Miracle-dz/UniFAR-FTUs huggingface dataset:
SPATIOTEMPORAL VARIATION IN LINEAR NATURAL SELECTION ON BODY COLOR IN WILD GUPPIES (POECILIA RETICULATA)

We conducted 10 mark–recapture experiments in natural populations of Trinidadian guppies to test hypotheses concerning the role of viability selection in geographic patterns of male color variation. Previous work has reported that male guppies are more colorful in low‐predation sites than in high‐predation sites. This pattern of phenotypic variation has been theorized to reflect differences in the balance between natural (viability) selection that disfavors bright male color (owing to predation) and sexual selection that favors bright color (owing to female choice). Our results support the prediction that male color is disfavored by viability selection in both predation regimes. However, it does not support the prediction that viability selection against male color is weaker in low‐predation experiments. Instead, some of the most intense bouts of selection against color occurred in low‐predation experiments. Our results illustrate considerable spatiotemporal variation in selection among experiments, but such variation was not generally correlated with local patterns of color diversity. More complex selective interactions, possibly including the indirect effects of predators on variation in mating behavior, as well as other environmental factors, might be required to more fully explain patterns of secondary sexual trait variation in this system.
Circadian phase resetting by a single short-duration light exposure.

BACKGROUND. In humans, a single light exposure of 12 minutes and multiple-millisecond light exposures can shift the phase of the circadian pacemaker. We investigated the response of the human circadian pacemaker to a single 15-second or 2-minute light pulse administered during the biological night. METHODS. Twenty-six healthy individuals participated in a 9-day inpatient protocol that included assessment of dim light melatonin onset time (DLMO time) before and after exposure to a single 15-second (n = 8) or 2-minute (n = 12) pulse of bright light (9,500 lux; 4,100 K fluorescent) or control background dim light (<3 lux; n = 6). Phase shifts were calculated as the difference in clock time between the two phase estimates. RESULTS. Both 15-second and 2-minute exposures induced phase delay shifts [median (± SD)] of -34.8 ± 47.2 minutes and -45.4 ± 28.4 minutes, respectively, that were significantly (P = 0.04) greater than the control condition (advance shift: +22.3 ± 51.3 minutes) but were not significantly different from each other. Comparisons with historic data collected under the same conditions confirmed a nonlinear relationship between exposure duration and the magnitude of phase shift. CONCLUSIONS. Our results underscore the exquisite sensitivity of the human pacemaker to even short-duration single exposures to light. These findings may have real-world implications for circadian disruption induced by exposure to brief light stimuli at night. TRIAL REGISTRATION. The study was registered as a clinical trial on www.clinicaltrials. org, NCT #01330992. FUNDING. Funding for this study was provided by NSBRI HFP02802 and NIH P01-AG09975, R01-HL114088 (EBK), RC2-HL101340-0 (EBK, SWL, SAR, REK), K02-HD045459 (EBK), K24-HL105664 (EBK), T32-HL07901 (MSH, SAR), HL094654 (CAC), and AG044416 (JFD). The project described was supported by NIH grant 1UL1 TR001102-01, 8UL1TR000170-05, UL1 RR 025758, Harvard Clinical and Translational Science Center, from the National Center for Advancing Translational Science.
Use of a Low-Cost, Commercially Available Gaming Console (Wii) for Rehabilitation of an Adolescent With Cerebral Palsy

Background and Purpose: The purpose of this retrospective and prospective case report is to describe the feasibility and outcomes of using a low-cost, commercially available gaming system (Wii) to augment the rehabilitation of an adolescent with cerebral palsy. Patient and Setting: The patient was an adolescent with spastic diplegic cerebral palsy classified as GMFCS level III who was treated during a summer session in a school-based setting. Intervention: The patient participated in 11 training sessions, 2 of which included other players. Sessions were between 60 and 90 minutes in duration. Training was performed using the Wii sports games software, including boxing, tennis, bowling, and golf. He trained in both standing and sitting positions. Outcomes: Three main outcome measures were used: (1) visual-perceptual processing, using a motor-free perceptual test (Test of Visual Perceptual Skills, third edition); (2) postural control, using weight distribution and sway measures; and (3) functional mobility, using gait distance. Improvements in visual-perceptual processing, postural control, and functional mobility were measured after training. Discussion and Conclusions: The feasibility of using the system in the school-based setting during the summer session was supported. For this patient whose rehabilitation was augmented with the Wii, there were positive outcomes at the impairment and functional levels. Multiple hypotheses were proposed for the findings that may be the springboard for additional research. To the authors’ knowledge, this is the first published report on using this particular low-cost, commercially available gaming technology for rehabilitation of a person with cerebral palsy.
A Low Complexity Algorithm for Selective AF-OFDM System

A low complexity algorithm is proposed for joint allocation of power profiles at the source and relay nodes and subcarrier assignment for single user amplify and forward (AF) cooperative communication using orthogonal frequency division multiplexing (OFDM) system. The relay uses AF cooperative relaying to transmit messages on a set of available subcarriers with diversity. The remaining subcarriers are used for direct transmission without diversity. The objective is to allocate the resources to maximize the sum rate subject to individual power constraint on each node. We formulate such a problem as subcarrier based resource allocation that seeks joint optimization of subcarrier assignment and power profiles at the source and relay nodes. The algorithm is based on an ordering of the channel gain's ratio and splitting them into two partitions, then searching for the partition that maximizes the sum rate. Simulation results demonstrate the merit of the proposed algorithm.
DNA Methylation Precedes Chromatin Modifications under the Influence of the Strain-Specific Modifier Ssm1

ABSTRACT Ssm1 is responsible for the mouse strain-specific DNA methylation of the transgene HRD. In adult mice of the C57BL/6 (B6) strain, the transgene is methylated at essentially all CpGs. However, when the transgene is bred into the DBA/2 (D2) strain, it is almost completely unmethylated. Strain-specific methylation arises during differentiation of embryonic stem (ES) cells. Here we show that Ssm1 causes striking chromatin changes during the development of the early embryo in both strains. In undifferentiated ES cells of both strains, the transgene is in a chromatin state between active and inactive. These states are still observed 1 week after beginning ES cell differentiation. However, 4 weeks after initiating differentiation, in B6, the transgene has become heterochromatic, and in D2, the transgene has become euchromatic. HRD is always expressed in D2, but in B6, it is expressed only in early embryos. The transgene is already more methylated in B6 ES cells than in D2 ES cells and becomes increasingly methylated during development in B6, until essentially all CpGs in the critical guanosine phosphoribosyl transferase core are methylated. Clearly, DNA methylation of HRD precedes chromatin compaction and loss of expression, suggesting that the B6 form of Ssm1 interacts with DNA to cause strain-specific methylation that ultimately results in inactive chromatin.
UK public health plan aims to save 300 000 lives in next decade

The director of the US National Institutes of Health, Harold Varmus, has published a clarification of his original proposal to offer “the international scientific community free, fast, and full access to the entire biomedical literature” through a single electronic database called E-biomed (1 May, p 1165). The clarification seeks “to restate …
Long run equilibrium: convergence within an urban and rural regional economy

Purpose – To test the economic theory that economies with greater stability and diversity are also economies that are more insulated from economic shocks. Design/methodology/approach – Uses persistence profiles derived from the cointegrated systems of two regional economies within the state of Oregon; the urban Portland Metropolitan Area (PMA) and the rural Southwest (SW) region. Findings – The results of the above process illustrate that the more stable and diverse PMA responds with a smaller frequency and returns to equilibrium more quickly than the SW. Research limitations/implications – This paper only provides one set of observations, which is insufficient to prove the theory, but does enable a more extensive time series approach than that has been done previously. Also regional economies typically become more diversified over time, so the level of diversity can only be measured in relative terms not absolute. Practical implications – The paper reveals the benefits a diversified a diversified economy has in creating stable employment opportunities, as deviations in unemployment rates decline as diversification increases. Originality/value – The paper takes a widely accepted time series econometrics technique from macroeconomic literature, cointegration, and applies it at a regional level. Cointegration combined with persistence profiles enables the integration of both the time dynamics of an economy and their inter-industry linkages to be analyzed. This methodology dramatically increases the depth of possible analysis into the stability/diversity debate that has been waged over the last 70 years.
Novel , Real-Time Cell Analysis for Measuring Viral Cytopathogenesis and the Efficacy of Neutralizing Antibodies to the 2009 Influenza A ( H 1 N 1 ) Virus

A novel electronic cell sensor array technology, the real-time cell analysis (RTCA) system, was developed to monitor cell events. Unlike the conventional methods labeling the target cells with fluorescence, luminescence, or light absorption, the RTCA system allows for label-free detection of cell processes directly without the incorporation of labels. Here, we used this new format to measure the cytopathic effect (CPE) of the 2009 influenza A (H1N1) virus and the efficacy of neutralizing antibodies in human sera to this virus. The real-time dynamic monitoring of CPE was performed on MDCK cell cultures infected with the H1N1 virus, ranging from 5.50610 to 5.50610 copies/mL. The resulting CPE kinetic curves were automatically recorded and were both time and viral load dependent. The CPE kinetics were also distinguishable between different H1N1 stains, as the onset of CPE induced by the A/Shanghai/37T/2009 H1N1 virus was earlier than that of the A/ Shanghai/143T/2009 H1N1 virus. Furthermore, inhibition of H1N1 virus-induced CPE in the presence of human specific antisera was detected and quantified using the RTCA system. Antibody titers determined using this new neutralization test correlated well with those obtained independently via the standard hemagglutination inhibition test. Taken together, this new CPE assay format provided label-free and high-throughput measurement of viral growth and the effect of neutralizing antibodies, illustrating its potential in influenza vaccine studies. Citation: Tian D, Zhang W, He J, Liu Y, Song Z, et al. (2012) Novel, Real-Time Cell Analysis for Measuring Viral Cytopathogenesis and the Efficacy of Neutralizing Antibodies to the 2009 Influenza A (H1N1) Virus. PLoS ONE 7(2): e31965. doi:10.1371/journal.pone. 0031965 Editor: Suryaprakash Sambhara, Centers for Disease Control and Prevention, United States of America Received September 12, 2011; Accepted January 19, 2012; Published February 20, 2012 Copyright: 2012 Tian et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The study was supported by the National Major Science and Technology Project–Prevention and Treatment of AIDS, Viral Hepatitis, and Other Major Infectious Diseases (Grant NO. 2009ZX10004-211), China ministry of health, and by the grant from the Shanghai Medical College of Fudan University (Grant NO. 09L-34), Shanghai, China. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: ywhu@shaphc.org . These authors contributed equally to this work.
Transcription-Dependent Nuclear-Cytoplasmic Trafficking Is Required for the Function of the von Hippel-Lindau Tumor Suppressor Protein

ABSTRACT Mutation of the von Hippel-Lindau tumor suppressor gene (vhl) causes the von Hippel-Lindau cancer syndrome as well as sporadic renal clear cell carcinoma. To pursue our study of the intracellular localization of VHL protein in relation to its function, we fused VHL to the green fluorescent protein (GFP) to produce the VHL-GFP fusion protein. Like VHL, VHL-GFP binds to elongins B and C and Cullin-2 and regulates target gene product levels, including levels of vascular endothelial growth factor and glucose transporter 1. VHL-GFP localizes predominantly to the cytoplasm, with some detectable nuclear signal. Inhibition of transcription by actinomycin D or 5,6-dichlorobenzimidazole riboside (DRB) causes VHL to be redistributed to the nucleus. A cellular fusion assay was used to demonstrate that inhibition of transcription induces a decrease in the nuclear export rate of VHL. The dependence of transcription for trafficking is lost with a deletion of exon 2, a region with a mutation causing a splice defect in the VHL gene in sporadic renal clear cell carcinoma. Addition of a strong nuclear export signal (NES) derived from the Rev protein results in complete nuclear exclusion and abrogates the redistribution of VHL-GFP-NES into the nucleus upon inhibition of transcription. Leptomycin B, which inhibits NES-mediated nuclear export, reverts the distribution of VHL-GFP-NES to that of VHL-GFP and restores sensitivity to actinomycin D and DRB. Uncoupling of VHL-GFP trafficking to transcription either by an exon 2 deletion or fusion to NES abolishes VHL function. We suggest that VHL function requires not only nuclear or cytoplasmic localization, but also exon 2-mediated transcription-dependent trafficking between these two cellular compartments.
The varicella-zoster virus (VZV) open reading frame 47 (ORF47) protein kinase is dispensable for viral replication and is not required for phosphorylation of ORF63 protein, the VZV homolog of herpes simplex virus ICP22

To investigate the role of varicella-zoster virus (VZV) open reading frame 47 (ORF47) protein kinase during infection, a VZV mutant was generated in which two contiguous stop codons were introduced into ORF47, thus eliminating expression of the ORF47 kinase. ORF47 kinase was not essential for the growth of VZV in cultured cells, and the growth rate of the VZV mutant lacking ORF47 protein was indistinguishable from that of parental VZV. Nuclear extracts from cells infected with parental VZV contained several phosphorylated proteins which were not detected in extracts from cells infected with the ORF47 mutant. The herpes simplex virus type 1 (HSV-1) UL13 protein (the homolog of VZV ORF47 protein) is responsible for the posttranslational processing associated with phosphorylation of HSV-1 ICP22 (the homolog of VZV ORF63 protein). Immunoprecipitation of 32P-labeled proteins from cells infected with parental virus and those infected with ORF47 mutant virus yielded similar amounts of the VZV phosphoproteins encoded by ORF4, ORF62, ORF63, and ORF68 (VZV gE), and the electrophoretic migration of these proteins was not affected by the lack of ORF47 kinase. Therefore, while the VZV ORF47 protein is capable of phosphorylating several cellular or viral proteins, it is not required for phosphorylation of the ORF63 protein in virus-infected cells.
Associations Between School Connection and Depressive Symptoms From Adolescence Through Early Adulthood: Moderation by Early Adversity

&NA; Depressive symptomatology is one of the most common and costly threats to American mental health, making the elucidation of environmental influences on depressive symptoms particularly important. Using the National Longitudinal Study of Adolescent Health, this study explores the interaction between environmental risk and protective factors in the etiology of depressive symptoms by asking whether school connection is associated with lower levels of depressive symptoms through early adulthood, and whether connection serves as a protective or promotive factor for youth who experienced early adversity. Findings highlight the importance of school connection in promoting long‐term mental health for all youth and suggest that policies and practice supporting school connection may be effective intervention strategies for youth at risk for depressive symptomatology.
Sound Source Localization for HRI Using FOC-Based Time Difference Feature and Spatial Grid Matching

In human-robot interaction (HRI), speech sound source localization (SSL) is a convenient and efficient way to obtain the relative position between a speaker and a robot. However, implementing a SSL system based on TDOA method encounters many problems, such as noise of real environments, the solution of nonlinear equations, switch between far field and near field. In this paper, fourth-order cumulant spectrum is derived, based on which a time delay estimation (TDE) algorithm that is available for speech signal and immune to spatially correlated Gaussian noise is proposed. Furthermore, time difference feature of sound source and its spatial distribution are analyzed, and a spatial grid matching (SGM) algorithm is proposed for localization step, which handles some problems that geometric positioning method faces effectively. Valid feature detection algorithm and a decision tree method are also suggested to improve localization performance and reduce computational complexity. Experiments are carried out in real environments on a mobile robot platform, in which thousands of sets of speech data with noise collected by four microphones are tested in 3D space. The effectiveness of our TDE method and SGM algorithm is verified.
T-S fuzzy-model-based output feedback MPC for networked control systems with disturbance

This paper investigates output feedback model predictive control (MPC) for nonlinear networked control systems (NCSs) with bounded disturbance where data quantization and packet loss may occur simultaneously. A Takagi-Sugeno (T-S) fuzzy model is exploited to describe the nonlinear system which can be turned into a linear one. The quantization error is treated as sector bound uncertainties and a binary Markov chain is introduced to characterize packet loss of NCSs. By applying the notion of quadratic boundedness (QB), a state estimator can be off-line designed and the estimation error bound can be obtained. The on-line MPC optimization problem which minimizes an upper bound of the expect value of the infinite horizon performance cost is solved based on the obtained estimation state. A new technique for refreshing the estimation error bound, which plays the key role of guaranteeing the recursive feasibility of optimization problem, is provided. A numerical example is given to illustrate the effectiveness of the proposed output feedback MPC approach.
Robust Adaptive Inverse Control of a Class of Nonlinear Systems With Prandtl-Ishlinskii Hysteresis Model

The exhibition of hysteresis effects in smart actuators highly affect the accuracy and stability of the control systems. The common approaches are the use of inverse hysteresis as a compensator. However, when the hysteresis is unknown, the inverse compensation will introduce notably inverse compensation error with an estimated inverse construction. The challenge is that the expression for the inverse compensation error is required for stability analysis. In this note, by developing an error expression of the inverse compensation, an inverse based robust adaptive control approach is proposed, leading to a strict stability proof. Simulation results show that the proposed controller has certain advantages comparing with the one without using an inverse compensator.
Evidence for a Late Supernova Injection of 60Fe into the Protoplanetary Disk

High-precision 60Fe-60Ni isotope data show that most meteorites originating from differentiated planetesimals that accreted within 1 million years of the solar system's formation have 60Ni/58Ni ratios that are ∼25 parts per million lower than samples from Earth, Mars, and chondrite parent bodies. This difference indicates that the oldest solar system planetesimals formed in the absence of 60Fe. Evidence for live 60Fe in younger objects suggests that 60Fe was injected into the protoplanetary disk ∼1 million years after solar system formation, when 26Al was already homogeneously distributed. Decoupling the first appearance of 26Al and 60Fe constrains the environment where the Sun's formation could have taken place, indicating that it occurred in a dense stellar cluster in association with numerous massive stars.
Can vaccines against canine visceral leishmaniasis interfere with the serological diagnostics recommended by the Brazilian Ministry of Health

The objective of the current research was to assess seroconversion in dogs immunized with Leishmune® and Leish Tec® vaccines using rapid chromatographic immunoassay DPP® (Dual Path Platform) (DPP CVL) and enzyme immunoassay (EIE) up to one year after the vaccination protocol. The study sample comprised 28 dogs divided into two groups, each group immunized with an anti-CVL vaccine and clinically monitored for one year through clinical evaluation and laboratory tests. 22 (78.5%) dog were monitored. During the evaluation time (T1-30 days, T2-6 months, and T3-1 year after vaccination) the results for all dogs were negative for CVL, except for one animal vaccinated with Leish tec® that seroconverted in the DPP CVL test at T2. Subsequent examinations of this dog were negative. Our results showed that in a non-endemic area, even at different evaluation times, dogs vaccinated against CVL with Leishmune® or Leish tec® did not seroconvert in the serological protocol used by the Brazilian Ministry of Health (DPP/EIE).
A Two-Point Method for PTZ Camera Calibration in Sports

Calibrating narrow field of view soccer cameras is challenging because there are very few field markings in the image. Unlike previous solutions, we propose a two-point method, which requires only two point correspondences given the prior knowledge of base location and orientation of a pan-tilt-zoom (PTZ) camera. We deploy this new calibration method to annotate pan-tilt-zoom data from soccer videos. The collected data are used as references for new images. We also propose a fast random forest method to predict pan-tilt angles without image-to-image feature matching, leading to an efficient calibration method for new images. We demonstrate our system on synthetic data and two real soccer datasets. Our two-point approach achieves superior performance over the state-of-the-art method.