bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient and Accurate Extracting of Unstructured EHRs on Cancer Therapy Responses for the Development of RECIST Natural Language Processing Tools: Part I, the Corpus
Authors: Li Yalun , Luo Yung-Hung , Wampfler Jason A. , Rubinstein Samuel M. , Tiryaki Firat , Ashok Kumar , Warner Jeremy L. , Xu Hua , Yang Ping 
Published: May 2020

PURPOSE Electronic health records (EHRs) are created primarily for nonresearch purposes; thus, the amounts of data are enormous, and the data are crude, heterogeneous, incomplete, and largely unstructured, presenting challenges to effective analyses for timely, reliable results. Particularly, research dealing with clinical notes relevant to patient care and outcome is seldom conducted, due to the complexity of data extraction and accurate annotation in the past. RECIST is a set of widely accepted research criteria to evaluate tumor response in patients undergoing antineoplastic therapy. The aim for this study was to identify textual sources for RECIST information in EHRs and to develop a corpus of pharmacotherapy and response entities for development of natural language processing tools. METHODS We focused on pharmacotherapies and patient responses, using 55,120 medical notes (n = 72 types) in Mayo Clinic’s EHRs from 622 randomly selected patients who signed authorization for research. Using the Multidocument Annotation Environment tool, we applied and evaluated predefined keywords, and time interval and note-type filters for identifying RECIST information and established a gold standard data set for patient outcome research. RESULTS Key words reduced clinical notes to 37,406, and using four note types within 12 months postdiagnosis further reduced the number of notes to 5,005 that were manually annotated, which covered 97.9% of all cases (n = 609 of 622). The resulting data set of 609 cases (n = 503 for training and n = 106 for validation purpose), contains 736 fully annotated, deidentified clinical notes, with pharmacotherapies and four response end points: complete response, partial response, stable disease, and progressive disease. This resource is readily expandable to specific drugs, regimens, and most solid tumors. CONCLUSION We have established a gold standard data set to accommodate development of biomedical informatics tools in accelerating research into antineoplastic therapeutic response.
Pathogenic Variants in CHEK2 Are Associated With an Adverse Prognosis in Symptomatic Early-Onset Breast Cancer
Authors: Greville-Heygate Stephanie L. , Maishman Tom , Tapper William J. , Cutress Ramsey I. , Copson Ellen , Dunning Alison M. , Haywood Linda , Jones Louise J. , Eccles Diana M. 
Published: May 2020

PURPOSE Checkpoint kinase 2 ( CHEK2) is frequently included in multigene panels. We describe the associated outcomes among carriers of CHEK2 pathogenic variants in young patients with symptomatic breast cancer. PATIENTS AND METHODS Participants (N = 2,344) in the Prospective Outcomes in Sporadic Versus Hereditary Breast Cancer study had a diagnosis of primary invasive breast cancer at age ≤ 40 years. Summary statistics were used to compare tumor characteristics among CHEK2+ carriers with those who were CHEK2−. Kaplan-Meier curves were used to demonstrate overall survival (OS) and distant disease-free survival. RESULTS Overall, 53 of the 2,344 participants (2.3%) had a pathogenic CHEK2 variant. CHEK2+-associated tumors were significantly more likely to be grade 2, estrogen receptor and progesterone receptor–positive compared with CHEK2− tumors (grade 2, n = 28 of 52 [53.8%] v n = 803 of 2,229 [36.0%]; P = .029). CHEK2-associated tumors were significantly more likely to have nodal involvement (N1, n = 37 of 53 [69.8%] v 1,169 of 2,253 [51.9%]; P = .0098) and demonstrated a trend toward multifocality. A higher proportion of participants with CHEK2+ variants with invasive breast cancer were obese than were those with CHEK2− variant (28.3% v 18.8%; P = .039). Univariate and multivariable analyses revealed that OS and distant disease-free survival were significantly worse in CHEK2+ versus CHEK2− carriers (OS hazard ratio, 1.58; 95% CI, 1.01 to 2.48; P = .043). CONCLUSION This work highlights the adverse prognosis associated with breast cancer in carriers of CHEK2 pathogenic variants. It also identifies a potential association among obesity, family history, and breast cancer risk in young CHEK2 gene carriers.
Selective Progesterone Receptor Modulators—Mechanisms and Therapeutic Utility
Authors: Islam Md Soriful , Afrin Sadia , Jones Sara Isabel , Segars James 
Published: May 2020

AbstractSelective progesterone receptor modulators (SPRMs) are a new class of compounds developed to target the progesterone receptor (PR) with a mix of agonist and antagonist properties. These compounds have been introduced for the treatment of several gynecological conditions based on the critical role of progesterone in reproduction and reproductive tissues. In patients with uterine fibroids, mifepristone and ulipristal acetate have consistently demonstrated efficacy, and vilaprisan is currently under investigation, while studies of asoprisnil and telapristone were halted for safety concerns. Mifepristone demonstrated utility for the management of endometriosis, while data are limited regarding the efficacy of asoprisnil, ulipristal acetate, telapristone, and vilaprisan for this condition. Currently, none of the SPRMs have shown therapeutic success in treating endometrial cancer. Multiple SPRMs have been assessed for efficacy in treating PR-positive recurrent breast cancer, with in vivo studies suggesting a benefit of mifepristone, and multiple in vitro models suggesting the efficacy of ulipristal acetate and telapristone. Mifepristone, ulipristal acetate, vilaprisan, and asoprisnil effectively treated heavy menstrual bleeding (HBM) in patients with uterine fibroids, but limited data exist regarding the efficacy of SPRMs for HMB outside this context. A notable class effect of SPRMs are benign, PR modulator-associated endometrial changes (PAECs) due to the actions of the compounds on the endometrium. Both mifepristone and ulipristal acetate are effective for emergency contraception, and mifepristone was approved by the US Food and Drug Administration (FDA) in 2012 for the treatment of Cushing’s syndrome due to its additional antiglucocorticoid effect. Based on current evidence, SPRMs show considerable promise for treatment of several gynecologic conditions.
The Changing Face of Adrenoleukodystrophy
Authors: Zhu Jia , Eichler Florian , Biffi Alessandra , Duncan Christine N , Williams David A , Majzoub Joseph A 
Published: May 2020

AbstractAdrenoleukodystrophy (ALD) is a rare X-linked disorder of peroxisomal oxidation due to mutations in ABCD1. It is a progressive condition with a variable clinical spectrum that includes primary adrenal insufficiency, myelopathy, and cerebral ALD. Adrenal insufficiency affects over 80% of ALD patients. Cerebral ALD affects one-third of boys under the age of 12 and progresses to total disability and death without treatment. Hematopoietic stem cell transplantation (HSCT) remains the only disease-modifying therapy if completed in the early stages of cerebral ALD, but it does not affect the course of adrenal insufficiency. It has significant associated morbidity and mortality. A recent gene therapy clinical trial for ALD reported short-term MRI and neurological outcomes comparable to historical patients treated with HSCT without the associated adverse side effects. In addition, over a dozen states have started newborn screening (NBS) for ALD, with the number of states expecting to double in 2020. Genetic testing of NBS-positive neonates has identified novel variants of unknown significance, providing further opportunity for genetic characterization but also uncertainty in the monitoring and therapy of subclinical and/or mild adrenal insufficiency or cerebral involvement. As more individuals with ALD are identified at birth, it remains uncertain if availability of matched donors, transplant (and, potentially, gene therapy) centers, and specialists may affect the timely treatment of these individuals. As these promising gene therapy trials and NBS transform the clinical management and outcomes of ALD, there will be an increasing need for the endocrine management of presymptomatic and subclinical adrenal insufficiency. (Endocrine Reviews 41: 1 – 17, 2020)
Mental health considerations for children & adolescents in COVID-19 Pandemic
Authors: Imran Nazish , Zeshan Muhammad , Pervaiz Zainab 
Published: May 2020

Children are not indifferent to the significant psychological impact of the COVID-19 Pandemic. They experience fears, uncertainties, substantial changes to their routines, physical and social isolation alongside high level of parental stress. Understanding their emotions and responses is essential to properly address their needs during this pandemic. In this article, we highlight children’s vulnerability, provide an overview of common symptoms of distress in different age groups, and summarize the interventions and resources available to promote child mental health and wellbeing during these challenging times. We advocate that prioritizing mental health including child & adolescent mental health is an essential component of any universal, community led response to COVID-19 Pandemic.
doi: https://doi.org/10.12669/pjms.36.COVID19-S4.2759
How to cite this:Imran N, Zeshan M, Pervaiz Z. Mental health considerations for children & adolescents in COVID-19 Pandemic. Pak J Med Sci. 2020;36(COVID19-S4):COVID19-S67-S72. doi: https://doi.org/10.12669/pjms.36.COVID19-S4.2759
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Population dynamics and predatory impact of the alien jellyfish Aurelia solida (Cnidaria, Scyphozoa) in the Bizerte Lagoon (southwestern Mediterranean Sea)
Authors: GUEROUN SONIA K.M. , MOLINERO JUAN CARLOS , PIRAINO STEFANO , DALY YAHIA MOHAMED NEJIB 
Published: May 2020

Understanding the life cycle strategies and predatory impact of alien jellyfish species is critical to mitigate the impact these organisms may have on local populations, biodiversity, and ultimately on the functioning of food webs. In the Mediterranean Sea, little is known about the dynamics of alien jellyfish, although this area is a biodiversity hotspot and one of the most threatened by an increasing number of alien jellyfish. Here, we investigated the population dynamics and predatory impact of a non-indigenous scyphomedusa, Aurelia solida Browne 1905, in the Bizerte Lagoon, Tunisia. The study was based on a bimonthly survey performed over two consecutive years, from November 2012 to August 2014. Field observations showed that the planktonic phase of A. solida occurs from winter to early summer. Prey composition was investigated by means of gut content and field zooplankton analyses. Calanoid copepods, mollusc larvae and larvaceans represented the main food items of A. solida. To determine the jellyfish feeding rate and their predatory impact on zooplankton populations, the digestion time for zooplankton prey was assessed at three different temperatures: 13, 18 and 23 °C in laboratory conditions, corresponding to the average range of temperatures encountered by A. solida in the Bizerte Lagoon. We found that A. solida consumed 0.5–22.5% and 0.02–37.3% of the daily zooplankton standing stock in 2013 and 2014, respectively. These results indicate a non-negligible but restricted seasonal grazing impact on some mesozooplankton groups, explained by the relatively short lifespan of the medusa stage (5–6 months).
Characterising demographics, knowledge, practices and clinical care among patients attending sickle cell disease clinics in Eastern Uganda
Authors: Olupot-Olupot Peter , Wabwire Ham , Ndila Carolyne , Adong Ruth , Ochen Linus , Amorut Denis , Abongo Grace , Okalebo Charles B. , Akello Sarah Rachael , Oketcho Joy B. , Okiror William , Asio Sarah , Odiit Amos , Alaroker Florence , Nyutu Gideon , Maitland Kathryn , Williams Thomas N. 
Published: May 2020

Background: In Uganda to date, there are neither established registries nor descriptions of facility-based sickle cell disease (SCD) patient characteristics beyond the central region. Here, we summarize data on the baseline clinical characteristics and routine care available to patients at four clinics in Eastern Uganda as a prelude to a clinical trial. Methods: Between February and August 2018, we conducted a cross-sectional survey of patients attending four SCD clinics in Mbale, Soroti, Atutur and Ngora, all in Eastern Uganda, the planned sites for an upcoming clinical trial (H-PRIME: ISRCTN15724013). Data on socio-demographic characteristics, diagnostic methods, clinic schedules, the use of prophylactic and therapeutic drugs, clinical complications and patient understanding of SCD were collected using a structured questionnaire. Results: Data were collected on 1829 patients. Their ages ranged from 0 to 64 years with a median (IQR) of 6 (3-11) years. 50.9% of participants were male. The majority (1151; 62.9%) reported a positive family history for SCD. Approximately half knew that SCD is inherited from both parents but a substantial proportion did not know how SCD is transmitted and small numbers believed that it is acquired by either transfusion or from other people. Only 118/1819 (6.5%) participants had heard about or were using hydroxyurea while 356/1794 (19.8%) reported stigmatization. Participants reported a median of three (IQR 1-4) hospital admissions during the preceding 12 months; 80.8% had been admitted at least once, while 14.2% had been admitted more than five times. Pain was the most common symptom, while 83.9% of those admitted had received at least one blood transfusion. Conclusion: The majority of patients attending SCD clinics in Eastern Uganda are children and few are currently being treated with hydroxyurea. The data collected through this facility-based survey will provide background data that will be useful in planning for the H-PRIME trial.
ESTUDOS DE GÊNERO NA GEOGRAFIA: UMA ANÁLISE FEMINISTA DA PRODUÇÃO DO ESPAÇO
Authors: Reis Maíra Lopes 
Published: May 2020

Resumo: O presente texto se trata de um estudo teórico, com iniciativa de associar a análise do espaço geográfico e gênero enquanto categoria analítica, tendo em vista, que os referenciais que abordam esses temas vêm crescendo, tornando mais rico o debate dessa nova maneira de estudar as manifestações geográficas. Discute-se o conceito de gênero, a partir da construção histórica da opressão feminina dentro do contexto da sociedade de classe, e no processo de organização do espaço geográfico. Como forma de unir a categoria de gênero ao conceito de espaço, aborda-se as relações de gênero como agentes estruturantes na construção do espaço, e a Geografia enquanto uma ciência que deve ampliar suas reflexões sobre estas relações, entendendo-as como parte das práticas espaciais que permite desvendar a base da organização geográfica das sociedades e a estrutura de poder entre os gêneros.Palavras-chave: Geografia; gênero, espaço; geográfico.
ASPECTOS TEÓRICOS DA HISTÓRIA DA CARTOGRAFIA: VINTE ANOS DEPOIS
Authors: Novaes André Reyes , Dawl Ed 
Published: May 2020

Para a décima sexta Conferência Internacional sobre História da Cartografia, ocorrida em Viena em 1995, Ed Dahl convidou três colegas - Matthew Edney, Christian Jacob, and Catherine Delano Smith – para apresentarem artigos em uma sessão especial sobre o papel da teoria na história da cartografia. Naquela ocasião, ele afirmou que os aspectos teóricos dos trabalhos em história da cartografia seguiam uma “área pouco enfatizada e desenvolvida” (Dahl, Imago Mundi, 1996:185). Os três artigos e cinco comentários foram publicados na Imago Mundi em 1996 e o debate circulou por muitos espaços acadêmicos.
PAÍS E PAISAGEM NA ALMA DO POVO NORTE-AMERICANO
Authors: Ratzel Friedrich 
Published: May 2020

Texto traduzido pelos Professores Jörn Seemann (Ball State University) e Breno Viotto Pedrosa (Universidade Federal do Rio Grande do Sul) do original “Land und Landschaft in der nordamerikanischen”, publicado na Deutsche Monatsschrift für das gesamte Leben der Gegenwart, v.10, p.523-538, 1902
ENTRE SILÊNCIOS E PROTESTOS: UMA REFLEXÃO SOBRE ESCRITA PRETA NO CIBERESPAÇO
Authors: Raul Jessica Mara 
Published: May 2020

Mulheres negras têm, historicamente, se mobilizado em diversos espaços políticos na busca por justiça social e, com a proliferação de smartphones e tablets ampliaram a possibilidade de registro e divulgação quase simultânea de eventos nas plataformas de redes sociais, encurtando a distância entre um evento e sua publicização (TAYLOR, 2017). Mesmo diante das disputas necessárias com as plataformas e infraestruturas digitais, como os GAFA (Google, Amazon, Facebook e Apple), podemos observar a ascensão do ciberespaço como ambiente de articulação das mulheres negras. Este artigo se apoia em uma pesquisa qualitativa aplicada à internet, de caráter exploratório, com o objetivo de analisar a utilização das redes sociais, a partir das quais se pode verificar as “pedagogias negras”. Para tanto, busca-se identificar as ações de mulheres negras por autodefinição e autorrepresentação (COLLINS, 2016) e sua utilização para a construção de outras representações da comunidade negra no Brasil e de si mesmas. Apoiado do pressuposto de que a atuação dessas sujeitas viabilizam a disseminação de práticas educativas no que tange às relações raciais no Brasil, se pretende problematizar a potencialidade da ação de mulheres negras no ciberespaço. Assim, a escrita “ciber-ativista” (CARDOSO, 2018) se efetua enquanto prática de intervenção que perceptivelmente já contribui para a transformação das discussões sobre negritude e gênero no Brasil, configurando-se em resposta inovadora às suas representações estereotipadas, perpetuadas ao longo da história nacional.
PUNKS, SAPATONAS E WELFARE QUEENS - POTENCIAL RADICAL DA POLÍTICA QUEER?
Authors: Cohen Cathy , De Almeida Valeria Lima 
Published: May 2020

Trata-se de uma tradução do artigo "Punks, bulldaggers e welfare queens - the radical potential of queer politics?", da cientista política estadunidense Cathy Cohen. O artigo problematiza a abordagem de "opressão única" da teoria queer, trazendo também para a discussão de sujeitos sexualmente marginalizados outras categorias identitárias não comumente vistas como queer, sugerindo a ampliação desse conceito e trazendo uma abordagem interseccional para o ativismo queer.
WEBSÉRIE ‘FALA PRETA: VOZES DO PRESENTE – MULHERES QUE INSPIRAM MULHERES’
Authors: Olivatto Bruno , Santos Elaine Amazonas Alves dos , Santana Edilene 
Published: May 2020

‘Fala Preta: vozes do presente – mulheres que inspiram mulheres’ é uma websérie audiovisual, de curta-metragem, estruturada em 05 episódios, produzida pelo Centro de Estudos e Assessoria Pedagógica/CEAP, ONG fundada pelos Jesuítas, atuante há 26 anos na cidade de Salvador, Bahia. A obra é resultante de edital público, executado no ano 2019, promovido pela Secretaria de Promoção da Igualdade Racial/SEPROMI, do Governo do Estado da Bahia. A iniciativa intenciona visibilizar, por amplificação das vozes de mulheres negras, suas percepções sobre questões de gênero, raça, classe, sexualidade, saúde, empreendedorismo, entre outros temas que orbitam diretamente o seu cotidiano das relações sociais. Esta produção audiovisual foi precedida de rodas temáticas de conversa, contando com a participação de 40 mulheres negras, por 12 encontros presenciais físicos, ao longo de 03 meses, realizados na sede do CEAP. A websérie ‘Fala Preta’ é produto cultural de valorização das histórias de vida dessas mulheres, trazendo realce de suas narrativas críticas e testemunhos diários de superação, bem como acentua protagonismos e (re)existências empreendidas em seus diferentes e desafiadores contextos sociais, desde o familiar ao profissional, passando pelas suas relações com a escola, com movimentos sociais e suas práticas de sobrevivência material e existencial. Trata-se de dispositivo formativo acionador de reflexões em torno, especialmente, de questões como machismo, sexismo, patriarcado, racismo estrutural, entre outros.
PEDAGOGIA SURDA E VISUALIDADES: RASTROS CULTURAIS IMAGÉTICOS INDICADORES DE APRENDIZAGEM NA CIBERCULTURA
Authors: Colacique Rachel Capucho , Amaral Mirian Maia 
Published: May 2020

Este artigo, inspirado numa pesquisa de doutorado que procurou investigar o papel preponderante das visualidades para a aprendizagem das pessoas surdas, em diferentes “espaçostempos” educativos, tem como objetivo central identificas rastros culturais produzidos pelos praticantes surdos, indicadores de aprendizagem, na imbricação cibercultura/cidade. Para isso, buscamos amparo em posicionamentos que norteiam os estudos da visualidade e da pedagogia surda (Ströbel, 2008, 2009); Perlin, 2006; Skliar, 1997), ancorados nos princípios da multirreferencialidade, que exige a adoção de um olhar plural, a partir de sistemas de referências distintos (Ardoino,1998), e nas pesquisas com os cotidianos (Alves, 2012; Certeau, 2013; Andrade, Caldas e Alves, 2019), que enfatizam as práticas pedagógicas, o que possibilitou-nos apreender algumas produções que circulam pela Internet, cujas conversas e narrativas dos praticantes culturais nos forneceram indícios de aprendizagens, que podem auxiliar a prática didática a partir das imagens visuais.
Power and energy scaling of rod-type cryogenic Yb:YLF regenerative
amplifiers
Authors: Demirbas Umit , Cankaya Huseyin , Pergament Mikhail , Kärtner Franz X. 
Published: May 2020

We numerically investigate the power and energy scaling potential of
cryogenic Yb:YLF regenerative amplifiers in rod geometry. Our approach
is based on solving the coupled set of equations describing thermal
behavior of the material and its effect on spectroscopic properties,
gain, and overall amplification. The approach is first benchmarked
with earlier experimental data. By carefully analyzing the sensitivity
of the system to operation parameters, we see that the relatively low
gain nature of the Yb:YLF and the onset of thermal effects are the
main factors that limited the performance in earlier experimental
work. We show that usage of dual-rod geometry promises much improved
performance. Specifically, we demonstrate that sub-250 fs pulses with
an average power of up to 270 W and a peak power above 500 GW can be
extracted directly from a single-stage Yb:YLF regenerative amplifier
employing dual Yb:YLF rods. We further show that by adjusting the spot
size in the regenerative amplifier, one can operate the amplifier in
either high-energy mode (

>

100

m
J

at 1 kHz) or high-average-power mode (

>

25

m
J

at 10 kHz, with

>

250

W

). We also discuss pros and cons of
Yb:YLF with respect to Yb:YAG, and underline the need for measurement
of population and photo-elastic-effect-induced lensing in Yb:YLF to
obtain a better understanding of Yb:YLF systems. The findings
presented in this work can be used for the design and development of
next-generation high-average and peak-power Yb:YLF amplifier
systems.
A figura incerta do antilivro
Authors: Silva Rui 
Published: May 2020

Recensão crítica de Nicholas Thoburn, Anti-Book: On the Art and Politics of Radical Publishing. Minneapolis, University of Minnesota Press, 2016, 398 pp. ISBN 978-0-8166-2196-5
DOI: https://doi.org/10.14195/2182-8830_7-1_15
No bounds for the bound book: a digital refresh to reload the page
Authors: Reina Patrícia 
Published: May 2020

Review of Kiene Brillenburg Wurth, Kári Driscoll and Jessica Pressman (eds.), Book Presence in a Digital Age. London: Bloomsbury Academic, 2018, 280 pp. ISBN 978-1-5013-2118-4.
DOI: https://doi.org/10.14195/2182-8830_7-1_16