Miracle-dz/UniFAR-FTUs huggingface dataset:
Linkages between lake shrinkage/expansion and sublacustrine permafrost distribution determined from remote sensing of interior Alaska, USA

Linkages between permafrost distribution and lake surface‐area changes in cold regions have not been previously examined over a large scale because of the paucity of subsurface permafrost information. Here, a first large‐scale examination of these linkages is made over a 5150 km2 area of Yukon Flats, Alaska, USA, by evaluating the relationship between lake surface‐area changes during 1979–2009, derived from Landsat satellite data, and sublacustrine groundwater flow‐path connectivity inferred from a pioneering, airborne geophysical survey of permafrost. The results suggest that the shallow (few tens of meters) thaw state of permafrost has more influence than deeper permafrost conditions on the evolving water budgets of lakes on a multidecadal time scale. In the region studied, these key shallow aquifers have high hydraulic conductivity and great spatial variability in thaw state, making groundwater flow and associated lake level evolution particularly sensitive to climate change owing to the close proximity of these aquifers to the atmosphere.
Coprolite morphotypes from the Upper Cretaceous of Sweden: novel views on an ancient ecosystem and implications for coprolite taphonomy

Coprolites (fossilized faeces) are common, yet previously unreported, elements in the Campanian (Upper Cretaceous) shallow-marine strata of Asen, southern Sweden. They are associated with a diverse vertebrate fauna and comprise at least seven different morphotypes that suggest a variety of source animals. Their faecal origin is corroborated by several lines of evidence, including chemical composition (primarily calcium phosphate), external morphology and nature of the inclusions. Preservation in a fossil coquina, interpreted as a taphocoenosis, suggests early lithification promoted by rapid entombment. This would have prevented disintegration of the faecal matter and facilitated transportation and introduction to the host sediment. The coprofabrics can generally be correlated to specific gross morphologies, supporting a morphology-determined coprolite classification. Moreover, having been deposited under presumably comparable taphonomic conditions, variations in coprofabrics infer differences in diet and/or digestive efficiency of the host animal. Size and morphology of the coprolites imply that most, if not all, were produced by vertebrates and the largest specimens infer a host animal of considerable size. Two spiralled coprolite morphotypes yield bone fragments and scales of bony fish, suggesting that the producers were piscivorous sharks. Other coprolites contain inclusions interpreted as the remains of shelled invertebrates, thus indicating that they may have derived from durophagous predators and/or scavengers. The occurrence of small scrapes, tracks and traces on several specimens suggest manipulation of the faeces by other (presumably coprophagous) organisms after deposition. The collective data from the Asen coprolites provide new insights into a shallow-water Late Cretaceous marine ecosystem hitherto known solely from body fossils. (Less)
Third Report on Chicken Genes and Chromosomes 2015

Opening insights into new technologies in avian genomics The chicken has long been a model organism for genetic and developmental studies. It is now beginning to take its place as a model genome, opening up the fields of phylogenetics and comparative genomics like never before. This report comes at a time of huge technological advances (particularly in sequencing methodologies) and summarizes the current efforts to complete the gaps in the genome. It describes the progress that has been made in genomic annotation, particularly with respect to noncoding RNAs and genetic variants. Reviews of comparative genomics, avian evolution and sex determination are included as well as transcriptomic case studies and developments in epigenetic studies. The Third Report on Chicken Genes and Chromosomes also features the National Avian Research Facility and how it has developed into a resource for the study of avian biology, genetics, infection and disease. In this volume researchers interested in genetics, genomics and evolution will find detailed information that has not been available until now.
Ice streaming in the Laurentide Ice Sheet: A first comparison between data‐calibrated numerical model output and geological evidence

Despite the importance of rapidly‐flowing ice streams to ice sheet mass balance, their incorporation into numerical ice sheet models is a major scientific challenge. This introduces large uncertainties in model output and inhibits a more complete understanding of the role of ice streams in overall ice sheet stability. Recent computational advances have enabled more realistic representations of ice streaming but few studies have attempted to compare model output against known locations of ice streams. This paper compares predictions of ice streaming derived from a large ensemble analysis of a Glacial Systems Model of the Laurentide Ice Sheet against independent geological evidence compiled from previously published studies. Although the precise dating of paleo‐ice stream locations is problematic, our analysis includes comparisons at six different time‐steps (18 to 10 cal ka BP) during deglaciation. Results indicate that the model is successful in predicting all of the major marine‐terminating ice streams but there is mixed success in simulating terrestrial ice streams in the right place and at the right time, which is vital in guiding future model development. The model also reveals that whilst some ice streams persist throughout deglaciation the focus of mass loss associated with ice streaming switches through time with dynamic changes in ice stream catchments and tributaries. This implies that major changes in ice stream activity are to be expected in a deglaciating ice sheet, with important implications for contemporary ice sheet dynamics.
A New Surgical Technique of Combination Retroperitoneal with Transperitoneal Laparoscopic Nephroureterectomy in a Single Position and Comparative Outcomes

Background: The traditional surgical treatment for upper urinary tract urothelial carcinoma (UTUC) is time-consuming owing to changing the surgical position and larger surgical trauma because of open surgery in handling the distal ureter. Therefore, we created a new surgical technique of combination retroperitoneal with transperitoneal (CRT) laparoscopic nephroureterectomy (LNU) in a single position and here report our early outcomes. Methods: From January 2017 to December 2019, a total of 106 patients underwent LNU by a single surgeon at our department, of whom 50 patients underwent standard technique and 56 patients underwent CRT technique. Relevant clinical data were collected including each patient ’ s characteristics, surgical outcomes, and follow-up results. A comparative analysis between standard LNU cases and CRT LNU cases was performed. Results: LNU was performed successfully on all 106 patients. There was no signi ﬁ cant difference in patients ’ characteristics. Compared to the standard group, patients in the CRT group had shorter operative time ( P =0.001), less estimated blood loss (EBL) ( P <0.001), lower visual analogue scale (VAS) pain score ( P =0.020) and less scarring ( P =0.013). The median time of surgical drain stay decreased from 5 to 2 days ( P =0.004) and median hospital stay after surgery decreased from 5 to 3 days ( P =0.001). The complication rates did not show statistical differences between the two groups within the ﬁ rst 30 days postoperatively ( P =0.263). For the long-term complications, the incidence of abdomen bulge or incisional hernia in the CRT group was less than that in the standard group ( P <0.001). Conclusion: The CRT technique, which combines both the advantages of retroperitoneal and transperitoneal approaches, is a more minimally invasive, simpli ﬁ ed and effective way to perform the LNU.
Composition and evolution of fluids during skarn development in the Monte Capanne thermal aureole, Elba Island, central Italy

We describe the chemistry of the fluids circulating during skarn formation by focusing on fluids trapped in calcsilicate minerals of the inner thermal aureole of the Late Miocene Monte Capanne intrusion of western Elba Island (central Italy). Primary, CH4-dominant, C-O-H-S-salt fluid inclusions formed during prograde growth of the main skarn-forming mineral phases: grossular ⁄andradite and vesuvianite. The variable phase ratios attest to heterogeneous entrapment of fluid, with co-entrapment of an immiscible hydrocarbon‐brine mixture. Chemical elements driving skarn metasomatism such as Na, K, Ca, S and Cl, Fe and Mn were dominantly partitioned into the circulating fluid phase. The high salinity (apparent salinity between 58 and 70 wt% NaCl eq.) and the C-component of the fluids are interpreted as evidence for a composite origin of the skarn-forming fluids that involves both fluids derived from the crystallizing intrusion and contributions from metamorphic devolatilization. Oxidation of a Fe-rich brine in an environment dominated by fluctuation in pressure from lithostatic to hydrostatic conditions (maintained by active crack-sealing) contributed to skarn development. Fluid infiltration conformed to a geothermal gradient of about 100� Ck m )1 , embracing the transition from high-temperature contact metamorphism and fluid-assisted skarn formation (at ca 600� C) to a barren hydrothermal stage (at ca 200� C).
Neurology of the cryopyrin‐associated periodic fever syndrome

The cryopyrin‐associated periodic fever syndrome (CAPS) is an autosomal dominant autoinflammatory disorder caused by mutations in the NLRP3 gene and is typified by recurrent episodes of systemic inflammation resulting in fever, urticarial rash and arthralgia. In addition to these systemic aspects, CAPS has multiple neurological manifestations. The largest case series to date is presented focusing on the neurological features of this disorder.
Total C and N storage and organic C pools of a Red-Yellow Podzolic under conventional and no tillage at the Atlantic Forest Zone, south-eastern Brazil

A 15-year experiment in a clayey Red-Yellow Podzolic in the tropical highlands of Vicosa, Brazil, was studied in 2000, aiming to evaluate the impact of different management systems (no tillage, disk plowing, heavy scratcher + disk plowing, and heavy scratched) on the total organic carbon (TOC), total nitrogen (TN), and several organic carbon pools. A natural forest, adjacent to the experimental area, was used as reference. The greatest TOC and TN as well as microbial biomass C (CMB), light fraction C (CFL), and labile organic carbon (CL) stocks were observed in the Atlantic Forest, compared with all other systems. The long-term cultivation (±70 years) of this area, prior to the installation of the experiment, has led to soil degradation, slowing the C recovery. No tillage had the higher C and N stocks and greater CL pool at the surface (0–10 cm), indicating improvement in soil nutrient status, although none of the systems presented potential to sequester C-CO2. Sustainable tropical agricultural systems should involve high residue input and conservative soil management in order to act as a C-CO2 sink. The C stocks in the CMB, CFL, and CL compartments were more reduced in relation to the natural vegetation with higher intensity management than the TOC stocks. This result indicates that these C compartments are more sensitive to changes in the soil management.
Baimazhai, Yunnan Province, China: A Hydrothermally Modified Magmatic Nickel-Copper-PGE Sulfide Deposit

The Baimazhai Ni-Cu-PGE (platinum-group-elements) sulfide deposit, southeast Yunnan Province, is hosted in mafic-ultramafic intrusions of the Permian Emeishan large igneous province, with which it is temporally and genetically related. The typical orthomagmatic sulfide ores of the Baimazhai deposit locally exhibit peculiar textural features, and are intimately associated with hydrothermal minerals such as biotite, amphibole, and chlorite. This suggests that magmatic sulfide ores were subjected to hydrothermal alteration and subsequent redistribution, resulting in enrichment in Cu, Pd, and Au. Whole-rock 40Ar-39Ar age data yielded plateau ages of about 160-170 Ma, at odds with the established Permian age of the host intrusions and the Emeishan large igneous province. We interpret these younger ages as due to thermal resetting during post-Permian tectonothermal events such as the Jurassic Cretaceous Yanshanian orogeny, and propose a model in which tectonic movements and hydrothermal fluids modified the pre-existing magmatic sulfides. Given the high degree of overprinting, we suggest two possible scenarios: (1) sulfide disseminations that surround the massive magmatic ores are the result of deformation and hydrothermal alteration; and (2) both magmatic massive and disseminated sulfides were produced initially, in which case the scale and metasomatic remobilization would have been smaller, but still detectable.
Do I misconstrue? Sarcasm detection, emotion recognition, and theory of mind in Huntington disease.

OBJECTIVE Emotion recognition has been widely studied in Huntington disease (HD), but only a few studies have investigated more complex social cognition and, when so, exclusively in manifest HD. The present study sought to investigate social-cognitive functions in a large, consecutive cohort of premanifest and manifest HD gene expansion carriers using tests assessing sarcasm detection, theory of mind (ToM), and emotion recognition. METHOD Fifty manifest, 50 premanifest HD gene expansion carriers, and 39 at risk gene expansion negative healthy controls were included. All participants were tested with sarcasm detection, ToM, and emotion recognition tasks. Between-group comparisons of test performances and correlation analyses of test performances and disease burden scores were made. RESULTS Group comparisons showed significant differences in performances on the social-cognitive tests between manifest HD gene expansion carriers and healthy controls, but differences in performances between premanifest HD gene expansion carriers and healthy controls were not statistically significant. Correlation analysis showed that the worse test performances were associated with higher disease burden scores in all HD gene expansion carriers. CONCLUSION Our findings support a theory of impaired social-cognitive functions in the early stages of HD. Test performances decreased with increasing disease burden in all HD gene expansion carriers, suggesting that social-cognitive tests may be useful for tracking disease progression. Simple emotion recognition tasks are just as sensitive for measuring social-cognitive deficits as more complex measures, but knowledge of the quality of social-cognitive impairments in HD can be of great importance to both patients and caregivers.
TMEM184B promotes pruriceptive neuron specification to allow itch sensitivity

Nociceptive and pruriceptive neurons in the dorsal root ganglia (DRG) convey sensations of pain and itch to the spinal cord, respectively. One subtype of mature DRG neurons, marked by Somatostatin ( Sst ) expression, is responsible for sensing mediators of acute itch and atopic dermatitis, including the cytokine IL-31. How itch-sensitive (pruriceptive) neurons are specified is unclear. Here we show that Tmem184b , a gene with roles in axon degeneration and nerve terminal maintenance, is required for the expression of a large cohort of itch receptors, including those for IL-31, Leukotriene C4, and Histamine. Mice lacking Tmem184b fail to respond to IL31, but maintain normal responses to pain and mechanical force, indicating a specific behavioral defect in pruriception. Lineage-tracing studies using Sst -driven Cre recombinase show a loss of pruriceptive neurons in Tmem184b -mutant mice, suggesting a defect in neuron subtype specification. We identify an early failure of proper Wnt-dependent transcriptional signatures and signaling components in Tmem184b mutant mice that can explain the improper DRG neuronal subtype specification. Lentiviral re-expression of Tmem184b in mutant embryonic neurons restores Wnt signatures, whereas re-expression of Tmem184b in adult DRG fails to restore itch responses. Together, these data demonstrate that Tmem184b promotes adult somatosensation through developmental Wnt signaling and specification of pruriceptive neurons. Our data illuminate a new key regulatory step in the processes controlling the establishment of diversity in the somatosensory system. , nociceptive terminals in the epidermis show swollen endings, and mice show deficits in broad measures of sensorimotor behavior (Bhattacharya et al., 2016). Here we show that Tmem184b controls the expression of a large cohort of sensory receptors in the DRG, specifically those in the NP3/C2 population mediating pruriception. We found specific behavioral defects in acute itch, but not pain, when Tmem184b is absent, showing that Tmem184b is required for proper pruriception. Tmem184b loss causes a reduction in the total number of NP3/C2 neurons in adults. We show that Tmem184b is required in embryonic neurons for expression of critical drivers of sensory neurogenesis, suggesting an early role for Tmem184b in sensory development. Rescue experiments in both adults and embryos support a primary role for Tmem184b in pruriceptive neuron specification through control of Wnt signaling. Our data identify a critical role for Tmem184b in the establishment of the neurons responsible for primary pruriception.
Bibliometric study of ‘overviews of systematic reviews’ of health interventions: Evaluation of prevalence, citation and journal impact factor

Overviews synthesising the results of multiple systematic reviews help inform evidence‐based clinical practice. In this first of two companion papers, we evaluate the bibliometrics of overviews, including their prevalence and factors affecting citation rates and journal impact factor (JIF). We searched MEDLINE, Epistemonikos and Cochrane Database of Systematic Reviews (CDSR). We included overviews that: (a) synthesised reviews, (b) conducted a systematic search, (c) had a methods section and (d) examined a healthcare intervention. Multivariable regression was conducted to determine the association between citation density, JIF and six predictor variables. We found 1218 overviews published from 2000 to 2020; the majority (73%) were published in the most recent 5‐year period. We extracted a selection of these overviews (n = 541; 44%) dated from 2000 to 2018. The 541 overviews were published in 307 journals; CDSR (8%), PLOS ONE (3%) and Sao Paulo Medical Journal (2%) were the most prevalent. The majority (70%) were published in journals with impact factors between 0.05 and 3.97. We found a mean citation count of 10 overviews per year, published in journals with a mean JIF of 4.4. In multivariable analysis, overviews with a high number of citations and JIFs had more authors, larger sample sizes, were open access and reported the funding source. An eightfold increase in the number of overviews was found between 2009 and 2020. We identified 332 overviews published in 2020, which is equivalent to one overview published per day. Overviews perform above average for the journals in which they publish.
Assessing the Mutagenic Potential of Surface Sediments from Beijing Guanting Reservoir to Salmonella typhimurium

Mutagenicity of organic extracts from Beijing Guanting Reservoir sediments was investigated with TA98 and TA100 of Salmonella typhimurium. TA98 and TA100 were employed to detect frameshift mutation and base-pair substitution mutation, respectively. For TA100, no positive result was found, while TA98 was more sensitive and pro-mutagenic frameshift mutagens were mainly detected in sediments. Sediments from northern and southern Guanting Reservoir were at potential mutagenic risk. No mutagenicity was found in the sediments from the entrance of the tributaries, but strong mutagenicity was observed in the sediments from the outlet of the reservoir. Chemical analysis was also performed, and poor correlation was found between mutagenicity and organochlorine pesticides (OCPs). However, significant positive correlation was found for polycyclic aromatic hydrocarbons (PAHs) (r = 0.603–0.946), which showed that PAHs were dominated for the tested mutagenicity in the sediments. Polychlorinated biphenyls (PCBs) might induce mutagenicity or promote the mutagenicity of other substances.
Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome

Significance Transposable elements (TEs) are genetic units that can selfishly propagate in a host genome. Despite often being considered “junk,” TEs can occasionally acquire useful functions such as regulating expression of nearby host genes. Here, we study gibbons, small apes whose genome contains a unique TE called LAVA (LINE-AluSz-VNTR-AluLIKE). We present evidence indicating that several LAVA insertions function as gene regulatory elements in the gibbon genome. Two of these insertions were also favored/preserved by natural selection, further indicating their functional importance for gibbons. Both of these LAVA elements were found inside genes that facilitate correct repair of DNA breaks, suggesting that LAVA’s incorporation in these genes may have influenced the regulation of biological processes that are crucial for maintaining genome integrity. Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. The LAVA retrotransposon is thought to have played a role in the emergence of the highly rearranged structure of the gibbon genome by disrupting transcription of cell cycle genes. In this study, we investigated whether LAVA may have also contributed to the evolution of gene regulation by adopting enhancer function. We characterized fixed and polymorphic LAVA insertions across multiple gibbons and found 96 LAVA elements overlapping enhancer chromatin states. Moreover, LAVA was enriched in multiple transcription factor binding motifs, was bound by an important transcription factor (PU.1), and was associated with higher levels of gene expression in cis. We found gibbon-specific signatures of purifying/positive selection at 27 LAVA insertions. Two of these insertions were fixed in the gibbon lineage and overlapped with enhancer chromatin states, representing putative co-opted LAVA enhancers. These putative enhancers were located within genes encoding SETD2 and RAD9A, two proteins that facilitate accurate repair of DNA double-strand breaks and prevent chromosomal rearrangement mutations. Co-option of LAVA in these genes may have influenced regulation of processes that preserve genome integrity. Our findings highlight the importance of considering lineage-specific TEs in studying evolution of gene regulatory elements.