Small mammal abundances are frequently limited by resource availability but predators can exert strong lethal (direct mortality) and non-lethal limitations (e.g. depressed site-level activity). Artificially increasing resource availability for small mammals provides a unique opportunity to examine predator-prey interactions. We monitored the 3-year response of arboreal rodents and their predators at nest platforms (n = 598; 23 young forest sites), using annual inspections and remote cameras (n = 168). One year after adding nest platforms we found a 2.9 to 9.2-fold increase in red tree vole (Arborimus longicaudus) use at the site-level, but little use by potential predators. Predator use of nest platforms began in year two and increased in year three of the study. Most potential nest predators were positively correlated with tree vole presence at nest platforms but effect size and direction varied with temporal grain considered (e.g. hour vs day time-bin widths). Flying squirrels (Glaucomys humboldtensis) were positively correlated with disturbances caused by digging birds. Using a Cormack-Jolly-Seber model and encounter histories produced from visual re-captures of marked tree voles, we estimated apparent annual survival to be 0.099 ± 0.057 (x̄ ± 1 SE) for females and 0.005 ± 0.014 for males. Weasels (Mustela spp.), an active seeking predator, preyed upon tree voles most frequently with 10% of weasel detections resulting in mortality of a tree vole (n = 8) whereas owls, an ambush predator, did not prey upon tree voles at nest platforms even though they were detected at similar frequencies as weasels. Weasels also exerted potential non-lethal effects and we observed a >10-fold reduction in the number of tree vole detections per week after weasel detection. Our evidence indicates that predators exert direct and indirect effects on tree vole populations with active seeking predators being the most important predators at nest sites.

We seek to explain why the hydrogen bond possesses unusual strength in small water clusters that account for many of the complex behaviors of water. We have investigated and visualized the donation of covalent character from covalent (sigma) to hydrogen-bonds, by calculating the eigenvector coupling properties of QTAIM, stress tensor σ(r) and Ehrenfest Force F(r) on the F(r) molecular graph. The next generation 3-D bond-path framework sets are presented and only the F(r) bond-path framework sets reproduce the earlier finding on the coupling between covalent (sigma) and hydrogen-bonds that possess a degree of covalent character. The directional character of the covalent (sigma) and hydrogen-bonds 3-D bond-path framework sets for the F(r) explains differences found in the earlier results from QTAIM and the stress tensor σ(r).

Pipeline transmission is one of the most important ways of oil and gas transportation, and its safety is majorly threatened by fatigue fracture that generally occurs in heat-affected zone (HAZ) adjacent to the welded joint of the pipeline. Therefore, studying the fatigue properties of HAZ is important. In this work, the microstructure and mechanical properties in the HAZ of a X80 pipe were accurately simulated by thermal simulation. The fatigue life and crack growth rate of typical sub-HAZ were tested. Results showed that the fine grain HAZ had the lowest strength and fatigue life. By contrast, the coarse grain HAZ had the highest strength, but its fatigue life was lower than that of the intercritical HAZ. Furthermore, the microstructure of each sub-HAZ and its effect on fatigue properties were discussed in detail. The results will reveal the effects of microstructure and mechanical properties on the service safety of pipeline transportation.

Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across non-model organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effective population size, inbreeding, demographic history, and population structure, that are critical for conservation efforts. Moreover, population genomics studies can identify particular genetic loci and variants responsible for inbreeding depression or adaptation to changing environments, allowing for conservation efforts to estimate the capacity of populations to evolve and adapt in response to environmental change and to manage for adaptive variation. While connections from basic research to applied wildlife conservation have been slow to develop, these connections are increasingly strengthening. Here we review the primary areas in which population genomics approaches can be applied to wildlife conservation and management, highlight examples of how they have been used, and provide recommendations for building on the progress that has been made in this field.

1. Understanding how invasive species respond to novel environments is limited by a lack of sensitivity and throughput in conventional biomonitoring methods. Arthropods in particular are often difficult to monitor due to small size, rapid lifecycles, and/or visual similarities with co-occurring species. This is true for the agromyzid leafminer, Liriomyza sativae, a global pest of vegetable and nursery industries that has recently established in Australia. 2. A highly robust method based on environmental DNA (eDNA) was developed exploiting traces of DNA left inside ‘empty’ leaf mines, which are easier to collect and persist longer in the environment than the insect. This extended the window of possible diagnosis to at least 28 days since a leaf mine became empty. The test allowed for visually indistinguishable leafmining damage caused by L. sativae to be genetically differentiated from that of other flies. 3. Field application resulted in the identification of new local plant hosts for L. sativae, including widely distributed weeds and common garden crops, with important implications for the pest’s ability to spread. Moreover, the test allowed for the confirmation of L. sativae on an island with a previously unconfirmed population. 4. The developed eDNA method is likely to become an important tool for L. sativae and other leafmining species of biosecurity significance, which, historically, have been difficult to detect, diagnose and monitor. More generally, eDNA is emerging as a highly sensitive and labour-efficient surveillance tool for difficult to survey species to improve outcomes for agricultural industries, global health, and the environment.

Monarch butterflies are known for their spectacular annual migration in eastern North America, with millions of monarchs flying up to 4,500 kilometers to overwintering sites in central Mexico. Monarchs also live west of the Rocky Mountains, where they travel shorter distances to overwinter along the Pacific Coast. It is often assumed that eastern and western monarchs form distinct evolutionary units, but genomic studies to support this notion are lacking. We used a tethered flight mill to show that migratory eastern monarchs have greater flight performance than western monarchs, consistent with their greater migratory distances. However, analyzing more than 20 million SNPs in 43 monarch genomes, we found no evidence for genomic differentiation between eastern and western monarchs. Genomic analysis also showed identical and low levels of genetic diversity, and demographic analyses indicated similar effective population sizes and ongoing gene flow between eastern and western monarchs. Gene expression analysis of a subset of candidate genes during active flight revealed differential gene expression related to non-muscular motor activity. Our results demonstrate that eastern and western monarchs maintain migratory differences despite ongoing gene flow, and suggest that migratory differences between eastern and western monarchs are not driven by select major-effects alleles. Instead, variation in migratory distance and destination may be driven by environmentally induced differential gene expression, or by many alleles of small effect.

Skin drug delivery is an emerging route in the drug development, due to its great advantages, thus leading to an urgent need to understand the behaviour of active pharmaceutical ingredients into/through the skin. This knowledge is crucial in the early stages of product design and development. Yet, given the skin barrier properties as one of the first body’s natural defence systems, it can act as an obstacle to the successful outcome of a skin drug therapy. To unravel the mechanisms underlying this barrier, reductionist strategies have designed several models with different levels of complexity and integrity, using non-biological and biological components. Besides the detail of information and resemblance to the in vivo Human skin that each in vitro model offers, the technical and economic efforts required should be considered when selecting the most adequate model for the intended research. This review provides an outline of the most commonly applied skin models, including healthy and diseased conditions, lab developed systems and commercialized models, their advantages and limitations and, also an overview of the new trends in skin engineered models.

Using monotonicity methods, the Lagrange multiplier rule and some variational arguments, we consider a type of localization results pertaining to the existence of critical points to action functionals on a closed ball. A variant of the Schechter critical point theorem on a ball in Hilbert and Banach spaces is obtained. Applications to nonlinear Dirichlet problem and to partial difference equations are given in the final part of this paper.

Our interest itself of this paper is strongly inspired from an open problem in the paper published by D’Abbicco. In this article, we would like to study the Cauchy problem for a weakly coupled system of semi-linear structurally damped wave equations. The main goal is to find the threshold, which classifies the global (in time) existence of small data solutions or the nonexistence of global solutions under the growth condition of the nonlinearities.

A document by Mo Faheem. Click on the document to view its contents.

In this paper, we obtain a Korovkin type approximation theorem via Abel convergence. As an application of this theorem, we construct a non-tensor product BBH type operators in multivariate case. Finally, we proved that our new approximation result works but its classical case does not work.

In the paper, we consider a three-dimensional model of fluid-solid interaction when a thermo-electro-magneto-elastic body occupying a bounded region Ω+ is embedded in an inviscid fluid occupying an unbounded domain $\Omega^{-}=^3 \setminus $. In this case, we have a six-dimensional thermo-electro-magneto-elastic field (the displacement vector with three components, electric potential, magnetic potential, and temperature distribution function) in the domain Ω+, while we have a scalar acoustic pressure field in the unbounded domain Ω−. The physical kinematic and dynamic relations are described mathematically by appropriate boundary and transmission conditions. With the help of the potential method and theory of pseudodifferential equations, we prove the uniqueness and existence theorems for the corresponding boundary-transmission problems in appropriate Sobolev-Slobodetskii and Hölder continuous function spaces.

Background and Purpose Alzheimer’s disease (AD) pathogenesis involves amyloid-β (Aβ) aggregation where the intermediate oligomers are considered the prime toxic species. Here, we aimed to identify an effective peptide sequence from a medicinal plant-derived enzyme having anti-amyloidogenic properties against Aβ. Experimental Approach LC-MS/MS followed by computational analysis identified the active peptide (termed here as Pactive). Visualization techniques along with biophysical and biochemical approaches were used to determine the anti-amyloidogenic potency of the purified enzyme and peptides identified from the enzyme. Cytotoxicity was measured on SHSY-5Y cell lines. Interaction studies were done with bio-layer interferometry (BLI) and bio-stability of the peptide was assessed by NMR. Pactive induced conformational alterations of Aβ monomer and oligomers was determined with DSC and NMR. Key Results A small heptameric peptide (Pactive) identified form a medicinal plant-derived fibrinolytic enzyme proved to be a multifunctional inhibitor against Aβ aggregation. The results suggested that Pactive arrests Aβ molecules in non-toxic off-pathway oligomers that can no longer participate in the cytotoxic fibrillation pathway. Mechanistically, Pactive binding induces conformational alterations in the Aβ molecule, thus modulating its hydrophobicity, one of the key players in inducing aggregation. Conclusions and Implications The study identified a natural peptide Pactive (GFLLHQK) that displays potential anti-amyloidogenic properties against Aβ aggregation. The bio-stability of Pactive in human blood serum as well as its non-toxic nature makes it a promising therapeutic candidate against Alzheimer’s, for which no disease-modifying treatments are available till date.

Abstract Background Malaria in pregnancy is one of the serious global problems of our time. There were wide concerns about IPT-DP versus IPT-SP for prevention of malaria during pregnancy. Objectives To assess the current latest evidence on the efficacy and safety of dihydroartemisinin-piperaquine versus sulfadoxine-pyrimethamine for malaria in pregnancy. Search Strategy The Cochrane Library, EMBASE, PubMed and Web of science were searched from the earliest publication date available to July 4, 2019 Selection Criteria We included randomized controlled trials comparing dihydroartemisinin-piperaquine with sulfadoxine-pyrimethamine for malaria in pregnancy. Data Collection and Analysis Outcomes were analyzed using Risk ratios (RR) and 95% confidence intervals (CI). We did subgroup analysis about different intervals, including 4-6 or 8 weeks. Main Results A total of five studies with 4660 HIV-uninfected pregnant women in area of high malaria-transmission intensity were included in final synthesis. Meta-analysis showed dihydroartemisinin-piperaquine for intermittent preventive treatment resulted in lower rates of placental malaria (RR=0.50; 95%CI, 0.43–0.59) and infection with malaria parasites at delivery (RR=0.05; 95%CI, 0.01–0.24). In the subgroup analysis, dihydroartemisinin-piperaquine for intermittent preventive treatment at 4-6 weeks of administration was associated with a better effect for infection with malaria parasites at delivery. Conclusions Dihydroartemisinin-piperaquine was a promising alternative drug to sulfadoxine-pyrimethamine for intermittent preventive treatment in settings with high sulfadoxine-pyrimethamine resistance, especially at 4-6 weeks of administration. Based on real-world and other epidemiological settings, more data will be needed to identify the risk of adverse effects.

Objective Since the outbreak of Coronavirus Disease 2019 (COVID-19) in Singapore in January 2020, our maternity centre at Singapore General Hospital has devised and implemented contingency protocols to manage COVID-19 suspected or infected pregnant mothers. These aimed to deliver effective care while ensuring the safety of our front-line healthcare workers. Methods The epidemiology and pathogenicity of SARS-COV-2 was compared to the Severe Acute Respiratory Syndrome outbreak in 2003. Our protocols were constructed following multidisciplinary discussions. These workflow processes include triage, isolation, determination of admission criteria and subsequent secured transfers to dedicated isolation wards. Intrapartum management policies including mode of delivery were reviewed with the focus on minimising maternal-fetal transmission. Postpartum care (breastfeeding and skin-to-skin contact) policies were re-evaluated. Results The Centre conducted several multidisciplinary in-situ simulations which identified potential latent threats and deficiencies in infection containment. These were gaps in communication and co-ordination between operating theatre, obstetrics and neonatal teams resulting in delayed transfers. A particular vulnerability was the consistent breaches observed in the donning and doffing of personal protective equipment. This led to a need for additional personnel to guide and police strict adherence among healthcare workers. Conclusion Operational readiness leverage on robust contingency protocols which must be subjected to simulation and scrutiny with subsequent revision. We recommend deploying additional supervisory manpower to maintain strict adherence to infection prevention protocols. Effective preparation is key in maintaining high clinical standards of obstetric care while ensuring safety of healthcare workers during this ongoing pandemic. Funding No funding nor conflicts of interest.

A document by Oleg Volkov. Click on the document to view its contents.

Mini-commentary on BJOG-19-1139.R1: Mesh inlay, mesh kit or native tissue repair for women having repeat anterior or posterior prolapse surgery: randomised controlled trial (PROSPECT)

Wind erosion has become one of the major causes of land degradation on the Qinghai-Tibet Plateau (QTP). Assessing wind erosion dynamics is critical to forecast wind erosion and formulate desertification control strategies. In this study, the spatial and temporal variations in wind erosion on the QTP from 1980 to 2015 were evaluated by the revised wind erosion equation (RWEQ). Furthermore, the relative contributions of climate change and human activities to wind erosion were analysed to identify the drivers. The results showed that wind erosion intensity on the QTP increased continuously from southeast to northwest. Areas with moderate or high soil erosion intensity (>25 t∙hm2∙a-1), accounting for 53.48% of the region, were mainly distributed on the western and northern parts of the plateau. The mean annual soil wind erosion modulus (SWEM) of the total region during 1980-2015 was 32.08 t∙hm2∙a-1, with an obvious decline at a rate of approximately 0.14 t∙hm2∙a-1 in this period. However, 9.99% of the study area showed a relatively significant increase, and these areas were mostly located in the northwestern part of the region. Climate change, especially variation in wind speed, was the dominant factor that affected wind erosion over the whole plateau, whereas the impacts of human activities such as grazing and ecological restoration policies and programmes were comparatively small and usually more localized.

ABSTRACTAnalogous to human leukocyte antigens, blood group antigens are surface markers on the erythro-cyte cell membrane whose structures differ among individuals and which can be serologically identified. The Blood Group Antigen Gene Mutation Database (BGMUT) is an online repository of allelic variations in genes that determine the antigens ofvarious human blood group systems. The database is manually curated with allelic information collated from scientific literature and from direct submissions from research laboratories. Currently, the database documents sequence variations of a total of 1251 alleles of all 40 gene loci that together are known to affect antigens of 30 human blood group systems. When available, information on the geographic or ethnic prevalence of an allele is also provided. The BGMUT website also has general in-formation on the human blood group systems and the genes responsible for them. BGMUT is a part ofthe dbRBC resource of the National Center for Biotechnology Information, USA, and is available online at  http://www.ncbi.nlm.nih.gov/projects/gv/rbc/xslcgi.fcgi?cmd=bgmut. The database should be of use to members of the transfusion medicine community, those interested in studies of genetic variation and related topics such as human migrations, and students as well as members of the general public.INTRODUCTIONThe BGMUT Blood Group Antigen Gene Mutation Database documents variations in genes that encode antigens for human blood groups. It is a part of the dbRBC resource (1) of the National Center for Biotechnology Information (NCBI) of USA and can be freely accessed online at http://www.ncbi.nlm.nih.gov/projects/gv/rbc/xslcgi.fcgi?cmd=bgmut.Recent documentation of the extent and the surprisingly high numbers of mutations in the human genome have suggested that, perhaps with the exception of identical twins, no two individuals bear exact copies of chromosomal DNA. In those studies, DNA of random subjects is compared but more often phenotypic differences observed in disease states, whether single gene inherited disorders or in association studies of complex conditions are taken as criteria for selection of individuals whose DNA is examined for sequence changes. In the latter studies, large fragments of DNA are usually examined and compared statistically to matched control individuals. Changes in blood group phenotypes are another criterion for selection of subjects who may show differences in sequences of two or more defined sets of genes. These genes encode a group of red cell membrane proteins that are polymorphic in the population and are defined as blood group antigens; in addition, these genes may encode certain glycosyl transferases that are involved in the synthesis of red cell membrane glycans whose structures also differ among individuals. The former group consists of structural molecules, channels, adhesion molecules or enzymes and, excluding their red cell membrane location, can be considered as representative of any human protein, whereas the latter are similar tomost other glycosyl transferases. Evidence suggests that sequence changes in these proteins or even their absence,such as in null phenotypes, is not, in most cases, physiologically harmful. The proteins or the glycans fulfill their role as blood group antigens because they are polymorphic in the population and their sequence changes can be readily predictedby serological approaches; they are known as ‘antigens ’because in the course of transfusion, or pregnancy, the presence of a variant protein epitope is recognized as‘non-self’ and may ultimately result in an adverse immunological reaction. The use of transfusion being ubiquitous in the practice of medicine, populations world-wide are serologically tested and variant antigens and their genes, in contrast to many other variant genes arebeing documented in a large number of diverse populations. Although some variants occur rarely and, may onlybe observed in a single individual or family, others appearin unexpectedly large populations, such as the MiIIIphenotype encoded by the MiIIIGYPAgene, in Taiwan (incidence can be as high as 88% among Ami tribes) (2).For many alleles, the database also provides informationon the geographic or ethnic origin of alleles and/or theirassociated serological phenotypes when such informationwas presented in the publications describing the alleles.  This may be of use to those interested in populationmigrations.HISTORY AND CURRENT STATEBGMUT was developed in 1999 as a locus-specific gene mutation database under the aegis of the HumanVariation Genome Society. It was curated under the direction of one of the authors (OOB) with original information contributed by more than a dozen blood group system experts. The database was hosted online by the Department of Biochemistry at the Albert Einstein College of Medicine, New York. BGMUT was identifiedas one of three model locus-specific databases from morethan 200 in a scholarly review (3). In 2006, BGMUTbecame a part of the dbRBC resource of the NCBI.  At dbRBC, curatorship and direction for maintenanceof the database has been provided by another of the authors (WH). The number of alleles in BGMUT has ap-proximately doubled since 2004 when the database wasfirst described in a scholarly publication (4). This publica-tion has been referred to many times in the scientific literature indicating that BGMUT has been a usefulresource. Links to BGMUT database records are availableon relevant pages of the Wikipedia online encyclopedia,and on many of NCBI’s online resources. BGMUT is alsoa part of the PhenCode project which attempts to integrate genetic variation data with the UCSC Genome Browser (5).As of August 2011, BGMUT had 1251 alleles belongingto 40 genes that are together responsible for 30 humanblood group systems (Table 1). Alleles of some genes, such as ABO and RHCE/D which are, respectively, responsible for the ABO and Rh blood group systemsmost frequently examined in the populations, are morenumerous than those of others (Table 1). As per theInternational Society for Blood Transfusion, there are 30human blood group systems (http://ibgrl.blood.co.uk/ISBT%20Pages/ISBT%20Terminology%20Pages/Table%20of%20blood%20group%20systems.htm), all of whichare covered by BGMUT. The Globoside (GLOB) system iscurrently considered a part of the P1PK system inBGMUT, which additionally considers the system of T and Tn antigens as a separate blood group system.DATABASE ARCHITECTUREBGMUT is accessible online for view, search or for ad-ministration as a website in the form of HTML (hyper-text markup language) pages (Figures 1 and 2).  A Microsoft SQL Server relational database is used fordata storage. Programmatic code in SQL (structuredquery language), C++and XSLT (extensible structuredlanguage transformations) languages is used for inter-action with the SQL Server database and for renderingBGMUT’s web-based interface. Raw data on all or asubset of the alleles described in BGMUT can be down-loaded as tab-delimited or comma-separated (CSV) textformats from the BGMUT website. Compilations ofallelic sequences for the ABO, H, MNS and Rh systemsin the Microsoft Excel format are also available fordownload.DATABASE CURATION AND ALLELE SUBMISSIONThe BGMUT database is curated manually. Allelic information is periodically collated from scientific literature, asis the case for a majority of the alleles listed in BGMUT, or is obtained as direct submissions from researchers through the database website. During the process ofcuration, good quality of methods used in a study is ascertained. The new candidate allele’s sequence that has been published and/or submitted to a publicly available repository such as NCBI’s GenBank is compared to BGMUT’s reference allele for the gene sequence. The sequence positions and the kinds of the deduced aminoacid changes are also verified. Authors are consulted incase of a question or disagreement. For direct submission of information on a new allele for inclusion in the database, a scientific publication describing the allele is not required. However, submitters are encouraged to deposit the allele’s sequence in a publicly available repository. In the absence of a scientific publication, this is arequirement.ALLELES IN BGMUTAlleles in BGMUT are grouped by the blood group system that the genes they belong to affect. For each allele in the database, BGMUT provides details on the nucleotide changes and the deduced amino acid changes in the protein encoded by the gene the allele belongs to. These changes are in context of a ‘reference’ allele that itself is included in BGMUT, and is the same for all alleles of agene. Besides the information on the sequence changes, BGMUT also details for an allele the frequency of occurrence, the associated blood group phenotype, references to the studies that identified and characterized the allele and accession numbers of the relevant sequences in NCBI GenBank when such information is available. GenBank accession numbers, however, are not available for many alleles because though they have been described in published literature, their sequences were not deposited inthe repository by the authors. When known, the regions of the gene or cDNA that were sequenced to identify the allele, the prevalence of the allele in different geographical regions or ethnic populations and association of the allele with diseases are also noted. Often, a name is also provided for an allele. Names make it easier to refer to alleles and can indicate the associated phenotype and/or nucleotide or amino acidvariation. Table 1. Blood group systems in the BGMUT database

ABSTRACTThe Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-through put gene expression data. GEO provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-through put gene expression and genomic hybridization experiments.GEO is not intended to replace in house gene expression databases that benefit from coherent data sets,and which are constructed to facilitate a particular analytic method, but rather complement these byacting as a tertiary, central data distribution hub. The three central data entities of GEO are platforms,samples and series, and were designed with gene expression and genomic hybridization experiments in mind. A platform is, essentially, a list of probes that define what set of molecules may be detected. A sample describes the set of molecules that are being probed and references a single platform used to generate its molecular abundance data. A seriesorganizes samples into the meaningful data setswhich make up an experiment. The GEO repository ispublicly accessible through the World Wide Web a thttp://www.ncbi.nlm.nih.gov/geo.BACKGROUNDMolecular biological experiments utilizing high-through puthybridization array- and sequencing-based techniques havebecome extremely popular in recent years (1–3). These tech-niques have been used to measure the molecular abundance ofmRNA and genomic DNA either in absolute or relative terms.Mainly contributing to this popularity is the highly parallelnature of these techniques and the concomitant conservation oftime and resources brought about by the large number ofsimultaneous (or near-simultaneous) molecular samplingevents performed under very similar conditions.For a number of years there has been a growing desire forthese high-throughput data sets to be made publicly availableonce research findings have been published in the scientific literature—similar to journal and public funding requirementsfor the public release of biological sequence data. There have also been calls for the establishment of a public repository for (at least the gene expression microarray subset of) these data sets (4–6),and journals and public funding agencies have begun to makepublic availability of high-throughput data a condition of publication (7) or funding (e.g. NINDS request for proposalsBAA-RFP-NIH-NINDS-01–03, p. 76 at http://www.ninds.nih.gov/funding/2rfp_01_03.pdf), respectively. Recognizing the desire that this data should be made widely available, several laboratories and institutions have constructed primary and secondary Internet resources to distribute these high-throughput data sets(Table 1). Over the last several years, there has been an international effort to catalog the minimal set of information which is necessary in order for microarray experiments to be properly interpreted and to be comparable with one another (6). The codification and publication of this set of guidelines will be invaluable as aguide for high-throughput gene expression and genomic hybridization data producers and data repositories. We feel,however, that over-zealous application of these guidelines insetting standards and requirements must be avoided because it will stifle a rapidly developing and technically challenging field.  Therefore, our primary goal in creating the Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo) was to attempt to cover the broadest spectrum of high-through put experimental methods possible and remain flexible and responsive to future trends, rather than setting rigid requirements and standards for entry. In taking this approach, however, we recognize that there are obvious, inherent limitations to functionality and analysis that can be provided on such heterogeneous data sets.Hence, GEO is not intended to replace or match primary and secondary resources that operate on homogeneous data sets, but instead to serve as a complementary tertiary resource for the storage and retrieval of public high throughput gene expression and genomic hybridization data.REPOSITORY DESIGN GEO segregates data into three principle components, platform,sample and series (Table 2), each of which is accessioned(i.e. given a unique and constant identifier) in a relational data-base (Fig. 1). To achieve an open and flexible design that allows storage and retrieval of very diverse data types, the data are not fully granulated within the database. Instead, a tab-delimited ASCII table is stored for each platform and each sample. The table consists of multiple columns with accompanying column header names. The data within this table are currently partially extracted for indexing, but may be further extracted for more extensive search and retrieval. In addition, any number of supplementary columns may be provided by the submitter for the inclusion of additional, submitter-defined information.An instance of a platform is, essentially, a list of probes that define what set of molecules may be detected in any experiment utilizing that platform. For example, the platform data table may contain GEO-defined columns identifying the position and biological reagent contents of each probe (spot) such as a GenBank accession number, open reading frame (ORF) name and clone identifier, as well as submitter-defined columns.Platform accession numbers have a ‘GPL’ prefix.An instance of a sample describes the derivation of the set of molecules that are being probed and utilize platforms to generate molecular abundance data. Each sample has one, and only one, parent platform which must be previously defined.For example, a sample data table may contain columns indicating the final, relevant abundance value of the corresponding spot defined in its platform, as well as any other GEO-defined(e.g. raw signal, background signal) and submitter-defined columns. Sample accession numbers have a ‘GSM’ prefix.An instance of a series organizes samples into the meaningful data sets which make up an experiment, and are bound together by a common attribute. Series accession number shave a ‘GSE’ prefix.

This paper investigated the rate of gully formation and development, and its impacts on land competition and crop yield reduction in the Genbo Wonz Watershed, north-west highlands of Ethiopia. Geometrical gully dimension measurements, field observations and satellite imagery assessment have been performed selecting 22 gullies. As a result, road construction and design problems of soil and water conservation practices (SWCPs) were found to be important causes of gully formation and development. The total volume of soil loss from 22 gullies in three decades was ~340, 957 t, changing ~10 ha agricultural land to unproductive land. The annual rate of gully erosion was found to be ~62 t ha-1 with an average gully density of 16.4 m ha-1. Gully erosion also results in loss of 24 t yr-1 Teff grain yield (Eragrostis teff, E. abysainica) and 14 t yr-1 animals forage. To arrest the problem, proper design of SWCPs within farmlands, appropriate runoff discharge mechanisms along roads and controlled grazing systems within the grazing lands ought to be executed.

Fungi form diverse communities and play essential roles in many terrestrial ecosystems, yet there are methodological challenges in taxonomic and phylogenetic placement of fungi from environmental sequences. To address such challenges we investigated spatio-temporal structure of a fungal community using soil metabarcoding with four different sequencing strategies: short amplicon sequencing of the ITS2 region (300-400 bp) with Illumina MiSeq, Ion Torrent Ion S5, and PacBio RS II, as well as long amplicon sequencing of the full ITS and partial LSU regions (1200-1600 bp) with PacBio RS II. Resulting community structure and diversity depended more on statistical method than sequencing technology. The use of long-amplicon sequencing enables construction of a phylogenetic tree from metabarcoding reads, which facilitates taxonomic identification of sequences. However, long reads present issues for denoising algorithms in diverse communities. We present a solution that splits the reads into shorter homologous regions prior to denoising, and then reconstructs the full denoised reads. In the choice between short and long amplicons, we suggest a hybrid approach using short amplicons for sampling breadth and depth, and long amplicons to characterize the local species pool for improved identification and phylogenetic analyses.

Clustering is an important technique in data mining. It separates data points into different groups or clusters in such a way that objects in the same group are more similar to each other in some sense than with the objects in other groups. Gabor face clustering using affinity propagation and structural similarity index is composed of: A representation based on Gabor filters which has been shown to perform very well in face features, Affinity propagation clustering algorithm which is flexible, high speed, and does not require to specify the number of clusters, and structural similarity index which is a very powerful method for measuring the similarity between two images. Experimental results on two benchmark face datasets (LFW and IJB-B) show that our method outperforms well known clustering algorithms such as k-means, spectral clustering and Agglomerative

Abstract Rationale, aims and objectives: Sri Lanka has a well-established government-funded universal health coverage which provides free health care to all citizens. The aim of this qualitative study was to examine the out-of-pocket expenses incurred by patients with cirrhosis during admission to a tertiary care government hospital in Sri Lanka, and the impact such expenses might have on equity of care and patient outcome. Methods This is a qualitative study conducted among patients with cirrhosis admitted to a tertiary-care hospital, their caregivers and physicians. Quota sampling was used until data saturation was achieved. Data was collected through individual interviews and small group discussions using directed and open-ended questions. Thematic framework method was used to analyze data. Out-of-pocket expenses incurred by patients, its impact on equity of patient care and outcome were investigated. Results Costs for laboratory investigations, drugs purchased from the private sector and hired caretakers for hospitalized patients were reported as direct expenses. Loss of work and other sources of income were the primary indirect expenses. The impact of such expenses was higher in patients and families from lower socioeconomic categories, especially among those who were dependent on a daily income. Health care workers actively tried to minimize these out-of-pocket expenses, resulting in choice on investigations, drugs and other interventions often being made by the clinician and occasionally not being discussed with the patient, resulting in poor patient satisfaction. Conclusion This study reveals a substantial direct and indirect economic impact on patients despite being cared for in a government hospital with universal health coverage. The impact was more in patients from lower socioeconomic strata, potentially resulting in inequity in the care provided as well as the health outcomes.