Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding and Controlling Angular Momentum Coupled Optical Waves in Chirally-Coupled-Core (CCC) Fibers.

Understanding and Controlling Angular Momentum Coupled Optical Waves in Chirally-Coupled-Core(CCC) Fibers by Xiuquan Ma Chair: Almantas Galvanauskas In this dissertation a new type of fiber structure — so called Chirally-Coupled-Core (CCC) fiber — is extensively explored. Work presented here establishes theoretical, numerical and experimental foundations of describing optical phenomena in these novel structures, and provides with methods and tools required to design them. CCC fibers have been a very interesting topic of study due to their unusual symmetry (they are helically symmetric), novel nature of wave interactions within them, and the technological importance of their applications. We have discovered that operation of CCC fibers is based on optical wave interactions that involve both orbital and spin angular momentum of the propagating modes. This is the first and so far the only known example when optical angular momentum is involved in optical interactions. In this thesis we first show experimental evidence of multitude of optical resonances that cannot be explained within the framework of conventional phase-matched interactions. Then we show that these observations can be explained through opticalangular momentum assisted optical interactions of optical waves in these structures.
Developmental Origin and Evolution of Bacteriocytes in the Aphid–Buchnera Symbiosis

Symbiotic relationships between bacteria and insect hosts are common. Although the bacterial endosymbionts have been subjected to intense investigation, little is known of the host cells in which they reside, the bacteriocytes. We have studied the development and evolution of aphid bacteriocytes, the host cells that contain the endosymbiotic bacteria Buchnera aphidicola. We show that bacteriocytes of Acyrthosiphon pisum express several gene products (or their paralogues): Distal-less, Ultrabithorax/Abdominal-A, and Engrailed. Using these markers, we find that a subpopulation of the bacteriocytes is specified prior to the transmission of maternal bacteria to the embryo. In addition, we discovered that a second population of cells is recruited to the bacteriocyte fate later in development. We experimentally demonstrate that bacteriocyte induction and proliferation occur independently of B. aphidicola. Major features of bacteriocyte development, including the two-step recruitment of bacteriocytes, have been conserved in aphids for 80–150 million years. Furthermore, we have investigated two cases of evolutionary loss of bacterial symbionts: in one case, where novel extracellular, eukaryotic symbionts replaced the bacteria, the bacteriocyte is maintained; in another case, where symbionts are absent, the bacteriocytes are initiated but not maintained. The bacteriocyte represents an evolutionarily novel cell fate, which is developmentally determined independently of the bacteria. Three of five transcription factors we examined show novel expression patterns in bacteriocytes, suggesting that bacteriocytes may have evolved to express many additional transcription factors. The evolutionary transition to a symbiosis in which bacteria and an aphid cell form a functional unit, similar to the origin of plastids, has apparently involved extensive molecular adaptations on the part of the host cell.
Marine Vehicle Sensor Network Architecture and Protocol Designs for Ocean Observation

The micro-scale and meso-scale ocean dynamic processes which are nonlinear and have large variability, have a significant impact on the fisheries, natural resources, and marine climatology. A rapid, refined and sophisticated observation system is therefore needed in marine scientific research. The maneuverability and controllability of mobile sensor platforms make them a preferred choice to establish ocean observing networks, compared to the static sensor observing platform. In this study, marine vehicles are utilized as the nodes of mobile sensor networks for coverage sampling of a regional ocean area and ocean feature tracking. A synoptic analysis about marine vehicle dynamic control, multi vehicles mission assignment and path planning methods, and ocean feature tracking and observing techniques is given. Combined with the observation plan in the South China Sea, we provide an overview of the mobile sensor networks established with marine vehicles, and the corresponding simulation results.
Physiological Responses and Tolerance Mechanisms to Cadmium in Conyza canadensis

Experiments were conducted to examine the effects of different concentrations of Cd on the performance of the Cd accumulator Conyza canadensis. Cd accumulation in roots and leaves (roots > leaves) increased with increasing Cd concentration in soil. High Cd concentration inhibited plant growth, increased the membrane permeability of leaves, and caused a significant decline in plant height and chlorophyll [chlorophyll (Chl) a, Chl b, and total Chl] content. Leaf ultrastructural analysis of spongy mesophyllic cells revealed that excessive Cd concentrations cause adverse effects on the chloroplast and mitochondrion ultrastructures of C. canadensis. However, the activities of antioxidant enzymes, such as superoxide dismutase, catalase, peroxidase, total non-protein SH compounds, glutathione, and phytochelatin (PC) concentrations, showed an overall increase. Specifically, the increase in enzyme activities demonstrated that the antioxidant system may play an important role in eliminating or alleviating the toxicity of Cd in C. canadensis. Furthermore, results demonstrate that PC synthesis in plant cells is related to Cd concentration and that PC production levels in plants are related to the toxic effects caused by soil Cd level. These findings demonstrate the roles played by these compounds in supporting Cd tolerance in C. canadensis.
A case-based recommender for task assignment in heterogeneous computing systems

Case-based reasoning (CBR) is a knowledge-based problem-solving technique, which is based on reuse of previous experiences. We propose a new model for static task assignment in heterogeneous computing systems. The proposed model is a combination of the case based reasoning and the learning automata model. In this new model a learning automata model is used as adaptation mechanism, which adapts previously experienced cases to the problem to be solved. The objective of the proposed model is to reduce the number of iterations required to find a semioptimum solution. The application is modeled as a set of independent tasks and the heterogeneous computing system is modeled as a network of machines. Using computer simulation, it is shown that the combined model outperforms the model that only uses learning automata.
Antiplatelet agents and proton pump inhibitors – personalizing treatment

Introduction: Antiplatelet therapy remains one of the cornerstones in the management of non-cardioembolic ischemic stroke. However, a significant percentage of patients have concomitant gastroesophageal reflux or peptic ulcer disease that requires acid-reducing medications, the most powerful and effective being the proton pump inhibitors (PPIs). Antiplatelet efficacy, at least in vivo, and particularly for clopidogrel, has been shown to be reduced with concomitant proton pump inhibitor use. Whether this is clinically relevant is not clear from the limited studies available. Methods: We conducted an extensive review of studies available on Medline related to pharmacodynamic interactions between the antiplatelet medications and proton pump inhibitors as well as clinical studies that addressed this potential interaction. Results: Based on the present pharmacodynamic and clinical studies we did not find a significant interaction that would reduce the efficacy of antiplatelet agents with concomitant user of proton pump inhibitors. Conclusions: Patients on antiplatelet agents after a transient ischemic attack or ischemic stroke can safely use aspirin, and extended release dipyridamole/aspirin with proton pump inhibitors. Patients on clopidogrel may use other acid-reducing drugs besides proton pump inhibitors. In rare cases where proton pump inhibitors and clopidogrel have to be used concurrently, careful close monitoring for recurrent vascular events is required.
Evaluation of a pilot Pressure Ulcer Prevention Initiative (PUPI) for patients with traumatic spinal cord injury.

OBJECTIVE The purpose of this study was to determine whether implementation of a Pressure Ulcer Prevention Initiative (PUPI) changed the assessment and treatment of patients with a traumatic spinal cord injury (SCI) in an acute care setting, and improved patient outcomes. METHOD The success of implementation was evaluated by examining the percentage of patients with completed occupational therapist (OT) skin care assessments and prescriptions for therapeutic support surfaces (TSS; i.e., mattresses) before implementation (historical, cohort 1) and after implementation (experimental, cohort 2). Patient outcomes were evaluated by examining changes in PU incidence, severity, timing and recurrence, as well as PU prevalence and satisfaction with life in the community. RESULTS Final analysis included 70 patients in cohort 1 and 73 in cohort 2. OT skin care assessment documentation (31% to 60%; p<0.001) and TSS prescriptions (31% to 60%; p=0.02) significantly increased following the implementation. The PU incidence based on patient charts (both nursing and OT assessments) did not increase significantly (26% to 36%; p=0.2). However, documented PU incidence according to OT assessments showed a substantial increase (14% to 33%; p=0.002). No effect of the PUPI was seen on immediate or long-term patient outcomes during the study period. CONCLUSION PUPI was successful in changing clinical practice in PU prevention but no statistically significant improvements in PU-related patient outcomes were demonstrated. Results from this study identified facilitators and barriers to implementation and highlighted the complexity and difficulty of instituting effective preventative or therapeutic interventions for this population in an acute care setting. This information will assist with refinements of the PUPI and inform similar future initiatives.
Neural representation of time in cortico-basal ganglia circuits

Encoding time is universally required for learning and structuring motor and cognitive actions, but how the brain keeps track of time is still not understood. We searched for time representations in cortico-basal ganglia circuits by recording from thousands of neurons in the prefrontal cortex and striatum of macaque monkeys performing a routine visuomotor task. We found that a subset of neurons exhibited time-stamp encoding strikingly similar to that required by models of reinforcement-based learning: They responded with spike activity peaks that were distributed at different time delays after single task events. Moreover, the temporal evolution of the population activity allowed robust decoding of task time by perceptron models. We suggest that time information can emerge as a byproduct of event coding in cortico-basal ganglia circuits and can serve as a critical infrastructure for behavioral learning and performance.
The capacity of string-duplication systems

It is known that the majority of the human genome consists of repeated sequences. Furthermore, it is believed that a significant part of the rest of the genome also originated from repeated sequences and has mutated to its current form. In this paper, we investigate the possibility of constructing an exponentially large number of sequences from a short initial sequence and simple duplication rules, including those resembling genomic duplication processes. In other words, our goal is to find out the capacity, or the expressive power, of these string-duplication systems. Our results include the exact capacities, and bounds on the capacities, of four fundamental string-duplication systems.
Effect and Localization of Trifluralin in Plasmodium falciparum Gametocytes: An Electron Microscopic Study 1

Trifluralin, a herbicide which is known to bind to plant and algal tubulin, induced ultrastructural changes in the microtubules of the mature Plasmodium falciparum gametocytes in vitro. Trifluralin treatment led to disassembly of the well ordered subpellicular microtubules, whereas it had no effect on microtubules of human platelets or of rat neuronal cells in vitro. The disassembled microtubules showed fragmented large tubular structures, which frequently were associated with the pellicular membranes. Electron microscopic autoradiography showed radioactive trifluralin associated with the microtubule fragments. These results provide evidence that trifluralin selectively binds to microtubules in malaria parasites and causes disruption of their structure.
Bayesian Group Nonnegative Matrix Factorization for EEG Analysis

We propose a generative model of a group EEG analysis, based on appropriate kernel assumptions on EEG data. We derive the variational inference update rule using various approximation techniques. The proposed model outperforms the current state-of-the-art algorithms in terms of common pattern extraction. The validity of the proposed model is tested on the BCI competition dataset.
Listening effort with cochlear implant simulations.

PURPOSE Fitting a cochlear implant (CI) for optimal speech perception does not necessarily optimize listening effort. This study aimed to show that listening effort may change between CI processing conditions for which speech intelligibility remains constant. METHOD Nineteen normal-hearing participants listened to CI simulations with varying numbers of spectral channels. A dual-task paradigm combining an intelligibility task with either a linguistic or nonlinguistic visual response-time (RT) task measured intelligibility and listening effort. The simultaneously performed tasks compete for limited cognitive resources; changes in effort associated with the intelligibility task are reflected in changes in RT on the visual task. A separate self-report scale provided a subjective measure of listening effort. RESULTS All measures showed significant improvements with increasing spectral resolution up to 6 channels. However, only the RT measure of listening effort continued improving up to 8 channels. The effects were stronger for RTs recorded during listening than for RTs recorded between listening. CONCLUSION The results suggest that listening effort decreases with increased spectral resolution. Moreover, these improvements are best reflected in objective measures of listening effort, such as RTs on a secondary task, rather than intelligibility scores or subjective effort measures.
Temperature Dependence of Accommodation and Excitation in Space-Clamped Axons

Accommodation and excitation in space-clamped squid axons were studied with the double sucrose gap technique, using linear current ramps, short (50 µsec) square wave pulses, and rheobasic square wave pulses as stimuli. The temperature was varied from 5° to 35°C. Experimental results showed a Q 10 for accommodation which was 44% higher than that for excitation. Yet calculations on the basis of the Hodgkin-Huxley equations predict equal Q 10's for excitation and accommodation. Although the Hodgkin-Huxley equations are spectacularly successful for so many nerve phenomena, the differences between calculations of accommodation and these experiments, which were designed to test the equations, show that the equations need modification in this area.
Metabolic Profiling of Hypoxic Cells Revealed a Catabolic Signature Required for Cell Survival

Hypoxia is one of the features of poorly vascularised areas of solid tumours but cancer cells can survive in these areas despite the low oxygen tension. The adaptation to hypoxia requires both biochemical and genetic responses that culminate in a metabolic rearrangement to counter-balance the decrease in energy supply from mitochondrial respiration. The understanding of metabolic adaptations under hypoxia could reveal novel pathways that, if targeted, would lead to specific death of hypoxic regions. In this study, we developed biochemical and metabolomic analyses to assess the effects of hypoxia on cellular metabolism of HCT116 cancer cell line. We utilized an oxygen fluorescent probe in anaerobic cuvettes to study oxygen consumption rates under hypoxic conditions without the need to re-oxygenate the cells and demonstrated that hypoxic cells can maintain active, though diminished, oxidative phosphorylation even at 1% oxygen. These results were further supported by in situ microscopy analysis of mitochondrial NADH oxidation under hypoxia. We then used metabolomic methodologies, utilizing liquid chromatography–mass spectrometry (LC-MS), to determine the metabolic profile of hypoxic cells. This approach revealed the importance of synchronized and regulated catabolism as a mechanism of adaptation to bioenergetic stress. We then confirmed the presence of autophagy under hypoxic conditions and demonstrated that the inhibition of this catabolic process dramatically reduced the ATP levels in hypoxic cells and stimulated hypoxia-induced cell death. These results suggest that under hypoxia, autophagy is required to support ATP production, in addition to glycolysis, and that the inhibition of autophagy might be used to selectively target hypoxic regions of tumours, the most notoriously resistant areas of solid tumours.
System-Level Synthesis of Ultra Low-Power Wireless Sensor Network Node Controllers: A Complete Design-Flow. (Synthèse de haut-niveau de contrôleurs ultra-faible consommation pour des réseaux de capteurs: un flot de conception complet)

Wireless Sensor Networks (WSN) is a new and challenging research field for embedded system design automation. Engineering a WSN node platform is a tough challenge, as the design must enforce many severe constraints among which energy consumption is often the most critical one due to the small size of a node and its difficult access after deployment. WSN nodes have until now been designed using commercial low-power microcontrollers (MCUs). These MCUs are not well-suited for WSN node design as they are based on a general purpose compute engine and consume too much power w.r. t. WSN node's power budget. In this thesis, we propose a complete system-level designflow for an alternative approach based on the concept of power-gated hardware micro-tasks. In this approach, WSN node architecture is made of several micro-tasks that are activated on an event-driven basis, each of them being dedicated to a specific task of the system (such as event-sensing, MAC, routing, etc.). These hardware micro-tasks are controlled by a hardware scheduler (called the System Monitor) that is automatically generated from a system-level description of the WSN node task graph in the form of a textual Domain Specific Language (DSL). By combining hardware specialization with power-gating, we can drastically reduce both dynamic and static energy of a WSN node controller. The results show that dynamic power savings by one to two orders of magnitude are possible w.r. t. the software implementations based on MCUs such as the MSP430. Similarly, static power savings of one order of magnitude are also obtained due to the reduction in data memory size and power-gating.
DISRUPTION OF SKELETAL MYOCYTES INITIATES SUPEROXIDE RELEASE: CONTRIBUTION OF NAD(P)H OXIDASE

Generation of reactive oxygen species (ROS) as an early local reaction to muscle crush injury has frequently been predicted. However, although it is known that severe inflammatory reactions occurring after major muscle trauma originate mainly from early local incidents within the injured tissue, no detailed studies exist on the local generation of ROS in response to myocyte destruction thus far. Therefore, in this study, ROS formation after lethal mechanical damage was examined using a model of scraping injury to cultured C2C12 skeletal myocytes and superoxide detection by lucigenin chemiluminescence, nitrotetrazolium blue chloride reduction, or electron spin resonance spectroscopy. Mechanical rupture of myocytes resulted in an immediate release of superoxide from the damaged cells that could be substantially blocked by the superoxide scavengers superoxide dismutase (51%), tiron (95%), and MAMA/NO (93%) and by hypoxia (83% inhibition). Superoxide generation was primarily confined to the myocytes' membrane fraction and 7- to 8-fold enhanced by the addition of NADH or NADPH. The NADPH-enhanced superoxide generation could largely be diminished by the NAD(P)H oxidase inhibitors diphenyleneiodonium and apocynin in cell lysates (97% and 35% inhibition, respectively) and in isolated membrane fractions (61% and 63% inhibition). We thus conclude that immediately after myocyte damage, large amounts of superoxide are formed that predominantly originate from membrane-bound electron-transferring enzymes, especially NAD(P)H oxidase. This suggests a decisive role of ROS in the pathogenesis of tissue trauma, with superoxide being an initiator of the signaling mechanism from injured myocytes to the surrounding tissue and, potentially, to the whole body.ABBREVIATIONS-DPI, diphenyleneiodonium chloride; ESR, electron spin resonance; NBT, nitrotetrazolium blue chloride; NOX, NADPH oxidase; ROS, reactive oxygen species; SOD, superoxide dismutase
TSearch: Target-Oriented Low-Delay Node Searching in DTNs With Social Network Properties

Node searching in delay tolerant networks is of great importance for different applications, in which a locator node finds a target node in person. In the previous distributed node searching method, a locator traces the target along its movement path from its most frequently visited location. For this purpose, nodes leave traces during their movements and also store their long-term movement patterns in their frequently visited locations (i.e., preferred locations). However, such tracing leads to a long delay and high overhead on the locator by long-distance moving. Our trace data study confirms these problems and provides the foundation of our design of a new node searching method, called target-oriented method (TSearch). By leveraging social network properties, TSearch aims to enable a locator to directly move toward the target. Nodes create encounter records (ERs) indicating the locations and times of their encounters and make the ERs easily accessible by locators through message exchanges or a hierarchical structure. In node searching, a locator follows the target's latest ER, the latest ERs of its friends (i.e., frequently meeting nodes), its preferred locations, and the target's possible locations deduced from additional information for node searching. Extensive trace-driven and real-world experiments show that TSearch achieves significantly higher success rate and lower delay in node searching compared with previous methods.
Impacts of electrical properties and reliability on Ge MOS capacitors with surface pretreatment

Surface pretreatments with NO, N<inf>2</inf>O and NH<inf>3</inf>, are employed to prepare HfTiO/GeOxNy stack gate dielectric on n-Ge substrate. Impact of surface pretreatment on the electrical properties and reliability of the Ge MOS capacitors have been investigated. Excellent performances of Al/HfTiO/GeOxNy/n-Ge MOS capacitor with wet NO surface pretreatment have been achieved with an equivalent oxide thickness of 1.88 nm, physical thickness of 7.2 nm, equivalent permittivity of ∼ 34.5, interface -state density of 2.1×10<sup>11</sup> eV<sup>−1</sup>cm<sup>−2</sup>, equivalent oxide charge of −7.64×10<sup>11</sup> cm-2 and gate leakage current of 4.97×10<sup>−5</sup> A/cm<sup>2</sup> at Vg = 1 V. Experimental results also indicate that the wet NO surface pretreatment can lead to excellent reliability.