Miracle-dz/UniFAR-FTUs huggingface dataset:
Conservative site-specific and single-copy transgenesis in human LINE-1 elements

Genome engineering of human cells plays an important role in biotechnology and molecular medicine. In particular, insertions of functional multi-transgene cassettes into suitable endogenous sequences will lead to novel applications. Although several tools have been exploited in this context, safety issues such as cytotoxicity, insertional mutagenesis and off-target cleavage together with limitations in cargo size/expression often compromise utility. Phage λ integrase (Int) is a transgenesis tool that mediates conservative site-specific integration of 48 kb DNA into a safe harbor site of the bacterial genome. Here, we show that an Int variant precisely recombines large episomes into a sequence, termed attH4X, found in 1000 human Long INterspersed Elements-1 (LINE-1). We demonstrate single-copy transgenesis through attH4X-targeting in various cell lines including hESCs, with the flexibility of selecting clones according to transgene performance and downstream applications. This is exemplified with pluripotency reporter cassettes and constitutively expressed payloads that remain functional in LINE1-targeted hESCs and differentiated progenies. Furthermore, LINE-1 targeting does not induce DNA damage-response or chromosomal aberrations, and neither global nor localized endogenous gene expression is substantially affected. Hence, this simple transgene addition tool should become particularly useful for applications that require engineering of the human genome with multi-transgenes.
A Tabu Search Algorithm for the Protein Folding Problem

Protein folding problem is one of the central problems in the cross-discipline field involving biology, computational physics and computer science. In this paper, based on the heuristic physical model, a three-dimensional AB mode-based protein folding problem is converted from a nonlinear constraint-satisfied problem to an unconstrained optimization problem, which can be solved by the gradient method. However, in the course of solution using the gradient method, it is often possible for the calculation of gradient method to fall into the trap of local minimum. To jump out of the trap of local minimum and guide the search to the points with better prospects, we proposed a heuristic Tabu search method. The computational results show that our algorithm can outperform nPERM algorithm and HSA algorithm in terms of finding states with lower energy for the four benchmark sequences.
On the Degrees of Freedom of MIMO X Networks With Non-Cooperation Transmitters

This paper proposes novel transmission schemes for a class of interference networks that can achieve new tradeoff regions between the sum of degrees of freedom (sum-DoF) and channel state information (CSI) feedback delay with distributed and temperately-delayed CSI at the transmitter (CSIT). A significant impact of the results is they reveal that distributed and temperately-delayed CSIT contributes to achieve better sum-DoF than that without CSIT in a certain class of interference networks. Specifically, a distributed space-time interference alignment (STIA) scheme is proposed for the two-user multiple-input multiple-output (MIMO) X channel via a novel precoding method called <italic>Cyclic Zero-padding</italic>. The achieved sum-DoFs herein for certain antenna configurations are greater than the best known sum-DoFs in literature with delayed CSIT. Furthermore, we propose a distributed retrospective interference alignment (RIA) scheme that achieves more than 1 sum-DoF for the <inline-formula> <tex-math notation="LaTeX">${K}$ </tex-math></inline-formula>-user single-input single-output (SISO) X network. Finally, we extend the distributed STIA to the <inline-formula> <tex-math notation="LaTeX">${M} \times {N}$ </tex-math></inline-formula> user multiple-input single-output (MISO) X network, where each transmitter has <inline-formula> <tex-math notation="LaTeX">${N} -1$ </tex-math></inline-formula> antennas and each receiver has a single antenna, yielding the same sum-DoF as that in the global and instantaneous CSIT case. The discussion and result of the MISO X network can be extended to the MIMO case due to the spatial scale invariance property.
Tumor Suppressor Function of PGP9.5 Is Associated with Epigenetic Regulation in Prostate Cancer—Novel Predictor of Biochemical Recurrence after Radical Surgery

Background: The expression level of protein G product 9.5 (PGP9.5) is downregulated because of promoter CpG hypermethylation in several tumors. We speculated that impaired regulation of PGP9.5 through epigenetic pathways is associated with the pathogenesis of prostate cancer. Methods: CpG methylation of the PGP9.5 gene was analyzed in cultured prostate cancer cell lines, 226 localized prostate cancer samples from radical prostatectomy cases, and 80 benign prostate hyperplasia (BPH) tissues. Results: Following 5-aza-2′-deoxycytidune treatment, increased PGP9.5 mRNA transcript expression was found in the LNCaP and PC3 cell lines. With bisulfite DNA sequencing, partial methylation of the PGP9.5 promoter was shown in LNCaP whereas complete methylation was found in PC3 cells. After transfection of PGP9.5 siRNA, cell viability was significantly accelerated in LNCaP but not in PC3 cells as compared with control siRNA transfection. Promoter methylation of PGP9.5 was extremely low in only one of 80 BPH tissues, whereas it was found in 37 of 226 prostate cancer tissues. Expression of the mRNA transcript of PGP9.5 was significantly lower in methylation (+) than methylation (−) prostate cancer tissues. Multivariate analysis of biochemical recurrence (BCR) after an radical prostatectomy revealed pT category and PGP9.5 methylation as prognostically relevant. Further stratification with the pT category in addition to methylation status identified a stepwise reduction of BCR-free probability. Conclusion: This is the first clinical and comprehensive study of inactivation of the PGP9.5 gene via epigenetic pathways in primary prostate cancer. Impact: CpG methylation of PGP9.5 in primary prostate cancer might become useful as a molecular marker for early clinical prediction of BCR after radical prostatectomy. Cancer Epidemiol Biomarkers Prev; 21(3); 487–96. ©2012 AACR.
Rethinking conceptualisations of adult-imposed restriction and children's experiences of autonomy in outdoor space

This paper calls for more sensitive understandings of children's experiences of autonomy and restriction in outdoor space. The study with children and adults living in a suburban area of Cape Town, South Africa, suggests that the imposition of adult structure and surveillance on childhood should not be automatically perceived as negative. The children's experiences were more nuanced and must be contextualised with reference to the predominant concern with (in)security in these suburban geographies. The notion of accompanied mobility is then considered to suggest how children's outdoor mobility might be framed as a collective or community responsibility, as opposed to an individualistic concern of parents.
Plato, Dewey, and the Problem of the Teacher's Authority

An examination of contemporary publications in the philosophy of education reveals that the authority of the teacher is being eroded. As teachers derive their authority from the democratic state and its compulsory education laws, the undermining of their authority indicates the undermining of the authority of the democratic state and its laws. A comparison between Plato and Dewey from this point of view reveals that this state of affairs is the upshot of the collision between the principle of authority and the principle of liberty, and that this collision constitutes the basic problem of democracy as well as of education for democracy. The challenge to contemporary education is consequently that of exploring ways leading to the rehabilitation of the authority of the teacher.
Self-assembly of the plant cell wall requires an extensin scaffold

Cytokinesis partitions the cell by a cleavage furrow in animals but by a new cross wall in plants. How this new wall assembles at the molecular level and connects with the mother cell wall remains unclear. A lethal Arabidopsis embryogenesis mutant designated root-, shoot-, hypocotyl-defective (rsh) provides some clues: RSH encodes extensin AtEXT3, a structural glycoprotein located in the nascent cross wall or “cell plate” and also in mature cell walls. Here we report that electron micrographs of rsh mutant cells lacking RSH extensin correspond to a wall phenotype typified by incomplete cross wall assembly. Biochemical characterization of the purified RSH glycoprotein isolated from wild-type Arabidopsis cell cultures confirmed its identity as AtEXT3: a (hydroxy)proline-rich glyco protein comprising 11 identical amphiphilic peptide repeats with a 28-residue periodicity: SOOOOKKHYVYKSOOOOVKHYSOOOVYH (O = Hyp), each repeat containing a hydrophobic isodityrosine cross-link motif (YVY, underlined). Atomic force microscopy of RSH glycoprotein imaged its propensity for self-assembly into a dendritic scaffold. Extensin peroxidase catalyzed in vitro formation of insoluble RSH gels with concomitant tyrosine cross-linking, hence this likelihood in muro. We conclude that self-assembling amphiphiles of lysine-rich RSH extensin form positively charged scaffolds in the cell plate. These react with negatively charged pectin to create an extensin pectate coacervate that may template further orderly deposition of the new cross wall at cytokinesis.
Effectiveness of a school district closure for pandemic influenza A (H1N1) on acute respiratory illnesses in the community: a natural experiment.

BACKGROUND Following detection of pandemic influenza A H1N1 (pH1N1) in Dallas/Fort Worth, Texas, a school district (intervention community, [IC]) closed all public schools for 8 days to reduce transmission. Nearby school districts (control community [CC]) mostly remained open. METHODS We collected household data to measure self-reported acute respiratory illness (ARI), before, during, and after school closures. We also collected influenza-related visits to emergency departments (ED(flu)). RESULTS In both communities, self-reported ARIs and ED(flu) visits increased from before to during the school closure, but the increase in ARI rates was 45% lower in the IC (0.6% before to 1.2% during) than in the CC (0.4% before to 1.5% during) (RRR(During)(/Before) = 0.55, P < . 001; adjusted OR(During/Before) = 0.49, P < . 03). For households with school-aged children only (no children 0-5 years), IC had even lower increases in adjusted ARI than in the CC (adjusted OR(During/Before) = 0.28, P < . 001). The relative increase of total ED(flu) visits in the IC was 27% lower (2.8% before to 4.4% during) compared with the CC (2.9% before to 6.2% during). Among children aged 6-18 years, the percentage of ED(flu) in IC remained constant (5.1% before vs 5.2% during), whereas in the CC it more than doubled (5.2% before vs 10.9% during). After schools reopened, ARI rates and ED(flu) visits decreased in both communities. CONCLUSIONS Our study documents a reduction in ARI and ED(flu) visits in the intervention community. Our findings can be used to assess the potential benefit of school closures during pandemics.
An Instinct for Spiritual Quests: Quiet Religion

John Dewey notes the following in his book A Common Faith: "Any activity pursued in behalf of an ideal end against obstacles and in spite of threats of per sonal loss because of conviction of its general and enduring value is religious in quality" (1934, 27). By "ideal end" he is suggesting something of importance to us, something fundamentally worthy of enhancing the human condition. Dewey certainly captures what I have in mind by spiritual quests as they are natural ized and linked to human needs, cognitive capacity, and neural structures; these qualifications are consistent with Dewey's orientation, along with self-corrective inquiry, nonviolence, and humility. Spiritual quests are not an aberration or a pathological state. They are, rather, a fundamental human need. Moreover, conversions to "seeing" events in a certain way are at the basis of scientific and other forms of human experience, as well as spiritual quests. The pursuit of knowledge has "conversion-like" experiences associated with it (Bloom 2007; Heelan 1994). Religious quests are vital human activities and cut across the sciences and humanities. Religious sensibility is one thing; religious tyranny, quite another. Religious sensibility, at its normative best, is humble and pluralistic. The approach that I suggest avoids dismissive positivism and dogmatic theological fundamental ism and replaces them with a pious naturalism. What underlie spiritual quests are (1) heightened vigilance and some discomfort or unrest about human existence, (2) a search to come to terms with this fact, and (3) the much-appreciated moments of peace and quietude that are necessary for human well-being. What is important is to bring ideas to the lifeblood of experience, to the everyday, to bring the conception of vulnerability and hypothesis-testing inquiry to cover the whole range of human experience, including spiritual inquiry. Thus, in what follows, I suggest, first, that spiritual quests are fundamental to the human condition and then that certain cognitive categories and a basic instinctive response predispose us to express this human need. Diverse brain
Beyond the Constituent - A Dependency Grammar Analysis of Chains

Abstract The paper introduces a unit of syntax beyond the constituent called the chain . A number of mechanisms are shown to be sensitive to chains, e.g. the formation of predicates and idioms, the ellipses of gapping, pseudogapping and VP-ellipsis, and the elided material of stripping and answer fragments. The presentation is couched in a surface syntax, dependency-based framework, as opposed to a constituency-based one. While the chain can be defined in a manner consistent with constituency, doing so requires that one adopt some controversial assumptions about the nature of constituency structure. The potential of the chain concept is great; it is the tool necessary to address the manner in which semantic compositionality occurs in the syntax.
Teachers as Designers: Integrating Robotics in Early Childhood Education.

This article presents a constructionist approach to introducing technology, in particular robotics, in the early childhood classroom. The authors demonstrate how this approach is well suited, since the four basic tenets of constructionism have a long-standing tradition in early childhood education: (a) learning by designing meaningful projects to share in the community, (b) using concrete objects to build and explore the world, (c) the identification of powerful ideas that are both personally and epistemologically significant, and (d) the importance of self-reflection as part of the learning process. This article introduces a methodology for teaching preservice teachers to integrate technology in the classroom. It also describes four different experiences in which preservice teachers designed and integrated robotic projects done with LEGO Mindstorms and ROBOLAB to engage their young students in exploring and learning new concepts and ways of thinking.
A Literature Review on Supervised Machine Learning Algorithms and Boosting Process

Data mining is one amid the core research areas in the field of computer science. Yet there is a knowledge data detection process helps the data mining to extract hidden information from the dataset there is a big scope of machine learning algorithms. Especially supervised machine learning algorithms gain extensive importance in data mining research. Boosting action is regularly helps the supervised machine learning algorithms for rising the predictive / classification veracity. This survey research article prefer two famous supervised machine learning algorithms that is decision trees and support vector machine and presented the recent research works carried out. Also recent improvement on Adaboost algorithms (boosting process) is also granted. From this survey research it is learnt that connecting supervised machine learning algorithm with boosting process increased prediction efficiency and there is a wide scope in this research element.
Human-computer dance interaction with realtime accelerometer control

Motion-capture-based character animations are widely used in computer graphics and interactive games.In this paper, we show a novel approach to create dancing character animations that react to input music and an accelerometer manipulated by a user. Since the sensor reads express intensities of users' body movements, the system can synthesize character motions whose intensities are synchronized to those of users. Our system consists of analysis phase and synthesis phase. In the analysis phase, the musical beat and segments are detected from input sound, and motion rhythm and intensities are found from motion capture data. With the results of this analysis, we generate a motion graph that can generate character motions matched to the musical rhythm. In synthesis phase, the system receives the output data from an accelerometer and traverses the motion graph according to the matching result between the sensor data and the motion intensity. As the result, our system adds an interactive component to live dancing performed by virtual characters.
Norwegian monitoring programme on the inorganic and organic contaminants in fish caught in the Barents Sea, Norwegian Sea and North Sea, 1994–2001

The results from part of a monitoring programme of contaminant levels in fish and other seafood products initiated by the Directorate of Fisheries in Norway in 1994 are presented. Concentrations of 22 elements (four are presented here: As, Cd, Hg and Pb) and HCB, HCH, PCB 28, 52, 101, 105, 118, 138, 153, 156, 180, pp-DDD, p-DDE, p-DDT, sum DDT and 137Cs were determined in 17 species of fish caught in three sampling locations: the Barents Sea, the Norwegian Sea and the North Sea. The fish species analysed in the survey were limited to species of commercial importance for Norway with catching volumes of at least 10 000 metric tons year−1. The survey started in 1994 and is expected to continue beyond 2010. The analyses were carried out on 25 individual fish from each species and each sampling location, and the locations were representative of commercial fishing grounds for the species in question. The concentrations of contaminants found were considerably lower than the maximum levels permissible in fish set by CODEX and the European Union for contaminants in seafood products.
Intracellular mechanism of action of sympathetic hepatic nerves on glucose and lactate balance in perfused rat liver.

In rat liver perfused in situ stimulation of the nerve plexus around the hepatic artery and the portal vein caused an increase in glucose output and a shift from lactate uptake to output. The effects of nerve stimulation on some key enzymes, metabolites and effectors of carbohydrate metabolism were determined and compared to the actions of glucagon, which led to an increase not only of glucose output but also of lactate uptake. 1. Nerve stimulation caused an enhancement of the activity of glycogen phosphorylase a to 300% and a decrease of the activity of glycogen synthase I to 40%, while it left the activity of pyruvate kinase unaltered. Glucagon, similarly to nerve action, led to a strong increase of glycogen phosphorylase and to a decrease of glycogen synthase; yet in contrast to the nerve effect it lowered pyruvate kinase activity clearly. 2. Nerve stimulation increased the levels of glucose 6-phosphate and of fructose 6-phosphate to 200% and 170%, respectively; glucagon enhanced the levels to about 400% and 230%, respectively. The levels of ATP and ADP were not altered, those of AMP were increased slightly by nerve stimulation. 3. Nerve stimulation enhanced the levels of the effectors fructose 2,6-bisphosphate and cyclic AMP only slightly to 140% and 125%, respectively; glucagon lowered the level of fructose 2,6-bisphosphate to 15% and increased the level of cyclic AMP to 300%. 4. In calcium-free perfusions the metabolic responses to nerve stimulation showed normal kinetics, if calcium was re-added 3 min before, but delayed kinetics, if it was re-added 2 min after the onset of the stimulus. The delay may be due to the time required to refill intracellular calcium stores. The hemodynamic alterations dependent on extracellular calcium were normal in both cases. The activation of glycogen phosphorylase, the inhibition of glycogen synthase and the increase of glucose 6-phosphate can well explain the enhancement of glucose output following nerve stimulation. The unaltered activity of pyruvate kinase and the marginal increase of fructose 2,6-bisphosphate cannot be the cause of the nerve-stimulation-dependent shift from lactate uptake to output. The very slight increase of the level of cyclic AMP after nerve stimulation cannot elicit the observed activation of glycogen phosphorylase. (ABSTRACT TRUNCATED AT 400 WORDS)
Vertebral Reconstruction Using the Telescopic Plate Spacer-Thoracolumbar (TPS-TL) Device

Study Design Retrospective study of surgical technique and outcome. Objective The authors conducted a study to evaluate the ability of the TPS-TL (telescopic plate spacer-thoracolumbar) implant to correct kyphotic deformity and restore vertebral body height after vertebrectomy in the thoracolumbar spine. Summary of Background Data TPS-TL is a novel vertebral body replacement device that consists of an expandable cage with an integrated plate component for transvertebral screw fixation. Methods This is a retrospective study of 20 patients who underwent anterior column reconstruction with TPS-TL after a 1 or 2 level thoracolumbar vertebrectomy. Preoperative and postoperative sagittal alignment and vertebral body heights were radiologically analyzed in all patients. The mean follow-up was 14 months. Results Preoperative and postoperative Cobb angles were measured to assess sagittal alignment. The average preoperative Cobb angle was 16.0±7 degrees. This was reduced to 9.8±10 degrees at the final follow-up (P<0.001). Percent of ideal vertebral body height was used to assess postoperative restoration of vertebral body height. This value was obtained by creating a ratio of the height of the effected vertebral levels to the height of the adjacent normal vertebral bodies. The mean percent of ideal vertebral body height improved from a preoperative value from 86.2±2% to 93.1±6% at the final follow-up (P<0.001). Conclusions The TPS-TL implant is effective in restoring vertebral body height and correcting kyphotic deformity after thoracolumbar vertebrectomy.
X-RAY VARIABILITY OF σ ORIONIS YOUNG STARS AS OBSERVED WITH ROSAT

We used the Aladin Virtual Observatory tool and High Resolution Imager ROSAT archival data to search for X-ray variability in scale of days in 23 young stars in the σ Orionis cluster and a background galaxy. Five stars displayed unambiguous flares and had probabilities pvar≫ 99% of being actual variables. Two of the detected flares were violent and long lasting, with maximum duration of six days and amplitude of eight times above the quiescent level. We classified another four stars as possible X-ray variables, including the binary system formed by the B2Vp star σ Ori E and its close late-type companion. This makes a minimum frequency of high-amplitude X-ray variability in excess of a day of 39% among σ Orionis stars. The incidence of this kind of X-ray variability seems to be lower among classical T Tauri stars with mid-infrared flux excesses than among fast-rotating, disk-less young stars.