bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical application of genomic profiling in breast cancer and the TAILORx trial
Authors: Sparano Joseph A. 
Published: May 2015

Abstract
Breast cancer is characterized by clinical and molecular heterogeneity. Microarray-based gene expression has identified distinct expression profiles associated differing prognosis and response to therapy. Newer technologies now permit evaluation not only of gene expression, but also single nucleotide polymorphisms, gene copy number, genomic mutations, and epigenomic or microRNA patterns that modulate gene expression. These state-of-the-art molecular approaches offer new insights into the pathogenesis of breast cancers, and offer the promise to improve the prevention, diagnosis, and management of the disease. Although many gene expression assays have been shown to provide prognostic information that is complementary to classical clinicopathologic features, the clinical utility of such assays is uncertain — that is, how do the results alter patient care, and do patients benefit from that change? Most attention has focused on using these assays to reduce overtreatment in patients with estrogen-receptor positive, lymph node negative breast cancer, which accounts for about one-half of all breast cancers, and about 8% of all cancers in the United States. Evidence suggest that some assays do have clinical utility when used appropriately, usually by reducing overtreatment with chemotherapy in patients who may otherwise have an excellent prognosis with local therapy plus endocrine therapy alone — or “treatment sparing”. Other potential examples of clinical utility include “treatment selection” (selecting individuals for chemotherapy when standard clinicopathologic features would have suggested otherwise) and “treatment direction” (selecting individuals for chemotherapy when clinicopathologic features suggested therapeutic equipoise). There are three breast cancer clinical trials which have integrated multiparameter assays into the clinical decision making, including the TAILORx and CHORUS trials (which use the 21 gene assay) and the MINDACT trial (which uses the 70 gene assay). The results of these trials will inform us regarding the clinical utility of these assays, and provide a valuable resource for evaluating other clinical cancer tests in the future.
The quantitatively analysis of epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC) and its correlation with response rate of EGFR tyrosine kinase inhibitors (TKI)
Authors: Li Jun , Chen Zhao , Sun Daqiang , Xu Meilin , Zhang Xun , Xu Junpu 
Published: May 2015

Abstract
Background and Purpose: Lung cancer is the most frequent malignant tumor in China. Epidermal growth factor receptor (EGFR) had been validated as one of the most important therapeutic targets of non-small cell lung cancer (NSCLC), and tyrosine kinase inhibitors (TKI) have improved the overall outlook and quality of life for most of EGFR mutation positive NSCLC patients; however, the fact that 30% of EGFR mutation positive patients still do not response to TKIs. The current diagnostic test qualitatively measures the overall EGFR mutation status of the cancer tissue, ignored the impacts of nonmutated, TKI-unresponsive cancer cells.
274 NSCLC patients were recruited for the study to carry out the mutation analysis and its correlation with the response rate to EGFR TKIs with a novel quantitative methodology.
Experimental Procedures: 1) Selection of paraffin sections of each recruited patients by pathologist to ensure the tumor cells exceeds 70% of total tissue; 2) Extraction of genomic DNA from paraffin sections; 3) Construction of plasmids of both mutated transcripts and wild-type transcripts for each mutation to be analyzed; 4) Real-time PCR amplification of extracted genomic DNA samples with both mutated probes and wild-type probes, and measurement of mutated copy numbers and wild-type copy numbers of each sample with standard curves made by mutated plasmids and wild-type plasmids respectively; 5) Confirmation of the mutation status of each sample with sequencing; 6) Calculation of the percentage of mutated EGFR copy numbers among the total EGFR copy numbers to derive quantitatively mutation data of each patient sample; 7) Observation of EGFR mutations and its demographic features with quantitative data; 8) Evaluation of the outcomes of the therapy with EGFR TKIs (including gefitinib and erlotinib) and analysis of the correlation of increased EGFR mutated transcripts with response rate to EGFR TKIs
Summary of New Data: 1) 94 recruited samples was detected with EGFR mutation among total samples, the mutation ratio various from 5% to 90%; 2) The most frequently detected EGFR mutations among the 94 samples are deletions of Exon 19 (56 cases) and L858R (23 cases); 3) The mutation positive NSCLC patients are divided into 4 groups: a) low mutation rate + gefitinib; b) high mutation rate + gefitinib; c) low mutation ratio + erlotinib; d) high mutation rate + erlotinib. There are significant differences between group a and group b, group c and group d. 4) There is no significant difference between various EGFR mutation types against response rate to TKIs.
Conclusions: 1) The EGFR mutation ratios in NSCLC patients are various; 2) The EGFR mutation ratio is significant correlated with the response rate to TKIs.
This talk is also presented as Poster B36.
Molecular biomarker analyses using circulating tumor cells
Authors: Atwal Siminder K. , Chen Daniel , Lackner Mark , Punnoose Elizabeth 
Published: May 2015

Abstract
Background: Evaluation of cancer biomarkers from blood and other accessible tissues could significantly enable biomarker assessment by providing a relatively noninvasive source of representative tumor material. Circulating tumor cells (CTCs) isolated from blood of metastatic cancer patients hold significant promise in this regard.
Methodology/Principal Findings: Using a tumor-cell spike-in model system we evaluated CTC capture on different CTC technology platforms, including CellSearch® and two biochip platforms, and used the isolated CTCs to develop and optimize assays for molecular characterization of CTCs. We report similar performance for the various platforms tested in capturing CTCs, and find that capture efficiency is dependent on the level of EpCAM expression. We demonstrate that captured CTCs are amenable to biomarker analyses such as HER2 status, qRT-PCR for breast cancer subtype markers, KRAS mutation detection, and EGFR staining by immunofluorescence (IF). We demonstrate that cell surface expression of EGFR can be quantitated in CTCs from metastatic lung cancer patient samples. In addition, we determined HER2 status by IF and FISH in CTCs from metastatic breast cancer patients and in the majority of patients (89%) found concordance with HER2 status from patient tumor tissue, while in a subset of patients (11%), HER2 status had changed from the primary tumor at diagnosis. Surprisingly, we found CTC counts to be higher in ER+ patients in comparison to HER2+ and triple negative patients despite their more aggressive phenotype. This may be explained by our findings that the basal-like molecular subtype of breast cancer has low EpCAM expression and a more mesenchymal phenotype and CTCs will likely not be efficiently captured using EpCAM alone in tumors that arise from this subtype.
Conclusions/Significance: Our data suggests that molecular characterization from captured CTCs is possible and can inform us of the patients’ current biomarker status. In this regard, CTCs hold significant promise as a source of tumor material to facilitate clinical biomarker evaluation. However, limitations exist from a purely EpCAM-based capture system and addition of antibodies to mesenchymal markers in addition to EpCAM could further improve CTC capture efficiency to enable routine biomarker analysis from CTCs.
ICZN rules—a farewell to Tubificidae (Annelida, Clitellata)
Authors: ERSÉUS CHRISTER , WETZEL MARK J. , GUSTAVSSON LENA 
Published: May 2015

Morphological and molecular characters support that the former clitellate family Naididae Ehrenberg, 1828 is nested within another family, Tubificidae Vejdovský, 1876. To avoid paraphyly of the latter, it has been suggested that the two should be regarded as a single taxon. A recent decision by the International Commission of Zoological Nomenclature [2007; opinion 2167 (Case 3305)] ruled against a proposed reversal of the nomenclatural priority of Naididae over Tubificidae, with the consequence that all former tubificids should now be regarded as members of the Naididae whenever these two names are regarded as synonyms. The paper is a plea to clitellate researchers to conform to this ruling.
Priority of Geranoaetus Kaup, 1844 over Tachytriorchis Kaup, 1844 (Aves: Accipitridae) based on the first reviser principle
Authors: DO AMARAL FÁBIO RAPOSO , SHELDON FREDERICK H. , GAMAUF ANITA , HARING ELISABETH , RIESING MARTIN J. , SILVEIRA LUÍS F. , WAJNTAL ANITA 
Published: May 2015

The generic name Geranoaetus Kaup, 1844 (type species: Falco aguia Temminck = Spizaetus melanoleucus Vieillot) generally has been applied only to its type species, G. melanoleucus, although inclusion of fossil species in the genus has been suggested (Wetmore 1933; Amadon 1963). Although Geranoaetus is still recognized by some authors (e.g., Thiollay 1994; Remsen et al. 2010), others consider it a junior synonym of the genus Buteo Lacépedè, 1799, because of similarities to some species in that genus (e.g., Wetmore 1933; Hellmayr & Conover 1949; Clark 2006). Recent studies of the molecular phylogenetics of buteonine hawks (Riesing et al. 2003; Lerner et al. 2008; Amaral et al. 2006, 2009) unanimously agree on the lack of monophyly of three buteonine genera, namely Buteo, Leucopternis Kaup, 1847 and Buteogallus Lesson, 1830, as currently recognized (Remsen et al. 2010).
Selenops muehlmannorum spec. nov from Southern Laos (Araneae: Selenopidae)
Authors: JÄGER PETER , PRAXAYSOMBATH BOUNTHOB 
Published: May 2015

The spider fauna of Laos was for a long time neglected in terms of arachnological investigations. Only recently the spider fauna is investigated, new species are described, new records are listed and illustrations of species are provided for identification purposes (Jäger 2007; Jäger & Praxaysombath 2009, in press). Currently, 150 spider species are recorded for Laos.
Generalizing Cloud Overlap Treatment to Include the Effect of Wind Shear
Authors: Di Giuseppe Francesca , Tompkins Adrian M. 
Published: May 2015

Abstract
Six months of CloudSat and CALIPSO observations have been divided into over 8 million cloud scenes and collocated with ECMWF wind analyses to identify an empirical relationship between cloud overlap and wind shear for use in atmospheric models. For vertically continuous cloudy layers, cloud decorrelates from maximum toward random overlap as the layer separation distance increases, and the authors demonstrate a systematic impact of wind shear on the resulting decorrelation length scale. As expected, cloud decorrelates over smaller distances as wind shear increases. A simple, empirical linear fit parameterization is suggested that is straightforward to add to existing radiation schemes, although it is shown that the parameters are quite sensitive to the processing details of the cloud mask data and also to the fitting method used. The wind shear–overlap dependency is implemented in the radiation scheme of the ECMWF Integrated Forecast System. It has a similar-magnitude impact on the radiative budget as that of switching from a fixed decorrelation length scale to the latitude-dependent length scale presently used in the operational model, altering the zonal-mean, top-of-atmosphere, equator-to-midlatitude gradient of shortwave radiation by approximately 2 W m−2.
Formation and Maintenance of the Tropical Cold-Point Tropopause in a Dry Dynamic-Core GCM
Authors: Kim Joowan , Son Seok-Woo 
Published: May 2015

Abstract
The formation of the tropical cold-point tropopause (CPT) is examined using a dry primitive equation model driven by the Held–Suarez forcing. Without moist and realistic radiative processes, the dry model successfully reproduces the zonal-mean structure of the CPT. The modeled CPT is appreciably colder (~10 K) than the prescribed equilibrium temperature, and it is maintained by upwelling in the tropical upper troposphere and lower stratosphere (UTLS). A transient simulation starting from an axisymmetric steady state without the CPT shows that the evolution and maintenance of the CPT are closely related to the zonal-mean-flow response to wave driving in the stratosphere. The transformed Eulerian-mean analysis indicates that the wave driving is mostly due to convergence of synoptic-scale waves originating from the midlatitude troposphere and propagating into the subtropical UTLS in this model simulation. The modeled CPT also shows a large sensitivity to increased baroclinicity in the equilibrium temperature. Although planetary-scale waves are not considered in this simulation, the result confirms that wave-driven upwelling in the tropical UTLS is a crucial process for the formation and maintenance of the CPT. In addition, it also implies that synoptic-scale waves may play a nonnegligible role in this mechanism, particularly in the seasons when planetary-scale wave activity in the lower stratosphere is weak.
Palladium-catalyzed 5-exo-Selective Reductive Mizoroki–Heck Reaction of Aryl Chlorides with 2,5-Norbornadiene
Authors: Aida Fuyuki , Sone Hisashi , Ogawa Ryuhei , Hamaoka Takeharu , Shimizu Isao 
Published: May 2015

Abstract
5-exo-Selective reductive Mizoroki–Heck reaction of 4-tert-butyl-1-chlorobenzene with 2,5-norbornadiene has been achieved by [PdCl2(PCy3)2]/HCO2Na to give 5-exo-(4-tert-butylphenyl)-2-norbornene in 95% yield. When Cs2CO3 is used as a base in the absence of a reducing reagent, an exo-benzocyclobutene-fused norbornene, 6-tert-butyl-1,4,4a,8b-tetrahydro-1,4-methanobiphenylene is produced in 62% yield.
Resolvent Flows for Convex Functionals and p-Harmonic Maps
Authors: Kuwae Kazuhiro 
Published: May 2015

Abstract
We prove the unique existence of the (non-linear) resolvent associated to a coercive proper lower
semicontinuous function satisfying a weak notion of p-uniform λ-convexity on a complete metric space, and
establish the existence of the minimizer of such functions as the large time limit of the resolvents, which
generalizing pioneering work by Jost for convex functionals on complete CAT(0)-spaces. The results can be
applied to Lp-Wasserstein space over complete p-uniformly convex spaces. As an application, we solve an
initial boundary value problem for p-harmonic maps into CAT(0)-spaces in terms of Cheeger type p-Sobolev
spaces.
The Assessment of Susceptibility on Drainage in an Aquifer on the Basis of Pumping Tests in a Lignite Mine / Ocena Podatności Ośrodka Wodonośnego Na Odwodnienie Na Podstawie Próbnych Pompowań W Kopalni Węgla Brunatnego
Authors: Polak Krzysztof , Kaznowska-Opala Karolina , Pawlecka Katarzyna , Różkowski Kazimierz , Klich Jerzy 
Published: May 2015

Abstract
Drainage of the rock mass is a key component affecting the safety of mining operations and is associated with the removal of the overburden, dumping and excavation of useful minerals. The primary method of drainage in lignite coal mines are bored wells. The efficiency of drainage of rock mass depends on their accurate positioning and quality of workmanship.
The paper presents the current state of knowledge concerning the distribution of the components of drawdown (1) in pumping well (Walton, 1955; Bruin & Hudson, 1961; Kruseman & de Ridder, 1991; Avci, 1992; Atkinson, 1994; Helweg, 1994; Kawecki, 1995; Singh, 2002; Dufresne, 2011) and their dependence on the hydrogeological parameters of the drained aquifer (Fig. 2).
The results of pumping tests conducted in drainage wells operating in lignite mines are also presented. The subject of analysis was the geohydraulic resistance coefficient B, describing the resistance of the aquifer under laminar flow. This coefficient also takes the hydrogeological parameters into account which determines the dynamics and range of influence of drainage (12, 13). The value of the parameter and its spatial variability can be used for planning, designing and evaluating the effectiveness of wells drainage
In view of the results of the pumping tests, classification of aquifer susceptibility to drainage was proposed, which can be used to support decision-making in the scope of expansion of the drainage system, the necessary timing and dynamics of pumping water. The classification is preliminary and is the starting point for the development of methods to rationalize functioning costs of the drainage systems.
The Impact of the Estimation of the Parameters Values on the Accuracy of Predicting the Impacts of Mining Exploitation / Wpływ Oszacowania Wartości Parametrów Modelu Na Dokładność Prognozowania Wpływów Eksploatacji Górniczej
Authors: Niedojadło Zygmunt , Gruszczyński Wojciech 
Published: May 2015

Abstract
The possibility of the assessment of the probability that the acceptable values of deformation indexes will be exceeded and the introduction of the coefficient of safety are more and more seriously considered in case of predicting the impacts of exploitation both on the surface and the shaft tube. This article presents the mentioned above issue focusing on the authors’ project of the exploitation in the protective pillars of the shafts of the Legnica and Głogów Copper Area (LGOM). To assess the accuracy of the predicted deformation indexes Monte Carlo method (often used in statistics) was proposed as well as the strict and approximate analysis using the law of error propagation. The values of vertical strains were analysed, as the most important at the assessment of the state of deformation of the shaft tube. The comparison of the results obtained with different methods confirmed the correctness of the carried out calculations. The applied methods allowed the analysis of the impact of individual parameters of the model on the prediction of the accuracy of forecast. This article makes the continuation of the solutions of the article (Niedojadło & Gruszczyński, 2010) thus some contents essential for the continuity of understanding were repeated here.
Feasibility Analysis of Groundwater Abstraction for Gas Shale Fracturing in the Lublin Basin (Eastern Poland) / Ocena Możliwości Poboru Wód Podziemnych Do Szczelinowania Łupków Gazonośnych W Basenie Lubelskim (Wschodnia Polska)
Authors: Duda Robert , Macuda Jan 
Published: May 2015

Abstract
Natural gas extraction from shale rock necessitates hydraulic fracturing of rocks, which involves large amounts of fracture fluids made of 90.5% of water. The authors focus on feasibility of groundwater abstraction for the purpose of applying fracture fluids in wells of the Lublin Basin - area of perspective unconventional gas exploitation from the Ordovician and the Silurian shales. These data refer to the expected specific capacity of wells abstracting groundwater from main useful aquifers. Specific capacity of a well (q) belongs to high-certainty empirical parameters, characterizing water-bearing capacity of rocks at a regional scale. The spatial evaluation of q was based on respective data coming from 7 sheets of the Hydrogeological Map of Poland (scale 1:200,000) covering research area. Specific capacity q was calculated for wells abstracting water from the Upper Cretaceous, Tertiary and Quaternary aquifers in areas presented on particular sheets of the map. Authors determined the variability distribution and the cumulative probability plots of q values, indicating a range which corresponded to a sum of standard deviation (SD) above and below median (X̄), i.e. X̄ ± 1SD. On the total the interval included 68.2% of data. The results reveal that 0.6 ≤ q ≤ 40 m3h-1 per 1 meter of drawdown for the Upper Cretaceous rocks in the eastern part of the area, and 1.1 ≤ q ≤ 110 m3h-1 per 1 meter in the western part, being a result of more intense fracturing and fissuring. Owing to the scarcity of data, q values of wells screened at the Tertiary and Quaternary aquifers are given jointly for the whole area: 0.8 ≤ q ≤ 20 and 1.0 ≤ q ≤ 10 m3h-1 per 1 meter, respectively. The obtained specific capacities are high. When the wells are properly designed, their discharges may reach about ca. 100 m3h-1.
Determining the Optimum Cut-Off Grades in Sulfide Copper Deposits / Określanie Optymalnej Wartości Odcięcia Zawartości Procentowej Pierwiastka Użytecznego W Złożach Siarczku Miedzi
Authors: Rahimi Esmaeil , Oraee Kazem , Shafahi Zia Aldin , Ghasemzadeh Hasan 
Published: May 2015

Abstract
Optimum cut-off grades determination in mining life affects production planning and ultimate pit limit and it is also important from social, economical and environmental aspects. Calculation of optimum cut-off grades has been less considered for mines containing various mineral processing methods. In this paper, an optimization technique is applied to obtain optimum cut-off grades for both concentration and heap leaching processes. In this technique, production costs and different recoveries of heap leaching method directed into modeling different annual cash flows in copper mines. Considering the governing constraints, the Lagrange multiplier method is practiced to optimize the cut-off grades in which the objective function is supposed to maximize Net Present Value. The results indicate the effect of heap leaching process on the optimum cut-off grades of primary and secondary sulfide deposits.
The Modernization of the Energy Sector in Denmark / Modernizacja Sektora Energii W Danii
Authors: Frączek Paweł 
Published: May 2015

Abstract
Denmark is among the leaders who change their energy policy to guarantee its stable and sustainable character. The consistent pursuit of an energy policy enabled the country to lower both the level of its energy consumption and greenhouse gas emissions, while providing grounds for economic development. The study demonstrates that the main factors which led to the transition of Danish energy policy were the oil crisis of the 1970s as well as public expectations regarding their energy policy which was to be based on the concept of stability and sustainability.
Das Landesbibliotheksgesetz Rheinland-Pfalz
Authors: Steinhauer Eric W. 
Published: May 2015

Zusammenfassung:
Das neue Landesbibliotheksgesetz Rheinland-Pfalz fasst erstmals alle relevanten bibliotheksrechtlichen Vorschriften in einem einzigen Gesetz zusammen. Schwerpunkte des Gesetzes sind die Aufgaben des Landesbibliothekszentrums Rheinland-Pfalz, das Pflichtexemplarrecht sowie Regelungen über Bibliotheken als Bildungseinrichtungen und als Orte des kulturellen Gedächtnisses. Der Beitrag stellt das neue Gesetz in seinen Grundzügen vor und gibt kurze juristische Erläuterungen.
Auf „vier Rädern“ in die Cloud?
Authors: Degkwitz Andreas 
Published: May 2015

Zusammenfassung:
Die Bibliothekssysteme der nächsten Generation der weltweit größten Anbieter Ex Libris und OCLC sind cloud-basierte Systeme. Damit verbinden sich für Bibliotheken neue Herausforderungen. Über Fragen des Datenschutzes und der Datensicherheit hinaus spielen die damit einhergehende Standardisierung von Abläufen und Workflows sowie Katalogisierung und Metadatenmanagement eine zentrale Rolle. Mit dem DFG-Projekt „Cloudbasierte Infrastruktur für Bibliotheksdaten“ (CIB) wird ein virtueller „Deutscher Datenraum“ entwickelt, in dem die bibliothekarischen Metadaten der Katalogisierungsumgebungen von ALMA (Ex Libris) und WMS (OCLC) sowie von künftigen Systemanbietern synchronisiert zur Verfügung stehen. Wie wirken sich diese Entwicklungen auf die deutsche Katalogisierungspraxis aus? Wie und in welche Richtung wird sich künftiges Metadatenmanagement verändern? Unter diesen und weiteren Gesichtspunkten soll die Frage beantwortet werden, ob Bibliotheken auf „vier Rädern“ in der Cloud ankommen.