Current methods of gene prediction,their strengths and weaknesses

While the genomes of many organisms have been sequenced over the last few years, transforming such raw sequence data into knowledge remains a hard task. A great number of prediction programs have been developed that try to address one part of this problem, which consists of locating the genes along a genome. This paper reviews the existing approaches to predicting genes in eukaryotic genomes and underlines their intrinsic advantages and limitations. The main mathematical models and computational algorithms adopted are also briefly described and the resulting software classified according to both the method and the type of evidence used. Finally, the several difficulties and pitfalls encountered by the programs are detailed, showing that improvements are needed and that new directions must be considered.     

FRET microscopy in the living cell: different approaches, strengths and weaknesses

New imaging methodologies in quantitative fluorescence microscopy, such as F?rster resonance energy transfer (FRET), have been developed in the last few years and are beginning to be extensively applied to biological problems. FRET is employed for the detection and quantification of protein interactions, and of biochemical activities. Herein, we review the different methods to measure FRET in microscopy, and more importantly, their strengths and weaknesses. In our opinion, fluorescence lifetime imaging microscopy (FLIM) is advantageous for detecting inter-molecular interactions quantitatively, the intensity ratio approach representing a valid and straightforward option for detecting intra-molecular FRET. Promising approaches in single molecule techniques and data analysis for quantitative and fast spatio-temporal protein-protein interaction studies open new avenues for FRET in biological research.     

An appraisal of the strengths and weaknesses of newborn and juvenile rat models for researching gastrointestinal development

Research on the impact of bioactive compounds on the development and functional maturation of the gastrointestinal (GI) tract using newborn and juvenile rats has greatly contributed to the knowledge of GI physiology and to the improved clinical management of both premature and full-term newborns. Of the animal models available, two types have been described for use with young rats--maintenance models and substitution models. Maintenance models are those in which the young are reared with the dam and therefore benefit from continuation of natural nutrition and maternal care. Substitution models are those in which the young are reared in the absence of the dam using artificially formulated milk delivered by various means into specific GI sites. In this review, we describe these models and their operation, and discuss the strengths and weaknesses of each. Attention is also given to questions of scientific validity and some animal welfare issues raised by the use of these models.     

Environmental metabolomics: a SWOT analysis (strengths, weaknesses, opportunities, and threats)

Metabolomic approaches have the potential to make an exceptional contribution to understanding how chemicals and other environmental stressors can affect both human and environmental health. However, the application of metabolomics to environmental exposures, although getting underway, has not yet been extensively explored. This review will use a SWOT analysis model to discuss some of the strengths, weaknesses, opportunities, and threats that are apparent to an investigator venturing into this relatively new field. SWOT has been used extensively in business settings to uncover new outlooks and identify problems that would impede progress. The field of environmental metabolomics provides great opportunities for discovery, and this is recognized by a high level of interest in potential applications. However, understanding the biological consequence of environmental exposures can be confounded by inter- and intra-individual differences. Metabolomic profiles can yield a plethora of data, the interpretation of which is complex and still being evaluated and researched. The development of the field will depend on the availability of technologies for data handling and that permit ready access metabolomic databases. Understanding the relevance of metabolomic endpoints to organism health vs adaptation vs variation is an important step in understanding what constitutes a substantive environmental threat. Metabolomic applications in reproductive research are discussed. Overall, the development of a comprehensive mechanistic-based interpretation of metabolomic changes offers the possibility of providing information that will significantly contribute to the protection of human health and the environment.     

Meniscal pathology - the evidence for treatment

Whilst arthroscopic surgery for the treatment of meniscal tears is the most commonly performed orthopaedic surgery, meniscal tears at the knee are frequently identified on magnetic resonance imaging in adults with and without knee pain. The evidence for arthroscopic treatment of meniscal tears is controversial and lacks a supporting evidence base; it may be no more efficacious than conservative therapies. Surgical approaches to the treatment of meniscal pathology can be broadly categorised into those in which partial menisectomy or repair are performed. This review highlights that the major factor determining the choice of operative approach is age: meniscal repair is performed exclusively on younger populations, while older populations are subject to partial menisectomy procedures. This is probably because the meniscus is less amenable to repair in the older population where other degenerative changes co-exist. In middle-aged to older adults, arthroscopic partial menisectomy (APM) may treat the meniscus tear, but does not address the degenerative whole organ disease of knee osteoarthritis. Thus far, there is no convincing evidence that operative approaches are superior to conservative measures as the first-line treatment of older people with knee pain and meniscal tears. However, in two randomised controlled trials (RCTs) approximately one-third of subjects in the exercise groups had persisting knee pain with some evidence of improvement following APM, although the characteristics of this subgroup are unclear. From the available data, a first-line trial of conservative therapy, which includes weight loss, is recommended for the treatment of degenerative meniscal tears in older adults. The exception to this may be when mechanical symptoms, such as knee locking, predominate. Although requiring corroboration by RCTs, there is accumulating evidence from cohort studies and case series that meniscal repair rather than APM may improve function and reduce the long-term risk of knee osteoarthritis in young adults. There is no clear evidence from RCTs that one surgical method of meniscal repair is superior to another.     

Flexural and bond strengths of relined denture polymers assessed by four‐point bending tests and Weibull analysis

doi: 10.1111/j.1741‐2358.2011.00515.x Flexural and bond strengths of relined denture polymers assessed by four‐point bending tests and Weibull analysis Objectives: The aim of this study was to (1) investigate the flexural strengths of three denture resins i.e. heat, photopolymerised and microwaved and how it was affected by relining with auto‐ and visible light–polymerised hard reliners, (2) investigate the bond strengths between denture resins and hard reliners and (3) interpret the results of both tests by utilising Weibull analysis. Materials and methods: Specimens (65 × 10 × 2.5 mm) from denture resins, relined and bonded combinations were tested using a four‐point bending test in a universal testing machine and a crosshead speed of 5 mm/min. Ten specimens for each bulk resin and denture resin–reliner combination for a total of 150 were tested. Results: Statistical analysis indicated significant differences between bulk materials (p < 0.001) and between reliners (p < 0.001) for flexural and bond strength tests. Conclusion: It was concluded that (1) the four‐point flexural strength was different between the denture base materials, (2) flexure strength between bulk and relined or between relined with autopolymerised and photopolymerised bases was different, (3) flexural strength among relined denture bases was different and (4) bond strengths among relined denture bases were different.     

Fast Coding Unit Encoding Mechanism for Low Complexity Video Coding

In high efficiency video coding (HEVC), coding tree contributes to excellent compression performance. However, coding tree brings extremely high computational complexity. Innovative works for improving coding tree to further reduce encoding time are stated in this paper. A novel low complexity coding tree mechanism is proposed for HEVC fast coding unit (CU) encoding. Firstly, this paper makes an in-depth study of the relationship among CU distribution, quantization parameter (QP) and content change (CC). Secondly, a CU coding tree probability model is proposed for modeling and predicting CU distribution. Eventually, a CU coding tree probability update is proposed, aiming to address probabilistic model distortion problems caused by CC. Experimental results show that the proposed low complexity CU coding tree mechanism significantly reduces encoding time by 27% for lossy coding and 42% for visually lossless coding and lossless coding. The proposed low complexity CU coding tree mechanism devotes to improving coding performance under various application conditions.     

Age and reproduction in birds - hypotheses and tests

It is well known that reproductive performance improves with age in birds. Many hypotheses, involving factors such as differential survival, delayed breeding, breeding experience, foraging ability and reproductive effort, have been proposed to explain this pattern. Although these hypotheses are not mutually exclusive, they can be classified in three major groups relating to progressive appearance or disappearance of phenotypes, age-related improvements of competence, and optimization of reproductive effort. However, a closer examination of the literature reveals that only few studies have rigorously tested the hypotheses. Future work should focus on carefully designed tests that critically investigate the hypotheses.     

Coding polymorphism for phylogeny reconstruction

The methodology of coding polymorphic taxa has received limited attention to date. A search of the taxonomic literature revealed seven types of coding methods. Apart from ignoring polymorphic characters (sometimes called the fixed-only method), two main categories can be distinguished: methods that identify the start of a new character state with the origin of an evolutionary novelty, and methods that identify the new state with the fixation of a novelty. The methods of the first category introduce soft reversals, yielding signals that support cladograms incompatible with true phylogenies. We conclude that coding the plesiomorphy is the method to be preferred, unless the ancestral state is unknown, in which case coding as ambiguous is recommended. This holds for coding polymorphism in species as well as in supraspecific taxa. In this light we remark on methods proposed by previous authors.     

The pathology clinic - pathologists should see patients

This invited review describes why and how a pathologist should talk to patients in order to enhance the patient care pathway. The pathologist-patient interaction should become a natural extension to multidisciplinary team decision making, and also become the forum in which patients are helped to understand important aspects of their conditions and the pathological basis for their treatment plans. There is a vast amount of information available through the internet and to digest this can be a difficult process for a patient who is already having to cope with a medical condition. The pathologist is often best placed to sieve through this information and offer the patient the relevant detail necessary to understand the condition and the management pathway. Pathologists can provide up-to-date, simple information about malignant and even certain significant benign conditions, and they can do this with the help of several pictorial tools. In this way, the pathologist becomes an even more active member of a clinical team and helps both clinicians and patients to deal with illnesses in a novel way hitherto not considered.     

Optimum strengths for bones liable to fatigue and accidental fracture

Limb bones are liable to fail by fatigue, due to stresses imposed repeatedly in activities such as running. They may also be broken by larger stresses which occur occasionally in accidents. Too weak a bone will probably fail but too strong a bone is unduly heavy. A mathematical model predicts optimum strengths for bones subject to the hazards both of fatigue and of accidents. When accidents are mild and predictable, fatigue is the more important hazard. When they are large and unpredictable they are the more important hazard and stronger bones are generally preferred, but in extreme cases it may become advantageous to dispense with the bone. There is a restricted range of circumstances in which fatigue and accidents are both important hazards. The strengths of many limb bones seem surprisingly low, in the light of the theory and of current knowledge of the fatigue properties of bone.     

Partial Purification and Characterization of Messenger RNA Coding 14-3-2 Protein from Rat Brain

14-3-2 Protein (neuron-specific enolase) is a neuron-specific protein. Using a reticulocyte lysate cell-free system for translation of 14-3-2 protein mRNA, we have partially purified this mRNA by several procedures, including formamide sucrose density centrifugation, formamide polyacrylamide gel electrophoresis (PAGE) and polyuridylic acid (poly(U))-Sepharose affinity chromatography. Using mRNA obtained by these procedures, we could increase the translation ratio of 14-3-2 protein synthesized/total soluble protein synthesized to 7.31%. The overall purification was 37.8-fold. The size of 14-3-2 protein mRNA appears to be about 19-20S, because translation activity of mRNA obtained by sucrose density gradient centrifugation or formamide PAGE was the most active in this RNA size.