gebhart/patrepeval huggingface dataset:
COMA: Communication and Obfuscation Management Architecture (2019)

In this paper, we introduce a novel Communication and Obfuscation Management Architecture (COMA) to handle the storage of the obfuscation key and to secure the communication to/from untrusted yet obfuscated circuits. COMA addresses three challenges related to the obfuscated circuits: First, it removes the need for the storage of the obfuscation unlock key at the untrusted chip. Second, it implements a mechanism by which the key sent for unlocking an obfuscated circuit changes after each activation (even for the same device), transforming the key into a dynamically changing license. Third, it protects the communication to/from the COMA protected device and additionally introduces two novel mechanisms for the exchange of data to/from COMA protected architectures: (1) a highly secure but slow double encryption, which is used for exchange of key and sensitive data (2) a high-performance and low-energy yet leaky encryption, secured by means of frequent key renewal. We demonstrate that compared to state-of-the-art key management architectures, COMA reduces the area overhead by 14%, while allowing additional features including unique chip authentication, enabling activation as a service (for IoT devices), reducing the side channel threats on key management architecture, and providing two new means of secure communication to/from an untrusted chip.
Vaccine and abscopal effects result from <i>in situ</i> vaccination with nanosecond electric pulse treatment for breast cancer in mice (2020)

Abstract An electrical engineering technology, nanosecond electric pulse (nsEP), has been studied to ablate local tumor in a non-thermal and minimally invasive manner. Recently, several groups including our lab discovered that animals with complete tumor ablation following nsEP treatment were protected from a second tumor challenge. Therefore, nsEP tumor ablation is also a novel in situ vaccination approach. Breast cancer is considered a low immunogenic tumor with only a small subset of patients responsive to immune checkpoint inhibitors. We found nsEP treatment resulted in not only a potent in situ vaccine effect in a poorly immunogenic 4T1 mouse breast cancer model but also an abscopal effect, a rejection of distant untreated tumor lesion. We further examined the impact of nsEP on cancer cell death, tumor microenvironment (TME) modification, the dynamic changes of local and systemic immune response. 4T1 cells treated with nsEP did not show apoptotic death markers but released damage-associated molecular patterns, including calreticulin, high mobility group protein B1, and ATP. In contrast to abundant immune suppressor cells in untreated breast TME, nsEP treatment led to a significant reduction of both myeloid-derived suppressor cells and regulatory T cells. Conversely, the ratio of tumor associated macrophages M1-like verse M2-like was reversed. An increase of tissue-resident memory T cells was observed in draining lymph nodes. In summary, our results suggest that nsEP is a novel non-drug immunogenic cell death inducer and in situ vaccination approach. Further elucidation of its mechanisms and the development of an in vivo nsEP delivery system suitable for patients is critical to warrant this novel technology toward a clinical trial.
Influence of Physical Layer Configuration on Performance of Elastic Optical OFDM Networks (2014)

We study how the physical layer characteristics and novel digital impairment mitigation techniques impact the performance of elastic optical OFDM networks. The relationship between bandwidth blocking ratio (BBR) and fiber type, span length, dispersion management, FEC and intra-channel nonlinearity compensation are evaluated through cross-layer network simulations, which integrate closed-form expressions of quality of transmission into routing, modulation level and spectrum allocation (RMSA). An adaptive FEC assisted RMSA is proposed and proved to improve the network performance by optimizing the FEC overhead assignment for individual paths. Numerical simulations also show considerable performance improvement by deploying shorter span-length fiber links without dispersion management, and imperceptible influence of intra-channel nonlinearity compensation for flexible grid networks under very heavy traffic. These results provide valuable suggestions for physical layer fiber deployment and application of novel impairment mitigation techniques on elastic optical networks, such as intra-channel nonlinearity compensation as well as soft-decision FEC.
Rheological modeling of carbon nanotube aggregate suspensions (2008)

This paper is concerned with the rheological modeling of untreated carbon nanotubes (CNTs) suspended within an epoxy resin. The untreated CNT suspensions exhibited significant steady shear thinning and contained optically resolvable aggregate structures. A simple orientation model, based on a Fokker–Planck advection-diffusion description, failed to capture the experimentally observed rheological responses for untreated CNT suspensions. A new model named the “aggregation∕orientation” (AO) model has been developed to describe the experimental findings. The model integrated elements of both a standard orientation model and aggregation modeling concepts within the Fokker–Planck formalism. A hierarchy of states between CNTs that are free from entanglement and a complete CNT network was incorporated into the AO model, thereby enabling different microstructure populations to exist for different shear conditions. Using a small number of adjustable parameters, it was found that the experimental data could be fitted with reasonable precision.
In Silico-Mediated Virtual Screening and Molecular Docking Platforms for Discovery of Non β-Lactam Inhibitors of Y-49 β-Lactamase from Mycobacterium Tuberculosis (2018)

Tuberculosis (TB) is caused by Mycobacterium tuberculosis, and remains a major, worldwide health concern. The emergence of M. tuberculosis strains that are resistant to front line antimicrobacterial drugs such as isoniazid and rifampicin have greatly complicated efforts to control the spread of TB. Of the various resistance mechanisms, the most effective involves the production of -lactamases that hydrolyze -lactam antibiotics. One approach to overcoming resistance to -lactam antibiotics is to find new drugs or additives that can prevent the -lactam antibiotic from being hydrolyzed by -lactamases. The spectrum of anti-TB drugs consisting of non -lactam scaffolds has been expanded by the development of new boronic acid derivatives and cationic peptidic inhibitors that proved effective in neutralizing bacterial resistance, especially when administered in combination with antibiotics. The intrinsic resistance to -lactam antibiotics was due mainly to the presence of a chromosomally-encoded gene (blaC) in M. tuberculosis for a Class A, Ambler -lactamase (BlaC). The BlaC enzyme has already been validated as one of the leading targets of tuberculosis therapy. In the search for new -lactamase inhibitors we employed the on-line server Pharmit (pharmit.csb.pitt.edu) to discover new 3-D pharmacophores and search different databases of chemical libraries, and commercial compounds. Autodock Vina was employed to perform molecular docking of selected compounds from ChEMBL/ MolPort/ZINC databasesusingthe M. tuberculosis -lactamase 3M6B.pdb as the target protein. This combination of 3-D pharmacophore screening and molecular docking lead to the discovery of natural products, and novel, small molecules inhibitors of Y-49-lactamase from Mycobacterium tuberculosis. Notably new 3D-pharmacophores derived from hydroxyphenylglycine and fragments from the family of biphenyls, aromatic ketones, and stilbenes emerged as potential inhibitors of the recombinant Y-49 -lactamase exhibiting in vitro inhibitory constants (Ki), in the low 5uM-200uM range. These newly discovered pharmacophore features enabled by in silico screening are extending the chemical space for discovery of novel and potent inhibitors of -lactamases.
Supplementary Figures from LKB1 Expression Correlates with Increased Survival in Patients with Advanced Non–Small Cell Lung Cancer Treated with Chemotherapy and Bevacizumab (2023)

&lt;p&gt;Bonanno L. et al. Supplementary Figures&lt;/p&gt;
First isolation of Clostridium difficile 027 in Japan (2007)

We report the first isolation of a variant strain of Clostridium difficile from a patient with pseudomembranous colitis in Japan. The strain was chararacterised as North American pulsed field gel electrophoresis type 1 (NAP1), PCR ribotype 027, toxinotype III.
Time course of thrombin-induced increase in endothelial permeability: relationship to Ca2+i and inositol polyphosphates (1992)

The temporal relationship between the alpha-thrombin-induced increase in transendothelial permeability and the alpha-thrombin-mediated changes in several key transmembrane signaling events was examined in confluent monolayers of bovine pulmonary artery endothelial cells (BPAEC). The time courses of inositol 1,4,5-trisphosphate [Ins(1,4,5)P3] generation, changes in cytosolic [Ca2+] ([Ca2+]i), and reorganization of cytoskeletal F-actin were determined to assess the relationship between these events and the onset of the alpha-thrombin-induced increase in endothelial permeability. alpha-Thrombin (10(-7) M) increased the transendothelial 125I-albumin clearance rate half-maximally by approximately 1 min and maximally by approximately 2 min (160% over control level). The increase in permeability occurred concomitantly with reorganization of F-actin cytoskeleton (i.e., loss of peripheral band and increased stress fiber density) and increased actin polymerization. Stimulation of fura-2-loaded BPAEC with 10(-7) M alpha-thrombin produced a typical biphasic rise in [Ca2+]i. The initial rapid increase in [Ca2+]i peaked by approximately 16 s after thrombin challenge and the [Ca2+]i response showed a slow decrease to half-maximal within 50 s. The alpha-thrombin-induced increase in permeability as well as the increase in [Ca2+]i were consistently preceded by increased Ins(1,4,5)P3 generation detectable within 10 s after thrombin challenge. These results indicate that alpha-thrombin triggers a cascade of events (i.e., Ins(1,4,5)P3 generation and the ensuing rise in [Ca2+]i), which may comprise the second messengers that mediate F-actin reorganization and the increase in endothelial permeability.
Effect of Cell-Based Intercellular Delivery of Transcription Factor GATA4 on Ischemic Cardiomyopathy (2007)

Recent loss-of-function studies highlight the importance of the transcription factor GATA4 in the myocardial response to injury in the adult heart. However, the potential effects of gain-in-function of GATA4 overexpression, and transcription factors in general, is hindered by the fact that transcription factors are neither secreted nor taken up by cells. Chimeric proteins incorporating motifs of cell-penetrating proteins are secreted from cells and internalized by surrounding cells. We engineered a chimeric protein consisting of GATA4 and the cell-penetrating protein VP22. Cardiac fibroblasts stably transfected with the GATA4:VP22, GFP:VP22, or green fluorescent protein (GFP) constructs were transplanted into Lewis rats 1 month after left anterior descending ligation. GATA4:VP22 expression in the border zone was associated with increased cardiac myosin expression and cardiac myocyte size (30 mum versus 19 mum, P<0.01). Compared with the GFP:VP22 control group, 6 weeks after cardiac fibroblast transplantation (10 weeks after myocardial infarction), animals that received GATA4:VP22-expressing cardiac fibroblasts demonstrated increased cardiac function and less negative remodeling. These data demonstrate a novel strategy for transcription factor delivery to injured myocardium and indicate that the delivery of GATA4 locally to the infarct border zone induces multiple local effects in the border zone cardiac myocytes resulting in beneficial ventricular remodeling and improved global left ventricular function.
Azobenzene containing polymers: what is yet viable with aged liquid crystals (2006)

A Commentary on the paper ”Photochromic liquid crystalline polymers. Main chain and side chain polymers containing azobenzene mesogens„, by A. S. Angeloni, D. Caretti, C. Carlini, E. Chiellini, G. Galli, A. Altomare, R. Solaro and M. Laus. First published in Liquid Crystals, 4, 513‐527 (1989).
Knockdown of apoptosis signal‐regulating kinase 1 modulates basal glycogen synthase kinase‐3β kinase activity and regulates cell migration (2010)

GSK-3β is a basally active kinase. Axin forms a complex with GSK-3β and β-catenin; this complex promotes the GSK-3β-dependent phosphorylation of β-catenin, thereby inducing its degradation. However, the inhibition of GSK-3β provokes cell migration via the dysregulation of β-catenin. In this study, we determined that the level of apoptosis signal-regulating kinase 1 (ASK1) was lower in a metastatic breast cancer cell line, compared to that of non-metastatic cancer cell lines and the knockdown of ASK1 not only induces β-catenin activation via the inhibition of GSK-3β and collapsing the subsequent protein complex by regulating Axin dynamics, but also stimulates cell migration. Together, the blockage of the GSK-3β-β-catenin pathway resulting from the knockdown of ASK1 modulates the migration of breast cancer cells.
Toward the Development of a Novel Electro-Fenton System for Eliminating Toxic Organic Substances from Water. Part 2. Preparation, Characterization, and Evaluation of Iron-Impregnated Carbon Felts as Cathodic Electrodes (2015)

New results are presented on the preparation and performance of iron-impregnated carbon electrodes for a novel electro-Fenton “filter”-type device, reported in a previous publication. Two composite Fe/carbon-felt electrodes were prepared via different procedures: one prepared under oxidizing conditions (i.e., dissolved oxygen) through immersion of carbon felt in an iron ethanolic solution (CFm-Fe), and another prepared under reduced oxidative conditions (nitrogen, ammonia, etc.) leading to in situ formation of iron nanoparticles on the carbon surface (CFm-nFe). The cathodes were characterized by X-ray diffraction (XRD), N2 adsorption–desorption (BET), scanning electron microscopy (SEM), Raman microspectroscopy, and linear sweep voltammetry (LSV). The stability and oxidation performance of these electrodes were evaluated by measuring the leaching of iron species and the degradation in aqueous medium of a common pharmaceutical compound (diclofenac), respectively. The results show that the flow-through operation leads to increased solute removal, attributed to the enhanced electrosorption on the charged electrodes and the synergistic degradation/mineralization of diclofenac due to Fenton reactions on the composite cathodes. The CFm-nFe composite cathode was the most stable, exhibiting high sorption capacity (59.2 mgDCF gCFm–1) and significant degradation/mineralization efficiency (63.7 and 31.6%, respectively) at low applied potential (1.0 V/Ag/AgCl), neutral pH and high initial pollutant concentration (∼34 mg L–1). The results demonstrate the capability of the electro-Fenton process, implemented in the novel “filter”-type device, to decontaminate neutral waters polluted by diclofenac and similar organic compounds with no addition of chemicals and with reduced energy expenditure. Research and development (R&D) needs are also outlined.
Characteristics of a cold-sensitive cell division mutant of Escherichia coli K-12. (1977)

The culture of cold-sensitive division mutant, cs 2-29 consists of many normal cells and some filaments at 37°C. When an exponentially growing culture of cs 2-29 at 37°C was shifted to 20°C, the number of viable cells increased about 1.5-fold and the cells formed multinucleated filaments lacking septa. After the increase in optical density terminated at 20°C, normal cells separated from the end of filaments and the number of colony formers gradually increased. The number of viable cells of cs 2-29 increased normally at 25°, 30° and 37°C but not at 20°C in NBT medium. When chloramphenicol was added to the culture simultaneously with the temperature shift to 37°C after 6 hr of incubation at 20°C, the filamentous cells of cs 2-29 failed to divide. Strain cs 2-29 could divide at 20°C in NBT medium containing D-pantoyl lactone and also in semi-synthetic medium supplemented with sodium acetate as a carbon source. The mutant accepted both chromosomal and plasmid markers at reduced frequencies. The cs gene has been located between metE and rha, a previously undescribed region involved in septation. The mutated gene in this strain was designated as fcsA. The decrease of conjugation ability of cs 2-29 appears to be co-transducible with the cs gene.
A Framework for Robot Self-Assessment of Expected Task Performance (2022)

We propose a self-assessment framework which enables a robot to estimate how well it will be able to perform a known or possibly novel task. The robot simulates the task to generate a state distribution of possible outcomes and determines (1) the likelihood of overall success, (2) the most probable failure location, and (3) the expected time to task completion. We evaluate the framework on the “FetchIt!” mobile manipulation challenge which requires the robot to fetch a variety of parts around a small enclosed arena. By comparing the simulated and actual task resulting state distributions, we show that the robot can effectively assess its expected performance which can be communicated to humans.
Three-Dimensional Structure of Leucocin A in Trifluoroethanol and Dodecylphosphocholine Micelles:  Spatial Location of Residues Critical for Biological Activity in Type IIa Bacteriocins from Lactic Acid Bacteria<sup>,</sup> (1997)

The first three-dimensional structure of a type IIa bacteriocin from lactic acid bacteria is reported. Complete 1H resonance assignments of leucocin A, a 37 amino acid antimicrobial peptide isolated from the lactic acid bacterium Leuconostoc gelidum UAL187, were determined in 90% trifluoroethanol (TFE)-water and in aqueous dodecylphosphocholine (DPC) micelles (1:40 ratio of leucocin A:DPC) using two-dimensional NMR techniques (e.g., DQF-COSY, TOCSY, NOESY). Circular dichroism spectra, NMR chemical shift indices, amide hydrogen exchange rates, and long-range nuclear Overhauser effects indicate that leucocin A adopts a reasonably well defined structure in both TFE and DPC micelle environments but exists as a random coil in water or aqueous DMSO. Distance geometry and simulated annealing calculations were employed to generate structures for leucocin A in both lipophilic media. While some differences were noted between the structures calculated for the two different solvent systems, in both, the region encompassing residues 17-31 assumes an essentially identical amphiphilic alpha-helix conformation. A three-strand antiparallel beta-sheet domain (residues 2-16), anchored by the disulfide bridge, is also observed in both media. In TFE, these two regions have a more defined relationship relative to each other, while, in DPC micelles, the C-terminus is folded back onto the alpha-helix. The implications of these structural features with regard to the antimicrobial mechanism of action and target recognition are discussed.
Prognosis for patients who have osteosarcoma with skip metastasis. (1990)

We analyzed the cases of twenty-three patients who had Stage-IIB osteosarcoma and skip metastasis to determine the rates of disease-free and long-term survival. The regimens of preoperative and postoperative chemotherapy varied. The patterns of relapse and long-term survival were studied in relation to the skip lesions, and these patterns were compared with those of 224 patients who had Stage-II osteosarcoma but no skip lesion. Of the twenty-three patients who had a skip lesion, twenty-two had either a local recurrence or a distant metastasis; twenty-two patients died, and one remained disease-free at thirty-eight months. Kaplan-Meier analysis showed significant differences in the rates of local recurrence and distant metastasis (Mantel-Cox test statistic, p less than 0.0001) and in the over-all survival (Mantel-Cox test statistic, p less than 0.0001) between the patients who had and those who did not have skip metastasis. The cases of fourteen patients who had skip metastasis from a lesion in the distal end of the femur were compared with those of eighty-seven patients who had a similarly situated primary lesion but no skip metastasis. The difference was significant, although less so than when lesions in all anatomical sites were analyzed. The follow-up data indicated that the use of adjuvant chemotherapy did not improve the poor prognosis of patients who had skip metastasis. Therefore, we regard a skip lesion, along with regional lymphatic metastasis or metastasis to a distant organ, as another criterion for considering an osteosarcoma to be Stage III.
The Effect of Combined C-Peptide and Zinc on Cellular Function (2011)

The average adult human has approximately 5 L of blood, of which, nearly 40–45% is comprised of the red blood cell (RBC). The physiological significance of the RBC, its ability to carry and deliver oxygen to organs and tissues that may be hypoxic, is without question. Indeed, the idea of the RBC playing a role in such an important and complex mechanism may seem difficult to understand given that this cell has no nucleus or mitochondria. In fact, to some, this 7 or 8 μm-sized cell, whose life span in a healthy human is about 110–120 days, is nothing more than a simple cell with minimal machinery whose function is solely that of oxygen delivery. However, since the early 1990s, there has been a significant increase in the number of reports providing strong evidence that the RBC, in addition to its role as a deliverer of oxygen, is also a participant in overall blood flow itself [1, 2].
New insights into the pathogenesis of urinary tract infection (2005)

Drug Prescribing for Patients with Chronic Kidney Disease in General Practice: a Cross-Sectional Study
The Properties of LPCVD SiO2 Film Deposited by SiH2Cl2 and  N 2 O  Mixtures (1981)

The distribution of Cl in LPCVD film deposited by and was measured by IMMA. Cl was distributed broadly near the interface even in unannealed film. In thick LPCVD films on Si, surface roughness was observed after thermal oxidation. Cl was markedly piled up near the interface between the thermally grown oxide and the Si substrate. In thin films, surface roughness induced by oxidation was not observed. Cl distribution after oxidation was almost the same as that of unannealed film. The Cl pile‐up is not caused by oxidation, but by the existence of the interface. The cause of surface roughness is attributed to a smaller concentration of oxygen than Cl at the interface.
Endoscopic diagnosis and treatment of a giant duodenal lipoma presenting with gastrointestinal bleeding (2013)

A 66-year-old man presented with fatigue and acute upper gastrointestinal bleeding (hemoglobin 92 g/L). He had melena but no signs of hematemesis. Upper gastrointestinal endoscopy revealed a 35 × 15-mm large polypoid lesion with multiple ulcerations in the second part of the duodenum ([Fig. 1]). No biopsy samples were taken due to the risk of bleeding. The diagnosis was unclear and the patient underwent endoscopic ultrasound, which demonstrated a hyperechoic lesion measuring 11 × 19 mm in diameter in the submucosa in the duodenal wall with intact muscularis propria ([Fig. 2]), suggestive of a lipoma. A subsequent capsule endoscopy excluded distal causes of bleeding in the small intestine. Next, the lesion was removed endoscopically using an endoloop and snare without any complication ([Fig. 3]). The resected lesion exhibited multiple ulcerated areas ( [Fig.4]). Histological examination demonstrated a duodenal lipoma with large blood vessels in contact with these ulcerated areas ([Fig. 5]).