Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating Mangrove Forest Volume Using Terrestrial Laser Scanning and UAV-Derived Structure-from-Motion

Mangroves provide a variety of ecosystem services, which can be related to their structuralcomplexity and ability to store carbon in the above ground biomass (AGB). Quantifying AGB inmangroves has traditionally been conducted using destructive, time-consuming, and costlymethods, however, Structure-from-Motion Multi-View Stereo (SfM-MVS) combined withunmanned aerial vehicle (UAV) imagery may provide an alternative. Here, we compared the abilityof SfM-MVS with terrestrial laser scanning (TLS) to capture forest structure and volume in threemangrove sites of differing stand age and species composition. We describe forest structure in termsof point density, while forest volume is estimated as a proxy for AGB using the surface differencingmethod. In general, SfM-MVS poorly captured mangrove forest structure, but was efficient incapturing the canopy height for volume estimations. The differences in volume estimations betweenTLS and SfM-MVS were higher in the juvenile age site (42.95%) than the mixed (28.23%) or mature(12.72%) age sites, with a higher stem density affecting point capture in both methods. These resultscan be used to inform non-destructive, cost-effective, and timely assessments of forest structure orAGB in mangroves in the future.
Submillisecond Firing Synchrony between Different Subtypes of Cortical Interneurons Connected Chemically But Not Electrically

Synchronous firing is commonly observed in the brain, but its underlying mechanisms and neurobiological meaning remain debated. Most commonly, synchrony is attributed either to electrical coupling by gap junctions or to shared excitatory inputs. In the cerebral cortex and hippocampus, fast-spiking (FS) or somatostatin-containing (SOM) inhibitory interneurons are electrically coupled to same-type neighbors, and each subtype-specific network tends to fire in synchrony. Electrical coupling across subtypes is weak or absent, but SOM–FS and FS–FS pairs are often connected by inhibitory synapses. Theoretical studies suggest that purely inhibitory coupling can also promote synchrony; however, this has not been confirmed experimentally. We recorded from 74 pairs of electrically noncoupled layer 4 interneurons in mouse somatosensory cortex in vitro, and found that tonically depolarized FS–FS and SOM–FS pairs connected by unidirectional or bidirectional inhibitory synapses often fired within 1 ms of each other. Using a novel, jitter-based measure of synchrony, we found that synchrony correlated with inhibitory coupling strength. Importantly, synchrony was resistant to ionotropic glutamate receptors antagonists but was strongly reduced when GABAA receptors were blocked, confirming that in our experimental system IPSPs were both necessary and sufficient for synchrony. Submillisecond firing lags emerged in a computer simulation of pairs of spiking neurons, in which the only assumed interaction between neurons was by inhibitory synapses. We conclude that cortical interneurons are capable of synchronizing both within and across subtypes, and that submillisecond coordination of firing can arise by mutual synaptic inhibition alone, with neither shared inputs nor electrical coupling.
The phase structure of low dimensional large N gauge theories on tori

In this paper we continue our study of the thermodynamics of large N gauge theories on compact spaces. We consider toroidal compactifications of pure SU(N) Yang-Mills theories and of maximally supersymmetric Yang-Mills theories dimensionally reduced to 0+1 or 1+1 dimensions, and generalizations of such theories where the adjoint fields are massive. We describe the phase structure of these theories as a function of the gauge coupling, the geometry of the compact space and the mass parameters. In particular, we study the behavior of order parameters associated with the holonomy of the gauge field around the cycles of the torus. Our methods combine analytic analysis, numerical Monte Carlo simulations, and (in the maximally supersymmetric case) information from the dual gravitational theories.
Parylene Technology for Neural Probes Applications

Neural probes are important tools in detecting and studying neuron activities. Although people have been working on neural probe development for a long time, the current neural probes (including metal-wire probes and silicon neural probes) are still far from being satisfactory. An ideal neural probe array should have good biocompatibility, high-density electrodes with high signal-to-noise ratio, flexible cables for interconnections, integrated electronics, and even integrated actuators to track neuron movement. The work of this thesis focused on applying parylene technology to neural probes development to make a new generation of neural probes with better functions. With the properties of high electrical resistivity, mechanical flexibility, biocompatibility, low coefficient of friction, and an easy deposition/etching process, parylene is a good material for neural probe applications. In this thesis, we have designed, fabricated, and characterized a new parylene neural probe with a long, flexible parylene cable for a neural prosthesis system. Parylene layers are first used on the silicon probe shank with multiple electrodes as insulation and protective layers. And long parylene flexible cables are first monolithically integrated with silicon neural probes. A 96-electrode high-density, 3-D neural probe array for chronic implantation has been demonstrated. Different types of electrolysis actuators (including a silicon diaphragm actuator and a parylene balloon actuator) have been made and tested. The research on electrolysis-based actuators shows their great potential to be used for movable neural probes. Compared with the traditional silicon neural probes (e.g., the Michigan probes, the Utah electrode arrays), our microfabricated neural probes have much longer and stronger probe shanks (8 or 12 mm long, able to penetrate the human pia) and much longer flexible parylene cable (about 7 or 12 cm, long enough to go through a percutaneous connector and the human skull). At the same time, our new probe arrays are shown to have better biocompatibility (being totally covered with parylene material), lower stress, better penetration ability, and greater flexibility for making high-density 3-D arrays and for use in chronic neural signal recording implantation.
Petrogenesis of the Cenozoic alkaline volcanic rock series of the České Středohoří Complex (Bohemian Massif), Czech Republic: A case for two lineages

Cenozoic České Středohoří volcanic complex (CSVC) of the Bohemian Massif (Czech Republic) forms the eastern part of the Central European Volcanic Province and is associated with the Ohře/Eger graben which belongs to the rift system stretching from Spain and France through Germany to the Czech Republic and Poland. CSVC is about 90 km long and up to 25 km wide. The main pulse of the magmatic activities took place from Late Eocene to Middle Miocene and peaked from ∼32 to ∼24 Ma. CSVC is composed of lava flows, volcanosedimentary deposits and subvolcanic intrusions. The volcanic rocks are sodic (Na2O>K2O) alkaline silica-undersaturated types, which form two main associations: (1) basanite-phonolite and (2) subordinate trachybasalt-trachyte series, which differ particularly by the major element variations and Nd-Sr isotopic compositions. The mafic rocks strongly predominate over the felsic types (∼6%). The intermediate rocks are rare. Petrological modeling using MELTS software shows that both suites were generated from two distinct parental magmas (basanitic and basalt/trachybasaltic) by fractional crystallization without noticeable crustal contamination. Some phonolites, particularly their abundances of several incompatible trace elements such as heavy REE and Zr, were modified by late- to post-magmatic fluids. The compositional differences among the mafic rocks are, in part, related to variably metasomatically enriched lithospheric mantle. The Nd-Sr isotopic and trace element composition of the mafic magma indicates that the mantle source was slightly heterogeneous amphibole-and/or phlogopite-bearing garnet peridotite. The presence of garnet, amphibole and/or phlogopite indicates lithospheric melting took place close to the asthenosphere-lithosphere boundary. The lithospheric mantle source was probably metasomatically enriched by fluids or melts from an upwelling asthenospheric mantle. The enrichment may have taken place during the later stages of the Variscan orogeny. The two mafic parent magmas may be derived from a similar source which showed subtle differences in the source mineralogy mode and Nd-Sr isotopic compositions.
The mechanism of flight guidance in honeybee swarms: subtle guides or streaker bees?

SUMMARY When a honeybee swarm takes off to fly to its new home site, less than 5% of the bees in the swarm have visited the site and thereby know in what direction the swarm must fly. How does the small minority of informed bees indicate the swarm's flight direction to the large majority of uninformed bees? Previous simulation studies have suggested two possible mechanisms of visual flight guidance: the informed bees guide by flying in the preferred direction but without an elevated speed (subtle guide hypothesis) or they guide by flying in the preferred direction and with an elevated speed (streaker bee hypothesis). We tested these hypotheses by performing a video analysis that enabled us to measure the flight directions and flight speeds of individual bees in a flying swarm. The distributions of flight speed as a function of flight direction have conspicuous peaks for bees flying toward the swarm's new home, especially for bees in the top of the swarm. This is strong support for the streaker bee hypothesis.
PROFILE MEASUREMENT OF MICRO-ASPHERIC SURFACE BY A SMALL-SCALE MEASURING INSTRUMENT

INTRODUCTION Along with the miniaturization of optical devices such as medical endoscopes and fiber-optic communication systems, micro-aspheric lenses (1 mm in diameter) have become very important parts [1]. Micro-aspheric lenses are necessary for downsizing and higher image quality. Form accuracy of micro-aspheric lenses is required to be better than 100 nm to make the most of those devises. However, the 100 nm form accuracy is very hard to achieve because aspheric surface profiles are complicated. On the other hand, accurate profile measurement of the aspheric surfaces for realizing on-line assessment is a big challenge. Scanning probe measurement systems with a contact stylus are practical and suitable for profile measurement of aspheric surfaces [2]. We have developed a novel measurement system for micro-aspheric profiles that employs a contact stylus [3]. Contact styli are capable of measuring complicated surfaces that have steep slope such as aspheric surfaces as long as the probe spheres at probe tips contact with the measuring objects. However, lateral resolution of measuring instruments that employ contact styli is restricted by the radius of probe sphere. Most of commercial styli do not have high enough resolution to be employed for micro-aspheric surface scanning. In this research, a micro-stylus, which is composed of a micro-glass-ball and a micro-stylus, is fabricated and it is applied to the micro-aspheric profile measurement system.
Alterations in autobiographical memory for a blast event in Operation Enduring Freedom and Operation Iraqi Freedom veterans with mild traumatic brain injury.

OBJECTIVE Although loss of consciousness associated with moderate or severe traumatic brain injury (TBI) is thought to interfere with encoding of the TBI event, little is known about the effects of mild TBI (mTBI), which typically involves only transient disruption in consciousness. METHOD Blast-exposed Afghanistan and Iraq War veterans were asked to recall the blast event. Participants were stratified based on whether the blast was associated with probable mTBI (n = 50) or not (n = 25). Narratives were scored for organizational structure (i.e., coherence) using the Narrative Coherence Coding Scheme (Reese et al., 2011) and episodic recollection using the Autobiographical Interview Coding Procedures (Levine et al., 2002). RESULTS The mTBI group produced narratives that were less coherent but contained more episodic details than those of the no-TBI group. CONCLUSION These results suggest that mTBI interferes with the organizational quality of memory in a manner that is independent of episodic detail generation.
Assessment of the Performance of Water Supply and Management in Zanzibar A Case of Urban West Region, Unguja

The study intends to assess the performance of water supply and management in Zanzibar. This study is conducted in Zanzibar. The study used descriptive survey, based on crosssectional design. The study uses a total of 95 samples. The information was collected using questionnaire, structured interview and documentation. The study results indicate that the performance of water supply and management in the study area is not conducive. This is due to the fact that single source of water is in the study area, poor water accessibility in the study area, rough using of water in the study area with minimal water storage devices in the study area. On the side of the factors for improving water supply and management in the study area, it was highly agreed that rain water harvesting, paying for water services, waste water re-use and household water storage were agreed as the factors for improving water supply and management in the study area. Lastly on the matter of the challenges facing water supply and management in the study area, it was found that technological failure in the study area, population growth in the study area and financial and human resource shortage on water related sectors were the major challenges faces water supply and management in the study area. The study recommends that it is important for the government, to privatize the important social services such as water so that to diversify the sources of clean and safe water in the study area. In addition to that there is the need provide enough budgets for education and training on how to implement the factors as well as buying required technology and knowhow on how to implement the project.
Complete Genome Sequence of the BTEX-Degrading Bacterium Pseudoxanthomonas spadix BD-a59

ABSTRACT Pseudoxanthomonas spadix BD-a59, able to metabolize all six BTEX (benzene, toluene, ethylbenzene, and o-, m-, and p-xylene) compounds, was isolated from gasoline-contaminated sediment. Here, we report the complete 3.45-Mb genome sequence and annotation of strain BD-a59. These advance the understanding of strain BD-a59's genomic properties and pollutant metabolic versatility.
Development of an Integrated In Situ Analyzer for Quantitative Analysis of Microbial ATP in Aquatic Environments

An integrated and miniaturized device for in situ quantitative analysis of microbial ATP was developed in this study. The device can perform extracellular ATP elimination, cell lysis and ATP quantification in a microfluidic chip. A pattern of a microchannel has been optimized to measure luminescence caused by luciferin-luciferase reaction. As a result of evaluation of the developed microfluidic device, 10 nM to 100 muM of ATP was successfully quantified. Environmental samples and bacterial culture media were also analyzed by the microfluidic device. Towards in situ calibration of the ATP quantitative analysis device, a prototype of caged ATP based online calibration component was also fabricated and evaluated.
Software Defect Prediction using Feature Selection and Random Forest Algorithm

Software testing is the most important task in software production and it takes a lot of time, cost and effort. Thus, we need to reduce these resources. Software Defect Prediction (SDP) mechanisms are used to enhance the work of SQA process through the prediction of defective modules, many approaches have been conducted by researchers in order to predict the fault-proneness modules. This paper proposed an approach for the SDP purpose, it employs two existed algorithms to have a high performance, that are the Bat-based search Algorithm (BA) for the feature selection process, and the Random Forest algorithm (RF) for the prediction purpose. This paper also has tested a number of feature selection algorithms and classifiers to see their effectiveness in this problem.
BIST ATIC SAR INTERFEROMETRY USING ENVISAT AND A GROUND BASED RECEIVER: FIRST RESULTS

Bistatic SAR systems are an emerging research field, in which context the Universitat Politecnica de Catalunya is developing a ground based bistatic system using ESA’s ENVISAT and ERS-2 as transmitters. The spatial resolution of this configuration is similar to that of their monostatic counterpart, although foreshortening effects have a lesser impact. The formulation of the interferometric phase has been generalized to the bistatic case, as well as the geometric and volumetric decorrelation factors. UPC’s RSLab has developed a dual-channel receiver prototype to perform bistatic experiments. First single-pass interferometric images corresponding to a local test-site are presented and compared to a synthetic interferogram.
In Vitro Amplification of Misfolded Prion Protein Using Lysate of Cultured Cells

Protein misfolding cyclic amplification (PMCA) recapitulates the prion protein (PrP) conversion process under cell-free conditions. PMCA was initially established with brain material and then with further simplified constituents such as partially purified and recombinant PrP. However, availability of brain material from some species or brain material from animals with certain mutations or polymorphisms within the PrP gene is often limited. Moreover, preparation of native PrP from mammalian cells and tissues, as well as recombinant PrP from bacterial cells, involves time-consuming purification steps. To establish a convenient and versatile PMCA procedure unrestricted to the availability of substrate sources, we attempted to conduct PMCA with the lysate of cells that express cellular PrP (PrPC). PrPSc was efficiently amplified with lysate of rabbit kidney epithelial RK13 cells stably transfected with the mouse or Syrian hamster PrP gene. Furthermore, PMCA was also successful with lysate of other established cell lines of neuronal or non-neuronal origins. Together with the data showing that the abundance of PrPC in cell lysate was a critical factor to drive efficient PrPSc amplification, our results demonstrate that cell lysate in which PrPC is present abundantly serves as an excellent substrate source for PMCA.
Nuclear Factor-κB Activation and Postischemic Inflammation Are Suppressed in CD36-Null Mice after Middle Cerebral Artery Occlusion

CD36, a class-B scavenger receptor involved in multiple functions, including inflammatory signaling, may also contribute to ischemic brain injury through yet unidentified mechanisms. We investigated whether CD36 participates in the molecular events underlying the inflammatory reaction that accompanies cerebral ischemia and may contribute to the tissue damage. We found that activation of nuclear factor-κB, a transcription factor that coordinates postischemic gene expression, is attenuated in CD36-null mice subjected to middle cerebral artery occlusion. The infiltration of neutrophils and the glial reaction induced by cerebral ischemia were suppressed. Treatment with an inhibitor of inducible nitric oxide synthase, an enzyme that contributes to the tissue damage, reduced ischemic brain injury in wild-type mice, but not in CD36 nulls. In contrast to cerebral ischemia, the molecular and cellular inflammatory changes induced by intracerebroventricular injection of interleukin-1β were not attenuated in CD36-null mice. The findings unveil a novel role of CD36 in early molecular events leading to nuclear factor-κB activation and postischemic inflammation. Inhibition of CD36 signaling may be a valuable therapeutic approach to counteract the deleterious effects of postischemic inflammation.
Analytical Tools for the Study of Cellular Glycosylation in the Immune System

It is becoming increasingly clear that glycosylation plays important role in intercellular communication within the immune system. Glycosylation-dependent interactions are crucial for the innate and adaptive immune system and regulate immune cell trafficking, synapse formation, activation, and survival. These functions take place by the cis or trans interaction of lectins with glycans. Classical immunological and biochemical methods have been used for the study of lectin function; however, the investigation of their counterparts, glycans, requires very specialized methodologies that have been extensively developed in the past decade within the Glycobiology scientific community. This mini-review intends to summarize the available technology for the study of glycan biosynthesis, its regulation and characterization for their application to the study of glycans in immunology.
Brain regions that process case: Evidence from basque

The aim of this event‐related fMRI study was to investigate the cortical networks involved in case processing, an operation that is crucial to language comprehension yet whose neural underpinnings are not well‐understood. What is the relationship of these networks to those that serve other aspects of syntactic and semantic processing? Participants read Basque sentences that contained case violations, number agreement violations or semantic anomalies, or that were both syntactically and semantically correct. Case violations elicited activity increases, compared to correct control sentences, in a set of parietal regions including the posterior cingulate, the precuneus, and the left and right inferior parietal lobules. Number agreement violations also elicited activity increases in left and right inferior parietal regions, and additional activations in the left and right middle frontal gyrus. Regions‐of‐interest analyses showed that almost all of the clusters that were responsive to case or number agreement violations did not differentiate between these two. In contrast, the left and right anterior inferior frontal gyrus and the dorsomedial prefrontal cortex were only sensitive to semantic violations. Our results suggest that whereas syntactic and semantic anomalies clearly recruit distinct neural circuits, case, and number violations recruit largely overlapping neural circuits and that the distinction between the two rests on the relative contributions of parietal and prefrontal regions, respectively. Furthermore, our results are consistent with recently reported contributions of bilateral parietal and dorsolateral brain regions to syntactic processing, pointing towards potential extensions of current neurocognitive theories of language. Hum Brain Mapp, 2012. © 2011 Wiley Periodicals, Inc.