gebhart/patrepeval huggingface dataset:
Preparation, characterization and properties of nitrogen rich glasses in alkaline earth-Si-O-N systems (2009)

Nitrogen rich glasses in the systems Ca-Si-O-N, Sr-Si-O-N and AE-Ca-Si-O-N (AE = Mg, Sr and Ba) have been prepared using a novel glass-synthesis route. The limits of the glass forming regions in the Ca and Sr systems and substitution limits in the AE-Ca-Si-O-N systems have been determined and physical properties of the glasses measured. Transparent glasses were obtained for a few specific compositions in the Ca-Si-O-N and Mg-Ca-Si-O-N systems. All other glasses were found to be translucent gray to opaque black, with the coloration of the glasses depending on the modifier. Small inclusions of Ca/Sr silicides and, in much smaller amounts, elemental Si are believed to be responsible for their poor transparency. A large glass forming region was found for the Ca-Si-O-N system, with glasses retaining up to 58 e/o N and 42 e/o Ca. In comparison, a more narrow glass forming region was found for the corresponding Sr system, with glasses retaining up to 45 e/o N and 39 e/o Sr. The glass formation was found to depend on reaction kinetics and precursors used. A strong exothermic reaction was observed at temperatures 650–1000oC, providing improved conditions for reaction kinetics upon further heating. Physical property measurements for the Ca and Sr glasses showed that glass transition and crystallization temperatures, viscosity, hardness, Young’s modulus and shear modulus depend strongly on the nitrogen content and that these properties increase approximately linearly with increasing nitrogen content. Glass density and refractive index are also dependent on the modifier element and content, in particular for the Sr glasses. Glasses AE-Ca-Si-O-N, with approximately constant (Ca/AE): Si:O:N ratios, showed that mixed modifier glass properties, such as density, molar volume, glass transition temperature, hardness, refractive index can be related to the effective cation field strength of the modifiers.
Characterization of a modified human tissue plasminogen activator comprising a kringle-2 and a protease domain. (1990)

To study structure/function relationships of tissue plasminogen activator (t-PA) activity, one of the simplest modified t-PA structures to activate plasminogen in a fibrin-dependent manner was obtained by constructing an expression vector that deleted amino acid residues 4-175 from the full-length sequence of t-PA. The expression plasmid was introduced into a Syrian hamster cell line, and stable recombinant transformants, producing high levels of the modified plasminogen activator, were isolated. The resulting molecule, mt-PA-6, comprising the second kringle and serine protease domains of t-PA, produced a doublet of plasminogen activator activity having molecular masses of 40 and 42 kDa. The one-chain mt-PA-6 produced by cultured Syrian hamster cells was purified in high yield by affinity and size exclusion chromatography. The purified mt-PA-6 displayed the same two types of microheterogeneity observed for t-PA. NH2-terminal amino acid sequencing demonstrated that one-chain mt-PA-6 existed in both a GAR and a des-GAR form. Purified mt-PA-6 also existed in two glycosylation forms that accounted for the 40- and 42-kDa doublet of activity produced by the cultured Syrian hamster cells. Separation of these two forms by hydrophobic interaction chromatography and subsequent tryptic peptide mapping demonstrated that both forms contained N-linked glycosylation at Asn448; in addition, some mt-PA-6 molecules were also glycosylated at Asn184. Plasmin treatment of one-chain mt-PA-6 converted it to a two-chain molecule by cleavage of the Arg275-Ile276 bond. This two-chain mt-PA-6, like t-PA, had increased amidolytic activity. The fibrinolytic specific activities of the one- and two-chain forms of mt-PA-6 were similar and twice that of t-PA. The plasminogen activator activity of one-chain mt-PA-6 was enhanced greater than 80-fold by CNBr fragments of fibrinogen, and the one-chain enzyme lysed human clots in vitro in a dose-dependent manner. The ability to produce and purify a structurally simple plasminogen activator with desirable fibrinolytic properties may aid in the development of a superior thrombolytic agent for the treatment of acute myocardial infarction.
KDR activation in astrocytic neoplasms (1999)

The findings of the current study strongly support the hypothesis that the onset of angiogenesis is an important event during the disease progression of gliomas.
Preparation of Arabidopsis mesophyll protoplasts with high rates of photosynthesis (2007)

A simple and quick method is described for rapid isolation of metabolically active mesophyll protoplasts from leaves of Arabidopsis thaliana . The optimal composition of the digestion medium, period of digestion and stability of protoplast preparation were examined. A large number of protoplasts could be prepared within an hour. The isolated protoplasts were intact, stable and metabolically very active, as indicated by their high rates of photosynthetic oxygen evolution. The important factors during the preparation of protoplasts are short time of digestion, composition of medium, use of nylon nets for filtration, centrifugation at low speed and use of pH 7.0 for storage. The highest rate of photosynthesis obtained in these experiments was 130 ± 4 μmol O 2 evolved mg −1 Chl h −1 , at 1 m M sodium bicarbonate and at a light intensity of 600 μE m −2 s −1 . The present technique of isolation can be very useful for making Arabidopsis protoplasts for studies on not only metabolic processes, such as photosynthesis, but also metabolomics, proteomics and genomics.
The Short Apical Membrane Half-life of Rescued ΔF508-Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Results from Accelerated Endocytosis of ΔF508-CFTR in Polarized Human Airway Epithelial Cells (2005)

The most common mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene in individuals with cystic fibrosis, DeltaF508, causes retention of DeltaF508-CFTR in the endoplasmic reticulum and leads to the absence of CFTR Cl(-) channels in the apical plasma membrane. Rescue of DeltaF508-CFTR by reduced temperature or chemical means reveals that the DeltaF508 mutation reduces the half-life of DeltaF508-CFTR in the apical plasma membrane. Because DeltaF508-CFTR retains some Cl(-) channel activity, increased expression of DeltaF508-CFTR in the apical membrane could serve as a potential therapeutic approach for cystic fibrosis. However, little is known about the mechanisms responsible for the short apical membrane half-life of DeltaF508-CFTR in polarized human airway epithelial cells. Accordingly, the goal of this study was to determine the cellular defects in the trafficking of rescued DeltaF508-CFTR that lead to the decreased apical membrane half-life of DeltaF508-CFTR in polarized human airway epithelial cells. We report that in polarized human airway epithelial cells (CFBE41o-) the DeltaF508 mutation increased endocytosis of CFTR from the apical membrane without causing a global endocytic defect or affecting the endocytic recycling of CFTR in the Rab11a-specific apical recycling compartment.
Intermediate-representation recovery from low-level code (2006)

The goal of our work is to create tools that an analyst can use to understand the workings of COTS components, plugins, mobile code, and DLLs, as well as memory snapshots of worms and virus-infected code. This paper describes how static analysis provides techniques that can be used to recover intermediate representations that are similar to those that can be created for a program written in a high-level language.
AUTOMATED RFID-BASED IDENTIFICATION SYSTEM FOR STEEL COILS (2012)

This paper describes the radio frequency identification (RFID)-based steel coil identification system for supply chain management in the steel and iron industry. During crane operation, coil information is automatically updated by reading an RFID tag which is attached to the coil. One of the technical challenges associated with the RFID-based coil identification is the fall of the identification performance due to neighboring metallic objects. In order to cope with this problem, a system was developed in two directions. First, an effective tag attachment method considering the work process and the environmental conditions was proposed. Second, an antenna case was developed to improve the reading performance by minimizing the influence from the attached surface and focusing the RF signal to the target tag. The simulation and experimental results at the POSCO steel company verify that the proposed system can sense the target RFID tag successfully.
Quantum Computing and Quantum Measurement with Mesoscopic Josephson Junctions (2000)

Recent experimental demonstrations of quantum coherence of the charge and flux states of Josephson junctions show that the quantum Josephson dynamics can be used to develop scalable quantum logic circuits. In this work, I review the basic concepts of Josephson tunneling and Josephson-junction qubits, and discuss two problems of this tunneling motivated by quantum computing applications. One is the theory of photon-assisted resonant flux tunneling in SQUID systems used to demonstrate quantum coherence of flux. Another is the problem of quantum measurement of charge with the SET electrometer. It is shown that the SET electrometer at the Coulomb blockade threshold is the quantum-limited detector with energy sensitivity reaching ħ/√3 in the resonant-tunneling regime.
ATP6S1 elicits potent humoral responses associated with immune-mediated tumor destruction (2002)

An important goal of cancer immunology is the identification of antigens associated with tumor destruction. Vaccination with irradiated tumor cells engineered to secrete granulocyte/macrophage colony-stimulating factor (GM-CSF) generates potent, specific, and long-lasting antitumor immunity in multiple murine tumor models. A phase I clinical trial of this vaccination strategy in patients with advanced melanoma demonstrated the consistent induction of dense CD4(+) and CD8(+) T lymphocyte and plasma cell infiltrates in distant metastases, resulting in extensive tumor destruction, fibrosis, and edema. Antimelanoma antibody and cytotoxic T cell responses were associated with tumor cell death. To characterize the targets of these responses, we screened an autologous cDNA expression library prepared from a densely infiltrated metastasis with postvaccination sera from a long-term responding patient. High-titer IgG antibodies detected ATP6S1, a putative accessory unit of the vacuolar H(+)-ATPase complex. A longitudinal analysis of this patient revealed an association between the vaccine-induced increase in antibodies to ATP6S1 and tumor destruction. Three additional vaccinated melanoma patients and three metastatic non-small cell lung carcinoma patients vaccinated with autologous GM-CSF-secreting tumor cells similarly showed a correlation between humoral responses to ATP6S1 and tumor destruction. Moreover, a chronic myelogenous leukemia patient who experienced a complete remission after CD4(+) donor lymphocyte infusions also developed high-titer antibodies to ATP6S1. Lastly, vaccination with GM-CSF-secreting B16 melanoma cells stimulated high-titer antibodies to ATPS1 in a murine model. Taken together, these findings demonstrate that potent humoral responses to ATP6S1 are associated with immune-mediated destruction of diverse tumors.
Extracellular Regulation of Myostatin: A Molecular Rheostat for Muscle Mass (2010)

Myostatin (MSTN) is a transforming growth factor-ß family member that plays a critical role in regulating skeletal muscle mass. Genetic studies in multiple species have demonstrated that mutations in the Mstn gene lead to dramatic and widespread increases in muscle mass as a result of a combination of increased fiber numbers and increased fiber sizes. MSTN inhibitors have also been shown to cause significant increases in muscle growth when administered to adult mice. As a result, there has been an extensive effort to understand the mechanisms underlying MSTN regulation and activity with the goal of developing the most effective strategies for targeting this signaling pathway for clinical applications. Here, I review the current state of knowledge regarding the regulation of MSTN extracellularly by binding proteins and discuss the implications of these findings both with respect to the fundamental physiological role that MSTN plays in regulating tissue homeostasis and with respect to the development of therapeutic agents to combat muscle loss.
RETRACTED: Increased muscle PGC-1α expression protects from sarcopenia and metabolic disease during aging (2009)

Aging is a major risk factor for metabolic disease and loss of skeletal muscle mass and strength, a condition known as sarcopenia. Both conditions present a major health burden to the elderly population. Here, we analyzed the effect of mildly increased PGC-1alpha expression in skeletal muscle during aging. We found that transgenic MCK-PGC-1alpha animals had preserved mitochondrial function, neuromuscular junctions, and muscle integrity during aging. Increased PGC-1alpha levels in skeletal muscle prevented muscle wasting by reducing apoptosis, autophagy, and proteasome degradation. The preservation of muscle integrity and function in MCK-PGC-1alpha animals resulted in significantly improved whole-body health; both the loss of bone mineral density and the increase of systemic chronic inflammation, observed during normal aging, were prevented. Importantly, MCK-PGC-1alpha animals also showed improved metabolic responses as evident by increased insulin sensitivity and insulin signaling in aged mice. Our results highlight the importance of intact muscle function and metabolism for whole-body homeostasis and indicate that modulation of PGC-1alpha levels in skeletal muscle presents an avenue for the prevention and treatment of a group of age-related disorders.
Increased expression of Gi alpha 2 in mouse embryo stem cells promotes terminal differentiation to adipocytes (1993)

The level of Gs alpha activity has been shown to modulate the rate of adipogenesis in mouse embryo fibroblast 3T3-L1 cells (H.-Y. Wang, D. C. Watkins, and C. C. Malbon. Nature Lond. 358: 334-337, 1992). For the current work the role of Gi alpha 2, a G protein mediator of inhibitory control of adenylyl cyclase, in regulating terminal differentiation of these cells was explored by stable transfection of fibroblasts expressing wild-type and a constitutively active mutant of Gi alpha 2 (Q205L). Under the influence of the cytomegalovirus promoter, the expression vector yielded a 1.7-fold (Q205L mutant Gi alpha 2) and 2.2-fold (wild-type Gi alpha 2) increase in steady-state levels of these G protein alpha-subunits. Elevation of Gi alpha 2 expression or expression of constitutively active Gi alpha 2 (Q205L) promoted lipid accumulation in these clones, the hallmark of terminal differentiation of 3T3-L1 fibroblasts to adipocytes. Increasing Gi alpha 2 activity promotes adipogenic conversion, as was previously observed by decreasing Gs alpha either by inducers of differentiation or by oligodeoxynucleotides antisense to Gs alpha. Thus Gs alpha and Gi alpha 2 are shown to be counterregulatory with respect to promoting differentiation of 3T3-L1 mouse embryo fibroblasts to adipocytes in the absence of exogenously added inducers of differentiation. This is the first report demonstrating the induction of terminal differentiation of cells by the overexpression of a G protein alpha-subunit, further implicating G proteins as regulators of complex biological responses such as adipogenesis.
Correlation analysis of riboflavin, RFT2 and Helicobater pylori in gastric carcinoma. (2015)

The results indicate that RFT2 plays an important role in gastric carcinogenesis by modulating riboflavin absorption. H.pylori infection affects plasma riboflavin level and the prognosis of patients with gastric cancer.
Linear clinical progression, independent of age of onset, in Niemann–Pick disease, type C (2009)

Niemann-Pick disease, type C is a neurodegenerative, lysosomal storage disorder with a broad clinical spectrum and a variable age of onset. The absence of a universally accepted clinical outcome measure is an impediment to the design of a therapeutic trial for NPC. Thus, we developed a clinical severity scale to characterize and quantify disease progression. Clinical signs and symptoms in nine major (ambulation, cognition, eye movement, fine motor, hearing, memory, seizures, speech, and swallowing) and eight minor (auditory brainstem response, behavior, gelastic cataplexy, hyperreflexia, incontinence, narcolepsy, psychiatric, and respiratory problems) domains were scored. Data were collected from 18 current NPC patients and were extracted from records of 19 patients. Both patient cohorts showed a linear increase in severity scores over time. Cross-sectional evaluation of current patients showed a linear increase in the severity score. Longitudinal chart review of historical data demonstrated that although age of onset varied significantly, the rate of progression appeared linear, independent of age of onset, and similar in all patients. Combining the data from both cohorts, disease progression could be modeled by the following equation: ŝ(t0+x) = ŝ(t0) + 1.87x; where ŝ(t0) is the initial score and ŝ(t0+x) is the predicted future score after x years. Our observation that disease progression is similar across patients and independent of age of onset is consistent with a biphasic pathological model for NPC. This scale may prove useful in the characterization of potential biomarkers, and as an outcome measure to monitor disease progression in NPC patients.
Negative regulatory sequences in the lin-14 3'-untranslated region are necessary to generate a temporal switch during Caenorhabditis elegans development. (1991)

The heterchronic gene lin-14 controls the temporal sequence of developmental events in the Caenorhabditis elegans postembryonic cell lineage. It encodes a nuclear protein that normally is present in most somatic cells of late embryos and L1 larvae but is absent at later stages. Two lin-14 gain-of-function mutations delete 3'-untranslated sequences causing an inappropriately high level of the lin-14 nuclear protein late in development. These mutations identify a negative regulatory element that controls the formation of the lin-14 protein temporal gradient. The 21-kb lin-14 gene is differentially spliced to generate three lin-14 transcripts that encode protein products with variable amino-terminal regions and a constant carboxy-terminal region. The sequence of the gene revealed no protein sequence similarity to any proteins in various data bases.
Dynamic analysis of a genomic island in Magnetospirillum sp. strain AMB‐1 reveals how magnetosome synthesis developed (2006)

The entire structure of a 98 kb genomic region that abounds in genes related to magnetosome synthesis was first described in the Magnetospirillum sp. strain AMB-1. The deletion of this 98 kb genomic region and the circular form after excision from the chromosome was detected by PCR amplification. This strongly suggests that the region has undergone a lateral gene transfer. The region has the characteristics of a genomic island: low GC content, location between two repetitive sequences, and the presence of an integrase in the flanking region of the first repetitive sequence. This 98 kb genomic region has the potential for transfer by the integrase activity. Comparative genome analysis revealed other regions with a high concentration of orthologs in magnetic bacteria besides the 98 kb region, and magnetosome synthesis seemed to need not only the exogenous 98 kb region, but also other orthologs and individually originating genes.
Learning gender with support faces (2002)

Nonlinear support vector machines (SVMs) are investigated for appearance-based gender classification with low-resolution "thumbnail" faces processed from 1,755 images from the FERET (FacE REcognition Technology) face database. The performance of SVMs (3.4% error) is shown to be superior to traditional pattern classifiers (linear, quadratic, Fisher linear discriminant, nearest-neighbor) as well as more modern techniques, such as radial basis function (RBF) classifiers and large ensemble-RBF networks. Furthermore, the difference in classification performance with low-resolution "thumbnails" (21/spl times/12 pixels) and the corresponding higher-resolution images (84/spl times/48 pixels) was found to be only 1%, thus demonstrating robustness and stability with respect to scale and the degree of facial detail.
High‐speed photodamage cell selection using bromodeoxyuridine/Hoechst 33342 photosensitized cell killing (1988)

One of the major drawbacks of droplet sorting in a flow cytometer is the relatively low sorting speed. Thus, we have developed an alternative, faster sorting technique: photodamage cell sorting. In a photodamage cell sorter all unwanted cells, as detected with the first, measuring laser, are killed with the second, damaging laser. Thus, the cells need to be photosensitive to the second laser. In addition, a mechanism is needed to switch this laser on and off based on the sorting criteria. In our photodamage cell sorter, the ZAPPER, we use an acousto-optic crystal to switch the laser beam. Cells are made photosensitive by vital staining with photosensitizers. With cells grown in the presence of 5-bromo-2'-deoxyuridine (BrdUrd) and stained with Hoechst 33342 (H42) at least a 5-decade cell reduction is accomplished after irradiation with 400 mW UV light. With this system, sorting rates have been achieved of 30,000 cells per second. Due to the selection based on photodynamic killing, this sorting technique is restricted to the selection of viable cells. Photodamage cell sorting seems well suited for isolating viable cells occurring in low percentages or for the sorting of large numbers of cells. Another application can be the sorting of large or fragile cells.
Purely Functional Data Structures (1998)

Most books on data structures assume an imperative language like C or C++. However, data structures for these languages do not always translate well to functional languages such as Standard ML, Haskell, or Scheme. This book describes data structures from the point of view of functional languages, with examples, and presents design techniques so that programmers can develop their own functional data structures. It includes both classical data structures, such as red-black trees and binomial queues, and a host of new data structures developed exclusively for functional languages. All source code is given in Standard ML and Haskell, and most of the programs can easily be adapted to other functional languages. This handy reference for professional programmers working with functional languages can also be used as a tutorial or for self-study.