gebhart/patrepeval huggingface dataset:
Parametric deconvolution of positive spike trains (2000)

This paper describes a parametric deconvolution method (PDPS) appropriate for a particular class of signals which we call spike-convolution models. These models arise when a sparse spike train —Dirac deltas according to our mathematical treatment —is convolved with a fixed point-spread function, and additive noise or measurement error is superimposed.We view deconvolution as an estimation problem, regarding the locations and heights of the underlying spikes, as well as the baseline and the measurement error variance as unknown parameters.Our estimation scheme consists of two parts: model fitting and model selection.To fit a spike-convolution model of a specific order, we estimate peak locations by trigonometric moments, and heights and the baseline by least squares. The model selection procedure has two stages. Its first stage is so designed that we expect a model of a somewhat larger order than the truth to be selected. In the second stage, the final model is obtained using backwards deletion. This results in not only an estimate of the model order, but also an estimate of peak locations and heights with much smaller bias and variation than that found in a direct trigonometric moment estimate. A more efficient maximum likelihood estimate can be calculated from these estimates using a Gauss–Newton algorithm. We also present some relevant results concerning the spectral structure of Toeplitz matrices which play a key role in the estimation. Finally, we illustrate the behavior of these estimates using simulated and real DNA sequencing data.
Graphene as a lubricant on Ag for electrical contact applications (2015)

The potential of graphene as a solid lubricant in sliding Ag-based electrical contacts has been investigated. Graphene was easily and quickly deposited by evaporating a few droplets of a commercial graphene solution in air. The addition of graphene reduced the friction coefficient in an Ag/Ag contact with a factor of ~10. The lubricating effect was maintained for more than 150,000 cycles in a pin-on-disk test at 1 N. A reduction in friction coefficient was also observed with other counter surfaces such as steel and W but the life time was strongly dependent on the materials combination. Ag/Ag contacts exhibited a significantly longer life time than steel/Ag and W/Ag contacts. The trend was explained by an increased affinity for metal–carbon bond formation.
DEFECTIVE KERNEL MUTANTS OF MAIZE II. MORPHOLOGICAL AND EMBRYO CULTURE STUDIES (1980)

This report presents the initial results of our study of the immature kernel stage of 150 defective kernel maize mutants. They are single gene, recessive mutants that map throughout the genome, defective in both endosperm and embryo development and, for the most part, lethal (Neuffer and Sheridan 1980). All can be distinguished on immature ears, and 85% of them reveal a mutant phenotype within 11 to 17 days post-pollination. Most have immature kernels that are smaller and lighter in color than their normal counterparts. Forty of the mutants suffer from their defects early in kernel development and are blocked in embryogenesis before their primordia differentiate, or, if primordia are formed, they are unable to germinate when cultured as immature embryos or tested at maturity; a few begin embryo degeneration prior to the time that mutant kernels became visually distinguishable. The others express the associated lesion later in kernel development and form at least one leaf primordium by the time kernels are distinguishable and will germinate when cultured or tested at maturity. In most cases, on a fresh weight basis, the mutants have embryos that are more severely defective than the endosperm; their embryos usually are no more than one-half to two-thirds the size, and lag behind by one or two developmental stages. in comparison with embryos in normal kernels from the same ear. One hundred and two mutants were examined by culturing embryos on basal and enriched media; 21 simply enlarged or completely failed to grow on any of the media tested; and 81 produced shoots and roots on at least one medium. Many grew equally well on basal and enriched media; 16 grew at a faster rate on basal medium and 23 displayed a superior growth on enriched medium. Among the latter group, 10 may be auxotrophs. One of these mutants and another mutant isolated by E. H. Coe are proline-requiring mutants, allelic to pro-1. Considering their diversity of expression as evidenced by their differences in morphological appearance, degree of defectiveness and response to embryo culturing, we believe that they represent many different gene loci.
Hyaluronan and a cell-associated hyaluronan binding protein regulate the locomotion of ras-transformed cells. (1991)

Hyaluronan (HA) and one of its cell binding sites, fibroblast hyaluronan binding protein (HABP), is shown to contribute to the regulation of 10T1/2 cell locomotion that contain an EJ-ras-metallothionein (MT-1) hybrid gene. Promotion of the ras-hybrid gene with zinc sulfate acutely stimulates, by 6-10-fold, cell locomotion. After 10 h, locomotion drops to two- to threefold above that of uninduced cells. Several observations indicate increased locomotion is partly regulated by HA. These include the ability of a peptide that specifically binds HA (HABR) to reduce locomotion, the ability of HA (0.001-0.1 micrograms/ml), added at 10-30 h after induction to stimulate locomotion back to the original, acute rate, and the ability of an mAb specific to a 56-kD fibroblast HABP to block locomotion. Further, both HA and HABP products are regulated by induction of the ras gene. The effect of exogenous HA is blocked by HABR, is dose-dependent and specific in that chondroitin sulfate or heparan have no significant effect. Stimulatory activity is retained by purified HA and lost upon digestion with Streptomyces hyaluronidase indicating that the activity of HA resides in its glycosaminoglycan chain. Uninduced cells are not affected by HA, HABR, or mAb and production of HA or HABP is not altered during the experimental period. These results suggest that ras-transformation activates an HA/HABP locomotory mechanism that forms part of an autocrine motility mechanism. Reliance of induced cells on HA/HABP for locomotion is transient and specific to the induced state.
A new pattern matching approach to the recognition of printed Arabic (1998)

The paper presents a new segmentation-free approach to the Arabic optical character recognition. Extended with a suitable pre-and post-processing the method offers a simple and fast framework to develop a full OCR system. The method was developed primarily for the Naskhi font, it is however robust and flexible and can be easily extended.
Notes on the flotation processes ore extraction (1909)

The ordinary processes of ore-dressing, depending on separation by virtue of the difference in specific gravity of the constituents of an ore, are not suitable for all classes of ores. For example, those in which the valuable minerals are “ shot” or finely disseminated through the enclosing rock, necessitating very fine crushing to set them free, or those in which the minerals are of a very friable character and therefore produce a lot of slimes in crushing, are refractory types of ore, often impossible of treatment by the simple methods the writer sketched in his paper of February 1908.

A great deal of attention had been paid of late years to these refractory types, and many ingenious processes have been invented for their treatment. Among the most recent and most successful of these special processes stand those depending on the separation of the valuable minerals from the gangue by the floatation of the former.

The floatation processes are also applicable to the treatment of tailings (the waste product from other processes of extraction), providing the tailings are produced in sufficient quantity and hold sufficient mineral to warrant the expense of installing the necessary auxiliary plant. The Elmore Oil Plant (not now working), erected at the St David's Gold Mine, North Wales, for the treatment of cupriferous tailings, and the Delprat Plant, treating zinciferous tailings at the Broken Hill Proprietary Mines, New South Wales, may be cited as instances in point.

In this paper the expressions “ ore,” “ mineral,” and
Endoglycosidase and Glycoamidase Release of N‐Linked Glycans (2010)

Nearly all proteins entering the lumen of the endoplasmic reticulum (ER) become glycosylated en route to a cellular organelle, the plasma membrane, or the extracellular space. Many glycans can be attached to proteins, but the most common are the N-linked glycans (oligosaccharides). These chains are added very soon after a protein enters the ER, but they undergo extensive remodeling (processing), especially in the Golgi. Processing changes the sensitivity of the N-glycan to enzymes that cleave entire sugar chains or individual monosaccharides, which also changes the migration of the protein on SDS gels. These changes can be used to indicate when a protein has passed a particular subcellular location. This unit details some of the methods used to track a protein as it traffics from the ER to the Golgi toward its final location.
Prolyl isomerases catalyze antibody folding in vitro (1993)

Some slow-folding phases in the in vitro refolding of proteins originate from the isomerization of prolyl-peptide bonds, which can be accelerated by a class of enzymes called prolyl isomerases (PPIs). We used the in vitro folding of an antibody Fab fragment as a model system to study the effect of PPI on a folding reaction that is only partially reversible. We show here that members of both subclasses of PPIs, cyclophilin and FK 506 binding protein (FKBP), accelerate the refolding process and increase the yield of correctly folded molecules. An acceleration of folding was not observed in the presence of the specific inhibitor cyclosporin A, but still the yield of correctly folded molecules was increased. Bovine serum albumin (BSA) increased the yield comparable to cyclophilin but, in contrast, did not influence the rate of reactivation. These effects were observed only when cyclophilin or BSA were present during the first few seconds of refolding. However, the rate-limiting reactivation reaction is still accelerated when PPI is added several minutes after starting refolding. In contrast, the prokaryotic chaperone GroEL influences the refolding yield when added several minutes after initiating refolding. The results show that PPIs influence the folding of Fab in two different ways. (1) They act as true catalysts of protein folding by accelerating the rate-limiting isomerization of Xaa-Pro peptide bonds. Proline isomerization is obviously a late folding step and has no influence on the formation of aggregates within the first seconds of the refolding reaction.(ABSTRACT TRUNCATED AT 250 WORDS)
Multiplexed DNA Detection with DNA-Functionalized Silver and Silver/Gold Nanoparticle Superstructure Probes (2012)

E-mail: jslee79@korea.ac.krReceived October 20, 2011, Accepted November 21, 2011DNA-functionalized silver and silver/gold bimetallic nanoparticle superstructure probes with controllable sizesand optical properties are synthesized using monothiol DNA and dithiothreitol. The superstructures exhibit avery narrow size distribution, which can be easily controlled by balancing the ratio of dithiothreitol and DNA.These superstructures assemble reversibly in a highly cooperative manner, and are SERS active. Multiplexedcolorimetric detection of DNA targets using these superstructure probes has been demonstrated to identify threedifferent DNA target sequences that are associated with three lethal diseases, respectively.Key Words : DNA, SPR, Nanoparticle superstructure, Multiplexing, Colorimetric detectionIntroductionSequence-specific detection of multiple DNA targets inparallel has long been an intensive focus of research such asdisease diagnosis, forensic analysis, genomics, and biowar-fare defence.
Complete Genome Sequence of a Pseudomonas putida Clinical Isolate, Strain H8234 (2013)

We report the complete genome sequence of Pseudomonas putida strain H8234, which was isolated from a hospital patient presenting with bacteremia. This strain has a single chromosome (6,870,827 bp) that contains 6,305 open reading frames. The strain is not a pathogen but exhibits multidrug resistance associated with 40 genomic islands.
Association of the Metabolic Syndrome With History of Myocardial Infarction and Stroke in the Third National Health and Nutrition Examination Survey (2003)

These results indicate a strong, consistent relationship of the metabolic syndrome with prevalent MI and stroke.
Techniques for estimating the residual range of an electric vehicle (2001)

This paper presents an algorithm that has been developed to estimate the residual range of an electric vehicle, i.e., the distance that can still be covered with the energy stored inside the battery. The algorithm takes into account the complexity of the behavior of electrochemical batteries, with special reference to lead-acid batteries, as well as the main issues related to different driving styles. This paper also discusses some of the experimental results obtained by the use of the algorithm in several urban test trips made using two different types of electric vehicles.
[Influence of FasL overexpression in transgenic mice on the immune regulative function of Sertoli cell]. (2004)

FasL overexpression can influence the cytokine's secretion in the process of anti-infection immunity and further affects the immune balance of testis locality. Not all FasL over expression is benefit to body's anti-infection immune response.
Selective butyrylcholinesterase inhibition elevates brain acetylcholine, augments learning and lowers Alzheimer β-amyloid peptide in rodent (2005)

Like acetylcholinesterase, butyrylcholinesterase (BChE) inactivates the neurotransmitter acetylcholine (ACh) and is hence a viable therapeutic target in Alzheimer's disease, which is characterized by a cholinergic deficit. Potent, reversible, and brain-targeted BChE inhibitors (cymserine analogs) were developed based on binding domain structures to help elucidate the role of this enzyme in the central nervous system. In rats, cymserine analogs caused long-term inhibition of brain BChE and elevated extracellular ACh levels, without inhibitory effects on acetylcholinesterase. In rat brain slices, selective BChE inhibition augmented long-term potentiation. These compounds also improved the cognitive performance (maze navigation) of aged rats. In cultured human SK-N-SH neuroblastoma cells, intra- and extracellular beta-amyloid precursor protein, and secreted beta-amyloid peptide levels were reduced without affecting cell viability. Treatment of transgenic mice that overexpressed human mutant amyloid precursor protein also resulted in lower beta-amyloid peptide brain levels than controls. Selective, reversible inhibition of brain BChE may represent a treatment for Alzheimer's disease, improving cognition and modulating neuropathological markers of the disease.
An Algorithm for the Automatic Approximate Minimization of Boolean Functions (1968)

Abstract—There are several algorithms that determine directly an irredundant normal form (INF) of a Boolean function without generating the entire set of prime implicants. These algorithms can generate solutions for the minimization problem much more rapidly than the algorithms determining minimum normal forms (MNF), and the cost of these solutions is, in many cases, very close to the minimum.
A phase I study of trastuzumab-MCC-DM1 (T-DM1), a first-in-class HER2 antibody-drug conjugate (ADC), in patients (pts) with HER2+ metastatic breast cancer (BC) (2007)

1042 Background: ADCs utilize tumor-specific and/or over-expressed surface antigens that undergo internalization to deliver highly potent anti-tumor agents via linkage to antigen-specific monoclonal antibodies (MoAbs). T-DM1 contains the humanized anti-HER2 MoAb trastuzumab (T) previously demonstrated to prolong survival in HER2+ BC to which a highly potent antimicrotubule drug (DM1) derived from maytansine has been chemically linked. Maytansine has been studied as a free drug with responses noted in breast and lung cancer pts; principal adverse events (AEs) were nausea, vomiting, diarrhea, and neuropathy. The MCC linker employed in T-DM1 provides a stable bond between T and DM1 that is designed to prolong exposure and reduce the toxicity of T-DM1 while maintaining activity; T-DM1 is the first ADC with an MCC linker in clinical trials. T-DM1 has activity in T-resistant HER2+ BC xenografts; its principal preclinical toxicities were reversible transaminase elevations, reversible decreases in platelets, and neuropathy. Methods: This ongoing first-in-human phase I study is evaluating the safety and pharmacokinetics (PK) of T-DM1 given IV q3 weeks to pts with HER2+ metastatic BC who have progressed on a T-containing regimen. Results: Seven pts (median age 58 (range 47–70); all PS 0–1; median number prior chemo regimens 6 (range 5–11)) have received 24 doses of T-DM1 at 5 dose levels (0.3–4.8 mg/kg). Related grade (gr) 1–2 AEs include elevations in hepatic transaminases (2 pts), fatigue (2 pts), anemia (1 pt), and thrombocytopenia (TCP, 1 pt). Related gr 3–4 AEs have been limited to rapidly reversible gr 4 TCP at 4.8 mg/kg (1 pt). There has been no cardiac toxicity. Consistent with preclinical modeling, dose dependent decrease in clearance was observed for T-DM1 across dose levels. One pt at 2.4 mg/kg has maintained an ongoing partial response for 6 cycles. Conclusions: At these initial doses, gr =2 AEs related to T-DM1 have been infrequent and manageable; gr 4 (dose-limiting) rapidly reversible TCP was seen at 4.8 mg/kg. T-DM1 PK is consistent with q3-week dosing. Objective tumor response has been observed. Enrollment is ongoing to determine the maximum tolerated dose of q3-week T-DM1. No significant financial relationships to disclose.
A systematic review of clinical studies on dynamic magnetic resonance imaging of pelvic organ prolapse: the use of reference lines and anatomical landmarks (2009)

Only few studies have compared pelvic organ prolapse stages as assessed by dynamic MR imaging and clinical examination in a standardized manner. The available evidence suggests that prolapse assessment on dynamic MR imaging may be useful in the posterior compartment, but clinical assessment and dynamic MR imaging seem interchangeable in the anterior and central compartment.
Nanopore with Transverse Nanoelectrodes for Electrical Characterization and Sequencing of DNA (2007)

Nanopore DNA sequencing devices show promise for rapidly decoding genetic information, although single nucleotide detection appears to be beyond the sensitivity of present transmembrane current measurement schemes. In this paper, a nanodevice combining nanoelectrodes with a nanopore was made to measure the nucleotide dependent transverse tunneling currents during the translocation of DNA through the nanopore. A custom high speed, low noise, integrated circuit current amplifier was designed and fabricated to measure the tunneling current. This nanodevice was characterized electrically using 2 nm to 20 nm gold nanoparticles as an artificial construct for DNA using both DC and AC detection schemes. Measured transverse tunneling currents were found to be quantized, probably according to the number of nanoparticles residing within the pore.
Development of flexible-heteroarotinoids for kidney cancer (2009)

Potential chemopreventive and therapeutic value of the lead Flexible Heteroarotinoid (Flex-Het), SHetA2, was indicated by growth inhibition of multiple cancer cell lines. The objective of this study was to evaluate the SHetA2 mechanism and in vivo activity in kidney cancer. SHetA2 induced apoptosis in the Caki-1 kidney cancer cell line through reduction of Bcl-2 protein and induction of PARP-1 and caspase 3 cleavages, whereas normal kidney epithelial cells exhibited resistance. Both normal and cancerous cells underwent G(1) arrest and loss of Cyclin D1. Tubule differentiation was induced in organotypic cultures and xenograft tumors in association with increases in E-Cadherin mRNA and protein expression. SHetA2 repressed activity of nuclear factor-κB, a transcription factor that regulates apoptosis, Bcl-2, growth, Cyclin D1, differentiation, and E-Cadherin in the opposite manner as SHetA2. Glutathione binding and generation of reactive oxygen species were not required for these activities. Oral SHetA2 inhibited growth in one of two renal cancer xenograft models without causing mortality or weight loss. Structure function analysis of related Flex-Hets for potential improvement of SHetA2 pharmaceutical properties showed that compounds with increased hydrophilicity slightly reduced the growth inhibition efficacy, but retained the differential effect on cancer over normal cells. Flex-Hets and metabolites were not mutagenic in the Ames test. In conclusion, SHetA2 regulates growth, differentiation, and apoptosis in kidney cancer cells through multiple molecular events downstream of nuclear factor-κB repression. Increasing the hydrophilicity of Flex-Hets does not attenuate the differential effect on cancer cells over normal cells, thus offering alternatives for improvement of therapeutic value.
A Fabry-Perot interferometry based MRI-compatible miniature uniaxial force sensor for percutaneous needle placement (2013)

Robot-assisted surgical procedures, taking advantage of the high soft tissue contrast and real-time imaging of magnetic resonance imaging (MRI), are developing rapidly. However, it is crucial to maintain tactile force feedback in MRI-guided needle-based procedures. This paper presents a Fabry-Perot interference (FPI) based system of an MRI-compatible fiber optic sensor which has been integrated into a piezoelectrically actuated robot for prostate cancer biopsy and brachytherapy in 3T MRI scanner. The opto-electronic sensing system design was minimized to fit inside an MRI-compatible robot controller enclosure. A flexure mechanism was designed that integrates the FPI sensor fiber for measuring needle insertion force, and finite element analysis was performed for optimizing the correct force-deformation relationship. The compact, low-cost FPI sensing system was integrated into the robot and calibration was conducted. The root mean square (RMS) error of the calibration among the range of 0-10 Newton was 0.318 Newton comparing to the theoretical model which has been proven sufficient for robot control and teleoperation.
Cleaning power and abrasivity of a new toothpaste based on ion-exchange resins. (2004)

This study demonstrated that the use of a dentifrice based on an ion-exchange mixture was not effective at removing stains and abrasion was most insignificant when compared to other commercially available toothpastes.
Modeling time-constrained multiple-access message transmission by generalized stochastic Petri nets (2003)

Generalized stochastic Petri nets were used to model time-constrained message transmission over a single multiple-access channel to get the performance limits, which show the percentage of successful message transmission. These Petri net models reflect different assumptions about the laxity and length distributions of real-time messages. The results from the Petri net models are shown to agree with those from queuing system models.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>