Miracle-dz/UniFAR-FTUs huggingface dataset:
Reflection and Transmission Imaging of Thin Films

An experimental system was designed, built and used to determine the optical constants of matenals in the Vacuum Ultraviolet region of the electromagnetic spectrum. An optical analysis chamber was designed to mount onto the back end of an existing monochromatic VUV imaging beam system, which covers a wavelength range from 30-200nm. The chamber may accommodate three different expenmental configurations, allowing transmission and reflection measurements to be taken separately or at the same time. A versatile computational analysis system was developed to process the data obtained with this experimental system Recorded CCD images are aligned using a novel interpolation method, and reflection or transmission values are calculated from these. A Kramers-Kromg analysis program was developed and used to obtain a complete set of optical constants in the VUV region if reflection data is available over a sufficiently extensive wavelength range. The absorption coefficient of aluminium in the region between 30 and 85 5nm was determined to demonstrate the capabilities of the suite of expenmental and computational analysis systems. The absorption coefficient of aluminium is shrouded in controversy in this region of the spectrum due to two papers with conflicting results ref [19] & [21].
Inventory of Agaricomycetidae and Phallomycetidae under different conservation strategies by the United States Fish and Wildlife Service at Cabo Rojo, Puerto Rico Refuge

This thesis would not have been possible without the financial support of US Fish and Wildlife Services (Permit No. 2016-04), the Department of Natural and Environmental Resources (Permit No. 2015-IC-10) and the Department of Biology at University of Puerto Rico, Mayaguez Campus for providing the laboratory facilities.
Phenotypic and genotypic chactracterization of Campylobacter isolated from poultry

Phenotypic and genotypic characterization of Campylobacter isolated from poultry Wedad Ahmed, Helmut Hotzel, Ashraf A. Abd El-Tawab, Fatma I. El Hofy, Mona M. Sobhy 1 Friedrich-Loeffler-Institute, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany 2 Department of Microbiology, Faculty of Veterinary Medicine, Benha University, PO Box 13736, Moshtohor Toukh, Egypt 3 Department of Reproductive Diseases, ARRI, ARC, 12556 Giza, Egypt
Co-regulation of hormone receptors, neuropeptides, and steroidogenic enzymes across the vertebrate social behavior network

The vertebrate basal forebrain and midbrain contain a set of interconnected nuclei that control social behavior. Conserved anatomical structures and functions of these nuclei have now been documented among fish, amphibians, reptiles, birds and mammals, and these brain regions have come to be known as the vertebrate social behavior network (SBN). While it is known that nuclei (nodes) of the SBN are rich in steroid and neuropeptide activity linked to behavior, simultaneous variation in the expression of neuroendocrine genes among several SBN nuclei has not yet been described in detail. In this study, we use RNA-seq to profile gene expression across seven brain regions representing five nodes of the vertebrate SBN in a passerine bird, the wire-tailed manakin Pipra filicauda. Using weighted gene co-expression network analysis (WGCNA), we reconstructed sets of coregulated genes, revealing striking patterns of variation in neuroendocrine gene expression across the SBN. We describe regional expression variation networks comprising a broad set of hormone receptors, neuropeptides, steroidogenic enzymes, catecholamines, and other neuroendocrine signaling molecules. Our findings highlight how heterogeneity of brain gene expression across the SBN can provide functional insights into the neuroendocrine and genetic mechanisms that underlie vertebrate social behavior.
Disassembly of Fragmented Bat Communities in Orange Walk District, Belize

The assembly, or disassembly, of ecological communities is thought to be driven by competition, environmental filtering, and dispersal limitation. These processes leave patterns in the functional, phylogenetic, and taxonomic diversity of communities. Bat communities in the tropics tend to have many species that are niche specialists with varying dispersal propensities. We investigated the effects of fragmentation on bat communities in an isolated forest fragment and a nearby larger forest preserve in Belize. Over four field seasons (2014–2017), we captured over 1,480 individuals from 32 species using mist nets and harp traps. The community in the fragment was a nested subset of species (20) compared to the preserve (30), and species richness was relatively stable over time. Functional richness was higher in the preserve than in the fragment, and species in the preserve were more closely related phylogenetically than expected by chance. Closely related species and species with different diet guilds co-occurred at both sites more often than distant relatives and those with the same diet guild. Bat species with flexible roost use had higher abundance in the fragment than the preserve, while closely related roost-specialist species had higher abundance in the preserve. Local extirpation and decreased dispersal are the most likely mechanisms of community disassembly in this system, and variation in roosting habits results in nonrandom community composition. These results have significant implications for the effects of ongoing deforestation and habitat fragmentation in Belize and adjacent dry forest areas.
Simultaneous Determination of Testosterone, 5α-Androstan-17µ-ol-3-one, 5α-Androstane-3α,17µ-diol and 5a-Androstane-3µ,17µ-diol in Plasma of Adult Male Rabbits by Radioimmunoassay11

A simultaneous radioimmunoassay procedure for plasma testosterone (T), 5α-androstan- 17²-ol-3-one (DHT), 5α-androstane-3α,17²-diol (3αol), and 5α-androstan-3α,17²-diol (3βol) isdescribed in this report. Peripheral plasma concentrations of T, DHT, 3αol, and 3αol were 1.16 ± 0.26, 0.49 ± 0.15, 0.17 ± 0.03, and 0.24 ± 0.04 ng⁄ml, respectively, in adult male rabbits. In contrast, T, DHT, 3αol, and 3αol peripheral plasma concentrations in dexamethasone-treated castrate rabbits were 0.07 ± 0.01, 0.02 ± 0.01, 0.07 ± 0.01, and 0.05 ± 0.01 ng⁄ml, respectively. These results represent the first simultaneous measurement of T, DHT, 3αol, and 3βol in peripheral plasma of any male vertebrate. Moreover, we suggest that DHT, 3αol, and 3βol represent the unidentified immunoreactive material found in peripheral plasma of male rabbits by Falvo and Nalbandov (1). (Endocrinology97:787, 1975)
LRIT3 is Required for Nyctalopin Expression and Normal ON and OFF Pathway Signaling in the Retina

Abstract The first retinal synapse, photoreceptor→bipolar cell (BC), is both anatomically and functionally complex. Within the same synaptic region, a change in presynaptic glutamate release is sensed by both ON BCs (DBCs) via the metabotropic glutamate receptor 6 (mGluR6), and OFF BCs (HBCs) via ionotropic glutamate receptors to establish parallel signaling pathways that preferentially encode light increments (ON) or decrements (OFF), respectively. The synaptic structural organization of ON and OFF-type BCs at the photoreceptor terminal differs. DBCs make an invaginating synapse that contains a diverse but incompletely understood complex of interacting proteins (signalplex). HBCs make primarily flat contacts that contain an apparent different set of proteins that is equally uncharacterized. LRIT3 is a synaptic protein known to be essential for ON pathway visual function. In both male and female mice, we demonstrate that LRIT3 interacts with and is required for expression of nyctalopin, and thus TRPM1 at all DBC dendritic tips, but DBC signalplex components are not required for LRIT3 expression. Using whole-cell and multielectrode array (MEA) electrophysiology and glutamate imaging, we demonstrate that the loss of LRIT3 impacts both ON and OFF signaling pathway function. Without LRIT3, excitatory input to type 1 BCs is reduced, as are the visually evoked responses of many OFF retinal ganglion cells (RGCs). We conclude that the absence of LRIT3 expression disrupts excitatory input to OFF BCs and, thus disrupts the normal function of OFF RGCs.
The co-crystal tetra­aqua­bis(2-oxido-3,5-dinitro­benzoato)bis­(2-oxido-3,5-dinitro­benzoic acid)tricopper–diaqua­bis(2-hydr­oxy-3,5-dinitro­benzoato)(2-oxido-3,5-dinitro­benzoic acid)copper–water (0.54/0.92/4): a reformulation?

In the title compound, [Cu3(C7H3N2O7)2(C7H2N2O7)2(H2O)4]0.54[Cu(C7H3N2O7)2(H2O)2]0.92·4H2O, the CuII ion located on an inversion centre has a fractional site occupancy of 0.54. When this CuII ion is present, a trinuclear complex also involving two adjacent CuII ions arises; when it is not, then the result is two discrete mononuclear complexes. A very similar structure was reported previously by Valigura, Melnik, Koman, Martiŝka, Korabik, Mrozinski & Glowiak [Inorg. Chem. Commun. (2004), 7, 548–552]. However, in their material, arising from a different synthesis, the CuII ion with \overline{1} site symmetry is fully occupied, and thus only a trinuclear complex is formed. Here, the mononuclear CuII complex assumes a square-pyramidal coordination geometry, formed by two water mol­ecules and two 3,5-dinitro­salicylate anions, one of which is monodentate and the other bidentate.
A common framework for visual crowding in typical and amblyopic vision

Amblyopia is a developmental disorder of vision characterised by reduced acuity in one eye despite optical correction. When associated with strabismus, foveal vision is impaired by crowding: objects that are readily recognised in isolation become indistinguishable in clutter. In typical vision, crowding is minimal in the fovea and increases in the visual periphery. According to pooling accounts, the increase of crowding in the periphery arises from the integration of adjacent objects to promote perceptual homogeneity where sampling is insufficient and neurons have large receptive fields. It is unclear whether amblyopic crowding represents the same process. In this thesis I characterise amblyopic crowding, and investigate whether it can be understood within the same pooling framework as peripheral crowding. First, I show that amblyopic crowding systematically shifts the appearance of crowded objects to promote perceptual homogeneity, matching the perceptual effects in the periphery. A model simulating pooled responses of populations of visual neurons accurately characterises these effects in amblyopic and peripheral crowding, suggesting a common underlying mechanism. Second, I investigate the pattern of amblyopic crowding across the visual field and its neural correlates. I show that amblyopic crowding is elevated relative to typical vision in both fovea and periphery. At a group level, the increase of crowding in amblyopia and the typical periphery matches the increase of fMRI population receptive field (pRF) estimates in V1, V2, and V3, but at an individual level there is no correlation. Finally, I investigate the effects of higher-level grouping processes by examining whether uniformity in global clutter configuration modulates amblyopic crowding. I find that in most cases, clutter disrupts recognition in amblyopia regardless of global configuration, suggesting that contrary to the periphery, amblyopic crowding is largely unaffected by higher-level grouping processes. Therefore, on the whole pooling provides a successful framework for both amblyopic and peripheral crowding
Helping is Green, But Justice is Red: The Influence of Synesthesia on Educational and Vocational Foci in a Collegiate Population

Synesthesia is a rare condition in which the senses of an individual are perceived to be combined, creating associations between various stimuli and sensations. To date, fifty-four types of synesthesia have been discovered, and objective tests exist for twenty of these (Eaglemen, 2007). While past research has been conducted on the underlying causes and influencers of synesthesia, little has been done to investigate the greater implications and applications that come with it. Synesthesia has been associated with heightened memory and enhanced learning, so it is not unreasonable to predict that a synesthete may develop prowess in certain skills associated with their type of synesthesia (e.g. a person with number-space synesthesia being better at mathematics or a person with personality-color synesthesia taking interest in sociology or psychology.) This study investigated the potential connections between synesthesia and educational and vocational interests in a sample of undergraduates from Texas State University. Twohundred and eighty participants completed an online survey, which included questions about demographics, symptoms of synesthesia, and their educational and vocational interests (measured via the Holland Occupational Themes questionnaire [Holland, 1985]). In this sample, approximately 45% (127 participants) self-reported at least one symptom of synesthesia. Participants’ data were examined using quantitative and qualitative methods. Results suggested that, in certain cases, experiences with synesthesia influenced participants’ interests and career goals. The results of this study contribute to a greater understanding of a special group of people who experience the world differently. These findings may have broader implications for educational advisement and career counseling for synesthetes.
Unraveling Diagnostic Biomarkers of Schizophrenia Through Structure-Revealing Fusion of Multi-Modal Neuroimaging Data

Fusing complementary information from different modalities can lead to the discovery of more accurate diagnostic biomarkers for psychiatric disorders. However, biomarker discovery through data fusion is challenging since it requires extracting interpretable and reproducible patterns from data sets, consisting of shared/unshared patterns and of different orders. For example, multi-channel electroencephalography (EEG) signals from multiple subjects can be represented as a third-order tensor with modes: subject, time, and channel, while functional magnetic resonance imaging (fMRI) data may be in the form of subject by voxel matrices. Traditional data fusion methods rearrange higher-order tensors, such as EEG, as matrices to use matrix factorization-based approaches. In contrast, fusion methods based on coupled matrix and tensor factorizations (CMTF) exploit the potential multi-way structure of higher-order tensors. The CMTF approach has been shown to capture underlying patterns more accurately without imposing strong constraints on the latent neural patterns, i.e., biomarkers. In this paper, EEG, fMRI and structural MRI (sMRI) data collected during an auditory oddball task (AOD) from a group of subjects consisting of patients with schizophrenia and healthy controls, are arranged as matrices and higher-order tensors coupled along the subject mode, and jointly analyzed using structure-revealing CMTF methods (also known as advanced CMTF (ACMTF)) focusing on unique identification of underlying patterns in the presence of shared/unshared patterns. We demonstrate that joint analysis of the EEG tensor and fMRI matrix using ACMTF reveals significant and biologically meaningful components in terms of differentiating between patients with schizophrenia and healthy controls while also providing spatial patterns with high resolution and improving the clustering performance compared to the analysis of only the EEG tensor. We also show that these patterns are reproducible, and study reproducibility for different model parameters. In comparison to the joint independent component analysis (jICA) data fusion approach, ACMTF provides easier interpretation of EEG data by revealing a single summary map of the topography for each component. Furthermore, fusion of sMRI data with EEG and fMRI through an ACMTF model provides structural patterns; however, we also show that when fusing data sets from multiple modalities, hence of very different nature, preprocessing plays a crucial role.
Computer Study of the Ionic Mechanisms of Organophosphorous-Caused Long-QT Syndrome (LQTS)

Abstract : An important clinical marker of organophosphorous (OP)-caused cardiac toxicity is long-QT syndrome, the prolongation of the repolarization period in the ventricles, as measured in an electrocardiogrant The primary membrane currents responsible for this condition are two potassium currents, IKr and IKs This computer simulation investigated the effect of the modulation of the membrane currents most likely affected by the OP on the action potential in a two-dimensional slab of cardiac tissue. We have shown that modulation and reduction of the potassium currents, changes in the background current, and calcium overload of the cells mimic the experimentally observed change in slope of the depolarization in the presence of OPs as well as the prolongation and change in the shape of the plot of repolarization voltage vs. time. These changes are precursors to the onset of Torsade de Pointes and ventricular fibrillation and suggest the required pharmacology of antidotes for force protection. Based on these results, an estimated dose-response curve is presented.
Helicon sources with m = 1 and m = 2 helical antenna coupling*Helicon sources with m = 1 and m = 2 helical antenna coupling

Pulsed helicon discharges produced through m = 1 or m = 2 helical antennas are investigated. Special attention is paid to the axial asymmetry, which is characteristic for helicon sources with helical antenna coupling. The axial profiles of the RF wave fields as well as the energy deposition profiles reveal that the RF power is predominantly absorbed via helicon modes with positive azimuthal mode numbers m (m = +1, +2) travelling in positive magnetic field direction. This can be attributed to the fact that the helicon modes with negative m are strongly damped or even evanescent if the radial plasma density gradient is steep enough. In particular, we examined the RF power absorption in the m = 1 helicon discharge, that cannot be understood in terms of collisions. Various non-collisional absorption mechanisms as well as absorption via excitation of Trivelpiece–Gould waves are discussed. We also present first measurements carried out on the large-volume plasma injected from the m = 1 helicon source into a diffusion chamber.
MLFatigueDetection Machine Learning Based Walking Fatigue Detection

Leg fatigue can influence the gait patterns, therefore declining the postural stability and the motor performance, increasing the risk of falls. In order to improve the earlier detection of risks and the application of fall prevention strategies, automated solutions based on gait analysis must be developed. A sector of the population at risk is the workforce where a majority of workers admits to be fatigued and where falls can lead to serious workplace injuries or even deaths. In these cases, having the ability to detect if the user is fatigued in real time by simply using the motion sensors on the smartphone and processing it with machine learning can lead to the prevention of falls and the consequences these bring. Phones and wearable devices were studied for their ability to be used to extract inertial sensor’s data to provide enough information for the fatigue detection. Supervised machine learning algorithms, such as Support Vector Machines (SVM) and Neural Networks, will be used to process this information for fatigue level classification. Their performance will then be compared to find the best algorithm for fatigue detection. In addition to this comparative work, different conditions for the data collection and processing were tested in an effort to discover the optimal conditions for the implementation of the algorithms.
The complete chloroplast genome of Pterospermum kingtungense, a Critically Endangered species

Abstract Pterospermum kingtungense (Pterospermum, Sterculiaceae) is a Critically Endangered species. In this study, we reported a complete chloroplast genome of P. kingtungense based on high-throughput sequencing data. The size of chloroplast genome was 162,929 bp, including a large single-copy region (LSC: 91,535 bp) and a small single-copy region (SSC: 20,464 bp), separated by a pair of inverted repeats (IRa and IRb: 25,465 bp). The genome encoded 126 genes in total, including 81 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the P. kingtungense chloroplast genome is 36.39%. The phylogenetic tree showed P. kingtungense clustered together with the family Sterculiaceae.
Partial cutting in mixedwood stands: Effects of treatment configuration and intensity on stand structure, regeneration, and tree mortality

ABSTRACT In temperate and boreal mixedwood forests of eastern North America, partial disturbances such as insect outbreaks and gap dynamics result in the development of irregular forest structures. From a forest ecosystem management perspective, management of these forests should therefore include silvicultural regimes that incorporate medium- to high-retention harvesting. We present 12-year results of a field experiment undertaken to evaluate the effects of variable retention harvesting on stand structure, recruitment, and mortality. Treatments were gap harvesting (GAP), diameter-limit harvesting (DL), careful logging (CL), and careful logging followed by scarification (CL + SCAR), and an unharvested control. Although post-harvest basal area in the GAP treatment was significantly lower than that of controls, it maintained a diameter distribution profile and densities of balsam fir regeneration similar to those of pre-harvest conditions. Lower retention treatments (DL, CL, and CL + SCAR) tended to favor regeneration of pioneer, shade-intolerant species. Except for black spruce (for which mortality was highest in DL), stem mortality was similar among harvesting treatments. From an ecosystem management perspective, this study suggests that gap harvesting can maintain, in the short term, forest stand composition and structure similar to unharvested forests, and could be used where management objectives include the maintenance of late successional forest conditions.