Miracle-dz/UniFAR-FTUs huggingface dataset:
Incorporating Knowledge into Structural Equation Models Using Auxiliary Variables

In this paper, we extend graph-based identification methods by allowing background knowledge in the form of non-zero parameter values. Such information could be obtained, for example, from a previously conducted randomized experiment, from substantive understanding of the domain, or even an identification technique. To incorporate such information systematically, we propose the addition of auxiliary variables to the model, which are constructed so that certain paths will be conveniently cancelled. This cancellation allows the auxiliary variables to help conventional methods of identification (e.g., single-door criterion, instrumental variables, half-trek criterion), as well as model testing (e.g., d-separation, over-identification). Moreover, by iteratively alternating steps of identification and adding auxiliary variables, we can improve the power of existing identification methods via a bootstrapping approach that does not require external knowledge. We operationalize this method for simple instrumental sets (a generalization of instrumental variables) and show that the resulting method is able to identify at least as many models as the most general identification method for linear systems known to date. We further discuss the application of auxiliary variables to the tasks of model testing and z-identification.
Handling tRNA introns, archaeal way and eukaryotic way

Introns are found in various tRNA genes in all the three kingdoms of life. Especially, archaeal and eukaryotic genomes are good sources of tRNA introns that are removed by proteinaceous splicing machinery. Most intron-containing tRNA genes both in archaea and eukaryotes possess an intron at a so-called canonical position, one nucleotide 3′ to their anticodon, while recent bioinformatics have revealed unusual types of tRNA introns and their derivatives especially in archaeal genomes. Gain and loss of tRNA introns during various stages of evolution are obvious both in archaea and eukaryotes from analyses of comparative genomics. The splicing of tRNA molecules has been studied extensively from biochemical and cell biological points of view, and such analyses of eukaryotic systems provided interesting findings in the past years. Here, I summarize recent progresses in the analyses of tRNA introns and the splicing process, and try to clarify new and old questions to be solved in the next stages.
Determination and Toxicology Studies of Quaternary Ammonium Salts in Solution after Organoclay Processing

Organoclays have potential to be used as additives in various facade paints and other finishing materials. Such new innovative materials must be rigorously tested for them to have no impact on environment. Focus of this study was to develop HPLC – TOF/MS method for determining quaternary ammonium salts in various material washing solutions and to determine organoclay toxicity by performing acute toxicity test on Daphnia magna. From the obtained results, it was possible to conclude that organoclays can be safely used as additives in various materials with low or no impact on environment. We determined that organoclays are significantly less toxic then some quaternary ammonium salts on its own.
On the Physics of Anomalies of Boron Nanosegregation at Dislocations in FeAl

We present results of the constructive critical analysis and interpretation of some recent studies (Blavette, Sauvage, Wilde and others) at the atomic scale (using three-dimensional atom-probe field-ion microscopy) of impurity nanosegregation at dislocations, including “Cottrell atmospheres”, and grain boundaries in deformed intermetallics and metallic materials, and their relevance to mechanical properties and diffusion processes.
Improving Quality of Care in Patients with Liver Cirrhosis

Liver cirrhosis is a major chronic disease in the field of digestive diseases. It causes more than one million deaths per year. Despite established evidence based guidelines, the adherence to standard of care or quality indicators are variable. Complete adherence to the recommendations of guidelines is less than 50%. To improve the quality of care in patients with cirrhosis, we need a more holistic view. Because of high rate of death due to cardiovascular disease and neoplasms, the care of comorbid conditions and risk factors such as smoking, hypertension, high blood sugar or cholesterol, would be important in addition to the management of primary liver disease. Despite a holistic multidisciplinary approach for this goal, the management of such patients should be patient centered and individualized. The diagnosis of underlying etiology and its appropriate treatment is the most important step. Definition and customizing the quality indicators for quality measure in patients are needed. Because most suggested quality indicators are designed for measuring the quality of care in decompensated liver cirrhosis, we need special quality indicators for compensated and milder forms of chronic liver disease as well. Training the patients for participation in their own management, design of special clinics with dedicated health professionals in a form of chronic disease model, is suggested for improvement of quality of care in this group of patients. Special day care centers by a dedicated gastroenterologist and a trained nurse may be a practical model for better management of such patients.
IGF expression in HPV-related and HPV-unrelated human cancer cells

The human Igf-1 gene not only produces insulin-like growth factor-I (IGF-I), but also different carboxy-terminal extensions, known as E peptides, through alternative splicing. We and others have shown that human Eb peptide (hEb) derived from Igf-1 has intrinsic biological activity and is localized to nuclei of transfected cells. Since hEb actions can complement the activity of IGF-I itself, the aim of the present study was to compare IGF-I isoforms at the endogenous protein and transcript level in cancer cell lines, including HeLa, U2OS, HepG2 and K562 cells. Quantitative real-time PCR (qRT-PCR) using Igf-1 isoform specific primers was performed to determine expression patterns, using β-actin as a reference gene. The overall relative Igf-1 transcript level was different across the cell lines, with ~80-fold higher expression in K562 (130.2±31.2) than in U2OS cells (1.7±1.1). The relative copy number of Igf-1b was the highest in HepG2 (69.9±28.6) and K562 cells (28.3±6.7), whereas the relative copy numbers of Igf-1a and Igf-1c were significantly higher in K562 cells compared to all other cell lines. Immunoblotting using total cell lysates, cytoplasmic and nuclear fractions were carried out to determine the level and distribution of IGF-I proteins. K562 cells exhibited the highest level of hEb in total cell lysates and nuclear fractions and no cell lines displayed hEb in the cytoplasmic fractions. In contrast, IGF-IA was the highest in HeLa cells and was enriched only in the cytoplasmic fraction. Since relatively low IGF-1A transcript level but relatively high pro-IGF-1A protein level is plausible, we hypothesized that these transcripts could be processed with higher efficiency and/or the protein product may be stabilized by viral HPV oncogenes in HeLa cells. We assert that while it is important to analyze Igf-1 transcript level, it may be more relevant to determine the IGF isoforms at the protein level.
Exploring the Effects of Errors in Assessment and Time Requirements of Learning Objects in a Peer-Based Intelligent Tutoring System

We revisit a framework for designing peer-based intelligent tutoring systems motivated by McCalla's ecological approach, where learning is facilitated by the previous experiences of peers with a corpus of learning objects. Prior research demonstrated the value of a proposed algorithm for modeling student learning and for selecting the most beneficial learning objects to present to new students. In this paper, we first adjust the validation of this approach to demonstrate its ability to cope with errors in assessing the learning of student peers. We then deepen the representation of learning objects to reflect the expected time to completion and demonstrate how this may lead to more effective selection of learning objects for students, and thus more effective learning. As part of our exploration of these new adjustments, we offer insights into how the size of learning object repositories may affect student learning, suggesting future extensions for the model and its validation.
Measuring Work Productivity With a Mental Health Self-Report Measure

Objective: To determine whether the Social Role (SR) Scale of the Outcome Questionnaire (OQ) can predict work productivity. Methods: Employees at Utah State Hospital completed the OQ and the Work Productivity and Activity Impairment Scale (WPAI) once monthly for four months. Results: The SR predicted the WPAI Presenteeism and Activity Impairment scales. Conclusions: The SR can be used to estimate work productivity using tools like the Productivity Calculator. Specific relationships among measures and suggestions for future research are discussed.
Influence of nanoparticles of Сu 7 GeS 5 I superionic conductor on dielectric properties of planar-oriented nematic liquid crystal 6СВ

The influence of Сu7GeS5I nanoparticles on the dielectric properties of planaroriented liquid crystal 6CB has been investigated within the frequency range 6.10 6 Hz at the temperature 293 K. The concentration of nanoparticles varied within the range 0 to 0.1 wt. %. It has been shown that the Сu7GeS5I nanoparticles considerably less increase the conductivity of the liquid crystal (only by 1.3 times at their maximum concentration) than Сu7PS6 ones, influence of which on the conductivity of the same liquid crystal we investigated earlier (24-fold increase in the conductivity at the same concentration of nanoparticles). It has been assumed that the main mechanism of conductivity changes when introducing Сu7GeS5I nanoparticles is the transfer of charge through nanoparticles. This mechanism of charge transfer is characterized by a rather strong dependence of the conductivity of the liquid crystal on the frequency and is experimentally observed especially at the maximum concentration of nanoparticles.
Percutaneous Image-Guided Musculoskeletal Tumor Treatments.

OBJECTIVE The purpose of this article is to review the current guidelines and recommendations for percutaneous image-guided treatment of musculoskeletal tumors. CONCLUSION With the ongoing technologic advances, it is essential that the musculoskeletal interventionalist is familiar with the current tools and techniques available for the treatment of soft-tissue and bone tumors. Fortunately, many of these tools are readily available in a standard interventional radiology department and can be easily applied to the musculoskeletal system.
Type III IFNs Are Commonly Induced by Bacteria-Sensing TLRs and Reinforce Epithelial Barriers during Infection

Type III IFNs (IFN-λs) are secreted factors that are well-known for their antiviral activities. However, their regulation and functions during bacterial infections are unclear. In this article, we report that the regulation of IFN-λ genes did not track with mechanisms that control type I IFN expression in response to TLRs. Whereas type I IFNs were only expressed from TLRs present on endosomes, type III IFNs could be induced by TLRs that reside at the plasma membrane and that detect various bacterial products. The mechanisms that regulate type III IFN gene expression tracked with those that promote inflammatory cytokine and chemokine expression. Importantly, rIFN-λs enhanced epithelial barriers in vitro, preventing transcellular bacteria dissemination. We therefore propose that in addition to their functions in cell-intrinsic antiviral immunity, type III IFNs protect epithelial barrier integrity, an activity that would benefit the host during any infectious encounter.
PERCEPTUAL EFFECTS OF PACKET LOSS ON H.264/AVC ENCODED VIDEOS

Video communication over IP (Internet Protocol) networks has grown significantly in recent years. However, the Quality of Experience (QoE) associated with video over IP can vary dramatically. This is mainly due to bandwidth restrictions and the fluctuating Quality of Service (QoS). Investigating the perceptual effects of packet loss could lead to a better understanding of the QoE experienced by the end-user. In this paper, we present the results obtained from a series of subjective video quality tests that evaluated the quality of H.264/AVC videos distorted by several packet loss patterns. We draw some interesting conclusions concerning the impact on perceptual quality of (1) transmission-related factors such as the loss distribution and the lost pictures percentage; and (2) content-related factors such as the scene cut position in the video sequence and the spatial position of the loss in the picture.
The singular value decomposition and long and short spaces of noisy matrices

Using geometrical, algebraic, and statistical arguments, it is clarified why and when the singular value decomposition is successful in so-called subspace methods. First the concepts of long and short spaces are introduced, and a fundamental asymmetry in the consistency properties of the estimates is discussed. The model, which is associated with the short space, can be estimated consistently, but the estimates of the original data, which follow from the long space, are always inconsistent. An expression is found for the asymptotic bias in terms of canonical angles, which can be estimated from the data. This allows all equivalent reconstructions of the original signals to be described as a matrix ball, the center of which is the minimum variance estimate. Remarkably, the canonical angles also appear in the optimal weighting that is used in weighted subspace fitting approaches. The results are illustrated with a numerical simulation. A number of examples are discussed. >
COADAPTATION AND TAXONOMIC DIFFERENTIATION OF SPERM AND SPERMATHECAE IN FEATHERWING BEETLES

Sperm and spermathecae in minute beetles that inhabit the island of Sri Lanka (Ceylon) show diagnostic differences in form among closely related species and are highly coadapted morphologically in each species. Complementary morphological relationships between sperm and spermathecae are previously unreported in insects and are of unusual evolutionary interest. Beetles belonging to the genus Bambara (Coleoptera: Ptiliidae, commonly known as featherwing beetles) are less than a millimeter long and live in decaying litter on the forest floor in tropical and subtropical regions of the world. The beetles are often abundant but most species are still unnamed, including seven of the eight species of the Bambara invisibilis group in Sri Lanka with which this report is concerned. The eight species are closely related and remarkably similar externally (Dybas, in prep.), but they can be separated by constant differences in the form of the spermatheca (sperm storage organ) of the female. The taxonomic usefulness of this structure has also been demonstrated in other genera of the family (Besuchet and Sundt, 1971). We now report that each species in the invisibilis group on Sri Lanka differs from all others in external morphology of the sperm as well. Differences in sperm of closely related species of animals have been reported previously (Friend, 1936; Hirth, 1960; McFarlane, 1963; Forman, 1968; Genoways, 1973; Linzey and Layne, 1974) but the differences that characterize the sperm of Bambara species on Sri Lanka are more striking than any previously discovered. Moreover, in each species the form of the sperm is highly coadapted structurally with that of the spermatheca, suggesting an important functional morphological relationship between these complementary male and female reproductive structures.
Meningococcal Meningitis

Meningococcal disease may present as meningitis, septicemia, or a combination of the two. Generally, meningitis has a gradual onset, with fever, headache, and neck stiffness as the most frequent clinical symptoms. By contrast, fulminant septicemia may develop within hours, and is characterized by petechial bleedings and shock. It is of vital importance to diagnose and treat meningococcal disease rapidly. The diagnosis is based on the culture of Neisseria meningitides from blood or cerebrospinal fluid, or on the polymerase chain reaction (PCR) of spinal fluid. Cefotaxime or ceftriaxone are usually recommended as antibacterial treatment. There is a vaccine effective against disease with serogroups A, C, Y, and W.
Ray-Traced Collision Detection for Deformable Bodies

This paper presents a new approach to collision detection and modeling between deformable volumetric bod- ies. It allows deep intersections while alleviating the difﬁculties of distance ﬁeld update. A ray is shot from each surface vertex in the direction of the inward normal. A collision is detected when the ﬁrst intersection be- longs to an inward surface triangle of another body. A contact force between the vertex and the matching point is then created. Experiments show that this approach is fast and more robust than traditional proximity-based collisions.
Evaluation of alpha and gamma aluminum oxide nanoparticle accumulation, toxicity, and depuration in Artemia salina larvae

In this study, Artemia salina (crustacean filter feeders) larvae were used as a test model to investigate the toxicity of aluminum oxide nanoparticles (Al2O3 NPs) on marine microorganisms. The uptake, toxicity, and elimination of α‐Al2O3 (50 nm and 3.5 μm) and γ‐Al2O3 (5 nm and 0.4 μm) NPs were studied. Twenty‐four and ninety‐six hour exposures of different concentrations of Al2O3 NPs to Artemia larvae were conducted in a seawater medium. When suspended in water, Al2O3 NPs aggregated substantially with the sizes ranging from 6.3 nm to >0.3 µm for spherical NPs and from 250 to 756 nm for rod‐shaped NPs. The phase contrast microscope images showed that NPs deposited inside the guts as aggregates. Inductively coupled plasma mass spectrometry analysis showed that large particles (3.5 μm α‐Al2O3) were not taken up by Artemia, whereas fine NPs (0.4 μm γ‐Al2O3) and ultra‐fine NPs (5 nm γ‐Al2O3 and 50 nm α‐Al2O3) accumulated substantially. Differences in toxicity were detected as changing with NP size and morphology. The malondialdehyde levels indicated that smaller γ‐Al2O3 (5 nm) NPs were more toxic than larger γ‐Al2O3 (0.4 µm) particulates in 96 h. The highest mortality was measured as 34% in 96 h for γ‐Al2O3 NPs (5 nm) at 100 mg/L (LC50 > 100 mg/L). γ‐Al2O3 NPs were more toxic than α‐Al2O3 NPs at all conditions. © 2013 Wiley Periodicals, Inc. Environ Toxicol 30: 109–118, 2015.
Near-Infrared Subarcsecond Observations of Ultracompact H II Regions

We present adaptive optics (AO) assisted J, H, and K/K′ images of eight ultracompact H II (UC H II) regions taken with the ALFA and ADONIS AO systems at Calar Alto and La Silla observatories. The images show details of the stellar population and the near-IR morphology of UC H II regions with unprecedented resolution. We have searched for the ionizing sources of the regions using near-IR photometry. The spectral type of the ionizing and most luminous stars inferred from our photometry has been compared with spectral type estimates from IRAS and published radio-continuum measurements. We find that the photometric near-IR spectral types are earlier than estimates from radio and IRAS data. This difference is alleviated when stellar spherical models including line blanketing and stellar winds instead of non-LTE plane-parallel models are used to derive the radio- and IRAS-based spectral types. We also made an attempt to correlate the properties of the near-IR ionizing population with MSX data and published CS measurements. No correlation was found. We note that in two of the regions (G309.92+0.48 and G61.48+0.09B1), the best candidate to ionize the region is possibly a supergiant.
Intrafamilial transmission of extended-spectrum-beta-lactamase-producing Escherichia coli and Salmonella enterica Babelsberg among the families of internationally adopted children.

OBJECTIVES International adoption from developing countries has become an increasing phenomenon in recent years. Given the high prevalence of multidrug-resistant (MDR) bacteria in these countries, the adopted children represent a group at risk for both carriage and infection with MDR bacteria. The dynamics of intrafamilial transmission of MDR bacteria after adoption was studied in a prospective study from January 2002 to January 2005. METHODS Stool samples, taken at the first visit to the outpatient adoption practice and subsequently every month, from the adopted children of an orphanage of Bamako (Mali) and from all the members of their adoptive families were screened for MDR bacteria and bacterial pathogens. Bacteria were characterized by standard biochemical methods, disc diffusion antibiograms, PFGE and plasmid analysis. beta-Lactamase genes were sought by PCR. RESULTS Over the study period, 52 ESBL-producing Enterobacteriaceae (E-ESBL), with Escherichia coli (56%) being the most prevalent, were isolated from 24/25 adoptees at arrival in France. During follow-up, the transmission of ESBL-producing E. coli and Salmonella enterica Babelsberg between the adoptees and their adoptive family members has clearly been demonstrated for 5/22 families (23%). The mean duration of the carriage for the adopted children was 9 months (1-15 months). CTX-M-15 was the most prevalent resistance gene among the E-ESBLs (93%), while SHV-12 was found among the S. enterica Babelsberg studied. CONCLUSIONS International travellers, transfer of patients and now adoption may contribute to the global emergence of MDR bacteria. Thus, in addition to the usual screening of adopted children for infectious diseases, additional screening for MDR bacteria should be recommended, at least for children coming from countries with a high prevalence of MDR bacteria.
Duration of asthma and lung function in life-long nonsmoking adults.

BACKGROUND The airways of adult or elderly asthmatics are likely candidates for airway remodeling, resulting in persistent airflow obstruction. This population can provide a good model for cross-sectional evaluation of the effect of asthma duration on airflow. METHODS We evaluated postbronchodilator airflow and lung volumes at baseline and after a short course of oral prednisone in a group of 42 never-smokers with persistent mild or moderate asthma aged 55 years or older. Patients were grouped as having short duration asthma (SDA, <14 years) or long duration asthma (LDA, > or =14 years) according to the median duration of the disease (14 years) of the sample. RESULTS There were no significant differences in patient characteristics or asthma severity indices between the groups. After a short course of prednisone, forced expiratory volume in 1 second (FEV1) and the ratio of FEV to forced vital capacity (FVC) were significantly higher for the SDA group. Only 3 patients presented persistent airflow limitation (FEV1/FVC% < 75%). An inverse correlation was demonstrated between duration of asthma and postbronchodilator FEV1 (% predicted) (r = -0.43, P = .01) and FEV1/FVC% (r = -0.50, P = .003). CONCLUSION Our data show a close relationship between duration of disease and loss of lung function, supporting the concept of asthma as a slow, progressive disease at least among those patients with a mild-to-moderate severity. Permanent airflow obstruction in mild or moderate asthma is unusual, but can occur in a small number suffering from the disease for years.