Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantification and localization of gait variability as biomarkers for mild traumatic brain injury

ii To my parents, for believing in me. iii ACKNOWLEDGMENTS I would like to acknowledge and thank the individuals at the MRI Research Facility and the 3D Bio-Motion Research Lab at the University of Iowa for their expertise and assistance with this project. In particular, I would like to acknowledge John Meusch for his assistance in the collection and post processing of the motion capture data and for the inspired conversations. Also, their collaborative work with the imaging protocol and analysis, especially Jinsuh Kim for his reporting of the MRI-DTI findings. I would like to thank Joe Ekdahl and Vincent Magnotta for their assistance and patience scheduling MRIs. I would like to acknowledge my advisors, Salam Rahmatalla and Deema Fattal, and thank them for teaching me the value of hard work and a positive attitude. I would also like to acknowledge the members of my committee, Edwin Dove, Nicole Grosland, and David Wilder, for their presence and involvement in my education and for their continual support and guidance. I would also like to pray for the U.S. military and the individuals who so willingly serve and protect our country. It is my hope that this work contributes to the ever growing knowledge of mild traumatic brain injury, and that someday these courageous men and women will benefit from improved diagnosis and treatment and lead lives free of the persistent and debilitating effects of mild traumatic brain injury. iv ABSTRACT Motion capture technology and Magnetic Resonance Imaging with Diffusion Tensor Imaging (MRI-DTI) were used in this work to detect subtle abnormalities in patients with mild traumatic brain injury (MTBI). A new concept, termed dynamic variability, is introduced in this work to quantify and localize gait variability. Three chronic MTBI patients were recruited from the Veterans Affair Medical Center in Iowa City, IA, and three healthy controls with height, weight, and gender matched to the patients were recruited from the Reserve Officers' Training Corps in Iowa City, IA. Kinematic and kinetic data of the subjects were collected during the performance of three gait testing scenarios. The first test involved single-task walking and was used as a baseline. The second and third tests were dual tasks that involved walking while performing a cognitive or motor task and were designed to magnify gait abnormalities. The results showed that MTBI patients had reduced gait velocity, shortened stride length, and larger step width; findings that are …
Three-Dimensional Nonrigid MR-TRUS Registration Using Dual Optimization

In this study, we proposed an efficient nonrigid magnetic resonance (MR) to transrectal ultrasound (TRUS) deformable registration method in order to improve the accuracy of targeting suspicious regions during a three dimensional (3-D) TRUS guided prostate biopsy. The proposed deformable registration approach employs the multi-channel modality independent neighborhood descriptor (MIND) as the local similarity feature across the two modalities of MR and TRUS, and a novel and efficient duality-based convex optimization-based algorithmic scheme was introduced to extract the deformations and align the two MIND descriptors. The registration accuracy was evaluated using 20 patient images by calculating the TRE using manually identified corresponding intrinsic fiducials in the whole gland and peripheral zone. Additional performance metrics [Dice similarity coefficient (DSC), mean absolute surface distance (MAD), and maximum absolute surface distance (MAXD)] were also calculated by comparing the MR and TRUS manually segmented prostate surfaces in the registered images. Experimental results showed that the proposed method yielded an overall median TRE of 1.76 mm. The results obtained in terms of DSC showed an average of 80.8±7.8% for the apex of the prostate, 92.0±3.4% for the mid-gland, 81.7±6.4% for the base and 85.7±4.7% for the whole gland. The surface distance calculations showed an overall average of 1.84±0.52 mm for MAD and 6.90±2.07 mm for MAXD.
Predicting Commitment in Adult and Traditional-Age Students: Applying Rusbult's Investment Model to the Study of Retention.

Rusbult's Investment Model, a theoretical model of commitment based on notions of social exchange and interdependence theory, was used to predict college commitment in traditional-age and adult college students. A questionnaire assessing rewards, costs, investments, alternatives, and commitment to college was administered to 216 traditional-age students (83 males and 133 females) who attended regular weekday classes at a midsized private university in the Northeast and 204 adult students (77 males and 127 females) enrolled in a Saturday College program designed for older adults wishing to complete their baccalaureate degree by attending Saturday classes. Rewards, investments of time and money, and investments represented by potential losses upon leaving proved to be significant predictors of commitment for traditional-age students. Rewards, investments represented by potential losses upon leaving, and few perceived acceptable alternatives were determined to be significant predictors of commitment for adult students. Costs did not affect commitment for either traditional-age or adult students. It was concluded that increasing traditional-age and adult students' commitment to their college may require policies and procedures developed in consideration for the differences between the two age groups. (Contains 31 references.) (MN) *********************************************************************** Reproductions supplied by EDRS are the best that can be made from the original document. ***********************************************************************
Autophagy Regulates Endoplasmic Reticulum Homeostasis and Calcium Mobilization in T Lymphocytes

Macroautophagy (hereafter referred to as autophagy) is an evolutionarily conserved intracellular bulk degradation pathway that plays critical roles in eliminating intracellular pathogens, presenting endogenous Ags, and regulating T lymphocyte survival and proliferation. In this study, we have investigated the role of autophagy in regulating the endoplasmic reticulum (ER) compartment in T lymphocytes. We found that ER content is expanded in mature autophagy-related protein (Atg) 7-deficient T lymphocytes. Atg7-deficient T cells stimulated through the TCR display impaired influx, but not efflux, of calcium, and ER calcium stores are increased in Atg7-deficient T cells. Treatment with the ER sarco/ER Ca2+-ATPase pump inhibitor thapsigargin rescues the calcium influx defect in Atg7-deficient T lymphocytes, suggesting that this impairment is caused by an intrinsic defect in ER. Furthermore, we found that the stimulation-induced redistribution of stromal interaction molecule-1, a critical event for the store-operated Ca2+ release-activated Ca2+ channel opening, is impaired in Atg7-deficient T cells. Together, these findings indicate that the expanded ER compartment in Atg7-deficient T cells contains increased calcium stores, and the inability of these stores to be depleted causes defective calcium influx in these cells. Our results demonstrate that autophagy plays an important role in maintaining ER and calcium homeostasis in T lymphocytes.
Sequence Based Analysis reveals a polyphyletic origin of Vibrio vulnificus biotype 2

vulnificus biotype 2 Eva Sanjuán, Fernando González-Candelas , and Carmen Amaro. Departamento de Microbiología, Facultad de Biología, Universidad de Valencia, Valencia, España. (eva.sanjuan@uv.es, Carmen.amaro@uv.es) 2 Unidad mixta “Genómica y Salud” Centro Superior de Investigación en Salud Pública-Universidad de Valencia/Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Valencia, España. (Fernando.gonzalez@uv.es) 3 CIBER de Epidemiología y Salud Pública, Valencia, España.
Simulation software for a network modelling lab

We introduce a software application that simulates the most common types of queues. It also compares the simulation results with the values that the mathematical model predicts for specific types of queues. Thus, the software we have developed has two academic aspects. The first one applies to its ability to simulate most of the queuing processes that take place in computer networks. Therefore someone who studies network modelling or computer performance analysis may use it to derive some practical results in a very convenient way. The second aspect of the software refers to the part of the application that simulates specific types of queue and it can be used as a guide for teaching network modelling. We believe that it is very easy for someone to understand the aspects of queuing theory even though he/she is not familiar with it.
Multiple association analysis via simulated annealing (MASSA)

SUMMARY Genome-wide association studies are now technically feasible and likely to become a fundamental tool in unraveling the ultimate genetic basis of complex traits. However, new statistical and computational methods need to be developed to extract the maximum information in a realistic computing time. Here we propose a new method for multiple association analysis via simulated annealing that allows for epistasis and any number of markers. It consists of finding the model with lowest Bayesian information criterion using simulated annealing. The data are described by means of a mixed model and new alternative models are proposed using a set of rules, e.g. new sites can be added (or deleted), or new epistatic interactions can be included between existing genetic factors. The method is illustrated with simulated and real data. AVAILABILITY An executable version of the program (MASSA) running under the Linux OS is freely available, together with documentation, at http://www.icrea. es/pag.asp? id=Miguel.Perez.
Multi-agent physical a* using large pheromones

This paper introduces the notion of large pheromones as a model of communication and global knowledge sharing in multi-agent systems. With pheromones, agents communicate by writing and reading data at the nodes of the graph that constitutes their environment [2]. Unlike ordinary pheromones where only a limited amount of data can be written in each node, in the large pheromones model, there is no restriction on the amount of data that can be written in the the nodes and thus each agent can write its entire knowledge in a node. We apply this model of communication to the multi-agent physical A* algorithm (MAPHA*) which is the multi agent version of Physical-A* (PHA*) [1]. These algorithms modify the A* algorithm to find shortest paths in physical environments with mobile agents that move around the environment and explore unknown territories. These algorithms are designed to minimize the travel effort of the agents. We will show that increasing the amount of data that can be stored at each of the pheromones dramatically reduces the travel effort of the agents. With maximal usage of this model with unlimited size of pheromones the behavior of a multi-agent system is almost as good as with complete knowledge sharing between the agents.
Trajectory generation in joint space using modified hidden Markov model

Human guide robots need to generate a trajectory from human training. The popular work space methods have to calculate the inverse kinematics. While the joint space methods need the dynamic time warping. These destroy the accuracy of the trajectory model. In this paper, we use Lloyd's algorithm to hidden Markov model (HMM). The advantages of the method over the other HMM are the time difference does not affects the HMM training, and the training data can be generated in joint space. We also modify the traditional HMM such that the model in the joint space works similar as the task space. Simulation and experimental results show that the modified HMM with Lloyd's algorithm in joint space is effective to generate the desired trajectory.
1 Balance Sheet Effects and Financial Propagation : Evidence from Industrial and Emerging Markets

This paper examines the balance sheet effects with particular attention to the development of the financial system. Our results indicate that the macroeconomic cycles are more volatile in financially underdeveloped economies. We also found that net worth measured by stock prices plays a role in propagating real and credit cycles. The sensitivity to the change in net worth is particularly large in financially underdeveloped economies. Asymmetric behavior of the responses across boom and crash periods is found to be significant with production and credit cycles associated with the low level of financial development. This evidence supports the prediction of financial propagation mechanism caused by the balance sheet effects. Key word: Financial propagation, Balance sheet effect, and Credit booms JEL classification: F2, F4, E3 1 I thank Graciela Kaminsky, Holger Wolf, Fred Joutz, Jorge Soares, Sylvain Leduc, and participants at the Fall 2000 Macro-International seminar at George Washington University and the Bank of Japan for many helpful comments. I benefited from a discussion with Pamela Labadie at earlier stage of the paper. I am also grateful to the participants of the Friday international meeting for their suggestions and support.
Starvation‐induced MTMR13 and RAB21 activity regulates VAMP8 to promote autophagosome–lysosome fusion

Autophagy, the process for recycling cytoplasm in the lysosome, depends on membrane trafficking. We previously identified Drosophila Sbf as a Rab21 guanine nucleotide exchange factor (GEF) that acts with Rab21 in endosomal trafficking. Here, we show that Sbf/MTMR13 and Rab21 have conserved functions required for starvation‐induced autophagy. Depletion of Sbf/MTMR13 or Rab21 blocked endolysosomal trafficking of VAMP8, a SNARE required for autophagosome–lysosome fusion. We show that starvation induces Sbf/MTMR13 GEF and RAB21 activity, as well as their induced binding to VAMP8 (or closest Drosophila homolog, Vamp7). MTMR13 is required for RAB21 activation, VAMP8 interaction and VAMP8 endolysosomal trafficking, defining a novel GEF‐Rab‐effector pathway. These results identify starvation‐responsive endosomal regulators and trafficking that tunes membrane demands with changing autophagy status.
Content-adaptive reference frame compression based on intra-frame prediction for multiview video coding

This paper presents a content-adaptive reference frame compression scheme to alleviate the large overhead of external memory communication during the Motion and Disparity Estimation process in Multiview Video Coding (MVC). Our scheme is based on a simplified intra-prediction process to reduce the spatial redundancy of the reference samples. The intra-prediction residue is compressed by a path composed of non-linear quantization and Huffman-based entropy encoder. Four different quantization strengths and Huffman tables were statistically defined. They are dynamically selected according to a content adaptation strategy, which classifies the original blocks based on their spatial homogeneity. Experimental results show that the proposed content-adaptive compression scheme is able to reduce the external memory accesses by up to 63% along with negligible losses in the MVC encoder rate-distortion performance. Compared to the best available related work [12] our content-adaptive reference frame compression achieves 39% reduced external memory accesses, while still providing a BD-PSNR increase of 0.03dB.
Stresshantering als mediator in de relatie tussen persoonlijkheid en posttraumatische stress-stoornis.

Dit onderzoek trachtte de geldigheid te onderzoeken van een verklarend model dat de relaties tussen persoonlijkheid, stresshantering en posttraumatische stressstoornis (PTSS) beschrijft. Er werd een partiële mediatie verwacht door emotiegerichte stresshantering in de relatie tussen neuroticisme en extraversie enerzijds en PTSS anderzijds. Tevens werd onderzocht of er sprake is van een verschil in stresshantering tussen personen met PTSS en personen zonder PTSS. Hiertoe werden 150 mannen geworven in Servië, die allen het uiteenvallen van voormalig Joegoslavië hebben meegemaakt. Deze groep bestond uit patiënten met PTSS, personen die hersteld zijn van PTSS en personen met een oorlogstrauma, maar zonder PTSS. Bovendien werd een Nederlandse controlegroep met 21 gezonde mannelijke respondenten betrokken in het onderzoek. Er werden verbanden aangetoond tussen neuroticisme en extraversie enerzijds en PTSS anderzijds. Neuroticisme bleek bovendien voorspellend te zijn voor emotiegerichte stresshantering, extraversie echter niet. Er werd geen verband gevonden tussen emotiegerichte stresshantering en PTSS, waardoor mediatieanalyse overbodig werd. Bovendien werd aangetoond dat personen met PTSS en met herstelde PTSS meer gebruik maakten van emotiegerichte stresshantering dan gezonde respondenten zonder trauma. Alternatieve verklaringen voor de gevonden resultaten en beperkingen en implicaties van het onderzoek PTSD and with recovered PTSD made more use of emotion-focused coping as compared to healthy respondents without trauma. Alternative explanations for the results found and limitations and implications of the study are discussed.
Redundancy and access permissions in decentralized file systems

This thesis solves two open problems of peer-to-peer file systems. It proposes a resource-efficient system for the reliable redundant storage of data. The system is evaluated with network traces of real peer-to-peer systems using different redundancy algorithms. Furthermore, this thesis presents a scheme to enforce of POSIX access permissions. It only relies on cryptography and uses nearly no asymmetric cryptography. Both systems do not depend on any central components.
Updating Systematic Reviews: An International Survey

Background Systematic reviews (SRs) should be up to date to maintain their importance in informing healthcare policy and practice. However, little guidance is available about when and how to update SRs. Moreover, the updating policies and practices of organizations that commission or produce SRs are unclear. Methodology/Principal Findings The objective was to describe the updating practices and policies of agencies that sponsor or conduct SRs. An Internet-based survey was administered to a purposive non-random sample of 195 healthcare organizations within the international SR community. Survey results were analyzed using descriptive statistics. The completed response rate was 58% (n = 114) from across 26 countries with 70% (75/107) of participants identified as producers of SRs. Among responders, 79% (84/107) characterized the importance of updating as high or very-high and 57% (60/106) of organizations reported to have a formal policy for updating. However, only 29% (35/106) of organizations made reference to a written policy document. Several groups (62/105; 59%) reported updating practices as irregular, and over half (53/103) of organizational respondents estimated that more than 50% of their respective SRs were likely out of date. Authors of the original SR (42/106; 40%) were most often deemed responsible for ensuring SRs were current. Barriers to updating included resource constraints, reviewer motivation, lack of academic credit, and limited publishing formats. Most respondents (70/100; 70%) indicated that they supported centralization of updating efforts across institutions or agencies. Furthermore, 84% (83/99) of respondents indicated they favoured the development of a central registry of SRs, analogous to efforts within the clinical trials community. Conclusions/Significance Most organizations that sponsor and/or carry out SRs consider updating important. Despite this recognition, updating practices are not regular, and many organizations lack a formal written policy for updating SRs. This research marks the first baseline data available on updating from an organizational perspective.
Structural Similarity and Classification of Protein Interaction Interfaces

Interactions between proteins play a key role in many cellular processes. Studying protein-protein interactions that share similar interaction interfaces may shed light on their evolution and could be helpful in elucidating the mechanisms behind stability and dynamics of the protein complexes. When two complexes share structurally similar subunits, the similarity of the interaction interfaces can be found through a structural superposition of the subunits. However, an accurate detection of similarity between the protein complexes containing subunits of unrelated structure remains an open problem. Here, we present an alignment-free machine learning approach to measure interface similarity. The approach relies on the feature-based representation of protein interfaces and does not depend on the superposition of the interacting subunit pairs. Specifically, we develop an SVM classifier of similar and dissimilar interfaces and derive a feature-based interface similarity measure. Next, the similarity measure is applied to a set of 2,806×2,806 binary complex pairs to build a hierarchical classification of protein-protein interactions. Finally, we explore case studies of similar interfaces from each level of the hierarchy, considering cases when the subunits forming interactions are either homologous or structurally unrelated. The analysis has suggested that the positions of charged residues in the homologous interfaces are not necessarily conserved and may exhibit more complex conservation patterns.
A Market-Oriented Strategy for Small and Medium Scale Enterprises

The paper examines the economic rationale for intervention in support of small and medium scale enterprises (SME), on both theoretical and empirical grounds. It argues that the justification for SME interventions lies in market, and institutional failures that bias the size distribution of firms, rather than on any inherent economic benefits provided by small firms. The role of the state is mainly to provide an enabling business environment that opens access to markets, and reduces policy-induced biases against small firms. Governments can accelerate the development of markets for financial, and non-financial services suited to SMEs by promoting innovation in products, and delivery mechanisms, and, by building institutional capacity. Improving the development impact of SME strategies will require much more attention to the monitoring, and evaluation of intervention outcomes.
Using language clues to discover crosscutting concerns

Researchers have developed ways to describe a concern, to store a concern, and even to keep a concern's code quickly available while updating it. Work on identifying concerns (semi-)automatically, however, has yet to gain attention and practical use, even though it is a desirable prerequisite to all of the above activities, particularly for legacy applications. This paper describes a concern identification technique that leverages the natural language processing (NLP) information in source code. Developers often use NLP clues to help understand software, because NLP helps them identify concepts that are semantically related. However, few analyses use NLP to understand programs, or to complement other program analyses. We have observed that an NLP technique called lexical chains offers the NLP equivalent of a concern. In this paper, we investigate the use of lexical chaining to identify crosscutting concerns, present the design and implementation of an algorithm that uses lexical chaining to expose concerns, and provide examples of concerns that our tool is able to discover automatically.