Development Of New Protocols Research Articles

Artificial intelligence as an emerging technology in the current care of neurological disorders.

Artificial intelligence (AI) has influenced all aspects of human life and neurology is no exception to this growing trend. The aim of this paper is to guide medical practitioners on the relevant aspects of artificial intelligence, i.e., machine learning, and deep learning, to review the development of technological advancement equipped with AI, and to elucidate how machine learning can revolutionize the management of neurological diseases. This review focuses on unsupervised aspects of machine learning, and how these aspects could be applied to precision neurology to improve patient outcomes. We have mentioned various forms of available AI, prior research, outcomes, benefits and limitations of AI, effective accessibility and future of AI, keeping the current burden of neurological disorders in mind. The smart device system to monitor tremors and to recognize its phenotypes for better outcomes of deep brain stimulation, applications evaluating fine motor functions, AI integrated electroencephalogram learning to diagnose epilepsy and psychological non-epileptic seizure, predict outcome of seizure surgeries, recognize patterns of autonomic instability to prevent sudden unexpected death in epilepsy (SUDEP), identify the pattern of complex algorithm in neuroimaging classifying cognitive impairment, differentiating and classifying concussion phenotypes, smartwatches monitoring atrial fibrillation to prevent strokes, and prediction of prognosis in dementia are unique examples of experimental utilizations of AI in the field of neurology. Though there are obvious limitations of AI, the general consensus among several nationwide studies is that this new technology has the ability to improve the prognosis of neurological disorders and as a result should become a staple in the medical community. AI not only helps to analyze medical data in disease prevention, diagnosis, patient monitoring, and development of new protocols, but can also assist clinicians in dealing with voluminous data in a more accurate and efficient manner.

Variable performance of metamorphosis success indicators in an in vitro culture of freshwater mussel glochidia

The in vitro cultivation of parasitic larvae (glochidia) is becoming an important constituent of culture methods of freshwater mussels (order Unionida) worldwide. Despite rapid methodological progress, published methods for the vast majority of freshwater mussel species do not exist. In the present study, we tested the performance of current approaches to evaluate in vitro culture success quantification. A full factorial design was used to culture Anodonta anatina glochidia in vitro in separate media (M199 and DMEM), antibiotic concentrations and postincubation treatments (dilution methods). The glochidia metamorphosis success (the proportion of successfully transformed glochidia) in each treatment was quantified at two different time points, and the postlarval growth (8 days) of the juveniles was also estimated. The results showed a significant effect of medium type on metamorphosis success at the first time point (day 13) (M199 = 60.98 ± 20.20%, DMEM = 36.10 ± 23.61%; generalized mixed effect models, GLMMs, p < .001) but not at the second (day 21). Similarly, the dilution approach showed a significant variation in metamorphosis success only at the first quantification time point (water and medium = 33.97 ± 24.16%, water only = 63.11 ± 16.03%; GLMM p < .001). In contrast, the postlarval growth quantification showed an increased growth increment in the juveniles in the M199 medium (M199: 65.90 ± 24.20 μm, DMEM = 52.90 ± 19.84 μm; linear mixed effect model p < .001). The study shows that with current methods, the metamorphosis success assessment of in vitro culture protocols can be influenced by the effects of assessment time and dilution approach, two aspects that are not well standardized in the current methodology. Greater emphasis should be placed on the optimization of indicators with direct links to the final criteria, such as postlarval growth or physiology-based parameters. The optimization of metamorphosis success and viability indicators can be an important step towards the increased efficacy of current juvenile production by in vitro techniques and the development of new protocols.

Metal and Non-Metal Catalysts in the Synthesis of Five-Membered S-Heterocycles.

A wide variety of biological activities are exhibited by N, O and S containing heterocycles and recently, many reports appeared for the synthesis of these heterocycles. The synthesis of heterocycles with the help of metal and non-metal catalyst has become a highly rewarding and important method in organic synthesis. This review article concentrated on the synthesis of S-heterocylces in the presence of metal and non-metal catalyst. The synthesis of five-membered S-heterocycles is described here. There is a need for the development of rapid, efficient and versatile strategy for the synthesis of heterocyclic rings. Metal, non-metal and organocatalysis involving methods have gained prominence because traditional conditions have disadvantages such as long reaction times, harsh conditions and limited substrate scope. The metal-, non-metal-, and organocatalyst assisted organic synthesis is a highly dynamic research field. For ßthe chemoselective and efficient synthesis of heterocyclic molecules, this protocol has emerged as a powerful route. Various methodologies in the past few years have been pointed out to pursue more sustainable, efficient and environmentally benign procedures and products. Among these processes, the development of new protocols (catalysis), which avoided the use of toxic reagents, are the focus of intense research.

An Analysis of the Impact of Transient Faults on the Performance of the CAN-FD Protocol

The increasing complexity of distributed real-time control systems in the vehicular area has led to the development of new protocols, such as controller area network with a flexible data rate (CAN-FD), that provides high-bandwidth communication with FD rate. Different topologies are used to interconnect electronic control units in safety-critical applications in the automotive area and the applied communication protocols, such as CAN-FD, must comply with reliability requirements. Moreover, the functional operations must be tested to their limits, since they require appropriate assessment techniques for different application scenarios. Recent research has highlighted that power switching systems cause transient faults that affect the communication network. In light of this concern, this paper explores the IEC/TS 62228:2007 and ISO 26262-3/4/9:2018 standards that can act as guidelines for the development of a test method and testing board for evaluating the impact of electrical fast transients on the performance of a distributed automotive control system. Metrics such as difference jitter, average jitter, and packet loss, are used to determine the fault impact on the control law of a critical vehicular control system. The experiments that were conducted show that during the four test scenarios in which the testing board was used, the average jitter increased from 10.41 to 29.05% in the worst case scenario. These results highlight the importance of carrying out consistent tests to prevent critical situations and that these data can be used in software requirements specification phases to improve reliability in vehicular control systems.

Mapping the Mechanome-A Protocol for Simultaneous Live Imaging and Quantitative Analysis of Cell Mechanoadaptation and Ingression.

Mechanomics, the mechanics equivalent of genomics, is a burgeoning field studying mechanical modulation of stem cell behavior and lineage commitment. Analogous to mechanical testing of a living material as it adapts and evolves, mapping of the mechanome necessitates the development of new protocols to assess changes in structure and function in live stem cells as they adapt and differentiate. Previous techniques have relied on imaging of cellular structures in fixed cells and/or live cell imaging of single cells with separate studies of changes in mechanical and biological properties. Here we present two complementary protocols to study mechanobiology and mechanoadaptation of live stem cells in adherent and motile contexts. First, we developed and tested live imaging protocols for simultaneous visualization and tracking of actin and tubulin mechanoadaptation as well as shape and volume of cells and their nuclei in adherent model embryonic murine mesenchymal stem cells (C3H/10T1/2) and in a neuroblastoma cell line. Then we applied the protocol to enable quantitative study of primary human mesenchymal stem cells in a motile state, e.g., ingression in a three-dimensional, in vitro cell culture model. Together, these protocols enable study of emergent structural mechanoadaptation of the cell's own cytoskeletal machinery while tracking lineage commitment using phenotypic (quantitative morphology measures) and genotypic (e.g., reverse transcription Polymerase Chain Reaction, rtPCR) methods. These tools are expected to facilitate the mapping of the mechanome and incipient mechanistic understanding of stem cell mechanobiology, from the cellular to the tissue and organ length scales.

Innate Immune Cells in Immune Tolerance After Liver Transplantation.

Currently, liver transplantation is the most effective treatment for end-stage liver disease. Immunosuppressive agents are required to be taken after the operations, which have significantly reduced rejection rates and improved the short-term (<1 year) survival rates. However, post-transplant complications related to the immunosuppressive therapy have led to the development of new protocols aimed at protecting renal function and preventing de novo cancer and dysmetabolic syndrome. Donor specific immune tolerance, which means the mature immune systems of recipients will not attack the grafts under the conditions without any immunosuppression therapies, is considered the optimal state after liver transplantation. There have been studies that have shown that some patients can reach this immune tolerance state after liver transplantation. The intrahepatic immune system is quite different from that in other solid organs, especially the innate immune system. It contains a variety of liver specific cells, such as liver-derived dendritic cells, Kupffer cells, liver sinusoidal endothelial cells, liver-derived natural killer (NK) cells, natural killer T (NKT) cells, and so on. Depending on their specific structures and functions, these intrahepatic innate immune cells play important roles in the development of intrahepatic immune tolerance. In this article, in order to have a deeper understanding of the tolerogenic functions of liver, we summarized the molecular mechanisms of immune tolerance induced by intrahepatic innate immune cells after liver transplantation.

Bitcoin private key locked transactions

Bitcoin smart contracts allow the development of new protocols on top of Bitcoin itself. This usually involves the definition of complex scripts, far beyond the requirement of a single signature. In this paper we introduce the concept of private key locked transactions, a novel type of transactions that allows the atomic verification of a given private key (belonging to an asymmetric key pair) during the payment execution.

Promoting Intermolecular C-N Bond Formation under the Auspices of Iodine(III).

The quest for the development of new protocols that provide general conditions for oxidative carbon-nitrogen bond formation has grown over recent years. Within this context, due to feasibility and benignity considerations in biochemical sciences, reactions that rely on main group oxidants as the only promoters have received particular interest. We have recently found that simple protonolysis events enable the incorporation of nitrogenated groups of the bissulfonimide family into the coordination sphere of common iodine(III) complexes such as diacetoxy iodobenzene. The products of the type ArI(OAc)(NTs2) represent rare examples of iodine(III) compounds displaying reactive iodine-nitrogen single bonds. Further protonolysis furnishes the corresponding iodine(III) compounds ArI(NTs2)2 containing two defined iodine-nitrogen single bonds for unprecedented dual transfer of both nitrogenated groups. It is of great synthetic importance that these new compounds contain iodine-nitrogen entities, which upon dissociation in solution lead to electrophilic iodine centers and nucleophilic nitrogen groups. This has enabled the development of a body of conceptually new amination reactions, which do not rely on conventional electrophilic nitrogen reagents but rather employ iodine(III) as an electrophilic activator and bissulfonimides as the source of subsequent nucleophilic amination. Additional diversification arises from the ambident nature of bissulfonimines enabling oxygenation pathways. The exciting chemistry covered in this Account comprises structural features of the reagents (including X-ray analysis), scope and limitation in synthetic amination of different hydrocarbons (including sp-, sp2-, and sp3-hybridized centers as in acetylenes, alkenes, enols, butadienes, allenes, arenes, and alkylketones), and physical-organic and theoretical analysis of the underlying reaction mechanisms. The oxidative transformations with all their rich diversifications originate from the versatile redox chemistry of the iodine(III) and iodine(I) pair, which shares several aspects of transition metal high oxidation state chemistry. For the present aryliodine(III) reagents, steric and electronic fine-tuning is possible through accurate engineering of the arene substituent. In addition to the general reactivity of the I-N bond, chiral aryliodine(III) reagents with defined stereochemical information in the aryl backbone are conceptually compatible with this approach. Thus, the development of enantioselective amination reactions with up to 99% ee was also successful. Several of the active enantioselective reagents have been isolated and structurally characterized. Following this approach for the important class of chiral vicinal diamines, an unprecedented direct diamination of alkenes could be conducted in an enantioselective catalytic manner under full intermolecular reaction control. This latter reaction is based on the precise engineering of a chiral aryliodine(III) catalyst in combination with bismesylimide as nitrogen source. It is the consequence of the precise understanding of the reaction behavior of structurally defined bisimidoiodine(III) reagents.

Synchronized biphotonic process triggering C[sbnd]C coupling catalytic reactions

Activation of aryl(Ar)-halides for CC coupling catalytic reactions using visible light has become one of the most challenging tasks in organic synthesis since it offers effective and safer alternatives to traditional dehalogenation protocols. The insufficient energy provided by visible light to cleave such strong CH alogen bonds certainly makes necessary the development of new protocols to overcome this limitation. We report here the application of photon upconversion (UC) technology based on triplet-triplet annihilation (TTA) to a CC coupling catalytic reaction, a possibility that has not been investigated to date. This synchronized biphotonic process (TTA-UC) activates successfully Ar-halides with visible light. Based on product analysis and spectroscopic experiments, a cascade process combining photophysical and photochemical steps is proposed for the mechanism rationalization. Visible light, ambient temperature and pressure, low-loading metal-free photocatalysts and no additives make this protocol very attractive for applications to the synthesis of fine chemical building blocks, pharmaceuticals, agrochemicals or new materials.

Data Analysis of Multiplex Sequencing at SOLiD Platform: A Probabilistic Approach to Characterization and Reliability Increase

New sequencing technologies such as Illumina/Solexa, SOLiD/ABI, and 454/Roche, revolutionized the biological researches. In this context, the SOLiD platform has a particular sequencing type, known as multiplex run, which enables the sequencing of several samples in a single run. It implies in cost reduction and simplifies the analysis of related samples. Meanwhile, this sequencing type requires an additional filtering step to ensure the reliability of the results. Thus, we propose in this paper a probabilistic model which considers the intrinsic characteristics of each sequencing to characterize multiplex runs and filter low-quality data, increasing the data analysis reliability of multiplex sequencing performed on SOLiD. The results show that the proposed model proves to be satisfactory due to: 1) identification of faults in the sequencing process; 2) adaptation and development of new protocols for sample preparation; 3) the assignment of a degree of confidence to the data generated; and 4) guiding a filtering process, without discarding useful sequences in an arbitrary manner.

Hydrogen‐Transfer‐Mediated α‐Functionalization of 1,8‐Naphthyridines by a Strategy Overcoming the Over‐Hydrogenation Barrier

AbstractA general catalytic hydrogen transfer‐mediated α‐functionalization of 1,8‐naphthyridines is reported for the first time that benefits from a hydrogen transfer‐mediated activation mode for non‐activated pyridyl cores. The pyridyl α‐site selectively couples with the C8‐site of various tetrahydroquinolines (THQs) to afford novel α‐functionalized tetrahydro 1,8‐naphthyridines, a class of synthetically useful building blocks and potential candidates for the discovery of therapeutic and bio‐active products. The utilization of THQs as inactive hydrogen donors (HDs) appears to be a key strategy to overcome the over‐hydrogenation barrier and address the chemoselectivity issue. The developed chemistry features operational simplicity, readily available catalyst and good functional group tolerance, and offers a significant basis for further development of new protocols to directly transform or functionalize inert N‐heterocycles.

Hydrogen-Transfer-Mediated α-Functionalization of 1,8-Naphthyridines by a Strategy Overcoming the Over-Hydrogenation Barrier.

A general catalytic hydrogen transfer-mediated α-functionalization of 1,8-naphthyridines is reported for the first time that benefits from a hydrogen transfer-mediated activation mode for non-activated pyridyl cores. The pyridyl α-site selectively couples with the C8-site of various tetrahydroquinolines (THQs) to afford novel α-functionalized tetrahydro 1,8-naphthyridines, a class of synthetically useful building blocks and potential candidates for the discovery of therapeutic and bio-active products. The utilization of THQs as inactive hydrogen donors (HDs) appears to be a key strategy to overcome the over-hydrogenation barrier and address the chemoselectivity issue. The developed chemistry features operational simplicity, readily available catalyst and good functional group tolerance, and offers a significant basis for further development of new protocols to directly transform or functionalize inert N-heterocycles.

Oxygenation via C-H/C-C Bond Activation with Molecular Oxygen.

The selective oxidation of organic molecules is a fundamentally important component of modern synthetic chemistry. In the past decades, direct oxidative C-H and C-C bond functionalization has proved to be one of the most efficient and straightforward methods to synthesize complex products from simple and readily available starting materials. Among these oxidative processes, the use of molecular oxygen as a green and sustainable oxidant has attracted considerable attention because of its highly atom-economical, abundant, and environmentally friendly characteristics. The development of new protocols using molecular oxygen as an ideal oxidant is highly desirable in oxidation chemistry. More importantly, the oxygenation reaction of simple molecules using molecular oxygen as the oxygen source offers one of the most ideal processes for the construction of O-containing compounds. Aerobic oxidation and oxygenation by enzymes, such as monooxygenase, tyrosinase, and dopamine β-monooxygenase, have been observed in some biological C-H bond hydroxylation processes. Encouraged by these biological transformations, transition-metal- or organocatalyst-catalyzed oxygenation through dioxygen activation has attracted academic and industrial prospects. In this Account, we describe some advances from our group in oxygenation via C-H/C-C bond activation with molecular oxygen as the oxidant and oxygen source for the synthesis of O-containing compounds. Under an atmosphere of O2 (1 atm) or air (1 atm), we have successfully incorporated one or two O atoms from O2 into simple and readily available substrates through C-H, C-C, C═C, and C≡C bond cleavage by transition-metal catalysis, organocatalysis, and photocatalysis. Moreover, we have devised cyclization reactions with molecular oxygen to construct O-heterocycles. Most of these transformations can tolerate a broad range of functional groups. Furthermore, on the basis of isotope labeling experiments, electron paramagnetic resonance spectral analysis, and other mechanistic studies, we have demonstrated that a single electron transfer process via a carbon radical, peroxide radical, or hydroxyl radical is involved in these aerobic oxidation and oxygenation reactions. These protocols provide new approaches for the green synthesis of various α-keto amides, α-keto esters, esters, ketones, aldehydes, formamides, 2-oxoacetamidines, 2-(1H)-pyridones, phenols, tertiary α-hydroxy carbonyls, p-quinols, β-azido alcohols, benzyl alcohols, tryptophols, and oxazoles, which have potential applications in the preparation of natural products, bioactive compounds, and functional materials. In most cases, inexpensive and low-toxicity Cu, Fe, Mn, or NHPI was found to be an efficient catalyst for the transformation. The high efficiency, low cost, high oxygen atom economy, broad substrate scope, and practical operation make the developed oxygenation system very attractive and practical. Moreover, the design of new types of molecular-oxygen- or air-based oxidation and oxygenation reactions can be anticipated.

2-3-10. Development of cerebral activity examination that is simple and robust against repetition by using wearable NIRS

Monitoring of cerebral activity during long-term therapy such as occupational therapy is useful for the development of new protocols and assessments of the therapy. For clinical use, the authors tried to develop an examination by using a wearable Near infra-red Spectroscopy (NIRS) device with a neurocognitive task that is robust against repetition (habituation). The study was approved by the Ethics Committee of Gunma University Graduate School. Participants were fourteen healthy university students. We used a WOT-100, ten channel wearable NIRS device. Each participant underwent three tasks (deceitful reverse rock paper scissors, Stroop test, animal Stroop test) on a zero day, one week after, two weeks after, and three weeks after. Then the integral values of the oxyhemoglobin during the task were calculated. Stroop task was the only task with minimum habituation especially in the right frontal lobes. We concluded that the Stroop task was the most favorable of the three at this time.

High content analysis in amyotrophic lateral sclerosis.

Amyotrophic lateral sclerosis (ALS) is a devastating disease characterized by the progressive loss of motor neurons. Neurons, astrocytes, oligodendrocytes and microglial cells all undergo pathological modifications in the onset and progression of ALS. A number of genes involved in the etiopathology of the disease have been identified, but a complete understanding of the molecular mechanisms of ALS has yet to be determined. Currently, people affected by ALS have a life expectancy of only two to five years from diagnosis. The search for a treatment has been slow and mostly unsuccessful, leaving patients in desperate need of better therapies. Until recently, most pre-clinical studies utilized the available ALS animal models. In the past years, the development of new protocols for isolation of patient cells and differentiation into relevant cell types has provided new tools to model ALS, potentially more relevant to the disease itself as they directly come from patients. The use of stem cells is showing promise to facilitate ALS research by expanding our understanding of the disease and help to identify potential new therapeutic targets and therapies to help patients. Advancements in high content analysis (HCA) have the power to contribute to move ALS research forward by combining automated image acquisition along with digital image analysis. With modern HCA machines it is possible, in a period of just a few hours, to observe changes in morphology and survival of cells, under the stimulation of hundreds, if not thousands of drugs and compounds. In this article, we will summarize the major molecular and cellular hallmarks of ALS, describe the advancements provided by the in vitro models developed in the last few years, and review the studies that have applied HCA to the ALS field to date.

Defined three-dimensional culture conditions mediate efficient induction of definitive endoderm lineage from human umbilical cord Wharton's jelly mesenchymal stem cells.

BackgroundWharton’s jelly-derived mesenchymal stem cells (WJ-MSCs) are gaining increasing interest as an alternative source of stem cells for regenerative medicine applications. Definitive endoderm (DE) specification is a prerequisite for the development of vital organs such as liver and pancreas. Hence, efficient induction of the DE lineage from stem cells is crucial for subsequent generation of clinically relevant cell types. Here we present a defined 3D differentiation protocol of WJ-MSCs into DE cells.MethodsWJ-MSCs were cultured in suspension to generate spheroids, about 1500 cells each, for 7 days. The serum-free differentiation media contained specific growth factors, cytokines, and small molecules that specifically regulate signaling pathways including sonic hedgehog, bone morphogenetic protein, Activin/Wnt, and Notch.ResultsWe obtained more than 85 % DE cells as shown with FACS analysis using antibodies directed against the DE marker CXCR4. In addition, biochemical and molecular analysis of bona-fide DE markers revealed a time-course induction of Sox17, CXCR4, and FoxA2. Focused PCR-based array also indicated a specific induction into the DE lineage.ConclusionsIn this study, we report an efficient serum-free protocol to differentiate WJ-MSCs into DE cells utilizing 3D spheroid formation. Our approach might aid in the development of new protocols to obtain DE-derivative lineages including liver-like and pancreatic insulin-producing cells.Electronic supplementary materialThe online version of this article (doi:10.1186/s13287-016-0426-9) contains supplementary material, which is available to authorized users.

Fine Design of Photoredox Systems for Catalytic Fluoromethylation of Carbon-Carbon Multiple Bonds.

Trifluoromethyl (CF3) and difluoromethyl (CF2H) groups are versatile structural motifs, especially in the fields of pharmaceuticals and agrochemicals. Thus, the development of new protocols for tri- and difluoromethylation of various skeletons has become a vital subject to be studied in the field of synthetic organic chemistry. For the past decades, a variety of fluoromethylating reagents have been developed. In particular, bench-stable and easy-to-use electrophilic fluoromethylating reagents such as the Umemoto, Yagupolskii-Umemoto, Togni, and Hu reagents serve as excellent fluoromethyl sources for ionic and carbenoid reactions. Importantly, the action of catalysis has become a promising strategy for developing new fluoromethylations. For the past several years, photoredox catalysis has emerged as a useful tool for radical reactions through visible-light-induced single-electron-transfer (SET) processes. Commonly used photocatalysts such as [Ru(bpy)3](2+) and fac-[Ir(ppy)3] (bpy = 2,2'-bipyridine; ppy = 2-pyridylphenyl) have potential as one-electron reductants strong enough to reduce those fluoromethylating reagents, resulting in facile generation of the corresponding fluoromethyl radicals. Therefore, if we can design proper reaction systems, efficient and selective radical fluoromethylation would proceed without any sacrificial redox agents, i.e., via a redox-neutral process under mild reaction conditions: irradiation with visible light, including sunlight, below room temperature. It should be noted that examples of catalytic fluoromethylation of compounds with carbon-carbon multiple bonds have been limited until recent years. In this Account, we will focus on our recent research on photoredox-catalyzed fluoromethylation of carbon-carbon multiple bonds. First, choices of the photocatalyst and the fluoromethylating reagent and the basic concept involving a redox-neutral oxidative quenching cycle are explained. Then photocatalytic trifluoromethylation of olefins is discussed mainly. Trifluoromethylative difunctionalization reactions, i.e., simultaneous introduction of the CF3 group and a different functional group across carbon-carbon double bonds, are in the middle of the discussion. Oxy-, amino-, and ketotrifluoromethylation allow us to synthesize various organofluorine compounds bearing C(sp(3))-CF3 bonds. In addition, the synthesis of valuable trifluoromethylated alkenes is also viable when the olefins have an appropriate leaving group or undergo deprotonation. The present reaction system features high functional group compatibility and high regioselectivity. Furthermore, future prospects, especially trifluoromethylative difunctionalization of alkynes and difluoromethylation of alkenes, are also discussed.

Lessons for livestock genomics from genome and transcriptome sequencing in cattle and other mammals.

BackgroundDecreasing sequencing costs and development of new protocols for characterizing global methylation, gene expression patterns and regulatory regions have stimulated the generation of large livestock datasets. Here, we discuss experiences in the analysis of whole-genome and transcriptome sequence data.MethodsWe analyzed whole-genome sequence (WGS) data from 132 individuals from five canid species (Canis familiaris, C. latrans, C. dingo, C. aureus and C. lupus) and 61 breeds, three bison (Bison bison), 64 water buffalo (Bubalus bubalis) and 297 bovines from 17 breeds. By individual, data vary in extent of reference genome depth of coverage from 4.9X to 64.0X. We have also analyzed RNA-seq data for 580 samples representing 159 Bos taurus and Rattus norvegicus animals and 98 tissues. By aligning reads to a reference assembly and calling variants, we assessed effects of average depth of coverage on the actual coverage and on the number of called variants. We examined the identity of unmapped reads by assembling them and querying produced contigs against the non-redundant nucleic acids database. By imputing high-density single nucleotide polymorphism data on 4010 US registered Angus animals to WGS using Run4 of the 1000 Bull Genomes Project and assessing the accuracy of imputation, we identified misassembled reference sequence regions.ResultsWe estimate that a 24X depth of coverage is required to achieve 99.5 % coverage of the reference assembly and identify 95 % of the variants within an individual’s genome. Genomes sequenced to low average coverage (e.g., <10X) may fail to cover 10 % of the reference genome and identify <75 % of variants. About 10 % of genomic DNA or transcriptome sequence reads fail to align to the reference assembly. These reads include loci missing from the reference assembly and misassembled genes and interesting symbionts, commensal and pathogenic organisms.ConclusionsAssembly errors and a lack of annotation of functional elements significantly limit the utility of the current draft livestock reference assemblies. The Functional Annotation of Animal Genomes initiative seeks to annotate functional elements, while a 70X Pac-Bio assembly for cow is underway and may result in a significantly improved reference assembly.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0237-6) contains supplementary material, which is available to authorized users.

Historical development of institutional arrangements for forest monitoring and REDD + MRV in Peru: Discursive-institutionalist perspectives

The goal of reducing emissions from deforestation and forest degradation, and the roles of conservation, sustainable management of forests and enhancement of forest carbon stocks in developing countries (REDD+) under UNFCCC has triggered a new discussion on forest resource assessments in these countries. The international process on measurement, reporting and verification of REDD+ outcomes (REDD+ MRV) expands the scope of forest inventories to include quantification of forest carbon stocks and their changes for results-based REDD+ payments. UNFCCC decisions also specify methods to be used, and actors to be involved. Although forest management in developing countries has clearly been influenced by international processes in the past, exactly how and to what extent REDD+ MRV has affected institutional arrangements for forest assessments in developing countries remains unknown. Using as a theoretical framework Discursive-Institutionalism, a concept derived from political science, this paper examines (1) the historical evolution of institutional arrangements for forest inventories in Peru; and (2) how and to what extent their development has been shaped by international processes on forests, and, more recently, specifically by REDD+ MRV. The findings show that the international REDD+ MRV discussion has expanded the objectives of forest assessments in Peru, inspired the mobilization of new actors and resources, and spawned the development of new protocols for forest assessments. However, the ‘depth’ of these changes is not yet extensive, since the new rules for forest inventories have not yet been formally adopted, and the institutes envisaged to implement forest inventories, including measurement of carbon stocks and their changes, have not been established.

Recent Advances in Transition-Metal-Catalyzed Synthesis of Coumarins

Coumarin is a privileged scaffold found in a large number of biologically active natural products, pharmaceuticals and agrochemicals, and functionalized coumarins are also widely employed as materials. For this reason, considerable interest has been focused on the development of new protocols to access this heterocyclic moiety in the past few decades. Among the numerous methods developed so far, transition-metal-catalyzed reactions are the most attractive methodologies for the synthesis of coumarins under rather mild reaction conditions. This review provides an overview of the recent developments in this field. 1 Introduction 2 Palladium Catalysis 3 Platinum Catalysis 4 Cobalt Catalysis 5 Copper Catalysis 6 Gold Catalysis 7 Iron Catalysis 8 Nickel Catalysis 9 Rhodium Catalysis 10 Ruthenium Catalysis 11 Zinc Catalysis 12 Conclusion