Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Glioblastoma Patients' Plasma Revealed the Presence of MicroRNAs with a Prognostic Impact on Survival and Those of Viral Origin

Background Glioblastoma multiforme (GBM) is among the most aggressive cancers with a poor prognosis in spite of a plethora of established diagnostic and prognostic biomarkers and treatment modalities. Therefore, the current goal is the detection of novel biomarkers, possibly detectable in the blood of GBM patients that may enable an early diagnosis and are potential therapeutic targets, leading to more efficient interventions. Experimental Procedures MicroRNA profiling of 734 human and human-associated viral miRNAs was performed on blood plasma samples from 16 healthy individuals and 16 patients with GBM, using the nCounter miRNA Expression Assay Kits. Results We identified 19 miRNAs with significantly different plasma levels in GBM patients, compared to the healthy individuals group with the difference limited by a factor of 2. Additionally, 11 viral miRNAs were found differentially expressed in plasma of GBM patients and 24 miRNA levels significantly correlated with the patients’ survival. Moreover, the overlap between the group of candidate miRNAs for diagnostic biomarkers and the group of miRNAs associated with survival, consisted of ten miRNAs, showing both diagnostic and prognostic potential. Among them, hsa miR 592 and hsa miR 514a 3p have not been previously described in GBM and represent novel candidates for selective biomarkers. The possible signalling, induced by the revealed miRNAs is discussed, including those of viral origin, and in particular those related to the impaired immune response in the progression of GBM. Conclusion The GBM burden is reflected in the alteration of the plasma miRNAs pattern, including viral miRNAs, representing the potential for future clinical application. Therefore proposed biomarker candidate miRNAs should be validated in a larger study of an independent cohort of patients.
Graph Cuts Segmentation by Using Local Texture Features of Multiresolution Analysis

SUMMARY This paper proposes an approach to image segmentation using Iterated Graph Cuts based on local texture features of wavelet coefficients. Using Haar Wavelet based Multiresolution Analysis, the lowfrequency range (smoothed image) is used for the n-link and the highfrequency range (local texture features) is used for the t-link along with the color histogram. The proposed method can segment an object region having not only noisy edges and colors similar to the background, but also heavy texture change. Experimental results illustrate the validity of our method.
Direct Visualization of Protease Action on Collagen Triple Helical Structure

Enzymatic processing of extracellular matrix (ECM) macromolecules by matrix metalloproteases (MMPs) is crucial in mediating physiological and pathological cell processes. However, the molecular mechanisms leading to effective physiological enzyme-ECM interactions remain elusive. Only scant information is available on the mode by which matrix proteases degrade ECM substrates. An example is the enzymatic degradation of triple helical collagen II fragments, generated by the collagenase MMP-8 cleavage, during the course of acute inflammatory conditions by gelatinase B/MMP-9. As is the case for many other matrix proteases, it is not clear how MMP-9 recognizes, binds and digests collagen in this important physiological process. We used single molecule imaging to directly visualize this protease during its interaction with collagen fragments. We show that the initial binding is mediated by the diffusion of the protease along the ordered helix on the collagen ¾ fragment, with preferential binding of the collagen tail. As the reaction progressed and prior to collagen degradation, gelatin-like morphologies resulting from the denaturation of the triple helical collagen were observed. Remarkably, this activity was independent of enzyme proteolysis and was accompanied by significant conformational changes of the working protease. Here we provide the first direct visualization of highly complex mechanisms of macromolecular interactions governing the enzymatic processing of ECM substrates by physiological protease.
Smart server: Concepts and applications

The Internet has become a critical tool for information and communication that has reached much of the developed world. It is comprised of numerous components, of which the World Wide Web (WWW) is the largest and fastest growing. Efficient functionality of the WWW depends on a multitude of web servers in operation throughout the world. A web server, in and of itself, is frequently inefficient. We propose several concepts—all of which involve the assimilation of computational intelligence into a web server—that will ultimately improve its performance. A web server would then become a “smart” server that will learn during its operation and subsequently adapt its components and behavior to optimize many of its functions and modes of operation. Furthermore, it will be more secure, robust, and reliable via a hierarchical security system. A smart server will ultimately be more efficient, thus providing an enhanced experience for the multitude of people making use of the WWW every day. © 2007 Wiley Periodicals, Inc. Int J Int Syst 22: 1139–1154, 2007.
Control system design and kinematic analysis for a 4-DOF light weight manipulator

Light weight manipulator is characteristic of high load to weight ratio and high speed operation capability, so it has good prospect for application in warehousing logistics and agricultural picking. In this paper, a 4-DOF lightweight arm is designed and its control system and kinematics are studied. Firstly, the control system of the manipulator is determined. A distributed control system (DCS) based on the CAN (controller area network) bus is proposed in order to realize coordinated multi-axis control, the upper computer performs trajectory planning task of the manipulator, the actuator adopts PVT interpolation mode by which the upper computer sends trajectory segment message to the actuator via CAN bus. Secondly, the kinematics and trajectory planning of the manipulator is analyzed and studied. According to the link structure of the manipulator, the joint structure model is established and its kinematics is analyzed. The inverse kinematics of the manipulator is solved by geometry method to meet the task requirement. The motion trajectory of the manipulator is planned by the polynomial interpolation in the joint space. Finally, the simulation results show that the kinematic planning method is effective and the actual operation test shows that the manipulator can realize the action quickly and accurately to satisfy the operational requirement in the actual working environment.
ESTIMATES BASED ON RANDOM ASSIGNMENT IN EVALUATIONS OF SCHOOL CHOICE ? A WITHIN-STUDY COMPARISON

The ability of nonexperimental estimators to match impact estimates derived from random assignment is examined using data from the evaluation of two interdistrict magnet schools. As in previous within-study comparisons, nonexperimental estimates differ from estimates based on random assignment when nonexperimental estimators are implemented without pretreatment measures of academic performance. With comparison groups consisting of students drawn from the same districts or districts with similar student body characteristics as the districts where treatment group students reside, using pretreatment test scores reduces the bias in nonexperimental methods between 64 and 96 percent. Adding pretreatment test scores does not achieve as much bias reduction when the comparison group consists of students drawn from districts with different student body characteristics than the treatment group students’ districts. The results suggest that using pretreatment outcome measures and comparison groups that are geographically aligned with the treatment group greatly improves the performance of nonexperimental estimators.
Biogas Engine Waste Heat Recovery Using Organic Rankine Cycle

Italy is a leading country in the biogas sector. Energy crops and manure are converted into biogas using anaerobic digestion and, then, into electricity using internal combustion engines (ICEs). Therefore, there is an urgent need for improving the efficiency of these engines taking the real operation into account. To this purpose, in the present work, the organic Rankine cycle (ORC) technology is used to recover the waste heat contained in the exhaust gases of a 1 MW el biogas engine. The ICE behavior being affected by the biogas characteristics, the ORC unit is designed, firstly, using the ICE nameplate data and, then, with data measured during a one-year monitoring activity. The optimum fluid and the plant configuration are selected in both cases using an “in-house” optimization tool. The optimization goal is the maximization of the net electric power while the working fluid is selected among 115 pure fluids and their mixtures. Results show that a recuperative ORC designed using real data guarantees a 30% higher net electric power than the one designed with ICE nameplate conditions.
Identi ® cation and functional characterization of a new member of the human Mcm protein family : hMcm 8

The six minichromosome maintenance proteins (Mcm2±7) are required for both the initiation and elongation of chromosomal DNA, ensuring that DNA replication takes place once, and only once, during the S phase. Here we report on the cloning of a new human Mcm gene (hMcm8) and on characterisation of its protein product. The hMcm8 gene contains the central Mcm domain conserved in the Mcm2±7 gene family, and is expressed in a range of cell lines and human tissues. hMcm8 mRNA accumulates during G1/S phase, while hMcm8 protein is detectable throughout the cell cycle. Immunoprecipitationbased studies did not reveal any participation of hMcm8 in the Mcm3/5 and Mcm2/4/6/7 subcomplexes. hMcm8 localises to the nucleus, although it is devoid of a nuclear localisation signal, suggesting that it binds to a nuclear protein. In the nucleus, the hMcm8 structure-bound fraction is detectable in S, but not in G2/M, phase, as for hMcm3. However, unlike hMcm3, the hMcm8 structure-bound fraction is not detectable in G1 phase. Overall, our data identify a new Mcm protein, which does not form part of the Mcm2±7 complex and which is only structurebound during S phase, thus suggesting its speci®c role in DNA replication.
Lipopolysaccharide Analogs Improve Efficacy of Acellular Pertussis Vaccine and Reduce Type I Hypersensitivity in Mice

ABSTRACT Pertussis is an infectious disease of the respiratory tract that is caused by the gram-negative bacterium Bordetella pertussis. Although acellular pertussis (aP) vaccines are safe, they are not fully effective and thus require improvement. In contrast to whole-cell pertussis (wP) vaccines, aP vaccines do not contain lipopolysaccharide (LPS). Monophosphoryl lipid A (MPL) and Neisseria meningitidis LpxL2 LPS have been shown to display immune-stimulating activity while exerting little endotoxin activity. Therefore, we evaluated whether these LPS analogs could increase the efficacy of the aP vaccine. Mice were vaccinated with diphtheria-tetanus-aP vaccine with aluminum, MPL, or LpxL2 LPS adjuvant before intranasal challenge with B. pertussis. Compared to vaccination with the aluminum adjuvant, vaccination with either LPS analog resulted in lower colonization and a higher pertussis toxin-specific serum immunoglobulin G level, indicating increased efficacy. Vaccination with either LPS analog resulted in reduced lung eosinophilia, reduced eosinophil numbers in the bronchoalveolar lavage fluid, and the ex vivo production of interleukin-4 (IL-4) by bronchial lymph node cells and IL-5 by spleen cells, suggesting reduced type I hypersensitivity. Vaccination with either LPS analog increased serum IL-6 levels, although these levels remained well below the level induced by wP, suggesting that supplementation with LPS analogs may induce some reactogenicity but reactogenicity considerably less than that induced by the wP vaccine. In conclusion, these results indicate that supplementation with LPS analogs forms a promising strategy that can be used to improve aP vaccines.
Impact of Obesity on Pregnancy Outcome in Different Ethnic Groups: Calculating Population Attributable Fractions

Objectives To quantify the proportion of adverse pregnancy outcome attributable to maternal obesity. Design Cross sectional analysis of routine obstetric dataset. Setting Guy’s and St Thomas’s NHS Foundation Trust (GSTFT). Population 23,668 women who had singleton deliveries at GSTFT between 2004 and 2008. Methods Logistic regression was used to estimate the association between BMI and outcome in different ethnic groups. Adjusted odds ratios, and the proportions of obese women, were used to calculate population attributable risk fractions (PAFs). Main Outcome Measures (i) Maternal outcomes: diabetes, type of delivery, post-partum haemorrhage, and preterm delivery. (ii) Perinatal outcomes: macrosomia, low birth weight, admission to neonatal intensive care/special care baby unit, and perinatal death. Results The prevalence of maternal obesity was 14%. Increasing BMI was independently associated with increasing risk of adverse obstetric and neonatal outcome. At the individual level, the effect of obesity on diabetes was highest in Asian women compared to white women (p for interaction = 0.03). Calculation of population attributable risk fractions demonstrated that one third of diabetes cases and one in six Caesarean sections could be avoided in this population if all obese women were of normal BMI. At the population level, the contribution of obesity to diabetes was highest for Black women (42%), and lowest for oriental women (8%). Seven percent of neonatal macrosomia in all the population, and 13% in Black mothers, were attributable to obesity. Conclusions Preventing obesity prior to pregnancy will substantially reduce the burden of obstetric and neonatal morbidity in this population. This reduction will be higher in Black women.
QMapper for Smart Grid: Migrating SQL-based Application to Hive

Apache Hive has been widely used by Internet companies for big data analytics applications. It can provide the capability of compiling high-level languages into efficient MapReduce workflows, which frees users from complicated and time consuming programming. The popularity of Hive and its HiveQL-compatible systems like Impala and Shark attracts attentions from traditional enterprises as well. However, enterprise big data processing systems such as Smart Grid applications often have to migrate their RDBMS-based legacy applications to Hive rather than directly writing new logic in HiveQL. Considering their differences in syntax and cost model, manual translation from SQL in RDBMS to HiveQL is very difficult, error-prone, and often leads to poor performance. In this paper, we propose QMapper, a tool for automatically translating SQL into proper HiveQL. QMapper consists of a rule-based rewriter and a cost-based optimizer. The experiments based on the TPC-H benchmark demonstrate that, compared to manually rewritten Hive queries provided by Hive contributors, QMapper dramatically reduces the query latency on average. Our real world Smart Grid application also shows its efficiency.
Lck-Dependent Tyrosine Phosphorylation of Diacylglycerol Kinase α Regulates Its Membrane Association in T Cells1

TCR engagement triggers phospholipase Cγ1 activation through the Lck-ZAP70-linker of activated T cell adaptor protein pathway. This leads to generation of diacylglycerol (DAG) and mobilization of intracellular Ca2+, both essential for TCR-dependent transcriptional responses. TCR ligation also elicits transient recruitment of DAG kinase α (DGKα) to the lymphocyte plasma membrane to phosphorylate DAG, facilitating termination of DAG-regulated signals. The precise mechanisms governing dynamic recruitment of DGKα to the membrane have not been fully elucidated, although Ca2+ influx and tyrosine kinase activation were proposed to be required. We show that DGKα is tyrosine phosphorylated, and identify tyrosine 335 (Y335), at the hinge between the atypical C1 domains and the catalytic region, as essential for membrane localization. Generation of an Ab that recognizes phosphorylated Y335 demonstrates Lck-dependent phosphorylation of endogenous DGKα during TCR activation and shows that pY335DGKα is a minor pool located exclusively at the plasma membrane. Our results identify Y335 as a residue critical for DGKα function and suggest a mechanism by which Lck-dependent phosphorylation and Ca2+ elevation regulate DGKα membrane localization. The concerted action of these two signals results in transient, receptor-regulated DGKα relocalization to the site at which it exerts its function as a negative modulator of DAG-dependent signals.
Efficient reconstruction of nonrigid shape and motion from real-time 3D scanner data

We present a new technique for reconstructing a single shape and its nonrigid motion from 3D scanning data. Our algorithm takes a set of time-varying unstructured sample points that capture partial views of a deforming object as input and reconstructs a single shape and a deformation field that fit the data. This representation yields dense correspondences for the whole sequence, as well as a completed 3D shape in every frame. In addition, the algorithm automatically removes spatial and temporal noise artifacts and outliers from the raw input data. Unlike previous methods, the algorithm does not require any shape template but computes a fitting shape automatically from the input data. Our reconstruction framework is based upon a novel topology-aware adaptive subspace deformation technique that allows handling long sequences with complex geometry efficiently. The algorithm accesses data in multiple sequential passes, so that long sequences can be streamed from hard disk, not being limited by main memory. We apply the technique to several benchmark datasets, significantly increasing the complexity of the data that can be handled efficiently in comparison to previous work.
The ‘dark side of the moon’: a critical look at teacher knowledge construction in collaborative settings

Over the last two decades or so teacher knowledge construction has gained a prominent place in the research literature of teaching and teacher education, as well as in the design of pre-service and professional development programmes. The vast majority of research programmes have focused on first person accounts of the challenges, affordances and assets of doing collaborative teacher research, as well as on the barriers, impediments and confusions that teacher researchers face ‘on the way’. However, of central concern is what conditions in the collaborative process play out in collaborative teacher research and knowledge construction to transform it into a professional learning experience. Drawing on five enquiry study groups this issue attends to critical aspects in the co-construction of knowledge in teacher enquiry groups. The five contributors to this issue focus on the different ‘sides’ of knowledge construction, as shaped by the unique contexts within which their enquiry groups were situated. Conversation and dialogue are at the core of knowledge construction. Michal Zellermayer and Edith Tabak’s study, ‘Knowledge construction in a teachers’
Influence of channel prediction using theoretical autocorrelation on MIMO capacity in line-of-sight environment

In this report, we investigate prediction accuracy of fading channels in line-of-sight (LOS) environment when using autoregressive (AR) model. We especially evaluate the accuracy of the predicted channel in LOS environment when applying the theoretical autocorrelation formula of the LOS environment to the AR model. The influence of the prediction methods on MIMO capacities is also investigated. The simulation results clarify that the channel prediction using the LOS formula is superior to that using the NLOS formula especially when predicting the future channel at the large time interval.
Knowing about Environmental Knowing

This paper reviews the 15 years of concentrated research on environmental cognition, including recent developments in theory construction. Included are discussions on the content of environmental representations, cognitive mapping, environmental meaning and symbolism, individual and group differences, eplanatory variables, differences due to characteristics of the physical environment, and the role of environmental cognition in urban spatial behavior. It is argued that people remember buildings less for their architectural form than for their use significance, that people conceive of cities in terms of basic dichotomies of human experiences, that environmental meaning and symbolism are more im-portant in experience than concrete aspects of orientation and cognitive mapping, that developmental changes occur in a stage-sequence pattern, that with increasing mobility peoples images of the environment shift from social and physical conceptions to symbolic conceptions, and that a complete explanation of environmental cognition must take into account both internal organismic variables and external environmental variables. Finally, a framework for organizing existing findings is proposed and new lines of research are suggested.
Argentina's Escuela Normal de Paraná and its disciples: mergers of liberalism, Krausism, and Comtean positivism in Sarmiento's temple for civilizing the nation, 1870 to 1916

Positivism, the predominant philosophy of Latin America's elites at the end of the nineteenth century, found its exemplary expression in Brazil's castilhismo and Mexico's porfiriato. Argentina, in contrast, seemed to have deviated from the norm of ‘enlightened dictatorships’. After the end of the Rosas tyranny in 1852, authoritarianism had been discredited. Early positivism, as embodied by Teacher-President Sarmiento, could barely be distinguished from liberalism and no single political philosophy was able to exert hegemony. However, the significance of ‘scientific politics’ should not be downplayed. As this article argues, the merger, in the 1880s, of Comtean positivism and teacher training revolutionised education policies that aimed at erasing frontier backwardness and inserting future generations into an export-led economy, oligarchic polity, and homogenous national organism. Normal schools, especially Sarmiento's Escuela de Paraná, acted as laboratories for the assimilation, merger, and contestation of European, North American, and autochthonous scientific, philosophical, and pedagogical traditions.
Draft Genome Sequence of Escherichia coli Strain ATCC 23506 (Serovar O10:K5:H4)

ABSTRACT We report the 5.101-Mbp high-quality draft assembly of the Escherichia coli strain ATCC 23506 (serovar O10:K5:H4, also known as NCDC Bi 8337-41) genome. This uropathogenic strain, commonly referred to as E. coli K5, produces N-acetyl heparosan, a glycosaminoglycan-like capsular polysaccharide and precursor to the anticoagulant pharmaceutical heparin. Metabolic reconstruction of this genome will enable the prediction of gene deletions and overexpressions that lead to increased heparosan production.