A biochemical hypothesis on the formation of fingerprints using a turing patterns approach

<p>Abstract</p> <p>Background</p> <p>Fingerprints represent a particular characteristic for each individual. Characteristic patterns are also formed on the palms of the hands and soles of the feet. Their origin and development is still unknown but it is believed to have a strong genetic component, although it is not the only thing determining its formation. Each fingerprint is a papillary drawing composed by papillae and rete ridges (crests). This paper proposes a phenomenological model describing fingerprint pattern formation using reaction diffusion equations with Turing space parameters.</p> <p>Results</p> <p>Several numerical examples were solved regarding simplified finger geometries to study pattern formation. The finite element method was used for numerical solution, in conjunction with the Newton-Raphson method to approximate nonlinear partial differential equations.</p> <p>Conclusions</p> <p>The numerical examples showed that the model could represent the formation of different types of fingerprint characteristics in each individual.</p

Cisplatin-induced emesis: systematic review and meta-analysis of the ferret model and the effects of 5-HT3 receptor antagonists

PURPOSE: The ferret cisplatin emesis model has been used for ~30 years and enabled identification of clinically used anti-emetics. We provide an objective assessment of this model including efficacy of 5-HT(3) receptor antagonists to assess its translational validity. METHODS: A systematic review identified available evidence and was used to perform meta-analyses. RESULTS: Of 182 potentially relevant publications, 115 reported cisplatin-induced emesis in ferrets and 68 were included in the analysis. The majority (n = 53) used a 10 mg kg(−1) dose to induce acute emesis, which peaked after 2 h. More recent studies (n = 11) also used 5 mg kg(−1), which induced a biphasic response peaking at 12 h and 48 h. Overall, 5-HT(3) receptor antagonists reduced cisplatin (5 mg kg(−1)) emesis by 68% (45–91%) during the acute phase (day 1) and by 67% (48–86%) and 53% (38–68%, all P < 0.001), during the delayed phase (days 2, 3). In an analysis focused on the acute phase, the efficacy of ondansetron was dependent on the dosage and observation period but not on the dose of cisplatin. CONCLUSION: Our analysis enabled novel findings to be extracted from the literature including factors which may impact on the applicability of preclinical results to humans. It reveals that the efficacy of ondansetron is similar against low and high doses of cisplatin. Additionally, we showed that 5-HT(3) receptor antagonists have a similar efficacy during acute and delayed emesis, which provides a novel insight into the pharmacology of delayed emesis in the ferret

α-Actinin and Filamin Cooperatively Enhance the Stiffness of Actin Filament Networks

BACKGROUND: The close subcellular proximity of different actin filament crosslinking proteins suggests that these proteins may cooperate to organize F-actin structures to drive complex cellular functions during cell adhesion, motility and division. Here we hypothesize that alpha-actinin and filamin, two major F-actin crosslinking proteins that are both present in the lamella of adherent cells, display synergistic mechanical functions. METHODOLOGY/PRINCIPAL FINDINGS: Using quantitative rheology, we find that combining alpha-actinin and filamin is much more effective at producing elastic, solid-like actin filament networks than alpha-actinin and filamin separately. Moreover, F-actin networks assembled in the presence of alpha-actinin and filamin strain-harden more readily than networks in the presence of either alpha-actinin or filamin. SIGNIFICANCE: These results suggest that cells combine auxiliary proteins with similar ability to crosslink filaments to generate stiff cytoskeletal structures, which are required for the production of internal propulsive forces for cell migration, and that these proteins do not have redundant mechanical functions

Management Impacts on Forest Floor and Soil Organic Carbon in Northern Temperate Forests of the US

<p>Abstract</p> <p>Background</p> <p>The role of forests in the global carbon cycle has been the subject of a great deal of research recently, but the impact of management practices on forest soil dynamics at the stand level has received less attention. This study used six forest management experimental sites in five northern states of the US to investigate the effects of silvicultural treatments (light thinning, heavy thinning, and clearcutting) on forest floor and soil carbon pools.</p> <p>Results</p> <p>No overall trend was found between forest floor carbon stocks in stands subjected to partial or complete harvest treatments. A few sites had larger stocks in control plots, although estimates were often highly variable. Forest floor carbon pools did show a trend of increasing values from southern to northern sites. Surface soil (0-5 cm) organic carbon content and concentration were similar between treated and untreated plots. Overall soil carbon (0-20 cm) pool size was not significantly different from control values in sites treated with partial or complete harvests. No geographic trends were evident for any of the soil properties examined.</p> <p>Conclusions</p> <p>Results indicate that it is unlikely that mineral soil carbon stocks are adversely affected by typical management practices as applied in northern hardwood forests in the US; however, the findings suggest that the forest floor carbon pool may be susceptible to loss.</p

The distributed p-median problem in computer networks

Many distributed services in computer networks rely on a set of active facilities that are selected among a potentially large number of candidates. The active facilities then contribute and cooperate to deliver a specific service to the users of the distributed system. In this scenario graph partitioning or clustering is often adopted to determine the most efficient locations of the facilities. The identification of the optimal set of facility locations is known as the p-median problem in networks, is NP-hard and is typically solved by using heuristic methods. The goal is to select p locations among all candidate network nodes such that some cost function is minimised. A typical example of such a function is the overall communication cost to deliver the service to the users of the distributed system. Locating facilities in near-optimal locations has been extensively studied for different application domains. Most of these studies have investigated sequential algorithms and centralised approaches. However, centralised approaches are practically infeasible in large-scale and dynamic networks, where the problem is inherently distributed or because of the large communication overhead and memory requirements for gathering complete information about the network topology and the users. In this work distributed approaches to the p-median problem are investigated. Two solutions are proposed for addressing the facility locations problem in a fully distributed environment. Two different iterative heuristic approaches are applied to gradually improve a random initial solution and to converge to a final solution with a local minimum of the overall cost. While the first approach adopts a fine granularity by identifying a single change to improve the solution at each iteration, the second approach applies changes to every component of the solution at each iteration. An experimental comparative analysis based on simulations has shown that the approach with a finer granularity is able to deliver a better optimisation of the overall cost with longer convergence time. Both approaches have excellent scalability and provide an effective tool to optimise the facility locations from within the network. No prior knowledge of the system is required, no data needs to be gathered in a centralised server and the same process is used to identify and to deploy the facility locations solution in the network since the process is fully decentralised

Decreasing trends in cardiovascular mortality in Turkey between 1988 and 2008.

BACKGROUND: Cardiovascular disease (CVD) mortality increased in developed countries until the 1970s then started to decline. Turkey is about to complete its demographic transition, which may also influence mortality trends. This study evaluated trends in coronary heart disease (CHD) and stroke mortality between 1988 and 2008. METHODS: The number of deaths by cause (ICD-8), age and sex were obtained from the Turkish Statistical Institute (TurkStat) annually between 1988 and 2008. Population statistics were based on census data (1990 and 2000) and Turkstat projections. European population standardised mortality rates for CHD and stroke were calculated for men and women over 35 years old. Joinpoint Regression was used to identify the points at which a statistically significant (p < 0.05) change of the trend occurred. RESULTS: The CHD mortality rate increased by 2.9% in men and 2.0% in women annually from 1988 to 1994, then started to decline. The annual rate of decline for men was 1.7% between 1994-2008, whilst in women it was 2.8% between 1994-2000 and 6.7% between 2005-2008 (p < 0.05 for all periods).Stroke mortality declined between 1990-1994 (annual fall of 3.8% in both sexes), followed by a slight increase between 1994-2004 (0.6% in men, 1.1% in women), then a further decline until 2008 (annual reduction of 4.4% in men, 7.9% in women) (p < 0.05 for all periods). CONCLUSIONS: A decrease in CVD mortality was observed from 1995 onwards in Turkey. The causes need to be explored in detail to inform future policy priorities in noncommunicable disease control

Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing

Pacific herring (Clupea pallasii) support commercially and culturally important fisheries but have experienced significant additional pressure from a variety of anthropogenic and environmental sources. In order to provide genomic resources to facilitate organismal and population level research, high-throughput pyrosequencing (Roche 454) was carried out on transcriptome libraries from liver and testes samples taken in Prince William Sound, the Bering Sea, and the Gulf of Alaska. Over 40,000 contigs were identified with an average length of 728 bp. We describe an annotated transcriptome as well as a workflow for single nucleotide polymorphism (SNP) discovery and validation. A subset of 96 candidate SNPs chosen from 10,933 potential SNPs, were tested using a combination of Sanger sequencing and high-resolution melt-curve analysis. Five SNPs supported between-ocean-basin differentiation, while one SNP associated with immune function provided high differentiation between Prince William Sound and Kodiak Island within the Gulf of Alaska. These genomic resources provide a basis for environmental physiology studies and opportunities for marker development and subsequent population structure analysis

Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization

<p>Abstract</p> <p>Background</p> <p>Direct gene synthesis is becoming more popular owing to decreases in gene synthesis pricing. Compared with using natural genes, gene synthesis provides a good opportunity to optimize gene sequence for specific applications. In order to facilitate gene optimization, we have developed a stand-alone software called Visual Gene Developer.</p> <p>Results</p> <p>The software not only provides general functions for gene analysis and optimization along with an interactive user-friendly interface, but also includes unique features such as programming capability, dedicated mRNA secondary structure prediction, artificial neural network modeling, network & multi-threaded computing, and user-accessible programming modules. The software allows a user to analyze and optimize a sequence using main menu functions or specialized module windows. Alternatively, gene optimization can be initiated by designing a gene construct and configuring an optimization strategy. A user can choose several predefined or user-defined algorithms to design a complicated strategy. The software provides expandable functionality as platform software supporting module development using popular script languages such as VBScript and JScript in the software programming environment.</p> <p>Conclusion</p> <p>Visual Gene Developer is useful for both researchers who want to quickly analyze and optimize genes, and those who are interested in developing and testing new algorithms in bioinformatics. The software is available for free download at <it><url>http://www.visualgenedeveloper.net</url></it>.</p

PCR diagnostics and monitoring of adenoviral infections in hematopoietic stem cell transplantation recipients

After stem cell transplantation, human patients are prone to life-threatening opportunistic infections with a plethora of microorganisms. We report a retrospective study on 116 patients (98 children, 18 adults) who were transplanted in a pediatric bone marrow transplantation unit. Blood, urine and stool samples were collected and monitored for adenovirus (AdV) DNA using polymerase chain reaction (PCR) and real-time PCR (RT-PCR) on a regular basis. AdV DNA was detected in 52 (44.8%) patients, with mortality reaching 19% in this subgroup. Variables associated with adenovirus infection were transplantations from matched unrelated donors and older age of the recipient. An increased seasonal occurrence of adenoviral infections was observed in autumn and winter. Analysis of immune reconstitution showed a higher incidence of AdV infections during periods of low T-lymphocyte count. This study also showed a strong interaction between co-infections of AdV and BK polyomavirus in patients undergoing hematopoietic stem cell transplantations