bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome‐wide admixture and ecological niche modelling reveal the maintenance of species boundaries despite long history of interspecific gene flow
Authors: De La Torre Amanda R. , Roberts David R. , Aitken Sally N. 
Published: March 2014

AbstractThe maintenance of species boundaries despite interspecific gene flow has been a continuous source of interest in evolutionary biology. Many hybridizing species have porous genomes with regions impermeable to introgression, conferring reproductive barriers between species. We used ecological niche modelling to study the glacial and postglacial recolonization patterns between the widely hybridizing spruce speciesPicea glaucaandP. engelmanniiin western North America. Genome‐wide estimates of admixture based on a panel of 311 candidate gene single nucleotide polymorphisms (SNP) from 290 genes were used to assess levels of admixture and introgression and to identify loci putatively involved in adaptive differences or reproductive barriers between species. Our palaeoclimatic modelling suggests that these two closely related species have a long history of hybridization and introgression, dating to at least 21 000 years ago, yet species integrity is maintained by a combination of strong environmental selection and reduced current interspecific gene flow. Twenty loci showed evidence of divergent selection, including six loci that were both Fstoutliers and associated with climatic gradients, and fourteen loci that were either outliers or showed associations with climate. These included genes responsible for carbohydrate metabolism, signal transduction and transcription factors.
Interplay of transcriptional and small RNA‐dependent control mechanisms regulates chitosugar uptake in Escherichia coli and Salmonella
Authors: Plumbridge Jacqueline , Bossi Lionello , Oberto Jacques , Wade Joseph T. , Figueroa‐Bossi Nara 
Published: March 2014

SummaryEscherichia coli and Salmonella can use chitin‐derived oligosaccharides as carbon and nitrogen sources. Chitosugars traverse the outer membrane through a dedicated chitoporin, ChiP, and are transported across the cytoplasmic membrane by the chitobiose transporter (ChbBCA). Previous work revealed that synthesis of the chitoporin, ChiP, requires transcription of the chbBCARFG operon. A sequence from the chbBC portion of the transcript was shown to act as a decoy target for a regulatory small RNA, ChiX, that normally blocks chiP expression. ChiX is destabilized and degraded upon pairing with chbBC RNA. Here, we show that the chiP gene, like the chbBCARFG operon, is also downregulated at the transcriptional level by the NagC repressor. NagC repression is critical in maintaining chiP mRNA levels low enough, relative to ChiX, to allow full silencing by this sRNA. We also show that pairing of ChiX to chbBC RNA downregulates chbC under uninduced conditions, that is, when ChiX is in excess to the decoy sequence. Hence, under these conditions, chbBC RNA is not just a decoy, but a true target of ChiX regulation. Altogether these findings underscore the importance of stoichiometry in dictating the strength of the sRNA response and in differentiating the regulator from the regulatory target.
Gene expression related to seed shattering and the cell wall in cultivated and weedy rice
Authors: Nunes A. L. , Delatorre C. A. , Merotto A. 
Published: March 2014

AbstractSeed shattering is an evolutionary trait that is essential to the survival of wild and weedy rice. Discovery of the qSH1 gene in rice subspecies Japonica and Sh4 in the rice subspecies Indica indicated the possibility that seed shattering is governed by major genes in a qualitative manner. However, observation of the large variability of seed shattering in weedy rice has led us to hypothesise that other genes related to abscission layer integrity could also be important in the regulation of seed shattering in rice. Gene expression 10 days after pollination and nucleotide composition revealed that qSH1 and Sh4 that are described as major players in seed shattering were not important in weedy rice. High expression of the gene OsCPL1 was positively associated with the occurrence of high seed shattering in weedy rice, which did not concur in previous studies of cultivated rice. This result is related to the absence of four SNPs and an indel in the OsCPL1 gene in weedy rice that are related to seed shattering in previous studies. Analysis of the expression of six genes related to cell wall synthesis/degradation revealed the importance of the genes OsXTH8 and OsCel9D in seed shattering in weedy rice. Therefore, in addition to qSH1 and Sh4, the genes OsCPL1, OsXTH8 and OsCel9D should be considered in studies of rice evolution and in the development of mitigation approaches of gene flow in transgenic rice.
Hierarchical Models for Estimating State and Demographic Trends in US Death Penalty Public Opinion
Authors: Shirley Kenneth E. , Gelman Andrew 
Published: March 2014

SummaryOne of the longest running questions that has been regularly included in US national public opinion polls is ‘Are you in favor of the death penalty for persons convicted of murder?’. Because the death penalty is governed by state laws rather than federal laws, it is of special interest to know how public opinion varies by state, and how it has changed over time within each state. We combine dozens of national polls taken over a 50-year span and fit a Bayesian multilevel logistic regression model to estimate support for the death penalty as a function of the year, the state, state level variables and various individual level demographic variables. Among our findings were that support levels in northeastern and southern states have moved in opposite directions over the past 50 years, support among blacks has decreased relative to non-blacks, but at slightly different rates for men and women, and support among some education groups varies widely by region. Throughout the paper, we highlight the use of a variety of analytical and graphical tools for model understanding, including average predictive comparisons, finite population contrasts for overparameterized models and graphical summaries of posterior distributions of group level variance parameters.
Disseminated Cunninghamella bertholletiae infection with septic pulmonary embolism after allogeneic bone marrow transplantation
Authors: Matsumoto K. , Yamamoto W. , Ohgusa E. , Tanaka M. , Maruta A. , Ishigatsubo Y. , Kanamori H. 
Published: March 2014

AbstractMucormycosis in immunocompromised patients is often reported. We report a patient who developed non‐thrombotic pulmonary embolism due to Cunninghamella bertholletiae after allogeneic stem cell transplantation.
Using decision support for population tracking of adherence to recommended asthma guidelines
Authors: Ahmed Sara , Tamblyn Robyn , Winslade Nancy 
Published: March 2014

ObjectiveDecision support systems linked to administrative databases provide a unique opportunity to monitor adherence to guidelines and target disease management strategies towards patients not receiving guideline-based therapy. The objective of this study was to evaluate the discrepancy between actual asthma treatments prescribed by primary care physicians compared to those recommended by evidence-based guidelines using a decision support tool linked to a provincial health administrative database.DesignThe drug and medical services information of individuals with asthma was identified from the provincial health database and was pushed through an asthma decision support system (ADSS). Recommendations aimed at optimising asthma treatment were generated on two index dates, 15 September 2007 (index date 1) and 15 March 2008 (index date 2).SettingPrimary care settings in a large Canadian metropolitan area.ParticipantsIndividuals with asthma and provincial health insurance primary and secondary outcome measures: well controlled asthma.Results16 803 eligible individuals were identified on index date 1, and 18 103 on index date 2. The distribution of recommendation categories was similar on both index dates. 94% were classified as well controlled and 7% as not well controlled. Among well-controlled individuals, the largest proportion was in the maintain treatment category (63.8%), followed by the maintain/decrease treatment category (28.2%) and the decrease treatment category (2.7%). Almost all individuals who were not well controlled had the recommendation to increase treatment (88%) with a small proportion in the refer category (1%).ConclusionsThe ADSS was able to identify subgroups of patients from an administrative database that could benefit from a medication review and possible change. Decision support systems linked to an administrative database can be used to identify individuals with uncontrolled asthma or prescriptions that deviate from recommended treatment. When connected to the point of care, this can provide an opportunity for physicians to intervene early.
Endoscopic CO2 Laser Management of Chemoradiation-related Cricopharyngeal Stenosis
Authors: Silver Natalie , Gal T. J. 
Published: March 2014

Objective: Treatment of head and neck cancer with chemoradiation (CRT) can result in strictures of the cervical esophagus, often at the level of the cricopharyngeus. The objective of this study is to assess the feasibility of endoscopic CO2 laser cricopharyngeal myotomy for stricture ablation in the setting of prior CRT. Methods: A retrospective review of patients who underwent endoscopic CO2 laser cricopharyngeal myotomy for dysphagia after radiation for squamous cell carcinoma of the head and neck (SCCHN). Pre- and postoperative barium swallow and swallowing assessment were performed before and after surgery. Outcomes and complication rates were examined. Results: Endoscopic CO2 laser cricopharyngeal myotomy was performed in 10 patients with dysphagia secondary to cricopharyngeal stenosis/stricture, which developed following treatment for SCCHN with chemoradiation. All patients demonstrated radiographic improvement in stricture, with complete resolution of stricture in 9 of 10 patients. All patients noted improvement in dysphagia with 9 of 10 patients demonstrating significant advancement of diet by modified barium swallow. No complications were observed. Conclusion: Endoscopic CO2 cricopharyngeal myotomy can be performed safely in the setting of prior CRT, with significant improvement in swallowing in select patients. Indications and technical considerations will be discussed.
Bone Conduction Hearing: Device Auditory Capability to Aid in Device Selection
Authors: Syms Mark J. , Hernandez Kelly E. 
Published: March 2014

ObjectiveTo obtain identical laboratory measures of 8 (surgical and nonsurgical) bone conduction devices and relate them to clinical function.Study DesignEach device was measured with a single laboratory system and characterized with descriptive statistics.SettingLaboratory.Subjects and MethodsSeven surgical devices (Intenso, BP110, BP100, and Cordelle [Cochlear, Denver, Colorado]; Ponto Pro and Ponto Pro Power [Oticon Medical, Somerset, New Jersey]; and Alpha 2 [Sophono, Inc, Boulder, Colorado]) and 1 nonsurgical dental device (SoundBite; Sonitus Medical, Inc, San Mateo, California) constituted the independent variables. Measured maximum output and gain parameters were the dependent variables.ResultsMaximum output varied across devices in the pure‐tone average (PTA; 500‐3000 Hz) frequency range (mean, 109.7 dB re 1 µN; range, 98.8‐119.2 dB) and in the above‐PTA (4000‐8000 Hz) frequency range (mean, 102.6 dB re 1 µN; range, 88.99‐119.6 dB). Maximum gain varied in the PTA frequency range (mean, 40 dB; range, 29.1‐49.1 dB) and was higher in the frequency range above the PTA (mean, 32.0 dB; range, 20.8‐46.0 dB).ConclusionAll devices have sufficient maximum output and gain for the PTA frequency range for single‐sided deafness (SSD). The devices differed in maximum output and gain for the frequency range above the PTA, a consideration for accommodating presbycusis and optimizing auditory function for SSD. The surgical devices have less maximum output and gain in the above‐PTA range than in the PTA range. The nonsurgical dental device had the highest output (up to 30 dB higher) and gain (up to 26 dB higher) in the above‐PTA range.
Pneumatic thigh compression reduces calf volume and augments the venous return
Authors: Lattimer Christopher R , Kalodiki Evi , Azzam Mustapha , Geroulakos George 
Published: March 2014

Objectives Reactive hyperaemia following thigh compression increases arterial inflow and venous outflow. The net effect can be measured by changes in calf volume quantified using air-plethysmography. The objective was to investigate the effect of thigh compression on venous return. Method The right legs of 19 consecutive volunteers (14 male), median age 31 (25–56) years, were studied in the supine position using air-plethysmography. The clinical, etiological, anatomical, pathophysiological (CEAP) class was C0. A thigh-cuff, 12 cm wide, was inflated in increments of 10 mmHg, from 0 to 80 mmHg. After each inflation step, the calf volume increased to a plateau and was recorded. At 80 mmHg, the thigh-cuff was deflated suddenly with the calf volume decreasing until baseline. Calf volume changes were recorded and stored for analysis. Results There was a stepwise increase in the venous volume of the calf with each incremental rise in thigh-cuff pressure up to 80 mmHg (p < .0005, Friedman). The median (interquartile range) increase in venous volume from 0 to 80 mmHg was 87 (65–113) mL (p < .0005, Wilcoxon). The volume change below the original baseline following thigh-cuff release was −16 (−12 to −25) mL (p < .0005, Wilcoxon). Conclusions Once optimised, intermittent pneumatic compression of the thigh may have a therapeutic role in augmenting the venous return and reducing leg swelling in patients.
Comparison of Landing Biomechanics Between Male and Female Dancers and Athletes, Part 2
Authors: Liederbach Marijeanne , Kremenic Ian J. , Orishimo Karl F. , Pappas Evangelos , Hagins Marshall 
Published: March 2014

Background: Fatigue is strongly linked to an increased risk of injuries, including anterior cruciate ligament (ACL) ruptures. Part 1 of this study identified differences in the biomechanics of landing from a jump between dancers and team athletes, particularly female athletes, which may explain the epidemiological differences in ACL injuries between dancers and team athletes and the lack of a sex disparity within dancers. However, it is not known if these biomechanical variables change differently between team athletes and dancers in the face of fatigue. Purpose/Hypothesis: The purpose of this study was to compare dancers’ and team athletes’ resistance to fatigue and its effect on the biomechanics of single-legged drop landings. The primary hypotheses were that dancers may be more resistant than team athletes to the onset of fatigue and/or may have different biomechanical responses than athletes in landing tasks once fatigue has been achieved. Study Design: Controlled laboratory study. Methods: Kinematics and kinetics were recorded as 40 elite modern and ballet dancers (20 men and 20 women) and 40 team sport athletes (20 men and 20 women; National Collegiate Athletic Association Division I-III) performed single-legged drop landings from a 30-cm platform before and after a fatigue protocol consisting of step-ups and vertical jumps. Unfatigued and fatigued joint kinematics and kinetics were compared between groups and sexes with multivariate analyses of variance, followed by pairwise t tests as appropriate. Results: Dancers took longer ( P = .023) than team athletes to reach a similar state of fatigue. Multiple kinetic (eg, increased peak knee valgus moment; P < .001) and kinematic (eg, increased lateral and forward trunk flexion; P < .001 and P = .002, respectively) parameters of landing changed with fatigue, such that both fatigued dancers and athletes landed with mechanics that were more at risk for ACL injuries as compared with before fatigue. Conclusion: Dancers took significantly longer to reach fatigue than team athletes. Female athletes consistently exhibited landing patterns associated with a risk for ACL injuries when compared with the other 3 groups. Fatigue changed landing mechanics similarly in both dancers and athletes, such that all groups landed with worse alignment after being fatigued. Clinical Relevance: Dancers are more resistant to lower extremity fatigue than athletes, and this may partially explain the lower incidence of ACL injuries in both male and female dancers compared to team athletes. The extensive training in landing technique and daily practice that dancers undergo from a young age may be responsible for the higher levels of endurance.
Side peak cancellation method for sine-BOC(m,n)-modulated GNSS signals
Authors: Attia Salim , Rouabah Khaled , Chikouche Djamel , Flissi Mustapha 
Published: March 2014

Abstract
In this paper, we propose an efficient scheme for side peak cancelation in binary offset carrier (m,n) (BOC(m,n)) with integer modulation order. The proposed scheme reduces significantly the width of the main peak of the auto-correlation function (ACF) and thus the range of influence of the multipath (MP) in BOC-modulated signals. It is based on the use of reference ACFs like that of ideal pseudo random noise (PRN) code generated by linear feedback shift register (LFSR) and used in global positioning system (GPS) and the Russian Globalnaya Navigatsionnaya Sputnikovaya Sistema (GLONASS). In MP environment, the proposed method is used in combination with fast iterative maximum likelihood algorithm (FIMLA) that is adapted to future modernized GPS and Galileo signals. As a result, the obtained ACF of the proposed scheme does not contain any side peaks, and thus, the discriminator function (DF) has no ambiguity in the delay-locked loop (DLL) code tracking operation. The simulation results show that the proposed technique has superior performances in MP mitigation and permits the same resistance to noise compared to the traditional techniques.
Genetic polymorphisms in warfarin and tacrolimus-related genes VKORC1, CYP2C9 and CYP3A5 in the Greek-Cypriot population
Authors: Hadjipanagi Despina , Chrysanthou Stephanie , Voskarides Konstantinos , Deltas Constantinos 
Published: March 2014

Abstract

Background
Two variants in the gene encoding the cytochrome P450 2C9 enzyme (CYP2C9) are considered the most significant genetic risk factors associated with bleeding after warfarin prescription. A variant in the vitamin K epoxide reductase (VKORC1) has been also associated by several studies with warfarin response. Another variant in the P450 3A5 enzyme (CYP3A5) gene is known to affect the metabolism of many drugs, including tacrolimus.

Findings
We conducted a population genetic study in 148 unrelated healthy Greek-Cypriot volunteers (through PCR-RFLP assays), in order to determine the frequencies of the above pharmacogenetics variants and to compare allele frequencies with those in other major ethnic groups. The allele frequencies of CYP2C9*2, CYP2C9*3 and CYP3A5*3 were found to be 0.162, 0.112 and 0.943 respectively, whereas VKORC1 - 1639A was 0.534. The latter frequency differs significantly when compared with Caucasians, Asians and Africans (p < 0.001) and is still significant when compared with the geographically and culturally closely related to Greek-Cypriots, Hellenes of Greece (p = 0.01). Interestingly ~18% of our population are carriers of four or three risk alleles regarding warfarin sensitivity, therefore they have a high predisposition for bleeding after taking high or even normal warfarin doses.

Conclusions
Our data show no significant difference in the frequency of CYP2C9 and CYP3A5 allelic variants when compared to the Caucasian population, but differ significantly when compared with Africans and Asians (p < 0.001). Also, the frequency of variant VKORC1 - 1639A differs between Greek-Cypriots and every other population we compared. Finally, about 1/5 Greek-Cypriots carry three or four risk alleles and ~50% of them carry at least two independent risk alleles regarding warfarin sensitivity, a potentially high risk for over-anticoagulation.
Trastuzumab emtansine: mechanisms of action and drug resistance
Authors: Barok Mark , Joensuu Heikki , Isola Jorma 
Published: March 2014

AbstractTrastuzumab emtansine (T-DM1) is an antibody-drug conjugate that is effective and generally well tolerated when administered as a single agent to treat advanced breast cancer. Efficacy has now been demonstrated in randomized trials as first line, second line, and later than the second line treatment of advanced breast cancer. T-DM1 is currently being evaluated as adjuvant treatment for early breast cancer. It has several mechanisms of action consisting of the anti-tumor effects of trastuzumab and those of DM1, a cytotoxic anti-microtubule agent released within the target cells upon degradation of the human epidermal growth factor receptor-2 (HER2)-T-DM1 complex in lysosomes. The cytotoxic effect of T-DM1 likely varies depending on the intracellular concentration of DM1 accumulated in cancer cells, high intracellular levels resulting in rapid apoptosis, somewhat lower levels in impaired cellular trafficking and mitotic catastrophe, while the lowest levels lead to poor response to T-DM1. Primary resistance of HER2-positive metastatic breast cancer to T-DM1 appears to be relatively infrequent, but most patients treated with T-DM1 develop acquired drug resistance. The mechanisms of resistance are incompletely understood, but mechanisms limiting the binding of trastuzumab to cancer cells may be involved. The cytotoxic effect of T-DM1 may be impaired by inefficient internalization or enhanced recycling of the HER2-T-DM1 complex in cancer cells, or impaired lysosomal degradation of trastuzumab or intracellular trafficking of HER2. The effect of T-DM1 may also be compromised by multidrug resistance proteins that pump DM1 out of cancer cells. In this review we discuss the mechanism of action of T-DM1 and the key clinical results obtained with it, the combinations of T-DM1 with other cytotoxic agents and anti-HER drugs, and the potential resistance mechanisms and the strategies to overcome resistance to T-DM1.
Renal replacement therapy for critically ill patients: an intermittent continuity
Authors: Ricci Zaccaria , Romagnoli Stefano 
Published: March 2014

AbstractChoice of the right renal replacement therapy for severe acute kidney injury in critically ill patients has been investigated many times in the last two decades. Although some questions have been answered, in current practice many different approaches are still used in the ICU. One basic and important issue is the frequency of renal replacement delivery: apart from pathophysiological speculations, in terms of hard outcomes (namely mortality and length of hospital stay) should dialysis be delivered continuously or intermittently? The authors of the CONVINT study provided a (last) response to this debate: in expert hands, the two treatments provide similar outcomes. This study confirms previous studies and is also important for other aspects, such as the possibility that the two modalities are complementary and may be indicated for different purposes.