bluuebunny/crossref_metadata_2025 huggingface dataset:
41 UPDATING THE ZONA-FREE METHOD FOR MOUSE CLONING USING HM1 EMBRYONIC STEM CELLS
Authors: Lagutina I. , Lizier M. , Paulis M. , Lucchini F. , Castelli A. , Susani L. , Galli C. , Vezzoni P.
Published: December 2014

The zona-free method of SCNT designed for bovine and pig cloning (Booth et al. 2001; Vajta et al. 2001; Oback et al. 2003) was successfully used for horse (Galli et al. 2003). Although simple and efficient in farm animals, its application in the mouse met several problems (Ribas et al. 2005, 2006). The aim of our work was to produce cloned mice using HM1 embryonic stem (ES)cells adapting a zona-free method. Seven- to 24-week-old superovulated B6D2F1 female mice were used as oocytes donors. Cumulus cells were removed by 0.3% hyaluronidase and the zona pellucida by 0.5% pronase in KSOM-HEPES (KSOM-H) 1 h later (Ribas et al. 2006) or immediately after hyaluronidase treatment at 37°C. The HM1 ES cells were cultured in KnockOut DMEM supplemented with leukemia inhibitory factor and 15% fetal bovine serum with or without 2i (Ying et al. 2008) and were synchronized at M phase by 3 ng mL–1 nocodazole for 3 h before fusion. Only spherical cells were selected for NT. Metaphase II chromosome spindle complexes were removed by micromanipulation in KSOM-H medium with 5 μg mL–1 cytochalasin B. Lectin-treated enucleated oocytes were attached to the donor cells in KSOM-H with nocodazole and fused by 2 pulses of 1.3 kV cm–1 DC for 30 μs in 0.3 M mannitol medium. Following 10- to 15-min incubation in KSOM-H, the fusion was assessed and repeated if the constructs were nonfused. Cloned embryos were activated in 1 mM SrCl2 in Ca2+-free KSOM medium for 2 to 2.5 or 5 to 6 h and cultured in 20-μL KSOM droplets using the well-of-the-well (WOW) method (Vajta et al. 2000) under mineral oil at 37°C and 5% CO2. Day 4 compacted morulae and blastocysts were surgically transferred into the uterus of Day-2.5 pseudopregnant recipients that were sacrificed on Day 19.5 to examine fetal development. The donor mice age was important for oocyte survival: ~16% of oocytes of 7- to 10-week-old mice lysed before or during fusion in 33% of experiments (n experiments = 15), whereas oocytes of older mice were not sensitive to enzymatic treatment and electric impulses even after 3 fusion rounds (n = 19). The time of pronase treatment did not affect oocyte survival, whereas extending the time between hyaluronidase treatment and enucleation revealed self-activation in ~25% of oocytes. The fusion efficiency of ES cells was significantly lower compared with serum-starved fibroblasts (61%, n = 623 v. 100%, n = 80). The duration of SrCl2 treatment did not affect embryo development (cleavage: 82% v. 84%; Day 4 blastocysts: 49% v. 52%). ES cell culture with 2i increased Day 4 blastocyst development (60.7% v. 50.4%; P = 0.07), and their ability to implant (52.6% v. 38.2%; P = 0.06). Moreover, only NT embryos derived from 2i-ES cells developed to term (8.2%, n = 5; P = 0.08), and produced live fetuses (4.9%, n = 3). In light of these results, the fusion of ES cells remains the critical step in the mouse zona-free protocol.Partially supported by grant Superpig from Regione Lombardia.
66 EFFECT OF ADDITION OF CHOLESTEROL-LOADED CYCLODEXTRIN BEFORE FREEZING ON QUALITY AND FERTILITY OF STALLION FROZEN SEMEN
Authors: Papa F. O. , Ramires Neto C. , Sancler-Silva Y. F. R. , Resende H. L. , Monteiro G. A. , Freitas-Dell'aqua C. P. , Alvarenga M. A.
Published: December 2014

The aim of the present study was to evaluate the effect of cholesterol-loaded cyclodextrin on the quality and fertility of stallion frozen semen. Three ejaculates from each of 4 stallions were used. The semen was diluted (1 : 1) with a skim milk-based extender (Botu-SemenTM, Botupharma, Brazil). The samples were divided into 2 groups: control group (CG), composed of semen diluted only with extender, and treated group (TG), composed of semen diluted with extender plus 750 mg mL–1 of cholesterol-loaded cyclodextrin. Both groups were incubated for 15 min at 20°C. The semen was frozen with Botu-CryoTM (Botupharma, Brazil) extender according to the manufacturer's protocol in 0.5-mL straws containing 100 × 106 of total sperm. The sperm kinetic parameters were analysed by computer-assisted semen analysis, and plasma membrane integrity by flow cytometer (propidium iodide and fluorescein isothiocyanate -PSA) on post-thaw. The fertility trial was carried out inseminating 2 cycles of 20 mares (total of 40 cycles) immediately post-ovulation using 4 straws of CG or TG (400 × 106 total sperm), one from each stallion in a randomised design. Comparison of sperm parameters was performed by t-test and fertility by Fisher's exact test. No difference (P > 0.05) was observed in total motility (%, CG = 57.9 ± 6.5 v. TG = 60.2 ± 6.7), progressive motility (%, CG = 26.9 ± 4.8 v. TG = 28.5 ± 4.8), percentage of rapid sperm (%, CG = 43.5 ± 8.8 v. TG = 45.7 ± 7.6), membrane integrity (%, CG = 20.1 ± 5.1 v. TG = 20.3 ± 6.3), and fertility (CG = 60% v. TG = 70%) between the groups. The results of this study showed that the use of cholesterol-loaded cyclodextrin did not affect sperm kinetic parameters and fertility in stallion with good quality in post-thaw semen. Further studies must be performed with stallions sensitive to freeze-thawing process.
7 PREGNANCY RATES IN BEEF HEIFERS SYNCHRONIZED WITH A SHORTENED OESTRADIOL-BASED TREATMENT THAT PROVIDES FOR A PROLONGED PROESTRUS
Authors: Menchaca A. , Nuñez-Olivera R. , Cuadro F. , Bo G.
Published: December 2014

An oestradiol-based protocol (named J-Synch) has been developed recently with the aim of providing for a longer proestrus, enhancing the development of the dominant follicle before ovulation, and increasing pregnancy rates following fixed-time AI (FTAI) in heifers (de la Matta and Bo 2012 Taurus 55, 17–23). Two experiments were performed in Uruguay with 1953 Angus × Hereford crossbred heifers to compare pregnancy rates obtained with the J-Synch protocol with the conventional 7-day oestradiol-based protocol. A secondary objective was to determine the effects of the time of FTAI and the addition of eCG at the time progestin device removal on pregnancy rates. In Experiment 1, 966 heifers received a DIB device (0.5 g of progesterone, Syntex, Buenos Aires, Argentina) plus 2 mg of oestradiol benzoate IM (Syntex) on Day 0. Heifers in the conventional treatment group (n = 485) received cloprostenol (500 μg, Ciclase DL, Syntex) and oestradiol cypionate (0.5 mg, Cipiosyn, Syntex) IM and had their DIB removed on Day 7 a.m. Heifers in this group were then subdivided to be FTAI on Day 9 a.m. or p.m. (i.e. 48 or 56 h after DIB removal). Heifers in the J-Synch treatment group (n = 481) received cloprostenol IM and DIB removal on Day 6 p.m. and received gonadotropin-releasing hormone (100 μg gonadorelin acetate, Gonasyn Gdr, Syntex) on Day 9 a.m.; heifers were then FTAI on Day 9 a.m. or p.m. (i.e. 60 or 72 h after DIB removal). All heifers in this experiment were also treated with 300 IU of eCG (Novormon, Syntex) at DIB removal. In Experiment 2, 987 heifers were treated with the J-Synch protocol as described in Experiment 1. At device removal (Day 6 p.m.), heifers were divided to receive (n = 488) or not (n = 499) 300 IU of eCG IM at that time and were further subdivided to receive gonadotropin-releasing hormone and FTAI on Day 9 a.m. or p.m. (i.e. 60 or 72 h after DIB removal). Pregnancy rates were determined by ultrasonography 30 days after FTAI. Data were analysed using logistic regression, and results are shown in Table 1. J-Synch-treated heifers tended (P < 0.1) to have higher pregnancy rates following FTAI, whereas time of FTAI only affected pregnancy rates following the conventional 7-day treatment (P < 0.05). However, removal of eCG from the J-Synch protocol in Experiment 2 resulted in reduced pregnancy rates when inseminations were done on Day 9 p.m. (P < 0.05). In summary, the addition of eCG to the J-Synch protocol provided for a wider window of insemination times facilitating FTAI in large groups of beef heifers.

Table 1.Effect of length of progestin insertion, time of insemination and eCG treatment on pregnancy rates in beef heifers
74 EFFECT OF POWDERED EGG YOLK IN THE EXTENDER AND DONOR AGE ON FRESH AND THAWED SPERM MORPHOMETRY IN SMALL RUMINANTS
Authors: Palomo M. J. , Garcia W. , Tabarez A.
Published: December 2014

Our aim was to reduce heterogeneity and microbiological contamination risk on small ruminant semen cryopreservation by replacement of fresh egg yolk by pasteurized powdered egg yolk, assessing simultaneously the effect of the donor age (1 year v. 2 years old) on sperm head morphometry of fresh and thawed sperm. Briefly, fresh ejaculates from 8 rams and from 8 bucks were collected in autumn during 2 consecutive years. Immediately after collection, ejaculates from each species were mixed in equal quantities, and pooled semen was centrifuged twice (600 g for 10 min). Then the pellet was split into 2 aliquots and resuspended in an extender containing 15% (v/v) of fresh or powdered egg yolk supplemented with 5% glycerol in a Tris-based medium. Afterward, sperm samples were refrigerated at 5°C for 4 h before being frozen in nitrogen liquid vapours. Buck and ram sperm-head morphometry was analysed by computer-assisted sperm analysis (ISAS®) on fresh and thawed sperm previously stained with Diff Quick®, and the data were analysed using ANOVA (mean ± s.e., n = 6). From ram sperm studies, no differences were found between fresh and post-thaw sperm, neither between egg yolk-based extenders or donor ages, showing the following mean values of head length (8.4 ± 0.0 μm), width (4.9 ± 0.0 μm), area (34.2 ± 0.1 μm2), perimeter (23.4 ± 0.1 μm), ellipticity (1.7 ± 0.0), elongation (0.2 ± 0.0), rugosity (0.8 ± 0.0), and regularity (0.9 ± 0.0). Likewise buck semen did not show significant differences on sperm-head dimensions after cryopreservation, only on head-shape parameters as ellipticity, elongation, and regularity between fresh and thawed sperm from 2-year-old donors, independently of egg yolk used as cryoprotectant. However, the age of the buck had a significant effect on all assessed morphometric parameters in fresh and thawed sperms, except regularity (Table 1). Our results suggest that, from a morphometric point of view, the powdered egg yolk can be used satisfactory on small ruminant sperm cryopreservation, but in goats, the head changes due to the donor age should be considered.

Table 1.Effect of fresh v. powdered egg yolk (EY) in the extender and donor age on fresh and thawed buck-sperm morphometry

Research supported by INIA (RZ2009–00008–00–00), Generalitat de Catalunya (2009SGR0621 and CUR-DIUE), and FSE and Fundación Carolina.
9 TIMED ARTIFICIAL INSEMINATION IN BLOCKS: A NEW ALTERNATIVE TO IMPROVE FERTILITY IN BEEF COWS
Authors: Pfeifer L. F. M. , Castro N. A. , Siqueira L. G. B. , Lagos K. R. , Bagon A. , Singh J.
Published: December 2014

The objective of this study was to evaluate whether timed artificial insemination (TAI) according to the diameter of the dominant preovulatory follicle (POF) would improve pregnancy rates in beef cows. In Experiment 1, a retrospective meta-analysis of 5 oestradiol- or gonadotropin-releasing hormone-based TAI experiments from 2011 to 2014 was performed to evaluate the interval from luteolysis to ovulation. In these experiments, crossbred cows (Gyr × Holstein; n = 60) were examined by ultrasonography at 12-h intervals from progesterone-releasing device (CIDR) removal to ovulation. A linear regression model was used to predict the effect of POF diameter on the time of ovulation. Cows with a larger POF at the time of AI ovulated earlier than cows with smaller POF (y = –8.25x + 115.22; R2 = 0.93; P < 0.0001). In Experiment 2, lactating Nelore cows (Bos indicus; n = 59) on random days of the oestrous cycle were given 2 mg of oestradiol benzoate IM and a CIDR device (Day 0) to synchronize follicular waves. The CIDR were removed, and cows were given 500 μg of d-Cloprostenol (prostaglandin F2α) IM, 1 mg of oestradiol cypionate IM, and 300 IU of eCG IM on Day 8. On the morning of Day 10 (07:00 a.m.), the diameter of the POF was assessed by ultrasonography, and cows were randomised into Control (n = 29) and Block (n = 30) groups. 1) Control-group cows were TAI 48 h after CIDR removal (08:00 a.m. on Day 10), and Block-group cows were inseminated at 4 time points according to the diameter of the POF: B0 (POF ≥15 mm, TAI at 08:00 a.m. on Day 10, n = 6), B1 (POF 13 to 14 mm, TAI at 02:00 p.m. on Day 10, n = 8), B2 (POF 11 to 12 mm, TAI at 08:00 a.m. on Day 11, n = 11), and B3 (POF ≤ 10 mm, TAI at 02:00 p.m. on Day 11, n = 5). Pregnancy status was assessed 30 days post-AI by ultrasonography. No differences were detected in the diameter of the POF 48 h after CIDR removal (P = 0.77) or ovulation rate (P = 0.65; combined ovulation rate 52/59, 88%) between Control and Block groups. Block group had a higher pregnancy rate than Control (22/30, 73% v. 13/29, 45%, respectively; P = 0.02). In conclusion, our results document that interval from luteolysis to ovulation depends on the size of preovulatory follicle, timing of AI in relation to ovulation time is critical, and AI time according to the diameter of the POF can be an effective tool to improve fertility of cows in TAI protocols.
Kant (vs. Leibniz, Wolff and Lambert) on real definitions in geometry
Authors: Heis Jeremy
Published: December 2014

This paper gives a contextualized reading of Kant’s theory of real definitions in geometry. Though Leibniz, Wolff, Lambert and Kant all believe that definitions in geometry must be ‘real’, they disagree about what a real definition is. These disagreements are made vivid by looking at two of Euclid’s definitions. I argue that Kant accepted Euclid’s definition of circle and rejected his definition of parallel lines because his conception of mathematics placed uniquely stringent requirements on real definitions in geometry. Leibniz, Wolff and Lambert thus accept definitions that Kant rejects because they assign weaker roles to real definitions.
Population-based structural variation discovery with Hydra-Multi
Authors: Lindberg Michael R. , Hall Ira M. , Quinlan Aaron R.
Published: December 2014

Summary: Current strategies for SNP and INDEL discovery incorporate sequence alignments from multiple individuals to maximize sensitivity and specificity. It is widely accepted that this approach also improves structural variant (SV) detection. However, multisample SV analysis has been stymied by the fundamental difficulties of SV calling, e.g. library insert size variability, SV alignment signal integration and detecting long-range genomic rearrangements involving disjoint loci. Extant tools suffer from poor scalability, which limits the number of genomes that can be co-analyzed and complicates analysis workflows. We have developed an approach that enables multisample SV analysis in hundreds to thousands of human genomes using commodity hardware. Here, we describe Hydra-Multi and measure its accuracy, speed and scalability using publicly available datasets provided by The 1000 Genomes Project and by The Cancer Genome Atlas (TCGA).

Availability and implementation:  Hydra-Multi is written in C++ and is freely available at https://github.com/arq5x/Hydra.

Contact:  aaronquinlan@gmail.com or ihall@genome.wustl.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Safety and clinical outcomes of carbapenem de-escalation as part of an antimicrobial stewardship programme in an ESBL-endemic setting
Authors: Lew Kaung Yuan , Ng Tat Ming , Tan Michelle , Tan Sock Hoon , Lew Ee Ling , Ling Li Min , Ang Brenda , Lye David , Teng Christine B.
Published: December 2014

Objectives

To evaluate the safety and clinical outcomes of patients who received carbapenem de-escalation as guided by an antimicrobial stewardship programme (ASP) in a setting where ESBL-producing Enterobacteriaceae are endemic.

Methods

Patients receiving meropenem or imipenem underwent a prospective ASP review for eligibility for de-escalation according to defined institutional guidelines. Patients in whom carbapenem was de-escalated or not de-escalated, representing the acceptance and rejection of the ASP recommendation, respectively, were compared. The primary outcome was the clinical success rate; secondary outcomes included the 30 day readmission and mortality rates, the duration of carbapenem therapy, the incidence of adverse drug reactions due to antimicrobials, the acquisition of carbapenem-resistant Gram-negative bacteria and the occurrence of Clostridium difficile-associated diarrhoea (CDAD).

Results

The de-escalation recommendations for 300 patients were evaluated; 204 (68.0%) were accepted. The patient demographics and disease severity were similar. The clinical success rates were similar [de-escalated versus not de-escalated, 183/204 (89.7%) versus 85/96 (88.5%), P = 0.84], as was the survival at hospital discharge [173/204 (84.8%) versus 79/96 (82.3%), P = 0.58]. In the de-escalated group, the duration of carbapenem therapy was shorter (6 versus 8 days, P < 0.001), the rate of adverse drug reactions was lower [11/204 (5.4%) versus 12/96 (12.5%), P = 0.037], there was less diarrhoea [9/204 (4.4%) versus 12/96 (12.5%), P = 0.015], there was a lower incidence of carbapenem-resistant Acinetobacter baumannii acquisition [4/204 (2.0%) versus 7/96 (7.3%), P = 0.042] and there was a lower incidence of CDAD [2/204 (1.0%) versus 4/96 (4.2%), P = 0.081].

Conclusions

This study suggests that the ASP-guided de-escalation of carbapenems led to comparable clinical success, fewer adverse effects and a lower incidence of the development of resistance. This approach is safe and practicable, and should be a key component of an ASP.
Spontaneous Decompression Fracture in Thyroid Eye Disease
Authors: Richardson Marc A. , Lewis Kyle T.
Published: December 2014

This is a case of a 44-year-old female with a history of Graves’ orbitopathy presented to the emergency department after waking from a nap with sudden onset of left facial and periorbital swelling, ecchymosis, and subconjunctival hemorrhage. A CT scan obtained in the emergency department revealed a left blowout fracture and enlarged extraocular muscles. The patient lives with her mother and both adamantly denied any trauma. The patient had sustained a spontaneous orbital fracture; a process reported but few times in the medical literature.
Let Us Use LET
Authors: Sherman Joshua M. , Sheppard Patrick , Hoppa Eric , Krief William , Avarello Jahn
Published: December 2014

Background

Well-managed pain is associated with faster recovery, fewer complications, and decreased use of resources. In children, pain relief is also associated with higher patient and parent satisfaction. Studies have shown that there are deficiencies in pediatric pain management. LET gel (lidocaine 4%, epinephrine 0.1%, and tetracaine 0.5%) is a topical anesthetic that is routinely used before laceration repair.

Objective

The aim of this study was to determine if educational initiatives as part of a quality improvement initiative lead to increased rates of early topical anesthetic usage in a large urban pediatric emergency department.

Methods

The initiative consisted of an educational session and a triage booth poster. We then reviewed the charts of patients with facial and scalp lacerations for the month before the initiative, the month after the initiative, and 1 year after the initiative. We assessed if LET gel usage and time to administration improved and were sustainable.

Results

We reviewed 138 charts. Before the initiative, only 57.4% received LET gel before facial laceration repair with a mean time to application of 58.3 minutes. One month after the initiative, there was an increase in LET gel application by 20.1% with a reduction in time to application by 35.9 minutes (P < 0.05). In addition, these improvements were significantly sustainable. One year after the interventions, 82.4% received LET before facial laceration repair, and the time to LET application was 27.8 minutes.

Conclusions

Simple educational initiatives can improve the use of topical anesthetics. By using educational tools as part of a quality improvement initiative, we were able to significantly improve the rates of LET gel application for facial lacerations in children and decrease the time to administration.
Infectious disease, behavioural flexibility and the evolution of culture in primates
Authors: McCabe Collin M. , Reader Simon M. , Nunn Charles L.
Published: December 2014

Culturally transmitted traits are observed in a wide array of animal species, yet we understand little about the costs of the behavioural patterns that underlie culture, such as innovation and social learning. We propose that infectious diseases are a significant cost associated with cultural transmission. We investigated two hypotheses that may explain such a connection: that social learning and exploratory behaviours (specifically, innovation and extractive foraging) either compensate for existing infection or increase exposure to infectious agents. We used Bayesian comparative methods, controlling for sampling effort, body mass, group size, geographical range size, terrestriality, latitude and phylogenetic uncertainty. Across 127 primate species, we found a positive association between pathogen richness and rates of innovation, extractive foraging and social learning. This relationship was driven by two independent phenomena: socially contagious diseases were positively associated with rates of social learning, and environmentally transmitted diseases were positively associated with rates of exploration. Because higher pathogen burdens can contribute to morbidity and mortality, we propose that parasitism is a significant cost associated with the behavioural patterns that underpin culture, and that increased pathogen exposure is likely to have played an important role in the evolution of culture in both non-human primates and humans.
Top-predator control-induced trophic cascades: an alternative hypothesis to the conclusion of Colmanet al.
Authors: Allen Benjamin L.
Published: December 2014

Colmanet al.(2014Proc. R. Soc. B281, 20133094. (doi:10.1098/rspb.2013.3094)) recently argued that observed positive relationships between dingoes and small mammals were a result of top-down processes whereby lethal dingo control reduced dingoes and increased mesopredators and herbivores, which then suppressed small mammals. Here, I show that the prerequisite negative effects of dingo control on dingoes were not shown, and that the same positive relationships observed may simply represent well-known bottom-up processes whereby more generalist predators are found in places with more of their preferred prey. Identification of top-predator control-induced trophic cascades first requires demonstration of some actual effect of control on predators, typically possible only through manipulative experiments with the ability to identify cause and effect.
Senescence rates and late adulthood reproductive success are strongly influenced by personality in a long-lived seabird
Authors: Patrick Samantha C. , Weimerskirch Henri
Published: December 2014

Studies are increasingly demonstrating that individuals differ in their rate of ageing, and this is postulated to emerge from a trade-off between current and future reproduction. Recent theory predicts a correlation between individual personality and life-history strategy, and from this comes the prediction that personality may predict the intensity of senescence. Here we show that boldness correlates with reproductive success and foraging behaviour in wandering albatrosses, with strong sex-specific differences. Shy males show a strong decline in reproductive performance with age, and bold females have lower reproductive success in later adulthood. In both sexes, bolder birds have longer foraging trips and gain more mass per trip as they get older. However, the benefit of this behaviour appears to differ between the sexes, such that it is only matched by high reproductive success in males. Together our results suggest that personality linked foraging adaptations with age are strongly sex-specific in their fitness benefits and that the impact of boldness on senescence is linked to ecological parameters.
Host and pathogen ecology drive the seasonal dynamics of a fungal disease, white-nose syndrome
Authors: Langwig Kate E. , Frick Winifred F. , Reynolds Rick , Parise Katy L. , Drees Kevin P. , Hoyt Joseph R. , Cheng Tina L. , Kunz Thomas H. , Foster Jeffrey T. , Kilpatrick A. Marm
Published: December 2014

Seasonal patterns in pathogen transmission can influence the impact of disease on populations and the speed of spatial spread. Increases in host contact rates or births drive seasonal epidemics in some systems, but other factors may occasionally override these influences. White-nose syndrome, caused by the emerging fungal pathogen
Pseudogymnoascus destructans
, is spreading across North America and threatens several bat species with extinction. We examined patterns and drivers of seasonal transmission of
P. destructans
by measuring infection prevalence and pathogen loads in six bat species at 30 sites across the eastern United States. Bats became transiently infected in autumn, and transmission spiked in early winter when bats began hibernating. Nearly all bats in six species became infected by late winter when infection intensity peaked. In summer, despite high contact rates and a birth pulse, most bats cleared infections and prevalence dropped to zero. These data suggest the dominant driver of seasonal transmission dynamics was a change in host physiology, specifically hibernation. Our study is the first, to the best of our knowledge, to describe the seasonality of transmission in this emerging wildlife disease. The timing of infection and fungal growth resulted in maximal population impacts, but only moderate rates of spatial spread.
Natural Variation in Preparation for Nutrient Depletion Reveals a Cost-Benefit Tradeoff
Authors: Wang Jue , Atolia Esha , Hua Bo , Savir Yonatan , Escalante-Chong Renan , Springer Michael
Published: December 2014

Maximizing growth and survival in the face of a complex, time-varying environment is a common problem for single-celled organisms in the wild. When offered two different sugars as carbon sources, microorganisms first consume the preferred sugar, then undergo a transient growth delay, the “diauxic lag”, while inducing genes to metabolize the less preferred sugar. This delay is commonly assumed to be an inevitable consequence of selection to maximize use of the preferred sugar. Contrary to this view, we found that many natural isolates of Saccharomyces cerevisiae display short or non-existent diauxic lags when grown in mixtures of glucose (preferred) and galactose. These strains induce galactose-utilization (GAL) genes hours before glucose exhaustion, thereby “preparing” for the transition from glucose to galactose metabolism. The extent of preparation varies across strains, and seems to be determined by the steady-state response of GAL genes to mixtures of glucose and galactose rather than by induction kinetics. Although early GAL induction gives strains a competitive advantage once glucose runs out, it comes at a cost while glucose is still present. Costs and benefits correlate with the degree of preparation: strains with higher expression of GAL genes prior to glucose exhaustion experience a larger upfront growth cost but also a shorter diauxic lag. Our results show that classical diauxic growth is only one extreme on a continuum of growth strategies constrained by a cost-benefit tradeoff. This type of continuum is likely to be common in nature, as similar tradeoffs can arise whenever cells evolve to use mixtures of nutrients.
Detecting the anomaly zone in species trees and evidence for a misleading signal in higher-level skink phylogeny (Squamata: Scincidae)
Authors: Linkem Charles W. , Minin Vladimir , Leaché Adam D.
Published: December 2014

The anomaly zone presents a major challenge to the accurate resolution of many parts of the Tree of Life. The anomaly zone is defined by the presence of a gene tree topology that is more probable than the true species tree. This discrepancy can result from consecutive rapid speciation events in the species tree. Similar to the problem of long-branch attraction, including more data (loci) will only reinforce the support for the incorrect species tree. Empirical phylogenetic studies often implement coalescent based species tree methods to avoid the anomaly zone, but to this point these studies have not had a method for providing any direct evidence that the species tree is actually in the anomaly zone. In this study, we use 16 species of lizards in the family Scincidae to investigate whether nodes that are difficult to resolve are located within the anomaly zone. We analyze new phylogenomic data (429 loci), using both concatenation and coalescent based species tree estimation, to locate conflicting topological signal. We then use the unifying principle of the anomaly zone, together with estimates of ancestral population sizes and species persistence times, to determine whether the observed phylogenetic conflict is a result of the anomaly zone. We identify at least three regions of the Scindidae phylogeny that provide demographic signatures consistent with the anomaly zone, and this new information helps reconcile the phylogenetic conflict in previously published studies on these lizards. The anomaly zone presents a real problem in phylogenetics, and our new framework for identifying anomalous relationships will help empiricists leverage their resources appropriately for overcoming this challenge.
Individual Earnings Mobility and the Persistence of Earnings Inequalities in Australia
Authors: Gregg Paul , Scutella Rosanna , Vittori Claudia
Published: December 2014

This paper assesses earnings mobility among workers in Australia between 2001/2 and 2008/9 using HILDA household panel data. We examine the pattern of individuals' earnings growth and explore the importance of mobility as an equaliser of longer‐term earnings. We find that progressive earnings growth decreased overall inequality even after considering the re‐ranking that occurred in the distribution. This was partly driven by growth of earnings with age and partly by step changes associated with job‐to‐job moves, promotions and taking on more responsibility. Shocks also acted against this equalising process, most notably job loss, which had substantial negative effects on earnings and disproportionately fell on lower‐waged workers.
Prevalence, Genetic Diversity, and Antibiotic Resistance of Bacillus cereus Isolated from Korean Fermented Soybean Products
Authors: Kim Cheol‐Woo , Cho Seung‐Hak , Kang Suk‐Ho , Park Yong‐Bae , Yoon Mi‐Hye , Lee Jong‐Bok , No Wan‐Seob , Kim Jung‐Beom
Published: December 2014

Bacillus cereus contamination is a major food safety problem for Korean fermented soybean products, but few studies have assessed its potential to cause foodborne illness. The objectives of this study were to investigate the prevalence and characteristics of B. cereus isolated from Korean fermented soybean products. B. cereus was detected in 110 of 162 (67.9%) samples. The highest B. cereus frequency was observed in deonjang (68 of 93 samples, 73.1%) and cheonggukjang (18 of 25, 72.0%); however, nonhemolytic enterotoxin was detected only in 22 of 162 samples (13.6%). Although the tested B. cereus isolates showed diverse pulsotypes according to repetitive sequence‐PCR banding patterns, they displayed similar antibiotic sensitivity spectra. The low frequency of enterotoxin detection suggests that the potential risk of B. cereus foodborne illness associated with Korean fermented soybean products is lower than generally presumed. However, considering the prevalence of B. cereus and the high content of fermented soybean products in the Korean diet, it is necessary to constantly monitor the level of contamination with B. cereus and its toxins in such Korean food products.
Methicillin‐Resistant Staphylococcus aureus in Raw Meats and Prepared Foods in Public Hospitals in Salvador, Bahia, Brazil
Authors: Costa Wellington Luis Reis , Ferreira Jeane dos Santos , Carvalho Joelza Silva , Cerqueira Ellayne Souza , Oliveira Lucimara Cardoso , Almeida Rogeria Comastri de Castro
Published: December 2014

This study investigated the presence of methicillin‐resistant Staphylococcus aureus (MRSA) in raw meat and fish and foods prepared from them for patient consumption in public hospitals in Salvador, Bahia, in northeastern Brazil. A total of 114 samples of raw meat and fish (chicken, n = 30; beef, n = 30; pork, n = 24; and fish, n = 30) and 63 samples of prepared foods (made with chicken, n = 15; beef, n = 15; pork, n = 15; and fish, n = 18) were collected from the kitchens of 10 different hospitals. Of the 114 investigated raw meat and fish samples, 28.1% were positive for MRSA, which comprised 23.3% beef, 23.3% chicken, 37.5% pork, and 30% fish samples. Of the prepared foods, 9.5% were positive for MRSA, which comprised 5.6% chicken products, 6.7% pork products, and 22.2% fish products. MRSA contamination was not detected in prepared beef dishes. A statistical analysis showed no association between the presence of MRSA and the type of raw food (P > 0.05). The high prevalence of MRSA among the raw foods tested and the presence of the microorganism in prepared foods emphasizes the necessity of enforcing hygienic practices within hospital kitchens.
The Influence of Country, Industry, and Topic Factors on IFRS Policy Choice
Authors: Stadler Christian , Nobes Christopher W.
Published: December 2014

This paper proposes a framework for understanding management's decision‐making on observable accounting policy choices. The framework is used to hypothesize how country, industry, and topic factors influence policy choice under International Financial Reporting Standards (IFRS). The hypotheses are tested on the choices made by the largest firms from 10 jurisdictions on a comprehensive set of IFRS policy topics, which are hand‐collected from the financial statements. The results are consistent with the framework: country factors are particularly influential when the choice does not affect an important accounting number; and industry and topic factors influence the choice on some topics. Overall, we find that country factors have the greatest influence on IFRS policy choice.
Payout Policy Relevance and Accounting‐based Valuation
Authors: Clubb Colin , Walker Martin
Published: December 2014

DeAngelo and DeAngelo (2006) (D&D) argue ‘payout policy is not irrelevant and investment is not the sole determinant of value, even in frictionless markets’. Consistent with this view, we argue that the concept of a perfect capital market in Miller and Modigliani (1961) (M&M) and Fama and Miller (1972) can be extended to allow for managerial moral hazard if managers are assumed not to participate in securities trading. An updated version of the M&M valuation model is presented and the possibility of managerial free cash flow (FCF) retention through operating expense manipulation and sub‐optimal investment policies is discussed. Our analysis supports D&D's argument that payout policy is relevant and indicates that value relevance of payout depends on the quality of earnings measurement and the optimality of investment policy. Following this, we develop a framework for analyzing valuation and informational roles of payout in accounting‐based valuation models and apply this framework to the Ohlson (1995) and Feltham and Ohlson (1996) models. This analysis shows how these models permit payout valuation relevance due to managerial FCF retention but not payout informational relevance. Finally, we consider how the Feltham and Ohlson (1996) model can be extended to incorporate time variation in expected profitability of capital investment caused by time variation in managerial FCF retention activities and show that this explicitly affects payout value relevance. We conclude that the development of models where payout plays an explicit valuation role due to issues of moral hazard is an important direction for future research.
A WebGIS‐based teaching assistant system for geography field practice (TASGFP)
Authors: Wang Jiechen , Ni Haochen , Rui Yikang , Cui Can , Cheng Liang
Published: December 2014

Field practice is an important part of training geography research talents. However, traditional teaching methods may not adequately manage, share and implement instruction resources and thus may limit the instructor's ability to conduct field instruction. A possible answer is found in the rapid development of computer‐assisted instruction (CAI), a new teaching mode for the Information Age. A “virtual field trip” is an amalgam of Internet and multimedia techniques with great potential for geography field instruction, as it can arouse students' enthusiasm and immerse them in learning. However, limited by available technology, virtual field trips have disadvantages in terms of content presentation, data organisation, and loss or inadequate representation of spatial information. To overcome the above shortcomings, a map‐based, spatially correlated design method was proposed for a CAI system in geography. By integrating spatial information technology (Geographic Information System, Global Positioning System, remote sensing, etc) and information delivery methods (web services, databases, etc), a WebGIS‐based teaching assistant system for geography field practice (TASGFP) was established, realising an effective spatial management scheme and forming a shared platform for instruction material. Its efficiency was verified through the actual application, although there remains room for improvement. Nevertheless, the TASGFP stands as an effective CAI tool in geography instruction.
Is there an Appalachian disparity in dental caries in Pennsylvania schoolchildren?
Authors: Polk Deborah E. , Kim Sunghee , Manz Michael , Weyant Robert J.
Published: December 2014

Objectives

To determine whether there is an Appalachian disparity in caries prevalence or extent in children living in Pennsylvania.

Methods

We conducted a cross‐sectional clinical assessment of caries in a sample representing 1st, 3rd, 9th, and 11th grade students across Pennsylvania. We used logistic regression and zero‐inflated negative binomial regression controlling for age to examine the association of residence in an Appalachian county with caries prevalence and extent in the primary and permanent dentitions.

Results

Compared with children living outside Appalachia, more children living in Appalachia had a dft >0 (OR = 1.37, 95% CI = 1.07–1.76) and more had a DMFT >0 (OR = 1.32, 95% CI = 1.06–1.64). In addition, compared with children living outside Appalachia, children living in Appalachia had a greater primary but not permanent caries extent (IRR = 1.10, 95% CI = 1.01–1.19).

Conclusions

We found Appalachian disparities in caries prevalence in both the primary and permanent dentitions and an Appalachian disparity in caries extent in the primary dentition. None of the disparities was moderated by age. This suggests that the search for the mechanism or mechanisms for the Appalachian disparities should focus on differential exposures to risk factors occurring prior to and at the start of elementary school.
Prevalence, Determinants, and Prognostic Significance of Pulmonary Hypertension in Elderly Patients Admitted with Acute Decompensated Heart Failure: A Report from the BIO‐HF Registry
Authors: Vanhercke Daniel , Pardaens Sofie , Weytjens Caroline , Vande Kerckhove Barbara , De Laet Nancy , Janssens Emilie , Van Camp Guy , De Sutter Johan
Published: December 2014

Purpose

Pulmonary hypertension (PHT) is a predictor of mortality and morbidity in patients with chronic heart failure (HF). However, the prevalence, determinants, and prognostic significance of PHT in elderly patients admitted with acute decompensated HF are unclear.

Methods

We prospectively evaluated 401 patients aged ≥75 years (mean age 83 ± 5 years, 50% women) with acute HF, who were discharged alive, and whose tricuspid regurgitation (TR) gradient was measured by echocardiography during hospitalization. PHT was defined as a TR gradient ≥30 mmHg. The endpoint was all‐cause mortality.

Results

PHT was found in 280/401 patients (69%), including in 67% of patients with HF with reduced ejection fraction (HFrEF) and 73% of patients with HF with preserved ejection fraction (HFpEF) (P = 0.19). Clinical characteristics and comorbidities were similar between patients with and without PHT. The prevalence of PHT increased with increasing severity of mitral regurgitation (MR) (mild: 65%; moderate: 67%; severe: 85%; P < 0.01). After a mean follow‐up of 405 ± 399 days, 118 patients (30%) had died. In a multivariate Cox regression analysis, that included age, sex, serum creatinine, TR gradient, comorbidities, and medications at discharge, age (hazard ratio [HR] 1.07, 95% confidence interval [CI] 1.03–1.11, P < 0.001), serum creatinine (HR 1.41, 95% CI 1.15–1.73, P < 0.01), and PHT (HR 1.60, 95% CI 1.03–2.49, P < 0.01) were independent predictors of all‐cause mortality.

Conclusion

In elderly patients admitted with acute HF, PHT is common, mainly associated with the severity of MR and associated with a worse outcome after discharge.
The spatial and signal characteristics of physiologic high frequency oscillations
Authors: Alkawadri Rafeed , Gaspard Nicolas , Goncharova Irina I. , Spencer Dennis D. , Gerrard Jason L. , Zaveri Hitten , Duckrow Robert B. , Blumenfeld Hal , Hirsch Lawrence J.
Published: December 2014

Objectives

To study the incidence, spatial distribution, and signal characteristics of high frequency oscillations (HFOs) outside the epileptic network.

Methods

We included patients who underwent invasive evaluations at Yale Comprehensive Epilepsy Center from 2012 to 2013, had all major lobes sampled, and had localizable seizure onsets. Segments of non–rapid eye movement (NREM) sleep prior to the first seizure were analyzed. We implemented a semiautomated process to analyze oscillations with peak frequencies >80 Hz (ripples 80–250 Hz; fast ripples 250–500 Hz). A contact location was considered epileptic if it exhibited epileptiform discharges during the intracranial evaluation or was involved ictally within 5 s of seizure onset; otherwise it was considered nonepileptic.

Results

We analyzed recordings from 1,209 electrode contacts in seven patients. The nonepileptic contacts constituted 79.1% of the total number of contacts. Ripples constituted 99% of total detections. Eighty‐two percent of all HFOs were seen in 45.2% of the nonepileptic contacts (82.1%, 47%, 34.6%, and 34% of the occipital, parietal, frontal, and temporal nonepileptic contacts, respectively). The following sublobes exhibited physiologic HFOs in all patients: Perirolandic, basal temporal, and occipital subregions. The ripples from nonepileptic sites had longer duration, higher amplitude, and lower peak frequency than ripples from epileptic sites. A high HFO rate (>1/min) was seen in 110 nonepileptic contacts, of which 68.2% were occipital. Fast ripples were less common, seen in nonepileptic parietooccipital regions only in two patients and in the epileptic mesial temporal structures.

Conclusions

There is consistent occurrence of physiologic HFOs over vast areas of the neocortex outside the epileptic network. HFOs from nonepileptic regions were seen in the occipital lobes and in the perirolandic region in all patients. Although duration of ripples and peak frequency of HFOs are the most effective measures in distinguishing pathologic from physiologic events, there was significant overlap between the two groups.
Positional cloning of the sex‐linked giant egg (Ge) locus in the silkworm, Bombyx mori
Authors: Fujii T. , Abe H. , Kawamoto M. , Banno Y. , Shimada T.
Published: December 2014

The giant egg (Ge) locus is a Z‐linked mutation that leads to the production of large eggs. Cytological observations suggest that an unusual translocation of a large fragment of the W chromosome bearing a putative egg size‐determining gene, Esd, gave rise to giant egg mutants. However, there is currently no molecular evidence confirming either a W–Z translocation or the presence of Esd on the W chromosome. To elucidate the origin of giant egg mutants, we performed positional cloning. We observed that the Bombyx mori. orthologue of the human Phytanoyl‐CoA dioxygenase domain containing 1 gene (PHYHD1) is disrupted in giant egg mutants. PHYHD1 is highly conserved in eukaryotes and is predicted to be a Fe(II) and 2‐oxoglutarate‐dependent oxygenase. Exon skipping in one of the two available Ge mutants is probably caused by the insertion of a non‐long terminal repeat transposon into intron 4 in the vicinity of the 5′ splice site. Segmental duplication in Ge2, an independent allele, was caused by unequal recombination between short interspersed elements inserted into introns 3 and 5. Our results indicate that (1) Bombyx PHYHD1 is responsible for the Ge mutants and that (2) the Ge locus is unrelated to the W‐linked putative Esd. To our knowledge, this is the first report describing the phenotypic defects caused by mutations in PHYHD1 orthologues.
Sparse evidence of MERS‐CoV infection among animal workers living in Southern Saudi Arabia during 2012
Authors: Memish Ziad A. , Alsahly Ahmad , Masri Malak al , Heil Gary L. , Anderson Benjamin D. , Peiris Malik , Khan Salah Uddin , Gray Gregory C.
Published: December 2014

Middle East respiratory syndrome coronavirus (MERS‐CoV) is an emerging viral pathogen that primarily causes respiratory illness. We conducted a seroprevalence study of banked human serum samples collected in 2012 from Southern Saudi Arabia. Sera from 300 animal workers (17% with daily camel exposure) and 50 non‐animal‐exposed controls were examined for serological evidence of MERS‐CoV infection by a pseudoparticle MERS‐CoV spike protein neutralization assay. None of the sera reproducibly neutralized the MERS‐CoV‐pseudotyped lentiviral vector. These data suggest that serological evidence of zoonotic transmission of MERS‐CoV was not common among animal workers in Southern Saudi Arabia during July 2012.
The role of the small GTPase Rab31 in cancer
Authors: Chua Christelle En Lin , Tang Bor Luen
Published: December 2014

Members of the small GTPase family Rab are emerging as potentially important factors in cancer development and progression. A good number of Rabs have been implicated or associated with various human cancers, and much recent excitement has been associated with the roles of the Rab11 subfamily member Rab25 and its effector, the Rab coupling protein (RCP), in tumourigenesis and metastasis. In this review, we focus on a Rab5 subfamily member, Rab31, and its implicated role in cancer. Well recognized as a breast cancer marker with good prognostic value, recent findings have provided some insights as to the mechanism underlying Rab31's influence on oncogenesis. Levels of Oestrogen Receptor α (ERα)‐ responsive Rab31 could be elevated through stabilization of its transcript by the RNA binding protein HuR, or though activation by the oncoprotein mucin1‐C (MUC1‐C), which forms a transcriptional complex with ERα. Elevated Rab31 stabilizes MUC1‐C levels in an auto‐inductive loop that could lead to aberrant signalling and gene expression associated with cancer progression. Rab31 and its guanine nucleotide exchange factor GAPex‐5 have, however, also been shown to enhance early endosome‐late endosome transport and degradation of the epidermal growth factor receptor (EGFR). The multifaceted action and influences of Rab31 in cancer is discussed in the light of its new interacting partners and pathways.