Miracle-dz/UniFAR-FTUs huggingface dataset:
Cation- and lattice-site-selective magnetic depth profiles of ultrathin 
Fe3O4
(001) films

A detailed understanding of ultrathin film surface properties is crucial for the proper interpretation of spectroscopic, catalytic and spin-transport data. We present x-ray magnetic circular dichroism (XMCD) and x-ray resonant magnetic reflectivity (XRMR) measurements on ultrathin $\mathrm{Fe_3O_4}$ films to obtain magnetic depth profiles for the three resonant energies corresponding to the different cation species $\mathrm{Fe^{2+}_{oct}}$, $\mathrm{Fe^{3+}_{tet}}$ and $\mathrm{Fe^{3+}_{oct}}$ located on octahedral and tetrahedral sites of the inverse spinel structure of $\mathrm{Fe_3O_4}$. By analyzing the XMCD spectrum of $\mathrm{Fe_3O_4}$ using multiplet calculations, the resonance energy of each cation species can be isolated. Performing XRMR on these three resonant energies yields magnetic depth profiles that correspond each to one specific cation species. The depth profiles of both kinds of $\mathrm{Fe^{3+}}$ cations reveal a $\mathrm{3.9 \pm 1~A}$-thick surface layer of enhanced magnetization, which is likely due to an excess of these ions at the expense of the $\mathrm{Fe^{2+}_{oct}}$ species in the surface region. The magnetically enhanced $\mathrm{Fe^{3+}_{tet}}$ layer is additionally shifted about $\mathrm{3\pm 1.5~A}$ farther from the surface than the $\mathrm{Fe^{3+}_{oct}}$ layer.
Charge Transport Mechanism in p-Channel Tin Monoxide Thin-Film Transistors

In this letter, we report on the charge transport mechanism in the p-type tin monoxide (SnO) thin-film transistors (TFTs) over a wide range of operation regimes and temperatures. From the temperature-dependent field-effect conductance measurements, the variable range hopping and the trap-limited band transport are considered as dominant charge transport mechanisms in the SnO TFT at temperatures below ~ 200 K (−73 °C) and above ~273 K (0 °C), respectively, in the subthreshold and transition regions. In the above-threshold region, the intrinsic field-effect mobility (<inline-formula> <tex-math notation="LaTeX">$\mu _{\mathsf {FEi}})$ </tex-math></inline-formula> decreases with an increase in temperature with a prefactor <inline-formula> <tex-math notation="LaTeX">$\gamma \sim $ </tex-math></inline-formula>-0.36 in the <inline-formula> <tex-math notation="LaTeX">$\mu _{\mathsf {FEi}}\sim {T}^{\gamma }$ </tex-math></inline-formula> law at temperatures (<inline-formula> <tex-math notation="LaTeX">${T}\text{s}$ </tex-math></inline-formula>) between RT and 353 K (80 °C). The observed temperature and gate overdrive voltage dependence of <inline-formula> <tex-math notation="LaTeX">$\mu _{\mathsf {FEi}}$ </tex-math></inline-formula> suggests that the acoustic phonon scattering is the dominant physical mechanism limiting <inline-formula> <tex-math notation="LaTeX">$\mu _{\mathsf {FEi}}$ </tex-math></inline-formula> in the p-type SnO TFT at realistic operating conditions [in the above-threshold region and at temperatures ranging from RT to 353 K (80 °C)].
Changes in T1 and T2 Observed in Brain Magnetic Resonance Imaging With Delivery of High Concentrations of Oxygen

Objective: The aim of this study was to clarify the relative contributions of the amount of oxygen in the blood, and vasoconstriction/dilation responsible for changes in T1 and T2 observed in brain during hyperoxia. Methods: T1 and T2 values of the cerebral cortex and pituitary gland in mice were determined in room air. After room air was changed to either 100% oxygen (n = 8) or carbogen (n = 8), T1 and T2 values were again determined. Changes in each value with both gases were compared. Results: In both challenges, T1 values of the cerebral cortex decreased, whereas significant T2 prolongation of the cerebral cortex and pituitary gland was demonstrated. However, both cortex and pituitary gland displayed similar responses in T1 and T2 values when exposed to 100% oxygen or carbogen. Conclusions: Reduction of T1 was introduced by the increased amount of dissolved oxygen in blood, and the increased fraction of oxyhemoglobin caused T2 prolongation. The contribution of vasoconstriction/dilation by carbogen to changes in T1 and T2 may be negligible.
Preventing vaccinia virus class‐I epitopes presentation by HSV‐ICP47 enhances the immunogenicity of a TAP‐independent cancer vaccine epitope

Herpes simplex virus protein ICP47, encoded by US12 gene, strongly downregulates major histocompatibility complex (MHC) class‐I antigen restricted presentation by blocking transporter associated with antigen processing (TAP) protein. To decrease viral vector antigenic immunodominance and MHC class‐I driven clearance, we engineered recombinant vaccinia viruses (rVV) expressing ICP47 alone (rVV‐US12) or together with endoplasmic reticulum (ER)‐targeted Melan‐A/MART‐127–35 model tumor epitope (rVV‐MUS12). In this study, we show that antigen presenting cells (APC), infected with rVV‐US12, display a decreased ability to present TAP dependent MHC class‐I restricted viral antigens to CD8+ T‐cells. While HLA class‐I cell surface expression is strongly downregulated, other important immune related molecules such as CD80, CD44 and, most importantly, MHC class‐II are unaffected. Characterization of rVV‐MUS12 infected cells demonstrates that over‐expression of a TAP‐independent peptide, partially compensates for ICP47 induced surface MHC class‐I downregulation (30% vs. 70% respectively). Most importantly, in conditions where clearance of infected APC by virus‐specific CTL represents a limiting factor, a significant enhancement of CTL responses to the tumor epitope can be detected in cultures stimulated with rVV‐MUS12, as compared to those stimulated by rVV‐MART alone. Such reagents could become of high relevance in multiple boost protocols required for cancer immunotherapy, to limit vector‐specific responsiveness.
Neural plasticity detected in short‐and long‐term cochlear implant users using PET

The interaction of listening to words and watching sign language in short-term and long-term cochlear implant (CI) users who have learned sign language after becoming deaf was measured using PET. In short-term CI users the auditory cortex was inactive while in long-term CI users it was fully activated with the simultaneous presentation of auditory and visual input. The result suggests the possibility that the interference of rival modalities may be diminished with experience and the preference switchover from the visual input to the auditory input could be accomplished by means of the neural plasticity persisting in the mature human auditory cortex.
Association study of MICA gene polymorphisms with rheumatoid arthritis susceptibility in south Tunisian population

The aim of this study was to investigate the role of major histocompatibility complex (MHC) class I chain‐related gene A (MICA) polymorphisms, important in natural killer (NK) cell function, in patients with rheumatoid arthritis (RA). A transmembrane (TM) alanine‐encoding GCT repeats, termed A4, A5, A5.1, A6 and A9 in the MICA gene, and single‐nucleotide polymorphisms (SNPs): the Met129Val polymorphism (rs1051792) and the nonsynonymously coding SNP (rs1051794) were genotyped in 142 patients with RA and 123 unrelated healthy individuals using, respectively, PCR fluorescent method, nested PCR‐RFLP and allele specific PCR (ASP). Association was assessed based on the χ2 test, genotype relative risk (GRR) and odds ratio (OR) with 95% confidence intervals (CIs). Our results show a trend of association of the different MICA genotypes G/G, G/A and A/A (P = 0.029) which did not attain the significance after Bonferroni's correction (pc = 0.08). Although, we revealed a significant association of the genotype A/A of MICA‐250 in patients with RA compared to healthy controls (pc = 0.033). In contrast, no significant differences between alleles and genotypes frequencies were found either with MICA‐TM or MICA met129 val (P > 0.05) in our sample. Moreover, stratification of patients with RA according to clinical and immunological data for the different polymorphisms studied shows a significant association of both MICA‐250 G allele (pc = 0.0075) and MICA‐250 GG genotype (pc = 0.008) and both allelic (val) (pc = 0.021) and genotypic (val/val) distribution (pc = 0.0095) for MICA met129 val in the RF‐positive subgroup compared to RF‐negative patients with RA. In contrast, we found a strong association of the MICA‐TM A9 allele in RF‐negative patients with RA (pc = 0.0003). This study indicates the involvement of the MICA‐250 polymorphism in the genetic susceptibility and severity to RA and suggests that variations in MICA‐TM and MICA met129 val may have an effect on RA severity in our south Tunisian sample.
Mouse models in non‐alcoholic fatty liver disease and steatohepatitis research

Non‐alcoholic fatty liver disease (NAFLD) represents a histological spectrum of liver disease associated with obesity, diabetes and insulin resistance that extends from isolated steatosis to steatohepatitis and cirrhosis. As well as being a potential cause of progressive liver disease in its own right, steatosis has been shown to be an important cofactor in the pathogenesis of many other liver diseases. Animal models of NAFLD may be divided into two broad categories: those caused by genetic mutation and those with an acquired phenotype produced by dietary or pharmacological manipulation. The literature contains numerous different mouse models that exhibit histological evidence of hepatic steatosis or, more variably, steatohepatitis; however, few replicate the entire human phenotype. The genetic leptin‐deficient (ob/ob) or leptin‐resistant (db/db) mouse and the dietary methionine/choline‐deficient model are used in the majority of published research. More recently, targeted gene disruption and the use of supra‐nutritional diets to induce NAFLD have gained greater prominence as researchers have attempted to bridge the phenotype gap between the available models and the human disease. Using the physiological processes that underlie the pathogenesis and progression of NAFLD as a framework, we review the literature describing currently available mouse models of NAFLD, highlight the strengths and weaknesses of established models and describe the key findings that have furthered the understanding of disease pathogenesis.
Uropathogenic, Escherichia coli can express serologically identical pili of different receptor binding specificities

Uropathogenic Escherichia coli frequently express P‐pilus adhesins that recognize Galα(1–4)Gal‐containing glycoconjugates. The P‐pilus adhesin of the, E. coli isolate J96 is encoded by the pap gene cluster and has been shown to agglutinate P1‐erythrocytes. We now describe a novel gene cluster from J96, prs, which is responsible for the agglutination of sheep erythrocytes. The structurally related gene clusters both expressed pili exhibiting the F13 antigen. Analysis of mutants of cloned prs sequences, together with trans‐complementation of pap and prs genes, identified the sheep‐specific adhesin as the 37‐kD PrsG protein. The prsG gene occupies the equivalent position in prs as occupied by papG, which specifies the Galeα(1–4)Gal‐specific adhesion of pap. PrsG was shown to be structurally distinct from PapG since PapG‐specific antiserum did not cross‐react with PrsG. Using a solid phase glycolipid receptor binding assay, PrsG was found to specify preferential binding to the Forssman antigen, a major constituent of sheep erythrocyte membranes. The binding epitope was identified as the GaINAcα(1–3)GaINAc moiety. This is the first direct evidence that serologically identical pili may present antigenically distinct adhesins, each capable of binding to a specific receptor.
Purification and Characterization of Novel Antifungal Compounds from the Sourdough Lactobacillus plantarum Strain 21B

ABSTRACT Sourdough lactic acid bacteria were selected for antifungal activity by a conidial germination assay. The 10-fold-concentrated culture filtrate of Lactobacillus plantarum 21B grown in wheat flour hydrolysate almost completely inhibited Eurotium repens IBT18000, Eurotium rubrum FTDC3228,Penicillium corylophilum IBT6978, Penicillium roqueforti IBT18687, Penicillium expansum IDM/FS2,Endomyces fibuliger IBT605 and IDM3812, Aspergillus niger FTDC3227 and IDM1, Aspergillus flavus FTDC3226,Monilia sitophila IDM/FS5, and Fusarium graminearum IDM623. The nonconcentrated culture filtrate ofL. plantarum 21B grown in whole wheat flour hydrolysate had similar inhibitory activity. The activity was fungicidal. Calcium propionate at 3 mg ml−1 was not effective under the same assay conditions, while sodium benzoate caused inhibition similar toL. plantarum 21B. After extraction with ethyl acetate, preparative silica gel thin-layer chromatography, and chromatographic and spectroscopic analyses, novel antifungal compounds such as phenyllactic and 4-hydroxy-phenyllactic acids were identified in the culture filtrate of L. plantarum 21B. Phenyllactic acid was contained at the highest concentration in the bacterial culture filtrate and had the highest activity. It inhibited all the fungi tested at a concentration of 50 mg ml−1 except forP. roqueforti IBT18687 and P. corylophilumIBT6978 (inhibitory concentration, 166 mg ml−1). L. plantarum 20B, which showed high antimold activity, was also selected. Preliminary studies showed that phenyllactic and 4-hydroxy-phenyllactic acids were also contained in the bacterial culture filtrate of strain 20B. Growth of A. niger FTDC3227 occurred after 2 days in breads started with Saccharomyces cerevisiae 141 alone or with S. cerevisiae andLactobacillus brevis 1D, an unselected but acidifying lactic acid bacterium, while the onset of fungal growth was delayed for 7 days in bread started with S. cerevisiae and selectedL. plantarum 21B.
Impaired lymphatic contraction associated with immunosuppression

To trigger an effective immune response, antigen and antigen-presenting cells travel to the lymph nodes via collecting lymphatic vessels. However, our understanding of the regulation of collecting lymphatic vessel function and lymph transport is limited. To dissect the molecular control of lymphatic function, we developed a unique mouse model that allows intravital imaging of autonomous lymphatic vessel contraction. Using this method, we demonstrated that endothelial nitric oxide synthase (eNOS) in lymphatic endothelial cells is required for robust lymphatic contractions under physiological conditions. By contrast, under inflammatory conditions, inducible NOS (iNOS)-expressing CD11b+Gr-1+ cells attenuate lymphatic contraction. This inhibition of lymphatic contraction was associated with a reduction in the response to antigen in a model of immune-induced multiple sclerosis. These results suggest the suppression of lymphatic function by the CD11b+Gr-1+ cells as a potential mechanism of self-protection from autoreactive responses during on-going inflammation. The central role for nitric oxide also suggests that other diseases such as cancer and infection may also mediate lymphatic contraction and thus immune response. Our unique method allows the study of lymphatic function and its molecular regulation during inflammation, lymphedema, and lymphatic metastasis.
Identification of domains in canine parvovirus VP2 essential for the assembly of virus-like particles

Canine parvovirus capsids are composed of 60 copies of VP2 and 6 to 10 copies of VPl. To locate essential sites of interaction between VP2 monomers, we have analyzed the effects of a number of VP2 deletion mutants representing the amino terminus and the four major loops of the surface, using as an assay the formation of virus-like particles (VLPs) expressed by recombinant baculoviruses. For the amino terminus we constructed three mutants with progressively larger deletions, i.e., 9, 14, and 24 amino acids. Deletions of 9 and 14 amino acids did not affect the morphology and assembly capabilities of the mutants. However, the mutant with the 24-amino-acid deletion did not show hemagglutination properties or correct VLP morphology, stressing again the relevance of the RNER domain in canine parvovirus functionality. Three of the four mutants with deletions in the loops failed to make correct VLPs, indicating that these regions are essential for correct capsid assembly and morphology. Only the mutant with the deletion in loop 2 was able to assemble in regular VLPs, suggesting that this loop has little or no effect in capsid morphogenesis. Further research has demonstrated that this region can tolerate the insertion of foreign epitopes that are correctly exposed in the surface of the capsid. This result opens the door to the use of these VLPs for antigen delivery.
Application of Fisher Linear Discriminant Analysis to Speech/Music Classification

This paper proposes the application of Fisher linear discriminants to the problem of speech/music classification. Fisher linear discriminants can classify between two different classes, and are based on the calculation of some kind of centroid for the training data corresponding with each one of these classes. Based on that information a linear boundary is established, which will be used for the classification process. Some results will be given demonstrating the superior behavior of this classification algorithm compared with the well-known K-nearest neighbor algorithm. It will also be demonstrated that it is possible to obtain very good results in terms of probability of error using only one feature extracted from the audio signal, being thus possible to reduce the complexity of this kind of systems in order to implement them in real-time
The macrocyclic tetrapeptide [D‐Trp]CJ‐15,208 produces short‐acting κ opioid receptor antagonism in the CNS after oral administration

Cyclic peptides are resistant to proteolytic cleavage, therefore potentially exhibiting activity after systemic administration. We hypothesized that the macrocyclic κ opioid receptor (KOR)‐selective antagonist [D‐Trp]CJ‐15,208 would demonstrate antagonist activity after systemic, that is, s.c. and oral (per os, p. o.), administration.
Main Immunogenic Region of Torpedo Electroplax and Human Muscle Acetylcholine Receptor: Localization and Microheterogeneity Revealed by the Use of Synthetic Peptides

Abstract: Most anti‐nicotinic acetylcholine receptor (AChR) antibodies in myasthenia gravis are directed against an immunodominant epitope or epitopes [main immunogenic region (MIR)] on the AChR α‐subunit. Thirty‐two synthetic peptides, corresponding to the complete Torpedoα‐subunit sequence and to a segment of human muscle α‐subunit, were used to map the epitopes for 11 monoclonal antibodies (mAbs) directed against the Torpedo and/or the human MIR and for a panel of anti‐AChR mAbs directed against epitopes on the α‐subunit other than the MIR. A main constituent loop of the MIR was localized within residues α67‐76. Residues 70 and 75, which are different in the Torpedo and human α‐subunits, seem to be crucial in determining the binding profile for several mAbs whose binding to the peptides correlated very well with their binding pattern to native Torpedo and human AChRs. This strongly supports the identification of the peptide loop α67‐76 as the actual location of the MIR on the intact AChR molecule. Residues 75 and 76 were necessary for binding of some mAbs and irrelevant for others, in agreement with earlier suggestions that the MIR comprises overlapping epitopes. Structural predictions for the sequence segment α67‐76 indicate that this segment has a relatively high segmental mobility and a very strong turning potential centered around residues 68‐71. The most stable structure predicted for this segment, in both the Torpedo and human α‐subunits, is a hairpin loop, whose apex is a type I β‐turn and whose arms are β‐strands. This loop is highly hydrophilic, and its apex is negatively charged. All these structural properties have been proposed as characteristic of antibody binding sites. We also localized the epitopes for mAbs against non‐MIR regions. Among these, the epitope for a monoclonal antibody (mAb 13) that noncompetitively inhibits channel function was localized within residues α331‐351.
Coordination and Deployment of Mobile Agents on Dependable Systems

This paper presents a framework for enabling mobile agents to be organized dynamically and autonomously with two unique compositions and interagent interactions on dependable distributed systems. The first enable an agent to contain other agents inside it and migrate to another agent or computer with its inner agents. It provides a powerful approach to composing and deploying large-scale mobile software. The second enable an agent to define its destination according to another agent's location with several policies to support adaptation on distributed systems. It also introduces several higher-level coordinations between mobile agents, e.g., master-slave and redundancy, which are useful to implement dependable systems. This paper also describes a prototype implementation of the framework with mobile agent technology and several applications of it.
A dynamical mean-field theory for learning in restricted Boltzmann machines

We define a message-passing algorithm for computing magnetizations in restricted Boltzmann machines, which are Ising models on bipartite graphs introduced as neural network models for probability distributions over spin configurations. To model nontrivial statistical dependencies between the spins’ couplings, we assume that the rectangular coupling matrix is drawn from an arbitrary bi-rotation invariant random matrix ensemble. Using the dynamical functional method of statistical mechanics we exactly analyze the dynamics of the algorithm in the large system limit. We prove the global convergence of the algorithm under a stability criterion and compute asymptotic convergence rates showing excellent agreement with numerical simulations.
PMLRAR homodimers: distinct DNA binding properties and heteromeric interactions with RXR.

Fusion proteins (named PMLRAR) between PML and the retinoic acid receptor alpha (RAR alpha) are generated as a result of the t(15;17) chromosomal translocation found in acute promyelocytic leukemia (APL). We show here that PMLRAR proteins exist in solution as stable homodimers whose formation is mediated by a presumptive coiled coil in the PML moiety. In contrast to RAR alpha, which requires heterodimerization with RXR for efficient DNA binding, PMLRAR homodimers can bind to target sequences in the absence of RXR, and the binding pattern of PMLRAR homodimeric complexes to directly repeated motif (DR) response elements with 1–5 bp spacers is different from that of RAR/RXR heterodimeric complexes. We show that the presence of RXR induces the formation of PMLRAR/RXR heteromeric complexes which bind to DNA via one RAR DNA binding domain (DBD) and one RXR DBD, like ‘classical’ RAR/RXR heterodimers. PMLRAR interaction with RXR occurs in solution and in transfected cultured Cos cells, and PMLRAR is able to sequester RXR efficiently in the cytoplasm, suggesting that dominant ‘inactivation’ of RXR may be a possible mechanism of action for PMLRAR. Accordingly, we show that PMLRAR can both prevent the binding of the vitamin D3 receptor (VDR) to a target sequence in vitro and inhibit vitamin D3‐dependent activation of a VDR‐responsive reporter gene in transfected cells. These results suggest that both the distinct DNA binding properties of PMLRAR homodimers and the sequestration of RXR by PMLRARs may contribute to the molecular mechanisms which underlie the pathogenesis of APL. We also report that RXR alpha transcripts are down‐regulated by RA‐treatment in promyelocytic cells.