Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of the Escherichia coli nrd operon: role of DNA supercoiling

An in vitro RNA transcription assay was used to investigate the regulation of the expression of the nrd promoter. Using a linear DNA template, we found that Fis protein, which has a positive effect on expression of the nrd promoter in an nrd-lacZ fusion in vivo, had a moderate negative effect in vitro. However, with a supercoiled DNA template as substrate, we found that Fis had a concentration-dependent positive effect on nrd transcription in vitro. This positive effect was not present on two templates that had 35- or 37-bp insertions between the Fis binding site and the nrd promoter. In the absence of Fis protein, a dramatic decrease in transcription was observed in templates with reduced supercoiling generated by the treatment with wheat germ topoisomerase I. Templates with insertions of 35 bp into an HpaII site at -102 or 37 bp into the MnlI site at -33 bp from the start of transcription failed to exhibit the DNA supercoiling sensitivity of the nrd promoter. Analysis of cells containing either of these two nrd-lacZ fusion constructs that has an insertion at the regulatory region by flow cytometry indicated that these two constructs, unlike the parental construct, were not cell cycle regulated.
Outcomes of kidney transplantations in children weighing 15 kilograms or less: a retrospective cohort study

Kidney transplantation (KT) is often delayed in small children because of fear of postoperative complications. We report early‐ and long‐term outcomes in children transplanted at ≤15 kg in the two largest Belgian pediatric transplant centers. Outcomes before (period 1) and since the introduction of basiliximab and mycophenolate‐mofetil in 2000 (period 2) were compared. Seventy‐two KTs were realized between 1978 and 2016: 38 in period 1 and 34 in period 2. Organs came from deceased donors in 48 (67%) cases. Surgical complications occurred in 25 KTs (35%) with no significant difference between the two periods. At least one acute rejection (AR) occurred in 24 (33%) KTs with significantly less patients experiencing AR during period 2: 53% and 12% in period 1 and, period 2 respectively (P < 0.001). Graft survival free of AR improved significantly in period 2 compared with period 1: 97% vs. 50% at 1 year; 87% vs. 50% at 10 years post‐KT (P = 0.003). Graft survival tended to increase over time (period 1: 74% and 63% at 1 and 5 years; period 2: 94% and 86% at 1 and 5 years; P = 0.07), as well as patient survival. Kidney transplantation in children ≤15 kg remains a challenging procedure with 35% of surgical complications. However, outcomes improved and are nowadays excellent in terms of prevention of AR, patient and graft survival.
Testing the interspecific body size principle in ungulates: the smaller they come, the harder they groom

Tick removal grooming may be centrally regulated by an internal timing mechanism operating to remove ticks before they attach and engorge (programmed grooming model) and/or evoked by cutaneous stimulation from tick bites (stimulus-driven model). The programmed grooming model predicts that organismic and environmental factors that impact the cost-benefit ratio of grooming (e.g. body size and habitat) will influence the rate of tick removal grooming. The body size principle predicts that smaller-sized animals, because of their greater surface-to-mass ratio, should engage in more frequent tick removal grooming than larger-bodied animals in order to compensate for higher costs of tick infestation. The body size principle may be tested intraspecifically between young and adult animals, or interspecifically among species of contrasting body sizes. To rigorously test the interspecific body size prediction, we observed the programmed grooming (oral and scratch grooming) of 25 species (or subspecies) of bovids at a tick-free zoological park in which stimulus-driven grooming was ruled out. Multiple correlation analysis revealed highly significant negative correlations between species-typical mass and mean species grooming rates when habitat was controlled for in the model. Species-typical habitat type (classified along a gradient from most open to most closed) was positively correlated with mean oral grooming rate, indicating that species tended to groom at a higher rate in woodland and forest habitats (where typical tick density would be high) compared with more open environments. Species mass accounted for up to two-thirds of the variation in grooming rate across species, whereas habitat accounted for ca. 20% of variation in oral grooming. Similar results were obtained when the analysis was expanded to include 36 species/subspecies of six different families. The body size principle can therefore account for a large proportion of species-typical differences in programmed grooming rate among ungulates. However, to understand the tick defence adaptations of very large mammals that rarely or never engage in oral or scratch grooming (e.g. elephants, giraffes, rhinoceros), alternative tick defence strategies must be considered, such as thick skin, wallowing, rubbing and tolerance of oxpeckers and other tick-eating birds. Copyright 2000 The Association for the Study of Animal Behaviour.
Impact of Repetitive Elements on the Y Chromosome Formation in Plants

In contrast to animals, separate sexes and sex chromosomes in plants are very rare. Although the evolution of sex chromosomes has been the subject of numerous studies, the impact of repetitive sequences on sex chromosome architecture is not fully understood. New genomic approaches shed light on the role of satellites and transposable elements in the process of Y chromosome evolution. We discuss the impact of repetitive sequences on the structure and dynamics of sex chromosomes with specific focus on Rumex acetosa and Silene latifolia. Recent papers showed that both the expansion and shrinkage of the Y chromosome is influenced by sex-specific regulation of repetitive DNA spread. We present a view that the dynamics of Y chromosome formation is an interplay of genetic and epigenetic processes.
COMMITTEE ON NUTRITION STANDARDS FOR NATIONAL SCHOOL LUNCH AND BREAKFAST PROGRAMS

Copyright © National Academy of Sciences. Permission is granted for this material to be shared for noncommercial, educational purposes, provided that this notice appears on the reproduced materials, the Web address of the online, full authoritative version is retained, and copies are not altered. To disseminate otherwise or to republish requires written permission from the National Academies Press. ISBN: 0-309-14437-X, 388 pages, 6 x 9, (2009)
Visual areas in the dorsal and medial extrastriate cortices of the marmoset

To define the number and limits of the visual areas in the primate extrastriate cortex, the visuotopy of the dorsal convexity and medial wall was studied by electrophysiological recordings in five marmosets anaesthetised with sufentanil and nitrous oxide and paralysed with pancuronium bromide. We identified five visuotopic representations in and around the densely myelinated zone between visual area 2 (V2) and the posterior parietal cortex. Most of the densely myelinated zone is formed by the homologue of the owl monkey's dorsomedial area (DM); thus, we also termed this area DM in the marmoset. Within DM, the lower quadrant representation is continuous, with central vision represented laterally, peripheral vision medially, the horizontal meridian caudally, and the vertical meridian rostrally. In contrast, the upper quadrant representation is split, with the central portion represented at the lateral edge of DM on the dorsal surface, and the periphery along the midline. Two other visual field representations, corresponding to the dorsointermediate area (DI) and to a new subdivision termed the dorsoanterior area (DA), are also densely myelinated but can be distinguished from DM based on the separation of the bands of Baillerger and visual topography. In addition, a homologue of the medial visual area (M) was identified. Our results reveal a highly complex visuotopy in primate cortex, with local discontinuities in representation and borders between areas that are often not coincident with either the horizontal or the vertical meridian. The topography of the dorsal extrastriate cortex in the marmoset strongly suggests that both visual area 3 (V3) and the parieiooccipital area (PO) of other primates are portions of a single visuotopic representation, DM, and calls into question the, existence of visual areas with partial or quadrantic representations of the visual field. © 1995 Wiley‐Liss, Inc.
Dynamic Selling Mechanisms for Product Differentiation and Learning

We consider a firm that designs a menu of vertically differentiated products for a population of customers with heterogeneous quality sensitivities. The firm faces an uncertainty about production costs, and we formulate this uncertainty as a belief distribution on a set of cost models. Over a time horizon of T periods, the firm can dynamically adjust its menu and make noisy observations on the underlying cost model through customers’ purchasing decisions. We characterize how optimal product differentiation depends on the “informativeness” of quality choices, formally measured by a contrast-to-noise ratio defined on the firm’s feasible quality set. We prove that, if there exist informative quality choices, then the optimal product differentiation policy improves the product quality to accelerate information accumulation and exercises the most extreme experimentation on less quality-sensitive customers. We design a minimum quality standard (MQS) policy that mimics the aforementioned features of the optimal policy and show that the MQS policy is near-optimal. We also prove that, if there exists a certain continuum of informative quality choices, then even a myopic policy that makes no attempt to learn exhibits near-optimal profit performance. This stands in stark contrast to the poor performance of myopic policies in pricing and learning problems in the absence of product differentiation.
Sensitivity of the classification of psoriatic arthritis criteria in early psoriatic arthritis.

Psoriatic arthritis (PsA) is defined as an inflammatory arthritis associated with cutaneous psoriasis, usually seronegative for rheumatoid factor (RF) (1). The clinical presentation of PsA varies. Patients have a peripheral arthritis (oligoarthritis or polyarthritis), enthesitis, dactylitis, sacroiliitis, and spondylitis, occurring alone or in combination (1). Epidemiologic and genetic research in PsA has been hampered by the lack of validated or widely agreed upon classification criteria for PsA. Although a number of classification criteria have been proposed (2), none have been widely agreed upon or validated (3). Recently, the Classification of Psoriatic Arthritis (CASPAR) Study Group published new criteria for the classification of PsA that were derived from a data set of 588 patients with PsA and 536 controls with other inflammatory arthritis (2). The sensitivity and specificity of the CASPAR criteria in the original study were 91.4% and 98.7%, respectively (2). However, patients with PsA had longstanding disease with a mean disease duration of 12.5 years. It was therefore recommended that the criteria be tested in early PsA. The concept of early PsA is new and there have not been many studies on early PsA. The definition of early PsA has been extrapolated from early rheumatoid arthritis, and the usual definition is inflammatory arthritis associated with psoriasis, usually negative for RF with disease duration 2 years (4,5), although studies have used varying cutoffs (6,7). The objective of the present study was to determine the sensitivity of the CASPAR criteria in patients with early PsA. Patients and Methods
Effects of Ficus thonningii extracts on the gastrointestinal tract and clinical biochemistry of suckling rats.

BACKGROUND Ficus thonningii is commonly used in traditional medicine across the African continent. We investigated the effects of crude Ficus thonningii extracts on growth, morphology and morphometry of the abdominal viscera and clinical biochemistry of neonatal rats. MATERIALS AND METHODS Forty, 6-day old Sprague Dawley rat pups were orally gavaged once daily with either low (50 mg.kg(-1) b.w) or high (500 mg.kg(-1) b.w) doses of aqueous or methanolic F. thonningii leaf extracts while the control received distilled water. After 7 days of treatment, the pups were euthanased and gross morphometric measurements of the abdominal visceral organs were recorded. Samples of the liver, caecum and proximal small intestine were processed for histology. Plasma biochemical parameters were analysed colorimetrically. RESULTS High methanolic doses of F. thonningii extracts exhibited trophic effects on the stomach while both aqueous and methanolic extracts had trophic effects on the ceacal mucosa of rats. No significant growth-promoting effects were observed in other visceral organs. Histological analysis revealed no mucosal damage or necrosis. Clinical biochemistry parameters were not abnormally altered. There was a significant decrease (p<0.05, ANOVA) in the plasma concentration of non-fasting glucose in the high methanolic group but triglycerides and cholesterol were unaltered. CONCLUSION The findings suggest that at low doses, F. thonningii extracts can be safely used without the risk of any disruption in the structural integrity of the neonatal rat GIT and function of the liver and kidneys.
Correcting False Memories

While often impressive, memory is far from perfect. For example, the sentence “The karate champion hit the cinder block” is often misremembered as “The karate champion broke the cinder block” (Brewer, 1977). Hearing a list of related words such as “bed, rest, tired …” leads people to claim “sleep” was presented when in fact it was not (Roediger & McDermott, 1995). Answering the question “How fast was the white sports car going when it passed the barn while traveling along the country road? ” increases witnesses’ later reports of having seen a non-existent barn in an earlier video (Loftus, 1975, p. 566). These examples represent just a few of the many ways in which memory can go astray. Not only are these errors easily created, they often become vivid false memories held with high confidence. For example, false memories for non-presented words like “sleep” are so vivid that people often claim to remember which of two voices said the word (Payne, Elie, Blackwell, & Neuschatz, 1996). False memories can be strikingly persistent. Warnings about memory errors are rarely effective (McDermott & Roediger, 1998), especially after the study phase (Greene, Flynn, & Loftus, 1982). Re-exposure to events is insufficient; hearing “bed, rest, tired …” again reduces, but does not eliminate, false memories for “sleep” (McDermott, 1996; Watson, McDermott, & Balota, 2004). Even interventions that pinpoint specific contradictions between subjects’ memories and the original events are inadequate; many errors remain uncorrected even after subjects place an X next to each false memory (McConnell & Hunt, 2007). Despite much evidence that false memories are difficult to correct, a finding from another literature allows a surprising prediction about the correction of false memories. In a prototypical experiment demonstrating the hypercorrection effect, participants answer general knowledge questions and rate their confidence in each response before viewing the correct answer. High-confidence errors are more likely to be corrected on a second test than are incorrect guesses (Butterfield & Metcalfe, 2001). Someone who strongly believes that Sydney is the capital of Australia will benefit more from the feedback “Canberra” than someone who simply guessed “Sydney. ” The parallel in the false memory domain would be surprising, predicting that confidently-held false memories should be corrected more often than other errors. To examine this, we created false memories using sentences that encourage inferences; for example, “The clumsy chemist had acid on his coat” is often misremembered as “The clumsy chemist spilled acid on his coat. ” We examined ability to correct false memories as a function of initial confidence in the errors.
Detection of low spatial frequencies: A single filter or multiple filters?

Ever since it was first reported that the contrast sensitivity for low spatial frequency sinusoidal gratings falls off with a slope approximating unity it has been suggested that this may represent gradient detection by a single spatial filter tuned to higher spatial frequencies. We have further investigated this possibility using aperiodic as well as periodic stimuli. Experiments are presented that involve manipulations of luminance, field size and spatial adaptation, and the results are consistent with a multiple filter model accounting for the detection of low spatial frequency (0.2‐2 c/deg) periodic and aperiodic stimuli.
Assessment and modulation of resting-state neural networks after stroke.

PURPOSE OF REVIEW Stroke is a major cause of disability; however, most patients experience spontaneous partial recovery of functions in subacute to chronic phases. Poststroke loss and recovery of functions have been increasingly correlated with brain-wide alterations in the connectivity of neural networks, which is described in this review. Elucidation of the mechanisms of functional brain remodeling could reveal targets and strategies for more effective neurorehabilitation. RECENT FINDINGS Data from recent resting-state functional MRI, electroencephalography, magnetoencephalography, and optical imaging studies in patients and animal models have demonstrated that loss of function after stroke is closely associated with disrupted connectivity in large-scale networks beyond the lesion territory. Restoration of functional connectivity in the surviving networks appears to be critical for functional recovery, and this may be promoted with specific therapeutic strategies, such as robot-assisted training and noninvasive brain stimulation. The adaptability of functional networks relies on the structural integrity of neuronal pathways, but the relationship between the two remains incompletely understood. Furthermore, disturbed neurovascular coupling after stroke can confound hemodynamically based measurements of functional connectivity. SUMMARY Identification of key network processes in adaptive brain plasticity can aid in the prediction of functional outcome and the development of therapeutic interventions to support and promote recovery after stroke.
Ultrastructure of the calcium‐sequestering gastrodermal cell in the hydroid Hydractinia symbiolongicarpus (Cnidaria, Hydrozoa)

Large, free‐floating crystals of calcium carbonate occur in vacuoles of gastrodermal cells of the hydroid Hydractinia symbiolongicarpus. Here, morphological details about the process by which these cells accumulate and sequester calcium are provided by a cytochemical method designed to demonstrate calcium at the ultrastructural level. Electron‐dense material presumably indicative of the presence of calcium was EGTA‐sensitive and was shown by parallel electron energy loss spectroscopy (EELS) and energy spectroscopic imaging (ESI) to contain calcium. Calcium occurred in only one cell type, the endodermally derived gastrodermal cell. In these cells, the electron‐dense material appeared first as a fine precipitate in the cytosol and nucleus and later as larger deposits and aggregates in the vacuole. During the life cycle, gastrodermal cells of the uninduced planula and the planula during metamorphic induction sequestered calcium. In primary polyps and polyps from established colonies, gastrodermal cells sequestered calcium, but the endodermal secretory cells did not. Our observations support the hypothesis that gastrodermal cells function as a physiological sink for calcium that enters the organism in conjunction with calcium‐requiring processes such as motility, secretion, and metamorphosis. J. Morphol. 260:255–270, 2004. © 2004 Wiley‐Liss, Inc.
Implementation of analysis of data storage and retrieval using Rainbow technology

In the present day context, users are making use of public storage services in the cloud and local storage devices such as CD's and DVD's. Fortunately, with the advancement in the techniques of compression and encryption it will become possible to store data equivalent to CD's or DVD's on a piece of paper in the near future. The applications are to well-established recording technologies, including magnetic tape and magnetic disk systems as well as CD/DVD/Blue-Ray optical data-storage systems. This technique is named as RAINBOW TECHNOLOGY. It is named as such since it mainly uses colors, color combinations and geometric shapes to store the data elements. The Rainbow technology is feasible because the output is in the form of printed text, which is readable by human eyes. By printing the encoded in a denser way, much higher capacities can be achieved. Paper is, of course, bio-degradable, unlike CDs or DVDs and sheets of paper also cost a fraction of the cost of a CD & DVD.
Maternal serum biochemical markers in pregnancies with fetal parvovirus B19 infection

Hydrops fetalis and fetal death caused by fetal parovirus B19 infection have been reported to be associated with elevated maternal serum alpha‐fetoprotein (AFP), based on a total of six cases. It has been suggested that the absence of AFP elevation may be reassuring. Maternal serum levels of the Down syndrome screening markers unconjugated oestriol and human chorionic gonadotropin in cases of fetal parvovirus infection have not been previously reported. We report four cases of hydrops fetalis and fetal death caused by fetal parvovirus infection, each with unremarkable second‐trimester levels of AFP, unconjugated oestriol, and human chorionic gonadotropin.
Protein kinase A and TORC1 activate genes for ribosomal biogenesis by inactivating repressors encoded by Dot6 and its homolog Tod6

Genes required for ribosome biogenesis in yeast, referred to collectively as the Ribi regulon, are tightly regulated in coordination with nutrient availability and cellular growth rate. The promoters of a significant fraction of Ribi genes contain one or more copies of the RNA polymerases A and C (PAC) and/or ribosomal RNA-processing element (RRPE) motifs. Prompted by recent studies showing that the yeast protein Dot6 and its homolog Tod6 can bind to a PAC motif sequence in vitro and are required for efficient Ribi gene repression in response to heat shock, we have examined the role of Dot6 and Tod6 in nutrient control of Ribi gene expression in vivo. Our results indicate that PAC sites function as Dot6/Tod6-dependent repressor elements in vivo. Moreover, Dot6 and Tod6 mediate different nutrient signals, with Tod6 responsible for efficient repression of Ribi genes after inhibition of the nitrogen-sensitive TORC1 pathway and Dot6 responsible for repression after inhibition of the carbon-sensitive protein kinase A signaling pathway. Consistently, Dot6 and Tod6 are required for efficient repression of Ribi gene repression immediately after nutrient deprivation and for successful adaptation to nutrient limitation. Thus, these results establish Dot6/Tod6 as a direct link between nutrient availability, Ribi gene regulation, and growth control.
NoCmodel: An extensible framework for Network-on-Chips modeling

Network-on-Chips (NoC) is an emerging concept to address the growing complexity in digital electronics systems. However, current design methodology is based on traditional HDL languages written manually or with the help of code generation tools. In order to deal with NoC design and management we create NoCModel: an extensible framework for NoC modeling based on Python language, with support for simulation and code generation. This paper presents the motivation behind the build and use of this tool, the capabilities currently present in it, an explanation of the core and its add-ons and some results obtained from it.