Miracle-dz/UniFAR-FTUs huggingface dataset:
The Feasibility of Using Inherent Optical Properties and the Apparent Optical Property Remote Sensing Reflectance to Estimate Suspended Particulate Matter, Particularly for Use in Airborne Hydrographic Surveys

ii ACKNOWLEDGMENTS . iv DEDICATION . v LIST OF TABLES . xiii LIST OF ILLUSTRATIONS . xviii LIST OF ABBREVIATIONS . xxiii CHAPTER I INTRODUCTION . 1 Overview . 1 Airborne Hydrographic Surveys . 5 Hypotheses and Objectives . 7 Hypothesis 1. Sequential Profiling . 8 Objective 1 . 8 Objective 2 . 8 Objective 3 . 9 Hypothesis 2: SPM Algorithm Development from Inherent Optical Properties . 11 Objective 1. 11 Objective 2 . 11 Hypothesis 3: SPM Algorithm Development from Apparent Optical Property Rrs . 14 Objective 1 . 14 vii Hypothesis 4: SPM Distribution and Physical Properties . 16 Objective 1 . 16 Objective 2 . 17 Objective 3 . 17 Research Site . 19 Uncertainty . 20 Environmental Uncertainty . 22 CHAPTER II – METHODS: SENSORS, FILTRATION AND PROFILER CONFIGURATION . 24 Introduction . 24 Filtration Method . 25 Vertical Profiling . 27 DH4 (WET_Labs, 2010c) . 32 CTD (Sea-Bird Electronics, 2010, 2011b) . 32 BB9 (WET_Labs, 2008b) . 32 AC9 (WET_Labs, 2008a) and ACS (WET_Labs, 2009) . 34 LISST 100X (Type B) (Sequoia_Scientific). 37 Transmissometer (WET_Labs, 2010b, 2011) . 40 Fluorimeters (Chelsea_Technologies_Group_Ltd; WET_Labs, 2010a; WET_Labs_Inc., 2011) . 41 viii The Use of Multiple Profilers and Data Types . 41 Methods of Improving Profile Data and Filter Sample Spatial Relationships . 45 Uncertainties Related to Profiler Configuration . 48 Uncertainties Related to Downcast and Upcast Profile Data . 50 Deck – Based Hyperspectral Observations . 60 Field Measurements: ASD . 61 Field Measurements: HyperSAS. 67 Uncertainty related to Hyperspectral Observations . 69 Conclusions . 70 CHAPTER III METHODS II: ANALYZING THE SEQUENTIAL DEPLOYMENT OF PROFILERS . 72 Introduction . 72 Uncertainties Related to Sequential Deployments of the Optical Profiler . 72 Uncertainties Related to Observations from Different Profilers Deployed Sequentially: Salinity . 78 Uncertainties Related to Observations from Different Profilers Deployed Sequentially: Attenuation & Fluorescence . 93 Conclusions and Project Related Procedures . 95 CHAPTER IV – METHODS III: PERFORMANCE EVALUATIONS OF IOP SENSORS . 97
DEM, tide and velocity over Sulzberger ice shelf, West Antarctica

Arctic and Antarctic ice sheets preserve more than 77% of the global fresh water and could raise global sea level by several meters if completely melted. Ocean tides near and under ice shelves shifts the grounding line position significantly and are one of current limitations to study glacier dynamics and mass balance. The Sulzberger ice shelf is an area of ice mass flux change in West Antarctica and has not yet been well studied. In this study, we use repeat-pass synthetic aperture radar (SAR) interferometry data from the ERS-1 and ERS-2 tandem missions for generation of a high-resolution (60-m) Digital Elevation Model (DEM) including tidal deformation detection and ice stream velocity of the Sulzberger Ice Shelf. Other satellite data such as laser altimeter measurements with fine foot-prints (70-m) from NASA’s ICESat are used for validation and analyses. The resulting DEM has an accuracy of –0.57±5.88 m and is demonstrated to be useful for grounding line detection and ice mass balance studies. The deformation observed by InSAR is found to be primarily due to ocean tides and atmospheric pressure. The 2-D ice stream velocities computed agree qualitatively with previous methods on part of the Ice Shelf from passive microwave remote-sensing data (i.e., LANDSAT).
Identification of three late expression factor genes within the 33.8- to 43.4-map-unit region of Autographa californica nuclear polyhedrosis virus

A transient transactivation assay system was used in combination with an overlapping Autographa californica nuclear polyhedrosis virus clone library to identify genes involved in late and very late baculovirus gene expression. We have identified three genes within the 33.8- to 43.4-map-unit region of the A. californica nuclear polyhedrosis virus genome which contribute to expression from promoters of the vp39 major capsid protein and polyhedrin genes. One of these three genes corresponds to the previously identified DNA polymerase gene, while the other two genes encode previously unidentified polypeptides of 59,418 and 8,706 Da. None of these genes were required for expression from the early etl promoter.
NUMA-aware graph-structured analytics

Graph-structured analytics has been widely adopted in a number of big data applications such as social computation, web-search and recommendation systems. Though much prior research focuses on scaling graph-analytics on distributed environments, the strong desire on performance per core, dollar and joule has generated considerable interests of processing large-scale graphs on a single server-class machine, which may have several terabytes of RAM and 80 or more cores. However, prior graph-analytics systems are largely neutral to NUMA characteristics and thus have suboptimal performance. This paper presents a detailed study of NUMA characteristics and their impact on the efficiency of graph-analytics. Our study uncovers two insights: 1) either random or interleaved allocation of graph data will significantly hamper data locality and parallelism; 2) sequential inter-node (i.e., remote) memory accesses have much higher bandwidth than both intra- and inter-node random ones. Based on them, this paper describes Polymer, a NUMA-aware graph-analytics system on multicore with two key design decisions. First, Polymer differentially allocates and places topology data, application-defined data and mutable runtime states of a graph system according to their access patterns to minimize remote accesses. Second, for some remaining random accesses, Polymer carefully converts random remote accesses into sequential remote accesses, by using lightweight replication of vertices across NUMA nodes. To improve load balance and vertex convergence, Polymer is further built with a hierarchical barrier to boost parallelism and locality, an edge-oriented balanced partitioning for skewed graphs, and adaptive data structures according to the proportion of active vertices. A detailed evaluation on an 80-core machine shows that Polymer often outperforms the state-of-the-art single-machine graph-analytics systems, including Ligra, X-Stream and Galois, for a set of popular real-world and synthetic graphs.
Isolation and Characterization of the Gene Cluster for Biosynthesis of the Thiopeptide Antibiotic TP-1161

ABSTRACT Recently, we isolated a new thiopeptide antibiotic, TP-1161, from the fermentation broth of a marine actinomycete typed as a member of the genus Nocardiopsis. Here we report the identification, isolation, and analysis of the TP-1161 biosynthetic gene cluster from this species. The gene cluster was identified by mining a draft genome sequence using the predicted structural peptide sequence of TP-1161. Functional assignment of a ∼16-kb genomic region revealed 13 open reading frames proposed to constitute the TP-1161 biosynthetic locus. While the typical core set of thiopeptide modification enzymes contains one cyclodehydratase/dehydrogenase pair, paralogous genes predicted to encode additional cyclodehydratases and dehydrogenases were identified. Although attempts at heterologous expression of the TP-1161 gene cluster in Streptomyces coelicolor failed, its identity was confirmed through the targeted gene inactivation in the original host.
Targeted disruption of an orthologue of DOMAINS REARRANGED METHYLASE 2, OsDRM2, impairs the growth of rice plants by abnormal DNA methylation.

Recent methylome analyses of the entire Arabidopsis thaliana genome using various mutants have provided detailed information about the DNA methylation pattern and its function. However, information about DNA methylation in other plants is limited, partly because of the lack of mutants. To study DNA methylation in rice (Oryza sativa) we applied homologous recombination-mediated gene targeting to generate targeted disruptants of OsDRM2, a rice orthologue of DOMAINS REARRANGED METHYLASE 1 and 2 (DRM1/2), which encode DNA methyltransferases responsible for de novo and non-CG methylation in Arabidopsis. Whereas Arabidopsis drm1 drm2 double mutants showed no morphological alterations, targeted disruptants of rice OsDRM2 displayed pleiotropic developmental phenotypes in both vegetative and reproductive stages, including growth defects, semi-dwarfed stature, reductions in tiller number, delayed heading or no heading, abnormal panicle and spikelet morphology, and complete sterility. In these osdrm2 disruptants, a 13.9% decrease in 5-methylcytosine was observed by HPLC analysis. The CG and non-CG methylation levels were reduced in RIRE7/CRR1 retrotransposons, and in 5S rDNA repeats. Associated transcriptional activation was detected in RIRE7/CRR1. Furthermore, de novo methylation by an RNA-directed DNA methylation (RdDM) process involving transgene-derived exogenous small interfering RNA (siRNA) was deficient in osdrm2-disrupted cells. Impaired growth and abnormal DNA methylation of osdrm2 disruptants were restored by the complementation of wild-type OsDRM2 cDNA. Our results suggest that OsDRM2 is responsible for de novo, CG and non-CG methylation in rice genomic sequences, and that DNA methylation regulated by OsDRM2 is essential for proper rice development in both vegetative and reproductive stages.
NBER WORKING PAPER SERIES THE MACROECONOMIC EFFECTS OF OIL SHOCKS: WHY ARE THE 2000S SO DIFFERENT FROM THE 1970S?

We are grateful for helpful comments and suggestions to Julio Rotemberg, John Parsons, Lutz Kilian, José de Gregorio, Gauti Eggertson and participants at NBER ME Meeting, the NBER Conference on "International Dimensions of Monetary Policy'', and seminars at CREI-UPF. We thank Davide Debortoli for excellent research assistance, and the NSF and the Banque de France Foundation for financial assistance. The views expressed herein are those of the author(s) and do not necessarily reflect the views of the National Bureau of Economic Research.
The Dynamic Brain: From Spiking Neurons to Neural Masses and Cortical Fields

The cortex is a complex system, characterized by its dynamics and architecture, which underlie many functions such as action, perception, learning, language, and cognition. Its structural architecture has been studied for more than a hundred years; however, its dynamics have been addressed much less thoroughly. In this paper, we review and integrate, in a unifying framework, a variety of computational approaches that have been used to characterize the dynamics of the cortex, as evidenced at different levels of measurement. Computational models at different space–time scales help us understand the fundamental mechanisms that underpin neural processes and relate these processes to neuroscience data. Modeling at the single neuron level is necessary because this is the level at which information is exchanged between the computing elements of the brain; the neurons. Mesoscopic models tell us how neural elements interact to yield emergent behavior at the level of microcolumns and cortical columns. Macroscopic models can inform us about whole brain dynamics and interactions between large-scale neural systems such as cortical regions, the thalamus, and brain stem. Each level of description relates uniquely to neuroscience data, from single-unit recordings, through local field potentials to functional magnetic resonance imaging (fMRI), electroencephalogram (EEG), and magnetoencephalogram (MEG). Models of the cortex can establish which types of large-scale neuronal networks can perform computations and characterize their emergent properties. Mean-field and related formulations of dynamics also play an essential and complementary role as forward models that can be inverted given empirical data. This makes dynamic models critical in integrating theory and experiments. We argue that elaborating principled and informed models is a prerequisite for grounding empirical neuroscience in a cogent theoretical framework, commensurate with the achievements in the physical sciences.
Wavelet-based noise removal for biomechanical signals: a comparative study

The purpose of this paper is to present wavelet-based noise removal (WBNR) techniques to remove noise from biomechanical acceleration signals obtained from numerical differentiation of displacement data. Manual and semiautomatic methods were used to determine thresholds for both orthogonal and biorthogonal filters. This study also compares the performance of WBNR approaches with four automatic conventional noise removal techniques used in biomechanics. The conclusion of this work is that WBNR techniques are very effective in removing noise from differentiated signals with sharp transients while leaving these transients intact. For biomechanical signals with certain characteristics, WBNR techniques perform better than conventional methods, as indicated by quantitative merit measures.
Antibiotic Susceptibility of Tropheryma whipplei in MRC5 Cells

ABSTRACT Whipple's disease is considered a rare chronic disease with a broad spectrum of clinical manifestations. Several antibiotics have been used for the treatment of this disease, and the current reference treatment was determined empirically on the basis of only a few clinical observations. Patients should be treated for months, and many relapse after antibiotic withdrawal. We report here the first extensive study on the susceptibilities of three reference strains of Tropheryma whipplei to antibiotic in cell culture by using a real-time PCR assay as previously described. We found that doxycycline, macrolides, ketolides, aminoglygosides, penicillin, rifampin, teicoplanin, chloramphenicol, and trimethoprim-sulfamethoxazole were active, with MICs ranging from 0.25 to 2 μg/ml. Vancomycin was somewhat active at an MIC of 10 μg/ml. We found heterogeneity in the susceptibility to imipenem, with one strain being susceptible and the two other strains being resistant. Cephalosporins, colimycine, aztreonam, and fluoroquinolones were not active. We also demonstrated that a combination of doxycycline and hydroxychloroquine was bactericidal. This combination has been shown to be active in the treatment of patients suffering from chronic infections with Coxiella burnetii, a bacterium that is also found intracellularly in acidic vacuoles. We believe, then, that this combination therapy should be further evaluated in clinical trials for the treatment of Whipple's disease.
Exact Post Model Selection Inference for Marginal Screening

We develop a framework for post model selection inference, via marginal screening, in linear regression. At the core of this framework is a result that characterizes the exact distribution of linear functions of the response $y$, conditional on the model being selected (``condition on selection" framework). This allows us to construct valid confidence intervals and hypothesis tests for regression coefficients that account for the selection procedure. In contrast to recent work in high-dimensional statistics, our results are exact (non-asymptotic) and require no eigenvalue-like assumptions on the design matrix $X$. Furthermore, the computational cost of marginal regression, constructing confidence intervals and hypothesis testing is negligible compared to the cost of linear regression, thus making our methods particularly suitable for extremely large datasets. Although we focus on marginal screening to illustrate the applicability of the condition on selection framework, this framework is much more broadly applicable. We show how to apply the proposed framework to several other selection procedures including orthogonal matching pursuit, non-negative least squares, and marginal screening+Lasso.
Hysteroscopy: A necessary method for detecting uterine pathologies in post-menopausal women with abnormal uterine bleeding or increased endometrial thickness

Objective: To investigate the histologic and hysteroscopic findings of post-menopausal women with uterine bleeding and asymptomatic women with increased endometrial thickness equal or more than 5 mm. Materials and Methods: This cross-sectional study was performed between May 2014 and June 2015 on 110 post-menopausal women aged 40-82 years. The women were divided into two groups: Women with abnormal uterine bleeding (AUB group) and asymptomatic women with increased endometrial thickness (asymptomatic group). Results: Among the participants, 67 women had AUB and 43 women were asymptomatic. In the AUB group sensitivity, specificity, and positive and negative predictive values of hysteroscopy for normal findings were 98%, 100%, 100% and 90%, respectively. In the asymptomatic group, the same parameters were 98%, 100%, 100% and 85%, respectively. The sensitivity, specificity, and positive and negative predictive values of hysteroscopy for polyps and myomas were 100%. Also, the sensitivity, specificity, and positive and negative predictive values were 100% in hyperplasia cases found during hysteroscopy in both groups. Conclusion: Increased endometrial thickness in postmenopausal women with or without AUB is mostly due to benign lesions such as polyps and submucosal myomas. Hysteroscopy is a safe and reliable method for evaluating and treating these lesions.
A method to estimate groundwater depletion from confining layers

Although depletion of storage in low‐permeability confining layers is the source of much of the groundwater produced from many confined aquifer systems, it is all too frequently overlooked or ignored. This makes effective management of groundwater resources difficult by masking how much water has been derived from storage and, in some cases, the total amount of water that has been extracted from an aquifer system. Analyzing confining layer storage is viewed as troublesome because of the additional computational burden and because the hydraulic properties of confining layers are poorly known. In this paper we propose a simplified method for computing estimates of confining layer depletion, as well as procedures for approximating confining layer hydraulic conductivity (K) and specific storage (Ss) using geologic information. The latter makes the technique useful in developing countries and other settings where minimal data are available or when scoping calculations are needed. As such, our approach may be helpful for estimating the global transfer of groundwater to surface water. A test of the method on a synthetic system suggests that the computational errors will generally be small. Larger errors will probably result from inaccuracy in confining layer property estimates, but these may be no greater than errors in more sophisticated analyses. The technique is demonstrated by application to two aquifer systems: the Dakota artesian aquifer system in South Dakota and the coastal plain aquifer system in Virginia. In both cases, depletion from confining layers was substantially larger than depletion from the aquifers.
Tractable Lineages on Treelike Instances: Limits and Extensions

Query evaluation on probabilistic databases is generally intractable (#P-hard). Existing dichotomy results have identified which queries are tractable (or safe), and connected them to tractable lineages. In our previous work, using different tools, we showed that query evaluation is linear-time on probabilistic databases for arbitrary monadic second-order queries, if we bound the treewidth of the instance. In this paper, we study limitations and extensions of this result. First, for probabilistic query evaluation, we show that MSO tractability cannot extend beyond bounded treewidth: there are even FO queries that are hard on any efficiently constructible unbounded-treewidth class of graphs. This dichotomy relies on recent polynomial bounds on the extraction of planar graphs as minors, and implies lower bounds in non-probabilistic settings, for query evaluation and match counting in subinstance-closed families. Second, we show how to explain our tractability result in terms of lineage: the lineage of MSO queries on bounded-treewidth instances can be represented as bounded-treewidth circuits, polynomial-size OBDDs, and linear-size d-DNNFs. By contrast, we can strengthen the previous dichotomy to lineages, and show that there are even UCQs with disequalities that have superpolynomial OBDDs on all unbounded-treewidth graph classes; we give a characterization of such queries. Last, we show how bounded-treewidth tractability explains the tractability of the inversion-free safe queries: we can rewrite their input instances to have bounded-treewidth.
Speed impairs attending on the left: comparing attentional asymmetries for neglect patients in speeded and unspeeded cueing tasks

Visuospatial neglect after stroke is often characterized by a disengage deficit on a cued orienting task, in which individuals are disproportionately slower to respond to targets presented on the contralesional side of space following an ispilesional cue as compared to the reverse. The purpose of this study was to investigate the generality of the finding of a disengage deficit on another measure of cued attention, the temporal order judgment (TOJ) task, that does not depend upon speeded manual responses. Individuals with right hemisphere stroke with and without spatial neglect and older healthy controls (OHC) were tested with both a speeded RT cueing task and an unspeeded TOJ-with-cuing task. All stroke patients evidenced a disengage deficit on the speeded RT cueing task, although the size and direction of the bias was not associated with the severity of neglect. In contrast, few neglect patients showed a disengage deficit on the TOJ task. This discrepancy suggests that the disengage deficit may be related to task demands, rather than solely due to impaired attentional mechanisms per se. Further, the results of our study show that the disengage deficit is neither necessary nor sufficient for neglect to manifest.
Loose associations to increase utility in data publishing

Data fragmentation has been proposed as a solution for protecting the confidentiality of sensitive associations when releasing data for publishing or external storage. To enrich the utility of data fragments, a recent approach has put forward the idea of complementing a pair of fragments with some non-precise, hence loose information on the association between them. Starting from the observation that in presence of multiple fragments the publication of several independent associations between pairs of fragments can cause improper leakage of sensitive information, in this paper we extend loose associations to operate over an arbitrary number of fragments.We first illustrate how the publication of multiple loose associations between different pairs of fragments can potentially expose sensitive associations, and describe an approach for defining loose associations among an arbitrary set of fragments. We investigate how tuples in fragments can be grouped for producing loose associations so to increase the utility of queries executed over fragments. We then provide a heuristics for performing such a grouping and producing loose associations satisfying a given level of protection for sensitive associations, while achieving utility for queries over different fragments. We also illustrate the result of an extensive experimental effort over both synthetic and real datasets, which shows the efficiency and the enhanced utility provided by our proposal.