Miracle-dz/UniFAR-FTUs huggingface dataset:
Prokaryotic diversity and community composition in the Salar de Uyuni, a large scale, chaotropic salt flat

Salar de Uyuni (SdU), with a geological history that reflects 50 000 years of climate change, is the largest hypersaline salt flat on Earth and is estimated to be the biggest lithium reservoir in the world. Its salinity reaches saturation levels for NaCl, a kosmotropic salt, and high concentrations of MgCL2 and LiCl, both salts considered important chaotrophic stressors. In addition, extreme temperatures, anoxic conditions, high UV irradiance, high albedo and extremely low concentrations of phosphorous, make SdU a unique natural extreme environment in which to contrast hypotheses about limiting factors of life diversification. Geophysical studies of brines from different sampling stations show that water activity is rather constant along SdU. Geochemical measurements show significant differences in magnesium concentration, ranging from 0.2 to 2M. This work analyses the prokaryotic diversity and community structure at four SdU sampling stations, selected according to their location and ionic composition. Prokaryotic communities were composed of both Archaea (with members of the classes Halobacteria, Thermoplasmata and Nanohaloarchaea, from the Euryarchaeota and Nanohaloarcheota phyla respectively) and Bacteria (mainly belonging to Bacteroidetes and Proteobacteria phyla). The important differences in composition of microbial communities inversely correlate with Mg2+ concentration, suggesting that prokaryotic diversity at SdU is chaotropic dependent.
Luminescent chemodosimeters for bioimaging.

Yuming Yang,†,§ Qiang Zhao,‡,§ Wei Feng,† and Fuyou Li*,† †Department of Chemistry and State Key Laboratory of Molecular Engineering of Polymers and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China ‡Key Laboratory for Organic Electronics and Information Displays (KLOEID) and Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210046, P. R. China.
Impact of MODTRAN®5.1 on Atmospheric Compensation

MODTRANreg Version 5.1 includes many new capabilities tailored to enhance and facilitate atmospheric compensation. For the thermal region, the new 0.1 cm-1 band model provides the finer spectral resolution required for analysis of state-of-the-art long-wave and mid-wave hyper- and ultraspectral imagers (e.g. AIRS). A new MODTRANreg 5.1 atmospheric correction data (.acd) output file includes the specific radiative transfer quantities employed in the atmospheric compensation of solar region hyperspectral imager (e.g. MODIS, MAS) measurements; namely, DISORT-generated spectral spherical albedos and both sun-to-ground and atmospherically embedded observer-to-ground diffuse transmittances. Properly coupled observer-to-ground-to-sun path diffuse and direct transmittances are obtained when the MODTRANreg correlated-k model is used to generate the . acd output. Other MODTRANreg 5.1 features impacting both multi- and hyper-spectral atmospheric correction include the regeneration of molecular databases using HITRAN2004 with updates through January 2007, output of spectral channel brightness temperatures, input options facilitating perturbation of atmospheric profiles, and introduction of the O2 - O2 visible absorption continuum. Details of these capabilities are presented in the forward simulation mode along with applications in the reverse remote sensing mode to current satellite and aircraft sensors.
Vibrio vulnificus: new insights into a deadly opportunistic pathogen.

Vibrio vulnificus is a Gram-negative aquatic bacterium first isolated by the United States (US) Centers for Disease Control and Prevention (CDC) in 1964. This bacterium is part of the normal microbiota of estuarine waters and occurs in high numbers in molluscan shellfish around the world, particularly in warmer months. Infections in humans are derived from consumption of seafood produce and from water exposure. Vibrio vulnificus is a striking and enigmatic human pathogen, yet many aspects related to its biology, genomics, virulence capabilities and epidemiology remain elusive and poorly understood. This pathogen is responsible for over 95% of seafood-related deaths in the United States, and carries the highest fatality rate of any food-borne pathogen. Indeed, infections associated with this pathogen that progress to primary septicaemia have a similar case fatality rate to category BSL 3 and 4 pathogens, such as anthrax, bubonic plague, Ebola and Marburg fever. Interestingly, V. vulnificus infections disproportionately affect males (∼85% of cases) and older patients (> 40 years), especially those with underlying conditions such as liver diseases, diabetes and immune disorders. New insights from molecular studies and comparative genomic approaches have offered tantalising insights into this pathogen. A recent increase and geographical spread in reported infections, in particular wound cases, underlines the growing international importance of V. vulnificus, particularly in the context of coastal warming. We outline and explore here a range of current data gaps regarding this important pathogen, and provide some current thoughts on approaches to elucidate key aspects associated with this bacterium.
Cerebrovascular disease, APOE ϵ4 allele and cognitive decline in a cognitively normal population

Abstract Objectives: To investigate whether cerebrovascular disease (CVD) and apolipoprotein E (APOE) ϵ4 allele were associated with cognitive decline and whether the relationship between CVD and cognitive decline varied by APOE ϵ4 status. Methods: A total of 809 cognitively normal community-dwelling residents aged >75 years were followed to detect subjects with cognitive decline, defined as follow-up. Mini-mental state examination (MMSE) score was >10% decease of the baseline score. Logistic and multinomial logistic models were developed to estimate odds ratio (OR) and 95% confidence interval (CI) of cognitive decline related to a history of CVD and APOE ϵ4 by taking into account major potential confounders including baseline MMSE score. Results: During the mean 3.5 years of follow-up, 190 subjects experienced cognitive decline. Multi-adjusted ORs (95% CIs) of overall cognitive decline were 2.27 (1.23–4.17) for CVD and 1.69 (1.13–2.54) for APOE ϵ4, but no interaction was detected. Multinomial logistic analysis led to the CVD-related ORs of 1.42 (0.75–2.67) for cognitive decline without progression to dementia and 3.41 (1.55–7.55) for the decline progressing to dementia; similar analysis from a separate model led to adjusted OR of 2.28 (0.88–5.87; p=0.09) for the decline progressing to Alzheimer's disease. The risk effects of CVD on cognitive decline with progression to dementias were statistically significant mainly among individuals without APOE ϵ4 allele. Conclusions: CVD is a major risk factor for cognitive decline associated with progression to dementia and Alzheimer's disease. There appears no interaction between CVD and APOE ϵ4 on cognitive decline in very old people.
Identification of Syntrophobacteraceae as major acetate‐degrading sulfate reducing bacteria in Italian paddy soil

Methane is an important greenhouse gas and acetate is the most important intermediate (average 70%) of the carbon flow to CH4 in paddy fields. Sulfate (e.g., gypsum) application can reduce CH4 emissions up to 70%. However, the effect of gypsum application on acetate degradation and the microbial communities involved are unclear. Therefore, we studied acetate-dependent sulfate reduction in anoxic microcosms of Italian rice paddy soil, combining profiling of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts and rRNA based stable isotope probing (SIP) analysis. Methane production was completely inhibited by gypsum in the absence of exogenous acetate. Amended acetate (either 13 C labelled or non-labelled) was stoichiometrically coupled to sulfate reduction or CH4 production. With methyl fluoride in the presence of sulfate, added propionate and butyrate were incompletely oxidized to acetate, which transiently accumulated. After the depletion of propionate and butyrate the accumulated acetate was rapidly consumed. The relative abundance of dsrB and 16S rRNA genes and transcripts from Syntrophobacteraceae (Desulfovirga spp., Syntrophobacter spp. and unclassified Syntrophobacteraceae) increased upon addition of gypsum and acetate. Simultaneously, Syntrophobacteraceae affiliated species were significantly labelled with 13 C. In addition, minor groups like Desulforhabdus spp. , Desulfobacca spp. and Desulfotomaculum spp. substantially incorporated 13 C into their nucleic acids. The relative abundance of Desulfovibrio spp. slightly increased upon gypsum amendments. However, 13 C labelling of Desulfovibrio spp. was only moderate. In summary, Syntrophobacteraceae affiliated species were identified as the major acetotrophic sulfate reducers (SRB) in Italian paddy soil. The identification of these SRB as dominant acetate degraders well explained the scenarios of competition between SRB and acetoclastic methanogens as observed in rice paddy soil.
Functionalizing nanoparticles with biological molecules: developing chemistries that facilitate nanotechnology.

Chemistries that Facilitate Nanotechnology Kim E. Sapsford,† W. Russ Algar, Lorenzo Berti, Kelly Boeneman Gemmill,‡ Brendan J. Casey,† Eunkeu Oh, Michael H. Stewart, and Igor L. Medintz*,‡ †Division of Biology, Department of Chemistry and Materials Science, Office of Science and Engineering Laboratories, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States ‡Center for Bio/Molecular Science and Engineering Code 6900 and Division of Optical Sciences Code 5611, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States College of Science, George Mason University, 4400 University Drive, Fairfax, Virginia 22030, United States Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Sacramento, California 95817, United States Sotera Defense Solutions, Crofton, Maryland 21114, United States
Dexamethasone and lenalidomide have distinct functional effects on erythropoiesis

Corticosteroids and lenalidomide decrease red blood cell transfusion dependence in patients with Diamond-Blackfan anemia (DBA) and myelodysplastic syndrome (MDS), respectively. We explored the effects of dexamethasone and lenalidomide, individually and in combination, on the differentiation of primary human bone marrow progenitor cells in vitro. Both agents promote erythropoiesis, increasing the absolute number of erythroid cells produced from normal CD34+ cells and from CD34+ cells with the types of ribosome dysfunction found in DBA and del(5q) MDS. However, the drugs had distinct effects on the production of erythroid progenitor colonies; dexamethasone selectively increased the number of burst-forming units-erythroid (BFU-E), whereas lenalidomide specifically increased colony-forming unit-erythroid (CFU-E). Use of the drugs in combination demonstrated that their effects are not redundant. In addition, dexamethasone and lenalidomide induced distinct gene-expression profiles. In coculture experiments, we examined the role of the microenvironment in response to both drugs and found that the presence of macrophages, the central cells in erythroblastic islands, accentuated the effects of both agents. Our findings indicate that dexamethasone and lenalidomide promote different stages of erythropoiesis and support the potential clinical utility of combination therapy for patients with bone marrow failure.
Land use/cover characterizaitoin with MODIS time series data with hybrid classification mothed over Australia for 2001 and 2003

Improved and up-to-date land use/land cover (LULC) data sets are needed over the whole country of Australia to support science and policy applications focused on understanding the role and response of the LULC to environmental change. The main goal of this study was to map LULC in Australia using MODIS 250 m Normalized Difference Vegetation Index (NDVI), Land Surface Vegetation Index (LSWI) and reflectance time series data of 2000 and 2003. NDVI time-series were filtered by the Savitzky-Golay algorithm in the present study to smooth out noise. A combination of unsupervised ISODATA and a hierarchical decision tree classification were performed on 2 years 12-month time-series MODIS data. Also, Australian Vegetation Map and other land use/land cover data set were used as labeling reference during the classification process. The MODIS land cover products were evaluated using existing land use/cover data derived from Landsat TM as reference data (AUS-2000), also LULC information derived from 11 scenes of Landsat-5 TM data were used as validation data source. The overall classification accuracy was 76.4%. It turned out that our result is acceptable because the relative high resolution of MODIS data and more prior knowledge was applied.
Monitoring a tunneling in an urbanized area with Terrasar-X interferometry — Surface deformation measurements and atmospheric error treatment

We present results from a deformation monitoring to demonstrate potential and limitations of TerraSAR-X interferometry to measure vertical displacements due to the tunneling of main sewerage pipes along the river Emscher in Germany. In spite of higher sensitivity for deformation gradients the potential for deformation monitoring benefits from high spatial and temporal resolution of the TerraSAR-X data. We analyzed a large stack of TerraSAR-X stripmap scenes to derive regional pattern of vertical displacements with differential SAR Interferometry and small-scale displacements and deformation of objects (infrastructure and houses) in time series of SAR-scenes with Persistent Scatterer Interferometry (PSI). First results from PSI are promising with a great number of detected PS. We show deformation measurements with Artificial Corner Reflectors. Short-time interferograms (11 or 22 days) show high coherence for large areas and therefore are likely less infected by unwrapping errors. Atmospheric errors are important for X-Band SAR. Expected deformation in our application is in the range of mm to cm, similar to tropospheric delay features in their spatial and temporal extent. The atmospheric phase screen in PSI and stacking procedures are smoothing the nonuniform deformation history of progressing tunneling.
Transition metal-mediated synthesis of monocyclic aromatic heterocycles.

Heterocycles constitute the largest and the most diverse family of organic compounds. Among them, aromatic heterocycles represent structural motifs found in a great number of biologically active natural and synthetic compounds, drugs, and agrochemicals. Moreover, aromatic heterocycles are widely used for synthesis of dyes and polymeric materials of high value. 1 There are numerous reports on employment of aromatic heterocycles as intermediates in organic synthesis. 2 Although, a variety of highly efficient methodologies for synthesis of aromatic heterocycles and their derivatives have been reported in the past, the development of novel methodologies is in cuntinious demand. Particlularly, development of new synthetic approaches toward heterocycles, aiming at achieving greater levels of molecular complexity and better functional group compatibilities in a convergent and atom economical fashions from readily accessible starting materials and under mild reaction conditions, is one of a major research endeavor in modern synthetic organic chemistry. Transition metal-catalyzed transformations, which often help to meet the above criteria, are among the most attractive synthetic tools. Several excellent reviews dealing with transition metal-catalyzed synthesis of heterocyclic compounds have been published in literature during recent years. Many of them highlighted the use of a particular transition metal, such as gold,3 silver,4 palladium,5 copper,6 cobalt,7 ruthenium,8 iron,9 mercury,10 rare-earth metals,11 and others. Another array of reviews described the use of a specific kind of transformation, for instance, intramolecular nucleophilic attack of heteroatom at multiple C–C bonds,12 Sonogashira reaction,13 cycloaddition reactions,14 cycloisomerization reactions,15 C–H bond activation processes,16 metathesis reactions,17 etc. Reviews devoted to an application of a particular type of starting materials have also been published. Thus, for example, applications of isocyanides,18 diazocompounds,19 or azides20 have been discussed. In addition, a significant attention was given to transition metal-catalyzed multicomponent syntheses of heterocycles.21 Finally, syntheses of heterocycles featuring formation of intermediates, such as nitrenes,22 vinylidenes,23 carbenes, and carbenoids24 have also been reviewed. The main focus of the present review is a transition metal-catalyzed synthesis of aromatic monocyclic heterocycles. The organization of the review is rather classical and is based on a heterocycle, categorized in the following order: (a) ring size of heterocycle, (b) number of heteroatoms, (c) type of heterocycle, and (d) a class of transformation involved. A brief mechanistic discussion is given to provide information about a possible reaction pathway when necessary. The review mostly discusses recent literature, starting from 200425 until the end of 2011, however, some earlier parent transformations are discussed when needed.
ICT literacy, resilience and online learning self-efficacy between Chinese rural and urban primary school students

In the process of large-scale online education during the COVID-19 pandemic, students’ online learning has caused widespread public concerns. This study investigated the relationships between Chinese rural and urban primary school students’ information communications technology (ICT) literacy, student resilience, and online learning self-efficacy in a large-scale online education environment during the pandemic in China. We compared 5,037 primary school students in rural areas to 5,045 primary school students in urban areas with matching gender and grade in nine regions in China’s Guangdong province, using a survey comprising an ICT literacy scale, a student resilience scale, an online learning self-efficacy scale, and an ICT devices scale. The ICT literacy, resilience and online learning self-efficacy of primary school students in rural areas were significantly lower than those in urban areas (p < 0.01). The primary school students’ ICT literacy was significantly associated with student resilience and online learning self-efficacy. Student resilience played a mediating role between ICT literacy and online learning self-efficacy, while the rural/urban area factor moderated the relationship between ICT literacy and student resilience. These findings suggest that ICT literacy is more scarce and important for primary school students in rural areas of China than for those in urban areas. Improving ICT literacy among primary school students can enhance students’ resilience and thus improve their online learning self-efficacy, especially in rural areas.
Comammox Nitrospira Clade B is the most abundant complete ammonia oxidizer in a dairy pasture soil and inhibited by dicyandiamide and high ammonium concentrations

The recent discovery of comammox Nitrospira, a complete ammonia oxidizer, capable of completing the nitrification on their own has presented tremendous challenges to our understanding of the nitrification process. There are two divergent clades of comammox Nitrospira, Clade A and B. However, their population abundance, community structure and role in ammonia and nitrite oxidation are poorly understood. We conducted a 94-day microcosm study using a grazed dairy pasture soil amended with urea fertilizers, synthetic cow urine, and the nitrification inhibitor, dicyandiamide (DCD), to investigate the growth and community structure of comammox Nitrospira spp. We discovered that comammox Nitrospira Clade B was two orders of magnitude more abundant than Clade A in this fertile dairy pasture soil and the most abundant subcluster was a distinctive phylogenetic uncultured subcluster Clade B2. We found that comammox Nitrospira Clade B might not play a major role in nitrite oxidation compared to the role of canonical Nitrospira nitrite-oxidizers, however, comammox Nitrospira Clade B is active in nitrification and the growth of comammox Nitrospira Clade B was inhibited by a high ammonium concentration (700 kg synthetic urine-N ha–1) and the nitrification inhibitor DCD. We concluded that comammox Nitrospira Clade B: (1) was the most abundant comammox in the dairy pasture soil; (2) had a low tolerance to ammonium and can be inhibited by DCD; and (3) was not the dominant nitrite-oxidizer in the soil. This is the first study discovering a new subcluster of comammox Nitrospira Clade B2 from an agricultural soil.
Editorial: Model-informed drug development and evidence-based translational pharmacology

Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Melbourne, VIC, Australia, Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Fudan University, Shanghai, China, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China, Department of Drug Discovery and Development, Harrison College of Pharmacy, Auburn University, Auburn, AL, United States, Department of Pharmacology, School of Pharmaceutical Science, Shandong University, Jinan, China, Malaya Translational and Clinical Pharmacometrics Group, Faculty of Pharmacy, University of Malaya, Kuala Lumpur, Malaysia, Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, University of Malaya, Kuala Lumpur, Malaysia, Integrated Drug Development, Certara, NJ, United States
Paraoxonase 1 gene (Gln 192 -Arg) polymorphism and the risk of coronary artery disease in type 2 diabetes mellitus

Background: Paraoxonase 1 (PON1) is reported to have an antioxidant and cardioprotective properties. Recently, an association of glutamine (Gln) or (type A)/arginine (Arg) or (type B) polymorphism at position 192 of PON1 gene has been suggested with coronary artery disease (CAD) among patients with diabetes mellitus (DM). However, conflicting results have also been reported. Objectives: To investigate the relationship between PON1 gene (Gln192-Arg) poly-morphism and the presence, extent and severity of CAD in type 2 DM. Methods: The study comprised 180 patients recruited from those undergoing coronary angiography for suspected CAD, who were divided according to the presence or absence of CAD and DM into 4 groups; Group I (n = 40 patients) nondiabetic subjects without CAD, Group II (n = 45 patients) diabetic patients without CAD, Group III (n = 47 patients) non diabetic patients with CAD and Group IV (n = 48 patients) diabetic patients with CAD. PON1 (Gln192-Arg) genotype was assessed using polymerase chain reaction (PCR) followed by AlwI digestion. Results: The frequency of Gln allele (Type A) was significantly higher in group I and group II compared to group III and group IV (62.5%, 60% vs 38.3%, 31.25% respectively, p 100 mg/dL [OR 4.31, CI (1.25 - 12.5), P < 0.001], high density lipoprotein (HDL) cholesterol <40 mg/dL [OR 5.11, CI (1.79 - 16.33), P < 0.001] and PON1 192 Arg allele [OR 4.62, CI (1.67 - 13.57), P < 0.001] were significantly independent predictors of CAD. Conclusion: Arg allele of PON1 192 gene polymorphism is an independent risk factor for CAD and it is associated not only with the presence of CAD but also with its extent and severity and its impact is clearly more pronounced in diabetic patients.