Miracle-dz/UniFAR-FTUs huggingface dataset:
Infrastructure for Metagenome Data Management and Analysis

Metagenome sequencing projects are generating unprecedented amounts of data. Public sequence archive databases are challenged with large-scale data management issues including data storage, quick search and retrieval of the sequence data for further analysis. The sequence data is linked to the rich set of metadata attributes such as geochemical and ecological parameters for environmental projects and clinical patient information for human microbiome studies. That complex collection of heterogeneous information has to be integrated, organized and presented to the users in a meaningful and the most useful way. For the last 20 years The National Center for Biotechnology Information (NCBI) has been developing the infrastructure that allows an easy storage and distribution of various types of bimolecular data as well as data integration and easy navigation in complex information space. Here we describe NCBI resources that are used for metagenomics data management.
Designing Podcasts for Clinical Nurse Specialist Education

This is the first in a series of occasional articles in this column related to using educational technology in clinical nurse specialist education. In 2005, the New Oxford American Dictionary nominated several words for its Word of the Year including persistent vegetative state, Sudoku, bird flu, and trans fat. But ‘‘podcast’’ won. The editor-in-chief of the dictionary wrote that the word was considered in 2004, but they found that not enough people were using the word or familiar with it to recognize it as Word of the Year. In 1 short year, podcasts became so common that the editors selected the word over all of these other additions to Americans’ everyday language. Now, podcasting is becoming a common instructional delivery method in higher education. In the New Oxford American Dictionary, podcast is defined as ‘‘a digital recording of a radio broadcast or similar program, made available on the Internet for downloading to a personal audio player. ’’ Thus, there are 3 elements to podcastingVthe audio/video content, publication through Web syndication, and a mobile device for playback. When students choose to use a handheld digital device for playback, they can be mobile while listening or even watching, depending on their environment and activity. By December 2009, Apple sold more than 228 million iPods. These sales figures excluded the iPhone, which also plays podcasts. Of course, Apple is not the only company that makes handheld digital players, but it is certainly the largest, accounting for more than 73% of the market share in the United States. Coupled with other types of handheld digital players, it is safe to say that portable devices are ubiquitous and prevalent among graduate students. Podcasting is just emerging in the higher education literature, andmost publications are opinion, anecdotal experiences, or ‘‘how-to’’ articles. In 2009, Hew conducted a structured, 3-stage search of education databases and proceedings, netting 153 articles. However, he retained only 30 articles that met his inclusion criteria of being an empirical and original study of podcasting in K-12 and higher education. Hew did not search the healthcare databases, but a January 2010 search of CINAHL using the keyword ‘‘podcast*’’ and no year restriction led to 126 articles, but only 7 were classified as research. Similarly, in Medline OVID, Current
The involvement of people with lifelong disability and communication impairment in lecturing to speech-language pathology students

In order to provide appropriate service and support to people with lifelong disability, including those who use augmentative and alternative communication (AAC), speech-language pathologists need to develop positive attitudes to people with disability and a holistic approach. The aim of this paper was to explore final year students' and new graduates' perceptions of the impact of lectures by people with lifelong disability on their attitudes and learning. Fourteen final year speech-language pathology students and nine graduates who had been practising for a year participated in four focus groups to discuss their perceptions of four 50-minute lectures by people with lifelong disability and communication impairment. A content analysis of the focus group transcripts revealed five themes; understanding the perspectives of people with disability, seeing the person as a whole, attitudes, working in the field, and gaps in the lectures. Overall there were few differences between the groups that were not accounted for by clinical experience. Participants agreed that the lectures were interesting and informative and provided new insights into lifelong disability, but were an adjunct to a learning process that also required theoretical lectures or clinical practice.
Requirements for translocation of periplasmic domains in polytopic membrane proteins

Periplasmic domains of cytoplasmic membrane proteins require export signals for proper translocation. These signals were studied by using a MalF-alkaline phosphatase fusion in a genetic selection that allowed the isolation of mislocalization mutants. In the original construct, alkaline phosphatase is fused to the second periplasmic domain of the membrane protein, and its activity is thus confined exclusively to the periplasm. Mutants that no longer translocated alkaline phosphatase were selected by complementation of a serB mutation. A total of 11 deletions in the amino terminus were isolated, all of which spanned at least the third transmembrane segment. This domain immediately precedes the periplasmic domain to which alkaline phosphatase was fused. Our results obtained in vivo support the model that amino-terminal membrane-spanning segments are required for translocation of large periplasmic domains. In addition, we found that the inability to export the alkaline phosphatase domain could be suppressed by a mutation, prlA4, in the secretion apparatus.
A low-latency low-complexity scheme for efficient channel state feedback in MIMO multiuser communications

In order to exploit the full degrees of freedom of multi-antenna multi-user systems, accurate channel state information at the transmitter is needed. We consider a low latency and low complexity design for a closed-loop channel state information feedback scheme, where user terminals feed back their channel state information simultaneously to a multi-antenna base station. The underlying theoretical problem consists of the lossy transmission of multiple independent analog sources over a Gaussian MIMO Multi-Access Channel (MIMO-MAC), under a Mean-Square Error (MSE) criterion. We analyze distortion exponent, i.e., the order of decrease of the channel state information MSE for increasing channel SNR, and design very simple "almost uncoded" schemes that outperform conventional approaches such as finite-rate feedback and uncoded "analog" feedback.
Multiple kernel learning with adaptive kernel method for computer-aided detection of colonic polyps

Computer-aided detection (CAD) of colonic polyps, as a second reader for computed tomographic colonography (CTC) screening, has earned extensive research interest over the past decades. False positive (FP) reduction in the CAD system plays a crucial role in detecting the polyps. To improve the performance of FP reduction and better assist the physician's diagnosis, we propose a multiple kernel learning (MKL) with adaptive kernel method for CAD of colonic polyps, called AK-MKL method. Using the multiple kernel learning technique, the AK-MKL method learns a synthesized classifier which is an optimal combination of a collection of base classifiers. Performance evaluation for the presented AK-MKL method was performed on a CTC database. In terms of the AUC (area under the curve of receiver operating characteristic) merit, the experimental results showed that our AK-MKL method achieves better performance, compared with other two different methods, named the basic multiple kernel learning method (MKL) and the SVM with adaptive kernel (AK-SVM) method, respectively.
Using Rules for Assessing and Improving Data Quality: A Case Study for the Norwegian State of Estate Report

The Norwegian State of Estate (SoE) report service – a service providing information about central government properties in Norway – is a result of integrating cross-domain government data originating from the Norwegian cadastral system, Business Entity Register, Building Accessibility Register and Statsbygg’s property management system. This paper presents a rule-based approach to assess and improve the quality of the data upon which the SoE service is built. The approach develops a set of rules to specify a common data schema, rules for data quality assessment, and three dedicated measurement metrics for data integration. Application scenarios of the approach in identify-ing data inconsistencies in the sources are exemplified with strategies to improve data quality.
Intranasal delivery of tapentadol hydrochloride–loaded chitosan nanoparticles: formulation, characterisation and its in vivo evaluation

Abstract The aim of the present investigation was to formulate tapentadol hydrochloride–loaded chitosan nanoparticles (CS-NPs) for nose to brain delivery. Chitosan nanoparticles were prepared using ionotropic gelation technique. Optimisation of the formulation and process parameters was done using Box–Behnken Design. The entrapment efficiency, drug loading, Z-average size and zeta potential of the optimised batch were 63.49 ± 1.61%, 17.25 ± 1.38%w/w, 201.2 ± 1.5 nm and +49.3 mV, respectively. In-vitro release study showed 84.04 ± 1.53% drug release after 28 h, while ex vivo studies indicated higher permeation of CS-NPs through nasal mucosa. The nanoparticles exhibited good mucoadhesiveness, haemocompatibility and safety as evidenced by histopathology. The results of the pharmacodynamic study revealed prolongation of the analgesic activity. The intranasal instillation of CS-NPs resulted in the higher concentrations in brain compared to the drug solution and intravenous administration of CS-NPs. In a nutshell, intranasal administration of tapentadol hydrochloride–loaded CS-NPs is a promising approach for effective pain management.
Differential Regulation of Lipid and Protein Kinase Activities of Phosphoinositide 3-Kinase γ in Vitro

Abstract G protein sensitive phosphoinositide 3-kinase γ(PI3Kγ) has been characterised as a pleiotropic signalling protein expressing lipid kinase and protein kinase activities. Whereas the regulation of the lipid kinase activity has been investigated in detail, the regulatory features of PI3Kγ protein kinase activity are unknown. Here we report that Gβγ subunits of heterotrimeric G proteins induce a biphasic response of PI3Kγ autophosphorylation in vitro, which contrasts the regulatory effects of the G proteins on PI3Kγ lipid kinase activity. In addition to autophosphorylation PI3Kγ is able to catalyse transphosphorylation of the adapter protein p101 and the protein kinase MEK-1. In the presence of the p101, Gβγ affects PI3Kγ protein kinase activities in a complex manner. In summary, the differential regulatory effects of heterotrimeric G proteins on PI3Kγ lipid and protein kinase activities in vitro reflect the functional diversity of the enzyme observed in vivo.
Soft-actuators in cyclic motion: Analytical optimization of stiffness and pre-load

In this paper, we study the role of soft actuation in the reduction of the energy cost for mechanical systems that perform cyclic tasks. The objective is to determine the optimal stiffness value and spring pre-load such that a given cost functional is minimized. For the analysis, we consider both fully actuated and underactuated mechanical systems using elastic actuators which, depending on how and where the springs are placed w.r. t. the actuator and the load, can be Series Elastic Actuators (SEAs) or Parallel Elastic Actuators (PEAs). The energy consumption depends not only on the actuation parameters but also on the trajectories followed to perform a given cyclic task. We show that the general problem in which both joint trajectories and actuation parameters are the optimization variables, can be cast as a simpler problem in which optimization regards only joint trajectories. Simulations of fully actuated and underactuted compliant robots are reported to demonstrate the effectiveness of the method. Although the stiffness optimization method is analytical in nature, it is directly applicable to existing systems whose model is unknown. A model-free experimental application on a prototype of a hopping robot with SEA is presented.
Biblioteki metagenomowe jako zrodlo genow przydatnych w biotechnologii

The vast majority of microorganisms cannot be cultured under laboratory conditions. It was estimated that over 99% of microbial genetic information are inaccessible due to the inability to isolate and culture bacteria. It is also widely known that among those uncultured organisms there are such that bear the genes which are interesting from the biotechnological point of view, i.e. coding for novel enzymes (lipases, amylases, cellulases, polymerases etc.), responsible for resistance to various chemical substances (heavy metals, aromatic compounds, pesticides, antibiotics), or the genes encoding the elements of biosynthetic pathways (for instance producing novel antibiotics). Recently, the methods have been developed that allow (i) isolation and purification of environmental DNA, (ii) construction of random fragment libraries of such DNA, and (iii) effective screening of those libraries in search for interesting genes. These methods are collectively known as ‘metagenomics’ or ‘environmental genomics’. We aim to review the metagenomic methods, which will be done in Part I of our paper, and to present the up – to – date achievements and future perspectives for obtaining biotechnologically important genes from environmental samples in Part II. The main attention will be paid to soil metagenomics, as this kind of environment seems to be the most promising in terms of microbial biodiversity and the spectrum of biochemical reactions performed by inhabiting bacteria. We will treat the perspectives for isolation of novel, useful genes such as those coding for biosynthesis of antibiotics, organic compounds degrading pathways, and heavy metal resistance and prospects for their biotechnological application. Assessing the microbial biodiversity through metagenomic methods will also be covered.
High field human imaging

This review article examines the state of knowledge regarding human imaging using MRI at high main magnetic field strengths. The article starts with a summary of the technical issues associated with magnetic field strengths in the range of 3–8 T, including magnet characteristics and the properties of radiofrequency magnetic fields, with special reference to sensitivity, power deposition, and homogeneity. The published data on tissue‐water relaxation times in the brain is tabulated and the implications for contrast and pulse sequence implementation is elucidated. The behavior of the major fast imaging sequences, fast low angle shot (FLASH), rapid acquisition with relaxation enhancement (RARE), and echo planar imaging (EPI), is examined in this context. A number of anatomical images from 3 T systems are presented as examples. Particular attention is given to various forms of vascular imaging, namely, time of flight angiography, venography, and arterial spin labeling. The most complex changes in contrast with main magnetic field strength are in activation studies utilizing the blood oxygen level dependent mechanism, which are examined in detail. Improvements in spatial specificity are emphasized, particularly in conjunction with spin‐echo imaging. The article concludes with a discussion of the current status and the potential impact of technical developments such as parallel imaging. J. Magn. Reson. Imaging 2003;18:519–529. © 2003 Wiley‐Liss, Inc.
Alterations in the relative abundance of gene transcripts in preimplantation bovine embryos cultured in medium supplemented with either serum or PVA

In preimplantation bovine embryos, the relative abundance of various developmentally important gene transcripts was determined by a semi‐quantitative RT‐PCR assay to analyze the effects of two medium supplements, serum or polyvinyl alcohol (PVA). Development to morula, blastocyst, and hatched blastocyst stages was higher (P ≤ 0.05) in medium supplemented with serum than in medium supplemented with PVA. Connexin43 mRNA expression virtually disappeared from the 8–16 cell stage onward, but reappeared in the hatched blastocyst in serum‐supplemented medium, whereas it was detected in PVA‐derived embryos throughout development. No differences were found for plakophilin mRNA between both culture groups. Desmocollin II mRNA showed a sharp increase at the blastocyst stage in both groups with a higher transcription level in PVA‐generated embryos. A significant difference in desmocollin III transcripts was detectable at the 8–16‐cell stage between serum‐ and PVA‐derived embryos. Transcripts for desmoglein 1 and desmocollin I were not detected at any preimplantation stage, irrespective of medium supplementation. The relative abundance of glucosetransporter‐1 mRNA was significantly increased at the 8–16‐cell stage in embryos produced in medium supplemented with PVA, but not serum. Heat shock protein and poly(A)polymerase mRNA were continuously expressed during preimplantation development in both culture groups. Although poly(A)polymerase mRNA was significantly elevated in PVA‐ over serum‐derived embryos, heat shock protein mRNA expression was significantly enhanced in serum‐generated embryos over PVA‐derived embryos. Interferon tau mRNA showed a significant increase at the hatched blastocyst stage only in PVA‐supplemented medium. These data suggest that alterations in mRNA expression are associated with culture environment. Timing and magnitude of the alterations varied among the different transcripts and were significantly affected by the presence of exogenous protein in a stage‐specific manner, predominantly at critical developmental time points. Mol. Reprod. Dev. 53:8–18, 1999. © 1999 Wiley‐Liss, Inc.
Temporal patterns in the occurrence of selected tropical fishes in mangrove creeks: implications for the fisheries management in north Brazil

Com o objetivo de examinar padroes temporais em recrutamento de uma ictiofauna tropical, pescarias experimentais foram realizadas entre setembro 2003 e Julio 2004 em canais de mare com vegetacao de mangue no estuario do rio Curuca, Para, Norte do Brasil. Juvenis ocorreram durante todo o ano, entretanto com maior intensidade no periodo de recrutamento, durante a transicao da estacao chuvosa para a seca (Anchovia clupeoides, Cetengraulis edentulus, Rhinosardinia amazonica, Mugil sp.). O recrutamento foi continuo para Colomesus psittacus e Anchoa hepsetus. Sciades herzbergii apresentou dois picos de recrutamento (estacao chuvosa e seca), entretanto Cathorops sp. teve somente um (estacao chuvosa). A presenca continua de juvenis nos manguezais sugere que o manejo da pesca em regioes tropicais com vegetacao de mangue deveria se direcionar em definir grandes areas de protecao ao lugar de epocas de defeso.
Subcortical shape analysis of progressive mild cognitive impairment in Parkinson's disease

Cortical neural correlates of ongoing cognitive decline in Parkinson's disease (PD) have been suggested; however, the role of subcortical structures in longitudinal change of cognitive dysfunction in PD has not been fully investigated. Here, we used automatic analysis to explore subcortical brain structures in patients with PD with mild cognitive impairment that converts into PD with dementia.
The Intermediate Filament Protein, Vimentin, in the Lens Is a Target for Cross-linking by Transglutaminase*

Mere addition of Ca2+ to a lens cortical homogenate (bovine) generates a series of products composed of a variety of high molecular weight vimentin species. The Ca2+-induced cross-linking of this cytoskeletal element seems to be mediated by the intrinsic transglutaminase of lens, because the reaction could be blocked at the monomeric state of vimentin by the inclusion of small synthetic substrates of the enzyme dansylcadaverine or dansyl-ε-aminocaproyl-Gln-Gln-Ile-Val. These compounds are known to compete against the Gln or Lys functionalities of proteins that would participate in forming theN ε(γ-glutamyl)lysine protein-to-protein cross-links. The cytosolic transglutaminase-catalyzed reactions could be reproduced with purified bovine lens vimentin and also with recombinant human vimentin preparations. Employing the latter system, we have titrated the transglutaminase-reactive sites of vimentin and, by sequencing the dansyl-tracer-labeled segments of the protein, we have shown that residues Gln453 and Gln460 served as acceptor functionalities and Lys97, Lys104, Lys294, and Lys439 as electron donor functionalities in vimentin. The transglutaminase-dependent reaction of this intermediate filament protein might influence the shape and plasticity of the fiber cells, and the enzyme-catalyzed cross-linking of vimentin, in conjunction with other lens constituents, may contribute to the process of cataract formation.
A 274µW clock synchronized wireless body area network IC with super-regenerative RSSI for biomedical ad-hoc network system

A clock synchronized multi-node wireless body area network (WBAN) transceiver IC with super-regenerative RSSI is proposed for biomedical ad-hoc network system. The ad-hoc network makes stable communication even in the harsh human body channel condition (<−50 dB attenuation) with low-power consumption. The proposed system consists of two types of IC - a hub and node IC. The hub IC broadcasts the 240 MHz clock signal to the whole node ICs and gather the measured data through body channel communication (BCC). In the node IC, it has 2 key building blocks; 1) Injection locking clock synchronization receiver, and 2) Super-regenerative RSSI (SR-RSSI) and OOK receiver. As a result, the 240 MHz clock is exactly synchronized in the node IC with 90 µW power consumption. And a channel-condition-adapted ad-hoc network is constructed based on the SR-RSSI data. SR-RSSI consumes 184 µW concurrent achieving OOK receiver functionality for the ad-hoc network. The proposed WBAN IC is fabricated in 0.18 µm CMOS technology.
Lot quality assurance sampling for monitoring immunization coverage in Madras City.

OBJECTIVE To explore the usefulness of Lot Quality Assurance Sampling (LQAS) to identify divisions in a city that had immunization coverage levels of 80% for any of the four EPI vaccines. METHODS Only 43 divisions were considered for the study, the stratification factor being the death rate. The hypothesis that 80% coverage is 'unacceptable' was stipulated. Critical value (the number of unimmunized children) was chosen as 3. A simple random sample of 36 children in the age-group 12-23 months was taken from each selected division. Since sampling frames of children were not available, a simple random sample of 36 households was selected. Immunization status of each child was assessed by interviewing the child's mother/guardian. If the number of unimmunized children exceeded 3, then the division was regarded having coverage level 80% and rejected. RESULTS The coverage was classified as unacceptable(i. e., below 80%) in 19 divisions for Polio and DPT vaccines, in 26 divisions for Measles vaccine and in 4 divisions for BCG vaccine. The average time spent for undertaking the LQAS survey was 6 man-days per division. CONCLUSION This study demonstrated the utility of the LQAS technique in identifying 'unsatisfactory' pockets in Madras City, when the overall coverage was satisfactory. The technique will have greater application with an increase in the number of large units (cities/districts) having an overall coverage of 90% or more.