Miracle-dz/UniFAR-FTUs huggingface dataset:
Ensuring transparency in computational modeling

Computational models are of great s Cien tifiC and societal importance because they are used every day in a wide variety of products and policies. However, computational models are not pure abstractions, but rather they are tools constructed and used by humans. As such, computational models are only as good as their inputs and assumptions, including the values of those who build and use them. The role of ethics and values in the process of computational modeling can have farreaching consequences, but this is still a significantly understudied topic in need of further research. This article focuses on one particular value, transparency, documenting both why models should and how models can be transparent. Transparency is the capacity of a model to be clearly understood by all stakeholders, especially users of the model. Transparent models require that modelers are aware of the assumptions built into their models, and that they clearly communicate these assumptions to users. It is important that computational modelers recognize the potential for and importance of building computational models to be transparent. This article builds on an earlier article that makes the argument that computational models should be designed transparently to ensure parity and understanding among stakeholders, including modelers, clients, users, and those affected by the model. Data from an empirical study of computational modelers working in a corporate research laboratory is used to support this argument by demonstrating the importance of transparency from political, economic, and legal perspectives. This article also illustrates how transparency can be embedded in computational models throughout the stages of the modeling process.
Increased THEMIS First Exon Usage in CD4+ T-Cells Is Associated with a Genotype that Is Protective against Multiple Sclerosis

Multiple sclerosis is an autoimmune disease of the central nervous system. Genome wide association studies have identified over 100 common variants associated with multiple sclerosis, the majority of which implicate immunologically relevant genes, particularly those involved in T-cell development. SNP rs13204742 at the THEMIS/PTPRK locus is one such variant. Here, we have demonstrated mutually exclusive use of exon 1 and 2 amongst 16 novel THEMIS isoforms. We also show inverse correlation between THEMIS expression in human CD4+ T-cells and dosage of the multiple sclerosis risk allele at rs13204742, driven by reduced expression of exon 1- containing isoforms. In silico analysis suggests that this may be due to cell-specific, allele-dependent binding of the transcription factors FoxP3 and/or E47. Research exploring the functional implications of GWAS variants is important for gaining an understanding of disease pathogenesis, with the ultimate aim of identifying new therapeutic targets.
Diversity and community structure of beetles and their role as bioindicators in Ashtoum El- Gamil protectorate Port Said, Egypt

The diversity of invertebrate fauna across many different types of environments means that invertebrates are likely to be sensitive indicators of land use. Particularly, on a global scale beetles meet most of bio indication criteria. The aim of the present study is to investigate the effects of different aspects of disturbance on beetle diversity and community structure, as well as evaluate the beetles assemblages as bioindicators in Ashtoum El-Gamil protectorate using pitfall traps. A total of 658 adult specimens were collected seasonally from 12 sites belonging to 22 species and 13 families. Beetles abundance showed spatially significant difference among different study sites; where, (P< 0.05). The most abundant site was the disturbed site of Quail farm (90 individuals); while, the natural sites were the lowest (6). The ordination result of the DCA analysis for beetles species sampled during the study period separated the natural sites with their characteristic species from the disturbed sites. Also, The CCA showed that the plant species Mesembryanthemum forsskalei & Sarcornia fruticos and sand percentage of the soil parameters (P < 0.01) were correlated with the natural sites. In conclusion, it was found that there is a significant effect of disturbance on the species composition of beetles in Ashtoum El-
Biocompatibility of Resin-based Dental Materials

Oral and mucosal adverse reactions to resin-based dental materials have been reported. Numerous studies have examined the biocompatibility of restorative dental materials and their components, and a wide range of test systems for the evaluation of the biological effects of these materials have been developed. This article reviews the biological aspects of resin-based dental materials and discusses the conventional as well as the new techniques used for biocompatibility assessment of dental materials.
Evaluation of the TriSpan Neck Bridge Device for the Treatment of Wide-Necked Aneurysms: An Experimental Study in Canines

Background and Purpose — Many wide-necked aneurysms are difficult or impossible to treat with the Guglielmi detachable coil (GDC). The purpose of this study was to evaluate the use of a neck bridging device, the TriSpan coil, in combination with standard GDCs for the treatment of wide-necked aneurysms in an experimental canine aneurysm model. Methods — Of 24 experimental aneurysms in 12 animals, 19 (7 lateral and 12 terminal) were treated with the TriSpan coil in conjunction with standard GDCs. Digital subtraction angiography (DSA) was performed on all animals immediately after treatment. In 6 animals, follow-up DSA and histological evaluation were performed 4 weeks after treatment. In the remaining 6, DSA was done at both 90 and 180 days after treatment. Histological evaluation was done immediately after the 180-day angiographic evaluation. Results — The TriSpan was easy to use in conjunction with the standard GDC. Because of their geometry, some lateral aneurysms were difficult or impossible to treat with this device. Greater than 90% aneurysm occlusion was obtained in all 19 aneurysms. In no instance was there evidence of coil migration, herniation, or aneurysm recanalization. Histological evaluation of the tissue surrounding the TriSpan coil showed tissue responses similar to that seen with standard GDCs. Conclusions — These results show that the TriSpan coil in conjunction with standard GDCs can be used safely and effectively for the treatment of wide-necked aneurysms in this canine model. Positioning and deployment of the neck bridge in aneurysms having an acute angle with the long axis of their parent artery are difficult or impossible. It is likely that this device, used in conjunction with the standard GDC, will allow treatment of some wide-necked aneurysms that are not treatable with the GDC alone.
Growth stimulatory precipitates of CA2+ and pyrophosphate

Inorganic pyrophosphate (PPi) forms an insoluble precipitate with calcium in growth medium when its concentration exceeds about 0.1 mM. This PPi precipitate can reproduce the effects of 10% calf serum on all cell processes examined in Balb/c 3T3 cells, including hexose uptake and metabolism to lactate, 3H‐uridine, and 3H‐choline uptake, and the incorporation of 3H‐leucine and 3H‐thymidine into trichloroacetic acid (TCA)‐insoluble material. Concentrations of PPi insufficient to form a precipitate are without effect on cell metabolism. The precipitates are most effective when prepared with concentrations of PPi just sufficient to result in precipitate formation and become considerably less effective as the PPi concentration increases, even though the quantity of precipitate formed continues to increase with PPi concentration up to 1 mM PPi. Precipitates formed at low PPi concentrations consist largely of Ca2+ (81% of cations). PPi (77% of anions), and Pi (23% of anions). Precipitates formed with higher concentrations of PPi contain proportionately less Ca2+ and Pi and more monovalent cations and PPi. We have distinguished cell surface‐bound PPi from intracellular PPi by differential extraction. The quantity of surface‐bound PPi increases sharply when the PPi concentration reaches the point of precipitate formation. If the precipitate is prevented from binding to the cell surface by inverting monolayer cultures in precipitate‐containing medium, the cells are not stimulated. These findings suggest that the binding of PPi precipitate to the cell surface is involved in the stimulation of cell metabolism by PPi. PPi precipitates do not absorb serum mitogens or inhibitors from the culture medium, nor do they affect the binding of 125I‐platelet‐derived growth factor to its specific cell‐surface receptor, suggesting that PPi precipitates do not act directly through either of these mitogen‐receptor systems. In analogy to cell stimulation by epidermal growth factor and by antigens, we suggest that PPi may be active only in the form of a precipitate because multivalent binding of receptors with formation of clusters is required for stimulation. The inhibitory effects of high concentrations of PPi may be due to interference by free PPi with formation of active receptor clusters.
An OS-based alternative to full hardware coherence on tiled CMPs

The interconnect mechanisms (shared bus or crossbar) used in current chip-multiprocessors (CMPs) are expected to become a bottleneck that prevents these architectures from scaling to a larger number of cores. Tiled CMPs offer better scalability by integrating relatively simple cores with a lightweight point-to-point interconnect. However, such interconnects make snooping impractical and, thus, require alternative solutions to cache coherence. This paper proposes a novel, cost-effective mechanism to support shared-memory parallel applications that forgoes hardware maintained cache coherence. The proposed mechanism is based on the key ideas that mapping of lines to physical caches is done at the page level with OS support and that hardware supports remote cache accesses. It allows only some controlled migration and replication of data and provides a sufficient degree of flexibility in the mapping through an extra level of indirection between virtual pages and physical tiles. We evaluate the proposed tiled CMP architecture on the Splash-2 scientific benchmarks and ALPBench multimedia benchmarks against one with private caches and a distributed directory cache coherence mechanism. Experimental results show that the performance degradation is as little as 0%, and 16% on average, compared to the cache coherent architecture across all benchmarks for 16 and 32 processors.
Histopathological examination of two cases of anterior staphyloma associated with Peters' anomaly and persistent hyperplastic primary vitreous

AIMS To clarify the developmental mechanism and critical period for the uncommon complex of Peters' anomaly and persistent hyperplastic primary vitreous (PHPV). METHODS Two eyes with Peters' anomaly and PHPV were histologically examined by serial section. One eye was enucleated at age 7 months (case 1) and the other at age 4 months (case 2) owing to severe anterior staphyloma. RESULTS In both eyes, defects in the endothelium, Descemet's membrane, and posterior stroma were observed in the central cornea, and the degenerative lens adhered to the posterior surface of the defective corneal stroma. Also, in both eyes, the anterior chamber space was not formed and the undifferentiated iris stroma adhered to the posterior surface of the peripheral cornea. Mesenchymal tissue containing melanocytes was observed behind the degenerative lens, and the pigment epithelium was absent at the lower nasal side of the ciliary body in case 1. In case 2, mesenchymal tissue containing scattered melanocytes in the vitreous cavity was seen on the posterior retina. Based on the histological findings, both cases were diagnosed as Peters' anomaly caused by the faulty separation of the lens vesicle, PHPV, maldevelopment of the iris and ciliary body, and goniodysgenesis. CONCLUSION Migratory disorders of neural crest cells from 4 to 7 weeks of gestation may be responsible for various ocular anomalies including Peters' anomaly and PHPV, as observed in these cases.
Benthic primary production in coastal salt marsh systems

by LILIANA EUGENIA VELASQUEZ (Under the Direction of Samantha B. Joye) ABSTRACT Benthic microalgae are a central component of shallow coastal habitats and they may account for a significant fraction of the total primary production in these ecosystems. While several factors act in concert to generate the high photosynthetic rates observed in benthic microalgae, available data suggest light is of primary importance. Nutrient availability may also be important because increasing human population in the coastal zone has led to an oversupply of nutrients to aquatic habitats, in particular estuaries. The present study focused on the effects of light and nutrients on benthic primary production at two coastal Georgia sites: the Duplin River and the Satilla River. Benthic primary production and biomass along the Duplin varied over space and time. Nutrient addition experiments led to increased primary production by benthic microalgae (indicating nutrient limitation) with the addition of nitrogen and phosphorus at Sapelo Island but not at the Satilla River site.
Nitration of proteins in bronchoalveolar lavage fluid from patients with acute respiratory distress syndrome receiving inhaled nitric oxide.

Inhaled nitric oxide (.NO) is used to improve gas exchange and reduce pulmonary vascular resistance (PVR) in patients with the acute respiratory distress syndrome (ARDS). Although controlled studies have shown no survival benefit, some investigators have suggested that inhaled.NO may have antiinflammatory properties under these circumstances. In contrast, others have speculated that.NO given by inhalation could be cytotoxic, as it combines with superoxide at near diffusion-limited rates to produce the highly reactive oxidant peroxynitrite (ONOO(-)). We therefore quantified levels of 3-nitrotyrosine, a marker for ONOO(-) formation, in bronchoalveolar lavage fluid (BAL) from patients with ARDS receiving inhaled.NO, and from patients with comparable lung injury who were not so treated. We also measured levels of 3-chlorotyrosine as an index of neutrophil activation to assess indirectly the effects of inhaled.NO on lung inflammation. Patients receiving . NO had increased levels of 3-nitrotyrosine (6.76 +/- 2.79 versus 0.4 +/- 0.15 nmol/mg of protein, p < 0.05) and 3-chlorotyrosine (7.97 +/- 2.74 versus 1. 53 +/- 1.09 nmol/mg of protein, p < 0.05) in BAL protein compared with controls. In patients with ARDS, inhaled.NO increases the formation of 3-nitrotyrosine and is accompanied by an increase in levels of 3-chlorotyrosine (a marker of neutrophil activation). The possible long-term consequences of these observations remain to be evaluated.
Data-Driven Content Analysis of Social Media

Researchers have long measured people’s thoughts, feelings, and personalities using carefully designed survey questions, which are often given to a relatively small number of volunteers. The proliferation of social media, such as Twitter and Facebook, offers alternative measurement approaches: automatic content coding at unprecedented scales and the statistical power to do open-vocabulary exploratory analysis. We describe a range of automatic and partially automatic content analysis techniques and illustrate how their use on social media generates insights into subjective well-being, health, gender differences, and personality.
Multimodal learning with deep Boltzmann machines

Data often consists of multiple diverse modalities. For example, images are tagged with textual information and videos are accompanied by audio. Each modality is characterized by having distinct statistical properties. We propose a Deep Boltzmann Machine for learning a generative model of such multimodal data. We show that the model can be used to create fused representations by combining features across modalities. These learned representations are useful for classification and information retrieval. By sampling from the conditional distributions over each data modality, it is possible to create these representations even when some data modalities are missing. We conduct experiments on bimodal image-text and audio-video data. The fused representation achieves good classification results on the MIR-Flickr data set matching or outperforming other deep models as well as SVM based models that use Multiple Kernel Learning. We further demonstrate that this multimodal model helps classification and retrieval even when only unimodal data is available at test time.
Structure-Function Relationship of Cytoplasmic and Nuclear IκB Proteins: An In Silico Analysis

Cytoplasmic IκB proteins are primary regulators that interact with NF-κB subunits in the cytoplasm of unstimulated cells. Upon stimulation, these IκB proteins are rapidly degraded, thus allowing NF-κB to translocate into the nucleus and activate the transcription of genes encoding various immune mediators. Subsequent to translocation, nuclear IκB proteins play an important role in the regulation of NF-κB transcriptional activity by acting either as activators or inhibitors. To date, molecular basis for the binding of IκBα, IκBβ and IκBζ along with their partners is known; however, the activation and inhibition mechanism of the remaining IκB (IκBNS, IκBε and Bcl-3) proteins remains elusive. Moreover, even though IκB proteins are structurally similar, it is difficult to determine the exact specificities of IκB proteins towards their respective binding partners. The three-dimensional structures of IκBNS, IκBζ and IκBε were modeled. Subsequently, we used an explicit solvent method to perform detailed molecular dynamic simulations of these proteins along with their known crystal structures (IκBα, IκBβ and Bcl-3) in order to investigate the flexibility of the ankyrin repeat domains (ARDs). Furthermore, the refined models of IκBNS, IκBε and Bcl-3 were used for multiple protein-protein docking studies for the identification of IκBNS-p50/p50, IκBε-p50/p65 and Bcl-3-p50/p50 complexes in order to study the structural basis of their activation and inhibition. The docking experiments revealed that IκBε masked the nuclear localization signal (NLS) of the p50/p65 subunits, thereby preventing its translocation into the nucleus. For the Bcl-3- and IκBNS-p50/p50 complexes, the results show that Bcl-3 mediated transcription through its transactivation domain (TAD) while IκBNS inhibited transcription due to its lack of a TAD, which is consistent with biochemical studies. Additionally, the numbers of identified flexible residues were equal in number among all IκB proteins, although they were not conserved. This could be the primary reason for their binding partner specificities.
An Entropy Model for Artificial Grammar Learning

A model is proposed to characterize the type of knowledge acquired in artificial grammar learning (AGL). In particular, Shannon entropy is employed to compute the complexity of different test items in an AGL task, relative to the training items. According to this model, the more predictable a test item is from the training items, the more likely it is that this item should be selected as compatible with the training items. The predictions of the entropy model are explored in relation to the results from several previous AGL datasets and compared to other AGL measures. This particular approach in AGL resonates well with similar models in categorization and reasoning which also postulate that cognitive processing is geared towards the reduction of entropy.
A comprehensive model for ultrawideband propagation channels

This paper describes a comprehensive statistical model for UWB propagation channels that is valid for a frequency range from 3-10 GHz. It is based on measurements and simulations in the following environments: residential indoor, office indoor, built-up outdoor, industrial indoor, farm environments, and body area networks. The model is independent of the used antennas. It includes the frequency dependence of the pathloss, as well as several generalizations of the Saleh-Valenzuela model, like mixed Poisson times of arrival and delay dependent cluster decay constants. The model can thus be used for realistic performance assessment of UWB systems. It was accepted by the IEEE 802.15. 4a working group (WG) as standard model for evaluation of UWB system proposals
Variability in active galactic nuclei: confrontation of models with observations

The variability of active galactic nuclei (AGN) has long held the promise of shedding light on their detailed structure, and possibly other astrophysical phenomena. Different emission mechanisms lead to different patterns of variability in flux, which are in principle easily distinguishable. Recent predictions for the expected spectrum of variations for various models are now in such a form that they can be compared with the observed statistical properties of AGN light curves from large-scale monitoring programmes. In this paper, we use the results of a long-term monitoring programme of a large sample of quasars and Seyfert galaxies, as well as individual light curves from the literature, to distinguish between the various model predictions. The results favour a model based on accretion disc instability over the starburst model, where the variation comes from a succession of supernova bursts, but it also appears that much of the observed variation in quasars is due to gravitational microlensing.
Systolic and diastolic blood pressure, mean arterial pressure and pulse pressure for prediction of cardiovascular events and mortality in a Middle Eastern population

Abstract We compared systolic (SBP) and diastolic blood pressure (DBP), mean arterial pressure (MAP) and pulse pressure (PP) as independent predictors of cardiovascular disease (CVD), total and CVD mortality among an Iranian population. The study conducted among 5991 subjects aged ≥ 30 years without baseline CVD and antihypertensive medication. The mean of two measurements of SBP and DBP, in sitting position, was considered the subject's blood pressure. During a median follow-up of 8.7 years, 346 CVD and 157 deaths, 63 attributed to CVD, occurred. Hazard ratios (HRs) of each outcome were calculated for a one standard deviation (SD) increase in each blood pressure (BP) measures. In multivariate models, all BP measures were associated with increased risk of CVD regardless of age. In those aged < 60 years, SBP, DBP, PP and MAP were associated with total mortality (p < 0.05), but in subjects aged ≥ 60 years, only SBP and PP increased risk of total mortality significantly. In multivariate analyses, a 1SD increase in SBP, PP and MAP were associated with 35%, 31% and 28% increased risk of CVD mortality (p < 0.05). In terms of fitness and discrimination of models, DBP, PP and MAP were not superior to SBP. In conclusion, our findings provided further evidence from a Middle Eastern population, in support of SBP predictability for CVD events and CVD and all-cause mortality compared with other BP measures.
Prevalence of hypertension amongst spouses in urban area of Nagpur city, Maharashtra, India

Clinicians, epidemiologists and other students of human biology share an interest in studies of family clusters of heart disease and its antecedents. The recent inclusion of husband and wife pairs (spouse pairs) has added a new dimension to earlier studies of first degree relatives. Blood pressure is influenced by environmental factors operating within genetic limits. The study of cohabiting couples can identify environmental factors.