Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

Orthology assignment is ideally suited for functional inference. However, because predicting orthology is computationally intensive at large scale, and most pipelines relatively in accessible, less precise homology-based functional transfer is still the default for (meta-)genome annotation. We therefore developed eggNOG-mapper, a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters and phylogenies from eggNOG. To validate our method, we benchmarked Gene Ontology predictions against two widely used homology-based approaches: BLAST and InterProScan. Compared to BLAST, eggNOG-mapper reduced by 7% the rate of false positive assignments, and increased by 19% the ratio of curated terms recovered over all terms assigned per protein. Compared to InterProScan, eggNOG-mapper achieved similar proteome coverage and precision, while predicting on average 32 more terms per protein and increasing by 26% the rate of curated terms recovered over total term assignments per protein. Through strict orthology assignments, eggNOG-mapper further renders more specific annotations than possible from domain similarity only (e.g. predicting gene family names). eggNOG-mapper runs ~15x than BLAST and at least 2.5x faster than InterProScan. The tool is available standalone or as an online service at http://eggnog-mapper.embl. de.
Spectroscopy

—The dynamic quenching of dual fluorescence is simulated based on solving a system of equations for matrix elements of the statistical operator of a five(cid:2)level model molecule three levels of which belong to its excited states. It is assumed that one of the excited states is resonantly populated by monochromatic irradia(cid:2) tion, while the other two states are populated as a result of subsequent relaxation processes. These two states are initial states for transitions that emit dual fluorescence photons. Expressions for the population of the excited molecular states in the case of steady(cid:2)state fluorescence are obtained taking into account their decay (quenching) due to collisions with foreign molecules of the environment. As applied to molecules with intramolecular hydrogen bonds, the dual fluorescence quenching is described more completely and in more detail compared to the description given in the literature based on the molecular model with two excited levels
P/M processing of soft magnetic materials

A brief introduction to magnetism is given to provide a background to soft magnetic materials made by powder metallurgy (P/M). Iron powder and iron powder mixed with ferrophosphorus can be sintered to give acceptable magnetic induction and to provide mechanical strength. These sintered materials are used for flux return paths. Polymer coating of individual iron powder particles provides a low core loss at high frequencies and these materials can compete favorably with laminated steels in rotating machinery.
Antennas for light and plasmons

Antennas have been used for over a century as emitters, scatterers and receivers of electromagnetic waves. All wireless communication devices, such as radio, mobile phones and satellite communication are strongly dependent on the capability of an antenna to localize propagating electromagnetic waves to a fraction of its wavelength. Because Maxwell's equations are scale-invariant the principles of antenna designs at radio frequencies (106 Hz) can also be applied at optical frequencies (1014 Hz) [1]. Over the course of the last two decades, novel developments in nanotechnology have enabled the fabrication of antennas in the optical regime, and various optical antenna structures have been developed that have the potential to advance many light based technologies [2-5]. The power of optical antennas lies in their capability to manipulate light at the nanoscale. This freedom of controlling light at the nanoscale enables the creation of novel field distributions, where light can be focused to a fraction of the wavelength. Controlling the polarization state of these sub-wavelength spots is of interest for many future applications, including quantum computing. In this thesis the far- and near-fields of optical antennas are experimentally and numerically studied. We determine and manipulate several parameters which determine the resonance behavior of single and coupled antenna systems. With a newly developed optical technique, we are able to measure and manipulate the optical state of the near- and far-field of an array of optical antennas. With this technique we can make a phased antenna array for light, and manipulate the optical state of light at the nanoscale. We experimentally demonstrate how the fundamental properties of light at any point in space have become programmable parameters.
Initial cultivation of a temperate‐region soil immediately accelerates aggregate turnover and CO2 and N2O fluxes

The immediate effects of tillage on protected soil C and N pools and on trace gas emissions from soils at precultivation levels of native C remain largely unknown. We measured the response to cultivation of CO2 and N2O emissions and associated environmental factors in a previously uncultivated U.S. Midwest Alfisol with C concentrations that were indistinguishable from those in adjacent late successional forests on the same soil type (3.2%). Within 2 days of initial cultivation in 2002, tillage significantly (P 50.001, n 54) increased CO2 fluxes from 91 to 196mgCO2-Cm � 2 h � 1 and within the first 30 days higher fluxes because of cultivation were responsible for losses of 85gCO2-Cm � 2 . Additional daily C losses were sustained during a second and third year of cultivation of the same plots at rates of 1.9 and 1.0gCm � 2 day � 1 , respectively. Associated with the CO2 responses were increased soil temperature, substantially reduced soil aggregate size (mean weight diameter decreased 35% within 60 days), and a reduction in the proportion of intraaggregate, physically protected light fraction organic matter. Nitrous oxide fluxes in cultivated plots increased 7.7-fold in 2002, 3.1-fold in 2003, and 6.7-fold in 2004 and were associated with increased soil NO3 concentrations, which approached 15lgNg � 1 . Decreased plant N uptake immediately after tillage, plus increased mineralization rates and fivefold greater nitrifier enzyme activity, likely contributed to increased NO3 concentrations. Our results demonstrate that initial cultivation of a soil at precultivation levels of native soil C immediately destabilizes physical and microbial processes related to C and N retention in soils and accelerates trace gas fluxes. Policies designed to promote long-term C sequestration may thus need to protect soils from even occasional cultivation in order to preserve sequestered C.
Potent antimicrobial and antibiofilm activities of bacteriogenically synthesized gold–silver nanoparticles against pathogenic bacteria and their physiochemical characterizations

The objective of this study was to develop a bimetallic nanoparticle with enhanced antibacterial activity that would improve the therapeutic efficacy against bacterial biofilms. Bimetallic gold–silver nanoparticles were bacteriogenically synthesized using γ-proteobacterium, Shewanella oneidensis MR-1. The antibacterial activities of gold–silver nanoparticles were assessed on the planktonic and biofilm phases of individual and mixed multi-cultures of pathogenic Gram negative (Escherichia coli and Pseudomonas aeruginosa) and Gram positive bacteria (Enterococcus faecalis and Staphylococcus aureus), respectively. The minimum inhibitory concentration of gold–silver nanoparticles was 30–50 µM than that of other nanoparticles (>100 µM) for the tested bacteria. Interestingly, gold–silver nanoparticles were more effective in inhibiting bacterial biofilm formation at 10 µM concentration. Both scanning and transmission electron microscopy results further accounted the impact of gold–silver nanoparticles on biocompatibility and bactericidal effect that the small size and bio-organic materials covering on gold–silver nanoparticles improves the internalization and thus caused bacterial inactivation. Thus, bacteriogenically synthesized gold–silver nanoparticles appear to be a promising nanoantibiotic for overcoming the bacterial resistance in the established bacterial biofilms.
Phosphoinositide-3-Kinase Signaling in Human Natural Killer Cells: New Insights from Primary Immunodeficiency

Human natural killer (NK) cells play a critical role in the control of viral infections and malignancy. Their importance in human health and disease is illustrated by severe viral infections in patients with primary immunodeficiencies that affect NK cell function and/or development. The recent identification of patients with phosphoinositide-3-kinase (PI3K)-signaling pathway mutations that can cause primary immunodeficiency provides valuable insight into the role that PI3K signaling plays in human NK cell maturation and lytic function. There is a rich literature that demonstrates a requirement for PI3K in multiple key aspects of NK cell biology, including development/maturation, homing, priming, and function. Here, I briefly review these previous studies and place them in context with recent findings from the study of primary immunodeficiency patients, particularly those with hyperactivating mutations in PI3Kδ signaling.
Is There ‘Anther-Anther Interference’ within a Flower? Evidences from One-by-One Stamen Movement in an Insect-Pollinated Plant

The selective pressure imposed by maximizing male fitness (pollen dispersal) in shaping floral structures is increasingly recognized and emphasized in current plant sciences. To maximize male fitness, many flowers bear a group of stamens with temporally separated anther dehiscence that prolongs presentation of pollen grains. Such an advantage, however, may come with a cost resulting from interference of pollen removal by the dehisced anthers. This interference between dehisced and dehiscing anthers has received little attention and few experimental tests to date. Here, using one-by-one stamen movement in the generalist-pollinated Parnassia palustris, we test this hypothesis by manipulation experiments in two years. Under natural conditions, the five fertile stamens in P. palustris flowers elongate their filaments individually, and anthers dehisce successively one-by-one. More importantly, the anther-dehisced stamen bends out of the floral center by filament deflexion before the next stamen's anther dehiscence. Experimental manipulations show that flowers with dehisced anther remaining at the floral center experience shorter (1/3–1/2 less) visit durations by pollen-collecting insects (mainly hoverflies and wasps) because these ‘hungry’ insects are discouraged by the scant and non-fresh pollen in the dehisced anther. Furthermore, the dehisced anther blocks the dehiscing anther's access to floral visitors, resulting in a nearly one third decrease in their contact frequency. As a result, pollen removal of the dehiscing anther decreases dramatically. These results provide the first direct experimental evidence that anther-anther interference is possible in a flower, and that the selection to reduce such interferences can be a strong force in floral evolution. We also propose that some other floral traits, usually interpreted as pollen dispensing mechanisms, may function, at least partially, as mechanisms to promote pollen dispersal by reducing interferences between dehisced and dehiscing anthers.
FUNCTIONAL NEUROANATOMY

FUNCTIONAL NEUROANATOMY By Wendell J. S. Krieg. 3rd ed. (Pp xviii + 874; 429 figures; tables; diachrome booklet. $14.00.) Evanston, Illinois: Brain Books. 1966. This textbook clearly is the product of much of the author's professional lifetime, his magnum opus-a thorough, unusually personal work and one exceptionally devoted to teaching. The illustrations are not photographs, but most of the drawings, reconstructions, phantoms and sections, many differentially coloured according to function, and all in remarkable detail, are didactically excellent. In addition to a textbook of anatomy at a gross and microscopic level, Professor Krieg has included a laboratory manual, an atlas in multiple planes, and a review guide with progressively condensed material and its own summarizing illustrations. Though a lengthy and up-to-date bibliography is appended, the textual material is presented in a readymade and unnecessarily dogmatic manner. Perhaps the clarity and coherence of such a presentation have, as a beginning, certain pedagogic advantages when contrasted with the collection of poorly related facts often presented to students. Nevertheless, the author, in his endeavour to relate all structures to their functions, seems to attempt too much. Discussions involving physiology and neurology contain statements generally conceived to be untrue, and others that are purely speculative, viz., normally tonus is present in postural muscles, cerebellar basket cells spread excitation, flower spray endings on the muscle spindle record maximal contraction, it is possible to keep denervated muscles alive indefinitely by electrical stimulation. Omitted are discussions of the neuroanatomical correlates of memory, of inhibition as an active process of great importance, and of the wealth of new material being revealed by the electron microscope. The index has a large number of entries without page numbers, alphabetical misplacements and mis-spellings, and is, inconveniently, not at the very end of the book. Those students, at any stage, who are learning or relearning neuroanatomy would profit from this book which will, in any case, be more popular with them than with professional neuroanatomists. It is interesting reading, provocative, and well worth its reasonable price. Still, correlations of anatomy and function are probably best achieved by dialogues between the anatomist and a physiologist or neurologist with complementary interests. R. R. YOUNG
Outlaw Distributions and Locally Decodable Codes

Locally decodable codes (LDCs) are error correcting codes that allow for decoding of a single message bit using a small number of queries to a corrupted encoding. Despite decades of study, the optimal trade-off between query complexity and codeword length is far from understood. In this work, we give a new characterization of LDCs using distributions over Boolean functions whose expectation is hard to approximate (in~$L_\infty$~norm) with a small number of samples. We coin the term `outlaw distributions' for such distributions since they `defy' the Law of Large Numbers. We show that the existence of outlaw distributions over sufficiently `smooth' functions implies the existence of constant query LDCs and vice versa. We give several candidates for outlaw distributions over smooth functions coming from finite field incidence geometry, additive combinatorics and from hypergraph (non)expanders. We also prove a useful lemma showing that (smooth) LDCs which are only required to work on average over a random message and a random message index can be turned into true LDCs at the cost of only constant factors in the parameters.
Improvement in cognitive function after surgery for low-grade glioma.

OBJECTIVECognition is a key component in health-related quality of life (HRQoL) and is currently incorporated as a major parameter of outcome assessment in patients treated for brain tumors. The effect of surgery on cognition and HRQoL remains debatable. The authors investigated the impact of resection of low-grade gliomas (LGGs) on cognition and the correlation with various histopathological markers.METHODSA retrospective analysis of patients with LGG who underwent craniotomy for tumor resection at a single institution between 2010 and 2014 was conducted. Of 192 who underwent resective surgery for LGG during this period, 49 had complete pre- and postoperative neurocognitive evaluations and were included in the analysis. These patients completed a full battery of neurocognitive tests (memory, language, attention and working memory, visuomotor organization, and executive functions) pre- and postoperatively. Tumor and surgical characteristics were analyzed, including volumetric measurements and histopathological markers (IDH, p53, GFAP). RESULTSPostoperatively, significant improvement was found in memory and executive functions. A subgroup analysis of patients with dominant-side tumors, most of whom underwent intraoperative awake mapping, revealed significant improvement in the same domains. Patients whose tumors were on the nondominant side displayed significant improvement only in memory functions. Positive staining for p53 testing was associated with improved language function and greater extent of resection in dominant-side tumors. GFAP positivity was associated with improved memory in patients whose tumors were on the nondominant side. No correlation was found between cognitive outcome and preoperative tumor volume, residual volume, extent of resection, or IDH1 status.CONCLUSIONSResection of LGG significantly improves memory and executive function and thus is likely to improve functional outcome in addition to providing oncological benefit. GFAP and pP53 positivity could possibly be associated with improved cognitive outcome. These data support early, aggressive, surgical treatment of LGG.
Evaluating the use of high-pressure coolant in turning process of Inconel 625 nickel-based alloy

The automotive, aerospace and energy industries have lately increased their search for materials which must have high mechanical resistance/weight ratio and capability to maintain the mechanical properties in high temperatures and at corrosive environments in order to produce critical parts of their equipment. The nickel-based alloys are one type of materials which have been a good answer for this search. On the other hand, the very good mechanical properties of these alloys make their manufacturing very difficult, especially when machining processes are used. Among other problems in the machining of these alloys, due to the high mechanical resistance in high temperature, tool lives used to be much shorter than when steel alloys are machined, forcing cutting speeds to be much lower and, consequently, to have less productive processes. The main goal of this work was to test an alternative to increase tool life in the turning of Inconel 625 nickel-based alloy by the use of high-pressure coolant. This system was tested using different directions of the fluid flow (toward the rake face, toward the flank face and directing the fluid simultaneously toward these two tool faces) compared to the conventional way of applying fluid. The results show that the use of high-pressure coolant harms the notch wear development and, consequently, increases tool life with simultaneous improvement of workpiece surface roughness in some cases. However, the application of high-pressure coolant over both flank and rake faces at the same time did not provide any improvement.
Congenital heart defects and extracardiac malformations.

OBJECTIVE To review the association between congenital heart defects and extracardiac malformations. DATA SOURCES Scientific articles were searched in the Medline, Lilacs, and SciELO databases, using the descriptors "congenital heart disease," "congenital heart defects," "congenital cardiac malformations," "extracardiac defects," and "extracardiac malformations. " All case series that specifically explored the association between congenital heart defects and extracardiac malformations were included. DATA SYNTHESIS Congenital heart diseases are responsible for about 40% of birth defects, being one of the most common and severe malformations. Extracardiac malformations are observed in 7 to 50% of the patients with congenital heart disease, bringing a greater risk of comorbidity and mortality and increasing the risks related to heart surgery. Different studies have attempted to assess the presence of extracardiac abnormalities in patients with congenital heart disease. Among the changes described, those of the urinary tract are more often reported. However, no study has evaluated all patients in the same way. CONCLUSIONS Extracardiac abnormalities are frequent among patients with congenital heart disease, and patients with these alterations may present an increased risk of morbimortality. Therefore, some authors have been discussing the importance and cost-effectiveness of screening these children for other malformations by complementary exams.
Physico-mechanical characterization and biodegradability behavior of polypropylene/poly(L-lactide) polymer blends

Abstract Partially biodegradable polymer films from the blends of polypropylene (PP) and poly(L-lactide) (PLLA) were prepared in an internal mixer by melt blending technique, with and without compatibilizer, maleic anhydride grafted polypropylene (MAPP), followed by compression molding. With regard to tensile properties, 80/20 (PP/PLLA) and 80/20/6 (PP/PLLA/MAPP) were found as the optimum blends with best combination of the ingredients. Therefore, the blend samples, namely, PP80 (80% PP+20% PLLA) and PP80C6 (80% PP+20% PLLA+6 phr MAPP) were selected as ‘optimized’ blends and further characterized for their physical, chemical, morphological, and thermal properties. X-ray diffraction studies showed that neat PP and PP80C6 had the same crystallite size indicating compatibility between PP and PLLA due to MAPP. Fourier transform infrared spectroscopy and scanning electron microsopy investigations revealed that the two polymers were completely immiscible in absence of the compatibilizer. Bacterial biodegradation of the samples was performed by exposure to Pseudomonas stutzeri for 60 days and measured in terms of weight loss, optical density, and thermal stability of the samples before and after degradation. The results showed that 80/20 (PP/PLLA) blends undergo considerable degradation. Reduction in thermal stability of the film samples was also observed through thermogravimetric analysis, which was useful in accelerating their biodegradation.
Content of available forms of some micronutrients in soil after long-term differentiated fertilization.

The objective of this study has been to follow modifications in the content of Cu, Zn and Mn in the topmost layer of soil which had been fertilized for many years with farmyard manure and mineral fertilizers or with mineral fertilizers alone. Soil samples were collected in 2002-2005 from a trial established in 1986 on proper brown podsolic soil, according to the random block design with four replication. The first factor consisted of organic fertilization (manure applied every two years or without manure). The second factor involved different rates of mineral fertilization. Rates of nutrients in the mineral fertilizers were identical in both experimental series – with or without manure. In each year, the same crop was grown on both fields, in a crop rotation system: sugar beet (2002), spring barley (2003), maize (2004) and spring wheat (2005). Plant available forms of nutrients were extracted from soil in 1 mol HCl dm -3 solution. After extraction, the content of metals was determined by atomic absorption spectrophotometry. The results underwent statistical processing using analysis of variance for a two-factor experiment. The content of available forms of copper, zinc and manganese in soil regularly amended with manure was evidently higher than analogous concentrations determined in soil receiving only mineral fertilization since 1986. Manure most strongly improved the concentration of Cu (nearly 1.7-fold), while producing the weakest influence on manganese (over 1.3-fold more). In absolute values, however, the increase in availability of manganese was the highest, reaching on average 52 mg kg -1 of soil. Differentiated mineral fertilization with nitrogen or potassium as well as manganese and liming to a lesser extent than manure modified the availability of Cu, Zn and Mn in soil. Among these nutrients, nitrogen most often increased the content of plant assimilable forms of metals in soil, which may have been caused by its acidifying influence.