Simple Fragment Research Articles

Step-by-step strategy in the management of residual hepatolithiasis using post-operative cholangioscopy.

Hepatolithiasis is the presence of calculi within the intrahepatic bile duct specifically located proximal to the confluence of the left and right hepatic ducts. The ultimate goal of hepatolithiasis treatment is the complete removal of the stone, the correction of the associated strictures and the prevention of recurrent cholangitis. Although hepatectomy could effectively achieve the above goals, it can be restricted by the risk of insufficient residual liver volume, and has a 15.6% rate of residual hepatolithiasis. With improvements in minimally invasive surgery, post-operative cholangioscopy (POC), provides an additional option for hepatolithiasis treatment with higher clearance rate and fewer severe complications. POC is very safe, and can be performed repeatedly until full patient benefit is achieved. During POC three main steps are accomplished: first, the analysis of the residual hepatolithiasis distribution indirectly by imaging methods or directly endoscopic observation; second, the establishment of the surgical pathway to relieve the strictures; and third, the removal of the stone by a combination of different techniques such as simple basket extraction, mechanical fragmentation, electrohydraulic lithotripsy or laser lithotripsy, among others. In summary, a step-by-step strategy of POC should be put forward to standardize the procedures, especially when dealing with complicated residual hepatolithiasis. This review briefly summarizes the classification, management and complications of hepatolithiasis during the POC process.

Insecticide resistance in Trialeurodes vaporariorum populations and novel diagnostics for kdr mutations.

Neonicotinoids, pyrethroids and ketoenols are currently used for the control of Trialeurodes vaporariorum (Hemiptera: Aleyrodidae). In this study, insecticide resistance status and mechanisms were investigated using classical bioassays and molecular techniques. Dose-response bioassays were performed on 19 Greek populations, among the 35 different whitefly populations used for the whole analysis. Resistance factors scaled up to 207-, 4657- and 59-fold for imidacloprid, bifenthrin and spiromesifen, respectively. Molecular assays were used to investigate the frequency of known resistance mutations. A simple polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay was developed for detecting the pyrethroid-resistant alleles r1 (mutation L925I) and r2 (mutation T929I) of the para-type voltage-gated sodium channel gene (VGSC). Both alleles were present at high frequencies (on average 65% and 33%, respectively) in 14 populations from Greece. The M918 L pyrethroid resistance mutation was not detected in any of the Greek populations. Sequencing and a Taqman allelic discrimination were used to monitor the frequency of the mutation E645K of the acetyl-coenzyme A carboxylase gene (ACC) recently linked to spiromesifen resistance. This mutation was detected in 20 of the 24 populations examined in ∼38% frequency among the 433 individuals tested. However, its association with the spiromesifen resistance phenotype was not confirmed in the Greek populations. Finally, two homologues of the CYP6CM1 Bemisia tabaci P450, the known neonicotinoid metabolizer, were found upregulated in two T. vaporariorum neonicotinoid-resistant populations; they were both functionally expressed in Escherichia coli, but the recombinant proteins encoded did not metabolize those neonicotinoid insecticides tested. The development of simple diagnostics and their use alongside classical and molecular techniques for the early detection of resistant populations are of great importance for pest management strategies. The practical implications of our results are discussed in light of whitefly control. © 2017 Society of Chemical Industry.

Differential eNOS-signalling by platelet subpopulations regulates adhesion and aggregation.

In addition to maintaining haemostasis, circulating blood platelets are the cellular culprits that form occlusive thrombi in arteries and veins. Compared to blood leucocytes, which exist as functionally distinct subtypes, platelets are considered to be relatively simple cell fragments that form vascular system plugs without a differentially regulated cellular response. Hence, investigation into platelet subpopulations with distinct functional roles in haemostasis/thrombosis has been limited. In our present study, we investigated whether functionally distinct platelet subpopulations exist based on their ability to generate and respond to nitric oxide (NO), an endogenous platelet inhibitor. Utilizing highly sensitive and selective flow cytometry protocols, we demonstrate that human platelet subpopulations exist based on the presence and absence of endothelial nitric oxide synthase (eNOS). Platelets lacking eNOS (approximately 20% of total platelets) fail to produce NO and have a down-regulated soluble guanylate cyclase-protein kinase G (sGC-PKG)-signalling pathway. In flow chamber and aggregation experiments eNOS-negative platelets primarily initiate adhesion to collagen, more readily activate integrin αIIbβ3 and secrete matrix metalloproteinase-2, and form larger aggregates than their eNOS-positive counterparts. Conversely, platelets having an intact eNOS-sGC-PKG-signalling pathway (approximately 80% of total platelets) form the bulk of an aggregate via increased thromboxane synthesis and ultimately limit its size via NO generation. These findings reveal previously unrecognized characteristics and complexity of platelets and their regulation of adhesion/aggregation. The identification of platelet subpopulations also has potentially important consequences to human health and disease as impaired platelet NO-signalling has been identified in patients with coronary artery disease.

Stereoselective synthesis and anticancer activity of broussonetine analogues

The stereoselective synthesis of two broussonetine analogues 14·HCl and ent-14·HCl with differing stereochemistry of the polyhydroxylated pyrrolidine core and a simple C13 alkyl fragment has been achieved. For their construction, the known oxazolidinones 15 and 16 were chosen as appropriate advanced scaffolds. The common hydrophobic side chain was incorporated at an early stage of the synthesis through Grubbs’ cross metathesis chemistry. The required pyrrolidine skeleton was then formed by the cyclization of open chain intermediates 17 and 18. Four synthesized compounds were screened in vitro for antiproliferative/cytotoxic activity against six cancer cell lines by MTT assay. Compounds 14·HCl (HeLa and A-549) and ent-14·HCl (Caco-2 and Jurkat) showed comparable or higher potency than conventional anticancer agent cisplatin on at least two evaluated cancer cells, respectively.

Effect of Methotrexate and Omega-3 Combination on Cytogenetic Changes of Bone Marrow and Some Enzymatic Antioxidants: An Experimental Study

Effect of Methotrexate and Omega-3 Combination on Cytogenetic Changes of Bone Marrow and Some Enzymatic Antioxidants: An Experimental Study

Effect of Methotrexate and Omega-3 Combination on Cytogenetic Changes of Bone Marrow and Some Enzymatic Antioxidants: An Experimental Study

Effect of Methotrexate and Omega-3 Combination on Cytogenetic Changes of Bone Marrow and Some Enzymatic Antioxidants: An Experimental Study

Formal Verification of an Executable LTL Model Checker with Partial Order Reduction

We present a formally verified and executable on-the-fly LTL model checker that uses ample set partial order reduction. The verification is done using the proof assistant Isabelle/HOL and covers everything from the abstract correctness proof down to the generated SML code. Building on Doron Peled’s paper “Combining Partial Order Reductions with On-the-Fly Model-Checking”, we formally prove abstract correctness of ample set partial order reduction. This theorem is independent of the actual reduction algorithm. We then verify a reduction algorithm for a simple but expressive fragment of Promela. We use static partial order reduction, which allows separating the partial order reduction and the model checking algorithms regarding both the correctness proof and the implementation. Thus, the Cava model checker that we verified in previous work can be used as a back end with only minimal changes. Finally, we generate executable SML code using a stepwise refinement approach. We test our model checker on some examples, observing the effectiveness of the partial order reduction algorithm.

Hot-Spotting with Thermal Scanning: A Ligand- and Structure-Independent Assessment of Target Ligandability.

Evaluating the ligandability of a protein target is a key component when defining hit-finding strategies or when prioritize among drug targets. Computational as well as biophysical approaches based on nuclear magnetic resonance (NMR) fragment screening are powerful approaches but suffer from specific constraints that limit their usage. Here, we demonstrate the applicability of high-throughput thermal scanning (HTTS) as a simple and generic biophysical fragment screening method to reproduce assessments from NMR-based screening. By applying this method to a large set of proteins we can furthermore show that the assessment is predictive of the success of high-throughput screening (HTS). The few divergences for targets of low ligandability originate from the sensitivity differences of the orthogonal biophysical methods. We thus applied a new strategy making use of modulations in the solvent structure to improve assay sensitivity. This novel approach enables improved ligandability assessments in accordance with NMR-based assessments and more importantly positions the methodology as a valuable option for biophysical fragment screening.

Discovery of a new hypotrich ciliate from petroleum contaminated soil.

Pollution after oil spill represents extreme habitat for survival and is a major concern for loss of species diversity in the affected area. In this study, we investigated soil samples collected from a petrochemical industry, Ulsan, South Korea. The soil was in the phase of recovery from the contamination of crude oil spill. Detailed investigation, based on morphology, ontogenesis, and molecular phylogenetic methods, resulted in discovery of a novel hypotrich ciliate, i.e., Metasterkiella koreana n. gen., n. sp., which is morphologically characterized by a semirigid body, undulating membranes in Oxytricha pattern, 18 frontal-ventral-transverse cirri with cirrus V/3 placed posteriorly, one right and one left row of marginal cirri, four dorsal kineties, two dorsomarginal rows, and caudal cirri at the end of dorsal kineties 1, 2, and 4. Interestingly, during ontogenesis, formation of three common anlagen for the proter and the opisthe and involvement of cirrus V/3 in anlagen formation was observed. The dorsal ontogenesis was typical of oxytrichids, i.e., simple fragmentation of dorsal kinety 3 and formation of dorsomarginal rows close to the right marginal row. The new species was found to be similar with Sterkiella subtropica, except for some minor differences in morphometry, and at gene level with only one base pair difference. In phylogenetic analyses, based on SSU rRNA gene sequence, M. koreana cluster in a clade away from Sterkiella species, which could be explained by the differences in the morphogenetic pattern between these two genera. It is proposed that S. subtropica probably belongs to Metasterkiella; however, we do not perform changes and wait for the reinvestigation of its morphogenetic pattern.

Predicting "Hot" and "Warm" Spots for Fragment Binding.

Computational fragment mapping methods aim to predict hotspots on protein surfaces where small fragments will bind. Such methods are popular for druggability assessment as well as structure-based design. However, to date researchers developing or using such tools have had no clear way of assessing the performance of these methods. Here, we introduce the first diverse, high quality validation set for computational fragment mapping. The set contains 52 diverse examples of fragment binding "hot" and "warm" spots from the Protein Data Bank (PDB). Additionally, we describe PLImap, a novel protocol for fragment mapping based on the Protein-Ligand Informatics force field (PLIff). We evaluate PLImap against the new fragment mapping test set, and compare its performance to that of simple shape-based algorithms and fragment docking using GOLD. PLImap is made publicly available from https://bitbucket.org/AstexUK/pli .

Habitat modification and alpha-beta diversity in trap nesting bees and wasps (Hymenoptera: Aculeata) in southern Brazil

The global decline in biodiversity has been mainly attributed to the expansion of agricultural areas that transform continuous forest ecosystems into mosaic landscapes of simple agricultural and natural forest fragments. Considering this, the objective of this research was to evaluate if habitat modification affects trap nesting bees and wasps richness and abundance. An assemblage of bees and wasps that nest in pre-existing cavities was studied. The tested hypothesis was that species composition, richness and evenness are affected with habitat modification. Trap nests with different diameters were used to capture these insects in forests and in organic fields in Southern Brazil. Species composition in these areas was different, which led to the acceptance of the hypothesis that it is affected with habitat modification. The opposite occurred with alpha diversity because there was no significant difference between the richness of these areas. The most abundant genus, both in the forest areas and in the growing areas, was Trypoxylon, suggesting that the degree of impact on the Araucaria forest fragments is one of the factors that makes the diversity of these areas similar (in addition to the organic fields) since wasps of this genus usually occur in impacted areas.

Description and Molecular Phylogeny of a Novel Hypotrich Ciliate from the Soil of Marche Region, Italy; Including Notes on the MOSYSS Project.

The morphology and morphogenesis during cell division of a new stylonychine hypotrich, Rigidocortex quadrinucleatus n. sp., were investigated using live observation and protargol staining. The new species was isolated from soil samples collected from an organic farm in the Marche Region, Italy, in framework of the MOSYSS project. Rigidocortex quadrinucleatus is characterized as follows: cell size about 180×80μm invivo; four ellipsoidal macronuclear nodules; 44 adoral membranelles: 18 fronto-ventral-transverse cirri consisting of three frontal, four frontoventral, one buccal, three ventral, two pretransverse, and five transverse cirri; dorsal kinety 3 with multiple fragmentation; resting cyst with hyaline ridges. Rigidocortex quadrinucleatus mainly differs from the type species R.octonucleatus in having four (vs. eight) macronuclear nodules. Rigidocortex quadrinucleatus can be easily confused with Sterkiella cavicola since both have a rather similar ventral ciliature; however, they can be separated by the slightly higher number of cirri in the left marginal row that runs along the posterior cell's margin in R.quadrinucleatus. Morphogenesis on the ventral surface is highly similar to that of Sterkiella species, but differs significantly on the dorsal surface (multiple vs. simple fragmentation of dorsal kinety 3). Phylogenetic analyses based on SSU rRNA gene sequences consistently place the new species within the stylonychine oxytrichids, clustering closer to Gastrostyla steinii than to S.cavicola.

An Enumerative Combinatorics Model for Fragmentation Patterns in RNA Sequencing Provides Insights into Nonuniformity of the Expected Fragment Starting-Point and Coverage Profile.

RNA sequencing (RNA-seq) has emerged as the method of choice for measuring the expression of RNAs in a given cell population. In most RNA-seq technologies, sequencing the full length of RNA molecules requires fragmentation into smaller pieces. Unfortunately, the issue of nonuniform sequencing coverage across a genomic feature has been a concern in RNA-seq and is attributed to biases for certain fragments in RNA-seq library preparation and sequencing. To investigate the expected coverage obtained from fragmentation, we develop a simple fragmentation model that is independent of bias from the experimental method and is not specific to the transcript sequence. Essentially, we enumerate all configurations for maximal placement of a given fragment length, F, on transcript length, T, to represent every possible fragmentation pattern, from which we compute the expected coverage profile across a transcript. We extend this model to incorporate general empirical attributes such as read length, fragment length distribution, and number of molecules of the transcript. We further introduce the fragment starting-point, fragment coverage, and read coverage profiles. We find that the expected profiles are not uniform and that factors such as fragment length to transcript length ratio, read length to fragment length ratio, fragment length distribution, and number of molecules influence the variability of coverage across a transcript. Finally, we explore a potential application of the model where, with simulations, we show that it is possible to correctly estimate the transcript copy number for any transcript in the RNA-seq experiment.

INTRODUCTION IN TECHNOLOGY CONCEPTUALIZATION THE SUBJECT DOMAIN OF SOCIOLOGY: EXPANSION OF THE THEORY (in the example of relationship/kinship)

Presented article is the second of two articles, the aim of which is to introduce the reader has no special mathematical training, with the possibilities of application of mathematical methods developed in the scientific direction of “Conceptual analysis and design of systems of organizational management (CAD SOM)”, designed to solve a variety of tasks, such as technical and humanitarian spheres on the basis of the proposed methodological approach to the mathematization of the theoretical knowledge. At the heart of this methodological approach is a process of conceptualization, which is understood as a theoretical study of qualitative aspects of a selected domain using mathematical forms (axiomatic) theory, the locking connection between the concepts of logical derivability characterizing this subject area. Designed axiomatic theory – conceptual scheme – is the basis for building database structures, decision-making processes, a variety of phenomena subject area, structure and genesis of domain analysis and other tasks. One of the main advantages of the sending of methodological approach is the ability to work with complex regions based on the controlled synthesis tool terminal theory of conceptual schemes, explicated simple fragments of the subject area. Given the non-mathematical preparation of the reader, the contents of the methods illustrated by conceptualizing a conceptually simple subject areas – areas related relations, as well as the choice of one of the most simple goals conceptualization – structuring the domain and build a variety of its phenomena. The first article was given a brief description of mathematical methods, describes the main stages of the conceptualization of the subject areas, ranging from the definition of the boundaries of the domain and ending with the theory of the synthesis of the terminal and determine its compliance with the tasks of conceptualizing. In the chosen example – areas related relations – have been considered in detail first, most important, the steps taken and the impact of technology on these stages of conceptualizing solutions. They discussed the definition of family relationship and the concept of “relative”, identifies the major errors and their consequences are discussed various options for positing the core of the conceptual scheme, carried out a precise definition of the content to rely in this case the basic concepts and their properties. In the second article concludes with a discussion of issues related to the behest of basic sets – namely, issues of formation of so-called “Declaration on the base set” terminological problems and questions refer to basic sets. Described final core of the conceptual scheme, carried out an axiomatic study of selected domain. The basic attention in second article is given to expansion of the theory and difficulties with which thus the conceptualist – researcher collides. By the example of the entered terms – “blood family”, “the connected family”, “family balls”, “generations of ancestors”, “genealogical trees and rhizomes”, “binding generations”, “related clans” – are shown opportunities of directions of expansion of the axiomatic theory. Influence of definition of concept “relative” on carrying out of border between relatives and nonrelatives is shown. For demonstration of variants of erosion of kinship, concepts of species “sorodstvennikov” are entered. At the end of the article briefly reviews the steps required for the synthesis of conceptual schemes. In the presentation of possible mathematical omitted entries, and the deployment of the theory described in the attributive form – in terms of empirically determined characteristics.

Duplex PCR-RFLP for the Simultaneous Genotyping of Single Nucleotide Polymorphisms in ADH1B and ALDH2 Genes.

Single nucleotide polymorphisms (SNPs) in ADH1B and ALDH2, which encode alcohol dehydrogenase 1B and aldehyde dehydrogenase 2, respectively, are responsible for ethanol-metabolizing activity and alcohol-related disease. We developed a simple and rapid polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) method for the simultaneous genotyping of the genes in a single-tube reaction. Using an alkaline lysate of a human hair root as a template, SNP-containing regions of each gene were PCR-amplified simultaneously. The PCR products were directly applied to double restriction digestion, followed by agarose gel band analysis. The duplex PCR-RFLP allows for the simultaneous and accurate determination of the SNP genotypes of ADH1B and ALDH2 within 1.2 h.

Solar wind ion impacts into ice surfaces: A molecular-dynamics study using the REAX force field

Molecular dynamics simulation is used to study the effects of solar-wind ion irradiation on an ice target, focusing on the effects of nuclear energy deposition. A reactive force field (REAX) interatomic interaction potential is employed that allows us to model the breaking and formation of molecular bonds and hence to follow the chemistry occurring in the target. As ions we study H and He ions as typical constituents of the solar wind, and Ne as an example of a heavier ion; they impact at the speed of maximum flux in the solar wind, 400 km/s. The ice consists of a mixture of H2O, CO2, CH3OH and NH3. We find that molecular dissociations occur within 0.2 ps after ion impact and new products are formed up to a time of 1 ps; only water has a slower dynamics, due to highly mobile H atoms allowing for late recombinations. The number of dissociations, and hence also of product molecules increases from H over He to Ne ion projectiles and can be quantified by the amount of energy deposited in the target by these ions. The most abundant products formed include CO, OH and NH2. Reaction products are most complex for Ne impact, and include H3O, formaldehyde (H2CO), HO2, and NO. Formaldehyde is important as it is formed relatively frequently and is known as a precursor in the formation of sugars. In addition, molecules containing all CHON elements are formed, among which are CH2NO, CONH, methanolamine (CH5NO), and ethyne (C2H2). Repeated impacts generate novel, and more complex product species; we found CN, CH4, CH3NO, methylamine (CH3NH2), and acetamide (CH3CONH2), among others; the complex species are formed less frequently than the simple fragments. Sputtering occurs for all projectiles, even H. The ejecta are either original molecules – in particular CO2 – or simple fragments; only few product molecules are emitted.

Identification of Covalent Binding Sites Targeting Cysteines Based on Computational Approaches.

Covalent drugs have attracted increasing attention in recent years due to good inhibitory activity and selectivity. Targeting noncatalytic cysteines with irreversible inhibitors is a powerful approach for enhancing pharmacological potency and selectivity because cysteines can form covalent bonds with inhibitors through their nucleophilic thiol groups. However, most human kinases have multiple noncatalytic cysteines within the active site; to accurately predict which cysteine is most likely to form covalent bonds is of great importance but remains a challenge when designing irreversible inhibitors. In this work, FTMap was first applied to check its ability in predicting covalent binding site defined as the region where covalent bonds are formed between cysteines and irreversible inhibitors. Results show that it has excellent performance in detecting the hot spots within the binding pocket, and its hydrogen bond interaction frequency analysis could give us some interesting instructions for identification of covalent binding cysteines. Furthermore, we proposed a simple but useful covalent fragment probing approach and showed that it successfully predicted the covalent binding site of seven targets. By adopting a distance-based method, we observed that the closer the nucleophiles of covalent warheads are to the thiol group of a cysteine, the higher the possibility that a cysteine is prone to form a covalent bond. We believe that the combination of FTMap and our distance-based covalent fragment probing method can become a useful tool in detecting the covalent binding site of these targets.

A Genetic Map Between Gossypium hirsutum and the Brazilian Endemic G. mustelinum and Its Application to QTL Mapping.

Among the seven tetraploid cotton species, little is known about transmission genetics and genome organization in Gossypium mustelinum, the species most distant from the source of most cultivated cotton, G. hirsutum. In this research, an F2 population was developed from an interspecific cross between G. hirsutum and G. mustelinum (HM). A genetic linkage map was constructed mainly using simple sequence repeat (SSRs) and restriction fragment length polymorphism (RFLP) DNA markers. The arrangements of most genetic loci along the HM chromosomes were identical to those of other tetraploid cotton species. However, both major and minor structural rearrangements were also observed, for which we propose a parsimony-based model for structural divergence of tetraploid cottons from common ancestors. Sequences of mapped markers were used for alignment with the 26 scaffolds of the G. hirsutum draft genome, and showed high consistency. Quantitative trait locus (QTL) mapping of fiber elongation in advanced backcross populations derived from the same parents demonstrated the value of the HM map. The HM map will serve as a valuable resource for QTL mapping and introgression of G. mustelinum alleles into G. hirsutum, and help clarify evolutionary relationships between the tetraploid cotton genomes.

Guidelines for laboratory diagnosis of factor XIII deficiency

Factor XIII (FXIII) deficiency is an extremely rare hemorrhagic disorder with an approximate worldwide incidence of one per two million. With current tests, diagnosis of this disease can be made more precisely. However, factors such as the number of patients with FXIII deficiency (FXIIID), available diagnostic coagulation tests and the number of molecular studies have affected the diagnosis of FXIIID in different parts of the world. Various laboratory approaches can be used, including screening and diagnosis of the disorder in countries with a relatively high rate of FXIIID and recurrent mutation(s) with a simple polymerase chain reaction-restriction fragment length polymorphism analysis or polymerase chain reaction-sequencing for detection of one or a few specific mutations. In other countries, two different laboratory approaches can be used, depending on available coagulation tests. In less-equipped coagulation laboratories, the clot solubility test remains the only diagnostic test for FXIIID. Even in these countries, at least one referral laboratory should perform FXIII activity and, if possible, confirmation of FXIIID by molecular analysis. In countries with well equipped coagulation laboratories, FXIII activity should be used to screen suspected FXIIID patients; more specific tests such as molecular analysis should be used for confirmation. This study suggests a simple, reliable and flexible algorithm for early diagnosis of FXIIID, and may, with one-time diagnosis of FXIIID, reduce the rate of morbidity and mortality in patients with the disorder.

The undecidability theorem for the Horn-like fragment of linear logic (Revisited)

There has been an increased interest in the decision problems for linear logic and its fragments. Here, we give a fully self-contained, easy-to-follow, but fully detailed, direct and constructive proof of the undecidability of a very simple Horn-like fragment of linear logic, which is accessible to a wide range of people. Namely, we show that there is a direct correspondence between terminated computations of a Minsky machine M and cut-free linear logic derivations for a Horn-like sequent of the form \begin{equation*} \bang{\Phi_M},\ l_1 \vdash l_0, \end{equation*} where ΦM consists only of Horn-like implications of the following simple forms \begin{equation*} (l \llto l'),\ \ ((l\otimes r) \llto l'),\ \ (l\llto (r\otimes l')),\ \ and \ \ (l\llto (l'\oplus l'')), \end{equation*} where l1, l0, l, l′, l″ and r stand for literals.Neither negation, nor &, nor constants, nor embedded implications/bangs are used here.Furthermore, our particular correspondence constructed above provides decidability for each of the Horn-like fragments whenever we confine ourselves to any two forms of the above Horn-like implications, along with the complexity bounds that come from the proof.