Miracle-dz/UniFAR-FTUs huggingface dataset:
Long-Term Environmental Correlates of Invasion by Lantana camara (Verbenaceae) in a Seasonally Dry Tropical Forest

Invasive species, local plant communities and invaded ecosystems change over space and time. Quantifying this change may lead to a better understanding of the ecology and the effective management of invasive species. We used data on density of the highly invasive shrub Lantana camara (lantana) for the period 1990–2008 from a 50 ha permanent plot in a seasonally dry tropical forest of Mudumalai in southern India. We used a cumulative link mixed-effects regression approach to model the transition of lantana from one qualitative density state to another as a function of biotic factors such as indicators of competition from local species (lantana itself, perennial grasses, invasive Chromolaena odorata, the native shrub Helicteres isora and basal area of native trees) and abiotic factors such as fire frequency, inter-annual variability of rainfall and relative soil moisture. The density of lantana increased substantially during the study period. Lantana density was negatively associated with the density of H. isora, positively associated with basal area of native trees, but not affected by the presence of grasses or other invasive species. In the absence of fire, lantana density increased with increasing rainfall. When fires occurred, transitions to higher densities occurred at low rainfall values. In drier regions, lantana changed from low to high density as rainfall increased while in wetter regions of the plot, lantana persisted in the dense category irrespective of rainfall. Lantana seems to effectively utilize resources distributed in space and time to its advantage, thus outcompeting local species and maintaining a population that is not yet self-limiting. High-risk areas and years could potentially be identified based on inferences from this study for facilitating management of lantana in tropical dry forests.
Modeling processes related to corrosion of steel reinforcement and damage in concrete

Aggressive environmental conditions, such as exposure to the sea climate or use of deicing salts, have considerable influence on durability of reinforced concrete structures due to reinforcement corrosion-induced damage. In the present paper, a recently developed coupled three-dimensional chemo-hygro-thermo-mechanical model for concrete is briefly discussed. The model was implemented into a 3D FE code and its application is illustrated through a numerical example of a beam-end specimen exposed to aggressive corrosion conditions. Damage of concrete cover due to expansion of corrosion products and transport of rust through concrete pores and cracks are predicted. Subsequently, the influence of corrosion induced damage of concrete cover on bond resistance of deformed steel reinforcement is studied. The comparison between numerical results and experimental evidence shows that the complex coupled mathematical model is able to realistically predict phenomena related to corrosion of steel reinforcement and their consequences on the corrosion induce damage of concrete.
Controlled growth and doping of core-shell GaAs-based nanowires

The use of compound semiconductor heterostructures to create electron confinement has enabled the highest frequency and lowest noise semiconductor electronics in existence. Modem technology uses two-dimensional electron gasses and there is considerable interest to explore one-dimensional electron confinement. This thesis develops the materials science toolkit needed to fabricate, characterize, and control the compositional, structural and electronic properties of core-shell GaAs/AlGaAs nanowires towards studying quasi-one-dimensional confinement and developing high mobility electronics First, nanowire growth kinetics were studied to optimize nanowire morphology. Variations in nanowire diameter were eliminated by understanding the role Ga adatom diffusion on sidewall deposition and vertical growth was enabled by understanding the importance of Ga and As mass-transport to nanowire nucleation. These results demonstrate that arrays of vertically-aligned GaAs nanowires can be produced. Then, the deposition of epitaxial AlGaAs shells on GaAs nanowires was demonstrated. By reducing the nanowire aerial density the stability of the nanowire geometry was maintained. A variety of analytical electron microscopy techniques confirmed the shell deposition to be uniform, epitaxial, defect-free, and nearly atomic sharp. These results demonstrate that core-shell nanowires possess a core-shell interface free of many of the imperfections that lithographically-defined nanowires possess. Finally, the adverse effect of the Au seed nanoparticle during n-type doping was identified and n-type doping was achieved via the removal of the Au nanoparticle prior to doping. A combination of energy dispersive X-ray spectroscopy, current-voltage, capacitancevoltage, and Kelvin probe force microscopy demonstrated that if the Au seed nanoparticle is present during the shell deposition, Au diffuses from the seed nanoparticle and creates a rectifying IV behavior. A process was presented to remove the Au nanoparticle prior to shell deposition and was shown to produce uniform n-type doping. The conductivity of GaAs/n-GaAs nanowires was calculated as a function of donor concentration and geometric factors taking into account the effects of Fermi level pinning. The control demonstrated over all of these parameters is sufficient enough for core-shell nanowires to be considered candidates for high mobility electronics. Thesis Supervisor: Silvija Gradecak Title: Assistant Professor of Materials Science and Engineering Table of
Death by a thousand cuts: behaviour and attitudes that inhibit enterprise information asset management

Introduction. Data, information and knowledge together constitute one of four vital business assets that enable every business activity, business process and business decision. The effective management of information assets contributes to realising business benefit. Method. This paper describes the findings of qualitative empirical research conducted with executive managers from various industries to elicit their views on the day-to-day information asset management behaviour in their organisations. Personal interviews were conducted with Clevel executives and managers in law firms in Australia, the United States and South Africa. Analysis. Qualitative analysis was carried out on the data, using the NVivo qualitative analysis program. Results. The attitudes and behaviour of individuals in organisations can be categorised as contributing to either ‘digital landfill’ or a ‘bunker information’ mentality and are related to the ownership of the information assets (supported by the psychological ownership theory) and the value people place on them. Conclusion. An attitude behaviour outcome model was developed, which can be used to guide managers in understanding the behaviour and attitudes that lead to ‘death by a thousand cuts’. The study is subject to limitations of qualitative research, such as the lack of generalisation based on findings from a limited number of participants.
The Ionisation of Atmospheric Air

MESSRS. ELSTER AND GEITEL have published an important paper in the Physikalische Zeitschrift (No. 9, pp. 522-530), “Ueber die radioaktive Emanation in der atmospharischen Luft. ” They find that the abnormal conducting power of the stagnant air-of cellars and caves, and the amount of induced radio-activity which can be obtained from such air upon a negatively charged rod suspended in it vary greatly in different regions. In some places such air is no more active than ordinary atmospheric air. Air sucked through a pipe of which one end is buried in the ground is generally active, like the air of most cellars and caves; tests of the activity of samples of such ground-air from different localities showed great variations, some being no more active than ordinary air. The activity of ground-air falls off at a rate comparable with the rate of decay of the radium eman. If a portion of the soil of a region in which the ground-air is radio-active is isolated, it gives to a volume of air in contact with it abnormal conductivity which reaches its maximum in a few days. The soil retains this power for many months at least. The phenomena are all most readily explained by supposing that substances, which have the power of producing a radio-active emanation like that of radium, are distributed in varying amount among the materials composing the soils of different regions. In the latter part of the paper is an account of some interesting observations on the dependence of the radio-activity of atmospheric air upon meteorological conditions. The increase of the activity of the air which generally accompanies a fall of the barometer is attributed to the escape of ground-air into the atmosphere.
Indispensable Role of Proteases in Plant Innate Immunity

Plant defense is achieved mainly through the induction of microbe-associated molecular patterns (MAMP)-triggered immunity (MTI), effector-triggered immunity (ETI), systemic acquired resistance (SAR), induced systemic resistance (ISR), and RNA silencing. Plant immunity is a highly complex phenomenon with its own unique features that have emerged as a result of the arms race between plants and pathogens. However, the regulation of these processes is the same for all living organisms, including plants, and is controlled by proteases. Different families of plant proteases are involved in every type of immunity: some of the proteases that are covered in this review participate in MTI, affecting stomatal closure and callose deposition. A large number of proteases act in the apoplast, contributing to ETI by managing extracellular defense. A vast majority of the endogenous proteases discussed in this review are associated with the programmed cell death (PCD) of the infected cells and exhibit caspase-like activities. The synthesis of signal molecules, such as salicylic acid, jasmonic acid, and ethylene, and their signaling pathways, are regulated by endogenous proteases that affect the induction of pathogenesis-related genes and SAR or ISR establishment. A number of proteases are associated with herbivore defense. In this review, we summarize the data concerning identified plant endogenous proteases, their effect on plant-pathogen interactions, their subcellular localization, and their functional properties, if available, and we attribute a role in the different types and stages of innate immunity for each of the proteases covered.
Flatworm-specific transcriptional regulators promote the specification of tegumental progenitors in Schistosoma mansoni

Schistosomes infect more than 200 million people. These parasitic flatworms rely on a syncytial outer coat called the tegument to survive within the vasculature of their host. Although the tegument is pivotal for their survival, little is known about maintenance of this tissue during the decades schistosomes survive in the bloodstream. Here, we demonstrate that the tegument relies on stem cells (neoblasts) to specify fusogenic progenitors that replace tegumental cells lost to turnover. Molecular characterization of neoblasts and tegumental progenitors led to the discovery of two flatworm-specific zinc finger proteins that are essential for tegumental cell specification. These proteins are homologous to a protein essential for neoblast-driven epidermal maintenance in free-living flatworms. Therefore, we speculate that related parasites (i.e., tapeworms and flukes) employ similar strategies to control tegumental maintenance. Since parasitic flatworms infect every vertebrate species, understanding neoblast-driven tegumental maintenance could identify broad-spectrum therapeutics to fight diseases caused by these parasites.
How Do We Study the Dynamic Structure of Unstructured Proteins: A Case Study on Nopp140 as an Example of a Large, Intrinsically Disordered Protein

Intrinsically disordered proteins (IDPs) represent approximately 30% of the human genome and play key roles in cell proliferation and cellular signaling by modulating the function of target proteins via protein–protein interactions. In addition, IDPs are involved in various human disorders, such as cancer, neurodegenerative diseases, and amyloidosis. To understand the underlying molecular mechanism of IDPs, it is important to study their structural features during their interactions with target proteins. However, conventional biochemical and biophysical methods for analyzing proteins, such as X-ray crystallography, have difficulty in characterizing the features of IDPs because they lack an ordered three-dimensional structure. Here, we present biochemical and biophysical studies on nucleolar phosphoprotein 140 (Nopp140), which mostly consists of disordered regions, during its interaction with casein kinase 2 (CK2), which plays a central role in cell growth. Surface plasmon resonance and electron paramagnetic resonance studies were performed to characterize the interaction between Nopp140 and CK2. A single-molecule fluorescence resonance energy transfer study revealed conformational change in Nopp140 during its interaction with CK2. These studies on Nopp140 can provide a good model system for understanding the molecular function of IDPs.
Downregulation of SPINK13 Promotes Metastasis by Regulating uPA in Ovarian Cancer Cells

Background/Aims: Ovarian cancer (OC) is the fifth leading cause of cancer-related death in women, and it is difficult to diagnose at an early stage. The purpose of this study was to explore the prognostic biological markers of OC. Methods: Univariate Cox regression analysis was used to identify genes related to OC prognosis from the Cancer Genome Atlas(TCGA) database. Immunohistochemistry was used to analyse the level of SPINK13 in OC and normal tissues. Cell proliferation, apoptosis and invasion were performed using MTT assay, flow cytometric analysis and Transwell assay, respectively. Results: We identified the Kazal-type serine protease inhibitor-13 (SPINK13) gene related to OC prognosis from the Cancer Genome Atlas (TCGA) database by univariate Cox regression analysis. Overexpression of SPINK13 was associated with higher overall survival rate in OC patients. Immunohistochemistry showed that the level of SPINK13 protein was significantly lower in OC tissues than in normal tissues (P < 0.05). In vitro experiments showed that the overexpression of SPINK13 inhibited cellular proliferation and promoted apoptosis. Moreover, SPINK13 inhibited cell migration and epithelial to mesenchymal transition (EMT). SPINK13 was found to inhibit the expression of urokinase-type plasminogen activator (uPA), while recombinant uPA protein could reverse the inhibitory effect of SPINK13 on OC metastasis. Conclusion: These results indicate that SPINK13 functions as a tumour suppressor. The role of SPINK13 in cellular proliferation, apoptosis and migration is uPA dependent, and SPINK13 may be used as a potential biomarker for diagnosis and targeted therapy in OC.
The N-Terminal β-Sheet of Peroxiredoxin 4 in the Large Yellow Croaker Pseudosciaena crocea Is Involved in Its Biological Functions

Peroxiredoxins (Prxs) are thiol-specific antioxidant proteins that exhibit peroxidase and peroxynitrite reductase activities involved in the reduction of reactive oxygen species. The peroxiredoxin Prx4 from the large yellow croaker Pseudosciaena crocea is a typical 2-Cys Prx with an N-terminal signal peptide. We solved the crystal structure of Prx4 at 1.90 Å and revealed an N-terminal antiparallel β-sheet that contributes to the dimer interface. Deletion of this β-sheet decreased the in vitro peroxidase activity to about 50% of the wild-type. In vivo assays further demonstrated that removal of this β-sheet led to some impairment in the ability of Prx4 to negatively regulate nuclear factor-κB (NF-κB) activity and to perform its role in anti-bacterial immunity. These results provide new insights into the structure and function relationship of a peroxiredoxin from bony fish.
Atlantic Origin of the Arctic Biota? Evidence from Phylogenetic and Biogeographical Analysis of the Cheilostome Bryozoan Genus Pseudoflustra

The intricate geological evolution of the Arctic Ocean is paralleled by complexities in the biogeographical and phylogenetical histories of the Arctic biota, including bryozoans. Here we present revised taxonomic descriptions for all known species of the bryozoan genus Pseudoflustra, and use the present-day distributions and phylogenetic relationships between these species to infer the historical biogeography of the genus. Nine species belonging to the genus Pseudoflustra are recognized in the Arctic and North Atlantic. One new species, previously identified as Ichthyaria aviculata, is described as Pseudoflustra radeki sp. nov. Another species, previously assigned to Smittoidea as S. perrieri, is transferred to Pseudoflustra. Biogeographical analysis of Pseudoflustra reveals that species distributions mostly match current patterns pertaining in the North Atlantic and Arctic Ocean. Distributions were probably shaped by recent geological history as present-day current directions in the Arctic Ocean are believed to have been similar for at least the last 120 000 years. Phylogenetic analysis of Pseudoflustra places the five Arctic-North Atlantic species in a clade crownward of a paraphyletic grouping of North Atlantic species. Given that the Arctic Ocean was fully glaciated until 18 000 years, the most likely explanation for this phylogeographical pattern is that species of Pseudoflustra colonized the Arctic relatively recently from North Atlantic sources. However, a fuller understanding of the origin of Pseudoflustra in the Arctic will require molecular and fossil data, neither of which are currently available.
Articular Contact Area and Pressure in Posteromedial Rotatory Instability of the Elbow

Background: Joint incongruity in posteromedial rotatory instability (PMRI) has been theorized to determine early articular degenerative changes. Our hypothesis was that the articular contact area and contact pressure differ significantly between an intact elbow and an elbow affected by PMRI. Methods: Seven cadaveric elbows were tested under gravity varus stress using a custom-made machine designed to simulate muscle loads and allow passive elbow flexion (0° to 90°). The mean contact area and contact pressure data were collected and processed using the Tekscan sensor and software. After testing the intact specimen (intact elbow), a PMRI injury was simulated (PMRI elbow) and the specimen was tested again. Results: The PMRI elbows were characterized by initial joint subluxation and significantly elevated articular contact pressure. Both worsened, corresponding with a reduction in contact area, as the elbow was flexed from 0° until the joint subluxation and incongruity spontaneously reduced (at a mean [and standard error] of 60° ± 5° of flexion), at which point the mean contact pressure decreased from 870 ± 50 kPa (pre-reduction) to 440 ± 40 kPa (post-reduction) (p < 0.001) and the mean contact area increased from 80 ± 8 mm2 to 150 ± 58 mm2 (p < 0.001). This reduction of the subluxation was also followed by a shift of the contact area from the coronoid fracture edge toward the lower portion of the coronoid. At the flexion angle at which the PMRI elbows reduced, both the contact area and the contact pressure of the intact elbows differed significantly from those of the PMRI elbows, both before and after the elbow reduction (p < 0.001). Conclusions: The reduction in contact area and increased contact pressures due to joint subluxation and incongruity could explain the progressive arthritis seen in some elbows affected by PMRI. Clinical Relevance: This biomechanical study suggests that the early degenerative changes associated with PMRI reported in the literature could be subsequent to joint incongruity and an increase in contact pressure between the coronoid fracture surface and the trochlea.
Vacuum-Sealed and Gas-Filled Micromachined Devices

In the field of micromachining, microsensor packaging is one of the least investigated, although one of the most important and challenging, technology areas. In particular, hermetic packaging is a key aspect of many microelectromechanical systems (MEMS). By hermetically sealing microsystems and protecting them from harmful environmental influences, their reliability and lifetime can be significantly increased. In addition, some MEMS need a specific gas or pressure environment within the package to function properly. In this thesis, techniques for forming low-pressure encapsulated and gas-filled micromachined devices using silicon fusion and anodic bonding are investigated. Particular attention is given to techniques that provide hermetically sealed electrical feedthrough conductors. The low-pressure encapsulation of electrically operated silicon resonators and the sealing of cavities with carbon dioxide (CO2) are presented, both performed at the wafer level. The silicon resonators were encapsulated in a low-pressure cavity between two glass lids with metal electrodes for electrostatic excitation and capacitive detection. The final cavity pressure obtained was 1 mbar. The effect of squeeze-film damping due to oscillation close to the lid walls was investigated and a theoretical model for damping was presented. The development of a novel electronic circuitry based on discontinuous, “burst” excitation eliminated the need for feedthrough conductors by placing the electrodes outside the low-pressure cavity and suppressed the crosstalk between excitation and detection. Using this technique, a fully low-pressure resonant fluid density sensor was fabricated. A large cavity recess of 100 μm could be formed in the glass to reduce squeeze-film damping. The feedback control together with the detection electronics enabled on-line density measurements. The encapsulated sensor showed high performance with density sensitivities of –200 ppm (kg m), a high quality factor of 3400, low temperature sensitivities of –29 ppm °C in the range 20-100 °C and proven long-term stability. The CO2 chambers were filled with CO2 during an anodic bonding procedure performed at overpressure up to 2 bar in a CO2 atmosphere. The CO2 chambers are used as optical gas filters. To increase the transmission, the silicon wafer was coated with silicon dioxide as an antireflective coating and the glass wafer was thinned down to 125 μm. The fusion and anodic bonding techniques led to very good air-tight gas cavity chambers with an internal pressure of 1 bar. These optical gas filters were integrated in an infrared gas analysis system to provide a reference signal for measuring the CO2 concentration in patient airways during anesthesia or intensive care. Thierry Corman, Instrumentation Laboratory, Department of Signals, Sensors and Systems, Royal Institute of Technology, SE-100 44 Stockholm, Sweden