Miracle-dz/UniFAR-FTUs huggingface dataset:
Neurobiological bases of reading disorder part II: The importance of developmental considerations in typical and atypical reading

Decoding-based reading disorder (RD; aka developmental dyslexia) is one of the most common neurodevelopmental disorders, affecting approximately 5-10% of school-aged children across languages. Even though neuroimaging studies suggest an impairment of the left reading network in RD, the onset of this deficit and its developmental course, which may include constancy and change, is largely unknown. There is now growing evidence that the recruitment of brain networks underlying perceptual, cognitive and linguistic processes relevant to reading acquisition varies with age. These age-dependent changes may in turn impact the neurocognitive characteristics of RD observed at specific developmental stages. Here we synthesize findings from functional and structural magnetic resonance imaging (MRI) studies to increase our understanding of the developmental time course of the neural bases underlying (a)typical reading. We first provide an overview of the brain bases of typical and atypical (impaired) reading. Next we describe how the understanding of RD can be deepened through scientific attention to age effects, for example, by integrating findings from cross-sectional studies of RD at various ages. Finally, we accent findings from extant longitudinal studies that directly examine developmental reading trajectories beginning in the preliterate stage at both group and individual levels. Although science is at the very early stage of understanding developmental aspects of neural deficits in RD, evidence to date characterizes RD by atypical brain maturation. We know that reading impairment may adversely impact multiple life domains such as academic achievement and social relationships, and unfortunately, that these negative outcomes can persist and compound into adulthood. We contend that exploring the developmental trajectories of RD will contribute to a greater understanding of how neural systems support reading acquisition. Further, we propose and cite evidence that the etiology of RD can be better investigated by distinguishing primary deficits from secondary impairments unfolding along development. These exciting and modern investigatory efforts can also indirectly contribute to a centered practice of early and accurate identification and optimal intervention to support the development of foundational pre-literacy skills and fluent reading. In sum, integrating a developmental understanding into the science and practice of reading acquisition and intervention is both possible and necessary.
Lanthanide binding and IgG affinity construct: Potential applications in solution NMR, MRI, and luminescence microscopy

Paramagnetic lanthanide ions when bound to proteins offer great potential for structural investigations that utilize solution nuclear magnetic resonance spectroscopy, magnetic resonance imaging, or optical microscopy. However, many proteins do not have native metal ion binding sites and engineering a chimeric protein to bind an ion while retaining affinity for a protein of interest represents a significant challenge. Here we report the characterization of an immunoglobulin G‐binding protein redesigned to include a lanthanide binding motif in place of a loop between two helices (Z‐L2LBT). It was shown to bind Tb3+ with 130 nM affinity. Ions such as Dy3+, Yb3+, and Ce3+ produce paramagnetic effects on NMR spectra and the utility of these effects is illustrated by their use in determining a structural model of the metal‐complexed Z‐L2LBT protein and a preliminary characterization of the dynamic distribution of IgG Fc glycan positions. Furthermore, this designed protein is demonstrated to be a novel IgG‐binding reagent for magnetic resonance imaging (Z‐L2LBT:Gd3+ complex) and luminescence microscopy (Z‐L2LBT: Tb3+ complex).
Weight misperception and health risk behaviors among early adolescents.

OBJECTIVES To examine associations between weight misperception and youth health risk and protective factors. METHODS Three thousand ten US seventh-graders (72.1% white, mean age: 12.7 years) self-reported height, weight, risk, and protective factors. Analyses were conducted to determine cross-sectional and longitudinal associations between weight overestimation and health risk and protective factors. RESULTS Risk and protective factors had significant cross-sectional associations with weight overestimation. However, only depressive symptoms and reduced optimism predicted weight overestimation in eighth grade. Weight overestimation did not predict engagement in risky behaviors. CONCLUSIONS Weight overestimation and risk factors appear to co-occur, suggesting a constellation of risk that warrants further research.
Factors involved in anaerobic growth of Saccharomyces cerevisiae

Life in the absence of molecular oxygen requires several adaptations. Traditionally, the switch from respiratory metabolism to fermentation has attracted much attention in Saccharomyces cerevisiae, as this is the basis for the use of this yeast in the production of alcohol and in baking. It has also been clear that under anaerobic conditions the yeast is not able to synthesize sterols and unsaturated fatty acids and that for anaerobic growth these have to be added to the media. More recently it has been found that many more factors play a role. Several other biosynthetic reactions also require molecular oxygen and the yeast must have alternatives for these. In addition, the composition of the cell wall and cell membrane show major differences when aerobic and anaerobic cells are compared. All these changes are reflected by the observation that the transcription of more than 500 genes changes significantly between aerobically and anaerobically growing cultures. In this review we will give an overview of the factors that play a role in the survival in the absence of molecular oxygen. Copyright © 2007 John Wiley & Sons, Ltd.
Hepatic Fat Quantification: A Prospective Comparison of Magnetic Resonance Spectroscopy and Analysis Methods for Chemical-Shift Gradient Echo Magnetic Resonance Imaging With Histologic Assessment as the Reference Standard

ObjectiveThe aims of this study were to assess the confounding effects of hepatic iron deposition, inflammation, and fibrosis on hepatic steatosis (HS) evaluation by magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) and to assess the accuracies of MRI and MRS for HS evaluation, using histology as the reference standard. Materials and MethodsIn this institutional review board–approved prospective study, 56 patients gave informed consents and underwent chemical-shift MRI and MRS of the liver on a 1.5-T magnetic resonance scanner. To estimate MRI fat fraction (FF), 4 analysis methods were used (dual-echo, triple-echo, multiecho, and multi-interference), and MRS FF was calculated with T2 correction. Degrees of HS, iron deposition, inflammation, and fibrosis were analyzed in liver resection (n = 37) and biopsy (n = 19) specimens. The confounding effects of histology on fat quantification were assessed by multiple linear regression analysis. Using the histologic degree of HS as the reference standard, the accuracies of each method in estimating HS and diagnosing an HS of 5% or greater were determined by linear regression and receiver operating characteristic analyses. ResultsIron deposition significantly confounded estimations of FF by the dual-echo (P < 0.001) and triple-echo (P = 0.033) methods, whereas no histologic feature confounded the multiecho and multi-interference methods or MRS. The MRS (r = 0.95) showed the strongest correlation with histologic degree of HS, followed by the multiecho (r = 0.92), multi-interference (r = 0.91), triple-echo (r = 0.90), and dual-echo (r = 0.85) methods. For diagnosing HS, the areas under the curve tended to be higher for MRS (0.96) and the multiecho (0.95), multi-interference (0.95), and triple-echo (0.95) methods than for the dual-echo method (0.88) (P ≥ 0.13). ConclusionThe multiecho and multi-interference MRI methods and MRS can accurately quantify hepatic fat, with coexisting histologic abnormalities having no confounding effects.
Obesity and weight gain among former World Trade Center workers and volunteers

ABSTRACT A high prevalence of obesity has been observed among former World Trade Center (WTC) workers and volunteers. We hypothesized that unemployment and disability status would predict obesity. We surveyed 220 participants at the 
 Mount Sinai WTC Clinical Center to assess their obesity and current employment and disability status, WTC occupational exposure level, medical comorbidities, and dietary and exercise habits. Bivariate and logistic regression multivariate analyses were used to explore associated risk factors. Obesity was associated with active employment status. Other significant covariates included non-Latino African American race, having a high number of comorbid chronic diseases, low exercise frequency, and not drinking any glass of juice daily. The association of obesity with active employment suggests that interventions that favor healthy habits among actively employed individuals are warranted.
Applying Convolutional Neural Networks to Per-pixel Orthoimagery Land Use Classification

Recently, the proliferation of Convolutional Neural Networks has spurred research in a wide range of fields such as image recognition, voice synthesis, and various other classification tasks. Over the last several years, the availability of satellite and other forms of orthoimagery has also increased due to the decreasing cost of capturing devices. The amount of annotated or labeled orthoimagery has not kept pace with the increased availability of imagery, largely due to the time complexity of labeling such data. Land cover usage classifications in particular would have many uses in agriculture. The United States Department of Agriculture’s National Agricultural Statistics Service provides land cover usage data at a resolution of 30 meters, which compared with for example a 1 meter imagery resolution, leaves a large discrepancy between the quality of the raw image data and the labeling data. This research uses these low quality labels along with high quality image data to train a model that attempts to perform per-pixel land use classification, in hopes to create a classifier that is able to predict several different classes of land use, up to or beyond the resolution accuracy of the much less adequate label data set. It is important to note however, that it is very difficult to evaluate if a model provides relatively better classifications based on the semantics of the input image, due to the low resolution of the image labels. This is because, an individual pixel in the image label will only represent one class per NxN meter area in the case of our data set, a 30x30 meter area. That individual pixel may be a poor representation of features actually represented in the higher resolution image data. Thusly, we will attempt to demonstrate that, with enough data, a model may generate higher a resolution classification than the original imagery labels with a reasonable margin of error, and attempt to define a way to evaluate the effectiveness of the model despite the poor resolution of the image labels.
Characterization of Two Novel Pyrogenic Toxin Superantigens Made by an Acute Rheumatic Fever Clone of Streptococcus pyogenes Associated with Multiple Disease Outbreaks

ABSTRACT The pathogenesis of acute rheumatic fever (ARF) is poorly understood. We identified two contiguous bacteriophage genes, designated speL and speM, encoding novel inferred superantigens in the genome sequence of an ARF strain of serotype M18 group A streptococcus (GAS). speL and speM were located at the same genomic site in 33 serotype M18 isolates, and no nucleotide sequence diversity was observed in the 33 strains analyzed. Furthermore, the genes were absent in 13 non-M18 strains tested. These data indicate a recent acquisition event by a distinct clone of serotype M18 GAS. speL and speM were transcribed in vitro and upregulated in the exponential phase of growth. Purified SpeL and SpeM were pyrogenic and mitogenic for rabbit splenocytes and human peripheral blood mononuclear cells in picogram amounts. SpeL preferentially expanded human T cells expressing T-cell receptors Vβ1, Vβ5. 1, and Vβ23, and SpeM had specificity for Vβ1 and Vβ23 subsets, indicating that both proteins had superantigen activity. SpeL was lethal in two animal models of streptococcal toxic shock, and SpeM was lethal in one model. Serologic studies indicated that ARF patients were exposed to serotype M18 GAS, SpeL, and SpeM. The data demonstrate that SpeL and SpeM are pyrogenic toxin superantigens and suggest that they may participate in the host-pathogen interactions in some ARF patients.
Space-Frequency Decomposition and Time-Reversal Imaging

This paper presents two novel time-reversal algorithms: Space-frequency DORT (SF-DORT) and SF-multiple signal classification (SF-MUSIC) to image targets based on the SF multistatic scattering data matrix. Singular value decomposition is applied to this matrix to obtain the left unitary matrix, the vectors of which are classified into the signal-subspace vectors corresponding to the targets and the noise-subspace ones. Numerical simulations show that the imaging performances of the SF-MUSIC and the SF-DORT are similar to those of the time-reversal MUSIC (TR-MUSIC) and the time-domain DORT (TD-DORT), respectively. However, the new algorithms require only one single SF measurement by the TR array, in contrast to N measurements needed in the TR-MUSIC and the TD-DORT, when the TR array has N antennas.
The Rac1 Inhibitor NSC23766 Suppresses CREB Signaling by Targeting NMDA Receptor Function

NMDA receptor signaling plays a complex role in CREB activation and CREB-mediated gene transcription, depending on the subcellular location of NMDA receptors, as well as how strongly they are activated. However, it is not known whether Rac1, the prototype of Rac GTPase, plays a role in neuronal CREB activation induced by NMDA receptor signaling. Here, we report that NSC23766, a widely used specific Rac1 inhibitor, inhibits basal CREB phosphorylation at S133 (pCREB) and antagonizes changes in pCREB levels induced by NMDA bath application in rat cortical neurons. Unexpectedly, we found that NSC23766 affects the levels of neuronal pCREB in a Rac1-independent manner. Instead, our results indicate that NSC23766 can directly regulate NMDA receptors as indicated by their strong effects on both exogenous and synaptically evoked NMDA receptor-mediated currents in mouse and rat neurons, respectively. Our findings strongly suggest that Rac1 does not affect pCREB signaling in cortical neurons and reveal that NSC23766 could be a novel NMDA receptor antagonist.
Modeling and Analysis of Eddy-Current Damping Effect in Horizontal Motions for a High-Precision Magnetic Navigation Platform

Recent advancements in micro/nano-domain technologies have led to a renewed interest in ultra-high resolution magnetic navigation platforms. A magnetic navigation platform (MNP) has been developed at the MagLev Microrobotics Lab of the University of Waterloo, Waterloo, ON, Canada. This platform consists of two separate basic components: a magnetic drive unit and a microrobot. The magnetic drive unit produces and regulates the magnetic field for noncontact propelling of the microrobot in an enclosed environment. The MNP is equipped with an eddy-current damper to enhance its inherent damping factor in the microrobot's horizontal motions. This paper deals with the modeling and analysis of an eddy-current damper that is formed by a conductive plate placed below the levitated microrobot to overcome inherent dynamical vibrations and improve motion precision. The modeling of eddy-current distribution in the conductive plate is investigated by solving the diffusion equation for vector magnetic potential. An analytical expression for the horizontal damping force is presented and experimentally validated. It is demonstrated that eddy-current damping is a key technique to increase the damping coefficient in a noncontact way and improve levitation performance. This damping can be widely used in applications of magnetic actuation systems in micromanipulation and microfabrication.
Predicting the Outcome of H-1 B Visa Applications CS 229 Term Project Final Report

In our project, we aim to predict the outcome of H-1B visa applications that are filed by many high-skilled foreign nationals every year. We framed the problem as a classification problem and applied Naive Bayes, Logistic Regression, SVM and Neural Network in order to output a predicted case status of the application. The input to our algorithm is the attributes of the applicant which will be further explained in the following parts.
MvfR, a key Pseudomonas aeruginosa pathogenicity LTTR‐class regulatory protein, has dual ligands

MvfR (PqsR), a Pseudomonas aeruginosa LysR‐type transcriptional regulator, plays a critical role in the virulence of this pathogen. MvfR modulates the expression of multiple quorum sensing (QS)‐regulated virulence factors; and the expression of the phnAB and pqsA‐E genes that encode functions mediating 4‐hydroxy‐2‐alkylquinolines (HAQs) signalling compounds biosynthesis, including 3,4‐dihydroxy‐2‐heptylquinoline (PQS) and its precursor 4‐hydroxy‐2‐heptylquinoline (HHQ). PQS enhances the in vitro DNA‐binding affinity of MvfR to the pqsA‐E promoter, to suggest it might function as the in vivo MvfR ligand. Here we identify a novel MvfR ligand, as we show that HHQ binds to the MvfR ligand‐binding‐domain and potentiates MvfR binding to the pqsA‐E promoter leading to transcriptional activation of pqsA‐E genes. We show that HHQ is highly produced in vivo, where it is not fully converted into PQS, and demonstrate that it is required for MvfR‐dependent gene expression and pathogenicity; PQS is fully dispensable, as pqsH– mutant cells, which produce HHQ but completely lack PQS, display normal MvfR‐dependent gene expression and virulence. Conversely, PQS is required for full production of pyocyanin. These results uncover a novel biological role for HHQ; and provide novel insights on MvfR activation that may aid in the development of therapies that prevent or treat P. aeruginosa infections in humans.
Resistance Performance of a Ship in Model-Scaled Brash Ice Fields Using CFD and DEM Coupling Model

The brash ice channel formed with icebreaker navigation is a normal working scenario for ice-going vessels. Therefore, it is necessary to study brash ice resistance in this condition. In this study, CFD and DEM coupling methods were adopted to investigate the resistance performance of a ship sailing in model-scaled brash ice fields, considering the collision force and friction resistance, among the brash ice, and the water resistance and hydrodynamic force of brash ice, which make up physical scenarios of navigation in the brash ice channel. To study the effect of aforementioned parameters on the average total resistance, the time step, iteration, and brash ice stiffness were analyzed; we found that a time step of 0.02 s, iteration of 10, and brash ice stiffness of 1000 N/m that showed better repeatability of the physical phenomenon, and it was used to reproduce working conditions created in the HSVA ice tank test. The error between the numerical simulation results and the test results is less than 5%, which shows the robustness of the present coupling strategy. Finally, the effects of ship–ice friction coefficient, ice thickness, ice shape, brash ice channel width, and ice concentration on the resistance of the ship were investigated and verified with the published results.
A comparison of orally administered misoprostol and membrane sweeping for labour induction in uncomplicated, singleton post-term pregnancies

Objectives. This study assessed the efficacy of the two outpatient processes of single-dose 50 μg oral misoprostol (OM) and membrane sweeping (MS) on the outcome of labour induction and the possibility of reducing the need for hospital admission for cervical ripening/labour induction in uncomplicated post-term singleton pregnancies at a tertiary health institution in south-western Nigeria. Methods. A total of 100 patients were equally randomised into the two groups between April 2007 and March 2010. Primary outcome measures were delivery within 48 hours after the start of induction and route of delivery. Secondary outcome measures were time interval from induction to onset of labour (latency period), time interval from start of induction to delivery (duration of labour), need for oxytocin augmentation, labour complications, Apgar scores at 1 and 5 minutes, and need for neonatal intensive care unit (NICU) admission. Results. Both groups were similar at the baseline with regard to age, parity and days beyond 40 weeks’ gestation. There was a significantly shorter induction to onset of labour (latency) interval in the OM group, with a mean of 17.0 hours compared with 31.9 hours in the MS group (p=0.005), with 82.0% of the patients in the OM group in spontaneous labour within the latency period of 18 hours as opposed to 32.6% of the MS group (p<0.005). Forty-two patients in the OM group and 40 in the MS group had a vaginal delivery (84.0% v. 87.0%, p=0.361), with 12 and 20 patients in the OM and MS groups, respectively, requiring oxytocin augmentation (p=0.023). The duration of labour was significantly shorter in the OM group, in which 78.6% of those who had a vaginal delivery achieved it within 9 hours, compared with 57.5% in the MS group (p=0.036). Overall, neonatal outcomes and need for NICU admission were similar and comparable in the two groups. On a preference scale, 43% of the women in the MS group felt positive about the intervention, compared with 92% of the women in the OM group. Conclusion. The study demonstrated a shorter latency period, less need for oxytocin augmentation and shorter duration of labour in patients who received OM. The two induction agents were similar with regard to neonatal outcomes and need for NICU admission. Both showed good safety profiles for outpatient care, although further assessment of the safety profile with larger studies will be needed. More patients felt positive about the intervention in the OM group than in the MS group. S Afr J OG 2013;19(1):4-7. DOI:10.7196/SAJOG.584
Proximity ligation assays: a recent addition to the proteomics toolbox

An essential skill for every researcher is to learn how to select and apply the most appropriate methods for the questions they are trying to answer. With the extensive variety of methods available, it is increasingly important to scrutinize the advantages and disadvantages of these techniques prior to making a decision on which to use. In this article, we describe an approach to evaluate methods by reducing them into subcomponents. This is exemplified by a brief description of some commonly used proteomics methods. The same approach can also be used in method development by rearranging subcomponents in order to create new methods, as demonstrated with the development of proximity ligation assays (PLAs). PLA is a method as designed in our laboratory for detection of proteins, protein–protein interactions and post-translational modifications. Fundamentally, protein-recognition events are converted into detectable DNA molecules. The technique uses protein–DNA conjugates as binders for the targets of interest. Binding of two or more conjugates to the target results in assembly of an assay-specific DNA molecule. Subsequent amplification of the DNA molecule generates a signal that can be detected using PCR, for detection of minute amounts of proteins in serum, or standard fluorescence microscopy for detection of protein–protein interactions in tissue sections. Lastly, we apply the approach of recombining subcomponents to develop a few novel hypothetical methods hoping this might stimulate the readers to utilize this approach themselves.