bluuebunny/crossref_metadata_2025 huggingface dataset:
Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers
Authors: Scott Alison Dawn , Stenz Noah , Baum David A.
Published: November 2015

Summary

Whereas polyploidy is common and an important evolutionary factor in most land plant lineages it is a real rarity in gymnosperms. Coast redwood (Sequoia sempervirens) is the only hexaploid conifer and one of just two naturally polyploid conifer species. Numerous hypotheses about the mechanism of polyploidy inSequoiaand parental genome donors have been proffered over the years, primarily based on morphological and cytological data, but it remains unclear howSequoiabecame polyploid and why this lineage overcame an apparent gymnosperm barrier to whole-genome duplication (WGD).

We sequenced transcriptomes and used phylogenetic inference, Bayesian concordance analysis, and paralog age distributions to resolve relationships among gene copies in hexaploid coast redwood and its close relatives.

Our data show that hexaploidy in the coast redwood lineage is best explained by autopolyploidy or, if there was allopolyploidy, this was restricted to within the Californian redwood clade. We found that duplicate genes have more similar sequences than would be expected given evidence from fossil guard cell size which suggest that polyploidy dates to the Eocene.

Conflict between molecular and fossil estimates of WGD can be explained if diploidization occurred very slowly following whole genome duplication. We extrapolate from this to suggest that the rarity of polyploidy in conifers may be due to slow rates of diploidization in this clade.
Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites
Authors: Savic Daniel , Roberts Brian S. , Carleton Julia B. , Partridge E. Christopher , White Michael A. , Cohen Barak A. , Cooper Gregory M. , Gertz Jason , Myers Richard M.
Published: November 2015

Transcription factors (TFs) bind to thousands of DNA sequences in mammalian genomes, but most of these binding events appear to have no direct effect on gene expression. It is unclear why only a subset of TF bound sites are actively involved in transcriptional regulation. Moreover, the key genomic features that accurately discriminate between active and inactive TF binding events remain ambiguous. Recent studies have identified promoter-distal RNA polymerase II (RNAP2) binding at enhancer elements, suggesting that these interactions may serve as a marker for active regulatory sequences. Despite these correlative analyses, a thorough functional validation of these genomic co-occupancies is still lacking. To characterize the gene regulatory activity of DNA sequences underlying promoter-distal TF binding events that co-occur with RNAP2 and TF sites devoid of RNAP2 occupancy using a functional reporter assay, we performed cis-regulatory element sequencing (CRE-seq). We tested more than 1000 promoter-distal CCAAT/enhancer-binding protein beta (CEBPB)-bound sites in HepG2 and K562 cells, and found that CEBPB-bound sites co-occurring with RNAP2 were more likely to exhibit enhancer activity. CEBPB-bound sites further maintained substantial cell-type specificity, indicating that local DNA sequence can accurately convey cell-type–specific regulatory information. By comparing our CRE-seq results to a comprehensive set of genome annotations, we identified a variety of genomic features that are strong predictors of regulatory element activity and cell-type–specific activity. Collectively, our functional assay results indicate that RNAP2 occupancy can be used as a key genomic marker that can distinguish active from inactive TF bound sites.
ISO 9001: 2008 implementation and impact on the University of Nairobi: a case study
Authors: Moturi Christopher , Mbithi Peter M. F.
Published: November 2015

Purpose

– The purpose of this paper is to present the experience and impact of implementing the ISO 9001: 2008 Standard at the University of Nairobi, in relation to effectiveness on service delivery, operational performance, automation, implementation challenges and related emerging issues.

Design/methodology/approach

– The paper adopted a case study design approach based on qualitative analysis of internal audit reports, internal surveys and feedback, surveillance audits conducted by the certifying body, and rankings by external bodies, over a period of seven years.

Findings

– Significant achievements have been realized with regard to institutionalization of quality into the university processes, work environment, documentation and record management, customer satisfaction, infrastructure and facilities, use of ICT as a prime mover of performance improvement, and ranking of the university. Opportunities for improvement as well as critical success factors are presented.

Practical implications

– The paper reports successes that may encourage other institutions of higher learning that are not certified to implement Quality Management Systems (QMSs) according to ISO 9001 Standard by focusing on specific factors.

Originality/value

– This paper shows how an ISO 9001 certified QMS can improve internal institutional practices and avoid frequently experienced drawbacks.
The impact of ISO 9001 implementation on organizational performance in Kenya
Authors: Ochieng Jacqueline , Muturi David , Njihia Samuel N.
Published: November 2015

Purpose

– The purpose of this paper is to establish the effect of ISO 9001 implementation on the performance of organizations in Kenya. It specifically targeted organizations listed on the Nairobi Securities Exchange (NSE) which is the leading securities exchange in East Africa.

Design/methodology/approach

– The survey made use of web content analysis to collect data from these organizations’ web sites. Data were collected on net profit, turnover and net assets over a four-year period (2010-2013). The research used statistical data analysis to investigate the association between ISO 9001 implementation and performance.

Findings

– Results of the survey reveal that ISO 9001 certification influenced return on net assets of the organizations thereby influencing their performance. There was significant differences in net asset value among organizations with ISO 9001 certification and those that did not possess the certification. On profit and revenue, there were no significant differences between the ISO 9001 certified and non-certified organizations.

Research limitations/implications

– The research findings are limited to those organizations listed in the NSE and may not be generalized to other organizations. The study is further limited by the number of organizations participating in the study which was 20.

Practical implications

– The findings of the study provide justification for adoption of ISO 9001 standard in organizations in all key sectors of the Kenyan economy for sustained quality management practices. The ISO 9001 certified companies will enhance their quality management practices to achieve the successes documented in this paper while those yet to embrace the standards will draw lessons from such successes which may offer them compelling arguments to adopt them.

Originality/value

– Since the adoption and uptake of ISO certification in Kenya over a decade ago, no study has been carried out that directly relates ISO certification to organizational performance. This study will thus be useful as a starting point in documenting the ISO standard’s impact.
Making sense of opportunities in building material production
Authors: Isaksson Raine
Published: November 2015

Purpose

– Breakthrough improvement requires management decisions, which indicates that making sense of existing opportunities is important. This is a particular challenge when the improvement is a possibility and not a problem. The purpose of this paper is to propose the practice of doing an Opportunity Study as the way to create a sense of management urgency for realising dormant possibilities.

Design/methodology/approach

– A process-based Opportunity Study is presented consisting of a Diagnosing-Analysing-Solving (DAS) approach. Benchmarks are defined and compared with the actual performance resulting in a quantifiable improvement potential (D). Main causes are analysed (A), which leads to proposed solutions (S). The Opportunity Study practice is applied to a cement milling process, a cement plant and a supply network for cement-based building products.

Findings

– Results indicate that applying DAS methodology highlights realisable opportunities in all of the studied cases. This seems to be a necessary, but not sufficient criterion to create a sense of urgency for facts based change.

Research limitations/implications

– The results indicate that there is need for further research for looking at the process of sense making and to what extent facts alone can drive change initiatives.

Practical implications

– Results indicate that by a simple review, focusing on what a system can do instead of which the problems are, valuable opportunities for improvement could be detected.

Originality/value

– The paper highlights the value of focusing on opportunities.
Strategic alliances on performance of retail firms in Nairobi County, Kenya
Authors: Muange Rosemary , Maru Loice C.
Published: November 2015

Purpose

– The purpose of this paper is to determine the effect of strategic alliances on firm performance and the moderating effect of firm size in retail firms in Nairobi County in Kenya.

Design/methodology/approach

– Resource Dependency Theory was used to guide the study. The study adopted explanatory research design. Questionnaires were used to collect data from sample of 216 respondents through stratified and simple random sampling technique. The study used inferential statistics to test hypotheses.

Findings

– Study findings indicated that joint marketing alliances, procurement-supplier alliances, joint manufacturing alliances and technology development alliances have significant and positive effect on firm performance. Based on the findings, creating a joint marketing, procurement-supplier, joint manufacturing and technology development alliances mostly enhance firm performance.

Research limitations/implications

– The study considered only one county out of 47, although this county hosts the capital city, where most of the firms considered are located. It therefore is representative of all counties and firms considered in this study. It also considered top management staff and thus may have an effect since the lower cadre staff were not considered. However, most of the required information was expected from top management since these are the ones who make decisions, and hence most affected by strategic alliances.

Practical implications

– This study has practical implication on firm performance because it has established that strategic alliance improves on overall firm performance. This manifests itself in terms of improve productivity, production efficiency and profitability. It also helps in the availability of products to the end users.

Social implications

– Through improved productivity, efficiency and profitability, this translates to improved terms of payment of staff and hence improved quality of lives of their families and communities within which they live. It also enables the firms to participate more in corporate social responsibility projects which in turn improves the standard of living of the communities around them.

Originality/value

– The study has provided an empirical insight on the importance of strategic alliance on firm performance. This is the first study done in the Kenyan context concerning strategic alliances formed by firms to improve on their performance especially on retail firms.
Negative Externalities of Rail Noise and Housing Values: Evidence from the Cessation of Railway Operations in Singapore
Authors: Diao Mi , Qin Yu , Sing Tien Foo
Published: November 2015

The governments of Malaysia and Singapore reached a landmark agreement in May 2010 to end the operations of nearly 80‐year‐old railway lines and stations in Singapore. In our study, the cessation of the railway services operated by Keretapi Tanah Malaya (KTM), a firm owned by the Malaysian government, with effect from July 1, 2011 is used in a quasi‐experiment design to test the effects of the removal of train noise externalities on real estate values. Based on the nonlanded private housing transactions data from January 2005 to June 2013, we find that average prices for houses located within a 400‐m boundary from the railway lines increased by 3.5% relative to prices for houses located outside the 400‐m boundary after the cessation agreement has been announced. The removal of train noise externalities increases housing prices in the affected area by 13.7% on average in the postcessation period of the KTM railway services. Realized economic benefits associated with the railway services cessation were estimated at S$0.36 billion based on houses sold in the post cessation period of the KTM railway services.
Gastrointestinal perforation after liver transplantation
Authors: Fang Cheng , Yan Sheng , Liu Jianhua , Zheng Shusen
Published: November 2015

Aim

The aim of the present study was to evaluate the risk factors and outcomes of gastrointestinal perforation post‐liver transplantation.

Patients and Methods

Eleven patients were found to have complications as a result of gastrointestinal perforation post‐liver transplantation at our centre from May 2008 to February 2014. Seven of these patients were selected for statistical analysis. Each patient was randomly matched with six recipients in age (± 10 years), primary disease and sex. Factors, including cold ischaemic time, blood loss volume, previous hepatobiliary surgery history and 1‐year survival rate, were compared between the two groups.

Results

The sites of perforation were the stomach (n = 2), duodenum (n = 2), jejunum (n = 1), ileum (n = 3) and colon (n = 3). Univariate analysis showed a significant difference in previous hepatobiliary surgery history (P < 0.01). No difference was found in portal venous cross‐clamp time, cold ischaemic time, model for end‐stage liver disease score, body mass index, steroid therapy or blood type incompatibility. Previous hepatobiliary surgery history was found to be an independent risk factor in the multivariate analysis (P < 0.05). The 1‐year survival rate was lower in the perforation group (P < 0.01).

Conclusion

Gastrointestinal perforation leads to a high rate of morbidity and mortality, and significantly decreases graft and recipient survival. A history of hepatobiliary surgery is a risk factor of this complication. Careful dissection and avoiding iatrogenic injury during operation are important.
Efficacy and functional outcome of flexible ureteroscopy for renal stones in patients with a solitary kidney
Authors: Liao Wenbiao , Xiong Yunhe , Yang Sixing , Song Chao , Liu Lingqi , Meng Lingchao
Published: November 2015

Aim

The aim of the present study was to evaluate the efficacy and functional outcome of flexible ureteroscopy (fURS) for renal stones in patients with a solitary kidney.

Patients and Methods

From February 2011 to February 2015, 60 patients with a solitary kidney underwent fURS for the treatment of renal stones. Factors, such as operation duration, complications and stone‐free rate (SFR), were analysed. Changes in the renal function were evaluated by comparing preoperative and postoperative glomerular filtration rates (GFR) and serum creatinine. The stage of chronic kidney disease (CKD) was measured to evaluate the influence of fURS on renal function.

Results

The total SFR were 76.67 per cent and 93.33 per cent after the first and final procedures, respectively. Postoperative minor complications, classified as Clavien grade II, were recorded in 4.2 per cent (2/48) and 25 per cent (3/12) of patients with renal stones < 2 cm and > 2 cm, respectively. Serious complications, classified as Clavien grade III, occurred in 8.3 per cent (1/12) with renal stones > 2 cm. For patients with renal stones < 2 cm, the preoperative and postoperative mean GFR, as well as serum creatinine, had statistical difference (P < 0.05). For patients with a solitary kidney with stage 5 CKD, fURS did not improve the renal function regardless of the stone size.

Conclusion

fURS is a more effective and safer procedure, with a higher SFR and a lower rate of complications in treating stones < 2 cm in a solitary kidney than those > 2 cm. For patients with a solitary kidney with stage 5 CKD, fURS did not improve the renal function regardless of the stone size.
Male fertility following spinal cord injury: an update
Authors: Ibrahim E. , Lynne C. M. , Brackett N. L.
Published: November 2015

Spinal cord injury (SCI) occurs most often in young men at the peak of their reproductive health. The majority of men with SCI cannot father children naturally. Three major complications contribute to infertility in men with SCI: erectile dysfunction, ejaculatory dysfunction, and abnormal semen quality. Erectile dysfunction can be managed by regimens available to the general population, including oral administration of phosphodiesterase‐5 (PDE‐5) inhibitors, intracavernosal injections, vacuum devices, and penile prostheses. Semen may be obtained from anejaculatory men with SCI via the medically assisted ejaculation methods of penile vibratory stimulation (PVS) or electroejaculation (EEJ). Sperm retrieval is also possible via prostate massage or surgical sperm retrieval. Most men with SCI have abnormal semen quality characterized by normal sperm concentrations but abnormally low sperm motility and viability. Accessory gland dysfunction has been proposed as the cause of these abnormalities. Leukocytospermia is evident in most SCI patients. Additionally, elevated concentrations of pro‐inflammatory cytokines and elevated concentrations of inflammasome components are found in their semen. Neutralization of these constituents has resulted in improved sperm motility. There is a recent and alarming trend in the management of infertility in couples with SCI male partners. Although many men with SCI have sufficient motile sperm in their ejaculates for attempting intrauterine insemination (IUI) or even intravaginal insemination, surgical sperm retrieval is often introduced as the first and only sperm retrieval method for these couples. Surgical sperm retrieval commits the couple to the most advanced, expensive, and invasive method of assisted conception: in vitro fertilization with intracytoplasmic sperm injection (IVF/ICSI). Couples should be informed of all options, including semen retrieval by PVS or EEJ. Intravaginal insemination or IUI should be considered when indicated.
Variable selection and estimation in high‐dimensional models
Authors: Horowitz Joel L.
Published: November 2015

Models with high‐dimensional covariates arise frequently in economics and other fields. Often, only a few covariates have important effects on the dependent variable. When this happens, the model is said to be sparse. In applications, however, it is not known which covariates are important and which are not. This paper reviews methods for discriminating between important and unimportant covariates with particular attention given to methods that discriminate correctly with probability approaching 1 as the sample size increases. Methods are available for a wide variety of linear, nonlinear, semiparametric and nonparametric models. The performance of some of these methods in finite samples is illustrated through Monte Carlo simulations and an empirical example.
Association between green tea/coffee consumption and biliary tract cancer: A population‐based cohort study in Japan
Authors: Makiuchi Takeshi , Sobue Tomotaka , Kitamura Tetsuhisa , Ishihara Junko , Sawada Norie , Iwasaki Motoki , Sasazuki Shizuka , Yamaji Taiki , Shimazu Taichi , Tsugane Shoichiro
Published: November 2015

Green tea and coffee consumption may decrease the risk of some types of cancers. However, their effects on biliary tract cancer (BTC) have been poorly understood. In this population‐based prospective cohort study in Japan, we investigated the association of green tea (total green tea, Sencha, and Bancha/Genmaicha) and coffee consumption with the risk for BTC and its subtypes, gallbladder cancer, and extrahepatic bile duct cancer. The hazard ratios and 95% confidence intervals were calculated using the Cox proportional hazard model. A total of 89 555 people aged 45–74 years were enrolled between 1995 and 1999 and followed up for 1 138 623 person‐years until 2010, during which 284 cases of BTC were identified. Consumption of >720 mL/day green tea was significantly associated with decreased risk compared with consumption of ≤120 mL/day (hazard ratio = 0.67 [95% confidence interval, 0.46–0.97]), and a non‐significant trend of decreased risk associated with increased consumption was observed (P‐trend = 0.095). In the analysis according to the location of the primary tumor, consuming >120 mL green tea tended to be associated with decreased risk of gallbladder cancer and extrahepatic bile duct cancer. When Sencha and Bancha/Genmaicha were analyzed separately, we observed a non‐significant trend of decreased risk of BTC associated with Sencha but no association with Bancha/Genmaicha. For coffee, there was no clear association with biliary tract, gallbladder, or extrahepatic bile duct cancer. Our findings suggest that high green tea consumption may lower the risk of BTC, and the effect may be attributable to Sencha consumption.
Postprandial capillary–venous glucose gradient in Type 1 diabetes: magnitude and clinical associations in a real world setting
Authors: Lee I. , Lunt H. , Chan H. , Heenan H. , Berkeley J. , Frampton C. M. A.
Published: November 2015

Aims

To determine the magnitude of the peripheral glucose gradient in patients with Type 1 diabetes in a real world setting and to explore its relationship with insulin dose and macronutrient intake.

Methods

All patients used mealtime analogue insulin. The glucose gradient was assessed using antecubital fossa venous and finger‐stick capillary samples, collected concurrently at room temperature. Baseline sampling occurred before the administration of an insulin dose and breakfast of the patient's choosing. Breakfast was consumed an average of 15 min after baseline. The macronutrient content of breakfast was documented. Sampling was repeated 1 and 2 h after baseline.

Results

The mean (95% CI) plasma capillary–venous glucose gradient values for 43 patients were: pre‐breakfast, 0.21 (0.08–0.34) mmol/l; 1 h after baseline, 0.87 (0.66–1.07) mmol/l; and 2 h after baseline, 0.52 (0.33–0.71) mmol/l. Glucose gradient and dietary carbohydrate intake (g/kg body weight) were positively correlated at both 1 h (P < 0.01) and 2 h after baseline (P < 0.01). No relationship was observed between this gradient and mealtime insulin dose, or the glucose concentration at either time point.

Conclusions

In patients with Type 1 diabetes, a clinically significant glucose gradient is present after the ingestion of a carbohydrate‐rich meal. As postprandial capillary and venous plasma glucose concentrations are not equivalent, defining the site of sample collection is important.
THE EVOLUTIONARY LOGIC OF HONORING SUNK COSTS
Authors: Eswaran Mukesh , Neary Hugh M.
Published: November 2015

Although economics claims that sunk costs should not figure in current decision‐making, there is ample evidence to suggest that people squander resources by honoring bygones. We argue that such wastage of resources was tolerated in our evolutionary past by Nature because it served fitness‐enhancing functions. In this study, we propose and model one such function. We demonstrate how the honoring of sunk costs could have arisen as a commitment device that Nature found expedient for scenarios where conflicts over temptations between the emotional and rational centers of the brain might sabotage long‐term investments. By applying this idea to the self‐concept, we argue that this model provides a rationale for cognitive dissonance, a well‐established phenomenon in social psychology. (JELD01, D03)
Assessing the spatial variability of density dependence in waterfowl populations
Authors: Roy Christian , McIntire Eliot J. B. , Cumming Steven G.
Published: November 2015

Population models commonly assume that the demographic parameters are spatially invariant, but there is considerable evidence that population growth rate (r) and the strength of density dependence (β) can vary over a species' range. To address this issue we developed a spatially explicit Gompertz population model based on the spatially varying coefficients approach to assess the spatial variation in population drivers. The model was fit to spatially stratified time series population estimates of the mallardAnas platyrhynchosin western North America. We included precipitation during the previous year and spring maximum temperature in the current year as environmental factors in the density dependent population model. Because density dependent models can give biased estimates for time series of abundance data, we fit a naïve model without informative priors and a model where we constrained the mean and variance ofrto biologically realistic values that were derived via a comparative demography approach. In the naïve model,rand β were not separately identifiable and their values were overestimated, leading to unrealistic population growth. The naïve model also implied spatial variation in populationrand the return time to equilibrium [1⁄(– β)] across the survey area. In contrast, in the informative model,rand the return time to equilibrium did not vary markedly among populations and were generally equal across populations. The effects of the climatic factors were similar across models. Population growth rates in the Prairie‐pothole region were positively correlated with precipitation, while in Alaska rates were positively correlated with spring temperature. Although it has been argued in the past that adding ecological realism could help avoid the pitfalls associated with density dependent models, our results demonstrate that imposing constraints on the population parameters is still the best course of action.
Incorporating biotic factors in species distribution modeling: are interactions with soil microbes important?
Authors: Bueno de Mesquita Clifton P. , King Andrew J. , Schmidt Steven K. , Farrer Emily C. , Suding Katharine N.
Published: November 2015

It is increasingly recognized that species distributions are driven by both abiotic factors and biotic interactions. Despite much recent work incorporating competition, predation, and mutualism into species distribution models (SDMs), the focus has been confined to aboveground macroscopic interactions. Biotic interactions between plants and soil microbial communities are understudied as potentially important drivers of plant distributions. Some soil bacteria promote plant growth by cycling nutrients, while others are pathogenic; thus they have a high potential for influencing plant occurrence. We investigated the influence of soil bacterial clades on the distributions of bryophytes and 12 vascular plant species in a high elevation talus‐field ecosystem in the Rocky Mountain Front Range, Colorado, USA. We used an information‐theoretic criterion (AICc) modeling approach to compare SDMs with the following different sets of predictors: abiotic variables, abiotic variables and other plant abundances, abiotic variables and soil bacteria clade relative abundances, and a full model with abiotic factors, plant abundances, and bacteria relative abundances. We predicted that bacteria would influence plant distributions both positively and negatively, and that these interactions would improve prediction of plant species distributions. We found that inclusion of either plant or bacteria biotic predictors generally improved the fit, deviance explained, and predictive power of the SDMs, and for the majority of the species, adding information on both other plants and bacteria yielded the best model. Interactions between the modeled species and biotic predictors were both positive and negative, suggesting the presence of competition, parasitism, and facilitation. While our results indicate that plant–plant co‐occurrences are a stronger driver of plant distributions than plant–bacteria co‐occurrences, they also show that bacteria can explain parts of plant distributions that remain unexplained by abiotic and plant predictors. Our results provide further support for including biotic factors in SDMs, and suggest that belowground factors be considered as well.
Historical dynamics of Batrachochytrium dendrobatidis in Amazonia
Authors: Becker C. Guilherme , Rodriguez David , Lambertini Carolina , Toledo L. Felipe , Haddad Célio F. B.
Published: November 2015

The Amazon forest is known for its astonishing amphibian diversity, yet the potential distribution and underlying impacts of the most important amphibian pathogen is unknown for most of Amazonia. In this retrospective survey of preserved Leptodactylus frogs, collected over a 119 yr period, we used quantitative PCR to detect the fungal pathogen Batrachochytrium dendrobatidis (Bd) and performed spatial scan analyses to identify spatiotemporal clusters of Bd. We also quantified the potential effect of environmental factors on the likelihood of Bd occurrence and generated an updated suitability map for Bd in the Amazon that included our retrospective sampling. We detected Bd in lowland Amazon as early as 1935, in the state of Pará, Brazil, and we found low prevalence (∼ 3.8%) over time. We identified two statistically significant spatiotemporal clusters of Bd: a recent and narrow cluster in the Amazon River delta and a spatiotemporally broad cluster in the southern edge of Amazon and Brazilian savanna. Furthermore, we found an increase in Bd‐positive samples in the southwestern Amazon after the 1990s, coinciding with reported amphibian declines in neighboring high elevation sites on Andean slopes of Peru. Spatial regressions indicated that higher human interference, higher precipitation, and lower temperatures were significant predictors of Bd occurrence. Environmental niche modeling predicted some narrow areas of suitable climates along the Amazon's periphery and generally low climatic suitability for Bd in the central Amazon; although, we found clusters of Bd‐positive samples with unexpectedly high infection loads in areas of predicted low suitability. Our study indicates that accelerated human development may put Amazonian amphibians at risk from Bd introductions, and it highlights the potential need to monitor Bd dynamics near Amazonian port cities.
Cryptochrome 1b: a possible inducer of visual lateralization in pigeons?
Authors: Ströckens Felix , Güntürkün Onur
Published: November 2015

The visual system of adult pigeons shows a lateralization of object discrimination with a left hemispheric dominance on the behavioural, physiological and anatomical levels. The crucial trigger for the establishment of this asymmetry is the position of the embryo inside the egg, which exposes the right eye to light falling through the egg shell. As a result, the right‐sided retina is more strongly stimulated with light during embryonic development. However, it is unknown how this embryonic light stimulation is transduced to the brain as rods and cones are not yet functional. A possible solution could be the blue‐light‐sensitive molecule cryptochrome 1 (Cry1), which is expressed in retinal ganglion cells (RGCs) of several mammalian and avian species. RGCs have been shown to be functional during the time of induction of asymmetry and possess projections to primary visual areas. Therefore, Cry1‐containing RGCs could be responsible for induction of asymmetry. The aim of this study was to identify the expression pattern of the Cry1 subtype Cry1b in the retina of embryonic, post‐hatch and adult pigeons by immunohistochemical staining and to show whether Cry1b‐containing RGCs project to the optic tectum. Cry1b‐positive cells were indeed mainly found in the RGC layer and to lesser extent in the inner nuclear layer at all ages, including the embryonic stage. Tracing in adult animals revealed that at least a subset of Cry1b‐containing RGCs project to the optic tectum. Thus, Cry1b‐containing RGCs within the embryonic retina could be involved in the induction of asymmetries in the visual system of pigeons.
Intact working memory in non‐manifesting LRRK2 carriers – an fMRI study
Authors: Thaler Avner , Helmich Rick C. , Or‐Borichev Ayelet , van Nuenen Bart F.L. , Shapira‐Lichter Irit , Gurevich Tanya , Orr‐Urtreger Avi , Marder Karen , Bressman Susan , Bloem Bastiaan R. , Giladi Nir , Hendler Talma , Mirelman Anat ,   the LRRK2 Ashkenazi Jewish consortium
Published: November 2015

Cognitive impairments are prevalent in patients with Parkinson's disease. Mutations in the leucine‐rich repeat kinase 2 (LRRK2) gene are the most common cause of genetic Parkinsonism. Non‐manifesting carriers of the G2019S mutation in the LRRK2 gene were found to have lower executive functions as measured by the Stroop task. This exploratory study aimed to assess whether the cognitive impairment in non‐manifesting carriers is specific for executive functions or includes other cognitive domains such as working memory. We recruited 77 non‐manifesting first‐degree relatives of Parkinson's disease patients (38 carriers). A block‐design fMRI N‐back task, with 0‐back, 2‐back and 3‐back conditions, was used in order to assess working memory. Participants were well matched on the Montreal Cognitive Assessment, University of Pennsylvania Smell Identification Test, Unified Parkinson's Disease Rating Scale part III, digit span, age, gender and Beck Depression Inventory. The task achieved the overall expected effect in both groups with longer reaction times and lower accuracy rates with increasing task demands. However, no whole‐brain or region‐of‐interest between‐groups differences were found on any of the task conditions. These results indicate that non‐manifesting carriers of the G2019S mutation in the LRRK2 gene have a specific cognitive profile with executive functions, as assessed by the Stroop task, demonstrating significant impairment but with working memory, as assessed with the N‐back task, remaining relatively intact. These finding shed light on the pre‐motor cognitive changes in this unique ‘at risk’ population and should enable more focused cognitive assessments of these cohorts.
Examining the Reliability of Student Growth Percentiles Using Multidimensional IRT
Authors: Monroe Scott , Cai Li
Published: November 2015

Student growth percentiles (SGPs, Betebenner, 2009) are used to locate a student's current score in a conditional distribution based on the student's past scores. Currently, following Betebenner (2009), quantile regression (QR) is most often used operationally to estimate the SGPs. Alternatively, multidimensional item response theory (MIRT) may also be used to estimate SGPs, as proposed by Lockwood and Castellano (2015). A benefit of using MIRT to estimate SGPs is that techniques and methods already developed for MIRT may readily be applied to the specific context of SGP estimation and inference. This research adopts a MIRT framework to explore the reliability of SGPs. More specifically, we propose a straightforward method for estimating SGP reliability. In addition, we use this measure to study how SGP reliability is affected by two key factors: the correlation between prior and current latent achievement scores, and the number of prior years included in the SGP analysis. These issues are primarily explored via simulated data. In addition, the QR and MIRT approaches are compared in an empirical application.
Optogenetic stimulation of cholinergic brainstem neurons during focal limbic seizures: Effects on cortical physiology
Authors: Furman Moran , Zhan Qiong , McCafferty Cian , Lerner Benjamin A. , Motelow Joshua E. , Meng Jin , Ma Chanthia , Buchanan Gordon F. , Witten Ilana B. , Deisseroth Karl , Cardin Jessica A. , Blumenfeld Hal
Published: November 2015

Focal temporal lobe seizures often cause impaired cortical function and loss of consciousness. Recent work suggests that the mechanism for depressed cortical function during focal seizures may depend on decreased subcortical cholinergic arousal, which leads to a sleep‐like state of cortical slow‐wave activity. To test this hypothesis, we sought to directly activate subcortical cholinergic neurons during focal limbic seizures to determine the effects on cortical function. Here we used an optogenetic approach to selectively stimulate cholinergic brainstem neurons in the pedunculopontine tegmental nucleus during focal limbic seizures induced in a lightly anesthetized rat model. We found an increase in cortical gamma activity and a decrease in delta activity in response to cholinergic stimulation. These findings support the mechanistic role of reduced subcortical cholinergic arousal in causing cortical dysfunction during seizures. Through further work, electrical or optogenetic stimulation of subcortical arousal networks may ultimately lead to new treatments aimed at preventing cortical dysfunction during seizures.
Aberrant topological patterns of brain structural network in temporal lobe epilepsy
Authors: Yasuda Clarissa Lin , Chen Zhang , Beltramini Guilherme Coco , Coan Ana Carolina , Morita Marcia Elisabete , Kubota Bruno , Bergo Felipe , Beaulieu Christian , Cendes Fernando , Gross Donald William
Published: November 2015

Objective

Although altered large‐scale brain network organization in patients with temporal lobe epilepsy (TLE) has been shown using morphologic measurements such as cortical thickness, these studies, have not included critical subcortical structures (such as hippocampus and amygdala) and have had relatively small sample sizes. Here, we investigated differences in topological organization of the brain volumetric networks between patients with right TLE (RTLE) and left TLE (LTLE) with unilateral hippocampal atrophy.

Methods

We performed a cross‐sectional analysis of 86 LTLE patients, 70 RTLE patients, and 116 controls. RTLE and LTLE groups were balanced for gender (p = 0.64), seizure frequency (Mann‐Whitney U test, p = 0.94), age (p = 0.39), age of seizure onset (p = 0.21), and duration of disease (p = 0.69). Brain networks were constructed by thresholding correlation matrices of volumes from 80 cortical/subcortical regions (parcellated with Freesurfer v5.3 https://surfer.nmr.mgh.harvard.edu/) that were then analyzed using graph theoretical approaches.

Results

We identified reduced cortical/subcortical connectivity including bilateral hippocampus in both TLE groups, with the most significant interregional correlation increases occurring within the limbic system in LTLE and contralateral hemisphere in RTLE. Both TLE groups demonstrated less optimal topological organization, with decreased global efficiency and increased local efficiency and clustering coefficient. LTLE also displayed a more pronounced network disruption. Contrary to controls, hub nodes in both TLE groups were not distributed across whole brain, but rather found primarily in the paralimbic/limbic and temporal association cortices. Regions with increased centrality were concentrated in occipital lobes for LTLE and contralateral limbic/temporal areas for RTLE.

Significance

These findings provide first evidence of altered topological organization of the whole brain volumetric network in TLE, with disruption of the coordinated patterns of cortical/subcortical morphology.
Potential pitfalls of CRISPR/Cas9‐mediated genome editing
Authors: Peng Rongxue , Lin Guigao , Li Jinming
Published: November 2015

Recently, a novel technique named the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR‐associated protein (Cas)9 system has been rapidly developed. This genome editing tool has improved our ability tremendously with respect to exploring the pathogenesis of diseases and correcting disease mutations, as well as phenotypes. With a short guide RNA, Cas9 can be precisely directed to target sites, and functions as an endonuclease to efficiently produce breaks in DNA double strands. Over the past 30 years, CRISPR has evolved from the ‘curious sequences of unknown biological function’ into a promising genome editing tool. As a result of the incessant development in the CRISPR/Cas9 system, Cas9 co‐expressed with custom guide RNAs has been successfully used in a variety of cells and organisms. This genome editing technology can also be applied to synthetic biology, functional genomic screening, transcriptional modulation and gene therapy. However, although CRISPR/Cas9 has a broad range of action in science, there are several aspects that affect its efficiency and specificity, including Cas9 activity, target site selection and short guide RNA design, delivery methods, off‐target effects and the incidence of homology‐directed repair. In the present review, we highlight the factors that affect the utilization of CRISPR/Cas9, as well as possible strategies for handling any problems. Addressing these issues will allow us to take better advantage of this technique. In addition, we also review the history and rapid development of the CRISPR/Cas system from the time of its initial discovery in 2012.
Kinship moderates the association between a demented individual's behavioral disturbance and a caregiver's burden: Findings from a national survey in Taiwan
Authors: Lin Linen Nymphas , Wu Shwu‐Chong
Published: November 2015

Aim

The present study aimed to assess the moderating role of kinship between the behavioral disturbance of care recipients (CRs) with dementia and the caregivers' (CGs') burden in Taiwan.

Methods

The data of 965 CG‐CR dyads on the behavioral disturbance of CR with dementia, CG burden, CG kinship to CR and other relevant variables were obtained from the Assessment of the National Long‐Term Care Need in Taiwan (ANLTCNT). To test the moderating effect of CG‐CR kinship on the association between behavioral disturbance of CR and CG burden, a series of hierarchical multiple linear regression models were used after controlling for potential factors associated with CG burden.

Results

Different kinships had significant differences in terms of burden, except for relational burden. The interaction terms (of CRs' behavioral disturbance by kinship) were not significant on burden of time and emotional burden. On relational burden, the impact of CRs' behavioral disturbance on CG burden was significantly higher for a wife than for a daughter‐in‐law or a son. The impact of CRs' behavioral disturbance on financial burden was lower for a wife than for a daughter‐in‐law. In terms of the total burden, the impact of CRs' behavioral disturbance was higher for a daughter than for a son.

Conclusion

These findings highlight the importance of CG kinship to CR moderating the association between the CRs' level of behavioral disturbance and the CGs' relational, financial, and total burden, when refining kinship‐oriented interventions for community services to CRs with dementia and their CGs. Geriatr Gerontol Int 2016; 16: 1272–1280.
Effects of spousal illness on self‐rated health in older couples: Role of sex and proximity to adult children
Authors: Saito Tami , Wakui Tomoko , Kai Ichiro
Published: November 2015

Aims

The present study examined the impact of serious spousal illness or hospitalization on community‐dwelling older adults' self‐rated health (SRH), and explored the moderating effects of sex and residential proximity to adult children using a prospective and representative survey design.

Methods

The sample was obtained from a 2‐year longitudinal survey of non‐institutionalized men and women aged 65 years and older carried out in the Fukui Prefecture, Japan (n = 1573). The effect of serious spousal illness or hospitalization on SRH during the survey period was examined after controlling for baseline SRH, sex, age, socioeconomic status, chronic illness and other baseline covariates.

Results

Overall, 15.7% of respondents had experienced a serious spousal illness or hospitalization within the previous year. After controlling for covariates, spousal illness had a significant negative effect on SRH at follow‐up (P = 0.031). More serious effects of spousal illness were found in older adults whose children lived farther than 30 min away than in couples who lived with their children (P = 0.009). However, there was no significant interaction effect between sex and spousal illness.

Conclusions

Serious spousal illness could cause deterioration in the health of older spouses, particularly for older parents whose children live a distance away. Geriatr Gerontol Int 2016; 16: 1332–1338.
A trade‐off between overheating and camouflage on shorebird eggshell colouration
Authors: Gómez Jesús , Pereira Ana I. , Pérez‐Hurtado Alejandro , Castro Macarena , Ramo Cristina , Amat Juan A.
Published: November 2015

In ground‐nesting birds egg colour and appearance may have evolved due to opposite selection pressures. Pigmentation and spottiness make the eggs darker and have been suggested to improve camouflage. However darker and more spotted eggs may reach higher temperatures when not attended by adults and receiving direct sunlight, which may be lethal for embryos. Some authors suggested that this trade‐off may not exist because eggshell pigments mainly reflect in the infrared region of the solar spectrum, but have not considered that wavelengths in the visible part of the spectrum may also contribute to overheating. To test the occurrence of a trade‐off between camouflage and overheating of eggs, we took digital images to analyse colour and camouflage in 93 nests of four shorebird species (two stilts and two plovers) in two regions (tropical and mediterranean sites). We predicted that these species (closely related) may have evolved different eggshell designs depending on solar radiation, which is supposed to be stronger in the Tropics. To record egg temperatures, we placed Japanese quail eggs in natural nests of shorebirds, and registered temperatures using a datalogger. We found that darker and more spotted eggs reached higher temperatures than lighter ones, and that after controlling for environmental temperatures, eggs overheated more in the Tropics, likely because of a more intense solar radiation. We also found that tropical shorebirds’ eggshells have darker spots and lighter backgrounds. Overall, darker eggs were better camouflaged. Taken together, our results show that the benefits of increasing pigmentation of eggshell backgrounds and spottiness for a better camouflage are counteracted by the increased risks of overheating when eggs remain exposed to direct solar radiation.
Clear cell adenocarcinoma arising from adenomyotic cyst: A case report and literature review
Authors: Baba Akira , Yamazoe Shinji , Dogru Murat , Ogawa Mariko , Takamatsu Kiyoshi , Miyauchi Jun
Published: November 2015

Ovaries are the primary sites of cancerous disease that is derived from endometriosis. Uterine cancer originating from endometriosis is very rare. The most frequent histological subtype of cancer derived from endometriosis is endometrioid adenocarcinoma, a subtype of clear cell carcinoma which is exceedingly rare. We report a case of a 40‐year‐old Japanese woman with a six year history of uterine leiomyoma. The patient was clinically and radiologically suspected to have degenerative uterine myoma with a possible malignant association and underwent a transabdominal total hysterectomy. Histopathological examination of the specimens revealed clear cell adenocarcinoma arising from the adenomyotic cyst. A literature review of clear cell adenocarcinomas arising from uterine adenomyotic cysts (cystic adenomyosis), emphasizes the clinically and radiologically important features of this very rare entity. Clear cell carcinoma association should be suspected in patients who are under follow‐up for uterine myomas and present with cystic uterine changes with solid component on magnetic resonance imaging or computed tomography scans.