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This paper introduces a novel method for characterizing fracture mechanisms in multi-component materials using 3D image data gained by X-ray computed tomography (CT) measurements. In mineral liberation, the understanding of these mechanisms is crucial, particularly whether fractures occur along the boundaries of mineral phases (intergranular fracture) and/or within mineral phases (transgranular fracture). Conventional techniques for analyzing fracture mechanisms are focused on globally comparing the surface exposure of mineral phases extracted from image measurements before and after fracture. Instead, we present a virtual reassembling algorithm based on image registration techniques, which is applied to 3D data of multi-component materials before and after fracture in order to determine and characterize the individual fracture surfaces. This enables us to conduct a local quantitative analysis of fracture mechanisms by voxelwise comparing adjacent regions at fracture surfaces. A quantitative analysis of fracture mechanisms is especially important in the context of recycling processes. As primary deposits are decreasing worldwide and the focus is shifting on reducing wast, the interest in secondary raw materials has increased. However, lower-concentrated, but valuable materials are often overlooked in recycling routes designed for higher-concentration materials and dissipate. Therefore, efforts are being made to enrich valuable elements, such as lithium, as engineered artificial minerals through pyrometallurgical processes. The subsequent liberation through comminution processes, such as crushing, is essential for the recovery of valuable minerals. A better understanding of crushing processes, especially fracture mechanisms in slags, is crucial for the success of recycling. The reassembling algorithm presented in this paper is evaluated through a simulation study, followed by an application to a naturally occurring ore and a slag resulting from a recycling process. • Development of an algorithm for the characterisation of fracture mechanisms. • Analysis of fracture mechanisms by voxel-wise comparison of fracture surfaces. • Quantification of inter- and/or transgranular fracture in multi-component materials. • Insight into comminution processes for the recycling of valuable minerals from slag. [ABSTRACT FROM AUTHOR]

Segmentation of mm-resolution image data of irregularly shaped objects poses challenges to existing segmentation algorithms. This is especially true, when imperfections like noise, uneven lightning or traces of sample preparation are present in the image data. In this paper, considering electron micrographs of femoral quadriceps nerve sections of mice, a segmentation method to extract single axons surrounded by myelin sheaths is developed which is able to cope with various imperfections and artefacts. This approach successfully combines established methods like local thresholding and marker-based watershed transform to achieve a reliable segmentation of the given data. Indeed, the resulting segmentation map can be used to quantitatively determine geometrical characteristics of the axons and myelin sheaths. This is exemplified by modelling the joint probability distribution of axon area and myelin sphericity using a parametric copula approach, and by analysing the evolution of the model parameters for image data obtained from mice of different ages. [ABSTRACT FROM AUTHOR]

The unfolded protein response is an intricate system of sensor proteins in the endoplasmic reticulum (ER) that recognizes misfolded proteins and transmits information via transcription factors to either regain proteostasis or, depending on the severity, to induce apoptosis. The main transmembrane sensor is IRE1α, which contains cytoplasmic kinase and RNase domains relevant for its activation and the mRNA splicing of the transcription factor XBP1. Mast cell leukemia (MCL) is a severe form of systemic mastocytosis. The inhibition of IRE1α in the MCL cell line HMC-1.2 has anti-proliferative and pro-apoptotic effects, motivating us to elucidate the IRE1α interactors/regulators in HMC-1.2 cells. Therefore, the TurboID proximity labeling technique combined with MS analysis was applied. Gene Ontology and pathway enrichment analyses revealed that the majority of the enriched proteins are involved in vesicle-mediated transport, protein stabilization, and ubiquitin-dependent ER-associated protein degradation pathways. In particular, the AAA ATPase VCP and the oncoprotein MTDH as IRE1α-interacting proteins caught our interest for further analyses. The pharmacological inhibition of VCP activity resulted in the increased stability of IRE1α and MTDH as well as the activation of IRE1α. The interaction of VCP with both IRE1α and MTDH was dependent on ubiquitination. Moreover, MTDH stability was reduced in IRE1α-knockout cells. Hence, pharmacological manipulation of IRE1α–MTDH–VCP complex(es) might enable the treatment of MCL. [ABSTRACT FROM AUTHOR]

Autophagy is a ubiquitous catabolic process, which causes cellular bulk degradation through vesicular engulfment of obsolete, damaged or harmful cytoplasmic components. While autophagy regulates cellular homeostasis during development and in youth, there is mounting evidence that autophagy becomes increasingly dysfunctional with age. Recent work in Caenorhabditis elegans even suggests that late‐life dysfunctional autophagy exhibits detrimental effects that drive the ageing process. Other studies link elevated autophagy closely to increased health and longevity. This review aims to put these apparently opposing views into perspective and define our current understanding of the role of autophagy during ageing. [ABSTRACT FROM AUTHOR]

Background. Posttonsillectomy hemorrhage (PTH) is the most feared complication. Dissection near the tonsillar capsule under microscopic view (TEmic) could be assumed to decrease PTH compared to traditional tonsillectomy (TEtrad). Methods. In this study, patients were evaluated with respect to the need for surgical control (R/N: return/no return to theater (RTT): the day of surgery [0] or thereafter [1]). The findings at resection site and pain were measured. Results. 869 patients were included (183 TEmic; 686 TEtrad). PTH requiring RTT was not seen in the TEmic group on the day of surgery (R0) while PTH requiring RTT subsequently (R1) was seen in 1.1% of the cases. In the TEmic group, hemorrhages without a need for surgical control were observed in 0.6% (N0) and 3.4% (N1), respectively. The corresponding rates for TEtrad were as follows: R0, 0.3%; R1, 1.7%; N0, 0.6%; and N1, 3.6% (p>0.05). Postoperative edema and local infection at resection site were proven to be predictive of PTH (p=0.007). Conclusion. Microscope assistance in tonsillectomy did not statistically have an influence on the PTH even though there was a trend towards lower PTH rate in the TEmic group. Benefit for TEmic was observed in high-volume and long experienced surgeons. [ABSTRACT FROM AUTHOR]

Background: Antigen (Ag)/IgE-mediated mast cell (MC) responses play detrimental roles in allergic diseases. MC activation via the high-affinity receptor for IgE (FceRI) is controlled by the Src family kinase Lyn. Lyn-deficient (-/-) bone marrow-derived MCs (BMMCs) have been shown by various laboratories to exert stronger activation of the PI3K pathway, degranulation, and production of pro-inflammatory cytokines compared to wild-type (wt) cells. This mimics the phenotype of BMMCs deficient for the SH2-containing inositol-5'-phosphatase 1 (SHIP1). In this line, Lyn has been demonstrated to tyrosine-phosphorylate and activate SHIP1, thereby constituting a negative feedback control of PI3K-mediated signals. However, several groups have also reported on Lyn-/- BMMCs degranulating weaker than wt BMMCs. Results: Lyn-/- BMMCs, which show a suppressed degranulation response, were found to exhibit abrogated tyrosine phosphorylation of SHIP1 as well. This indicated that even in the presence of reduced SHIP1 function MC degranulation is dependent on Lyn function. In contrast to the reduced immediate secretory response, pro-inflammatory cytokine production was augmented in Lyn-/- BMMCs. For closer analysis, Lyn/SHIP1-double-deficient (dko) BMMCs were generated. In support of the dominance of Lyn deficiency, dko BMMCs degranulated significantly weaker than SHIP1-/- BMMCs. This coincided with reduced LAT1 and PLC-γ1 phosphorylation as well as Ca2+ mobilization in those cells. Interestingly, activation of the NFκB pathway followed the same pattern as measured by IκBα phosphorylation/degradation as well as induction of NFκB target genes. This suggested that Ag-triggered NFκB activation involves a Ca2+-dependent step. Indeed, IκBα phosphorylation/degradation and NFκB target gene induction were controlled by the Ca2+-dependent phosphatase calcineurin. Conclusions: Lyn deficiency is dominant over SHIP1 deficiency in MCs with respect to Ag-triggered degranulation and preceding signaling events. Moreover, the NFκB pathway and respective targets are activated in a Lyn- and Ca2+-dependent manner, reinforcing the importance of Lyn for MC activation. [ABSTRACT FROM AUTHOR]

Background DNA methylation (DNAm) has important regulatory roles in many biological processes and diseases. It is the only epigenetic mark with a clear mechanism of mitotic inheritance and the only one easily available on a genome scale. Aberrant cytosine-phosphate-guanine (CpG) methylation has been discussed in the context of disease aetiology, especially cancer. CpG hypermethylation of promoter regions is often associated with silencing of tumour suppressor genes and hypomethylation with activation of oncogenes. Supervised principal component analysis (SPCA) is a popular machine learning method. However, in a recent application to phenotype prediction from DNAm data SPCA was inferior to the specific method EVORA. Results We present Model-Selection-SPCA (MS-SPCA), an enhanced version of SPCA. MS-SPCA applies several models that perform well in the training data to the test data and selects the very best models for final prediction based on parameters of the test data. We have applied MS-SPCA for phenotype prediction from genome-wide DNAm data. CpGs used for prediction are selected based on the quantification of three features of their methylation (average methylation difference, methylation variation difference and methylation-age-correlation). We analysed four independent case-control datasets that correspond to different stages of cervical cancer: (i) cases currently cytologically normal, but will later develop neoplastic transformations, (ii, iii) cases showing neoplastic transformations and (iv) cases with confirmed cancer. The first dataset was split into several smaller case-control datasets (samples either Human Papilloma Virus (HPV) positive or negative). We demonstrate that cytology normal HPV+ and HPV- samples contain DNAm patterns which are associated with later neoplastic transformations. We present evidence that DNAm patterns exist in cytology normal HPV- samples that (i) predispose to neoplastic transformations after HPV infection and (ii) predispose to HPV infection itself. MS-SPCA performs significantly better than EVORA. Conclusions MS-SPCA can be applied to many classification problems. Additional improvements could include usage of more than one principal component (PC), with automatic selection of the optimal number of PCs. We expect that MS-SPCA will be useful for analysing recent larger DNAm data to predict future neoplastic transformations. [ABSTRACT FROM AUTHOR]

In drug discovery, the characterisation of the precise modes of action (MoA) and of unwanted off-target effects of novel molecularly targeted compounds is of highest relevance. Recent approaches for identification of MoA have employed various techniques for modeling of well defined signaling pathways including structural information, changes in phenotypic behavior of cells and gene expression patterns after drug treatment. However, efficient approaches focusing on proteome wide data for the identification of MoA including interference with mutations are underrepresented. As mutations are key drivers of drug resistance in molecularly targeted tumor therapies, efficient analysis and modeling of downstream effects of mutations on drug MoA is a key to efficient development of improved targeted anti-cancer drugs. Here we present a combination of a global proteome analysis, reengineering of network models and integration of apoptosis data used to infer the mode-of-action of various tyrosine kinase inhibitors (TKIs) in chronic myeloid leukemia (CML) cell lines expressing wild type as well as TKI resistance conferring mutants of BCR-ABL. The inferred network models provide a tool to predict the main MoA of drugs as well as to grouping of drugs with known similar kinase inhibitory activity patterns in comparison to drugs with an additional MoA. We believe that our direct network reconstruction approach, demonstrated on proteomics data, can provide a complementary method to the established network reconstruction approaches for the preclinical modeling of the MoA of various types of targeted drugs in cancer treatment. Hence it may contribute to the more precise prediction of clinically relevant on- and off-target effects of TKIs. [ABSTRACT FROM AUTHOR]

This study investigated the influence of viscose fibre (VF) geometry on the microstructures and resulting properties of high-density polyethylene (HDPE) composites. Seven types of viscose fibres varying in cross-section shape, linear density, and length were pelletised, compounded into HDPE with a twin-screw extruder, and injection moulded. The microstructures of the composites were characterised by investigating their cross-sections and by extracting the fibres and measuring their lengths using optical microscopy (OM). The mechanical and thermal properties of the composites were characterised using differential scanning calorimetry (DSC), tensile tests, Charpy impact tests, and dynamic mechanical analysis (DMA). The composites prepared using cylindrical fibres with a linear density of 1.7 dtex exhibited the best fibre dispersion, highest orientation, and lowest fibre–fibre contact area. The decrease in the linear density of the cylindrical fibres resulted in increasingly worse dispersion and orientation, while composites containing non-cylindrical fibres exhibited a comparably larger fibre–fibre contact area. The initial fibre length of about 3 to 10 mm decreased to the mean values of 0.29 mm to 0.41 mm during processing, depending on the initial geometry. In general, cylindrical fibres exhibited a superior reinforcing effect in comparison to non-cylindrical fibres. The composites containing cylindrical fibres with a linear density of 1.7 dtex and a length of 5 mm exhibited the best reinforcing effect with an increase in tensile modulus and strength of 323% and 141%, respectively. [ABSTRACT FROM AUTHOR]

Activation of mast cells (MCs) can be achieved by the high-affinity receptor for IgE (FceRI) as well as by additional receptors such as the lipopolysaccharide (LPS) receptor and the receptor tyrosine kinase Kit (stem cell factor [SCF] receptor). Thus, pharmacological interventions which stabilize MCs in response to different receptors would be preferable in diseases with pathological systemic MC activation such as systemic mastocytosis. 1,4-Benzodiazepines (BDZs) have been reported to suppress MC effector functions. In the present study, our aim was to analyze molecularly the effects of BDZs on MC activation by comparison of the effects of the two BDZs Ro5-4864 and clonazepam, which markedly differ in their affinities for the archetypical BDZ recognition sites, i.e., the GABAA receptor and TSPO (previously termed peripheral-type BDZ receptor). Ro5-4864 is a selective agonist at TSPO, whereas clonazepam is a selective agonist at the GABAA receptor. Ro5-4864 suppressed pro-inflammatory MC effector functions in response to antigen (Ag) (degranulation/cytokine production) and LPS and SCF (cytokine production), whereas clonazepam was inactive. Signaling pathway analyses revealed inhibitory effects of Ro5-4864 on Ag-triggered production of reactive oxygen species, calcium mobilization and activation of different downstream kinases. The initial activation of Src family kinases was attenuated by Ro5-4864 offering a molecular explanation for the observed impacts on various downstream signaling elements. In conclusion, BDZs structurally related to Ro5-4864 might serve as multifunctional MC stabilizers without the sedative effect of GABAA receptorinteracting BDZs. [ABSTRACT FROM AUTHOR]

Abstract: Objective: In recent years, several surgical disciplines adopted endoscopic techniques. Presently, natural orifice approaches are under exploration to reduce surgical access trauma. We have developed a trans-oral endoscopic approach for endoscopic mediastinal surgery and have tested this new technique in preclinical studies for feasibility and safety. Methods: We conducted an experimental anatomical study in fresh-frozen cadavers. By a midline, sublingual incision, we placed an optical scissor through a 6.0-mm trocar in the pretracheal region and created a working space; two additional trocars were placed by bi-vestibular incisions in the oral cavity. We visualized and followed the trachea down to the main bronchi. Paratracheal and subcarinal lymph nodes were resected bilaterally; the specimen could be removed through the midline channel. In an additional animal study in pigs, we tested the feasibility and safety for this surgical approach. Anatomical dissection allowed an estimate of collateral damage. Results: In all cases, we could reach the target region endoscopically, and no conversion was necessary. Landmarks (the brachiocervical trunk, the azygos vein, and the pulmonary artery) were visualized easily and kept intact. A working space in the mediastinum could be established by the insufflation of air at 6–8mmHg. It was possible to harvest the specimen through the midline channel. Anatomical dissection of the cervical access route as well as of the mediastinal region showed no collateral damage. In the animal study, we encountered seroma of the surgical field due to the conditions of the animal model. The other outcomes with respect to pain and food intake were normal until the third postoperative day. No local infections occurred. Intraoperative gas exchange was normal and was not influenced by CO2 insufflation with respect to blood gas analysis. Conclusion: These preclinical studies showed that the mediastinum could be reached by a trans-oral endoscopic approach, based on natural orifice surgery. Complete compartment resection of the paratracheal and subcarinal lymph node stations was possible in a well-defined and clearly visible working space. This approach may enhance the extent of mediastinal resections in oncologic surgery. [Copyright &y& Elsevier]

Abstract: Two approaches for the replacement of the toxic KCN etching step in the production of CuInS2 (CIS) absorber layers are presented. The electrochemical conditioning in acidic V2+/V3+ electrolyte comprises two treatment stages, the first one being the removal of covellite (CuS) at moderate anodic potentials and the second one the dissolution of a small sacrificial layer of CIS together with copper sulphide remnants at more aggressive potentials. This procedure yields absorber layers which are 3.3% efficient in photoelectrochemical solar cells (PECS) and 8% efficient in solid-state devices. The other approach is a combined electrochemical/chemical conditioning where the free energy of formation of a Cu–EDTA complex contributes to the copper sulphide dissolution and facilitates the removal of Cu–S phases at moderate electrochemical potentials. CIS films after this conditioning yield 1.44% in PECS. To cite this article: T. Wilhelm et al., C. R. Chimie 9 (2006) . [Copyright &y& Elsevier]

It is argued to study better non-binary (weighted) food webs where links are measured quantitatively, instead of binary (unweighted) food webs where links are just present or absent. Binary webs can simply be deduced from the more general non-binary ones: if a flux is larger than a critical flux value (below denoted by “cut”) a link is drawn, otherwise it is not. However, the amount of a flux between two nodes critically depends on the biomass of these nodes. Unfortunately, a clear definition of what to subsume into one node is missing up to now. The simplest (and probably most important) statistical description of non-binary food webs is given by the flux distribution function. However, this function may strongly be changed by just merging two nodes into one (as we have shown). In order to solve this decisive problem we propose to setup food webs with all nodes containing the same amount of biomass: equal-node-webs. A simple merging of just two nodes is forbidden here, because such a merged node would contain more biomass. The best basis for such a new food web theory would be provided by empirical equal-node-webs, established by field ecologists. However, such data has not been available up to now. Nevertheless, we demonstrate some advantages of studying equal-node-webs. For that purpose, first we show—by means of two example food webs—how equal-node-webs can be deduced from already published non-binary webs. Second, we describe the deduced equal-node-webs by their flux distribution functions as well as by different statistical measures. It is shown that equal-node-webs are more scale invariant than common non-binary food webs. Therefore, equal-node-webs provide a crucial, trustworthy basis for sound statistical descriptions and comparative analyses of food webs.Moreover, the article contains a new detailed comparison between a highly productive lake and a low productive one. It is shown that the food web of the latter has a higher complexity than that of the former. [Copyright &y& Elsevier]

Since the early days of the discovery of the genetic code nonrandom patterns have been searched for in the code in the hope of providing information about its origin and early evolution. Here we present a new classification scheme of the genetic code that is based on a binary representation of the purines and pyrimidines. This scheme reveals known patterns more clearly than the common one, for instance, the classification of strong, mixed, and weak codons as well as the ordering of codon families. Furthermore, new patterns have been found that have not been described before: Nearly all quantitative amino acid properties, such as Woese’s polarity and the specific volume, show a perfect correlation to Lagerkvist’s codon-anticodon binding strength. Our new scheme leads to new ideas about the evolution of the genetic code. It is hypothesized that it started with a binary doublet code and developed via a quaternary doublet code into the contemporary triplet code. Furthermore, arguments are presented against suggestions that a “simpler” code, where only the midbase was informational, was at the origin of the genetic code. [ABSTRACT FROM AUTHOR]

Paine [Ecology 69 (1988) 1648] called for a “dynamic rather than static” food web theory which should also take into account the “interaction strength” between the nodes. Here we face the challenge: an elementary food web model is presented which is both, dynamic and non-binary. We introduce the complexity measure for non-binary food webs “medium articulation” which resolves a contradiction in the discussion of stability of ecosystems. We propose a possible standard for establishment of food webs which avoids arbitrariness of both, nodes and links. After consideration of non-binary webs, binary webs are deduced by removing small fluxes and setting remaining fluxes to 1. Comparing both network types, it is argued that non-binary webs are more important than binary webs. [Copyright &y& Elsevier]

In mast cells (MCs), the TEC family kinase (TFK) BTK constitutes a central regulator of antigen (Ag)-triggered, FcεRI-mediated PLCγ phosphorylation, Ca2+ mobilization, degranulation, and pro-inflammatory cytokine production. Less is known about the function of BTK in the context of stem cell factor (SCF)-induced KIT signaling. In bone marrow-derived MCs (BMMCs), Ag stimulation caused intense phosphorylation of BTK at Y551 in its active center and at Y223 in its SH3-domain, whereas in response to SCF only Y223 was significantly phosphorylated. Further data using the TFK inhibitor Ibrutinib indicated that BTK Y223 is phosphorylated by a non-BTK TFK upon SCF stimulation. In line, SCF-induced PLCγ1 phosphorylation was stronger attenuated by Ibrutinib than by BTK deficiency. Subsequent pharmacological analysis of PLCγ function revealed a total block of SCF-induced Ca2+ mobilization by PLC inhibition, whereas only the sustained phase of Ca2+ flux was curtailed in Ag-stimulated BMMCs. Despite this severe stimulus-dependent difference in inducing Ca2+ mobilization, PLCγ inhibition suppressed Ag- and SCF-induced degranulation and pro-inflammatory cytokine production to comparable extents, suggesting involvement of additional TFK(s) or PLCγ-dependent signaling components. In addition to PLCγ, the MAPKs p38 and JNK were activated by Ag in a BTK-dependent manner; this was not observed upon SCF stimulation. Hence, FcεRI and KIT employ different mechanisms for activating PLCγ, p38, and JNK, which might strengthen their cooperation regarding pro-inflammatory MC effector functions. Importantly, our data clearly demonstrate that analyzing BTK Y223 phosphorylation is not sufficient to prove BTK activation. Unlabelled Image • In contrast to Ag, SCF hardly induces BTK Y551 phosphorylation in BMMCs. • SCF/KIT signaling uses non-BTK TFKs for activating PLCγ1 tyrosine phosphorylation. • Synergistic quality of Ag plus SCF-induced TNF-α production is independent of BTK. • Analysis of BTK Y223 phosphorylation is not sufficient to prove BTK activation. [ABSTRACT FROM AUTHOR]

The endoplasmic reticulum (ER) is a dynamic organelle that responds to demand in secretory proteins by undergoing expansion. The mechanisms that control the homeostasis of ER size and function involve the activation of the unfolded protein response (UPR). The UPR plays a role in various effector functions of immune cells. Mast cells (MCs) are highly granular tissue-resident cells and key drivers of allergic inflammation. Their diverse secretory functions in response to activation through the high-affinity receptor for IgE (FcεRI) suggest a role for the UPR in their function. Using human cord blood-derived MCs, we found that FcεRI triggering elevated the expression level and induced activation of the UPR transducers IRE1α and PERK, accompanied by expansion of the ER. In mouse bone marrow-derived MCs and peritoneal MCs, the ER underwent a more moderate expansion, and the UPR was not induced following MC activation. The deletion of IRE1α in mouse MCs did not affect proliferation, survival, degranulation, or cytokine stimulation following FcεRI triggering, but it did diminish the surface expression of TLR4 and the consequent response to LPS. A similar phenotype was observed in human MCs using an IRE1α inhibitor. Our data indicate that the ER of MCs, primarily of humans, undergoes a rapid remodeling in response to activation that promotes responses to TLR4. We suggest that IRE1α inhibition can be a strategy for inhibiting the hyperactivation of MCs by LPS over the course of allergic responses. [ABSTRACT FROM AUTHOR]

Faithful DNA repair is essential to maintain genome integrity. Ultraviolet (UV) irradiation elicits both the recruitment of DNA repair factors and the deposition of histone marks such as monoubiquitylation of histone H2A at lesion sites. Here, we report how a ubiquitin E3 ligase complex specific to DNA repair is remodeled at lesion sites in the global genome nucleotide excision repair (GG-NER) pathway. Monoubiquitylation of histone H2A (H2A-ubiquitin) is catalyzed predominantly by a novel E3 ligase complex consisting of DDB2, DDB1, CUL4B, and RING1B (UV-RING1B complex) that acts early during lesion recognition. The H2A-ubiquitin binding protein ZRF1 mediates remodeling of this E3 ligase complex directly at the DNA lesion site, causing the assembly of the UV-DDB-CUL4A E3 ligase complex (DDB1-DDB2-CUL4A-RBX1). ZRF1 is an essential factor in GG-NER, and its function at damaged chromatin sites is linked to damage recognition factor XPC. Overall, the results shed light on the interplay between epigenetic and DNA repair recognition factors at DNA lesion sites. [ABSTRACT FROM AUTHOR]

Headaches are a common complaint in HIV positive patients attending emergency services. A thorough understanding of the differential diagnoses, initial investigations and empirical management of this presentation is essential for the assessing physician. We discuss a case of a patient with known advanced HIV infection presenting with headache to the emergency department. Given the range of possible diagnoses, broad-spectrum antimicrobial therapy was initially commenced. This was stopped when magnetic resonance imaging confirmed a diagnosis of venous sinus thrombosis. Anticoagulation therapy was started in accordance with current clinical guidelines after discussing the rationale and options for treatment with the patient. Here, we review the guidelines and supporting evidence for management of venous sinus thrombosis, and consider the challenges and strategies for engaging a patient with previous poor attendance in their ongoing care. [ABSTRACT FROM AUTHOR]

Background: Expansion of multi-C2H2 domain zinc finger (ZNF) genes, including the Krüppel-associated box (KRAB) subfamily, paralleled the evolution of tetrapodes, particularly in mammalian lineages. Advances in their cataloging and characterization suggest that the functions of the KRAB-ZNF gene family contributed to mammalian speciation. Results: Here, we characterized the human 8q24.3 ZNF cluster on the genomic, the phylogenetic, the structural and the transcriptome level. Six (ZNF7, ZNF34, ZNF250, ZNF251, ZNF252, ZNF517) of the seven locus members contain exons encoding KRAB domains, one (ZNF16) does not. They form a paralog group in which the encoded KRAB and ZNF protein domains generally share more similarities with each other than with other members of the human ZNF superfamily. The closest relatives with respect to their DNA-binding domain were ZNF7 and ZNF251. The analysis of orthologs in therian mammalian species revealed strong conservation and purifying selection of the KRAB-A and zinc finger domains. These findings underscore structural/functional constraints during evolution. Gene losses in the murine lineage (ZNF16, ZNF34, ZNF252, ZNF517) and potential protein truncations in primates (ZNF252) illustrate ongoing speciation processes. Tissue expression profiling by quantitative real-time PCR showed similar but distinct patterns for all tested ZNF genes with the most prominent expression in fetal brain. Based on accompanying expression signatures in twenty-six other human tissues ZNF34 and ZNF250 revealed the closest expression profiles. Together, the 8q24.3 ZNF genes can be assigned to a cerebellum, a testis or a prostate/thyroid subgroup. These results are consistent with potential functions of the ZNF genes in morphogenesis and differentiation. Promoter regions of the seven 8q24.3 ZNF genes display common characteristics like missing TATA-box, CpG island-association and transcription factor binding site (TFBS) modules. Common TFBS modules partly explain the observed expression pattern similarities. Conclusions: The ZNF genes at human 8q24.3 form a relatively old mammalian paralog group conserved in eutherian mammals for at least 130 million years. The members persisted after initial duplications by undergoing subfunctionalizations in their expression patterns and target site recognition. KRAB-ZNF mediated repression of transcription might have shaped organogenesis in mammalian ontogeny. [ABSTRACT FROM AUTHOR]

Background. Preoperative imaging of the nose and paranasal sinus is standard in otorhinolaryngology. Previous studies on phantoms demonstrated the potential for dose reduction of cone beam computed tomography (CBCT) by varying the application parameters. Methodology. Based on previous studies, the standard protocol of paranasal sinus imaging by CBCT was altered. One hundred and fifty examinations using the old protocol (01/2010-01/2011, high dosage) and 150 examinations using the new protocol (09/2012-09/2013, low dosage) were evaluated and compared for the visibility of 17 anatomical structures, the Lund-Mackay Score, and technical parameters. Results. Alteration of the protocol resulted in a significant reduction in dosage (6.64mGy versus 2.88 mGy). Both groups showed the sameamount of pathology (Lund-Mackay Score: 4.95±3.79 versus 5.26±5.77; p = 0.558). There was a significant better visibility of the anatomical structures (all visible = 1, nothing visible = 4) (results: 1.25 versus 1.17; p = 0.001) in the low-dosage group. Conclusion. Despite a significant reduction in the applied dosage, reliable visualization of the bony anatomy of the anterior skull base is possible by CBCT. This demonstrates the need for the discussion of the required clinical imaging quality. [ABSTRACT FROM AUTHOR]

The widespread second messenger molecule cyclic di-GMP (cdG) regulates the transition from motile and virulent lifestyles to sessile, biofilm-forming ones in a wide range of bacteria. Many pathogenic and commensal bacterial-host interactions are known to be controlled by cdG signaling. Although the biochemistry of cyclic dinucleotide metabolism is well understood, much remains to be discovered about the downstream signaling pathways that induce bacterial responses upon cdG binding. As part of our ongoing research into the role of cdG signaling in plant-associated Pseudomonas species, we carried out an affinity capture screen for cdG binding proteins in the model organism Pseudomonas fluorescens SBW25. The flagella export AAA + ATPase FliI was identified as a result of this screen and subsequently shown to bind specifically to the cdG molecule, with a KD in the low micromolar range. The interaction between FliI and cdG appears to be very widespread. In addition to FliI homologs from diverse bacterial species, high affinity binding was also observed for the type III secretion system homolog HrcN and the type VI ATPase ClpB2. The addition of cdG was shown to inhibit FliI and HrcN ATPase activity in vitro. Finally, a combination of site-specific mutagenesis, mass spectrometry, and in silico analysis was used to predict that cdG binds to FliI in a pocket of highly conserved residues at the interface between two FliI subunits. Our results suggest a novel, fundamental role for cdG in controlling the function of multiple important bacterial export pathways, through direct allosteric control of export ATPase proteins. [ABSTRACT FROM AUTHOR]

Background: Gene reshuffling, point mutations and horizontal gene transfer contribute to bacterial genome variation, but require the genome to rewire its transcriptional circuitry to ensure that inserted, mutated or reshuffled genes are transcribed at appropriate levels. The genomes of Epsilonproteobacteria display very low synteny, due to high levels of reshuffling and reorganisation of gene order, but still share a significant number of gene orthologs allowing comparison. Here we present the primary transcriptome of the pathogenic Epsilonproteobacterium Campylobacter jejuni, and have used this for comparative and predictive transcriptomics in the Epsilonproteobacteria. Results: Differential RNA-sequencing using 454 sequencing technology was used to determine the primary transcriptome of C. jejuni NCTC 11168, which consists of 992 transcription start sites (TSS), which included 29 putative non-coding and stable RNAs, 266 intragenic (internal) TSS, and 206 antisense TSS. Several previously unknown features were identified in the C. jejuni transcriptional landscape, like leaderless mRNAs and potential leader peptides upstream of amino acid biosynthesis genes. A cross-species comparison of the primary transcriptomes of C. jejuni and the related Epsilonproteobacterium Helicobacter pylori highlighted a lack of conservation of operon organisation, position of intragenic and antisense promoters or leaderless mRNAs. Predictive comparisons using 40 other Epsilonproteobacterial genomes suggests that this lack of conservation of transcriptional features is common to all Epsilonproteobacterial genomes, and is associated with the absence of genome synteny in this subdivision of the Proteobacteria. Conclusions: Both the genomes and transcriptomes of Epsilonproteobacteria are highly variable, both at the genome level by combining and division of multicistronic operons, but also on the gene level by generation or deletion of promoter sequences and 5' untranslated regions. Regulatory features may have evolved after these species split from a common ancestor, with transcriptome rewiring compensating for changes introduced by genomic reshuffling and horizontal gene transfer [ABSTRACT FROM AUTHOR]

Molecular interaction networks establish all cell biological processes. The networks are under intensive research that is facilitated by new high-throughput measurement techniques for the detection, quantification, and characterization of molecules and their physical interactions. For the common model organism yeast Saccharomyces cerevisiae, public databases store a significant part of the accumulated information and, on the way to better understanding of the cellular processes, there is a need to integrate this information into a consistent reconstruction of the molecular interaction network. This work presents and validates RefRec, the most comprehensive molecular interaction network reconstruction currently available for yeast. The reconstruction integrates protein synthesis pathways, a metabolic network, and a protein-protein interaction network from major biological databases. The core of the reconstruction is based on a reference object approach in which genes, transcripts, and proteins are identified using their primary sequences. This enables their unambiguous identification and non-redundant integration. The obtained total number of different molecular species and their connecting interactions is ∼67,000. In order to demonstrate the capacity of RefRec for functional predictions, it was used for simulating the gene knockout damage propagation in the molecular interaction network in ∼590,000 experimentally validated mutant strains. Based on the simulation results, a statistical classifier was subsequently able to correctly predict the viability of most of the strains. The results also showed that the usage of different types of molecular species in the reconstruction is important for accurate phenotype prediction. In general, the findings demonstrate the benefits of global reconstructions of molecular interaction networks. With all the molecular species and their physical interactions explicitly modeled, our reconstruction is able to serve as a valuable resource in additional analyses involving objects from multiple molecular -omes. For that purpose, RefRec is freely available in the Systems Biology Markup Language format. [ABSTRACT FROM AUTHOR]

Recent analyses indicate that differences in protein concentrations are only 20%-40% attributable to variable mRNA levels, underlining the importance of posttranscriptional regulation. Generally, protein concentrations depend on the translation rate (which is proportional to the translational activity, TA) and the degradation rate. By integrating 12 publicly available large-scale datasets and additional database information of the yeast Saccharomyces cerevisiae, we systematically analyzed five factors contributing to TA: mRNA concentration, ribosome density, ribosome occupancy, the codon adaptation index, and a newly developed "tRNA adaptation index." Our analysis of the functional relationship between the TA and measured protein concentrations suggests that the TA follows Michaelis-Menten kinetics. The calculated TA, together with measured protein concentrations, allowed us to estimate degradation rates for 4,125 proteins under standard conditions. A significant correlation to recently published degradation rates supports our approach. Moreover, based on a newly developed scoring system, we identified and analyzed genes subjected to the posttranscriptional regulation mechanism, translation on demand. Next we applied these findings to publicly available data of protein and mRNA concentrations under four stress conditions. The integration of these measurements allowed us to compare the condition-specific responses at the posttranscriptional level. Our analysis of all 62 proteins that have been measured under all four conditions revealed proteins with very specific posttranscriptional stress response, in contrast to more generic responders, which were nonspecifically regulated under several conditions. The concept of specific and genegeneric responders is known for transcriptional regulation. Here we show that it also holds true at the posttranscriptional level. [ABSTRACT FROM AUTHOR]

Systematic chromatin immunoprecipitation (chIP-chip) experiments have become a central technique for mapping transcriptional interactions in model organisms and humans. However, measurement of chromatin binding does not necessarily imply regulation, and binding may be difficult to detect if it is condition or cofactor dependent. To address these challenges, we present an approach for reliably assigning transcription factors (TFs) to target genes that integrates many lines of direct and indirect evidence into a single probabilistic model. Using this approach, we analyze publicly available chIP-chip binding profiles measured for yeast TFs in standard conditions, showing that our model interprets these data with significantly higher accuracy than previous methods. Pooling the high-confidence interactions reveals a large network containing 363 significant sets of factors (TF modules) that cooperate to regulate common target genes. In addition, the method predicts 980 novel binding interactions with high confidence that are likely to occur in so-far untested conditions. Indeed, using new chIP-chip experiments we show that predicted interactions for the factors Rpn4p and Pdr1p are observed only after treatment of cells with methyl-methanesulfonate, a DNA-damaging agent. We outline the first approach for consistently integrating all available evidences for TF-target interactions and we comprehensively identify the resulting TF module hierarchy. Prioritizing experimental conditions for each factor will be especially important as increasing numbers of chIP-chip assays are performed in complex organisms such as humans, for which "standard conditions" are ill defined. [ABSTRACT FROM AUTHOR]

Summary: Many large ‘omics’ datasets have been published and many more are expected in the near future. New analysis methods are needed for best exploitation. We have developed a graphical user interface (GUI) for easy data analysis. Our discovery of all significant substructures (DASS) approach elucidates the underlying modularity, a typical feature of complex biological data. It is related to biclustering and other data mining approaches. Importantly, DASS-GUI also allows handling of multi-sets and calculation of statistical significances. DASS-GUI contains tools for further analysis of the identified patterns: analysis of the pattern hierarchy, enrichment analysis, module validation, analysis of additional numerical data, easy handling of synonymous names, clustering, filtering and merging. Different export options allow easy usage of additional tools such as Cytoscape. [ABSTRACT FROM PUBLISHER]

Ischemic stroke is known to cause the accumulation of misfolded proteins and loss of calcium homeostasis leading to impairment of endoplasmic reticulum (ER) function. The unfolded protein response (UPR) is an ER-located and cytoprotective pathway that aims to resolve ER stress. Transmembrane BAX inhibitor-1 motif-containing (TMBIM) protein family member TMBIM3/GRINA is highly expressed in the brain and mostly located at the ER membrane suppressing ER calcium release by inositol-1,4,5-trisphosphate receptors. GRINA confers neuroprotection and is regulated by erythropoietin (EPO) after murine cerebral ischemia. However, the role of GRINA and the impact of EPO treatment on the post-ischemic UPR have not been elucidated yet. We subjected GRINA-deficient (Grina−/−) and wildtype mice to transient (30 min) middle cerebral artery occlusion (tMCAo) followed by 6 h or 72 h of reperfusion. We administered EPO or saline 0, 24 and 48 h after tMCAo/sham surgery. Oxygen–glucose deprivation (OGD) and pharmacological stimulation of the UPR using Tunicamycin and Thapsigargin were carried out in primary murine cortical mixed cell cultures. Treatment with the PERK-inhibitor GSK-2606414, IRE1a-RNase-inhibitor STF-083010 and EPO was performed 1 h prior to either 1 h, 2 h or 3 h of OGD. We found earlier and larger infarct demarcations in Grina−/− mice compared to wildtype mice, which was accompanied by a worse neurological outcome and an abolishment of EPO-mediated neuroprotection after ischemic stroke. In addition, GRINA-deficiency increased apoptosis and the activation of the corresponding PERK arm of the UPR after stroke. EPO enhanced the post-ischemic activation of pro-survival IRE1a and counteracted the pro-apoptotic PERK branch of the UPR. Both EPO and the PERK-inhibitor GSK-2606414 reduced cell death and regulated Grina mRNA levels after OGD. In conclusion, GRINA plays a crucial role in post-ischemic UPR and the use of both GSK-2606414 and EPO might lead to neuroprotection. [ABSTRACT FROM AUTHOR]

Motivation: DiProGB is an easy to use new genome browser that encodes the primary nucleotide sequence by thermodynamical and geometrical dinucleotide properties. The nucleotide sequence is thus converted into a sequence graph. This visualization, supported by different graph manipulation options, facilitates genome analyses, because the human brain can process visual information better than textual information. Also, DiProGB can identify genomic regions where certain physical properties are more conserved than the nucleotide sequence itself. Most of the DiProGB tools can be applied to both, the primary nucleotide sequence and the sequence graph. They include motif and repeat searches as well as statistical analyses. DiProGB adds a new dimension to the common genome analysis approaches by taking into account the physical properties of DNA and RNA. [ABSTRACT FROM PUBLISHER]