Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of human leukocyte antigen‐A24‐restricted epitope peptides derived from gene products upregulated in lung and esophageal cancers as novel targets for immunotherapy

For the development of cancer vaccine therapies, we have searched for possible epitope peptides that can elicit cytotoxic T lymphocytes (CTL) to the TTK protein kinase (TTK), lymphocyte antigen 6 complex locus K (LY6K) and insulin‐like growth factor (IGF)‐II mRNA binding protein 3 (IMP‐3), which were previously identified to be transactivated in the majority of lung and esophageal cancers. We screened 31, 17 and 17 candidate human leukocyte antigen (HLA)‐A*2402‐binding peptides to parts of TTK, LY6K and IMP‐3, respectively. As a result, we successfully established strong CTL clones stimulated by TTK‐567 (SYRNEIAYL), LY6K‐177 (RYCNLEGPPI) and IMP‐3‐508 (KTVNELQNL) that have specific cytotoxic activities against the HLA‐A24‐positive target cells pulsed with the candidate peptides. Subsequent analysis of the CTL clones also revealed their cytotoxic activities against lung and esophageal tumor cells that endogenously express TTK, LY6K or IMP‐3. A cold target inhibition assay further confirmed that the CTL cell clones specifically recognized the MHC class I–peptide complex. Our results strongly imply that TTK, LY6K and IMP‐3 are novel tumor‐associated antigens recognized by CTL, and TTK‐567 (SYRNEIAYL), LY6K‐177 (RYCNLEGPPI) and IMP‐3‐508 (KTVNELQNL) are HLA‐A24‐restricted epitope peptides that can induce potent and specific immune responses against lung and esophageal cancer cells expressing TTK, LY6K and IMP‐3. (Cancer Sci 2007; 98: 1803–1808)
Blimp-1-Dependent Repression of Pax-5 Is Required for Differentiation of B Cells to Immunoglobulin M-Secreting Plasma Cells

ABSTRACT B-cell lineage-specific activator protein (BSAP), encoded by the Pax-5 gene, is critical for B-cell lineage commitment and B-cell development but is not expressed in terminally differentiated B cells. We demonstrate a direct connection between BSAP and B-lymphocyte-induced maturation protein 1 (Blimp-1), a transcriptional repressor that is sufficient to drive plasmacytic differentiation. Blimp-1 binds a site on the Pax-5 promoter in vitro and in vivo and represses the Pax-5 promoter in a binding-site-dependent manner. By ectopically expressing Blimp-1 or a competitive inhibitor of Blimp-1, we show that Blimp-1 is both necessary and sufficient to repress Pax-5 during plasmacytic differentiation of primary splenic B cells. Blimp-1-dependent repression of Pax-5 is sufficient to regulate BSAP targets CD19 and J chain and is necessary but not sufficient to induce XBP-1. We further show that repression of Pax-5 is required for Blimp-1 to drive differentiation of splenocytes to immunoglobulin M-secreting cells. Thus, repression of Pax-5 plays a critical role in the Blimp-1-dependent program of plasmacytic differentiation.
Globotriaosylceramide, Gb3, is an alternative functional receptor for Shiga-like toxin 2e

We reexamined the binding specificity of the Shiga-like toxin variant associated with porcine edema disease, SLT2e, which is reported to be more cytotoxic for Vero cells than for HeLa cells, by using receptor-deficient cells and a liposomal insertion system for purified glycolipids. We found that SLT2e preferentially uses globotetraosylceramide as a receptor but can also cause cytotoxicity by using globotriaosylceramide, the SLT2 receptor. We conclude that the differential cytotoxicity of SLT2e on HeLa and Vero cells is a function of both the receptor preference of the toxin and the specific glycolipid content of the target cells being used.
Compensation for phonetic nuisance variability in speaker recognition using DNNs

In this paper, a new way of using phonetic DNN in text-independent speaker recognition is examined. Inspired by the Subspace GMM approach to speech recognition, we try to extract i-vectors that are invariant to the phonetic content of the utterance. We overcome the assumption of Gaussian distributed senones by combining DNN with UBM posteriors and we form a complete EM algorithm for training and extracting phonetic content compensated i-vectors. A simpliﬁed version of the model is also presented, where the phonetic content and speaker subspaces are learned in a decoupled way. Covariance adaptation is also examined, where the covariance matrices are reesti-mated rather than copied from the UBM. A set of primary experimental results is reported on NIST-SRE 2010, with modest improvement when fused with the standard i-vectors.
Effect of Porphyromonas gingivalis-induced inflammation on the development of rheumatoid arthritis.

BACKGROUND Periodontitis is an extra-synovial chronic inflammatory condition, which has been proposed to be inter-related with rheumatoid arthritis. OBJECTIVE We investigated the effect of an established extra-synovial chronic inflammatory lesion on the induction and severity of experimental arthritis. MATERIALS AND METHODS Chronic inflammatory lesions were induced by the implantation of polyurethane sponges impregnated with heat-killed Porphyromonas gingivalis into the backs of DA rats. Thirty-five days later, adjuvant arthritis (AA) was induced in the rats by injecting a mycobacterium cell wall in complete Freund's adjuvant. The development of arthritis was then monitored for 2 weeks. RESULTS Histological assessment of the implanted sponges confirmed that a chronic inflammatory lesion had been established after 21 days. Following induction of adjuvant arthritis, the severity of disease was scored and paw swelling was measured. Severe arthritis developed more rapidly in animals with a pre-existing P. gingivalis-induced inflammatory lesion elsewhere. CONCLUSIONS The results show that a pre-existing extra-synovial chronic inflammatory lesion induced by P. gingivalis promotes the development of arthritis in an animal model. These findings provide further evidence for a relationship between the presence of periodontal pathogen-associated inflammation and the development of rheumatoid arthritis.
Molecular typing of Treponema pallidum strains from patients with neurosyphilis in Pretoria, South Africa

Objective: To evaluate the molecular typing system for Treponema pallidum using cerebrospinal fluid (CSF) specimens obtained from patients with neurosyphilis in Pretoria, South Africa. Methods: CSF specimens were collected from 32 men and 18 women with suspected late neurosyphilis. Typing of T pallidum involved PCR amplification and restriction analysis of the tprE, G and J genes and determination of the number of 60 base pair tandem repeats within the arp gene by PCR amplification. Results: Of 13 typeable specimens, 4 strain types were identified: 2i, 3e, 14a and 17e. Subtype 14a was identified in 7 specimens (53.8%), subtype 3e in 4 specimens (30.7%) and subtypes 17e and 2i in 1 specimen (7.6%) each. Conclusions: This study shows that the typing system can be applied to specimens which may contain low numbers of spirochaetes such as CSF.
A Y-slot wideband circularly polarized antenna for non-contact health monitoring applications

The primary object of this paper is to investigate the polarization mismatch effects between transmitter and receiver antennas in noncontact monitoring applications. It is shown that circularly-polarized antennas have better performance compared to similar linearly-polarized ones in the presence of the human body. A novel y-slot wideband CP antenna is proposed. The antenna consists of a u-shaped feed, a y-slot, and a parasitic stub. Simulation results show a bandwidth of 82% (3-7.2 GHz) for VSWR<;2:1 with a 3 dB axial ratio (AR) bandwidth of 33% (4.6-6.4 GHz). The proposed antenna has a low profile with an overall size of 28 mm×28 mm×1.6 mm.
Role of temperature‐dependent viscosity and surface plates in spherical shell models of mantle convection

Layered viscosity, temperature-dependent viscosity, and surface plates have an important effect on the scale and morphology of structure in spherical models of mantle convection. We find that long-wavelength structures can be produced either by a layered viscosity with a weak upper mantle or temperature-dependent viscosity even in the absence of surface plates, corroborating earlier studies, However,combining the layered viscosity structure with a temperature-dependent viscosity results in structure with significantly shorter wavelengths. Our models show that the scale of convection is mainly controlled by the surface plates, supporting the previous two-dimensional studies. Our models with surface plates: layered and temperature-dependent viscosity, and internal heating explain mantle structures inferred from seismic tomography. The models show that hot upwellings initiate at the core-mantle boundary (CMB) with linear structures, and as they depart from CMB, the linear upwellings quickly change into quasi-cylindrical plumes that dynamically interact with the ambient mantle and surface plates while ascending through the mantle. A linear upwelling structure is generated again at shallow depths (<200 km) in the vicinity of diverging plate margins because of the surface plates. At shallow depths, cold downwelling sheets form at converging plate margins. The evolution of downwelling sheets depends on the mantle rheology. The temperature-dependent viscosity strengthens the downwelling sheets so that the sheet structure can be maintained throughout the mantle. The tendency for linear upwelling and downwelling structures to break into plume-like structures is stronger at higher Rayleigh numbers. Our models also show that downwellings tp first-order control surface plate motions and the locations and horizontal motion of upwellings. Upwellings tend to form at stagnation points predicted solely from the buoyancy forces of downwellings. Temperature-dependent viscosity greatly enhances tb: ascending velocity of developed upwelling plumes, and this may reduce the influence of global mantle flow on the motion of plumes. Our results can explain the anticorrelation between hotspot distribution and fast seismic wave speed anomalies in the lower mantle and may also have significant implications to the observed stationarity of hotspots.
ON GEODESICS IN THE SPACE OF KÄHLER METRICS

We show that geodesics in the space of Kähler metrics are of class C1,1, provided that the manifold has nonnegative bisectional curvature. X.X. Chen has proved that these geodesics have bounded mixed complex derivatives (without any curvature assumption). We also analyze his proof of this, and of the fact that the space of Kähler metrics with the distance defined by its Riemannian structure is a metric space.
A Conceptual and Empirical Review of the Structure of Assessment Center Dimensions

Although the design, scoring, and interpretation of assessment centers (ACs) commonly focuses on job-relevant dimensions, over three decades of past studies have questioned the evidentiary basis underlying dimension-based interpretations of ACs. This review combines multiple approaches to examine the structure of AC dimensions. First, we consulted the AC, job performance, leadership, and personality literatures to articulate competing models of the dimensions underlying AC ratings. Next, meta-analytic confirmatory factor analysis (CFA) was used to compare the fit of these models to existing AC data. The results supported a model including administrative skills, relational skills, and drive. Third, socioanalytic theory was used as a basis to examine the nomological network of these three broad factors, specifically their relationships with general mental ability and the five factor model of personality. The analyses supported the nomological network of drive and administrative skills but less so for relational skills. These findings are discussed with regard to the construct-related validity of AC dimensions, the fidelity of ACs to the broader criterion domain, and the value of applying generalizable models to the analysis of AC ratings.
Long interspersed repeated DNA (LINE) causes polymorphism at the rat insulin 1 locus

The insulin 1, but not the insulin 2, locus is polymorphic (i.e., exhibits allelic variation) in rats. Restriction enzyme analysis and hybridization studies showed that the polymorphic region is 2.2 kilobases upstream of the insulin 1 coding region and is due to the presence or absence of an approximately 2.7-kilobase repeated DNA element. DNA sequence determination showed that this DNA element is a member of a long interspersed repeated DNA family (LINE) that is highly repeated (greater than 50,000 copies) and highly transcribed in the rat. Although the presence or absence of LINE sequences at the insulin 1 locus occurs in both the homozygous and heterozygous states, LINE-containing insulin 1 alleles are more prevalent in the rat population than are alleles without LINEs. Restriction enzyme analysis of the LINE-containing alleles indicated that at least two versions of the LINE sequence may be present at the insulin 1 locus in different rats. Either repeated transposition of LINE sequences or gene conversion between the resident insulin 1 LINE and other sequences in the genome are possible explanations for this.
Rules for type-checking of parametric polymorphism in EMF generics

The Eclipse infrastructure for modeling is based on EMF, an implementation of Essential MOF, the OMG standard for metamodeling. A recent addition to EMF has been parametric polymorphism (also known as “parameterized types” or “generics”) thus achieving the same benefits realized in other generic type systems (most notably, Java 5). To our knowledge, this is the first formal account in the literature of the resulting type system, including the well-formedness rules (WFRs) for type expressions. We offer an initial formalization of the type system of EMF Generics by formulating those WFRs in OCL (Object Constraint Language). The insights thus gained are applicable to solve the type-checking problem for custom DSLs (Domain Specific Languages).
Structural diversity of leucine-rich repeat proteins.

The superfamily of leucine-rich repeat proteins can be subdivided into at least six subfamilies, characterised by different lengths and consensus sequences of the repeats. It was proposed that the repeats from different subfamilies retain a similar superhelical fold, but differ in the three-dimensional structures of individual repeats. The sequence-structure relationship of three new subfamilies was examined by molecular modelling. I provide structural models for the repeats of all subfamilies. The models enable me to explain residue conservations within each subfamily. Furthermore, the difference in the packing explains why the repeats from different subfamilies never occur simultaneously in the same protein. Finally, these studies suggest different evolutionary origins for the different subfamilies. The approach used for the prediction of the leucine-rich repeat protein structures can be applied to other proteins containing internal repeats of about 20 to 30 residue in length.
Optimal Design of Tubular Transverse Flux Motors With Low Cogging Forces for Direct Drive Applications

Linear permanent magnet (PM) motors have increasingly been used in high-performance applications where high accuracy and fast dynamic response are required. However, the presence of cogging force in linear motors compromises position and speed control accuracy, which can be particularly troublesome at low speeds. This paper presents analysis and minimization of cogging force associated with a tubular PM motor with transverse flux configuration. An analytical criterion is brought forward, which allows the impact prediction of leading design parameters on the cogging force in an accurate way. And the validity and results are verified by extensive three-dimensional numerical computations and experimental measurements. It is shown that the cogging force increases along with the PM height. And it is highlighted that the cogging force amplitude is a sinusoidal function of the stator segment length, which is quite different from that in conventional PM machines. This work has provided a basis for cogging force reduction, and will aid the design process of the transverse flux motor, especially when targeting high-performance direct drive applications.
A New Decentralized Cryptographic Access Control Solution for Smart-phones

As the wireless technologies are becoming more and more popular and the number of cloud providers increases due to the growing demand of services and new emerging concepts like “Cloud computing”, security concerns are gaining a leading role. Data storage follows deprecated systems which make the cloud more vulnerable to data leakage. Besides, commmon cellphones have evolved to small pocket computers known as smart-phones, running their own Operating System. These devices are suffering every year an increment of cyber-attacks owing to weaknesses regarding the Operating System policy and the fact of using wireless standards such as GSM, UMTS, LTE, Wiﬁ or Bluetooth. Over this document, we propose a new access control solution based on a cryptographic system managed by the end-user to add extra security to one’s personal information on the cloud. It is orientated to smart-phones and takes into account the computational limitations these devices may have.
Analysis of the antigen specificity of the human serum immunoglobulin G immune response to complicated gonococcal infection

The antigen-specific basis of human serum immunoglobulin G antibody response to complicated gonococcal infection was studied in 13 patients by using the Western blot technique for transfer of proteins from sodium dodecyl sulfate-polyacrylamide gels to nitrocellulose paper. Of 13 patients (8 with disseminated gonococcal infection, 4 with pelvic inflammatory disease, 1 with gonococcal epididymitis), 12 reacted with protein I antigens and 9 with lipopolysaccharide (LPS). Sera from eight patients reacted with both protein I and LPS, whereas sera from four reacted only with protein I, and one sera reacted with LPS alone. One serum with antibody to both protein I and LPS by Western blot analysis was tested for bactericidal activity before and after adsorption of antibody to LPS. Removal of antibody to LPS reduced the bactericidal titer of this serum from 1:100 to 1:50, indicating that antibody to both antigens may be bactericidal for Neisseria gonorrhoeae.
Reconfigurable communications satellite: SoftSAT

It is generally impossible to exchange, repair, or upgrade onboard equipment in orbit, and communications satellites are designed for fifteen or more years of life. Consequently, orbiting communications satellites cannot follow unforeseen changes in terrestrial communications. Moreover, because of long lead times and high costs of satellite development, it is difficult to implement the latest technology at launch. And even if the latest communications technology were implemented at the time of launch, the configuration on orbit has limited capability for configuration change to parallel the endless evolution in terrestrial communications technology. In this paper, we propose a reconfigurable communication satellite system based on formation flying and inter-satellite communications technology. The satellite is composed of a group of satellites. The functions implemented by each satellite are defined by the OSI (Open Systems Interconnection) reference model. The discussion centers on a three satellite constellation or cluster having relatively close spacing; but the concept may be applied to larger clusters and spacings. Satellites implementing higher OSI layers are small and also on a size reducing trend. Replacing or adding small satellite elements might enable the cluster as a whole to keep pace with frequent paradigm shifts of terrestrial networks.
Bacterial Meningitis Caused by Veillonella Parvula

A three‐year‐old girl injured her right eyelid with a toothbrush. The wound was sutured. Swelling of the eyelid, high fever and vomiting developed in spite of oral antibiotics for seven days. The findings of the cerebrospinal fluid (CSF) were white blood cells (WBC) 26,368/mm3 (90% polymorphs), protein 127 mg/d, and sugar 0 mg/dl. Although Cram negative organisms were seen on the smear, aerobic culture was sterile. Later culture of CSF on admission grew anaerobic bacteria: Veillonella parvula. Intravenous administration of penicillins with cefotaxime (CTX), or of fosfomycin (FOM) were ineffective. Chloramphen‐icol (CP) cured the patient without neurological sequelae. There were no abnormal findings on brain CT scan. This is the first report of Veillonella meningitis. V. parvula appeared to have invaded the CSF from the abscess of the eyelid. It is necessary to consider anaerobic meningitis when there is a preceding pyogenic infection in the head.
Endothelial focal adhesions and barrier function

Focal adhesions composed of integrins provide an important structural basis for anchoring the endothelial lining to its surrounding matrices in the vascular wall. Complex molecular reactions occur at the endothelial cell–matrix contact sites in response to physical and chemical stress present in the circulatory system. Recent experimental evidence points to the importance of focal adhesions in the regulation of microvascular barrier function. On one hand, the adhesive interaction between integrins and their extracellular ligands is essential to the maintenance of endothelial barrier properties, and interruption of integrin–matrix binding leads to leaky microvessels. On the other hand, focal adhesion assembly and activation serve as important signalling events in modulating endothelial permeability under stimulatory conditions in the presence of angiogenic factors, inflammatory mediators, or physical forces. The focal responses show distinctive patterns with different temporal characteristics, whereas focal adhesion kinase (FAK) plays a central role in initiating and integrating various signalling pathways that ultimately affect the barrier function. The molecular basis of focal adhesion‐dependent microvascular permeability is currently under investigation, and advances in the technologies of computerized quantitative microscopy and intact microvessel imaging should aid the establishment of a functional significance for focal adhesions in the physiological regulation of microvascular permeability.
“There’s Not Enough Knowledge Out There”: Examining Older Adults’ Perceptions of Digital Technology Use and Digital Inclusion Classes

Older adults’ definitions of digital technology, and experiences of digital inclusion sessions, were examined using qualitative approaches. Seventeen older adults (aged between 54 and 85 years) participated in two focus groups that each lasted approximately 90 min to explore how older adults understood technology within their lived experience. Interpretative phenomenological analysis yielded two main themes: thirst for knowledge and a wish list for digital technology sessions. A separate content analysis was performed to identify what technology older adults identified as digital technology. This analysis revealed that the older adults most frequently defined digital technology as computers and telephones. The findings support the conclusions that this group of older adults, some of whom were “successful users,” have a wide knowledge of digital technology, are interested in gaining more skills, and desire knowledge acquisition through personalized one-to-one learning sessions.