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BACKGROUND: Patients with psychosis and patients with depression exhibit widespread neurobiological abnormalities. The analysis of dynamic functional connectivity (dFC) allows for the detection of changes in complex brain activity patterns, providing insights into common and unique processes underlying these disorders. METHODS: We report the analysis of dFC in a large sample including 127 patients at clinical high risk for psychosis, 142 patients with recent-onset psychosis, 134 patients with recent-onset depression, and 256 healthy control participants. A sliding window-based technique was used to calculate the time-dependent FC in resting-state magnetic resonance imaging data, followed by clustering to reveal recurrent FC states in each diagnostic group. RESULTS: We identified 5 unique FC states, which could be identified in all groups with high consistency (mean r = 0.889 [SD = 0.116]). Analysis of dynamic parameters of these states showed a characteristic increase in the lifetime and frequency of a weakly connected FC state in patients with recent-onset depression (p < .0005) compared with the other groups and a common increase in the lifetime of an FC state characterized by high sensorimotor and cingulo-opercular connectivities in all patient groups compared with the healthy control group (p < .0002). Canonical correlation analysis revealed a mode that exhibited significant correlations between dFC parameters and clinical variables (r = 0.617, p < .0029), which was associated with positive psychosis symptom severity and several dFC parameters. CONCLUSIONS: Our findings indicate diagnosis-specific alterations of dFC and underline the potential of dynamic analysis to characterize disorders such as depression and psychosis and clinical risk states.

Extracellular vesicles (EVs) are important mediators of communication between cells. Here, we reveal a new mode of intercellular communication by melanosomes, large EVs secreted by melanocytes for melanin transport. Unlike small EVs, which are disintegrated within the receiver cell, melanosomes stay intact within them, gain a unique protein signature, and can then be further transferred to another cell as “second-hand” EVs. We show that melanoma-secreted melanosomes passaged through epidermal keratinocytes or dermal fibroblasts can be further engulfed by resident macrophages. This process leads to macrophage polarization into pro-tumor or pro-immune cell infiltration phenotypes. Melanosomes that are transferred through fibroblasts can carry AKT1, which induces VEGF secretion from macrophages in an mTOR-dependent manner, promoting angiogenesis and metastasis in vivo. In melanoma patients, macrophages that are co-localized with AKT1 are correlated with disease aggressiveness, and immunotherapy non-responders are enriched in macrophages containing melanosome markers. Our findings suggest that interactions mediated by second-hand extracellular vesicles contribute to the formation of the metastatic niche, and that blocking the melanosome cues of macrophage diversification could be helpful in halting melanoma progression.

Der vorliegende Beitrag hat zwei miteinander verbundene Ziele. Als Reaktion auf das häufige Plädoyer für ein stärkeres Einbeziehen des Texts und der Textlinguistik in den Fremdsprachenunterricht wird erstens eine an der Universität Bergen, Norwegen, durchgeführte Unterrichtsreihe im Bereich der kontrastiven Textlinguistik bzw. Textgrammatik vorgestellt und erörtert. Zweitens wird im Rahmen eines Pretest/Posttest/Follow-up-Test-Designs geprüft, inwieweit die Vermittlung der Vorfeld-Funktionen bei der Textvernetzung im norwegischen und im deutschen argumentativen Text dazu beiträgt, dass sich norwegische Deutschstudierende textlinguistischer Unterschiede bewusst werden und dies in ihrer Schreibpraxis umsetzen.

Der vorliegende Beitrag hat zwei miteinander verbundene Ziele. Als Reaktion auf das häufige Plädoyer für ein stärkeres Einbeziehen des Texts und der Textlinguistik in den Fremdsprachenunterricht wird erstens eine an der Universität Bergen, Norwegen, durchgeführte Unterrichtsreihe im Bereich der kontrastiven Textlinguistik bzw. Textgrammatik vorgestellt und erörtert. Zweitens wird im Rahmen eines Pretest/Posttest/Follow-up-Test-Designs geprüft, inwieweit die Vermittlung der Vorfeld-Funktionen bei der Textvernetzung im norwegischen und im deutschen argumentativen Text dazu beiträgt, dass sich norwegische Deutschstudierende textlinguistischer Unterschiede bewusst werden und dies in ihrer Schreibpraxis umsetzen.

Der vorliegende Beitrag hat zwei miteinander verbundene Ziele. Als Reaktion auf das häufige Plädoyer für ein stärkeres Einbeziehen des Texts und der Textlinguistik in den Fremdsprachenunterricht wird erstens eine an der Universität Bergen, Norwegen, durchgeführte Unterrichtsreihe im Bereich der kontrastiven Textlinguistik bzw. Textgrammatik vorgestellt und erörtert. Zweitens wird im Rahmen eines Pretest/Posttest/Follow-up-Test-Designs geprüft, inwieweit die Vermittlung der Vorfeld-Funktionen bei der Textvernetzung im norwegischen und im deutschen argumentativen Text dazu beiträgt, dass sich norwegische Deutschstudierende textlinguistischer Unterschiede bewusst werden und dies in ihrer Schreibpraxis umsetzen.

Minimizing the difference of two submodular (DS) functions is a problem that naturally occurs in various machine learning problems. Although it is well known that a DS problem can be equivalently formulated as the minimization of the difference of two convex (DC) functions, existing algorithms do not fully exploit this connection. A classical algorithm for DC problems is called the DC algorithm (DCA). We introduce variants of DCA and its complete form (CDCA) that we apply to the DC program corresponding to DS minimization. We extend existing convergence properties of DCA, and connect them to convergence properties on the DS problem. Our results on DCA match the theoretical guarantees satisfied by existing DS algorithms, while providing a more complete characterization of convergence properties. In the case of CDCA, we obtain a stronger local minimality guarantee. Our numerical results show that our proposed algorithms outperform existing baselines on two applications: speech corpus selection and feature selection., Comment: Removed minor errors in Proposition 2.7, Theorem 4.3 and Corollary 4.4. Key results unchanged (see Erratum on p.4). Also fixed typos

We explore a method of statistical estimation called Maximum Entropy on the Mean (MEM) which is based on an information-driven criterion that quantifies the compliance of a given point with a reference prior probability measure. At the core of this approach lies the MEM function which is a partial minimization of the Kullback-Leibler divergence over a linear constraint. In many cases, it is known that this function admits a simpler representation (known as the Cram\'er rate function). Via the connection to exponential families of probability distributions, we study general conditions under which this representation holds. We then address how the associated MEM estimator gives rise to a wide class of MEM-based regularized linear models for solving inverse problems. Finally, we propose an algorithmic framework to solve these problems efficiently based on the Bregman proximal gradient method, alongside proximal operators for commonly used reference distributions. The article is complemented by a software package for experimentation and exploration of the MEM approach in applications.

This paper provides a variational analysis of the unconstrained formulation of the LASSO problem, ubiquitous in statistical learning, signal processing, and inverse problems. In particular, we establish smoothness results for the optimal value as well as Lipschitz properties of the optimal solution as functions of the right-hand side (or measurement vector) and the regularization parameter. Moreover, we show how to apply the proposed variational analysis to study the sensitivity of the optimal solution to the tuning parameter in the context of compressed sensing with subgaussian measurements. Our theoretical findings are validated by numerical experiments.

Grape phylloxera (Daktulosphaira vitifoliae, syn. Viteus vitifoliae), a destructive root and foliar pest of grapevines, occurs in almost all viticulture regions worldwide. However, certain regions have remained "phylloxera free." Until recently, this included Washington state (United States), where this insect is regulated as a quarantine pest by Washington State Department of Agriculture. In 2019, established phylloxera populations were discovered in Washington. Phylloxera is typically managed by using resistant or tolerant rootstocks. In Washington, most wine grapes are grown on their own roots of the susceptible species Vitis vinifera instead of grafted rootstock, and thus, are at high risk of vine death should they become infested with phylloxera. This article reports development of a phylloxera risk map for Washington state using geographical soil texture (sand content) and soil temperature data. Weighted averages of soil texture data (mapping year: 2016, depth: 0-100 cm) were obtained from United States Department of Agriculture-Natural Resource Conservation Service (USDA-NRCS) and soilgrids. Soil temperature data were obtained from over 200 weather stations of Washington State University's AgWeatherNet network. Threshold-based classifications were performed in Quantum GIS software on the rasterized soil sand content and temperature independently to derive low, moderate, and high-risk areas, with risk defined as site suitability for optimal phylloxera development. The validation identified 22 out of 23 confirmed phylloxera-positive sites as "high risk," and one site as "moderate risk" when considering soil sand content alone. Soil temperature data alone classified 10 sites as "high risk" and 13 sites as "low risk." When soil sand content was combined with soil temperature (as a risk modifier), 10 sites were classified as "high risk," 12 sites as "high-moderate risk" and one site as "moderate-low" risk. Ground-truth comparisons of confirmed positive sites for p

(1) Background: A reliable non-invasive distinction between low- and high-risk pancreatic intraductal papillary mucinous neoplasms (IPMN) is needed to effectively detect IPMN with malignant potential. This would improve preventative care and reduce the risk of developing pancreatic cancer and overtreatment. The present study aimed at exploring the presence of autoreactive antibodies in the blood of patients with IPMN of various grades of dysplasia. (2) Methods: A single-center cohort was studied composed of 378 serum samples from patients with low-grade IPMN (n = 91), high-grade IPMN (n = 66), IPMN with associated invasive cancer (n = 30), pancreatic ductal adenocarcinoma (PDAC) stages T1 (n = 24) and T2 (n = 113), and healthy controls (n = 54). A 249 full-length recombinant human protein microarray was used for profiling the serum samples. (3) Results: 14 proteins were identified as potential biomarkers for grade distinction in IPMN, yielding high specificity but mediocre sensitivity. (4) Conclusions: The identified autoantibodies are potential biomarkers that may assist in the detection of malignancy in IPMN patients.

Pacific Northwest Extension Publishing PNW 749, published Jan. 2021.

University of Idaho Extension PNW 749S, Spanish-language edition, published Jan. 2021.

The projection onto the epigraph or a level set of a closed proper convex function can be achieved by finding a root of a scalar equation that involves the proximal operator as a function of the proximal parameter. This paper develops the variational analysis of this scalar equation. The approach is based on a study of the variational-analytic properties of general convex optimization problems that are (partial) infimal projections of the the sum of the function in question and the perspective map of a convex kernel. When the kernel is the Euclidean norm squared, the solution map corresponds to the proximal map, and thus the variational properties derived for the general case apply to the proximal case. Properties of the value function and the corresponding solution map -- including local Lipschitz continuity, directional differentiability, and semismoothness -- are derived. An SC$^1$ optimization framework for computing epigraphical and level-set projections is thus established. Numerical experiments on 1-norm projection illustrate the effectiveness of the approach as compared with specialized algorithms

Image deblurring is a notoriously challenging ill-posed inverse problem. In recent years, a wide variety of approaches have been proposed based upon regularization at the level of the image or on techniques from machine learning. We propose an alternative approach, shifting the paradigm towards regularization at the level of the probability distribution on the space of images. Our method is based upon the idea of maximum entropy on the mean wherein we work at the level of the probability density function of the image whose expectation is our estimate of the ground truth. Using techniques from convex analysis and probability theory, we show that the method is computationally feasible and amenable to very large blurs. Moreover, when images are imbedded with symbology (a known pattern), we show how our method can be applied to approximate the unknown blur kernel with remarkable effects. While our method is stable with respect to small amounts of noise, it does not actively denoise. However, for moderate to large amounts of noise, it performs well by preconditioned denoising with a state of the art method., Comment: 34 pages, 7 figures

In orthopaedic medicine, connective tissues are often affected by traumatic or degenerative injuries, and surgical intervention is required. Rotator cuff tears are a common cause of shoulder pain and disability among adults. The development of graft materials for bridging the gap between tendon and bone after chronic rotator cuff tears is essentially required. The limiting factor for the clinical success of a tissue engineering construct is a fast and complete vascularization of the construct. Otherwise, immigrating cells are not able to survive for a longer period of time, resulting in the failure of the graft material. The femur chamber allows the observation of microhaemodynamic parameters inside implants located in close vicinity to the femur in repeated measurements in vivo. We compared a porous polymer patch (a commercially available porous polyurethane-based scaffold from Biomerix™) with electrospun polycaprolactone (PCL) fibre mats and chitosan (CS)-graft-PCL modified electrospun PCL (CS-g-PCL) fibre mats in vivo. By means of intravital fluorescence microscopy, microhaemodynamic parameters were analysed repetitively over 20 days at intervals of 3 to 4 days. CS-g-PCL modified fibre mats showed a significantly increased vascularization at Day 10 compared with Day 6 and at Day 14 compared with the porous polymer patch and the unmodified PCL fibre mats at the same day. These results could be verified by histology. In conclusion, a clear improvement in terms of vascularization and biocompatibility is achieved by graft-copolymer modification compared with the unmodified material. © 2019 The Authors Journal of Tissue Engineering and Regenerative Medicine Published by John Wiley & Sons Ltd

Deep neural networks perform well on real world data but are prone to adversarial perturbations: small changes in the input easily lead to misclassification. In this work, we propose an attack methodology not only for cases where the perturbations are measured by $\ell_p$ norms, but in fact any adversarial dissimilarity metric with a closed proximal form. This includes, but is not limited to, $\ell_1, \ell_2$, and $\ell_\infty$ perturbations; the $\ell_0$ counting "norm" (i.e. true sparseness); and the total variation seminorm, which is a (non-$\ell_p$) convolutional dissimilarity measuring local pixel changes. Our approach is a natural extension of a recent adversarial attack method, and eliminates the differentiability requirement of the metric. We demonstrate our algorithm, ProxLogBarrier, on the MNIST, CIFAR10, and ImageNet-1k datasets. We consider undefended and defended models, and show that our algorithm easily transfers to various datasets. We observe that ProxLogBarrier outperforms a host of modern adversarial attacks specialized for the $\ell_0$ case. Moreover, by altering images in the total variation seminorm, we shed light on a new class of perturbations that exploit neighboring pixel information.

Michael Dreher,1 Pierre-Charles Neuzeret,2 Wolfram Windisch,3 Dagmar Martens,2 Gerhard Hoheisel,4 Andreas Gröschel,5 Holger Woehrle,6 Thomas Fetsch,7 Andrea Graml,2 Thomas Köhnlein8 1Department of Pneumology and Intensive Care Medicine, University Hospital Aachen, Aachen, Germany; 2ResMed, Martinsried, Germany; 3Department of Pneumology, Cologne Merheim Hospital, Kliniken Der Stadt Köln gGmbH, Witten/Herdecke University, Cologne, Germany; 4Studienzentrum, Leipzig, Germany; 5Mvz Aaz, Aachen, Germany; 6Sleep and Ventilation Center Blaubeuren, Respiratory Center Ulm, Ulm, Germany; 7The Clinical Research Institute, Munich, Germany; 8Facharztzentrum Teuchern, Teuchern, GermanyCorrespondence: Michael DreherDepartment of Pneumology and Intensive Care Medicine, University Hospital Aachen, Pauwelsstraße 30, Aachen D- 52057, GermanyTel +49 241 80 88763Fax +49 241 80 82153Email mdreher@ukaachen.deBackground: Non-invasive ventilation (NIV) has been shown to improve survival and quality of life in COPD patients with chronic hypercapnic respiratory failure. However, the proportion of COPD patients with chronic hypercapnia is not yet known and clinical data enabling better identification of patients are scarce. The HOmeVent registry was initiated to determine the prevalence of chronic hypercapnia in COPD in an outpatient setting and to evaluate the predictors of hypercapnia.Methods: HOmeVent is a multicenter, prospective, observational, non-interventional patient registry that includes COPD patients in GOLD stage 3 or 4. Eligible patients were identified and enrolled in an outpatient setting during routine clinic visits. Assessments included blood gas analyses, pulmonary function testing and quality of life assessment.Results: Ten outpatient clinics in Germany enrolled 231 COPD patients in the registry (135 in GOLD stage 3 (58%) and 96 in GOLD stage 4 (42%)). Arterial carbon dioxide pressure (PaCO2) was ≥45 mmHg in 58 patients (25%); of

Transcriptional profiling was performed on 452 RNA preparations isolated from various types of pancreatic tissue from tumour patients and healthy donors, with a particular focus on peritumoral samples. Pancreatic ductal adenocarcinomas (PDAC) and cystic tumours were most different in these non-tumorous tissues surrounding them, whereas the actual tumours exhibited rather similar transcript patterns. The environment of cystic tumours was transcriptionally nearly identical to normal pancreas tissue. In contrast, the tissue around PDAC behaved a lot like the tumour, indicating some kind of field defect, while showing far less molecular resemblance to both chronic pancreatitis and healthy tissue. This suggests that the major pathogenic difference between cystic and ductal tumours may be due to their cellular environment rather than the few variations between the tumours. Lack of correlation between DNA methylation and transcript levels makes it unlikely that the observed field defect in the peritumoral tissue of PDAC is controlled to a large extent by such epigenetic regulation. Functionally, a strikingly large number of autophagy-related transcripts was changed in both PDAC and its peritumoral tissue, but not in other pancreatic tumours. A transcription signature of 15 autophagy-related genes was established that permits a prognosis of survival with high accuracy and indicates the role of autophagy in tumour biology.

Transcriptional profiling was performed on 452 RNA preparations isolated from various types of pancreatic tissue from tumour patients and healthy donors, with a particular focus on peritumoral samples. Pancreatic ductal adenocarcinomas (PDAC) and cystic tumours were most different in these non-tumorous tissues surrounding them, whereas the actual tumours exhibited rather similar transcript patterns. The environment of cystic tumours was transcriptionally nearly identical to normal pancreas tissue. In contrast, the tissue around PDAC behaved a lot like the tumour, indicating some kind of field defect, while showing far less molecular resemblance to both chronic pancreatitis and healthy tissue. This suggests that the major pathogenic difference between cystic and ductal tumours may be due to their cellular environment rather than the few variations between the tumours. Lack of correlation between DNA methylation and transcript levels makes it unlikely that the observed field defect in the peritumoral tissue of PDAC is controlled to a large extent by such epigenetic regulation. Functionally, a strikingly large number of autophagy-related transcripts was changed in both PDAC and its peritumoral tissue, but not in other pancreatic tumours. A transcription signature of 15 autophagy-related genes was established that permits a prognosis of survival with high accuracy and indicates the role of autophagy in tumour biology.

[Background] Variable domains of camelid heavy-chain antibodies, commonly named nanobodies, have highbiotechnological potential. In view of their broad range of applications in research, diagnostics and therapy,engineering their stability is of particular interest. One important aspect is the improvement of thermostability,because it can have immediate effects on conformational stability, protease resistance and aggregation pro-pensity of the protein, [Methods] We analyzed the sequences and thermostabilities of 78 purified nanobody binders. From this data,potentially stabilizing amino acid variations were identified and studied experimentally.Results:Some mutations improved the stability of nanobodies by up to 6.1 °C, with an average of 2.3 °C acrosseight modified nanobodies. The stabilizing mechanism involves an improvement of both conformational stabilityand aggregation behavior, explaining the variable degree of stabilization in individual molecules. In some in-stances, variations predicted to be stabilizing actually led to thermal destabilization of the proteins. The reasonsfor this contradiction between prediction and experiment were investigated., [Conclusions] The results reveal a mutational strategy to improve the biophysical behavior of nanobody bindersand indicate a species-specificity of nanobody architecture, [General significance] This study illustrates the potential and limitations of engineering nanobody thermostabilityby merging sequence information with stability data, an aspect that is becoming increasingly important with therecent development of high-throughput biophysical methods

Generalized matrix-fractional (GMF) functions are a class of matrix support functions introduced by Burke and Hoheisel as a tool for unifying a range of seemingly divergent matrix optimization problems associated with inverse problems, regularization and learning. In this paper we dramatically simplify the support function representation for GMF functions as well as the representation of their subdifferentials. These new representations allow the ready computation of a range of important related geometric objects whose formulations were previously unavailable.

BACKGROUND: As treatments for constipation become increasingly available, it is important to know when to progress along the treatment algorithm if the patient is not better. AIM: To establish the definition of failure of a treatment to provide adequate relief (F-PAR) to support this management and referral process in patients with chronic constipation. METHODS: We conducted an international Delphi Survey among gastroenterologists and general practitioners with a special interest in chronic constipation. An initial questionnaire based on recognised rating scales was developed following a focus group. Data were collected from two subsequent rounds of questionnaires completed by all authors. Likert scales were used to establish a consensus on a shorter list of more severe symptoms. RESULTS: The initial focus group yielded a first round questionnaire with 84 statements. There was good consensus on symptom severity and a clear severity response curve, allowing 67 of the symptom-severity pairings to be eliminated. Subsequently, a clear consensus was established on further reduction to eight symptom statements in the final definition, condensed by the steering committee into five diagnostic statements (after replicate statements had been removed). CONCLUSIONS: We present an international consensus on chronic constipation, of five symptoms and their severities, any of which would be sufficient to provide clinical evidence of treatment failure. We also provide data representing an expert calibration of commonly used rating scales, thus allowing results of clinical trials expressed in terms of those scales to be converted into estimates of rates of provision of adequate relief.

DNA sequencing has advanced to a state that permits studying the genomes of individual patients as nearly a matter of routine. Towards analysing a tissue's protein content in a similar manner, we established a method for the production of microarrays that represent full-length proteins as they are encoded in individual specimens, exhibiting the particular variations, such as mutations or splice variations, present in these samples. From total RNA isolates, each transcript is copied to a specific location on the array by an on-chip polymerase elongation reaction, followed by in situ cell-free transcription and translation. These microarrays permit parallel analyses of variations in protein structure and interaction that are specific to particular samples.

After World War II, a widely circulated rumour claimed that the type-XXI submarine U 2511 had made a blind attack on the British cruiser NORFOLK during the final phase of the war. An investigation carried out in 1998 came to the conclusion that, on the basis of the spatiotemporal data, this episode was impossible and therefore a myth. The article begins with a critical look at the basic information supplied by the various sources, as well as at the arguments that led to the verdict passed by the 1998 study. The focus then turns to the description of a scenario in which the known data are summarised in a logically conceivable set of proceedings. The scenario is not a historical reconstruction of the event but a concrete model of what would have been spatiotemporally plausible according to the data. The results clearly indicate that there is no sufficient or solid basis for concluding that the encounter between the U 2511 and the NORFOLK was a mere invention.

Using the electrospinning process the geometry of a heart valve is not replicable by just one manufacturing process. To produce heart valve scaffolds the heart valve leaflets and the vessel have to be produced in separated spinning processes. For the final product of a heart valve they have to be mated afterwards. In this work an already existing three-axes laser was enhanced to laser weld those scaffolds. The automation control software is based on the robot operating system (ROS). The mechatronically control is done by an Arduino Mega. A graphical user interface (GUI) is written with Python and Kivy.

Many diagnostic and therapeutic concepts require antibodies of high specificity. Recombinant binder libraries and related selection approaches allow the efficient isolation of antibodies against almost every target of interest. Nevertheless, it cannot be guaranteed that selected antibodies perform well and interact specifically enough with analytes unless an elaborate characterisation is performed. Here, we present an approach to shorten this process by combining the selection of suitable antibodies with the identification of informative target molecules by means of antibody microarrays, thereby reducing the effort of antibody characterisation by concentrating on relevant molecules. In a pilot scheme, a library of 456 single-chain variable fragment (scFv) binders to 134 antigens was used. They were arranged in a microarray format and incubated with the protein content of clinical tissue samples isolated from pancreatic ductal adenocarcinoma and healthy pancreas, as well as recurrent and non-recurrent bladder tumours. We observed significant variation in the expression of the E3 ubiquitin-protein ligase (CHFR) as well as the glutamate receptor interacting protein 2 (GRIP2), for example, always with more than one of the scFvs binding to these targets. Only the relevant antibodies were then characterised further on antigen microarrays and by surface plasmon resonance experiments so as to select the most specific and highest affinity antibodies. These binders were in turn used to confirm a microarray result by immunohistochemistry analysis.

The CRISPR/Cas9 system is a recently developed genome editing technique. In this study, we used a modified CRISPR system, which employs the fusion of inactive Cas9 (dCas9) and the FokI endonuclease (FokI-dCas9) to correct the most common variant (allele frequency 21.4%) in the phenylalanine hydroxylase (PAH) gene - c.1222C>T (p.Arg408Trp) - as an approach toward curing phenylketonuria (PKU). PKU is the most common inherited diseases in amino acid metabolism. It leads to severe neurological and neuropsychological symptoms if untreated or late diagnosed. Correction of the disease-causing variants could rescue residual PAH activity and restore normal function. Co-expression of a single guide RNA plasmid, a FokI-dCas9-zsGreen1 plasmid, and the presence of a single-stranded oligodeoxynucleotide in PAH_c.1222C>T COS-7 cells - an in vitro model for PKU - corrected the PAH variant and restored PAH activity. Also in this system, the HDR enhancer RS-1 improved correction efficiency. This proof-of-concept indicates the potential of the FokI-dCas9 system for precision medicine, in particular for targeting PKU and other monogenic metabolic diseases.

BACKGROUND: The majority of colorectal cancer (CRC) cases are preventable by early detection and removal of precancerous polyps. Even though CRC is the second most common internal cancer in Australia, only 30 per cent of the population considered to have risk factors participate in stool-based test screening programs. Evidence indicates a robust, blood-based, diagnostic assay would increase screening compliance. A number of potential diagnostic blood-based protein biomarkers for CRC have been reported, but all lack sensitivity or specificity for use as a stand-alone diagnostic. The aim of this study was to identify and validate a panel of protein-based biomarkers in independent cohorts that could be translated to a reliable, non-invasive blood-based screening test. PRINCIPAL FINDINGS: In two independent cohorts (n = 145 and n = 197), we evaluated seven single biomarkers in serum of CRC patients and age/gender matched controls that showed a significant difference between controls and CRC, but individually lack the sensitivity for diagnostic application. Using logistic regression strategies, we identified a panel of three biomarkers that discriminated between controls and CRC with 73% sensitivity at 95% specificity, when applied to either of the two cohorts. This panel comprised of Insulin like growth factor binding protein 2 (IGFBP2), Dickkopf-3 (DKK3), and Pyruvate kinase M2(PKM2). CONCLUSIONS: Due to the heterogeneous nature of CRC, a single biomarker is unlikely to have sufficient sensitivity or specificity for use as a stand-alone diagnostic screening test and a panel of markers may be more effective. We have identified a 3 biomarker panel that has higher sensitivity and specificity for early stage (Stage I and -II) disease than the faecal occult blood test, raising the possibility for its use as a non-invasive blood diagnostic or screening test.

Our ability to engineer organisms with new biosynthetic pathways and genetic circuits is limited by the availability of protein characterization data and the cost of synthetic DNA. With new tools for reading and writing DNA, there are opportunities for scalable assays that more efficiently and cost effectively mine for biochemical protein characteristics. To that end, we have developed the Multiplex Library Synthesis and Expression Correction (MuLSEC) method for rapid assembly, error correction, and expression characterization of many genes as a pooled library. This methodology enables gene synthesis from microarray-synthesized oligonucleotide pools with a one-pot technique, eliminating the need for robotic liquid handling. Post assembly, the gene library is subjected to an ampicillin based quality control selection, which serves as both an error correction step and a selection for proteins that are properly expressed and folded in E. coli. Next generation sequencing of post selection DNA enables quantitative analysis of gene expression characteristics. We demonstrate the feasibility of this approach by building and testing over 90 genes for empirical evidence of soluble expression. This technique reduces the problem of part characterization to multiplex oligonucleotide synthesis and deep sequencing, two technologies under extensive development with projected cost reduction.

Despite improved therapeutic regimens, primary CNS lymphoma (PCNSL) remains a therapeutic challenge. A prognostic classification of PCNSL patients may represent an important step towards optimised patient-adapted therapy. However, only higher age and low Karnofsky Performance Status (KPS) have repeatedly been reported to be associated with shorter overall survival (OS). Here we characterised microRNA (miRNA) fingerprints in the blood of PCNSL patients with short-term survival (STS) versus long-term survival (LTS) to assess their potential as novel prognostic biomarkers. Blood was collected from patients enrolled in the G-PCNSL-SG1 trial, a phase III study for patients with newly diagnosed PCNSL. miRNAs were extracted from the blood and analysed by next generation sequencing. The STS group comprised 20 patients with a median OS of 3months and was compared to 20 LTS patients with a median OS of 55months. The cohorts were balanced for age and KPS. Twelve annotated miRNAs were significantly deregulated between the two groups. Among them, miR-151a-5p and miR-151b exhibited the most prominent differences. Importantly, the combination of several miRNA allowed for a good separation between short- and long-term survivors with maximal Area Under Curve (AUC) above 0.75. Besides the known miRNAs we identified putative novel miRNA candidates with potential regulatory influence of PCNSL. Finally, the differential regulation of the most promising candidate miRNAs was confirmed by real-time polymerase chain reaction (PCR) in a validation cohort consisting of 20 STS and LTS patients. In conclusion, peripheral blood miRNA expression patterns hold promise as a prognostic tool in PCNSL patients.

http://name.umdl.umich.edu/IC-UMMU-X-11-01664%5D11_01664, https://quod.lib.umich.edu/cgi/i/image/api/thumb/ummu/11-01664/11_01664/!250,250, The University of Michigan Library provides access to these materials for educational and research purposes. These materials may be protected by copyright. If you decide to use any of these materials, you are responsible for making your own legal assessment and securing any necessary permission. If you have questions about the collection, please contact the Library Information Technology.; 2010 Horst Hoheisel, https://www.lib.umich.edu/about-us/policies/copyright-policy

http://name.umdl.umich.edu/IC-UMMU-X-11-01664%5D11_01664, https://quod.lib.umich.edu/cgi/i/image/api/thumb/ummu/11-01664/11_01664/!250,250, The University of Michigan Library provides access to these materials for educational and research purposes. These materials may be protected by copyright. If you decide to use any of these materials, you are responsible for making your own legal assessment and securing any necessary permission. If you have questions about the collection, please contact the Library Information Technology.; 2010 Horst Hoheisel, https://www.lib.umich.edu/about-us/policies/copyright-policy

Pancreatic ductal adenocarcinoma (PDAC) has an extremely poor prognosis. To improve the prognosis, novel molecular markers and targets for earlier diagnosis and adjuvant and/or neoadjuvant treatment are needed. Recent advances in human genome research and high-throughput molecular technologies make it possible to cope with the molecular complexity of malignant tumors. With DNA array technology, mRNA expression levels of thousand of genes can be measured simultaneously in a single assay. As several studies using microarrays in PDAC have already been published, this review attempts to compare the published data and therefore to validate the results. In addition, the applied techniques are discussed in the context of pancreatic malignancies., Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

The epidermal growth factor receptor 2, ERBB2, is a well-validated target for cancer diagnostics and therapy. Recent studies suggest that the over-expression of this receptor in various cancers might also be exploited for antibody-based payload delivery, e.g. antibody drug conjugates. In such strategies, the full-length antibody format is probably not required for therapeutic effect and smaller tumor-specific affinity proteins might be an alternative. However, small proteins and peptides generally suffer from fast excretion through the kidneys, and thereby require frequent administration in order to maintain a therapeutic concentration. In an attempt aimed at combining ERBB2-targeting with antibody-like pharmacokinetic properties in a small protein format, we have engineered bispecific ERBB2-binding proteins that are based on a small albumin-binding domain. Phage display selection against ERBB2 was used for identification of a lead candidate, followed by affinity maturation using second-generation libraries. Cell surface display and flow-cytometric sorting allowed stringent selection of top candidates from pools pre-enriched by phage display. Several affinity-matured molecules were shown to bind human ERBB2 with sub-nanomolar affinity while retaining the interaction with human serum albumin. Moreover, parallel selections against ERBB2 in the presence of human serum albumin identified several amino acid substitutions that dramatically modulate the albumin affinity, which could provide a convenient means to control the pharmacokinetics. The new affinity proteins competed for ERBB2-binding with the monoclonal antibody trastuzumab and recognized the native receptor on a human cancer cell line. Hence, high affinity tumor targeting and tunable albumin binding were combined in one small adaptable protein.

We describe a method for pooling and sequencing DNA from a large number of individual samples while preserving information regarding sample identity. DNA from 576 individuals was arranged into four 12 row by 12 column matrices and then pooled by row and by column resulting in 96 total pools with 12 individuals in each pool. Pooling of DNA was carried out in a two-dimensional fashion, such that DNA from each individual is present in exactly one row pool and exactly one column pool. By considering the variants observed in the rows and columns of a matrix we are able to trace rare variants back to the specific individuals that carry them. The pooled DNA samples were enriched over a 250 kb region previously identified by GWAS to significantly predispose individuals to lung cancer. All 96 pools (12 row and 12 column pools from 4 matrices) were barcoded and sequenced on an Illumina HiSeq 2000 instrument with an average depth of coverage greater than 4,000×. Verification based on Ion PGM sequencing confirmed the presence of 91.4% of confidently classified SNVs assayed. In this way, each individual sample is sequenced in multiple pools providing more accurate variant calling than a single pool or a multiplexed approach. This provides a powerful method for rare variant detection in regions of interest at a reduced cost to the researcher.

Pancreatic ductal adenocarcinoma (PDAC) has an extremely poor prognosis. To improve the prognosis, novel molecular markers and targets for earlier diagnosis and adjuvant and/or neoadjuvant treatment are needed. Recent advances in human genome research and high-throughput molecular technologies make it possible to cope with the molecular complexity of malignant tumors. With DNA array technology, mRNA expression levels of thousand of genes can be measured simultaneously in a single assay. As several studies using microarrays in PDAC have already been published, this review attempts to compare the published data and therefore to validate the results. In addition, the applied techniques are discussed in the context of pancreatic malignancies., Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

KRAS mutations are major factors involved in initiation and maintenance of pancreatic tumors. The impact of different mutations on patient survival has not been clearly defined. We screened tumors from 171 pancreatic cancer patients for mutations in KRAS and CDKN2A genes. Mutations in KRAS were detected in 134 tumors, with 131 in codon 12 and only 3 in codon 61. The GGT>GAT (G12D) was the most frequent mutation and was present in 60% (80/134). Deletions and mutations in CDKN2A were detected in 43 tumors. Analysis showed that KRAS mutations were associated with reduced patient survival in both malignant exocrine and ductal adenocarcinomas (PDAC). Patients with PDACs that had KRAS mutations showed a median survival of 17 months compared to 30 months for those without mutations (log-rank P = 0.07) with a multivariate hazard ratio (HR) of 2.19 (95% CI 1.09-4.42). The patients with G12D mutation showed a median survival of 16 months (log-rank-test P = 0.03) and an associated multivariate HR 2.42 (95% CI 1.14-2.67). Although, the association of survival in PDAC patients with CDKN2A aberrations in tumors was not statistically significant, the sub-group of patients with concomitant KRAS mutations and CDKN2A alterations in tumors were associated with a median survival of 13.5 months compared to 22 months without mutation (log-rank-test P = 0.02) and a corresponding HR of 3.07 (95% CI 1.33-7.10). Our results are indicative of an association between mutational status and survival in PDAC patients, which if confirmed in subsequent studies can have potential clinical application.

In 1988 the preceding journal of Nature Biotechnology, Bio/Technology, reported a work by Hopp and co-workers about a new tag system for the identification and purification of recombinant proteins: the FLAG-tag. Beside the extensively used hexa-his tag system the FLAG-tag has gained broad popularity due to its small size, its high solubility, the presence of an internal Enterokinase cleavage site, and the commercial availability of high-affinity anti-FLAG antibodies. Surprisingly, considering the heavy use of FLAG in numerous laboratories world-wide, we identified in insect cells a post-translational modification (PTM) that abolishes the FLAG-anti-FLAG interaction rendering this tag system ineffectual for secreted proteins. The present publication shows that the tyrosine that is part of the crucial FLAG epitope DYK is highly susceptible to sulfation, a PTM catalysed by the enzyme family of Tyrosylprotein-Sulfo-transferases (TPSTs). We showed that this modification can result in less than 20% of secreted FLAG-tagged protein being accessible for purification questioning the universal applicability of this established tag system.

Nanostructured carbonaceous materials, that is, carbon materials with a feature size on the nanometer scale and, in some cases, functionalized surfaces, already play an important role in a wide range of emerging fields, such as the search for novel energy sources, efficient energy storage, sustainable chemical technology, as well as organic electronic materials. Furthermore, such materials might offer solutions to the challenges associated with the on-going depletion of nonrenewable energy resources or climate change, and they may promote further breakthroughs in the field of microelectronics. However, novel methods for their preparation will be required that afford functional carbon materials with controlled surface chemistry, mesoscopic morphology, and microstructure. A highly promising approach for the synthesis of such materials is based on the use of well-defined molecular precursors. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nanostructured carbonaceous materials, that is, carbon materials with a feature size on the nanometer scale and, in some cases, functionalized surfaces, already play an important role in a wide range of emerging fields, such as the search for novel energy sources, efficient energy storage, sustainable chemical technology, as well as organic electronic materials. Furthermore, such materials might offer solutions to the challenges associated with the on-going depletion of nonrenewable energy resources or climate change, and they may promote further breakthroughs in the field of microelectronics. However, novel methods for their preparation will be required that afford functional carbon materials with controlled surface chemistry, mesoscopic morphology, and microstructure. A highly promising approach for the synthesis of such materials is based on the use of well-defined molecular precursors. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome scale applications. This situation has triggered several initiatives involving large scale generation and validation of antibodies, for example the Swedish Human Protein Atlas and the German Antibody Factory. Antibodies targeting specific subproteomes are being pursued by members of Human Proteome Organisation (plasma and liver proteome projects) and the United States National Cancer Institute (cancer-associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality-controlled protein-binding reagents for the whole human proteome. An ultimate PAR database resource would allow consumers to visit one online warehouse and find all available affinity reagents from different providers together with documentation that facilitates easy comparison of their cost and quality. However, in contrast to, for example, nucleotide databases among which data are synchronized between the major data providers, current PAR producers, quality control centers, and commercial companies all use incompatible formats, hindering data exchange. Here we propose Proteomics Standards Initiative (PSI)-PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI-PAR format is maintained by the Human Proteome Organisation PSI and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI-molecular interaction, which is a widely accepted and established community standard for molecular interaction data. Further information

Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome scale applications. This situation has triggered several initiatives involving large scale generation and validation of antibodies, for example the Swedish Human Protein Atlas and the German Antibody Factory. Antibodies targeting specific subproteomes are being pursued by members of Human Proteome Organisation (plasma and liver proteome projects) and the United States National Cancer Institute (cancer-associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality-controlled protein-binding reagents for the whole human proteome. An ultimate PAR database resource would allow consumers to visit one online warehouse and find all available affinity reagents from different providers together with documentation that facilitates easy comparison of their cost and quality. However, in contrast to, for example, nucleotide databases among which data are synchronized between the major data providers, current PAR producers, quality control centers, and commercial companies all use incompatible formats, hindering data exchange. Here we propose Proteomics Standards Initiative (PSI)-PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI-PAR format is maintained by the Human Proteome Organisation PSI and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI-molecular interaction, which is a widely accepted and established community standard for molecular interaction data. Further information, QC 20110114

Only limited data have been published about the therapeutic use of anakinra in patients with psoriatic arthritis. We undertook this study to evaluate the efficacy and safety of anakinra in patients with active psoriatic arthritis. In a prospective open-label single-center study, 20 patients were treated with 100 mg anakinra everyday either alone or in combination with ongoing methotrexate over 6 months. Safety and efficacy was evaluated using Psoriasis Arthritis Response Criteria (PsARC), Disease Activity Score (DAS) 28, American College of Rheumatology (ACR), European League Against Rheumatism (EULAR), Psoriasis Area and Severity Index Score, Dactylitis Score and Health Assessment Questionnaire (HAQ), and the C-reactive protein, and erythrocyte sedimentation rate. Of the 20 patients enrolled, six completed 24 weeks, 18 completed 12 weeks, and 19 completed 4 weeks of treatment. Early-treatment termination was mainly due to inefficacy (13 patients) and only one drop-out occurred because of an unrelated adverse event. Six patients fulfilled continuously the PsARC until week 24. A moderate EULAR response was achieved by four patients and a good EULAR response by three patients in week 24. Five patients reached ACR 20, four patients ACR 50, and two patients ACR 70 in week 24. HAQ improved slightly throughout the study (n = 19, mean (SD); baseline, 1.127 (0.671); week 24, 1.055 (0.812)) just as DAS 28 (n = 16; baseline, 4.7(1.5); week 24, 4.0(2.0)). Only nine patients showed skin manifestations affecting > 3% of their body surface area which improved in two, worsened in four, stabilized in two patients, and newly evolved in one patient. Adverse events were mainly mild (95%). Fifteen (75%) patients showed injection site reactions. No serious infections occurred. Anakinra was well tolerated with no occurrence of serious drug-associated adverse events and lead to improvement of signs and symptoms in nine out of 19 patients, therefore providing a potential therapeutic option

We currently face a dramatic loss of natural services, such as fish resources, fertile soils, and climate regulation. In order to sustainably manage these services,the resilience approach is increasingly being put forward. The cultural presumptions of this approach frequently go unnoticed. However, they lead to both a partial organismicconcept of ecological units and a one-sided concept of a highly bounded man-nature relationship - and thus to potentially inad equate recommendations for environmental management.

Only limited data have been published about the therapeutic use of anakinra in patients with psoriatic arthritis. We undertook this study to evaluate the efficacy and safety of anakinra in patients with active psoriatic arthritis. In a prospective open-label single-center study, 20 patients were treated with 100 mg anakinra everyday either alone or in combination with ongoing methotrexate over 6 months. Safety and efficacy was evaluated using Psoriasis Arthritis Response Criteria (PsARC), Disease Activity Score (DAS) 28, American College of Rheumatology (ACR), European League Against Rheumatism (EULAR), Psoriasis Area and Severity Index Score, Dactylitis Score and Health Assessment Questionnaire (HAQ), and the C-reactive protein, and erythrocyte sedimentation rate. Of the 20 patients enrolled, six completed 24 weeks, 18 completed 12 weeks, and 19 completed 4 weeks of treatment. Early-treatment termination was mainly due to inefficacy (13 patients) and only one drop-out occurred because of an unrelated adverse event. Six patients fulfilled continuously the PsARC until week 24. A moderate EULAR response was achieved by four patients and a good EULAR response by three patients in week 24. Five patients reached ACR 20, four patients ACR 50, and two patients ACR 70 in week 24. HAQ improved slightly throughout the study (n = 19, mean (SD); baseline, 1.127 (0.671); week 24, 1.055 (0.812)) just as DAS 28 (n = 16; baseline, 4.7(1.5); week 24, 4.0(2.0)). Only nine patients showed skin manifestations affecting > 3% of their body surface area which improved in two, worsened in four, stabilized in two patients, and newly evolved in one patient. Adverse events were mainly mild (95%). Fifteen (75%) patients showed injection site reactions. No serious infections occurred. Anakinra was well tolerated with no occurrence of serious drug-associated adverse events and lead to improvement of signs and symptoms in nine out of 19 patients, therefore providing a potential therapeutic option

Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome scale applications. This situation has triggered several initiatives involving large scale generation and validation of antibodies, for example the Swedish Human Protein Atlas and the German Antibody Factory. Antibodies targeting specific subproteomes are being pursued by members of Human Proteome Organisation (plasma and liver proteome projects) and the United States National Cancer Institute (cancer-associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality-controlled protein-binding reagents for the whole human proteome. An ultimate PAR database resource would allow consumers to visit one on-line warehouse and find all available affinity reagents from different providers together with documentation that facilitates easy comparison of their cost and quality. However, in contrast to, for example, nucleotide databases among which data are synchronized between the major data providers, current PAR producers, quality control centers, and commercial companies all use incompatible formats, hindering data exchange. Here we propose Proteomics Standards Initiative (PSI)-PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI-PAR format is maintained by the Human Proteome Organisation PSI and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI-molecular interaction, which is a widely accepted and established community standard for molecular interaction data. Further information

Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome scale applications. This situation has triggered several initiatives involving large scale generation and validation of antibodies, for example the Swedish Human Protein Atlas and the German Antibody Factory. Antibodies targeting specific subproteomes are being pursued by members of Human Proteome Organisation (plasma and liver proteome projects) and the United States National Cancer Institute (cancer-associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality-controlled protein-binding reagents for the whole human proteome. An ultimate PAR database resource would allow consumers to visit one on-line warehouse and find all available affinity reagents from different providers together with documentation that facilitates easy comparison of their cost and quality. However, in contrast to, for example, nucleotide databases among which data are synchronized between the major data providers, current PAR producers, quality control centers, and commercial companies all use incompatible formats, hindering data exchange. Here we propose Proteomics Standards Initiative (PSI)-PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI-PAR format is maintained by the Human Proteome Organisation PSI and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI-molecular interaction, which is a widely accepted and established community standard for molecular interaction data. Further information