Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparing Label-Free Quantitative Peptidomics Approaches to Characterize Diurnal Variation of Peptides in the Rat Suprachiasmatic Nucleus

Mammalian circadian rhythm is maintained by the suprachiasmatic nucleus (SCN) via an intricate set of neuropeptides and other signaling molecules. In this work, peptidomic analyses from two times of day were examined to characterize variation in SCN peptides using three different label-free quantitation approaches: spectral count, spectra index and SIEVE. Of the 448 identified peptides, 207 peptides were analyzed by two label-free methods, spectral count and spectral index. There were 24 peptides with significant (adjusted p-value < 0.01) differential peptide abundances between daytime and nighttime, including multiple peptides derived from secretogranin II, cocaine and amphetamine regulated transcript, and proprotein convertase subtilisin/kexin type 1 inhibitor. Interestingly, more peptides were analyzable and had significantly different abundances between the two time points using the spectral count and spectral index methods than with a prior analysis using the SIEVE method with the same data. The results of this study reveal the importance of using the appropriate data analysis approaches for label-free relative quantitation of peptides. The detection of significant changes in so rich a set of neuropeptides reflects the dynamic nature of the SCN and the number of influences such as feeding behavior on circadian rhythm. Using spectral count and spectral index, peptide level changes are correlated to time of day, suggesting their key role in circadian function.
An Algorithm to Evaluate Quantified Boolean Formulae

The high computational complexity of advanced reasoning tasks such as belief revision and planning calls for efficient and reliable algorithms for reasoning problems harder than NP. In this paper we propose Evaluate, an algorithm for evaluating Quantified Boolean Formulae, a language that extends propositional logic in a way such that many advanced forms of propositional reasoning, e.g., reasoning about knowledge, can be easily formulated as evaluation of a QBF. Algorithms for evaluation of QBFs are suitable for the experimental analysis on a wide range of complexity classes, a property not easily found in other formalisms. Evaluate is based on a generalization of the Davis-Putnam procedure for SAT, and is guaranteed to work in polynomial space. Before presenting Evaluate, we discuss all the abstract properties of QBFs that we singled out to make the algorithm more efficient. We also briefly mention the main results of the experimental analysis, which is reported elsewhere.
In search of no-loss strategies for the game of tic-tac-toe using a customized genetic algorithm

The game of Tic-tac-toe is one of the most commonly known games. This game does not allow one to win all the time and a significant proportion of games played results in a draw. Thus, the best a player can hope is to not lose the game. This study is aimed at evolving a number of no-loss strategies using genetic algorithms and comparing them with existing methodologies. To efficiently evolve no-loss strategies, we have developed innovative ways of representing and evaluating a solution, initializing the GA population, developing GA operators including an elite preserving scheme. Interestingly, our GA implementation is able to find more than 72 thousands no-loss strategies for playing the game. Moreover, an analysis of these solutions has given us insights about how to play the game to not lose it. Based on this experience, we have developed specialized efficient strategies having a high win-to-draw ratio. The study and its results are interesting and can be encouraging for the techniques to be applied to other board games for finding efficient strategies.
Spinal Dorsal Horn Calcium Channel α2δ-1 Subunit Upregulation Contributes to Peripheral Nerve Injury-Induced Tactile Allodynia

Peripheral nerve injury induces upregulation of the calcium channel α2δ-1 structural subunit in dorsal root ganglia (DRG) and dorsal spinal cord of spinal nerve-ligated rats with neuropathic pain, suggesting a role of the calcium channel α2δ-1 subunit in central sensitization. To investigate whether spinal dorsal horn α2δ-1 subunit upregulation derives from increased DRG α2δ-1 subunit and plays a causal role in neuropathic pain development, we examined spinal dorsal hornα2δ-1 subunit expression with or without dorsal rhizotomy in spinal nerve-ligated rats and its correlation with tactile allodynia, a neuropathic pain state defined as reduced thresholds to non-noxious tactile stimulation. We also examined the effects of intrathecal α2δ-1 antisense oligonucleotides on α2δ-1 subunit expression and neuropathic allodynia in the nerve-ligated rats. Our data indicated that spinal nerve injury resulted in time-dependentα2δ-1 subunit upregulation in the spinal dorsal horn that correlated temporally with neuropathic allodynia development and maintenance. Dorsal rhizotomy diminished basal level expression and blocked injury-induced expression of the spinal dorsal hornα2δ-1 subunit and reversed injury-induced tactile allodynia. In addition, intrathecal α2δ-1 antisense oligonucleotides blocked injury-induced dorsal horn α2δ-1 subunit upregulation and diminished tactile allodynia. These findings indicate that α2δ-1 subunit basal expression occurs presynaptically and postsynaptically in spinal dorsal horn. Nerve injury induces mainly presynaptic α2δ-1 subunit expression that derives from increased α2δ-1 subunit in injured DRG neurons. Thus, changes in presynaptic α2δ-1 subunit expression contribute to injury-induced spinal neuroplasticity and central sensitization that underlies neuropathic pain development and maintenance.
Discussion Paper Series Cores of Non-Atomic Market Games

We study the cores of non-atomic market games, a class of transferable utility cooperative games introduced by Aumann and Shapley [2], and, more in general, of those games that admit a na-continuous and concave extension to the set of ideal coalitions, studied by Einy, Moreno, and Shitovitz [12]. We show that the core of such games is norm compact and we provide some representation results. We also give a Multiple Priors interpretation of some of our results.
Self-Regulation, Mediators, and E-Learning: A Field Experiment in Rural Belize

Can lessons from IS research be applied on a small scale in rural environments to help a country develop? Students in rural schools in Belize often lack access to well-trained subject experts, score lower on national exams, and enroll in secondary schools at a lower rate than urban students. Utilizing mobile Internet technologies, students living without electricity can now access educational resources similar to urban students. How best to utilize these resources to improve students’ learning outcomes remains to be solved. This article first describes and compares a theory originating in the developed world (self-regulated learning) with one originating in the developing world (minimally invasive education). Second, it presents a framework combining constructs from both theories. Finally, it focuses on learning outcomes as measured by students’ cognitive ability, self-efficacy and motivation and compares a self-organized learning environment with one enhanced by self-regulated strategies, through a quasi-experimental design.
Attractive Interactions among Intermediate Filaments Determine Network Mechanics In Vitro

Mechanical and structural properties of K8/K18 and vimentin intermediate filament (IF) networks have been investigated using bulk mechanical rheometry and optical microrheology including diffusing wave spectroscopy and multiple particle tracking. A high elastic modulus G 0 at low protein concentration c, a weak concentration dependency of G 0 (G 0∼c 0.5±0.1) and pronounced strain stiffening are found for these systems even without external crossbridgers. Strong attractive interactions among filaments are required to maintain these characteristic mechanical features, which have also been reported for various other IF networks. Filament assembly, the persistence length of the filaments and the network mesh size remain essentially unaffected when a nonionic surfactant is added, but strain stiffening is completely suppressed, G 0 drops by orders of magnitude and exhibits a scaling G 0∼c 1.9±0.2 in agreement with microrheological measurements and as expected for entangled networks of semi-flexible polymers. Tailless K8Δ/K18ΔT and various other tailless filament networks do not exhibit strain stiffening, but still show high G 0 values. Therefore, two binding sites are proposed to exist in IF networks. A weaker one mediated by hydrophobic amino acid clusters in the central rod prevents stretched filaments between adjacent cross-links from thermal equilibration and thus provides the high G 0 values. Another strong one facilitating strain stiffening is located in the tail domain with its high fraction of hydrophobic amino acid sequences. Strain stiffening is less pronounced for vimentin than for K8/K18 due to electrostatic repulsion forces partly compensating the strong attraction at filament contact points.
Postural Stability in Young Adults with Down Syndrome in Challenging Conditions

To evaluate postural control and performance in subjects with Down syndrome (SwDS), we measured postural sway (COP) in quiet stance in four 20-second tests: with eyes open or closed and on hard or foam surface. Ten SwDS and eleven healthy subjects participated, aged 29.8 (4.8) and 28.4 (3.9), respectively. The time-series recorded with the sampling rate of 100 Hz were used to evaluate postural performance (COP amplitude and mean velocity) and strategies (COP frequency, fractal dimension and entropy). There were no intergroup differences in the amplitude except the stance on foam pad with eyes open when SwDS had larger sway. The COP velocity and frequency were larger in SwDS than controls in all trials on foam pad. During stances on the foam pad SwDS increased fractal dimension showing higher complexity of their equilibrium system, while controls decreased sample entropy exhibiting more conscious control of posture in comparison to the stances on hard support surface. This indicated that each group used entirely different adjustments of postural strategies to the somatosensory challenge. It is proposed that the inferior postural control of SwDS results mainly from insufficient experience in dealing with unpredictable postural stimuli and deficit in motor learning.
Long Non-Coding RNA LSINCT5 Predicts Negative Prognosis and Exhibits Oncogenic Activity in Gastric Cancer

AbstractLong non-coding RNAs (lncRNAs) are recently discovered RNA transcripts that are aberrantly expressed in many tumor types. Numerous studies have suggested that lncRNAs can be utilized for cancer diagnosis and prognosis. LSINCT5 (long stress-induced non-coding transcript 5) is dramatically upregulated in breast and ovarian cancer and affects cellular proliferation. However, the expression pattern of LSINCT5 in gastrointestinal cancer and the association between aberrant expression of LSINCT5 in gastrointestinal cancer and malignancy, metastasis, or prognosis remain unknown.LSINCT5 expression was detected in gastrointestinal cancer and paired adjacent normal tissue samples or cell lines using reverse transcription quantitative PCR (RT-qPCR). We also investigated the potential relationship between tumor LSINCT5 levels and clinicopathological features of gastrointestinal cancer. Finally, we assessed whether LSINCT5 influences in vitro cell proliferation.The expression of LSINCT5 is significantly upregulated in gastrointestinal cancer tissues and cell lines relative to their normal counterparts. In addition, increased LSINCT5 expression was correlated with a larger tumor size, deeper tumor depth, and advanced clinical stage. Kaplan–Meier analysis indicated that gastric cancer (GC) and colorectal cancer (CRC) patients with higher LSINCT5 expression levels have worse disease-free survival (DFS) and disease-specific survival (DSS) rates. Moreover, multivariate analysis revealed that increased expression of LSINCT5 is an independent predictor of DFS and DSS rates in GC patients. The ectopic expression of LSINCT5 in gastrointestinal cancer cell lines resulted in an increase in cellular proliferation; conversely, knock down of LSINCT5 significantly inhibited proliferation.These results suggest that LSINCT5 may represent a novel prognostic indicator and a target for gene therapy in gastrointestinal cancer.
VLSI structures for bit-serial modular multiplication using basis conversion

This paper proposes design techniques for the efficient VLSI implementation of bit-serial multiplication over a modulus. These techniques reduce multiplication into simple cyclic shifts, where the number representation of the data is chosen appropriately. This representation will, in general, be highly redundant, implying a relatively poor throughput for the multiplier. It is then shown how, by splitting the multiplier into two pipelined multipliers, the throughput of the unit can be increased, whilst still retaining a cyclic-shift implementation. The split multiplier requires a mid-computation basis conversion, and the two number representations, used within the unit, are only moderately redundant. Thus, high-throughput, bit-serial multipliers are achieved, with most of the complexity contained within systolic basis converter modules. The multipliers are applicable to the VLSI implementation of high-throughput, signal processing operations performed over finite fields, in particular, transform and filter operations.
O-Linked-N-Acetylglucosamine Cycling and Insulin Signaling Are Required for the Glucose Stress Response in Caenorhabditis elegans

In a variety of organisms, including worms, flies, and mammals, glucose homeostasis is maintained by insulin-like signaling in a robust network of opposing and complementary signaling pathways. The hexosamine signaling pathway, terminating in O-linked-N-acetylglucosamine (O-GlcNAc) cycling, is a key sensor of nutrient status and has been genetically linked to the regulation of insulin signaling in Caenorhabditis elegans. Here we demonstrate that O-GlcNAc cycling and insulin signaling are both essential components of the C. elegans response to glucose stress. A number of insulin-dependent processes were found to be sensitive to glucose stress, including fertility, reproductive timing, and dauer formation, yet each of these differed in their threshold of sensitivity to glucose excess. Our findings suggest that O-GlcNAc cycling and insulin signaling are both required for a robust and adaptable response to glucose stress, but these two pathways show complex and interdependent roles in the maintenance of glucose–insulin homeostasis.
Training transfer between card sorting and false belief understanding: helping children apply conflicting descriptions.

Two studies investigated the parallel developmental progress in theory of mind and executive control, as exemplified by correlations between the Dimensional Change Card Sorting task (DCCS; Frye, Zelazo, & Palfai, 1995) and the false-belief task. Experiment 1 with sixty 3-year-old children confirmed earlier studies (e.g., Perner & Lang, 2002), suggesting that children's problem with the DCCS lies in the redescription of stimulus objects. Experiment 2 with forty-four 3- to 4-year-olds reinforced the correlational evidence for a developmental link by showing transfer of training: False-belief training improved DCCS performance, and DCCS training significantly increased children's performance on the false-belief task. Results are discussed in relation to 5 theories explaining the existing correlational evidence.
Online speaker adaptation and tracking for real-time speech recognition

This paper describes a low-latency online speaker adaptation framework. The main objective is to apply fast speaker adaptation to a real-time (RT) large vocabulary continuous speech recognition (LVCSR) engine. In this framework, speaker adaptation is performed on speaker turns generated by online speaker change detection and speaker clustering. To maximize long-term system performance, the adaptation statistics for known speakers are updated continuously while new speakers are actively discovered. In contrast to existing approaches, a re-decode of an utterance after adaptation is eliminated from the process. We demonstrate that the framework can be easily incorporated into every pass of a multi-pass decoder. We applied the framework to the BBN Audio Indexer which is a real-time end-to-end audio indexing system that runs at around 0.6xRT. The result is an 8%-12% relative word-error-rate reduction on broadcast news benchmark tests for English, Chinese, and Arabic, with less than 0.1xRT cost in real-time throughput.
Collaboration Around a Tabletop Display : Supporting Interpersonal Interactions

This paper explores the use of a tabletop display to support collaboration. The research goal was to investigate participants’ collaborative interactions while they worked cooperatively around a tabletop display. In particular, non-verbal interactions of participants were examined to elucidate issues surrounding awareness of intent. Two different input device strategies were explored for interaction with the tabletop display. Stylus and mouse based interaction models were developed to allow multiple people to simultaneously interact with the system using either one or two devices. The results demonstrated that users exhibited a high degree of physical interactivity when working around the table and that the stylus-based approach encouraged non-verbal communication between participants. In particular, physical gestures and eye contact afforded by the tabletop enhanced users’ awareness of their partner’s intent. Overall, we found that the tabletop display was a natural medium to support collaboration and that the stylus was an effective device to support seamless interactions.
Transmissibility of the Influenza Virus in the 1918 Pandemic

BACKGROUND With a heightened increase in concern for an influenza pandemic we sought to better understand the 1918 Influenza pandemic, the most devastating epidemic of the previous century. METHODOLOGY/PRINCIPAL FINDINGS We use data from several communities in Maryland, USA as well as two ships that experienced well-documented outbreaks of influenza in 1918. Using a likelihood-based method and a nonparametric method, we estimate the serial interval and reproductive number throughout the course of each outbreak. This analysis shows the basic reproductive number to be slightly lower in the Maryland communities (between 1.34 and 3.21) than for the enclosed populations on the ships (R(0) = 4.97, SE = 3.31). Additionally the effective reproductive number declined to sub epidemic levels more quickly on the ships (within around 10 days) than in the communities (within 30-40 days). The mean serial interval for the ships was consistent (3.33, SE = 5.96 and 3.81, SE = 3.69), while the serial intervals in the communities varied substantially (between 2.83, SE = 0.53 and 8.28, SE = 951.95). CONCLUSIONS/SIGNIFICANCE These results illustrate the importance of considering the population dynamics when making statements about the epidemiological parameters of Influenza. The methods that we employ for estimation of the reproductive numbers and the serial interval can be easily replicated in other populations and with other diseases.
An SDP-Based Divide-and-Conquer Algorithm for Large-Scale Noisy Anchor-Free Graph Realization

We propose the DISCO algorithm for graph realization in $\mathbb{R}^d$, given sparse and noisy short-range intervertex distances as inputs. Our divide-and-conquer algorithm works as follows. When a group has a sufficiently small number of vertices, the basis step is to form a graph realization by solving a semidefinite program. The recursive step is to break a large group of vertices into two smaller groups with overlapping vertices. These two groups are solved recursively, and the subconfigurations are stitched together, using the overlapping atoms, to form a configuration for the larger group. At intermediate stages, the configurations are improved by gradient descent refinement. The algorithm is applied to the problem of determining protein moleculer structure. Tests are performed on molecules taken from the Protein Data Bank database. For each molecule, given 20-30% of the inter-atom distances less than 6A that are corrupted by a high level of noise, DISCO is able to reliably and efficiently reconstruct the conformation of large molecules. In particular, given 30% of distances with 20% multiplicative noise, a 13000-atom conformation problem is solved within an hour with a root mean square deviation of 1.6A.
Automatic Clustering of Flow Cytometry Data with Density-Based Merging

The ability of flow cytometry to allow fast single cell interrogation of a large number of cells has made this technology ubiquitous and indispensable in the clinical and laboratory setting. A current limit to the potential of this technology is the lack of automated tools for analyzing the resulting data. We describe methodology and software to automatically identify cell populations in flow cytometry data. Our approach advances the paradigm of manually gating sequential two-dimensional projections of the data to a procedure that automatically produces gates based on statistical theory. Our approach is nonparametric and can reproduce nonconvex subpopulations that are known to occur in flow cytometry samples, but which cannot be produced with current parametric model-based approaches. We illustrate the methodology with a sample of mouse spleen and peritoneal cavity cells.
Unsupervised Method of Object Retrieval Using Similar Region Merging and Flood Fill

In this work; we address a novel interactive framework for object retrieval using unsupervised similar region merging and flood fill method which models the spatial and appearance relations among image pixels. Efficient and effective image segmentation is usually very hard for natural and complex images. This paper presents a new technique for similar region merging and objects retrieval. The users only need to roughly indicate the after which steps desired objects boundary is obtained during merging of similar regions. A novel similarity based region merging mechanism is proposed to guide the merging process with the help of mean shift technique. A region R is merged with its adjacent regions Q if Q has highest similarity with R among all Q’s adjacent regions. The proposed method automatically merges the regions that are initially segmented through mean shift technique, and then effectively extracts the object contour by merging all similar regions. Extensive experiments are performed on 22 object classes (524 images total) show promising results.