Miracle-dz/UniFAR-FTUs huggingface dataset:
Antimicrobial resistance and genotyping of Mycobacterium leprae in Venezuela

Leprosy is a neglected tropical disease that leads to physical disability and social discrimination. The active surveillance of new cases and vigilance for drug resistance can decrease the incidence, and improve the clinical outcomes of people affected by it. We analyzed, with molecular biology techniques, a set of skin biopsy samples from 25 Venezuelan patients. The patients had been diagnosed with leprosy in 2014 and early 2015, and 15 were relapse cases. The samples were tested for molecular drug resistance to dapsone, rifampicin, and fluoroquinolones. In addition, we performed molecular epidemiology analysis through multiple-locus variable-number tandem repeat analysis (MLVA) and single nucleotide polymorphism (SNP) typing. We did not find evidence of drug resistance and 76% of the samples (n = 16) had isolates belonging to SNP type 3. Genotype profiles allowed us to rule out the possibility of re-infection in a patient with persistent symptoms after treatment, as well as that of household transmission in two more patients. Although our sampling is relatively small, very similar or even identical Mycobacterium leprae genotypes were observed in Miranda State. The presence of this cluster is highly suggestive of high rates of local transmission and, in turn, the need to better control this disease. Finally, the copy number distribution of minisatellite 18–8 in a considerable number of SNP type 3 strains strongly suggests the presence of a sublineage of this disease that is particular to Venezuela.
Effective collision strengths for fine-structure transitions for the electron impact excitation of N II

We present effective collision strengths for the electron impact excitation of singly ionized nitrogen which have been calculated using the R-matrix method. The 23 lowest LS states are included in the expansion of the total wavefunction. These target states arise from the 2s 2 2p 2 ,2 s2p 3 and 2s 2 2p3l(l = s, p, d) configurations, leading to 41 fine structure levels and 820 possible transitions. The fine-structure collision strengths were obtained by transforming to a jj-coupling scheme using the JAJOM program of Saraph and have been determined at a sufficiently fine energy mesh to delineate properly the resonance structure. The effective collision strengths were calculated by averaging the electron collision strengths over a Maxwellian distribution of velocities. Tabulations of the non-zero effective collision strengths are given for electron temperatures (Te )i n the range log10 Te(K) = 2.0−5.5.
In-silico Analysis of Human Papillomavirus – 45 E6, E7 & L1 Proteins as Potential Immunogens

Globally, cervical cancer is the fourth most common cancer among women. After being cloned from a recurring cervical lesion in 1987, Human papillomavirus (HPV) type-45 was identified as a high-risk HPV type. It is the third most common cancer-causing HPV subtype, after HPV-16 and HPV-18. Immunogenic epitopes and structural features provide the most useful information for vaccine development. Computational algorithms provide quick, simple, trustworthy, and cost-efficient methods for predicting immunogenic epitopes. In this study, both B and T cell epitopes have been identified as potential immunogens that can elicit a response from the host system. Three potential B-cell epitopes, i.e., SIAGQYRGQCNTCCDQ, LQEIVLHLEPQNELDP, and DSTVYLPPPSVARVVS, were identified in this study. A potential epitope for E6 (ATLERTEVY) was predicted to 8 MHC-I alleles (HLA-A*30:02, HLA-B*15:01, HLA-A*01:01, HLA-A*26:01, HLA-A*32:01, HLA-B*35:01, HLA-B*58:01, HLA-A*11:01) and for L1 epitope (NVFPIFLQM) was predicted for 4 MHC-I alleles (HLA-A*30:02, HLA-A*32:01, HLA-B*53:01, HLA-B*51:01). To conclude, the epitopes identified here might potentially be useful for developing a cervical cancer vaccine against HPV-45 strains, but in vitro and in vivo trials are needed to validate their safety and efficacy.
AG-Index: Adjacent Edge Hash Index for Graph Databases

Many queries have been proposed to retrieve graphs. Among others, subgraph query is a fundamental one: given a graph database and a query graph, find the graphs in the database containing the query graph. Most existing works follow the filtering-and-verification framework, where a core task is to reduce the number of candidate graphs. This paper follows the framework and we propose a novel index, namely AG-Index. It indexes adjacent edge pairs of data graphs and can significantly reduce the number of candidate graphs. Our experiments show that our AG-Index outperforms several existing techniques on real-life datasets and synthetic datasets.
Domain Kinetics in Lithium Niobate Single Crystals with Photoresist Dielectric Layer

The influence of the artificial surface layer (photoresist film) on the domain kinetics was studied in congruent lithium niobate single crystals. The switching current data was fitted by modified Kolmogorov-Avrami formula. The qualitative change of the domain structure evolution for photoresist film thickness above 2 μm was revealed by in situ optical visualization and analysis of the switching current data. The linear dependence of the threshold field increase on the film thickness was found. The quasi-regular nanodomain structures on Z+ polar surface were studied by scanning probe and Raman confocal microscopy and the domain evolution scenario was revealed.
Enhanced Raman scattering by spatially distributed atomic coherence

We demonstrate experimentally an enhancement in Raman scattering in Rb atomic vapor due to the atomic coherence initially prepared by a weak write laser. We find that the enhanced Raman scattering depends on the spatial distribution of the atomic spin coherence and can be explained with a simple picture of three-wave mixing. This effect can in principle be used to have a light conversion efficiency near unity in Raman process. Such an enhanced Raman scattering may have practical applications in quantum information, nonlinear optics, and laser spectroscopy.
Linear Statistical Inference and Its Applications

"C. R. Rao would be found in almost any statistician's list of five outstanding workers in the world of Mathematical Statistics today. His book represents a comprehensive account of the main body of results that comprise modern statistical theory. " -W. G. Cochran "[C. R. Rao is] one of the pioneers who laid the foundations of statistics which grew from ad hoc origins into a firmly grounded mathematical science. " -B. Efrom Translated into six major languages of the world, C. R. Rao's Linear Statistical Inference and Its Applications is one of the foremost works in statistical inference in the literature. Incorporating the important developments in the subject that have taken place in the last three decades, this paperback reprint of his classic work on statistical inference remains highly applicable to statistical analysis. Presenting the theory and techniques of statistical inference in a logically integrated and practical form, it covers: * The algebra of vectors and matrices * Probability theory, tools, and techniques * Continuous probability models * The theory of least squares and the analysis of variance * Criteria and methods of estimation * Large sample theory and methods * The theory of statistical inference * Multivariate normal distribution Written for the student and professional with a basic knowledge of statistics, this practical paperback edition gives this industry standard new life as a key resource for practicing statisticians and statisticians-in-training.
Cutting corners: The impact of storage and DNA extraction on quality and quantity of DNA in honeybee (Apis mellifera) spermatheca

The purpose of our study was to investigate methods of short-term storage that allow preservation, transport and retrieval of genetic information contained in honeybee queen’s spermatheca. Genotyping of the honeybee colony requires well ahead planned sample collection, depending on the type of data to be acquired. Sampling and genotyping of spermatheca’s content instead of individual offspring is timesaving, allowing answers to the questions related to patriline composition immediately after mating. Such procedure is also cheaper and less error prone. For preservation either Allprotect Tissue Reagent (Qiagen) or absolute ethanol were used. Conditions during transportation were simulated by keeping samples 6–8 days at room temperature. Six different storing conditions of spermathecas were tested, complemented with two DNA extraction methods. We have analysed the concentration of DNA, RNA, and proteins in DNA extracts. We also analysed how strongly the DNA is subjected to fragmentation (through amplification of genetic markers ANT2 and tRNAleu-COX2) and whether the quality of the extracted DNA is suitable for microsatellite (MS) analysis. Then, we tested the usage of spermatheca as a source of patriline composition in an experiment with three instrumentally inseminated virgin queens and performed MS analysis of the extracted DNA from each spermatheca, as well as queens’ and drones’ tissue. Our results show that median DNA concentration from spermathecas excised prior the storage, regardless of the storing condition and DNA extraction method, were generally lower than median DNA concentration obtained from spermathecas dissected from the whole queens after the storage. Despite the differences in DNA yield from the samples subjected to different storing conditions there was no significant effect of storage method or the DNA extraction method on the amplification success, although fewer samples stored in EtOH amplified successfully in comparison to ATR storing reagent. However, we recommend EtOH as a storing reagent due to its availability, low price, simplicity in usage in the field and in the laboratory, and capability of good preservation of the samples for DNA analysis during transport at room temperature.
In plateaus, land cover replaced climate as the vital environmental factor on the spatial composition of bumblebees with the altitude rising

Bumblebees show a series of advantages over other pollinating insects in offering pollination services for both the ecosystem and agricultural production, especially in high‐altitude areas. With climate warming, their diversity at high altitudes will be threatened. Therefore, more attention should be paid to the management of bumblebee resources at high altitudes to prevent their decline here. Discovering drivers responsible for the spatial variation of biodiversity is a benefit for developing appropriate management. Here, based on the bumblebee diversity on three plateau areas with an altitude gradient, the roles of different environmental factors, the climate, land cover, topography, habitat heterogeneity and soil, in the bumblebee composition were assessed by generalised dissimilarity modelling. And the relative importance of variables was evaluated by the impact on the magnitude of total biological change and the per cent change in deviance explained by models. According to the results, in the low‐altitude area, the climate played a vital role and the most important variable was the climate variable. Then, with the altitude rising, the effect of land cover continually increased. In the medium‐altitude area, the effects of different factors were detected to be similar, and the most important variables were a climate variable and a land cover variable. In the high‐altitude area, land cover finally replaced the climate as the most important factor, and one land cover variable was assessed as the most important variable. Our study revealed that the relative importance of different environmental factors on the biodiversity of bumblebees can differ as the altitude rises.
Recent progress in local reconstruction

While classic CT theory targets exact reconstruction of a whole cross-section or of an entire object from complete projections, practical applications often focus on much smaller internal ROIs. Traditional CT methods cannot exactly reconstruct an internal ROI only from local truncated projections associated with x-rays through the ROI, because this interior problem does not have a unique solution. When applying approximate local CT algorithms for interior reconstruction from truncated projection data, features outside the ROI may create artifacts overlapping inside features, rendering the images inaccurate or useless. Recently, novel solutions for the interior problem were published by our group with numerical results demonstrating that the interior problem can be solved in a theoretically exact and numerically stable fashion aided by some prior knowledge, such as a small known sub-region inside the ROI or the ROI can modeled by piecewise constant/polynomial function. In this invited paper, we will review the recent progress in local reconstruction. The topic includes lambda tomography, analytic and iterative interior reconstructions, with an emphasis on total variation minimization based soft-threshold methods and statistical based interior reconstruction algorithms.
Mass, linear momentum and kinetic energy of bipolar flows in protoplanetary nebulae

We have studied the CO emission from protoplanetary nebulae (PPNe). Our sample is composed of 37 objects and includes, we think, all well identied PPNe detected in CO, together with the two yellow hypergiants emitting in CO and one young PN. We present a summary of the existing CO data, including accurate new observations of the 12 CO and 13 CO J = 1{0 and J = 2{1 lines in 16 objects. We identify in the nebulae a slowly expanding shell (represented in the spectra by a central core) and a fast outflow (corresponding to the line wings), that in the well studied PPNe is known to be bipolar. Excluding poor data, we end up with a sample of 32 sources (including the 16 observed by us); fast flows are detected in 28 of these nebulae, being absent in only 4. We present a method to estimate from these data the mass, \scalar" momentum and kinetic energy of the dierent components of the molecular outflows. We argue that the uncertainties of our method can hardly lead to signicant overestimates of these parameters, although underestimates may be present in not well studied objects. The total nebular mass is often as high as 1 M, and the mass-loss rate, that (presumably during the last stages of the AGB phase) originated the nebula, had typical values 10 4 M yr 1 . The momentum corresponding to this mass ejection process in most studied nebulae is accurately coincident with the maximum momentum that radiation pressure, acting through absorption by dust grains, is able to supply (under expected conditions). We estimate that this high-eciency process lasts about 1000{10 000 yr, after which the star has ejected a good fraction of its mass and the AGB phase ends. On the other hand, the fast molecular outflows, that have probably been accelerated by shock interaction with axial post-AGB jets, carry a signicant fraction of the nebular mass, with a very high momentum (in most cases between 10 37 and 10 40 gc m s 1 ) and very high kinetic energy (usually between 10 44 and 10 47 erg). In general, yellow hypergiants and post-AGB objects with low initial mass show nebular masses and momenta that are, respectively, higher and lower than these values. We compare the momenta of the fast outflows with those that can be supplied by radiation pressure, taking into account the expected short acceleration times and some eects that can increase the momentum transfer. We nd that in about 80% of PPNe, the fast molecular flows have too high momenta to be powered by radiation pressure. In some cases the momentum of the outflow is1000 larger than that carried by radiation pressure; such high factors are dicult to explain even under exceptional conditions. Wind interaction is the basic phenomenon in the PN shaping from the former AGB envelopes; we conclude that this interaction systematically takes place along a dominant direction and that this process is not powered by radiation pressure. Due to the lack of theoretical studies, the possible momentum source remains a matter of speculation.
Species mixtures increase fine root length to support greater stand productivity in a natural boreal forest

Species mixtures have been widely reported to increase aboveground productivity; however, how tree species mixtures affect root systems in natural forests remains unclear. We hypothesize that mixtures have a greater fine root length compared to single species‐dominated stands to support their greater productivity. Here, we collected monthly root images from the minirhizotrons installed in 18 stands either dominated by Populus tremuloides, Pinus banksiana, and their mixtures for three years (2015–2017) in post‐fire boreal forests of two stand ages (8 and 34 years old) to test our hypotheses. We found that the fine root length was higher in mixtures than in single species‐dominated stands, and the magnitude of mixture effects was greater in the 34‐ than in the 8‐year‐old stands in the third year. The mixture effects on fine root length revealed a positive relationship with forest net primary productivity. Root length production, which is the growth of new roots within a year, was not affected by tree species mixtures except for the 8‐year‐old stand in 2015. Tree species mixtures did not affect root length turnover. Root length and root biomass were not significantly correlated at stand level. Synthesis. Our results show that tree species mixtures positively affect fine root length, with that positive effect increasing with stand development in the studied natural forests. Our results suggest that the greater root length in species mixtures supported the greater forest productivity in species mixtures as the greater root length benefits plant uptake of nutrients and water. Therefore, conserving tree species diversity has implications for improving forest productivity and carbon sequestration in forest ecosystems.
Algebraic properties of multilinear constraints

In this paper the different algebraic varieties that can be generated from multiple view geometry with uncalibrated cameras have been investigated. The natural descriptor, V-n, to work with is the image of P-3 in P-2 x P-2 x . x P-2 under a corresponding product of projections, (A(1) x A(2) x . x A(m)). Another descriptor, the variety V-b, is the one generated by all bilinear forms between pairs of views, which consists of all points in P-2 x P-2 x . x P-2 where all bilinear forms vanish. Yet another descriptor, the variety V-t, is the variety generated by all trilinear forms between triplets of views. It has been shown that when m = 3, V-b is a reducible variety with one component corresponding to V-t and another corresponding to the trifocal plane. Furthermore, when m = 3, V-t is generated by the three bilinearities and one trilinearity, when m = 4, V-t is generated by the six bilinearities and when m greater than or equal to 4, V-t can be generated by the ((m)(2)) bilinearities. This shows that four images is the generic case in the algebraic setting, because V-t can be generated by just bilinearities. Furthermore, some of the bilinearities may be omitted when m greater than or equal to 5. (C) 1997 by B. G. Teubner Stuttgart - John Wiley & Sons Ltd. (Less)
Routing problems: a historical perspective

This paper presents an historical perspective on routing problems. Today a well-established class of optimization problems, routing problems have played a pivotal role in the development of Logistics as a discipline, even influencing other sectors not directly connected to management studies. The aim of this paper is to provide an overview of the evolution of this topic, starting from seminal contributions by Euler and Hamilton, and illustrating the most recent applications. This article is based on a longer article originally published in Italian (Bruno et al. 2010).
Publications of the Astronomical Society of the Pacific 98:1220-1231, November 1986 OPTIMAL EXTRACTION OF SINGLE-OBJECT SPECTRA FROM OBSERVATIONS WITH TWO-DIMENSIONAL DETECTORS

Spectrographs on large telescopes are frequently equipped with two-dimensional detectors, able to form independent spectra in a number of contiguous spatial columns along the slit. If the projected column width is sufficiently small that a typical seeing disk illuminates several adjacent columns, a signal-to-noise ratio enhancement for observations of a stellar object is obtained by using appropriate weights in the combination of these individual column spectra, instead of using simple coadding. The enhancement is most significant for faint objects, i.e., those for which statistical noise from the underlying sky (and detector noise if applicable) is comparable to the VN noise due to the object itself. The calculation and use of such column weights is described, covering both photoncounting detectors and CCDs. The combination of spectra from separate successive runs also benefits from the use of weights, since the quality of some runs is often better than others. A scheme for calculation of run weights is given. To illustrate the use of column and run weights, a specific spectroscopic observation of a QSO is discussed. The general criteria for the gains to be expected from use of weighting are given. The gain in signal-to-noise ratio is not dramatic (typically ~ 10% for a faint object) but this would be equivalent to an extra 20% observing time and is obtained merely by following the reduction procedure as outlined. The gain due to weighting is substantially larger if the unweighted reduction includes all columns with detectable signal. Methods for analysis of absorption-line spectra to give wavelength, equivalent width, broadening, and asymmetry of detected absorption lines are given. The wavelengths of lines are derived from the median rather than the centroid because it is less affected by noise and by wings or continuum fluctuations near the edges of the line. These procedures for the extraction of absorption-line parameters can be applied whether or not the weighting scheme given here has been used to produce the spectrum.
Secrecy Performance Analysis of Heterogeneous Networks With Unreliable Wireless Backhaul and Imperfect Channel Estimation

Wireless backhaul is an economical and flexible alternative to wired backhaul, however, it experiences impairments. This research proposes a new secure heterogeneous system model with unreliable wireless backhaul and imperfect channel estimation over Nakagami-$m$ fading channel. To improve the system secrecy performance, we propose three small-cell transmitter selection schemes under channel estimation imperfections and wireless backhaul impairments, namely Optimum Selection (OS), Sub-optimum Selection (SS) and Minimum-Eavesdropping Selection (MES). Novel closed-form expressions of secrecy outage probability (SOP) are derived for these three selection schemes in both practical and ideal scenarios. The novel theoretical analysis and simulation results show the impact of wireless backhaul uncertainties and channel estimation errors on system secrecy performance. In addition, we investigate how the number of small-cell transmitters affects the system secrecy performance. The asymptotic behaviour is provided to obtain insights into the system performance. The analytical derivations and asymptotic expressions are validated by Monte Carlo simulations. Our novel theoretical analysis can guide different physical layer security (PLS) designs.