Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary and conservation genetics of the Seychelles warbler (Acrocephalus sechellensis)

In this thesis, I investigated how evolutionary forces and conservation action interact to shape neutral and adaptive genetic variation within and among populations. To accomplish this, I studied an island species, the Seychelles warbler (Acrocephalus sechellensis), with microsatellite markers and major histocompatibility complex (MHC) genes as measures of neutral and adaptive variation respectively. First, I used museum DNA and historical records to reveal a recent bottleneck that provides context for the contemporary genetic variation observed in this species. I then determined the impact of four translocations on genetic diversity over two decades. I found that diversity does not differ significantly between islands but the use of smaller founder sizes in two translocations has caused population divergence. These results indicate that stochastic genetic capture is important in translocations and that future assisted gene flow between populations may be necessary. As a tool for conservation practitioners, I wrote a technical report of the most recent translocation - to Fregate Island - detailing practicalities and outcomes to help inform future translocation policy. Using two translocation events as experiments, I then tested whether MHC-based social mate choice acts to maintain MHC diversity in the Seychelles warbler, finding that male age and heterozygosity, but not MHC, predicted pairing success. Lastly, I investigated survival and reproductive consequences of Ase-ua4, an MHC class I allele previously shown to confer a survival advantage in the Seychelles warbler. I found widespread patterns of allele frequency increase within cohorts consistent with the survival effect, but no overall increase in population allele frequency over time. I investigated potential antagonistic reproductive mechanisms, but found no clear evidence for why this allele is not driven towards fixation. Collectively, my results provide an interesting case study of the evolutionary conservation approach, whilst providing insight into the importance of maintaining genetic variation in natural populations.
The tasman front

Detailed and repeated vertical temperature sections obtained in August 1975 across the Tasman Front (previously called the Mid Tasman Convergence) show the front to be more sharply defined than previously thought. Velocities in the associated frontal jet up to 0.65 m.s‐1and isopycnal slopes in the front of up to 8 × 10‐3 were observed. The repeated sections showed only small frontal movement in a 2‐week period. Re‐examination of available data in the Tasman Front region shows high spatial and temporal variability in the front. Part of the variability is shown to be topographically induced, particularly on the western flanks of the two major ridge systems. Other contributing processes are largely unknown, although some of the variability probably arises from the highly variable East Australian Current system from which the front is thought to derive. Seasonal changes in frontal intensity may occur and the appearance of the front as a surface feature in winter can be related to seasonal changes in the upper.
Formation of Macroscale Flux Transfer Events at Mercury

Flux transfer events (FTEs) are magnetic flux ropes that are produced via magnetic reconnection at the planetary magnetopause where the solar wind directly interacts with the magnetosphere. Previous observations show that FTEs with a duration of several seconds, corresponding to a spatial scale of ∼0.5–1 RM, can occur at Mercury. However, the formation of these macroscale FTEs at a small dimensional magnetopause with a radius of ∼1.5 RM remains unclear. Here, we report the observations of active magnetic reconnection events at Mercury’s magnetopause by the MESSENGER spacecraft. The reconnection process is dominated by the formation of a series of multi-scale FTEs. Ion-scale flux ropes, typically with durations of ∼1 s or less, may be produced by the tearing instability in the thin current sheet near the subsolar position. Moreover, the commonly observed macroscale FTEs consist of three to tens of successive small-scale FTEs. We propose that macroscale FTEs at Mercury are generated by the interaction and merging of multiple ion-scale flux ropes, probably through two or more steps. This is distinct from the formation of typical FTEs, mainly between a pair of X-lines, at Earth’s magnetopause. Thus, the formation and evolution of FTEs may differ among planetary magnetospheres with a vast range of scale sizes. We further conclude that Mercury’s magnetopause is a natural plasma laboratory to study flux rope dynamics and evolution for the upcoming Bepi-Colombo mission.
Maternal age is not a predominant determinant of progeny sex ratio variation in ungulates

A. J. Mark Hewison, Inst. de Recherche sur les Grands Mammifères, INRA, BP 27, 31326 Castanet-Tolosan, France (hewison@toulouse.inra.fr). – Jean-Michel Gaillard and Pierrick Blanchard, Uni . Claude Bernard, Lyon 1, Unité Mixte de Recherche ‘‘Biométrie et Biologie E oluti e’’, 43 Bl d du 11 no embre 1918, 69622 Villeurbanne, France. – Marco Festa-Bianchet, Dépt de biologie, Uni . de Sherbrooke, Sherbrooke, PQ, J1K 2R1, Canada.
Within-Host Population Dynamics and the Evolution and Maintenance of Microparasite Virulence

We examine effects of the vertebrate immune system on the evolution and maintenance of virulence of microparasites (viruses, bacteria, or unicellular eukaryotes). We employ a mathematical model of the within-host population dynamics of an invading microparasite and the immune response. In this model, the virulence of the parasite is proportional to its rate of replication within the host. We show that if the rate of transmission of parasites from infected hosts is proportional to their within-host density, then the total transmission reaches a maximum for parasites with intermediate rather than low or high virulence. When hosts can only be infected with a single parasite strain, then parasites having intermediate virulence not only release the most transmissible forms from individual infected hosts but also drive other parasite strains to extinction in the population at large. We interpret the results of our analysis of the properties of this model as support for the proposition that the immune system may be responsible for the evolution and maintenance of the virulence of those microparasites that it controls and clears.
Physics puzzles on membrane domains posed by cell biology

Clusters, rafts, nanodomains, and patches are names frequently used to depict cell membranes. This wide vocabulary emphasizes the heterogeneous organization of membrane constituents, which is essential for cellular functions such as signalling, trafficking and adhesion. Despite their diversity, cell membrane domains might share similar physical grounds. In an attempt to integrate them in a general framework, we review here recent studies on domains in adhering and non-adhering membranes. We show that a broad range of biological studies challenged the concepts of membrane physics at thermodynamic equilibrium and enriched the classical physical-chemistry approaches on model systems.
Mitochondrial DNA differentiation between populations of black sea bass (Centropristis striata) across Cape Hatteras, North Carolina (USA)

Phylogeographical ‘breaks’ often occur at biogeographical province boundaries, suggesting common causative factors. Cape Hatteras, North Carolina, on the US Atlantic coast, separates water masses of sharply differing temperature and divides the Virginian and Carolinian provinces, but has not often been detected as a phylogeographical break. We studied the black sea bass, Centropristis striata (Linnaeus, 1758), a species with philopatric adults but long‐lived planktonic larvae. An earlier study of only two Atlantic populations, and lower‐resolution mitochondrial RFLP markers, showed strong separation between the Gulf of Mexico and the Atlantic, but not across Cape Hatteras.
A flood-free period combined with early planting is required to sustain yield of pre-rice sweet sorghum (Sorghum bicolor L. Moench)

Abstract Understanding the responses of sweet sorghum to flooding and the characters associated with flooding tolerance may be a useful strategy for pre-rice production and help meet demand for biofuel feedstock. Three sweet sorghum genotypes (Bailey, Keller and Wray) and five flooding treatments including non-flooding control, continuous flooding extended from 30, 45, 60 and 75 days after emergence to harvest were conducted under greenhouse conditions. Flooding decreased leaf dry weight (22–60%), leaf area (10–70%), number of node per stalk (1–5%), shoot dry weight (5–20%) and stalk yield (2–22%) with highest reduction in 30 days after emergence flooding treatment. Flooding later than 30 days after emergence did not significantly affect shoot growth, yield and yield components. Brix value, sucrose content and total sugar content were not significantly affected. All studied cultivars had similar shoot growth response. Flooding induced development of roots in water; root length, root dry weight, nodal root and lateral root number and interconnection of aerenchyma spaces from roots in flooded soil to stalk base above water level but suppressed root growth in flooded soil. The acclimation traits were highest in Keller, flooding from 30 days after emergence but there was a lack of root development in 75 days after emergence flooding treatments. These findings indicate the effect of waterlogging on sweet sorghum growth and yield strongly depends on the growth stage at which it occurs. There were genetic variations in root morphological and anatomical responses to flooding of sweet sorghum. The development of nodal and lateral roots and aerenchyma formation from flooded plant parts to stalk bases above water level may distribute to flooding tolerance in sweet sorghum. Based on the results, a flood-free period of at least 30 days after emergence is required to sustain yield of pre-rice sweet sorghum and early planting is highly recommended.
Hypoxia delays mating in the broad-nosed pipefish

Abstract Courtship is an important part of the reproductive process, ensuring reproductive compatibility and conveying individual quality. One factor in aquatic environments that has the potential to influence courtship behaviours and mating propensity is the level of dissolved oxygen. Furthermore, hypoxic areas are currently spreading due to anthropogenic disturbance, such as eutrophication. In marine environments, hypoxia often occurs in shallow coastal regions that are particularly important areas for reproduction. Here, we investigated how types of reproductive behaviour were affected by mild hypoxia using the well-studied broad-nosed pipefish, Syngnathus typhle. More precisely, we investigated the impact of acute hypoxia on the reproductive behaviour preceding mating, and on the probability of mating, as well as on the latency until these occurred. We found that the latency period to courting and copulation occurring was prolonged in the low-oxygen environment. However, the total time spent courting as well as the probability of mating was unaffected by hypoxia. Other types of reproductive behaviour found in this species, such as dancing, and the unique male pouch-flap behaviour, were also unaffected by the low-oxygen treatment. We conclude that although latency to courting and copulating was prolonged in the hypoxic environment, most reproductive behaviour investigated was unaffected by hypoxia. Thus, hypoxia commonly occurring in shallow coastal regions has the potential to delay certain components of reproduction, but overall the broad-nosed pipefish shows robustness to hypoxic conditions.
Internet of Things with Wireless Sensor Network Potential Business Possibility

Wireless Sensor Network is an exciting part of the Internet of Things to study because of its versatility in various types of industries. The existence of wireless sensor networks is believed to develop similar to the evolution of computer network systems when they were first connected and eventually became what we call today the Internet (World Wide Web). The source of information from the wireless sensor network will be more precious than the current internet information source, and this will change the World Wide Web to what is called the World Wide Sensor Network (WWSN). This paper focuses on the impact of this transformation process, the parties involved, the operational and business models possibility.
The Role of the Surgery in the Case of an Intramedullary Spinal Cord Metastasis as a Primary Presentation of a Malignant Disease

Introduction: Spinal cord metastases represent a small proportion of intramedullary tumors. The occurrence of such lesion over the course of malignant disease is usually a predictor for shortened life expectancy and is often associated with severe neurological deficits. Treatment options include microsurgical excision, radio-, chemo- or palliative therapy. Despite these possibilities the optimal management of patients with intramedullary spinal cord metastases (ISCM) is difficult due to the wide variety of clinical situations and the lack of controlled studies on the results of different therapeutic options. Materials: We are presenting a case of a 68-year-old male with gradually increasing spinal neurological deficit – axial low back pain, numbness and muscle weakness in both legs and gait disturbance. Arterial hypertension was pointed as the only comorbidity of the patient. The MRI showed an intramedullary solitary lesion in the lumbar intumescence at the level of Th12 and L1 vertebra. Results: The patient underwent surgery and the tumor was totally excised. The symptoms improved dramatically. The histology evidence a metastasis from a lung adenocarcinoma. Six months later he presented with severe back pain, progression of the paresis and urinary retention. Tumour recurrence was detected by MRI. After careful decision making and taking into consideration the risk of permanent neurological deficit a reoperation was performed. The lesion was gross-totally removed with improvement in functions and no neurological deterioration registered in the postoperative period. Conclusion: It is possibly the symptoms from an intramedullary metastatic lesion to precede the detection of the primary tumour. The low frequency of occurrence and the absence of a manifested and diagnosed primary malignant process should not stop us thinking in the direction of metastasis. Surgical resection with function preservation is highly aimed. Operation and even reoperation in some cases is acceptable.
Urban Mobility and Activity Space

Recent theoretical and methodological advances in urban sociology, including spatially located data, provide new opportunities to consider the joint influence of mobility and place in urban social life. This review defines the concept of activity space, describes its origins in urban sociology, and examines the extent to which activity space approaches advance sociological research in four substantive domains—spatial inequality and segregation, social connectedness and engagement, crime and offending patterns, and health and health-related behavior. It next describes the evolution of methods for location tracking and new approaches that hold promise for maximizing urban mobility and activity space contributions. It then discusses how location data may be augmented to enhance our sociological understanding of the structure, meaning, and implications of the places people visit or traverse in daily life. We close with new directions for activity space research, emphasizing how such work could enable comparative contextual research.
Field Application and Validation of a Seismic Bedload Transport Model

Bedload transport drives morphological changes in gravel‐bed streams and sediment transfer in catchments. The large impact forces associated with bedload motion and its highly dynamic spatiotemporal nature make it difficult to monitor bedload transport in the field. In this study, we revise a physically‐based model of bedload‐induced seismic ground motion proposed by Tsai et al. (2012) and apply it to invert bedload flux from seismic measurements alongside an Alpine stream. First, we constrain the seismic response of a braided river reach with a simple active experiment using a series of large‐rock impacts. This allows the characterization of surface wave propagation and attenuation with distance from the impact source. Second, we distinguish bedload‐generated ground vibrations from those caused by turbulent flow using frequency‐based scaling relationships between seismic power and discharge. Finally, absolute bedload transport rates are quantified from seismic measurements using inverse modeling based on a simplified formulation of bedload particle motion. The results are verified with a large data set of bedload samples (between 0.01 and 1 kg/m/s), demonstrating that seismic measurements can provide an indirect measure for bedload flux with an uncertainty of less than one order of magnitude. Larger deviations may be due to the contribution of turbulent flow effects and remaining uncertainties in particle impact mechanics (elasticity and velocity). When constraining these uncertainties, seismic monitoring may provide an accurate and continuous means to investigate bedload dynamics in gravel‐bed streams.
A summary of the database pertaining to the phylogeny of the major groups of parasitic platyhelminths, with a revised classification

A previously published phylogenetic systematic analysis of the major groups of parasitic platyhelminths was based on 39 anatomical characters. The resulting phylogenetic tree had a consistency index, which indicates the degree of fit of the data to the tree hypothesis, of 95% due to two postulated cases of convergence. That tree is evaluated in light of 49 additional anatomical characters and 32 ultrastructural characters. The additional anatomical characters support the original hypothesis with a consistency index of 100%, indicating no additional convergence in the data. The total anatomical database has a consistency index of 97.8%. The ultrastructural characters provide a best fit to a phylogenetic tree of 94.1 %, due to two postulated cases of convergent evolution. That tree is the same as the one supported by the anatomical data. The combined database thus comprises 120 characters having a consistency index of 96.7%, due to four postulated cases of convergent evolution. A classification of the major.
Predictors of HIV knowledge and testing among female adolescents and emerging adults in Tajikistan

ABSTRACT Over the past decade, incidence of human immunodeficiency virus (HIV) has increased significantly in Tajikistan, with female adolescents and emerging adults (i.e., 15–24 years old) particularly vulnerable for acquiring HIV. This study sought to examine whether HIV knowledge and HIV testing among female youth in Tajikistan have increased between 2012 and 2017 using national data from the Demographic and Health Surveys (DHS). In addition, predictors of HIV knowledge and testing were examined. Results suggest that between 2012 and 2017, self-reported HIV testing prevalence increased from 10% to 15% among female adolescents and emerging adults. In addition, HIV knowledge increased significantly among female youth from 2012 to 2017; however, many respondents still displayed limited knowledge about the modes of HIV transmission and effective prevention methods. In order to reduce incidence of HIV among youth in Tajikistan, greater efforts are needed to engage women in education and prevention efforts, as well as to understand the unique vulnerabilities that place some subgroups at increased risk for infection.
Incidence of vibrios of public health significance in the farming phase of tiger shrimp (Penaeus monodon)

The incidence of some of the human pathogenic vibrios in the cultured tiger shrimp (Penaeus monodon) was evaluated during the farming phase in practice at a commercial semi-intensive shrimp farm off Uttarakannada, Karnataka (India). Possible sources of these human pathogens were also evaluated. Vibrio alginolyticus was found to be the most common Vibrio member (57% incidence). Vibrio cholerae, V parahemolyticus and V vulnificus were the other species encountered. All these occurred in shrimp pond sediment, pond water and the feed used (clam meat and formulated feed). Vibrio mimicus was encountered only in the dam meat used as a shrimp feed. A poor correlation between the faecal coliform level and the occurrence of these pathogenic vibrios was apparent, implying natural occurrence of these vibrios in the brackishwater/shrimp culture environment.
Epidermal Growth Factor Stimulates Chloride Transport in Primary Cultures of Weanling and Adult Rabbit Colonocytes

Objectives: We have shown that Ca2+-dependent regulation of Cl− secretion in the mammalian colon exhibits age dependence. Because epidermal growth factor (EGF) has a well-established role in growth and can increase intracellular calcium [Ca2+]i, it is conceivable that its developmental influence may extend to the regulation of intestinal ion transport. In this study, we examined the role of EGF in the regulation of Cl− transport in the developing rabbit distal colon. Materials and Methods: Because serum contains growth factors, which could have confounded our studies, we first established an optimal milieu for testing EGF in primary cultures of adult rabbit distal colonocytes by culturing them for 24 h in media containing 0%, 1%, 5%, and 20% serum. Chloride transport (millimoles per second) and [Ca2+]i were measured with use of the fluorescent indicator N-(ethoxycarbonylmethyl)-6-methoxyquinolinium bromide (MQAE) and Fura-2AM, respectively. Results: Serum depletion had no effect on cell number, DNA content, or basal Cl− transport, but it significantly affected cell viability. In media with 0%, 1%, or 20% serum, bethanechol, 8BrcAMP, taurodeoxycholate, and EGF stimulated Cl− transport to a similar extent. EGF maximally stimulated Cl− transport at 16.3 nmol/L and 20 minutes. Bethanechol, but not EGF, increased [Ca2+]i. EGF did not alter bethanechol-stimulated Cl− transport or [Ca2+]i. EGF acts via an EGF-receptor and mitogen activated protein kinase (MAPK) signaling pathway, since stimulation of Cl− transport was abolished by genistein, AG1478, and PD98059. Weanling and adult colonocytes, cultured in 1% serum, showed similar basal and EGF-stimulated Cl− transport. Conclusions: EGF stimulates rabbit colonic Cl− transport via a Ca2+-independent, tyrosine kinase- and MAPK-dependent pathway, and its effects are not age dependent.