bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enriching the ant tree of life: enhanced UCE bait set for genome‐scale phylogenetics of ants and other Hymenoptera
Authors: Branstetter Michael G. , Longino John T. , Ward Philip S. , Faircloth Brant C. 
Published: January 2017

Summary

Targeted enrichment of conserved genomic regions (e.g. ultraconserved elements or UCEs) has emerged as a promising tool for inferring evolutionary history in many organismal groups. Because the UCE approach is still relatively new, much remains to be learned about how best to identify UCE loci and design baits to enrich them.

We test an updated UCE identification and bait design workflow for the insect order Hymenoptera, with a particular focus on ants. The new strategy augments a previous bait design for Hymenoptera by (i) changing the parameters by which conserved genomic regions are identified and retained, and (ii) increasing the number of genomes used for locus identification and bait design. We perform in vitro validation of the approach in ants by synthesizing an ant‐specific bait set that targets UCE loci and a set of ‘legacy’ phylogenetic markers. Using this bait set, we generate new data for 84 taxa (16/17 ant subfamilies) and extract loci from an additional 17 genome‐enabled taxa. We then use these data to examine UCE capture success and phylogenetic performance across ants. We also test the workability of extracting legacy markers from enriched samples and combining the data with published datasets.

The updated bait design (hym‐v2) contained a total of 2590‐targeted UCE loci for Hymenoptera, significantly increasing the number of loci relative to the original bait set (hym‐v1; 1510 loci). Across 38 genome‐enabled Hymenoptera and 84 enriched samples, experiments demonstrated a high and unbiased capture success rate, with the mean locus enrichment rate being 2214 loci per sample. Phylogenomic analyses of ants produced a robust tree that included strong support for previously uncertain relationships. Complementing the UCE results, we successfully enriched legacy markers, combined the data with published Sanger datasets and generated a comprehensive ant phylogeny containing 1060 terminals.

Overall, the new UCE bait design strategy resulted in an enhanced bait set for genome‐scale phylogenetics in ants and other Hymenoptera. Our in vitro tests demonstrate the utility of the updated design workflow, providing evidence that this approach could be applied to any organismal group with available genomic information.
Novel, continuous monitoring of fine‐scale movement using fixed‐position radiotelemetry arrays and random forest location fingerprinting
Authors: Harbicht Andrew B. , Castro‐Santos Theodore , Ardren William R. , Gorsky Dimitry , Fraser Dylan J. 
Published: January 2017

Summary

Radio‐tag signals from fixed‐position antennas are most often used to indicate presence or absence of individuals, or to estimate individual activity levels from signal strength variation within an antenna's detection zone. The potential of such systems to provide more precise information on tag location and movement has not been explored in great detail in an ecological setting.

By reversing the roles that transmitters and receivers play in localization methods common to the telecommunications industry, we present a new telemetric tool for accurately estimating the location of tagged individuals from received signal strength values. The methods used to characterize the study area in terms of received signal strength are described, as is the random forest model used for localization. The resulting method is then validated using test data before being applied to true data collected from tagged individuals in the study site.

Application of the localization method to test data withheld from the learning dataset indicated a low average error over the entire study area (<1 m), whereas application of the localization method to real data produced highly probable results consistent with field observations.

This telemetric approach provided detailed movement data for tagged fish along a single axis (a migratory path) and is particularly useful for monitoring passage along migratory routes. The new methods applied in this study can also be expanded to include multiple axes (x, y, z) and multiple environments (aquatic and terrestrial) for remotely monitoring wildlife movement.
The decision‐making process for breast reconstruction after cancer surgery: Representations of heterosexual couples in long‐standing relationships
Authors: Fasse Léonor , Flahault Cécile , Vioulac Christel , Lamore Kristopher , Van Wersch Anna , Quintard Bruno , Untas Aurélie 
Published: January 2017

ObjectivesMost people deal with intrusive life events such as cancer and the care trajectory together with their intimate partners. To our knowledge, no research has studied the involvement of the partner in the decision‐making process regarding breast reconstruction (BR) after cancer. This study aimed to gain a better understanding of the couples’ decision‐making process for BR in the cancer context and particularly to investigate the partners’ involvement in this process.MethodEighteen participants (nine women who underwent a mastectomy following a first breast cancer and their intimate partners) took part in this study. We conducted semidirective interviews, and a general inductive approach was chosen to capture the representations of the couples.ResultsThe women in the sample were aged between 33 and 66 years (M = 54, SD = 7.5) and their partner between 40 and 76 years (M = 59, SD = 11.6). The duration of their intimate relationship was on average 18 years (SD = 10.4; minimum = 4; maximum = 33). The analysis revealed 11 major themes. The two most salient ones were ‘external influence’ and ‘implication of the partner’. The exploration of the subthemes revealed that the decision‐making process is often reported as an interrelated experience by the couples and as a dyadic stressor. The partner's role is depicted as consultative and mostly supportive.ConclusionThese results provide new insights on the involvement of the partner in decision‐making. Thus, it now seems crucial to develop a prospective study, which will help understand the progression of the decision‐making process over time.
Statement of contribution

What is already known on this subject?

Most people deal with intrusive life events such as cancer and the care trajectory together with their intimate partners. Shared decision‐making between patients and physicians is now the ‘gold standard’ in Western Europe and the United States. However, in the context of breast reconstruction (BR) after cancer, factors guiding the decision‐making process for BR, especially the potential involvement of the partner, are not very well understood.

What does this study add?

Provides a qualitative insight on the specific nature of heterosexual couples’ representations regarding the decision‐making process for breast reconstruction after cancer.

Reveals that the decision‐making process is often reported as an interrelated experience by the couples and as a dyadic stressor.

Underlines the consultative function of partners with women engaged in breast reconstruction.
Parent–child value similarity in families with young children: The predictive power of prosocial educational goals
Authors: Döring Anna K. , Makarova Elena , Herzog Walter , Bardi Anat 
Published: January 2017

Value transmission from one generation to the next is a key issue in every society, but it is not clear which parents are the most successful in transmitting their values to their children. We propose parents’ prosocial educational goals as key predictors of parent–child value similarity. Accordingly, we hypothesized that the more parents wanted their children to endorse values of self‐transcendence (helping, supporting, and caring for others) and the less parents wanted their children to endorse the opposing values of self‐enhancement (striving for power and achievement), the higher would be parent–child overall value similarity. Findings from two studies of families – Study 1: 261 Swiss families, children aged 7–9 years; Study 2: 157 German families, children aged 6–11 years – confirmed this hypothesis. The effect was even stronger after controlling for values that prevail in the Swiss and German society, respectively. We integrate evidence from this study of values in families with young children with existing findings from studies with adolescent and adult children, and we discuss potential pathways from parents’ educational goals to parent–child value similarity.
Suppression of carboxylesterases by imatinib mediated by the down‐regulation of pregnane X receptor
Authors: Luo Wenjing , Xin Yu , Zhao Xia , Zhang Feng , Liu Changqing , Fan Hongwei , Xi Tao , Xiong Jing 
Published: January 2017

Background and PurposeImatinib mesylate (IM) is a first‐line treatment for chronic myeloid leukaemia (CML) as a specific inhibitor of BCR‐ABL tyrosine kinase. As IM is widely used in CML, in combination with other drugs, the effects of IM on drug‐metabolizing enzymes (DMEs) are crucial to the design of rational drug administration. Carboxylesterases (CESs) are enzymes catalysing the hydrolytic biotransformation of several clinically useful drugs. Although IM is known to inhibit cytochromes P450 (CYPs), its effects on DMEs, and CESs in particular, are still largely undefined.Experimental ApproachHepatoma cell lines (HepG2 and Huh7) and primary mouse hepatocytes were used. mRNA and protein expression were evaluated by quantitative RT‐PCR and Western blot analysis. Reporter luciferase activity was determined by transient co‐transfection experiment. Pregnane X receptor (PXR) expression was regulated by overexpression and RNA interference. The activity of CESs was determined by enzymic and toxicological assays. Mice were treated with a range of doses of IM to analyse expression of CESs in mouse liver.Key ResultsThe expression and activity of CESs were markedly repressed by IM, along with the down‐regulation of PXR and inhibited expression and activity of CYP3A4 and P‐gp.Conclusions and ImplicationsDown‐regulation of PXR mediates IM‐induced suppression of CESs. IM may inhibit expression of other genes targeted by PXR, thus inducing a wide range of potential drug–drug interactions during treatment of CML. The data deserve further elucidation including clinical trials.
Protein arginine deiminase 4 inhibition is sufficient for the amelioration of collagen-induced arthritis
Authors: Willis V C , Banda N K , Cordova K N , Chandra P E , Robinson W H , Cooper D C , Lugo D , Mehta G , Taylor S , Tak P P , Prinjha R K , Lewis H D , Holers V M 
Published: January 2017

Summary
Citrullination of joint proteins by the protein arginine deiminase (PAD) family of enzymes is recognized increasingly as a key process in the pathogenesis of rheumatoid arthritis. This present study was undertaken to explore the efficacy of a novel PAD4-selective inhibitor, GSK199, in the murine collagen-induced arthritis model of rheumatoid arthritis. Mice were dosed daily from the time of collagen immunization with GSK199. Efficacy was assessed against a wide range of end-points, including clinical disease scores, joint histology and immunohistochemistry, serum and joint citrulline levels and quantification of synovial autoantibodies using a proteomic array containing joint peptides. Administration of GSK199 at 30 mg/kg led to significant effects on arthritis, assessed both by global clinical disease activity and by histological analyses of synovial inflammation, pannus formation and damage to cartilage and bone. In addition, significant decreases in complement C3 deposition in both synovium and cartilage were observed robustly with GSK199 at 10 mg/kg. Neither the total levels of citrulline measurable in joint and serum, nor levels of circulating collagen antibodies, were affected significantly by treatment with GSK199 at any dose level. In contrast, a subset of serum antibodies reactive against citrullinated and non-citrullinated joint peptides were reduced with GSK199 treatment. These data extend our previous demonstration of efficacy with the pan-PAD inhibitor Cl-amidine and demonstrate robustly that PAD4 inhibition alone is sufficient to block murine arthritis clinical and histopathological end-points.
Determinants of the increase in ketone concentration during SGLT2 inhibition in NGT, IFG and T2DM patients
Authors: Al Jobori Hussein , Daniele Giuseppe , Adams John , Cersosimo Eugenio , Triplitt Curtis , DeFronzo Ralph A. , Abdul‐Ghani Muhammad 
Published: January 2017

AimTo examine metabolic factors that influence ketone production after sodium‐glucose cotransport inhibitor (SGLT2) administration.Research design and methodsFasting plasma glucose (FPG), insulin, glucagon, free fatty acid and ketone concentrations were measured in 15 type 2 diabetes mellitus (T2DM) and 16 non‐diabetic subjects before and at day 1 and day 14 after treatment with empagliflozin.ResultsEmpagliflozin caused a 38 mg/dL reduction in FPG concentration in T2DM patients. However, it caused only a small but significant (7 mg/dL) reduction in the FPG concentration in impaired fasting glucose (IFG) subjects and did not affect FPG concentration in normal glucose tolerant (NGT) subjects. Empagliflozin caused a significant increase in mean plasma glucagon, free fatty acid (FFA) and ketone concentrations in T2DM subjects. However, empagliflozin did not cause a significant change in mean plasma insulin, glucagon or ketone concentrations in non‐diabetic subjects. An index that integrates change in plasma glucose, insulin and FFA concentration at day 1 strongly correlates with plasma ketone concentration at day 1 (r = 0.85,
P
< .001) and day 14 (r = 0.63, r = 0.01) and predicts, with 86% sensitivity and 83% specificity, subjects at the top tertile for plasma ketone concentration after empagliflozin treatment.ConclusionResults of the present study demonstrate that SGLT2 inhibition exerts different metabolic effects in non‐diabetic individuals as compared to diabetic patients.
Hybridisation and lack of prezygotic barriers betweenPhymata pennsylvanicaandamericana
Authors: PUNZALAN DAVID , ROWE LOCKE 
Published: January 2017

1. The persistence of both geographical and reproductive boundaries between related species poses a fundamental puzzle in biology. Reproductive interactions between species can have a substantial impact on the maintenance of a boundary, potentially contributing to its collapse (e.g. via hybridisation) or facilitating reproductive isolation (e.g. via reinforcement).2. The degree to which two parapatric insect species in the genusPhymataare reproductively isolated was evaluated and several mechanisms that could contribute to the maintenance of species boundaries were assessed.3. Behavioural assays showed no indication of species‐assortative mating, nor any fecundity costs associated with heterospecific mating. Thus, there was no evidence of prezygotic mechanisms of reproductive isolation between the two species.4.In laboratory crosses, it was found that the two species were indeed capable of producing viableF1hybrids. Morphologically, these hybrids were phenotypically intermediate to the two parental species, and similar to the phenotypes seen in natural populations thought to occur in a hybrid zone.F1hybrids did not show reduced viability, although there was some suggestion of ‘hybrid breakdown’, evident from the lower viability observed for progeny of ‘natural hybrids’.5. Collectively, we show that despite genetically based morphological differences between species,P. americanaandpennsylvanicacan, and probably do hybridise. More studies are needed to understand the mechanisms that maintain the distinct phenotypes and geographical ranges of these species, despite the considerable potential for introgression.
Private Law, Regulation, and Justice
Authors: Hesselink Martijn W. 
Published: January 2017

AbstractThis paper critically engages with the European Regulatory Private Law thesis (ERPL). The main strength of ERPL is that it offers an entirely new perspective on European private law. However, as a complete theory of European private law, ERPL is too one‐sided, both from a descriptive and from a normative point of view. With its strong focus on the private law locked up in regulatory silos for specific market sectors, it obscures the reality of the consumer acquis and its transformative force. A fuller picture would include the contours of a loosely coherent system of European private law that is currently emerging. The main pillars of that pragmatic system are (for now) the withdrawal rights, unfair term control, and remedies for nonconformity. Moreover, the contribution of European private law to access justice cannot be the only standard for its evaluation and critique; at least as important are interpersonal justice and democratic legitimacy.
The EU's Private Law in the Regulated Sectors: Competitive Market Handmaiden or Institutional Platform?
Authors: Svetiev Yane 
Published: January 2017

AbstractThe article contests the claim that EU private law is narrowly circumscribed by a market rationality. Such a claim tracks broader criticism of EU functional legal integration, although it tends to obscure the underlying transformative pressures on private law and regulation and the role EU law plays in coping with such pressures. To offer a number of counter‐narratives, the article draws on examples from the regulated sectors, including telecommunications and energy, to reveal their experimentalist features. These suggest that EU private law is constructed through a process of error‐corrections, which allows for mutual adjustment of instruments and hybridisation of EU and local policy goals. The process results in more finely grained assemblages of autonomy and regulation to respond to concrete problems or newly salient policy goals, so that markets are understood as social institutions that are always works‐in‐progress rather than convergence points. Thus, EU private law provides a platform for transnational market‐building through innovating institutions that promote various normative and policy commitments despite the interdependencies that could undermine them.
An ultrasound‐guided, tendon‐sparing, lateral approach to injection of the navicular bursa
Authors: Nottrott K. , De Guio C. , Khairoun A. , Schramme M. 
Published: January 2017

SummaryBackgroundNavicular disease in the horse often requires injection of the navicular bursa. We have developed an ultrasound‐guided, lateral needle approach to navicular bursocentesis, which avoids penetration of the deep digital flexor tendon (DDFT) and the need for radiographic control.ObjectivesTo describe and evaluate the feasibility and efficacy of an ultrasound‐guided, lateral bursocentesis technique.Study designCadaveric and in vivo experiments.MethodsThe navicular bursa in 62 cadaveric forelimbs of 31 horses and in both forelimbs of 26 live horses, positioned with the foot flexed in a navicular block, were submitted to lateral, ultrasound‐guided injection of 1.5 ml radiocontrast agent. Lateromedial radiographs were taken to locate the contrast. A second injection of 0.5 ml methylene blue was administered during needle withdrawal in cadaveric limbs to investigate the needle pathway during dissection.ResultsContrast agent was successfully deposited in the navicular bursa in 104 of 114 (91%) limbs and in the navicular bursa alone in 89 of 114 (78%) limbs. Dissection showed no evidence of penetration of the DDFT in cadaver limbs. Failure to inject the navicular bursa was significantly associated with poor quality of the ultrasound image (P = 0.04) and resulted in aberrant injection of the distal interphalangeal joint in five of 114 (4%) limbs, the peribursal soft tissues in four of 114 (4%) limbs and the digital flexor tendon sheath in one of 114 (0.9%) limbs. Synovial fluid was observed at the needle hub in 58% of live horses.Main limitationsIt is unknown whether injection results obtained in the limbs of horses without disease can be extrapolated to horses with clinical disease of the podotrochlear apparatus. The localisation of contrast medium on radiographs may not accurately reflect the behaviour of local anaesthetic solution or therapeutic medications injected in the navicular bursa.ConclusionsThis lateral, ultrasound‐guided technique for injecting the navicular bursa is effective, does not penetrate the DDFT and avoids exposure of personnel to radiation.
Long‐term follow‐up of Norwegian horses affected with acquired equine polyneuropathy
Authors: Hanche‐Olsen S. , Kielland C. , Ihler C. F. , Hultin Jäderlund K. 
Published: January 2017

SummaryBackgroundAcquired equine polyneuropathy (AEP), a neurological disease clinically characterised by knuckling of metatarsophalangeal joints, has been described in numerous Nordic horses during the last 20 years. Although clinical recovery has been reported, large‐scale data on long‐term follow‐up of survivors have been lacking.ObjectivesTo describe long‐term survival of AEP affected horses registered in Norway, with a focus on athletic performance and possible residual clinical signs connected to the disease.Study designA retrospective cohort study.MethodsThe study includes 143 horses recorded with AEP in Norway from 2000 to 2012, with the follow‐up period continuing until 2015. Participating owners of survivors completed a standardised questionnaire, providing information on disease and convalescence, management, performance‐level and possible residual clinical signs. To investigate the follow‐up of survivors, we performed 2 multivariable linear regression models.ResultsThe follow‐up time of survivors was 1.0–14.5 years (median 5.3, interquartile range 2.5–7.2). Fifty‐seven horses survived and all but 3 horses returned to previous or higher level of performance. However, possible disease‐related residual clinical signs were reported in 14/57 horses. Forty‐nine of the survivors were in athletic use at time of contact. The majority of survivors were categorised with low severity‐grades at time of diagnosis and the initial grade was significantly associated with time to resumed training. Only 3 horses had experienced relapse/new attack during the follow‐up period.Main limitationAthletic performance was judged by owners, which renders a possible source of bias.ConclusionsAlthough AEP is a potential fatal disease, most survivors will recover and return to minimum previous level of athletic performance. Some horses display residual clinical signs, but often without negative effect on performance and relapse of disease is rare.