Miracle-dz/UniFAR-FTUs huggingface dataset:
National and subnational incidence, mortality and associated factors of colorectal cancer in China: A systematic analysis and modelling study

Background Due to their known variation by geography and economic development, we aimed to evaluate the incidence and mortality of colorectal cancer (CRC) in China over the past decades and identify factors associated with CRC among the Chinese population to provide targeted information on disease prevention. Methods We conducted a systemic review and meta-analysis of epidemiolocal studies on the incidence, mortality, and associated factors of CRC among the Chinese population, extracting and synthesising data from eligible studies retrieved from seven global and Chinese databases. We pooled age-standardised incidence rates (ASIRs) and mortality rates (ASMRs) for each province, subregion, and the whole of China, and applied a joinpoint regression model and annual per cent changes (APCs) to estimate the trends of CRC incidence and mortality. We conducted random-effects meta-analyses to assess the effect estimates of identified associated risk factors. Results We included 493 articles; 271 provided data on CRC incidence or mortality, and 222 on associated risk factors. Overall, the ASIR of CRC in China increased from 2.75 to 19.39 (per 100 000 person-years) between 1972 and 2019 with a slowed-down growth rate (APC1 = 5.75, APC2 = 0.42), while the ASMR of CRC decreased from 12.00 to 7.95 (per 100 000 person-years) between 1974 and 2020 with a slight downward trend (APC = -0.89). We analysed 62 risk factors with synthesized data; 16 belonging to the categories of anthropometrics factors, lifestyle factors, dietary factors, personal histories and mental health conditions were graded to be associated with CRC risk among the Chinese population in the meta-analysis limited to the high-quality studies. Conclusions We found substantial variation of CRC burden across regions and provinces of China and identified several associated risk factors for CRC, which could help to guide the formulation of targeted disease prevention and control strategies. Registration PROSPERO: CRD42022346558.
Prospects for Free Trade in the Americas

Negotiations on a Free Trade Area of the Americas (FTAA) were officially launched at the Santiago Summit in April 1998. This study examines the prospects for the FTAA in light of recent economic and political turmoil in Latin America and the continuing impasse over US "fast-track" authority. The study evaluates progress to date in the trade talks and proposals for accelerating the target date of January 2005 for concluding negotiations, and it takes into account the results of the April 2001 Quebec Summit. It surveys regional interests in the wide-ranging negotiating agenda and assesses the "readiness" of countries to participate in a hemisphere-wide free trade zone (based on updated "readiness indicators" originally developed by Hufbauer and Schott in their 1994 study, Western Hemisphere Economic Integration).
Global atmospheric temperature monitoring with satellite microwave measurements - Method and results 1979-84

Abstract A method for measuring global atmospheric temperature anomalies to a high level of precision from satellites is demonstrated. Global data from the Microwave Sounding Units (MSUs), flying on NOAA satellites since late 1978, have been analysed to determine the extent to which these data can reveal atmospheric temperature anomalies on bidaily and longer time scales for regional and larger space scales. The global sampling provided by the MSUs is an important asset, with most of the earth sampled bidaily from each of (typically) two instruments flying concurrently on separate satellites at different solar times. The primary source of tropospheric thermal information is from the MSU 53.74 GHz channel. This channel is primarily sensitive to thermal emission from molecular oxygen in the middle troposphere, with relatively little sensitivity to water vapor, the earth's surface, and cloud (especially cirrus) variations. The long-term stability of the oxygen mixing ratio in the atmosphere makes it an ideal.
RNase III participates in control of quorum sensing, pigmentation and oxidative stress resistance in Rhodobacter sphaeroides

RNase III is a dsRNA‐specific endoribonuclease, highly conserved in bacteria and eukarya. In this study, we analysed the effects of inactivation of RNase III on the transcriptome and the phenotype of the facultative phototrophic α‐proteobacterium Rhodobacter sphaeroides. RNA‐seq revealed an unexpectedly high amount of genes with increased expression located directly downstream to the rRNA operons. Chromosomal insertion of additional transcription terminators restored wild type‐like expression of the downstream genes, indicating that RNase III may modulate the rRNA transcription termination in R. sphaeroides. Furthermore, we identified RNase III as a major regulator of quorum‐sensing autoinducer synthesis in R. sphaeroides. It negatively controls the expression of the autoinducer synthase CerI by reducing cerI mRNA stability. In addition, RNase III inactivation caused altered resistance against oxidative stress and impaired formation of photosynthetically active pigment‐protein complexes. We also observed an increase in the CcsR small RNAs that were previously shown to promote resistance to oxidative stress. Taken together, our data present interesting insights into RNase III‐mediated regulation and expand the knowledge on the function of this important enzyme in bacteria.
The Probable Range Concept Applied to the Biostratigraphy of Marine Microfossils

The probable range of a taxon is its most frequently observed range defined for a set of geologic sections. The probable range concept is defined and demonstrated using two applications, both based on Deep Sea Drilling Project data. The first uses a Cenozoic and Mesozoic North Atlantic Ocean data set (calcareous nannoplankton, 228 taxa, 55 sections). The major result is a standardized rangechart at a definable level of minimum confidence for the data set that shows excellent correlation when compared with published range data. The second application uses a Pacific Ocean data set (calcareous nannoplankton, planktonic foraminifera, Radiolaria, 330 taxa, 32 sections). The application results in an estimated maximum attainable resolution of 100,000 years for the Tertiary. The quantitative application of the probable range concept offers the improvement of resolution beyond the 100,000 year level, equally reliable alternatives to standard biostratigraphic zonations, and objective limits of confidence or risk of error in using biostratigraphic sequence trends for age and paleoenvironmental interpretations.
FACTORS PREDICTING APPARENT OPHIDIOMYCOSIS IN WILD BROWN WATERSNAKES (NERODIA TAXISPILOTA)

Abstract: Ophidiomycosis, also known as snake fungal disease, is caused by Ophidiomyces ophidiicola and is a threat to snake conservation worldwide. Ophidiomycosis has been reported throughout much of the eastern US, and outbreaks have been associated with local population declines of already strained populations. Previous studies report significant variability in ophidiomycosis among species sampled, with higher prevalence typically observed in Nerodia spp. Although ophidiomycosis can lead to morbidity and mortality in affected individuals, little is known about disease dynamics in free-ranging populations. Herein, we examine how individual-specific factors (e.g., life stage [immature, mature], contaminant status, sex, hemograms) may be associated with ophidiomycosis status in the brown watersnake (Nerodia taxispilota). During 2018–19, we sampled 97 N. taxispilota from five locations along the Savannah River in South Carolina and Georgia, US. Ophidiomyces ophidiicola DNA was detected in 66 snakes for a prevalence of 68% (95% confidence interval, 59–77). Mature snakes had a significantly higher risk of apparent ophidiomycosis (skin lesions present and quantitative PCR [qPCR], positive) relative to immature snakes. Snakes classified as having possible (skin lesions present, but qPCR negative) or apparent ophidiomycosis exhibited a relative azurophilia and heterophilia compared with individuals classified as negative (P≤0.037). Nerodia taxispilota in this region appear to have a high prevalence of apparent ophidiomycosis (22%; 95% CI, 14–31), similar to previous reports from the southeastern US. Additional epidemiologic investigations are warranted to further elucidate other individual-specific and environmental factors that may dictate disease risk and outcomes in affected populations.
Negative Perceptions of Peer Relationships as Mechanisms in the Association Between Maltreatment Timing and the Development of Psychopathology

Abstract:Despite findings that developmental timing of maltreatment is a critical factor in predicting subsequent outcomes, children's developmental stage is understudied in maltreatment research. Moreover, childhood maltreatment is associated with the development of maladaptive peer relationships and psychopathology, with social cognition identified as a process underlying this risk. The current study uses structural equation modeling to examine the impact of developmental timing of maltreatment (i.e., infancy through preschool versus elementary and middle-school years) on psychopathology via negative perceptions of peer relationships. Multi-informant methods were used to assess 680 socioeconomically disadvantaged children. Results did not support differential effects of early versus later maltreatment on children's internalizing symptomatology or disruptive behavior, but indicated that chronic maltreatment, relative to episodic maltreatment, has more severe consequences for children's internalizing symptomatology. Results further support the mediating role of children's perceptions of relationships in the effect of maltreatment on negative developmental outcomes.
VARIDT 3.0: the phenotypic and regulatory variability of drug transporter

Abstract The phenotypic and regulatory variability of drug transporter (DT) are vital for the understanding of drug responses, drug-drug interactions, multidrug resistances, and so on. The ADME property of a drug is collectively determined by multiple types of variability, such as: microbiota influence (MBI), transcriptional regulation (TSR), epigenetics regulation (EGR), exogenous modulation (EGM) and post-translational modification (PTM). However, no database has yet been available to comprehensively describe these valuable variabilities of DTs. In this study, a major update of VARIDT was therefore conducted, which gave 2072 MBIs, 10 610 TSRs, 46 748 EGRs, 12 209 EGMs and 10 255 PTMs. These variability data were closely related to the transportation of 585 approved and 301 clinical trial drugs for treating 572 diseases. Moreover, the majority of the DTs in this database were found with multiple variabilities, which allowed a collective consideration in determining the ADME properties of a drug. All in all, VARIDT 3.0 is expected to be a popular data repository that could become an essential complement to existing pharmaceutical databases, and is freely accessible without any login requirement at: https://idrblab.org/varidt/.
Comparison of Tonotopic and Default Frequency Fitting for Speech Understanding in Noise in New Cochlear Implantees: A Prospective, Randomized, Double-Blind, Cross-Over Study

Objectives: While cochlear implants (CIs) have provided benefits for speech recognition in quiet for subjects with severe-to-profound hearing loss, speech recognition in noise remains challenging. A body of evidence suggests that reducing frequency-to-place mismatch may positively affect speech perception. Thus, a fitting method based on a tonotopic map may improve speech perception results in quiet and noise. The aim of our study was to assess the impact of a tonotopic map on speech perception in noise and quiet in new CI users. Design: A prospective, randomized, double-blind, two-period cross-over study in 26 new CI users was performed over a 6-month period. New CI users older than 18 years with bilateral severe-to-profound sensorineural hearing loss or complete hearing loss for less than 5 years were selected in the University Hospital Centre of Rennes in France. An anatomical tonotopic map was created using postoperative flat-panel computed tomography and a reconstruction software based on the Greenwood function. Each participant was randomized to receive a conventional map followed by a tonotopic map or vice versa. Each setting was maintained for 6 weeks, at the end of which participants performed speech perception tasks. The primary outcome measure was speech recognition in noise. Participants were allocated to sequences by block randomization of size two with a ratio 1:1 (CONSORT Guidelines). Participants and those assessing the outcomes were blinded to the intervention. Results: Thirteen participants were randomized to each sequence. Two of the 26 participants recruited (one in each sequence) had to be excluded due to the COVID-19 pandemic. Twenty-four participants were analyzed. Speech recognition in noise was significantly better with the tonotopic fitting at all signal-to-noise ratio (SNR) levels tested [SNR = +9 dB, p = 0.002, mean effect (ME) = 12.1%, 95% confidence interval (95% CI) = 4.9 to 19.2, standardized effect size (SES) = 0.71; SNR = +6 dB, p < 0.001, ME = 16.3%, 95% CI = 9.8 to 22.7, SES = 1.07; SNR = +3 dB, p < 0.001 ME = 13.8%, 95% CI = 6.9 to 20.6, SES = 0.84; SNR = 0 dB, p = 0.003, ME = 10.8%, 95% CI = 4.1 to 17.6, SES = 0.68]. Neither period nor interaction effects were observed for any signal level. Speech recognition in quiet (p = 0.66) and tonal audiometry (p = 0.203) did not significantly differ between the two settings. 92% of the participants kept the tonotopy-based map after the study period. No correlation was found between speech-in-noise perception and age, duration of hearing deprivation, angular insertion depth, or position or width of the frequency filters allocated to the electrodes. Conclusion: For new CI users, tonotopic fitting appears to be more efficient than the default frequency fitting because it allows for better speech recognition in noise without compromising understanding in quiet.
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase

Abstract The presence of ATP is known to stimulate helicase activity of the Dengue Virus Non-structural protein 3 helicase (NS3h), and the presence of RNA stimulates NS3h ATPase activity, however this coupling is still mechanistically unclear. Here we use atomistic models and molecular dynamics simulations to evaluate the single-stranded RNA (ssRNA)-length dependence of the NS3h–ssRNA binding affinity and its modulation by bound ATP. Considering complexes with 7, 11, 16 and 26 nucleotides (nts), we observe that both the binding affinity and its modulation by bound ATP are augmented with increased ssRNA lengths. In models with at least 11 nts bound, the binding of ATP results in a shift from a tightly bound to a weakly bound state. We find that the weakly bound state persists during both the ADP-Pi- and ADP-bound stages of the catalytic cycle. We obtain the equilibrium association constants for NS3h binding to an ssRNA 10-mer in vitro, both in the absence and presence of ADP, which further support the alternation between tightly and weakly bound states during the catalytic cycle. The length of bound ssRNA is critical for understanding the NS3h–RNA interaction as well as how it is modulated during the catalytic cycle.
Scan-by-scan averaging CFAR

The main shortcoming of currently working CFAR procedures based on the slidingwindow concept is a substantial performance degradation in the presence of nonhomogeneous background interference. Alternative procedures, based on clutter maps, exploit the intrinsic local homogeneity of the radar environment, thus yielding enhanced robustness and, at the same time, little loss of detectability with respect to optimum detectors. The paper analyses one such procedure and shows that it works well under quite general conditions; plots are given of detection probability against the average signal-to-noise ratio for several values of false alarm probability. The problem of the self-masking target is also investigated and the performance impairment due to such phenomena is assessed; plots of detection performance against the number of scans for which the target persists in the same map cell are given for several values of the system parameters.
miRNAs from Inflamed Gingiva Link Gene Signaling to Increased MET Expression

Several array-based microRNA (miRNA) expression studies independently showed increased expression of miRNAs hsa-miR-130a-3p, -142-3p, -144-3p, -144-5p, -223-3p, -17-5p, and -30e-5p in gingiva affected by periodontal inflammation. We aimed to determine direct target genes and signaling pathways regulated by these miRNAs to identify processes relevant to gingival inflammatory responses and tissue homeostasis. We transfected miRNA mimics (mirVana) for each of the 7 miRNAs separately into human primary gingival fibroblasts cultured from 3 different donors. Following RNA sequencing, differential gene expression and second-generation gene set enrichment analyses were performed. miRNA inhibition and upregulation was validated at the transcript and protein levels using quantitative reverse transcriptase polymerase chain reaction, Western blotting, and reporter gene assays. All 7 miRNAs significantly increased expression of the gene MET proto-oncogene, receptor tyrosine kinase (MET). Expression of known periodontitis risk genes CPEB1, ABCA1, and ATP6V1C1 was significantly repressed by hsa-miR-130a-3p, -144-3p, and -144-5p, respectively. The genes WASL, ENPP5, ARL6IP1, and IDH1 showed the most significant and strongest downregulation after hsa-miR-142-3p, -17-5p, -223-3p, and -30e-5p transfection, respectively. The most significantly regulated gene set of each miRNA related to cell cycle (hsa-miRNA-144-3p and -5p [Padj = 4 × 10−40 and Padj = 4 × 10−6], -miR-17-5p [Padj = 9.5 × 10−23], -miR-30e-5p [Padj = 8.2 × 10−18], -miR-130a-3p [Padj = 5 × 10−15]), integrin cell surface interaction (-miR-223-3p [Padj = 2.4 × 10−7]), and interferon signaling (-miR-142-3p [Padj = 5 × 10−11]). At the end of acute inflammation, gingival miRNAs bring together complex regulatory networks that lead to increased expression of the gene MET. This underscores the importance of mesenchymal cell migration and invasion during gingival tissue remodeling and proliferation in restoring periodontal tissue homeostasis after active inflammation. MET, a receptor of the mitogenic hepatocyte growth factor fibroblast secreted, is a core gene of this process.
Geometric and structural river channel complexity and the prediction of urban inundation

Recent research modelling floodplain inundation processes has concentrated on issues surrounding the level of physical, topographical, and numerical solver complexity needed to represent floodplain flows adequately. However, during flooding episodes the channel typically still conveys the bulk of the flow. Despite this, the effect of channel physical processes and topographic complexity on model results has been largely unexplored. To address this, the impact of channel cross‐section geometry, channel long‐profile variability and the representation of hydraulic structures on floodplain inundation are explored using a coupled dynamic 1D‐2D hydraulic model (ESTRY‐TUFLOW) of the Carlisle floods of January 2005. These simulations are compared with those from a simplified 1D‐2D model, LISFLOOD‐FP. In this case, the simpler model is sufficient to simulate the far‐field peak flood elevations. However, comparison of channel dynamics suggests that the full shallow water approximation used by ESTRY‐TUFLOW gives a more robust performance when models calibrated on maximum floodplain water elevations are used to predict channel water levels. Examination of the response of ESTRY‐TUFLOW to variations in channel geometric complexity shows that downstream variations in the channel long profile are more important than cross‐section variability for obtaining a dataset‐independent calibration. The results show, in general, that as model physical complexity is increased, calibrated parameters become less ‘effective’, and as a consequence, the values of performance measures reduce less rapidly away from the optimum value. This means that often more physically complex models are less likely to yield different optimum parameter values when calibrated on different datasets resulting in a more robust numerical model. Lastly, the inclusion of bridge structures can simulate substantial local backwatering effects, but the variability in observed water and wrack marks is such that it is not possible to discern the effect of the bridges at this site in the post‐event observational dataset. Copyright © 2011 John Wiley & Sons, Ltd.
Live-cell imaging unveils distinct R-loop populations with heterogeneous dynamics

Abstract We have developed RHINO, a genetically encoded sensor that selectively binds RNA:DNA hybrids enabling live-cell imaging of cellular R-loops. RHINO comprises a tandem array of three copies of the RNA:DNA hybrid binding domain of human RNase H1 connected by optimized linker segments and fused to a fluorescent protein. This tool allows the measurement of R-loop abundance and dynamics in live cells with high specificity and sensitivity. Using RHINO, we provide a kinetic framework for R-loops at nucleoli, telomeres and protein-coding genes. Our findings demonstrate that R-loop dynamics vary significantly across these regions, potentially reflecting the distinct roles R-loops play in different chromosomal contexts. RHINO is a powerful tool for investigating the role of R-loops in cellular processes and their contribution to disease development and progression.
Ancestry testing of “Old Tom,” a killer whale central to mutualistic interactions with human whalers

Abstract Cooperative hunting between humans and killer whales (Orcinus orca) targeting baleen whales was reported in Eden, New South Wales, Australia, for almost a century. By 1928, whaling operations had ceased, and local killer whale sightings became scarce. A killer whale from the group, known as “Old Tom,” washed up dead in 1930 and his skeleton was preserved. How these killer whales from Eden relate to other populations globally and whether their genetic descendants persist today remains unknown. We extracted and sequenced DNA from Old Tom using ancient DNA techniques. Genomic sequences were then compared with a global dataset of mitochondrial and nuclear genomes. Old Tom shared a most recent common ancestor with killer whales from Australasia, the North Atlantic, and the North Pacific, having the highest genetic similarity with contemporary New Zealand killer whales. However, much of the variation found in Old Tom’s genome was not shared with these widespread populations, suggesting ancestral rather than ongoing gene flow. Our genetic comparisons also failed to find any clear descendants of Tom, raising the possibility of local extinction of this group. We integrated Traditional Custodian knowledge to recapture the events in Eden and recognize that Indigenous Australians initiated the relationship with the killer whales before European colonization and the advent of commercial whaling locally. This study rectifies discrepancies in local records and provides new insight into the origins of the killer whales in Eden and the history of Australasian killer whales.