bluuebunny/crossref_metadata_2025 huggingface dataset:
Ancient river systems and phylogeographical structure in the spring salamander, Gyrinophilus porphyriticus
Authors: Kuchta Shawn R. , Haughey Michael , Wynn Addison H. , Jacobs Jeremy F. , Highton Richard
Published: November 2015

Aim

The river drainages of the Appalachian Mountains have experienced a dynamic history as glacial cycles, stream capture and other geological processes have led to the fragmentation and fusion of formerly isolated palaeodrainages. Some ancient rivers have gone extinct, including portions of the great Teays River. Here we investigate the contribution of contemporary and historical drainages to patterns of phylogeographical structure in the spring salamander complex, Gyrinophilus porphyriticus.

Location

Eastern North America, USA.

Methods

Sampling spanned the range of the G. porphyriticus complex, and included representative samples of the cave species of Gyrinophilus as well. Molecular sequence data included the mitochondrial DNA locus cytochrome b and the nuclear locus recombination‐activating gene 1 (RAG‐1). Time‐calibrated phylogenies were inferred, and Bayes‐LAGRANGE was used to reconstruct ancestral distributions. Contemporary and historical river influences on patterns of genetic diversity were tested using distance‐based redundancy analysis (db‐RDA).

Results

The G. porphyriticus complex originated prior to the Pleistocene glacial cycles, and historical river systems explained more genetic variation than did contemporary drainages or geographical distance. Patterns of genetic variation suggest that extinct or remodelled palaeodrainages, including the Teays River, played an important role in structuring contemporary patterns of genetic variation.

Main conclusions

The hydrogeological history of eastern North American drainage basins has been instrumental in structuring patterns of regional biodiversity in freshwater species. Here we show that hydrological remodelling has also left its genetic signature in the semi‐aquatic spring salamander complex, G. porphyriticus. Historical drainages accounted for the largest fraction of phylogeographical structure, more so than did contemporary drainages or geographical distance, with spatial and temporal patterns of variation associated with the extinct Teays River.
Moderate alcohol drinking in pregnancy increases risk for children's persistent conduct problems: causal effects in a Mendelian randomisation study
Authors: Murray Joseph , Burgess Stephen , Zuccolo Luisa , Hickman Matthew , Gray Ron , Lewis Sarah J.
Published: November 2015

Background

Heavy alcohol use during pregnancy can cause considerable developmental problems for children, but effects of light‐moderate drinking are uncertain. This study examined possible effects of moderate drinking in pregnancy on children's conduct problems using a Mendelian randomisation design to improve causal inference.

Methods

A prospective cohort study (ALSPAC) followed children from their mother's pregnancy to age 13 years. Analyses were based on 3,544 children whose mothers self‐reported either not drinking alcohol during pregnancy or drinking up to six units per week without binge drinking. Children's conduct problem trajectories were classified as low risk, childhood‐limited, adolescence‐onset or early‐onset‐persistent, using six repeated measures of the Strengths and Difficulties Questionnaire between ages 4–13 years. Variants of alcohol‐metabolising genes in children were used to create an instrumental variable for Mendelian randomisation analysis.

Results

Children's genotype scores were associated with early‐onset‐persistent conduct problems (OR = 1.29, 95% CI = 1.04–1.60, p = .020) if mothers drank moderately in pregnancy, but not if mothers abstained from drinking (OR = 0.94, CI = 0.72–1.25, p = .688). Children's genotype scores did not predict childhood‐limited or adolescence‐onset conduct problems.

Conclusions

This quasi‐experimental study suggests that moderate alcohol drinking in pregnancy contributes to increased risk for children's early‐onset‐persistent conduct problems, but not childhood‐limited or adolescence‐onset conduct problems.
Monitoring and mechanisms of organophosphate resistance in San Jose scale, Diaspidiotus perniciosus (Hemiptera: Diaspididae)
Authors: Buzzetti K. A. , Chorbadjian R. A. , Fuentes‐Contreras E. , Gutiérrez M. , Ríos J. C. , Nauen R.
Published: November 2015

San Jose scale, Diaspidiotus perniciosus (Comstock), is a serious pest in Chilean apple tree orchards, and a number of organophosphate insecticides were used to control them for decades. Recently, control failures with these insecticides were reported and linked to insecticide resistance development. In this study, 40 San Jose scale field populations were collected and their susceptibility to two commonly used organophosphate insecticides, that is chlorpyrifos and methidathion, was assessed. The obtained bioassay data suggest moderate levels of resistance to both insecticides when compared to a reference susceptible strain. The highest resistance ratio (RR) detected for chlorpyrifos and methidathion was 31‐fold and 11‐fold, respectively. The bioassay results suggest the occurrence of a significant cross‐resistance between both compounds. Biochemical measurements revealed a role for esterases in conferring resistance to organophosphates, but not modified acetylcholinesterase. The spatial spread and extend of insecticide resistance were also evaluated. Our result shows that no autocorrelation can be assumed, and then, insecticide resistance is caused by random factors.
A real‐time PCR toolbox for accurate identification of invasive fruit fly species
Authors: Dhami M. K. , Gunawardana D. N. , Voice D. , Kumarasinghe L.
Published: November 2015

Significant plant pests such as fruit flies that travel with fresh produce between countries as eggs or larvae pose a great economic threat to the agriculture and fruit industry worldwide. Time‐limited and expensive quarantine decisions require accurate identification of such pests. Immature stages are often impossible to identify, making them a serious concern for biosecurity agencies. Use of COI barcoding PCR, often the only molecular identification resource, is time‐consuming. We assess the suitability of the COI barcoding region for real‐time PCR assays to identify four pest fruit fly species (Family: Tephritidae), in a diagnostic framework. These species, namely Mediterranean fruit fly (Ceratitis capitata), Queensland fruit fly (Bactrocera tryoni), African invader fly (Bactrocera invadens) and Island fly (Dirioxa pornia) each provide a different set of genetic species delimitation problems. We discuss the benefits and limitations of using a single‐gene TaqMan™ real‐time approach for such species. Our results indicate that COI‐based TaqMan™ real‐time PCR assays, in particular for genetically distinct species, provide an accurate, sensitive and rapid diagnostic tool.
The development of a non‐invasive model to predict the presence of non‐alcoholic steatohepatitis in patients with non‐alcoholic fatty liver disease
Authors: Goh George BB , Issa Danny , Lopez Rocio , Dasarathy Srinivasan , Dasarathy Jaividhya , Sargent Ruth , Hawkins Carol , Pai Rish K , Yerian Lisa , Khiyami Amer , Pagadala Mangesh R , Sourianarayanane Achuthan , Alkhouri Naim , McCullough Arthur J
Published: November 2015

Background:

Non‐alcoholic steatohepatitis (NASH) is an advanced and aggressive form of non‐alcoholic fatty liver disease (NAFLD), which remains difficult to diagnose without a liver biopsy. Hyperferritinemia has increasingly been associated with the presence of NASH. Hence, we sought to explore the relationship between ferritin and NASH and to develop a composite model based on ferritin to predict the presence of NASH.

Methods:

A total of 405 patients with biopsy‐proven NAFLD were enrolled in the study. Comparison was explored to assess differences between patients with and without NASH, upon which a scoring model was established using variables found to be independent predictors of NASH.

Results:

Among all patients with NAFLD, 291 (72%) had biopsy‐proven NASH, and 114 (28%) had non‐NASH. Mean age was 48 ± 12 years, and 56% were female. Ferritin was significantly higher in NASH compared with non‐NASH patients (184 vs 126, respectively; P < 0.001) but lacked diagnostic accuracy for predicting NASH alone (area under the curve [AUC 0.62]). The addition of other significant variables such as aspartate aminotransferase, body mass index, platelet count, diabetes, and hypertension to ferritin improved the prediction of NASH with an AUC 0.81 (95% confidence interval: 0.76–0.86). Internal validation of the model using imputed data sets demonstrated that AUC did not change materially.

Conclusions:

While higher ferritin was significantly associated with NASH, ferritin alone lacked diagnostic accuracy to predict NASH. However, incorporating several easily obtainable variables with ferritin allowed the construction of a novel scoring system that can be easily applied in the clinical setting to guide management of NAFLD.
Additive impact of pre‐liver transplant metabolic factors on survival post‐liver transplant
Authors: Adams Leon A , Arauz Oscar , Angus Peter W , Sinclair Marie , MacDonald Graeme A , Chelvaratnam Utti , Wigg Alan J , Yeap Sze , Shackel Nicholas , Lin Linda , Raftopoulos Spiro , McCaughan Geoffrey W , Jeffrey Gary P ,   on behalf of the Australian New Zealand Liver Transplant Study Group
Published: November 2015

Background and Aim:

Diabetes at time of liver transplantation is associated with reduced post‐transplant survival. We aimed to assess whether additional metabolic conditions such as obesity or hypertension had additive prognostic impact on post‐transplantation survival.

Methods:

A multi‐center cohort study of 617 adult subjects undergoing liver transplantation between 2003 and 2009 has been used. Dry body mass index was calculated following adjustment for ascites.

Results:

After a median follow‐up of 5.8 years (range 0–10.5), 112 (18.2%) patients died. Diabetes was associated with reduced post‐transplant survival (hazard ratio 1.89, 95% confidence interval [CI] 1.25–2.86, P = 0.003), whereas obesity, hypertension, dyslipidemia, and the metabolic syndrome itself were not (P > 0.3 for all). Patients with concomitant diabetes and obesity had lower survival (adjusted Hazard Ratio [aHR] 2.40, 95%CI 1.32–4.38, P = 0.004), whereas obese non‐diabetic patients or diabetic non‐obese patients had similar survival compared with non‐diabetic, non‐obese individuals. The presence of hypertension or dyslipidemia did not impact on survival in patients with diabetes (P > 0.1 for both). Obese diabetic patients had longer intensive care and hospital stays than non‐obese diabetic or obese, non‐diabetic patients (P < 0.05). The impact of concomitant obesity and diabetes on survival was greater in subjects aged 50+ years (52.6% 5‐year survival, aHR 3.04, 95% CI 1.54–5.98) or those transplanted with hepatocellular carcinoma (34.1% 5‐year survival, aHR 3.35, 95% CI 1.31–5.57). Diabetes without obesity was not associated with an increased mortality rate in these sub‐groups.

Conclusions:

Concomitant diabetes and obesity but not each condition in the absence of the other is associated with reduced post‐liver transplant survival. The impact of diabetes and obesity is greater in older patients and those with hepatocellular carcinoma.
Adverse metabolic phenotype of adolescent girls with non‐alcoholic fatty liver disease plus polycystic ovary syndrome compared with other girls and boys
Authors: Ayonrinde Oyekoya T , Adams Leon A , Doherty Dorota A , Mori Trevor A , Beilin Lawrence J , Oddy Wendy H , Hickey Martha , Sloboda Deborah M , Olynyk John K , Hart Roger
Published: November 2015

Background and Aims:

Non‐alcoholic fatty liver disease (NAFLD) and polycystic ovary syndrome (PCOS) share risk associations of adiposity and insulin resistance. We examined the impact of a PCOS diagnosis on the metabolic phenotype of adolescent girls with NAFLD and compared this to girls without PCOS or NAFLD and to age‐matched boys.

Methods:

Community‐based adolescents from the Raine Cohort participated in assessments for NAFLD (572 girls and 592 boys) and PCOS (244 girls). One hundred and ninety‐nine girls attended both assessments.

Results:

Amongst the 199 girls, PCOS was diagnosed in 16.1% and NAFLD in 18.6%. NAFLD was diagnosed in 10.1% of the boys. NAFLD was more prevalent in girls with PCOS than girls without PCOS (37.5% vs 15.1%, P = 0.003). Girls with NAFLD plus PCOS had greater adiposity (waist circumference, body mass index, suprailiac skinfold thickness [SST], serum androgens, high‐sensitivity C‐reactive protein, ferritin, homeostasis model assessment for insulin resistance (HOMA‐IR), and lower serum sex hormone binding globulin levels than girls with NAFLD without a PCOS diagnosis (all P < 0.05). Girls with NAFLD plus PCOS had similar adiposity, HOMA‐IR, and adiponectin levels to boys with NAFLD, but more adiposity, serum leptin and HOMA‐IR than both girls and boys without NAFLD. PCOS (odds ratios 2.99, 95% confidence intervals 1.01–8.82, P = 0.048) and SST (odds ratios 1.14, 95% confidence intervals 1.08–1.20, P < 0.001) independently predicted NAFLD in adolescent girls, however, serum androgens and HOMA‐IR levels did not.

Conclusions:

Adolescent girls with NAFLD plus PCOS have a similar metabolic phenotype to boys with NAFLD. Increasing SST and pre‐existing PCOS independently predict NAFLD in adolescent girls.
Valuable New Resistances Ensure Improved Management of Sclerotinia Stem Rot (Sclerotinia sclerotiorum) in Horticultural and Oilseed Brassica Species
Authors: You Ming Pei , Uloth Margaret B. , Li Xi Xiang , Banga Surinder S. , Banga Shashi K. , Barbetti Martin J.
Published: November 2015

Field resistances against Sclerotinia rot (SR) (Sclerotinia sclerotiorum) were determined in 52 Chinese genotypes of Brassica oleracea var. capitata, 14 Indian Brassica juncea genotypes carrying wild weedy Brassicaceae introgression(s) and four carrying B‐genome introgression, 22 Australian commercial Brassica napus varieties, and 12 B. napus and B. juncea genotypes of known resistance. All plants were individually inoculated by securing an agar disc from a culture of S. sclerotiorum growing on a glucose‐rich medium to the stem above the second internode with Parafilm tape. Mean stem lesion length across tested genotypes ranged from <1 to >68 mm. While there was considerable diversity within the germplasm sets from each country, overall, 65% of the B. oleracea var. capitata genotypes from China showed the highest levels of stem resistance, a level comparable with the highest resistance ever recorded for oilseed B. napus or B. juncea from China or Australia. One Indian B. juncea line carrying weedy introgression displayed a significant level of both stem and leaf resistance. However, the vast majority of commercial Australian oilseed B. napus varieties fell within the most susceptible 40% of genotypes tested for stem disease. There was no correlation between expressions of stem versus leaf resistance, suggesting their independent inheritance. A few Chinese B. oleracea var. capitata genotypes that expressed combined extremely high‐level stem (≤1 mm length) and leaf (≤0.5 mean number of infections/plant) resistance will be particularly significant for developing new SR‐resistant horticultural and oilseed Brassica varieties.
A molecular phylogeny of Chinese orchids
Authors: Li Ming‐He , Zhang Guo‐Qiang , Lan Si‐Ren , Liu Zhong‐Jian ,   China Phylogeny Consortium
Published: November 2015

We estimated the molecular phylogenetic relationships of the Chinese members of the family Orchidaceae. Within the Tree of Life for the Genera of Chinese Vascular Plants usingatpB, rbcL, matK, ndhF, andmatR, the currently delimited subfamilies, tribes, and subtribes are highly supported as monophyletic except for the perplexing Epidendroideae. Five genes (rbcL,matK,psaB,ycf1, andXdh), which are more universally used in Orchidaceae, were further analyzed to reconstruct the phylogeny of Epidendroideae. The reconstructed trees were in strong agreement and showed significant support for the tribal and subtribal clades. Based on the highly supported circumscription and arrangement of the suprageneric levels in the Tree of Life and reconstructed trees, we have proposed a new phylogenetic classification of Chinese Orchidaceae that includes five subfamilies, 17 tribes, and 21 subtribes.
Spatial distribution and association patterns in a tropical evergreen broad‐leaved forest of north‐central Vietnam
Authors: Nguyen Hong Hai , Uria‐Diez Jaime , Wiegand Kerstin
Published: November 2015

Questions

What are the prevailing types of intraspecific spatial distributions and interspecific association patterns at species and life stage levels of trees in a tropical rain forest? Which ecological processes could structure these patterns? Possible processes include dispersal limitation, self‐thinning, facilitation and competition between species and life stages.

Location

A tropical broad‐leaved forest in north‐central Vietnam.

Methods

We used univariate and bivariate pair‐correlation functions to investigate the spatial distribution and association patterns of 18 abundant tree species. To disentangle first‐ and second‐order effects, we used a scale separation approach with the heterogeneous Poisson process as null model.

Results

(1) Sixteen of 18 species had aggregated patterns at various scales and regardless of their abundance. (2) Significant and aggregated patterns were found in 64% of all specific life stages. (3) At scales up to 15 m, 12.4% species pairs showed significant associations, among that 71% were spatial attractions, 5% were spatial repulsions and 24% were non‐essential interactions. (4) In different life stage associations, attractions (81%) predominated over repulsions (19%) at small scales of up to 15 m.

Conclusions

Our findings provide evidence that dispersal limitation may regulate the spatial patterns of tree species. Moreover, positive spatial associations between tree species and life stages suggest the presence of species herd protection and/or facilitation in this forest stand, while the persistence of intraspecific aggregation through life stages suggests a very late onset or even absence of self‐thinning. Habitat heterogeneity plays an important role for species distribution patterns, and the spatial segregation occurs at a scale around 15 m in this forest.
Evaluating the performance of selection scans to detect selective sweeps in domestic dogs
Authors: Schlamp Florencia , van der Made Julian , Stambler Rebecca , Chesebrough Lewis , Boyko Adam R. , Messer Philipp W.
Published: November 2015

Selective breeding of dogs has resulted in repeated artificial selection on breed‐specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analysed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks.
Sodium modelling to reduce intradialytic hypotension during haemodialysis for acute kidney injury in the intensive care unit
Authors: Lynch Katherine E. , Ghassemi Fatimah , Flythe Jennifer E. , Feng Mengling , Ghassemi Marzyeh , Celi Leo Anthony , Brunelli Steven M.
Published: November 2015

Aim

Intradialytic hypotension often complicates haemodialysis for patients with acute kidney injury (AKI) and may impact renal recovery. Sodium modelling is sometimes used as prophylaxis against intradialytic hypotension in the chronic haemodialysis population, but there is little evidence for its use among critically ill patients with AKI.

Methods

A retrospective cohort with AKI requiring intermittent haemodialysis in the intensive care unit from 2001 to 2008 was used to study the association of prophylactic sodium modelling and multiple outcomes. Outcomes included a composite of in‐hospital death or dialysis dependence at hospital discharge, as well as intradialytic hypotension, ultrafiltration goal achievement and net ultrafiltration volume. Associations were estimated using logistic regression, mixed linear models and generalized estimating equations adjusting for demographic and clinical characteristics.

Results

One hundred and ninety‐one individuals who underwent 892 sessions were identified; sodium modelling was prescribed in 27.1% of the sessions. In adjusted analyses, sodium modelling was not significantly associated with intradialytic hypotension (P = 0.67) or with the ultrafiltration goal achievement (P = 0.06). Sodium modelling during the first dialysis session was numerically associated with lower risk for the composite of in‐hospital death or dialysis dependence: adjusted odds ratio (95% confidence interval) 0.39 (0.15–1.02; P = 0.06); however, this association did not reach statistical significance.

Conclusion

We did not observe statistically significant associations between sodium modelling and improved outcomes among AKI patients receiving intermittent dialysis in the intensive care unit. However, suggestive findings warrant further study.
Network analyses support the role of prey preferences in shaping resource use patterns within five animal populations
Authors: Lemos‐Costa Paula , Pires Mathias M. , Araújo Márcio S. , de Aguiar Marcus A. M. , Guimarães Paulo R.
Published: November 2015

Individual variation is an inherent aspect of animal populations and understanding the mechanisms shaping resource use patterns within populations is crucial to comprehend how individuals partition resources. Theory predicts that differences in prey preferences among consumers and/or differences in the likelihood of adding new resources to their diets are key mechanisms underlying intrapopulation variation in resource use. We developed network models based on optimal diet theory that simulate how individuals consume resources under varying scenarios of individual variation in prey preferences and in the willingness of consuming alternate resources. We then investigated how the structure of individual–resource networks generated under each model compared to the structure of observed networks representing five classical examples of individual diet variation. Our results support the notion that, for the studied populations, individual variation in prey preferences is the major factor explaining patterns in individual–resource networks. In contrast, variation in the willingness of adding prey does not seem to play an important role in shaping patterns of resource use. Individual differences in prey preferences in the studied populations may be generated by complex behavioral rules related to cognitive constraints and experience. Our approach provides a pathway for mapping foraging models into network patterns, which may allow determining the possible mechanisms leading to variation in resource use within populations.
Minimum mycophenolic acid levels are associated with donor‐specific antibody formation
Authors: Filler Guido , Todorova Ekaterina Kirilova , Bax Kevin , Alvarez‐Elías Ana Catalina , Huang Shih‐Han Susan , Kobrzynski Marta Caroline
Published: November 2015

Although de novo DSA are associated with inferior graft survival, there are no effective strategies to prevent their formation. Underexposure to MPA (prodrug: MMF) also contributes to rejection rates early after transplantation, but the effect of this phenomenon on the formation of DSA long‐term post‐transplantation is unknown. Data are expressed as mean (standard deviation). All available data from 32 renal transplant recipients (age at transplantation 7.5 [4.5] yr) on tacrolimus and MPA immunosuppression with an average follow‐up of 9.4 (s.d. 4.6) yr were analyzed. DSA were measured using the Luminex assay (>500 MFI was considered DSA‐positive). Tacrolimus and MPA levels were measured with the Abbot Tacro II and EMIT assay, respectively. Among 1964 MPA and 3462 tacrolimus trough levels, the average MPA trough level was 3.2 (1.5) mg/L and the average tacrolimus level was 6.7 (2.8) ng/mL. At last follow‐up, only 5/32 patients had undetectable DSA, with 5/32 having no class I antibodies and 6/32 having no class II antibodies. DSA formation was associated with a lower minimum MPA trough level (0.27 [0.23] vs. 0.47 [0.18] mg) and cystatin C eGFR (48 [21] vs. 70 [23] mL/min/1.73 m2) for class I DSA formers. The average eGFR of patients without class I DSA was 70 (23) mL/min/1.73 m2, whereas the average eGFR of patients with class I DSA was 48 (21) mL/min/1.73 m2 (p = 0.0071). MPA trough levels <1.3 mg/L long‐term post‐transplantation are associated with the formation of DSA. The association between the formation of DSA and minimum MPA exposure may support a strategy for preventing the formation of DSA.
Psychological distance modulates the performance of the embodiment effect: Evidence from behavioral and ERP studies
Authors: Wang Hanlin , Mo Lei , Luo Qiuling , Xiang Yanhui , Hu Yunyang
Published: November 2015

Research on embodied cognition suggests the ubiquity of embodiment effects during interaction with the environment. However, construal level theory (CLT) holds that these effects could be moderated by the psychological distance between self and objects and are attenuated by higher‐level mental construal. The current research explored the “action‐evaluation” embodiment effect in the evaluation of words located at different spatial distances. Results showed that for “short‐distance” words, the response model conflicted with this embodiment effect slower reaction time and induced a larger P2 component than the opposite response model. However, evaluation of “long‐distance” words was not significantly influenced by the response model. The results are consistent with CLT and suggest that the action‐evaluation embodiment effect influences the coding and execution of evaluating actions, but only for stimuli at close psychological distance locations.
Interaction of threat and verbal working memory in adolescents
Authors: Patel Nilam , Vytal Katherine , Pavletic Nevia , Stoodley Catherine , Pine Daniel S. , Grillon Christian , Ernst Monique
Published: November 2015

Threat induces a state of sustained anxiety that can disrupt cognitive processing, and, reciprocally, cognitive processing can modulate an anxiety response to threat. These effects depend on the level of cognitive engagement, which itself varies as a function of task difficulty. In adults, we recently showed that induced anxiety impaired working memory accuracy at low and medium but not high load. Conversely, increasing the task load reduced the physiological correlates of anxiety (anxiety‐potentiated startle). The present work examines such threat‐cognition interactions as a function of age. We expected threat to more strongly impact working memory in younger individuals by virtue of putatively restricted cognitive resources and weaker emotion regulation. This was tested by examining the influence of age on the interaction of anxiety and working memory in 25 adolescents (10 to 17 years) and 25 adults (22 to 46 years). Working memory load was manipulated using a verbal n‐back task. Anxiety was induced using the threat of an aversive loud scream and measured via eyeblink startle. Findings revealed that, in both age groups, accuracy was lower during threat than safe conditions at low and medium but not high load, and reaction times were faster during threat than safe conditions at high load but did not differ at other loads. Additionally, anxiety‐potentiated startle was greater during low and medium than high load. Thus, the interactions of anxiety with working memory appear similar in adolescents and adults. Whether these similarities reflect common neural mechanisms would need to be assessed using functional neuroimaging.
Ibuprofen intake increases exercise time to exhaustion: A possible role for preventing exercise‐induced fatigue
Authors: Lima F. D. , Stamm D. N. , Della Pace I. D. , Ribeiro L. R. , Rambo L. M. , Bresciani G. , Ferreira J. , Rossato M. F. , Silva M. A. , Pereira M. E. , Ineu R. P. , Santos A. R. , Bobinski F. , Fighera M. R. , Royes L. F. F.
Published: November 2015

Although the intake of nonsteroidal anti‐inflammatory drugs (NSAIDs) intake by athletes prevents soreness, little is known concerning their role in exercise performance. This study assessed the effects of ibuprofen intake on an exhaustive protocol test after 6 weeks of swimming training in rats. Animals were divided into sedentary and training groups. After training, animals were subdivided into two subsets: saline or ibuprofen. Afterwards, three repeated swimming bouts were performed by the groups. Ibuprofen (15 mg/kg) was administered once a day. Pain measurements were performed and inflammatory and oxidative stress parameters were assayed in cerebral cortex and gastrocnemius muscle. Training, ibuprofen administration, or both combined (P < 0.05; 211 ± 18s, 200 ± 31s, and 279 ± 23s) increased exercise time to exhaustion. Training decreased the acetylcholinesterase (AChE) activity (P < 0.05; 149 ± 11) in cerebral cortex. Ibuprofen intake decreased the AChE activity after exhaustive protocol test in trained and sedentary rats (P < 0.05; 270 ± 60; 171 ± 38; and 273 ± 29). It also prevented neuronal tumor necrosis factor‐α (TNF‐α) and interleukin (IL 1β) increase. Fatigue elicited by this exhaustive protocol may involve disturbances of the central nervous system. Additive anti‐inflammatory effects of exercise and ibuprofen intake support the hypothesis that this combination may constitute a more effective approach. In addition, ergogenic aids may be a useful means to prevent exercise‐induced fatigue.
Stress‐related growth following sport injury: Examining the applicability of the organismic valuing theory
Authors: Wadey R. , Podlog L. , Galli N. , Mellalieu S. D.
Published: November 2015

This study explored the applicability of organismic valuing theory (OVT) to stress‐related growth (SRG) following sport injury. Specifically, the direct and indirect relationships between need satisfaction (i.e., autonomy, competence, and relatedness), SRG, and subjective well‐being (i.e., positive affect) were examined. Previously injured athletes (n = 520), ranging from 18 to 59 years of age (Mage = 23.3 years; standard deviation = 6.5), completed three measures: needs satisfaction scale, stress‐related growth scale, and positive affect scale. Structural equation modeling with maximum likelihood estimation revealed a significant positive relationship between competence and relatedness and SRG, and between SRG and positive affect. In line with OVT, SRG was also found to mediate the relationship between need satisfaction (competence and relatedness) and subjective well‐being. The findings offer preliminary support for the applicability of OVT in aiding our understanding of the antecedents and consequences of SRG. Future avenues of research are discussed, together with recommended methodologies to further extend and refine knowledge and understanding of the phenomenon of SRG following sport injury.
Evaluation of methods for calculating maximum allowable standing height in amputees competing in Paralympic athletics
Authors: Connick M. J. , Beckman E. , Ibusuki T. , Malone L. , Tweedy S. M.
Published: November 2015

The International Paralympic Committee has a maximum allowable standing height (MASH) rule that limits stature to a pre‐trauma estimation. The MASH rule reduces the probability that bilateral lower limb amputees use disproportionately long prostheses in competition. Although there are several methods for estimating stature, the validity of these methods has not been compared. To identify the most appropriate method for the MASH rule, this study aimed to compare the criterion validity of estimations resulting from the current method, the Contini method, and four Canda methods (Canda‐1, Canda‐2, Canda‐3, and Canda‐4). Stature, ulna length, demispan, sitting height, thigh length, upper arm length, and forearm length measurements in 31 males and 30 females were used to calculate the respective estimation for each method. Results showed that Canda‐1 (based on four anthropometric variables) produced the smallest error and best fitted the data in males and females. The current method was associated with the largest error of those tests because it increasingly overestimated height in people with smaller stature. The results suggest that the set of Canda equations provide a more valid MASH estimation in people with a range of upper limb and bilateral lower limb amputations compared with the current method.
Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high‐density, high‐resolution consensus genetic map
Authors: Tayeh Nadim , Aluome Christelle , Falque Matthieu , Jacquin Françoise , Klein Anthony , Chauveau Aurélie , Bérard Aurélie , Houtin Hervé , Rond Céline , Kreplak Jonathan , Boucherot Karen , Martin Chantal , Baranger Alain , Pilet‐Nayel Marie‐Laure , Warkentin Thomas D. , Brunel Dominique , Marget Pascal , Le Paslier Marie‐Christine , Aubert Grégoire , Burstin Judith
Published: November 2015

Single nucleotide polymorphism (SNP) arrays represent important genotyping tools for innovative strategies in both basic research and applied breeding. Pea is an important food, feed and sustainable crop with a large (about 4.45 Gbp) but not yet available genome sequence. In the present study, 12 pea recombinant inbred line populations were genotyped using the newly developed GenoPea 13.2K SNP Array. Individual and consensus genetic maps were built providing insights into the structure and organization of the pea genome. Largely collinear genetic maps of 3918–8503 SNPs were obtained from all mapping populations, and only two of these exhibited putative chromosomal rearrangement signatures. Similar distortion patterns in different populations were noted. A total of 12 802 transcript‐derived SNP markers placed on a 15 079‐marker high‐density, high‐resolution consensus map allowed the identification of ohnologue‐rich regions within the pea genome and the localization of local duplicates. Dense syntenic networks with sequenced legume genomes were further established, paving the way for the identification of the molecular bases of important agronomic traits segregating in the mapping populations. The information gained on the structure and organization of the genome from this research will undoubtedly contribute to the understanding of the evolution of the pea genome and to its assembly. The GenoPea 13.2K SNP Array and individual and consensus genetic maps are valuable genomic tools for plant scientists to strengthen pea as a model for genetics and physiology and enhance breeding.
Flux balance analysis of primary metabolism in the diatom Phaeodactylum tricornutum
Authors: Kim Joomi , Fabris Michele , Baart Gino , Kim Min K. , Goossens Alain , Vyverman Wim , Falkowski Paul G. , Lun Desmond S.
Published: November 2015

Diatoms (Bacillarophyceae) are photosynthetic unicellular microalgae that have risen to ecological prominence in oceans over the past 30 million years. They are of interest as potential feedstocks for sustainable biofuels. Maximizing production of these feedstocks will require genetic modifications and an understanding of algal metabolism. These processes may benefit from genome‐scale models, which predict intracellular fluxes and theoretical yields, as well as the viability of knockout and knock‐in transformants. Here we present a genome‐scale metabolic model of a fully sequenced and transformable diatom: Phaeodactylum tricornutum. The metabolic network was constructed using the P. tricornutum genome, biochemical literature, and online bioinformatic databases. Intracellular fluxes in P. tricornutum were calculated for autotrophic, mixotrophic and heterotrophic growth conditions, as well as knockout conditions that explore the in silico role of glycolytic enzymes in the mitochondrion. The flux distribution for lower glycolysis in the mitochondrion depended on which transporters for TCA cycle metabolites were included in the model. The growth rate predictions were validated against experimental data obtained using chemostats. Two published studies on this organism were used to validate model predictions for cyclic electron flow under autotrophic conditions, and fluxes through the phosphoketolase, glycine and serine synthesis pathways under mixotrophic conditions. Several gaps in annotation were also identified. The model also explored unusual features of diatom metabolism, such as the presence of lower glycolysis pathways in the mitochondrion, as well as differences between P. tricornutum and other photosynthetic organisms.
Glycomapping the fine specificity of monoclonal and polyclonal Lewis antibodies with type‐specific Lewis kodecytes and function‐spacer‐lipid constructs printed on paper
Authors: Williams Eleanor , Korchagina Elena , Frame Tom , Ryzhov Ivan , Bovin Nicolai , Henry Stephen
Published: November 2015

BACKGROUND

Lewis serologic reagents frequently give inaccurate phenotyping results. Furthermore these serologic reagents are often used in nonserologic assays such as inhibition and immunohistochemistry. In both scenarios knowledge of the fine specificity and cross‐reactivity of these reagents will improve the quality of results obtained.

STUDY DESIGN AND METHODS

A range of contemporary and historical workshop and developmental Lewis reagents including mouse monoclonal (MoAb) and human and goat polyclonal (PoAb) reagents were evaluated. All were evaluated both against Lewis kodecytes expressing only single Lea, Leb, ALeb, BLeb, Lex, Ley, ALey, or BLey antigens and against the same antigens inkjet printed on a paper‐based microplate and analyzed by enzyme immunoassay. Nine clinical samples were also evaluated. A kodecyte antigen dilution sensitivity assay was used to establish the ratio of Leb antigen between group A1/A2 and O RBCs.

RESULTS

A continuum of cross‐reactivity from Lex through to H was observed with MoAbs. All PoAb and few MoAb anti‐Lea samples and reagents cross‐reacted to some degree with Leb antigen. Some PoAb and MoAb anti‐Leb did not cross‐react with Lea. All polyclonal goat anti‐Leb reagents showed substantial activity against ALeb and BLeb, while no MoAb reagent had this activity. A1 RBCs had less than half the Leb antigen of A2/O RBCs.

CONCLUSIONS

Substantial cross‐reactivity of both MoAbs and PoAbs with related antigens highlights the risks of using serologic reagents in nonserologic assays or against synthetic antigens. The lack of ALeb activity in anti‐Leb MoAbs explains their poor performance against blood group A1 Le(a–b+) phenotypes.
Ecophysiological factors contributing to the invasion ofPanicum maximuminto nativeMiscanthus sinensisgrassland in Taiwan
Authors: Ho C‐Y , Tsai M‐Y , Huang Y‐L , Kao W‐Y
Published: November 2015

Panicum maximum(guinea grass), a native grass of Africa, has invaded and displaced the nativeMiscanthus sinensisgrassland at Dadu terrace in central Taiwan. The Dadu terrace has distinct wet and dry seasons and is prone to fire during the dry seasons. We compared photosynthesis and growth, as well as the growth response to two water treatments, betweenP. maximumandM. sinensisplants to understand ecophysiological factors contributing to the successful invasion of the grass. In comparison withM. sinensis,P. maximumhad a significantly higher photosynthetic rate, larger specific leaf area and a higher leaf area/total biomass ratio, and thus grew faster and higher, and accumulated more biomass under well‐watered conditions. The growth ofP. maximumwas more susceptible thanM. sinensisto drought stress. Faster growth of seedlings and more biomass accumulation of mature plants would giveP. maximuma highly competitive advantage overM. sinensisfor resource acquisition in the Dadu terrace during the wet season, which might contribute to the successful invasion ofP. maximuminto the grassland ofM. sinensis.
Rat‐to‐Chinese tree shrew heart transplantation is a novel small animal model to study non‐Gal‐mediated discordant xenograft humoral rejection
Authors: Chen WeiLi , Wu Yuan , Shimizu Akira , Lian YinLong , Tasaki Masayuki , Villani Vincenzo , Moran Shannon , Xia JunJie , Yamada Kazuhiko , Qi ZhongQuan
Published: November 2015

Since α‐1,3‐galactosyltransferase knockout (GalT‐KO) pigs became available, there has been an increasing interest in non‐Gal natural antibody (nAb)‐mediated xenograft rejection. To better understand mechanisms of non‐Gal nAb‐mediated rejection, a simple small animal model without gene manipulation would be extremely valuable. Here, we tested whether the Chinese tree shrew (CTS), which is a small‐sized mammal that is phylogenetically close to primates, could serve as a model for discordant xenograft rejection.

Methods

Study 1: Expression of α‐Gal antigens in hearts and kidneys of CTSs and rats was assessed by IB4 lectin binding. Presence of anti‐Gal and anti‐non‐Gal IgM and IgG nAb in CTS sera was tested by FACS using Gal+ and GalTKO PBMC as well as BSA‐ELISA. Study 2: Rat hearts were transplanted into CTS recipients (group 1, n = 7), and CTS hearts were transplanted in rats [n = 10; seven received no immunosuppression (group 2) and three received FK506 + leflunomide (group 3)].

Results

Study 1: Both CTSs and rats had α‐Gal expression in hearts and kidneys. ELISA showed CTSs do not have anti‐Gal nAb, and flow cytometry indicated CTSs have anti‐non‐Gal IgM and IgG nAb in serum. Study 2: Rat hearts in CTSs were uniformly rejected within 35 mins, while CTS hearts in rats continued beating until day 5 without immunosuppression, and up to day 8 with immunosuppression.

Conclusion

Rat‐to‐CTS heart transplantation is a discordant xenotransplant model, CTS‐to‐Rat heart transplantation is a concordant xenotransplant model. CTSs are valuable small animals to study mechanisms and strategies to avoid non‐Gal nAb‐mediated xenograft rejection.
East Asian allopatry and north Eurasian sympatry in Long‐tailed Tit lineages despite similar population dynamics during the late Pleistocene
Authors: Song Gang , Zhang Ruiying , DuBay Shane G. , Qu Yanhua , Dong Lu , Wang Wenjuan , Zhang Yanyun , Lambert David M. , Lei Fumin
Published: November 2015

Eurasia is a large continent characterized by heterogeneous environments. Glacial cycles during the late Pleistocene have had variable impacts on the avifauna across Eurasia. Bird populations from South‐East Asia show stability through the Last Glacial Maximum (LGM), while populations from Europe exhibit evidence of post‐LGM expansion. We investigated the phylogeography of the Long‐tailed Tit (Aegithalos caudatus), which spans the longitudinal breadth of Eurasia to test how climatic history and regional topographical complexity affected populations and diversification within the species complex. Our results show that two lineages from central and southern China (lineages C and D) segregate geographically, while lineages across northern Eurasia (lineage A and B) show substantial sympatry. Bayesian estimates for the timing of diversification suggest that the four lineages diverged during the middle Pleistocene, splitting in parallel and undergoing concurrent demographic histories since divergence. A. caudatus lineages experienced similar and synchronous population size dynamics during glacial cycles before the LGM. We conclude that the difference in geo‐topologic complexity may be an important factor that led to the variation in secondary admixture between northern Eurasian and eastern Asian lineages.
Magnetic resonance: Using computer simulations and visualizations to connect quantum theory with classical concepts
Authors: Engelhardt Larry
Published: November 2015

We discuss how computers can be used to solve the ordinary differential equations that provide a quantum mechanical description of magnetic resonance. By varying the parameters in these equations and visually exploring how these parameters affect the results, students can quickly gain insights into the nature of magnetic resonance that go beyond the standard presentation found in quantum mechanics textbooks. The results were generated using an IPython notebook, which we provide as an online supplement with interactive plots and animations.
A demonstration of the conservation of the orbital angular momentum of Earth
Authors: Pellizza Leonardo J. , Mayochi Mariano G. , Ciocci Brazzano Ligia , Pedrosa Susana E.
Published: November 2015

We describe a simple but quantitative experiment to demonstrate the conservation of angular momentum. We measure the correlation of the apparent radius and angular velocity of the Sun with respect to the stars, due to the conservation of the angular momentum of Earth in its orbit. We also determine the direction of Earth's angular momentum vector and show that it is conserved. The experiment can be performed using a small telescope and a digital camera. It is conceptually simple, allowing students to get direct physical insight from the data. The observations are performed near the resolution limit imposed by the atmosphere, and in the presence of strong competing effects. These effects necessitate a careful experimental setup and allow students to improve their skills in experimentation.
Undergraduate physics laboratory: Electrophoresis in chromatography paper
Authors: Hyde Alexander , Batishchev Oleg
Published: November 2015

An experiment studying the physical principles of electrophoresis in liquids was developed for an undergraduate laboratory. We have improved upon the standard agarose gel electrophoresis experimental regime with a straightforward and cost-effective procedure, in which drops of widely available black food coloring were separated by electric field into their dye components on strips of chromatography paper soaked in a baking soda/water solution. Terminal velocities of seven student-safe dyes were measured as a function of the electric potential applied along the strips. The molecular mobility was introduced and calculated by analyzing data for a single dye. Sources of systematic and random errors were investigated.
Calculating helium atomic excited states in coordinate space
Authors: Hall Shane , Siegel P. B.
Published: November 2015

Two coupled Schrödinger equations are used to calculate excited states of atomic helium. Using product state functions for the two-electron state, the shooting method is used to numerically determine the energies of the allowed singlet and triplet levels. The calculations agree well with the data, and the coordinate-space basis yields Schrödinger equations for helium that are familiar to students who have used similar methods for the hydrogen atom.