Miracle-dz/UniFAR-FTUs huggingface dataset:
HA-1 and the SMCY-derived peptide FIDSYICQV (H-Y) are immunodominant minor histocompatibility antigens after bone marrow transplantation.

BACKGROUND Allogeneic bone marrow donors can be incompatible at different levels. Even HLA-identical pairs will be still incompatible for numerous minor histocompatibility antigens (mHag). Nevertheless, some incompatibilities are found to be associated with an increased risk of graft-versus-host disease (GVHD), which could be related to the way the immune system recognizes these antigens. METHODS We determined the specificity of cytotoxic T-cell clones isolated during acute GVHD or during bone marrow graft rejection in patients (n=14) transplanted with marrow from donors who were histoincompatible for different minor and/or major histocompatibility antigens. RESULTS We found a clear hierarchy among the different types of histoincompatibilities. In three combinations mismatched for a class I allele, all 27 clones isolated during GVHD were specific for the incompatible HLA molecule. In the 11 class I-identical combinations, 14 different mHags were recognized. The mHag HA-1, known to have a significant impact on the development of GVHD, was recognized in the two HA-1-incompatible combinations. In one of these combinations, which was sex mismatched, all 56 clones analyzed were directed against HA-1, demonstrating the dominance of this mHag. In the four HA-1-compatible, sex-mismatched combinations, the anti-H-Y response was directed against one immunodominant epitope rather than against multiple Y-chromosome-encoded epitopes. All male specific cytotoxic T lymphocytes (n=15) recognized the same high-performance liquid chromatography-purified peptide fraction presented by T2 cells. Moreover, all cytotoxic T lymphocytes tested (n=6) were specific for the SMCY-derived peptide FIDSYICQV, originally described as being the H-Y epitope recognized in the context of HLA-A*0201. CONCLUSIONS Some histocompatibility antigens are recognized in an immunodominant fashion and will therefore be recognized in the majority of mismatched combinations. Only for such antigens, correlations between mismatches and the occurrence of GVHD or graft rejections will be found.
Dexamethasone Rapidly Induces a Novel Ras Superfamily Member-related Gene in AtT-20 Cells*

Differential display was used to identify a new Ras superfamily gene (Dexras1) induced by dexamethasone (Dex) in AtT-20 cells. Treatment of AtT-20 cells with Dex for 30 min resulted in increased mRNA for Dexras1; the highest concentrations appeared after 2 h of treatment. The gene was also identified in mouse heart, brain, liver, and kidney and furthermore was induced in these tissues after Dex treatment. The deduced protein shows regions of homology characteristic of members of the Ras superfamily of small GTPases. Highest homology (36% identity, 57% positives) was found with human Rap-2b, followed closely by a number of other Ras subfamily members, suggesting that Dexras1 is probably a member of the Ras subfamily of GTPases (members include Ras and Rap). Dexras1is the first Ras superfamily member identified that is induced in response to steroids. The function of this gene is unknown; however, its wide distribution and rapid induction by Dex suggests the possibility of a role in glucocorticoid action in a variety of tissues.
Community structure of shallow rocky shore fish in a tropical bay of the southwestern Atlantic

Southwestern Atlantic Ocean rocky shores sustain important reef fish communities. However, those communities in tropical regions are not well understood, especially in Brazil. In this present article we assess community parameters of reef fishes such as composition, trophic organization and their relationships with physical and biological factors on four tropical rocky shores in Todos os Santos Bay, southwestern Atlantic. During six months, a total of 80 visual censuses were performed, in which 3,582 fish belonging to 76 species were recorded. Territorial herbivorous fish and turf algae were dominant at all the sites. The spatial variability of fish community structure was related to the benthic cover composition and depth. The high abundance of territorial herbivores and mobile invertebrate feeders could be associated with high levels of turf cover, low wave exposure and shallow waters. Moreover, this fact could be a consequence of the low density of roving herbivores and large carnivores probably due to the pressure of intense fishing activity. Thus complementary studies are needed to evaluate the actual conservation status of these rocky shore reefs, singularly located habitats connecting inner and outer reefs in Todos os Santos Bay.
Least squares estimate of the initial phases in STFT based speech enhancement

In this paper, we consider single-channel speech enhancement in the short time Fourier transform (STFT) domain. We suggest to improve an STFT phase estimate by estimating the initial phases. The method is based on the harmonic model and a model for the phase evolution over time. The initial phases are estimated by setting up a least squares problem between the noisy phase and the model for phase evolution. Simulations on synthetic and speech signals show a decreased error on the phase when an estimate of the initial phase is included compared to using the noisy phase as an initialisation. The error on the phase is decreased at input SNRs from -10 to 10 dB. Recon-structing the signal using the clean amplitude, the mean squared error is decreased and the PESQ score is increased.
On the decidability of shared memory consistency verification

We view shared memories as structures, which define relations over the set of programs and their executions. An implementation is modeled by a transducer, where the relation it realizes is its language. This approach allows us to cast shared memory verification as language inclusion. We show that a specification can be approximated by an infinite hierarchy of finite-state transducers, called the memory model machines. Also, checking whether an execution is generated by a sequentially consistent memory is approached through a constraint satisfaction formulation. It is proved that if a memory implementation generates a non interleaved sequential and unambiguous execution, it necessarily generates one such execution of bounded size. Our paper summarizes the key results from the first author's dissertation, and may help a practitioner understand with clarity what "sequential consistency checking is undecidable" means.
Joint sparsity models for wideband array processing

Recent work has demonstrated the power of sparse models and representations in signal processing applications and has provided the community with computational tools to use it. In this paper we explore the use of sparsity in localization and beamforming when capturing multiple broadband sources using a sensor array. Specifically, we reformulate the wideband signal acquisition as a joint/group sparsity problem in a combined frequency-space domain. Under this formulation the signal is sparse in the spatial domain but has common support in all frequencies. Using techniques from the model-based compressive sensing literature we demonstrate that it is possible to robustly capture, localize and often reconstruct multiple signals present in the scene.
Positronen-Emissions-Tomografie bei Substanzmissbrauch und Sucht

Zusammenfassung Die neurofunktionelle Bildgebung mittels Positronen- Emissions-Tomografie (PET) hat in den letzten zwei Dekaden einen maßgeblichen Beitrag zur Erforschung der neurobiologischen Grundlagen von Substanzmissbrauch und Abhängigkeit geleistet. So ist es möglich, neben der Identifikation wichtiger Netzwerkstrukturen (z. B. Belohnungssystem und frontolimbische Schleifen) auch die beteiligten Neurotransmittersysteme (z. B. mesolimbische dopaminerge Projektionen) experimentell in vivo zu untersuchen. Derzeit wird die PET zunehmend in der Therapieforschung zur biologischen Evaluation potenzieller „Anti- Craving“-Substanzen eingesetzt. Der vorliegende Artikel gibt einen kurzgefassten Überblick über den aktuellen Stand der PET-Forschung bei Substanzmissbrauch und Abhängigkeitserkrankungen.
Analysis of training parameters for classifiers based on Haar-like features to detect human faces

This paper analyzes the performance of the Haar-like feature based classifier for detection of face with fewer features. The lower dimensional feature space representation of the image may reduce the computational burden compromising the accuracy in detection of faces with varying orientations. In this work we train the classifier with positive instances of different orientations under such feature constraint. The training parameters like maximum deviation and maximum angle are varied to form different classifiers. Experimental results show optimum values of the design parameters can produce good performance of the classifier to detect frontal as well as tilted human faces.
Antimicrobial resistance in sexually transmitted infections in the developed world: implications for rational treatment

Purpose of review Public health control of bacterial sexually transmitted infections (STIs) is dependent on the delivery of effective therapy and so will be compromised by the emergence of resistance. The scope of the problem and the implications for treatment that follow are discussed in this review. Recent findings Emerging resistance has been documented in all the bacterial STIs, but is considered rare and unconfirmed in Chlamydia trachomatis whereas is of global concern in Neisseria gonorrhoeae. Azithromycin resistance has now been recognized in Mycoplasma genitalium, Treponema pallidum and N. gonorrhoeae, questioning its widespread use for chlamydial infection and threatening its future use. Rapidly increasing levels of decreased susceptibility to the extended-spectrum cephalosporins in N. gonorrhoeae and emerging treatment failures to both cefixime and ceftriaxone, without an obvious alternative agent, are of considerable concern. Implications for treatment include choice and timing of any change in therapy, reintroduction of test of cure and definition of treatment failure in an era of molecular testing. Summary Emerging resistance in all bacterial STIs and the particular problem of resistant gonorrhoea will present a challenge to maintain antimicrobial therapy at the forefront of public health control.
Glucosyltransferase mediates adhesion of Streptococcus gordonii to human endothelial cells in vitro

Human umbilical vein endothelial cells (HUVEC) were used as an experimental host model to investigate the mechanism(s) of streptococcal adhesion in infective endocarditis. Adhesion activity of Streptococcus gordonii was maximal during the logarithmic phase of growth and was greatly reduced or eliminated by pretreatment of bacteria with heat, formaldehyde, or trypsin. At saturating numbers of streptococci, an average of 81 bacteria were bound per HUVEC. Streptococcal adhesion was inhibited by low-molecular-weight dextran and heparin but not by sucrose, fibronectin, or laminin. Adhesion was also prevented by pretreatment of HUVEC with proteins dissociated from the surface of S. gordonii with 10 mM EDTA or isolated from spent culture medium. Western blot (immunoblot) assays detected a single adhesion protein of 153 kDa (AP153) on HUVEC after incubation with unfractionated extracts of streptococci. The adhesin exhibited glucosyltransferase (GTF) activity when incubated with sucrose and Triton X-100 after sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The AP153 was purified by affinity chromatography on dextran beads and show to have binding activity for HUVEC, GTF activity, an amino acid composition similar to that reported for GTF of S. gordonii, and the ability to inhibit S. gordonii adhesion. Incubation of the streptococci with antibodies to the adhesin inhibited bacterial attachment to HUVEC monolayers. These results indicate that surface-localized GTF mediates adhesion of S. gordonii to HUVEC in vitro and may serve as a mechanism for colonization of the endocardium in infective endocarditis.
Surface Reconstruction from Unorganized Points Using Self-Organizing Neural Networks

We introduce a novel technique for surface reconstruction from unorganized points by applying Kohonen’s self-organizing map. The topology of the surface is predetermined, and a neural network learning algorithm is carried out to obtain correct 3D coordinates at each vertex of the surface. Edge swap and multiresolution learning are proposed to make the algorithm more effective and more efficient. The whole algorithm is very simple to implement. Experimental results have shown our techniques are successful.
Current issues in biomechanics

Part I: Mechanics of Human Motion Chapter 1. Biomechanics of Distance Running, Keith R. Williams Chapter 2. Biomechanics of the Foot During Locomotion, Mary M. Rogers. Chapter 3. Human Gait: From Clinical Interpretation to Computer Simulation, Christopher L. Vaughan and Michael D. Sussman Chapter 4. Low Back Biomechanics in and The Prevention of Injury Through Safer Lifting, Stuart M. McGill and Robert W. Norman Part II: Basic Tissue Biomechanics Chapter 5. Ligament Biomechanics, David Hawkins Chapter 6. Skeletal Adaptation to Functional Stimuli, Ted S. Gross and Stephen D. Bain Chapter 7. Skeletal Muscle Mechanics and Movement, Robert J. Gregor Part III: Neuromotor Elements Chapter 8. Neuromuscular Basis of the Maximum Voluntary Force Capacity of Muscle, Roger M. Enoka and Andrew J. Fuglevand Chapter 9. Ligamentous Mechanoreceptors and Knee Joint Function: The Neurosensory Hypothesis, Mark D. Grabiner.
Quantitative cell polarity imaging defines leader-to-follower transitions during collective migration and the key role of microtubule-dependent adherens junction formation

The directed migration of cell collectives drives the formation of complex organ systems. A characteristic feature of many migrating collectives is a ‘tissue-scale’ polarity, whereby ‘leader’ cells at the edge of the tissue guide trailing ‘followers’ that become assembled into polarised epithelial tissues en route. Here, we combine quantitative imaging and perturbation approaches to investigate epithelial cell state transitions during collective migration and organogenesis, using the zebrafish lateral line primordium as an in vivo model. A readout of three-dimensional cell polarity, based on centrosomal-nucleus axes, allows the transition from migrating leaders to assembled followers to be quantitatively resolved for the first time in vivo. Using live reporters and a novel fluorescent protein timer approach, we investigate changes in cell-cell adhesion underlying this transition by monitoring cadherin receptor localisation and stability. This reveals that while cadherin 2 is expressed across the entire tissue, functional apical junctions are first assembled in the transition zone and become progressively more stable across the leader-follower axis of the tissue. Perturbation experiments demonstrate that the formation of these apical adherens junctions requires dynamic microtubules. However, once stabilised, adherens junction maintenance is microtubule independent. Combined, these data identify a mechanism for regulating leader-to-follower transitions within migrating collectives, based on the relocation and stabilisation of cadherins, and reveal a key role for dynamic microtubules in this process.
Richness and distribution of tropical oyster parasites in two oceans

SUMMARY Parasites can exert strong effects on population to ecosystem level processes, but data on parasites are limited for many global regions, especially tropical marine systems. Characterizing parasite diversity and distributions are the first steps towards understanding the potential impacts of parasites. The Panama Canal serves as an interesting location to examine tropical parasite diversity and distribution, as it is a conduit between two oceans and a hub for international trade. We examined metazoan and protistan parasites associated with ten oyster species collected from both Panamanian coasts, including the Panama Canal and Bocas del Toro. We found multiple metazoan taxa (pea crabs, Stylochus spp., Urastoma cyrinae). Our molecular screening for protistan parasites detected four species of Perkinsus (Perkinsus marinus, Perkinsus chesapeaki, Perkinsus olseni, Perkinsus beihaiensis) and several haplosporidians, including two genera (Minchinia, Haplosporidium). Species richness was higher for the protistan parasites than for the metazoans, with haplosporidian richness being higher than Perkinsus richness. Perkinsus species were the most frequently detected and most geographically widespread among parasite groups. Parasite richness and overlap differed between regions, locations and oyster hosts. These results have important implications for tropical parasite richness and the dispersal of parasites due to shipping associated with the Panama Canal.
Boolean Propagation Based on Literals for Quantified Boolean Formulae

This paper proposes a new set of propagation rules for quantified Boolean formulae based on literals and generated automatically thanks to quantified Boolean formulae certificates. Different decompositions by introduction of existentially quantified variables are discussed in order to construct complete systems. This set of rules is compared with already proposed quantified Boolean propagation rule sets and Stalmarck's method.
A Hierarchical-Spectrum Model of Mental Disorders: Genetic, Developmental, and Interpersonal Perspectives

The current project aimed to determine whether a recently developed explanatory model for comorbidity patterns--labeled the Hierarchical-Spectrum Model (HSM)--could serve as a useful organizing framework for research on psychopathology. The HSM accounts for the high co-occurrence of depressive and anxiety disorders by representing them as facets of an overarching Internalizing dimension; likewise, the substance use and antisocial behavior disorders are represented as facets of an Externalizing dimension. In latent variable modeling terms, the HSM parses the shared and unique variance of disorders into transdiagnostic latent factors (i.e., Internalizing and Externalizing dimensions) and diagnosis-specific residuals, respectively. This project integrated the HSM quantitative structure with prominent genetic and psychosocial theories of psychopathology. Results from Study 1 demonstrated that the relationship of early environmental adversity with psychopathology in young adulthood is partly mediated by the transdiagnostic dimensions. At the same time, early adversity was associated with several residual variances of the HSM, signaling the presence of diagnosis-specific pathways from early adversity to mental disorder. Study 2 conceptualized the stress generation hypothesis, which posits that people with a history of depression, relative to their never-depressed counterparts, experience more stressful life events dependent at least in part on their own behavior, through the lens of the HSM. Results revealed stress generating effects of the Internalizing and Externalizing dimensions, suggesting that the stress generation phenomenon is not specific to any one diagnostic category. Yet, the diagnosis-specific components of major depression and dysthymia also contributed to stress generation over and above the effects of the transdiagnostic dimensions, suggesting there is some pathology unique to depression that confers vulnerability to stress exposure. In Study 3, a daily diary methodology was used to examine day-to-day fluctuations of HSM symptoms. Consistent with expectations, elevated daily stress levels predicted increases in both Internalizing and Externalizing symptoms. Further, a widely studied polymorphism in the serotonin transporter gene (5-HTTLPR) moderated the relationship between daily stress and Internalizing, but not Externalizing, symptoms. Together, the current findings suggest that the HSM has the potential to be a useful framework for research, treatment, and classification in clinical psychology.
Is diabetes prevalence higher among HIV-infected individuals compared with the general population? Evidence from MMP and NHANES 2009–2010

Background Nationally representative estimates of diabetes mellitus (DM) prevalence among HIV-infected adults in the USA are lacking, and whether HIV-infected adults are at increased risk of DM compared with the general adult population remains controversial. Methods We used nationally representative survey (2009–2010) data from the Medical Monitoring Project (n=8610 HIV-infected adults) and the National Health and Nutrition Examination Survey (n=5604 general population adults) and fit logistic regression models to determine and compare weighted prevalences of DM between the two populations, and examine factors associated with DM among HIV-infected adults. Results DM prevalence among HIV-infected adults was 10.3% (95% CI 9.2% to 11.5%). DM prevalence was 3.8% (CI 1.8% to 5.8%) higher in HIV-infected adults compared with general population adults. HIV-infected subgroups, including women (prevalence difference 5.0%, CI 2.3% to 7.7%), individuals aged 20–44 (4.1%, CI 2.7% to 5.5%), and non-obese individuals (3.5%, CI 1.4% to 5.6%), had increased DM prevalence compared with general population adults. Factors associated with DM among HIV-infected adults included age, duration of HIV infection, geometric mean CD4 cell count, and obesity. Conclusions 1 in 10 HIV-infected adults receiving medical care had DM. Although obesity contributes to DM risk among HIV-infected adults, comparisons to the general adult population suggest that DM among HIV-infected persons may develop at earlier ages and in the absence of obesity.
Transductive Learning of Structural SVMs via Prior Knowledge Constraints

Reducing the number of labeled examples required to learn accurate prediction models is an important problem in structured output prediction. In this paper we propose a new transductive structural SVM algorithm that learns by incorporating prior knowledge constraints on unlabeled data. Our formulation supports dierent types of prior knowledge constraints, and can be trained eciently. Experiments on two citation and advertisement segmentation tasks show that our transductive structural SVM can learn eectively from unlabeled data, achieving similar prediction accuracies when compared against other state-of-art algorithms.
Gray Matter Pathology in MS: Neuroimaging and Clinical Correlations

It is abundantly clear that there is extensive gray matter pathology occurring in multiple sclerosis. While attention to gray matter pathology was initially limited to studies of autopsy specimens and biopsies, the development of new MRI techniques has allowed assessment of gray matter pathology in vivo. Current MRI techniques allow the direct visualization of gray matter demyelinating lesions, the quantification of diffuse damage to normal appearing gray matter, and the direct measurement of gray matter atrophy. Gray matter demyelination (both focal and diffuse) and gray matter atrophy are found in the very earliest stages of multiple sclerosis and are progressive over time. Accumulation of gray matter damage has substantial impact on the lives of multiple sclerosis patients; a growing body of the literature demonstrates correlations between gray matter pathology and various measures of both clinical disability and cognitive impairment. The effect of disease modifying therapies on the rate accumulation of gray matter pathology in MS has been investigated. This review focuses on the neuroimaging of gray matter pathology in MS, the effect of the accumulation of gray matter pathology on clinical and cognitive disability, and the effect of disease-modifying agents on various measures of gray matter damage.