Miracle-dz/UniFAR-FTUs huggingface dataset:
NUTMEG: a neuromagnetic source reconstruction toolbox.

We have developed an analysis toolbox called NUTMEG (Neurodynamic Utility Toolbox for Magnetoencephalography) for reconstructing the spatiotemporal dynamics of neural activations and overlaying them onto structural MR images. The toolbox runs under MATLAB in conjunction with SPM2 and can be used with the Linux/UNIX, Mac OS X, and even Windows platforms. Currently, evoked magnetic field data from 4-D Neuroimaging, CTF, and KIT systems can be imported to the toolbox for analysis. NUTMEG uses an eigenspace vector beamforming algorithm to generate a tomographic reconstruction of spatiotemporal magnetic source activity over selected time intervals and spatial regions. The MEG coordinate frame is coregistered with an anatomical MR image using fiducial locations and, optionally, head shape information. This allows the reconstruction to be superimposed onto an MRI to provide a convenient visual correspondence to neuroanatomy. Navigating through the MR volume automatically updates the displayed time series of activation for the selected voxel. Animations can also be generated to view the evolution of neural activity over time. Since NUTMEG displays activations using SPM2's engine, certain SPM functions such as brain rendering and spatial normalization may be applied as well. Finally, as a MATLAB package, the end user can easily add customized functions. Source code is available at http://bil.ucsf. edu/ and distributed under a BSD-style license.
Establishment of an indicator cell line to quantify Bovine Foamy Virus infection

A cell line derived from baby hamster kidney (BHK‐21) cells was transfected with the enhanced green fluorescent protein gene driven by the bovine foamy virus (BFV) long terminal repeat (LTR) to establish a BFV indicator cell line (BICL). Among 48 clones, one clone was chosen for its little constitutive enhanced green fluorescent protein (EGFP) expression and high level of EGFP expression after activation by BFV infection. By detecting the EGFP expression of the BFV indicator cell line, the titers of BFV were quantified by the end point method. As a result, the titer determined by the EGFP based assay 5–6 days post infection (d.p.i.) was 100 fold higher than traditional assays measuring cytopathic effects 8–9 d.p.i. Moreover, the EGFP based assay was also used to determine the titer of those cells infected by BFV without inducing cytopathic effects. Using this simple and rapid assay, we examined the in vitro host range of BFV. It was found that BFV can productively infect various cell lines derived from bovine, human, rat and monkey. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
What Drives People to Play Wii Game? - The Trend of Human-Computer Interaction on Video Game Design

An apparatus and method for treating and reusing the wastewater discharged from agricultural animal farms. The apparatus and method of the present invention is designed to be a zero discharge system in which no wastewater will be discharged or spray irrigated. The wastewater effluent is first passed through a mechanical screen were bulk solids are separated and partially de-watered. The screened effluent is then directed to a primary plastic-lined earthen lagoon where it undergoes aerobic digestion utilizing specially selected bacteria. After treatment in the primary lagoon, the wastewater effluent is used to wash the floors of the hog houses or undergoes a purification phase including solids separation/denitrification, filtration and sterilization. The solids separation/denitrification phase (clarification) preferably takes place in an anoxic environment in preferably above-ground tanks where suspended solids removal will occur as well as denitrification for nitrate reduction. The clarification process may be facilitated through use of polymer addition. The majority of solids will be sent to a plurality of drying beds for de-watering and subsequent removal.
Effect of Trans-resveratrol on Rotenone-induced Cytotoxicity in Human Breast Adenocarcinoma Cells

Rotenone, a botanical insecticide is known to cause apoptosis in various cell types. Trans-resveratrol, a natural phytophenol present in red grapes and wine, is also well documented for its antioxidant, anti-inflammatory, anti-mutagenic, and anticarcinogenic activities. Therefore, the present investigations were carried out to assess the protective effect of trans-resveratrol against rotenone-induced cell death in human breast adenocarcinoma (MCF-7) cells. MCF-7 cells were exposed with various concentrations of rotenone for 24 h, and the loss in percent cell viability was evaluated by MTT [3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide] and neutral red uptake (NRU) assays. A significant decrease in percent cell viability in MCF-7 cells was observed at 50 μM and above concentrations of rotenone, as compared to untreated control. Furthermore, various concentrations (5, 10, and 25 μM) of trans-resveratrol were used to see its protective role on cell viability in rotenone-induced cell death in MCF-7 cells. Pre- or post- treatment of trans-resveratrol for 24 h was given to the cells. The data exhibited a significant dose dependent increase in the percent cell viability under pre- and post-treatment conditions. However, post-treatment of trans-resveratrol for 24 h after rotenone exposure to the cells was relatively less effective. Overall, the results suggest that trans-resveratrol significantly protects MCF-7 cells from rotenone-induced cell death. This model can be used as an effective and economical alternative to animal models for screening the antioxidant activity of a variety of natural compounds/drugs.
The Mechanism of Dynein Light Chain LC8-mediated Oligomerization of the Ana2 Centriole Duplication Factor*

Background: Ana2 is a conserved centriole duplication factor involved in nascent centriole biogenesis. Results: Two sites in the central domain of Ana2 (Ana2M) bind LC8 and form an Ana2M4-LC88 complex. Conclusion: LC8 potentiates Ana2 tetramerization. Significance: LC8-potentiated Ana2 tetramerization is expected to increase the avidity of Ana2 for centriole factors, including Sas-6, and may drive binding factor oligomerization. Centrioles play a key role in nucleating polarized microtubule networks. In actively dividing cells, centrioles establish the bipolar mitotic spindle and are essential for genomic stability. Drosophila anastral spindle-2 (Ana2) is a conserved centriole duplication factor. Although recent work has demonstrated that an Ana2-dynein light chain (LC8) centriolar complex is critical for proper spindle positioning in neuroblasts, how Ana2 and LC8 interact is yet to be established. Here we examine the Ana2-LC8 interaction and map two LC8-binding sites within the central region of Ana2, Ana2M (residues 156–251). Ana2 LC8-binding site 1 contains a signature TQT motif and robustly binds LC8 (KD of 1.1 μm), whereas site 2 contains a TQC motif and binds LC8 with lower affinity (KD of 13 μm). Both LC8-binding sites flank a predicted ∼34-residue α-helix. We present two independent atomic structures of LC8 dimers in complex with Ana2 LC8-binding site 1 and site 2 peptides. The Ana2 peptides form β-strands that extend a central composite LC8 β-sandwich. LC8 recognizes the signature TQT motif in the first LC8 binding site of Ana2, forming extensive van der Waals contacts and hydrogen bonding with the peptide, whereas the Ana2 site 2 TQC motif forms a uniquely extended β-strand, not observed in other dynein light chain-target complexes. Size exclusion chromatography coupled with multiangle static light scattering demonstrates that LC8 dimers bind Ana2M sites and induce Ana2 tetramerization, yielding an Ana2M4-LC88 complex. LC8-mediated Ana2 oligomerization probably enhances Ana2 avidity for centriole-binding factors and may bridge multiple factors as required during spindle positioning and centriole biogenesis.
Provider and Care Workforce Influences on Quality of Home-Care Services in England

Abstract A key trend in home care in recent years in England has been movement away from “in-house” service provision by local government authorities (e.g., counties) towards models of service commissioning from independent providers. A national survey in 2003 identified that there were lower levels of satisfaction and perceptions of quality of care among older users of independent providers compared with in-house providers. This paper reports the results of a study that related service users views of 121 providers with the characteristics of these providers. For the most part, characteristics associated with positive perceptions of quality were more prevalent among in-house providers. Multivariate analyses of independent providers suggested that aspects of the workforce itself, in terms of age and experience, provider perceptions of staff turnover, and allowance of travel time, were the most critical influences on service user experiences of service quality.
The Effect of Visuospatial Neglect on Functional Outcome and Discharge Destination: An Exploratory Study

ABSTRACT Background and Purpose: The purpose of this study was to evaluate the effect of visuospatial neglect on functional outcome and discharge destination in individuals with right brain damage. Methods: Sixteen subjects agreed to participate in the study and 6 of these subjects demonstrated visuospatial neglect. During two different data collection periods, participants were evaluated with the Rivermead Behavioral Inattention Test, the Functional Independence Measure (FIM), the Mini-Mental State Examination, the Berg Balance Scale, and the Chedoke-McMaster Impairment Inventory. Results: Admission and discharge FIM scores were significantly lower for subjects with visuospatial neglect. The discharge destination for the group with visuospatial neglect demonstrated a trend toward supported living (i.e., long-term care). The groups did not differ significantly in onset to rehabilitation admission interval or length of rehabilitation stay. Conclusions: The presence of visuospatial neglect may predict the need for greater amounts of caregiver assistance at discharge.
The influence of aortic dimensions on calculated wall shear stress in the mouse aortic arch

In this paper, the influence of the aortic dimensions of an investigated mouse on its resulting wall shear stress (WSS) was studied. A numerical model of a mouse aortic arch was created based on a micro-CT scan of a vascular corrosion cast of an 8-week-old wild type mouse. This model was then rescaled to obtain five models with aortic root diameters corresponding to five different stages in the mouse life cycle varying from late fetal (0.7 mm) to old adult (1.5 mm). Consistent with literature, WSS values much higher than those normally encountered in humans were found. WSS was found to decrease rapidly in early life stages and to reach a plateau in adulthood, thus supporting a mediating role for WSS in arterial growth. Our results show that WSS values for mice should be interpreted very cautiously, and if possible an animal-specific geometry with animal-specific boundary conditions should be used.
Investigación en redes sociales digitales: consideraciones metodológicas desde el paradigma estructural

In recent years, virtual communities such as Facebook, Twitter, YouTube and Instagram have changed the way we interact with others. This phenomenon, along with the emergence of new techniques and procedures to analyse the large volume of relational data generated by these platforms, challenges us with some theoretical, methodological and ethical issues. This paper is aimed to support students and scholars interested in this topic to develop their research as well as to demonstrate the potential of structural analysis for the study of digital networks. This paper is intended to: (a) demonstrate the link between conventional social network research and digital networks research; (b) address relevant methodological aspects for the design of a structural investigation; (c) introduce some of the main programs used to extract, analyse and display data from digital networks. Data from a case study will be used to illustrate the potential of structural analysis applied to the digital environments.
Performance of an abbreviated version of the Lubben Social Network Scale among three European community-dwelling older adult populations.

PURPOSE There is a need for valid and reliable short scales that can be used to assess social networks and social supports and to screen for social isolation in older persons. DESIGN AND METHODS The present study is a cross-national and cross-cultural evaluation of the performance of an abbreviated version of the Lubben Social Network Scale (LSNS-6), which was used to screen for social isolation among community-dwelling older adult populations in three European countries. Based on the concept of lack of redundancy of social ties we defined clinical cut-points of the LSNS-6 for identifying persons deemed at risk for social isolation. RESULTS Among all three samples, the LSNS-6 and two subscales (Family and Friends) demonstrated high levels of internal consistency, stable factor structures, and high correlations with criterion variables. The proposed clinical cut-points showed good convergent validity, and classified 20% of the respondents in Hamburg, 11% of those in Solothurn (Switzerland), and 15% of those in London as at risk for social isolation. IMPLICATIONS We conclude that abbreviated scales such as the LSNS-6 should be considered for inclusion in practice protocols of gerontological practitioners. Screening older persons based on the LSNS-6 provides quantitative information on their family and friendship ties, and identifies persons at increased risk for social isolation who might benefit from in-depth assessment and targeted interventions.
Data Centers as Software Defined Networks: Traffic Redundancy Elimination with Wireless Cards at Routers

We propose a novel architecture of data center networks (DCN), which adds wireless network card to both servers and routers. Existing traffic redundancy elimination (TRE) mechanisms reduce link loads and increase network capacity in several environments by removing strings that have appeared in earlier packets through encoding and decoding them several hops downstream. This article is the first to explore TRE mechanisms in large-scale DCNs and the first to exploit cooperative TRE among servers. Moreover, it also achieves the `logically centralized' control over the physically distributed states in emerging software defined networks (SDN) paradigm, by sharing information among servers and routers in data centers with wireless cards. We first formulate the TREDaCeN (TRE in Data Center Networks) problem and reduce the cycle cover problem to prove that finding an optimal caching task assignment for TREDaCeN problem is NP-hard. We further describe an offline TREDaCeN algorithm which is proved to have good approximation ratio. We then discuss efficient online zero-delay and semi-distributed implementations of TREDaCeN supported by physical proximity of servers and routers, enabling status updates in a single wireless transmission, using an efficient prioritized schedule. We also address online cache replacement and consistency of information in servers and routers with and without delay. Our framework is tested on different parameters and shows superior performance in comparison to other mechanisms (imported directly to this setting). Our results show the robustness and the trade-off between the `logically centralized' implementation and the overhead on handling inconsistency of distributed information in DCN.
Escaping free-energy minima

We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the FES, allowing the efficient exploration and accurate determination of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.
Conflicts, Commitments, and Cliques in the University: Moral Seduction as a Threat to Trustee Independence

The ability of trustees to make independent judgments in the best interests of the university is a fundamental characteristic of an effective governing board. Trustee independence is increasingly threatened, however, as the university becomes more deeply embedded in government, industry, networks, and the professions. This topic is investigated through analysis of qualitative interviews, focus group observations, and informant-produced documents from 59 public university presidents. It is argued that threats to trustee independence are produced primarily through a process of moral seduction that allows trustees to engage in self-interested decision making while maintaining an ethical self-concept. The article then provides a conceptual model to frame our understanding of how important social actors seek to capture and co-opt boards of trustees to serve external interests and describes how the institutional mechanism of moral seduction creates important policy considerations.
Collaboration and end-user information management tools

Knowledge and information workers work as individuals within virtual team structures. Those teams may be small, or they may in fact form part of larger groups which continue to share similar objectives. Knowledge workers therefore acquire and manage personal and group information which they may choose to manage themselves using Personal and small-Group Information Management tools and techniques (PIM, GIM). This paper summarises some earlier research into PIM and GIM before addressing its objectives, which are to:  Consider the use of PIM / GIM techniques as the basis for collaboration within those virtual teams  Discuss collaboration and community involvement in the actual development of PIM/GIM tools  Identify the need for formalisms and abstraction skills in effective personal information management.
Complex-valued hough transforms for circles

This paper proposes the use of complex variables to represent votes in the Hough transform for circle detection. Replacing the positive numbers classically used in the parameter space of the Hough transforms by complex numbers allows cancellation effects when adding up the votes. Cancellation and the computation of shape likelihood via a complex number's magnitude square lead to more robust solutions than the “classic” algorithms, as shown by computational experiments on synthetic and real datasets. We note a resemblance to methods used in quantum theory.
Mathematics Teachers' Instructional Practices in an Era of High-Stakes Testing

This study explored mathematics teachers' instructional practices in the context of high-stakes testing. Data were obtained from a survey instrument given to a stratified sample of Mississippi and Tennessee teachers who teach the same content tested on their state's high school graduation examination. An analysis showed teachers using a balance of standards-based and traditional practices and tools, including textbook-based assignments, calculators, open-response questions, supplementary materials, and multiple-choice questions. Over 90% of teachers from both states felt that an “interest in helping my students attain test scores that will allow them to graduate high school” was a factor influencing their instructional practices. This was followed by an “interest in helping my school improve high school graduation examination scores,” and “belief these are the best instructional practices. ”
Cholera forecast for Dhaka, Bangladesh, with the 2015-2016 El Niño: Lessons learned

A substantial body of work supports a teleconnection between the El Niño-Southern Oscillation (ENSO) and cholera incidence in Bangladesh. In particular, high positive anomalies during the winter (Dec-Feb) in sea surface temperatures (SST) in the tropical Pacific have been shown to exacerbate the seasonal outbreak of cholera following the monsoons from August to November. Climate studies have indicated a role of regional precipitation over Bangladesh in mediating this long-distance effect. Motivated by this previous evidence, we took advantage of the strong 2015–2016 El Niño event to evaluate the predictability of cholera dynamics for the city in recent times based on two transmission models that incorporate SST anomalies and are fitted to the earlier surveillance records starting in 1995. We implemented a mechanistic temporal model that incorporates both epidemiological processes and the effect of ENSO, as well as a previously published statistical model that resolves space at the level of districts (thanas). Prediction accuracy was evaluated with “out-of-fit” data from the same surveillance efforts (post 2008 and 2010 for the two models respectively), by comparing the total number of cholera cases observed for the season to those predicted by model simulations eight to twelve months ahead, starting in January each year. Although forecasts were accurate for the low cholera risk observed for the years preceding the 2015–2016 El Niño, the models also predicted a high probability of observing a large outbreak in fall 2016. Observed cholera cases up to Oct 2016 did not show evidence of an anomalous season. We discuss these predictions in the context of regional and local climate conditions, which show that despite positive regional rainfall anomalies, rainfall and inundation in Dhaka remained low. Possible explanations for these patterns are given together with future implications for cholera dynamics and directions to improve their prediction for the city.
On Literary Works as Simulations that Run on Minds

This commentary discusses Oatley's proposal that literary works considered as simulations that run on minds can fulfill similar epistemic functions as computer simulations of mental processes. Whereas in computer simulation, both the input data and the computations to be performed on these data are explicit, only the input is explicitly known in the case of mental simulation. For this reason, literary simulations cannot play exactly the same epistemic role as computer simulations. Still, literary simulations can provide knowledge (e.g., about the phenomenal quality of emotions or about possible emotional dynamics) that is relevant for emotion science: it adds to the corpus of facts about emotions that need to be explained, and it may suggest hypotheses about the constitution of the mechanisms that generate emotions. In addition, the hypotheses suggested by a literary simulation can be tested in new mental simulations. However, at least for the purpose of hypothesis testing, the simulation of a multiplicity of experimentally manipulated scenarios should be more revealing than that of a single literary work describing only one possible course of events.
Supporting Array Programming in X10

Effective support for array-based programming has long been one of the central design concerns of the X10 programming language. After significant research and exploration, X10 has adopted an approach based on providing arrays via user definable and extensible class libraries. This paper surveys the range of array abstractions available to the programmer in X10 2.4 and describes the key language features and language implementation techniques necessary to make efficient and productive implementations of these abstractions possible.