Miracle-dz/UniFAR-FTUs huggingface dataset:
Polymorphic Nature of Human T-Cell Leukemia Virus Type 1 Particle Cores as Revealed through Characterization of a Chronically Infected Cell Line

ABSTRACT Human T-cell leukemia virus type 1 (HTLV-1) is the etiological agent of adult T-cell leukemia (ATL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). HTLV-1 cell-to-cell transmission is dependent on the release of infectious virus particles into the virological synapse. The HTLV-1 particle structure is still poorly understood, and previous studies analyzed viruses produced by transformed lymphocytic cell lines chronically infected with HTLV-1, particularly the MT-2 cell line, which harbors truncated proviruses and expresses aberrant forms of the Gag protein. In this study, we demonstrate that the chronically infected SP cell line harbors a relatively low number of proviruses, making it a more promising experimental system for the study of the HTLV-1 particle structure. We first identified the genomic sites of integration and characterized the genetic structure of the gag region in each provirus. We also determined that despite encoding a truncated Gag protein, only the full-length Gag protein was incorporated into virus particles. Cryo-transmission electron microscopy analyses of the purified virus particles revealed three classes of particles based upon capsid core morphology: complete cores, incomplete cores, and particles without distinct electron densities that would correlate with the capsid region of a core structure. Observed cores were generally polygonal, and virus particles were on average 115 nm in diameter. These data corroborate particle morphologies previously observed for MT-2 cells and provide evidence that the known poor infectivity of HTLV-1 particles may correlate with HTLV-1 particle populations containing few virus particles possessing a complete capsid core structure. IMPORTANCE Studies of retroviral particle core morphology have demonstrated a correlation between capsid core stability and the relative infectivity of the virus. In this study, we used cryo-transmission electron microscopy to demonstrate that HTLV-1 particles produced from a distinct chronically infected cell line are polymorphic in nature, with many particles lacking organized electron densities that would correlate with a complete core structure. These findings have important implications for infectious HTLV-1 spread, particularly in the context of cell-to-cell transmission, a critical step in HTLV-1 transmission and pathogenesis.
Microglia contribute to circuit defects in Mecp2 null mice independent of microglia-specific loss of Mecp2 expression

Microglia, the resident CNS macrophages, have been implicated in the pathogenesis of Rett Syndrome (RTT), an X-linked neurodevelopmental disorder. However, the mechanism by which microglia contribute to the disorder is unclear and recent data suggest that microglia do not play a causative role. Here, we use the retinogeniculate system to determine if and how microglia contribute to pathogenesis in a RTT mouse model, the Mecp2 null mouse (Mecp2tm1.1Bird/y). We demonstrate that microglia contribute to pathogenesis by excessively engulfing, thereby eliminating, presynaptic inputs at end stages of disease (≥P56 Mecp2 null mice) concomitant with synapse loss. Furthermore, loss or gain of Mecp2 expression specifically in microglia (Cx3cr1CreER;Mecp2fl/yor Cx3cr1CreER; Mecp2LSL/y) had little effect on excessive engulfment, synapse loss, or phenotypic abnormalities. Taken together, our data suggest that microglia contribute to end stages of disease by dismantling neural circuits rendered vulnerable by loss of Mecp2 in other CNS cell types. DOI: http://dx.doi. org/10.7554/eLife.15224. 001
Role of neuroinflammation in neurodegenerative diseases (Review)

Neurodegeneration is a phenomenon that occurs in the central nervous system through the hallmarks associating the loss of neuronal structure and function. Neurodegeneration is observed after viral insult and mostly in various so-called 'neurodegenerative diseases', generally observed in the elderly, such as Alzheimer's disease, multiple sclerosis, Parkinson's disease and amyotrophic lateral sclerosis that negatively affect mental and physical functioning. Causative agents of neurodegeneration have yet to be identified. However, recent data have identified the inflammatory process as being closely linked with multiple neurodegenerative pathways, which are associated with depression, a consequence of neurodegenerative disease. Accordingly, pro-inflammatory cytokines are important in the pathophysiology of depression and dementia. These data suggest that the role of neuroinflammation in neurodegeneration must be fully elucidated, since pro-inflammatory agents, which are the causative effects of neuroinflammation, occur widely, particularly in the elderly in whom inflammatory mechanisms are linked to the pathogenesis of functional and mental impairments. In this review, we investigated the role played by the inflammatory process in neurodegenerative diseases.
Modeling and control of FAST-Hex: A fully-actuated by synchronized-tilting hexarotor

We present FAST-Hex, a novel UAV concept which is able to smoothly change its configuration from underactuated to fully actuated by using only one additional motor that tilts all propellers at the same time. FAST-Hex can adapt to the task at hand by finely tuning its configuration from the efficient (but underactuated) flight (typical of coplanar multi-rotor platforms) to the full-pose-tracking (but less efficient) flight, which is attainable by non-coplanar multi-rotors. We also introduce a novel full-pose geometric controller for generic multi-rotors (not only the FAST-Hex) that outperforms classical inverse dynamics approaches. The controller receives as input any reference pose in ℝ3×SO(3) (3D position + 3D orientation). Exact tracking is achieved if the reference pose is feasible with respect to the propeller spinning rate saturations. In case of unfeasibility a new feasible desired trajectory is generated online giving priority to the positional part. The new controller is tested with the FAST-Hex but can be used for many other multi-rotor platforms: underactuated, slightly fully-actuated and completely fully-actuated.
TraceME: Traceability Management in Eclipse

In this demo we present TraceME (Traceability Management in Eclipse), an Eclipse plug-in, that supports the software engineer in capturing and maintaining traceability links between different types of artifacts. A comparative analysis of the functionalities of the tools supporting traceability recovery highlights that TraceME is the more comprehensive tool for supporting such a critical activity during software development.
Thermal plasmonic interconnects in graphene

Baoan Liu,1 Yongmin Liu,2 and Sheng Shen1,* 1Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA 2Department of Mechanical & Industrial Engineering, Department of Electrical & Computer Engineering, Northeastern University, Boston, Massachusetts 02115, USA (Received 12 March 2014; revised manuscript received 7 October 2014; published 10 November 2014)
Long-Time Treatment by Low-Dose N-Acetyl-L-Cysteine Enhances Proinflammatory Cytokine Expressions in LPS-Stimulated Macrophages

N-acetyl-L-cysteine is known to act as a reactive oxygen species scavenger and used in clinical applications. Previous reports have shown that high-dose N-acetyl-L-cysteine treatment inhibits the expression of proinflammatory cytokines in activated macrophages. Here, we have found that long-time N-acetyl-L-cysteine treatment at low-concentration increases phosphorylation of extracellular signal-regulated kinase 1/2 and AKT, which are essential for the induction of proinflammatory cytokines including interleukin 1β and interleukin 6 in lipopolysaccharide-stimulated RAW264.7 cells. Furthermore, long-time N-acetyl-L-cysteine treatment decreases expressions of protein phosphatases, catalytic subunit of protein phosphatase-2A and dual specificity phosphatase 1. On the other hand, we have found that short-time N-acetyl-L-cysteine treatment at low dose increases p53 expression, which inhibits expressions of proinflammatory cytokines. These observations suggest that long-time low-dose N-acetyl-L-cysteine treatment increases expressions of proinflammatory cytokines through enhancement of kinase phosphorylation.
Bilateral Proprioceptive Evaluation in Individuals With Unilateral Chronic Ankle Instability.

CONTEXT Despite extensive research on chronic ankle instability, the findings regarding proprioception have been conflicting and focused only on the injured limb. Also, the different components of proprioception have been evaluated in isolation. OBJECTIVE To evaluate bilateral ankle proprioception in individuals with unilateral ankle instability. DESIGN Cohort study. SETTING Research laboratory center in a university. PATIENTS OR OTHER PARTICIPANTS Twenty-four individuals with a history of unilateral ankle sprain and chronic ankle instability (mechanical ankle instability group, n = 10; functional ankle instability [FAI] group, n = 14) and 20 controls. MAIN OUTCOME MEASURE(S) Ankle active and passive joint position sense, kinesthesia, and force sense. RESULTS We observed a significant interaction between the effects of limb and group for kinesthesia (F = 3.27, P = .049). Increased error values were observed in the injured limb of the FAI group compared with the control group (P = .031, Cohen d = 0.47). Differences were also evident for force sense (F = 9.31, P < .001): the FAI group demonstrated increased error versus the control group (injured limb: P < .001, Cohen d = 1.28; uninjured limb: P = .009, Cohen d = 0.89) and the mechanical ankle instability group (uninjured limb: P = .023, Cohen d = 0.76). CONCLUSIONS Individuals with unilateral FAI had increased error ipsilaterally (injured limb) for inversion movement detection (kinesthesia) and evertor force sense and increased error contralaterally (uninjured limb) for evertor force sense.
Correct Transaction Handling for 2xx Responses to Session Initiation Protocol (SIP) INVITE Requests

This document normatively updates RFC 3261, the Session Initiation Protocol (SIP), to address an error in the specified handling of success (200 class) responses to INVITE requests. Elements following RFC 3261 exactly will misidentify retransmissions of the request as a new, unassociated, request. The correction involves modifying the INVITE transaction state machines. The correction also changes the way responses that cannot be matched to an existing transaction are handled to address a security risk.
PyPy's approach to virtual machine construction

The PyPy project seeks to prove both on a research and a practical level the feasibility of constructing a virtual machine (VM) for a dynamic language in a dynamic language - in this case, Python. The aim is to translate (i.e. compile) the VM to arbitrary target environments, ranging in level from C/Posix to Smalltalk/Squeak via Java and CLI/. NET, while still being of reasonable efficiency within these environments.A key tool to achieve this goal is the systematic reuse of the Python language as a system programming language at various levels of our architecture and translation process. For each level, we design a corresponding type system and apply a generic type inference engine - for example, the garbage collector is written in a style that manipulates simulated pointer and address objects, and when translated to C these operations become C-level pointer and address instructions.
Synthesis, crystal structures and optical properties of rare earth silicate oxyapatite

The silicate oxyapatite materials are known for their structural flexibilities, high melting temperatures and good chemical stabilities. Therefore, various applications for this group of materials have been explored. In the present work, synthesis methods, crystal structures and the optical properties including potential optical applications of silicate oxyapatite Sr2Y8(SiO4)6O2 based materials are studied. Pure Sr2Y8(SiO4)6O2 powders are synthesized by both solid state reaction and sol-gel method. The crystal structure characterizations of Sr2Y8(SiO4)6O2 show that its symmetry belongs to P63/m. The general formula of silicate oxyapatite materials is A4A6(SiO4)6O2 and in the current case, half of A sites are occupied by Sr while the other half of A sites and all the A sites are filled by Y. The crystal structures and the photoluminescent properties of Eu doped Sr2Y8(SiO4)6O2 with different Eu concentrations are investigated. The XRD and Rietveld refinement revealed that most Eu cations entered A sites in low europium concentration (x = 0~0.5). At increased Eu concentration (x > 0.5), Eu cations also occupy A sites but the preference to the A sites still maintained. Photoluminescent properties vary with Eu concentrations according to photoluminescent spectra. Sr2Y6Eu2(SiO4)6O2 from sol-gel method appears to be the one with the strongest emission in nearly pure red color, whose intensity is comparable to commercial fluorescent lamp phosphor Eu:Y2O3, demonstrating potential as a red phosphor for the white LEDs. The translucent silicate oxyapatite Sr2Y8(SiO4)6O2 ceramic with a low porosity of about 0.7% is successfully fabricated by employing the spark plasma sintering. The total forward transmittance is about 52% but the in-line transmittance is much lower. Calculation reveals that influence of residual pores on the in-line transmittance is more significant than that of the birefringence effect. Though previous studies of translucent ceramics fabricated by spark plasma sintering with luminescent properties are limited, the translucent Ce doped Sr2Y8(SiO4)6O2 ceramics with different Ce concentration are fabricated by spark plasma sintering in this work and their photoluminescent properties are studied. The energy transfer process between Ce cations at A and A is revealed.
Neurophysiological Differences between Flail Arm Syndrome and Amyotrophic Lateral Sclerosis

There are many clinical features of flail arm syndrome (FAS) that are different from amyotrophic lateral sclerosis (ALS), suggesting they are probably different entities. Studies on electrophysiological differences between them are limited at present, and still inconclusive. Therefore, we aimed to find clinical and neurophysiological differences between FAS and ALS. Eighteen healthy control subjects, six FAS patients and forty-one ALS patients were recruited. The upper motor neuron signs (UMNS), split-hand index (SI), resting motor threshold (RMT), central motor conduction time (CMCT) were evaluated and compared. There was no obvious upper motor neuron signs in FAS. The SI and RMT level in FAS was similar to control subjects, but significantly lower than that of in ALS. Compared with control group, the RMT and SI in ALS group were both significantly increased to higher level. However, no significant difference of CMCT was found between any two of these three groups. The differences in clinical and neurophysiological findings between FAS and ALS, argue against they are the same disease entity. Since there was no obvious UMNS, no split-hand phenomenon, and no obvious changes of RMT and CMCT in FAS patients, the development of FAS might be probably not originated from motor cortex.
The ghost crab Ocypode mortoni George, 1982 (Crustacea: Decapoda: Ocypodidae): redescription, distribution at its type locality, and the phylogeny of East Asian Ocypode species

The ghost crab Ocypode mortoni George, 1982 was first described from the sandy shores of Sai Wan, Hong Kong, andalthough also identified from South China and Japan, has not been subsequently recorded in Hong Kong. The taxonomicstatus of O. mortoni is not clear as its original morphological description was not detailed, and there remains no informa-tion on its vertical and horizontal ecological distribution in Hong Kong. In the present study, O. mortoni was found to belocally rare in Hong Kong, only present at three of seven surveyed sites. It was always sympatric with the common O. ceratophthalmus (Pallas, 1772) at the same tidal level, and there appeared to be no clear habitat/niche distinction. Relativeabundance of O. mortoni vs. O. ceratophthalmus was at most 31%: 69% based on quantitative transect survey data fromSai Wan. Molecular phylogenetic analyses on 24 haplotypes (from 28 individuals) of 636-basepair (bp) mitochondrial cy-tochrome oxidase I (COI) gene of Ocypode spp. in East Asia show O. mortoni is a valid species most closely related to O. stimpsoni Ortmann, 1897, with an average difference of 37.64 bp, and nucleotide divergence of 6.25%. The two species are very similar morphologically, but adults of O. mortoni develop ocular stylets.
Unsupervised Adaptation for Deep

Recent ground-breaking works have shown that deep neural networks can be trained end-to-end to regress dense disparity maps directly from image pairs. Computer generated imagery is deployed to gather the large data corpus required to train such networks, an additional fine-tuning allowing to adapt the model to work well also on real and possibly diverse environments. Yet, besides a few public datasets such as Kitti, the ground-truth needed to adapt the network to a new scenario is hardly available in practice. In this paper we propose a novel unsupervised adaptation approach that enables to fine-tune a deep learning stereo model without any ground-truth information. We rely on off-the-shelf stereo algorithms together with state-of-the-art confidence measures, the latter able to ascertain upon correctness of the measurements yielded by former. Thus, we train the network based on a novel loss-function that penalizes predictions disagreeing with the highly confident disparities provided by the algorithm and enforces a smoothness constraint. Experiments on popular datasets (KITTI 2012, KITTI 2015 and Middlebury 2014) and other challenging test images demonstrate the effectiveness of our proposal.
Pretense, Pride And Prejudice In Qualitative Leadership Research: An Appraisal And Two Examples From Europe

In this paper we identify a number of prevailing epistemological inconsistencies in qualitative leadership research and suggest some emendations. We first analyze current research practices in the leadership field. We note that few qualitative studies are conducted and that many such so-called qualitative studies adhere wholly or partly to a positivist paradigm. We evoke possible rationales for this, i.e. we uncover mechanisms by which the positivist paradigm maintains its dominant position. Subsequently we propose an alternative research paradigm, social constructionism, and purport why this paradigm may be particularly suited to leadership research. By means of two practical personal research experiences we provide the reader with concrete examples of social constructionist leadership research and of what issues, barriers and satisfactions researchers might face during such a research journey. We conclude with some pragmatic ideas as to how scholars could be introduced to constructionist epistemologies and encouraged to apply interpretative research stances to leadership themes more often.
Markups Across Space and Time ∗

We study the behavior of markups in the retail sector. Markups are measured with gross margins computed at the product level using the replacement cost for every item. We find that: (1) markups are relatively stable over time and mildly procyclical; (2) there is a large regional dispersion in markups; (3) regions with higher incomes have higher markups; (4) these higher markups do not result from less intense competition or regional differences in marginal costs; and (5) regional differences in markups are due to variations in assortment, not to deviations from uniform pricing practices. We propose a simple model consistent with these facts.
Fixing sensor-related energy bugs through automated sensing policy instrumentation

As mobile applications (apps) become more and more complex, many apps contain various energy bugs, which may cause energy wastes that might reduce the battery life to as short as several hours. Among them, sensor-related bugs such as sensor data underutilization is one of the most common energy bugs. Instead of trying to detect these energy bugs, this paper proposes a method to fix sensor data underutilization automatically through instrumentation of existing apps. App-specific energy-aware sensing policies can be written to the apps via an automated instrumentation process, which can also be customized by users if needed. The proposed technique is easy to apply as it does not need to modify the operating system or the apps. At the same time, it also works for existing legacy apps, which makes it practical and feasible for a wide-range of mobile apps. Experimental results on popular Android apps show that we are able to achieve significant energy savings through automated instrumentation and rebuilding the targeted apps.
Linear and non‐linear contributions to oxygen transport and utilization during moderate random exercise in humans

What is the central question of this study? The pulmonary oxygen uptake ( pV̇O2 ) data used to study the muscle aerobic system dynamics during moderate‐exercise transitions is classically described as a mono‐exponential function controlled by a complex interaction of the oxygen delivery–utilization balance. This elevated complexity complicates the acquisition of relevant information regarding aerobic system dynamics based on pV̇O2 data during a varying exercise stimulus. What is the main finding and its importance? The elevated complexity of pV̇O2 dynamics is a consequence of a multiple‐order interaction between muscle oxygen uptake and circulatory distortion. Our findings challenge the use of a first‐order function to study the influences of the oxygen delivery–utilization balance over the pV̇O2 dynamics.
Smart Control of Monte Carlo Simulations for Astroparticle Physics

Imaging Air Cherenkov Telescopes, such as VERITAS and MAGIC, rely on models for signal separation and energy estimation. These models are fit to simulated airshowers, each of which is associated with a single initial particle of known type and energy. Simulating an airshower from such primary particles requires the execution of fine-grained stochastic processes to emulate the behaviour of millions of secondary particles. In this work we explore the smart control of simulator runs to reduce the overall runtime of data generation whilst producing the most useful example set for model fitting. We give an overview of the approach and provide an evaluation using data from the widely used CORSIKA shower simulation.
Ephedra: SPARQL Federation over RDF Data and Services

Knowledge graph management use cases often require addressing hybrid information needs that involve a multitude of data sources, a multitude of data modalities (e.g., structured, keyword, geospatial search), and availability of computation services (e.g., machine learning and graph analytics algorithms). Although SPARQL queries provide a convenient way of expressing data requests over RDF knowledge graphs, the level of support for hybrid information needs is limited: existing query engines usually focus on retrieving RDF data and only support a set of hard-coded built-in services accessible via SPARQL 1.1 queries. To deal with this problem, we present Ephedra: a SPARQL federation engine aimed at processing hybrid queries, which provides a flexible declarative mechanism for including hybrid services into a SPARQL federation.