Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Power of Truncated SVD for General High-rank Matrix Estimation Problems

We show that given an estimate $\widehat{A}$ that is close to a general high-rank positive semi-definite (PSD) matrix $A$ in spectral norm (i.e., $\|\widehat{A}-A\|_2 \leq \delta$), the simple truncated SVD of $\widehat{A}$ produces a multiplicative approximation of $A$ in Frobenius norm. This observation leads to many interesting results on general high-rank matrix estimation problems, which we briefly summarize below ($A$ is an $n\times n$ high-rank PSD matrix and $A_k$ is the best rank-$k$ approximation of $A$): (1) High-rank matrix completion: By observing $\Omega(\frac{n\max\{\epsilon^{-4},k^2\}\mu_0^2\|A\|_F^2\log n}{\sigma_{k+1}(A)^2})$ elements of $A$ where $\sigma_{k+1}\left(A\right)$ is the $\left(k+1\right)$-th singular value of $A$ and $\mu_0$ is the incoherence, the truncated SVD on a zero-filled matrix satisfies $\|\widehat{A}_k-A\|_F \leq (1+O(\epsilon))\|A-A_k\|_F$ with high probability. (2)High-rank matrix de-noising: Let $\widehat{A}=A+E$ where $E$ is a Gaussian random noise matrix with zero mean and $\nu^2/n$ variance on each entry. Then the truncated SVD of $\widehat{A}$ satisfies $\|\widehat{A}_k-A\|_F \leq (1+O(\sqrt{\nu/\sigma_{k+1}(A)}))\|A-A_k\|_F + O(\sqrt{k}\nu)$. (3) Low-rank Estimation of high-dimensional covariance: Given $N$ i.i. d. ~samples $X_1,\cdots,X_N\sim\mathcal N_n(0,A)$, can we estimate $A$ with a relative-error Frobenius norm bound? We show that if $N = \Omega\left(n\max\{\epsilon^{-4},k^2\}\gamma_k(A)^2\log N\right)$ for $\gamma_k(A)=\sigma_1(A)/\sigma_{k+1}(A)$, then $\|\widehat{A}_k-A\|_F \leq (1+O(\epsilon))\|A-A_k\|_F$ with high probability, where $\widehat{A}=\frac{1}{N}\sum_{i=1}^N{X_iX_i^\top}$ is the sample covariance.
The Centrioles, Centrosomes, Basal Bodies, and Cilia of Drosophila melanogaster

Centrioles play a key role in the development of the fly. They are needed for the correct formation of centrosomes, the organelles at the poles of the spindle that can persist as microtubule organizing centers (MTOCs) into interphase. The ability to nucleate cytoplasmic microtubules (MTs) is a property of the surrounding pericentriolar material (PCM). The centriole has a dual life, existing not only as the core of the centrosome but also as the basal body, the structure that templates the formation of cilia and flagellae. Thus the structure and functions of the centriole, the centrosome, and the basal body have an impact upon many aspects of development and physiology that can readily be modeled in Drosophila. Centrosomes are essential to give organization to the rapidly increasing numbers of nuclei in the syncytial embryo and for the spatially precise execution of cell division in numerous tissues, particularly during male meiosis. Although mitotic cell cycles can take place in the absence of centrosomes, this is an error-prone process that opens up the fly to developmental defects and the potential of tumor formation. Here, we review the structure and functions of the centriole, the centrosome, and the basal body in different tissues and cultured cells of Drosophila melanogaster, highlighting their contributions to different aspects of development and cell division.
Glucose-ABL1-TOR Signaling Modulates Cell Cycle Tuning to Control Terminal Appressorial Cell Differentiation

The conserved target of rapamycin (TOR) pathway integrates growth and development with available nutrients, but how cellular glucose controls TOR function and signaling is poorly understood. Here, we provide functional evidence from the devastating rice blast fungus Magnaporthe oryzae that glucose can mediate TOR activity via the product of a novel carbon-responsive gene, ABL1, in order to tune cell cycle progression during infection-related development. Under nutrient-free conditions, wild type (WT) M. oryzae strains form terminal plant-infecting cells (appressoria) at the tips of germ tubes emerging from three-celled spores (conidia). WT appressorial development is accompanied by one round of mitosis followed by autophagic cell death of the conidium. In contrast, Δabl1 mutant strains undergo multiple rounds of accelerated mitosis in elongated germ tubes, produce few appressoria, and are abolished for autophagy. Treating WT spores with glucose or 2-deoxyglucose phenocopied Δabl1. Inactivating TOR in Δabl1 mutants or glucose-treated WT strains restored appressorium formation by promoting mitotic arrest at G1/G0 via an appressorium- and autophagy-inducing cell cycle delay at G2/M. Collectively, this work uncovers a novel glucose-ABL1-TOR signaling axis and shows it engages two metabolic checkpoints in order to modulate cell cycle tuning and mediate terminal appressorial cell differentiation. We thus provide new molecular insights into TOR regulation and cell development in response to glucose.
A usability study of workspace awareness widgets

Groupware systems that use large shared workspaces generally provide only limited awareness information about other collaborators in the workspace. We are designing a set of groupware widgets to provide this missing information. This paper describes a usability study of a number of such widgets. The study has both validated our intuitions about the need for workspace awareness information, and revealed the strengths and weaknesses of several current designs.
Genetics of body shape and armour variation in threespine sticklebacks

Patterns of genetic variation and covariation can influence the rate and direction of phenotypic evolution. We explored the possibility that the parallel morphological evolution seen in threespine stickleback (Gasterosteus aculeatus) populations colonizing freshwater environments is facilitated by patterns of genetic variation and covariation in the ancestral (marine) population. We estimated the genetic (G) and phenotypic (P) covariance matrices and directions of maximum additive genetic (gmax) and phenotypic (pmax) covariances of body shape and armour traits. Our results suggest a role for the ancestral G in explaining parallel morphological evolution in freshwater populations. We also found evidence of genetic constraints owing to the lack of variance in the ancestral G. Furthermore, strong genetic covariances and correlations among traits revealed that selective factors responsible for threespine stickleback body shape and armour divergence may be difficult to disentangle. The directions of gmax and pmax were correlated, but the correlations were not high enough to imply that phenotypic patterns of trait variation and covariation within populations are very informative of underlying genetic patterns.
Source code analysis with LDA

Latent Dirichlet allocation (LDA) has seen increasing use in the understanding of source code and its related artifacts in part because of its impressive modeling power. However, this expressive power comes at a cost: The technique includes several tuning parameters whose impact on the resulting LDA model must be carefully considered. The aim of this work is to provide insights into the tuning parameters' impact. Doing so improves the comprehension of both researchers who look to exploit the power of LDA in their research and those who interpret the output of LDA‐using tools. It is important to recognize that the goal of this work is not to establish values for the tuning parameters because there is no universal best setting. Rather, appropriate settings depend on the problem being solved, the input corpus (in this case, typically words from the source code and its supporting artifacts), and the needs of the engineer performing the analysis. This work's primary goal is to aid software engineers in their understanding of the LDA tuning parameters by demonstrating numerically and graphically the relationship between the tuning parameters and the LDA output. A secondary goal is to enable more informed setting of the parameters. Copyright © 2016 John Wiley & Sons, Ltd.
Western Pacific Oceanic Heat Content: A Better Predictor of La Niña Than of El Niño

The western equatorial Pacific oceanic heat content (warm water volume in the west or WWVw) is the best El Niño–Southern Oscillation (ENSO) predictor beyond 1‐year lead. Using observations and selected Coupled Model Intercomparison Project Phase 5 simulations, we show that a discharged WWVw in boreal fall is a better predictor of La Niña than a recharged WWVw for El Niño 13 months later, both in terms of occurrence and amplitude. These results are robust when considering the heat content across the entire equatorial Pacific (WWV) at shorter lead times, including all Coupled Model Intercomparison Project Phase 5 models or excluding Niño‐Niña and Niña‐Niño phase transitions. Suggested mechanisms for this asymmetry include (1) the negatively skewed WWVw distribution with stronger discharges related to stronger wind stress anomalies during El Niño and (2) the stronger positive Bjerknes feedback loop during El Niño. The possible role of stronger subseasonal wind variations during El Niño is also discussed.
Análisis de opiniones en Internet a partir de la red social Twitter.

The high level of acceptance of social networks as a way to broadcast information has caused a great number of users to employ them to express their opinions about current issues. This paper introduces a procedure able to evaluate public opinion on products, brands, people, etc. So that, the messages displayed on the social network Twitter are analyzed to obtain the relevant information of the web sites referenced by these messages. Therefore, an assessment process has been developed using machine learning models plus natural language processing techniques. Finally, some guidelines are proposed to improve the assessment process by means of Soft Computing techniques, to obtain a final evaluation through a set of heteroge-
Flash Flood Verification: Pondering Precipitation Proxies

Quantitative precipitation estimate (QPE) exceedances of numerous different heavy precipitation thresholds—including spatially varying average recurrence interval (ARI) and flash flood guidance (FFG) thresholds—are compared among each other and against reported and warned flash floods to quantify existing deficiencies with QPEs and to identify best practices for using QPE for flash flood forecasting and analysis. QPEs from three different sources—NCEP Stage IV Precipitation Analysis (ST4), Climatology Calibrated Precipitation Analysis (CCPA), and Multi-Radar Multi-Sensor (MRMS) QPE—are evaluated across the United States from January 2015 to June 2017. In addition to evaluating different QPE sources, threshold types, and magnitudes, QPE accumulation interval lengths from hourly to daily are considered. Systematic errors with QPE sources are identified, including a radar distance dependence on extreme rainfall frequency in MRMS, spurious occurrences of locally extreme precipitation in the complex terrain of the West in ST4, and insufficient QPEs for many legitimate heavy precipitation events in CCPA. Overall, flash flood warnings and reports corresponded to each other far more than any QPE exceedances. Correspondence between all sources was at a maximum in the East and worst in the West, with ST4, CCPA, and MRMS QPE exceedances locally yielding maximal correspondence in the East, Plains, and West, respectively. Surprisingly, using a fixed 2.5 in. (24 h)−1 proxy outperformed shorter accumulation exceedances and the use of ARIs and FFGs. On regional scales, different ARI exceedances achieved superior performance to the selection of any fixed threshold; FFG exceedances were consistently too rare to achieve optimal correspondence with observed flash flooding.
Soil nitrogen and water dynamics in crops following perennial pastures under drought conditions

Perennial pasture phases may increase the sustainability of cropping rotations by increasing out of season water use, reducing leakage to the water table, and improving ground cover over the summer months. The dominant perennial pasture species used is lucerne (Medicago sativa). The perennial grasses phalaris (Phalaris aquatica) and cocksfoot (Dactylis glomerata) are broadly adapted but have been studied less extensively in cropping rotations. The effects of lucerne, phalaris, cocksfoot and mixtures of these species, on soil mineral N and water was studied in the field at Junee Reefs in southern NSW (530 mm annual rainfall) by deep coring at sowing and harvest. Potential N mineralisation was assessed by incubation studies in the laboratory. During three dry seasons (2001-3) soil water was very low for most treatments, having been depleted prior to the beginning of the experimental period. Nitrogen mineralisation dynamics were strongly influenced by residue decomposition, explained by time of pasture removal and summer rainfall. In 2001 the rate of N mineralisation was significantly higher following pastures containing cocksfoot. In following seasons substantial amounts of N were mineralised following all perennial pastures. The rates were not significantly different. There was little correlation between potential mineralisation measured in the laboratory and actual mineralisation measured in the field. Drought conditions prevented soil N mineralisation over summer. Incrop mineralisation and crop N accumulation was high after lucerne, leading to haying-off of wheat crops, but perennial grass pastures provided sufficient mineral N to following wheat crops under drought conditions.
Toward Adaptive Sleep Schedules for Balancing Energy Consumption in Wireless Sensor Networks

In this work, we assume a geographic area populated by tiny sensors, each perhaps no larger than a dime. In order to save their energy, the sensors spend most of their lifetime in sleep mode and wake up for short periods of time to participate in various tasks supportive of the overall mission of the network. We assume that the tasks to be performed stipulate QoS parameters expressed in terms of the minimum number of sensors that need to monitor their sensing area. Since only awake sensors participate in tasks, the Effective Sensor Density (ESD), defined as the density of awake sensors, is an important network parameter that obviously depends on the sleep schedules adopted in the network. The first main contribution of this work is to provide a mathematical analysis of ESD from the perspective of the monitored events. We also provide design guidelines to determine deployment-time sensor density and an associated sleep schedule that probabilistically keeps the ESD at a level needed by QoS requirements. We also propose a fully distributed sleep schedule which adaptively adjusts the duty cycles of sensors within the same sensing area based on the relative difference in their remaining energy budget. The main advantage of the proposed adaptive scheme is to balance energy consumption among sensors, thus promoting the functional longevity of the sensor network without adversely affecting the ESD.
How do we treat fetal and neonatal alloimmune thrombocytopenia?

Fetal and neonatal alloimmune thrombocytopenia (FNAIT) is a potentially devastating disease, seen in one in 800 to 1000 neonates. FNAIT is the most common cause of early‐onset isolated severe neonatal thrombocytopenia in maternity wards. The complication of this disorder most to be feared is intracranial hemorrhage, leading to death or to neurologic sequels. As there is no systematic screening of at‐risk pregnancies, FNAIT is often discovered when signs of bleeding are observed during pregnancy or at delivery. Platelet transfusion is required in case of bleeding or severe thrombocytopenia (<30 × 109/L) during the 48‐hour‐postdelivery period. Diagnosis of alloimmunization is important for management of the index case and for subsequent pregnancies, due to the increasing severity of this syndrome as it recurs. Noninvasive antenatal therapy is based on maternal perfusion of intravenous immunoglobulins and risk stratification. In our experience, the addition of corticoids during the last trimester significantly improves the efficiency of treatment. Follow‐up of antibody concentration during pregnancy may constitute a useful variable for therapy effectiveness.
Serum Myeloperoxidase Levels Independently Predict Endothelial Dysfunction in Humans

Background—In vitro and animal studies demonstrate that myeloperoxidase catalytically consumes nitric oxide as a substrate, limiting its bioavailability and function. We therefore hypothesized that circulating levels of myeloperoxidase would predict risk of endothelial dysfunction in human subjects. Methods and Results—Serum myeloperoxidase was measured by enzyme-linked immunoassay, and brachial artery flow–mediated dilation and nitroglycerin-mediated dilation were determined by ultrasound in a hospital-based population of 298 subjects participating in an ongoing study of the clinical correlates of endothelial dysfunction (age, 51±16; 61% men, 51% with cardiovascular disease). A strong inverse relation between brachial artery flow–mediated dilation and increasing quartile of serum myeloperoxidase level was observed (11.0±6.0%, 9.4±5.3%, 8.6±5.8%, and 6.4±4.5% for quartiles 1 through 4, respectively; P<0.001 for trend). Using the median as a cut point to define endothelial dysfunction, increasing quartile of myeloperoxidase predicted endothelial dysfunction after adjustment for classic cardiovascular disease risk factors, C-reactive protein levels, prevalence of cardiovascular disease, and ongoing treatment with cardiovascular medications (OR, 6.4; 95% CI, 2.6 to 16; P=0.001 for highest versus lowest quartile). Conclusions—Serum myeloperoxidase levels serve as a strong and independent predictor of endothelial dysfunction in human subjects. Myeloperoxidase-mediated endothelial dysfunction may be an important mechanistic link between oxidation, inflammation, and cardiovascular disease.
Oxidative Stress Induced in Sunflower Seedling Roots by Aqueous Dry Olive-Mill Residues

The contamination of soils with dry olive-mill residue can represent a serious problem as being an environmental stressor in plants. It has been demonstrated that inoculation of aqueous extract of olive oil-mill residue (ADOR) with saprobe fungi removes some phenolic compounds. In this paper we studied the effect of ADOR uninoculated or inoculated with saprobe fungi in sunflower seedling roots. The germination and root growth, O2·- generation, superoxide dismutase (SOD) and extracellular peroxidases (EC-POXs) activities, and the content of some metabolites involved in the tolerance of stress were tested. The roots germinated in ADOR uninoculated show a decrease in meristem size, resulting in a reduction of the root length and fresh weight, and in the number of layers forming the cortex, but did not alter the dry weight, protein and soluble amino acid content. ADOR caused the decreases in O2·- generation and EC-POX′s activities and protein oxidation, but enhanced SOD activity, lipid peroxidation and proline content. Fluorescence imaging showed that ADOR induced O2·- and H2O2 accumulation in the roots. The increase in SOD and the decrease in EC-POX′s activities might be involved in the enhancement of H2O2 content and lipid peroxidation. Control roots treated with ADOR for 10 min show an oxidative burst. Roots germinated in ADOR inoculated with saprobe fungi partially recovered normal levels of ROS, morphological characteristics and antioxidant activities. These results suggested that treatment with ADOR caused a phytotoxic effect during germination inducing an oxidative stress. The inoculation of ADOR with saprobe fungi limited the stress.
The Tor and cAMP-dependent protein kinase signaling pathways coordinately control autophagy in Saccharomyces cerevisiae

Macroautophagy (hereafter autophagy) is a conserved membrane trafficking pathway responsible for the turnover of cytosolic protein and organelles during periods of nutrient deprivation. This pathway is also linked to a number of processes important for human health, including tumor suppression, innate immunity and the clearance of protein aggregates. As a result, there is tremendous interest in autophagy as a potential point of therapeutic intervention in a variety of pathological states. To achieve this goal, it is imperative that we develop a thorough understanding of the normal regulation of this process in eukaryotic cells. The Tor protein kinases clearly constitute a key element of this control as Tor activity inhibits this degradative process in all organisms examined, from yeast to man. Here, we discuss recent work indicating that the cAMP-dependent protein kinase (PKA) also plays a critical role in controlling autophagy in the budding yeast, Saccharomyces cerevisiae. A model describing how PKA activity might influence this degradative process, and how this control might be integrated with that of the Tor pathway, is presented.
Phosphorylation of eIF4GII and 4E-BP1 in response to nocodazole treatment: A reappraisal of translation initiation during mitosis

Translation mechanisms at different stages of the cell cycle have been studied for many years, resulting in the dogma that translation rates are slowed during mitosis, with cap-independent translation mechanisms favored to give expression of key regulatory proteins. However, such cell culture studies involve synchronization using harsh methods, which may in themselves stress cells and affect protein synthesis rates. One such commonly used chemical is the microtubule de-polymerization agent, nocodazole, which arrests cells in mitosis and has been used to demonstrate that translation rates are strongly reduced (down to 30% of that of asynchronous cells). Using synchronized HeLa cells released from a double thymidine block (G1/S boundary) or the Cdk1 inhibitor, RO3306 (G2/M boundary), we have systematically re-addressed this dogma. Using FACS analysis and pulse labeling of proteins with labeled methionine, we now show that translation rates do not slow as cells enter mitosis. This study is complemented by studies employing confocal microscopy, which show enrichment of translation initiation factors at the microtubule organizing centers, mitotic spindle, and midbody structure during the final steps of cytokinesis, suggesting that translation is maintained during mitosis. Furthermore, we show that inhibition of translation in response to extended times of exposure to nocodazole reflects increased eIF2α phosphorylation, disaggregation of polysomes, and hyperphosphorylation of selected initiation factors, including novel Cdk1-dependent N-terminal phosphorylation of eIF4GII. Our work suggests that effects on translation in nocodazole-arrested cells might be related to those of the treatment used to synchronize cells rather than cell cycle status.
Pediatric prenatal diagnosis of congenital heart disease

Purpose of review Fetal cardiology is a rapidly evolving field. Imaging technology continues to advance as do approaches to in-utero interventions and care of the critically ill neonate, with even greater demand for improvement in prenatal diagnosis of congenital heart disease (CHD) and arrhythmias. Recent findings Reviewing the advances in prenatal diagnosis of CHD in such a rapidly developing field is a broad topic. Therefore, we have chosen to focus this review of recent literature on challenges in prenatal detection of CHD, challenges in prenatal counseling, advances in fetal arrhythmia diagnosis, and potential benefits to patients with CHD who are identified prenatally. Summary As methods and tools to diagnose and manage CHD and arrhythmias in utero continue to improve, future generations will hopefully see a reduction in both prenatal and neonatal morbidity and mortality. Prenatal diagnosis can and should be used to optimize location and timing of delivery and postnatal interventions. Video abstract http://links.lww. com/MOP/A21