Miracle-dz/UniFAR-FTUs huggingface dataset:
Determination of Dynamical Conservation in Human Cyclophilin Isoforms

Among the peptidyl prolyl isomerases, the Cyclophilin family of proteins has been linked to various cellular activities such as regulation of homeostasis, mitochondrial permeability, and cell death. Their functionality spans throughout the cell and throughout all cell types as different isoforms. Previous studies done on Cyclophilin A revealed an interesting contact ensemble when bound to a substrate. Because of the similarity of CypA to its homologues, it is believed that they too will exhibit the same contact dynamics. We have defined the dynamics of cyclophilin isoforms through Molecular Dynamics simulations and determined their contact dynamics, characterizing their contact ensembles, and their relative dynamical conservation to each other. INDEX WORDS: Cyclophilin isoforms, Cis-trans isomerization, Peptidyl-prolyl cis-trans isomerase, Contact Dynamics, Dynamical conservation, Dynamical Conservation Index DETERMINATION OF DYNAMICAL CONSERVATION IN HUMAN CYCLOPHILIN ISOFORMS
POTENTIAL CHEMOPREVENTIVE AGENT: STUDY OF APOPTOSIS IN THE EXTRACTS OF SPONGE-ASSOCIATED FUNGI FROM YOGYAKARTA AGAINST CERVICAL CANCER HeLa CELL LINE

Background: Cervical cancer is one of the leading-cancers affecting women. Cancer drugs that do not originate from natural ingredient, chemotherapy drugs, have side and resistant effects. Thus study about the natural products treating cancer cells is needed. Secondary metabolites isolated from sponge-associated fungi are expected to have a potency to fight cancer cells. In addition, the production of anticancer compounds from microorganisms has several advantages, including rapid growth and can be manipulated to increase productivity. The isolation and testing cytotoxicity against 3 fungal isolates from Yogyakarta have been done on the previous research. All three isolates have a potential candidate as anticancer drug. Aims: The purpose of this advanced study was studying bioactive compounds induced apoptosis pathway of sponge-associated fungi against cervical cancer HeLa cells. Methods: This study has been carried out for approximately 5 months. The method conducted in this research including the sponge cultivation (covers growth and isolation of secondary metabolites), the mycelium extraction of fungi, the cytotoxicity assay against HeLa cells using MTT Assay and Apoptosis Staining was to see the induction of apoptosis pathway. Results: Based on the research showed that ethyl acetate extract from mycelium is 0.22 grams. The cytotoxicity assay from mycelium extract showed IC50 value of 164 μg/mL against HeLa cell line. Conclusion: The findings is carrying to a possibility to develop the extracts of sponge-associated fungi as candidate of anti-cancer compound. By apoptosis staining, showed the cells coloured green are still alive, and cells undergoing apoptosis have nucleus that appears orange to red. We assuming that the apoptosis was caused by the possibility of peptide compounds that induce apoptosis through the mitochondrial pathway, by increasing the activity of the protein expression of apoptosis, which are Bcl-2 and Bcl-xl.
Characterization of kerogens by matrix‐assisted laser desorption ionization mass spectroscopy

Two kerogen samples from shales of different geological age, selected from each of Types I, II and III, have been characterized by matrix-assisted laser desorption ionization mass spectroscopy (MALDI-MS). A Kratos Kompact MALDI III time-of-flight mass spectrometer equipped with a nitrogen laser operated at 337 nm was used on samples mounted in a matrix of sinapinic acid. The spectrometer was used in linear mode with a mass range up to 270 000 u and an ion extraction voltage of 20 kV. Individual spectra from 50 laser shots at low laser fluence were summed for each spectrum. The present study is a first attempt at characterizing kerogens by MALDI-MS. At low mass (200–500 u) families of peaks consisting of overlapping homologous series of apparently polar compounds have been observed: these peaks appear to be distinct from those due to the matrix material. In higher mass regions of the spectra, continua of masses extending from 1000 u up to around 10 000 u were observed; ions at higher masses were separated to baseline up to masses of 50 000 u. Evidence was found for a relationship between the minimum laser power sufficient for activating the MALDI-ionization process and the geological age of the kerogens; the laser power decreased as the geological age increased. In the case of one kerogen, a high laser fluence was used to generate molecular ions up to the detection limit of the mass spectrometer, in excess of 260 000 u. This paper presents results from a preliminary study of kerogens which requires an in-depth examination of the desorption process in complex mixtures.
Isospora machadoae sp. nov. (Protozoa: Apicomplexa: Eimeriidae), a new coccidian species from white-necked thrushes Turdus albicolis (Passeriformes: Turdidae) of South America

A new coccidian species parasitizing white-necked thrushes Turdus albicollis Vieillot, 1818 is described from the Parque Nacional do Itatiaia, in Southeastern Brazil. Isospora machadoae sp. nov. has oocysts that are sub-spherical, 22.2 × 21.2 μm, with bilayered wall, ~1.3 μm thick. Outer layer is rough with micropyle and micropyle cap. Oocyst residuum is absent, but one or two polar granules are present. Sporocysts are ellipsoidal, 13.3 × 9.7 μm. The Stieda body is flattened to half-moon-shaped and substieda body rounded. Sporocyst residuum is present, composed of scattered spherules of different sizes. Sporozoites are vermiform with a refractile body and a nucleus. These parasitized thrushes had no apparent clinical signs of coccidiosis or high densities of oocysts in feces. This condition may be associated with a specific low pathogenicity of I. machadoae sp. nov. and/or with the conserved habitat of these birds, which ensures the ecological niches and thus the immunocompetence to wildlife.
The 13C content of the orchid Epipactis palustris (L.) Crantz responds to light as in autotrophic plants

Abstract Most temperate green orchids form mycorrhizae with rhizoctonias fungi and are considered autotrophic. Some orchids, however, associate with fungi that also form ectomycorrhizae with surrounding trees and derive part of their carbon from these fungi. This evolutionarily derived condition, called mixotrophy, is characterized by natural 13C enrichment and high N content. Some orchid genera display both syndromes depending on species. Here, we further document the isotopic features of a rhizoctonias-associated species, Epipactis palustris, in a genus otherwise encompassing many mixotrophic orchids. First, E. palustris in two wetland sites from Northern Europe displayed similar to slightly-depleted 13C abundance and identical N content as compared with surrounding autotrophic plants, confirming published results on this species. Second, some individuals growing in darker conditions (63% reduced irradiation) revealed a decrease of 13C abundance as expected (and observed at the same place) for autotrophic plants. The latter result expands previous observations on other rhizoctonias-associated orchid species. We discuss our results in relationship with the current views of the two nutritional syndromes of green orchids (especially, with the doubts on autotrophy of rhizoctonias-associated species) and in the framework of the phylogeny of Epipactis that evolved secondarily mixotrophy. The latter observation entails that the tribe Neottieae repeatedly evolved mixotrophy.
Canadian goldenrod residues and extracts inhibit the growth of Streptomyces scabiei, the causal agent of potato common scab

Abstract Common scab is one of the most important diseases affecting potato crops worldwide. Using fresh residues and/or bio-products of Canadian goldenrod (Solidago canadensis) may offer an alternative to harmful conventional fumigants. In this study, we aimed to: (i) conduct a preliminary investigation of the utilization of S. canadensis to reduce common scab severity (Experiment 1), and (ii) determine the allopathic potentials of S. canadensis extracts on Streptomyces scabiei (also known as S. scabies), the most important soil pathogen responsible for causing common scab in North America (Experiment 2). Compared with control plants, preliminary results showed that adding 1.2 kg of fresh S. canadensis residue per m2 reduced scab severity by about 45% (Experiment 1). Furthermore, hexane and dichloromethane extracts of S. canadensis, at a concentration of 200 µg·mL−1, inhibited the growth of S. scabiei by about 97% (Experiment 2). These results were comparable with those using tetracycline (2.5 µg·mL−1), a known inhibitor of S. scabiei. Both experiments suggested that S. canadensis may represent a new approach for controlling potato common scab. More studies are required to better understand the mechanisms involved in S. canadensis induced reduction of common scab in order to standardize the approaches.
Multi-Level Clustering-Based Outlier's Detection (MCOD) Using Self-Organizing Maps

Outlier detection is critical in many business applications, as it recognizes unusual behaviours to prevent losses and optimize revenue. For example, illegitimate online transactions can be detected based on its pattern with outlier detection. The performance of existing outlier detection methods is limited by the pattern/behaviour of the dataset; these methods may not perform well without prior knowledge of the dataset. This paper proposes a multi-level outlier detection algorithm (MCOD) that uses multi-level unsupervised learning to cluster the data and discover outliers. The proposed detection method is tested on datasets in different fields with different sizes and dimensions. Experimental analysis has shown that the proposed MCOD algorithm has the ability to improving the outlier detection rate, as compared to the traditional anomaly detection methods. Enterprises and organizations can adopt the proposed MCOD algorithm to ensure a sustainable and efficient detection of frauds/outliers to increase profitability (and/or) to enhance business outcomes.
Artificial Intelligence Enabled Routing in Software Defined Networking

Software defined networking (SDN) is an emerging networking architecture that separates the control plane from the data plane and moves network management to a central point, called the controller. The controller is responsible for preparing the flow tables of each switch in the data plane. Although dynamic routing can perform rerouting in case of congestion by periodically monitoring the status of each data flow, problems concerning a suitable monitoring period duration and lack of learning ability from past experiences to avoid similar but ineffective route decisions remain unsolved. This paper presents an artificial intelligence enabled routing (AIER) mechanism with congestion avoidance in SDN, which can not only alleviate the impact of monitoring periods with dynamic routing, but also provide learning ability and superior route decisions by introducing artificial intelligence (AI) technology. We evaluate the performance of the proposed AIER mechanism on the Mininet simulator by installing three additional modules, namely, topology discovery, monitoring period, and an artificial neural network, in the control plane. The effectiveness and superiority of our proposed AIER mechanism are demonstrated by performance metrics, including average throughput, packet loss ratio, and packet delay versus data rate for different monitoring periods in the system.
Energy-aware Aperiodic Task Servers for Firm Real-time Energy harvesting Systems

This paper proposes new scheduling approaches for servicing aperiodic tasks in a real-time system powered by renewable energy. We show that, the arriving aperiodics, if serviced naively, could cause the system to run out of power. We describe how to adjust the classical BG (Background Server) and TBS (Total Bandwidth Server) so as to work together with two energy-aware real-time schedulers, namely Green-RTO and Green-BWP. Their objective is threefold: (i) to guarantee a prespecified Quality of Service (QoS) level - measured in terms of success deadline ratio - for the periodic tasks, (ii) to minimize the response time of the aperiodic tasks, and (iii) to achieve perpetual energy autonomy for the whole system. We describe the results of both theoretical and experimental studies in order to bring to light the effectiveness of these aperiodic task servers which are specifically suited to firm real-time energy harvesting systems.
Einkorn (Triticum monococcum ssp. monococcum) in vitro propagation sterilization protocol

Einkorn is one of the oldest and important wheat species because of its increasing economic value, agronomical technical properties, and health and sanitary effects. Therefore, a faster tissue culture production protocol which may ensure a fast einkorn production is desired. The tissue culture process first requires an efficient sterilization technique of the explant to eliminate contamination factors in this hulled species. In this study, we, thus, aimed to determine the effective einkorn sterilization process for the removal of contaminating microorganisms without the loss of germination capacity and viability. We tested 22 following sterilant combinations with different concentration and exposure time: Ethanol, Commercial Bleach, Tween 20, Mercury (II) Chloride, and Sterile Distilled Water. On the other hand, obtained the data were analyzed by one-way ANOVA and Duncan test, where p≤0.05 was accepted significant. Forty percent commercial bleach which were applied fifteen minutes eliminated all microorganisms with a 92.6% seed germination. The second-best technique was one minute exposure of 70% ethanol which were followed by 10 minutes exposure of 20% commercial bleach. This assured up to 89% germination and no contamination. The worst results came from the mercury (II) chloride with 0% contamination and ≤ 25% germination rate. Mercury (II) Chloride was both highly toxic on the seeds and reduced the contamination. Commercial Bleach and Ethanol Chemicals were less toxic while providing an acceptable sterilization.
Participatory on - Farm Evaluation and Demonstration of Improved Forage Species under Rain Fed Condition in Hamer Woreda of South Omo Zone

Participatory field experiment was conducted at Dimeka zuriya peasant associations of Hamer woreda of South Omo zone in the 2014 main cropping season at on farm condition under rain fed using the improved legume forage species to identify the adaptable and high biomass yielding forage species. The field experiment was laid out in a randomized complete block design (RCBD) with three replications where trial agro pastoralists farm were considered as replications. The improved legume forage species tested were Lablab purpureus, Lablab intoritum, and Vigna unguiculata. Each improved legume species was planted in a single plot area of 3 m x 4m. The average fresh biomass yield (FBY) and dry matter yield (DMY) of the tested species were 20 tone/ha, 14.84 tone/ha and 12 tone/ha and 7.2 tone /ha, 4.5 tone/ha and 6.8 tone /ha for Labalab purpureus, Lablab intoritum and Vigna unguiculata.
Massively parallel single cell lineage tracing using CRISPR/Cas9 induced genetic scars

A key goal of developmental biology is to understand how a single cell transforms into a full-grown organism consisting of many different cell types. Single-cell RNA-sequencing (scRNA-seq) has become a widely-used method due to its ability to identify all cell types in a tissue or organ in a systematic manner 1–3. However, a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here, we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses, LINNAEUS (LINeage tracing by Nuclease-Activated Editing of Ubiquitous Sequences) can be used as a systematic approach for identifying the lineage origin of novel cell types, or of known cell types under different conditions.
Analysis of phenolic compounds in Carica papaya, Zingiber officinale, Ipomoea batatas and Myrothamnus flabellifolius using RP-HPLC-UV/VIS-DAD, and in vitro evaluation of antifungal activity on plant pathogenic fungi of economic importance

iv ACKNOWLEDGEMENTS . v DEDICATION. vi LIST OF TABLES . xiii LIST OF FIGURES . xiv LIST OF APPENDICES . xvi CHAPTER 1: INTRODUCTION . 1 1.1 Background of the Study . 1 1.2 Statement of the Problem . 3 1.3 Justification of the study . 3 1.4 Main Objective . 4 1.5 Specific Objectives . 5 1.6 Research Hypotheses. 5 CHAPTER 2: LITERATURE REVIEW . 6 2.
Subjective well-being among women with disabilities

Women with disabilities are individuals who have double vulnerabilities. These vulnerabilities are arguably resulting from their condition as disabled persons and their status as a woman. Both women with innate disabilities factors and accident factors have a similarly negative view of their condition. This study aimed to describe subjective well-being in women with disabilities. The research method used was qualitative phenomenology. The data was obtained through semi-structured interviews. This study included six women with disabilities aged between 20 to 30 years who lived in Yogyakarta. The data from interviews were analyzed with thematic analysis. The results showed that subjective well-being in women with disabilities was influenced by cognitive component (life satisfaction), which was indicated by self-acceptance, positive social relations, and perceived gratitude. Besides, the affective component also played a role. This component included positive affect, which was indicated by a sense of attention that the participant received, a feeling of excitement, pleasure, and a feeling of pride. Negative affect was indicated by feelings of sadness because of past negative relationships and feelings of disappointment.
Porous Texture of CuO Prepared from Copper Oxalate Precursor

The porous texture of CuO obtained from CuC2O4 • 0.5H2O as a precursor, as well as the interconnection between the texture of the initial oxalate and that of the copper oxide obtained, has been studied by physisorption, XRD, XPS and SEM methods. The dimensions of the particle aggregates and the crystalline particles were altered as a consequence of the thermal decomposition of CuC2O4 • 0.5H2O to CuO, and this led to an increase of ca. 1.5-times in the specific surface of the CuO obtained relative to that of the initial substance. The comparatively non-uniform sizes of the intra-aggregate mesopores in CuC2O4 • 0.5H2O were transformed into considerably smaller intra-aggregate mesopores in CuO. A finite increase in the volume of the intra-crystallite pores in CuO was also observed, although this did not change the average size of the intra-crystallite pores in the oxide obtained nor the character of the pore-size distribution with respect to the starting material. In addition, as a result of the thermal decomposition of CuC2O4 • 0.5H2O, the mesoporosity of the prepared oxide also developed. However, the CuO component retained the textural type characteristic of the initial CuC2O4 • 0.5H2O.
Linking species thermal tolerance to elevational range shifts in upland dung beetles

Climate warming has been proposed as the main cause of the recent range shifts seen in many species. Although species’ thermal tolerances are thought to play a key role in determining responses to climate change, especially in ectotherms, empirical evidence is still limited. We investigate the connection between species’ thermal tolerances, elevational range and shifts in the lower elevational limit of dung beetle species (Coleoptera, Aphodiidea) in an upland region in the northwest of England. We measured thermal tolerances in the laboratory, and used current and historical distribution data to test specific hypotheses about the area’s three dominant species, particularly the species most likely to suffer from warming: Agollinus lapponum. We found marked differences between species in their minimum and maximum thermal tolerance and in their elevational range and patterns of abundance. Overall, differences in thermal limits among species matched the abundance patterns along the elevation gradient expected if distributions were constrained by climate. A. lapponum abundance increased with elevation and this species showed lower maximum and minimum thermal limits than Acrossus depressus, for which abundance declined with elevation. Consistent with lower tolerance to high temperature, we recorded an uphill retreat of the low elevation limit of A. lapponum (177 m over 57 years) in line with the increase in summer temperature observed in the region over the same period. Moreover, this species has been replaced at low and mid-elevations by the other two warm-tolerant species (A. depressus and Agrilinus ater). Our results provide empirical evidence that species’ thermal tolerance constrains elevational ranges and contributes to explain the observed responses to climate warming. A mechanistic understanding of how climate change directly affects species, such as the one presented here, will provide a robust base to inform predictions of how individual species and whole assemblages may change in the future.
William A. F. Browne: Earliest Documented Use of Rehabilitative Art in Great Britain

Abstract Art therapy is a recognized primary or adjunctive treatment modality that traces its modern roots to the mid-twentieth century. However, art therapy has its origins, at least, in the 1840s. William A. F. Browne, the first medical superintendent of Crichton Royal Institution in Dumfries, Scotland, in 1839, was a reformer. He was part of a larger movement known as moral treatment which advocated the elimination of restraints and fear as methods of control of patients, treating patients humanely and with respect, and the introduction of a multitude of therapeutic activities, including artistic endeavors. Browne’s efforts stand apart from others in that he encouraged art as a rehabilitative activity, even for non-artists.
Identification of resistance to Aspergillus flavus infection in cotton germplasm

ABSTRACT Natural resistance in cottonseed to Aspergillus flavus infection has not been explored to date. A green fluorescent protein (GFP) expressing A. flavus strain was used to assess the resistance of seed from 35 cotton varieties from Gossypium arboreum, G. barbadense, and G. hirsutum. Mature cotyledons devoid of seed coat were wounded, inoculated, and assessed for innate resistance to A. flavus infection. Of the initial 35 varieties tested, we observed a range of resistance to infection in representatives of all three species. A subset of 15 representatives was further analyzed. Within this group, G. arboreum cultivar A2 186 and G. hirsutum cultivar SA 1582 were most resistant to fungal infection. The most susceptible cultivar in this group was G. hirsutum SA 1595. The remaining 12 representatives tested in the secondary screen (3 G. arboreum, 3 G. barbadense, and 6 G. hirsutum lines) exhibited intermediate resistance. We did not observe any relationship between species and resistance. Within each species, there was a range of responses to fungal infection. Future studies using this methodology to screen additional diploid and tetraploid cotton lines may enable us to identify naturally resistant germplasm that can be used to develop cotton with enhanced resistance to fungal infection.