Miracle-dz/UniFAR-FTUs huggingface dataset:
Basic Research on Explosive Forming of Magnesium Alloy Plate

This study has investigated the plastic forming of magnesium alloys plate. It is not easy to perform the cold-worked with the usual plastic forming method although magnesium alloys have the advantages in terms of strength-to-weight ratio. Therefore, explosive forming method which is one of the plastic forming methods with a specific forming mechanism has been applied. At first, numerical simulations have been conducted to clarify the optimal combination conditions, and then we have verified practical effectiveness of this proposed method by using experimental study.
TANK-Binding Kinase-1 Plays an Important Role during In Vitro and In Vivo Type I IFN Responses to DNA Virus Infections1

TANK-binding kinase-1 (TBK1) and the inducible IκB kinase (IKK-i) have recently been shown to activate type I IFN responses elicited by intracellular detection of RNA or DNA from infecting viruses. Detection of viral RNA is mediated by retinoic acid inducible gene-I or melanoma differentiation-associated gene-5 pathways in which TBK1 and IKK-i have been demonstrated to play redundant roles in IFN activation. In this study, we have examined whether such redundancy occurs in the type I IFN response to DNA viral challenges by examining induction of IFNs and IFN-mediated signaling and gene programs in TBK1−/− macrophages. In contrast to the normal IFN responses in TBK1−/− macrophages infected with an RNA virus, IFN responses were severely abrogated during DNA virus infections in TBK1−/− macrophages. Because both TBK1 and IKK-i are expressed in macrophages, our studies suggest that TBK1 and IKK-i differ functionally in DNA virus-mediated IFN responses; however, they are redundant in RNA virus-mediated IFN responses. Confirmatively, reconstitution of TBK1−/−IKK-i−/− fibroblasts revealed that TBK1 rescued IFN responses to transfected B-DNA to a much stronger degree than IKK-i. Finally, we demonstrate the requirement for the TBK1-IFN regulatory factor-3 pathway in host defense against a DNA virus infection in vivo.
Auditory Sketches: Very Sparse Representations of Sounds Are Still Recognizable

Sounds in our environment like voices, animal calls or musical instruments are easily recognized by human listeners. Understanding the key features underlying this robust sound recognition is an important question in auditory science. Here, we studied the recognition by human listeners of new classes of sounds: acoustic and auditory sketches, sounds that are severely impoverished but still recognizable. Starting from a time-frequency representation, a sketch is obtained by keeping only sparse elements of the original signal, here, by means of a simple peak-picking algorithm. Two time-frequency representations were compared: a biologically grounded one, the auditory spectrogram, which simulates peripheral auditory filtering, and a simple acoustic spectrogram, based on a Fourier transform. Three degrees of sparsity were also investigated. Listeners were asked to recognize the category to which a sketch sound belongs: singing voices, bird calls, musical instruments, and vehicle engine noises. Results showed that, with the exception of voice sounds, very sparse representations of sounds (10 features, or energy peaks, per second) could be recognized above chance. No clear differences could be observed between the acoustic and the auditory sketches. For the voice sounds, however, a completely different pattern of results emerged, with at-chance or even below-chance recognition performances, suggesting that the important features of the voice, whatever they are, were removed by the sketch process. Overall, these perceptual results were well correlated with a model of auditory distances, based on spectro-temporal excitation patterns (STEPs). This study confirms the potential of these new classes of sounds, acoustic and auditory sketches, to study sound recognition.
Feasibility of high pressure freezing with freeze substitution after long‐term storage in chemical fixatives

Fixation of biological samples is an important process especially related to histological and ultrastructural studies. Chemical fixation was the primary method of fixing tissue for transmission electron microscopy for many years, as it provides adequate preservation of the morphology of cells and organelles. High pressure freezing (HPF) and freeze substitution (FS) is a newer alternative method that rapidly freezes non‐cryoprotected samples that are then slowly heated in the FS medium, allowing penetration of the tissue to insure adequate fixation. This study addresses several issues related to tissue preservation for electron microscopy. Using mice liver tissue as model the difference between samples fixed chemically or with HPF immediately after excision, or stored before chemical or HPF fixation were tested with specific focus on the nuclear membrane. Findings are that immediate HPF is the method of choice compared to chemical fixation. Of the chemical fixatives, immediate fixation with 2.5% glutaraldehyde (GA)/formaldehyde (FA) is the best in preserving membrane morphology, 2.5% GA can be used as alternative for stored and then chemically processed samples, with 10% formalin being suitable as a storage medium only if followed by HPF fixation. Overall, storage leads to lower ultrastructural preservation, but HPF with FS can minimize these artifacts relative to other processing protocols. Microsc. Res. Tech. 76:942–946, 2013. © 2013 Wiley Periodicals, Inc.
Wiring variations that enable and constrain neural computation in a sensory microcircuit

Neural network function can be shaped by varying the strength of synaptic connections. One way to achieve this is to vary connection structure. To investigate how structural variation among synaptic connections might affect neural computation, we examined primary afferent connections in the Drosophila olfactory system. We used large-scale serial section electron microscopy to reconstruct all the olfactory receptor neuron (ORN) axons that target a left-right pair of glomeruli, as well as all the projection neurons (PNs) postsynaptic to these ORNs. We found three variations in ORN→PN connectivity. First, we found a systematic co-variation in synapse number and PN dendrite size, suggesting total synaptic conductance is tuned to postsynaptic excitability. Second, we discovered that PNs receive more synapses from ipsilateral than contralateral ORNs, providing a structural basis for odor lateralization behavior. Finally, we found evidence of imprecision in ORN→PN connections and show how this can diminish network performance.
α-N-Methylation of Damaged DNA-binding Protein 2 (DDB2) and Its Function in Nucleotide Excision Repair*

Background: Because its N terminus adopts an APK motif, DDB2 might be α-N-methylated. Results: We examined the nature of DDB2 α-N-methylation, the enzyme involved in this methylation and its function in DNA repair. Conclusion: DDB2 could be α-N-methylated by NRMT, and this methylation facilitated the recruitment of DDB2 to DNA damage foci. Significance: This work expands the function of protein α-N-methylation to DNA repair. DDB2 exhibits a high affinity toward UV-damaged DNA, and it is involved in the initial steps of global genome nucleotide excision repair. Mutations in the DDB2 gene cause the genetic complementation group E of xeroderma pigmentosum, an autosomal recessive disease manifested clinically by hypersensitivity to sunlight exposure and an increased predisposition to skin cancer. Here we found that, in human cells, the initiating methionine residue in DDB2 was removed and that the N-terminal alanine could be methylated on its α-amino group in human cells, with trimethylation being the major form. We also demonstrated that the α-N-methylation of DDB2 is catalyzed by the N-terminal RCC1 methyltransferase. In addition, a methylation-defective mutant of DDB2 displayed diminished nuclear localization and was recruited at a reduced efficiency to UV-induced cyclobutane pyrimidine dimer foci. Moreover, loss of this methylation conferred compromised ATM (ataxia telangiectasia mutated) activation, decreased efficiency in cyclobutane pyrimidine dimer repair, and elevated sensitivity of cells toward UV light exposure. Our study provides new knowledge about the posttranslational regulation of DDB2 and expands the biological functions of protein α-N-methylation to DNA repair.
Starcode: sequence clustering based on all-pairs search

Motivation: The increasing throughput of sequencing technologies offers new applications and challenges for computational biology. In many of those applications, sequencing errors need to be corrected. This is particularly important when sequencing reads from an unknown reference such as random DNA barcodes. In this case, error correction can be done by performing a pairwise comparison of all the barcodes, which is a computationally complex problem. Results: Here, we address this challenge and describe an exact algorithm to determine which pairs of sequences lie within a given Levenshtein distance. For error correction or redundancy reduction purposes, matched pairs are then merged into clusters of similar sequences. The efficiency of starcode is attributable to the poucet search, a novel implementation of the Needleman–Wunsch algorithm performed on the nodes of a trie. On the task of matching random barcodes, starcode outperforms sequence clustering algorithms in both speed and precision. Availability and implementation: The C source code is available at http://github.com/gui11aume/starcode. Contact: guillaume.filion@gmail.com
PIIN Suppression Using Random Diagonal Code for Spectral Amplitude Coding Optical CDMA System

A new code for spectral-amplitude coding optical code-division multiple-access system is proposed called Random diagonal (RD) code. This code is constructed using code segment and data segment. One of the important properties of this code is that the cross correlation at data segment is always zero, which means that Phase Intensity Induced Noise (PIIN) is reduced. For the performance analysis, the effects of phase-induced intensity noise, shot noise, and thermal noise are considered simultaneously. Bit-error rate (BER) performance is compared with Hadamard and Modified Frequency Hopping (MFH) codes. It is shown that the system using this new code matrices not only suppress PIIN, but also allows larger number of active users compare with other codes. Simulation results shown that using point to point transmission with three encoded channels, RD code has better BER performance than other codes, also its found that at 0 dbm PIIN noise are 10 -10 and 10 -11 for RD and MFH respectively. Keywords—OCDMA, MFH, PIIN, and BER.
Definition and specification of accrual failure detectors

For many years, people have been advocating the development of failure detection as a basic service, but, unfortunately, without meeting much success so far. We believe that this comes from the fact that important system engineering issues have not yet been addressed adequately, thus preventing the definition of a truly generic service. Ultimately, our goal is to define a service that is both simple and expressive, yet powerful enough to support the requirements of many distributed applications. To this end, we consider an alternative interaction model between the service and the applications, called accrual failure detectors. Roughly, an accrual failure detector associates to each process a real value representing a suspicion level, instead of the traditional binary information (i.e., trust vs. suspect). In this paper, we provide a rigorous definition for accrual failure detectors, demonstrate that changing the interaction model leads to no loss in computational power, discuss quality of service issues, and present several possible implementations.
Infrared High-Index Coating Materials, PbTe and Pb1−xGexTe: Properties and Applications

The greater value of refractive index for high-index layers in thin-film interference filters operating in the infrared has an incomparable advantage. Lead telluride (PbTe), which is much superior to other infrared high-index coating materials due to its high index and advantage of fundamental absorption edges, has played an important role in filters employed in the infrared radiometer and other instruments launched in space atmosphere sounding research projects. In this chapter, we summarized some recent achievements in the investigations into another infrared high-index coating material — lead germanium telluride (Pb 1 (cid:1) x Ge x Te), a pseudo-binary alloy of PbTe and GeTe. It can be revealed that the layers of Pb 1 (cid:1) x Ge x Te exhibit the tunable optical properties, such as temperature coefficient of refractive index and fundamental absorption edge, as well as mechanical properties, such as the hardness and Young ’ s modulus, corresponding to its intrinsic ferroelectric phase transition. Some important applications in thin-film interference filters were also demonstrated for its tremendous potential, such as a stable narrow bandpass interference filter without temperature-induced wavelength shift and a tunable infrared short wavelength cutoff filter. Furthermore, it is also revealed that electron beam evaporation is a more effective congruent-transfer technique to deposit the layers of Pb 1 (cid:1) x Ge x Te.
Comparison of Histopathological Findings with Duplex Sonography of the Temporal Arteries in Suspected Giant Cell Arteritis

Abstract Introduction: In clinical practice the temporal artery biopsy (TAB) in suspected giant cell arteritis (GCA) is still believed to be the “gold standard”. The purpose of this study was to compare the histopathological findings of the TAB with duplex sonography of the temporal artery. Patients and Methods: In our retrospective study we analysed 85 consecutive patients (52 female, mean age 71.5, range 55 – 91 years; 33 male, mean age 71.6, range 44 – 91 years) with suspected GCA who underwent TAB in our clinic between January 1999 – February 2011. All patients received a preoperative duplex sonography, 57 patients including description of the temporal arteries. Results: 38 of 85 (44.7 %) of the artery biopsies were proven positive for GCA by histopathology. Interpretation of the duplex sonography was congruent of histopathological interpretation of the biopsy in 39 patients (68.4 %) and incongruent in 18 patients (31.6 %). Sensitivity of duplex-sonography was 44.4 %, specificity 90 %, positive predictive value 80 %. Discussion: Duplex sonography is a non-invasive and very helpful diagnostic tool to guide the clinician in cases of suspected GCA but needs considerable skills. It shows a good specificity and relatively high positive predictive value as there are only few false positive results. A negative report however does not rule out GCA, so that in our opinion the TAB – at least in those cases – should still be performed.
The inhibition of IGF‐1 signaling promotes proteostasis by enhancing protein aggregation and deposition

The discovery that the alteration of aging by reducing the activity of the insulin/IGF‐1 signaling (IIS) cascade protects nematodes and mice from neurodegeneration‐linked, toxic protein aggregation (proteotoxicity) raises the prospect that IIS inhibitors bear therapeutic potential to counter neurodegenerative diseases. Recently, we reported that NT219, a highly efficient IGF‐1 signaling inhibitor, protects model worms from the aggregation of amyloid b peptide and polyglutamine peptides that are linked to the manifestation of Alzheimer's and Huntington's diseases, respectively. Here, we employed cultured cell systems to investigate whether NT219 promotes protein homeostasis (proteostasis) in mammalian cells and to explore its underlying mechanisms. We found that NT219 enhances the aggregation of misfolded prion protein and promotes its deposition in quality control compartments known as “aggresomes. ” NT219 also elevates the levels of certain molecular chaperones but, surprisingly, reduces proteasome activity and impairs autophagy. Our findings show that IGF‐1 signaling inhibitors in general and NT219 in particular can promote proteostasis in mammalian cells by hyperaggregating hazardous proteins, thereby bearing the potential to postpone the onset and slow the progression of neurodegenerative illnesses in the elderly. —Moll, L. , Ben‐Gedalya, T. , Reuveni, H. , Cohen, E. The inhibition of IGF‐1 signaling promotes proteostasis by enhancing protein aggregation and deposition. FASEB J. 30, 1656–1669 (2016). www.fasebj. org
A phase I factorial design study of dose-dense temozolomide alone and in combination with thalidomide, isotretinoin, and/or celecoxib as postchemoradiation adjuvant therapy for newly diagnosed glioblastoma

External beam radiation therapy (XRT) with concomitant temozolomide and 6 cycles of adjuvant temozolomide (5/28-day schedule) improves survival in patients with newly diagnosed glioblastoma compared with XRT alone. Studies suggest that dose-dense temozolomide schedules and addition of cytostatic agents may further improve efficacy. This factorial design phase I/II protocol tested dose-dense temozolomide alone and combined with cytostatic agents. Patients with newly diagnosed glioblastoma received fractionated XRT to 60 Gy concomitant with temozolomide (75 mg/m2/day for 42 days). In the phase I portion, patients with stable disease or radiologic response 1 month after chemoradiation were randomized to adjuvant temozolomide alone (150 mg/m2/day, 7/14-day schedule) or with doublet combinations of thalidomide (400 mg/day), isotretinoin (100 mg/m2/day), and/or celecoxib (400 mg twice daily), or all 3 agents. Toxicity was assessed after 4 weeks. Among 54 patients enrolled (median age, 52 years; median Karnofsky performance status, 90), adjuvant treatment was not administered to 12 (22%), primarily because of disease progression (n = 10). All combinations were well tolerated. Grade 3/4 lymphopenia developed in 63% of patients, but no related infections occurred. One patient treated with temozolomide plus isotretinoin plus thalidomide had dose-limiting grade 3 fatigue and rash, and 1 patient receiving all 4 agents had dose-limiting grade 4 neutropenia. Venous thrombosis occurred in 7 patients, 4 of whom received thalidomide. From study entry, median survival was 20 months and the 2-year survival rate was 40%. Multiple cytostatic agents can be safely combined with dose-dense temozolomide. The factorial-based phase II portion of this study is currently ongoing.
Transform features for texture classification and discrimination in large image databases

Proposes a method for classification and discrimination of textures based on the energies of image subbands. The authors show that with this relatively simple feature set, effective texture discrimination can be achieved. In the paper, subband-energy feature sets extracted from the following typical image decompositions are compared: wavelet subband, uniform subband, discrete cosine transform (DCT), and spatial partitioning. The authors report that over 90% correct classification was attained using the feature set in classifying the full Brodatz [1965] collection of 112 textures. Furthermore, the subband energy-based feature set can be readily applied to a system for indexing images by texture content in image databases, since the features can be extracted directly from spatial-frequency decomposed image data. The authors also show that to construct a suitable space for discrimination, Fisher discrimination analysis (Dillon and Goldstein, 1984) can be used to compact the original features into a set of uncorrelated linear discriminant functions. This procedure makes it easier to perform texture-based searches in a database by reducing the dimensionality of the discriminant space. The authors also examine the effects of varying training class size, the number of training classes, the dimension of the discriminant space and number of energy measures used for classification. The authors hope that the performance for texture discrimination of these simple energy-based features will allow images in a database to be efficiently and effectively indexed by contents of their textured regions. <<ETX>>
The carbon source influences the efflux pump-mediated antimicrobial resistance in clinically important Gram-negative bacteria.

OBJECTIVES Multidrug efflux pumps are proteins known to play an important role in resistance in bacteria. These proteins are located in the inner membrane (IM), together with many other proteins, including inducible permeases that participate in the uptake of non-phosphotransferase system (PTS) carbohydrates (i.e. carbohydrates uptaken by mechanisms other than the PTS). However, lipid bilayer space in the IM is limited. Therefore, we examined whether the overexpression of unrelated IM proteins is able to interfere with the efflux-mediated resistance mechanism, consequently increasing the susceptibility towards different antimicrobial compounds. METHODS We cultured bacteria under different conditions that increase the synthesis of unrelated IM proteins, either by using a non-PTS carbohydrate as the sole carbon source or by artificially overexpressing IM proteins, prior to determining the resistance to different antimicrobial compounds by disc diffusion assays. RESULTS We observed that efflux-pump-mediated resistance is affected by the carbon source in all the strains tested, exhibiting increased susceptibility when a non-PTS carbohydrate was used as the sole carbon source. Moreover, when we artificially overexpressed an unrelated IM protein, we also observed decreased efflux-mediated resistance. CONCLUSIONS These results strongly suggest that overexpression of IM proteins, by using a non-PTS carbohydrate as the sole carbon source, or by artificially introducing a high number of copies of an unrelated IM protein, competes with the antibiotic efflux systems, thereby decreasing the efflux-mediated resistance to different antimicrobial compounds. This sort of competition arises because of the limited available space in the bacterial IM, or by an unknown mechanism.
A Swarm-inspired Technique for Self-Organizing and Consolidating Data Centre Servers

This paper proposes a swarm-inspired data centre self-organizing and consolidation technique which aims at reducing the power demand in data centres while ensuring the workload execution within the established performance parameters. Each data centre server is managed by an intelligent agent that implements a bird's migration-inspired behaviour to decide on the appropriate server consolidation actions. The selected actions are executed to achieve an optimal utilization of server computing resources thus lowering power demand. The data centre servers self-organize in logical clusters according to the birds V-formation self-organizing migration model. The results are promising showing that by using the proposed swarm-inspired solution, the data centre Deployed Hardware Utilization Ratio Green Indicator increases compared to the widely used Fit First consolidation algorithm. The average power saving of the proposed technique is around 40% of the power demanded by the data centre computing resources and about 16% of its total power demand including the IT facility, when comparing to OpenNebula Fit First consolidation technique. This paper is an extended version of the one published in WIMS'12 proceedings showing more details about the swarm-inspired consolidation technique and the defined algorithms.
Attitude control of a quadrotor

This study includes altitude stabilization, hovering control any desired position and attitude control of quadrotor. Classically PD controller derived and applied to this system. Inverse dynamic control, feedback linearization control and sliding mode control methods have used to derive as nonlinear controllers. Linear and nonlinear control techniques applied to attitude control of this vehicle. Derived control methods have been performed using computer simulations and compared the results according to this study objective.