenza virus reminded us once again of the need for a universal influenza vaccine that can elicit heterosubtypic protection. Here, we show the superior immunogenicity and immunoprotective capacity of the full-length matrix protein 2 ectodomain (M2e) peptide coupled to keyhole limpet haemocyanin (KLH) compared with the N-terminal 9 aa residues of M2e (SP1). Immunization with M2e-KLH protected mice against a lethal challenge with influenza A virus and significantly reduced weight loss and lung virus titres. In addition, passive transfer of serum raised in rabbits against M2e-KLH protected mice against a lethal influenza virus challenge, whereas serum from rabbits immunized with SP1-KLH did not. Nevertheless, immunofluorescence staining revealed that rabbit serum raised against SP1-KLH bound specifically to infected Madin-Darby canine kidney cells. We conclude that the peptide SP1 contains an immunogenic epitope that is not sufficient for immunoprotection.
Radial Head Fractures (2000)

Summary: Radial head fractures are the most common fractures of the elbow. Because of the variety of fracture types and associated injuries, treatment of radial head fractures is variable. The biomechanical role of the radial head in elbow and forearm stability is becoming better recognized. Preserving the radial head can improve stability of the elbow and hopefully decrease the chance of posttraumatic instability and arthritis. Therefore, radial head preservation techniques, such as open reduction with internal fixation or metallic radial head replacement, are becoming more common. The authors review the current treatment of radial head fractures.
Stem Cells: Supramolecular Hydrogels for Long‐Term Bioengineered Stem Cell Therapy (Adv. Healthcare Mater. 2/2015) (2015)

K. Kim, Y. C. Sung, S. K. Hahn, and co-workers develop supramolecular hydrogels for long-term engineered mesenchymal stem cell (eMSC) therapy using the host-guest chemistry of cucurbit[6]uril and diaminohexane on page 237. The eMSCs can produce enhanced green fluorescence protein within the hydrogels in mice for more than 60 days. This platform technology is successfully applied to the treatment of cancer, reflecting the feasibility for various cell therapy and tissue engineering.
Hard and Transparent Films Formed by Nanocellulose–TiO2 Nanoparticle Hybrids (2012)

The formation of hybrids of nanofibrillated cellulose and titania nanoparticles in aqueous media has been studied. Their transparency and mechanical behavior have been assessed by spectrophotometry and nanoindentation. The results show that limiting the titania nanoparticle concentration below 16 vol% yields homogeneous hybrids with a very high Young's modulus and hardness, of up to 44 GPa and 3.4 GPa, respectively, and an optical transmittance above 80%. Electron microscopy shows that higher nanoparticle contents result in agglomeration and an inhomogeneous hybrid nanostructure with a concomitant reduction of hardness and optical transmittance. Infrared spectroscopy suggests that the nanostructure of the hybrids is controlled by electrostatic adsorption of the titania nanoparticles on the negatively charged nanocellulose surfaces.
Differential contribution of GABAA receptor subtypes to the anticonvulsant efficacy of benzodiazepine site ligands (2006)

Non-selective benzodiazepines, such as diazepam, interact with equivalent affinity and agonist efficacy at GABA(A) receptors containing either an alpha1, alpha2, alpha3 or alpha5 subunit. However, which of these particular subtypes are responsible for the anticonvulsant effects of diazepam remains uncertain. In the present study, we examined the ability of diazepam to reduce pentylenetetrazoLe (PTZ)-induced and maximal electroshock (MES)-induced seizures in mice containing point mutations in single (alpha1H101R, alpha2H101R or alpha5H105R) or multiple (alpha125H-->R) alpha subunits that render the resulting GABA(A) receptors diazepam-insensitive. Furthermore, the anticonvulsant properties of diazepam, the alpha1- and alpha3-selective compounds zolpidem and TP003, respectively, and the alpha2/alpha3 preferring compound TP13 were studied against PTZ-induced seizures. In the transgenic mice, no single subtype was responsible for the anticonvulsant effects of diazepam in either the PTZ or MES assay and neither the alpha3 nor alpha5 subtypes appeared to confer anticonvulsant activity. Moreover, whereas the alpha1 and alpha2 subtypes played a modest role with respect to the PTZ assay, they had a negligible role in the MES assay. With respect to subtype-selective compounds, zolpidem and TP003 had much reduced anticonvulsant efficacy relative to diazepam in both the PTZ and MES assays whereas TP13 had high anticonvulsant efficacy in the PTZ but not the MES assay. Taken together, these data not only indicate a role for alpha2-containing GABA(A) receptors in mediating PTZ and MES anticonvulsant activity but also suggest that efficacy at more than one subtype is required and that these subtypes act synergistically.
Hydrogen uptake in high-strength steel corroded in actual use environment and in laboratory corrosion condition, and interpretation of diffusive hydrogen in Thermal-Desorption-Spectroscopy-based Gas Chromatograph. (2018)

The theme of this paper is the hydrogen uptake in high-strength steel mainly for spring and stabilizer of automobile, when used in actual use environment and/or corroded in laboratory-simulating accelerated corrosion environment. In addition, this report gives a new interpretation to diffusive hydrogen concentration measured with Gas-Chromatograph-based Thermo-Desorption-Spectroscopy. When hydrogen in corroded steel (bcc-based ferrite, bainite or martensite) is measured after removing corrosion layer, hydrogen signal often appears at 300 to 400℃, in addition to both diffusive hydrogen signal at below 200℃ and non-diffusive hydrogen signal at over 400℃. However, the hydrogen signal at 300 to 400℃ has not been defined correctly, and it has been regarded as a long-standing unclear problem. Through experimental data and evidence, it is shown that the hydrogen peaks at 300 to 400℃ is based on inevitably-remaining deeply-rooted rust of FeOOH which cannot be removed perfectly from corroded steel sample even with a careful hand-polishing. The hydrogen spectrum appearing at around 300 to 400℃ has no relation to both diffusive hydrogen and non-diffusive hydrogen, and it is generated inside Gas Chromatograph, and therefore, it is not involved with hydrogen embrittlement at all.
Development of PRPK Directed Phthalimides (2021)

Abstract Immunomodulatory drugs (IMiDs) thalidomide, lenalidomide, and pomalidomide (Pom) bind to cereblon (CRBN) and trigger proteasomal degradation of neo-substrates IKZF1/3 leading to multiple myeloma (MM) cell apoptosis. Pomalidomide (Pom) also binds albeit weakly to p53-related protein kinase (PRPK, aka TP53RK), an understudied kinase reported to be associated with poor prognosis in MM patients. Here, we developed a series of IMiDs based on Pom and conducted a structure-activity relationship (SAR) study to identify a potent and selective PRPK binder. Structural analysis showed that IMiDs bind PRPK in a fundamentally different way from CRBN, and suggested specific derivatization to improve affinity. We employed a structure-guided strategy to develop compound TXM-02-118, which exhibited nanomolar affinityfor PRPK in binding assays, and showed high selectivity for PRPK over CRBN. Overall, the work represents an initial effort to develop tool compounds for studying PRPK. Moreover, it illustrates how a single class of molecules can use different recognition elements to bind diverse targets using fundamentally different binding poses. This has broad implications for chemical probe and lead compound selectivity profiling, and argues for more wide-spread use of global proteomics or similar methodologies.
Design of a Triple-Band Shared-Aperture Antenna With High Figures of Merit (2021)

This communication develops a triple-band shared-aperture antenna operating at X/K/Ka-band with high figures of merit such as high aperture reuse efficiency and simple configuration to achieve high gain. The proposed antenna is implemented by integrating a Fabry–Perot (FP) cavity antenna operating at X-band into a dual-band reflectarray antenna enabled by frequency selective surfaces (FSSs). The unit cells (UCs) to form the phase-shifting surfaces for the dual-band reflectarray antenna can offer partial reflectance/transmission abilities at X-band simultaneously, thereby enabling the implementation of an FP cavity antenna. The frequency responses of the proposed antenna are highly independent at X/K/Ka-band, which facilitates the design and optimization. For demonstration, a prototype has been described, fabricated, and measured. The simulated results present 3 dB gain bandwidths of 11.2% (8.4–9.4 GHz), 10.0% (24–26.6 GHz), and 13.3% (35–40 GHz), which are all experimentally verified. The measured results also present a peak gain of 16.8 dBi at 9.0 GHz, 23.8 dBi at 26 GHz, and 26.7 dBi at 38 GHz.
Tyrosine 981, a Novel Ret Autophosphorylation Site, Binds c-Src to Mediate Neuronal Survival (2004)

The glial cell line-derived neurotrophic factor (GDNF) family ligands (GFLs) are neurotrophic factors that influence several aspects of the developing and injured nervous system. GFLs signal through a common receptor tyrosine kinase (Ret) and one of the four ligand-binding co-receptors (GFRalpha1 to 4). Ligand-induced translocation of Ret to lipid rafts, where it interacts with the nonreceptor tyrosine kinase Src, is a prerequisite for full biological activity of these neurotrophic factors. This interaction and subsequent activation of Src are required for GFL-mediated neuronal survival, neurite outgrowth, or cell proliferation. Here we show by multiple approaches that Ret tyrosine 981 constitutes the major binding site of the Src homology 2 domain of Src and therefore the primary residue responsible for Src activation upon Ret engagement. Other tyrosines such as 1015 and 1029 may contribute to the overall interaction between Ret and Src, as judged by overexpression experiments. By generating a phosphospecific antibody, we demonstrate that tyrosine 981 is a novel autophosphorylation site in Ret. Importantly, we also show that this tyrosine becomes phosphorylated in dissociated sympathetic neurons after ligand stimulation. Mutation of tyrosine 981 to phenylalanine reduces GDNF-mediated survival in a transfected cerebellar granule neuron paradigm.
Meeting Report--NASA Radiation Biomarker Workshop (2008)

A summary is provided of presentations and discussions from the NASA Radiation Biomarker Workshop held September 27-28, 2007, at NASA Ames Research Center in Mountain View, California. Invited speakers were distinguished scientists representing key sectors of the radiation research community. Speakers addressed recent developments in the biomarker and biotechnology fields that may provide new opportunities for health-related assessment of radiation-exposed individuals, including for long-duration space travel. Topics discussed include the space radiation environment, biomarkers of radiation sensitivity and individual susceptibility, molecular signatures of low-dose responses, multivariate analysis of gene expression, biomarkers in biodefense, biomarkers in radiation oncology, biomarkers and triage following large-scale radiological incidents, integrated and multiple biomarker approaches, advances in whole-genome tiling arrays, advances in mass-spectrometry proteomics, radiation biodosimetry for estimation of cancer risk in a rat skin model, and confounding factors. Summary conclusions are provided at the end of the report.
Reliable Geofence Activation with Sparse and Sporadic Location Measurements (2022)

Geofences are a fundamental tool of location-based services. A geofence is usually activated by detecting a location measurement inside the geofence region. However, location measurements such as GPS often appear sporadically on smart-phones, partly due to weak signals or privacy preservation. Users may restrict location sensing, or conserve energy, because sensing locations can consume a significant amount of battery. These unpredictable, and sometimes long, gaps between measurements mean that entry into a geofence can go completely undetected. In this paper we argue that short term location prediction can help alleviate this problem by computing the probability of entering a geofence in the future. Complicating this prediction approach is the fact that another location measurement could appear at any time, making the prediction redundant and wasteful. Therefore, we develop a framework that accounts for uncertain location predictions and the possibility of new measurements to trigger geofence activations. Our framework optimizes over the benefits and costs of correct and incorrect geofence activations, leading to an algorithm that reacts intelligently to the uncertainties of future movements and measurements.
Natural Apocarotenoids and Their Synthetic Glycopeptide Conjugates Inhibit SARS-CoV-2 Replication (2021)

The protracted global COVID-19 pandemic urges the development of new drugs against the causative agent SARS-CoV-2. The clinically used glycopeptide antibiotic, teicoplanin, emerged as a potential antiviral, and its efficacy was improved with lipophilic modifications. This prompted us to prepare new lipophilic apocarotenoid conjugates of teicoplanin, its pseudoaglycone and the related ristocetin aglycone. Their antiviral effect was tested against SARS-CoV-2 in Vero E6 cells, using a cell viability assay and quantitative PCR of the viral RNA, confirming their micromolar inhibitory activity against viral replication. Interestingly, two of the parent apocarotenoids, bixin and β-apo-8'carotenoic acid, exerted remarkable anti-SARS-CoV-2 activity. Mechanistic studies involved cathepsin L and B, as well as the main protease 3CLPro, and the results were rationalized by computational studies. Glycopeptide conjugates show dual inhibitory action, while apocarotenoids have mostly cathepsin B and L affinity. Since teicoplanin is a marketed antibiotic and the natural bixin is an approved, cheap and widely used red colorant food additive, these readily available compounds and their conjugates as potential antivirals are worthy of further exploration.
Downhole seismic sources for Reverse 3D-VSP surveys (2011)

Acquisition of Reverse 3D-VSP with Downhole seismic sources and large amount of surface seismic sensors is desirable in many instances. A non exhaustive overview of existing powerful prototype downhole seismic source devices is presented, as well as the main results obtained in a recent past, as well as the emerging technology which can contribute to industrialise the Reverse 3D-VSP method. Discussion with industry is welcome
Clinical experience with uridine triacetate for 5-FU overexposure: An update. (2013)

e20592 Background: 5-Fluorouracil (5-FU) is broadly used to treat solid tumors. It is typically administered by IV infusion, at or near its maximum tolerated dose, over several days. The use of infusion pumps increases the possibility of life-threatening or lethal toxicity due to errors in pump programming, infusion reservoir errors and dosage miscalculations. Partial or total dihydropyrimidine dehydrogenase (DPD) deficiency, which predisposes patients (up to 3% of the population) to impaired 5-FU elimination, can also result in serious or lethal toxicity, Uridine triacetate is an orally bioavailable direct biochemical antagonist of 5-FU toxicity that has been used successfully to treat patients in emergency overdose situations as well as patients with known or suspected overexposure to 5-FU due to DPD deficiency or other causes. Approximately 100 patients at excess risk of 5-FU toxicity due to 5-FU overdose, accidental Xeloda (capecitabine) ingestion, or possible DPD deficiency (rapid onset of severe toxicities) have been treated with uridine triacetate using a common treatment regimen and protocol. More than 80 of these cases have occurred since uridine triacetate data were presented at ASCO in 2009. Methods: Uridine triacetate was provided under emergency IND provisions or an expanded access protocol when requested by qualified clinical sites following 5-FU overexposures, most due to infusion pump errors. Patients received uridine triacetate (10g q6h for 20 doses) as soon as possible after recognition of the overdose or possible clearance defect. Clinical outcomes, including safety and resumption of chemotherapy, were monitored. Results: To date, 98 patients overexposed to 5-FU have been treated with uridine triacetate. 96 of these 98 patients recovered fully. Reductions in or absence of GI, hematologic, and other toxicities associated with 5-FU poisoning were observed. Adverse events attributable to urdine triacetate were infrequent and mild in severity. Conclusions: Uridine triacetate appears to be a safe and effective life-saving antidote for 5-FU overexposure in emergency situations.
Protective Function of von Hippel-Lindau Protein against Impaired Protein Processing in Renal Carcinoma Cells (1999)

The absence of functional von Hippel-Lindau (VHL) tumor suppressor gene leads to the development of neoplasias characteristic of VHL disease, including renal cell carcinoma (RCC). Here, we compared the sensitivity of RCC cells lacking VHL gene function with that of RCC cells expressing the wild-type VHL gene (wtVHL) after exposure to various stresses. While the response to most treatments was not affected by the VHL gene status, glucose deprivation was found to be much more cytotoxic for RCC cells lacking VHL gene function than for wtVHL-expressing cells. The heightened sensitivity of VHL-deficient cells was not attributed to dissimilar energy requirements or to differences in glucose uptake, but more likely reflects a lesser ability of VHL-deficient cells to handle abnormally processed proteins arising from impaired glycosylation. In support of this hypothesis, other treatments which act through different mechanisms to interfere with protein processing (i.e., tunicamycin, brefeldin A, and azetidine) were also found to be much more toxic for VHL-deficient cells. Furthermore, ubiquitination of cellular proteins was elevated in VHL-deficient cells, particularly after glucose deprivation, supporting a role for the VHL gene in ubiquitin-mediated proteolysis. Accordingly, the rate of elimination of abnormal proteins was lower in cells lacking a functional VHL gene than in wtVHL-expressing cells. Thus, pVHL appears to participate in the elimination of misprocessed proteins, such as those arising in the cell due to the unavailability of glucose or to other stresses.