Miracle-dz/UniFAR-FTUs huggingface dataset:
Yield Stress Fluids Slowly Yield to Analysis

The behavior of a type of complex fluid (exemplified by mayonnaise and concrete) can depend on the sample's flow history. We are surrounded in everyday life by yield stress fluids: materials that behave as solids under small stresses but flow like liquids beyond a critical stress. For example, paint must flow under the brush, but remain fixed in a vertical film despite the force of gravity. Food products (such as mayonnaise), other consumer products (such as toothpaste), concrete, and even radioactive nuclear waste sludge exhibit yield stresses. The yield stress may serve to keep particulate fillers from settling, as in many consumer products and gelled propellants, or determine whether bubbles remain trapped in cement. For handling and using these materials, it is paramount to know the stress at which the material starts to flow, but a consensus on the mechanical behavior of these materials is only slowly emerging.
Underestimated phenomena: Higher cortical dysfunctions during migraine aura

Introduction Aura occurs in 20–30% of patients with migraine. Some descriptions of aura go far beyond the most frequent visual and sensory symptoms, suggesting the involvement of different cortical areas. The aim of this prospective study was to evaluate the frequency and types of disorders of higher cortical functions (HCF) that occur during visual and/or sensory aura. Methods We interviewed 60 patients with visual and/or sensory aura about HCF disorders of praxia, gnosia, memory, and speech, during aura. Patients were divided into two groups, with and without HCF disorders, and were compared in terms of demographic data and aura characteristics. Results From all 60 patients, 65% reported at least one HCF disorder during aura. The patients with HCF disorders had longer-lasting auras (28.51 ± 16.39 vs. 19.76 ± 11.23, p = 0.016). The most common HCF disorders were motor dysphasia (82.05%) and dysnomia (30.74%). Motor dysphasia was more often reported by patients with visual as well as sensory aura (p = 0.002). The number of HCF disorders correlated with the aura duration (p = 0.003). Conclusion According to our results, HCF disorders during aura occur more often than previously thought. The aura duration has some influence on the HCF disorders.
DICER1 Mutations in Familial Pleuropulmonary Blastoma

A rare form of lung cancer in children is associated with mutational disruption of an enzyme that generates small noncoding RNAs. Pleuropulmonary blastoma (PPB) is a rare pediatric lung tumor that is often part of an inherited cancer syndrome. PPBs consist of mesenchymal cells that are susceptible to malignant transformation and cysts lined by epithelial cells. In a subset of patients, overgrowth of the cysts by mesenchymal cells leads to sarcoma formation. Here, we show that 11 multiplex PPB families harbor heterozygous germline mutations in DICER1, a gene encoding an endoribonuclease critical to the generation of small noncoding regulatory RNAs. Expression of DICER1 protein was undetectable in the epithelial component of PPB tumors but was retained in the malignant mesenchyme (sarcoma). We hypothesize that loss of DICER1 in the epithelium of the developing lung alters the regulation of diffusible factors that promote mesenchymal proliferation.
Discriminative subnetwork mining for multiple thresholded connectivity-networks-based classification of mild cognitive impairment

Recent studies on brain connectivity networks have suggested that many brain diseases, such as, Alzheimer's disease (AD) and mild cognitive impairment (MCI), are related with large-scale connectivity networks, rather than individual brain regions. However, it is challenging to find those networks from the whole connectivity network due to the complexity of brain networks. In this paper, we propose a novel method to mine the discriminative subnetworks for classifying MCI patients from healthy controls (HC). Specifically, we first apply multiple thresholds to generate multiple thresholded connectivity networks, and extract a set of frequent subnetworks from each of the two groups (i.e., MCI and HC), respectively. Then, we measure the discriminative ability of those frequent subnetworks using graph-kernel-based classification method and select the most discriminative subnetworks for subsequent classification. The results on the functional connectivity networks of 12 MCI and 25 HC show that our method can obtain a competitive results compared with state-of-the-art methods on MCI classification.
Bacteriophages Encode Factors Required for Protection in a Symbiotic Mutualism

Attacks Wasps The bacterium Hamiltonella defensa infects aphids and carries virulence determinants from a bacteriophage virus. Oliver et al. (p. 992) have now found that the toxin-bearing phage does not harm the aphid host of the bacterium, but targets the larvae of parasitoid wasps that infest the aphids. If an aphid population is not infested by wasps, the allied bacteriophage is shed by the bacterium, presumably because there is a cost to carrying it. If the wasps then resume their predation, the aphids are no longer protected and succumb to the parasitoid. A virus endows a bacterial symbiont of an aphid with virulence factors that kill parasitoid wasps. Bacteriophages are known to carry key virulence factors for pathogenic bacteria, but their roles in symbiotic bacteria are less well understood. The heritable symbiont Hamiltonella defensa protects the aphid Acyrthosiphon pisum from attack by the parasitoid Aphidius ervi by killing developing wasp larvae. In a controlled genetic background, we show that a toxin-encoding bacteriophage is required to produce the protective phenotype. Phage loss occurs repeatedly in laboratory-held H. defensa–infected aphid clonal lines, resulting in increased susceptibility to parasitism in each instance. Our results show that these mobile genetic elements can endow a bacterial symbiont with benefits that extend to the animal host. Thus, phages vector ecologically important traits, such as defense against parasitoids, within and among symbiont and animal host lineages.
Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima

Now Shown in 3D With the advent of systems-wide technologies and the development of analytical methods, data produced by analyzing individual or small groups of molecular components can be integrated to reassemble whole biological systems. Zhang et al. (p. 1544) have undertaken a major technological challenge: to integrate biochemical data with experimentally determined or predicted three-dimensional structures of all proteins involved in the central metabolism of a bacterial cell. This integration of large-scale data sets provides evolutionary and functional insights and furthers our understanding of the molecular assembly of complex biological networks. Protein structure and biochemical data generate a three-dimensional view of the metabolic network of a bacterial cell. Metabolic pathways have traditionally been described in terms of biochemical reactions and metabolites. With the use of structural genomics and systems biology, we generated a three-dimensional reconstruction of the central metabolic network of the bacterium Thermotoga maritima. The network encompassed 478 proteins, of which 120 were determined by experiment and 358 were modeled. Structural analysis revealed that proteins forming the network are dominated by a small number (only 182) of basic shapes (folds) performing diverse but mostly related functions. Most of these folds are already present in the essential core (~30%) of the network, and its expansion by nonessential proteins is achieved with relatively few additional folds. Thus, integration of structural data with networks analysis generates insight into the function, mechanism, and evolution of biological networks.
Dynamics of Chemical Bonding Mapped by Energy-Resolved 4D Electron Microscopy

Watching Graphite Breathe Electron microscopy is best known for its capacity to resolve spatial features. In a variant of the technique termed electron energy loss spectroscopy (EELS), the kinetic energy dissipated as the electron probe beam penetrates a sample can be quantified to characterize the material's underlying electronic structure. Carbone et al. (p. 181) have achieved femtosecond time resolution in an EELS study of graphite, and thereby traced the correlated motion of electrons and nuclei when the sample is heated by laser irradiation. The laser pulse induces rapid compression and then expansion of the layers in graphite's sheet structure. Concurrently, EELS uncovers shifts in delocalized electronic excitations, or plasmons. Layer compression coincides with a population shift from surface to bulk (that is, interlayer) plasmons, with the reverse shift accompanying expansion. Femtosecond tracking of an electron probe beam reveals correlated electronic and nuclear motion in laser-heated graphite. Chemical bonding dynamics are fundamental to the understanding of properties and behavior of materials and molecules. Here, we demonstrate the potential of time-resolved, femtosecond electron energy loss spectroscopy (EELS) for mapping electronic structural changes in the course of nuclear motions. For graphite, it is found that changes of milli–electron volts in the energy range of up to 50 electron volts reveal the compression and expansion of layers on the subpicometer scale (for surface and bulk atoms). These nonequilibrium structural features are correlated with the direction of change from sp2 [two-dimensional (2D) graphene] to sp3 (3D-diamond) electronic hybridization, and the results are compared with theoretical charge-density calculations. The reported femtosecond time resolution of four-dimensional (4D) electron microscopy represents an advance of 10 orders of magnitude over that of conventional EELS methods.
(+)‐Methamphetamine‐induced monoamine reductions and impaired egocentric learning in adrenalectomized rats is independent of hyperthermia

Methamphetamine (MA) is widely abused and implicated in residual cognitive deficits. In rats, increases in plasma corticosterone and egocentric learning deficits are observed after a 1‐day binge regimen of MA (10 mg/kg × 4 at 2‐h intervals). The purpose of this experiment was to determine if adrenal inactivation during and following MA exposure would attenuate the egocentric learning deficits in the Cincinnati water maze (CWM). In the first experiment, the effects of adrenalectomy (ADX) or sham surgery (SHAM) on MA‐induced neurotoxicity at 72 h were determined. SHAM‐MA animals showed typical patterns of hyperthermia, whereas ADX‐MA animals were normothermic. Both SHAM‐MA‐ and ADX‐MA‐treated animals showed increased neostriatal glial fibrillary acidic protein and decreased monoamines in the neostriatum, hippocampus, and entorhinal cortex. In the second experiment, SHAM‐MA‐ and ADX‐MA‐treated groups showed equivalently impaired CWM performance 2 weeks post‐treatment (increased latencies, errors, and start returns) compared to SHAM‐saline (SAL) and ADX‐SAL groups with no effects on novel object recognition, elevated zero maze, or acoustic startle/prepulse inhibition. Post‐testing, monoamine levels remained decreased in both MA‐treated groups in all three brain regions, but were not as large as those observed at 72‐h post‐treatment. The data demonstrate that MA‐induced learning deficits can be dissociated from drug‐induced increases in plasma corticosterone or hyperthermia, but co‐occur with dopamine and serotonin reductions. Synapse 64:773–785, 2010. © 2010 Wiley‐Liss, Inc.
Analysis and efficient control design for generator-side converters of PMSG-based wind and tidal stream turbines

Mitigation of climate change has stimulated an increased penetration of renewable generation into electricity grids. A substantial amount of the future energy mix is projected to come from renewable sources such as offshore wind, but marine energy may be an important contributor due to the great potential of wave and tidal stream generation. Wind and tidal stream turbines feature similarities: electric machines used, system configuration and control schemes-aiming to extract maximum power from the wind or flow. In this line, individual channel analysis and design (ICAD), a frequency domain framework with the help of which the investigation of the potential and limitations for control design of multivariable systems can be assessed, is employed for turbines based on permanent magnet synchronous generators. Through ICAD, a formal evaluation of the internal coupling of the turbine generator is performed. Results offer formal insight into control strategies based on vector control - with emphasis made on the generator-side of the full power converter. The analysis shows that the use of decoupling loops is not necessary to ensure a satisfactory performance. This is further examined through a simulation carried out in MATLAB/Simulink, showing the effectiveness of the approach.
Meta‐analysis: A need for well‐defined usage in ecology and conservation biology

Meta-analysis is a powerful research summarization technique. In the medical field, for example, meta-analysis is an indispensable tool as part of systematic reviews for healthcare decision making. The advantages of meta-analysis have also been recognized in the fields of ecology and conservation biology with the method becoming increasingly popular since the 1990s. “Meta-analysis”, however, is not well-defined in these fields, but is regularly confused with other summary analysis techniques, such as multiple regression methods, vote-counting or other quantitative analyses. We argue that this vague and inconsistent utilization of the term is problematic, because a meta-analysis typically provides scientifically rigorous results. We therefore advocate a consistent and well-defined usage of the term in our disciplines, based on the standardized definition applied in the medical sciences. We searched the Web of Knowledge for meta-analyses in the subject area “biodiversity conservation” and evaluated the usage of the term “meta-analysis”. Based on meta-analysis literature from the medical sciences, we determined steps that in our opinion are mandatory when performing meta-analysis and rated articles according to these steps. In the first round of rating, we assessed the usage of four “technical” steps that are normally applied in meta-analytical software. In the second round, we only evaluated the highly rated articles from the first round. We considered three steps regarding more qualitative aspects of interpretation and results presentation. Of the 133 evaluated articles in the first round, only 45% fulfilled all technical requirements for a meta-analysis, while 25% did not fulfill any of the requisite steps. In the second round, only one article of 83 fulfilled all requisite steps, while 22% did not fulfill any requirement. Our findings highlight the ambiguous and vague usage of the term “meta-analysis” in ecology and conservation biology and underline the importance of a consistent and clear definition. We conclude with recommendations on how the term should be applied in the future.
A Spindle Assembly Checkpoint Protein Functions in Prophase I Arrest and Prometaphase Progression

BubR1 Broadens Its Remit During mitosis in mammalian somatic cells, BubR1 is indispensable for spindle assembly checkpoint signaling and for establishing contacts between chromosomes and spindle microtubules. Homer et al. (p. 991) found that in mouse oocytes during meiosis I, BubR1 was not only required to sustain prophase I arrest but also for promoting the completion of meiosis I. Both effects converge on the Cdh1 coactivator of the multimeric ubiquitin ligase, known as the anaphase-promoting complex, and both functions are required for the production of fertilizable eggs. A protein vital for correct segregation of chromosomes in mitosis is also needed to complete meiosis in mouse oocytes. Two critical stages of mammalian oocyte regulation are prophase I arrest, which is important for sustaining the oocyte pool, and the progression through meiosis I (MI) to produce fertilizable eggs. We have found that the spindle assembly checkpoint protein BubR1 regulates both stages in mouse oocytes. We show that oocytes depleted of BubR1 cannot sustain prophase I arrest and readily undergo germinal vesicle breakdown, a marker for reentry into MI. BubR1-depleted oocytes then arrest before completing MI, marked by failure of polar body extrusion. Both meiotic defects in BubR1-depleted oocytes are due to reduced activity of the master regulator known as the anaphase-promoting complex (APC), brought about through diminished levels of the APC coactivator Cdh1.
Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions

Lysine Acetylation Catalog Covalent posttranslational modification is an essential cellular regulatory mechanism by which the activity of proteins can be controlled. Advances in mass spectrometry made it possible for Choudhary et al. (p. 834, published online 16 July) to assess the prevalence of lysine acetylation throughout the whole proteome. Acetylation is much more widespread than previously appreciated and occurs on proteins participating in all sorts of biological functions. Acetylation can influence susceptibility of proteins to phosphorylation and occurs frequently on enzymes that control the modification of other proteins by covalent ubiquitination and on proteins that form large macromolecular complexes. The findings also help to characterize the actions of lysine deacetylase inhibitors, which have shown clinical promise in treatments for cancer. A proteomic-scale analysis of protein acetylation suggests that it is an important biological regulatory mechanism. Lysine acetylation is a reversible posttranslational modification of proteins and plays a key role in regulating gene expression. Technological limitations have so far prevented a global analysis of lysine acetylation’s cellular roles. We used high-resolution mass spectrometry to identify 3600 lysine acetylation sites on 1750 proteins and quantified acetylation changes in response to the deacetylase inhibitors suberoylanilide hydroxamic acid and MS-275. Lysine acetylation preferentially targets large macromolecular complexes involved in diverse cellular processes, such as chromatin remodeling, cell cycle, splicing, nuclear transport, and actin nucleation. Acetylation impaired phosphorylation-dependent interactions of 14-3-3 and regulated the yeast cyclin-dependent kinase Cdc28. Our data demonstrate that the regulatory scope of lysine acetylation is broad and comparable with that of other major posttranslational modifications.
Voltage-gated sodium channels: the search for subtype-selective analgesics

Background: Primary afferent or sensory neurons innervate almost all the tissues of the body. They are vital in receiving sensory information and conveying this to the spinal cord and subsequently to the brain, where the higher centres convert this afferent input into an ‘understanding’ of its nature. The nociceptors are a subset of sensory neurons responsible for the transmission of ‘painful’ stimuli into the CNS. Objective/methods: Voltage-gated sodium channels (VGSCs) are pivotal in the transduction of noxious signals at the terminals of the nociceptors and the transmission of the signal along the axon and into the spinal cord and brain. There are nine functional members of the VGSC family. This review aims to briefly summarise the biology of the family, discuss those VGSCs involved in the transduction and transmission of nociceptive signals and to highlight the potential and also the challenges in seeking subtype-selective VGSC modulators for the effective treatment of pain. Results/conclusion: Robust evidence from preclinical models – and better yet, overwhelming human clinical genetic data – provides a compelling rationale for the involvement of VGSCs in nociceptive processing. Some compounds showing a low degree of subtype selectivity have been progressed into clinical development, but the results have been disappointing. It is likely that the high degree of structural homology within the VGSC family is a causative factor in making the discovery of subtype-selective modulators extremely challenging. A much greater understanding of the structure – function relationship for VGSCs and pharmacological modulators is needed if we are to design the compounds that will target those channels involved in nociceptive signalling whilst sparing those in the heart and brain. Only then will we be able to deliver a quantum leap in analgesic pharmacotherapy, providing the effective and well-tolerated drugs that the patient needs.
Detection of 16 Gamma-Ray Pulsars Through Blind Frequency Searches Using the Fermi LAT

Gamma-Ray Pulsar Bonanza Most of the pulsars we know about were detected through their radio emission; a few are known to pulse gamma rays but were first detected at other wavelengths (see the Perspective by Halpern). Using the Fermi Gamma-Ray Space Telescope, Abdo et al. (p. 840, published online 2 July; see the cover) report the detection of 16 previously unknown pulsars based on their gamma-ray emission alone. Thirteen of these coincide with previously unidentified gamma-ray sources, solving the 30-year-old mystery of their identities. Pulsars are fast-rotating neutron stars. With time they slow down and cease to radiate; however, if they are in a binary system, they can have their spin rates increased by mass transfer from their companion stars, starting a new life as millisecond pulsars. In another study, Abdo et al. (p. 845) report the detection of gamma-ray emission from the globular cluster 47 Tucanae, which is coming from an ensemble of millisecond pulsars in the cluster's core. The data imply that there are up to 60 millisecond pulsars in 47 Tucanae, twice as many as predicted by radio observations. In a further companion study, Abdo et al. (p. 848, published online 2 July) searched Fermi Large Area Telescope data for pulsations from all known millisecond pulsars outside of stellar clusters, finding gamma-ray pulsations for eight of them. Their properties resemble those of other gamma-ray pulsars, suggesting that they share the same basic emission mechanism. Indeed, both sets of pulsars favor emission models in which the gamma rays are produced in the outer magnetosphere of the neutron star. Most of these identifications correspond to gamma-ray sources long suspected to be pulsars. Pulsars are rapidly rotating, highly magnetized neutron stars emitting radiation across the electromagnetic spectrum. Although there are more than 1800 known radio pulsars, until recently only seven were observed to pulse in gamma rays, and these were all discovered at other wavelengths. The Fermi Large Area Telescope (LAT) makes it possible to pinpoint neutron stars through their gamma-ray pulsations. We report the detection of 16 gamma-ray pulsars in blind frequency searches using the LAT. Most of these pulsars are coincident with previously unidentified gamma-ray sources, and many are associated with supernova remnants. Direct detection of gamma-ray pulsars enables studies of emission mechanisms, population statistics, and the energetics of pulsar wind nebulae and supernova remnants.