pinecone/core-2020-05-10-deduplication huggingface dataset:
Investigating the information gaps in refugee integration

Refugee integration processes and systems are complex for refugees. They find them difficult to navigate and thus often end up disadvantaged. This paper presents the first set of findings from an ongoing information behavior research study into refugee integration. The study explores the situational experiences of refugees and asylum seekers engaging with the integration processes and systems through individual semi-structured interviews. Dervin’s sense-making methodology was used to elicit the information gaps. The findings reveals refused asylum situation during integration and highlight information needs embedded in processes and systems of refugee integration. The results have implications for reducing the complexity of service provision during refugee integration. In addition, the approach expands previous studies and highlights the depth a situational investigation can bring to information behaviour studies
Practices of Metadata Use in Research Information Management Systems

This poster reports on a study that examines the practices of metadata use in a research information management (RIM) system ResearchGate. Understanding these practices can help institutional repositories to better align their RIM metadata models with researchers? needs and priorities. The study identified three categories of RIM system users. The study?s preliminary findings suggest that community members are more willing to share their personal information and provide full-texts of their works on
ResearchGate compared to readers and personal record managers.This research is supported by an OCLC/ALISE Library and Information Research Grant for 2016 and a National Leadership Grant from the IMLS of the U.S. Government (grant # LG-73-16-0006-16)
Proteomic profiling of 13 paired ductal infiltrating breast carcinomas and non-tumoral adjacent counterparts.

According to recent statistics, breast cancer remains one of the leading causes of death among women in Western countries. Breast cancer is a complex and heterogeneous disease, presently classified into several subtypes according to their cellular origin. Among breast cancer histotypes, infiltrating ductal carcinoma represents the most common and potentially aggressive form. Despite the current progress achieved in early cancer detection and treatment, including the new generation of molecular therapies, there is still need for identification of multiparametric biomarkers capable of discriminating between cancer subtypes and predicting cancer progression for personalized therapies. One established step in this direction is the proteomic strategy, expected to provide enough information on breast cancer profiling. To this aim, in the present study we analyzed 13 breast cancer tissues and their matched non-tumoral tissues by 2-DE. Collectively, we identified 51 protein spots, corresponding to 34 differentially expressed proteins, which may represent promising candidate biomarkers for molecular-based diagnosis of breast cancer and for pattern discovery. The relevance of these proteins as factors contributing to breast carcinogenesis is discussed
Contribution of laser microdissection-based technology to proteomic analysis in hepatocellular carcinoma developing on cirrhosis.

International audienceHepatocellular carcinoma (HCC) is a major cause of cancer worldwide. Proteomic studies provide opportunities to uncover targets for the diagnosis and treatment of this disease. However, in HCC developing in a setting of cirrhosis, the detection of proteome alterations may be hampered by the increased cellular heterogeneity of tissue when analysing global liver homogenates. The aim of this study was to evaluate whether the identification of proteome alterations in these HCC cases was improved when the differential protein profile between tumour and non-tumour areas of liver was determined using hepatocytes isolated by laser microdissection (LM). Differential profiles established with LM-hepatocytes and liver section homogenates using 2-DE and MS exhibited noticeable differences: 30% of the protein spots with deregulated expression in tumorous LM-samples did not display any modification in homogenates; conversely 15% of proteins altered in tumorous homogenates were not impaired in LM-hepatocytes. These alterations resulted from the presence in cirrhotic liver of fibrotic stroma which displayed a protein pattern different from that determined in LM-hepatocytes. In conclusion, our data demonstrate the interest of LM in distinguishing between fibrotic and hepatocyte proteome alterations and thus the benefit of LM to proteome studies of HCC developing in a context of cirrhosis
Proteomics in chronic wound research : potentials in healing and health

Chronic wounds, such as venous and diabetic leg ulcers, represent a significant health and financial burden to individuals and healthcare systems. In worst case scenarios this condition may require the amputation of an affected limb, with significant impact on patient quality of life and health. Presently there are no clinical biochemical analyses used in the diagnosis and management of this condition; moreover few biochemical therapies are accessible to patients. This presents a significant challenge in the efficient and efficacious treatment of chronic wounds by medical practitioners. A number of protein-centric investigations have analysed the wound environment and implicated a suite of molecular species predicted to be involved in the initiation or perpetuation of the condition. However, comprehensive proteomic investigation is yet to be engaged in the analysis of chronic wounds for the identification of molecular diagnostic/prognostic markers of healing or therapeutic targets. This review examines clinical chronic wound research and recommends a path towards proteomic investigation for the discovery of medically significant targets. Additionally, the supplementary documents associated with this review provide the first comprehensive summary of protein-centric, small molecule and elemental analyses in clinical chronic wound research
Differential occurrence of S100A7 in breast cancer tissues: A proteomic-based investigation

PURPOSE: The present study reports for the first time a large-scale proteomic screening of the occurrence, subcellular localization and relative quantification of the S100A7 protein among a group of 100 patients, clinically grouped for the diagnosis of infiltrating ductal carcinoma (IDC).\ud
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EXPERIMENTAL DESIGN: To this purpose, the methods of differential proteomics, Western blotting, and immunohistochemistry were used.\ud
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RESULTS: The identity of two isoforms of the protein was assessed by mass spectrometry and immunologically confirmed. Moreover, we proved by immunocytochemical applications the exclusive localization of the protein within the neoplastic cells. The correlation of S100A7 expression levels with the collective profile of cancer patients' proteomics predicted functional interactions, distinct for the two isoforms. The S100A7b isoform was significantly correlated with specific protein clusters (calcium binding, signaling and cell motion, heat shock and folding) and intercrossing pathways (antioxidant, metabolic and apoptotic pathways), while the more acidic isoform was correlated with a narrow number of proteins mainly unrelated to the b isoform.\ud
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CONCLUSIONS AND CLINICAL RELEVANCE: This study is the first proteomic-based report on S100A7 in a large series of IDC patients. The correlation with in silico data may significantly contribute the knowledge of possible pathways for S100A7, providing novel insights into the mechanism of action of this protein. We suggest that each S100A7 isoform is involved in critical phases of the breast cancer growth and progression, probably through interaction with different partner proteins
Opportunities and challenges of proteomics in pediatric patients: circulating biomarkers after hematopoietic stem cell transplantation as a successful example

Biomarkers have the potential to improve diagnosis and prognosis, facilitate-targeted treatment, and reduce health care costs. Thus, there is great hope that biomarkers will be integrated in all clinical decisions in the near future. A decade ago, the biomarker field was launched with great enthusiasm because MS revealed that blood contains a rich library of candidate biomarkers. However, biomarker research has not yet delivered on its promise due to several limitations: (i) improper sample handling and tracking as well as limited sample availability in the pediatric population, (ii) omission of appropriate controls in original study designs, (iii) lability and low abundance of interesting biomarkers in blood, and (iv) the inability to mechanistically tie biomarker presence to disease biology. These limitations as well as successful strategies to overcome them are discussed in this review. Several advances in biomarker discovery and validation have been made in hematopoietic stem cell transplantation, the current most effective tumor immunotherapy, and these could serve as examples for other conditions. This review provides fresh optimism that biomarkers clinically relevant in pediatrics are closer to being realized based on: (i) a uniform protocol for low-volume blood collection and preservation, (ii) inclusion of well-controlled independent cohorts, (iii) novel technologies and instrumentation with low analytical sensitivity, and (iv) integrated animal models for exploring potential biomarkers and targeted therapie
Formalin-fixed paraffin-embedded tissue: The holy grail of clinical proteomics

Tissue is the most relevant biological material to gather insight in disease mechanisms by means of omics technologies. However, fresh frozen tissue, which is generally regarded as the best imaginable source for such studies, is often not available. In case it is available, the different ways of storage (e.g. -20°C, -80°C, liquid nitrogen, etc.) hamper the conduction of reproducible multicenter studies because of different protein degradation rates. Formalin-fixed paraffin-embedded (FFPE) tissue on the contrary is considered as a valuable alternative for fresh frozen tissue, because only a few standard operation procedures are applied worldwide for the preparation of these tissues and because they are all stored in the same way. However, a study on the impact of the different preparation protocols for FFPE tissue was still lacking. Therefore, Bronsert et al. in this issue [Bronsert, P., Weißer, J., Biniossek, M. L., Kuehs, M. et al., Proteomics Clin. Appl. 2014, 8 786-804] conducted such a study that provides proof that there is no significant effect between these sample preparations procedures, and thereby they further open the gate for FFPE tissues to enter the field of clinical proteomics.status: publishe
Surfaceome of classical Hodgkin and non-Hodgkin lymphoma

PURPOSE: Classical Hodgkin lymphoma (cHL) is characterized by a low percentage of tumor cells in a background of diverse, reactive immune cells. cHL cells commonly derive from preapoptotic germinal-center B cells and are characterized by the loss of B cell markers and the varying expression of other hematopoietic lineage markers. This phenotypic variability and the scarcity of currently available cHL-specific cell surface markers can prevent clear distinction of cHL from related lymphomas.\ud
EXPERIMENTAL DESIGN: We applied the Cell Surface Capture (CSC) technology to directly measure the pool of cell surface exposed proteins in four cHL and four non-Hodgkin lymphoma (NHL) cell lines.\ud
RESULTS: More than 1 000 membrane proteins, including 178 CD annotated proteins, were identified and allowed the generation of lymphoma surfaceome maps. The functional properties of identified cell surface proteins enable, but also limit the information exchange of lymphoma cells with their microenvironment.\ud
CONCLUSIONS AND CLINICAL RELEVANCE: Selected candidate proteins with potential diagnostic value were evaluated on a tissue microarray (TMA). Primary lymphoma tissue of 126 different B cell derived lymphoma cases were included in the TMA analysis. The TMA analysis indicated gamma-glutamyltranspeptidase 1 as a potential additional marker that can be included in a panel of markers for differential diagnosis of cHL versus NHL. This article is protected by copyright. All rights reserved
Metabolic and Molecular Regulation of Dietary Polyunsaturated Fatty Acids on Prostate Cancer

Purpose

The aim of this study is to investigate the role of n-3 and n-9 fatty acids in crucial processes involved in prostate cancer cell growth through a large-scale proteomic analysis.
Experimental design

We used a label-free protein quantification method to profile global protein expression of fish oil and oleic acid treated PCa cells and validated a panel of differentially expressed proteins by either Western blot or multiple reaction monitoring. Bioinformatic analysis was also performed to uncover the pathways involved in fatty acid metabolism.
Results

Fish oil, not oleic acid, suppresses prostate cancer cell viability. Assessment of fatty acid synthesis pathway activity also shows that oleic acid is a more potent inhibitor than fish oil on de novo fatty acid synthesis. Although fatty acid synthase activity decreases with fish oil treatment, the inhibition of its activity occurs over time while reduction in viability occurs within 24 h. Bioinformatic analysis revealed the pathways altered by these fatty acid treatments.
Conclusions and clinical relevance

This study suggests that suppression of cell viability by fish oil is independent of fatty acid synthase and fish oil regulates prostate cancer cells through activation of other pathways depending upon length of exposure to fish oil
Development of a MALDI MS-based platform for early detection of acute kidney injury

PURPOSE: Septic acute kidney injury (AKI) is associated with poor outcome. This can partly be attributed to delayed diagnosis and incomplete understanding of the underlying pathophysiology. Our aim was to develop an early predictive test for AKI based on the analysis of urinary peptide biomarkers by MALDI-MS.
EXPERIMENTAL DESIGN: Urine samples from 95 patients with sepsis were analyzed by MALDI-MS. Marker search and multimarker model establishment were performed using the peptide profiles from 17 patients with existing or within the next 5 days developing AKI and 17 with no change in renal function. Replicates of urine sample pools from the AKI and non-AKI patient groups and normal controls were also included to select the analytically most robust AKI markers.
RESULTS: Thirty-nine urinary peptides were selected by cross-validated variable selection to generate a support vector machine multidimensional AKI classifier. Prognostic performance of the AKI classifier on an independent validation set including the remaining 61 patients of the study population (17 controls and 44 cases) was good with an area under the receiver operating characteristics curve of 0.82 and a sensitivity and specificity of 86% and 76%, respectively.
CONCLUSION AND CLINICAL RELEVANCE: A urinary peptide marker model detects onset of AKI with acceptable accuracy in septic patients. Such a platform can eventually be transferred to the clinic as fast MALDI-MS test format
Elevated levels of protein AMBP in cerebrospinal fluid of women with preeclampsia compared to normotensive pregnant women

Purpose: To investigate the cerebrospinal fluid (CSF) proteome of patients with preeclampsia (PE) and normotensive pregnant women, in order to provide a better understanding of brain involvement in PE. Experimental design: Ninety-eight CSF samples (43 women with PE and 55 normotensive controls) were analyzed by LC-MS/MS proteome profiling. CSF was obtained during the spinal puncture before caesarean delivery. Results: Eight proteins were higher abundant and 17 proteins were lower abundant in patients with PE. The most significantly differentially abundant protein was protein AMBP (alpha-1-microglobulin/bikunin precursor). This finding was validated by performing an ELISA experiment (p = 0.002). Conclusions and clinical relevance: The current study showed a clear difference between the protein profiles of CSF from patients with PE and normotensive pregnant women. Protein AMBP is a precursor of a heme-binding protein that counteracts the damaging effects of free hemoglobin, which may be related to the presence of free hemoglobin in CSF. Protein levels showed correlations with clinical symptoms during pregnancy and postpartum. To our knowledge, this is the first LC-MS/MS proteome profiling study on a unique set of CSF samples from (severe) preeclamptic patients and normotensive pregnant women
Nipple aspirate fluid - a liquid biopsy for diagnosing breast health

YesPurpose: Nipple secretions are protein-rich and a potential source of breast cancer biomarkers for breast cancer screening. Previous studies of specific proteins have shown limited correlation with clinicopatholigical features. Our aim, in this pilot study, was to investigate the intra- and inter-patient protein composition of nipple secretions and the implications for their use as liquid biopsies.
Experimental design: Matched pairs of NAF (n=15) were characterised for physicochemical properties and SDS PAGE. Four pairs were selected for semi-quantitative proteomic profiling and trypsin-digested peptides analysed using 2D LC Orbitrap Fusion mass spectrometry. The resulting data was subject to bioinformatics analysis and statistical evaluation for functional significance.
Results: A total of 1990 unique proteins were identified many of which are established cancer associated markers. Matched pairs shared the greatest similarity (average Pearson correlation coefficient of 0.94), but significant variations between individuals was observed.
Conclusions: This was the most complete proteomic study of NAF to date providing a valuable source for biomarker discovery. The high level of milk proteins in healthy volunteer samples compared to the cancer patients was associated with galactorrhoea. Using matched pairs increased confidence in patient-specific protein levels but changes relating to cancer stage require investigation of a larger cohort.Proteomics research was supported by Yorkshire Cancer Research projects, BPP047 and B381PA.Author tried other journals but only got accepted in this one. Not OA compliant but forced to use the title for publication. No funds for OA fee. SN
Article has now been published online and is a CCBY paper so now allowed to include the final version. ET 15/08/17Gol
Evaluation of the Endo-Lysosomal System and the Ubiquitin-Proteasome System in Neurodegenerative Diseases

Neurodegeneration is the process of neuronal cell loss where the symptoms will reflect the regions affected. Neurodegenerative disorders including Alzheimer’s disease (AD), Parkinson’s disease (PD) and frontotemporal dementia (FTD) are all characterised by an accumulation of protein aggregates suggesting impaired production or turnover of these proteins. Hence, dysfunctional proteostasis is implicated in neurodegenerative disorders. In AD, there is a decreased turnover of endocytic and autophagic vesicles and an accumulation of endo-lysosomal proteins and ubiquitin in brain tissue. Lysosomal dysfunction has been indicated in PD by the link of disease risk and genetic alterations associated with lysosomal storage disorders as well as by decreased expression of lysosomal proteins in disease afflicted regions. Disease causing mutations and genetic risk factors in FTD suggest altered function of the autophagic and endo-lysosomal system to be involved in the pathogenesis.
The aim of this thesis was to examine dysfunctional proteostasis in neurodegenerative diseases by developing assays to monitor proteins from the autophagic and endo-lysosomal system and the ubiquitin-proteasome system in human cerebrospinal fluid (CSF). Proteins from the endo-lysosomal system and the ubiquitin-proteasome system have been identified and quantified in CSF using mass spectrometry (MS)-based proteomics. Principally, three methods have been developed; 1) lysosomal membrane protein LAMP2 was purified from CSF by immunoprecipitation followed by tryptic digestion and quantification by liquid chromatography (LC)
and parallel reaction monitoring MS (PRM-MS); 2) full length ubiquitin was isolated from CSF by solid-phase extraction (SPE) followed by quantification by LC PRM-MS; and 3) finally, a panel of endo-lysosomal proteins, e.g., LAMP2, and ubiquitin, were analysed using tryptic digestion, peptide isolation by SPE and quantification by LC PRM-MS. CSF samples from cohorts including subjects with AD, PD, clinical FTD subtypes and FTD mutation carriers, as well as controls, were analysed with the developed assays.
In AD the CSF levels of several endo-lysosomal proteins, including LAMP2, were elevated compared to controls. CSF ubiquitin was also found to be elevated in AD compared to controls. In contrast, CSF levels of endo-lysosomal proteins and ubiquitin in PD were found to be decreased. Investigation in clinical subtypes of FTD and mutation carriers showed limited alterations in the CSF levels of endo-lysosomal proteins, suggesting dysfunctional proteostasis not to be readily detected in CSF in FTD. Our results showing altered CSF levels of proteins
involved in proteostasis in AD and PD might indicate pathological alterations in the autophagic and endo-lysosomal system and the ubiquitin-proteasome system. Although further studies are needed, CSF ubiquitin in AD and endo-lysosomal proteins and ubiquitin in PD might serve as potential biomarkers in these disorders
A Flow Time Model for Melt-Cast Insensitive Explosive Process

International audienceDiphasic flows of concentrated suspensions of melt-cast insensitive explosives exhibit specific rheological properties. In order to limit the handling of pyrotechnical products presenting a risk with respect to the mechanical and thermal shocks, a lot of work has been undertaken for many years in the civil engineering sector. The objective of this study is to propose a predictive model of the flow time of a concentrated suspension through a nozzle located at the bottom of a tank. Similar to our industrial process, the suspension is made out of insensitive energetic materials and flows under gravity. Experimental results are compared to three models (Quemada, Krieger-Dougherty, and Mooney) predicting the viscosity μ of a suspension as a function of the solid volume fraction ϕ, the maximum packing density ϕm and the viscosity μ0 of the interstitial liquid. De Larrard's model is used to calculate ϕm. The value of viscosity measured for the pure liquid is close to the one predicted by the Bernoulli theorem, where liquids are considered as incompressible and inviscid. Finally, it was found that the Quemada's model gives a fair agreement between predictions and experiments
Suppressing hydrogen evolution by aqueous silicon powder dispersions by controlled silicon surface oxidation

Aqueous silicon dispersions are used to produce pyrotechnic time delay compositions. The propensity of silicon to react with water and to produce hazardous hydrogen gas must be suppressed. To this end, the effect of air heat treatment temperature on the rate of corrosion of silicon was investigated. It was found that four hour heat treatments at temperatures below 350 °C provided significant passivation. This is attributed to the removal of the hydroxyl groups present on the SiO2 surface scale layer. It was found that thickening the silica layer, by heat treatment at higher temperatures, causes a further reduction in the amount of hydrogen released. However, differential thermal analysis (DTA) studies showed that excessive silicon surface oxidation increased the ignition temperature and reduced the heat release of a near-stoichiometric silicon-lead chromate pyrotechnic composition.http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1521-4087hb2013ai201