Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring Microbial Genome Sequences to Identify Protein Families on the Grid

The analysis of microbial genome sequences can identify protein families that provide potential drug targets for new antibiotics. With the rapid accumulation of newly sequenced genomes, this analysis has become a computationally intensive and data-intensive problem. This paper describes the development of a Web-service-enabled, component-based, architecture to support the large-scale comparative analysis of complete microbial genome sequences and the subsequent identification of orthologues and protein families (Microbase). The system is coordinated through the use of Web-service-based notifications and integrates distributed computing resources together with genomic databases to realize all-against-all comparisons for a large volume of genome sequences and to present the data in a computationally amenable format through a Web service interface. We demonstrate the use of the system in searching for orthologues and candidate protein families, which ultimately could lead to the identification of potential therapeutic targets.
Saying What You're Looking For: Linguistics Meets Video Search

We present an approach to searching large video corpora for clips which depict a natural-language query in the form of a sentence. Compositional semantics is used to encode subtle meaning differences lost in other approaches, such as the difference between two sentences which have identical words but entirely different meaning: The person rode the horse versus The horse rode the person. Given a sentential query and a natural-language parser, we produce a score indicating how well a video clip depicts that sentence for each clip in a corpus and return a ranked list of clips. Two fundamental problems are addressed simultaneously: detecting and tracking objects, and recognizing whether those tracks depict the query. Because both tracking and object detection are unreliable, our approach uses the sentential query to focus the tracker on the relevant participants and ensures that the resulting tracks are described by the sentential query. While most earlier work was limited to single-word queries which correspond to either verbs or nouns, we search for complex queries which contain multiple phrases, such as prepositional phrases, and modifiers, such as adverbs. We demonstrate this approach by searching for 2,627 naturally elicited sentential queries in 10 Hollywood movies.
A small (2.4 Mb) Bacillus cereus chromosome corresponds to a conserved region of a larger (5.3 Mb) Bacillus cereus chromosome

We have determined the sizes of the chromosomes of six Bacillus cereus strains (range 2.4–4.3 Mb) and constructed a physical map of the smallest B. cereus chromosome (2.4 Mb). This map was compared to those of the chromosomes of four B. cereus strains and one B. thuringiensis strain previously determined to be 5.4‐6.3 Mb. Of more than 50 probes, 30 were localized to the same half of the larger B. cereus and B. thuringiensis chromosomes. All 30 were also present on the small chromosome. Twenty of the probes present on the other half of the larger chromosomes were either present on extrachromosomal DNA, or absent from the B. cereus strain carrying the small chromosome. We propose that the genome of B. cereus and B. thuringiensis has one constant part and another less stable part which is more easily mobilized into other genetic elements. This part of the genome is localized to one region of the chromosome and may be subject to deletions or more frequent relocations between the chromosome and episomal elements of varying sizes up to the order of megabases.
Pharmacological Modulation of AMPAR Rescues Intellectual Disability-Like Phenotype in Tm4sf2−/y Mice

Abstract Intellectual disability affects 2‐3% of the world's population and typically begins during childhood, causing impairments in social skills and cognitive abilities. Mutations in the TM4SF2 gene, which encodes the TSPAN7 protein, cause a severe form of intellectual disability, and currently, no therapy is able to ameliorate this cognitive impairment. We previously reported that, in cultured neurons, shRNA‐mediated down‐regulation of TSPAN7 affects AMPAR trafficking by enhancing PICK1‐GluA2 interaction, thereby increasing the intracellular retention of AMPAR. Here, we found that loss of TSPAN7 function in mice causes alterations in hippocampal excitatory synapse structure and functionality as well as cognitive impairment. These changes occurred along with alterations in AMPAR expression levels. We also found that interfering with PICK1‐GluA2 binding restored synaptic function in Tm4sf2−/y mice. Moreover, potentiation of AMPAR activity via the administration of the ampakine CX516 reverted the neurological phenotype observed in Tm4sf2−/y mice, suggesting that pharmacological modulation of AMPAR may represent a new approach for treating patients affected by TM4SF2 mutations and intellectual disability.
Web page rank prediction with markov models

In this paper we propose a method for predicting the ranking position of a Web page. Assuming a set of successive past top-k rankings, we study the evolution of Web pages in terms of ranking trend sequences used for Markov Models training, which are in turn used to predict future rankings. The predictions are highly accurate for all experimental setups and similarity measures.
In fl ation in the Euro Area : A Case for Monetary Indicators ? ∗

This paper examines inflation indicators for the euro area by studying the relationship between inflation, output, money and interest rates, using data spanning 1980—2001. The central finding is that both the output gap and the real money gap (the difference between the real money stock and the long-run equilibrium real money stock) contain considerable information regarding future inflation. In contrast, the Eurosystem’s money-growth indicator (the difference between nominal money growth and a reference value), the prominent “first pillar” in its monetary strategy, contains little information about future inflation, and no information beyond that contained in the output and real money gaps. The predictive performance of the output gap has improved compared to that in a previous version of this paper, most likely because of better estimation methods. JEL Classification Numbers: E42, E52, E58
A Comparative Analysis of RE Approaches for MAS

Poor requirements are one of the principal reasons for collapse of software projects. Detecting the requirements errors at the final stage intensifies the efforts of developers that may delay system delivery and overrun cost. Therefore to reduce the development time and cost, it necessitates a systematic and structured Requirement Engineering (RE) approach to establish a comprehensive understanding of the requirements addressed by a software product. Agent-based technology for software development has been recognized as a promising and pioneering paradigm for next generation systems. It was observed that a number of RE approaches in literature, are the rich sources of techniques facilitating various phases of RE. This work presents a year-wise comparative analysis of these RE approaches that could provide systematic guidelines to developers for an effective application of RE to Multi-Agent System (MAS).
A REPLANNING ALGORITHM FOR DECISION THEORETIC HIERARCHICAL PLANNING: PRINCIPLES AND EMPIRICAL EVALUATION

In this article, we present a replanning algorithm for a decision-theoretic hierarchical planner, illustrate the experimental methodology we designed to investigate its performance, and provide an evaluation of the algorithm. The methodology relies on an agent-based framework, in which plan failures can emerge from the interplay of the agent and the environment. Given this framework, the performance of the replanning algorithm is compared with the one of planning from scratch the solution to the planning problem by executing experiments in different domains. The empirical evaluation shows the superiority of replanning with respect to planning from scratch. However, the observation of significant differences in the data collected across planning domains confirm the importance of empirical evaluation in practical systems.
Sensitization, pathologic, and imaging findings comparing symptomatic and quiescent failed renal allografts

Late allograft failure (LAF) is a common cause of end stage renal disease. These patients face interrelated challenges regarding immunosuppression management, risk of graft intolerance syndrome (GIS), and sensitization. This retrospective study analyzes sensitization, pathology, imaging, and transfusion requirements in 33 LAFs presenting either with GIS (22) or grafts remaining quiescent (11). All patients underwent immunosuppression weaning to discontinuation at LAF. Profound increases in sensitization were noted for all groups and occurred in the GIS group prior to transplant nephrectomy (TxN). Patients with GIS experienced a major upswing in sensitization at, or before the time of their symptomatic presentation. For both GIS and quiescent grafts, sensitization appeared to be closely linked to immunosuppression withdrawal. Most transfusion naïve patients became highly sensitized. Fourteen patients in the GIS group underwent TxN which revealed grade II acute cellular rejection or worse, with grade 3 chronic active T‐cell‐mediated rejection. Blinded comparisons of computed tomography scan of GIS group revealed swollen allografts with fluid collections compared with the quiescent allografts (QAs), which were shrunken and atrophic. The renal volume on imaging and weight of explants nearly matched. Future studies should focus on interventions to avoid sensitization and GIS.
CORRELATION MODEL FOR SHADOW FADING IN MOBILE RADIO SYSTEMS

I. , and CRAIG-RYAN, s. P.: ‘High-gain, broad spectral bandwidth erbium-doped fibre amplifier pumped near 1.5&, Electron. Lett. , 1989,25, pp. 91@911 MILLER, c. A. , BRIERLEY, M. c. , and FRANCE, P. w. : ‘Optical amplification in an erbium-doped fluorozirconate fibre between 1480nm and 1600nm’. ECOC ’88,1988, part I , pp. 6669 4 SNITZER, E. , and TUMMINELLI, R. : SO,-clad fibres with selectively volatilized soft glass cores’, Opt. Lerr. , 1989, 14, pp. 757-759 5 YAMADA, M. , SHIMIZU, M. , HORIGUCHI, M. , OKAYASU, M. , and SUGITA, E. : ‘Gain characteristics of an Er”-doped multicomponent glass single-mode optical fibre’, IEEE Photonics Technol. Lett. , 1990, 2, pp. 656-658 6 LINES, M. E. , MACCHESNEY, I. B. , LYONS, K . B. , BRUCE, A. I. , MILLER, A. E. , and NASSAU, K . : ‘Calcium aluminate glasses as potential ultralow-loss optical material at 1.5-1.9pm: J . Non-Cryst. Solids, 1989,107, pp. 251-260
Collagen-Glycosaminoglycan Matrix Implantation Promotes Angiogenesis following Surgical Brain Trauma

Surgical brain injury (SBI) is unavoidable during many neurosurgical procedures intrinsically linked to postoperative neurological deficits. We have previously demonstrated that implantation of collagen glycosaminoglycan (CG) following surgical brain injury could significantly promote functional recovery and neurogenesis. In this study we further hypothesized that this scaffold may provide a microenvironment by promoting angiogenesis to favor neurogenesis and subsequent functional recovery. Using the rodent model of surgical brain injury as we previously established, we divided Sprague-Dawley male rats (weighting 300–350 g) into three groups: (1) sham (2) surgical injury with a lesion (L), and (3) L with CG matrix implantation (L + CG). Our results demonstrated that L + CG group showed a statistically significant increase in the density of vascular endothelial cells and blood vessels over time. In addition, tissue concentrations of angiogenic growth factors (such as VEGF, FGF2, and PDGF) significantly increased in L + CG group. These results suggest that implantation of a CG scaffold can promote vascularization accompanied by neurogenesis. This opens prospects for use of CG scaffolds in conditions such as brain injury including trauma and ischemia.
Model-Based Bayesian Reinforcement Learning in Large Structured Domains

Model-based Bayesian reinforcement learning has generated significant interest in the AI community as it provides an elegant solution to the optimal exploration-exploitation tradeoff in classical reinforcement learning. Unfortunately, the applicability of this type of approach has been limited to small domains due to the high complexity of reasoning about the joint posterior over model parameters. In this paper, we consider the use of factored representations combined with online planning techniques, to improve scalability of these methods. The main contribution of this paper is a Bayesian framework for learning the structure and parameters of a dynamical system, while also simultaneously planning a (near-)optimal sequence of actions.
Detecting and quantifying unusual interactions by correlating salient motion

A significant problem in scene interpretation is efficient bottom-up extraction and representation of salient features. In this paper, we address the problem of correlating salient motion at a spatio-temporal level and also across spatially separated regions since it is in the interactions that more sophisticated scene interpretation can be found. We show that it is possible to spatio-temporally locate and detect salient motion events and interactions in two contrasting scenarios using the same hierarchical co-occurrence framework. Thus generating a concise description of a dynamic scene from the sequence data alone. Results show it is possible to reduce a highly populated multi-dimensional co-occurrence matrix representing correlations between salient motion regions, to a one dimensional vector with clearly separable unusual activity. The results also show that the method inherently provides a quantifiable measure of the saliency of an interaction through its frequency of occurrence.
Some Considerations About Processing Singing Voice for Music Retrieval

The audio processing and post-processing of singing hold a fundamental role in the context of query-by-humming applications. Through the analysis of a sung query, we should perform some kind of meta-information extraction and this topic deserves the interest of the present paper. Considering the raw output of a pitch tracking algorithm, the issues of note estimation and the study of singing accuracy have been addressed. Further, we report an experiment on the deviations from pure tone intonation in performances of untrained singers.
Ethanolic Extract of Bark from Salix aegyptiaca Ameliorates 1,2-dimethylhydrazine-induced Colon Carcinogenesis in Mice by Reducing Oxidative Stress

ABSTRACT We have previously shown that ethanolic extract from bark (EEB) of Salix aegyptiaca (Musk Willow) can inhibit proliferation and motility and induce apoptosis in colon cancer cells. Tandem mass spectrometry revealed EEB to be rich in catechin, catechol, and salicin. The present study investigated the chemopreventive effect of HPLC-fingerprinted EEB on 1,2-dimethylhydrazine (DMH)-induced aberrant crypt foci (ACF) formation in mice. DMH (20 mg/kg body weight) was weekly injected subcutaneously to mice for the first 2 weeks. EEB (100 and 400 mg/kg body weight) was provided orally from the 7th to 14th week, after which colon tissues were evaluated histologically and biochemically. DMH treatment induced high number of ACF; EEB significantly reduced the number and multiplicity of ACF, along with a restoration in goblet cells and mucin accumulation. EEB supplementation improved the markers of inflammation (myeloperoxidase and neutrophil infiltration) and oxidative stress. More importantly, EEB amplified apoptosis of neoplastic cells in the colon mucosa of DMH-treated mice. It also lowered levels of markers for early transformation events such as EGFR, nuclear β-catenin, and COX-2 in colon cancer cell lines HT-29 and HCT-116. The innocuity of EEB (up to 1600 mg/kg) to mice reinforces its potential as a chemopreventive agent.
The Sonoda–Tajima Cell Collection: A Human Genetics Research Resource with Emphasis on South American Indigenous Populations

The Sonoda–Tajima Cell Collection includes cell samples obtained from a range of ethnic minority groups across the world but in particular from South America. The collection is made all the more valuable by the fact that some of these ethnic populations have since died out, and thus it will be impossible to prepare a similar cell collection again. The collection was donated to our institute, a public cell bank in Japan, by Drs Sonoda and Tajima to make it available to researchers throughout the world. The original cell collection was composed of cryopreserved peripheral blood samples that would obviously have been rapidly exhausted if used directly. We, therefore, immortalized some samples with the Epstein–Barr virus and established B-lymphoblastoid cell lines (B-LCLs). As there is continuing controversy over whether the B-LCL genome is stably maintained, we performed an array comparative genomic hybridization (CGH) analysis to confirm the genomic stability of the cell lines. The array CGH analysis of the B-LCL lines and their parental B cells demonstrated that genomic stability was maintained in the long-term cell cultures. The B-LCLs of the Sonoda–Tajima Collection will therefore be made available to interested scientists around the world. At present, 512 B-LCLs have been developed, and we are willing to increase the number if there is sufficient demand.
THE ROLE OF MERGER STAGE ON GALAXY RADIO SPECTRA IN LOCAL INFRARED-BRIGHT STARBURST GALAXIES

An investigation of the steep, high-frequency (i.e., ν ∼ 12 GHz) radio spectra among a sample of 31 local infrared-bright starburst galaxies is carried out in light of their Hubble-Space-Telescope-based merger classifications. Radio data covering as many as 10 individual bands allow for spectral indices to be measured over three frequency bins between 0.15 and 32.5 GHz. Sources having the flattest spectral indices measured at ∼2 and 4 GHz, arising from large free–free optical depths among the densest starbursts, appear to be in ongoing through post-stage mergers. The spectral indices measured at higher frequencies (i.e., ∼12 GHz) are steepest for sources associated with ongoing mergers in which their nuclei are distinct, but share a common stellar envelope and/or exhibit tidal tails. These results hold after excluding potential active galactic nuclei based on their low 6.2 μm polycyclic aromatic hydrocarbon equivalent widths. Consequently, the low-, mid-, and high-frequency spectral indices each appear to be sensitive to the exact merger stage. It is additionally shown that ongoing mergers, whose progenitors are still separated and share a common envelope and/or exhibit tidal tails, also exhibit excess radio emission relative to what is expected given the far-infrared/radio correlation, suggesting that there may be a significant amount of radio emission that is not associated with ongoing star formation. The combination of these observations, along with high-resolution radio morphologies, leads to a picture in which the steep high-frequency radio spectral indices and excess radio emission arise from radio continuum bridges and tidal tails that are not associated with star formation, similar to what is observed for so-called “taffy” galaxies. This scenario may also explain the seemingly low far-infrared/radio ratios measured for many high-z submillimeter galaxies, a number of which are merger-driven starbursts.
Refinement of an MTF-based speech dereverberation method using an optimal inverse-MTF filter

We previously proposed a speech dereverberation method based on the modulation transfer function (MTF). This method consists of power envelope restoration and carrier regeneration processes, and reduces both the loss due to degraded power envelopes and the loss of speech intelligibility. In the power envelope restoration, however, whether adaptive time-frequency division provides the best representation is still uncertain and the improvement in restoration accuracy tends to lessen as the reverberation time drastically increases. In this paper, with regard to these issues, we explain how the power envelope restoration can be improved and show that power envelope inverse filtering can be redesigned as an optimal inverse MTF.
Impaired APP activity and altered Tau splicing in embryonic stem cell-derived astrocytes obtained from an APPsw transgenic minipig

ABSTRACT Animal models of familial juvenile onset of Alzheimer's disease (AD) often fail to produce diverse pathological features of the disease by modification of single gene mutations that are responsible for the disease. They can hence be poor models for testing and development of novel drugs. Here, we analyze in vitro-produced stem cells and their derivatives from a large mammalian model of the disease created by overexpression of a single mutant human gene (APPsw). We produced hemizygous and homozygous radial glial-like cells following culture and differentiation of embryonic stem cells (ESCs) isolated from embryos obtained from mated hemizygous minipigs. These cells were confirmed to co-express varying neural markers, including NES, GFAP and BLBP, typical of type one radial glial cells (RGs) from the subgranular zone. These cells had altered expression of CCND1 and NOTCH1 and decreased expression of several ribosomal RNA genes. We found that these cells were able to differentiate into astrocytes upon directed differentiation. The astrocytes produced had decreased α- and β-secretase activity, increased γ-secretase activity and altered splicing of tau. This indicates novel aspects of early onset mechanisms related to cell renewal and function in familial AD astrocytes. These outcomes also highlight that radial glia could be a potentially useful population of cells for drug discovery, and that altered APP expression and altered tau phosphorylation can be detected in an in vitro model of the disease. Finally, it might be possible to use large mammal models to model familial AD by insertion of only a single mutation. Summary: Insight into astrocyte and radial glia pathology in an in vitro culture system derived from the APPsw pig.
Facebook Advertisements for Inexpensive Participant Recruitment Among Women in Early Pregnancy

Facebook advertisements were used to recruit nulliparous women in the first 20 weeks of pregnancy for an online survey about their childbirth preferences. A campaign of ads was targeted to women, aged 18 to 44 years, residing in the United States. The ads were viewed 10,577,381 times by 7,248,985 unique Facebook users over 18 weeks in 2011. The ad campaign yielded 6,094 clicks by 5,963 unique users at a mean cost of $0.63 per click and a unique click-through rate of 0.08%. Of those who clicked through to the study site, 18% (n = 1,075) consented to participate. The participant pool was reduced to 344 women after application of strict eligibility criteria. Participants represented 43 states and the District of Columbia, their mean age was 20.9 years (Mdn = 19.0, SD = 4.0), and their mean weeks’ gestation was 11.5 (SD = 5.8). The campaign cost was $3,821.81 or $11.11 per eligible participant.