Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of critical molecules involved in host-parasite interactions of Tritrichomonas foetus

27 THESIS ABSTRACT Trichomonads have attracted considerable attention over the years as parasites of human and veterinary importance. Unlike the human infecting parasite Trichomonas vaginalis, Tritrichomonas foetus can be found in a range of distantly related mammals. Initially identified as a commensal organism of the nasal cavity and digestive tract of pigs, T. foetus later became notorious as a parasite of high veterinary importance, parasitising the urogenital tract of cattle and thus contribute to infertility. Within the last decade T. foetus was also identified as the causative agent of large bowel diarrhoea in domestic cats. Current prevalence has seen feline trichomoniasis as a global veterinary problem and bovine trichomoniasis appears to be re-emerging as a serious disease burden in cattle. Although it is not unusual for a parasite to have a wide host range, the diverse tissue tropism, routes of transmission and pathogenicity of T. foetus isolates within different hosts is confounding. This in part, could be attributed to the limited knowledge of molecules governing T. foetus host-specificity and biological variation. Recent comparative genotypic and transcriptomic analysis of T. foetus have revealed a high degree of similarity exists between T. foetus isolates. However, they have been unable to define the dynamic molecules involved in driving this host-specificity. Quantitative proteomic analysis could address this and may shed light on the molecules governing T. foetus host-specificity. Therefore, this thesis aimed to provide an in-depth quantitative proteomic analysis of T. foetus baseline proteomes from three distinct hosts to enhance the understanding of T. foetus. To achieve this, experimental investigations were performed into aspects of parasite genotypic variation and virulence, all of which have generated quantitative proteomic data. Firstly, quantitative proteomic analysis using gel-based, two-dimensional gel electrophoresis (2DE) was undertaken using whole cell lysates from two parasitic bovine and feline T. foetus isolates. Both isolates exhibited largely similar proteomes with only 24 spots identified as having a four-fold or greater change. However, deeper analysis using 2DE zymography and protease-specific fluorogenic
CRISPR/Cas12a-assisted PCR tagging of mammalian genes

Here we describe a simple strategy for tagging of genes in mammalian cells. The method enables efficient creation of endogenously expressed protein fusions. Only PCR for the generation of a DNA fragment is required. This avoids the handling of RNAs, recombinant proteins or cloning of plasmids. The fragment, termed ‘PCR cassette’, is then transfected into cells along with a CRISPR/Cas12a helper plasmid and integrates into the target locus specified by sequences provided by the oligonucleotides used for PCR. The method is robust and works in all cell lines tested with tagging efficiency of up to 20% without selection, and up to 60% when selection markers are used.
Selection Internal Control over Financial Reporting Framework in the Republic of Indonesia using Analytic Hierarchy Process Approach

System of the internal control over financial reporting (ICOFR) on state finance management in the Republic of Indonesia had been designed using soft system methodology. ICOFR framework in the Republic of Indonesia was needed. Based on questionnaire, we found risk focus, applicability, harmony with PP No. 60/2018, can be applied in entity and transactional level, and can be applied IT environment as criteria. We found understandability, clarity of control components, and effectiveness assessment as sub criterion of criterion applicability and we found general control and application control as sub criterion of criterion â€˜can be applied in IT environmentâ€™. The Analytic Hierarchy Process (AHP) methodology areÂ used to choose best alternative. Calculations of the results by Expert Choice software indicated COSO ranked 1st, COBIT ranked 2rd, and CoCo ranked 3th. Â
A review of neurotransmitter mechanisms associated with visual cortical plasticity in animal models of deprivation amblyopia

A review of research literature concerning neurotransmitters involved in deprivation amblyopia was conducted. Stimulus deprivation amblyopia was induced in 6 kittens using opaque contact lens occlusion. The kittens were reared in the dark for 18 hours a day and wore the contact lenses, while exposed to room light, for six hours a day, five days a week from age 5 weeks to age 19 weeks. During this period of time, the kittens were also trained and tested for monocular acuities in the non-occluded eye. Visually evoked potentials were recorded from these kittens at the end of the occlusion period and suggested the presence of stimulus deprivation amblyopia.
Higher-level pattern features provide additional information to birds when recognizing and rejecting parasitic eggs

Despite a recent explosion of research on pattern recognition, in both neuroscience and computer vision, we lack a basic understanding of how most animals perceive and respond to patterns in the wild. Avian brood parasites and their hosts provide an ideal study system for investigating the mechanisms of pattern recognition. The cuckoo finch, Anomalospiza imberbis, and its host the tawny-flanked prinia, Prinia subflava, lay highly polymorphic eggs with a great deal of variation in colour and patterning, with the cuckoo finch capable of close egg mimicry. Behavioural experiments in Zambia have previously shown that prinias use colour and multiple ‘low-level’ (occurring in early stages of visual processing) pattern attributes, derived from spatial frequency analysis, when rejecting foreign eggs. Here, we explore the extent to which host birds might also use ‘higher-level’ pattern attributes, derived from a feature detection algorithm, to make rejection decisions. Using a SIFT-based pattern recognition algorithm, NaturePatternMatch, we show that hosts are more likely to reject a foreign egg if its higher-level pattern features—which capture information about the shape and orientation of markings—differ from those of the host eggs. A revised statistical model explains about 37% variance in egg rejection behaviour, and differences in colour, low-level and higher-level pattern features all predict rejection, accounting for 42, 44 and 14% of the explained variance, respectively. Thus, higher-level pattern features provide a small but measurable improvement to the original model and may be especially useful when colour and low-level pattern features provide hosts with little information. Understanding the relative importance of low- and higher-level pattern features is a valuable goal for future work on animal coloration, especially in the contexts of mimicry, camouflage and individual recognition. This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
Changes in Water Soluble Protein Profile of Antarctic Cyanobacterium Nostoc Commune under Temperature Downshift from 25° to 5 °C

Abstract The cyanobacterium Nostoc commune (Nostocales) is an isolate from the Schirmacher Oasis Antarctica. The cyanobacterium is psychrotropic in nature; and maintained in laboratory at 25 °C temperature, in unialgal form. Here, we studied the change in protein profile of water soluble proteins from exponentially growing N. commune upon downshift from its optimum growth temperature (25 °C) to a low temperature (5 °C). Experimental set up used to analyze the proteome were- a sudden shift to low temperature (i.e., cold shock), after short- (8 days) and long-term acclimation (7 weeks) to low temperature (5 °C). Cold-shock resulted in an increase in Low molecular weight proteins (LMWPs) with clouding of diffused proteins. Further increase in the duration of incubation period (short- and long-term acclimation) caused dissociation of proteins, indicated by NaCl (50–600mM) induced dissociation of proteins. That is, high molecular weight proteins (HMWPs) dissociated into LMWPs resulting in an increased number of protein bands. This was further confirmed by addition of LMWPs (≤10KDa) resulting in re-association of proteins into HMWPs. Hence, we report that the cold-induced synthesis of LMWPs (≤10kDa) is a strategy adopted by the N. commune to survive at low temperature of Antarctica.
Resting‐state functional connectivity modulates the BOLD activation induced by nucleus accumbens stimulation in the swine brain

While it is known that the clinical efficacy of deep brain stimulation (DBS) alleviates motor-related symptoms, cognitive and behavioral effects of DBS and its action mechanism on brain circuits are not clearly understood. By combining functional magnetic resonance imaging (fMRI) and DBS, we investigated the pattern of blood-oxygenation-level-dependent (BOLD) signal changes induced by stimulating the nucleus accumbens and how inter-regional resting-state functional connectivity is related with the stimulation DBS effect in a healthy swine model. We found that the pattern of stimulation-induced BOLD activation was diffused across multiple functional networks including the prefrontal, limbic, and thalamic regions, altering inter-regional functional connectivity after stimulation. Furthermore, our results showed that the strength of the DBS effect is closely related to the strength of inter-regional resting-state functional connectivity including stimulation locus and remote brain regions. Our results reveal the impact of nucleus accumbens stimulation on major functional networks, highlighting functional connectivity may mediate the modulation effect of DBS via large-scale brain networks.
A Wave Energy Research Centre in Albany, Australia

II. ABSTRACT This paper presents some of the research currently undertaken by the newly established Wave Energy Research Centre at the University of Western Australia to support Carnegie Clean Energy in deploying a 1.5MW grid connected wave energy converter in Torbay, Albany, Western Australia. This includes the modelling of the wave resources in Torbay, wave tank testing and hydrodynamic modelling to characterise and predict the motion of the wave energy converter and some aspects of geotechnical engineering to optimise the foundations of the device.
A Delay Sensitive Framework for Effective Healthcare using Machine Learning

This paper proposes a delay-sensitive framework for the Healthcare Industry that can effectively predict diseases at an early stage. The framework utilizes Machine Learning (ML) techniques to integrate the Internet of Things (IoT), Cloud Computing, and ML in the medical field. The primary objective is to reduce the delay on the user's end while using Smart Healthcare services and provide the quickest response to the patient. The proposed framework can contribute to the better and optimal integration of emerging technologies in the Healthcare sector. The methodology involves collecting data from various sources, using ML algorithms, preprocessing feature extraction, and model training. The major findings indicate that the proposed framework can effectively predict diseases early and improve the quality of healthcare services. The interpretations and implications of the study highlight the importance of integrating emerging technologies in the Healthcare sector to provide better healthcare services to patients.
A Proposed Model of Secure Academic Transcript Records with Blockchain Technology in Higher Education

: The higher education institution today is a concern to become an institution that gives birth to people who can compete in the current era. Stakeholders at the higher education institution will see how the data produced by graduates can be trusted and no data manipulation takes place at the higher education institution. Based on this problem, this article explains how higher education institutions use blockchain technology that is able to maintain data security and prevent data manipulation, especially in academic transcript ﬁles. Academic transcript records become an output from students after completing a semester or level of education at the higher education institution. In general, academic transcript records are used when students complete a study at a higher education institution as a document requirement for access to the company where they work. Thus academic transcript reports become important for companies to ﬁnd out if this student is competent in a certain area. In this case, accurate and valid data is certainly needed and the truth can be trusted. This qualitative research contributes to the higher education institution through a proposed blockchain technology model, especially in academic transcript records, so that the results of the proposed model ensure that data manipulation does not occur in data in academic transcript records. The results of this model will be used as design material for application design, so that the blockchain platform can be used in higher education institutions, especially when publishing valid academic transcript records that can be trusted with the data.
Mitochondrial phylogeny and biogeography of the genus Gobio (Teleostei: Cyprinidae) in Turkey

Species of the cyprinid genus Gobio Cuvier, 1816 are widely distributed in freshwater lakes and rivers in Turkey, which is a hotspot for freshwater fish diversity and endemism. The mitochondrial 16S, coxI and cytb genes were sequenced for 217 individuals representing 15 species of Gobio from Turkey. A total of 23 haplotypes were identified for each mitochondrial gene. The genetic distance matrices show that Turkish Gobio species are clustered into three groups (northwestern, central and northeastern Anatolia). Phylogenetic trees constructed with combined dataset by using maximum parsimony, maximum likelihood and Bayesian inference methods revealed that the Turkish Gobio species belongs to three well-supported groups in accordance with their geographic distribution: Group I comprises species found in Central Anatolia, Group II species ranging from eastern Thrace to western Anatolia (northwestern Group) and Group III contains only one species from Western Transcaucasia (northeastern Group). The estimated divergence times between the three Gobio groups, calculated using a conventional 1% rate of mutation for a fish mitochondrial cytb gene per million years, coincide with the late Miocene period in which the tectonic uplift of Anatolia and global climate fluctuations occurred. The relatively low genetic distance between Gobio species in the Turkish Lake District indicate that they are not good species.
The stem rust fungus Puccinia graminis f . sp . tritici induces waves of small RNAs with opposing 1 profiles during wheat infection 2

19 The fungus Puccinia graminis f. sp. tritici (Pgt) causes devastating stem rust disease on wheat. Infection 20 occurs when rust spores germinate on the leaf surface and subsequently, specialized infection structures called 21 haustoria form inside host cells followed by sporulation. Small RNA and transcriptome sequencing during 22 Pgt-wheat infection reveals that the Pgt RNA interference (RNAi) machinery has functionally diversified. A 23 number of Pgt RNAi genes are strongly up-regulated during late infection compared to the start of infection. 24 This coincides with the production of two distinct Pgt small RNA (sRNA) profiles. At the start of infection, 25 Pgt induces predominantly 21 nt sRNAs with a 5‘ uracil derived from genes. In contrast, during late infection 26 Pgt induces 22 nt sRNAs with a 5‘ adenine derived from repeats. Strikingly, over 85% of Pgt sRNAs are 27 differentially expressed during infection, compared to only 4% of wheat sRNAs. Using chromatin 28 conformation capture assay data (Hi-C), we define Pgt centromeres and show that sRNAs up-regulated during 29 late infection are derived from those repeat-rich, gene-poor and transcriptionally silent centromeric regions. 30 We conclude that the Pgt RNAi machinery is highly regulated, resulting in differential accumulation of sRNA 31 types throughout the infection cycle. Such tight temporal control of the RNAi machinery has thus far not been 32 observed in fungi and might ensure genome stability during sporulation in rust fungi. 33
Music Therapy as Treatment of Negative Symptoms for Adult Patients Diagnosed with Schizophrenia—Study Protocol for a Randomized, Controlled and Blinded Study

Background: Three Cochrane reviews show that music therapy has a positive effect on schizophrenia concerning general functioning and positive/negative symptoms. This study aims to replicate these results in the Danish health system, a requirement for recommendation in guidelines from the Danish National Board of Health. Methods: The study is a randomized, controlled multi-site study, with a blinded design, aiming to include 90 participants who are 18–65 years in age, diagnosed according to ICD-10 with a schizophrenia diagnosis. The participants are randomized to one of two different music therapy activities for 25 weekly sessions. The study interventions are added to standard care. Outcome measures are rated at baseline, after 15 sessions and post therapy. A qualitative interview is performed as a one month follow up at the end of study. The primary intended outcome is a reduction in negative symptoms. The secondary intended outcome is progression in quality of life, alliance and psychosocial functioning. Results: As this study is still running, the results are not yet available. Conclusion: The study will investigate the direct effects of music therapy on negative symptoms as part of schizophrenia in a blinded, randomized trial. If proven effective, music therapy can be added to the small treatment armamentarium of effective therapies for negative symptoms in patients with schizophrenia.
Underwater Caging and Capture for Autonomous Underwater Vehicles

In this paper, we consider the problem of caging and eventual capture of an underwater entity using multiple Autonomous Underwater Vehicles (AUVs) in a 3D water volume We solve this problem both with and without taking bathymetry into account. Our proposed algorithm for range-limited sensing in 3D environments captures a finite-speed entity based on sparse and irregular observations. After an isolated initial sighting of the entity, the uncertainty of its whereabouts grows while deployment of the AUV system is underway. To contain the entity, an initial cage, or barrier of sensing footprints, is created around the initial sighting, using islands and other terrain as part of the cage if available. After the initial cage is established, the system waits for a second sighting, and the possible opportunity to create a smaller, shrinkable cage. This process continues until at some point it is possible to create this smaller cage, resulting in capture, meaning the entity is sensed directly and continuously. We present a set of algorithms for addressing the scenario above, and illustrate their performance on a set of examples. The proposed algorithm is a combination of solutions to the min-cut problem, the set cover problem, the linear bottleneck assignment problem and the Thomson problem.
Validation of Abbott Diagnostics turbidimetric cystatin C assay and enzymatic creatinine assay using the Architect c8000 analyzer

Objective: Estimation of glomerular filtration rate (GFR) is an important tool in the diagnosis and management of chronic kidney disease. Today creatinine is the most frequently used marker for kidney function though several studies indicate that cystatin C is a superior marker. The purpose of this study was to validate Abbott Diagnostics turbidimetric cystatin C assay and enzymatic creatinine assay. Methods: The validation was performed by studies of CV for the two methods and correlations between the two and other available methods for assessing GFR. The stability of cystatin C at room temperature was also evaluated. Results: Both methods showed good precision. The Abbott cystatin C assay generally gave lower values and thereby higher estimated GFRs than the correlated Gentian method. The Abbott enzymatic creatinine assay gave higher values than the correlated Jaffe method. Those results are generally unexpected, but in this study the cause is an automatically applied negative intercept used together with the Jaffe method. Cystatin C showed high stability when stored at room temperature. Conclusions: Estimated GFRs tend to differ depending on the choice of method for analyzing cystatin C or creatinine and this study gives an overview of the range of variation. The study also enlightens the need for an international calibrator for the cystatin C methods presented by different manufacturers.
Flexible, fast and selective genetic manipulation of the vertebrate CNS with misPiggy

In utero electroporation is increasingly used for manipulation of gene expression in the mammalian central nervous system. Here we created a transposon-based single plasmid system, that allows long-term conditional loss- and gain-of-function experiments across major CNS cell types. The system is widely applicable across species, allowing fast, flexible and cheap cell manipulation in previously non-transgenic species.
Leptin gene polymorphism of Ongole Grade cattle based on single nucleotide polymorphism

Point mutation on exon 2 of leptin gene, which changes amino acid encoding from Arginine to Cysteine, may alters the physiological function of the leptin hormone. This study aimed to identify leptin gene polymorphism of Ongole Grade (OG) cattle based on Single Nucleotide Polymorphism (SNP). The DNA sample was taken from 48 head of OG cattle at Balai Pengembangan Perbibitan Ternak Sapi Potong(BPPT SP) Cijeungjing West Java, which was isolated from white blood cell using the high salt method. Amplification of DNA was done by Polymerase Chain Reaction (PCR), followed by direct sequencing to obtain nucleotide sequence. The SNP analysis was carried out from alignment of sequencing result using Bioedit and MEGA 5.2 program. The results indicated in exon 2 leptin gene of OG cattle there was one synonymous SNPs that did not changeamino acids Serine encoding on g.1025T >C/S17S, while two non synonymous SNPaltered amino acids encoding, those were g.1047C> T /R25C and g.1048G>A/R25H. Those mutations changed amino acids encoding from Arginine to Cysteine and Arginine to Histidine respectively.In OG cattle, the frequency of A allele (44.8%) was higher than C allele (33.3%) and T allele (21.9%). Six genotypes were also identified, i.e. AA (41.7%), CC (20.8%), CT (20.8%), CA(4.2%), TT (10.4%) and TA (2.1 %). Heterozigosity of OG cattle based on leptin gene was 0.65 that was a high category. The A allele was a specific allele on Indonesian local cattle.
Synthesis of a 33‐yr series of whole‐lake experiments: Effects of nutrients, grazers, and precipitation‐driven water color on chlorophyll

We conducted a 33‐yr series of whole‐lake experiments to measure ecosystem responses to food web structure and nutrient load, compare aquatic and terrestrial carbon flows to consumers, and evaluate indicators of ecosystem resilience. These manipulations showed that chlorophyll responded to nutrient loading and to grazing controlled by a trophic cascade. In this article, we synthesized experimental results using a new analysis of heretofore unrecognized variation in water color, measured as light absorbance at 440 nm. Long‐term data revealed fluctuations in precipitation that drive water color variation. We compared effects of nutrient loading, zooplankton biomass, zooplankton body size, and water color on chlorophyll. Water color was an important factor in the chlorophyll response. This driver of the chlorophyll response to manipulation was not resolved until decades of data were available. A long‐term context enriched insights from ecosystem experiments and exemplified the complementarity of experimental and long‐term approaches in limnology.