gebhart/patrepeval huggingface dataset:
LeProT1, a Transporter for Proline, Glycine Betaine, and γ-Amino Butyric Acid in Tomato Pollen (1999)

During maturation, pollen undergoes a period of dehydration accompanied by the accumulation of compatible solutes. Solute import across the pollen plasma membrane, which occurs via proteinaceous transporters, is required to support pollen development and also for subsequent germination and pollen tube growth. Analysis of the free amino acid composition of various tissues in tomato revealed that the proline content in flowers was 60 times higher than in any other organ analyzed. Within the floral organs, proline was confined predominantly to pollen, where it represented >70% of total free amino acids. Uptake experiments demonstrated that mature as well as germinated pollen rapidly take up proline. To identify proline transporters in tomato pollen, we isolated genes homologous to Arabidopsis proline transporters. LeProT1 was specifically expressed both in mature and germinating pollen, as demonstrated by RNA in situ hybridization. Expression in a yeast mutant demonstrated that LeProT1 transports proline and gamma-amino butyric acid with low affinity and glycine betaine with high affinity. Direct uptake and competition studies demonstrate that LeProT1 constitutes a general transporter for compatible solutes.
Mechanical, dielectric, and electromechanical properties of silicone dielectric elastomer actuators (2013)

ABSTRACT Silicone elastomer actuators were investigated to develop a simple and industrially scalable product with improved mechanical properties, such as a low modulus, high tearing strength, and good resilience, and enhanced electromechanical actuation properties. Silicone elastomers were fabricated via a hydrosilylation addition reaction with a vinyl‐end‐functionalized poly(dimethyl siloxane) (V), a multivinyl‐functionalized silicone resin, and a crosslinker in the presence of a platinum catalyst. For the larger electromechanical actuation response, the silicone dielectric elastomer actuator had to have a larger molecular weight of poly(dimethyl siloxane), a smaller hardener content, and a resin‐free composition. However, the silicone elastomer actuators needed to include a small amount of resin to improve the tearing strength. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2014 , 131 , 40030.
Modeling and detection of oil in sea water (2013)

The challenge of a deep-water oil leak is that a significant quantity of oil remains in the water column and possibly changes properties. There is a need to quantify the oil settled within the water column and determine its physical properties to assist in the oil recovery. There are currently no methods to map acoustically submerged oil in the sea. In this paper, high-frequency acoustic methods are proposed to localize the oil polluted area and characterize the parameters of its spatial covariance, i.e., variance and correlation. A model is implemented to study the underlying mechanisms of backscattering due to spatial heterogeneity of the medium and predict backscattering returns. An algorithm for synthetically generating stationary, Gaussian random fields is introduced which provides great flexibility in implementing the physical model of an inhomogeneous field with spatial covariance. A method for inference of spatial covariance parameters is proposed to describe the scattering field in terms of its second-order statistics from the backscattered returns. The results indicate that high-frequency acoustic methods not only are suitable for large-scale detection of oil contamination in the water column but also allow inference of the spatial covariance parameters resulting in a statistical description of the oil field.
A terrorizmus elleni fellépés eszközrendszerének fejlődése, különös tekintettel a terrorizmus finanszírozása elleni küzdelemre = The development of measures for combating terrorism with special respect to the fight against financing terrorism (2012)

Az előiranyzott munkaterv szerint reszt vettunk a Nemzetkozi Buntetőjogi Tarsasag (AIDP) egisze alatt a 2009. szeptember 20-27. kozott Isztambulban megrendezesre kerult XVIII. Nemzetkozi Buntetőjogi Kongresszuson. A 2009. evben anyaggyűjtesi es adatfeldolgozasi, rendszerezesi munkalatok kerultek napirendre annak erdekeben, hogy előkeszitesre keruljon a terrorizmus osszefuggeseben fentebb reszletezett temateruletek osszehasonlito jogi szempontok szerint tortenő tovabbgondolasa. 2009. novembereben Europai es Nemzetkozi Buntetőjog cimmel megrendezett konferencian mutattuk be a kutatas eredmenyeit. 2010.-nem a konferencia anyagat a Jog-Allam-Politika szakfolyoiratban tettuk kozze. Ennek kereteben megjelent publikaciokat korabban ismertettuk. Az előiranyzott munkaterv szerint 2010. juniusaban kutatast vegeztunk a Columbia Egyetem konyvtaraban. 2011. juniusaban a kutatasi tervnek megfelelően latogatast tettunk a Bűnugyi Tudomanyok Nemzetkozi Intezeteben (Syracusa, Olaszorszag), ahol a zaro tanulmany elkeszitesehez meg hianyzo szakmai anyagokat beszereztuk. Az eredeti kutatasi tervben rogzitettek szerint a munka eredmenyeit osszefoglalo zarotanulmanyt 2011 julius honapban veglegesitettuk. Ennek kereteben onallo fejezetet szenteltunk a terrorizmus fogalma, a terrorizmus kriminologiai es A zaro-tanulmany monografikus feldolgozasban az UNIVERSITAS-GYŐR Nonprofit Kft. gondozasaban 2011. nyaran nyomtatasban is megjelent. | Pursuant to the original research plan, the final summary of the results stemming from the research project was made in April 2011. This material discusses the mainstreams of our work in single chapters, where the concept of terrorism, the criminological and criminal policy aspects of terrorism, as well as the national and international means and legislative efforts of fighting against terrorism are focused upon. The monographical version of this summary has been finally published by UNIVERSITAS-GYŐR Nonprofit Ltd. in the end of summer 2011.
Toward a cost-effective DSM organization that exploits processor-memory integration (2002)

Dramatic increases in the number of transistors that can be integrated on a VLSI chip will soon allow commodity microprocessors to include both processor and a sizable fraction of main memory on chip. Distributed Shared-Memory (DSM) multiprocessors typically use the latest off-the-shelf microprocessors and thus will be affected by the upcoming processor-memory integration. In this paper, we explore how a cache-coherent DSM machine built around Processor-In-Memory (PIM) chips might be cost-effectively organized. To take advantage of the close coupling between processor and memory, we propose tagging the memory and organizing it as a cache. Furthermore, commercial considerations dictate the use of off-the-shelf hardware largely designed for uniprocessors. Consequently, we keep the directory control off-chip. To keep the multiprocessor cheap and simple, and to allow for reconfigurability, directory control is performed by chips that are identical to the ones used as compute nodes. As a result, the machine hardware can be easily reconfigured for computing or coherence-handling depending on the needs of the application. We also propose a cache coherence protocol that is tailored to our architecture: it uses the memory very efficiently while exploiting the large caching space available. Overall, the resulting machine is simple and inexpensive, and delivers performance that is comparable to, and higher than, the more expensive traditional COMA and CC-NUMA organizations, respectively.
Tovara virginiana (L.) Raf. (2005)

https://thekeep.eiu.edu/herbarium_specimens_byname/13632/thumbnail.jpg
Storage coding for wear leveling in flash memories (2009)

NAND flash memories are currently the most widely used flash memories. In a NAND flash memory, although a cell block consists of many pages, to rewrite one page, the whole block needs to be erased and reprogrammed. Block erasures determine the longevity and efficiency of flash memories. So when data is frequently reorganized, which can be characterized as a data movement process, how to minimize block erasures becomes an important challenge. In this paper, we show that coding can significantly reduce block erasures for data movement, and present several optimal or nearly optimal algorithms. While the sorting-based non-coding schemes require O(n log n) erasures to move data among n blocks, coding-based schemes use only O(n) erasures and also optimize the utilization of storage space.
HBV-RNA, Quantitative HBsAg, Levels of HBV in Peripheral Lymphocytes and HBV Mutation Profiles in Chronic Hepatitis B (2022)

A comprehensive characterization of chronic HBV (CHB) patients is required to guide therapeutic decisions. The cumulative impact of classical and novel biomarkers on the clinical categorization of these patients has not been rigorously assessed. We determined plasma HBV-RNA and HBsAg levels, HBV in peripheral lymphocytes (PBMCs) and HBV mutation profiles in CHB patients. Patient demographics (n = 139) and classical HBV biomarkers were determined during a clinical routine. HBV-RNA in plasma and HBV-DNA in PBMCs were determined by RT-PCR. HBsAg levels were determined using Architect. In samples with HBV-DNA viral load >1000 IU/mL, genotype mutations in precore (PC), basal core promoter (BCP), HBsAg and Pol regions were determined by sequencing. Most patients (n = 126) were HBeAg-negative (HBeAgNeg) with significantly lower levels of HBV-RNA, HBV-DNA and HBsAg compared to HBeAg-positive (HBeAgPos) patients (p < 0.05). HBV genotype D prevailed (61/68), and >95% had BCP/PC mutations. Escape mutations were identified in 22.6% (13/63). HBeAgNeg patients with low levels of HBsAg (log IU ≤ 3) were older and were characterized by undetectable plasma HBV-DNA and undetectable HBV-RNA but not undetectable HBV-DNA in PBMCs compared to those with high HBsAg levels. In >50% of the studied HBeAgNeg patients (66/126), the quantitation of HBsAg and HBV-RNA may impact clinical decisions. In conclusion, the combined assessment of classical and novel serum biomarkers, especially in HBeAgNeg patients, which is the largest group of CHB patients in many regions, may assist in clinical decisions. Prospective studies are required to determine the real-time additive clinical advantage of these biomarkers.
Abstract SY16-02: Clinical whole exome interpretation for precision cancer medicine (2015)

Abstract Translating whole exome sequencing (WES) for prospective clinical use may impact the care of cancer patients. However, since this approach greatly expands the quantity of genomic data generated for an individual patient, multiple innovations are necessary for clinical implementation. These include clinical analysis and interpretation of large scale WES data, effective representation of WES data in a clinical environment for physician consumption, and development of knowledge-sharing platforms to ensure effective curation of clinically relevant variants. Here, we describe heuristic methods for the clinical interpretation of WES data. We also discuss approaches that may facilitate physician understanding of WES data in a clinical setting. Finally, we review existing knowledge bases and emerging mechanisms for crowdsourcing variant curation that may enable prospective WES-scale genomic profiling. Overall, this methodology may inform the widespread implementation of precision cancer medicine. Citation Format: Eliezer M. Van Allen. Clinical whole exome interpretation for precision cancer medicine. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr SY16-02. doi:10.1158/1538-7445.AM2015-SY16-02
Topological Origin of Fragility, Network Adaptation, and Rigidity and Stress Transitions in Especially Homogenized Nonstoichiometric Binary GexS100–x Glasses B (2014)

Binary GeₓS₁₀₀–ₓ glasses reveal a richness of elastic and chemical phase transitions driven by network topology. With increasing Ge content (x), well-defined rigidity at xc(1) = 19.3(5)% and a stress transition at xc(2) = 24.9(5)% are observed in Raman scattering. In modulated DSC measurements, the nonreversing enthalpy of relaxation at Tg reveals a square-well-like minimum (reversibility window) with window walls that coincide with the two elastic phase transitions. Molar volumes show a trapezoidal-like minimum (volumetric window) with edges that nearly coincide with the reversibility window. These optical, thermal, and volumetric results are consistent with an isostatically rigid elastic phase (intermediate phase, IP) present between the rigidity (xc(1)) and stress (xc(2)) transitions. Complex Cₚ measurements show melt fragility index, m(x) to also show a global minimum in the reversibility window with m < 20, underscoring that melt dynamics encode the elastic behavior of the glass formed at Tg. The strong nature of melts formed in the IP has an important practical consequence; they lead to slow homogenization (over days not hours) of nonstoichiometric Ge–S batch compositions reacted at high temperatures. Homogenization of chalcogenide melts/glasses over a scale of a few micrometers is a prerequisite to observe the intrinsic physical properties of these materials.
The hinge region operates as a stability switch in cGMP‐dependent protein kinase Iα (2007)

The molecular mechanism of cGMP-dependent protein kinase activation by its allosteric regulator cyclic-3',5'-guanosine monophosphate (cGMP) has been intensely studied. However, the structural as well as thermodynamic changes upon binding of cGMP to type I cGMP-dependent protein kinase are not fully understood. Here we report a cGMP-induced shift of Gibbs free enthalpy (DeltaDeltaGD) of 2.5 kJ.mol-1 as determined from changes in tryptophan fluorescence using urea-induced unfolding for bovine PKG Ialpha. However, this apparent increase in overall stability specifically excluded the N-terminal region of the kinase. Analyses of tryptic cleavage patterns using liquid chromatography-coupled ESI-TOF mass spectrometry and SDS/PAGE revealed that cGMP binding destabilizes the N-terminus at the hinge region, centered around residue 77, while the C-terminus was protected from degradation. Furthermore, two recombinantly expressed mutants: the deletion fragment Delta1-77 and the trypsin resistant mutant Arg77Leu (R77L) revealed that the labile nature of the N-terminus is primarily associated with the hinge region. The R77L mutation not only stabilized the N-terminus but extended a stabilizing effect on the remaining domains of the enzyme as well. These findings support the concept that the hinge region of PKG acts as a stability switch.
Detailed Evaluation of Data Analysis Tools for Subtyping of Bacterial Isolates Based on Whole Genome Sequencing: Neisseria meningitidis as a Proof of Concept (2019)

Whole genome sequencing is increasingly recognized as the most informative approach for characterization of bacterial isolates. Success of the routine use of this technology in public health laboratories depends on the availability of well-characterized and verified data analysis methods. However, multiple subtyping workflows are now often being used for a single organism, and differences between them are not always well described. Moreover, methodologies for comparison of subtyping workflows, and assessment of their performance are only beginning to emerge. Current work focuses on the detailed comparison of WGS-based subtyping workflows and evaluation of their suitability for the organism and the research context in question. We evaluated the performance of pipelines used for subtyping of <i>Neisseria meningitidis</i>, including the currently widely applied cgMLST approach and different SNP-based methods. In addition, the impact of the use of different tools for detection and filtering of recombinant regions and of different reference genomes were tested. Our benchmarking analysis included both assessment of technical performance of the pipelines and functional comparison of the generated genetic distance matrices and phylogenetic trees. It was carried out using replicate sequencing datasets of high- and low-coverage, consisting mainly of isolates belonging to the clonal complex 269. We demonstrated that cgMLST and some of the SNP-based subtyping workflows showed very good performance characteristics and highly similar genetic distance matrices and phylogenetic trees with isolates belonging to the same clonal complex. However, only two of the tested workflows demonstrated reproducible results for a group of more closely related isolates. Additionally, results of the SNP-based subtyping workflows were to some level dependent on the reference genome used. Interestingly, the use of recombination-filtering software generally reduced the similarity between the gene-by-gene and SNP-based methodologies for subtyping of <i>N. meningitidis</i>. Our study, where <i>N. meningitidis</i> was taken as an example, clearly highlights the need for more benchmarking comparative studies to eventually contribute to a justified use of a specific WGS data analysis workflow within an international public health laboratory context.
A Cloud-Based Multi-threaded Implementation of View Synthesis System (2017)

In multiview video applications, view synthesis is a computationally intensive task that needs to be done correctly and efficiently in order to deliver a seamless user experience. In order to provide fast and efficient view synthesis, in this paper, we present a cloud-based implementation that will be especially beneficial to mobile users whose devices may not be powerful enough for high quality view synthesis. Our proposed implementation balances the view synthesis algorithm's components across multiple threads and utilizes the computational capacity of modern CPUs for faster and higher quality view synthesis. For arbitrary view generation, we utilize the depth map of the scene from the cameras' viewpoint and estimate the depth information conceived from the virtual camera. The estimated depth is then used in a backward direction to warp the cameras' image onto the virtual view. Finally, we use a depth-aided inpainting strategy for the rendering step to reduce the effect of disocclusion regions (holes) and to paint the missing pixels. For our cloud implementation, we employed an automatic scaling feature to offer elasticity in order to adapt the service load according to the fluctuating user demands. Our performance results using 4 multiview videos over 2 different scenarios show that our proposed system achieves average improvement of around 1.7 times for speedup, 50% and 52% for efficiency and resource utilization, respectively.
A multi-agent based Tourism Kiosk on Internet (2002)

We discuss the implementation of a multi agent based Tourism Kiosk for Hong Kong tourism industry on the Internet. This system allows the users to retrieve the most updated information about Hong Kong through any Java enabled Web browser. The complete system consists of a set of software agents who handle various information categories, such as hotels, shopping centres, and cinemas, etc. The Knowledge Query and Manipulation Language (KQML) was selected as the agent communication language to develop our system, which takes care the exchange of information among agents. The users are able to send their queries to the system, then the system will dispatch one or more agents, depending on the analysis of the query, to search for and retrieve information for the users.
WebKDD 2004 (2004)

In this report, we summarize the contents and outcomes of the recent WebKDD 2004 workshop that was held in conjunction with the 10th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2004), August 22-25, 2004, in Seattle, Washington. We also reflect on the trend in participation levels in the WebKDD series of workshops over the last six years, and indicate new directions in Web mining research as reflected in the latest workshop.
Optical Interconnects Facilitate The Way To Massive Parallelism (1988)

The importance and complexity of interconnections in computers increase tremendously if one considers the von Neumann digital computer in connection with parallel computers with many tightly coupled processors. There is an indication that processing and interconnecting aspects will merge in future computer architecture. Parallel computers are able to perform a myriad of processing tasks such as &quot;computational seismics&quot;, chemical reaction and aerodynamic simulation, dynamic imaging and robot vision. Such systems, comprised of many tightly coupled processors can meet the computational performance goals, required for these processing tasks. However a major problem is the construction of a suitable interconnection network which provides fast and flexible interprocessor communications at a reasonable cost. The cost-effectiveness of any arbitrary network design is governed by factors such as the number of processors applied, the computational tasks to be performed, the required speed of the interprocessor data transfers, the complexity of the actual hardware topology of the network and any cost constraints on its construction. The Delft Parallel Processor [DPP], which has been operational since 1981, is a modest size MIMD computer with a powerful interprocessor interconnection topology. (MIMD = Multiple-Instruction stream, Multiple-Data stream). In the DPP architecture, multiple data streams are realized by means of plural parallel data channels (one per data stream), with a branch-off per channel to each Processing Element [PE] to fetch the data on which to operate. A fast and efficient exchange of information within the DPP is performed by this &apos;full interconnectivity&apos; Multiple-Broadcast [MB] interconnection topology. In the case of many processors, this MB interconnect has to be realized by means of Optical Interconnects [01&apos;s], to validate at several levels the quality and flexibility of communication systems for both interconnection topologies and data flow protocols. Conventional Electrical Interconnects [Us] and switching technologies are now becoming an insuperable bottleneck at several levels. The implementation of high speed, multi-pin, silicon and GaAs VLSI/VHSI circuits is one extreme; the choice of a massively reconfigurable parallel interconnection scheme is another. Optimum routing methods are hard to define. The application of wired Ors for the board-to-board interconnects and Local Area Networks [LAN&apos;s] is the most promising. Structured optical waveguide techniques, image mapping optics, optical starcouplers and free space holographic for the inner- and interchip communication may be the future, although coupling between opto-electronic components and/or waveguides still requires critical alignment.
Surrogate Internal Standard (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.