Miracle-dz/UniFAR-FTUs huggingface dataset:
A Transcription Elongation Factor That Links Signals from the Reproductive System to Lifespan Extension in Caenorhabditis elegans

In Caenorhabditis elegans and Drosophila melanogaster, the aging of the soma is influenced by the germline. When germline-stem cells are removed, aging slows and lifespan is increased. The mechanism by which somatic tissues respond to loss of the germline is not well-understood. Surprisingly, we have found that a predicted transcription elongation factor, TCER-1, plays a key role in this process. TCER-1 is required for loss of the germ cells to increase C. elegans' lifespan, and it acts as a regulatory switch in the pathway. When the germ cells are removed, the levels of TCER-1 rise in somatic tissues. This increase is sufficient to trigger key downstream events, as overexpression of tcer-1 extends the lifespan of normal animals that have an intact reproductive system. Our findings suggest that TCER-1 extends lifespan by promoting the expression of a set of genes regulated by the conserved, life-extending transcription factor DAF-16/FOXO. Interestingly, TCER-1 is not required for DAF-16/FOXO to extend lifespan in animals with reduced insulin/IGF-1 signaling. Thus, TCER-1 specifically links the activity of a broadly deployed transcription factor, DAF-16/FOXO, to longevity signals from reproductive tissues.
Distributive Network Utility Maximization Over Time-Varying Fading Channels

Distributed network utility maximization (NUM) has received an increasing intensity of interest over the past few years. Distributed solutions (e.g., the primal-dual gradient method) have been intensively investigated under fading channels. As such distributed solutions involve iterative updating and explicit message passing, it is unrealistic to assume that the wireless channel remains unchanged during the iterations. Unfortunately, the behavior of those distributed solutions under time-varying channels is in general unknown. In this paper, we shall investigate the convergence behavior and tracking errors of the iterative primal-dual scaled gradient algorithm (PDSGA) with dynamic scaling matrices (DSC) for solving distributive NUM problems under time-varying fading channels. We shall also study a specific application example, namely the multicommodity flow control and multicarrier power allocation problem in multihop ad hoc networks. Our analysis shows that the PDSGA converges to a limit region rather than a single point under the finite state Markov chain (FSMC) fading channels. We also show that the order of growth of the tracking errors is given by O(T̅/N̅), where T̅ and N̅ are the update interval and the average sojourn time of the FSMC, respectively. Based on this analysis, we derive a low complexity distributive adaptation algorithm for determining the adaptive scaling matrices, which can be implemented distributively at each transmitter. The numerical results show the superior performance of the proposed dynamic scaling matrix algorithm over several baseline schemes, such as the regular primal-dual gradient algorithm.
Heparan Sulfate Proteoglycans May Promote or Inhibit Cancer Progression by Interacting with Integrins and Affecting Cell Migration

The metastatic disease is one of the main consequences of tumor progression, being responsible for most cancer-related deaths worldwide. This review intends to present and discuss data on the relationship between integrins and heparan sulfate proteoglycans in health and cancer progression. Integrins are a family of cell surface transmembrane receptors, responsible for cell-matrix and cell-cell adhesion. Integrins' main functions include cell adhesion, migration, and survival. Heparan sulfate proteoglycans (HSPGs) are cell surface molecules that play important roles as cell receptors, cofactors, and overall direct or indirect contributors to cell organization. Both molecules can act in conjunction to modulate cell behavior and affect malignancy. In this review, we will discuss the different contexts in which various integrins, such as α5, αV, β1, and β3, interact with HSPGs species, such as syndecans and perlecans, affecting tissue homeostasis.
Ontology Based Patterns for Collaborative Process Management

Collaboration within and between organisations requires knowledge and skills that collaborating partners do not always possess. In an effort to capture best practice collaboration knowledge, we propose patterns as models of repeatable collaboration processes for recurring high-value collaborative tasks. We present a pattern-based approach, associated ontology and tool which act as a platform that can intelligently match collaboration contexts and requirements to collaboration patterns, make intelligent inferences about applying patterns to solve problems at successive levels of abstraction and recommend either workflows or less structured actions as solutions to collaboration contexts.
Vestibular and oculomotor influences on visual dependency

Participants made verticality judgments using the rod-and-disk test, a test of visual dependence, and then repeated after caloric irrigation. If the combination of rotating disk and caloric increased the slow-phase velocity of the torsional nystagmus the tilt in subjective verticality increased, whereas reductions in eye velocity were associated with reduced tilt. Thus visual dependency measures are not only modulated by perceptual style but can also reflect local vestibulo-ocular function, specifically torsional eye movements.
Neurodiverse Self-Discovery and Social Acceptance in Curious Incident and Marcelo in the Real World

Abstract:The article compares the identities and coming-of-age experiences of neurodiverse young adult protagonists in two novels, Mark Haddon's The Curious Incident of the Dog in the Night-Time and Francisco X. Stork's Marcelo in the Real World. While Christopher in Curious Incident encourages readers to consider the world from a neurodiverse point of view and see the potential value of neurodiversity for the individual himself, it also portrays his autistic traits as the dominant aspects of his identity, and it is difficult to see how others may accept his difference or recognize him as having value in society. In Marcelo in the Real World, on the other hand, Marcelo is a more fully developed character who makes significant progress toward successfully integrating into mainstream society while also retaining who he is as a neurodiverse individual. Both novels feature neurodiverse characters in ways that can promote understanding of neurological difference; however, neurodiversity as it is represented in the character of Marcelo is more nuanced and demonstrates that neurodiverse individuals can be both valued by and contribute to society whilst not having to change who they are.
Beyond Statistical Significance: Implications of Network Structure on Neuronal Activity

It is a common and good practice in experimental sciences to assess the statistical significance of measured outcomes. For this, the probability of obtaining the actual results is estimated under the assumption of an appropriately chosen null-hypothesis. If this probability is smaller than some threshold, the results are deemed statistically significant and the researchers are content in having revealed, within their own experimental domain, a “surprising” anomaly, possibly indicative of a hitherto hidden fragment of the underlying “ground-truth”. What is often neglected, though, is the actual importance of these experimental outcomes for understanding the system under investigation. We illustrate this point by giving practical and intuitive examples from the field of systems neuroscience. Specifically, we use the notion of embeddedness to quantify the impact of a neuron's activity on its downstream neurons in the network. We show that the network response strongly depends on the embeddedness of stimulated neurons and that embeddedness is a key determinant of the importance of neuronal activity on local and downstream processing. We extrapolate these results to other fields in which networks are used as a theoretical framework.
The on-line cross entropy method for unsupervised data exploration

We investigate the use of the new Cross Entropy method as a tool for exploratory data analysis. We show how this method can be used to perform linear projections such as principal component analysis, exploratory projection pursuit and canonical correlation analysis. We further go on to show how topology preserving mappings can be created usin the cross entropy method. We also show how the cross entropy method can be used to train deep architecture nets which are one of the main current research directions for creating true artificial intelligence. Finally we show how the cross entropy method can be used to optimize parameters for latent variable models.
Proteomic Analysis of a Fraction with Intact Eyespots of Chlamydomonas reinhardtii and Assignment of Protein Methylation

Flagellate green algae possess a visual system, the eyespot. In Chlamydomonas reinhardtii it is situated at the edge of the chloroplast and consists of two carotenoid rich lipid globule layers subtended by thylakoid membranes (TM) that are attached to both chloroplast envelope membranes and a specialized area of the plasma membrane (PM). A former analysis of an eyespot fraction identified 203 proteins. To increase the understanding of eyespot related processes, knowledge of the protein composition of the membranes in its close vicinity is desirable. Here, we present a purification procedure that allows isolation of intact eyespots. This gain in intactness goes, however, hand in hand with an increase of contaminants from other organelles. Proteomic analysis identified 742 proteins. Novel candidates include proteins for eyespot development, retina-related proteins, ion pumps, and membrane-associated proteins, calcium sensing proteins as well as kinases, phosphatases and 14-3-3 proteins. Methylation of proteins at Arg or Lys is known as an important posttranslational modification involved in, e.g., signal transduction. Here, we identify several proteins from eyespot fractions that are methylated at Arg and/or Lys. Among them is the eyespot specific SOUL3 protein that influences the size and position of the eyespot and EYE2, a protein important for its development.
Mean-Field-Type Games in Engineering

A mean-field-type game is a game in which the instantaneous payoffs and/or the state dynamics functions involve not only the state and the action profile but also the joint distributions of state-action pairs. This article presents some engineering applications of mean-field-type games including road traffic networks, multi-level building evacuation, millimeter wave wireless communications, distributed power networks, virus spread over networks, virtual machine resource management in cloud networks, synchronization of oscillators, energy-efficient buildings, online meeting and mobile crowdsensing.
Insulin resistance, diabetes, and the insulin-regulated trafficking of GLUT-4

AB~T~S affects ~,5% of people in the United States of America and the incidence is much higher in sporadic populations such as Pima Indians in North America and Australian Aborigines. There are two major forms of diabetes, referred to as insulin-dependent diabetes (IDD) ~ and non-insulin-dependent diabetes (NIDD). The etiology of these diseases is quite different despite similarities in their pathophysiologies. IDD often arises in early life and is due to autoimmune destruction of pancreatic/3 cells resulting in partial or complete loss of/3 cell function. NIDD is more common in later life (>40 yr) and ,x,85 % of all diabetics have this form. The increased prevalence of NIDD in developed countries together with its association with heart disease and stroke makes this one of the most devastating diseases in the western world. NIDD appears to be due to a defect in glucose disposal (DeFronzo et al., 1992). Both glucose per se and insulin, play important roles in facilitating glucose uptake into target organs (for review see DeFronzo et ai., 1992). Following ingestion of a carbohydrate meal, glucose uptake into many organs is increased simply due to the elevated blood glucose. A more pronounced increase which is evoked by insulin, is observed specifically in muscle and adipose tissue. The net result is that in the postprandial state, glucose is rapidly and efficiently cleared from the blood and stored primarily in muscle and adipose. Each of these processes is defective in NIDD making it extremely difficult to identify the primary lesion. Studies in first degree relatives of NIDDs indicate that one of the earliest detectable defects is impaired insulin action in muscle and adipose tissue or insulin resistance (Martin et al., 1992). Thus, identifying the physiological and molecular biological processes that control insulin-stimulated glucose utilization in these organs is of major significance.
Neurobiology of Disease Microglia Disrupt Mesolimbic Reward Circuitry in Chronic Pain

X Anna M. W. Taylor,1,2 X Annie Castonguay,3,4 Alison J. Taylor,2 Niall P. Murphy,2 Atefeh Ghogha,2 Christopher Cook,1 Lihua Xue,5 X Mary C. Olmstead,6 X Yves De Koninck,3,4 Christopher J. Evans,2 and X Catherine M. Cahill1,5 1Department of Anesthesiology and Perioperative Care, University of California Irvine, Irvine, California 92697, 2Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, 3Institut Universitaire en Santé Mentale de Québec 2601, Chemin de la Canardiere, Québec G1J 2G3, Canada, 4Department of Psychiatry and Neuroscience, Université Laval, Québec G1V OA6, Canada, 5Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada, and 6Department of Psychology, Queen’s University, Kingston, Ontario K7L 3N6, Canada
The Buddha on Meditation and States of Consciousness

There is inevitably great difficulty in translating from noumenat experience to the realm of discourse, from raw reality to abstract concept. Experience is the forerunner of all spiritual teachings, though similar experiences may come to be articulated differently; the Vedas say, "The Truth is one, only thesages call it by different names," In any given exploration of higher states of consciousness, the version set down in words is of necessity an arbitrary, and perhaps nebulous, delimitation of states, their characteristics, and their bounds. Lao Tzu recognizes this dilemma in the Tao Te Ching:
Examining the Impact of University Sports Success on Freshman ACT Scores: An Empirical Analysis

My study presents a model in which incoming freshman ACT scores are a function of football, basketball, and baseball regular season and postseason success, using academic variables as controls. I contribute to the existing literature by including baseball in the analysis in addition to football and basketball, using ACT scores instead of SAT scores, using a unique and expanded set of variables to measure sports success, and more recent data. For the time period 2006-2014, I find weak evidence that supports the hypothesis that athletic success positively influences ACT scores.
Career Counseling Interventions for Video Game Players

Video games are becoming ubiquitous in Western societies. However, this virtual leisure has received little attention from researchers in career counseling, leaving career counselors relatively unprepared to work with video game players. In this article, we propose three types of interventions to capitalize on the benefits of playing video games to foster the career counseling process. The first intervention aims to identify and transfer the skills that video game players develop through their leisure activity. The second intervention highlights how video game players’ narrative may reveal vocational personality types. The third intervention proposes to turn career counseling tasks into a game to increase motivation to achieve it. The strengths and limitations of these interventions are underlined, as well as the potential of career counseling sessions to help remedy problematic video game play.
MRI-Compatible Pneumatic Robot for Transperineal Prostate Needle Placement

Magnetic resonance imaging (MRI) can provide high-quality 3-D visualization of prostate and surrounding tissue, thus granting potential to be a superior medical imaging modality for guiding and monitoring prostatic interventions. However, the benefits cannot be readily harnessed for interventional procedures due to difficulties that surround the use of high-field (1.5T or greater) MRI. The inability to use conventional mechatronics and the confined physical space makes it extremely challenging to access the patient. We have designed a robotic assistant system that overcomes these difficulties and promises safe and reliable intraprostatic needle placement inside closed high-field MRI scanners. MRI compatibility of the robot has been evaluated under 3T MRI using standard prostate imaging sequences and average SNR loss is limited to 5%. Needle alignment accuracy of the robot under servo pneumatic control is better than 0.94 mm rms per axis. The complete system workflow has been evaluated in phantom studies with accurate visualization and targeting of five out of five 1 cm targets. The paper explains the robot mechanism and controller design, the system integration, and presents results of preliminary evaluation of the system.
Multi-document summarization of scientific corpora

In this paper, we investigated four approaches for scientific corpora summarization when only gold-standard keyterms available. MEAD with built-in default vocabulary, MEAD with corpus specific vocabulary extracted by Keyphrase Extraction Algorithm (KEA), LexRank (a state-of-the-art summarization algorithm based on random walk) and W3SS (summarization algorithm based on keyword density) are tested on two Computer Science research paper collections. We use a content evaluation method, pyramid method, instead of the well-known ROUGE metrics since there are no gold-standard summaries available for our data. Evaluations with pyramid method indicates that including a corpus specific vocabulary to the traditional summarization methods improves the performance but not significantly. On the other hand, visual inspection shows us that current content evaluation methods, which use only the gold-standard keyterm information, are not intuitive and focus must turn into better evaluation techniques especially for the multi-document summarization problem. Even though the pyramid method looks for important keyterms in the resulting summaries, it cannot distinguish between a general introductory sentence about the area and a specific sentence on the core idea, if they both contain the same keyterm. Also, our results show that the state of the art summarization method LexRank is not feasible for scientific corpus summarization because of its high computational cost.
Propose a Wall Shear Stress Divergence to Estimate the Risks of Intracranial Aneurysm Rupture

Although wall shear stress (WSS) has long been considered a critical indicator of intracranial aneurysm rupture, there is still no definite conclusion as to whether a high or a low WSS results in aneurysm rupture. The reason may be that the effect of WSS direction has not been fully considered. The objectives of this study are to investigate the magnitude of WSS (|WSS|) and its divergence on the aneurysm surface and to test the significance of both in relation to the aneurysm rupture. Patient-specific computational fluid dynamics (CFD) was used to compute WSS and wall shear stress divergence (WSSD) on the aneurysm surface for nineteen patients. Our results revealed that if high |WSS| is stretching aneurysm luminal surface, and the stretching region is concentrated, the aneurysm is under a high risk of rupture. It seems that, by considering both direction and magnitude of WSS, WSSD may be a better indicator for the risk estimation of aneurysm rupture (154).
Characterizing Uronate Dehydrogenase from P. syringae as a Step Towards Expressing a Retro-Biosynthetically Derived Glucaric Acid Pathway in E. coli

Retro-biosynthesis is a novel pathway design method that integrates biocatalysis (in particular, functional group specificity and reactivity of enzymes) and organic chemistry. Using this method, several novel pathways have been designed in this laboratory for the microbial production of glucaric acid. In addition to design, efforts have been made in order to express these pathways inside E. col. For the production of glucaric acid in E. coil, toxicity of this organic acid as well as the uptake efficiency of glucose, the starting substrate, when in the presence of glucaric acid was assessed. Furthermore, a benchmark pathway for glucaric acid production that utilizes known reaction steps from different source organisms was designed. The design and expression of this pathway will be compared to the retro-biosynthetic pathway. The ease of design and expression will be analyzed in order to confirm the validity of retro-biosynthesis. Toxicity results showed that glucaric acid concentrations, up to 40 mM, do not affect growth of E. coli DH1OB cells. Furthermore, cells take up equal amounts of glucose even when glucaric acid is available, indicating that glucose is preferentially utilized by cells and that glucaric acid, once produced by cells, would not affect further production. Finally, efforts have been made in order to express the benchmark pathway in E. coli. The entire pathway requires expression of three enzymes. The final reaction step requires uronate dehydrogenase in order to convert glucuronic acid to the desired product, glucaric acid. Although the function and approximate molecular weight of uronate dehydrogenase is known, its DNA sequence is not. Isolating the gene encoding the enzyme can be facilitated by a partial digestion of the genomic DNA of the source organism, P. syringae. A screening method for uronate dehydrogenase activity has also been developed and optimized. Using this screening method, the library was constructed in E. coli. Once colonies that contain uronate dehydrogenase are selected, this enzyme's sequence can be determined and the benchmark pathway can be closer to becoming expressed. Thesis Supervisor: Kristala Jones Prather Title: Joseph R. Mares (1924) Assistant Professor of Chemical Engineering
Delay Models of Single-Source Single-Relay Cooperative ARQ Protocols in Slotted Radio Networks With Poisson Frame Arrivals

In conventional (noncooperative) automatic repeat request (ARQ) protocols for radio networks, the corrupted data frames that cannot be correctly decoded at the destination are retransmitted by the source. In cooperative ARQ protocols, data frame retransmissions may be performed by a neighboring node (the relay) that has successfully overheard the source's frame transmission. One advantage of the latter group of ARQ protocols is the spatial diversity provided by the relay. The first delay model for cooperative ARQ protocols is derived in this paper. The model is analytically derived for a simple set of retransmission rules that make use of both uncoded and coded cooperative communications in slotted radio networks. The model estimates the delay experienced by Poisson arriving frames, whose retransmissions (when required) are performed also by a single relay. Saturation throughput, data frame latency, and buffer occupancy at both the source and relay are quantified and compared against two noncooperative ARQ protocols.