Improving inferences from short‐term ecological studies with Bayesian hierarchical modeling: white‐headed woodpeckers in managed forests

Pilot studies are often used to design short‐term research projects and long‐term ecological monitoring programs, but data are sometimes discarded when they do not match the eventual survey design. Bayesian hierarchical modeling provides a convenient framework for integrating multiple data sources while explicitly separating sample variation into observation and ecological state processes. Such an approach can better estimate state uncertainty and improve inferences from short‐term studies in dynamic systems. We used a dynamic multistate occupancy model to estimate the probabilities of occurrence and nesting for white‐headed woodpeckers Picoides albolarvatus in recent harvest units within managed forests of northern California, USA. Our objectives were to examine how occupancy states and state transitions were related to forest management practices, and how the probabilities changed over time. Using Gibbs variable selection, we made inferences using multiple model structures and generated model‐averaged estimates. Probabilities of white‐headed woodpecker occurrence and nesting were high in 2009 and 2010, and the probability that nesting persisted at a site was positively related to the snag density in harvest units. Prior‐year nesting resulted in higher probabilities of subsequent occurrence and nesting. We demonstrate the benefit of forest management practices that increase the density of retained snags in harvest units for providing white‐headed woodpecker nesting habitat. While including an additional year of data from our pilot study did not drastically alter management recommendations, it changed the interpretation of the mechanism behind the observed dynamics. Bayesian hierarchical modeling has the potential to maximize the utility of studies based on small sample sizes while fully accounting for measurement error and both estimation and model uncertainty, thereby improving the ability of observational data to inform conservation and management strategies.     

Establishment and Characterization of UTI and CAUTI in a Mouse Model

Urinary tract infections (UTI) are highly prevalent, a significant cause of morbidity and are increasingly resistant to treatment with antibiotics. Females are disproportionately afflicted by UTI: 50% of all women will have a UTI in their lifetime. Additionally, 20-40% of these women who have an initial UTI will suffer a recurrence with some suffering frequent recurrences with serious deterioration in the quality of life, pain and discomfort, disruption of daily activities, increased healthcare costs, and few treatment options other than long-term antibiotic prophylaxis. Uropathogenic Escherichia coli (UPEC) is the primary causative agent of community acquired UTI. Catheter-associated UTI (CAUTI) is the most common hospital acquired infection accounting for a million occurrences in the US annually and dramatic healthcare costs. While UPEC is also the primary cause of CAUTI, other causative agents are of increased significance including Enterococcus faecalis. Here we utilize two well-established mouse models that recapitulate many of the clinical characteristics of these human diseases. For UTI, a C3H/HeN model recapitulates many of the features of UPEC virulence observed in humans including host responses, IBC formation and filamentation. For CAUTI, a model using C57BL/6 mice, which retain catheter bladder implants, has been shown to be susceptible to E. faecalis bladder infection. These representative models are being used to gain striking new insights into the pathogenesis of UTI disease, which is leading to the development of novel therapeutics and management or prevention strategies.     

盆底肌力强度对产后压力性尿失禁发生的预测作用研究

目的:探讨盆底肌力强度对产后压力性尿失禁发生的预测作用。方法:2013年4月至2014年3月,随机抽取200例在本院产检和分娩的产妇,收集其临床资料,并在产后6个月检测其盆底肌力强度,根据产妇是否有压力性尿失禁分为尿失禁组和非尿失禁组,运用双变量分析、分类和回归树等统计方法,建立一个产后压力性尿失禁的预测模型。结果:尿失禁组和非尿失禁组在慢性咳嗽、孕前已有尿失禁症状、孕期有新发尿失禁症状以及盆底肌力强度等4项因素中有统计学差异(P0.05);分类与回归树预测模型提示盆底肌力强度小于等于35.5 cm H2O、孕前已有尿失禁症状、新生儿出生体重大于2988 g及孕期有新发尿失禁症状对产后尿失禁有预测作用,其中盆底肌力强度的预测作用最显著。结论:根据预测模型筛选出产后压力性尿失禁的高危人群,及早对其进行干预,对减少产后压力性尿失禁的发生率有一定的临床意义,而预测模型的构建还需进一步的研究和验证。     

Greenhouse gas fluxes from an Australian subtropical cropland under long‐term contrasting management regimes

The long‐term effects of conservation management practices on greenhouse gas fluxes from tropical/subtropical croplands remain to be uncertain. Using both manual and automatic sampling chambers, we measured N₂O and CH₄ fluxes at a long‐term experimental site (1968–present) in Queensland, Australia from 2006 to 2009. Annual net greenhouse gas fluxes (NGGF) were calculated from the 3‐year mean N₂O and CH₄ fluxes and the long‐term soil organic carbon changes. N₂O emissions exhibited clear daily, seasonal and interannual variations, highlighting the importance of whole‐year measurement over multiple years for obtaining temporally representative annual emissions. Averaged over 3 years, annual N₂O emissions from the unfertilized and fertilized soils (90 kg N ha^?1 yr^?1 as urea) amounted to 138 and 902 g N ha^?1, respectively. The average annual N₂O emissions from the fertilized soil were 388 g N ha^?1 lower under no‐till (NT) than under conventional tillage (CT) and 259 g N ha^?1 higher under stubble retention (SR) than under stubble burning (SB). Annual N₂O emissions from the unfertilized soil were similar between the contrasting tillage and stubble management practices. The average emission factors of fertilizer N were 0.91%, 1.20%, 0.52% and 0.77% for the CT‐SB, CT‐SR, NT‐SB and NT‐SR treatments, respectively. Annual CH₄ fluxes from the soil were very small (?200–300 g CH₄ ha^?1 yr^?1) with no significant difference between treatments. The NGGF were 277–350 kg CO₂‐e ha^?1 yr^?1 for the unfertilized treatments and 401–710 kg CO₂‐e ha^?1 yr^?1 for the fertilized treatments. Among the fertilized treatments, N₂O emissions accounted for 52–97% of NGGF and NT‐SR resulted in the lowest NGGF (401 kg CO₂‐e ha^?1 yr^?1 or 140 kg CO₂‐e t^?1 grain). Therefore, NT‐SR with improved N fertilizer management practices was considered the most promising management regime for simultaneously achieving maximal yield and minimal NGGF.     

Modelling the effects on phytoplankton communities of changing mixed depth and background extinction coefficient on three contrasting lakes in the English Lake District

1. The process‐based phytoplankton community model, PROTECH, was used to model the response of algal biomass to a range of mixed layer depths and extinction coefficients for three contrasting lakes: Blelham Tarn (eutrophic), Bassenthwaite Lake (mesotrophic) and Ullswater (oligotrophic). 2. As expected, in most cases biomass and diversity decreased with decreasing light availability caused by increasing the mixed depth and background extinction coefficient. The communities were generally dominated by phytoplankton tolerant of low light. Further, more novel, factors were identified, however. 3. In Blelham Tarn in the second half of the year, biomass and diversity did not generally decline with deeper mixing and the community was dominated by nitrogen‐fixing phytoplankton because that nutrient was limiting to growth. 4. In Bassenthwaite Lake, changing mixed depth influenced the retention time so that, as the mixed depth declined, the flushing rate in the mixed layer increased to the point that only fast‐growing phytoplankton could dominate. 5. In the oligotrophic Ullswater, changing the mixed depth had a greater effect through nutrient supply rather than light availability. This effect was observed when the mixed layer was relatively shallow (<5.5 m) and the driver for this was that the inflowing nutrients were added to a smaller volume of water, thus increasing nutrient concentrations and algal growth. 6. Therefore, whilst changes in mixed depth generally affect the phytoplankton via commonly recognized factors (light availability, sedimentation rate), it also affected phytoplankton growth and community composition through other important factors such as retention time and nutrient supply.     

Digestion in the common marmoset (Callithrix jacchus), a gummivore–frugivore

Wild common marmosets (Callithrix jacchus) feed on fruits, insects, and gums, all of which provide different digestive challenges. Much of the ingested mass of fruits consists of seeds. In general, seeds represent indigestible bulk to marmosets and could inhibit feeding if they are not eliminated rapidly. In contrast, gums are β‐linked polysaccharides that require microbial fermentation. Their digestion would benefit from an extended residence time within the gut. Earlier research found that mean retention time (MRT) for a liquid digestive marker (cobalt EDTA) was significantly longer than MRT for a particulate marker (chromium‐mordanted fiber), suggesting that common marmosets preferentially retain liquid digesta. We conducted two four‐day‐long digestion trials on 13 individually housed adult common marmosets fed a single‐item, purified diet in order to examine the relations among MRT of cobalt EDTA and chromium‐mordanted fiber, food dry matter intake (DMI), and apparent digestibility of dry matter (ADDM). We compared the MRT values with the data from the previous study mentioned above and a study using polystyrene beads. There were no significant correlations among MRT, ADDM, or DMI, although increases in DMI between trials were associated with decreases in MRT. ADDM was consistent within individuals between trials; but the mean values ranged from 75.0 to 83.4% among individuals. We found no difference in MRT between the liquid (17.5±1.6 hr) and particulate (17.9±1.4 hr) markers. Although these values were not significantly different than found previously, the MRT for chromium‐mordanted fiber tended to be longer. This probably reflects the relatively small size of the chromium‐mordanted fiber particles used in this study. An inverse relationship between particle size and MRT was evident; the mean MRT of polysterene beads, the largest marker, was only 8.3±1.5 hr. Marmosets appear to retain liquids and small particles within the gut longer than large particles. Am. J. Primatol. 71:957–963, 2009. © 2009 Wiley‐Liss, Inc.     

A longitudinal study of urinary dipstick parameters in wild chimpanzees (Pan troglodytes verus) in Côte d'Ivoire

We performed 796 dip‐stick tests on urine from 100 wild West African chimpanzees (Pan troglodytes verus) from 4 habituated groups in the tropical rain forest of Taï National Park, Cote d'Ivoire, to establish reference values for health monitoring. Specific gravity was also measured on 359 urine samples from 62 chimpanzees. The effect of age, sex, group, month, estrus, pregnancy, meat consumption, and acute respiratory disease on pH, leucocytes, protein, blood, hemoglobin, and glucose was examined using ordinal logistic regression. The presence of nitrite, ketones, bilirubin, and urobilinogen in urine was also recorded. Outbreak of acute respiratory disease did not influence any of the urinary parameters. Thirty‐seven percent of the samples had a pH <7 and the whole range of pH was found through the year, in all age groups, and in both sexes. Meat consumption lowered the urinary pH. Our results show that all pH levels must be considered normal for the West African chimpanzee subspecies P. troglodytes verus living in the rainforest. We also found a cluster of glucose‐positive samples at a specific point in time which was not attributed to diabetes mellitus. These findings highlight that there are differences in normal physiological parameters among wild chimpanzees living in different habitats. Am. J. Primatol. 72:689–698, 2010. © 2010 Wiley‐Liss, Inc.     

Protein disulfide isomerase chaperone ERP‐57 decreases plasma membrane expression of the human GnRH receptor

Retention of misfolded proteins by the endoplasmic reticulum (ER) is a quality control mechanism involving the participation of endogenous chaperones such as calnexin (CANX). CANX interacts with and restricts plasma membrane expression (PME) of the gonadotropin releasing hormone receptor (GnRHR), a G protein‐coupled receptor. CANX also interacts with ERP‐57 a thiol oxidoreductase chaperone present in the ER. CANX along with ERP‐57 promotes the formation of disulfide bond bridges in nascent proteins. The human GnRH receptor (hGnRHR) is stabilized by two disulfide bond bridges (C¹⁴‐C²⁰⁰ and C¹¹⁴‐C¹⁹⁶), that, when broken, lead to a decrease in receptor expression at the plasma membrane. To determine if the presence of chaperones CANX and ERP‐57 exerts an influence over membrane routing and second messenger activation, we assessed the effect of various mutants including those with broken disulfide bridges (Cys → Ala) along with the hGnRHR. The effect of chaperones on mutants was insignificant, whereas the over expression of ERP‐57 led to an hGnRHR retention. This effect was further enhanced by cotransfection with cDNA for CANX showing receptor retention by ERP‐57 augmented by CANX, suggesting utilization of these chaperones for quality control of the GnRHR. Copyright © 2009 John Wiley & Sons, Ltd.     

Maternal and paternal hybrid triploids of tetras

Hybrid maternal triploids were generated by crossing grey-body and red or yellow-tailed Buenos Aires tetra Hemigrammus caudovittatus (BT) males with albino or black Gymnocorymbus ternetzi [widow tetra (WT)] females and retaining the second polar body by heat shock (HS) or cold shock (CS). Paternal triploids were also generated using 2·5% polyethylene glycol (PEG) incubated BT semen to facilitate the entry of two sperm into an egg of WT. Optimum temperature for CS was identified as 6° C and the optimum age for thermal shocking the zygote as 3 min after fertilization. At hatching, survival was 25, 17 and 5% for the HS, CS and paternal triploids, respectively. At maturity, it was further reduced to >2% and the maturity inordinately delayed. With the presence of undifferentiated 'steriles' and almost total absence of females, the expected sex ratio was distorted. Triploid males produced spermatocytes, spermatids but not spermatozoa. Triploidy was confirmed by phenotypic markers, karyotyping, erythrocyte measurement and molecular markers. The fusiform body shape of WT was a dominant phenotypic trait over the typical piscine slender body shape of BT. Polymerase chain reaction products of the genomic DNA of the triploids amplified by OPF6 primer were 300, 450 and 1000 bp length, characteristic of BT, and 500 and 800 bp, typical of WT and thereby confirmed the biparental genomic contribution to the triploids. Analyses of genomic DNA of selected progenies using DMRT-1 marker showed that (1) like the diploid BT males, the hybrid triploid males were also true genetic males, and amplified 237 and 300 bp products but (2) the triploid steriles amplified all the three products of 100, 237 and 300 bp indicating that they were mosaics but the diploid steriles failed to amplify.