Miracle-dz/UniFAR-FTUs huggingface dataset:
Clustering With Orthogonal AutoEncoder

Recently, clustering algorithms based on deep AutoEncoder attract lots of attention due to their excellent clustering performance. On the other hand, the success of PCA-Kmeans and spectral clustering corroborates that the orthogonality of embedding is beneficial to increase the clustering accuracy. In this paper, we propose a novel dimensional reduction model, called Orthogonal AutoEncoder (OAE), which encourages the orthogonality of the learned embedding. Furthermore, we propose a joint deep Clustering framework based on Orthogonal AutoEncoder (COAE), and this new framework is capable of extracting the latent embedding and predicting the clustering assignment simultaneously. The COAE stacks a fully connected clustering layer on top of the OAE, where the activation function of the clustering layer is the multinomial logistic regression function. The loss function of the COAE contains two terms: the reconstruction loss and the clustering-oriented loss. The first one is a data-dependent term in order to prevent overfitting. The other one is the cross entropy between the predicted assignment and the auxiliary target distribution. The network parameters of the COAE can be effectively updated by the mini-batch stochastic gradient descent algorithm and the back-propagation approach. The experiments on benchmark datasets empirically demonstrate that the COAE can achieve superior or competitive clustering performance as state-of-the-art deep clustering frameworks. The implementation of our algorithm is available at https://github.com/WangDavey/COAE
The relationship between plasma lipids, oxidant–antioxidant status, and glycated proteins in individuals at risk for atherosclerosis

Objective: Ageing is one of the major risks for atherosclerosis. The age-related changes of interactions between plasma lipids, oxidative stress, antioxidant defense, and glycation processes are still not established while we age. Thus, the aim of the study was to analyze such relationships in individuals at risk for atherosclerosis due to their age. Methods: Elderly and middle-aged persons with no acute disease or severe chronic disorder were assessed. Fasting plasma lipids (total cholesterol (T-C), high-density lipoprotein-cholesterol (HDL-C), low-density lipoprotein-cholesterol, and triacylglycerols), thiobarbituric acid reacting substances (TBARS), plasma total antioxidant status (TAS), and glucose and glycated proteins (fructosamine (FA) and glycated hemoglobin (HbA1c)) were determined. An oral glucose tolerance test allowed exclusion of persons with type 2 diabetes. Results: Lipid profiles were significantly profitable, increased HDL-C especially (p<0.0001), in the elderly versus middle-aged group. Decreased TBARS and TAS were found in the elderly versus middle-aged group (p=0.0001 and p=0.00002, respectively). Increased fructosamine was found in the elderly (255±30 μmol/L) versus middle-aged (236±33 μmol/L) group (p=0.006). Multiple regression analysis showed that in the middle-aged group TBARS correlated with T-C and HDL-C, and in the elderly group with HbA1c and FA independently of other factors. Conclusion: The factors which have an impact on oxidant–antioxidant status are crucial to understanding the pathomechanisms of senescence as well as the development of chronic diseases. Healthy aging may be maintained throughout proper lipid control. Moreover, data support the premise that the balance between lipid metabolism and oxidative stress may play a role in the initial phases of glycation plasma proteins particularly among elderly persons.
On the development of a sliding mode observer-based fault diagnosis scheme for a wind turbine benchmark model

This paper addresses the design of an observer-based fault diagnosis scheme, which is applied to some of the sensors and actuators of a wind turbine benchmark model. The methodology is based on a modified sliding mode observer (SMO) that allows accurate reconstruction of multiple sensor or actuator faults occurring simultaneously. The faults are reconstructed using the equivalent output error injection signal. A well-known validated wind turbine benchmark model, developed by Aalborg University and KK-electronic a/c, is utilized to evaluate the FDD scheme. Different sensors and actuator fault scenarios are simulated in the drive train, generator, and pitch & blade subsystems of the benchmark model, and attempts have been made to estimate these faults via the proposed modified SMO. The simulation results confirm the effectiveness of the proposed diagnosis scheme, and the faults are well detected, isolated, and reconstructed in the presence of the measurement noise.
The Solution of Parametrized Symmetric Linear Systems

We compare the Lanczos and MINRES methods for the solution of symmetric linear systems with a linear parameter arising from structural engineering. We show a connection with the Pade-via-Lanczos method. We propose an error estimation for the solution in finite precision arithmetic. The use of reorthogonalization is discussed and practical algorithms are given. The theory is illustrated with numerical examples.
Reduction in Cardiovascular Death After Kidney Transplantation

Background. Cardiovascular (CVS) disease is the commonest cause of death after kidney transplantation. In the general population, CVS mortality has reduced significantly over the last two decades; however, this trend has not been specifically examined in the kidney transplant population. Methods: We studied all patients in Australia and New Zealand with a functioning kidney transplant between 1980 and 2007 and examined trends in the cause and timing of all 2195 deaths recorded after kidney transplantation in the Australia and New Zealand Dialysis and Transplant registry. Poisson regression was used to compare death rates over the time periods. Results: CVS events were the commonest cause of death throughout all the time points examined; however, CVS death rates significantly decreased with an adjusted risk ratio of 0.61 (95% confidence interval, 0.38–0.96; P=0.034) for 2005 to 2007 era. In comparison, death rates due to malignancy have increased significantly over this period. Decreased CVS death rates have occurred despite increasing comorbidity at the time of transplantation. Factors associated with CVS death were older recipient age, preexisting CVS disease, and diabetes mellitus. There was a significantly lower CVS death rate in patients with a glomerular filtration rate >48 mL/min compared with those with poor renal function (risk ratio, 0.66; 95% confidence interval, 0.45–0.95; P=0.024). Conclusions: These trends suggest improvements in CVS risk management and outcomes in the kidney transplant population in Australia and New Zealand.
EpCAM‐ and EGFR‐targeted selective gene therapy for biliary cancers using Z33‐fiber‐modified adenovirus

A critical issue in adenovirus (Ad)‐based cancer gene therapy is to improve the specificity of gene delivery to cancer cells for better efficacy and safety. We explored methods of retargeting Ad vectors for selective gene therapy of human biliary cancers using the Ad incorporating an IgG Fc‐binding motif (Z33) from the Staphylococcus protein A (Ad‐FZ33) combined with tumor‐specific antibodies. Flow cytometry analysis revealed high‐expression levels of epithelial cell adhesion molecule (EpCAM) and epidermal growth factor receptor (EGFR) on human biliary cancer cells. Ad‐FZ33 expressing LacZ combined with antibodies against EpCAM or EGFR, followed by β‐gal assay, demonstrated highly efficient gene transduction in these biliary cancer cells, compared to the treatment with control antibody or without antibody. Ad‐FZ33 expressing uracil phosphoribosyl transferase (UPRT), an enzyme which greatly enhances the toxicity of 5‐fluorouracil (FU), combined with antibodies against EpCAM or EGFR, remarkably enhanced the sensitivity of biliary cancer cells to 5‐FU. By contrast, the treatment did not affect the 5‐FU sensitivity of the cells not expressing EpCAM or EGFR including normal hepatocytes. Finally, treatments with the UPRT‐expressing Ad‐FZ33 with antibodies against EpCAM or EGFR, followed by 5‐FU administration, significantly suppressed the growth of biliary cancer xenografts in nude mice. These results indicate that the gene therapy mediated by the Z33 fiber modified Ad with anti‐EpCAM or anti‐EGFR antibodies offers a potentially effective therapeutic modality against biliary cancers.
Determinants of Antiretroviral Therapy Initiation and Treatment Outcomes for People Living With HIV in Vietnam

Abstract Objectives: This study explores patient characteristics that are significantly associated with very late combination antiretroviral therapy (cART) initiation (CD4 count ≤100 cells/mm3) and examines the association between patient characteristics and treatment outcomes, CD4 recovery, and mortality. Design: Data were obtained from the clinical records of 2,198 HIV/AIDS patients in 13 outpatient clinics across 6 provinces in Vietnam. Methods: Multivariate logistic regression and Cox proportional hazards regression were used to identify patient characteristics that are significantly associated with very late cART initiation and to measure relationships between patient characteristics and treatment outcomes. Results: Very late cART initiation was significantly associated with being male compared with female (odds ratio [OR], 0.36; 95% CI, 0.23–0.58), becoming HIV infected through injecting drugs (OR, 2.13; 95% CI, 1.09–4.14), and having opportunistic infections at cART initiation (OR, 1.69; 95% CI, 1.02–2.86). Being male (female vs male: hazard ratio [HR], 0.45; 95% CI, 0.20–0.98), very late cART initiation (timely vs late: HR, 0.18; 95% CI, 0.04–0.72), low baseline body mass index (BMI) (HR, 0.95; 95% CI, 0.92–0.98), and later baseline WHO clinical stage (WHO clinical stage IV vs combined group of stage I and II: HR, 5.70; 95% CI, 3.90–7.80) were significantly associated with death, whereas being female compared with male (HR, 1.51; 95% CI, 1.14–1.99) and timely cART initiation (HR, 35.45; 95% CI, 13.67–91.91) were significant predictors of CD4 recovery. Conclusions: Timely testing of patients for HIV, increasing use of CD4 count testing services, and starting cART earlier are essential to reduce mortality and improve treatment outcomes.
ESET/SETDB1 gene expression and histone H3 (K9) trimethylation in Huntington's disease

Chromatin remodeling and transcription regulation are tightly controlled under physiological conditions. It has been suggested that altered chromatin modulation and transcription dysfunction may play a role in the pathogenesis of Huntington's disease (HD). Increased histone methylation, a well established mechanism of gene silencing, results in transcriptional repression. ERG-associated protein with SET domain (ESET), a histone H3 (K9) methyltransferase, mediates histone methylation. We show that ESET expression is markedly increased in HD patients and in transgenic R6/2 HD mice. Similarly, the protein level of trimethylated histone H3 (K9) was also elevated in HD patients and in R6/2 mice. We further demonstrate that both specificity protein 1 (Sp1) and specificity protein 3 (Sp3) act as transcriptional activators of the ESET promoter in neurons and that mithramycin, a clinically approved guanosine–cytosine-rich DNA binding antitumor antibiotic, interferes with the DNA binding of these Sp family transcription factors, suppressing basal ESET promoter activity in a dose dependent manner. The combined pharmacological treatment with mithramycin and cystamine down-regulates ESET gene expression and reduces hypertrimethylation of histone H3 (K9). This polytherapy significantly ameliorated the behavioral and neuropathological phenotype in the R6/2 mice and extended survival over 40%, well beyond any existing reported treatment in HD mice. Our data suggest that modulation of gene silencing mechanisms, through regulation of the ESET gene is important to neuronal survival and, as such, may be a promising treatment in HD patients.
Bronchial hyperresponsiveness and airway inflammation markers in nonasthmatics with allergic rhinitis.

We read with interest the article by POLOSA et al. [1] in which methacholine and adenosine monophosphate (AMP) responsiveness and induced sputum cell counts were measured in 12 subjects with allergic rhinitis due to Parietaria pollen. The subjects had no symptoms of asthma and apparently no cough. However, if a provocative concentration of methacholine causing a 20% fall in forced expiratory volume in one second #8 mg.mL by the method they use is abnormal, eight of the 12 subjects had hyperresponsiveness and might have had asthma, if asthma is defined by variable airflow limitation [2]. Such variable airflow limitation has been identified in similar subjects by abnormal diurnal variation of peak expiratory flow (PEF) or hyperresponsiveness to physical stimuli like hyperventilation of cold dry air [3]. Also, they could have had symptoms of variable airflow limitation but failed to recognize, or to admit to, these [4]. All of the rhinitic subjects had sputum cosinophilia. Are the authors sure there was no contamination with postnasal drip? Assuming there was none, if abnormal sputum cell counts are used to diagnose bronchitis, they all had an eosinophilic bronchitis. Such an eosinophilic bronchitis has previously been reported in subjects with asymptomatic methacholine hyperresponsiveness [5] and in patients with a chronic cough without hyperresponsiveness to methacholinc or AMP [6±8]. Treatment with inhaled steroid or avoidance of the cause [9] can reverse the eosinophilia and improve the degree of airway responsiveness. R. Leigh, M. Kelly, F.E. Hargreave Asthma Research Group, St. Joseph©s Hospital and McMaster University, 50 Charlton Avenue East, Hamilton, ON, Canada, L8N 4A6. Fax: 001 9055216037
Alternative derivation of the Ruska/Langmuir reduced-brightness/spot-blurring formula, and some related comments

This conference poster present an alternative derivation of a well known formula that relates both to the concept of reduced brightness in a charge-particle (CP) beam and to the blurring of field-ion image spots. It is then argued that field ion images provide a practical illustration of some aspects of CP optics, including the issue of whether reduced brightness is always a conserved quantity.
Topical Tenofovir Disoproxil Fumarate Nanoparticles Prevent HIV-1 Vaginal Transmission in a Humanized Mouse Model

ABSTRACT Preexposure prophylaxis (PrEP) with 1% tenofovir (TFV) vaginal gel has failed in clinical trials. To improve TFV efficacy in vaginal gel, we formulated tenofovir disoproxil fumarate nanoparticles in a thermosensitive (TMS) gel (TDF-NP-TMS gel). TDF-NPs were fabricated using poly(lactic-co-glycolic acid) (PLGA) polymer and an ion-pairing agent by oil-in-water emulsification. The efficacy of TDF-NP-TMS gel was tested in humanized bone marrow-liver-thymus (hu-BLT) mice. Hu-BLT mice in the treatment group (Rx; n = 15) were administered TDF-NP-TMS gel intravaginally, having TDF at 0.1%, 0.5%, and 1% (wt/vol) concentrations, whereas the control (Ctr; n = 8) group received a blank TMS gel. All Rx mice (0.1% [n = 4], 0.5% [n = 6], and 1% [n = 5]) were vaginally challenged with two transmitted/founder (T/F) HIV-1 strains (2.5 × 105 50% tissue culture infectious doses). Rx mice were challenged at 4 h (0.1%), 24 h (0.5%), and 7 days (1%) posttreatment (p.t.) and Ctr mice were challenged at 4 h p.t. Blood was drawn weekly for 4 weeks postinoculation (p.i.) for plasma viral load (pVL) using reverse transcription-quantitative PCR. Ctr mice had positive pVL within 2 weeks p.i. Rx mice challenged at 4 h and 24 h showed 100% protection and no detectable pVL throughout the 4 weeks of follow-up (P = 0.009; Mantel-Cox test). Mice challenged at 7 days were HIV-1 positive at 14 days p.i. Further, HIV-1 viral RNA (vRNA) in vaginal and spleen tissues of Rx group mice with negative pVL were examined using an in situ hybridization (ISH) technique. The detection of vRNA was negative in all Rx mice studied. The present studies elucidate TDF-NP-TMS gel as a long-acting, coitus-independent HIV-1 vaginal protection modality.
PATCH SHAPE, CONNECTIVITY, AND FORAGING BY OLDFIELD MICE (PEROMYSCUS POLIONOTUS)

Abstract We examined how corridors and patch shape affect foraging by the oldfield mouse (Peromyscus polionotus) by deploying foraging trays and live traps in experimental landscapes with 3 different patch types: patches connected with a corridor, unconnected patches with projecting corridorlike portions (“winged” patches), and unconnected rectangular patches. Corridors did not lead to different levels of activity of P. polionotus among the 3 patch types. Rather, corridors influenced activity by changing patch shape: foraging in seed trays and total number of captures of P. polionotus tended to be greater at the patch center than at the patch edge, but only in connected and winged patches where corridors or wings increased the amount of patch edge relative to the amount of core habitat in the patch. P. polionotus avoided open microhabitats near the patch edge in winged and connected patches, but not open microhabitats near the patch interior, suggesting that predation risk caused shifts in foraging near edges in connected and winged patches. Foraging in corridors and wings was generally low, suggesting that both are high-risk habitats where predation risk is not ameliorated by proximity to vegetative cover. By changing patch shape, corridors caused changes in within-patch activity of P. polionotus, changing foraging patterns and potentially altering the dynamics of P. polionotus and the seeds they consume.
Design, Synthesis and Evaluation of New 2, 6-Dihydroimidazo[1, 2-c]Pyrimido[5, 4-e]-Pyrimidine-5(3H)-thiones as Possible Antihistaminic/Antiasthmatic Agents§

A series of new 10-(alkylamino)-8-methyl-2, 6-dihydroimidazo[1, 2-c]pyrimido[5, 4-e]pyrimidine-5(3H)-thiones (4a-g) were subjected to molecular property prediction (drug-likeness, lipophilicity and solubility parameters) using Osiris Property Explorer, ALOGPS 2.1, Molinspiration and ACD/Chemsketch 12.0 software programmes. The calculated drug-related properties of the designed molecules were similar to those found in most marketed drugs. Amongst the proposed analogues, four promising candidates were chosen (4a-d) for synthesis on the basis of Lipinski's ‘Rule of Five’ and drug-likeness scores. The significant biological activity of the test compounds in two in vitro modes (isolated guinea pig tracheal chain preparation, isolated guinea pig ileum) supports the promise and accuracy of the prediction. Among them, 4a was the most potent antihistaminic (IC50 value of 30.2 μM; standard, chlorpheniramine maleate showed an IC50 of 14.1 μM).
A Small Open Economy in the Great Depression: The Case of Switzerland

In historical accounts of the world economic crisis of the 1930s, Switzerland is known for its staunch defense of the gold standard and the rise of corporatist policies. Yet, so far, the literature has not discussed the implications of these two features. This paper tries to show how the combination of hard-currency policy and nominal rigidities introduced by corporatist policies proved to be fatal for growth. Estimating a New Keynesian small open economy model for the period 1926-1938, we show that the decision to participate in the Gold Bloc after 1933 at an overvalued currency can be identified as the main reason for the unusual long lasting recession and that price rigidities from 1931 to 1936 significantly slowed down the adjustment process.
Meta-Analysis of Finfish Abundance at Offshore Wind Farms

Abstract Offshore wind farms are becoming increasingly common in the coastal margins of marine ecosystems worldwide. Yet, the effects that wind farm structures have on fish populations remain unclear. To explore potential effects, a meta-analysis of studies that have examined the abundance of finfish inside of wind farms compared to nearby reference sites was conducted. Using well-established meta-analytic methods, the overall effect size across all studies was calculated, and then changes in effect size for soft-bottom and complex-bottom oriented species were explored in association with several covariates including characteristics of the wind farm (depth, distance from shore, wind farm age), the sampling design (season, gear type, and distance from the turbine sampled), and ecosystem level characteristics (functional feeding group and fishing presence/absence). The overall effect size was positive and significantly different from zero, indicating greater abundance of fish inside of wind farms. Likewise, positive and significant effect sizes were noted for several covariates for both soft-bottom and complex-bottom species. The findings of this study underscore the need for regional, national, and international collaboration on monitoring approaches and data sharing in order to develop a more holistic understanding of how offshore wind farms affect living marine resources.
Regulation of Prolactin Secretion by Dopamine at the Level of the Hypothalamus in the Turkey

Avian prolactin (PRL) secretion is regulated by vasoactive intestinal peptide (VIP) neurons residing in the infundibular nuclear complex (INF) of the hypothalamus. This VIPergic activity is modulated by stimulatory dopaminergic inputs. Dynorphin, serotonin (5-HT), dopamine (DA) and VIP all appear to stimulate PRL secretion along a hypothalamic pathway, expressing ĸ opioid, serotonergic, dopaminergic and VIPergic receptors in succession, with the VIPergic system as the final mediator. Electrical stimulation (ES) within the turkey hypothalamus at the level of the medial preoptic area (POA), the ventromedial hypothalamic nucleus (VMN), the INF or the median eminence (ME) results in the release of PRL. When the selective D1 DA receptor antagonist SCH-23390 HCl was infused intraventricularly at the rate of 10 nmol/min, ES in the POA or VMN was unable to increase PRL levels, while ES in the INF and ME did increase PRL to the same level as that of controls. These results were interpreted to suggest that the D1 DA receptors involved in PRL release lie caudally to the VMN and dorsally to the INF. Bilateral microinjections (50 ng) of the D1 DA receptor agonist SKF-38393 HCl into the POA or VMN failed to produce any increase in PRL, while similar microinjections in the INF increased PRL significantly within 15 min. Bilateral microinjections of the D1 DA antagonist (50 ng) into the INF blocked the rise in PRL associated with ES in the POA. Bilateral microinjections of a D2 DA antagonist (50 ng) into the INF failed to block PRL secretion induced by ES in the POA. Tract tracing, using double-label immunocytochemistry, revealed the presence of a monosynaptic dopaminergic pathway projecting from the POA to the INF. These data imply that the only hypothalamic D1 DA receptors involved in the regulation of avian PRL secretion are those residing within the INF in the same region as the VIP neurons known to be involved in PRL secretion.