Miracle-dz/UniFAR-FTUs huggingface dataset:
Rotavirus Infection Induces the Unfolded Protein Response of the Cell and Controls It through the Nonstructural Protein NSP3

ABSTRACT The unfolded protein response (UPR) is a cellular mechanism that is triggered in order to cope with the stress caused by the accumulation of misfolded proteins in the endoplasmic reticulum (ER). This response is initiated by the endoribonuclease inositol-requiring enzyme 1 (IRE1), activating transcription factor 6 (ATF6), and PKR-like ER kinase, which increase the expression of the genes involved in the folding and degradation processes and decrease the protein input into the ER by inhibiting translation. It has been shown that viruses both induce and manipulate the UPR in order to protect the host cells from an ER stress-mediated death, thus permitting the translation of viral proteins and the efficient replication of the virus. To understand the cellular events that occur during the rotavirus replication cycle, we examined the activation of the three UPR arms following infection, using luciferase reporters driven by promoters of the ER stress-responsive genes and real-time reverse transcription-PCR to determine the levels of the stress-induced mRNAs. Our findings indicated that during rotavirus infection two of the three arms of the UPR (IRE1 and ATF6) become activated; however, these pathways are interrupted at the translational level by the general inhibition of protein synthesis caused by NSP3. This response seems to be triggered by more than one viral protein synthesized during the replication of the virus, but not by the viral double-stranded RNA (dsRNA), since cells transfected with psoralen-inactivated virions, or with naked viral dsRNA, did not induce UPR.
Single cell isolation from micro-fluid utilizing femtosecond laser-induced impulsive force

We demonstrated a new single cell isolation method utilizing femtosecond laser-induced deposition. Micro sphere was dispersed in an aqueous solution as a phantom of the cell and it was introduced into mm-sized well. The well was placed upside down on a microscope stage and then the laser was shot near the air/liquid surface. The laser-shot caused a droplet formation on the surface and the sphere near the laser focus was drawn into the droplet. Fall of the droplet resulted in transfer of the sphere from the liquid layer to the target substrate. Spatial selectivity of intake of the sphere would range 50–130 μm. Since diameter of the typical animal cell is to be 30 μm, the selectivity could be comparable to the single animal cell but also larger biological samples such as cell aggregation.
Wide field interferometric imaging with single-mode fibers

Classical single-mode fiber interferometers, using one fiber per aperture, have very limited imaging capabilities and small field of view. Observations of extended sources (resolved by one aperture) cannot be fully corrected for wavefront aberrations: accurate measurements of object visibilities are then made very difficult from ground-based fiber interferometers. These limitations are very severe for the new generation of interferometers, which make use of large telescopes equipped with adaptive optics, but can be overcome by using several fibers per aperture. This technique improves the wide field imaging capabilities of both ground-based and space interferometers.
Making the Most of a Web Search Session

We tackle problems related to Web query formulation: given the set of keywords from a search session, 1) we find a maximum promising Web query, and, 2) we construct a family of promising Web queries covering all keywords. A query is promising if it fulfills user-defined constraints on the number of returned hits. We assume a real-world setting where the user is not given direct access to a search engine's index, i.e., querying is possible only through an interface. The goal to be optimized is the overall number of submitted Web queries. For both problems we develop search strategies based on co-occurrence probabilities. The achieved performance gain is substantial: compared to the uninformed baselines without co-occurrence probabilities the expected savings are up to 50% in the number of submitted queries, index accesses, and runtime.
Production and bond strength of similar-titanium ultrasonic welded joints

The joinability of unalloyed titanium and the bond strength of similar titanium welded joints by ultrasonic welding were investigated. It turned out that sound welded joints of similar titanium were obtained by using the jig for fixing both base metals. In the case of non-fixing and fixing the lower base metal, sound welded joints were not usually obtained due to the slip between the two base metals. Producing welded joints having sufficient bond strength required a certain threshold value of the ultrasonic energy. When the ultrasonic welding was carried out under the condition where the ultrasonic energy was higher than a threshold value (approximately 2000 W s), the welded joints were fractured within the titanium base metal but not at the interface. The values of the bond strength were associated with the fixing method and the surface roughness of the base metals. The bond interface was joined metallurgically for the most part, although some small voids were observed on the bond interface by SEM and EPMA observation.
Taking Stock of the Drosophila Research Ecosystem

With a century-old history of fundamental discoveries, the fruit fly has long been a favored experimental organism for a wide range of scientific inquiries. But Drosophila is not a “legacy” model organism; technical and intellectual innovations continue to revitalize fly research and drive advances in our understanding of conserved mechanisms of animal biology. Here, we provide an overview of this “ecosystem” and discuss how to address emerging challenges to ensure its continued productivity. Drosophila researchers are fortunate to have a sophisticated and ever-growing toolkit for the analysis of gene function. Access to these tools depends upon continued support for both physical and informational resources. Uncertainty regarding stable support for bioinformatic databases is a particular concern, at a time when there is the need to make the vast knowledge of functional biology provided by this model animal accessible to scientists studying other organisms. Communication and advocacy efforts will promote appreciation of the value of the fly in delivering biomedically important insights. Well-tended traditions of large-scale tool development, open sharing of reagents, and community engagement provide a strong basis for coordinated and proactive initiatives to improve the fly research ecosystem. Overall, there has never been a better time to be a fly pusher.
Controlling the surface wettability of the polymer dielectric for improved resolution of inkjet-printed electrodes and patterned channel regions in low-voltage solution-processed organic thin film transistors

A facile method for realizing both inkjet printed electrodes with improved resolution and patterned semiconductor islands was developed to fabricate all solution processed low-voltage organic thin film transistors (OTFTs). By reducing the surface wettability of the polymer gate dielectric layer through coating of a self-assembled monolayer (SAM), fine and narrow inkjet printed source/drain electrodes (a line width of about 35 μm) and short channels (about 15 μm) were formed with very good yield and uniformity using an inkjet printer with a 10 pL drop volume print head and limited registration accuracy. The coated SAM layer was then selectively removed by ultraviolet ozone treatment to create patterned wettable and less wettable regions to form self-assembled organic semiconductor islands. The fabricated low voltage OTFTs present a high quality semiconductor/dielectric interface and good device performance.
Dissociated repetition deficits in aphasia can reflect flexible interactions between left dorsal and ventral streams and gender-dimorphic architecture of the right dorsal stream

Assessment of brain-damaged subjects presenting with dissociated repetition deficits after selective injury to either the left dorsal or ventral auditory pathways can provide further insight on their respective roles in verbal repetition. We evaluated repetition performance and its neural correlates using multimodal imaging (anatomical MRI, DTI, fMRI, and18FDG-PET) in a female patient with transcortical motor aphasia (TCMA) and in a male patient with conduction aphasia (CA) who had small contiguous but non-overlapping left perisylvian infarctions. Repetition in the TCMA patient was fully preserved except for a mild impairment in nonwords and digits, whereas the CA patient had impaired repetition of nonwords, digits and word triplet lists. Sentence repetition was impaired, but he repeated novel sentences significantly better than clichés. The TCMA patient had tissue damage and reduced metabolism in the left sensorimotor cortex and insula. DTI showed damage to the left temporo-frontal and parieto-frontal segments of the arcuate fasciculus (AF) and part of the left ventral stream together with well-developed right dorsal and ventral streams, as has been reported in more than one-third of females. The CA patient had tissue damage and reduced metabolic activity in the left temporoparietal cortex with additional metabolic decrements in the left frontal lobe. DTI showed damage to the left temporo-parietal and temporo-frontal segments of the AF, but the ventral stream was spared. The direct segment of the AF in the right hemisphere was also absent with only vestigial remains of the other dorsal subcomponents present, as is often found in males. fMRI during word and nonword repetition revealed bilateral perisylvian activation in the TCMA patient suggesting recruitment of spared segments of the left dorsal stream and right dorsal stream with propagation of signals to temporal lobe structures suggesting a compensatory reallocation of resources via the ventral streams. The CA patient showed a greater activation of these cortical areas than the TCMA patient, but these changes did not result in normal performance. Repetition of word triplet lists activated bilateral perisylvian cortices in both patients, but activation in the CA patient with very poor performance was restricted to small frontal and posterior temporal foci bilaterally. These findings suggest that dissociated repetition deficits in our cases are probably reliant on flexible interactions between left dorsal stream (spared segments, short tracts remains) and left ventral stream and on gender-dimorphic architecture of the right dorsal stream.
On incentive compatibility of deadline differentiated pricing for deferrable demand

A large fraction of the total electric load is comprised of end-use devices whose demand is inherently deferrable in time. While this latent flexibility in demand can be leveraged to absorb variability in supply from renewable generation, the challenge lies in designing incentives to induce the desired response in demand. In the following, we study a novel forward market, where consumers consent to deferred service of pre-specified loads in exchange for a reduced per-unit price for energy. The longer a customer is willing to defer, the larger the reduction in price. The proposed deadline-differentiated forward contract provides a guarantee on the aggregate quantity to be delivered by a consumer-specified deadline. Under the earliest-deadline-first (EDF) scheduling policy, which is shown to be optimal for the supplier, we explicitly characterize differentiated prices yielding an efficient competitive equilibrium between supply and demand. We also show that such prices are incentive compatible (IC) in that every consumer would like to reveal her true deadline type to the supplier, provided that the other consumers are truth-telling.
Functional Neuroimaging Distinguishes Posttraumatic Stress Disorder from Traumatic Brain Injury in Focused and Large Community Datasets

Background Traumatic brain injury (TBI) and posttraumatic stress disorder (PTSD) are highly heterogeneous and often present with overlapping symptomology, providing challenges in reliable classification and treatment. Single photon emission computed tomography (SPECT) may be advantageous in the diagnostic separation of these disorders when comorbid or clinically indistinct. Methods Subjects were selected from a multisite database, where rest and on-task SPECT scans were obtained on a large group of neuropsychiatric patients. Two groups were analyzed: Group 1 with TBI (n=104), PTSD (n=104) or both (n=73) closely matched for demographics and comorbidity, compared to each other and healthy controls (N=116); Group 2 with TBI (n=7,505), PTSD (n=1,077) or both (n=1,017) compared to n=11,147 without either. ROIs and visual readings (VRs) were analyzed using a binary logistic regression model with predicted probabilities inputted into a Receiver Operating Characteristic analysis to identify sensitivity, specificity, and accuracy. One-way ANOVA identified the most diagnostically significant regions of increased perfusion in PTSD compared to TBI. Analysis included a 10-fold cross validation of the protocol in the larger community sample (Group 2). Results For Group 1, baseline and on-task ROIs and VRs showed a high level of accuracy in differentiating PTSD, TBI and PTSD+TBI conditions. This carefully matched group separated with 100% sensitivity, specificity and accuracy for the ROI analysis and at 89% or above for VRs. Group 2 had lower sensitivity, specificity and accuracy, but still in a clinically relevant range. Compared to subjects with TBI, PTSD showed increases in the limbic regions, cingulum, basal ganglia, insula, thalamus, prefrontal cortex and temporal lobes. Conclusions This study demonstrates the ability to separate PTSD and TBI from healthy controls, from each other, and detect their co-occurrence, even in highly comorbid samples, using SPECT. This modality may offer a clinical option for aiding diagnosis and treatment of these conditions.
Association of the single‐nucleotide polymorphism and haplotype of the interleukin 18 gene with atopic dermatitis in Koreans

Background IL‐18 is a proinflammatory cytokine that plays an important role for T‐helper type 1 (Th1) and Th2 cytokine in the presence/absence of IL‐12. It has been recently shown that human IL‐18 plays a role in atopic dermatitis (AD) by enhancing IL‐4 and IL‐13 production and by stimulating the synthesis of IgE.
A Rapid Technique Using Handheld Instrument for Mapping Corrosion of Steel in Reinforced Concrete / Eine Schnellmethode zur Bestimmung der örtlichen Verteilung der Korrosion des Stahles in bewehrtem Beton mit Hilfe eines Handgerätes

This paper presents a rapid technique using a handheld instrument for mapping corrosion of steel in reinforced concrete structures. The technique involves a short time galvanostatic pulse measurement followed with the numerical calculation of the effective polarization current from the measured ohmic and polarized potential responses, so as to be able to estimate the true values of ohmic and polarization resistances related to the confined area. Owing to its rapidity (in a few seconds per measurement), this technique provides a useful tool for mapping electrochemical characteristics of reinforcement steel in concrete structures, including half-cell potential, ohmic resistivity and corrosion rate. These three corrosion-related parameters supply better information to an inspector for condition assessment of reinforced concrete structures. The results from comparative measurements on both small and large reinforced concrete slabs show that the corrosion rate measured by the new developed rapid technique is quite comparable with that measured by the Spanish Gecor instrument, which uses the modulated confinement technique. The technique has been used in a number of real concrete structures. The results show that the corrosion extent measured by the new rapid technique is in reasonably good agreement with those by the other techniques and visual observations.
Single IFFT block based reduced complexity Partial Transmit Sequence technique for PAPR reduction in OFDM

This paper discusses a novel, reduced complexity implementation of the Partial Transmit Sequence technique (PTS) for reducing the Peak to Average Power Ratio (PAPR) of OFDM signals. The original PTS provides good PAPR reduction at the cost of computational complexity. The use of large number of IFFT blocks in PTS has been replaced by a single IFFT block. The parallel processing of the PTSs has been replaced by serial processing. Reducing the number of IFFT blocks and replacing parallel processing by serial processing reduces the computational complexity. The simulation results demonstrate that the proposed technique provides performance as good as standard PTS.
The HlyU Protein Is a Positive Regulator of rtxA1, a Gene Responsible for Cytotoxicity and Virulence in the Human Pathogen Vibrio vulnificus

ABSTRACT Vibrio vulnificus is an opportunistic human pathogen that preferentially infects compromised iron-overloaded patients, causing a fatal primary septicemia with very rapid progress, resulting in a high mortality rate. In this study we determined that the HlyU protein, a virulence factor in V. vulnificus CMCP6, up-regulates the expression of VV20479, a homologue of the Vibrio cholerae RTX (repeats in toxin) toxin gene that we named rtxA1. This gene is part of an operon together with two other open reading frames, VV20481 and VV20480, that encode two predicted proteins, a peptide chain release factor 1 and a hemolysin acyltransferase, respectively. A mutation in rtxA1 not only contributes to the loss of cytotoxic activity but also results in a decrease in virulence, whereas a deletion of VV20481 and VV20480 causes a slight decrease in virulence but with no effect in cytotoxicity. Activation of the expression of the rtxA1 operon by HlyU occurs at the transcription initiation level by binding of the HlyU protein to a region upstream of this operon.
Activation of the nuclear receptor PPARα regulates lipid metabolism in foetal liver from diabetic rats: implications in diabetes‐induced foetal overgrowth

Peroxisome proliferator‐activated receptor α (PPARα) is a crucial regulator of liver lipid metabolism. As maternal diabetes impairs foetal lipid metabolism and growth, we aimed to determine whether PPARα activation regulates lipid metabolism in the foetal liver from diabetic rats as well as foetal weight and foetal liver weight.
Outbreak column 17: Situational Awareness for healthcare outbreaks

Outbreak column 17 introduces the utility of Situation Awareness (SA) for outbreak management. For any given time period, an individual or team’s SA involves a perception of what is going on, meaning derived from the perception and a prediction of what is likely to happen next. The individual or team’s SA informs, but is separate to, both the decisions and actions that follow. The accuracy and completeness of an individual or team’s SA will therefore impact on the effectiveness of decisions and actions taken. SA was developed by the aviation industry and is utilised in situations which, like outbreaks, have dynamic, i.e. continuously changing problem spaces, and wherein a loss of SA is likely to lead to both poor decision-making and actions with potentially fatal consequences. The potential benefits of using SA for outbreaks are discussed and include: (1) retrospectively to identify if poor decision-making was a result of a poor SA; (2) prospectively to identify where the system is weakest; and (3) as a teaching tool to improve the skills of individuals and teams in developing a shared understanding of the here and now.
Modeling of Hybrid Damping Scheme Using Smart Magnetostrictive Composites for Flexible Manipulator

In this article a method called, hybrid damping has been proposed to check the high amplitude non-linear vibration within a desired limit using smart magnetostrictive composite materials. For this, a flexible manipulator of large length has been modeled using a finite element method (FEM) which compared the efficiency, computation time, and damping performance corresponding to different actuations. Hybrid damping is an interactive combination of active and passive damping. An active damping scheme is employed to control the induced strains in the passive damping coating. Smart magnetostrictive material, Terfenol-D, is used to achieve active damping in the link. Fabrication of Terfenol-D based composite actuator which is used in the experiment is also discussed. Such materials can be used as an intelligent distributed layer over the link to introduce distributed control of vibration. For passive damping, a layer of strain dependent nanocomposite damping material poly-ethylene poly-ethylene glycol (PPEPEG) is used. Mathematical modeling of hybrid damping is done following a FEM and integrated with the manipulator. Simulations are first done to demonstrate the effectiveness of vibration attenuation. Experiments are conducted to validate the simulation results. It is observed that the hybrid damping scheme is able to damp vibration in the manipulator efficiently.
Differential chromosome control of ploidy in the yeast Saccharomyces cerevisiae

In Saccharomyces cerevisiae, aneuploidy is well tolerated and stable. We analysed whether the induced loss of a disomic chromosome favours endo‐reduplication of the remaining chromosome or the cells prefer to retain the acquired euploidy. Chromosome VIII disomes and trisomes were tagged with GFP (green fluorescent protein), DsRed (red fluorescent protein) and BFP (blue fluorescent protein) integrated at the thr1 locus, using our newly designed STIK (specific targeted integration of kanamycin resistance‐associated, non‐selectable DNA) plasmid system. A knockout cassette for centromere 8 was constructed with the hygromycin‐B marker, which was transformed into the strains. The transformants lost sensitivity to hygromycin, thereby indicating the event of centromere replacement. Quantitative PCR and Southern analysis were performed for chromosome VIII copy number determination by probing the markers located on both the right (ARG4 and THR1) and left (GUT1) arm whereas, for chromosome V, markers such as HIS1, located on right arm, and URA3, on left arm, were used. The loss of an extranumerary chromosome VIII in a disome and trisome leads to stable euploidy. Furthermore, in a wild‐type diploid, deletion of a copy of chromosome VIII, leads to monosomy, and restoration of euploidy after 22 generations, by reduplication of chromosome VIII, and consequent loss of heterozygosis (LOH). However, chromosome V knockouts in chromosome VIII trisome, still showed LOH and duplication of chromosome V, with return to the original aneuploid condition. These results suggest that yeast cells could control the integrity of their genetic complement acting at the individual chromosome level. Copyright © 2005 John Wiley & Sons, Ltd.
A Proof-Theoretic Subsumption Reasoner for Hybrid EL-TBoxes

Hybrid EL-TBoxes combine general concept inclusions (GCIs), which are interpreted with descriptive semantics, with cyclic concept definitions, which are interpreted with greatest fixpoint (gfp) semantics. We introduce a proof-theoretic approach that yields a polynomial-time decision procedure for subsumption in EL w.r. t. hybrid TBoxes, and present preliminary experimental results regarding the performance of the reasoner Hyb that implements this decision procedure.