bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying biases at different spatial and temporal scales of diversification: a case study in the Neotropical parrotlet genus Forpus
Authors: Smith Brian Tilston , Ribas Camila C. , Whitney Bret M. , HernÁndez‐baÑos Blanca E. , Klicka John 
Published: November 2012

AbstractThe temporal origins of the extraordinary biodiversity of the Neotropical region are highly debated. Recent empirical work has found support for alternative models on the tempo of speciation in Neotropical species further fuelling the debate. However, relationships within many Neotropical lineages are poorly understood, and it is unclear how this uncertainty impacts inferences on the evolution of taxa in the region. We examined the robustness of diversification patterns in the avian genus Forpus by testing whether the use of different units of biodiversity (i.e. biological species and statistically inferred species) impacted diversification rates and inferences regarding important biogeographic breaks in the genus. We found that the best‐fit model of diversification for the biological species data set was a declining rate of diversification; whereas a model of constant diversification was the best‐fit model for statistically inferred species or subspecies. Moreover, the relative importance of different landscape features in delimiting genetic structure across the landscape varied across data sets with differing units of biodiversity. Patterns based on divergence times among biological species indicated old speciation events across major geographic and river barriers. In contrast, data sets more inclusive of the diversity in Forpus illustrate the role of both old divergence across major landscape features and more recent divergences that are possibly attributed to Pleistocene climatic changes. Overall, these results indicate that conflicting models on the temporal origins of Neotropical birds may be attributable to sampling biases.
Amplicon‐pyrosequencing‐based detection of compositional shifts in bryophyte‐associated fungal communities along an elevation gradient
Authors: Davey Marie L. , Heegaard Einar , Halvorsen Rune , Kauserud Håvard , Ohlson Mikael 
Published: November 2012

AbstractAlthough bryophytes are a dominant vegetation component of boreal and alpine ecosystems, little is known about their associated fungal communities. HPLC assays of ergosterol (fungal biomass) and amplicon pyrosequencing of the ITS2 region of rDNA were used to investigate how the fungal communities associated with four bryophyte species changed across an elevational gradient transitioning from conifer forest to the low‐alpine. Fungal biomass and OTU richness associated with the four moss hosts did not vary significantly across the gradient (P > 0.05), and both were more strongly affected by host and tissue type. Despite largely constant levels of fungal biomass, distinct shifts in community composition of fungi associated with Hylocomium, Pleurozium and Polytrichum occurred between the elevation zones of the gradient. This likely is a result of influence on fungal communities by major environmental factors such as temperature, directly or indirectly mediated by, or interacting with, the response of other components of the vegetation (i.e. the dominant trees). Fungal communities associated with Dicranum were an exception, exhibiting spatial autocorrelation between plots, and no significant structuring by elevation. Nevertheless, the detection of distinct fungal assemblages associated with a single host growing in different elevation zones along an elevational gradient is of particular relevance in the light of the ongoing changes in vegetation patterns in boreal and alpine systems due to global climate warming.
Asymmetric hybridization and gene flow between Joshua trees (Agavaceae: Yucca) reflect differences in pollinator host specificity
Authors: Starr Tyler N. , Gadek Katherine E. , Yoder Jeremy B. , Flatz Ramona , Smith Christopher I. 
Published: November 2012

AbstractThe angiosperms are by far the largest group of terrestrial plants. Their spectacular diversity is often attributed to specialized pollination. Obligate pollination mutualisms where both a plant and its pollinator are dependent upon one another for reproduction are thought to be prone to rapid diversification through co‐evolution and pollinator isolation. However, few studies have evaluated the degree to which pollinators actually mediate reproductive isolation in these systems. Here, we examine evidence for hybridization and gene flow between two subspecies of Joshua tree (Yucca brevifolia brevifolia and Yucca brevifolia jaegeriana) pollinated by two sister species of yucca moth. Previous work indicated that the pollinators differ in host specificity, and DNA sequence data suggested asymmetric introgression between the tree subspecies. Through intensive sampling in a zone of sympatry, a large number of morphologically intermediate trees were identified. These included trees with floral characters typical of Y. b. jaegeriana, but vegetative features typical of Y. b. brevifolia. The opposite combination—Y. b. brevifolia flowers with Y. b. jaegeriana vegetative morphology—never occurred. Microsatellite genotyping revealed a high frequency of genetically admixed, hybrid trees. Coalescent‐based estimates of migration indicated significant gene flow between the subspecies and that the direction of gene flow matches differences in pollinator host fidelity. The data suggest that pollinator behaviour determines the magnitude and direction of gene flow between the two subspecies, but that specialized pollination alone is not sufficient to maintain species boundaries. Natural selection may be required to maintain phenotypic differences in the face of ongoing gene flow.
Nus transcription elongation factors and RNase III modulate small ribosome subunit biogenesis in Escherichia coli
Authors: Bubunenko Mikhail , Court Donald L. , Al Refaii Abdalla , Saxena Shivalika , Korepanov Alexey , Friedman David I. , Gottesman Max E. , Alix Jean‐Hervé 
Published: November 2012

SummaryEscherichia coli NusA and NusB proteins bind specific sites, such as those in the leader and spacer sequences that flank the 16S region of the ribosomal RNA transcript, forming a complex with RNA polymerase that suppresses Rho‐dependent transcription termination. Although antitermination has long been the accepted role for Nus factors in rRNA synthesis, we propose that another major role for the Nus‐modified transcription complex in rrn operons is as an RNA chaperone insuring co‐ordination of 16S rRNA folding and RNase III processing that results in production of proper 30S ribosome subunits. This contrarian proposal is based on our studies of nusA and nusB cold‐sensitive mutations that have altered translation and at low temperature accumulate 30S subunit precursors. Both phenotypes are suppressed by deletion of RNase III. We argue that these results are consistent with the idea that the nus mutations cause altered rRNA folding that leads to abnormal 30S subunits and slow translation. According to this idea, functional Nus proteins stabilize an RNA loop between their binding sites in the 5′ RNA leader and on the transcribing RNA polymerase, providing a topological constraint on the RNA that aids normal rRNA folding and processing.
Effect of lateral positioning on gastroesophageal reflux (GER) and underlying mechanisms in GER disease (GERD) patients and healthy controls
Authors: Loots C. , Smits M. , OMARI T. , Bennink R. , Benninga M. , VAN WIJK M. 
Published: November 2012

AbstractBackground  Posture has been shown to influence the number of transient lower esophageal sphincter relaxation (TLESRs) and gastroesophageal reflux (GER), however, the physiology explaining the influence of right lateral position (RLP), and left lateral position (LLP) is not clear. The aim of this study was to determine the influence of RLP and LLP on TLESRs and GERD after a meal in GER disease (GERD) patients and healthy controls (HC) while monitoring gastric distension and emptying.Methods  Ten GERD patients and 10 HC were studied for 90 min (30 min test meal infusion, 30 min postprandial in either RLP or LLP (randomly assigned) and 30 min in alternate position). The study was repeated on a separate day in reverse position order. TLESRs, GER, and gastric emptying rate were recorded using manometry, multichannel intraluminal impedance, and 13C‐octanoate breath tests. Gastric distension was visualized by five serial gastric volume scintigraphy scans during the first 30 min.Key Results  Gastroesophageal reflux, (GER) disease patients had increased numbers of TLESRs in RLP compared to LLP in the first postprandial hour [5 (4–14) and 4.5 (2–6), respectively, P = 0.046] whereas the number of TLESRs was not different in RLP and LLP [4 (2–4) and 4 (3–6), respectively, P = 0.7] in HC. Numbers of GER increased similar to TLESRs in GERD patients. In GERD patients, gastric emptying reached peak 13CO2 excretion faster and proximal gastric distension was more pronounced.Conclusions & Inferences  In GERD patients, TLESRs, GER, distension of proximal stomach, and gastric emptying are increased in RLP compared to LLP. This effect is not seen in HC.
miR‐370 modulates insulin receptor substrate‐1 expression and inhibits the tumor phenotypes of oral carcinoma
Authors: Chang K‐W , Chu T‐H , Gong N‐R , Chiang W‐F , Yang C‐C , Liu C‐J , Wu C‐H , Lin S‐C 
Published: November 2012

BackgroundMicroRNAs play important roles in carcinogenesis. A preliminary screening study suggested that down‐regulation of miR‐370 occurs in oral squamous cell carcinoma (OSCC) tissue. Insulin receptor substratre‐1 (IRS‐1) is the substrate of insulin‐like growth factor receptor (IGFR), which modulates AKT/mTOR activation in malignancies. The relationship between miR‐370 and IRS‐1, and their functional roles in OSCC pathogenesis are unclear.Materials and MethodsPrimary OSCC specimens were examined for miR‐370 expression. Exogenous expression of miR‐370 was established using both stable subclones and transient expression, and these were used to gain insights into miR‐370's functions in OSCC cells. Knockdown of miR‐370 and IRS‐1 was also carried out in OSCC cells using a small interference oligonucleotide approach.ResultsSquamous cell carcinoma tissues with perineural invasion had lowered miR‐370 expression compared with contrasting OSCC. OSCC cells also exhibited lower miR‐370 expression than normal oral keratinocytes, and this can be reversed by treatment with 5‐aza‐2′‐deoxycytidine. Exogenous miR‐370 expression decreases the migration and anchorage‐independent growth of OSCC cells, which implies a suppressor role for miR‐370. The enhancement of anchorage‐independent growth of OSCC cells through miR‐370 inhibiting can be reduced by knockdown of IRS‐1 expression.ConclusionThis study concludes that miR‐370 is able to target IRS‐1 for oral tumorigenesis.
Socioeconomic burden of lymphatic filariasis in Georgetown, Guyana
Authors: Tyrell Ede 
Published: November 2012

AbstractObjectiveTo assess the socioeconomic impact of lymphatic filariasis (LF) in Guyana.MethodsObservational, cross‐sectional study of 50 persons with chronic LF attending the Filariasis Clinic who were selected as the cases; and 50 persons with chronic skin conditions but no chronic LF, attending the Skin Clinic who were selected as the controls. The two groups were assessed using semi‐structured interviews.ResultsSocioeconomic impact was statistically significant, especially with respect to ‘having to change jobs’ and experiencing major emotional and financial changes (P < 0.05). Fifty‐six per cent of cases reported a major change since their diagnosis, whereas only 32% of controls did. Cases were less likely to be able to dress themselves and walk inside and outside the house than controls; they were three times more likely to spend money on transportation than controls (OR, 3.04 95% CI 1.11, 8.44).ConclusionPatients with chronic LF face a considerable burden, which should be addressed as part of the Elimination Programme. One way in which this can be done is to provide free transportation for patients with chronic LF to and from Filariasis Clinics.
Interleukin‐1β blockade improves cardiac remodelling after myocardial infarction without interrupting the inflammasome in the mouse
Authors: Toldo Stefano , Mezzaroma Eleonora , Van Tassell Benjamin W. , Farkas Daniela , Marchetti Carlo , Voelkel Norbert F. , Abbate Antonio 
Published: November 2012

New Findings
What is the central question of this study?The formation of the cryopyrin inflammasome in the heart induces an intense inflammatory response during acute myocardial infarction, which mediates further damage and promotes adverse cardiac remodelling. The present study investigates the role of interleukin‐1β in mediating the pathological effects of the inflammasome in the heart.
What is the main finding and its importance?Blockade of interleukin‐1β improves cardiac remodelling after acute myocardial infarction in the mouse by inhibiting apoptosis without affecting the formation or the activity of the inflammasome in the heart. These findings suggest that interleukin‐1β mediates the deleterious effects on the heart during the sterile inflammatory response.
The formation of the cryopyrin inflammasome in the heart induces an intense inflammatory response during acute myocardial infarction (AMI), which mediates further damage and promotes adverse cardiac remodelling. Active interleukin‐1β (IL‐1β) is a key product of the inflammasome, being cleaved by active caspase‐1. The aim of this study was to dissect the role of IL‐1β from that of the inflammasome by using a neutralizing monoclonal antibody directed against IL‐1β and measuring the intensity of the inflammatory response, the activity of caspase‐1 in the inflammasome, cardiomyocyte apoptosis and cardiac remodelling in a mouse model of non‐reperfused AMI. A mouse monoclonal IgG2a antibody directed against IL‐1β (IL‐1β‐AB; 10 mg kg−1) was given i.p. immediately after surgery and repeated 1 week later. Cardiac tissue was analysed at 72 h after surgery in a subgroup of mice for inflammasome aggregates and caspase‐1 activity (inflammasome) and for DNA fragmentation and caspase‐3 activity (apoptosis). All sham‐operated mice were alive at 10 weeks, whereas 40% of the control‐antibody‐treated mice and 30% of the IL‐1β‐AB‐treated mice died during the 4 weeks after surgery. When compared with vehicle, treatment with the IL‐1β‐AB did not affect inflammasome formation or caspase‐1 activation in the heart tissue at 72 h after AMI nor circulating plasma IL‐6 levels, but did inhibit cardiomyocyte apoptosis, limit left ventricular enlargement by 40% (P < 0.01) and improve systolic dysfunction by 17% (P < 0.01) after AMI. These findings suggest that IL‐1β mediates the deleterious effects on the heart during the sterile inflammatory response.
Increasing brain serotonin corrects CO2 chemosensitivity in methyl‐CpG‐binding protein 2 (Mecp2)‐deficient mice
Authors: Toward Marie A. , Abdala Ana P. , Knopp Sharon J. , Paton Julian F. R. , Bissonnette John M. 
Published: November 2012

New Findings
What is the central question of this study?Mice deficient in methyl‐CpG‐binding protein 2 (Mecp2; a model of Rett syndrome) display reduced CO2 chemosensitivity, which may contribute to their breathing abnormalities. Patients and mice show reduced levels of brain 5‐HT, which is important in central chemosensitivity. It is not known whether increasing 5‐HT in this mouse model would improve their respiratory response to CO2.
What is the main finding and its importance?We show, for the first time, that females heterozygous for the Mecp2 mutation have a higher hypocapnic threshold for apnoeas versus wild‐type mice and that increasing 5‐HT in Mecp2‐null males, with citalopram, can correct CO2 chemosensitivity, a finding that may be important clinically.
Mice deficient in the transcription factor methyl‐CpG‐binding protein 2 (Mecp2), a mouse model of Rett syndrome, display reduced CO2 chemosensitivity, which may contribute to their breathing abnormalities. In addition, patients with Rett syndrome and male mice that are null for Mecp2 show reduced levels of brain serotonin (5‐HT). Serotonin is known to play a role in central chemosensitivity, and we hypothesized that increasing the availability of 5‐HT in this mouse model would improve their respiratory response to CO2. Here we determined the apnoeic threshold in heterozygous Mecp2‐deficient female mice and examined the effects of blocking 5‐HT reuptake on the CO2 response in Mecp2‐null male mice. Studies were performed in B6.129P2(C)‐Mecp2τm1.1Bird null males and heterozygous females. In an in situ preparation, seven of eight Mecp2‐deficient heterozygous females showed arrest of phrenic nerve activity when arterial CO2 was lowered to 3%, whereas the wild‐types maintained phrenic nerve amplitude at 53 ± 3% of maximal. In vivo plethysmography studies were used to determine CO2 chemosensitivity in null males. These mice were exposed sequentially to 1, 3 and 5% CO2. The percentage increase in minute ventilation in response to increased inspired CO2 was less in Mecp2−/y than in Mecp2+/y mice. Pretreatment with citalopram, a selective 5‐HT reuptake inhibitor (2.5 mg kg−1 i.p.), 40 min prior to CO2 exposure, in Mecp2−/y mice resulted in an improvement in CO2 chemosensitivity to wild‐type levels. These results suggest that decreased 5‐HT in Mecp2‐deficient mice reduces CO2 chemosensitivity, and restoring 5‐HT levels can reverse this effect.
Similar skeletal muscle angiogenic and mitochondrial signalling following 8 weeks of endurance exercise in mice: discontinuous versus continuous training
Authors: Malek Moh H. , Hüttemann Maik , Lee Icksoo , Coburn Jared W. 
Published: November 2012

New Findings
What is the central question of this study?Little is known about skeletal muscle adaptation to discontinuous endurance training. Despite little research, it has been suggested that accumulating 30 min of endurance exercise daily may result in similar adaptations in the working muscle to a 30 min exercise bout.
What is the main finding and its importance?The unique finding of the present investigation was that 10 min of continuous endurance training performed three times daily results in similar adaptations of the angiogenic and mitochondrial signalling pathways to 30 min of continuous exercise. Taken together, these adaptations in the working muscle improved exercise tolerance.
Little is known about skeletal muscle adaptation to discontinuous endurance training. It has been suggested that accumulating 30 min of endurance exercise daily may result in similar adaptations in the working muscle to a 30 min exercise bout. The purposes of the present investigation, therefore, were to conduct an 8 week continuous or discontinuous endurance training regimen and determine the following: (i) whether treadmill exercise capacity differs between the two training regimens; and (ii) whether the angiogenic and mitochondrial signalling pathways are differentially activated in the two training regimens. Twenty‐four young adult male FVB/NJ mice were randomized into the following three groups: control; continuous treadmill endurance training for 30 min five times a week; or discontinuous treadmill endurance training for a total of 30 min five times per week for three 10 min intervals with 2 h rest between intervals. After the intervention, endurance capacity increased by 60% (P < 0.001) in both exercise groups compared to control animals. For the quadriceps muscle, anti‐angiogenic regulators (thrombospondin‐1 and ADAMTS1) were reduced by 50–70% (P < 0.001) with either exercise regimen. In addition, phosphorylation of p38 mitogen‐activated protein kinase signalling increased by 50–300% (P < 0.001), which corresponded to an increase in peroxisome proliferator‐activated receptor γ coactivator 1 β (PGC‐1β) protein expression. These findings suggest that accumulating 30 min of endurance exercise in 10 min sessions results in similar endurance training adaptations in skeletal muscle to a 30 min exercise bout.
Quality of descriptions of treatments: a review of published randomised controlled trials
Authors: Schroter Sara , Glasziou Paul , Heneghan Carl 
Published: November 2012

ObjectivesTo be useable in clinical practise, treatments studied in trials must provide sufficient information to enable clinicians and researchers to replicate. We sought to assess the completeness of treatment descriptions in published randomised controlled trials (RCTs) using a checklist and to determine the extent to which peer reviewers and editors comment on the quality of reporting of treatments.DesignA cross-sectional study.SettingTrials published in theBMJ, a general medical journal.ParticipantsFifty-one trials published in theBMJwere independently evaluated by two raters using a checklist. Reviewers’ and editors’ comments were also assessed for statements on treatment descriptions.Primary and secondary outcome measuresProportion of trials rated as replicable (primary outcome).ResultsFor 57% (29/51) of the papers, published treatment descriptions were not considered sufficient to allow replication. Most poorly described aspects were the actual procedures involved including the sequencing of the technique (what happened and when) and the physical or informational materials used (eg, training materials): 53% and 43% not clear, respectively. For a third of treatments, the dose/duration of individual sessions was not clear and for a quarter the schedule (interval, frequency, duration or timing) was not clear. Although the majority of problems were not picked up by reviewers and editors, when they were detected only about two-thirds were fixed before publication.ConclusionsJournals wanting to publish the research of use to practising healthcare professionals need to pay more attention to descriptions of treatments. Our checklist, may be useful for reviewers, and editors and could help ensure that important details of treatments are provided before papers are in the public domain.
Dimensions of the posterior cerebral circulation: an analysis based on advanced non-invasive imaging
Authors: Rai Ansaar T , Rodgers Daniel , Williams Eric A , Hogg Jeffery P 
Published: November 2012

BackgroundOur goal was to provide measurements of the posterior cerebral circulation using non-invasive imaging and advanced software analysis tools.Methods100 consecutive patients aged ≥40 years (50 men and 50 women) who had undergone CT angiography (CTA) but had no vascular abnormality were analyzed. Specific software was used to make vessel measurements along the center line. The length of the intracranial vertebral artery (VA), the basilar artery (BA) and the distance from the mid-basilar artery to the posterior cerebral artery (mBA-PCA) was recorded. Vessel diameter was measured at the proximal and distal ends of these vessel lengths. Vessel taper was calculated as the change in diameter in millimeters per centimeter of length.ResultsThe mean lengths of the intracranial VA, the BA and the mBA-PCA were 40±10.6 mm, 27.3±5.7 mm and 25.6±4.3 mm, respectively. The proximal and distal diameters were 3.9±0.8 mm and 2.8±0.6 mm for the VA and 3.6±0.6 mm and 3.1±0.5 mm for the BA, respectively. The mean mid-BA diameter and the proximal PCA diameter were 3.2±0.5 mm and 2.2±0.4 mm, respectively. There was a significant increase in arterial caliber in patients aged ≥60 years compared with those aged 40–59 years. Men also tended to have longer vessels with a larger diameter than women.ConclusionsAdvanced software and non-invasive imaging can be used to perform accurate vessel analysis. The posterior circulation measurements showed an increase in arterial caliber with age. This baseline information may be useful in planning neurovascular procedures and endovascular device development.