bluuebunny/crossref_metadata_2025_split huggingface dataset:
EM-mosaic detects mosaic point mutations that contribute to congenital heart disease
Authors: Hsieh Alexander , Morton Sarah U. , Willcox Jon A. L. , Gorham Joshua M. , Tai Angela C. , Qi Hongjian , DePalma Steven , McKean David , Griffin Emily , Manheimer Kathryn B. , Bernstein Daniel , Kim Richard W. , Newburger Jane W. , Porter George A. , Srivastava Deepak , Tristani-Firouzi Martin , Brueckner Martina , Lifton Richard P. , Goldmuntz Elizabeth , Gelb Bruce D. , Chung Wendy K. , Seidman Christine E. , Seidman J. G. , Shen Yufeng 
Published: April 2020

Abstract
Background
The contribution of somatic mosaicism, or genetic mutations arising after oocyte fertilization, to congenital heart disease (CHD) is not well understood. Further, the relationship between mosaicism in blood and cardiovascular tissue has not been determined.

Methods
We developed a new computational method, EM-mosaic (Expectation-Maximization-based detection of mosaicism), to analyze mosaicism in exome sequences derived primarily from blood DNA of 2530 CHD proband-parent trios. To optimize this method, we measured mosaic detection power as a function of sequencing depth. In parallel, we analyzed our cohort using MosaicHunter, a Bayesian genotyping algorithm-based mosaic detection tool, and compared the two methods. The accuracy of these mosaic variant detection algorithms was assessed using an independent resequencing method. We then applied both methods to detect mosaicism in cardiac tissue-derived exome sequences of 66 participants for which matched blood and heart tissue was available.

Results
EM-mosaic detected 326 mosaic mutations in blood and/or cardiac tissue DNA. Of the 309 detected in blood DNA, 85/97 (88%) tested were independently confirmed, while 7/17 (41%) candidates of 17 detected in cardiac tissue were confirmed. MosaicHunter detected an additional 64 mosaics, of which 23/46 (50%) among 58 candidates from blood and 4/6 (67%) of 6 candidates from cardiac tissue confirmed. Twenty-five mosaic variants altered CHD-risk genes, affecting 1% of our cohort. Of these 25, 22/22 candidates tested were confirmed. Variants predicted as damaging had higher variant allele fraction than benign variants, suggesting a role in CHD. The estimated true frequency of mosaic variants above 10% mosaicism was 0.14/person in blood and 0.21/person in cardiac tissue. Analysis of 66 individuals with matched cardiac tissue available revealed both tissue-specific and shared mosaicism, with shared mosaics generally having higher allele fraction.

Conclusions
We estimate that ~ 1% of CHD probands have a mosaic variant detectable in blood that could contribute to cardiac malformations, particularly those damaging variants with relatively higher allele fraction. Although blood is a readily available DNA source, cardiac tissues analyzed contributed ~ 5% of somatic mosaic variants identified, indicating the value of tissue mosaicism analyses.
“Pick up anything that moves”: a qualitative analysis of a police crackdown against people who use drugs in Tijuana, Mexico
Authors: Morales Mario , Rafful Claudia , Baker Pieter , Arredondo Jaime , Kang Sunyou , Mittal Maria L. , Rocha-Jiménez Teresita , Strathdee Steffanie A. , Beletsky Leo 
Published: April 2020

Abstract
Background
Homeless people who use drugs (PWUD) are often displaced, detained, and/or forced into drug treatment during police crackdowns. Such operations follow a zero-tolerance approach to law enforcement and have a deleterious impact on the health of PWUD. In Mexico, municipal police officers (MPOs) conducted the largest crackdown documented at the Tijuana River Canal (Tijuana Mejora) to dismantle an open drug market. We analyzed active-duty MPOs’ attitudes on the rationale, implementation, and outcomes of the crackdown. We also included the involvement of non-governmental allies in the disguised imprisonment as drug treatment referral and potential legal consequences of having illegally detained PWUD.

Methods
Between February–June 2016, 20 semi-structured interviews were conducted with MPOs in Tijuana. Interviews were transcribed, translated and coded using a consensus-based approach. Emergent themes, trends and frameworks were analyzed through a hermeneutic grounded theory protocol.

Results
Participants recognized the limitations of Tijuana Mejora in effectively controlling crime and addressing drug treatment solutions. MPOs perceived that the intent of the operation was to displace and detain homeless PWUD, not to assist or rehabilitate them. The police operation was largely justified as a public safety measure to reduce the risk of injury due to flooding, decrease drug consumption among PWUD and protect local tourism from PWUD. Some participants perceived the crackdown as a successful public health and safety measure while others highlighted occupational risks to MPOs and potential human rights violations of PWUD.

Conclusions
Tijuana Mejora illustrated why public and private actors align in enforcing zero-tolerance drug policy. Perceptions of care are often based on captivity of the diseased, not in health and well-being of PWUD. Officer perceptions shed light on the many limitations of this punitive policing tool in this context. A shift towards evidence-based municipal strategies to address drug use, wherein police are perceived as partners in harm reduction rather than antagonists, is warranted.
Physical property evolution of granite during experimental chemical stimulation
Authors: Farquharson Jamie I. , Kushnir Alexandra R. L. , Wild Bastien , Baud Patrick 
Published: April 2020

AbstractThe Soultz-sous-Forêts geothermal reservoir (France)—in particular, the GPK-4 well—has been proposed as a target for chemical stimulation under the DESTRESS Horizon-2020 framework. With a combination of batch reaction tests and acid flow-through experiments using hydrochloric acid (HCl) at different molarities and temperatures, we investigate the potential for acid-induced permeability enhancement of a granite analogous to the Soultz-sous-Forêts reservoir rock, by means of acid stimulation. In the batch reaction experiments, we find that the propensity for increase or decrease in porosity and permeability depends on the physico-chemical properties of the starting material: unaltered granite underwent a significant increase in both porosity and permeability relative to its initial state, altered granite exhibited a moderate increase in both porosity and permeability (modulated slightly by HCl molarity), whereas initially more porous and permeable thermally and naturally fractured granite exhibited an increase in porosity accompanied by a relative decrease in permeability. The extent to which permeability increased or decreased appears to be tied to the initial fluid-flow characteristics of the material. Using a new, custom-built acid permeameter, flow-through tests were performed on unaltered granite, while the acid was sampled at regular time intervals. Element release into solution recorded throughout the experiments, indicated dissolution of granite minerals. Despite this operative micromechanism, however, the absolute change in sample permeability is limited, both at room temperature and at $$100\, ^{\circ } \hbox {C}$$

100

∘

C

. Ultimately, these data suggest that the potential for geothermal reservoir enhancement using HCl is low at Soultz-sous-Forêts. Nevertheless, the possibility remains that a more targeted thermal or chemical stimulation approach—or hybrid thereof—could prove effective in the future.
Knockdown of long non-coding RNA HOTAIR reverses cisplatin resistance of ovarian cancer cells through inhibiting miR-138-5p-regulated EZH2 and SIRT1
Authors: Zhang Yun , Ai Hao , Fan Xue , Chen Suxian , Wang Yadi , Liu Lili 
Published: April 2020

Abstract
Background
Cisplatin resistance (DDP-resistance) remains one of the major causes of poor prognosis in females with ovarian cancer. Long non-coding RNAs (lncRNAs) have been shown to participate in the regulation of cellular processes, including chemoresistance. The aim of this study was to explore the role of HOX transcript antisense RNA (HOTAIR) in DDP-resistant ovarian cancer cells.

Methods
DDP-resistant ovarian cancer cell lines (SKOV3/DDP and A2780/DDP) were established. Real-time PCR, western blot, dual-luciferase reporter assay, and flow cytometry were then used to evaluate the effect of HOTAIR/miR-138-5p axis on chemoresistance of DDP-resistant ovarian cancer cells to DDP.

Results
We found that HOTAIR was upregulated in DDP-resistant cells, while miR-138-5p was downregulated. Knockdown of HOTAIR increased the expression of miR-138-5p in DDP-resistant cells and miR-138-5p is directly bound to HOTAIR. Upregulation of miR-138-5p induced by HOTAIR siRNA or by its mimics enhanced the chemosensitivity of DDP-resistant cells and decreased the expression of EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit) and SIRT1 (sirtuin 1). Furthermore, the HOTAIR silencing-induced chemosensitivity of DDP-resistant cells was weakened by miR-138-5p inhibitor.

Conclusions
These data demonstrate that HOTAIR acts as a sponge of miR-138-5p to prevent its binding to EZH2 and SIRT1, thereby promoting DDP-resistance of ovarian cancer cells. Our work will shed light on the development of therapeutic strategies for ovarian cancer treatment.
A feasibility, acceptability and fidelity study of a multifaceted behaviour change intervention targeting free-living physical activity and sedentary behaviour in community dwelling adult stroke survivors
Authors: Moore Sarah A. , Avery Leah , Price Christopher I. M. , Flynn Darren 
Published: April 2020

Abstract
Background
Despite the benefits of physical activity for walking ability, balance, and mood, less than 30% of stroke survivors engage in recommended levels of physical activity with high levels of sedentary behaviour observed. This study aims to assess the feasibility, acceptability and fidelity of a theory- and evidence-based multifaceted behaviour change intervention targeting free-living physical activity and sedentary behaviour after stroke.

Methods
This study will be set in community stroke services in the North East of England and will assess the feasibility of a behaviour change intervention targeting free-living physical activity and sedentary behaviour of stroke survivors and consultation behaviour of the healthcare professionals to support stroke survivors to make these lifestyle changes. Up to 35 stroke survivors currently receiving stroke rehabilitation within the study catchment area with capacity and no contraindications to increasing physical activity/reducing sedentary behaviour will be recruited. Stroke survivors will receive a supported self-management physical activity/sedentary behaviour programme incorporating provision of information, goal setting, action planning, barrier identification, coping planning, self-monitoring and feedback on physical activity and sedentary behaviour. The programme will be supported by up to 12 healthcare professionals (HCPs) recruited from the community stroke services taking part in the study. The HCPs will deliver at least two face-to-face sessions (baseline, review and subsequent reviews if necessary) and provide a range of personalised tools to support each individual stroke survivor (e.g. workbook, self-monitoring tools, information on local resources). The consultation behaviour of the HCPs will be targeted via a training programme incorporating face-to-face training, a training manual and individual feedback on intervention programme delivery from the study research team. The feasibility, acceptability and fidelity of the study protocol will be assessed.

Discussion
The most effective methods of supporting stroke survivors to alter physical activity and sedentary behaviour have yet to be established. This study will establish the feasibility of delivering a complex theory- and evidence-based intervention targeting the behaviour of both stroke survivors and HCPs and assess whether it is acceptable to the target populations. Findings will inform the iterative development of the intervention before a larger scale evaluation.

Trial registration
Trial register: Trial identifier: ISRCTN35516780, date of registration: 24/10/2018
The limitations to our understanding of peer review
Authors: Tennant Jonathan P. , Ross-Hellauer Tony 
Published: April 2020

AbstractPeer review is embedded in the core of our knowledge generation systems, perceived as a method for establishing quality or scholarly legitimacy for research, while also often distributing academic prestige and standing on individuals. Despite its critical importance, it curiously remains poorly understood in a number of dimensions. In order to address this, we have analysed peer review to assess where the major gaps in our theoretical and empirical understanding of it lie. We identify core themes including editorial responsibility, the subjectivity and bias of reviewers, the function and quality of peer review, and the social and epistemic implications of peer review. The high-priority gaps are focused around increased accountability and justification in decision-making processes for editors and developing a deeper, empirical understanding of the social impact of peer review. Addressing this at the bare minimum will require the design of a consensus for a minimal set of standards for what constitutes peer review, and the development of a shared data infrastructure to support this. Such a field requires sustained funding and commitment from publishers and research funders, who both have a commitment to uphold the integrity of the published scholarly record. We use this to present a guide for the future of peer review, and the development of a new research discipline based on the study of peer review.
Successful treatment of pleuroperitoneal communication with pleurodesis using autologous blood in a patient with severe heart failure undergoing peritoneal dialysis: a case report and brief literature review
Authors: Tatematsu Satoru , Hosoya Koji , Ryuzaki Munekazu 
Published: April 2020

Abstract
Background
Pleuroperitoneal communication is a potential complication of peritoneal dialysis (PD). Of the various treatment strategies for pleuroperitoneal communication, successful treatment with pleurodesis using autologous blood has rarely been reported.

Case presentation
A 58-year-old man with end-stage kidney disease secondary to diabetic nephropathy and severe heart failure was placed on PD. He developed right-sided hydrothorax after the commencement of PD. Technetium-99m macro-aggregated human serum albumin peritoneal scintigraphy revealed pleuroperitoneal communication. PD was temporarily discontinued and substituted with hemodialysis. Subsequently, the levels of pleural fluid decreased. However, the resumption of PD exacerbated the hydrothorax. After thoracentesis, 50 mL of autologous blood was instilled into the right pleural cavity. There were no complications related to the procedure. PD was reinitiated 5 days after pleurodesis. Repeated chest X-rays did not depict any evidence of recurrent hydrothorax over the subsequent 10 months.

Conclusions
Pleurodesis using autologous blood was effective for pleuroperitoneal communication and was evidently safe in our patient. It should be considered in patients with severe heart failure since it is minimally invasive.
Application of Adomian decomposition method to free vibration analysis of thin isotropic rectangular plates submerged in fluid
Authors: Sobamowo Gbeminiyi M. , Salawu Saheed A. , Yinusa Ahmed A. 
Published: April 2020

AbstractInvestigating dynamic free vibration response of isotropic thin rectangular plate resting on two-parameter elastic foundation is of interest in the field of geotechnics, structure, highway, railway and mechanical engineering. This study employs analytical approach to the investigation of free vibration analysis of isotropic rectangular plate submerged in fluid and resting on combined elastic foundations under different support conditions. The nonlinear partial differential equation of the system is transformed into nonlinear ordinary differential equation using the Galerkin method of separation. The resulting ordinary differential equation is solved using Adomian decomposition method (ADM). The reliability of the solutions obtained is validated with numerical and existing results as reported in the literature. Also, the bending moment and stress are analysed. The analytical solutions are used for the investigation of dynamic behaviour of plates in fluid, effect of aspect ratio, effect of elastic foundation parameters on natural frequency and effect of bending moment and stress on the mode of the vibrating plate. From the results, it is observed that the increase in elastic foundation parameter increases the natural frequency. Increasing the aspect ratio increases the natural frequency. Increasing the combined elastic foundation parameters increases the natural frequency. Natural frequency of plates reduces when submerged in fluid with the mode shapes not significantly affected. The node and antinodes of the mode shapes are affected by moment and stress. It is expected that the present study will add to the existing knowledge in the field of vibration of plates.
Tobacco Smoking a Potential Risk Factor in Transmission of COVID-19 Infection
Authors: Ahmed Naseer , Maqsood Afsheen , Abduljabbar Tariq , Vohra Fahim 
Published: April 2020

Corona Virus disease 2019 (COVID-19) is a global pandemic and is caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) group of viruses. To date, April 25, 2020, more than 2.4 million humans are infected and more than a hundred thousand deaths have been reported from more than 200 countries from COVID-19. There is no evidence-based treatment for the infection and prevention of transmission using social distancing, isolation and hygiene measures is widely recommended. Tobacco smoking is rampant in communities around the globe and the addiction to tobacco results in deaths of more than 8 million individuals each year. As COVID-19 transmits through salivary droplets and causes severe lung pneumonia, tobacco smokers are also at high risk of severe COVID-19 infection due to poor lung function, cross-infection and susceptible hygiene habits. Smoking tobacco (cigarette, e-cigarettes or waterpipe) produces exhaled smoke, coughing or sneezing, aerosols containing SARS-CoV-2 in the surroundings and contaminating surfaces. Therefore, smoking tobacco is a possible mode of transmission for the virus for both active and passive smokers. Smoking should be considered a risk factor for the disease transmission until further availability of evidence and measures to limit its direct and indirect effects should be implemented within the community.
doi: https://doi.org/10.12669/pjms.36.COVID19-S4.2739
How to cite this:Ahmed N, Maqsood A, Abduljabbar T, Vohra F. Tobacco Smoking a Potential Risk Factor in Transmission of COVID-19 Infection. Pak J Med Sci. 2020;36(COVID19-S4):COVID19-S104-S107. doi: https://doi.org/10.12669/pjms.36.COVID19-S4.2739
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Covid-19: Invisible, Elusive and the Advancing Enemy
Authors: Shafi Khalid Mahmood , Meo Anusha Sultan , Khalid Rohaan 
Published: April 2020

doi: https://doi.org/10.12669/pjms.36.COVID19-S4.2758
How to cite this:Shafi KM, Meo AS, Khalid R. Covid-19: Invisible, Elusive and the Advancing Enemy. Pak J Med Sci. 2020;36(COVID19-S4):COVID19-S138-S139. doi: https://doi.org/10.12669/pjms.36.COVID19-S4.2758
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Combinations of propolis and Ca(OH)2 in dental pulp capping treatment for the stimulation of reparative dentin formation in a rat model
Authors: Rahayu Retno Pudji , Pribadi Nirawati , Widjiastuti Ira , Nugrahani Nur Ariska 
Published: April 2020

Background:Caries in the dental pulp result in inflammation and damage to the pulp tissue. During inflammation of the pulp, various inflammatory mediators and growth factors are released, including IL-8, IL-10, TLR-2, VEGF and TGF-β through the NF-kB pathway. In the present study, therapy for pulpal caries was performed through pulp capping by giving a combination of propolis and calcium hydroxide (Ca(OH)2). This treatment was expected to stimulate the formation of reparative dentin as an anti-inflammatory material to prevent pulp tissue damage.Methods:28 Wistar rats were divided into four groups and treated with Ca(OH)2 with or without the addition of propolis for either 7 or 14 days. Immunohistochemical examination was used to determine the expression of IL-8, IL-10, TLR-2, VEGF, TGF-β in the four treatment groups.Results:The group treated with a combination of propolis and Ca(OH)2 for 7 days showed that the expression of IL-10, IL-8, TLR-2, VEGF, TGF-β increased significantly compared to the treatment group treated with only Ca(OH)2. The expression of IL-10, TLR-2, TGF-β, VEGF increased in the treatment group treated with propolis and Ca(OH)2 for 14 days, while the expression of IL-8 in the decreased significantly.Conclusions:Administration of a combination of propolis and Ca(OH)2 has efficacy in the pulp capping treatment process because it has anti-bacterial and immunomodulatory properties. The results show that it is able to stimulate the process of pulp tissue repair through increased expression of IL-10, TGF-β, VEGF, TLR -2 and decreased expression of IL-8.
Cooking with biomass fuel and cardiovascular disease: a cross-sectional study among rural villagers in Phitsanulok, Thailand
Authors: Juntarawijit Chudchawal , Juntarawijit Yuwayong 
Published: April 2020

Background: Burning biomass fuel is a major source of indoor air pollution; about 40% of Thai people still use biomass for cooking. There is increasing evidence of the association between biomass smoke exposure and serious health effects including cardiovascular disease. The object of this cross-sectional study was to investigate the association between biomass use for household cooking and cardiovascular outcome, including coronary heart disease, hypertension, high cholesterol, diabetes mellitus, and stroke among rural villagers in Phitsanulok, Thailand. Methods: Data from 1078 households were collected using a face-to-face interview questionnaire. Results: After being adjusted for gender, age, cigarette smoke, secondhand smoke, and exposure to other sources of air pollution, it was found that the family members of cooks using biomass fuel were at risk of coronary heart disease (CHD; OR=4.35; 95%CI 0.10–18.97), high blood pressure (HBP; OR=1.61; 95%CI 1.10–2.35), high cholesterol (HC; OR=2.74; 95%CI 1.66–4.53), and diabetes (OR= 1.88; 95%CI 1.03–3.46). Compared to LPG use, using wood was associated with stroke (OR=7.64; 95%CI 1.18–49.61), and using charcoal was associated with HC (OR=1.52; 95%CI 1.04–2.24). Compared to never user, household cooks who sometimes use charcoal had an increased risk of HBP (OR=2.04; 95%CI 1.32–3.15), HC (OR=2.61; 95%CI 1.63–4.18), and diabetes (OR=2.09; 95%CI 1.17–3.73); and cooks who often use charcoal had an elevated risk of stroke (OR=3.17; 95%CI 1.04–9.71), and HC (OR=1.52; 95%CI 1.02–2.27) to their family members. Conclusions: The study results were consistent with those found in studies from other parts of the world, and supports that exposure to biomass smoke increase cardiovascular diseases. The issue should receive more attention, and promotion of clean fuel use is a prominent action.