Miracle-dz/UniFAR-FTUs huggingface dataset:
Small flies to tackle big questions: assaying complex bacterial virulence mechanisms using Drosophila melanogaster

A successful raid on a fortress requires ingenious strategies in addition to a large number of soldiers. When a microorganism faces a potential host many factors are important, including not only the capacity to proliferate but also the ability to hide, escape or subvert the defence arsenal of the infected organism. This ability confers microbial pathogenicity and relies on complex virulence mechanisms, which are tightly regulated during the course of the infection. The amazing versatility of some microbes that can infect a wide broad of hosts undoubtedly relies on virulence factors intent on fighting evolutionarily conserved innate immune mechanisms. This makes the use of alternative invertebrate models, which are of outstanding interest because they demand less ethical consideration and lower experimental costs, extremely relevant. These simpler organisms are used to analyse genes and mechanisms involved in resistance or tolerance to microorganisms. They can also be used to study bacterial virulence factors that allow proliferation or persistence in the host. In particular, the Drosophila fruit fly has a complex immune response (similar to the mammalian innate immune response) and is particularly appropriate for deciphering many events underlying bacterial pathogenicity from acute virulence to biofilm formation. As highlighted in this review, Drosophila has been notably extensively used to study virulence traits of the opportunistic bacteria Pseudomonas aeruginosa, such as proliferation or persistence, translocation through an epithelial barrier, subversion of the phagocytic machinery, in vivo biofilm formation and enhanced virulence provided by commensal flora or a polymicrobial community. Moreover, these small flies now appear to be a useful system for assaying chemicals with therapeutic potential.
A Binaural CI Research Platform for Oticon Medical SP/XP Implants Enabling ITD/ILD and Variable Rate Processing

We present the first portable, binaural, real-time research platform compatible with Oticon Medical SP and XP generation cochlear implants. The platform consists of (a) a pair of behind-the-ear devices, each containing front and rear calibrated microphones, (b) a four-channel USB analog-to-digital converter, (c) real-time PC-based sound processing software called the Master Hearing Aid, and (d) USB-connected hardware and output coils capable of driving two implants simultaneously. The platform is capable of processing signals from the four microphones simultaneously and producing synchronized binaural cochlear implant outputs that drive two (bilaterally implanted) SP or XP implants. Both audio signal preprocessing algorithms (such as binaural beamforming) and novel binaural stimulation strategies (within the implant limitations) can be programmed by researchers. When the whole research platform is combined with Oticon Medical SP implants, interaural electrode timing can be controlled on individual electrodes to within ±1 µs and interaural electrode energy differences can be controlled to within ±2%. Hence, this new platform is particularly well suited to performing experiments related to interaural time differences in combination with interaural level differences in real-time. The platform also supports instantaneously variable stimulation rates and thereby enables investigations such as the effect of changing the stimulation rate on pitch perception. Because the processing can be changed on the fly, researchers can use this platform to study perceptual changes resulting from different processing strategies acutely.
Understanding object descriptions in robotics by open-vocabulary object retrieval and detection

We address the problem of retrieving and detecting objects based on open-vocabulary natural language queries: given a phrase describing a specific object, for example “the corn flakes box”, the task is to find the best match in a set of images containing candidate objects. When naming objects, humans tend to use natural language with rich semantics, including basic-level categories, fine-grained categories, and instance-level concepts such as brand names. Existing approaches to large-scale object recognition fail in this scenario, as they expect queries that map directly to a fixed set of pre-trained visual categories, for example ImageNet synset tags. We address this limitation by introducing a novel object retrieval method. Given a candidate object image, we first map it to a set of words that are likely to describe it, using several learned image-to-text projections. We also propose a method for handling open vocabularies, that is, words not contained in the training data. We then compare the natural language query to the sets of words predicted for each candidate and select the best match. Our method can combine category- and instance-level semantics in a common representation. We present extensive experimental results on several datasets using both instance-level and category-level matching and show that our approach can accurately retrieve objects based on extremely varied open-vocabulary queries. Furthermore, we show how to process queries referring to objects within scenes, using state-of-the-art adapted detectors. The source code of our approach will be publicly available together with pre-trained models at http://openvoc.berkeleyvision. org and could be directly used for robotics applications.
Herpes Simplex Virus 1 UL34 Protein Regulates the Global Architecture of the Endoplasmic Reticulum in Infected Cells

ABSTRACT Upon herpes simplex virus 1 (HSV-1) infection, the CD98 heavy chain (CD98hc) is redistributed around the nuclear membrane (NM), where it promotes viral de-envelopment during the nuclear egress of nucleocapsids. In this study, we attempted to identify the factor(s) involved in CD98hc accumulation and demonstrated the following: (i) the null mutation of HSV-1 UL34 caused specific dispersion throughout the cytoplasm of CD98hc and the HSV-1 de-envelopment regulators, glycoproteins B and H (gB and gH); (ii) as observed with CD98hc, gB, and gH, wild-type HSV-1 infection caused redistribution of the endoplasmic reticulum (ER) markers calnexin and ERp57 around the NM, whereas the UL34-null mutation caused cytoplasmic dispersion of these markers; (iii) the ER markers colocalized efficiently with CD98hc, gB, and gH in the presence and absence of UL34 in HSV-1-infected cells; (iv) at the ultrastructural level, wild-type HSV-1 infection caused ER compression around the NM, whereas the UL34-null mutation caused cytoplasmic dispersion of the ER; and (v) the UL34-null mutation significantly decreased the colocalization efficiency of lamin protein markers of the NM with CD98hc and gB. Collectively, these results indicate that HSV-1 infection causes redistribution of the ER around the NM, with resulting accumulation of ER-associated CD98hc, gB, and gH around the NM and that UL34 is required for ER redistribution, as well as for efficient recruitment to the NM of the ER-associated de-envelopment factors. Our study suggests that HSV-1 induces remodeling of the global ER architecture for recruitment of regulators mediating viral nuclear egress to the NM. IMPORTANCE The ER is an important cellular organelle that exists as a complex network extending throughout the cytoplasm. Although viruses often remodel the ER to facilitate viral replication, information on the effects of herpesvirus infections on ER morphological integrity is limited. Here, we showed that HSV-1 infection led to compression of the global ER architecture around the NM, resulting in accumulation of ER-associated regulators associated with nuclear egress of HSV-1 nucleocapsids. We also identified HSV-1 UL34 as a viral factor that mediated ER remodeling. Furthermore, we demonstrated that UL34 was required for efficient targeting of these regulators to the NM. To our knowledge, this is the first report showing that a herpesvirus remodels ER global architecture. Our study also provides insight into the mechanism by which the regulators for HSV-1 nuclear egress are recruited to the NM, where this viral event occurs.
APPLICATION Synchrony : quantifying variability in space and time

1. There is growing recognition that linking patterns to their underlying processes in interconnected and dynamic ecological systems requires data sampled atmultiple spatial and temporal scales. 2. However, spatially explicit and temporally resolved data sets can be difficult to analyze using classical statistical methods because the data are typically autocorrelated and thus violate the assumption of independence. 3. Here, we describe the synchrony package for the R programming environment, which provides modern parametric and nonparametric methods for (i) quantifying temporal and spatial patterns of autoand cross-correlated variability in univariate, bivariate, andmultivariate data sets, and (ii) assessing their statistical significance viaMonte Carlo randomizations. 4. We illustrate how the methods included in the package can be used to investigate the causes of spatial and temporal variability in ecological systems through a series of examples, and discuss the assumptions and caveats of each statistical procedure in order to provide a practical guide for their application in the real world.
A Forced Alignment Based Approach for English Passage Reading Assessment

SUMMARY This paper presents our investigation into improving the performance of our previous automatic reading quality assessment system. The method of the baseline system is calculating the average value of the Phone Log-Posterior Probability (PLPP) of all phones in the voice to be assessed, and the average value is used as the reading quality assessment feature. In this paper, we presents three improvements. First, we cluster the triphones, and then calculate the average value of the normalized PLPP for each classiﬁcation separately, and use this average values as the multi-dimensional assessment features instead of the original one-dimensional assessment feature. This method is simple but e ﬀ ective, which made the score di ﬀ erence of the machine scoring and manual scoring decrease by 30.2% relatively. Second, in order to assess the reading rhythm, we train Gaussian Mixture Models (GMM), which contain the information of each triphone’s relative duration under standard pronunciation. Using the GMM, we can calculate the probability that the relative duration of each phone is conform to the standard pronunciation, and the average value of the probabilities is added to the assessment feature vector as a dimension of feature, which decreased the score di ﬀ erence between the machine scoring and manual scoring by 9.7% relatively. Third, we detect Filled Pauses (FP) by analyzing the formant curve, and then calculate the relative duration of FP, and add the relative duration of FP to the assessment feature vector as a dimension of feature. This method made the score di ﬀ erence between the machine scoring and manual scoring be further decreased by 10.2% relatively. Finally, when the feature vector extracted by the three methods are used together, the score di ﬀ erence between the machine scoring and manual scoring was decreased by 43.9% relatively compared to the baseline system. key words: CALL, automatic assessment, forced alignment, formant
Multiview Shooting Geometry for Multiscopic Rendering with Controlled Distortion

A fundamental element of stereoscopic and/or autostereoscopic image production is the geometrical analysis of the shooting and viewing conditions in order to obtain a qualitative 3D perception experience. This paper firstly compares the perceived depth with the shot scene depth from the viewing and shooting geometries for a couple of shooting and rendering devices. This yields a depth distortion model whose parameters are expressed from the geometrical characteristics of shooting and rendering devices. Secondly, these expressions are inverted in order to design convenient shooting layouts yielding chosen distortions on specific rendering devices. Thirdly, this design scheme provides three shooting technologies (3D computer graphics software, photo rail, and camera box system) producing qualitative 3D content for various kinds of scenes (real or virtual, still or animated), complying with any prechosen distortion when rendered on any specific multiscopic technology or device formerly specified.
Estrogen-induced gonadotropin release in ovariectomized rhesus monkeys and its advancement by progesterone.

The effects of estradiol-17 3 (E2) and progesterone (P), administered sc in silastic capsules, on the serum levels of LH and FSH were studied oven four days in two groups of intact rhesus monkeys on days 3 to 9 of the intermenstrual period and in ovaniectomized (ovx) animals. In the intact females (N = 5, Group 1), simultaneous LH and FSH surges occurred approximately 48 h after E2 treatment was begun (serum E2 levels of 200 to 400 pg/mI). With this same E2 treatment was accompanied by P (serum levels of 4 to 6 ng/ml, Group 2), LH release was blocked in 6 of 6 animals. In ovx animals (N = 9, Group 3), E2 alone produced an LH surge at 72 h (P>0.05 Group 1 vs 3), and a slight release of FSH with LH in 6 of the 9 animals. P administered simultaneously with E2 to these same ovx animals (Group 4) advanced (P<0.01 Group 3 vs 4) rather than blocked the LH surge. LH release occurred at 30 h and was again accompanied by a slight elevation of FSH in 4 of the 9 animals. P also failed to block the LH surge in 7 of 8 ovx animals pretreated for 11 days with 50 to 100 pg/mI of E2 (Group 5). Again the LH surge was advanced (P<0.01 Group 3 vs 5) to approximately 30 h and under these circumstances was accompanied by a distinct release of FSH. Th se data show that P advances the E2 -induced release of LH in ovx rhesus monkeys. In intact females, however, it produces a different effect which cannot be replicated in ovx animals treated with tonic levels of 50 to 100 pg/mI E2 for two weeks.
From Reference Model to Component Model

Stable component models are an essential prerequisite for developingcustomer-individual business applications. Thereby the information for theidentification and specification of their components is gained from domainmodels. Reference models constitute a potential source for building enterprisespecificdomain models. Based on the analysis of existing reference models,this article shows how information available through reference models can beused for the development of stable component models. The derivation ofinformation required for the identification and specification of reusablebusiness components is discussed using example reference modellingtechniques. Additionally, potential extensions of existing reference modellingtechniques are shown.
Single-Filter Structure With Tunable Operating Frequency in Noncontiguous Bands

In this paper, we present a frequency-tunable substrate-integrated waveguide bandpass filter of which the operating frequency band can be switched between S-band and X-band. One of unique features of the presented filter is that a single-filter structure can replace a filter bank composed of an S-band filter, an X-band filter, and two switches at input and output ports for selecting one of two filters. In addition, the filter can tune the center frequency in each band. This paper provides the design method, fabrication, and measurement of the presented filter structure.
Microarray analysis of Mu transposition in Salmonella enterica, serovar Typhimurium: transposon exclusion by high‐density DNA binding proteins

All organisms contain transposons with the potential to disrupt and rearrange genes. Despite the presence of these destabilizing sequences, some genomes show remarkable stability over evolutionary time. Do bacteria defend the genome against disruption by transposons? Phage Mu replicates by transposition and virtually all genes are potential insertion targets. To test whether bacteria limit Mu transposition to specific parts of the chromosome, DNA arrays of Salmonella enterica were used to quantitatively measure target site preference and compare the data with Escherichia coli. Essential genes were as susceptible to transposon disruption as non‐essential ones in both organisms, but the correlation of transposition hot spots among homologous genes was poor. Genes in highly transcribed operons were insulated from transposon mutagenesis in both organisms. A 10 kb cold spot on the pSLT plasmid was near parS, a site to which the ParB protein binds and spreads along DNA. Deleting ParB erased the plasmid cold spot, and an ectopic parS site placed in the Salmonella chromosome created a new cold spot in the presence of ParB. Our data show that competition between cellular proteins and transposition proteins on plasmids and the chromosome is a dominant factor controlling the genetic footprint of transposons in living cells.
A hybrid power system using alternative energy facilities in isolated island

A hybrid power system uses many wind turbine generators in isolated small islands. The output power of wind turbine generators is mostly fluctuating and has an effect on system frequency. In order to solve this problem, we propose a new power system using renewable energy in small, isolated islands. The system can supply high-quality power using an aqua electrolyzer, fuel cell, renewable energy, and diesel generator. The generated hydrogen by an aqua electrolyzer is used as fuel for a fuel cell. The simulation results are given to demonstrate the availability of the proposed system in this paper.
Frame-based SAR processing and automatic moving targets parameters extraction

Synthetic aperture radar is a very popular and widely used instrument for various remote sensing tasks. In the paper, we propose several novel ideas for improvement of the efficiency of the modern SAR systems. At first, the problem of the automatic image stitching is considered. Instead of the common cross-correlation based solution the local features detection and description techniques are proposed. Secondly, we analyze the problem of the moving target parameters estimation. It is shown that the optical flow techniques can be used for the automatic extraction of the moving target shifts from the sequence of SAR looks. Experimental examples with real SAR data are illustrated and comprehensively discussed.
Circuit optimization for minimisation of power consumption under delay constraint

We address the problem of optimization of VLSI circuits to minimize power consumption while meeting performance goals. We present a method of estimating power consumption of a basic or complex CMOS gate which takes the internal capacitances of the gate into account. This method is used to select an ordering of series-connected transistors found in CMOS gates to achieve lower power consumption. We describe a multipass algorithm which makes use of transistor reordering to optimize performance and power consumption of circuits and which has a linear time complexity per pass. The algorithm has been benchmarked on several large examples and the results are presented.
Acoustic Word Embeddings for ASR Error Detection

This paper focuses on error detection in Automatic Speech Recognition (ASR) outputs. A neural network architecture is proposed, which is well suited to handle continuous word representations, like word embeddings. In a previous study, the authors explored the use of linguistic word embeddings, and more particularly their combination. In this new study, the use of acoustic word embeddings is explored. Acoustic word embeddings offer the opportunity of an a priori acoustic representation of words that can be compared, in terms of similarity, to an embedded representation of the audio signal. First, we propose an approach to evaluate the intrinsic performances of acoustic word embeddings in comparison to orthographic representations in order to capture discriminative phonetic information. Since French language is targeted in experiments, a particular focus is made on homophone words. Then, the use of acoustic word embeddings is evaluated for ASR error detection. The proposed approach gets a classification error rate of 7.94% while the previous state-of-the-art CRFbased approach gets a CER of 8.56% on the outputs of the ASR system which won the ETAPE evaluation campaign on speech recognition of French broadcast news.
Autoimmune liver diseases and inflammatory bowel diseases in children: current issues and future perspectives

Abstract Inflammatory bowel diseases (IBDs) represent a group of intestinal disorders with a chronic and relapsing inflammation of the gut, and with a potential risk of systemic involvement of other organs and systems. Over the pediatric age, an incidence higher than 20% of developing extraintestinal manifestation during follow-up has been reported. The liver and the biliary system are frequently involved, and primary sclerosing cholangitis (PSC) is the most predominant entity with an incidence rate of 6.4–7.8% in children. PSC recognizes a multifactorial pathogenesis, and so far a not fully known mechanism for this association. The peculiar phenotype and the distinct clinical course of patients with IBD and PSC-associated make this ‘linkage’ an attractive study model to better understand mechanisms underlying these diseases. Approaching to these patients is complex and multidisciplinary, and a unique therapeutic strategy has not been standardized yet. New medications are being studied; however, further studies are needed to fully understand the pathogenesis and to improve the care of these patients. The aim of this paper is to review the recent literature regarding hepatobiliary involvement in IBD patients, with particular attention to PSC, and to provide the latest information for a correct diagnosis and appropriate management.
Mitochondrial fission is required for cardiomyocyte hypertrophy via a Ca 2 +-calcineurin signalling pathway

∞Corresponding authors: Dr. Beverly A Rothermel. Department of Internal Medicine (Cardiology Division), University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8573, USA. Tel: +1-214-6487429; E-mail: Beverly.Rothermel@UTSouthwestern.eduor Dr. Sergio Lavandero. Advanced Center for Chronic Diseases (ACCDiS), Facultad Ciencias Quimicas y Farmaceuticas &, Facultad de Medicina, Universidad de Chile, Olivos 1007, Santiago 8380492, Chile. Tel. +562-2978 2919; E-mail: slavander@uchile.cl
Performance evaluation of the universal filtered multi-carrier communications under various multipath fading propagation conditions

The Universal filtered multi-carrier (UFMC) which filtering successive sub-bands for supporting sliced spectrum is one of the enabling approaches for the fifth generation (5G) mobile networks. The UFMC system not only provides a flexibility of filtering arbitrary number of subcarriers to diminish out of band (OoB) leakage, but also maintains the orthogonality between subbands and subcarriers inside one sub-band at the same time. The simulation is conducted that utilizing the physical downlink shared channel (PDSCH) processing of the long-term evolution (LTE) system with the UFMC and orthogonal frequency-division multiplexing (OFDM) schemes under various multipath fading propagation conditions.