bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leveraging Bayesian networks and information theory to learn risk factors for breast cancer metastasis
Authors: Jiang Xia , Wells Alan , Brufsky Adam , Shetty Darshan , Shajihan Kahmil , Neapolitan Richard E. 
Published: July 2020

Abstract
Background
Even though we have established a few risk factors for metastatic breast cancer (MBC) through epidemiologic studies, these risk factors have not proven to be effective in predicting an individual’s risk of developing metastasis. Therefore, identifying critical risk factors for MBC continues to be a major research imperative, and one which can lead to advances in breast cancer clinical care. The objective of this research is to leverage Bayesian Networks (BN) and information theory to identify key risk factors for breast cancer metastasis from data.

Methods
We develop the Markov Blanket and Interactive risk factor Learner (MBIL) algorithm, which learns single and interactive risk factors having a direct influence on a patient’s outcome. We evaluate the effectiveness of MBIL using simulated datasets, and compare MBIL with the BN learning algorithms Fast Greedy Search (FGS), PC algorithm (PC), and CPC algorithm (CPC). We apply MBIL to learn risk factors for 5 year breast cancer metastasis using a clinical dataset we curated. We evaluate the learned risk factors by consulting with breast cancer experts and literature. We further evaluate the effectiveness of MBIL at learning risk factors for breast cancer metastasis by comparing it to the BN learning algorithms Necessary Path Condition (NPC) and Greedy Equivalent Search (GES).

Results
The averages of the Jaccard index for the simulated datasets containing 2000 records were 0.705, 0.272, 0.228, and 0.147 for MBIL, FGS, PC, and CPC respectively. MBIL, NPC, and GES all learned that grade and lymph_nodes_positive are direct risk factors for 5 year metastasis. Only MBIL and NPC found that surgical_margins is a direct risk factor. Only NPC found that invasive is a direct risk factor. MBIL learned that HER2 and ER interact to directly affect 5 year metastasis. Neither GES nor NPC learned that HER2 and ER are direct risk factors.

Discussion
The results involving simulated datasets indicated that MBIL can learn direct risk factors substantially better than standard Bayesian network learning algorithms. An application of MBIL to a real breast cancer dataset identified both single and interactive risk factors that directly influence breast cancer metastasis, which can be investigated further.
Genome-wide identification and transcript profiles of walnut heat stress transcription factor involved in abiotic stress
Authors: Liu Xuejiao , Meng Panpan , Yang Guiyan , Zhang Mengyan , Peng Shaobing , Zhai Mei Zhi 
Published: July 2020

Abstract
Background
Walnut (Juglans regia) is an important tree cultivated worldwide and is exposed to a series of both abiotic and biotic stress during their life-cycles. The heat stress transcription factors (HSFs) play a crucial role in plant response to various stresses by regulating the expression of stress-responsive genes. HSF genes are classified into 3 classes: HSFA, HSFB, and HSFC. HSFA gene has transcriptional activation function and is the main regulator of high temperature-induced gene expression. HSFB gene negatively regulates plant resistance to drought and NaCl. And HSFC gene may be involved in plant response to various stresses. There are some reports about the HSF family in herbaceous plants, however, there are no reports about the HSFs in walnut.

Result
In this study, based on the complete genome sequencing of walnut, the bioinformatics method was used and 29 HSF genes were identified. These HSFs covered 18 HSFA, 9 HSFB, and 2 HSFC genes. Phylogenetic analysis of these HSF proteins along with those from Arabidopsis thaliana showed that the HSFs in the two species are closely related to each other and have different evolutionary processes. The distribution of conserved motifs and the sequence analysis of HSF genes family indicated that the members of the walnut HSFs are highly conserved. Quantitative Real-Time PCR (qRT-PCR) analysis revealed that the most of walnut HSFs were expressed in the walnut varieties of ‘Qingxiang’ and ‘Xiangling’ under high temperature (HT), high salt and drought stress, and some JrHSFs expression pattern are different between the two varieties.

Conclusion
The complex HSF genes family from walnut was confirmed by genome-wide identification, evolutionary exploration, sequence characterization and expression analysis. This research provides useful information for future studies on the function of the HSF genes and molecular mechanism in plant stress response.
Increased expression of hypoxia inducible factor-1 alpha and vascular endothelial growth factor is associated with diabetic gastroparesis
Authors: Wu Xueping , Yang Zhifang , Li Zhihong , Yang Ling , Wang Xinyan , Wang Congrong , Gu Jun 
Published: July 2020

Abstract
Background
Gastroparesis is a recognized complication of diabetes but its pathogenic mechanism incompletely understood. Our aim was to determine whether HIF-1α and VEGF are secreted from gastric tissue is a fundamental factor that drives diabetic gastroparesis.

Methods
Diabetes was induced in Sprague-Dawley by a single intraperitoneal injection of 65 mg/kg streptozotocin. After 4 and 12 weeks, rats were euthanized for assaying body weight, blood glucose, gastric acid secretion and gastric emptying. Morphologic changes in gastric mucosa were observed by the light microscope. Expression of HIF-1α and VEGF were assessed using immunohistochemistry, RT-PCR and Western blot analyses.

Results
Compared with control group, blood glucose were significantly increased and body weight were markedly decreased in streptozotocin-induced diabetes. Gastric emptying was significantly decreased in diabetic rats compared to the control group at different times. The number of parietal cells was obviously decreased, and vacuolated degeneration in diabetic rats. Gastric acid secretion in diabetic group was significantly decreased, and expression of HIF-1α and VEGF were significantly increased in the diabetic group.

Conclusion
These results indicated that overexpression of HIF-1α and VEGF in the gastric mucosa and played a pivotal role in the progression of diabetic gastroparesis.
Multifocal tuberculosis simulating a cancer-a case report
Authors: Wang Congxiao , Luan Ying , Liu Shifeng , Zhao Mingwei , Zhang Hao , Li Wei , Li Zixiang , Hu Xiaokun , Peng Lijing 
Published: July 2020

Abstract
Background
Tuberculosis is a disease that may affect any organ of the body. Multifocal tuberculosis involving multiple systems with associated symptoms are rare, which makes the diagnosis challenging. Distinguishing multifocal tuberculosis from lesions metastatic from system malignancy is difficult. Single detection method is difficult to make a diagnosis. A combination of multiple methods is essential.

Case presentation
A 17-year-old male presented with a 20 days weakness of lower limbs, which aggravated for 6 days. The PET/CT showed increased metabolism of ileocecal intestinal and terminal ileum wall, multiple enlarged lymph node (LNs), multiple osteolytic bone lesions, and soft tissue intensity belong T7 and T8 vertebrae. To confirm the diagnosis of the disease, a biopsy of the mediastinum lymph nodes was carried out. Polymerase chain reaction (PCR) test of the specimen was positive for the Mycobacterium tuberculosis, the T-SPOT and Xpert MTB/RIF test were also positive, which suggested the presence of Mycobacterium tuberculosis. The final diagnosis was multifocal tuberculosis, the patients received the resection of the mass in the spine. Anti-tuberculosis drugs were given. The myodynamia and muscle tension of the patients recovered following the therapy.

Conclusions
Our results indicated that Multifocal tuberculosis should also be taken into consideration when lesions metastatic from system malignancy were suspected from images results even without the clinical symptoms of tuberculosis, and combination of multiple diagnosis methods were essential for the diagnosis of multifocal disease.
Three-year outcome of aflibercept treatment for Japanese patients with neovascular age-related macular degeneration
Authors: Itagaki Kanako , Sekiryu Tetsuju , Kasai Akihito , Sugano Yukinori , Ogasawara Masashi , Saito Masaaki 
Published: July 2020

Abstract
Background
To evaluate the three-year outcome after intravitreal aflibercept injection (IAI) for neovascular age-related macular degeneration (nAMD).

Methods
Forty-nine treatment-naïve nAMD patients (50 eyes) were enrolled in this prospective study. The eyes received IAI at two-month intervals in the first year. The treatment regimen was changed to IAI based on a treat-and-extend approach in the second and third years.

Results
Twenty-nine eyes of 28 patients were successfully followed up over 36 months. The nAMD subtypes included 15 eyes with typical AMD and 14 eyes with polypoidal choroidal vasculopathy. The number of IAIs performed over the 3 years was 17.2 ± 3.1 (mean ± standard deviation). The mean logMAR, which was 0.42 at baseline, improved to 0.19 (P = 0.001) at 12 months, and 0.26 (P = 0.049) at 36 months. The central retinal thickness (CRT) was 329 ± 120 μm at baseline, 151 ± 38 μm (P < 0.001) at 12 months, and 143 ± 61 μm (P < 0.001) at 36 months. The mean subfoveal choroidal thickness (SFCT) was 288 ± 97 μm at baseline, 243 ± 82 μm (P < 0.001) at 12 months, and 208 ± 63 μm (P < 0.01) at 36 months. The changes in logMAR, CRT, and SFCT over the study period did not differ between typical AMD and PCV.

Conclusion
Long-term aflibercept injection can achieve visual improvement and reduce the thickness of the retina and choroid in nAMD. Morphological improvement of these tissues may not be sufficient to sustain earlier visual improvement over the long-term.
Veganism and paediatric food allergy: two increasingly prevalent dietary issues that are challenging when co-occurring
Authors: Protudjer Jennifer L. P. , Mikkelsen Andrea 
Published: July 2020

AbstractVegan diets – defined as the exclusion of all foods of animal origin from the diet- are becoming popular. In recent years, the prevalence of food allergy has also increased, and disproportionately affects children. When vegan diets and food allergy co-occur, this combination can be challenging and pose risks of nutritional deficiencies, particularly during childhood. In this paper, we aim to summarise the major concerns regarding vegan diets and food allergy, review the literature on this topic, and provide some suggestions for healthcare providers, particularly dietitians and nutritionists, who work with food allergic, vegan patients and their family. When working with this patient population, a regular and complete medical nutrition history, including screening for any possible nutritional deficiencies, is warranted. Likewise, the routine tracking of serum markers (especially iodine, iron, zinc, calcium, Vitamins B12, D, B2, and A, selected n-3 fatty acids and protein, which are more abundant in animal vs. plant foods) and symptoms of co-morbid diseases, including asthma, is important, as comorbid diseases may increase energy and nutrient requirements. For infants and children, anthropometry ought to be tracked longitudinally at regular intervals to identify any deviations from the child’s previous growth pattern, and to accommodate any increased requirements for growth and development. Correct diagnoses, education and allergy management must be disseminated to the family in a clear and appropriate manner. Children with allergy may have increased nutritional needs due to comorbidity. This is complicated by coincident food allergy and vegan diet as both impose diet restrictions (limiting sources of important nutrients, need for dietary variety and/or increased consumption due to reduced bioavaliability).
LncRNA PLAC2 upregulates miR-663 to downregulate TGF-β1 and suppress bladder cancer cell migration and invasion
Authors: Zhang Zhenxing , Ao Ping , Han Hui , Zhang Qi , Chen Yang , Han Jie , Huang Qunlian , Huang Houbao , Zhuo Dong 
Published: July 2020

Abstract
Background
The roles of lncRNA PLAC2 in bladder cancer (BC) were explored.

Methods
The expression of PLAC2 in two types of tissue of BC patients was detected by RT-qPCR and the expression data were compared by paired t test. The 56 patients were staged according to the AJCC criteria, and 12, 15, 15 and 14 cases were classified into stage I-IV, respectively. The expression of TGF-β1 and miR-663 in BC tissues were also detected by RT-qPCR experiments.

Results
Our data showed that the expression levels of PLAC2 were significantly lower in BC tissues than that in non-cancer tissues. The expression of PLAC2 was not affect by clinical stages and low expression levels of PLAC2 predicted lower survival rate. The expression of PLAC2 was positively correlated with miR-663 and inversely correlated with TGF-β1 in BC tissues. In BC cells, downregulated TGF-β1 and upregulated miR-663 were observed after the overexpression of PLAC2. Overexpression of PLAC2 also resulted in suppressed invasion and migration of BC cells. Overexpression of miR-663 resulted in downregulated TGF-β1 but did not affect the expression of PLAC2. Overexpression of TGF-β1 reduced the inhibitory effects of overexpression of PLAC2 and miR-663 on cell migration and invasion.

Conclusion
PLAC2 can upregulate miR-663 to downregulate TGF-β1 and suppress BC cell migration and invasion.
Computer-aided design of polyetheretherketone for application to removable pediatric space maintainers
Authors: Guo Hui , Wang Yong , Zhao Yijiao , Liu He 
Published: July 2020

AbstractBackgroundThe premature loss of primary teeth is a common problem in pediatric dentistry, resulting in disruption of the arch integrity. Hence, space maintainers (SM) used for maintaining spaces are necessary. However, current methods of making removable space maintainers (RSM) have some limitations.MethodsDigital models of dentition defects were obtained by using a scanning technique coupled with laser medical image reconstruction. The digital RSMs were designed using the 3Shape software. They were manufactured using two methods: polyetheretherketone (PEEK), and conventional methods (20 RSMs per group). For qualitative evaluation, the Likert five-point scale was used by 10 experts to obtain a score for 40 RSMs. The spaces between the tissue surfaces of the RSMs and the models were replaced using silicone, and the maximum and mean distances, as well as the standard deviation, were measured. A three-dimensional variation analysis was used to measure these spaces. The student’s t-test and Satterthwaite t-test were used to compare the differences in the spaces for the various materials.ResultsThe PEEK RSMs were found to fit the models well. In the qualitative assessment, the mean experts’ scores for the PEEK and conventional groups were 1.80 ± 0.40 and 1.82 ± 0.40, and there was no significant difference between the two groups (p = 0.875). In the quantitative assessment, the mean spaces for the PEEK digital RSMs and the conventional RSMs were 44.32 ± 1.75 μm, and 137.36 ± 18.63 μm, respectively, and the differences were statistically significant (p < 0.001). In addition, there were significant differences in the maximum space and the standard deviation between the two groups.ConclusionDigitally designed and integrated RSMs were found to be superior to those produced using the conventional method. 3D variation analysis results showed that the mean distances and standard deviations of the PEEK groups were significantly smaller than those of conventional group (p < 0.01). A PEEK-manufactured RSM produced using CAD/CAM would be extremely suitable for clinical applications.
Using flexible regression models for calculating hospital’s production functions
Authors: Reyes-Santías Francisco , Cordova-Arevalo Octavio , Rivo-Lopez Elena 
Published: July 2020

AbstractBackgroundThe relative lack of flexibility of parametric models has led to the development of nonparametric regression techniques based on the family of generalized additive models. However, despite the potential advantages of using Generalized Additive Model (GAM) in practice many models have, until now, not been sufficiently explored in health economics problems.It could be interesting to calculate a new flexible hospital production function by means of a GAM including interactions and to compare it with the classic model Cobb-Douglas in the prediction of the behavior of productive factors.MethodThe flexible model considered has been the AM including the beds-facultative interaction. The covariates “Hospital”, being a categorical variable and “Year” being a continuous variable, have also been included in the model. Based on the estimation of the model penalized thin plate splines will be used to represent smoothed functions. In this configuration, the smoothed parameters will be estimated via REML.ResultsCobb-douglas model fits well for the production functions of the more general clinical and surgical services, while the GAM adjusts better in the case of more specialized medical services.ConclusionsGeneralized Additive Models are more flexible than parametric models, providing a better fit in the presence of non-linear relationships and thus allowing more accurate prediction values. The results of this study suggest that AM is a promising technique for the areas of research and application in health economics.
A prospective evaluation of inter-rater agreement of routine medical records audits at a large general hospital in São Paulo, Brazil
Authors: Mafra Ana Carolina Cintra Nunes , Miraglia João Luiz , Colugnati Fernando Antonio Basile , Padilha Gilberto Soares Lourenço , Tadeucci Renata Rafaella Santos , Almeida Ederson , Bracco Mario Maia 
Published: July 2020

Abstract
Background
The quality of patient medical records is intrinsically related to patient safety, clinical decision-making, communication between health providers, and continuity of care. Additionally, its data are widely used in observational studies. However, the reliability of the information extracted from the records is a matter of concern in audit processes to ensure inter-rater agreement (IRA). Thus, the objective of this study is to evaluate the IRA among members of the Patient Health Record Review Board (PHRRB) in routine auditing of medical records, and the impact of periodic discussions of results with raters.

Methods
A prospective longitudinal study was conducted between July of 2015 and April of 2016 at Hospital Municipal Dr. Moysés Deutsch, a large public hospital in São Paulo. The PHRRB was composed of 12 physicians, 9 nurses, and 3 physiotherapists who audited medical records monthly, with the number of raters changing throughout the study. PHRRB meetings were held to reach a consensus on rating criteria that the members use in the auditing process. A review chart was created for raters to verify the registry of the patient’s secondary diagnosis, chief complaint, history of presenting complaint, past medical history, medication history, physical exam, and diagnostic testing. The IRA was obtained every three months. The Gwet’s AC1 coefficient and Proportion of Agreement (PA) were calculated to evaluate the IRA for each item over time.

Results
The study included 1884 items from 239 records with an overall full agreement among raters of 71.2%. A significant IRA increase of 16.5% (OR = 1.17; 95% CI = 1.03—1.32; p = 0.014) was found in the routine PHRRB auditing, with no significant differences between the PA and the Gwet’s AC1, which showed a similar evolution over time. The PA decreased by 27.1% when at least one of the raters was absent from the review meeting (OR = 0.73; 95% CI = 0.53—1.00; p = 0.048).

Conclusions
Medical record quality has been associated with the quality of care and could be optimized and improved by targeted interventions. The PA and the Gwet’s AC1 are suitable agreement coefficients that are feasible to be incorporated in the routine PHRRB evaluation process.
Experiences with health care and health-related quality of life of patients with hematologic malignancies in Mexico
Authors: Doubova Svetlana V. , Terreros-Muñoz Eduardo , Delgado-Lòpez Nancy , Montaño-Figueroa Efreen Horacio , Infante-Castañeda Claudia , Pérez-Cuevas Ricardo 
Published: July 2020

Abstract
Background
In Mexico, patients with hematologic malignancies (HMs) are characterized by being at high risk and advanced stages at diagnosis and by having a low cure rate; yet information on their experiences with health care and health-related quality of life (HRQL) is scarce. We aimed to evaluate experiences with health care and HRQL of patients with HMs and the association between these patient-reported measures.

Methods
We conducted a cross-sectional survey in two public oncology hospitals in Mexico City. The study included outpatient cancer patients aged ≥18 years with a diagnosis of leukemia, lymphoma, or multiple myeloma. We used a patient-centered quality of cancer care questionnaire to assess patient experiences with receiving 1) timely care; 2) clear information; 3) information for treatment decision-making; 4) care to address biopsychosocial needs; and 5) respectful and coordinated care. We applied the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire (EORTC QLQ-C30) to measure HRQL. We performed a multiple linear regression to evaluate the association between patient-reported experiences (independent variables) and the QLQ-C30 summary score (dependent variable).

Results
Of the 515 participating HM patients, 46.6% had lymphoma, 34% leukemia, and 19.4% multiple myeloma; 70.9% were at advanced stages or at high risk. Additionally, 15.1% had anxiety and 12.8% had depression. Over one third (35.9%) reported receiving clear information, 28.5% timely care, 20.6% information for treatment decision-making, 23.7% care that addressed their biopsychosocial needs, and 31% respectful and coordinated care. The mean QLQ-C30 summary score was 71.9 points. Timely care, clear information, and care that addresses biopsychosocial needs were associated with higher HRQL.

Conclusions
Health care services for HM patients at public oncology hospitals in Mexico need improvement. Notably, providing timely care, clear information, and care that addresses patients’ biopsychosocial needs can increase the likelihood of better HRQL. Health care providers should measure and improve the experiences of HM patients with health care.