Patent pools and clearinghouses in the life sciences

The biopharmaceutical industry is slowly absorbing the idea of collaborative patent licensing models. Recently, two patent pools for developing countries have been launched: the Pool for Open Innovation against Neglected Tropical Diseases initiated by GlaxoSmithKline (GSK), which is referred to as the BIO Ventures for Global Health (BVGH) pool, and the Medicines Patent Pool (MPP) initiated by UNITAID. Various organizations have recommended using pools or clearinghouses beyond the humanitarian dimension where many patents are owned by many different actors. As a first attempt, MPEG LA, which administers patent pools in various technology fields, is now setting up a clearinghouse for patents related to molecular diagnostics. These examples as well as the results from an empirical study provide useful insights for the design and administration of future pools and clearinghouses in the life sciences.     

Metagenomic abundance estimation and diagnostic testing on species level

One goal of sequencing-based metagenomic community analysis is the quantitative taxonomic assessment of microbial community compositions. In particular, relative quantification of taxons is of high relevance for metagenomic diagnostics or microbial community comparison. However, the majority of existing approaches quantify at low resolution (e.g. at phylum level), rely on the existence of special genes (e.g. 16S), or have severe problems discerning species with highly similar genome sequences. Yet, problems as metagenomic diagnostics require accurate quantification on species level. We developed Genome Abundance Similarity Correction (GASiC), a method to estimate true genome abundances via read alignment by considering reference genome similarities in a non-negative LASSO approach. We demonstrate GASiC’s superior performance over existing methods on simulated benchmark data as well as on real data. In addition, we present applications to datasets of both bacterial DNA and viral RNA source. We further discuss our approach as an alternative to PCR-based DNA quantification.     

Ethical issues in the diagnostic genetic testing process

The diagnostic genetic testing process has certain unique ethical features and deserves special consideration. The purpose of this study was to determine through empirical research, using focussed interview, what ethical issues are involved in the diagnostic genetic testing process. This article describes views and perceptions of adult patients, parents of child patients and various personnel groups (n=30). The ethical issues were analysed classified into three main categories: a) personnel characteristics, including personality, professional skills, morals and values; b) realization of ethical principles in the examination process, with subcategories of knowledge, autonomy, data protection and equity; and c) consequences of genetic testing, including patients' control over their own lives, manifestation of heterogeneity and outlook on the world. Problematic ethical issues in all three main categories were described in a more many-sided way by parents and personnel than by adult patients. In the future, attention should be paid to the content areas highlighted by the study, in both clinical practice and further studies.     

Interpretation of diagnostic testing strategies for production and economic usefulness

Veterinarians providing reproductive services use a variety of diagnostic testing methods, including physical examination, laboratory testing, diagnostic imaging, and performance record evaluation. The diagnostic end point may be a physical diagnosis of pregnancy, attainment of puberty, or adequate quality and quantity of sperm; furthermore, it may be a medical diagnosis of reproductive tract pathology, presence of an infectious pathogen, or abnormal hormonal status. Proper interpretation of test results requires an understanding of how sensitivity and specificity (as measures of test accuracy), and prevalence of the condition, affect the interpretation of an individual result. For many diagnostic questions, the proper use of more than one test, either in series or in parallel, allows veterinarians to optimize their diagnostic accuracy and the economic return for the testing strategy.     

Exercise testing as a diagnostic entity in mitochondrial myopathies

Exercise intolerance is one of the most common symptoms in patients with mitochondrial myopathies (MM). At the whole body level, this is characterized by a reduction in maximal oxygen consumption (VO2max) with an excessive carbon dioxide production (VCO2), increased rating of perceived exertion and a hyperdynamic circulatory response at a given exercise intensity. Fewer patients with MM display overt muscle atrophy and weakness even in the absence of a peripheral neuropathy. At the level of the skeletal muscle, the abnormal exercise response in MM patients is characterized by an increase in; delivery of oxygen relative to extraction (reduced myoglobin or hemoglobin desaturation), lactate production, phosphocreatine hydrolysis and time of post-exercise PCr and ADP recovery. Classically, the characterization of exercise intolerance is performed using cycle ergometry with measurements of VO2, VCO2, respiratory exchange ratio (RER = VCO2/VO2), heart rate, minute ventilation, rating of perceived exertion, and cardiac output (where available). Exercise protocols to maximum or for a given time period at a set workload can differentiate MM from controls with a sensitivity of 0.63-0.75 and a specificity of 0.70-0.90. Modified hand-grip exercise protocols, especially if coupled with simultaneous measurements of myoglobin/hemoglobin desaturation (near infra-red spectroscopy) or venous oxygenation, can achieve similar or higher levels of sensitivity and specificity. Similarly, exercise coupled with muscle phosphocreatine/Pi ratios, PCr, pH or ADP recovery kinetics, determined using magnetic resonance spectroscopy are useful in differentiating MM, but are limited by availability, experience and cost. In summary, aerobic exercise testing with some measurement of oxygen consumption can be performed in most institutions and can provide valuable information in the both the work-up of patients with suspected MM as well as in the monitoring of therapy in such patients.     

Current and future hepatitis C virus diagnostic testing: problems and advancements

Serological antibody assays used in hepatitis C virus diagnosis have improved in sensitivity and specificity. However, detection of active viremia or monitoring levels of virus during or after patient treatment is most commonly undertaken using nucleic acid-based technologies. Advancements in diagnostic technologies and implications for managing patients with hepatitis C in various clinical settings are discussed.     

Routine diagnostic testing of Y chromosome deletions in male infertile and subfertile

Male factor infertility elucidated about half the couple of infertility and in around 50% of cases, its etiology remains unknown. The aim of this study was to investigate a predisposing genetic background for Yq deletions and male infertility and effectiveness of molecular genetic approaches have uncovered several etiopathogenetic factors, such as microdeletions of Yq chromosome. The Y chromosome microdeletions removing the azoospermia factor (AZF) regions, which are most common molecular genetic causes of oligospermia or azoospermia. However, with the analysis of Yq deletions, we are able to obtain a better understanding of the clinical significance of genetic anomaly and to the identifying of fertility candidate genes in the AZF regions. Molecular genetic approaches, becomes a routine diagnostic test, that provides an etiology for spermatogenic disturbances, and prognosis for testicular sperm retrieval according to the type of deletion.     

The Evidence Based Medicine approach to diagnostic testing: practicalities and limitations

Evidence-Based Medicine (EBM) has become a popular approach to medical decision making and is increasingly part of undergraduate and postgraduate medical education. EBM follows four steps: 1. formulate a clear clinical question from a patient's problem; 2. search the literature for relevant clinical articles; 3. evaluate (critically appraise) the evidence for its validity and usefulness; 4. implement useful findings into clinical practice. This review describes the concepts, terminology and skills taught to attendees at EBM courses, focusing specifically on the approach taken to diagnostic questions. It covers how to ask an answerable clinical question, search for evidence, construct diagnostic critically appraised topics (CATs), and use sensitivity, specificity, likelihood ratios, kappa and phi statistics. It familiarises readers with the lexicon and techniques of EBM and allows better understanding of the needs of EBM practitioners.     

Improved diagnostic accuracy by repetitive ultrasonic pregnancy testing in sheep

Operator effects and instrument accuracy in using the Scanopreg ultrasonic pregnancy detector in sheep bred at synchronized estrus were studied in three experiments. In the first study, four operators tested the same 101 ewes at 60 and 80 days after breeding. The only significant difference among the four operators was that one operator consistently underestimated pregnancy. Operators did not differ in their diagnoses between days 60 and 80. In the second study, there were no differences between two operators who tested 239 ewes 90 days after breeding. In the third study, one operator tested 318 ewes 60, 70 and 90 days after breeding. The accuracy of diagnosis of pregnancy was at least 90% on each day tested; the corresponding diagnoses of nonpregnancy were 52, 76 and 79% correct. Some ewes that were initially diagnosed as nonpregnant were correctly recognized as pregnant when tested later than day 60. Most of the missed pregnancies were in ewes carrying a single lamb. A second Scanopreg test on day 90 of ewes not diagnosed pregnant on day 60 or 70 identified additional ewes as pregnant. Paired tests (days 70 and 90) recognized 99% of the ewes that eventually lambed.     

Compartmentalized ATP pools produced from adenosine are nuclear pools

Incubation of African green monkey kidney (BS-C-1) cells and mouse fibroblasts (3T6) in the presence of adenosine for 4 hours resulted in increases in the nuclear compartment pools of adenosine 5'-triphosphate (ATP) and nuclear ATP/adenosine 5'-diphosphate (ADP) ratios. Adenine and inosine, which yield increases in total cellular ATP pools and ATP/ADP ratios similar to those promoted by adenosine, do not produce similar increases in the nuclear compartment. Adenosine-promoted increases in nuclear ATP pools were higher in the untransformed, serially propagated, BS-C-1 cells than in the spontaneously transformed 3T6 cells. Adenosine-promoted compartmentalized ATP pools in primary chick embryo fibroblasts were reduced upon transformation of these cells with Rous sarcoma virus, resulting in free mixing of all of the ATP pools synthesized from various salvage precursors. The growth regulatory properties of the nuclear compartment pools of adenine nucleotides is suggested by the big increases in nuclear ATPase and adenosine 5'-monophosphate (AMP) deaminase activities upon the entry of 3T6 cells into the S phase of their cycle. These enzymatic activities would tend to lower the nuclear ATP/ADP ratios and reduce the total adenine nucleotide pools in these nuclei respectively--conditions which were shown by earlier in vitro studies to be favorable to DNA replication.     

Developments in immunological technologies leading to improvements in point-of-care diagnostic testing

Rapid and accurate point of care testing is of great concern, especially in terms of detecting infectious disease outbreaks in developing countries having high population burdens. While numerous detection systems are currently available, care must be taken in choosing those that are reliable and have proven acceptable levels of sensitivity and specificity, based on adequate laboratory and pre-clinical trial testing. Two papers in the current issue show significant advances in technology that could bring Point-of-Care Diagnostic Testing closer to reality for cholera and environmental mycobacteria.     

Synaptic vesicle pools and dynamics

Synaptic vesicles release neurotransmitter at chemical synapses, thus initiating the flow of information in neural networks. To achieve this, vesicles undergo a dynamic cycle of fusion and retrieval to maintain the structural and functional integrity of the presynaptic terminals in which they reside. Moreover, compelling evidence indicates these vesicles differ in their availability for release and mobilization in response to stimuli, prompting classification into at least three different functional pools. Ongoing studies of the molecular and cellular bases for this heterogeneity attempt to link structure to physiology and clarify how regulation of vesicle pools influences synaptic strength and presynaptic plasticity. We discuss prevailing perspectives on vesicle pools, the role they play in shaping synaptic transmission, and the open questions that challenge current understanding.     

Synaptic vesicle pools

Communication between cells reaches its highest degree of specialization at chemical synapses. Some synapses talk in a 'whisper'; others 'shout'. The 'louder' the synapse, the more synaptic vesicles are needed to maintain effective transmission, ranging from a few hundred (whisperers) to nearly a million (shouters). These vesicles reside in different 'pools', which have been given a bewildering array of names. In this review, we focus on five tissue preparations in which synaptic vesicle pools have been identified and thoroughly characterized. We argue that, in each preparation, each vesicle can be assigned to one of three distinct pools.     

Patent Deployment Strategies and Patent Value in LED Industry

This study applies two variables in the measurement of company patent deployment strategies: patent family depth and earn plan ratio. Patent family depth represents the degree to which certain fields and markets are valued by the patent owner. Earn plan ratio defined as the ratio of the number of patent forward citations to patent family size. Earn plan ratio indicates the degree to which a patent family could be cited by later innovators and competitors. This study applies a logistic regression model in the analysis LED industry data. The results demonstrate that patent value has a positive relationship with the patent family depth, and earn plan ratio.     

Two synaptic vesicle pools,vesicle recruitment and replenishment of pools at the Drosophila neuromuscular junction

Drosophila neuromuscular junctions (DNMJs) are malleable and its synaptic strength changes with activities. Mobilization and recruitment of synaptic vesicles (SVs), and replenishment of SV pools in the presynaptic terminal are involved in control of synaptic efficacy. We have studied dynamics of SVs using a fluorescent styryl dye, FM1-43, which is loaded into SVs during endocytosis and released during exocytosis, and identified two SV pools. The exo/endo cycling pool (ECP) is loaded with FM1-43 during low frequency nerve stimulation and releases FM1-43 during exocytosis induced by high K⁺. The ECP locates close to release sites in the periphery of presynaptic boutons. The reserve pool (RP) is loaded and unloaded only during high frequency stimulation and resides primarily in the center of boutons. The size of ECP closely correlates with the efficacy of synaptic transmission during low frequency neuronal firing. An increase of cAMP facilitates SV movement from RP to ECP. Post-tetanic potentiation (PTP) correlates well with recruitment of SVs from RP. Neither PTP nor post-tetanic recruitment of SVs from RP occurs in memory mutants that have defects in the cAMP/PKA cascade. Cyotochalasin D slows mobilization of SVs from RP, suggesting involvement of actin filaments in SV movement. During repetitive nerve stimulation the ECP is replenished, while RP replenishment occurs after tetanic stimulation in the absence of external Ca²⁺. Mobilization of internal Ca²⁺ stores underlies RP replenishment. SV dynamics is involved in synaptic plasticity and DNMJs are suitable for further studies.