Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of a Fourier transform IR system for measurements of N2O fluxes using micrometeorological methods, an ultralarge chamber system, and conventional field chambers

Measurements of the sources and sinks of biogenic trace gases such as N2O and CH4 from terrestrial ecosystems are important in explaining and predicting the influence of these gases on global warming. Because of their biological origins the fluxes of these gases often show high spatial and temporal variation. Traditional methods of flux measurement use different types of field chambers or micrometeorologically based methods. These methods have several shortcomings and may not always be applicable to flux measurements of trace gases such as N2O or CH4. Fourier transform infrared (FTIR) spectroscopy, due to its path-integrating and multicomponent nature, shows unique potential for the measurement of fluxes of greenhouse gases from various ecosystems. To assess this potential, we have used a medium resolution (1 cm−1) FTIR spectrometer to test its suitability for area-integrated measurements, simultaneous multicomponent measurements, and continuous real-time measurements of trace gas fluxes. We have tested three different configurations: a conventional field chamber where the FTIR is used to continuously and simultaneously monitor the concentration changes of several gases, a megachamber method using a large tent as field chamber with the FTIR optical path within the chamber, and a micrometeorological flux gradient method. The three configurations are described and discussed and their performance is demonstrated in measurements of fluxes of N2O from a fertilized grassland and CH4 from a forest soil.
Inter-species association mapping links splice site evolution to METTL16 and SNRNP27K

Eukaryotic genes are interrupted by introns that are removed from transcribed RNAs by splicing. Patterns of splicing complexity differ between species, but it is unclear how these differences arise. We used inter-species association mapping with Saccharomycotina species to correlate splicing signal phenotypes with the presence or absence of splicing factors. Here, we show that variation in 5’ splice site sequence preferences correlate with the presence of the U6 snRNA N6-methyladenosine methyltransferase METTL16 and the splicing factor SNRNP27K. The greatest variation in 5’ splice site sequence occurred at the +4 position and involved a preference switch between adenosine and uridine. Loss of METTL16 and SNRNP27K orthologs, or a single SNRNP27K methionine residue, was associated with a preference for +4 U. These findings are consistent with splicing analyses of mutants defective in either METTL16 or SNRNP27K orthologs and models derived from spliceosome structures, demonstrating that inter-species association mapping is a powerful orthogonal approach to molecular studies. We identified variation between species in the occurrence of two major classes of 5’ splice sites, defined by distinct interaction potentials with U5 and U6 snRNAs, that correlates with intron number. We conclude that variation in concerted processes of 5’ splice site selection by U6 snRNA is associated with evolutionary changes in splicing signal phenotypes.
Pleistocene evolution: Northern hemisphere ice sheets and North Atlantic Ocean

We analyze five high-resolution time series spanning the last 1.65 m.y. : benthic foraminiferal δ18O and δ13O, percent CaCO3, and estimated sea surface temperature (SST) at North Atlantic Deep Sea Drilling Project site 607 and percent CaCO3 at site 609. Each record is a multicore composite verified for continuity by splicing among multiple holes. These climatic indices portray changes in northern hemisphere ice sheet size and in North Atlantic surface and deep circulation. By tuning obliquity and precession components in the δ18O record to orbital variations, we have devised a time scale (TP607) for the entire Pleistocene that agrees in age with all K/Ar-dated magnetic reversals to within 1.5%. The Brunhes time scale is taken from Imbrie et al. [1984], except for differences near the stage 17/16 transition (0.70 to 0.64 Ma). All indicators show a similar evolution from the Matuyama to the Brunhes chrons: orbital eccentricity and precession responses increased in amplitude; those at orbital obliquity decreased. The change in dominance from obliquity to eccentricity occurred over several hundred thousand years, with fastest changes around 0.7 to 0.6 Ma. The coherent, in-phase responses of δ18O, δ13O, CaCO3 and SST at these rhythms indicate that northern hemisphere ice volume changes have controlled most of the North Atlantic surface-ocean and deep-ocean responses for the last 1.6 m.y. The δ13O, percent CaCO3, and SST records at site 607 also show prominent changes at low frequencies, including a prominent long-wavelength oscillation toward glacial conditions that is centered between 0.9 and 0.6 Ma. These changes appear to be associated neither with orbital forcing nor with changes in ice volume.
Identification and validation of obesity related genes signature based on microenvironment phenotypes in prostate adenocarcinoma

Background: The role of obesity related genes (ORGs) in the immune checkpoint inhibitors (ICIs) treatment of prostate adenocarcinoma (PRAD) has not yet been proved by research. Methods: We comprehensively evaluated the ORGs patterns in PRAD based on tumor microenvironment (TME) phenotypes and immunotherapy efficacies. Then we constructed a ORGs risk score for prognosis and a ORGs signature for accurate prediction of TME phenotype and immunotherapy efficacy in order to evaluate individual patients. Results: Two distinct ORGs patterns were generated. The two ORGs patterns were consistent with inflammatory and non-inflammatory TME phenotypes. ORGs patterns had an important role for predicting immunotherapy efficacies. Next, we constructed a ORGs risk score for predicting each patient’s prognosis with high performance in TCGA-PRAD. The ORGs risk score could be well verified in the external cohorts including GSE70769 and GSE21034. Then, we developed a ORGs signature and found it was significantly positively correlated with tumor-infiltrating lymphocytes in TCGA-PRAD. We found that each patient in the high-risk ORGs signature group represented a non-inflamed TME phenotype on the single cell level. The patients with high ORGs signature had more sensitivity to immunotherapy. And those ORGs were verified. Conclusions: ORGs pattern depicts different TME phenotypes in PRAD. The ORGs risk score and ORGs signature have an important role for predicting prognosis and immunotherapy efficacies.
Kinematics of subduction and subduction-induced flow in the upper mantle

[1] Results of fluid dynamical experiments are presented to model the kinematics of lithospheric subduction in the upper mantle. The experiments model a dense high-viscosity plate (subducting lithosphere) overlying a less dense low-viscosity layer (upper mantle). The overriding lithosphere is not incorporated. Several important features of slab behavior were investigated including the temporal variability of hinge line migration, the kinematic behavior of the slab and the subduction-induced upper mantle flow. Both fixed and free trailing edge boundary conditions of the subducting plate were investigated. Results show that hinge line retreat is a natural consequence of subduction of a negatively buoyant slab. The migration rate increases until the slab approaches the upper-lower mantle discontinuity, resulting in a decrease in migration rate followed by a renewed increase and finally approaching a steady state. Slab retreat results in mantle flow, with material initially located underneath the slab flowing around the lateral slab edges toward the mantle wedge. Experimental results indicate that all rollback-induced flow occurs around the lateral slab edges, forcing the hinge line to attain a convex shape toward the direction of retreat. No signs for poloidal flow underneath the slab tip have been detected. Only a small component of toroidal-type flow was observed underneath slanting slab tips. For a fixed trailing edge, the slab does not sink vertically downward, but sinks at an angle in a regressive manner. For a free trailing edge, slab sinking is oriented more vertically while the surface part of the subducting plate is pulled into the subduction zone.
Impact of informal care on the mental health of caregivers during the COVID-19 pandemic

Abstract Background Informal care can affect the mental health of caregivers. The COVID-19 pandemic precipitated many people into informal care. Little is known about the longitudinal effect of informal care throughout the pandemic. We investigate changes in mental health in relation to changes in informal care between July 2020 and September 2021. Methods Using data from Understanding Society, we applied fixed-effects modelling to assess mental health variations associated with changes in caregiving among 13 557 participants (50 430 observations). Hours of weekly care were categorized as 0, 1–19, ≥20. Mental health was measured using the General Health Questionnaire (GHQ-12) as a continuous score and a binary indicator. Main analyses were stratified by gender. Results Compared to when delivering 0 hours care/week, the GHQ-12 scores of women providing care for 1–19 hours/week were 0.46 points higher (95%CI: −0.11, 1.09), while their mental health scores were 0.99 higher (95%: 0.08, 1.90) when caring for ≥20 hours/week. Changes on the binary GHQ-12 measure were only evident for women when providing ≥20 hours of weekly care. These changes were not substantial among men. Conclusion Informal care adversely impacted the mental health of women carers during the COVID-19 pandemic. Support programmes for informal carers should focus on alleviating caregiving loads in women.
Collective motion in hcp-Fe at Earth's inner core conditions.

Earth's inner core is predominantly composed of solid iron (Fe) and displays intriguing properties such as strong shear softening and an ultrahigh Poisson's ratio. Insofar, physical mechanisms to explain these features coherently remain highly debated. Here, we have studied longitudinal and shear wave velocities of hcp-Fe (hexagonal close-packed iron) at relevant pressure-temperature conditions of the inner core using in situ shock experiments and machine learning molecular dynamics (MLMD) simulations. Our results demonstrate that the shear wave velocity of hcp-Fe along the Hugoniot in the premelting condition, defined as T/Tm (Tm: melting temperature of iron) above 0.96, is significantly reduced by ~30%, while Poisson's ratio jumps to approximately 0.44. MLMD simulations at 230 to 330 GPa indicate that collective motion with fast diffusive atomic migration occurs in premelting hcp-Fe primarily along [100] or [010] crystallographic direction, contributing to its elastic softening and enhanced Poisson's ratio. Our study reveals that hcp-Fe atoms can diffusively migrate to neighboring positions, forming open-loop and close-loop clusters in the inner core conditions. Hcp-Fe with collective motion at the inner core conditions is thus not an ideal solid previously believed. The premelting hcp-Fe with collective motion behaves like an extremely soft solid with an ultralow shear modulus and an ultrahigh Poisson's ratio that are consistent with seismic observations of the region. Our findings indicate that premelting hcp-Fe with fast diffusive motion represents the underlying physical mechanism to help explain the unique seismic and geodynamic features of the inner core.
Effect on the Skin Microbiota of Oral Minocycline for Rosacea

In the rosacea an unstable skin microbiota is significant for disease progression. However, data on the influence on the skin microbiota of treatment with systemic antibiotics are limited. This single-arm trial recruited patients with rosacea. Oral minocycline 50 mg was administered twice daily for 6 weeks. The lesions on the cheek and nose were sampled for 16S rRNA amplicon sequencing and metagenomic sequencing at baseline, 3 weeks and 6 weeks of treatment. Physiological parameters were detected using non-invasive instruments. After treatment, distribution of the Investigator Global Assessment scores changed significantly. For the skin microbiota, a notable increase in α-diversity and a shift of structure were observed after treatment. Treatment was accompanied by a reduction in the relative abundance of Cutibacterium and Staphylococcus, indicating negative correlations with increased bacterial metabolic pathways, such as butyrate synthesis and L-tryptophan degradation. The increased butyrate and tryptophan metabolites would be conducive to inhibiting skin inflammation and promoting skin barrier repair. In addition, the abundance of skin bacterial genes related to tetracycline resistance and multidrug resistance increased notably after antibiotic treatment. SIGNIFICANCE The effect on the skin microbiota of oral minocycline for rosacea remains unclear. A single-arm trial was conducted among 36 patients with rosacea treated with oral minocycline 50 mg twice daily for 6 weeks, to assess the efficacy and safety of oral minocycline. Genetic sequencing of skin lesions on the cheeks and nose was also performed at different times during oral treatment with minocycline to investigate alterations in the diversity, structure and composition of skin microbiota. Alterations in microbial metabolism and drug resistance were observed, which might guide the clinical selection of antibiotic.
Monitoring Debris Flows Using Spatial Filtering and Entropy Determination Approaches

We developed an automatic debris flow warning system in this study. The system uses a fixed video camera mounted over mountainous streams with a high risk for debris flows. The focus of this study is to develop an automatic algorithm for detecting debris flows with a low computational effort which can facilitate real-time implementation. The algorithm is based on a moving object detection technique to detect debris flow by comparing among video frames. Background subtraction is the kernel of the algorithm to reduce the computational effort, but non-rigid properties and color similarity of the object and the background color introduces some difficulties. Therefore, we used several spatial filtering approaches to increase the performance of the background subtraction. To increase the accuracy entropy is used with histogram analysis to identify whether a debris flow occurred. The modified background subtraction approach using spatial filtering and entropy determination is adopted to overcome the error in moving detection caused by non-rigid and similarities in color properties. The results of this study show that the approach described here can improve performance and also reduce the computational effort.
Comparison of Initial Growth Responses to Water Availability of Two Chinese Desert Dune Species and Nine Cultivated Species

Seed traits and germination responses to water availability can be related to seedling emergence and survival in sand and thus can affect the adaptability of species to desert dune environments. Water absorption by seeds, germination speed, responses of germination to water stress (imposed using polyethylene glycol-6000), and the effects of irrigation on seedling emergence and survival in sand were compared among two desert dune herbs from northeastern China (Astragalus adsurgens and Melilotus albus) and nine cultivated species (lettuce, carrot, turnip, sesame, Welsh onion, radish, cucumber, barley, and snap bean). Seeds that germinated rapidly after irrigation, those that germinated under low water potential, and those with small dry weight tended to produce emergent seedlings in response to a smaller amount of irrigation. However, these seedlings did not survive long, indicating that ready seedling emergence did not always promote seedling establishment. Drought resistance of seedlings was not correlated with seed traits or germination responses. The results indicated that the desert dune species were not less sensitive to water deficiency than the cultivated species at the initial growth stage. This may result from the fact that precipitation occurs predominantly during the summer in the desert dunes of northeastern China. As a result, species tend not to suffer from water deficiency during the initial growth stage.
Quantitative Assessment of Systematic Bias: A Guide for Researchers

Observational research provides valuable opportunities to advance oral health science but is limited by vulnerabilities to systematic bias, including unmeasured confounding, errors in variable measurement, or bias in the creation of study populations and/or analytic samples. The potential influence of systematic biases on observed results is often only briefly mentioned among the discussion of limitations of a given study, despite existing methods that support detailed assessments of their potential effects. Quantitative bias analysis is a set of methodological techniques that, when applied to observational data, can provide important context to aid in the interpretation and integration of observational research findings into the broader body of oral health research. Specifically, these methods were developed to provide quantitative estimates of the potential magnitude and direction of the influence of systematic biases on observed results. We aim to encourage and facilitate the broad adoption of quantitative bias analyses into observational oral health research. To this end, we provide an overview of quantitative bias analysis techniques, including a step-by-step implementation guide. We also provide a detailed appendix that guides readers through an applied example using real data obtained from a prospective observational cohort study of preconception periodontitis in relation to time to pregnancy. Quantitative bias analysis methods are available to all investigators. When appropriately applied to observational studies, findings from such studies can have a greater impact in the broader research context.
Association of hypoxia-inducible factor 1α expression with susceptibility to hepatitis B virus-related hepatocellular carcinoma: A meta-analysis

Hypoxia-inducible factor 1α (HIF-1α) triggers tumorigenesis and progression in hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). Inconsistent findings have been reported on the influence of HIF-1α over-expression on the clinical outcomes of HBV-related HCC. This study aims to clarify the role of HIF-1α overexpression in the tumorigenesis and prognosis of HBV-induced HCC. Systematic and comprehensive search of online papers was carried out to elucidate the contribution of HIF-1α expression to susceptibility of HBV-induced HCC. STATA 12.0 software was utilized to analyze available data extracted from all eligible literature. Publication bias and sensitivity were comprehensively analyzed. A total of 23 published studies involving 2244 subjects were finally screened. The HIF-1α expression was remarkably upregulated in HBV-induced HCC tissues than in normal liver tissues, non-tumorous tissues, paraneoplastic tissues, and non-HBV HCC tissues. The high HIF-1α expression tended to be positively related to capsular infiltration (odds ratio (OR) 1.767; 95% confidence interval (CI) 1.058, 2.950). The HIF-1α expression was relevant to lymph node metastasis (OR 3.778; 95% CI 1.666, 8.568). High levels of HIF-1α expression tended to be closely implicated in portal vein invasion (OR 6.728, 95% CI 2.191, 20.656) but were irrelevant to alpha-fetoprotein, cirrhosis, Edmondson grading, tumor size, age, gender, and histological grade. Analysis of pooled data showed that HIF-1α was not statistically relevant to poor overall survival in HBV-related HCC. Our data provides compelling evidence that HIF-1α overexpression may imply a greater probability of invasion and metastasis in patients with HBV-induced HCC.
A Novel Fluorescence-Based Leak Test Method for Rectal Anastomoses Using Aerosolized Indocyanine Green

BACKGROUND: The intraoperative air leak test is commonly performed during rectal surgery to evaluate anastomotic integrity. However, its drawbacks include occasional difficulties in visualizing the exact point of the leak while maintaining the pelvis under saline, the need for repeat testing to identify the leak point, and a lack of continuous visualization of the leak point. OBJECTIVE: To evaluate the feasibility and clinical applicability of using aerosolized indocyanine green, a fluorescent tracer, for detecting rectal anastomotic leakage. DESIGN: Animal preclinical study. SETTING: Animal laboratory at Kagawa University. PATIENTS: Six healthy adult female beagles were included. INTERVENTIONS: An anastomotic leakage model with a single air leak point was created in each dog. Indocyanine green was aerosolized using a nebulizer kit with a stream of carbon dioxide flowing at 1.5 to 2.0 L/min. The aerosol was administered into the rectum transanally, and laparoscopic observations were performed. MAIN OUTCOME MEASURES: Air leak points were observed using a near-infrared fluorescence laparoscope, after which the presence of corresponding indocyanine green fluorescence was verified. RESULTS: Aerosolized indocyanine green was visualized laparoscopically at all anastomosis sites but not elsewhere. The median time from the administration of the aerosol to its visualization was 4.5 seconds. Pathological examinations were performed 4 weeks postsurgery in all dogs, and no histological abnormalities related to aerosolized indocyanine green administration were observed at the anastomosis sites. LIMITATIONS: The leak points were surgically created and did not occur naturally. CONCLUSIONS: Visualization of air leaks at the sites of rectal anastomosis was laparoscopically achievable by administering aerosolized indocyanine green transanally into the rectum in our canine model. This novel fluorescent leak test could be a valid alternative to established methods. Video Abstract Video Abstract1_ifl9093zKaltura
A Feasibility Study of Time-Lapse Seismic Noise Interferometry for CO2 Monitoring at Ketzin

Since 2008, CO2 has been injected at the demonstration site for CO2 sequestration in Ketzin, Germany. Since 2009, a permanent array of seismic receivers installed by TNO at the injection site has recorded passive data continuously. It is the intention of TNO to use seismic interferometry (SI) by cross-correlation applied to the recorded ambient noise as a cost-effective technique for time-lapse monitoring. Under specific conditions, SI by cross-correlation can retrieve reflection data that may be interpreted in terms of subsurface layer properties. To assess the feasibility of this monitoring technique, we model base and monitor passive experiments for recording the response from noise sources and cross-correlate the recorded synthetic traces. The best results are obtained when the stationary-phase regions for the Green's functions are sampled densely enough by noise sources and, at the same time, the noise contributions from non-stationary regions cancel to a sufficient extent. Conversely, non-favourable noise conditions will cause wrong retrieval of the Green's functions and possibly deteriorate the monitoring potential of the technique. However, we show that being selective with the recorded noise in terms of illumination characteristics prior to correlation will improve the retrieved reflection data for further monitoring interpretation.