gebhart/patrepeval huggingface dataset:
High accuracy android malware detection using ensemble learning (2015)

With over 50 billion downloads and more than 1.3 million apps in Google's official market, Android has continued to gain popularity among smartphone users worldwide. At the same time there has been a rise in malware targeting the platform, with more recent strains employing highly sophisticated detection avoidance techniques. As traditional signature‐based methods become less potent in detecting unknown malware, alternatives are needed for timely zero‐day discovery. Thus, this study proposes an approach that utilises ensemble learning for Android malware detection. It combines advantages of static analysis with the efficiency and performance of ensemble machine learning to improve Android malware detection accuracy. The machine learning models are built using a large repository of malware samples and benign apps from a leading antivirus vendor. Experimental results and analysis presented shows that the proposed method which uses a large feature space to leverage the power of ensemble learning is capable of 97.3–99% detection accuracy with very low false positive rates.
Water-Soluble [2.2]Paracyclophane Chromophores with Large Two-Photon Action Cross Sections (2004)

A series of alpha,omega-donor-substituted distyrylbenzene dimers held together by the [2.2]paracyclophane core were designed, synthesized, and characterized. Different substituents were chosen to modulate the strength of the donor nitrogen groups and to allow the molecules to be either neutral and soluble in nonpolar organic solvents or charged and water-soluble. The specific neutral structures are (in order of decreasing donor strength) 4,7,12,15-tetra[N,N-bis(6' '-chlorohexyl)-4'-aminostyryl]-[2.2]paracyclophane (1N), 4,7,12,15-tetra[(N-(6' '-chlorohexyl)carbazol-3'-yl)vinyl]-[2.2]paracyclophane (2N), and 4,7,12,15-tetra[N,N-bis(4' '-(6' ''-chlorohexyl)phenyl)-4'-aminostyryl]-[2.2]paracyclophane (3N). The charged species are 4,7,12,15-tetra[N,N-bis(6' '-(N,N,N-trimethylammonium)hexyl)-4'-aminostyryl]-[2.2]paracyclophane octaiodide (1C), 4,7,12,15-tetra[(N-(6' '-(N,N,N-trimethylammonium)hexyl)carbazol-3'-yl)vinyl]-[2.2]paracyclophane octaiodide (2C), and 4,7,12,15-tetra[N,N-bis(4' '-(6' ''-(N,N,N-trimethylammonium)hexyl)phenyl)-4'-aminostyryl]-[2.2]paracyclophane octaiodide (3C). Two-photon excitation spectra, measured using the two-photon induced fluorescence technique, show in toluene the following trend for the two-photon cross sections (delta): 3N > 2N > 1N. In water the delta values follow the same order, 3C approximately 2C > 1C, but are smaller (approximately one-third). Significantly, the fluorescence quantum yield (eta) in water decreases much more for 1, relative to 2 and 3. The two-photon action cross sections (deltaeta) of 2C and 3C are 294 GM and 359 GM, respectively. These values are among the highest reported thus far. These results show that, to maximize the deltaeta in this class of chromophores, one needs to fine-tune the magnitude of the charge transfer character of the excited state, to minimize fluorescence quenching in polar media.
The intracellular precursor of IL-1 beta is associated with microtubules in activated U937 cells. (1989)

Treatment of the human histiocytic leukemia cell line U937 with PMA and LPS results in the induction of expression of IL-1. Rabbit polyclonal antibodies raised against mature rIL-1 have been used to investigate the intracellular location of the IL-1 beta precursor in U937 cells. The pattern of indirect immunofluorescence staining seen with these antibodies overlaps substantially with that seen by using a mAb raised against beta-tubulin. Depolymerization of tubulin by incubation of the cells at 0 degrees C before fixation results in the disruption of the pattern of IL-1 staining. IL-1 beta precursor in extracts of activated U937 cells is shown to co-cycle with exogenously added tubulin through two rounds of in vitro depolymerization/polymerization. In addition, immunoprecipitation of IL-1 from cell extracts at 30 degrees C but not at 0 degrees C results in co-precipitation of tubulin. Thus the IL-1 beta precursor is shown in vivo and in vitro to associate with the microtubules of the cytoskeleton.
Direct Synthesis of Acyl Azides from Carboxylic Acids Using 2-Azido-1,3-dimethylimidazolinium Chloride (2010)

Abstract Acyl azides were directly synthesized from carboxylic acids by the treatment with 2-azido-1,3-dimethylimidazolinium chloride (ADMC, 1) and amine. This procedure resulted in acyl azides in good yields and was applied to the amidation of amino acid derivatives without racemization of the products.
Prostate Segmentation with Texture Enhanced Active Appearance Model (2010)

Prostate contour segmented from Trans Rectal Ultra Sound (TRUS) and Magnetic Resonance (MR) images could improve inter-modality registration accuracy and reduce computational complexity of the procedure. However, prostate segmentation in each of these modalities is a challenging task in presence of imaging artifacts, intensity heterogeneities, and large inter patient shape variabilities of the prostate. We propose to use Haar wavelet approximation coefficients to extract texture features of the prostate region in both modalities to guide a deformable parametric model to segment the prostate in a multi-resolution framework. Principal Component Analysis (PCA) of the shape and texture information of the prostate region obtained from the training data aids contour propagation of the deformable parametric model. Prior knowledge of the optimization space is utilized for optimal segmentation of the prostate. Our method achieves a mean Dice Similarity Coefficient (DSC) value of 0.95±0.01, with mean segmentation time of 0.72±0.05 seconds in a leave-one-out validation framework with 25 TRUS images grabbed from a video sequence. DSC value of 0.88 ± 0.06 with a mean segmentation time of 0.81 ± 0.02 seconds was recorded for MR images when validated with 15 central slice images of 15 datasets from the MICCAI prostate segmentation challenge 2009. Our proposed method performs computationally efficient accurate multi-modal prostate segmentation in presence of intensity heterogeneities and imaging artifacts.
P19-50 LB. Role of vaccine-induced innate and adaptive immunity in controlling mucosal transmission of SIV in macaques (2009)

Background Mucosal immunity is critical in AIDS virus infection because most transmission is through mucosal surfaces and the GI mucosa is a major reservoir for virus replication. There is window in time in which mucosal T cells could potentially eradicate a nascent local mucosal infection before it disseminates. In most vaccine work, adjuvant-induced innate immunity was of interest only to improve adaptive immunity. Here, in addition to adaptive immunity, we also examine direct adjuvant effects on innate immune protection.
Concepts and Methods to Access Novel Antibiotics from Actinomycetes (2018)

Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics. Currently uncultured actinobacteria can be made available by bioprospecting extreme or simply habitats other than soil. Furthermore, bioinformatic analysis of genomes reveals most producers to harbour many more biosynthetic gene clusters than compounds identified from any single strain, which translates into a silent biosynthetic potential of the microbial world for the production of yet unknown natural products. This review covers discovery strategies and innovative methods recently employed to access the untapped reservoir of natural products. The focus is the order of actinomycetes although most approaches are similarly applicable to other microbes. Advanced cultivation methods, genomics- and metagenomics-based approaches, as well as modern metabolomics-inspired methods are highlighted to emphasise the interplay of different disciplines to improve access to novel natural products.
Simplified purification of equine chorionic gonadotropin (eCG)––an example of the use of magnetic microsorbents for the isolation of glycoproteins from serum (2011)

Classical purification of the glycoprotein equine chorionic gonadotropin (eCG) from serum includes pH fractionation with metaphosphoric acid, two ethanol precipitation steps as well as dialysis followed by fixed-bed chromatography. A simplified process requiring only 1/3 of the solvent and improving the yield from 53 to 65% has been developed. The process comprises an ultra-/diafiltration step after the first ethanol precipitation, directly followed by an adsorption/desorption procedure based on magnetic microadsorbents with N,N-diethyl-ammonium functionalization. The process reaches an overall purification factor of eCG of more than 1800 and an average product activity of 1300 IU(ELISA)/mg. After adapting the parameters of the fractionation and the type of magnetic microadsorbents, the new concept is likely to be transferable to other serum proteins.
CCDC 291708: Experimental Crystal Structure Determination (2006)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Catastrophic Cervical Spine Injuries in Contact Sports (2016)

<b>Study Design</b> Systematic review. <b>Objectives</b> To determine the incidence of catastrophic cervical spine injuries (CCSIs) among elite athletes participating in contact team sports and whether the incidence varies depending on the use of protective gear or by player position. <b>Methods</b> Electronic databases and reference lists of key articles published from January 1, 2000, to January 29, 2016, were searched. <b>Results</b> Fourteen studies were included that reported CCSI in rugby (<i>n</i> = 10), American football (<i>n</i> = 3), and Irish hurling (<i>n</i> = 1). Among Rugby Union players, incidence of CCSI was 4.1 per 100,000 player-hours. Among National Football League players, the CCSI rate was 0.6 per 100,000 player-exposures. At the collegiate level, the CCSI rate ranged from 1.1 to 4.7 per 100,000 player-years. Mixed populations of elite and recreational rugby players in four studies report a CCSI rate of 1.4 to 7.2 per 100,000 player-years. In this same population, the scrum accounted for 30 to 51% of total reported CCSIs in Rugby Union versus 0 to 4% in Rugby League. The tackle accounted for 29 to 39% of injuries in Rugby Union and 78 to 100% of injuries in Rugby League. Making a tackle was responsible for 29 to 80% of injuries in American football. <b>Conclusion</b> CCSIs are infrequent among elite athletes. There is insufficient evidence to determine the effect of protective gear (e.g., helmets, padding) on CCSI incidence. Scrum and tackle in rugby and tackling in American football account for the majority of CCSIs in each respective sport.
Preferential Platination of an Activated Cellular Promoter by cis-Diamminedichloroplatinum (1999)

This study examines how accessibility to cisplatin on various genomic regions in T47D breast cancer cells, including the retinoic acid receptor beta gene promoter and coding region and the dihydrofolate reductase gene promoter and coding region, is affected by treatment of the cells with 9-cis retinoic acid, a treatment that activates the retinoic acid receptor beta gene promoter in these cells. A PCR-based assay was used to measure cisplatin adduct density based on the inhibition of PCR amplification of templates from cisplatin treated versus untreated cells. Treatment of cells with 9-cis retinoic acid enhanced accessibility to cisplatin on the retinoic acid receptor beta gene promoter region, but not on the coding regions of that gene nor on the dihydrofolate reductase gene promoter or coding regions, where accessibilities to cisplatin remained 2-4 times lower than on the activated retinoic acid receptor beta gene promoter. Examination of smaller regions within this promoter region showed a repression of platination in the 500 bp region surrounding the TATA box in cells prior to 9-cis retinoic acid treatment, which was abolished following promoter activation. Differences in sequence composition between the various regions could not fully account for differences in platination, suggesting that structural features such as bends in retinoic acid receptor beta gene promoter DNA following gene activation, create energetically favorable sites for platination, and contribute to the cytotoxicity of the drug.
Push-SAGA: A Decentralized Stochastic Algorithm With Variance Reduction Over Directed Graphs (2021)

In this letter, we propose Push-SAGA, a decentralized stochastic first-order method for finite-sum minimization over a directed network of nodes. Push-SAGA combines node-level variance reduction to remove the uncertainty caused by stochastic gradients, network-level gradient tracking to address the distributed nature of the data, and push-sum consensus to tackle directed information exchange. We show that Push-SAGA achieves linear convergence to the exact solution for smooth and strongly convex problems and is thus the first linearly-convergent stochastic algorithm over arbitrary strongly connected directed graphs. We also characterize the regime in which Push-SAGA achieves a linear speed-up compared to its centralized counterpart and achieves a network-independent convergence rate. We illustrate the behavior and convergence properties of Push-SAGA with the help of numerical experiments on strongly convex and non-convex problems.
Impact of the COVID-19 epidemic at a high-volume facility in gynecological oncology in Tokyo, Japan: a single-center experience (2020)

During the epidemic phase of an emerging infectious disease, we found that COVID-19 has several other effects besides its incidence. The postponing treatment was the most common, therefore, treatment of ovarian tumors and ovarian cancer was considered to be the most likely to be affected among gynecological diseases. Protocols that allow for easy over-diagnosis can be disadvantageous, mainly because of treatment delays, and therefore, the protocols must be developed in light of the local infection situation.
Disorder‐Induced Quantum Griffiths Singularity Revealed in an Artificial 2D Superconducting System (2020)

Disorder-induced Griffiths singularity of quantum phase transition (QPT) is a crucial issue in 2D superconductors (2DSC). In a superconducting system, the strength of disorder is found to be associated with the vortex pinning energy, which is closely related to the quantum Griffiths singularity; however, a direct study to elucidate the role of vortex pinning energy on the quantum Griffiths singularity in 2DSC remains to be undertaken. Here, an artificial 2DSC system is designed by randomly depositing superconducting nanoislands on 2Delectron gas (2DEG). Quantum Griffiths singularity is present in a graphene/Pb-islands-array hybrid, where the superconducting behavior transits to weakly localized metallic behavior induced by the vertical magnetic field and exhibits critical behavior with a diverging dynamical critical exponent approaching zero temperature. Compared to the study of graphene/Sn-islands-array hybrid where the sharp QPT is observed, the vortex pinning energy acquired from the Arrhenius plot analysis is greater in graphene/Pb-islands-array hybrid, which may contribute to the presence of the quantum Griffiths singularity. This work may provide a comprehensive interpretation of the QPT in 2DSC.
Cell equalization in battery stacks through State Of Charge estimation polling (2010)

Differences in chemical characteristics, operating temperature or different internal resistance can cause differences in cell remaining capacity, leading to overcharging or overdischarging of respectively most charged and most discharged cells, decreasing the total stack storage capacity, shortening the battery lifetime and, eventually, permanently damaging the cells. The system proposed in this paper uses the switching capacitor method for cell equalization during bidirectional operations and it relies on a State Of Charge (SOC) estimator in order to select the target cell for charge distribution. The SOC estimator, based on an Extended Kalman Filter (EKF), polls cells sequentially and updates simple coulomb-counting SOC estimators. The polling limits the speed of equalization but it reduces the computational load of multiple EKF for every cell in the stack.
Tumor-specific down-regulation of the tumor necrosis factor-related apoptosis-inducing ligand decoy receptors DcR1 and DcR2 is associated with dense promoter hypermethylation. (2002)

TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) induces apoptosis in a large variety of cancer cells but not in most normal human cells. This feature makes TRAIL, a potential antitumor agent. TRAIL can bind to four different receptors, two pro-apoptotic death receptors (DRs), DR4 and DR5, and two antiapoptotic decoy receptors (DcRs), DcR1 and DcR2. Normal cells express all four of the receptors. The increased TRAIL sensitivity of tumor cells has been postulated to result from the lack of DcR expression. We studied the tumor-specific down-regulation of the TRAIL receptors DcR1 and DcR2, as well as DR4 and DR5, in a group of pediatric tumor cell lines [nine neuroblastoma and three peripheral primitive neuro-ectodermal tumors (PNETs)] and three cell lines from adult tumors. Lack of expression of DcR1 and DcR2 was widespread (13 of the 15 cell lines and 10 of 15, respectively), both in the adult tumor cell lines and in the pediatric tumor lines. DR4 and DR5 were expressed in 8 of 15 and 12 of 15 cell lines, respectively. To understand the tumor-specific down-regulation of the TRAIL receptors, the promoter regions were studied for possible methylation changes of their CpG islands. All normal tissues were completely unmethylated, whereas in the tumor cell lines, we found frequent hypermethylation of the promoter. For DcR1 and DcR2, we found dense hypermethylation in 9 (69%) of 13 and 9 (90%) of 10 of nonexpressing cell lines, respectively. DR4 and DR5 were methylated in 5 (71%) of 7 and 2 (67%) of 3 nonexpressing cell lines, respectively. Treatment with the demethylating agent 5-aza-2'deoxycytidine resulted in partial demethylation and restored mRNA expression. In addition, we performed mutation analysis of the death domains of DR4 and DR5 by sequencing exon 9. Mutations were not present in any of the neuroblastoma or PNET cell lines. A panel of 28 fresh neuroblastoma tumor samples also lacked expression of DcR1 and DcR2 in 85 and 74% of cases, respectively. Hypermethylation was observed in 6 (21%) of 28 for DcR1 and 7 (25%) of 28 for DcR2. DR4 and DR5 were both expressed in 22 of 28 tumors, and no promoter methylation was observed. These data suggest that hypermethylation of the promoters of DcR1 and DcR2 is important in the down-regulation of expression in neuroblastoma and other tumor types.
Effect of human epidermal growth factor on the tumor cell line A431: in vivo analysis of tumor growth inhibition and gene expression (2012)

The historical tag of the epidermal growth factor (EGF) as carcinogenesis promoter has not been uniformly reproduced, since, in some experiments, malignant cells are bound to growth inhibition and apoptosis. The present study intends to obtain additional data on the interaction of EGF with cancer cells by analyzing its effect in vitro on the growth of cultured A431 cells, and in vivo on nude mice xenotransplanted with this cell line; identifying, in addition, the gene expression patterns for a selected group of genes related to EGF and cancer pathways in the solid tumor. EGF-treated animals showed significantly smaller tumor volumes than controls, suggesting cellular growth inhibition mediated by this factor. Similar results were obtained regarding the proliferation of cultured A431 when treated with 2.2, 33 and 165 nM of EGF. These results may imply a common mechanism for the EGF-mediated growth inhibition of A431 cells in both biological conditions (in vivo and in vitro). The action of EGF at nanomolar concentrations may trigger a transient recovery of the tumor suppressor ability of tumor cells through the reduction of the biological action of mutated TP53, cell cycle arrest due to a decrease in Cdk4 expression levels and the initiation of caspase through the activation of CASP9.
Combined density and size-based sorting in deterministic lateral displacement devices (2013)

We present a deterministic-lateral-displacement (DLD) device that extends the capabilities of this traditionally sizebased particle separation technique to also be sensitive to density. By the use of T-shaped posts instead of the normally cylindrical posts the particle trajectory through the device will be a function of its vertical position which in turn is determined by the buoyancy of the particles. The potential lies in fast sorting of complex biological samples together with diagnosis and treatment-monitoring of diseases affecting cell-density, eg. cancer, sickle-cell anemia and malaria. We demonstrate proof-of-principle of combined size-and-density-based sorting, specifically particles of identical size but different density.
Life‐Threatening Ventricular Tachyarrhythmias Associated with Holiday Heart Syndrome: Treatment with the Automatic Implantable Cardioverter Defibrillator (1989)

Holiday heart syndrome is defined as the occurrence of cardiac arrhythmia in aicohol users without overt heart disease after the ingestion of alcohol. Additionally, alcohol has been implicated as a potential etiology of sudden cardiac death in susceptible individuals. We report on a 53‐year‐old black woman with mild nonischemic dilated congestive cardiomyopathy and alcohol‐provoked ventricular tachyarrhythmias who received an automatic implantable Cardioverter defibrillator (AICD). She subsequently had recurrent cardiac arrest during bouts of alcohol intoxication and with out‐of‐hospital AICD rescue. Electrophysiological study using alcohol infusion confirmed alcohol as the etiology of arrhythmogenicity. We propose that holiday heart be expanded to include people with overt heart disease. These individuals have a high risk of sudden cardiac death after alcohol ingestion, irrespective of underlying cardiac substrate; the AICD is an effective back‐up modality of therapy.
20-Gbaud QPSK coherent radio transmission at 325 GHz with high-gain antennas (2014)

High-speed coherent transmission at 325 GHz is successfully demonstrated with a 20-Gbaud QPSK signal. A frequency-locked terahertz signal can be provided by an optical-modulation-based optical frequency comb signal. A high-gain antenna with a gain of 46 dBi is suitable to extend the transmission distance up to 15 m without requiring a terahertz amplifier.
[Genotype-phenotype correlation in ADPKD: a possible role for NGAL?]. (2015)

This is the first study to evaluate plasma NGAL in the context of genotype-phenotype correlation. In ADPKD, NGAL levels were higher in patients already on Renal Replacement Therapy (RRT) compared to their affected relatives not on RRT. WT relatives had normal NGAL and CysC levels: these could be considered a better CTR group because they share the same genetic background with ADPKD subjects. No differences were found in NGAL levels between PKD1 and PKD2 patients in CKD stage II-III. Furthermore, the results indicate that NGAL correlates closely with renal function and CysC levels.