Miracle-dz/UniFAR-FTUs huggingface dataset:
A stochastic, evolutionary model for range shifts and richness on tropical elevational gradients under Quaternary glacial cycles

Quaternary glacial–interglacial cycles repeatedly forced thermal zones up and down the slopes of mountains, at all latitudes. Although no one doubts that these temperature cycles have left their signature on contemporary patterns of geography and phylogeny, the relative roles of ecology and evolution are not well understood, especially for the tropics. To explore key mechanisms and their interactions in the context of chance events, we constructed a geographical range-based, stochastic simulation model that incorporates speciation, anagenetic evolution, niche conservatism, range shifts and extinctions under late Quaternary temperature cycles along tropical elevational gradients. In the model, elevational patterns of species richness arise from the differential survival of founder lineages, consolidated by speciation and the inheritance of thermal niche characteristics. The model yields a surprisingly rich variety of realistic patterns of phylogeny and biogeography, including close matches to a variety of contemporary elevational richness profiles from an elevational transect in Costa Rica. Mountaintop extinctions during interglacials and lowland extinctions at glacial maxima favour mid-elevation lineages, especially under the constraints of niche conservatism. Asymmetry in temperature (greater duration of glacial than of interglacial episodes) and in lateral area (greater land area at low than at high elevations) have opposing effects on lowland extinctions and the elevational pattern of species richness in the model—and perhaps in nature, as well.
Interactive Effects of Secondary Macronutrients and Micronutrients on the Grain Yield, Nutrient Uptake and Use Efficiencies of Maize in the Guinea Savannas of Nigeria

To close the nutrient-related yield gaps in maize, balanced nutrition using primary and secondary macronutrients as well as micronutrients is recommended. Multi-nutrient diagnostic field trials were conducted in Guinea Savanna of Nigeria to assess the interactive effects of macronutrients and micronutrients on maize grain yields, nutrient uptake as well as N, P and K use efficiencies. The treatments consisted of a control (zero fertilizer applied), an NPK treatment and 10 other treatments in which macronutrient (Mg, S) and/or micronutrients (B, and Zn) were added to the NPK. The experiment was laid out in Randomized Complete Block Design with 3 replications. Data collected were subjected to mixed model with nutrient management strategy as fixed effects while replication nested in location and interaction between location and nutrient management strategy as random effects. The results revealed significant effects (P < 0.05) of nutrient management strategy on maize yield, nutrient uptake and nutrient use efficiencies of N, P and K. The study revealed that yield advantage over the recommended NPK fertilizer as a result of application macronutrients and micronutrients were highest with Mg in Lere (2.4 t ha−1), S + B + Zn in Faskari (2.8 t ha−1), S + B in Doguwa (1.5 t ha−1) and S + Zn in Toro (2.4 t ha−1). Addition of Mg, S and B significantly increases macronutrient uptakes over the recommended NPK only. Agronomic use efficiency, internal utilization efficiency, apparent recovery efficiency and partial factor productivity were significantly increased with the addition of S, Mg, and B but were not improved with Zn application. It was concluded that nutrient limitations to maize in the Guinea Savanna go beyond N, P and K. This study recommends that S, Mg, and B are needed to improve maize productivity and engender improve the use efficiency of NPK fertilizers.
Antifungal activity of essential oils from Iranian plants against fluconazole-resistant and fluconazole-susceptible Candida albicans

Objective: The purpose of this study was to assay the antifungal activity of selected essential oils obtained from plants against both fluconazole (FLU)-resistant and FLU-susceptible C. albicans strains isolated from HIV positive patients with oropharyngeal candidiasis (OPC). Materials and Methods: The essential oils were obtained by hydrodistillation method from Myrtus communis (My. communis), Zingiber officinale roscoe (Z. officinale roscoe), Matricaria chamomilla (Ma. chamomilla), Trachyspermum ammi (T. ammi) and Origanum vulgare (O. vulgare). The susceptibility test was based on the M27-A2 methodology. The chemical compositions of the essential oils were obtained by gas chromatography- mass spectroscopy (GC-MS). Results: In GC-MS analysis, thymol (63.40%), linalool (42%), α-pinene (27.87%), α-pinene (22.10%), and zingiberene (31.79%) were found to be the major components of T. ammi, O. vulgare, My. communis, Ma. chamomilla and Z. officinale roscoe, respectively. The results showed that essential oils have different levels of antifungal activity. O. vulgare and T. ammi essential oils were found to be the most efficient (P<0.05). The main finding was that the susceptibilities of FLU-resistant C. albicans to essential oils were higher than those of the FLU-susceptible yeasts. Conclusion: Results of this study indicated that the oils from medicinal plants could be used as potential anti FLU-resistant C. albicans agents.
Direct prediction of profiles of sequences compatible with a protein structure by neural networks with fragment‐based local and energy‐based nonlocal profiles

Locating sequences compatible with a protein structural fold is the well‐known inverse protein‐folding problem. While significant progress has been made, the success rate of protein design remains low. As a result, a library of designed sequences or profile of sequences is currently employed for guiding experimental screening or directed evolution. Sequence profiles can be computationally predicted by iterative mutations of a random sequence to produce energy‐optimized sequences, or by combining sequences of structurally similar fragments in a template library. The latter approach is computationally more efficient but yields less accurate profiles than the former because of lacking tertiary structural information. Here we present a method called SPIN that predicts Sequence Profiles by Integrated Neural network based on fragment‐derived sequence profiles and structure‐derived energy profiles. SPIN improves over the fragment‐derived profile by 6.7% (from 23.6 to 30.3%) in sequence identity between predicted and wild‐type sequences. The method also reduces the number of residues in low complex regions by 15.7% and has a significantly better balance of hydrophilic and hydrophobic residues at protein surface. The accuracy of sequence profiles obtained is comparable to those generated from the protein design program RosettaDesign 3.5. This highly efficient method for predicting sequence profiles from structures will be useful as a single‐body scoring term for improving scoring functions used in protein design and fold recognition. It also complements protein design programs in guiding experimental design of the sequence library for screening and directed evolution of designed sequences. The SPIN server is available at http://sparks‐lab.org. Proteins 2014; 82:2565–2573. © 2014 Wiley Periodicals, Inc.
What can be learned by measuring the fluxes of the 7 Be and the pep solar neutrino lines

Measurements of the interaction rates of the solar neutrino lines of {sup 7}Be and pep can be used, independent of solar models, to test whether electron flavor is conserved, to determine survival probabilities of electron-type neutrinos at specific energies, and to test for the existence of sterile neutrinos. We present analytic descriptions of these tests. We also illustrate by numerical simulations, assuming matter-enhanced and vacuum neutrino oscillations, what measurements of solar neutrino lines can teach us about neutrino masses and mixing angles. {copyright} {ital 1997} {ital The American Physical Society}
BANDWIDTH STEALING VIA LINK-TARGETED ROQ ATTACKS

We present a scheme that enables a set of flows to acquire an unfair share of bandwidth by mounting an adversarial distributed Reduction of Quality (RoQ) attack on flows competing for that bandwidth. This adversarial behavior stands in sharp contrast to other network exploits, e.g., Denial-ofService (DoS) attacks, whose aim is to simply take down a resource, or severely limit access to a service. The extent to which the scheme we expose is successful in slowing down competing flows determines the amount of “stolen bandwidth. ” We present two schemes for the construction of a RoQ attack stream that would evade detection, and thus would challenge counter-DoS techniques. Our results show the vulnerability of the Internet to the distributed nature of RoQ attacks, which could be mounted through a relatively small number of zombie clients, motivating the need for the development of counter measures. We validate our findings through simple analysis, simulations and real Internet experiments.
Salmonella Paratyphi A Rates, Asia

Little is known about the causes of enteric fever in Asia. Most cases are believed to be caused by Salmonella enterica serovar Typhi and the remainder by S. Paratyphi A. We compared their incidences by using standardized methods from population-based studies in China, Indonesia, India, and Pakistan.
DigSee: disease gene search engine with evidence sentences (version cancer)

Biological events such as gene expression, regulation, phosphorylation, localization and protein catabolism play important roles in the development of diseases. Understanding the association between diseases and genes can be enhanced with the identification of involved biological events in this association. Although biological knowledge has been accumulated in several databases and can be accessed through the Web, there is no specialized Web tool yet allowing for a query into the relationship among diseases, genes and biological events. For this task, we developed DigSee to search MEDLINE abstracts for evidence sentences describing that ‘genes’ are involved in the development of ‘cancer’ through ‘biological events’. DigSee is available through http://gcancer.org/digsee.
Memory fast-forward: A low cost special function unit to enhance energy efficiency in GPU for big data processing

Big data processing, e.g., graph computation and MapReduce, is characterized by massive parallelism in computation and a large amount of fine-grained random memory accesses often with structural localities due to graph-like data dependency. Recently, GPU is gaining more and more attention for servers due to its capability of parallel computation. However, the current GPU architecture is not well suited to big data workloads due to the limited capability of handling a large number of memory requests. In this paper, we present a special function unit, called memory fast-forward (MFF) unit, to address this problem. Our proposed MFF unit provides two key functions. First, it supports pointer chasing which enables computation threads to issue as many memory requests as possible to increase the potential of coalescing memory requests. Second, it coalesces memory requests bound for the same cache block, often due to structural locality, thereby reducing memory traffics. Both pointer chasing and memory request coalescing contribute to reducing memory stall time as well as improving the real utilization of memory bandwidth, by removing duplicate memory traffics, thereby improving performance and energy efficiency. Our experiments with graph computation algorithms and real graphs show that the proposed MFF unit can improve the energy efficiency of GPU in graph computation by average 54.6% at a negligible area cost.
Effects of increases in dietary fat intake on plasma lipid and lipoprotein cholesterol concentrations and associated enzyme activities in cats.

OBJECTIVE To determine the effects of increases in dietary intake of polyunsaturated and saturated fatty acids on plasma lipid and lipoprotein concentrations and activity of associated enzymes in healthy domestic cats. ANIMALS 16 healthy adult sexually intact female cats. PROCEDURES A baseline diet (40% energy from fat) and 4 test diets, with increased amounts of fat (51% and 66% energy from fat) from the addition of polyunsaturated and saturated fatty acids, were fed for 6 weeks each. Plasma cholesterol, triglyceride, and lipoprotein cholesterol concentrations, along with activities of lipoprotein lipase, hepatic lipase, and lecithin-cholesterol acyl transferase, were measured at the end of each feeding period. RESULTS Diet, amount of fat, or ratio of polyunsaturated to saturated fatty acids had no effect on plasma concentrations of cholesterol, triglycerides, and very-low-density or high-density lipoproteins or the activity of lecithin-cholesterol acyl transferase. Low-density lipoprotein concentrations were significantly lower in cats fed a high-fat diet containing polyunsaturated fatty acids. Lipoprotein concentration and hepatic lipase activity were significantly higher in cats fed the fat-supplemented diets, and this was unrelated to whether diets were enriched with polyunsaturated or saturated fatty acids. CONCLUSIONS AND CLINICAL RELEVANCE Diets containing up to 66% of energy from fat were tolerated well by healthy cats and did not affect plasma lipid concentrations. Therefore, high-fat diets probably will not contribute to hypercholesterolemia or hypertriglyceridemia in cats.
Energy-delay considerations in coded packet flows

We consider a line of terminals which is connected by packet erasure channels and where random linear network coding is carried out at each node prior to transmission. In particular, we address an online approach in which each terminal has local information to be conveyed to the base station at the end of the line and provide a queueing theoretic analysis of this scenario. First, a genie-aided scenario is considered and the average delay and average transmission energy depending on the link erasure probabilities and the Poisson arrival rates at each node are analyzed. We then assume that all nodes cannot send and receive at the same time. The transmitting nodes in the network send coded data packets before stopping to wait for the receiving nodes to acknowledge the number of degrees of freedom, if any, that are required to decode correctly the information. We analyze this problem for an infinite queue size at the terminals and show that there is an optimal number of coded data packets at each node, in terms of average completion time or transmission energy, to be sent before stopping to listen.
Herschel : the first science highlights Special feature L etter to the E ditor Properties of compact 250 μ m emission and H II regions in M 33 ( HERM 33 ES )

Aims. Within the framework of the HERM33ES key program, using the high resolution and sensitivity of the Herschel photometric data, we study the compact emission in the Local Group spiral galaxy M 33 to investigate the nature of the compact SPIRE emission sources. We extracted a catalogue of sources at 250 μm in order to investigate the nature of this compact emission. Taking advantage of the unprecedented Herschel resolution at these wavelengths, we also focus on a more precise study of some striking Hα shells in the northern part of the galaxy. Methods. We present a catalogue of 159 compact emission sources in M 33 identified by SExtractor in the 250 μm SPIRE band that is the one that provides the best spatial resolution. We also measured fluxes at 24 μm and Hα for those 159 extracted sources. The morphological study of the shells also benefits from a multiwavelength approach including Hα, far-ultraviolet from GALEX, and infrared from both Spitzer IRAC 8 μm and MIPS 24 μm in order to make comparisons. Results. For the 159 compact sources selected at 250 μm, we find a very strong Pearson correlation coefficient with the MIPS 24 μm emission (r24 = 0.94) and a rather strong correlation with the Hα emission, although with more scatter (rHα = 0.83). The morphological study of the Hα shells shows a displacement between far-ultraviolet, Hα, and the SPIRE bands. The cool dust emission from SPIRE clearly delineates the Hα shell structures. Conclusions. The very strong link between the 250 μm compact emission and the 24 μm and Hα emissions, by recovering the star formation rate from standard recipes for H ii regions, allows us to provide star formation rate calibrations based on the 250 μm compact emission alone. The different locations of the Hα and far-ultraviolet emissions with respect to the SPIRE cool dust emission leads to a dynamical age of a few Myr for the Hα shells and the associated cool dust.
A modeling study on the use of passive microwave data for the monitoring of sparsely vegetated land surfaces

Presents some aspects of a scheme which uses remote sensing measurements to control the simulations of a coupled land surface process and passive microwave radiative transfer model. Based on an iterative minimization procedure, the scheme estimates model input parameters or initial conditions. The study focuses on the feasibility of the scheme and its sensitivity to errors. It is shown that important parameters can be retrieved with the scheme, and that the parameters to which the simulations are most sensitive, are also those which are more liable to be retrieved satisfactorily in the presence of noise.
Discovering in Formative Knowledge using Combined Mining Approach

mining applications involve complex data like multiple heterogeneous data sources, different user preference and create decision making activities. The comprehensive, useful information may not be obtained by using the single data mining method in the form of informative patterns as that would consume more time and space. Combined mining is a hybrid mining approach for mining informative patterns from single or multiple data sources, many features abstraction and merging multiple methods as per the requirements. Some concepts show hybrid or combined mining approach. In this paper, multi method combined mining methodology is designed. Proposed method combine apriori algorithm with Multi-Objective Evolutionary Algorithm. It helps to improve searching for the exact products from complex data. Proposed method combine apriori algorithm with multi-objective evolutionary algorithm to improve searching of documents from complex data. It addressed challenging problems in combined mining and summarized and proposed effective pattern merging and interaction paradigms, combined pattern types, such as pair patterns and cluster patterns, interestingness measures. In the proposed method, by using apriori algorithm, calculate the support and confidence of the frequent item set which improve results of searching by a using multi-objective evolutionary algorithm. Keywordsmining approach, Multi-objective Evolutionary algorithm, Apriori algorithm, Knowledge Discovery combined mining, complex data, data mining, multiple source data mining.
ABNORMAL PGE2 REGULATION OF MONOCYTE TNF-α LEVELS IN TRAUMA PATIENTS PARALLELS DEVELOPMENT OF A MORE MACROPHAGE-LIKE PHENOTYPE

Some trauma patients’ monocytes (MO) increase TNF-α levels concomitant to augmenting production of the TNF-α inhibitor prostaglandin E2 (PGE2), suggesting posttrauma MO insensitivity to PGE2 effects. This study assesses additional posttrauma MO PGE2 insensitivity effects on altering TNF-α form (membrane versus secreted), down-regulating MO receptor expression, and depressing MO APC function. Posttrauma MO TNF-α insensitivity to exogenous and autocrine PGE2 correlated to accumulation of TNF-α primarily as a membrane-bound cytokine (mTNF-α). MO retention of mTNF-α correlated with unfavorable clinical outcomes and loss of antigen-presenting cell (APC) function as assessed by depressed MLR and dendritic cell (DC) differentiation. MO TNF-α sensitivity to down-regulation by IL-10 was retained, suggesting that PGE2-related functions are specifically altered in these patients’ MO. Freshly isolated MO from all trauma patients had decreased expression of Toll-like receptor 4 (TLR4) for gram-negative bacteria. Exogenous PGE2 at high (10−6M) or low (10−8M) concentrations decreased normals’ and further decreased APC-competent patients’ MO TLR4 expression but had no effect on TLR2. Patients’ APC-dysfunctional MO failed to further down-regulate their TLR4 expression in response to additional PGE2, demonstrating another form of PGE2 insensitivity. One of the primary MO prostaglandin receptors, eicosanoid receptor 4 (EP4), was decreased on patients’ APC dysfunctional MO, suggesting that depressed EP4 expression could contribute to PGE2 insensitivity in patients’ MO. The APC dysfunctional MO’s dysregulation of TLR4 expression paralleled increased macrophage-like characteristics such as increased CD64 expression density, elevated mTNF-α production, and increased PGE2 levels. Increased PGE2 levels still decreased patients’ MO APC functions but failed to depress either MO TLR4 expression or mTNF-α levels, suggesting differential involvement of EP receptors in postinjury PGE2-mediated effects.
Pathoadaptive Mutations in Salmonella enterica Isolated after Serial Passage in Mice

How pathogenic bacteria adapt and evolve in the complex and variable environment of the host remains a largely unresolved question. Here we have used whole genome sequencing of Salmonella enterica serovar Typhimurium LT2 populations serially passaged in mice to identify mutations that adapt bacteria to systemic growth in mice. We found unique pathoadaptive mutations in two global regulators, phoQ and stpA, which increase the competitive indexes of the bacteria 3- to 5-fold. Also, all mouse-adapted lineages had changed the orientation of the hin invertable element, resulting in production of a FliC type of flagellum. Competition experiments in mice with locked flagellum mutants showed that strains expressing the FliC type of flagellum had a 5-fold increase in competitive index as compared to those expressing FljB type flagellum. Combination of the flagellum cassette inversion with the stpA mutation increased competitive indexes up to 20-fold. These experiments show that Salmonella can rapidly adapt to a mouse environment by acquiring a few mutations of moderate individual effect that when combined confer substantial increases in growth.
Advanced Packaging and Heterogeneous Integration to Reboot Computing

In the past several decades on-chip dimensions have scaled over 2000X, while dimensions on printed circuit board have scaled 4-5X. This modest scaling of packaging dimensions has severely limited system scaling. To address this, we have proposed a disruptive package-free integration scheme. We replace the traditional organic printed circuit board (PCB) with silicon interconnect fabric (SiIF) and replace the traditional package by directly mounting bare chiplets on to the SiIF. Fine pitch solderless copper pillar connections increase IO density by 20-80X and the inter-chiplet spacing is reduced by 10-20X. This enables highly parallel communication instead of serialized links. This achieves higher bandwidth/mm (~100X) and lower latency (~25X) and lower communication energy per bit (~200X). This integration technology allows us to challenge the conventional communication-limited architectures in a substantial way. The ability to heterogeneously integrate diverse dies with arbitrarily fine granularity, but on a wafer scale, reduces the cost of processor-memory communication energy opening new compute paradigms. In addition, the superior heat spreading properties of the SiIF compared to organic PCBs allows us to run the cores harder. The heterogeneous integration property of our scheme, allows for an intimate mingling of heterogeneous processor cores, FPGAs and memory types opening new avenues to reboot computing.