bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reducing Interface Traps with High Density Hydrogen Treatment to Increase Passivated Emitter Rear Contact Cell Efficiency
Authors: Yang Chih-Cheng , Chen Po-Hsun , Chang Ting-Chang , Su Wan-Ching , Chen Sung-Yu , Liu Shui-Chin , Chou Sheng-Yao , Tan Yung-Fang , Lin Chun-Chu , Wu Pei-Yu , Tsai Tsung-Ming , Huang Hui-Chun 
Published: December 2019

AbstractIn this work, a high-density hydrogen (HDH) treatment is proposed to reduce interface traps and enhance the efficiency of the passivated emitter rear contact (PERC) device. The hydrogen gas is compressed at pressure (~ 70 atm) and relatively low temperature (~ 200 °C) to reduce interface traps without changing any other part of the device’s original fabrication process. Fourier-transform infrared spectroscopy (FTIR) confirmed the enhancement of Si–H bonding and secondary-ion mass spectrometry (SIMS) confirmed the SiN/Si interface traps after the HDH treatment. In addition, electrical measurements of conductance-voltage are measured and extracted to verify the interface trap density (Dit). Moreover, short circuit current density (Jsc), series resistance (Rs), and fill factor (F.F.) are analyzed with a simulated light source of 1 kW M−2 global AM1.5 spectrum to confirm the increase in cell efficiency. External quantum efficiency (EQE) is also measured to confirm the enhancement in conversion efficiency between different wavelengths. Finally, a model is proposed to explain the experimental result before and after the treatment.
A qualitative transcriptional signature for the histological reclassification of lung squamous cell carcinomas and adenocarcinomas
Authors: Li Xin , Shi Gengen , Chu Qingsong , Jiang Wenbin , Liu Yixin , Zhang Sainan , Zhang Zheyang , Wei Zixin , He Fei , Guo Zheng , Qi Lishuang 
Published: December 2019

AbstractBackgroundTargeted therapy for non-small cell lung cancer is histology dependent. However, histological classification by routine pathological assessment with hematoxylin-eosin staining and immunostaining for poorly differentiated tumors, particularly those from small biopsies, is still challenging. Additionally, the effectiveness of immunomarkers is limited by technical inconsistencies of immunostaining and lack of standardization for staining interpretation.ResultsUsing gene expression profiles of pathologically-determined lung adenocarcinomas and squamous cell carcinomas, denoted as pADC and pSCC respectively, we developed a qualitative transcriptional signature, based on the within-sample relative gene expression orderings (REOs) of gene pairs, to distinguish ADC from SCC. The signature consists of two genes,KRT5andAGR2, which has the stable REO pattern ofKRT5 > AGR2in pSCC andKRT5 < AGR2in pADC. In the two test datasets with relative unambiguous NSCLC types, the apparent accuracy of the signature were 94.44 and 98.41%, respectively. In the other integrated dataset for frozen tissues, the signature reclassified 4.22% of the 805 pADC patients as SCC and 12% of the 125 pSCC patients as ADC. Similar results were observed in the clinical challenging cases, including FFPE specimens, mixed tumors, small biopsy specimens and poorly differentiated specimens. The survival analyses showed that the pADC patients reclassified as SCC had significantly shorter overall survival than the signature-confirmed pADC patients (log-rankp = 0.0123, HR = 1.89), consisting with the knowledge that SCC patients suffer poor prognoses than ADC patients. The proliferative activity, subtype-specific marker genes and consensus clustering analyses also supported the correctness of our signature.ConclusionsThe non-subjective qualitative REOs signature could effectively distinguish ADC from SCC, which would be an auxiliary test for the pathological assessment of the ambiguous cases.
Long noncoding RNAs in lipid metabolism: literature review and conservation analysis across species
Authors: Muret Kevin , Désert Colette , Lagoutte Laetitia , Boutin Morgane , Gondret Florence , Zerjal Tatiana , Lagarrigue Sandrine 
Published: December 2019

Abstract
Background
Lipids are important for the cell and organism life since they are major components of membranes, energy reserves and are also signal molecules. The main organs for the energy synthesis and storage are the liver and adipose tissue, both in humans and in more distant species such as chicken. Long noncoding RNAs (lncRNAs) are known to be involved in many biological processes including lipid metabolism.

Results
In this context, this paper provides the most exhaustive list of lncRNAs involved in lipid metabolism with 60 genes identified after an in-depth analysis of the bibliography, while all “review” type articles list a total of 27 genes. These 60 lncRNAs are mainly described in human or mice and only a few of them have a precise described mode-of-action. Because these genes are still named in a non-standard way making such a study tedious, we propose a standard name for this list according to the rules dictated by the HUGO consortium. Moreover, we identified about 10% of lncRNAs which are conserved between mammals and chicken and 2% between mammals and fishes. Finally, we demonstrated that two lncRNA were wrongly considered as lncRNAs in the literature since they are 3′ extensions of the closest coding gene.

Conclusions
Such a lncRNAs catalogue can participate to the understanding of the lipid metabolism regulators; it can be useful to better understand the genetic regulation of some human diseases (obesity, hepatic steatosis) or traits of economic interest in livestock species (meat quality, carcass composition). We have no doubt that this first set will be rapidly enriched in coming years.
Challenges of one-year longitudinal follow-up of a prospective, observational cohort study using an anonymised database: recommendations for trainee research collaboratives
Authors:   STARSurg Collaborative, Nepogodiev Dmitri 
Published: December 2019

Abstract
Background
Trainee research collaboratives (TRCs) have pioneered high quality, prospective ‘snap-shot’ surgical cohort studies in the UK. Outcomes After Kidney injury in Surgery (OAKS) was the first TRC cohort study to attempt to collect one-year follow-up data. The aims of this study were to evaluate one-year follow-up and data completion rates, and to identify factors associated with improved follow-up rates.

Methods
In this multicentre study, patients undergoing major gastrointestinal surgery were prospectively identified and followed up at one-year following surgery for six clinical outcomes. The primary outcome for this report was the follow-up rate for mortality at 1 year. The secondary outcome was the data completeness rate in those patients who were followed-up. An electronic survey was disseminated to investigators to identify strategies associated with improved follow-up.

Results
Of the 173 centres that collected baseline data, 126 centres registered to participate in one-year follow-up. Overall 62.3% (3482/5585) of patients were followed-up at 1 year; in centres registered to collect one-year outcomes, the follow-up rate was 82.6% (3482/4213). There were no differences in sex, comorbidity, operative urgency, or 7-day postoperative AKI rate between patients who were lost to follow-up and those who were successfully followed-up. In centres registered to collect one-year follow-up outcomes, overall data completeness was 83.1%, with 57.9% (73/126) of centres having ≥95% data completeness. Factors associated with increased likelihood of achieving ≥95% data completeness were total number of patients to be followed-up (77.4% in centres with < 15 patients, 59.0% with 15–29 patients, 51.4% with 30–59 patients, and 36.8% with > 60 patients, p = 0.030), and central versus local storage of patient identifiers (72.5% vs 48.0%, respectively, p = 0.006).

Conclusions
TRC methodology can be used to follow-up patients identified in prospective cohort studies at one-year. Follow-up rates are maximized by central storage of patient identifiers.
Joint model robustness compared with the time-varying covariate Cox model to evaluate the association between a longitudinal marker and a time-to-event endpoint
Authors: Arisido Maeregu W. , Antolini Laura , Bernasconi Davide P. , Valsecchi Maria G. , Rebora Paola 
Published: December 2019

AbstractBackgroundThe recent progress in medical research generates an increasing interest in the use of longitudinal biomarkers for characterizing the occurrence of an outcome. The present work is motivated by a study, where the objective was to explore the potential of the long pentraxin 3 (PTX3) as a prognostic marker of Acute Graft-versus-Host Disease (GvHD) after haematopoietic stem cell transplantation. Time-varying covariate Cox model was commonly used, despite its limiting assumptions that marker values are constant in time and measured without error. A joint model has been developed as a viable alternative; however, the approach is computationally intensive and requires additional strong assumptions, in which the impacts of their misspecification were not sufficiently studied.MethodsWe conduct an extensive simulation to clarify relevant assumptions for the understanding of joint models and assessment of its robustness under key model misspecifications. Further, we characterize the extent of bias introduced by the limiting assumptions of the time-varying covariate Cox model and compare its performance with a joint model in various contexts. We then present results of the two approaches to evaluate the potential of PTX3 as a prognostic marker of GvHD after haematopoietic stem cell transplantation.ResultsOverall, we illustrate that a joint model provides an unbiased estimate of the association between a longitudinal marker and the hazard of an event in the presence of measurement error, showing improvement over the time-varying Cox model. However, a joint model is severely biased when the baseline hazard or the shape of the longitudinal trajectories are misspecified. Both the Cox model and the joint model correctly specified indicated PTX3 as a potential prognostic marker of GvHD, with the joint model providing a higher hazard ratio estimate.ConclusionsJoint models are beneficial to investigate the capability of the longitudinal marker to characterize time-to-event endpoint. However, the benefits are strictly linked to the correct specification of the longitudinal marker trajectory and the baseline hazard function, indicating a careful consideration of assumptions to avoid biased estimates.
Development of the DAGIS intervention study: a preschool-based family-involving study promoting preschoolers’ energy balance-related behaviours and self-regulation skills
Authors: Ray Carola , Kaukonen Riikka , Lehto Elviira , Vepsäläinen Henna , Sajaniemi Nina , Erkkola Maijaliisa , Roos Eva 
Published: December 2019

AbstractBackgroundPreschoolers’ energy balance-related behaviours (EBRBs) and self-regulation skills are important for their later health. Few preschool-based interventions aiming to promote preschoolers’ EBRBs and self-regulation skills, simultaneously reducing differences in EBRBs, due to children’s socio-economic status (SES) background, have been conducted. This study will present the Increased Health and Wellbeing in Preschools (DAGIS) intervention development process applying the Intervention Mapping (IM) framework.MethodsThe development of the DAGIS intervention study, a preschool level clustered randomized controlled trial (RCT), was based on the IM framework. The protocol in IM guides the development process of an intervention through six steps: needs assessment and logic model of the problem, programme outcomes and objectives, design of the programme, production, implementation plan, and evaluation plan.ResultsThe needs assessment, part of the step 1 in IM, yielded the base for the DAGIS logic model of change. The model includes objectives related to changes in children’s EBRBs, self-regulation skills, and in psychosocial and physical environment that is determined by parents and early educators. A 22-week programme was developed, and materials for preschools and families were produced. A feasibility study of the recruitment processes, acceptability of the materials and methods, and implementation was conducted. The DAGIS intervention study was conducted September 2017–May 2018 as a clustered RCT including a comprehensive effectiveness and process evaluation. The process evaluation was run throughout the intervention targeting preschools and families.ConclusionA preschool-based family-involving programme was developed in the DAGIS intervention study by applying the IM protocol. It was a time- and resource-consuming process. However, the systematic planning, development, and running of the programme have reinforced a comprehensive evaluation, which is a strength in the intervention. The results from the evaluation will enhance the knowledge of how to promote EBRBs and self-regulation skills among preschoolers, and diminish SES differences in them.Trial registrationISRCTN57165350(Prospectively registered January the 8th, 2015).
Influence of psychiatric or social backgrounds on clinical decision making: a randomized, controlled multi-centre study
Authors: Yamauchi Yosuke , Shiga Takashi , Shikino Kiyoshi , Uechi Takahiro , Koyama Yasuaki , Shimozawa Nobuhiko , Hiraoka Eiji , Funakoshi Hiraku , Mizobe Michiko , Imaizumi Takahiro , Ikusaka Masatomi 
Published: December 2019

Abstract
Background
Frequent and repeated visits from patients with mental illness or free medical care recipients may elicit physicians’ negative emotions and influence their clinical decision making. This study investigated the impact of the psychiatric or social background of such patients on physicians’ decision making about whether to offer recommendations for further examinations and whether they expressed an appropriate disposition toward the patient.

Methods
A randomized, controlled multi-centre study of residents in transitional, internal medicine, or emergency medicine was conducted in five hospitals. Upon randomization, participants were stratified by gender and postgraduate year, and they were allocated to scenario set 1 or 2. They answered questions pertaining to decision-making based on eight clinical vignettes. Half of the eight vignettes presented to scenario set 1 included additional patient information, such as that the patient had a past medical history of schizophrenia or that the patient was a recipient of free care who made frequent visits to the doctor (biased vignettes). The other half included no additional information (neutral vignettes). For scenario set 2, the four biased vignettes presented to scenario set 1 were neutralized, and the four neutral vignettes were rendered biased by providing additional information. After reading, participants answered decision-making questions regarding diagnostic examination, interventions, or patient disposition. The primary analysis was a repeated-measures ANOVA on the mean management accuracy score, with patient background information as a within-subject factor (no bias, free care recipients, or history of schizophrenia).

Results
A total of 207 questionnaires were collected. Repeated-measures ANOVA showed that additional background information had influence on mean accuracy score (F(7, 206) = 13.84, p <  0.001 partial η2 = 0.063). Post hoc pairwise multiple comparison test, Sidak test, showed a significant difference between schizophrenia and no bias condition (p <  0.05). The ratings for patient likability were lower in the biased vignettes compared to the neutral vignettes, which was associated with the lower utilization of medical resources by the physicians.

Conclusions
Additional background information on past medical history of schizophrenia increased physicians’ mistakes in decision making. Patients’ psychiatric backgrounds should not bias physicians’ decision-making. Based on these findings, physicians are recommended to avoid being influenced by medically unrelated information.
Towards the automation of early-stage human embryo development detection
Authors: Raudonis Vidas , Paulauskaite-Taraseviciene Agne , Sutiene Kristina , Jonaitis Domas 
Published: December 2019

Abstract
Background
Infertility and subfertility affect a significant proportion of humanity. Assisted reproductive technology has been proven capable of alleviating infertility issues. In vitro fertilisation is one such option whose success is highly dependent on the selection of a high-quality embryo for transfer. This is typically done manually by analysing embryos under a microscope. However, evidence has shown that the success rate of manual selection remains low. The use of new incubators with integrated time-lapse imaging system is providing new possibilities for embryo assessment. As such, we address this problem by proposing an approach based on deep learning for automated embryo quality evaluation through the analysis of time-lapse images. Automatic embryo detection is complicated by the topological changes of a tracked object. Moreover, the algorithm should process a large number of image files of different qualities in a reasonable amount of time.

Methods
We propose an automated approach to detect human embryo development stages during incubation and to highlight embryos with abnormal behaviour by focusing on five different stages. This method encompasses two major steps. First, the location of an embryo in the image is detected by employing a Haar feature-based cascade classifier and leveraging the radiating lines. Then, a multi-class prediction model is developed to identify a total cell number in the embryo using the technique of deep learning.

Results
The experimental results demonstrate that the proposed method achieves an accuracy of at least 90% in the detection of embryo location. The implemented deep learning approach to identify the early stages of embryo development resulted in an overall accuracy of over 92% using the selected architectures of convolutional neural networks. The most problematic stage was the 3-cell stage, presumably due to its short duration during development.

Conclusion
This research contributes to the field by proposing a model to automate the monitoring of early-stage human embryo development. Unlike in other imaging fields, only a few published attempts have involved leveraging deep learning in this field. Therefore, the approach presented in this study could be used in the creation of novel algorithms integrated into the assisted reproductive technology used by embryologists.
New considerations on pathways involved in acute traumatic coagulopathy: the thrombin generation paradox
Authors: Gangloff Cedric , Mingant Fanny , Theron Michael , Galinat Hubert , Grimault Ollivier , Ozier Yves , Pichavant-Rafini Karine 
Published: December 2019

AbstractBackgroundAn acute traumatic coagulopathy (ATC) is observed in about one third of severely traumatized patients. This early, specific, and endogenous disorder is triggered by the association of trauma and hemorrhage. The early phase of this condition is characterized by the expression of a bleeding phenotype leading to hemorrhagic shock and the late phase by a prothrombotic profile leading to multiple organ failure. The physiopathology of this phenomenon is still poorly understood. Hypotheses of disseminated intravascular coagulation, activated protein C-mediated fibrinolysis, fibrinogen consumption, and platelet functional impairment were developed by previous authors and continue to be debated. The objective of this study was to observe general hemostasis disorders in case of ATC to confront these hypotheses.MethodFour groups of 15 rats were compared: C, control; T, trauma; H, hemorrhage; and TH, trauma and hemorrhage. Blood samples were drawn at baseline and 90 min. Thrombin generation tests, platelet aggregometry, and standard hemostasis tests were performed.ResultsSignificant differences were observed between the baseline and TH groups for aPTT (17.9 ± 0.8 s vs 24.3 ± 1.4 s,p< 0.001, mean ± SEM), MAP (79.7 ± 1.3 mmHg vs 43.8 ± 1.3 mmHg,p< 0.001, mean ± SEM), and hemoglobin (16.5 ± 0.1 g/dL vs 14.1 ± 0.3 g/dL,p< 0.001, mean ± SEM), indicating the presence of an hemorrhagic shock due to ATC. Compared to all other groups, coagulation factor activities were decreased in the TH group, but endogenous thrombin potential was (paradoxically) higher than in group C (312 ± 17 nM/min vs. 228 ± 23 nM/min;p= 0.016; mean ± SEM). We also observed a subtle decrease in platelet count and function in case of ATC and retrieved an inversed linear relationship between fibrinogen concentration and aPTT (intercept, 26.53 ± 3.16; coefficient, − 3.40 ± 1.26; adjustedR2: 0.1878;p= 0.0123).ConclusionsThe clinical-biological profile that we observed, combining normal thrombin generation, fibrinogen depletion, and a hemorrhagic phenotype, reinforced the hypothesis of activated protein C mediated-fibrinolysis. The key role of fibrinogen, but not of the platelets, was confirmed in this study. The paradoxical preservation of thrombin generation suggests a protective mechanism mediated by rhabdomyolysis in case of major trauma. Based on these results, we propose a new conception concerning the pathophysiology of ATC.
N-myc downstream-regulated gene 1 inhibits the proliferation of colorectal cancer through emulative antagonizing NEDD4-mediated ubiquitylation of p21
Authors: Zhang Sen , Yu Chaoran , Yang Xiao , Hong Hiju , Lu Jiaoyang , Hu Wenjun , Hao Xiaohui , Li Shuchun , Aikemu Batuer , Yang Guang , He Zirui , Zhang Luyang , Xue Pei , Cai Zhenghao , Ma Junjun , Zang Lu , Feng Bo , Yuan Fei , Sun Jing , Zheng Minhua 
Published: December 2019

Abstract
Background
N-myc downstream-regulated gene 1 (NDRG1) has been shown to play a key role in tumor metastasis. Recent studies demonstrate that NDRG1 can suppress tumor growth and is related to tumor proliferation; however, the mechanisms underlying these effects remain obscure.

Methods
Immunohistochemistry (IHC) was used to detect NDRG1 and p21 protein expression in colorectal cancer tissue, and clinical significance of NDRG1 was also analyzed. CCK-8 assay, colony formation assay, flow cytometry, and xenograft model were used to assess the effect of NDRG1 on tumor proliferation in vivo and in vitro. The mechanisms underlying the effect of NDRG1 were investigated using western blotting, immunofluorescence, immunoprecipitation, and ubiquitylation assay.

Results
NDRG1 was down-regulated in CRC tissues and correlated with tumor size and patient survival. NDRG1 inhibited tumor proliferation through increasing p21 expression via suppressing p21 ubiquitylation. NDRG1 and p21 had a positive correlation both in vivo and in vitro. Mechanistically, E3 ligase NEDD4 could directly interact with and target p21 for degradation. Moreover, NDRG1 could emulatively antagonize NEDD4-mediated ubiquitylation of p21, increasing p21 expression and inhibit tumor proliferation.

Conclusion
Our study could fulfill potential mechanisms of the NDRG1 during tumorigenesis and metastasis, which may serve as a tumor suppressor and potential target for new therapies in human colorectal cancer.