Impacts of extreme climate on Australia's green cover (2003-2018): A MODIS and mascon probe

Australia as a continent represents a semi-arid environment that is generally water-limited. Changes in rainfall pattern will inevitably occur due to rising temperatures caused by climate change, which has a direct impact on the distribution of Australia's vegetation (green cover). As variability in rainfall continues to increase, i.e., in frequency and/or magnitude, due to climate change, extreme climate events such as droughts are predicted to become more pervasive and severe that will have an adverse effect on vegetation. This study investigates the effects of extreme climate on Australia's green cover during 2003-2018 for the end of rainy seasons of April and October in the northern and southern parts, respectively, to (i) determine the state of vegetation and its changes, (ii) identify "hotspots", i.e., regions that constantly experienced statistically significant decrease in NDVI, and (iii), relate changes in the identified hotspots to GRACE-hydrological changes. These are achieved through the exploitation of the statistical tools of Principal Component Analysis (PCA) and Mann-Kendel Test on Gravity Recovery and Climate Experiment (GRACE) hydrological products on the one hand, and the utilization of Australia's rainfall product and Moderate Resolution Imaging Spectroradiometer Normalized Difference Vegetation Index (MODIS-NDVI) used here with its native spatial resolution of 0.002413^∘ × 0.002413^∘ on the other hand. Differences between 3-year intervals from 2003 to 2018 for both April and October datasets are used to quantify vegetation variations. Through area change analysis, the vegetation differences (2003-2018) indicate that April exhibited larger increase (13.77% of total vegetation area) than decrease (7.83%) compared to October, which experienced slightly larger decrease (9.41%) than increase (8.71%). South Australia and Western Australia emerge as "hotspots" in which vegetation statistically decreased in October, with no noticeable change in April. GRACE-based hydrological changes in both hotspots reflect a decreasing trend (2003-2009) and increasing trend (2009-2012) that peaks in 2011, which then transitions towards a gradually decreasing trend after 2012. Australia-wide climate variability (ENSO and IOD) influenced vegetation variations during the data period 2003 to 2018.

Anakinra in hospitalized patients with severe COVID-19 pneumonia requiring oxygen therapy: Results of a prospective, open-label, interventional study

Objective

The aim of this study was to evaluate the efficacy of anakinra in patients who were admitted to hospital for severe COVID-19 pneumonia requiring oxygen therapy.

Methods

A prospective, open-label, interventional study in adults hospitalized with severe COVID-19 pneumonia was conducted. Patients in the interventional arm received subcutaneous anakinra (100 mg twice daily for 3 days, followed by 100 mg daily for 7 days) in addition to standard treatment. Main outcomes were the need for mechanical ventilation and in-hospital death. Secondary outcomes included successful weaning from supplemental oxygen and change in inflammatory biomarkers. Outcomes were compared with those of historical controls who had received standard treatment and supportive care.

Results

A total of 69 patients were included: 45 treated with anakinra and 24 historical controls. A need for mechanical ventilation occurred in 14 (31%) of the anakinra-treated group and 18 (75%) of the historical cohort (p < 0.001). In-hospital death occurred in 13 (29%) of the anakinra-treated group and 11 (46%) of the historical cohort (p = 0.082). Successful weaning from supplemental oxygen to ambient air was attained in 25 (63%) of the anakinra-treated group compared with 6 (27%) of the historical cohort (p = 0.008). Patients who received anakinra showed a significant reduction in inflammatory biomarkers.

Conclusion

In patients with severe COVID-19 pneumonia and high oxygen requirement, anakinra could represent an effective treatment option and may confer clinical benefit.

Trial registration number

ISRCTN74727214.

Endocrinological Abnormalities and Growth Impairment in Human Immunodeficiency Virus-Infected Children

Background Pediatric human immunodeficiency virus (HIV) is an important emerging disease and many children are surviving into adulthood with effective antiretroviral therapy. Growth dysregulation is common in these children and endocrine abnormalities are likely to be a possible comorbidity. There is a paucity of data on these endocrinological abnormalities in this population. Against this background, a study to evaluate the endocrinological profile in HIV-infected children and its relationship with growth failure was performed.

Methods A cross-sectional descriptive study was performed in children less than 18 years attending the pediatric HIV clinic at a tertiary care hospital in central India. Blood samples for T3, T4, thyroid-stimulating hormone (TSH), growth hormone (GH), dehydroepiandrosterone (DHEA), cortisol, and insulin-like growth factor-binding protein 3 (IGFBP3) were collected during routine visit, preserved at –70°C, and subsequently assayed. Statistical analysis for the data with respect to the endocrinological abnormalities and growth failure was performed.

Results A total of 100 children were included in the study. The prevalence of growth failure was high. Nineteen percent children had height less than − 3 standard deviation (SD) and 59% children had height less than 2SD. The prevalence of endocrinological abnormalities was also high. Fifty-four percent children had low T3 levels, 12% had low T4 levels, 4% had high TSH levels, 44% had low cortisol levels, and 25% had low DHEA. Fifty-eight percent children had low GH levels, while IGFBP3 levels were low in the entire cohort. There was a statistically significant association between growth failure and levels of T3 and GH.

Conclusion Our results show a high prevalence of growth failure and endocrinological abnormalities in HIV-infected children. A significant association between growth failure and endocrine abnormalities was found for T3 and GH.

Prevalence, predictors and challenges of gestational diabetes mellitus screening among pregnant women in northern Tanzania

OBJECTIVES

To determine the prevalence and predictors of gestational diabetes mellitus (GDM) as well as acceptability of returning for glucose tolerance testing among pregnant women in Moshi municipality, northern Tanzania.

METHODS

Cross-sectional study from October 2015 to April 2016 among women with gestation age of 24-28 weeks of pregnancy attending at Kilimanjaro Christian Medical Centre (KCMC) referral hospital, Majengo and Pasua Health Centres. Women were interviewed and requested to return the next day (window within a month, depending on gestational age) for fasting plasma glucose (FPG) testing, followed immediately by a 75 g oral glucose tolerance test (OGTT). GDM was diagnosed using the 2013 WHO criteria. Logistic regression was conducted to reveal independent predictors for GDM.

RESULTS

Of 433 interviewed women, 100 (23%) did not return for FPG and OGTT testing. The prevalence of GDM among the 333 screened women was 19.5%, and 3% had diabetes in pregnancy (DIP). GDM was significantly associated with age ≥35 years (adjusted OR 6.75), pre-pregnancy obesity (AOR 2.22) and history of abortion (AOR 2.36).

CONCLUSION

Prevalence of GDM is high in Moshi. We recommend introduction of routine screening for hyperglycaemia during pregnancy along with strategies for follow-up to prevent long-term effects of GDM and DIP in women and their children.

Chest wall lymphomas: Fine needle aspiration cytodiagnosis and review of the literature

OBJECTIVE

Compared to other chest wall malignancies, lymphoma is a common disease. However, published literature on a series of lymphoma cases involving the chest wall is scarce. The aim of the present study, was to describe experience with chest wall swellings diagnosed as lymphoid neoplasms on fine needle aspiration (FNA) cytology.

METHODS

Eleven chest wall swellings were diagnosed as lymphoid neoplasms on FNA over a period of 15 years (January 2000-December 2014). The age of patients ranged from 19 to 73 years (median, 46). The male-to -emale ratio was 7:4. Ten cases had an anterior or lateral chest wall mass, and one swelling was in the scapular region. Six cases had concurrent lymphadenopathy, and one had bone involvement. The FNA smears were reviewed and classified under WHO Classification of Hematopoietic Neoplasms. The histopathological diagnoses were available in eight cases.

RESULTS

The preliminary cytodiagnoses in 11 cases of chest wall lymphoid neoplasms were anaplastic large cell lymphoma (ALCL) in two cases, and ALCL/malignant melanoma, ALCL/T-cell-rich-B-cell lymphoma (TCRBCL)/Hodgkin's lymphoma (HL), plasmacytoma/neuroendocrine carcinoma, Hodgkin's lymphoma, small cell NHL/CLL, NHL, suggestive of NHL, post-transplant peripheral T-cell lymphoma (PTCL), and a malignant plasma cell tumour in one case each. The reviewed cytodiagnoses of lymphoid neoplasms were as follows: ALCL ( five cases), centroblastic lymphoma (two cases), and small cell lymphoma/CLL, post-transplant peripheral T-cell lymphoma, Hodgkin's lymphoma and plasmacytoma (one case each). Histopathological diagnoses available in eight cases confirmed the presence of lymphoid neoplasms.

CONCLUSION

A variety of lymphoid neoplasms involved the chest wall, and among them, ALCL was a common form.

Noncoding RNAs that associate with YB-1 alter proliferation in prostate cancer cells

The highly conserved, multifunctional YB-1 is a powerful breast cancer prognostic indicator. We report on a pervasive role for YB-1 in which it associates with thousands of nonpolyadenylated short RNAs (shyRNAs) that are further processed into small RNAs (smyRNAs). Many of these RNAs have previously been identified as functional noncoding RNAs (http://www.johnlab.org/YB1). We identified a novel, abundant, 3'-modified short RNA antisense to Dicer1 (Shad1) that colocalizes with YB-1 to P-bodies and stress granules. The expression of Shad1 was shown to correlate with that of YB-1 and whose inhibition leads to an increase in cell proliferation. Additionally, Shad1 influences the expression of additional prognostic markers of cancer progression such as DLX2 and IGFBP2. We propose that the examination of these noncoding RNAs could lead to better understanding of prostate cancer progression.

Genome-wide transcript profiling reveals novel breast cancer-associated intronic sense RNAs

Non-coding RNAs (ncRNAs) play major roles in development and cancer progression. To identify novel ncRNAs that may identify key pathways in breast cancer development, we performed high-throughput transcript profiling of tumor and normal matched-pair tissue samples. Initial transcriptome profiling using high-density genome-wide tiling arrays revealed changes in over 200 novel candidate genomic regions that map to intronic regions. Sixteen genomic loci were identified that map to the long introns of five key protein-coding genes, CRIM1, EPAS1, ZEB2, RBMS1, and RFX2. Consistent with the known role of the tumor suppressor ZEB2 in the cancer-associated epithelial to mesenchymal transition (EMT), in situ hybridization reveals that the intronic regions deriving from ZEB2 as well as those from RFX2 and EPAS1 are down-regulated in cells of epithelial morphology, suggesting that these regions may be important for maintaining normal epithelial cell morphology. Paired-end deep sequencing analysis reveals a large number of distinct genomic clusters with no coding potential within the introns of these genes. These novel transcripts are only transcribed from the coding strand. A comprehensive search for breast cancer associated genes reveals enrichment for transcribed intronic regions from these loci, pointing to an underappreciated role of introns or mechanisms relating to their biology in EMT and breast cancer.

An in-depth map of polyadenylation sites in cancer

We present a comprehensive map of over 1 million polyadenylation sites and quantify their usage in major cancers and tumor cell lines using direct RNA sequencing. We built the Expression and Polyadenylation Database to enable the visualization of the polyadenylation maps in various cancers and to facilitate the discovery of novel genes and gene isoforms that are potentially important to tumorigenesis. Analyses of polyadenylation sites indicate that a large fraction (∼30%) of mRNAs contain alternative polyadenylation sites in their 3' untranslated regions, independent of the cell type. The shortest 3' untranslated region isoforms are preferentially upregulated in cancer tissues, genome-wide. Candidate targets of alternative polyadenylation-mediated upregulation of short isoforms include POLR2K, and signaling cascades of cell-cell and cell-extracellular matrix contact, particularly involving regulators of Rho GTPases. Polyadenylation maps also helped to improve 3' untranslated region annotations and identify candidate regulatory marks such as sequence motifs, H3K36Me3 and Pabpc1 that are isoform dependent and occur in a position-specific manner. In summary, these results highlight the need to go beyond monitoring only the cumulative transcript levels for a gene, to separately analysing the expression of its RNA isoforms.

Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs

Deep sequencing studies frequently identify small RNA fragments of abundant RNAs. These fragments are thought to represent degradation products of their precursors. Using sequencing, computational analysis, and sensitive northern blot assays, we show that constitutively expressed non-coding RNAs such as tRNAs, snoRNAs, rRNAs and snRNAs preferentially produce small 5' and 3' end fragments. Similar to that of microRNA processing, these terminal fragments are generated in an asymmetric manner that predominantly favors either the 5' or 3' end. Terminal-specific and asymmetric processing of these small RNAs occurs in both mouse and human cells. In addition to the known processing of some 3' terminal tRNA-derived fragments (tRFs) by the RNase III endonuclease Dicer, we show that several RNase family members can produce tRFs, including Angiogenin that cleaves the TψC loop to generate 3' tRFs. The 3' terminal tRFs but not the 5' tRFs are highly complementary to human endogenous retroviral sequences in the genome. Despite their independence from Dicer processing, these tRFs associate with Ago2 and are capable of down regulating target genes by transcript cleavage in vitro. We suggest that endogenous 3' tRFs have a role in regulating the unwarranted expression of endogenous viruses through the RNA interference pathway.

miRNA-939 regulates human inducible nitric oxide synthase posttranscriptional gene expression in human hepatocytes

Human inducible nitric oxide synthase (hiNOS) gene expression is regulated by transcriptional and posttranscriptional mechanisms. The purpose of this study was to determine whether specific microRNA (miRNA) directly regulate hiNOS gene expression. Sequence analysis of the 496-bp hiNOS 3'-untranslated region (3'-UTR) revealed five putative miR-939 binding sites. The hiNOS 3'-UTR conferred significant posttranscriptional blockade of luciferase activity in human A549, HCT8, and HeLa cells. The hiNOS 3'-UTR also exerted basal and cytokine-stimulated posttranscriptional repression in an orientation-dependent manner. Functional studies demonstrated that transfection of miR-939 into primary human hepatocytes (HCs) significantly inhibited cytokine-induced NO synthesis in a dose-dependent manner that was abrogated by a specific miR-939 inhibitor. MiR-939 (but not other miRNAs) abolished cytokine-stimulated hiNOS protein in human HC, but had no effect on hiNOS mRNA levels. Site-directed mutagenesis of miR-939 bindings sites at +99 or +112 bp in the hiNOS 3'-UTR increased reporter gene expression. Furthermore, intact miR-939 binding sites at +99 or +112 positions were required for posttranscriptional suppression by miR-939. Cytokine stimulation directly increased miR-939 levels in human HC. Transfection of miR-939 inhibitor (antisense miR-939) enhanced cytokine-induced hiNOS protein and increased NO synthesis in vitro in human HC. Finally, cytokine or LPS injection in vivo in mice increased hepatic miR-939 levels. Taken together, these data identify that miR-939 directly regulates hiNOS gene expression by binding in the 3'-UTR to produce a translational blockade. These findings suggest dual regulation of iNOS gene expression where cytokines induce iNOS transcription and also increase miR-939, leading to translational inhibition in a check-and-balance system.

Validation of the Roche AMPLICOR HIV DNA test version 1.5 for early infant diagnosis of HIV in Papua New Guinea

Human immunodeficiency virus (HIV) is a significant public health issue in Papua New Guinea (PNG). After heterosexual transmission (90%), the second most common route of transmission is vertically from mother to child (3.5%). Before the introduction of molecular methods of HIV testing in PNG, diagnosing exposed infants was problematic because there were no reliable assays available for accurate early infant HIV detection. This study aimed to validate and assess a global gold standard for virological early infant HIV diagnosis in PNG: the AMPLICOR HIV DNA v1.5 assay (Roche) using dried blood spot (DBS) specimens. The assay was validated in three ways: by testing well-characterized DBS and kit controls and by blinded retesting of 42 patient specimens. The assay was further investigated by comparison with a serological assay. The results indicated that the assay was robust and highly reproducible using DBS and kit controls, with 100% sensitivity and specificity. Of the 42 infant DBS specimens that were retested blindly, 100% of the test results were concordant with diagnostic results. Among the 42 infant specimens tested with the Amplicor HIV DNA v1.5 assay we found that 33% of infants (n = 14) were HIV PCR positive and 67% (n = 28) negative. The earliest point of HIV detection established for this study was three months of age. This pilot study indicates that HIV-infected infants in PNG can be effectively diagnosed using virological testing and can thus be started earlier on treatment than was previously possible with serological testing.

Evaluation of an electrostatic dust removal system with potential application in next-step fusion devices

The ability to manage inventories of carbon, tritium, and high-Z elements in fusion plasmas depends on means for effective dust removal. A dust conveyor, based on a moving electrostatic potential well, was tested with particles of tungsten, carbon, glass, and sand. A digital microscope imaged a representative portion of the conveyor, and dust particle size and volume distributions were derived before and after operation. About 10 mm(3) volume of carbon and tungsten particles were moved in under 5 s. The highest driving amplitude tested of 3 kV was the most effective. The optimal driving frequency was 210 Hz (maximum tested) for tungsten particles, decreasing to below 60 Hz for the larger sand particles. Measurements of particle size and volume distributions after 10 and 100 cycles show the breaking apart of agglomerated carbon and the change in particle distribution over short timescales (<1 s).

Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation

The emerging discoveries on the link between polyadenylation and disease states underline the need to fully characterize genome-wide polyadenylation states. Here, we report comprehensive maps of global polyadenylation events in human and yeast generated using refinements to the Direct RNA Sequencing technology. This direct approach provides a quantitative view of genome-wide polyadenylation states in a strand-specific manner and requires only attomole RNA quantities. The polyadenylation profiles revealed an abundance of unannotated polyadenylation sites, alternative polyadenylation patterns, and regulatory element-associated poly(A)(+) RNAs. We observed differences in sequence composition surrounding canonical and noncanonical human polyadenylation sites, suggesting novel noncoding RNA-specific polyadenylation mechanisms in humans. Furthermore, we observed the correlation level between sense and antisense transcripts to depend on gene expression levels, supporting the view that overlapping transcription from opposite strands may play a regulatory role. Our data provide a comprehensive view of the polyadenylation state and overlapping transcription.

New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism

Small (<200 nucleotide) RNA (sRNA) profiling of human cells using various technologies demonstrates unexpected complexity of sRNAs with hundreds of thousands of sRNA species present. Genetic and in vitro studies show that these RNAs are not merely degradation products of longer transcripts but could indeed have a function. Furthermore, profiling of RNAs, including the sRNAs, can reveal not only novel transcripts, but also make clear predictions about the existence and properties of novel biochemical pathways operating in a cell. For example, sRNA profiling in human cells indicated the existence of an unknown capping mechanism operating on cleaved RNA, a biochemical component of which was later identified. Here we show that human cells contain a novel type of sRNA that has non-genomically encoded 5' poly(U) tails. The presence of these RNAs at the termini of genes, specifically at the very 3' ends of known mRNAs, strongly argues for the presence of a yet uncharacterized endogenous biochemical pathway in cells that can copy RNA. We show that this pathway can operate on multiple genes, with specific enrichment towards transcript-encoding components of the translational machinery. Finally, we show that genes are also flanked by sense, 3' polyadenylated sRNAs that are likely to be capped.

Evidence-based management of heart failure in clinical practice: a review of device-based therapy use

BACKGROUND

Heart failure is a growing health issue and is associated with significant mortality risk. Device therapy is efficacious in preventing sudden death in patients with heart failure; however, this evidence comes from rigorous clinical trials. It is unclear how device therapy is utilized in 'real-world' practice. The primary objective was to characterize patterns of device use in patients with heart failure at risk of sudden death and to identify barriers to guideline-driven prescription of implantable cardioverter-defibrillators.

METHODS

We report a cross-sectional study of patients attending general cardiology clinic over a 3-month period.

RESULTS

Of 1003 consecutive patients attending the cardiology clinic, 176 had heart failure. Of these, 66 were potentially eligible for device therapy, but only 16 of these had actually undergone device implantation. Potentially eligible non-recipients were older (P < 0.001), more likely to have ischaemic cardiomyopathy (P= 0.002), less likely to be prescribed spironolactone (P= 0.005) or warfarin (P= 0.02), and less likely to have a widened QRS > 120 ms (P= 0.005). There was a high prevalence of underuse of evidence-based pharmacotherapies among patients with heart failure.

CONCLUSION

There is substantial underuse of device therapy in patients with heart failure. Strikingly, whereas patients with symptoms of heart failure were more likely to receive a device, those being managed for ischaemic heart disease were not. There is also a high prevalence of failure to prescribe evidence-based pharmacotherapy in a tertiary hospital general cardiology clinic. This may be explained in part by the lack of a patient database to record treatment contraindications and to alert clinicians to possible gaps in patient therapy.

A sensitive non-radioactive northern blot method to detect small RNAs

The continuing discoveries of potentially active small RNAs at an unprecedented rate using high-throughput sequencing have raised the need for methods that can reliably detect and quantitate the expression levels of small RNAs. Currently, northern blot is the most widely used method for validating small RNAs that are identified by methods such as high-throughput sequencing. We describe a new northern blot-based protocol (LED) for small RNA (∼15–40 bases) detection using digoxigenin (DIG)-labeled oligonucleotide probes containing locked nucleic acids (LNA) and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide for cross-linking the RNA to the membrane. LED generates clearly visible signals for RNA amounts as low as 0.05 fmol. This method requires as little as a few seconds of membrane exposure to outperform the signal intensity using overnight exposure of isotope-based methods, corresponding to ∼1000-fold improvement in exposure-time. In contrast to commonly used radioisotope-based methods, which require freshly prepared and hazardous probes, LED probes can be stored for at least 6 months, facilitate faster and more cost-effective experiments, and are more environmentally friendly. A detailed protocol of LED is provided in the Supplementary Data.