Miracle-dz/UniFAR-FTUs huggingface dataset:
STATUS OF PLANT DIVERSITY AT KUFRI (SOONE VALLEY) PUNJAB, PAKISTAN AND PREVAILING THREATS THEREIN

To examine the species composition in the Soone Valley, Punjab, Pakistan, the Kufri site was selected on the basis of some ecological attributes i.e., topography, soil type and the nature of prevailing disturbances. Data regarding the composition of plant diversity revealed that among the woody leguminous plants Acacia modesta was the most commonly occurring species. Propsopis juliflora occurred very commonly and formed mono-species stands, while Dalbergia sissoo was absent altogether. Among the herbaceous weedy legumes Medicago polymorpha and Melilotus indica were commonly found during the winter seasons. At higher altitudes Olea ferruginea formed a good association with Acacia modesta. Throughout the examined site, Dodonaea viscosa and Justicia adhatoda occurred very abundantly, because both species had resistance for grazing and fuel needs. Cutting of woody plants and shrubs for fuel purposes and their lopping for grazing the domestic animals are the two major threats to the entire local vegetation in this valley. Accidental fires caused by careless honey hunters also, sometimes become uncontrollable and wipe out most of the vegetation to a large extent.
Ethical Dilemmas Experienced by Australian Rehabilitation Counsellors

Private sector rehabilitation counsellors operate in a dynamic and complex environment in which their decisions are influenced by several stakeholder interests including workers’ compensation authority regulators, scheme appointed agents, employers, and injured workers. The potentially competing interests of all parties often challenge the values and professional responsibilities of rehabilitation counsellors. The current study aimed to address the gap identified in the literature concerning ethical dilemmas unique to private sector rehabilitation counselling in Australia. A qualitative methodology was adopted to examine: a) the types of ethical dilemmas most encountered by rehabilitation counsellors working in the context of private sector settings; and b) rehabilitation counsellors' preferred methods for resolving ethical dilemmas in this context. Findings revealed that rehabilitation counsellors interviewed had experienced an array of ethical dilemmas in their practice, reflecting some of the inherent challenges in Australia’s private rehabilitation sector. The findings have implications for the ethics education and professional development of rehabilitation counsellors, and provide a foundation for future ethics research in rehabilitation counselling.
Impact of Bt-engineered cotton on target and non-target arthropods, toxin flow through different trophic levels and seedcotton yield

Insect-resistant genetically engineered cottons expressing ? -endotoxins from the bacterium, Bacillus thuringiensis (Bt) have been adopted on a large scale worldwide. The effects of Bt cotton on non-target insect pests, generalist predators, arthropod diversity and toxin flow through different trophic levels under insecticide protected and unprotected conditions was studied. The populations of major non-target insect pests (leafhoppers, whiteflies, ash weevils, aphids, dusky and red cotton bug, and green bug) and the generalist predators (ladybirds, chrysopids, and spiders) did not differ significantly between the Bt and non-Bt cottons, while their numbers were lower in insecticide protected than under unprotected conditions, except for aphids and whiteflies. Although, Bt toxin was detected in some insect species, no significant differences were observed in their abundance on Bt and non-Bt cottons. Species richness and diversity of plant inhabiting and soil dwelling arthropods was similar in Bttransgenic and non-transgenic cottons, except in a few cases. The Bt-transgenic cotton was effective for the management of bollworms, without any major adverse effects on the non-target arthropods.
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

NCBI's reference sequence (RefSeq) database () is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. The database includes 3774 organisms spanning prokaryotes, eukaryotes and viruses, and has records for 2 879 860 proteins (RefSeq release 19). RefSeq records integrate information from multiple sources, when additional data are available from those sources and therefore represent a current description of the sequence and its features. Annotations include coding regions, conserved domains, tRNAs, sequence tagged sites (STS), variation, references, gene and protein product names, and database cross-references. Sequence is reviewed and features are added using a combined approach of collaboration and other input from the scientific community, prediction, propagation from GenBank and curation by NCBI staff. The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence.
Bacterial Cellulose Templates for Nano-Hydroxyapatite Fibre Synthesis

Guided bone regeneration is a medical procedure which induces in vivo re-growth of bone using membranes and osteopromoting fillers. In this work, bacterial cellulose fibres were isolated and used as a basis for biomimetic hydroxyapatite growth, with the ultimate goal of producing GBR filler materials. Acetobacter xylinum generated BC using various carbon sources. Fibres were treated with phosphoric acid to phosphorylate functional groups and preconditioned with calcium to nucleate the HA. Simulated body fluid (SBF) furthered the growth. Over 14 days, the product was characterized via EDX, SEM, FTIR, and XRD. The effect of media composition, phosphorylation time, pre-treatment, and structure on the resultant composites was examined. Samples possessed a Ca-to-P ratio as high as 1.45±0.92, encompassing the HA standard of 1.67. Higher ratios were observed on the surface of pellicles, implying crystal deposition. Results indicate potential in threedimensional samples and a basis for further BC-HA scaffold optimization for GBR.
Evolution of Picornaviruses: Impacts of Recombination and Selection

EVOLUTION OF PICORNAVIRUSES: IMAPCTS OF RECOMBINATION AND SELECTION Nicole Lewis-Rogers Department of Microbiology and Molecular Biology Doctor of Philosophy Picornaviruses are responsible for some of the most common and debilitating diseases affecting humans and animals worldwide. The objectives of this dissertation research were (1) estimate phylogenetic relationships among 11 picornavirus genera and within three species: foot-and-mouth disease virus (FMDV: Aphthovirus) which afflicts cloven-hoofed animals and human rhinovirus A and B (HRV: Enterovirus) which cause the common cold; (2) better understand the impact recombination has on genomic organization and evolution; (3) characterize where positive and purifying selection has occurred in proteins and how selection has influenced phenotype. The dissertation includes four studies. The first chapter provides an overview of the evolutionary significance of recombination, its detection and estimation, and its effect on phylogenetic analysis in four biological systems: bacteria, viruses, mitochondria, and the human genome. Chapter two investigates the interand intra-serotypic relationships within FMDV by examining 12 genes. Gene sequences were analyzed to assess recombination breakpoint locations, genetic diversity, and natural selection in FMDV. Recombination breakpoints were located throughout the genome. Paraphyletic relationships among serotypes were not as prevalent as previously reported, suggesting that convergent evolution was prevalent. Purifying selection was the dominant evolutionary force influencing both genotype and phenotype. Chapter three examines interand intraspecific relationships of HRV using 11 genes. Similar hypotheses were tested as in chapter two. No recombination was detected and phylogenetic relationships among enteroviruses, HRV-A, and HRV-B remain unresolved. The evolution of HRV-A major serotypes appeared to be under extensive purifying selection, HRV-A minor serotypes under predominantly positive selection, and a nearly equal influence from both kinds of selection was evident for HRV-B serotypes. Chapter four examines phylogenetic relationships among genera using three conserved genes. The hypothesis of cospeciation between picornaviruses and their hosts was also tested. The deepest split in the family separated Hepatovirus, „Tremovirus‟, Parechovirus, and seal picornavirus type 1 from the remainder of the family. Enterovirus and „Sapelovirus‟ were sister taxa. Cardiovirus, „Senecavirus‟, Aphthovirus, Erbovirus, Teschovirus, and Kobuvirus were derived from a common ancestor with Kobuvirus occupying a basal position relative to the other genera in this clade. My analyses suggest that picornaviruses have not cospeciated with their known hosts.
Optimization of circulating miRNA library preparation for next-generation sequencing and an exploratory pharmacogenomics investigation of psoriatic arthritis patients treated with IL-12/23 or IL-17 inhibitors

Optimization for circulating miRNA library preparations, multiplexing capacity, and sequencing with the Ion Torrent System was executed in order to process patient samples effectively. Multiple modifications were attempted in two published protocols before miRNA library preparations reached adequate quality for sequencing. A cohort of nine psoriatic arthritis patients, recruited for a pharmacogenomics investigation of treatment with IL-12/23 or IL-17 inhibitors, had blood samples drawn at baseline, as well as one- and three-month post treatment. The pharmacogenomics samples from baseline were sequenced and the resultant data underwent several analyses in order to identify predictive miRNA markers or profiles. Differential miRNA expression analyses were performed both between the American College of Rheumatology response criteria groupings and on clinical datasets, followed by a comprehensive literature review to examine potential implications of identified miRNAs. Pathway analyses, network analyses, and an in silico functional enrichment analysis were performed on the data to identify associations with signalling cascades, collectively targeted genes, and biological functions, respectively. The results of this exploratory study demonstrate the potential of the miRNA sequencing framework for identifying predictive miRNA markers and profiles associated with response to pharmaceuticals.
Using radiofrequency ablation for conventional endoscopic treatment refractory bleeding from radiation proctitis: A single center cohort

The treatment of bleeding in patients with radiation proctitis is clinically challenging, with no effective management strategy currently available for controlling bleeding refractory to conventional medications and endoscopic hemostatic tools. Bleeding has been controlled in a small number of patients using radiofrequency ablation (RFA) in western countries. However, there is limited experience with RFA treatment in Asia. Therefore, the aim of our study was to report on our treatment of refractory bleeding in three patients with radiation proctitis using RFA. All three patients in our case series were referred to Chia‐yi Christian Hospital for RFA treatment. Patients' medical records were reviewed to confirm persistent bleeding after treatment with medical and conventional endoscopy. A pre‐RFA colonoscopy was performed to confirm the severity of radiation proctitis and to exclude other causes of bleeding. RFA was performed using a Halo90 system, with an energy setting of 12 J/cm2, applied twice to every area of bleeding on the mucosa per treatment session. All patients received one RFA session, with follow‐up treatment as needed. Clinical symptoms, diarrhea, bleeding, tenesmus, and transfusion dependence were recorded. Our study included one patient with uterine cancer and two patients with prostate cancer, with all patients having severe symptoms of radiation proctitis, with more than six bloody stool passages per day and all were transfusion‐dependent. All patients had failed to respond to medication treatment and endoscopic argon plasma coagulation. Two patients had also undergone hyperbaric oxygen treatment prior to RFA, with no response. At the time of RFA treatment, bleeding had persisted for eight, six, and four months among the three patients. Overt and persistent bleeding from the telangiectasia was identified by colonoscopy in all three patients. Post‐RFA treatment, complete or near‐complete control of the bleeding was obtained during the follow‐up period, with no patients requiring further transfusion. No RFA‐associated complications were noted, including stricture or perforation. RFA can safely and effectively be used to control bleeding from radiation proctitis that has been refractory to conventional endoscopic hemostatic tools. Further accumulation of more evidence is warranted.
The role of SNARE proteins in CD4+ T-helper cell subsets

It is well established that CD4+ T-helper cells are vital in the adaptive immune response and mediate the clearance of persistent pathogens. Specific T-helper cell phenotypes that secrete distinct profiles of cytokines are generated in response to infection. These cytokines orchestrate homeostasis and pathogen clearance through autocrine and endocrine signalling. Dysregulation of this process can lead to inflammation and autoimmune disease. Secretion of cytokines is facilitated by highly regulated SNARE proteins. SNAREs have been shown to form specific partnerships and facilitate membrane-membrane fusion required for the exocytosis of cytokines and other proteins from immune cells. Using an optimised in vitro model, isolated CD4+ T cells were polarised into T-helper cell subsets in order to profile SNARE expression and regulation. Syntaxin-11 (STX11) was identified as a candidate regulatory SNARE in Th1 and Th17 cells. Further investigation in vivo using two mouse models of inflammation suggested that STX11 was regulated in Th17/Th1 mediated disease. Finally, we examined Th1 and Th17 responses in STX11 deficient mice and demonstrated that in the absence of STX11, T helper cell secreted increased levels of IFN-� and were unable to differentiate into a Th17 subset. The elucidation of SNARE trafficking pathways in CD4+ T-helper cells may represent potential therapeutic targets for blocking cytokine secretion from targeted cells and control inflammation. It may also lead to a better understanding of SNARE deficient immune disorders such as familial haemophagocytic lymphohistocytosis - 4 (FHL-4), characterised by over production of cytokines and high number of activated lymphocytes due to STX11 deficiency.
“Study of Neuromuscular and Proprioceptive Training Program on Postural Stability in Active Middle-Aged Men”

Background: The risk of falling increases with age, and the outcome might sometimes be severe injury or even death. Objectives: This study was designed to determine whether a 12-week neuromuscular and proprioceptive training (NPT) plan was impressive on postural stability of active middle-aged men. Methods: The study had a quasi-experimental design with a control group. In 2016, 50 middle-aged males of the Ukrainian Sports Medicine Center (Kiev) were randomly divided to experimental (performed the NPT program, rather than general warm-up routines) and control groups (maintained the general warm-up routines). The mean center of pressure (CoP) ﬂuctuations of postural stabilitywasassessedduringeyesopen(EO)andclosed(EC)usingaforceplatforminthetwodirections,beforeandafterthe12-week study. Results: TheinterventionleadstoasigniﬁcantimprovementinthemeanCoPvelocityinbothplanes(P< 0.05)intheexperimental group compared to the control. All CoP parameters used in this study showed very large correlations. Conclusions: The NPT program had a positive eﬀect on postural stability. This may have a direct impact on reducing lower limb injury in middle-aged men.
Form and function in the hominoid tarsal skeleton

This thesis explores form variation in the adult tarsal skeleton of extant and fossil hominoids. Three dimensional coordinate data were obtained from five bones of the foot: the calcaneus, talus, cuboid, navicular and medial cuneiform. The comparative sample was made up of Homo sapiens, Pan troglodytes troglodytes, Pan paniscus, Gorilla gorilla gorilla and Pongo pygmaeus. The fossil sample consisted of tarsal remains assigned to a number of Late Pliocene taxa: Australopithecus afarensis, Australopithecus africanus, Paranthropus robustus and Homo habilis. Statistical shape analysis was conducted using geometric morphometric techniques. The first section of analysis explores sexual dimorphism in the extant hominoid foot. It is found that there is no shape dimorphism in the forefoot, and a marginal amount in the hindfoot of Gorilla and Pongo only. Such differences are likely to be linked to high degrees of body mass dimorphism in those taxa. The section concludes that shape dimorphism is unlikely to be an important factor in explaining differences between fossil hominin pedal remains. The second section explores the inter-specific relationship between the tarsals of the extant hominoids. It is found that shape differences between taxa closely mirror those differences already described in the literature. However, it is found that the phenetic relationship between the taxa varies from bone to bone, and, furthermore, does not match the consensus molecular phylogeny. The section concludes that some tarsals are more specialised and remodelled than others, and thus great caution should be taken when considering isolated fossil pedal specimens. The third section incorporates the fossil specimens into the study. It is found that the morphology of the A. africanus and H. habilis tarsals are very similar, and fall within extant hominoid intra-specific ranges of variation. However, the morphology of the A. afarensis tarsals are considerably distinct, and show a different overall pattern to those of A. africanus and H. habilis. The section concludes that all taxa were mosaic in their affinities, but were mosaic in different ways. This thesis concludes that it is likely that there were at least two distinct ways in which the tarsals of different hominin taxa had adapted to bipedal locomotion. This finding supports recent new discoveries suggesting a far wider degree of taxonomic diversity in the African fossil hominin record than had previously been thought.
Antimicrobial activity of selected plant spices marketed in the west Anatolia

Herbs and spices are sources of many bioactive compounds that can improve the taste of foods as well as influence digestion and metabolism processes. The present study was performed to evaluate the antimicrobial activity of ten Turkish medicinal plant spices, used in the traditional system of medicine, against 10 pathogenic bacterial species and yeast, C. albicans, using the agar well diffusion method. Anti-candidal activity was detected in 8 plants. Extracts of Alchemilla vulgaris, Laurus nobilis, Melissa officinalis, Silybum marianum, Camellia sinensis (5a), Camellia sinensis (5b), Rosmarinus officinalis, Hibiscus sp. and Foeniculum vulgare showed broad-spectrum antimicrobial activity with inhibition zones ranging from 4 to 32 mm, except Erica vulgaris. The most resistant microorganisms were Escherichia coli and Salmonella typhimurium. The most susceptible organisms were Kocuria rhizophila and Candida albicans. Minimum Inhibitory Concentrations (MIC) of crude extracts were determined for the three highly active plants showing activity against Staphylococcus aureus, Escherichia coli; Kocuria rhizophila, Bacillus cereus, Enterococcus faecalis and Candida albicans. MICs of active extracts ranged from 2.92 to 10≤mg/mL against one or other test bacteria. © 2010 Friends Science Publishers Key Word: Antimicrobial activity; Spices; Resistant; Microorganisms; West Anatolia
The Effect of Supplemental Probiotics and Spray-Dried Egg Proteins on Piglet Growth Performance Characteristics

This study evaluated the use of a supplemental probiotic, containing spray-dried egg proteins and several different dried bacteria. The objectives of this study were to determine if the probiotic supplement affected growth performance of the piglets, fecal consistency, and the number of Escherichia coli and Lactobacillus species present in the feces. The supplemental probiotic was administered at three intervals with fecal samples being collected at four intervals. Weights were collected at five intervals. There were no differences (P > 0.05) in 21-day, weaning, nursery, or finishing floor weights between treatment and control groups. There were no differences (P > 0.05) in fecal scores in the farrowing house, nursery, or finishing floor between treatment and control groups. There were no differences (P > 0.05) in the number of Escherichia coli or Lactobacillus species present in the fecal material, between treatment and control groups, at all intervals measured.
Effect of prey on predation, growth and biology of green lacewing (Chrysoperla zastrowi sillemi)

The larvae of the polyphagous predator, green lacewing [Chrysoperla zastrowi sillemi (Esben-Petersen)] was reared on natural prey including cabbage aphid (Brevicoryne brassicae), bean aphid (Aphis craccivora), nymphs of okra jassid (Amrasca biguttula biguttula), eggs and neonate larvae of Spodoptera litura and eggs of Corcyra cephalonica to study the effect of prey regimes on the predation and the biology of the predator. The lacewing grub preyed significantly highest number of prey units (415.50 eggs/ grub) of C. cephalonica eggs which was significantly more than the S. litura eggs (250.60 eggs/ grub), A. biguttula biguttula (185.00 nymphs/ grub), B. brassicae (127.50 aphids/grub), A. craccivora (119.00 aphids/grub) and neonates of S.litura (62.25 larvae/grub). The larval duration varied from 7.50 to 15.235 days on different preys which was seven day less in the grubs reared on eggs than the grubs fed on insect as prey. Larval survival was significantly highest (97.82%) on C. cephalonica eggs. The pupal period varied from 7.50 days to 8.63 days. The grubs reared on eggs of C. cephalonica and S. litura showed longer pupal period. On insects as prey, the growth index (GI) of larvae was significantly less (5.56–8.58) compared to the larvae reared on egg-hosts. The weight of grubs preying on other hosts was 35–50% less compared to those reared on C. cephalonica eggs. Relative inadequacy of lepidopteran neonates and aphids except B. brassicae as prey for the young larvae adversely affected the larval survival, GI and adult emergence may be due to reduced nutritional support exerting adverse effect on growth and causing moulting distress.