bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration of anatomy ontology data with protein–protein interaction networks improves the candidate gene prediction accuracy for anatomical entities
Authors: Fernando Pasan C. , Mabee Paula M. , Zeng Erliang 
Published: October 2020

AbstractBackgroundIdentification of genes responsible for anatomical entities is a major requirement in many fields including developmental biology, medicine, and agriculture. Current wet lab techniques used for this purpose, such as gene knockout, are high in resource and time consumption. Protein–protein interaction (PPI) networks are frequently used to predict disease genes for humans and gene candidates for molecular functions, but they are rarely used to predict genes for anatomical entities. Moreover, PPI networks suffer from network quality issues, which can be a limitation for their usage in predicting candidate genes. Therefore, we developed an integrative framework to improve the candidate gene prediction accuracy for anatomical entities by combining existing experimental knowledge about gene-anatomical entity relationships with PPI networks using anatomy ontology annotations. We hypothesized that this integration improves the quality of the PPI networks by reducing the number of false positive and false negative interactions and is better optimized to predict candidate genes for anatomical entities. We used existing Uberon anatomical entity annotations for zebrafish and mouse genes to construct gene networks by calculating semantic similarity between the genes. These anatomy-based gene networks were semantic networks, as they were constructed based on the anatomy ontology annotations that were obtained from the experimental data in the literature. We integrated these anatomy-based gene networks with mouse and zebrafish PPI networks retrieved from the STRING database and compared the performance of their network-based candidate gene predictions.ResultsAccording to evaluations of candidate gene prediction performance tested under four different semantic similarity calculation methods (Lin, Resnik, Schlicker, and Wang), the integrated networks, which were semantically improved PPI networks, showed better performances by having higher area under the curve values for receiver operating characteristic and precision-recall curves than PPI networks for both zebrafish and mouse.ConclusionIntegration of existing experimental knowledge about gene-anatomical entity relationships with PPI networks via anatomy ontology improved the candidate gene prediction accuracy and optimized them for predicting candidate genes for anatomical entities.
The algal selenoproteomes
Authors: Jiang Liang , Lu Yiqian , Zheng Lin , Li Gaopeng , Chen Lianchang , Zhang Maona , Ni Jiazuan , Liu Qiong , Zhang Yan 
Published: October 2020

Abstract
Background
Selenium is an essential trace element, and selenocysteine (Sec, U) is its predominant form in vivo. Proteins that contain Sec are selenoproteins, whose special structural features include not only the TGA codon encoding Sec but also the SECIS element in mRNA and the conservation of the Sec-flanking region. These unique features have led to the development of a series of bioinformatics methods to predict and research selenoprotein genes. There have been some studies and reports on the evolution and distribution of selenoprotein genes in prokaryotes and multicellular eukaryotes, but the systematic analysis of single-cell eukaryotes, especially algae, has been very limited.

Results
In this study, we predicted selenoprotein genes in 137 species of algae by using a program we previously developed. More than 1000 selenoprotein genes were obtained. A database website was built to record these algae selenoprotein genes (www.selenoprotein.com). These genes belong to 42 selenoprotein families, including three novel selenoprotein gene families.

Conclusions
This study reveals the primordial state of the eukaryotic selenoproteome. It is an important clue to explore the significance of selenium for primordial eukaryotes and to determine the complete evolutionary spectrum of selenoproteins in all life forms.
Interdisciplinary clinical debriefing in the emergency department: an observational study of learning topics and outcomes
Authors: Coggins Andrew , Santos Aaron De Los , Zaklama Ramez , Murphy Margaret 
Published: October 2020

AbstractBackgroundDefined as a ‘guided reflective learning conversation’, ‘debriefing’ is most often undertaken in small groups following healthcare simulation training. Clinical debriefing (CD) following experiences in the working environment has the potential to enhance learning and improve performance.MethodsPrior to the study, a literature review was completed resulting in a standardised approach to CD that was used for training faculty. A pilot study of CD (n = 10) was then performed to derive a list of discussion topics and optimise the faculty training. The resulting debriefing approach was based on the “S.T.O.P.” structure (Summarise the case; Things that went well; Opportunities for improvement; Points of action). A debriefing aid, with suggested scripting, was provided. A subsequent observational study assessed CD within 1-h of clinical events. ‘Significantly distressing’ or ‘violent’ events were excluded. Data was collected on participant characteristics, discussion topics, and team recommendations. Study forms were non-identifiable. Subsequent analysis was performed by two investigators using content analysis of the debriefing forms (n = 71). Discussion topics (learning points) were coded using a modified version of the Promoting Excellence and Reflective Learning in Simulation (PEARLS) framework. One month after completion of the study, ED management staff were surveyed for reports of “harm” as the result of CD.ResultsDuring the study period, 71 CDs were recorded with a total of 506 participants. Mean debriefing length was 10.93 min (SD 5.6). Mean attendance was 7.13 (SD 3.3) participants. CD topics discussed were divided into ‘plus’ (well-done) and ‘delta’ (need to improve) groupings. 232 plus domains were recorded of which 195 (84.1%) aligned with the PEARLS debriefing framework, suggesting simulation debriefing skills may be translatable to a clinical setting. Topics discussed outside the PEARLS framework included family issues, patient outcome and environmental factors. CD reports led to preventative interventions for equipment problems and to changes in existing protocols. There were no recorded incidents of participant harm resulting from CD.ConclusionsTopics discussed in CD predominantly aligned to those commonly observed in simulation-based medical education. Collective recommendations from CD can be used as evidence for improving existing protocols and models of care.
Effects of kidney function, serum albumin and hemoglobin on dementia severity in the oldest old people with newly diagnosed Alzheimer’s disease in a residential aged care facility: a cross-sectional study
Authors: Wu Jia-Jyun , Weng Shuo-Chun , Liang Chih-Kuang , Lin Chu-Sheng , Lan Tsuo-Hung , Lin Shih-Yi , Lin Yu-Te 
Published: October 2020

Abstract
Background
Chronic kidney disease (CKD), low serum albumin, and anemia are known risk factors for cognitive decline in older people. We investigated the association between kidney function and cognitive impairment severity in oldest-old people with a diagnosis of Alzheimer’s disease (AD).

Methods
A cross-sectional study of patients aged 80 years and older was conducted at a veterans’ home in Taiwan between 2012 and 2016. Their estimated glomerular filtration rate (eGFR) was determined using the Modification of Diet in Renal Diseases (MDRD) equation. Cognitive function was evaluated with the Mini-Mental State Examination (MMSE) and Clinical Dementia Rating (CDR).

Results
A total of 84 patients (age mean ± SD, 86.6 ± 3.9 years) had MMSE scores of 10.1 ± 6.7, and CDR scores of 1.6 ± 0.7. The average eGFR was 61.7 ± 21.5 mL/min/1.73m2. The mean hemoglobin concentration was 12.7 ± 1.7 g/dl, and the mean albumin concentration was 4.5 ± 4.8 g/dl. Multivariate regression analyses showed that scores of CDR were significantly correlated with eGFR after adjustment for potential confounders. The scores of MMSE were significantly correlated with serum albumin and hemoglobin after adjustment for potential confounders.

Conclusions
We found dementia severity was significantly associated with kidney function, serum albumin, and hemoglobin in the oldest-old with AD. We recommend that oldest-old people with a diagnosis of AD be evaluated to determine kidney function, as well as nutritional and hematological status. Further study is needed to establish whether prevention of CKD deterioration, and correction of malnutrition and anemia may help to slow cognitive decline in oldest-old people with dementia.
Impact of the implementation of new guidelines on the management of patients with HIV infection at an advanced HIV clinic in Kinshasa, Democratic Republic of Congo (DRC)
Authors: Mangana F. , Massaquoi L. D. , Moudachirou R. , Harrison R. , Kaluangila T. , Mucinya G. , Ntabugi N. , Van Cutsem G. , Burton R. , Isaakidis P. 
Published: October 2020

Abstract
Background
HIV continues to be the main determinant morbidity with high mortality rates in Sub-Saharan Africa, with a high number of patients being late presenters with advanced HIV. Clinical management of advanced HIV patients is thus complex and requires strict adherence to updated, empirical and simplified guidelines. The current study investigated the impact of the implementation of a new clinical guideline on the management of advanced HIV in Kinshasa, Democratic Republic of Congo (DRC).

Methods
A retrospective analysis of routine clinical data of advanced HIV patients was conducted for the periods; February 2016 to March 2017, before implementation of new guidelines, and November 2017 to July 2018, after the implementation of new guidelines. Eligible patients were patients with CD4 < 200 cell/μl and presenting with at least 1 of 4 opportunistic infections. Patient files were reviewed by a medical doctor and a committee of 3 other doctors for congruence. Statistical significance was set at 0.05%.

Results
Two hundred four and Two hundred thirty-one patients were eligible for inclusion before and after the implementation of new guidelines respectively. Sex and age distributions were similar for both periods, and median CD4 were 36 & 52 cell/μl, before and after the new guidelines implementation, respectively. 40.7% of patients had at least 1 missed/incorrect diagnosis before the new guidelines compared to 30% after new guidelines, p < 0.05. Clinical diagnosis for TB and toxoplasmosis were also much improved after the implementation of new guidelines. In addition, only 63% of patients had CD4 count test results before the new guidelines compared to 99% of patients after new guidelines. Death odds after the implementation of new guidelines were significantly lower than before new guidelines in a multivariate regression model that included patients CD4 count and 10 other covariates, p < 0.05.

Conclusions
Simplification and implementation of a new and improved HIV clinical guideline coupled with the installation of laboratory equipment and point of care tests potentially helped reduce incorrect diagnosis and improve clinical outcomes of patients with advanced HIV. Regulating authorities should consider developing simplified versions of guidelines followed by the provision of basic diagnostic equipment to health centers.
MS Spasticity: Take Control (STC) for ambulatory adults: protocol for a randomized controlled trial
Authors: Hugos Cinda L. , Cameron Michelle H. 
Published: October 2020

Abstract
Background
Spasticity affects 60–80% of people with multiple sclerosis (MS), impacting activity, participation and quality of life. We developed the group delivered spasticity self-management program, “MS Spasticity: Take Control” (STC), with DVDs for education and lower extremity stretching. STC is based on an international guideline and recommendations from systematic reviews and emphasizes the importance of stretching with specific stretching exercises. Our pilot trial (n = 38) compared STC followed by one month of home stretching practice to unguided use of the National MS Society (NMSS) brochure titled “Stretching for People with MS: An Illustrated Manual,” also followed by one month of home stretching practice. In this pilot trial, STC showed promising effects on the impact of spasticity (MS Spasticity Scale-88) and other self-report and physical performance measures. We will now carry out a fully-powered trial to evaluate the effect of STC compared to a comparably delivered control program on the impact and severity of spasticity in people with MS and self-reported lower extremity spasticity.

Methods
Two hundred-twenty ambulatory adults with MS self-reported spasticity interfering with daily activities will be randomized 1:1 to STC or control, using the same NMSS brochure used in the pilot study, with both programs delivered in groups with trained facilitators. Outcomes are the impact of spasticity with the MS Spasticity Scale-88, the severity of spasticity with the Numeric Rating Scale for Spasticity, other self-report questionnaires, and physical performance walking measures at baseline and one and 6 months after the interventions.

Discussion
Stretching is the cornerstone of spasticity management. Stretching takes time and energy every day. Unfortunately, beyond the logical expectation that regular stretching should help prevent muscle shortening and contractures in the presence of spasticity, there is very little data on the effects of stretching on spasticity in people with MS or any other condition. Our pilot trial of STC suggested that education and stretching help reduce the impact of spasticity. To definitively determine if this education and instructional program with daily stretching practice is effective, a fully powered trial with a comparable control intervention and facilitators who did not create STC is needed. Here we report the protocol for this trial.

Trial registration
NCT03166930 May 25, 2017.
Rationale and design of ePPOP-ID: a multicenter randomized controlled trial using an electronic-personalized program for obesity in pregnancy to improve delivery
Authors: Deruelle Philippe , Lelorain Sophie , Deghilage Sylvie , Couturier Emmanuelle , Guilbert Elodie , Berveiller Paul , Sénat Marie Victoire , Vayssière Christophe , Sentilhes Loïc , Perrotin Franck , Gallot Denis , Chauleur Céline , Sananes Nicolas , Roth Emmanuel , Luton Dominique , Caputo Marie , Lorio Elodie , Chatelet Carla , Couster Julien , Timbely Oumar , Doret-Dion Muriel , Duhamel Alain , Pigeyre Marie 
Published: October 2020

AbstractBackgroundPre-pregnancy obesity and excessive gestational weight gain (GWG) are established risk factors for adverse pregnancy, delivery and birth outcomes. Pregnancy is an ideal moment for nutritional interventions in order to establish healthier lifestyle behaviors in women at high risk of obstetric and neonatal complications.MethodsElectronic-Personalized Program for Obesity during Pregnancy to Improve Delivery (ePPOP-ID) is an open multicenter randomized controlled trial which will assess the efficacy of an e-health web-based platform offering a personalized lifestyle program to obese pregnant women in order to reduce the rate of labor procedures and delivery interventions in comparison to standard care. A total of 860 eligible pregnant women will be recruited in 18 centers in France between 12 and 22 weeks of gestation, randomized into the intervention or the control arm and followed until 10 weeks of postpartum.The intervention is based on nutrition, eating behavior, physical activity, motivation and well-being advices in which personalization is central, as well as the use of a mobile/tablet application. Inputs includes data from the medical record of participants (medical history, anthropometric data), from the web platform (questionnaires on dietary habits, eating behavior, physical activity and motivation in both groups), and adherence to the program (time of connection for the intervention group only). Data are collected at inclusion, 32 weeks, delivery and 10 weeks postpartum. As primary outcome, we will use a composite endpoint score of obstetrical interventions during labor and delivery, defined as caesarean section and instrumental delivery (forceps and vacuum extractor). Secondary outcomes will consist of data routinely collected as part of usual antenatal and perinatal care, such as GWG, hypertension, preeclampsia, as well as fetal and neonatal outcomes including premature birth, gestational age at birth, birth weight, macrosomia, Apgar score, arterial umbilical cord pH, neonatal traumatism, hyperbilirubinemia, respiratory distress syndrome, transfer in neonatal intensive care unit, and neonatal adiposity. Post-natal outcomes will be duration of breastfeeding, maternal weight retention and child weight at postnatal visit.DiscussionThe findings of the ePPOP-ID trial will help design e-health intervention program for obese women in pregnancy.Trial registrationClinicalTrials.govIdentifier:NCT02924636/ October 5th 2016.
Mitochondrial apurinic/apyrimidinic endonuclease 1 enhances mtDNA repair contributing to cell proliferation and mitochondrial integrity in early stages of hepatocellular carcinoma
Authors: Bazzani Veronica , Barchiesi Arianna , Radecka Dorota , Pravisani Riccardo , Guadagno Antonio , Di Loreto Carla , Baccarani Umberto , Vascotto Carlo 
Published: October 2020

AbstractBackgroundHepatocellular carcinoma (HCC) is the leading cause of primary liver cancers. Surveillance of individuals at specific risk of developing HCC, early diagnostic markers, and new therapeutic approaches are essential to obtain a reduction in disease-related mortality. Apurinic/apyrimidinic endonuclease 1 (APE1) expression levels and its cytoplasmic localization have been reported to correlate with a lower degree of differentiation and shorter survival rate. The aim of this study is to fully investigate, for the first time, the role of the mitochondrial form of APE1 in HCC.MethodsAs a study model, we analyzed samples from a cohort of patients diagnosed with HCC who underwent surgical resection. Mitochondrial APE1 content, expression levels of the mitochondrial import protein Mia40, and mtDNA damage of tumor tissue and distal non-tumor liver of each patient were analyzed. In parallel, we generated a stable HeLa clone for inducible silencing of endogenous APE1 and re-expression of the recombinant shRNA resistant mitochondrially targeted APE1 form (MTS-APE1). We evaluated mtDNA damage, cell growth, and mitochondrial respiration.ResultsAPE1’s cytoplasmic positivity in Grades 1 and 2 HCC patients showed a significantly higher expression of mitochondrial APE1, which accounted for lower levels of mtDNA damage observed in the tumor tissue with respect to the distal area. In the contrast, the cytoplasmic positivity in Grade 3 was not associated with APE1’s mitochondrial accumulation even when accounting for the higher number of mtDNA lesions measured. Loss of APE1 expression negatively affected mitochondrial respiration, cell viability, and proliferation as well as levels of mtDNA damage. Remarkably, the phenotype was efficiently rescued in MTS-APE1 clone, where APE1 is present only within the mitochondrial matrix.ConclusionsOur study confirms the prominent role of the mitochondrial form of APE1 in the early stages of HCC development and the relevance of the non-nuclear fraction of APE1 in the disease progression. We have also confirmed overexpression of Mia40 and the role of the MIA pathway in the APE1 import process. Based on our data, inhibition of the APE1 transport by blocking the MIA pathway could represent a new therapeutic approach for reducing mitochondrial metabolism by preventing the efficient repair of mtDNA.
Swept-source OCT findings in shaken baby syndrome: case report
Authors: Ksiaa Imen , Ghachem Mohamed , Besbes Habib , Khochtali Sana , Chouchane Slaheddine , Khairallah Moncef 
Published: October 2020

Abstract
Background
Our purpose was to document the swept source optical coherence tomography (SSOCT) findings in a patient with Shaken baby syndrome (SBS).

Case presentation
SSOCT was obtained without sedation in a six-month-old girl with bilateral multilayered retinal hemorrhages due to SBS. It documented vitreoretinal interface abnormalities, including internal limiting membrane (ILM) detachment with retinal traction, in association with other specific changes in the inner and outer retinal layers. Six weeks later, retinal hemorrhages had substantially resolved, and there was optic disc pallor. OCT showed ILM reattachment with release of retinal traction and the development of severe diffuse retinal atrophy involving the fovea.

Conclusions
SS OCT can provide useful information in SBS, revealing a wide variety of vitreoretinal interface, inner, and outer retinal changes not detected by clinical examination. It also may have a prognostic value over follow-up.
Limbal stem cell deficiency secondary to systemic paclitaxel (Taxol) for breast cancer: a case report
Authors: Sekhon Amardeep , Wang Jeff Y. F. , Tan Johnson C. H. , Holland Simon P. , Yeung Sonia N. 
Published: October 2020

Abstract
Background
Paclitaxel (PTX) is an antineoplastic drug widely used in treatments for ovarian, breast, and small-cell lung cancer. Although ocular effects associated with PTX have been previously described, very few studies have specifically reported systemic PTX as a contributing factor for limbal stem cell deficiency (LSCD), which is characterized by the loss of stem cell and barrier function of the limbus leading to progressive pain and reduction in visual acuity. Described here is a unique case where a patient was diagnosed with LSCD secondary to PTX use for the treatment of breast cancer, at doses of PTX far lower than what is reported in current literature.

Case presentation
A 73-year-old woman with a previous diagnosis of breast cancer with liver metastasis presented with a complaint of increasing pain in the left eye more than the right, along with decreasing visual acuity in both eyes following 3 months of PTX therapy for recurrent liver metastases. Upon examination, best-corrected visual acuity was 20/100 in the right eye and counting fingers on the left. Peripheral neovascularization, stromal scarring, and features of limbal stem cell deficiency (LSCD) were noted on the right cornea. A central neurotrophic ulcer with thinning to 50% and 360 degrees of conjunctivalization were noted on the left. After the discontinuation PTX with doxorubicin as the substitute, there was no further progression of her LSCD, and stabilization of her ocular surface was achieved.

Conclusion
Although chemotherapy induced LSCD is a relatively rare adverse event, it is essential for clinicians starting new chemotherapy agents to consider the potential ocular toxicities that may result in their use. Ophthalmology review is recommended for patients after starting PTX therapy to assess for signs of LSCD, particularly in patients where drug toxicity can be aggravated due to impaired hepatic function.