Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential Regulation of Retinoblastoma Protein Function by Specific Cdk Phosphorylation Sites (*)

The retinoblastoma tumor suppressor protein, RB, contains at least three distinct protein binding domains. The A/B pocket binds proteins with the LXCXE motif, the C pocket binds the nuclear c-Abl tyrosine kinase, and the large A/B pocket binds the transcription factor E2F. Dissociation of RB from its targets is observed as RB becomes phosphorylated during G/S progression. There are 16 Cdk consensus phosphorylation sites in RB. It was previously unknown whether the many phosphorylation sites had redundant or distinct functions in the regulation of RB. Using RB mutant proteins lacking specific phosphorylation sites, we show that each of the binding domains is inhibited by different sites. Thr-821/826 phosphorylation is required to inhibit the binding to LXCXE containing proteins. Mutation of these two sites does not interfere with the hyperphosphorylation of RB. However, this phosphorylated mutant retains the ability to bind T-Ag, E7, and Elf-1, all of which contain the LXCXE motif. In contrast, Ser-807/811 phosphorylation is required to disrupt c-Abl binding. Mutation of Ser-807/811 and Thr-821/826 does not abolish the regulation of E2F binding. Taken together, these results show that the protein binding domains of RB are each regulated by distinct Cdk phosphorylation sites.
Periorbital edema as the presenting sign of dermatomyositis

Background Periorbital edema can occur in dermatomyositis, which is characterized by symmetric macular erythema, Gottron's papules, Gottron's sign, periungual telangiectasia, heliotrope rash, and poikilodermatous macules on the shoulders, arms, or upper back (shawl sign).
Development and validation of a gene expression tumour classifier for cancer of unknown primary

Summary Accurate identification of the primary tumour in cancer of unknown primary (CUP) is required for effective treatment selection and improved patient outcomes. The aim of this study was to develop and validate a gene expression tumour classifier and integrate it with histopathology to identify the likely site of origin in CUP. RNA was extracted from 450 formalin fixed, paraffin embedded samples of known origin comprising 18 tumour groups. Whole genome expression analysis was performed using a bead-based array. Classification of the tumours made use of a binary support vector machine, together with recursive feature elimination. A hierarchical tumour classifier was developed and incorporated with conventional histopathology to identify the origins of metastatic tumours. The classifier demonstrated an accuracy of 88% for correctly predicting the tumour type on a validation set of known tumours (n = 94). For CUP samples (n = 49) having a final clinical diagnosis, the classifier improved the accuracy of histology alone for both single and multiple predictions. Furthermore, where histology alone could not suggest any specific diagnosis, the classifier was able to correctly predict the primary site of origin. We demonstrate the integration of gene expression profiling with conventional histopathology to aid the investigation of CUP.
Clinical applications of vibration therapy in orthopaedic practice.

BACKGROUND Vibration therapy (VT) has been proposed as an option to improve physical performance and reduce the negative effects of ageing on bone, muscles and tendons. Several discrepancies exist on the type of applications, frequency and magnitude. These differences reflex on the contradictory clinical results in literature. Aim of the present study is to carry on an exhaustive review to focus on technical options on the market, clinical applications in orthopaedic practice and expected outcomes. METHODS a literature review using the key words "vibration therapy" and "whole-body vibration" and "orthopaedics" was performed. After checking the available abstracts 71 full text articles were evaluated. RESULTS fifty-one articles focused on the effects of VT on muscles and tendons reporting ways of action and clinical outcomes. In a similar way 20 studies focused on the influence of VT on bone tissue with regard on ways of action and clinical trials. CONCLUSIONS VT provides anabolic mechanical signals to bone and musculo-tendinous system. The best effects seem to be achieved with devices that deliver low-intensity stimuli at high frequencies providing linear horizontal displacement.
A Comparative Genomics Approach to the Evolution of Eukaryotes and their Mitochondria 1

The Organelle Genome Megasequencing Program (OGMP) investigates mitochondrial genome diversity and evolution by systematically determining the complete mitochondrial DNA (mtDNA) sequences of a phylogenetically broad selection of protists. The mtDNAs of lower fungi and choanoflagellates are being analyzed by the Fungal Mitochondrial Genome Project (FMGP), a sister project to the OGMP. Some of the most interesting protists include the jakobid flagellates Reclinomonas americana, Malawimonas jakobiformis, and Jakoba libera, which share ultrastructural similarities with amitochondriate retortamonads, and harbor mitochondrial genes not seen before in mtDNAs of other organisms. In R. americana and J. libera, gene clusters are found that resemble, to an unprecedented degree, the contiguous ribosomal protein operons str, S10, spc, and alpha of eubacteria. In addition, their mtDNAs code for an RNase P RNA that displays all the elements of a bacterial minimum consensus structure. This structure has been instrumental in detecting the rnpB gene in additional protists. Gene repertoire and gene order comparisons as well as multiple‐gene phylogenies support the view of a single endosymbiotic origin of mitochondria, whose closest extant relatives are Rickettsia‐type α‐Proteobacteria.
The KCl cotransporter, KCC2, is highly expressed in the vicinity of excitatory synapses in the rat hippocampus

Immunocytochemical visualization of the neuron‐specific K+/Cl– cotransporter, KCC2, at the cellular and subcellular level revealed an area‐ and layer‐specific diffuse labelling, and a discrete staining outlining the somata and dendrites of some interneurons in all areas of the rat hippocampus. KCC2 was highly expressed in parvalbumin‐containing interneurons, as well as in subsets of calbindin, calretinin and metabotropic glutamate receptor 1a‐immunoreactive interneurons. During the first 2 postnatal weeks, an increase of KCC2 staining was observed in the molecular layer of the dentate gyrus, correlating temporally with the arrival of entorhinal cortical inputs. Subcellular localization demonstrated KCC2 in the plasma membranes. Immunoreactivity in principal cells was responsible for the diffuse staining found in the neuropil. In these cells, KCC2 was detected primarily in dendritic spine heads, at the origin of spines and, at a much lower level on the somata and dendritic shafts. KCC2 expression was considerably higher in the somata and dendrites of interneurons, most notably of parvalbumin‐containing cells, as well as in the thorny excrescences of CA3 pyramidal cells and in the spines of spiny hilar and stratum lucidum interneurons. The data indicate that KCC2 is highly expressed in the vicinity of excitatory inputs in the hippocampus, perhaps in close association with extrasynaptic GABAA receptors. A high level of excitation is known to lead to a simultaneous net influx of Na+ and Cl–, as evidenced by dendritic swelling. KCC2 located in the same microenvironment may provide a Cl– extrusion mechanism to deal with both ion and water homeostasis in addition to its role in setting the driving force of Cl– currents involved in fast postsynaptic inhibition.
Adaptations of Pseudomonas aeruginosa to the Cystic Fibrosis Lung Environment Can Include Deregulation of zwf, Encoding Glucose-6-Phosphate Dehydrogenase

ABSTRACT Cystic fibrosis (CF) patients are highly susceptible to chronic pulmonary disease caused by mucoid Pseudomonas aeruginosa strains that overproduce the exopolysaccharide alginate. We showed here that a mutation in zwf, encoding glucose-6-phosphate dehydrogenase (G6PDH), leads to a ∼90% reduction in alginate production in the mucoid, CF isolate, P. aeruginosa FRD1. The main regulator of alginate, sigma-22 encoded by algT (algU), plays a small but demonstrable role in the induction of zwf expression in P. aeruginosa. However, G6PDH activity and zwf expression were higher in FRD1 strains than in PAO1 strains. In PAO1, zwf expression and G6PDH activity are known to be subject to catabolite repression by succinate. In contrast, FRD1 zwf expression and G6PDH activity were shown to be refractory to such catabolite repression. This was apparently not due to a defect in the catabolite repression control (Crc) protein. Such relaxed control of zwf was found to be common among several examined CF isolates but was not seen in other strains of clinical and environmental origin. Two sets of clonal isolates from individual CF patient indicated that the resident P. aeruginosa strain underwent an adaptive change that deregulated zwf expression. We hypothesized that high-level, unregulated G6PDH activity provided a survival advantage to P. aeruginosa within the lung environment. Interestingly, zwf expression in P. aeruginosa was shown to be required for its resistance to human sputum. This study illustrates that adaptation to the CF pulmonary environment by P. aeruginosa can include altered regulation of basic metabolic activities, including carbon catabolism.
Extended-spectrum β-lactamases, transferable quinolone resistance, and virulotyping in extra-intestinal E. coli in Uruguay.

INTRODUCTION To characterize extended-spectrum β-lactamases (ESBLs) and plasmid-mediated quinolone resistance (PMQR) genes in Escherichia coli isolates obtained from extra-intestinal samples in three Uruguayan hospitals. METHODOLOGY Fifty-five ESBL-producing E. coli isolates were studied. Virulence genes, ESBLs, and PMQR genes were detected by polymerase chain reaction. ESBL-producing isolates were compared by pulsed-field gel electrophoresis. Multi-locus sequence typing was also performed on 13 selected isolates. RESULTS Thirty-seven isolates harbored blaCTX-M-15 (67.3%), eight blaCTX-M-2 (14.6%), five blaCTX-M-14 (9.1%), three carried both blaCTX-M-2 and blaCTX-M-14, one blaCTX-M-9, and one blaCTX-M-8. Among the CTX-M-15 producers, 92% belonged to sequence types ST131 and ST405, and carried aac(6')Ib-cr as well. Isolates harboring blaCTX-M-2, blaCTX-M-14, blaCTX-M-9, or blaCTX-M-8 were found to be genetically unrelated. CONCLUSIONS The successful dissemination of CTX-M-15-producing E.coli isolates seems to be linked to the spreading of high-risk clones and horizontal gene transfer. A trade-off between carrying more antibiotic resistance and less virulence-related genes could partially account for the evolutionary advantages featured by successful clones.
The Rural Superintendency and the Need for a Critical Leadership of Place

This article examines how school superintendents and parents in high-needs rural districts conceptualized educational quality. Specifically, this comparative case study of two rural school superintendents presents a contextualized understanding of rural superintendents’ and other educators’ mainstream views of educational quality, parents and other rural community members’ place-based views, and the tensions among these. Primary data sources featured interviews with two superintendents and their constituents, including Board of Education members, principals, teachers, parents, and community members. Findings indicated that both superintendents worked to create an aspirational culture in which education was the way out of poverty for their students, aspirations that were frequently at tension with community values. This article concludes with a proposed critical leadership and pedagogy of place that may help superintendents navigate these tensions.
Industrial Ecology Education at Tsinghua University

As a leading university in engineering education in China, Tsinghua University implemented industrial ecology (IE) education in the 1990s. This article describes the evolution of IE education at Tsinghua. Tsinghua mainstreams IE education into green education and engineering education not only by establishing independent courses of IE for both undergraduate and graduate students, but also by incorporating IE principles and knowledge modules into an increasing number of courses. During 2002–2015, a total of 1,023 undergraduates from 33 schools and departments participated in an IE course. To cope with the diversity of participants, four knowledge modules were customized for an undergraduate course: concepts and history; methods and tools; topics and applications; and policy and perspectives. Meanwhile, an interdisciplinary teaching method was adopted by inviting experts from diverse disciplines and organizing group discussions. Though the course has received strong positive feedback, four challenges still remain in IE education: defining the knowledge boundary, presenting an integrated view, utilizing an interdisciplinary methodology, and cultivating a class culture.
Assessment of technical efficiency of NIS with the use of DEA

This paper examines the technical efficiency of innovation systems. Based upon the European Innovation Scoreboard, the efficiency of investment in innovation is examined with the use of DEA model. It is observed that the so called laggards in innovation are often efficient in their use of resources, whereas leaders of innovation fall short in the area of returns to scale and congestion.
Integrated electricity and heating load control based on smart grid technology

This paper aims at the difficulties in peak load supply and wind power integration with combined heat and power (CHP) widely used in North of China. Currently CHP units are excluded for electricity peak regulation and wind power is abandoned at the time of low electricity demand. In this paper, a method of integrated electricity and heating load control based on smart grid technology is proposed with introduction of electric heat pumps (EHPs) considering the heating delay due to heating distance. According to aforementioned methodologies, integrated electricity and heating load control is enabled: Firstly, in the electricity peak load or low wind power, heating water from CHP units is suggested to be shaved so as to increase its power output and reduce the peak of electricity load or compensate wind power equivalently; Secondly, taking account of heating delay due to heating distance, EHPs can supply heating by electricity to replace parts of CHP's heating water in the electricity valley load, so that the valley of electricity load is increased or excess wind power is utilized. At last, a numerical simulation concerning CHP, wind power turbines and condensing unit is performed to illustrate the result of this paper, it shows that the peak load can be cut equivalently and the capacity of integrated wind power is increased while the abandoned wind power is reduced. Moreover less energy consumption is realizable by this new method.
Effect of bepridil in atrial fibrillation inducibility facilitated by vagal nerve stimulation. - Prevention of vagal nerve activation-induced shortening of the atrial action potential duration -.

BACKGROUND Because bepridil blocks multiple myocardial ionic channels, including the muscarinic acetylcholine receptor-operated potassium current (I(KAch)), bepridil is expected to suppress atrial fibrillation (AF) mediated by vagal nerve stimulation (VNS). METHODS AND RESULTS The therapeutic effects of bepridil were studied with a special focus on heart rate variability (HRV) in a canine model of AF. During VNS, AF was induced in 9 of 9 experiments before, vs 3 of 9 experiments after administration of bepridil (P<0.01). During 350 ms atrial pacing, VNS shortened the right and left atrial monophasic action potentials at 90% repolarization (MAP90) by -31+/-8% and -22+/-12%, respectively, vs -10+/-13% and -6+/-8%, respectively, after bepridil (P<0.01, N=9). Bepridil prolonged the sinus cycle length, although it had no significant effect on the conduction time measured at 300 ms pacing. Statistically insignificant change was observed in the VNS-induced slowing of the sinus cycle length and in the VNS-induced increase in high frequency amplitude of HRV before (1.2+/-0.7 to 5.3+/-4.0 ms) vs after (1.7+/-0.8 to 5.4+/-2.3 ms) bepridil administration. CONCLUSIONS Bepridil prevented the VNS-induced shortening of atrial MAP90 and suppressed the inducibility of AF during VNS in two-thirds of the experiments. As far as this study shows, it may be possible that inhibition of I(KAch) played a part in this antifibrillatory effect.
Development of chimeric laccases by directed evolution

DNA recombination methods are useful tools to generate diversity in directed evolution protein engineering studies. We have designed an array of chimeric laccases with high‐redox potential by in vitro and in vivo DNA recombination of two fungal laccases (from Pycnoporus cinnabarinus and PM1 basidiomycete), which were previously tailored by laboratory evolution for functional expression in Saccharomyces cerevisiae. The laccase fusion genes (including the evolved α‐factor prepro‐leaders for secretion in yeast) were subjected to a round of family shuffling to construct chimeric libraries and the best laccase hybrids were identified in dual high‐throughput screening (HTS) assays. Using this approach, we identified chimeras with up to six crossover events in the whole sequence, and we obtained active hybrid laccases with combined characteristics in terms of pH activity and thermostability. Biotechnol. Bioeng. 2012; 109: 2978–2986. © 2012 Wiley Periodicals, Inc.
IgG and IgA subclass antibodies against Aspergillus umbrosus in farmer's lung disease

Fifty patients with farmer's lung disease (FL), 20 asymptomatic exposed farmers, and 18 healthy controls were investigated for total IgG and total IgA, as well as subclass antibody levels against Aspergillus umbrosus, the most common fungus to which FL patients in Finland have been exposed. Enzyme‐linked immunosorbent assay (ELISA) revealed significantly elevated levels of specific total IgG and IgA antibodies in the sera of patients during the acute phase of the disease. Both IgG1 and IgG2 subclass antibodies and both IgA1 and IgA2 subclass antibodies were significantly associated with the disease. The antibody levels decreased during the first 3 months, when mould exposure was avoided and when an oral 6‐week steroid treatment was administered. During the next 12 month follow‐up, the mean antibody levels continued to decrease, even though re‐exposure might have occurred. The results (with sensitivity 94% and specificity 95%) imply that in addition to the measurement of A. umbrosus‐specific IgG, determination of both A. umbrosus‐specific IgG1 and IgA might also be useful in the scrodiagnosis of acute stage of FL.
Spatiotemporal flow of information in the early visual pathway

The spatial components of a visual scene are processed neurally in a sequence of coarse features followed by fine features. This coarse‐to‐fine temporal stream was initially considered to be a cortical function, but has recently been demonstrated in the dorsal lateral geniculate nucleus. The goal of this study was to test the hypothesis that coarse‐to‐fine processing is present at earlier stages of visual processing in the retinal ganglion cells that supply lateral geniculate nucleus (LGN) neurons. To compare coarse‐to‐fine processing in the cat's visual system, we measured the visual responses of connected neuronal pairs from the retina and LGN, and separate populations of cells from each region. We found that coarse‐to‐fine processing was clearly present at the ganglion cell layer of the retina. Interestingly, peak and high‐spatial‐frequency cutoff responses were higher in the LGN than in the retina, indicating that there was a progressive cascade of coarse‐to‐fine information from the retina to the LGN to the visual cortex. The analysis of early visual pathway receptive field characteristics showed that the physiological response interplay between the center and surround regions was consistent with coarse‐to‐fine features and may provide a primary role in the underlying mechanism. Taken together, the results from this study provided a framework for understanding the emergence and refinement of coarse‐to‐fine processing in the visual system.
A Dominant Allele of PDR1 Alters Transition Metal Resistance in Yeast*

A yeast mutant was found to have defective growth on low iron medium despite a normal high affinity iron transport system. The phenotype results from a gain of function mutation inPDR1, which encodes a transcription factor that acts as a regulator of pleiotropic drug resistance in Saccharomyces cerevisiae. The mutant allele, PDR1(R821H), was found to result in increased expression of at least 19 genes, three of which are ATP-binding cassette (ABC) transporters. Expression of at least six genes was required to show the low iron growth defect. Wild type cells transformed with the PDR1(R821H) allele or a PDR1 dominant allele (PDR1–3) showed the low iron growth defect as well as increased resistance to drugs such as cycloheximide and oligomycin. Transformation of PDR1(R821H) into Δccc1 cells, which were previously shown to have increased sensitivity to high iron medium because of defective vacuolar iron storage (Li, L., Chen, O. S., Ward, D. M., and Kaplan, J. (2001) J. Biol. Chem. 276, 29515–29519), conferred resistance to high iron medium. Cells expressingPDR1(R821H) also showed increased resistance to copper and manganese because of increased metal export. These results suggest that expression of PDR1-regulated genes affects both efflux and storage of transition metals.
Desmoid-type fibromatoses involving the brachial plexus: treatment options and assessment of c-KIT mutational status.

OBJECT Desmoid-type fibromatoses are a locally invasive soft-tissue lesion that is most commonly encountered in abdominal sites. The tumor also affects head and neck areas, particularly the supraclavicular region, where it may encase and distort the brachial plexus and compromise neurovascular structures. Neurosurgeons may be called on to treat desmoid-type fibromatoses in these sites. The authors describe their experience in treating four patients with desmoid-type fibromatoses involving the brachial plexus and report the results of immunohistochemical analysis of the tumors. METHODS Gross-total excision with nerve sparing was the first-line therapy of choice, although the surgery was challenging. Intraoperative identification of the site of tumor origin from musculoaponeurotic tissues by the neurosurgeon was necessary in two of the four cases to achieve a correct frozen section or final pathological diagnosis. Immunostaining for c-KIT (CD117) was undertaken in all cases in light of a previous report of positive CD117 immunoreactivity in abdominal desmoid-type fibromatoses. All four tumors manifested weak focal immunostaining for c-KIT. One of the patients was given adjuvant imatinib mesylate therapy, with limited success. Subsequent polymerase chain reaction testing revealed that three of the four tumors manifested a single base pair change in exon 10 of the c-KIT gene (A to C in two cases and A to G in one case). There was local recurrence in three patients, despite gross-total excision. With the combination of surgery and radiation therapy, local disease control was achieved in three of the four patients. CONCLUSIONS This represents the first report of c-KIT sequencing in desmoid-type fibromatoses and suggests a possible biological basis for continuing to explore the use of adjuvant imatinib mesylate therapy.