Miracle-dz/UniFAR-FTUs huggingface dataset:
Research proposal : Evaluating multi-modal deep learning systems with microworlds

My research focuses on the evaluation of multi-modal deep neural networks with respect to various symbolic/linguistic understanding and generalisation abilities. Instead of real-world data, I work on a system which automatically generates artificial toy data by randomly sampling an internal world model representation. Although simple, their structural complexity is still sufficient to generate a broad variety of interesting instances involving many aspects of language. In contrast to the classic image captioning task, a deep network here is asked to decide about the agreement of a given statement and the presented image. By controlling the content of training and test instances, I make sure that achieving good performance clearly indicates the learning of genuine concept understanding. Moreover, such a setup makes a more detailed investigation of the process and content of learning possible.
Generación automática de resümenes personalizados

En la actualidad los servicios de informacion presentes en la Web y en particular los periodicos digitales ofrecen a los usuarios una seleccion de documentos basada en criterios bastante simples que lleva a los usuarios a recibir una gran cantidad de informacion irrelevante. Nuestro trabajo pretende disminuir la sobrecarga de los usuarios de dos maneras: aportando un modelo de usuario mas completo que permita definir mejor los intereses de los usuarios y construyendo un generador de resumenes automatico que permita al usuario detectar las noticias que realmente le interesan mediante la visualizacion de resumenes adaptados a su modelo. Se han obtenido resultados alentadores en una evaluacion de los distintos tipos de resumenes para varios modelos de usuario. El trabajo esta enmarcado dentro del sistema Hermes, un enviador personalizado de noticias que maneja informacion en ingles y en espanol.
Lesional CD4+ IFN-γ+ cytotoxic T lymphocytes in IgG4-related dacryoadenitis and sialoadenitis

Objectives IgG4-related disease (IgG4-RD) is a chronic, systemic, inflammatory condition of unknown aetiology. We have recently described clonally expanded circulating CD4+ cytotoxic T lymphocytes (CTLs) in IgG4-RD that infiltrate affected tissues where they secrete interleukin (IL)-1β and transforming growth factor -β1 (TGF-β1). In this study, we sought to examine the role of CD4+ CTLs in the pathogenesis of IgG4-related dacryoadenitis and sialoadenitis (IgG4-DS) and to determine whether these cells secrete interferon-gamma (IFN-γ) at lesional sites. Methods Salivary glands of 25 patients with IgG4-DS, 22 patients with Sjögren's syndrome (SS), 12 patients with chronic sialoadenitis (CS) and 12 healthy controls were analysed in this study. Gene expression analysis was performed on submandibular glands (SMGs) from five patients with IgG4-DS, three with CS and three healthy controls. Infiltrating CD4+ CTLs were examined by quantitative multicolour imaging in tissue samples from 20 patients with IgG4-DS, 22 patients with SS, 9 patients with CS and 9 healthy controls. Results In IgG4-DS tissues, nine genes associated with CD4+ CTLs were overexpressed. The expression of granzyme A (GZMA) mRNA was significantly higher in samples from patients with IgG4-RD compared with corresponding tissues from SS and healthy controls. Quantitative imaging showed that infiltrating CD4+ GZMA+ CTLs were more abundant in patients with IgG4-DS than in the other groups. The ratio of CD4+GZMA+ CTLs in SMGs from patients with IgG4-DS correlated with serum IgG4 concentrations and the number of affected organs. A large fraction of CD4+GZMA+ CTLs in SMGs from patients with IgG4-DS secreted IFN-γ. Conclusions The pathogenesis of IgG4-DS is associated with tissue infiltration by CD4+GZMA+ CTLs that secrete IFN-γ.
A simple protocol for deniable authentication based on ElGamal cryptography

Deniable authentication is different from traditional authentication in that the receiver cannot prove the source of a given message to a third party. This article presents a new deniable authentication protocol, based on ElGamal cryptography. The protocol meets the two properties of deniable authentication and can withstand person‐in‐middle (PIM) attacks. Compared with previous schemes, it is simpler and more efficient. © 2005 Wiley Periodicals, Inc. NETWORKS, Vol. 45(4), 193–194 2005
Permittivity and tan delta characteristics of epoxy nanocomposites in the frequency range of 1 MHz-1 GHz

To achieve a compact and reliable design of electrical equipment for the present day requirements, there is an urgent need for better and smart insulating materials and in this respect, the reported enhancements in dielectric properties obtained for polymer nanocomposites seems to be very encouraging. To further understand the dielectric behavior of polymer nanocomposites, this experimental work reports the trends of dielectric permittivities and tan delta (loss tangent) of epoxy nanocomposites with single nano-fillers of Al2O3 and TiO2at low filler concentrations (0.1%, 0.5%, 1% & 5%) over a frequency range of 1 MHz-1 GHz. Results show that the nanocomposites demonstrate some very different dielectric characteristics when compared to those for polymer microcomposites. Unlike the usual expectations of increasing permittivity with increasing filler concentration in polymer microcomposites, it has been seen that up to a certain nano-filler concentration and depending on the permittivity of the nano-filler, the permittivities of the epoxy nanocomposites are less than that of the unfilled epoxy at all the measured frequencies. This suggests that there is a very strong dependence of the filler concentration and nano-filler permittivity on the final permittivity of the nanocomposites at all these frequencies. But, in the case of tan delta behavior in nanocomposites, significant effects of filler concentrations were not observed with both Al2O3 and TiO2 fillers. Tan delta values in nanocomposites with Al2O3 fillers are found to be marginally lower at all filler concentrations when compared with the value for unfilled epoxy. But, in TiO2Oepoxy nanocomposites, although the variations in tan delta are not significant with respect to unfilled epoxy, some interesting trends are observed with respect to the frequencies of measurement.
S 5 H / DMR 6 Encodes a Salicylic Acid 5-Hydroxylase That Fine-Tunes Salicylic Acid Homeostasis 1 [ OPEN ]

Yanjun Zhang, Li Zhao, Jiangzhe Zhao, Yujia Li, Jinbin Wang, Rong Guo, Susheng Gan, Chang-Jun Liu, and Kewei Zhang Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 Department of Biosciences, Brookhaven National Laboratory, Upton, New York 11973
JITL based Fault Detection of DAB DC-DC Converter with EPS Control

As the most important part of the power system, the reliability of dual-active-bridge (DAB) DC-DC converter determines the safe operation of equipment. Thus, this paper proposes a fault detection scheme based on just-in-time-learning (JITL) in DAB DC-DC converter with extended-phase-shift (EPS) control. The performance of the DAB DC-DC converter under the two different control methods are analyzed, and the faults in the primary circuit are detected using JITL method. The simulation model is established using Matlab and the experimental results are analyzed to verify the effectiveness of the method.
Antibody fragments as tools in crystallography

While antibody‐based therapeutics have become firmly established as front‐line drugs, the use of antibodies as research tools in small molecule drug discovery is still in its infancy. In this review we focus on the use of antibody fragments as crystallization chaperones to aid the structural determination of otherwise ‘uncrystallizable’ or ‘undruggable’ target proteins. We also highlight a potential application for this technology, in which antibody‐mediated structures may be used to inform the design of new chemical entities.
Fermentation quality and in vitro methane production of sorghum silage prepared with cellulase and lactic acid bacteria

Objective The effects of lactic acid bacteria (LAB) and cellulase enzyme on fermentation quality, microorganism population, chemical composition and in vitro gas production of sorghum silages were studied. Methods Commercial inoculant Lactobacillus plantarum Chikuso 1 (CH), local selected strain Lactobacillus casei (L. casei) TH 14 and Acremonium cellulase (AC) were used as additives in sorghum silage preparation. Results Prior to ensiling Sorghum contained 104 LAB and 106 cfu/g fresh matter coliform bacteria. The chemical compositions of sorghum was 26.6% dry matter (DM), 5.2% crude protein (CP), and 69.7% DM for neutral detergent fiber. At 30 days of fermentation after ensiling, the LAB counts increased to a dominant population; the coliform bacteria and molds decreased to below detectable level. All sorghum silages were good quality with a low pH (<3.5) and high lactic acid content (>66.9 g/kg DM). When silage was inoculated with TH14, the pH value was significantly (p<0.05) lower and the CP content significantly (p<0.05) higher compared to control, CH and AC-treatments. The ratio of in vitro methane production to total gas production and DM in TH 14 and TH 14+AC treatments were significantly (p<0.05) reduced compared with other treatments while in vitro dry matter digestibility and gas production did not differ among treatments. Conclusion The results confirmed that L. casei TH14 could improve sorghum silage fermentation, inhibit protein degradation and decrease methane production.
The relation between major histocompatibility complex (MHC) restriction and the capacity of Ia to bind immunogenic peptides

The capacity of purified I-Ad, I-Ed, I-Ak, and I-Ek to bind to protein derived peptides that have been previously reported to be T cell immunogens has been examined. For each of the 12 peptides studied strong binding to the relevant Ia restriction element was observed. All the peptides bound more than one Ia molecule; however, for 11 of 12 peptides, the dominant binding was to the restriction element, whereas in one instance the dominant binding was to a nonrestriction element. When the peptides were used to inhibit the presentation of antigen by prefixed accessory cells to T cells, an excellent correlation was found between the capacity of a peptide to inhibit the binding of an antigen to purified Ia and the capacity of the peptide to inhibit accessory cell presentation of the antigen. Thus, the binding of peptide to purified Ia is immunologically relevant, and Ia seems to be the only saturable molecule on the surface of the accessory cell involved in antigen presentation. Inhibition analysis also indicated that all peptides restricted to a particular Ia molecule competitively inhibited one another, suggesting that each Ia restriction element has a single binding site for antigen. Cross-linking of labeled peptides to Ia followed by electrophoretic analysis and autoradiography suggested that this single binding site is made up of portions of both alpha and beta chains of Ia.
Interactive Visualization of Metabolic Pathways

This work enriches the visualization of complex graphs from the biomedical domain called metabolic pathways by means of interactive linked views in 2D and 3D. Due to the high degree of complexity of pathways biologists are restrained by currently available systems in the process of hypothesis generation and validation. We propose an interactive visual data mining process that is supported by the integration of methods as detail-ondemand, focus and context, and semantic zoom. CR
Characterization of the specific O-polysaccharide structure and biosynthetic gene cluster of Yersinia pseudotuberculosis serotype O:15

Yersinia pseudotuberculosis serotyping scheme contains 21 serotypes based on the distribution of about 30 different O-factors within the species. The chemical structures of LPSs and the genetic basis of their biosynthesis has been determined for a number of Y. pseudotuberculosis strains representing different serotypes; thus, an overall picture of the relationship between genetics and structures is emerging. In this work, we have performed a structural and genetic analysis of the Y. pseudotuberculosis serotype O:15 O-specific polysaccharide. Our results showed that the set-up of the Y. pseudotuberculosis O:15 gene cluster is a hybrid between those of Y. pseudotuberculosis serotypes O:1b and O:5a, possibly due to a single recombination event. The hybrid nature could also be seen in the structure of the O-specific polysaccharide repeating unit pentasaccharide. It contains a tetrameric backbone identical to that of O:5a while the branching paratofuranose residue is identical to that of O:1b.
Flexing DNA: HMG-box proteins and their partners.

The initiation of transcription by RNA polymerase II is controlled by the assembly of the basal transcription machinery, which integrates inputs from transcription factors bound to promoters and enhancers. Overall, a typical gene may depend on the binding of tens of transcription factors to its controlling-sequence elements. Combinatorial assembly ensures that each gene can exhibit a distinctive and sometimes variable pattern of expression, despite the fact that the number of transcription factors is much lower than the number of genes.
Tele-rehabilitation for back pain in Korean farmers

Back pain is a common musculoskeletal problem for farmers. Tele-rehabilitation for back pain could be useful for people living in rural area distant from hospital. Each session composed of self-assessment of back pain, education, stretching, core exercise, cool down exercise and homework using videoconferencing and Kinect-guided exercise. The outcome measure was visual analogue scale, Oswestry Disability Index, isometric back extensor strength, and pain pressure threshold of paraspainl muscles at baseline, after completion of 3 sessions, and after completion of 7 sessions. A total of 4 men (mean age, 64.8 ± 8.8) and 12 women (mean age, 67.4 ± 9.1) were participated in tele-rehabilitation program. After 7 consecutive sessions of tele-rehabilitation, participants had significant improvement on outcome measures including Oswestry Disability Index, isometric back extensor strength and pain pressure threshold on right L2 and left L4 paraspinal muscles. We showed tele-rehabilitation for back pain could be effective.
Chlamydia pneumoniae infection‐related hemophagocytic lymphohistiocytosis and acute encephalitis and poliomyelitis‐like flaccid paralysis

A 3‐year‐old male presented with Chlamydia pneumoniae infection‐related hemophagocytic lymphohistiocytosis (HLH). The patient developed an episode of HLH with severe skin eruption following C. pneumoniae pneumonia. Symptoms responded to steroid/cyclosporine A therapy, but the patient slowly lost consciousness and developed systemic flaccid paralysis. He was diagnosed with encephalitis/myelitis by brain and spinal MRI. Neurological symptoms and signs gradually resolved. We thought that the immune response to C. pneumoniae infection triggered the development of HLH, associated with unusual neurological complications. This report describes a novel case of C. pneumoniae‐associated HLH and with poliomyelitis like flaccid paralysis. Pediatr Blood Cancer 2011;56:853–855. © 2010 Wiley‐Liss, Inc.
REDUCTION OF STRIPING NOISE IN OVERLAPPING LIDAR INTENSITY DATA BY RADIOMETRIC NORMALIZATION

Abstract. To serve seamless mapping, airborne LiDAR data are usually collected with multiple parallel strips with one or two cross strip(s). Nevertheless, the overlapping regions of LiDAR data strips are usually found with unbalanced intensity values, resulting in the appearance of stripping noise. Despite that physical intensity correction methods are recently proposed, some of the system and environmental parameters are assumed as constant or not disclosed, leading to such an intensity discrepancy. This paper presents a new normalization technique to adjust the radiometric misalignment found in the overlapping LiDAR data strips. The normalization technique is built upon a second-order polynomial function fitted on the joint histogram plot, which is generated with a set of pairwise closest data points identified within the overlapping region. The method was tested on Teledyne Optech’s Gemini dataset (at 1064 nm wavelength), where the LiDAR intensity data were first radiometrically corrected based on the radar (range) equation. Five land cover features were selected to evaluate the coefficient of variation (cv) of the intensity values before and after implementing the proposed method. Reduction of cv was found by 19% to 59% in the Gemini dataset, where the striping noise was significantly reduced in the radiometrically corrected and normalized intensity data. The Gemini dataset was also used to conduct land cover classification, and the overall accuracy yielded a notable improvement of 9% to 18%. As a result, LiDAR intensity data should be pre-processed with radiometric correction and normalization prior to any data manipulation.
Placement: From Wirelength to Detailed Routability

: Research on the placement problem in physical design has evolved timely in the recent few decades from traditional wirelength-driven, to routability-driven and then to detailed-routability driven. In this paper, we will focus on the interconnect and routing issues in placement, and study and survey on the development and progress of related works on this important problem
The interdomain linker of Escherichia coli initiation factor IF3: a possible trigger of translation initiation specificity

Initiation factor IF3 is responsible for the accuracy of translation initiation in bacteria, by destabilizing complexes involving non‐initiator tRNA and/or non‐start codons. This proofreading is performed on the 30S subunit to which IF3 binds selectively. IF3 has an unusual architecture, with two globular domains connected by a mobile, positively charged linker. Here, we have investigated the function of this flexible tether by probing its conformation when IF3 is bound to the ribosomal RNA. Using site‐directed mutagenesis of the linker region, we have also selectively modified its length, its flexibility and its chemical composition. The function of the mutant genes was assayed in vivo, and the structural and biochemical properties of some of the corresponding variant proteins were characterized in vitro. The two isolated domains of IF3 were also co‐expressed in order to test the requirement for their covalent attachment. The results indicate that the physical link between the two domains of IF3 is essential for the function of this protein, but that the exact length and chemical composition of the linker can be varied to a large extent. A model is presented in which the extended linker would act as a ‘strap’, triggering a conformational change in the 30S subunit, which would then ensure initiator tRNA selection.
Autoactivation of Type-1 Parathyroid Hormone Receptors Containing a Tethered Ligand*

Interactions between the N-terminal residues of parathyroid hormone (PTH) and the region of the PTH receptor containing the extracellular loops and transmembrane domains are thought to be critical for receptor activation. We evaluated this hypothesis by replacing the large N-terminal extracellular domain of the human type 1 PTH receptor (hP1Rc-WT) with residues 1–9 of PTH (AVSEIQLMH) using a tetraglycine linker between His-9 of the ligand and Glu-182 of the receptor near the extracellular terminus of transmembrane domain-1. Expression of this construct, hP1Rc-Tether(1–9), in COS-7 cells resulted in basal cAMP levels that were 10-fold higher than those seen in control cells transfected with hP1Rc-WT. Extending the ligand sequence to include Asn-10 and the activity-enhancing substitution of Leu-11 → Arg yielded hP1Rc-[Arg11]Tether(1–11), for which we observed basal cAMP levels that were 50-fold higher than those seen with P1Rc-WT. An alanine-scan analysis of hP1Rc-[Arg11]Tether(1–11) revealed that Gln-6 and His-9 were not critical for autoactivation, whereas Val-2, Ile-5, and Met-8 were. The data show that tethered PTH/PTH receptors can autoactivate. Analysis of the structure-activity relationships in these tethered receptor constructs can provide new information concerning how the N-terminal residues of PTH interact with the extracellular loops and transmembrane regions of the PTH-1 receptor, particularly in regard to receptor activation.
Bidirectional current-fed converter for integration of dc micro-grid with ac grid

Most of the loads found in various commercial installations require front end ac-dc conversion. Various storage systems and renewable sources interact with these loads and the ac grid through dc-ac converters. These multistage conversions reduce system efficiency. To avoid this, an ac distribution system can be replaced by a dc distribution system within a commercial facility. It results in improved system efficiency and reliability. This paper proposes a three-phase current-fed converter, interfacing a dc distribution system with a utility ac grid. It has bidirectional power flow capability. The converter injects or draws low ripple current from a dc micro-grid, while maintaining high power factor and low current distortion on ac grid side. It has improved reliability and size over conventional VSC. The steady state and dynamic performance of the converter is studied using MATLAB Simulink. The converter also has a limited capacity of supplying or absorbing reactive power. These limits are computed for both inversion and rectification modes of operation.
Simulating the function of sodium/proton antiporters

Significance Understanding the molecular nature of the function of transporters is of significant interest in view of their biological importance. However, the actual structure–function relationship of transporters is far from being clear. To advance this understanding, we simulated the activity of the Na+/H+ antiporter NhaA by a Monte Carlo approach, based on the calculated coarse-grained electrostatic landscape of the system. The simulations reproduce the observed trend and provide a powerful insight into the origin of the transporting function and the molecular basis of its control. We also show that a large conformational alternation is essential for the transporter function. The approach used should be useful for general studies of other transporters. The molecular basis of the function of transporters is a problem of significant importance, and the emerging structural information has not yet been converted to a full understanding of the corresponding function. This work explores the molecular origin of the function of the bacterial Na+/H+ antiporter NhaA by evaluating the energetics of the Na+ and H+ movement and then using the resulting landscape in Monte Carlo simulations that examine two transport models and explore which model can reproduce the relevant experimental results. The simulations reproduce the observed transport features by a relatively simple model that relates the protein structure to its transporting function. Focusing on the two key aspartic acid residues of NhaA, D163 and D164, shows that the fully charged state acts as an Na+ trap and that the fully protonated one poses an energetic barrier that blocks the transport of Na+. By alternating between the former and latter states, mediated by the partially protonated protein, protons, and Na+ can be exchanged across the membrane at 2:1 stoichiometry. Our study provides a numerical validation of the need of large conformational changes for effective transport. Furthermore, we also yield a reasonable explanation for the observation that some mammalian transporters have 1:1 stoichiometry. The present coarse-grained model can provide a general way for exploring the function of transporters on a molecular level.