Miracle-dz/UniFAR-FTUs huggingface dataset:
The brain anatomy of attention-deficit/hyperactivity disorder in young adults – a magnetic resonance imaging study

Background This is one of the first studies to examine the structural brain anatomy and connectivity associated with an ADHD diagnosis and child as well as adult ADHD symptoms in young adults. It was hypothesized that an adult ADHD diagnosis and in particular childhood symptoms, are associated with widespread changes in the brain macro- and microstructure, which can be used to develop a morphometric biomarker for ADHD. Methods Voxel-wise linear regression models were used to examine structural and diffusion-weighted MRI data in 72 participants (31 young adults with ADHD and 41 controls without ADHD) in relation to diagnosis and the number of self-reported child and adult symptoms. Results Findings revealed significant associations between ADHD diagnosis and widespread changes to the maturation of white matter fiber bundles and gray matter density in the brain, such as structural shape changes (incomplete maturation) of the middle and superior temporal gyrus, and fronto-basal portions of both frontal lobes. ADHD symptoms in childhood showed the strongest association with brain macro- and microstructural abnormalities. At the brain circuitry level, the superior longitudinal fasciculus (SLF) and cortico-limbic areas are dysfunctional in individuals with ADHD. The morphometric findings predicted an ADHD diagnosis correctly up to 83% of all cases. Conclusion An adult ADHD diagnosis and in particular childhood symptoms are associated with widespread micro- and macrostructural changes. The SLF and cortico-limbic findings suggest complex audio-visual, motivational, and emotional dysfunctions associated with ADHD in young adults. The sensitivity of the morphometric findings in predicting an ADHD diagnosis was sufficient, which indicates that MRI-based assessments are a promising strategy for the development of a biomarker.
De novo Transcriptome Assembly of Floral Buds of Pineapple and Identification of Differentially Expressed Genes in Response to Ethephon Induction

A remarkable characteristic of pineapple is its ability to undergo floral induction in response to external ethylene stimulation. However, little information is available regarding the molecular mechanism underlying this process. In this study, the differentially expressed genes (DEGs) in plants exposed to 1.80 mL·L−1 (T1) or 2.40 mL·L−1 ethephon (T2) compared with Ct plants (control, cleaning water) were identified using RNA-seq and gene expression profiling. Illumina sequencing generated 65,825,224 high-quality reads that were assembled into 129,594 unigenes with an average sequence length of 1173 bp. Of these unigenes, 24,775 were assigned to specific KEGG pathways, of which metabolic pathways and biosynthesis of secondary metabolites were the most highly represented. Gene Ontology (GO) analysis of the annotated unigenes revealed that the majority were involved in metabolic and cellular processes, cell and cell part, catalytic activity and binding. Gene expression profiling analysis revealed 3788, 3062, and 758 DEGs in the comparisons of T1 with Ct, T2 with Ct, and T2 with T1, respectively. GO analysis indicated that these DEGs were predominantly annotated to metabolic and cellular processes, cell and cell part, catalytic activity, and binding. KEGG pathway analysis revealed the enrichment of several important pathways among the DEGs, including metabolic pathways, biosynthesis of secondary metabolites and plant hormone signal transduction. Thirteen DEGs were identified as candidate genes associated with the process of floral induction by ethephon, including three ERF-like genes, one ETR-like gene, one LTI-like gene, one FT-like gene, one VRN1-like gene, three FRI-like genes, one AP1-like gene, one CAL-like gene, and one AG-like gene. qPCR analysis indicated that the changes in the expression of these 13 candidate genes were consistent with the alterations in the corresponding RPKM values, confirming the accuracy and credibility of the RNA-seq and gene expression profiling results. Ethephon-mediated induction likely mimics the process of vernalization in the floral transition in pineapple by increasing LTI, FT, and VRN1 expression and promoting the up-regulation of floral meristem identity genes involved in flower development. The candidate genes screened can be used in investigations of the molecular mechanisms of the flowering pathway and of various other biological mechanisms in pineapple.
Direct Camera Pose Tracking and Mapping With Signed Distance Functions

In many areas, the ability to create accurate 3D models is of great interest, for example, in computer vision, robotics, architecture, and augmented reality. In this paper we show how a textured indoor environment can be reconstructed in 3D using an RGB-D camera. Real-time performance can be achieved using a GPU. We show how the camera pose can be estimated directly using the geometry that we represent as a signed distance function (SDF). Since the SDF contains information about the distance to the surface, it defines an error-metric which is minimized to estimate the pose of the camera. By iteratively estimating the camera pose and integrating the new depth images into the model, the 3D reconstruction is computed on the fly. We present several examples of 3D reconstructions made from a handheld and robot-mounted depth sensor, including detailed reconstructions from medium-sized rooms with almost drift-free pose estimation. Furthermore, we demonstrate that our algorithm is robust enough for 3D reconstruction using data recorded from a quadrocopter, making it potentially useful for navigation applications. (Less)
A mesoscale investigation of the endothelial glycocalyx and its interaction with blood flow

Polymer brushes are dense matrices of grafted macromolecules. In addition to brushes finely designed in laboratory, various examples are offered by Nature, as the endothelial glycocalyx, decorating the lumen of mammalian blood vessels. The interaction of such network with the flowing plasma and cells is still partially unknown.The present thesis, by mean of Dissipative Particle Dynamics simulations, proposes a coarse-grained model for the self-consistent analysis of a dense polymer brush under parabolic flow. Our mesoscale investigation highlights the relevance of collective effects, driven by hydrodynamics, and proposes novel interpretations regarding the rich phenomenology of the brush-flow system.Preliminary results are also provided for the interplay between a mesoscopic deformable flowing object (prototype of a red blood cell) and the grafted polymers.
Independent component analysis - an innovative technique for wireless MIMO OFDM systems

This paper investigates the application of independent component analysis (ICA) on multiple-input multiple-output (MIMO) orthogonal frequency division multiplexing (OFDM) wireless communication systems. We present first the ICA based blind equalization for MIMO OFDM systems, where the non-redundant linear precoding is employed to resolve the ambiguity in the ICA equalized signal and reduce peak-to-average power ratio (PAPR) of OFDM signal. Then we discuss the application of ICA to the blind compensation for both frequency-dependent and frequency-independent inphase/quadrature (I/Q) imbalance in MIMO OFDM systems. Simulation results show that the ICA based equalization approach provides a much better performance than that of the subspace method with significant PAPR reduction. In addition, the ICA based I/Q compensation approach outperforms not only previous methods, but also the case with perfect channel state information and no I/Q imbalance due to additional frequency diversity gains.
Linear Free Energy Relationship Correlation of the Distribution of Solutes between Water and Sodium Dodecyl Sulfate (SDS) Micelles and between Gas and SDS Micelles

Data have been assembled from the published literature on the water-to-micellar sodium dodecyl sulfate (SDS) partition coefficient data for more than 200 compounds and on the gas-to-micellar SDS partition coefficient data for more than 140 compounds. It is shown that an Abraham solvation equation with only five descriptors can be used to correlate the observed partition coefficient data to within a standard deviation of 0.22 log units. Micellar electrokinetic chromatographic (MEKC) retention factor data measured on a micellar SDS pseudostationary phase was also gathered from the literature. The water-to-micellar SDS partition coefficient and MEKC retention factor data were combined into a single database and correlated with the Abraham model. The derived correlation described the 486 experimental values to within a standard deviation of 0.15 log units. The micellar SDS system has been compared to various liquid phases in terms of solubility of gases and vapors and has been shown to be a very selective system-more so than room-temperature ionic liquids.
Compositional Type Systems for Stack-Based Low-Level Languages

It is widely believed that low-level languages with jumps must be difficult to reason about by being inherently non-modular. We have recently argued that this in untrue and proposed a novel method for developing compositional natural semantics and Hoare logics for low-level languages and demonstrated its viability on the example of a simple low-level language with expressions (Saabas & Uustalu 2005). The central idea is to use the implicit structure of finite disjoint unions present in low-level code as an (ambiguous) phrase structure.Here we apply our method to a stack-based language and develop it further. We define a compositional natural semantics and Hoare logic for this language and go then on to show that, in addition to Hoare logics, one can also derive compositional type systems as weaker specification languages with the same method. We describe type systems for stack-error freedom and secure information flow.
A Stochastic Finite-State Word-Segmentation Algorithm for Chinese

We present a stochastic finite-state model for segmenting Chinese text into dictionary entries and productively derived words, and providing pronunciations for these words; the method incorporates a class-based model in its treatment of personal names. We also evaluate the system's performance, taking into account the fact that people often do not agree on a single segmentation.
Biconnectivity approximations and graph carvings

A spanning tree in a graph is the smallest connected spanning subgraph. Given a graph, how does one find the smallest (i.e., least number of edges) 2-connected spanning subgraph (connectivity refers to both edge and vertex connectivity, if not specified)? Unfortunately, the problem is known to be NP-hard. We consider the problem of finding an approximation to the smallest 2-connected subgraph, by an efficient algorithm. For 2-edge connectivity our algorithm guarantees a solution that is no more than 3/2 times the optimal. For 2-vertex connectivity our algorithm guarantees a solution that is no more than 5/3 times the optimal. The previous best approximation factor is 2 for each of these problems. The new algorithms (and their analyses) depend upon a structure called a carving of a graph, which is of independent interest. We show that approximating the optimal solution to within an additive constant is NP-hard as well. We also consider the case where the graph has edge weights. We show that an approximation factor of 2 is possible in polynomial time for finding a k-edge connected spanning subgraph. This improves an approximation factor of 3 for k=2 due to [FJ81], and extends it for any k (with an increased running time though).
Chronic Hypoxia–Induced Upregulation of Store-Operated and Receptor-Operated Ca2 Channels in Pulmonary Arterial Smooth Muscle Cells: A Novel Mechanism of Hypoxic Pulmonary Hypertension

Chronic hypoxic pulmonary hypertension is associated with profound vascular remodeling and alterations in Ca2+ homeostasis in pulmonary arterial smooth muscle cells (PASMCs). Recent studies show that transient receptor potential (TRPC) genes, which encode store-operated and receptor-operated cation channels, play important roles in Ca2+ regulation and cell proliferation. However, the influence of chronic hypoxia on TRPC channels has not been determined. Here we compared TRPC expression, and store- and receptor-operated Ca2+ entries in PASMCs of normoxic and chronic hypoxic rats. Reverse-transcription polymerase chain reaction (RT-PCR), Western blot, and immunostaining showed consistently that TRPC1, TRPC3, and TRPC6 were expressed in intralobar pulmonary arteries (PAs) and PASMCs. Application of 1-oleoyl-2-acetyl-sn-glycerol (OAG) to directly activate receptor-operated channels, or thapsigargin to deplete Ca2+ stores, caused dramatic increase in cation entry measured by Mn2+ quenching of fura-2 and by Ca2+ transients. OAG-induced responses were ≈700-fold more resistant to La3+ inhibition than thapsigargin-induced responses. siRNA knockdown of TRPC1 and TRPC6 specifically attenuated thapsigargin- and OAG-induced cation entries, respectively, indicating that TRPC1 mediates store-operated entry and TRPC6 mediates receptor-operated entry. In hypoxic PAs, there were 2- to 3-fold increases in TRPC1 and TRPC6 expression. They were accompanied by significant increases in basal, OAG-induced, and thapsigargin-induced cation entries in hypoxic PASMCs. Moreover, removal of Ca2+ or inhibition of store-operated Ca2+ entry with La3+ and SK&F-96365 reversed the elevated basal [Ca2+]i in PASMCs and vascular tone in PAs of chronic hypoxic animals, but nifedipine had minimal effects. Our results for the first time to our knowledge show that both store- and receptor-operated channels of PASMCs are upregulated by chronic hypoxia and contribute to the enhanced vascular tone in hypoxic pulmonary hypertension.
CorpoMate: A framework for building linguistic corpora from the web

A linguistic corpus is a collection of an ample number of text documents serving as a data source for sampling human language, usually in computational linguistics. Conventional methods of building such a corpus involve frequent human intervention and poses difficulties during reproduction. To address the issues, the paper introduces CorpoMate, an extensible framework with a pipeline-inspired and modular architecture for automating the creation of linguistic corpora, from web resources via crawling websites or parsing feeds. It performs the necessary pre-processing as well as related tasks according to programmable queues of standard or customized tasks with easily swappable tools and, can export aggregated data into widely-accepted formats. Results from experiments performed on text processing tools and performance tests on the asynchronous, rule-based web crawling system justify the importance of having swappable tools along with the feasibility of the architecture described in the paper.
A Novel Modular Bioreactor to In Vitro Study the Hepatic Sinusoid

We describe a unique, versatile bioreactor consisting of two plates and a modified commercial porous membrane suitable for in vitro analysis of the liver sinusoid. The modular bioreactor allows i) excellent control of the cell seeding process; ii) cell culture under controlled shear stress stimulus, and; iii) individual analysis of each cell type upon completion of the experiment. The advantages of the bioreactor detailed here are derived from the modification of a commercial porous membrane with an elastomeric wall specifically moulded in order to define the cell culture area, to act as a gasket that will fit into the bioreactor, and to provide improved mechanical robustness. The device presented herein has been designed to simulate the in vivo organization of a liver sinusoid and tested by co-culturing endothelial cells (EC) and hepatic stellate cells (HSC). The results show both an optimal morphology of the endothelial cells as well as an improvement in the phenotype of stellate cells, most probably due to paracrine factors released from endothelial cells. This device is proposed as a versatile, easy-to-use co-culture system that can be applied to biomedical research of vascular systems, including the liver.
A RECENT STUDY OF CHOLERA WITH REFERENCE TO AN OUTBREAK IN TAIWAN IN 1962.

During the summer of 1962, cholera broke out in Taiwan after an absence of 16 years. This paper gives a full description of the prompt and energetic measures that were instituted to control the outbreak; these included the designation of emergency areas, the immediate detection and isolation of patients and probable carriers, and mass vaccination.In all, over 160 000 rectal swabs and stool specimens were examined for cholera organisms. The author's egg-starch medium, described in detail, proved very satisfactory for this purpose. During the main epidemic (July-September) 383 confirmed cases of cholera and 380 carriers were identified. While the over-all carrier: case ratio was thus approximately 1:1 the ratios in different age-groups varied considerably, being as high as 4:1 in children aged 0-4 years and as low as 0.3:1 in persons aged 55-59 years. The author suggests possible reasons for the older persons' tendency to develop clinical disease rather than become carriers.There were only 24 deaths in the outbreak (a fatality rate of 6%). The efficacy of vaccination was difficult to determine precisely, but in general more deaths and more cases occurred among the non-vaccinated than among the vaccinated.
Variational Inference for Logical Inference

Functional Distributional Semantics is a framework that aims to learn, from text, semantic representations which can be interpreted in terms of truth. Here we make two contributions to this framework. The first is to show how a type of logical inference can be performed by evaluating conditional probabilities. The second is to make these calculations tractable by means of a variational approximation. This approximation also enables faster convergence during training, allowing us to close the gap with state-of-the-art vector space models when evaluating on semantic similarity. We demonstrate promising performance on two tasks.
Protein-specific Scoring Method for Ligand Discovery

Protein-based virtual screening plays an important role in modern drug discovery process. Most protein-based virtual screening experiments are carried out with docking programs. The accuracy of a docking program highly relies on the incorporated scoring function based on various energy terms. The existing scoring functions deal all the energy terms with the equal weight function or other weight function derived by physical characteristics. These existing scoring functions are not protein dependent. We expect that a protein-specific scoring function, which can reflect the protein characteristics, may improve the docking results. Therefore, we propose a protein-specific rescoring approach to select potential ligands by adjusting the weights of energy terms. The protein-specific scoring function is based on the linear regression analysis associated with an outlier detection approach. The scoring function incorporated in DOCK program is used as the model system. The performance of our method was evaluated by the DUD docked data set, which contains 40 protein targets. The study results show that this method can improve the enrichment factors for most of the 40 protein targets. We further expend the protein-specific scoring function to a larger database, and the results also show significant improvement. Our method is not limited to improving the DOCK scoring function. It can be adopted to improve other programs such as GOLD and Glide. We believe that this method can be applied to virtual screening experiments and elevates the hits rate significantly, which can be beneficial to the modern drug discovery process.
Prospective study of nosocomial pneumonia and of patient and circuit colonization during mechanical ventilation with circuit changes every 48 hours versus no change.

Circuits on mechanical ventilators with cascade humidifiers are routinely changed every day or every other day, although humidifying cascades have been considered unlikely to increase the risk of respiratory infection because they do not generate aerosols. Moreover, changing ventilator tubings every 24 rather than every 48 h increases the risk of ventilator-associated pneumonia. To study the effects of ventilator circuit changes on the rate of nosocomial pneumonia and on patient and circuit colonization, 73 consecutive patients requiring continuous mechanical ventilation for more than 48 h were randomly assigned to either ventilator circuit changes every 48 h (Group 1, n = 38) or no change (Group 2, n = 35). Patients dying or being weaned before 96 h were not analyzed (Group 1 n = 3; Group 2 n = 7; leaving Group 1 n = 35 and Group 2 n = 28; p = 0.13). Ventilator-associated pneumonia was defined as the occurrence during mechanical ventilation or within 48 h after weaning of a new and persistent infiltrate on chest X-ray, purulent tracheal secretions, and a positive culture of a protected brush specimen (greater than or equal to 10(3) cfu/ml). Bacterial colonization was assessed every 48 h by quantitative cultures of pharyngeal swab, tracheal aspirate, humidifying cascade, and expiratory tubing trap. The two groups were similar in terms of age, indication for and duration of ventilation, and severity of illness. (ABSTRACT TRUNCATED AT 250 WORDS)
An irreversible constitutive model for fibrous soft biological tissue : A 3-D microfiber approach with demonstrative application to abdominal aortic aneurysms

1742-7061/$ see front matter 2011 Acta Material doi:10.1016/j.actbio. 2011.02. 015 ⇑ Address: KTH Solid Mechanics, Osquars Backe 1, S Tel. : +46 87907793. E-mail address: tg@hallf.kth. se Understanding the failure and damage mechanisms of soft biological tissue is critical to a sensitive and specific characterization of tissue injury tolerance and its relation to biological responses. Despite increasing experimental and analytical efforts, failure-related irreversible effects of soft biological tissue are still poorly understood. There is still no clear definition of what ‘‘damage’’ of a soft biological material is, and conventional macroscopic indicators, as known from damage of engineering materials for example, may not identify the tissue’s tolerance to injury appropriately. To account for the complex three-dimensional arrangement of collagen, a microfiber model approach is applied, where constitutive relations for collagen fibers are integrated over the unit sphere, which in turn defines the tissue’s macroscopic properties. A collagen fiber is represented by a bundle of proteoglycan cross-linked collagen fibrils that undergoes irreversible deformations when exceeding its elastic tensile limit. The proposed constitutive model is able to predict strain stiffening at physiological strain levels and does not exhibit a clear macroscopic elastic limit, two typical features known from soft biological tissue testing. An elastic-predictor/plastic-corrector implementation of the model is followed and constitutive parameters are estimated from in vitro test data from a particular abdominal aortic aneurysm (AAA). Damage-based structural instabilities of the AAA under different inflation conditions are investigated, where the collagen orientation density has been estimated from its in vivo stress state. 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.