gebhart/patrepeval huggingface dataset:
Type Synthesis of Vehicle Planar Suspension Mechanism Using Graph Theory (1993)

This paper presents a graph theory-based approach to optimum type synthesis of vehicle suspension mechanisms using an expert system. Kinematic chain isomorphism is identified, using an extended degree method to facilitate the enumeration of kinematic structures. Rules representing design criteria and the flow value theory based on energy loss calculation are incorporated in the rule base to evaluate and select mechanisms among those that are enumerated in the database. Statistical variance calculation serves to complement the flow value theory. A new method called the extended flow value method is devised for isomorphism checking of labeled graphs. In the spirit of increasing emphasis on the riding quality of vehicles, several novel suspension configurations are created to ensure maintenance ease and vibration damping efficiency.
Nomenclature and classification of potentially malignant disorders of the oral mucosa (2007)

At a workshop coordinated by the WHO Collaborating Centre for Oral Cancer and Precancer in the UK issues related to terminology, definitions and classification of oral precancer were discussed by an expert group. The consensus views of the Working Group are presented here. The term, 'potentially malignant disorders', was recommended to refer to precancer as it conveys that not all disorders described under this term may transform into cancer. Critically evaluating all definitions proposed so far for oral leukoplakia, the Working Group agreed that the term leukoplakia should be used to recognize 'white plaques of questionable risk having excluded (other) known diseases or disorders that carry no increased risk for cancer'. An outline was proposed for diagnosing oral leukoplakia that will prevent other oral white disorders being misclassified as leukoplakia. The Working Group discussed the caveats involved in the current use of terminology and classification of oral potentially malignant disorders, deficiencies of these complex systems, and how they have evolved over the past several decades. The terminology presented in this report reflects our best understanding of multi-step carcinogenesis in the oral mucosa, and aspires to engender consistency in use.
The Identification of Speech in Noise by Cochlear Implant Patients and Normal-Hearing Listeners Using 6-Channel Signal Processors (1998)

Our results extend the range of stimulus conditions, from quiet to modest amounts of noise, in which the CIS strategy allows the best performing patients to extract most, if not all, of the information available to normal-hearing subjects listening to speech processed into six channels.
Fur functions as an activator and as a repressor of putative virulence genes in <i>Neisseria meningitidis</i> (2004)

Fur is a well-known iron-responsive repressor of gene transcription, which is used by many bacteria to respond to the low-iron environment that pathogens encounter during infection. Four promoters of Neisseria meningitidis predicted to have Fur-binding boxes were selected to study the molecular interactions between Fur and the promoter regions of genes expected to play a central role in survival and pathogenesis. We demonstrate that Fur acts not only as a repressor, but also as an activator of gene expression both in vivo and in vitro. We report that Fur binds to operators located upstream of three promoters that are positively regulated in vivo by Fur and iron, whereas Fur binds to an operator overlapping the classically iron-repressed tbp promoter. Deletion of the upstream operator in the norB promoter abolished activation of transcription in vivo in response to iron and in vitro in response to Fur. The role of such a dual mechanism of Fur regulation during infection is discussed.
Early Detection of Rock Movement with Time Domain Reflectometry (1994)

Remote operation of a time domain reflectometry (TDR) system demonstrates the effectiveness of telemetric monitoring for early detection of rock movement. During field testing reported here, TDR data were related to shear deformation above a longwall caving operation using a correlation between the signature reflection coefficient and shear deformation established through laboratory measurements. A 175‐m (575 ft) long vertical coaxial TDR cable was grouted into the rock mass above the longwall coal‐mining operation and attached to the aboveground‐pulsing instrument. TDR data were then remotely acquired twice daily by an operator some 500 km away. Comparison of TDR signature changes with longwall‐face location showed that localized changes were detected four days before surface subsidence occurred when mining was still 64 m (210 ft) away. Since the mining was moving toward the cable at a rate of 10 m/day, a warning interval is expected to be larger for premined sites with lower deformation rates.
Rationale for Development of a Synthetic Vaccine Against <i>Plasmodium falciparum</i> Malaria (1985)

Protective immunity against malaria can be obtained by vaccination with irradiated sporozoites. The protective antigens known as circumsporozoite (CS) proteins, are polypeptides that cover the surface membrane of the parasite. The CS proteins contain species-specific immunodominant epitopes formed by tandem repeated sequences of amino acids. Here it is shown that the dominant epitope of Plasmodium falciparum is contained in the synthetic dodecapeptide Asn-Ala-Asn-Pro-Asn-Ala-Asn-Pro-Asn-Ala-Pro or (NANP)3. Monoclonal antibodies and most or all polyclonal human antibodies to the sporozoites react with (NANP)3, and polyclonal antibodies raised against the synthetic peptide (NANP)3 react with the surface of the parasite and neutralize its infectivity. Since (NANP)3 repeats are present in CS proteins of P. falciparum from many parts of the world, this epitope is a logical target for vaccine development.
THE ELECTROCARDIOGRAM AS A SAFEGUARD IN PERICARDIOCENTESIS (1956)

• Damage to the myocardium during pericardial paracentesis has occasionally been severe enough to result in pericardial tamponade and death. Anamil experiments here described showed that contact of the tip of the needle with the myocardium could be detected electrocardiographically if the needle was connected in such a way as to constitute an exploring electrode with the machine set as in recording chest leads. Contact with the myocardium is indicated by elevation of the S-T or the P-R segment, depending on whether the ventricle or the auricle is disturbed. This technique has been used in 40 cases of pericardial paracentesis. All were without complication, though the ventricular cavity was entered inadvertently in six instances. The danger of unintended puncture of the ventricle can be minimized by recognizing the existence of a lag between the appearance of changes in the electrocardiogram and the communication of this fact to the operator.
Reexamination of spectroscopic properties of ceruloplasmin freshly isolated with a novel very rapid single-step procedure. (1988)

A novel, single-step, chromatographic procedure for the purification of ceruloplasmin is described. The procedure consists of a single chromatographic step, leading in approximately 5 hours from 2 liters of plasma to an electrophoretically homogeneous ceruloplasmin preparation which exhibits different spectroscopic properties with respect to the protein obtained with more lengthy, currently available procedures. The method is suitable for either small or large scale purification from various vertebrate plasma.
<b>Effect of Hydrophilic Components of the Extracellular Matrix on Quantifiable Diffusion-Weighted Imaging of Human Gliomas:</b> Preliminary Results of Correlating Apparent Diffusion Coefficient Values and Hyaluronan Expression Level (2003)

Hyaluronan as one of the main hydrophilic components of the extracellular matrix in gliomas likely contributes to differences in the ADC values between high- and low-grade glial tumors.
Solid phase purification in automated DNA sequencing (1993)

A solid phase purification method has been utilized to investigate the effect of template DNA and other contaminants present in enzymatic DNA sequencing reactions upon data quality in automated DNA sequence analysis. The primer oligonucleotide is prepared with an internal biotin group and one of four fluorescent tags at the 5' terminus. The fluorescently labeled DNA fragments produced in the sequencing reactions are separated from other reaction components, including template DNA, using superparamagnetic streptavidin beads. Template DNA and other reaction components may then be added back to the purified material to assess their effect upon sequence data. It is found that band intensity and base calling accuracy are decreased by the presence of the template DNA and other reaction components.
Simulating the swelling and deformation behaviour in soft tissues using a convective thermal analogy (2002)

The advantage of the proposed thermal analogy technique over previous studies is that it accounts for the convective diffusion of ion concentrations and the Donnan osmotic pressure in the interstitial fluid.
Frontotemporal lobar degeneration through loss of progranulin function (2006)

The striking clinical and pathological features of frontotemporal lobar degeneration (FTLD) have attracted much attention ever since Arnold Pick reported the first disease cases and Alois Alzheimer described the characteristic nerve cell inclusions of Pick's disease. We now know that FTLD is a common cause of dementia, especially in the population below the age of 65 (Neary et al ., 2005). Clinically, it encompasses cases of frontotemporal dementia (FTD), semantic dementia (SD) and primary progressive aphasia (PPA). Of these, FTD is the most common. It is characterized by progressive behavioural and personality disturbances, which evolve gradually into cognitive impairment and dementia. SD is characterized by a loss of conceptual knowledge, whereas in PPA progressive language impairment usually precedes the behavioural symptoms. In some patients, behavioural symptoms are also associated with a parkinsonian syndrome or with motor neuron disease (MND).

Pathologically, FTLD is characterized by the severe degeneration of frontal and/or temporal regions of the cerebral cortex. It can be divided into three broad subtypes, based on the presence of abnormal inclusions inside nerve cells. Filamentous cytoplasmic inclusions made of hyperphosphorylated tau protein characterize a proportion of cases with FTLD, including Pick's disease (Spillantini et al ., 1998). In recent years, it has become apparent that a substantial number of disease cases is characterized by the presence of tau-negative, ubiquitin-positive inclusions (FTLD-U) (Hodges et al ., 2004). The third subtype, FTLD lacking distinctive histopathology, where abnormal inclusions are not observed, now appears to be much less common than believed previously (Mackenzie et al ., 2006 a ).

FTLD has a substantial genetic component, in that up to 40% of cases are inherited in a dominant manner (Rosso et al ., 2003). Several disease loci and genes have been identified on chromosomes 3, 9 and 17. Mutations in the Tau gene on …
Tyrosine Kinase Receptor with Extensive Homology to EGF Receptor Shares Chromosomal Location with <i>neu</i> Oncogene (1985)

A novel potential cell surface receptor of the tyrosine kinase gene family has been identified and characterized by molecular cloning. Its primary sequence is very similar to that of the human epidermal growth factor receptor and the v-erbB oncogene product; the chromosomal location of the gene for this protein is coincident with the neu oncogene, which suggests that the two genes may be identical.
Implementing fault-tolerant replicated objects using Psync (2003)

Psync is an IPC protocol that explicitly preserves the partial order of messages exchanged among a set of processes. A description is given of how Psync can be used to implement replicated objects in the presence of network and host failures. Unlike conventional algorithms that depend on an underlying mechanism that totally orders messages for implementing replicated objects, the authors' approach exploits the partial order provided by Psync to achieve additional concurrency.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Expression of NPAT, a novel substrate of cyclin E-CDK2, promotes S-phase entry (1998)

To understand the mechanisms by which CDKs regulate cell cycle progression, it is necessary to identify and characterize the physiological substrates of these kinases. We have developed a screening method to identify novel CDK substrates. One of the cDNAs identified in the screen is identical to the recently isolated NPAT gene. Here we show that NPAT associates with cyclin E-CDK2 in vivo and can be phosphorylated by this CDK. The protein level of NPAT peaks at the G1/S boundary. Overexpression of NPAT accelerates S-phase entry, and this effect is enhanced by coexpression of cyclin E-CDK2. These results suggest that NPAT is a substrate of cyclin E-CDK2 and plays a role in S-phase entry.
MStream: Fast Anomaly Detection in Multi-Aspect Streams (2021)

Given a stream of entries in a multi-aspect data setting i.e., entries having multiple dimensions, how can we detect anomalous activities in an unsupervised manner? For example, in the intrusion detection setting, existing work seeks to detect anomalous events or edges in dynamic graph streams, but this does not allow us to take into account additional attributes of each entry. Our work aims to define a streaming multi-aspect data anomaly detection framework, termed MStream which can detect unusual group anomalies as they occur, in a dynamic manner. MStream has the following properties: (a) it detects anomalies in multi-aspect data including both categorical and numeric attributes; (b) it is online, thus processing each record in constant time and constant memory; (c) it can capture the correlation between multiple aspects of the data. MStream is evaluated over the KDDCUP99, CICIDS-DoS, UNSW-NB 15 and CICIDS-DDoS datasets, and outperforms state-of-the-art baselines.
Analysis of, and Software Development for, ChIP-Seq and RNA-Seq Data. (2012)

With the recent, rapid progress in high throughput DNA sequencing technology, deep sequencing has made it possible to perform unbiased genome-wide protein-DNA interaction studies (ChIP-Seq) and transcript expression (RNA-Seq) profiling. My thesis focuses on the data analysis and software development for ChIP-Seq and RNA-Seq. The second chapter of my dissertation focuses on applying bioinformatics approaches to integrate sequencing and phylogenetic conservation data to help to predict the genome position of a Gata3 enhancer element that is active exclusively in the T cell lineage. I also performed in vivo imaging to confirm the T cell specificity of the regulatory element. The third chapter consists of a ChIP-Seq study in which I mapped the in vivo binding sites of TR4, an orphan nuclear receptor, in four human ENCODE (ENCyclopedia Of DNA Elements) consortium cell lines. From these data, I discovered that TR4 preferentially binds to and is predicted to regulate genes that play crucial roles in RNA transcription and processing. In the fourth chapter, I performed an analysis of RNA-seq data from differentiating human CD34+ hematopoietic progenitor cells derived from the (fetal) umbilical cord and (adult) bone marrow. Analysis results revealed potential novel isoforms of several known erythroid regulatory proteins and these potential isoforms are supported by the identification of cloned ESTs in the sequence databases. In Chapter 5, I developed a bioinformatics software pipeline to prioritize ChIP-Seq peaks by incorporating external annotation data to facilitate more efficient downstream validation experiments. The developed ChIP-Seq pipeline estimates and adjusts for variation among biological replicates and incorporates peak location relative to gene structure to prioritize resulting peaks. It was then utilized to illustrate its performance with highly localized transcription factor binding (narrow peaks) and more broadly peaked histone modification profiles from ChIP-Seq data. Taken together, we have demonstrated that an integrative approach incorporating greater functional annotation advances our ability to effectively utilize and interpret data from massively parallel sequencing experiments of protein-DNA interactions. Finally, chapter 6 provides an overall summary and conclusions from my research with ChIP-Seq and RNA-Seq data.
Control of NO/sub x/ by positive and negative pulsed corona discharges (1990)

The pulse-induced plasma chemical process (PPCP) is a novel means of processing with great potential in various applications including the removal of NO, SO/sub 2/, HCl, and Hg vapor and other gaseous pollutants from combustion gases, the composition of gaseous and solid substances, the production of ultrafine particulate materials, the treatment of surfaces, etc. An investigation of the DENOX and DESOX of combustion gas by PPCP was conducted, confirming that DENOX is possible by both positive and negative pulsings and DESOX only by positive pulsing. NO is oxidized by PPCP to NO/sub 2/, which is removed again by PPCP. The reaction speed for PPCP with positive pulsing is more than one order of magnitude higher than that with negative pulsing applicable to electrostatic precipitators. The reaction speed is greatly enhanced by raising the peak field intensity, which requires the use of a very sharp pulses. The speed is also enhanced by raising pulse frequency, lowering the gas temperature, and using sharp corona wires. The oxidation of NO and removal of NO/sub 2/ can proceed without O/sub 2/ and moisture, but is greatly enhanced by them. The addition of NH/sub 3/ also enhances NO/sub 2/ removal, possibly by its NO/sub 2/-scavenging effect from the gas phase, while it does not enhance NO oxidation. The combination of PPCP with the electron-beam DENOX and DESOX does not produce a nonlinear enhancing effect beyond the independent effect of PPCP alone.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Reducing Common-Mode Voltage in Three-Phase Sine-Triangle PWM With Interleaved Carriers (2010)

Interleaving pulse width modulation (PWM) waveforms is a proven method to reduce ripple in dc-dc converters. The present study explores interleaving for three-phase motor drives. Fourier analysis shows that interleaving the carriers in conventional uniform PWM significantly reduces the common-mode voltage. New digital signal processor (DSP) hardware supports interleaving directly with changes to just two registers at setup time, so no additional computation time is needed during operation. The common-mode voltage reduction ranges from 36% at full modulation to 67% when idling with zero modulation. Third-harmonic injection slightly reduces the advantage (to 25% at full modulation). However, the maximum RMS common-mode voltage is still less than 20% of the bus voltage under all conditions. The disadvantage of the proposed approach is an increase in current ripple at the switching frequency. Simulations verify the findings. Experiments on a motor drive that uses a commercially available motor-control DSP, connected to a 5 hp motor, agree well with calculations and simulations.
Scalability of Quasi-Hysteretic FSM-Based Digitally Controlled Single-Inductor Dual-String Buck LED Driver to Multiple Strings (2013)

There has been growing interest in single-inductor multiple-output (SIMO) dc-dc converters due to its reduced cost and smaller form factor in comparison with using multiple single-output converters. An application for such a SIMO-based switching converter is to drive multiple LED strings in a multichannel LED display. This paper proposes a quasi-hysteretic finite-state-machine-based digitally controlled single-inductor dual-output buck switching LED driver operating in discontinuous conduction mode (DCM) and extends it to drive multiple outputs. Based on the time-multiplexing control scheme in DCM, a theoretical upper limit of the total number of outputs in a SIMO buck switching LED driver for various backlight LED current values can be derived analytically. The advantages of the proposed SIMO LED driver include reducing the controller design complexity by eliminating loop compensation, driving more LED strings without limited by the maximum LED current rating, performing digital dimming with no additional switches required, and optimization of local bus voltage to compensate for variability of LED forward voltage VF in each individual LED string with smaller power loss. Loosely binned LEDs with larger VF variation can, therefore, be used for reduced LED costs.
Generalized FDTD-ADI: an unconditionally stable full-wave Maxwell's equations solver for VLSI interconnect modeling (2000)

The finite-difference time-domain (FDTD) method of solving the full-wave Maxwell's equations has been recently extended to provide accurate and numerically stable operation for time steps exceeding the Courant limit. The elimination of an upper bound on the size of the time step was achieved using an alternating-implicit direction (ADI) time-stepping scheme. This greatly increases the computational efficiency of the FDTD method for classes of problems where the cell size of the three-dimensional space lattice is constrained to be much smaller than the shortest wavelength in the source spectrum. One such class of problems is the analysis of high-speed VLSI interconnects where full-wave methods are often needed for the accurate analysis of parasitic electromagnetic wave phenomena. In this paper, we present an enhanced FDTD-ADI formulation which permits the modeling of realistic lossy materials such as semiconductor substrates and metal conductors as well as artificial lossy materials needed for perfectly matched layer (PML) absorbing boundary conditions. Simulations using our generalized FDTD-ADI formulation are presented to demonstrate the accuracy and extent to which the computational burden is reduced by the ADI scheme.
The relationship between the "TATA" sequence and transcription initiation sites at the HIS4 gene of Saccharomyces cerevisiae. (1985)

Transcription of the HIS4 gene begins at a single site (I) at position -60 from the ATG that begins translation. We have made linker insertions/deletions in the 5' noncoding region to identify the elements required for the specificity of transcription initiation. Although there are four sequences that begin TATA and are near the start of transcription (-170, -132, -123, and -102) only the sequence at -123 (TATA-123) is required for transcription initiation. By inserting synthetic oligonucleotides into a mutant from which TATA-123 had been deleted, we found that just TATA or TATAA does not work but that TATAAA functions almost as well as the wild-type sequence. This hexamer does not work in the opposite orientation (TTTATA). When a synthetic TATA sequence is placed upstream from the normal site, the site of initiation also moves upstream in a roughly cometric way even when TATA-123 is present. Analysis of transcripts in strains where the distance between the TATA sequence and the wild-type site of transcription initiation (I site) has been altered shows that in yeast, unlike higher cells, transcription does not initiate at a strictly defined distance from the TATA sequence. Constructions that alter the distance between the TATA and the I site or remove the I site change the pattern of transcription initiation without affecting the level of HIS4 expression. Deletions that eliminate the I site produce heterogeneous transcripts and deletions that substantially shorten the distance between TATA-123 and the I site initiate at multiple sites downstream from the I site. Thus, both the TATA and the sequences downstream from it determine the pattern of transcription initiation.