Related Files Research Articles

Effectiveness of neoadjuvant concurrent chemoradiotherapy versus up-front proctectomy in clinical stage II-III rectal cancer: A population-based study

Neoadjuvant concurrent chemoradiotherapy (NCCRT) is currently the preferred treatment for rectal cancer of clinical stage II-III based on its efficacy in clinical trials. The population-based effectiveness of NCCRT is rarely reported on in the literature. The purpose of our study is to investigate the nationwide population-based effectiveness of NCCRT as compared with up-front proctectomy. In this retrospective cohort study, we identified the study population by linking datasets including the cancer registry, death registry and other related files in Taiwan. We identified all patients with rectal adenocarcinoma of American Joint Committee on Cancer clinical stage II or III who were diagnosed in 2007 or 2008 and received either NCCRT or up-front proctectomy. We included patients' age, gender, residence, socioeconomic status and clinical stage as covariables. We used overall survival as the measure of effectiveness. The Cox proportional-hazards regression model was used for statistical analyses. We further conducted sensitivity analyses, one in only those who received optimal postoperative chemotherapy and one in two subgroups matched for propensity score. We included 1933 patients (NCCRT: 424; up-front proctectomy: 1509) in the study population. NCCRT was associated with improved survival as compared with up-front proctectomy (adjusted hazard ratio of death 0.656; 95% confidence interval 0.495-0.871). Our results were robust in the sensitivity analyses. We demonstrated that the use of neoadjuvant concurrent systemic therapy and radiotherapy is associated with better effectiveness in rectal adenocarcinoma of clinical stage II-III as compared with up-front proctectomy. Further studies are needed to elucidate the subgroups most likely to benefit and to clarify NCCRT's cost-effectiveness.

Towards visual analytics for digging into human rights violations data

Towards visual analytics for digging into human rights violations data

The Research and Implementation of XBRL Data Service Platform

As there is no convenient and custom XBRL data service in the present market, in this article we designed the XBRL Data Service Platform in the perspective that a computer application can get the needed XBRL data conveniently. The platform parses the XBRL taxonomy and instance first, and then store the XBRL data in the combination of relational database and file system. The platform is designed in 3-tier architecture to provide data service. The work of Data Access Tier and Model Tier is to query and encapsulate the XBRL data; the Business Logical Tier is to complete the main logical work, to invoke the Data Access Tier to get the data, and then assembly and serialize the data, and return the result to the View Tier at last; View Tier opens the API list to public as web service, users may invoke the interface with an application. The test work shows that XBRL Data Service Platforms interface is simple and definite, and its function to get XBRL data is powerful. With the platform users can get both the specific XBRL data segments and the complete XBRL files as their needs. Furthermore, all the data requests are completed in a short response time.

WinPyrox: A Windows program for pyroxene calculation classification and thermobarometry

A Microsoft Visual Basic program, called WinPyrox, has been developed to calculate structural formulas of both wet-chemical and microprobe-derived pyroxene analyses. Based on the standard International Mineralogical Association (IMA-88) nomenclature scheme, WinPyrox primarily calculates and classifies pyroxene groups and then determines a specific pyroxene name with its possible modifiers. It is developed to predict cation site-allocations at the different structural positions, including T , M 1, and M 2 sites, as well as to estimate end-members, molar fractions, end-member activities, components and activities, and single-clinopyroxene and two-pyroxene thermobarometers. The program allows the user to edit and load Microsoft Excel files to calculate electron-microprobe pyroxene analyses for different ferric iron estimation methods and normalization schemes. This software generates and stores all the calculated results in the output of a Microsoft Excel file, which can be displayed and processed by any other software for verification, general data manipulation, and graphing purposes. The compiled program code is distributed as a self-extracting setup file, including a help file, test data files, and related graphic files, which are designed to produce a high-quality printout from the Golden Software’s Grapher software. The self-extracting setup file, which is approximately 12 Mb, may be downloaded from or can be obtained from author on request.

E-Book versus Printed Materials: Preferences of University Students

Reading habits, accessing resources, and material preferences change rapidly in a digital world. University students, as digital natives, are accessing countless resources, from lecture notes to research papers electronically. The change of reading habits with a great scale has led to differentiation on accessibility of resources, archiving them and usage of related technologies. The purpose of this study is to examine the e-book usage preferences versus printed material along with reading habits in a context of different variables. Additionally, different uses of e-books in a variety of faculties have been the focus of this study. The participants comprised of 222 students, studying in 36 different universities across Turkey. A questionnaire was developed specifically for the study. The questionnaire consisted of three parts: Printed book reading habits, e-book reading habits (methods of reaching e-books, aim of usage etc.), and technological knowledge (e-book related tools and file formats etc.). According to the results of study, approximately 68% of university students stated that they read one book in a week and 62% indicated that they are e-book readers. Moreover, there was a significant relationship between social environment and reading habits of students. University students put forward accessibility advantage (68%) of e-book and stated that they mostly read e-book for research (81%). E-book format which is most commonly preferred among students is Portable Document Format (pdf) (73%), while the computer is the most commonly used e-book medium (60%).

Users’ recognition in web using web mining techniques

The rapid growth of the web and the lack of structure or an integrated schema create various issues to access the information for users. All users’ access on web information are saved in the related server log files. The circumstance of using these files is implemented as a resource for finding some patterns of user's behavior. Web mining is a subset of data mining and it means the mining of the related data from WWW, which is categorized into three parts including web content mining, web structure mining and web usage mining, based on the part of data, which is mined. It seems necessary to have a technique, which is capable of learning the users’ interests and based on the interests, which could filter the unrelated interests automatically or it could offer the related information to the user in reasonable amount of time. The web usage mining makes a profile from users to recognize them and it has direct relationship to web personalizing. The primary objective of personalizing systems is to prepare the thing, which is required by users, without asking them explicitly. In the other way, formal models prepare the possibility of system’s behavior modeling. The Petri and queue nets as some samples of these models can analyze the user's behavior in web. The primary objective of this paper is to present a colored Petri net to model the user's interactions for offering a list of pages recommendation to them in web. Estimating the user's behavior is implemented in some cases like offering the proper pages to continue the browse in web, ecommerce and targeted advertising. The preliminary results indicate that the proposed method is able to improve the accuracy criterion 8.3% rather static method.

IMPLEMENTASI PROGRAM JAMINAN KESEHATAN MASYARAKAT DIRUMAH SAKIT UMUM DAERAH Dr. SOETOMO SURABAYA (Studi Iniplementasi Program Jamkesmas Pada Aspek Pelayanan Bagi Pasien Luar Provinsi Di Rumah Sakit Umum Daerah Dr. Soetomo Surabaya)

RSUD Dr. Soetomo was the biggest hospital at East Indonesia that selected become one of recommended hospital to Jamkesmas patient from around of East Indonesia. That reason tfiat make searcher will concern searching to implementation Jamksesmas program that have been in Dr. Soetomo Hospital Surabaya especially to one of provinces patient. Problem resume in that searching was how did factors support and blocked implementation Jamkesmas program in Dr. Soetomo hospital The goal of this research is to descript about implementation of Jamkesmas program and factors that support and blocked to service aspect by patients from other. Method that have been used in this research was qualitative searching metode in the descript if type. Collecting file was did with indeepth interview technique, observation and documentation. Definite informan technique used key informan, that he or she know much about the field of this research titan other people around. File analyst process was did collecting also combain file that be goten and set up relation file network Searching product show that Jamkesmas program implementation and Dr. Soetomo hospital was transmission and consistency in communication, staff quality and quality progress method in staff sources, responding Jamkesmas subject and commitment disposition subject, level coordination and service standard in bureaucracy. Structure and factor blocked Jamkesmas program implementation was clear communication, staff quantity in the sources of staff and facility.

A flexible and extensible approach to automated CAD/CAM format classification

There are hundreds of distinct 3D, CAD and engineering file formats. As engineering design and analysis has become increasingly digital, the proliferation of file formats has created many problems for data preservation, data exchange, and interoperability. In some situations, physical file objects exist on legacy media and must be identified and interpreted for reuse. In other cases, file objects may have varying representational expressiveness.We introduce the problem of automated file recognition and classification in emerging digital engineering environments, where all design, manufacturing and production activities are “born digital.” The result is that massive quantities and varieties of data objects are created during the product lifecycle.This paper presents an approach to automated identification of engineering file formats. This work operates independent of any modeling tools and can identify families of related file objects as well as variations in versions. This problem is challenging as it cannot assume any a priori knowledge about the nature of the physical file object. Applications for these methods include support for a number of emerging applications in areas such as forensic analysis, data translation, as well as digital curation and long-term data management.

A Method of Geospatial Data Files Conversion Based on Semantic

Data conversion is a necessary step to establish a unified data storage and management mode. Based on the analysis of the structure of Shapefile and the principle of semantic conversion, this paper proposes a method of geospatial data files conversion based on semantic. This method to a relational database file shape file conversion, the application of this method can not only increase the data read speed, and ease of data management and sharing.

Exploring Family Relations between International Patent Applications

In the international system for granting patents for inventions, first patent filings can be followed by subsequent filings at other patent offices within one year. Each such group of related filings constitutes a patent family. Tests are developed as to whether the observed number of first filings that leads to subsequent filings (r) is in agreement with a random process of assignment of the hits from the subsequent filings. An exact expression for the random distribution can be used for small sized data sets. Its behaviour and also the behaviour of an asymptotic Poisson approximation as well as a censored binomial distribution for r are assessed. The approach is stimulated by the Fisher-Wright model in population genetics and possible parallel applications to other biological processes are sought, such as transformations of stem cells and cancer.

Racial Disparities in Gastrointestinal Cancers-Related Mortality in the US Population

Racial difference in cancer-related mortality has been described in epidemiological studies and evidence points towards higher mortalities in the minorities. To determine the magnitude of racial disparities and sex differences in GI cancer-related mortalities in the US population, we analyzed the data using the third National Health and Nutrition Examination Survey (NHANES III) and related mortality data files. NHANES III and its related public linked mortality files were used for this study. Our study cohort included subjects who were ≥18 years and were part of the longitudinal mortality follow-up database. The overall GI cancers related mortality was calculated using combined mortality from malignant neoplasm of esophagus, stomach, colon, liver and pancreas. The evaluation of independent predictors of overall GI cancer-related mortality and of each individual GI cancer was carried out using the Cox proportional hazards model. A total of 13,221 individuals were included in the analyses with the average person year follow-up of 13.9 years. During the follow-up period, 4,146 subjects died. Of these, 199 were from GI-related cancers. Non-Hispanic black (NHB) had significantly higher overall GI-cancer related mortality compared to non-Hispanic white (NHW, adjusted hazard ratio, aHR: 2.31, 95% CI 1.57-3.38, p < 0.001). Subgroup analyses by sex demonstrated higher mortality from gastric, colorectal and primary liver cancer related mortality in NHB men compared to NHW men. Esophageal and pancreatic cancer mortalities were higher in NHB women compared to NHW women. Overall GI cancer-related mortality is significantly higher among NHB compared to NHW in the U.S. population.

TARİHİ YARIMADA'NIN BAZI BİLİNMEYEN BİZANS DÖNEMİ SARNIÇLARI

Due to the absence of systematical archaeological excavations elsewhere in Istanbul, like other archaeological discoveries, surviving remains of Byzantine cisterns sometimes appear during the rescue excavations for construction activities at Historical Peninsula. However, even if these remains are well documented, the valuable data usually stays in the related official archive files and cannot be introduced to the academic community. Construction of modern buildings over these remains may be allowed with permissions by government authorities on condition of their protection. Today, many remnants of these unpublished structures preserved under the basements of many commercial and residential buildings, but these are unlikely to be detected unless a systematical research is undertaken in the archives. In this article, a group of previously unpublished cisterns or currently published works which include brief descriptions without further details in order to provide data for purpose of the research will be introduced.

Identifying Protein Complexes From Interactome Based on Essential Proteins and Local Fitness Method

High-throughput experimental technologies, along with computational predictions, have promoted the emergence of large-scale interactome for numerous organisms. Identification of protein complexes from these interactome networks is crucial to understand principles of cellular organization and predict protein functions. Protein complexes are generally considered as dense subgraphs. However, the real protein complexes do not always have highly connected topologies. In this paper, a novel protein complex identifying method, named EPOF, is proposed, using essential proteins and the local metric of vertex fitness. In EPOF, cliques in the subnetwork which is consisted by the essential proteins are firstly considered as seeds, which are ordered according to their size and the number of their neighbors. A protein complex is extended from a seed based on the evaluation of its neighbors' fitness value. Then, the similar procedure is applied to the cliques identified in the subnetwork which is consisted by the proteins which is not clustered in the first step. When EPOF identifies complexes by expanding essential protein cliques, the essential proteins have higher priority and lower threshold. When it identifies complexes by expanding nonessential protein cliques, the nonessential proteins have higher priority and lower threshold. Finally, the last step, we output the identified complexes set. The proposed algorithm EPOF is applied to the unweighted and weighted interaction networks of S. cerevisiae and detects many well known protein complexes. We compare the performances of EPOF to other ten previous algorithms, including EAGLE, NFC, MCODE, DPClus, IPCA, CPM, MCL, CMC, SPICi, and Core-Attachment. Experimental results show that EPOF outperforms other previous competing algorithms in terms of matching with known complexes, sensitivity, specificity, f-measure, function enrichment and accuracy. The program and related files available on https://github.com/gangchen/epof.

스캐닝 기법을 이용한 실행 소프트웨어를 담을 수 있는 기능성 USB 솔루션 개발

The technology suggested in this study is the method to contain executable software in a portable storage devices like the USB and install an application program to operate it in any client devices. To solve this problem, we can store pre-scanned information on the above client`s files, registry, and services in the device before installing the proper application program to be installed using the scanning method and manage in the USB the resources that generated and changed by post-scanning the information after installing the above application program in the client`s device. After that, necessary files in the client to be used can be copied for using, and after use, related files are deleted, and it also includes the process to return to the previous system environment. This method is advantageous in that once any sort of application programs needed to be installed gets to be installed in an external portable storage devices like the USB, the application program installed can be operated in any computer not raising any issues like illegal copy.

Selected FINRA notices and disciplinary actions, October‐December 2011

PurposeThe purpose of this paper is to provide summaries of selected Financial Industry Regulatory Authority (FINRA) regulatory notices and disciplinary actions issued in October, November, and December 2011.Design/methodology/approachThe paper provides Regulatory Notice 11‐49, October 2011, Advertising Regulation; Regulatory Notice 11‐52, November 2011, Senior Designations; Regulatory Notice 11‐54, November 2011, Branch Office Inspections; and the description of one disciplinary action in which a firm was sanctioned and an individual fined.FindingsNotice 11‐49: to inform firms of recent developments regarding the application of rules governing communications with the public, FINRA is proving guidance to firms on communication with the public regarding exchange‐traded products, treasury inflation‐protected securities (TIPS), use of “FINRA” in firm trademarks, and identification of related prior filings when submitting new filings for review. Notice 11‐52: FINRA reminds firms of their supervisory obligations regarding the use of certifications and designations that imply expertise, certification, training or specialty in advising senior investors. Notice 11‐54: FINRA and the Securities and Exchange Commission's Office of Compliance Inspections and Examinations provide broker‐dealer firms with information on developing effective policies and procedures for branch office inspections and remind firms of supervisory requirements under FINRA's supervision rule and notes common deficiencies and strong compliance practices. Trade Reporting Notice on TRACE Reporting Issues: FINRA answers selected member firm detailed questions on reporting issues related to The Trade Reporting and Compliance Engine (TRACE), the vehicle developed by FINRA to facilitate the mandatory reporting of over the counter secondary market transactions in eligible fixed income securities. All broker/dealers who are FINRA member firms have an obligation to report transactions in corporate bonds to TRACE under an SEC approved set of rules.Originality/valueThese are direct excerpts designed to provide a useful digest for the reader and an indication of regulatory trends.

A Weighted Power Framework for Integrating Multisource Information: Gene Function Prediction in Yeast

Predicting the functions of unannotated genes is one of the major challenges of biological investigation. In this study, we propose a weighted power scoring framework, called weighted power biological score (WPBS), for combining different biological data sources and predicting the function of some of the unclassified yeast Saccharomyces cerevisiae genes. The relative power and weight coefficients of different data sources, in the proposed score, are estimated systematically by utilizing functional annotations [yeast Gene Ontology (GO)-Slim: Process] of classified genes, available from Saccharomyces Genome Database. Genes are then clustered by applying k-medoids algorithm on WPBS, and functional categories of 334 unclassified genes are predicted using a P-value cutoff 1 ×10(-5). The WPBS is available online at http://www.isical.ac.in/~ shubhra/WPBS/WPBS.html, where one can download WPBS, related files, and a MATLAB code to predict functions of unclassified genes.

A novel research approach to enhance research group‐level science data management

AbstractThis poster will report an alternative approach compared with large‐scale collection, technology development, or discipline informatics projects by exploring the enhancement of science data management at the research group level. An academic‐year‐long project involving both information and technical analysts demonstrated that flexible introduction of IT in the form of a relational database solution presents an opportunity to incorporate data‐related practices, behavior, and schemes into a tool. The project team used cognitive work analysis and participatory design research methods to sensitively analyze research practice and then design and introduce a prototype tool. Iterative analysis and design cycles captured and incorporated the complex practices of researchers who struggle with the accumulation of samples and related digital data files from years of research. Design research processes will be analyzed according to project developments and research group reaction to the proposed data management tool design and preliminary attempt at implementation.

Evaporation Correction Methods for Microwave Retrievals of Surface Precipitation Rate

Active and passive microwave remote sensing estimates of surface precipitation based on signals from hydrometeors aloft require correction for evaporated precipitation that would otherwise reach the ground. This paper develops and compares two near-surface evaporation correction methods using two years of data from 509 globally distributed rain gauges and three passive millimeter-wave Advanced Microwave Sounding Units (AMSUs) aboard National Oceanic and Atmospheric Administration (NOAA) satellites (NOAA-15, NOAA-16, and NOAA-18). The first type of correction is a scale factor that minimizes the bias between the means of annual AMSU and rain gauge precipitation accumulations (in millimeters per year) for each of 12 infrared-based surface classifications. The scale factor for the second correction method is computed using a neural network trained using both surface classification and annual average relative humidity pro files. AMSU surface precipitation retrievals using both methods were compared to the annual accumulations for 509 rain gauges uncorrected for wind effects, where different data were used for training and accuracy evaluation. The rms annual accumulation retrieval errors for AMSU using surface classification and relative humidity corrections were 236 and 222 mm/y, respectively, compared to 190 mm/y for corresponding Global Precipitation Climatology Project data, which utilizes more satellite sensors and over 6500 rain gauges.

Managerial Attitudes and Merger Outcomes: Evidence from Corporate Takeover Filings

We examine the textual content of merger and acquisition related SEC filings in an effort to understand the role of managerial attitudes and beliefs in merger negotiations and outcomes. Using a textual algorithm to identify the degree to which filings of bidders and targets exhibit negative/cautious tones vs. positive/optimistic tones, we find that bidders employing the most optimistic language in their filings actually experience the worst long-run performance following the transactions. In contrast, bidding managers who appear to acknowledge and understand the risks of the transactions experience relatively better post-merger performance. For targets, we use the tone of their filings as a measure of how positive or negative their management teams are towards the proposed transaction. We find that target filings are more negative for deals with lower initial premiums, and that negative filings are associated with lower deal completion rates. For completed mergers, bidders are more likely to increase premia for resistant targets. Thus our analysis of the textual content of merger filings appears to give us a new method for investigating the role of bidder and target attitudes and beliefs on merger outcomes.

Correlated evolution of transcription factors and their binding sites

The interaction between transcription factor (TF) and transcription factor binding site (TFBS) is essential for gene regulation. Mutation in either the TF or the TFBS may weaken their interaction and thus result in abnormalities. To maintain such vital interaction, a mutation in one of the interacting partners might be compensated by a corresponding mutation in its binding partner during the course of evolution. Confirming this co-evolutionary relationship will guide us in designing protein sequences to target a specific DNA sequence or in predicting TFBS for poorly studied proteins, or even correcting and rescuing disease mutations in clinical applications. Based on six, publicly available, experimentally validated TF-TFBS binding datasets for the basic Helix-Loop-Helix (bHLH) family, Homeo family, High-Mobility Group (HMG) family and Transient Receptor Potential channels (TRP) family, we showed that the evolutions of the TFs and their TFBSs are significantly correlated across eukaryotes. We further developed a mutual information-based method to identify co-evolved protein residues and DNA bases. This research sheds light on the dynamic relationship between TF and TFBS during their evolution. The same principle and strategy can be applied to co-evolutionary studies on protein-DNA interactions in other protein families. All the datasets, scripts and other related files have been made freely available at: http://jjwanglab.org/co-evo. junwen@uw.edu. Supplementary data are available at Bioinformatics online.