gebhart/patrepeval huggingface dataset:
Fabrication of large preforms for low-loss single-mode optical fibers by a hybridized process (1996)

A hybridized fabrication process for single-mode optical fibers has been studied. The process consists of direct overcladding a VAD derived core rod with a porous body made from commercial silica powder by means of the cold isostatic pressing technique. By using a mixture of main silica powder with an average particle diameter of 10 µm and 1 w t% of fine silica powder with an average particle diameter of 0.04 µm and a core rod having a core/cladding diameter ratio of 1/2.4 as starting materials, large preforms for 300 km fibers were fabricated, which were drawn into fibers with attenuation losses of 0.350 dB/km at 1.31 µm and 0.232 dB/km at 1.55 µm. In the process, a special rubber mold with a structure in which both ends of the core rod are pressed by hydrostatic pressure makes the fabrication of large hybridized soot preforms possible, plastic deformation of the porous body during degreasing being remarkably reduced by using a suitable content of glycerol.
Classification as an Approach To Requirements Analysis (1990)

Oassification schemes have proven immensely useful in computerized systems for problem solving in the physical and biological sciences. A typical example is found in the medical domain where various taxonomies have been created for diseases, symptOms, laboratory tests, drugs, and so forth. These taxonomies may be used for characterizing specific clinical situations in expert systems that assist physicians and other health professionals in diagnosis and treatment. Oassification can be divided into several phases. The activities in the first phase are to find a category structure which can fit observations. This phase is called analysis, or typology, clumping, regionalization, etc., or (construction) in our paper, depending on the field to which it is applied. There are many approaches to this cluster analysis. These include approaches such as numerical taxonomy and conceptual clustering. Once this category structure has been established, the next phase is to classify new observations, that is, recognize them as members of one category or another. There are two different situations for the activities in this phase: 1) when the category structure is completely known, this kind of activity is called classification, indexing, or classifying in this paper, and 2) if category structure is partly known or only part of the information of the observation is known, this kind of activity is called discriminant analysis [AND73] [GOR81]. Oancey [CLA84] has characterized classification problem solving as making a selection from a set of pre-enumerated solutions (in contrast to constructing new solutions). If the problem solver has a priori knowledge of existing solutions and is able to relate these to the problem description by data abstraction and refinement, then the problem can be solved using classification. Other artificial intelligence researchers, especially those investigating machine learning, have developed new techniques such as conceptual clustering [MIC86] (in contrast to numerical/statistical clustering), which might be used for developing classification schemes for problem solving.
FGFR3, HRAS, KRAS, NRAS and PIK3CA Mutations in Bladder Cancer and Their Potential as Biomarkers for Surveillance and Therapy (2010)

The mutation assays present a companion diagnostic to define patients for targeted therapies. In addition, the assays are a potential biomarker to detect recurrences during surveillance. We showed that 88% of patients presenting with low-grade NMI-BC are eligible for such a follow-up. This may contribute to a reduction in the number of cystoscopical examinations.
Slicing the universe at affordable cost: the quest for the MUSE image slicer (2004)

The introduction of Image Slicers in Astronomy has been growing rapidly in the recent years. These optical devices allow the simultaneous observation on the same detector matrix of two-dimensional sky maps and the spectral decomposition of light on all of their angular samples, therefore dramatically reducing the observation times and getting rid of the spectro-photometric variations of the atmosphere. Today the implementation of Image Slicers is planned on various ground and space telescopes, covering a spectral domain ranging from blue to mid-IR wavelengths. Among such different projects, we describe the Image Slicer of MUSE (Multi Unit Spectroscopic Explorer), a second-generation Integral-Field Spectrograph for the VLT combining a 1’ x 1’ Field of View with a spatial resolution of 0.2” and a spectral resolution of 3000. The most efficient principle of an Image Slicer consists in a combination of several different optical channels, each made of three mini-mirrors having different tilts and curvatures. After a brief presentation of the MUSE Image Slicer requirements, we will explain the followed logic in order to optimize the opto-mechanical design and cost of the Slicer: indeed one of MUSE peculiarity is the total number of its individual modules, that is 24. The realization of such series at an affordable cost actually is a design driver of the study. The communication also deals with the used optical design models, the expected performance, the candidate technologies for the manufacturing of all the components, and the future development of a prototype of this critical optical subsystem.
A Phase II Study of Etanercept (Enbrel), a Tumor Necrosis Factor α Inhibitor in Patients with Metastatic Breast Cancer (2004)

Our study shows the safety and biological activity of Etanercept in breast cancer and provides data to assess pharmacodynamic endpoints of different schedules of Etanercept and combinations with chemotherapy or other biological therapies.
Molecular Analysis of the Hotspot of Recombination in the Murine Major Histocompatibility Complex (1986)

Biological and serological assays have been used to define four subregions for the I region of the major histocompatibility complex (MHC) in the order I-A, I-B, I-J, and I-E. The I-J subregion presumably encodes the I-J polypeptide of the elusive T-cell suppressor factors. Restriction enzyme site polymorphisms and DNA sequence analyses of the I region from four recombinant mouse strains were used to localize the putative I-B and I-J subregions to a 1.0-kilobase (kb) region within the E beta gene. Sequencing this region from E beta clones derived from the two mouse strains: B10.A(3R), I-Jb and B10.A(5R), I-Jk initially used to define the I-J subregion revealed that these regions are identical, hence the distinct I-Jb and I-Jk molecules cannot be encoded by this DNA. In addition, the DNA sequence data also refute the earlier mapping of the I-B subregion. Analysis of the DNA sequences of three parental and four I region recombinants reveals that the recombinant events in three of the recombinant strains occurred within a 1-kb region of DNA, supporting the proposition that a hotspot for recombination exists in the I region. The only striking feature of this hotspot is a tetramer repeat (AGGC)n that shows 80 percent homology to the minisatellite sequence which may facilitate recombination in human chromosomes.
Thiamin-Binding Protein from Sunflower Seeds. (1998)

A thiamin-binding protein was isolated from sunflower seeds. Its molecular mass was estimated to be 230 kDa by gel filtration. The protein was suggested to be composed of six subunits, which consisted of polypeptides linked by disulfide bond(s). The protein contained a large amount of glutamine or glutamic acid (19.9 mol%) and asparagine or aspartic acid (11.1 mol%). The levels of tryptophan and valine in the protein were low. These properties of the thiamin-binding protein were similar to those of helianthinin. Optimum pH for the thiamin-binding activity of the protein was 8.0 to 9.0. The thiamin-binding activity was not inhibited by thiamin monophosphate, thiamin pyrophosphate, oxythiamin, or pyrithiamin. These properties of the thiamin-binding protein from sunflower seeds were similar to those from buckwheat seeds, but not to those from rice seeds and sesame seeds.
Biochemical and Functional Characterization of Membrane Blebs Purified from Neisseria meningitidis Serogroup B (2005)

Studies with purified aggregates of endotoxin have revealed the importance of lipopolysaccharide-binding protein (LBP)-dependent extraction and transfer of individual endotoxin molecules to CD14 in Toll-like receptor 4 (TLR4)-dependent cell activation. Endotoxin is normally embedded in the outer membrane of intact Gram-negative bacteria and shed membrane vesicles ("blebs"). However, the ability of LBP and CD14 to efficiently promote TLR4-dependent cell activation by membrane-associated endotoxin has not been studied extensively. In this study, we used an acetate auxotroph of Neisseria meningitidis serogroup B to facilitate metabolic labeling of bacterial endotoxin and compared interactions of purified endotoxin aggregates and of membrane-associated endotoxin with LBP, CD14, and endotoxin-responsive cells. The endotoxin, phospholipid, and protein composition of the recovered blebs indicate that the blebs derive from the bacterial outer membrane. Proteomic analysis revealed an unusual enrichment in highly cationic (pI > 9) proteins. Both purified endotoxin aggregates and blebs activate monocytes and endothelial cells in a LBP-, CD14-, and TLR4/MD-2-dependent fashion, but the blebs were 3-10-fold less potent when normalized for the amount of endotoxin added. Differences in potency correlated with differences in efficiency of LBP-dependent delivery to and extraction of endotoxin by CD14. Both membrane phospholipids and endotoxin are extracted by LBP/soluble CD14 (sCD14) treatment, but only endotoxin.sCD14 reacts with MD-2 and activates cells. These findings indicate that the proinflammatory potency of endotoxin may be regulated not only by the intrinsic structural properties of endotoxin but also by its association with neighboring molecules in the outer membrane.
Evaluation of Double Stranded RNA for the Prevention of Infectious Myonecrosis Virus (IMNV) in Litopenaeus vannamei (2011)

Double stranded RNA was synthesized in vitro with sequences corresponding to portions of the IMNV genome and were injected into shrimp prior to challenge with IMNV. This is the first time these methods have been used to prevent IMN in shrimp.
Pulse pileup statistics for energy discriminating photon counting x‐ray detectors (2011)

A computationally efficient multinomial approximation of the count statistics that is based on the mean output spectrum can accurately predict imaging performance. This enables photon counting system designers to directly relate the effect of pileup to its impact on imaging statistics and how to best take advantage of the benefits of energy discriminating photon counting detectors, such as material separation with spectral imaging.
The Balance between Protein Synthesis and Degradation in Chloroplasts Determines Leaf Variegation inArabidopsis yellow variegatedMutants (2007)

An Arabidopsis thaliana leaf-variegated mutant yellow variegated2 (var2) results from loss of FtsH2, a major component of the chloroplast FtsH complex. FtsH is an ATP-dependent metalloprotease in thylakoid membranes and degrades several chloroplastic proteins. To understand the role of proteolysis by FtsH and mechanisms leading to leaf variegation, we characterized the second-site recessive mutation fu-gaeri1 (fug1) that suppressed leaf variegation of var2. Map-based cloning and subsequent characterization of the FUG1 locus demonstrated that it encodes a protein homologous to prokaryotic translation initiation factor 2 (cpIF2) located in chloroplasts. We show evidence that cpIF2 indeed functions in chloroplast protein synthesis in vivo. Suppression of leaf variegation by fug1 is observed not only in var2 but also in var1 (lacking FtsH5) and var1 var2. Thus, suppression of leaf variegation caused by loss of FtsHs is most likely attributed to reduced protein synthesis in chloroplasts. This hypothesis was further supported by the observation that another viable mutation in chloroplast translation elongation factor G also suppresses leaf variegation in var2. We propose that the balance between protein synthesis and degradation is one of the determining factors leading to the variegated phenotype in Arabidopsis leaves.
Porous silicon structures for low-cost diffraction-based biosensing (2010)

We present a strategy for label-free biosensing using porous silicon diffraction gratings. The gratings are fabricated using a cost-effective, high-throughput stamping technique. Unlike traditional diffraction-based biosensors that rely on microcontact printing or lithography to create gratings for the localization of analytes on the top surface of the grating, in our structure analytes are free to infiltrate the porous network and increase the effective refractive index of the grating. The large surface area of porous silicon available for molecular binding offers the potential for enhanced diffraction response compared to nonporous gratings with limited surface area. Small molecule detection of 3-aminopropyltriethoxysilane is demonstrated.
Standardization of the Chloramine-T Method of Protein Iodination (1970)

SummaryA method is described for the controlled iodination of proteins. The potential, EMF, of the reaction mixture is monitored and used to determine the minimum amount of chloramine-T required for acceptable iodination. The method has been applied to the iodination of bovine serum albumin, ovalbumin, Salmonella flagella, and other proteins.
New Transition-Metal-Dependent DNAzymes as Efficient Endonucleases and as Selective Metal Biosensors (2002)

Like proteins and RNA molecules, many DNA molecules have now been shown to catalyze a variety of reactions and are thus called DNAzymes. With limited building blocks, DNAzymes need to recruit other cofactors in order to match other enzymes in terms of reaction diversity and catalytic efficiency. Several unique properties make transition-metal ions an ideal choice of cofactor for DNAzymes. Indeed, new DNAzymes that bind transition-metal ions with high affinity and selectivity have been obtained through the use of a powerful combinatorial biology tool called in vitro selection. This accomplishment now makes it possible to obtain different classes of metallo-DNAzymes in the laboratory within a short period of time. It also offers a rare opportunity to compare and contrast structural and functional properties of metal-binding sites in proteins and in DNAzymes. The resulting transition-metal-dependent DNAzymes have displayed high activity toward cleavage of DNA and RNA and thus hold promise for their biochemical and pharmaceutical applications. Finally, the use of DNAzymes as a new class of highly sensitive and selective biosensors for metal ions has been demonstrated recently.
Amyotrophic Lateral Sclerosis (2017)

Progress has been made in understanding the genetic defects and the pathophysiology of this crippling motor neuron disease (commonly called Lou Gehrig’s disease). However, this information has not yet led to a successful intervention that alters the course of the disease.
Ribosomal protein L7a gene is up-regulated but not fused to the tyrosine kinase receptor as chimeric trk oncogene in human colorectal carcinoma. (2000)

Ribosomal protein L7a (rp L7a) was identified in a subtractive hybridization screen as a gene up-regulated in human colorectal cancer. Expression of rp L7a was greater than 2-fold higher in tumors compared to adjacent normal mucosa in 72% of the patients studied (n=36). rp L7a was also up-regulated in concomitant polyps. The number of patients with rp L7a T/N ratio of >2 was significantly higher in the female (16/18) than in the male (10/18). rp L7a expression was also significantly higher in females with lymph node involvement compared to males. These results indicate that rp L7a expression is related to tumor growth in colorectal cancer especially in females, where it may also be related to tumor spread. There was no correlation of rp L7a expression with tumor cell differentiation. We also show that rp L7a does not exist as a fusion oncogene (trk-2h) in colorectal cancer.
Transcriptional regulation of zwf, encoding glucose‐6‐phosphate dehydrogenase, from the cyanobacterium Nostoc punctiforme strain ATCC 29133 (1996)

The gene encoding glucose-6-phosphate dehydrogenase (G6PD), zwf, in Nostoc punctiforme strain ATCC 29133 is part of a four-gene operon that also encodes fructose bisphosphatase (fbp), transaldolase (tal) and a gene product termed OpcA, which is contranscribed with zwf and essential for G6PD activity. The effect of exogenous nitrogen and carbon sources on transcription of these genes was investigated. Growth in the presence of ammonium yielded low levels of transcripts encoding all genes of the operon, while growth under nitrogen-fixing conditions resulted in a large increase of transcripts encoding for fbp and zwf-opcA. When cells are grown in the presence of fructose, levels of transcripts encoding tal and zwf-opcA were increased, relative to levels in ammonium-grown cells. These results indicate that this facultatively heterotrophic cyanobacterium can respond to changes in its environment by altering transcription of genes involved in carbon catabolism. Primer extension identified five 5' ends corresponding to the major regulated transcripts which we conclude arise from independent transcriptional start points.
5-Methylcytosine as an Endogenous Mutagen in the Human LDL Receptor and p53 Genes (1990)

Direct genomic sequencing revealed that cytosine residues known to have undergone a germ-line mutation in the low density lipoprotein receptor gene or somatic mutations in the p53 tumor suppressor gene were methylated in all normal human tissues analyzed. Thus, these mutations should be scored as transitions from 5-methylcytosine to thymine rather than from cytosine to thymine. Methylated cytosines occur exclusively at CpG dinucleotides, which, although markedly underrepresented in human DNA, are sites for more than 30 percent of all known disease-related point mutations. Thus, 5-methylcytosine functions as an endogenous mutagen and carcinogen in humans, in that methylation seems to increase the potential for mutation at cytosine residues at least by a factor of 10.
Nuclear Roundness Factor Measurement for Assessment of Prognosis of Patients With Prostatic Carcinoma. I. Testing Of A Digitization System (1988)

Standard pathological grading systems for prostatic carcinoma based upon glandular architectural pattern or nuclear anaplasia have failed to predict the prognosis of individual patients. Quantitative morphometric analysis of nuclear shape has predicted the outcome of patients with prostatic carcinoma when evaluated by some but not all reported studies. Calculation of nuclear roundness factor by different investigators was complicated by equipment differences and lack of standardized methods for acquiring and reporting data. We have improved our system for nuclear contour digitization and determined its theoretical limitations by digitizing standardized objects. Measurement errors were independent of orientation or location of an object within a microscopic or digitizer tablet field, speed of digitization and introduction of a microscope extension tube and light emitting diode cursor. Perimeters and areas of circles and squares of actual or digitizer-projected diameter or sidelength greater than five mm. were measured with a reproducibility and accuracy of greater than or equal to 90%. When a microscopic circle of diameter similar to prostatic carcinoma nuclei was digitized at a magnification of 2580 X, perimeter and area measurements differed within or between observers by less than 5% and were more than 95% accurate. In order to calculate accurately and evaluate NRF for use in assessing the prognosis of patients with prostatic carcinoma investigators must precisely describe their digitization system, standardization method and observer reproducibility and accuracy when measuring circles that approximate the projected size of prostatic carcinoma nuclei.
A Syndrome of Methylmalonic Aciduria, Homocystinuria, Megaloblastic Anemia and Neurologic Abnormalities in a Vitamin B12-Deficient Breast-Fed Infant of a Strict Vegetarian (1978)

Original Article from The New England Journal of Medicine — A Syndrome of Methylmalonic Aciduria, Homocystinuria, Megaloblastic Anemia and Neurologic Abnormalities in a Vitamin B12-Deficient Breast-Fed Infant of a Strict Vegetarian
Wavelength-tolerant optical access architectures featuring N-dimensional addressing and cascaded arrayed waveguide gratings (1998)

This paper describes two- and three-stage wavelength routed optical access networks, which offer wavelength tolerance by using coarse passband-flattened arrayed waveguide grating routers. An N-dimensional addressing strategy enables 6912 customers to be bidirectionally accessed with multi-Gb/s data using only 24 wavelengths and 1.6 nm spacing. These architectures are designed to map onto standard access network topologies, allowing elegant upgradability from legacy passive optical network (PON) infrastructures at low cost.
SU11248 is a novel FLT3 tyrosine kinase inhibitor with potent activity in vitro and in vivo (2003)

FLT3 (fms-related tyrosine kinase/Flk2/Stk-2) is a receptor tyrosine kinase (RTK) primarily expressed on hematopoietic cells. In blasts from acute myelogenous leukemia (AML) patients, 2 classes of FLT3 activating mutations have been identified: internal tandem duplication (ITD) mutations in the juxtamembrane domain (25%-30% of patients) and point mutations in the kinase domain activation loop (7%-8% of patients). FLT3-ITD mutations are the most common molecular defect identified in AML and have been shown to be an independent prognostic factor for decreased survival. FLT3-ITD is therefore an attractive molecular target for therapy. SU11248 is a recently described selective inhibitor with selectivity for split kinase domain RTKs, including platelet-derived growth factor receptors, vascular endothelial growth factor receptors, and KIT. We show that SU11248 also has potent activity against wild-type FLT3 (FLT3-WT), FLT3-ITD, and FLT3 activation loop (FLT3-Asp835) mutants in phosphorylation assays. SU11248 inhibits FLT3-driven phosphorylation and induces apoptosis in vitro. In addition, SU11248 inhibits FLT3-induced VEGF production. The in vivo efficacy of SU11248 was investigated in 2 FLT3-ITD models: a subcutaneous tumor xenograft model and a bone marrow engraftment model. We show that SU11248 (20 mg/kg/d) dramatically regresses FLT3-ITD tumors in the subcutaneous tumor xenograft model and prolongs survival in the bone marrow engraftment model. Pharmacokinetic and pharmacodynamic analysis in subcutaneous tumors showed that a single administration of an efficacious drug dose potently inhibits FLT3-ITD phosphorylation for up to 16 hours following a single dose. These results suggest that further exploration of SU11248 activity in AML patients is warranted.
Appearance-based eye gaze estimation (2003)

We present a method for estimating eye gaze direction, which represents a departure from conventional eye gaze estimation methods, the majority of which are based on tracking specific optical phenomena like corneal reflection and the Purkinje images. We employ an appearance manifold model, but instead of using a densely sampled spline to perform the nearest manifold point query, we retain the original set of sparse appearance samples and use linear interpolation among a small subset of samples to approximate the nearest manifold point. The advantage of this approach is that since we are only storing a sparse set of samples, each sample can be a high dimensional vector that retains more representational accuracy than short vectors produced with dimensionality reduction methods. The algorithm was tested with a set of eye images labelled with ground truth point-of-regard coordinates. We have found that the algorithm is capable of estimating eye gaze with a mean angular error of 0.38 degrees, which is comparable to that obtained by commercially available eye trackers.