bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of mutation rate on estimators of genetic differentiation - lessons from Arabidopsis thaliana
Authors: Kronholm Ilkka , Loudet Olivier , de Meaux Juliette 
Published: May 2010

Abstract

Background
The analysis of molecular variation within and between populations is crucial to establish strategies for conservation as well as to detect the footprint of spatially heterogeneous selection. The traditional estimator of genetic differentiation (F

ST
) has been shown to be misleading if genetic diversity is high. Alternative estimators of F

ST
have been proposed, but their robustness to variation in mutation rate is not clearly established. We first investigated the effect of mutation and migration rate using computer simulations and examined their joint influence on Q

ST
, a measure of genetic differentiation for quantitative traits. We further used experimental data in natural populations of Arabidopsis thaliana to characterize the effect of mutation rate on various estimates of population differentiation. Since natural species exhibit various degrees of self-fertilisation, we also investigated the effect of mating system on the different estimators.

Results
If mutation rate is high and migration rate low, classical measures of genetic differentiation are misleading. Only Φ
ST
, an estimator that takes the mutational distances between alleles into account, is independent of mutation rate, for all migration rates. However, the performance of Φ
ST
depends on the underlying mutation model and departures from this model cause its performance to degrade. We further show that Q

ST
has the same bias. We provide evidence that, in A. thaliana, microsatellite variation correlates with mutation rate. We thereby demonstrate that our results on estimators of genetic differentiation have important implications, even for species that are well established models in population genetics and molecular biology.

Conclusions
We find that alternative measures of differentiation like F'

ST
and D are not suitable for estimating effective migration rate and should not be used in studies of local adaptation. Genetic differentiation should instead be measured using an estimator that takes mutation rate into account, such as Φ
ST
. Furthermore, in systems where migration between populations is low, such as A. thaliana, Q

ST
< F

ST
cannot be taken as evidence for homogenising selection as has been traditionally thought.
Torsional stability of interference screws derived from bovine bone - a biomechanical study
Authors: Bauer Joscha , Efe Turgay , Herdrich Silke , Gotzen Leo , El-Zayat Bilal Farouk , Schmitt Jan , Timmesfeld Nina , Schofer Markus Dietmar 
Published: May 2010

Abstract

Background
In the present biomechanical study, the torsional stability of different interference screws, made of bovine bone, was tested. Interference screws derived from bovine bone are a possible biological alternative to conventional metallic or bioabsorbable polymer interference screws.

Methods
In the first part of the study we compared the torsional stability of self-made 8 mm Interference screws (BC) and a commercial 8 mm interference screw (Tutofix®). Furthermore, we compared the torsional strength of BC screws with different diameters. For screwing in, a hexagon head and an octagon head were tested. Maximum breaking torques in polymethyl methacrylate resin were recorded by means of an electronic torque screw driver. In the second part of the study the tibial part of a bone-patellar tendon-bone graft was fixed in porcine test specimens using an 8 mm BC screw and the maximum insertion torques were recorded. Each interference screw type was tested 5 times.

Results
There was no statistically significant difference between the different 8 mm interference screws (p = 0.121). Pairwise comparisons did not reveal statistically significant differences, either. It was demonstrated for the BC screws, that a larger screw diameter significantly leads to higher torsional stability (p = 9.779 × 10-5). Pairwise comparisons showed a significantly lower torsional stability for the 7 mm BC screw than for the 8 mm BC screw (p = 0.0079) and the 9 mm BC screw (p = 0.0079). Statistically significant differences between the 8 mm and the 9 mm BC screw could not be found (p = 0.15). During screwing into the tibial graft channel of the porcine specimens, insertion torques between 0.5 Nm and 3.2 Nm were recorded. In one case the hexagon head of a BC screw broke off during the last turn.

Conclusions
The BC screws show comparable torsional stability to Tutofix® interference screws. As expected the torsional strength of the screws increases significantly with the diameter. The safety and in vivo performance of products derived from xenogeneic bone should be the focus of further investigations.
Prostate apoptosis response protein 4 sensitizes human colon cancer cells to chemotherapeutic 5-FU through mediation of an NFκB and microRNA network
Authors: Wang Bi-Dar , Kline Christina Leah B. , Pastor Danielle M. , Olson Thomas L. , Frank Bryan , Luu Truong , Sharma Arun K. , Robertson Gavin , Weirauch Matthew T. , Patierno Steven R. , Stuart Joshua M. , Irby Rosalyn B. , Lee Norman H. 
Published: May 2010

AbstractBackgroundDiminished expression or activity of prostate apoptosis response protein 4 (Par-4) has been demonstrated in a number of cancers, although reports on Par-4 expression during colon cancer progression are lacking. An understanding of the molecular events in conjunction with the genetic networks affected by Par-4 is warranted.ResultsColon cancer specimens derived from patients have significantly diminished expression of Par-4 mRNA relative to paired normal colon. Hence, the functional consequences of reintroducing Par-4 into HT29 colon cancer cells were assessed. Overexpression augmented the interaction of Par-4 with NFκB in the cytosol but not nucleus, and facilitated apoptosis in the presence of 5-fluorouracil (5-FU). Analogous findings were obtained when AKT1 pro-survival signaling was inhibited. Transcriptome profiling identified ~700 genes differentially regulated by Par-4 overexpression in HT29 cells. Nearly all Par-4-regulated genes were shown by promoter analysis to containcis-binding sequences for NFκB, and meta-analysis of patient expression data revealed that one-third of these genes exist as a recurrent co-regulated network in colon cancer specimens. Sets of genes involved in programmed cell death, cell cycle regulation and interestingly the microRNA pathway were found overrepresented in the network. Noteworthy, Par-4 overexpression decreased NFκB occupancy at the promoter of one particular network geneDROSHA, encoding a microRNA processing enzyme. The resulting down-regulation ofDROSHAwas associated with expression changes in a cohort of microRNAs. Many of these microRNAs are predicted to target mRNAs encoding proteins with apoptosis-related functions. Western and functional analyses were employed to validate several predictions. For instance, miR-34a up-regulation corresponded with a down-regulation of BCL2 protein. Treating Par-4-overexpressing HT29 cells with a miR-34a antagomir functionally reversed both BCL2 down-regulation and apoptosis by 5-FU. Conversely, bypassing Par-4 overexpression by direct knockdown ofDROSHAexpression in native HT29 cells increased miR-34a expression and 5-FU sensitivity.ConclusionOur findings suggest that the initiation of apoptotic sensitivity in colon cancer cells can be mediated by Par-4 binding to NFκB in the cytoplasm with consequential changes in the expression of microRNA pathway components.
A multiplex reverse transcription-nested polymerase chain reaction for detection and differentiation of wild-type and vaccine strains of canine distemper virus
Authors: Si Wei , Zhou Shun , Wang Zhao , Cui Shang-jin 
Published: May 2010

Abstract
A multiplex reverse transcription-nested polymerase chain reaction (RT-nPCR) method was developed for the detection and differentiation of wild-type and vaccine strains of canine distemper virus (CDV). A pair of primers (P1 and P4) specific for CDV corresponding to the highly conserved region of the CDV genome were used as a common primer pair in the first-round PCR of the nested PCR. Primers P2 specific for CDV wild-type strains, were used as the forward primer together with the common reverse primer P4 in the second round of nested PCR. Primers P3, P5 specific for CDV wild-type strain or vaccine strain, were used as the forward primer together with the common reverse primer P4+P6 in the second round of nested PCR. A fragment of 177 bp was amplified from vaccine strain genomic RNA, and a fragment of 247 bp from wild-type strain genomic RNA in the RT-nPCR, and two fragments of 247 bp and 177 bp were amplified from the mixed samples of vaccine and wild-type strains. No amplification was achieved for uninfected cells, or cells infected with Newcastle disease virus (NDV), canine parvovirus (CPV), canine coronavirus (CCV), rabies virus (RV), or canine adenovirus (CAV). The RT-nPCR method was used to detect 30 field samples suspected of canine distemper from Heilongjiang and Jilin Provinces, and 51 samples in Shandong province. As a result of 30 samples, were found to be wild-type-like, and 5 to be vaccine-strain-like. The RT-nPCR method can be used to effectively detect and differentiate wild-type CDV-infected dogs from dogs vaccinated with CDV vaccine, and thus can be used in clinical detection and epidemiological surveillance.
Human neutrophil integrin α9β1: up-regulation by cell activation and synergy with β2 integrins during adhesion to endothelium under flow
Authors: Mambole Agnès , Bigot Sylvain , Baruch Dominique , Lesavre Philippe , Halbwachs-Mecarelli Lise 
Published: May 2010

Abstract
α9β1 is the main β1 integrin of human activated neutrophils; and α9β1/VCAM-1 interactions participate to neutrophilrolling on endothelial cells.
Neutrophil β1 integrin expression and contribution to cell adhesion were revisited in this study. α9β1 and α5β1 appeared here as the main β1 integrins expressed on the membrane of resting platelet-depleted neutrophils—α6β1 representing &lt;15% and α2β1 undetectable. Neutrophil activation slightly enhanced α5 expression, did not change α6, but resulted in a two- to threefold increase of α9β1, which then became the major β1 integrin of the neutrophil membrane. α9β1 was the only β1 integrin to be up-regulated after transendothelial migration across TNF-α-activated HUVECs. As α9β1 binds VCAM-1, we analyzed its participation to neutrophil adhesion to TNF-α-activated endothelial cells. Blocking anti-α9 mAb had little effect on neutrophil static adhesion, contrasting with the strong inhibition by anti-β2 mAb. Under flow conditions, the anti-α9 mAb had no effect by itself on neutrophil adhesion to activated HUVECs but enhanced the blocking effect of anti-β2 antibodies significantly and further enhanced the velocity of β2–blocked rolling neutrophils. In conclusion, we describe here for the first time a nearly exclusive up-regulation of α9β1 expression among all β1 integrins during neutrophil activation and transendothelial migration and a possibly important synergy between α9β1 and β2 integrins in stabilizing neutrophil adhesion to endothelium under flow conditions.
Proximal Alternating Minimization and Projection Methods for Nonconvex Problems: An Approach Based on the Kurdyka-Łojasiewicz Inequality
Authors: Attouch Hédy , Bolte Jérôme , Redont Patrick , Soubeyran Antoine 
Published: May 2010

We study the convergence properties of an alternating proximal minimization algorithm for nonconvex structured functions of the type: L(x,y)=f(x)+Q(x,y)+g(y), where f and g are proper lower semicontinuous functions, defined on Euclidean spaces, and Q is a smooth function that couples the variables x and y. The algorithm can be viewed as a proximal regularization of the usual Gauss-Seidel method to minimize L. We work in a nonconvex setting, just assuming that the function L satisfies the Kurdyka-Łojasiewicz inequality. An entire section illustrates the relevancy of such an assumption by giving examples ranging from semialgebraic geometry to “metrically regular” problems. Our main result can be stated as follows: If L has the Kurdyka-Łojasiewicz property, then each bounded sequence generated by the algorithm converges to a critical point of L. This result is completed by the study of the convergence rate of the algorithm, which depends on the geometrical properties of the function L around its critical points. When specialized to [Formula: see text] and to f, g indicator functions, the algorithm is an alternating projection mehod (a variant of von Neumann's) that converges for a wide class of sets including semialgebraic and tame sets, transverse smooth manifolds or sets with “regular” intersection. To illustrate our results with concrete problems, we provide a convergent proximal reweighted ℓ1 algorithm for compressive sensing and an application to rank reduction problems.
Spending Constraint Utilities with Applications to the Adwords Market
Authors: Vazirani Vijay V. 
Published: May 2010

The notion of a “market” has undergone a paradigm shift with the Internet. Totally new and highly successful markets have been defined and launched by Internet companies, which already form an important part of today's economy and are projected to grow considerably in the future. Another major change is the availability of massive computational power for running these markets in a centralized or distributed manner. In view of these new realities, the study of market equilibria, an important, though essentially nonalgorithmic, theory within mathematical economics, needs to be revived and rejuvenated via an inherently algorithmic approach. Such a theory should not only address traditional market models, but also define new models for some of the new markets. We present a new, natural class of utility functions that allow buyers to explicitly provide information on their relative preferences as a function of the amount of money spent on each good. These utility functions offer considerable expressivity, especially in Google's Adwords market. In addition, they lend themselves to efficient computation, while retaining some of the nice properties of traditional models. The latter include weak gross substitutability, and the uniqueness and continuity of equilibrium prices and utilities.
Repeated colonoscopic screening of patients with acromegaly: 15-year experience identifies those at risk of new colonic neoplasia and allows for effective screening guidelines
Authors: Dworakowska D , Gueorguiev M , Kelly P , Monson J P , Besser G M , Chew S L , Akker S A , Drake W M , Fairclough P D , Grossman A B , Jenkins P J 
Published: May 2010

ObjectiveIt is suggested that patients with acromegaly have an increased risk of colorectal cancer and pre-malignant adenomatous polyps. However, the optimum frequency with which colonoscopic screening should be offered remains unclear.DesignTo determine the optimum frequency for repeated colonoscopic surveillance of acromegalic patients.MethodsWe retrospectively reviewed the case records of all patients with acromegaly seen in our centre since 1992: 254 patients had at least one surveillance colonoscopy, 156 patients had a second surveillance colonoscopy, 60 patients had a third surveillance colonoscopy and 15 patients had a fourth surveillance colonoscopy.ResultsThe presence of hyperplastic or adenomatous polyps was assessed in all patients, while one cancer was detected at the second surveillance. At the third surveillance, mean (±s.d.) serum IGF1 levels (ng/ml) in patients with hyperplastic polyps were significantly higher than those with normal colons (P<0.05). The presence of an adenoma rather than a normal colon at the first colonoscopy was associated with a significantly increased risk of adenoma at the second (odds ratio (OR) 4.4, 95% confidence interval (CI) 1.9–10.4) and at the third (OR 8.8, 95% CI 2.9–26.5) screens. Conversely, a normal colon at the first surveillance gave a high chance of normal findings at the second (78%) or third surveillance (78%), and a normal colon at the second colonoscopy was associated with normality at the third colonoscopy (81%).ConclusionsRepeated colonoscopic screening of patients with acromegaly demonstrated a high prevalence of new adenomatous and hyperplastic colonic polyps, dependent on both the occurrence of previous polyps and elevated IGF1 levels.
Antioxidant adaptive responses of extraembryonic tissues from cloned and non-cloned bovine conceptuses to oxidative stress during early pregnancy
Authors: Al-Gubory Kaïs H , Garrel Catherine , Delatouche Laurent , Heyman Yvan , Chavatte-Palmer Pascale 
Published: May 2010

AbstractPlacental oxidative stress has been suggested as a key factor in early pregnancy failure. Abnormal placental development limits success in pregnancies obtained by somatic cell nuclear transfer (SCNT). Malondialdehyde (MDA) content, an index of oxidative stress, and superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX) activities were determined in bovine extraembryonic tissues of SCNT or artificial insemination (AI) conceptuses. Chorionic tissues of SCNT and AI conceptuses show no difference in MDA content at day 32 of pregnancy. MDA content in chorionic tissues of SCNT and AI conceptuses decreased from day 32 to 62 of pregnancy. MDA content was lower in chorionic tissues of SCNT conceptuses than that in chorionic tissues of AI conceptuses at day 62 of pregnancy. SOD1, SOD2 and GPX activities in chorionic tissues of SCNT conceptuses were not different from those in chorionic tissues of AI conceptuses at both gestational ages. CAT activity in chorionic tissues of SCNT conceptuses was lower at day 32, and it was higher at day 62 of pregnancy than that in chorionic tissues of AI conceptuses. CAT and GPX activities increased in chorionic tissues of SCNT conceptuses with gestational age. SOD1 activity decreased while that of SOD2 and GPX increased in chorionic tissues of AI conceptuses with gestational age. At day 62 of pregnancy, MDA content and enzyme activities in cotyledonary tissues were not different between AI and SCNT conceptuses. Different antioxidant mechanisms may operate within the chorion of AI and SCNT conceptuses. Further experiments are required to elucidate this point.
The Ecology of Health Policymaking and Reform in the U.S.A.
Authors: Ubokudom Sunday E , Khubchandani Jagdish 
Published: May 2010

AbstractThis article demonstrates how constitutional, political, legal, economic, technological, social and cultural, physical, demographic, and global factors affect health policymaking in the U.S.A. The ecological factors that influence health policy in the U.S. are uniquely different from those of other countries. Therefore, even though a number of problems may be common to health systems worldwide, these problems may require different solutions in the different countries, or in different sections of the same country. The article concludes that the above ecological factors, individually or collectively, cause U.S. health policies to be inconsistent. For example, policies were adopted in the past to promote the concentrated interests of health providers. Recently, the rise of opposing concentrated interests, a lingering economic recession, a weakened resistance to change, and policy learning from the practices of other industrialized countries and from scholarly publications give us hope that reform, although still difficult to achieve, may finally be in sight.
A New Approach to Producing Geographic Profiles of HIV Prevalence: An Application to Malawi
Authors: Ivaschenko Oleksiy , Lanjouw Peter 
Published: May 2010

AbstractSubnational estimates of HIV prevalence can inform the design of policy responses to the HIV epidemic. Such responses also benefit from a better understanding of the correlates of HIV status, including the association between HIV and geographical characteristics of localities. In recent years, several countries in Africa have implemented household surveys (such as DHS surveys) that include HIV testing of the adult population, providing estimates of HIV prevalence rates at the subnational level. These surveys are known to have nonresponse bias, but are nonetheless thought to represent a marked improvement over alternatives such as sentinel surveys. At present, however, most countries are not in a position to regularly field such household surveys. This paper proposes a new approach to the estimation of HIV prevalence for relatively small geographic areas in settings where national population‐based surveys of prevalence are not available. The proposed approach aims to overcome some of the difficulties with prevailing methods of deriving HIV prevalence estimates (at both national and subnational levels) directly from sentinel surveys. The paper also outlines some of the limitations of the proposed approach.
Public‐Private Partnership for TB Control in Bangladesh: Role of Private Medical Practitioners in the Management of TB Patients
Authors: Ullah Abu Naser Zafar , Huque Rumana , Begum Vikarunnessa , Newell James , Gerein Nancy 
Published: May 2010

AbstractBackground: Despite enormous efforts, Bangladesh has one of the highest burdens of tuberculosis (TB) in the world. Treatment in the private sector is common and popular among TB patients in South‐Asian countries, including Bangladesh, even though the quality of diagnosis and treatment of TB patients has been shown to be poor in several such countries. The Bangladesh National Tuberculosis Programme (NTP) has recently shown considerable interest in exploring policy options to address this problem. Consequently, the NTP and Non‐Governmental Organisation (NGO) partners planned to develop a public‐private partnership (PPP) model for effective involvement of private medical practitioners (PMPs) in TB control. However, there was a lack of solid data on TB case management practice by PMPs which was needed to appraise the potential role and contribution of PMPs in TB control. The purpose of the study is therefore to assess the knowledge, attitudes and practices of PMPs on TB control in an urban setting in Bangladesh in order to inform development of a public‐private collaboration model. Methods: A cross sectional study was carried out in four areas of Dhaka city involving the NTP and three NGO partners. A mapping of PMPs was carried out: of the 250 PMPs identified, 97 showed an interest in becoming involved in the public‐private collaboration model and agreed to be interviewed. Information was also collected from focus group discussions with PMPs, and through a workshop. Results: PMPs were not aware of the NTP‐recommended regimen for treating TB: their prescribing patterns varied widely and were not related to the TB case categorisation. X‐ray was the preferred investigation of PMPs, who sent TB suspects to their preferred private‐run laboratory for diagnostic tests. Virtually no PMP had knowledge of the Bangladesh national policy for TB control (based on the WHO DOTS strategy), and the great majority did not know the locations of neighbouring DOTS centres. The quality of care provided by the public sector was perceived as poor by PMPs, who were therefore reluctant to refer TB patients to the NTP. Conclusions: There is enormous potential for improving TB treatment and control through partnerships between the NTP and PMPs, if the issues identified in this study are adequately addressed. PMPs must be encouraged to follow NTP guidelines for diagnosis and treatment. They should be motivated to refer patients to nearby DOTS centres. Proper training is required for PMPs to enhance their knowledge on diagnosis, treatment, and follow‐up. Appropriate tools and protocols and customised training packages need to be developed, focusing on appropriate diagnosis and treatment, including ways to refer patients to DOTS centres for diagnosis and treatment supervision.