Miracle-dz/UniFAR-FTUs huggingface dataset:
Metagenomic analysis of gut microbial communities from a Central Asian population

Objective Changes in the gut microbiota are increasingly recognised to be involved in many diseases. This ecosystem is known to be shaped by many factors, including climate, geography, host nutrition, lifestyle and medication. Thus, knowledge of varying populations with different habits is important for a better understanding of the microbiome. Design We therefore conducted a metagenomic analysis of intestinal microbiota from Kazakh donors, recruiting 84 subjects, including male and female healthy subjects and metabolic syndrome (MetS) patients aged 25–75 years, from the Kazakh administrative centre, Astana. We characterise and describe these microbiomes, the first deep-sequencing cohort from Central Asia, in comparison with a global dataset (832 individuals from five countries on three continents), and explore correlations between microbiota, clinical and laboratory parameters as well as with nutritional data from Food Frequency Questionnaires. Results We observe that Kazakh microbiomes are relatively different from both European and East Asian counterparts, though similar to other Central Asian microbiomes, with the most striking difference being significantly more samples falling within the Prevotella-rich enterotype, potentially reflecting regional diet and lifestyle. We show that this enterotype designation remains stable within an individual over time in 82% of cases. We further observe gut microbiome features that distinguish MetS patients from controls (eg, significantly reduced Firmicutes to Bacteroidetes ratio, Bifidobacteria and Subdoligranulum, alongside increased Prevotella), though these overlap little with previously published reports and thus may reflect idiosyncrasies of the present cohort. Conclusion Taken together, this exploratory study describes gut microbiome data from an understudied population, providing a starting point for further comparative work on biogeography and research on widespread diseases. Trial registration number ISRCTN37346212; Post-results.
Solar Irradiance Anomalies Caused by Clear-Sky Transmission Variations above Mauna Loa: 1958–99

Abstract The clear-sky transmission of the atmosphere contributes to determining the amount of solar irradiance that reaches various levels in the atmosphere, which in turn is fundamental to defining the climate of the earth. As of the end of 1999, sustained clear-sky solar transmission over the mid-Pacific, as viewed from Mauna Loa, Hawaii, reached its highest level of clarity since before the eruption of Mount Pinatubo in 1991 and appears to be continuing to increase toward baseline levels established during 1958–62 and not sustained since. This record is used to answer the question as to impact of transmission variations, which can be attributed to either upward scattering or absorption above the station, on the net solar irradiance at 3.4 km, the altitude of the isolated mountain-top observing site. Net solar irradiance at a given level describes the total solar irradiance absorbed below that level. Monthly mean net solar anomalies caused by transmission variations, relative to the 1958–62 baseline, r.
Sea‐ice draft from submarine‐based sonar: Establishing a consistent record from analog and digitally recorded data

Measurements of arctic sea‐ice draft have been taken by Navy submarines for nearly five decades. The data are in two inherently different forms, analog paper charts and digitally recorded data. “Raw” analog drafts digitized from paper charts are biased toward thicker ice by over 30 cm compared with the digital drafts. This is due to the coarser temporal resolution of the paper charts compared the digital data. We examine coincident analog and digital data to determine how they can be made equivalent in mean draft and draft distribution (the histogram of draft vs. fractional frequency of observation). Image processing techniques are used to thin vertical features in the scanned chart images; this produces a “final” analog mean draft that is essentially unbiased (2 ± 6 cm) relative to the digital mean and final draft distributions that are in good agreement.
Sedimentology, isotopes and palynology of late Holocene cores from Lake Sibaya and the Kosi Bay system (KwaZulu-Natal, South Africa)

This study documents a multi-proxy palaeoecological record spanning 2000 years for the northern KwaZulu-Natal coastal plain. Data are presented from cores recovered from Lake Sibaya and the northernmost coastal flats of the Kosi lake system. Sedimentation rates are higher in the dated Sibaya core than in the Kosi core. Carbon isotopic values from all three cores suggest that C3 plants have been the dominant biomass, with some C4 plant input at certain depths/times in the cores. Low nitrogen isotopic data in the cores suggest that nitrogen fixation processes occur in both systems. Due to high sample distance and often low pollen concentration, palynological data are restricted to a single core at Lake Sibaya. The pollen assemblages reflecting changes from greater forest abundances to greater savanna grassland abundances support results from a previous palynological study at the lake. The relative proportion of carbon in the samples decreases during the same time frame, potentially reflecting a decline in biomass volumes at the two ecosystems. Human impact is evidenced by the appearance of pine and probable maize pollen in the upper section of the core.
Improved Methods for PCA-Based Reconstructions: Case Study Using the Steig et al. (2009) Antarctic Temperature Reconstruction

AbstractA detailed analysis is presented of a recently published Antarctic temperature reconstruction that combines satellite and ground information using a regularized expectation–maximization algorithm. Though the general reconstruction concept has merit, it is susceptible to spurious results for both temperature trends and patterns. The deficiencies include the following: (i) improper calibration of satellite data; (ii) improper determination of spatial structure during infilling; and (iii) suboptimal determination of regularization parameters, particularly with respect to satellite principal component retention. This study proposes two methods to resolve these issues. One utilizes temporal relationships between the satellite and ground data; the other combines ground data with only the spatial component of the satellite data. Both improved methods yield similar results that disagree with the previous method in several aspects. Rather than finding warming concentrated in West Antarctica, the authors fi.
Methane fluxes from the littoral zone of hypereutrophic Taihu Lake, China

[1] Methane (CH4) fluxes were measured in hypereutrophic Meiliang Bay of Taihu Lake with static chambers for 1 year. The results showed that the macrophyte-covered infralittoral zones were the “hotspots” of CH4 emission in water systems. There were large temporal variations for CH4 fluxes, ranging from −1.7 to 131 mg CH4 m−2 h−1, in the macrophyte-covered littoral zone. The highest CH4 emissions occurred during the period of the summer algal bloom. The amount of CH4 flux from June to September accounted for about 50–90% of the annual fluxes. CH4 fluxes from the bare infralittoral zone (−0.2∼4.2 mg CH4 m−2 h−1) were low and close to those in the pelagic zone. The difference in CH4 fluxes between macrophyte-covered and bare infralittoral zones indicated that vegetation in the inundated area played an essential role in CH4 production. In the infralittoral zone, the redox condition (DO, Eh), temperature, and primary production controlled CH4 fluxes; these variables explained 47% of flux variation, whereas such influences were not detected in the pelagic zone.
Primer registro fósil de Tayassu pecari (Link) (Mammalia, Artiodactyla) en la Argentina

Resumen. Se da a conocer el primer registro fosil de Tayassu pecari (Link) en la Argentina, consistente en premolares y molares aislados provenientes de sedimentos de la Fm. Yupoi (Pleistoceno tardio), en la provincia de Corrientes. Desde una perspectiva paleoambiental, la presencia de este taxon (adaptado fundamentalmente a climas humedos y ambientes boscosos y selvaticos) en la Formacion Yupoi, junto con otras evidencias paleofaunisticas (registros de Dolichotis, Tolypeutes y Galea en la Formacion Toropi, y Toxodon en la Formacion Yupoi) y sedimentologicas, apoya la hipotesis de condiciones climatico-ambientales algo mas humedas que las inferidas para la Formacion Toropi (Pleistoceno medio). El desarrollo de climas mas calidos y humedos durante la sedimentacion de la Fm. Yupoi habria favorecido el ingreso de elementos brasilicos a la Mesopotamia, probablemente durante el ultimo interglacial (ca. 130 ka). Esto concuerda con la informacion paleofaunistica obtenida por diversos autores para otros sectores de la Mesopotamia, el sector occidental de Uruguay y el sur de Brasil. Abstract. FIRST FOSSIL RECORD OF TAYASSU PECARI (LINK) (MAMMALIA, ARTIODACTYLA) IN ARGENTINA. The first fossil record of Tayassu pecari (Link) in Argentina is reported, represented by isolated molars and premolars from the Yupoi Formation (late Pleistocene), Corrientes Province. From a palaeoenvironmental point of view, the presence of this taxon (mainly adapted to humid climate and woodland and forest environments) in the Yupoi Formation, together with other paleofaunistic remains (Dolichotis, Tolypeutes and Galea Meyen in the Toropi Formation, and Toxodon in the Yupoi Formation) as well as sedimentological evidences, supports the hypothesis of more humid climatic conditions than those inferred in the Toropi Formation (middle Pleistocene). The development of warmer and humid weather during the sedimentation of the Yupoi Formation may have allowed migration of “brazilian” faunas to the Mesopotamia, probably during the last interglacial (ca. 130 ka). This hypothesis is supported by the palaeofaunistic evidence obtained by other authors in other areas of the Argentine Mesopotamia, western Uruguay and southern Brazil.
Atmospheric Loading of Polycyclic Aromatic Hydrocarbons to Lake Michigan as Recorded in the Sediments

Five sediment cores from a north−south transect of Lake Michigan were collected using box cores deployed from the RV Lake Guardian and from a submersible (Johnson Sea Link II, RV Seward Johnson). The sediments, analyzed for PAHs (n = 28) and 210Pb to obtain accumulation rates and inventories of PAHs, were used to determine the role of the atmosphere in contaminant loading to Lake Michigan. The accumulation of PAHs in the sediments increased dramatically around 1900, reached a plateau around 1930−1975, and decreased slightly in recent time. Surface sediment accumulation rates and inventories for ∑PAHs (n = 17 parent), corrected for sediment focusing with 210Pb, equaled 50−70 ng cm-2 yr-1 and 5000−7000 ng cm-2, respectively. The relative abundances of individual PAH compounds from Lake Michigan sediments, PM-10 aerosol of Chicago, and a coke oven signature are statistically similar establishing a linkage between combustion sources in the south, atmospheric deposition, and sediment accumulation. Further supp.
University of Birmingham The state of mixed methods research in nursing

Aims: To consider the scope and quality of mixed methods research in nursing. Design: Focused mapping review and synthesis (FMRS). Data sources: Five purposively selected journals: International Journal of Nursing Studies , Journal of Nursing Scholarship , Journal of Advanced Nursing , Worldviews on Evidence-Based Nursing , and Journal of Mixed Methods Research . Review methods: In the target journals, titles and abstracts from papers published between 2015–2018 were searched for the words
Timing of the Jiufotang Formation (Jehol Group) in Liaoning, northeastern China, and its implications

The timing of the Jiufotang Formation remains speculative despite recent progress in the study of the Jehol Biota. In this paper we contribute to this topic with 40Ar/39Ar dating on K‐feldspar (sanidine and orthoclase) from tuffs interbedded within the fossil‐bearing shales of the Jiufotang Formation, from the upper part of the Jehol Group in Chaoyang, Liaoning, northeastern China. 40Ar/39Ar step heating analyses of K‐feldspar and the SHRIMP U‐Pb zircon data indicate that tuffs at the Shangheshou section erupted at 120.3 ± 0.7 million years ago. This result confirms an Aptian age for the Jiufotang Formation that was mainly based on biostratigraphic evidence. It also places stringent controls on the age of the fossils from the formation, providing a minimum age (120 Ma) for the four‐winged dinosaur, Microraptor, and the seed‐eating bird, Jeholornis.
How Good are we at Distinguishing Musical Temperaments?

An off-the-shelf digital organ controlled by a MIDI sequence was used to obtain recordings of an excerpt of early music that differed only in the chosen musical temperament. At the same time, the recording of slow chromatic scales made it possible to accurately identify the fundamental frequencies of the organ notes, and these frequencies were in agreement with the theoretical values of the temperaments indicated by the manufacturer of the organ. An Odd One Out test was conducted with the musical recordings to assess the extent to which listeners differentiate between the equal temperament and ﬁve other more or less unequal temperaments. Three-sound series were presented, with equal temperament twice and unequal temperament once. The middle interval always contained the equal temperament recording, the listener was asked to indicate which sound was different from it. Over forty participants, including non-musicians and early music professionals, took this test. It turned out that participants overwhelmingly discriminated between equal and other temperaments, with discrimination rates increasing when temperaments were varied in the usual ”musicologi-cal” order from least unequal to most unequal. Those who had the most difﬁculty distinguishing temperaments were non-musicians, but those who had the least were not early music professionals.
Reduced precipitation over large water bodies in the Brazilian Amazon shown from TRMM data

Tropical Rainfall Measurement Mission (TRMM) data show lower rainfall over large water bodies in the Brazilian Amazon. Mean annual rainfall (P), number of wet days (rainfall > 2 mm) (W) and annual rainfall accumulated over 3‐hour time intervals (P3hr) were computed from TRMM 3B42 data for 1998–2009. Reduced rainfall was marked over the Rio Solimões/Amazon, along most Amazon tributaries and over the Balbina reservoir. In a smaller test area, a heuristic argument showed that P and W were reduced by 5% and 6.5% respectively. Allowing for TRMM 3B42 spatial resolution, the reduction may be locally greater. Analyses of diurnal rainfall patterns showed that rainfall is lowest over large rivers during the afternoon, when most rainfall is convective, but at night and early morning the opposite occurs, with increased rainfall over rivers, although this pattern is less marked. Rainfall patterns reported from studies of smaller Amazonian regions therefore exist more widely.
Melt water driven stream and groundwater stage fluctuations on a glacier forefield (Dammagletscher, Switzerland)

In many mountain regions, large land areas with heterogeneous soils have become ice‐free with the ongoing glacier retreat. On these recently formed proglacial fields, the melt of the remaining glaciers typically drives pronounced diurnal stream level fluctuations that propagate into the riparian zone. This behaviour was measured on the Damma glacier forefield in central Switzerland with stage recorders in the stream and groundwater monitoring wells along four transects. In spite of the large groundwater stage variations, radon measurements in the near‐stream riparian zone indicate that there is little mixing between stream water and groundwater on daily time scales. At all four transects, including both losing and gaining reaches, the groundwater level fluctuations lagged the stream stage variations and were often damped with distance from the stream. Similar behaviours have been modelled using the diffusion equation in coastal regions influenced by tidal sea level variations. We thus tested the ability of such a model to predict groundwater level fluctuations in proglacial fields. The model reproduced several key features of the observed fluctuations at three of four locations, although discrepancies also arise due to non representative input data and model simplifications. Nevertheless, calibration of the model for the individual transects yielded realistic estimates of hydraulic diffusivities between the stream and groundwater monitoring wells. We conclude that studying diurnal groundwater fluctuations can provide important information about the subsurface hydrology of alpine watersheds dominated by glacier melt. Copyright © 2012 John Wiley & Sons, Ltd.
Implementation of CRISPR-Cas13a system in fission yeast and its 2 repurposing for precise RNA editing 3 4

27 In contrast to genome editing that introduces genetic changes at DNA level, 28 disrupting or editing genes’ transcripts provides a distinctive approach to perturb a 29 genetic system, offering benefits complementary to classic genetic approaches. To 30 develop a new toolset for manipulation of RNA, we first implemented a member of 31 type VI CRISPR systems, Cas13a from Leptotrichia shahii (LshCas13a) in 32 Schizosaccharomyces pombe , an important model organism employed by biologists to 33 study key cellular mechanisms conserved from yeast to humans. While it was shown 34 to knock down targeted endogenous genes’ transcripts, differently from previous 35 studies in E. coli , no collateral cleavage of other non-specific RNA by activated 36 Cas13a-crRNA complex was detected in fission yeast. Second, we engineered a 37 RNA-editing system by tethering an inactive form of LshCas13a (dCas13) to the 38 catalytic domain of human Adenosine Deaminase Act on RNA 2 (hADAR2d), which 39 was shown to be programmable with crRNA to target messenger RNAs and precisely 40 edit specific nucleotide residues. We optimized the system parameters using a 41 dual-florescence reporter and demonstrated its utility in editing of randomly selected 42 endogenous genes’ transcripts. Our engineered RNA-editing system enables a new 43 toolset for transcriptomic manipulation that is widely applicable in basic genetic and 44 biotechnological research. 45 46 47 48
University of Birmingham Pulmonary MicroRNA changes alter angiogenesis in chronic obstructive pulmonary disease and lung cancer

: The pulmonary endothelium is dysfunctional in chronic obstructive pulmonary disease (COPD), a known risk factor for lung cancer. The pulmonary endothelium is altered in emphysema, which is disproportionately affected by cancers. Gene and microRNA expression differs between COPD and non-COPD lung. We hypothesised that the alteration in microRNA expression in the pulmonary endothelium contributes to its dysfunction. A total of 28 patients undergoing pulmonary resection were recruited and endothelial cells were isolated from healthy lung and tumour. MicroRNA expression was compared between COPD and non-COPD patients. Positive ﬁndings were conﬁrmed by quantitative polymerase chain reaction (qPCR). Assays assessing angiogenesis and cellular migration were conducted in Human Umbilical Vein Endothelial Cells ( n = 3–4) transfected with microRNA mimics and compared to cells transfected with negative control RNA. Expression of miR-181b-3p, miR-429 and miR-23c (all p < 0.05) was increased in COPD. Over-expression of miR-181b-3p was associated with reduced endothelial sprouting ( p < 0.05). miR-429 was overexpressed in lung cancer as well and exhibited a reduction in tubular formation. MicroRNA-driven changes in the pulmonary endothelium thus represent a novel mechanism driving emphysema. These processes warrant further study to determine if they may be therapeutic targets in COPD and lung cancer.
Significance of nitrogen dioxide absorption in estimating aerosol optical depth and size distributions

Abstract Concurrent measurements of spectral direct beam solar radiation and columnar nitrogen dioxide (NO2) content at a suburban site, McMaster University, in Hamilton, Ontario, were used to determine the effect of NO2 absorption upon aerosol optical depths, derived size distributions, and the columnar particle number density and mass. Aerosol optical depths were reduced by 22–47, 12–25, 3–6% and 1% at wavelengths of 400, 500, 610 and 670 nm, respectively, when the gaseous absorption was included. The smaller reductions refer to average NO2 amounts (3 × 10−3 atm‐cm) and the larger to high amounts (>6 × 10−3 atm‐cm). Columnar number density was reduced by 51–95% and mass by 13–26%. At high NO2 amounts the inclusion of NO2 absorption narrowed the size distribution derived from median optical depths and changed it from bimodal to unimodal.
Adherence to preventive medications in asthmatic children at a tertiary care teaching hospital in Malaysia

Purpose: Asthma affects an estimated 300 million people worldwide. Poor adherence to prescribed preventive medications, especially among children with asthma, leads to increased mortality and morbidity. The purpose of this study was to assess the adherence and persistence levels of asthmatic children at the Universiti Kebangsaan Malaysia Medical Center (UKMMC), a tertiary care teaching hospital
research paper series

China has transitioned from being an almost autarkic economy to become the world’s largest exporter in less than three decades. Given this unique transformation, this paper investigates if the key stylized facts that characterize the behavior of ﬁrms’ exports around the world, can also describe China’s experience after joining the World Trade Organization. We ﬁnd that, consistent with received wisdom, relatively few Chinese ﬁrms engage in exporting, and those doing so, are on average, larger and more productive than their domestic counterparts. However, unlike other large and developed countries, a substantial share of Chinese exporters sell the majority of their output abroad. In fact, the distribution of Chinese exporters according to their export intensity —the share of their revenues accounted for by exports— is strikingly bimodal. In con-trast to recent work that has focused on the technological factors that explain the prevalence of high-intensity exporters, we instead concentrate on the role played by China’s heterodox trade policy regime in promoting pure exporters. Our empirical analysis suggests that trade policy has played an instrumental role in fostering a dual export sector. Notably, nine out of ten manufacturing exporters in China are eligible to enjoy ﬁscal incentives contingent on export performance.
Evolution of convex lens-shaped networks under the curve shortening flow

We consider convex symmetric lens-shaped networks in R2 that evolve under the curve shortening flow. We show that the enclosed convex domain shrinks to a point in finite time. Furthermore, after appropriate rescaling the evolving networks converge to a self-similarly shrinking network, which we prove to be unique in an appropriate class. We also include a classification result for some self-similarly shrinking networks.