bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systems genetics analysis identifies calcium-signaling defects as novel cause of congenital heart disease
Authors: Izarzugaza Jose M. G. , Ellesøe Sabrina G. , Doganli Canan , Ehlers Natasja Spring , Dalgaard Marlene D. , Audain Enrique , Dombrowsky Gregor , Banasik Karina , Sifrim Alejandro , Wilsdon Anna , Thienpont Bernard , Breckpot Jeroen , Gewillig Marc ,   Competence Network for Congenital Heart Defects, Germany, Abdul-Khaliq Hashim , Kramer Hans-Heiner , Berger Felix , Stiller Brigitte , Bauer Ulrike , Pickardt Thomas , Klaassen Sabine , Brook J. David , Hitz Marc-Phillip , Larsen Lars A. , Brunak Søren 
Published: August 2020

Abstract
Background
Congenital heart disease (CHD) occurs in almost 1% of newborn children and is considered a multifactorial disorder. CHD may segregate in families due to significant contribution of genetic factors in the disease etiology. The aim of the study was to identify pathophysiological mechanisms in families segregating CHD.

Methods
We used whole exome sequencing to identify rare genetic variants in ninety consenting participants from 32 Danish families with recurrent CHD. We applied a systems biology approach to identify developmental mechanisms influenced by accumulation of rare variants. We used an independent cohort of 714 CHD cases and 4922 controls for replication and performed functional investigations using zebrafish as in vivo model.

Results
We identified 1785 genes, in which rare alleles were shared between affected individuals within a family. These genes were enriched for known cardiac developmental genes, and 218 of these genes were mutated in more than one family. Our analysis revealed a functional cluster, enriched for proteins with a known participation in calcium signaling. Replication in an independent cohort confirmed increased mutation burden of calcium-signaling genes in CHD patients. Functional investigation of zebrafish orthologues of ITPR1, PLCB2, and ADCY2 verified a role in cardiac development and suggests a combinatorial effect of inactivation of these genes.

Conclusions
The study identifies abnormal calcium signaling as a novel pathophysiological mechanism in human CHD and confirms the complex genetic architecture underlying CHD.
RETRACTED ARTICLE: Long non-coding RNA LINC00525 regulates the proliferation and epithelial to mesenchymal transition of human glioma cells by sponging miR-338-3p
Authors: Wan Yilv , Liang Feng , Wei Minjun , Liu Ying 
Published: August 2020

AbstractLong non-coding RNA (LncRNA) LINC00525 has been shown to be upregulated in several human cancers and deduced to possess caner regulatory role. The regulation of molecular mechanics of human glioma by lncRNA-LINC00525 through microRNA sponging in glioma is elusive. The lncRNA-LINC00525 showed significant (P < 0.05) upregulation in glioma cancer cells. The upregulation of lncRNA-LINC00525 was upto 6.6-fold in glioma cells relative to the normal cells. Knockdown of lncRNA-LINC00525 significantly declined the proliferation of the glioma cancer cells. Additionally, the colony formation was inhibited by around 60% in glioma cells. The wound healing and transwell assays revealed significant (P < 0.05) inhibition of migration and invasion potential under lncRNA-LINC00525 knockdown. The western blotting study of biomarkers of epithelial to mesenchymal transition (EMT) revealed that lncRNA-LINC00525 gene silencing reduced the expression of mesenchymal molecular markers but increased the protein levels of epithelial markers. miR-338-3p was predicted to be interacting with lncRNA-LINC00525 in glioma and was shown to mediated the regulatory role of lncRNA-LINC00525. Taken together, the results of present study are supportive of the prognostic applicability of lncRNA-LINC00525 against human glioma together with its therapeutic potential against the said malignancy.
Anthracycline-based and gemcitabine-based chemotherapy in the adjuvant setting for stage I uterine leiomyosarcoma: a retrospective analysis at two reference centers
Authors: Fucà Giovanni , Fabbroni Chiara , Mancari Rosanna , Manglaviti Sara , Bogani Giorgio , Fumagalli Elena , Bertulli Rossella , Morosi Carlo , Collini Paola , Raspagliesi Francesco , Colombo Nicoletta , Casali Paolo G. , Sanfilippo Roberta 
Published: August 2020

Abstract
Background
Radically resected early uterine leiomyosarcoma (eULMS) is still marked by a poor prognosis. Adjuvant strategies investigated up to now have not been corroborated by controlled studies. We retrospectively reviewed the clinical outcome of eULMS patients treated with adjuvant anthracycline-based or gemcitabine-based chemotherapy at two Italian reference centers.

Methods
In this explorative, retrospective, cohort analysis, we included all the consecutive patients with radically resected eULMS treated at two centers between 1997 and 2017.

Results
A total of 109 consecutive patients were included. Sixty-six (60%) received an anthracycline-based regimen, whereas 43 (40%) received a gemcitabine-based regimen. Median disease-free survival (DFS) was 41.3 months with anthracycline-based regimens compared to 20.9 months with gemcitabine-based regimens (HR: 0.49; 95% CI: 0.30–0.80; P = 0.004). In the multivariable model, anthracycline-based regimens were independently associated with a better DFS. No difference in terms of overall survival was observed.

Conclusions
DFS was not the same by using an anthracycline-based or a gemcitabine-based adjuvant chemotherapy for patients with radically resected eULMS. The results of our study are in line with recent prospective controlled evidence in limb and superficial trunk soft tissue sarcomas. The role of anthracycline-based adjuvant chemotherapy should still be viewed as a research issue in eULMS.
Thermal impacts of basaltic lava flows to buried infrastructure: workflow to determine the hazard
Authors: Tsang Sophia W. R. , Lindsay Jan M. , Kennedy Ben , Deligne Natalia I. 
Published: August 2020

AbstractLava flows can cause substantial physical damage to elements of the built environment. Often, lava flow impacts are assumed to be binary, i.e. cause complete damage if the lava flow and asset are in contact, or no damage if there is no direct contact. According to this paradigm, buried infrastructure would not be expected to sustain damage if a lava flow traverses the ground above. However, infrastructure managers (“stakeholders”) have expressed concern about potential lava flow damage to such assets. We present a workflow to assess the thermal hazard posed by lava flows to buried infrastructure. This workflow can be applied in a pre-defined scenario. The first step in this workflow is to select an appropriate lava flow model(s) and simulate the lava flow’s dimensions, or to measure an in situ lava flow’s dimensions. Next, stakeholders and the modellers collaborate to identify where the lava flow traverses buried network(s) of interest as well as the thermal operating conditions of these networks. Alternatively, instead of direct collaboration, this step could be done by overlaying the flow’s areal footprint on local infrastructure maps, and finding standard and maximum thermal operating conditions in the literature. After, the temperature of the lava flow at the intersection point(s) is modelled or extracted from the results of the first step. Fourth, the lava flow-substrate heat transfer is calculated. Finally, the heat transfer results are simplified based on the pre-identified thermal operating conditions. We illustrate how this workflow can be applied in an Auckland Volcanic Field (New Zealand) case study. Our case study demonstrates considerable heat is transferred from the hypothetical lava flow into the ground and that maximum operating temperatures for electric cables are exceeded within 1 week of the lava flow front’s arrival at the location of interest. An exceedance of maximum operating temperatures suggests that lava flows could cause thermal damage to buried infrastructure, although mitigation measures may be possible.
Weak and strong singularities problems to Liénard equation
Authors: Xin Yun , Hu Guixin 
Published: August 2020

AbstractThis paper is devoted to an investigation of the existence of a positive periodic solution for the following singular Liénard equation: $$ x''+f\bigl(x(t)\bigr)x'(t)+a(t)x= \frac{b(t)}{x^{\alpha }}+e(t), $$

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where the external force $e(t)$
e
(
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may change sign, α is a constant and $\alpha >0$
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0
. The novelty of the present article is that for the first time we show that weak and strong singularities enables the achievement of a new existence criterion of positive periodic solution through an application of the Manásevich–Mawhin continuation theorem. Recent results in the literature are generalized and significantly improved, and we give the existence interval of periodic solution of this equation. At last, two examples and numerical solution (phase portraits and time portraits of periodic solutions of the example) are given to show applications of the theorem.
Antimicrobial resistance preparedness in sub-Saharan African countries
Authors: Elton Linzy , Thomason Margaret J. , Tembo John , Velavan Thirumalaisamy P. , Pallerla Srinivas Reddy , Arruda Liã Bárbara , Vairo Francesco , Montaldo Chiara , Ntoumi Francine , Abdel Hamid Muzamil M. , Haider Najmul , Kock Richard , Ippolito Giuseppe , Zumla Alimuddin , McHugh Timothy D. ,   the PANDORA-ID-NET consortium
Published: August 2020

Abstract
Background
Antimicrobial resistance (AMR) is of growing concern globally and AMR status in sub-Saharan Africa (SSA) is undefined due to a lack of real-time data recording, surveillance and regulation. World Health Organization (WHO) Joint External Evaluation (JEE) reports are voluntary, collaborative processes to assess country capacities and preparedness to prevent, detect and rapidly respond to public health risks, including AMR. The data from SSA JEE reports were analysed to gain an overview of how SSA is working towards AMR preparedness and where strengths and weaknesses lie.

Methods
SSA country JEE AMR preparedness scores were analysed. A cumulative mean of all the SSA country AMR preparedness scores was calculated and compared to the overall mean SSA JEE score. AMR preparedness indicators were analysed, and data were weighted by region.

Findings
The mean SSA AMR preparedness score was 53% less than the overall mean SSA JEE score. East Africa had the highest percentage of countries reporting having AMR National Action Plans in place, as well as human and animal pathogen AMR surveillance programmes. Southern Africa reported the highest percentage of countries with training programmes and antimicrobial stewardship.

Conclusions
The low mean AMR preparedness score compared to overall JEE score, along with the majority of countries lacking implemented National Action Plans, suggests that until now AMR has not been a priority for most SSA countries. By identifying regional and One Health strengths, AMR preparedness can be fortified across SSA with a multisectoral approach.
Effect of sodium silicate on early growth stages of wheat under drought stress
Authors: Lee Sang Gyu , Lee Hyeri , Lee Byung Cheon , Lee Hojoung , Moon Jun Cheol , Choi Changhyun , Chung Namhyun 
Published: August 2020

AbstractWheat yield is decreasing due to climate change, and a method to prevent decreasing yield during drought stress is desirable. In this study, wheat cultivars (Koso and Jokyung) were treated with 15% polyethylene glycol-6000 (PEG) and PEG + Si solution (6.5, 8.7, 13.1 and 26.1 mM). The effect of Si treatment on the alleviation of drought stress was measured using the germination test, shoot relative water content (RWC), seedling stage observation, and quantitative real time polymerase chain reaction (qRT-PCR). The results of root/shoot length ratio and shoot length ratio showed that Si treatment induced the alleviation of drought stress in Jokyung cultivar. The result of qRT-PCR showed the alleviation of drought stress in Koso cultivar. In addition, the results with shoot RWC and seedling stage observation showed that the alleviation effects of Si treatment was observed with both Koso and Jokyung cultivar at the high concentration of Si (26.1 mM). All these results suggest that Si treatment at a high concentration could be employed to alleviate drought stress in wheat.
Interpersonal reactivity index adaptation among expectant seroconcordant couples with HIV in Zambézia Province, Mozambique
Authors: Sack Daniel E. , Frisby Michael B. , Diemer Matthew A. , De Schacht Caroline , Graves Erin , Kipp Aaron M. , Emílio Almiro , Matino Ariano , Barreto Ezequiel , Van Rompaey Sara , Wallston Kenneth A. , Audet Carolyn M. 
Published: August 2020

Abstract
Background
The ability to understand another’s emotions and act appropriately, empathy, is an important mediator of relationship function and health intervention fidelity. We adapted the Interpersonal Reactivity Index (IRI) – an empathy scale – among seroconcordant expectant couples with HIV in the Homens para Saúde Mais (HoPS+) trial – a cluster randomized controlled trial assessing couple-based versus individual treatment on viral suppression – in Zambézia Province, Mozambique.

Methods
Using baseline data from 1332 HoPS+ trial participants (666 couples), an exploratory factor analysis assessed culturally relevant questions from the IRI. Because empathy is interdependent among couples, we validated the results of the exploratory factor analysis using a dyadic confirmatory factor analysis (CFA) with dyadic measurement invariance testing. Finally, we assessed the relationship between scores on our final scale and basic demographic characteristics (sex, age, education, and depression) using t-tests.

Results
We found two subscales: 1) a seven-item cognitive empathy subscale (Cronbach’s alpha 0.78) and 2) a six-item affective empathy subscale (Cronbach’s alpha 0.73). The dyadic CFA found acceptable model fit and metric invariance across partners (Comparative Fit Index (CFI) = 0.914, Tucker Lewis Index = 0.904, Root Mean Squared Error of Approximation = 0.056, ΔCFI = 0.011). We observed higher cognitive (p: 0.012) and affective (p: 0.049) empathy among males and higher cognitive (p: 0.031) and affective (p: 0.030) empathy among younger participants. More educated participants had higher affective empathy (p: 0.017) and depressed participants had higher cognitive empathy (p: < 0.001). This two-subscale, 13-item version of the IRI measures cognitive and affective empathy in HoPS+ trial participants and adults while accounting for the interdependent nature of empathy within partner dyads.

Conclusions
This scale will allow us to assess the interplay between empathy and other psychometric constructs (stigma, social support, etc.) in the HoPS+ trial and how each relates to retention in HIV, adherence to treatment, and prevention of maternal to child HIV transmission. Furthermore, this scale can be adapted for other sub-Saharan African populations, which will allow researchers to better assess HIV-related intervention efficacy.

Trial registration
This study is within the context of the HoPS+ trial, registered at ClinicalTrials.gov as number NCT03149237. Registered May 11, 2017.
Comprehensive analysis of diverse low-grade neuroepithelial tumors with FGFR1 alterations reveals a distinct molecular signature of rosette-forming glioneuronal tumor
Authors: Lucas Calixto-Hope G. , Gupta Rohit , Doo Pamela , Lee Julieann C. , Cadwell Cathryn R. , Ramani Biswarathan , Hofmann Jeffrey W. , Sloan Emily A. , Kleinschmidt-DeMasters Bette K. , Lee Han S. , Wood Matthew D. , Grafe Marjorie , Born Donald , Vogel Hannes , Salamat Shahriar , Puccetti Diane , Scharnhorst David , Samuel David , Cooney Tabitha , Cham Elaine , Jin Lee-way , Khatib Ziad , Maher Ossama , Chamyan Gabriel , Brathwaite Carole , Bannykh Serguei , Mueller Sabine , Kline Cassie N. , Banerjee Anu , Reddy Alyssa , Taylor Jennie W. , Clarke Jennifer L. , Oberheim Bush Nancy Ann , Butowski Nicholas , Gupta Nalin , Auguste Kurtis I. , Sun Peter P. , Roland Jarod L. , Raffel Corey , Aghi Manish K. , Theodosopoulos Philip , Chang Edward , Hervey-Jumper Shawn , Phillips Joanna J. , Pekmezci Melike , Bollen Andrew W. , Tihan Tarik , Chang Susan , Berger Mitchel S. , Perry Arie , Solomon David A. 
Published: August 2020

AbstractTheFGFR1gene encoding fibroblast growth factor receptor 1 has emerged as a frequently altered oncogene in the pathogenesis of multiple low-grade neuroepithelial tumor (LGNET) subtypes including pilocytic astrocytoma, dysembryoplastic neuroepithelial tumor (DNT), rosette-forming glioneuronal tumor (RGNT), and extraventricular neurocytoma (EVN). These activatingFGFR1alterations in LGNET can include tandem duplication of the exons encoding the intracellular tyrosine kinase domain, in-frame gene fusions most often withTACC1as the partner, or hotspot missense mutations within the tyrosine kinase domain (either at p.N546 or p.K656). However, the specificity of these differentFGFR1events for the various LGNET subtypes and accompanying genetic alterations are not well defined. Here we performed comprehensive genomic and epigenomic characterization on a diverse cohort of 30 LGNET withFGFR1alterations. We identified that RGNT harbors a distinct epigenetic signature compared to other LGNET withFGFR1alterations, and is uniquely characterized byFGFR1kinase domain hotspot missense mutations in combination with eitherPIK3CAorPIK3R1mutation, often with accompanyingNF1orPTPN11mutation. In contrast, EVN harbors its own distinct epigenetic signature and is characterized byFGFR1-TACC1fusion as the solitary pathogenic alteration. Additionally, DNT and pilocytic astrocytoma are characterized by either kinase domain tandem duplication or hotspot missense mutations, occasionally with accompanyingNF1orPTPN11mutation, but lacking the accompanyingPIK3CAorPIK3R1mutation that characterizes RGNT. The glial component of LGNET withFGFR1alterations typically has a predominantly oligodendroglial morphology, and many of the pilocytic astrocytomas withFGFR1alterations lack the biphasic pattern, piloid processes, and Rosenthal fibers that characterize pilocytic astrocytomas withBRAFmutation or fusion. Together, this analysis improves the classification and histopathologic stratification of LGNET withFGFR1alterations.
Multi Region-Based Feature Connected Layer (RB-FCL) of deep learning models for bone age assessment
Authors: Wibisono Ari , Mursanto Petrus 
Published: August 2020

AbstractPrediction of bone age from an x-ray is one of the methods in the medical field to support predicting endocrine gland disease, growth abnormalities, and genetic disorders. A decision support system to predict the bone age from the x-ray image has been implemented. It utilizes traditional machine learning methods and deep learning. We propose the Region-Based Feature Connected Layer (RB-FCL) from the essential segmented region of hand x-ray. We treat the deep learning models as the feature extraction for each region of the hand x-ray bone. The Feature Connected Layers are the output from the trained important region, such as 1-radius-ulna, 2-carpal, 3-metacarpal, 4-phalanges, and 5-ephypisis. DenseNet121, InceptionV3, and InceptionResNetV2 are the deep learning models that we used to train the critical region. From the evaluation results, the Mean Absolute Error (MAE) results produced is 6.97. This result is better compared to standard deep learning models, which are 9.41.
Trends of Mycobacterium tuberculosis and rifampicin resistance in Adigrat General Hospital, Eastern zone of Tigrai, North Ethiopia
Authors: Abay Getachew Kahsu , Abraha Bahlbi Hailay 
Published: August 2020

Abstract
Background
Tuberculosis is an infectious disease usually caused by Mycobacterium tuberculosis bacteria. The global emergence of mono- or multidrug-resistant tuberculosis and extensively drug-resistant forms of tuberculosis pose a considerable challenge to tuberculosis control programs. There has been no reliable and organized data on trends and drug resistance of Mycobacterium tuberculosis in the study area. Therefore, this study aimed to determine the trends of Mycobacterium tuberculosis and rifampicin resistance in the Adigrat General Hospital, eastern Zone of Tigrai, North Ethiopia.

Methods
A hospital-based retrospective cross-sectional study was conducted at Adigrat General Hospital from January 2015 to 2018.Data was collected retrospectively from the GeneXpert™ TB registration book using a data extraction format. Data was entered into Epi-Info 3.1 and subsequently exported and analyzed using SPSS Version 20.The results were summarized using descriptive statistics, tables, and figures. Bivariate and multi-variant regression analysis was employed to measure the association between dependent and independent variables. P values < 0.05 were considered statistically significant.

Result
A total of 5944 Mycobacterium tuberculosis presumptive patients were included in the study. The majority of the study participants were male (58.1%) with participants’ median age of 40.0 (IQR 26–57) years, the majority were 30–44 years. The overall positive cases of Mycobacterium tuberculosis was 24.3% (1446) with a total of 132 (9.1%) found to be resistant to rifampicin. Of the total confirmed positive cases 8.7% (103/1188) and 11.2% (29/258) were rifampicin resistance of presumptive tuberculosis and presumptive drug resistance tuberculosis patients respectively. Age, the reason for diagnosis, site of presumptive tuberculosis, and/or being HIV infected showed significant association with our dependent variable; however, only age and being HIV infected were associated with rifampicin resistance.

Conclusion
In our study, the overall trends of Mycobacterium tuberculosis and rifampicin resistance were found to be high. Rifampicin resistance is more common in patients with HIV and presumptive drug resistance tuberculosis individuals. Therefore, maximizing early detection of drug-resistant and strengthening tuberculosis infection control activities are recommended to reduce the burden of this contagious and potentially deadly disease.