Miracle-dz/UniFAR-FTUs huggingface dataset:
Motor and Executive Function at 6 Years of Age After Extremely Preterm Birth

BACKGROUND. Studies of very preterm infants have demonstrated impairments in multiple neurocognitive domains. We hypothesized that neuromotor and executive-function deficits may independently contribute to school failure. METHODS. We studied children who were born at ≤25 completed weeks' gestation in the United Kingdom and Ireland in 1995 at early school age. Children underwent standardized cognitive and neuromotor assessments, including the Kaufman Assessment Battery for Children and NEPSY, and a teacher-based assessment of academic achievement. RESULTS. Of 308 surviving children, 241 (78%) were assessed at a median age of 6 years 4 months. Compared with 160 term classmates, 180 extremely preterm children without cerebral palsy and attending mainstream school performed less well on 3 simple motor tasks: posting coins, heel walking, and 1-leg standing. They more frequently had non–right-hand preferences (28% vs 10%) and more associated/overflow movements during motor tasks. Standardized scores for visuospatial and sensorimotor function performance differed from classmates by 1.6 and 1.1 SDs of the classmates' scores, respectively. These differences attenuated but remained significant after controlling for overall cognitive scores. Cognitive, visuospatial scores, and motor scores explained 54% of the variance in teachers' ratings of performance in the whole set; in the extremely preterm group, additional variance was explained by attention-executive tasks and gender. CONCLUSIONS. Impairment of motor, visuospatial, and sensorimotor function, including planning, self-regulation, inhibition, and motor persistence, contributes excess morbidity over cognitive impairment in extremely preterm children and contributes independently to poor classroom performance at 6 years of age.
Glucagon-stimulated phosphorylation of pyruvate kinase in hepatocytes.

A 32P-labeled pyruvate kinase (L-type isozyme) was elicited in response to glucagon and has been isolated from suspensions of hepatocytes incubated with inorganic [32P]phosphate. The pyruvate kinase in crude extracts of hepatocytes was stabilized by ammonium sulfate fractionation, 30% glycerol, and 50 mM KF and the enzyme was isolated by immunoprecipitation with anti-liver pyruvate kinase immunoglobulin. In the absence of glucagon, incorporation of 32P into pyruvate kinase was linear for up to 60 min. However, addition of 1 pM glucagon to hepatocytes incubated in the presence of inorganic [32P]phosphate resulted in a 3-fold increase in the incorporation of 32P into pyruvate kinase within 5 min. Immunoelectrophoresis of the hepatocyte extracts followed by autoradiography demonstrates that 32P is located with the pyruvate kinaseanti-liver pyruvate kinase immunoglobulin precipitation band. Furthermore, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the isolated immune complex indicates that 32P is covalently bound to the dissociated subunits of pyruvate kinase. Incubation of the hepatocytes in 1 pM glucagon resulted in a 60% decrease of pyruvate kinase activity when assayed in subsaturating concentrations of phosphoenolpyruvate and in the absence of the activator fructose 1,6-bisphosphate. Furthermore, the pyruvate kinase in glucagon-treated hepatocytes has a decreased affinity for phosphoenolpyruvate and a decreased affinity for fructose 1,6-bisphosphate. Both the rapid decrease in pyruvate kinase activity and the rapid increase in phosphorylation of the enzyme in response to addition of glucagon are consistent with phosphorylation of pyruvate kinase being a hormone-sensitive biochemical modification to regulate its activity in uivo.
Effect of Acid Suppression on Molecular Predictors for Esophageal Cancer

Background: Gastroesophageal reflux disease is a risk factor for the development of Barrett's esophagus and esophageal adenocarcinoma. The effect of antireflux therapy on the incidence of esophageal adenocarcinoma is unknown. Acid exposure in vitro induces hyperproliferation via a cyclooxygenase-2 (COX-2) dependent mechanism. Epidemiologic and animal studies suggest that COX inhibitors decrease the incidence of esophageal adenocarcinoma. Aim: To study the differential effect of complete compared with incomplete acid suppression on proliferation, apoptosis, and COX-2. Patients and Methods: Fifty-one patients with Barrett's esophagus who underwent pH monitoring were divided into two groups according to their DeMeester score: 32 acid-suppressed patients (group 1) and 19 patients with abnormally high acid exposure (group 2). Slides from biopsies taken 3 months before and 4 and 12 months after pH monitoring were stained for Mcm2, COX-2, c-myc, and cleaved caspase-3 (marker of apoptosis). Results: There was no evidence of a difference between the two groups in terms of age, gender ratio, medication, dysplasia status, and the expression levels of any marker before pH monitoring. In group 1, Mcm2 expression decreased in the luminal surface and throughout the tissue 12 months after monitoring when compared with the two previous time points (P < 0.05). The levels of COX-2 increased overtime (P < 0.01 in group 1, not significant in group 2). There was no correlation between Mcm2 and COX-2 expression. Acid suppression had no effect on c-myc or apoptosis. Conclusion: Long-term acid suppression reduces proliferation in Barrett's esophagus samples but has no advantageous effect on c-myc, apoptosis, or COX-2. (Cancer Epidemiol Biomarkers Prev 2006;15(2):288–93)
Production , Isolation and Purification of Peroxidase Using Bacillus Subtilis

Peroxidases are classified as oxido reductases which are used for catalyzing various oxidative reactions. They are isolated from various sources like plants, animals and microbes. Peroxidases have wide applications in many areas like industrial, medical and food processing. In the present study, Bacillus subtilis was employed for the production of peroxidases. B.subtilis was isolated from soil using the Serial dilution method. Identification of B.subtilis was done by performing various staining techniques and biochemical assays. Pure cultures of B.subtilis were obtained and screened for the production of peroxidases and those cultures which produced the same were selected for further study. B.subtilis produced 0.00045 units of peroxidase per ml of fermentation media. Optimization studies were performed and it was found that the optimum conditions for the production of peroxidase are pH-6, Temperature-370C. Purification of peroxidase enzyme was done using Salt precipitation, dialysis and Ion exchange chromatographic techniques. Quantification of the resultant peroxidase was done by Lowry's method. Kinetics of the peroxidase enzyme were also studied . Enzyme immobilization was done and was found that the peroxidase activity increased after immobilization.
The Rsm regulon of plant growth-promoting Pseudomonas fluorescens SS101: role of small RNAs in regulation of lipopeptide biosynthesis

The rhizobacterium Pseudomonas fluorescens SS101 inhibits growth of oomycete and fungal pathogens, and induces resistance in plants against pathogens and insects. To unravel regulatory pathways of secondary metabolite production in SS101, we conducted a genome‐wide search for sRNAs and performed transcriptomic analyses to identify genes associated with the Rsm (repressor of secondary metabolites) regulon. In silico analysis led to the identification of 16 putative sRNAs in the SS101 genome. In frame deletion of the sRNAs rsmY and rsmZ showed that the Rsm system regulates the biosynthesis of the lipopeptide massetolide A and involves the two repressor proteins RsmA and RsmE, with the LuxR‐type transcriptional regulator MassAR as their most likely target. Transcriptome analyses of the rsmYZ mutant further revealed that genes associated with iron acquisition, motility and chemotaxis were significantly upregulated, whereas genes of the type VI secretion system were downregulated. Comparative transcriptomic analyses showed that most, but not all, of the genes controlled by RsmY/RsmZ are also controlled by the GacS/GacA two‐component system. We conclude that the Rsm regulon of P. fluorescens SS101 plays a critical role in the regulation of lipopeptide biosynthesis and controls the expression of other genes involved in motility, competition and survival in the plant rhizosphere.
Precise and Ultrafast Molecular Sieving Through Graphene Oxide Membranes

Graphene oxide membranes allow only very small hydrated molecules and ions to pass with an accelerated transport rate. [Also see Perspective by Mi] Graphene-based materials can have well-defined nanometer pores and can exhibit low frictional water flow inside them, making their properties of interest for filtration and separation. We investigate permeation through micrometer-thick laminates prepared by means of vacuum filtration of graphene oxide suspensions. The laminates are vacuum-tight in the dry state but, if immersed in water, act as molecular sieves, blocking all solutes with hydrated radii larger than 4.5 angstroms. Smaller ions permeate through the membranes at rates thousands of times faster than what is expected for simple diffusion. We believe that this behavior is caused by a network of nanocapillaries that open up in the hydrated state and accept only species that fit in. The anomalously fast permeation is attributed to a capillary-like high pressure acting on ions inside graphene capillaries. On the Fast Track Membranes based on graphene can simultaneously block the passage of very small molecules while allowing the rapid permeation of water. Joshi et al. (p. 752; see the Perspective by Mi) investigated the permeation of ions and neutral molecules through a graphene oxide (GO) membrane in an aqueous solution. Small ions, with hydrated radii smaller than 0.45 nanometers, permeated through the GO membrane several orders of magnitude faster than predicted, based on diffusion theory. Molecular dynamics simulations revealed that the GO membrane can attract a high concentration of small ions into the membrane, which may explain the fast ion transport.
Age and growth of the white shark, Carcharodon carcharias, in the western North Atlantic Ocean

Age and growth estimates for the white shark (Carcharodon carcharias) in the western North Atlantic Ocean (WNA) were derived from band pair counts on the vertebral centra of 81 specimens collected between 1963 and 2010. We used two previously published criteria to interpret band pairs and assessed the validity of each method using Δ14C levels from a recent bomb radiocarbon validation study and existing Δ14C reference chronologies in the WNA. Although both criteria produced age estimates consistent, to varying degrees, with different reference chronologies, only one was considered valid when life history information was used to select the appropriate reference chronology and minimum/maximum ages based on bomb carbon values were taken into consideration. These age estimates, validated up to 44 years, were used to develop a growth curve for the species, which was best described using the Schnute general model (sexes combined). These results indicate that white sharks grow more slowly and live longer than previously thought.
A study of the Naive Bayes classifier for analyzing imaginary movement EEG signals using the Periodogram as spectral estimator

This study aims at applying algorithms for the spectral estimation and the classification of EEG signals during imaginary movements. Accordingly, it was used a database created by Graz University of Technology for the BCI Competition II. The database was created through an experiment in which an individual was asked to imagine the movement of her right or left hand while the EEG signal reading (Electroencephalogram) was being performed directly on the scalp by using three bipolar electrodes. In order to analyze the EEG signals for spectral estimation, it was used the Periodogram method computed in three different frequencies in μ-rythm (8 a 13Hz) and β-rythm (14 a 25Hz) frequencies to generate the Naive Bayes classifier entries. This database enabled to obtain a hit rate higher than 80%, which is consistent with results from the literature. Systems based on Brain-Computer Interface (BCI) can appropriate these algorithms to trigger and control devices through mental intentions only.
Effects of abstinence on the brain: quantitative magnetic resonance imaging and magnetic resonance spectroscopic imaging in chronic alcohol abuse.

BACKGROUND Structural brain damage, especially to white matter, is well documented in chronic alcohol abuse. There is also evidence for brain metabolic abnormalities in this condition. It is unknown, however, to what extent these structural and metabolic changes are present in treated alcohol abusers who achieve long-term abstinence versus treatment-naïve, heavily drinking individuals. METHODS This study compared 12 recovering alcoholics with 8 actively heavily drinking subjects. Participants underwent magnetic resonance (MR) imaging and proton MR spectroscopic imaging of the brain. Semiautomated image segmentation techniques yielded volumes for gray matter, white matter, white matter lesions, and cerebral spinal fluid in multiple brain regions defined by Talairach stereotaxic coordinates. Automated spectral processing methods yielded gray and white matter concentrations of the metabolites N-acetylaspartate, creatine, and choline for the same regions. RESULTS Recovering alcoholics had greater volumes of frontal white matter, but the opposite was true for white matter in a "remainder" region encompassing the basal frontal and temporal lobes, the cerebellum, and the brainstem. Recovering alcoholics also had smaller volumes of white matter lesions in whole brain, in occipital and mesial parietal regions, and in the remainder region. Recovering alcoholics had greater gray matter volumes in the orbital frontal pole and postcentral gyrus, but smaller gray matter volumes in the anterior cingulate. Whole-brain and regional metabolite concentrations did not differ significantly between the two groups. CONCLUSIONS White and gray matter volumes in different regions of the brain were greater or smaller in recovering, treated alcoholics. The findings suggest region-specific structural recovery from chronic alcohol-induced brain injury, but also region-specific long-term structural damage in abstinent alcoholics. White matter lesions were widespread in active drinkers and may partly resolve during long-term abstinence. Proton MR spectroscopic measures, as applied in this cross-sectional study, were largely ineffective in revealing metabolic effects of abstinence on the alcohol-damaged brain.
Editorial: Cancer-Associated Defects in the DNA Damage Response: Drivers for Malignant Transformation and Potential Therapeutic Targets

Transformation of normal cells into cancer cells almost invariably goes along with increased levels of DNA damage. An important source of DNA damage is the enhanced activity of growth-promoting transcription factors, such as MYC. Oncogenic activation of these transcription factors aberrantly stimulates DNA replication, which leads to replication stress and ensuing DNA breaks. Cells respond to this type of stress by activation of the DNA damage response (DDR). The DDR is a complex signaling network, displaying multiple levels of cross-talk and feed-back control. Its kinase-driven signaling axes ensure rapid responses to DNA lesions, which is complemented by its transcriptional axis that warrants maintained signaling. Ultimately, activation of the DDR prevents further proliferation and thus provides time to repair genotoxic lesions, and in case of excessive levels of DNA damage promotes permanent cell cycle exit (senescence) or programmed cell death (apoptosis). Activation of the DDR thus prevents the outgrowth of incipient tumor cells, early during tumorigenesis.
Neonatal deafening alters nonpyramidal dendrite orientation in auditory cortex: A computer microscope study in the rabbit

In order to examine the influence of afferent input on nonpyramidal dendrite development in the auditory cortex, unilateral deafening was carried out in neonatal rabbits at birth, approximately 6 days prior to the onset of hearing. Deafening was produced by surgical removal of the incus and stapes ossicles, aspiration of the cochlear perilymph, and kanamycin injection into the oval window. At 60 days of age, acoustic stimulation of the deafened ear was unable to evoke auditory brainstem responses. The brains of experimental and littermate control rabbits were processed according to the Golgi‐Cox Nissl method. The dendritic systems of lamina III/IV spine‐free nonpyramidal cells in the auditory cortex contralateral to the deafened ear were digitized from 340‐μm‐thick coronal sections with the aid of a computer microscope. Three‐dimensional spatial and statistical analyses revealed that nonpyramidal dendrite length in neonatally deafened rabbits increased 27% relative to littermate controls. A fan‐in projection analysis revealed that the increased dendrite length in the deafened animals was maximum in the tangential direction and toward the white matter. Computer rotation of digitized neurons from neonatally deafened rabbits also revealed evidence of abnormal dendritic growth in the form of recurved dendrites. We interpret our results to indicate that unilateral cochlear destruction early in development causes a reorganization of the ascending auditory pathway which extends to the contralateral cerebral cortex. Because the auditory cortex contralateral to the deafened ear still receives acoustic input from the undamaged ipsilateral ear, normal nonpyramidal dendritic growth in the auditory cortex is, in part, dependent upon afferent activity arising from both ears.
Energy Contribution of Octanoate to Intact Rat Brain Metabolism Measured by 13C Nuclear Magnetic Resonance Spectroscopy

Glucose is the dominant oxidative fuel for brain, but studies have indicated that fatty acids are used by brain as well. We postulated that fatty acid oxidation in brain could contribute significantly to overall energy usage and account for non-glucose-derived energy production. [2,4,6,8-13C4]octanoate oxidation in intact rats was determined by nuclear magnetic resonance spectroscopy. We found that oxidation of 13C-octanoate in brain is avid and contributes ∼20% to total brain oxidative energy production. Labeling patterns of glutamate and glutamine were distinct, and analysis of these metabolites indicated compartmentalized oxidation of octanoate in brain. Examination of liver and blood spectra revealed that label from 13C-octanoate was incorporated into glucose and ketones, which enabled calculation of its overall energy contribution to brain metabolism: glucose (predominantly unlabeled) and 13C-labeled octanoate can account for the entire oxidative metabolism of brain. Additionally, flux through anaplerotic pathways relative to tricarboxylic acid cycle flux (Y) was calculated to be 0.08 ± 0.039 in brain, indicating that anaplerotic flux is significant and should be considered when assessing brain metabolism. Y was associated with the glutamine synthesis compartment, consistent with the view that anaplerotic flux occurs primarily in astrocytes.
JIRCD: An open letter to the journal

Your emergence is a significant and exciting accomplishment. It is also an indicator of healthy growth in the area of qualitative research in communication disorders. Your presence shows that qualitative research in speech-language pathology now has sufficient prestige and viability to have its own journal, its own voice. But that’s not all. Your dedication to interaction research is also significant. By focusing on interaction, you are challenging our field’s long and constrained tradition of subscribing to the medical model – a tradition that harks back to our very beginnings as a profession. Your emphasis on interaction invites contributors to portray and treat communication disorders in their social/cultural milieu rather than as if they were diseases that are biologically defined and impairment-based. Good for you! Your gestation period was too long, or so it seems to those of us celebrating your birth. Despite pressures against it, there has been considerable qualitative research over the last 30 years. During this period a number of ethnographic studies have been published in different areas of our field, including aphasia (Le Dorze and Brassard 1995; Parr 1994, 1997), childhood language disorders (Crago and Cole 1991), stuttering (Corcoran and Stewart 1998; St Louis 2001), autism (Ochs and Solomon 2004; Ochs et al. 2004) and hearing impairment
Typing of Mycobacterium avium Subspecies paratuberculosis Isolates from Newfoundland Using Fragment Analysis

Short Sequence Repeat (SSR) typing of Mycobacterium avium subspecies paratuberculosis (Map) isolates is one of the most commonly used method for genotyping this pathogen. Currently used techniques have challenges in analyzing mononucleotide repeats >15 bp, which include some of the Map SSRs. Fragment analysis is a relatively simple technique, which can accurately measure the size of DNA fragments and can be used to calculate the repeat length of the target SSR loci. In the present study, fragment analysis was used to analyze 4 Map SSR loci known to provide sufficient discriminatory power to determine the relationship between Map isolates. Eighty-five Map isolates from 18 animals from the island of Newfoundland were successfully genotyped using fragment analysis. To the best of our knowledge, this is the first report on Map SSR diversity from Newfoundland dairy farms. Previously unreported Map SSR-types or combinations were also identified during the course of the described work. In addition, multiple Map SSR-types were isolated from a single animal in many cases, which is not a common finding.
Gastric carcinoma with invasive micropapillary pattern and its association with lymph node metastasis

Ushiku T, Matsusaka K, Iwasaki Y, Tateishi Y, Funata N, Seto Y & Fukayama M (2011) Histopathology 59, 1081–1089 Gastric carcinoma with invasive micropapillary pattern and its association with lymph node metastasis
A Photogrammetric Method for Single Image Orientation and Measurement

The aim of this paper is to present a photogrammetric method for determining the dimensions of flat surfaces, such as billboards, based on a single digital image. A mathematical model was adapted to generate linear equations for vertical and horizontal lines in the object space. These lines are identified and measured in the image and the rotation matrix is computed using an indirect method. The distance between the camera and the surface is measured using a lasermeter, providing the coordinates of the camera perspective center. Eccentricity of the lasermeter center related to the camera perspective center is modeled by three translations, which are computed using a calibration procedure. Some experiments were performed to test the proposed method and the achieved results are within a relative error of about 1 percent in areas and distances in the object space. This accuracy fulfills the requirements of the intended applications.
Phase change during a cyclic quantum evolution.

A new geometric phase factor is defined for any cyclic evolution of a quantum system. This is independent of the phase factor relating the initial and final state vectors and the Hamiltonian, for a given projection of the evolution on the projective space of rays of the Hilbert space. Some applications, including the Aharonov-Bohm effect, are considered. For the special case of adiabatic evolution, this phase factor is a gauge-invariant generalization of the one found by Berry.