bluuebunny/crossref_metadata_2025 huggingface dataset:
Çalışanın İş Sağlığı ve Güvenliği için Uygunluk Tespiti: Görüntü ve Ses İşleme ile Yorgunluk Tespiti ve Kişiye Özel Raporlama
Authors: Yapıcı Abdulkadir , Üstün Rumeysa , Özcan Hikmetcan
Published: July 2024

Günümüzde teknolojinin ilerlemesi, iş sağlığı ve güvenliği alanında çalışanların güvenliğini artırmaya yönelik yeni sistemlerin ortaya çıkmasına olanak tanımıştır. Ancak, tüm bu güvenlik önlemleri alındığında bile, işçinin yorgunluğunun güvenlikte kritik bir rol oynadığı unutulmamalıdır. Yorgun bir işçi, ne kadar güvenlik protokolü olursa olsun, bu protokolleri uygulamakta zorlanabilir. Bu nedenle, özellikle dikkat ve özen gerektiren endüstriyel görevlerde, çalışanların yorgun olup olmadığını belirlemenin hayati öneme sahip olduğu kabul edilmektedir. Çalışmada, işçilerin uzun ve kısa vadede işlerini sağlıklı bir şekilde sürdürebilmeleri adına yorgunluk tespitine odaklanıldı. Bu bağlamda, gerçek zamanlı video görüntülerini kullanarak, görüntü işleme teknikleriyle yüz tespiti gerçekleştirildi ve yüzdeki belirli referans noktaları haritalandı. Göz ve ağız açıklığı ile başın eğiklik seviyesi, yorgunluk belirtileri olarak belirlendi ve bu parametreler eşik değerlere göre değerlendirildi. Ayrıca, işçinin dikkatini ve bilgisini ölçmek amacıyla yorgunluk tespit sırasında iş sağlığı ve güvenliğiyle ilgili sesli ve görsel sorular da soruldu. Böylelikle işçinin belirli iş aktiviteleri ve ekipmanlar için ne kadar hazır olduğu belirlenmeye çalışıldı. Ek olarak, önerilen sistemde kullanılan yüz tanıma ile bireysel yorgunluk raporları hazırlandı. Deneysel çalışmalar sonucunda, önerilen sistemin öznel veri setindeki performansı doğruluk %80, kesinlik %85, duyarlılık %73 ve F1 skoru %75 olarak hesaplanmıştır. YawDD veri seti üzerinde ise doğruluk %95.99, kesinliği %96.83, duyarlılığı %95.58 ve F1 skoru %95.59 olarak belirlenmiştir.
Theoretical study of Dy3+, Na+: PbGa2S4 mid-infrared laser based on experimental parameters
Authors: Yu Xue-Zhou , Huang Chang-Bao , Wu Hai-Xin , Hu Qian-Qian , Liu Guo-Jin , Li Ya , Zhu Zhi-Cheng , Qi Hua-Bei , Ni You-Bao , Wang Zhen-You ,   Crystal Lab of Laser Technology Research Center, Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China,   University of Science and Technology of China, Hefei 230026, China
Published: July 2024

According to the absorption spectra of Dy3+, Na+: PbGa2S4 crystal elements, as well as the theoretical calculations obtained from Judd-Ofelt analysis, we derive partial fluorescence absorption and emission cross sections. For energy levels that cannot be directly measured, we employ the reciprocal method to calculate their respective absorption cross-section and emission cross-section. Combing the experimental measurements and the calculation results, the experimental setup, which can generate a 4.3-μm mid-infrared laser through directly pumping dysprosium and Dy3+, Na+: PbGa2S4 crystals by 1.3 μm and 1.7 μm diode lasers, is investigated through numerical simulation. The spatial distributions of laser power, gain coefficient, and absorption coefficient within the crystal are obtained through numerical calculation. Furthermore, the effects of pumping power, crystal length, and output mirror reflectance on laser performance are analyzed. In this model, a 2.9-μm laser oscillation is introduced in the optical path and the changes of output power before and after introduction are observed. Our results demonstrate that the introduction of 2.9-μm laser oscillation effectively facilitates the particle number transfer from the 6H13/2 level to the ground state 6H15/2, thereby reducing the self-terminating phenomenon during the transition between the 6H11/2 and 6H13/2 levels, and enhancing both output power and slope efficiency of the laser system. Numerical results indicate that maximum power output for the 1.3μm diode laser pumping is achieved at 103 mW with a pumping threshold of 12 mW and a slope efficiency of 2.8%, while for the 1.7-μm diode laser pumping, the power output reaches up to 315 mW with a pumping threshold of 46 mW and a slope efficiency of 8%. Additionally, the calculation results show that the optimal crystal length is 17 mm for the 1.3 μm diode laser pumping, and 32 mm for the 1.7 μm diode laser pumping. Finally, the best reflectance value for the output mirror is 0.92. These numerical results are of great significance for guiding the crystal processing and the selection of optical path structure parameters.
The Jag2/Notch1 signaling axis promotes sebaceous gland differentiation and controls progenitor proliferation
Authors: Abidi Syeda Nayab Fatima , Chan Sara , Seidel Kerstin , Lafkas Daniel , Vermeulen Louis , Peale Frank , Siebel Christian W
Published: July 2024

The sebaceous gland (SG) is a vital appendage of the epidermis, and its normal homeostasis and function is crucial for effective maintenance of the skin barrier. Notch signaling is a well-known regulator of epidermal differentiation, and has also been shown to be involved in postnatal maintenance of SGs. However, the precise role of Notch signaling in regulating SG differentiation in the adult homeostatic skin remains unclear. While there is evidence to suggest that Notch1 is the primary Notch receptor involved in regulating the differentiation process, the ligand remains unknown. Using monoclonal therapeutic antibodies designed to specifically inhibit of each of the Notch ligands or receptors, we have identified the Jag2/Notch1 signaling axis as the primary regulator of sebocyte differentiation in mouse homeostatic skin. Mature sebocytes are lost upon specific inhibition of the Jag2 ligand or Notch1 receptor, resulting in the accumulation of proliferative stem/progenitor cells in the SG. Strikingly, this phenotype is reversible, as these stem/progenitor cells re-enter differentiation when the inhibition of Notch activity is lifted. Thus, Notch activity promotes correct sebocyte differentiation, and is required to restrict progenitor proliferation.
Reliability and validity of “My Jump 2” application for countermovement jump free arm and interlimb jump symmetry in different sports of professional athletes
Authors: Peng Yong , Sun Shaotong , Wang Yudi , Qin Ya xuan , Qin Di
Published: July 2024

Background

Vertical jumping is an important evaluation tool to measure muscle strength and power as well as lower limb symmetry. It is of practical importance and value to develop and utilize a portable and low-cost mobile application (APP) to evaluate jumping. The “My Jump 2” app is an iPhone camera-based application for measuring jumping movements, which is applied to the countermovement jump (CMJ) vertical jumps of the lower limbs of athletes in different sports. The validity of this application and previous versions applied to different forms of vertical jump tests has been preliminarily demonstrated in different population, which has an obvious progress in research. Therefore, the reliability and validity of the jump height, time of flight parameters and symmetry of the CMJ vertical jump of athletes in different sports are needed to be verified by more experiments.

Purpose

The purpose of this study is to verify whether “My Jump 2” can effectively and reliably assess jump height, flight practice and lower limb symmetry in CMJAM (countermovement jump free arm) tests in fencing, swimming and diving athletes.

Methods

Seventy-nine fencers, swimmers and divers with training experience participated in this study. They completed a total of three CMJAM vertical jump and lower limb symmetry tests in 1 day, while being assessed by using the “My Jump 2” application and a force platform. The intra-group correlation coefficient (ICC) was used to verify reliability, while the Cronbach’s alpha and coefficient of variation (CV%) was used to analyze the stability of the CMJAM vertical jump test over three jumps. The Pearson correlation coefficient was used to verify the strength of the relationship between methods (i.e., concurrent validity), and the Bland-Altman plot was used to represent consistency, meanwhile, the t-test was used to determine the systematic bias between methods.

Results

Compared with the force platform, the cumulative height values of the total number of jumps (r = 0.999; p = 0.000), the cumulative time to vacate (r = 0.999; p = 0.000) for the CMJAM test obtained by the “My Jump 2” application, the height (ICC = 0.999–1, p = 0.000), the time to vacate flight (ICC = 0.999–1, p = 0.000), contact time symmetry (ICC = 0.976–0.994, p = 0.000), and flight time symmetry (ICC = 0.921–0.982, p = 0.000), respectively. Showed high correlation between the results of “my jump 2” app and the force platform.

Conclusion

The “My Jump 2” application is a valid tool to assess CMJAM vertical jump and lower limb symmetry in fencing, swimming and diving athletes with training experience.
The Impact of the Christian School of Alexandria on Christianity: The First Councils of Nicaea and the First Councils of Istanbul
Authors: AYTEPE Nesim
Published: July 2024

Stratejik konumu, zengin kültürel ve entelektüel mirası sayesinde İskenderiye, bilim, felsefe ve inancın kesiştiği antik çağın en önemli merkezlerinden biri olarak bilinmektedir. Bu zengin birikim sayesinde şehir, daha sonra kurulacak
olan İskenderiye Okulu için sağlam bir temel oluşturmuştur. Okul, bilim, felsefe ve din gibi çeşitli alanlarda önemli katkılarda bulunmuş, hem entelektüel hem de kurumsal bir yapı inşa etmiştir. İskenderiye Okulu kendisinden sonra
gelen birçok eğitim kurumu için model olmuş, farklı din ve inanç sistemlerine sahip toplulukların kendi okullarını kurmalarında teşvik edici bir misyon üstlenmiştir. Bu kurumlardan birisi de Hıristiyan düşüncesinin gelişiminde
merkezi bir rol oynayan İskenderiye Hıristiyan Okuludur. Antik dönem İskenderiye Okulunun kültürel ve medolojik mirası üzerine kurulmuş olan İskenderiye Hıristiyan Okulu, Hıristiyan inancının dinamiklerini referans alımıştır. İskenderiye
Okulunun oluşturduğu zengin kültürel ortamdan etkilenen bu okul, Hıristiyan tarihi ve teolojisi üzerinde önemli bir etki bırakmıştır. Bu çalışma, İskenderiye Hıristiyan Okulunun Hıristiyanlık doktrinlerinin şekillenmesindeki merkezi
rolünü ve bu süreçte Birinci İznik ve İstanbul Konsilleri ile olan ilişkisini incelemeyi amaçlamaktadır. İznik Konsili ve İstanbul Konsili, Hıristiyan inancının temel öğretilerini belirlemiş, özellikle teslis doktrinin resmi olarak
kabu edilmesinde kritik roller oynamıştır. Bu çalışma, söz konusu okulun, Hıristiyan teolojisinin ve özellikle teslis doktrininin resmi kabulünde oynadığı kritik rolü detaylı bir şekilde analiz etmeyi hedeflemektedir.
Heavy Metal Pollution in Gas Flare-Impacted Soils: An Assessment Using Pollution Indices in Obunagha, Bayelsa State, Nigeria
Authors: Silver Wurutuawei T. , Young Erepamowei , Imomotimi Ajoko T. , Angaye Woyengidoubara Terah , Ebong Christopher Unyime
Published: July 2024

Gas flaring is the controlled burning of natural gas which occurs as a result of the activities of oil exploration and exploitation using flare stacks. In Nigeria, gas flaring activities is high and it mainly takes place in the Niger Delta region. The aim of this study was to investigate the bioavailability and concentration of heavy metals pollution of gas flare-impacted soils using pollution indices such as contamination factor, geo-accumulation index and pollution load index. Soil samples were collected with soil auger at depths of 0-15 cm from distances of 200 m, 500 m, 1000 m, 2000 m, and 3000 m away from the flaring point. Flame atomic absorption spectrometry was used to assess the presence of the following heavy metals in the soils: cadmium, chromium, nickel, zinc, copper, and manganese. The findings revealed that Fe (90% bioavailability) had the highest bioavailability among the metals tested in the soils, while Cr (45%) had the lowest. The metals bioavailability decreased in the order of Fe>Mn>Cu>Cd>Ni>Zn>Cr. The geo-accumulation index revealed that the soils were practically uncontaminated by Zn and Cu at all distances, moderately polluted by Cd and Ni at 1000 m and 2000 m and strongly polluted with Cd at a distance of 200 m. The Contamination factor results were consistent with the geo-accumulation index results. The pollutant load index (PLI) was found to be high but decreasing (1.37-0.49) as the distance from the flare point increased, indicating that the research region was polluted. In conclusion, the study's overall findings suggested that the soils were contaminated with heavy metals (particularly Cd) as a result of nearby gas flaring. As a result, the area must be appropriately monitored and managed to prevent future soil contamination by heavy metals to a level that is hazardous to human health.
Growth, Decomposition, and Instability Analysis of Pearl Millet in Jodhpur Region and Rajasthan, India
Authors: Bairwa Kailash Chand , Balai Harkesh Kumar , Meena M. L. , Bairwa S. K. , Prasad Dasharath
Published: July 2024

Aims: The main purpose of this study was to examine the growth, instability and source of output growth in area, production and productivity of pearl millet in Jodhpur & Barmer districts, Jodhpur Region and entire Rajasthan.
Study Design: The present study was completely based on secondary time series data.
Place & Duration of Study: This study area was covered to Jodhpur & Barmer districts, Jodhpur Region and entire Rajasthan. The entire study period was divided into three sub-periods viz., period-I (2006-07 to 2013-14), Period-II (2014-15 to 2021-22) and Overall period (2006-07 to 2021-22).
Methodology: The time series data were analyzed using statistical tools exponential growth model, Cuddy-Della Valle instability index and Minhas & Vaidyanthan decomposition model to accomplish the study’s objectives.
Results: The results of the study indicated that highest growth rate were observed in the productivity (36.20%) and production (30.83%) of pearl millet in Barmer district during period-I. The maximum variability was observed in production (77.88%) and productivity (77.30%) of pearl millet in Barmer district during period-II. The yield effect (300.43%) was reported as major contributor to boost-up the production of pearl millet in selected study area. The state government should establish Agri-Export Zones for millet crops in the state.
Conclusion: The highest growth rate was recorded in pearl millet’s productivity in Barmer district. The highest instability was reported in production of pearl millet in Barmer district. Yield effect was major source of output growth in production of pearl millet in Barmer district.
Contribution of Goods and Services Tax (GST) Revenue: India’s March towards $5 Trillion Economy
Authors: Dhotre Avinash C. , Chinchodkar Kishor N. , Ghodake Abhijeet D. , Shinde Bhausaheb N.
Published: July 2024

This research emphasis on GST’s revenue contributes to India’s march towards $ 5 trillion economy. GST is an indirect tax in nature and levied on goods and services except alcoholic liquors and petroleum products. The dream of $ 5 trillion economy is too difficult for India. While perceiving such dream, GST would contribute to achieve it. In this study we focused on monthly collection of GST revenue, GST revenue Y-o-Y, GDP growth Y-o-Y, payment of GST in last six years, and the contribution to GST revenue from different business constitution. The GST slab rate of 18% and 28% are charged on luxuries goods and services will help to generate high revenue. After analysis, we found that the revenue of GST is increasing every year. The revenue was Rs. 1.46 Trillion in the month November of F. Y. 2022-23 and highly increased to Rs. 1.68 Trillion in the month November of F.Y. 2023-24. It shows 15% growth from November 2022-23 to November 2024. The share of GST revenue is huge in the development of economy.
Research on the Influence of Digital Economy on Technological Complexity of China's Manufacture Exports
Authors: Mengyuan Cheng , Jifeng Zhang
Published: July 2024

This paper provides an empirical analysis of the relationship between China's digital economy and the improvement of technical complexity of China's manufacturing exports. First, the direct effect of digital economy on the enhancement of technical complexity of manufacturing exports is tested by constructing a fixed effect model; Second, the indirect effect of digital economy on the enhancement of technical complexity of manufacturing exports is tested by constructing a mediating effect model; Third, a heterogeneity model is constructed to test the differentiated impact of digital economy on the technical complexity of manufacturing exports. Empirical results suggest that: (1) the digital economy can effectively enhance the technological complexity of China's manufacturing exports; (2) product innovation is an important transmission mechanism for the digital economy to promote the enhancement of the technological complexity of manufacturing exports; (3) this enhancement effect is stronger in the economically developed regions.
Comparative Analysis of Morphometric and Meristic Characters in Oreochromis niloticus (Linnaeus, 1758), Nile Tilapia across Diverse Ecological Zones in Nigeria
Authors: H. A. Adedeji, , M. Kefas, , T. A. Idowu, , O. A. Sogbesan,
Published: July 2024

The present study investigated the comparative analysis of morphometric and meristic characteristics in Oreochromis niloticus (Linnaeus, 1758) from six lakes in different ecological zones across Nigeria. A total of 347 samples were collected. Twenty-nine morphometric characters were measured to the nearest 0.01 cm using Vernier calipers and nine meristic characters were counted in all the collected individuals. The results of the univariate analysis of variance (ANOVA) revealed that all observed morphometric and meristic characters were significantly different (P=0.05) across the study sites. Notably, O. niloticus from Asejire Lake had significantly higher values in all the morphometric characters. The multivariate analysis of variance (MANOVA) identified three morphometric and four meristic characters as the most discriminating traits among the studied populations. These findings align with previous research highlighting the utility of morphometric and meristic data in delineating fish populations based on habitat differences and genetic compositions. Significant differences in head-related (head length), swimming-related (anal fin length and caudal peduncle length), and feeding-related (both left and right gill raker) measurements further underscored environmental influences on morphological variation. The study suggests that ecological factors such as food availability and environmental conditions contribute to the observed variations. This research provides valuable insights into the population dynamics and adaptation strategies of O. niloticus in diverse aquatic environments across Nigeria
Morphological and Physico-chemical Properties of Soils of Amtur-3 Micro-Watershed on Schistose Landscape in Bailhongal taluk of Belagavi District, Karnataka, India
Authors: Fathima Firdosh , Hebbara M. , Manjunatha M. V. , Kuligod V. B. , Rajkumara S.
Published: July 2024

Aims: To assess the morphological and physico-chemical properties of two soil series viz., KKT (Kabulayathkatti tanda) and SDH (Singadahalli) of Amtur-3 micro-watershed developed on schistose landscape in northern transition zone of Karnataka.
Place and Duration of Study: The study was carried out in the Amtur-3 micro-watershed (4D5B8t04) located in Bailhongal taluk of Belagavi district, Karnataka during 2022-2024.
Methodology: Horizon-wise soil samples were collected from the two representative pedons viz., KKT (Kabulayathkatti tanda) and SDH (Singadahalli) soil series, were identified, characterized and classified up to family level according to revisions in Soil Taxonomy using morphological, physical and chemical properties.
Results: The soils of these two series were sandy clay loam to clay in texture, neutral in soil reaction and had low salt content. Calcium and magnesium were the dominant cations followed by sodium and potassium. Both the soil series belonged to the order Inceptisol.
Digitalisation, Banking Stability and Nigeria's Economic Growth Trajectory
Authors: Enebeli-Uzor Sunday
Published: July 2024

The integration of digital technologies in banking operations has become a cornerstone of economic policy to promote financial stability and foster economic growth. This study examines the interplay between digitalisation and banking industry stability and economic growth in Nigeria. Annual time series data spanning 1981 to 2022, except for the digitalisation variable (web payment) which covers a shorter period, was collected from the Central Bank of Nigeria’s Statistical Bulletin. Using the Least Squares estimator to analyse the multiple regression model, the study found that digitalisation and financial deepening negatively impact economic growth due to digital prematurity and financial shallowness. However, bank stability and bank assets positively influence economic growth. The study concludes that although digitalisation and financial deepening have the potential to enhance growth, as seen in studies for other nations, Nigeria’s digital maturity level is too low to propel economic growth effectively. Nonetheless, stability in the Nigerian banking industry and bank assets contribute positively to the country’s economic growth trajectory. The study suggests that banks should invest more in digital transformation to foster economic growth. Additionally, banks should provide more credit to private sector and integrate the unbanked population into formal banking processes to enhance financial deepening, which is a key driver of growth in both aspiring and regional peer countries of Nigeria. Finally, banks should continue to build a strong asset base, not only for regulatory purposes but also to leverage large assets for valuation benefits, collateral for loans, risk exposure diversity, competitive advantage, and growth opportunities.
Biological Control by Microorganisms
Authors: Harper David R
Published: June 2013

Biological control is the use of natural enemies to reduce the numbers of a damaging organism, which can be anything from a bacterium to a rabbit. Such natural enemies include pathogenic and competitor microorganisms. Biological control agents can be both less toxic and more flexible than chemical pesticides, although given the complexities of biological systems a relatively high level of understanding of the target organism is required. Although they may be more sympathetically regulated, their high specificity can impose limitations on commercial development. Biological control includes a wide range of approaches, from natural predators to biologically produced molecules. The focus of this article is on microorganisms, including viruses, bacteria, fungi and protozoans. Though many of these cause disease in or poison their target through toxin production, others may act by a different route, for example, by outcompeting the target organism or by excluding it from an ecological niche.

Key Concepts:

Biological control is use of material of biological origin to control the numbers or effects of a target organism.

Biological control includes the use of predators, competitors, pathogens and compounds of biological origin.

Microorganisms used include viruses, bacteria, fungi and protozoans. These may cause disease, or may compete with or otherwise limit the target organism.

Biological controls tend to be highly specific. Although this generally makes them environmentally benign, it also means that they need to be used in a highly informed way.

Both specificity and the cost and nature of the agents used have limited the use of biological control. All approaches combined account for only approximately 5% of the global pesticides market, although this figure is rising.
Complement Regulatory Proteins and Related Diseases
Authors: Meri Seppo , Jarva Hanna
Published: June 2013

Many regulatory proteins exist to prevent excessive complement activation and to protect our cells and tissues from inappropriate damage. The classical and lectin pathways are inhibited by C1 inhibitor (C1 INH) and C4b‐binding protein (C4bp). Deficiencies in C1 INH predispose to hereditary angiooedema (HAE). Factor H(FH) is the main inhibitor of the alternative pathway amplification cascade. Mutations and polymorphisms in FH predispose to meningococcal infections, dense deposit disease (also called membranoproliferative glomerulonephritis type II), partial lipodystrophy, atypical haemolytic uraemic syndrome (aHUS) and age‐related macular degeneration. aHUS can also be the consequence of mutations in factor I (C4b/C3b inactivator) or membrane cofactor protein (CD46). Two other membrane regulators, decay‐accelerating factor (CD55) and protectin (CD59), have glycosylphosphatidylinositol (GPI)‐anchors, whose acquired deficiency from bone marrow‐derived cells can lead to paroxysmal nocturnal haemoglobinuria (PNH). Cell damage and vascular thromboses are characteristic for PNH and aHUS.

Key Concepts:

Several complement inhibitors are needed because the complement system has a strong potential to cause inflammation and tissue damage.

The default of the complement system – in the absence of regulators – is to become activated and stay in a state of activation.

The alternative pathway factor H can discriminate between activators (nonhost) and nonactivators (host) to prevent attack against viable endogenous cells and structures.

Loss of complement inhibitor function usually predisposes to a spectrum of distinct diseases.

The diseases are characterised by ‘innate autoreactivity’, that is, attack against endogenous cells and tissues.

Anaemia, thrombocytopenia and endothelial cell damage are common features and lead, in severe cases, to thrombotic microangiopathy.

Inability to control complement activation may also lead to secondary complement deficiency and increased susceptibility to infections.

Complement regulators have cross‐inhibitory activity to kinin (C1INH) and coagulation (FH) systems. Loss of function thus predisposes, for example, to bradykinin formation (in HAE) and thrombosis (aHUS).

Initiation of complement dysregulation‐related diseases and disease attacks usually requires triggering factors (e.g. infection, trauma, medication and stress).

The emergence of therapeutic complement inhibitors and replacement therapy helps in controlling excessive disease‐related complement activation.
Rhynie Chert
Authors: Trewin Nigel H
Published: June 2013

The Rhynie chert of Aberdeenshire, Scotland, UK contains exceptionally well‐preserved Early Devonian (c. 407 Ma) fossil plants and arthropods. The chert is a siliceous rock resulting from the alteration of sinter deposited around surface vents by hydrothermal hot springs, and the cherts lie within shales and sandstones deposited by floods from a river system. The seven embryophyte plants include primitive rhyniophytes and early lycopods. Both sporophyte and gametophyte generations are preserved for several plants. Saprophytic, parasitic and symbiotic fungi are associated with the plants. The terrestrial fauna is dominated by arthropods with trigonotarbids, mites, myriapods and primitive hexapods, and freshwater pools contained branchiopod crustaceans and a euthycarcinoid. The biota comprises the oldest well‐preserved terrestrial ecosystem on Earth, and the primitive terrestrial plants form the cornerstone of palaeobotany.

Key Concepts:

The Rhynie chert contains the oldest well preserved terrestrial ecosystem on Earth.

Silica preserves delicate 3D structures in plants and arthropods.

The earliest full sporophte/gametophyte plant life histories are preserved.

Superb preservation reveals many organisms with their earliest known occurrence in the chert.

The advanced ecological relationships in the Rhynie chert indicate a long pre‐Devonian period of terrestrial colonisation by plants and arthropods.

The ecosytem has many features in common with modern plant litter communities.
Flavivirus Infections in Humans
Authors: Roehrig John T , Barrett Alan DT
Published: June 2013

Flaviviruses are enveloped, positive‐stranded
ribonucleic acid
viruses that are globally emerging and cause significant human disease in the form of encephalitis or haemorrhagic fever. The medically important flaviviruses are dengue, yellow fever, Japanese encephalitis, St. Louis encephalitis, tick‐borne encephalitis (TBE) and West Nile viruses. Most flaviviruses are maintained in animal reservoirs in nature and are transmitted to humans primarily through the bite of an infected mosquito or tick. Human‐to‐human transmission can also occur through transfusion or transplantation of infected tissue. Vaccines are available for only yellow fever and Japanese and TBE; however, new vaccines for dengue and West Nile are in clinical trials in humans. Disease diagnosis can be difficult as all flaviviruses are antigenically and genetically closely related. There are no effective antiviral therapies that exist for any flavivirus so the main approach to disease control is through vaccination and vector control.

Key Concepts:

Flaviviruses are important global human pathogens that primarily cause encephalitis and haemorrhagic disease.

Flaviviruses are enveloped, positive‐stranded RNA viruses.

Most human flaviviral infections are asymptomatic.

Flaviviruses are primarily transmitted to man by the bite of an infected mosquito or tick and are maintained in nature in animal reservoirs.

Flaviviruses can also be transmitted between humans by transfusion or transplantation of contaminated tissue.

All flaviviruses are closely related so diagnosis of human disease can be difficult.

Most flaviviral diseases are considered emerging infections.

There are no effective drugs or treatments for flaviviral infections.

Approved human flaviviral vaccines are available for Japanese encephalitis, tick‐borne encephalitis and yellow fever.

Control of flavivirus outbreaks largely depend on vector‐control measures.
RNA
Editing: Evolutionary Implications
Authors: Gray Michael W
Published: June 2013

The term ‘
ribonucleic acid (RNA)
editing’ describes a variety of mechanistically unrelated biochemical activities that alter RNA molecules after transcription by addition, deletion or substitution of nucleotides. Examples include insertion and deletion of uridine residues in the mitochondrial
messenger RNAs (mRNAs)
of kinetoplastid protozoa; cytidine‐to‐uridine deamination of specific residues in the mitochondrial mRNAs and
transfer RNAs (tRNAs)
of land plants; conversion of adenosine to inosine via deamination in the nuclear transcripts of metazoan animals; and replacement of nonbase‐paired nucleotides at the 5′ and 3′ ends of certain mitochondrial tRNAs. A three‐stage ‘constructive neutral evolution’ (CNE) model, illustrated by specific examples, can explain in a general way how RNA‐editing systems might arise and become fixed. The CNE model proposes that potential editing systems arise before there is an actual requirement for editing, thereby serving to relax functional constraints at the genome level because harmful/lethal mutations are able to be reversed at the level of the corresponding transcript.

Key Concepts:

RNA editing is a process (typically post‐transcriptional) that alters the nucleotide sequence of an RNA molecule relative to the corresponding gene sequence.

Two general types of RNA editing are recognised: (1) insertional, in which nucleotides are added to (and also deleted from) internal positions and (2) substitutional, in which one nucleotide type replaces another at particular positions.

All types of cellular RNA (messenger, transfer and ribosomal) may undergo editing, as well as intron, noncoding and viral sequences.

RNA‐editing systems are almost exclusively restricted to eukaryotes, and are especially prominent in chloroplasts and mitochondria.

RNA‐editing systems are clearly derived traits, arising relatively recently within particular eukaryotic lineages.

RNA‐editing systems are mechanistically diverse and biochemically distinct, pointing to numerous separate evolutionary origins.

A ‘constructive neutral evolution’ (CNE) model provides a general explanation for the emergence of diverse RNA‐editing systems.

A basic tenet of the CNE model is that potential RNA‐editing systems arise before there is a need for editing.

The emergence of an RNA‐editing system allows fixation of otherwise deleterious mutations that can be ‘repaired’ by RNA editing.
Locus Control Regions (
LCRs
)
Authors: Bulger Michael , Groudine Mark
Published: June 2013

Locus control regions (LCRs) are defined as
deoxyribonucleic acid
sequence elements that confer high‐level, tissue‐specific expression to stably integrated transgenes in a position‐independent manner. As such, LCRs mediate gene activation and render a high proportion of genomic integration sites permissive for such expression, and are distinguished from transcriptional enhancers, which like LCRs are capable of mediating gene activation over large genomic distances. The mechanistic basis for the functional distinction between LCRs and enhancers is unclear. LCRs appear to subsume the separate functions of both transcriptional enhancers and chromatin insulators, but may be qualitatively different from either of these classes of regulatory elements. At their native loci, however, LCRs may only be required for a subset of the activities that they display in transgenic contexts.

Key Concepts:

LCRs are
cis
‐acting DNA regulatory elements that have been identified at a number of tissue‐specific gene loci in vertebrates.

LCRs are defined by their activity in transgenic assays, where in addition to activating transcription of linked transgenes, they are capable of rendering most integration sites permissive for expression.

The mechanistic basis for LCR function in transgenes is unknown, and there is evidence both for LCRs representing simply a very strong enhancer and for LCRs harbouring an activity entirely distinct from that of enhancers, involving the long‐range propagation of an ‘open’ chromatin structure.

At the endogenous loci from which LCRs have been derived, they appear to be required for a variety of different functions, not all of which correspond to their activity in transgenes.

LCR function has been correlated with the regulation of nuclear localisation of linked genes.
Bitter Taste Sensitivity in Humans and Chimpanzees
Authors: Behrens Maik , Meyerhof Wolfgang
Published: June 2013

Bitter taste receptors (TAS2Rs) serve an important function during evolution. They are designed to detect toxic plant metabolites before ingestion. With respect to bitter taste receptors the genetic repertoire of animal species is highly diverse reflecting the species differences in their metabolic requirements, the variety of habitats and evolutionary history. Over the recent years, an incredible amount of data on human bitter taste receptor pharmacology, biochemistry and structural features has accumulated. It became apparent that
TAS2R
gene expression is not restricted to the oral cavity, but includes several nongustatory tissues, thus expanding the presumed roles of TAS2Rs. By comparing the bitter taste receptor genes of humans with our closest relative, the chimpanzee, we learn about some of the evolutionary forces that shaped the development of modern human beings. This article discusses the current knowledge on bitter taste physiology, TAS2R function and evolutionary conservation of human and chimpanzee
TAS2R
genes.

Key Concepts:

Taste physiology and hedonics of bitter taste appear similar in humans and chimpanzees.

Human bitter taste receptors can be grouped into generalists and specialists depending on their tuning breadth.

Similar to the human situation, bitter tasting abilities of the chimpanzee are in some instances individual.

Dynamic evolution of human and chimpanzee TAS2R genes is earmarked by regional diversification.

The rate of TAS2R gene pseudogenisation indicates relaxed evolutionary constraints in the primate lineage.
Gene Conversion During Primate Evolution
Authors: Satta Yoko
Published: June 2013

Gene conversion is a nonreciprocal recombination process; the term originally referred to distorted segregation of alleles in gametocytes. In evolutionary studies, however, gene conversion often means ‘the transfer of
deoxyribonucleic acid (DNA)
sequence information from one locus to another’. In evolutionary processes, gene conversion is frequently observed between tandemly duplicated sequences or between homologous sequences on the same or on different chromosome(s). Gene conversion between functional loci has three significant roles: (1) Gene conversion generally works to maintain sequence and functional similarity in the ‘coevolution’ of interacting molecules. (2) Gene conversion often takes place between a functional gene and a pseudogene, and such events mainly cause diseases, especially in humans. Rarely, such conversions may confer a novel function to a converted gene. (3) Gene conversion erases advantageous sequence divergence between genes. In these cases, negative selection against for conversion maintains the advantageous divergence, and the converted genes are eliminated from a population.

Key Concepts:

Concerted evolution is one of evolutionary mechanisms acting on multigene families, and it maintains homogeneity among members of the family within a species.

Coevolution at the molecular level means that two or more molecules that interact with each other evolve in a harmonious way.

A nonprocessed pseudogene is a functionless gene caused by detrimental mutations such as nonsense mutations, frameshift mutations (causing a premature stop codon) or mutations in the regulatory region (silencing the expression).

A processed pseudogene is a retrotransposed mRNA of a particular gene. They are randomly inserted into the genome and do not have regulatory elements; therefore, they usually are not expressed.

Paralogues are homologous genes within a species that originate from gene duplication.

Orthologues are homologous genes found in different species that are transmitted to daughter species during speciation.

Gametologues are homologous genes on a pair of sex chromosomes, for example, the X and Y chromosomes in mammals or the Z and W chromosomes in birds.
Gene Therapy for Primary Immunodeficiency
Authors: Booth Claire , Gaspar H Bobby , Thrasher Adrian J
Published: June 2013

Primary immunodeficiencies represent a spectrum of disorders characterised by impaired development and function of the immune system with the more severe forms being lethal in infancy. Haematopoietic stem cell transplant is a curative treatment for many of these conditions but is limited by the availability of suitable donors and toxicities associated with cytoreductive chemotherapy and human leucocyte antigen disparity. Gene therapy strategies offer an alternative management option and have been developed for a number of disorders, with clinical trials underway for adenosine deaminase‐deficient‐severe combined immune deficiency (SCID), X‐linked SCID, X‐linked chronic granulomatous disease and Wiskott–Aldrich Syndrome. Initial trials using gammaretroviral vector‐mediated gene transfer showed impressive efficacy but were complicated by vector insertion driven leukaemia in some patients. Newer designs using modified vectors are likely to have an improved safety profile and the results of ongoing clinical trials may pave the way for gene therapy as a feasible management option for some children with PIDs.

Key Concepts:

In gene therapy, a patient's own haematopoietic stem cells are harvested, transduced with a viral vector containing a corrected copy of the defective gene and then returned to the patient.

A gene therapy procedure can be curative for patients with specific forms of severe combined immune deficiency (SCID), namely adenosine deaminase‐deficient SCID (ADA‐SCID) or X‐linked SCID.

Gene therapy also potentially offers definitive treatment for some non‐SCID PIDs including CGD and WAS although clinical trials are at early stages and those performed using gammaretroviral vectors offered only transient clinical benefit, if any.

Owing to the nature of the gammaretroviral vectors used in early trials several patients treated developed leukaemias or myelodysplasia.

Lentiviral vectors with an improved biosafety profile have since been developed, which reduce the risk of this happening again.

Targeted gene correction where the gene of interest is corrected
in situ
using meganuclease technology is currently being investigated as a future strategy, which may improve both the safety and efficacy of gene therapy procedures.
Animal Social Networks
Authors: Downing Beatrice C , Royle Nick J
Published: June 2013

Social network analysis (SNA) is a powerful tool that allows researchers to understand and quantify the structure and dynamics of animal societies. It is particularly useful for studying the transmission of disease, information and culture in groups and within populations and the evolution of cooperation, but is likely to be applicable for almost any subject that involves animals interacting with one another. Social networks can be potentially constructed using any association or interaction as long as a significant proportion of the focal group/population is individually identifiable. Once networks are constructed summary metrics can be extracted and used to answer the questions of interest. Care must be taken to make sure that the metrics used are appropriate for the hypotheses under test. The continuous advances in technology mean that SNA is becoming more and more widespread and increasingly relevant to understanding animal societies.

Key Concepts:

All animal societies can potentially be studied using social network analysis.

Social networks incorporate all the relationships among individuals within a group at the same time, rather than focussing on relationships between pairs of individuals, so are more realistic than traditional approaches.

Social network analysis has provided important insights into a wide‐range of areas, from the structure of complex societies to the transmission of information and disease within groups and the evolution of cooperation.

It is possible to incorporate spatial and temporal information when analysing networks of social relationships.

Social network analysis can also be useful in conservation, for example, management of endangered species, as well as theoretical studies.

There are many ways of building networks and numerous network metrics available for describing nodes and networks, making social network analysis valuable for many research questions.

Advances in technology are making it easier to apply social network analysis to animal societies.
Immune Evasion by Viruses
Authors: Simmons Ruth A , Willberg Christian B , Paul Klenerman
Published: June 2013

When a virus infects a host, a complex immune response develops to eliminate the invading pathogen. Viruses, in turn, have evolved a profusion of strategies to escape from the immune system. Mechanisms of viral evasion can be separated into those that occur at the cellular level and those that are important at the systemic level. Viruses can avoid detection by both innate and adaptive immune responses. Pattern recognition receptors in infected cells, interferons, dendritic cells, T cell receptors and antibodies are all targets of viral evasion proteins. Viruses can express proteins that directly interfere with host processes or mimic host proteins and compete to bind specific receptors. Pathogens are also able to directly deplete immune cells, and prevent their recruitment to the site of infection. In a state of latency, viruses remain dormant and undetectable in host cells. The diversity of these mechanisms has allowed us to dissect the immune system further and understand how viruses persist despite such a strong counterattack by the immune system.

Key Concepts:

Viruses have evolved a plethora of mechanisms to inhibit every step of the innate and adaptive immune responses.

Viruses avoid detection by pattern recognition receptors, T cell receptors and antibodies by modifying the ligands for these receptors.

Different viruses target every stage of antigen processing and presentation by MHC molecules, thus inhibiting recognition by T cells.

Interferons, cytokines and chemokines are mimicked or blocked by viral proteins to prevent the efficient development of an immune response.

Through repression of their replication, viruses are able to enter latency and remain dormant inside the cell, remaining undetectable.
Genetic, Epigenetic and Environmental Influences on Human Tooth Size, Shape and Number
Authors: Townsend Grant C , Brook Alan H
Published: June 2013

Studies of twins are helping to unravel the roles of genetic, epigenetic and environmental influences on human tooth size, shape and number. There is a relatively strong genetic contribution to variation in these dental phenotypes but comparisons between monozygotic cotwins are also highlighting the roles of environmental and epigenetic factors. Furthermore, by viewing the dentition as a complex adaptive system, with multiple interacting components, a clearer picture is emerging of how common dental anomalies develop and are associated with one another. This article concentrates on providing a synthesis of relevant findings and concepts about variation in the human dentition at a phenotypic level. We focus on patterning within the dentition and dental asymmetry, as well as emphasising the importance of assessing the magnitude of errors when measuring or scoring dental features. We also provide links to several articles published in the Encyclopedia of Life Sciences that cover the molecular aspects of dental development.

Key Concepts:

There are distinct patterns of variation within the human dentition that conform to ‘morphogenetic fields’.

Patterns of phenotypic variation correspond with the relative amount of time that each tooth germ spends in the soft tissue phase before mineralisation.

A unifying aetiological model, incorporating thresholds, serves to explain the relationships between tooth size, shape and number in males and females.

Tooth size variation shows a relatively strong genetic component but epigenetic and environmental factors can also contribute to phenotypic variation.

Interrelationships exist between dental crown size and morphological dental features, such as the Carabelli trait.

Discordance in the expression of missing or extra teeth between monozygotic cotwins indicates involvement of epigenetic influences on dental development.

Studies of dizygotic opposite sex twins indicate that hormonal influencesin uterocan influence dental development.

The magnitude of fluctuating dental asymmetry reflects the effects of epigenetic and environmental influences during development.

Dental development is a multilevel process involving interacting genetic, epigenetic and environmental factors over an extended period.

The dentition fulfils the characteristics of a complex adaptive system.