Genomic predictions based on a joint reference population for the Nordic Red cattle breeds

The main aim of this study was to compare accuracies of imputation and genomic predictions based on single and joint reference populations for Norwegian Red (NRF) and a composite breed (DFS) consisting of Danish Red, Finnish Ayrshire, and Swedish Red. The single nucleotide polymorphism (SNP) data for NRF consisted of 2 data sets: one including 25,000 markers (NRF25K) and the other including 50,000 markers (NRF50K). The NRF25K data set had 2,572 bulls, and the NRF50K data set had 1,128 bulls. Four hundred forty-two bulls were genotyped in both data sets (double-genotyped bulls). The DFS data set (DSF50K) included 50,000 markers of 13,472 individuals, of which around 4,700 were progeny-tested bulls. The NRF25K data set was imputed to 50,000 density using the software Beagle. The average error rate for the imputation of NRF25K decreased slightly from 0.023 to 0.021, and the correlation between observed and imputed genotypes changed from 0.935 to 0.936 when comparing the NRF50K reference and the NRF50K-DFS50K joint reference imputations. A genomic BLUP (GBLUP) model and a Bayesian 4-component mixture model were used to predict genomic breeding values for the NRF and DFS bulls based on the single and joint NRF and DFS reference populations. In the multiple population predictions, accuracies of genomic breeding values increased for the 3 production traits (milk, fat, and protein yields) for both NRF and DFS. Accuracies increased by 6 and 1.3 percentage points, on average, for the NRF and DFS bulls, respectively, using the GBLUP model, and by 9.3 and 1.3 percentage points, on average, using the Bayesian 4-component mixture model. However, accuracies for health or reproduction traits did not increase from the multiple population predictions. Among the 3 DFS populations, Swedish Red gained most in accuracies from the multiple population predictions, presumably because Swedish Red has a closer genetic relationship with NRF than Danish Red and Finnish Ayrshire. The Bayesian 4-component mixture model performed better than the GBLUP model for most production traits for both NRF and DFS, whereas no advantage was found for health or reproduction traits. In general, combining NRF and DFS reference populations was useful in genomic predictions for both the NRF and DFS bulls.

Effects of Clostridium butyricum on growth performance, immune function, and cecal microflora in broiler chickens challenged with Escherichia coli K88

This study was conducted to investigate the effects of Clostridium butyricumon growth performance, immune function, and cecal microflora in broiler chickens challenged with Escherichia coli K88. Three hundred sixty 1-d-old broiler chickens were randomly divided into 4 treatments: negative control (NC) birds were fed a basal diet and not challenged with E. coli K88; positive control (PC) birds were fed a basal diet and challenged with E. coli K88; C. butyricum treatment (CB) birds were fed a diet containing 2 × 10(7) cfu C. butyricum/kg of diet and challenged with E. coli K88; and colistin sulfate treatment (CS) birds were fed a diet containing 20 mg of colistin sulfate/kg of diet and challenged with E. coli K88. Birds fed CB had greater (P < 0.05) BW than the PC birds from 3 to 21 d postchallenge. Birds fed CB had greater (P < 0.05) serum IgA and IgY at 14 d postchallenge, greater (P < 0.05) serum IgM at 21 d postchallenge, and greater (P < 0.05) mucosal secreted IgA at 3 and 7 d postchallenge than the PC birds. Birds fed CB had greater concentrations of serum complement component 3 at 14 d postchallenge, and greater (P < 0.05) concentrations of serum complement component 4 at 3, 7, and 14 d postchallenge than the PC birds. Birds in the CS or CB treatments had less cecal E. coli population at 3, 7, and 21 d postchallenge, and less cecal Clostridium perfringens counts at 21 d postchallenge compared with the PC birds. The CB treatment increased (P < 0.05) the population of cecal Lactobacillus at 3 d postchallenge and the number of cecal Bifidobacterium at 3, 14, and 21 d postchallenge in comparison with the PC treatment. The results indicate that dietary supplementation of CB promotes growth performance, improves immune function, and benefits the cecal microflora in Escherichia coli K88-challenged chickens.

Representation of information about family relatives as structured data in electronic health records

BACKGROUND

The ability to manage and leverage family history information in the electronic health record (EHR) is crucial to delivering high-quality clinical care.

OBJECTIVES

We aimed to evaluate existing standards in representing relative information, examine this information documented in EHRs, and develop a natural language processing (NLP) application to extract relative information from free-text clinical documents.

METHODS

We reviewed a random sample of 100 admission notes and 100 discharge summaries of 198 patients, and also reviewed the structured entries for these patients in an EHR system's family history module. We investigated the two standards used by Stage 2 of Meaningful Use (SNOMED CT and HL7 Family History Standard) and identified coverage gaps of each standard in coding relative information. Finally, we evaluated the performance of the MTERMS NLP system in identifying relative information from free-text documents.

RESULTS

The structure and content of SNOMED CT and HL7 for representing relative information are different in several ways. Both terminologies have high coverage to represent local relative concepts built in an ambulatory EHR system, but gaps in key concept coverage were detected; coverage rates for relative information in free-text clinical documents were 95.2% and 98.6%, respectively. Compared to structured entries, richer family history information was only available in free-text documents. Using a comprehensive lexicon that included concepts and terms of relative information from different sources, we expanded the MTERMS NLP system to extract and encode relative information in clinical documents and achieved a corresponding precision of 100% and recall of 97.4%.

CONCLUSIONS

Comprehensive assessment and user guidance are critical to adopting standards into EHR systems in a meaningful way. A significant portion of patients' family history information is only documented in free-text clinical documents and NLP can be used to extract this information.

Observation of a charged charmoniumlike structure in e+ e- → (D* D*)± π∓ at √s = 4.26 GeV

We study the process e+ e- →(D* D*)± π∓ at a center-of-mass energy of 4.26 GeV using a 827  pb(-1) data sample obtained with the BESIII detector at the Beijing Electron Positron Collider. Based on a partial reconstruction technique, the Born cross section is measured to be (137±9±15)  pb. We observe a structure near the (D* D*)± threshold in the π∓ recoil mass spectrum, which we denote as the Zc±(4025). The measured mass and width of the structure are (4026.3±2.6±3.7)  MeV/c2 and (24.8±5.6±7.7)  MeV, respectively. Its production ratio σ(e+ e- → Zc±(4025)π∓ → (D* D*)± π∓)/σ(e+ e- → (D* D*)± π∓) is determined to be 0.65±0.09±0.06. The first uncertainties are statistical and the second are systematic.

Normative reference of short-term heart rate variability and estimation of cardiovascular autonomic neuropathy prevalence in Chinese people

BACKGROUND

The cardiovascular autonomic neuropathy (CAN) prevalence is rapidly growing in all populations worldwide. This study aimed to evaluate the reference values for the short-term heart rate variable (HRV) and estimate CAN prevalence in our cross-sectional dataset.

METHODS

We conducted a large-scale, community-based, cross-sectional study in a Chinese population. Of 2,092 subjects available for data analysis, 371 healthy subjects were selected to reference the values for the short-term HRV. The short-term HRV analysis was performed for all subjects using a computer-aided examination and evaluation system for spectral analysis to investigate changes in autonomic regulation.

RESULTS

In the total sample, the reference value for total power was more than 356.13 ms(2). The cutoff points of 55.45 and 36.64 ms(2) were set for low frequency (LF) and high frequency (HF), respectively. The cutoff points of LFn and HFn were 6.40 and 4.83 ν, respectively. The normative reference of LF/HF ranged from 0.3 to 6.5. Using HRV test (model 1), the estimated age-adjusted CAN prevalence in the total sample was 16.83 %. The estimated age-adjusted CAN prevalence values were 31.07, 21.97 and 20.81 % in DM, HT, and MS patients, respectively.

CONCLUSION

Our findings provided reference values for short-term HRV. The estimated CAN prevalence was high in the Chinese population.

Observation of e+e- → γX(3872) at BESIII

With data samples collected with the BESIII detector operating at the BEPCII storage ring at center-of-mass energies from 4.009 to 4.420 GeV, the process e+e-→ γX(3872) is observed for the first time with a statistical significance of 6.3σ. The measured mass of the X(3872) is (3871.9 ± 0.7s tat ± 0.2 syst)  MeV/c(2), in agreement with previous measurements. Measurements of the product of the cross section σ[e+e- → γX(3872)] and the branching fraction B[X(3872)→π+π-J/ψ] at center-of-mass energies 4.009, 4.229, 4.260, and 4.360 GeV are reported. Our measurements are consistent with expectations for the radiative transition process Y(4260) → γX(3872).

Search for quantum black hole production in high-invariant-mass lepton+jet final states using pp collisions at √s=8 TeV and the ATLAS detector

This Letter presents a search for quantum black-hole production using 20.3 fb-1 of data collected with the ATLAS detector in pp collisions at the LHC at √s = 8 TeV. The quantum black holes are assumed to decay into a final state characterized by a lepton (electron or muon) and a jet. In either channel, no event with a lepton-jet invariant mass of 3.5 TeV or more is observed, consistent with the expected background. Limits are set on the product of cross sections and branching fractions for the lepton+jet final states of quantum black holes produced in a search region for invariant masses above 1 TeV. The combined 95% confidence level upper limit on this product for quantum black holes with threshold mass above 3.5 TeV is 0.18 fb. This limit constrains the threshold quantum black-hole mass to be above 5.3 TeV in the model considered.

Thermoporometry characterization of silica microparticles and nanowires

We present the results of a systematic study on the porosity of silica microparticles and nanowires prepared by glancing angle deposition-metal-assisted chemical etching (GLAD-MACE) and interference lithography-metal-assisted chemical etching (IL-MACE) techniques using the thermoporometry (TPM) method. Good agreement was obtained between our TPM results and published data provided by the suppliers of silica microparticles. TPM characterization of the GLAD-MACE and IL-MACE nanowires was carried out on the basis of parameters obtained from TPM experiments on microparticles. Our nanowires showed a similar trend but lower values of the pore volume and surface area than nanowires prepared by MACE with AgNO3 solution. We attribute the enhanced bioanalysis performance of the GLAD-MACE nanowires based devices to the increased pore volume and total surface area of the nanowires.

Mutation p.S335X in GATA4 reduces its DNA binding affinity and enhances cell apoptosis associated with ventricular septal defect

Genetic mutations in GATA4, a transcriptional factor, have been found to cause congenital heart diseases. The underlying mechanism, however, remains largely unknown. We previously reported 7 heterozygous variants in patients with ventricular septal defects (VSD). Here we functionally characterized a de novo mutation p.S335X and demonstrated that this mutation led to the pre-termination of its translation, producing a truncated GATA4 lacking a conservative region at C-terminus. Truncated GATA4 did not disturb its subcellular localization; however, it delayed the cardiomyocyte differentiation in P19cl6 model and prohibited Bcl2 expression that led to apoptosis proved by fragmented genomic DNA and positive TUNEL staining in H9C2 cells. By ChIP assay, we showed that GATA4 without C-terminus reduced its DNA binding affinity and suppressed the expressions of its target genes. These findings suggest that C-terminus of GATA4 is critical to maintain DNA binding, and genetic mutations in this region may affect genes important for myocyte apoptosis and differentiation associated with congenital heart defects.

Spectral measurement of electron antineutrino oscillation amplitude and frequency at Daya Bay

A measurement of the energy dependence of antineutrino disappearance at the Daya Bay reactor neutrino experiment is reported. Electron antineutrinos (ν¯(e)) from six 2.9  GW(th) reactors were detected with six detectors deployed in two near (effective baselines 512 and 561 m) and one far (1579 m) underground experimental halls. Using 217 days of data, 41 589 (203 809 and 92 912) antineutrino candidates were detected in the far hall (near halls). An improved measurement of the oscillation amplitude sin(2)2θ(13)=0.090(-0.009)(+0.008) and the first direct measurement of the ν¯(e) mass-squared difference |Δm(ee)2|=(2.59(-0.20)(+0.19))×10(-3)  eV2 is obtained using the observed ν¯(e) rates and energy spectra in a three-neutrino framework. This value of |Δm(ee)2| is consistent with |Δm(μμ)2| measured by muon neutrino disappearance, supporting the three-flavor oscillation model.

Search for dark matter in events with a hadronically decaying W or Z boson and missing transverse momentum in pp collisions at √s=8 TeV with the ATLAS detector

A search is presented for dark matter pair production in association with a W or Z boson in pp collisions representing 20.3  fb(-1) of integrated luminosity at √s=8  TeV using data recorded with the ATLAS detector at the Large Hadron Collider. Events with a hadronic jet with the jet mass consistent with a W or Z boson, and with large missing transverse momentum are analyzed. The data are consistent with the standard model expectations. Limits are set on the mass scale in effective field theories that describe the interaction of dark matter and standard model particles, and on the cross section of Higgs production and decay to invisible particles. In addition, cross section limits on the anomalous production of W or Z bosons with large missing transverse momentum are set in two fiducial regions.

Observation of a charged (DD*)± mass peak in e+ e- → πDD* at sqrt[s] = 4.26 GeV

We report on a study of the process e+ e- → π± (DD*)∓ at sqrt[s] = 4.26  GeV using a 525 pb(-1) data sample collected with the BESIII detector at the BEPCII storage ring. A distinct charged structure is observed in the (DD*)∓ invariant mass distribution. When fitted to a mass-dependent-width Breit-Wigner line shape, the pole mass and width are determined to be Mpole = (3883.9±1.5(stat)±4.2(syst))  MeV/c2 and Γpole = (24.8±3.3(stat)±11.0(syst))  MeV. The mass and width of the structure, which we refer to as Zc(3885), are 2σ and 1σ, respectively, below those of the Zc(3900) → π± J/ψ peak observed by BESIII and Belle in π+ π- J/ψ final states produced at the same center-of-mass energy. The angular distribution of the πZc(3885) system favors a JP = 1+ quantum number assignment for the structure and disfavors 1- or 0-. The Born cross section times the DD* branching fraction of the Zc(3885) is measured to be σ(e+ e- → π± Zc(3885)∓)×B(Zc(3885)∓ → (DD*)∓) = (83.5±6.6(stat)±22.0(syst))   pb. Assuming the Zc(3885) → DD* signal reported here and the Zc(3900) → πJ/ψ signal are from the same source, the partial width ratio (Γ(Zc(3885) → DD*)/Γ(Zc(3900) → πJ/ψ)) = 6.2±1.1(stat)±2.7(syst) is determined.