nils-herrmann/clean_scirepeval huggingface dataset:
Simple Random Sampling Estimation of the Number of Local Optima
Venue: PPSN

We evaluate the performance of estimating the number of local optima by estimating their proportion in the search space using simple random sampling (SRS) The performance of this method is compared against that of the jackknife method. The methods are used to estimate the number of optima in two landscapes of random instances of some combinatorial optimisation problems. SRS provides a cheap, unbiased and accurate estimate when the proportion is not exceedingly small. We discuss choices of confidence interval in the case of extremely small proportion. In such cases, the method more likely provides an upper bound to the number of optima and can be combined with other methods to obtain a better lower bound. We suggest that SRS should be the first choice for estimating the number of optima when no prior information is available about the landscape under study.
ON SIMPLE RANDOM SAMPLING WITH REPLACEMENT

In simple random sampling with replacement, Basu (1958) and Des Raj and Khamis (1958) showed that for estimating the population mean, the average of distinct units is more efficient than the overall sample mean. In this paper, a detailed treatment of the above problem is given, and the exact expression for the variance of above estimator is derived. The relative efficiency of the above estimator with other estimators is also considered. An improved estimator of the population variance is obtained. Finally, a comparison between the two simple random sampling schemes (with and without replacement) is made.
Multilayer fluorescence imaging on a single pixel detector.
Venue: Biomedical optics express

A critical challenge for fluorescence imaging is the loss of high frequency components in the detection path. Such a loss can be related to the limited numerical aperture of the detection optics, aberrations of the lens, and tissue turbidity. In this paper, we report an imaging scheme that integrates multilayer sample modeling, ptychography inspired recovery procedures, and lensless single pixel detection to tackle this challenge. In the reported scheme, we directly placed a 3D sample on top of a single pixel detector. We then used a known mask to generate speckle patterns in 3D and scanned this known mask to different positions for sample illumination. The sample was then modeled as multiple layers and the captured 1D fluorescence signals were used to recover multiple sample images along the z axis. The reported scheme may find applications in 3D fluorescence sectioning, time resolved and spectrum resolved imaging. It may also find applications in deep tissue fluorescence imaging using the memory effect.
Indel variant analysis of short read sequencing data with Scalpel
Venue: Nature Protocols

As the second most common type of variation in the human genome, insertions and deletions (indels) have been linked to many diseases, but the discovery of indels of more than a few bases in size from short read sequencing data remains challenging. Scalpel (http:/scalpel.sourceforge.net) is an open source software for reliable indel detection based on the microassembly technique. It has been successfully used to discover mutations in novel candidate genes for autism, and it is extensively used in other large scale studies of human diseases. This protocol gives an overview of the algorithm and describes how to use Scalpel to perform highly accurate indel calling from whole genome and whole exome sequencing data. We provide detailed instructions for an exemplary family based de novo study, but we also characterize the other two supported modes of operation: single sample and somatic analysis. Indel normalization, visualization and annotation of the mutations are also illustrated. Using a standard server, indel discovery and characterization in the exonic regions of the example sequencing data can be completed in ~5 h after read mapping.
Examining Leadership Articles: Which Characteristics and How Leadership Comprises?

Bu arastirmada, Turkiye'deki bilimsel dergilerde yayinlanan liderlik konulu makalelerin; calisma alanlarinin, kullanilan yontem ve orneklem buyuklugu gibi metodolojik ozelliklerinin, calismalarin yapildigi egitim kademelerinin, calismaya konu olan oznelerin ve bu calismalarda liderligin hangi sifatlari aldiginin belirlenmesi amaclanmistir. Arastirmanin evrenini 2002 yilindan itibaren Ulusal Akademik Ag ve Bilgi Merkezi (ULAKBIM)'nde dizinlenen ve Sosyal ve Beseri Bilimler Veri Tabaninda yer alan liderlik konulu 410 makale olusturmaktadir. Durum calismasi deseninde tasarlanan arastirmanin orneklemi, olcut ornekleme yontemi kullanilarak belirlenmistir. Calismanin ornekleminin belirlenmesinde; liderlik kavraminin, kendini niteleyen baska bir kavramla birlikte calisma basliginda yer almasi olcut olarak kabul edilmistir. Belirtilen olcutu saglayan 117 makale arastirmanin ornekleminde yer almistir. Arastirmanin sonucunda; diger alanlarla kiyaslandiginda liderligin en fazla egitim alaninda incelendigi tespit edilmistir. Liderlik arastirmalarinin cogunlugunda 76.1) nicel arastirma yontemleri kullanilmistir. Nicel arastirmalar icinde ise en cok iliskisel tarama modeli tercih edilmistir. Iliskisel tarama modelini kullanan arastirmalar, nicel liderlik arastirmalarinin 51'ini; liderlik arastirmalarinin tamaminin 38'ini olusturmustur. Liderlik etik, donusumcu, paternalist, vizyoner gibi 53 sifatla nitelendirilmistir. Donusumcu liderligi farkli sekillerde adlandiran tum arastirmalar degerlendirildiginde, arastirmalarin dortte birinin donusumcu liderlik ile ilgili oldugu sonucuna varilmistir
Insights into global diatom distribution and diversity in the world's ocean
Venue: Proceedings of the National Academy of Sciences

Diatoms, considered one of the most diverse and ecologically important phytoplanktonic groups, contribute around 20% of global primary productivity. They are particularly abundant in nutrient rich coastal ecosystems and at high latitudes. Here, we have explored the dataset generated by Tara Oceans from a wide range of oceanic regions to characterize diatom diversity patterns on a global scale. We confirm the dominance of diatoms as a major photosynthetic group and identify the most widespread and diverse genera. We also provide a new estimate of marine planktonic diatom diversity and a global view of their distribution in the world's ocean. Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of ~12 million diatom V9 18S ribosomal DNA (rDNA) ribotypes, derived from 293 size fractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs) Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron. We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered.
NbCZF1, a Novel C2H2 Type Zinc Finger Protein, as a New Regulator of SsCut Induced Plant Immunity in Nicotiana benthamiana.
Venue: Plant cell physiology

SsCut, which functions as an elicitor, can induce plant immunity. In this study, we utilized Nicotiana benthamiana and virus induced gene silencing to decrease the expression of 2,500 genes individually. Using this forward genetics approach, several genes were identified that, when silenced, compromised SsCut triggered cell death based on a cell death assay. A C2H2 type zinc finger gene was isolated from N. benthamiana Sequence analysis indicated that the gene encodes a 27 kDa protein with 253 amino acids containing two typical C2H2 type zinc finger domains; this gene was named NbCZF1 We found that SsCut induced cell death could be inhibited by virus induced gene silencing of NbCZF1 in N. benthamiana In addition, SsCut induces stomatal closure, accompanied by reactive oxygen species (ROS) production by NADPH oxidases and nitric oxide (NO) production. NbCZF1 silenced plants showed impaired SsCut induced stomatal closure, decreased SsCut induced production of ROS and NO in guard cells and reduced SsCut induced resistance against Phytophthora nicotianae Taken together, these results demonstrate that the NbCZF1 ROS NO pathway mediates multiple SsCut triggered responses, including stomatal closure, hypersensitive responses and defense related gene expression. This is the first report describing the function of a C2H2 type zinc finger protein in N. benthamiana.
Investigation into gas production from natural gas hydrate: A review

Natural gas hydrates (NGHs) which extensively exist in sea floor and permafrost regions, are considered as an alternative energy in the future for the fossil fuels approaching depletion with the gradually increasing energy consumption. Because of the particularity of NGH stabilizing only in the conditions of the high pressure and the low temperature, the exploitation of NGH is distinguished from those of petroleum and natural gas. Researchers over the world are devoting themselves to developing the technologies of NGH exploitation. However, till now, few NGH exploitation technology is identified and employed to exploit commercially NGH. Although there do be two cases of short term NGH exploitation in Mackenzie Delta (CAN) Alaska North Slope (USA) and Nankai Trough (JAP) in the past 10years. It is mainly because some characteristics of the flow (gas, water, gas hydrate slurry, quicksand, etc. the issues of heat and mass transfer, the risk assessment and the economic evaluation are still not comprehensively recognized. Presently, the researches of NGH exploitation are mainly carried out from three aspects, numerical simulation and analysis, experimental simulation and field trial exploitation for the different technologies. In this paper, we comprehensively review the relevant studies of NGHs and propose our comments. We not only represent the achievements for the NGH exploitation researches, but also discuss the limitations and challenges, raise some questions and put forward some suggestions from our points of view.
Assessment of gas production from natural gas hydrate using depressurization, thermal stimulation and combined methods

The largest sources of hydrocarbons worldwide are distributed in the permafrost and submarine sediments in the form of methane hydrates, but exploitation of these hydrocarbons is still years away from being economical, safe, and commercially viable; thus, further research is needed. To analyze the characteristics of methane hydrate (MH) dissociation and evaluate the gas production during the application of different MH decomposition methods, this study firstly compared MH dissociation during depressurization, thermal stimulation, and combined method (depressurization thermal stimulation) treatments using magnetic resonance imaging (MRI) in situ observation. In particular, the influences of back pressure and temperature on hydrate dissociation, the hydrate saturation, the rate of hydrate dissociation and MRI images from each of the three methods were investigated. The results proved that during application of the depressurization and combined methods at different back pressures (2.2 2.6 MPa) the MH dissociation proceeded via radial dissociation rather than axial dissociation; moreover, during the application of the thermal stimulation method at different dissociation temperatures (278.15 288.15 K) the MH dissociated uniformly. Overall, a combination of depressurization and thermal stimulation at the initial stage of hydrate decomposition was proposed and comparison of the three methods demonstrated that the combined method had obvious advantages for methane treatment. Specifically, the combined method was capable of solving the problems related to low gas production and poor energy efficiency that were encountered when using either the depressurization or thermal stimulation method alone.
The music of trees: the intergenerative tie between primary care and public health
Venue: London journal of primary care

Stories help us frame and understand complex ideas and challenges. Metaphors are particularly powerful linguistic devices that guide and extend our thinking by bridging conceptual domains, for example to consider the brain as a digital computer. Trees are widely used as metaphors for broad concepts like evolution, history, society, and even life itself, i.e. 'the tree of life' Tree like diagrams of roots and branches are used to demonstrate historical and cultural relationships, for example, between different species or different languages. In this paper, we describe a theatrical character called a tree doctor which is a living metaphor. A human being, namely the author, lectures, acts or dances as a tree and offers lessons to Homo Sapiens about 'holistic' ideas of health. The character teaches us to not only see the value of our relationships to trees, but the importance of seeing forests as well the individual trees. The metaphorical statement that we should not 'miss the forest for the trees' means we should learn to think of health embedded in systems and communities. In medicine, we too often focus on individual molecules, pharmaceuticals, or even patients and miss the bigger picture of public and environmental health. In a time of great ecological system change, the tree doctor points to broad ethical responsibility for each other and future generations of humans and other living creatures. The character embraces arts and particularly music as a powerful way of infusing purpose and improving the qualities of our lives together, especially as we age. The tree doctor knows the value of intergenerational relationships. But it also points to intergenerative innovations across many cultural domains, disciplines and professions. The tree doctor supports primary care and empowers the value of intergenerational relationships, art and music in the recommendations doctors make to patients to improve their health and well being.
The Non convex Geometry of Low rank Matrix Optimization

This work considers two popular minimization problems: (i) the minimization of a general convex function $f(\mathbf{X} with the domain being positive semi definite matrices; (ii) the minimization of a general convex function $f(\mathbf{X} regularized by the matrix nuclear norm \mathbf{X}|_* with the domain being general matrices. Despite their optimal statistical performance in the literature, these two optimization problems have a high computational complexity even when solved using tailored fast convex solvers. To develop faster and more scalable algorithms, we follow the proposal of Burer and Monteiro to factor the low rank variable \mathbf{X} \mathbf{U}\mathbf{U}\top (for semi definite matrices) or \mathbf{X}\mathbf{U}\mathbf{V}\top (for general matrices) and also replace the nuclear norm \mathbf{X}|_* with \mathbf{U}|_F^2+\mathbf{V}|_F^2)/2$ In spite of the non convexity of the resulting factored formulations, we prove that each critical point either corresponds to the global optimum of the original convex problems or is a strict saddle where the Hessian matrix has a strictly negative eigenvalue. Such a nice geometric structure of the factored formulations allows many local search algorithms to find a global optimizer even with random initializations.
Total Variation Regularized Low Rank Matrix Factorization for Hyperspectral Image Restoration
Venue: IEEE Transactions on Geoscience and Remote Sensing

In this paper, we present a spatial spectral hyperspectral image (HSI) mixed noise removal method named total variation (TV) regularized low rank matrix factorization (LRTV) In general, HSIs are not only assumed to lie in a low rank subspace from the spectral perspective but also assumed to be piecewise smooth in the spatial dimension. The proposed method integrates the nuclear norm, TV regularization, and L1 norm together in a unified framework. The nuclear norm is used to exploit the spectral low rank property, and the TV regularization is adopted to explore the spatial piecewise smooth structure of the HSI. At the same time, the sparse noise, which includes stripes, impulse noise, and dead pixels, is detected by the L1 norm regularization. To tradeoff the nuclear norm and TV regularization and to further remove the Gaussian noise of the HSI, we also restrict the rank of the clean image to be no larger than the number of endmembers. A number of experiments were conducted in both simulated and real data conditions to illustrate the performance of the proposed LRTV method for HSI restoration.
A family of subgradient based methods for convex optimization problems in a unifying framework
Venue: Optim. Methods Softw.

We propose a new family of subgradient and gradient based methods which converges with optimal complexity for convex optimization problems whose feasible region is simple enough. This includes cases where the objective function is non smooth, smooth, have composite/saddle structure, or are given by an inexact oracle model. We unified the way of constructing the subproblems which are necessary to be solved at each iteration of these methods. This permitted us to analyse the convergence of these methods in a unified way compared to previous results which required different approaches for each method/algorithm. Our contribution rely on two well known methods in non smooth convex optimization: the mirror descent method (MDM) by Nemirovski Yudin and the dual averaging method by Nesterov. Therefore, our family of methods includes them and many other methods as particular cases. For instance, the proposed family of classical gradient methods and its accelerations generalize Devolder et al.'s, Nesterov's primal/dual gradient methods, and Tseng's accelerated proximal gradient methods. Also our family of methods can partially become special cases of other universal methods, too. As an additional contribution, the novel extended MDM removes the compactness assumption of the feasible region and the fixation of the total number of iterations which is required by the original MDM in order to attain the optimal complexity.
Guia de recomendaciones para diseno de software centrado en el usuario

En este libro se aborda toda la tematica relacionada con las interfaces del usuario y su proceso de desarrollo. Se profundiza sobre la etapa de diseno de interfaces especificas, brindando una serie de recomendaciones que permitan alcanzar la calidad de uso del producto. El libro presenta una organizacion que consiste en seis capitulos, acompanados por ejercitacion, casos de estudio y referencias especificas a cada uno. En el capitulo 1 se introducen los conceptos basicos de la Interaccion Hombre Computadora. Se incluye una breve referencia a su evolucion, se aborda el paradigma de independencia de dialogo y metricas de evaluacion de una interfaz. El capitulo 2 abarca el proceso de diseno de la interfaz de usuario, haciendo hincapie en las caracteristicas mas importantes, el ciclo de vida de la interfaz de usuario y la prototipacion como metodologia de desarrollo de una interfaz de usuario. Desde el capitulo 3 al 5, el libro se adentra en recomendaciones de diseno para interfaces especificas como interfaces visuales, iconicas e interfaces para la Web. En el capitulo 6 y ultimo se introducen los conceptos de accesibilidad y las normas internacionales para construir interfaces accesibles. Al finalizar cada capitulo, se dispone de un conjunto de ejercicios practicos y un caso de estudio relacionado con la tematica. En general, versan sobre la aplicacion de las recomendaciones a versiones prototipicas de sistemas desarrollados por los alumnos durante la cursada de la materia. Se han seleccionado para estos casos las mejores entregas de las distintas cohortes del dictado de la materia de Diseno Centrado en el Usuario. Se incluye tambien un anexo con el glosario de terminos y la resolucion de las ejercitaciones planteadas en cada capitulo.
Phytochemical Proximate and Mineral contents of Leaves and Back of Ficus Capensis

The phytochemical, proximate and mineral contents of Ficus capensis (leaves bark) were analyzed, using Trease and Evans and Harboure procedure, the Association of Official Analytical Chemist (AOAC) method and Atomic Absorption Spectrophotometry and Flame Photometry respectively. This study is aimed at evaluating (using ethanol and water as solvents) the nutrient composition, phytochemical constituents and minerals present. The results of the phytochemical screening showed the presence of tannins, terpenoids, alkaloids, flavonoids, cardiac glycosides and reducing sugars, with steroids and anthraquinones absent in the water extract of the leaves and bark of Ficus capensis. Saponin was however present in the bark but absent in the leaves (water extract) of the plants. Terpenoids, flavonoids, steroids, cardiac glycosides and reducing sugars were present in ethanol extract of the leaves and bark, while anthraquinones were absent. Alkaloids were present in the ethanol extracts of the bark but absent in leaves. The proximate analysis of the leaves and bark of Ficus capensis yielded 25.80% and 10% for moisture, 17.47% and 3.73% for proteins, 1.80% and 2% for crude fat, 11.00% and 10.95% for ash, 41.00% and 20.5% for crude fiber and 2.93% and 52.82% for carbohydrates respectively. The mineral analysis of the leaves and bark of the plant yielded calcium 2640.00mg/kg and 1772mg/kg, magnesium2383.00mg/kg and 1605mg/kg, iron25.00mg/kg and 6.6mg/kg, zinc 29.30mg/kg and 4.4mg/kg, copper 14.60mg/kg and 6mg/kg and phosphorus 1012mg/kg and 305mg/kg. Manganese was absent in the bark but yielded 1.1mg/kg in the leaves. Sodium and potassium were not detected in the leaves but yielded the values 97.2mg/kg and 126.4mg/kg in the bark. The presence of some phytochemicals (saponins, alkaloids, flavonoids, cardiac glycosides, tannins and terpenoids) and some essential minerals proves that it is really an alternative source of medicine.(c) JASEM http:/dx.doi.org/10.4314/jasem.v19i4.10