Guidelines: basic principles of neurorehabilitation for patients with acquired brain injury. Recommendations of the Spanish Society of Neurorehabilitation

INTRODUCTION

We present the Spanish Society of Neurorehabilitation's guidelines for adult acquired brain injury (ABI) rehabilitation. These recommendations are based on a review of international clinical practice guidelines published between 2013 and 2020.

DEVELOPMENT

We establish recommendations based on the levels of evidence of the studies reviewed and expert consensus on population characteristics and the specific aspects of the intervention or procedure under research.

CONCLUSIONS

All patients with ABI should receive neurorehabilitation therapy once they present a minimal level of clinical stability. Neurorehabilitation should offer as much treatment as possible in terms of frequency, duration, and intensity (at least 45-60minutes of each specific form of therapy that is needed). Neurorehabilitation requires a coordinated, multidisciplinary team with the knowledge, experience, and skills needed to work in collaboration both with patients and with their families. Inpatient rehabilitation interventions are recommended for patients with more severe deficits and those in the acute phase, with outpatient treatment to be offered as soon as the patient's clinical situation allows it, as long as intensity criteria can be maintained. The duration of treatment should be based on treatment response and the possibilities for further improvement, according to the best available evidence. At discharge, patients should be offered health promotion, physical activity, support, and follow-up services to ensure that the benefits achieved are maintained, to detect possible complications, and to assess possible changes in functional status that may lead the patient to need other treatment programmes.

Assessment of milk metabolites as biomarkers for predicting feed efficiency in dairy sheep

Estimating feed efficiency (FE) in dairy sheep is challenging due to the high cost of systems that measure individual feed intake. Identifying proxies that can serve as effective predictors of FE could make it possible to introduce FE into breeding programs. Here, 39 Assaf ewes in first lactation were evaluated regarding their FE by 2 metrics, residual feed intake (RFI) and feed conversion ratio (FCR). The ewes were classified into high, medium and low groups for each metric. Milk samples of the 39 ewes were subjected to untargeted metabolomics analysis. The complete milk metabolomic signature was used to discriminate the FE groups using partial least squares discriminant analysis. A total of 41 and 26 features were selected as the most relevant features for the discrimination of RFI and FCR groups, respectively. The predictive ability when utilizing the complete milk metabolomic signature and the reduced data sets were investigated using 4 machine-learning algorithms and a multivariate regression method. The Orthogonal Partial Least Square algorithm outperformed other ML algorithms for the FCR prediction in the scenarios using the complete milk metabolite signature (r2 = 0.62 ± 0.06) and the 26 selected features (0.62 ± 0.15). Regarding RFI predictions, the scenarios using the 41 selected features outperformed the scenario with the complete milk metabolite signature, where the Multilayer feedforward artificial neural network (r2 = 0.18 ± 0.14) and extreme gradient boosting (r2 = 0.17 ± 0.15) outperformed other algorithms. The functionality of the selected metabolites implied that the metabolism of glucose, galactose, fructose, sphingolipids, amino acids, insulin, and thyroid hormones was at play. Compared with the use of traditional methods, practical applications of these biomarkers might simplify and reduce costs in selecting feed-efficient ewes.

Demonstrating Agreement between Radio and Fluorescence Measurements of the Depth of Maximum of Extensive Air Showers at the Pierre Auger Observatory

We show, for the first time, radio measurements of the depth of shower maximum (X_{max}) of air showers induced by cosmic rays that are compared to measurements of the established fluorescence method at the same location. Using measurements at the Pierre Auger Observatory we show full compatibility between our radio and the previously published fluorescence dataset, and between a subset of air showers observed simultaneously with both radio and fluorescence techniques, a measurement setup unique to the Pierre Auger Observatory. Furthermore, we show radio X_{max} resolution as a function of energy and demonstrate the ability to make competitive high-resolution X_{max} measurements with even a sparse radio array. With this, we show that the radio technique is capable of cosmic-ray mass composition studies, both at Auger and at other experiments.

Epigenetic regulation of functional candidate genes for milk production traits in dairy sheep subjected to protein restriction in the prepubertal stage

BACKGROUND

As the prepubertal stage is a crucial point for the proper development of the mammary gland and milk production, this study aims to evaluate how protein restriction at this stage can affect methylation marks in milk somatic cells. Here, 28 Assaf ewes were subjected to 42.3% nutritional protein restriction (14 animals, NPR) or fed standard diets (14 animals, C) during the prepubertal stage. During the second lactation, the milk somatic cells of these ewes were sampled, and the extracted DNA was subjected to whole-genome bisulfite sequencing.

RESULTS

A total of 1154 differentially methylated regions (DMRs) were identified between the NPR and C groups. Indeed, the results of functional enrichment analyses of the genes harboring these DMRs suggested their relevant effects on the development of the mammary gland and lipid metabolism in sheep. The additional analysis of the correlations of the mean methylation levels within these DMRs with fat, protein, and dry extract percentages in the milk and milk somatic cell counts suggested associations between several DMRs and milk production traits. However, there were no phenotypic differences in these traits between the NPR and C groups.

CONCLUSION

In light of the above, the results obtained in the current study might suggest potential candidate genes for the regulation of milk production traits in the sheep mammary gland. Further studies focusing on elucidating the genetic mechanisms affected by the identified DMRs may help to better understand the biological mechanisms modified in the mammary gland of dairy sheep as a response to nutritional challenges and their potential effects on milk production.

Transcriptome analysis of perirenal fat from Spanish Assaf suckling lamb carcasses showing different levels of kidney knob and channel fat

Introduction

Suckling lamb meat is highly appreciated in European Mediterranean countries because of its mild flavor and soft texture. In suckling lamb carcasses, perirenal and pelvic fat depots account for a large fraction of carcass fat accumulation, and their proportions are used as an indicator of carcass quality.

Material and Methods

This study aimed to characterize the genetic mechanisms that regulate fat deposition in suckling lambs by evaluating the transcriptomic differences between Spanish Assaf lambs with significantly different proportions of kidney knob and channel fat (KKCF) depots in their carcasses (4 High-KKCF lambs vs. 4 Low-KKCF lambs).

Results

The analyzed fat tissue showed overall dominant expression of white adipose tissue gene markers, although due to the young age of the animals (17-36 days), the expression of some brown adipose tissue gene markers (e.g., UCP1, CIDEA) was still identified. The transcriptomic comparison between the High-KKCF and Low-KKCF groups revealed a total of 80 differentially expressed genes (DEGs). The enrichment analysis of the 49 DEGs with increased expression levels in the Low-KKCF lambs identified significant terms linked to the biosynthesis of lipids and thermogenesis, which may be related to the higher expression of the UCP1 gene in this group. In contrast, the enrichment analysis of the 31 DEGs with increased expression in the High-KKCF lambs highlighted angiogenesis as a key biological process supported by the higher expression of some genes, such as VEGF-A and THBS1, which encode a major angiogenic factor and a large adhesive extracellular matrix glycoprotein, respectively.

Discussion

The increased expression of sestrins, which are negative regulators of the mTOR complex, suggests that the preadipocyte differentiation stage is being inhibited in the High-KKCF group in favor of adipose tissue expansion, in which vasculogenesis is an essential process. All of these results suggest that the fat depots of the High-KKCF animals are in a later stage of development than those of the Low-KKCF lambs. Further genomic studies based on larger sample sizes and complementary analyses, such as the identification of polymorphisms in the DEGs, should be designed to confirm these results and achieve a deeper understanding of the genetic mechanisms underlying fat deposition in suckling lambs.

Influence of a temporary restriction of dietary protein in prepubertal ewe lambs on first lactation milk traits and response to a mammary gland inflammatory challenge

This study evaluated the influence of a temporary nutritional protein restriction (NPR) performed, under commercial conditions, in prepubertal female lambs on first lactation milk production traits and the inflammatory response triggered by an inflammatory challenge of the. From 40 Assaf female lambs, we defined a control group (Cn = 20), which received a standard diet for replacement lambs and the NPR group (n = 20), which received the same diet but without soybean meal between 3 and 5 months of age. About 150 days after lambing, 24 of these ewes (13 NPR, 11C) were subjected to an intramammary infusion of E. coli lipopolysaccharide (LPS). Our dynamic study identified indicator traits of local (SCC) and systemic (rectal T^a, IL-6, CXCL8, IL-10, IL-36RA, VEGF-A) response to the LPS challenge. The NPR did not show significant effects on milk production traits and did not affect the SCC and rectal T^a after the LPS challenge. However, the NPR had a significant influence on 8 of the 14 plasma biomarkers analysed, in all the cases with higher relative values in the C group. The effects observed on VEGF-A (involved in vasculogenesis during mammary gland development and vascular permeability) and IL-10 (a regulatory cytokine classically known by its anti-inflammatory action) are the most remarkable to explain the differences found between groups. Whereas further studies should be undertaken to confirm these results, our findings are of interest considering the current concern about the future world's demand for protein and the need for animal production systems to evolve toward sustainability.

Limits to Gauge Coupling in the Dark Sector Set by the Nonobservation of Instanton-Induced Decay of Super-Heavy Dark Matter in the Pierre Auger Observatory Data

Instantons, which are nonperturbative solutions to Yang-Mills equations, provide a signal for the occurrence of quantum tunneling between distinct classes of vacua. They can give rise to decays of particles otherwise forbidden. Using data collected at the Pierre Auger Observatory, we search for signatures of such instanton-induced processes that would be suggestive of super-heavy particles decaying in the Galactic halo. These particles could have been produced during the post-inflationary epoch and match the relic abundance of dark matter inferred today. The nonobservation of the signatures searched for allows us to derive a bound on the reduced coupling constant of gauge interactions in the dark sector: α_{X}≲0.09, for 10^{9}≲M_{X}/GeV<10^{19}. Conversely, we obtain that, for instance, a reduced coupling constant α_{X}=0.09 excludes masses M_{X}≳3×10^{13}  GeV. In the context of dark matter production from gravitational interactions alone, we illustrate how these bounds are complementary to those obtained on the Hubble rate at the end of inflation from the nonobservation of tensor modes in the cosmological microwave background.

Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms

Wallachian and Sumava sheep are autochthonous breeds that have undergone a significant bottleneck effect and subsequent restoration efforts. The first objective of this study was to evaluate the degree of genetic variability of both breeds and, therefore, the current management of the breeding. The second was to determine whether these two breeds still retain their genetic uniqueness in relation to each other and other breeds, despite regenerative interventions. Our data consisted of 48 individuals of Sumava and 37 individuals of Wallachian sheep. The comparison data contained 25 other breeds (primarily European) from the HapMap dataset generated by the International Sheep Genomics Consortium. When comparing all 27 breeds, the Czech breeds clustered with 15 other breeds and formed a single branch with them according to Nei's distances. At the same time, however, the clusters of both breeds were integral and easily distinguishable from the others when displayed with principal component analysis (PCA). Population substructure analysis did not show any common genetic ancestry of the Czech national breeds and breeds used for regeneration or, eventually, breeds whose ancestral population was used for regeneration. The average values of F_ST were higher in Wallachian sheep (F_ST = 0.14) than in Sumava sheep (F_ST = 0.08). The linkage disequilibrium (LD) extension per autosome was higher in Wallachian than in Sumava sheep. Consequently, the N_e estimates five generations ago were 68 for Sumava versus 34 for Wallachian sheep. Both native Czech breeds exhibit a wide range of inbreeding based on the excess of homozygosity (F_HOM) among individuals, from -0.04 to 0.16 in Sumava and from -0.13 to 0.12 in Wallachian. Average inbreeding based on runs of homozygosity was 0.21 in Sumava and 0.27 in Wallachian. Most detected runs of homozygosity (ROH) were less than 5 Mb long for both breeds. ROH segments longer than 15 Mb were absent in Wallachian sheep. Concerning putative selection signatures, a total of 471 candidate genes in Wallachian sheep within 11 hotspots and 653 genes within 13 hotspots in Sumava sheep were identified. Czech breeds appear to be well differentiated from each other and other European breeds. Their genetic diversity is low, especially in the case of the Wallachian breed. Sumava is not so threatened by low diversity but has a larger share of the non-native gene pool.

Low-density SNP panel for efficient imputation and genomic selection of milk production and technological traits in dairy sheep

The present study aimed to ascertain how different strategies for leveraging genomic information enhance the accuracy of estimated breeding values for milk and cheese-making traits and to evaluate the implementation of a low-density (LowD) SNP chip designed explicitly for that aim. Thus, milk samples from a total of 2,020 dairy ewes from 2 breeds (1,039 Spanish Assaf and 981 Churra) were collected and analyzed to determine 3 milk production and composition traits and 2 traits related to milk coagulation properties and cheese yield. The 2 studied populations were genotyped with a customized 50K Affymetrix SNP chip (Affymetrix Inc.) containing 55,627 SNP markers. The prediction accuracies were obtained using different multitrait methodologies, such as the BLUP model based on pedigree information, the genomic BLUP (GBLUP), and the BLUP at the SNP level (SNP-BLUP), which are based on genotypic data, and the single-step GBLUP (ssGBLUP), which combines both sources of information. All of these methods were analyzed by cross-validation, comparing predictions of the whole population with the test population sets. Additionally, we describe the design of a LowD SNP chip (3K) and its prediction accuracies through the different methods mentioned previously. Furthermore, the results obtained using the LowD SNP chip were compared with those based on the 50K SNP chip data sets. Finally, we conclude that implementing genomic selection through the ssGBLUP model in the current breeding programs would increase the accuracy of the estimated breeding values compared with the BLUP methodology in the Assaf (from 0.19 to 0.39) and Churra (from 0.27 to 0.44) dairy sheep populations. The LowD SNP chip is cost-effective and has proven to be an accurate tool for estimating genomic breeding values for milk and cheese-making traits, microsatellite imputation, and parentage verification. The results presented here suggest that the routine use of this LowD SNP chip could potentially increase the genetic gains of the breeding selection programs of the 2 Spanish dairy sheep breeds considered here.

Describing post-polio syndrome

INTRODUCTION

Patients presenting sequelae of poliomyelitis may present new symptoms, known as post-polio syndrome (PPS).

OBJECTIVE

To identify the clinical and functional profile and epidemiological characteristics of patients presenting PPS.

PATIENTS AND METHODS

We performed a retrospective study of 400 patients with poliomyelitis attended at the Institut Guttmann outpatient clinic, of whom 310 were diagnosed with PPS. We describe patients' epidemiological, clinical, and electromyographic variables and analyse the relationships between age of poliomyelitis onset and severity of the disease, and between sex, age of PPS onset, and the frequency of symptoms.

RESULTS

PPS was more frequent in women (57.7%). The mean age at symptom onset was 52.4 years, and was earlier in women. Age at primary infection >2 years was not related to greater poliomyelitis severity. The frequency of symptoms was: pain in 85% of patients, loss of strength in 40%, fatigue in 65.5%, tiredness in 57.8%, cold intolerance in 20.2%, dysphagia in 11.7%, cognitive complaints in 9%, and depressive symptoms in 31.5%. Fatigue, tiredness, depression, and cognitive complaints were significantly more frequent in women. Fifty-nine percent of patients presented electromyographic findings suggestive of PPS.

CONCLUSIONS

While the symptoms observed in our sample are similar to those reported in the literature, the frequencies observed are not. We believe that patients' clinical profile may be very diverse, giving more weight to such objective parameters as worsening of symptoms or appearance of weakness; analysis of biomarkers may bring us closer to an accurate diagnosis.

Study on the concordance between different SNP-genotyping platforms in sheep

Different SNP genotyping technologies are commonly used in multiple studies to perform QTL detection, genotype imputation, and genomic predictions. Therefore, genotyping errors cannot be ignored, as they can reduce the accuracy of different procedures applied in genomic selection, such as genomic imputation, genomic predictions, and false-positive results in genome-wide association studies. Currently, whole-genome resequencing (WGR) also offers the potential for variant calling analysis and high-throughput genotyping. WGR might overshadow array-based genotyping technologies due to the larger amount and precision of the genomic information provided; however, its comparatively higher price per individual still limits its use in larger populations. Thus, the objective of this work was to evaluate the accuracy of the two most popular SNP-chip technologies, namely, Affymetrix and Illumina, for high-throughput genotyping in sheep considering high-coverage WGR datasets as references. Analyses were performed using two reference sheep genome assemblies, the popular Oar_v3.1 reference genome and the latest available version Oar_rambouillet_v1.0. Our results demonstrate that the genotypes from both platforms are suggested to have high concordance rates with the genotypes determined from reference WGR datasets (96.59% and 99.51% for Affymetrix and Illumina technologies, respectively). The concordance results provided in the current study can pinpoint low reproducible markers across multiple platforms used for sheep genotyping data. Comparing results using two reference genome assemblies also informs how genome assembly quality can influence genotype concordance rates among different genotyping platforms. Moreover, we describe an efficient pipeline to test the reliability of markers included in sheep SNP-chip panels against WGR datasets available on public databases. This pipeline may be helpful for discarding low-reliability markers before exploiting genomic information for gene mapping analyses or genomic prediction.

Genome-wide association studies (GWAS) and post-GWAS analyses for technological traits in Assaf and Churra dairy breeds

This study aimed to perform a GWAS to identify genomic regions associated with milk and cheese-making traits in Assaf and Churra dairy sheep breeds; second, it aimed to identify possible positional and functional candidate genes and their interactions through post-GWAS studies. For 2,020 dairy ewes from 2 breeds (1,039 Spanish Assaf and 981 Churra), milk samples were collected and analyzed to determine 6 milk production and composition traits and 6 traits related to milk coagulation properties and cheese yield. The genetic profiles of the ewes were obtained using a genotyping chip array that included 50,934 SNP markers. For both milk and cheese-making traits, separate single-breed GWAS were performed using GCTA software. The set of positional candidate genes identified via GWAS was subjected to guilt-by-association-based prioritization analysis with ToppGene software. Totals of 84 and 139 chromosome-wise significant associations for the 6 milk traits and the 6 cheese-making traits were identified in this study. No significant SNPs were found in common between the 2 studied breeds, possibly due to their genetic heterogeneity of the phenotypes under study. Additionally, 63 and 176 positional candidate genes were located in the genomic intervals defined as confidence regions in relation to the significant SNPs identified for the analyzed traits for Assaf and Churra breeds. After the functional prioritization analysis, 71 genes were identified as promising positional and functional candidate genes and proposed as targets of future research to identify putative causative variants in relation to the traits under examination. In addition, this multitrait study allowed us to identify variants that have a pleiotropic effect on both milk production and cheese-related traits. The incorporation of variants among the proposed functional and positional candidate genes into genomic selection strategies represent an interesting approach for achieving rapid genetic gains, specifically for those traits difficult to measure, such as cheese-making traits.

Measurement of the Fluctuations in the Number of Muons in Extensive Air Showers with the Pierre Auger Observatory

We present the first measurement of the fluctuations in the number of muons in extensive air showers produced by ultrahigh energy cosmic rays. We find that the measured fluctuations are in good agreement with predictions from air shower simulations. This observation provides new insights into the origin of the previously reported deficit of muons in air shower simulations and constrains models of hadronic interactions at ultrahigh energies. Our measurement is compatible with the muon deficit originating from small deviations in the predictions from hadronic interaction models of particle production that accumulate as the showers develop.

A multiple-phenotype imputation procedure as a method for prediction of cheese-making efficiency in Spanish Assaf sheep

Sheep milk is mainly intended to manufacture a wide variety of high-quality cheeses. The ovine cheese industry would benefit from an improvement, through genetic selection, of traits related to the milk coagulation properties (MCPs) and cheese yield-related traits, broadly denoted as "cheese-making traits." Considering that routine measurements of these traits needed for genetic selection are expensive and time-consuming, this study aimed to evaluate the accuracy of a cheese-making phenotype imputation method based on the information from official milk control records combined with the pH of the milk. For this study, we analyzed records of milk production traits, milk composition traits, and measurements of cheese-making traits available from a total of 1,145 dairy ewes of the Spanish Assaf sheep breed. Cheese-making traits included five related to the MCPs and two cheese yield-related traits. The milk and cheese-making phenotypes were adjusted for significant effects based on a general linear model. The adjusted phenotypes were used to define a multiple-phenotype imputation procedure for the cheese-making traits based on multivariate normality and Markov chain Monte Carlo sampling. Five of the seven cheese-making traits considered in this study achieved a prediction accuracy of 0.60 computed as the correlation between the adjusted phenotypes and the imputed phenotypes. Particularly the logarithm of curd-firming time since rennet addition (logK20) (0.68), which has been previously suggested as a potential candidate trait to improve the cheese ability in this breed, and the logarithm of the ratio between the rennet clotting time and the curd firmness at 60 min (logRCT/A60) (0.65), which has been defined by other studies as an indicator trait of milk coagulation efficiency. This study represents a first step toward the possible use of the phenotype imputation of cheese-making traits to develop a practical methodology for the dairy sheep industry to impute cheese-making traits only based on the analysis of a milk sample without the need of pedigree information. This information could be also used in future planning of specific breeding programs considering the importance of the cheese-making efficiency in dairy sheep and highlights the potential of phenotype imputation to leverage sample size on expensive, hard-to-measure phenotypes.

Estimation of genetic parameters for cheese-making traits in Spanish Churra sheep

The global production of sheep milk is growing, and the main industrial use of sheep milk is cheese making. The Spanish Churra sheep breed is one of the most important native dairy breeds in Spain. The present study aimed to estimate genetic parameters for a wide range of traits influencing the cheese-making ability of Churra sheep milk. Using a total of 1,049 Churra ewes, we studied the following cheese-making traits: 4 traits related to milk coagulation properties (rennet coagulation time, curd-firming time, and curd firmness at 30 and 60 min after addition of rennet), 2 traits related to cheese yield (individual laboratory cheese yield and individual laboratory dried curd yield), and 3 traits measuring curd firmness over time (maximum curd firmness, time to attain maximum curd firmness, and syneresis). In addition, a list of milk traits, including the native pH of the milk and several milk production and composition traits (milk yield; the fat, protein, and dried extract percentages; and the somatic cell count), were also analyzed for the studied animals. After discarding the noncoagulating samples (only 3.7%), data of 1,010 ewes were analyzed with multiple-trait animal models by using the restricted maximum likelihood method to estimate (co)variance components, heritabilities, and genetic correlations. In general, the heritability estimates were low to moderate, ranging from 0.08 (for the individual laboratory dried curd yield trait) to 0.42 (for the fat percentage trait). High genetic correlations were found within pairs of related traits (i.e., 0.93 between fat and dried extract percentages, -0.93 between the log of the curd-firming time and curd firmness at 30 min, 0.70 between individual laboratory cheese yield and individual laboratory dried curd yield, and -0.94 between time to attain maximum curd firmness and syneresis). Considering all the information provided here, we suggest that in addition to the current consideration of the protein percentage trait for improving cheese yield traits, the inclusion of the pH of milk as a measured trait in the Churra dairy breeding program would represent an efficient strategy for improving the cheese-making ability of milk from this breed.

Features of the Energy Spectrum of Cosmic Rays above 2.5×10^{18} eV Using the Pierre Auger Observatory

We report a measurement of the energy spectrum of cosmic rays above 2.5×10^{18}  eV based on 215 030 events. New results are presented: at about 1.3×10^{19}  eV, the spectral index changes from 2.51±0.03(stat)±0.05(syst) to 3.05±0.05(stat)±0.10(syst), evolving to 5.1±0.3(stat)±0.1(syst) beyond 5×10^{19}  eV, while no significant dependence of spectral features on the declination is seen in the accessible range. These features of the spectrum can be reproduced in models with energy-dependent mass composition. The energy density in cosmic rays above 5×10^{18}  eV is [5.66±0.03(stat)±1.40(syst)]×10^{53}  erg Mpc^{-3}.

The Milk Microbiota of the Spanish Churra Sheep Breed: New Insights into the Complexity of the Milk Microbiome of Dairy Species

Simple Summary

In the last decade, the number of studies focused on the study of the microbiota of different tissues, organs, or physiological fluids has considerably increased. The milk of dairy species is an important and continuous source of commensal, mutualistic and potentially probiotic bacteria. Second-generation sequencing technologies have been applied to characterise the milk microbiota of dairy cows, whereas the study of the sheep milk microbiota is scarce. In the present study, we aimed to explore the bacterial diversity and composition of milk samples from the Churra sheep breed, a rustic autochthonous breed from the region of Castilla y León (Spain). Moreover, this study tries to clarify the complex bacterial composition of sheep milk comparing the results presented here with previous research on the milk microbiota of the Assaf sheep breed. This assessment has shown that the milk microbiota of ewes from one flock of the Assaf breed is more diverse than the milk microbiota reported here for two different flocks of Churra sheep. The study also provides a step into a better understanding of the link between the bacterial milk composition in these two sheep breeds and somatic cell count, an indicator trait of subclinical mastitis resistance in dairy sheep.

Abstract

Milk from healthy animals has classically been considered a sterile fluid. With the development of massively parallel sequencing and its application to the study of the microbiome of different body fluids, milk microbiota has been documented in several animal species. In this study, the main objective of this work was to access bacterial profiles of healthy milk samples using the next-generation sequencing of amplicons from the 16S rRNA gene to characterise the milk microbiome of the Churra breed. A total of 212 samples were collected from two Churra dairy farms with a different management system. The core milk microbiota in Churra ewes includes lesser genera (only two taxa: Staphylococcus and Escherichia/Shigella) than studies reported in other dairy species or even in a previous study in Assaf sheep milk. We found that diversity values in the two flocks of Churra breed were lower than the diversity of the milk microbiota in Assaf. The non-metric multidimensional scaling (NMDS) ordination using Bray-Curtis distance separates samples based on their microbiota composition. The information reported here might be used to understand the complex issue of milk microbiota composition.

Public health impact and treatment of insomnia

A growing number of people are concerned about their sleep in the United States. There are an estimated 40 million US citizens with chronic sleep disorders. The cost to society of sleep disorders has been estimated at greater than $90 billion US dollars. Despite this enormous cost to society, there remains a pervasive lack of attention provided to medical management of this problem. This is compounded by inadequate funding of sleep disorders research. There are treatments available to improve insomnia. These include different behavioral and pharmacologic regimes that can be used separately or in combination. Successful treatment requires thorough knowledge of the differential diagnosis of insomnia. The greatest public health challenge in the management of insomnia is how to develop effective educational programs that will allow the general public to improve their sleep. This will require greater cooperation from primary care providers and the government. Sleep disorders are the most important public health problem not being addressed in the United States.

Extended gamma-ray sources around pulsars constrain the origin of the positron flux at Earth

The unexpectedly high flux of cosmic-ray positrons detected at Earth may originate from nearby astrophysical sources, dark matter, or unknown processes of cosmic-ray secondary production. We report the detection, using the High-Altitude Water Cherenkov Observatory (HAWC), of extended tera-electron volt gamma-ray emission coincident with the locations of two nearby middle-aged pulsars (Geminga and PSR B0656+14). The HAWC observations demonstrate that these pulsars are indeed local sources of accelerated leptons, but the measured tera-electron volt emission profile constrains the diffusion of particles away from these sources to be much slower than previously assumed. We demonstrate that the leptons emitted by these objects are therefore unlikely to be the origin of the excess positrons, which may have a more exotic origin.

Identification of a new Y chromosome haplogroup in Spanish native cattle

The aim of this work was to perform a thorough analysis of the diversity of Y-haplotypes in Spanish cattle. A total of 207 Bos taurus males were sampled across 25 European breeds, with a special focus on rare, local Spanish populations. Animals were genotyped with five Y-specific microsatellites (INRA189, UMN0103, UMN0307, BM861 and BYM1), two indels (ZFY10 and USP9Y) and one SNP (UTY19). A new haplogroup, distinct from those described by Götherström et al. (2005), was identified and named Y1.2. Samples representing the three B. taurus Y-haplogroups were genotyped for four additional Y chromosome SNPs (rs121919254, rs121919281, rs121919323 and rs137049553). Among these SNPs, only rs121919281 was informative in B. taurus and helped to confirm the new Y1.2 haplogroup. Analysis of a larger dataset of standardized haplotypes for 1507 individuals from 57 populations from Spain, other European countries and Africa showed the new Y1.2 haplogroup to be found exclusively in Spanish breeds. This finding reinforces the importance of local Spanish cattle as reservoirs of genetic diversity as well as the importance of the Iberian Peninsula in the history of cattle.

Testing Hadronic Interactions at Ultrahigh Energies with Air Showers Measured by the Pierre Auger Observatory

Ultrahigh energy cosmic ray air showers probe particle physics at energies beyond the reach of accelerators. Here we introduce a new method to test hadronic interaction models without relying on the absolute energy calibration, and apply it to events with primary energy 6-16 EeV (E_{CM}=110-170  TeV), whose longitudinal development and lateral distribution were simultaneously measured by the Pierre Auger Observatory. The average hadronic shower is 1.33±0.16 (1.61±0.21) times larger than predicted using the leading LHC-tuned models EPOS-LHC (QGSJetII-04), with a corresponding excess of muons.

Measurement of the Radiation Energy in the Radio Signal of Extensive Air Showers as a Universal Estimator of Cosmic-Ray Energy

We measure the energy emitted by extensive air showers in the form of radio emission in the frequency range from 30 to 80 MHz. Exploiting the accurate energy scale of the Pierre Auger Observatory, we obtain a radiation energy of 15.8±0.7(stat)±6.7(syst)  MeV for cosmic rays with an energy of 1 EeV arriving perpendicularly to a geomagnetic field of 0.24 G, scaling quadratically with the cosmic-ray energy. A comparison with predictions from state-of-the-art first-principles calculations shows agreement with our measurement. The radiation energy provides direct access to the calorimetric energy in the electromagnetic cascade of extensive air showers. Comparison with our result thus allows the direct calibration of any cosmic-ray radio detector against the well-established energy scale of the Pierre Auger Observatory.

Behavioural linear standardized scoring system of the Lidia cattle breed by testing in herd: estimation of genetic parameters

Docility is very important for cattle production, and many behavioural tests to measure this trait have been developed. However, very few objective behavioural tests to measure the opposite approach 'aggressive behaviour' have been described. Therefore, the aim of this work was to validate in the Lidia cattle breed a behavioural linear standardized scoring system that measure the aggressiveness and enable genetic analysis of behavioural traits expressing fearless and fighting ability. Reproducibility and repeatability measures were calculated for the 12 linear traits of this scoring system to assess its accuracy, and ranged from 85.3 and 94.2%, and from 66.7 to 97.9%, respectively. Genetic parameters were estimated using an animal model with a Bayesian approach. A total of 1202 behavioural records were used. The pedigree matrix contained 5001 individuals. Heritability values (with standard deviations) ranged between 0.13 (0.04) (Falls of the bull) and 0.41 (0.08) (Speed of approach to horse). Genetic correlations varied from 0.01 (0.07) to 0.90 (0.13). Finally, an exploratory factor analysis using the genetic correlation matrix was calculated. Three main factors were retained to describe the traditional genetic indexes aggressiveness, strength and mobility.

Search for patterns by combining cosmic-ray energy and arrival directions at the Pierre Auger Observatory

Energy-dependent patterns in the arrival directions of cosmic rays are searched for using data of the Pierre Auger Observatory. We investigate local regions around the highest-energy cosmic rays with [Formula: see text] eV by analyzing cosmic rays with energies above [Formula: see text] eV arriving within an angular separation of approximately 15[Formula: see text]. We characterize the energy distributions inside these regions by two independent methods, one searching for angular dependence of energy-energy correlations and one searching for collimation of energy along the local system of principal axes of the energy distribution. No significant patterns are found with this analysis. The comparison of these measurements with astrophysical scenarios can therefore be used to obtain constraints on related model parameters such as strength of cosmic-ray deflection and density of point sources.

Contribution of Lidia cattle breed historical castes to the paternal genetic stock of Spain

The main objective of this work was to determine whether the five founding castes defined in the Lidia cattle breed actually have an important contribution to the Spanish paternal genetic stock as well as to the paternal genetic origin support. A total of 1300 Bos taurus male individuals were genotyped for five microsatellites (INRA189, UMN0103, UMN0307, BM861 and BYM1) and one indel (ZFY10). Microsatellite and indel alleles were combined into haplotypes, identifying a total of 38 haplotypes, 11 of them belonging to haplogroup Y1 and 27 to haplogroup Y2. Ten different haplotypes were found in the Lidia cattle breed, with five being exclusive to this breed. Our results agree with different male genetic stocks in the Lidia breed: one hypothetically representing the ancient Iberian bovine genetic stock (Gallardo, Navarra and Cabrera castes and some encastes from Vistahermosa) and a second one that is the result of the more recent breeding strategy of choosing the most aggressive individuals from traditional herds (including some Vistahermosa encastes and the Vazqueña caste). In terms of conservation, it would be better to not consider this breed as a unit but to consider the caste, or even better the encaste, as the target of putative conservation efforts.

Measurement of the proton-air cross section at √s=57 TeV with the Pierre Auger Observatory

We report a measurement of the proton-air cross section for particle production at the center-of-mass energy per nucleon of 57 TeV. This is derived from the distribution of the depths of shower maxima observed with the Pierre Auger Observatory: systematic uncertainties are studied in detail. Analyzing the tail of the distribution of the shower maxima, a proton-air cross section of [505±22(stat)(-36)(+28)(syst)] mb is found.

Referred sensations and neuropathic pain following spinal cord injury

It has been proposed that painful and non-painful referred sensations (RSs) are associated with reorganization of sensory pathways in patients with complete spinal cord injury (SCI). In order to investigate the referred sensation (RS) phenomenon and its correlation with neuropathic pain (NP) 48 patients with complete SCI, 24 with chronic NP and 24 without pain or paraesthesias were studied using clinical examination and neurophysiological tests. Patients reporting RSs were re-examined at 2 and 10weeks after the first examination. We defined the presence of RS as sensations perceived below the injury level in response to touch and pinprick stimuli in various body points above the injury level. The examination was carried out by one researcher applying the stimuli to the patient under two visual conditions (open and closed eyes), and then asking the patient to make tactile self-stimulation. Seven patients with SCI and NP (29%) reported RS below the injury level. RS were well located and consistently evoked at repeated examinations. Touch and pinprick stimulation elicited similar RS that were non-painful in six patients and painful in one. Visual feedback did not change RS perception and characteristics. None of the patients in the SCI group without NP presented RS. In conclusion, our results indicate that RS is relatively frequent in patients with complete SCI and NP. The common occurrence of RS in patients with NP and the location of the sensations in the same area as NP suggest that pain and RS share common pathophysiological mechanisms.

Measurement of the depth of maximum of extensive air showers above 10{18} eV

We describe the measurement of the depth of maximum, X{max}, of the longitudinal development of air showers induced by cosmic rays. Almost 4000 events above 10;{18} eV observed by the fluorescence detector of the Pierre Auger Observatory in coincidence with at least one surface detector station are selected for the analysis. The average shower maximum was found to evolve with energy at a rate of (106{-21}{+35}) g/cm{2}/decade below 10{18.24+/-0.05} eV, and (24+/-3) g/cm{2}/decade above this energy. The measured shower-to-shower fluctuations decrease from about 55 to 26 g/cm{2}. The interpretation of these results in terms of the cosmic ray mass composition is briefly discussed.

Do multimodal evoked potentials add information to MRI in clinically isolated syndromes?

The role of multimodal evoked potentials (MMEPs) in establishing multiple sclerosis (MS) diagnosis and prognosis has diminished nowadays. The objective of this article is to evaluate whether MMEPs add information to MRI in identifying patients with higher risk of relapse or development of disability after a clinically isolated syndrome (CIS). Patients who underwent visual, somato-sensory and brainstem auditory evoked potentials (EPs) were identified from a cohort of consecutive CIS. Patients also underwent brain MRI within 3 months of first attack. We analysed time to second attack and to Expanded Disability Status Scale (EDSS) score of 3.0 according to number of Barkhof criteria and number of abnormal MMEPs. A complete study was performed in 245 patients who were followed for a mean of 76.4 months (interquartile range: 61 to 96). Seventy-one patients (29%) had the three EPs normal, 115 patients (47%) had one abnormal EP; 40 patients (16%) had two; and 19 patients (8%) had three abnormal EPs. Baseline MRI determined the risk for converting to clinically definite MS and correlated with disability according to previous studies. EPs individually did not modify the risk of conversion or disability. However, the presence of three abnormal EPs increased the risk of reaching moderate disability (hazard ratio 7.0; 1.4—34.9) independently of baseline MRI. In conclusion, in the presence of three abnormal EPs could help identify CIS patients with a higher risk of developing disability, independently of MRI findings. However, the utility of MMEPs is limited by the low percentage of CIS patients having the three abnormal at baseline.

Observation of the suppression of the flux of cosmic rays above 4 x 10 (19) eV

The energy spectrum of cosmic rays above 2.5 x 10;{18} eV, derived from 20,000 events recorded at the Pierre Auger Observatory, is described. The spectral index gamma of the particle flux, J proportional, variantE;{-gamma}, at energies between 4 x 10;{18} eV and 4 x 10;{19} eV is 2.69+/-0.02(stat)+/-0.06(syst), steepening to 4.2+/-0.4(stat)+/-0.06(syst) at higher energies. The hypothesis of a single power law is rejected with a significance greater than 6 standard deviations. The data are consistent with the prediction by Greisen and by Zatsepin and Kuz'min.

Upper limit on the diffuse flux of ultrahigh energy tau neutrinos from the Pierre Auger Observatory

The surface detector array of the Pierre Auger Observatory is sensitive to Earth-skimming tau neutrinos that interact in Earth's crust. Tau leptons from nu(tau) charged-current interactions can emerge and decay in the atmosphere to produce a nearly horizontal shower with a significant electromagnetic component. The data collected between 1 January 2004 and 31 August 2007 are used to place an upper limit on the diffuse flux of nu(tau) at EeV energies. Assuming an E(nu)(-2) differential energy spectrum the limit set at 90% C.L. is E(nu)(2)dN(nu)(tau)/dE(nu)<1.3 x 10(-7) GeV cm(-2) s(-1) sr(-1) in the energy range 2 x 10(17) eV< E(nu)< 2 x 10(19) eV.

Do oligoclonal bands add information to MRI in first attacks of multiple sclerosis?

BACKGROUND

To evaluate whether oligoclonal bands (OB) add information to MRI in predicting both a second attack and development of disability in patients with clinically isolated syndromes (CIS).

METHODS

From 1995 to 2006, 572 patients with CIS were included in a prospective study. Patients underwent brain MRI and determination of OB within 3 months of first attack. The number and location of lesions and presence of OB were studied. We analyzed time to second attack and to Expanded Disability Status Scale 3.0 according to number of Barkhof criteria (BC) and the presence or absence of OB.

RESULTS

We studied 415 (73%) patients with CIS with both baseline MRI and determination of OB. Patients were followed for a mean of 50 months (SD 31). Compared to the reference group with 0 BC at baseline MRI, patients with one to two BC showed a hazard ratio (HR) for conversion to CDMS of 3.8 (2.0 to 7.2) and patients with three to four BC of 8.9 (4.8 to 16.4). Of the total cohort, OB were positive in 61% of the patients. However, broken down by MRI group, OB were positive in 31% of those with no BC; 69% of those with one to two BC; and 85% of those with three or four BC. The presence of OB increased the risk of a second relapse (HR 1.7; 1.1 to -2.7) independently of baseline MRI but did not modify the development of disability.

CONCLUSIONS

Presence of oligoclonal bands doubles the risk for having a second attack, independently of MRI, but does not seem to influence the development of disability.

Polyregional and hemispheric syndromes: a study of these uncommon first attacks in a CIS cohort

Clinically isolated syndromes (CIS) classically refer to optic neuritis (ON), brainstem or spinal cord syndromes. Less common first episodes suggestive of central nervous system (CNS) demyelination, such as hemispheric or clinically polyregional syndromes, have been only slightly studied. The aim of this study was to describe these CIS topographies in our cohort of patient with a CIS. We evaluated 320 patients with a CIS, and classified the topographies of the attacks according to clinical symptoms only into CIS of the optic nerve (123), brainstem (78), spinal cord (89), hemispheric (6), polyregional (12) or undetermined (12) topographies. Patients underwent brain MRI within three months of their first attack, and again 12 months later. Conversion to multiple sclerosis (MS), determined either clinically or by magnetic resonance imaging (MRI), was evaluated according to topography. Hemispheric and polyregional syndromes were closer to brainstem or spinal cord syndromes than ON in clinical and MRI conversion terms, although a statistical analysis was not performed because of the small number of patients. There are differences between several studies in the definition, and, therefore, the prevalence of these so-called atypical CIS. Consensus on the denomination and definition of these syndromes must be reached. Multiple Sclerosis 2007; 13: 731-736. http://msj.sagepub.com

Baseline MRI predicts future attacks and disability in clinically isolated syndromes

OBJECTIVE

To determine the relation between baseline MRI and both conversion to multiple sclerosis (MS) and development of disability in a cohort of patients with clinically isolated syndromes (CIS).

METHODS

From 1995 to 1998, 175 consecutive patients with CIS underwent brain MRI within 3 months of their first attack and again 12 months and 5 years later. We studied the number and location of lesions at baseline and development of new T2 lesions. We also analyzed conversion to MS and development of disability (Expanded Disability Status Scale [EDSS] > or = 3.0).

RESULTS

We included 156 patients with CIS followed for a median of 7 years. Compared to the reference group with 0 Barkhof criteria at baseline MRI, patients with one or two Barkhof criteria showed an adjusted hazard ratio (HR) of 6.1 (2.2 to 16.6) and patients with three to four Barkhof criteria of 17.0 (6.7 to 43) for conversion to MS and differentiated patients with low, medium, and high conversion risk. EDSS at year 5 correlated with baseline number of Barkhof criteria (r = 0.46, p < 0.0001). When categorizing by number of baseline lesions, similar results were seen. Patients with a baseline MRI with three to four Barkhof criteria had an adjusted HR of 3.9 (1.1 to 13.6) for reaching EDSS > or = 3.0. Only 10% of the latter had disability at year 5, but 40% reached this at 8 years.

CONCLUSIONS

Baseline MRI determines the risk for converting to clinically definite multiple sclerosis and correlates with disability at 5 years. The proportion of patients developing disability is low during the first 5 years but rapidly increases shortly after.

Sleep-disordered breathing and upper-airway anomalies in first-degree relatives of ALTE children

From 1985 through 1995, 348 infants aged 3 wk-3 mo were referred to the Stanford Sleep Clinic for "apparent life-threatening events" (ALTE). A small group of 48 infants with no history of sleep-disordered breathing (SDB) was also recruited and used as controls (they comprised group C). We conducted a systematic investigation of relatives (parents, siblings, and grandparents) of the infants, including a clinical evaluation, craniofacial investigation, and the completion of an extensive (189-question) validated sleep/wake questionnaire. All data were calculated before the subdivision of ALTE infants into two groups. The subdivision was based on a blind scoring of the infants' polygraphic recordings; 42.5% of the infants were negative for SDB (Group A), whereas 57.5% of the infants were positive for SDB (Group B). Groups A and C were not significantly different from each other. Forty-three percent of the relatives of Group B infants had been treated for SDB (with nasal CPAP, surgical or dental appliance treatments) compared with 7.1% of Group A relatives. Clinical investigation indicated a significantly higher presence of small upper airways in the families of infants with SDB. About twice as many relatives reported the presence of asthma in Group B compared with Group A. Naso-oro-maxillomandibular anatomic traits that may lead to small upper airways in parents may be risk factors for abnormal breathing during sleep in their infants.

Apparent life-threatening events, facial dysmorphia and sleep-disordered breathing

A standardized clinical evaluation and questionnaire was, beginning in 1985, applied to infants referred for an apparent life-threatening event (ALTE). All children who underwent this "core evaluation protocol" during a 10-year period were reviewed. Documentation of clinical complaints, symptoms and signs of sleep-disordered breathing, sleep/wake evaluation, systematic evaluation of the face and naso-oro-pharynx, nocturnal polygraphic recording, and systematic follow-up was conducted. A total of 346 infants had complete data sets, with a smaller group of 46 age-matched healthy infants as controls. A scorer blind to the clinical data analyzed the polygraphic investigation and divided the 346 referred into two groups. Group A, 42.6% of the population, included infants with no abnormal findings based on nocturnal polygraphic recording. These infants were no different from controls at initial evaluation and during follow-up. Group B, 57.4% of the population, included infants who had obstructive breathing during sleep which became more obvious over time. Two-thirds of these infants not only had clinical symptoms of sleep-disordered breathing but also had mild facial dysmorphia that could be seen clearly at 6 months of age.

CONCLUSION

A subgroup of infants with apparent life-threatening events present an indication of a sleep-disordered breathing syndrome which is associated with a mild dysmorphia. This mild facial dysmorphia needs to be recognized early to distinguish these infants from other infants with apparent life-threatening events and to initiate appropriate treatment.

Pediatric sleep-related breathing disorders

Sleep-related breathing disorders (SRBD) can occur at any age. Obstructive sleep apnea, upper airway resistance syndrome and obstructive hypopnea syndrome all lie on the pathological continuum of SRBD. These disorders can have a great impact on a child's quality of life and can progress to significant complications. The symptoms, signs, work-up, and treatment of SRBD in children are discussed.

Narcolepsy in children: a practical guide to its diagnosis, treatment and follow-up

Narcolepsy is a neurological syndrome characterised by daytime somnolence and cataplexy which often begins in childhood. Failing to recognise the condition may lead to mislabelling a child as lazy or depressed. The diagnostic criteria for narcolepsy vary with age. In children 8 years and older a Multiple Sleep Latency Test with an average latency of less than 8 minutes, and 2 or more sleep onset REM episodes supports the diagnosis. Human leucocyte antigen (HLA) marker DQbeta1 -0602 has been associated with narcolepsy. The current evidence supports the hypothesis that transmission of narcolepsy is multifactorial. with at least two genes, one of which is non-HLA related. The goal of all therapeutic approaches in narcolepsy is to control the narcoleptic symptoms and allow the patient to continue to fully participate in personal and academic activities. This usually requires a combination of behavioural therapy along with medication. Medications for patients with excessive sleepiness are usually stimulants, including amphetamines. However, a novel wake promoting agent, modafinil, is now available. Cataplexy can be controlled by medications with noradrenergic reuptake-blocking properties, such as clomipramine and fluoxetine, through their active metabolites. Increased awareness of narcolepsy is important to allow earlier diagnosis. Research on the effects different medications have, specifically on children with narcolepsy, has been very limited.