Miracle-dz/UniFAR-FTUs huggingface dataset:
Long-term exposure to more frequent disturbances increases baseline carbon in some ecosystems: Mapping and quantifying the disturbance frequency-ecosystem C relationship

Disturbance regimes have a major influence on the baseline carbon that characterizes any particular ecosystem. Often regimes result in lower average regional baseline C (compared to those same systems if the disturbance processes were lessened/removed). However, in infrequently disturbed systems the role of disturbance as a “background” process that influences broad-scale, baseline C levels is often neglected. Long-term chronosequences suggest disturbances in these systems may serve to increase regional biomass C stocks by maintaining productivity. However, that inference has not been tested spatially. Here, the large forested system of southeast Alaska, USA, is utilized to 1) estimate baseline regional C stocks, 2) test the fundamental disturbance-ecosystem C relationship, 3) estimate the cumulative impact of disturbances on baseline C. Using 1491 ground points with carbon measurements and a novel way of mapping disturbance regimes, the relationship between total biomass C, disturbance exposure, and climate was analyzed statistically. A spatial model was created to determine regional C and compare different disturbance scenarios. In this infrequently disturbed ecosystem, higher disturbance exposure is correlated with higher biomass C, supporting the hypothesis that disturbances maintain productivity at broad scales. The region is estimated to potentially contain a baseline 1.21–1.52 Pg biomass C (when unmanaged). Removal of wind and landslides from the model resulted in lower net C stocks (-2 to -19% reduction), though the effect was heterogeneous on finer scales. There removal of landslides alone had a larger effect then landslide and wind combined removal. The relationship between higher disturbance exposure and higher biomass within the broad ecosystem (which, on average, has a very low disturbance frequency) suggest that disturbances can serve maintain higher levels of productivity in infrequently disturbed but very C dense ecosystems. Carbon research in other systems, especially those where disturbances are infrequent relative to successional processes, should consider the role of disturbances in maintaining baseline ecosystem productivity.
Real-Time PCR based test for the early diagnosis of Haplosporidium pinnae affecting fan mussel Pinna nobilis

Noble pen shell or fan mussel, Pinna nobilis Linnaeus (1758), protected since 1992, was incorporated into the Spanish Catalogue of Threatened Species (Category: Vulnerable, Royal Decree 139/2011). The status is presently in the process of being catalogued as critically endangered, pending approval by Spanish Government (https://www.mapama.gob.es/es/biodiversidad/participacion-publica/Borrador_OM_situacion_critica.aspx). The International Union for the Conservation of Nature (IUCN) alerted the countries of the Mediterranean basin to the “emergent situation” due to serious mortality events suffered by the fan mussel, putting it in serious risk of extinction. Thus, emergency actions have been implemented by Spanish authorities in which several research institutes from all over the country are involved. The parasite, Haplosporidium pinnae, was recently characterized by histology, TEM, SEM and molecular biology techniques and it was considered responsible for the mass mortality of P. nobilis in the Mediterranean Sea. In this context, the aim of this study has been to develop species-specific quantitative PCR (qPCR) protocol carrying out a fast, specific and effective molecular diagnose of H. pinnae. In this sense, the detection limit for qPCR was equal to 30 copies of SSU rDNA / ng of DNA using plasmid alone and when 100ng DNA of non-infected oyster were added. The qPCR assay revealed that 94% of the 32 analysed mantle tissues of fan mussel were infected by H. pinnae, showing a high sensitivity and specificity for its detection (100% if we don't consider negative and too much degraded samples). This technique will allow us to make quicker follow-ups of the disease, allowing us to get a better understanding of its evolution in order to help in the rescue of P. nobilis populations
Role of deformable cancer cells on wall shear stress-associated-VEGF secretion by endothelium in microvasculature

Endothelial surface layer (glycocalyx) is the major physiological regulator of tumor cell adhesion to endothelium. Cancer cells express vascular endothelial growth factor (VEGF) which increases the permeability of a microvessel wall by degrading glycocalyx. Endothelial cells lining large arteries have also been reported, in vitro and in vivo, to mediate VEGF expression significantly under exposure to high wall shear stress (WSS) > 0.6 Pa. The objective of the present study is to explore whether local hemodynamic conditions in the vicinity of a migrating deformable cancer cell can influence the function of endothelial cells to express VEGF within the microvasculature. A three-dimensional model of deformable cancer cells (DCCs) migrating within a capillary is developed by applying a massively parallel hemodynamics application to simulate the fluid-structure interaction between the DCC and fluid surrounding the DCC. We study how dynamic interactions between the DCC and its local microenvironment affect WSS exposed on endothelium, under physiological conditions of capillaries with different diameters and flow conditions. Moreover, we quantify the area of endothelium affected by the DCC. Our results show that the DCC alters local hemodynamics in its vicinity up to an area as large as 40 times the cancer cell lateral surface. In this area, endothelium experiences high WSS values in the range of 0.6–12 Pa. Endothelial cells exposed to this range of WSS have been reported to express VEGF. Furthermore, we demonstrate that stiffer cancer cells expose higher WSS on the endothelium. A strong impact of cell stiffness on its local microenvironment is observed in capillaries with diameters <16 μm. WSS-induced-VEGF by endothelium represents an important potential mechanism for cancer cell adhesion and metastasis in the microvasculature. This work serves as an important first step in understanding the mechanisms driving VEGF-expression by endothelium and identifying the underlying mechanisms of glycocalyx degradation by endothelium in microvasculature. The identification of angiogenesis factors involved in early stages of cancer cell-endothelium interactions and understanding their regulation will help, first to develop anti-angiogenic strategies applied to diagnostic studies and therapeutic interventions, second to predict accurately where different cancer cell types most likely adhere in microvasculature, and third to establish accurate criteria predisposing the cancer metastasis.
Ovarian reserve in women with sickle cell disease

BACKGROUND It has been proposed that ovarian sickling and/or iron overload in women with sickle cell disease (SCD) could contribute to gonadal dysfunction, but there are very few published studies. We hypothesised that the above phenomena might impair ovarian reserve. METHODS A total of 50 SCD patients were case-matched by age, ethnicity, and presence of regular cycles (28±5 days) with 73 patients without a known haemoglobinopathy who required anti-Müllerian hormone (AMH) assessment in a gynaecology clinic. SCD patients had AMH levels taken as part of routine care. The patients were case-controlled and matched with patients who had no haemoglobinopathy in a tertiary centre over a period of one year. RESULTS The mean AMH in the SCD case group was 7.6 pmol/l compared with 13.4 pmol/l in the control group (p<0.001). The AMH distributions were subsequently categorised. This showed that SCD patients had a significantly higher chance of having lower AMH in comparison with the control group (OR 2.6 (CI 1.1-6.5, P = 0.02). The proportion of women with AMH > 20 pmol/l was significantly lower in the SCD group (6%) in comparison with the control group (19%) (P = 0.04). CONCLUSIONS This is the first study showing that women of reproductive age with SCD are more likely to have a low ovarian reserve at a younger age in comparison with patients with no haemoglobinopathy.
Extraction-free whole transcriptome gene expression analysis of FFPE sections and histology-directed subareas of tissue

We describe the use of a ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq™, to profile formalin-fixed paraffin-embedded (FFPE) tissue, including H&E stained FFPE tissue, by directly lysing tissue scraped from slides without extracting RNA or converting the RNA to cDNA. The correlation of measured gene expression changes in unfixed and fixed samples using blocks prepared from a pellet of a single cell type was R2 = 0.97, demonstrating that no significant artifacts were introduced by fixation. Fixed and fresh samples prepared in an equivalent manner produced comparable sequencing depth results (+/-20%), with similar %CV (11.5 and 12.7%, respectively), indicating no significant loss of measurable RNA due to fixation. The sensitivity of the TempO-Seq assay was the same whether the tissue section was fixed or not. The assay performance was equivalent for human, mouse, or rat whole transcriptome. The results from 10 mm2 and 2 mm2 areas of tissue obtained from 5 μm thick sections were equivalent, thus demonstrating high sensitivity and ability to profile focal areas of histology within a section. Replicate reproducibility of separate areas of tissue ranged from R2 = 0.83 (lung) to 0.96 (liver) depending on the tissue type, with an average correlation of R2 = 0.90 across nine tissue types. The average %CVs were 16.8% for genes expressed at greater than 200 counts, and 20.3% for genes greater than 50 counts. Tissue specific differences in gene expression were identified and agreed with the literature. There was negligible impact on assay performance using FFPE tissues that had been archived for up to 30 years. Similarly, there was negligible impact of H&E staining, facilitating accurate visualization for scraping and assay of small focal areas of specific histology within a section.
A simulation environment for studying transcutaneous electrotactile stimulation

Transcutaneous electrical nerve stimulation (TENS) allows the artificial excitation of nerve fibres by applying electric-current pulses through electrodes on the skin’s surface. This work involves the development of a simulation environment that can be used for studying transcutaneous electrotactile stimulation and its dependence on electrode layout and excitation patterns. Using an eight-electrode array implementation, it is shown how nerves located at different depths and with different orientations respond to specific injected currents, allowing the replication of already reported experimental findings and the creation of new hypotheses about the tactile sensations associated with certain stimulation patterns. The simulation consists of a finite element model of a human finger used to calculate the distribution of the electric potential in the finger tissues neglecting capacitive effects, and a cable model to calculate the excitation/inhibition of action potentials in each nerve.
Improving estimates of district HIV prevalence and burden in South Africa using small area estimation techniques

Many countries, including South Africa, have implemented population-based household surveys to estimate HIV prevalence and the burden of HIV infection. Most household HIV surveys are designed to provide reliable estimates down to only the first subnational geopolitical level which, in South Africa, is composed of nine provinces. However HIV prevalence estimates are needed down to at least the second subnational level in order to better target the delivery of HIV care, treatment and prevention services. The second subnational level in South Africa is composed of 52 districts. Achieving adequate precision at the second subnational level therefore requires either a substantial increase in survey sample size or use of model-based estimation capable of incorporating other pre-existing data. Our purpose is demonstration of the efficacy of relatively simple small-area estimation of HIV prevalence in the 52 districts of South Africa using data from the South African National HIV Prevalence, Incidence and Behavior Survey, 2012, district-level HIV prevalence estimates obtained from testing of pregnant women who attended antenatal care (ANC) clinics in 2012, and 2012 demographic data. The best-fitting model included only ANC prevalence and dependency ratio as out-of-survey predictors. Our key finding is that ANC prevalence was the superior auxiliary covariate, and provided substantially improved precision in many district-level estimates of HIV prevalence in the general population. Inclusion of a district-level spatial simultaneously autoregressive covariance structure did not result in improved estimation.
The influence of immigrant generation on obesity among Asian Americans in California from 2013 to 2014

Objectives We aimed to examine the association between immigrant generation and obesity among Californian adults and Asian Americans. Methods We pooled weighted data (n = 2,967) on Asian Americans from the 2013–2014 California Health Interview Survey. Overweight and obesity were defined using body mass indices (BMI) of 25 kg/m2 and 30 kg/m2, respectively, in non-Asians, compared with BMI of 23 kg/m2 (for being overweight) and 27.5 kg/m2 (for being obese) in Asians. First-generation or immigrant Asian Americans were defined as those born outside of the U.S. Second-generation Asian Americans were defined as those born in the U.S. with at least one foreign-born parent. All other Asian participants were classified as third-generation or higher. Multiple logistic regression analyses were used with adjustment for age, sex, family income, smoking status, marital status, education, physical activity, and fast food consumption. Results Overall, 23.3% of the Asian population was obese, and 40.0% was overweight. The percentage of 1st, 2nd, and 3rd generation were 72.7%, 22.6%, and 4.6%, respectively. Overall, 1st generation of Asians had lower odds of being obese compared to Whites (OR = 0.34, 95%CI = 0.26–0.45). Multiple logistic regression analyses showed that overall, 2nd generation (OR = 1.69, 95%CI = 1.10–2.60) and 3rd generation (OR = 2.33, 95%CI = 1.29–4.22) Asians had higher odds of being obese compared to 1st generation Asians. Among Chinese, compared to the 1st generation, the 3rd generation had increased likelihood of being obese (OR = 6.29, 95%CI = 2.38–16.6). Conclusion Compared to Whites, Hispanics, and Blacks, Asian immigrants are less likely to be obese. Among Asians, 2nd and 3rd generations were more likely to be obese compared to 1st generation. The obesity rate seems to increase the longer Asian immigrants remain in the U.S.
Gata6, Nanog and Erk signaling control cell fate in the inner cell mass through a tristable regulatory network

During blastocyst formation, inner cell mass (ICM) cells differentiate into either epiblast (Epi) or primitive endoderm (PrE) cells, labeled by Nanog and Gata6, respectively, and organized in a salt-and-pepper pattern. Previous work in the mouse has shown that, in absence of Nanog, all ICM cells adopt a PrE identity. Moreover, the activation or the blockade of the Fgf/RTK pathway biases cell fate specification towards either PrE or Epi, respectively. We show that, in absence of Gata6, all ICM cells adopt an Epi identity. Furthermore, the analysis of Gata6+/− embryos reveals a dose-sensitive phenotype, with fewer PrE-specified cells. These results and previous findings have enabled the development of a mathematical model for the dynamics of the regulatory network that controls ICM differentiation into Epi or PrE cells. The model describes the temporal dynamics of Erk signaling and of the concentrations of Nanog, Gata6, secreted Fgf4 and Fgf receptor 2. The model is able to recapitulate most of the cell behaviors observed in different experimental conditions and provides a unifying mechanism for the dynamics of these developmental transitions. The mechanism relies on the co-existence between three stable steady states (tristability), which correspond to ICM, Epi and PrE cells, respectively. Altogether, modeling and experimental results uncover novel features of ICM cell fate specification such as the role of the initial induction of a subset of cells into Epi in the initiation of the salt-and-pepper pattern, or the precocious Epi specification in Gata6+/− embryos.
Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia

Grain yield is a trait of paramount importance in the breeding of all cereals. In wheat (Triticum aestivum L.), yield has steadily increased since the Green Revolution, though the current rate of increase is not forecasted to keep pace with demand due to growing world population and affluence. While several genome-wide association studies (GWAS) on yield and related component traits have been performed in wheat, the previous lack of a reference genome has made comparisons between studies difficult. In this study, a GWAS for yield and yield-related traits was carried out on a population of 324 soft red winter wheat lines across a total of four rain-fed environments in the state of Virginia using single-nucleotide polymorphism (SNP) marker data generated by a genotyping-by-sequencing (GBS) protocol. Two separate mixed linear models were used to identify significant marker-trait associations (MTAs). The first was a single-locus model utilizing a leave-one-chromosome-out approach to estimating kinship. The second was a sub-setting kinship multi-locus method (FarmCPU). The single-locus model identified nine significant MTAs for various yield-related traits, while the FarmCPU model identified 74 significant MTAs. The availability of the wheat reference genome allowed for the description of MTAs in terms of both genetic and physical positions, and enabled more extensive post-GWAS characterization of significant MTAs. The results indicate promising avenues for increasing grain yield by exploiting variation in traits relating to the number of grains per unit area, as well as phenological traits influencing grain-filling duration of genotypes.
The impact of an insecticide treated bednet campaign on all-cause child mortality: A geospatial impact evaluation from the Democratic Republic of Congo

Objective To test the impact of a nationwide Long-Lasting Insecticidal Nets [LLINs] distribution program in the Democratic Republic of Congo [DRC] on all-cause under-five child mortality exploiting subnational variation in malaria endemicity and the timing in the scale-up of the program across provinces. Design Geospatial Impact Evaluation using a difference-in-differences approach. Setting Democratic Republic of the Congo. Participants 52,656 children sampled in the 2007 and 2013/2014 DRC Demographic and Health Surveys. Interventions The analysis provides plausibly causal estimates of both average treatment effects of the LLIN distribution campaign and geospatial heterogeneity in these effects based on malaria endemicity. It compares the under-five, all-cause mortality for children pre- and post-LLIN campaign relative to children in those areas that had not yet been exposed to the campaign using a difference-in-differences model and controlling for year- and province-fixed effects, and province-level trends in mortality. Results We find that the campaign led to a 41% decline [3.7 percentage points, 95% CI 1.3 to 6.0] in under-5 mortality risk among children living in rural areas with malaria ecology above the sample median. Results were robust to controlling for household assets and the presence of other health aid programs. No effect was detected in children living in areas with malaria ecology below the median. Conclusion The findings of this paper make important contributions to the evidence base for the effectiveness of large scale-national LLIN campaigns against malaria. We found that the program was effective in areas of the DRC with the highest underlying risk of malaria. Targeting bednets to areas with greatest underlying risk for malaria may help to increase the efficiency of increasingly limited malaria resources but should be balanced against other malaria control concerns.
How people living with diabetes in Indonesia learn about their disease: A grounded theory study

Background Diabetes education has been found to impact positively on self-management by people with diabetes although little is known about the process by which they assimilate information. The aim of this study was to generate a theory explaining the process by which people with diabetes learn about their disease in Indonesia. Methods This study employed a grounded theory methodology influenced by constructivism and symbolic interactionism. A total of twenty-eight face-to-face or telephone interviews with participants from Indonesia that included people with diabetes, healthcare professionals, health service providers and families of people with diabetes were conducted in both Indonesia and Australia. Results This study discloses a core category of Learning, choosing, and acting: self-management of diabetes in Indonesia as the basic social process of how people learn about their diabetes. The process includes five distinctive major categories. People with diabetes acted after they had received recommendations that they considered to be trustworthy. Factors that influenced their choice of recommendations to adopt are also identified. Conclusions Awareness of the complexity involved in their decision making will assist healthcare professionals to engage effectively with people living with diabetes.
Detection of ON1 and novel genotypes of human respiratory syncytial virus and emergence of palivizumab resistance in Lebanon

Respiratory syncytial virus (RSV) is a common cause of respiratory tract infections in children and immunocompromised individuals. A multi-center surveillance of the epidemiologic and molecular characteristics of RSV circulating in Lebanon was performed. The attachment (G) and fusion (F) glycoproteins were analyzed and compared to those reported regionally and globally. 16% (83/519) of the nasopharyngeal swabs collected during the 2016/17 season tested positive for RSV; 50% (27/54) were RSV-A and 50% (27/54) were RSV-B. Phylogenetic analysis of the G glycoprotein revealed predominance of the RSVA ON1 genotype, in addition to two novel Lebanese genotype variants, hereby named LBA1 and LBA2, which descended from the ON1 and NA2 RSV-A genotypes, respectively. RSV-B strains belonged to BA9 genotype except for one BA10. Deduced amino acid sequences depicted several unique substitutions, alteration of glycosylation patterns and the emergence of palivizumab resistance among the Lebanese viruses. The emergence of ON1 and other novel genotypes that are resistant to palivizumab highlights the importance of monitoring RSV globally.