gebhart/patrepeval huggingface dataset:
Auxin-Mediated Transcriptional System with a Minimal Set of Components Is Critical for Morphogenesis through the Life Cycle in Marchantia polymorpha (2015)

The plant hormone auxin regulates many aspects of plant growth and development. Recent progress in Arabidopsis provided a scheme that auxin receptors, TIR1/AFBs, target transcriptional co-repressors, AUX/IAAs, for degradation, allowing ARFs to regulate transcription of auxin responsive genes. The mechanism of auxin-mediated transcriptional regulation is considered to have evolved around the time plants adapted to land. However, little is known about the role of auxin-mediated transcription in basal land plant lineages. We focused on the liverwort Marchantia polymorpha, which belongs to the earliest diverging lineage of land plants. M. polymorpha has only a single TIR1/AFB (MpTIR1), a single AUX/IAA (MpIAA), and three ARFs (MpARF1, MpARF2, and MpARF3) in the genome. Expression of a dominant allele of MpIAA with mutations in its putative degron sequence conferred an auxin resistant phenotype and repressed auxin-dependent expression of the auxin response reporter proGH3:GUS. We next established a system for DEX-inducible auxin-response repression by expressing the putatively stabilized MpIAA protein fused with the glucocorticoid receptor domain (MpIAA(mDII)-GR). Repression of auxin responses in (pro)MpIAA:MpIAA(mDII)-GR plants caused severe defects in various developmental processes, including gemmaling development, dorsiventrality, organogenesis, and tropic responses. Transient transactivation assays showed that the three MpARFs had different transcriptional activities, each corresponding to their phylogenetic classifications. Moreover, MpIAA and MpARF proteins interacted with each other with different affinities. This study provides evidence that pleiotropic auxin responses can be achieved by a minimal set of auxin signaling factors and suggests that the transcriptional regulation mediated by TIR1/AFB, AUX/IAA, and three types of ARFs might have been a key invention to establish body plans of land plants. We propose that M. polymorpha is a good model to investigate the principles and the evolution of auxin-mediated transcriptional regulation and its roles in land plant morphogenesis.
The Role of GIS and Other Spatial Technologies in Natural Disaster Reduction (1996)

The central thesis of this paper is that more appropriate, accurate and current information on both hazard agents and the communities at risk is the key to reducing the impact of natural disasters. Over the two decades, 1976 to 1996, a wide range of technologies has been introduced to enhance the collection of information, especially on the hazard phenomenon. There has been, however, a significant lack of integration of these technologies and the information that they generate, especially in the emergency management field. The need for information integration has grown apace with the development of a risk-based view of emergency management in place of the traditional hazard-based view. This new and more holistic approach has been made possible by the application of geographic information systems (GIS) as an analytical and decision support tool.
Bayesian Predictive Profiles With Applications to Retail Transaction Data (2001)

Massive transaction data sets are recorded in a routine manner in telecommunications, retail commerce, and Web site management. In this paper we address the problem of inferring predictive individual profiles from such historical transaction data. We describe a generative mixture model for count data and use an an approximate Bayesian estimation framework that effectively combines an individual's specific history with more general population patterns. We use a large real-world retail transaction data set to illustrate how these profiles consistently outperform non-mixture and non-Bayesian techniques in predicting customer behavior in out-of-sample data.
<i>Through</i> versus <i>Cross</i> Electron Delocalization in Polytriacetylene Oligomers: A Computational Analysis (2005)

Herein, we report a systematic theoretical investigation of the molecular and electronic properties of unsubstituted polytriacetylene (PTA) and iso-polytriacetylene (iso-PTA) oligomers, which are characterized by through and cross pi-conjugation pathways, respectively. The goal of the study is to compare through versus cross conjugation on the basis of the computed molecular geometries of the neutral, anionic, and cationic species, the electron affinities, ionization potentials, excitation energies, and nonlinear optical properties for oligomers up to the nonamer. Differences in the effective conjugation length are directly related to electron delocalization in cross- and through-conjugated pathways. As in the through-conjugated oligomers, that is, the PTAs, the frontier orbitals of the iso-PTA oligomers are delocalized along the entire carbon backbone, suggesting that pi-delocalization can extend through cross-linked carbon atoms. However, in contrast to the PTA oligomers, the bond lengths remain strictly constant and the reduction of the energy gap beyond the trimer is completely due to the correlation contribution. On the other hand, in the anions and cations, the bond lengths do change significantly with increasing chain length. Therefore, oxidation or reduction of the iso-PTA oligomer appears to switch on delocalization through cross-linked carbon atoms. Obviously, the effective conjugation length is specific and depends on the observable considered.
Replacement of anticodon loop nucleotides to produce functional tRNAs: amber suppressors derived from yeast tRNAPhe. (1982)

The method of anticodon loop replacement has been used to make derivatives of yeast tRNAPhe. By constructing tRNAs with a CUA anticodon, complementary to the amber (UAG) terminator, functional amber suppressor tRNAs were produced. The activity of these tRNAs was assayed in a mammalian cell-free protein synthesizing system. The level of suppression reflects the efficiency of codon recognition. tRNAs were constructed with either A, C, U, or G on the 3' side of the CUA anticodon. The tRNAs containing the purines were efficient amber suppressors, whereas those containing pyrimidines were inefficient.
Ultrastructural distribution of histones within Ehrlich tumor cell nucleoli: a cytochemical and immunocytochemical study. (1989)

We investigated the ultrastructural distribution of histones within Ehrlich tumor cell nucleoli by means of three cytochemical methods and by a Lowicryl post-embedding immunogold labeling procedure involving anti-histone (H2B, H3, H4) antisera as well as antibodies to synthetic peptides of histones. With the two technical approaches, labeling was particularly concentrated over the perinucleolar chromatin and over its intranucleolar invaginations which penetrate the nucleolar body and come in close contact with the fibrillar centers. Furthermore, the high-resolution immunocytochemical technique revealed the presence of a small amount of the three histones in the fibrillar centers, preferentially located towards their peripheral regions. In addition, colocalization of DNA at all the histone-positive sites could be visualized after double immunogold staining using a monoclonal anti-DNA antibody and the anti-histone antisera. These results appear to indicate that all the DNA detected within the nucleolus was associated with histones. This finding suggests that the ribosomal DNA, including transcriptionally active genes, is bound to histones.
A comparison of five clock scoring methods using ROC (receiver operating characteristic) curve analysis (2001)

While substantial differences among the clock scoring methods were evident in our sample, the accuracy of each was modest at best. Unless further studies in relevant settings suggest otherwise, we caution on the use of clock drawing alone to screen for dementia.
Unsupervised Low Latency Speech Enhancement With RT-GCC-NMF (2019)

In this paper, we present RT-GCC-NMF: a real-time (RT), two-channel blind speech enhancement algorithm that combines the non-negative matrix factorization (NMF) dictionary learning algorithm with the generalized cross-correlation (GCC) spatial localization method. Using a pre-learned universal NMF dictionary, RT-GCC-NMF operates in a frame-by-frame fashion by associating individual dictionary atoms to target speech or background interference based on their estimated time-delay of arrivals. We evaluate RT-GCC-NMF on two-channel mixtures of speech and real-world noise from the signal separation and evaluation campaign (SiSEC). We demonstrate that this approach generalizes to new speakers, acoustic environments, and recording setups from very little training data, and outperforms all but one of the algorithms from the SiSEC challenge in terms of overall perceptual evaluation methods for audio source separation (PEASS) scores and compares favourably to the ideal binary mask baseline. Over a wide range of input signal to noise ratios (SNRs), we show that this approach simultaneously improves the PEASS and SNR-based blind source separation eval objective quality metrics as well as the short-time objective intelligibility (STOI) and extended STOI objective speech intelligibility metrics. A flexible, soft masking function in the space of NMF activation coefficients offers real-time control of the tradeoff between interference suppression and target speaker fidelity. Finally, we use an asymmetric short-time Fourier transform to reduce the inherent algorithmic latency of RT-GCC-NMF from 64 ms to 2 ms with no loss in performance. We demonstrate that latencies within the tolerable range for hearing aids are possible on current hardware platforms.
Defining cell-type specificity at the transcriptional level in human disease (2013)

Cell-lineage-specific transcripts are essential for differentiated tissue function, implicated in hereditary organ failure, and mediate acquired chronic diseases. However, experimental identification of cell-lineage-specific genes in a genome-scale manner is infeasible for most solid human tissues. We developed the first genome-scale method to identify genes with cell-lineage-specific expression, even in lineages not separable by experimental microdissection. Our machine-learning-based approach leverages high-throughput data from tissue homogenates in a novel iterative statistical framework. We applied this method to chronic kidney disease and identified transcripts specific to podocytes, key cells in the glomerular filter responsible for hereditary and most acquired glomerular kidney disease. In a systematic evaluation of our predictions by immunohistochemistry, our in silico approach was significantly more accurate (65% accuracy in human) than predictions based on direct measurement of in vivo fluorescence-tagged murine podocytes (23%). Our method identified genes implicated as causal in hereditary glomerular disease and involved in molecular pathways of acquired and chronic renal diseases. Furthermore, based on expression analysis of human kidney disease biopsies, we demonstrated that expression of the podocyte genes identified by our approach is significantly related to the degree of renal impairment in patients. Our approach is broadly applicable to define lineage specificity in both cell physiology and human disease contexts. We provide a user-friendly website that enables researchers to apply this method to any cell-lineage or tissue of interest. Identified cell-lineage-specific transcripts are expected to play essential tissue-specific roles in organogenesis and disease and can provide starting points for the development of organ-specific diagnostics and therapies.
Reactivity within a confined self-assembled nanospace (2007)

Confined nanospaces in which reactions can take place, have been created by various approaches such as molecular capsules, zeolites and micelles. In this tutorial review we focus on the application of self-assembled nanocapsules with well-defined cavities as nanoreactors for organic and metal catalysed transformations. The self-assembly of nanocapsules based on noncovalent bonds such as hydrogen bonds and metal-ligand interactions is discussed to introduce the properties of the building blocks and capsules thereof. We will elaborate on the encapsulation effects that can be expected when reactions are carried out in a capsule-protected environment. Subsequently, literature examples will be described in which self-assembled nanocapsules are applied as nanoreactors, for various types of organic and metal catalysed reactions.
A Temperature-Independent Interrogation Technique for FBG Sensors Using Monolithic Multilayer Piezoelectric Actuators (2016)

In this paper, a temperature-independent technique for measurements of ac signals, such as voltage and electrical current, with fiber Bragg grating (FBG) sensors is presented. This technique is based on a twin-grating scheme, in which the measured quantity is obtained from the optical power of convolution between a sensing FBG and a tunable FBG. The proposed interrogator employs a low-voltage monolithic multilayer piezoelectric actuator (MMPA) to sweep the tunable FBG over the wavelength range of the sensing FBG, in order to obtain the convolution function accurately. A dedicated microcontrolled optoelectronic system with a firmware-based tracking routine is responsible for keeping the tunable FBG following the sensing FBG over temperature-induced wavelength shifts with subpicometric resolution, while the dc level of convolution is controlled precisely at the highest sensitivity point of operation. The MMPA employed allows the tracking of the tunable FBG after the sensing FBG over a maximum temperature difference that ranges from -29 °C to +90 °C. The proposed interrogator presents lower cost compared with the systems that employ frequency-scanning devices, such as high-speed Fabry-Perot tunable filters.
Recent Trends in Electrospinning of Polymer Nanofibers and their Applications as Templates for Metal Oxide Nanofibers Preparation (2016)

Scientists have been paying a special attention for the synthesis of one-dimensional (1D) morphologies to attain new phenomena and novel physicochemical characteristics of materials. Furthermore, 1D nanostructures exhibit long axial ratio, which has a great influence on the physical and chemical properties of materials. It is worth mentioning that electrospinning is one of the most common and efficient techniques used for the preparation of 1D polymer composite nanofibers. Using electrospinning, nanofibers were fabricated by electrostatic stretching of polymer viscous solution by applying a high voltage. This chapter discusses the synthesis of metal oxide nanofibers such as tin oxide (SnO2), zinc oxide (ZnO), titanium oxide (TiO2), and nickel oxide (NiO) using electrospinning process of polymer solution containing metal precursors and followed by annealing procedures to eliminate the polymer galleries, which were chosen as a sacrificial template for the preparation of metal oxide nanofibers. SEM, XRD, and XPS are equipped to characterize the electrospun metal oxide nanofibers and the results settle the formation of homogeneously distributed metal oxide nanofibers.
Encyclopedia of Biomaterials and Biomedical Engineering (2008)

Antimineralization Treatment. Artificial Neural Networks: An Overview. Bioactive Materials and Scaffolds for Tissue Engineering. Biomaterials, Immune Response. Bioresorbable Polymers, An Overview. Cell-Material Interaction. Compression of Digital Biomedical Signals. Electromyography. Magnetic Resonance Microscopy. Melt Spinning. Polyamides (Synthetic and Natural). Repair and Regeneration of Peripheral Nerves: Historical Perspective. Sterilization of Biomedical Materials. Supercritical Fluid Processing. Ultrasonic Therapy, Bone Healing. Wear Debris, Bone Resorption Animal Models. Zirconia Ceramics.
Application of phase-change materials in memory taxonomy (2017)

Phase-change materials are suitable for data storage because they exhibit reversible transitions between crystalline and amorphous states that have distinguishable electrical and optical properties. Consequently, these materials find applications in diverse memory devices ranging from conventional optical discs to emerging nanophotonic devices. Current research efforts are mostly devoted to phase-change random access memory, whereas the applications of phase-change materials in other types of memory devices are rarely reported. Here we review the physical principles of phase-change materials and devices aiming to help researchers understand the concept of phase-change memory. We classify phase-change memory devices into phase-change optical disc, phase-change scanning probe memory, phase-change random access memory, and phase-change nanophotonic device, according to their locations in memory hierarchy. For each device type we discuss the physical principles in conjunction with merits and weakness for data storage applications. We also outline state-of-the-art technologies and future prospects.
1,4‐Di‐ <i>O</i> ‐Alkyl Threitols from Tartaric Acid: 1,4‐Di‐ <i>O</i> ‐Benzyl‐ <scp>L</scp> ‐Threitol (2003)

Abstract 1,4‐Di‐ O ‐alkyl threitols from tartaric acid: 1,4‐di‐ O ‐benzyl‐ L ‐threitol intermediate: Dimethyl 2,3‐ O ‐isopropylidene‐ L ‐tartrate. reactant: L ‐tartaric acid (101 g, 0.673 mol) intermediate: 2,3‐Di‐ O ‐isopropylidene‐ L ‐threitol. intermediate: 1,4‐di‐ O ‐benzyl‐2,3‐ O ‐isopropylidene‐ L ‐threitol product: 1,4‐Di‐ O ‐benzyl‐ L ‐threitol
Vectors for Cu<sup>2+</sup>‐inducible production of glutathione <i>S</i>‐transferase‐fusion proteins for single‐step purification from yeast (1994)

We describe six new yeast episomal vectors which encode glutathione S-transferase (GST) affinity tags. These allow for the production of GST-fusion proteins in Saccharomyces cerevisiae under the control of the CUP1 promoter. Affinity chromatography with glutathione-Sepharose permits convenient purification of the fusion protein from a yeast lysate. The presence of a protease cleavage site facilitates subsequent removal of the GST tag. The expression and single-step purification of both GST and a functional GST-metallothionein fusion from yeast are shown as an example of the application of these vectors.
Architectural characteristics and hardware cost of a class of interconnection networks (2002)

A new class of interconnection networks is proposed for interconnecting the processors of a general purpose parallel computer which is based on the hierarchical application of a complete graph compound. The systematic construction of this new class of interconnection networks, RCC, is shown and its properties are derived and are compared favorably to other interconnection networks. A specific instance of this class, RCC-CUBE, is shown to have desirable network properties such as small diameter, small degree, high density, and high bandwidth. The hardware cost and physical time performance are estimated for RCC-CUBE and compared to those of the hypercube and the 2-D mesh demonstrating an overall cost-effectiveness for RCC-CUBE. Thus, the RCC-CUBE appears to be a good candidate for next generation massively parallel computer systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
CloudSim: a toolkit for modeling and simulation of cloud computing environments and evaluation of resource provisioning algorithms (2010)

Abstract Cloud computing is a recent advancement wherein IT infrastructure and applications are provided as ‘services’ to end‐users under a usage‐based payment model. It can leverage virtualized services even on the fly based on requirements (workload patterns and QoS) varying with time. The application services hosted under Cloud computing model have complex provisioning, composition, configuration, and deployment requirements. Evaluating the performance of Cloud provisioning policies, application workload models, and resources performance models in a repeatable manner under varying system and user configurations and requirements is difficult to achieve. To overcome this challenge, we propose CloudSim: an extensible simulation toolkit that enables modeling and simulation of Cloud computing systems and application provisioning environments. The CloudSim toolkit supports both system and behavior modeling of Cloud system components such as data centers, virtual machines (VMs) and resource provisioning policies. It implements generic application provisioning techniques that can be extended with ease and limited effort. Currently, it supports modeling and simulation of Cloud computing environments consisting of both single and inter‐networked clouds (federation of clouds). Moreover, it exposes custom interfaces for implementing policies and provisioning techniques for allocation of VMs under inter‐networked Cloud computing scenarios. Several researchers from organizations, such as HP Labs in U.S.A., are using CloudSim in their investigation on Cloud resource provisioning and energy‐efficient management of data center resources. The usefulness of CloudSim is demonstrated by a case study involving dynamic provisioning of application services in the hybrid federated clouds environment. The result of this case study proves that the federated Cloud computing model significantly improves the application QoS requirements under fluctuating resource and service demand patterns. Copyright © 2010 John Wiley & Sons, Ltd.
위계적선형모형을 활용한 국민의 경찰신뢰도 영향요인 분석 (2015)

국가 내 도시마다 처한 특수성이 다르고 문화가 다르기 때문에 이를 고려하면 경찰신뢰에 영향을 미치는 요인을 더욱 명확히 밝혀낼 수 있다. 이 연구에서는 2012년도 한국종합사회조사(Korea General Social Survey)에서 추출한 변수와 통계청을 통해 얻은 16개 시도의 거시지표를 활용하여 경찰신뢰에 영향을 미치는 변수를 파악하고자 했다. 거시지표 투입에 적합한 위계적 선형 모델(Hierachical Lineal Model)의 검증을 위해 Stata ver.12가 사용되었다. 분석결과, 개인수준의 변수만을 투입한 모델에서는 기혼여부와 사회신뢰와 대인신뢰 정도, 사회에 대한 공정성 평가 등이 경찰신뢰에 영향을 미치는 것으로 나타났다. 다음으로 지역수준의 변수만을 투입한 모델에서는 18대 대선 투표율과 검거율이 경찰신뢰에 영향을 미쳤다. 주목할 만한 것은 개인수준의 변수가 통제된 통합모델에서 지역수준의 변수 가운 데 검거율만이 통계적유의도를 유지했다는 점이다. 이는 다른 요인들이 모두 통제된후에도, 경찰이 지역사회 치안과 안보라는 본연의 업무에서 성과를 보이는 것이 경찰신뢰의 증진에 매우 중요할 수 있음을 보여준다고 할 수 있다. 이 연구는 시민들의 경찰에 대한 신뢰를 증진시키기 위해서는, 무엇보다도 실질적으로 사회의 안전을 보장할 수 있는 성과적 측면이 요구된다는 점을 시사한다.
State-plane analysis of zero-current-switching resonant DC/DC power converters (1989)

The state-plane analysis for the buck, boost, buck/boost, and Cuk zero-current-switching resonant DC/DC power converters is presented. Simple visual criteria are introduced to determine whether the converter is operating in a mode producing voltage conversion. It is shown that the voltage conversion takes place within the converters if and only if both horizontal and vertical straight-line segments are present in the state-plane graph. The boundary of energy conversion is identified from the state plane by the evaporation of one or both straight-line segments. Formulas are found for the normalized switching frequency at this boundary that depend on the value of normalized switching voltage.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Fine-grained and efficient lineage querying of collection-based workflow provenance (2010)

The management and querying of workflow provenance data underpins a collection of activities, including the analysis of workflow results, and the debugging of workflows or services. Such activities require efficient evaluation of lineage queries over potentially complex and voluminous provenance logs. Näive implementations of lineage queries navigate provenance logs by joining tables that represent the flow of data between connected processors invoked from workflows. In this paper we provide an approach to provenance querying that: (i) avoids joins over provenance logs by using information about the workflow definition to inform the construction of queries that directly target relevant lineage results; (ii) provides fine grained provenance querying, even for workflows that create and consume collections; and (iii) scales effectively to address complex workflows, workflows with large intermediate data sets, and queries over multiple workflows.