bluuebunny/crossref_metadata_2025 huggingface dataset:
Reproducibility of peripheral arterial tonometry measurements in male cardiovascular patients
Authors: Nil Markus , Schäfer Daniela , Radtke Thomas , Saner Hugo , Wilhelm Matthias , Eser Prisca
Published: September 2014

Background

Assessment of endothelial function of the microvasculature by peripheral arterial tonometry (EndoPAT®) has gained increasing popularity in patients with cardiovascular risk factors. Only limited knowledge about its reproducibility in patients with coronary artery disease (CAD) is available. We therefore aimed to quantify reproducibility of EndoPAT® parameters in patients with stable CAD.

Design

EndoPAT® measurements were performed repeatedly in 78 male patients (age 66 ± 8 years) with CAD on stable medication. We calculated overall mean, standard deviation (SD), coefficient of variation (CV) and intraclass correlation coefficient (ICC) of the following parameters: reactive hyperemic index (RHI), PAT ratio of the postocclusion period 90–150 s as used for calculation of the RHI (PAT ratio90–150 s) and 90–120 s (PAT ratio90–120 s) as used for the often employed Framingham RHI (F‐RHI), as well as PAT ratio of the peak hyperemic response (PAT ratiopeak response). Additionally, least significant changes (LSC) for individual subjects and minimum sample sizes for parallel and cross‐over design studies were calculated.

Results

Mean RHI was 1·84 (SD 0·36). For RHI, PAT ratio90–150 s, PAT ratio90–120 s, and PAT ratiopeak response the CVs were 17·0%, 25·4%, 26·1%, and 25·0%, respectively. The ICCs were 0·45, 0·49, 0·48 and 0·51, respectively, and LSC for RHI was 47·2%.

Conclusions

CV of RHI in our population was moderate; however, we consider this precision insufficient to monitor changes in individual patients, as they would need to exceed 47% to show a significant change. Further, the poor ICCs reflect the difficulty of detecting treatment effects in homogenous populations, such as patients with stable CAD.
Does probability of occurrence relate to population dynamics?
Authors: Thuiller Wilfried , Münkemüller Tamara , Schiffers Katja H. , Georges Damien , Dullinger Stefan , Eckhart Vincent M. , Edwards Thomas C. , Gravel Dominique , Kunstler Georges , Merow Cory , Moore Kara , Piedallu Christian , Vissault Steve , Zimmermann Niklaus E. , Zurell Damaris , Schurr Frank M.
Published: September 2014

Hutchinson defined species' realized niche as the set of environmental conditions in which populations can persist in the presence of competitors. In terms of demography, the realized niche corresponds to the environments where the intrinsic growth rate (r) of populations is positive. Observed species occurrences should reflect the realized niche when additional processes like dispersal and local extinction lags do not have overwhelming effects. Despite the foundational nature of these ideas, quantitative assessments of the relationship between range‐wide demographic performance and occurrence probability have not been made. This assessment is needed both to improve our conceptual understanding of species' niches and ranges and to develop reliable mechanistic models of species geographic distributions that incorporate demography and species interactions.

The objective of this study is to analyse how demographic parameters (intrinsic growth rate r and carrying capacity K ) and population density (N ) relate to occurrence probability (Pocc ). We hypothesized that these relationships vary with species' competitive ability. Demographic parameters, density, and occurrence probability were estimated for 108 tree species from four temperate forest inventory surveys (Québec, western USA, France and Switzerland). We used published information of shade tolerance as indicators of light competition strategy, assuming that high tolerance denotes high competitive capacity in stable forest environments.

Interestingly, relationships between demographic parameters and occurrence probability did not vary substantially across degrees of shade tolerance and regions. Although they were influenced by the uncertainty in the estimation of the demographic parameters, we found that r was generally negatively correlated with Pocc, while N, and for most regions K, was generally positively correlated with Pocc. Thus, in temperate forest trees the regions of highest occurrence probability are those with high densities but slow intrinsic population growth rates. The uncertain relationships between demography and occurrence probability suggests caution when linking species distribution and demographic models.
Neurophysiological evidence for the presence of cannabinoid CB1 receptors in the laterodorsal tegmental nucleus
Authors: Soni Neeraj , Satpathy Shankha , Kohlmeier Kristi A.
Published: September 2014

Marijuana, which acts within the endocannabinoid (eCB) system as an agonist of the cannabinoid type 1 receptor (CB1R), exhibits addictive properties and has powerful actions on the state of arousal of an organism. The laterodorsal tegmental nucleus (LDT), as a component of the reticular activating system, is involved in cortical activation and is important in the development of drug addiction‐associated behaviours. Therefore, eCBs might exert behavioural effects by actions on the LDT; however, it is unknown whether eCBs have actions on neurons in this nucleus. Accordingly, whole‐cell voltage‐ and current‐clamp recordings were conducted from mouse brain slices, and responses of LDT neurons to the CB1R agonist WIN‐2 were monitored. Our results showed that WIN‐2 decreased the frequency of spontaneous and miniature inhibitory postsynaptic currents (sIPSCs and mIPSCs). Ongoing activity of endogenous eCBs was confirmed as AM251, a potent CB1R antagonist, elicited sIPSCs. WIN‐2 reduced the firing frequency of LDT neurons. In addition, our RT‐PCR studies confirmed the presence of CB1R transcript in the LDT. Taken together, we conclude that CB1Rs are functionally active in the LDT, and their activation changes the firing frequency and synaptic activity of neurons in this nucleus. Therefore, endogenous eCB transmission could play a role in processes involving the LDT, such as cortical activation and motivated behaviours and, further, behavioural actions of marijuana are probably mediated, in part, via cellular actions within the LDT induced by this addictive and behavioural state‐altering drug.
Multiple mandibular ossifying fibromas in a yearlingBelgianDraught horse filly
Authors: Crijns C. P. , Vlaminck L. , Verschooten F. , van Bergen T. , De Cock H. E. , Huylebroek F. , Pool R. , Gielen I.
Published: September 2014

A yearlingBelgianDraught horse filly was presented with a history of bilateral, progressive, painful swelling of the mandible, fever and anorexia. Radiographs and computed tomographic images showed an expansile lesion with a coalescing, well‐defined cystic pattern at the level of the horizontal ramii of the mandible. The histopathological findings confirmed the diagnoses of bilateral, multiple ossifying fibroma. This report indicates that ossifying fibroma should be included in a differential diagnosis if multiple expansile lesions of the jaw are present.
Effects of woody debris and the supply of terrestrial invertebrates on the diet and growth of brown trout (Salmo trutta) in a boreal stream
Authors: Gustafsson Pär , Greenberg Larry A. , Bergman Eva
Published: September 2014

Changes to the riparian vegetation of forest streams during timber harvesting may have considerable impacts on stream biota, but few studies have attempted to separate the effects of individual factors that are altered during clear‐felling operations.

We studied the effects of large wood and terrestrial invertebrate supply, two factors affected by forest harvesting, on the growth and diet of two size classes of brown trout (Salmo trutta) during a two‐month (June–August) field enclosure experiment. Twelve 20‐m‐long enclosed stream reaches were used in a 2 × 2 factorial design, with large wood either absent or added to mimic pre‐modern forestry conditions, and terrestrial invertebrate inputs either reduced or maintained at ambient levels.

The addition of large wood had a positive effect on the growth of large trout but no effect on small trout, whereas terrestrial invertebrate input had no effect on the growth of either size class. Growth rates were highest in the treatment with ambient terrestrial invertebrate inputs and added wood, were lowest in the treatment with reduced terrestrial invertebrate inputs and no added wood and were intermediate in the other two treatments.

Dietary analyses showed no difference in treatments with and without added wood, perhaps because instream wood influences growth by producing profitable stream positions for trout, rather than by acting as a source of prey. Terrestrial invertebrate inputs affected the diet, as trout in enclosures with reduced inputs had a lower proportion of terrestrial invertebrate biomass in the diet than trout in enclosures with ambient terrestrial inputs.

Our results suggest that leaving woody debris in streams when harvesting forests may enhance trout growth and that this is probably due to the physical changes in depth and current velocity caused by the wood rather than to changes in dietary prey composition.
Microrefuges from drying for invertebrates in a seasonal wetland
Authors: Strachan Scott R. , Chester Edwin T. , Robson Belinda J.
Published: September 2014

Seasonally intermittent freshwater environments show large temporal changes in area and environmental conditions (which may be harsh). We investigated whether microhabitats that retain moisture could provide a refuge during drying in a seasonal wetland.

We investigated occupancy by invertebrates of three potential microrefuge types: surface depressions, shallow cracks and deeper fissures in the sediment of a wetland in Western Australia. Our aims were to determine whether the assemblages occupying these microrefuges differed and whether they changed as the wetland dried and reflooded.

Ten microrefuges of each type were sampled for invertebrates, sediment and temperature during each of three hydrological phases: the damp phase (surface water absent but sediment moist), the dry phase (groundwater at its lowest level) and the reflooded phase (surface water present). Sediment samples taken from each microrefuge in the damp and dry phases were reflooded in the laboratory to reveal species aestivating or present as eggs, and sediment organic matter content was measured.

Sediment organic matter content did not change between wetland phases. The invertebrate assemblage in the microrefuges showed almost complete species turnover between phases. Invertebrate composition differed between microrefuges, and temperature in the deeper fissures was on average >10 °C lower than in surface depressions and shallow cracks.

Microcrustaceans and gastropods survived the drier months as resting stages in the microrefuges and either emerged or hatched from eggs upon reflooding. Several species, including isopods and caddisflies, were collected only from cracks and fissures as the wetland dried. During drying, a high diversity of carnivorous species was observed in the microrefuges.

Sediment microrefuges apparently underpin resistance to drought by invertebrates in South Lake. Those species that depend on sediment fissures to survive may be threatened by the declining groundwater table in the region. Changes to wetland hydrology and other human activities that affect wetland sediment or vegetation will affect the range of microrefuges available to invertebrates to survive drying and may thus alter wetland biodiversity.
Viral attack exacerbates the susceptibility of a bloom‐forming alga to ocean acidification
Authors: Chen Shanwen , Gao Kunshan , Beardall John
Published: September 2014

Both ocean acidification and viral infection bring about changes in marine phytoplankton physiological activities and community composition. However, little information is available on how the relationship between phytoplankton and viruses may be affected by ocean acidification and what impacts this might have on photosynthesis‐driven marine biological CO2 pump. Here, we show that when the harmful bloom alga Phaeocystis globosa is infected with viruses under future ocean conditions, its photosynthetic performance further decreased and cells became more susceptible to stressful light levels, showing enhanced photoinhibition and reduced carbon fixation, up‐regulation of mitochondrial respiration and decreased virus burst size. Our results indicate that ocean acidification exacerbates the impacts of viral attack on P. globosa, which implies that, while ocean acidification directly influences marine primary producers, it may also affect them indirectly by altering their relationship with viruses. Therefore, viruses as a biotic stressor need to be invoked when considering the overall impacts of climate change on marine productivity and carbon sequestration.
Bone disease in patients with haemophilia A and B – where are we now?
Authors: Anagnostis P. , Karras S. N. , Goulis D. G.
Published: September 2014

It is evident that haemophilia A and B are associated with decreased bone mass in both adults and children. Decreased physical activity and vitamin D deficiency are some of the major factors leading to bone loss. Hepatitis C virus (HCV) infection may also contribute to low bone mineral density (BMD). However, definite conclusions regarding the exact prevalence and pathogenesis of osteoporosis cannot be conducted yet, due to the small sample size and significant heterogeneity among studies. Discordant findings with regard to the skeletal site of low BMD have also been reported. Furthermore, data on fracture risk are sparse. The use of the Fracture Risk Assessment Tool (FRAX) for assessing fracture risk, regular BMD assessment at the age of 25 and thereafter, careful evaluation of risk factors associated with bone loss and optimal calcium and vitamin D intake are recommended. Long‐term prophylactic factor replacement therapy, resistance exercise and bisphosphonates, in severe cases of increased fracture risk, can prevent bone loss.
Effect of alternate night nocturnal home hemodialysis on anemia control in patients with end‐stage renal disease
Authors: Poon Clara K. Y. , Tang Hon‐Lok , Wong Joseph H. S. , Law Wai‐Ping , Lam Chung‐Man , Yim Ka‐Fai , Cheuk Au , Lee William , Chau Ka‐Foon , Tong Matthew K. L. , Fung Samuel K. S.
Published: September 2014

Nocturnal home hemodialysis (NHHD) has shown promising results in various clinical parameters. Whether NHHD provide benefit in anemia management remains controversial. This study aims to investigate whether anemia and erythropoiesis‐stimulating agent (ESA) requirement are improved in patients receiving alternate night NHHD compared with conventional hemodialysis (CHD). In this retrospective controlled study, a clinical data of 23 patients receiving NHHD were compared with 25 in‐center CHD patients. Hemoglobin level, ESA requirement, iron profile, and dialysis adequacy indexes were compared between the two groups. Hemoglobin level increased from baseline of 9.37 ± 1.39 g/dL to 11.34 ± 2.41 g/dL at 24 months (P < 0.001) and ESA requirement decreased from 103.44 ± 53.55 U/kg/week to 47.33 ± 50.62 U/kg/week (P < 0.001) in NHHD patients. ESA requirement further reduced after the first year of NHHD (P = 0.037). Standard Kt/V increased from baseline of 2.02 ± 0.28 to 3.52 ± 0.30 at 24 months (P < 0.001). At 24 months, hemoglobin level increased by 1.98 ± 2.74 g/dL in the NHHD group while it decreased by 0.20 ± 2.32 g/dL in the CHD group (P = 0.007). ESA requirement decreased by 53.49 ± 55.50 U/kg/week in NHHD patients whereas it increased by 16.22 ± 50.01 U/kg/week in CHD patients (P < 0.001). Twenty‐six percent of NHHD patients were able to stop ESA compared with none in the CHD group. Standard Kt/V showed greater increase in the NHHD group. (1.49 ± 0.36 in NHHD vs. 0.18 ± 0.31 in CHD, P = 0.005). NHHD with an alternate night schedule improves anemia and reduces ESA requirement as a result of enhanced uremic clearance. This benefit extended beyond the first year of NHHD.
Increased T‐cell turnover is associated with spondyloarthritis in virally suppressed patients with HIV‐1 infection
Authors: Lu I‐N , Meyer‐Olson D , Stoll M , Witte T , Schmidt RE , Baerlecken NT
Published: September 2014

Objectives

Spondyloarthritis (SpA) is one of the most frequently observed inflammatory joint diseases in HIV‐1‐seropositive patients. T‐cells were described frequently as one of the major driving forces in SpA, therefore we tried to look for T‐cell aberrancies in our HIV‐positive patients with SpA.

Methods

A total of 1098 files for HIV‐positive patients who attended the HIV out‐patient clinic of the Department of Clinical Immunology and Rheumatology at the Medical University Hanover for at least one visit between January 2004 and December 2010 were screened for the presence of a diagnosis of SpA. A cross‐sectional study was conducted to investigate aberrancies in T‐cell homeostasis induced by HIV‐1 in these subjects.

Results

The prevalence of SpA in the HIV‐positive patients was 1.6% (18 of 1098). Interestingly, the percentage of patients with SpA who were human leucocyte antigen (HLA)‐B27 negative in our HIV‐positive cohort was 80%. Despite combination antiretroviral therapy (cART) and viral suppression, an incomplete immune recovery of T‐cell naïve/memory distribution and turnover, as identified by intracellular Ki‐67 expression, was observed in HIV‐positive patients with SpA.

Conclusions

Independent of HLA‐B27 status and despite cART, HIV‐positive patients can develop SpA and exhibit an increased T‐cell turnover rate.
Private Dependence, Public Personhood: Rethinking “Nested Obligations”
Authors: Back Laura
Published: September 2014

This paper responds to Love's Labor, Eva Feder Kittay's seminal contribution to feminist disability theory, arguing that Kittay's “nested obligations” approach creates a two‐tiered system of justice in which care relationships built around private dependence and private obligation are figured as wholly prepolitical, to the detriment of both gender justice and disability justice. I suggest that centering the civic membership of the disabled person allows us to keep what is valuable in Kittay's contribution, namely her theorization of the nature of care and its political significance, and her call for collective support of care relationships, while omitting the nesting of obligations and resituating care recipients and care workers as equal and interdependent.
Low incubation investment in the burrow‐nesting Crab PloverDromas ardeolapermits extended foraging on a tidal food resource
Authors: De Marchi Giuseppe , Chiozzi Giorgio , Dell'Omo Giacomo , Fasola Mauro
Published: September 2014

We usedGPSdata‐loggers, video‐recordings and dummy eggs to assess whether foraging needs may force the low incubation attentiveness (< 55%) of the Crab PloverDromas ardeola, a crab‐eating wader of the Indian Ocean that nests colonially in burrows. The tidal cycle was the major determinant of the time budget and some foraging trips were more distant from the colony than previously known (up to 26 km away and lasting up to 45 h). The longest trips were mostly made by off‐duty parents, but on‐duty parents also frequently left the nest unattended while foraging for 1–7 h. However, the time spent at the colony area (47%) and the time spent roosting on the foraging grounds (16%) would have allowed almost continuous incubation, as in other species with shared incubation. Therefore, the low incubation attentiveness is not explained by the need for long foraging trips but is largely dependent on a high intermittent rhythm of incubation with many short recesses (5.8 ± 2.6 recesses/h) that were not spent foraging but just outside the burrow or thermoregulating at the seashore. As a result, the eggs were warmed on average only 1.7 °C above burrow temperature, slightly more during high tide periods and when burrow temperature was lower between 20:00 and 10:00 h, only partly counteracting the temperature fluctuations of the incubation chamber. These results suggest that low incubation attentiveness is due to the favourable thermal conditions provided by safe nesting burrows and by the hot tropical breeding season, a combination that allows simultaneous foraging by parents and the exploitation of distant foraging grounds. Why Crab Plovers engage in many short recesses from incubation still remains to be clarified but the need to thermoregulate at the seashore and to watch for predators may play a role.
On Families of Distributions with Shape Parameters
Authors: Jones M. C.
Published: September 2014

Univariate continuous distributions are one of the fundamental components on which statistical modelling, ancient and modern, frequentist and Bayesian, multi‐dimensional and complex, is based. In this article, I review and compare some of the main general techniques for providing families of typically unimodal distributions on with one or two, or possibly even three, shape parameters, controlling skewness and/or tailweight, in addition to their all‐important location and scale parameters. One important and useful family is comprised of the ‘skew‐symmetric’ distributions brought to prominence by Azzalini. As these are covered in considerable detail elsewhere in the literature, I focus more on their complements and competitors. Principal among these are distributions formed by transforming random variables, by what I call ‘transformation of scale’—including two‐piece distributions—and by probability integral transformation of non‐uniform random variables. I also treat briefly the issues of multi‐variate extension, of distributions on subsets of and of distributions on the circle. The review and comparison is not comprehensive, necessarily being selective and therefore somewhat personal. © 2014 The Authors. International Statistical Review © 2014 International Statistical Institute
An integrative review of ethnic and cultural variation in socialization and children's self‐regulation
Authors: LeCuyer Elizabeth A. , Zhang Yi
Published: September 2014

Aim

To examine the evidence for cross‐cultural variation in socialization and children's normative self‐regulation, based on a contextual‐developmental perspective.

Background

Nurses and healthcare workers in multi‐cultural societies must understand diversity in socializing influences (including parenting) and in children's behaviour. A contextual‐developmental perspective implies that normative cultural and ethnic values will influence socializing processes and behaviour, which in turn will influence children's self‐regulation.

Design

Integrative review.

Data sources

Studies were located using five major search engines from 1990–2011. Domains of a contextual‐developmental perspective and a comprehensive definition of self‐regulation assisted the generation of search terms.

Review methods

Selected studies compared at least two ethnic or cultural groups and addressed contextual‐developmental domains: (1) culturally specific social values, beliefs, or attitudes; (2) socializing behaviours; and (3) children's normative self‐regulation.

Results

Eleven studies about children's self‐regulation were found to have data consistent with a contextual‐developmental perspective. Studies used descriptive correlational or comparative designs with primarily convenience sampling; eight confirmed stated hypotheses, three were exploratory. Findings across studies evidenced coherent patterns of sociocultural influence on children's attention, compliance, delay of gratification, effortful control and executive function.

Conclusion

A contextual‐developmental perspective provided a useful perspective to examine normative differences in values, socializing behaviours and children's self‐regulation. This perspective and these findings are expected to guide future research, to assist nurses and healthcare providers to understand diversity in parenting and children's behaviour.
Rising incidence of early‐onset colorectal cancer in Australia over two decades: Report and review
Authors: Young Joanne P , Win Aung Ko , Rosty Christophe , Flight Ingrid , Roder David , Young Graeme P , Frank Oliver , Suthers Graeme K , Hewett Peter J , Ruszkiewicz Andrew , Hauben Ehud , Adelstein Barbara‐Ann , Parry Susan , Townsend Amanda , Hardingham Jennifer E , Price Timothy J
Published: September 2014

The average age at diagnosis for colorectal cancer (CRC) in Australia is 69, and the age‐specific incidence rises rapidly after age 50 years. The incidence has stabilized or is declining in older age groups in Australia during recent decades, possibly related to the increased uptake of screening and high‐risk surveillance. In the same time frame, a rising incidence of CRC in younger adults has been well‐documented in the United States. This rise in incidence in the young has not been reported from other countries that share long‐term exposure to westernised urban lifestyles. Using data from the Australian Institute of Health and Welfare, we examined trends in national incidence rates for CRC under age 50 years and observed that rates in people under age 40 years have been rising for the last two decades. We further performed a review of the literature regarding CRC in young adults to outline the extent of current understanding, explore potential risk factors such as obesity, alcohol, and sedentary lifestyles, and to identify the questions remaining to be addressed. Although absolute numbers might not justify a population screening approach, the dispersal of young adults with CRC across the primary health‐care system decreases probability of their recognition. Patient and physician awareness, aided by stool and emerging blood‐screening tests and risk profiling tools, have the potential to aid in identification of those young adults who would most benefit from a colonoscopy through early detection of CRCs or by removal of advanced polyps.
Labor Embodied in Trade
Authors: Simas Moana , Wood Richard , Hertwich Edgar
Published: September 2014

Global production chains carry environmental and socioeconomic impacts embodied in each traded good and service. Even though labor and energy productivities tend to be higher for domestic production in high‐income countries than those in emerging economies, this difference is significantly reduced for consumption, when including imported products to satisfy national demand. The analysis of socioeconomic and environmental aspects embodied in consumption can shed a light on the real level of productivity of an economy, as well as the effects of rising imports and offshoring. This research introduces a consumption‐based metric for productivity, in which we evaluate the loss of productivity of developed nations resulting from imports from less‐developed economies and offshoring of labor‐intensive production. We measure the labor, energy, and greenhouse gas emissions footprints in the European Union's trade with the rest of the world through a multiregional input‐output model. We confirm that the labor footprint of European imports is significantly higher than the one of exports, mainly from low‐skilled, labor‐intensive primary sectors. A high share of labor embodied in exports is commonly associated with low energy productivities in domestic industries. Hence, this reconfirms that the offshoring of production to cheaper and low‐skilled, labor‐abundant countries offsets, or even reverts, energy efficiency gains and climate‐change mitigation actions in developed countries.
ZmGns, a maize class I β‐1,3‐glucanase, is induced by biotic stresses and possesses strong antimicrobial activity
Authors: Xie Yu‐Rong , Raruang Yenjit , Chen Zhi‐Yuan , Brown Robert L. , Cleveland Thomas E.
Published: September 2014

Plant β‐1,3‐glucanases are members of the pathogenesis‐related protein 2 (PR‐2) family, which is one of the 17 PR protein families and plays important roles in biotic and abiotic stress responses. One of the differentially expressed proteins (spot 842) identified in a recent proteomic comparison between five pairs of closely related maize (Zea maysL.) lines differing in aflatoxin resistance was further investigated in the present study. Here, the corresponding cDNA was cloned from maize and designated asZmGns.ZmGnsencodes a protein of 338 amino acids containing a potential signal peptide. The expression ofZmGnswas detectible in all tissues studied with the highest level in silks.ZmGnswas significantly induced by biotic stresses including three bacteria and the fungusAspergillus flavus.ZmGnswas also induced by most abiotic stresses tested and growth hormones including salicylic acid.In vivo, ZmGns showed a significant inhibitory activity against the bacterial pathogenPseudomonas syringaepv.tomatoDC3000 and fungal pathogenBotrytis cinereawhen it overexpressed inArabidopsis. Its high level of expression in the silk tissue and its induced expression by phytohormone treatment, as well as by bacterial and fungal infections, suggest it plays a complex role in maize growth, development, and defense.
Population transcriptomics reveals a potentially positive role of expression diversity in adaptation
Authors: Xu Qin , Xing Shilai , Zhu Caiyun , Liu Wei , Fan Yangyang , Wang Qian , Song Zhihong , Yang Wenhui , Luo Fan , Shang Fei , Kang Lifang , Chen Wenli , Yan Juan , Li Jianqiang , Sang Tao
Published: September 2014

While it is widely accepted that genetic diversity determines the potential of adaptation, the role that gene expression variation plays in adaptation remains poorly known. Here we show that gene expression diversity could have played a positive role in the adaptation of Miscanthus lutarioriparius. RNA‐seq was conducted for 80 individuals of the species, with half planted in the energy crop domestication site and the other half planted in the control site near native habitats. A leaf reference transcriptome consisting of 18,503 high‐quality transcripts was obtained using a pipeline developed for de novo assembling with population RNA‐seq data. The population structure and genetic diversity of M. lutarioriparius were estimated based on 30,609 genic single nucleotide polymorphisms. Population expression (Ep) and expression diversity (Ed) were defined to measure the average level and the magnitude of variation of a gene expression in the population, respectively. It was found that expression diversity increased while genetic diversity decreased after the species was transplanted from the native habitats to the harsh domestication site, especially for genes involved in abiotic stress resistance, histone methylation, and biomass synthesis under water limitation. The increased expression diversity could have enriched phenotypic variation directly subject to selections in the new environment.
LRRK2 pathobiology in Parkinson's disease
Authors: Martin Ian , Kim Jungwoo Wren , Dawson Valina L. , Dawson Ted M.
Published: September 2014

Mutations in the catalytic Roc‐COR and kinase domains of leucine‐rich repeat kinase 2 (LRRK2) are a common cause of familial Parkinson's disease (PD). LRRK2 mutations cause PD with age‐related penetrance and clinical features identical to late‐onset sporadic PD. Biochemical studies support an increase in LRRK2 kinase activity and a decrease in GTPase activity for kinase domain and Roc‐COR mutations, respectively. Strong evidence exists that LRRK2 toxicity is kinase dependent leading to extensive efforts to identify selective and brain‐permeable LRRK2 kinase inhibitors for clinical development. Cell and animal models of PD indicate that LRRK2 mutations affect vesicular trafficking, autophagy, protein synthesis, and cytoskeletal function. Although some of these biological functions are affected consistently by most disease‐linked mutations, others are not and it remains currently unclear how mutations that produce variable effects on LRRK2 biochemistry and function all commonly result in the degeneration and death of dopamine neurons. LRRK2 is typically present in Lewy bodies and its toxicity in mammalian models appears to be dependent on the presence of α‐synuclein, which is elevated in human iPS‐derived dopamine neurons from patients harboring LRRK2 mutations. Here, we summarize biochemical and functional studies of LRRK2 and its mutations and focus on aberrant vesicular trafficking and protein synthesis as two leading mechanisms underlying LRRK2‐linked disease.

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LRRK2 mutations are a common cause of both familial and sporadic Parkinson's disease. Here, we review evidence describing the effects of these mutations on LRRK2 kinase and GTPase activities as a key driver of LRRK2 toxicity. We also discuss the reported impact of pathogenic mutations on cellular pathways which provide important clues on mechanisms of disease development.
Metabolomic comparison between cells over‐expressing isocitrate dehydrogenase 1 and 2 mutants and the effects of an inhibitor on the metabolism
Authors: Wen He , Cho Hye Rim , Yun Taeho , Kim Hyeonjin , Park Chul‐Kee , Lee Se‐Hoon , Choi Seung Hong , Park Sunghyouk
Published: September 2014

The R132H and R172K mutations of isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) have neomorphic activity of generating 2‐hydroxyglutarate (2‐HG) which has been implicated in the oncogenesis. Although similarities in structure and enzyme activity for the two isotypic mutations have been suggested, the difference in their cellular localization and biochemical properties suggests differential effects on the metabolic oncogenesis. Using U87 cells transfected with either wild‐type (WT) and mutant (MT) IDH genes, the MT‐IDH1 and MT‐IDH2 cells were compared with NMR‐based metabolomics. When normalized with the respective WT‐IDH cells, the general metabolic shifts of MT‐IDH1 and IDH2 were almost opposite. Subsequent analysis with LC‐MS and metabolic pathway mapping showed that key metabolites in pentose phosphate pathway and tricarboxylic acid cycle are disproportionately altered in the two mutants, suggesting different activities in the key metabolic pathways. Notably, lactate level was lower in MT‐IDH2 cells which produced more 2‐HG than MT‐IDH1 cells, indicating that the Warburg effects can be overridden by the production of 2‐HG. We also found that the effect of a mutant enzyme inhibitor is mainly reduction of the 2‐HG level rather than general metabolic normalization. Overall, the metabolic alterations in the MT‐IDH1 and 2 can be different and seem to be commensurate with the degree of 2‐HG production.

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The R132H and R172K mutations of isocitrate dehydrogenase 1 and 2, respectively, (IDH1 and IDH2) have neomorphic activity of generating 2‐hydroxyglutarate (2‐HG) which has been implicated in oncogenesis. The mutant cell's metabolic shifts from the respective wild type cells were almost opposite, with lactate level being lower in the IDH2 mutant only, implicating an overridden Warburg effect. The metabolic effect of an IDH1 mutant inhibitor was limited to 2‐HG lowering.
Exotic grassland species have stronger priority effects than natives regardless of whether they are cultivated or wild genotypes
Authors: Wilsey Brian J. , Barber Kaitlin , Martin Leanne M.
Published: September 2014

During community assembly, early arriving exotic species might suppress other species to a greater extent than do native species. Because most exotics were intentionally introduced, we hypothesize there was human selection on regeneration traits during introduction. This could have occurred at the across‐ or within‐species level (e.g. during cultivar development).

We tested these predictions by seeding a single species that was either native, exotic ‘wild‐type’ (from their native range), or exotic ‘cultivated’ using 28 grassland species in a glasshouse experiment. Priority effects were assessed by measuring species’ effect on establishment of species from a seed mix added 21 d later.

Exotic species had higher germination and earlier emergence dates than native species, and differences were found in both ‘wild’ and ‘cultivated’ exotics. Exotic species reduced biomass and species diversity of later arriving species much more than native species, regardless of seed source.

Results indicate that in situations in which priority effects are likely to be strong, effects will be greater when an exotic species arrives first than when a native species arrives first; and this difference is not merely a result of exotic species cultivation, but might be a general native–exotic difference that deserves further study.
THE ‘EXTENDEDNESS’ OF SCIENTIFIC EVIDENCE
Authors: Kerr Eric , Gelfert Axel
Published: September 2014

In recent years, the idea has been gaining ground that our traditional conceptions of knowledge and cognition are unduly limiting, in that they privilege what goes on inside the ‘skin and skull’ (Clark 1997: 82) of an individual reasoner. Instead, it has been argued, knowledge and cognition need to be understood as embodied (involving both mind and body), situated (being dependent on the complex interplay between the individual and its environment), and extended (that is, continuous with, rather than separate from, the world ‘outside’). Whether these various interrelations and dependencies are ‘merely’ causal, or are in a more fundamental sense constitutive of knowledge and cognition, is as much a matter of controversy as the degree to which they pose a challenge to ‘traditional’ conceptions of cognition, knowledge and the mind. In this paper we argue that when the idea of ‘extendedness’ is applied to a core concept in epistemology and the philosophy of science—namely, scientific evidence—things appear to be on a much surer footing. The evidential status of data gathered through extended processes—including its utility as justification or warrant—do not seem to be weakened by virtue of being extended, but instead are often strengthened because of it. Indeed, it is often precisely by virtue of this extendedness that scientific evidence grounds knowledge claims, which individuals may subsequently ascribe to themselves. The functional equivalence between machine‐based gathering, filtering, and processing of data and human interpretation and assessment is the crucial factor in deciding whether evidence has been gathered, rather than the distinction between intra‐ and extracranial processes or individual and social processes (or combinations thereof). To prioritize biological processes here, and to assert the superiority of human cognitive capacities seems both arbitrary and unwarranted with respect to gathering evidence, and ultimately would lead to an unattractive skepticism about many of the methods used in science to gather evidence. In other words, conceiving of scientific evidence as ‘impersonal’ (or at least not necessarily personal) not only better captures the character of evidence‐gathering in practice, but also makes sense of a large amount of evidence‐gathering that ‘personal’ accounts fail to either acknowledge or accurately describe. Whilst we suggest it is likely that all internally‐distributed evidence‐gathering processes are merely contingently internal processes, a significant number of externally‐distributed evidence‐gathering processes are necessarily externally‐distributed. Some evidence can only be gathered by extended epistemic agents.
JFGI: FROM DISTRIBUTED COGNITION TO DISTRIBUTED RELIABILISM*
Authors: Michaelian Kourken
Published: September 2014

While, prima facie, virtue/credit approaches in epistemology would appear to be in tension with distributed/extended approaches in cognitive science, Pritchard () has recently argued that the tension here is only apparent, at least given a weak version of distributed cognition, which claims merely that external resources often make critical contributions to the formation of true belief, and a weak virtue theory, which claims merely that, whenever a subject achieves knowledge, his cognitive agency makes a significant contribution to the formation of a true belief. But the significance of the role played by the subject's cognitive agency in distributed cognitive systems is in fact highly variable: at one extreme, formation of a true belief seems clearly to be significantly creditable to the subject's agency; at the other extreme, however, the subject's agency plays such a peripheral role that it is at best unclear whether it should receive significant credit for formation of a true belief. The compatibility of distributed cognition and virtue epistemology thus turns on what it takes for a contribution to the formation of true belief to count as significant. This article argues that the inevitable vagueness of this notion suggests retreating from virtue epistemology to a form of process reliabilism and explores the prospects for a distributed reliabilist epistemology designed to fit smoothly with distributed cognition. In effect, distributed reliabilism radicalizes Goldberg's recent extended reliabilist view (Goldberg ) by allowing the process the reliability of which determines the epistemic status of a subject's belief to extend to include not only processing performed by other subjects but also processing performed by non‐human technological resources.
EMPIRICISM FOR CYBORGS
Authors: Toon Adam
Published: September 2014

One important debate between scientific realists and constructive empiricists concerns whether we observe things using instruments. This paper offers a new perspective on the debate over instruments by looking to recent discussion in philosophy of mind and cognitive science. Realists often speak of instruments as ‘extensions’ to our senses. I ask whether the realist may strengthen her view by drawing on the extended mind thesis. Proponents of the extended mind thesis claim that cognitive processes can sometimes extend beyond our brains and bodies into the environment. I suggest that the extended mind thesis offers a way to make sense of realists’ talk of instruments as extensions to the senses and that it provides the realist with a new argument against the constructive empiricist view of instruments.
COGNITIVE PENETRATION, THE DOWNGRADE PRINCIPLE, AND EXTENDED COGNITION
Authors: Vahid Hamid
Published: September 2014

It has been argued that just as, say, prejudice or wishful thinking can generate ill‐founded beliefs, the same is true of experiences. The idea is that the etiology of cognitively penetrated experiences can downgrade their justificatory force. This view, known as the Downgrade Principle, seems to be compatible with both internalist and externalist conceptions of epistemic justification. An assessment of the credentials of the Downgrade Principle is particularly important in view of the fact that not all cases of cognitive penetration are epistemically malignant. There are good and bad cases of cognitive penetration. I argue that a proper assessment of the Downgrade Principle will have to address two fundamental questions. I identify two general ways of responding to these questions and show why they fail. It will be maintained that an explanationist conception of justification has a better chance of accounting for the distinction between good and bad cases of cognitive penetration. The Downgrade Principle is then discussed in the context of the extended cognition thesis (ECT). In particular, I look at the sensorimotor theory of perception, as a way of broadening the scope of (ECT) to include conscious perceptual experience, that sees senses as ways of exploring the environment mediated by different patterns of sensorimotor contingency. I suggest possible ways in which one could distinguish between good and bad cases of cognitive penetration on such a view compatible with the explanationist view of epistemic justification.
Understanding how visual attention locks on to a location: Toward a computational model of the N2pc component
Authors: Tan Mingxuan , Wyble Brad
Published: September 2014

Competing theories regarding the neural mechanism underlying the N2pc suggest that it reflects target enhancement or distractor suppression, but we suggest a different theory. In our study, participants viewed a bilateral dual‐stream rapid serial visual presentation (RSVP). Each trial had either one or two targets (T1, T2) presented either in the same or different streams. We found that the N2pc elicited by T1 was not affected by an immediately following T2 at the same location. However, if T2 was on the opposite hemifield, a second N2pc was elicited. These results suggest that the N2pc reflects neural processes involved in localizing a target to initiate the deployment of attention, rather than the sustained enhancement of processing at that location or distractor inhibition. We have created a computational model of a convergent gradient‐filter model of attention that reproduces the observed event‐related potential traces and makes five testable predictions to be addressed in future work.
The Evaluation of Evidence for Auto-Correlated Data in Relation to Traces of Cocaine on Banknotes
Authors: Wilson Amy , Aitken Colin , Sleeman Richard , Carter James
Published: September 2014

Much research in recent years for evidence evaluation in forensic science has focused on methods for determining the likelihood ratio in various scenarios. When the issue in question is whether evidence is associated with a person who is or is not associated with criminal activity then the problem is one of discrimination. A procedure for the determination of the likelihood ratio is developed when the evidential data are believed to be driven by an underlying latent Markov chain. Three other models that assume auto-correlated data without the underlying Markov chain are also described. The performances of these four models and a model assuming independence are compared by using data concerning traces of cocaine on banknotes.
Group Sequential Method for Observational Data by Using Generalized Estimating Equations: Application to Vaccine Safety Datalink
Authors: Cook Andrea J. , Wellman Robert D. , Nelson Jennifer C. , Jackson Lisa A. , Tiwari Ram C.
Published: September 2014

Post-market medical product surveillance is important for detecting rare adverse events that are not identified during preapproval. The goal of surveillance is to assess over time for elevated rates of adverse events for new medical products. These studies utilize administrative databases from multiple large health plans. We propose a group sequential method using a permutation approach with generalized estimating equations to account for confounding. A simulation study is conducted to evaluate the performance of the group sequential generalized estimating equation method compared with two other approaches. The methods are then applied to a vaccine safety application from the Vaccine Safety Datalink.
A qualitative study of citizens' experience of participating in health counseling
Authors: Andersen Lotte Nygaard , Andersen Stinne Sonne , Muurholm Britt , Roessler Kirsten Kaya
Published: September 2014

Individual health counseling is a form of intervention designed to minimize the effects of chronic health disease and to offer a path towards good health practices. The aim of the present study was to explore the experiences of those persons who participated in health counseling in order to assess the psychosocial significance of the counseling upon their health behavior. In addition the study was concerned with the factors which underlay peoples' decision to sign up for health counseling. The research involved 11 semi‐structured interviews with individuals who had participated in a municipality based health counseling program. Data was analyzed using Malterud's systemic text condensation and a theoretical framework around Bandura's social cognitive theory. Analysis revealed that an approach tailored to each individual with minor short‐term goals accompanied by feeling supported by the counselor produced the greatest impact on behavior. Receiving feedback from the counselor and feeling positive about the relationship were seen as essential. These aspects were also crucial in the decision to undertake health counseling. The study indicates that whether individual's sign up on their own initiative or conversely are invited to join the program has no influence upon their motivation to change their behavior. Overall the respondents demonstrated improvement in their behavior and attitudes towards their health. However, the study also indicates that this form of intervention is less or even ineffective without the support of the individual's immediate family.