bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of functional genetic variation in exome sequence analysis
Authors: Jaffe Andrew , Wojcik Genevieve , Chu Audrey , Golozar Asieh , Maroo Ankit , Duggal Priya , Klein Alison P 
Published: December 2011

Abstract
Recent technological advances have allowed us to study individual genomes at a base-pair resolution and have demonstrated that the average exome harbors more than 15,000 genetic variants. However, our ability to understand the biological significance of the identified variants and to connect these observed variants with phenotypes is limited. The first step in this process is to identify genetic variation that is likely to result in changes to protein structure and function, because detailed studies, either population based or functional, for each of the identified variants are not practicable. Therefore algorithms that yield valid predictions of a variant’s functional significance are needed. Over the past decade, several programs have been developed to predict the probability that an observed sequence variant will have a deleterious effect on protein function. These algorithms range from empirical programs that classify using known biochemical properties to statistical algorithms trained using a variety of data sources, including sequence conservation data, biochemical properties, and functional data. Using data from the pilot3 study of the 1000 Genomes Project available through Genetic Analysis Workshop 17, we compared the results of four programs (SIFT, PolyPhen, MAPP, and VarioWatch) used to predict the functional relevance of variants in 101 genes. Analysis was conducted without knowledge of the simulation model. Agreement between programs was modest ranging from 59.4% to 71.4% and only 3.5% of variants were classified as deleterious and 10.9% as tolerated across all four programs.
Advantages of adjuvant chemotherapy for patients with triple-negative breast cancer at Stage II: usefulness of prognostic markers E-cadherin and Ki67
Authors: Kashiwagi Shinichiro , Yashiro Masakazu , Takashima Tsutomu , Aomatsu Naoki , Ikeda Katsumi , Ogawa Yoshinari , Ishikawa Tetsuro , Hirakawa Kosei 
Published: December 2011

Abstract
Introduction
Triple-negative breast cancer (TNBC), which is characterized by negativity for estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 (HER2), is a high risk breast cancer that lacks specific targets for treatment selection. Chemotherapy is, therefore, the primary systemic modality used in the treatment of this disease, but reliable parameters to predict the chemosensitivity of TNBC have not been clinically available.

Methods
A total of 190 TNBC patients who had undergone a curative resection of a primary breast cancer were enrolled. The adjuvant chemotherapy was performed for 138 (73%) of 190 TNBC cases; 60 cases had an anthracyclin-based regimen and 78 a 5-fluorouracil-based regimen. The prognostic value of E-cadherin, Ki67 and p53 expression in the outcome of TNBC patients with adjuvant chemotherapy was evaluated by immunohistochemistry.

Results
The adjuvant therapy group, especially those with Stage II TNBC, had a more favorable prognosis than the surgery only group (P = 0.0043), while there was no significant difference in prognosis between the anthracyclin-based regimen and 5-fluorouracil-based regimen. Patients with E-cadherin-negative and Ki67-positive expression showed significantly worse overall survival time than those with either E-cadherin-positive or Ki67-negative expression (P < 0.001). Multivariate analysis showed that the combination of E-cadherin-negative and Ki67-positive expression was strongly predictive of poor overall survival (P = 0.004) in TNBC patients receiving adjuvant chemotherapy. In contrast, p53 status was not a specific prognostic factor.

Conclusions
Adjuvant therapy is beneficial for Stage II TNBC patients. The combination of E-cadherin and Ki67 status might be a useful prognostic marker indicating the need for adjuvant chemotherapy in Stage II TNBC patients.
Are synonymous codons indeed synonymous?
Authors: Venetianer Pál 
Published: December 2011

AbstractIt has long been known that the distribution and frequency of occurence of synonymous codons can vary greatly among different species, and that the abundance of isoaccepting tRNA species could also be very different. The interaction of these two factors may influence the rate and efficiency of protein synthesis and therefore synonymous mutations might influence the fitness of the organism and cannot be treated generally as ‘neutral’ in an evolutionary sense. These general effects of synonymous mutations, and their possible role in evolution, have been discussed in several recent papers. This review, however, will only deal with the influence of synonymous codon replacements on the expression of individual genes. It will describe the possible mechanisms of such effects and will present examples demonstrating the existence and effects of each of these mechanisms.
Ambulatory arterial stiffness indexes in acromegaly
Authors: Dassie Francesca , Grillo Andrea , Carretta Renzo , Fabris Bruno , Macaluso Loredana , Bardelli Moreno , Martini Chiara , Paoletta Agostino , Vettor Roberto , Sicolo Nicola , Fallo Francesco , Maffei Pietro 
Published: December 2011

ObjectiveAcromegaly is associated with increased cardiovascular morbidity and mortality and with specific heart and vascular abnormalities. The aim of our study was to investigate arterial stiffness using the ambulatory arterial stiffness index (AASI) and symmetric AASI (Sym-AASI), two indexes derived from 24-h ambulatory blood pressure monitoring (ABPM), in a group of normotensive and hypertensive patients with active acromegaly, compared with normotensive controls (NOR-CTR) or hypertensive controls (HYP-CTR).Subjects and methodsNinety-six consecutive patients with active acromegaly (46 males, mean age 49±14 years) underwent 24-h ABPM and evaluation of cardiovascular risk factors. Based on ABPM measurement, acromegalic patients were divided into 64 normotensive (normotensive acromegalic patients (NOR-ACRO)) and 32 hypertensive (hypertensive acromegalic patients (HYP-ACRO)) patients, and were compared with 35 normotensive (NOR-CTR) and 34 hypertensive (HYP-CTR) age-, sex,- and ABPM-matched control subjects.ResultsThe AASI and Sym-AASI indexes were significantly higher in acromegalic patients than in controls, either in the normotensive (NOR-ACRO vs NOR-CTR, P<0.0001 for AASI and P=0.005 for Sym-AASI) or in the hypertensive (HYP-ACRO vs HYP-CTR, P=0.01 for AASI and P=0.01 for Sym-AASI) group. Multiple logistic regression analysis showed a significant association of the highest AASI tertile with serum IGF1 (P=0.034) in the whole acromegalic group.ConclusionAASIs are increased in acromegaly, independent of blood pressure (BP) elevation, and may have an important role in predicting cardiovascular risk in this disease.
Calcium and Magnesium Prophylaxis for Oxaliplatin-Related Neurotoxicity: Is It a Trade-off Between Drug Efficacy and Toxicity?
Authors: Khattak Muhammad Adnan 
Published: December 2011

Abstract
Oxaliplatin-based chemotherapy regimens are the current standard treatment in the management of colorectal cancer. Neurotoxicity is the major cause of treatment delay, dose reduction, and cessation of oxaliplatin. Evidence regarding the role of calcium and magnesium prophylaxis to prevent oxaliplatin-related neurotoxicity is conflicting and further randomized data are needed to answer this question accurately. The purpose of this paper is to provide a critical overview of various studies that have been conducted so far to evaluate the preventative role of calcium and magnesium prophylaxis against oxaliplatin-related neurotoxicity.
Patient-Centered Cancer Treatment Planning: Improving the Quality of Oncology Care. Summary of an Institute of Medicine Workshop
Authors: Balogh Erin P. , Ganz Patricia A. , Murphy Sharon B. , Nass Sharyl J. , Ferrell Betty R. , Stovall Ellen 
Published: December 2011

Abstract
The Institute of Medicine's National Cancer Policy Forum recently convened a workshop on patient-centered cancer treatment planning, with the aim of raising awareness about this important but often overlooked aspect of cancer treatment. A primary goal of patient-centered treatment planning is to engage patients and their families in meaningful, thorough interactions with their health care providers to develop an accurate, well-conceived treatment plan, using all available medical information appropriately while also considering the medical, social, and cultural needs and desires of the patient and family. A cancer treatment plan can be shared among the patient, family, and care team in order to facilitate care coordination and provide a roadmap to help patients navigate the path of cancer treatment. There are numerous obstacles to achieving patient-centered cancer treatment planning in practice. Some of these challenges stem from the patient and include patients' lack of assertiveness, health literacy, and numeracy, and their emotional state and concurrent illnesses. Others are a result of physician limitations, such as a lack of time to explain complex information and a lack of tools to facilitate treatment planning, as well as insensitivity to patients' informational, cultural, and emotional needs. Potential solutions to address these obstacles include better training of health care providers and patients in optimal communication and shared decision making, and greater use of support services and tools such as patient navigation and electronic health records. Other options include greater use of quality metrics and reimbursement for the time it takes to develop, discuss, and document a treatment plan.
Study of the Inferior Alveolar Canal and Mental Foramen on Digital Panoramic Images
Authors: Pria Carlos M , Masood Farah , Beckerley Joy M , Carson Robert E 
Published: December 2011

ABSTRACT

Objectives
To study the radiographic location of the mental foramen and appearance of the inferior alveolar canal and the relationship between image gray values and the clarity of inferior alveolar canal on the digital panoramic images and to evaluate if the histogram equalization of the digital image would improve the visualization of the inferior alveolar canal outline on the digital panoramic images in the mandible.

Methods
Five hundred digital panoramic images were evaluated by two examiners using a specific inclusion criteria. Only the right side of the mandible was studied. Chi-square analyses were used for comparisons of distributions. Mean and median pixel values were analyzed separately with a one-way analysis of variance. Also, percentages were calculated to report the usefulness of the histogram equalization for visualization of canal.

Results
Results show variation in location of mental foramen. Most frequent location of the mental foramen was reported as first and second premolar region. Chi-square analysis showed that the frequency of occurrence of the mental foramen was equally probable for any of the three locations. The study did not find significant usefulness of the gray values obtained from the histogram equalization in predicting the clarity of inferior alveolar canal outlines.

Clinical significance
Knowing the normal relationship and the anatomical variation of the maxillofacial structures for each patient is important for surgical implant treatment planning to avoid future complications. It is also important to be familiar with the advantages and limitations of diagnostic aids available before making treatment planning decisions based on such findings.

How to cite this article
Pria CM, Masood F, Beckerley JM, Carson RE. Study of the Inferior Alveolar Canal and Mental Foramen on Digital Panoramic Images. J Contemp Dent Pract 2011;12(4):265-271.
Limonov's "It's Me, Eddie" and the Autobiographical Mode
Authors: Ryan-Hayes Karen 
Published: December 2011

The publication of Eduard Limonov'sIt's Me, Eddie ("Eto ia- Edichka) in 1980 aroused impassioned polemics that have not been entirely quelled after more than a decade. Critical discourse on the book tends to superlatives and hyperbole; it has been lauded as "the quintessential novel of the third wave emigration" and reviled as pornographic slander. Limonov's heavy use of mat, his inclusion of numerous explicitly erotic scenes and his avowal of leftist political tendencies all contributed to establishing It's Me, Eddie's infamy.
Detecting multiple causal rare variants in exome sequence data
Authors: Ye Kenny Q. , Engelman Corinne D. 
Published: December 2011

AbstractRecent advances in sequencing technology have presented both opportunities and challenges, with limited statistical power to detect a single causal rare variant with practical sample sizes. To overcome this, the contributors to Group 1 of Genetic Analysis Workshop 17 sought to develop methods to detect the combined signal of multiple causal rare variants in a biologically meaningful way. The contributors used genes, genome location proximity, or genetic pathways as the basic unit in combining the information from multiple variants. Weaknesses of the exome sequence data and the relative strengths and weaknesses of the five approaches are discussed. Genet. Epidemiol. 35:S18–S21, 2011. © 2011 Wiley Periodicals, Inc.
Soil particle accumulation in termite (Macrotermes bellicosus) mounds and the implications for soil particle dynamics in a tropical savanna Ultisol
Authors: Abe Susumu S. , Kotegawa Takashi , Onishi Taisuke , Watanabe Yoshinori , Wakatsuki Toshiyuki 
Published: December 2011

AbstractThis study investigated the influence of mound‐building termites on soil particle dynamics on the land surface and in soil‐forming processes by examining the amount of soil particles in mound structures of Macrotermes bellicosus in a highly weathered Ultisol of tropical savanna. Soil particle turnover via the mounds was estimated using particle stock data and soil turnover data from previous studies. A 4‐ha study plot with six mounds of relatively uniform shape and size was investigated. Soil mass constituting the mounds was 6,166 ± 1,581 kg mound−1 within which the mound wall and nest body accounted for 5,002 ± 1,289 and 1,164 ± 293 kg, respectively. The mound wall contained a significantly larger amount of clay (252 ± 9.97 g kg−1) balanced with a lower sand content (676 ± 26.5 g kg−1) than in the adjacent surface (Ap1) horizon, (46.4 ± 12.8 g clay kg−1; 866 ± 83.2 g sand kg−1); the nest body had much higher clay content (559 ± 51.0 g kg−1) but less sand (285 ± 79.2 g kg−1) than the mound wall. As a result, the mounds of M. bellicosus accumulated clay of 2,874 ± 781 kg ha−1 (corresponding to 2.52% of clay stock in the Ap1 horizon) along with an estimated clay turnover rate of 169 kg ha−1 year−1. These findings suggest a positive feedback effect from termite mound‐building activity on soil particle dynamics in tropical savanna ecosystems: M. bellicosus preferentially use subsoil material for mound construction, resulting in relocation of illuvial clay in the subsoil to the land surface where clay eluviation from the surface soil and its illuviation in the subsoil are major soil‐forming processes.
Treatment effect of adalimumab and infliximab in Japanese psoriasis patients: Results in a single community‐based hospital
Authors: NODA Shinji , MIZUNO Kyoko , ADACHI Makoto 
Published: December 2011

ABSTRACTBecause adalimumab and infliximab were approved in Japan for psoriasis treatment only 1 year ago, therapeutic efficacy of these agents is not well studied in a Japanese psoriasis population. Moreover, the evaluation of scalp psoriasis treated with biologics has never been reported in these subjects. In this study, 21 patients with moderate to severe plaque psoriasis were assigned to receive adalimumab 40 mg every other week with an initial loading dose of 80 mg (n = 11), or infliximab 5 mg/kg at weeks 0, 2, 6, 14 and 22 (n = 10). The treatment efficacy was evaluated by the proportion of patients who achieved at least 75% improvement in Psoriasis Area and Severity Index (PASI 75) and Psoriasis Scalp Severity Index score (PSSI 75) from baseline at weeks 4, 8, 16 and 24. A patient selection bias existed between the two groups in body surface area and PASI (44.0 ± 24.7 vs 30.2 ± 13.5, P = 0.12 and 22.2 ± 9.3 vs 15.6 ± 7.75, P = 0.09, respectively). At week 16, 81.8% of adalimumab‐treated patients and 60.0% of infliximab‐treated patients achieved PASI 75 response, but no statistically significant difference was found between these response rates. There was a tendency toward a reduced PSSI 75 response rate in the adalimumab‐treated group compared to the infliximab‐treated group (54.5% vs 90% at week 16, P = 0.15). In conclusion, both of the tumor necrosis factor‐α inhibitors demonstrated good therapeutic response similar to that in the previously reported randomized controlled trials, without any severe adverse reactions. Treatment response in scalp lesions tended to be lower in adalimumab‐treated patients, possibly because of delayed treatment onset of adalimumab.
Total population investigation of dental hospitalizations in Indigenous children under five years in Western Australia using linked data
Authors: Slack‐Smith LM , Read AW , Colvin LJ , Leonard H , Kilpatrick N , McAullay D , Messer LB 
Published: December 2011

AbstractBackground:  The aim of this study was to compare dental hospital admissions in a total state birth population of Indigenous and non‐Indigenous children aged under five years in Western Australia.Methods:  Midwives’ notification data were linked to databases of deaths, admissions, birth defects and intellectual disability. Births during 1980–1995 were followed until five years of age (n = 383 665). Dental admissions were classified by ICD‐9 principal diagnosis categories.Results:  There were 738 dental admissions for 665 children aged up to five years of Indigenous mothers (n = 20 921). Indigenous children comprised 6.3% of all children having a dental admission in this age group; 3.2% of children with Indigenous mothers had a dental admission compared with 2.7% of non‐Indigenous children. Overall, 8.7% (n = 58) of Indigenous children with a dental admission had a birth defect and 5.5% (n = 23) had an intellectual disability (compared to 8.8% and 3.2%). Indigenous children were four times more likely to be diagnosed with oral soft tissue diseases than non‐Indigenous children, and less likely to be categorized as having diseases of the dental hard tissues. Indigenous children were more likely to have a longer dental admission.Conclusions:  These analyses provide important findings regarding hospital admissions for Indigenous children. Admissions for disorders of the soft tissues are more common in Indigenous children.
Kähler groups, real hyperbolic spaces and the Cremona group. With an appendix by Serge Cantat
Authors: Delzant Thomas , Py Pierre 
Published: December 2011

AbstractGeneralizing a classical theorem of Carlson and Toledo, we prove thatanyZariski dense isometric action of a Kähler group on the real hyperbolic space of dimension at least three factors through a homomorphism onto a cocompact discrete subgroup of PSL2(ℝ). We also study actions of Kähler groups on infinite-dimensional real hyperbolic spaces, describe some exotic actions of PSL2(ℝ) on these spaces, and give an application to the study of the Cremona group.
Antibiotics in Feed Induce Prophages in Swine Fecal Microbiomes
Authors: Allen Heather K. , Looft Torey , Bayles Darrell O. , Humphrey Samuel , Levine Uri Y. , Alt David , Stanton Thaddeus B. 
Published: December 2011

ABSTRACT

Antibiotics are a cost-effective tool for improving feed efficiency and preventing disease in agricultural animals, but the full scope of their collateral effects is not understood. Antibiotics have been shown to mediate gene transfer by inducing prophages in certain bacterial strains; therefore, one collateral effect could be prophage induction in the gut microbiome at large. Here we used metagenomics to evaluate the effect of two antibiotics in feed (carbadox and ASP250 [chlortetracycline, sulfamethazine, and penicillin]) on swine intestinal phage metagenomes (viromes). We also monitored the bacterial communities using 16S rRNA gene sequencing. ASP250, but not carbadox, caused significant population shifts in both the phage and bacterial communities. Antibiotic resistance genes, such as multidrug resistance efflux pumps, were identified in the viromes, but in-feed antibiotics caused no significant changes in their abundance. The abundance of phage integrase-encoding genes was significantly increased in the viromes of medicated swine over that in the viromes of nonmedicated swine, demonstrating the induction of prophages with antibiotic treatment. Phage-bacterium population dynamics were also examined. We observed a decrease in the relative abundance of
Streptococcus
bacteria (prey) when
Streptococcus
phages (predators) were abundant, supporting the “kill-the-winner” ecological model of population dynamics in the swine fecal microbiome. The data show that gut ecosystem dynamics are influenced by phages and that prophage induction is a collateral effect of in-feed antibiotics.

IMPORTANCE
This study advances our knowledge of the collateral effects of in-feed antibiotics at a time in which the widespread use of “growth-promoting” antibiotics in agriculture is under scrutiny. Using comparative metagenomics, we show that prophages are induced by in-feed antibiotics in swine fecal microbiomes and that antibiotic resistance genes were detected in most viromes. This suggests that in-feed antibiotics are contributing to phage-mediated gene transfer, potentially of antibiotic resistance genes, in the swine gut. Additionally, the so-called “kill-the-winner” model of phage-bacterium population dynamics has been shown in aquatic ecosystems but met with conflicting evidence in gut ecosystems. The data support the idea that swine fecal
Streptococcus
bacteria and their phages follow the kill-the-winner model. Understanding the role of phages in gut microbial ecology is an essential component of the antibiotic resistance problem and of developing potential mitigation strategies.
Are We There Yet?: the Impact of the Lisbon Treaty on the EU Children's Rights Agenda
Authors: Stalford Helen , Schuurman Mieke 
Published: December 2011

AbstractThe EU's Lisbon Treaty presents the most important opportunity for the development of children's rights since the EU's existence. This article sets out the broader constitutional changes made that are of relevance to children and the implications of changes to the legislative procedure, including a discussion on whether the new Citizens' Initiative might be exploited as a lobbying tool for specific children's rights issues and its relation to the right of children to participate. The impact of the EU's enhanced fundamental rights agenda on children's rights is assessed, including the Charter of Fundamental Rights, the General Principles of EU Law and the ECHR. In addition, the Lisbon Treaty presents new opportunities for integrating children's rights into all stages of the decision-making and implementation process. It also provides sharper tools to develop adequate non-legislative responses to the diverse range of needs that children have, such as policy, budgetary and research initiatives.