Miracle-dz/UniFAR-FTUs huggingface dataset:
Health system preparedness challenges before earthquakes based on the WHO framework : a qualitative study in the Iranian context

Preparedness is a key component of disaster management. One of the main responsibilities of the health system is to improve preparedness to respond effectively to disasters. This study identified the challenges of the Iranian health system before possible earthquakes in Tehran based on the WHO framework. Materials and Methods. For this qualitative study, in-depth and semis-structured interviews with 17 health experts and authorities were conducted. Purposive sampling was performed to select the participants. The data were analyzed using framework analysis. Results. The main themes were weak communication infrastructures, inappropriate assessment of specialized training courses and lack of a clear scenario, integrated urban commanding, extrasectoral coordination, and data banks for public volunteers. Conclusion. The Iranian Ministry of Health and Medical Education and other organizations that are responsible for disasters will not be able to play an effective role in managing disasters unless National Disaster Management Organization clarifies the roles they are to play when disasters strike through a roadmap at the national level.
Autoantibodies in haemolytic uraemic syndrome (HUS)

Summary Haemolytic uraemic syndrome (HUS) is a severe disease with renal failure, microangiopathic anemia and thrombocytopenia. Several mechanisms leading to HUS have been identified, like infections with enterohaemorrhagic Escherichia coli, as well as genetic mutations of complement genes, which result in defective complement control on the surface of host cells. The complement system forms the first defense line of innate immunity and mediates the attack against foreign microorganisms. Defective regulation of this cascade results in attack of self cells and in autoimmune disease. Apparently, the alternative pathway convertase C3bBb is central for the pathophysiology of HUS as gene mutations of the components (C3 and Factor B) or of regulators (Factor H, Factor I and MCP/CD46) are observed in the genetic form of HUS. Recently, a novel mechanism leading to atypical HUS (aHUS) was identified, in form of autoantibodies that bind the complement inhibitor Factor H. Here we summarize the current concept of HUS and focus in particular on the novel subgroup of aHUS patients with IgG autoantibodies to Factor H which develop on the genetic background of CFHR1/CFHR3 deficiency, and which define a new subform termed DEAP-HUS (deficient for CFHR proteins and Factor H autoantibody positive).
Scatter and cross-talk corrections in simultaneous Tc-99m/I-123 brain SPECT using constrained factor analysis and artificial neural networks

Simultaneous imaging of Tc-99m and I-123 would have a high clinical potential in the assessment of brain perfusion (Tc-99m) and neurotransmission (I-123) but is hindered by cross-talk between the two radionuclides. Monte Carlo simulations of 15 different dual-isotope studies were performed using a digital brain phantom. Several physiologic Tc-99m and I-123 uptake patterns were modeled in the brain structures. Two methods were considered to correct for cross-talk from both scattered and unscattered photons: constrained spectral factor analysis (SFA) and artificial neural networks (ANN). The accuracy and precision of reconstructed pixel values within several brain structures were compared to those obtained with an energy windowing method (WSA). In I-123 images, mean bias was close to 10% in all structures for SFA and ANN and between 14% (in the caudate nucleus) and 25% (in the cerebellum) for WSA. Tc-99m activity was overestimated by 35% in the cortex and 53% in the caudate nucleus with WSA, but by less than 9% in all structures with SFA and ANN. SFA and ANN performed well even in the presence of high-energy I-123 photons. The accuracy was greatly improved by incorporating the contamination into the SFA model or in the learning phase for ANN. SFA and ANN are promising approaches to correct for cross-talk in simultaneous Tc-99m/I-123 SPECT.
Dating phototrophic microbial lineages with reticulate gene histories

Phototrophic bacteria are among the most biogeochemically significant organisms on Earth and are physiologically related through the use of reaction centers to collect photons for energy metabolism. However, the major phototrophic lineages are not closely related to one another in bacterial phylogeny, and the origins of their respective photosynthetic machinery remain obscured by time and low sequence similarity. To better understand the co‐evolution of Cyanobacteria and other ancient anoxygenic phototrophic lineages with respect to geologic time, we designed and implemented a variety of molecular clocks that use horizontal gene transfer (HGT) as additional, relative constraints. These HGT constraints improve the precision of phototroph divergence date estimates and indicate that stem green non‐sulfur bacteria are likely the oldest phototrophic lineage. Concurrently, crown Cyanobacteria age estimates ranged from 2.2 Ga to 2.7 Ga, with stem Cyanobacteria diverging ~2.8 Ga. These estimates provide a several hundred Ma window for oxygenic photosynthesis to evolve prior to the Great Oxidation Event (GOE) ~2.3 Ga. In all models, crown green sulfur bacteria diversify after the loss of the banded iron formations from the sedimentary record (~1.8 Ga) and may indicate the expansion of the lineage into a new ecological niche following the GOE. Our date estimates also provide a timeline to investigate the temporal feasibility of different photosystem HGT events between phototrophic lineages. Using this approach, we infer that stem Cyanobacteria are unlikely to be the recipient of an HGT of photosystem I proteins from green sulfur bacteria but could still have been either the HGT donor or the recipient of photosystem II proteins with green non‐sulfur bacteria, prior to the GOE. Together, these results indicate that HGT‐constrained molecular clocks are useful tools for the evaluation of various geological and evolutionary hypotheses, using the evolutionary histories of both genes and organismal lineages.
Psychological Climate and Work Attitudes

In this field study, the authors explore how choosing one context over another influences both research results and implications. Using both quantitative and qualitative data, the authors examine context from both an organizational and a business-unit perspective by studying relationships between five psychological climate variables and outcomes of job satisfaction, affective commitment, and intent to leave. Results show different contextual influences between the organization and two business units, suggesting that different bundles of psychological climate variables yield similar outcomes depending on the context studied. These results bolster the contention that researchers need to identify the right context in field research.
Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae)

Next‐generation sequencing allows the discovery of large numbers of single nucleotide polymorphisms (SNPs) in species where little genomic information was previously available. Here, we assembled, de novo, over 130 mb of non‐normalized cDNA using 454 pyrosequencing data from dwarf and normal lake whitefish and backcross hybrids. Our main goals were to gather a large data set of SNP markers, document their distribution within coding regions, evaluate the effect of species divergence on allele frequencies and combine results with previous genomic studies to identify candidate genes underlying the adaptive divergence of lake whitefish. We identified 6094 putative SNPs in 2674 contigs (mean size: 576 bp, range: 101–6116) and 1540 synonymous and 1734 non‐synonymous mutations for a genome‐wide non‐synonymous to synonymous substitution rate ratio (pN/pS) of 0.37. As expected based on the young age (<15 000 years) of whitefish species pair, the overall level of divergence between them was relatively weak. Yet, 89 SNPs showed pronounced allele frequency differences between sympatric normal and dwarf whitefish. Among these, SNPs in genes annotated to energy metabolic functions were the most abundant and this, in addition to previous experimental data at the gene expression and phenotypic level, brings compelling evidence that genes involved in energy metabolism are prime candidates explaining the adaptive divergence of lake whitefish species pairs. Finally, we unexpectedly identified 44 contigs annotated to transposable elements and these were predominantly composed of backcross hybrids sequences. This indicates an elevated activity of transposable elements, which could potentially contribute to the reduced fitness of hybrids previously documented.
Interstitial pneumonia with autoimmune features: a critical appraisal of the new definition

Purpose of review We review the newly formulated and published research classification criteria for interstitial pneumonia with autoimmune features and appraise these criteria in light of findings from recent investigations. Recent findings Previous studies demonstrated that interstitial pneumonia may be caused by an autoimmune process with a variety of names and criteria utilized for this entity. To standardize terminology and provide a definition for future research, a multidisciplinary task force formulated criteria by which patients with interstitial lung disease and autoimmune features might be recognized. The interstitial pneumonia with autoimmune features criteria require the presence of an interstitial pneumonia on chest imaging or surgical lung biopsy, exclusion of an alternate cause, the absence of a defined connective tissue disease and at least one feature suggestive of autoimmunity from at least two of three domains: clinical with specific extra-thoracic features, serologic with positive autoantibodies and morphologic as demonstrated by chest imaging, histopathology, or multicompartment involvement. Although recent studies provide insight into features of significance, these criteria have not undergone formal validation. Summary A uniform name and set of research criteria for interstitial pneumonia with autoimmune features may identify patients with treatment responsive interstitial lung disease and an improved prognosis. These criteria require validation before they can be applied in the clinical setting.
Changes in Gait over a 30-min Walking Session in Obese Females

Purpose This study assessed the biomechanical gait changes in obese and normal-weight female adult subjects after a commonly recommended 30-min walking session. Hip and knee adduction and extensor moments, which are the primary modulators of frontal and sagittal plane load distribution, were hypothesized to increase in obese females after a 30-min walking period, resulting in more stress across the hip and knee joint. Methods Ten obese (37.7 ± 4.8 yr of age, body mass index [BMI] = 36.1 ± 4.2 kg·m−2) and 10 normal-weight control female subjects (38.1 ± 4.5 yr of age, BMI = 22.6 ± 2.3 kg·m−2) walked 30 min continuously on the treadmill at their self-selected speed. V˙O2max was estimated using Ebbeling protocol. A three-dimensional pre- and posttreadmill gait analysis was conducted using infrared markers and force plates to calculate hip and knee moments. Results Knee extensor moments increased in both obese, pretreadmill (0.54 ± 0.28 N·m·kg−1) to posttreadmill (0.78 ± 0.43 N·m·kg−1) (P = 0.01), and control subjects, pretreadmill (0.57 ± 0.34 N·m·kg−1) to posttreadmill (0.80 ± 0.49 N·m·kg−1) (P = 0.02). Hip extensor moments decreased for both obese and control subjects. Knee adduction moments did not change in either obese or control subjects. Knee extensor and adductor moments showed good to moderate relationships with V˙O2max, but not BMI or waist circumference. Conclusion Obese and normal-weight subjects experienced an increase in knee extensor moments after 30 min of walking similarly; therefore, clinicians do not need special consideration for obese individuals when recommending 30-min walking sessions. Fitness may be the important factor in judging the implications of exercise on joint mechanics and parameters of a walking program.
Qualitative assessment of supplemental amino acid needs for growing lambs fed urea as the sole nitrogen source.

The qualitative amino acid adequacy of ruminally synthesized protein for growing lambs was evaluated by nitrogen retention responses to abomasal infusions of amino acids. The experimental animals were fed a controlled level of semipurified diet containing urea as the sole nitrogen source. Methionine alone con sistently increased nitrogen retention above isonitrogenous urea-infused controls. Lysine produced a positive nitrogen retention response only after supplemental methionine was provided. Threonine increased nitrogen retention only when infused concurrently with methionine and lysine. The data suggested that the limiting order of essential amino acids for growing lambs fed urea as the sole nitrogen source was: 1) methio nine, 2) lysine and 3) threonine. An abomasal supplement of the combination of methionine, lysine and threonine increased nitrogen retention 60% above the urea infusion control values. Tryptophan, histidine or leucine did not significantly in fluence nitrogen retention when infused with methionine, lysine and threonine. Methionine was also shown to be the first limiting essential amino acid when non specific amino nitrogen needs were supplied by glutamic acid. Plasma amino acid patterns appeared responsive to infusions and may provide an index of amino acid status in the growing lamb.
The most common sponges on the Great Barrier Reef seabed, Australia, include species new to science (Phylum Porifera)

We describe two new species amongst the most common sponges living on the seabed (inter-reef) of the Great Barrier Reef (GBR) collected during a multi-agency survey (GBR Seabed Biodiversity Project 2003–2006) of the shelf benthic biota using a trawl and dredge at 1254 sites. More than 1,200 sponge morphospecies (operational taxonomic units or OTUs) were recognised, many of which are potentially new species. This paper describes five of the most common sponges, two of which are new to science, Dercitus xanthus sp. nov. and Paracornulum fistulosum sp. nov. Taxonomic revisions of the three other most common species (Coscinoderma nardorus (Lendenfeld, 1886), Spheciospongia vagabunda (Ridley, 1884) and Xenospongia patelliformis Gray, 1858), reveal new characters not previously recorded. Extensive distribution maps are provided for these species within the GBR Marine Park. Analysis of the physical data associated with the biota revealed these species had strong preference for sand and carbonate sediments. As colonisers of the soft seabed these most prevalent species provide important habitat stabilisation, enabling succession communities to more readily establish on the seabed. This wide-scale study along the length and breadth of the GBR provides a concise and encompassing view of the distribution and diversity of the seabed benthos, and has significant implications for the conservation and management of the GBR World Heritage Area.
Remediation of total petroleum hydrocarbons using combined in-vessel composting and oxidation by activated persulfate

This study was investigated the efficiency of activated persulfate and ‎in-vessel composting for removal of total petroleum hydrocarbons. ‎Remediation by activated persulfate with ferrous sulfate as pre-treatment was done at batch system. In the chemical oxidation, various variables including persulfate concentrations (10-3000 mg/g as waste), pH (3-7), ferrous sulfate (0.5-4 mg/g as waste)and temperature (20-60°C) were studied. In the biological system, premature compost was added as an amendment. The filter cake to compost ratio were 1:0 (as control) and 1:5 to 15 (as dry basis). C: N: P ratio and moisture content were 100:5:1 and 45-60%, respectively. The results showed that acidic pH (pH=3) had high efficiency for the removal of total petroleum hydrocarbons by activated persulfate. Temperature had the significant effect during the persulfate oxidation. When ferrous sulfate was used as an activator for degradation at acidic condition and 60°C, removal efficiency increased to 47.32%. The results of biological process showed that the minimum total petroleum hydrocarbons removal in all reactors was 62 percent. The maximum and minimum removal efficiency was obtained at 1:5 (69.46%) and 1:10 (62.42%) mixing ratios, respectively. Kinetic study showed that second order kinetic model (R2>0.81) shows the best agreement with the experimental data and the rate of TPH degradation at low mixing ratio (1:3) was faster than high mixing ratio (1:15). Therefore, according to the results, in-vessel composting after pre-treatment by activated persulfate is suggested as an efficient process for degradation of total petroleum hydrocarbons.
Human milk oligosaccharides are resistant to enzymatic hydrolysis in the upper gastrointestinal tract.

BACKGROUND Human milk oligosaccharides (HMOs) show a complexity and variety not found in milk of any other species. Although progress has been made in the past 3 decades with regard to identification and structural characterization of HMOs, not much is known about the physiologic functions of HMOs. OBJECTIVE As a prerequisite for biological activity in infant metabolism, HMOs have to resist enzymatic hydrolysis in the gastrointestinal tract. To assess the extent to which selected HMOs are hydrolyzed, we carried out in vitro digestion studies using enzyme preparations of human and porcine pancreas and intestinal brush border membranes (BBMs). DESIGN Fractions of HMOs, including structurally defined isolated oligosaccharides, were digested for up to 20 h with human pancreatic juice and BBMs prepared from human or porcine intestinal tissue samples. HMOs were incubated by using a porcine pancreatic homogenate and BBMs as enzyme sources. HMOs and digestion products were identified by mass spectrometry and anion-exchange chromatography. Additionally, free D-glucose, L-fucose, and N-acetylneuraminic acid were determined enzymatically. RESULTS Whereas maltodextrin (control) was rapidly and completely hydrolyzed, neutral and acidic HMOs showed a profound resistance against pancreatic juice and BBM hydrolases. However, cleavage of most of the HMOs was achieved by using a pancreatic homogenate containing intracellular, including lysosomal, enzymes in addition to secreted enzymes. CONCLUSIONS The results of this study strongly suggest that HMOs are not hydrolyzed by enzymes in the upper small intestine. Although intact HMOs may be absorbed, we postulate that a majority of HMOs reach the large intestine, where they serve as substrates for bacterial metabolism. Therefore, HMOs might be considered the soluble fiber fraction of human milk.
A Topographical Map of the Causal Network of Mechanisms Underlying the Relationship Between Major Depressive Disorder and Coronary Heart Disease

Objective: Major depressive disorder (MDD) and coronary heart disease (CHD) are both clinically important public health problems. Depression is linked with a higher incidence of ischaemic cardiac events and MDD is more prevalent in patients with CHD. No single comprehensive model has yet described the causal mechanisms linking MDD to CHD. Several key mechanisms have been put forward, comprising behavioural mechanisms, genetic mechanisms, dysregulation of immune mechanisms, coagulation abnormalities and vascular endothelial dysfunction, polyunsaturated omega-3 free fatty acid deficiency, and autonomic mechanisms. It has been suggested that these mechanisms form a network, which links MDD and CHD. The aim of this review is to examine the causal mechanisms underlying the relationship between MDD and CHD, with the aim of constructing a topological map of the causal network which describes the relationship between MDD and CHD. Methods: The search term ‘depression and heart disease’ was entered into an electronic multiple database search engine. Abstracts were screened for relevance and individually selected articles were collated. Results: This review introduces the first topological map of the causal network which describes the relationship between MDD and CHD. Conclusions: Viewing the causal pathways as an interdependent network presents a new paradigm in this field and provides fertile ground for further research. The causal network can be studied using the methodology of systems biology, which is briefly introduced. Future research should focus on the creation of a more comprehensive topological map of the causal network and the quantification of the activity between each node of the causal network.
Dietary fiber and progression of atherosclerosis: the Los Angeles Atherosclerosis Study.

BACKGROUND Several epidemiologic studies found weak protective relations between dietary fiber intake and the risk of cardiovascular disease events. However, few of the studies addressed possible mechanisms of the effect. OBJECTIVE In the present study, we estimated relations between the progression of atherosclerosis and the intake of selective dietary fiber fractions. Mediation of the relations by serum lipids was also investigated. DESIGN Participants who were free of heart disease and aged 40-60 y were recruited into the cohort (n = 573; 47% women). The intima-media thickness (IMT) of the common carotid arteries was measured ultrasonographically at the baseline examination and at 2 follow-up examinations (n = 500), dietary intakes were assessed with six 24-h recalls (3 at baseline and 3 at the first follow-up examination), and blood samples were analyzed at baseline and at both follow-up examinations. RESULTS A significant inverse association was observed between IMT progression and the intakes of viscous fiber (P = 0.05) and pectin (P = 0.01). Correction for measurement error increased the magnitude of these estimated effects. The ratio of total to HDL cholesterol was inversely related to the intakes of total fiber (P = 0.01), viscous fiber (P = 0.05), and pectin (P = 0.01). The magnitude of the association between IMT progression and the intakes of viscous fiber and pectin was attenuated by adjustment for serum lipids. CONCLUSIONS The intake of viscous fiber, especially pectin, appears to protect against IMT progression. Serum lipids may act as a mediator between dietary fiber intake and IMT progression.