Miracle-dz/UniFAR-FTUs huggingface dataset:
AVclass2: Massive Malware Tag Extraction from AV Labels

Tags can be used by malware repositories and analysis services to enable searches for samples of interest across different dimensions. Automatically extracting tags from AV labels is an efficient approach to categorize and index massive amounts of samples. Recent tools like AVclass and Euphony have demonstrated that, despite their noisy nature, it is possible to extract family names from AV labels. However, beyond the family name, AV labels contain much valuable information such as malware classes, file properties, and behaviors. This work presents AVclass2, an automatic malware tagging tool that given the AV labels for a potentially massive number of samples, extracts clean tags that categorize the samples. AVclass2 uses, and helps building, an open taxonomy that organizes concepts in AV labels, but is not constrained to a predefined set of tags. To keep itself updated as AV vendors introduce new tags, it provides an update module that automatically identifies new taxonomy entries, as well as tagging and expansion rules that capture relations between tags. We have evaluated AVclass2 on 42M samples and showed how it enables advanced malware searches and to maintain an updated knowledge base of malware concepts in AV labels.
Scattering and absorption invariance of nonmagnetic particles under duality transformations

We revisit the total scatterings (in terms of extinction, scattering, and absorption cross sections) by arbitrary clusters of nonmagnetic particles that support optically induced magnetic responses. Our reexamination is conducted from the perspective of the electromagnetic duality symmetry, and it is revealed that all total scattering properties are invariant under duality transformations. This secures that, for self-dual particle clusters, the total scattering properties are polarization independent for any fixed incident direction, while, for non-self-dual particle clusters, two scattering configurations that are connected to each other through a duality transformation would exhibit identical scattering properties. This electromagnetic duality induced invariance is irrelevant to specific particle distributions or wave incident directions, which is illustrated for both random and periodic clusters.
μ⋆ masses: weak-lensing calibration of the Dark Energy Survey Year 1 redMaPPer clusters using stellar masses

We present the weak-lensing mass calibration of the stellar-mass-based μ⋆ mass proxy for redMaPPer galaxy clusters in the Dark Energy Survey Year 1. For the first time, we are able to perform a calibration of μ⋆ at high redshifts, z > 0.33. In a blinded analysis, we use ∼6000 clusters split into 12 subsets spanning the ranges 0.1 ≤ z < 0.65 and μ⋆ up to ${\sim} 5.5 \times 10^{13} \, \mathrm{M}_{\odot }$, and infer the average masses of these subsets through modelling of their stacked weak-lensing signal. In our model, we account for the following sources of systematic uncertainty: shear measurement and photometric redshift errors, miscentring, cluster-member contamination of the source sample, deviations from the Navarro–Frenk–White halo profile, halo triaxiality, and projection effects. We use the inferred masses to estimate the joint mass–μ⋆–z scaling relation given by $\langle M_{200c} | \mu _{\star },z \rangle = M_0 (\mu _{\star }/5.16\times 10^{12} \, \mathrm{M_{\odot }})^{F_{\mu _{\star }}} ((1+z)/1.35)^{G_z}$. We find $M_0= (1.14 \pm 0.07) \times 10^{14} \, \mathrm{M_{\odot }}$ with $F_{\mu _{\star }}= 0.76 \pm 0.06$ and Gz = −1.14 ± 0.37. We discuss the use of μ⋆ as a complementary mass proxy to the well-studied richness λ for: (i) exploring the regimes of low z, λ < 20 and high λ, z ∼ 1; and (ii) testing systematics such as projection effects for applications in cluster cosmology.
The unequal variance t-test is an underused alternative to Student's t-test and the Mann–Whitney U test

Often in the study of behavioral ecology, and more widely in science, we require to statistically test whether the central tendencies (mean or median) of 2 groups are different from each other on the basis of samples of the 2 groups. In surveying recent issues of Behavioral Ecology (Volume 16, issues 1–5), I found that, of the 130 papers, 33 (25%) used at least one statistical comparison of this sort. Three different tests were used to make this comparison: Student’s t-test (67 occasions; 26 papers), Mann–Whitney U test (43 occasions; 21 papers), and the t-test for unequal variances (9 occasions; 4 papers). My aim in this forum article is to argue for the greater use of the last of these tests. The numbers just related suggest that this test is not commonly used. In my survey, I was able to identify tests described simply as ‘‘t-tests’’ with confidence as either a Student’s t-test or an unequal variance t-test because the calculation of degrees of freedom from the 2 sample sizes is different for the 2 tests (see below). Hence, the neglect of the unequal variance t-test illustrated above is a real phenomenon and can be explained in several (nonexclusive ways) ways: 1. Authors are unaware that Student’s t-test is unreliable
Constraint-Based Regularization of Neural Networks

We propose a method for efficiently incorporating constraints into a stochastic gradient Langevin framework for the training of deep neural networks. Constraints allow direct control of the parameter space of the model. Appropriately designed, they reduce the vanishing/exploding gradient problem, control weight magnitudes and stabilize deep neural networks and thus improve the robustness of training algorithms and the generalization capabilities of the trained neural network. We present examples of constrained training methods motivated by orthogonality preservation for weight matrices and explicit weight normalizations. We describe the methods in the overdamped formulation of Langevin dynamics and the underdamped form, in which momenta help to improve sampling efficiency. The methods are explored in test examples in image classification and natural language processing.
Mapping dark matter and finding filaments: calibration of lensing analysis techniques on simulated data

We quantify the performance of mass mapping techniques on mock imaging and gravitational lensing data of galaxy clusters. The optimum method depends upon the scientific goal. We assess measurements of clusters’ radial density profiles, departures from sphericity, and their filamentary attachment to the cosmic web. We find that mass maps produced by direct (KS93) inversion of shear measurements are unbiased, and that their noise can be suppressed via filtering with mrlens. Forward-fitting techniques, such as lenstool, suppress noise further, but at a cost of biased ellipticity in the cluster core and overestimation of mass at large radii. Interestingly, current searches for filaments are noise-limited by the intrinsic shapes of weakly lensed galaxies, rather than by the projection of line-of-sight structures. Therefore, space-based or balloon-based imaging surveys that resolve a high density of lensed galaxies could soon detect one or two filaments around most clusters.
Field margin vegetation enhances biological control and crop damage suppression from multiple pests in organic tomato fields

Ephemeral cropping systems are characterized by frequent disturbances of ecological processes, which may compromise the conservation of plant and arthropod diversity and the ecosystem services they may provide. Conservation biological control practices include habitat manipulations that provide non‐pest resources and selectively enhance natural enemies' effectiveness. This study, conducted in eight commercial fields of organically grown tomato, compared the effectiveness of sown flower strips with semi‐natural margins in regulating natural enemy abundance, biocontrol, and crop damage. During repeated visits, the abundance of different arthropod groups was recorded. Crop surveys included measurement of aphid abundance, parasitism, and leaf and fruit damage from sap‐sucking and lepidopteran pests. Semi‐natural habitats were associated with higher vegetation diversity, but natural enemies were more strongly associated with sown strips during flowering. Sap‐sucking pests were always recorded in higher abundance in flower strips, but crop damage in the plots adjacent to these strips was lower, suggesting that these strips may act as a trap‐crop. The inclusion of floral supplements enhanced the parasitism rate of aphids in the crop, and reduced the rate of increase of lepidopteran‐caused foliar damage with time. Early in the growing season, semi‐natural strips showed significantly lower levels of crop damage and aphid counts, suggesting that these habitats may be important during early crop colonization by natural enemies. These results indicate that the inclusion of flower strips enhances the conservation of arthropod functional diversity in ephemeral crops, and that diverse mechanisms are important for controlling different pests. However, the efficacy of habitat manipulation is likely to be greater when it is complemented with the conservation of diverse semi‐natural vegetation in the pre‐existing field margin.
Genetic and morphological variation in Dunlin Calidris alpina breeding in the Palearctic tundra

The extensive overlap in morphological characters between populations of Dunlin Calidris alpina imposes problems of determining the origin of migrating and wintering birds. The morphology of the birds also varies between the sexes, and the sex of a Dunlin may often be difficult to determine. To clarify if mitochondrial DNA can be used to identify which breeding areas migrating Dunlin come from, we investigated the occurrence of different mtDNA haplotypes in Dunlin from eight breeding areas on the Russian and Siberian tundra. Four haplotypes were found and at most sites more than one haplotype occurred. The European haplotype predominated in the area west of the Taymyr Peninsula, the Siberian haplotype in central Siberia (from the Taymyr Peninsula to the Lopatka Peninsula) and the Beringian haplotype in eastern Siberia. One individual of an Alaskan haplotype, not detected previously among breeding birds outside North America, was found on Wrangel Island. The sex of each bird was identified genetically and the morphology of males and females was analysed separately. Birds with the European haplotype were generally smaller than birds with the Beringian or Alaskan haplotypes. Birds possessing the Siberian haplotype showed intermediate values in most cases. After compensating for differences between sites, males with the Siberian haplotype had significantly longer bills than males having the European haplotype. Multiple regressions indicate that mitochondrial DNA analysis improves models estimating the breeding origin of migrating Dunlin.
Functional group bridge for simultaneous regression and support estimation

This paper is motivated by studying differential brain activities to multiple experimental condition presentations in intracranial electroencephalography (iEEG) experiments. Contrasting effects of experimental conditions are often zero in most regions and nonzero in some local regions, yielding locally sparse functions. Such studies are essentially a function‐on‐scalar regression problem, with interest being focused not only on estimating nonparametric functions but also on recovering the function supports. We propose a weighted group bridge approach for simultaneous function estimation and support recovery in function‐on‐scalar mixed effect models, while accounting for heterogeneity present in functional data. We use B‐splines to transform sparsity of functions to its sparse vector counterpart of increasing dimension, and propose a fast nonconvex optimization algorithm using nested alternative direction method of multipliers (ADMM) for estimation. Large sample properties are established. In particular, we show that the estimated coefficient functions are rate optimal in the minimax sense under the L2 norm and resemble a phase transition phenomenon. For support estimation, we derive a convergence rate under the L∞$L_{\infty }$ norm that leads to a selection consistency property under δ‐sparsity, and obtain a result under strict sparsity using a simple sufficient regularity condition. An adjusted extended Bayesian information criterion is proposed for parameter tuning. The developed method is illustrated through simulations and an application to a novel iEEG data set to study multisensory integration.
Measurements of natural mortality for Pacific sardine (Sardinops sagax)

The northern stock of Pacific sardine (Sardinops sagax) in the California Current Ecosystem is periodically assessed to provide harvest guidelines for the United States and Canadian fisheries. The assessment model incorporates the estimates of abundance from acoustic-trawl method (ATM) and other surveys and many parameters including a constant value for the instantaneous natural mortality coefficient (M). Here, the ATM-estimated length-structured sardine abundances for 2006–2011 are combined to directly estimateM. The stock was dominated by the 2003, 2004, and 2005 year classes (2003–2005 cohort) from 2006 to 2010 and by the 2009 and 2010 year classes in 2011. Insignificant recruitments during 2006–2010 allowed the 2003–2005 cohort to be tracked andM to be estimated. The bootstrap distributions of estimatedM encompass the assessment-assumed value of 0.4. The measurements suggest thatM is high for a new cohort, declines duringmid-life, then increases as the fish approach their longevity. ThemeanM for the entire period, 0.52, is 30%higher than the one currently assumed for the assessment, reflecting the steeper decline in the ATM-estimated biomass versus that in the assessment model.
Galaxy cluster cores as seen with VLT/MUSE: New strong-lensing analyses of RX J2129.4+0009, MS 0451.6−0305 & MACS J2129.4−0741

We present strong-lensing analyses of three galaxy clusters, RX J2129.4+0009 (z = 0.235), MS 0451.6−0305 (z = 0.55), and MACS J2129.4−0741 (z = 0.589), using the powerful combination of Hubble Space Telescope (HST) multi-band observations, and Multi-Unit Spectroscopic Explorer (MUSE) spectroscopy. In RX J2129, we newly spectroscopically confirm 15 cluster members. Our resulting mass model uses 8 multiple image systems as we include a galaxy-galaxy lensing system North-East of the cluster, and is composed of 71 haloes including one dark matter cluster-scale halo and 2 galaxy-scale haloes optimized individually. For MS 0451, we report the spectroscopic identification of 2 new systems of multiple images in the Northern region, and 112 cluster members. Our mass model uses 16 multiple image systems, and 146 haloes, including 2 large-scale haloes, and 7 galaxy-scale haloes independently optimized. For MACS J2129, we report the spectroscopic identification of one new multiple image system at z = 4.41, and newly measure spectroscopic redshifts for 4 cluster members. Our mass model uses 14 multiple image systems, and is composed of 151 haloes, including 2 large-scale haloes and 4 galaxy-scale haloes independently optimized. Our best models have rms of 0.29″,0.6″, 0.74″ in the image plane for RX J2129, MS 0451, and MACS J2129 respectively. This analysis presents a detailed comparison with the existing literature showing excellent agreements, and discuss specific studies of lensed galaxies, e.g. a group of submilimeter galaxies at z = 2.9 in MS 0451, and a bright z = 2.1472 red singly imaged galaxy in MACS J2129.
EVfold.org: Evolutionary Couplings and Protein 3D Structure Prediction

Recently developed maximum entropy methods infer evolutionary constraints on protein function and structure from the millions of protein sequences available in genomic databases. The EVfold web server (at EVfold.org) makes these methods available to predict functional and structural interactions in proteins. The key algorithmic development has been to disentangle direct and indirect residue-residue correlations in large multiple sequence alignments and derive direct residue-residue evolutionary couplings (EVcouplings or ECs). For proteins of unknown structure, distance constraints obtained from evolutionarily couplings between residue pairs are used to de novo predict all-atom 3D structures, often to good accuracy. Given sufficient sequence information in a protein family, this is a major advance toward solving the problem of computing the native 3D fold of proteins from sequence information alone. Availability EVfold server at http://evfold.org/ Contact evfoldtest@gmail.com Abbreviations DI direct information EC evolutionary coupling EV evolutionary MSA multiple sequence alignment PLM pseudo-likelihood maximization PPV positive predictive value (number of true positives divided by the sum of true and false positives) TM-score template modeling score
In situ plant water balance studies using a portable NMR spectrometer.

A portable 1 H NMR spectrometer has been applied to whole plants in situ, i.e. in climate rooms and in a greenhouse, to study plant water relations under these conditions. The spectrometer consists of a 30 kg permanent magnet system of 0.235 T, modified Bruker Minispec electronics, and a standard XT pc for spectrometer control. Unattended, the system automatically measures the xylem sap stream and tissue water content in a well-defined section of the plant stem. Because of the small size of the magnet these measurements can be made at different positions on the plant stem or on different plants in succession. Magnetic field drift due to the varying climates that occur in greenhouses was corrected by field locking
Methylation sensitive amplified polymorphism (MSAP) reveals that alkali stress triggers more DNA hypomethylation levels in cotton (Gossypium hirsutum L.) roots than salt stress

Cytosine-5 hypomethylation or hypermethylation have been shown to regulate plant development and abiotic stress-responsive genes expression. However, some combinatory stresses in plants like saline and alkaline could have varied responses that could contribute to their adaptive evolution trends. We evaluated root and leaf DNA methylation patterns of cotton in salt (S, 9:1 molar ratio of NaCl to Na 2 SO 4 , pH 6.96) and alkali (A, 9:1 molar ratio of NaHCO 3 to Na 2 CO 3 , with higher pH 9.21) stresses using methylation sensitive amplified polymorphism (MSAP) method and found out that in general, demethylation events occurred more than methylation events in both leaves and roots samples. In addition, the total methylation variation frequency was only 1.38% in leaves and 2.2% in roots under salt stress. However, the alkali stress triggered more alterations and decreased the DNA methylation level significantly (P<0.05) compared to salt stress. This was up to 2.59% and 12.44% in the scored CCGG sites in leaves and roots, respectively. These results suggest that more adaptive and possibly complex gene expression alterations could be occurring in the tolerance of the cotton root in response to salt and alkali stresses coupled with DNA methylation alterations, although exclusion physiological mechanisms cannot be ruled out. Key words : Salt stress, alkali stress, Gossypium hirsutum L. , DNA methylation, methylation sensitive amplified polymorphism (MSAP).
Eipo plant nomenclature and classification compared with other folk taxonomic systems

Abstract Hiepko, P.: Eipo plant nomenclature and classification compared with other folk taxonomic systems. — Willdenowia 36 (Special Issue): 447–453. — ISSN 0511-9618; © 2006 BGBM Berlin-Dahlem. doi:10.3372/wi.36. 36142 (available via http://dx.doi.org/) Ethnobotanical data collected among the Eipo people in the Central Highlands of West New Guinea are compared with the theoretical model of ethnotaxonomic systems developed by Berlin and co-workers based on ethnobotanical studies in Central and South America. The Eipo plant nomenclature appears to fit well in Berlin's general principles and corroborates the existence of universals in folk classification systems.
Collection of Xylem Sap at Flow Rate Similar to in vivo Transpiration Flux

We have explored a method to collect xylem sap using a Scholander pressure chamber for potted plants. Intact root system in pots which fitted the pressure chamber was pressurised at a pneumatic pressure numerically equal to the absolute value of shoot water potential. The rate of xylem flow obtained from the stem stump under such pressure was found similar to the rate of transpiration before detopping. The rate of pressurised flow from detopped roots was linearly related to the pressure applied in both well-watered and soil-dried plants. The osmotic concentration of the xylem sap was negatively related to the rate of volume flow, suggesting the necessity to collect xylem sap at in vivo flow rate if original solute concentration is to be evaluated. The concentration of ABA in the xylem sap, however, did not show such a relationship with water flux. Both well-watered and soil-dried plants showed the concentration of ABA in xylem sap largely stable with a range of volume flow rate, indicating a linear relationship between the rate of ABA delivery through xylem and that of volume flow. We also compared the concentrations of ABA in xylem sap sequentially collected from pressurised roots with that from detached shoots of the same plants. The concentration of ABA in the initial saps from shoots showed to be similar to that from roots. However, a decrease in the concentration of ABA in the xylem sap collected from detached leaf or twig was observed when more volume of sap was collected, which might also be dependent on the plant species and the volume of xylem vessels concerned.
Effects of pioneer shrubs on the recruitment of the fleshy-fruited tree Olea europaea ssp. cuspidata in Afromontane savanna

Abstract Question: Is seedling recruitment of a fleshy-fruited tree in degraded Afromontane savanna dependent on shelter from pioneer shrubs, and is shelter availability related to shrub traits? Location: Degraded montane savanna in northern Ethiopia (13°36′ N, 39°21′ E). Method: Nurse plants of Olea europaea ssp. cuspidata seedlings were recorded using T-square plotless sampling and clustered according to shrub traits, using Ward's method after Principal Components Analysis. Facilitation was further examined through experimental planting and Kaplan-Meier survival analysis. Results: Both in grazed and protected areas, Olea recruits were found exclusively under shrubs, primarily under Euclea racemosa although Acacia etbaica was more abundant. Olea recruitment is distributed randomly at landscape scale, but depends on shelter at patch scale. Shelter ability is related to shrub shape and species identity. Dense multi-stemmed shrubs with a wide base and crown on a mulch-rich mound are key recruitment foci. Euclea shrubs have these favoured traits and probably act as preferential perching sites for avian seed dispersers. Soil and organic matter accumulation under Euclea shrubs may also create favourable conditions for Olea germination and survival. Experimentally planted seedlings had a better chance for survival under Euclea. Conclusions: Olea regeneration is probably subject to both passive (disperser-mediated) and active facilitation. Small changes of shrub traits can alter the suitability of a patch for Olea recruitment. Protection of shrubs can increase facilitation for seedlings, while pruning may reduce competition for saplings and thus enhance forest succession. Planting of raised Olea seedlings under Euclea shrubs in years with a good rainy season may further assist forest restoration. Abbreviation: TSB = Byth robust T-square estimator. Nomenclature: Hedberg & Edwards (1989); Hedberg et al. (2003); Klopper et al. (2005).