Miracle-dz/UniFAR-FTUs huggingface dataset:
Left Ventricular T-Cell Recruitment Contributes to the Pathogenesis of Heart Failure

Background—Despite the emerging association between heart failure (HF) and inflammation, the role of T cells, major players in chronic inflammation, has only recently begun to be explored. Whether T-cell recruitment to the left ventricle (LV) participates in the development of HF requires further investigation to identify novel mechanisms that may serve for the design of alternative therapeutic interventions. Methods and Results—Real-time videomicroscopy of T cells from nonischemic HF patients or from mice with HF induced by transverse aortic constriction revealed enhanced adhesion to activated vascular endothelial cells under flow conditions in vitro compared with T cells from healthy subjects or sham mice. T cells in the mediastinal lymph nodes and the intramyocardial endothelium were both activated in response to transverse aortic constriction and the kinetics of LV T-cell infiltration was directly associated with the development of systolic dysfunction. In response to transverse aortic constriction, T cell–deficient mice (T-cell receptor, TCR&agr;−/−) had preserved LV systolic and diastolic function, reduced LV fibrosis, hypertrophy and inflammation, and improved survival compared with wild-type mice. Furthermore, T-cell depletion in wild-type mice after transverse aortic constriction prevented HF. Conclusions—T cells are major contributors to nonischemic HF. Their activation combined with the activation of the LV endothelium results in LV T-cell infiltration negatively contributing to HF progression through mechanisms involving cytokine release and induction of cardiac fibrosis and hypertrophy. Reduction of T-cell infiltration is thus identified as a novel translational target in HF.
Making Neural Programming Architectures Generalize via Recursion

Empirically, neural networks that attempt to learn programs from data have exhibited poor generalizability. Moreover, it has traditionally been difficult to reason about the behavior of these models beyond a certain level of input complexity. In order to address these issues, we propose augmenting neural architectures with a key abstraction: recursion. As an application, we implement recursion in the Neural Programmer-Interpreter framework on four tasks: grade-school addition, bubble sort, topological sort, and quicksort. We demonstrate superior generalizability and interpretability with small amounts of training data. Recursion divides the problem into smaller pieces and drastically reduces the domain of each neural network component, making it tractable to prove guarantees about the overall system's behavior. Our experience suggests that in order for neural architectures to robustly learn program semantics, it is necessary to incorporate a concept like recursion.
Breast Field Cancerization: Isolation and Comparison of Telomerase-Expressing Cells in Tumor and Tumor Adjacent, Histologically Normal Breast Tissue

Telomerase stabilizes chromosomes by maintaining telomere length, immortalizes mammalian cells, and is expressed in more than 90% of human tumors. However, the expression of human telomerase reverse transcriptase (hTERT) is not restricted to tumor cells. We have previously shown that a subpopulation of human mammary epithelial cells (HMEC) in tumor-adjacent, histologically normal (TAHN) breast tissues expresses hTERT mRNA at levels comparable with levels in breast tumors. In the current study, we first validated a reporter for measuring levels of hTERT promoter activity in early-passage HMECs and then used this reporter to compare hTERT promoter activity in HMECs derived from tumor and paired TAHN tissues 1, 3, and 5 cm from the tumor (TAHN-1, TAHN-3, and TAHN-5, respectively). Cell sorting, quantitative real-time PCR, and microarray analyses showed that the 10% of HMECs with the highest hTERT promoter activity in both tumor and TAHN-1 tissues contain more than 95% of hTERT mRNA and overexpress many genes involved in cell cycle and mitosis. The percentage of HMECs within this subpopulation showing high hTERT promoter activity was significantly reduced or absent in TAHN-3 and TAHN-5 tissues. We conclude that the field of “normal tissue” proximal to the breast tumors contains a population of HMECs similar in hTERT expression levels and in gene expression to the HMECs within the tumor mass and that this population is significantly reduced in tissues more distal to the tumor. Mol Cancer Res; 9(9); 1209–21. ©2011 AACR.
Modelling of fume formation in arc welding: the influence of oxygen

A zero-dimensional model that couples chemical kinetics and particle growth is used to investigate the influence of oxygen in the formation of fume in arc welding. A three-dimensional computational model of the arc, which includes the vaporization of the wire electrode, is used to provide the input parameters to the zero-dimensional model. In the presence of oxygen, FeO nanoparticles are produced, which are smaller and more numerous than the Fe nanoparticles formed in the absence of oxygen.
Disruption of the Saccharomyces cerevisiae Homologue to the Murine Fatty Acid Transport Protein Impairs Uptake and Growth on Long-chain Fatty Acids*

The yeast Saccharomyces cerevisiae is able to utilize exogenous fatty acids for a variety of cellular processes including β-oxidation, phospholipid biosynthesis, and protein modification. The molecular mechanisms that govern the uptake of these compounds in S. cerevisiae have not been described. We report the characterization of FAT1, a gene that encodes a putative membrane-bound long-chain fatty acid transport protein (Fat1p). Fat1p contains 623 amino acid residues that are 33% identical and 54% with similar chemical properties as compared with the fatty acid transport protein FATP described in 3T3-L1 adipocytes (Schaffer and Lodish (1994) Cell 79, 427-436), suggesting a similar function. Disruption of FAT1 results in 1) an impaired growth in YPD medium containing 25 μM cerulenin and 500 μM fatty acid (myristate (C14:0), palmitate (C16:0), or oleate (C18:1)); 2) a marked decrease in the uptake of the fluorescent long-chain fatty acid analogue boron dipyrromethene difluoride dodecanoic acid (BODIPY-3823); 3) a reduced rate of exogenous oleate incorporation into phospholipids; and 4) a 2-3-fold decrease in the rates of oleate uptake. These data support the hypothesis that Fat1p is involved in long-chain fatty acid uptake and may represent a long-chain fatty acid transport protein.
Detection of human herpesvirus 7 DNA in peripheral blood reflects mainly CD4+ cell count in patients infected with HIV

The opportunistic behavior and the potential interactions of human herpesvirus 7 (HHV‐7) with human immunodeficiency virus (HIV)‐1 in HIV‐1‐infected patients were investigated in comparison with HHV‐6, another human roseolovirus. Roseolovirus DNAs were detected and quantified in peripheral blood mononuclear cells (PBMCs) from 198 HIV‐seronegative healthy blood donors, 38 HIV‐1‐infected patients classified as long‐term non‐progressors, and 99 HIV‐1‐infected patients classified as progressors. The rate of HHV‐7 DNA detection was higher in healthy donors (78%) than in long‐term non‐progressors (47%; P = 0.0003) or in progressors (52%; P < 0.0001). HHV‐7 cell load was higher in healthy donors (median: 212 EqCop/106 PBMCs) and in long‐term non‐progressors (median: 105 EqCop/106 PBMCs) than in progressors (median: 48 EqCop/106 PBMCs; P < 0.0001 and P = 0.015, respectively). Among progressors, HHV‐7 detection was correlated positively with the CD4+ T‐lymphocyte count (P = 0.028). Neither HHV‐7 detection rate nor cell load was correlated with the HIV‐1 plasma load. As a whole, HHV‐6 detection rate and cell load were lower than the HHV‐7 counterparts, albeit exhibiting similar differences between healthy donors, long‐term non‐progressors, and progressors. In conclusion, HHV‐7 infection does not appear to be stimulated by HIV‐1 infection, nor interact with it. Rather, HHV‐7 detection rate and cell load reflect CD4+ T‐lymphocyte count, with higher values in healthy donors and long‐term non‐progressors than in progressors. J. Med. Virol. 76:223–228, 2005. © 2005 Wiley‐Liss, Inc.
On designing and evaluating speech event detectors

We study issues related to designing speech event detectors for automatic speech recognition. Event detection is a critical component of a recently proposed automatic speech attribute transcription (ASAT) paradigm for speech research. Similar to keyword spotting and non-keyword rejection, a good detector needs to effectively detect speech attributes of interest while rejecting extraneous events. We compare frame and segment based detectors, study their properties in detecting manners of articulation, and propose new performance measures. We test these detectors on the TIMIT database with several evaluation criteria. Our results indicate that segment based detectors outperform frame based detectors in several key aspects of speech detector design. We also show that the performance can be significantly enhanced by incorporating discriminative training into designing speech event detectors.
Preoperative Differential Diagnosis of Canine Adrenal Tumors Using Triple-Phase Helical Computed Tomography.

OBJECTIVE To characterize the computed tomography (CT) findings for canine adrenal tumors, including cortical adenoma, cortical adenocarcinoma, and pheochromocytoma, and to evaluate the feasibility and usefulness of preoperative triple-phase helical CT for differentiation of tumor types and surgical planning. STUDY DESIGN Retrospective study. ANIMALS Dogs with adrenal tumors (n=36). METHODS All dogs underwent triple-phase helical CT, followed by adrenalectomy and histopathological diagnosis of the resected mass. Precontrast images, arterial, venous, and delayed phase images were obtained. In all cases, morphological characteristics and CT values and calculations, including the percentage enhancement washout ratio, relative percentage washout, enhancement washin, and enhancement washout, were analyzed and compared among the tumor types. RESULTS Of the 36 dogs with adrenal masses, cortical adenocarcinoma was most commonly diagnosed (16 dogs), followed by pheochromocytoma (13 dogs), and cortical adenoma (7 dogs). The precontrast minimum CT value and enhancement washout between venous and delayed phases in the cortical adenoma were significantly higher than those in the cortical adenocarcinoma. The maximum CT values of the precontrast image and arterial and venous phases, the enhancement washin and washouts, percentage enhancement washout ratio, and relative percentage washout in the pheochromocytomas were significantly higher than those in cortical adenocarcinoma. CONCLUSION The differential diagnosis of canine adrenal tumors was feasible based on triple-phase CT findings, including morphological features, CT values, and intratumoral contrast attenuation. Preoperative diagnosis using triple-phase helical CT may be useful for surgical planning in dogs with adrenal tumors.
The Functional Interplay between Protein Kinase CK2 and CCA1 Transcriptional Activity Is Essential for Clock Temperature Compensation in Arabidopsis

Circadian rhythms are daily biological oscillations driven by an endogenous mechanism known as circadian clock. The protein kinase CK2 is one of the few clock components that is evolutionary conserved among different taxonomic groups. CK2 regulates the stability and nuclear localization of essential clock proteins in mammals, fungi, and insects. Two CK2 regulatory subunits, CKB3 and CKB4, have been also linked with the Arabidopsis thaliana circadian system. However, the biological relevance and the precise mechanisms of CK2 function within the plant clockwork are not known. By using ChIP and Double–ChIP experiments together with in vivo luminescence assays at different temperatures, we were able to identify a temperature-dependent function for CK2 modulating circadian period length. Our study uncovers a previously unpredicted mechanism for CK2 antagonizing the key clock regulator CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1). CK2 activity does not alter protein accumulation or subcellular localization but interferes with CCA1 binding affinity to the promoters of the oscillator genes. High temperatures enhance the CCA1 binding activity, which is precisely counterbalanced by the CK2 opposing function. Altering this balance by over-expression, mutation, or pharmacological inhibition affects the temperature compensation profile, providing a mechanism by which plants regulate circadian period at changing temperatures. Therefore, our study establishes a new model demonstrating that two opposing and temperature-dependent activities (CCA1-CK2) are essential for clock temperature compensation in Arabidopsis.
Resource efficient mobile communications for crowd-sensing

Due to continuously growing communication traffic of emerging mobile phone applications, resource-efficient communication is a key to affordable network services with high Quality of Experience. While some communication traffic requires immediate resource allocations (such as voice services), an increasing number of mobile phone applications produce a lot of background communication traffic (e.g. social network apps, crowd sensing services). In this paper we discuss the predictive Channel-Aware Transmission (pCAT) scheme, which leverages the fact, that favorable channel conditions require much less spectrum resource allocation than bad channel conditions. By leveraging the knowledge of user trajectories and recurring spots with favorable channel conditions, the so-called LTE connectivity hot spots, background traffic transmissions can be scheduled by the client according to expected channel quality and application data priority. Thereby, the spectrum consumption of background traffic of applications can be reduced significantly. At the same time, the efficient usage of spectrum resources has also an impact on the battery lifetime of the mobile devices. By introducing the Context-Aware Power Consumption Model (CoPoMo) for LTE communications, we highlight, how decisions about the spectrum resource allocation by the network will impact the battery lifetime. One case study will show, that by simply changing the resource allocation scheme and without the need for spending more spectrum resources, the power consumption can be reduced by more than 70% using the Energy-Efficient Scheduling (EES) introduced in this paper.
Latent epistatic interaction model identifies loci associated with human working memory

Background Epistatic interactions among genomic loci are expected to explain a large fraction of the heritability of complex diseases and phenotypic traits of living organisms. Although epistasis detection methods are continually being developed, the current state of the art is exhaustive search methods, which become infeasible when the number of analyzed loci is large. Results We develop a novel latent interaction-based selection method for polymorphic loci as the first stage of a two-stage epistasis detection approach. Given a continuous phenotype and a single-nucleotide polymorphism (SNP), we rank the SNPs according to their interaction potential. When tested on simulated datasets and compared to standard marginal association and exhaustive search methods, our procedure significantly outperforms main-effect heuristics, especially in the presence of linkage disequilibrium (LD), which is explicitly accounted for in our model. Applied to real human genotype data, we prioritized several SNP pairs as candidates for epistatic interactions that influence human working memory performance, some of which are known to be connected to this phenotype. Conclusions The proposed method improves two-stage epistasis detection. Its linear runtime and increased statistical power contribute to reducing the computational complexity and to addressing some of the statistical challenges associated with the genome-wide search for epistatic loci.
Non-oscillation of half-linear differential equations with periodic coefficients

We consider half-linear Euler type differential equations with general periodic coefficients. It is well-known that these equations are conditionally oscillatory, i.e., there exists a border value given by their coefficients which separates oscillatory equations from non-oscillatory ones. In this paper, we study oscillatory properties in the border case. More precisely, we prove that the considered equations are non-oscillatory in this case. Our results cover the situation when the periodic coefficients do not have any
One hundred in-patient suicides

Background The study aimed to define the characteristics and assess the clinical predictability and possible prevention of psychiatric in-patient suicides. Method The coroner's files on all suicides in the Greater Montreal Region from 1 April 1986 to 31 March 1991 were examined. The medical records of each case of suspected in-patient suicide were then reviewed and rated for predictability and preventive measures taken. Results A total of 3079 suicides were recorded over this five-year period (mean annual rate of 16.4 per 100 000 inhabitants). Of these, 104 (3.4%) involved hospital in-patients. Nearly half (48%) of these in-patient suicides occurred outside the hospital setting. The methods most frequently employed were hanging (36%) and jumping from high places (24%). Patients suffering from an affective disorder (45%) or schizophrenia (35%) comprised the majority of the sample. Suicides were significantly more predictable in general hospital psychiatric wards. Suicide prevention measures did not differ significantly across settings. Conclusions The majority of in-patient suicides were not highly predictable. For highly predictable suicides, the results underline the importance of actively treating and protecting these patients.
Pegasparaginase: where do we stand?

The use of unmodified asparaginases (ASP) in the management of pediatric and adult acute lymphoblastic leukemia (ALL) is well established. Despite its well-proven clinical efficacy, the use of unmodified Escherichia coli ASP (EC-ASP) has been limited by frequent toxicities, especially the development of hypersensitivity reactions and neutralizing antibodies, and by the need for frequent administration. To overcome these limitations, EC-ASP enzyme was covalently linked to monomethoxypolyethylene glycol (PEG), forming the pegylated ASP (PEG-ASP) (Oncaspar®). PEG-ASP has a prolonged half-life and is associated with decreased immunogenicity when compared with EC-ASP. Clinical trials have demonstrated the efficacy, safety and tolerability of PEG-ASP administered intramuscularly, subcutaneously or intravenously as part of multi-agent chemotherapy regimens in the management of newly diagnosed and relapsed pediatric and adult ALL. Here we discuss the pharmacology, pharmacokinetics, clinical trial results and potential side effects of PEG-ASP.
Multi-class support vector machine

We propose a transformation from the multi-class support vector machine (SVM) classification problem to the single-class SVM problem which is more convenient for optimization. The proposed transformation is based on simplifying the original problem and employing the Kesler construction which can be carried out by the use of properly defined kernel only. The experiments conducted indicate that the proposed method is comparable with the one-against-all decomposition solved by the state-of-the-art sequential minimal optimizer algorithm.
Dual role of ERK5 in the regulation of T cell receptor expression at the T cell surface

Regulation of the levels of the TCR/CD3 complex at the cell surface is critical to proper T cell development and mature T cell activation. We provide evidence that the MAPK ERK5 regulates the surface expression of the TCR/CD3 complex by controlling the degradation of the CD3ζ chain and the recovery of the complex after anti‐CD3ɛ stimulation. ERK5 knockdown led to TCR/CD3 up‐regulation at the cell surface and increased amounts of the CD3ζ chain. Inhibition of the MEK5‐dependent phosphorylation status of the kinase domain of ERK5 in human T CD4+ cells reduced CD3ζ ubiquitination and degradation, limiting TCR/CD3 down‐regulation in anti‐CD3‐stimulated cells. Moreover, TCR/CD3 recovery at the cell surface, after anti‐CD3ɛ treatment, is impaired by ERK5 knockdown or pharmacological inhibition of autophosphorylation in the ERK5 C‐terminal region. ERK5 loss in thymocytes augmented cellular CD3ζ and increased cell surface levels of TCR/CD3 on CD4+CD8+ thymocytes. This correlated with enhanced generation of CD4+CD8−CD25+ thymocytes. Our findings define ERK5 as a novel kinase that modulates the levels of TCR/CD3 at the cell surface by promoting CD3ζ degradation and TCR/CD3 recovery after TCR stimulation.
Relevance and Diversity of Nitrospira Populations in Biofilters of Brackish RAS

Lithoautotrophic nitrite-oxidizing bacterial populations from moving-bed biofilters of brackish recirculation aquaculture systems (RAS; shrimp and barramundi) were tested for their metabolic activity and phylogenetic diversity. Samples from the biofilters were labeled with 13C-bicarbonate and supplemented with nitrite at concentrations of 0.3, 3 and 10 mM, and incubated at 17 and 28°C, respectively. The biofilm material was analyzed by fatty acid methyl ester - stable isotope probing (FAME-SIP). High portions of up to 45% of Nitrospira-related labeled lipid markers were found confirming that Nitrospira is the major autotrophic nitrite oxidizer in these brackish systems with high nitrogen loads. Other nitrite-oxidizing bacteria such as Nitrobacter or Nitrotoga were functionally not relevant in the investigated biofilters. Nitrospira-related 16S rRNA gene sequences were obtained from the samples with 10 mM nitrite and analyzed by a cloning approach. Sequence studies revealed four different phylogenetic clusters within the marine sublineage IV of Nitrospira, though most sequences clustered with the type strain of Nitrospira marina and with a strain isolated from a marine RAS. Three lipids dominated the whole fatty acid profiles of nitrite-oxidizing marine and brackish enrichments of Nitrospira sublineage IV organisms. The membranes included two marker lipids (16∶1 cis7 and 16∶1 cis11) combined with the non-specific acid 16∶0 as major compounds and confirmed these marker lipids as characteristic for sublineage IV species. The predominant labeling of these characteristic fatty acids and the phylogenetic sequence analyses of the marine Nitrospira sublineage IV identified organisms of this sublineage as main autotrophic nitrite-oxidizers in the investigated brackish biofilter systems.
Surface Field Measurements From a Buried UHF Transmitter: Theory, Modeling and Experimental Results

Electromagnetic interference between a direct ray and a lateral wave was postulated theoretically but has been only observed near to the ground surface in a forest canopy. This communication reports surface measurements of the electric field profile from a 433 MHz transmitter buried up to 600 mm in sand (relative permittivity 2.13, conductivity 10−4 S/m). A strong interference pattern with nulls greater than −20 dB were observed extending laterally to more than 5 m. This interference was evident when both the transmitter and receiver lay on the surface and when separated by an above ground conducting shield. Forward modeling using the impedance method and the finite integral technique adequately predict the interference pattern. These observations impact open-pit mining, surface and buried wireless sensor networks, and under-road communications systems.