Miracle-dz/UniFAR-FTUs huggingface dataset:
Deformation and metamorphism in convergent orogens: a model for uplift and exhumation of metamorphic terrains

Summary A conceptual model is presented for deformation, uplift and exhumation in convergent orogens based on flexural models of foreland basin subsidence, the role of inherited rifted margins in convergent orogens, critical wedge theory and the use of P-T-t data to construct particle paths within the deforming orogen. Three states of overthrust orogens can be defined, based on the relative rates of mass loss by erosion and mass addition by accretion and underplating. Rapid exhumation of metamorphic terrains is most likely in the steady state, where erosion balances accretion; a constructive state, where mass addition outweighs erosion, initially results in deep burial and relatively little exhumation; a destructive state, where mass loss outweighs mass addition, results in slow exhumation or subsidence of metamorphic rocks, depending on whether mass is lost by erosion or redistributed during extension. In order to test these predictions, reliable P-T-t data are required on peak metamorphism, pluton emplacement, cooling, exhumation, and uplift, for a range of localities within an orogen.
Identification of intermediate-risk patients with acute symptomatic pulmonary embolism

The identification of normotensive patients with acute pulmonary embolism (PE) at high risk of adverse PE-related clinical events (i.e. intermediate-risk group) is a major challenge. We combined individual patient data from six studies involving 2874 normotensive patients with PE. We developed a prognostic model for intermediate-risk PE based on the clinical presentation and the assessment of right ventricular dysfunction and myocardial injury. We used a composite of PE-related death, haemodynamic collapse or recurrent PE within 30 days of follow-up as the main outcome measure. The primary outcome occurred in 198 (6.9%) patients. Predictors of complications included systolic blood pressure 90–100 mmHg (adjusted odds ratio (aOR) 2.45, 95% CI 1.50–3.99), heart rate ≥110 beats per min (aOR 1.87, 95% CI 1.31–2.69), elevated cardiac troponin (aOR 2.49, 95% CI 1.71–3.69) and right ventricular dysfunction (aOR 2.28, 95% CI 1.58–3.29). We used these variables to construct a multidimensional seven-point risk index; the odds ratio for complications per one-point increase in the score was 1.55 (95% CI 1.43–1.68; p<0.001). The model identified three stages (I, II and III) with 30-day PE-related complication rates of 4.2%, 10.8% and 29.2%, respectively. In conclusion, a simple grading system may assist clinicians in identifying intermediate-risk PE. A simple grading system to identify intermediate-risk pulmonary embolism http://ow.ly/uItnL
Key Generation From Wireless Channels: A Review

Key generation from the randomness of wireless channels is a promising alternative to public key cryptography for the establishment of cryptographic keys between any two users. This paper reviews the current techniques for wireless key generation. The principles, performance metrics and key generation procedure are comprehensively surveyed. Methods for optimizing the performance of key generation are also discussed. Key generation applications in various environments are then introduced along with the challenges of applying the approach in each scenario. The paper concludes with some suggestions for future studies.
Reducing FIFO buffer power using architectural alternatives at RTL

NoC has a significant impact on the power, area and performance of multi-core architectures. The contribution of NoC in the total power budget of a CMP is approximately 30 to 40% [1], and the input buffers of router consume most of it. Therefore, the designers need to design a low power communication architecture of NoC by reducing the power consumption of buffers. In the existing techniques, virtual channel buffer power has been optimized by employing buffer sharing, power gating with flexible virtual channels and Dynamic Voltage Frequency Scaling (DVFS). In this paper, we have proposed a) Routing Logic enabled clock gating at input channel buffers b) Further, we applied the clock gating on FPGA slices on our proposed design. Our approach provides a significant improvement in FIFO buffer power in 2D NoC as the FIFO power is optimized by 10.70%. Furthermore, 37% of improvement in dynamic power has been achieved by applying clock gating on slices and block RAM on our proposed routing logic enabled input channel buffers clock gating technique.
Complete Genome Sequence of a Novel Human Betapapillomavirus, HPV-159

ABSTRACT A novel human papillomavirus (HPV), now officially recognized as HPV-159, isolated from an anal swab, was fully cloned, sequenced, and genetically characterized. HPV-159 has a genomic organization that is typical of cutaneotrophic HPV types, and it belongs to the genus Betapapillomavirus.
Assessment of in vivo frequency of mutated T cells in patients with systemic lupus erythematosus

The frequency of mutant T cells (FMC) in blood lymphocytes from patients with systemic lupus erythematosus (SLE) was measured by growing cells in the presence and in the absence of 6-thioguanine. Patients with SLE had a spectrum of FMC ranging from normal to about 100 times normal. This high FMC among cells from SLE patients appears to reflect excessive in vivo activation and proliferation during the course of the disease. This represents the first demonstration of such a T cell abnormality in SLE; it supports the hypothesis that SLE T cells demonstrate increased in vivo division and/or survival.
PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

Restriction-site associated genomic markers are a powerful tool for investigating evolutionary questions at the population level, but are limited in their utility at deeper phylogenetic scales where fewer orthologous loci are typically recovered across disparate taxa. While this limitation stems in part from mutations to restriction recognition sites that disrupt data generation, an alternative source of data loss comes from the failure to identify homology during bioinformatic analyses. Clustering methods that allow for lower similarity thresholds and the inclusion of indel variation will perform better at assembling RADseq loci at the phylogenetic scale. PyRAD is a pipeline to assemble de novo RADseq loci with the aim of optimizing coverage across phylogenetic data sets. It utilizes a wrapper around an alignment-clustering algorithm which allows for indel variation within and between samples, as well as for incomplete overlap among reads (e.g., paired-end). Here I compare PyRAD with the program Stacks in their performance analyzing a simulated RADseq data set that includes indel variation. Indels disrupt clustering of homologous loci in Stacks but not in PyRAD, such that the latter recovers more shared loci across disparate taxa. I show through re-analysis of an empirical RADseq data set that indels are a common feature of such data, even at shallow phylogenetic scales. PyRAD utilizes parallel processing as well as an optional hierarchical clustering method which allow it to rapidly assemble phylogenetic data sets with hundreds of sampled individuals. Availability Software is written in Python and freely available at http://www.dereneaton. com/software/ Supplement Scripts to completely reproduce all simulated and empirical analyses are available in the Supplementary Materials.
Investigating the driving forces of deforestatiom in the state of Minas Gerais, Brazil

In 2003, the government of Minas Gerais, Brazil, devised a vegetation monitoring system that provides important information to the government agencies such as land-cover maps, deforestation rates, volume estimates and carbon stocks. Nevertheless, the main factors behind deforestation in the region are still unidentified as well as in each scale these factors operate. The main goal of this study was to explore the spatial variability of the driving forces behind deforestation at three different scales using Ordinary Least Square (OLS) and Geographically Weighted Regression (GWR) techniques. Scales correspond to three aggregation levels: the municipalities (Aggregation level 1), the microregions (Aggregation level 2) and the watersheds (Aggregation level 3). The datasets was provided by the state’s monitoring system and public agencies. The results reveal that the driving forces of deforestation are agricultural area, charcoal production, and monoculture forest area at Aggregation level 1 while charcoal production and monoculture forest area dominate at Aggregation levels 2 and 3. The GWR results present significant improvement compared to the OLS results. Additionally, the GWR technique provide useful insights for the government decision-makers about the spatial relationships between dominant driving forces and deforested areas at multiple scales. This study also confirms the influence of the modifiable areal unit problem (MAUP) in OLS and GWR models.
Optical Color Gradients in Star-forming Ring Galaxies

We compute radial color gradients produced by an outwardly propagating circular wave of star formation and compare our results with color gradients observed in the classical ring galaxy, the "Cartwheel. " We invoke two independent models of star formation in the ring galaxies. The first one is the conventional density wave scenario, in which an intruder galaxy creates a radially propagating density wave accompanied by an enhanced star formation following the Schmidt's law. The second scenario is a pure self-propagating star formation model, in which the intruder sets off only the first burst of stars at the point of impact. Both models give essentially the same results. Systematic reddening of B-V, V-K colors toward the center, such as that observed in the Cartwheel, can be obtained only if the abundance of heavy elements in the star-forming gas is a few times below solar. The B-V and V-K color gradients observed in the Cartwheel can be explained as a result of mixing of stellar populations born in a star-forming wave propagating through a low-metallicity gaseous disk, and a preexisting stellar disk of the size of the gaseous disk with color properties typical to those observed in nearby disk galaxies.
Inter‐annual variability of summertime CO concentrations in the Northern Hemisphere explained by boreal forest fires in North America and Russia

Background measurements of Carbon Monoxide in the extra‐tropical Northern Hemisphere during the 1990s showed no clear trends, but significant inter‐annual variations. In this study, the measured summertime averaged CO concentrations north of 30° N were correlated with area burned by forest fires in North America and Russia. According to a linear regression analysis, 14% of the CO variability in the extra‐tropical Northern Hemisphere can be explained by boreal forest area burnt in North America, 53% by area burnt in Russia, and 63% by the combination of both. There are strong indications that the officially reported Russian fire areas are significantly underestimated. By statistically correcting these areas, we can show that, on the average, boreal burning provides a summertime CO source term comparable with all anthropogenic sources in the United States and Europe.
A field-grown transgenic tomato line expressing higher levels of polyamines reveals legume cover crop mulch-specific perturbations in fruit phenotype at the levels of metabolite profiles, gene expression, and agronomic characteristics

Genetic modification of crop plants to introduce desirable traits such as nutritional enhancement, disease and pest resistance, and enhanced crop productivity is increasingly seen as a promising technology for sustainable agriculture and boosting food production in the world. Independently, cultural practices that utilize alternative agriculture strategies including organic cultivation subscribe to sustainable agriculture by limiting chemical usage and reduced tillage. How the two together affect fruit metabolism or plant growth in the field or whether they are compatible has not yet been tested. Fruit-specific yeast S-adenosylmethionine decarboxylase (ySAMdc) line 579HO, and a control line 556AZ were grown in leguminous hairy vetch (Vicia villosa Roth) (HV) mulch and conventional black polyethylene (BP) mulch, and their fruit analysed. Significant genotype×mulch-dependent interactions on fruit phenotype were exemplified by differential profiles of 20 fruit metabolites such as amino acids, sugars, and organic acids. Expression patterns of the ySAMdc transgene, and tomato SAMdc, E8, PEPC, and ICDHc genes were compared between the two lines as a function of growth on either BP or HV mulch. HV mulch significantly stimulated the accumulation of asparagine, glutamate, glutamine, choline, and citrate concomitant with a decrease in glucose in the 556AZ fruits during ripening as compared to BP. It enables a metabolic system in tomato somewhat akin to the one in higher polyamine-accumulating transgenic fruit that have higher phytonutrient content. Finally, synergism was found between HV mulch and transgenic tomato in up-regulating N:C indicator genes PEPC and ICDHc in the fruit.
Cellular mechanisms underlying cholinergic and noradrenergic modulation of neuronal firing mode in the cat and guinea pig dorsal lateral geniculate nucleus

The functional properties, ionic basis, and possible convergence and interaction of postsynaptic actions mediated by muscarinic and alpha 1- adrenergic receptors were examined in cat and guinea pig dorsal lateral geniculate (LGNd) neurons maintained in thalamic slices in vitro. The possible involvement of GTP-binding proteins was also examined. Extracellular recordings from cat LGNd revealed the presence of two subpopulations of neurons. The most prevalent generated rhythmic high- frequency (300–500 Hz) bursts of two to six action potentials each, with an interburst frequency of 1–3 Hz. Intracellular recordings revealed that this activity is typical of thalamocortical relay cells in the apparent absence of neuromodulatory input. Application of ACh or noradrenaline (NA) to rhythmically oscillating neurons in the cat LGNd resulted in cessation of this activity followed by the appearance of single spike firing. Intracellular recordings revealed that this change in firing mode was associated with a depolarization of the neuron out of the range of intrinsic rhythmic oscillation and into or near the single spike firing mode. The voltage characteristics of the current underlying the cholinergic and noradrenergic slow depolarization were investigated in guinea pig LGNd neurons. Application of the muscarinic agonist acetyl-beta-methylcholine (MCh) to presumed relay neurons resulted in a hyperpolarization due to the activation of an outward K+ current. This response was followed by a slow depolarization due to reduction of a relatively non-voltage-dependent potassium current distinct from IM and IAHP. Application of NA resulted in a slow depolarization that was also associated with reduction of this relatively linear K+ current. The MCh- and NA-induced slow depolarizations displayed the property of occlusion, indicating convergence of action. However, these responses were mediated by pharmacologically distinct receptors since the MCh-induced reduction in K+ current was blocked by scopolamine while that induced by NA was blocked by the alpha 1-adrenoceptor antagonist prazosin. Intracellular diffusion of GTP-gamma-S resulted in the inward current responses to NA and MCh being irreversible, suggesting the possible involvement of a G- protein. Prior exposure to pertussis toxin did not affect the inward current response to NA and MCh, while the outward K+ current responses induced by application of MCh or the GABAB agonist baclofen were blocked. These results reveal that activation of muscarinic or alpha 1- adrenergic postsynaptic receptors in the LGNd result in a shift in firing mode from rhythmic oscillation to tonic single spike activity through a decrease in a relatively linear K+ current mediated through a pertussis toxin-insensitive G-protein. (ABSTRACT TRUNCATED AT 400 WORDS)
Can the behaviour of threespine stickleback parasitized with Schistocephalus solidus be replicated by manipulating host physiology?

ABSTRACT Sticklebacks infected by the parasitic flatworm Schistocephalus solidus show dramatic changes in phenotype, including a loss of species-typical behavioural responses to predators. The timing of host behaviour change coincides with the development of infectivity of the parasite to the final host (a piscivorous bird), making it an ideal model for studying the mechanisms of infection-induced behavioural modification. However, whether the loss of host anti-predator behaviour results from direct manipulation by the parasite, or is a by-product (e.g. host immune response) or side effect of infection (e.g. energetic loss), remains controversial. To understand the physiological mechanisms that generate these behavioural changes, we quantified the behavioural profiles of experimentally infected fish and attempted to replicate these in non-parasitized fish by exposing them to treatments including immunity activation and fasting, or by pharmacologically inhibiting the stress axis. All fish were screened for the following behaviours: activity, water depth preference, sociability, phototaxis, anti-predator response and latency to feed. We were able to change individual behaviours with certain treatments. Our results suggest that the impact of S. solidus on the stickleback might be of a multifactorial nature. The behaviour changes observed in infected fish might result from the combined effects of modifying the serotonergic axis, lack of energy and activation of the immune system. Summary: Hypotheses regarding causes of the behavioural modifications in threespine stickleback parasitized with the flatworm Schistocephalus solidus are tested by analyzing behaviour changes induced by experimental manipulations.
Local active information storage as a tool to understand distributed neural information processing

Every act of information processing can in principle be decomposed into the component operations of information storage, transfer, and modification. Yet, while this is easily done for today's digital computers, the application of these concepts to neural information processing was hampered by the lack of proper mathematical definitions of these operations on information. Recently, definitions were given for the dynamics of these information processing operations on a local scale in space and time in a distributed system, and the specific concept of local active information storage was successfully applied to the analysis and optimization of artificial neural systems. However, no attempt to measure the space-time dynamics of local active information storage in neural data has been made to date. Here we measure local active information storage on a local scale in time and space in voltage sensitive dye imaging data from area 18 of the cat. We show that storage reflects neural properties such as stimulus preferences and surprise upon unexpected stimulus change, and in area 18 reflects the abstract concept of an ongoing stimulus despite the locally random nature of this stimulus. We suggest that LAIS will be a useful quantity to test theories of cortical function, such as predictive coding.
Fast Multiplication Without Carry-Propagate Addition

Conventional schemes for fast multiplication accumulate the partial products in redundant form (carry-save or signed-digit) and convert the result to conventional representation in the last step. This step requires a carry-propagate adder which is comparatively slow and occupies a significant area of the chip in a VLSI implementation. A report is presented on a multiplication scheme (left-to-right, carry-free, LRCF) that does not require this carry-propagate step. The LRCF scheme performs the multiplication most-significant bit first and produces a conventional sign-and-magnitude product (most significant n bits) by means of an on-the-fly conversion. The resulting implementation is fast and regular and is very well suited for VLSI. The LRCF scheme for general radix r and a radix-4 signed-digit implementation are presented. >
Measuring Inhomogeneity in Spatial Distributions

The spatial distribution of nodes in wireless networks has important impact on network performance properties, such as capacity and connectivity. Although random sample models based on a uniform distribution are widely used in the research community, they are inappropriate for scenarios with clustered, inhomogeneous node distribution. This paper proposes a well-defined measure for the level of inhomogeneity of a node distribution. It is based on the local deviation of the actual value of the density of nodes from its expected value. Desired properties of the measure are defined and mathematically proven to be fulfilled. The inhomogeneity measure is also compared to human perception of inhomogeneity gained via an online survey. The results reveal that the measure well fits human perception, although there are notable deviations if linear operations are applied.
New color-based tracking algorithm for joints of the upper extremities

To track the joints of the upper limb of stroke sufferers for rehabilitation assessment, a new tracking algorithm which utilizes a developed color-based particle filter and a novel strategy for handling occlusions is proposed in this paper. Objects are represented by their color histogram models and particle filter is introduced to track the objects within a probability framework. Kalman filter, as a local optimizer, is integrated into the sampling stage of the particle filter that steers samples to a region with high likelihood and therefore fewer samples is required. A color clustering method and anatomic constraints are used in dealing with occlusion problem. Compared with the general basic particle filtering method, the experimental results show that the new algorithm has reduced the number of samples and hence the computational consumption, and has achieved better abilities of handling complete occlusion over a few frames.
Chapter 2 Interpretation of Urine Electrolytes and Osmolality

A. S. Reddi, Fluid, Electrolyte and Acid-Base Disorders, DOI 10.1007/978-1-4614-9083-8_2, © Springer Science+Business Media New York 2014 Measurement of urine Na + , Cl − , and K + is rather common in hospitalized patients, and these urine electrolytes are useful in the diagnostic evaluation of volume status, hyponatremia , acute kidney injury (AKI) , metabolic alkalosis, hypokalemia and urine anion gap (urine net charge). A spot urine sample is generally adequate for determination of these electrolytes. In addition, urine creatinine is determined to calculate the fractional excretion of Na + , K + , or other electrolytes. Also, urine osmolality is helpful in the differential diagnosis of hyponatremia , polyuria, and AKI. Table 2.1 summarizes the clinical applications of urine electrolytes and osmolality.
Structural basis for substrate recognition by the human N-terminal methyltransferase 1

Here, Dong et al. report the first crystal structures of human NTMT1 in complex with cofactor SAH and six substrate peptides. They also demonstrate that NTMT1 contains two characteristic structural elements (a β hairpin and an N-terminal extension) that contribute to its substrate specificity, thus advancing our understanding of the molecular mechanism of N-terminal methylation.