bluuebunny/crossref_metadata_2025_split huggingface dataset:
Next-generation sequencing of non-small cell lung cancer using a customized, targeted sequencing panel: Emphasis on small biopsy and cytology
Authors: DiBardino David M. , Rawson David W. , Saqi Anjali , Heymann Jonas J. , Pagan Carlos A. , Bulman William A. 
Published: March 2017

Background:
Next-generation sequencing (NGS) with a multi-gene panel is now available for patients with lung adenocarcinoma, but the performance characteristics and clinical utility of this testing are not well-described. We present the results of an extended 467 gene panel in a series of advanced, highly selected nonsmall cell lung cancer (NSCLC) patients using a range of specimens, including predominantly small biopsy and cytology specimens.

Materials and Methods:
A retrospective review of 22 NSCLC biopsies sent for NGS using an extended gene panel from January 2014 to July 2015. The customized NGS panel sequences 467 cancer-associated genes with exonic and intronic sequences obtained from purified tumor DNA. Genomic alterations, patient characteristics, and success of testing were determined.

Results:
The majority of samples tested were metastatic lung adenocarcinoma on final pathology. Of the 22 specimens tested, 5 (22.7%) were surgical resections and 17 (77.3%) were small biopsy and cytology specimens. Twenty-one (95%) of the specimens were adequate for full sequencing and yielded a total of 204 genomic alterations (average 8.9 per tumor), of which 17 (average 0.81 per tumor) were actionable and/or clinically relevant. Genomic alterations were found most commonly in the TP53, EGFR, EPHB1, MLL3, APC, SETD2, KRAS, DNMT3A, RB1, CDKN2A, ARID1A, EP300, KDM6B, RAD50, STK11, and BRCA2 genes.

Conclusions:
NGS using a comprehensive gene panel was performed successfully in 95% of all NSCLC cases in this series, including 94% small biopsy and cytology specimens and 100% surgical resections. This custom assay was performed on a range of tumor specimens and demonstrates that small specimens are able to provide a similar depth of information as larger ones. As many patients present at an advanced stage and only small specimens are obtained, the information these provide has the potential for guiding treatment in highly selected patients with advanced lung adenocarcinoma.
Role of neoadjuvant chemotherapy in advanced carcinoma of the hypopharynx and larynx
Authors: Joshi Poonam , Joshi Amit , Norohna Vanita , Chaturvedi Pankaj , Patil Vijay , Agarwal Jai Prakash , Juvekar Shashikant , Prabhash Kumar 
Published: March 2017

Abstract
Bacground: To assess the response rate and impact of neoadjuvant chemotherapy (NACT) in advanced carcinoma of the hypopharynx and larynx. Materials and Methods: This is a retrospective case series of 80 patients with locally advanced laryngopharynx carcinoma who received NACT from April 2010 to October 2011 at our tertiary care center. The patients received NACT either for achieving resectability or for organ preservation. Results: Majority of the patients (60%) had T4 a disease. Grade 3 and 4 neutropenia was seen in 18%, febrile neutropenia in 4%, mucositis in 4%, diarrhea in 5%, and vomiting in 3% patients. Resectability could be achieved in 34%, and larynx was preserved in 51% patients at a mean follow-up of 13 months. Conclusions: NACT was safe with acceptable toxicity. Majority of the patients who achieved resectability had oropharyngeal involvement. NACT followed by concurrent chemoradiotherapy could provide a high rate of organ preservation.
Surgical management of bronchopulmonary carcinoids: A single center experience
Authors: Jakhetiya Ashish , Garg Pankaj Kumar , Pandey Rambha , Ramanathan Palaniappan , Kumar Sunil , Nath Debojit , Pandey Durgatosh 
Published: March 2017

Abstract
Introduction: Bronchopulmonary carcinoids are uncommon tumors with relatively indolent biological behavior but a distinct malignant potential. Surgery is the mainstay of treatment. Our aim was to study preoperative characteristics, surgical approaches, and outcome in patients with bronchopulmonary carcinoid tumors. Patients and Methods: This retrospective study was done in the Department of Surgical Oncology of a Tertiary Teaching Hospital of North India. The case records of all the patients who underwent surgical treatment for lung neoplasms and were diagnosed to have bronchopulmonary carcinoids were reviewed. Details concerning the clinical presentation, preoperative therapy, operative procedure, postoperative complications, and outcome were retrieved from the case records. Results: Sixteen patients who underwent surgical treatment were found to have bronchopulmonary carcinoids on histopathological examination. The median age of the patients was 34 years (range 18–62 years). There were 11 men and five women. All patients were symptomatic, and the median duration of symptoms was 12 months (range 6–72 months) before presentation. Six patients had received antitubercular treatment before presentation, and one patient had been treated with chemotherapy due to misdiagnosis. Surgical procedures included six pneumonectomies (one with carinoplasty), four bilobectomies, three lobectomies, and three bronchoplastic procedures (two with lobectomy and one with bilobectomy). There was no postoperative mortality; three patients had morbidity in the form of lobar collapse, prolonged pleural collection, and surgical site infection. With a median follow-up time of 11 months (range 2–85 months), all the 16 patients are alive and disease-free. Conclusions: Delayed presentation and misdiagnosis of bronchial carcinoid are major concerns in North India. Adequate surgical resection can be performed without undue morbidity and is associated with good long-term results.
Classification of Simple Weight Modules over the Schrödinger Algebra
Authors: Bavula V. V. , Lu T. 
Published: March 2017

AbstractA classification of simple weight modules over the Schrödinger algebra is given. The Krull and the global dimensions are found for the centralizer (H) (and some of its prime factor algebras) of the Cartan element H in the universal enveloping algebra of the Schrödinger (Lie) algebra. The simple (H)-modules are classified. The Krull and the global dimensions are found for some (prime) factor algebras of the algebra (over the centre). It is proved that some (prime) factor algebras of and (H) are tensor homological/Krull minimal.
Gas chromatography vs. quantum cascade laser-based N2O flux measurements using a novel chamber design
Authors: Brümmer Christian , Lyshede Bjarne , Lempio Dirk , Delorme Jean-Pierre , Rüffer Jeremy J. , Fuß Roland , Moffat Antje M. , Hurkuck Miriam , Ibrom Andreas , Ambus Per , Flessa Heinz , Kutsch Werner L. 
Published: March 2017

Abstract. Recent advances in laser spectrometry offer new opportunities to investigate the soil–atmosphere exchange of nitrous oxide. During two field campaigns conducted at a grassland site and a willow field, we tested the performance of a quantum cascade laser (QCL) connected to a newly developed automated chamber system against a conventional gas chromatography (GC) approach using the same chambers plus an automated gas sampling unit with septum capped vials and subsequent laboratory GC analysis. Through its high precision and time resolution, data of the QCL system were used for quantifying the commonly observed nonlinearity in concentration changes during chamber deployment, making the calculation of exchange fluxes more accurate by the application of exponential models. As expected, the curvature values in the concentration increase was higher during long (60 min) chamber closure times and under high-flux conditions (FN2O > 150 µg N m−2 h−1) than those values that were found when chambers were closed for only 10 min and/or when fluxes were in a typical range of 2 to 50 µg N m−2 h−1. Extremely low standard errors of fluxes, i.e., from  ∼  0.2 to 1.7 % of the flux value, were observed regardless of linear or exponential flux calculation when using QCL data. Thus, we recommend reducing chamber closure times to a maximum of 10 min when a fast-response analyzer is available and this type of chamber system is used to keep soil disturbance low and conditions around the chamber plot as natural as possible. Further, applying linear regression to a 3 min data window with rejecting the first 2 min after closure and a sampling time of every 5 s proved to be sufficient for robust flux determination while ensuring that standard errors of N2O fluxes were still on a relatively low level. Despite low signal-to-noise ratios, GC was still found to be a useful method to determine the mean the soil–atmosphere exchange of N2O on longer timescales during specific campaigns. Intriguingly, the consistency between GC and QCL-based campaign averages was better under low than under high N2O efflux conditions, although single flux values were highly scattered during the low efflux campaign. Furthermore, the QCL technology provides a useful tool to accurately investigate the highly debated topic of diurnal courses of N2O fluxes and its controlling factors. Our new chamber design protects the measurement spot from unintended shading and minimizes disturbance of throughfall, thereby complying with high quality requirements of long-term observation studies and research infrastructures.
Understanding Student-Teachers’ Performances within an Inquiry-Based Practicum
Authors: Rivera Pilar Mendez , Gomez Francisco Perez 
Published: March 2017

The role of an inquiry-based practicum in the education of future teachers has been identified as a key component to foster student-teachers’ abilities to face problems, try to solve them, work on doubts and produce situated and valuable learning from their own practices (Cochran-Smith & Little, 2001; Beck, 2001). The interaction between mentors and student-teachers involved in this process requires feeding the mutual understanding to collaboratelly make decisions to work on difficulties. In this reflective study, the practicum was the perfect scenario to evaluate how student-teachers and mentors engaged in inquiry-based work to face problems on a daily basis in schools in the context of teachers education. This article shows how a group of 12 students-teachers and their mentors experienced difficulties within an inquiry-based practicum in an undergraduate program while conducting an instructional intervention, designing, implementing and applying a project relevant to their teaching context. Given the qualitative nature of this study, some stages of the process were analysed over a period of a year bringing as a result relevant insights to enhance their teaching practicum-process in Colombian public schools.
Metáforas gramaticais como recurso para empacotamento no texto acadêmico
Authors: Ninin Maria Otília Guimarães , Joseph Norma Lírio de Leão , Maciel Alda Maria Coimbra 
Published: March 2017

Escrita acadêmica não é uma tarefa fácil a graduandos de qualquer curso, embora convivam com textos dessa natureza ao longo de toda a graduação. Muitos estudos têm se concentrado nas discussões sobre resenhas, abstractse resumos, introduções de teses e dissertações, buscando suas características e modos de construir o significado do texto. No entanto, ainda são escassas as pesquisas que se debruçam sobre a seção de revisão da literatura. Nessa direção, este capítulo, a partir da análise de seções teóricas de diferentes gêneros da área de Letras/Linguística, à luz do conceito de metáfora gramatical (HALLIDAY, 1994; 2004; EGGINS; MARTIN, 1997; TAVERNIERS, 2003; SCHLEPPEGRELL, 2004; RAVELLI, 1988; SARDINHA, 2007), pretende mostrar como se realiza essa escrita e como pode ser viável, por meio de atividades de revisão do texto, propiciar aos alunos o aprendizado de uma escrita mais encapsulada, com maior densidade lexical, característica fundamental para a qualidade do texto científico.
ESBOÇO DA MORFOLOGIA DA LÍNGUA SURUÍ- AIKEWÁRA, COM BASE NO CLÁSSICO TRABALHO DE RODRIGUES “A ESTRUTURA DO TUPINAMBÁ”
Authors: Lopes Jorge Domingues 
Published: March 2017

Este artigo apresenta uma descrição de aspectos da morfologia da língua Suruí-Aikewára, língua pertencente ao subramo IV da família linguística Tupí-Guaraní (Rodrigues 1984/1985), tendo como referência o clássico estudo de Rodrigues (2010 [1981]), “A estrutura do Tupinambá”.
ANÁLISE E DESCRIÇÃO DA FONOLOGIA SEGMENTAL DO MANXINERU
Authors: Couto Fábio Pereira 
Published: March 2017

Neste artigo apresentamos a descrição da língua Manxineru, variedade da língua Yine (família Aruák), falada no sudeste do Estado do Acre, Brasil. Este trabalho foi pensado e elaborado não só como forma de descrever e divulgar a minha pesquisa desenvolvida em dissertação de mestrado em 2012 e ampliada em tese de doutorado em andamento, mas também com a intenção de contribuir para os estudos de línguas e para conhecimento da língua Manxineru. A descrição fonológica feita nesta pesquisa foi desenvolvida sob o viés da fonética articulatória e em uma perspectiva fonológica, considerando princípios de análise fonêmica, que tem, como orientação fundamental, a distribuição dos sons em sequências sonoras mais largas, tais quais sílabas e palavras.
Fostering Elite Athlete Development and Recreational Sport Participation: a Successful Club Environment
Authors: Galatti Larissa Rafaela , Côté Jean , Reverdito Riller Silva , Allan Veronica , Seoane Antonio Montero , Paes Roberto Rodrigues 
Published: March 2017

The overall aim of this article was to present a positive case study about how a sport club can foster both elite athlete development in parallel with offering a diverse range of sport activities to attract and maintain a greater number of children and youth for continued participation in a long term sport program. To this end, an in-depth case study was conducted of a model Spanish Basketball Club, considered an example of success in achieving consistent level of performance and high rates of participation among their youth. Data were collected from in-depth interviews with administrators, setting observation, and analysis of current and archived club documents. The results show that the club has created changes over the years that have led to a clear organizational structure with a philosophy that connects its youth development teams and elite teams. An increase focus on youth development, the addition of recreational activities, and the implementation of a coach education program have been linked to enhanced participation rate and performance.
The endochondral bone protein CHM1 sustains an undifferentiated, invasive phenotype, promoting lung metastasis in Ewing sarcoma
Authors: von Heyking Kristina , Calzada‐Wack Julia , Göllner Stefanie , Neff Frauke , Schmidt Oxana , Hensel Tim , Schirmer David , Fasan Annette , Esposito Irene , Müller‐Tidow Carsten , Sorensen Poul H. , Burdach Stefan , Richter Günther H. S. 
Published: March 2017

Ewing sarcomas (ES) are highly malignant, osteolytic bone or soft tissue tumors, which are characterized by EWS–ETS translocations and early metastasis to lung and bone. In this study, we investigated the role of the BRICHOS chaperone domain‐containing endochondral bone protein chondromodulin I (CHM1) in ES pathogenesis. CHM1 is significantly overexpressed in ES, and chromosome immunoprecipitation (ChIP) data demonstrate CHM1 to be directly bound by an EWS–ETS translocation, EWS‐FLI1. Using RNA interference, we observed that CHM1 promoted chondrogenic differentiation capacity of ES cells but decreased the expression of osteolytic genes such as HIF1A, IL6, JAG1, and VEGF. This was in line with the induction of the number of tartrate‐resistant acid phosphatase (TRAP+)‐stained osteoclasts in an orthotopic model of local tumor growth after CHM1 knockdown, indicating that CHM1‐mediated inhibition of osteomimicry might play a role in homing, colonization, and invasion into bone tissues. We further demonstrate that CHM1 enhanced the invasive potential of ES cells in vitro. This invasiveness was in part mediated via CHM1‐regulated matrix metallopeptidase 9 expression and correlated with the observation that, in an xenograft mouse model, CHM1 was essential for the establishment of lung metastases. This finding is in line with the observed increase in CHM1 expression in patient specimens with ES lung metastases. Our results suggest that CHM1 seems to have pleiotropic functions in ES, which need to be further investigated, but appears to be essential for the invasive and metastatic capacities of ES.
The role of DYNAMO in situ observations in improving NASA CERES‐like daily surface and atmospheric radiative flux estimates
Authors: Wang Hailan , Su Wenying , Loeb Norman G. , Achuthavarier Deepthi , Schubert Siegfried D. 
Published: March 2017

AbstractThe daily surface and atmospheric radiative fluxes from NASA Clouds and the Earth's Radiant Energy System (CERES) Synoptic 1 degree (SYN1deg) Ed3A are among the most widely used data to study cloud‐radiative feedback. The CERES SYN1deg data are based on Fu‐Liou radiative transfer computations that use specific humidity (Q) and air temperature (T) from NASA Global Modeling and Assimilation Office (GMAO) reanalyses as inputs and are therefore subject to the quality of those fields. This study uses in situ Q and T observations collected during the Dynamics of the Madden‐Julian Oscillation (DYNAMO) field campaign to augment the input stream used in the NASA GMAO reanalysis and assess the impact on the CERES daily surface and atmospheric longwave estimates. The results show that the assimilation of DYNAMO observations considerably improves the vertical profiles of analyzed Q and T over and near DYNAMO stations by moistening and warming the lower troposphere and upper troposphere and drying and cooling the mid‐upper troposphere. As a result of these changes in Q and T, the computed CERES daily surface downward longwave flux increases by about 5 W m−2, due mainly to the warming and moistening in the lower troposphere; the computed daily top‐of‐atmosphere (TOA) outgoing longwave radiation increases by 2–3 W m−2 during dry periods only. Correspondingly, the estimated local atmospheric longwave radiative cooling enhances by about 5 W m−2 (7–8 W m−2) during wet (dry) periods. These changes reduce the bias in the CERES SYN1deg‐like daily longwave estimates at both the TOA and surface and represent an improvement over the DYNAMO region.
Revisiting the contribution of transpiration to global terrestrial evapotranspiration
Authors: Wei Zhongwang , Yoshimura Kei , Wang Lixin , Miralles Diego G. , Jasechko Scott , Lee Xuhui 
Published: March 2017

AbstractEven though knowing the contributions of transpiration (T), soil and open water evaporation (E), and interception (I) to terrestrial evapotranspiration (ET = T + E + I) is crucial for understanding the hydrological cycle and its connection to ecological processes, the fraction of T is unattainable by traditional measurement techniques over large scales. Previously reported global mean T/(E + T + I) from multiple independent sources, including satellite‐based estimations, reanalysis, land surface models, and isotopic measurements, varies substantially from 24% to 90%. Here we develop a new ET partitioning algorithm, which combines global evapotranspiration estimates and relationships between leaf area index (LAI) and T/(E + T) for different vegetation types, to upscale a wide range of published site‐scale measurements. We show that transpiration accounts for about 57.2% (with standard deviation ± 6.8%) of global terrestrial ET. Our approach bridges the scale gap between site measurements and global model simulations,and can be simply implemented into current global climate models to improve biological CO2 flux simulations.
Temporal variation of the shallow subsurface at the Aquistore CO2 storage site associated with environmental influences using a continuous and controlled seismic source
Authors: Ikeda Tatsunori , Tsuji Takeshi , Takanashi Mamoru , Kurosawa Isao , Nakatsukasa Masashi , Kato Ayato , Worth Kyle , White Don , Roberts Brian 
Published: March 2017

AbstractThe development of reliable systems for monitoring injected CO2 is essential in carbon capture and storage projects. We applied time‐lapse surface wave analysis to measure temporal variations of the shallow subsurface among 11 periods (0.2–21.6 days) of continuous seismic data acquired from 2014 to 2016 at the Aquistore CO2 storage site in Canada. We focused on monitoring environmental influences on shallow seismic velocity, which are unrelated to CO2 injection into deep reservoirs. A continuous, controlled seismic source system called Accurately Controlled Routinely Operated Signal System was used to enhance the temporal resolution and source repeatability. Observed phase velocities were clearly higher in winter than in warmer seasons. The seasonal variation could be reproduced by an increase in the shallow S wave velocity during winter associated with the greater extent of freezing of partially saturated rock. We also observed gradual increases or decreases in phase velocities as the seasons changed, which could be related to gradual freezing or melting of ice. Our monitoring system thus could be effective for monitoring temporal variations of the shallow subsurface associated with the degree of freezing. Furthermore, the high temporal stability of our monitoring approach in warm seasons may make it possible to immediately identify CO2 leakage in the shallow subsurface.
New insights on tsunami genesis and energy source
Authors: Song Y. Tony , Mohtat Ali , Yim Solomon C. 
Published: March 2017

AbstractConventional tsunami theories suggest that earthquakes with significant vertical motions are more likely to generate tsunamis. In tsunami models, the vertical seafloor elevation is directly transferred to the sea‐surface as the only initial condition. However, evidence from the 2011 Tohoku earthquake indicates otherwise; the vertical seafloor uplift was only 3–5 m, too small to account for the resultant tsunami. Surprisingly, the horizontal displacement was undeniably larger than anyone's expectation; about 60 m at the frontal wedge of the fault plate, the largest slip ever recorded by in situ instruments. The question is whether the horizontal motion of seafloor slopes had enhanced the tsunami to become as destructive as observed. In this study, we provide proof: (1) combining various measurements from the 2011 Tohoku event, we show that the earthquake transferred a total energy of 3.1e + 15 joule to the ocean, in which the potential energy (PE) due to the vertical seafloor elevation (including seafloor uplift/subsidence plus the contribution from the horizontal displacement) was less than a half, while the kinetic energy (KE) due to the horizontal displacement velocity of the continental slope contributed a majority portion; (2) using two modern state‐of‐the‐art wave flumes and a three‐dimensional tsunami model, we have reproduced the source energy and tsunamis consistent with observations, including the 2004 Sumatra event. Based on the unified source energy formulation, we offer a competing theory to explain why some earthquakes generate destructive tsunamis, while others do not.