Body growth, hematological profile, and clinical biochemistry of heifer calves sired by a bull or its clone

The aim of this paper was to compare body growth, hematological profile development, and clinical biochemistry in the female progeny of a sire with the female progeny of its clone. Sixteen Friesian female calves, 9 daughters from a tested bull (BULL) and 7 from its somatic cell nuclear transfer clone (CLONE) were monitored from birth to 60 wk of life. Body weight (BW), wither height (WH), hip height (HH), body length (BL), and hearth girth (HG) were measured at birth and 4, 8, 12, 16, 20, 24, 36, and 50 wk. Blood samples were taken from jugular vein at 12 to 48 h from birth and 1, 2, 3, 4, 8, 12, 16, 20, 24, and 36 wks of age, to be analyzed for hematological, serum protein, and metabolic profiles. At the same time, rectal temperature (RT) was recorded. Age at puberty was assessed on surviving heifers by measuring weekly plasma progesterone levels. Data were evaluated using a mixed model, taking into account the repeated measures in time on the calf. For each variable, different covariance structures were tested, choosing the best according to the Akaike's Information Criteria. Significant was set at P < 0.05, and a trend was considered for P < 0.10. At 24 wk of age, WH was lower in CLONE daughters than BULL daughters. Around 20 wk of age, there was a trend for lower BW in CLONE daughters than BULL daughters, confirmed from differences in HG. There was no difference in RT due to sire effect. Blood glucose concentration decreased in both groups during the first 4 wk of life; at birth, only a trend for higher blood glucose in CLONE daughters was recorded, whereas an opposite trend was observed for plasma creatinine. Total leukocyte count did not differ between progenies. Circulating lymphocytes tended to be lower in CLONE than BULL daughters. The neutrophil: lymphocyte ratio tended to be higher in CLONE than BULL calves. No difference was demonstrated for erythrocyte features, whereas mean platelet volume tended to be lower in CLONE than BULL progeny. From these results, there were no differences between progenies from BULL and its clone that suggest welfare problems in the first 6 mo of life.     

Induced immotility during long-term storage at +5 degrees C does not prolong survival of dog spermatozoa

This study investigated whether the immotility induced by the CLONE chilled semen extender prolongs the lifespan of dog spermatozoa stored at 5 degrees C, compared with a Tris-egg yolk-glucose (TG) extender, which maintains motility. Pooled semen was split in four aliquots, centrifuged, and the four sperm pellets mixed with TG extender; with the CLONE chilled semen (CL) extender; with TG extender mixed with an activator (TG+A(TG)); or with the CLONE extender mixed with the CLONE activator (CL+A(CL)). Samples were stored at 5 degrees C for 23 days and examined 12 times for sperm motility, plasma membrane and acrosome integrity, glucose consumption, and DNA fragmentation index (DFI). The experiment was performed in triplicate. Glucose consumption was not significantly different between extenders until the period 15-23 days, when it was higher in CL and CL+A(CL) than in TG (P=0.0055) and TG+A(TG) (P=0.0010). No breakdown of DNA chromatin (P>0.05) occurred until day 14. Spermatozoa preserved in TG or TG+A(TG) showed better values for all the different parameters throughout the experiment compared with sperm subjected to CL or CL+A(CL). In conclusion, the immotility induced by the CLONE chilled semen extender during long-term cold storage at 5 degrees C did not prolong the lifespan of spermatozoa compared with the lifespan following storage in Tris-egg yolk-glucose. In addition, our results indicate that good quality dog semen may possibly be stored for up to 14 days in TG extender at 5 degrees C, with retained fertilizing capacity. In vivo studies should, however, be performed to further support this conclusion.     

In vitro characteristics of canine spermatozoa subjected to two methods of cryopreservation

The in vitro viability of canine spermatozoa was evaluated after freezing-thawing using the Andersen method, and the commercial CLONE method. These methods differ in the extenders used, number of dilution steps, and equilibration times as well as in both freezing and thawing techniques and rates. Insemination with semen frozen-thawed by either method gives high whelping rates in practice, implying that dog spermatozoa can retain their fertilizing ability after being subjected to widely different preservation methods. The in vitro viability of spermatozoa processed by these methods has not been previously evaluated in detail. Three ejaculates were collected from each of 5 fertile dogs. Each ejaculate was divided into 2 parts and frozen in medium straws according to the 2 methods. Two straws were thawed and examined from each freezing batch. Sperm motility was assessed in the undiluted semen, and in frozen-thawed semen immediately after thawing, and after storage for 3, 6 and 24 h at room temperature (Straw 1) or 1, 2 and 3 h at 37 degrees C (Straw 2, thermoresistance test). The integrity of the sperm plasma membrane was evaluated in undiluted, in equilibrated (diluted and chilled), and in frozen-thawed spermatozoa using fluorophore probes. The acrosome morphology of frozen-thawed spermatozoa was assessed using a commercial stain (Spermac). Motility immediately after thawing was significantly higher with the CLONE method (75.3% [SD = 4.0] for Straw 1 and 73.7% [SD = 3.2] for Straw 2) than with the Andersen method (70.0% [SD = 5.1] and 69.7% [SD = 3.2]). Motility decreased during storage after thawing. Spermatozoa frozen-thawed using the CLONE method showed a significantly lower thermoresistance. The proportion of spermatozoa with intact plasma membrane was not affected by the equilibration procedure used with either method but was significantly decreased (P < 0.001) after thawing with both methods. The percentage of spermatozoa exhibiting changes thought to represent different stages of acrosomal degradation, was 45.7% (SD = 5.3) using the Andersen method and 44.1% (SD = 9,4) using the CLONE method. Both cryopreservation methods thus resulted in high initial post-thaw sperm motility and membrane integrity but low thermoresistance, and under both methods a large proportion of sperm cells were undergoing acrosomal degradation. The methods differed significantly in terms of their effect on sperm motility but not on plasma membrane integrity or acrosomal morphology.     

Plasma estrone sulfate,clinical biochemistry,and milk yield of dairy cows carrying a fetus from a bull or its clone

The aim of this article was to compare plasma estrone sulfate (E₁SO₄), clinical biochemistry, and milk yield of dairy cows carrying a female fetus from a bull (BULL) or from its clone (CLONE), evaluating also the relationship between the former variables and the birth weight of the newborn. Sixteen recipient dairy Friesian heifers (10 BULL and 7 CLONE) received a female embryo, obtained by in vitro embryo production and sexing by polymerase chain reaction with the semen of the BULL or the CLONE. Blood samples on all cows were obtained before feed distribution in the morning from jugular vein from 4 weeks before to 4 weeks after calving, to be analyzed for metabolic profile. The samples from late gestation were also analyzed for E₁SO₄ concentration. To separately assess the effect of calf birth weight (CBW), data were categorized as follows: low (<39 kg; BWT-A), mid (39–46 kg; BWT-B), and high (>46 kg; BWT-C). The plasma concentrations of β-hydroxybutyric acid (BHB, P = 0.019), Na (P = 0.002), Cl (P = 0.026), strong cation–anion balance (P = 0.020), total bilirubin (P = 0.054), and α₁-globulin (P = 0.044) were higher in prepartum BULL recipients than those in CLONE, whereas BHB (P = 0.021) and Mg (P = 0.090) were higher in postpartum BULL recipients, while no differences were recorded in the remaining postpartum parameters. The CBW class had significant interaction with week of gestation on antepartum plasma estrone sulfate (P = 0.021), whereas CBW per se affected antepartum plasma BHB (P = 0.021), and nonesterified fatty acids (NEFA; P = 0.011) being higher in BWT-C which also had the lower NEFA concentration during postpartum. Milk yield was unaffected by the sire used, both for quantitative and qualitative aspects. Cows carrying heavier fetus (BWT-C) had a different lactation affected by month compared with the other 2 CBW groups. From these results, there were no differences between BULL and CLONE recipients. Estrone sulfate, BHB, and NEFA may be used to predict CBW and provide different nutritional management during gestation.     

The dynamics of hemispheric restructuring during human short-term adaptation

In work studied intimate (hidden) mechanism conversion information in the making new adaptive program and evidence role different stage of sleep in this process, which conclude in reorganization information on degree its value for organism. Discovered, that evaluation received information on criterion novelty occur in 2 day, but its selection on criterion emotional (biological) value for organism--in 3 day adaptation. Evaluation novelty realize left hemisphere, but its emotional (biological) value--right hemisphere brain. Reveal functional inequivalence of cerebral hemisphere under adaptation in process emergence creation new program reaction in change condition existence. Herewith left-hemisphere mechanism direct on reproduction already have available program reaction (how genetic bolt, so and newly obtained), but right-hemisphere--on production new adaptive program (perception and conversion enter information).     

Post-thaw evaluation of dog spermatozoa using new triple fluorescent staining and flow cytometry

A new triple fluorescent staining method was developed to evaluate frozen-thawed dog spermatozoa. This method was used to compare functional parameters of canine spermatozoa cryopreserved using 2 different freezing-thawing protocols. One ejaculate from each of 10 dogs was split into 2 aliquots and processed using the Andersen method or the CLONE method. Semen samples were evaluated immediately after thawing and after 3 h of incubation at 37 degrees C. Plasma membrane integrity and acrosomal status of the spermatozoa were evaluated simultaneously by flow cytometry using a combination of 3 fluorescent dyes: Carboxy-SNARF-1 (SNARF), to identify the live spermatozoa; propidium iodide (PI), which only stains dead cells or cells with damaged membranes; and fluorescein isothiocyanate (FITC)-conjugated Pisum sativum agglutinin (PSA), which binds to the acrosomal content of spermatozoa with damaged plasma and outer acrosomal membranes. The accuracy of this new staining method in quantifying the proportions of live and dead spermatozoa by flow cytometry was evaluated by comparing it with the staining technique using carboxyfluorescein diacetate and propidium iodide (CFDA-PI), which yielded high correlation coefficients. The triple-stained sperm samples were also analyzed by epifluorescence microscopy, and both methods proved to be highly correlated. Post-thaw progressive motility and plasma membrane integrity were similar for the 2 freezing procedures, but the proportion of damaged acrosomes after thawing was lower using the Andersen method and the spermatozoa had a higher thermoresistance. This new triple staining method for assessing canine sperm viability and acrosomal integrity provides an efficient procedure for evaluating frozen-thawed dog semen samples either by flow cytometry or fluorescence microscopy.     

Comparison of fertility data from vaginal vs intrauterine insemination of frozen-thawed dog semen: a retrospective study

Fertility data from 327 artificial inseminations (AIs) using frozen-thawed dog semen are presented here. The AIs were performed in 274 bitches using semen from 185 males of 76 breeds. The data cover all AIs conducted during 1983 through 1995 at Cryogenetic Laboratories (CLONE) in the United States with AKC-registered and research bitches, and all AIs carried out at the Department of Obstetrics and Gynecology at the Swedish University of Agricultural Sciences in Uppsala, Sweden, using semen frozen by CLONE, in 0.5-mL straws. Semen was frozen using a standardized, three-step liquid nitrogen vapor freezing method. Whelping rates > 70% were obtained when post-thaw motility was 40% or higher. The inseminations were made either directly into the uterus using transcervical catheterization with the Norwegian catheter (NIU; 167 AIs) or a fiberoptic endoscope (EIU; 19 AIs), or in the cranial vagina (VAG; 141 AIs). Resulting whelping rates were 84.4% (NIU), 58.9% (VAG; P < 0.001), and 57.9% (EIU). Increasing the number of VAG AIs per cycle from 1 to 2 enhanced the whelping rate (P < 0.05). The mean interval from the first AI to whelping was 61.8 +/- 2.4 d, and was longer for VAG AIs (62.7 +/- 2.7 d) than for NIU AIs (61.2 +/- 2.1 d; P < 0.001). The mean interval from the last AI was 60.1 +/- 1.9 d, and did not differ between VAG AIs (60.2 +/- 2.2 d) and NIU AIs (60.0 +/- 1.6 d). Gestation length was not influenced by breed or litter size. A total of 1158 pups resulted from the 327 AIs. Litter size was 5.4 +/- 3.0 (NIU), 4.0 +/- 2.7 (VAG; P < 0.001), and 6.0 +/- 2.1 (EIU). Litter size was also influenced by breed (P = 0.006) and, for VAG AIs, by the number of inseminations performed per cycle (P = 0.009). This study is the largest that has been carried out on frozen-thawed dog semen AI. It shows that using a good method for cryopreservation, together with nonsurgical intrauterine AI employing the Norwegian catheter, can yield whelping rates and litter sizes similar to those reported from well-controlled natural matings. Furthermore, this is the first study to show that intrauterine deposition of frozen-thawed dog semen results in a significantly higher whelping rate and larger litter size than vaginal deposition.     

CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes

Background  

Online Mendelian Inheritance in Man (OMIM) is a computerized database of information about genes and heritable traits in human populations, based on information reported in the scientific literature. Our objective was to establish an automated text-mining system for OMIM that will identify genetically-related cancers and cancer-related genes. We developed the computer program CGMIM to search for entries in OMIM that are related to one or more cancer types. We performed manual searches of OMIM to verify the program results.     

COMBOSA3D: combining sequence alignments with three-dimensional structures

COMBOSA3D is a program that allows sequence conservation to be viewed in its proper three-dimensional environment. It superimposes sequence alignment information onto a protein structure using a customizable color scheme, which is also applied to a textual sequence alignment for reference. AVAILABILITY: The program can be tested at http://www.bioinformatics.org/combosa3d/, and the source code is freely available.     

Magnetic Resonance Imaging in Multiple Sclerosis – Patients' Experiences,Information Interests and Responses to an Education Programme

Background

Magnetic resonance imaging (MRI) is a key diagnostic and monitoring tool in multiple sclerosis (MS) management. However, many scientific uncertainties, especially concerning correlates to impairment and prognosis remain. Little is known about MS patients'' experiences, knowledge, attitudes, and unmet information needs concerning MRI.

Methods

We performed qualitative interviews (n = 5) and a survey (n = 104) with MS patients regarding MRI patient information, and basic MRI knowledge. Based on these findings an interactive training program of 2 hours was developed and piloted in n = 26 patients.

Results

Interview analyses showed that patients often feel lost in the MRI scanner and left alone with MRI results and images while 90% of patients in the survey expressed a high interest in MRI education. Knowledge on MRI issues was fair with some important knowledge gaps. Major information interests were relevance of lesions as well as the prognostic and diagnostic value of MRI results. The education program was highly appreciated and resulted in a substantial knowledge increase. Patients reported that, based on the program, they felt more competent to engage in encounters with their physicians.

Conclusion

This work strongly supports the further development of an evidence-based MRI education program for MS patients to enhance participation in health-care.     

ANGSD: Analysis of Next Generation Sequencing Data

Background

High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultaneously.

Results

We present a multithreaded program suite called ANGSD. This program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly on the raw sequencing data or by using genotype likelihoods.

Conclusions

The open source c/c++ program ANGSD is available at http://www.popgen.dk/angsd. The program is tested and validated on GNU/Linux systems. The program facilitates multiple input formats including BAM and imputed beagle genotype probability files. The program allow the user to choose between combinations of existing methods and can perform analysis that is not implemented elsewhere.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0356-4) contains supplementary material, which is available to authorized users.     

Information literacy in an inquiry course for first-year science undergraduates: a simplified 3C approach

In this article, we describe a simplified approach to teach students to assess information obtained from diverse sources. Three broad categories (credibility, content, and currency; 3C) were used to evaluate information from textbooks, monographs, popular magazines, scholarly journals, and the World Wide Web. This 3C approach used in an inquiry course for freshmen in an undergraduate science program can be readily transferred to other settings.     

Efficiency of genomic selection in an established commercial layer breeding program

Background

In breeding programs for layers, selection of hens and cocks is based on recording phenotypic data from hens in different housing systems. Genomic information can provide additional information for selection and/or allow for a strong reduction in the generation interval. In this study, a typical conventional layer breeding program using a four-line cross was modeled and the expected genetic progress was derived deterministically with the software ZPLAN+. This non-genomic reference scenario was compared to two genomic breeding programs to determine the best strategy for implementing genomic information in layer breeding programs.

Results

In scenario I, genomic information was used in addition to all other information available in the conventional breeding program, so the generation interval was the same as in the reference scenario, i.e. 14.5 months. Here, we assumed that either only young cocks or young cocks and hens were genotyped as selection candidates. In scenario II, we assumed that breeders of both sexes were used at the biologically earliest possible age, so that at the time of selection only performance data of the parent generation and genomic information of the selection candidates were available. In this case, the generation interval was reduced to eight months. In both scenarios, the number of genotyped male selection candidates was varied between 800 and 4800 males and two sizes of the calibration set (500 or 2000 animals) were considered. All genomic scenarios increased the expected genetic gain and the economic profit of the breeding program. In scenario II, the increase was much more pronounced and even in the most conservative implementation led to a 60% improvement in genetic gain and economic profit. This increase was in all cases associated with higher breeding costs.

Conclusions

While genomic selection is shown to have the potential to improve genetic gain in layer breeding programs, its implementation remains a business decision of the breeding company; the possible extra profit for the breeding company depends on whether the customers of breeding stock are willing to pay more for improved genetic quality.     

Effectiveness of a Pilot Partner Notification Program for New HIV Cases in Barcelona,Spain

Background

An estimated 30% of HIV cases in the European Union are not aware of their serological status. This study aimed to assess the effectiveness of a pilot HIV partner notification program.

Methods

HIV cases diagnosed between January 2012 and June 2013 at two healthcare settings in Barcelona were invited to participate in a prospective survey. We identified process and outcome measures to evaluate this partner notification program, including the number of partners identified per interviewed index case, the proportion of partners tested for HIV as a result of the partner notification, and the proportion of new HIV diagnoses among their sex or needle-sharing partners.

Results

Of the 125 index cases contacted, 108 (86.4%) agreed to provide information about partners. A total of 199 sexual partners were identified (1.8 partners per interviewed index case). HIV outcome was already known for 58 partners (70.7% were known to be HIV-positive), 141 partners were tested as result of partner notification, and 26 were newly diagnosed with HIV. The case-finding effectiveness of the program was 18.4%.

Conclusion

This pilot program provides evidence of the effectiveness of a partner notification program implemented in healthcare settings. This active partner notification program was feasible, acceptable to the user, and identified a high proportion of HIV-infected patients previously unaware of their status.     

Impact of an Educational Program to Reduce Healthcare Resources in Community-Acquired Pneumonia: The EDUCAP Randomized Controlled Trial

Background

Additional healthcare visits and rehospitalizations after discharge are frequent among patients with community-acquired pneumonia (CAP) and have a major impact on healthcare costs. We aimed to determine whether the implementation of an individualized educational program for hospitalized patients with CAP would decrease subsequent healthcare visits and readmissions within 30 days of hospital discharge.

Methods

A multicenter, randomized trial was conducted from January 1, 2011 to October 31, 2014 at three hospitals in Spain. We randomly allocated immunocompetent adults patients hospitalized for CAP to receive either an individualized educational program or conventional information before discharge. The educational program included recommendations regarding fluid intake, adherence to drug therapy and preventive vaccines, knowledge and management of the disease, progressive adaptive physical activity, and counseling for alcohol and smoking cessation. The primary trial endpoint was a composite of the frequency of additional healthcare visits and rehospitalizations within 30 days of hospital discharge. Intention-to-treat analysis was performed.

Results

We assigned 102 patients to receive the individualized educational program and 105 to receive conventional information. The frequency of the composite primary end point was 23.5% following the individualized program and 42.9% following the conventional information (difference, -19.4%; 95% confidence interval, -6.5% to -31.2%; P = 0.003).

Conclusions

The implementation of an individualized educational program for hospitalized patients with CAP was effective in reducing subsequent healthcare visits and rehospitalizations within 30 days of discharge. Such a strategy may help optimize available healthcare resources and identify post-acute care needs in patients with CAP.

Trial Registration

Controlled-Trials.com ISRCTN39531840     

The information transmitted at final position in visually triggered forearm movements

Visually triggered forearm movements were analyzed by an Information Theory approach. Human subjects made smooth movements which were characterized by moderate speeds, ranging about 100 degrees per second, by continuity in the position and velocity traces, and attainment of final average EMG levels before completion of the movement. We calculated the information transmitted by final position, biceps EMG, triceps EMG, and the ratio of the EMGs. The results were: (1) The information transmitted by final joint angle increased with number of targets but gradually levelled off. The maximum value was slightly over 3 bits, corresponding to an equivalent number of less than nine independent arm positions for a single movement. (2) The information transmitted by the ratio of the EMGs exceeds that transmitted by the biceps or triceps alone. (3) A previous theoretical prediction based on a spring model (Sakitt, 1980a) gives a moderately good fit to the experimental EMG ratio as a function of final position over a large range of angles. Our results lend consistency to two ideas about the nature of visually triggered forearm movements. First, our finding about the EMG ratio suggests that the basic motor program for final position is probably in terms of relative allocation of innervations, rather than looking up individual values. Second, single movements of this kind transmit surprisingly little information. If this is the case, it suggests that very fine accuracy is not achieved by a single program but requires feedback in order to program and execute additional movement.Laboratoire de Physiologie Neurosensorielle, CNRS, Paris, France     

Delay and characteristics of scorpion bite management in the Sidi-Bouzid region

Scorpion envenomation represents a potential danger in the 2/3 of Tunisia's territory but Sidi Bouzid area is the most infected with 1/6 of the piqued in Tunisia. The purpose of the study was to assess the result of a program for scorpion control in Sidi Bouzid and especially the delay from being stung to access to health care service. The analysis of data related to program shows that the delay was decreased only in 4 districts out of 11. This situation should be explained by such factors as information and behaviour of population, access to health care.... It is necessary to increase the action recommended by the program and to behold specific characteristics of each district.     

AUGUSTUS at EGASP: using EST,protein and genomic alignments for improved gene prediction in the human genome

Background

A large number of gene prediction programs for the human genome exist. These annotation tools use a variety of methods and data sources. In the recent ENCODE genome annotation assessment project (EGASP), some of the most commonly used and recently developed gene-prediction programs were systematically evaluated and compared on test data from the human genome. AUGUSTUS was among the tools that were tested in this project.

Results

AUGUSTUS can be used as an ab initio program, that is, as a program that uses only one single genomic sequence as input information. In addition, it is able to combine information from the genomic sequence under study with external hints from various sources of information. For EGASP, we used genomic sequence alignments as well as alignments to expressed sequence tags (ESTs) and protein sequences as additional sources of information. Within the category of ab initio programs AUGUSTUS predicted significantly more genes correctly than any other ab initio program. At the same time it predicted the smallest number of false positive genes and the smallest number of false positive exons among all ab initio programs. The accuracy of AUGUSTUS could be further improved when additional extrinsic data, such as alignments to EST, protein and/or genomic sequences, was taken into account.

Conclusion

AUGUSTUS turned out to be the most accurate ab initio gene finder among the tested tools. Moreover it is very flexible because it can take information from several sources simultaneously into consideration.

     

Web-based weight management programs in an integrated health care setting: a randomized, controlled trial

Objective: To assess the efficacy of a Web‐based tailored behavioral weight management program compared with Web‐based information‐only weight management materials. Research Methods and Procedures: Participants, 2862 eligible overweight and obese (BMI = 27 to 40 kg/m²) members from four regions of Kaiser Permanente's integrated health care delivery system, were randomized to receive either a tailored expert system or information‐only Web‐based weight management materials. Weight change and program satisfaction were assessed by self‐report through an Internet‐based survey at 3‐ and 6‐month follow‐up periods. Results: Significantly greater weight loss at follow‐up was found among participants assigned to the tailored expert system than among those assigned to the information‐only condition. Subjects in the tailored expert system lost a mean of 3 ± 0.3% of their baseline weight, whereas subjects in the information‐only condition lost a mean of 1.2 ± 0.4% (p < 0.0004). Participants were also more likely to report that the tailored expert system was personally relevant, helpful, and easy to understand. Notably, 36% of enrollees were African‐American, with enrollment rates higher than the general proportion of African Americans in any of the study regions. Discussion: The results of this large, randomized control trial show the potential benefit of the Web‐based tailored expert system for weight management compared with a Web‐based information‐only weight management program.