Miracle-dz/UniFAR-FTUs huggingface dataset:
A new species of the genus Phymorhynchus (Neogastropoda: Raphitomidae) from a hydrothermal vent in the Manus Back-Arc Basin

During an investigation carried out by the Institute of Oceanology, Chinese Academy of Sciences (IOCAS), three living raphitomid specimens were collected from a hydrothermal vent site in the Manus Back-Arc Basin. Observations of the shell, external anatomy and radular morphology reveal that they represent an undescribed species of the genus Phymorhynchus Dall, 1908. In this paper, we describe and illustrate this species as Phymorhynchus oculatus sp. nov. The new species is most similar in general shell shape to Phymorhynchus buccinoides Okutani, Fujikura & Sasaki, 1993, but can be distinguished from it by having spiral cords over the whole shell surface and much longer marginal tooth with a distal barb. A list of species of Phymorhynchus from vent/seep habitats is also given.
Effects of sufentanil pretreatment on myocardial ischemia-reperfusion injury in rats

Objective To investigate the effects of sufentanil pretreatment(SPC) on myocardial ischemiareperfusion (I/R) injury in rats. Methods Thirty-six male SD rats weighing 250-350 g were randomized into 6 groups (n = 6 each) : group Ⅰ sham operation (S) ;group Ⅱ I/R ;group Ⅲ ischemic pretreatment + I/R (IPC) ;groupⅣ,Ⅴ,Ⅵ SPC (0.05, 0.2 and 1.0 μg·kg-1·min-1) + I/R (SPCI,2,3). The animals were anesthetized with pentobarbital sodium 60 mg/kg intraperitoneally. The left anterior descending branch of coronary artery was temporarily ligated for 30 min followed by 120 min reperfusion. In group Ⅲ (IPC) the animals were subjected to 3 episodes of 5 min myocardial iscbemia at 5 min intervals before I/R. In group Ⅳ, Ⅴ and Ⅵ (SPCI, 2,3) the animals received 3 episodes of 5 min sufentanil infusion at 0.05, 0.2 and 1.0 μg·kg-1· min-1 respectively at 5 min intervals before I/R. HR, LVSP, LVEDP and ± dp/dtmax were measured and left ventricular developed pressure (LVDP) was calculated immediately before (T0), at the end of 30 min ischemia (T1) and at 30 (T2) 60 (T3) and 120 min of reperfusion (T4). The severity of arrhythmia was assessed at T2 . The animals were killed at T4. Plasma MDA concentration and SOD activity were determined. The infarct size (IS) and the area at risk (AAR) were measured by TIC staining. Results The plasma SOD activity was significantly decreased in group Ⅱ-Ⅵ as compared with group S. The plasma MDA concentration was significantly increased by I/R in group Ⅱ as compared with group S. IPC and SPC attenuated the I/R-induced increase in plasma MDA concentration in group Ⅲ , Ⅳ, Ⅴ and Ⅵ. The arrhytlunia score and IS/AAB were significantly lower in group IPC and SPC1,2,3 than in group I/R.Conclusion Sufentanil pretreatment can protect myocardium against I/B injuryat the dose of 0.05,0.2 and 1.0 μg·kg-1·min-1 in rats. Key words: Sufentanil; Myocardial reperfusion injury
Genome-Wide Identification of the Dehydrin Genes in the Cucurbitaceae Species

Dehydrins (DHNs) are hydrophilic proteins with conserved lysine-rich K-segment, which belong to Group II of the late embryogenesis abundant (LEA) protein family. DHNs are considered as molecular chaperons playing important roles in abiotic stress tolerance. In this study, DHN genes were identified through genome-wide searches in five Cucurbitaceae species, including cucumber, wild cucumber, melon, watermelon, and bitter gourd. Three to five DHN genes were found in each of the five species, which were further divided into several protein architecture types based on the presence and order of the major conserved motifs such as K-, Y-, and S-segments. In silico expression profiling using RNA-Seq data revealed high expression of SK3-type DHN gene and low expression of other type DHN genes in cucumber and melon. In silico promoter analysis identified a number of cis-acting element-like sequences related to abiotic stress-response such as DRE and ABRE in 2-kb putative promoter sequences. DHN genes identified in this study will be valuable for understanding the stress response mechanism as well as assisting molecular breeding in Cucurbitaceae crops.
Elucidating the immunomodulatory mechanisms of the KSHV protein vOX2

CD200 is a transmembrane protein with known immunoregulatory activities exerted via its receptor, CD200R. The Kaposi’s sarcoma associated-herpesvirus (KSHV) ORF K14 lytic cycle gene product, vOX2, shares 36% protein identity with cellular CD200. Both vOX2 and CD200 ligate CD200R with similar affinity. The main aim of this project was to determine whether vOX2 and CD200 regulate the function of human leukocytes. Thus, vOX2, CD200 and an inactive KSHV protein KCPmut were fused to the Fc region of human IgG1. vOX2:Fc and CD200:Fc exerted no effect upon isolated neutrophils, but suppressed granulocyte oxidative activity in whole blood by up to 25%. B lymphoblastoid cells were engineered to express full-length vOX2 or CD200 and utilized as antigen-presenting cells for Epstein Barr Virus-specific human T cell clones. vOX2 and CD200 suppressed IFNγ production by up to 50% in seven CD8\(^+\) CD200R\(^+\) T cell clones and one CD4\(^+\) CD200R\(^+\) clone. Mechanistically, vOX2 and CD200 suppressed the phosphorylation of ERK1/2, p38 and Akt kinases. This is the first evidence of a role for both cellular CD200 and KSHV vOX2 in negatively modulating antigen-specific T cell activity. The negative regulation of T cells by vOX2 probably contributes to KSHV evasion of antigen-specific T cell responses during lytic replication.
Biological and physical characterization of the seabed surrounding Ascension Island from 100–1000 m

Recent studies have improved our understanding of nearshore marine ecosystems surrounding Ascension Island (central Atlantic Ocean), but little is known about Ascension's benthic environment beyond its shallow coastal waters. Here, we report the first detailed physical and biological examination of the seabed surrounding Ascension Island at 100–1000 m depth. Multibeam swath data were used to map fine scale bathymetry and derive seabed slope and rugosity indices for the entire area. Water temperature and salinity profiles were obtained from five Conductivity, Temperature, Depth (CTD) deployments, revealing a spatially consistent thermocline at 80 m depth. A camera lander (Shelf Underwater Camera System; SUCS) provided nearly 400 images from 21 sites (100 m transects) at depths of 110–1020 m, showing high variability in the structure of benthic habitats and biological communities. These surveys revealed a total of 95 faunal morphotypes (mean richness >14 per site), complemented by 213 voucher specimens constituting 60 morphotypes collected from seven targeted Agassiz trawl (AGT) deployments. While total faunal density (maximum >300 m−2 at 480 m depth) increased with rugosity, characteristic shifts in multivariate assemblage structure were driven by depth and substratum type. Shallow assemblages (~100 m) were dominated by black coral (Antipatharia sp.) on rocky substrata, cup corals (Caryophyllia sp.) and sea urchins (Cidaris sp.) were abundant on fine sediment at intermediate depths (250–500 m), and shrimps (Nematocarcinus spp.) were common at greater depths (>500 m). Other ubiquitous taxa included serpulid and sabellid polychaetes and brittle stars (Ophiocantha sp.). Cold-water corals (Lophelia cf. pertusa), indicative of Vulnerable Marine Ecosystems (VMEs) and representing substantial benthic carbon accumulation, occurred in particularly dense aggregations at <350 m but were encountered as deep as 1020 m. In addition to enhancing marine biodiversity records at this locality, this study provides critical baseline data to support the future management of Ascension's marine environment.
Sequences of mitochondrial DNA suggest that Echinocardium cordatum is a complex of several sympatric or hybridizing species: A pilot study

Sequence data from the 16S ribosomal gene of the mitochondrial genome were obtained for 10 individuals of the irregular sea urchin Echinocardium cordatum (Pennant 1777) (Loveniidae, Spatangoida), with one individual of Echinocardium flavescens (O.F. Muller, 1776) as an outgroup, plus one individual of Abatus cordatus (Verrill, 1876) (Schizasteridae, Spatangoida) as a more distant outgroup. Eighteen additional individuals were analysed for their Taa 1 restriction digestion profile at the same locus. This preliminary data set gave unexpected results. Eight different E. cordatum haplotypes were found and their phylogenetic relation- ships were established. They form two well supported monophyletic groups, clades A and B. Haplotypes of Glade A were found only in the samples from the Atlantic ocean, whereas haplotypes of Glade B were found in both Mediterranean and Atlantic locations. A and B haplotypes are found sympatrically in an Atlantic sample. Clade B can be divided in Glade B1 (two haplotypes) and Glade B2 (four haplotypes). Using fossil evidence within the genus Echinocardium, we inferred that more than six million years separate clades A and B, and more than two million years separate clades B 1 and B2. These large divergence times, the absence of haplotypes dis- playing nucleotide sequences intermediate between these groups of haplotypes, and the reduced divergence within each Glade suggest that they belong to different taxa, which were probably geographically separated in the past. Sequence data or genotypes from nuclear markers are necessary to establish if these putative pairs of taxa are now hybridising or sympatric species.
The complete mitochondrial genome of Axis porcinus (Mammalia: Cervidae) from Victoria, Australia, using MiSeq sequencing

Abstract The mitochondrial genome of the hog deer (Axis porcinus) was sequenced using an Illumina MiSeq. The assembled genome consists of 16,351 bp, and shared a 99.8% similarity to the published chital deer (Axis axis) genome, suggesting that they belong to the same species. Further research is ongoing to understand why these mitochondrial genomes are highly similar.
ATP-activated currents and calcium signalling in adult murine supporting cells

Purinergic P2 receptors are present in the adult organ of Corti however their role and cellular effects of their stimulation are unclear. To date studies have been hampered by the relative difficulty of accessing intact adult organ of Corti tissue. In this study a novel dissection technique which enabled easy access to the apical turn of the adult mouse organ of Corti was used. The goal of the current study was to determine the distribution of P2 receptors and determine the effect of ATP on membrane conductances in inner sulcus (IS) supporting cells and supporting cells surrounding the IHC afferent synapse in the adult mouse organ of Corti. Purinergic P2 receptors were localized immunohistochemically and functionally to multiple supporting cells of the organ of Corti. In patch clamp electrophysiology recordings application of extracellular ATP to gap junction coupled IS cells, elicited inward currents and transiently increased resting membrane resistance while making the resting zero current potential more positive. Transmitted brightfield imaging showed that the electrophysiological changes were accompanied by a decrease in cytoplasmic Brownian movement. In IS cells decoupled with gap junction blockers stimulation with ATP elicited monophasically declining membrane currents. In contrast in decoupled border cells surrounding the IHC afferent synapse ATP activated biphasic currents. The initial component of the currents elicited in border cells desensitized during sustained stimulation and showed high inward rectification, characteristic of some P2X receptor subtypes. In contrast the delayed component was identified as a Ca2+-activated Cl- channel. It is argued that these conductances could help decrease the potassium concentration around the IHCs during periods of sustained IHC stimulation and thus affect the membrane potential of these sensory cells. In addition, actively propagating, gap junction-mediated, extracellular ATP-independent Ca2+ waves were observed to propagate along the organ of Corti in the IS and Deiters’ cell regions. These increases in intracellular Ca2+ levels were periodic. Currently the role of the waves is unclear, however increases in intracellular Ca2+ of a similar frequency and periodicity have been linked to the regulation of gene expression. Thus the observed waves could be a new mechanism regulating gene expression in the organ of Corti.
Antioxidant activity of inulin derivatives with quaternary ammonium

In this paper, three inulin derivatives with quaternary ammonium, including 2-(N,N,N-triethylamine)acetyl inulin chloride (TAIL), 2-imidazoleacetyl inulin chloride (IAIL), and 2-(1-methylimidazole)acetyl inulin chloride (MIAIL) were synthesized via reaction of chloracetyl inulin (CAIL) with tertiary amine. Their antioxidant activity against hydroxyl radicals and superoxide radicals were evaluated in vitro, respectively. Results showed that IAIL had the best scavenging ability on scavenging hydroxyl radicals and superoxide radicals, and the scavenging index is 86.7% and 67.8% at 1.6 mg/mL, respectively. These data indicate that all of the inulin derivatives have better antioxidant activities than inulin, and the quaternary ammonium and imidazole will improve the antioxidant activity of inulin derivatives.
Two new species of Macrorrhyncha Winnertz (Diptera: Keroplatidae) from Turkey, with redescription of Macrorrhyncha thracica Bechev, stat. n. and a key to the Western Palaearctic species of the genus

Tribe Orfeliini (Diptera, Keroplatidae) includes 52 genera (EVENHUIS 2006), only 4 of which have elongated mouthparts: Antlemon LOEW, 1871, Asindulum LATREILLE, 1805, Macrorrhyncha WINNERTZ, 1846 and Cloeophoromyia MATILE, 1970. Detailed data on the morphology and diagnoses of these genera are given in MATILE (1975) for Asindulum and Macrorrhyncha, MATILE (1977) for Antlemon and MATILE (1970) for the Afrotropical Cloeophoromyia. The adults of the genera Antlemon, Asindulum and Macrorrhyncha are known as flower visitors (BECHEV 2010) and are probably pollinators. The genus Macrorrhyncha is known from one species in the Nearctic, five in the Eastern Palaearctic, sixteen in the Western Palaearctic and one in the Oriental Region, in SE China (EVENHUIS 2006). A key to the western Palaearctic species is given in CHANDLER et al. (2005) and to the species in Japan in UETSUGI (2005). In this study two new species from southwest Asiatic Turkey are described and Macrorrhyncha geranias thracica BECHEV is raised to species level based on the study of type material. With these actions the number of the Palaearctic species increases to twenty five.
Dactylogyrus oryziasi n. sp. (Monogenea: Dactylogyridae) from Oryzias latipes (Beloniformes: Adrianichthyidae) in Japan

Dactylogyrus oryziasi n. sp. (Monogenea: Dactylogyridae) is described from the gills of the southern medaka Oryzias latipes (Temminck and Schlegel, 1846) (Beloniformes: Adrianichthyidae) collected from an irrigation canal, Tokushima city, Tokushima Prefecture, Shikoku, Japan. This new species resembles Dactylogyrus rysavyi Ergens, 1970 in having a coiled penis passing through a tube of an accessory piece associated with a sigmoid rod, and shapes of haptoral parts, but these species differ from each other by turns of the penis and a connection point between the rod and tube of the accessory piece. This is the first record of Dactylogyrus from beloniform fish.
The effects of physical activity level, sex, and different exercise protocols on monocyte TLR expression

It has been suggested that moderate exercise contributes to protection against the development of chronic diseases by anti-inflammatory mechanisms that include elevations of anti-inflammatory cytokines and also reduction of the expression of Toll- Like Receptors (TLRs). However, prolonged strenuous exercise has been shown to reduce the function of some immune cells, decrease virus protection and consequently may account for the reason athletes appear more vulnerable to catching Upper Respiratory Tract Infections (URTI). Although it has been proven that some exercise is better than no exercise, it is not clear yet what is the right amount of exercise to elicit beneficial immune responses and to help prevent the development of diseases. Therefore, the general aim of the studies in this thesis was to evaluate the impact of different types of exercise on monocyte TLR expression in participants with different fitness levels. It was found that different acute exercise protocols elicit different changes in TLR2 and TLR4 expression, where an acute bout of strenuous exercise reduced TLR4 expression for a few hours after the completion of the exercise (Chapter 5); however, short two bouts of exhaustive exercise separated by 2 hours did not change TLR4 expression (Chapter 6). In addition, changes in TLR4 expression were related to sex and the physical activity level of the participants (Chapter 4), and should therefore be considered separately when analysing TLR4 expression. Furthermore, high-intensity intermittent training improves participants’ aerobic capacity and modifies the monocyte subpopulation concentration in the blood, with no changes in TLR4 expression. Further research needs to be done in this area to achieve a conclusive finding about changes in TLR4 expression and monocyte subsets after different training protocols, and possible relationships to cytokine production.
Effects of zinc fortification on the plasma fatty acid composition of beninese school children: A randomised, double-blind controlled trial

V OPSOMMING . VII LIST OF ABBREVIATIONS . IX LIST OF SYMBOLS AND UNITS . XI CHAPTER 1: INTRODUCTION . 18 1.1 Background . 18 1.2 Rationale of the study . 20 1.3 Study site . 20 1.4 Research aim . 21 1.5 Research objectives . 21 1.6 Ethical approval . 22 1.7 Dissertation outline . 22 1.8 Research outputs . 22 1.9 Research team . 22 REFERENCES . 24 CHAPTER 2: LITERATURE REVIEW . 26 2.
Human-Exoskeleton Interaction

It is hypothesized that healthy humans can reduce their energy expenditure during walking by wearing an exoskeleton. Exoskeletons are often designed for mechanical efficiency at joint level. This approach disregards the energy savings mechanisms in the human leg like bi-articular muscles and tendons. We use the muscle-reflex model to simulate the experiments by Cain et al. with an ankle exoskeleton actuated by a pneumatic muscle that supports plantarflexion. The muscle-reflex model predicts muscle activations and metabolic rate. The reflexcontrol parameters of the model were optimized for walking with and without support from an exoskeleton. The simulated exoskeleton uses either the EMG signal from the soleus muscle (proportional myoelectric control), or a footswitch to trigger the actuation of the pneumatic muscle. Cain et al. did find an experimental reduction in soleus muscle activation of 41.4 percent for the proportional myoelectric control and 13.0 percent for the footswitch control, where the optimization outcomes of simulated walking predicted a reduction of 42.8 percent and 25.9 percent respectively. 3.
Extraction of type A and type B gelatin from jellyfish (Lobonema smithii).

Type A (acid treated process) and type B (alkaline treated process) gelatin were extracted from the umbrella of desalted jellyfish (Lobonema smithii) by sulfuric acid and sodium hydroxide, respectively, at different temperatures (60 and 75°C) and times (6 and 12 h). The condition of H2SO4 and NaOH used were adjusted to pH 2 and pH 14, respectively. The degree of hydrolysis of type B jellyfish gelatin (77.13%) was greater than that of type A gelatin (65.30%) at 75°C for 12 h. The highest content of soluble protein (203.12 mg/ml) of type A jellyfish gelatin was lower than that of type B jellyfish gelatin (350.02 mg/ml) treated at 75°C for 12 h. The type A of jellyfish gelatin exhibited gel formation only at the condition of 75°C for 6 and 12 h, but type B jellyfish gelatin had no gel formation at all conditions used. The hue color of type A and type B jellyfish gelatin had values in the range of 47.28-83.64 and 82.89-88.58, respectively. In summary only type A jellyfish gelatin exhibiting gel formation can be produced by sulfuric acid hydrolysis (pH 2) at a temperature of 75°C for 12 h.
Assessment of kallikrein-related peptidases 4 and 6 (KLK4 and KLK6) as candidate biomarkers in prostate and ovarian cancer

The protein expression of KLK4 and KLK6 was analyzed in normal and cancerous human prostate and ovarian tissues by IHC using specific antibodies. KLK4 expression was significantly up-regulated in early-stage but not in late-stage prostate cancer, indicating that differential expression of KLK4 carries stage-related prognostic information. In ovarian cancer tumor tissues, only stromal cell-associated KLK6 expression was significant for OS and PFS, indicating that KLK6 expressed by stromal cells may contribute to the aggressiveness of ovarian cancer and may have significant prognostic value.
Structural and biochemical characterization of cell cycle regulatory proteins and associated signaling receptors

This thesis is a collection of three different projects to characterize the biochemical and structural features of proteins important in cancer development. A new hypothesis about the interaction of shugoshin and Mad2 and their role in mitosis is supported by NMR and ITC binding studies Shugoshin binds Mad2 at the binding site of the so called safty belt. To determine the structural basis of the binding mechanisms of a new small molecule inhibitor for CDK2, crystallization of the complex was attempted. This interaction was chosen to prove a novel NMR-based drug screening method. Protein binding is monitored via a simple 1D proton NMR signal of tryptophan and permits rapid screening of potential ligands. The method also provides quantitative characterization of the antagonist-protein interactions in the form of KDs. As a prerequisite for X-ray crystallography and NMR spectroscopy an expression system for the IGF-1 Receptor was established.
Abiotic factors, not herbivorous pressure, are primarily responsible for the performance of an invasive aquatic plant

Morphological performance of invasive plants can be determined by abiotic factors (e.g. water temperature) and biotic factors (e.g. herbivory). This study investigates the performance of an exotic plant in its native and introduced environments. The questions of study are: Is the performance of Egeria densa in both its native and introduced areas associated with abiotic and/or biotic factors? Is the performance of this plant better in the native or in the introduced area? In order to answer these questions, E. densa individuals collected in France (introduced range) were compared with individuals collected in Brazil (native range). The results demonstrate that E. densa populations sampled in its native areas included a higher percentage of plants grazed than in the introduced range populations, but they also exhibited a superior performance in terms of length and dry mass. In both regions, the performance of the plants was associated mainly with abiotic factors. Whereas the higher temperature in its native area may have promoted greater growth in terms of length and dry mass, a lower temperature and high levels of ammonium in French waters might have reduced the development of this plant in its introduced range. The lower performance of E. densa in France should not be associated with abiotic factors alone, since other factors can also be involved, as limited resources or low clonal adaptation. Thus, future studies concerning E. densa performance in France should consider these factors in order to assist in understanding the nature of the plant’s invasiveness in this region.