Miracle-dz/UniFAR-FTUs huggingface dataset:
Influences of multiwalled carbon nanotubes and plant residue chars on bioaccumulation of polycyclic aromatic hydrocarbons by Chironomus plumosus larvae in sediment

Carbonaceous materials (CMs), including carbon nanotubes (CNTs), and black carbon have been suggested as potential remediation materials for hydrophobic organic contaminants (HOCs) in sediments or soils. However, the concentration‐dependent and potential effects of CMs on the decrease in HOC bioavailability are not well understood. In this research, the effects of two types of multiwalled CNTs (MWNT‐1 and MWNT‐2) and chars (char‐stalk produced from stalk and char‐wood from wood) on the bioaccumulation of polycyclic aromatic hydrocarbons (PAHs), including phenanthrene, pyrene, and chrysene, in the benthic organism Chironomus plumosus larvae were studied. When CM content was 1.5% or less in sediments, biota‐sediment accumulation factor (BSAF) values for PAHs decreased sharply as CM increased. However, when char and MWNT‐1 content was greater than 1.5% in sediments, reduction rates of BSAF were slight. Furthermore, when MWNT‐2 content was greater than 1.5%, BSAF values were elevated. This indicated that the MWNT‐associated PAHs may have been absorbed by larvae through particle ingestion, and suggested that some CNTs may not be suitable for the remediation of HOC‐contaminated sediments because they probably could increase the exposure risk of PAHs to benthic organisms, possibly because of their unique structure. Environ. Toxicol. Chem. 2012;31:202–209. © 2011 SETAC
Diagnosis of Leptospirosis: Comparison between Microscopic Agglutination Test, IgM-ELISA and IgM Rapid Immunochromatography Test

Background Leptospirosis is diagnosed on clinical grounds, and confirmed by microscopic agglutination test (MAT). IgM-ELISA (Serion-Virion) and immunochromatography test (Leptocheck-WB) are two immunodiagnostic assays for leptospirosis. Their sensitivity, specificity and applicability in Sri Lanka have not been systematically evaluated. Methods Clinically diagnosed leptospirosis patients (n = 919) were recruited from three hospitals in the Western Province of Sri Lanka, during June 2012 to December 2013. MAT, IgM-ELISA and Leptocheck-WB were performed on all patient sera. MAT titer of ≥400 in single sample, four-fold rise or seroconversion ≥100 in paired samples were considered as positive for MAT. For diagnostic confirmation, MAT was performed during both acute and convalescent phases. Anti-leptospiral IgM ≥20 IU/ml and appearance of a band in the test window were considered as positive for IgM-ELISA and Leptocheck-WB test respectively. Patients with an alternative diagnosis (n = 31) were excluded. Data analysis was performed using two methods, i) considering MAT as reference standard and ii) using Bayesian latent class model analysis (BLCM) which considers each test as imperfect. Results MAT, IgM-ELISA and Leptocheck-WB positivity were 39.8%, 45.8% and 38.7% respectively during the acute phase. Acute-phase MAT had specificity and sensitivity of 95.7% and 55.3% respectively, when compared to overall MAT positivity. IgM-ELISA and Leptocheck-WB had similar diagnostic sensitivity when compared with acute-phase MAT as the gold standard, although IgM-ELISA showed higher specificity (84.5%) than Leptocheck-WB (73.3%). BLCM analysis showed that IgM-ELISA and Leptocheck-WB had similar sensitivities (86.0% and 87.4%), while acute-phase MAT had the lowest sensitivity (77.4%). However, acute-phase MAT had high specificity (97.6%), while IgM-ELISA and Leptocheck-WB showed similar but lower specificity (84.5% and 82.9%). Conclusions Both IgM-ELISA and Leptocheck-WB shows similar sensitivities and specificities. IgM-ELISA may be superior to MAT during the acute phase and suitable for early diagnosis of leptospirosis. Leptocheck-WB is suitable as a rapid immunodiagnostic screening test for resource limited settings.
Empirical Knowledge and Genetic Algorithms for Selection of Amide I Frequencies in Protein Secondary Structure Prediction

Here we investigate an extension of a previously suggested "automatic amide I frequency selection procedure" where we introduce an additional criterion utilizing empirical knowledge on regions within the amide I band (1600--1700 cm-1) found to be particularly sensitive to protein secondary structure. We show that the genetic algorithm provides a solution with good protein secondary structure prediction accuracy.Based on an evaluation set of 13 protein infrared spectra from proteins not contained in the reference set, it is demonstrated that our method is capable of making good predictions for proteins it has never seen before during training. In the present study, where the genetic algorithm is guided towards a solution with a higher number of empirically determined, structure sensitive amide I frequencies selected, minor improvement in prediction accuracy for α-helix and s-sheet structure could be achieved compared to our previous study, where no such knowledge has been provided. Despite the very limited number of protein spectra in the reference set (18), the neural networks were able to generalize with an overall average of standard errors of prediction of 4.36 % based on the evaluation set of protein spectra, which is even better than that achieved during the analysis based on the reference set of protein spectra (4.8 %). This clearly indicates the potential of our approach once more protein infrared spectra are available to base the analysis on.
The Serotonin Transporter Gene: Polymorphism and Haplotype Analysis in Russian Suicide Attempters

The focus on gender-specific genes associated with female suicide is justified by the possible dimorphic nature of the serotonergic system and by the greater number of suicide attempts in females. We performed analysis of the promoter (5-HTTLPR) and intron 2 (STin2 VNTR) polymorphisms and haplotypes of the serotonin transporter gene in Russian suicide attempters, separately in men and women. Our findings indicate the contribution of the SLC6A4 gene to susceptibility for suicidal behavior in women, but not in men. The L/L genotype (p = 0.013, OR = 2.09) and L10 haplotype (p = 0.04, OR = 1.77) were associated with suicide in Russian women only. Further investigations of this gene in different phenotypic groups are necessary.
An Investigation of the Interaction of Reinforced Concrete Frames With Masonry Filler Walls

Abstract : The beneficial effects on frame stiffness and strength which result from providing in-filled masonry walls in all frame openings are investigated. Tests to failure were conducted on eight one-story, one-bay frames; 13 five-story, one-bay frames; and six two-story, three-bay reinforced concrete frames. The test results are presented, including load-deflection relationships, load-reinforcement strain curves, load-wall strain data, and information on cracking in both the wall elements and frame elements. Analyses are presented enabling the calculation of the response of the framewall systems to horizontal loadings. The response to loads smaller than those cracking can be approximated as that of a cantilever beam, and the post cracking behavior approximates the response of a frame with knee braces. The forces causing diagonal cracking and failure in the wall elements were related to the results of tests of masonry specimens. The masonry walls led to an order of magnitude increase in stiffness and a significant increase in strength over unfilled frames, but the ductility was reduced. (Author)
Three-Dimensional Anatomic Finite Element Modelling of Hemi-Arthroplasty of Human Hip Joint

Linear elastic finite element (FE) study was performed to investigate the contact mechanics and stress distribution of hemi-arthroplasty hip resurfacing using a metallic component. Three dimensional anatomic, three and two dimensional axisymmetric FE models were analyzed and compared in this study. The contact mechanics results show a good agreement between three FE models with approximately 0.5% difference between three-dimensional, anatomic and axisymmetric models and approximately 7% difference between three-dimensional, anatomic and two-dimensional, axisymmetric models. Significant differences were found in the maximum predicted von Mises stresses between anatomic and axisymmetric, finite element models. Stress shielding in the bone tissue was found to occur with the hip hemi-resurfacing prosthesis considered in this study. However, the stress shielding was shown to be less than those reported in literature for the MOM hip resurfacings and conventional total hip replacements.
Hierarchical multivariate mixture generalized linear models for the analysis of spatial data: An application to disease mapping

Disease mapping of a single disease has been widely studied in the public health setup. Simultaneous modeling of related diseases can also be a valuable tool both from the epidemiological and from the statistical point of view. In particular, when we have several measurements recorded at each spatial location, we need to consider multivariate models in order to handle the dependence among the multivariate components as well as the spatial dependence between locations. It is then customary to use multivariate spatial models assuming the same distribution through the entire population density. However, in many circumstances, it is a very strong assumption to have the same distribution for all the areas of population density. To overcome this issue, we propose a hierarchical multivariate mixture generalized linear model to simultaneously analyze spatial Normal and non‐Normal outcomes. As an application of our proposed approach, esophageal and lung cancer deaths in Minnesota are used to show the outperformance of assuming different distributions for different counties of Minnesota rather than assuming a single distribution for the population density. Performance of the proposed approach is also evaluated through a simulation study.
Reliability study on technology trends beyond 20nm

In this work, an assessment of different technology trends (planar CMOS, FinFET and III-V MOSFETs) has been carried out in front of some different reliability scenarios (variability and soft errors). The logic circuits based on FinFET devices have presented the best overall behavior, since we have obtained the best performance and variability robustness. Meanwhile, the III-V/Ge-based circuits have shown the best electrical masking in front of soft errors disturbances.
Rates of at-risk drinking among patients presenting to the emergency department with occupational and nonoccupational injury.

OBJECTIVES To compare the characteristics and rates of at-risk drinking among patients presenting to the emergency department (ED) with occupational and nonoccupational injury. METHODS Cross-sectional survey of injured patients presenting to a university hospital ED. Injured patients were prospectively identified, and consenting patients completed a survey including questions regarding quantity/frequency of alcohol use, TWEAK, CAGE, and work-relatedness of injury. Major trauma and motor-vehicle collisions were excluded. Demographic and injury information was obtained from the medical record. Patients with a TWEAK score > or =3, CAGE score > or =2, or who exceeded NIAAA quantity/frequency guidelines were defined as at-risk drinkers. Analysis utilized the Student t-test for continuous variables, and frequency and chi-square analysis for categorical variables. RESULTS Among 3,476 enrolled patients, 766 (22%) had work injuries and 2,710 (78%) had nonwork injuries. Patients with work injuries were as likely as patients with nonwork injuries to be at-risk drinkers; 35% of patients with an occupational injury and 36% of those with a nonoccupational injury were at-risk drinkers (odds ratio = 0.96). CONCLUSIONS Patients presenting to the ED with an occupational injury have rates of at-risk drinking similar to other injury patients, and may be an important group in which to target brief alcohol interventions.
The nuclear mRNA export receptor Mex67‐Mtr2 of Trypanosoma brucei contains a unique and essential zinc finger motif

Trypanosoma brucei is the causative agent of Human African Trypanosomiasis. Trypanosomes are early diverged protozoan parasites and show significant differences in their gene expression compared with higher eukaryotes. Due to a lack of individual gene promoters, large polycistronic transcripts are produced and individual mRNAs mature by trans‐splicing and polyadenylation. In the absence of transcriptional control, regulation of gene expression occurs post‐transcriptionally mainly by control of transcript stability and translation. Regulation of mRNA export from the nucleus to the cytoplasm might be an additional post‐transcriptional event involved in gene regulation. However, our knowledge about mRNA export in trypanosomes is very limited. Although export factors of higher eukaryotes are reported to be conserved, only a few orthologues can be readily identified in the genome of T. brucei. Hence, biochemical approaches are needed to identify the export machinery of trypanosomes. Here, we report the functional characterization of the essential mRNA export factor TbMex67. TbMex67 contains a unique and essential N‐terminal zinc finger motif. Furthermore, we could identify two interacting export factors namely TbMtr2 and the karyopherin TbIMP1. Our data show that the general heterodimeric export receptor Mex67‐Mtr2 is conserved throughout the eukaryotic kingdom albeit exhibiting parasite‐specific features.
Comprehension and Risk Elicitation in the Field: Evidence from Rural Senegal

In the past decade, it has become increasingly common to use simple laboratorygames and decision tasks as a device for measuring both the preferences and understanding ofrural populations in the developing world. In this paper, we report the results observed with threedistinct risk elicitation mechanisms, using samples drawn from the rural population in Senegal,West Africa. We test the understanding of and the level of meaningful responses to the typicalHolt-Laury task, to an adaptation of a simple binary mechanism pioneered by Gneezy andPotters in 1997, and to a non-incentivized willingness-to-risk scale. We find a low level ofunderstanding with the Holt-Laury task and an unlikely-to-be-accurate pattern with thewillingness-to-risk question. Our analysis indicates that the simple binary mechanism hassubstantially more predictive power than does the Holt-Laury mechanism. Our study is acautionary note regarding utilizing either relatively sophisticated risk-elicitation mechanisms ornon-incentivized questions in the rural developing world.
GATA3 abnormalities and the phenotypic spectrum of HDR syndrome

We report on GATA3 analysis and the phenotypic spectrum in nine Japanese families with the HDR syndrome (hypoparathyroidism, sensorineuraldeafness, andrenal dysplasia) (MIM 146255). Fluorescence in situ hybridisation and microsatellite analyses showed heterozygous gross deletions including GATA3 in four families. Sequence analysis showed heterozygous novel mutations in three families: a missense mutation within the first zinc finger domain at exon 4 (T823A, W275R), an unusual mutation at exon 4 (900insAA plus 901insCCT or C901AACCCT) resulting in a premature stop at codon 357 with loss of the second zinc finger domain, and a nonsense mutation at exon 6 (C1099T, R367X). No GATA3 abnormalities were identified in the remaining two families. The triad of HDR syndrome was variably manifested by patients with GATA3 abnormalities. The results suggest that HDR syndrome is primarily caused by GATA3 haploinsufficiency and is associated with a wide phenotypic spectrum.
Trunk Muscle Recruitment Patterns in Patients With Low Back Pain Enhance the Stability of the Lumbar Spine

Study Design. A comparative study of trunk muscle recruitment patterns in healthy control subjects and patients with chronic low back pain was conducted. Objective. To assess trunk muscle recruitment in patients with low back pain. Summary of Background Data. Conflicting evidence has been reported on the level and pattern of trunk muscle recruitment in patients with low back pain. The disparities can be explained partly by methodologic differences. It was hypothesized that trunk muscle recruitment patterns may be altered in patients with low back pain to compensate for reduced spinal stability. Methods. For this study, 16 patients with low back pain and 16 matched control subjects performed slow trunk motions about the neutral posture and isometric ramp contractions while seated upright. Ratios of electromyographic amplitudes and estimated moment contributions of antagonist over agonist muscles and of segmentally inserting muscles over muscles inserting on the thorax and pelvis only were calculated. In addition, model simulations were performed to assess the effect of changes in muscle recruitment on spinal stability. Results. The ratios of antagonist over agonist, and of lumbar over thoracic erector spinae electromyographic amplitude and estimated moment contributions were greater in the patients than in the control subjects. The simulation model predicted that these changes would effectively increase spinal stability. Conclusions. Trunk muscle recruitment patterns in patients with low back pain are different from those in healthy control subjects. The differences are likely to be functional with respect to enhancement of spinal stability in the patients.
Relation of driving status to incident life space constriction in community-dwelling older persons: a prospective cohort study.

BACKGROUND Maintaining spatial movement through the environment is an important feature of healthy aging. We examined whether being licensed to drive is associated with maintaining spatial movement in older persons initially reporting maximum spatial mobility. METHODS From the Rush Memory and Aging Project, 571 nondemented, community-dwelling older persons were identified with (i) baseline data on driving status, (ii) baseline report of spatial mobility to the largest life space zone, and (iii) at least one annual follow-up evaluation. Incident constriction of life space was the primary outcome of interest. RESULTS Over an average follow-up of 4.3 years, 303 participants reported incident constriction of life space. In a proportional hazards model adjusted for age, sex, and education, having a valid driver's license at baseline was associated with a decreased hazard of reporting a life space constriction (hazard ratio = 0.39; 95% confidence interval = 0.29-0.54). Results were unchanged after controlling for number of vascular risk factors and vascular diseases, low visual acuity, social isolation, and gait speed. Of participants reporting incident life space constriction, 188 subsequently reported reexpansion of spatial mobility to the largest zone of life space. Having a valid driver's license was associated with a greater likelihood of life space recovery (hazard ratio = 2.00; 95% confidence interval = 1.27-3.17). CONCLUSION In older persons, having a valid driving license was associated with reduced hazard of reporting life space constriction and a greater likelihood of life space recovery if incident life space constriction occurred.
Identification of the functional components of the Ras signaling pathway regulating pituitary cell-specific gene expression

Ras, a small GTP-binding protein, is required for functional receptor tyrosine kinase signaling. Ultimately, Ras alters the activity of specific nuclear transcription factors and regulates novel patterns of gene expression. Using a rat prolactin promoter construct in transient transfection experiments, we show that both oncogenic Ras and activated forms of Raf-1 kinase selectively stimulated the cellular rat prolactin promoter in GH4 rat pituitary cells. We also show that the Ras signal is completely blocked by an expression vector encoding a dominant-negative Raf kinase. Additionally, using a molecular genetic approach, we determined that inhibitory forms of p42 mitogen-activated protein kinase and an Ets-2 transcription factor interfere with both the Ras and the Raf activation of the rat prolactin promoter. These findings define a functional requirement for these signaling constituents in the activation of the prolactin gene, a cell-specific gene which marks the lactotroph pituitary cell type. Further, this analysis allowed us to order the components in the Ras signaling pathway as it impinges on regulation of prolactin gene transcription as Ras-->Raf kinase-->mitogen-activated protein kinase-->Ets. In contrast, we show that intact c-Jun expression inhibited the Ras-induced activation of the prolactin promoter, defining it as a negative regulator of this pathway, whereas c-Jun was able to enhance the Ras activation of an AP-1-driven promoter in GH4 cells. These data show that c-Jun is not the nuclear mediator of the Ras signal for the highly specialized, pituitary cell-specific prolactin cellular promoter. Thus, we have defined a model system which provides an ideal paradigm for studying Ras/Raf signaling pathways and their effects on neuroendocrine cell-specific gene regulation.
Priming of code-switches in sentences: The role of lexical repetition, cognates, and language proficiency – CORRIGENDUM

An error was made in the preparation of Figure 3 in the article by Kootstra et al., published online on January 4, 2012. The figure should not have presented odds ratios, but odds. The correct version of Figure 3 is given below. This new figure leads to the same interpretation as in the original article, so our conclusions remain the same.
Computer program ANIZC for the calculation of diffraction contrast factors of dislocations in elastically anisotropic cubic, hexagonal and trigonal crystals

The computer program ANIZC has been developed using the Pascal programming language for the calculation of diffraction contrast factors of dislocations in elastically anisotropic cubic, hexagonal and trigonal crystals. The contrast factor is obtained numerically by integrating the angular part of the distortion tensor in the slip plane. The distortion tensor is calculated by solving the sextic equation provided by the mechanical equilibrium of a single dislocation in an infinite anisotropic medium. The contrast factors can be used for the interpretation of strain anisotropy as obtained from peak profile measurements made on either single crystals, textured polycrystals or powders.
Current Advances in the Cognitive Neuroscience of Music

The study of music perception and cognition is one of the oldest topics in experimental psychology. The last 20 years have seen an increased interest in understanding the functional neuroanatomy of music processing in humans, using a variety of technologies including fMRI, PET, ERP, MEG, and lesion studies. We review current findings in the context of a rich intellectual history of research, organized by the cognitive systems underlying different aspects of human musical behavior. We pay special attention to the perception of components of musical processing, musical structure, laterality effects, cultural issues, links between music and movement, emotional processing, expertise, and the amusias. Current trends are noted, such as the increased interest in evolutionary origins of music and comparisons of music and language. The review serves to demonstrate the important role that music can play in informing broad theories of higher order cognitive processes such as music in humans.