The impact of methodology on the reproducibility and rigor of DNA methylation data

Epigenetic modifications are crucial for normal development and implicated in disease pathogenesis. While epigenetics continues to be a burgeoning research area in neuroscience, unaddressed issues related to data reproducibility across laboratories remain. Separating meaningful experimental changes from background variability is a challenge in epigenomic studies. Here we show that seemingly minor experimental variations, even under normal baseline conditions, can have a significant impact on epigenome outcome measures and data interpretation. We examined genome-wide DNA methylation and gene expression profiles of hippocampal tissues from wild-type rats housed in three independent laboratories using nearly identical conditions. Reduced-representation bisulfite sequencing and RNA-seq respectively identified 3852 differentially methylated and 1075 differentially expressed genes between laboratories, even in the absence of experimental intervention. Difficult-to-match factors such as animal vendors and a subset of husbandry and tissue extraction procedures produced quantifiable variations between wild-type animals across the three laboratories. Our study demonstrates that seemingly minor experimental variations, even under normal baseline conditions, can have a significant impact on epigenome outcome measures and data interpretation. This is particularly meaningful for neurological studies in animal models, in which baseline parameters between experimental groups are difficult to control. To enhance scientific rigor, we conclude that strict adherence to protocols is necessary for the execution and interpretation of epigenetic studies and that protocol-sensitive epigenetic changes, amongst naive animals, may confound experimental results.

Prevalence of laboratory markers of human respiratory viruses in monkeys of Adler primate center

Introduction. The relevance of studying the circulation of human respiratory viruses among laboratory primates is associated with the need to test vaccines and antiviral drugs against these infections on monkeys.The aim of this work was to study the prevalence of serological and molecular markers of human respiratory viral infections in laboratory primates born at the Adler Primate Center and in imported monkeys.Material and methods. Blood serum samples (n = 1971) and lung autopsy material (n = 26) were obtained from different monkey species. These samples were tested for the presence of serological markers of measles, parainfluenza (PI) types 1, 2, 3, influenza A and B, respiratory syncytial (RS) and adenovirus infections using enzyme immunoassay (ELISA). Detection of RS virus, metapneumovirus, PI virus types 1–4, rhinovirus, coronavirus, and adenoviruses B, C, E and bocavirus nucleic acids in this material was performed by reverse transcription polymerase chain reaction (RT-PCR).Results and discussion. The overall prevalence of antibodies (Abs) among all monkeys was low and amounted 11.3% (95% CI: 9.2–13.7%, n = 811) for measles virus, 8.9% (95% CI: 6.2–12.2%, n = 381) for PI type 3 virus, 2.5% (95% CI: 0.8–5.6%, n = 204) for PI type 1 virus, and 7.7% (95% CI: 3.8–13.7%, n = 130) for adenoviruses. When testing 26 autopsy lung samples from monkeys of different species that died from pneumonia, 2 samples from Anubis baboons (Papio аnubis) were positive for of parainfluenza virus type 3 RNA.Conclusion. Our data suggest the importance of the strict adherence to the terms of quarantine and mandatory testing of monkey sera for the presence of IgM antibodies to the measles virus that indicate the recent infection. The role of PI virus type 3 in the pathology of the respiratory tract in Anubis baboons has been established.

No substantial excess all-cause mortality among cardiac implantable electronic device patients during the first COVID‑19 lockdown in the Leiden area

In the Netherlands, the coronavirus disease 2019 (COVID‑19) pandemic has resulted in excess mortality nationwide. Chronic heart disease patients are at risk for a complicated COVID‑19 course. The current study investigates all-cause mortality among cardiac implantable electronic device (CIED) patients during the first peak of the pandemic and compares the data to the statistics for the corresponding period in the two previous years. Data of adult CIED patients undergoing follow-up at the Leiden University Medical Centre were analysed. All-cause mortality between 1 March and 31 May 2020 was evaluated and compared to the data for the same period in 2019 and 2018. At the beginning of the first peak of the pandemic, 3,171 CIED patients (median age 70 years; 68% male; 41% ischaemic aetiology) were alive. Baseline characteristics of the 2019 (n = 3,216) and 2018 (n = 3,169) cohorts were comparable. All-cause mortality during the peak of the pandemic was 1.4% compared to 1.6% and 1.4% in the same period in 2019 and 2018, respectively (p = 0.84). During the first peak of the COVID‑19 pandemic, there was no substantial excess mortality among CIED patients in the Leiden area, despite the fact that this is group at high risk for a complicated course of a COVID‑19 infection. Strict adherence to the preventive measures may have prevented substantial excess mortality in these vulnerable patients.

Muslim philanthropy: living beyond a Western definition

The commonly used definition of philanthropy used in Western scholarship excludes many Muslim acts of philanthropy. This definition privileges Western scholarly framing of philanthropy, which has been heavily informed by scientific approaches to philanthropy. This article argues that this framing of philanthropy limits our understanding of Muslim philanthropy and should not be privileged over other cultural and religious traditions’ notions of philanthropy. Muslim philanthropy is explored by examining theological and cultural sources in order to point towards a broader conception of philanthropy within an Islamic context. It illustrates the challenges of strict adherence to the Western definition of philanthropy for scholars of Muslim philanthropy. Ultimately, the article suggests a framework that the field of philanthropic studies can use to go beyond its Western-centric definition to be more inclusive of other cultural and faith perspectives, and proposes that Muslim philanthropy should be interpreted as a discursive tradition.

Natural regeneration in logging gaps of different sizes in Subri River Forest Reserve (Ghana)

Subri River Forest Reserve (SR) is the most extensive forest area in Ghana with an accompanying rich floral species. Over the years, logging from both legally prescribed and illegal operations remain the predominant forest disturbance in SR. Gap creation following logging is crucial in determining tree species composition and diversity. Hence, the study evaluated the composition and diversity of naturally regenerated tree species in logging gaps of different sizes and, again examined the roles of these tree species in fulfilling the economic and ecological agenda of sustainable forest management after logging in SR. Twelve gaps were randomly selected: 4 each were grouped into small size (≤ 200 m2), medium size (201–300 m2), and large size (≥ 300 m2). Data were gathered from 1 m2 circular area at gap centres and repeatedly inside 1 m width strip along 20 m individual N-S-E-W transects. Species diversity differed significantly between gap sizes. Higher diversity indices were measured in large size gaps. Gap sizes shared similar species. There were significant differences among various height groupings of tree species across all three gap sizes. Pioneers preferred medium to large size gaps, while shade-tolerant tree species preferred small size gaps for their abundance. Vulnerable and Lower Risk Near Threatened tree species under Conservation Status and, Premium and Commercial tree species under Utilisation Status preferred small size gaps for their proliferation and conservation. Therefore, we recommend the single tree-based selective logging for ensuring creations of small to medium size (200–300 m2) gaps through adjustments to the logging permit process, revision of Allocation Quota Permit, strict adherence to the 40-year polycyclic selection system, along with more dedicated enforcement and monitoring. Changes along these protocols would tremendously facilitate natural regeneration of different suites of timber species resulting in the improvement of the overall biodiversity conservation associated with the forest, more sustainable forest harvests and more income to those who receive permits.

Gluten-related immunogenic peptides in stool as means to monitor compliance with gluten-free diet in children with newly dia gnosed coeliac disease

Objectives and study: To compare the values of gluten-related immunogenic peptides (GIP) in stool and anti-tissue transglutaminase IgA antibodies (anti-tTG IgA) in blood in children newly diagnosed with coeliac disease (CD). Methods: All children (2–15 y) newly diagnosed with CD between May 2018 and May 2020 at our clinic who complied with the inclusion criteria were invited to join the prospective study. During workup for CD, a stool sample to measure GIP was taken together with a blood sample to measure anti-tTG IgA. All newly diagnosed children were invited 4 months later for a check-up. Children and their caregivers were asked about known non-compliance with the gluten-free diet (GFD), a blood sample was taken to measure the anti-tTG IgA, and a stool sample was collected to measure GIP. Blood was evaluated for anti-tTG IgA by ELISA, and the stool was tested by quantitative Sandwich ELISA designed to detect and quantify GIP using the G12 antibody. Values of GIP and anti-tTG IgA were compared in terms of their relation to the upper limit of normal (ULN) of the particular method. Results: 29 children (18 girls) were enrolled in the study. The values of GIP in stool at the time of diagnosis were above the ULN (0.15 µg/g) in all children. Average 4.21, median 3.29, standard deviation (SD) 3.7. After the four months, all but three (89.7%) had values of GIP in the reference range. Average 0.29, median 0.12, SD 0.73. Similarly, anti-tTG IgA values were above the ULN (9.9 U/mL) at the time of diagnosis in all children. Average 164, median 195, SD 49. Although the anti-tTG IgA levels were lower at check-up in all but one child, only 10 (34.5%) showed values within the normal range, with an average of 27.9, median 12.0, and SD 38.9. All children declared strict adherence to GFD. Discussion: Using the GIP concentration in stool, adherence to GFD in our cohort of children is very good, better than that described in literature. Conclusion: Measuring GIP in stool could prove a more sensitive indicator of adherence to GFD in the early months after the diagnosis of CD when anti-tTG IgA are still elevated above the ULN due to their well-described gradual decrease after GFD initiation.

Strict Adherence to Anti-Epidemic Measures Prevents ICU Staff from SARS-Cov2 Infection

During the first wave of the SARS Cov-2 virus pandemic, we faced a rapidly spreading infection in the Czech Republic. The lack of experience with a pandemic of such magnitude and the inconsistent information on the situation in China and Italy meant that we were forced to introduce an effective anti-epidemic measures in a very short period to protect our patients. One of the key measures that significantly contributed to the successful management of the first wave of the pandemic was to prevent the spread among healthcare professionals who directly cared for patients with active infection. During and after the first wave of the pandemic, we conducted a local observational study to assess the infection rate in ICU health care professionals who were in direct contact with infected patients. We believe that the successful management of the first wave of the pandemic and the experience gained by the entire team will help to manage the further course of this pandemic as well as other epidemics in the future. Here we bring our own experience from University Hospital ICU, which was selected to treat critically ill Covid-19 positive patients from whole region.

Incidence of COVID-19 after pulmonary function tests: a retrospective cohort study

Introduction: It has been proposed that exposure to pulmonary function tests (PFT) could be associated with a higher risk of viral transmission. The risk of the Coronavirus Disease 2019 (COVID-19) transmission after performing PFT is unknown. We aimed to assess the incidence of COVID-19 after a PFT at an academic teaching facility in Buenos Aires, Argentina. Materials and methods: We conducted a retrospective cohort study including all consecutive adult patients that performed PFT between April 1, 2020 and September 30, 2020. Patients with prior COVID-19 were excluded. We defined a 15-day time window to ascertain PFT related COVID-19. The primary outcome was ascertained by consulting a national database, which has information on all patients with nasopharyngeal swabs for SARS-CoV-2 in Argentina. Results: We included 278 patients who performed a PFT. Fifty percent were women, the mean age was 54 years (SD 18), and the main comorbidities were obesity (31%), smoking (31%), hypertension (29%), and chronic lung disease (28%). The main indication for performing PFT was anesthetic preoperative risk assessment. Swabs were collected from 27 patients (10%). Twenty-two swabs (8%) were taken according to surgical protocols; five swabs (2%) were taken due to clinical suspicion of COVID-19, with only one testing positive. The cumulative incidence of COVID-19 after PFT was 0.36% (95% CI 0.01-20%). None of the technicians developed symptomatic disease. Conclusion: Given the right setting and strict adherence to international recommendations, the SARS-CoV-2 infection after having a PFT appears to be low, which follows that these procedures can be performed safely for both patients and staff.

Efficiency and Safety of Binocular Cataract Phacoemulsification

A literature review is presented on the comparative assessment of two options for conducting cataract phacoemulsification — monocular phacoemulsification of cataract, (delayed sequential bilateral cataract surgery, DSBCS) and binocular phacoemulsification of cataract (immediate sequential bilateral cataract surgery, ISBCS). It has been established that to date in the literature there is a sufficient amount of data indicating the positive aspects of ISBCS, associated with faster rehabilitation, better functional results, as well as time, financial, and economic aspects. The safety of ISBCS is determined by the minimum likelihood of postoperative bilateral endophthalmitis with careful selection of patients, the required surgeon qualifications and strict adherence to the surgical protocol. Comparatively, in accordance with the results obtained, postoperative refractive indices, the value of the maximum corrected distance visual acuity, the frequency of complications and the degree of patient satisfaction were the same regardless of whether the bilateral cataract surgery was performed simultaneously or sequentially. The effectiveness of ISBCS is determined by quick rehabilitation, the need for only one pair of glasses, a decrease in visits to the clinic, the absence of anisometropia between operations, as well as only one general anesthesia (if necessary). The experience of clinics where such procedures were carried out shows that after ISBCS, minor refractive errors occur, while they are almost always symmetrical, characterized by a slight deviation from the target refraction and rapid recovery of binocular and stereoscopic vision. In financial terms, in accordance with the calculations carried out, the cost of DSBCS in various countries may be higher than the cost of ISBCS by 10.8–47.9 %. In absolute terms, simultaneous cataract surgery on two eyes (Finland) saved €449 per patient in medical costs and €739 after travel and home care costs were included. Taking into account the cost of lost work time, the savings were €849 per patient. The wider distribution of ISBCS is associated with the approval of the ophthalmological community and insurance companies, as well as the development of standardized teaching materials for practicing ophthalmologists.

IMPLIKASI YURIDIS TRANSFORMASI UNIT SYARIAH PERUSAHAAN ASURANSI/REASURANSI KE DALAM PERUSAHAAN ASURANSI/REASURANSI SYARIAH

In this article the author examines the juridical implications of transforming Units of Insurance/Reinsurance Company into Sharia Insurance/Reinsurance Company. It peruses two different models, the pure model, and the acquisition model. Both have its own strong and weak points. The pure models show its strongest point in being simpler about Sharia compliance. Its weakness, however, is the requirement of priory obtaining permit in principle and business permits. In contrast, the superiority of the acquisition model lies in its simplicity of licensing and conversion permits. Its disadvantage is in the complexity of contract conversion. Regarding assets and liabilities, strict adherence to the Sharia principles, voluntarisms, and avoidance of the mixing of halal and haram, is a pre-requisite