Miracle-dz/UniFAR-FTUs huggingface dataset:
Monocytes and macrophages in flow: an ESCCA initiative on advanced analyses of monocyte lineage using flow cytometry

In April 2013, a symposium was organized to highlight different aspects of differentiation and activation of the monocyte‐macrophage lineage as analyzed on the flow cytometer. Characterization of this lineage requires knowledge of the maturation process from their progenitors that are present in bone marrow up to the mature monocytic cells in peripheral blood, because each monocytic lineage cell with an aberrant phenotype refers to the corresponding maturation stage. A standardized quantitative analysis will facilitate the monitoring of the pathological processes and the clinical features, such as the outcome of treatment. However, changes in marker expression by variation in intensity, asynchronism, and lineage infidelity must be considered. The dynamics of normal marker expressions in early differentiation stages, e.g. molecules like HLA II, CD64 or CD14, give rise to a hypothesis on their possible role in monocyte ontogeny. Besides their usual role in tissue homeostasis, mature macrophages may also play a similar role in hematopoiesis. This meeting highlighted the large potential of flow cytometric tools available for monitoring of all these aspects in the monocytic and macrophage cell lineage. © 2015 International Clinical Cytometry Society
Not All Offspring Are Created Equal: Variation in Larval Characteristics in a Serially Spawning Damselfish

The way organisms allocate their resources to growth and reproduction are key attributes differentiating life histories. Many organisms spawn multiple times in a breeding season, but few studies have investigated the impact of serial spawning on reproductive allocation. This study investigated whether resource allocation was influenced by parental characteristics and prior spawning history in a serial spawning tropical damselfish (Pomacentrus amboinensis). The offspring attributes of isolated parents of known characteristics were monitored over a 6-week breeding period in the field. Smaller females produced larvae of longer length and larger energy reserves at hatching. This finding is contrary to several other studies that found larger females produce offspring of greater quality. We found that resource allocation in the form of reproductive output was not influenced by the number of spawning events within the breeding season, with larger females producing the greatest number of offspring. Larval characteristics changed as spawning progressed. There was a general decline in length of larvae produced, with an increase in the size of the larval yolk-sac, for all females regardless of size as spawning progressed. This trend was accentuated by the smallest females. This change in larval characteristics may reflect a parental ability to forecast unfavourable conditions as the season progresses or a mechanism to ensure that some will survive no matter what conditions they encounter. This study highlights the importance of accounting for temporal changes in reproductive allocation in studies of reproductive trade-offs and investigations into the importance of parental effects.
Effects of Nested Interruptions on Task Resumption: A Laboratory Study With Intensive Care Nurses

Objective: Interruptions to secondary tasks resulting in multiple tasks to resume may tax working memory. The objective of this research is to study such interruptions experienced by intensive care unit (ICU) nurses. Background: ICU nurses are frequently interrupted, resulting in a switch from primary to secondary tasks. In two recent studies, we observed that some of these secondary tasks also get interrupted, resulting in multiple tasks that have to be resumed, a phenomenon we refer to as nested interruptions. Although completing multiple secondary tasks in a serial fashion during an interruption period can create context-switching costs, we hypothesize that nested interruptions tax the working memory even more than just performing multiple secondary tasks sequentially because the nurse would have to encode in working memory the resumption goals for both the primary and the interrupted secondary tasks. Method: We conducted a laboratory study with 30 ICU nurses, who performed an electronic order-entry task under three interruption conditions: (a) baseline—no secondary task during the interruption period; (2) serial—performance of two tasks one after the other during the interruption period; and (3) nested—performance of two tasks during the interruption period, one of which was also interrupted. Results: Nested interruptions resulted in significantly longer primary-task resumption lag and less accurate task resumption compared with both the serial interruption and baseline conditions. Conclusion: The nested nature of interruptions adds to the resumption lag and diminishes resumption accuracy by likely populating the working memory with goals associated with interrupted secondary tasks.
Optimize Parallel Data Access in Big Data Processing

Recent years the Hadoop Distributed File System(HDFS) has been deployed as the bedrock for many parallel big data processing systems, such as graph processing systems, MPI-based parallel programs and scala/java-based Spark frameworks, which can efficiently support iterative and interactive data analysis in memory. The first part of my dissertation mainly focuses on studying parallel data accession distributed file systems, e.g, HDFS. Since the distributed I/O resources and global data distribution are often not taken into consideration, the data requests from parallel processes/executors will unfortunately be served in a remoter imbalanced fashion on the storage servers. In order to address these problems, we develop I/O middleware systems and matching-based algorithms to map parallel data requests to storage servers such that local and balanced data access can be achieved. The last part of my dissertation presents our plans to improve the performance of interactive data access in big data analysis. Specifically, most interactive analysis programs will scan through the entire data set regardless of which data is actually required. We plan to develop a content-aware method to quickly access required data without this laborious scanning process.
Maximum Weight Spectrum Codes

In the recent work [ 9 ], a combinatorial problem concerning linear codes over a finite field \begin{document}$\mathbb{F}_q$\end{document} was introduced. In that work the authors studied the weight set of an \begin{document}$[n,k]_q$\end{document} linear code, that is the set of non-zero distinct Hamming weights, showing that its cardinality is bounded above by \begin{document}$\frac{q^k-1}{q-1}$\end{document} . They showed that this bound was sharp in the case \begin{document}$ q = 2 $\end{document} , and in the case \begin{document}$ k = 2 $\end{document} . They conjectured that the bound is sharp for every prime power \begin{document}$ q $\end{document} and every positive integer \begin{document}$ k $\end{document} . In this work we quickly establish the truth of this conjecture. We provide two proofs, each employing different construction techniques. The first relies on the geometric view of linear codes as systems of projective points. The second approach is purely algebraic. We establish some lower bounds on the length of codes that satisfy the conjecture, and the length of the new codes constructed here are discussed.
The Problem of Carbapenemase-Producing-Carbapenem-Resistant-Enterobacteriaceae Detection

ABSTRACT The emergence and spread of carbapenemase-producing carbapenem-resistant Enterobacteriaceae (CP-CRE) are a significant clinical and public health concern. Reliable detection of CP-CRE is the first step in combating this problem. There are both phenotypic and molecular methods available for CP-CRE detection. There is no single detection method that is ideal for all situations.
Linking the fine‐scale social environment to mating decisions: a future direction for the study of extra‐pair paternity

Variation in extra‐pair paternity (EPP) among individuals of the same population could result from stochastic demography or from individual differences in mating strategies. Although the adaptive value of EPP has been widely studied, much less is known about the characteristics of the social environment that drive the observed patterns of EPP. Here, we demonstrate how concepts and well‐developed tools for the study of social behaviour (such as social network analysis) can enhance the study of extra‐pair mating decisions (focussing in particular on avian mating systems). We present several hypotheses that describe how characteristics of the social environment in which individuals are embedded might influence the levels of EPP in a socially monogamous population. We use a multi‐level social approach (Hinde, 1976) to achieve a detailed description of the social structure and social dynamics of individuals in a group. We propose that the pair‐bond, the direct (local) social environment and the indirect (extended) social environment, can contribute in different ways to the variation observed in the patterns of EPP, at both the individual and the population level. A strength of this approach is that it integrates into the analysis (indirect) interactions with all potential mates in a population, thus extending the current framework to study extra‐pair mating behaviour. We also encourage the application of social network methods such as temporal dynamic analysis to depict temporal changes in the patterns of interactions among individuals in a group, and to study how this affects mating behaviour. We argue that this new framework will contribute to a better understanding of the proximate mechanisms that drive variation in EPP within populations in socially monogamous species, and might ultimately provide insights into the evolution and maintenance of mating systems.
CDC42 regulates the expression of superficial zone molecules in part through the actin cytoskeleton and myocardin‐related transcription factor‐A

Osteoarthritis (OA) is a degenerative disease that initially manifests as loss of the superficial zone (SZ) of articular cartilage. SZ chondrocytes (SZC) differ in morphology from other chondrocytes as they are elongated and oriented parallel to the tissue surface. Proteoglycan 4 (PRG4) and tenascin C (TNC) are molecules expressed by SZC, which have been shown to be chondroprotective. Identification of the signalling pathway(s) regulating expression of SZ molecules may lead to a therapeutic target that can be used to delay or prevent the onset of OA. The hypothesis of this study is that expression of SZ molecules are regulated in part, by the CDC42‐actin‐myocardin‐related transcription factor‐A (MRTF‐A) signaling pathway. SZC from bovine metacarpal‐phalangeal joints were isolated and grown in monolayer culture. Each target in the CDC42‐actin‐MRTF‐A pathway was inhibited and the effect on cell shape, actin cytoskeleton status, and expression of PRG4 and TNC were determined. Treatment with the CDC42 inhibitor ML141 decreased PRG4 and TNC expression, and correlated with increased cell circularity and G‐/F‐actin ratio. PRG4 and TNC expression were differentially regulated by actin depolymerizing agents, latrunculin B and cytochalasin D. Chemical inhibition of MRTF‐A resulted in decreased expression of both PRG4 and TNC; however, specific knockdown by small interfering RNA only decreased expression of TNC indicating that TNC, but not PRG4, is regulated by MRTF‐A. Although PRG4 and TNC expression are both regulated by CDC42 and actin, it appears to occur through different downstream signaling pathways. Further study is required to elucidate the pathway regulating PRG4. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:2421–2430, 2018.
Modeling and control of a PV based QZSI for grid connected applications

This paper proposes modeling and control system design for PV based Quasi-Z-Source Inverter (QZSI) for grid connected applications. The control system is designed based on the dynamical characteristics of the converter and introduces two cascaded controllers. Firstly, output current controller designed in the stationary frame. The second is DC-link voltage controller. Also, Modified Direct Incremental Conductance Maximum Power Point Tracking (MDIC-MPPT) method is proposed for rapid and accurate maximum power point optimization allowing wide DC-link voltage and Shoot-Through (ST) duty ratio ranges, minimize the voltage stress on the inverter bridge, and prevent overlap between ST duty ratio and Modulation index (M). Simulation results are presented to validate the controller's design. The obtained results are encouraging and promising for practical implementation.
Goodput-Aware Load Distribution for Real-Time Traffic over Multipath Networks

Load distribution is a key research issue in deploying the limited network resources available to support traffic transmissions. Developing an effective solution is critical for enhancing traffic performance and network utilization. In this paper, we investigate the problem of load distribution for real-time traffic over multipath networks. Due to the path diversity and unreliability in heterogeneous overlay networks, large end-to-end delay and consecutive packet losses can significantly degrade the traffic flow's goodput, whereas existing studies mainlyfocus on the delay or throughput performance. To address the challenging problems, we propose a Goodput-Aware Load distribuTiON (GALTON) model that includes three phases: (1) path status estimation to accurately sense the quality of each transport link, (2) flow rate assignment to optimize the aggregate goodput of input traffic, and (3) deadline-constrained packet interleaving to mitigate consecutive losses. We present a mathematical formulation for multipath load distribution and derive the solution based on utility theory. The performance of the proposed model is evaluated through semi-physical emulations in Exata involving both real Internet traffic traces and H.264 video streaming. Experimental results show that GALTON outperforms existing traffic distribution models in terms of goodput, video Peak Signal-to-Noise Ratio (PSNR), end-to-end delay, and aggregate loss rate.
Imaging EGFR distribution using surface-enhanced Raman spectroscopy

The purpose of this study is to explore the feasibility of using Surface Enhanced Raman Spectroscopy (SERS) to image the distribution of Epidermal Growth Factor Receptor (EGFR) in cells. To accomplish this task, 30 nm gold nanoparticles (AuNPs) tagged with antibodies to EGFR (1012 per ml) are incubated with cells (106 per ml) of the A431 human epidermoid carcinoma cell line and normal human bronchial epithelial (NHBE) cells. Using the 632.8 nm excitation line of a He-Ne laser, Raman spectroscopy measurements are performed using a point mapping scheme. SERS signals are observed with an overall enhancement of 4-7 orders of magnitude. Raman intensity maps of the 1480 and 1583 cm-1 peaks correlate well with the expected distribution of AuNPs and EGFR. Normal cells show little to no enhancement. The results therefore present a simple yet effective means to image EGFR over-expression.
The Use of Biophysical Flow Models in the Surgical Management of Patients Affected by Chronic Thromboembolic Pulmonary Hypertension

Introduction: Chronic Thromboembolic Pulmonary Hypertension (CTEPH) results from progressive thrombotic occlusion of the pulmonary arteries. It is treated by surgical removal of the occlusion, with success rates depending on the degree of microvascular remodeling. Surgical eligibility is influenced by the contributions of both the thrombus occlusion and microvasculature remodeling to the overall vascular resistance. Assessing this is challenging due to the high inter-individual variability in arterial morphology and physiology. We investigated the potential of patient-specific computational flow modeling to quantify pressure gradients in the pulmonary arteries of CTEPH patients to assist the decision-making process for surgical eligibility. Methods: Detailed segmentations of the pulmonary arteries were created from postoperative chest Computed Tomography scans of three CTEPH patients. A focal stenosis was included in the original geometry to compare the pre- and post-surgical hemodynamics. Three-dimensional flow simulations were performed on each morphology to quantify velocity-dependent pressure changes using a finite element solver coupled to terminal 2-element Windkessel models. In addition to transient flow simulations, a parametric modeling approach based on constant flow simulations is also proposed as faster technique to estimate relative pressure drops through the proximal pulmonary vasculature. Results: An asymmetrical flow split between left and right pulmonary arteries was observed in the stenosed models. Removing the proximal obstruction resulted in a reduction of the right-left pressure imbalance of up to 18%. Changes were also observed in the wall shear stresses and flow topology, where vortices developed in the stenosed model while the non-stenosed retained a helical flow. The predicted pressure gradients from constant flow simulations were consistent with the ones measured in the transient flow simulations. Conclusion: This study provides a proof of concept that patient-specific computational modeling can be used as a noninvasive tool for assisting surgical decisions in CTEPH based on hemodynamics metrics. Our technique enables determination of the proximal relative pressure, which could subsequently be compared to the total pressure drop to determine the degree of distal and proximal vascular resistance. In the longer term this approach has the potential to form the basis for a more quantitative classification system of CTEPH types.
Does Perceived Stress Mediate the Association Between Workplace Bullying and Long-Term Sickness Absence?

Objective: To examine if perceived stress mediated the association between workplace bullying and subsequent long-term sickness absence. Methods: The PRISME cohort was established in 2007 and re-examined in 2009. Questionnaire data about workplace bullying and perceived stress were obtained from 4114 individuals. Participants were followed in registers on long-term sickness absence (≥30 consecutive days of sickness absence). Results: Workplace bullying was associated with subsequent sickness absence (odds ratio [OR] = 2.05; 95% confidence interval [CI]: 1.57 to 2.65) and concurrent high perceived stress levels (OR = 2.34; 95% CI: 1.86 to 2.96). A high perceived stress level was also associated with subsequent sickness absence (OR = 1.33; 95% CI: 1.13 to 1.56). Perceived stress explained 13% (95% CI: 6 to 23%) of the total association between bullying and sickness absence. Conclusions: The association between workplace bullying and subsequent long-term sickness absence may be partially mediated by perceived stress.
Empirical determination of thresholds for optimal dialogue act classification

We present recent experiments which build on our work in the area of Dialogue Act (da) tagging. Identifying the dialogue acts of utterances is recognised as an important step towards understanding the content and nature of what speakers say. We describe a simple dialogue act classifier based on purely intra-utterance features — principally word n-gram cue phrases. Such a classifier performs surprisingly well, rivalling scores obtained using far more sophisticated language modelling techniques for the corpus we address. The approach requires the use of thresholds effecting the selection of n-gram cues, which have previously been manually supplied. We here describe a method of automatically determining these thresholds to optimise classifier performance.
Alterations in the Quinolone Resistance-Determining Regions and Fluoroquinolone Resistance in Clinical Isolates and Laboratory-Derived Mutants of Mycoplasma bovis: Not All Genotypes May Be Equal

ABSTRACT Mycoplasma bovis is considered a major contributor to respiratory diseases in young cattle. Resistant M. bovis isolates have increasingly been reported worldwide due to extensive use of antimicrobials to treat bovine pneumonia. The frequency of isolates resistant to fluoroquinolones varies considerably from one country to another. The MICs of isolates collected in France have only increased from “very low” to “low. ” The present study was conducted to investigate whether alterations in the quinolone resistance-determining regions (QRDRs) could account for this slight modification in susceptibility. No correlation between QRDR alterations and increased MICs was evidenced in clinical isolates. In addition, all clinical isolates were subtyped, and the tendencies of the different sequence types to develop resistance through mutations in QRDRs under selective pressure in vitro were examined. In vitro, 3 hot spots for mutations in QRDRs (position 83 in GyrA and positions 80 and 84 in ParC) were associated with a high level of resistance when cumulated. We showed that the point mutations in the QRDRs observed in vitro were different (in location and selection rapidity) between the different subtypes. Our in vitro observations were corroborated by the recent detection of a clinical isolate highly resistant to fluoroquinolones (MIC ≥ 16 μg/ml) and belonging to the subtype which easily accumulates QRDR alterations in vitro. The current increased prevalence of this subtype in clinical isolates highlights the urgent need to control fluoroquinolone usage in veterinary medicine.
WUW (What Users Want): A Service to Enhance Users' Satisfaction in Content-Based Peer-to-Peer Networks

Peer-to-Peer (P2P) architectures are more and more used in Content Delivery Net- works (CDN), because the traditional client-server architectures are burdened by high distribution and maintenance cost, whereas in P2P systems those costs are almost negli- gible. In general, such applications do not take into account user preferences, other than QoS-related parameters. As users resources are the richness of P2P systems, we think it is important to satisfy their preferences concerning the usage of their resources. In this work we propose WUW (What Users Want), a service to improve users' satisfaction in a personal way. WUW runs on top of unstructured P2P systems, and its main goal is to allow users to strategically impact their local neighborhoods according to their own personal preferences. We present first results of experiments, deployed in a cluster, obtained with the prototype implementation of our service, which runs on top of Bit- Torrent, the most used file sharing protocol. We show that BitTorrent performances are not affected by the users strategic choices introduced by WUW. The advantage of our approach is that, without loosing performance, users can chose the peers they want to collaborate with according to their personal preferences.
Number 2 Feibi Recipe Reduces PM2.5-Induced Lung Injury in Rats

Air pollution is the main cause of respiratory diseases. Fine particulates with the diameter below 2.5 μm can get into the alveoli and then enter the blood circulation through the lung tissue ventilation function and cause multiple systemic diseases especially the respiratory diseases. This study investigated the pathological mechanism of the lungs injury in rats induced by PM2.5 and the effect and mechanism of the Chinese herbal medicine number 2 Feibi Recipe (number 2 FBR) on lungs injury. In this experiment, Wistar rats were used. Lungs injury was induced by PM2.5. Number 2 FBR was used to treat the rats. The result showed that number 2 FBR could improve the lung injury in the rats. Meanwhile, it significantly reduced pathological response and inflammatory mediators including interleukin-6 (IL-6), interleukin-13 (IL-13), interleukin-17 (IL17), monocyte chemotactic protein-1 (MCP-1), and transforming growth factor-α (TNF-α) and upregulated glutathione peroxidase (GSH-Px) in the PM2.5 induced lung injury in the rats. Collectively, number 2 FBR appears to attenuate the lungs injury in rats induced by PM2.5.