Modeling missing pedigree with metafounders and validating single-step genomic predictions in a small dairy cattle population with a great influence of foreign genetics.

Genetic improvement in small countries rely heavily on foreign genetics. In an importing country such as Uruguay, consideration of unknown parent groups (UPG) for foreign sires is essential. However, the use of UPG in genomic model evaluations may lead to bias in genomic estimated breeding values (GEBV). The objective of this study was to study different models including UPG or metafounders (MF) in the Uruguayan Holstein evaluation and to analyze bias, dispersion, and accuracy of GEBV predictions in BLUP and single-step genomic BLUP (ssGBLUP). A gamma matrix (Γ) was estimated either by using base allele population frequencies obtained by bounded linear regression (MFbounded), or by using 2 values to design Γ (i.e., a single value for the diagonal and a different value for the off-diagonal [MFrobust]). Both Γ estimators performed well in terms of GEBV predictions, but MFbounded was the best option. There is, however, some bias whose origin was not completely understood. UPG or MF seem to model correctly genetic progress for unknown parents except for the very first groups (earlier time period). As for validation bulls, bias was observed across all models, whereas for validation cows it was only observed with UPG in BLUP. Overdispersion was found in all models, but it was mostly detected in validation bulls. Ratio of accuracies indicated that ssGBLUP gave better predictions than BLUP.

Observation on temperature and strain dependency of Brillouin dynamic grating in a few-mode fiber with a ring-cavity configuration.

We experimentally conduct Brillouin dynamic grating (BDG) operation using a 1-km-long four-mode fiber. By employing a simplified ring-cavity configuration with single-end pumping, the BDG is effectively generated in $ {{\rm LP}_{01}} $LP01 mode within a range of 250 m, and three higher-order modes, namely, $ {{\rm LP}_{11b}} $LP11b, $ {{\rm LP}_{21a}} $LP21a, and $ {{\rm LP}_{02}} $LP02, are chosen as probes to analyze the BDG with a spatial resolution of 1 m. To the best of our knowledge, this is the first time to characterize the responses of BDG frequency to temperature and strain for different modes in a conventional few-mode fiber. By employing the pump-probe pair of $ {{\rm LP}_{01}}{{\rm - LP}_{02}} $LP01-LP02 mode, the highest temperature and strain sensitivities of 3.21 MHz/°C and $ - 0.0384\;{\rm MHz}/{\unicode{x00B5}}{\unicode{x03B5}} $-0.0384MHz/µÎµ have been achieved. Also, the performance of simultaneously distributed temperature and strain sensing based on BDG is evaluated.

Mode-selective few-mode Brillouin fiber lasers based on intramodal and intermodal SBS.

Mode-selective fiber lasers have advantages in a number of applications. Here we propose and experimentally demonstrate a transverse mode-selective few-mode Brillouin fiber laser using the mode-selective photonic lantern. We generated the lowest three orders of linearly polarized (LP) modes based on both intramodal and intermodal stimulated Brillouin scattering (SBS). Their slope efficiencies, optical spectra, mode profiles, and linewidths were measured.

Creating oscillons and oscillating kinks in two scalar field theories.

Oscillons are time-dependent, localized in space, extremely long-lived states in nonlinear scalar-field models, while kinks are topological solitons in one spatial dimension. In the present work, we show new classes of oscillons and oscillating kinks in a system of two nonlinearly coupled scalar fields in 1+1 spatiotemporal dimensions. The solutions contain a control parameter, the variation of which produces oscillons and kinks with a flat-top shape. The model finds applications in condensed matter, cosmology, and high-energy physics.

Using modified fish scale waste from Sardinella brasiliensis as a low-cost adsorbent to remove dyes from textile effluents.

Textile industry wastewater has become a cause of concern to environmentalists due to its toxic composition and the difficulty of breaking down certain dyes. In this study, modified fish scales of Sardinella brasiliensis (SSb) were used as an alternative for a low-cost adsorbent to remove dyes from textile wastewaters. Adsorption efficiency was assessed by measuring the general, kinetic, and thermodynamic physico-chemical parameters of adsorption isotherms, using Reactive Turquoise Blue 15 (RTB15) and Reactive Red 120 (RR120) dyes as adsorbate models, as local textile industries commonly use these dyes. The isothermal data from the batch experiments were inserted in the Langmuir, Freundlich, and Langmuir-Freundlich (SIPS) equations; the Langmuir isotherm equation showed the most appropriate. The thermodynamic parameters showed that adsorption of dyes by the modified SSb adsorbent was an endothermic yet spontaneous process in the case of RR120. Sorbent-based on SSb material was concluded as adsorbing both of the tested dyes. Because of its abundant availability, and the small amount of activation needed to turn it into an adsorbent, this biowaste can be employed as a low-cost alternative for removal of dyes in the treatment of textile wastewater.

Bacterial short-chain fatty acid metabolites modulate the inflammatory response against infectious bacteria.

Short-chain fatty acids (SCFAs), predominantly acetic, propionic, and butyric acids, are bacterial metabolites with an important role in the maintenance of homeostasis due to their metabolic and immunomodulatory actions. Some evidence suggests that they may also be relevant during infections. Therefore, we aimed to investigate the effects of SCFAs in the effector functions of neutrophils to an opportunistic pathogenic bacterium, Aggregatibacter actinomycetemcomitans. Using a subcutaneous model to generate a mono, isolated infection of A. actinomycetemcomitans, we demonstrated that the presence of the SCFAs in situ did not affect leukocyte accumulation but altered the effector mechanisms of migrating neutrophils by downregulating the production of cytokines, their phagocytic capacity, and killing the bacteria, thus impairing the containment of A. actinomycetemcomitans. Similar effects were observed with bacteria-stimulated neutrophils incubated with SCFAs in vitro. These effects were independent of free-fatty acid receptor 2 (FFAR2) activation, the main SCFA receptor expressed on neutrophils, occurring possibly through inhibition of histone deacetylases because similar effects were obtained by using histone deacetylase inhibitors, such as SAHA, MS-275, and RGFP 966. Considering the findings of this study, we hypothesized that in an infectious condition, SCFAs may exert a detrimental effect on the host by inhibiting neutrophil's effector functions.

Genetic parameter estimation for long endurance trials in the Uruguayan Criollo horse.

The aim of this study was to estimate the genetic parameters of performance in a 750-km, 15-day ride in Criollo horses. Heritability (h2 ) and maternal lineage effects (mt2 ) were obtained for rank, a relative placing measure of performance. Additive genetic and maternal lineage (rmt) correlations among five medium-to-high intensity phase ranks (pRK) and final rank (RK) were also estimated. Individual records from 1,236 Criollo horses from 1979 to 2012 were used. A multivariate threshold animal model was applied to the pRK and RK. Heritability was moderate to low (0.156-0.275). Estimates of mt2 were consistently low (0.04-0.06). Additive genetic correlations between individual pRK and RK were high (0.801-0.924), and the genetic correlations between individual pRKs ranged from 0.763 to 0.847. The pRK heritabilities revealed that some phases were explained by a greater additive component, whereas others showed stronger genetic relationships with RK. Thus, not all pRK may be considered as similar measures of performance in competition.

Soil forensics: How far can soil clay analysis distinguish between soil vestiges?

Soil traces are useful as forensic evidences because they frequently adhere to individuals and objects associated with crimes and can place or discard a suspect at/from a crime scene. Soil is a mixture of organic and inorganic components and among them soil clay contains signatures that make it reliable as forensic evidence. In this study, we hypothesized that soils can be forensically distinguished through the analysis of their clay fraction alone, and that samples of the same soil type can be consistently distinguished according to the distance they were collected from each other. To test these hypotheses 16 Oxisol samples were collected at distances of between 2m and 1.000m, and 16 Inceptisol samples were collected at distances of between 2m and 300m from each other. Clay fractions were extracted from soil samples and analyzed for hyperspectral color reflectance (HSI), X-ray diffraction crystallographic (XRD), and for contents of iron oxides, kaolinite and gibbsite. The dataset was submitted to multivariate analysis and results were from 65% to 100% effective to distinguish between samples from the two soil types. Both soil types could be consistently distinguished for forensic purposes according to the distance that samples were collected from each other: 1000m for Oxisol and 10m for Inceptisol. Clay color and XRD analysis were the most effective techniques to distinguish clay samples, and Inceptisol samples were more easily distinguished than Oxisol samples. Soil forensics seems a promising field for soil scientists as soil clay can be useful as forensic evidence by using routine analytical techniques from soil science.

All-fiber few-mode multicore photonic lantern mode multiplexer.

The emergence of space division multiplexing (SDM) for ultrahigh capacity networks has heralded pioneering Petabit-class optical transmission systems. In parallel to novel SDM fibers, a new class of components to enable scalable, low-loss schemes for unlocking fiber capacity is being developed. In this work, an all-fiber mode selective photonic lantern mode multiplexer designed for launching into few-mode multicore fibers is demonstrated. This device is capable of selectively exciting LP01, LP11a and LP11b modes in a seven-core configuration, resulting in 21 spatial channels, with less than 38 dB core-to-core crosstalk and insertion loss below 0.4 dB. The multicore photonic lantern multiplexer is scalable to larger number of cores and modes per core, and can be easily integrated with emerging ultra-high bandwidth few-mode multicore optical communication systems.

Versatile supercontinuum generation in parabolic multimode optical fibers.

We demonstrate that the pump's spatial input profile can provide additional degrees of freedom in tailoring at will the nonlinear dynamics and the ensuing spectral content of supercontinuum generation in highly multimoded optical fibers. Experiments and simulations carried out at 1550 nm indicate that the modal composition of the input beam can substantially alter the soliton fission process as well as the resulting Raman and dispersive wave generation that eventually lead to supercontinuum in such a multimode environment. Given the multitude of conceivable initial conditions, our results suggest that it is possible to pre-engineer the supercontinuum spectral content in a versatile manner.

Tailoring frequency generation in uniform and concatenated multimode fibers.

We demonstrate that frequency generation in multimode parabolic-index fibers can be precisely engineered through appropriate fiber design. This is accomplished by exploiting the onset of a geometric parametric instability that arises from resonant spatiotemporal compression. By launching the output of an amplified Q-switched microchip laser delivering 400 ps pulses at 1064 nm, we observe a series of intense frequency sidebands that strongly depend on the fiber core size. The nonlinear frequency generation is analyzed in three fiber samples with 50 µm, 60 µm, and 80 µm core diameters. We further demonstrate that by cascading fibers of different core sizes, a desired frequency band can be generated from the frequency lines parametrically produced in each section. The observed frequency shifts are in good agreement with analytical predictions and numerical simulations. Our results suggest that core scaling and fiber concatenation can provide a viable avenue in designing optical sources with tailored output frequencies.

Reduced-symmetry LMA rod-type fiber for enhanced higher-order mode delocalization.

We present a novel design of a micro-structured large-pitch, large-mode-area (LMA) asymmetric rod-type fiber. By reducing the cladding symmetry through six high-refractive index germanium-doped silica inclusions, the fiber features strong higher-order mode (HOM) delocalization, leading to a potentially enhanced preferential gain for the fundamental mode in active fibers. In addition, high resolution spatially and spectrally (S2) resolved mode analysis measurements confirm HOM contributions below 1% and LP1m-like HOM contributions below the detection limit. This proposed fiber design enables single-mode operation, with near-diffraction-limited beam quality of M2=1.3 and an effective mode area of 2560 µm2 at 1064 nm. This design opens new insights into improving the threshold-like onset of modal instabilities in high-power fiber lasers and fiber amplifiers by efficiently suppressing LP11 modes.

Instant and efficient second-harmonic generation and downconversion in unprepared graded-index multimode fibers.

We show that germanium-doped graded-index multimode silica fibers can exhibit relatively high conversion efficiencies (∼6.5%) for second-harmonic generation when excited at 1064 nm. This frequency-doubling behavior is also found to be accompanied by an effective downconversion. As opposed to previous experiments carried out in single- and few-mode fibers where hours of preparation were required, in our system, these χ(2) related processes occur almost instantaneously. The efficiencies observed in our experiments are, to the best of our knowledge, among the highest ever reported in unprepared fibers.

Nonlinear pulse compression to 43 W GW-class few-cycle pulses at 2 µm wavelength.

High-average power laser sources delivering intense few-cycle pulses in wavelength regions beyond the near infrared are promising tools for driving the next generation of high-flux strong-field experiments. In this work, we report on nonlinear pulse compression to 34.4 µJ-, 2.1-cycle pulses with 1.4 GW peak power at a central wavelength of 1.82 µm and an average power of 43 W. This performance level was enabled by the combination of a high-repetition-rate ultrafast thulium-doped fiber laser system and a gas-filled antiresonant hollow-core fiber.

Visible supercontinuum generation in a graded index multimode fiber pumped at 1064 nm.

We observe efficient supercontinuum generation that extends into the visible spectral range by pumping a low differential mode group delay graded index multimode fiber in the normal dispersion regime. For a 28.5 m long fiber, the generated spectrum spans more than two octaves, starting from below 450 nm and extending beyond 2400 nm. The main nonlinear mechanisms contributing to the visible spectrum generation are attributed to multipath four-wave mixing processes and periodic spatio-temporal breathing dynamics. Moreover, by exploiting the highly multimodal nature of this system, we demonstrate versatile generation of visible spectral peaks in shorter fiber spans by altering the launching conditions. A nonlinearly induced mode cleanup was also observed at the pump wavelength. Our results could pave the way for high brightness, high power, and compact, multi-octave continuum sources.

Few-mode erbium-doped fiber amplifier with photonic lantern for pump spatial mode control.

We demonstrate a few-mode erbium-doped fiber amplifier employing a mode-selective photonic lantern for controlling the modal content of the pump light. Amplification of six spatial modes in a 5 m long erbium-doped fiber to ∼6.2 dBm average power is obtained while maintaining high modal fidelity. Through mode-selective forward pumping of the two degenerate LP21 modes operating at 976 nm, differential modal gains of <1 dB between all modes and signal gains of ∼16 dB at 1550 nm are achieved. In addition, low differential modal gain for near-full C-band operation is demonstrated.

Mode-selective amplification in a large mode area Yb-doped fiber using a photonic lantern.

We demonstrate selective spatial mode amplification in a few mode, double-clad Yb-doped large mode area (LMA) fiber, utilizing an all-fiber photonic lantern. Amplification to multi-watt output power is achieved while preserving high spatial mode selectivity. We observe gain values of over 12 dB for all modes: LP01, LP11a, and LP11b, when amplified individually. Additionally, we investigate the simultaneous amplification of LP01+LP11a and LP11a+LP11b, and the resultant mode competition. The proposed architecture allows for the reconfigurable excitation of spatial modes in the LMA fiber amplifiers, and represents a promising method that could enable dynamic spatial mode control in high power fiber lasers.

Influence of the number of daily pills and doses on adherence to antiretroviral treatment: a 7-year study.

WHAT IS KNOWN AND OBJECTIVE: Antiretroviral treatment (ART) is hampered by complicated regimens, high pill burden, drug-drug interactions, and frequent short- and long-term adverse effects, leading to decreased adherence. Over recent years, considerable effort has been directed at developing regimens that are less burdening. We undertook a 7-year retrospective study of the records of 264 HIV-infected subjects enrolled in a pharmaceutical care programme to document the progress made and to study the influence of the number of ART pills and doses on the level of treatment adherence. METHODS: Antiretroviral dispensing records were analysed for the number of pills and doses administered and the ART adherence rate estimated. RESULTS AND DISCUSSION: In 2005, the patients took a mean of 6·2 pills daily (CI 95%: 5·9-6·6), and 92·9% of them were on a twice-a-day (BID) dosage regimen. By 2012, the mean number of pills was reduced to 4·1 (CI 95%: 3·8-4·4), and only 50·9% were on a BID regimen. No statistically significant relation was observed between number of daily pills and doses and ART adherence reached by the patients in any of the analyses performed. WHAT IS NEW AND CONCLUSIONS: There has been a continuous reduction in the number of pills and doses of antiretrovirals taken by individual patients over the last 7 years due largely to the introduction of improved treatments and regimens. More daily pills or doses was not associated with worse ART adherence in our pharmaceutical care programme.

Genetic variability in isolates of Chromobacterium violaceum from pulmonary secretion, water, and soil.

Chromobacterium violaceum is a free-living Gram-negative bacillus usually found in the water and soil in tropical regions, which causes infections in humans. Chromobacteriosis is characterized by rapid dissemination and high mortality. The aim of this study was to detect the genetic variability among C. violaceum type strain ATCC 12472, and seven isolates from the environment and one from a pulmonary secretion from a chromobacteriosis patient from Ilhéus, Bahia. The molecular characterization of all samples was performed by polymerase chain reaction (PCR) sequencing and 16S rDNA analysis. Primers specific for two ATCC 12472 pathogenicity genes, hilA and yscD, as well as random amplified polymorphic DNA (RAPD), were used for PCR amplification and comparative sequencing of the products. For a more specific approach, the PCR products of 16S rDNA were digested with restriction enzymes. Seven of the samples, including type-strain ATCC 12472, were amplified by the hilA primers; these were subsequently sequenced. Gene yscD was amplified only in type-strain ATCC 12472. MspI and AluI digestion revealed 16S rDNA polymorphisms. This data allowed the generation of a dendogram for each analysis. The isolates of C. violaceum have variability in random genomic regions demonstrated by RAPD. Also, these isolates have variability in pathogenicity genes, as demonstrated by sequencing and restriction enzyme digestion.

Comparative evaluation of total RNA extraction methods in Theobroma cacao using shoot apical meristems.

Theobroma cacao is a species of great economic importance with its beans used for chocolate production. The tree has been a target of various molecular studies. It contains many polyphenols, which complicate the extraction of nucleic acids with the extraction protocols requiring a large amount of plant material. These issues, therefore, necessitate the optimization of the protocols. The aim of the present study was to evaluate different methods for extraction of total RNA from shoot apical meristems of T. cacao 'CCN 51' and to assess the influence of storage conditions for the meristems on the extraction. The study also aimed to identify the most efficient protocol for RNA extraction using a small amount of plant material. Four different protocols were evaluated for RNA extraction using one shoot apical meristem per sample. Among these protocols, one that was more efficient was then tested to extract RNA using four different numbers of shoot apical meristems, subjected to three different storage conditions. The best protocol was tested for cDNA amplification using reverse transcription-polymerase chain reaction; the cDNA quality was determined to be satisfactory for molecular analyses. The study revealed that with the best RNA extraction protocol, one shoot apical meristem was sufficient for extraction of high-quality total RNA. The results obtained might enable advances in genetic analyses and molecular studies using reduced amount of plant material.