bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ada-WHIPS: Explaining AdaBoost Classification with Applications in the Health Sciences
Authors: Hatwell Julian , Gaber Mohamed Medhat , Azad R.M. Atif 
Published: February 2020

Abstract
Background

Computer Aided Diagnostics (CAD) can support medical practitioners to make critical decisions about their patients' disease conditions. Practitioners require access to the chain of reasoning behind CAD to build trust in the CAD advice and to supplement their own expertise. Yet, CAD systems might be based on black box machine learning (ML) models and high dimensional data sources (electronic health records, MRI scans, cardiotocograms, etc). These foundations make interpretation and explanation of the CAD advice very challenging. This challenge is recognised throughout the machine learning research community. eXplainable Artificial Intelligence (XAI) is emerging as one of the most important research areas of recent years, because it addresses the interpretability and trust concerns of medical practitioners and other critical decision makers. Method

In this work, we focus on AdaBoost, a black box model that has been widely adopted in the CAD literature. We address the challenge -- to explain AdaBoost classification -- with a novel algorithm that extracts simple, logical rules from AdaBoost models. Our algorithm, \textit{Adaptive-Weighted High Importance Path Snippets} (Ada-WHIPS), makes use of AdaBoost's adaptive classifier weights; using a novel formulation, Ada-WHIPS uniquely redistributes the weights among individual decision nodes at the internals of the AdaBoost model. Then, a simple heuristic search of the weighted nodes finds a single rule that dominated the model's decision. We compare the explanations generated by our novel approach with the state of the art in an experimental study. We evaluate the derived explanations with simple statistical tests of well-known quality measures, precision and coverage, and a novel measure \textit{stability} that is better suited to the XAI setting. Results

In this paper, our experimental results demonstrate the benefits of using our novel algorithm for explaining AdaBoost classification. The simple rule-based explanations have better generalisation (mean coverage 15\%-68\%) while remaining competitive for specificity (mean precision 80\%-99\%). A very small trade-off in specificity is shown to guard against over-fitting. Conclusions

This research demonstrates that interpretable, classification rule-based explanations can be generated for computer aided diagnostic tools based on AdaBoost, and that a tightly coupled, AdaBoost-specific approach can outperform model-agnostic methods.
Recurrent disc herniation following percutaneous endoscopic lumbar discectomy preferentially occurs when Modic changes are present
Authors: Hao Lu , Li Shengwen , Liu Junhui , Shan Zhi , Fan Shunwu , Zhao Fengdong 
Published: February 2020

Abstract
Objective: To investigate the relationship between Modic changes (MCs) and recurrent lumbar disc herniation (rLDH), and that between the herniated disc component and rLDH following percutaneous endoscopic lumbar discectomy (PELD).
Methods: We included 102 (65 males, 37 females, aged 20–66 yrs) inpatients who underwent PELD from August 2013 to August 2016. All patients underwent CT and MRI preoperatively. The presence and type of Modic changes were assessed. During surgery the herniated disc component of each patient was classified into two groups: nucleus pulposus group, hyaline cartilage group. The association of herniated disc component with Modic changes was investigated. The incidence of recurrent disc herniation was assessed based on more than 2-year follow-up.
Results: In total, 11 patients were lost to follow up; the other 91 were followed up during 24–60 months. Of the 91 patients, 99 discs underwent PELD; 28/99 (28.3%) had MCs. Type I and II MCs were seen in 9 (9.1%) and 19 (19.2%), respectively; no type III MCs were found. Among 28 endplates with MCs, according to the herniated disc component, 18/28 (64.3%) showed evidence of hyaline cartilage in the intraoperative specimens, including 6/9 and 12/19 endplates with type I and II MCs, respectively. Among 71 endplates without MCs, 14/71 (19.7%) showed evidence of hyaline cartilage in the intraoperative specimens. Hyaline cartilage was more common in patients with MCs (P<0.05). We found 2 cases of rLDH in the non-MC group (n=71); 6 cases rLDH were found in the MC group (n=28), including 2 and 4 cases for types I and II, respectively. There was no significant difference between types I and II (P>0.05). rLDH was more common in patients with MCs (P<0.05). We found 5 rLDH cases in the hyaline cartilage group (n=32); 3 rLDH cases were found in the nucleus pulposus group (n=67). rLDH was more common in the hyaline cartilage group (P<0.05).
Conclusions: MCs were associated with the herniated cartilage disc component. rLDH following PELD preferentially occurs when MCs or the herniated cartilage are present. Patients with MCs following PELD might require a second operation.
FHIR PIT: an open software application for spatiotemporal integration of clinical data and environmental exposures data
Authors: Xu Hao , Cox Steven , Stillwell Lisa , Pfaff Emily , Champion James , Ahalt Stanley C. , Fecho Karamarie 
Published: February 2020

Abstract
Background: Informatics tools to support the integration and subsequent interrogation of spatiotemporal data such as clinical data and environmental exposures data are lacking. Such tools are needed to support research in environmental health and any biomedical field that is challenged by the need for integrated spatiotemporal data to examine individual-level determinants of health and disease. Results: We have developed an open-source software application—FHIR PIT (Health Level 7 Fast Healthcare Interoperability Resources Patient data Integration Tool)—to enable studies on the impact of individual-level environmental exposures on health and disease. FHIR PIT was motivated by the need to integrate patient data derived from our institution’s clinical warehouse with a variety of public data sources on environmental exposures and then openly expose the data via ICEES (Integrated Clinical and Environmental Exposures Service). FHIR PIT consists of transformation steps or building blocks that can be chained together to form a transformation and integration workflow. Several transformation steps are generic and thus can be reused. As such, new types of data can be incorporated into the modular FHIR PIT pipeline by simply reusing generic steps or adding new ones. We have validated FHIR PIT in the context of a driving use case designed to investigate the impact of airborne pollutant exposures on asthma. Specifically, we replicated published findings demonstrating racial disparities in the impact of airborne pollutants on asthma exacerbations.Conclusions: While FHIR PIT was developed to support our driving use case, the software can be used to integrate any type and number of spatiotemporal data sources at a level of granularity that enables individual-level study. We expect FHIR PIT to facilitate research in environmental health and numerous other biomedical disciplines.
Newborn feeding recommendations and practices increase the risk of development of overweight and obesity
Authors: Watchmaker Brittany , Boyd Bridget , Dugas Lara 
Published: February 2020

Abstract
Background: The prevalence of obesity among infants less than 2 years of age has increased by more than 60 percent over the last three decades. Obese infants and toddlers are at an increased risk for staying overweight into adolescence and adulthood. Metabolic programming has been demonstrated in animal models whereby early life feeding habits result in life-long changes in hormone balance and metabolism. Our study explores if newborn over-nutrition on the first day of life (DOL1) is associated with risk for future overweight and obesity in childhood.

Methods: Retrospective chart data was collected for full-term formula-fed infants born between January 2008 and December 2012 who continued care at the same institution. Data included the volume of formula (ml) consumed on DOL1 as well as subsequent yearly BMI measures from well child check-ups. (WCC). Overfeeding was categorized as any feed greater than or equal to 30 ml on any of the first seven feeds while controlling for birth weight.

Results: The final data set included 1106 infants (547 male; 559 female). 1023 of the 1106 newborns (93%) were overfed at least once during DOL1, while 789 of 1106 (71%) were overfed 3 or more times during their first 7 feeds. After adjusting for birth weight, infants who were overfed 5 of the first 7 feeds were 5 times as likely to be overweight or obese at their 4th year well child check-up (p<0.05) compared to children not overfed. Infants who were overfed on all 7 of their first 7 feeds were 7 times more likely to be overweight or obese at their 4th year WCC (p=0.017).

Conclusions: Infants overfed on DOL1 were significantly more likely to be overweight or obese at their 4 th year WCC, compared to infants not overfed on their first day of life. Newborn families may benefit from counseling regarding age-appropriate volumes of formula during this early critical and impressionable time period. Future studies will aim to look at effect of smaller feeding bottle size on DOL1 on reducing overfeeding practices and future overweight and obesity.
MicroRNA-491-5p inhibit gastric cancer development by targeting EMT, cell adhesion genes and IFITM2
Authors: Wei zhijian , Zhang lixiang , Li angqing , li chuanhong , han wenxiu , Xu A-Man 
Published: February 2020

Abstract
Background: Gastric cancer (GC) is one of the deadliest cancers in China. And, it can be regulated by MicroRNAs (miRNAs) generally. miR-491-5p function as a tumor suppressor in different types of cancer, but we still don’t know the role of miR-491-5p in gastric cancer. Methods: Functional experiments including CCK-8 assay and transwell assay were performed. Furthermore, the underlying mechanism was explored through qRT-PCR and western blot assay. In addition, the function of miR-491-5p was also identified in vivo.Results: In this study, we found that high level of miR-491-5p caused a weak cell proliferation, migration and invasion abilities. In order to explore the role of miR-491-5p in vivo, we set a xenograft mouse model, and also found that high level of miR-491-5p suppressed tumor growth. Moreover, we found that miR-491-5p regulate the tumor development thought regulate the expression of EMT(Epithelial-mesenchymal transition), cell adhesion genes and IFITM2. Conclusions: These data show that miR-491-5p function as a tumor suppressor in GC both in vitro and in vivo.
Gut microbiota regulates autism-like behavior by mediating vitamin B6 metabolism in EphB6-deficient mice
Authors: Li Jian-Ming , Li Ying , Luo Zheng-Yi , Hu Yu-Ying , Bi Yue-Wei , Yang Jian-Ming , Zou Wen-Jun , Song Yun-Long , Li Shi , Shen Tong , Li Shu-Ji , Huang Lang , Zhou Ai-Jun , Gao Tian-Ming 
Published: February 2020

Abstract
Background
Autism spectrum disorder (ASD) is a developmental disorder with limited effective pharmacological treatments for the core autistic symptoms so far. Increasing evidences, especially the clinical studies in ASD patients, suggest a functional link between gut microbiota and development of ASD. However, the mechanisms linking gut microbiota and brain dysfunctions (gut-brain axis) in ASD are still not well-established. With genetic mutations and down-regulated expression in patients with ASD, EPHB6 , which is also important in homeostasis of gut, has been generally considered to be a candidate gene for ASD. Nonetheless, the role and mechanism of EPHB6 involved in regulating gut microbiota and development of ASD have been unclear.
Results
Here, we found deletion of EphB6 induced autism-like behavior and disturbed gut microbiota in mice. More importantly, transplanting fecal microbiota from EphB6-deficient mice resulted in autism-like behavior in antibiotics-treated C57BL/6J mice. Meanwhile, transplanting fecal microbiota from wild-type mice ameliorated autism-like behavior in EphB6-deficient mice. At the metabolic levels, disturbed gut microbiota led to vitamin B6 and dopamine defects in EphB6-deficient mice. At the cellular levels, excitation/inhibition (E/I) imbalance in medial prefrontal cortex was induced by gut microbiota-mediated defects of vitamin B6 metabolism in EphB6-deficient mice.
Conclusions
Our study uncovers a key role for gut microbiota in regulation of autism-like social behavior by mediating vitamin B6 metabolism, dopamine synthesis and E/I balance in EphB6-deficient mice, suggesting new strategies for understanding and treatment of ASD.
Comparison of three methods for monitoring dentin erosion progression
Authors: Pinto Shelon Cristina Souza , Lima Suellen Nogueira Linares , Nassif Maria Vitoria , Zakian Christian , Chew Hooi Pin , Pretty Ian , Ellwood Roger , Sampaio José Eduardo Cezar , Bandeca Matheus 
Published: February 2020

Abstract
Background: Clinical assessment and monitoring of dental erosion in vivo is challenging, although a number of clinical indices have been proposed but these are unlikely to be sensitive enough to quantify erosion with sufficient sensitivity to allow comparison of different therapies. In this respect, some of the techniques predominantly employed for the assessment of dental caries such as Quantitative light- induced fluorescence (QLF) and Optical coherence tomography (OCT) may also have utility for the assessment for erosion both in vivo and in vitro. The aim of the present study was to test three techniques (QLF, OCT and SMH) for the assessment of dentine erosion in a product testing model, using dentifrices to reduce erosion susceptibility. Dentine erosion was evaluated comparing the methods. Methods: Human dentine specimens were treated with one of two dentifrice slurries or mineral water (control group), followed by an erosive challenge and storage overnight in artificial saliva. These procedures were performed over 5 days. The following two dentifrices were tested: Duraphat™ 5000 (5000ppm Sodium Fluoride) and Colgate Sensitive Pro-Relief™ (8% arginine plus calcium carbonate and 1450ppm Fluoride). All groups showed a progressivedecrease in SMH and increase in scattering for OCT (P<0.05) indicating mineral loss. Results: The two dentifrice groups demonstrated significantly less softening than the control group (P<0.05). No statistically significantdifferences were detected for dentine erosion using QLF (P>0.05). Conclusion: SMH and OCT techniques were able to detect a significant protective effect against in vitro erosion whensamples were pre-treated with either dentifrice formulation. Dentifrices containing high concentrations of fluoride andarginine associated with calcium carbonate and fluoride have a protective effect against dentinal erosion.
Effective treatment of progressive nodular histiocytosis by intermediate-dose cytarabine: a case report and literature review
Authors: Wang Ji-nuo , Qiu Yu , Sun Jian , Niu Na , Jiao Yang , Zhu Tie-nan , Li Jian , Zhou Dao-bin , Cao Xin-xin 
Published: February 2020

Abstract
Background

Progressive nodular histiocytosis (PNH) is a rare, clinically distinct non-Langerhans cell histiocytosis, affecting the skin and mucous membranes with no signs of spontaneous regression of the lesions, without any other system involved. Patients typically have hundreds of lesions of superficial xanthomatous papules to nodules and deep larger fibrous nodules. So far, very few universally accepted reports of PNH existed and no effective treatment have been reported to reverse the progressive clinical course.

Results

Twenty-five PNH cases were identified so far, with a median age of 34 years. 14 patients were male. All patients presented as papules and nodules over the skin and/or mucosal surfaces, including face (39%), fingers or palm (16%), laryngeal (12%) and eyes (8%). 7 cases (28%) reported PNH with systematic diseases. Treatment efficacy using steroids, chemotherapy or surgical excision were disappointing in previous case reports. One patient with laryngeal involvement died due to airway obstruction. In our case, traditional chemotherapy achieved favorable therapeutic effect with intermediate-dose cytarabine confirmed by clinical symptoms of the patient, as well as PET/CT imaging.

Conclusions

PNH is a rare, proliferative disorder with disfiguring lesions and deteriorative quality of life. Intermediate-dose cytarabine should be considered as a treatment option for PNH patients.
Prevalence and factors associated with suicidal behavior among adolescents with epilepsy at Mulago and Butabika national referral hospitals in Uganda.
Authors: Kuteesa Hillary , Abbo Catherine , Muhwezi Winstons W 
Published: February 2020

Abstract
Background Suicide is the 3 rd leading cause of death among young people. Patients with epilepsy are 2 times more likely to have suicidal ideation and 3 times more likely to plan suicide attempt. In addition to seizures, these young people experience a variety of psychiatric illnesses like depression and anxiety. Social support and coping are known to have an effect on suicidal behavior in adolescents with epilepsy. There’s scanty data on this subject in Uganda. The purpose of this study was to determine the prevalence of suicidal behavior among adolescents with epilepsy at Butabika and Mulago National Referral Hospitals and associated factors. Methods Between 1 st August 2017 and 1 st February 2018, we sampled 223 adolescents from Butabika and Mulago National Referral Hospitals using a cross sectional study design. We used a Demographics Questionnaire, Mini International Neuropsychiatric Interview for Children and Adolescents-DSM-IV-TR version (MINI-KID), Brief COPE, and Multidimensional Scale of Perceived Social Support (MSPSS) to collect data. Data Entry was done using Epi Data and analyzed with Stata version 14. The dependent variable was suicidal behavior and independent variables were socio-demographic characteristics of adolescents and caregivers, epilepsy related factors, psychiatric co morbidity, coping strategies and perceived social support. Bi-variate and Multi-variate analyses were done to describe the associations between the dependent and independent variables. Results Of the 223 adolescents we recruited, (123)55.2% were male, 52.9% were aged 14-17 years. The prevalence of suicidal behavior was 30.5%. Major depression was most strongly associated with suicidal behavior (aOR=9.3, CI=4.3-20.1, p<0.001). Adolescents having post primary education were more likely to have suicidal behavior (aOR=2.2, CI=1.0-4.9, p=0.046). Venting as a coping strategy was found to increase the likelihood of having suicidal behavior (aOR=2.7, CI=1.2-6.2, p=0.017) whereas perceived family social support (aOR=0.4, CI=0.2-0.8, p=0.017) and the use of the active coping strategy (aOR=0.4, CI=0.2-0.9, p=0.033) were protective against suicidal behavior. Conclusions Prevalence of suicidal behavior in adolescents with epilepsy is high. Major depression is associated with suicidal behavior while perceived family social support is protective against suicidal behavior.
HLA-Mismatched GPBSCs infusion therapy in refractory Epstein-Barr virus-associated hemophagocytic lymphohistiocytosis: A observational study from a single center
Authors: Song Yue , Wang Jingshi , Wang Yini , Wang Zhao 
Published: February 2020

Abstract
Background: Hemophagocytic lymphohistiocytosis (HLH) is a severe or even fatal inflammatory state. Epstein–Barr virus (EBV) infection associated HLH (EBV-HLH) is one of the most common secondary HLH and suffers a very poor prognosis. Allo-HSCT is often required for refractory EBV-HLH, but some patients still cannot proceed to the next allo-HSCT due to various factors. This study aimed to observe the efficacy of HLA-mismatched granulocyte colony-stimulating factor (G-CSF) mobilized peripheral blood stem cells (GPBSCs) infusion for refractory EBV-HLH. Methods: A retrospective case-control study of refractory EBV-HLH patients with GPBSCs infusion from HLA-mismatched donors after chemotherapy (as GPBSCs group) and sole chemotherapy (as control group) was performed. Efficacy was evaluated 2 and 4 weeks and all patients were followed up until 1 January 2018. Results: There were 15 cases who accepted infusion between March 2016 and June 2017 and 19 were randomly selected from refractory EBV-HLH patients who underwent salvage therapy during the same period for the control group. In GPBSCs group, WBC (p=0.029), Fbg (p=0.041), ferritin (p=0.041) improved significantly after treatment. The overall response rate was 66.7% (CR 26.7%, PR 40.0%). However, there is no significant differences in changes of WBC, HGB, PLT, TG, Fbg, Ferritin, AST, ALT, T-bil between two groups. Only the Fbg level was recovered better in the GPBSCs infusion group (p=0.017). In the GPBSCs group, EBV-DNA decreased significantly after 2 weeks (p=0.010) and 4 weeks (p=0.002) after treatment, and the effect of the decrease was significantly better than that of the chemotherapy alone group in 2 weeks but not 4 weeks (p2w=0.017, p4w=0.145). The median survival time in the infusion group was 20.4 weeks [6.7, 92.1], and the median survival time in the control group was 10.8 weeks [0.6-116.4]. In the short-term, the infusion group’s survival rate was better (2-month 93.33% vs. 52.63%, p=0.002; 3-month 86.67% vs. 47.09%, p=0.006), but there was no difference in OS (p=0.259). Conclusions: Infusing GPBSCs combined with chemotherapy is effective, especially in decreasing EBV-DNA, performs better than chemotherapy alone, and improve short term survival rate. GPBSCs infusion is suggested as a bridging treatment method to allo-HSCT.
Upregulation of lncRNA DQ679794 contributes to preventing the progression of hepatocellular carcinoma both in vitro and in vivo
Authors: Lin Ze-wei , Ren Qing-qi , Huang Zhi-feng , Liu Ji-kui 
Published: February 2020

Abstract
Background Hepatocellular carcinoma (HCC) is an aggressive tumor with a poor prognosis. Long noncoding RNAs (lncRNAs) are key regulators of tumor development. However, lncRNA profiles in HCC remain largely unknown. In previous studies, we found that lncRNA DQ786243 plays an important role in the pathogenesis of HCC and promotes the development of HCC. In this study, we investigated the role of lncRNA DQ679794 in the pathogenesis of HCC. Methods and Results We first used quantitative real-time PCR among 64 paired HCC tissues, and the level of lncRNA DQ679794 was found to be significantly lower in tumors than in normal tissues. In addition, the effects of lncRNA DQ679794 were assessed by overexpression in vitro and in vivo . We found that the level of apoptosis was increased and that cell proliferation was weakened in HepG2 cells overexpressing DQ679794. Finally, the transplanted tumor experiment confirmed that after the overexpression of lncRNA DQ679794, the growth of transplanted tumors formed by liver cancer cells was inhibited. Conclusion This study suggests that lncRNA DQ679794 is an oncogene that inhibits tumor progression, and we believe that lncRNAs may be a key regulatory center in HCC progression.