gebhart/patrepeval huggingface dataset:
SNP Chip Analysis of Myelodysplastic Syndromes Disclosed High Frequency of Uniparental Disomy and a Novel Dominant Mutation as the Target of 11q UPD. (2007)

Abstract Myelodysplastic syndromes (MDS) are clonal disorders of hematopoietic progenitors characterized by ineffective hematopoiesis and high propensity to leukemias. One of the prominent features of MDS is the high frequency of copy number changes that result in genetic imbalances. Loss of heterozygosity (LOH) may be also closely related to the pathogenesis of MDS, but genome-wide LOH mapping of MDS is still unexplored. We developed a robust program, CNAG/AsCNAR, to explore genetic alterations of the cancer genome, using Affymetrix® GeneChip® SNP arrays. Implementing a series of data compensation algorithms, it enables accurate copy number estimation in cancer genomes. In addition, by sensing subtle distortions in allele-specific signals caused by allelic imbalance using anonymous controls, sensitive detection of LOH is enabled with accurate determination of allele-specific copy numbers even in the face of up to 70% normal cell contamination. Using GeneChip with CNAG/AsCNAR analysis, we analyzed a total of 172 MDS and MDS/MPD specimens in order to identify relevant potential target genes for development of MDS. Nnumerous copy number alterations were sensitively detected in MDS genomes, however more interesting finding was the high frequency of copy number neutral LOH (Uniparental disomy, UPD) observed in 51 of 172 (∼30%) MDS cases. They preferentially involved 1p, 1q, 4q, 7q, 11q, 17p and other chromosomal segments, which were associated with homozygous mutations of tumor suppressor genes and oncogenes, including TP53 (17p UPD), AML1/RUNX1 (in 21q UPD), Nras and cMPL (1p UPD), JAK-2 (9p UPD), and FLT3 (13q UPD). In addition we identified the target of 11q UPD, internally called mds11, which showed homozygous mutations in 8 of 9 MDS cases with 11q UPD (CMML=5, RAEB=3, overt leukemia=1). Mutations of mds11 were rare in non-11q UPD cases (1/163), demonstrating the mutation is tightly linked to 11q UPD. NIH-3T3 cells transduced with these mutatnts showed increased colony formation in soft agar and were tumorigenic in nude mice. To investigate the functions of these mutants in hematopoietic cells, we introduced this mutant gene into c-kit(+)Sca1(+)Lin(−) murine bone marrow cells, and examined their replating capacities in methylcellurose culture, where all the mutants showed enhanced capacities. These observations also present a novel examples that duplication of a dominant mutation (11qUPD) with exclusioin of the wild-type allele is an important mechanism of tumorigenesis. In conclusion, UPD is an important mechanism of development of MDS, in which both gain-of-function and loss-of-function mutations are duplicated with exclusion of wild-type allele. Analysis of 11q UPD disclosed novel gain-of-function mutations. Identification of the targets of UPDs in 1q, 4q and 7q should also be important to gain a novel insight into the pathogenesis of MDS.
Secreted frizzled related proteins inhibit fibrosis in vitro but appear redundant in vivo (2014)

Although SFRP1 counteracts the effect of TGFβ1 in pulmonary cells in vitro; loss of neither SFRP1 nor FRZB alters fibrotic outcomes in the lungs in vivo. The lack of in vivo effect in the absence of specific SFRPs suggests functional redundancy within this family of Wnt antagonists.
A Chemical Approach to the Identification of Tensin-Binding Proteins (2007)

Many protein-protein interactions are mediated by small modular domains, which recognize short peptide motifs in their partner proteins. However, for the great majority of these domains, the identity of their partner proteins remains unknown. In this work, a chemical/bioinformatics approach has been developed to identify phosphotyrosyl (pY) proteins that bind to tensin, a protein involved in the formation of actin cytoskeleton and signal transduction. A pY peptide library was chemically synthesized and screened against the Src homology 2 (SH2) domain of tensin to identify the peptide motifs that bind to the SH2 domain. Next, protein databases were searched for proteins containing the SH2 domain-binding peptide motifs. Finally, the potential tensin-binding proteins were confirmed (or disproved) by in vitro pull-down and coimmunoprecipitation assays. This procedure identified phosphoinositide-dependent kinase-1 and downstream of tyrosine kinase 2 as novel tensin-binding proteins. In addition, a cell-permeable pY peptide was designed as tensin SH2 domain inhibitor, which caused the disruption of actin filaments in NIH 3T3 cells. This method should be generally applicable to other modular domains that recognize small peptide motifs.
Compared to Subcutaneous Tenofovir, Oral Tenofovir Disoproxyl Fumarate Administration Preferentially Concentrates the Drug into Gut-Associated Lymphoid Cells in Simian Immunodeficiency Virus-Infected Macaques (2012)

To compare tissue-based pharmacokinetics and efficacy of oral tenofovir disoproxyl fumarate (TDF) versus subcutaneous tenofovir (TFV), macaques were treated for 2 weeks starting 1 week after simian immunodeficiency virus inoculation. Despite lower plasma TFV levels in the oral TDF arm, similar TFV diphosphate levels and antiviral activities were measured in lymphoid cells of most tissues. In intestinal tissues, however, oral TDF resulted in higher active drug levels, associated with lower virus levels and better immune preservation.
Generalized rainbows and unfolded glories of oblate drops: organization for multiple internal reflections and extension of cusps into Alexander's dark band (1994)

Oblate drops of water can produce caustics where, unlike a simple Airy caustic, more than two rays merge. We extend previous treatments of generalized primary rainbows based on catastrophe optics [Opt. Lett. 10, 588 (1985); Proc. R. Soc. (London) A 438, 397 (1992)] to rays having (p - 1) = 2 to 5 internal reflections. The analysis is for a horizontally illuminated ellipsoid with a vertical symmetry axis. Aspect ratios causing a vanishing of the vertical curvature at the equator for the outgoing wave front are found from generalized ray tracing. In response to infinitesimal deformation, the axial caustic of real glory rays unfolds producing cusps. Laboratory observations with laser illumination demonstrate that cusps resulting from rays with five internal reflections extend into Alexander's dark band when the drop's aspect ratio is near 1.08. The evolution of this p = 6 scattering pattern as cusps meet the quinary rainbow is suggestive of an E(6) catastrophe. For ellipsoids of varying aspect ratio and refractive index N, there is an organizing singularity associated with an exceptionally flat outgoing wave front from spheres with N = p.
Progression of atherosclerosis: the cell biology (1987)

The sequence of events during atherogenesis has been deduced from serial changes that occur in animal models of atherosclerosis and from autopsy studies in humans. In vitro studies have provided insight into the mechanisms of the major features of atherosclerosis. One of the earliest events in atherogenesis is adhesion of monocytes to intact endothelium, followed by migration along a chemotactic gradient into the intima, where they become macrophages. These events appear to be modulated by lipoproteins. Subendothelial macrophages accumulate cholesteryl ester and become the foam cells of the fatty streak. Smooth muscle cells proliferate in response to stimulation by mitogens. Later, intimal macrophages and smooth muscle cells also accumulate lipid, by apparently different mechanisms. Later, lipoproteins accumulate in the extracellular space where they are bound to proteoglycans. Strategies to prevent atherosclerosis should be targeted towards specific events in the cell biology of this disease.
Studies of Organic Catalytic Reactions. VI. The Function of Pyridine and Copper in the Rosenmund-von Braun Reaction (1968)

Abstract The Rosenmund-von Braun reaction with aryl halide, with its Ar-X+CuCN-Base→Ar-CN+CuX-Base, has been studied in nitrobenzene in place of an organic base at 160–180°C. The free nitriles formed during the reaction were determined exactly by gas chromatography. In the use of bases with suitable coordination forces to CuCN, the reactivity of the base for the substitution was found to be in the order: prim.&amp;gt;sec.&amp;gt;tert. A steric hindrance of the base was observed, and the reactivity of the pyridine homologue followed the order: pyridine&amp;gt;quinoline&amp;gt;α-picoline&amp;gt;2, 6-lutidine. Ortho-substituted groups in the halobenzene seem to manifest no steric hindrance on the reaction. From the results of the kinetic study, it can be said that CuCN participates in the reaction essentially in the form of a Base(1 mol)-CuCN complex. The overall reaction is second-order, dc⁄dt=k[Complex][Ar-X]. The rate-determining step may be in the halogen exchange stage in the intervening complex, Base-CuCN-Ar-X, where the plane including CN-Cu-X and that of the benzene ring may be nearly perpendicular to each other. When an excess of CuCN over the base is used, the base is liberated from the Base-CuX complex, after the displacement, and then coordinates to the unreacted CuCN again.
Imoox – Eine Mooc-Plattform Mit Oer? (2018)

Die TU Graz betreibt zusammen mit der Universität Graz seit 2014 die nachwievor einzige MOOC-Plattform in Österreich mit dem Namen iMooX (https://imoox.at). Hier werden freie Online-Kurse vorwiegend in deutscher Sprache frei zur Verfügung gestellt und damit dem öffentlichen Bildungsauftrag der Universität nachgekommen („Third Mission“). Darüber hinaus haben sich die beiden Universitäten dazu verpflichtet, dass sämtliche Lehr- und Lerninhalte unter einer Creative-Commons-Lizenz anzubieten sind, um eine möglichste weite Verbreitung und auch Anwendung dieser in andern Bildungskontexten zu ermöglichen. Dies unterscheidet die Plattform deutlich von ihren internationalen Konkurrenten (Udacitx, edX, ...). In dem Vortrag sollen mehrere Fragen angesprochen werden: Warum ist es notwendig, die Bildungsinhalte offen zu lizenzieren bzw. als OER anzubieten? Welche Effekte der Verbreitung und Anwendung der offenen Online-Kurse konnten bisher beobachtet werden? Welche Änderungen im Geschäftsmodell ergeben sich dadurch, da z. B. ein direkter Verkauf der Inhalte nicht möglich ist? Es sollen die bisherigen Erfahrungen und die positiven Effekte die durch OER erzielt werden übersichtlich dargestellt werden. Insbesondere zeigt sich, dass durch die offene Lizenzierung anderen Bildungsträger möglich ist, die Inhalte nicht nur zu verwenden, sondern auch mit neuen didaktischen Konzepten (z. B. Inverse Blended Learning) einzusetzen. Neben der Rechtssicherheit bilden also neue Geschäftsmodelle, neue didaktische Konzepte und neue Möglichkeiten der Verbreitung von Bildungsangeboten den Schwerpunkt des Vortrages.
Asynchronous Cellular Automaton-Based Neuron: Theoretical Analysis and On-FPGA Learning (2013)

A generalized asynchronous cellular automaton-based neuron model is a special kind of cellular automaton that is designed to mimic the nonlinear dynamics of neurons. The model can be implemented as an asynchronous sequential logic circuit and its control parameter is the pattern of wires among the circuit elements that is adjustable after implementation in a field-programmable gate array (FPGA) device. In this paper, a novel theoretical analysis method for the model is presented. Using this method, stabilities of neuron-like orbits and occurrence mechanisms of neuron-like bifurcations of the model are clarified theoretically. Also, a novel learning algorithm for the model is presented. An equivalent experiment shows that an FPGA-implemented learning algorithm enables an FPGA-implemented model to automatically reproduce typical nonlinear responses and occurrence mechanisms observed in biological and model neurons.
Linear Generalized Synchronization of Chaotic Systems with Adaptive Control (2006)

A new method—adaptive control for constructing a response system was developed to implement linear generalized synchronization(GS)with the drive system.The method was proved to be effective based on the Lyapunov stability theory and Barbalat lemma.The Chua's circuit was taken for illustration and verification.Furthermore,the results of the numerical simulation indicate that the method driven here can be applied well to the secure communication.
Biobarriers for groundwater treatment: a review (2012)

Biobarriers (BBs) are a new type of in situ technology for the remediation of contaminated groundwater. In recent years, this remediation technique has been more and more used in place of traditional Pump & Treat systems or other in situ technologies both in the USA and Europe. This work reviews the main experiences of BBs. The literature contains reports about tests and application at different scales (laboratory, pilot and full scale), which have been analyzed according to the aim of the study, the operative conditions adopted, the filling material, the inoculation procedure, the electron acceptor and the nutrient delivery systems. Operative conditions were extremely varied. Lab scale experiments pointed out good results in terms of pollutant removal efficiency. Pilot scale tests and full-scale applications confirmed the results obtained at lab scale, but also pointed out the importance of design for a proficient remediation system. The experiences underlined some possible critical issues: (a) the filling material must ensure proper hydraulic properties, but it also must be capable of keeping biomass in the reactive zone; (b) inoculation is a critical step and measurements should be carried out to check the initial distribution of microorganisms and its evolution over time; (c) electron acceptor and nutrient supply is usually required, but oxygenation into anaerobic aquifers can be critical.
Use of Mycophenolate in Pediatric Liver Transplantation (1998)

552 Mycophenolate mofetil (MMF) is a new immunosuppressant that may diminish the frequency of rejection post liver transplant (LTx) and permit the use of lower doses of steroids which induce growth retardation in children. Purpose - To examine whether addition of MMF immediately after Ltx is associated with lower frequency of rejection and less prednisone(Pred). Methods - We retrospectively examined the charts of the last 33 Pediatric Ltx done over 5 years. MMF was used with FK-506 or Cyclosporin for the past 20 months. MMF dose was 600 mg/kg/dose twice daily, tapered 50% at 3 months, stopped at 6 months. Results - Overall, there was no significant difference between patients (pt) given MMFor not with respect to age, weight, dose of Pred(1,3,6 and 12 months post LTx), and number of rejection episodes(Table). Severity of rejection was not different between groups. Number of infections (CMV, EBV, HCV) and use of OKT3 were not different among groups. MMF was tolerated well.Conclusions - In this retrospective study in Pediatric LTx patients, addition of MMF immediately after surgery to either FK-506 or Cyclosporine did not result in fewer episodes of rejection or lower doses of Pred during the first year after transplant. A randomized prospective study is warranted.
Application Security: Building in Security during the Development Stage (2004)

Abstract Early networks — such as the postal system — relied on the manual delivery of messages to the intended recipient. Message integrity and confidentiality were ensured using sealed envelopes and, in some cases, primitive forms of cryptography. As electronic networks evolved, so did cryptography. New algorithms and protocols were developed, eventually to the point that today direct attacks on encrypted messages are extremely rare.
Engineering Nutritionally Improved Edible Plant Oils (2023)

In contrast to traditional breeding, which relies on the identification of mutants, metabolic engineering provides a new platform to modify the oil composition in oil crops for improved nutrition. By altering endogenous genes involved in the biosynthesis pathways, it is possible to modify edible plant oils to increase the content of desired components or reduce the content of undesirable components. However, introduction of novel nutritional components such as omega-3 long-chain polyunsaturated fatty acids needs transgenic expression of novel genes in crops. Despite formidable challenges, significant progress in engineering nutritionally improved edible plant oils has recently been achieved, with some commercial products now on the market.
Improved Performance of GaAs-Based Terahertz Emitters via Surface Passivation and Silicon Nitride Encapsulation (2010)

We have improved the stability and performance of terahertz (THz) photoconductive (Auston) switches using a combination of (NH <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$_{4}$</tex></formula> ) <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX"> $_{2}$</tex></formula> S surface passivation (SP) and silicon nitride (Si <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$_{3}$</tex> </formula> N <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$_{4}$</tex></formula> ) encapsulation. The influences of SP and encapsulation on the ultrafast electron dynamics in GaAs were examined using THz emission spectroscopy and optical pump–THz probe spectroscopy. The power of THz radiation from the surface of photoexcited GaAs increased by a factor of 5 after passivation and encapsulation, while the process lengthened the trapping time for photoexcited charge carriers. By fabricating and assessing the performance of photoconductive switches, we found that passivation and encapsulation increased the average THz power generated fourfold.
PMTest (2019)

Recent non-volatile memory technologies such as 3D XPoint and NVDIMMs have enabled persistent memory (PM) systems that can manipulate persistent data directly in memory. This advancement of memory technology has spurred the development of a new set of crash-consistent software (CCS) for PM - applications that can recover persistent data from memory in a consistent state in the event of a crash (e.g., power failure). CCS developed for persistent memory ranges from kernel modules to user-space libraries and custom applications. However, ensuring crash consistency in CCS is difficult and error-prone. Programmers typically employ low-level hardware primitives or transactional libraries to enforce ordering and durability guarantees that are required for ensuring crash consistency. Unfortunately, hardware can reorder instructions at runtime, making it difficult for the programmers to test whether the implementation enforces the correct ordering and durability guarantees. We believe that there is an urgent need for developing a testing framework that helps programmers identify crash consistency bugs in their CCS. We find that prior testing tools lack generality, i.e., they work only for one specific CCS or memory persistency model and/or introduce significant performance overhead. To overcome these drawbacks, we propose PMTest (available at https://pmtest.persistentmemory.org), a crash consistency testing framework that is both flexible and fast. PMTest provides flexibility by providing two basic assertion-like software checkers to test two fundamental characteristics of all CCS: the ordering and durability guarantee. These checkers can also serve as the building blocks of other application-specific, high-level checkers. PMTest enables fast testing by deducing the persist order without exhausting all possible orders. In the evaluation with eight programs, PMTest not only identified 45 synthetic crash consistency bugs, but also detected 3 new bugs in a file system (PMFS) and in applications developed using a transactional library (PMDK), while on average being 7.1× faster than the state-of-the-art tool.
Gateway Binary Vectors with the Bialaphos Resistance Gene,bar, as a Selection Marker for Plant Transformation (2010)

We constructed two series of Gateway binary vectors, pGWBs and R4pGWBs, possessing the bialaphos resistance gene (bar) as a selection marker for plant transformation. The reporters and tags employed in this system are sGFP, GUS, LUC, EYFP, ECFP, G3GFP, mRFP, TagRFP, 6xHis, FLAG, 3xHA, 4xMyc, 10xMyc, GST, T7 and TAP. Selection of Arabidopsis transformants with BASTA was successfully carried out using both plate-grown and soil-grown seedlings. Transformed rice calli and suspension-cultured tobacco cells were selected on plates containing BASTA or glufosinate-ammonium. These vectors are compatible with existing pGWB and R4pGWB vectors carrying kanamycin and hygromycin B resistance.
Simplifying Collection of Corneal Specimens in Cases of Suspected Bacterial Keratitis (2003)

Identification of the causative organisms in suspected bacterial keratitis traditionally involves collecting multiple corneal scrapes, which are plated directly onto different solid agar culture media. Difficulties have been reported with this practice, so the development of a simpler diagnostic method in suspected bacterial keratitis would be useful. It is unclear whether a single corneal scrape sent to the microbiology laboratory in a liquid transport culture medium (indirect method) is as reliable for the diagnosis of bacterial keratitis as inoculation of multiple scrapes directly onto agar plates (direct method). To investigate this, bacterial recovery was assessed following transfer and transport of different concentrations and types of bacteria from an artificially contaminated surgical blade into brain heart infusion (BHI). Bacterial recovery rates between the proposed (indirect) and standard (direct) method were then compared after the in vitro inoculation of pig corneas and following specimen collection in patients with presumed bacterial ulcerative keratitis. Recovery of bacteria from contaminated surgical blades was found to be the same from both solid and liquid culture media. There was no significant difference in the numbers of positive cultures from solid (direct) and liquid (indirect) culture media, both in the experimental pig cornea inoculation study (P = 0.34) and in experiments with patients with clinical infections (P = 0.4), with an 85.2% agreement between methods (kappa = 0.61, P < 0.0001). In conclusion, therefore, the collection of two corneal scrapes, one used for Gram staining and the other transported in BHI followed by plating and subculturing in an enrichment medium, provides a simple method for the investigation of presumed bacterial keratitis.