Miracle-dz/UniFAR-FTUs huggingface dataset:
A Resource for Discovering Specific and Universal Biomarkers for Distributed Stem Cells

Specific and universal biomarkers for distributed stem cells (DSCs) have been elusive. A major barrier to discovery of such ideal DSC biomarkers is difficulty in obtaining DSCs in sufficient quantity and purity. To solve this problem, we used cell lines genetically engineered for conditional asymmetric self-renewal, the defining DSC property. In gene microarray analyses, we identified 85 genes whose expression is tightly asymmetric self-renewal associated (ASRA). The ASRA gene signature prescribed DSCs to undergo asymmetric self-renewal to a greater extent than committed progenitor cells, embryonic stem cells, or induced pluripotent stem cells. This delineation has several significant implications. These include: 1) providing experimental evidence that DSCs in vivo undergo asymmetric self-renewal as individual cells; 2) providing an explanation why earlier attempts to define a common gene expression signature for DSCs were unsuccessful; and 3) predicting that some ASRA proteins may be ideal biomarkers for DSCs. Indeed, two ASRA proteins, CXCR6 and BTG2, and two other related self-renewal pattern associated (SRPA) proteins identified in this gene resource, LGR5 and H2A.Z, display unique asymmetric patterns of expression that have a high potential for universal and specific DSC identification.
Microsurgical Treatment of Basilar Apex Aneurysms: Perioperative and Long-term Clinical Outcome

OBJECTIVEWe sought to analyze the perioperative and long-term clinical outcome data for patients with microsurgically treated basilar apex aneurysms. METHODSWe identified 98 consecutively treated basilar apex aneurysms in patients prospectively enrolled in a cerebral aneurysm database. RESULTSFifty patients presented with subarachnoid hemorrhage, and 19 aneurysms were giant. Eighty-four of 98 aneurysms were directly clipped. Surgical morbidity was 19.4% for the entire cohort and 8.8% for the unruptured, nongiant subgroup. The most common complication resulting in long-term morbidity was perforator injury. Sixty-seven percent of patients with clipped aneurysms were independent at discharge; this fraction increased to 79.0% at the 3-month follow-up examination. Good long-term outcomes (modified Rankin Scale score ≤2) were achieved in 56 (70%) of 80 cases. The mean Barthel Index of surviving patients was 95.8 ± 15.0 (median = 100, n = 66). Patients with unruptured, nongiant lesions fared considerably better than patients in other cohorts. Ninety-three percent of this subgroup was independent at discharge; this fraction increased to 100% at the 3-month follow-up examination (n = 27). In univariate analyses, poor clinical grade, giant aneurysm size, major operative complications, and operations performed early in the series were associated with worse outcomes. In the multivariate analysis, unruptured giant aneurysm status was found to confer a tremendous risk for poor outcome (risk ratio, 80.0; 95% confidence interval, 8.0–800.7; P < 0.01). Surviving patients were observed for a mean clinical follow-up period of 7.4 ± 3.7 years. The annual rate of postoperative subarachnoid hemorrhage was 0.18% for all clipped aneurysms and 0% for completely clipped lesions. CONCLUSIONIn comparison to data from the existing literature regarding Guglielmi detachable coil embolization of basilar apex aneurysms, the data presented suggest that surgical clipping should be an important component of a multimodality approach to the treatment of patients with basilar apex aneurysms.
The Contribution of Greenhouse Gas Emissions on Future Acid Rain in States of Gulf Cooperation Council: Measures to Adopt

Air pollution is one of the serious problems facing the world. This is mainly due to production and consumption of fossil fuels. Sulphur dioxide (SO2) and oxides of nitrogen (NOx) emissions could affect human health and destroy vegetation through acid deposition and cause transboundary air pollution. Currently, there are no regional ambient SO2 and NOx regulations and control measures of many developing countries including GCC countries. This paper reviewed the experiences of the past acid rain pollution problems in United States, Canada, Europe, Japan and China. In addition, the plausible control measures through application of air pollution abatement technologies, market based regulations were discussed. The study recommended that suitable and locally based measures could be adopted by GCC states to prevent future occurrence of acid rain within the region and beyond.
Role for Bcl-xL in delayed eosinophil apoptosis mediated by granulocyte-macrophage colony-stimulating factor and interleukin-5.

Eosinophils are potent inflammatory cells involved in allergic reactions. Inhibition of apoptosis of purified eosinophils by certain cytokines has been previously shown to be an important mechanism causing tissue eosinophilia. To elucidate the role of Bcl-2 family members in the inhibition of eosinophil apoptosis, we examined the expression of the known anti-apoptotic genes Bcl-2, Bcl-xL, and A1, as well as Bax and Bcl-xS, which promote apoptosis in other systems. We show herein that freshly isolated human eosinophils express significant amounts of Bcl-xL and Bax, but only little or no Bcl-2, Bcl-xS, or A1. As assessed by reverse transcription-polymerase chain reaction, immunoblotting, flow cytometry, and immunocytochemistry, we show that spontaneous eosinophil apoptosis is associated with a decrease in Bcl-xL mRNA and protein levels. In contrast, stimulation of the cells with granulocyte-macrophage colony-stimulating factor (GM-CSF) or interleukin-5 (IL-5) results in maintenance or upregulation of Bcl-xL mRNA and protein levels. Moreover, Bcl-2 protein is not induced by GM-CSF or IL-5 in purified eosinophils. Bcl-2 protein is also not expressed in tissue eosinophils as assessed by immunohistochemistry using two different eosinophilic tissue models. Furthermore, Bcl-xL antisense but not scrambled phosphorothioate oligodeoxynucleotides can partially block the cytokine-mediated rescue of apoptotic death in these cells. These data suggest that Bcl-xL acts as an anti-apoptotic molecule in eosinophils.
Gamma‐Aminobutyric Acid (Gaba) Receptors Rho (Gabrr) Gene Polymorphisms and Risk for Migraine

The possible role of gammaaminobutyric acid (GABA) in the pathogenesis of migraine has been suggested by a number of biochemical, pharmacological, neurophysiological and experimental data. We investigated the possible association between the most common single nucleotide polymorphisms (SNPs) in the GABA receptor rho1, 2, and 3 genes (GABRR1, GABRR2, and GABRR3) and the risk of developing migraine.
Spectral and higher-order statistical analysis of the ECG: Application to the study of ischemia in rabbit isolated hearts

There are many different approaches for heart beat classification. Probably the main task is extraction of relevant features from the beat. The present paper is focused on the study of ECG cross spectral coherence and higher-order cumulants and their ability to classify normal and ischemic cardiac beats. Using these parameters as the input for neural network classifier allows achieving classification error only 4%. Thus, they can be successfully used to solve this task.
Using run time traces in automated programming tutoring

Running test cases against a student's solution of a programming assignment is one of the easiest ways to generate feedback. If black-box tests are used, students may have difficulties to retrace the complete system behaviour and to find erroneous programming statements. This paper discusses the use of automated trace generation for assisting students in this task. Both manual and automated trace interpretation is discussed and evaluated by examples.
Historie H1°: a major player in cell differentiation?

Histone H1° was initially described as a member of the lysine‐rich histone class, typically present in nondividing mammalian cells. Since then it has been found in almost every animal or plant species studied. The protein accumulates in terminally differentiated cells that have stopped dividing. It has also been implicated in changes in chromatin structure and function accompanying malignant transformation. Despite its involvement in these fundamental cellular processes, its precise role remains elusive, as do the molecular mechanisms via which it acts. This review is an attempt to summarize and critically discuss the huge relevant literature, trying to highlight the problems that still await answers. —Zlatanova, J., Doenecke, D. , Histone H1°: a major player in cell differentiation? FASEB J. 8, 1260‐1268 (1994)
Defense from the Group A Streptococcus by active and passive vaccination with the streptococcal hemoprotein receptor.

BACKGROUND The worldwide burden of the Group A Streptococcus (GAS) primary infection and sequelae is considerable, although immunization programs with broad coverage of the hyper variable GAS are still missing. We evaluate the streptococcal hemoprotein receptor (Shr), a conserved streptococcal protein, as a vaccine candidate against GAS infection. METHODS Mice were immunized intraperitoneally with purified Shr or intranasally with Shr-expressing Lactococcus lactis. The resulting humoral response in serum and secretions was determined. We evaluated protection from GAS infection in mice after active or passive vaccination with Shr, and Shr antiserum was tested for bactericidal activity. RESULTS A robust Shr-specific immunoglobulin (Ig) G response was observed in mouse serum after intraperitoneal vaccination with Shr. Intranasal immunization elicited both a strong IgG reaction in the serum and a specific IgA reaction in secretions. Shr immunization in both models allowed enhanced protection from systemic GAS challenge. Rabbit Shr antiserum was opsonizing, and mice that were administrated with Shr antiserum prior to the infection demonstrated a significantly higher survival rate than did mice treated with normal rabbit serum. CONCLUSIONS Shr is a promising vaccine candidate that is capable of eliciting bactericidal antibody response and conferring immunity against systemic GAS infection in both passive and active vaccination models.
Effect of Punica granatum L. Flower Water Extract on Five Common Oral Bacteria and Bacterial Biofilm Formation on Orthodontic Wire

Background: Use of herbal extracts and essences as natural antibacterial compounds has become increasingly popular for the control of oral infectious diseases. Therefore, finding natural antimicrobial products with the lowest side effects seems necessary. The present study sought to assess the effect of Punica granatum L. water extract on five oral bacteria and bacterial biofilm formation on orthodontic wire. Methods: Antibacterial property of P. granatum L. water extract was primarily evaluated in brain heart infusion agar medium using well-plate method. The minimum inhibitory concentration and minimum bactericidal concentration were determined by macro-dilution method. The inhibitory effect on orthodontic wire bacterial biofilm formation was evaluated using viable cell count in biofilm medium. At the final phase, samples were fixed and analyzed by Scanning Electron Microscopy. Results: The growth inhibition zone diameter was proportional to the extract concentration. The water extract demonstrated the maximum antibacterial effect on Streptococcus sanguinis ATCC 10556 with a minimum inhibitory concentration of 6.25 mg/ml and maximum bactericidal effect on S. sanguinis ATCC 10556 and S. sobrinus ATCC 27607 with minimum bactericidal concentration of 25 mg/ml. The water extract decreased bacterial biofilm formation by S. sanguinis, S. sobrinus, S. salivarius, S. mutans ATCC 35608 and E. faecalis CIP 55142 by 93.7–100%, 40.6–99.9%, 85.2–86.5%, 66.4–84.4% and 35.5–56.3% respectively. Conclusion: Punica granatum L. water extract had significant antibacterial properties against 5 oral bacteria and prevented orthodontic wire bacterial biofilm formation. However, further investigations are required to generalize these results to the clinical setting.
Transarterial Chemoembolization Using Gelatin Sponges or Microspheres Plus Lipiodol-Doxorubicin versus Doxorubicin-Loaded Beads for the Treatment of Hepatocellular Carcinoma

Objective To retrospectively compare treatment of hepatocellular carcinoma (HCC) with transarterial chemoembolization (TACE) using gelatin sponges or microspheres plus lipiodol-doxorubicin vs. doxorubicin-loaded drug-eluting beads (DEB). Materials and Methods A total of 158 patients with HCC received TACE from November 2010 to November 2011 were enrolled in this study, including 64 (40.5%) received TACE with lipiodol-doxorubicin and gelatin sponges (group A), 41 (25.9%) received TACE with lipiodol-doxorubicin and microspheres (group B), and 53 (33.5%) received TACE with doxorubicin-loaded DEB (group C). Tumor response and adverse events (AEs) were evaluated. Results No significant difference was found at baseline among the three groups. The doxorubicin dosage in group C was significantly (p < 0.001) higher compared to the dose used in groups A or B (median, 50 mg vs. 31 mg or 25 mg). Significantly (p < 0.001) more patients in group C achieved complete response compared to those in groups A or B (32.1% vs. 6.3% or 2.4%). Significantly (p < 0.001) less patients in group C had progressive disease compared to those in groups A or B (34.0% vs. 57.8% or 68.3%). Minor AEs were more common in groups A and B compared to group C, with rates of 54.7%, 34.1%, and 5.7%, respectively. Conclusion In patients with HCC, TACE with DEB offers better safety and efficacy profiles compared to either TACE with gelatin sponges or TACE with microspheres.
On the optimization of SiGe and III-V compound hetero-junction Tunnel FET devices

We investigate the operation and performance of planar SiGe/Si and In<sub>0.53</sub>Ga<sub>0.47</sub>As/In<sub>0.7</sub>Ga<sub>0.3</sub>As/In<sub>0.53</sub>Ga<sub>0.47</sub>As hetero-junction Semiconductor on Insulator (ScOI) Tunnel FET (TFET) devices. The alignment between the hetero-junction, the gate edge and the source junction is systematically shifted to search for the highest ON-current and the lowest Subthreshold Swing (SS). A slight positive misalignment between the hetero-junction and the metallurgical junction is beneficial to improve I<sub>ON</sub> but for the considered devices the ON-current at V<sub>DD</sub>=0.5V and I<sub>oFF</sub>=1pA/μm hardly exceeds 1μA/μm. Furthers reduction of the band gap by lattice strain appears mandatory to exceed this limit in the explored material systems.
Optimizing preprocessing and analysis pipelines for single‐subject fMRI. I. Standard temporal motion and physiological noise correction methods

Subject‐specific artifacts caused by head motion and physiological noise are major confounds in BOLD fMRI analyses. However, there is little consensus on the optimal choice of data preprocessing steps to minimize these effects. To evaluate the effects of various preprocessing strategies, we present a framework which comprises a combination of (1) nonparametric testing including reproducibility and prediction metrics of the data‐driven NPAIRS framework (Strother et al. [2002]: NeuroImage 15:747–771), and (2) intersubject comparison of SPM effects, using DISTATIS (a three‐way version of metric multidimensional scaling (Abdi et al. [2009]: NeuroImage 45:89–95). It is shown that the quality of brain activation maps may be significantly limited by sub‐optimal choices of data preprocessing steps (or “pipeline”) in a clinical task‐design, an fMRI adaptation of the widely used Trail‐Making Test. The relative importance of motion correction, physiological noise correction, motion parameter regression, and temporal detrending were examined for fMRI data acquired in young, healthy adults. Analysis performance and the quality of activation maps were evaluated based on Penalized Discriminant Analysis (PDA). The relative importance of different preprocessing steps was assessed by (1) a nonparametric Friedman rank test for fixed sets of preprocessing steps, applied to all subjects; and (2) evaluating pipelines chosen specifically for each subject. Results demonstrate that preprocessing choices have significant, but subject‐dependant effects, and that individually‐optimized pipelines may significantly improve the reproducibility of fMRI results over fixed pipelines. This was demonstrated by the detection of a significant interaction with motion parameter regression and physiological noise correction, even though the range of subject head motion was small across the group (≪ 1 voxel). Optimizing pipelines on an individual‐subject basis also revealed brain activation patterns either weak or absent under fixed pipelines, which has implications for the overall interpretation of fMRI data, and the relative importance of preprocessing methods. Hum Brain Mapp, 2012. © 2011 Wiley Periodicals, Inc.
Konsep Pendidikan Islam Ibnu Khaldun Relevansinya Terhadap Pendidikan Nasional

Ibn Khaldun with all efforts to find a concept of Islamic education with some of them about the idea of learning known as malakah theory, generalization, tadarruj, and continuity, which until now is still used as a guide in the world of education. For this research trying to uncover the relationship between Islam Ibn Khaldun's Concept of Education in Relevance o f National Education. This study aims to provide an overview of the reasons behind Ibn Khaldun's ideas with regard to the concept of Islamic education and describes the relevance of the concept of Islamic education Ibn Khaldun to the National Education. This research is a library research by using the method of collecting data is documentation research method, the research model by searching the data using the record of events that have passed such monumental works of Ibn Khaldun. From the analysis that has been done can be concluded that there is relevance of Ibn Khaldun's concept of Islamic education to national education is characterized among other things by the similarity of the concept that the main object of education is a human being, in which man is composed of several basic elements are interrelated and can not be separated from each other.
The (Re)Turn to History: A Comment on Wiebe E. Bijker, "Do Not Despair: There Is Life After Constructivism"

What was distinctive about the concept of a socio-technical system that was developed in these studies was the way in which it overlayed a meticulous dissection of the labor process, its stages, divisions and relations of command, with an equally fine-meshed network of intra-psychical, inter-individual, and inter-group forces, tensions, conflicts, and anxieties. Trist and his colleagues thus claimed that the technology did not determine the relations of work. (Rose 1989,91)
Capturing and using software architecture knowledge for architecture-based software development

Management of architecture knowledge is vital for improving an organization's architectural capabilities. Despite the recognition of the importance of capturing and reusing architecture knowledge, there is no suitable support mechanism. We have developed a conceptual framework to provide appropriate guidance and tool support for making tacit or informally described architecture knowledge explicit. This framework identifies different approaches to capturing implicit architecture knowledge. We discuss different usages of the captured knowledge to improve the effectiveness of architecture processes. This paper also presents a prototype of a Web-based architecture knowledge management tool to support the storage and retrieval of the captured knowledge. The paper concludes with open issues that we plan to address in order to successfully transfer this support mechanism for capturing and using architecture knowledge to the industry.
SWAT: a lightweight load balancing method for multitenant databases

Multitenant databases achieve cost efficiency through the consolidation of multiple small tenants. However, performance isolation is an inherent problem in multitenant databases due to resource sharing among the tenants. That is, a bursty workload from a co-located tenant, i.e., a noisy neighbor, may affect the performance of the other tenants sharing the same system resources. We address this issue by using a load balancing method that is based on database replica swap. Unlike the traditional data migration-based load balancing, replica swap-based load balancing does not incur data movement, which makes it highly resource- and time-efficient. We propose a novel method of choosing which tenants should be subject to swaps. Our experimental results show that swap-based load balancing effectively reduces the number of SLA violations, which is the main performance metric we choose.
Leveraging Social Bookmarks from Partially Tagged Corpus for Improved Web Page Clustering

Automatic clustering of Web pages helps a number of information retrieval tasks, such as improving user interfaces, collection clustering, introducing diversity in search results, etc. Typically, Web page clustering algorithms use only features extracted from the page-text. However, the advent of social-bookmarking Web sites, such as StumbleUpon.com and Delicious.com, has led to a huge amount of user-generated content such as the social tag information that is associated with the Web pages. In this article, we present a subspace based feature extraction approach that leverages the social tag information to complement the page-contents of a Web page for extracting beter features, with the goal of improved clustering performance. In our approach, we consider page-text and tags as two separate views of the data, and learn a shared subspace that maximizes the correlation between the two views. Any clustering algorithm can then be applied in this subspace. We then present an extension that allows our approach to be applicable even if the Web page corpus is only partially tagged, that is, when the social tags are present for not all, but only for a small number of Web pages. We compare our subspace based approach with a number of baselines that use tag information in various other ways, and show that the subspace based approach leads to improved performance on the Web page clustering task. We also discuss some possible future work including an active learning extension that can help in choosing which Web pages to get tags for, if we only can get the social tags for only a small number of Web pages.
Hierarchical Label Propagation and Discovery for Machine Generated Email

Machine-generated documents such as email or dynamic web pages are single instantiations of a pre-defined structural template. As such, they can be viewed as a hierarchy of template and document specific content. This hierarchical template representation has several important advantages for document clustering and classification. First, templates capture common topics among the documents, while filtering out the potentially noisy variabilities such as personal information. Second, template representations scale far better than document representations since a single template captures numerous documents. Finally, since templates group together structurally similar documents, they can propagate properties between all the documents that match the template. In this paper, we use these advantages for document classification by formulating an efficient and effective hierarchical label propagation and discovery algorithm. The labels are propagated first over a template graph (constructed based on either term-based or topic-based similarities), and then to the matching documents. We evaluate the performance of the proposed algorithm using a large donated email corpus and show that the resulting template graph is significantly more compact than the corresponding document graph and the hierarchical label propagation is both efficient and effective in increasing the coverage of the baseline document classification algorithm. We demonstrate that the template label propagation achieves more than 91% precision and 93% recall, while increasing the label coverage by more than 11%.