gebhart/patrepeval huggingface dataset:
Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves (2009)

Little is known about the role of proteins that lack primary sequence homology with any known motifs (proteins with unknown functions, PUFs); these comprise more than 10% of all proteins. This paper offers a generalized experimental strategy for identifying the functions of such proteins, particularly in relation to metabolism. Using this strategy, we have identified a novel regulatory function for Arabidopsis locus At3g30720 (which we term QQS for qua-quine starch). QQS expression, revealed through global mRNA profiling, is up-regulated in an Arabidopsis Atss3 mutant that lacks starch synthase III and has increased leaf starch content. Analysis of public microarray data using MetaOmGraph (metnetdb.org), in combination with transgenic Arabidopsis lines containing QQS promoter-GUS transgenes, indicated that QQS expression responds to a variety of developmental/genetic/environmental perturbations. In addition to the increase in the Atss3 mutant, QQS is up-regulated in the carbohydrate mutants mex1 and sis8. A 586 nt sequence for the QQS mRNA was identified by 5' and 3' RACE experiments. The QQS transcript is predicted to encode a protein of 59 amino acids, whose expression was confirmed by immunological Western blot analysis. The QQS gene is recognizable in sequenced Arabidopsis ecotypes, but is not identifiable in any other sequenced species, including the closely related Brassica napus. Transgenic RNA interference lines in which QQS expression is reduced show excess leaf starch content at the end of the illumination phase of a diurnal cycle. Taken together, the data identify QQS as a potential novel regulator of starch biosynthesis.
Heat Shock Protein 90: A Potential Therapeutic Target in Leukemic Progenitor and Stem Cells Harboring Mutant BCR-ABL Resistant to Kinase Inhibitors (2007)

Development of drug resistance has become a major obstacle for tyrosine kinase inhibitors (TKIs) in the treatment of Philadelphia chromosome-positive (Ph(+)) chronic myelogenous leukemia (CML) and other cancers. The BCR-ABL-T315I mutant does not respond to clinically available TKIs, although some newly developed anti-BCR-ABL-T315I TKIs are now being tested in patients. TKIs transiently inhibit kinase activity of BCR-ABL, but do not reduce the level of the BCR-ABL protein. Elimination of mutant BCR-ABL protein would provide a new therapeutic strategy for treating Ph(+) leukemia. We recently showed that inhibition of heat shock protein 90 (Hsp90) by a novel Hsp90 inhibitor, IPI- 504, causes BCR-ABL protein degradation, decreased numbers of leukemia stem cells, and prolonged survival of mice with CML induced by BCR-ABL-T315I. Here we discuss further the mechanisms and effectiveness of Hsp90 inhibition in suppression of survival and proliferation of leukemic progenitor and stem cells in CML mice, and the potential of this anti-Hsp90 strategy in treating CML patients, including those who have developed resistance to TKIs.
Crafting qualities in designing QR-coded embroidery and bedtime stories (2014)

There is a renewed interest into crafts and what it can mean when integrating new technologies\ninto textiles. This paper proposes to embed craft qualities and sustainable values into designing\nsmart textile projects. Our design iterations QR-Coded Embroidery and Bedtime Stories combine\ntextiles, augmented reality and a storytelling service. Those concepts were inspired by traditional\ncrafts. We use crafts and craftsmanship as an inspiration for designing due to their long sustainable\nhistory and the deep qualities they embed. In this article we describe our design rationale with a design critique based on our own reflections and on those of five crafting experts. We point out specific craft qualities identified in the original inspiration the Muhu Skirt and the following two design iterations. We reflect on how craft qualities were incorporated, lost or gained in the transfer between the iterations. In conclusion we reflect on the impact of the used approach to our projects creating the basis for a craftsmanship approach towards the sustainability of smart textile services.
Comparison of ridge- and intensity-based perspiration liveness detection methods in fingerprint scanners (2006)

Fingerprint scanners can be spoofed by fake fingers using moldable plastic, clay, Play-Doh, wax or gelatin. Liveness detection is an anti-spoofing method which can detect physiological signs of life from fingerprints to ensure only live fingers can be captured for enrollment or authentication. Our laboratory has demonstrated that the time-varying perspiration pattern can be used as a measure to detect liveness for fingerprint systems. Unlike spoof or cadaver fingers, live fingers have a distinctive spatial perspiration phenomenon both statically and dynamically. In this paper, a new intensity based approach is presented which quantifies the grey level differences using histogram distribution statistics and finds distinct differences between live and non-live fingerprint images. Based on these static and dynamic features, we generate the decision rules to perform liveness classification. These methods were tested on optical, capacitive DC and electro-optical scanners using a dataset of about 58 live fingerprints, 50 spoof (made from Play-Doh and Gelatin) and 25 cadaver fingerprints. The dataset was divided into three sets: training set, validation set and test set. The training set was used to generate the classification tree model while the best tree model was decided by the validation set. Finally, the test set was used to estimate the performance. The results are compared with the former ridge signal algorithm with new extracted features. The outcome shows that the intensity based approach and ridge signal approach can extract simple features which perform with excellent classification (about 90%~100%) for some scanners using a classification tree. The proposed liveness detection methods are purely software based, efficient and easy to be implemented for commercial use. Application of these methods can provide anti-spoofing protection for fingerprint scanners.
Design alternatives for wireless local area networks (2001)

Abstract In this paper an overview of the wireless local area network (LAN) area is provided. The two types of wireless LAN topologies used today, infrastructure and ad hoc, are presented. The requirements that a wireless LAN is expected to meet are discussed. These requirements impact on the implementation of both the Physical and MAC layer of a wireless LAN. The unique characteristics of wireless physical layers are discussed and the five technology alternatives used today are presented. MAC layer issues are discussed and the two existing standards, IEEE 802.11 and HIPERLAN 1, are examined. Polling‐based MAC protocols (RAP, GRAP) are also reviewed. Finally, an introduction is made to wireless technologies that interact with WLANs, such as personal area networking (PAN) and wireless ATM and an overview of HIPERLAN 2, a WLAN using ATM technology, is provided. Copyright © 2001 John Wiley & Sons, Ltd.
[Cloning of human lysosomal acid beta-glucosidase gene and its expression in COS7 cells]. (2009)

In this study, we amplified human lysosomal acid beta-glucosidase (GlcCerase) gene by RT-PCR from human placenta, and analyzed the sequence of the PCR product cloned in pMD-19T. The gene identity was 99% comparable to that of the reported human GlcCerase cDNA sequence in GenBank. The GlcCerase gene digested with Xho I was subcloned into eukaryotic express vector pEGFP-C1 to generate recombinant expression vector pEGFP-GlcCerase. After identified the recombinant plasmid by restriction enzyme digestion, we transfected pEGFP-GlcCerase into COS7 cells by liposome. GlcCerase mRNA was expressed and the activity of GlcCerase was also detected in COS7 cells. This study would lay a foundation for the function of GlcCerase and its production by transgenic bioreactor.
Developmental gene regulation in <i>Giardia lamblia</i>: first evidence for an encystation‐specific promoter and differential 5′ mRNA processing (1999)

Giardia lamblia must encyst to survive in the environment and subsequently infect new hosts. We investigated the expression of glucosamine-6-phosphate isomerase (Gln6PI), the first enzyme required for biosynthesis of N-acetylgalactosamine, for the major cyst wall polysaccharide. We isolated two Gln6PI genes that encode proteins with large areas of identity, but distinctive central and terminal regions. Both recombinant enzymes have comparable kinetics. Interestingly, these genes have distinct patterns of expression. Gln6PI-A has a conventional, short 5' untranslated region (UTR), and is expressed at a low level during vegetative growth and encystation. The Gln6PI-B gene has two transcripts - one is expressed constitutively and the second species is highly upregulated during encystation. The non-regulated Gln6PI-B transcript has the longest 5'-UTR known for Giardia and is 5' capped or blocked. In contrast, the Gln6PI-B upregulated transcript has a short, non-capped 5'-UTR. A small promoter region (< 56 bp upstream from the start codon) is sufficient for the regulated expression of Gln6PI-B. Gln6PI-B also has an antisense overlapping transcript that is expressed constitutively. A shorter antisense transcript is detected during encystation. This is the first report of a developmentally regulated promoter in Giardia, as well as evidence for a potential role of 5' RNA processing and antisense RNA in differential gene regulation.
Wireless security techniques for coordinated manufacturing and on-line hardware trojan detection (2012)

This paper addresses the hardware Trojan (HT) attacks that impose severe threats to the security and integrity of wireless networks and systems. We first develop HT attack models by embedding a single HT gate in the target design that triggers advanced malicious attacks. We place the one-gate HT trigger in such a way that it exhibits rare switching activities, consumes ultra-low leakage power, and hides from delay characterizations. Therefore, the HT attack models are capable of bypassing the widely used side channel-based HT detection schemes. Furthermore, based on the HT attack models, we investigate the potential on-line threat models during the system operation and develop an in-field trusted HT detection approach using physical unclonable functions (PUFs). We evaluate the effectiveness of the HT attack and defense models on a set of ISCAS'85, ISCAS'89, and ITC'99 benchmarks.
Variational Quantum Linear Solver (2023)

Previously proposed quantum algorithms for solving linear systems of equations cannot be implemented in the near term due to the required circuit depth. Here, we propose a hybrid quantum-classical algorithm, called Variational Quantum Linear Solver (VQLS), for solving linear systems on near-term quantum computers. VQLS seeks to variationally prepare <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow class="MJX-TeXAtom-ORD"><mml:mo stretchy="false">|</mml:mo></mml:mrow><mml:mi>x</mml:mi><mml:mo fence="false" stretchy="false">&#x27E9;</mml:mo></mml:math> such that <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>A</mml:mi><mml:mrow class="MJX-TeXAtom-ORD"><mml:mo stretchy="false">|</mml:mo></mml:mrow><mml:mi>x</mml:mi><mml:mo fence="false" stretchy="false">&#x27E9;</mml:mo><mml:mo>&#x221D;</mml:mo><mml:mrow class="MJX-TeXAtom-ORD"><mml:mo stretchy="false">|</mml:mo></mml:mrow><mml:mi>b</mml:mi><mml:mo fence="false" stretchy="false">&#x27E9;</mml:mo></mml:math>. We derive an operationally meaningful termination condition for VQLS that allows one to guarantee that a desired solution precision <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>&#x03F5;</mml:mi></mml:math> is achieved. Specifically, we prove that <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>C</mml:mi><mml:mo>&#x2A7E;</mml:mo><mml:msup><mml:mi>&#x03F5;</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mrow class="MJX-TeXAtom-ORD"><mml:mo>/</mml:mo></mml:mrow><mml:msup><mml:mi>&#x03BA;</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:math>, where <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>C</mml:mi></mml:math> is the VQLS cost function and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>&#x03BA;</mml:mi></mml:math> is the condition number of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>A</mml:mi></mml:math>. We present efficient quantum circuits to estimate <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>C</mml:mi></mml:math>, while providing evidence for the classical hardness of its estimation. Using Rigetti's quantum computer, we successfully implement VQLS up to a problem size of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mn>1024</mml:mn><mml:mo>&#x00D7;</mml:mo><mml:mn>1024</mml:mn></mml:math>. Finally, we numerically solve non-trivial problems of size up to <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mn>2</mml:mn><mml:mrow class="MJX-TeXAtom-ORD"><mml:mn>50</mml:mn></mml:mrow></mml:msup><mml:mo>&#x00D7;</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mrow class="MJX-TeXAtom-ORD"><mml:mn>50</mml:mn></mml:mrow></mml:msup></mml:math>. For the specific examples that we consider, we heuristically find that the time complexity of VQLS scales efficiently in <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>&#x03F5;</mml:mi></mml:math>, <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>&#x03BA;</mml:mi></mml:math>, and the system size <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>N</mml:mi></mml:math>.
Evaluation of the number of positive cells from flow cytometric immunoassays by mathematical modeling of cellular autofluorescence (1994)

A method for automated evaluation of the percentage of positive cells from flow cytometric immunofluorescence histograms is presented. The method is based on a suitable mathematical representation of cellular autofluorescence distribution which is used to identify the negative cell distribution in the test histogram. An algorithm is developed and implemented in a computer program that quantifies the positive cells from the routinely available control and test histograms. Its accuracy is compared to that of the other currently used automated methods of analysis on the basis of a set of histograms with overlapping distributions and with known percentages of positive cells, generated by artificial mixing of real data.
An Auto-Scaling Framework for Containerized Elastic Applications (2017)

Mechanisms for automatic resource provisioning in cloud environment have been widely studied. However, most current work are based on Virtual Machines(VMs) and few auto-scaling systems dedicated for containerized environment have been presented. This paper proposes an auto-scaler that caters for containerized elastic applications. We devise a hybrid scaling strategy based on a resource demand prediction model to meet Service Level Agreements(SLAs) in face of quickly varying workloads. We implemented our system in a private container-centric cloud environment and experimental results demonstrate that our auto-scaling framework out-performs existing rule-based approaches.
Cache memory design for the data transport to array processors (2002)

An array memory architecture which provides parallel and random access to data matrices as needed by array processors for real-time image processing is described. The array memory serves as a cache for array processors. The architecture consists of an array of memory blocks and a logic which allows simultaneous access for read and write. Parallel access to several memory blocks provides the necessary high data rate for parallel operating processing units. A standard cell CMOS-VLSI chip of an array memory with 2048 picture elements (pels) and parallel access to four pels is realized. The chip provides a 100 M pels/s data output rate using on-chip RAM macros with a 40-ns access time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
SARS-CoV2-mediated suppression of NRF2-signaling reveals potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate (2020)

Antiviral strategies to inhibit Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) and the pathogenic consequences of COVID-19 are urgently required. Here, we demonstrate that the NRF2 antioxidant gene expression pathway is suppressed in biopsies obtained from COVID-19 patients. Further, we uncover that NRF2 agonists 4-octyl-itaconate (4-OI) and the clinically approved dimethyl fumarate (DMF) induce a cellular antiviral program that potently inhibits replication of SARS-CoV2 across cell lines. The inhibitory effect of 4-OI and DMF extends to the replication of several other pathogenic viruses including Herpes Simplex Virus-1 and-2, Vaccinia virus, and Zika virus through a type I interferon (IFN)-independent mechanism. In addition, 4-OI and DMF limit host inflammatory responses to SARS-CoV2 infection associated with airway COVID-19 pathology. In conclusion, NRF2 agonists 4-OI and DMF induce a distinct IFN-independent antiviral program that is broadly effective in limiting virus replication and in suppressing the pro-inflammatory responses of human pathogenic viruses, including SARS-CoV2.
Phosphorylation of the Hinge Domain of the Nuclear Hormone Receptor LRH-1 Stimulates Transactivation (2006)

The nuclear receptor LRH-1 (NR5A2) functions to regulate expression of a number of genes associated with bile acid homeostasis and other liver functions, but mechanisms that modulate its activity remain unclear. We have found that mitogenic stimuli, including treatment with phorbol myristate (PMA), increase LRH-1 transactivation. This response maps to the hinge and ligand binding domains of LRH-1 and is blocked by the mitogen-activated protein kinase ERK1/2 inhibitor U0126. LRH-1 is a phosphoprotein and hinge domain serine residues at 238 and 243 are required for effective phosphorylation, both in vitro and in cells. Preventing phosphorylation of these residues by mutating both to alanine decreases PMA-dependent LRH-1 transactivation and mimicking phosphorylation by mutation to positively charged aspartate residues increases basal transactivation. Although serine phosphorylation of the hinge of SF-1 (NR5A1), the closest relative of LRH-1, confers a similar response, the specific targets differ in the two closely related orphan receptors. These results define a novel pathway for the modulation of LRH-1 transactivation and identify specific LRH-1 residues as downstream targets of mitogenic stimuli. This pathway may contribute to recently described proliferative functions of LRH-1.
Unsupervised Machine Learning for Developing Personalised Behaviour Models Using Activity Data (2017)

The goal of this study is to address two major issues that undermine the large scale deployment of smart home sensing solutions in people's homes. These include the costs associated with having to install and maintain a large number of sensors, and the pragmatics of annotating numerous sensor data streams for activity classification. Our aim was therefore to propose a method to describe individual users' behavioural patterns starting from unannotated data analysis of a minimal number of sensors and a "blind" approach for activity recognition. The methodology included processing and analysing sensor data from 17 older adults living in community-based housing to extract activity information at different times of the day. The findings illustrate that 55 days of sensor data from a sensor configuration comprising three sensors, and extracting appropriate features including a "busyness" measure, are adequate to build robust models which can be used for clustering individuals based on their behaviour patterns with a high degree of accuracy (>85%). The obtained clusters can be used to describe individual behaviour over different times of the day. This approach suggests a scalable solution to support optimising the personalisation of care by utilising low-cost sensing and analysis. This approach could be used to track a person's needs over time and fine-tune their care plan on an ongoing basis in a cost-effective manner.
ChemInform Abstract: Nearly Centrosymmetric (S)‐7‐(2,6‐Dichlorobenzyl)‐8‐(3‐oxocyclopentyl)‐ 1,3‐dipropyl‐7H‐purine‐2,6‐dione. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Intraband and interband processes in the infrared spectrum of metallic aluminum (1986)

The dielectric function of polycrystalline metallic aluminum derived by Shiles et al. [Phys. Rev. B 22, 1612 (1980)] from room-temperature ultrahigh-vacuum reflectance measurements has been analyzed into intraband and interband components and compared with theoretical predictions of Szmulowicz and Segall [Phys. Rev. B 24, 892 (1981)]. For this analysis, a new approach was developed, which utilizes experimental data over a larger energy range than in previous studies. To within experimental uncertainty, the resulting intraband component is consistent with a Drude model having a plasma frequency ${\ensuremath{\Omega}}_{p}$=12.5\ifmmode\pm\else\textpm\fi{}0.3 eV and relaxation time \ensuremath{\tau}=(1.06\ifmmode\pm\else\textpm\fi{}0.12)\ifmmode\times\else\texttimes\fi{}${10}^{\mathrm{\ensuremath{-}}14}$ sec. These values are in accord with the bulk static conductivity which in turn is in agreement with the inertial sum rule on the real part of the dielectric function. The interband contribution was found to consist of a broad background with two superimposed peaks: the well-known ``0.8 \ensuremath{\mu}m'' absorption at \ensuremath{\sim}1.5 eV and a weaker absorption in the vicinity of 0.4 eV. This interband spectrum is in good agreement in regard to both peak position and oscillator strength with the one-electron augmented-plane-wave model calculations for the optical conductivity by Szmulowicz and Segall. The total experimental intraband and interband oscillator strengths for the conduction electrons are 1.9 and 1.2 electrons/per atom, respectively.
Matching network design using genetic algorithms for impedance constrained thinned arrays (2003)

This paper investigates a technique for optimizing matching networks for thinned aperiodic dipole arrays to achieve a 2:1 or better VSWR for each antenna element over the entire scan range of the array. The thinned array is optimized via a genetic algorithm to have a suppressed grating lobe over the scan range of the array. In addition, the genetic algorithm places restrictions on the driving point impedance of each element so that they are well behaved during scanning. The impedance constraint allows a three element reactive matching network to be optimized for each element of the array using a separate genetic algorithm.