nils-herrmann/clean_scirepeval huggingface dataset:
Simultaneous subtyping and pathotyping of the novel reassortant influenza A (H5N8) virus from clinical samples using a diagnostic microarray
Venue: BioChip Journal

Highly pathogenic avian influenza (HPAI) viruses cause economic losses in the poultry industry and pose a severe threat to human health. Rapid and accurate diagnostic methods are important because they can help prevent further spread of the virus and reduce the time required for eradication of the virus. We developed a low density microarray for the rapid detection and identification of avian influenza virus subtypes H5, H7, and H9 and their pathotypes in a previous study. In the present study, we report the development of updated probe sets and evaluation of the diagnostic microarray using H5N8 clade 2.3.4.4 HPAI viruses including clinical samples, without the need for egg propagation. Cy3 labeled DNA targets were obtained by reverse transcription polymerase chain reaction using Cy3 labeled universal primers, and labeled amplicons were hybridized to the microarray. All positive samples from RT PCR showed H5 specific and highly pathogenic pattern in the microarray, without purification of PCR products. Furthermore, it allowed for specific detection of the subtype and pathotype from low DNA concentration samples that did not allow direct sequence analysis. Therefore, this diagnostic microarray has enormous potential for the rapid subtyping and pathotyping from clinical samples without the need for culture.
Event sampled direct adaptive NN state feedback control of uncertain strict feedback system
Venue: 2016 IEEE 55th Conference on Decision and Control (CDC)

In this paper, neural networks (NNs) are utilized in the backstepping approach to design a control input by approximating unknown dynamics of the strict feedback nonlinear system with event sampled inputs. The system state vector is assumed to be measurable. As part of the controller design, first, local input to state like stability (ISS) for a continuously sampled controller that has been injected with bounded measurement errors is demonstrated and, subsequently, an event execution control law is derived such that the measurement errors are guaranteed to remain bounded. Lyapunov theory is used to demonstrate that the tracking errors and the NN weight estimation errors for each NN are locally uniformly ultimately bounded (UUB) in the presence bounded disturbances, NN reconstruction errors, as well as errors introduced by event sampling. Simulation results are provided to illustrate the effectiveness of the proposed controller.
Adaptive decision feedback equalizer for SISO communication channel using combined FIR neural network and fast block LMS algorithm
Venue: 2016 IEEE Annual India Conference (INDICON)

In this paper, an adaptive nonlinear decision feedback equalizer(DFE) is designed using three blocks that is feed forward filter, feedback filter and single layer neural network architecture with functional expansions of input patterns. Fast Block Least Mean Square (FBLMS) is used to update coefficients of all filters used in the design and the algorithm is based on block processing using FFT and IFFT which substantially reduces Bit Error. Thus the adaptive DFE as a part of the demodulator will improve the error performance of the receiver. The performance of the DFE is evaluated in terms of BER and eye diagrams for the BPSK modulated transmitted data sequence. Non linear minimum phase time invariant channel model is used for Single Input Single Output (SISO) communication systems which introduces ISI in the modulated data stream. The comparison results are obtained by using other coefficients update algorithms like LMS and Block LMS in presence of additive white Gaussian noise.
New construction of eigenstates and separation of variables for SU(N) quantum spin chains

A bstractWe conjecture a new way to construct eigenstates of integrable XXX quantum spin chains with SU(N) symmetry. The states are built by repeatedly acting on the vacuum with a single operator Bgood(u) evaluated at the Bethe roots. Our proposal serves as a compact alternative to the usual nested algebraic Bethe ansatz. Furthermore, the roots of this operator give the separated variables of the model, explicitly generalizing Sklyanin's approach to the SU(N) case. We present many tests of the conjecture and prove it in several special cases. We focus on rational spin chains with fundamental representation at each site, but expect many of the results to be valid more generally.
Cyclic Di GMP Regulated Periplasmic Proteolysis of a Pseudomonas aeruginosa Type Vb Secretion System Substrate
Venue: Journal of bacteriology

We previously identified a second messenger regulated signaling system in the environmental bacterium Pseudomonas fluorescens which controls biofilm formation in response to levels of environmental inorganic phosphate. This system contains the transmembrane cyclic di GMP (c di GMP) receptor LapD and the periplasmic protease LapG. LapD regulates LapG and controls the ability of this protease to process a large cell surface adhesin protein, LapA. While LapDG orthologs can be identified in diverse bacteria, predictions of LapG substrates are sparse. Notably, the opportunistic pathogen Pseudomonas aeruginosa harbors LapDG orthologs, but neither the substrate of LapG nor any associated secretion machinery has been identified to date. Here, we identified P. aeruginosa CdrA, a protein known to mediate cell cell aggregation and biofilm maturation, as a substrate of LapG. We also demonstrated LapDG to be a minimal system sufficient to control CdrA localization in response to changes in the intracellular concentration of c di GMP. Our work establishes this biofilm signaling node as a regulator of a type Vb secretion system substrate in a clinically important pathogen.  Here, the biological relevance of a conserved yet orphan signaling system in the opportunistic pathogen Pseudomonas aeruginosa is revealed. In particular, we identified the adhesin CdrA, the cargo of a two partner secretion system, as a substrate of a periplasmic protease whose activity is controlled by intracellular c di GMP levels and a corresponding transmembrane receptor via an inside out signaling mechanism. The data indicate a posttranslational control mechanism of CdrA via c di GMP, in addition to its established transcriptional regulation via the same second messenger.
Incidence and Risk Factors for Atrial Fibrillation in Korea: the National Health Insurance Service Database (2002 2010)
Venue: Korean circulation journal

Atrial fibrillation (AF) is a common arrhythmia that is known as an important independent risk factor for stroke. However, limited information is available on AF in Korea. This study evaluated the incidence of AF, its associated co morbidities and risk factors for AF in Korea.  The National Health Insurance Service database between 2002 and 2010 was used in the study. Individuals<30 years old and those diagnosed with AF between 2002 and 2004 were excluded. Hazard ratios (HRs) according to co morbidities and risk factors for AF were determined using a Cox proportional hazard model. Population attributable fractions (PAFs) of AF risk factors were determined.  During a 6 year follow up period, 3517 (1.7% developed AF. The incidence rates in men and women aged 30 39 years were 0.82 and 0.55 per 1000 person years, respectively; the incidence rates further increased with age to 13.09 and 11.54 per 1000 person years in men and women aged>=80 years, respectively. The risk factors for incident AF were age, sex, body mass index (BMI) hypertension, ischemic heart disease (IHD) and heart failure. After adjusting for variables related to AF, the risk of AF was significantly associated with hypertension (HR 1.667) IHD (HR 1.639) heart failure (HR 1.521) and the PAFs for age, sex, BMI, hypertension, IHD, heart failure and diabetes mellitus were 30.6% 10.1% 3.4% 16.6% 8.2% 5.3% and 0.8% respectively.  Incidence of AF increased with age and was higher in men than in women. A larger proportion of AF events was attributable to hypertension than to other co morbidities.
A review on soil structure interaction analysis of laterally loaded piles
Venue: Innovative Infrastructure Solutions

Soil structure interaction plays an important role in the behavior of structure under static or dynamic loading. It influences the behavior of soil, as well as the response of pile under loading. The analysis is highly essential for predicting a more accurate structural behavior so as to improve the safety of structures under extreme loading conditions. The soil pile system behavior is predominantly nonlinear and this makes the problem complicated. In a laterally loaded pile the load is resisted by the soil pile interaction effect, which in turn depends on soil properties, pile material, pile diameter, loading type and bed slope of ground. The difficulty in the accountability of the influencing factors necessitates a careful study on soil structure interaction problem. The analysis became easier with the debut of powerful computers and simulation tools such as finite element analysis software. A detailed literature review on soil structure interaction analysis of laterally loaded piles is presented in this paper.
An experimental investigation of transient dynamics of pile supported structures in liquefiable soils.

Unsatisfactory performance of pile supported structures in liquefiable areas (ranging from tilting/settlement to complete collapse) is still observed after most major earthquakes. As a result, further research is required in this subject. This thesis therefore aims to study the response of pile supported structures during seismic liquefaction. The ground liquefies progressively in a top down fashion when the soil transform from solid material to liquid like material. This is referred to as transient behaviour (from no liquefaction to full liquefaction state) and is particularly focused in this work. In practice, piles are usually analysed as laterally loaded beams using Beam on Nonlinear Winkler Foundation model where earthquake loading is applied in a pseudo static way. Therefore, this study reviews methods of analysis of laterally loaded pile. Six different field case records were analysed using different approaches and the results were compared. Large scale shake table experiments were also conducted consisting of four pile models (two single piles and two pile groups of 2x2) placed in a rigid soil container with energy absorbing boundaries. Redhill 110 sand was used and earthquake motions were applied to liquefy the soil. It was observed that the bending moment along the piles changed with the progression of liquefaction and the maximum bending moment occurred in the transient phase. It was also observed that the time taken to reach liquefaction may affect the amplification of the bending moment. Design of piles requires soil parameters and as a result, a series of multi stage soil element tests were carried out on four different types of sands; Redhill 110 sand, Japanese silica sand No. 8, Assam sand, and Ganga sand where the sands were first liquefied and then tests were carried out to obtain stress strain of liquefied sand (post liquefaction) The results showed that the post liquefaction behaviour of sand depends on the soil relative density. Furthermore, the results from the Redhill 110 sand were used to back analyse the shake table test results. Finally, a method has been proposed to incorporate transient behaviour of pile in liquefiable soils, based on an assessment of the estimated dynamics amplification factors in the shake table tests.  Dynamic soil pile interaction, Liquefaction, Shake table test, multi stage soil element test, transient dynamics, dynamic amplification factors.
Behavior of pile foundations in liquefied and laterally spreading ground. eScholarship

ASCE/AEG/UMKC Geotechnical Conference April 6, 2002 University Center, Pierson Auditorium University of Missouri at Kansas City Behavior of Pile Foundations in Liquefied and Laterally Spreading Ground By Priyanshu Singh 1 Scott J. Brandenberg 1 Ross W. Boulanger 2 Bruce L. Kutter 3 ABSTRACT Methods for predicting the performance of pile foundations in liquefying and laterally spreading ground during earthquakes have developed considerably in recent years. Nonetheless, the mechanisms of soil pile interaction in liquefied soil are still not well understood and the accuracy of design methods remains to be quantified. Subsequently, a series of dynamic centrifuge model experiments are being performed at UC Davis to study the behavior of single piles and pile groups in a soil profile comprised of a nonliquefied crust spreading laterally over a loose saturated sand layer. This paper will discuss some recent findings on the lateral resistance of liquefied soil, present initial evaluations of simplified pushover design methods against centrifuge test data, and summarize current recommendations for engineering practice.  Extensive damage to pile supported structures in areas of liquefaction and lateral spreading has been observed in many earthquakes around the world. A review of case histories and physical modeling studies shows that many important lessons and insights have been learned in recent years, but that numerous questions remain regarding the mechanisms of soil pile interaction in liquefied soil for many situations. In addition, the accuracy of our evolving design methods remains to be quantified. Predicting the behavior of a pile foundation in liquefying ground during an earthquake requires consideration of design motions, free field site response, superstructure response, and soil pile superstructure interaction. Evaluating pile performance requires consideration of the inertial and kinematic loads imposed on the piles and their pile cap connections, transient or permanent deformations of the pile foundation, the influence of the pile foundation on the dynamic Graduate student, Dept. of Civil Environmental Engrg. University of California, Davis, CA. Associate Professor, Dept. of Civil Environmental Engrg. University of California, Davis, CA. Professor, Department of Civil Environmental Engineering, University of California, Davis, CA.
Evaluation of the allowable axial bearing capacity of a single pile subjected to machine vibration by numerical analysis
Venue: International Journal of Geo Engineering

AbstractThe purpose of this study is to analyze the changes in the vertical load of the pile when the additional vibration load due to mechanical vibration acted to the single pile supporting a vibration machine, and to review the validity of the typical calculation method for the axial bearing capacity of a single pile supporting the vibration machine by numerical analysis. Firstly, the 3D numerical model for the load displacement behavior of a single pile was constituted. After the model was statically loaded to the allowable load in static analysis, the axial vibration due to machine vibration was added to the pile top in dynamic analysis. In these procedures, the static analysis was verified with the centrifuge test results for a single pile. Based on the analysis results, it was found that the additional dynamic load caused by machine vibration is about 6% of the allowable static load. It was thought that the design concepts of the machine foundation, assuming that the additional dynamic load due to machine vibration equals to 50% of the static load in current code, is excessively conservative.
Optimization of pile design for offshore wind turbine jacket foundations

The aim of this study is to use numerical methods of structural design optimization to design piles for offshore wind turbine jacket foundations. Pile mass is minimized with constraints on axial and lateral capacity. Results indicate that accurate knowledge about soil characteristics can translate into significant cost reductions. NOMENCLATURE d External diameter of the pile (m) di Internal diameter of the pile (m) l Length of the pile (m) t Thickness of pile wall (m) INTRODUCTION Foundation and substructure for offshore wind turbines can amount to more than 20 of the capital expenditure in a project. Pile anchoring a jacket foundation to the seabed requires to first perform a geological survey to map the soil characteristics and then design a pile with sufficient capacity to carry the loads from the substructure. Structural optimization  is the science of achieving the optimal load carrying structure. Given an objective such as compliance or cost, and some constraints such as limitations on the maximum stress or displacement, the optimal structure is defined as the one that minimizes the objective function while satisfying the constraints. A pile foundation is a slender hollow cylinder that is inserted into the soil. Anchoring by driven piles has been used extensively in the oil and gas industry, and in the last decade also for offshore wind turbines using either monopiles or piled jacket foundations. Pile foundation design is considered in this study according to the current state of practice for offshore foundations, see eg.   Axial and lateral capacities are calculated based on shaft friction and end bearing resistance and lateral resistance respectively. The obtained ultimate loads formulate the design basis.
Observations on Pile Design and Construction Practices in India

This paper reviews the design and construction practices on pile foundation being adopted in India observed over the last three decades. The factors that affect the choice of the pile have been discussed highlighting the necessity of initial field tests prior to the detailed design. A case study is presented where choice of the pile was made based on initial field tests on piles of promising types. The common problems faced during pile construction in each type of pile with possible remedial measures that can improve the performance are described. Various issues in pile design are reviewed with some of the experimental and numerical work carried out on lateral load on piles in slope, pile group effect under lateral load, negative drag force, rock socketed pile, etc. Finally, the need for more such full scale field tests and monitoring with instrumentation is emphasized to achieve an optimum pile design along with few case studies on such tests carried out. The review reveals remarkable improvements, both in the design and construction, comparable with that in other countries.
Assessment of Trace Elements in Tissues of Fish Species: Multivariate Study and Safety Evaluation

Levels of As, Cd, Cr, Cu, Li, Mn, Mo, Ni, Pb, Sb and Se in muscle, gill, stomach, liver, kidney and gonad tissues of six different fish species Caranx latus, Bagre marinus, Archosargus rhomboidalis, Lutjanus synagris, Scomberomorus cavalla and Sphyraena guachancho) from the Todos os Santos Bay (Bahia State, Brazil) were evaluated. The elements were determined by inductively coupled plasma mass spectrometry (ICP MS) after wet digestion using reflux system with a cold finger. The detected concentration ranges were as follows (mg kg 1 dry weight) 0.49 27.31 for As, 0.013 1.12 for Cd, 0.38 6.05 for Cr, 0.17 28.12 for Cu, 0.092 1.19 for Li, 0.16 55.9 for Mn, 0.034 1.24 for Mo, 0.067 15.57 for Ni, 0.013 0.60 for Pb, 0.144 for Sb and 0.57 14.6 for Se. Highest concentrations of trace elements were observed in kidney, liver and gill tissues.
Correlacao entre a capacidade vital lenta e o tempo maximo de fonacao em idosos

Objetivos: verificar a relacao existente entre a capacidade vital lenta e o tempo maximo de fonacao em idosos. Metodo: o estudo foi do tipo analitico e observacional, de corte transversal, realizado na Universidade aberta a Terceira Idade na instituicao de origem, no periodo de junho a outubro de 2014. Participaram 61 idosos do sexo feminino, nao tabagistas. Foram excluidos portadores de Doenca Pulmonar Obstrutiva Cronica e/ou doencas respiratorias, individuos com problemas neurologicos ou de audicao e profissionais da voz. Todos os participantes foram avaliados quanto a capacidade vital lenta e tempo maximo de fonacao. Foram coletados ainda os seguintes dados: sexo, peso, estatura, idade e indice de massa corporea. Resultados: os dados demonstram que os valores de capacidade vital lenta e tempo maximo de fonacao estao reduzidos na terceira idade. Alem disso, existe uma correlacao positiva entre a capacidade vital lenta e o tempo maximo de fonacao do /s/ e /z/ no sexo feminino. Conclusoes: com o envelhecimento, medidas de respiracao e voz podem estar reduzidas. Alem disso, existe uma associacao entre a capacidade vital lenta e o tempo maximo de fonacao em mulheres idosas, sugerindo a influencia que a respiracao exerce sobre a fonacao nesta populacao especifica.
Respuesta de la glucosa sanguinea en el ejercicio fisico maximo

Existen datos contradictorios en la respuesta aguda al ejercicio fisico maximo. Algunos factores incluyen dieta previa, condiciones de la prueba, protocolo de estudio, duracion e intensidad.  Evaluar la respuesta de la glucosa sanguinea al ejercicio fisico maximo sobre banda sin fi n en sujetos fisicamente acondicionados y sedentarios.  En la presente investigacion participaron dos grupos: Grupo I formado por 11 atletas corredores de medio y gran fondo, cuyo nivel de actividad fisica fue considerado como excelente y Grupo II constituido por 12 varones considerados como sedentarios.  La respuesta de la glucosa al ejercicio fisico maximo fue mayor en los acondicionados (D 58 mg/dL) que en los sedentarios (D 45 mg/dL) El estudio resulto ser signifi cativo (p 0.05) al comparar individuos acondicionados con sedentarios.  La cantidad de glucosa se incremento probablemente a una mayor respuesta en los receptores hepaticos y musculares de catecolaminas (epinefrina y norepinefrina) factor mediante el cual el organismo sustrae hidratos de carbono como fuente de energia al aumentar el numero de receptores en los acondicionados.
Recognizing Human Actions in the Motion Trajectories of Shapes
Venue: IUI

People naturally anthropomorphize the movement of nonliving objects, as social psychologists Fritz Heider and Marianne Simmel demonstrated in their influential 1944 research study. When they asked participants to narrate an animated film of two triangles and a circle moving in and around a box, participants described the shapes' movement in terms of human actions. Using a framework for authoring and annotating animations in the style of Heider and Simmel, we established new crowdsourced datasets where the motion trajectories of animated shapes are labeled according to the actions they depict. We applied two machine learning approaches, a spatial temporal bag of words model and a recurrent neural network, to the task of automatically recognizing actions in these datasets. Our best results outperformed a majority baseline and showed similarity to human performance, which encourages further use of these datasets for modeling perception from motion trajectories. Future progress on simulating human like motion perception will require models that integrate motion information with top down contextual knowledge.