bluuebunny/crossref_metadata_2025_split huggingface dataset:
Poly(dimethylsiloxane)-based microdevices for studying plant reproduction
Authors: Arata Hideyuki , Higashiyama Tetsuya 
Published: March 2014

Long-term holding and precise handling of growing plant tissues during in vitro cultivation has been a major hurdle for experimental studies related to plant development and reproduction. In the present review, we introduce two of our newly developed poly(dimethylsiloxane)-based microdevices: a T-shaped microchannel device for pollen tube chemoattraction and a microcage array for long-term live imaging of ovules. Their design, usage and advantages are described, and future prospects of experimental approaches to plant reproduction using such microdevices are discussed.
Right Ventricular Reverse Remodeling after Pulmonary Endarterectomy: Magnetic Resonance Imaging and Clinical and Right Heart Catheterization Assessment
Authors: Berman Marius , Gopalan Deepa , Sharples Linda , Screaton Nick , Maccan Caroline , Sheares Karen , Pepke‐Zaba Joanna , Dunning John , Tsui Steven , Jenkins David P. 
Published: March 2014

The objective of this study was to assess the effect of pulmonary endarterectomy (PEA) on right ventricular (RV) reverse remodeling using magnetic resonance imaging (MRI) and to correlate MRI findings with clinical and hemodynamic outcomes postsurgery. We performed a retrospective analysis in 72 patients undergoing PEA surgery in whom MRI and right heart catheterization (RHC) were performed preoperation and 3 months postoperation. RV volumes and mass were assessed by MRI. Continuous variables were expressed as means, changes were compared with a paired t test, and associations between the variables were explored using Pearson correlation coefficients. The mean age was 57 years, and 51% were male. Both RV end‐diastolic volume (EDV; 176–117 mL; P < 0.001) and RV end‐systolic volume (ESV; 129–64 mL; P < 0.001) reduced significantly following PEA. Preoperative pulmonary artery pressure (PAP) correlated moderately with ESV (r = 0.46, P < 0.001). Postoperatively, PAP correlated with EDV (r = 0.45, P < 0.001) and ESV (r = 0.44, P < 0.001). Moderate correlation was present between hemodynamic parameters: PAP, pulmonary vascular resistance, and right atrial pressure with pre‐ and postoperation end‐systolic and end‐diastolic RV mass (P < 0.001). RHC and MRI measurements of cardiac output and RV volumes were significantly different (P < 0.001). In conclusion, RV reverse remodeling, as measured by improvement in RV volumes and mass by MRI, was observed for 3 months in patients who underwent PEA surgery. This is the largest series of patients with pre‐ and post‐PEA MRI assessment so far reported. MRI detects changes in parameters reflecting cardiac remodeling and pulmonary clearance, but measurements are significantly different from those of RHC.
Accepting Inequality Deters Responsibility: How Power Distance Decreases Charitable Behavior
Authors: Winterich Karen Page , Zhang Yinlong 
Published: March 2014

Abstract
Could power distance, which is the extent that inequality is expected and accepted, explain why some countries and consumers are more likely to engage in prosocial behavior, including donations of both money and time? This research proposes that higher power distance results in weaker perceptions of responsibility to aid others, which decreases charitable behavior. Both correlational and causal evidence is provided in a series of five studies that examine country-level power distance as well as individual and temporarily salient power distance belief. Consistent with the mediating role of perceived responsibility, results reveal that uncontrollable needs and communal relationship norms are boundary conditions that overcome the negative effect of power distance on charitable behavior. These results explain differences in charitable giving across cultures and provide implications for nonprofit organizations soliciting donations.
Basin Hopping Graph: a computational framework to characterize RNA folding landscapes
Authors: Kucharík Marcel , Hofacker Ivo L. , Stadler Peter F. , Qin Jing 
Published: March 2014

Abstract
Motivation: RNA folding is a complicated kinetic process. The minimum free energy structure provides only a static view of the most stable conformational state of the system. It is insufficient to give detailed insights into the dynamic behavior of RNAs. A sufficiently sophisticated analysis of the folding free energy landscape, however, can provide the relevant information.
Results: We introduce the Basin Hopping Graph (BHG) as a novel coarse-grained model of folding landscapes. Each vertex of the BHG is a local minimum, which represents the corresponding basin in the landscape. Its edges connect basins when the direct transitions between them are ‘energetically favorable’. Edge weights endcode the corresponding saddle heights and thus measure the difficulties of these favorable transitions. BHGs can be approximated accurately and efficiently for RNA molecules well beyond the length range accessible to enumerative algorithms.
Availability and implementation: The algorithms described here are implemented in C++ as standalone programs. Its source code and supplemental material can be freely downloaded from http://www.tbi.univie.ac.at/bhg.html .
Contact: qin@bioinf.uni-leipzig.de
Supplementary information: Supplementary data are available at Bioinformatics online.
DBatVir: the database of bat-associated viruses
Authors: Chen Lihong , Liu Bo , Yang Jian , Jin Qi 
Published: March 2014

Abstract
Emerging infectious diseases remain a significant threat to public health. Most emerging infectious disease agents in humans are of zoonotic origin. Bats are important reservoir hosts of many highly lethal zoonotic viruses and have been implicated in numerous emerging infectious disease events in recent years. It is essential to enhance our knowledge and understanding of the genetic diversity of the bat-associated viruses to prevent future outbreaks. To facilitate further research, we constructed the database of bat-associated viruses (DBatVir). Known viral sequences detected in bat samples were manually collected and curated, along with the related metadata, such as the sampling time, location, bat species and specimen type. Additional information concerning the bats, including common names, diet type, geographic distribution and phylogeny were integrated into the database to bridge the gap between virologists and zoologists. The database currently covers &gt;4100 bat-associated animal viruses of 23 viral families detected from 196 bat species in 69 countries worldwide. It provides an overview and snapshot of the current research regarding bat-associated viruses, which is essential now that the field is rapidly expanding. With a user-friendly interface and integrated online bioinformatics tools, DBatVir provides a convenient and powerful platform for virologists and zoologists to analyze the virome diversity of bats, as well as for epidemiologists and public health researchers to monitor and track current and future bat-related infectious diseases.
Database URL: http://www.mgc.ac.cn/DBatVir/
Epigenetic Modifications are Associated with Inter-species Gene Expression Variation in Primates
Authors: Zhou Xiang , Cain Carolyn E. , Myrthil Marsha , Lewellen Noah , Michelini Katelyn , Davenport Emily R. , Stephens Matthew , Pritchard Jonathan K. , Gilad Yoav 
Published: March 2014

AbstractChanges in gene regulation level have long been thought to play an important role in evolution and speciation, especially in primates. Over the past decade, comparative genomic studies have revealed extensive inter-species differences in gene expression levels yet we know much less about the extent to which regulatory mechanisms differ between species. To begin addressing this gap, we performed a comparative epigenetic study in primate lymphoblastoid cell lines (LCLs), to query the contribution of RNA polymerase II (Pol II) and four histone modifications (H3K4me1, H3K4me3, H3K27ac, and H3K27me3) to inter-species variation in gene expression levels. We found that inter-species differences in mark enrichment near transcription start sites are significantly more often associated with inter-species differences in the corresponding gene expression level than expected by chance alone. Interestingly, we also found that first-order interactions among the histone marks and Pol II do not markedly contribute to the degree of association between the marks and inter-species variation in gene expression levels, suggesting that the marginal effects of the five marks dominate this contribution.
Tissue tropism and vertical transmission ofCoxiellainRhipicephalus sanguineusandRhipicephalus turanicusticks
Authors: Lalzar Itai , Friedmann Yael , Gottlieb Yuval 
Published: March 2014

SummaryArthropod symbionts present tissue tropism that corresponds to the nature of the association and the mode of transmission between host generations. In ticks, however, our knowledge of symbiont tissue tropism and function is limited. Here, we quantified and localized previously describedCoxiella‐like symbionts in several organs of the tickRhipicephalus turanicus. Quantitative polymerase chain reaction revealed high densities ofCoxiellain the female gonads, and both male and femaleMalpighian tubules. Using fluorescencein situhybridization and transmission electron microscopy, we further showed that in the gonads of bothRh. turanicusandRh. sanguineus,Coxielladoes not colonize the primary oocytes but is found later in young and mature oocytes in a specific distribution, suggesting controlled vertical transmission. This method revealed the presenceCoxiellain the distal part of theMalpighian tubules, suggesting a possible role in nitrogen metabolism. While testingRickettsiasymbionts, no specific tissue tropism was found, but a slightly higher densities in the tick gut. The low density ofRickettsiain the female ovaries suggests competition betweenRickettsiaandCoxiellafor vertical transmission. The described tissue distribution supports an obligatory role forCoxiellain ticks.
Identification of key nitrous oxide production pathways in aerobic partial nitrifying granules
Authors: Ishii Satoshi , Song Yanjun , Rathnayake Lashitha , Tumendelger Azzaya , Satoh Hisashi , Toyoda Sakae , Yoshida Naohiro , Okabe Satoshi 
Published: March 2014

SummaryThe identification of the key nitrous oxide (N2O) production pathways is important to establish a strategy to mitigate N2O emission. In this study, we combined real‐time gas‐monitoring analysis, 15N stable isotope analysis, denitrification functional gene transcriptome analysis and microscale N2O concentration measurements to identify the main N2O producers in a partial nitrification (PN) aerobic granule reactor, which was fed with ammonium and acetate. Our results suggest that heterotrophic denitrification was the main contributor to N2O production in our PN aerobic granule reactor. The heterotrophic denitrifiers were probably related to Rhodocyclales bacteria, although different types of bacteria were active in the initial and latter stages of the PN reaction cycles, most likely in response to the presence of acetate. Hydroxylamine oxidation and nitrifier denitrification occurred, but their contribution to N2O emission was relatively small (20–30%) compared with heterotrophic denitrification. Our approach can be useful to quantitatively examine the relative contributions of the three pathways (hydroxylamine oxidation, nitrifier denitrification and heterotrophic denitrification) to N2O emission in mixed microbial populations.
Statistical Classification Methods for Estimating Ancestry Using Morphoscopic Traits,
Authors: Hefner Joseph T. , Ousley Stephen D. 
Published: March 2014

AbstractAncestry assessments using cranial morphoscopic traits currently rely on subjective trait lists and observer experience rather than empirical support. The trait list approach, which is untested, unverified, and in many respects unrefined, is relied upon because of tradition and subjective experience. Our objective was to examine the utility of frequently cited morphoscopic traits and to explore eleven appropriate and novel methods for classifying an unknown cranium into one of several reference groups. Based on these results, artificial neural networks (aNNs), OSSA, support vector machines, and random forest models showed mean classification accuracies of at least 85%. The aNNs had the highest overall classification rate (87.8%), and random forests show the smallest difference between the highest (90.4%) and lowest (76.5%) classification accuracies. The results of this research demonstrate that morphoscopic traits can be successfully used to assess ancestry without relying only on the experience of the observer.
Inhibition ofListeria monocytogenesandSalmonellaby Combinations of Oriental Mustard, Malic Acid, and EDTA
Authors: Olaimat Amin N. , Holley Richard A. 
Published: March 2014

AbstractThe antimicrobial activities of oriental mustard extract alone or combined with malic acid and EDTA were investigated againstSalmonellaspp. orListeria monocytogenesat different temperatures. Five strainSalmonellaorL. monocytogenescocktails were separately inoculated in Brain Heart Infusion broth containing 0.5% (w/v) aqueous oriental mustard extract and incubated at 4 °C to 21 °C for 21 d. For inhibitor combination tests,Salmonella Typhimurium02:8423 andL. monocytogenes2–243 were individually inoculated in Mueller Hinton broth containing the mustard extract with either or both 0.2% (w/v) malic acid and 0.2% (w/v) EDTA and incubated at 10 °C or 21 °C for 10 to 14 d. Mustard extract inhibited growth of theL. monocytogenescocktail at 4 °C up to 21 d (2.3 log10CFU/mL inhibition) or at 10 °C for 7 d (2.4 log10CFU/mL inhibition).Salmonellaspp. viability was slightly, but significantly reduced by mustard extract at 4 °C by 21 d. Although hydrolysis of sinigrin in mustard extract by both pathogens was 2 to 6 times higher at 21 °C than at 4 °C to 10 °C, mustard was not inhibitory at 21 °C, perhaps because of the instability of its hydrolysis product (allyl isothiocyanate). At 21 °C, additive inhibitory effects of mustard extract with EDTA or malic acid led to undetectable levels ofS.TyphimuriumandL. monocytogenesby 7 d and 10 d, respectively. At 10 °C,S.Typhimuriumwas similarly susceptible, but combinations of antimicrobials were not more inhibitory toL. monocytogenesthan the individual agents.
Sub‐surface Property, Free‐entry Mineral Staking and Settler Colonialism in Canada
Authors: Hoogeveen Dawn 
Published: March 2014

AbstractThis article examines mineral rights and claim staking in northern Canada, with a focus on settler colonialism and how liberal understandings of property are embedded in the legal geography of the right to explore for minerals. The history of these legal systems is explained through the “free‐entry” principle understood as the right to stake a mineral claim without consulting with private landholders or Indigenous peoples. Free‐entry debate highlights how ideologies of property are assumed neutral through staking regulations. Based on an analysis of interviews with key informants involved in mining regulation, I analyze the geographic stratification of land into two categories, above and below the surface, as an avenue to understand how dominant ideologies of property reveal a critical site of contestation.
Retrospective evaluation of methotrexate elimination when co‐administered with proton pump inhibitors
Authors: Reeves David J. , Moore Elizabeth S. , Bascom Devon , Rensing Brandon 
Published: March 2014

AimsThe aim was to assess potential interaction between methotrexate (MTX) and proton pump inhibitors (PPIs) in patients receiving high‐dose MTX.MethodsRecords of 56 adults receiving 201 cycles of MTX were reviewed to determine effects of PPI administration on MTX elimination. Repeated‐measures logistic regressions and Cox regressions were performed to evaluate the possible drug interaction.ResultsDespite a significant difference between those receiving a PPI and not receiving a PPI in median MTX levels at 24 (8.0 vs. 3.9 μmol l−1, respectively, P = 0.013) and 72 h after MTX administration (0.08 vs. 0.05 μmol l−1, respectively, P = 0.037), there was no difference between those receiving a PPI and not receiving a PPI in the proportion of patients experiencing delayed elimination at 24 (19.2% vs. 20.2%, respectively, P = 1.000) and 72 h (36.2% vs. 33.7%, respectively, P = 0.765). When data were analysed using Cox regression, controlling for multiple cycles of MTX per patient, PPI use was not a significant predictor of time to MTX < 0.1 μmol l−1. When the clustering effect of multiple cycles of MTX per patient was controlled for, co‐administration of PPIs was not a significant predictor of MTX level (P = 0.969). A comparison of patients with delayed elimination at any time point and those without delayed elimination indicated that PPI use was not a significant predictor of delayed elimination (P = 0.607).ConclusionsThis study does not support previous findings of a significant interaction between PPIs and MTX. Based on these results, the clinical significance of any potential interaction is likely to be small.
Simple lifestyle recommendations and the outcomes of gestational diabetes. A 2×2 factorial randomized trial
Authors: Bo S. , Rosato R. , Ciccone G. , Canil S. , Gambino R. , Poala C. B. , Leone F. , Valla A. , Grassi G. , Ghigo E. , Cassader M. , Menato G. 
Published: March 2014

AbstractThe benefits of exercise and behavioural recommendations in gestational diabetes mellitus (GDM) are controversial. In a randomized trial with a 2×2 factorial design, we examined the effect of exercise and behavioural recommendations on metabolic variables, and maternal/neonatal outcomes in 200 GDM patients. All women were given the same diet: group D received dietary recommendations only; group E was advised to briskly walk 20‐min/day; group B received behavioural dietary recommendations; group BE was prescribed the same as B + E. Dietary habits improved in all groups. In a multivariable regression model, fasting glucose did not change. Exercise, but not behavioural recommendations, was associated with the reduction of postprandial glucose (p < 0001), glycated haemoglobin (HbA1c; p < 0.001), triglycerides (p = 0.02) and C‐reactive protein (CRP; p < 0.001) and reduced any maternal/neonatal complications (OR = 0.50; 95%CI=0.28–0.89;p = 0.02). In GDM patients a simple exercise programme reduced maternal postprandial glucose, HbA1c, CRP, triglycerides and any maternal/neonatal complications, but not fasting glucose values.
Clinical efficacy of a computerised device (STA™) and a pressure syringe (VarioJect INTRA™) for intraligamentary anaesthesia
Authors: Kämmerer P. W. , Schiegnitz E. , von Haussen T. , Shabazfar N. , Kämmerer P. , Willershausen B. , Al‐Nawas B. , Daubländer M. 
Published: March 2014

AbstractIntroductionTo evaluate the impact of experience whilst using different devices for intraligamentary anaesthesia, dental students tested clinical anaesthetic efficacy of a mechanical (PDL‐S) and a computer‐controlled (CCLAD) application system in restorative patients.Material and methodsIn a prospective study, 41 Patients in need of restorative treatment in lower posterior mandible were randomised into three groups (PDL‐S: teeth n = 22; CCLAD: teeth n = 20; inferior alveolar nerve block (IANB): teeth n = 20). Dental last year students conducted anaesthesia and dental treatment. Primary objectives were differences in pain during treatment [numeric rating scale (NRS)] as well as in anaesthetic efficacy (complete/sufficient vs. insufficient/no effect) between PDL‐S and CCLAD. Pain of injection, need for second injections, amount of anaesthetic solution and duration of local numbness were assessed. IANB as gold standard was compared to each system descriptively.ResultsPDL‐S had a significant lower pain during treatment (P = 0.017) but a similar anaesthetic efficacy (P = 0.175) compared to the CCLAD system. Concerning pain of injection (P = 0.42), quantity of second injections (P = 0.232), amount of used solution (P = 0.073) as well as duration of local numbness (P = 0.253), no differences were seen. When comparing both periodontal ligament injection (PDL)‐systems with IANB, pain rating was higher when using CCLAD. Injection pain, amount of used solution as well as soft tissue anaesthesia was less for PDL‐S and CCLAD.DiscussionBoth PDL techniques showed a good success for dental routine treatments. Although, compared to the mechanic device, the CCLAD system might need more clinical daily experience.ConclusionWe recommend including specific trainings in intraligamentary anaesthesia in the dental curriculum.
Long‐term follow‐up of bone density, general and reproductive health in female survivors after treatment for haematological malignancies
Authors: Naessén Sabine , Bergström Ingrid , Ljungman Per , Landgren Britt‐Marie 
Published: March 2014

AbstractThe purpose of this study was to assess the ovarian function, fertility and bone mineral density in women who previously had treatment for different haematological malignancies (HMs). The overall survival and cure rates of patients with HMs have improved dramatically. The treatment affects fertility and bone density. Fifty‐two premenopausal women, from Stockholm region, were included in the study between 1998 and 2002, followed until 2011. The diagnoses were acute lymphoblastic leukaemia (n = 6), acute myeloid leukaemia (n = 10), chronic lymphocytic leukaemia (n = 1), chronic myeloid leukaemia (n = 12), Hodgkin lymphoma (n = 12) and non‐Hodgkin lymphoma (n = 11). Before treatment, women without children (43/52), when possible, were offered fertility preservation options. The mean age at diagnosis was 27, at final evaluation 39 yr. Thirty‐seven patients received HSCT; 26 allogeneic, 11 autologous. Before allogeneic HSCT, nineteen patients had myeloablative conditioning; seven had reduced‐intensity conditioning. Eleven patients got total body irradiation. Eight patients were transplanted with grafts from an HLA‐identical sibling donor, while 18 had unrelated donors. All women were in a menopausal state post‐therapy. Hormone replacement therapy (HRT) was given, and bone mineral density (BMD) was measured every other year. The serum levels of parathyroid hormone (PTH), free and bound calcium was within normal range. BMD measurements showed a slight increase over time in the spine with a mean of 0.015 g/cm2/yr. Four spontaneous pregnancies resulted in two babies and two discontinued pregnancies; two pregnancies were achieved with oocyte donation and surrogacy and one woman adopted a child. HRT sustains BMD in long‐term survivors from HMs. This study highlights the importance of HRT and fertility issues in this patient group.