bluuebunny/crossref_metadata_2025_split huggingface dataset:
Congruification: support for time scaling large phylogenetic trees
Authors: Eastman Jonathan M. , Harmon Luke J. , Tank David C. 
Published: March 2013

Summary

Approaches for efficient statistical estimation of large phylogenies are now available (Bioinformatics, 2006, 22, 2688), and yet we lack adequate tools for synthesizing information from previous analyses into large timetrees. Here, we present a cross‐platform r tool that integrates with tree of life efforts by mapping divergence times from an existing timetree (a ‘reference’) to another uncalibrated phylogeny (a ‘target’) that samples from the same lineage. Leveraging existing methods for rate‐smoothing phylograms, this tool enables the rapid generation of very large timetrees where direct estimation of the timing of lineage diversification is either impracticable or impossible.

The primary output of the tool is to return divergence times for nodes resolved as concordant between the reference and target. Given the computed set of secondary calibrations, post hoc tree transformation can be accomplished using existing resources that assume either a strict or relaxed evolutionary clock.

Our software is provided open source in the geiger package (http://cran.r-project.org/package=geiger) and is thoroughly demonstrated in the Supporting Information.
Motivational interviewing to enhance nicotine patch treatment for smoking cessation among homeless smokers: a randomized controlled trial
Authors: Okuyemi Kolawole S. , Goldade Kate , Whembolua Guy‐Lucien , Thomas Janet L. , Eischen Sara , Sewali Barrett , Guo Hongfei , Connett John E. , Grant Jon , Ahluwalia Jasjit S. , Resnicow Ken , Owen Greg , Gelberg Lillian , Des Jarlais Don 
Published: March 2013

AbstractAimsTo assess the effects of adding motivational interviewing (MI) counseling to nicotine patch for smoking cessation among homeless smokers.DesignTwo‐group randomized controlled trial with 26‐week follow‐up.Participants and settingA total of 430 homeless smokers from emergency shelters and transitional housing units in Minneapolis/St Paul, Minnesota, USA.Intervention and measurementsAll participants received 8‐week treatment of 21‐mg nicotine patch. In addition, participants in the intervention group received six individual sessions of MI counseling which aimed to increase adherence to nicotine patches and to motivate cessation. Participants in the standard care control group received one session of brief advice to quit smoking. Primary outcome was 7‐day abstinence from cigarette smoking at 26 weeks, as validated by exhaled carbon monoxide and salivary cotinine.FindingsUsing intention‐to‐treat analysis, verified 7‐day abstinence rate at week 26 for the intervention group was non‐significantly higher than for the control group (9.3% versus 5.6%, P = 0.15). Among participants who did not quit smoking, reduction in number of cigarettes from baseline to week 26 was equally high in both study groups (−13.7 ± 11.9 for MI versus −13.5 ± 16.2 for standard care).ConclusionsAdding motivational interviewing counseling to nicotine patch did not increase smoking rate significantly at 26‐week follow‐up for homeless smokers.
Long‐Term Outcomes of Dental Implants with a Titanium Plasma‐Sprayed Surface: A 20‐Year Prospective Case Series Study in Partially Edentulous Patients
Authors: Chappuis Vivianne , Buser Ramona , Brägger Urs , Bornstein Michael M. , Salvi Giovanni E. , Buser Daniel 
Published: March 2013

AbstractBackgroundLong‐term studies of ≥10 years are important milestones to get a better understanding of potential factors causing implant failures or complications.PurposeThe present study investigated the long‐term outcomes of titanium dental implants with a rough, microporous surface (titanium plasma sprayed [TPS]) and the associated biologic and technical complications in partially edentulous patients with fixed dental prostheses over a 20‐year follow‐up period.Materials and MethodsSixty‐seven patients, who received 95 implants in the 1980s, were examined with well‐established clinical and radiographic parameters. Based on these findings, each implant was classified as either successful, surviving, or failed.ResultsTen implants in nine patients were lost during the observation period, resulting in an implant survival rate of 89.5%. Radiographically, 92% of the implants exhibited crestal bone loss below 1 mm between the 1‐ and 20‐year follow‐up examinations. Only 8% yielded peri‐implant bone loss of >1 mm and none exhibited severe bone loss of more than 1.8 mm. During the observation period, 19 implants (20%) experienced a biologic complication with suppuration. Of these 19 implants, 13 implants (13.7%) had been treated and were successfully maintained over the 20‐year follow‐up period. Therefore, the 20‐year implant success rate was 75.8 or 89.5% depending on the different success criteria. Technical complications were observed in 32%.ConclusionThe present study is the first to report satisfactory success rates after 20 years of function of dental implants with aTPSsurface in partially edentulous patients.
Resolving the relationships of apid bees (Hymenoptera: Apidae) through a direct optimization sensitivity analysis of molecular, morphological, and behavioural characters
Authors: Payne Ansel 
Published: March 2013

AbstractPhylogenetic analyses that incorporate the most character information also provide the most explanatory power. Here I demonstrate the value of such an approach through a direct optimization sensitivity analysis of apid bee phylogeny. Whereas prior studies have relied solely on one class of data or the other, this analysis combines previously published molecular, morphological, and behavioural characters into a single supermatrix. The final dataset includes 191 ingroup and 30 outgroup taxa, and includes data from seven unaligned gene sequences (18S, 28S, wingless, EF1‐α, polII, Nak, LW rhodopsin), 209 adult and larval morphological characters, and two behavioural characters. Nine different sets of transformation cost parameters are evaluated, along with their relative degrees of character incongruence. The preferred parameter set returns a strict consensus tree somewhat similar to, but more resolved than, a previous parsimony tree based on molecules alone. I also describe the effects of including EF1‐α and LW rhodopsin intron sequences on the outcome of the direct optimization analysis. By accounting for more evidence, this study provides the most comprehensive treatment yet of apid phylogenetic relationships.
Conflicting and Complementary Ethics of Animal Welfare Considerations in Reintroductions
Authors: HARRINGTON LAUREN A. , MOEHRENSCHLAGER AXEL , GELLING MERRYL , ATKINSON ROB P. D. , HUGHES JOELENE , MACDONALD DAVID W. 
Published: March 2013

AbstractDespite differences in focus, goals, and strategies between conservation biology and animal welfare, both are inextricably linked in many ways, and greater consideration of animal welfare, although important in its own right, also has considerable potential to contribute to conservation success. Nevertheless, animal welfare and animal ethics are not always considered explicitly within conservation practice. We systematically reviewed the recent scientific peer‐reviewed and online gray literature on reintroductions of captive‐bred and wild‐caught animals (mammals, birds, amphibians, and reptiles) to quantify the occurrence of animal welfare issues. We considered monitoring that could be indicative of the animal's welfare status and supportive management actions that could improve animal welfare (regardless of whether the aim was explicitly animal‐welfare orientated). Potential welfare issues (of variable nature and extent) were recorded in 67% of 199 projects reviewed; the most common were mortality >50%, dispersal or loss of animals, disease, and human conflict. Most (>70%) projects monitored survival, 18% assessed body condition, and 2% monitored stress levels. Animal welfare, explicitly, was referred to in 6% of projects. Supportive actions, most commonly use of on‐site prerelease pens and provision of supplemental food or water, were implemented in 79% of projects, although the extent and duration of support varied. Practitioners can address animal‐welfare issues in reintroductions by considering the potential implications for individual animals at all stages of the release process using the decision tree presented. We urge practitioners to report potential animal‐welfare issues, describe mitigation actions, and evaluate their efficacy to facilitate transparent evaluation of common moral dilemmas and to advance communal strategies for dealing with them. Currently, comparative mortality rates, health risks, postrelease stress, effectiveness of supportive measures, and behavior of individuals warrant further research to improve animal welfare in reintroductions and to increase success of such projects.Ética Conflictiva y Complementaria al Considerar el Bienestar Animal en Reintroducciones
Partial anterior sacrectomy with nerve preservation to treat locally advanced rectal cancer
Authors: Evans M. D. , Harji D. P. , Sagar P. M. , Wilson J. , Koshy A. , Timothy J. , Giannoudis P. V. 
Published: March 2013

AbstractAimMost studies that have reported outcomes after composite abdomino‐sacral resection for locally advanced/recurrent rectal cancer have involved resections below the S2/3 disc space. Involvement of the sacrum above this level is uncommon and, until recently, was considered a contraindication to resection.MethodWe report here a surgical technique to deal with high sacral involvement with an anterior approach and maintenance of sacropelvic stability.ResultsThe operative findings confirmed a locally perforated rectal cancer with an associated abscess cavity and direct invasion into S2. Given the likelihood that a complete dislocation of the sacrum would cause significant neurological damage and pelvic instability without oncological benefit, we opted for a partial high anterior sacrectomy with nerve preservation. The patient made an uncomplicated recovery without neurological deficit and was able to walk with the aid of crutches from postoperative day 3.ConclusionWhile a high sacral transection is appropriate for some patients with locally advanced/recurrent rectal cancer, operative decisions and options should be tailored to each individual.
Mesenchymal stem cell transfusion for desensitization of positive lymphocyte cross‐match before kidney transplantation: outcome of 3 cases
Authors: Saadi G. , Fadel F. , El Ansary M. , El‐Hamid S. Abd 
Published: March 2013

AbstractObjectivesDonor specific antibodies (DSA) and a positive cross‐match are contraindications for kidney transplantation. Trials of allograft transplantation across theHLAbarrier have employed desensitization strategies, including the use of plasmapheresis, intravenous immunoglobulins, anti‐B‐cell monoclonal antibodies and splenectomy, associated with high‐intensity immunosuppressive regimens. Our case 1 report suffered from repeatedly positive lymphocyte cross match after 1st renal transplantation. Graft nephrectomy could not correct the state of sensitization. Splenectomy was done in a trial to get rid of the antibody producing clone. Furthermore plasmapheresis with low doseIVIGcould not as well revert the state of sensitization for the patient.Material and methodsAbout 50 millions donor specificMSCs were injected to the patient.ResultsMSCs transfusion proved to be the only procedure which could achieve successful desensitization before performing the second transplantation owing to their immunosuppressive properties.ConclusionThis case indicates thatDS‐MSCs is a potential option for anti‐HLAdesensitization. In cases 2 and 3IV DS‐MSCs transfusion was selected from the start as a successful line of treatment for pre renal transplantation desensitization to save other unnecessary lines of treatment that were tried in case 1.
Tocotrienols promote apoptosis in human breast cancer cells by inducing poly(ADP‐ribose) polymerase cleavage and inhibiting nuclear factor kappa‐B activity
Authors: Loganathan R. , Selvaduray K. R. , Nesaretnam K. , Radhakrishnan A. K. 
Published: March 2013

AbstractObjectivesTocotrienols and tocopherols are members of the vitamin E family, with similar structures; however, only tocotrienols have been reported to achieve potent anti‐cancer effects. The study described here has evaluated anti‐cancer activity of vitamin E to elucidate mechanisms of cell death, using human breast cancer cells.Materials and methodsAnti‐cancer activity of a tocotrienol‐rich fraction (TRF) and a tocotrienol‐enriched fraction (TEF) isolated from palm oil, as well as pure vitamin E analogues (α‐tocopherol, α−, δ− and γ−tocotrienols) were studied using highly aggressive triple negative MDA‐MB‐231 cells and oestrogen‐dependent MCF‐7 cells, both of human breast cancer cell lines. Cell population growth was evaluated using a Coulter particle counter. Cell death mechanism, poly(ADP‐ribose) polymerase cleavage and levels of NF‐κB were determined using commercial ELISA kits.ResultsTocotrienols exerted potent anti‐proliferative effects on both types of cell by inducing apoptosis, the underlying mechanism of cell death being ascertained using respective IC50 concentrations of all test compounds. There was marked induction of apoptosis in both cell lines by tocotrienols compared to treatment with Paclitaxel, which was used as positive control. This activity was found to be associated with cleavage of poly(ADP‐ribose) polymerase (a DNA repair protein), demonstrating involvement of the apoptotic cell death signalling pathway. Tocotrienols also inhibited expression of nuclear factor kappa‐B (NF‐κB), which in turn can increase sensitivity of cancer cells to apoptosis.ConclusionTocotrienols induced anti‐proliferative and apoptotic effects in association with DNA fragmentation, poly(ADP‐ribose) polymerase cleavage and NF‐κB inhibition in the two human breast cancer cell lines.
Effects of simvastatin and rosuvastatin on RAS protein, matrix metalloproteinases and NF‐κB in lung cancer and in normal pulmonary tissues
Authors: Falcone D. , Gallelli L. , Di Virgilio A. , Tucci L. , Scaramuzzino M. , Terracciano R. , Pelaia G. , Savino R. 
Published: March 2013

AbstractObjectivesIn this study, we have evaluated effects of 24‐hour treatments with simvastatin or rosuvastatin on RAS protein, NF‐κB and MMP expression in LC tissues obtained from 12 patients undergoing thoracic surgery.Materials and methodsNormal and lung tumour tissues obtained from each sample were exposed to simvastatin (2.5–30 μm) or rosuvastatin (1.25–30 μm) and western blot analysis was then performed.ResultsWe documented increased expression of proteins, MMP‐2, MMP‐9 and NF‐κB‐p65 in LC tissues, with respect to normal tissues (P < 0.01). In the malignant tissues, simvastatin and rosuvastatin significantly (P < 0.01) and dose‐dependently reduced RAS protein, MMP‐2/9 and NF‐κB‐p65 expression.ConclusionsIn conclusion, our results suggest that simvastatin and rosuvastatin could play a role in LC treatment by modulation of RAS protein, MMP‐2/9 and NF‐κB‐p65.
The role of parenting and dopamine D4 receptor gene polymorphisms in children's inhibitory control
Authors: Smith Heather J. , Kryski Katie R. , Sheikh Haroon I. , Singh Shiva M. , Hayden Elizabeth P. 
Published: March 2013

AbstractTemperamental effortful control has important implications for children's development. Although genetic factors and parenting may influence effortful control, few studies have examined interplay between the two in predicting its development. The current study investigated associations between parenting and a facet of children's effortful control, inhibitory control (IC), and whether these associations were moderated by whether children had a 7‐repeat variant of the DRD4 exon III VNTR. A community sample of 409 3‐year‐olds completed behavioural tasks to assess IC, and observational measures of parenting were also collected. Negative parenting was associated with lower child IC. The association between children's IC and positive parenting was moderated by children's DRD4 7‐repeat status, such that children with at least one 7‐repeat allele displayed lower IC than children without this allele when positive parenting was lower. These effects appeared to be primarily influenced by parent support and engagement. Results extend recent findings suggesting that some genetic polymorphisms may increase vulnerability to contextual influences.
Effortful control and parenting: Associations with HPA axis reactivity in early childhood
Authors: Kryski Katie R. , Dougherty Lea R. , Dyson Margaret W. , Olino Thomas M. , Laptook Rebecca S. , Klein Daniel N. , Hayden Elizabeth P. 
Published: March 2013

AbstractWhile activation of the hypothalamic‐pituitary‐adrenal (HPA) axis is an adaptive response to stress, excessive HPA axis reactivity may be an important marker of childhood vulnerability to psychopathology. Parenting, including parent affect during parent–child interactions, may play an important role in shaping the developing HPA system; however, the association of parent affect may be moderated by child factors, especially children's emerging self‐regulatory skills. We therefore tested the relationship between parent affectivity and 160 preschoolers’ cortisol reactivity during a laboratory visit, examining children's effortful control (EC) as a moderator. Greater parent negative affectivity was related to greater initial and increasing cortisol over time, but only when children were low in EC. Higher parent positive affectivity was related to a higher baseline cortisol for children with low EC and lower baseline cortisol for children with high EC. Results indicate that children's EC moderates the extent to which parent affect shapes stress reactive systems in early childhood.
Florivores on the dioecious shrub Eurya japonica and the preferences and performances of two polyphagous geometrid moths on male and female plants
Authors: Tsuji Kaoru , Sota Teiji 
Published: March 2013

AbstractFlowers of dioecious plants have sexually dimorphic traits that may affect florivore performances, and florivores may have preferences to plant sex that are correlated with their performance on different plant sexes. We investigated the florivory on a polygamodioecious evergreen shrub Eurya japonica in Japan to reveal florivores and their feeding patterns involved in sexually biased florivory on E. japonica flowers. Flowers of E. japonica were infested by lepidopteran and dipteran larvae and hemipteran insects. Lepidopteran larvae were chewers, dipteran larvae were gall makers and hemipteran insects were suckers. Chewed flowers were most frequent among infested flowers. Of florivores, lepidopteran larvae, mostly of Geometridae, were the important florivore that damaged flowers by chewing. Florivores infested male flower buds more often than female flower buds, but only a geometrid larvae Chloroclystis excise, which exclusively uses flower buds, showed the biased infection on male flowers. Rearing experiments for two other geometrid moths which use both leaves and flowers showed that the preference and performance of Ourapteryx nivea that fed mainly leaves did not differ between the plant sexes, whereas the development of Alcis angulifera larvae which fed both leaves and flowers was slower when they fed female than male leaves and flower buds. In addition, A. angulifera larvae fed fewer flower buds on female than on male plants. These results show that the male‐biased florivory on E. japonica trees is attributed mainly to the specialist florivore and also feeding preference for male flowers in an opportunistic florivore that feed both leaves and flowers.
Dynamics of intracellular calcium in cultured human keratinocytes after localized cell damage
Authors: Tsutsumi Moe , Goto Makiko , Denda Mitsuhiro 
Published: March 2013

AbstractRecovery of cultured keratinocytes after scratch damage is considered to be a wound‐healing model. In this study, we observed changes in intracellular calcium concentration ([Ca2+]i) in cultured human keratinocytes after scratch damage. Immediately after scratch damage, a wave of increased [Ca2+]i radiated outward from the damaged area and then disappeared gradually. But, [Ca2+]i remained elevated in a peripheral layer of cells around the damaged area for several minutes. This layer did not appear in calcium‐free medium. When the culture was switched to calcium‐free medium for 30 min immediately after scratch damage, then switched back to standard (Ca2+‐containing) medium, the recovery ratio after 24 h was approximately 25% lower than that of the culture in standard medium throughout. We speculate that delineation of damage sites by a layer of cells with increased [Ca2+]i might be part of a signalling pathway that appropriately directs the wound‐healing process in epidermis.
Interference fit effect on improving fatigue life of a holed single plate
Authors: Croccolo D. , De Agostinis M. , Ceschini L. , Morri A. , Marconi A. 
Published: March 2013

ABSTRACTThis paper deals with the influence of interference fit coupling on the fatigue strength of holed plates made of a medium‐carbon forging steel (35 KB2), heat treated by quenching followed by tempering, up to a hardness of about 350 BH, obtaining a sorbitic microstructure. Tensile and impact tests showed an ultimate tensile strength of about 1100 MPa, a yield strength of about 1000 MPa, an elongation to failure of 15% and an impact toughness KV of 43 J at room temperature. Axial fatigue tests were performed on holed specimens with or without a pin, made of the same material, press fitted and still left into their central hole. The tension–tension fatigue tests have been performed with a stress ratio R = 0.1. The effect on fatigue strength was investigated both experimentally and numerically. Three different conditions were investigated by using open hole specimens, specimens with 0.6% of nominal specific interference and specimens with 2% of nominal specific interference. The experimental stress‐life (S–N) curves pointed out an increased fatigue life of the interference fit specimens, compared with the open hole ones. The numerical investigation was performed in order to analyse the stress field by applying an elastic plastic 2D simulation, with commercial finite element software. The stress history and distribution around the interference‐fitted hole indicate a significant reduction of the stress amplitude produced by the external loading (remote stress) because a residual and compressive stress field is generated by the pin insertion.
Decision to transfer to an emergency department from residential aged care: A systematic review of qualitative research
Authors: Arendts Glenn , Quine Susan , Howard Kirsten 
Published: March 2013

AimIf developing policies to optimize quality acute care within residential aged care facilities (RACF) is a goal, understanding the factors that influence the decision to transfer a resident from RACF to hospital emergency departments is important. The aim of the present study was to review the published literature pertaining to transfer decisions.MethodsWe carried out a systematic review of the qualitative literature to ascertain key influences on transfer decisions amongst three key stakeholder groups – residents, their family and carers.ResultsFrom 11 papers we found two themes encompassing seven domains of influence. Transfers are influenced by an expectation or goal of improved resident clinical or quality of life outcomes – these are domains within the “resident dominant” theme. However, transfers also occur where there is no expectation of resident benefit. These domains, such as inadequate facility resourcing and care planning, are categorized within the “resident subordinate” theme.ConclusionTransfer decisions are often influenced by considerations beyond expected benefit to the individual resident. Conceptualizing influences on transfer decisions within this framework might assist clinicians and policy makers in the design and delivery of services for RACF residents. Geriatr Gerontol Int 2013; 13: 825–833.