Miracle-dz/UniFAR-FTUs huggingface dataset:
A climatology of the winter low‐level jet over the Red Sea

This study presents the first climatology of the low‐level jet (LLJ) over the southern part of the Red Sea during the winter season. ERA‐Interim pressure levels with 25 hPa vertical resolution were analysed for a 10‐year period from 2006 to 2015. The jet was found to be a relatively frequent phenomenon, occurring on 37% of all 6‐hr time steps in all 10 years in the south at 13.5°N and 43°E, decreasing to 15% of the data farther north at 19.5°N and 39°E. The core of the jet was usually close to the ground, with occurrence maximized at the 925 and 950 hPa levels corresponding roughly to 540–800 m above sea level. The study defined three criteria for the jet based on peak wind speeds. The jets that met the weaker criterion were frequent north of the straight of Bab el Mandeb in the far southern part of the Red Sea. The jets that met the two stronger criteria were more frequent further north approximately between 14°–17°N and 39°–42°E. Although the jet was present in the strait of Bab el Mandeb as found in earlier studies, the extension of the jet so much farther north suggests that other processes besides channelling must be acting to produce this jet. It also appears that the jet plays a significant role in moisture advection towards the central Red Sea region, which can contribute towards precipitation there as it was found that the moisture concentration increased in that region when the LLJ was present. It must be noted, however, that the present study relied upon reanalysis data to document the jet. Upper level observations in the region are scarce, so caution should be used in the interpretation of the results.
Amphibian molecular ecology and how it has informed conservation

Molecular ecology has become one of the key tools in the modern conservationist's kit. Here we review three areas where molecular ecology has been applied to amphibian conservation: genes on landscapes, within‐population processes, and genes that matter. We summarize relevant analytical methods, recent important studies from the amphibian literature, and conservation implications for each section. Finally, we include five in‐depth examples of how molecular ecology has been successfully applied to specific amphibian systems.
Effect of nitric oxide synthase inhibition on haemodynamics and outcome of patients with persistent cardiogenic shock complicating acute myocardial infarction: a phase II dose-ranging study.

AIMS Previous studies suggested haemodynamic benefits and, possibly, mortality reduction with the use of nitric oxide synthase (NOS) inhibition in patients with acute myocardial infarction (AMI) complicated by cardiogenic shock (CS). We assessed preliminary efficacy and safety of four doses of l-n-monomethyl-arginine (l-NMMA), a non-selective NOS inhibitor, in patients with AMI complicated by CS despite an open infarct-related artery. METHODS AND RESULTS Patients (n = 79) were randomly assigned to a bolus and 5 h infusion of placebo or 0.15, 0.5, 1.0, or 1.5 mg/kg of l-NMMA. The primary outcome measure was absolute change in mean arterial pressure (MAP) at 2 h. Fifteen minutes after study drug initiation, mean change in MAP was -4.0 mmHg in the placebo group and 5.8 (P = 0.02), 4.8 (P = 0.02), 5.1 (P = 0.07), and 11.6 (P < 0.001) mmHg in the four l-NMMA groups, respectively (all vs. placebo). Mean change in MAP at 2 h was -0.4, 4.4, 1.8, -4.1, and 6.8 mmHg in the placebo and four l-NMMA groups, respectively (all P = NS). CONCLUSION l-NMMA resulted in modest increases in MAP at 15 min compared with placebo but there were no differences at 2 h.
A Unified Focusing Algorithm for Several Modes of SAR Based on FrFT

Many imaging algorithms for different modes, such as, stripmap synthetic aperture radar (SAR), spotlight SAR, sliding spotlight SAR, and terrain observation by progressive scans (TOPS) SAR, of SAR have been studied. This paper is to obtain a unified focusing algorithm (UFA) for these SAR modes based on fractional Fourier transform. By defining the rotation-center range, the stripmap SAR and spotlight SAR can be treated as special cases of sliding spotlight SAR or TOPS SAR. Then, a parameterized focusing algorithm determined by the rotation-center range is presented. Data of each mode can be focused by utilizing UFA and selecting parameters or rotation angles. Some application aspects of UFA are also analyzed. Simulation and real data results are presented to validate the analysis and the proposed method.
Data and Dynamics Driven Approaches for Modelling and Forecasting the Red Sea Chlorophyll

Data and Dynamics Driven Approaches for Modelling and Forecasting the Red Sea Chlorophyll Denis Dreano Phytoplankton is at the basis of the marine food chain and therefore play a fundamental role in the ocean ecosystem. However, the large-scale phytoplankton dynamics of the Red Sea are not well understood yet, mainly due to the lack of historical in situ measurements. As a result, our knowledge in this area relies mostly on remotelysensed observations and large-scale numerical marine ecosystem models. Models are very useful to identify the mechanisms driving the variations in chlorophyll concentration and have practical applications for fisheries operation and harmful algae blooms monitoring. Modelling approaches can be divided between physicsdriven (dynamical) approaches, and data-driven (statistical) approaches. Dynamical models are based on a set of differential equations representing the transfer of energy and matter between different subsets of the biota, whereas statistical models identify relationships between variables based on statistical relations within the available data. The goal of this thesis is to develop, implement and test novel dynamical and statistical modelling approaches for studying and forecasting the variability of chlorophyll concentration in the Red Sea. These new models are evaluated in term of their ability to efficiently forecast and explain the regional chlorophyll variability. We also propose innovative synergistic strategies to combine dataand physics-driven approaches to further enhance chlorophyll forecasting capabilities and efficiency.
Obesity and Barrett’s oesophagus: more than just reflux

Numerous studies have demonstrated an association between obesity and an increased risk of various epithelial malignancies.1 The factors underlying these associations are probably complex, and may relate to chronic inflammation, hyperinsulinaemia and increased production of adipokines and other adipose-derived hormones.2 Obesity is also associated with an increased risk of gastro-oesophageal reflux disease (GORD), an established risk factor for oesophageal adenocarcinoma. It is widely accepted that GORD is associated with and probably directly contributes to the development of Barrett’s oesophagus, the precursor lesion for oesophageal adenocarcinoma. It is not clear, however, whether obesity alone, independent of GORD, also plays a role in this metaplastic transformation. In the article by Jacobson et al ( see page 1460 ), data prospectively collected from the Nurses’ Health Study cohort were examined to study the relationship between obesity and Barrett’s oesophagus in women.3 More than 15 000 women who underwent upper endoscopy were included in the study, and data were collected on self-reported height and weight as well as self-measured waist and hip circumference. Body mass index (BMI) ⩾30 was associated with a significantly increased odds of Barrett’s oesophagus, and this association persisted even when the analyses were restricted only to patients (cases and controls) with a history of GORD symptoms. Interestingly, neither the waist-to-hip ratio (WHR) nor the waist circumference was independently associated with Barrett’s oesophagus. The authors used data from …
Fos Expression in Orexin Neurons Varies with Behavioral State

The neuropeptide orexin (also known as hypocretin) is hypothesized to play a critical role in the regulation of sleep–wake behavior. Lack of orexin produces narcolepsy, which is characterized by poor maintenance of wakefulness and intrusions of rapid eye movement (REM) sleep or REM sleep-like phenomena into wakefulness. Orexin neurons heavily innervate many aminergic nuclei that promote wakefulness and inhibit REM sleep. We hypothesized that orexin neurons should be relatively active during wakefulness and inactive during sleep. To determine the pattern of activity of orexin neurons, we recorded sleep–wake behavior, body temperature, and locomotor activity under various conditions and used double-label immunohistochemistry to measure the expression of Fos in orexin neurons of the perifornical region. In rats maintained on a 12 hr light/dark cycle, more orexin neurons had Fos immunoreactive nuclei during the night period; in animals housed in constant darkness, this activation still occurred during the subjective night. Sleep deprivation or treatment with methamphetamine also increased Fos expression in orexin neurons. In each of these experiments, Fos expression in orexin neurons correlated positively with the amount of wakefulness and correlated negatively with the amounts of non-REM and REM sleep during the preceding 2 hr. In combination with previous work, these results suggest that activation of orexin neurons may contribute to the promotion or maintenance of wakefulness. Conversely, relative inactivity of orexin neurons may allow the expression of sleep.
Maximum Entropy Discrimination Markov Networks

The standard maximum margin approach for structured prediction lacks a straightforward probabilistic interpretation of the learning scheme and the prediction rule. Therefore its unique advantages such as dual sparseness and kernel tricks cannot be easily conjoined with the merits of a probabilistic model such as Bayesian regularization, model averaging, and ability to model hidden variables. In this paper, we present a new general framework called maximum entropy discrimination Markov networks (MaxEnDNet, or simply, MEDN), which integrates these two approaches and combines and extends their merits. Major innovations of this approach include: 1) It extends the conventional max-entropy discrimination learning of classification rules to a new structural max-entropy discrimination paradigm of learning a distribution of Markov networks. 2) It generalizes the extant Markov network structured-prediction rule based on a point estimator of model coefficients to an averaging model akin to a Bayesian predictor that integrates over a learned posterior distribution of model coefficients. 3) It admits flexible entropic regularization of the model during learning. By plugging in different prior distributions of the model coefficients, it subsumes the well-known maximum margin Markov networks (M3N) as a special case, and leads to a model similar to an L1-regularized M3N that is simultaneously primal and dual sparse, or other new types of Markov networks. 4) It applies a modular learning algorithm that combines existing variational inference techniques and convex-optimization based M3N solvers as subroutines. Essentially, MEDN can be understood as a jointly maximum likelihood and maximum margin estimate of Markov network. It represents the first successful attempt to combine maximum entropy learning (a dual form of maximum likelihood learning) with maximum margin learning of Markov network for structured input/output problems; and the basic principle can be generalized to learning arbitrary graphical models, such as the generative Bayesian networks or models with structured hidden variables. We discuss a number of theoretical properties of this approach, and show that empirically it outperforms a wide array of competing methods for structured input/output learning on both synthetic and real OCR and web data extraction data sets.
A PCR-Based Method to Construct Lentiviral Vector Expressing Double Tough Decoy for miRNA Inhibition

DNA vector-encoded Tough Decoy (TuD) miRNA inhibitor is attracting increased attention due to its high efficiency in miRNA suppression. The current methods used to construct TuD vectors are based on synthesizing long oligonucleotides (~90 mer), which have been costly and problematic because of mutations during synthesis. In this study, we report a PCR-based method for the generation of double Tough Decoy (dTuD) vector in which only two sets of shorter oligonucleotides (< 60 mer) were used. Different approaches were employed to test the inhibitory potency of dTuDs. We demonstrated that dTuD is the most efficient method in miRNA inhibition in vitro and in vivo. Using this method, a mini dTuD library against 88 human miRNAs was constructed and used for a high-throughput screening (HTS) of AP-1 pathway-related miRNAs. Seven miRNAs (miR-18b-5p, -101-3p, -148b-3p, -130b-3p, -186-3p, -187-3p and -1324) were identified as candidates involved in AP-1 pathway regulation. This novel method allows for an accurate and cost-effective generation of dTuD miRNA inhibitor, providing a powerful tool for efficient miRNA suppression in vitro and in vivo.
XWRAP: an XML-enabled wrapper construction system for Web information sources

The paper describes the methodology and the software development of XWRAP, an XML-enabled wrapper construction system for semi-automatic generation of wrapper programs. By XML-enabled we mean that the metadata about information content that are implicit in the original Web pages will be extracted and encoded explicitly as XML tags in the wrapped documents. In addition, the query based content filtering process is performed against the XML documents. The XWRAP wrapper generation framework has three distinct features. First, it explicitly separates tasks of building wrappers that are specific to a Web source from the tasks that are repetitive for any source, and uses a component library to provide basic building blocks for wrapper programs. Second, it provides a user friendly interface program to allow wrapper developers to generate their wrapper code with a few mouse clicks. Third and most importantly, we introduce and develop a two-phase code generation framework. The first phase utilizes an interactive interface facility to encode the source-specific metadata knowledge identified by individual wrapper developers as declarative information extraction rules. The second phase combines the information extraction rules generated at the first phase with the XWRAP component library to construct an executable wrapper program for the given Web source. We report the initial experiments on performance of the XWRAP code generation system and the wrapper programs generated by XWRAP.
Asymptotic sum-capacity of MIMO two-way relay channels within 1/2 log 5/4 bit per user-antenna

We propose a novel space-division based network-coding scheme for multiple-input multiple-output (MIMO) two-way relay channels (TWRCs), in which two multi-antenna users exchange information via a multi-antenna relay. In the proposed scheme, the overall signal space at the relay is divided into two subspaces. In one subspace, the spatial streams of the two users have nearly orthogonal directions, and are completely decoded at the relay. In the other subspace, the signal directions of the two users are nearly parallel, and linear functions of the spatial streams are computed at the relay, following the principle of physical-layer network coding (PNC). Based on the recovered messages and message-functions, the relay generates and forwards network-coded messages to the two users. We show that, at high signal-to-noise ratio (SNR), the proposed scheme with optimized precoding achieves the asymptotic sum-rate capacity of MIMO TWRCs within 1/2 log(5/4) ≈ 0.161 bit per user-antenna, for any antenna configuration and any channel realization.
Collaborative thesaurus tagging the Wikipedia way

This paper explores the system of categories that is used to classify articles in Wikipedia. It is compared to collaborative tagging systems like del.icio. us and to hierarchical classification like the Dewey Decimal Classification (DDC). Specifics and commonalitiess of these systems of subject indexing are exposed. Analysis of structural and statistical properties (descriptors per record, records per descriptor, descriptor levels) shows that the category system of Wikimedia is a thesaurus that combines collaborative tagging and hierarchical subject indexing in a special way.
Evolutionary walks on rugged landscapes

The rapid evolution of antibody molecules during an immune response enables the immune system to respond efficiently to an immense variety of challenges. To investigate this response, a theory for molecular evolution in biological systems is developed and analyzed. A molecule can be represented as a sequence of Nletters, with each letter being chosen from an alphabet of size a; for protein molecules the alphabet consists of the twenty amino acids, while for nucleic acids it consists of the four base pairs. Together, these $a^N $ possibilities form a sequence space ${\bf S}$ It is assumed that a fitness can be assigned to each sequence in ${\bf S}$; for the immune response the fitness is just the chemical affinity of the antibody for the immunizing antigen.Evolution is assumed to occur by random point mutations that change a single letter in the sequence; this defines the set of one-mutant neighbors of a sequence. It is assumed that the original sequence will be replaced by the one-mutant neighbor if and o.
Dissolved carbon dioxide determines the productivity of a recombinant hemagglutinin component of an influenza vaccine produced by insect cells

Dissolved carbon dioxide (dCO2) accumulation during cell culture has been recognized as an important parameter that needs to be controlled for successful scale‐up of animal cell culture because above a certain concentration there are adverse effects on cell growth performance and protein production. We investigated the effect of accumulation of dCO2 in bioreactor cultures of expresSF+® insect cells infected with recombinant baculoviruses expressing recombinant influenza virus hemagglutinins (rHA). Different strategies for bioreactor cultures were used to obtain various ranges of concentrations of dCO2 (<50, 50–100, 100–200, and >200 mmHg) and to determine their effects on recombinant protein production and cell metabolic activity. We show that the accumulation of dCO2 at levels > 100 mmHg resulted in reduced metabolic activity, slowed cell growth, prolonged culture viability after infection, and decreased infection kinetics. The reduced rHA yields were not caused by the decrease in the extracellular pH that resulted from dCO2 accumulation, but were most likely due to the effect of dCO2 accumulation in cells. The results obtained here at the 2 L scale have been used for the design of large‐scale processes to manufacture the rHA based recombinant vaccine Flublok™ at the 2500 L scale Biotechnol. Bioeng. 2015;112: 2267–2275. © 2015 Wiley Periodicals, Inc.
Suicidal ideation and the risk of suicide in patients with fibromyalgia: a comparison with non-pain controls and patients suffering from low-back pain

Fibromyalgia is associated with an increased rate of mortality from suicide. In fact, this disease is associated with several characteristics that are linked to an increased risk of suicidal behaviors, such as being female and experiencing chronic pain, psychological distress, and sleep disturbances. However, the literature concerning suicidal behaviors and their risk factors in fibromyalgia is sparse. The objectives of the present study were to evaluate the prevalence of suicidal ideation and the risk of suicide in a sample of patients with fibromyalgia compared with a sample of healthy subjects and a sample of patients with chronic low-back pain. We also aimed to evaluate the relevance of pain intensity, depression, and sleep quality as variables related to suicidal ideation and risks. Logistic regression was applied to estimate the likelihood of suicidal ideation and the risk of suicide adjusted by age and sex. We also used two logistic regression models using age, sex, pain severity score, depression severity, sleep quality, and disease state as independent variables and using the control group as a reference. Forty-four patients with fibromyalgia, 32 patients with low-back pain, and 50 controls were included. Suicidal ideation, measured with item 9 of the Beck Depression Inventory, was almost absent among the controls and was low among patients with low-back pain; however, suicidal ideation was prominent among patients with fibromyalgia (P<0.0001). The risk of suicide, measured with the Plutchik Suicide Risk Scale, was also higher among patients with fibromyalgia than in patients with low-back pain or in controls (P<0.0001). The likelihood for suicidal ideation and the risk of suicide were higher among patients with fibromyalgia (odds ratios of 26.9 and 48.0, respectively) than in patients with low-back pain (odds ratios 4.6 and 4.7, respectively). Depression was the only factor associated with suicidal ideation or the risk of suicide.
Transport of angular momentum and chemical species by anisotropic mixing in stellar radiative interiors

Small levels of turbulence can be present in stellar radiative interiors due to, e.g., the instability of rotational shear. In this paper we estimate turbulent transport coefficients for stably stratified rotating stellar radiation zones. Stable stratification induces strong anisotropy with a very small ratio of radial-to-horizontal turbulence intensities. Angular momentum is transported mainly due to the correlation between azimuthal and radial turbulent motions induced by the Coriolis force. This non-diffusive transport known as the Λ-effect has outward direction in radius and is much more efficient compared to the effect of radial eddy viscosity. Chemical species are transported by small radial diffusion only. This result is confirmed using direct numerical simulations combined with the test-scalar method. As a consequence of the non-diffusive transport of angular momentum, the estimated characteristic time of rotational coupling (≲100 Myr) between radiative core and convective envelope in young solar-type stars is much shorter compared to the time-scale of Lithium depletion (∼1 Gyr) (© 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Automatic Detection of [T] Pronunciation Errors for Chinese Learners of English

—This study examines the types of errors produced by Chinese learners of English when attempting to pronounce [T] in reading passages and presents a system for automatically detecting these pronunciation errors. The system achieves an accuracy of 79.8%, compared to the inter-annotator exact agreement rate of 83.1%. In addition, speaker-level scores based on the total number of correct productions of [T] made by each speaker are generated from both the human and machine error annotations, and these are shown to have a strong correlation with each other (0.797).