Miracle-dz/UniFAR-FTUs huggingface dataset:
The Importance of LAT in the Activation, Homeostasis, and Regulatory Function of T Cells*

LAT (linker for activation of T cells) is a transmembrane adaptor protein that plays an essential role in TCR-mediated signaling and thymocyte development. Because LAT-deficient mice have an early block in thymocyte development, we utilized an inducible system to delete LAT in primary T cells to study LAT function in T cell activation, homeostasis, and survival. Deletion of LAT caused primary T cells to become unresponsive to stimulation from the TCR and impaired T cell homeostatic proliferation and long term survival. Furthermore, deletion of LAT led to reduced expression of Foxp3, CTLA-4, and CD25 in Treg cells and impaired their function. Consequently, mice with LAT deleted developed a lymphoproliferative syndrome similar to that in LATY136F mice, although less severe. Our data implicate that LAT has positive and negative roles in the regulation of mature T cells.
Lateral division of the lateral posterior region: Connections with area 18 in cats

Abstract To establish the topography of the lateral division of the lateral posterior region (LP1) projections to area 18, up to five different anatomical tracers were injected in separate rostrocaudal locations in area 18 of four adult cats, and patterns of retrogradely labeled LP1 cells were identified. LP1 inputs to area 18 arose from both caudal and rostral nuclei and were topological, organized in patterns that indicate that lower visual space is represented anteroventrally, and more central and upper visual space is represented caudodorsally. In the caudal LP1 nucleus, patches of labeled cells formed bands that ran parallel to the medial and lateral LPI borders and encompassed medial portions of the nucleus. In rostral LP1, the patches of labeled cells formed clusters giving the connections with area 18 a more modular appearance, and were nearer the lateral LP1 border. Injections made nearest area centralis representations in area 18 labeled more neurons than injections in cortex representing more peripheral visual space. Also, neighboring injections in area 18 labeled overlapping patches of cells, but no double-labeled cells were observed. These findings are consistent with previous conclusions based on electrophysiological mapping studies, that two retinotopically organized nuclei constitute LP1.
Monitoring of fatty aldehyde dehydrogenase by formation of pyrenedecanoic acid from pyrenedecanal

Fatty aldehyde dehydrogenase (EC 1.2.1.48) converts long-chain fatty aldehydes to the corresponding acids. Deficiency in this enzyme causes the Sjogren Larsson Syndrome, a rare inherited disorder characterized by ichthyosis, spasticity, and mental retardation. Using a fluorescent aldehyde, pyrenedecanal, and HPLC with fluorescence detection, we developed a novel method to monitor fatty aldehyde dehydrogenase activity by quantification of the product pyrenedecanoic acid together with the substrate pyrenedecanal and possible side products, such as aldehyde adducts. As shown with recombinant enzymes, pyrenedecanal showed a high preference for fatty aldehyde dehydrogenase compared with other aldehyde dehydrogenases. The method allowed detection of fatty aldehyde dehydrogenase activity in nanogram amounts of microsomal or tissue protein and microgram amounts of Sjogren Larsson syndrome patients' skin fibroblast protein. It could successfully be adapted for the analysis of fatty aldehyde dehydrogenase activity in gel slices derived from low-temperature SDS-PAGE, showing that fatty aldehyde dehydrogenase activity from solubilized rat liver microsomes migrates as a dimer. Thus, monitoring of pyrenedecanoic acid formation from pyrenedecanal by HPLC with fluorescence detection provides a robust and sensitive method for determination of fatty aldehyde dehydrogenase activity.
Role of the corpus callosum in bimanual coordination: a comparison of patients with congenital and acquired callosal damage

The objective of the study was to investigate temporal control in patients with congenital as compared to acquired pathology of the corpus callosum during two different bimanual paradigms: (i) a drawer‐opening task during which one hand opened a drawer while the other hand reached and grasped a small object, and (ii) rhythmical circling movements that were executed according to the in‐phase or antiphase mode. Synchronization values revealed that patients with acquired callosal dysfunction generally showed optimal behaviour during the goal‐directed and familiar drawer‐opening task but demonstrated strong tendencies towards desynchronization during circling movements, which became most apparent for antiphase coordination. Whereas one patient with callosal agenesis showed a similar performance, the other acallosal patients performed both activities successfully. These observations indicate that patients with congenital absence of the corpus callosum can make use of compensatory mechanisms for allowing temporal synchronization during bimanual movements whereas patients with acquired callosal dysfunction are severely hampered when the task places significant demands on the control processes. The data also underline that the ability of callosal patients to precisely time events in coordinated actions depend on the task constraints.
Validity and limitations of the Nidek NT‐4000 non‐contact tonometer: a clinical study

Using Goldmann applanation tonometry (GAT) as a gold standard, we evaluated the accuracy of Nidek NT‐4000 pneumotonometry (NPT) in adults without corneal disease. Bland and Altman analysis of serial intra‐ocular pressures (IOPs) measured with NPT and GAT in 10 healthy subjects revealed that the repeatability coefficients for the two methods were similar. NPT, GAT and ultrasonic pachymetry were then performed in 100 patients. Bland and Altman analysis showed that NPT yielded significantly higher readings than GAT [mean biases for right and left eye measurements were 1.37 mmHg (95% limits of agreement: −3.02–5.76) and 1.17 mmHg (95% limits of agreement: −2.76–5.11) respectively] and was more affected by corneal thickness variations. For detection of IOPs ≥21 mmHg, NPT displayed very high sensitivity (0.90) and good specificity (0.95). NPT may be useful in screening and clinical settings but borderline‐high IOP readings should be confirmed with GAT.
Intracellular Loop between Transmembrane Segments IV and V of Cystic Fibrosis Transmembrane Conductance Regulator Is Involved in Regulation of Chloride Channel Conductance State (*)

The cystic fibrosis transmembrane conductance regulator (CFTR) contains two membrane-spanning domains; each consists of six transmembrane segments joined by three extracellular and two intracellular loops of different length. To examine the role of intracellular loops in CFTR channel function, we studied a deletion mutant of CFTR (Δ19 CFTR) in which 19 amino acids were removed from the intracellular loop joining transmembrane segments IV and V. This mutant protein was expressed in a human embryonic kidney cell line (293 HEK). Fully mature glycosylated CFTR (170 kDa) was immunoprecipitated from cells transfected with wild-type CFTR cDNA, while cells transfected with the mutant gene expressed only a core-glycosylated form (140 kDa). The chloride efflux rate (measured by 6-methoxyl-N-(3-sulfopropyl) quinolinium SPQ fluorescence) from cells expressing wild-type CFTR increased 600% in response to forskolin. In contrast, Δ19 CFTR-expressing cells had no significant response to forskolin. Western blotting performed on subcellular membrane fractions showed that Δ19 CFTR was located in the same fractions as ΔF508 CFTR, a processing mutant of CFTR. These results suggest that Δ19 CFTR is located in the intracellular membranes, without reaching the cell surface. Upon reconstitution into lipid bilayer membranes, Δ19 CFTR formed a functional Cl channel with gating properties nearly identical to those of the wild-type CFTR channel. However, Δ19 CFTR channels exhibited frequent transitions to a 6-picosiemens subconductance state, whereas wild-type CFTR channels rarely exist in this subconductance state. These data suggest that the intracellular loop is involved in stabilizing the full conductance state of the CFTR Cl channel.
Relating parent and family functioning to the psychological adjustment of children with chronic health conditions: what have we learned? What do we need to know?

Reviewed research concerning the relationship of parent and family functioning to the psychological adjustment of children with chronic health conditions. More adaptive family relationships and parental psychological adjustment were associated with positive psychological adjustment while less adaptive family relationships (e.g., greater conflict and maternal psychological distress) consistently predicted problematic adjustment. Conclusions were limited by small, site-specific samples, reliance on self-report measures generally obtained from one parent, and general measures. Research progress would be enhanced by (a) more representative data sets; (b) process-oriented, illness-specific, and clinically relevant measures; (c) prospective analyses that clarify specific causal pathways between family functioning and children's adjustment; and (d) tests of interventions that modify risk and/or resistance factors.
Expression and prognostic value of epidermal growth factor receptor, transforming growth factor‐α, and c‐erb B‐2 in nephroblastoma

Wilms tumor is one of the most common solid tumors in children. A transforming growth factor‐α (TGF‐α)/epidermal growth factor receptor (EGF‐R) autocrine loop plays an important role in tumor growth. Abnormal expression of TGF‐α, EGF‐R and c‐erb B‐2 has been demonstrated in several human malignancies.
Crystal structure of an antigen-binding fragment bound to single-stranded DNA.

Antibodies to DNA are characteristic of the autoimmune disease systemic lupus erythematosus (SLE) and they also serve as models for the study of protein-DNA recognition. Anti-DNA antibodies often play an important role in disease pathogenesis by mediating kidney damage via antibody-DNA immune complex formation. The structural underpinnings of anti-DNA antibody pathogenicity and antibody-DNA recognition, however, are not well understood, due in part to the lack of direct, experimental three-dimensional structural information on antibody-DNA complexes. To address these issues for anti-single-stranded DNA antibodies, we have determined the 2.1 A crystal structure of a recombinant Fab (DNA-1) in complex with dT5. DNA-1 was previously isolated from a bacteriophage Fab display library from the immunoglobulin repertoire of an SLE-prone mouse. The structure shows that DNA-1 binds oligo(dT) primarily by sandwiching thymine bases between Tyr side-chains, which allows the bases to make sequence-specific hydrogen bonds. The critical stacking Tyr residues are L32, L49, H100, and H100A, while His L91 and Asn L50 contribute hydrogen bonds. Comparison of the DNA-1 structure to other anti-nucleic acid Fab structures reveals a common ssDNA recognition module consisting of Tyr L32, a hydrogen bonding residue at position L91, and an aromatic side-chain from the tip of complementarity determining region H3. The structure also provides a framework for interpreting previously determined thermodynamics data, and this analysis suggests that hydrophobic desolvation might underlie the observed negative enthalpy of binding. Finally, Arg side-chains from complementarity determining region H3 appear to play a novel role in DNA-1. Rather than forming ion pairs with dT5, Arg contributes to oligo(dT) recognition by helping to maintain the structural integrity of the combining site. This result is significant because antibody pathogenicity is thought to be correlated to the Arg content of anti-DNA antibody hypervariable loops.
Humoral immune responses to Shiga-like toxins and Escherichia coli O157 lipopolysaccharide in hemolytic-uremic syndrome patients and healthy subjects

Shiga-like-toxin (SLT)-producing Escherichia coli strains, especially serotype O157:H7, are important causes of bloody diarrhea and are associated with the development of hemolytic-uremic syndrome (HUS). Enzyme-linked immunosorbent assays (ELISAs) were developed for the serologic detection of immunoglobulin M (IgM), IgG, and IgA to Shiga toxin (ST) and SLT-I, IgG to SLT-II, and IgM and IgG reactive against E. coli O157 lipopolysaccharide (LPS). Serum samples were collected from 27 HUS patients (25 pediatric and 2 adult) and tested in the ELISAs. Of 27 patients, 10 (37%) were positive for at least one class of antibody to ST/SLT-I. None of the patients were positive for IgG antibody to SLT-II. Twenty-one of the 27 patients (78%) were positive for antibody to E. coli O157 LPS; 19 of 27 (70%) were positive for IgM, and 20 of 27 (74%) were positive for IgG. None of 48 control serum samples were positive in any of the toxin assays, and only 1 of 48 (2%) and 2 of 48 (4%) were positive for IgM and IgG, respectively, to E. coli O157 LPS. Twelve of the 24 patients (50%) from whom stool specimens were collected were positive by culture for E. coli O157. Overall, serology and culture produced confirmation of infection by SLT-producing organisms in 23 of 27 (85%) HUS patients. A combination of ELISA for antibodies to E. coli O157 LPS and culture provided evidence for 22 of 27 (82%) of these patients. The results indicate that while ELISAs for ST/SLT-I and SLT-II antibodies were of limited diagnostic value, the ELISAs for IgM and IgG to E. coli O157 LPS provided valuable and sensitive adjuncts to culture.
Synthetic Images of High-Throughput Microscopy for Validation of Image Analysis Methods

Automated image analysis provides a powerful tool when quantifying various characteristics of cell populations. Previously, the validation of image analysis results has been a task of expert biologist, who has manually analyzed the images and provided the ground truth to which the proposed analysis results have been compared. The traditional validation approach, prone to errors and variation, is unfeasible in the emergence of high-throughput measurement systems which make human-based analysis excessively laborious. The systems biology approach for studying, e.g., cellular activity massively in parallel, often lending on high-throughput microscopy, further increases the need for efficient, validated computational methods. As a solution for the problem, we propose a computational framework for simulating fluorescence microscopy images of cell populations. The simulation framework allows generation of synthetic images with realistic characteristics including the ground truth for validation. Thus, the simulation enables validation and performance analysis for various analysis algorithms. By creating a parameterized model of cells based on a given population, the simulator is able to create different cell types. The proposed modular framework, combined with the ability to create high-throughput measurements, provides a powerful tool for validating image analysis methods in traditional microscopy as well as in high content screening. Moreover, we use experimental data to study the validity of the proposed modeling approach.
Attracting Ellipsoid Method application to designing of sliding mode controllers

The Attracting Ellipsoid Method is applied for the design of sliding mode controllers for linear systems subjected to matched and unmatched perturbations. The existence of first order actuators is considered and their time constants are designed to provide quasi-optimal practical stability. The technique is based on the existence of an attracting (invariant) ellipsoid such that the convergence to a quasi-minimal region of the origin is guaranteed. The design procedure is given in terms of the solution of a set of Linear Matrix Inequalities. A benchmark example illustrating the design is given.
A transverse oscillation approach for estimation of three-dimensional velocity vectors, Part I: concept and simulation study

A method for 3-D velocity vector estimation using transverse oscillations is presented. The method employs a 2-D transducer and decouples the velocity estimation into three orthogonal components, which are estimated simultaneously and from the same data. The validity of the method is investigated by conducting simulations emulating a 32 × 32 matrix transducer. The results are evaluated using two performance metrics related to precision and accuracy. The study includes several parameters including 49 flow directions, the SNR, steering angle, and apodization types. The 49 flow directions cover the positive octant of the unit sphere. In terms of accuracy, the median bias is -2%. The precision of vx and vy depends on the flow angle β and ranges from 5% to 31% relative to the peak velocity magnitude of 1 m/s. For comparison, the range is 0.4 to 2% for vz. The parameter study also reveals, that the velocity estimation breaks down with an SNR between -6 and -3 dB. In terms of computational load, the estimation of the three velocity components requires 0.75 billion floating point operations per second (0.75 Gflops) for a realistic setup. This is well within the capability of modern scanners.
An approximation based algorithm for minimum bounding rectangle computation

Shape extraction and analysis is one of the most important task in image processing. The accuracy of the shape features extraction process increases the object recognition rate. Minimum Bounding Rectangle (MBR) is a tool that contributes to the increase of the accuracy of the shape features extraction, particularly it can be used to determine the real aspect ratio. This paper focuses on the improvement of the existing method. This is focused around the determination of the MBR's edges points, using a series of approximations. The proposed method gives more accurate MBR in all the tested situations. In order to demonstrate the accuracy of the proposed method, an experiment is setup based on the comparison of the manually drawn MBR and the ones generated by each of the methods. Results achieved showed that the proposed method outperforms existing method as it consistently produced results closest to the manually drawn MBR.
Comparison of the relative airways and systemic potencies of inhaled fenoterol and salbutamol in asthmatic patients.

BACKGROUND--There is controversy as to the relative safety of fenoterol and salbutamol. No differences have been found in the relative cardiac beta 1/beta 2 receptor activity of inhaled fenoterol and salbutamol in normal subjects. These initial findings have been extended by comparing the respective potencies of equivalent doses by weight of fenoterol and salbutamol in asthmatic subjects, in terms of airways and systemic responses. METHODS--Eighteen asthmatic patients of mean (SD) age 40 (14) years and a forced expiratory volume in one second (FEV1)% predicted of 56 (14)% (1.97 (0.66)1) were randomised to inhale fenoterol (100 micrograms/puff or 200 micrograms/puff), salbutamol, or placebo (100 micrograms/puff or 200 micrograms/puff) on three separate days. Dose-response curves were constructed using cumulative doses of 100 micrograms, 200 micrograms, 400 micrograms, 1000 micrograms, 2000 micrograms, and 4000 micrograms, and airways and systemic responses were measured 20 minutes after each dose with 40 minute increments. Dose ratios for the relative potency of fenoterol versus salbutamol were calculated from the dose-response curves using regression analysis of parallel slopes. RESULTS--There was no difference in bronchodilator potency between fenoterol and salbutamol (as median dose ratio): FEV1 1.1 (95% CI 0.4 to 4.6). In contrast, dose ratios for systemic responses showed that fenoterol was more potent than salbutamol: serum potassium 3.7 (95% CI 2.0 to 6.0), tremor 5.7 (95% CI 1.4 to 10.2), heart rate 1.6 (95% CI 1.0 to 2.3). At a conventional dose of 200 micrograms the only difference in response between the two drugs was observed for tremor (as mean difference): 0.23 log units (95% CI 0.06 to 0.41 log units). CONCLUSIONS--There was no difference in the bronchodilator potency between fenoterol and salbutamol on a microgram equivalent basis. In contrast, systemic potency was greater with fenoterol, although this difference was not clinically relevant at conventional dosages up to 200 micrograms.
β-Subunits of the SnRK1 Complexes Share a Common Ancestral Function Together with Expression and Function Specificities; Physical Interaction with Nitrate Reductase Specifically Occurs via AKINβ1-Subunit1[C][OA]

The SNF1/AMPK/SnRK1 kinases are evolutionary conserved kinases involved in yeast, mammals, and plants in the control of energy balance. These heterotrimeric enzymes are composed of one α-type catalytic subunit and two γ- and β-type regulatory subunits. In yeast it has been proposed that the β-type subunits regulate both the localization of the kinase complexes within the cell and the interaction of the kinases with their targets. In this work, we demonstrate that the three β-type subunits of Arabidopsis (Arabidopsis thaliana; AKINβ1, AKINβ2, and AKINβ3) restore the growth phenotype of the yeast sip1Δsip2Δgal83Δ triple mutant, thus suggesting the conservation of an ancestral function. Expression analyses, using AKINβ promoter∷β-glucuronidase transgenic lines, reveal different and specific patterns of expression for each subunit according to organs, developmental stages, and environmental conditions. Finally, our results show that the β-type subunits are involved in the specificity of interaction of the kinase with the cytosolic nitrate reductase. Together with previous cell-free phosphorylation data, they strongly support the proposal that nitrate reductase is a real target of SnRK1 in the physiological context. Altogether our data suggest the conservation of ancestral basic function(s) together with specialized functions for each β-type subunit in plants.
The Transformation Suppressor Pdcd4 Is a Novel Eukaryotic Translation Initiation Factor 4A Binding Protein That Inhibits Translation

ABSTRACT Pdcd4 is a novel transformation suppressor that inhibits tumor promoter-induced neoplastic transformation and the activation of AP-1-dependent transcription required for transformation. A yeast two-hybrid analysis revealed that Pdcd4 associates with the eukaryotic translation initiation factors eIF4AI and eIF4AII. Immunofluorescent confocal microscopy showed that Pdcd4 colocalizes with eIF4A in the cytoplasm. eIF4A is an ATP-dependent RNA helicase needed to unwind 5′ mRNA secondary structure. Recombinant Pdcd4 specifically inhibited the helicase activity of eIF4A and eIF4F. In vivo translation assays showed that Pdcd4 inhibited cap-dependent but not internal ribosome entry site (IRES)-dependent translation. In contrast, Pdcd4D418A, a mutant inactivated for binding to eIF4A, failed to inhibit cap-dependent or IRES-dependent translation or AP-1 transactivation. Recombinant Pdcd4 prevented eIF4A from binding to the C-terminal region of eIF4G (amino acids 1040 to 1560) but not to the middle region of eIF4G(amino acids 635 to 1039). In addition, both Pdcd4 and Pdcd4D418A bound to the middle region of eIF4G. The mechanism by which Pdcd4 inhibits translation thus appears to involve inhibition of eIF4A helicase, interference with eIF4A association-dissociation from eIF4G, and inhibition of eIF4A binding to the C-terminal domain of eIF4G. Pdcd4 binding to eIF4A is linked to its transformation-suppressing activity, as Pdcd4-eIF4A binding and consequent inhibition of translation are required for Pdcd4 transrepression of AP-1.