Miracle-dz/UniFAR-FTUs huggingface dataset:
Colorful Protein-Based Fluorescent Probes for Collagen Imaging

Real-time visualization of collagen is important in studies on tissue formation and remodeling in the research fields of developmental biology and tissue engineering. Our group has previously reported on a fluorescent probe for the specific imaging of collagen in live tissue in situ, consisting of the native collagen binding protein CNA35 labeled with fluorescent dye Oregon Green 488 (CNA35-OG488). The CNA35-OG488 probe has become widely used for collagen imaging. To allow for the use of CNA35-based probes in a broader range of applications, we here present a toolbox of six genetically-encoded collagen probes which are fusions of CNA35 to fluorescent proteins that span the visible spectrum: mTurquoise2, EGFP, mAmetrine, LSSmOrange, tdTomato and mCherry. While CNA35-OG488 requires a chemical conjugation step for labeling with the fluorescent dye, these protein-based probes can be easily produced in high yields by expression in E. coli and purified in one step using Ni2+-affinity chromatography. The probes all bind specifically to collagen, both in vitro and in porcine pericardial tissue. Some first applications of the probes are shown in multicolor imaging of engineered tissue and two-photon imaging of collagen in human skin. The fully-genetic encoding of the new probes makes them easily accessible to all scientists interested in collagen formation and remodeling.
Improving deep neural network acoustic modeling for audio corpus indexing under the IARPA babel program

This paper is focused on several techniques that improve deep neural network (DNN) acoustic modeling for audio corpus indexing in the context of the IARPA Babel program. Specifically, fundamental frequency variation (FFV) and channel-aware (CA) features and data augmentation based on stochastic feature mapping (SFM) are investigated not only for improved automatic speech recognition (ASR) performance but also for their impact to the ﬁnal spoken term detection on the pre-indexed audio corpus. Experimental results on development languages of Babel option period one show that the improved DNN acoustic models can reduce word error rates in ASR and also help the keyword search performance compared to already competitive DNN baseline systems.
Quality-Aware Target Coverage in Energy Harvesting Sensor Networks

Sensing coverage is a fundamental problem in wireless sensor networks for event detection, environment monitoring, and surveillance purposes. In this paper, we study the sensing coverage problem in an energy harvesting sensor network deployed for monitoring a set of targets for a given monitoring period, where sensors are powered by renewable energy sources and operate in duty-cycle mode, for which we first introduce a new coverage quality metric to measure the coverage quality within two different time scales. We then formulate a novel coverage quality maximization problem that considers both sensing coverage quality and network connectivity that consists of active sensors and the base station. Due to the NP-hardness of the problem, we instead devise efficient centralized and distributed algorithms for the problem, assuming that the harvesting energy prediction at each sensor is accurate during the entire monitoring period. Otherwise, we propose an adaptive framework to deal with energy prediction fluctuations, under which we show that the proposed centralized and distributed algorithms are still applicable. We finally evaluate the performance of the proposed algorithms through experimental simulations. Experimental results demonstrate that the proposed solutions are promising.
Antigen specificity of antihistone antibodies in systemic sclerosis

OBJECTIVES The aim of the study was to determine the prevalence and clinical significance of antibodies to individual histone components in systemic sclerosis (SSc). METHODS Serum samples from patients with limited cutaneous SSc (lSSc; n=42) and diffuse cutaneous SSc (dSSc; n=28) were examined for IgG and/or IgM antibodies to individual histone components and complexes by enzyme linked immunosorbent assay (ELISA). RESULTS The level of IgG antibody to total histones was significantly higher in lSSc and dSSc than in normal controls. The level of IgM antibody to total histones was significantly higher in lSSc, but not in dSSc, than in normal controls. IgG antibody to total histones tended to be increased in dSSc when compared with that in lSSc. On the other hand, IgM antibody to total histones tended to be increased in lSSc when compared with that in dSSc. Although SSc showed various antihistone specificities, H2B, H2A-H2B, (H2A-H2B)-dsDNA were main antigens recognised by IgG antibodies in both lSSc and dSSc. Although IgM antibodies to H2B and H2A-H2B were also detected in both lSSc and dSSc, serum samples from lSSc patients exhibited highest IgM reactivity with H1. CONCLUSION SSc may be included among conditions in which heterogeneous antihistone antibodies are produced. IgM antibodies to the most accessible histone H1 may be related to mild clinical features (lSSc) and IgG antibodies to the inner core molecules of native histone such as H2B or complexes including H2B may be associated with severe clinical features (dSSc) in Ssc.
Synchronization in the molting and spawning activity of northern krill (Meganyctiphanes norvegica) and its effect on recruitment

The molting, spawning, and recruitment of northern krill (Meganyctiphanes norvegica) were analyzed over an annual cycle (1999–2000) in the Clyde Sea (west coast of Scotland). Results supported the hypothesis of a functional relationship between egg production and molt development for the duration of the reproductive season (March to August), with one reproductive cycle being made up of two molt cycles. Females remained in reproductive condition throughout the reproductive season, and the timing of their spawning and molting was synchronized at the population level throughout this period. A semiempirical model predicted that the krill population produced an egg pulse every 20 to 26 d (depending on temperature), and three cohorts were evident in net samples taken later in the year. The likely date on which the first cohort was spawned was around 26 d after the main phytoplankton bloom, suggesting that the bloom triggered egg development in all adult females. Such a synchronized spawning period was observed directly in adult females 26 d after a bloom in March 2000. A total of three cohorts over the 6‐month reproductive season is less than the maximum of seven that would be possible if spawning occurred at a periodicity of between 20 and 26 d, suggesting that larval recruitment was not always successful. Analysis showed that successful recruitment was only achieved when chlorophyll a levels were adequate during both the period of egg maturation in the ovary and the subsequent development of larvae, especially the furcilia stages.
Homogeneous Superpixels from Random Walks

This paper presents a novel algorithm to generate homogeneous superpixels from the process of Markov random walks. We exploit Markov clustering (MCL) as the methodology, a generic graph clustering method based on stochastic flow circulation. In particular, we introduce a new graph pruning strategy called compact pruning in order to capture intrinsic local image structure, and thereby keep the superpixels homogeneous, i.e. uniform in size and compact in shape. Further, this new pruning scheme comes with three advantages: faster computation, smaller memory footprint, and straightforward parallel implementation. Through comparisons with other recent standard techniques, we show that the proposed algorithm achieves an optimal performance in terms of qualitative measure at a decent computational speed.
Improving opioid prescription practices and reducing patient risk in the primary care setting

Chronic pain is complex, and the patient suffering from chronic pain frequently experiences concomitant medical and psychiatric disorders, including mood and anxiety disorders, and in some cases substance use disorders. Ideally these patients would be referred to an interdisciplinary pain program staffed by pain medicine, behavioral health, and addiction specialists. In practice, the majority of patients with chronic pain are managed in the primary care setting. The primary care clinician typically has limited time, training, or access to resources to effectively and efficiently evaluate, treat, and monitor these patients, particularly when there is the added potential liability of prescribing opioids. This paper reviews the role of opioids in managing chronic noncancer pain, including efficacy and risk for misuse, abuse, and addiction, and discusses several models employing novel technologies and health delivery systems for risk assessment, intervention, and monitoring of patients receiving opioids in a primary care setting.
Looking for Transliterations in a Trilingual English, French and Japanese Specialised Comparable Corpus

Transliterations and cognates have been shown to be useful in the case of bilingual extraction from parallel corpora. Observation of transliterations in a trilingual English, French and Japanese specialised comparable corpus reveals evidences that they are likely to be used with comparable corpora too, since they are an important and relevant part of the common vocabulary, but they also yield links between Japanese and English/French corpora.
Phenotypic Polarization of Activated Astrocytes: The Critical Role of Lipocalin-2 in the Classical Inflammatory Activation of Astrocytes

Astrocytes provide structural and functional support for neurons, as well as display neurotoxic or neuroprotective phenotypes depending upon the presence of an immune or inflammatory microenvironment. This study was undertaken to characterize multiple phenotypes of activated astrocytes and to investigate the regulatory mechanisms involved. We report that activated astrocytes in culture exhibit two functional phenotypes with respect to pro- or anti-inflammatory gene expression, glial fibrillary acidic protein expression, and neurotoxic or neuroprotective activities. The two distinct functional phenotypes of astrocytes were also demonstrated in a mouse neuroinflammation model, which showed pro- or anti-inflammatory gene expression in astrocytes following challenge with classical or alternative activation stimuli; similar results were obtained in the absence of microglia. Subsequent studies involving recombinant lipocalin-2 (LCN2) protein treatment or Lcn2-deficient mice indicated that the pro- or anti-inflammatory functionally polarized phenotypes of astrocytes and their intracellular signaling pathway were critically regulated by LCN2 under in vitro and in vivo conditions. Astrocyte-derived LCN2 promoted classical proinflammatory activation of astrocytes but inhibited IL-4–STAT6 signaling, a canonical pathway involved in alternative anti-inflammatory activation. Our results suggest that the secreted protein LCN2 is an autocrine modulator of the functional polarization of astrocytes in the presence of immune or inflammatory stimuli and that LCN2 could be targeted therapeutically to dampen proinflammatory astrocytic activation and related pathologies in the CNS.
Individual Differences in the Mental Rotation Skills of Turkish Prospective Teachers.

This study investigated the effects of gender, academic performance and preschool education on mental rotation skills among Turkish prospective teachers. A total of 525 undergraduate students (364 female) from a government university located in western Turkey completed the Mental Rotation Test (MRT). A three-way [2 (gender) × 5 (academic performance) × 2 (preschool education)] between-subjects analysis of variance (ANOVA) revealed that males outperformed females in mental rotation performance (��= .86). Significant effects of preschool education and academic performance on MRT scores were also observed. Significant interactions were observed between gender and academic performance and academic performance and preschool education. There was also a significant three-way interaction of gender, academic performance and preschool education. An interaction between gender and preschool education failed to reach significance.
Receding Horizon Differential Dynamic Programming

The control of high-dimensional, continuous, non-linear dynamical systems is a key problem in reinforcement learning and control. Local, trajectory-based methods, using techniques such as Differential Dynamic Programming (DDP), are not directly subject to the curse of dimensionality, but generate only local controllers. In this paper, we introduce Receding Horizon DDP (RH-DDP), an extension to the classic DDP algorithm, which allows us to construct stable and robust controllers based on a library of local-control trajectories. We demonstrate the effectiveness of our approach on a series of high-dimensional problems using a simulated multi-link swimming robot. These experiments show that our approach effectively circumvents dimensionality issues, and is capable of dealing with problems of (at least) 24 state and 9 action dimensions.
Insulin prolongs the QTc interval in humans.

Insulin hyperpolarizes plasma membranes; we tested whether insulin affects ventricular repolarization. In 35 healthy volunteers, we measured the Q-T interval during electrocardiographic monitoring in the resting state and in response to hyperinsulinemia (euglycemic 1-mU. min(-1). kg(-1) insulin clamp). A computerized algorithm was used to identify T waves; Bazett's formula was employed to correct Q-T (QTc) by heart rate (HR). In the resting state, QTc was inversely related to indexes of body size (e.g., body surface area, r = -0.53, P = 0.001) but not to indexes of body fatness. During the clamp, HR (67 +/- 1 to 71 +/- 1 beats/min, P < 0.0001) and plasma norepinephrine levels (161 +/- 12 to 184 +/- 10 pg/ml, P < 0.001) increased. QTc rose promptly and consistently, averaging 428 +/- 6 ms between 30 and 100 min (P = 0.014 vs. the resting value of 420 +/- 5 ms). Fasting serum potassium (3.76 +/- 0.03 mM) declined to 3. 44 +/- 0.03 mM during insulin. After adjustment for body size, resting QTc was directly related to fasting plasma insulin (partial r = 0.43, P = 0.01); furthermore, QTc was inversely related to serum potassium levels both in the fasting state (partial r = -0.16, P < 0. 04) and during insulin stimulation (partial r = -0.47, P = 0.003). Neither resting nor clamp-induced QTc was related to insulin sensitivity. Physiological hyperinsulinemia acutely prolongs ventricular repolarization independent of insulin sensitivity. Both insulin-induced hypokalemia and adrenergic activation contribute to this effect.
Handling diversity in evolutionary multiobjective optimization

In evolutionary multiobjective optimisation (EMO), the diversity of the set of non-dominated solutions used to be handled by the niching and fitness sharing technique. The main downside of this technique is the need to set the niche radius. Quite recently, new techniques have emerged and proved to be more successful. The grid-based density of the adaptive grid algorithm (AGA), the crowding-distance technique of the nondominated sorting genetic algorithm (NSGA-II), and the archive truncation procedure of the strength Pareto evolutionary algorithm (SPEA2) are the latest successful methods that ensure a better diversity than the traditional less effective and computationally expensive niching method. In this work, a crowding-dispersion technique which is based on the Pareto potential regions (PPR), is proposed and compared to three recent techniques.
Interaction between UV-damaged DNA Binding Activity Proteins and the c-Abl Tyrosine Kinase*

The c-Abl tyrosine kinase is activated by some forms of DNA damage, including ionizing radiation, but not UV radiation. The functions of this activation in the damage response pathways remain obscure. To identify potential targets of c-Abl kinase, we utilized the yeast two-hybrid system to screen a murine cDNA library. One c-Abl binding protein of particular interest was the large subunit (DDB1) of the heterodimeric complex with UV-damaged DNA binding activity (UV-DDB). This complex binds with high specificity to DNA damaged by UV, is absent in a subset of xeroderma pigmentosum group E cells, and is required for global genomic repair of UV-induced damage. The association of c-Abl with DDB1 required the kinase domain of c-Abl and preserved the interaction between DDB1 and the small subunit (DDB2) of the UV-DDB complex. Significantly, overexpression of c-Abl increased tyrosine phosphorylation of DDB2 and suppressed UV-DDB activity. Conversely, a dominant negative, kinase-deficient allele of c-Abl decreased tyrosine phosphorylation of DDB2 and dramatically stimulated UV-DDB activity. These results suggest that one role of c-Abl may be to negatively regulate UV-DDB activity by phosphorylation of DDB2.
Age-related Volumetric Changes of Prefrontal Gray and White Matter from Healthy Infancy to Adulthood

Despite increasing evidence of the role of the prefrontal cortex in providing the neural substrate of higher cognitive function and neurodevelopment, little is known about neuroanatomic changes in prefrontal subregions during human development. In this prospective study, we evaluated prefrontal gray and white matter volume in healthy infants, children, adolescents, and adults. Magnetic resonance imaging was performed on 107 healthy people aged one month to 25 years. Gray and white matter volumes of the dorsolateral, dorsomedial, orbitolateral, and orbitomedial prefrontal cortex were quantified. The results indicated that both children and early adolescents had larger dorsolateral gray matter volume than infants and adults. Dorsolateral white matter volumes in children, early adolescents, and late adolescents were larger than those of infants. Dorsomedial white matter volumes of early adolescents, late adolescents, and adults were also larger than those of infants. There was no significant difference among age groups in both orbital prefrontal regions. These findings suggest that there are two important stages of structural change of the prefrontal cortex from infancy to young adulthood. First, growth spurts of both gray matter and white matter during the first 2 years of life have been shown to occur specifically in the dorsal prefrontal cortex. Second, gray matter changes have been shown to be regionally specific, with changes in the dorsal, but not orbital, prefrontal cortex peaking during late childhood or early adolescence. Thus, developmental differences within sectors of the prefrontal lobe and evidence of neural pruning and myelination may be useful in understanding the mechanisms of neurodevelopmental disorders.
Genetic Evidence for the Synonymy of Two Reticulitermes Species: Reticulitermes flavipes and Reticulitermes santonensis

Abstract By applying the 16S rRNA mitochondrial marker to 434 populations of Reticulitermes termites from North, Central, and South America; France; and Germany with other locations around the world that we have analyzed, identical DNA sequence data were obtained from Reticulitermes flavipes (Kollar) in North America and Germany and for Reticulitermes santonensis Feytaud from undisturbed (nonurban) forested locations in western France. We also discovered identical DNA sequence data from previously unidentified Reticulitermes specimens from South America and Easter Island. Haplotypes F, M, and GG were observed in France; haplotype F in Germany; and haplotype GG was found on Easter Island, Santiago, Chile, and Montevideo, Uruguay. All of these haplotypes are found in numerous states within the continental United States. In light of their well documented morphological, chemical, and phylogenetic relationships, coupled with this new data that directly link these disjunct groups, R. flavipes and R. santonensis should be synonymized. Compared with other studies that largely suggest phyletic similarities, this is the first study that specifically matches haplotypes from North America (where populations of R. flavipes are endemic) with populations in Europe (where R. flavipes, described as R. santonensis, is presumed exotic).
Quality of Life in Endometrial Cancer Survivors: What Does Obesity Have to Do with It?

Objective. Most women with type I endometrial cancer (EC) are obese, increasing the risk of morbidity and mortality in this population. The study objective was to evaluate the impact of obesity on quality of life (QOL) and general health status in EC survivors with early-stage disease. Methods. A prospective ancillary analysis of stage I/II EC survivors. The association of BMI with QOL questionnaire variables measured with the functional assessment of cancer therapy (subscales: physical (PWB), functional (FWB), social, and emotional well-being) and the physical (PCS) and mental component summary subscales of the short-form medical outcomes survey was determined. Results. 152 women completed both questionnaires; 81% were obese. After multiple linear regression, BMI was inversely associated with PWB (P = .001), FWB (P = 0.048), and PCS (P = .001). Conclusions. Despite the good prognosis associated with early-stage EC, QOL, and physical health are not optimized in obese survivors. This paper highlights the importance of incorporating health-related QOL assessments and obesity interventions during the survivorship period.
Advancements in 2D flexible nanoelectronics: from material perspectives to RF applications

In the past decade, two-dimensional (2D) atomic crystals have stimulated great interest in the electronic device community for their interesting physics and diverse applications. With the rapid growing market of wearable electronics and the internet of things, flexible nanoelectronics with high operation speed and low power consumption has become one of the most researched topics. In this regard, 2D atomic van der Waals crystals have emerged as promising candidates for such applications owing to their compelling capabilities including ultimate thickness scalability, superior mechanical flexibility and highly tunable electronic performance. In this review, state-of-the-art advancements in 2D flextronics based on chemical vapor deposition (CVD) monolayer graphene, CVD monolayer molybdenum disulphide (MoS2) and exfoliated few layer black phosphorus are presented with specific emphasis on radio frequency applications.
ThriftStore: Finessing Reliability Trade-Offs in Replicated Storage Systems

This paper explores the feasibility of a storage architecture that offers the reliability and access performance characteristics of a high-end system, yet is cost-efficient. We propose ThriftStore, a storage architecture that integrates two types of components: volatile, aggregated storage and dedicated, yet low-bandwidth durable storage. On the one hand, the durable storage forms a back end that enables the system to restore the data the volatile nodes may lose. On the other hand, the volatile nodes provide a high-throughput front-end. Although integrating these components has the potential to offer a unique combination of high throughput and durability at a low cost, a number of concerns need to be addressed to architect and correctly provision the system. To this end, we develop analytical and simulation-based tools to evaluate the impact of system characteristics (e.g., bandwidth limitations on the durable and the volatile nodes) and design choices (e.g., the replica placement scheme) on data availability and the associated system costs (e.g., maintenance traffic). Moreover, to demonstrate the high-throughput properties of the proposed architecture, we prototype a GridFTP server based on ThriftStore. Our evaluation demonstrates an impressive, up to 800 Mbps transfer throughput for the new GridFTP service.