scholarly journals MGnify: the microbiome analysis resource in 2020

2019 ◽  
Author(s):  
Alex L Mitchell ◽  
Alexandre Almeida ◽  
Martin Beracochea ◽  
Miguel Boland ◽  
Josephine Burgin ◽  
...  
Keyword(s):  
Metagenomic Data ◽  
Microbial Populations ◽  
Protein Database ◽  
Functional Annotations ◽  
Fine Grained ◽  
Microbiome Analysis ◽  
The Past ◽  
The Common ◽  
Microbiome Data ◽  
Assembly Analysis

Abstract MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility. MGnify's new analysis pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2) and expanded protein functional annotations. Biochemical pathways and systems predictions have also been added for assembled contigs. MGnify's growing focus on the assembly of metagenomic data has also seen the number of datasets it has assembled and analysed increase six-fold. The non-redundant protein database constructed from the proteins encoded by these assemblies now exceeds 1 billion sequences. Meanwhile, a newly developed contig viewer provides fine-grained visualisation of the assembled contigs and their enriched annotations.

scholarly journals Current Issues in Ciphertext Policy-Attribute Based Scheme for Cloud Computing: A Survey

2018 ◽  
Vol 7 (2.15) ◽  
pp. 64
Author(s):  
Norhidayah Muhammad ◽  
Jasni Mohamad Zain ◽  
Mumtazimah Mohamad
Keyword(s):  
Cloud Computing ◽  
Cloud Storage ◽  
Fine Grained ◽  
The Past ◽  
Attribute Based Encryption ◽  
Key Policy ◽  
The Common ◽  
Ciphertext Policy ◽  
Server Maintenance ◽  
Better Than

The use of cloud computing has increased exponentially in data resources storage over the past few years. Cloud storage reduces the overall costs of server maintenance, whereby companies only pay for the resources they actually use in the cloud storage. Despite this, security concerns in cloud computing must be a top priority. One of the common encryption methods in cloud security is Attribute Based Encryption (ABE). ABE contains two types, namely, Ciphertext Policy-Attribute Based Encryption (CP-ABE) and Key Policy- Attribute based Encryption (KP-ABE). CP-ABE is better than KP-ABE, especially in reduplication issues and fine-grained access. However, issues in CP_ABE need further improvement. Improvement for the CP-ABE scheme has been growing rapidly since 2010 to date, and five main issues need improvement. This paper reviews the proposed CP-ABE schemes during the past three years.  These schemes focus on solving the five issues identified inherent in the CP-ABE scheme. 

Mental time travel? A neurocognitive model of event simulation

2020 ◽  
Author(s):  
Donna Rose Addis
Keyword(s):  
Predictive Coding ◽  
Time Travel ◽  
Simulation System ◽  
Mental Time Travel ◽  
Event Representation ◽  
Conceptual Information ◽  
Fine Grained ◽  
The Past ◽  
The Future ◽  
General Capacity

Mental time travel (MTT) is defined as projecting the self into the past and the future. Despite growing evidence of the similarities of remembering past and imagining future events, dominant theories conceive of these as distinct capacities. I propose that memory and imagination are fundamentally the same process – constructive episodic simulation – and demonstrate that the ‘simulation system’ meets the three criteria of a neurocognitive system. Irrespective of whether one is remembering or imagining, the simulation system: (1) acts on the same information, drawing on elements of experience ranging from fine-grained perceptual details to coarser-grained conceptual information and schemas about the world; (2) is governed by the same rules of operation, including associative processes that facilitate construction of a schematic scaffold, the event representation itself, and the dynamic interplay between the two (cf. predictive coding); and (3) is subserved by the same brain system. I also propose that by forming associations between schemas, the simulation system constructs multi-dimensional cognitive spaces, within which any given simulation is mapped by the hippocampus. Finally, I suggest that simulation is a general capacity that underpins other domains of cognition, such as the perception of ongoing experience. This proposal has some important implications for the construct of ‘MTT’, suggesting that ‘time’ and ‘travel’ may not be defining, or even essential, features. Rather, it is the ‘mental’ rendering of experience that is the most fundamental function of this simulation system, enabling humans to re-experience the past, pre-experience the future, and also comprehend the complexities of the present.

Beyond Promoter: The Role of Macrophage in Invasion and Progression of Renal Cell Carcinoma

2020 ◽  
Vol 15 (7) ◽  
pp. 588-596
Author(s):  
Haibao Zhang ◽  
Guodong Zhu
Keyword(s):  
Renal Cell Carcinoma ◽  
Tumor Microenvironment ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Cell Formation ◽  
Biological Behavior ◽  
Tumor Stem Cell ◽  
The Past ◽  
The Common

Renal cell carcinoma (RCC) is one of the common urologic neoplasms, and its incidence has been increasing over the past several decades; however, its pathogenesis is still unknown up to now. Recent studies have found that in addition to tumor cells, other cells in the tumor microenvironment also affect the biological behavior of the tumor. Among them, macrophages exist in a large amount in tumor microenvironment, and they are generally considered to play a key role in promoting tumorigenesis. Therefore, we summarized the recent researches on macrophage in the invasiveness and progression of RCC in latest years, and we also introduced and discussed many studies about macrophage in RCC to promote angiogenesis by changing tumor microenvironment and inhibit immune response in order to activate tumor progression. Moreover, macrophage interactes with various cytokines to promote tumor proliferation, invasion and metastasis, and it also promotes tumor stem cell formation and induces drug resistance in the progression of RCC. The highlight of this review is to make a summary of the roles of macrophage in the invasion and progression of RCC; at the same time to raise some potential and possible targets for future RCC therapy.

Searching for Political Parties in the Past

2017 ◽  
Author(s):  
Piero Ignazi
Keyword(s):  
Eighteenth Century ◽  
Political Parties ◽  
Political Party ◽  
Ancient Greece ◽  
Political Community ◽  
Democratic Politics ◽  
The Political ◽  
The Past ◽  
The Common

Chapter 1 introduces the long and difficult process of the theoretical legitimation of the political party as such. The analysis of the meaning and acceptance of ‘parties’ as tools of expressing contrasting visions moves forward from ancient Greece and Rome where (democratic) politics had first become a matter of speculation and practice, and ends up with the first cautious acceptance of parties by eighteenth-century British thinkers. The chapter explores how parties or factions have been constantly considered tools of division of the ‘common wealth’ and the ‘good society’. The holist and monist vision of a harmonious and compounded society, stigmatized parties and factions as an ultimate danger for the political community. Only when a new way of thinking, that is liberalism, emerged, was room for the acceptance of parties set.

Can Groups Assert That P?

2019 ◽  
pp. 326-344
Author(s):  
Deborah Tollefsen
Keyword(s):  
Common Ground ◽  
Speech Act ◽  
Single Individual ◽  
Constitutive Rule ◽  
The Past ◽  
Group Members ◽  
The Common ◽  
Declarative Statement ◽  
John Macfarlane

When a group or institution issues a declarative statement, what sort of speech act is this? Is it the assertion of a single individual (perhaps the group’s spokesperson or leader) or the assertion of all or most of the group members? Or is there a sense in which the group itself asserts that p? If assertion is a speech act, then who is the actor in the case of group assertion? These are the questions this chapter aims to address. Whether groups themselves can make assertions or whether a group of individuals can jointly assert that p depends, in part, on what sort of speech act assertion is. The literature on assertion has burgeoned over the past few years, and there is a great deal of debate regarding the nature of assertion. John MacFarlane has helpfully identified four theories of assertion. Following Sandy Goldberg, we can call these the attitudinal account, the constitutive rule account, the common-ground account, and the commitment account. I shall consider what group assertion might look like under each of these accounts and doing so will help us to examine some of the accounts of group assertion (often presented as theories of group testimony) on offer. I shall argue that, of the four accounts, the commitment account can best be extended to make sense of group assertion in all its various forms.

scholarly journals A Theoretical Framework on the Determinants of Food Purchasing Behavior of the Elderly: A Bibliometric Review with Scientific Mapping in Web of Science

Foods ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 688
Author(s):  
Khaled Alhammadi ◽  
Luna Santos-Roldán ◽  
Luis Javier Cabeza-Ramírez
Keyword(s):  
Elderly Population ◽  
Web Of Science ◽  
The Elderly ◽  
Purchasing Behavior ◽  
Food Purchasing ◽  
The Past ◽  
Bibliometric Review ◽  
Food Market ◽  
The Common ◽  
Elderly Consumers

The past few years have seen significant demographic changes in most regions, including an increased elderly population. Subsequently, elderly citizens comprise an important market segment of consumers, with the food industry one of the most affected areas in this context. However, food market managers previously believed that elderly consumers’ needs were stereotyped in nature. The lack of focus on this sector, therefore, left elderly consumers as an untapped market, without realizing the financial independence of this segment regarding their nutrition. This research will attempt to provide the key determinant factors on elderly consumers’ behavior related to food. For that purpose, a complete literature review of more than 123 papers regarding these concepts has been carried out. Once analyzed, we highlight the common insights to give clear guidance for supermarket managers and food manufacturers to have a better knowledge of the reasons behind elderly people’s food acquisitions.

scholarly journals Chimera Spectrum Diagnostics for Peptides Using Two-Dimensional Partial Covariance Mass Spectrometry

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3728
Author(s):  
Taran Driver ◽  
Nikhil Bachhawat ◽  
Leszek J. Frasinski ◽  
Jonathan P. Marangos ◽  
Vitali Averbukh ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Peptide Sequence ◽  
Two Dimensional ◽  
Peptide Ions ◽  
Finite Mass ◽  
Protein Database ◽  
Spectra Analysis ◽  
Fragment Ions ◽  
Single Precursor ◽  
The Common

The rate of successful identification of peptide sequences by tandem mass spectrometry (MS/MS) is adversely affected by the common occurrence of co-isolation and co-fragmentation of two or more isobaric or isomeric parent ions. This results in so-called `chimera spectra’, which feature peaks of the fragment ions from more than a single precursor ion. The totality of the fragment ion peaks in chimera spectra cannot be assigned to a single peptide sequence, which contradicts a fundamental assumption of the standard automated MS/MS spectra analysis tools, such as protein database search engines. This calls for a diagnostic method able to identify chimera spectra to single out the cases where this assumption is not valid. Here, we demonstrate that, within the recently developed two-dimensional partial covariance mass spectrometry (2D-PC-MS), it is possible to reliably identify chimera spectra directly from the two-dimensional fragment ion spectrum, irrespective of whether the co-isolated peptide ions are isobaric up to a finite mass accuracy or isomeric. We introduce ‘3-57 chimera tag’ technique for chimera spectrum diagnostics based on 2D-PC-MS and perform numerical simulations to examine its efficiency. We experimentally demonstrate the detection of a mixture of two isomeric parent ions, even under conditions when one isomeric peptide is at one five-hundredth of the molar concentration of the second isomer.

scholarly journals B.05 Hemi-laryngopharyngeal spasm (HELPS) syndrome: The discovery, cure, and characterization of a new neurological condition

2017 ◽  
Vol 44 (S2) ◽  
pp. S11-S11
Author(s):  
C Honey ◽  
M Morrison
Keyword(s):  
Surgical Care ◽  
Review Of The Literature ◽  
The Past ◽  
First Case ◽  
Patient Reported ◽  
Operative Outcome ◽  
Small Cohort ◽  
The Common ◽  
Similar Motor

Background: We published the world’s first case of hemi-laryngpharyngeal spasm (HELPS) syndrome cured by microvascular decompression (MVD) of the Xth cranial nerve in 2016. We now present a small cohort of patients (n=3) successfully treated with surgery in order to better delineate the common characteristics of this syndrome, diagnostic tests of choice, nuances of their surgical care and outcomes of their treatment. Methods: The history and physical examination of three patients with HELPS syndrome are presented. Pre-operative laryngoscopy, neuroimaging, response to botox and intra-operative videos are detailed. Post-operative outcome and complications are presented. Results: Each patient reported similar motor (choking) and sensory (coughing) features in their history. Episodic choking relentlessly progressed over the years until it occurred while sleeping and with frightening severity prompting tracheostomy in one patient and intubation in another. A “tickling” sensation deep in the throat triggered episodic coughing that worsened over the years until it occurred while sleeping and with frightening severity (syncope and incontinence). Conclusions: A review of the literature suggests that patients with similar symptoms, often called episodic laryngospasm in the past, have been treated with psychotherapy or antacids. With the recognition that a clearly defined subset of these patients have HELPS syndrome, we can offer them the potential of a neurosurgical cure.

Expanding Evolutionary Psychology: toward a Better Understanding of Violence and Aggression

2003 ◽  
Vol 42 (1) ◽  
pp. 5-50 ◽  
Author(s):  
Iver Mysterud ◽  
Dag Viljen Poleszynski
Keyword(s):  
Evolutionary Psychology ◽  
Food Allergies ◽  
Sociocultural Factors ◽  
The Past ◽  
Physical Chemical ◽  
Reactive Hypoglycemia ◽  
Proximate Factors ◽  
Survival And Reproduction ◽  
The Common ◽  
Habitual Intake

The “mainstream” evolutionary psychology model is currently under criticism from scientists of other persuasions wanting to expand the model or to make it more realistic in various ways. We argue that focusing on the environment as if it consisted only of social (or sociocultural) factors gives too limited a perspective if evolutionary approaches are to understand the behavior of modern humans. Taking the case of violence, we argue that numerous novel environmental factors of nutritional and physical-chemical origin should be considered as relevant proximate factors. The common thesis presented here is that several aspects of the biotic or abiotic environment are able to change brain chemistry, thus predisposing individuals to violence and aggression in given contexts. In the past, aggressive behavior has had a number of useful functions that were of particular importance to our ancestors' survival and reproduction. However, some of the conditions in our novel environment, which either lowered the threshold for aggression or released such behavior in contexts which were adaptive in our evolutionary past, no longer apply. It is high time evolutionary approaches to violence are expanded to include the possibilities that violence may be triggered by nutritionally depleted foods, reactive hypoglycemia caused by habitual intake of foods with a high glycemic index (GI), food allergies/intolerances and exposure to new environmental toxins (heavy metals, synthetic poisons).

Communication Theory and Training Approaches for Multiculturally Diverse Organizations: Have Academics and Practitioners Missed the Connection?

2001 ◽  
Vol 30 (4) ◽  
pp. 445-455 ◽  
Author(s):  
Marguerite Arai ◽  
Maryanne Wanca-Thibault ◽  
Pamela Shockley-Zalabak
Keyword(s):  
Communication Theory ◽  
Diversity Training ◽  
Multicultural Training ◽  
Theory And Practice ◽  
Important Research ◽  
Human Communication ◽  
The Past ◽  
The Common ◽  
Multiculturally Diverse ◽  
And Training

While a number of articles have looked at the importance of multicultural training in the workplace over the past 30 years, there is little concrete agreement that documents the common fundamental elements of a “successful” diversity initiative. A review of the training literature suggests the importance of human communication theory and practice without including important research, methodologies, and practice from the communication discipline. This article examines formal diversity approaches, provides examples from the literature of several successful diversity initiatives in larger organizations, identifies the limited use of communication-based approaches in diversity training, and discusses the importance of integrating communication theory and practice in future training efforts.

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