scholarly journals Pan-genomics: Unmasking the gene diversity hidden in the bacteria species.

2013 ◽  
Author(s):  
Luis David Alcaraz
Keyword(s):  
Core Genome ◽  
Gene Diversity ◽  
Single Gene ◽  
Phenotypic Traits ◽  
Ongoing Debate ◽  
16S Rrna Sequence ◽  
Sequence Comparisons ◽  
Shared Information ◽  
The Common ◽  
Definition Of

The dramatic increase in genome sequencing during the last years has changed our ideas about bacteria diversity, from single gene to whole community DNA surveys; we have learned that the nature largest gene repository resides in bacteria. Comparison of bacteria genomes has contributed to understand the flexibility in size and gene content as well as the gene movement due to gene family expansions and Horizontal Gene Transfer. Bacteria species are currently defined by means of 16S rRNA sequence comparisons and some limited phenotypic traits. There is an ongoing debate about the biological and evolutive significance of the bacteria species, and thus the need of refine the definition of it using the most of the genomic shared information. When comparing multiple genomes of related strains we can divide the common shared features like the core genome, and the strain specific genes are known as accessory genome, both accessory and core genome as the total of the genetic composition are known as pan-genome. Here we present the possibilities using pan-genomics as a workhorse to describe both taxonomical and functional diversity within bacteria.

scholarly journals Pan-genomics: Unmasking the gene diversity hidden in the bacteria species

2014 ◽  
Author(s):  
Luis David Alcaraz
Keyword(s):  
Core Genome ◽  
Gene Diversity ◽  
Single Gene ◽  
Phenotypic Traits ◽  
Ongoing Debate ◽  
16S Rrna Sequence ◽  
Sequence Comparisons ◽  
Shared Information ◽  
Taxonomic Range ◽  
Definition Of

The dramatic increase in genome sequencing during the last years has changed our ideas about bacterial diversity, from single gene to whole community DNA surveys; we have learned that nature's lagest gene repository resides in bacteria resides in bacteria. Comparison of bacteria genomes has contributed to understand the flexibility in size and gene content as well as the gene movement due to gene family expansions and Horizontal Gene Transfer. Bacteria species are currently defined by means of 16S rRNA sequence comparisons and some limited phenotypic traits. There is an ongoing debate about the biological and evolutive significance of the bacteria species, and thus the need to refine the definition of it using the most of the genomic shared information across any taxonomic range. When comparing multiple genomes of related strains we can distinguish a set of common shared features which are known as the core genome. In the other hand, the set of strain specific genes are known as accessory genome. The accessory and core genome conform the total of the genetic composition, and are known as pan-genome. Here we present the possibilities using pan-genomics as a workhorse to describe both taxonomical and functional diversity within bacteria.

scholarly journals Pan-genomics: Unmasking the gene diversity hidden in the bacteria species

2014 ◽  
Author(s):  
Luis David Alcaraz
Keyword(s):  
Core Genome ◽  
Gene Diversity ◽  
Single Gene ◽  
Phenotypic Traits ◽  
Ongoing Debate ◽  
16S Rrna Sequence ◽  
Sequence Comparisons ◽  
Shared Information ◽  
Taxonomic Range ◽  
Definition Of

The dramatic increase in genome sequencing during the last years has changed our ideas about bacterial diversity, from single gene to whole community DNA surveys; we have learned that nature's lagest gene repository resides in bacteria resides in bacteria. Comparison of bacteria genomes has contributed to understand the flexibility in size and gene content as well as the gene movement due to gene family expansions and Horizontal Gene Transfer. Bacteria species are currently defined by means of 16S rRNA sequence comparisons and some limited phenotypic traits. There is an ongoing debate about the biological and evolutive significance of the bacteria species, and thus the need to refine the definition of it using the most of the genomic shared information across any taxonomic range. When comparing multiple genomes of related strains we can distinguish a set of common shared features which are known as the core genome. In the other hand, the set of strain specific genes are known as accessory genome. The accessory and core genome conform the total of the genetic composition, and are known as pan-genome. Here we present the possibilities using pan-genomics as a workhorse to describe both taxonomical and functional diversity within bacteria.

scholarly journals Logics of Common Ground

2017 ◽  
Vol 58 ◽  
pp. 859-904 ◽  
Author(s):  
Tim Miller ◽  
Jens Pfau ◽  
Liz Sonenberg ◽  
Yoshihisa Kashima
Keyword(s):  
Common Ground ◽  
Modal Logics ◽  
Joint Activities ◽  
Formal Definitions ◽  
Different Types ◽  
Agent Collaboration ◽  
Shared Information ◽  
Multi Agent ◽  
The Common ◽  
Definition Of

According to Clark's seminal work on common ground and grounding, participants collaborating in a joint activity rely on their shared information, known as common ground, to perform that activity successfully, and continually align and augment this information during their collaboration. Similarly, teams of human and artificial agents require common ground to successfully participate in joint activities. Indeed, without appropriate information being shared, using agent autonomy to reduce the workload on humans may actually increase workload as the humans seek to understand why the agents are behaving as they are. While many researchers have identified the importance of common ground in artificial intelligence, there is no precise definition of common ground on which to build the foundational aspects of multi-agent collaboration. In this paper, building on previously-defined modal logics of belief, we present logic definitions for four different types of common ground. We define modal logics for three existing notions of common ground and introduce a new notion of common ground, called salient common ground. Salient common ground captures the common ground of a group participating in an activity and is based on the common ground that arises from that activity as well as on the common ground they shared prior to the activity. We show that the four definitions share some properties, and our analysis suggests possible refinements of the existing informal and semi-formal definitions.

scholarly journals The proteome, not the transcriptome, predicts that oocyte superovulation affects embryonic phenotypes in mice

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Leila Taher ◽  
Steffen Israel ◽  
Hannes C. A. Drexler ◽  
Wojciech Makalowski ◽  
Yutaka Suzuki ◽  
...  
Keyword(s):  
Oocyte Quality ◽  
Phenotypic Traits ◽  
Oocyte Diameter ◽  
Common View ◽  
Molecular Embryology ◽  
The Common ◽  
Definition Of ◽  
Proteome Changes ◽  
Open Question ◽  
First Time

AbstractSuperovulation is the epitome for generating oocytes for molecular embryology in mice, and it is used to model medically assisted reproduction in humans. However, whether a superovulated oocyte is normal, is an open question. This study establishes for the first time that superovulation is associated with proteome changes that affect phenotypic traits in mice, whereas the transcriptome is far less predictive. The proteins that were differentially expressed in superovulated mouse oocytes and embryos compared to their naturally ovulated counterparts were enriched in ontology terms describing abnormal mammalian phenotypes: a thinner zona pellucida, a smaller oocyte diameter, increased frequency of cleavage arrest, and defective blastocyst formation, which could all be verified functionally. Moreover, our findings indicate that embryos with such abnormalities are negatively selected during preimplantation, and ascribe these abnormalities to incomplete ovarian maturation during the time of the conventional superovulation, since they could be corrected upon postponement of the ovulatory stimulus by 24 h. Our data place constraints on the common view that superovulated oocytes are suitable for drawing general conclusions about developmental processes, and underscore the importance of including the proteins in a modern molecular definition of oocyte quality.

SIMILARITIES AND DIFFERENT FEATURES OF HAND GESTURES IN AMERICAN AND KYRGYZ CULTURES

2019 ◽  
pp. 19-22
Author(s):  
Avtandil kyzy Ya
Keyword(s):  
Everyday Life ◽  
Facial Expressions ◽  
Main Part ◽  
Body Language ◽  
Hand Gestures ◽  
Common Definition ◽  
The World ◽  
The Common ◽  
Definition Of ◽  
Different Cultures

Abstract: This paper highlights similarities and different features of the category of kinesics “hand gestures”, its frequency usage and acceptance by different individuals in two different cultures. This study shows its similarities, differences and importance of the gestures, for people in both cultures. Consequently, kinesics study was mentioned as a main part of body language. As indicated in the article, the study kinesics was not presented in the Kyrgyz culture well enough, though Kyrgyz people use hand gestures a lot in their everyday life. The research paper begins with the common definition of hand gestures as a part of body language, several handshake categories like: the finger squeeze, the limp fish, the two-handed handshake were explained by several statements in the English and Kyrgyz languages. Furthermore, this article includes definitions and some idioms containing hand, shake, squeeze according to the Oxford and Academic Dictionary to show readers the figurative meanings of these common words. The current study was based on the books of writers Allan and Barbara Pease “The definite book of body language” 2004, Romana Lefevre “Rude hand gestures of the world”2011 etc. Key words: kinesics, body language, gestures, acoustics, applause, paralanguage, non-verbal communication, finger squeeze, perceptions, facial expressions. Аннотация. Бул макалада вербалдык эмес сүйлѳшүүнүн бѳлүгү болуп эсептелген “колдордун жандоо кыймылы”, алардын эки башка маданиятта колдонулушу, айырмачылыгы жана окшош жактары каралган. Макаланын максаты болуп “колдордун жандоо кыймылынын” мааниси, айырмасы жана эки маданиятта колдонулушу эсептелет. Ошону менен бирге, вербалдык эмес сүйлѳшүүнүн бѳлүгү болуп эсептелген “кинесика” илими каралган. Берилген макалада кѳрсѳтүлгѳндѳй, “кинесика” илими кыргыз маданиятында толугу менен изилденген эмес, ошого карабастан “кинесика” илиминин бѳлүгү болуп эсептелген “колдордун жандоо кыймылы” кыргыз элинин маданиятында кѳп колдонулат. Андан тышкары, “колдордун жандоо кыймылынын” бир нече түрү, англис жана кыргыз тилдеринде ма- селен аркылуу берилген.Тѳмѳнкү изилдѳѳ ишин жазууда чет элдик жазуучулардын эмгектери колдонулду. Түйүндүү сѳздѳр: кинесика, жандоо кыймылы, акустика,кол чабуулар, паралингвистика, вербалдык эмес баарлашуу,кол кысуу,кабыл алуу сезими. Аннотация. В данной статье рассматриваются сходства и различия “жестикуляции” и частота ее использования, в американской и кыргызской культурах. Следовательно, здесь было упомянуто понятие “кинесика” как основная часть языка тела. Как указано в статье, “кинесика” не была представлена в кыргызской культуре достаточно хорошо, хотя кыргызский народ часто использует жестикуляцию в повседневной жизни. Исследовательская работа начинается с общего определения “жестикуляции” как части языка тела и несколько категорий жестикуляции, таких как: сжатие пальца, слабое рукопожатие, рукопожатие двумя руками, были объяснены несколькими примерами на английском и кыргызском языках. Кроме того, эта статья включает определения слов “рука”, “рукопожатие”, “сжатие” и некоторые идиомы, содержащие данных слов согласно Оксфордскому и Академическому словарю, чтобы показать читателям их образное значение. Данное исследование было основано на книгах писателей Аллана и Барбары Пиз «Определенная книга языка тела» 2004 года, Романа Лефевра «Грубые жестикуляции мира» 2011 года и т.д. Ключевые слова: кинесика, язык жестов, жесты, акустика, аплодисменты, паралингвистика, невербальная коммуникация, сжатие пальца, чувство восприятия, выражение лиц.

Maṣlaḥa as Sovereignty: Fadlallah and Khomeini Compared

2017 ◽  
Vol 9 (1) ◽  
pp. 89-112
Author(s):  
Nachman Alexander
Keyword(s):  
Political Thought ◽  
Common Good ◽  
Islamic History ◽  
The Common Good ◽  
Islamic Political Thought ◽  
Popular Movement ◽  
The Common ◽  
Definition Of

This article examines how Fadlallah and Khomeini’s respective quests for sovereignty are reflected in their political thought, particularly vis-a-vis their notions of maṣlaḥa, which I define as the “common good.” I argue that if, to an extent, Islamic political thought seeks to maximise maṣlaḥa, then this can also constitute a claim to sovereignty, the definition of which remains multidimensional and contentious. By closely examining Fadlallah and Khomeini’s writings and pronouncements on governance, popular movement, and state, I attempt to reveal how discussions regarding Islamic governance demonstrate a broader claim to authority in Islamic history.

scholarly journals Viscoelastometric Testing to Assess Hemostasis of COVID-19: A Systematic Review

2021 ◽  
Vol 10 (8) ◽  
pp. 1740
Author(s):  
Marion Bareille ◽  
Michaël Hardy ◽  
Jonathan Douxfils ◽  
Stéphanie Roullet ◽  
Dominique Lasne ◽  
...  
Keyword(s):  
Systematic Review ◽  
Mechanical Strength ◽  
Small Sample ◽  
The Common ◽  
Small Sample Sizes ◽  
Definition Of ◽  
Reported Data ◽  
Prophylactic Anticoagulation ◽  
The Impact ◽  
Heparin Neutralization

Infection by SARS-CoV-2 is associated with a high risk of thrombosis. The laboratory documentation of hypercoagulability and impaired fibrinolysis remains a challenge. Our aim was to assess the potential usefulness of viscoelastometric testing (VET) to predict thrombotic events in COVID-19 patients according to the literature. We also (i) analyzed the impact of anticoagulation and the methods used to neutralize heparin, (ii) analyzed whether maximal clot mechanical strength brings more information than Clauss fibrinogen, and (iii) critically scrutinized the diagnosis of hypofibrinolysis. We performed a systematic search in PubMed and Scopus databases until December 31st, 2020. VET methods and parameters, and patients’ features and outcomes were extracted. VET was performed for 1063 patients (893 intensive care unit (ICU) and 170 non-ICU, 44 studies). There was extensive heterogeneity concerning study design, VET device used (ROTEM, TEG, Quantra and ClotPro) and reagents (with non-systematic use of heparin neutralization), timing of assay, and definition of hypercoagulable state. Notably, only 4 out of 25 studies using ROTEM reported data with heparinase (HEPTEM). The common findings were increased clot mechanical strength mainly due to excessive fibrinogen component and impaired to absent fibrinolysis, more conspicuous in the presence of an added plasminogen activator. Only 4 studies out of the 16 that addressed the point found an association of VETs with thrombotic events. So-called functional fibrinogen assessed by VETs showed a variable correlation with Clauss fibrinogen. Abnormal VET pattern, often evidenced despite standard prophylactic anticoagulation, tended to normalize after increased dosing. VET studies reported heterogeneity, and small sample sizes do not support an association between the poorly defined prothrombotic phenotype of COVID-19 and thrombotic events.

scholarly journals Chromosome-Level Assembly of the Common Lizard (Zootoca vivipara) Genome

2020 ◽  
Vol 12 (11) ◽  
pp. 1953-1960
Author(s):  
Andrey A Yurchenko ◽  
Hans Recknagel ◽  
Kathryn R Elmer
Keyword(s):  
Linkage Map ◽  
Single Copy ◽  
Phenotypic Traits ◽  
Sequencing Data ◽  
High Coverage ◽  
Squamate Reptiles ◽  
Common Lizard ◽  
Zootoca Vivipara ◽  
The Common ◽  
Chromosome Level

Abstract Squamate reptiles exhibit high variation in their phenotypic traits and geographical distributions and are therefore fascinating taxa for evolutionary and ecological research. However, genomic resources are very limited for this group of species, consequently inhibiting research efforts. To address this gap, we assembled a high-quality genome of the common lizard, Zootoca vivipara (Lacertidae), using a combination of high coverage Illumina (shotgun and mate-pair) and PacBio sequencing data, coupled with RNAseq data and genetic linkage map generation. The 1.46-Gb genome assembly has a scaffold N50 of 11.52 Mb with N50 contig size of 220.4 kb and only 2.96% gaps. A BUSCO analysis indicates that 97.7% of the single-copy Tetrapoda orthologs were recovered in the assembly. In total, 19,829 gene models were annotated to the genome using a combination of ab initio and homology-based methods. To improve the chromosome-level assembly, we generated a high-density linkage map from wild-caught families and developed a novel analytical pipeline to accommodate multiple paternity and unknown father genotypes. We successfully anchored and oriented almost 90% of the genome on 19 linkage groups. This annotated and oriented chromosome-level reference genome represents a valuable resource to facilitate evolutionary studies in squamate reptiles.

Classifying precontractual liability: a comparative analysis

Legal Studies ◽  
2001 ◽  
Vol 21 (2) ◽  
pp. 153-191 ◽  
Author(s):  
Joachim Dietrich
Keyword(s):  
Common Law ◽  
Civil Law ◽  
Tort Law ◽  
Contract Law ◽  
Common Elements ◽  
Ongoing Debate ◽  
Unjust Enrichment ◽  
The Common ◽  
Initial Focus

The common law has solved questions of liability arising in the context of precontractual negotiations by resort to a range of different doctrines and approaches, adopting in effect ‘piecemeal’ solutions to questions of precontractual liability. Consequently, debate has arisen as to how best to classify or categorise claims for precontractual work and as to which doctrines are best suited to solving problems arising from anticipated contracts. The purpose of this article is to consider this question of how best to classify (cases of) precontractual liability. The initial focus will be on the ongoing debate as to whether principles of contract law or principles of unjust enrichment can better solve problems of precontractual liability. I will be suggesting that unjust enrichment theory offers little by way of explanation of cases of precontractual liability and, indeed, draws on principles of contract law in determining questions of liability for precontractual services rendered, though it does so by formulating those principles under different guises. Irrespective, however, of the doctrines utilised by the common law to impose liability, it is possible to identify a number of common elements unifying all cases of precontractual liability. In identifying such common elements of liability, it is necessary to draw on principles of both contract and tort law. How, then, should cases of precontractual liability best be classified? A consideration of the issue of classification of precontractual liability from a perspective of German civil law will demonstrate that a better understanding of cases of precontractual liability will be gained by classifying such cases as lying between the existing categories of contract and tort.

Edges of Regression and Limit Normal Point of Conjugate Surfaces1

1998 ◽  
Vol 122 (4) ◽  
pp. 419-425 ◽  
Author(s):  
Ningxin Chen
Keyword(s):  
Differential Geometry ◽  
Contact Boundary ◽  
Boundary Line ◽  
Tangent Point ◽  
Common Tangent ◽  
Numerical Examples ◽  
Envelope Surface ◽  
The Common ◽  
Conjugate Surfaces ◽  
Definition Of

The presented paper utilizes the basic theory of the envelope surface in differential geometry to investigate the undercutting line, the contact boundary line and the limit normal point of conjugate surfaces in gearing. It is proved that (1) the edges of regression of the envelope surfaces are the undercutting line and the contact boundary line in theory of gearing respectively, and (2) the limit normal point is the common tangent point of the two edges of regression of the conjugate surfaces. New equations for the undercutting line, the contact boundary line and the limit normal point of the conjugate surfaces are developed based on the definition of the edges of regression. Numerical examples are taken for illustration of the above-mentioned concepts and equations. [S1050-0472(00)00104-5]

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