Miracle-dz/UniFAR-FTUs huggingface dataset:
Hyperbaric Oxygen Therapy's Effects on Cognition and Narrative Discourse in Severe TBI: A Case Study

The final copy of this thesis has been examined by the signatories, and we Find that both the content and the form meet acceptable presentation standards Of scholarly work in the above mentioned discipline. Discourse deficits following traumatic brain injury (TBI) have been found to negatively impact social reintegration and quality of life and are connected to underlying impairments in cognition. Hyperbaric oxygen therapy (HBOT) has been previously explored as a treatment for cognition in the TBI population, resulting in mixed outcomes. The present study examined the effect of HBOT on the cognitive and narrative discourse performance of an individual with chronic severe TBI. Multiple measurements of general cognition, receptive vocabulary, and discourse performance in the form of narrative storytelling were taken before and after HBOT. Hypotheses predicted that cognition would improve as a result of HBOT and facilitate enhanced narrative discourse performance; receptive vocabulary measures were not expected to improve on account of the participant's lack of deficits in this area. Narratives were divided into T-units and assessed for organization, efficiency, and thoroughness. One-tailed t-tests indicated significant improvement in overall cognition but only in one aspect of the three narrative discourse measures. Further examination revealed that only improvements in attention explained the gains in cognition. For this study's subject, HBOT likely increased attention but did not improve other areas of cognition measured, nor narrative discourse. Further studies incorporating more subjects and long-term outcome measurements are necessary for supporting these results and exploring HBOT's effect on additional cognitive components and narrative discourse performance in a larger population of individuals with chronic, severe TBI. iv Acknowledgements The author would like to thank her advisor Professor Kathryn Hardin for bringing this research opportunity to her attention; her advisors Dr. Kathryn Hardin for their support throughout the process; Paula Messamer for her extensive assistance and encouragement; and my fellow graduate students for generously volunteering their time to help with test administration and/or data analysis.
Contrasting losses and gains increases the predictability of behavior by frontal EEG asymmetry

Frontal asymmetry measured at rest using EEG is considered a stable marker of approach-avoidance behaviors and risk taking. We examined whether without salient cues of attention in the form of losses, predictability is reduced. Fifty-seven participants performed an experiential decision task in a gain-only, loss-only, and mixed (gains and losses) condition. Increased risk taking on the part of individuals with relatively high left frontal activation, as denoted by the Alpha band, was only observed in the task involving both gains and losses. Event-related potential analysis sheds light on the processes leading to this pattern. Left-frontal dominant individuals had increased fronto-central P300 activation following risky compared to safe outcomes, while right-frontal dominant individuals did not show a P300 difference following safe and risky outcomes. This interaction also only emerged when losses were contrasted with gains. The findings highlight the sensitivity of behavioral predictability to cues of valence.
A NEW CRYSTAL-CHEMICAL VARIATION OF THE ALUNITE-TYPE STRUCTURE IN MONOCLINIC PbZn0.5Fe3(AsO4)2(OH)6

The crystal structure of a segnitite-related mineral with composition Pb[Zn0.50.5]Fe3(AsO4)2(OH)6,  = vacancy, from Broken Hill, Australia, has been determined using single-crystal X-ray data. The mineral has monoclinic symmetry, space group C2/c, with a 25.8898(6), b 14.8753(2), c 12.1700(2) A, b 110.681(1)°, Z = 16. All crystals examined were found to be multiply twinned by 120° rotations about c*, which corresponds with ch of the hexagonal alunite-type subcell. The structure was determined on a twinned crystal with one dominant individual, and refined to R = 0.055 for 4089 reflections with F > 4sF. The general features of the monoclinic structure match those of the prototype rhombohedral alunite-type structure. This involves a rhombohedral stacking of hexagonal tungsten-bronze-type sheets of corner-connected octahedra that share their apical anions with AsO4 tetrahedra on either side of the layer of octahedra, with Pb atoms located between the layers. However, the structure differs from those of other alunite-type minerals in having zinc atoms ordered in trigonal bipyramidal sites in half of the available six-membered rings of the layers of octahedra. These sites are unoccupied in previously reported alunite-type structures. Ordered displacements of the Pb atoms occur in response to the Zn– ordering.
Markov chain Monte Carlo method for evaluating multi-frame data association hypotheses

This paper describes algorithms for probabilistically evaluating multi-frame data-association hypotheses formed in multiple-hypothesis, multiple-target tracking, using Markov chain Monte Carlo (MCMC) methods (also known as sequential Monte Carlo (SMC) methods). Each algorithm is designed to sequentially, randomly generate multi-frame data association hypotheses, and to converge to a stationary process with the a posteriori probabilities of the multi-frame hypotheses, as the stationary (target) probability distribution. The paper explores three sampling designs: the metropolis sampling, the metropolis sampling with Boltzman acceptance probability, and the metropolis-hasting sampling. Their performances are compared with each other and with the hypothesis evaluation obtained by a K-best hypothesis selection algorithm, using two simple examples.
On the intrinsic Rent parameter and spectra-based partitioning methodologies

The complexity of circuit designs requires a top-down approach to layout synthesis. A good partitioning hierarchy, as measured by the associated Rent parameter, will correspond to an area-efficient layout. The intrinsic Rent parameter of a netlist is defined as the minimum possible Rent parameter of any partitioning hierarchy for the netlist. Experimental results show that spectra-based ratio cut partitioning methods yield partitioning hierarchies with the lowest observed Rent parameter over all benchmarks and over all algorithms tested. For examples where the intrinsic Rent parameter is known, spectral ratio cut partitioning yields a Rent parameter essentially identical to this theoretical optimum. Additional theoretical results are provided to support the close relationship between spectral partitioning and the intrinsic Rent parameter. <<ETX>>
The Quiescent-Cell Expression System for Protein Synthesis in Escherichia coli

ABSTRACT The quiescent-cell expression system is a radical alternative to conventional fermentation for protein overproduction inEscherichia coli. It is dependent on the controlled overexpression of a small RNA called Rcd in hns mutant strains to generate nongrowing, quiescent cells which are not nutrient limited. Quiescent cells no longer produce biomass and have their metabolic resources channelled toward the expression of plasmid-based genes. The biosynthetic capacity of the system is demonstrated by its ability to express chloramphenicol acetyltransferase to more than 40% of total cell protein. Quiescent cells may provide an ideal environment for the expression of toxic as well as benign proteins.
Native Valve Endocarditis Caused by Corynebacterium striatum with Heterogeneous High-Level Daptomycin Resistance: Collateral Damage from Daptomycin Therapy?

ABSTRACT We describe a patient who developed Corynebacterium striatum native valve endocarditis after receiving two 6-week courses of daptomycin for the treatment of methicillin-resistant Staphylococcus aureus bacteremia and osteomyelitis. The organism exhibited in vitro heteroresistance to daptomycin, with two subpopulations showing daptomycin susceptibility (MIC of ≤0.094 μg/ml) and high-level resistance to daptomycin (MIC of ≥256 μg/ml). The selection of daptomycin-resistant Gram-positive skin flora with the potential of causing invasive disease may be a concern during prolonged courses of daptomycin.
Neglect benevolence in human control of swarms in the presence of latency

Autonomous swarm algorithms have been studied extensively in the past several years. However, there is little research on the effect of injecting human influence into a robot swarm-whether it be to update the swarm's current goals or reshape swarm behavior. While there has been growing research in the field of human-swarm interaction (HSI), no previous studies have investigated how humans interact with swarms under communication latency.We investigate the effects of latency both with and without a predictive display in a basic swarm foraging task to see if such a display can help mitigate the effects of delayed feedback of the swarm state. Furthermore, we introduce a new concept called neglect benevolence to represent how a human operator may need to give time for swarm algorithms to stabilize before issuing new commands, and we investigate it with respect to task performance. Our study shows that latency did affect a user's ability to control a swarm to find targets in the foraging task, and that the predictive display helped to remove these effects. We also found evidence for neglect benevolence, and that operators exploited neglect benevolence in different ways, leading to two different, but equally successful strategies in the target-searching task.
A MinMaxCut Spectral Method for Data Clustering and Graph Partitioning

The goal of data clustering can be formally stated as a min-max clustering principle: data points are grouped into clusters such that (a) between-cluster similarities are minimized while (b) within-cluster similarities are maximized. Existing methods typically focus on one of the above requirements. Here we propose a new method that emphasizes both requirements simultaneously. The MinMaxCut method uses pairwise similarities between all data objects. Viewing them as the adjacency matrix of a weighted graph, MinMaxCut is a graph partitioning method. An important feature is that the continuous solution of the cluster membership indicator vector is the eigenvector of the generalized graph Laplacian matrix; this simplifies the optimization of the min-max clustering objective function. We provide a comprehensive analysis of this principled clustering method; a systematic evaluation on clustering experiments on Internet newsgroups indicates that MinMaxCut outperforms other current popular partitioning/clustering methods.
Abstract Stack Graph to Detect Obfuscated Calls in Binaries

Information about calls to the operating system (or kernel libraries) made by a binary executable may be used to determine whether the binary is malicious. Being aware of this approach, malicious programmers hide this information by making such calls without using the call instruction. For instance, the ‘call addr’ instruction may be replaced by two push instructions and a return instruction, the first push pushes the address of instruction after the return instruction, and the second push pushes the address addr. The code may be further obfuscated by spreading the three instructions and by splitting each instruction into multiple instructions. This paper presents a method to statically detect obfuscated calls in binary code. The notion of abstract stack is introduced to associate each element in the stack to the instruction that pushes the element. An abstract stack graph is a concise representation of all abstract stacks at every point in the program. An abstract stack graph, created by
Non-Invasive Serum Amyloid A (SAA) Measurement and Plasma Platelets for Accurate Prediction of Surgical Intervention in Severe Necrotizing Enterocolitis (NEC)

Objective To evaluate the value of biomarkers to detect severe NEC. Summary Background Data The time point of surgery in necrotizing enterocolitis (NEC) is critical. Therefore, there is a need for markers that detect severe NEC, because clinical signs of severe NEC often develop late. This study evaluated the value of biomarkers reflecting intestinal cell damage and inflammation to detect severe NEC. Methods 29 neonates with NEC were included. Two definitions of moderate versus severe NEC were analyzed: medical NEC (n = 12) versus surgical or fatal NEC (n = 17); and Bell stage II NEC (n = 13) versus stage III NEC (n = 16). Urinary intestinal fatty acid binding protein (I-FABP), serum amyloid A (SAA), C3a and C5a, and fecal calprotectin were measured. C-reactive protein (CRP), white blood cell count (WBC) and platelet count data were measured in blood. Results In both definitions of moderate versus severe NEC, urinary SAA levels were significantly higher in severe NEC. A cut-off value of 34.4 ng/ml was found in surgical NEC versus medical NEC (sensitivity, 83%; specificity, 83%; LR+, 4.88 (95% CI, 1.37–17.0); LR−, 0.20 (95% CI, 0.07–0.60)) at diagnosis of NEC and at one day prior to surgery in neonates who were operated later on. Combination of urinary SAA and platelet count increased the accuracy, with a sensitivity, 94%; specificity, 83%; LR+, 5.53 (95% CI, 1.57–20.0); and LR−, 0.07 (95% CI, 0.01–0.48). Conclusion Urinary SAA is an accurate marker in differentiating severe NEC from moderate NEC; particularly if combined with serum platelet count.
Development of Manifest Strabismus and Reduced Visual Acuity Following Initial Normal Orthoptic Examination/Pseudo-strabismus Under the Age of 30 Months

Abstract Aim: To evaluate the incidence of manifest strabismus and the visual acuity found at 5-year vision screening in those who were referred with concerns of strabismus under the age of 30 months and were initially diagnosed by an orthoptist with either pseudo-strabismus or “no abnormality detected” (NAD). Method: Data were collected for children who were seen between April 2007 and March 2008 and diagnosed as above. Notes were retrieved and the database of visual acuity at screening was examined. Results: 248 children were diagnosed as NAD or pseudo-squint on their first visit. 82 were discharged at their first appointment and 166 were offered follow-up. Notes were retrieved for 208 (84%). Of those followed up, 4 (1.9%) were later found to have a heterotropia (2 esotropes, 2 exotropes). Vision screening results were available for 207 (83.5%). Of these, 172 (83%) passed and 35 (17%) failed vision screening. 2 were found to have microtropia and 1 was esotropic. There was no statistically significant difference in the rate of referral from visual screening between the general population and those who were seen and discharged on their first visit (x2 = 1.76, p = 0.67 risk ratio = 0.98 [95% CI 0.89 to 1.08]). Conclusion: The incidence of undiagnosed esotropia in this group is between 2.4% and 3.4%. The risk of failing visual screening is the same as the general population.
Binary Representation in Gene Expression Programming: Towards a Better Scalability

One of the main problems that arises when using gene expression programming (GEP) conditions in learning classifier systems is the increasing number of symbols present as the problem size grows. When doing model-building LCS, this issue limits the scalability of such a technique, due to the cost required. This paper proposes a binary representation of GEP chromosomes to palliate the computation requirements needed. A theoretical reasoning behind the proposed representation is provided, along with empirical validation.
Huntington’s Disease and Striatal Signaling

Huntington’s Disease (HD) is the most frequent neurodegenerative disease caused by an expansion of polyglutamines (CAG). The main clinical manifestations of HD are chorea, cognitive impairment, and psychiatric disorders. The transmission of HD is autosomal dominant with a complete penetrance. HD has a single genetic cause, a well-defined neuropathology, and informative pre-manifest genetic testing of the disease is available. Striatal atrophy begins as early as 15 years before disease onset and continues throughout the period of manifest illness. Therefore, patients could theoretically benefit from therapy at early stages of the disease. One important characteristic of HD is the striatal vulnerability to neurodegeneration, despite similar expression of the protein in other brain areas. Aggregation of the mutated Huntingtin (HTT), impaired axonal transport, excitotoxicity, transcriptional dysregulation as well as mitochondrial dysfunction, and energy deficits, are all part of the cellular events that underlie neuronal dysfunction and striatal death. Among these non-exclusive mechanisms, an alteration of striatal signaling is thought to orchestrate the downstream events involved in the cascade of striatal dysfunction.
Spatial discrimination of salt- and sodium-affected soil surfaces

Abstract Salinization-alkalinization is a time- and space-dynamic soil degradation process in semiarid regions. This study implements a synergistic approach to map salt- and sodium affected surfaces, combining digital image classification with field observation of soil degradation features and laboratory determinations. Salinity-alkalinity classes were established using the electrical conductivity (EC) and pH values. A neighbourhood operator, with spatial and spectral user-defined constraints determined the spectral objects constituting the training set. Six combined Landsat TM bands (1,2,4,5,6,7) provided the highest separability between salt- and sodium-affected soil classes. Although the overall accuracy was slightly low (64 per cent), accuracies of 100 per cent were obtained for some classes. Main causes of spectral confusions, masking different salinity-alkalinity degrees were the type and abundance of salt-tolerant vegetation cover, the topsoil textures, and the mixture of topsoil properties under f.
Chicxulub Crater: A possible Cretaceous/Tertiary boundary impact crater on the Yucatán Peninsula, Mexico

We suggest that a buried 180-km-diameter circular structure on the Yucatan Peninsula, Mexico, is an impact crater. Its size and shape are revealed by magnetic and gravity-field anomalies, as well as by oil wells drilled inside and near the structure. The stratigraphy of the crater includes a sequence of andesitic igneous rocks and glass interbedded with, and overlain by, breccias that contain evidence of shock metamorphism. The andesitic rocks have chemical and isotopic compositions similar to those of tektites found in Cretaceous/Tertiary (K/T) ejecta. A 90-m-thick K/T boundary breccia, also containing evidence of shock metamorphism, is present 50 km outside the crater's edge. This breccia probably represents the crater's ejecta blanket. The age of the crater is not precisely known, but a K/T boundary age is indicated. Because the crater is in a thick carbonate sequence, shock-produced CO2 from the impact may have caused a severe greenhouse warming.
PnpM, a LysR-Type Transcriptional Regulator Activates the Hydroquinone Pathway in para-Nitrophenol Degradation in Pseudomonas sp. Strain WBC-3

A LysR-type transcriptional regulator (LTTR), PnpR, has previously been shown to activate the transcription of operons pnpA, pnpB, and pnpCDEFG for para-nitrophenol (PNP) degradation in Pseudomonas sp. strain WBC-3. Further preliminary evidence suggested the possible presence of an LTTR additional binding site in the promoter region of pnpCDEFG. In this study, an additional LTTR PnpM, which shows 44% homology to PnpR, was determined to activate the expression of pnpCDEFG. Interestingly, a pnpM-deleted WBC-3 strain was unable to grow on PNP but accumulating hydroquinone (HQ), which is the catabolic product from PNP degradation by PnpAB and the substrate for PnpCD. Through electrophoretic mobility shift assays (EMSAs) and promoter activity detection, only PnpR was involved in the activation of pnpA and pnpB, but both PnpR and PnpM were involved in the activation of pnpCDEFG. DNase I footprinting analysis suggested that PnpR and PnpM shared the same DNA-binding regions of 27 bp in the pnpCDEFG promoter. In the presence of PNP, the protection region increased to 39 bp by PnpR and to 38 bp by PnpM. Our data suggested that both PnpR and PnpM were involved in activating pnpCDEFG expression, in which PNP rather than the substrate hydroquinone for PnpCD is the inducer. Thus, during the PNP catabolism in Pseudomonas sp. strain WBC-3, pnpA and pnpB operons for the initial two reactions were controlled by PnpR, while the third operon (pnpCDEFG) for HQ degradation was activated by PnpM and PnpR. This study builds upon our previous findings and shows that two LTTRs PnpR and PnpM are involved in the transcriptional activation of these three catabolic operons. Specifically, our identification that an LTTR, PnpM, regulates pnpCDEFG expression provides new insights in an intriguing regulation system of PNP catabolism that is controlled by two regulators.
Robust Smoothing of Quantitative Genomic Data Using Second-Generation Wavelets and Bivariate Shrinkage

Recent high-throughput nucleotide sequencing technologies provide large amounts of quantitative genomic data, and thus, biologists currently need to process vast quantities of the data on a regular basis. The first step of the process is almost always smoothing of the data because biomedical data generally tend to contain a lot of noise. In this first step, classical wavelet transforms are widely used; however, the second-generation wavelet transform has not been used in biomedical studies. Smoothing based on the second-generation wavelets is more effective than classical wavelets-based methods because it employs data-dependent wavelet functions and does not require predefined explicit base functions. Since biomedical data usually lack regularity, it is more useful in biomedical research to use the second-generation wavelets than to use the classical wavelets. Therefore, we propose a novel smoothing method based on the second-generation wavelets and bivariate shrinkage, which enables to determine robust thresholds for wavelet-based smoothing, and apply it to synthetic and real genomic data. Experimental results demonstrate the effectiveness of the proposed method.
Linear Moving Horizon Estimation With Pre-Estimating Observer

In this note, a moving horizon estimation (MHE) strategy for detectable linear systems is proposed. Like the idea of “pre-stabilizing” model-predictive control, the states are estimated by a forward simulation with a pre-estimating observer in the MHE formulation. Compared with standard linear MHE approaches, it has more degrees of freedom to optimize the noise filtering. Tuning parameters are chosen to minimize the effects of measurement noise and model errors, which is implemented by finding tightest estimation error bounds. The performance of the proposed observer is demonstrated on one linear discrete-time example.