Miracle-dz/UniFAR-FTUs huggingface dataset:
Lipopolysaccharide Disrupts Mitochondrial Physiology in Skeletal Muscle via Disparate Effects on Sphingolipid Metabolism

ABSTRACT Lipopolysaccharides (LPS) are prevalent pathogenic molecules that are found within tissues and blood. Elevated circulating LPS is a feature of obesity and sepsis, both of which are associated with mitochondrial abnormalities that are key pathological features of LPS excess. However, the mechanism of LPS-induced mitochondrial alterations remains poorly understood. Herein we demonstrate the necessity of sphingolipid accrual in mediating altered mitochondrial physiology in skeletal muscle following LPS exposure. In particular, we found LPS elicited disparate effects on the sphingolipids dihydroceramides (DhCer) and ceramides (Cer) in both cultured myotubes and in muscle of LPS-injected mice. Although LPS-treated myotubes had reduced DhCer and increased Cer as well as increased mitochondrial respiration, muscle from LPS-injected mice manifested a reverse trend, namely elevated DhCer, but reduced Cer as well as reduced mitochondrial respiration. In addition, we found that LPS treatment caused mitochondrial fission, likely via dynamin-related protein 1, and increased oxidative stress. However, inhibition of de novo sphingolipid biosynthesis via myriocin protected normal mitochondrial function in spite of LPS, but inhibition of DhCer desaturase 1, which increases DhCer, but not Cer, exacerbated mitochondrial respiration with LPS. In an attempt to reconcile the incongruent effects of LPS in isolated muscle cells and whole muscle tissue, we incubated myotubes with conditioned medium from treated macrophages. In contrast to direct myotube LPS treatment, conditioned medium from LPS-treated macrophages reduced myotube respiration, but this was again mitigated with sphingolipid inhibition. Thus, macrophage sphingolipid production appears to be necessary for LPS-induced mitochondrial alterations in skeletal muscle tissue.
The Size of Employee Stakeholding in Large UK Corporations

The existing debate about policies designed to foster the development of a stakeholder economy have largely avoided a fundamental question. How large is the financial stake employees currently hold in their companies? This paper addresses this question using data from the Datastream database, and finds that there is already a significant link between the pay of rank and file employees and the performance of their firms. We find that a doubling of firm value increases employee pay in these firms by approximately 14 percent. Firms with explicit profit- sharing arrangements have a performance elasticity of approximately 0.32, while firms without explicit profit-sharing arrangements have a performance elasticity of only 0.11. This indicates that flexibility of pay is not limited to the explicit profit-sharing awards. This is further substantiated by the finding that even after controlling for the levels of profit-sharing pay, the performance elasticity in the profit sharing firms is 0.27. These estimates are by no means a complete measure of the stakeholding relationship, but they do quantify the financial relationship between firms and a group of primary stakeholders: the workers.
Artificial Intelligence Support for Interferon Treatment Decision in Chronic Hepatitis B

Chronic hepatitis B can evolve to cirrhosis and liver cancer. Interferon is the only effective treatment, for carefully selected patients, but it is very expensive. Some of the selection criteria are based on liver biopsy, an invasive, costly and painful medical proce- dure. Therefore, developing efficient non-invasive selection systems, could be in the patients benefit and also save money. We investigated the possibility to create intelligent systems to assist the Interferon therapeutical decision, mainly by predicting with acceptable accuracy the results of the biopsy. We used a knowledge discovery in integrated medical data - imaging, clinical, and laboratory data. The resulted intelligent systems, tested on 500 patients with chronic hepatitis B, based on C5.0 decision trees and boosting, predict with 100% accuracy the results of the liver biopsy. Also, by integrating the other patients selection criteria, they offer a non-invasive support for the correct Interferon therapeutic decision. To our best knowledge, these decision systems outperformed all similar systems published in the literature, and offer a realistic opportunity to replace liver biopsy in this medical context. Keywords—Interferon, chronic hepatitis B, intelligent virtual biopsy.
Topics in Portfolio Choice: Qualitative Properties, Time Consistency and Investment Under Model Uncertainty

The study of expected utility maximization in continuous-time stochastic market models dates back to the seminal work of Merton 1969 and has since been central to the area of Mathematical Finance. The associated stochastic optimization problems have been extensively studied. The problem formulation relies on two strong underlying assumptions: the ability to specify the underpinning market model and the knowledge of the investor’s risk preferences. However, neither of these inputs is easily available, if at all. Resulting issues have attracted continuous attention and prompted very active and diverse lines of research. This thesis seeks to contribute towards this literature and questions related to both of the above issues are studied. Specifically, we study the implications of certain qualitative properties of the utility function; we introduce, and study various aspects of, the notion of robust forward investment criteria; and we study the investment problem associated with risk- and ambiguity-averse preference criteria defined in terms of quasiconcave utility functionals.
The Roles of Noradrenergic and Glucocorticoid Activation in the Development of Intrusive Memories

Intrusive memories are a common feature of many psychological disorders. Recent evidence has potentially extended cognitive models of intrusions by identifying the role of biological markers of arousal at the time of consolidation in subsequent memory for emotional events. This study investigated the role of arousal during consolidation in the development of intrusive memories. Seventy-eight university students (37 men and 41 women) viewed 20 negative and 20 neutral images. Half the participants then underwent a cold pressor test (High Stress), immersing their hand in ice water, while the remaining participants immersed their hand in warm water (Low Stress). Samples of salivary alpha-amylase (sAA) and cortisol were collected from participants at baseline and following the stressor challenge. Participants completed a delayed free recall test and intrusion questionnaires two days later. Participants in the High Stress condition reported more intrusions of negative images than participants in the Low Stress condition. An interaction variable in a linear regression of increased noradrenergic and cortisol values predicted intrusive memories of emotional stimuli for men but not women. These findings are consistent with recent evidence of the combined effects of noradrenaline and corticoid responses to stress on emotional memories, and also with increasing evidence of gender differences in how stress hormones influence formation of emotional memories. These findings point to possible mechanisms by which development of intrusions may be prevented after consolidation of traumatic experiences.
Further results on reconstruction methods for processing finite-length signals with perfect reconstruction filter banks

In de Queiroz and Rao (1995), new expressions were developed for the perfect reconstruction (PR) of the boundary regions of a finite-length signal after subband processing using uniform and paraunitary filter banks (PUFBs). The present paper points out an incorrect assertion in the previous paper regarding the sufficiency of its solution and presents the general existence (applicability) conditions for the method. Furthermore, we extend the method to encompass perfect reconstruction filter banks, i.e., not only the paraunitary case.
Mathematical Modeling of Heterogeneous Electrophysiological Responses in Human β-Cells

Electrical activity plays a pivotal role in glucose-stimulated insulin secretion from pancreatic -cells. Recent findings have shown that the electrophysiological characteristics of human -cells differ from their rodent counterparts. We show that the electrophysiological responses in human -cells to a range of ion channels antagonists are heterogeneous. In some cells, inhibition of small-conductance potassium currents has no effect on action potential firing, while it increases the firing frequency dramatically in other cells. Sodium channel block can sometimes reduce action potential amplitude, sometimes abolish electrical activity, and in some cells even change spiking electrical activity to rapid bursting. We show that, in contrast to L-type -channels, P/Q-type -currents are not necessary for action potential generation, and, surprisingly, a P/Q-type -channel antagonist even accelerates action potential firing. By including SK-channels and dynamics in a previous mathematical model of electrical activity in human -cells, we investigate the heterogeneous and nonintuitive electrophysiological responses to ion channel antagonists, and use our findings to obtain insight in previously published insulin secretion measurements. Using our model we also study paracrine signals, and simulate slow oscillations by adding a glycolytic oscillatory component to the electrophysiological model. The heterogenous electrophysiological responses in human -cells must be taken into account for a deeper understanding of the mechanisms underlying insulin secretion in health and disease, and as shown here, the interdisciplinary combination of experiments and modeling increases our understanding of human -cell physiology.
Linking live and replay scenes in broadcasted sports video

Content based video organization requires to understand semantical relationships such as identity and similarity between video segments. In particular, it is of great interest to identify scenes of the same event which may differ in their appearances. For broadcasted sports video, such scenes correspond to live and replay scenes that appear at different temporal positions. In this paper, we propose a method of linking up live and replay scenes by focusing on the domain knowledge about producing TV programs of sports: most of the replay scenes are sandwiched in between specific digital video effects. The replay scenes are linked with live scenes when the game is in play based on salient image features. We clarify the effectiveness of our method through fundamental experiments for American football games.
BIOINFORMATICS ORIGINAL PAPER

Motivation: With an increase in the number of known biological functions of non-coding RNAs, the importance of RNA sequence alignment has risen. RNA sequence alignment problem has been investigated by many researchers as a mono-objective optimization problem where contributions from sequence similarity and secondary structure are taken into account through a single objective function. Since there is a trade-off between these two objective functions, usually we cannot obtain a single solution that has both the best sequence similarity score and the best structure score simultaneously. Multi-objective optimization is a widely used framework for the optimization problems with conﬂicting objective functions. So far, no one has examined how good alignments we can obtain by applying multi-objective optimization to structural RNA sequence alignment problem. Results: We developed a pairwise RNA sequence alignment program, Cofolga2mo, based on multi-objective genetic algorithm (MOGA). We tested Cofolga2mo with a benchmark dataset which includes sequence pairs with a wide range of sequence identity, and we obtained at most 100 alignments for each inputted RNA sequence pair as an approximate set of weak Pareto optimal solutions. We found that the alignments in the approximate set give benchmark results comparable to those obtained by the state-of-the-art mono-objective RNA alignment algorithms. Moreover, we found that our algorithm is efﬁcient in both time and memory usage compared to the other methods. Availability: Our MOGA programs for structural RNA sequence alignment
Bench testing of auto-adjusting positive airway pressure devices

Continuous positive airway pressure devices are routinely used to treat sleep breathing disorders. Automated devices that adjust the therapeutic pressure have recently been proposed. The utility of such devices is still controversial, as rigorous clinical comparisons are difficult to perform as a result of patient and device differences. The current authors studied automated devices in a respiratory model that was able to mimic upper airway mechanics and to interact with pressure adjustment in a closed loop. Five auto-adjusted devices were submitted to this model, in order to determine their ability to detect respiratory events and adjust pressure accordingly. All apnoeas were suppressed, whilst the reaction to repetitive hypopnoeas was dependent on the airflow shape. In some devices, repetitive hypopnoeas were changed to flow limitation. Artificial snoring caused a pressure increase in four devices, and constant mask leak was not systematically compensated. Only one device did not raise pressure in response to central apnoeas with opened upper airways. These findings show that, in some devices, event classification failed and normal airflow was not fully restored, resulting in elevated residual event indices. In conclusion, this model is useful in order to reproducibly compare diagnostic and therapeutic capacities of commercial devices as a first step, before costly clinical studies.
Exploratory Study of Agile Methods in the Vietnamese Software Industry

This paper reports on exploratory research to examine the adoption of agile methods by the software industry in Vietnam. Agile methods for designing and developing software have existed for over a decade. Yet there is limited research or data about the adoption of agile practices in industry. Much of the existing literature focuses predominantly on adoption rates in America (USA). However, software design and development is increasingly a global endeavor. Outsourcing software design and development to firms in countries such as Vietnam is an important characteristic of global information technology. In response to these circumstances, an exploratory multi-site study into the adoption of agile methods was carried out in Vietnam using structured interviews. Outsourcing vendors reported additional challenges to incorporating agile methods into their software processes. The research offers additional data regarding the adoption of agile methods by industry, specifically regarding practices in Vietnam, and contributes to broadening the foundation for future research in global information systems.
From dusk till dawn: the Arabidopsis thaliana sugar starving responsive network

Plant growth and development are tightly controlled by photosynthetic carbon availability. The understanding of mechanisms governing carbon partitioning in plants will be a valuable tool in order to satisfy the rising global demand for food and biofuel. The goal of this study was to determine if sugar starvation responses were transcriptionally coordinated in Arabidopsis thaliana. A set of sugar-starvation responsive (SSR) genes was selected to perform a co-expression network analysis. Posteriorly, a guided-gene approach was used to identify the SSR-network from public data and to discover candidate regulators of this network. In order to validate the SSR network, a global transcriptome analysis was realized on three A. thaliana starch-deficient mutants. The starch-deficient phenotype in leaves induces sugar starvation syndrome at the end of the night due to the absence of photosynthesis. Promoter sequences of genes belonging to the SSR-network were analyzed in silico reveling over-represented motifs implicated in light, abscisic acid, and sugar responses. A small cluster of protein encoding genes belonging to different metabolic pathways, including three regulatory proteins, a protein kinase, a transcription factor, and a blue light receptor, were identified as the cornerstones of the SSR co-expression network. In summary, a large transcriptionally coordinated SSR network was identified and was validated with transcriptional data from three starch-deficient mutant lines. Candidate master regulators of this network were point out.
DC-Bus Voltage Balancing Algorithm for Three-Level Neutral-Point-Clamped (NPC) Traction Inverter Drive With Modified Virtual Space Vector

A modified-virtual-space-vector-based dc-link voltage balancing strategy is proposed in this paper for a three-level inverter. In the proposed strategy, the summation of the three-phase currents for virtual vector needs not to be zero and it also keeps the two capacitor voltages balanced with wider range of load variations. The duty cycles for all the power switches are also derived in this paper using a nearest three-voltage vector scheme. Due to the reduced use of the medium voltage vectors, the proposed control strategy can considerably decrease the neutral-point voltage fluctuation for lower power-factor-based loads as well. Detailed simulation and experimental studies are also carried out to show the effectiveness of the proposed system with a dc-link voltage balancing strategy with permanent magnet synchronous machine. Voltage and current harmonic distortions are also presented with change in modulation index. A Dspace-based real-time operating system is used for real-time implementation with a 6.0-kW surface permanent magnet synchronous motor.
An Investigation of Individual Preferences: Consistency Across Incentives and Stability Over Time

This study compares individual preferences across incentives (i.e., hypothetical vs. real incentives) and over time (i.e. elicitation at two different points in time) in a choice experiment involving charitable donating decisions. We provide evidence of hypothetical bias but little evidence of instability of individual giving. There is significant heterogeneity in individual preferences, with real incentives either dampening or pronouncing the observed donating behaviour. Neither hypothetical bias nor instability is observed when we examine the propensity of individuals to make internally consistent decisions over identical choices.
Reduced dose to urethra and rectum with the use of variable needle spacing in prostate brachytherapy: a potential role for robotic technology

Purpose Several robotic delivery systems for prostate brachytherapy are under development or in pre-clinical testing. One of the features of robotic brachytherapy is the ability to vary spacing of needles at non-fixed intervals. This feature may play an important role in prostate brachytherapy, which is traditionally template-based with fixed needle spacing of 0.5 cm. We sought to quantify potential reductions in the dose to urethra and rectum by utilizing variable needle spacing, as compared to fixed needle spacing. Material and methods Transrectal ultrasound images from 10 patients were used by 3 experienced planners to create 120 treatment plans. Each planner created 4 plan variations per patient with respect to needle positions: 125I fixed spacing, 125I variable spacing, 103Pd fixed spacing, and 103Pd variable spacing. The primary planning objective was to achieve a prostate V100 of 100% while minimizing dose to urethra and rectum. Results All plans met the objective of achieving prostate V100 of 100%. Combined results for all plans show statistically significant improvements in all assessed dosimetric variables for urethra (Umax, Umean, D30, D5) and rectum (Rmax, Rmean, RV100) when using variable spacing. The dose reductions for mean and maximum urethra dose using variable spacing had p values of 0.011 and 0.024 with 103Pd, and 0.007 and 0.029 with 125I plans. Similarly dose reductions for mean and maximum rectal dose using variable spacing had p values of 0.007 and 0.052 with 103Pd, and 0.012 and 0.037 with 125I plans. Conclusions The variable needle spacing achievable by the use of robotics in prostate brachytherapy allows for reductions in both urethral and rectal planned doses while maintaining prostate dose coverage. Such dosimetric advantages have the potential in translating to significant clinical benefits with the use of robotic brachytherapy.
Localized Attraction Correlates with Bacterial Adhesion to Glass and Metal Oxide Substrata

Bacterial adhesion to surfaces does not always proceed according to theoretical expectations. Discrepancies are often attributed to surface heterogeneities that provide localized, favorable sites for bacterial attachment. The presence of these favorable deposition sites for bacteria, however, has never been directly measured. Atomic force microscopy (AFM) was used to quantify the distribution of attractive sites on clean substrata. Surfaces of silica and three different metal oxides mapped by adhesion force with regular or colloidal AFM tips showed a heterogeneous distribution of adhesion forces. Adhesion forces were normally distributed based on a colloid probe, but regular tips revealed a proportionately larger number of relatively more adhesive sites. No correlation was found between the average adhesion force (tip or colloid) and macroscopic adhesion tests using five strains of bacteria. However, when AFM tip results were compared to bacterial adhesion data on the basis of only the stickiest sites (the 5% of sites with the largest adhesion force), there was a good correlation of AFM data with adhesion data. These results demonstrate for the first time how overall bacterial adhesion to a surface effectively correlates with a relatively small fraction of highly adhesive sites rather than averaged adhesion force as detected using AFM.
Rac1 Mediates Collapse of Microvilli on Chemokine-Activated T Lymphocytes

Lymphocytes circulate in the blood and upon chemokine activation rapidly bind, where needed, to microvasculature to mediate immune surveillance. Resorption of microvilli is an early morphological alteration induced by chemokines that facilitates lymphocyte emigration. However, the antecedent molecular mechanisms remain largely undefined. We demonstrate that Rac1 plays a fundamental role in chemokine-induced microvillar breakdown in human T lymphocytes. The supporting evidence includes: first, chemokine induces Rac1 activation within 5 s via a signaling pathway that involves Gαi. Second, constitutively active Rac1 mediates microvilli disintegration. Third, blocking Rac1 function by cell permeant C-terminal “Trojan” peptides corresponding to Rac1 (but not Rac2, Rho, or Cdc42) blocks microvillar loss induced by the chemokine stromal cell-derived factor 1α (SDF-1α). Furthermore, we demonstrate that the molecular mechanism of Rac1 action involves dephosphorylation-induced inactivation of the ezrin/radixin/moesin (ERM) family of actin regulators; such inactivation is known to detach the membrane from the underlying actin cytoskeleton, thereby facilitating disassembly of actin-based peripheral processes. Specifically, ERM dephosphorylation is induced by constitutively active Rac1 and stromal cell-derived factor 1α-induced ERM dephosphorylation is blocked by either the dominant negative Rac1 construct or by Rac1 C-terminal peptides. Importantly, the basic residues at the C terminus of Rac1 are critical to Rac1’s participation in ERM dephosphorylation and in microvillar retraction. Together, these data elucidate new roles for Rac1 in early signal transduction and cytoskeletal rearrangement of T lymphocytes responding to chemokine.