Miracle-dz/UniFAR-FTUs huggingface dataset:
Does an increase in water color intensity affect the lake trophic status and phytoplankton metrics

During the 11-year period covered by this study (2003–2013), high precipitation events increased the water level in the deep hardwater of Lake Rogoźno (Eastern Poland), causing its water to become browner. We investigated the effect of a change in water color on the physical, chemical, and biological parameters of the lake. The concentration of total phosphorus and nitrogen decreased, whereas the total phytoplankton biomass, coupled with a high biomass of flagellate species, increased, with the increase in water color intensity. Such changes had an effect on the determination of ecological status, based on selected phytoplankton metrics (i.e. , Polish, German, and Estonian) as well as the trophic status of Lake Rogoźno. The decrease of phosphorus concentration associated with an increase in water color intensity improved the trophic status of the lake based on Carlson's Trophic State Index. The changes in the phytoplankton community caused the deterioration of the ecological status of the lake when using the Polish and German indices adopted for clear water lakes. The use of the Estonian index, which is adapted to colored lakes, suggested that, despite the increase in water color intensity, the good ecological status of the lake was maintained or even improved. Our findings suggest that, in the event of a transformation like the one that occurred in the lake studied here, the use of only one index, adapted by state environmental monitoring programs in individual European countries, may be insufficient for the appropriate assessment of the ecological status of European lakes.
The Evaluation of Barringtonia asiatica on Indomethacin Induced Ulceration on Albino Rats.

Objective: The aim of this study was to evaluate the effect of Barringtonia asiatica hexane extract on animal induced ulceration Materials and Methods: In this study indomethacin was administered to induce gastric ulcer. Rats were divided into eight groups: Healthy animals, untreated animals (acetic acid-induced), treatment group of 100 mg/kg/ bwt, 200 mg/kg/bwt, 300 mg/kg/bwt, 400 mg/kg/bwt and 500 mg/kg/bwt and positive control group of Omeprazole 25 mg/kg/bwt was measured through histopathology examination and ulceration observation. Haematological parameters were also evaluated before and after treatments to indicate the safety profile of various concentration of Barringtonia asiatica extract. Results: The untreated animals developed more serious injuries (i.e., bigger and more severe ulcers) than the omeprazole control groups and extract treatment groups. The hexane crude extract of Barringtonia asiatica treatment with doses of 100 mg/kg/bwt, 200 mg/kg/bwt, 300 mg/kg/bwt, 400 mg/kg/bwt and 500 mg/kg/bwt were effective to heal the ulcer as shown by reduction of ulcer size (up to 13.94%, 33.46%, 51.87%, 64.34% and 86.54% respectively) compared to the untreated animals. The Barringtonia asiatica extract was as effective as omeprazole 2 mg/kg/bwt in alleviating ulcer severity as examined in histopathology result. There were no significant differences in haematological values. Hexane extract at doses of 100 mg/kg/bwt, 200 mg/kg/bwt, 300 mg/kg/bwt, 400 mg/kg/ bwt and 500 mg/kg/bwt demonstrated healing activity on indomethacin-induced gastric ulcer, with a similar or more effect to that of omeprazole at dose of 25 mg/kg/bwt. Conclusion: No adverse reaction was seen in all treatment groups, suggesting that Barringtonia asiatica hexane crude extract has a good safety profile in animal and ulcer induced.
Protein Phosphorylation in Cell Growth Regulation

Receptor and non-receptor tyrosine kinases protein tyrosine phosphatases in cell growth regulation role of JAK tyrosine in cytokine signal transduction mitogen-activated kinases and the control of cell growth role of the protein kinase C family in the regulation of gene expression phosphorylation of transcription factors and chromatin-associated proteins regulation of the NF-KE family of transcriptions factors by protein phosphorylation regulation of components in the translational machinery by protein phosphorylation structure and function of the interferon-induced protein kinase PKR and related enzymes protein kinase and phosphatases in cell cycle control.
Uncovering Deep Phylogenetic Signal in Plastid Genomes

Author(s): Lawrence, Travis Joseph | Advisor(s): Ardell, David H | Abstract: The overall aim of my dissertation is to show that a novel source of phylogenetic information from the plastid genome, the tRNA interaction network, coupled with machine-learning and distance-based methods, is capable of accurately reconstructing deep phylogenetic relationships. First, we review the history of the plastid genome as a source of phylogenetic information, discuss sources of systematic biases of plastid sequence data, and introduce the transfer RNA (tRNA) interaction network as a source of phylogenetic data.Second, I determine the phylogenetic origin of plastids withinthe Cyanobacteria tree of life (CyanoToL). Previous studies have strongly supported contradictory conclusions, with plastids branching either early or late within the CyanoToL. I begin by predicting structural features that determine the charging potential of a tRNA with its cognate amino acid, termed tRNA Class Informative Features (CIFs) for 113 Cyanobacterial genomes within eight Cyanobacterial clades. I show that predicted tRNA CIFs differ between Cyanobacterial clades in a phylogenetically informative way that can be exploited to accurately classify Cyanobacterial genomes using a machine-learning algorithm known as a multilayer perceptron (MLP), which we have named CYANO-MLP. I then use CYANO-MLP to test competing hypotheses of the origin of plastids by classifying 440 plastids genomes. I found support for the origin of plastids among a late-branching clade of starch-producing marine/freshwater diazotrophic cyanobacteria. Finally, I show that previously used phylogenetic models are unable to accommodate systematic biases possibly explaining conflicting hypotheses.Third, I use tRNA CIFs to determine the phylogenetic placement of gnetophytes, a small clade of plants, within the seed plant phylogeny. The location of gnetophytes has been contentious with phylogenomic studies supporting several relationships with cone-bearing seed plants (conifers). Here I use the Jensen-Shannon divergence to calculate a pairwise distance matrix between seed plant clades for plastid tRNA CIFs. Using standard distance-based phylogenetic algorithms I found support for gnetophytes as sister to conifers.Lastly, I describe the implementation of two software packages. The first is tsfm: tRNA structure function mapper, that provides methods for predicting tRNA CIFs. The second is a suite of tools modeled after GNU Textutils named, FAST: FAST Analysis of Sequences Toolbox, for processing of molecular sequence data on the command line.
Experimental evidence reveals impact of drought periods on dissolved organic matter quality and ecosystem metabolism in subalpine streams

Subalpine streams are predicted to experience lower summer discharge following climate change and water extractions. In this study, we aimed to understand how drought periods impact dissolved organic matter (DOM) processing and ecosystem metabolism of subalpine streams. We mimicked a gradient of drought conditions in stream‐side flumes and evaluated implications of drought on DOM composition, gross primary production, and ecosystem respiration. Our experiment demonstrated a production and release of DOM from biofilms and leaf litter decomposition at low discharges, increasing dissolved organic carbon concentrations in stream water by up to 50%. Absorbance and fluorescence properties suggested that the released DOM was labile for microbial degradation. Dissolved organic carbon mass balances revealed a high contribution of internal processes to the carbon budget during low flow conditions. The flumes with low discharge were transient sinks of atmospheric CO2 during the first 2 weeks of drought. After this autotrophic phase, the metabolic balance of these flumes turned heterotrophic, suggesting a nutrient limitation for primary production, while respiration remained high. Overall our experimental findings suggest that droughts in subalpine streams will enhance internal carbon cycling by transiently increasing primary production and more permanently respiration as the drought persists. We propose that the duration of a drought period combined with inorganic nutrient availability are key variables that determine if more carbon is respired in situ or exported downstream.
The skull of the carettochelyid turtle Anosteira pulchra from the Eocene (Uintan) of Wyoming and the carotid canal system of carettochelyid turtles

Abstract. Here we document the morphology of the only known skull of a carettochelyid turtle from North America. The specimen originates from the middle Eocene (early Uintan) Washakie Formation of Sweetwater County, Wyoming, and is referred to Anosteira pulchra based on temporal considerations. The skull of Anosteira pulchra broadly corresponds in its morphology to that of other carettochelyids but exhibits numerous differences that are related to it being more gracile. As a meaningful outgroup is lacking, it is not possible to determine if the gracile morphology seen in this taxon is apomorphic or plesiomorphic for the Anosteira–Allaeochelys clade. Anosteira pulchra and Carettochelys insculpta lack an ossified palatine canal. We conclude by reference to extant trionychids that the palatine (mandibular) canal is likely present but branches from the cerebral (pseudopalatine) canal following its exit from the sella turcica. As in trionychids, the vidian branch of the facial nerve (VII) of Anosteira pulchra and Carettochelys insculpta mostly traverses the palatine.
Reconciliation Between Economic Development and Sustainability: A Case Study in Vietnam

Sustainability has increasingly become an essential factor in economic development. Environmental pollution, climate change and natural resource exhaustion are currently serous challenges to sustainability development as well as human life. However, the reluctance of firms to respond to these issues is not uncommon. Reconciliation between economic development and sustainability is still a challenge for not only firms but also most countries worldwide, particularly developing countries. In this research, we employ a qualitative approach, using single case study method to examine the issue in the context of a developing country, Vietnam. Our findings show that the environmental disaster by the Formosa Ha Tinh Steel Corporation causes severely negative effects on the environment, economics and social life of local communities. The research also finds that corruptions and corporate unethical behaviours are among key hurdles to sustainability development in Vietnam. This study contributes to the existing literature on sustainability development by providing qualitative empirical evidence on the issue of reconciliation between economic development and sustainability in the context of a developing country. The study also identifies key hurdles to maintain a balance between economic development and environmental sustainability in a developing economy and recommends some possible solutions.
Tunnel‐dependent supercapacitance of MnO2: effects of crystal structure

A proportional relationship between the specific capacitance of MnO2 and the percentage of effective Mn centers that act as active sites in the Faradaic charge storage has been established on the basis of a tunnel structure–crystallization behavior correlation. A quantitative relationship between the effective Mn centers at the surfaces and in the tunnels can distinguish the specific capacitance values that arise from the adsorption/desorption and insertion/extraction processes, respectively, of different MnO2 crystallographic forms in the Faradaic charge storage. The different specific capacitance values between the MnO2 crystallographic forms are mainly attributed to the different effective utilizations of Mn centers in the size-limited tunnels. The present model demonstrates that increasing the percentage of effective Mn centers via decreasing the crystal size can facilitate obtaining MnO2-based electrode materials with higher specific capacitance values.
A cultural approach to wetlands restoration to assess its public acceptance

Ecological restoration (ER) of coastal wetlands is extremely important because they provide a huge variety of ecosystem services (ES), but they are the most degraded ecosystems in the world. However, coastal wetlands are usually located in largely modified and densely populated landscapes. Hence their restoration may conflict with cultural values. Therefore, considering the cultural dimension of ER is a way of increasing public acceptance of restoration projects. In this study, we assessed the public acceptance of a restoration project in a coastal wetland of Costa Brava (Spain). We combined the ES framework with a cultural approach, which is capable of considering interdisciplinarity, introducing barely assessed services like tranquility and facilitating further integration of the human dimension in the ES framework. We administered an open‐ended questionnaire to 232 visitors and the answers were submitted to a content analysis to get a post hoc classification of services and values. Our results show that visitors undervalue environmental values, while tranquility is the most commonly stated value. Moreover, place attachment is found to be the main driver to influence the perception of the ER. The study concluded that the project enjoys a high public acceptance. However, some disengagement exists between the goals of restoration and visitors’ perceptions, and this needs to be addressed. Sharing the decision‐making power with stakeholders and informing visitors about ES that are not easily perceived could be appropriate steps to take.
Is oxygen limitation in warming waters a valid mechanism to explain decreased body sizes in aquatic ectotherms?

Aim: The negative correlation between temperature and body size of ectothermic animals (broadly known as the temperature‐size rule or TSR) is a widely observed pattern, especially in aquatic organisms. Studies have claimed that the TSR arises due to decreased oxygen solubility and increasing metabolic costs at warmer temperatures, whereby oxygen supply to a large body becomes increasingly difficult. However, mixed empirical evidence has led to a controversy about the mechanisms affecting species’ size and performance under different temperatures. We review the main competing genetic, physiological and ecological explanations for the TSR and suggest a roadmap to move the field forward. Location: Global. Taxa: Aquatic ectotherms. Time period: 1980–present. Results: We show that current studies cannot discriminate among alternative hypotheses and none of the hypotheses can explain all TSR‐related observations. To resolve this impasse, we need experiments and field‐sampling programmes that specifically compare alternative mechanisms and formally consider energetics related to growth costs, oxygen supply and behaviour. We highlight the distinction between evolutionary and plastic mechanisms, and suggest that the oxygen limitation debate should separate processes operating on short, decadal and millennial time‐scales. Conclusions: Despite decades of research, we remain uncertain whether the TSR is an adaptive response to temperature‐related physiological (enzyme activity) or ecological changes (food, predation and other mortality), or a response to constraints operating at a cellular level (oxygen supply and associated costs). To make progress, ecologists, physiologists, modellers and geneticists should work together to develop a cross‐disciplinary research programme that integrates theory and data, explores time‐scales over which the TSR operates, and assesses limits to adaptation or plasticity. We identify four questions for such a programme. Answering these questions is crucial given the widespread impacts of climate change and reliance of management on models that are highly dependent on accurate representation of ecological and physiological responses to temperature.
Chain-growth versus step-growth polymerization in an aerosol photo-induced process

La ricerca mirava allo scopo di comprendere i fenomeni che governano la produzione di micro-particelle e nano-particelle polimeriche, destinate all'impiego nel settore farmaceutico, attraverso un processo di fotopolimerizzazione in aerosol. In particolare, sono stati analizzati i meccanismi di polimerizzazione radicalico acrilico e tiolenico per i quali si e cercato di produrre particelle piene, porose e a forma di capsula o a forma di caps. Oltre a cio, si e valutato l'effetto della composizione chimica della soluzione da nebulizzare sulla morfologia delle particelle ottenute. In entrambi, essa si e rivelata fortemente dipendente dalla scelta del co-solvente, sia per la capacita di solubilizzare i reagenti, sia per la sua tensione di vapore. Sono stati utilizzati etanolo, 1-propanolo e acetone per desumere conclusioni sui risultati. Alcuni parametri come il tempo di permanenza all'interno del reattore e la scelta del binomio di monomeri impiegati e risultata cruciale solo per il meccanismo tiolenico. La scelta del monomero acrilico e il rapporto monomero-solvente, invece, sono risultati decisivi per la produzione di particelle nanostrutturate con strutture complesse nel meccanismo radicalico acrilico. Nanoparticelle a forma di caps sono state ottenute con l'aggiunta di glicerolo alla soluzione tiolenica. Infine e stata studiata la possibilita di produrre strutture ibride tramite incorporazione in situ di particelle di argento nella matrice polimerica. L'esito e stato positivo con l'utilizzo di particelle di 50 nm nella matrice polimerica acrilica e negativo nei tentativi effettuati con il meccanismo tiolenico. La morfologia delle particelle e stata osservata con l'utilizzo di un microscopio a scansione elettronica (SEM) ed un microscopio elettronico a trasmissione (TEM).
ANTIMICROBIAL ACTIVITY OF CLEMENTINE PEEL ESSENTIAL OIL WITH ITS CYTOTOXIC AND IN VITRO WOUND HEALING POTENTIAL ON NIH-3T3 FIBROBLAST CELLS

Narenciye esansiyel yaglari cilt ve sac bakimi, uykusuzluk, sindirimin duzenlenmesi ve bagisiklik sisteminin gelistirilmesi gibi pek cok alanda kullanima sahiptir. Bu calisma, Turkiye’de yetistiriciligi yapilmakta olan bir mandalina turu olan klementin’in (Citrus clementina Hort. ex Tan) kabugundan elde edilen esansiyel yagin biyolojik aktivitelerinin belirlenmesi amaciyla planlanmistir. Klementin kabuk esansiyel yaginin (CPEO) antimikrobiyal aktivitesi E. coli, S. aureus ve bir maya turu olan C. albicans’a karsi disk difuzyon yontemi ile belirlenmistir. Sitotoksisitesi MTT kolorimetrik analizi ile NIH-3T3 fibroblast hucreleri kullanilarak tespit edilmistir. Ayrica stratch-yara iyilesme teknigi kullanilarak CPEO’nin fibroblast hucrelerinin gocu ve proliferasyonu uzerine etkinligi in vitro yara iyilesme aktivitesi olarak degerlendirilmistir. Sonuclara gore CPEO’nin kayda deger antimikrobiyal aktiviteye sahip oldugu gozlenmistir. En yuksek inhibisyon zonu C. albicans’a karsi 20.67±0.58 mm olarak olculmustur. Sitotoksik aktivite analizine gore IC50 degeri 52.50 µg/mL olarak belirlenmistir. CPEO icin IC50 degerinin altinda uygulanan dozlarda fibroblast hucreleri kontrol grubuna kiyasla daha hizli surede proliferasyon saglayarak yapay yaranin iyilesmesine yonelik yuksek hareket gostermistir. Mevcut calisma sonuclarina gore CPEO, patojenik mikroorganizmalara karsi sahip oldugu antimikrobiyal karakterin yani sira cilt uygulamalari ve yara iyilesmeye yonelik urunlerin gelistirilmesinde kullanilma potansiyeline sahiptir.
Databases for Antimicrobial Resistance Genes and Mobile Genetic Elements in Gut Microbiome

The human gut microbiota forms a large reservoir of antimicrobial resistance (AMR) genes. Also a number of these bacteria are endowed with metabolic potentials and added advantages which are often provided by mobile genetic elements (MGE). MGEs carry out extensive horizontal gene transfer (HGT) in gut and are believed to be agents of open source evolution. Regardless of their medical importance and biological significance, MGEs from the gut microbiome have not been methodically characterized. This research news scan highlights the Intestinal microbiome mobile element database (ImmeDB) associated with the collection, classification, and annotation of MGEs from gut microbiome using a novel “deletion-based” Split Read Insertion Detection (SRID) method. The database can help us screen already identified genomes for the valida-
EVALUATING THE EFFECT OF ISLAMIC FINANCING TO FINANCIAL DEVELOPMENT: EVIDENCE FROM OIC COUNTRIES

The development of Islamic finance is governed by Islamic laws (Shariah). The main principles that regulate all forms of transactions in Islamic banking activities include the prohibition of interest or usury (riba), the use of excessive risk (gharar), and gambling (maysir). The Islamic finance industry has become a prominent sector and is one of the fastest growing components of financial developments over the last decade in the global financial system. The availability of large numbers of Islamic finance products will increase significantly as there have been a growing demand throughout the world, especially in OIC participating countries. Hence, the objective of this study is to identify the important factors that enhances financial development in the selected OIC countries (Malaysia, Indonesia, Jordan, Kuwait, Saudi Arabia, Sudan and Yemen). Three indicators of financial development
Characterization of a respiratory burst oxidase homolog from Gracilariopsis lemaneiformis (Rhodophyta) during stress and phytohormone treatments

Abstract Plant respiratory burst oxidase homologs (rbohs), a source of reactive oxygen species (ROS), play a central role in the response to biotic and abiotic stresses in plants. Here, an rboh gene from the seaweed Gracilariopsis lemaneiformis (Glrboh) was characterized and analyzed in terms of its structure and changes in its expression profile in response to high salinity, high temperature and phytohormone treatments. The results show that high salinity and high temperature mostly induced Glrboh expression at the mRNA, protein and enzyme activity levels within 3–6 h, and the levels decreased thereafter, but there was an almost continuous decline in Glrboh mRNA during the 24 h following exposure to high temperature. Under heat stress, abscisic acid (ABA) dramatically enhanced the levels of Glrboh mRNA at 3 h and increased Glrboh protein expression and enzyme activity throughout most of the 24-h period. However, salicylic acid (SA) and methyl jasmonate (MJ) had only slight and varied effects on Glrboh expression. These results indicate that Glrboh is involved in heat and salt stress responses and that the phytohormone ABA is more closely related to ROS production in this alga than SA and MJ.
Object Detection System in Image Processing

An object detection system finds objects of the real world present either in a digital image or a video, where the object can belong to any class of objects namely humans, cars, etc. In order to detect an object in an image or a video the system needs to have a few components in order to complete the task of detecting an object, they are a model database, a feature detector, a hypothesiser and a hypothesiser verifier. This paper presents a review of the various techniques that are used to detect an object, localise an object, categorise an object, extract features, appearance information, and many more, in images and videos. The comments are drawn based on the studied literature and key issues are also identified relevant to the object detection. Information about the source codes and online datasets is provided to facilitate the new researcher in object detection area. An idea about the possible solution for the multi class object detection is also presented. This paper is suitable for the researchers who are the beginners in this domain.