Miracle-dz/UniFAR-FTUs huggingface dataset:
Chimeric genes as dominant selectable markers in plant cells

Opine synthases are enzymes produced in dicotyledonous plants as the result of a natural gene transfer phenomenon. Agrobacteria contain Ti plasmids that direct the transfer, stable integration and expression of a number of genes in plants, including the genes coding for octopine or nopaline synthase. This fact was used as the basis for the construction of a number of chimeric genes combining the 5′ upstream promoter sequences and most of the untranslated leader sequence of the nopaline synthase (nos) gene with the coding sequence of two bacterial genes: the aminoglycoside phosphotransferase (APH(3′)II) gene of Tn5 and the methotrexate‐insensitive dihydrofolate reductase (DHFR MtxR) of the R67 plasmid. The APH(3′)II enzyme inactivates a number of aminoglycoside antibiotics such as kanamycin, neomycin and G418. Kanamycin, G418 and methotrexate are very toxic to plants. The chimeric NOS‐APH(3′)II gene, when transferred to tobacco cells using the Ti plasmid as a gene vector, was expressed and conferred resistance to kanamycin to the plant cells. Kanamycin‐resistant tobacco cells were shown to contain a typical APH(3′)II phosphorylase activity. This chimeric gene can be used as a potent dominant selectable marker in plants. Similar results were also obtained with a NOS‐DHFR MtxR gene. Our results demonstrate that foreign genes are not only transferred but are also functionally expressed when the appropriate constructions are made using promoters known to be active in plant cells.
Tilapia chromosomal growth hormone gene expression accelerates growth in transgenic zebrafish (Danio rerio)

Gene transfer is economically important and model fish species has produced a great impact in modern biology and biotechnology. Transgenic zebrafish ( Danio rerio ) were generated through the co-injection of a GFP-expressing plasmid and an "all fish" transgene composed by the carp β-actin promoter and the chromosomal tilapia ( Oreochromis hornorum ) growth hormone gene. The GFP expression was a good indicator of stable transformation and allowed for high efficiency selection of transgenic fish. Transgenic F1 zebrafish grew 20% faster than full sibling non-transgenic controls.
Towards MRI-Based Autonomous Robotic US Acquisitions: A First Feasibility Study

Robotic ultrasound has the potential to assist and guide physicians during interventions. In this work, we present a set of methods and a workflow to enable autonomous MRI-guided ultrasound acquisitions. Our approach uses a structured-light 3D scanner for patient-to-robot and image-to-patient calibration, which in turn is used to plan 3D ultrasound trajectories. These MRI-based trajectories are followed autonomously by the robot and are further refined online using automatic MRI/US registration. Despite the low spatial resolution of structured light scanners, the initial planned acquisition path can be followed with an accuracy of 2.46 ± 0.96 mm. This leads to a good initialization of the MRI/US registration: the 3D-scan-based alignment for planning and acquisition shows an accuracy (distance between planned ultrasound and MRI) of 4.47 mm, and 0.97 mm after an online-update of the calibration based on a closed loop registration.
Lifts of Lipschitz maps and horizontal fractals in the Heisenberg group

We consider horizontal iterated function systems in the Heisenberg group $\mathbb{H}^1$, i.e. collections of Lipschitz contractions of $\mathbb{H}^1$ with respect to the Heisenberg metric. The invariant sets for such systems are so-called horizontal fractals. We study questions related to connectivity of horizontal fractals and regularity of functions whose graph lies within a horizontal fractal. Our construction yields examples of horizontal BV (bounded variation) surfaces in $\mathbb{H}^1$ that are in contrast with the non-existence of horizontal Lipschitz surfaces which was recently proved by Ambrosio and Kirchheim (Rectifiable sets in metric and Banach spaces. Math. Ann.318(3) (2000), 527–555).
Pharmaceutical treatment of asthma symptoms in elite athletes – doping or therapy?

Asthma, exercise‐induced bronchoconstriction, and airway hyper‐responsiveness are often found in elite athletes, perhaps as a consequence of their sport or maybe because asthma is a common disorder in young adults. Inhaled β2‐agonists (IBA) are frequently used in elite athletes, but due to regulations introduced by the International Olympic Committee, the use of anti‐asthmatic therapy might change. Drugs that make ergogenic effect persist are prohibited in all athletes, whether or not they take part in competitions and systemic steroids and β2‐agonists are among such drugs. On the other hand, opinion is more divided about the use of inhaled corticosteroids (ICS) and IBA. In humans, no effect has been found on the oxygen uptake, performance or distance run with therapeutic doses of IBA, either in asthmatics or non‐asthmatics, whereas others report an ergogenic effect and better lung function of high doses of a β2‐agonist in non‐asthmatics. Anti‐asthmatic treatment is necessary for asthmatics, but should not be used by non‐asthmatic elite athletes due to both possible systemic effects and furthermore, side effects of both ICS and IBA.
Forehead Electro-tactile Display for Vision Substitution

The Forehead Retina System-composed of a small camera and 512 electrodes on the forehead-captures the view in front, extracts outlines from the view, and converts the outlines to tactile sensation by electrical stimulation. Forehead skin was chosen for stimulation in consideration of usability. An electrotactile display was used so that the system becomes small and durable. A gel layer was designed to prevent an unpleasant sensation during stimulation. The system primarily aims to enable the visually impaired to "see" the surrounding environment.
Motor Cortex-Evoked Activity in Reciprocal Muscles Is Modulated by Reward Probability

Horizontal intracortical projections for agonist and antagonist muscles exist in the primary motor cortex (M1), and reward may induce a reinforcement of transmission efficiency of intracortical circuits. We investigated reward-induced change in M1 excitability for agonist and antagonist muscles. Participants were 8 healthy volunteers. Probabilistic reward tasks comprised 3 conditions of 30 trials each: 30 trials contained 10% reward, 30 trials contained 50% reward, and 30 trials contained 90% reward. Each trial began with a cue (red fixation cross), followed by blue circle for 1 s. The subjects were instructed to perform wrist flexion and press a button with the dorsal aspect of middle finger phalanx as quickly as possible in response to disappearance of the blue circle without looking at their hand or the button. Two seconds after the button press, reward/non-reward stimulus was randomly presented for 2-s duration. The reward stimulus was a picture of Japanese 10-yen coin, and each subject received monetary reward at the end of experiment. Subjects were not informed of the reward probabilities. We delivered transcranial magnetic stimulation of the left M1 at the midpoint between center of gravities of agonist flexor carpi radialis (FCR) and antagonist extensor carpi radialis (ECR) muscles at 2 s after the red fixation cross and 1 s after the reward/non-reward stimuli. Relative motor evoked potential (MEP) amplitudes at 2 s after the red fixation cross were significantly higher for 10% reward probability than for 90% reward probability, whereas relative MEP amplitudes at 1 s after reward/non-reward stimuli were significantly higher for 90% reward probability than for 10% and 50% reward probabilities. These results implied that reward could affect the horizontal intracortical projections in M1 for agonist and antagonist muscles, and M1 excitability including the reward-related circuit before and after reward stimulus could be differently altered by reward probability.
The Place of Modeling in Cognitive Science

I consider the role of cognitive modeling in cognitive science. Modeling, and the computers that enable it, are central to the field, but the role of modeling is often misunderstood. Models are not intended to capture fully the processes they attempt to elucidate. Rather, they are explorations of ideas about the nature of cognitive processes. In these explorations, simplification is essential-through simplification, the implications of the central ideas become more transparent. This is not to say that simplification has no downsides; it does, and these are discussed. I then consider several contemporary frameworks for cognitive modeling, stressing the idea that each framework is useful in its own particular ways. Increases in computer power (by a factor of about 4 million) since 1958 have enabled new modeling paradigms to emerge, but these also depend on new ways of thinking. Will new paradigms emerge again with the next 1,000-fold increase?
Studies on lens protein polypeptides.

Methods for the separation and identification of the polypeptide chains of each lens crystaUin are basic to the study of these proteins on polyribosomes. Rabbit lens proteins have been deaggregated, denatured, and reduced to polypeptide chains, and separated by polyacrylamide gel electrophoresis. Approximate molecular weights of the resultant chains have been calculated by the same system. Vigorous denaturation and reduction with sodium dodecyl sulfate and 2-mercaptoethanol disrupts all structure other than primary structure, degrading each protein to its component polypeptides. The separation method employed is almost exclusively dependent on molecular size. Deaggregated alpha crystaUin is a group of chains, each of about 20,000 molecular weight. The beta crystaUin region of the DEAE chromatogram yields three polypeptides of estimated molecular weights 21,000, 23,000, and 29,000. Preliminary studies on the four beta crystaUin peaks isolated, by DEAE-chromatography suggest that one or more may be composed of aggregates of different polypeptide chains. Gamma crystallins appear to be single polypeptide chain proteins of molecular weights from 18,000 to 21,000. Experiments performed on lens epithelium indicate that a significant percentage of their newly synthesized proteins are nuclear and cytoplasmic proteins other than the crystallins.
Effects of gliclazide add on metformin on serum omentin-1 levels in patients with type 2 diabetes mellitus

Background: Omentin is a newly identified adipokine that has beneficial influence against cardiovascular disorders. Hence, considering the impact of anti-diabetic drug on omentin levels may provide an adjuvant strategy to protect diabetic patients against valuable clinical hazards. Aim of the Study: To investigate the influence of metformin alone or in combination with gliclazide on the level of serum omentin among patients with type 2 diabetes mellitus (T2DM). Patients and Methods: A total of 70 newly diagnosed patients with T2DM were enrolled in this randomized, double-blind prospective study, and divided into two equal groups based on treatment regimen in which Group 1 treated with metformin (1000 mg) and Group 2 treated with metformin (1000 mg) plus gliclazide (80 mg). Blood glucose levels, HbA1C, insulin levels, and serum omentin-1 were measured at baseline and after 12 weeks of treatment. Result: Use of gliclazide as an add-on therapy to metformin in patients with T2DM result in better glycemic control evidenced by significant reductions in the levels of blood glucose levels and HbA1C and much more improvement in insulin sensitivity evidenced by significant decreased in insulin resistance index, whereas it has adverse impact on serum omentin-1 levels evidenced by significant decrement in omentin-1 level in comparison to their pretreatment levels among Group 2 patients. Conclusions: Adding of gliclazide to metformin in treatment of patients with T2DM might extend the therapeutic action of metformin in regarding much better controlling of glycemic indices, but, at the same time, it might attenuate the cardioprotective effects of metformin by its adverse influence on serum omentin-1 levels.
LightCycler Multiplex PCR for the Laboratory Diagnosis of Common Viral Infections of the Central Nervous System

ABSTRACT A conventional multiplex PCR assay that detects herpes simplex virus type 1 (HSV-1), HSV-2, varicella-zoster virus, and enteroviruses for the diagnosis of central nervous system infections was modified to be performed using the LightCycler system. The sensitivity of detection of each of the viruses using the LightCycler assay was compared to that of the conventional assay using external quality assessment material. The assays had equivalent sensitivities, but the LightCycler assay was more rapid, reduced the risk of contamination, and used an amplicon detection format that demonstrated greater discrimination than a gel electrophoresis method.
Developmental skills of 36-60-month-old children in Isfahan daycare centers in 2013

Background: Assessment of developmental skills is one of the most essential components of children's health evaluation. Since several pubertal disorders are caused by parental negligence in diagnosis, prevention, and treatment of childhood problems, failure to make a timely diagnosis of these problems could have adverse effects on the health of children in future. This study was conducted to determine the developmental skills of 36-60-month-old children in Isfahan. Materials and Methods: In this cross-sectional study, 196 children, aged 36-60 months, were recruited through random cluster sampling. “Ages and Stages” questionnaire was filled for each subject by their parents (father, mother, or both), and the frequency of developmental delay was determined based on cut-off points. The data were analyzed by descriptive statistics using SPSS 20.0. Results: About 52.6% of the children were male. Mean age of the children was 50.71 (SD = 8.16) months. The abnormal findings were in the five domains of communication (1.5%), gross motor (3.1%), fine motor (7.7%), problem solving (7.7%) and personal-social (2%). Conclusions: The results suggest that some of the children had scores below or equal to the cut-off points and needed more evaluation by a professional person. The domains in which the children had problems were fine motor, problem solving, and gross motor. Therefore, health staff should pay more attention to assessment of these domains and parents should be trained to develop their children's skills in these domains.
Modeled channel distributions explain extracellular recordings from cultured neurons sealed to microelectrodes

Amplitudes and shapes of extracellular recordings from single neurons cultured on a substrate embedded microelectrode depend not only on the volume conducting properties of the neuron-electrode interface, but might also depend on the distribution of voltage-sensitive channels over the neuronal membrane. In this paper, finite-element modeling is used to quantify the effect of these channel distributions on the neuron-electrode contact. Slight accumulation or depletion of voltage-sensitive channels in the sealing membrane of the neuron results in various shapes and amplitudes of simulated extracellular recordings. However, estimation of channel-specific accumulation factors from extracellular recordings can be obstructed by co-occuring ion currents and defect sealing. Experimental data from cultured neuron-electrode interfaces suggest depletion of sodium channels and accumulation of potassium channels.
The Extra-Cytoplasmic Function Sigma Factor SigX Modulates Biofilm and Virulence-Related Properties in Pseudomonas aeruginosa

SigX, one of the 19 extra-cytoplasmic function sigma factors of P. aeruginosa, was only known to be involved in transcription of the gene encoding the major outer membrane protein OprF. We conducted a comparative transcriptomic study between the wildtype H103 strain and its sigX mutant PAOSX, which revealed a total of 307 differentially expressed genes that differed by more than 2 fold. Most dysregulated genes belonged to six functional classes, including the “chaperones and heat shock proteins”, “antibiotic resistance and susceptibility”, “energy metabolism”, “protein secretion/export apparatus”, and “secreted factors”, and “motility and attachment” classes. In this latter class, the large majority of the affected genes were down-regulated in the sigX mutant. In agreement with the array data, the sigX mutant was shown to demonstrate substantially reduced motility, attachment to biotic and abiotic surfaces, and biofilm formation. In addition, virulence towards the nematode Caenorhabditis elegans was reduced in the sigX mutant, suggesting that SigX is involved in virulence-related phenotypes.
Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota

Recent work using culture-independent methods suggests that the lungs of cystic fibrosis (CF) patients harbor a vast array of bacteria not conventionally implicated in CF lung disease. However, sampling lung secretions in living subjects requires that expectorated specimens or collection devices pass through the oropharynx. Thus, contamination could confound results. Here, we compared culture-independent analyses of throat and sputum specimens to samples directly obtained from the lungs at the time of transplantation. We found that CF lungs with advanced disease contained relatively homogenous populations of typical CF pathogens. In contrast, upper-airway specimens from the same subjects contained higher levels of microbial diversity and organisms not typically considered CF pathogens. Furthermore, sputum exhibited day-to-day variation in the abundance of nontypical organisms, even in the absence of clinical changes. These findings suggest that oropharyngeal contamination could limit the accuracy of DNA-based measurements on upper-airway specimens. This work highlights the importance of sampling procedures for microbiome studies and suggests that methods that account for contamination are needed when DNA-based methods are used on clinical specimens.
Optimal CEO Compensation with Search: Theory and Empirical Evidence

We integrate an agency problem into search theory to study executive compensation in a market equilibrium. A CEO can choose to stay or quit and search after privately observing an idiosyncratic shock to the firm. The market equilibrium endogenizes CEOs’ and firms’ outside options and captures contracting externalities. We show that the optimal pay-to-performance ratio is less than one even when the CEO is risk neutral. Moreover, the equilibrium pay-toperformance sensitivity depends positively on a firm’s idiosyncratic risk, and negatively on the systematic risk. Our empirical tests using executive compensation data confirm these results.
Identification of a Complex that Binds to the CD154 3′ Untranslated Region: Implications for a Role in Message Stability During T Cell Activation1

CD154 expression is regulated throughout a time course of CD3-dependent T cell activation by differential mRNA decay. To understand the molecular basis of the “stability” phase of this pathway, experiments were conducted to identify sequences and specific complexes important in this regulation. Gel retardation assays using extracts from both Jurkat T cells and CD3-activated CD4+ T cells revealed a major complex (complex I) that bound a 65-bp highly CU-rich region of the CD154 3′ untranslated region. The specificity of the CU-rich element for complex-I formation was confirmed by disruption of this complex by oligo(dCT) competition. Formation of complex I strongly correlated with CD154 mRNA stability across a time course of T cell activation. UV cross-linking identified a major oligo(dCT)-sensitive species at ∼90 kDa that showed induced and increased expression in extracts from 24- and 48-hr anti-CD3-activated T cells, respectively. This protein was absent in equivalent extracts from resting or 2-h-activated T cells. Using an in vitro decay assay, we found that a CD154-specific transcript was more rapidly degraded in 2-h-activated extract and stabilized in the 24- and 48-h extracts compared to extracts from resting T cells. Disruption of complex I resulted in the rapid decay of a CD154-specific transcript demonstrating a functional role for complex I in mRNA stabilization in vitro. These studies support a model of posttranscriptional regulation of CD154 expression being controlled in part by the interaction of a poly(CU)-binding complex with a specific sequence in the 3′ untranslated region.
Ca-Signaling G-Protein[Ndash] coupled Receptors: A New Site of Local Anesthetic Action?

The role of Na channel inhibition in the mechanism of local anesthetic (LA) action is well established,1 and it seems clear that this is the primary mechanism explaining their antinociceptive and antidysrhythmic effects. Studies in neurons and cardiac tissue, more recently supplemented by molecular biologic research on isolated Na channels, have provided a wealth of support for this statement. However, this clarity of understanding (which is in sharp contrast with the muddled situation concerning volatile anesthetic action) has led to the assumption—rarely articulated but widely held—that all LA actions can be explained by Na channel block. This is certainly not the case.1 Indeed, LAs are known to have a variety of biologic effects mediated other than via tetrodotoxin (TTX)sensitive Na channels. Particularly exciting is the realization that some of these actions are of potential great importance for perioperative medicine: modulation of inflammatory responses and prevention of hypercoagulability are just 2 examples of obvious interest to the anesthesiologist. In this review, we will discuss evidence that G proteins that couple membrane receptors to intracellular effectors are affected by local anesthetics. Exploitation of this action might lead to new therapeutic opportunities for LAs or LA derivatives. Using LAs as lead compounds, such a program should eventually result in synthesis of drugs with the beneficial Gprotein–coupled receptor (GPCR)-inhibiting properties of LAs, but without the “side effect” of Na channel block.
Gastroprotective Effect of Fenugreek Seeds (Trigonella foenum graecum) on Experimental Gastric Ulcer in Rats

ABSTRACT The effect of fenugreek seeds (Trigonella foenum graecum) compared with ranitidine was studied on aspirin-induced gastric ulcer. The gel fraction isolated from the seeds showed significant ulcer protective effect. The cytoprotective effect of the seeds seemed to be not only due to the anti-secretory action but also due to the effects on mucosal glycoproteins. The fenugreek seed gel also prevented the rise in lipid peroxidation induced by aspirin presumably by enhancing antioxidant potential of the gastric mucosa thereby lowering mucosal injury. Histological studies revealed that the soluble gel fraction prevents lesion formation and is effective as ranitidine. These observations show that fenugreek seeds possess antiulcer potential.