Miracle-dz/UniFAR-FTUs huggingface dataset:
Transient assembly of F-actin by phagosomes delays phagosome fusion with lysosomes in cargo-overloaded macrophages

Dynamic remodelling of the cortical actin cytoskeleton is required for phagocytic uptake of pathogens and other particles by macrophages. Actin can also be nucleated de novo on membranes of nascent phagosomes, a process that can stimulate or inhibit phagosome fusion with lysosomes. Recently, phagosomes were shown to polymerize actin in transient pulses, called actin `flashing', whose function remains unexplained. Here, we investigated phagosomal actin dynamics in live macrophages expressing actin tagged with green fluorescent protein (GFP). We show that only immature phagosomes can transiently induce assembly of actin coat, which forms a barrier preventing phagosome-lysosome docking and fusion. The capacity of phagosomes to assemble actin is enhanced in cells exposed to increased phagocytic load, which also exhibit a delay in phagosome maturation. Parallel analysis indicated that polymerization of actin on macropinosomes also induces compression and propulsion. We show that dynamic interactions between membrane elastic tension and compression forces of polymerizing actin can also lead to macropinosome constriction and scission – a process that is obstructed on rigid phagosomes. We hypothesize that the rate of individual phagosome maturation, as well as the biogenesis and remodelling of macropinosomes, can be regulated by the extent and manner of actin assembly on their membrane.
Extending Languages by Leveraging Compilers: From Modelica to Optimica

Constructing compilers using ordinary object-oriented programming takes advantage of parser generators to construct abstract syntax trees (ASTs) and uses the Visitor design pattern to program traversals that resolve names and types and to generate code. Although this plain approach allows some reuse and modularization, it's possible to go much further by combining object orientation with recent advances in at tribute grammars to build highly extensible compilers.
Transcranial magnetic stimulation-induced global propagation of transient phase resetting associated with directional information flow

Electroencephalogram (EEG) phase synchronization analyses can reveal large-scale communication between distant brain areas. However, it is not possible to identify the directional information flow between distant areas using conventional phase synchronization analyses. In the present study, we applied transcranial magnetic stimulation (TMS) to the occipital area in subjects who were resting with their eyes closed, and analyzed the spatial propagation of transient TMS-induced phase resetting by using the transfer entropy (TE), to quantify the causal and directional flow of information. The time-frequency EEG analysis indicated that the theta (5 Hz) phase locking factor (PLF) reached its highest value at the distant area (the motor area in this study), with a time lag that followed the peak of the transient PLF enhancements of the TMS-targeted area at the TMS onset. Phase-preservation index (PPI) analyses demonstrated significant phase resetting at the TMS-targeted area and distant area. Moreover, the TE from the TMS-targeted area to the distant area increased clearly during the delay that followed TMS onset. Interestingly, the time lags were almost coincident between the PLF and TE results (152 vs. 165 ms), which provides strong evidence that the emergence of the delayed PLF reflects the causal information flow. Such tendencies were observed only in the higher-intensity TMS condition, and not in the lower-intensity or sham TMS conditions. Thus, TMS may manipulate large-scale causal relationships between brain areas in an intensity-dependent manner. We demonstrated that single-pulse TMS modulated global phase dynamics and directional information flow among synchronized brain networks. Therefore, our results suggest that single-pulse TMS can manipulate both incoming and outgoing information in the TMS-targeted area associated with functional changes.
MotionFlow: Visual Abstraction and Aggregation of Sequential Patterns in Human Motion Tracking Data

Pattern analysis of human motions, which is useful in many research areas, requires understanding and comparison of different styles of motion patterns. However, working with human motion tracking data to support such analysis poses great challenges. In this paper, we propose MotionFlow, a visual analytics system that provides an effective overview of various motion patterns based on an interactive flow visualization. This visualization formulates a motion sequence as transitions between static poses, and aggregates these sequences into a tree diagram to construct a set of motion patterns. The system also allows the users to directly reflect the context of data and their perception of pose similarities in generating representative pose states. We provide local and global controls over the partition-based clustering process. To support the users in organizing unstructured motion data into pattern groups, we designed a set of interactions that enables searching for similar motion sequences from the data, detailed exploration of data subsets, and creating and modifying the group of motion patterns. To evaluate the usability of MotionFlow, we conducted a user study with six researchers with expertise in gesture-based interaction design. They used MotionFlow to explore and organize unstructured motion tracking data. Results show that the researchers were able to easily learn how to use MotionFlow, and the system effectively supported their pattern analysis activities, including leveraging their perception and domain knowledge.
HacA-Independent Functions of the ER Stress Sensor IreA Synergize with the Canonical UPR to Influence Virulence Traits in Aspergillus fumigatus

Endoplasmic reticulum (ER) stress is a condition in which the protein folding capacity of the ER becomes overwhelmed by an increased demand for secretion or by exposure to compounds that disrupt ER homeostasis. In yeast and other fungi, the accumulation of unfolded proteins is detected by the ER-transmembrane sensor IreA/Ire1, which responds by cleaving an intron from the downstream cytoplasmic mRNA HacA/Hac1, allowing for the translation of a transcription factor that coordinates a series of adaptive responses that are collectively known as the unfolded protein response (UPR). Here, we examined the contribution of IreA to growth and virulence in the human fungal pathogen Aspergillus fumigatus. Gene expression profiling revealed that A. fumigatus IreA signals predominantly through the canonical IreA-HacA pathway under conditions of severe ER stress. However, in the absence of ER stress IreA controls dual signaling circuits that are both HacA-dependent and HacA-independent. We found that a ΔireA mutant was avirulent in a mouse model of invasive aspergillosis, which contrasts the partial virulence of a ΔhacA mutant, suggesting that IreA contributes to pathogenesis independently of HacA. In support of this conclusion, we found that the ΔireA mutant had more severe defects in the expression of multiple virulence-related traits relative to ΔhacA, including reduced thermotolerance, decreased nutritional versatility, impaired growth under hypoxia, altered cell wall and membrane composition, and increased susceptibility to azole antifungals. In addition, full or partial virulence could be restored to the ΔireA mutant by complementation with either the induced form of the hacA mRNA, hacA i, or an ireA deletion mutant that was incapable of processing the hacA mRNA, ireA Δ10. Together, these findings demonstrate that IreA has both HacA-dependent and HacA-independent functions that contribute to the expression of traits that are essential for virulence in A. fumigatus.
Simulation of crowd behaviors based on event reaction

We propose a new organization for virtual crowd responses to emergent events. In our approach, there are three main components: agent model, smart environment model and behavior model. The agent model is responsible for providing important information to the smart environment model and executing the corresponding actions. The smart environment model includes a set of smart objects and events and embeds the behavioral responses to inform the behavior model of behavior options. The behavior model adopts the rule-based module to generate appropriate behaviors according to the attributes and current state of agents. This scheme does not require complex reasoning and can run in real time. Furthermore, it can not only show plausible crowd behaviors and reflect the dynamic change of the emergent event, but is also much easier for extendibility and scalability. We demonstrate this approach in a scenario of agents reacting to a car accident.
Kinetic Spectrophotometric Determination of Ramipril in Commercial Dosage Forms

This paper presents a simple and sensitive kinetic spectrophotometric method for the determination of ramipril in commercial dosage forms. The method is based on the reaction of the drug with 1-chloro-2,4-dinitrobenzene (CDNB) in dimethylsulfoxide (DMSO) at 100 ± 1C. The reaction is followed spectrophotometrically by measuring the rate of change of the absorbance at 420 nm. Fixed-time (ΔA) and equilibrium methods are adopted for constructing the calibration curves. Both the calibration curves were found to be linear over the concentration ranges 20 220 μg/ml. The regression analysis of calibration data yielded the linear equations: Δ A = 6.30 × 10 + 1.54 × 10 C and A = 3.62 × 10 + 6.35 × 10 C for fixed time (Δ A) and equilibrium methods, respectively. The limits of detection (LOD) for fixed time and equilibrium methods are 1.47 and 1.05 μg/ml, respectively. The method has been successfully applied to the determination of ramipril in commercial dosage forms. Statistical comparison of the results shows that there is no significant difference between the proposed methods and Abdellatef’s spectrophotometric method. Keywords—Equilibrium method, Fixed-time (ΔA) method, Ramipril, Spectrophotometry.
Fine Haplotype Structure of a Chromosome 17 Region in the Laboratory and Wild Mouse

Extensive linkage disequilibrium among classical laboratory strains represents an obstacle in the high-resolution haplotype mapping of mouse quantitative trait loci (QTL). To determine the potential of wild-derived mouse strains for fine QTL mapping, we constructed a haplotype map of a 250-kb region of the t-complex on chromosome 17 containing the Hybrid sterility 1 (Hst1) gene. We resequenced 33 loci from up to 80 chromosomes of five mouse (sub)species. Trans-species single-nucleotide polymorphisms (SNPs) were rare between Mus m. musculus (Mmmu) and Mus m. domesticus (Mmd). The haplotypes in Mmmu and Mmd differed and therefore strains from these subspecies should not be combined for haplotype-associated mapping. The haplotypes of t-chromosomes differed from all non-t Mmmu and Mmd haplotypes. Half of the SNPs and SN indels but only one of seven longer rearrangements found in classical laboratory strains were useful for haplotype mapping in the wild-derived M. m. domesticus. The largest Mmd haplotype block contained three genes of a highly conserved synteny. The lengths of the haplotype blocks deduced from 36 domesticus chromosomes were in tens of kilobases, suggesting that the wild-derived Mmd strains are suitable for fine interval-specific mapping.
Local learning of item dissimilarity using content and link structure

In the Recommendation Problem, it is often important to find a set of items similar to a particular item or a group of items. This problem of finding similar items for the recommendation task may also be viewed as a link prediction problem in a network, where the items can be treated as the nodes. The strength of the edge connecting two items represents the similarity between the items. In this context, a central challenge is to suitably define an appropriate dissimilarity function between the items. For content based recommender systems, the dissimilarity function should take into account the individual attributes of the items. The same attribute may have different importances in different parts of the underlying network. We focus on the problem of learning a suitable dissimilarity function between items and address it by formulating it as a constrained optimization problem which captures the local weightages of the attributes in different regions of the graph. The constraints are imposed in such a way that the non-connected nodes show higher value of dissimilarity than the connected nodes. The local tuning of the weights learns the optimal value of weights in various parts of the network: from the portions having rich graph information to the portions having only content information. Detailed experimentation shows the superiority of the proposed algorithm over the Adamic Adar metric as well as logistic regression methodology.
Blind hyperspectral denoising

In this work we propose a new formulation for hyperspectral denoising based on the Blind Compressed Sensing (BCS) framework. BCS learns the sparsifying basis during signal recovery combining the advantages of standard sparse recovery with dictionary learning. We show that our proposed formulation yields better results than a state-of-the- art technique hyperspectral denoising both in terms of PSNR (more than 1dB improvement) and visual quality.
Usefulness of the maximum rate of pressure rise in the central and peripheral arteries after weaning from cardiopulmonary bypass in pediatric congenital heart surgery

Abstract The maximum rate of pressure rise (dP/dtmax) in radial artery has been proposed as a noninvasive surrogate of aortic dp/dtmax, reflecting left ventricular (LV) contractility in children. The aim of this study was to investigate relationship between aortic and radial dp/dtmax at weaning from cardiopulmonary bypass (CPB) and usefulness of these indices for estimating postoperative outcomes in pediatric congenital heart surgery. Aortic and radial arterial pressure waveforms were analyzed simultaneously during weaning from CPB in 29 congenital heart surgery. The maximum first derivatives of aortic and radial arterial waveforms were calculated and averaged from 3 consecutive respiratory cycles. We obtained the maximum vasoactive inotropic score during the first 36 postoperative hours, LV ejection fraction, and fractional shortening on transthoracic echocardiography performed within postoperative day 7. A significant difference between aortic and radial dP/dtmax was observed (mean difference 356 mm Hg/s, 44% of averages), and radial dP/dtmax was weakly correlated with aortic dP/dtmax (r =0.373, P = 0.047). Aortic dP/dtmax was significantly associated with the maximum vasoactive inotropic score (P < 0.001), postoperative LV ejection fraction (P = 0.018), and fractional shortening (P = 0.015); however, radial dP/dtmax was not. On Receiver operating characteristic analysis, aortic dP/dtmax had a greater area under the curve than radial dP/dtmax in predicting higher vasoactive inotropic score (0.827 vs 0.673). Immediately after CPB in pediatric congenital heart surgery, radial dP/dtmax may not replace aortic dP/dtmax because of a discrepancy between central and peripheral arterial waveforms. In this critical period, aortic dP/dtmax can be useful to estimate postoperative ventricular function rather than peripherally derived dP/dtmax.
Gain-Loss Framing in Interdependent Choice

Abstract Framing influences choice. However, little is known about the underlying mechanisms behind framing effects. We study gain-loss framing in binary modified dictator games. Subjects choose the selfish option more often in the loss frame compared to the gain frame. Recording visual fixations with eye-tracking, we find that dictators focus more on their own outcomes when facing losses. This suggests that losses to the own outcome are weighted more than losses to another player.
Exact Time Complexity of ZebraNet with Cover Times Jo

Population protocols are a communication model for large sensor networks with resource-limited mobile agents. The agents move asynchronously and communicate via pair-wise interactions. The original fairness assumption of this model involves a high level of asynchrony and prevents an evaluation of the convergence time of a protocol (via deterministic means). The introduction of some partial synchrony in the model, under the form of cover times, is an extension that allows evaluating the time complexities. In this paper, we take advantage of this extension and study a data collection protocol used in the ZebraNet project for the wild-life tracking of zebras in a reserve in central Kenya. In ZebraNet, sensors are attached to zebras and the sensed data is collected regularly by a mobile base station crossing the area. The data collection protocol of ZebraNet has been analyzed through simulations, but to our knowledge, this is the rst time, that a purely analytical study is presented. Our rst result is that, in the original protocol, some data may never be delivered to the base station. We then propose two slightly modi ed and correct protocols and we compute their worst case time complexities. Still, in both cases, the result is far from the optimal.
Corporate Associations and Consumer Product Responses: The Moderating Role of Corporate Brand Dominance

This study investigates the effect of corporate brand dominance—that is, the visibility of a company's corporate brand in product communications—on the relationship between corporate associations and product evaluations. The results show that corporate brand dominance determines the degree to which associations with the company's corporate ability and corporate social responsibility influence product attitudes, as well as the nature of the moderating effects of fit and involvement.
CMSC 858 F : Algorithmic Game Theory Fall 2010 Frugality & Profit Maximization in Mechanism Design Instructor :

Recall from the previous lecture that in combinatorial auction each bidder has an associated real-valued valuation function V defined for each subset of items S. An allocation of items S1, S2, . , Sn among the bidders with valuation function V1, V2, . , Vn respectively is socially efficient if the allocation maximizes the social welfare ∑ i Vi(Si). Combinatorial auction is a very general auction setting and it is well-known that if we use VCG payments, then this is incentive-compatible. However there are some issues. The two major issues in combinatorial auctions are,
DIFFERENCES BETWEEN INTERNATIONAL MOTOR CARRIERS AND NATIONAL MOTOR CARRIERS

Since non-manufacturing activities represent the majority of the North American economy, there is opportunity for research to focus on non-manufacturing settings, including transportation (Shields 1997). This study focuses on a single service industry: the motor carrier industry (SIC 4213). Restricting to a single industry reduces noise, thereby increasing statistical power, and consequently provides a higher likelihood of identifying valid relationships. The motor carrier industry is selected because of interest of the members of the industry in use of business initiatives that can potentially improve their competitive positions. Since deregulation, motor carriers have had to relearn state of the art competitive practices.
Precise Gridding of Microarray Images by Detecting and Correcting Rotations in Subarrays

DNA microarrays are an important tool for massive gene expression profiling and genotyping studies. A microarray consists of thousands of spots that must be scanned and digitized for further analysis. However, the mechanical constraints and other printing issues increase the difficulty in automatic analysis, most of the applications released up to now need different levels of human intervention, which inevitably reduce the efficiency and reproducibility of the entire process. In this paper, we present a precise microarray gridding method, in which potential problems in grid alignment and possible rotation in subarrays are detected and corrected. The gridding process is fully automatic, which eliminates the need for human intervention.
Efficient window for monolingual and crosslingual speaker identification using MFCC

In this paper an experimental evaluation of the various windowing techniques using mel-frequency cepstral coefficient (MFCC) for monolingual and crosslingual speaker identification is demonstrated. The set of windows presented here allows a tradeoff between main lobe bandwidth and side lobe ripple decay. The speaker identification study is conducted using randomly selected 50 speakers from IITG Multi-variability speaker recognition (IITG-MV) database, MFCC feature and Gaussian mixture model (GMM)-universal background model (UBM) classifier. Speaker identification system based on various windowing techniques shown to have considerably improved performance over baseline Hamming window technique.
Atrophy in the Medial Temporal Lobe is Specifically Associated With Encoding and Storage of Verbal Information in MCI and Alzheimer Patients

Background : Alzheimer’s dementia (AD) is characterized by a progressive decline in the encoding and storage of episodic memory. Word-list learning tests can characterize different aspects of episodic memory. Medial temporal lobe atrophy (MTA) seems to be an important anatomical feature of AD and its prodromal stage, mild cognitive impairment (MCI). The aim of this study is to define the relationships of the functional memory processes and MTA in patients with AD and MCI, while correcting for confounding factors. Methods : MTA was evaluated with a visual assessment scale using the MRIs of 53 patients diagnosed with AD or MCI and 19 controls. Rey’s Auditory Verbal Learning Test was used to assess the different aspects of memory processing, i.e., encoding, storage and retrieval. Multiple regression analysis was used to investigate the association of MTA with these different memory processes. In addition to general factors such as age, education and sex, white matter lesions, cortical and subcortical atrophy were evaluated for being confounders. Results : MTA was significantly associated with encoding (corrected beta = -0.45, sd = 0.11, P Conclusions : We can conclude that atrophy of the medial temporal lobe is associated with a decline in encoding and storage of verbal information in MCI and AD. doi:10.4021/jnr18w
Hyperphagia produced by lateral amygdalar lesions in dogs.

In our previous papers (Fonberg 1965, 1967) the assumption was made, that the baso-lateral part of amygdala consists of an inhibitory ali-mentary center, similar to the "satiety center" in the ventroinedial hy-pothalamus. This assumption was mostly based on the results of our earlier experiments on cats (Fonberg and Delgado 1960, 1961) which showed that stimullation of the baso-lateral partion of the amygdaloid complex inhibits the food intake and performance of instrumental ali-mentary reactions. These findings were confirmed on dogs (Fon~berg 1963), and on rats (Morgane 1962). Several authors described hyperphagia after amygdalar ablation (Ful-and others). In most of the studies, however, large amygdalar lesions or total ablation was performed, and strict localization was not the problem under study or yielded controversial results. For example Wood (1958) observed an increase of food intake after lesions situated in the central nucleus. On the other ha~nd, Green et al. (1957) on the basis of reconstruction of amygdalar lesions on cats stated that the junction between lateral and basal nucleus is crucial for the hyperphagia syndrome. Our recent experiments seem to show, that performing a small circumscribed lesion is a good methold to localize the specialized functions of the amygdala. It was found that lesions situated in the dorso-medial part of amygdala produce aphagia with subsequent hypophagia (Fonberg 1966, 1968, 1969ab). However, if lesion involved also the lateral nucleus, subsequent