gebhart/patrepeval huggingface dataset:
Finding Explicit and Implicit Knowledge (2010)

This chapter discusses two different types of text data mining focusing on the biomedical literature. One deals with explicit information or facts written in articles, and the other targets implicit information or hypotheses inferred from explicit information. A major difference between the two is that the former is bound to the contents within the literature, whereas the latter goes beyond existing knowledge and generates potential scientific hypotheses. As concrete examples applied to real-world problems, this chapter looks at two applications of text data mining: gene functional annotation and genetic association discovery, both considered to have significant practical importance.
Author Correction: Involvement of Innate Immune System in Late Stages of Inherited Photoreceptor Degeneration (2018)

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Ganglioside modulation of neural cell adhesion molecule and N-cadherin-dependent neurite outgrowth (1992)

We have used monolayers of control 3T3 cells and 3T3 cells expressing transfected human neural cell adhesion molecule (NCAM) or chick N-cadherin as a culture substrate for PC12 cells. NCAM and N-cadherin in the monolayer directly promote neurite outgrowth from PC12 cells via a G-protein-dependent activation of neuronal calcium channels. In the present study we show that ganglioside GM1 does not directly activate this pathway in PC12 cells. However, the presence of GM1 (12.5-100 micrograms/ml) in the co-culture was associated with a potentiation of NCAM and N-cadherin-dependent neurite outgrowth. Treatment of PC12 cells with GM1 (100 micrograms/ml) for 90 min led to trypsin-stable increases in both beta-cholera toxin binding to PC12 cells and an enhanced neurite outgrowth response to N-cadherin. The ganglioside response could be fully inhibited by treatment with pertussis toxin. These data are consistent with exogenous gangliosides enhancing neuritic growth by promoting cell adhesion molecule-induced calcium influx into neurons.
BEOL compatible high tunnel magneto resistance perpendicular magnetic tunnel junctions using a sacrificial Mg layer as CoFeB free layer cap (2015)

Perpendicularly magnetized MgO-based tunnel junctions are envisaged for future generation spin-torque transfer magnetoresistive random access memory devices. Achieving a high tunnel magneto resistance and preserving it together with the perpendicular magnetic anisotropy during BEOL CMOS processing are key challenges to overcome. The industry standard technique to deposit the CoFeB/MgO/CoFeB tunnel junctions is physical vapor deposition. In this letter, we report on the use of an ultrathin Mg layer as free layer cap to protect the CoFeB free layer from sputtering induced damage during the Ta electrode deposition. When Ta is deposited directly on CoFeB, a fraction of the surface of the CoFeB is sputtered even when Ta is deposited with very low deposition rates. When depositing a thin Mg layer prior to Ta deposition, the sputtering of CoFeB is prevented. The ultra-thin Mg layer is sputtered completely after Ta deposition. Therefore, the Mg acts as a sacrificial layer that protects the CoFeB from sputter-induced damage during the Ta deposition. The Ta-capped CoFeB free layer using the sacrificial Mg interlayer has significantly better electrical and magnetic properties than the equivalent stack without protective layer. We demonstrate a tunnel magneto resistance increase up to 30% in bottom pinned magnetic tunnel junctions and tunnel magneto resistance values of 160% at resistance area product of 5 Ω.μm2. Moreover, the free layer maintains perpendicular magnetic anisotropy after 400 °C annealing.
Transcription factors involved in pancreas development are expressed in paediatric solid pseudopapillary tumours (2008)

The clinical behaviour of SPT in the paediatric population is similar to its adult counterpart. Complete surgical resection is essential. PDX1 and Sox9 proteins are exclusively expressed in the cytoplasmic compartment in SPT, suggesting overexpression of the corresponding genes linked to beta-catenin mutations. These findings favour the hypothesis that SPT originates from transformation of normally quiescent pancreatic stem cells.
Knowledge Acquisition by Improved Fuzzy ID3 Algorithm and Stability Analysis for Jacket Tank Temperature Control (2000)

The extraction of knowledge from operation data is an important theme in an autonomous control system. An efficient method for making a decision tree for classification from data is the fuzzy ID3 algorithm using fuzzy sets. However, the definition of fuzzy sets greatly affects the generation of fuzzy trees. In this paper, we propose a new version of fuzzy ID3 algorithms to generate a fuzzy decision maximizing the expected value of transferred information by applying a random search method for determining the fuzzy set, and by using the improved fuzzy ID3 algorithm an automatic extraction of control knowledge from operational data by skilled operator of a jacket tank process. As a result, a fuzzy controller that can decide output of a control switch from both tank temperature error and differentiation of error is designed. Further, a method of analyzing the stability of the fuzzy control system by the modified fuzzy ID3 algorithm is proposed using the phase planes of tank temperature.
From<i>Drosophila</i>to Humans: Reflections on the Roles of the Prolyl Isomerases and Chaperones, Cyclophilins, in Cell Function and Disease (2012)

Despite remarkable advances in human genetics and other genetic model systems, the fruit fly, Drosophila melanogaster, remains a powerful experimental tool to probe with ease the inner workings of a myriad of biological and pathological processes, even when evolutionary forces impart apparent divergences to some of such processes. The understanding of such evolutionary differences provides mechanistic insights into genotype-phenotype correlations underpinning biological processes across metazoans. The pioneering work developed by the William Pak laboratory for the past four decades, and the work of others, epitomize the notion of how the Drosophila system breaks new fertile ground or complements research fields of high scientific and medical relevance. Among the three major genetic complementation groups produced by the Pak's laboratory and impairing distinct facets of photoreceptor neuronal function, the nina group (ninaA, …., ninaJ) selectively affects the biogenesis of G protein-coupled receptors (GPCRs), mediating the photoconversion and transduction of light stimuli. Among the nina genes identified, ninaA arguably assumes heightened significance for several reasons. First, it presents unique physiological selectivity toward the biogenesis of a subset of GPCRs, a standalone biological manifestation yet to be discerned for most mammalian homologues of NinaA. Second, NinaA belongs to a family of proteins, immunophilins, which are the primary targets for immunosuppressive drugs at the therapeutic forefront of a multitude of medical conditions. Third, NinaA closest homologue, cyclophilin B (CyPB/PPIB), is an immunophilin whose loss-of-function was found recently to cause osteogenesis imperfecta in the human. This report highlights advances made by studies on some members of immunophilins, the cyclophilins. Finally, it reexamines critically data and dogmas derived from past and recent genetic, structural, biological, and pathological studies on NinaA and few other cyclophilins that support some of such paradigms to be less than definite and advance our understanding of the roles of cyclophilins in cell function, disease, and therapeutic interventions.
Control of mobile robot by using evolutionary fuzzy controller (2002)

An evolutionary fuzzy controller that drives the output parameters of fuzzy logic system in such a way that the Lyapunov function and the system is exponentially stable is presented. The output parameters of the fuzzy logic system are updated for every sampling time in an evolutionary manner. Only part of the parameters associated with the current situation are considered and, thus, the presented evolutionary fuzzy controller significantly reduces the computation time and the output parameters of the fuzzy logic systems are updated with on-line evolution. Also, in order to guarantee the stable operation of the system when the evolution is progressed, the derivative of the Lyapunov function is maintained to be negative semi-definite by introducing the supervisory control input. The presented evolutionary fuzzy controller has been successfully tested on a simulation example of a mobile robot stabilizing problem.
Genotype Phenotype Correlation and Variability in Microcephaly Associated With Chorioretinopathy or Familial Exudative Vitreoretinopathy (2020)

Microcephaly due to mutations in KIF11, TUBGCP4, or TUBGCP6 can be associated with retinal disease on a spectrum from chorioretinal atrophy to FEVR-like posterior segment changes. Visually significant disease progression can occur and patients should be monitored closely by a team experienced in ophthalmic genetics.
Code specialization for red-black tree management algorithms (2013)

A lot of work is spent on low-level optimization for regular computations; from instruction scheduling and cache-aware design to intensive use of SIMD instructions. Meanwhile, irregular applications, especially pointer intensive ones, are often only optimized at algorithm or compilation levels, since not so much hardware or dedicated instructions are available for this kind of code. In this paper, we investigate a low-level optimization of associative arrays intensively used in complex applications such as dynamic compilers, using self-modifying code. We propose to encode Red-Black trees, widely used to implement asssociative arrays, as specialized binary code rather than data, in order to accelerate the tree traversal by taking advantage of the underlying hardware: program cache, processor fetch and decode. We show a 45% gain on an ARM Cortex-A9 processor and that we transfer most of the data-cache pressure to the program-cache, motivating future work on dedicated hardware.
Detection of Molecular Ions of Non-Covalent Complexes of RasGDP and RasGppNp by MALDI-TOFMS. (1996)

A detection of non-covalent complexes of Ras·GDP and Ras·GppNp (guanosine-5′-(β,γ-imido)-triphosphate; GTP analogue) using matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOFMS) is reported. The Ras proteins are bound to GDP or GppNp, non-covalently, with ionic bonds. The GDP-bound Ras is inactive, while the GTP-bound Ras is active. This paper shows the possibility of the detection of the active and inactive form of a regulatory protein, which is non-covalently bound with a nucleotide, with a small sample amount by MALDI-TOFMS analyses. It was also suggested that MALDI-TOFMS is promising for the estimation of the ratio of nucleotide bound Ras protein and free apo-Ras protein.
Cochlear implants (1976)

All presently devised single channel devices generate a primitive sensation of hearing by the mechanism of 'periodicity pitch'. No 'place pitch' encoding is possible. Although some enhancement of communicative skills with lip reading results, unaided speech discrimination is not possible. Definite psychological advantages for the totally deaf have been observed with these simple devices. Multiple segments of auditory nerve must be stimulated in a manner which will simulate the complex patterns of neural activity necessary for speech discrimination. Electrode optimization and the pathophysiological consequences of electrical stimulation of the auditory nerve can best be determined in animals. The perceptual consequences of electrical stimulation of the auditory nerve, however, can best be determined in man. How much we will have to innovate the methods of aural rehabilitation will depend upon how well we can generate perceptual speech patterns by electrical excitation of the auditory nerve.
Weight-Loss Drugs (2007)

Obesity is increasing in prevalence and its medical liabilities are largely related to central adiposity and the associated insulin resistance. The present drugs available for the treatment of obesity and metabolic syndrome are few in number and limited in efficacy. This chapter reviews the drugs approved by the US Food and Drug Administration (FDA) to treat obesity, drugs approved by the FDA for other indications than weight loss, drugs in the late development process that have not been approved by the FDA, drugs in earlier stages of drug development for which clinical information is limited, drugs that have been dropped from development, and new potential drug targets for which essentially no clinical data yet exist. We also review the nonprescription products sold for the treatment of obesity and metabolic syndrome. The developmental pipeline of drugs for the treatment of obesity and the metabolic syndrome is rich. Because drugs to treat obesity are being developed in an era characterized by more sophisticated tools for drug development than existed when hypertension drugs were being developed, much faster progress in developing safe and effective drugs for obesity and metabolic syndrome is anticipated. With safe and effective drugs available, we anticipate that the chronic treatment of obesity with weight loss medication will become as well-accepted and prevalent as is the chronic drug treatment of hypertension and diabetes in the medical practice of today.
Variable dimension quantization in the transform domain (2002)

Quantization is a critical procedure in lossy image compression. Linear (uniform) quantizers are used in most of the present image (sequence) compression standards for their simplicity and flexibility. Unfortunately, the resulting representation is often inefficient, preventing potentially significant gains in image compression. We introduce a new class of linear, low complexity, variable dimension quantizers (VDQ) that efficiently reduces the redundancy of the data stream while retaining the design flexibility and signal-to-noise performance of a linear quantizer. When applied to frequency domain representations in the JPEG image compression standard, this approach resulted in SNR improvements of almost 9 dB over the baseline quantizer at comparable bit rates. The algorithm presented is near optimal and runs in O(N) time, making it suitable for real time applications. Its low complexity and effectiveness make VDQ a promising alternative to conventional quantization for image codecs.
Growth of wurtzite Al<sub><i>x</i></sub>Ga<sub>1−<i>x</i></sub>P nanowire shells and characterization by Raman spectroscopy (2016)

The phonon energies of AlGaP in wurtzite crystal structure are generally not known, as opposed to their zincblende counterparts, because AlGaP crystallizes in zincblende phase in bulk and thin films structures. However, in nanowires AlGaP can be grown in wurtzite crystal structure. In this work we have grown wurtzite GaP/AlGaP/GaP core-shell nanowires by use of MOVPE. After developing suitable growth conditions, the Al composition was determined by STEM-EDX measurements and the wurtzite AlGaP phonon energies by Raman spectroscopy. Raman measurements show a peak shift with increasing Al composition in the AlGaP shell. We find that the phonon energies for wurtzite AlGaP are slightly lower than for zincblende AlGaP. Our results can be used to determine the Al composition in wurtzite AlGaP by Raman scattering.
High Surface Area Silicon Carbide Whiskers and Nanotubes Nanocast Using Mesoporous Silica (2004)

We report here the formation of high surface area silicon carbide materials comprising whiskers and nanotubes via a synthesis route, which utilizes mesoporous silica as sacrificial solid template. The silicon carbide materials are obtained via carbothermal reduction of mesoporous silica/carbon (i.e., SBA-15/sucrose) composites. Varying the carbothermal reduction conditions (i.e., temperature or duration) readily modifies the morphology of the silicon carbide so as to obtain whiskers or nanotubes. The whiskers, which grow in the [111] direction, are achieved by subjecting the mesoporous silica/carbon composites to carbothermal reduction at high temperature (1250 or 1300 °C) for reduction periods of up to 14 h. For reduction periods of up to 14 h, using the higher temperature (1300 °C) optimizes whisker formation. The diameter of the whiskers is 50−90 nm and their length is typically greater than 20 μm. The surface area of the whisker containing SiC materials varies between 120 and 145 m2/g, while their pore volume is ca. 0.42 cm3/g. Increasing the carbothermal reduction period to 20 h, at 1250 or 1300 °C, results in the formation of solid SiC nanotubes of diameter 60−100 nm and length greater than 10 μm. The formation of nanotubes is accompanied by an increase in the surface area (up to 190 m2/g) of the silicon carbide materials.
Amino Acid Substitutions in the <i>Caenorhabditis elegans</i> RNA Polymerase II Large Subunit AMA-1/RPB-1 that Result in α-Amanitin Resistance and/or Reduced Function (2011)

Mutations in the Caenorhabditis elegans RNA polymerase II AMA-1/RPB-1 subunit that cause α-amanitin resistance and/or developmental defects were isolated previously. We identified 12 of these mutations and mapped them onto the Saccharomyces cerevisiae RPB1 structure to provide insight into AMA-1 regions that are essential for development in a multicellular organism.
Crystallization behavior of sheared polyamide 66 (2018)

The application of fast scanning chip calorimetry (FSC) for analysis of sheared polyamide 66 (PA 66) provided quantitative insight to the effect of shear flow and flow-induced formation of crystallization precursors/nuclei on the subsequent crystallization in a wide range of temperatures. In the high-temperature, heterogeneous-nucleation range, there is a direct relationship between the amount of specific work supplied to the melt and the acceleration of crystallization, presumably due in part to increased nucleation density of the sheared samples. This information is directly applicable to polymer engineering applications where the formation of crystalline domains during processing often occurs at rapid-cooling conditions. Analysis of the structure at the micrometer-length scale of sheared PA 66 by polarized-light optical microscopy (POM) revealed large shish-kebab structures.
X-ray generation from 50-mJ, 120-ps KrF laser-produced plasmas (1992)

The generation of x rays from the interaction of low-energy (10–50 mJ) 120-ps KrF laser pulses with solid targets has been experimentally investigated. Conversion efficiency as a function of laser energy and detailed keV x-ray spectra have been obtained for targets (Fe, Ni, and Cu) with potential application in high-resolution x-ray lithography. Peak x-ray conversion efficiencies of over 3% in the 800–1400-eV photon energy band have been measured for laser intensities of 1.5 × 1014 W/cm2. In addition, transmission grating spectra have been obtained to characterize the overall distribution of x-ray emission at photon energies down to 100 eV.
Expression of the Caudal-Type Homeodomain Transcription Factors <i>CDX</i> 1/2 and Outcome in Carcinomas of the Ampulla of Vater (2005)

Expression of CDX was an independent marker of outcome in patients with resected adenocarcinoma of the ampulla of Vater. Expression of CDX may distinguish good prognosis intestinal-like tumors, which potentially arise within intestinal epithelium, from poorer prognosis pancreatobiliary tumors, which arise in adjacent pancreatic and/or biliary ductal epithelium.
[Lumbar interapophyseal septic arthritis. Apropos of 3 cases]. (1996)

Septic arthritis of spinal apophyseal joint, seldom described, mainly concern the lumbar spine. We report three cases. Inflammatory lesions of the paravertebral soft tissues were associated in each case; an epidural abscess was present twice. Our three cases were due to Staphylococcus aureus. The initial clinical features were consistent with a spondylodiscitis. Imaging led to the correct diagnosis in all cases. According to our observations and several others of the literature: facet joint lesions are visible too late on plain films. Bone scintigraphy is sensitive, but not specific. CT scan and MRI are the most contributive investigations. A pathologic aspect of the paravertebral soft tissues is visible less than one week after the beginning of the symptoms on CT scan and MRI. Lesions of the facet joint are detectable as soon as the first week on MRI, and after 15 days of clinical course on CT scan. Epidural abscess, when present, is best shown by MRI as early as the first week. CT scan can guide percutaneous needle biopsies of the paravertebral abscesses or of the concerned facet joint.
Expression and secretion in yeast of active insect defensin, an inducible antibacterial peptide from the fleshfly<i>Phormia terranovae</i> (1992)

Summary Insect defensin A is an inducible antibacterial peptide of the fleshfly Phormia terra-novae and has been recently characterized as a 40 residue basic peptide with six cysteines engaged in three intramolecular disulfide bridges. We report the expression of this peptide in Saccharomyces cerevisiae as a fusion protein carrying at its N-terminus leader sequences which are derived from the precursor of the yeast pheromone mating factor α (MFαl). These sequences allow the biologically active peptide to be secreted at high levels in a correctly processed form. Thus heterologous production of defensin A circumvents laborious purification of minute amounts of the peptide from its natural source. The insect defensin pro peptide can substitute for the MFαl pro peptide, indicating that yeast can process an insect pro sequence.
Multiplexed, high-throughput analysis of 3D microtissue suspensions (2010)

Three-dimensional (3D) tissue models have significantly improved our understanding of structure/function relationships and promise to lead to new advances in regenerative medicine. However, despite the expanding diversity of 3D tissue fabrication methods, approaches for functional assessment have been relatively limited. Here, we describe the fabrication of microtissue (μ-tissue) suspensions and their quantitative evaluation with techniques capable of analyzing large sample numbers and performing multiplexed parallel analysis. We applied this platform to 3D μ-tissues representing multiple stages of liver development and disease including: embryonic stem cells, bipotential hepatic progenitors, mature hepatocytes, and hepatoma cells photoencapsulated in polyethylene glycol hydrogels. Multiparametric μ-tissue cytometry enabled quantitation of fluorescent reporter expression within populations of intact μ-tissues (n≥ 10²-10³) and sorting-based enrichment of subsets for subsequent studies. Further, 3D μ-tissues could be implanted in vivo, respond to systemic stimuli, retrieved and quantitatively assessed. In order to facilitate multiplexed 'pooled' experimentation, fluorescent labeling strategies were developed and utilized to investigate the impact of μ-tissue composition and exposure to soluble factors. In particular, examination of drug/gene interactions on collections of 3D hepatoma μ-tissues indicated synergistic influence of doxorubicin and siRNA knockdown of the anti-apoptotic gene BCL-XL. Collectively, these studies highlight the broad utility of μ-tissue suspensions as an enabling approach for high n, populational analysis of 3D tissue biology in vitro and in vivo.