bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptive phenotypic plasticity in the Midas cichlid fish pharyngeal jaw and its relevance in adaptive radiation
Authors: Muschick Moritz , Barluenga Marta , Salzburger Walter , Meyer Axel 
Published: April 2011

AbstractBackgroundPhenotypic evolution and its role in the diversification of organisms is a central topic in evolutionary biology. A neglected factor during the modern evolutionary synthesis, adaptive phenotypic plasticity, more recently attracted the attention of many evolutionary biologists and is now recognized as an important ingredient in both population persistence and diversification. The traits and directions in which an ancestral source population displays phenotypic plasticity might partly determine the trajectories in morphospace, which are accessible for an adaptive radiation, starting from the colonization of a novel environment. In the case of repeated colonizations of similar environments from the same source population this "flexible stem" hypothesis predicts similar phenotypes to arise in repeated subsequent radiations. The Midas Cichlid (Amphilophusspp.) in Nicaragua has radiated in parallel in several crater-lakes seeded by populations originating from the Nicaraguan Great Lakes. Here, we tested phenotypic plasticity in the pharyngeal jaw of Midas Cichlids. The pharyngeal jaw apparatus of cichlids, a second set of jaws functionally decoupled from the oral ones, is known to mediate ecological specialization and often differs strongly between sister-species.ResultsWe performed a common garden experiment raising three groups of Midas cichlids on food differing in hardness and calcium content. Analyzing the lower pharyngeal jaw-bones we find significant differences between diet groups qualitatively resembling the differences found between specialized species. Observed differences in pharyngeal jaw expression between groups were attributable to the diet's mechanical resistance, whereas surplus calcium in the diet was not found to be of importance.ConclusionsThe pharyngeal jaw apparatus of Midas Cichlids can be expressed plastically if stimulated mechanically during feeding. Since this trait is commonly differentiated - among other traits - between Midas Cichlid species, its plasticity might be an important factor in Midas Cichlid speciation. The prevalence of pharyngeal jaw differentiation across the Cichlidae further suggests that adaptive phenotypic plasticity in this trait could play an important role in cichlid speciation in general. We discuss several possibilities how the adaptive radiation of Midas Cichlids might have been influenced in this respect.
Clarifying mammalian RISC assembly in vitro
Authors: Tan Grace S , Garchow Barry G , Liu Xuhang , Metzler David , Kiriakidou Marianthi 
Published: April 2011

Abstract

Background
Argonaute, the core component of the RNA induced silencing complex (RISC), binds to mature miRNAs and regulates gene expression at transcriptional or post-transcriptional level. We recently reported that Argonaute 2 (Ago2) also assembles into complexes with miRNA precursors (pre-miRNAs). These Ago2:pre-miRNA complexes are catalytically active in vitro and constitute non-canonical RISCs.

Results
The use of pre-miRNAs as guides by Ago2 bypasses Dicer activity and complicates in vitro RISC reconstitution. In this work, we characterized Ago2:pre-miRNA complexes and identified RNAs that are targeted by miRNAs but not their corresponding pre-miRNAs. Using these target RNAs we were able to recapitulate in vitro pre-miRNA processing and canonical RISC loading, and define the minimal factors required for these processes.

Conclusions
Our results indicate that Ago2 and Dicer are sufficient for processing and loading of miRNAs into RISC. Furthermore, our studies suggest that Ago2 binds primarily to the 5'- and alternatively, to the 3'-end of select pre-miRNAs.
A Parametric Study Delineating Irreversible Electroporation from Thermal Damage Based on a Minimally Invasive Intracranial Procedure
Authors: Garcia Paulo A , Rossmeisl John H , Neal Robert E , Ellis Thomas L , Davalos Rafael V 
Published: April 2011

Abstract

Background
Irreversible electroporation (IRE) is a new minimally invasive technique to kill undesirable tissue in a non-thermal manner. In order to maximize the benefits from an IRE procedure, the pulse parameters and electrode configuration must be optimized to achieve complete coverage of the targeted tissue while preventing thermal damage due to excessive Joule heating.

Methods
We developed numerical simulations of typical protocols based on a previously published computed tomographic (CT) guided in vivo procedure. These models were adapted to assess the effects of temperature, electroporation, pulse duration, and repetition rate on the volumes of tissue undergoing IRE alone or in superposition with thermal damage.

Results
Nine different combinations of voltage and pulse frequency were investigated, five of which resulted in IRE alone while four produced IRE in superposition with thermal damage.

Conclusions
The parametric study evaluated the influence of pulse frequency and applied voltage on treatment volumes, and refined a proposed method to delineate IRE from thermal damage. We confirm that determining an IRE treatment protocol requires incorporating all the physical effects of electroporation, and that these effects may have significant implications in treatment planning and outcome assessment. The goal of the manuscript is to provide the reader with the numerical methods to assess multiple-pulse electroporation treatment protocols in order to isolate IRE from thermal damage and capitalize on the benefits of a non-thermal mode of tissue ablation.
Role of adhesion molecules and inflammation in Venezuelan equine encephalitis virus infected mouse brain
Authors: Sharma Anuj , Bhomia Manish , Honnold Shelley P , Maheshwari Radha K 
Published: April 2011

Abstract

Background
Neuroinvasion of Venezuelan equine encephalitis virus (VEEV) and subsequent initiation of inflammation in the brain plays a crucial role in the outcome of VEEV infection in mice. Adhesion molecules expressed on microvascular endothelial cells in the brain have been implicated in the modulation of the blood brain barrier (BBB) and inflammation in brain but their role in VEEV pathogenesis is not very well understood. In this study, we evaluated the expression of extracellular matrix and adhesion molecules genes in the brain of VEEV infected mice.

Findings
Several cell to cell adhesion molecules and extracellular matrix protein genes such as ICAM-1, VCAM-1, CD44, Cadherins, integrins, MMPs and Timp1 were differentially regulated post-VEEV infection. ICAM-1 knock-out (IKO) mice infected with VEEV had markedly reduced inflammation in the brain and demonstrated a delay in the onset of clinical symptoms of disease. A differential regulation of inflammatory genes was observed in the IKO mice brain compared to their WT counterparts.

Conclusions
These results improve our present understanding of VEEV induced inflammation in mouse brain.
Impact of chromium histidinate on high fat diet induced obesity in rats
Authors: Tuzcu Mehmet , Sahin Nurhan , Orhan Cemal , Agca Can Ali , Akdemir Fatih , Tuzcu Zeynep , Komorowski James , Sahin Kazim 
Published: May 2011

Abstract

Background
Chromium (Cr) is an essential trace element that has garnered interest for use as a weight loss aid, but its molecular mechanism in obesity is not clear. In this study, an attempt has been made to investigate the effects of chromium histidinate (CrHis) on glucose transporter-2 (GLUT-2), nuclear factor erythroid 2-related factor 2 (Nrf2), heme oxygenase-1 (HO-1), nuclear factor-kappa B (NF-κB p65) and the oxidative stress marker 4-hydroxynonenal adducts (HNE) expressions in liver of rats fed high fat diet (HFD).

Methods
Male Wistar rats (n = 40, 8 wk-old) were divided into four groups. Group I was fed a standard diet (12% of calories as fat); Group II was fed a standard diet and supplemented with 110 μg CrHis/kg BW/d; Group III was fed a HFD (40% of calories as fat); Group IV was fed HFD and supplemented with 110 μg CrHis/kg BW/d.

Results
Rats fed HFD possessed greater serum insulin (40 vs.33 pmol/L) and glucose (158 vs. 143 mg/dL) concentration and less liver Cr (44 vs.82 μg/g) concentration than rats fed the control diet. However, rats supplemented with CrHis had greater liver Cr and serum insulin and lower glucose concentration in rats fed HFD (P < 0.05). The hepatic nuclear factor-kappa B (NF-κB p65) and HNE were increased in high fat group compared to control group, but reduced by the CrHis administration (P < 0.05). The levels of hepatic Nrf2 and HO-1 were increased by supplementation of CrHis (P < 0.05).

Conclusion
These findings demonstrate that supplementation of CrHis is protective against obesity, at least in part, through Nrf2-mediated induction of HO-1 in rats fed high fat diet.
Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons
Authors: Cambray Guillaume , Sanchez-Alberola Neus , Campoy Susana , Guerin Émilie , Da Re Sandra , González-Zorn Bruno , Ploy Marie-Cécile , Barbé Jordi , Mazel Didier , Erill Ivan 
Published: April 2011

Abstract

Background
Integrons are found in hundreds of environmental bacterial species, but are mainly known as the agents responsible for the capture and spread of antibiotic-resistance determinants between Gram-negative pathogens. The SOS response is a regulatory network under control of the repressor protein LexA targeted at addressing DNA damage, thus promoting genetic variation in times of stress. We recently reported a direct link between the SOS response and the expression of integron integrases in Vibrio cholerae and a plasmid-borne class 1 mobile integron. SOS regulation enhances cassette swapping and capture in stressful conditions, while freezing the integron in steady environments. We conducted a systematic study of available integron integrase promoter sequences to analyze the extent of this relationship across the Bacteria domain.

Results
Our results showed that LexA controls the expression of a large fraction of integron integrases by binding to Escherichia coli-like LexA binding sites. In addition, the results provide experimental validation of LexA control of the integrase gene for another Vibrio chromosomal integron and for a multiresistance plasmid harboring two integrons. There was a significant correlation between lack of LexA control and predicted inactivation of integrase genes, even though experimental evidence also indicates that LexA regulation may be lost to enhance expression of integron cassettes.

Conclusions
Ancestral-state reconstruction on an integron integrase phylogeny led us to conclude that the ancestral integron was already regulated by LexA. The data also indicated that SOS regulation has been actively preserved in mobile integrons and large chromosomal integrons, suggesting that unregulated integrase activity is selected against. Nonetheless, additional adaptations have probably arisen to cope with unregulated integrase activity. Identifying them may be fundamental in deciphering the uneven distribution of integrons in the Bacteria domain.
Differences between psychopathy and other personality disorders: evidence from neuroimaging
Authors: Sarkar Sagari , Clark Ben S. , Deeley Quinton 
Published: April 2011

SummaryICD-10 and DSM-IV-TR diagnostic guidelines do not list psychopathy as a distinct psychiatric entity. However, there are significant overlaps between psychopathy and DSM-IV-TR Cluster B personality disorders. Neuroimaging studies implicate deficits in structure and function of frontal and limbic regions in this group of personality disorders, while highlighting both distinctions and overlaps between syndromes. Here, these data are reviewed and implications for diagnosis and clinical practice are discussed.
Association of Comorbidities With Overall Survival in Myelodysplastic Syndrome: Development of a Prognostic Model
Authors: Naqvi Kiran , Garcia-Manero Guillermo , Sardesai Sagar , Oh Jeong , Vigil Carlos E. , Pierce Sherry , Lei Xiudong , Shan Jianqin , Kantarjian Hagop M. , Suarez-Almazor Maria E. 
Published: May 2011

PurposePatients with cancer often experience comorbidities that may affect their prognosis and outcome. The objective of this study was to determine the effect of comorbidities on the survival of patients with myelodysplastic syndrome (MDS).Patients and MethodsWe conducted a retrospective cohort study of 600 consecutive patients with MDS who presented to MD Anderson Cancer Center from January 2002 to December 2004. The Adult Comorbidity Evaluation-27 (ACE-27) scale was used to assess comorbidities. Data on demographics, International Prognostic Scoring System (IPSS), treatment, and outcome (leukemic transformation and survival) were collected. Kaplan-Meier methods and Cox regression were used to assess survival. A prognostic model incorporating baseline comorbidities with age and IPSS was developed to predict survival.ResultsOverall median survival was 18.6 months. According to the ACE-27 categories, median survival was 31.8, 16.8, 15.2, and 9.7 months for those with none, mild, moderate, and severe comorbidities, respectively (P < .001). Adjusted hazard ratios were 1.3, 1.6, and 2.3 for mild, moderate, and severe comorbidities, respectively, compared with no comorbidities (P < .001). A final pognostic model including age, IPSS, and comorbidity score predicted median survival of 43.0, 23.0, and 9.0 months for lower-, intermediate-, and high-risk groups, respectively (P < .001).ConclusionComorbidities have a significant impact on the survival of patients with MDS. Patients with severe comorbidity had a 50% decrease in survival, independent of age and IPSS risk group. A comprehensive assessment of the severity of comorbidities helps predict survival in patients with MDS.
Progression From High-Grade Prostatic Intraepithelial Neoplasia to Cancer: A Randomized Trial of Combination Vitamin-E, Soy, and Selenium
Authors: Fleshner Neil E. , Kapusta Linda , Donnelly Bryan , Tanguay Simon , Chin Joseph , Hersey Karen , Farley Anne , Jansz Ken , Siemens D. Robert , Trpkov Kiril , Lacombe Louis , Gleave Martin , Tu Dongsheng , Parulekar Wendy R. 
Published: May 2011

Purpose High-grade prostatic intraepithelial neoplasia (HGPIN) is a putative precursor of invasive prostate cancer (PCa). Preclinical evidence suggests vitamin E, selenium, and soy protein may prevent progression of HGPIN to PCa. This hypothesis was tested in a randomized phase III double-blind study of daily soy (40 g), vitamin E (800 U), and selenium (200 μg) versus placebo. Patients and Methods Three hundred three men in 12 Canadian centers were analyzed. The main eligibility criterion was confirmed HGPIN in at least one of two biopsies within 18 months of random assignment. Treatment was administered daily for 3 years. Follow-up prostate biopsies occurred at 6, 12, 24, and 36 months postrandomization. The primary end point was time to development of invasive PCa. Kaplan-Meier plots and log-rank tests were used to compare two treatment groups for this end point. Results For all patients, the median age was 62.8 years. The median baseline prostate-specific antigen (PSA; n = 302) was 5.41 ug/L; total testosterone (n = 291) was 13.4 nmol/L. Invasive PCa developed among 26.4% of patients. The hazard ratio for the nutritional supplement to prevent PCa was 1.03 (95% CI, 0.67 to 1.60; P = .88). Gleason score distribution was similar in both groups with 83.5% of cancers graded Gleason sum of 6. Baseline age, weight, PSA, and testosterone did not predict for development of PCa. The supplement was well tolerated with flatulence reported more frequently (27% v 17%) among men receiving micronutrients. Conclusion This trial does not support the hypothesis that combination vitamin E, selenium, and soy prevents progression from HGPIN to PCa.
Phase II Trial of Bevacizumab in Recurrent or Persistent Endometrial Cancer: A Gynecologic Oncology Group Study
Authors: Aghajanian Carol , Sill Michael W. , Darcy Kathleen M. , Greer Benjamin , McMeekin D. Scott , Rose Peter G. , Rotmensch Jacob , Barnes Mack N. , Hanjani Parviz , Leslie Kimberly K. 
Published: May 2011

Purpose Bevacizumab, a recombinant humanized monoclonal antibody against vascular endothelial growth factor-A (VEGF-A), has clinical activity in multiple tumor types. We conducted a phase II trial to assess the activity and tolerability of single-agent bevacizumab in recurrent or persistent endometrial cancer (EMC). Patients and Methods Eligible patients had persistent or recurrent EMC after receiving one to two prior cytotoxic regimens, measurable disease, and Gynecologic Oncology Group performance status of ≤ 2. Treatment consisted of bevacizumab 15 mg/kg intravenously every 3 weeks until disease progression or prohibitive toxicity. VEGF-A was assessed by immunohistochemistry in archival tumor and by enzyme-linked immunosorbent assay in pretreatment plasma. Primary end points were progression-free survival (PFS) at 6 months and overall response rate. Results Fifty-six patients were enrolled. Fifty-two patients were eligible and evaluable. Median age was 62 years, and prior treatment consisted of one or two regimens in 33 (63.5%) and 19 (36.5%) patients, respectively. Twenty-nine patients (55.8%) received prior radiation. Adverse events were consistent with those expected with bevacizumab treatment. No GI perforations or fistulae were seen. Seven patients (13.5%) experienced clinical responses (one complete response and six partial responses; median response duration, 6.0 months), and 21 patients (40.4%) survived progression free for at least 6 months. Median PFS and overall survival times were 4.2 and 10.5 months, respectively. Suggested associations were observed between high VEGF-A and adjusted hazard of death or tumor response when evaluated in tumor/plasma or plasma, respectively. Conclusion Bevacizumab is well tolerated and active based on PFS at 6 months in recurrent or persistent EMC and warrants further investigation.
Efficient Risk Estimation via Nested Sequential Simulation
Authors: Broadie Mark , Du Yiping , Moallemi Ciamac C. 
Published: April 2011

We analyze the computational problem of estimating financial risk in a nested simulation. In this approach, an outer simulation is used to generate financial scenarios, and an inner simulation is used to estimate future portfolio values in each scenario. We focus on one risk measure, the probability of a large loss, and we propose a new algorithm to estimate this risk. Our algorithm sequentially allocates computational effort in the inner simulation based on marginal changes in the risk estimator in each scenario. Theoretical results are given to show that the risk estimator has a faster convergence order compared to the conventional uniform inner sampling approach. Numerical results consistent with the theory are presented.This paper was accepted by Gérard Cachon, stochastic models and simulation.
The Impact of Demand Aggregation Through Delayed Component Allocation in an Assemble-to-Order System
Authors: Bernstein Fernando , DeCroix Gregory A. , Wang Yulan 
Published: April 2011

We consider an assemble-to-order system in which multiple products are assembled from a common component and a set of product-dedicated components. Component capacities are chosen prior to a finite-horizon selling season, and the common component is allocated to the products based on observed demands. We propose a collection of allocation mechanisms involving varying degrees of demand aggregation, ranging from a scheme under which all demands are observed prior to making the allocation decision to allocations made for each arriving demand. In this context, we explore the impact of the allocation scheme on sales, profits, and capacity decisions, including the degree of capacity imbalance. We find that the benefit from increased demand aggregation is closely linked to the degree of capacity imbalance: profit gains from delayed allocation tend to be higher in systems in which the optimal capacity portfolio is highly unbalanced when the allocation decision is made after observing all demands. We develop insights into what detailed system parameters lead to the largest gains from demand aggregation and also explore the trade-offs associated with the choice of an allocation scheme when customers exhibit impatience if the allocation scheme forces them to wait to be served. This paper was accepted by Ananth Iyer, operations and supply chain management.
Investigating the asymmetry of English sibilant assimilation: Acoustic and EPG data
Authors: Pouplier Marianne , Hoole Philip , Scobbie James M. 
Published: May 2011

AbstractWe present tongue-palate contact (EPG) and acoustic data on English sibilant assimilation, with a particular focus on the asymmetry arising from the order of the sibilants. It is generally known that /s#ʃ/ sequences may display varying degrees of regressive assimilation in fluent speech, yet for /ʃ#s/ it is widely assumed that no assimilation takes place, although the empirical content of this assumption has rarely been investigated nor a clear theoretical explanation proposed. We systematically compare the two sibilant orders in word-boundary clusters. Our data show that /s#ʃ/ sequences assimilate frequently and this assimilation is strictly regressive. The assimilated sequence may be indistinguishable from a homorganic control sequence by our measures, or it can be characterized by measurement values intermediate to those typical for /ʃ/ or /s/. /ʃ#s/ sequences may also show regressive assimilation, albeit less frequently and to a lesser degree. Assimilated /ʃ#s/ sequences are always distinguishable from /s#s/ sequences. In a few cases, we identify progressive assimilation for /ʃ#s/. We discuss how to account for the differences in degree of assimilation, and we propose that the order asymmetry may arise from the different articulatory control structures employed for the two sibilants in conjunction with phonotactic probability effects.