Miracle-dz/UniFAR-FTUs huggingface dataset:
CCL27 Is Downregulated by Interferon Gamma via Epidermal Growth Factor Receptor in Normal Human Epidermal Keratinocytes

The cutaneous T cell‐attracting chemokine (CTACK)/CCL27 is indispensable in skin inflammation. CTACK/CCL27 is exclusively produced by epidermal keratinocytes to attract CCR10‐expressing T lymphocytes to the skin. We investigated the mechanism of CTACK/CCL27 production from normal human epidermal keratinocytes (NHEKs) by the proinflammatory cytokines TNFα and IFNγ. CTACK/CCL27 production was induced by TNFα via ERK, JNK, p38, and NFκB. The induction of CTACK/CCL27 by TNFα was suppressed by IFNγ via a pathway dependent on JAK, STAT1, and STAT3. Our results also demonstrated that IFNγ and TNFα induced the phosphorylation of EGFR and the following phosphorylation of ERK, which is partly responsible for the suppressive effect of IFNγ on TNFα‐induced production of CTACK/CCL27. Peri‐lesional skin of psoriasis demonstrates early inflammatory changes as we have previously reported. CTACK/CCL27 expression was diffuse in the peri‐lesional epidermis, while it was restricted to basal layer in lesional epidermis, suggesting that CTACK/CCL27 expression was induced in the early stage of psoriatic plaque formation, and IFNγ could participate in the suppression of CTACK/CCL27 expression in the lesional epidermis, reflecting the later stage of psoriatic plaque formation. Our study suggests that CTACK/CCL27 may have a pivotal role in the early stage of psoriasis plaque formation, but should be downregulated in the later stage to induce inflammation characteristic for chronic psoriasis plaques. J. Cell. Physiol. 229: 1935–1945, 2014. © 2014 Wiley Periodicals, Inc.
Sequencing, Annotation, and Characterization of the Influenza Ferret Infectome

ABSTRACT Ferrets have become an indispensable tool in the understanding of influenza virus virulence and pathogenesis. Furthermore, ferrets are the preferred preclinical model for influenza vaccine and therapeutic testing. Here we characterized the influenza infectome during the different stages of the infectious process in ferrets with and without prior specific immunity to influenza. RNA from lung tissue and lymph nodes from infected and naïve animals was subjected to next-generation sequencing, followed by de novo data assembly and annotation of the resulting sequences; this process generated a library comprising 13,202 ferret mRNAs. Gene expression profiles during pandemic H1N1 (pdmH1N1) influenza virus infection were analyzed by digital gene expression and solid support microarrays. As expected during primary infection, innate immune responses were triggered in the lung tissue; meanwhile, in the lymphoid tissue, genes encoding antigen presentation and maturation of effector cells of adaptive immunity increased dramatically. After 5 days postinfection, the innate immune gene expression was replaced by the adaptive immune response, which correlates with viral clearance. Reinfection with homologous pandemic influenza virus resulted in a diminished innate immune response, early adaptive immune gene regulation, and a reduction in clinical severity. The fully annotated ferret infectome will be a critical aid to the understanding of the molecular events that regulate disease severity and host-influenza virus interactions among seasonal, pandemic, and highly pathogenic avian influenzas.
LPEseq: Local-Pooled-Error Test for RNA Sequencing Experiments with a Small Number of Replicates

RNA-Sequencing (RNA-Seq) provides valuable information for characterizing the molecular nature of the cells, in particular, identification of differentially expressed transcripts on a genome-wide scale. Unfortunately, cost and limited specimen availability often lead to studies with small sample sizes, and hypothesis testing on differential expression between classes with a small number of samples is generally limited. The problem is especially challenging when only one sample per each class exists. In this case, only a few methods among many that have been developed are applicable for identifying differentially expressed transcripts. Thus, the aim of this study was to develop a method able to accurately test differential expression with a limited number of samples, in particular non-replicated samples. We propose a local-pooled-error method for RNA-Seq data (LPEseq) to account for non-replicated samples in the analysis of differential expression. Our LPEseq method extends the existing LPE method, which was proposed for microarray data, to allow examination of non-replicated RNA-Seq experiments. We demonstrated the validity of the LPEseq method using both real and simulated datasets. By comparing the results obtained using the LPEseq method with those obtained from other methods, we found that the LPEseq method outperformed the others for non-replicated datasets, and showed a similar performance with replicated samples; LPEseq consistently showed high true discovery rate while not increasing the rate of false positives regardless of the number of samples. Our proposed LPEseq method can be effectively used to conduct differential expression analysis as a preliminary design step or for investigation of a rare specimen, for which a limited number of samples is available.
Joint Identification of Network Communities and Semantics via Integrative Modeling of Network Topologies and Node Contents

The objective of discovering network communities, an essential step in complex systems analysis, is two-fold: identification of functional modules and their semantics at the same time. However, most existing community-finding methods have focused on finding communities using network topologies, and the problem of extracting module semantics has not been well studied and node contents, which often contain semantic information of nodes and networks, have not been fully utilized. We considered the problem of identifying network communities and module semantics at the same time. We introduced a novel generative model with two closely correlated parts, one for communities and the other for semantics. We developed a co-learning strategy to jointly train the two parts of the model by combining a nested EM algorithm and belief propagation. By extracting the latent correlation between the two parts, our new method is not only robust for finding communities and semantics, but also able to provide more than one semantic explanation to a community. We evaluated the new method on artificial benchmarks and analyzed the semantic interpretability by a case study. We compared the new method with eight state-of-the-art methods on ten real-world networks, showing its superior performance over the existing methods.
My Relationship is Better than- and Not as Bad as--Yours is: The Perception of Superiority in Close Relationships

This research studies naturally occurring thoughts about relationships to test hypotheses regarding the tendency to perceive one 's own relationship as superior to others' relationships. Using a thought-listing technique, four experiments conducted in the United States and two experiments conducted in the Netherlands demonstrated that subjects hold more positive beliefs about their own relationships than other relationships (positive superiority) and hold fewer negative beliefs about their own relationships than other relationships (negative superiority). Also, subjects' beliefs about their own relationships are composed of far more positive than negative information (own relationship positivity), whereas perceptions of other relationships are dominated by negative information (other relationships negativity). These findings were obtained when subjects listed positive and negative thoughts regarding global features of relationships; parallel findings emerged for descriptions of constructive and destructive reactions to specific dissatisfying incidents.
An Effective DDoS Attack Detection and Packet-Filtering Scheme

A distributed denial-of-service (DDoS) attack presents a very serious threat to the stability of the Internet. In a typical DDoS attack, a large number of compromised hosts are amassed to send useless packets to jam a victim or its Internet connection, or both. Defense against DDoS attacks as well as identification of their sources comprise demanding challenges in the realm of Internet security studies. In this paper, effective measures are proposed for detecting attacks in routers through the use of queuing models, which help detect attacks closer to the attack sources. Utilizing these measures, an effective DDoS attack detection and packet-filtering scheme is proposed. The suggested approach is a cooperative technique among routers intended to protect the network from persistent and severe congestion arising from a rapid increase in attack traffic. Through computer simulations, it is shown that the proposed scheme can trace attacks near to the attack sources, and can effectively filter attack packets.
Functional MRI mapping of stimulus rate effects across visual processing stages

Functional magnetic resonance imaging (fMRI) was used to record cortical activation across multiple stages in the visual system during single character visual search and reversing checkerboard stimulation. Scanning used T2‐weighted, gradient echo sequences with late echo times (TE = 36 ms) with a voxel size of 0.94 * 1.88 mm in‐plane resolution, 4–5 mm deep, on a conventional scanner. A scout experiment recorded six slices to identify major regions of activation. Two slices were selected for extensive assessment. Character stimuli activated small (average 16 mm2), reliable, statistically defined regions of activation in the calcarine fissure, superior occipital cortex, and fusiform‐lingual gyrus. The results include: (1) for character search, the MRI signal change increased linearly from 2.1 to 3.1% for stimulation from 1 to 8 Hz; (2) the character rate effect was equivalent across three levels of the visual system; (3) the checkerboard stimuli showed broader, more intense primary visual activation and less intense secondary visual activation than did character search. Issues relating to fMRI signal variability across the imagining plane, statistical data analysis, signal sensitivity, statistical power, fMRI experimental protocols, and comparisons with positron emission tomography (PET) data are discussed. © 1994 Wiley‐Liss, Inc.
Maternal influence on the size and viability of Iceland cod Gadus morhua eggs and larvae

Size, condition, and age of female-Icelandic cod Gadus morhua were correlated to the size of their eggs and newly hatched larvae. A positive relationship was detected between egg size and some larval viability parameters, including the age at first feeding, successful development of a swimbladder, and specific growth rates during the first 15 days after hatching. These results reveal that the viability of cod larvae is related to attributes of the spawning females and that this information is important to our understanding of stock–recruitment relationships.
Quantifying Parkinson's disease progression by simulating gait patterns

Modern rehabilitation protocols of most neurodegenerative diseases, in particular the Parkinson Disease, rely on a clinical analysis of gait patterns. Currently, such analysis is highly dependent on both the examiner expertise and the type of evaluation. Development of evaluation methods with objective measures is then crucial. Physical models arise as a powerful alternative to quantify movement patterns and to emulate the progression and performance of specific treatments. This work introduces a novel quantification of the Parkinson disease progression using a physical model that accurately represents the main gait biomarker, the body Center of Gravity (CoG). The model tracks the whole gait cycle by a coupled double inverted pendulum that emulates the leg swinging for the single support phase and by a damper-spring System (SDP) that recreates both legs in contact with the ground for the double phase. The patterns generated by the proposed model are compared with actual ones learned from 24 subjects in stages 2,3, and 4. The evaluation performed demonstrates a better performance of the proposed model when compared with a baseline model(SP) composed of a coupled double pendulum and a mass-spring system. The Frechet distance measured differences between model estimations and real trajectories, showing for stages 2, 3 and 4 distances of 0.137, 0.155, 0.38 for the baseline and 0.07, 0.09, 0.29 for the proposed method.
Msl2 Is a Novel Component of the Vertebrate DNA Damage Response

hMSL2 (male-specific lethal 2, human) is a RING finger protein with ubiquitin ligase activity. Although it has been shown to target histone H2B at lysine 34 and p53 at lysine 351, suggesting roles in transcription regulation and apoptosis, its function in these and other processes remains poorly defined. To further characterize this protein, we have disrupted the Msl2 gene in chicken DT40 cells. Msl2−/− cells are viable, with minor growth defects. Biochemical analysis of the chromatin in these cells revealed aberrations in the levels of several histone modifications involved in DNA damage response pathways. DNA repair assays show that both Msl2−/− chicken cells and hMSL2-depleted human cells have defects in non-homologous end joining (NHEJ) repair. DNA damage assays also demonstrate that both Msl2 and hMSL2 proteins are modified and stabilized shortly after induction of DNA damage. Moreover, hMSL2 mediates modification, presumably ubiquitylation, of a key DNA repair mediator 53BP1 at lysine 1690. Similarly, hMSL1 and hMOF (males absent on the first) are modified in the presence of hMSL2 shortly after DNA damage. These data identify a novel role for Msl2/hMSL2 in the cellular response to DNA damage. The kinetics of its stabilization suggests a function early in the NHEJ repair pathway. Moreover, Msl2 plays a role in maintaining normal histone modification profiles, which may also contribute to the DNA damage response.
Information Yeast strains

Yeast strains. Mutations were introduced into the TIM15 gene by PCR-based mutagenesis to make genes for Tim15 5DE , Tim15 2RH , Tim15 D111A , and Tim15 Δ133-137. Yeast haploid strain (Δtim15/pRS316-Tim15) (Yamamoto et al, 2005), in which chromosomal disruption of the TIM15 gene was complemented with a URA3 plasmid harboring the TIM15 gene, was transformed with a TRP1 single-copy plasmid harboring the wild-type TIM15 gene or the mutant tim15 genes. Yeast strains dependent on mutated tim15 was selected on 0.1% 5′-fluoroorotic acid (5′-FOA) plates.
Multi-modal and multi-camera attention in smart environments

This paper considers the problem of multi-modal saliency and attention. Saliency is a cue that is often used for directing attention of a computer vision system, e.g., in smart environments or for robots. Unlike the majority of recent publications on visual/audio saliency, we aim at a well grounded integration of several modalities. The proposed framework is based on fuzzy aggregations and offers a flexible, plausible, and efficient way for combining multi-modal saliency information. Besides incorporating different modalities, we extend classical 2D saliency maps to multi-camera and multi-modal 3D saliency spaces. For experimental validation we realized the proposed system within a smart environment. The evaluation took place for a demanding setup under real-life conditions, including focus of attention selection for multiple subjects and concurrently active modalities.
Three mammalian tropomyosin isoforms have different regulatory effects on nonmuscle myosin-2B and filamentous β-actin in vitro

The metazoan actin cytoskeleton supports a wide range of contractile and transport processes. Recent studies have shown how the dynamic association with specific tropomyosin isoforms generates actin filament populations with distinct functional properties. However, critical details of the associated molecular interactions remain unclear. Here, we report the properties of actomyosin–tropomyosin complexes containing filamentous β-actin, nonmuscle myosin-2B (NM-2B) constructs, and either tropomyosin isoform Tpm1.8cy (b.–.b.d), Tpm1.12br (b.–.b.c), or Tpm3.1cy (b.–.a.d). Our results show the extent to which the association of filamentous β-actin with these different tropomyosin cofilaments affects the actin-mediated activation of NM-2B and the release of the ATP hydrolysis products ADP and phosphate from the active site. Phosphate release gates a transition from weak to strong F-actin–binding states. The release of ADP has the opposite effect. These changes in dominant rate-limiting steps have a direct effect on the duty ratio, the fraction of time that NM-2B spends in strongly F-actin–bound states during ATP turnover. The duty ratio is increased ∼3-fold in the presence of Tpm1.12 and 5-fold for both Tpm1.8 and Tpm3.1. The presence of Tpm1.12 extends the time required per ATP hydrolysis cycle 3.7-fold, whereas it is shortened by 27 and 63% in the presence of Tpm1.8 and Tpm3.1, respectively. The resulting Tpm isoform–specific changes in the frequency, duration, and efficiency of actomyosin interactions establish a molecular basis for the ability of these complexes to support cellular processes with widely divergent demands in regard to force production, capacity to move processively, and speed of movement.
Test Data Compression and Test Resource Partitioning for System-on-a-Chip Using Frequency-Directed Run-Length (FDR) Codes

Test data compression and test resource partitioning (TRP) are necessary to reduce the volume of test data for system-on-a-chip designs. We present a new class of variable-to-variable-length compression codes that are designed using distributions of the runs of 0s in typical test sequences. We refer to these as frequency-directed run-length (FDR) codes. We present experimental results for ISCAS 89 benchmark circuits and two IBM production circuits to show that FDR codes are extremely effective for test data compression and TRP. We derive upper and lower bounds on the compression expected for some generic parameters of the test sequences. These bounds are especially tight when the number of runs is small, thereby showing that FDR codes are robust, i.e., they are insensitive to variations in the input data stream. In order to highlight the inherent superiority of FDR codes, we present a probabilistic analysis of data compression for a memoryless data source. Finally, we derive entropy bounds for the benchmark test sets and show that the compression obtained using FDR codes is close to the entropy bounds.
High‐resolution image reconstruction with multisensors

This article considers the problem of reconstructing a high‐resolution image from multiple undersampled, shifted, degraded frames with subpixel displacement errors. This leads to a formulation involving a periodically shift‐variant system model. The maximum a posteriori (MAP) estimation scheme is used subject to the assumption that the original high‐resolution image is modeled by a stationary Markov‐Gaussian random field. The resulting MAP formulation is expressed as a complex linear matrix equation, where the characterizing matrix involves the periodic block Toeplitz with Toeplitz block (BTTB) blur matrix and banded‐BTTB inverse covariance matrix associated with the original image. By approximating the periodic‐BTTB and the banded‐BTTB matrices with, respectively, the periodic block circulant with circulant block (BCCB) and the banded‐BCCB matrices, it is shown that the computation‐intensive MAP formulation can be decomposed into a set of smaller matrix equations by using the two‐dimensional discrete Fourier transform. Exact solutions are also considered through the use of the preconditioned conjugate gradient algorithm. Computer simulations are given to illustrate the procedure. © 1998 John Wiley & Sons, Inc. Int J Imaging Syst Technol, 9, 294–304, 1998
Health-related quality of life in obese and overweight, treatment-seeking youth.

OBJECTIVE This study evaluated health related quality of life (HRQOL) in obese children using obesity-specific HRQOL measures and examined potential race and sex differences. PARTICIPANTS Two-hundred and four children aged 5.03 to 13.48 years (mean +/- SD = 10.18 +/- 1.95) and their parents participated. METHODS All participants enrolled in a family-based weight loss intervention study. Their height and weight were measured before and after the intervention, and demographic information was collected. Participants also completed a weight related quality of life measure; children completed a self-report version, and parents completed a parent-proxy version. RESULTS Higher child body mass index z-scores (BMIz) were related to poorer HRQOL per parent and child report. Males reported higher emotional functioning than females, and for race, African American parents reported higher physical functioning for their children than Caucasian parents. No difference in total HRQOL was found for race. CONCLUSIONS Childhood BMIz is inversely related to quality of life. Compared with male children, females have more impairment in quality of life. However, HRQOL did not differ by race. Also, although parent and child reports do overlap in certain areas, they also each provide unique information. Future researchers and clinicians would be wise to capture both child and parent perspectives regarding quality of life among obese children.
A Mentor-Based Targeted Intervention for High-Risk Latino College Freshmen

This article describes the implementation and evaluation of a pilot mentoring program that provided support for Latino college freshmen at risk for poor academic outcomes. Latino is a term used in the United States to identify persons of Spanish-speaking origin or descent who designate themselves as Mexican American, Chicano, Puerto Rican, Cuban, or of some other Hispanic Origin. The study illustrates specific ways in which a mentoring program can promote positive academic outcomes by targeting students at high psychosocial risk. Este artículo describe la ejecución y evaluación de un programa piloto de apoyo para estudiantes universitarios de primer año con riesgo de pobre logro académico. Latino es un término usado en los EUA para identificar personas con origen o descendencia de pais de lengua española o que se identifican como méxico-americanos, chicanos, puertorriqueños, cubanos o de algún otro origen hispano. Este estudio ilustra formas específicas en las que un programa de apoyo puede promover logros académicos positivos al concentrarse en estudiantes de alto riesgo psicosocial.