Miracle-dz/UniFAR-FTUs huggingface dataset:
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila

DroID (http://droidb.org/), the Drosophila Interactions Database, is a comprehensive public resource for Drosophila gene and protein interactions. DroID contains genetic interactions and experimentally detected protein–protein interactions curated from the literature and from external databases, and predicted protein interactions based on experiments in other species. Protein interactions are annotated with experimental details and periodically updated confidence scores. Data in DroID is accessible through user-friendly, intuitive interfaces that allow simple or advanced searches and graphical visualization of interaction networks. DroID has been expanded to include interaction types that enable more complete analyses of the genetic networks that underlie biological processes. In addition to protein–protein and genetic interactions, the database now includes transcription factor–gene and regulatory RNA–gene interactions. In addition, DroID now has more gene expression data that can be used to search and filter interaction networks. Orthologous gene mappings of Drosophila genes to other organisms are also available to facilitate finding interactions based on gene names and identifiers for a number of common model organisms and humans. Improvements have been made to the web and graphical interfaces to help biologists gain a comprehensive view of the interaction networks relevant to the genes and systems that they study.
What impact do student-led demonstrations versus teacher-led demonstrations have on the retention rate of AP biology students?

In this investigation strategies were implemented with the purpose of improving student engagement and learning in the biology classroom. I investigated whether or not a student-led demonstration versus a teacher-led demonstration had an impact on the retention rate of AP biology students. A progressive Bloom’s Taxonomy technique was used in accordance with a student-led demonstration. I believe that because of the student-led demonstrations and a progressive Bloom’s Taxonomy technique, students reached a higher level of Bloom’s Taxonomy, became self-sustained critical thinkers, and in turn supported their own higher level thinking. This led to an understanding of a topic and long term memory recognition. The participating student had a positive affect on him/herself, the teacher and also my colleagues.
Single‐shot magnetic resonance spectroscopic imaging with partial parallel imaging

A magnetic resonance spectroscopic imaging (MRSI) pulse sequence based on proton–echo‐planar‐spectroscopic‐imaging (PEPSI) is introduced that measures two‐dimensional metabolite maps in a single excitation. Echo‐planar spatial–spectral encoding was combined with interleaved phase encoding and parallel imaging using SENSE to reconstruct absorption mode spectra. The symmetrical k‐space trajectory compensates phase errors due to convolution of spatial and spectral encoding. Single‐shot MRSI at short TE was evaluated in phantoms and in vivo on a 3‐T whole‐body scanner equipped with a 12‐channel array coil. Four‐step interleaved phase encoding and fourfold SENSE acceleration were used to encode a 16 × 16 spatial matrix with a 390‐Hz spectral width. Comparison with conventional PEPSI and PEPSI with fourfold SENSE acceleration demonstrated comparable sensitivity per unit time when taking into account g‐factor–related noise increases and differences in sampling efficiency. LCModel fitting enabled quantification of inositol, choline, creatine, and N‐acetyl‐aspartate (NAA) in vivo with concentration values in the ranges measured with conventional PEPSI and SENSE‐accelerated PEPSI. Cramer–Rao lower bounds were comparable to those obtained with conventional SENSE‐accelerated PEPSI at the same voxel size and measurement time. This single‐shot MRSI method is therefore suitable for applications that require high temporal resolution to monitor temporal dynamics or to reduce sensitivity to tissue movement. Magn Reson Med, 2009. © 2008 Wiley‐Liss, Inc.
Induction of CD8+ T-cell responses against novel glioma-associated antigen peptides and clinical activity by vaccinations with {alpha}-type 1 polarized dendritic cells and polyinosinic-polycytidylic acid stabilized by lysine and carboxymethylcellulose in patients with recurrent malignant glioma.

PURPOSE A phase I/II trial was performed to evaluate the safety and immunogenicity of a novel vaccination with α-type 1 polarized dendritic cells (αDC1) loaded with synthetic peptides for glioma-associated antigen (GAA) epitopes and administration of polyinosinic-polycytidylic acid [poly(I:C)] stabilized by lysine and carboxymethylcellulose (poly-ICLC) in HLA-A2(+) patients with recurrent malignant gliomas. GAAs for these peptides are EphA2, interleukin (IL)-13 receptor-α2, YKL-40, and gp100. PATIENTS AND METHODS Twenty-two patients (13 with glioblastoma multiforme [GBM], five with anaplastic astrocytoma [AA], three with anaplastic oligodendroglioma [AO], and one with anaplastic oligoastrocytoma [AOA]) received at least one vaccination, and 19 patients received at least four vaccinations at two αDC1 dose levels (1 × or 3 × 10(7)/dose) at 2-week intervals intranodally. Patients also received twice weekly intramuscular injections of 20 μg/kg poly-ICLC. Patients who demonstrated positive radiologic response or stable disease without major adverse events were allowed to receive booster vaccines. T-lymphocyte responses against GAA epitopes were assessed by enzyme-linked immunosorbent spot and HLA-tetramer assays. RESULTS The regimen was well-tolerated. The first four vaccines induced positive immune responses against at least one of the vaccination-targeted GAAs in peripheral blood mononuclear cells in 58% of patients. Peripheral blood samples demonstrated significant upregulation of type 1 cytokines and chemokines, including interferon-α and CXCL10. Nine (four GBM, two AA, two AO, and one AOA) achieved progression-free status lasting at least 12 months. One patient with recurrent GBM demonstrated sustained complete response. IL-12 production levels by αDC1 positively correlated with time to progression. CONCLUSION These data support safety, immunogenicity, and preliminary clinical activity of poly-ICLC-boosted αDC1-based vaccines.
Möbius Transformations For Global Intrinsic Symmetry Analysis

The goal of our work is to develop an algorithm for automatic and robust detection of global intrinsic symmetries in 3D surface meshes. Our approach is based on two core observations. First, symmetry invariant point sets can be detected robustly using critical points of the Average Geodesic Distance (AGD) function. Second, intrinsic symmetries are self‐isometries of surfaces and as such are contained in the low dimensional group of Möbius transformations. Based on these observations, we propose an algorithm that: 1) generates a set of symmetric points by detecting critical points of the AGD function, 2) enumerates small subsets of those feature points to generate candidate Möbius transformations, and 3) selects among those candidate Möbius transformations the one(s) that best map the surface onto itself. The main advantages of this algorithm stem from the stability of the AGD in predicting potential symmetric point features and the low dimensionality of the Möbius group for enumerating potential self‐mappings. During experiments with a benchmark set of meshes augmented with human‐specified symmetric correspondences, we find that the algorithm is able to find intrinsic symmetries for a wide variety of object types with moderate deviations from perfect symmetry.
Context Independent Term Mapper for European Languages

In this paper the author presents a new context independent method for bilingual term mapping using maximised character alignment maps. The method tries to particularly address mapping of multi-word terms and compound terms that are extracted from comparable corpora. The method allows integrating linguistic resources (e.g., probabilistic dictionaries and character based transliteration systems) that significantly increase the mapping recall while maintaining a stable precision. The term mapping method has been automatically evaluated using the EuroVoc thesaurus with varying availability of linguistic resources and on terms extracted from Latvian-English medical domain comparable corpus collected from the Web. The paper shows that the results significantly outperform previously reported results on the same evaluation corpus.
A Quantitative Evaluation Model for Choosing Efficient Redundancy Strategies over Clouds

Reliability has always been one of the key issues that draw widespread concerns since the rise of cloud computing. While most cloud systems use replication to ensure high reliability, some scholars incline to try erasure codes in the interest of space efficiency. Comparison of performance and reliability between replication and erasure coding have been widely analyzed by many researchers, but effort to make a thorough understanding of this issue is quite few. In this paper, we defined a quantitative model aimed at comprehensively evaluating the relative merits of the two redundancy schemes in seven metrics (availability, reliability, storage, performance, bandwidth, energy and dollar cost) which will be detailed next, and we exploited this model to provide a reference for Cloud Service Providers (CSPs for short) to set up the right configurations for their cloud file systems. In addition, we presented a scheme to decide on which one of the two redundancy schemes more suitable for a given cloud storage system.
Counting channels: a tutorial guide on ion channel fluctuation analysis.

Ion channels open and close in a stochastic fashion, following the laws of probability. However, distinct from tossing a coin or a die, the probability of finding the channel closed or open is not a fixed number but can be modified (i.e., we can cheat) by some external stimulus, such as the voltage. Single-channel records can be obtained using the appropriate electrophysiological technique (e.g., patch clamp), and from these records the open probability and the channel conductance can be calculated. Gathering these parameters from a membrane containing many channels is not straightforward, as the macroscopic current I = iNP(o), where i is the single-channel current, N the number of channels, and P(o) the probability of finding the channel open, cannot be split into its individual components. In this tutorial, using the probabilistic nature of ion channels, we discuss in detail how i, N, and P(o max) (the maximum open probability) can be obtained using fluctuation (nonstationary noise) analysis (Sigworth FJ. G Gen Physiol 307: 97-129, 1980). We also analyze the sources of possible artifacts in the determination of i and N, such as channel rundown, inadequate filtering, and limited resolution of digital data acquisition by use of a simulation computer program (available at www.cecs.cl).
Automatic Liver Segmentation and Hepatic Fat Fraction Assessment in MRI

Automated assessment of hepatic fat fraction is clinically important. A robust and precise segmentation would enable accurate, objective and consistent measurement of liver fat fraction for disease quantification, therapy monitoring and drug development. However, segmenting the liver in clinical trials is a challenging task due to the variability of liver anatomy as well as the diverse sources the images were acquired from. In this paper, we propose an automated and robust framework for liver segmentation and assessment. It uses single statistical atlas registration to initialize a robust deformable model to get fine segmentation. Fat fraction map is computed by using chemical shift based method in the delineated region of liver. This proposed method is validated on 14 abdominal magnetic resonance (MR) volumetric scans. The qualitative and quantitative comparisons show that our proposed method can achieve better segmentation accuracy with less variance comparing with an automatic graph cut method. Experimental results demonstrate the promises of our assessment framework.
Relationship between hOGG 1 Ser 326 Cys gene polymorphism and coronary artery lesions in patients with diabetes mellitus

To study the relationship between human 8-oxoguanine glycosylase (hOGG1) Ser326Cys gene polymorphism and coronary artery lesions in patients with diabetes mellitus, we analyzed 323 patients with diabetic mellitus, who underwent coronary angiography. Using PCR-RFLP, these patients were grouped into three genotypes: Cys/Cys (n=85), Ser/Ser (n=121), and Ser/Cys (n=117). Several clinical data, including history of diseases and biochemical indices were recorded. hOGG1 mRNA expression and 8-hydroxy deoxyguanosine (8-OHdG) were measured by RT-PCR and ELISA, respectively. The quantities and severity of coronary artery with lesions were analyzed from coronary angiography. The Gensini and SYNTAX scores were detected by the unitary criteria. The 8-OHdG levels showed statistical difference among the three genotypes (F=21.56, P<0.05). Also, 8-OHdG in Cys/Cys genotype was higher than Ser/Ser and Ser/Cys genotype (q=2.32, q=3.12, P<0.05). In terms of the expression of hOGGl mRNA, the measure of hOGGl/β-actin showed significant difference among the three groups (F=12.56, P<0.05). On comparing two groups, hOGGl/β-actin in Cys/Cys genotype was higher thanSer/Ser and Ser/Cys genotypes (q=2.32, q=3.12, P<0.05). Percentage of 3-vessel lesions was high in Cys/Cys genotype and percentage of 1-vessel lesions was low in Ser/Cys genotype. Gensini and SYNTAX scores and ratio of complex lesions were significantly higher in the Cys/Cys genotype than the other two genotypes (FGensini=47.16, FSYNTAX=55.12; P<0.05). hOGG1 Ser326Cys polymorphism showed correlation with coronary artery lesions in patients with diabetes mellitus, and Cys/Cys genotype may have more impact on the severity of lesions.
A novel word reordering method for statistical machine translation

Word order differences between source and target languages pose a serious challenge to statistical machine translation (SMT). Pre-ordering, an approach that reorders source words into a target-word-like order as a preprocessing step, has been shown effective in handling word order between different languages and improving translation performance of SMT. In this paper, we propose a novel word reordering method based on the pre-ordering framework. Instead of using a supervised parser trained on a monolingual treebank, our method extracts bilingual structural information for reordering from automatically wordaligned sentence pairs into dependency-tree-like structures, then learns a reordering model by training a dependency parser on this extracted pseudo-treebank. Experiment results show that our pre-ordering method is effective in permuting source words to resemble word order of the target language, and improving translation quality.
Testing whether jumps have finite or infinite activity

We propose statistical tests to discriminate between the finite and infinite activity of jumps in a semimartingale discretely observed at high frequency. The two statistics allow for a symmetric treatment of the problem: we can either take the null hypothesis to be finite activity, or infinite activity. When implemented on high-frequency stock returns, both tests point toward the presence of infinite-activity jumps in the data.
Identifying new categories in community question answering archives: a topic modeling approach

Community Question Answering (CQA) services have evolved into a popular way of information seeking and providing. User-posted questions in CQA are generally organized into hierarchical categories. In this paper, we define and study a novel problem which is referred to as New Category Identification (NCI) in CQA question archives. New Category Identification is primarily concerned with detecting and characterizing new or emerging categories which are not included in the existing category hierarchy. We define this problem formally, and propose both unsupervised and semi-supervised topic modeling methods to solve it. Experiments with a ground-truth set built from Yahoo! Answers show that our methods identify and interpret new categories effectively.
The Reduction of the State Vector and Limitations on Measurement in the Quantum Mechanics of Closed Systems

Measurement is a fundamental notion in the usual approximate quantum mechanics of measured subsystems. Probabilities are predicted for the outcomes of measurements. State vectors evolve unitarily in between measurements and by reduction of the state vector at measurements. Probabilities are computed by summing the squares of amplitudes over alternatives which could have been measured but weren't. Measurements are limited by uncertainty principles and by other restrictions arising from the principles of quantum mechanics. This essay examines the extent to which those features of the quantum mechanics of measured subsystems that are explicitly tied to measurement situations are incorporated or modified in the more general quantum mechanics of closed systems in which measurement is not a fundamental notion. There, probabilities are predicted for decohering sets of alternative time histories of the closed system, whether or not they represent a measurement situation. Reduction of the state vector is a necessary part of the description of such histories. Uncertainty principles limit the possible alternatives at one time from which histories may be constructed. Models of measurement situations are exhibited within the quantum mechanics of the closed system containing both measured subsystem and measuring apparatus. Limitations are derived on the existence of records for the outcomes of measurements when the initial density matrix of the closed system is highly impure. (Festschrift for Dieter Brill).
BURSTY TOPIC DETECTION FROM TWITTER USING SPATIO-TEMPORAL HASHTAG CLUSTERING

Twitter Monitor, a system that performs trend detection over the Twitter stream. The system identifies emerging topics (i.e. ‘trends’) on Twitter in real time and provides meaningful analytics that synthesize an accurate description of each topic. In this paper, we focus on hierarchical spatio-temporal hashtag clustering techniques. Our system has the following features: (1) Exploring events (hashtag clusters) with different space granularity. Users can zoom in and out on maps to find out what is happening in a particular area. (2) Exploring events with different time granularity. Users can choose to see what is happening today or in the past week. (3) Efficient single-pass algorithm for event identification, which provides human-readable hashtag clusters. (4) Efficient event ranking which aims to find burst events and localized events given a particular region and time frame. To support aggregation with different space and time granularity, we propose a data structure called S TREAMCUBE, which is an extension of the data cube structure from the database community with spatial and temporal hierarchy. To achieve high scalability, we propose a divide-and-conquer method to construct the STREAMCUBE. To support flexible event ranking with different weights, we proposed a top-k based index. Keyword: Topic Sketch, tweet stream, bursty topic, real time
ERG is specifically associated with ETS-2 and ETV-4, but not with ETS-1, in prostate cancer

The erythroblast transformation-specific (ETS) family of transcription factors plays important roles in both physiological and pathological conditions. Even though many studies have focused on single ETS factors within a single tissue and within the context of specific promoters, the functional impact of multiple ETS members present within a specific cell type has not yet been investigated, especially in prostate cancer (PCa). As the most prominent gene rearrangement in PCa leads to the overexpression of the ETS-related gene (ERG), the aim of this study was to investigate whether ERG is part of a complex integrated transcriptional network that involves other ETS factors. More specifically, as the ETS family consists of 27 members, we focused our efforts initially on investigating whether ERG is associated with the three family members, ETS-1, ETS-2 and ETS variant gene-4 (ETV-4), in PCa as a proof of principle. Using western blot analysis, we show that ERG, ETS-1, ETS-2 and ETV-4 are expressed in PC3 cell nuclear extracts and in protein lysates prepared from human PCa prostatectomy specimens. Immunoprecipitations using an anti-ERG antibody were used with PC3 cell nuclear extracts as well as with a pooled protein lysate sample prepared from the PCa tissue samples of five patients. Importantly, our results revealed that ERG is specifically associated with ETS-2 and ETV-4, but not with ETS-1, in PC3 cell nuclear extracts and PCa tissue protein lysates. Our findings strongly support the notion that ERG is part of a complex integrated transcriptional network that involves other ETS factors, which are likely to cooperate or influence the activity of ERG in PCa. The functional impact of multiple ETS factors being associated with ERG in PCa requires further study, as it may provide insights into the mechanism by which ERG exerts its influence in PCa and may subsequently contribute to our understanding of the molecular basis of PCa.
Stochastic Modeling and Optimization in a Microgrid: A Survey

The future smart grid is expected to be an interconnected network of small-scale and self-contained microgrids, in addition to a large-scale electric power backbone. By utilizing microsources, such as renewable energy sources and combined heat and power plants, microgrids can supply electrical and heat loads in local areas in an economic and environment friendly way. To better adopt the intermittent and weather-dependent renewable power generation, energy storage devices, such as batteries, heat buffers and plug-in electric vehicles (PEVs) with vehicle-to-grid systems can be integrated in microgrids. However, significant technical challenges arise in the planning, operation and control of microgrids, due to the randomness in renewable power generation, the buffering effect of energy storage devices and the high mobility of PEVs. The two-way communication functionalities of the future smart grid provide an opportunity to address these challenges, by offering the communication links for microgrid status information collection. However, how to utilize stochastic modeling and optimization tools for efficient, reliable and economic planning, operation and control of microgrids remains an open issue. In this paper, we investigate the key features of microgrids and provide a comprehensive literature survey on the stochastic modeling and optimization tools for a microgrid. Future research directions are also identified.
Syntheses , Characterizations of Copper ( II ) with Amine Coupled Naphthoquinone Complex as Antioxidant

The presented study investigates application of Cu(II) complex (Cu-1) with Amine coupled to Naphthoquinone as Antioxidant agent. Cu-1 complex is synthesized with ligand L1 formed by amine coupling at C-2 positions of naphthoquinones. Cu-1 performs valence tautomeric distorted octahedral coordination established by IR, EPR, magnetic susceptibility measurements, and CV studies. Cu-1 also acts as functional model of SOD confirmed by DPPH method. Cu-1 with L-1 is tested for antioxidant activities. Their antioxidant activities are screened on DPPH assay. Both activities are compared & correlated with structures and etransfer routes.