gebhart/patrepeval huggingface dataset:
Database Management as a Service: Challenges and Opportunities (2009)

Data outsourcing or database as a service is a new paradigm for data management in which a third party service provider hosts a database as a service. The service provides data management for its customers and thus obviates the need for the service user to purchase expensive hardware and software, deal with software upgrades and hire professionals for administrative and maintenance tasks. Since using an external database service promises reliable data storage at a low cost it is very attractive for companies. Such a service would also provide universal access, through the Internet to private data storedat reliable and secure sites. A client would store their data, and not need to carry their data with them as they travel. They would also not need to log remotely to their home machines, which may suffer from crashes and be unavailable. However, recent governmental legislations, competition among companies, and database thefts mandate companies to use secure and privacy preserving data management techniques. The data provider, therefore, needs to guarantee that the data is secure, be able to execute queries on the data, and the results of the queries must also be secure and not visible to the data provider. Current research has been focused only on how to index and query encrypted data. However, querying encrypted data is computationally very expensive. \emph{Providing an efficient trust mechanism} to push both database service providers and clients to behave honestly has emerged as one of the most important problem before data outsourcing to become a viable paradigm. In this paper, we describe scalable privacy preserving algorithms for data outsourcing. Instead of encryption, which is computationally expensive, we use distribution on multiple data provider sites and information theoretically proven secret sharing algorithms as the basis for privacy preserving outsourcing. The technical contributions of this paper is the establishment and development of a framework for efficient fault-tolerant scalable and theoretically secure privacy preserving data outsourcing that supports a diversity of database operations executed on different types of data, which can even leverage publicly available data sets.
Face recognition from a single view based on flexible neural network matching (2002)

This work presents a model-based face recognition approach that uses a hierarchical Gabor wavelet representation and flexible neural network matching. The representation of local features is based on the Gabor wavelets transform of a number of scales and a number of orientations. The Gabor wavelet representation is used in a innovative self-organization flexible neural network matching approach that can provide robust recognition. The sparse centers of Gabor wavelets in the images and neurons placement are arranged according to the hexagonal grids. Neural network matching between the model and the input image is to find out the exact correspondence of local features and to map the model to the input image based on local similarity and neighborhood grouping of local features. Experimental results in recognizing faces that includes the variations of translation, rotation in plane, rotation in depth, and slightly changes of facial expressions are also presented.
Improvement of Fingerprint Sensor Reading Using FPGA Devices (2008)

In order to realize fingerprint recognition system in real time environment, we describe in this paper signal controller to read fingerprint sensor generated in FPGA devices. Basically this signal is generated using state machine. The simulation result for behavioral simulation and signal generation read by logic analyzer are presented in this paper. Initialization and reading time for 76800 pixels are 50.99 mS. It is faster than fingerprint sensor using USB connection, which is more than 250 ms.
Hypermethylation of O6-methylguanine-DNA methyltransferase promoter may predict nonrecurrence after chemotherapy in colorectal cancer cases. (2003)

Hypermethylation of the MGMT promoter may be predictive of a low risk of recurrence in CRC patients receiving adjuvant chemotherapy.
Discovery of GPR183 Agonists Based on an Antagonist Scaffold (2021)

The G protein-coupled receptor GPR183/EBI2, which is activated by oxysterols, is a therapeutic target for inflammatory and metabolic diseases where both antagonists and agonists are of potential interest. Using the piperazine diamide core of the known GPR183 antagonist (E)-3-(4-bromophenyl)-1-(4-(4-methoxybenzoyl)piperazin-1-yl)prop-2-en-1-one (NIBR189) as starting point, we identified and sourced 79 structurally related compounds that were commercially available. In vitro screening of this compound collection using a Ca<sup>2+</sup> mobilization assay resulted in the identification of 10 compounds with agonist properties. To enable establishment of initial structure-activity relationship trends, these were supplemented with five in-house compounds, two of which were also shown to be GPR183 agonists. Taken together, our findings suggest that the agonist activity of this compound series is dictated by the substitution pattern of one of the two distal phenyl rings, which functions as a molecular efficacy-switch.
Effective Learning and Filtering of Faulty Heart-Beats for Advanced ECG Arrhythmia Detection using MIT-BIH Database (2015)

Electrocardiogram (ECG) signal has been established as one of the most fundamental bio-signals for monitoring and assessing the health status of a person. ECG analysis flow relies on the detection of points of interest on the signal with the QRS complex, located around an R peak of the heart beat, being the most commonly used. Using the MIT-BIH arrhythmia database, we evaluate the accuracy of various R peak detectors, showing a large number, i.e. several thousands, of falsely detected peaks. Considering the medical significance of the ECG analysis, we propose a machine learning based classifier to be incorporated in the ECG analysis flow aiming at identifying and discarding heart beats based on erroneously detected R peaks. Using Support Vector Machines (SVMs) and extensive exploration, we deliver a tuned classifier that i) successfully filters up to 75% of the false beats, ii) while keeping the correct beats mis-classified as false lower than 0.01% and iii) the computational overhead of the classifier sufficiently low.
Microbial ecology and geoelectric responses across a groundwater plume (2015)

Abstract We have used geophysics, microbiology, and geochemistry to link large-scale (30+ m) geophysical self-potential (SP) responses at a groundwater contaminant plume with its chemistry and microbial ecology of groundwater and soil from in and around it. We have found that microbially mediated transformation of ammonia to nitrite, nitrate, and nitrogen gas was likely to have promoted a well-defined electrochemical gradient at the edge of the plume, which dominated the SP response. Phylogenetic analysis demonstrated that the plume fringe or anode of the geobattery was dominated by electrogens and biodegradative microorganisms including Proteobacteria alongside Geobacteraceae, Desulfobulbaceae, and Nitrosomonadaceae. The uncultivated candidate phylum OD1 dominated uncontaminated areas of the site. We defined the redox boundary at the plume edge using the calculated and observed electric SP geophysical measurements. Conductive soils and waste acted as an electronic conductor, which was dominated by abiotic iron cycling processes that sequester electrons generated at the plume fringe. We have suggested that such geoelectric phenomena can act as indicators of natural attenuation processes that control groundwater plumes. Further work is required to monitor electron transfer across the geoelectric dipole to fully define this phenomenon as a geobattery. This approach can be used as a novel way of monitoring microbial activity around the degradation of contaminated groundwater plumes or to monitor in situ bioelectric systems designed to manage groundwater plumes.
Video Rate Optical Coherence Tomography (1998)

We have developed an optical coherence tomography system which can image up to video rate. The system utilizes a high power broadband source and real time image acquisition hardware and features a high speed scanning delay line in the reference arm based on Fourier- transform pulse shaping technology. We detail the operation of the delay line and demonstrate real time imaging of in vivo human skin and Xenopus laevis embryo and in vitro samples of porcine gastrointestinal tissue
QT Dispersion: Problems of Methodology and Clinical Significance (1994)

QT Dispersion. QT dispersion is defined as the difference in QT interval between the different leads of the surface 12‐lead ECG. This may provide an indirect measure of the underlying inhomogeneity of myocardial repolarization, which is believed to be important in arrhylhmogenesis. Methodology for determining QT dispersion varies significantly between studies, and the results of these studies need to be interpreted in light of the methodology used. Although QT dispersion is developing into an important research tool, as yet it has no established role in clinical practice. Once standardization of methodology is achieved a clinical role may emerge, particularly in the assessment of patients before and after intervention aimed at reduction of arrhythmia risk.
Low level of antioxidant capacity biomarkers but not target overexpression predicts vulnerability to ROS-inducing drugs (2023)

Despite a strong rationale for why cancer cells are susceptible to redox-targeting drugs, such drugs often face tumor resistance or dose-limiting toxicity in preclinical and clinical studies. An important reason is the lack of specific biomarkers to better select susceptible cancer entities and stratify patients. Using a large panel of lung cancer cell lines, we identified a set of "antioxidant-capacity" biomarkers (ACB), which were tightly repressed, partly by STAT3 and STAT5A/B in sensitive cells, rendering them susceptible to multiple redox-targeting and ferroptosis-inducing drugs. Contrary to expectation, constitutively low ACB expression was not associated with an increased steady state level of reactive oxygen species (ROS) but a high level of nitric oxide, which is required to sustain high replication rates. Using ACBs, we identified cancer entities with a high percentage of patients with favorable ACB expression pattern, making it likely that more responders to ROS-inducing drugs could be stratified for clinical trials.
Immune Inhibitor A Metalloproteases Contribute to Virulence in Bacillus Endophthalmitis (2021)

Endophthalmitis is a devastating infection that can cause blindness. Over half of <i>Bacillus</i> endophthalmitis cases result in significant loss of useful vision. <i>Bacillus</i> produces many virulence factors that may contribute to retinal damage and robust inflammation. We analyzed <i>Bacillus</i> immune inhibitor A (InhA) metalloproteases in the context of this disease, hypothesizing that InhAs contribute to <i>Bacillus</i> intraocular virulence and inflammation. We analyzed phenotypes and infectivity of wild-type (WT), InhA1-deficient (Δ<i>inhA1</i>), InhA2-deficient (Δ<i>inhA2</i>), or InhA1, A2, and A3-deficient (Δ<i>inhA1-3</i>) Bacillus thuringiensis. <i>In vitro</i> analysis of growth, proteolysis, and cytotoxicity were compared. WT and InhA mutants were similarly cytotoxic to retinal cells. The Δ<i>inhA1</i> and Δ<i>inhA2</i> mutants entered log-phase growth earlier than WT B. thuringiensis. Proteolysis by the Δ<i>inhA1-3</i> mutant was decreased, but this strain grew similar to WT <i>in vitro</i>. Experimental endophthalmitis was initiated by intravitreally infecting C57BL/6J mice with 200 CFU of WT B. thuringiensis or InhA mutants. Eyes were analyzed for intraocular <i>Bacillus</i> and myeloperoxidase concentrations, retinal function loss, and gross histological changes. Eyes infected with the Δ<i>inhA1</i> or Δ<i>inhA2</i> mutant strains contained greater numbers of bacteria than eyes infected with WT throughout the infection course. Eyes infected with single mutants had inflammation and retinal function loss similar to eyes infected with the WT strain. Eyes infected with the Δ<i>inhA1-3</i> mutant cleared the infection. Quantitative real-time PCR (qRT-PCR) results suggested that there may be compensatory expression of the other InhAs in the single InhA mutant. These results indicate that together, the InhA metalloproteases contribute to the severity of infection and inflammation in <i>Bacillus</i> endophthalmitis.
A New Copper-Catalyzed [3 + 2] Cycloaddition:  Enantioselective Coupling of Terminal Alkynes with Azomethine Imines To Generate Five-Membered Nitrogen Heterocycles (2003)

A copper-catalyzed method for the regioselective 1,3-dipolar cycloaddition of azomethine imines to terminal alkynes has been developed. Through the use of a chiral phosphaferrocene-oxazoline ligand, a wide range of substrates can be coupled to generate useful heterocycles in very good enantiomeric excess.
hashFS: Applying Hashing to Optimize File Systems for Small File Reads (2010)

Today's file systems typically need multiple disk accesses for a single read operation of a file. In the worst case, when none of the needed data is already in the cache, the metadata for each component of the file path has to be read in. Once the metadata of the file has been obtained, an additional disk access is needed to read the actual file data. For a target scenario consisting almost exclusively of reading small files, which is typical in many Web 2.0 scenarios, this behavior severely impacts read performance. In this paper, we propose a new file system approach, which computes the expected location of a file using a hash function on the file path. Additionally, file metadata is stored together with the actual file data. Together, these characteristics allow a file to be read in with only a single disk access. The introduced approach is implemented extending the ext2 file system and stays very compatible with the Posix semantics. The results show very good random read performance nearly independent of the organization and size of the file set or the available cache size. In contrast, the performance of standard file systems is very dependent on these parameters.
Susceptibility to T Cell-Mediated Injury in Immune Complex Disease Is Linked to Local Activation of Renin-Angiotensin System: The Role of NF-AT Pathway (2002)

FcR provides a critical link between ligands and effector cells in immune complex diseases. Emerging evidence reveals that angiotensin (Ang)II exerts a wide variety of cellular effects and contributes to the pathogenesis of inflammatory diseases. In anti-glomerular basement membrane Ab-induced glomerulonephritis (GN), we have previously noted that FcR-deficient mice (gamma(-/-)) surviving from lethal initial damage still developed mesangial proliferative GN, which was drastically prevented by an AngII type 1 receptor (AT1) blocker. We further examined the mechanisms by which renin-Ang system (RAS) participates in this immune disease. Using bone marrow chimeras between gamma(-/-) and AT1(-/-) mice, we found that glomerular injury in gamma(-/-) mice was associated with CD4(+) T cell infiltration depending on renal AT1-stimulation. Based on findings in cutaneous delayed-type hypersensitivity, we showed that AngII-activated renal resident cells are responsible for the recruitment of effector T cells. We next examined the chemotactic activity of AngII-stimulated mesangial cells, as potential mechanisms coupling RAS and cellular immunity. Chemotactic activity for T cells and Th1-associated chemokine (IFN-gamma-inducible protein-10 and macrophage-inflammatory protein 1alpha) expression was markedly reduced in mesangial cells from AT1(-/-) mice. Moreover, this activity was mainly through calcineurin-dependent NF-AT. Although IFN-gamma-inducible protein-10 was NF-kappaB-dependent, macrophage-inflammatory protein 1alpha was dominantly regulated by NF-AT. Furthermore, AT1-dependent NF-AT activation was observed in injured glomeruli by Southwestern histochemistry. In conclusion, our data indicate that local RAS activation, partly via the local NF-AT pathway, enhances the susceptibility to T cell-mediated injury in anti-glomerular basement membrane Ab-induced GN. This novel mechanism affords a rationale for the use of drugs interfering with RAS in immune renal diseases.
Abstract 1156: Shed syndecan-1 downregulates histone acetyltransferase activity and shuttles HGF to the nucleus of tumor and host cells (2014)

Abstract The cell surface heparan sulfate proteoglycan syndecan-1 (CD138) is expressed by myeloma tumor cells, is proteolytically shed from the cell surface and accumulates in the serum. High levels of serum syndecan-1 are an independent indicator of poor prognosis. Our lab has demonstrated that shed syndecan-1 drives myeloma tumor progression in vivo, but the mechanism(s) mediating this are not fully understood. The role of heparan sulfate proteoglycans on the cell surface and in the extracellular matrix has been extensively studied, but their presence and function within the nucleus is often overlooked. However, recent findings indicate that nuclear heparan sulfate has important regulatory functions. Based on preliminary findings, we hypothesized that shed syndecan-1 binds to the tumor cell surface and translocates to the nucleus where it regulates gene expression thereby promoting aggressive tumor behavior. We utilized murine myeloma cells which were grown in the presence of medium containing human shed syndecan-1. Strikingly, the shed syndecan-1 was rapidly taken up by these cells and translocated to the nucleus. Additionally, exogenous human shed syndecan-1 added to murine stromal cells also bound to the cell surface and translocated to the nucleus. This is the first demonstration that shed proteoglycans can translocate to the nucleus of cells. When stromal cells were grown in the presence of tumor-derived shed syndecan-1, acetylated histone H3 was decreased. Additionally, tumor cells engineered to express high levels of shed SDC1 have a 58% reduction in histone acetyltransferase activity. This may be due to syndecan-1 directly binding to p300/CBP-associated factor, a HAT enzyme. Moreover, HGF bound to shed syndecan-1 was shuttled to the nucleus of myeloma cells as a complex. Shed syndecan-1 and HGF translocation to the nucleus is dependent on intact heparan sulfate chains present on the syndecan-1 core protein. These data reveal a novel mechanism of tumor-host crosstalk whereby syndecan-1, shed by tumor cells, alters histone acetyltransferase activity and shuttles heparin-binding factors to the nucleus to reprogram cells and alter gene expression. Therapeutic regulation of syndecan-1 shedding, its binding to the cell surface or translocation to the nucleus represent novel strategies to control the progression of myeloma and other cancers. Citation Format: Mark Stewart, Vishnu Ramani, Ralph Sanderson. Shed syndecan-1 downregulates histone acetyltransferase activity and shuttles HGF to the nucleus of tumor and host cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1156. doi:10.1158/1538-7445.AM2014-1156
Hormonal Characterization of a Nonrooting Naphthalene-Acetic Acid Tolerant Tobacco Mutant by an Immunoenzymic Method (1989)

The comparative analysis of plant hormones was undertaken on a 1-naphthaleneacetic acid tolerant mutant and normal tobacco (Nicotiana tabacum cv Xanthi) plantlets. The mutant plantlet was scrubby and impaired in its root morphogenesis. Degeneration of the root meristem was studied on tissue sections; it appeared very fast (as early as the 3rd or 4th day after sowing), after which the root was further transformed into a callus. Indoleacetic acid (IAA), abscisic acid (ABA), and the isopentenyladenine (iP)- and trans-zeatin(Z)-type cytokinin levels were measured in terminal buds and root tips 13 days after sowing, by enzyme linked immunosorbent assay of high performance liquid chromatography fractions. Some differences appeared between the apical buds of the two genotypes, but the mutant tobacco differed from the wild type mainly by the presence of higher levels of IAA, ABA, and iP + isopentenyladenosine (iPA) in its small root. Thus, the IAA, ABA, and iP + iPA contents were increased by a factor of 15, 7, and 24 times, respectively, in mutant root compared to wild-type tobacco roots. Previous work has shown that the mutation impairs membrane polarization effects induced by auxin at the cell level. The present results would favor the hypothesis that the mutation has also affected the control of growth regulator accumulation in tissues.
Detecting Vertical Zika Transmission: Emerging Diagnostic Approaches for an Emerged Flavivirus (2019)

Zika virus (Zika) was recently responsible for a massive epidemic that spread throughout Latin America and beyond. Though Zika is typically asymptomatic or self-limiting, the sheer numbers of Zika infections led to the identification of unexpected phenotypes including sexual transmission, Guillain-Barré syndrome, and teratogenicity. Thousands of infants in South, Central, and North America have now been born with microcephaly or one of a number of fetal anomalies constituting the congenital Zika syndrome (CZS). Diagnosing CZS is based on a combination of clinical risk assessment and laboratory testing (which includes determining whether the mother has experienced a possible Zika infection during her pregnancy). A newborn suspected of having congenital Zika infection (due to maternal Zika infection or a birth defect described in association with congenital Zika infection) is then specifically tested for presence of Zika virus in neonatal tissue or anti-Zika IgM in the blood or cerebrospinal fluid. Though the guidelines are clear, there is room for considerable practice variation to emerge from individualized patient-provider encounters, largely due to limitations in diagnostic testing for Zika. The natural history of Zika further obscures our ability to know who, when, and how to test. Molecular diagnostics are highly specific but may not serve well those with asymptomatic infection. Serologic assays expand the diagnostic window but are complicated by cross-reactivity among related flaviviruses and passive immunity transferred from mother to baby. Furthermore, existing and emerging diagnostic tools may not be widely available due to limitations in resources and infrastructure of health systems in affected areas. Improvements in assay parameters as well as advances in platforms and deployability hold promise for optimizing diagnostic approaches for congenital Zika infection. The diagnostic tools and technologies under development must be integrated with forthcoming clinical knowledge of congenital Zika infection to fully realize the value that laboratory testing holds for diagnosing <i>in utero</i> mother to child transmission but also for understanding, predicting, and managing the health outcomes due to congenital Zika infection.
Scientific Note: Effects of Nuclei Type on Characteristics of Creamed Honey (2017)

Creamed honey is a non-liquid form of honey. This type of honey is produced mainly by adding nuclei(i.e. previous creamed honey) to liquid honey. In this research, chemical characteristics of creamed honey produced using two nuclei types; 10% of creamed honey (M1), and 2.4% of powdered glucose (M2) at a storage temperature of 5°C were investigated. The sugar content, pH, and water percent were chemically analyzed. The results showed that sucrose, fructose and moisture percents were significantly higher in creamed honey produced using M1 by 1.09, 1.69 and 1.65%, respectively than M2. On the other hand, creamed honey produced using M2 had significantly higher glucose percent and pH by 2.4% and 0.53, respectively than M1. The study highlighted the noticeable impacts of nuclei type on characteristics of creamed honey. The results of this study have a special importance to creamed honey producers.