Miracle-dz/UniFAR-FTUs huggingface dataset:
MICROSATELLITE-BASED ANALYSIS OF TWO NIGERIAN INDIGENOUS GOAT BREEDS

This study was conducted to determine the genetic variation between Sahel and Red Sokoto goat breeds of Nigeria . One hundred and twenty goats, 60 each of both Sahel and Red Sokoto breeds obtained from Maigatari market in Jigawa State and Animal Science Departmental Farm in Zaria, Kaduna State, respectively. Tissue samples were collected randomly from each breed using an Allflex ear punch tissue sample collector and aliquoted into plastic tubes containing the Allflex preservative. DNA extraction, amplification and sequencing were carried out at the International Livestock Research Institute (ILRI), Nairobi, Kenya. The DNA was extracted from the tissue cells using the Pure Link™ Genomic DNA minikit according to the manufacturer’s specifications and protocol and were genotyped using 25 microsatellite markers as recommended by FAO/ISAG. Twenty three of the twenty five microsatellite markers used in this analysis had four or more alleles. The mean Shannon index, observed and expected heterozygosity and inbreeding coefficient (F is ) for Sahel goats were 1.642, 0.609, 0.700 and 0.143 respectively. For the Red Sokoto goats, the mean Shannon index, observed and expected heterozygosity and inbreeding coefficient (F is ) were 1.635, 0.644, 0.708 and 0.087, respectively. The genetic distance as well as the genetic differentiation (F st ) between the breeds was low, 0.04 and 0.026, respectively, however; the gene-flow (Nm) was high (5.78). This study has shown that Sahel and Red Sokoto goats have some genetic similarity owing to the fact that they have a common ancestry and are both Northern breeds. Measures to conserve the uniqueness/distinctiveness of these breeds should be sought through in-situ and ex-situ conservation. Gene flow between populations should be controlled by adopting effective breeding and management practices.
Passive Nonlinear Optical Isolators Bypassing Dynamic Reciprocity

Magnetic-free optical isolators are critical components for the realization of integrated optical systems. The underlying physics of passive nonlinear optical isolators is not solely about breaking the Lorentz reciprocity without requiring any external bias. Indeed, one major obstacle to the operation of Kerr-type nonlinear optical isolators was found to be the so-called dynamic reciprocity, of which the serious outcome is that a backward signal cannot be isolated in the presence of a forward strong signal. In this work, we advocate the novel concept of velocity-selective nonlinearity to bypass such dynamic reciprocity. Using a proof-of-principle platform with warm rubidium atoms in an asymmetric cavity, we experimentally achieve the isolation of a backward signal in the presence of a strong forward signal, with experimental observations in agreement with our theoretical simulations. This work has thus made one essential step towards functioning Kerr-type passive optical isolators.
Genetic Determinants of Salmonella and Campylobacter Required for In Vitro Fitness

Non-typhoidal Salmonella (NTS) and Campylobacter play a major role in foodborne illness caused by the consumption of food contaminated by pathogens worldwide. A comprehensive understanding of the genetic factors that increase the survival fitness of these foodborne pathogens will effectively help us formulate mitigation strategies without affecting the nutrition ecology. The objective of this study was to identify the genetic determinants of Salmonella and Campylobacter that are required for fitness under various in vitro conditions. For the purpose, we used a high throughput Transposon sequencing (Tn-seq) that utilizes next generation sequencing (NGS) to screen hundreds of thousands of mutants simultaneously. In Chapter 1, we reviewed the technical aspects of different Tn-seq methods along with their pros and cons and compressive summary of recently published studies using Tn-seq methods. In Chapter 2, we exposed complex Tn5 library of Salmonella Typhimurium 14028S (S. Typhimurium) to the mimicked host stressors in vitro conditions. Such as low acidic pH (pH 3) found in the stomach, osmotic (3% NaCl) and short chain fatty acid (SCFAs, 100 mM Propionate) found in intestine, and oxidation (1mM H2O2) and starvation (12-day survival in PBS) found in macrophage. There was an overlapping set of 339 conditionally essential genes (CEGs) required by S. Typhimurium to overcome these host stressors. In Chapter 3, we screened of S. Typhimurium Tn5 library for desiccation survival. Salmonella spp. is the most notable and frequent cause of contamination in low-water activity foods. We identified 61 genes and 6 intergenic regions required for fitness during desiccation stress. In Chapter 4, the essential genome of Campylobacter jejuni (C. jejuni) NCTC 11168 and C. jejuni 81-176 was investigated using Tn-seq. We identified 166 essential protein-coding genes and 20 essential transfer RNA (tRNA) in C. jejuni NCTC 11168 which were intolerant to Tn5 insertions during in vitro growth. The reconstructed library C. jejuni 81176 had 384 protein coding genes with zero Tn5 insertions. The genetic determinants Salmonella and Campylobacter identified in this study have high potential to be explored as food safety intervention, therapeutic and vaccine target to curb the spread of the foodborne pathogens making world a safer place.
Ensemble Chinese End-to-End Spoken Language Understanding for Abnormal Event Detection from Audio Stream

Conventional spoken language understanding (SLU) consist of two stages, the first stage maps speech to text by automatic speech recognition (ASR), and the second stage maps text to intent by natural language understanding (NLU). End-to-end SLU maps speech directly to intent through a single deep learning model. Previous end-to-end SLU models are primarily used for English environment due to lacking large scale SLU dataset in Chinese, and use only one ASR model to extract features from speech. With the help of Kuaishou technology, a large scale SLU dataset in Chinese is collected to detect abnormal event in their live audio stream. Based on this dataset, this paper proposed a ensemble end-to-end SLU model used for Chinese environment. This ensemble SLU models extracted hierarchies features using multiple pre-trained ASR models, leading to better representation of phoneme level and word level information. This work also showed a feasible way to build a end-to-end SLU system without transcribing audios. The proposed approached achieve 9.7\% increase of accuracy compared to previous end-to-end SLU model.
Olaparib treatment in older patients with ovarian cancer: need for ‘real-world’ data beyond clinical trials

Background Ageing is a risk factor for cancer. Worldwide, the number and proportion of adults aged ≥65 will increase, along with the incidence of ovarian cancer. Older adults are under-represented in randomised clinical trials (RCTs), and those who are enrolled have a good performance status and no major health issues. These patients are not representative of older patients seen in everyday clinical practice; therefore, age-specific data on efficacy and toxicity of olaparib in the ‘real-world’ setting are lacking. Methods This observational study was conducted in the Central Jutland Region in Denmark. Data in unselected older (≥65) patients with known BRCA mutation receiving olaparib maintenance treatment for platinum-sensitive relapsed ovarian cancer were registered between 2015 and 2019. Toxicity and progression-free survival (PFS) were registered. No geriatric assessment has been performed. Results In total, 20 consecutive patients ≥65 years were included with a median age of 75 years (range: 65–85). Most of the patients (18/20) had ECOG PS: 0–1. Treatment interruption and dose reduction occurred in 65% of the patients. Toxicities of any grade occurred in 18 (90%), whereas grade 3/4 toxicities occurred in 6 patients (30%). Treatment was terminated due to disease progression or unacceptable toxicity in 13 (65%) patients. The median PFS was 6 months (range: 2–31), and the median follow-up was 15 months (range: 3–30). Discussion Our ‘real-world’ experience shows that unselected older patients represent a significant larger proportion in real life than in RCTs; furthermore, older patients in a real-world setting may experience more side effects possibly affecting the quality of life. The median PFS data suggest that older patients may not derive the same clinical benefit than their fit and younger counterparts. There is a need to enrol vulnerable/frail older patients into RCTs, ensuring that data will also be applicable in standard clinical settings. Incorporating geriatric assessment into these trials should be encouraged.
A 31-Integrin Receptor forFibronectin inHuman Kidney Glomeruli

The fibronectin receptor (FNR) is a transmembrane heterodimeric glycoprotein which shares a common :3,-chain with several other members of the integrin family of adhesion receptors. The au-thors have prepared a membrane fraction of isolated human glomeruli, from which two proteins (apparent molecular weights 120 kd and 140 kd) bound to a fibronectin-column, and were selectively released by the synthetic peptide Arg- Gly-Asp-Ser. These molecules were labeled in immune overlays by an antibody raised against the FNR from human placenta that recognizes both the FNR-spe-cific a-chain and the group-specific f. ,-integrin chain. In sections of normal human kidneys this antibody labeled predominately the mesangia and the peripheral capillary walls of glomeruli by an immunoperoxidase procedure. Quantitative immunoelectron microscopy, using an indirect im-munogoldprocedure, revealed apreferential localization along the cell membranes of mesangial, epithelial, and endothelial cells that face the mesangial matrix or the glomerular basement membrane (GBM). In kidney biopsies from patients with various glomerular diseases (membra-nous and otherforms of glomerulonephritis, minimal change disease) the distribution was similar
Discovery and Characterization of Novel Sperm Development Patterns in the Nematode Rhabditis Sp. Sb347

Studies of gamete production in Caenorhabditis elegans self-fertile hermaphrodites have informed textbook descriptions of nematode reproduction and have significantly contributed to our understanding of fundamental cellular and developmental mechanisms. However, C. elegans is one species within a large phylum of mostly dioecious (male/female) species. Whether the C. elegans pattern of self-fertile hermaphroditism and gamete development is representative of other nematodes remains largely unexplored. In Chapter 1, we describe an alternative pattern of sperm production in the trioecious (male/female/hermaphrodite) nematode Rhabditis sp. SB347 that differs from C. elegans in two striking ways. First, instead of making a one-time switch from sperm to oocyte production, R. sp. SB347 hermaphrodites produce sperm and oocytes simultaneously. Secondly, instead of limiting germ cell proliferation to germline stem cells (GSCs), sperm production in R. sp. SB347 includes an additional population of mitotically dividing cells that are a developmental intermediate between GSCs and fully differentiated spermatocytes. These cells, which are present in males and hermaphrodites but not females, exhibit key characteristics of spermatogonia, the mitotic progenitors of spermatocytes in flies and vertebrates. Specifically, they amplify germ cell numbers, exist outside the stem cell niche, and synchronously develop and proliferate within germ cell clusters (or cysts). We next discovered that spermatogonia are a feature of sperm production in other trioecious species of the Rhabditis genus, but not in the male/female species Rhabditis axei. The discovery of simultaneous hermaphroditism and spermatogonia in a labcultivatable nematode suggests R. sp. SB347 as a richly informative species for comparative studies of gametogenesis. In Chapter 2, we assess whether C. elegans germ cell development genes have been conserved across species and identify homologs in R. sp. SB347. By comparing these homologs’ roles and expression patterns between species, we may better understand differences between these two divergent mechanisms of hermaphroditism and sperm production. Such molecular comparative analyses may also inform our understanding of germ cell evolution. Here we begin to develop tools to investigate expression of two conserved homologs, FBF and SPE-44. In Chapter 3, we consider what aspects about R. sp. SB347’s unique form of sperm development have not yet been fully explored. We report relevant preliminary data and recommend future directions for addressing these questions.
Dual role of Lin28a in the regulation of miRNA biogenesis during neuronal differentiation

XIII Lay abstract . XIV Chapter 1 . 1 1 Introduction . 1 1.1 miRNA biogenesis and function in vertebrate systems . 3 1.1.1 Transcriptional control of miRNA synthesis . 8 1.1.2 Post-transcriptional mechanisms regulating miRNA production . 10 1.1.2.1 Drosha mediated pri-miRNA processing in the cell nucleus . 11 1.1.2.2 Dicer-mediated pre-miRNA processing in the cell cytoplasm . 15 1.1.3 miRISC complex – executioner of miRNA function . 18 1.1. 4 Modifications of miRNAs and its role in biogenesis regulation . 22 1.2 The role of Lin28 in miRNA biogenesis . 24 1.2.1 Implications to let-7 levels . 25 1.2.2 Effect of Lin28-mRNA interaction on protein translation . 28 1.2. 3 Functional importance of the regulatory role of Lin28 . 30 1.2. 4 Structural determinants for Lin28 action . 32 1.2. 4.1 Role of the zinc-knuckle domain in substrate recognition and uridylation . 33 1.2. 4.2 Implications of the Cold Shock Domain’s role in structural rearrangement of RNA . 33 1.3 The role of miRNAs in the development and pathogenesis of the nervous system . 36
Ascorbic Acid Alleviates Toxicity Induced by Excess Copper in Brassica campestris Ssp. Chinensis Makino

ABSTRACT In this study, the changes in mineral elements content, chlorophyll, malondialdehyde (MDA), ascorbic acid (AsA), and deoxyribonucleic acid (DNA) methylation level were studied in leaves of three cultivars of non-heading Chinese cabbage (Brassica campestris ssp., chinensis Makino) under copper stress, and the role of exogenous AsA was also investigated. Under copper stress, the copper content in leaves increased significantly, while it is lowest in “Wutacai”, which showed the highest copper tolerance in the three cultivars of non-heading Chinese cabbage. Mineral elements such as iron (Fe), manganese (Mn), magnesium (Mg), sodium (Na), and potassium (K) reduced remarkably, the content of chlorophyll decreased, while MDA and DNA methylation level increased significantly. Compared with that under copper treatment, exogenous AsA decreased the contents of copper and MDA, and DNA methylation level, while increased the content of chlorophyll and other mineral contents, which implied that AsA alleviates copper stress in non-heading Chinese cabbage.
Expanding Metabolic Diversity of Two Archaeal Phyla: Nanoarchaeota and Korarchaeota

Culture independent studies have revealed a greater diversity of Archaea than the two kingdoms initially defined by Carl Woese. Culturing species from the newly discovered archaeal lineages, as with the majority of microbes, has been difficult. To overcome the culturing dilemma, metagenomics is being used to reconstruct environmental genomes. Two metagenomic studies are presented in this thesis, with the aim of recovering newly proposed archaeal genomes from the Nanoarchaeota and Korarchaeota. In the first study, a sediment sample, NZ13, was collected from a terrestrial New Zealand hot spring. Along with the sediment sample, two complex enrichments were sequenced on an Illumina MiSeq platform. Assembly and differential binning recovered two nearly complete genomes of a nanoarchaeote and a korarchaeote. The NZ13 nanoarchaeote is similar to other terrestrial nanoarchaeotes, which lack an ATP synthase and encode genes for glycolysis/gluconeogenesis and archaella. One notable difference is the NZ13 nanoarchaeote contains CRISPR genes, which are absent in other terrestrial nanoarchaeotes, although present in a marine nanoarchaeote, Nanoarchaeum equitans. The NZ13 korarchaeote mirrors Candidatus Korarchaeum cryptofilum, lacking genes for de novo synthesis of purines and several cofactors, while containing an abundance of peptide transporters and amino acid fermentation pathways. The second study focused on sulfide samples collected from deep-sea hydrothermal vent fields in southwestern Pacific Ocean along the Eastern Lau Spreading Center. Ten sulfide samples were sequenced on an Illumina HiSeq platform. Small ii subunit ribosomal RNA genes were extracted from the metagenome reads and aligned against the SILVA Ref NR 99 123 database. The preliminary results identified which samples could be prioritized for genome reconstruction of uncultured bacterial and archaeal lineages. Three uncultured bacteria, candidate division SR1, Gracilibacteria (GN02) and Parcubacteria (OD1) were identified in several samples. Many uncultured deep-sea hydrothermal archaeal lineages were identified in all samples. In particular, korarchaeotal sequences were in high relative archaeal abundances in two samples, ABE-1 and Vai Lili-2, while few nanoarchaeotal reads were classified.
The unconventional kinetoplastid kinetochore protein KKT4 tracks with dynamic microtubule tips

Kinetochores are multiprotein machines that drive chromosome segregation in all eukaryotes by maintaining persistent, load-bearing linkages between the chromosomes and the tips of dynamic spindle microtubules. Kinetochores in commonly studied eukaryotes are assembled from widely conserved components like the Ndc80 complex that directly binds microtubules. However, in evolutionarily-divergent kinetoplastid species such as Trypanosoma brucei, which causes sleeping sickness, the kinetochores assemble from a unique set of proteins lacking homology to any known microtubule-binding domains. Here we show that a kinetochore protein from T. brucei called KKT4 binds directly to microtubules, diffuses along the microtubule lattice, and tracks with disassembling microtubule tips. The protein localizes both to kinetochores and to spindle microtubules in vivo, and its depletion causes defects in chromosome segregation. We define a minimal microtubule-binding domain within KKT4 and identify several charged residues important for its microtubule-binding activity. Laser trapping experiments show that KKT4 can maintain load-bearing attachments to both growing and shortening microtubule tips. Thus, despite its lack of similarity to other known microtubule-binding proteins, KKT4 has key functions required for harnessing microtubule dynamics to drive chromosome segregation. We propose that it represents a primary element of the kinetochore-microtubule interface in kinetoplastids.
Baicalein Restores the Balance of Th17/Treg Cells via Aryl Hydrocarbon Receptor to Attenuate Colitis

As one of the ligands of aryl hydrocarbon receptor (AhR), baicalein, isolated from Scutellaria baicalensis Georgi, has been proved to exert potential therapeutic effects on ulcerative colitis (UC), but its therapeutic mechanism remains obscure. Authentically, ulcerative colitis can be alleviated by regulating the differentiation of naïve CD4+ T cells via AhR activation. So, our study planned to prove the hypothesis that baicalein protected mice against UC by regulating the balance of Th17/Treg cells via AhR activation. Immunofluorescence and western blot results showed that baicalein could promote AhR activation and induce it to transfer to the nucleus. We further determined the effect of baicalein on naïve CD4+ T cell differentiation in vitro by magnetic cell separation and drug intervention. The results showed that baicalein could promote Treg cell differentiation by activating AhR. In vivo study, UC mice were established by free drinking of dextran sulfate sodium (DSS) for 7 days and then were orally administrated by baicalein (10, 20, and 40 mg/kg), TCDD (AhR agonist), and CH223191 (antagonist). The results demonstrated that baicalein improved the symptoms of UC mice, regulated the balance of Th17/Treg cells, and restored the balance of proinflammatory cytokines such as IL-17, IL-6, and TNF-α; anti-inflammatory cytokines such as IL-10 and TGF-β; and epithelial protective cytokine IL-22 in UC mice, and these effects were related to AhR. Taken together, our research found that baicalein might be a potential drug for UC via regulating Treg cell differentiation and maintaining immune homeostasis and attempted to shed a light on the pivotal role of AhR in these effects.
Foraging strategy and food preference of Formica polyctena ants in different habitats and possibilities for their use in forest protection

Abstract Food availability is an important factor influencing the lives of ant colonies. Wood ants consume protein-rich and sugary foods. Protein-rich food is comprised primarily of insects, a considerable proportion of which the ants acquire by direct predation. They therefore play an important function in biological protection of forests. The objective of our study was to determine if workers activity is dependent on habitat type, size of the nest, bait size and food type (sugar, protein). We selected 23 nests in a spruce forest and placed food baits of various sizes and types near each nest. The results obtained show that the number of individuals on the baits was substantially higher in clearings than within mature forest. The number of worker ants recorded on the baits was slightly higher for larger nests. Bait size and type had no influence on the number of workers present. Because wood ants do not focus solely on food of a certain size or quality, they can effectively decrease the abundance of forest pests.
Adequacy of clinical information in X-ray referrals for traumatic ankle injury with reference to the Ottawa Ankle Rules—a retrospective clinical audit

Study Objective To assess the adequacy of clinical information with reference to the Ottawa Ankle Rules (OAR) in X-ray referrals for adults with traumatic ankle injury in the ED of a South Australian tertiary hospital and report upon referring trends between emergency department clinicians. Methods A retrospective clinical audit of adult ankle X-ray referrals in the emergency department was conducted. Eligible referrals were screened for their adherence to the OAR, patient details, clinical history and referrer. A logistic regression was used to determine the influence of these factors on the likelihood of being referred for X-rays despite not meeting the OAR criteria. Sensitivity, specificity, positive and negative likelihood ratios and their associated confidence intervals were calculated to assess the diagnostic accuracy of the OAR for those referred. Results Out of the 262 eligible referrals, 163 were deemed to have met the criteria for the OAR. Physiotherapists showed the highest OAR compliance of 77.3% and were the most accurate in their use of the rules, with a sensitivity of 0.86. Medical officers, registrars and interns were 2.5 times more likely to still refer a patient for X-ray if they did not meet the OAR criteria, compared to physiotherapists as the baseline. Patient age, duration of injury etc. were not significantly associated with likelihood of referral (even when they did not meet OAR criteria). The overall sensitivity, specificity, positive and negative likelihood ratios of the OAR were 0.59 (95% CI [0.47–0.71]), 0.37 (95% CI [0.30–0.44]), 0.93 (95% CI [0.76–1.16]) and 1.10 (95% CI [0.82–1.48]) respectively. Conclusion The results of this audit demonstrated poor sensitivity and moderate compliance by referrers with the rule. Reasonable evidence exists for the implementation of individual and/or institutional-based change strategies to improve clinician compliance and accuracy with use of the OAR.