bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of Cytochrome P450 Isoenzyme 2D6 (CYP2D6) Genotypes and Pharmacogenomic Impact on Primaquine Metabolism in an Active-Duty US Military Population
Authors: Spring Michele D , Sousa Jason C , Li Qigui , Darko Christian A , Morrison Meshell N , Marcsisin Sean R , Mills Kristin T , Potter Brittney M , Paolino Kristopher M , Twomey Patrick S , Moon James E , Tosh Donna M , Cicatelli Susan B , Froude Jeffrey W , Pybus Brandon S , Oliver Thomas G , McCarthy William F , Waters Norman C , Smith Philip L , Reichard Gregory A , Bennett Jason W 
Published: July 2019

AbstractBackgroundPlasmodium vivax malaria requires a 2-week course of primaquine (PQ) for radical cure. Evidence suggests that the hepatic isoenzyme cytochrome P450 2D6 (CYP2D6) is the key enzyme required to convert PQ into its active metabolite.MethodsCYP2D6 genotypes and phenotypes of 550 service personnel were determined, and the pharmacokinetics (PK) of a 30-mg oral dose of PQ was measured in 45 volunteers. Blood and urine samples were collected, with PQ and metabolites were measured using ultraperformance liquid chromatography with mass spectrometry.ResultsSeventy-six CYP2D6 genotypes were characterized for 530 service personnel. Of the 515 personnel for whom a single phenotype was predicted, 58% had a normal metabolizer (NM) phenotype, 35% had an intermediate metabolizer (IM) phenotype, 5% had a poor metabolizer (PM) phenotype, and 2% had an ultrametabolizer phenotype. The median PQ area under the concentration time curve from 0 to ∞ was lower for the NM phenotype as compared to the IM or PM phenotypes. The novel 5,6-ortho-quinone was detected in urine but not plasma from all personnel with the NM phenotype.ConclusionThe plasma PK profile suggests PQ metabolism is decreased in personnel with the IM or PM phenotypes as compared to those with the NM phenotype. The finding of 5,6-ortho-quinone, the stable surrogate for the unstable 5-hydroxyprimaquine metabolite, almost exclusively in personnel with the NM phenotype, compared with sporadic or no production in those with the IM or PM phenotypes, provides further evidence for the role of CYP2D6 in radical cure.Clinical Trials RegistrationNCT02960568.
A patient and public involvement investigation into healthy eating and weight management advice during pregnancy
Authors: Abayomi J C , Charnley M S , Cassidy L , Mccann M T , Jones J , Wright M , Newson L M 
Published: July 2019

AbstractObjectiveTo conduct patient and public involvement (PPI) to gain insight into the experience of healthy eating and weight management advice during pregnancy.DesignPPI in the planning and development of health interventions, aiming to ensure patient-centred care. Optimum nutrition and weight management are vital for successful pregnancy outcomes, yet many services report poor attendance and engagement.SettingCommunity venues in Liverpool and Ulster (UK).ParticipantsTwo PPI representatives were involved in all aspects of the study: design, interview questions, recruitment and collection/analysis of feedback.InterventionFeedback was collected via note taking during group discussions, two in Liverpool (n = 10 & 5); two in Ulster (n = 7 & 9) and an interview (n = 1, in Ulster).Main Outcome MeasuresTranscript data were collated and thematic analysis was applied in analysis.ResultsThematic analysis identified three themes: (i) weight gain is inevitable in pregnancy; (ii) healthy eating advice is important but currently lacks consistency and depth and (iii) expectations regarding the type of knowledge/support.ConclusionsPPI provides opportunity to enhance research design and offers valuable insight towards the needs of healthcare users. Pregnant women want positive health messages, with a focus on what they can/should do, rather than what they should not do. Midwives need to consider their communication with pregnant women, to ensure that their unique relationship is maintained, especially when the topics of diet and weight management are addressed. A well-designed digital intervention could improve access to pregnancy-specific nutrition information; empowering midwives to communicate patient-centred, healthy eating messages with confidence. This has the potential to change dietary and weight management behaviour in pregnant women.
What health records data are required for accurate prediction of suicidal behavior?
Authors: Simon Gregory E , Shortreed Susan M , Johnson Eric , Rossom Rebecca C , Lynch Frances L , Ziebell Rebecca , Penfold and Robert B 
Published: July 2019

Abstract

Objective
The study sought to evaluate how availability of different types of health records data affect the accuracy of machine learning models predicting suicidal behavior.

Materials and Methods
Records from 7 large health systems identified 19 061 056 outpatient visits to mental health specialty or general medical providers between 2009 and 2015. Machine learning models (logistic regression with penalized LASSO [least absolute shrinkage and selection operator] variable selection) were developed to predict suicide death (n = 1240) or probable suicide attempt (n = 24 133) in the following 90 days. Base models were used only historical insurance claims data and were then augmented with data regarding sociodemographic characteristics (race, ethnicity, and neighborhood characteristics), past patient-reported outcome questionnaires from electronic health records, and data (diagnoses and questionnaires) recorded during the visit.

Results
For prediction of any attempt following mental health specialty visits, a model limited to historical insurance claims data performed approximately as well (C-statistic 0.843) as a model using all available data (C-statistic 0.850). For prediction of suicide attempt following a general medical visit, addition of data recorded during the visit yielded a meaningful improvement over a model using all data up to the prior day (C-statistic 0.853 vs 0.838).

Discussion
Results may not generalize to setting with less comprehensive data or different patterns of care. Even the poorest-performing models were superior to brief self-report questionnaires or traditional clinical assessment.

Conclusions
Implementation of suicide risk prediction models in mental health specialty settings may be less technically demanding than expected. In general medical settings, however, delivery of optimal risk predictions at the point of care may require more sophisticated informatics capability.
Detecting conversation topics in primary care office visits from transcripts of patient-provider interactions
Authors: Park Jihyun , Kotzias Dimitrios , Kuo Patty , Logan IV Robert L , Merced Kritzia , Singh Sameer , Tanana Michael , Karra Taniskidou Efi , Lafata Jennifer Elston , Atkins David C , Tai-Seale Ming , Imel Zac E , Smyth Padhraic 
Published: July 2019

AbstractObjectiveAmid electronic health records, laboratory tests, and other technology, office-based patient and provider communication is still the heart of primary medical care. Patients typically present multiple complaints, requiring physicians to decide how to balance competing demands. How this time is allocated has implications for patient satisfaction, payments, and quality of care. We investigate the effectiveness of machine learning methods for automated annotation of medical topics in patient-provider dialog transcripts.Materials and MethodsWe used dialog transcripts from 279 primary care visits to predict talk-turn topic labels. Different machine learning models were trained to operate on single or multiple local talk-turns (logistic classifiers, support vector machines, gated recurrent units) as well as sequential models that integrate information across talk-turn sequences (conditional random fields, hidden Markov models, and hierarchical gated recurrent units).ResultsEvaluation was performed using cross-validation to measure 1) classification accuracy for talk-turns and 2) precision, recall, and F1 scores at the visit level. Experimental results showed that sequential models had higher classification accuracy at the talk-turn level and higher precision at the visit level. Independent models had higher recall scores at the visit level compared with sequential models.ConclusionsIncorporating sequential information across talk-turns improves the accuracy of topic prediction in patient-provider dialog by smoothing out noisy information from talk-turns. Although the results are promising, more advanced prediction techniques and larger labeled datasets will likely be required to achieve prediction performance appropriate for real-world clinical applications.
Identifying relations of medications with adverse drug events using recurrent convolutional neural networks and gradient boosting
Authors: Yang Xi , Bian Jiang , Fang Ruogu , Bjarnadottir Ragnhildur I , Hogan William R , Wu Yonghui 
Published: July 2019

AbstractObjectiveTo develop a natural language processing system that identifies relations of medications with adverse drug events from clinical narratives. This project is part of the 2018 n2c2 challenge.Materials and MethodsWe developed a novel clinical named entity recognition method based on an recurrent convolutional neural network and compared it to a recurrent neural network implemented using the long-short term memory architecture, explored methods to integrate medical knowledge as embedding layers in neural networks, and investigated 3 machine learning models, including support vector machines, random forests and gradient boosting for relation classification. The performance of our system was evaluated using annotated data and scripts provided by the 2018 n2c2 organizers.ResultsOur system was among the top ranked. Our best model submitted during this challenge (based on recurrent neural networks and support vector machines) achieved lenient F1 scores of 0.9287 for concept extraction (ranked third), 0.9459 for relation classification (ranked fourth), and 0.8778 for the end-to-end relation extraction (ranked second). We developed a novel named entity recognition model based on a recurrent convolutional neural network and further investigated gradient boosting for relation classification. The new methods improved the lenient F1 scores of the 3 subtasks to 0.9292, 0.9633, and 0.8880, respectively, which are comparable to the best performance reported in this challenge.ConclusionThis study demonstrated the feasibility of using machine learning methods to extract the relations of medications with adverse drug events from clinical narratives.
Implementation of a Blind Quality Control Program in Blood Alcohol Analysis
Authors: Moral Jackeline , Hundl Callan , Lee Dayong , Neuman Maddisen , Grimaldi Aimee , Cuellar Maria , Stout Peter 
Published: July 2019

Abstract
Declared proficiency tests are limited in their use for testing the performance of the entire system, because analysts are aware that they are being tested. A blind quality control (BQC) is intended to appear as a real case to the analyst to remove any intentional or subconscious bias. A BQC program allows a real-time assessment of the laboratory’s policies and procedures and monitors reliability of casework. In September 2015, the Houston Forensic Science Center (HFSC) began a BQC program in blood alcohol analysis. Between September 2015 and July 2018, HFSC submitted 317 blind cases: 89 negative samples and 228 positive samples at five target concentrations (0.08, 0.15, 0.16, 0.20 and 0.25 g/100 mL; theoretical targets). These blood samples were analyzed by a headspace gas chromatograph interfaced with dual-flame ionization detectors (HS-GC-FID). All negative samples produced `no ethanol detected’ results. The mean (range) of reported blood alcohol concentrations (BACs) for the aforementioned target concentrations was 0.075 (0.073–0.078), 0.144 (0.140–0.148), 0.157 (0.155–0.160), 0.195 (0.192–0.200) and 0.249 (0.242–0.258) g/100 mL, respectively. The average BAC percent differences from the target for the positive blind cases ranged from −0.4 to −6.3%, within our uncertainty of measurement (8.95–9.18%). The rate of alcohol evaporation/degradation was determined negligible. A multiple linear regression analysis was performed to compare the % difference in BAC among five target concentrations, eight analysts, three HS-GC-FID instruments and two pipettes. The variables other than target concentrations showed no significant difference (P > 0.2). While the 0.08 g/100 mL target showed a significantly larger % difference than higher target concentrations (0.15–0.25 g/100 mL), the % differences among the higher targets were not concentration-dependent. Despite difficulties like gaining buy-in from stakeholders and mimicking evidence samples, the implementation of a BQC program has improved processes, shown methods are reliable and added confidence to staff’s testimony in court.
Simplification of a species complex: Two new species of Leucothoidae (Crustacea: Amphipoda) previously attributed to Leucothoe spinicarpa (Abildgaard, 1789) in Florida, U.S.A.
Authors: White Kristine N 
Published: July 2019

Abstract
Leucothoe spinicarpa (Abildgaard, 1789) has long been thought of as a cosmopolitan species; however, relatively recent morphological studies have discovered a species complex previously attributed to L. spinicarpa. Despite this, several species remain hardly distinguishable from the general leucothoid form of L. spinicarpa. Morphological analyses reveal two distinct species in Tampa Bay, Florida, USA, which is supported by molecular mitochondrial COI and nuclear 18S ribosomal DNA data. Leucothoe tunicasp. nov. and L. machidaisp. nov. are described herein. Analyses of DNA sequences from specimens from Tampa Bay, FL, Big Pine Key, FL, and Belize of L. tunicasp. nov. demonstrate intraspecific genetic structure in morphologically identical populations. Therefore, the geographically distant populations of L. tunicasp. nov. thus represent one species with a wide distribution, whereas L. machidaisp. nov. has so far been collected only in Tampa Bay.
Proximity and learning: evidence from a post-WW2 intellectual reparations program
Authors: Bode Rasmus , Buenstorf Guido , Heinisch Dominik P 
Published: July 2019

Abstract
Prior work indicates that proximity facilitates learning, but proximity reflects individual choices. New data on a British post-World War 2 program to detain and interrogate German industrial experts allow us to minimize selection bias and to disentangle individual dimensions of proximity. Our empirical analysis of post-detention patenting activities suggests that cognitive proximity was more important for interactive learning than social and institutional proximity. Detention in the UK increased inventors’ subsequent likelihood of interacting with UK partners as well as their post-detention patent output.
Risk factors for acute exacerbation of idiopathic interstitial pneumonia in patients undergoing lung cancer treatment
Authors: Taya Tetsuya , Chiba Hirofumi , Yamada Gen , Takahashi Mamoru , Ikeda Kimiyuki , Mori Yuki , Otsuka Mitsuo , Takahashi Hiroki 
Published: July 2019

Abstract

Objective
Identifying risk factors for cancer treatment-related acute exacerbations (AEs) of idiopathic interstitial pneumonia (IIP) in patients with lung cancer.

Methods
We retrospectively reviewed clinical records of 98 patients with concurrent lung cancer and IIPs diagnosed and treated at the Sapporo Medical University Hospital from January 2010 to December 2014.

Results
Of the 98 patients with concurrent lung cancer and IIPs, 14 patients (14.3%) had AEs. A total of 10 patients died. The univariate analysis revealed that the patients with idiopathic pulmonary fibrosis (IPF) or usual interstitial pneumonia (UIP) patterns on chest computed tomography (CT) had significantly higher rates of AE than those with non-IPF or non-UIP patterns, respectively. Further, those with a reduced percentage of forced vital capacity (%FVC) predictive values or elevated Krebs von den Lungen-6 (KL-6) presented significantly higher rates of AE. Our multivariate analysis identified that UIP pattern on chest CT and each 10% decrease in %FVC were significant independent risk factors for AEs. Of the 14 patients who experienced AEs, 10 cases were associated with cancer treatment. The treatment-specific incidences were 3/40 (7.5%) for surgery, 5/50 (10.0%) for chemotherapy, and 2/26 (7.7%) for radiation therapy. After comparing the AE incidences in 55 cases receiving one treatment (monotherapy group) and in 29 cases receiving two types of treatment or more (multitherapy group), we found no significant differences.

Conclusions
Chest CT UIP patterns and reduced %FVC are independent risk factors for AE. Moreover, AE incidence did not increase in the multitherapy group compared with the monotherapy group.
Sample preparation utilizing sputter coating increases contrast of cellulose nanocrystals in the transmission electron microscope
Authors: Mulenos Marina R , Zechmann Bernd , Sayes Christie M 
Published: July 2019

Abstract
Cellulose nanocrystals (CNCs) are prepared for transmission electron microscopy (TEM) using positive or negative stains in an effort to increase the contrast between the specimen and background. When imaging CNCs, conventional stains have been shown to induce particle aggregation and produce artifacts. In this study, we report on methods used to image CNCs. To increase contrast and decrease artifacts and aggregation, sputter coating was used to coat the samples. CNCs were loaded onto copper grids and sputter coated with one of four different metals: iridium, carbon, gold, and titanium. The final layer was deposited at 5 nm to ensure surface homogeneity. The thin layer of conductive metal atoms deposited onto the specimen surface significantly increased contrast and improved image quality. The results presented here demonstrate the advantages of using sputter coating for imaging of highly crystalline cellulose materials with TEM.
The Association of Abdominal Adiposity With Mortality in Patients With Stage I–III Colorectal Cancer
Authors: Brown Justin C , Caan Bette J , Prado Carla M , Cespedes Feliciano Elizabeth M , Xiao Jingjie , Kroenke Candyce H , Meyerhardt Jeffrey A 
Published: July 2019

Abstract

Background
The quantity and distribution of adipose tissue may be prognostic measures of mortality in colorectal cancer patients, and such associations may vary by patient sex.

Methods
This cohort included 3262 stage I–III colorectal cancer patients. Visceral and subcutaneous adipose tissues were quantified using computed tomography. The primary endpoint was all-cause mortality. Restricted cubic splines estimated statistical associations with two-sided P values.

Results
Visceral adipose tissue was prognostic of mortality in a reverse L-shaped pattern (nonlinear P = .02); risk was flat to a threshold (∼260 cm2) then increased linearly. Subcutaneous adipose tissue was prognostic of mortality in a J-shaped pattern (nonlinear P &lt; .001); risk was higher at extreme (&lt;50 cm2) but lower at intermediate values (&gt;50 to ≤560 cm2). Patient sex modified the prognostic associations between visceral adipose tissue (Pinteraction = .049) and subcutaneous adipose tissue (Pinteraction = .04) with mortality. Among men, visceral adiposity was associated with mortality in a J-shaped pattern (nonlinear P = .003), whereas among women, visceral adiposity was associated with mortality in a linear pattern (linear P = .008). Among men, subcutaneous adiposity was associated with mortality in an L-shaped pattern (nonlinear P = .01), whereas among women, subcutaneous adiposity was associated with mortality in a J-shaped pattern (nonlinear P &lt; .001).

Conclusions
Visceral and subcutaneous adipose tissue were prognostic of mortality in patients with colorectal cancer; the shape of these associations were often nonlinear and varied by patient sex. These results offer insight into the potential biological mechanisms that link obesity with clinical outcomes in patients with cancer, suggesting that the dysregulated deposition of excess adiposity is prognostic of mortality.
Hyperglycemia During Childhood Cancer Therapy: Incidence, Implications, and Impact on Outcomes
Authors: Grimes Allison , Mohamed Ashraf , Sopfe Jenna , Hill Rachel , Lynch Jane 
Published: July 2019

Abstract
Hyperglycemia is a known complication of therapies used in the treatment of childhood cancer, particularly glucocorticoids and asparaginase. It has been linked to increased infection and reduced survival. With more limited data on hyperglycemia during childhood cancer treatment compared with adult cancer, impact on outcomes is less clear in this population. As additional glycemic-altering cancer agents including immune checkpoint inhibitors and targeted therapies make their way into pediatric cancer treatment, there is a more pressing need to better understand the mechanisms, risk factors, and adverse effects of hyperglycemia on the child with cancer. Thus, we utilized a systematic approach to review the current understanding of the incidence, implications, and outcomes of hyperglycemia during childhood cancer therapy.
High-Fat Diet Intake Promotes the Enlargement and Degenerative Changes in the Media of Intracranial Aneurysms in Rats
Authors: Shimizu Kampei , Miyata Haruka , Abekura Yu , Oka Mieko , Kushamae Mika , Kawamata Takakazu , Mizutani Tohru , Kataoka Hiroharu , Nozaki Kazuhiko , Miyamoto Susumu , Aoki Tomohiro 
Published: July 2019

Abstract
Subarachnoid hemorrhage due to rupture of intracranial aneurysms is a life-threatening disease. Although some previous reports have demonstrated an association between lipid accumulation and degenerative changes in aneurysmal walls in humans, epidemiological studies have failed to identify dyslipidemia as a risk factor for intracranial aneurysms. Thus, we examined whether an increase in serum cholesterol levels facilitates the progression of intracranial aneurysms in a rat model. Rats were given a high-fat diet (HFD) and subjected to an intracranial aneurysm model. The HFD elevated their serum cholesterol levels. The intracranial aneurysms induced at the anterior cerebral artery-olfactory artery bifurcation were significantly larger in the high-fat group than in the normal-chow group. Histological analysis demonstrated that the loss of medial smooth muscle layers was exacerbated in the high-fat group and indicated the presence of macrophage-derived foam cells in the lesions. In in vitro experiments, the expression levels of the pro-inflammatory genes induced by LPS in RAW264.7-derived foam cells were significantly higher than those in RAW264.7 cells. The combination of these results suggests that increased serum cholesterol levels facilitate degenerative changes in the media and the progression of intracranial aneurysms presumably through foam cell transformation.
A case report of retrograde intussusception 3 years post Roux-en-Y gastric bypass
Authors: Okal Fahad , Allarakia Jawad , Alghamdi Amer , Alqurashi Zahid , Aboalsamh Ghaleb , Abdelhady Ahmed 
Published: July 2019

Abstract
Retrograde jejuno-jejunal intussusception is a rare complication of bariatric surgeries. It causes acute sudden symptoms that require immediate surgical intervention. We report a case of a 46-year-old female who underwent Roux-en-Y gastric bypass (REYGP) 3 years prior. The patient presented to the emergency department with acute sudden abdominal pain, nausea and vomiting. Laparoscopically, intussuscepting small bowel segment was found gangrenous, and it was resected and end-to-end anastomoses were fashioned. The postoperative course was uneventful, and the patient remained asymptomatic for the 12 months of follow-up. Patients with retrograde intussusception experience an intolerable severe pain that necessitates surgical intervention. The etiology of intussusception as a complication after REYGP is unclear, yet theoretically some possible etiologies exist. The initial diagnosis of retrograde intussusception is made based on abdominal computed tomography. Early intervention significantly reduces morbidity and mortality.