bluuebunny/crossref_metadata_2025_split huggingface dataset:
Call for Data Standardization: Lessons Learned and Recommendations in an Imaging Study
Authors: Basu Amrita , Warzel Denise , Eftekhari Aras , Kirby Justin S. , Freymann John , Knable Janice , Sharma Ashish , Jacobs Paula 
Published: December 2019

PURPOSE Data sharing creates potential cost savings, supports data aggregation, and facilitates reproducibility to ensure quality research; however, data from heterogeneous systems require retrospective harmonization. This is a major hurdle for researchers who seek to leverage existing data. Efforts focused on strategies for data interoperability largely center around the use of standards but ignore the problems of competing standards and the value of existing data. Interoperability remains reliant on retrospective harmonization. Approaches to reduce this burden are needed. METHODS The Cancer Imaging Archive (TCIA) is an example of an imaging repository that accepts data from a diversity of sources. It contains medical images from investigators worldwide and substantial nonimage data. Digital Imaging and Communications in Medicine (DICOM) standards enable querying across images, but TCIA does not enforce other standards for describing nonimage supporting data, such as treatment details and patient outcomes. In this study, we used 9 TCIA lung and brain nonimage files containing 659 fields to explore retrospective harmonization for cross-study query and aggregation. It took 329.5 hours, or 2.3 months, extended over 6 months to identify 41 overlapping fields in 3 or more files and transform 31 of them. We used the Genomic Data Commons (GDC) data elements as the target standards for harmonization. RESULTS We characterized the issues and have developed recommendations for reducing the burden of retrospective harmonization. Once we harmonized the data, we also developed a Web tool to easily explore harmonized collections. CONCLUSION While prospective use of standards can support interoperability, there are issues that complicate this goal. Our work recognizes and reveals retrospective harmonization issues when trying to reuse existing data and recommends national infrastructure to address these issues.
Patterns of Care of Cancers and Radiotherapy in Ethiopia
Authors: Rick Tara , Habtamu Biruk , Tigeneh Wondemagegnhu , Abreha Aynalem , van Norden Yvette , Grover Surbhi , Assefa Mathewos , Incrocci Luca 
Published: December 2019

PURPOSE Radiotherapy (RT) is an essential component of cancer treatment. There is a lack of RT services in sub-Saharan Africa as well as limited knowledge regarding clinical practices. The purpose of this study was to identify and describe the patterns for RT treatment in Ethiopia. METHODS AND MATERIALS We performed a retrospective analysis of 1,823 patients treated with cobalt RT at a large referral hospital in Addis Ababa, Ethiopia, from May 2015 through January 2018. Paper charts were reviewed for patient and treatment characteristics. Descriptive statistics were computed using SPSS (IBM, Armonk, NY). RESULTS Among patients treated for cancer, 98% (n = 1,784) were adults, 78% (n = 1,426) were female, 5% (n = 85) were HIV positive, 30% (n = 555) were from Addis Ababa, and the median age was 48 years (interquartile range [IQR], 38-58 years). Cervical cancer was the most frequent cancer treated (47%, n = 851), followed by breast cancer (15%, n = 274) and head and neck cancer (10%, n = 184). Seventy-three percent of patients (n = 1,339) presented at a late stage, and 62% (n = 1,138) received palliative RT. The wait times were the shortest for patients receiving palliative treatment (median, 0 days; IQR, 0-15 days; n = 1,138), whereas wait times were longer for patients receiving curative treatment (median, 150 days; IQR, 60-210 days; n = 685). Three percent of patients (n = 56) had documented grade 3 or 4 acute toxicity; of these, 59% (n = 33) were patients with head and neck cancer. CONCLUSION Cervical cancer accounted for half of patients treated; thus, a majority of patients were adult females. Most patients had advanced-stage cancer, and goals of care were palliative. Wait times were long for patients with curative-intent cancer as a result of low capacity for RT services.
Identifying and Prioritizing Family Education Needs at Pediatric Oncology Centers in Central America and Mexico
Authors: McCann Erin , Fuentes-Alabí Soad , Antillón Federico , Vega-Vega Lourdes , Sanchez Maria Sabina , Albanti Irini 
Published: December 2019

PURPOSE The educational needs of parents at the time of their child’s cancer diagnosis are often unclear, and research on this topic in low- and middle-income countries is limited. This study evaluated the educational needs of families at major pediatric oncology centers in Central America and Mexico. METHODS A qualitative study involving 72 in-person interviews and 4 focus groups was conducted using a semistructured interview guide. Key informants included family members, physicians, nurses, psychosocial providers, foundation leadership, volunteers, and communication professionals. The study sites included pediatric oncology centers in El Salvador, Guatemala, Mexico, and Panama. NVivo was used for thematic analysis. RESULTS Across all sites, parents had common questions and educational needs. Questions from families focused on their child’s likelihood of dying from cancer and feelings of guilt that were based on their perception that they caused the disease. The origin of cancer, nutrition, and psychosocial support were the most important educational themes. However, the prioritization of different educational themes varied on the basis of cultural or social influences unique to each site. Some of these differences included a need for education surrounding amputations, sibling support, and alternative or traditional healers. CONCLUSION This study demonstrates that although many educational needs were consistent across hospitals, some of the educational priorities differed by site despite geographic proximity and shared language. Developing an educational program in resource-limited settings can be challenging, but it is an important contributor to improving childhood cancer outcomes that should be tailored to the specific needs of a site. This study can be used as a guide for other programs with limited resources wanting to develop relevant educational materials for families.
AMPK Subunits Harbor Largely Nonoverlapping Genetic Determinants for Body Fat Mass, Glucose Metabolism, and Cholesterol Metabolism
Authors: Randrianarisoa Elko , Lehn-Stefan Angela , Krier Johannes , Böhm Anja , Heni Martin , Hrabě De Angelis Martin , Fritsche Andreas , Häring Hans-Ulrich , Stefan Norbert , Staiger Harald 
Published: December 2019

Abstract

Context
Adenosine monophosphate (AMP)-activated protein kinase (AMPK) is a heterotrimeric enzyme and central regulator of cellular energy metabolism. The impact of single nucleotide polymorphisms (SNPs) in all 7 AMPK subunit genes on adiposity, glucose metabolism, and lipid metabolism has not yet been systematically studied.

Objective
To analyze the associations of common SNPs in all AMPK genes, and of different scores thereof, with adiposity, insulin sensitivity, insulin secretion, blood glucose, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, total cholesterol, and triglycerides.

Study Design and Methods
A cohort of 2789 nondiabetic participants from the Tübingen Family study of type 2 diabetes, metabolically characterized by oral glucose tolerance test and genotyped by genome-wide SNP array, was analyzed.

Results
We identified 6 largely nonoverlapping SNP sets across 4 AMPK genes (PRKAA1, PRKAA2, PRKAG2, PRKAG3) associated with adiposity, insulin sensitivity, insulin secretion, blood glucose, total/LDL cholesterol, or HDL cholesterol, respectively. A genetic score of body-fat-increasing alleles revealed per-allele effect sizes on body mass index (BMI) of +0.22 kg/m2 (P = 2.3 × 10–7), insulin sensitivity of −0.12 × 1019 L2/mol2 (P = 9.9 × 10–6) and 2-hour blood glucose of +0.02 mmol/L (P = 0.0048). Similar effects on blood glucose were observed with scores of insulin-sensitivity-reducing, insulin-secretion-reducing and glucose-raising alleles, respectively. A genetic cholesterol score increased total and LDL cholesterol by 1.17 mg/dL per allele (P = 0.0002 and P = 3.2 × 10–5, respectively), and a genetic HDL score decreased HDL cholesterol by 0.32 mg/dL per allele (P = 9.1 × 10–6).

Conclusions
We describe largely nonoverlapping genetic determinants in AMPK genes for diabetes-/atherosclerosis-related traits, which reflect the metabolic pathways controlled by the enzyme. Formation of trait-specific genetic scores revealed additivity of allele effects, with body-fat-raising alleles reaching a marked effect size. (J Clin Endocrinol Metab 105: 14–25, 2020)
Maternal Adipose Tissue Expansion, A Missing Link in the Prediction of Birth Weight Centile
Authors: Jarvie Eleanor M , Stewart Frances M , Ramsay Jane E , Brown E Ann , Meyer Barbara J , Olivecrona Gunilla , Griffin Bruce A , Freeman Dilys J 
Published: December 2019

Abstract

Context
Maternal body mass index (BMI) is associated with increased birth weight but does not explain all the variance in fetal adiposity.

Objective
To assess the contribution of maternal body fat distribution to offspring birth weight and adiposity.

Design
Longitudinal study throughout gestation and at delivery.

Setting
Women recruited at 12 weeks of gestation and followed up at 26 and 36 weeks. Cord blood was collected at delivery.

Patients
Pregnant women (n = 45) with BMI 18.0 to 46.3 kg/m2 and healthy pregnancy outcome.

Methods
Maternal first trimester abdominal subcutaneous and visceral adipose tissue thickness (SAT and VAT) was assessed by ultrasound.

Main Outcome Measures
Maternal body fat distribution, maternal and cord plasma glucose and lipid concentrations, placental weight, birth weight, and fetal adiposity assessed by cord blood leptin.

Results
VAT was the only anthropometric measure independently associated with birth weight centile (r2 adjusted 15.8%, P = .002). BMI was associated with trimester 2 and trimesters 1 through 3 area under the curve (AUC) glucose and insulin resistance (Homeostatic Model Assessment). SAT alone predicted trimester 2 lipoprotein lipase (LPL) mass (a marker of adipocyte insulin sensitivity) (11.3%, P = .017). VAT was associated with fetal triglyceride (9.3%, P = .047). Placental weight was the only independent predictor of fetal adiposity (48%, P &lt; .001). Maternal trimester 2 and AUC LPL were inversely associated with fetal adiposity (r = -0.69, P = .001 and r = -0.58, P = .006, respectively).

Conclusions
Maternal VAT provides additional information to BMI for prediction of birth weight. VAT may be a marker of reduced SAT expansion and increased availability of maternal fatty acids for placental transport.
The incidence and diagnostic relevance of chemical shift artefact in the magnetic resonance imaging characterisation of superficial soft tissue masses
Authors: Saifuddin Asif , Siddiqui Shuaib , Pressney Ian , Khoo Michael 
Published: December 2019

Objective:
Chemical shift artefact (CSA) is often encountered during MRI evaluation of superficial soft tissue masses. The study aim was to determine the incidence and diagnostic relevance of CSA in a consecutive series of superficial soft tissue masses referred to a specialist musculoskeletal sarcoma service.

Methods:
All patients referred over a 6 month period with a non-lipomatous superficial soft tissue mass were prospectively analysed. Patients characteristics (age, gender), lesion features (anatomical location, size, relationship to the skin and deep fascia), presence of CSA and final histopathological diagnosis were collected. The presence of CSA was statistically analysed against these clinical, imaging and histopathological variables.

Results:
128 patients fulfilled the inclusion criteria [63 males, 65 females; mean age = 50.6 years (7–96 years)]. CSA was present in 50 cases (39.1%) overall, but in 39 (41.5%) of 94 cases with histological diagnosis. There was no statistically significant relationship to any assessed variable apart from relationship to the deep fascia, CSA being more frequent in lesions contacting the fascia compared to lesions contacting both skin and fascia (p-value 0.02). In particular, the presence of CSA did not allow differentiation between non-malignant and malignant lesions.

Conclusion:
The presence of CSA is a not infrequent finding in the MRI assessment of superficial soft tissue masses but does not appear to be of any significance in differentiating between non-malignant and malignant lesions.

Advances in knowledge:
CSA is a relatively common finding in association with superficial soft tissue masses, but does not indicate a particular histological diagnosis or help in the differentiation of non-malignant from malignant lesions.
Family planning financing: tracking domestic family planning budget allocations at national and sub-national level in Kenya and Uganda
Authors: Ongwae Joshua 
Published: December 2019

Background: The Abuja Declaration committed African Union countries to allocate at least 15% of their budget to improving the health sector. Consequently, Deutsche Stiftung Weltbevoelkerung (DSW) has been undertaking annual budget studies in Kenya and Uganda to track financial allocation for health and family planning (FP). Methods: This study, carried out between the months of May and October 2017, involved budget analysis of general health and FP funding at national and sub-national level. The study covered the fiscal year 2017/18. However, for comparison purposes, fiscal years 2015/16 and 2016/17 were included in the analysis. Results: In Uganda, during the 2017/18 fiscal year, the government allocated 0.73% ($3.7 million) of its health sector budget ($506.7 million) to FP; of which 98.8% ($3.6 million) was allocated to National Medical Stores (NMS), mainly for the supply of reproductive health commodities. Analysis of four districts shows that only 0.5% ($7,966), 0.8% ($10,046), 0.9% ($9,663) and 1.9% ($35,395) of the health sector budget was allocated to FP in Kamuli, Mityana, Mukono and Tororo, respectively, during the 2017/18 fiscal year. In Kenya, the FP budget allocation at the national level reduced from $6.05 million in 2015/16 to $2.93 million in 2017/18. At the subnational level, there were combined increases in the estimated sub-national FP budget allocations in all eleven counties of 21.8% ($2.1 million), from $9.6 million (2016/17) to $11.7 million (2017/2018). Conclusions: The findings indicate an overall increase in FP allocations over the last three years in the two countries of study. Advocacy personnel should be enlightened on the budget making process, as it provides an excellent platform for advocating for budgetary increases.
The functional status, rehospitalization, and hospital cost reduction in geriatric patients after the implementation of the universal health coverage program in the national referral hospital Indonesia
Authors: Soejono Czeresna Heriawan , Sutanto Hari 
Published: December 2019

BACKGROUND Universal health coverage program (UHCP) might implicate negatively toward geriatric care with its impact on higher cost. The evaluation had to be made, especially in functional status, rehospitalization, and cost-effectiveness.
METHODS Retrospective cohort study with historical control was done. Seventy two geriatric inpatients in the pre-UHCP group and 86 in the UHCP group were recruited from Cipto Mangunkusumo Hospital, Jakarta, Indonesia. Subjects with geriatric syndromes admitted from July to December 2013 (pre-UHCP era) and January to June 2014 (UHCP era). Functional status changes, rehospitalization, and process indicators were observed. Cost reduction was calculated using the incremental cost-effectiveness ratio (ICER), whereby costs, functional status changes, and rehospitalization of both groups were used to identify the differences.
RESULTS Proportions of functional status increase were 35.3% and 34.8% in the pre- UHCP and UHCP groups, respectively (p = 1.00) and the decrease were 5.9% and 4.5% in the pre-UHCP and UHCP group, respectively (p = 1.00). Rehospitalization rates were 21.7% and 18.1% (p = 0.603) in the pre-UHCP and UHCP groups, respectively. Mean hospital expenses were between 17.1 million IDR (1,221 USD; 1 USD = 14,000 IDR) for the pre-UHCP group and 20.8 million IDR (1,486 USD) for the UHCP group. ICER showed that hospitalization cost was 3.7 million IDR (264 USD) higher to increase 1 activity of daily living score in the UHCP era. As for rehospitalization, the cost was 600,000 IDR (43 USD) less, with 3.6% smaller in readmission.
CONCLUSIONS There was no changes in patients’ functional status after the UHCP implementation. There was a reduction in rehospitalization with lower cost in the UHCP era.
Patient assessment of constipation quality of life questionnaire: validity and reliability for Indonesian population
Authors: Abdullah Murdani , Maulahela Hasan , Utari Amanda Pitarini , Kusumo Pratiwi Dyah , Soebandrio Amin , Achmad Ibrahim , William Andy , Makmun Dadang 
Published: December 2019

BACKGROUND Constipation is a condition commonly encountered by physicians, causing a significant reduction in patients’ quality of life. Therefore, successful management of constipation should also include increase the quality of life. The Patient Assessment of Constipation Quality of Life (PAC-QOL) questionnaire is a questionnaire developed to address this issue. However, this questionnaire had not been translated into the Indonesian language. This study was aimed to adapt PAC-QOL into Indonesian culture and perform the psychometric evaluation.
METHODS Translation and cultural adaptation were performed based on the linguistic validation guidelines by Acquadro et al in 2012. To perform the psychometric evaluation, a total of 64 subjects in Petamburan district in Jakarta, Indonesia, were recruited from February to March 2018. Test-retest reliability was assessed by completing the PACQOL twice with one-week interval. Subjects also completed the Short Form 36 (SF-36) Health Survey Questionnaire to assess concurrent validity. Internal consistency was analyzed with Cronbach’s alpha value (>0.7) and the intraclass correlation coefficient.
RESULTS The mean (standard deviation) overall average score was 1.52 (0.66), while the Cronbach’s alpha value for the overall average score was 0.910. Concurrently, the intraclass correlation coefficient for the overall score was 0.87. Simultaneously, several experts judged content validity to be adequate. All the questions had significant correlations with their respective domains. Moreover, each domain of PAC-QOL also had a significant correlation with several SF-36 domains.
CONCLUSIONS The psychometric evaluation performed in this study demonstrated that the Indonesian version of the PAC-QOL was valid and reliable, suggesting that this questionnaire can be used in daily clinical practice.
Object-independent piston diagnosing approach for segmented optical mirrors via deep convolutional neural network
Authors: Hui Mei , Li Weiqian , Liu Ming , Dong Liquan , Kong Lingqin , Zhao Yuejin 
Published: December 2019

Piston diagnosing approaches based on neural networks have shown great
success, while a few methods are heavily dependent on the imaging
target of the optical system. In addition, they are inevitably faced
with the interference of submirrors. Therefore, a unique
object-independent feature image is used to form an original kind of
data set. Besides, an extremely deep image-based convolutional neural
network (CNN) of 18 layers is constructed. Furthermore, 9600 images
are generated as a data set for each submirror with a special measure
of sensitive area extracting. The diversity of results among all the
submirrors is also analyzed to ensure generalization ability. Finally,
the average root mean square error of six submirrors between the real
piston values and the predicted values is approximately

0.0622

λ

. Our approach has the following
characteristics: (1) the data sets are object-independent and contain
more effective details, which behave comparatively better in CNN
training; (2) the complex network is deep enough and only a limited
number of images are required; (3) the method can be applied to the
piston diagnosing of segmented mirror to overcome the difficulty
brought by the interference of submirrors. Our method does not require
special hardware, and is fast to be used at any time, which may be
widely applied in piston diagnosing of segmented mirrors.
Coupling silica waveguides to photonic crystal waveguides through a multilayered Luneburg lens
Authors: Badri S. Hadi , M. Gilarlue M. 
Published: December 2019

We present a detailed analysis of a coupler based on the Luneburg lens to couple a silica waveguide to a photonic crystal (PhC) waveguide. The dependence of coupling efficiency on the lens’s truncation, cut position of the PhC structure, coupler tip width, and misalignment are investigated with a two-dimensional finite element method. We implement the lens with a concentric ring-based multilayer structure. We also present a method to replace layers with very narrow widths by layers of predetermined minimum widths in the structure of the lens. The coupling loss of the designed 2.7-µm-long coupler, connecting a 2.79-µm-wide silica waveguide to a PhC structure with a rod-type square lattice, is lower than 0.49 dB in the C-band. The average coupling loss in the entire S, C, L, and U bands of optical communications is 0.70 dB.
1030-nm passively Q-switched ytterbium-doped fiber laser using excited-state absorption of thulium fiber
Authors: Tsai Tzong-Yow , Lee Zhi-Cheng 
Published: December 2019

We demonstrated a pulsed ytterbium all-fiber laser passively

Q

-switched using excited-state absorption of thulium fiber and a mode-field-area mismatch. The absorption cross section of the excited state

3

F
4

was measured and determined to be the key factor inducing pulsing, and it was much higher than that of the ground state

3

H
6

over 0.95–1.15 µm. By successfully realizing the pulsed laser at 1030 nm, which is the most critical wavelength for

Q

-switching, we verified that the excite state

3

F
4

of

T
m

3
+

could be a full-range saturable-absorber

Q

-switch for a Yb fiber laser over 1.0–1.15 µm.
A brutal humanism for the new millennium? The legacy of Neorealism in contemporary cinema of migration
Authors: Johnson Rachel 
Published: December 2019

Abstract
This article proposes that the institutional construction of Italian cinema of migration in the new millennium may be conditioned by an enduring, implicit aspect of Neorealism's legacy: a 'brutal humanism' that posits the witnessing of bodies in crisis as an ethical act. Supplementing Karl Schoonover's theory of brutal humanism with Lacanian gaze theory, I argue that the Berlin International Film Festival's synopsis of a recent cause célèbre of Italian cinema, Fuocoammare (Fire at Sea) (Rosi, 2016), instantiates a 'brutal vision' directed towards the figure of the refugee, while the film text's depiction of the 'objective gaze' of these characters challenges such relations of power and looking. The article underlines the importance of competitive European film festivals and paratexts in the international circulation and ideological construction of Italian cinema, while arguing that the film text itself can offer a site of resistance to the meanings that institutions ascribe to it.
Commercialism and the quotidian
Authors: Bohlinger Vincent 
Published: December 2019

Abstract
This article examines Andy Warhol Eating a Hamburger in relation to the aesthetics of Andy Warhol's own filmmaking and contemporaneous American television commercials. I point to how the film's design – including the single long take, ambient sound, and Warhol's performance – draw upon and undermine American commercial culture.