Miracle-dz/UniFAR-FTUs huggingface dataset:
Developments in bridging education for Maori

Maori mainstream education is at crisis point; a situation reflected in recent figures showing that 35 per cent of Maori leave school without formal qualifications. The presenter, who works in the area of bridging education for under-qualified students wanting to move into tertiary study, believes Maori bridging programmes have a vital role to play in helping to solve this crisis. In examining current bridging education pedagogy and relating it to pedagogical theory and practice, it is concluded that mainstream bridging programmes do not cater for Maori needs and the development of initiatives intended to bridge this gap are discussed.
Analisis Hambatan Perkembangan Stadium Plasmodium Falciparum Terhadap Pemberian Ekstrak Daun Salam Badak (Acmena Acuminatissima) In Vitro

Background: The urgency generated by drug-resistant strains of malaria parasites has accelerated the need to find a new anti-malarial drug. Recent studies have shown that 80% ethanol extract Acmena acuminatissima has suitable antimalarial activities. Aim: To analyze the inhibitory effect of A. acuminatissima extract at the developmental stage of P. falciparum in infected erythrocytes in vitro. Methods: the synchronized culture of P. falciparum was incubated along with A. acuminatissima extract, and compared with negative controls. The effect on parasite growth was determined by observing the level of parasitemia and accumulation of various infective stages seen on thin blood smears after the incubation period of 12, 24, 36, and 48 hours using a light microscope with 1000 times magnification. Results: Within 48 hours of observation the difference was mainly in the proportion of ring-stage which was 2.75% in culture with the test compound and 41.41% in the negative control which showed that ethanol extract of A. acuminatissima inhibited the growth of parasites at the schizont stage into the ring stage. In trophozoite and schizonts stages of culture with test compounds, enlargement of digestive vacuole and vesiculation is obtained. Conclusion: A. acuminatissima inhibits the development of intraerythrocyt parasites at the schizonts stage and induced morphological changes.
Psychological distress increases needle sharing among cocaine users: Results from the COSMO study

Objective: Cocaine use and mental health disorders have both been separately identified as risk factors for blood borne virus infection. However, the contribution of specific underlying aspects of mental health to risks is not well documented. The aim of this study was to examine the association between psychological distress and risk behaviors for HIV and Hepatitis C infection among cocaine users. Methods: Individuals who either smoked or injected cocaine were recruited in community-based and addiction treatment programs located in downtown Montreal. Participants were asked to complete an interviewer-administered questionnaire assessing psychological distress based on the Kessler scale (K10). Three-month risk behaviors outcomes included drug injection material sharing (needle, dilution water, cooker, filters, backloading, frontloading or wash), and smoking equipment sharing. Socio-demographic data, severity of cocaine dependence and other substances use information were also collected. Statistical analyses were conducted using logistic regression. Results: Severe psychological distress was reported by 202 (34.3%) out of 589 participants (86.2% male; 76.6% ≥ 30y.o.). The prevalence of sharing was: 14.8% for needles, 24.9% for other injection equipment (378 injectors) and 68.3% for smoking material (508 smokers). Multivariate analysis showed that injectors with severe psychological distress were more likely to report needle sharing (Adjusted Odds Ratio (AOR): 2.1, 95% CI: 1.1-3.8). No significant association was found between K10 score and sharing of other paraphernalia. Conclusion: Severe psychological distress increases the risk of needle sharing, a major risk factor for HIV and HCV infection, but not sharing of other paraphernalia. These results suggest differential psychological mechanisms according to sharing practices. They also support the importance of screening for psychological distress in order to implement adequate preventive interventions aimed at cocaine users.
Generation of non-integrated iPSCs from achondroplasia patient skin and urine and gene correction in them using CRISPR-Cas9

Achondroplasia (ACH) is the most common genetic form of dwarfism and belong to dominant monogenetic disorder (MGD) caused by a mutation in the transmembrane region of fibroblast growth factor receptor 3 (FGFR3). Like many other MGDs, there are no effective therapeutic methods for ACH even though the cause of the mutation has been found. With the rapid development of stem cell biology and gene-editing technology, the research of ACH is not only important, but also provides theoretical and experimental basis for the investigation of other MGDs. In this study, we first acquired three different tissue samples from 3 ACH patients to culture somatic cells, including the most commonly used skin, the most easily available urine and large amount of acquired adipose tissue that can produce multipotent mesenchymal stem cells (AD-MSCs) with chondrocyte differentiation ability. We found that, like skin cells, urine cells were also very efficiently reprogrammed into iPSCs, which may provide a new donor cells for stem cell research of ACH. However, AD-MSCs cannot be reprogrammed into iPSCs. Given ACH is a chondrocyte generation disorder caused by FGFR3 mutation, our results suggested that perhaps the point mutation affected the reprogramming ability of AD-MSCs. By powerful gene-editing tool CRISPR-Cas9, we successfully obtained 2 completely corrected knock-in cell lines from urine-derived iPSCs. These corrected iPSCs still displayed pluripotency and maintained a normal karyotype. Sequencing analysis of potential offtarget sites suggested no off-target indels were identified. Our study is the first time to obtain ACH iPSCs from urine, the first to obtain non-integrated ACH iPSCs, and the first to perform gene correction in ACH research.
Coolpup.py: versatile pile-up analysis of Hi-C data

Motivation Hi-C is currently the method of choice to investigate the global 3D organisation of the genome. A major limitation of Hi-C is the sequencing depth required to robustly detect loops in the data. A popular approach used to mitigate this issue, even in single-cell Hi-C data, is genome-wide averaging (piling-up) of peaks, or other features, annotated in high-resolution datasets, to measure their prominence in less deeply sequenced data. However current tools do not provide a computationally efficient and versatile implementation of this approach. Results Here we describe coolpup.py – a versatile tool to perform pile-up analysis on Hi-C data. We demonstrate its utility by replicating previously published findings regarding the role of cohesin and CTCF in 3D genome organization, as well as discovering novel details of Polycomb-driven interactions. We also present a novel variation of the pile-up approach that can aid the in statistical analysis of looping interactions. We anticipate that coolpup.py will aid in Hi-C data analysis by allowing easy to use, versatile and efficient generation of pileups. Availability and implementation Coolpup.py is cross-platform, open-source and free (MIT licensed) software. Source code is available from https://github.com/Phlya/coolpuppy and it can be installed from the Python Packaging Index. Contact Ilya.Flyamer@igmm.ed.ac.uk
An integrated platform to systematically identify causal variants and genes for polygenic human traits

Genome-wide association studies (GWAS) have identified over 150,000 links between common genetic variants and human traits or complex diseases. Over 80% of these associations map to polymorphisms in non-coding DNA. Therefore, the challenge is to identify disease-causing variants, the genes they affect, and the cells in which these effects occur. We have developed a platform using ATAC-seq, DNaseI footprints, NG Capture-C and machine learning to address this challenge. Applying this approach to red blood cell traits identifies a significant proportion of known causative variants and their effector genes, which we show can be validated by direct in vivo modelling.
Gene expression response to a nematode parasite in novel and native eel hosts

Abstract Invasive parasites are involved in population declines of new host species worldwide. The high susceptibilities observed in many novel hosts have been attributed to the lack of protective immunity to the parasites which native hosts acquired during their shared evolution. We experimentally infected Japanese eels (Anguilla japonica) and European eels (Anguilla anguilla) with Anguillicola crassus, a nematode parasite that is native to the Japanese eel and invasive in the European eel. We inferred gene expression changes in head kidney tissue from both species, using RNA‐seq data to determine the responses at two time points during the early stages of infection (3 and 23 days postinfection). At both time points, the novel host modified the expression of a larger and functionally more diverse set of genes than the native host. Strikingly, the native host regulated immune gene expression only at the earlier time point and to a small extent while the novel host regulated these genes at both time points. A low number of differentially expressed immune genes, especially in the native host, suggest that a systemic immune response was of minor importance during the early stages of infection. Transcript abundance of genes involved in cell respiration was reduced in the novel host which may affect its ability to cope with harsh conditions and energetically demanding activities. The observed gene expression changes in response to a novel parasite that we observed in a fish follow a general pattern observed in amphibians and mammals, and suggest that the disruption of physiological processes, rather than the absence of an immediate immune response, is responsible for the higher susceptibility of the novel host.
The majority of the matrix protein TapA is dispensable for biofilm formation by Bacillus subtilis

Biofilm formation is a co-operative behaviour where microbial cells become embedded in an extracellular matrix. This biomolecular matrix plays a key role in the manifestation of the beneficial or detrimental outcome mediated by the collective of cells. Bacillus subtilis is an important bacterium for understanding the general principles of biofilm formation and is a plant growth-promoting organism. The protein components of the B. subtilis matrix include the secreted proteins BslA, which forms a hydrophobic coat over the biofilm, and TasA, which forms protease-resistant fibres needed for structuring. A third protein TapA (for TasA anchoring and assembly protein) is needed for biofilm formation and helps TasA fibre formation in vivo but is dispensable for TasA-fibre assembly in vitro. Here we show that TapA is subjected to proteolytic cleavage in the biofilm and that only the first 57 amino acids of the 253-amino acid protein are required for biofilm architecture. However, through the construction of a strain which lacks all eight extracellular proteases, we show that proteolytic cleavage by these enzymes is not a prerequisite for TapA function. It remains unknown why TapA is synthesized at a full length of 253 amino acids when the first 57 are sufficient for biofilm structuring, but the findings do not exclude the core conserved region of TapA having a second role beyond that of structuring the B. subtilis biofilm.
Identification and Functional Prediction of Drought-Responsive Long Non-Coding RNA in Tomato

In higher plants, several lines of evidence suggest that long non-coding RNAs (lncRNAs) may play important roles in the regulation of various biological processes by regulating gene expression. In this study, we identified a total of 521 lncRNAs, classified as intergenic, intronic, sense, and natural antisense lncRNAs, from RNA-seq data of drought-exposed tomato leaves. A further 244 drought-responsive tomato lncRNAs were predicted to be putative targets of 92 tomato miRNAs. Expression pattern and preliminary functional analysis of potential mRNA targets suggested that drought-responsive tomato lncRNAs play important roles in a variety of biological processes via lncRNA–mRNA co-expression. Taken together, these data present a comprehensive view of drought-responsive tomato lncRNAs that serve as a starting point for understanding the role of long intergenic non-coding RNAs in the regulatory mechanisms underlying drought responses in crops.
PENAMPILAN PERTUMBUHAN AYAM PERSILANGAN KAMPUNG DAN BANGKOK

This study was carried out for four months by using 48 chicks which consist of the progeny of interse Bangkok Chicken, interse Kampung Chicken, Crossing of Bangkok-Kampung and Crossing of Kampung Bangkok. Variables of the study were average body weight, feed Consumption and feed Efisiency. A Complete randomized design was used in this study. The result showed the highest average body weight and feed consumption in progeny interse Bangkok Chicken, however the best feed efisiency found in crossing of Kampung-Bangkok.
Florida's Pillar Coral (Dendrogyra cylindrus): The Roles of the Holobiont Partners in Bleaching, Recovery, and Disease Processes

Black band disease (BBD) affects many coral species worldwide and is considered a major contributor to the decline of reef-building coral. On the Florida Reef Tract BBD is most prevalent during summer and early fall when water temperatures exceed 29 C. BBD is rarely reported in pillar coral (Dendrogyra cylindrus) throughout the Caribbean, and here we document for the first time the appearance of the disease in this species on Florida reefs. The highest monthly BBD prevalence in the D. cylindrus population were 4.7% in 2014 and 6.8% in 2015. In each year, BBD appeared immediately following a hyperthermal bleaching event, which raises concern as hyperthermal seawater anomalies become more frequent.
Pituitary Magnetic Resonance Imaging in Patients with Isolated Hypogonadotrophic Hypogonadism: A Single Center Experience

Abstract Hypogonadism is a result of testicular/ovarian failure and/or insufficient pituitary stimulation. Various hypothalamo-pituitary abnormalities or lesions can contribute to hypogonadism. Benign or malign tumoural lesions of cellar or paracellar region, may lead to hypogonadism. Therefore, pituitary magnetic resonance imaging (MRI) is needed in patients with hypogonadism. In our study, we aimed to investigate our hypothalamo-pituitary MRI findings of hypogonadal patients. We evaluated 42 isolated hypogonadal patients followed in our clinic. These patients’ pituitary MRI findings were analyzed retrospectively. 80.9 % of isolated hypogonadotrophic patients’ were male, 19.1 % were female. Pituitary MRI findings of isolated hypogonadotrophic patients revealed that; 59.5% (n=25) were normal, 16.7 % (n=7) pituitary microadenoma, 11.9% (n=5) partial empty sella, 4.7% (n=2) pituitary macroadenoma, 2.4% empty sella (n=1), 2.4% (n=1) ectopic neuropituitary, and 2.4% (n=1) empty sella plus ectopic neuropituitary together. In half of the patients with isolated hypogonadotrophic hypogonadism, pituitary MRI findings may be normal. In these patients, if clinic and laboratory results are harmonious, to determine the diagnosis dynamic tests are required and appropriate therapy must be done, even if pituitary MRI is normal. Keywords: Hypogonadism, magnetic resonance imaging, microadenoma, macroadenoma
Bacterial virulence or exorbitant host response? On innate immunity against the streptococcal M1 protein.

Bacterial infection is inevitable throughout a lifetime. What differs between mild andserious infections is the pathogen responsible and how the host immune systemresponds to it. A fundamental role to prevent infection is a proper physical barrier such as the skin and mucosa. However, sometimes abrasions or injuries are still introduced, being potential ports of entry for pathogenic bacteria. An appropriate activation of innate immunity is necessary for bacterial elimination and wound healing. Special precautions are needed to prevent excessive host response that can result in severe tissue injury and aggravate the state of infection. This thesis has focused on studying the initial reactivity towards the streptococcal virulence factor M1 protein, and the consequent innate host response in vitro, modelling a streptococcal skin infection. The first part of the thesis describes the vigilant activity of keratinocytes triggering PAMP-signaling when encountering the streptococcal virulence factor. This signaling pathway resulted in cytokine release, especially IL-8, enabling recruitment and activation of leukocytes. We continued by studying the delicate balance between bacterial virulence and host response to avoid excessive inflammation. The bacterial protein was not cytotoxic, however, it completely abolished any wound-healing abilities of keratinocytes in vitro. We concluded that M1 protein can aggravate the state of streptococcal skin infection, and that it is rather a bacterial virulence mechanism than due to an exorbitant host response. Moreover, we decided to investigate if CAP, a partly ionized gas with antiseptic abilities, can also modulate the inflammatory activities triggered by the streptococcal M1 protein. For the first time, we have shown that CAP is able to modulate a specific bacterial virulence factor and abolish its detrimental activities in favor of the host. Our results also show that CAP exert its antivirulence and antimicrobial functions without disturbing fundamental innate immune responses. The final part of this thesis identifies new virulence factors of Leptospira responsible for triggering massive HBP release from neutrophils. Elevated HBP levels were found in serum samples from patients suffering from Leptospirosis and could potentially be a diagnostic biomarker for the disease. In conclusion, this thesis explores new mechanisms and host responses to combat bacterial virulence important for the pathology of infectious diseases. (Less)
Fungal connections between plants and biocrusts facilitate plants but have little effect on biocrusts

Species interactions may couple the resource dynamics of different primary producers and may enhance productivity by reducing loss from the system. In low‐resource systems, this biotic control may be especially important for maintaining productivity. In drylands, the activities of vascular plants and biological soil crusts can be decoupled in space because biocrusts grow on the soil surface but plant roots are underground, and decoupled in time due to biocrusts activating with smaller precipitation events than plants. Soil fungi are hypothesized to functionally couple the plants and biocrusts by transporting nutrients. We studied whether disrupting fungi between biocrusts and plants reduces nitrogen transfer and retention and decreases primary production as predicted by the fungal loop hypothesis. Additionally, we compared varying precipitation regimes that can drive different timing and depth of biological activities. We used field mesocosms in which the potential for fungal connections between biocrusts and roots remained intact or were impeded by mesh. We imposed a precipitation regime of small, frequent or large, infrequent rain events. We used 15N to track fungal‐mediated nitrogen (N) transfer. We quantified microbial carbon use efficiency and plant and biocrust production and N content. Fungal connections with biocrusts benefitted plant biomass and nutrient retention under favourable (large, infrequent) precipitation regimes but not under stressful (small, frequent) regimes, demonstrating context dependency in the fungal loop. Translocation of a 15N tracer from biocrusts to roots was marginally lower when fungal connections were impeded than intact. Under large, infrequent rains, when fungal connections were intact, the C:N of leaves converged towards the C:N of biocrusts, suggesting higher N retention in the plant, and plant above‐ground biomass was greater relative to the fungal connections‐impeded treatment. Carbon use efficiency in both biocrust and rooting zone soil was less C‐limited when connections were intact than impeded, again only in the large, infrequent precipitation regime. Synthesis. Although we did not find evidence of a reciprocal transfer of C and N between plants and biocrusts, plant production was benefited by fungal connections with biocrusts under favourable conditions.
Found in Transcription: Gene fusions arise through defects in RNA processing in the absence of chromosomal rearrangements

Recent advancements in high throughput sequencing analysis have enabled the characterization of cancer-driving fusions, improving our understanding of cancer development. Most fusion calling methods, however, examine either RNA or DNA information alone and are limited to a rigid definition of what constitutes a fusion. For this study we developed a pipeline that incorporates several fusion calling methods and considers both RNA and DNA to capture a more complete representation of the tumour fusion landscape. Interestingly, most of the fusions we identified were specific to RNA, with no evidence of corresponding genomic restructuring. Further, while the average total number of fusions in tumour and normal brain tissue samples is comparable, their overall fusion profiles vary significantly. Tumours have an over-representation of fusions occurring between coding genes, whereas fusions involving intergenic or non-coding regions comprised the vast majority of those in normals. Tumours were also more abundant in unique, sample-specific fusions compared to normals, though several fusions exhibited strong recurrence in the tumour type examined (diffuse intrinsic pontine glioma; DIPG) and were absent from both normal tissues and other cancers. Intriguingly, tumours also show broad up- or down-regulation of spliceosomal gene expression, which significantly correlates with fusion number (p=0.007). Our results show that RNA-specific fusions are abundant in both tumour and normal tissue and are associated with spliceosomal gene dysregulation. RNA-specific fusions should be considered as a potential mechanism that may contribute to cancer formation initiation and maintenance alongside more traditional structural events.
Factors influencing promotion and or appointments of political appointees in Tanzania

The discourse of political promotion and or appointment in work places has been doubtful for many decades. Despite many literatures narrating on the various systems of promotion, yet the perception of workers on credentials used for promotion has not been reflecting what ought to be done in accordance to the management professionalism. The study entails to find out if competence based was among the credentials used for appointing or promoting workers in work places. It further seeks to find out if appointment of political appointees was perceived to be, competent based. Therefore, this paper provides findings on the perception of workers on factors perceived to be used for promoting or appointing political appointees in Tanzania. The study used a purposeful sampling of a focus group of workers pursuing MBA degree at the Tumaini University. The students are employees of different places in Tanzania ranging from public and private sectors. The respondents emanates from 19 regions of Tanzania. The total sample of students was 40. Interview and questionnaire were the leading data collection strategies. Excel was the tool used for data presentation. The findings reveal that most workers perceive that promotion and appointments is related to religion relationships, intimacy relationships, corruption and tribalism.