Miracle-dz/UniFAR-FTUs huggingface dataset:
Interstitial lung disease: are we missing formes frustes of connective tissue disease?

Patients with connective tissue disease (CTD) may encompass a variety of respiratory manifestations, including: pleural disease; pulmonary hypertension; bronchial or bronchiolar disease; interstitial pneumonia; restrictive lung disease secondary to musculo-skeletal changes; and iatrogenic drug-induced lung disease. Patients also have an increased risk of opportunistic infections, often favoured by corticosteroids and/or immunosuppressive or immunomodulatory therapy 1, 2. The respective frequency of manifestations, their clinical and radiological presentations, response to treatment, and outcome are dependent on the underlying CTD. Rheumatoid arthritis may be responsible for a broad spectrum of manifestations, including: pleural effusion; chronic interstitial pneumonia; lung rheumatoid nodules; bronchiectasis; obstructive ventilatory defect due to constrictive bronchiolitis; laryngeal involvement; and opportunistic infections, such as mycobacterial infections facilitated by anti-tumour necrosis factor-α treatments. Systemic sclerosis may be commonly associated with chronic interstitial pneumonia (especially in patients with diffuse systemic sclerosis and anti-topoisomerase-1 antibodies), or pulmonary arterial hypertension (most frequently, but not exclusively, in patients with limited systemic sclerosis with anti-centromere antibodies), with both contributing to the unfavourable prognosis of the disease 3. Although less frequent among CTDs than rheumatoid arthritis and systemic sclerosis, the spectrum of idiopathic inflammatory myopathy (including dermatomyositis, polymyositis, and amyopathic dermatomyositis) may give rise to a variety of respiratory manifestations, which represent a common cause of death in these patients. These include interstitial lung disease (ILD), aspiration pneumonia, ventilatory failure secondary to diaphragmatic dysfunction 4, and rarely, acute respiratory distress syndrome, pleural effusion, pneumothorax, pulmonary hypertension 5, diffuse alveolar haemorrhage, and dyspnoea due to dermatopolymyositis-related cardiac disease 2, 6. In addition, some manifestations may be the consequence of treatment, such as drug-induced pneumonitis and opportunistic infections. First described in 1986 7, the high frequency of pneumomediastinum in dermatomyositis has been better appreciated more recently 8. The association of ILD and …
Dispersion and repulsion contributions to the solvation free energy: Comparison of quantum mechanical and classical approaches in the polarizable continuum model

We report a systematic comparison of the dispersion and repulsion contributions to the free energy of solvation determined using quantum mechanical self‐consistent reaction field (QM‐SCRF) and classical methods. In particular, QM‐SCRF computations have been performed using the dispersion and repulsion expressions developed in the framework of the integral equation formalism of the polarizable continuum model, whereas classical methods involve both empirical pairwise potential and surface‐dependent approaches. Calculations have been performed for a series of aliphatic and aromatic compounds containing prototypical functional groups in four solvents: water, octanol, chloroform, and carbon tetrachloride. The analysis is focused on the dependence of the dispersion and repulsion components on the level of theory used in QM‐SCRF computations, the contribution of those terms in different solvents, and the magnitude of the coupling between electrostatic and dispersion–repulsion components. Finally, comparison is made between the dispersion–repulsion contributions obtained from QM‐SCRF calculations and the results determined from classical approaches. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006
Endogenous versus exogenous markers of adult neurogenesis in canaries and other birds: Advantages and disadvantages

Although the existence of newborn neurons had originally been suggested, but not broadly accepted, based on studies in adult rodent brains, the presence of an active neurogenesis process in adult homoeothermic vertebrates was first firmly established in songbirds. Adult neurogenesis was initially studied with the tritiated thymidine technique, later replaced by the injection and detection of the marker of DNA replication 5‐bromo‐2′‐deoxyuridine (BrdU). More recently, various endogenous markers were used to identify young neurons or cycling neuronal progenitors. We review here the respective advantages and pitfalls of these different approaches in birds, with specific reference to the microtubule‐associated protein, doublecortin (DCX), that has been extensively used to identify young newly born neurons in adult brains. All these techniques of course have limitations. Exogenous markers label cells replicating their DNA only during a brief period and it is difficult to select injection doses that would exhaustively label all these cells without inducing DNA damage that will also result in some form of labeling during repair. On the other hand, specificity of endogenous markers is difficult to establish due to problems related to the specificity of antibodies (these problems can be, but are not always, addressed) and more importantly because it is difficult, if not impossible, to prove that a given marker exhaustively and specifically labels a given cell population. Despite these potential limitations, these endogenous markers and DCX staining in particular clearly represent a useful approach to the detailed study of neurogenesis especially when combined with other techniques such as BrdU. J. Comp. Neurol. 522:4100–4120, 2014. © 2014 Wiley Periodicals, Inc.
[Evaluation of "admission index of insulin resistance (AIRI)" as an early stage risk predictor in nondiabetic acute coronary syndromes].

OBJECTIVE Insulin resistance is a risk predictor for many cardiovascular diseases, but its effect on etiology and prognosis of diseases has not been clearly identified. In this study, we aimed to investigate whether admission index of insulin resistance (AIRI), recently and practically presented for determination of insulin resistance, could be a new risk predictor of early prognosis in nondiabetic acute coronary syndromes. METHODS One hundred and sixty nondiabetic patients admitted to the intensive coronary care unit and underwent coronary angiography with the diagnosis of acute myocardial infarction (AMI) (Group I; 72 patients; mean age - 58+/-12 years) or unstable angina pectoris (UAP) (Group II; 88 patients; mean age 58+/-10 years) were included in the study. In all patients blood glucose and insulin levels were measured on admission and AIRI was calculated by the formula of "admission glucose level X insulin level / normal blood glucose level (5 mmol/L) X normal insulin level (5 mU/L)" for each patient. After determining the left ventricular ejection fraction (LVEF) and wall motion score index (LVWMSI) echocardiographically and calculating the Gensini score index from coronary angiography, the patients were followed up for major cardiac events (heart failure, atrial fibrillation, reinfarction, life-threatening ventricular arrhythmias, atrio-ventricular block, need for revascularisation and mortality) for 30 days. RESULTS AIRI was found higher in Group I (7.2+/-5.3 versus 5.2+/-4.4, p< 0.01) than in Group II. AIRI was positively correlated with Gensini score and LVWMSI (r=0.41, p<0.01 and r=0.48, p<0.001, respectively) and negatively correlated with LVEF (r=-0.37, p=0.001) in Group I. In addition, it was seen that positive correlation of AIRI with Gensini score (r=0.23, p=0.01) and LVWMSI (r=0.43, p=0.0001) in Group I persisted on multivariate regression analysis. Again, AIRI was significantly correlated with heart failure (r=0.42, p<0.0001), atrial fibrillation (r=0.35, p=0.002) and reinfarction (r=0.23, p=0.04) in Group I. Along with this, in multivariate regression analysis, it was correlated with heart failure (r=0.21, p<0.007), atrial fibrillation (r=0.18, p=0.01) and reinfarction (r=0.18, p=0.01). On the other hand, there was no significant correlation between AIRI and these parameters in Group II. CONCLUSION AIRI can be used in early stage as a risk predictor to determine high-risk subgroups of nondiabetic patients presenting with AMI. Also AIRI, a parameter, which is practically calculated and easily used, is an independent risk factor detecting the extent of coronary artery disease and left ventricular dysfunction in patients with AMI.
Development of a speech-distortionless beamformer for two-microphone digital hearing aids

To enhance noise reduction performance for digital hearing aids (DHA), this study proposes a speech-distortionless beamformer which is realized by a sequential processing of fractional delay, subtraction and integration (FDSI). A Simulink model of this beamformer was constructed and its performance of speech quality enhancement was evaluated in various noisy circumstances including babble, car and traffic noises. In this simulation, null direction of the beamformer was fixed at 120° azimuth and noise source position was altered from 100 to 140° azimuth. The distance between two microphones also varies from 8 to 20 mm. Compared to conventional beamformers, the FDSI beamformer showed higher frequency-weighted segmental SNR (fwsegSNR) and lower weighted spectral slope (WSS) while perceptual evaluation of speech quality (PESQ) was almost same in every beamformer. These results imply that speech distortion was significantly reduced. Therefore, the FDSI beamformer has great promising for speech quality enhancement in DHA.
Supervised Bayesian sparse coding for classification

In this paper, we propose a supervised Bayesian sparse coding (SBSC) model for classification. The sparse coding with Laplacian scale mixture prior is formulated as a weighted l1 minimization problem. Category-specific discriminative dictionaries and regularization parameters are learned using variational EM algorithm from the training samples of each category. Instability of previous sparse coding methods is alleviated through the regularizer design. Classification of a test sample is done using the MAP estimate of the sparse codes. We have tested the model on different recognition tasks and demonstrated the effectiveness of the model.
Neural Networks and Continuous Time

The fields of neural computation and artificial neural networks have developed much in the last decades. Most of the works in these fields focus on implementing and/or learning discrete functions or behavior. However, technical, physical, and also cognitive processes evolve continuously in time. This cannot be described directly with standard architectures of artificial neural networks such as multi-layer feed-forward perceptrons. Therefore, in this paper, we will argue that neural networks modeling continuous time are needed explicitly for this purpose, because with them the synthesis and analysis of continuous and possibly periodic processes in time are possible (e.g. for robot behavior) besides computing discrete classification functions (e.g. for logical reasoning). We will relate possible neural network architectures with (hybrid) automata models that allow to express continuous processes.
French Tough-Movement Infinitives as Deverbal Nominals

In this paper, we argue that predicates of the tough-class in French embed not a verbal infinitive but rather, a gerundive verbal noun. This hypothesis allows us to capture a number of unexpected restrictions on French tough-movement discussed by Legendre (1986). We show that these restrictions are best described as the inability of French tough-movement infinitives to be followed by complements that are disallowed in their corresponding argument-taking event nominals. Our analysis of such infinitives as nominalized elements correctly predicts that they should never be selected by auxiliaries, and that they should have suppressed external arguments in the sense of Grimshaw (1990). This working paper is available in University of Pennsylvania Working Papers in Linguistics: http://repository.upenn. edu/pwpl/ vol15/iss1/3 U. Penn Working Papers in Linguistics, Volume 15.1, 2009 French Tough-Movement Infinitives as Deverbal Nominals J.-Marc Authier and Lisa A. Reed
Additional protein intake limits weight regain after weight loss in humans

Since long-term weight maintenance (WM) is a major problem, interventions to improve WM are needed. The aim of the study was to investigate whether the addition of protein to the diet might limit weight regain after a weight loss of 5–10 % in overweight subjects. In a randomised parallel study design, 113 overweight subjects (BMI 29·3 (SD 2·5) kg/m2); age 45·1 (SD 10·4) years) followed a very-low-energy diet for 4 weeks, after which there was a 6-month period of WM. During WM, subjects were randomised into either a protein group or a control group. The protein group received 30 g/d protein in addition to their own usual diet. During the very-low-energy diet, no differences were observed between the groups. During WM, the protein group showed a higher protein intake (18 % v. 15 %; P<0·05), a lower weight regain (0·8 v. 3·0 kg; P<0·05), a decreased waist circumference (−1·2 (SD 0·7) v. 0·5 (SD 0·5 ) cm; P<0·05) and a smaller increase in respiratory quotient (0·03 (SD 0·01) v. 0·07 0·01; (SD/)P <0·05) compared with the control group. Weight regain in the protein group consisted of only fat-free mass, whereas the control group gained fat mass as well. Satiety in the fasted state before breakfast increased significantly more in the protein group than in the control group. After 6 months follow-up, body weight showed a significant group × time interaction. A protein intake of 18 % compared with 15 % resulted in improved WM in overweight subjects after a weight loss of 7·5 %. This improved WM implied several factors, i.e. improved body composition, fat distribution, substrate oxidation and satiety.
Perspectives in Innate and Acquired Cardioprotection Past and present course of cardioprotection against ischemia-reperfusion injury

Liem DA, Honda HM, Zhang J, Woo D, Ping P. Past and present course of cardioprotection against ischemia-reperfusion injury. J Appl Physiol 103: 2129–2136, 2007. First published August 2, 2007; doi:10.1152/japplphysiol.00383. 2007. —Despite tremendous advances in cardiovascular research and clinical therapy, ischemic heart disease remains the leading cause of serious morbidity and mortality in western society and is growing in developing countries. For the past 5 decades, many scientists have studied the pathophysiology of myocardial ischemia-reperfusion (I/R) injury leading to infarction. With the exception of reperfusion therapy, attempts to salvage the myocardium during an acute myocardial infarction showed disappointing results in directly decreasing infarct size. Nevertheless, the phenomena of ischemic preconditioning and ischemic postconditioning show a consistent and robust cardioprotective effect in every used experimental animal model. As a result, many studies have focused on the intracellular protective signaling pathways that are involved in preconditioning and postconditioning. More recently, it has been suggested that components of the reperfusion injury salvage kinases pathway, protein kinase B, and the extracellular signal-regulated kinases can induce cardioprotection against I/R injury when they are activated during the postischemic reperfusion period. In addition, inhibition of mitochondrial permeability transition during postischemic reperfusion also shows a strong cardioprotective effect against I/R injury. The present mini-review highlights a short summary of the historical and present course of research into cardioprotection against myocardial I/R injury.
Ensuring Progress in Amnesiac Replicated Systems

Replication is used for providing highly available and fault-tolerant information systems, which are constructed on top of replication and recovery protocols. Important aspects when designing these systems are the failure model assumed and the progress condition assumed. Replicated transactional systems usually assume the crash-recovery with partial amnesia failure model, and the majority partition progress condition. But, despite the large use of such combination most of these works do not handle accurately a very special phenomenon that can lead to diverging states in different replicas causing, when happening, critical situations.
Continuous pLSI and Smoothing Techniques for Hybrid Music Recommendation

This paperpresentsan extendedprobabilisticlatent semantic indexing (pLSI) for hybrid music recommendation that deals with rating data provided by users and with contentbased data extracted from audio signals. The original pLSI can be applied to collaborative filtering by treating users and items as discrete random variables that follow multinomial distributions. In hybrid recommendation, it is necessary to deal with musical contents that are usually represented as continuous vectorial values. To do this, we propose a continuous pLSI that incorporates Gaussian mixture models. This extension, however, causes a severe local optima problem because it increases the number of parameters drastically. This is considered to be a major factor generating “hubs,” which are items that are inappropriately recommended to almost all users. To solve this problem, we tested three smoothing techniques: multinomial smoothing,Gaussian parametertying,andartist-baseditem clustering. The experimentalresults revealed that although the first method improved nothing, the others significantly improved the recommendation accuracy and reduced the hubness. This indicates that it is importantto appropriately limit the model complexity to use the pLSI in practical.
Potential role of Thermus thermophilus and T. oshimai in high rates of nitrous oxide (N2O) production in ∼80 °C hot springs in the US Great Basin

Ambient nitrous oxide (N2O) emissions from Great Boiling Spring (GBS) in the US Great Basin depended on temperature, with the highest flux, 67.8 ± 2.6 μmol N2O‐N m−2 day−1, occurring in the large source pool at 82 °C. This rate of N2O production contrasted with negligible production from nearby soils and was similar to rates from soils and sediments impacted with agricultural fertilizers. To investigate the source of N2O, a variety of approaches were used to enrich and isolate heterotrophic micro‐organisms, and isolates were screened for nitrate reduction ability. Nitrate‐respiring isolates were identified by 16S rRNA gene sequencing as Thermus thermophilus (31 isolates) and T. oshimai (three isolates). All isolates reduced nitrate to N2O but not to dinitrogen and were unable to grow with N2O as a terminal electron acceptor. Representative T. thermophilus and T. oshimai strains contained genes with 96–98% and 93% DNA identity, respectively, to the nitrate reductase catalytic subunit gene (narG) of T. thermophilus HB8. These data implicate T. thermophilus and T. oshimai in high flux of N2O in GBS and raise questions about the genetic basis of the incomplete denitrification pathway in these organisms and on the fate of biogenic N2O in geothermal environments.
Inflammatory bowel disease: a study of the association between anxiety and depression, physical morbidity, and nutritional status.

BACKGROUND The etiology of inflammatory bowel disease is unclear, and the role played by anxiety and depression is highly controversial. Anxiety and depression in patients with inflammatory bowel disease could be secondary to disabling symptoms, but the interaction between physical morbidity and psychologic illness in these subjects has not been sufficiently investigated. Patients with inflammatory bowel disease are nevertheless frequently undernourished, but there are no studies on the association between anxiety and depression and malnutrition. This study was designed to characterize anxiety and depression in subjects affected by inflammatory bowel disease and to establish the influence of physical morbidity and/or nutritional status on psychologic disorders. METHODS Seventy-nine consecutive patients, 43 with Crohn's disease (CD) and 36 with ulcerative colitis (UC), were enrolled in the study. An index of the disease activity and physical morbidity was obtained by the simplified Crohn's Disease Activity Index and Truelove-Witts criteria and using the Clinical Rating Scale. Thirty-six healthy volunteers were studied as controls. All the subjects were given the State and Trait Anxiety Inventory (STAI) test and the Zung self-rating Depression Scale. RESULTS The percentage of subjects with state anxiety was significantly higher in the CD (P < 0.001) and UC (P < 0.001) groups than in control subjects. There was no significant difference in trait anxiety among groups. The percentage of subjects with depression was significantly higher in the CD (P < 0.05) and UC (P < 0.05) groups than in control subjects. State anxiety and depression were significantly associated with physical morbidity and correlated with malnutrition in CD and UC patients. CONCLUSION Anxiety and depression in patients with inflammatory bowel disease could be reactive to the disabling symptoms and to malnutrition. As measured with the STAI, personality trait of anxiety does not seem to play an important role in inflammatory bowel disease.
3-Chloro-4-fluoroanilinium picrate

In the title picrate salt of a dihalogenated aniline derivative, C6H6ClF+·C6H2N3O7 −, the intracyclic C—C—C angles in the picrate anion cover a broad range [111.95 (12)–125.38 (13)°], while those in the aromatic cation span a much narrower range [118.25 (14)–122.33 (13)°]. In the crystal, classical N—H⋯O hydrogen bonds, as well as C—H⋯O contacts, connect the ions into layers parallel to (001).
The histone demethylase KDM5A is a key factor for the resistance to temozolomide in glioblastoma

Notwithstanding current multimodal treatment, including surgery, radiotherapy and chemotherapy with temozolomide (TMZ), median survival of glioblastoma (GBM) patients is about 14 months, due to the rapid emergence of cell clones resistant to treatment. Therefore, understanding the mechanisms underlying chemoresistance is mandatory to improve treatments' outcome. We generated TMZ resistant cells (TMZ-R) from a GBM cell line and from cancer stem cell-enriched cultures isolated from human GBMs. We demonstrated that TMZ resistance is partially reverted by “drug wash-out” suggesting the contribution of epigenetic mechanisms in drug resistance and supporting the possibility of TMZ rechallenge in GBM patients after prior drug exposure. The expression of histone lysine demethylase genes (KDMs) was increased in TMZ-R cells compared to parental cells, and TMZ resistance or restored sensitivity was mimicked by over-expressing or inactivating KDM5A. Methylation and expression of O6-methylguanine-DNA methyltransferase (MGMT) and drug efflux mechanisms were not altered in TMZ-R cells compared to parental TMZ sensitive cells. TMZ-R cells transiently acquired morphologic and molecular characteristics of differentiated tumor cells, features that were lost after drug wash-out. In conclusion, we demonstrated that treatment-induced TMZ resistance in GBM involves epigenetic mechanisms in a subset of slow-cycling and transiently partially differentiated cells that escape drug cytotoxicity, overcome G2 checkpoint and sustain clonal growth. We found that TMZ-R cells are sensitive to histone deacethylase inhibitors (HDACi) that synergize with TMZ. This strong synergism could be exploited to develop novel combined adjuvant therapies for this rapidly progressing and invariably lethal cancer.