Miracle-dz/UniFAR-FTUs huggingface dataset:
A Model of Fatigue Following Traumatic Brain Injury

Objective:Fatigue is one of the most frequent sequelae of traumatic brain injury (TBI), although its causes are poorly understood. This study investigated the interrelationships between fatigue and sleepiness, vigilance performance, depression, and anxiety, using a structural equation modeling approach. Methods:Seventy-two participants with moderate to severe TBI (78% males) were recruited a median of 305 days postinjury. They completed the Fatigue Severity Scale, a vigilance task, the Epworth Sleepiness Scale, and Hospital Anxiety and Depression Scale. A model of the interrelationships between the study variables was developed, tested, and modified with path analysis. Results:The modified model had a good overall fit (&khgr;22 = 1.3, P = .54; comparative fit index = 1.0; root-mean square error of approximation = 0.0; standardized root-mean square residual = 0.02). Most paths in this model were significant (P < .05). Fatigue predicted anxiety, depression, and daytime sleepiness. Depression predicted daytime sleepiness and poor vigilance, whereas anxiety tended to predict reduced daytime sleepiness. Conclusions:This model confirms the complexity of fatigue experience. It supports the hypothesis that fatigue after TBI is a cause, not a consequence, of anxiety, depression, and daytime sleepiness, which, in turn (especially depression), may exacerbate fatigue by affecting cognitive functioning. These findings suggest that to alleviate fatigue, it is important to address each of these factors. However, the findings need to be confirmed with a longitudinal research design.
Coaching: learning and using environment and agent models for advice

Coaching is a relationship where one agent provides advice to another about how to act. This thesis explores a range of problems faced by an automated coach agent in providing advice to one or more automated advice-receiving agents. The coach's job is to help the agents perform as well as possible in their environment. We identify and address a set of technical challenges: How can the coach learn and use models of the environment? How should advice be adapted to the peculiarities of the advice receivers? How can opponents be modeled, and how can those models be used? How should advice be represented to be effectively used by a team? This thesis serves both to define the coaching problem and explore solutions to the challenges posed. This thesis is inspired by a simulated robot soccer environment with a coach agent who can provide advice to a team in a standard language. This author developed, in collaboration with others, this coach environment and standard language as the thesis progressed. The experiments in this thesis represent the largest known empirical study in the simulated robot soccer environment. A predator-prey domain and a moving maze environment are used for additional experimentation. All algorithms are implemented in at least one of these environments and empirical validation is performed. In addition to the coach problem formulation and decompositions, the thesis makes several main technical contributions: (i) Several opponent model representations with associated learning algorithms, whose effectiveness in the robot soccer domain is demonstrated. (ii) A study of the effects and need for coach learning under various limitations of the advice receiver and communication bandwidth. (iii) The Multi-Agent Simple Temporal Network, a multi-agent plan representation which is refinement of a Simple Temporal Network, with an associated distributed plan execution algorithm. (iv) Algorithms for learning an abstract Markov Decision Process from external observations, a given state abstraction, and partial abstract action templates. The use of the learned MDP for advice is explored in various scenarios.
Video segmentation with the assistance of audio content analysis

Video structure extraction is essential to automatic content-based organization, retrieval and browsing of video. However, while many robust shot segmentation algorithms have been developed, it is still difficult to extract scene structures or group shots into scenes. We present a novel audio assisted video segmentation scheme, in which audio and color information is integrated in video scene extraction. A novel audio segmentation scheme is developed to segment audio tracks into speech, music, environmental sound and silence segments. A robust algorithm for shot grouping based on correlation analysis is also developed to further enhance the scene extraction accuracy.
Will mechanical dyssynchrony one day impact our management of chronic heart failure patients?

Mechanical dyssynchrony along with its role in cardiac resynchronization therapy (CRT) has been studied for over 10 years now.1 Although there are ‘believers’ in imaging techniques and echocardiography specifically, there are no recommendations for their use in clinical practice or guidelines for CRT.2 QRS duration remains the gold-standard for selecting patients for CRT and predicting their responses. ² The key importance of QRS width and morphology, so as to predict responses to CRT, has been demonstrated recently.3 According to the results of the RethinQ trial involving 172 patients with heart failure and narrow QRS, CRT did not improve peak oxygen consumption or LV remodelling at the 6-month follow-up.4 It has also been demonstrated that the correlation between mechanical dyssynchrony and QRS width was less than perfect.5 Thus, despite the 30% rate of non-response to CRT, it is challenging for imaging techniques to demonstrate substantial value, …
Le soulevé de sinus par voie crestale sans adjonction de matériaux de substitution osseuse : revue de la littérature

Introduction : Le souleve de sinus par voie crestale fait appel a des materiaux de substitution osseuse. Cependant, des etudes ont montre que cette technique utilisee sans greffe a des resultats similaires a des sites greffes. Le but de cette etude est de faire un etat des lieux des resultats de l’osteotomie crestale avec et sans greffe. Materiel et methode : une revue systematique de la litterature permet d’analyser les taux de survie, de succes et de complications chirurgicales d’implants places en site sous sinusiens atrophies sans materiaux de substitution osseuse. Resultats : Le taux de survie d’implants varie de 94% a 100% a 14 mois et a 10 ans respectivement selon differents auteurs. Quant au taux de succes, il varie de 91.6% a 24 mois a 100% a 36 mois selon les etudes. Le taux de perforations de la membrane varie de 26% a 3.7% voire a 0.0% selon les etudes. Discussion : Au vu des resultats de notre revue de la litterature, il ne semble pas y avoir de difference significative entre une implantation en secteurs maxillaires posterieurs atrophies faisant appel ou non a des materiaux de substitution osseuse.
Whole-Genome Comparison of Leucine-Rich Repeat Extensins in Arabidopsis and Rice. A Conserved Family of Cell Wall Proteins Form a Vegetative and a Reproductive Clade1,212

We have searched the Arabidopsis and rice (Oryza sativa) genomes for homologs of LRX1, an Arabidopsis gene encoding a novel type of cell wall protein containing a leucine-rich repeat (LRR) and an extensin domain. Eleven and eight LRX (LRR/EXTENSIN) genes have been identified in these two plant species, respectively. TheLRX gene family encodes proteins characterized by a short N-terminal domain, a domain with 10 LRRs, a cysteine-rich motif, and a variable C-terminal extensin-like domain. Phylogenetic analysis performed on the conserved domains indicates the existence of two major clades of LRX proteins that arose before the eudicot/monocot divergence and then diversified independently in each lineage. In Arabidopsis, gene expression studies by northern hybridization and promoter::uidA fusions showed that the two phylogenetic clades represent a specialization into “reproductive” and “vegetative” LRXs. The four Arabidopsis genes of the “reproductive” clade are specifically expressed in pollen, whereas the seven “vegetative” genes are predominantly expressed in various sporophytic tissues. This separation into two expression classes is also supported by previous studies on maize (Zea mays) and tomato (Lycopersicon esculentum)LRX homologs and by information on available rice ESTs. The strong conservation of the amino acids responsible for the putative recognition specificity of the LRR domain throughout the family suggests that the LRX proteins interact with similar ligands.
Nanoscale Pore Characteristics of the Upper Permian Mudrocks from a Transitional Environment in and around Eastern Sichuan Basin, China

Nanoscale pore characteristics of the Upper Permian Longtan transitional mudrocks and their equivalent strata Wujiaping Formation marine mudrocks in and around the eastern Sichuan Basin was investigated using field emission scanning electron microscopy (FE‐SEM) and low‐pressure N2 adsorption experiments. The results indicate that the Upper Permian mudrock is at a mature stage with total organic carbon (TOC) values ranging between 0.47% and 12.3%. The Longtan mudrocks mainly contain vitrinite, and their mineral composition is primarily clay. In contrast, the Wujiaping mudrocks are dominated by sapropelinite and solid bitumen, and their mineral compositions are mainly quartz and a notably high amount of pyrite. The FE‐SEM reveals that clay mineral pores and microcracks are the common pore types in the Longtan mudrocks. The specific surface area and pore volume depend on the clay content but are negatively correlated with the TOC. The generation of nanometer pores in the Longtan mudrocks is caused by high clay mineral contents. Meanwhile, the Wujiaping mudrock mainly contains OM pores, and the pore parameters are positively correlated with the TOC. The OM pore development exhibits remarkable differences in the Longtan and Wujiaping mudrocks, which might be related to their sedimentary facies and maceral fractions. Vitrinite and inertinite appear as discrete particles in these mudrocks and cannot generate pores during thermal maturation. Sapropelinite often contains many secondary pores, and solid bitumen with large particles, usually with several pores, is not the major contributor to the pore system of the investigated mudrock.
Statistical Analysis of Relational Data: Mining and Modeling Complex Networks

JAMES DAVID WILSON: Statistical analysis of relational data: mining and modeling complex networks (Under the direction of Andrew B. Nobel and Shankar Bhamidi) Networks have created many new and exciting areas of scientific inquiry, particularly in the field of statistics. The relational and often complex nature of network data requires the development of new statistical techniques that address analysis, modeling, and simulation. In this dissertation, we make contributions to the development and application of statistical methodology on network data. This work is divided into two related areas. The first part of the dissertation is devoted to the problem of community detection: the unsupervised clustering of vertices in a network. Community detection is a common and important first step in the analysis of networks because networks tend to cluster into densely connected groups of vertices that often closely associate with important physical patterns of a modeled system. We develop and evaluate two novel significance-based detection techniques the Extraction of Statistically Significant Communities (ESSC) algorithm, and Multilayer Extraction. The ESSC algorithm is a hypothesis testing approach for undirected networks, while Multilayer Extraction is a scorebased approach that identifies significant vertex-layer communities in multilayer networks. The performance and potential use of both methods are investigated through simulations and real data applications, and large graph consistency is established for the Multilayer Extraction algorithm. The second part of the dissertation is devoted to the simulation and modeling of networks with weighted edges. The generalized exponential random graph model (GERGM) was recently proposed to model networks with continuous-valued edges; however, current estimation algorithms for the GERGM only allow inference on a restricted family of model specifications. We develop a Metropolis-Hastings estimation method that greatly extends the family of weighted graphs that can be modeled under the GERGM framework. We show that new flexible model specifications are capable of avoiding the common problem likelihood degeneracy. Furthermore, new specifications
DNA repair and PARP in aging

Half a century ago, when the free radical theory of aging was first proposed, the damaging effects of reactive oxygen species (ROS) were in the focus of attention and considered the single most important determinant of aging. Two decades later, however, the disposable soma theory of aging redirected the attention to the potential impact of cellular maintenance and repair pathways that are both genetically and environmentally determined and are counteracting the damaging effects of ROS. In the present paper, recent experimental data linking DNA repair pathways with the aging process are summarised. Special attention is paid to poly(ADP-ribosyl)ation, a DNA-damage driven posttranslational modification of proteins.
Age-associated alterations in inducible gene transcription in human CD4+ T lymphocytes

Age associated immune dysregulation results in a pro-inflammatory state and increased susceptibility to infections and autoimmune diseases. Studies show that signaling initiated at the T cell antigen receptor (TCR) is impaired in CD4+ T cells from old compared to young mice. Here we examined TCR-inducible gene expression changes in CD4+ T cells during human aging. We reveal a dichotomy in gene expression mediated by the inducible transcription factor NF-κB. Most NF-κB target genes are not induced in a sustained manner in cells derived from older compared to younger individuals. However, a subset of NF-κB target genes including genes associated with chronic pro-inflammatory state in the elderly, such as interleukin 1 and 6, continue to be up-regulated even in the absence of NF-κB induction. In addition, we identify other widespread changes in gene expression between cells derived from older and younger individuals. Surprisingly, many of the most noteworthy age-associated changes in human CD4+ T cells differ from those seen in murine models. Our studies provide the first view of age-associated alteration of TCR-inducible gene expression in human CD4+ T cells.
Amyloid-like Fibrils from a Domain-swapping Protein Feature a Parallel, in-Register Conformation without Native-like Interactions*

The formation of amyloid-like fibrils is characteristic of various diseases, but the underlying mechanism and the factors that determine whether, when, and how proteins form amyloid, remain uncertain. Certain mechanisms have been proposed based on the three-dimensional or runaway domain swapping, inspired by the fact that some proteins show an apparent correlation between the ability to form domain-swapped dimers and a tendency to form fibrillar aggregates. Intramolecular β-sheet contacts present in the monomeric state could constitute intermolecular β-sheets in the dimeric and fibrillar states. One example is an amyloid-forming mutant of the immunoglobulin binding domain B1 of streptococcal protein G, which in its native conformation consists of a four-stranded β-sheet and one α-helix. Under native conditions this mutant adopts a domain-swapped dimer, and it also forms amyloid-like fibrils, seemingly in correlation to its domain-swapping ability. We employ magic angle spinning solid-state NMR and other methods to examine key structural features of these fibrils. Our results reveal a highly rigid fibril structure that lacks mobile domains and indicate a parallel in-register β-sheet structure and a general loss of native conformation within the mature fibrils. This observation contrasts with predictions that native structure, and in particular intermolecular β-strand interactions seen in the dimeric state, may be preserved in “domain-swapping” fibrils. We discuss these observations in light of recent work on related amyloid-forming proteins that have been argued to follow similar mechanisms and how this may have implications for the role of domain-swapping propensities for amyloid formation.
3D shape measurement of specular surface based on structured light coding method

Present a novel method for 3D shape measurement of specular surface based on structured light coding method. Coded fringe pattern are projected onto the high reflected surface of the measured object. The deflection fringe pattern that modulated by the object surface are captured by the CCD camera. Central perturbation phase-shift technology is adopted to fast retrieve the phase distribution on the deflection fringe pattern. Then the slope information can be obtained by analyzing the relationship between the phase deflection and the slope of the object surface. By combining the character of the phase-shifting fringe pattern and digital image processing technologies the boundary of the measured object can be picked up from the background before reconstruction, which can reduce the quantities of data to be processed and advance the reconstruction precision at the boundary. The improved wave-front reconstruction method is used to reconstruct the surface. With the application of this technology the 3D shape of specular surface can be precisely reconstructed.
A closed-loop wireless homecage for optogenetic stimulation experiments

This paper presents a smart EnerCage-homecage (HC) system for optogenetic stimulation, equipped with magnetic resonance based wireless power transmission (WPT), closed-loop power control, and data communication via Bluetooth Low Energy (BLE). The proposed system is encompassed with four rectangular slanted overlapping high-Q resonators and a wire-wound driver coil, all tuned at 13.56 MHz. An optical headstage is implemented capable of driving 4 micro light-emitting diodes (μ-LEDs) based on stimulation commands received via the BLE link on-the-fly, while being wirelessly powered in a closed-loop fashion. Measurements show that the entire headstage unit was provided with up to 51 mW throughout the homecage up to the maximum elevation of 10 cm, while the transmitter (Tx) power consumption changed from 1.5 W to 2.1 W (overall η, 2.4-3.4%).
Acute Versus Chronic Effects of Whey Proteins on Calcium Absorption in Growing Rats

The acute and chronic effects of whey proteins on calcium metabolism and bone were evaluated. In acute studies, 8-week-old male rats were gavaged with 50 mg whey protein concentrate (WPC) and 25 mg calcium. 45Ca was administered intravenously or orally. Kinetic studies were performed, and femurs were harvested. Four of seven WPCs significantly increased femur uptake of 45Ca compared with controls. One WPC at 50 mg enhanced calcium absorption over a range of calcium Intakes from 35.1 ± 9.4% to 42.4 ± 14.0% (P < 0.01). Three of the most effective WPCs were tested further in a chronic feeding study. One hundred 3-week-old rats were randomly divided into four adequate dietary calcium (ADC; 0.4% Ca) groups (control of 20% casein and three WPC groups with 1% substitution of casein with each of three WPCs) and two low calcium (LC; 0.2% Ca) groups (control of 20% casein and one WPC group with 1% substitution of casein with one WPC). After 8 weeks, there was no effect of WPCs on femur uptake of 45Ca among ADC groups and there was no effect of WPCs on calcium retention, femur breaking force, femur bone mineral density, or total femur calcium at either dietary calcium intake. However, whole body bone mineral content (BMC) was significantly higher (P < 0.05) in the three whey protein concentrate ADC groups compared with the ADC control group. Total BMC at the proximal tibia in whey protein ADC groups was increased, as shown by peripheral quantitative computed tomography. Our results indicate that the acute calcium absorption–enhancing effect of whey proteins did not persist through long-term feeding in rats. However, the initial enhancement of calcium absorption by whey protein was sufficient to Increase BMC.
Effects of Multiple Deletions of Murein Hydrolases on Viability, Septum Cleavage, and Sensitivity to Large Toxic Molecules in Escherichia coli

ABSTRACT The multiplicity of murein hydrolases found in most bacteria presents an obstacle to demonstrating the necessity of these potentially autolytic enzymes. Therefore, Escherichia coli mutants with deletions in multiple murein hydrolases, including lytic transglycosylases, amidases, and dd-endopeptidases, were constructed. Even a mutant from which seven different hydrolases were deleted was viable and grew at a normal rate. However, penicillin-induced lysis was retarded. Most of the mutants were affected in septum cleavage, which resulted in the formation of chains of cells. All three enzymes were shown to be capable of splitting the septum. Failure to cleave the septum resulted in an increase in outer membrane permeability, and thus the murein hydrolase mutants did not grow on MacConkey agar plates. In addition, the hydrolase mutants not only could be lysed by lysozyme in the absence of EDTA but also were sensitive to high-molecular-weight antibiotics, such as vancomycin and bacitracin, which are normally ineffective against E. coli.
Impact of channel estimation error on upper bound of rate loss for macro cell in a VFDM system

Vandermonde-subspace frequency division multiplexing (VFDM) is a newly-proposed spectrum sharing technology, where perfect channel state information (CSI) is required. In this paper, considering complex Gaussian distributed channel estimation error, we study the interference leakage from small cell (SC) to macro cell (MC) due to imperfect CSI. The probability density function (PDF) of the upper bound of interference leakage is carefully derived. With that PDF, the distribution of the rate loss upper bound is further achieved. Simulation results are presented to validate the correctness of the theoretical derivation and to discover the impact of imperfect CSI on the performance degradation of the MC.
Structured Open Urban Data: Understanding the Landscape

A growing number of cities are now making urban data freely available to the public. Besides promoting transparency, these data can have a transformative effect in social science research as well as in how citizens participate in governance. These initiatives, however, are fairly recent and the landscape of open urban data is not well known. In this study, we try to shed some light on this through a detailed study of over 9,000 open data sets from 20 cities in North America. We start by presenting general statistics about the content, size, nature, and popularity of the different data sets, and then examine in more detail structured data sets that contain tabular data. Since a key benefit of having a large number of data sets available is the ability to fuse information, we investigate opportunities for data integration. We also study data quality issues and time-related aspects, namely, recency and change frequency. Our findings are encouraging in that most of the data are structured and published in standard formats that are easy to parse; there is ample opportunity to integrate different data sets; and the volume of data is increasing steadily. But they also uncovered a number of challenges that need to be addressed to enable these data to be fully leveraged. We discuss both our findings and issues involved in using open urban data.