scholarly journals Knot localization in proteins

2013 ◽  
Vol 41 (2) ◽  
pp. 538-541 ◽  
Author(s):  
Eric J. Rawdon ◽  
Kenneth C. Millett ◽  
Joanna I. Sułkowska ◽  
Andrzej Stasiak
Keyword(s):  
Present Article ◽  
Protein A ◽  
Biological Role ◽  
Complete Analysis ◽  
Precise Localization ◽  
Limited Information ◽  
Linear Chains ◽  
Different Types ◽  
The Matrix ◽  
Knotted Protein

The backbones of proteins form linear chains. In the case of some proteins, these chains can be characterized as forming linear open knots. The knot type of the full chain reveals only limited information about the entanglement of the chain since, for example, subchains of an unknotted protein can form knots and subchains of a knotted protein can form different types of knots than the entire protein. To understand fully the entanglement within the backbone of a given protein, a complete analysis of the knotting within all of the subchains of that protein is necessary. In the present article, we review efforts to characterize the full knotting complexity within individual proteins and present a matrix that conveys information about various aspects of protein knotting. For a given protein, this matrix identifies the precise localization of knotted regions and shows the knot types formed by all subchains. The pattern in the matrix can be considered as a knotting fingerprint of that protein. We observe that knotting fingerprints of distantly related knotted proteins are strongly conserved during evolution and discuss how some characteristic motifs in the knotting fingerprints are related to the structure of the knotted regions and their possible biological role.

From Organizations of Processes to Organisms and Other Biological Individuals

2018 ◽  
Author(s):  
Argyris Arnellos
Keyword(s):  
Multicellular Organism ◽  
Collaborative Networks ◽  
Biological Role ◽  
Regulatory Processes ◽  
Different Types ◽  
Organizational Framework

The emphasis on the collaborative dimension of life overlooks the importance of biological individuals (conceived of as integrated, self-maintaining organizations) in the build-up of more complex collaborative networks in the course of evolution. This chapter proposes a process-based organizational ontology for biology, according to which the essential features of unicellular organismicality are captured by a self-maintaining organization of processes integrated by means of a special type of collaboration (realized through regulatory processes entailing an indispensable interdependence) between its constitutive and its interactive aspects. This ontology is then used to describe different types of collaborations among cells and to suggest the type that yields a multicellular organism. The proposed organizational framework enables us to critically assess hypercollaborative views of life, especially issues related to the distinction between biological individuals and organisms and between life and non-life, without however underestimating the central biological role of collaboration.

scholarly journals When Does HARKing Hurt? Identifying When Different Types of Undisclosed Post Hoc Hypothesizing Harm Scientific Progress

2017 ◽  
Vol 21 (4) ◽  
pp. 308-320 ◽  
Author(s):  
Mark Rubin
Keyword(s):  
Philosophy Of Science ◽  
Present Article ◽  
Literature Search ◽  
A Priori ◽  
Scientific Progress ◽  
Research Report ◽  
Research Results ◽  
Different Types ◽  
Replication Crisis ◽  
Post Hoc

Hypothesizing after the results are known, or HARKing, occurs when researchers check their research results and then add or remove hypotheses on the basis of those results without acknowledging this process in their research report ( Kerr, 1998 ). In the present article, I discuss 3 forms of HARKing: (a) using current results to construct post hoc hypotheses that are then reported as if they were a priori hypotheses; (b) retrieving hypotheses from a post hoc literature search and reporting them as a priori hypotheses; and (c) failing to report a priori hypotheses that are unsupported by the current results. These 3 types of HARKing are often characterized as being bad for science and a potential cause of the current replication crisis. In the present article, I use insights from the philosophy of science to present a more nuanced view. Specifically, I identify the conditions under which each of these 3 types of HARKing is most and least likely to be bad for science. I conclude with a brief discussion about the ethics of each type of HARKing.

scholarly journals Bird sounds in nature writing: Human perspective on animal communication

2009 ◽  
Vol 37 (3/4) ◽  
pp. 580-613 ◽  
Author(s):  
Kadri Tüür
Keyword(s):  
Present Article ◽  
Nature Writing ◽  
Animal Communication ◽  
Bird Song ◽  
Literary Analysis ◽  
Human Language ◽  
Different Types ◽  
Human Interpretation ◽  
Object Of Study

The object of study in the present article is birds, more precisely the sounds of birds as they are represented in Estonian nature writing. The evolutionary and structural parallels of bird song with human language are reviewed. Human interpretation of bird sounds raises the question, whether it is possible to transmit or “translate” signals between the Umwelts of different species. The intentions of the sender of the signal may remain unknown, but the signification process within human Umwelt can still be traced and analysed. By approaching the excerpts of nature writing using semiotic methodology, I attempt to demonstrate how bird sounds can function as different types of signs, as outlined by Thomas A. Sebeok. It is argued that the zoosemiotic treatment of nature writing opens up a number of interesting perspectives that would otherwise remain beyond the scope of traditional literary analysis.

COEVALNESS OF INSECT TRACE FOSSILS AND TRACE-BEARING ROCKS, A CASE STUDY FROM THE PLIO?-PLEISTOCENE OF SW SPAIN

Palaios ◽  
2021 ◽  
Vol 36 (3) ◽  
pp. 115-121
Author(s):  
EDUARDO MAYORAL ◽  
JORGE F. GENISE ◽  
FRANCISCO J. RODRÍGUEZ-TOVAR ◽  
ANA SANTOS
Keyword(s):  
Fossil Record ◽  
Field Research ◽  
Sw Spain ◽  
Modern Age ◽  
Different Types ◽  
The Matrix ◽  
Time Gap

ABSTRACT Plio?-Pleistocene outcrops located at the southwestern edge of the Guadalquivir Basin in the area of Lepe (Huelva, Spain) provide an interesting example for studying the contemporaneity of traces with the rocks that contain them. Two different types of cells compatible with the ichnogenera Celliforma (Type 1) and Palmiraichnus (Type 2) were found in these outcrops. Their walls were constructed with the same material as the matrix and our first research in the area showed no extant bees producing them suggesting that they were coeval with the trace-bearing rocks. The case of the “Palmiraichnus-like” Type 2 cells was misleading because of its similarity with Palmiraichnus described from the region in the Canary Islands and Balearic Archipelago (Spain). Two determining features were vital in clarifying this first appearance. In the Palmiraichnus-like cells we found remains of a larval cocoon in one cell that could be dated by C14, giving a modern age. In the Celliforma-like cells more field research in the area allow us to observe extant bees nesting in these rocks in autumn. Ichnological literature show a few cases of asynchronies involving extant traces found mostly in Paleozoic and Mesozoic rocks. In contrast, the case presented herein indicates the time gap between the bearing rocks and the Lepe traces was shorter (ca. 12 ky–2.6 My), enhancing the similarity of traces and rocks and thus their potential coevalness. This case may serve as a warning about other potential examples in the fossil record in which relatively short asynchronies between traces and paleosols exist.

scholarly journals Probable evidence of a Middle Palaeolithic site in the northern parts of the Susiana Plain, Khuzestan, Iran

2019 ◽  
Vol 46 ◽  
pp. 424-433
Author(s):  
Saeid Bahramiyan
Keyword(s):  
Raw Materials ◽  
Middle Palaeolithic ◽  
Limited Information ◽  
Zagros Mountains ◽  
Significant Progress ◽  
Khuzestan Province ◽  
Different Types ◽  
Northern Regions ◽  
Considerable Body ◽  
The Karkheh River

There is a considerable body of studies regarding the activities of the Pleistocene human population in the Zagros and Alborz regions of Iran, as well as significant progress in the Palaeolithic studies in other regions, such as the foothills, plains and deserts’ margins. However, some of these peripheral regions and foothills are still neglected, and the information about the Palaeolithic period in these areas is limited. Khuzestan province, especially its northern regions, is one of these unstudied regions, yet the limited information about this region seems very interesting. Khervali, located on the western foothills of the Zagros Mountains and on the northern heights of Susa, nearby the western bank of the Karkheh River, is one of the few Palaeolithic sites identified in recent years. The site was identified in 2012 and was systemically surveyed. Due to the extension of the site and the distribution of the artefacts, sampling all the site was not feasible, therefore, four sections of the site were chosen for taking the samples and a total of 330 stone artefacts were collected. The results of the techno-typology analyses, as well as the frequency of the flakes, the Levallois samples and different types of scrapers, revealed that the artefacts date to the middle Palaeolithic period, with considerable access to the local raw materials.

scholarly journals ANALYSIS OF STUDENT FORMULA CAR FOR OPTIMUM SAFETY AND PERFORMANCE

2020 ◽  
pp. 137-142
Author(s):  
Rabi Pathak
Keyword(s):  
Boundary Conditions ◽  
Weight Reduction ◽  
Structural Performance ◽  
Complete Analysis ◽  
Loading Conditions ◽  
Different Types ◽  
And Performance ◽  
Reliability Performance ◽  
Ansys Workbench

The Formula Student competitions are held everyyear. This paper is the result of the analysis done on the sample car design that can be presented in the Formula Student competition. The purpose of the paper is to provide a final summary on chassis analysis and structural performance. It also talks about all the important analysis that is to be done on a Formula Student car to make it safe and perform well on the track. The design has been made such that it focusses on maximum adjustability, reliability, performance, safety, weight reduction and ease of manufacturing. The analysis was done to make sure the objectives of design are fulfilled. After going through many papers, documents, blogs and videos we found that many people get confused about the loading conditions and boundary conditions for different types of tests so this paper prioritizes to make people understand about those conditions as well as about the major tests required to perform complete analysis of Formula Student cars. The weight of the chassis was calculated as 36 kg approximately according to the data obtained from design modeler of Ansys workbench as well as Solidworks. The design sustained all the loading conditions and passed all the tests. Thus, one of the objective of this paper is to help other universities and passionate students to successfully design and analyze their cars that can pass all necessary tests included in the paper. KEYWORDS—Formula Student; FEA; Boundary Conditions; Loading Conditions; Ansys; Solidworks

scholarly journals Explore the Effects of Fertilization on Polyphenols Content in Autumn of Forages from Hill Permanent Grassland by Principal Component & Classifications Analysis

2011 ◽  
Vol 68 (1) ◽  
Author(s):  
Monica HARMANESCU
Keyword(s):  
Colorimetric Method ◽  
Principal Component ◽  
Floristic Composition ◽  
Classification Analysis ◽  
Permanent Grassland ◽  
Different Types ◽  
The Matrix ◽  
Chemometric Techniques ◽  
First Time

Principal Components and Classification Analysis (PC&CA) represents one of the most utilised multivariate chemometric techniques, having the advantage to use many measurements for a single sample in the same time, being recommended for understanding better the complexity of one phenomenon. The aim of this paper was to use PC&CA to study the effects of different types of fertilizers on polyphenols content of forages harvested in autumn from permanent grassland. Gravimetrically was established the matrix of floristic composition. The experimental field was fertilized first time in 2003, organic and/or NPK mineral. The determination of polyphenols contents was made using UV-VIS SPECORD 205 spectrophotometer, in conformity to chemical Folin and Ciocalteu colorimetric method. The highest polyphenols content was identified in forages from unfertilized variant (108 µM gallic acid/g). PC&CA can be a useful tool in describing the modification of polyphenols contents of forages under the effects of organic and/or mineral fertilisation of permanent grassland.

scholarly journals Hot and crispy: CRISPR–Cas systems in the hyperthermophile Sulfolobus solfataricus

2013 ◽  
Vol 41 (6) ◽  
pp. 1422-1426 ◽  
Author(s):  
Jing Zhang ◽  
Malcolm F. White
Keyword(s):  
Present Article ◽  
Pyrococcus Furiosus ◽  
Sulfolobus Solfataricus ◽  
Host Genome ◽  
Current Understanding ◽  
Major Type ◽  
Crispr Locus ◽  
Defence System ◽  
Different Types ◽  
Foreign Dna

The CRISPR (clustered regularly interspaced short palindromic repeats) and Cas (CRISPR-associated) genes are widely spread in bacteria and archaea, representing an intracellular defence system against invading viruses and plasmids. In the system, fragments from foreign DNA are captured and integrated into the host genome at the CRISPR locus. The locus is transcribed and the resulting RNAs are processed by Cas6 into small crRNAs (CRISPR RNAs) that guide a variety of effector complexes to degrade the invading genetic elements. Many bacteria and archaea have one major type of effector complex. However, Sulfolobus solfataricus strain P2 has six CRISPR loci with two families of repeats, four cas6 genes and three different types of effector complex. These features make S. solfataricus an important model for studying CRISPR–Cas systems. In the present article, we review our current understanding of crRNA biogenesis and its effector complexes, subtype I-A and subtype III-B, in S. solfataricus. We also discuss the differences in terms of mechanisms between the subtype III-B systems in S. solfataricus and Pyrococcus furiosus.

Managing Digital Bonds in the Buyer-Supplier Relationships

2015 ◽  
pp. 107-128
Author(s):  
Jari Salo ◽  
Giuseppe Pedeliento ◽  
Robert Wendelin
Keyword(s):  
Case Studies ◽  
Customer Retention ◽  
Multiple Forms ◽  
Supplier Relationships ◽  
Strategic Actions ◽  
Limited Knowledge ◽  
It Systems ◽  
Different Types ◽  
The Matrix

Among the multiple forms of bonding which can help companies to build and maintain buyer-supplier relationships, digital bonds, i.e. ties between an industrial buyers and suppliers formed when the IT systems of the parties are shared and integrated, are increasingly recognized as a strategic mean of customer retention. Despite several studies have unveiled which factors enable and constrain the companies' adoption of IT systems, we still have limited knowledge of how different types of digital bonds can be strategically managed. In this chapter we first provide a digital bond matrix in which four different types of digital bonds are identified. Then the proposed matrix is empirically validated by analyzing four different case studies representative of each digital bond identified. Finally, the matrix is applied as a device to inform strategic actions and decisions that can/should be undertaken to improve firms' digital bonds portfolio.

Applying sustainability indicators in the analysis and segmentation of tourist demand - implications for marine visitor experiences on the Tremiti Islands, Italy.

2021 ◽  
pp. 192-204
Author(s):  
Nicolaia Iaffaldano ◽  
Sonia Ferrari
Keyword(s):  
National Park ◽  
Marine Reserve ◽  
Sustainability Indicators ◽  
High Quality ◽  
Visitor Experiences ◽  
Different Types ◽  
The Matrix ◽  
Crucial Information ◽  
Tourist Demand ◽  
Questionnaire Research

Abstract This chapter presents the findings of qualitative questionnaire research carried out in the Tremiti Islands Marine Reserve, which is part of Gargano National Park, Italy. The study have identified different segments of tourists visiting Tremiti by means of the model proposed by Arnegger et al. (2010), using the matrix suggested in the model. The model was used to understand and categorize visitor characteristics, their expectations and levels of satisfaction, and the strengths and weaknesses of local offerings. This is crucial information for the managers of the marine reserve who require thorough knowledge of the different types of visitors to adapt to the needs, expectations and preferences of the visitors in order to offer high-quality services and memorable experiences.

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