Miracle-dz/UniFAR-FTUs huggingface dataset:
SVM-based Method for Predicting Enzyme Function in a Hierarchical Context

Automatically categorizing enzyme into the Enzyme Commission (EC) hierar- chy is crucial to understand its specific molecular mechanism. Standard machine learning methods like support vector machine (SVM) and naive bayesian classifier have been suc- cessfully applied for this task. However, they treat each functional class independently, and ignore the inter-class relationships. In this paper, we develop a SVM-based method for prediction of enzyme function into the EC hierarchical context. Our method with low computational complexity is a modified version of a structured predictive model— Hierarchical Max-Margin Markov algorithm (HM 3 ). HM 3 , which is specially designed for the hierarchical multi-label classification, has been successfully used in many struc- tured pattern recognition problems, such as document categorization, web contend clas- sification, and enzyme function prediction. As input features for our predictive model, we use the conjoint triad feature (CTF). Our method has been validated on an enzyme benchmark dataset, the proteins in this benchmark dataset have less than 40% sequence identity to any other in a same functional class. Finally, for the first three EC digits, the predictive accuracy and the Matthew's correlation coefficient (MCC) of our method range from 78% to 100% and 0.76 to 1 respectively. Therefore we think our new method will be useful supplementary tools for the future studies in enzyme function prediction. Keywords: Enzyme function prediction; Conjoint triad feature; Structured hierarchical output; Support vector machine.
An inequality of Kostka numbers and Galois groups of Schubert problems

We show that the Galois group of any Schubert problem involving lines in projective space contains the alternating group. Using a criterion of Vakil and a special position argument due to Schubert, this follows from a particular inequality among Kostka numbers of two-rowed tableaux. In most cases, an easy combinatorial injection proves the inequality. For the remaining cases, we use that these Kostka numbers appear in tensor product decompositions of sl_2(C)-modules. Interpreting the tensor product as the action of certain commuting Toeplitz matrices and using a spectral analysis and Fourier series rewrites the inequality as the positivity of an integral. We establish the inequality by estimating this integral.
PTP‐SL and STEP protein tyrosine phosphatases regulate the activation of the extracellular signal‐regulated kinases ERK1 and ERK2 by association through a kinase interaction motif

Protein kinases and phosphatases regulate the activity of extracellular signal‐regulated kinases 1 and 2 (ERK1/2) by controlling the phosphorylation of specific residues. We report the physical and functional association of ERK1/2 with the PTP‐SL and STEP protein tyrosine phosphatases (PTPs). Upon binding, the N‐terminal domains of PTP‐SL and STEP were phosphorylated by ERK1/2, whereas these PTPs dephosphorylated the regulatory phosphotyrosine residues of ERK1/2 and inactivated them. A sequence of 16 amino acids in PTP‐SL was identified as being critical for ERK1/2 binding and termed kinase interaction motif (KIM) (residues 224–239); it was shown to be required for phosphorylation of PTP‐SL by ERK1/2 at Thr253. Co‐expression of ERK2 with catalytically active PTP‐SL in COS‐7 cells impaired the EGF‐induced activation of ERK2, whereas a PTP‐SL mutant, lacking PTP activity, increased the ERK2 response to EGF. This effect was dependent on the presence of the KIM on PTP‐SL. Furthermore, ERK1/2 activity was downregulated in 3T3 cells stably expressing PTP‐SL. Our findings demonstrate the existence of a conserved ERK1/2 interaction motif within the cytosolic non‐catalytic domains of PTP‐SL and STEP, which is required for the regulation of ERK1/2 activity and for phosphorylation of the PTPs by these kinases. Our findings suggest that PTP‐SL and STEP act as physiological regulators of the ERK1/2 signaling pathway.
Stationary planetary wave and nonmigrating tidal signatures in ionospheric wave 3 and wave 4 variations in 2007–2011 FORMOSAT‐3/COSMIC observations

The wave 3 and wave 4 modulations of the Equatorial Ionization Anomalies are a robust feature of the low‐latitude ionosphere, when viewed at constant local time. Although initially associated, respectively, with DE2 and DE3, nonmigrating diurnal tides in the mesosphere and lower thermosphere region, recent results have suggested that the wave 3 and wave 4 may also have significant contributions from other tidal and stationary planetary wave (SPW) signatures. We present observations of total electron content (TEC) variations associated with tidal and SPW signatures comprising the ionospheric wave 3 and wave 4 structures from FORMOSAT‐3/COSMIC from 2007 to 2011. We find that the wave 3 (wave 4) feature is comprised predominately by DE2 (DE3) and SPW3 (SPW4) signatures in TEC throughout all 5 years, with contributions from SE1 (SE2) being less significant. The wave 3 component also has recurring contributions from DW4 during December/January. The absolute amplitudes of all the aforementioned tidal and SPW signatures are directly related to the level of solar activity and the semiannual variation in zonal mean TEC. After normalizing by the zonal mean, the relative amplitudes of the wave 4 signatures are inversely related to solar activity through 2010, which is not seen with the wave 3‐related signatures. The seasonal variation and phases of the main constituents of wave 3 and wave 4 are consistent from year to year, as evidenced by the interannual recurrence in the peak and trough locations of wave 3 and wave 4.
Distributional Models and Deep Learning Embeddings: Combining the Best of Both Worlds

There are two main approaches to the distributed representation of words: low-dimensional deep learning embeddings and high-dimensional distributional models, in which each dimension corresponds to a context word. In this paper, we combine these two approaches by learning embeddings based on distributional-model vectors - as opposed to one-hot vectors as is standardly done in deep learning. We show that the combined approach has better performance on a word relatedness judgment task.
Learning incoherent sparse and low-rank patterns from multiple tasks

We consider the problem of learning incoherent sparse and low-rank patterns from multiple tasks. Our approach is based on a linear multi-task learning formulation, in which the sparse and low-rank patterns are induced by a cardinality regularization term and a low-rank constraint, respectively. This formulation is non-convex; we convert it into its convex surrogate, which can be routinely solved via semidefinite programming for small-size problems. We propose to employ the general projected gradient scheme to efficiently solve such a convex surrogate; however, in the optimization formulation, the objective function is non-differentiable and the feasible domain is non-trivial. We present the procedures for computing the projected gradient and ensuring the global convergence of the projected gradient scheme. The computation of projected gradient involves a constrained optimization problem; we show that the optimal solution to such a problem can be obtained via solving an unconstrained optimization subproblem and an Euclidean projection subproblem. In addition, we present two projected gradient algorithms and discuss their rates of convergence. Experimental results on benchmark data sets demonstrate the effectiveness of the proposed multi-task learning formulation and the efficiency of the proposed projected gradient algorithms.
Usefulness of Seminested Multiplex PCR in Surveillance of Imported Malaria in Spain

ABSTRACT The use of a new PCR-based method for the diagnosis of malaria in the Spanish Malaria Reference Laboratory has promoted an increase in confirmed cases of malaria. From August 1997 to July 1998, a total of 192 whole-blood samples and 71 serum samples from 168 patients were received from the hospitals of the Spanish National Health System. Most of the patients came from west-central African countries (85%). This molecular method showed more sensitivity and specificity than microscopy, detecting 12.4% more positive samples than microscopy and 13% of mixed infections undetectable by Giemsa stain. Plasmodium falciparum was the main species detected, with 68% of the total positive malaria cases, followed by Plasmodium malariae(29%), Plasmodium vivax (14%), and Plasmodium ovale (7%), including mixed infections in all cases. This report consists of the first wide, centralized survey of malaria surveillance in Spain. The reference laboratory conducted the analysis of all imported cases in order to detect trends in acquisition. The use of a seminested multiplex PCR permitted confirmation of the origins of the infections and the Plasmodium species involved and confirmation of the effectiveness of drug treatments. This PCR also allowed the detection of the presence in Spain of primaquine-tolerantP. vivax strains from west-central Africa, as well as the detection of a P. falciparum infection induced by transfusion.
A NEW APPROACH OF MODULAR WATERSHED MODELING WITHIN THE BILATERAL GLOBAL CHANGE PROGRAM WAVES IN NORTHEAST BRAZIL

The city of Picos and the Rio Guaribas Basin in the State of Piaui/Brazil is one of the focus areas within the international WAVES-program. With the investigation in focus areas on meso- and microscale level the statewide, macroscale WAVES-models are evaluated and calibrated. The description and modeling of different water flows in the Rio Guaribas Basin is performed by combining different models or working tools for each water compartment, so-called different modules within the WARIG-concept (WARIG- Modeling of Water Availability and Quality in Rio Guaribas Basin). In addition, the description of the actual water budget and the simulation of future water budgets support the regional development of the investigation area. Further on, results will be up-scaled and transferred to other areas with less data density.
Compressive sensing and 3-D radar imaging

Nonstandard image formation methods can enable fully three-dimensional fine resolution radar images of some objects of interest to be constructed from certain types of sparsely sampled three-dimensional apertures, which contain too little collected data to support traditional imaging methods. Such three-dimensional image products provide more target information than traditional SAR and ISAR imagery, and eliminate most of the difficulties associated with interpretation, mensuration, and recognition that result from overlay effects, self shadowing, scaling and viewing angle uncertainties.
Ethanol Differentially Enhances Hippocampal GABAAReceptor-Mediated Responses in Protein Kinase Cγ (PKCγ) and PKCε Null Mice

Ethanol intoxication results partly from actions of ethanol at specific ligand-gated ion channels. One such channel is the GABAA receptor complex, although ethanol's effects on GABAA receptors are variable. For example, we found that hippocampal neurons from selectively bred mice and rats with high hypnotic sensitivity to ethanol have increased GABAAreceptor-mediated synaptic responses during acute ethanol treatment compared with mice and rats that display low behavioral sensitivity to ethanol. Here we investigate whether specific protein kinase C (PKC) isozymes modulate hypnotic and GABAA receptor sensitivity to ethanol. We examined acute effects of ethanol on GABAAreceptor-mediated inhibitory postsynaptic currents (IPSCs) in mice lacking either PKCγ (PKCγ−/−) or PKCε (PKCε−/−) isozymes and compared the results to those from corresponding wild-type littermates (PKCγ+/+ and PKCε+/+). GABAA receptor-mediated IPSCs were evoked in CA1 pyramidal neurons by electrical stimulation in stratum pyramidale, and the responses were recorded in voltage-clamp mode using whole-cell patch recording techniques. Ethanol (80 mM) enhanced the IPSC response amplitude and area in PKCγ+/+mice, but not in the PKCγ−/− mice. In contrast, ethanol markedly potentiated IPSCs in the PKCε−/− mice, but not in PKCε+/+ littermates. There was a positive correlation between ethanol potentiation of IPSCs and the ethanol-induced loss of righting reflex such that mice with larger ethanol-induced increases in GABAA receptor-mediated IPSCs also had higher hypnotic sensitivity to ethanol. These results suggest that PKCγ and PKCε signaling pathways reciprocally modulate both ethanol enhancement of GABAA receptor function and hypnotic sensitivity to ethanol.
Microbial Biomass and Organic Nutrients in the Deep-Sea Sediments of the Central Indian Ocean Basin

Abstract In order to assess the impact of deep-sea mining on the in situ benthic life, we measured the microbial standing stock and concentration of organic nutrients in the deep-sea sediments of the Central Indian Ocean Basin in the Indian pioneer area. Sediments were collected using box core and grab samples during September 1996. The total bacterial numbers ranged from 1010–1011 cells per g−1 dry weight sediment. There was a marginal decrease in the number of bacteria from surface to 30 cm depth, though the subsurface section registered a higher number than did the surface. The highest numbers were encountered at depths of 4–8 cm. The retrievable number of bacteria were two orders less in comparison with the direct total counts of bacteria. An almost homogeneous distribution of bacteria, total organic carbon, living biomass, and lipids throughout the depth of cores indicates active microbial and benthic processes in the deep sea sediments. On the other hand, a uniform distribution of total counts of bacteria, carbohydrates, and total organic carbon in all the cores indicates their stable nature and suggests that they can serve as useful parameters for long-term monitoring of the area after the benthic disturbance. Further studies on temporal variability in this region would not only verify the observed norms of distribution of these variables but would also help to understand restabilization processes after the simulated benthic disturbance.
Study of mass transfer at the air‐water interface by an isotopic method

The calculation of the evaporation flux is based on certain assumptions concerning processes in the vicinity of the air-water interface. Most of the recently proposed evaporation theories differ mainly in the estimated contributions of molecular and turbulent mass transfer in the vapor phase just above the liquid surface. This paper will show that, by analyzing the hydrogen and oxygen stable isotope distribution in liquid and water vapor, the processes taking place on a very small scale near the liquid can be investigated. The effect of molecular mass transfer is directly obtained without having to perform difficult measurements in the air in the immediate vicinity of the water surface. Experiments are carried out in the Institut de Mecanique Statistique de la Turbulence air-water tunnel specially designed for the simulation of ocean-atmosphere energy exchanges. The wind velocities vary from 0.7 to 7 m/s. The experimental results obtained do not support the classical Reynolds analogy between momentum and mass transfer down to the interface and the theory proposed by Sheppard, but they are in agreement with Sverdrup's, Kitaigorodskiy and Volkov's, and Brutsaert's theories, all of which involve a layer just above the air-water interface through which mass transfer is dominated by molecular diffusion. The thickness of this layer in the two first theories is shown to decrease with increasing wind velocity. Direct application of Brutsaert's theory for roughness Reynolds numbers smaller than 1 is in good agreement with our experimental data.
Charge-sensitive TCP and rate control in the Internet

We investigate the fundamental problem of achieving the system optimal rates in a distributed environment, which maximize the total user utility, using only the information available at the end hosts. This is done by decomposing the system problem into two subproblems-network and user problems-and introducing an incentive-compatible pricing scheme, while maintaining proportional fairness. We demonstrate that when users update their parameters by solving their own optimization problem, at an equilibrium the system optimum is achieved. Furthermore, this algorithm does not require any explicit feedback from the network and can be deployed over the Internet with modifications only on the end hosts. In the second part of the paper we model as a noncooperative game the case where the choice of each user's action has nonnegligible effect on the price per unit flow at the resources and investigate the Nash equilibria of the game. We show, in the simple case of a single bottleneck, that there exists a unique Nash equilibrium of the game. Further, as the number of users increases, the unique Nash equilibrium approaches the system optimum.
Co‐Operative Movement

The co-operative movement first emerged in Europe during the nineteenth century. Although scholarly research remains in disagreement about exactly where the movement began, many trace its origins back to a number of cooperative experiences that developed in Britain and France in the eighteenth century, especially in the farming industry and consumer organizations (Holyoake 1908). Keywords: identity politics
Urban major road extraction from IKONOS imagery based on modified texture progressing analysis technique

A method for urban major road extraction from IKONOS imagery was proposed. The texture features of the image were first analyzed in three different levels. The first level calculated the Mahalanobis distance between test pixels and training pixels. The second level was the calculation results of Bhattacharyya distance between the distributions of the pixels in the training area and the pixels within a 3×3 window in the test area. The third level employed cooccurrence matrices over the texture cube built around one pixel, and then Bhattacharyya distance was used again. The processed results were thresholded and thinned, respectively. With the assistance of the geometrical characteristic of roads, the three resultant images corresponding to three levels were computed using fuzzy mathematics for their likelihood belonging to road and then merged together. A knowledge-based algorithm was used to link the segmented roads. The result was finally optimized by polynomial fitting. The experiment shows that the proposed method can effectively extract the urban major roads from the high-resolution imagery such as IKONOS.
Lexical Resources for Semantics Extraction

In this paper, we report our work on the creation of a number of lexical resources that are crucial for an interlingua based MT from English to other languages. These lexical resources are in the form of sub-categorization frames, verb knowledge bases and rule templates for establishing semantic relations and speech act like attributes. We have created these resources over a long period of time from Oxford Advanced Learners Dictionary (OALD) [1], VerbNet [2], Princeton WordNet 2.1 [3], LCS database [4], Penn Tree Bank [5], and XTAG lexicon [6]. On the challenging problem of generating interlingua from domain and structure unrestricted English sentences, we are able to demonstrate that the use of these lexical resources makes a difference in terms of accuracy figures.
Balancing on the Borderline – a Low‐cost Approach to Visualize the Red‐edge Shift for the Benefit of Aerial Archaeology

Scientists from different research disciplines have provided essential information that relates the biophysical characteristics of plants to their spectral reflectance. This fundamental understanding has facilitated the development of various non‐destructive sensing methods for detecting vegetation stresses, monitoring plant growth and calculating crop yield. Aerial archaeologists flying in small aeroplanes have only partially exploited this knowledge. Instead of basing archaeological interpretation on only direct visual inspection of the conventionally acquired colour photographs, this contribution briefly reviews the reflectance properties of plants and uses them to present a new low‐cost imaging technique beneficial for the detection of (faint) archaeologically induced vegetation marks. The new approach consists of three simultaneously operated digital still cameras, each of them capturing information in a different spectral waveband: the visible, near‐infrared and red‐edge spectral region. The latter two bands are used in the calculation of a R700/R800 vegetation index. Besides a theoretical underpinning, real‐world examples will assess the potential of this new approach in detection of vegetation marks and prove that this low‐cost, multispectral method might be beneficial in identifying and enhancing weak crop stresses that are lost when taking only the broad visible spectrum into account. In the final discussion, some thoughts on future archaeological aerial research are given. Copyright © 2011 John Wiley & Sons, Ltd.
The Keck Carbon Cycle AMS Laboratory, U.C.I.: Initial operation and a background surprise

Author(s): Southon, John R; Santos, Guaciara M; Druffel-Rodriguez, K C; Druffel, Ellen R. M; Trumbore, Susan E; Xu, Xiaomei; Griffin, Sheila; Ali, S; Mazon, M | Abstract: A new 14C accelerator mass spectrometry (AMS) laboratory for carbon cycle studies has been established at the University of California, Irvine. The 0.5 MV AMS system was installed in mid-2002 and has operated routinely sinceOctober of that year. This paper briefly describes the spectrometer and summarizes lessons learned during the first year of operation. In the process of setting up the system, we identified and largely suppressed a previously unreported radiocarbonAMS background: charge exchange tails from 14N beams derived from nitrogen-containing molecular ions produced near the entrance of the accelerator.
Importance of cystic pedicle dissection in laparoscopic cholecystectomy in order to avoid the common bile duct injuries

Abstract The dissection of the cystic pedicle represents the “main” issue in performing the cholecystectomy, as well as the surgical moment when many accidents may happen. The paper analyzes the most frequent causes, which can generate iatrogenic injuries of the common bile duct (CBD) during the dissection of the cystic pedicle, such as the ductal and vascular anatomical variants, the local pathological transformation, human errors, etc.
Cost Analysis of the MBMS Multicast Mode of UMTS

Along with the widespread deployment of the third generation cellular networks, the fast-improving capabilities of the mobile devices, content and service providers are increasingly interested in supporting multicast communications over wireless networks and in particular over universal mobile telecommunications system (UMTS). To this direction, the third generation partnership project (3 GPP) is currently standardizing the multimedia broadcast/multicast service (MBMS) framework of UMTS. In this paper, we present an overview of the MBMS multicast mode of UMTS. We analytically present the multicast mode of the MBMS and analyze its performance in terms of packet delivery cost under various network topologies, cell types and multicast users' distributions. Furthermore, for the evaluation of the scheme, we consider different transport channels for the transmission of the data over the UTRAN interfaces.