bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Impact of the Condenser on Cytogenetic Image Quality in Digital Microscope System
Authors: Ren Liqiang , Li Zheng , Li Yuhua , Zheng Bin , Li Shibo , Chen Xiaodong , Liu Hong 
Published: January 2015

Background: Optimizing operational parameters of the digital microscope system is an important technique to acquire high quality cytogenetic images and facilitate the process of karyotyping so that the efficiency and accuracy of diagnosis can be improved.OBJECTIVE: This study investigated the impact of the condenser on cytogenetic image quality and system working performance using a prototype digital microscope image scanning system.Methods: Both theoretical analysis and experimental validations through objectively evaluating a resolution test chart and subjectively observing large numbers of specimen were conducted.Results: The results show that the optimal image quality and large depth of field (DOF) are simultaneously obtained when the numerical aperture of condenser is set as 60%–70% of the corresponding objective. Under this condition, more analyzable chromosomes and diagnostic information are obtained. As a result, the system shows higher working stability and less restriction for the implementation of algorithms such as autofocusing especially when the system is designed to achieve high throughput continuous image scanning.Conclusions: Although the above quantitative results were obtained using a specific prototype system under the experimental conditions reported in this paper, the presented evaluation methodologies can provide valuable guidelines for optimizing operational parameters in cytogenetic imaging using the high throughput continuous scanning microscopes in clinical practice.
Evaluations of Auto-Focusing Methods under a Microscopic Imaging Modality for Metaphase Chromosome Image Analysis
Authors: Qiu Yuchen , Chen Xiaodong , Li Yuhua , Chen Wei R. , Zheng Bin , Li Shibo , Liu Hong 
Published: January 2015

Background: Auto-focusing is an important operation in high throughput imaging scanning. Although many auto-focusing methods have been developed and tested for a variety of imaging modalities, few investigations have been performed on the selection of an optimal auto-focusing method that is suitable for the pathological metaphase chromosome analysis under a high resolution scanning microscopic system.Objective: The purpose of this study is to investigate and identify an optimal auto-focusing method for the pathological metaphase chromosome analysis.Methods: In this study, five auto-focusing methods were applied and tested using metaphase chromosome images acquired from bone marrow and blood specimens. These methods were assessed by measuring a number of indices including execution time, accuracy, number of false maxima, and full width at half maximum (FWHM).Results: For the specific condition investigated in this study, the results showed that the Brenner gradient and threshold pixel counting methods were the optimal methods for acquiring high quality metaphase chromosome images from the bone marrow and blood specimens, respectively.Conclusions: Selecting an optimal auto-focusing method depends on the specific clinical tasks. This study also provides useful information for the design and implementation of the high throughput microscopic image scanning systems in the future digital pathology.
Rare e14a3 (b3a3) BCR-ABL Fusion in Chronic Myeloid Leukemia in India: The Threats and Challenges in Monitoring Minimal Residual Disease (MRD)
Authors: Vaniawala Salil , Acharya Arpan , Parekh Harsh , Mukhopadhyaya Pratap N. 
Published: January 2015

Objective: The primary objective of this work was to confirm the occurrence of rareBCR ABLfusion variant involving the a3 region of theABLgene in a patient positive for t(9;22) translocation but negative for common major and minor breakpoint cluster regions and the challenges and threats that it poses in a routine laboratory setting which use commercial kits for monitoring the minimal residual disease.Methods: A patient with elevated white blood cell count was subjected to classical cytogenetics, FISH as well as RT-PCR testing using commercial kits as well as published primers and in house testing protocol. PCR amplicon generated from in the process was sequenced and analyzed.Results: The translocation event in chromosome 9 and 22 could be successfully detected. BCR/ABL dual color, dual fusion probe generated a classical balanced translocation scenario within the nucleus of affected cells and presented a ‘1O1G2F’ signal pattern. RT-PCR with probes from commercial kit designed to detect common breakpoints within the M- and m-BCR regions involving e13a2, e14a2 and e1a2 fusion variants respectively failed to generate any signal. Further investigation revealed presence of the rare e14a3 (b3a3) fusion.Discussion: This is the first report of rare e14a3 fusion in the BCR ABL gene in a CML patient from India. The observation indicates the need for interrogating rare BCR ABL fusions when common breakpoint cluster regions are absent such that minimal residual disease (MRD), critical for disease monitoring, can be performed and false positive remission cases can be avoided. It also emphasizes the utility and significance of cytogenetics and FISH techniques in primary diagnosis of CML and use of RT-PCR based assays only for generating secondary information within special reference to MRD.Conclusions: The rare e14a3 (b3a3) fusion of theBCR ABLgene is present in Indian population as demonstrated from this first report and clinical laboratories using commercial kit that do not cover such rare fusions are likely to generate false result thereby declaring complete molecular remission in CML patients under therapy while conducting MRD assay using RT-PCR technology.
Basins of Attraction for Two-Species Competitive Model with Quadratic Terms and the Singular Allee Effect
Authors: Brett A. , Kulenović M. R. S. 
Published: January 2015

We consider the following system of difference equations:xn+1=xn2/B1xn2+C1yn2, yn+1=yn2/A2+B2xn2+C2yn2,  n=0, 1, …,  whereB1,C1,A2,B2,C2are positive constants andx0, y0≥0are initial conditions. This system has interesting dynamics and it can have up to seven equilibrium points as well as a singular point at(0,0), which always possesses a basin of attraction. We characterize the basins of attractions of all equilibrium points as well as the singular point at(0,0)and thus describe the global dynamics of this system. Since the singular point at(0,0)always possesses a basin of attraction this system exhibits Allee’s effect.
How Does Multistep Tumorigenesis Really Proceed?
Authors: Chaffer Christine L. , Weinberg Robert A. 
Published: January 2015

Abstract
Summary: Identifying the cancer cells-of-origin is of great interest, as it holds the potential to elucidate biologic mechanisms inherent in the normal cell state that have been co-opted to drive the oncogenic cell state. An emerging concept, proposed here, states that cancer stem cells, key players in cancer initiation and metastasis, arise when transit-amplifying cells with mutant genomes dedifferentiate and enter the stem cell state. This model contrasts with the notion that cancer stem cells are the direct products of neoplastically transformed normal tissue stem cells. Cancer Discov; 5(1); 22–4. ©2015 AACR.
Addressing the Controversy: Do Bisphosphonates Directly Affect Primary Tumors?
Authors: Sterling Julie A. 
Published: January 2015

Abstract
Summary: The recent article by Junankar and colleagues focuses on demonstrating the uptake of bisphosphonates (BP) into the primary tumor in both animal models and human samples. Interestingly, the authors were able to establish tumor-associated macrophages as the cell type that takes up the BPs. These studies are an important advancement for understanding the potential benefits of using BPs as adjuvant therapy in patients with cancer. Cancer Discov; 5(1); 14–5. ©2015 AACR.
See related article by Junankar and colleagues, p. 35
The Microsatellite Instable Subset of Colorectal Cancer Is a Particularly Good Candidate for Checkpoint Blockade Immunotherapy
Authors: Xiao Yanping , Freeman Gordon J. 
Published: January 2015

Abstract
Summary: The microsatellite instable (MSI) subset of colorectal cancer exhibits an active Th1/CTL immune microenvironment, probably due to recognition of a high number of tumor neoantigens. However, the high expression of checkpoint molecules PD-1, PD-L1, CTLA-4, LAG-3, and IDO in MSI colorectal cancer distinguishes MSI from microsatellite stable colorectal cancer and creates an immunosuppressive microenvironment that may help MSI tumors evade immune destruction by the infiltrating immune cells. Though colorectal cancer does not have a good response rate to PD-1 pathway immunotherapy, these results suggest that the MSI subset of colorectal cancer is a particularly good candidate for checkpoint immunotherapy. Cancer Discov; 5(1); 16–8. ©2015 AACR.
See related article by Llosa et al., p. 43
Expression Quantitative Trait Loci Acting Across Multiple Tissues Are Enriched in Inherited Risk for Coronary Artery Disease
Authors: Foroughi Asl Hassan , Talukdar Husain A. , Kindt Alida S.D. , Jain Rajeev K. , Ermel Raili , Ruusalepp Arno , Nguyen Khanh-Dung H. , Dobrin Radu , Reilly Dermot F. , Schunkert Heribert , Samani Nilesh J. , Braenne Ingrid , Erdmann Jeanette , Melander Olle , Qi Jianlong , Ivert Torbjörn , Skogsberg Josefin , Schadt Eric E. , Michoel Tom , Björkegren Johan L.M. 
Published: January 2015

Background—
Despite recent discoveries of new genetic risk factors, the majority of risk for coronary artery disease (CAD) remains elusive. As the most proximal sensor of DNA variation, RNA abundance can help identify subpopulations of genetic variants active in and across tissues mediating CAD risk through gene expression.

Methods and Results—

By generating new genomic data on DNA and RNA samples from the Stockholm Atherosclerosis Gene Expression (STAGE) study, 8156
cis
-acting expression quantitative trait loci (eQTLs) for 6450 genes across 7 CAD-relevant tissues were detected. The inherited risk enrichments of tissue-defined sets of these eQTLs were assessed using 2 independent genome-wide association data sets. eQTLs acting across increasing numbers of tissues were found increasingly enriched for CAD risk and resided at regulatory hot spots. The risk enrichment of 42 eQTLs acting across 5 to 6 tissues was particularly high (≤7.3-fold) and confirmed in the combined genome-wide association data from Coronary Artery Disease Genome Wide Replication And Meta-Analysis Consortium. Sixteen of the 42 eQTLs associated with 19 master regulatory genes and 29 downstream gene sets (n>30) were further risk enriched comparable to that of the 153 genome-wide association risk single-nucleotide polymorphisms established for CAD (8.4-fold versus 10-fold). Three gene sets, governed by the master regulators
FLYWCH1
,
PSORSIC3
, and
G3BP1
, segregated the STAGE patients according to extent of CAD, and small interfering RNA targeting of these master regulators affected cholesterol-ester accumulation in foam cells of the THP1 monocytic cell line.

Conclusions—

eQTLs acting across multiple tissues are significant carriers of inherited risk for CAD.
FLYWCH1
,
PSORSIC3
, and
G3BP1
are novel master regulatory genes in CAD that may be suitable targets.
Bibliografia w cyfrowej przestrzeni informacyjnej
Authors: Woźniak-­Kasperek Jadwiga 
Published: January 2015

Bibliography in a digital information environmentThe dynamically changing area of the digital, including web, information interacts with the bibliographic universe, bringing new opportunities as well as new problems for both the bibliographers and the users. The article analyzes the following issues: 1) The aim of bibliography. Bibliographies serve utilitarian purposes, they allow, or at the very least facilitate, the access to relevant publications; they connect the information with its potential recipient. But bibliographies fulfil more tasks. They are treasuries of memory, images of a widely understood culture in a certain time and place; documents of archival value meant to be preserved for future generations. 2) Bibliography and library catalogue. The dangers of identifying bibliography as library catalogue. 3) The form of bibliography. The advantages and disadvantages of the paper (printed) and the digital forms. Full­-text resource as the target standard of bibliographic services and an opportunity of computer-­aided indexing. The possibilities and advantages of using Web 2.0 tools in bibliographies. 4) Searching tools. Arrangements and indexes. Bibliografia w cyfrowej przestrzeni informacyjnejDynamicznie zmieniająca się przestrzeń informacji cyfrowej, w tym sieciowej, oddziałuje na uniwersum bibliograficzne, stając się źródłem zarówno nowych możliwości, jak i trudności, z którymi muszą się zmagać i bibliografowie, i użytkownicy. W artykule poddano analizie cztery grupy zagadnień: 1) Cele i zadania bibliografii. Bibliografie służą celom utylitarnym, umożliwiają, lub co najmniej ułatwiają, osobom zainteresowanym dotarcie do właściwych publikacji. Bibliografie mają też inne zadania. Są skarbnicami pamięci, obrazem stanu szeroko rozumianej kultury w określonym czasie i miejscu, dokumentem, który ma znamiona dokumentu archiwalnego, przeznaczonego do zachowania dla przyszłych pokoleń. 2) Bibliografia a katalog biblioteczny. Konsekwencje utożsamiania bibliografii i katalogów. 3) Postać bibliografii. Zalety i wady wersji drukowanych i cyfrowych. Dostęp do zasobów pełnotekstowych jako docelowy standard serwisów bibliograficznych i szansa na indeksowanie wspomagane komputerowo. Możliwości i zalety stosowania narzędzi Web 2.0 w bibliografiach. 4) Narzędzia wyszukiwawcze. Układy i indeksy.
Tekstowy korpus a dalše informaciske srědki wo hornjoserbskej rěči w interneće
Authors: Wölkowa Sonja 
Published: January 2015

The Upper Sorbian text corpus and further sources of information with regard to Upper Sorbian in the InternetIn the present era of globalisation and the omnipresence of the Internet, Sorbian linguistics faces new challenges along the lines “What is not in the Internet, does not exist”. The demand for digital sources of information with regard to Upper and Lower Sorbian and those accessible online as working tools and reference points for language practice and as a source for academic research increases. As a result of this ongoing development, the Foundation for the Sorbian People established a workgroup called “Sorbian in the new media” at the end of 2012, which has pointed out the creation of an online German­Upper Sorbian dictionary as the major task in this field of activities. The focus of this article, however, is the Upper-­Sorbian text corpus HoTKo, which has been created by the Sorbian Institute and which has been made available in co-­operation with the Institute of the Czech National Corpus at the Charles University in Prague. The article presents the history and development of the corpus, its extent and shape as well as its link to or incorporation into further planned digital projects of the Sorbian Institute with regard to the Upper Sorbian language.
Abstrakt i adnotacja jako element opisu dokumentu w bazie iSybislaw
Authors: Kowalski Paweł 
Published: January 2015

Abstract and annotation as an element of bibliographic description in the iSybislaw databaseAbstract (sometimes called summary) of a scientific publication is a brief text that contains keywords. It is one of the elements of a bibliographic description in the bibliographic database iSybislaw – a modern information retrieval system. In the paper definitions of terms such as abstract, annotation and summary along with their constitutive elements are presented. A characteristics of such short texts inserted in the iSybislaw database in the fields Abstract and Abstract 2 is also given. Based on some examples excerpted from the iSybislaw system a typology of short texts, which are elements of the database bibliographic description, is proposed. The material allows to list three kinds of texts that are being used in the iSybislaw database: annotations, abstracts and biographic annotations. Abstrakt i adnotacja jako element opisu dokumentu w bazie iSybislawPrzedmiotem analizy artykułu są krótkie teksty, które stanowią jeden z elementów opisu bibliograficznego w systemie wyszukiwawczym iSybislaw. W praktyce naukowej używane są różne terminy odnoszące się do takich tekstów (abstrakt, adnotacja, streszczenie). Autor podaje ich definicje oraz wskazuje elementy konstytutywne. Na podstawie przykładów wyekscerpowanych z systemu iSybislaw przedstawia ich typologię oraz omawia miejsce i funkcje w opisie bibliograficznym.
Słowa kluczowe, tagi…, i co dalej?
Authors: Babik Wiesław 
Published: January 2015

Keywords, tags... and what else?Keywords and their latest versions, called tags, are the object of this paper. Those expressions are treated as elements of the lexical systems of respective languages: the keyword language and the tag language. Our presentation of those vocabulary groups is intended to demonstrate that they are not homonymous, in structural or functional respects. Those two lexical resources are presented rather from the viewpoint of the theory of indexing and retrieval languages as well as the information search theories.Considering the future of the languages in question, the author presents the folksonomies and the possibilities of application of the respective vocabulary collections in the construction of tools required for semantization of the information retrieval environment in the Internet, including the construction of ontology and thought maps.Special attention was paid to the idea that keywords and tags are practically equivalent to specific “languages” which, similarly to natural languages, are subjected to continuous changes. For that reason, it is necessary to regularly monitor them and consider their practical application in document and information description and search.The works on keywords constitute a step towards the construction of linguistic tools for the needs of a semantic website. This paper is a contribution to the discussion on the development of keyword vocabularies created at the Institute of Slavic Studies of the Polish Academy of Sciences in Warsaw. Such vocabularies constitute part of the Slavic bibliographic information system. Słowa kluczowe, tagi…, i co dalej?Przedmiotem artykułu są słowa kluczowe oraz ich nowsza odmiana zwana tagami. Wyrażenia te zostały potraktowane jako elementy systemów leksykalnych odpowiednich języków: języka słów kluczowych oraz języka tagów. Prezentacja tych grup słownictwa ma na celu wykazanie, że nie są to homonimiczne grupy leksyki zarówno pod względem strukturalnym, jak i funkcjonalnym. Wymienione zasoby słownictwa zostały zaprezentowane z punktu widzenia teorii języków informacyjno-wyszukiwawczych oraz teorii wyszukiwania informacji.Biorąc pod uwagę przyszłość omawianych języków, zaprezentowano folksonomie oraz możliwości wykorzystania omówionych zbiorów słownictwa w budowie narzędzi do semantyzacji środowiska wyszukiwawczego w Internecie, w tym do budowy ontologii i map myśli.Szczególną uwagę zwrócono na to, że słowa kluczowe i tagi to w praktyce swoistego rodzaju „języki”, które, podobnie jak język naturalny, podlegają ciągłym zmianom, stąd potrzeba stałego śledzenia i uwzględniania pragmatyki ich stosowania w opisie i wyszukiwaniu dokumentów i informacji.Prace nad słowami kluczowymi stanowią krok w kierunku budowy lingwistycznych narzędzi na potrzeby semantycznego Web-u. Artykuł stanowi głos w dyskusji nad tworzonymi w Instytucie Slawistyki PAN w Warszawie słownikami słów kluczowych stanowiącymi element systemu slawistycznej informacji bibliograficznej.
Słowa kluczowe podawane przez autora publikacji jako podstawa opisu bibliograficznego w iSybislawie
Authors: Stanojević Marek , Kryżan­-Stanojević Barbara 
Published: January 2015

Author-provided keywords as the basis of bibliographical description in the iSybislaw bibliographyA bibliographer primarily relies on the abstract and keywords provided by the author of the original article. However the author-provided abstract and keywords are rarely sufficient. The bibliographer’s task is to ascertain that they correspond to the content of the article itself, as well as to find the closest equivalents in the language of the bibliography, Polish in our case. Additional confounding factors in determining the keywords corresponding most accurately to the submission in question include terminological inconsistencies within the works by certain authors, terminological inconsistencies within each of the languages as well as possible inconsistencies due to different theoretical backgrounds. This article deals with all of these issues on the basis of two pairs of examples. The first is the Polish term frazeologizm ‘idiom, phrase’ and the Croatian term frazem ‘idiom, phrase’. The second pair is the Polish term dialekt ‘dialect’ and the Croatian terms dijalekt/narječje ‘dialect/vernacular’. The complication inherent in the work of the bibliographer is due to, inter alia, the fact that the bibliographer’s strategy in prepairing the bibliographic description should enable the user to achieve the best possible effectiveness and efficiency in his/her search. Słowa kluczowe podawane przez autora publikacji jako podstawa opisu bibliograficznego w iSybislawieStreszczenie/abstrakt i słowa kluczowe podane przez autora w oryginalnym artykule są podstawą opracowania bibliograficznego, nie stanowią jednak wystarczającego źródła pracy bibliografa. Jego zadaniem jest przede wszystkim sprawdzenie, czy streszczenie/abstrakt i słowa kluczowe odpowiadają treści samego artykułu. Kolejne zadanie polega na odnalezieniu w języku bibliografii (w naszym przypadku jest to język polski) najbliższych ekwiwalentów słów kluczowych. Czynniki utrudniające dobór odpowiednich słów kluczowych z istniejącej bazy to brak ujednolicenia terminologicznego w pracach niektórych autorów, zróżnicowanie terminologiczne między językami, a także różnice terminologiczne związane z różnymi teoriami lingwistycznymi. W niniejszym artykule rozpatrywane są wszystkie te problemy na podstawie dwu przykładów. Pierwszy z nich stanowi para: polski termin frazeologizm i chorwacki termin frazem. Drugi reprezentowany jest przez polski termin dialekt i chorwackie terminy dijalekt/narječje. Problemy w pracy bibliografa wiążą się z opracowywaniem przez niego opisu bibliograficznego, który powinien zapewnić użytkownikowi jak największą skuteczność wyszukiwania informacji.
A Surface Wind Extremes (“Wind Lulls” and “Wind Blows”) Climatology for Central North America and Adjoining Oceans (1979–2012)
Authors: Malloy Jonny W. , Krahenbuhl Daniel S. , Bush Chad E. , Balling Robert C. , Santoro Michael M. , White Joshua R. , Elder Renée C. , Pace Matthew B. , Cerveny Randall S. 
Published: January 2015

AbstractThis study explores long-term deviations from wind averages, specifically near the surface across central North America and adjoining oceans (25°–50°N, 60°–130°W) for 1979–2012 (408 months) by utilizing the North American Regional Reanalysis 10-m wind climate datasets. Regions where periods of anomalous wind speeds were observed (i.e., 1 standard deviation below/above both the long-term mean annual and mean monthly wind speeds at each grid point) were identified. These two climatic extremes were classified as wind lulls (WLs; below) or wind blows (WBs; above). Major findings for the North American study domain indicate that 1) mean annual wind speeds range from 1–3 m s−1 (Intermountain West) to over 7 m s−1 (offshore the East and West Coasts), 2) mean durations for WLs and WBs are high for much of the southeastern United States and for the open waters of the North Atlantic Ocean, respectively, 3) the longest WL/WB episodes for the majority of locations have historically not exceeded 5 months, 4) WLs and WBs are most common during June and October, respectively, for the upper Midwest, 5) WLs are least frequent over the southwestern United States during the North American monsoon, and 6) no significant anomalous wind trends exist over land or sea.