Miracle-dz/UniFAR-FTUs huggingface dataset:
The current status and management of South Africa's chondrichthyan fisheries§

Chondrichthyans (sharks, skates, rays and chimaeras) are captured in many marine fisheries. Management and research efforts directed at chondrichthyan fishing are often neglected because of low product value, taxonomic uncertainty, low capture rates, and harvesting by multiple fisheries. In South Africa's diverse fishery sectors, which include artisanal as well as highly industrialised fisheries, 99 (49%) of 204 chondrichthyan species that occur in southern Africa are targeted regularly or taken as bycatch. Total reported dressed catch for 2010, 2011 and 2012 was estimated to be 3 375 t, 3 241 t and 2 527 t, respectively. Two‑thirds of the reported catch was bycatch. Regulations aimed at limiting chondrichthyan catches, coupled with species‑specific permit conditions, currently exist in the following fisheries: demersal shark longline, pelagic longline, recreational line, and beach‑seine and gillnet. Limited management measures are currently in place for chondrichthyans captured in other South African fisheries. Catch and effort dataseries suitable for stock assessments exist for fewer than 10 species. Stock assessments have been attempted for five shark species: soupfin Galeorhinus galeus, smoothhound Mustelus mustelus, white Carcharodon carcharias, spotted ragged‑tooth Carcharias taurus, and spotted gully Triakis megalopterus. Fishery‑independent surveys and fishery observer data, which can be used as a measure of relative abundance, exist for 67 species. Compared with most developing countries, South African shark fishing is relatively well controlled and managed. As elsewhere, incidental capture and bycatch remain challenges to the appropriate management of shark species. In 2013, South Africa's National Plan of Action for the Conservation and Management of Sharks (NPOA‑Sharks) was published. Implementation of the NPOA‑Sharks should help to improve chondrichthyan management in the near future.
Studies on Skeletal Muscle Histology of Datong Yaks at Different Development Stages

Datong yaks from plateau and cattle from plain at different development stages were researched to reveal the adaptation characteristics of yak skeletal muscle fiber structue to the plateau hypoxia environment and to reveal the developmental characteristics of yak in hypoxia environent.Muscle fiber diameter and surface area density skeletal muscle were assayed by histological method.Results showed as follows: Muscle fiber diameter of skeletal muscle in Datong yaks and plain cattle increased significantly(P0.01) but surface area density of skeletal muscle decreased strikingly(P0.01) following growth.Fiber diameter of skeletal muscle in Datong yaks was compared with that in plain cattle at the same ages.Results showed that skeletal muscle fiber diameters of yaks at 1-day-old,30-day-old,and adult were greater than those of cattle at the same ages,but the diameter of 180-day-old yaks was smaller than that of cattle.Compared with same age cattle,skeletal muscle surface area densities were smaller at 1-day-old,30-day-old,and adult yaks,but greater at 180 day.These results were opposite to the results about fiber diameter.
Analysis of 6-cys proteins and calcium fluxes during erythrocyte invasion by Plasmodium falciparum parasites

i DECLARATION iii PREFACE iv PUBLICATIONS v ACKNOWLEDGEMENTS vi TABLE OF CONTENTS vii LIST OF FIGURES x LIST OF TABLES xii CHAPTER 1 Literature Review 1 Malaria 1 Malaria control, cure, and prevention 2 The Plasmodium life cycle 4 Merozoite invasion of erythrocytes 8 Merozoite surface proteins 9 Erythrocyte binding antigens and reticulocyte binding protein homologs 12 Apical membrane antigen and rhoptry neck proteins 18 The 6-cys protein family 22 Signaling during erythrocyte invasion 26 Aims of research 30 Functional analysis of 6-cys domain proteins in blood-stage malaria parasite 31 Live-cell microscopic analysis of Ca signaling and its role in erythrocyte invasion 31 CHAPTER 2 Materials and Methods 41 Parasite media and solutions 41 Bacterial media 43 Molecular biology reagents 44 Recombinant protein expression reagents 46 Zeiss AxioObserver Z1 filter sets 47 Experimental procedures 48 Parasite culture techniques 48 Molecular biology techniques 51
Recent advances in breeding for quality chickens

White-feathered broilers dominate world poultry meat production owing to their rapid growth and high feed efficiency. However, consumers' preference for colour-feathered and slow-growing meat-type quality chickens is growing in certain regions of the world. Among them, the ‘Three Yellow’ of China and ‘Label Rouge’ in France are two famous examples. The appearance (plumage, skin, combs and so on), meat flavour, and meat texture are the main attributes that attract customers to purchase them. For practical breeding, quality chickens were initially produced by direct use of native chicken breeds, which are generally slowly-growing with poor feed conversion. Currently, the breeding for quality chickens in China is characterized with crossbreeding between native breeds and highly-selected lines with rapid growth rate or relatively high egg production. The breeding objectives focus on improving growth rate and reproductive efficiency while maintaining original appearance characters of native chicken such as plumage colour, body shape, comb shape, skin and shank colour and so on. The performances of native chickens have been greatly improved by crossbreeding. Two-way or three-way crossing is commonly used in producing commercial quality chickens in China. In some cases, the dw gene has been introduced into maternal line for better reproduction efficiency and lower feed cost. For future development, breeders and producers will place more and more breeding significance on meat quality traits, which include meat flavour, tenderness, fat deposition, muscle fibre composition, visual characters and so on. As evaluation of these traits is expensive and time-consuming, new molecular markers will play more important roles. Once reliable markers are identified, early marker assisted selection can be performed with great selection accuracy and without slaughtering. Attempts to identify candidate genes related to meat flavour, muscle fibre, lipid metabolism and other physical characters have brought great potentials for future breeding of quality chickens.
The study of candidate sialometabolism genes and sialometabolism gene regulation in Haemophilus influenzae

Sialic acid (SA) is a known major virulence factor of Haemophilus influenza (Hi). This study aims to analyse the functions of some candidate sialometabolism genes, and to further our current understanding on the Hi sialometabolism gene regulation. Two candidate sialometabolism genes (HI0227 and HI0148) and their adjacent ORFs (HI0228, HI0148.1 and HI0149) were studied. HI0148.1 and HI0149 are transcribed as a single gene in screened NTHi strains, and we refer to the combined ORF as NTHI0236 (the designation in strain 86-028NP). Across Hi strains screened, the sequences of HI0227, HI0148 and NTHI0236 are conserved. However, the sequence of HI0228 is heterogeneous. Mutants that lack the functions of HI0227, HI0228, HI0148 and NTHI0236 were compared to their respective wild type parent strains for ability to grow on SA (in aerobic and microaerophilic conditions), their ability to sialylate LPS and their ability to resist complement mediated killing. The mutants did not exhibit major differences in the tested aspects of sialometabolism compared to their respective wild type strains. Changes observed in some of the mutants in serum bactericidal assays and LPS profiles were due to the effect of phase variable genes. The sialometabolism functions of HI0227, HI0148, and NTHI0236 remain obscure, and we postulate that HI0228 is a pseudogene. Investigation of Hi sialometabolism gene regulation was conducted using mutants that lack different steps of the Neu5Ac catabolism pathway and the Neu5Ac activation pathway. The expression of nanE and siaP, respectively representing the Neu5Ac catabolism and transport operons, were assessed using RT-PCR and qPCR. We investigated a temporal/concentration effect of Neu5Ac on the expression of sialometabolism operons, which highlights the importance of studying the Hi sialometabolism gene regulation as a dynamic process. We further demonstrated that GlcN-6P, a Neu5Ac intermediate from the catabolism pathway, is likely the SIS sugar that interacts with SiaR, the repressor protein of the Hi sialometabolism operons. We postulate that upon binding of GlcN-6P to SiaR, the SiaR-mediated repression on the Hi sialometabolism operons is relieved, resulting in the induction of the expression of Neu5Ac catabolism and transport genes.
EVOLUTION OF FITNESS IN EXPERIMENTAL POPULATIONS OF DROSOPHILA PSEUDOOBSCURA

The genetic analysis of populations evolving by natural selection has been, in the past, mainly confined to natural populations (Dobzhansky, 1947a, 1952, 1956, 1958; Epling and Lower, 1957; Ford, 1953; Kettlewell, 1961; and others). Such natural systems, however, present many observational difficulties in respect to the numerous changes (new mutation, recombination, migration, selection, sampling effects) occurring in an evolving population. To achieve some measure of experimental control over these factors, it may prove of value to seek out actively changing laboratory populations which would permit testing for fitness changes as they are subjected to natural selection under varied conditions. Such evolving laboratory systems have already been described in Drosophila by observing the change in competitive success of a population both before and after laboratory "evolution. " Moore (1952) noted an increase in fitness of D. simulans that had been subjected to competition with D. melanogaster, as compared to D. simulans which had not been subjected to this competition. Buzzati-Traverso (1955) found an improvement of the competitive ability of a wild-type strain of D. melanogaster after it had been in competition with a mutant strain. Lewontin (1958) isolated Arrowhead third chromosomes from a polymorphic laboratory population of D. pseudoobscura and showed them to have acquired a competitive fitness supe-
Accompanying migration of natural enemies and biodiversity

It was found in radar observations and marine samples that the phenomena of accompanying migration by natural enemies (including aeronautic spiders) with their hosts was significant and spectacular. The phenomena shows that the interaction between different trophic levels of natural enemy insect and pest plant is undoubtedly of important ecological and behavioral significance. The great difference of natural enemy catches in aerial samples between different areas in the tropics and the temperate zone reflects the different backgrounds of biodiversity. The long term monitoring of bio flux in the low level atmosphere would provide reliable information on biodiversity.
The aortic and carotid sinus baroreflexes contribute equally to control blood pressure and heart rate variabilities

Baroreflexes are important in stabilizing blood pressure (BP). Disrupting the reflexes, e.g., via sinoaortic denervation (SAD), largely increases BP variability (BPV), which contributes to end‐organ damage. Because baroreflexes are often destructed separately in clinic, this study examines the individual role of aortic and carotid baroreflexes in BPV.
Integration of Germline and Somatic Variation in Tumor Data

During tumor inception and progression, culprit gene variants confer selective advantage to progenitor cancer cells, allowing them to outcompete normal cells and proliferate uncontrollably. Both regions of somatic amplification as well as germline DNA sequence changes may be variants that are positively selected by the tumor. Traditionally, these two variant classes have been studied independently. While many discoveries have been made in such a manner, independent examination of these classes possesses certain limitations. Integrated examination of these two classes holds the potential to reveal specific nucleotide alleles that are amplified in the tumor, which in turn may reveal proximal genes. We present methods that focus on such integration. The first, the Amplification Distortion Test (ADT), aims to detect nucleotide alleles that are selectively amplified across tumor samples. Motivated to apply ADT on nascent next generation sequencing data, we developed a novel Hidden Markov Model-based method—Haplotype Amplification in Tumor Sequences (HATS)—that analyzes tumor and matched normal sequence data, along with training data for linkage information, to infer amplified alleles and haplotypes in regions of copy number gain. HATS is designed to handle biases in read data as well as accommodate rare variants. We demonstrate that HATS infers the amplified alleles more accurately on simulated and real tumor data than does an alternate naive approach, especially at low to intermediate sequence coverage levels, and when allele-specific biases or stromal contamination is present. We present these methods with the motivation that they may aid the cancer community in identifying novel causal or associated putative variants.
Regular Use or on Demand of Inhaled Corticosteroids for the Management of Bronchial Asthma among Libyan Patients

Asthma is two stage process that can be defined as a chronic inflammatory disease and bronchial hyper-responsiveness that leads to reversible airways obstruction, either spontaneously or following medication [1]. Although everyone’s airway has the ability to obstruct in response to allergens, the asthmatic’s airways are very sensitive. As the airways become obstructed, more effort is required to force the air through and therefore breathing is very difficult together with wheezing and coughing. Asthma cannot be cured, but it can be managed and with proper treatment, people with asthma can get normal and active lives.
Histopathology and Bacterial Populations of Atypical Symptoms-Inducing Xanthomonas axonopodis pv. citri Strains in Leaves of Grapefruit and Mexican Lime

Histopathology of atypical symptoms-inducing Xanthomonas axonopodis pv. citri (Xac) strains XW47 (type Xac-A') and XW121 (type Xac-A') in citrus leaves was examined with light and electron microscopy, and compared with that of a typical Asiatic citrus canker strain XW19 (type Xac-A). Strain XW47 induces typical canker lesions on leaves of Mexican lime (Citrus aurantifolia) but causes flat necrotic lesions with water soaked margin on leaves of grapefruit (C. paradisi): whereas strain XW121 induces restricted and raised corky lesions without watersoaked margin on both citrus leaves. Light microscopic examinations showed that XW47 induced hyperplasia and hypertrophy of mesophyll cells and ruptures of the epidermis as those observed in Mexican lime leaves induced by XW19. However, neither hypertrophic cells nor eruption of the epidermis were observed in the brownish necrotic and hyperplastic mesophyll tissues induced by XW47 on grapefruit leaves. A distinct layer of lignified tissues around the brownish disintegrated erumpent tissues in which masses of fibrillar matrix agglutinated with bacterial cells was observed in the sections of a restricted and raised corky lesion induced by strain XW121. Bacterial populations of strain XW121 in mesophyll tissues were approximately 10^3 folds lower than those of XW19 and XW47 under a lower inoculum concentration, but increased to those of XW19 and XW47 under a higher inoculum concentration. Although XW19 and XW47 induced distinct symptoms on grapefruit leaves, no significant difference of bacterial growth was observed.
Seminal Receptacles in the Eastern Box Turtle, Terrapene carolina

Tubular albumen-secreting glands in the oviducts of the eastern box turtle (Terrapene carolina) can serve as seminal receptacles. The glands containing spermatozoa are restricted to the caudal portion of the albumen region of the oviduct, and open to the lumen of the oviduct either via breaks in the overlying mucosal epithelium or through ducts formed by invaginations of the mucosal epithelium. Spermatozoa were identified in the seminal receptacles of females isolated from males for varying periods up to 14 months.
Physiological variations of blood pressure according to gender and age among healthy young black Africans aged between 18 and 30 years in Côte d’Ivoire, West Africa

In Africa, abnormal high blood pressure is common and affects young subjects. The risk of organ damage and mortality increases with blood pressure level. Therefore, the purpose of this study was to assess the blood pressure profile of a black African population aged between 18 and 30 years in Côte d’Ivoire. Five hundred fifty‐one healthy black African students, men and women, with sedentary lifestyle, aged between 18 and 30 years were selected. Systolic (SBP) and diastolic (DBP) blood pressures and heart rate were recorded after 5 min of rest. Regression models were used to estimate the effects of age, gender, and body mass index (BMI) on SBP and DBP. Each increase of 1 year in age and 1 kg/m2 of BMI is significantly associated, respectively, with an increase of 20% (p = .002) and 17% (p = .008) in the risk of having an SBP ≥ 130 mmHg. The same risk is 3.8 times greater for men than women (p = .01). Among subjects with SBP < 120 mmHg, men have an SBP 5.22 mmHg higher than women (p < .001). The increase in the age of 1 year is significantly correlated with a rise of 36% of having a DBP ≥ 85 mmHg (p = .0001). Also, in men population, the age increase of 1 year is associated with a rise of 41% of having a DBP ≥ 85 mmHg (p = .0001). Among young black African students aged between 18 and 30 years in Côte d’Ivoire, SBP is positively associated with male gender, age, and BMI. For DBP, it is only an increase with age.
CD163 deficiency facilitates lipopolysaccharide‐induced inflammatory responses and endotoxin shock in mice

Septic (or endotoxin) shock is a severe systemic inflammatory disease caused by bacteraemia or endotoxaemia. Although it is known that increased serum levels of CD163 are observed in septic/endotoxin shock patients, the exact function and significance of CD163 in macrophage activation remain unclear. Therefore, in the current study, we tested whether CD163 contributes to the pathogenesis of endotoxin shock in mice.
Comparative Study between Metformin and Insulin in Controlling Gestational Diabetes Mellitus

Background: the use of antidiabetic drugs to control gestational diabetes was controversial. Some studies suggest a possible link between the use of oral antidiadetics and fetal anomalies, fetal macrosomia and neonatal hypoglycemia whereas others have demonstrated no such relationship. Objective: This study aims to assess the efficacy of metformin in controlling maternal blood glucose level compared to insulin in women with GDM. Patients and Methods: The present study included 116 pregnant women who have been diagnosed as gestational diabetics before 34 weeks gestation with singleton pregnancy. They had FBG level ranging from 90- 169 mg/ dl or 2-hour postprandial blood glucose level ranging from 110-176 mg/dl. The exclusion criteria include pregnant women with preexisting DM and underlying diseases known to affect fetal growth, preeclampsia, unbalanced chronic disease, twin pregnancy, or refused to participate. Results: Comparison of the baseline characteristics was performed between 2 groups and there were no significant differences between the two groups regarding maternal age, gravidity, parity, GA at time of diagnosis, GA at beginning of treatment, and BMI at time of diagnosis. Analysis of the results revealed that metformin was an effective medication for control of euglycemic with diet only.
Comunidad de Helmintos Parásitos del Sapo Espinoso Rhinella spinulosa (Wiegmann, 1834) (Anura: Bufonidae) de Perú

The aim of this study was to evaluate the community of metazoan parasites of thorny toad Rhinella spinulosa of Peru and elucidate whether sex and the total length of the hosts amphibians are structuring their communities of parasites. Ninety specimens of R. spinulosa were acquired during May 2009 to October 2010. The body cavity, gastrointestinal tract, bladder, lungs and muscles were examined to search for metazoan parasites. Seven taxa of metazoan parasites were collected: one digenean [Gorgoderina chilensis (Gorgoderidae) in the bladder] a cestode [Cylindrotaenia aff. americana (Proteocephalidae) in the small intestine], four nematodes [Aplectana hylambatis and A. vellardi (Cosmocercidae) in the large intestine, Hedruris moniezi (Hedruridae) in the stomach and Rhabdias aff. pseudosphaerocephala (Rhabdiasidae) in lungs] and one acanthocephalan [Pseudoacanthocephalus lutzi (Echinorhynchidae) in the small intestine]. A positive correlation was observed between length and mean abundance of R. aff. pseudosphaerocephala, and an association between sex and mean abundance of G. chilensis, A. hylambatis and R. aff. pseudosphaerocephala. G. chilensis showed dependence on the sex of R. spinulosa. The three levels of aggregation (dispersion index, index discrepancy of Poulin and K negative binomial equation) showed a contagious distribution. Most of the values of alpha diversity of parasitic infracommunities were lower than those of the community component.
Proteins of the canine seminal plasma

Studies have been performed to identify the proteins present in canine seminal plasma (SP) and relate them to sperm quality as well as to discover molecular markers of reproductive tract diseases. There is evidence that heparin-binding proteins, zinc-binding proteins, and lactoferrin as well as the matrix metalloproteinase, superoxide dismutase, catalase, and glutathione peroxidase enzymes are associated with canine sperm quality. Other studies indicate that prolactin and enzymes like arginine esterase, acid phosphatase, and alkaline phosphatase could be successfully used as biomarkers of reproductive disorders. Thus, the present literature review aims to address aspects related to proteins of the canine SP, their influence on fertility, and their importance as biomarkers of reproductive disorders.
An Overview of the Ilium of Anurans (Lissamphibia, Salientia), with a Critical Appraisal of the Terminology and Primary Homology of Main Ilial Features

ABSTRACT The ilium has been considered a ‘key’ element in anuran paleontology, but its terminology is inconsistent across the literature. Therefore, we here review the terminology used so far to describe anuran ilia and provide an annotated glossary of main ilial features. We also survey ilial morphology and comment on variation exhibited by each ilial feature among major anuran lineages. We do so with special consideration for myological correlates, provide muscle maps for a few species, and aim to clarify hypotheses of primary homology. We consider previous work that compartmentalizes part of the described variation into cladistic characters, with the intention of providing a starting point for using ilial features in future research on osteology-based phylogenetics of anurans. Finally, we remark on some aspects regarding the dorsal prominenceprotuberance complex.
Effects of Biological Factors on the Diversity of Arbuscular Mycorrhizal Fungi

Arbuscular Mycorrhizal (AM) fungi distribute in various ecosystems in the nature. The diversity of AM fungi was significantly influenced by ecological factors, such as animals, plants, microorganisms and anthropogenic factors. The advances in this field in the recent ten years were reviewed and problems were also discussed.