bluuebunny/crossref_metadata_2025 huggingface dataset:
Do directly acting antiviral agents for HCV increase the risk of hepatic decompensation and decline in renal function? Results from ERCHIVES
Authors: Butt A. A. , Ren Y. , Marks K. , Shaikh O. S. , Sherman K. E. ,   For the ERCHIVES study
Published: November 2016

Background

Directly acting antiviral agents (DAA) have been associated with hepatic decompensation, especially in patients with pre‐treatment cirrhosis, but this risk is not well defined.

Aim

To determine the incidence of hepatic decompensation, liver transplantation, death and worsening renal function in patients treated with a Paritaprevir/ritonavir, Ombitasvir, Dasabuvir (PrOD), sofosbuvir/simeprevir or sofosbuvir/ledipasvir regimen.

Methods

We followed ERCHIVES participants treated with the above regimens for up to 12 weeks post‐treatment. We excluded those with HIV, HBsAg+ and pre‐existing diagnosis of hepatic decompensation and hepatocellular carcinoma.

Results

Of 3728 persons on PrOD, 1578 on sofosbuvir/simeprevir and 10 440 on sofosbuvir/ledipasvir, incidence rates (95% CI) of hepatic decompensation/1000 patient‐years were 10.6 (5.89–17.36) for the PrOD, 32.4 (20.74–48.16) for the sofosbuvir/simeprevir and 13.0 (9.74–17.10) for the sofosbuvir/ledipasvir. Among those with baseline cirrhosis, these rates were 36.9 (19.1–64.5), 61.8 (38.2–94.5) and 41.1 (29.9–55.2) respectively, while among those without cirrhosis at baseline, these rates were 2.7 (0.6–8.0), 7.5 (1.5–21.8) and 2.7 (1.2–5.4). Advanced fibrosis was associated with increased risk of hepatic decompensation in all groups [HR (95% CI) per 0.5 unit increase in FIB‐4 score: PrOD 1.11 (1.07–1.16); sofosbuvir/simeprevir 1.03 (1.01–1.05); sofosbuvir/ledipasvir 1.02 (1.01–1.03)]. There were no deaths. Proportion of persons with eGFR decrease >30 ml/min/1.73 m2 was higher among the PrOD group, but presence of cirrhosis did not appear to affect this.

Conclusions

The incidence of hepatic decompensation in persons treated with PrOD, up to 12 weeks after completion of treatment, was comparable to those treated with sofosbuvir/ledipasvir regimen, and was lower than among those treated with a sofosbuvir/simeprevir regimen. Such risk was predominantly observed in those with pre‐treatment cirrhosis.
An interactive training programme to treat body image disturbance
Authors: Gledhill Lucinda J. , Cornelissen Katri K. , Cornelissen Piers L. , Penton‐Voak Ian S. , Munafò Marcus R. , Tovée Martin J.
Published: November 2016

Objectives

Anorexia nervosa (AN) is a life‐threatening mental health condition. A core feature is a disturbance of body image, such that sufferers see themselves as fatter than they actually are.

Design

We tested the effectiveness of a novel training programme to recalibrate our participants’ perception of body size.

Methods

In a novel adaptation of a cognitive bias training programme, participants judged the body size of a series of female bodies and were given feedback to improve their accuracy over four daily training sessions. In Study 1, we recruited young women with high concerns about their body size for a randomized controlled study. In Study 2, we then applied the training programme to a case series of women with atypical AN.

Results

In Study 1, the training programme significantly improved the body size judgements of women with high body concerns compared to controls. We also found evidence of improved body image and reduced eating concerns in this group. In Study 2, the programme again recalibrated the body size judgements of women with atypical AN. We also saw evidence of a clinically meaningful reduction in their body size and eating‐disordered concerns.

Conclusions

This training has the potential to be a valuable treatment used together with more traditional talking therapies.

Statement of contribution

What is already known on this subject?

A core feature of anorexia nervosa (AN) is an overestimation of body size; sufferers believe themselves to be larger than they are in reality. This study shows that an individual's perceptual boundary between what they classify as a fat versus a thin body is not immutable; it can be changed through a cognitive bias training programme.

What does this study add?

This means that body size overestimation may now be treatable.

Critically, as well as improving the accuracy of body size judgements, we also found a clinically significant improvement in participants’ eating‐disordered concerns.

This demonstrates that a targeted behavioural training regime can change body perception, and the central role that body overestimation has in eating‐disordered beliefs.
What affects perceptions of neighbourhood change?
Authors: Gosse Meghan , Ramos Howard , Radice Martha , Grant Jill L. , Pritchard Paul
Published: November 2016

Key Messages

Residents of Halifax do not perceive economic or social and cultural changes in their neighbourhoods; however, they do perceive those to the built environment.

When residents of Halifax perceive changes in their neighbourhoods, they tend to be positive about them.

Tabular and regression analysis show that sense of belonging increases positive perceptions of neighbourhood change and older age decreases positive views of change.
Inferior vena cava collapsibility index, renal dysfunction, and adverse outcomes in patients with broad spectrum cardiovascular disease
Authors: Kim Yong‐Hyun , Kim Sunwon , Kim Jin‐Seok , Lim Sang‐Yup , Shim Wan‐Joo , Ahn Jeong‐Cheon , Song Woo‐Hyuk
Published: November 2016

Aims

The clinical implication of the inferior vena cava collapsibility index (IVCCI) has not been well evaluated in patients with various cardiovascular diseases.

Method and results

The relationships between clinical characteristics and echocardiographic indicators of the systemic intravascular volume status [IVCCI; the ratio of the early transmitral and early myocardial diastolic velocities (E/Em)] were evaluated at baseline, and the clinical status during follow‐up was compared across the IVCCI levels. Among 1166 patients (mean age=63.8±13.4 years), 934, 171, and 61 had high (≥50%), intermediate (25%–50%), and low (<25%) IVCCIs, respectively. Age‐, sex‐, and body mass index‐adjusted serum creatinine (sCr) levels were highest in patients with low IVCCI (P=.002) and E/Em >15 (P<.001). During follow‐up (1108±463 days), 67 patients died, and 38 of these deaths were cardiovascular related. Age, body mass index, heart failure (HF), sCr levels, and a low IVCCI (vs high IVCCI: hazard ratio [HR]=3.193, 95% confidence interval [CI]=1.297–7.857, P=.012) were associated with all‐cause mortality in multivariable analysis. HF, diuretic use, and a low IVCCI (vs high IVCCI: HR=4.428, 95% CI=1.406–13.104, P=.007) were significantly associated with cardiovascular mortality.

Conclusion

A low IVCCI was significantly associated with reduced renal function and was an independent risk factor for adverse outcomes, regardless of underlying cardiovascular disease and renal function.
Castration alters the number and structure of dendritic spines in the male posterodorsal medial amygdala
Authors: Zancan Mariana , Dall'Oglio Aline , Quagliotto Edson , Rasia‐Filho Alberto A.
Published: November 2016

The posterodorsal medial amygdala (MePD) is responsive to androgens and participates in the integration of olfactory/vomeronasal stimuli for the display of sexual behavior in rats. Adult gonadectomy (GDX) affects the MePD structural integrity at the same time that impairs male mating behavior. At the cellular level, dendritic spines modulate excitatory synaptic transmission, strength, and plasticity. Here, we describe the effect of GDX on the number and shape of dendritic spines in the right and left MePD using confocal microscopy and 3D image reconstruction. Age‐matched adult rats were intact (n = 6), submitted to a sham procedure (n = 4) or castrated and studied 90 days after GDX (n = 5). The MePD neurons have a density of 1.1 spines/dendritic μm composed of thin, mushroom‐like, stubby/wide, and few ramified or atypical spines. Irrespective of brain hemisphere, GDX decreased the dendritic spine density in the MePD, but induced different effects on each spine type. That is, compared to control groups, GDX reduced (i) the number (up to 50%) of thin, mushroom‐like, and ramified spines, and (ii) the size and the neck length of thin spines as well as the head diameter of ramified spines. Besides, GDX increased the number of stubby/wide and atypical spines (up to 140% and 400%, respectively). These data show that GDX promotes a cellular and synaptic reorganization in a spine‐specific manner in the MePD. By altering the number and shape of these connectional elements, GDX can affect the neural transmission and hinder the function of integrated brain circuitries in the male brain.
Phosphorylation of H2A.XTyr39 positively regulates DNA damage response and is linked to cancer progression
Authors: Liu Yan , Long Yue‐Hong , Wang Shu‐Qing , Li Yu‐Feng , Zhang Jing‐Hua
Published: November 2016

Double‐stranded DNA breaks induce serine phosphorylation of histone H2A.X, producing γ‐H2A.X foci that are then recognized by DNA damage response pathway proteins. Formation of γ‐H2A.X is therefore critical for the repair of DNA double‐stranded breaks and maintenance of genomic stability, and defects in the recognition or repair of double‐stranded breaks can result in tumorigenesis. However, key details regarding the formation of γ‐H2A.X and its possible role in tumorigenesis remain elusive. Here, we report a previously unknown phosphorylation site on H2A.X, Tyr39. Phosphorylation at this site is induced by ionizing radiation and is a prerequisite for γ‐H2A.X formation. Increased phosphorylation of H2A.X at Tyr39 was observed in multiple cancer cell lines, and we found that H2AX Tyr39 phosphorylation positively correlated with histological grade, tumor size and tumor node metastasis stage, and negatively correlated with survival. We also identified a potential role for eyes absent 2 (EYA2) in regulating H2A.X Tyr39 phosphorylation. Our study supports an important role for H2AX Tyr39 phosphorylation in γ‐H2A.X formation and cancer progression.
Identification and management of elder physical abuse in the routine of dentistry – a systematic review
Authors: Silva Luanderson O. , Souza‐Silva Bianca N. , de Alcântara Rodrigues José Lucas , Rigo Lilian , Cericato Graziela O. , Franco Ademir , Paranhos Luiz R.
Published: November 2016

Objective

To perform a systematic search in the literature in order to verify whether the dentists are able to identify and manage cases elder physical abuse.

Background

Dentists may play an important legal role contributing to the management of abused patients through the identification of injuries in their face, head and neck.

Materials and methods

The present systematic review was performed following the PRISMA Statement and was registered in the PROSPERO database. A search was conducted in the following electronic databases: PubMed, LILACS, SciELO, Embase, Web of Science, OpenGrey, Google Scholar. Specifically, the last two databases were used to search the ‘grey literature’. The research question was based on the PVO strategy for systematic exploratory review. Two examiners determined the eligibility criteria for selecting the studies and performed all the research steps.

Results

The initial search resulted in 842 studies, from which eight were considered eligible. Six studies used questionnaires to assess the perception, knowledge and attitudes of dentists towards the identification and management of cases of elder abuse, while two studies assessed this information through personal interviews. Two studies were rated as high quality, while six studies reached moderate quality. Male and female dentists were assessed separately in six studies. Only three studies specified the aggressor.

Conclusion

The dentists revealed insufficient knowledge on elder abuse. Most of the dentists are not able to identify and manage these cases in the clinical routine.
Is There a Too‐Big‐to‐Fail Discount in Excess Returns on German Banks’ Stocks?
Authors: Nitschka Thomas
Published: November 2016

Since the global financial crisis, German and other European banks’ stocks have underperformed compared with the overall euro‐area stock market. Does this observation reflect the explicit state guarantee for too‐big‐to‐fail (TBTF) banks? In that case, investors have an incentive to hold stocks of systemically important banks because they provide insurance against disaster risk through the state guarantee. Indeed, recent studies reveal a TBTF discount in large US banks’ stock returns. Does this finding pertain to German (representing continental European) banks too? The main results of this paper suggest that it does. Risk‐adjusted returns on a German bank stock index were negative in the period from 1973 to 2014. The key driver of this finding is an unanticipated, adverse shock to the German banking sector at the beginning of the global financial crisis. This shock increased the probability of a bank default and thus the insurance value of government support.
Association between dental caries experience and sense of coherence among adolescents and mothers
Authors: Lage Carolina Freitas , Fulgencio Livia Bonfim , Corrêa‐Faria Patricia , Serra‐Negra Junia Maria , Paiva Saul Martins , Pordeus Isabela Almeida
Published: November 2016

Background

Sense of coherence (SOC) is associated with oral health.

Aim

Investigate associations between dental caries experience and SOC among mothers and adolescents.

Design

A cross‐sectional study was conducted with 1195 adolescents and their mothers. Data were collected through a questionnaire, the short version of the SOC and oral clinical examinations. The data were statistically analyzed using bivariate analysis, Poisson regression models with robust variance, and Spearman's correlation coefficient.

Results

The prevalence of dental caries experience was 41.8%. A moderate correlation was found between the SOC of mothers and adolescents (r = 0.563; P < 0.001). A higher mother's SOC (PR: 0.44; 95% CI: 0.36–0.53) and adolescent's SOC (PR: 0.46; 95% CI: 0.39–0.55) were protective factors against dental caries experience in the adolescents. The prevalence of dental caries experience was higher among adolescents with visible plaque (Model 1—PR: 1.77; 95% CI: 1.53–2.04; Model 2—PR: 1.59; 95% CI: 1.37–1.84) and those whose families were in a lower economic class (Model 1—PR: 1.56; 95% CI: 1.35–1.80; Model 2—PR: 1.57; 95% CI: 1.36–1.81).

Conclusion

Dental caries in adolescents was associated with social determinants evaluated through the sense of coherence.
Microstructure–Property Connections for Porous Ceramics: The Possibilities Offered by Micromechanics
Authors: Bruno Giovanni , Kachanov Mark
Published: November 2016

Microstructure of porous ceramics is highly “irregular”: it comprises pores and microcracks of diverse shapes and orientations. This makes their quantitative modeling challenging, and one often resorts to empirical relations containing fitting parameters and having somewhat uncertain range of applicability. We review the substantial progress made in modeling of “irregular” microstructures that does not seem to have been sufficiently utilized in the context of ceramics. We discuss the possibilities offered by micromechanics in developing microstructure–property relations for porous microcracked ceramics. After an overview of relevant micromechanics topics, we focus on several issues of specific interest for ceramics: nonlinear stress–strain behavior, effective elastic properties, and thermally induced microcracking. We discuss extraction of microscale parameters (such as strength of the intergranular cohesion, density of cracks and pores, etc.) from macroscopic data and identify the extent of uncertainty in this process. We also argue that there is no quantitative correlation between fracturing process and the loss of elastic stiffness.
Investigation into the Physiological Significance of the Phytohormone Abscisic Acid in Perkinsus marinus, an Oyster Parasite Harboring a Nonphotosynthetic Plastid
Authors: Sakamoto Hirokazu , Suzuki Shigeo , Nagamune Kisaburo , Kita Kiyoshi , Matsuzaki Motomichi
Published: November 2016

Some organisms have retained plastids even after they have lost the ability to photosynthesize. Several studies of nonphotosynthetic plastids in apicomplexan parasites have shown that the isopentenyl pyrophosphate biosynthesis pathway in the organelle is essential for their survival. A phytohormone, abscisic acid, one of several compounds biosynthesized from isopentenyl pyrophosphate, regulates the parasite cell cycle. Thus, it is possible that the phytohormone is universally crucial, even in nonphotosynthetic plastids. Here, we examined this possibility using the oyster parasite Perkinsus marinus, which is a plastid‐harboring cousin of apicomplexan parasites and has independently lost photosynthetic ability. Fluridone, an inhibitor of abscisic acid biosynthesis, blocked parasite growth and induced cell clustering. Nevertheless, abscisic acid and its intermediate carotenoids did not affect parasite growth or rescue the parasite from inhibition. Moreover, abscisic acid was not detected from the parasite using liquid chromatography mass spectrometry. Our findings show that abscisic acid does not play any significant roles in P. marinus.
Better Nurse Autonomy Decreases the Odds of 30‐Day Mortality and Failure to Rescue
Authors: Rao Aditi D. , Kumar Aparna , McHugh Matthew
Published: November 2016

Research Purpose

Autonomy is essential to professional nursing practice and is a core component of good nurse work environments. The primary objective of this study was to examine the relationship between nurse autonomy and 30‐day mortality and failure to rescue (FTR) in a hospitalized surgical population.

Study Design

This study was a secondary analysis of cross‐sectional data. It included data from three sources: patient discharge data from state administrative databases, a survey of nurses from four states, and the American Hospital Association annual survey from 2006–2007.

Methods

Survey responses from 20,684 staff nurses across 570 hospitals were aggregated to the hospital level to assess autonomy measured by a standardized scale. Logistic regression models were used to estimate the relationship between nurse autonomy and 30‐day mortality and FTR. Patient comorbidities, surgery type, and other hospital characteristics were included as controls.

Findings

Greater nurse autonomy at the hospital level was significantly associated with lower odds of 30‐day mortality and FTR for surgical patients even after accounting for patient risk and structural hospital characteristics. Each additional point on the nurse autonomy scale was associated with approximately 19% lower odds of 30‐day mortality (p < .001) and 17% lower odds of failure to rescue (p < .01).

Conclusions

Hospitals with lower levels of nurse autonomy place their surgical patients at an increased risk for mortality and FTR.

Clinical Relevance

Patients receiving care within institutions that promote high levels of nurse autonomy have a lower risk for death within 30 days and complications leading to death within 30 days. Hospitals can actively take steps to encourage nurse autonomy to positively influence patient outcomes.
Response to Karen Lebacqz and Stephen Palmquist
Authors: Green Ronald M.
Published: November 2016

I respond here to the essays by Karen Lebacqz and Stephen Palmquist, beginning with my debt of gratitude to Lebacqz for her understanding of the methodological depth I try to bring to the analysis of bioethical issues. I further illustrate that observation here by reviewing the logic of my approach to the issue of wrongful life. At the same time, in connection with human genetic enhancement, I acknowledge that I may have not properly appreciated the seriousness of the problem of sin. To Palmquist's assertion that my criticisms of Kant's treatments of grace miss the way Kant has confined himself to being a philosophical (as opposed to biblical) theologian, I argue that Kant's problem lies instead in his poor application of his own compelling insights about the depths of human sinning. I close with an appreciation of Palmquist's observation of some important points of contact between Kant's understanding of sin and that of Kierkegaard.
Functional connectivity alterations in patients with chronic hepatitis C virus infection: A multimodal MRI study
Authors: Kharabian Masouleh S. , Herzig S. , Klose L. , Roggenhofer E. , Tenckhoff H. , Kaiser T. , Thöne‐Otto A. , Wiese M. , Berg T. , Schroeter M. L. , Margulies D. S. , Villringer A.
Published: November 2016

Chronic hepatitis C virus (HCV) infection is associated with fatigue and depression. Cognitive impairments are also reported in a smaller number of HCV‐positive patients. Recent studies linked HCV to low‐grade inflammation in brain. Here, we test the hypothesis that chronic HCV is associated with 3T‐neuroimaging‐derived grey matter volume (GMV) and functional connectivity alterations in a sample of chronic HCV (1b), without severe liver disease. Regional GMV and resting‐state fMRI‐derived eigenvector centrality (EC) were compared between 19 HCV‐positive patients and 23 healthy controls (all females, 50‐69 and 52‐64 years, respectively), controlling for white matter hyperintensities and age. Standard tests were used to assess fatigue, depression and cognitive performance. Also, liver fibrosis stage and viral load were quantified among patients. In comparison with controls, HCV‐positive patients had higher scores in fatigue and depression, and worse alertness scores. The groups performed similarly in other cognitive domains. We report higher EC in a cluster in the right anterior superior parietal lobule in patients, while no differences are found in GMV. Post hoc functional connectivity analysis showed increased connectivity of this cluster with primary and secondary somatosensory cortex, and temporal and occipital lobes in patients. Higher mean EC in the superior parietal cluster, adjusted for mean framewise displacement, was associated with better memory and attention performance, but not with fatigue, depression, viral load or level of liver fibrosis, among patients. These results suggest a compensatory mechanism in chronic hepatitis C and explain equivocal results in the literature about cognitive deficits in infected persons. Further studies should define the relation of these connectivity changes to the brain's inflammatory activity.
Establishment limitation may be more important than species dispersal: insights from dry grasslands and old‐fields
Authors: Knappová Jana , Hemrová Lucie , Knapp Michal , Münzbergová Zuzana
Published: November 2016

Questions

Old‐fields and their succession often played crucial role in dynamics of species‐rich semi‐natural grasslands. Our objective was to assess whether colonization of old‐fields by grassland species is limited by the availability of seeds, dispersal abilities, habitat requirements of the species or biotic interactions. In particular, we asked following questions: (1) What are the main constrains limiting frequency of grassland species in old‐fields? (2) Is frequency in source habitat (grasslands) and target habitat (old‐fields) limited by the same factors/processes? And (3) how the results and their interpretation change after considering species phylogeny?

Location

Old‐fields and grasslands in northern Bohemia, Czech Republic, Europe.

Methods

Frequency in old‐fields and grasslands of 29 plant species was related to a set of species characteristics representing source, dispersal, abiotic and biotic limitation using phylogenetic regression.

Results

Species frequency in old‐fields was significantly correlated with frequency in grasslands. In general, habitat (biotic and abiotic) limitation was more important for frequency in both habitat types without phylogenetic correction. Specifically, frequency in both habitat types was mostly limited by soil preference and in grasslands also by niche width. Old‐fields were relatively more colonized by species with better competitiveness. Phylogenetic signal was not detected during phylogenetic regression.

Conclusions

To preserve high diversity in grasslands, the effort should be directed towards maintenance of soil quality (minimize the use of fertilizers, pesticides and heavy machinery). Colonization of old‐fields could be enhanced by reduction of competitive species by introduction of traditional management (e.g., mowing or grazing).
Private Law Firms in the Public Interest: The Organizational and Institutional Determinants of Pro Bono Participation, 1994–2005
Authors: Boutcher Steven A.
Published: November 2016

Despite longstanding concern that the commercialization of legal practice is antithetical to professionalism, corporate law firms have dramatically increased their pro bono participation over the past few decades. What explains this paradox? This article examines the organizational and institutional determinants of pro bono participation across an elite field of large law firms. I find that pro bono work is only partly rooted in internal organizational dynamics and that the institutional environment appears more important for explaining variation in pro bono participation. These findings indicate that large firms may be more drawn to pro bono work as a social process tied to professional status and legitimacy than to concrete, rational organizational goals. Moreover, these findings point to the importance of the interstitial space that these firms inhabit between the legal profession and corporate market as an especially important factor in facilitating, rather than dampening, pro bono participation.
Mourners in the Court: Victims in Death Penalty Trials, through the Lens of Performance
Authors: Kaufman Sarah Beth
Published: November 2016

This article presents findings from ethnographic research in death penalty trials around the United States, focusing on the role of victims and their supporters. Victim impact testimony (VIT) in death penalty sentencing has received intense legal scrutiny during the past thirty years. The ruling jurisprudence allows VIT with the explanation that it deserves parity with testimony about the defendant's background. Drawing on observations and interviews with participants in 15 death penalty trials, I demonstrate that this framing confuses the central role of victim supporters in the courtroom. Victim supporters function as mourners, which grants them a socially elevated position in the courtroom. I argue that the consequences of the institutionalization of VIT can only be understood through this lens.
Temperature‐compensated cell production rate and elongation zone length in the root of Arabidopsis thaliana
Authors: Yang Xiaoli , Dong Gang , Palaniappan K. , Mi Guohua , Baskin Tobias I.
Published: November 2016

To understand how root growth responds to temperature, we used kinematic analysis to quantify division and expansion parameters in the root of Arabidopsis thaliana. Plants were grown at temperatures from 15 to 30 °C, given continuously from germination. Over these temperatures, root length varies more than threefold in the wild type but by only twofold in a double mutant for phytochrome‐interacting factor 4 and 5. For kinematics, the spatial profile of velocity was obtained with new software, Stripflow. We find that 30 °C truncates the elongation zone and curtails cell production, responses that probably reflect the elicitation of a common pathway for handling severe stresses. Curiously, rates of cell division at all temperatures are closely correlated with rates of radial expansion. Between 15 to 25 °C, root growth rate, maximal elemental elongation rate, and final cell length scale positively with temperature whereas the length of the meristem scales negatively. Non‐linear temperature scaling characterizes meristem cell number, time to transit through either meristem or elongation zone, and average cell division rate. Surprisingly, the length of the elongation zone and the total rate of cell production are temperature invariant, constancies that have implications for our understanding of how the underlying cellular processes are integrated.
Poplar PtabZIP1‐like enhances lateral root formation and biomass growth under drought stress
Authors: Dash Madhumita , Yordanov Yordan S. , Georgieva Tatyana , Tschaplinski Timothy J. , Yordanova Elena , Busov Victor
Published: November 2016

Developing drought‐resistance varieties is a major goal for bioenergy crops, such as poplar (Populus), which will be grown on marginal lands with little or no water input. Root architecture can affect drought resistance, but few genes that affect root architecture in relation to water availability have been identified. Here, using activation tagging in the prime bioenergy crop poplar, we have identified a mutant that overcomes the block of lateral root (LR) formation under osmotic stress. Positioning of the tag, validation of the activation and recapitulation showed that the phenotype is caused by the poplar PtabZIP1‐like (PtabZIP1L) gene with highest homology to bZIP1 from Arabidopsis. PtabZIP1L is predominantly expressed in roots, particularly in zones where lateral root primordia (LRP) initiate and LR differentiate and emerge. Transgenics overexpressing PtabZIP1L showed precocious LRP and LR development, while PtabZIP1L suppression significantly delayed both LRP and LR formation. Transgenic overexpression and suppression of PtabZIP1L also resulted in modulation of key metabolites like proline, asparagine, valine and several flavonoids. Consistently, expression of both of the poplar Proline Dehydrogenase orthologs and two of the Flavonol Synthases genes was also increased and decreased in overexpressed and suppressed transgenics, respectively. These findings suggest that PtabZIP1L mediates LR development and drought resistance through modulation of multiple metabolic pathways.
IMAGING DIAGNOSIS—MAGNETIC RESONANCE IMAGING OF DIFFUSE LEPTOMENINGEAL OLIGODENDROGLIOMATOSIS IN A DOG WITH “DURAL TAIL SIGN”
Authors: Lobacz Monika Anna , Serra Fabienne , Hammond Gawain , Oevermann Anna , Haley Allison C.
Published: November 2016

A case of diffuse leptomeningeal oligodendrogliomatosis affecting the brain and spinal cord of a dog is presented. A 7.5‐year old, male neutered Staffordshire bull terrier presented for evaluation of a chronic history of tetraparesis and seizures, with a multifocal neuroanatomical localization was determined. Extra‐axial intradural lesions with an atypical presentation of a dural tail sign were seen on MRI. Histologically, the lesions were consistent with leptomeningeal oligodendrogliomatosis. To the authors’ knowledge, a dural tail sign has not previously been reported as an MRI characteristic of diffuse leptomeningeal oligodendrogliomatosis in dogs.
Effects of Residual Stress, Axial Stretch, and Circumferential Shrinkage on Coronary Plaque Stress and Strain Calculations: A Modeling Study Using IVUS-Based Near-Idealized Geometries
Authors: Wang Liang , Zhu Jian , Samady Habib , Monoly David , Zheng Jie , Guo Xiaoya , Maehara Akiko , Yang Chun , Ma Genshan , Mintz Gary S. , Tang Dalin
Published: November 2016

Accurate stress and strain calculations are important for plaque progression and vulnerability assessment. Models based on in vivo data often need to form geometries with zero-stress/strain conditions. The goal of this paper is to use IVUS-based near-idealized geometries and introduce a three-step model construction process to include residual stress, axial shrinkage, and circumferential shrinkage and investigate their impacts on stress and strain calculations. In Vivo intravascular ultrasound (IVUS) data of human coronary were acquired for model construction. In Vivo IVUS movie data were acquired and used to determine patient-specific material parameter values. A three-step modeling procedure was used to make our model: (a) wrap the zero-stress vessel sector to obtain the residual stress; (b) stretch the vessel axially to its length in vivo; and (c) pressurize the vessel to recover its in vivo geometry. Eight models were constructed for our investigation. Wrapping led to reduced lumen and cap stress and increased out boundary stress. The model with axial stretch, circumferential shrink, but no wrapping overestimated lumen and cap stress by 182% and 448%, respectively. The model with wrapping, circumferential shrink, but no axial stretch predicted average lumen stress and cap stress as 0.76 kPa and −15 kPa. The same model with 10% axial stretch had 42.53 kPa lumen stress and 29.0 kPa cap stress, respectively. Skipping circumferential shrinkage leads to overexpansion of the vessel and incorrect stress/strain calculations. Vessel stiffness increase (100%) leads to 75% lumen stress increase and 102% cap stress increase.
Elasticity Solutions to Nonbuckling Serpentine Ribbons
Authors: Yang Shixuan , Qiao Shutao , Lu Nanshu
Published: November 2016

Stretchable electronics have found wide applications in bio-mimetic and bio-integrated electronics attributing to their softness, stretchability, and conformability. Although conventional electronic materials are intrinsically stiff and brittle, silicon and metal membranes can be patterned into in-plane serpentine ribbons for enhanced stretchability and compliance. While freestanding thin serpentine ribbons may easily buckle out-of-plane, thick serpentine ribbons may remain unbuckled upon stretching. Curved beam (CB) theory has been applied to analytically solve the strain field and the stiffness of freestanding, nonbuckling serpentine ribbons. While being able to fully capture the strain and stiffness of narrow serpentines, the theory cannot provide accurate solutions to serpentine ribbons whose widths are comparable to the arc radius. Here we report elasticity solutions to accurately capture nonbuckling, wide serpentine ribbons. We have demonstrated that weak boundary conditions are sufficient for solving Airy stress functions except when the serpentine’s total curve length approaches the ribbon width. Slightly modified weak boundary conditions are proposed to resolve this difficulty. Final elasticity solutions are fully validated by finite element models (FEM) and are compared with results obtained by the curved beam theory. When the serpentine ribbons are embedded in polymer matrices, their stretchability may be compromised due to the fact that the matrix can constrain the in-plane rotation of the serpentine. Comparison between the analytical solutions for freestanding serpentines and the FEM solutions for matrix-embedded serpentines reveals that matrix constraint remains trivial until the matrix modulus approaches that of the serpentine ribbon.
Computational Biomechanics of Human Red Blood Cells in Hematological Disorders
Authors: Li Xuejin , Li He , Chang Hung-Yu , Lykotrafitis George , Em Karniadakis George
Published: November 2016

We review recent advances in multiscale modeling of the biomechanical characteristics of red blood cells (RBCs) in hematological diseases, and their relevance to the structure and dynamics of defective RBCs. We highlight examples of successful simulations of blood disorders including malaria and other hereditary disorders, such as sickle-cell anemia, spherocytosis, and elliptocytosis.
Eddy Viscosity and Reynolds Stress Models of Entropy Generation in Turbulent Channel Flows
Authors: Sun J. , Kuhn D. , Naterer G.
Published: November 2016

This paper presents new models of entropy production for incompressible turbulent channel flows. A turbulence model is formulated and analyzed with direct numerical simulation (DNS) data. A Reynolds-averaged Navier–Stokes (RANS) approach is used and applied to the turbulence closure of mean and fluctuating variables and entropy production. The expression of the mean entropy production in terms of other mean flow quantities is developed. This paper presents new models of entropy production by incorporating the eddy viscosity into the total shear stress. Also, the Reynolds shear stress is used as an alternative formulation. Solutions of the entropy transport equations are presented and discussed for both laminar and turbulent channel flows.
Arrangement Method of Offshore Topside Based on an Expert System and Optimization Technique
Authors: Kim Sung-Kyoon , Roh Myung-Il , Kim Ki-Su
Published: November 2016

An offshore platform has several modules that contain much of the equipment needed for oil and gas production, and these are placed on the limited space of the topside. Furthermore, the equipment layout should leave sufficient space in between to ensure operability, maintainability, and safety. Thus, the design problem to arrange the topside of an offshore platform can be difficult to solve due to the number of modules and equipment placed on the topside. This study proposes a method to arrange the offshore topside based on an expert system and multistage optimization in order to obtain the optimal arrangement that addresses various considerations and satisfies the given requirements. The proposed method consists of four components. First, an expert system is proposed to systematically computerize experts' knowledge and experience and to evaluate the feasibility of alternatives for the arrangement of the offshore topside. Second, a multistage optimization method is proposed to yield a better arrangement design by formulating the arrangement design problem as an optimization problem with two stages. Third, an arrangement template model (ATM) was proposed to store the arrangement data of the offshore topside. Fourth, the user interface was developed to run the expert system and for optimization. A prototype program was then developed to solve an floating, production, storage, and offloading (FPSO) topside problem in order to evaluate the applicability of the proposed method. The results showed that the proposed method can be used to obtain the optimal arrangement of an offshore topside.
Hydrogen Production by Carbon-Catalyzed Methane Decomposition Via Thermogravimetry
Authors: Shilapuram Vidyasagar , Ozalp Nesrin
Published: November 2016

Hydrogen is a high energy content fuel and methane is currently the most preferred feedstock for hydrogen production. Direct thermal splitting of methane offers the cleanest technique to produce hydrogen and carbon as coproduct fuel. Carbonaceous catalysts have significant impact on methane to hydrogen conversion. This study presents thermogravimetric experiment results of carbon-catalyzed methane decomposition using commercial catalyst. Results are presented in terms of carbon formation rate, amount of carbon deposition on the catalyst, sustainability factor, catalyst activity, and kinetics of the reaction. The results show that weight gain because of carbon formation depends on reaction temperature, methane volume percent in the feed gas, and nature of the carbonaceous catalyst. It was observed that the reaction rate was dominant at the beginning, and deactivation rate was dominant toward the end of reaction. X-ray diffraction (XRD) and scanning electron microscopic (SEM) analysis of deactivated catalytic samples show decreasing disorder with increasing reaction temperature. Finally, performance comparison of activated carbons (ACs) studied in literature shows that activated carbon sample chosen in this study outperforms in terms of carbon deposition, reaction rate, carbon weight gain, and sustainability factor.
Pressure Sensitive Paint Visualization of Pressure Distribution of Externally Pressurized Circular Thrust Gas Bearing With a Single Gas Supply Hole: Experimental Validation of Variation of Pressure Distribution by Supply Pressure
Authors: Ise Tomohiko , Kobayashi Shuma , Itoh Kazuhiro , Asami Toshihiko
Published: November 2016

This study investigated the use of pressure sensitive paint (PSP) as new measuring technique for measuring the pressure distribution of a gas bearing. An externally pressurized circular thrust gas bearing with single gas supply hole was used as the test bearing to investigate the suitability of this technique. The test bearing was 30 mm in diameter, with a gas supply hole of diameter 0.7 mm. A coat of PtTFPP, the substance used as the PSP, was applied to the bearing surface using an air-assisted spray. The PSP luminescence characteristics were calibrated before the tests because of their dependency on temperature and pressure. The pressure distribution was obtained by averaging 50 images captured by a 12-bit complementary metal-oxide semiconductor (CMOS) camera. These experimental results were compared with the results of a numerical analysis based on the divergence formulation method. There was good agreement between the experimental and analytical results, thus demonstrating the effectiveness of using PSP for pressure distribution measurements.
Aluminum oxide/titanium dioxide nanolaminates grown by atomic layer deposition: Growth and mechanical properties
Authors: Ylivaara Oili M. E. , Kilpi Lauri , Liu Xuwen , Sintonen Sakari , Ali Saima , Laitinen Mikko , Julin Jaakko , Haimi Eero , Sajavaara Timo , Lipsanen Harri , Hannula Simo-Pekka , Ronkainen Helena , Puurunen Riikka L.
Published: November 2016

Atomic layer deposition (ALD) is based on self-limiting surface reactions. This and cyclic process enable the growth of conformal thin films with precise thickness control and sharp interfaces. A multilayered thin film, which is nanolaminate, can be grown using ALD with tuneable electrical and optical properties to be exploited, for example, in the microelectromechanical systems. In this work, the tunability of the residual stress, adhesion, and mechanical properties of the ALD nanolaminates composed of aluminum oxide (Al2O3) and titanium dioxide (TiO2) films on silicon were explored as a function of growth temperature (110–300 °C), film thickness (20–300 nm), bilayer thickness (0.1–100 nm), and TiO2 content (0%–100%). Al2O3 was grown from Me3Al and H2O, and TiO2 from TiCl4 and H2O. According to wafer curvature measurements, Al2O3/TiO2 nanolaminates were under tensile stress; bilayer thickness and growth temperature were the major parameters affecting the stress; the residual stress decreased with increasing bilayer thickness and ALD temperature. Hardness increased with increasing ALD temperature and decreased with increasing TiO2 fraction. Contact modulus remained approximately stable. The adhesion of the nanolaminate film was good on silicon.
Peptide interactions with zigzag edges in graphene
Authors: Kuang Zhifeng , Kim Steve S. , Ngo Yen H. , McAlpine Michael C. , Farmer Barry L. , Naik Rajesh R.
Published: November 2016

Recognition and manipulation of graphene edges enable the control of physical properties of graphene-based devices. Recently, the authors have identified a peptide that preferentially binds to graphene edges from a combinatorial peptide library. In this study, the authors examine the functional basis for the edge binding peptide using experimental and computational methods. The effect of amino acid substitution, sequence context, and solution pH value on the binding of the peptide to graphene has been investigated. The N-terminus glutamic acid residue plays a key role in recognizing and binding to graphene edges. The protonation, substitution, and positional context of the glutamic acid residue impact graphene edge-binding. Our findings provide insights into the binding mechanisms and the design of peptides for recognizing and functionalizing graphene edges.
Draft Genome Sequence of Streptococcus agalactiae Serotype Ia Strain M19, a Multidrug-Resistant Isolate from a Cow with Bovine Mastitis
Authors: Yang Feng , Li Hongsheng , Zhang Shidong , Wang Xurong
Published: November 2016

Streptococcus agalactiae
is a major contagious pathogen causing bovine mastitis worldwide. We report here the draft sequence of
S. agalactiae
Ia strain M19, a multidrug-resistant isolate from a bovine mastitis case in Ningxia Hui autonomous region, China.
Complete Genome Sequence of
Alkaliphilus metalliredigens
Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds
Authors: Hwang C. , Copeland A. , Lucas S. , Lapidus A. , Barry K. , Detter J. C. , Glavina del Rio T. , Hammon N. , Israni S. , Dalin E. , Tice H. , Pitluck S. , Chertkov O. , Brettin T. , Bruce D. , Han C. , Schmutz J. , Larimer F. , Land M. L. , Hauser L. , Kyrpides N. , Mikhailova N. , Ye Q. , Zhou J. , Richardson P. , Fields M. W.
Published: November 2016

Alkaliphilus metalliredigens
strain QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum
Firmicutes
. QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms.
New aerobactin-mediated iron uptake system in a septicemia-causing strain of Enterobacter cloacae
Authors: Crosa L M , Wolf M K , Actis L A , Sanders-Loehr J , Crosa J H
Published: November 2016

Unlike the great majority of the aerobactin-producing enteric bacteria documented in the literature, Enterobacter cloacae EK33, isolated from a case of human neonatal meningitis, did not show any homology at the DNA level with the prototype aerobactin system encoded by the ColV-K30 plasmid. However, both the nuclear magnetic resonance spectrum and fast-atom bombardment mass spectrometry of the siderophore purified from EK33 confirmed its identity with aerobactin. Bioassay screening of a gene library of total DNA of EK33 led to the isolation of several aerobactin-positive clones. Under conditions of iron limitation, these clones expressed in Escherichia coli a protein of 72 kilodaltons that reacted with antiserum raised against the pColV-K30 74-kilodalton aerobactin receptor, while the original E. cloacae strain synthesized an 85-kilodalton protein which also cross-reacted with the antiserum. Restriction endonuclease analysis of the cloned DNA confirmed the structural differences between the two aerobactin genetic systems.
Molybdate transport by Bradyrhizobium japonicum bacteroids
Authors: Maier R J , Graham L
Published: November 2016

Bacteroid suspensions of Bradyrhizobium japonicum USDA 136 isolated from soybeans grown in Mo-deficient conditions were able to transport molybdate at a nearly constant rate for up to 1 min. The apparent Km for molybdate was 0.1 microM, and the Vmax was about 5 pmol/min per mg (dry weight) of bacteroid. Supplementation of bacteroid suspensions with oxidizable carbon sources did not markedly increase molybdate uptake rates. Anaerobically isolated bacteroids accumulated twice as much Mo in 1 h as aerobically isolated cells did, but the first 5 min of molybdate uptake was not dependent on the isolation condition with respect to O2. Respiratory inhibitors such as cyanide, azide, and hydroxylamine did not appreciably affect molybdate uptake, even at concentrations that inhibited O2 uptake. The uncouplers carbonyl cyanide m-chlorophenylhydrazone (CCCP) and carbonyl cyanide p-trifluoromethoxyphenylhydrazone (FCCP) and the ionophores nigericin and monensin significantly inhibited molybdate uptake. The electrogenic ionophores valinomycin and gramicidin stimulated molybdate uptake. Rapid pH shift experiments indicated that molybdate transport depends on a transmembrane proton gradient (delta pH), and it is probably transported electroneutrally as H2MoO4. Most of the 99MoO4(2-) taken up was not exchangeable with a 100-fold excess of unlabeled MoO4(2-). Tungstate was a competitive inhibitor of molybdate uptake, with a Ki of 0.034 microM, and vanadate inhibited molybdate uptake slightly.