Miracle-dz/UniFAR-FTUs huggingface dataset:
Safety and efficacy of alpha-1-antitrypsin augmentation therapy in the treatment of patients with alpha-1-antitrypsin deficiency

Correspondence: irina Petrache indiana University, Division of Pulmonary, Allergy, Critical Care and Occupational Medicine, van Nuys Medical Science Building, 635 Barnhill Drive, MS224, Indianapolis, IN 46202-5120, USA Tel +1 317 988 3811 Fax +1 317 988 3976 email ipetrach@iupui.edu Abstract: Alpha-1-antitrypsin deficiency (AATD), also known as alpha1-proteinase inhibitor deficiency, is an autosomal co-dominant condition. The genotypes associated with AATD include null, deficient, and dysfunctional alpha-1-antitrypsin (A1AT) variants, which result in low levels of circulating functional A1AT, unbalanced protease activity, and an increased risk of developing lung emphysema, the leading cause of morbidity in these patients. Furthermore, the most common abnormal genotype, Pi*ZZ may also cause trapping of abnormally folded protein polymers in hepatocytes causing liver dysfunction. A major focus of therapy for patients with lung disease due to AATD is to correct the A1AT deficiency state by augmenting serum levels with intravenous infusions of human plasma-derived A1AT. This strategy has been associated with effective elevations of A1AT levels and function in serum and lung epithelial fluid and observational studies suggest that it may lead to attenuation in lung function decline, particularly in patients with moderate impairment of lung function. In addition, an observational study suggests that augmentation therapy is associated with a reduction of mortality in subjects with AATD and moderate to severe lung impairment. More recent randomized placebo-controlled studies utilizing computer scan densitometry suggest that this therapy attenuates lung tissue loss. Augmentation therapy has a relative paucity of side effects, but it is highly expensive. Therefore, this therapy is recommended for patients with AATD who have a high-risk A1AT genotype with plasma A1AT below protective levels (11 μM) and evidence of obstructive lung disease. In this article, we review the published evidence of A1AT augmentation therapy efficacy, side effects, and safety profile.
Soil structure interaction in offshore wind turbine collisions

3651 ABSTRACT: Vessel impact is one of the load cases which should be accounted for in the design of an offshore wind turbine (OWT) according to design codes, but little guidance or information is given on the employed methodology. This study focuses on the evaluation of the distress induced in a wind turbine after a ship collision, thus providing an insight on the consequences of a collision event and on the main aspects to be considered when designing for this load case. In particular, the role of the foundation soil properties (site conditions) on the response of the structural system is investigated. Dynamic finite element analyses have been performed taking into account the geometric and material nonlinearity of the tower, and the effects of soil structure interaction (SSI) have been studied in two representative collision scenarios of a service vessel with the turbine: a moderate energy impact collision, characterized by a vessel drift velocity of 2 m/s; and a high energy impact collision, characterized by a velocity of 5 m/s. The results of the investigation show that SSI modifies the behaviour of the OWT mainly by introducing additional deformations at the OWT base and by absorbing a portion of ship impact energy in these deformations. Since moderate and high energy impacts both result in rather similar energy absorption by the foundation, disregarding the effects of SSI leads to substantial overestimation of permanent deformations in the case of a moderate energy impact.
Evidence based disease network construction towards drug repositioning

Drug repositioning is one of emerging approaches dedicated to find alternative usages of existing drugs efficiently and economically, especially with the advance in computational technology. The current progress made for computational drug repositioning is primarily focusing on informatics approach development/improvement or exploration on different type of data in order to identify possible drug candidates. Comparing to the existing studies, we proposed a novel method for constructing the disease based network by applying data extracted from the Semantic MEDLINE. Phenotypical associations (disease-disease associations) can be identified from this network, which can drive drug repositioning study by targeting on specific domain. In this paper, we successfully demonstrated the capability of the disease based network in hidden phenotypical association discovery to support drug repositioning in case studies.
Appearance change prediction for long-term navigation across seasons

Changing environments pose a serious problem to current robotic systems aiming at long term operation. While place recognition systems perform reasonably well in static or low-dynamic environments, severe appearance changes that occur between day and night, between different seasons or different local weather conditions remain a challenge. In this paper we propose to learn to predict the changes in an environment. Our key insight is that the occurring appearance changes are in part systematic, repeatable and therefore predictable. The goal of our work is to support existing approaches to place recognition by learning how the visual appearance of an environment changes over time and by using this learned knowledge to predict its appearance under different environmental conditions. We describe the general idea of appearance change prediction (ACP) and a novel implementation based on vocabularies of superpixels (SP-ACP). Despite its simplicity, we can further show that the proposed approach can improve the performance of SeqSLAM and BRIEF-Gist for place recognition on a large-scale dataset that traverses an environment under extremely different conditions in winter and summer.
Genetic structure in a tropical lek‐breeding bird, the blue manakin (Chiroxiphia caudata) in the Brazilian Atlantic Forest

Determining the genetic structure of tropical bird populations is important for assessing potential genetic effects of future habitat fragmentation and for testing hypotheses about evolutionary mechanisms promoting diversification. Here we used 10 microsatellite DNA loci to describe levels of genetic differentiation for five populations of the lek‐mating blue manakin (Chiroxiphia caudata), sampled along a 414‐km transect within the largest remaining continuous tract of the highly endangered Atlantic Forest habitat in southeast Brazil. We found small but significant levels of differentiation between most populations. FST values varied from 0.0 to 0.023 (overall FST = 0.012) that conformed to a strong isolation by distance relationship, suggesting that observed levels of differentiation are a result of migration–drift equilibrium. Nem values estimated using a coalescent‐based method were small (≤ 2 migrants per generation) and close to the minimum level required to maintain genetic similarity between populations. An implication of these results is that if future habitat fragmentation reduces dispersal between populations to even a small extent, then individual populations may undergo a loss of genetic diversity due to an increase in the relative importance of drift, since inbreeding effective population sizes are relatively small (Ne ~1000). Our findings also demonstrate that population structuring can occur in a tropical bird in continuous habitat in the absence of geographical barriers possibly due to behavioural features of the species.
Comparison of Assessment of Oxygen Consumption, Etest, and CLSI M38-A2 Broth Microdilution Methods for Evaluation of the Susceptibility of Aspergillus fumigatus to Posaconazole

ABSTRACT Posaconazole MICs for 50 Aspergillus fumigatus isolates with distinct genotypes were determined by three methods. MICs were ≥0.5 μg/ml for 5, 11, and 15 strains by the CLSI reference M38-A2, Etest (48-h), and oxygen consumption methods, respectively. The levels of categorical agreement between the results obtained by the CLSI method and those obtained by the oxygen consumption and Etest methods were 80 and 84%, respectively.
A Source Localization/Separation/Respatialization System Based on Unsupervised Classification of Interaural Cues

In this paper we propose a complete computational system for Auditory Scene Analysis. This time-frequency system localizes, separates, and spatializes an arbitrary number of audio sources given only binaural signals. The localization is based on recent research frameworks, where interaural level and time differences are combined to derive a confident direction of arrival (azimuth) at each frequency bin. Here, the power-weighted histogram constructed in the azimuth space is modeled as a Gaussian Mixture Model, whose parameter structure is revealed through a weighted Expectation Maximization. Afterwards, a bank of Gaussian spatial filters is configured automatically to extract the sources with significant energy accordingly to a posterior probability. In this frequency-domain framework, we also inverse a geometrical and physical head model to derive an algorithm that simulates a source as originating from any azimuth angle.
Modelling and measurement of elastic properties of hydrating cement paste

Durability and safety of concrete structures are fully governed by mechanical properties. This is especially true at early age, when cement matrix is not yet fully developed, and phase arrangement becomes critical for understanding mechanical behavior. This factor can be thoroughly examined only with the use of numerical models. This study is specifically focused on the prediction of effective elastic properties of cement paste by Finite Element method (FEM) based on its microstructure. The 3-D microstructure is an output of a vector microstructural model. Up to 5 million of overlapping spheres can exist in the computational volume of cement paste. The geometrical representation for FEM computation therefore becomes a challenge. In this study, at first, specific aspects of the FEM are investigated with respect to the early age microstructure. Mesh for such a complex microstructure poses a challenge, simplifications of the geometry have to be accepted. Sensitivity to mesh type, resolution, integration scheme and size of computational volume is tested. The most important factor in the prediction is identified as artificial connectivity, which is a result of insufficient resolution. It causes substantial overestimation of elastic properties at the beginning of hydration. A scheme to partially treat this effect is presented. In the second part of the work, the model is applied to study variations of microstructural parameters. These include the effect of flocculation, water/cement ratio, particle size distributions and number of hydrate clusters. It is shown, that the model is able to capture the differences in microstructural arrangements despite the resolution limitations, verified experimentally. As such, the model has the capability to be used for explanation of anomalies in the material structure.
HR: A System for Machine Discovery in Finite Algebras

We describe the HR concept formation program which invents mathematical definitions and conjectures in finite algebras such as group theory and ring theory. We give the methods behind and the reasons for the concept formation in HR, an evaluation of its performance in its training domain, group theory, and a look at HR in domains other than group theory.
American Journal of Epidemiology Original Contribution Cancer Risk after Exposure to Treatments for Ovulation Induction

Uncertainty continues as to whether treatments for ovulation induction are associated with increased risk of cancer. The authors conducted a long-term population-based historical cohort study of parous women. A total of 15,030 women in the Jerusalem Perinatal Study who gave birth in 1974–1976 participated in a postpartum survey. Cancer incidence through 2004 was analyzed using Cox's proportional hazards models, controlling for age and other covariates. Women who used drugs to induce ovulation (n ¼ 567) had increased risks of cancer at any site (multivariate hazard ratio (HR) ¼ 1.36, 95% confidence interval (CI): 1.06, 1.74). An increased risk of uterine cancer was found among women treated with ovulation-inducing agents No association was noted between use of ovulation-inducing agents and ovarian cancer (age-adjusted HR ¼ 0.61, 95% CI: 0.08, 4.42). Ovulation induction was associated with a borderline-significant increased risk of breast cancer (multivariate HR ¼ 1.42, 95% CI: 0.99, 2.05). Increased risks were also observed for malignant melanoma and non-Hodgkin lymphoma. These associations appeared stronger among women who waited more than 1 year to conceive. Additional follow-up studies assessing these associations by drug type, dosage, and duration are needed. Approximately 10% of couples in developed countries seek health care for infertility (1, 2). The use of fertility treatment has grown substantially in recent decades, as can be inferred from the increasing utilization of assisted reproductive technologies (3). It has been estimated that approximately 1% of US infants born in 2004 were conceived through assisted reproductive technologies (4). Ovulation-inducing drugs are widely used for ovarian follicle stimulation, either as independent therapies or during in vitro fertilization cycles. Clomiphene citrate, in use since the 1960s, is still considered the best initial treatment for the majority of women with anovulatory infertility (4). Clomiphene has also been widely used among couples with unexplained infertility (4). Similarly, human menopausal gonadotropins (nowadays partly replaced by recombinant follicle-stimulating hormone) have been used to promote ovulation since the early 1960s (5), and human chorionic gonadotropins have been used since 1932 (6). Despite this long-term use, the scientific literature provides inconsistent information on the association between ovulation induction treatment and cancer incidence. An increased risk of ovarian cancer following treatment has been suggested in previous studies (7, 8), while more recent studies suggest no association (9, 10) (Table 1). Some studies have suggested an increased risk of breast cancer following treatment with clomiphene (11, 12); however, in others, investigators have …
Modeling Fractal Structure of Systems of Cities Using Spatial Correlation Function

This paper proposes a new method to analyze the spatial structure of urban systems using ideas from fractals. Regarding a system of cities as a set of "particles" distributed randomly on a triangular lattice, we construct a spatial correlation function of cities. Suppose that the spatial correlation follows the power law. It can be proved that the correlation exponent is the second order generalized dimension. The spatial correlation model is applied to the system of cities in China. The results show that the Chinese urban system can be described by the correlation dimension ranging from 1.3 to 1.6. The fractality of self-organized network of cities in both the conventional geographic space and the "time" space is revealed with the empirical evidence. The spatial correlation analysis is significant in that it is applicable to both large and small sizes of samples and can be used to link different fractal dimensions in urban study, including box dimension and radial dimension.
Evaluation of Selenite Effects on Selenoproteins and Cytokinome in Human Hepatoma Cell Lines

The need to explore new alternative therapeutic strategies and chemoprevention methods for hepatocellular carcinoma is growing significantly. Selenium is a trace element that plays a critical role in physiological processes, and is used in cancer chemoprevention. The aim of this work was to test in vitro the effect of sodium selenite on the human hepatoma cell lines, HepG2 and Huh7, to assess its effect on the expression of GPX1, SELK and SELENBP1 and also to evaluate its action on inflammation determinants such as cytokines. Our results show that: (i) the increase observed for the GPX1 and SELK expression is correlated with an increase in the sodium selenite concentration, also evidencing an inverse association between the levels of these two proteins and SELENBP1; (ii) the selenium concentrations evaluated in protein extracts increase in proportional way with the selenite concentrations used in the treatment, suggesting that other selenoproteins can also be modulated and should be evaluated in further studies, and (iii) some cytokines, VEGF and three pro-inflammatory cytokines, i.e., IL-6, IL-8, and IL-17, decreased with an increasing selenite concentration. Finally, interactomic studies show that GPX1 and SELK, and the four pro-inflammatory cytokines are functionally correlated evidencing a putative anti-inflammatory role for the selenite.
Comparison of the efficacy of nalbuphine, tramadol, ondansetron and placebo in the treatment of postanesthetic shivering after spinal anesthesia for cesarean delivery

Background: Use of meperidine for the treatment of post-anesthetic shivering (PS) after neuraxial opioids is limited by risk of respiratory depression. Objective: To compare the efficacy of tramadol, nalbuphine, ondansetron and a placebo in the treatment of PS after spinal anesthesia in cesarean section patients. Methods: Two hundred eighty parturients who developed moderate to severe shivering and required treatment after cesarean delivery under spinal anesthesia with bupivacaine and intrathecal morphine 0.2 mg were randomized into 4 groups. Group T, Group N, Group O and Group P were given tramadol 0.5 mg/kg, nalbuphine 0.05 mg/kg, ondansetron 0.1 mg/kg and normal saline 5 mL IV, respectively. The patients were evaluated at 15 minutes after treatment and were observed for a recurrence of PS within 4 hours in a double-blinded fashion. Results: The treatment success rate (no or mild shivering) of PS in groups T, N, O and P were 88, 81, 61 and 36 %, respectively (p<0.001). The treatment success rate of groups T vs P, N vs P, O vs P, T vs O and N vs O were significantly different (p<0.001, 0.001, 0.003, <0.001, and 0.009, respectively). The success rate between groups T vs N was not significantly different (p=0.223). Recurrence rate of PS in groups T, N, O and P were 14 %, 15 %, 11 % and 28 %; p=0.329. Other side effects such as pruritus, nausea/vomiting, and dizziness were few and treatable. Conclusion: Tramadol, nalbuphine and ondansetron were efficacious in the treatment of PS after intrathecal morphine in cesarean section patients with low recurrence rates. Tramadol and nalbuphine were superior to ondansetron in the treatment of PS.
Development of stem cell therapy for stress urinary incontinence

Purpose of review In recent years, stem cell therapy has been investigated as a promising approach for the treatment of stress urinary incontinence (SUI). This article reviews the biology of stem cells and their applications as a cell-based treatment for SUI. The current status and future direction of this forefront research in urinary incontinence are also examined. Recent findings During the past decade, adult stem cells have been studied as a potential cell-based approach for the treatment of SUI. The results of current preclinical and clinical studies are presented. These studies demonstrated the improvement in histologic and functional outcomes with stem cell therapies for SUI. Adult stem cells may augment sphincter regeneration and also release trophic factors, promoting vessel and nerve integration into the generated tissues. So far, the findings of the clinical trials are less impressive than the results obtained with animal studies. Summary Although stem cell therapy holds much promise for SUI, the clinical applications in patients have been slow to materialize. This challenge, together with the currently limited data on basic science studies and clinical trials, will undoubtedly stimulate new investigations in the near future.
Islet Autotransplantation After Left Pancreatectomy for Non‐Enucleable Insulinoma

Insulinoma is a rare, almost always benign endocrine tumor of the pancreas, clinically characterized by hyperinsulinemic, hypoglycemic episodes. Surgical excision is the therapy of choice, which may lead to postpancreatectomy diabetes mellitus in the case of extensive pancreatic resection.
Knowledge-based music retrieval for places of interest

In this paper we address a particular recommendation task: retrieving musicians suited for a place of interest (POI). We present a knowledge-based framework built upon the DBpedia ontology linking items from different domains. Graph-based algorithms are used for ranking and filtering items in a target domain (music) with respect to their relatedness to an input item in a source domain (POIs). By conducting user studies we found that users appreciate and judge more valuable the suggestions generated by the proposed approach when a novel weight spreading activation algorithm is used to compute the matching between musicians and POIs. Moreover, users perceive compositions of the suggested musicians as suited for the POIs.
Returns Premia on Company Fundamentals

This paper studies the excess returns on stocks, associated to various company fundamentals on a panel of US stocks from 1979 to 2008. The returns premia are measured using a random coefficient panel data model on the individual stock level. We show that the HML and SMB factors in the Fama and French model probably have no particular economic meaning as sources of systematic risk other than being proxies for the impact of the book-to-price and size characteristics. While the book-to-price ratio, market capitalization, past year sales growth and the share of reinvested profits generate significant premia, earnings history and forecasts are of little predictive power. We statistically confirm the time-varying nature of the style premia but find no strong evidence for the value and growth momentum in a multivariate setting when the systematic risk is controlled for. Some of the premia are positively correlated with the market return and between each other, while others seem to be unrelated. Variations in premia associated with companies’ high internal growth and growth of sales are positively correlated between each other, with the market return and with the value premium. Variations of the size