bluuebunny/crossref_metadata_2025 huggingface dataset:
49 SUCCESSFUL CRYOPRESERVATION USING LOW ETHYLENE GLYCOL CONCENTRATION FOR IN VITRO-PRODUCED BOVINE EMBRYOS
Authors: Takayama M. , Sato S. , Nishimura Y. , Imai K. , Dochi O.
Published: December 2016

In vitro-produced (IVP) bovine embryos tend to have a lower survival rate after cryopreservation than in vivo embryos do. Therefore, the freezing medium (FM) and concentration of cryoprotectant are very important factors. This study was to investigate the effect of 1.2 M ethylene glycol (EG) with 0.1 M sucrose (SUC) on survival of IVP embryos after freezing. The COC were matured in 25 mM HEPES-buffered TCM199 (TCM199) supplemented with 5% calf serum (CS) and 0.02 AU mL−1 FSH. Oocytes (20 to 25) were cultured in 100-μL droplets of maturation medium for 20 h. After 6 h of gamete co-culture (5 × 106 sperm/mL), the presumptive zygotes were cultured in CR1aa medium supplemented with 5% CS for 9 days (fertilization = Day 0). Only the expanded blastocysts from Days 7 to 9 were used in this experiment and separated into 3 treatment groups. The first and second groups were frozen in Dulbecco’s phosphate-buffered saline (D-PBS) supplemented with 20% CS, 0.1 M SUC, and 1.2 or 1.5 M EG (groups 1.2 or 1.5 M EG), respectively. The third group was D-PBS supplemented with 20% fetal calf serum (FCS), 0.25 M SUC, and 1.4 M glycerol (group GLY). In each group, embryos were equilibrated with their FM for 10 min and loaded into 0.25-mL straws individually. These straws were placed into the cooling chamber of a programmable freezer precooled to −7°C. After 2 min, the straws were seeded and then held for a further 13 min at −7°C. Then, the straws were cooled to −30°C at −0.3°C/min before being plunged into liquid nitrogen. The cryopreserved embryos were thawed by allowing the straws to stand in air for 7 s and then warming them in a 30°C water bath for 20 s. The thawed embryos were washed twice using 38°C D-PBS supplemented with 20% FCS. Subsequently, they were immersed in the same medium, held at 38°C for 10 min, and then each embryo was cultured in 20-μL droplets of TCM199 supplemented with 20% FCS and 0.1 mM β-mercaptoethanol for 72 h. The rates of embryos developing to the re-expanded and hatching blastocyst stages were determined 72 h after thawing. All data were analysed by the chi-squared test with Yates’ correction. The re-expanded and hatching rates of frozen-thawed embryos after 72 h in culture were not significantly different between 1.2 M EG (n = 39: 71.8% and 69.2%), 1.5 M EG (n = 38: 76.3% and 63.2%), and 1.4 M GLY (n = 37: 75.7% and 64.9%) groups (P > 0.05). Survival and hatching rates according to embryo quality were also not significantly different between 1.2 M EG (good n = 18: 88.9% and 88.9%; fair n = 21: 57.1% and 52.4%), 1.5 M EG (good n = 19: 89.5% and 84.2%; fair n = 19: 63.2% and 42.1%), and 1.4 M GLY (good n = 18: 77.8% and 66.7%; fair n = 19: 73.7% and 63.2%) (P > 0.05). In conclusion, cryoprotectant type and concentration did not affect embryo survival or development after cryopreservation in this study. Therefore, the ethylene glycol concentration used for the cryopreservation of IVP embryos can be reduced.
79 THE CELL-CYCLE RELATED NUCLEAR LOCALIZATION OF PLATELET-ACTIVATING FACTOR IN BOVINE AND MURINE EMBRYO DEVELOPMENT
Authors: Vandenberghe L. T. M. , De Schauwer C. , Heindryckx B. , Van Soom A.
Published: December 2016

Platelet-activating factor (PAF) is a lipid mediator produced by a wide variety of cells and well known for its involvement in host defense and platelet aggregation. In embryo development, PAF functions as an embryotropin and a marker of embryo quality and viability in human and mice. However, only limited information is available concerning its function during in vitro culture of bovine embryos. Bovine and murine embryos were collected at different time points according to their development (4–8-16 cells-morula-blastocyst; 8–10 embryos per replicate; 4 replicates). Phospholipid expression and intracellular localization was evaluated by immunofluorescent staining and confocal scanning microscopy. In short, the zona pellucida of the embryos was removed using 0.5% protease (from Streptomyces griseus). After a recovery period of 30 min, embryos were fixed in 4% paraformaldehyde and permeabilized (0.5% Triton X-100 and 0.05% Tween20) overnight at 4°C. Subsequently, embryos were transferred to blocking solution (30% goat serum and 0.05% Tween20) overnight at 4°C to block nonspecific binding sites. Next, embryos were incubated overnight with primary antibody against PAF (1:100; Emelca Bioscience, Breda, the Netherlands) at 4°C, followed by 1 h of incubation with secondary goat anti-rabbit (Alexa Fluor 488; 1:500; Abcam, Cambridge, MA, USA). Nuclei were visualised by 20 min incubation with Hoechst 33342 (1:500, Molecular Probes) in the dark. As a negative control, the primary antibody was replaced with rabbit IgG whole molecule (Rockland Immunochemicals, Limerick, PA, USA). Using specific lipid antibodies, we were able to show that PAF accumulates in the nuclei of pre-implantation bovine and murine embryos. Suprisingly, the localization correlated with the cell cycle: a clear nuclear signal was observed during interphase and a redistribution to the cytoplasm happened upon nuclear envelope breakdown at mitosis. To confirm this finding, bovine blastocysts (10 embryos per replicate, 3 replicates) were incubated for 12 h with the microtubule destabilising agent nocodazole (2 μM; Sigma, Germany). Embryos were analysed using immunofluorescent staining as described above. Nocodazole treatment resulted in arrest of at least 20% of the embryonic cells at mitosis. Upon treatment, we were able to reproduce the cell-cycle dependent shuttling between M-phase and interphase nuclei of PAF. We are the first to attribute this unique feature of nucleo-cytoplasmic redistribution to an important embryonic growth factor such as PAF. Further research will be needed to unravel the exact pathway and function of PAF in the nucleus and its implications on embryonic development.
81 IMPROVEMENT OF DEVELOPMENTAL COMPETENCE OF BOVINE IN VITRO-PRODUCED EMBRYOS BY ADDING 2-METHOXYSTYPANDRONE IN MATURATION MEDIA
Authors: Mesalam A. , Khan I. , Lee K.-L. , Song S.-H. , Joo M.-D. , Chowdhury M. M. R. , Xu L. , Zhang S. , Jin J.-I. , Kong I.-K.
Published: December 2016

The 2-methoxystypandrone (2-MS) is a naphthoquinone isolated from Polygonum cuspidatum. The objective of this study was to investigate the effects of 2-MS on oocyte maturation, blastocyst development, and embryo quality in terms of cell number and gene expression in vitro. A total of 2364 oocytes were cultured in TCM-199 supplemented with 10% fetal bovine serum, 1 μg mL−1 oestradiol-17β, 10 μg mL−1 FSH, 10 ng mL−1 epidermal growth factor, 0.6 mM cysteine, and 0.2 mM sodium pyruvate and supplemented with different concentrations of 2-MS as following: 1.5 μM (n = 458), 1.0 (n = 493), 0.5 (n = 468), 0.1 (n = 470), and 0 μM (control, n = 475) followed by IVF and then culture in CR1-aa medium supplemented with 44 μg mL−1 sodium pyruvate, 14.6 μg mL−1 glutamine, 10 μL mL−1 penicillin-streptomycin, 3 mg mL−1 BSA, and 310 μg mL−1 glutathione for the first 3 days, and then the BSA was replaced with 10% FBS until Day 8. The differences in embryo development between experimental groups were analysed by one-way ANOVA. The Duncan’s multiple range tests were used to test the differences between the treatments. The level of statistical significance was set at P < 0.05. The results showed that the addition of 2-MS at 1.0 mM significantly improved (P < 0.05) the percentage of MII oocytes, which were identified by aceto-orcein staining, compared with that in the control (76.5 v. 65.4%, respectively), and remarkably (P < 0.05), improved blastocyst development rates (45.29%) compared with control (32.21%). Additionally, TUNEL assay demonstrated that treatment with 1.0 μM of 2-MS significantly improved the embryo quality by increasing total number of cells and reducing DNA damage. Immunofluorescent analysis showed that the protein levels of nuclear factor-kappa B (NFkB), inhibitor of kappa B kinase β (IkKβ), 8-oxoguanine, and cyclooxygenase-2 (COX2) declined significantly (P < 0.05) after 2-MS treatment compared with the control. These results were confirmed by qRT-PCR, which showed a significant decrease in the mRNA levels of NFkB, IkKβ, COX2, inducible nitric oxide synthase (iNOS), BCL2-associated X protein (BAX), caspase-3, and Janus kinase2 (JAK2) after 2-MS treatment; however, the mRNA level of the anti-apoptotic gene B-cell lymphoma2 (BCL2) was significantly higher than that in the control. In conclusion, the addition of 2-MS at the indicated concentration dramatically improves the developmental competence of bovine in vitro-produced embryos.
This work was supported by a grant from the Next-Generation BiogGeen21 (No. PJ01107703), IPET (No. 315017–5), BK21plus, and KGSP.
89 METHYLATION STATUS OF IGF2/H19 DMR3 REGION AFFECTS IN VITRO BLASTOCYST PRODUCTION IN GOAT (CAPRA HIRCUS)
Authors: Tiwari M. , Rawat N. , Vats P. , Nagoorvali D. , Mahajan M. , Chauhan M. S. , Manik R. S. , Singla S. K. , Palta P. , Singh M. K.
Published: December 2016

Parthenogenesis has been observed in lower animals but no known instance has been reported in mammals because both maternal and paternal genomes are a fundamental prerequisite for embryogenesis. A major reason for developmental failure of uniparental zygotes is expression of certain genes in a parent-of-origin-specific manner, i.e. genomic imprinting of genes. Out of many imprinted genes identified so far, IGF2/H19 have been extensively studied and known to play an important role in fetal and placental development. Gene IGF2 is expressed by the paternal allele, H19 is transcribed from the maternal allele, and the reciprocal expression of both genes is regulated by the DMR3 region placed upstream of the H19 gene. In the present study we compared the methylation status of IGF2/H19 DMR in parthenogenetic activated (PA) and IVF goat (Capra hircus) blastocyst through bisulphite sequencing. For this, immature oocytes of usable quality were subjected to in vitro maturation and subsequently used for embryo production through parthenogenesis (n = 993) (by calcium ionophore and 6-DMAP activation) and IVF (n = 1096). It was found that embryo production rate at all the embryonic stages (2-cell, 4-cell, 8–16-cell, morula, and blastocyst) was significantly higher (P < 0.05) in parthenogenesis (74.66 ± 3.35%, 61.90 ± 2.73%, 47.83 ± 2.95%, 38.13 ± 5.28%, and 21.11 ± 2.51%, respectively) as compared with IVF (55.21 ± 2.02%, 38.12 ± 2.48%, 28.53 ± 1.67%, 21.57 ± 1.59%, and 8.23 ± 1.02%, respectively). When blastocysts (n = 6 each) were subjected to TUNEL, it was found that PA blastocyst showed significantly higher (P < 0.05) total cell number (217.83 ± 18.80 v. 159.67 ± 13.94) and significantly low (P < 0.05) apoptotic index (2.04 ± 0.25 v. 4.03 ± 0.29) as compared with IVF blastocysts. For the methylation pattern study, we analysed 17 CpG sites on the DMR3 region of the IGF2/H19 gene. Variable methylation pattern was observed within these CpG sites in different clones (n = 15) of PA and IVF blastocyst. The DMR3 region of the IGF2/H19 gene was significantly hypermethylated (P < 0.05) in PA blastocysts as compared with IVF blastocysts (80.39 ± 2.96, 32.55 ± 4.37, respectively), which suggests higher expression of IGF2 in parthenotes. The result suggests IGF2 might play different roles in different species; the same expression pattern of IGF2 is observed in ovine, but a contrary result is found in porcine species. Our results signify the hypermethylation of IGF2/H19 DMR3, which leads to higher expression of IGF2 to support embryonic development at the blastocyst stage.
This work was supported by the NFBSFARA Project on Parthenogenetic Goat (CA-4002), New Delhi, India.
98 INFLUENCE OF INJECTION ALTRENOGEST IN UTERINE TONE AND EMBRYONIC VESICLE GROWTH IN RECIPIENT MARES
Authors: Vallejo Aristizabal V. H. , Mogollón Garcia H. D. , Dell'aqua Junior J. A.
Published: December 2016

The objective of this study was to compare the influence of injectable altrenogest on uterine tone (UT) and embryonic vesicle growth (EVG) in non-cyclic recipient mares in anestrus and transition with cyclic mares. This study was conducted in Brazil in the winter season (June to September) between 2011 and 2014. One-hundred fifty-five embryo transfers (ET) were made in crossbreed mares from 4 to 10 years of age, between 350 and 450 kg of weight. The recipient mares were distributed into 3 groups: G1: anestrus (n = 67), mares with follicles less than 15 mm and absence of corpus luteum; G2: transition (n = 14), mares with follicles between 15 and 20 mm and absence of corpus luteum; and G3: cyclic (n = 74), mares with follicles larger than 20 mm and presence of corpus luteum. On Day 0 (day of donor mare ovulation), recipient mares in G1 and G2 received a single IM dose of 17β-oestradiol (10 mg). Recipients were examined by ultrasound on Days 1 and 2 to evaluate the presence of uterine oedema. On Day 2, once oedema was confirmed, recipients were given 180 mg of altrenogest IM, and altrenogest treatment was repeated every 8 days until Day 90 of gestation. The G3 recipient mares were not treated with 17β-oestradiol and altrenogest. For mares in G1 and G2, ET was performed 6 days after the initiation of altrenogest treatment. For recipients in G3, ET was performed between Days 6 and 8. Uterine tone was evaluated before ET on a scale of 0 to 3 (tonus absent 0, and tonus intense 3). Conception rate was determined by ultrasound at Day 15. The diameter of the EVG was calculated by measuring the length and width of the embryonic vesicle on Days 15, 20, 25, 30, 35, 40, and 45 using ultrasonography. Analysis of the variables UT and EVG was performed with Proc Mixed. Results are represented as ± standard error of the mean. Statistical analysis for conception rate was made by chi-square distribution adjusted with the Fisher’s test when it was required. All data were analysed with the SAS statistical package. There was no difference (P > 0.05) in UT between recipient groups (G1: 2.6 ± 0.04; G2: 2.6 ± 0.09; G3: 2.5 ± 0.04). In addition, there was no effect of recipient group nor an interaction between recipient group and day of gestation for EVG (P > 0.05). However, conception rate was greater (P < 0.05) in G2 (11/14 = 78%) and G3 (44/74 = 59%) compared with G1 (26/67 = 39%). Results of the present study demonstrate the effectiveness of injectable altrenogest for use in managing anestrus and transition mares for ET.
How Australian mammals contributed to our understanding of sex determination and sex chromosomes
Authors: Graves Jennifer A. Marshall
Published: December 2016

Marsupials and monotremes can be thought of as independent experiments in mammalian evolution. The discovery of the human male-determining gene, SRY, how it works, how it evolved and defined our sex chromosomes, well illustrates the value of comparing distantly related animals and the folly of relying on humans and mice for an understanding of the most fundamental aspects of mammalian biology. The 25th anniversary of the discovery of SRY seems a good time to review the contributions of Australian mammals to these discoveries. The discovery of the mammalian sex determining gene, SRY, was a milestone in the history of human genetics. SRY opened up investigations into the pathway by which the genital ridge (bipotential gonad) becomes a testis. Studies of Australian mammals were important in the story of the discovery of SRY, not only in refuting the qualifications of the first candidate sex-determining gene, but also in confirming the ubiquity of SRY and raising questions as to how it works. Studies in marsupials also led to understanding of how SRY evolved from a gene on an autosome with functions in the brain and germ cells, and to identifying the ancestors of other genes on the human Y. The discovery that platypus have sex chromosomes homologous, not to the human XY, but to the bird ZW, dated the origin of the therian SRY and the XY chromosomes it defined. This led to important new models of how our sex chromosomes function, how they evolved, and what might befall this gene and the Y chromosome it defines.
IntegratedMRF: random forest-based framework for integrating prediction from different data types
Authors: Rahman Raziur , Otridge John , Pal Ranadip
Published: December 2016

IntegratedMRF is an open-source R implementation for integrating drug response predictions from various genomic characterizations using univariate or multivariate random forests that includes various options for error estimation techniques. The integrated framework was developed following superior performance of random forest based methods in NCI-DREAM drug sensitivity prediction challenge. The computational framework can be applied to estimate mean and confidence interval of drug response prediction errors based on ensemble approaches with various combinations of genetic and epigenetic characterizations as inputs. The multivariate random forest implementation included in the package incorporates the correlations between output responses in the modeling and has been shown to perform better than existing approaches when the drug responses are correlated. Detailed analysis of the provided features is included in the Supplementary Material.

Availability and Implementation

The framework has been implemented as a R package IntegratedMRF, which can be downloaded from https://cran.r-project.org/web/packages/IntegratedMRF/index.html, where further explanation of the package is available.

Supplementary information

Supplementary data are available at Bioinformatics online.
Effects of Cardiopulmonary Bypass on Renal Perfusion, Filtration, and Oxygenation in Patients Undergoing Cardiac Surgery
Authors: Lannemyr Lukas , Bragadottir Gudrun , Krumbholz Vitus , Redfors Bengt , Sellgren Johan , Ricksten Sven-Erik
Published: December 2016

Background

Acute kidney injury is a common complication after cardiac surgery with cardiopulmonary bypass. The authors evaluated the effects of normothermic cardiopulmonary bypass on renal blood flow, glomerular filtration rate, renal oxygen consumption, and renal oxygen supply/demand relationship, i.e., renal oxygenation (primary outcome) in patients undergoing cardiac surgery.

Methods

Eighteen patients with a normal preoperative serum creatinine undergoing cardiac surgery procedures with normothermic cardiopulmonary bypass (2.5 l · min−1 · m−2) were included after informed consent. Systemic and renal hemodynamic variables were measured by pulmonary artery and renal vein catheters before, during, and after cardiopulmonary bypass. Arterial and renal vein blood samples were taken for measurements of renal oxygen delivery and consumption. Renal oxygenation was estimated from the renal oxygen extraction. Urinary N-acetyl-β-d-glucosaminidase was measured before, during, and after cardiopulmonary bypass.

Results

Cardiopulmonary bypass induced a renal vasoconstriction and redistribution of blood flow away from the kidneys, which in combination with hemodilution decreased renal oxygen delivery by 20%, while glomerular filtration rate and renal oxygen consumption were unchanged. Thus, renal oxygen extraction increased by 39 to 45%, indicating a renal oxygen supply/demand mismatch during cardiopulmonary bypass. After weaning from cardiopulmonary bypass, renal oxygenation was further impaired due to hemodilution and an increase in renal oxygen consumption, accompanied by a seven-fold increase in the urinary N-acetyl-β-d-glucosaminidase/creatinine ratio.

Conclusions

Cardiopulmonary bypass impairs renal oxygenation due to renal vasoconstriction and hemodilution during and after cardiopulmonary bypass, accompanied by increased release of a tubular injury marker.
Activation of PKCα and PI3K Kinases in Hypertrophic and Nodular Port Wine Stain Lesions
Authors: Yin Rong , Gao Lin , Tan Wenbin , Guo Wei , Zhao Tao , Nelson Jhon Stuart , Wang Gang
Published: December 2016

Port wine stain (PWS) is a congenital, progressive vascular malformation. Many patients with PWS develop hypertrophy and discrete nodularity during their adult life, but the mechanism(s) remain incompletely understood. In this study, we attempted to investigate activation status of PKCα, PI3K, PDPK1 and PLC-γ and protein levels of PP2A and DAG to explore their potential roles in the formation of hypertrophic and nodular PWS lesions. We found phosphorylated levels of PKCα, PI3K, PDPK1, and PLC-γ and protein levels of PP2A and DAG showed moderate increases in the endothelial cells of hypertrophic PWS as compared to the adjacent normal skin. These increases extended throughout the entire stroma of blood vessels in PWS nodules. Many proliferating cells, such as fibroblasts, also showed strong activation of PKCα, PI3K, PDPK1 and PLC-γ and upregulations of PP2A and DAG in nodular PWS lesions. Our data showed that there is aberrant activation of PKCα, PI3K, PDPK1 and PLC-γ and upregulation of PP2A and DAG mainly in endothelial cells in hypertrophic PWS areas, but presenting in the entire vasculatures and surrounding fibroblasts in PWS nodules. Our data suggest that both PKCα and PI3K signaling pathways contribute to the development of hypertrophy and nodularity in adult PWS.
Follicular Malignant Melanoma: A Rare Morphologic Variant of Melanoma. Report of a Case and Review of the Literature
Authors: Chapman Iona , Horton Sharon , Liu Wenhua
Published: December 2016

Follicular malignant melanoma (FMM) is an exceedingly rare variant of melanoma. Only 8 cases have been reported in the literature thus far. Often bland on physical examination, FMM shows a striking histologic pattern, with atypical melanocytes sometimes consuming the entire follicle and extending into the dermis. Criteria have been suggested to help distinguish FMM from lentigo maligna melanoma; however, no clear criteria distinguish this cancer clinically. FMM cannot be distinguished from follicular metastases of melanoma based on histology, requiring close clinical correlation and detailed history taking on the part of the practitioner. In this publication, we present a case of FMM and a review of the literature. A 59-year-old man was incidentally found to have a small flesh-colored papule on the arm during a skin cancer screening. Biopsy revealed atypical melanocytes extending from the follicular infundibulum into the reticular dermis. Immunohistochemical staining confirmed the melanocytic origin of the neoplasm. The patient underwent wide local excision with 2-cm margins. Sentinel lymph node biopsy was negative for melanoma. We present this case to highlight an unusual type of melanoma and illustrate how it may be distinguished from other neoplasms.
A mouse model for chronic pain-induced increase in ethanol consumption
Authors: Butler Ryan K. , Knapp Darin J. , Ulici Veronica , Longobardi Lara , Loeser Richard F. , Breese George R.
Published: December 2016

Chronic pain conditions are often comorbid with alcohol abuse. “Self-medication” with alcohol introduces a host of problems associated with the abuse of alcohol which over time has the potential of exacerbating the painful condition. Despite the prevalence of chronic pain being associated with alcohol abuse, rodent models which mimic the comorbid conditions are lacking. In this study, we model osteoarthritis (OA) in C57BL/6J mice by surgically destabilizing the medial meniscus (DMM). Sham-operated mice served as controls. Thirteen weeks after surgery, DMM but not sham-operated mice exhibited pronounced incapacitance of the surgically manipulated hind limb compared with the nonsurgically manipulated hind limb. At this time, the mice were exposed to the 2-bottle ethanol choice, beginning with 2.5% with a gradual increasing to 20%. Compared with sham controls, DMM mice consumed more EtOH and preferred EtOH over water at the 20% EtOH concentration. Histological analysis verified that the DMM mice exhibited significant damage to the articular cartilage and osteophyte growth compared with sham controls and these measures of the severity of OA correlated with the amount of ethanol intake. Thus, the combination of the DMM model of OA with the enhanced two-bottle ethanol choice is a potential preclinical approach in mice by which the basis of the comorbid association of alcohol abuse and chronic pain conditions can be explored.
Who's your daddy?: paternal inheritance of metabolic disease risk
Authors: Isganaitis Elvira , Suehiro Harumi , Cardona Connie
Published: December 2016

Purpose of review

Although the importance of optimizing mothers’ health prior to conception and during pregnancy is now well accepted, recent data also implicate health and nutritional status of fathers as contributors to chronic disease risk in their progeny. This brief review will highlight recent epidemiological and experimental studies linking paternal overnutrition, undernutrition, and other forms of stress, to metabolic disease in the offspring.

Recent findings

The past 2 years have brought tremendous insights into the mechanisms by which paternal exposures can contribute to disease susceptibility in the next generation. Recent data, both from humans and experimental models, demonstrate that paternal obesity and undernutrition result in epigenetic reprogramming of male germ cells, notably altered DNA methylation, histone retention, and expression of small noncoding RNAs and transfer RNA fragments. Novel mechanisms have also been identified, such as epididymal transport vesicles, seminal fluid hormones and metabolites, and a unique seminal fluid microbiome.

Paternal nutritional and other perturbations are linked to risk of metabolic disease and obesity in offspring. Germ cell-dependent mechanisms have recently been linked to these intergenerational effects. Nongenetic, paternal inheritance of chronic disease has important implications for public health, and may provide novel opportunities for multigenerational disease prevention.
Association Between Clinical Nurse Specialist’s Presence and Open Visitation in US Intensive Care Units
Authors: Suba Sukardi , Donesky DorAnne , Scruth Elizabeth Ann , Carrieri-Kohlman Virginia
Published: December 2016

Background:

Current evidence shows that an open visitation policy can benefit patients and families during intensive care unit (ICU) stays. Therefore, an unrestricted visitation policy in the ICU has been proposed as part of patient-centered care.

Purpose:

The purpose of this secondary analysis is to explore the likelihood of an ICU with a clinical nurse specialist (CNS) having an open visitation policy when compared with an ICU without a CNS.

Design:

This is a secondary analysis of a survey conducted between 2008 and 2009, describing the ICU visitation practices in more than 600 hospitals across the United States.

Methods:

χ2 Analysis was performed comparing the presence of CNS in the ICU with visitation policies, with P < 0.05 considered statistically significant.

Results:

There were data from 347 hospitals used in the analysis, with 47 hospitals (13.5%) having open visitation policies. There were 108 hospitals (31%) that had a CNS present in the ICU; 14 of the hospitals (13%) had open visitation policies. No significant correlation was found between a CNS being present in the ICU and open visitation policy (odds ratio, 0.93; P = .83), regardless of hospital geographic regions.

Conclusions:

Although CNS presence was not associated with open visitation in this study, given the strong evidence to support the benefits to patients and the CNS role as a change agent in the hospital system, liberalization of visitation in the ICU is an area that could benefit from CNS advocacy.
Correlational Study of Diabetic Retinopathy and Hearing Loss
Authors: Ooley Caroline , Jun Weon , Le Kim , Kim Allen , Rock Nathan , Cardenal Molly , Kline Rebecca , Aldrich Drew , Hayes John
Published: December 2016

Purpose

Our research goal was to complete a retrospective chart review to determine if there is a correlation between the level of diabetic retinopathy and diabetic neurosensory hearing loss.

Methods

A retrospective analysis of 175 Department of Veterans Affairs Computerized Patient Record System charts was completed at the VA Portland Health Care System. Subjects were classified by degree of diabetic retinopathy as follows: no diabetic retinopathy (n = 80), mild nonproliferative diabetic retinopathy (n = 51), moderate nonproliferative diabetic retinopathy (n = 25), and combined severe nonproliferative diabetic retinopathy and proliferative diabetic retinopathy (PDR) (n = 17). Degree of sensorineural hearing was collected for each ear. Additionally, measures of diabetic control, including hemoglobin A1C, and creatinine, were recorded.

Results

After controlling for diabetic control, as measured by HbA1C and creatinine, level of diabetic retinopathy was significantly associated with hearing loss severity in both ears (right ear, P = .018 and left ear, P = .007).

Conclusions

When adjusted to include diabetes control, the severity of diabetic retinopathy showed a correlation with degree of hearing loss at most levels. Because of this association, recommendation for hearing evaluations may be considered for those with mild, moderate, or severe nonproliferative or proliferative diabetic retinopathy.
Brief Report: CD14+ Enriched Peripheral Cells Secrete Cytokines Unique to HIV-Associated Neurocognitive Disorders
Authors: Agsalda-Garcia Melissa A. , Sithinamsuwan Pasiri , Valcour Victor G. , Chalermchai Thep , Tipsuk Somporn , Kuroda Jason , Nakamura Christie , Ananworanich Jintanat , Zhang Guangxiang , Schuetz Alexandra , Slike Bonnie M. , Shiramizu Bruce ,   on behalf of the SEARCH 011 Study Group
Published: December 2016

Monocytes play a vital role in HIV-associated neurocognitive disorder (HAND), postulated to transport HIV into the brain and secrete pro-inflammatory cytokines. We analyzed cytokines released by cultured peripheral blood mononuclear cells enriched with the CD14+marker isolated from HIV-infected individuals with HAND and normal cognition (NC) in combination antiretroviral therapy naive and after 1 year on treatment. Interleukin-8 and monocyte chemoattractant protein-1 levels were higher in HAND compared with NC at baseline (P= 0.002 andP< 0.0001). These cytokines remained higher in HAND patients 1 year after combination antiretroviral therapy and were significant when NC patients who were initially HAND were excluded (P= 0.012 andP= 0.002). Both correlated with baseline CD14+peripheral blood mononuclear cell HIV DNA levels supporting the role of HIV DNA reservoir size and monocyte cytokines in HAND persistence.
In situ
developmental responses of tropical sea urchin larvae to ocean acidification conditions at naturally elevated
p
CO
2
vent sites
Authors: Lamare Miles D. , Liddy Michelle , Uthicke Sven
Published: December 2016

Laboratory experiments suggest that calcifying developmental stages of marine invertebrates may be the most ocean acidification (OA)-sensitive life-history stage and represent a life-history bottleneck. To better extrapolate laboratory findings to future OA conditions, developmental responses in sea urchin embryos/larvae were compared under ecologically relevant
in situ
exposures on vent-elevated
p
CO
2
and ambient
p
CO
2
coral reefs in Papua New Guinea.
Echinometra
embryos/larvae were reared in meshed chambers moored in arrays on either venting reefs or adjacent non-vent reefs. After 24 and 48 h, larval development and morphology were quantified. Compared with controls (mean pH
(T)
= 7.89–7.92), larvae developing in elevated
p
CO
2
vent conditions (pH
(T)
= 7.50–7.72) displayed a significant reduction in size and increased abnormality, with a significant correlation of seawater pH with both larval size and larval asymmetry across all experiments. Reciprocal transplants (embryos from vent adults transplanted to control conditions, and
vice versa
) were also undertaken to identify if adult acclimatization can translate resilience to offspring (i.e. transgenerational processes). Embryos originating from vent adults were, however, no more tolerant to reduced pH. Sea temperature and chlorophyll-
a
concentrations (i.e. larval nutrition) did not contribute to difference in larval size, but abnormality was correlated with chlorophyll levels. This study is the first to examine the response of marine larvae to OA scenarios in the natural environment where, importantly, we found that stunted and abnormal development observed
in situ
are consistent with laboratory observations reported in sea urchins, in both the direction and magnitude of the response.
Within-group behavioural consequences of between-group conflict: a prospective review
Authors: Radford Andrew N. , Majolo Bonaventura , Aureli Filippo
Published: December 2016

Conflict is rife in group-living species and exerts a powerful selective force. Group members face a variety of threats from extra-group conspecifics, from individuals looking for reproductive opportunities to rival groups seeking resources. Theory predicts that such between-group conflict should influence within-group behaviour. However, compared with the extensive literature on the consequences of within-group conflict, relatively little research has considered the behavioural impacts of between-group conflict. We give an overview of why between-group conflict is expected to influence subsequent behaviour among group members. We then use what is known about the consequences of within-group conflict to generate testable predictions about how between-group conflict might affect within-group behaviour in the aftermath. We consider the types of behaviour that could change and how the role of different group members in the conflict can exert an influence. Furthermore, we discuss how conflict characteristics and outcome, group size, social structure and within-group relationship quality might modulate post-conflict behavioural changes. Finally, we propose the need for consistent definitions, a broader range of examined behaviours and taxa, individual-focused data collection, complementary observational and experimental approaches, and a consideration of lasting effects if we are to understand fully the significant influence of between-group conflict on social behaviour.
Decline and recovery of a large carnivore: environmental change and long-term trends in an endangered brown bear population
Authors: Martínez Cano Isabel , Taboada Fernando González , Naves Javier , Fernández-Gil Alberto , Wiegand Thorsten
Published: December 2016

Understanding what factors drive fluctuations in the abundance of endangered species is a difficult ecological problem but a major requirement to attain effective management and conservation success. The ecological traits of large mammals make this task even more complicated, calling for integrative approaches. We develop a framework combining individual-based modelling and statistical inference to assess alternative hypotheses on brown bear dynamics in the Cantabrian range (Iberian Peninsula). Models including the effect of environmental factors on mortality rates were able to reproduce three decades of variation in the number of females with cubs of the year (
Fcoy
), including the decline that put the population close to extinction in the mid-nineties, and the following increase in brown bear numbers. This external effect prevailed over density-dependent mechanisms (sexually selected infanticide and female reproductive suppression), with a major impact of climate driven changes in resource availability and a secondary role of changes in human pressure. Predicted changes in population structure revealed a nonlinear relationship between total abundance and the number of
Fcoy
, highlighting the risk of simple projections based on indirect abundance indices. This study demonstrates the advantages of integrative, mechanistic approaches and provides a widely applicable framework to improve our understanding of wildlife dynamics.
Egg size investment in superb fairy-wrens: helper effects are modulated by climate
Authors: Langmore N. E. , Bailey L. D. , Heinsohn R. G. , Russell A. F. , Kilner R. M.
Published: December 2016

Natural populations might exhibit resilience to changing climatic conditions if they already show adaptive flexibility in their reproductive strategies. In cooperative breeders, theory predicts that mothers with helpers should provide less care when environmental conditions are favourable, but maintain high investment when conditions are challenging. Here, we test for evidence of climate-mediated flexibility in maternal investment in the cooperatively breeding superb fairy-wren
Malurus cyaneus
. We focus on egg size because in this species egg size influences offspring size, and females reduce egg investment when there are helpers at the nest. We report that females lay larger eggs during dry, hot conditions. However, the effect of temperature is modulated by the presence of helpers: the average egg size of females with helpers is reduced during cooler conditions but increased during hot conditions relative to females without helpers. This appears to reflect plasticity in egg investment rather than among female differences. Analysis of maternal survival suggests that helped females are better able to withstand the costs of breeding in hot conditions than females without helpers. Our study suggests that females can use multiple, independent cues to modulate egg investment flexibly in a variable environment.
Allee effect in polar bears: a potential consequence of polychlorinated biphenyl contamination
Authors: Pavlova Viola , Nabe-Nielsen Jacob , Dietz Rune , Sonne Christian , Grimm Volker
Published: December 2016

Polar bears (
Ursus maritimus
) from East Greenland and Svalbard exhibited very high concentrations of polychlorinated biphenyls (PCBs) in the 1980s and 1990s. In Svalbard, slow population growth during that period was suspected to be linked to PCB contamination. In this case study, we explored how PCBs could have impacted polar bear population growth and/or male reproductive success in Svalbard during the mid-1990s by reducing the fertility of contaminated males. A dose–response relationship linking the effects of PCBs to male polar bear fertility was extrapolated from studies of the effects of PCBs on sperm quality in rodents. Based on this relationship, an individual-based model of bear interactions during the breeding season predicted fertilization success under alternative assumptions regarding male–male competition for females. Contamination reduced pregnancy rates by decreasing the availability of fertile males, thus triggering a mate-finding Allee effect, particularly when male–male competition for females was limited or when infertile males were able to compete with fertile males for females. Comparisons of our model predictions on age-dependent reproductive success of males with published empirical observations revealed that the low representation of 10–14-year-old males among breeding males documented in Svalbard in mid-1990s could have resulted from PCB contamination. We conclude that contamination-related male infertility may lead to a reduction in population growth via an Allee effect. The magnitude of the effect is largely dependent on the population-specific mating system. In eco-toxicological risk assessments, appropriate consideration should therefore be given to negative effects of contaminants on male fertility and male mating behaviour.
Life-history characteristics influence physiological strategies to cope with hypoxia in Himalayan birds
Authors: Barve S. , Dhondt A. A. , Mathur V. B. , Cheviron Z. A.
Published: December 2016

Hypobaric hypoxia at high elevation represents an important physiological stressor for montane organisms, but optimal physiological strategies to cope with hypoxia may vary among species with different life histories. Montane birds exhibit a range of migration patterns; elevational migrants breed at high elevations but winter at low elevations or migrate further south, while high-elevation residents inhabit the same elevation throughout the year. Optimal physiological strategies to cope with hypoxia might therefore differ between species that exhibit these two migratory patterns, because they differ in the amount time spent at high elevation. We examined physiological parameters associated with blood-oxygen transport (haemoglobin concentration and haematocrit, i.e. the proportion of red blood cells in blood) in nine species of elevational migrants and six species of high-elevation residents that were sampled along a 2200 m (1000–3200 m) elevational gradient. Haemoglobin concentration increased with elevation within species regardless of migratory strategy, but it was only significantly correlated with haematocrit in elevational migrants. Surprisingly, haemoglobin concentration was not correlated with haematocrit in high-elevation residents, and these species exhibited higher mean cellular haemoglobin concentration than elevational migrants. Thus, alternative physiological strategies to regulate haemoglobin concentration and blood O
2
carrying capacity appear to differ among birds with different annual elevational movement patterns.
Measuring Mitochondrial Transmembrane Potential by TMRE Staining
Authors: Crowley Lisa C. , Christensen Melinda E. , Waterhouse Nigel J.
Published: December 2016

Adenosine triphosphate (ATP) is the main source of energy for metabolism. Mitochondria provide the majority of this ATP by a process known as oxidative phosphorylation. This process involves active transfer of positively charged protons across the mitochondrial inner membrane resulting in a net internal negative charge, known as the mitochondrial transmembrane potential (ΔΨm). The proton gradient is then used by ATP synthase to produce ATP by fusing adenosine diphosphate and free phosphate. The net negative charge across a healthy mitochondrion is maintained at approximately −180 mV, which can be detected by staining cells with positively charged dyes such as tetramethylrhodamine ethyl ester (TMRE). TMRE emits a red fluorescence that can be detected by flow cytometry or fluorescence microscopy and the level of TMRE fluorescence in stained cells can be used to determine whether mitochondria in a cell have high or low ΔΨm. Cytochrome c is essential for producing ΔΨm because it promotes the pumping the protons into the mitochondrial intermembrane space as it shuttles electrons from Complex III to Complex IV along the electron transport chain. Cytochrome c is released from the mitochondrial intermembrane space into the cytosol during apoptosis. This impairs its ability to shuttle electrons between Complex III and Complex IV and results in rapid dissipation of ΔΨm. Loss of ΔΨm is therefore closely associated with cytochrome c release during apoptosis and is often used as a surrogate marker for cytochrome c release in cells.
Gene-Centered Yeast One-Hybrid Assays
Authors: Fuxman Bass Juan I. , Reece-Hoyes John S. , Walhout Albertha J.M.
Published: December 2016

An important question when studying gene regulation is which transcription factors (TFs) interact with which cis-regulatory elements, such as promoters and enhancers. Addressing this issue in complex multicellular organisms is challenging as several hundreds of TFs and thousands of regulatory elements must be considered in the context of different tissues and physiological conditions. Yeast one-hybrid (Y1H) assays provide a powerful “gene-centered” method to identify the TFs that can bind a DNA sequence of interest. In this introduction, we describe the basic principles of the Y1H assay and its advantages and disadvantages and briefly discuss how it is complementary to “TF-centered” methods that identify protein–DNA interactions for a known protein of interest.
Bayesian method for the analysis of diffraction patterns using BLAND
Authors: Lesniewski Joseph E. , Disseler Steven M. , Quintana Dylan J. , Kienzle Paul A. , Ratcliff William D.
Published: December 2016

Rietveld refinement of X-ray and neutron diffraction patterns is routinely used to solve crystal and magnetic structures of organic and inorganic materials over many length scales. Despite its success over the past few decades, conventional Rietveld analysis suffers from tedious iterative methodologies, and the unfortunate consequence of many least-squares algorithms discovering local minima that are not the most accurate solutions. Bayesian methods which allow the explicit encoding of a priori knowledge pose an attractive alternative to this approach by enhancing the ability to determine the correlations between parameters and to provide a more robust method for model selection. Global approaches also avoid the divergences and local minima often encountered by practitioners of the traditional Rietveld technique. The goal of this work is to demonstrate the effectiveness of an automated Bayesian algorithm for Rietveld refinement of neutron diffraction patterns in the solution of crystallographic and magnetic structures. A new software package, BLAND (Bayesian library for analyzing neutron diffraction data), based on the Markov–Chain Monte Carlo minimization routine, is presented. The benefits of such an approach are demonstrated through several examples and compared with traditional refinement techniques.
Use of small-angle X-ray scattering to resolve intracellular structure changes of Escherichia coli cells induced by antibiotic treatment
Authors: von Gundlach A. R. , Garamus V. M. , Willey T. M. , Ilavsky J. , Hilpert K. , Rosenhahn A.
Published: December 2016

The application of small-angle X-ray scattering (SAXS) to whole Escherichia coli cells is challenging owing to the variety of internal constituents. To resolve their contributions, the outer shape was captured by ultra-small-angle X-ray scattering and combined with the internal structure resolved by SAXS. Building on these data, a model for the major structural components of E. coli was developed. It was possible to deduce information on the occupied volume, occurrence and average size of the most important intracellular constituents: ribosomes, DNA and proteins. E. coli was studied after treatment with three different antibiotic agents (chloramphenicol, tetracycline and rifampicin) and the impact on the intracellular constituents was monitored.
Coherent X-ray beam metrology using 2D high-resolution Fresnel-diffraction analysis
Authors: Ruiz-Lopez M. , Faenov A. , Pikuz T. , Ozaki N. , Mitrofanov A. , Albertazzi B. , Hartley N. , Matsuoka T. , Ochante R. , Tange Y. , Yabuuchi T. , Habara T. , Tanaka K. A. , Inubushi Y. , Yabashi M. , Nishikino M. , Kawachi T. , Pikuz S. , Ishikawa T. , Kodama R. , Bleiner D.
Published: December 2016

Direct metrology of coherent short-wavelength beamlines is important for obtaining operational beam characteristics at the experimental site. However, since beam-time limitation imposes fast metrology procedures, a multi-parametric metrology from as low as a single shot is desirable. Here a two-dimensional (2D) procedure based on high-resolution Fresnel diffraction analysis is discussed and applied, which allowed an efficient and detailed beamline characterization at the SACLA XFEL. So far, the potential of Fresnel diffraction for beamline metrology has not been fully exploited because its high-frequency fringes could be only partly resolved with ordinary pixel-limited detectors. Using the high-spatial-frequency imaging capability of an irradiated LiF crystal, 2D information of the coherence degree, beam divergence and beam quality factor M
2 were retrieved from simple diffraction patterns. The developed beam metrology was validated with a laboratory reference laser, and then successfully applied at a beamline facility, in agreement with the source specifications.
Accurate hydrogen parameters for the amino acidL-leucine
Authors: Binns Jack , Parsons Simon , McIntyre Garry J.
Published: December 2016

The structure of the primary amino acid L-leucine has been determined for the first time by neutron diffraction. This was made possible by the use of modern neutron Laue diffraction to overcome the previously prohibitive effects of crystal size and quality. The packing of the structure into hydrophobic and hydrophilic layers is explained by the intermolecular interaction energies calculated using the PIXEL method. Variable-temperature data collections confirmed the absence of phase transitions between 120 and 300 K in the single-crystal form.