bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precursor-induced conditional random fields: connecting separate entities by induction for improved clinical named entity recognition
Authors: Lee Wangjin , Choi Jinwook 
Published: July 2019

Abstract
Background
This paper presents a conditional random fields (CRF) method that enables the capture of specific high-order label transition factors to improve clinical named entity recognition performance. Consecutive clinical entities in a sentence are usually separated from each other, and the textual descriptions in clinical narrative documents frequently indicate causal or posterior relationships that can be used to facilitate clinical named entity recognition. However, the CRF that is generally used for named entity recognition is a first-order model that constrains label transition dependency of adjoining labels under the Markov assumption.

Methods
Based on the first-order structure, our proposed model utilizes non-entity tokens between separated entities as an information transmission medium by applying a label induction method. The model is referred to as precursor-induced CRF because its non-entity state memorizes precursor entity information, and the model’s structure allows the precursor entity information to propagate forward through the label sequence.

Results
We compared the proposed model with both first- and second-order CRFs in terms of their F1-scores, using two clinical named entity recognition corpora (the i2b2 2012 challenge and the Seoul National University Hospital electronic health record). The proposed model demonstrated better entity recognition performance than both the first- and second-order CRFs and was also more efficient than the higher-order model.

Conclusion
The proposed precursor-induced CRF which uses non-entity labels as label transition information improves entity recognition F1 score by exploiting long-distance transition factors without exponentially increasing the computational time. In contrast, a conventional second-order CRF model that uses longer distance transition factors showed even worse results than the first-order model and required the longest computation time. Thus, the proposed model could offer a considerable performance improvement over current clinical named entity recognition methods based on the CRF models.
A controlled field experiment to investigate the deterioration of earthen heritage by wind and rain
Authors: Richards J. , Zhao G. , Zhang H. , Viles H. 
Published: July 2019

Abstract
Earthen heritage constitutes 10% of sites on the World Heritage List and many of these sites are experiencing extensive deterioration caused by environmental forces, such as wind and rain. This study used a well-established test wall to investigate the impact of environmental conditions on the deterioration of earthen heritage at the remote and under-studied site of Suoyang Ancient City, Gansu Province, China, which is exhibiting widespread deterioration. Test walls have previously been used in earthen heritage research as they allow controlled experiments to be undertaken on complex, realistic structures without risking damage or loss of value to the historic material. This study used portable wind and rain erosion simulation devices to investigate experimentally (i) the comparative effect of wind, sediment-laden wind and wind-driven rain in causing deterioration to earthen heritage and (ii) how the incipient deterioration features produced by wind, sediment-laden wind and wind-driven rain on the test wall relate to the deterioration features recorded on the historic city walls. The test wall was subjected to low, medium and high intensities of clean wind, sediment-laden wind and wind-driven rain. The extent of deterioration produced was measured using repeat, high resolution laser scans before and after each test run. The deterioration features caused by each environmental force were notably different with clean wind removing the loose surface material, sediment-laden wind causing pitting and wind-driven rain causing incipient gullying. These incipient features compare well with more developed features seen on the historic walls. Wind-driven rain caused the greatest amount of deterioration while clean wind caused the least. However, as the frequency and duration of wind events at Suoyang is much greater than those of rain events, wind is likely to play an important role in the deterioration of earthen heritage over annual timescales. These findings show that conservation strategies at rammed earth sites like Suoyang need to address the impact of multiple environmental forces, such as clean wind, sediment laden wind and wind-driven rain.
Comparison of screening strategies for Lynch syndrome in patients with newly diagnosed endometrial cancer: a prospective cohort study in China
Authors: Chao Xiaopei , Li Lei , Wu Ming , Ma Shuiqing , Tan Xianjie , Zhong Sen , Bi Yalan , Lang Jinghe 
Published: July 2019

AbstractBackgroundThe prevalence of Lynch syndrome and screening strategies for this disorder in Chinese patients with endometrial cancer have seldom been investigated. Such data would be essential for the screening, prevention, genetic counseling, and treatment of Lynch syndrome. The purpose of this prospective study was to determine the accuracy of the mismatch repair (MMR) protein immunohistochemistry (IHC), microsatellite instability (MSI) test, and clinical diagnostic criteria in screening for Lynch syndrome‐associated endometrial cancer (LS‐EC) in a prospective Chinese cohort.MethodsAll patients with newly diagnosed endometrial cancer (EC) were evaluated using clinical diagnostic criteria (Amsterdam II criteria and the revised Bethesda guidelines), MSI test, and IHC of MMR proteins in tumor tissues. For all patients, the screening results were compared with results of germline sequencing for pathogenic variants of MMR genes.ResultsBetween December 2017 and August 2018, a total of 111 unselected patients with newly diagnosed EC were enrolled. Six patients (5.4%) harbored a pathogenic germline mutation of MMR genes: 1 had a mutation in MutL homolog 1 (MLH1), 2 in MutS homolog 2 (MSH2), and 3 in MutS homolog 6 (MSH6). The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for identifying LS‐EC were 33.3%, 88.6%, 14.3%, and 95.9%, for the clinical criteria, 66.7%, 75.0%, 14.3%, and 97.3% for IHC of MMR proteins, 100%, 89.9%, 33.3%, and 100% for MSI test, and 100%, 72.4%, 20.0% and 100% for combined IHC and MSI test, respectively. The combination of IHC and MSI test had higher sensitivity and PPV than the clinical criteria (p = 0.030). MSI test and IHC were highly concordant for LS‐EC screening (73/77, 94.8%).ConclusionThe accuracy of the combination of IHC of MMR proteins and MSI test for screening LS among Chinese patients with EC was superior to that of the clinical criteria.Trial registration NCT03291106. Registered on September 25, 2017
Impact of BRAF V600E and TERT Promoter Mutations on Response to Therapy in Papillary Thyroid Cancer
Authors: Trybek Tomasz , Walczyk Agnieszka , Gąsior-Perczak Danuta , Pałyga Iwona , Mikina Estera , Kowalik Artur , Hińcza Kinga , Kopczyński Janusz , Chrapek Magdalena , Góźdź Stanisław , Kowalska Aldona 
Published: July 2019

Abstract
In this study, we examined the relationship between coexisting BRAF V600E and TERT promoter mutations in papillary thyroid cancer (PTC) and response to therapy. PTC cases (n = 568) with known BRAF and TERT status, diagnosed from 2000 to 2012 and actively monitored at one institution, were reviewed retrospectively. Associations between BRAF V600E and TERT promoter mutations and clinicopathological features, Tumor-Node-Metastasis stage, initial risk, response to therapy, follow-up, and final disease outcome were assessed according to American Thyroid Association 2015 criteria and the American Joint Committee on Cancer/Tumor-Node-Metastasis (8th edition) staging system. Median follow-up was 120 months. TERT promoter mutations (any type) were detected in 13.5% (77/568) of PTC cases with known BRAF status. The C228T and C250T TERT hotspot mutations were found in 54 (9.5%) and 23 (4%) patients, respectively, and 22 other TERT promoter alterations were identified. Coexisting BRAF V600E and TERT hotspot promoter mutations were detected in 9.5% (54/568) of patients, and significantly associated with older patient age (P = 0.001), gross extrathyroidal extension (P = 0.003), tumor stage pT3-4 (P = 0.005), stage II to IV (P = 0.019), intermediate or high initial risk (P = 0.003), worse than excellent response to primary therapy (P = 0.045), recurrence (P = 0.015), and final outcome of no remission (P = 0.014). We conclude that coexisting BRAF V600E and TERT mutations in patients with PTC are associated with poor initial prognostic factors and clinical course and may be useful for predicting a worse response to therapy, recurrence, and poorer outcome than in patients without the above mutations.
The good, the bad and the slimy: experimental studies of hagfish digestive and nutritional physiology
Authors: Glover Chris N. , Weinrauch Alyssa M. 
Published: July 2019

ABSTRACT
The hagfishes provide valuable insight into the physiology of feeding, digestion and nutrient absorption by virtue of unusual and unique features of their biology. For example, members of this group undergo long periods of fasting, and are the only vertebrates known to absorb organic nutrients across their epidermal surface. Such properties engender significant attention from researchers interested in feeding and feeding-related processes; however, the practical realities of employing the hagfish as an experimental organism can be challenging. Many of the key tools of the experimental biologist are compromised by a species that does not readily feed in captivity, is difficult to instrument and which produces copious quantities of slime. This Commentary provides critical insight into the key aspects of hagfish feeding and digestive processes, and highlights the pitfalls of this group as experimental organisms. We also suggest key research gaps that, if filled, will lead to better understanding of hagfishes, and we consider how this group may advance our knowledge of feeding, digestion and nutrient absorption processes.
Correlates of Children’s Physical Activity: A Canadian Multisite Study
Authors: LAROUCHE RICHARD , BLANCHETTE SÉBASTIEN , FAULKNER GUY , RIAZI NEGIN , TRUDEAU FRANÇOIS , TREMBLAY MARK S. 
Published: July 2019

ABSTRACT

Purpose
To inform future physical activity (PA) interventions among children, we investigated the correlates of PA among 8- to 12-yr-olds in three regions of Canada: Ottawa, Trois-Rivières, and Vancouver.

Methods
We recruited 1699 children (55.0% girls) in 37 schools located in urban, suburban, and rural areas that differed in socioeconomic status. Children wore a sealed SC-StepRx pedometer capable of measuring moderate- to vigorous-intensity physical activity (MVPA) for seven consecutive days. Children and one of their parents/guardians completed a questionnaire that captured multiple potential PA correlates. Publicly available data on weather and neighborhood walkability were obtained. Multiply-imputed gender-stratified linear mixed models were used to examine the correlates of daily step counts and MVPA while controlling for age, site, type of urbanization, and area-level socioeconomic status.

Results
Each additional hour spent outdoors was associated with higher PA in boys (+769 steps per day; +3.7 min MVPA per day) and girls (+596 steps per day; +3.5 min·d−1). Boys’ PA declined with age (−500 steps per day; −3.7 min·d−1). Boys were less active if they had a long-standing injury/illness (−1862 steps per day; −3.7 min·d−1) or their parents reported driving to work (−835 steps per day; −4.4 min·d−1), were worried about traffic (−982 steps per day; −6.4 min·d−1), or about other people in their neighborhood (−1250 steps per day). Girls speaking neither English nor French at home were less active (−620 steps per day; −3.7 min·d−1). In girls, each degree Celsius increase in morning temperature was associated with 77 additional steps per day, and each kilometer increase in active school travel distance was associated with 0.5 more MVPA minutes per day.

Conclusion
Consistent with previous studies, our results suggest that PA interventions should aim to increase outdoor time. The observed gender differences in PA correlates suggest the need for a gender-sensitized approach to PA promotion.
Understanding the contribution of UK public health research to clinical guidelines: a bibliometric analysis
Authors: Guthrie Susan , Cochrane Gavin , Deshpande Advait , Macaluso Benoit , Larivière Vincent 
Published: July 2019

Background: There is an increasing need to understand the wider impacts of research on society and the economy. For health research, a key focus is understanding the impact of research on practice and ultimately on patient outcomes. This can be challenging to measure, but one useful proxy for changes in practice is impact on guidelines. Methods: The aim of this study is to map the contribution of UK research and UK research funders to the National Institute for Health and Clinical Excellence (NICE) public health guidelines, understanding areas of strengths and weakness and the level of collaboration and coordination across countries and between funders. The work consisted of two main elements: analysis of the references cited on NICE guidelines and interviews with experts in public health. Results: Across the papers cited on 62 NICE public health guidelines, we find that 28% of the papers matched include at least one UK affiliation, which is relatively high when compared to other health fields. In total, 165 unique funders were identified with more than three acknowledgements, based in 20 countries. 68% of papers which acknowledge funding cite at least one UK funder, and NIHR is the most highly cited funder in the sample. Conclusions: The UK makes an important contribution to public health research cited on NICE PH guidelines, although the research does not appear to be bibliometrically distinct from other research sectors, other than having a relatively low level of international collaboration. However, the extent to which NICE public health guidelines reflect practice at the local authority level is less clear. More research is needed to understand the sources of evidence to support public health decision making at the local level and how NICE guidance can be made more applicable, timely and accessible in this new context.
Does fluoroscopy prevent inadvertent parathyroidectomy in thyroid surgery?
Authors: DiMarco A , Chotalia R , Bloxham R , McIntyre C , Tolley N , Palazzo FF 
Published: July 2019

Introduction Near-infrared imaging may facilitate intraoperative identification of parathyroid glands by causing autofluorescence but its clinical value has not been established. Inadvertent parathyroidectomy occurs in 5–22% of thyroidectomies and is associated with temporary and permanent hypoparathyroidism. The aim of this study was to determine whether near-infrared imaging prevents inadvertent parathyroidectomy and early hypocalcaemia as a surrogate for permanent hypoparathyroidism. Materials and methods Near-infrared imaging was used in a prospective cohort of consecutive thyroidectomies. Thyroidectomies performed prior to the introduction of near-infrared imaging formed a control group. The thyroid bed and specimen were scanned with near-infrared imaging. Areas of autofluorescence on the specimen were examined and any parathyroid tissue found was autotransplanted. Inadvertent parathyroidectomy was therefore recorded as established intraoperatively by near-infrared imaging (allowing autotransplantation) or on subsequent histology (missed). Serum calcium and parathyroid hormone were measured on day one and at two weeks and six months postoperatively. Results A total of 269 patients were included: 106 near-infrared imaging and 163 controls. Inadvertent parathyroidectomy was detected by near-infrared imaging in two (and autotransplantation performed) and histologically (i.e. missed by near-infrared imaging in 13, 12.3% vs 17, 10.4% controls). Neither result was statistically significant (P = 0.08, 0.89). There was no significant difference in serum calcium or parathyroid hormone between near-infrared imaging and control groups at one day, two weeks or thereafter. Discussion Near-infrared imaging may detect inadvertent parathyroidectomy and may allow autotransplantation. It did not, however, reduce the incidence of missed inadvertent parathyroidectomy and no difference was seen in early hypocalcaemia or late hypoparathyroidism. Current near-infrared imaging technology does not appear to confer a clinical benefit sufficient to justify its use.
Effect of Lipoprotein(a) on the Diagnosis of Familial Hypercholesterolemia: Does It Make a Difference in the Clinic?
Authors: Chan Dick C , Pang Jing , Hooper Amanda J , Bell Damon A , Burnett John R , Watts Gerald F 
Published: July 2019

Abstract

BACKGROUND
Diagnostic tools for familial hypercholesterolemia (FH) rely on estimation of LDL cholesterol concentration. However, routine measurement or calculation of LDL cholesterol concentration using the Friedewald equation contains a cholesterol contribution from lipoprotein(a) [Lp(a)]. We investigated whether Lp(a) influences the phenotypic diagnosis of FH by commonly used clinical criteria.

METHODS
A cohort of 907 adult index patients attending a clinic were studied. The Dutch Lipid Clinic Network (DLCN) and Simon Broome (SB) diagnostic criteria were estimated before and after adjusting LDL cholesterol concentration for the cholesterol content (30%) of Lp(a). Diagnostic reclassification rates and area under the ROC (AUROC) curves in predicting an FH mutation were also compared.

RESULTS
Seventy-four patients defined by DLCN criteria (8.2%) and 207 patients defined by SB criteria (22.8%) were reclassified to “unlikely” FH after adjusting LDL cholesterol for Lp(a) cholesterol. The proportion of FH patients defined by DLCN (probable/definite) and SB (possible/definite) criteria decreased significantly in patients with increased Lp(a) (&gt;0.5 g/L; n = 330) after Lp(a) cholesterol adjustment (P &lt; 0.01). The overall reclassification rate was significantly higher in patients with Lp(a) concentration &gt;1.0 g/L (P &lt; 0.001). The AUROC curve for LDL cholesterol concentration ≥191 mg/dL (≥5.0 mmol/L), DLCN criteria, and SB criteria in predicting an FH mutation increased significantly after adjustment (P &lt; 0.001). There was no significant difference in AUROC curve before and after Lp(a) cholesterol adjustment at an LDL cholesterol concentration ≥251 mg/dL (≥6.5 mmol/L).

CONCLUSIONS
Adjusting LDL cholesterol concentration for Lp(a) cholesterol improves the diagnostic accuracy of DLCN and SB criteria, especially with Lp(a) &gt;1.0 g/L and LDL cholesterol &lt;251 mg/dL (&lt;6.5 mmol/L). Lp(a) should be measured in all patients suspected of having FH.
Isolated Intestinal Ganglioneuroma Mimicking Small Bowel Crohn's Disease
Authors: Badrinath Madhuri , Mandru Rachana , Lowe Dhruv , Manocha Divey , Achufusi Ted 
Published: July 2019

ABSTRACT
Ganglioneuromas (GNs) are hamartomatous tumors derived from the autonomic nervous system. GNs are frequently associated with neurofibromatosis-1 and multiple endocrine neoplasia type 2b and commonly present with constipation, abdominal pain, weight loss, obstruction, and gastrointestinal bleeding. We report a 40-year-old man with symptoms of chronic abdominal pain, weight loss, and diarrhea for 1 year. Imaging was suggestive of thickening of ileal wall with a stricture, and subsequent biopsy revealed intestinal GN. To our knowledge, this is the first case report of an isolated intestinal GN masquerading as Crohn's disease.
Utility of Endoscopic Retrograde Cholangiopancreatography in the Treatment of Intraductal Papillary Neoplasm of the Bile Duct
Authors: Patel Nicolas , Goodman Adam 
Published: July 2019

ABSTRACT
Intraductal papillary neoplasm of the bile duct is a rare bile duct tumor that displays a range of cytoarchitectural atypia and is recognized as a precursor of invasive carcinoma. We present a 71-year-old woman with a recent diagnosis of lung adenocarcinoma, who presented with acute cholangitis secondary to an obstructive intraductal papillary neoplasm of the bile duct. The patient underwent endoscopic retrograde cholangiopancreatography, which identified the lesion, and on biliary sweep, the polyp presented externally and she underwent successful polypectomy with resolution of the infection.
Intramural Hematoma Causing Hematochezia After Colonoscopy With Polypectomy
Authors: Gavrić Aleksandar , Dežman Rok , Stefanović Sebastian , Drnovšek Jan , Štabuc Borut 
Published: July 2019

ABSTRACT
Intramural hematoma of the colon is a rare complication of colonoscopy. We present a case of a 78-year-old woman on warfarin who presented with hematochezia and hypotension due to intramural hematoma of the sigmoid colon after colonoscopy with polypectomy of small polyps in the right colon.
Strongyloides stercoralis Hyperinfection and Concomitant Cytomegalovirus Gastroenteritis in an Immunocompromised Host
Authors: Crowe Brooks R. , Duenas Sean M. , Serrano Antonio , Kingsbery Joseph , Williams Renee 
Published: July 2019

ABSTRACT

Strongyloides stercoralis infection typically presents with nonspecific gastrointestinal symptoms and no definitive or pathognomonic endoscopic findings. Disease burden can vary depending on a patient's immune status. Immunocompromised patients with strongyloidiasis can develop tremendous disease burden, extraintestinal dissemination, and are at risk for coinfection with other organisms. We present the case of an immunocompromised patient presenting with multiple gastrointestinal complaints found to have S. stercoralis hyperinfection and concomitant cytomegalovirus gastroenteritis.
"Sou menos/Quando não sou líquida"
Authors: Silva Sandro Adriano da 
Published: July 2019

Este artigo pretende uma análise do poema “I”, da obra Alcoólicas (1989), de Hilda Hilst, considerando os elementos de sua configuração poética e presença de uma imaginação simbólica em torno do elemento água em sua face etílica. A arquitetônica do poema e o imaginário fundem-se na captação e expressão da experiência de um sujeito poético solitário que margeia sentidos de dissolvência pela embriaguez da subjetividade lírica diante do imponderável existir. E ainda assim celebra a Vida. É nessa faixa criadora que se situa Alcoólicas, cujos poemas afirmam-se na ubiquidade do arquétipo água – desde sempre apontado como arké, fonte ou origem da vida e da morte – que os nutre no essencial, violento e ambíguo confluir da atividade imaginante da poeta.
Palavras-chave: Poesia brasileira. Hilda Hilst. Alcoólicas. Poética. Imaginação simbólica.
Ciclos míticos do sul
Authors: Mora Arthur Katrein 
Published: July 2019

Ciclos míticos podem modificar uma linguagem – costumes, imaginário – para além do reconhecimento, alterando profundamente as relações de uma população com a sua terra. Relações estas que transitam entre tradição e progresso, manutenção e destruição, quebra e continuidade, e que permeiam a narrativa de Assim na terra, romance de Luiz Sérgio Metz. O espaço do Rio Grande do Sul, seus edifícios e seus personagens, além de seu processo histórico, encontra na literatura e em seu repertório de mitos, símbolos e tradições, um novo vigor que ilustra o consolo dos eufemismos frente ao esquecimento e a morte. Entre a afetividade poética dos espaços de Gaston Bachelard (1975) e as harmonias e redundâncias da imaginação simbólica de Gilbert Durand (1982;1988;1996), testemunhamos na obra de Metz uma jornada rumo à afirmação da saudade, intuição afetiva que dá sentido ao olvido e aos ciclos míticos da qual deriva.
Palavras-chave: imaginário, literatura gaúcha, ciclos míticos, Bachelard, Durand.