bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes by Clinical and Molecular Features in Children With Medulloblastoma Treated With Risk-Adapted Therapy: Results of an International Phase III Trial (SJMB03)
Authors: Gajjar Amar , Robinson Giles W. , Smith Kyle S. , Lin Tong , Merchant Thomas E. , Chintagumpala Murali , Mahajan Anita , Su Jack , Bouffet Eric , Bartels Ute , Schechter Tal , Hassall Tim , Robertson Thomas , Nicholls Wayne , Gururangan Sridharan , Schroeder Kristin , Sullivan Michael , Wheeler Greg , Hansford Jordan R. , Kellie Stewart J. , McCowage Geoffrey , Cohn Richard , Fisher Michael J. , Krasin Matthew J. , Stewart Clinton F. , Broniscer Alberto , Buchhalter Ivo , Tatevossian Ruth G. , Orr Brent A. , Neale Geoff , Klimo Paul , Boop Frederick , Srinivasan Ashok , Pfister Stefan M. , Gilbertson Richard J. , Onar-Thomas Arzu , Ellison David W. , Northcott Paul A. 
Published: January 2021

PURPOSE SJMB03 (ClinicalTrials.gov identifier: NCT00085202 ) was a phase III risk-adapted trial that aimed to determine the frequency and clinical significance of biological variants and genetic alterations in medulloblastoma. PATIENTS AND METHODS Patients 3-21 years old were stratified into average-risk and high-risk treatment groups based on metastatic status and extent of resection. Medulloblastomas were molecularly classified into subgroups (Wingless [WNT], Sonic Hedgehog [SHH], group 3, and group 4) and subtypes based on DNA methylation profiles and overlaid with gene mutations from next-generation sequencing. Coprimary study end points were (1) to assess the relationship between ERBB2 protein expression in tumors and progression-free survival (PFS), and (2) to estimate the frequency of mutations associated with WNT and SHH tumors. Clinical and molecular risk factors were evaluated, and the most robust were used to model new risk-classification categories. RESULTS Three hundred thirty eligible patients with medulloblastoma were enrolled. Five-year PFS was 83.2% (95% CI, 78.4 to 88.2) for average-risk patients (n = 227) and 58.7% (95% CI, 49.8 to 69.1) for high-risk patients (n = 103). No association was found between ERBB2 status and PFS in the overall cohort ( P = .74) or when patients were stratified by clinical risk ( P = .71). Mutations in CTNNB1 (96%), DDX3X (37%), and SMARCA4 (24%) were most common in WNT tumors and PTCH1 (38%), TP53 (21%), and DDX3X (19%) in SHH tumors. Methylome profiling classified 53 WNT (17.4%), 48 SHH (15.7%), 65 group 3 (21.3%), and 139 group 4 (45.6%) tumors. A comprehensive clinicomolecular risk factor analysis identified three low-risk groups (WNT, low-risk SHH, and low-risk combined groups 3 and 4) with excellent (5-year PFS > 90%) and two very high-risk groups (high-risk SHH and high-risk combined groups 3 and 4) with poor survival (5-year PFS < 60%). CONCLUSION These results establish a new risk stratification for future medulloblastoma trials.
Dust surface potential for the dusty plasma with negative ions and with a three-parameter non-Maxwell velocity distribution
Authors: Yao Guoxue , Du Jiulin 
Published: January 2021

Abstract
We study the dust surface potential for the complex dusty plasma with negative ions and with a three-parameter non-Maxwell velocity distribution. The plasma contains electrons, positive ions, negative ions, and negatively charged dust particles. By using the current equilibrium condition, we derive the relationship between the normalized dust surface potential and the dusty plasma parameters such as the normalized dust number density, the temperature ratio of negative ions to electrons, the density ratio of negative ions to positive ions, and the charge number of negative ions. The numerical analyses show that the relationship depends evidently on the three parameters in the non-Maxwell distribution when the dust surface potential is relatively smaller, but with the increase of the potential, such dependence will weaken soon. The dust surface potential is negative and increases monotonously with the increase of the dust density, and for the complex dusty plasma with the three-parameter non-Maxwell distribution, it is generally greater than that in the same plasma with the kappa-distribution and the Maxwellian distribution.
Microwave photonic notch filter with integrated phase-to-intensity modulation transformation and optical carrier suppression
Authors: Daulay Okky , Liu Gaojian , Marpaung David 
Published: January 2021

We demonstrate for the first time, to the best of our knowledge, an on-chip microwave photonic (MWP) notch filter with high stopband rejection and integrated optical carrier suppression in a phase modulator-based system. The notch filter was achieved through phase modulation to intensity modulation (PM-to-IM) transformation and dual-sideband-processing using a network of three ring resonators (RRs) in a low-loss silicon nitride (

S
i

3

N

4

) platform. We show simultaneous PM-to-IM conversion and optical carrier processing for enhancing the filter performance using a single RR. We achieve filtering with a high stopband rejection of

>

55

d
B

, an optical carrier suppression up to 3 dB, a radio frequency link gain of 3 dB, a noise figure of 31 dB, and a spurious-free dynamic range of

100

d
B

⋅

H
z

2

/

3

. These experiments point to the importance of vectorial spectral shaping of an MWP spectrum for advanced functionalities.
Prediction of neonatal morbidity and very preterm delivery using maternal steroid biomarkers in early gestation
Authors: Patil Avinash S. , Grotegut Chad A. , Gaikwad Nilesh W. , Dowden Shelley D. , Haas David M. 
Published: January 2021

Background
Preterm delivery is a common pregnancy complication that can result in significant neonatal morbidity and mortality. Limited tools exist to predict preterm birth, and none to predict neonatal morbidity, from early in pregnancy. The objective of this study was to determine if the progesterone metabolites 11-deoxycorticosterone (DOC) and 16-alpha hydroxyprogesterone (16α-OHP), when combined with patient demographic and obstetric history known during the pregnancy, are predictive of preterm delivery-associated neonatal morbidity, neonatal length of stay, and risk for spontaneous preterm delivery prior to 32 weeks’ gestation.

Methods and findings
We conducted a cohort study of pregnant women with plasma samples collected as part of Building Blocks of Pregnancy Biobank at the Indiana University School of Medicine. The progesterone metabolites, DOC and 16α-OHP, were quantified by mass spectroscopy from the plasma of 58 pregnant women collected in the late first trimester/early second trimester. Steroid levels were combined with patient demographic and obstetric history data in multivariable logistic regression models. The primary outcome was composite neonatal morbidity as measured by the Hassan scale. Secondary outcomes included neonatal length of stay and spontaneous preterm delivery prior to 32 weeks’ gestation. The final neonatal morbidity model, which incorporated antenatal corticosteroid exposure and fetal sex, was able to predict high morbidity (Hassan score ≥ 2) with an area under the ROC curve (AUROC) of 0.975 (95% CI 0.932, 1.00), while the model without corticosteroid and fetal sex predictors demonstrated an AUROC of 0.927 (95% CI 0.824, 1.00). The Hassan score was highly correlated with neonatal length of stay (p<0.001), allowing the neonatal morbidity model to also predict increased neonatal length of stay (53 [IQR 22, 76] days vs. 4.5 [2, 31] days, above and below the model cut point, respectively; p = 0.0017). Spontaneous preterm delivery prior to 32 weeks’ gestation was also predicted with an AUROC of 0.94 (95% CI 0.869, 1.00).

Conclusions
Plasma levels of DOC and 16α-OHP in early gestation can be combined with patient demographic and clinical data to predict significant neonatal morbidity, neonatal length of stay, and risk for very preterm delivery, though validation studies are needed to verify these findings. Early identification of pregnancies at risk for preterm delivery and neonatal morbidity allows for timely implementation of multidisciplinary care to improve perinatal outcomes.
Development and validation of a food and nutrition literacy questionnaire for Chinese school-age children
Authors: Liu Tan , Su Xiao , Li Niuniu , Sun Jing , Ma Guansheng , Zhu Wenli 
Published: January 2021

BackgroundThis study aimed to develop and validate the Food and Nutrition Literacy Questionnaire for Chinese School-age Children (FNLQ-SC).MethodsA comprehensive literature review and qualitative study were initially performed to identify the dimensions and core components of food and nutrition literacy. A cross-sectional survey of 4359 school-age children was conducted, and junior middle school students were used to analyze the reliability and validity of the questionnaire (n = 2452). The reliability of the questionnaire was determined by internal consistency, the construct validity was assessed by exploratory factor analysis (EFA) and confirmatory factor analysis (CFA), and the content validity was assessed by the Pearson correlation coefficient.ResultsFrom the literature review and qualitative methods, 19 core components of the FNLQ-SC were developed, including one dimension of food and nutrition knowledge and understanding, and four skill dimensions (ability of access, selection, preparing food and healthy eating). The overall FNLQ-SC questionnaire had acceptable internal consistency (Cronbach’s α = 0.698). The EFA of skill components extracted 5 factors that were included in the conceptual framework in a slightly different model, and the cumulative contribution of variance accounted for 50.60% of the overall variance. The CFA of skill components showed an acceptable fit in general and the root mean square error of approximation (RMSEA) was 0.070 (between 0.50 to 0.80). The communality was greater than 0.20 for all components. The Pearson correlation coefficients between each dimension and the overall questionnaire ranged from 0.370 to 0.877. The average FNLQ-SC score of all 4395 participants was 61.91 ± 9.22, and the score for the knowledge and understanding dimension was higher than that for the skill dimensions. Multiple linear regression analysis indicated that not only social demographic characteristics (being a girl, being an only child, living someplace other than at school, having an urban registered permanent residence status, being from an affluent family, and being cared for by parents/grandparents with a higher education level) but also the home food environment were predictors of food and nutrition literacy in school-age children (R2= 0.226,F= 81.401,P<0.05).ConclusionThe Food and Nutrition Literacy Questionnaire (FNLQ-SC) developed here had good reliability, and it can potentially be a useful instrument for assessing food and nutrition literacy among Chinese school-age children.
Characterization of cerebrospinal fluid (CSF) microbiota from patients with CSF shunt infection and reinfection using high throughput sequencing of 16S ribosomal RNAgenes
Authors: Whitlock Kathryn B. , Pope Christopher E. , Hodor Paul , Hoffman Lucas R. , Limbrick David L. , McDonald Patrick J. , Hauptman Jason S. , Ojemann Jeffrey G. , Simon Tamara D. ,   on behalf of the Cerebrospinal FLuId MicroBiota in Shunts Study (CLIMB) Group
Published: January 2021

Background
Nearly 20% of patients with cerebrospinal fluid (CSF) shunt infection develop reinfection. It is unclear whether reinfections are caused by an organism previously present or are independent infection events.

Objective
We used bacterial culture and high throughput sequencing (HTS) of 16S ribosomal RNA (rRNA) genes to identify bacteria present in serial CSF samples obtained from children who failed CSF shunt infection treatment. We hypothesized that organisms that persist in CSF despite treatment would be detected upon reinfection.

Design/methods
Serial CSF samples were obtained from 6 patients, 5 with 2 infections and 1 with 3 infections; the study was limited to those for which CSF samples were available from the end of infection and beginning of reinfection. Amplicons of the 16S rRNA gene V4 region were sequenced. Taxonomic assignments of V4 sequences were compared with bacterial species identified in culture.

Results
Seven infection dyads averaging 13.5 samples per infection were analyzed. A median of 8 taxa [interquartile range (IQR) 5–10] were observed in the first samples from reinfection using HTS. Conventional culture correlated with high abundance of an organism by HTS in all but 1 infection. In 6 of 7 infection dyads, organisms identified by culture at reinfection were detected by HTS of culture-negative samples at the end of the previous infection. The median Chao-Jaccard abundance-based similarity index for matched infection pairs at end of infection and beginning of reinfection was 0.57 (IQR 0.07–0.87) compared to that for unmatched pairs of 0.40 (IQR 0.10–0.60) [p = 0.46].

Conclusion(s)
HTS results were generally consistent with culture-based methods in CSF shunt infection and reinfection, and may detect organisms missed by culture at the end of infection treatment but detected by culture at reinfection. However, the CSF microbiota did not correlate more closely within patients at the end of infection and beginning of reinfection than between any two unrelated infections. We cannot reject the hypothesis that sequential infections were independent.
Comparison of acute appendicitis before and within lockdown period in COVID-19 era: A retrospective study from rural Nepal
Authors: Baral Suman , Chhetri Raj Kumar , Thapa Neeraj 
Published: January 2021

IntroductionThe world has been engulfed with the pandemic of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which have created significant impact in the emergency surgical health delivery including acute appendicitis. The main aim of this study was to compare the demographic and clinical parameters between two cohorts before the onset of lockdown and within the pandemic.MethodsA retrospective analysis was performed between two groups A and B, who presented with acute appendicitis three months prior to and after initiation of lockdown on March 24 2020 respectively in one of the tertiary centers of Nepal. These two cohorts were compared in demographics, clinicopathological characteristics and surgical aspects of acute appendicitis.ResultsThere were 42 patients in group A and 50 patients in group B. Mean age of the patients was 31.32±17.18 years with male preponderance in group B (N = 29). Mean duration of pain increased significantly in group B [57.8±25.9(B) vs 42.3±25.0(A) hours, P = 0.004] along with mean duration of surgery [51.06±9.4(B) vs 45.27±11.8(A) minutes, P = 0.015]. There was significant decrease in post-operative hospital stay among group B patients [3.04±1.1(B) vs 3.86±0.67(A) days, P = 0.0001]. Complicated cases increased in group B including appendicular perforation in 10 cases. Similarly, mean duration of presentation to hospital significantly increased in group B patients with perforation [69.6±21.01 vs 51.57±17.63 hours, P = 0.008].ConclusionDuring the adversity of the current pandemic, increased number of cases of acute appendicitis can be dealt with surgery as the chances of late presentation and complexity of the lesion exists.
Recurrent disease progression networks for modelling risk trajectory of heart failure
Authors: Lu Xing Han , Liu Aihua , Fuh Shih-Chieh , Lian Yi , Guo Liming , Yang Yi , Marelli Ariane , Li Yue 
Published: January 2021

Motivation
Recurrent neural networks (RNN) are powerful frameworks to model medical time series records. Recent studies showed improved accuracy of predicting future medical events (e.g., readmission, mortality) by leveraging large amount of high-dimensional data. However, very few studies have explored the ability of RNN in predicting long-term trajectories of recurrent events, which is more informative than predicting one single event in directing medical intervention.

Methods
In this study, we focus on heart failure (HF) which is the leading cause of death among cardiovascular diseases. We present a novel RNN framework named Deep Heart-failure Trajectory Model (DHTM) for modelling the long-term trajectories of recurrent HF. DHTM auto-regressively predicts the future HF onsets of each patient and uses the predicted HF as input to predict the HF event at the next time point. Furthermore, we propose an augmented DHTM named DHTM+C (where “C” stands for co-morbidities), which jointly predicts both the HF and a set of acute co-morbidities diagnoses. To efficiently train the DHTM+C model, we devised a novel RNN architecture to model disease progression implicated in the co-morbidities.

Results
Our deep learning models confers higher prediction accuracy for both the next-step HF prediction and the HF trajectory prediction compared to the baseline non-neural network models and the baseline RNN model. Compared to DHTM, DHTM+C is able to output higher probability of HF for high-risk patients, even in cases where it is only given less than 2 years of data to predict over 5 years of trajectory. We illustrated multiple non-trivial real patient examples of complex HF trajectories, indicating a promising path for creating highly accurate and scalable longitudinal deep learning models for modeling the chronic disease.
An Apparatus to Measure Gas Diffusion and Gas Permeability of Unsaturated Cap Barriers Subjected to Distortion
Authors: Rajesh S. , Khan V. 
Published: January 2021

AbstractLandfill cap barriers are commonly designed to limit infiltration into the landfill, sustain deformation, and prevent the migration of landfill gases to the atmosphere. The gas flow through the unsaturated cap barrier could be due to advection, diffusion, or both based on the degree of saturation of the cap barriers. In the present study, a custom-designed test setup is developed to measure the gas permeability and diffusion coefficient of unsaturated cap barriers sequentially under various settlement rate and distortion levels. The apparatus comprises cylindrical lower and upper chambers, perforated overlapping triangular plates, worm gear, screw jack, motor, controller, and sensors. The lower chamber equipped with an oxygen sensor will be used to measure the variation in the oxygen concentration inside the chamber, leading to the measurement of gas diffusion of cap barriers. The measured quantity of nitrogen gas stored in the gas reservoir is allowed to flow through the cap barrier, leading to the measurement of gas permeability by advection. The gas permeability and gas diffusion at various distortion levels can be determined with the help of perforated overlapping triangular plates and a calibrated screw jack-motor system. The usage of this test setup in assessing the gas flow characteristics of the unsaturated cap barrier under the chosen distortion level is briefly illustrated using two types of cap barriers (compacted clay liner and geosynthetic clay liner) at different moisture contents.
Diabetogenically beneficial gut microbiota alterations in third trimester of pregnancy
Authors: Amabebe Emmanuel , Anumba Dilly O 
Published: January 2021

Altered gut microbiota (dysbiosis), inflammation and weight gain are pivotal to the success of normal pregnancy. These are features of metabolic syndrome that ordinarily increase the risk of type 2 diabetes in non-pregnant individuals. Though gut microbiota influences host energy metabolism and homeostasis, the outcome (healthy or unhealthy) varies depending on pregnancy status. In a healthy pregnancy, the gut microbiota is altered to promote metabolic and immunological changes beneficial to the mother and foetus but could connote a disease state in non-pregnant individuals. During the later stages of gestation, metabolic syndrome-like features, that is, obesity-related gut dysbiotic microbiota, increased insulin resistance, and elevated pro-inflammatory cytokines, promote energy storage in adipose tissue for rapid foetal growth and development, and in preparation for energy-consuming processes such as parturition and lactation. The origin of this gestation-associated host–microbial interaction is still elusive. Therefore, this review critically examined the host–microbial interactions in the gastrointestinal tract of pregnant women at late gestation (third trimester) that shift host metabolism in favour of a diabetogenic or metabolic syndrome-like phenotype. Whether the diabetogenic effects of such interactions are indeed beneficial to both mother and foetus was also discussed with plausible mechanistic pathways and associations highlighted.

Lay summary
In non-pregnant women, increased blood glucose, fat accumulation, and prolonged immune response lead to obesity and diabetes. However, during the later stages of pregnancy, the changes in the body’s metabolism described previously do not lead to disease, instead pregnancy facilitates the storage of sufficient energy in fat cells for rapid growth and development of the foetus. The excess energy stores also prepares the mother for labour and breastfeeding. This review examines the role of the normal bacteria in the digestive tract in this beneficial energy accumulation and transfer between the mother and foetus without leading to obesity, diabetes and hypertension in pregnancy.
The First Live Birth in Lithuania After Application of Preimplantation Genetic Testing
Authors: Gudlevičienė Živilė , Baušytė Raminta , Dagytė Evelina , Balkelienė Danutė , Utkus Algirdas , Ramašauskaitė Diana 
Published: January 2021

Background. Preimplantation genetic testing (PGT) is a genetic testing procedure that is performed before the implantation of embryos for the identification of genetic abnormalities. It is commonly performed when one or both expecting parents have such abnormalities and are at a high risk of passing them to their offspring. The aim of this case report is to describe the first successful IVF/ICSI/PGT procedure in Lithuania.Case report. A 27-year-old woman and a 31-year-old man, a married couple, were referred to VUHSK Santaros Fertility Center after trying to conceive for 4 years. In a previous relationship, the woman got pregnant spontaneously and decided to terminate the pregnancy. The husband does not have any children. During the medical examination, the transvaginal ultrasound revealed a low antral follicle count and low anti-Müllerian hormone level for the woman. Semen analysis for the male patient showed severe oligoastenospermia, which confirmed the previous abnormal spermogram results. Chromosome analysis revealed normal karyotype for the woman (46,XX) and Robertsonian translocation for the husband (45,XY,der(13;14)(q10;q10)). After the interdisciplinary medical team counselling, an ICSI with PGT-SR was suggested for the couple. The woman underwent controlled ovarian hyperstimulation with GnRH antagonist protocol for 11 days. Only one embryo with no unbalanced rearrangements was identified and transferred to the woman. On the 14th day post oocyte retrieval, the first serum β-hCG result was received – 39.5 mIU/ml, and the normal gestational sac at 5 weeks and 3 days was confirmed by ultrasound examination.Conclusion: the first successful pregnancy was achieved in Lithuania and the first IVF/ICSI/PGT-SR newborn in Lithuania was born in 2019 – a vaginal birth of a healthy girl with gestational age of 38 weeks and 4 days and a weight of 2820 g; the Apgar score was 10/10. The IVF/ICSI/PGT procedure was successfully implemented by the multidisciplinary team in VUHSK.