bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of the Leray-Schauder degree for elliptic operators in unbounded domains
Authors: Volpert A.I. , Volpert V.A. 
Published: February 2017

This paper is devoted to a construction of the Leray–Schauder degree for quasilinear elliptic operators in unbounded domains. The main problem here is that such operators can not be reduced to compact ones and the usual theory (
see
[1]) can not be applied. In [2, 3] the Leray–Schauder degree was constructed in one dimensional case. To do this certain lower estimates of the operators were obtained and the approach of Skrypnik [4] was applied. In this paper we generalize these results to the multidimensional case. When the degree is defined the Leray–Schauder method can be used to prove the existence of solutions [3].

Résumé
Cet article est consacré à la construction du degré de Leray–Schauder pour les opérateurs elliptiques dans les domaines non bornés. Le problème essentiel ici est que ces opérateurs ne peuvent pas être réduits à des compacts. Par conséquent, on ne peut pas utiliser la théorie habituelle [1]. Dans [2, 3] le degré est construit pour les cas monodimen-sionnel. Pour cette construction, certaines estimations des opérateurs sont obtenues, et l’approche de Skrypnik [4] est utilisée. Dans cet article, nous généralisons ces résultats pour le cas multidimensionnel. Quand le degré est déterminé, la méthode de Leray–Schauder peut être appliquée pour prouver l’existence de solutions [3].
A uniqueness result in the theory of stereo vision: Coupling Shape from Shading and Binocular Information allows Unambiguous Depth Reconstruction
Authors: Chambolle Antonin 
Published: February 2017

We study here the mathematical consistency of coupling two classical methods in the theory of vision and surface reconstruction, namely the
shape from shading
theory and the theory of stereo vision. It is known that each of these approaches by itself is incomplete and leads to ill posed problems and multiple solutions, even under drastic simplifying assumptions. We show in this paper that, from a mathematical point of vue, these ambiguities disappear when both theories are cooperatively implemented. In section 2 we state our assumptions; then part 3 is devoted to the presentation of the binocular vision theory. Section 4 eventually studies, in the one and two dimensional case, how introducing the
shape from shading
tool leads to the uniqueness of the solution. In the annex (section 6), a few mathematical results are explained, and some experiments (in 1 D) are presented.

Résumé

Nous étudions ici la consistance mathématique du couplage de deux méthodes classiques de reconstruction visuelle, à savoir la théorie du
shape from shading
, qui vise à retrouver le relief d’une surface à partir des ombres et variations d’intensité lumineuse de son image, et la théorie de la vision binoculaire (la « vision stéréo » au sens usuel). Chacune de ces approches est incomplète et conduit à des problèmes mal posés à solutions multiples. Dans cet article nous montrons que d’un point de vue mathématique ces inconvénients disparaissent lorsqu’on met à contribution de manière coopérative les deux méthodes.

Dans la section 2 on établit un certain nombre d’hypothèses simplificatrices, puis la partie suivante 3 est consacrée à la présentation de notre modèle de vision binoculaire. Finalement nous montrons (section 4) dans les cas uni- et bidimensionnel, comment l’introduction du
shape from shading
supprime les ambiguités. Le détail des résultats mathématiques de trouve en annexe, ainsi que la présentation de quelques résultats de simulations numériques (en dimension un).
A notion of total variation depending on a metric with discontinuous coefficients
Authors: Amar M. , Bellettini G. 
Published: February 2017

Given a function

u:\mathrm{\Omega } \subseteq ℝ^{n}\rightarrow ℝ

, we introduce a notion of total variation of

u

depending on a possibly discontinuous Finsler metric. We prove some integral representation results for this total variation, and we study the connections with the theory of relaxation.

Résumé

Étant donnée une fonction

u:\mathrm{\Omega } \subseteq ℝ^{n}\rightarrow ℝ

, on définit une notion de variation totale de

u

, dépendant d’une métrique Finslérienne discontinue. On démontre quelques résultats de représentation intégrale pour cette variation totale et ses relations avec la théorie de la relaxation.
On the singular support of the distributional determinant
Authors: Müller Stefan 
Published: February 2017

Let

Ω ⊂ ℝ^n

be bounded and open, let

p ≧ n^2/(n + 1)

and let

u: Ω → ℝ^n

be in the Sobolevspace

W^{1, n} (Ω; ℝ^n)

. This paper discusses the singular part of the distributional determinant

\mathrm{Det\, D}u

and shows the existence of functions

u

for which that singular part is supported in a set of prescribed Hausdorff-dimension

α \in (0, n)

. For

n = 2

and simply connected

Ω

the problem is equivalent to analyzing

\mathrm{div} (bv) − b.\mathrm Dv

where

v\in W^{1, p} (Ω; ℝ^2)

with

\mathrm{div} b = 0

.

Résumé

Soit

Ω ⊂ ℝ^n

un ouvert borné, soit

p ≧ n^2/(n + 1)

et soit

u: Ω → ℝ^n

dans l’espace de Sobolev

W^{1, p} (Ω; ℝ^n)

. On construit des applications

u

dont le déterminant au sens de distributions

\mathrm{Det\, D}u

est une mesure de Radon positive, portée par un ensemble singulier dont la dimension de Hausdorff est arbitraire, strictement entre

0

et

n

.
Three or More Courses of Stereotactic Radiosurgery for Patients with Multiply Recurrent Brain Metastases
Authors: Kotecha Rupesh , Damico Nicholas , Miller Jacob A. , Suh John H. , Murphy Erin S. , Reddy Chandana A. , Barnett Gene H. , Vogelbaum Michael A. , Angelov Lilyana , Mohammadi Alireza M. , Chao Samuel T. 
Published: February 2017

Abstract

BACKGROUND: Although patients with brain metastasis are treated with primary stereotactic radiosurgery (SRS), the use of salvage therapies and their consequence remains understudied.

OBJECTIVE: To study the intracranial recurrence patterns and salvage therapies for patients who underwent multiple SRS courses.

METHODS: A retrospective review was performed of 59 patients with brain metastases who underwent ≥3 SRS courses for new lesions. Cox regression analyzed factors predictive for overall survival.

RESULTS: The median age at diagnosis was 52 years. Over time, patients underwent a median of 3 courses of SRS (range: 3-8) to a total of 765 different brain metastases. The 6-month risk of distant intracranial recurrence after the first SRS treatment was 64% (95% confidence interval: 52%-77%). Overall survival was 40% (95% confidence interval: 28%-53%) at 24 months. Only 24 patients (41%) had a decline in their Karnofsky Performance Status ≤70 at last office visit. Quality of life was preserved among 77% of patients at 12 months, with 45% experiencing clinically significant improvement during clinical follow-up. Radiation necrosis developed in 10 patients (17%). On multivariate analysis, gender (males, Hazard Ratio [HR]: 2.0, P < .05), Karnofsky Performance Status ≤80 (HR 3.2, P < .001), extracranial metastases (HR: 3.6, P < .001), and a distant intracranial recurrence ≤3 months from initial to repeat SRS (HR: 3.8, P < .001) were associated with a poorer survival.

CONCLUSION: In selected patients, performing ≥3 SRS courses controls intracranial disease. Patients may need salvage SRS for distant intracranial relapse, but focal retreatments are associated with modest toxicity, do not appear to negatively affect a patient's performance status, and help preserve quality of life.
Importance and Difficulties of Pursuing rTMS Research in Acute Stroke
Authors: Carey James R. , Chappuis Diane M. , Finkelstein Marsha J. , Frost Kate L. , Leuty Lynette K. , McNulty Allison L. , Oddsson Lars I. E. , Seifert Erin M. , Kimberley Teresa J. 
Published: February 2017

Abstract
Although much research has been done on repetitive transcranial magnetic stimulation (rTMS) in chronic stroke, only sparse research has been done in acute stroke despite the particularly rich potential for neuroplasticity in this stage. We attempted a preliminary clinical trial in one active, high-quality inpatient rehabilitation facility (IRF) in the -United States. But after enrolling only 4 patients in the grant period, the study was stopped because of low enrollment. The purpose of this paper is to offer a perspective describing the important physiologic rationale for including rTMS in the early phase of stroke, the reasons for our poor patient enrollment in our attempted study, and recommendations to help future studies succeed. We conclude that, if scientists and clinicians hope to enhance stroke outcomes, more attention must be directed to leveraging conventional rehabilitation with neuromodulation in the acute phase of stroke when the capacity for neuroplasticity is optimal. Difficulties with patient enrollment must be addressed by reassessing traditional inclusion and exclusion criteria. Factors that shorten patients’ length of stay in the IRF must also be reassessed at all policy-making levels to make ethical decisions that promote higher functional outcomes while retaining cost consciousness.
Persistent homology: a tool to universally measure plant morphologies across organs and scales
Authors: Li Mao , Frank Margaret H. , Coneva Viktoriya , Mio Washington , Topp Christopher N. , Chitwood Daniel H. 
Published: February 2017

AbstractGenetic contributions to plant morphology are not partitioned between shoots and roots. Yet, shoot and root architectures are rarely measured in the same plants. Even if shoot and root architectures are both studied, the application of mathematical methods flexible enough to accommodate the disparate topologies and shapes within a plant, and across scales, are lacking. Here, we advocate the use of persistent homology, a mathematical method robust to noise, invariant with respect to orientation, capable of application across diverse scales, and importantly, compatible with diverse functions to quantify disparate plant morphologies, architectures, and textures. To demonstrate the usefulness of this method, we apply persistent homology approaches to the shape of leaves, serrations, and root architecture as measured in the same plants of a domesticated tomato Solanum pennellii near-isogenic introgression line population under field conditions. We find that genetic contributions to morphology affect the plant in a concerted fashion, affecting both the shoot and root, revealing a pleiotropic basis to natural variation in tomato.
Extensive Copy Number Variation in Fermentation-Related Genes amongSaccharomyces cerevisiaeWine Strains
Authors: Steenwyk Jacob , Rokas Antonis 
Published: February 2017

AbstractDue to the importance ofSaccharomyces cerevisiaein wine-making, the genomic variation of wine yeast strains has been extensively studied. One of the major insights stemming from these studies is that wine yeast strains harbor low levels of genetic diversity in the form of single nucleotide polymorphisms (SNPs). Genomic structural variants, such as copy number (CN) variants, are another major type of variation segregating in natural populations. To test whether genetic diversity in CN variation is also low across wine yeast strains, we examined genome-wide levels of CN variation in 132 whole-genome sequences ofS. cerevisiaewine strains. We found an average of 97.8 CN variable regions (CNVRs) affecting ~4% of the genome per strain. Using two different measures of CN diversity, we found that gene families involved in fermentation-related processes such as copper resistance (CUP), flocculation (FLO), and glucose metabolism (HXT), as well as theSNOgene family whose members are expressed before or during the diauxic shift showed substantial CN diversity across the 132 strains examined. Importantly, these same gene families have been shown, through comparative transcriptomic and functional assays, to be associated with adaptation to the wine fermentation environment. Our results suggest that CN variation is a substantial contributor to the genomic diversity of wine yeast strains and identify several candidate loci whose levels of CN variation may affect the adaptation and performance of wine yeast strains during fermentation.
Predicting how and when hidden neurons skew measured synaptic interactions
Authors: Brinkman Braden A. W. , Rieke Fred , Shea-Brown Eric , Buice Michael A. 
Published: February 2017

AbstractA major obstacle to understanding neural coding and computation is the fact that experimental recordings typically sample only a small fraction of the neurons in a circuit. Measured neural properties are skewed by interactions between recorded neurons and the “hidden” portion of the network. To properly interpret neural data and determine how biological structure gives rise to neural circuit function, we thus need a better understanding of the relationships between measured effective neural properties and the true underlying physiological properties. Here, we focus on how the effective spatiotemporal dynamics of the synaptic interactions between neurons are reshaped by coupling to unobserved neurons. We find that the effective interactions from a pre-synaptic neuronr′to a post-synaptic neuronrcan be decomposed into a sum of the true interaction fromr′torplus corrections from every directed path fromr′torthrough unobserved neurons. Importantly, the resulting formula reveals when the hidden units have—or do not have—major effects on reshaping the interactions among observed neurons. As a particular example of interest, we derive a formula for the impact of hidden units in random networks with “strong” coupling—connection weights that scale with, whereNis the network size, precisely the scaling observed in recent experiments. With this quantitative relationship between measured and true interactions, we can study how network properties shape effective interactions, which properties are relevant for neural computations, and how to manipulate effective interactions.
An Evaluation of Machine-learning for Predicting Phenotype: Studies in Yeast, Rice, and Wheat
Authors: Grinberg Nastasiya F. , Orhobor Oghenejokpeme I. , King Ross D. 
Published: February 2017

AbstractIn phenotype prediction, the physical characteristics of an organism are predicted from knowledge of its genotype and environment. Such studies are of the highest societal importance, as they are of central importance to medicine, crop-breeding, etc. We investigated three phenotype prediction problems: one simple and clean (yeast), and the other two complex and real-world (rice and wheat). We compared standard machine learning methods (elastic net, ridge regression, lasso regression, random forest, gradient boosting machines (GBM), and support vector machines (SVM)), with two state-of-the-art classical statistical genetics methods (including genomic BLUP). Additionally, using the clean yeast data, we investigated how performance varied with the complexity of the biological mechanism, the amount of observational noise, the number of examples, the amount of missing data, and the use of different data representations. We found that for almost all phenotypes considered standard machine learning methods outperformed the methods from classical statistical genetics. On the yeast problem, the most successful method was GBM, followed by lasso regression, and the two statistical genetics methods; with greater mechanistic complexity GBM was best, while in simpler cases lasso was superior. When applied to the wheat and rice studies the best two methods were SVM and BLUP. The most robust method in the presence of noise, missing data, etc. was random forests. The classical statistical genetics method of genomic BLUP was found to perform well on problems where there was population structure, which suggests one way to improve standard machine learning methods when population structure is present. We conclude that the application of machine learning methods to phenotype prediction problems holds great promise.
Assessment of the World Largest Afforestation Program: Success, Failure, and Future Directions
Authors: Zhu J. J. , Zheng X. , Wang G.G. , Wu B.F. , Liu S.R. , Yan C.Z. , Li Y. , Sun Y.R. , Yan Q.L. , Zeng Y. , Lu S.L. , Li X. F. , Song L.N. , Hu Z. B. , Yang K. , Yan N.N. , Li X.S. , Gao T. , Zhang J. X. , Ellison Aaron M. 
Published: February 2017

AbstractThe Three-North Afforestation Program (TNAP), initiated in 1978 and scheduled to be completed in 2050, is the world’s largest afforestation project and covers 4.07 x 106km2(42.4%) of China. We systematically assessed goals and outcomes of the first 30 years of the TNAP using high-resolution remote sensing and ground survey data. With almost 23 billion dollars invested between 1978 and 2008, the forested area within the TNAP region increased by 1.20 × 107ha, but the proportion of high quality forests declined by 15.8%. The establishment of shelterbelts improved crop yield by 1.7%, much lower than the 5.9% expected once all crop fields are fully protected by shelterbelts. The area subjected to soil erosion by water decreased by 36.0% from 6.72 × 107to 4.27 × 107ha; the largest reductions occurred in areas where soil erosion had been most severe and forests contributed more than half of this improvement. Desertification area increased from 1978 to 2000 but decreased from 2000 to 2008; the 30-year net reduction was 13.0% (4.05×106ha), with 8.0% being accounted for by afforestation in areas with only slight, prior desertification. In addition to its direct impacts, the TNAP has enhanced people’s awareness of environmental protection and attracted consistent attention and long-term commitment from the Chinese government to the restoration and protection of fragile ecosystems in the vast Three-North region. The significant decline in forest quality, limited success in reducing desertification, and low coverage of shelterbelts are aspects of the TNAP in need of re-assessment, and additional ca. 34 billion dollars will be needed to ensure the completion of the TNAP.
Free energy based high-resolution modeling of CTCF-mediated chromatin loops for human genome
Authors: Dawson Wayne , Plewczynski Dariusz 
Published: February 2017

AbstractIn recent years, chromatin has been found to have considerable structural organization in the human genome with diverse parts of the chromatin interacting with each other to form what have been termed topologically associated domains (TADs). Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is a recent protein-specific method that measures these chromatin interactions via specific interactions such as CTCF-cohesin binding proteins or RNA polymerase II interactions. Unlike high-throughput chromosome conformation capture (Hi-C), which measures unspecific binding (all against all), ChIA-PET measures specific protein-protein contact interactions; hence physical bonds that reflect binding free energies. In this work, a thermodynamic method for computing the stability and dynamics of chromatin loops is proposed. The CTCF-mediated interactions, as observed in ChIA-PET experiments for human B-lymphoblastoid cells, are evaluated in terms of a chain folding polymer model and the experimentally observed frequency of contacts within the chromatin regions. To estimate the optimal free energy and a Boltzmann distribution of suboptimal structures, the approach uses dynamic programming with methods to handle degeneracy and heuristics to compute parallel and antiparallel chain stems and pseudoknots. Moreover, multiple loops mediated by CTCF protein binding that connects together more than one chain into multimeric islands are simulated using the model. Based on the thermodynamic properties of those topological three-dimensional structures, we predict the correlation between the relative activity of chromatin loop and the Boltzmann probability, or the minimum free energy, depending also on its genomic length. The results show that segments of chromatin where the structures show a more stable minimum free energy (for a given genomic distance) tend to be inactive, whereas structures that have lower stability in the minimum free energy (with the same genomic distance) tend to be active.
First indication of acetylcholine-based communication in honeybee haemocytes and its modulation by a neonicotinoid insecticide
Authors: Pamminger T. , Basley K. , Goulson D , Hughes WOH 
Published: February 2017

AbstractThere is growing concern that some managed and wild insect pollinator populations are in decline, potentially threatening biodiversity and sustainable food production on a global scale. In recent years, there has been increasing evidence that sub-lethal exposure to neurotoxic, neonicotinoid pesticides can negatively affect pollinator immunocompetence and amplify the effects of diseases, likely contributing to pollinator declines. Here we show that a range of non-neural tissues and haemocytes of the honeybeeApis melliferaexpress the nicotinic acetylcholine receptor that is the target of neonicotinoids. In addition, we demonstrate that the haemocytes, which form the cellular arm of the innate immune system, actively synthesize acetylcholine. This suggests the presence of a neural-independent acetylcholine-based immune signalling system in insects similar to that found in vertebrates. Lastly we establish that field-relevant doses of the neonicotinoid insecticide clothianidin alter this communication system. These findings provide a novel, mechanistically informed framework to understand the numerous siede-effects on insects of sub-lethal pesticide exposure, including immunosuppression. They support the growing evidence for acetylcholine-based immune regulation in invertebrates that operates independently of the nervous system.
Millennia of genomic stability within the invasive Para C Lineage ofSalmonella enterica
Authors: Zhou Zhemin , Lundstrøm Inge , Tran-Dien Alicia , Duchêne Sebastián , Alikhan Nabil-Fareed , Sergeant Martin J. , Langridge Gemma , Fotakis Anna K. , Nair Satheesh , Stenøien Hans K. , Hamre Stian S. , Casjens Sherwood , Christophersen Axel , Quince Christopher , Thomson Nicholas R. , Weill François-Xavier , Ho Simon Y.W. , Gilbert M. Thomas P. , Achtman Mark 
Published: February 2017

AbstractSalmonella entericaserovar Paratyphi C is the causative agent of enteric (paratyphoid) fever. While today a potentially lethal infection of humans that occurs in Africa and Asia, early 20thcentury observations in Eastern Europe suggest it may once have had a wider-ranging impact on human societies. We recovered a draft Paratyphi C genome from the 800-year-old skeleton of a young woman in Trondheim, Norway, who likely died of enteric fever. Analysis of this genome against a new, significantly expanded database of related modern genomes demonstrated that Paratyphi C is descended from the ancestors of swine pathogens, serovars Choleraesuis and Typhisuis, together forming the Para C Lineage. Our results indicate that Paratyphi C has been a pathogen of humans for at least 1,000 years, and may have evolved after zoonotic transfer from swine during the Neolithic period.One Sentence SummaryThe combination of an 800-year-oldSalmonella entericaParatyphi C genome with genomes from extant bacteria reshapes our understanding of this pathogen’s origins and evolution.