gebhart/patrepeval huggingface dataset:
Thymidylate synthase expression correlates closely with E2F1 expression in colon cancer. (2000)

Thymidylate synthase (TS) is thought to be one of the target genes that the E2F1 transcription factor binds to and regulates. However, the relationship between the expressions of TS and E2F1 in primary colon cancer specimens remains unclear. The aim of this study was to define the relation of TS and E2F1 gene expressions in tumor samples from 23 colon cancer patients. TS and E2F1 gene expressions were measured by TaqMan reverse transcription-PCR assay using glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as an internal standard and expressed as a TS:GAPDH or E2F1:GAPDH mRNA ratio. A close relationship was found between TS gene expression and E2F1 gene expression (r2 = 0.598, P < 0.001) in 23 tumor samples analyzed. Surprisingly, a high correlation between TS gene expression and E2F1 gene expression was observed even in advanced tumors from stage IV colon cancer patients. These results suggest that transcription of the TS gene may be regulated by E2F1 in primary colon cancer specimens and that this gene-regulatory pathway from E2F1 to TS may be highly conserved during malignant progression. Four of the 23 patients showed TS overexpression with increased E2F1 expression. These results suggest that the ability of a tumor to increase TS expression may possibly be due to an overexpression of E2F1. Although the number of patients was relatively small, our study provides new insights into the molecular mechanisms underlying the regulation of TS expression in colon cancers.
AIR CARGO REVENUE AND CAPACITY MANAGEMENT (2006)

The traditional air cargo supply chain is composed by the shippers, the freight forwarders and the airlines. The freight forwarders secure capacity with airlines in order to accommodate shippers' demand. They bid for capacity six to twelve months before the actual departure date of the aircraft, and confirm the needed capacity a few days before departure.\n\nWe address the freight forwarders' problem of confirming needed capacity based on balancing the costs of ordering too much capacity versus ordering too little. We use a Markov decision process to model the problem. We show the value function is convex in the state variables for lead times of one and two periods. We present the structure of the optimal policy and show it is stationary. In addition we present solutions to the case with subcontracting options and order due dates.\n\nWe also address the airlines' revenue management problem with respect to its cargo capacity available for free sale (after honoring committed capacity to freight forwarders), in particular the problems of (1) accepting/rejecting incoming bookings based on bid prices, and of (2) estimating the show-up rate (ratio of bookings handed in at departure over bookings on hand) with impact on overbooking.\n\nTo address the lumpiness of demand, we split the cargo into two categories: small cargo, composed of mail and small packages, and large cargo, composed of the bulk of commercial cargo. The small cargo is approximated with the passenger arrival, and we propose a new algorithm to solve the traditional probabilistic nonlinear problem from the passenger side. The large cargo is solved using a dynamic program, which is decomposed\nat the leg level using a fare-prorating scheme. The solution from our new approach is shown via simulation to be superior to two approaches currently used: the first come first serve, and the deterministic linear program.\n\nThe show-up rate is estimated using wavelets and we show that a discrete show-up rate is more suitable than the traditional Normal estimator used in practice. The new estimator results in considerable more potential revenue.
Directory-Based Information Services: Password Policies (2014)

This document extends Directory-Based Information Services (DBIS)
described in [draft-bannister-dbis-mapping-00] to support the shadow
databases. The shadow database schema SHALL be backwards compatible
with the Network Information Service [NIS] but stored within [X.500]
entries so that it may be resolved with the Lightweight Directory
Access Protocol [RFC4510]. A shadow database extends user login
accounts with credential policy data. This document represents shadow
database entries as an extended set of attributes that may be applied
to both passwd and group database entries for the management of
consistent password policies. This document describes configuration
maps [draft-bannister-dbis- mapping-00] for shadow databases, and
database entries referenced by those maps.
Thermolabile folding intermediates: inclusion body precursors and chaperonin substrates (1996)

An unexpected aspect of the expression of cloned genes is the frequent failure of newly synthesized polypeptide chains to reach their native state, accumulating instead as insoluble inclusion bodies. Amyloid deposits represent a related state associated with a variety of human diseases. The critical folding intermediates at the juncture of productive folding and the off-pathway aggregation reaction have been identified for the phage P22 tailspike and coat proteins. Though the parallel beta coil tailspike is thermostable, an early intracellular folding intermediate is thermolabile. As the temperature of intracellular folding is increased, this species partitions to inclusion bodies, a kinetic trap within the cell. The earliest intermediates along the in vitro aggregation pathway, sequential multimers of the thermolabile folding intermediates, have been directly identified by native gel electrophoresis. Temperature-sensitive folding (tsf) mutations identify sites in the beta coil domain, which direct the junctional intermediate down the productive pathway. Global suppressors of tsf mutants inhibit the pathway to inclusion bodies, rescuing the mutant chains. These mutants identify sites important for avoiding aggregation. Coat folding intermediates also partition to inclusion bodies as temperature is increased. Coat tsf mutants are suppressed by overexpression of the GroE chaperonin, indicating that the thermolabile intermediate is a physiological substrate for GroE. We suggest that many proteins are likely to have thermolabile intermediates in their intracellular folding pathways, which will be precursors to inclusion body formation at elevated temperatures and therefore substrates for heat shock chaperonins.
Insights into the Maize Pan-Genome and Pan-Transcriptome   (2014)

Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome. Stepwise iterative clustering of RTAs suggests, within the context of the genotypes used in this study, that the maize genome is restricted and further sampling of seedling RNA within this germplasm base will result in minimal discovery. Genome-wide association studies based on SNPs and transcript abundance in the pan-genome revealed loci associated with the timing of the juvenile-to-adult vegetative and vegetative-to-reproductive developmental transitions, two traits important for fitness and adaptation. This study revealed the dynamic nature of the maize pan-genome and demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.
The Numerical Solution of Integral Equations of the Second Kind (1997)

This book provides an extensive introduction to the numerical solution of a large class of integral equations. The initial chapters provide a general framework for the numerical analysis of Fredholm integral equations of the second kind, covering degenerate kernel, projection and Nystrom methods. Additional discussions of multivariable integral equations and iteration methods update the reader on the present state of the art in this area. The final chapters focus on the numerical solution of boundary integral equation (BIE) reformulations of Laplace's equation, in both two and three dimensions. Two chapters are devoted to planar BIE problems, which include both existing methods and remaining questions. Practical problems for BIE such as the set up and solution of the discretised BIE are also discussed. Each chapter concludes with a discussion of the literature and a large bibliography serves as an extended resource for students and researchers needing more information on solving particular integral equations.
A Meta-Analysis of the Clinical Effectiveness of School Scoliosis Screening (2010)

The use of the FBT alone in school scoliosis screening is insufficient. We need large, retrospective cohort studies with sufficient follow-up to properly assess the clinical effectiveness of school scoliosis screening.
Effect of Local TOF Kernel Miscalibrations on Contrast-Noise in TOF PET (2013)

TOF PET imaging requires specific calibrations: accurate characterization of the system timing resolution and timing offset is required to achieve the full potential image quality. Current system models used in image reconstruction assume a spatially uniform timing resolution kernel. Furthermore, although the timing offset errors are often pre-corrected, this correction becomes less accurate with the time since, especially in older scanners, the timing offsets are often calibrated only during the installation, as the procedure is time-consuming. In this study, we investigate and compare the effects of local mismatch of timing resolution when a uniform kernel is applied to systems with local variations in timing resolution and the effects of uncorrected time offset errors on image quality. A ring-like phantom was acquired on a Philips Gemini TF scanner and timing histograms were obtained from coincidence events to measure timing resolution along all sets of LORs crossing the scanner center. In addition, multiple acquisitions of a cylindrical phantom, 20 cm in diameter with spherical inserts, and a point source were simulated. A location-dependent timing resolution was simulated, with a median value of 500 ps and increasingly large local variations, and timing offset errors ranging from 0 to 350 ps were also simulated. Images were reconstructed with TOF MLEM with a uniform kernel corresponding to the effective timing resolution of the data, as well as with purposefully mismatched kernels. To CRC vs noise curves were measured over the simulated cylinder realizations, while the simulated point source was processed to generate timing histograms of the data. Results show that timing resolution is not uniform over the FOV of the considered scanner. The simulated phantom data indicate that CRC is moderately reduced in data sets with locally varying timing resolution reconstructed with a uniform kernel, while still performing better than non-TOF reconstruction. On the other hand, uncorrected offset errors in our setup have a larger potential for decreasing image quality and can lead to a reduction of CRC of up to 15% and an increase in the measured timing resolution kernel up to 40%. However, in realistic conditions in frequently calibrated systems, using a larger effective timing kernel in image reconstruction can compensate uncorrected offset errors.
A 1-Mb 28-nm 1T1MTJ STT-MRAM With Single-Cap Offset-Cancelled Sense Amplifier and <italic>In Situ</italic> Self-Write-Termination (2018)

1T1MTJ spin-transfer-torque (STT)-MRAM is a promising candidate for next-generation high-density embedded non-volatile memory. This paper presents a 1-Mb 28-nm 1T1MTJ STT-MRAM with improved sensing margin and reduced power consumption. An offset-cancelled sense amplifier is proposed, using only a single capacitor, to improve sensing margin and accelerate read speed. To save write power, an in situ write-self-termination method is proposed where the sense amplifier is reconfigured without area overhead to continuously monitor the write operation and shutoff the write drivers as soon as the magnetic transition occurs in the bitcell. A prototype chip achieves 2.8- and 3.6-ns read access time at 25 °C and 120 °C, respectively. The in situ write-self-termination scheme reduces write power by 47% and 60% with 20-ns write access time at 25 °C and 120 °C, respectively.
Application of the extracellular alpha-amylase gene from Streptococcus bovis 148 to construction of a secretion vector for yogurt starter strains (1997)

Streptococcus thermophilus ATCC 19258, Lactobacillus delbrueckii subsp. bulgaricus T-11, and Lactococcus lactis subsp. lactis IL1403 were transformed with the alpha-amylase gene (amyA) from Streptococcus bovis 148 by using a wide host-range vector, and all the transformants secreted the alpha-amylase successfully. Since the promoter and the secretion signal of the amyA gene were functional in these strains, we constructed a secretion vector using the expression elements of amyA. Trials to secrete foreign enzymes in yogurt starter strains were performed using this novel secretion vector.
Managing Complex Change in Clinical Study Metadata (2004)

In highly functional metadata-driven software, the interrelationships within the metadata become complex, and maintenance becomes challenging. We describe an approach to metadata management that uses a knowledge-base subschema to store centralized information about metadata dependencies and use cases involving specific types of metadata modification. Our system borrows ideas from production-rule systems in that some of this information is a high-level specification that is interpreted and executed dynamically by a middleware engine. Our approach is implemented in TrialDB, a generic clinical study data management system. We review approaches that have been used for metadata management in other contexts and describe the features, capabilities, and limitations of our system.
Establishing a sepsis-score for adult equine patients (2012)

Die Septikmie ist ein schwerwiegender und hufig lebensbedrohlicher klinischer Zustand. Um die Diagnose mglichst schnell zu stellen, den Schweregrad einer Septikmie sowie ihren Verlauf objektiv einzuschtzen und eine eventuell erforderliche Intensivtherapie zeitnah einleiten bzw. im weiteren Verlauf entsprechend modifizieren zu knnen, wird bei
Design of complex FIR filters with arbitrary complex frequency responses by two real Chebyshev approximations (1997)

The well-known Parks-McClellan program can only design linear phase real FIR filters, and the Remez exchange algorithm is not readily applied for general complex FIR filter design. Here the problem of designing complex FIR filters is solved by dividing the original complex approximation into two real ones such that the Remez exchange algorithm can be applied by slightly modifying the Parks-McClellan-McCalling program. Arbitrary frequency response complex FIR filters and complex all-pass filters can be easily designed by this efficient technique. This approach has several practical advantages such as fast design time and easy implementation with satisfactory performance.
Top-Gated Graphene Field-Effect Transistors Using Graphene on Si (111) Wafers (2010)

In this letter, we report the first experimental demonstration of wafer-scale ambipolar field-effect transistor (FET) on Si (111) substrates by synthesizing a graphene layer on top of 3C-SiC(111)/Si(111) substrates. With lateral scaling of the source-drain distance to 1 μm in a top-gated layout, the ON-state current of 225 μA/μm and peak transconductance of > 40 μS/μm were obtained at Vds = 2 V, which is the highest performance of graphene-on-Si FETs. The peak field-effect mobilities of 285 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Vs for holes and 175 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Vs for electrons were demonstrated, which is higher than that of ultra-thin-body SOI (n, p) MOSFETs.
Evolving Developing Spiking Neural Networks (2005)

Indirect encoding strategies aim at higher evolvability by reducing the dimensionality of the search space. If on one hand scalability is often improved for specific tasks, on the other the generality of these methods can be limited. In previous work, a development system was introduced and tested in the evolution of specific 2D morphologies of various size and complexity. Here the same model is used to instead specify the structure and properties of neuro-controllers for simulated Khepera robots. In this paper, we introduce a plastic spiking neural network model, particularly suited for evolution and development, testing its performance against direct encoding. Compared to previous work, the new task implies the solution of a functional problem. Nevertheless, results show similar conclusions regarding the improved scalability of the development system and its connection to regularity
Content Centric Services in Smart Cities (2012)

We expect around 9 billions people on the Earth within 2050, 70% of them living in urban environments. By that time, we have to be ready to support a never seen request for ICT services in order to improve the efficiency of future Smart Cities, thus allowing a pacific coexistence among humans. Inline with this premise, the present contribution proposes a novel service platform, based on the emerging content-centric networking paradigm. It can easily embrace all available, upcoming, and remote generation wireless techologies, while supporting, at the same time, ubiquitous and secure applications in many domains, such as: e-helthcare, intelligent transportation systems, entertainment, and many others. All details of the approach we propose, have been carefully described by means of pragmaticaluse-cases, thus making evident its effectivenes in future realistic urban environments.
Amodal Instance Segmentation With KINS Dataset (2019)

Amodal instance segmentation, a new direction of instance segmentation, aims to segment each object instance involving its invisible, occluded parts to imitate human ability. This task requires to reason objects' complex structure. Despite important and futuristic, this task lacks data with large-scale and detailed annotations, due to the difficulty of correctly and consistently labeling invisible parts, which creates the huge barrier to explore the frontier of visual recognition. In this paper, we augment KITTI with more instance pixel-level annotation for 8 categories, which we call KITTI INStance dataset (KINS). We propose the network structure to reason invisible parts via a new multi-task framework with Multi-View Coding (MVC), which combines information in various recognition levels. Extensive experiments show that our MVC effectively improves both amodal and inmodal segmentation. The KINS dataset and our proposed method will be made publicly available.
Enabling Secure and Privacy Preserving Identity Management via Smart Contract (2019)

Biometrics have been used increasingly heavily for identity authentication in many critical public services, such as border passes or security check points. However, traditional biometrics-based identity management systems collect and store personal biometrical data in a centralized server or database, and an individual has no control over how her biometrics will be used for what purpose. Such kind of systems can result in serious security and privacy issues for sensitive personal data. In this paper, we design a novel approach to leveraging biometrics and blockchain/smart contract to enable secure and privacy preserving identity management. The basic idea is to use blockchain to store an authority's attestation and the transformed value of an individual's biometrics. The stored data on the blockchain is then controlled by smart contracts which define various access control policies, e.g., access parties, access times, etc. The owner of the biometrical data can flexibly change the access control policies through a white list, a timer and other methods to any identity verifiers. We used the well-known Ethereum platform to implement the proposed approach and tested the effectiveness as well as the flexibility of various access control policies.
An image-reject downconverter with sideband selection for double-conversion receiver (2001)

An image-reject downconverter unit for a double-conversion receiver is presented. The circuit includes a LNA, image-reject mixers in Hartley configuration, a 3- stage polyphase filter, an IF-amplifier and a novel SAW driver. For LO generation the circuit includes a 6-GHz on-chip VCO, a divide-by-four circuit for quadrature LO and divide-by-16 for feeding an external PLL. Signal reversal switching in the LO buffer can be used for altering the location of image frequency. The circuit features 44-dB gain, 40-dB image rejection, 4.6-dB noise figure, 20-dBm OIP3 and it is fabricated in a 0.9- µm SiGe HBT technology.
SESCA: Predicting Circular Dichroism Spectra from Protein Molecular Structures (2019)

Circular dichroism (CD) spectroscopy is a highly sensitive but low-resolution technique to study the structure of proteins. Combined with molecular modeling or other complementary techniques, CD spectroscopy can provide essential information at higher resolution. To this end, we introduce a new computational method to calculate the electronic circular dichroism spectra of proteins from a structural model or ensemble using the average secondary structure composition and a precalculated set of basis spectra. The method is designed for model validation to estimate the error of a given protein structural model based on the measured CD spectrum. We compared the predictive power of our method to that of existing algorithms, namely, DichroCalc and PDB2CD, and found that it predicts CD spectra more accurately. Our results indicate that the derived basis sets are robust to both experimental errors in the reference spectra and the choice of the secondary structure classification algorithm. For over 80% of the globular reference proteins, our basis sets accurately predict the experimental spectrum solely from their secondary structure composition. For the remaining 20%, correcting for intensity normalization considerably improves the prediction power. Additionally, we show that the predictions for short peptides and an example complex of intrinsically disordered proteins strongly benefit from accounting for side-chain contributions and structural flexibility.