Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk of injuries before and after a diagnosis of cirrhosis: A population-based cohort study

Background: Cirrhosis is often asymptomatic prior to decompensation. Still, cognitive impairment and sarcopenia may be present before decompensation, possibly increasing the risk of injuries. We estimated the risk of injuries during the period shortly before and after cirrhosis diagnosis. Methods: All patients (N=59,329) with a diagnosis of cirrhosis from 1997 to 2019 were identified from the Swedish National Patient Register. We used a self-controlled case series design to compare the incidence rates (IR) of injuries during a “diagnostic period” (within 3 months before or after the cirrhosis diagnosis date) to a self-controlled “prediagnostic period” (the same 6 calendar months 3 years before diagnosis), using conditional Poisson regression. Injuries were ascertained from the National Patient Register. Results: We identified 23,733 (40.0%) patients with compensated and 35,595 (60.0%) with decompensated cirrhosis. There were 975 injuries (IR 2.8/1000 person-months) during the prediagnostic period, and 3610 injuries (IR 11.6/1000 person-months) identified during the diagnostic period. The IR ratio was 8.1 (95% CI 7.5–8.7) comparing the diagnostic period with the prediagnostic period. For patients with compensated cirrhosis, the risk increment of injuries was highest just before the diagnosis of cirrhosis, whereas the risk increase was highest shortly after the diagnosis for those with decompensation. Conclusions: The incidence of injuries increases shortly before and after the diagnosis of cirrhosis. These findings indicate that cirrhosis is frequently diagnosed in conjunction with an injury, and highlight the need for injury prevention after cirrhosis diagnosis, especially in patients with decompensation.
Subnano Te Cluster in Glass for Efficient Full‐Spectrum Conversion

Broadband near‐infrared (NIR) photonic materials have wide applications. Although extensive studies on rare‐earth, transition‐metal, and even semiconductor‐activated materials have enabled the development of a rich NIR material pool, developing broadband and efficient photonic candidates covering the NIR I and II regions from 750 to 1500 nm has been met with limited success. Here, it is reported that a subnano Te cluster with a characteristic configuration different from that of the ion state may fill the aforementioned gap. Further, a strategy is proposed for the in situ generation and stabilization of Te clusters by tuning the cluster evolution in glass. A novel active photonic glass embedded with a Te cluster is fabricated; it exhibits intense and broadband short‐wave NIR luminescence with a central wavelength at 1030 nm and a bandwidth exceeding 330 nm. Interestingly, the glass exhibited a full visible‐spectrum conversion ability from 300 to 800 nm. The application of this unique broadband excitation feature for night vision and tissue penetration is demonstrated using a smartphone as the excitation source. These findings demonstrate a fundamental principle of cluster design in glass for creating new properties and provide a new direction for developing novel cluster‐derived functional composite materials.
INTEGRATED SOLID WASTE MANAGEMENT: A FRAMEWORK FOR ANALYSIS

Owing to the number of potential impacts and the vast heterogeneity of state and local solid waste management programs, any careful attempt to assess the benefits and costs of solid waste management practices must begin with a fairly comprehensive organizational framework, one that is applicable to a wide range of available waste management options and that accounts for all possible impacts while taking care to avoid potential double-counting. This paper provides such a comprehensive framework by combining the traditional economic method of benefit-cost analysis with the more recent life-cycle approach found in systems analysis, resulting in a framework based on the flow of waste materials through generation, collection, processing, recovery, and/or disposal. The framework presented in this article is valuable to researchers, decision makers, and others who are interested in identifying and analyzing the large number and types of benefits and costs associated with integrated solid waste management systems.
sTREM2 is a plasma biomarker for human NASH and promotes hepatocyte lipid accumulation

Background: Pathogenetic mechanisms of the progression of NAFL to advanced NASH coupled with potential noninvasive biomarkers and novel therapeutic targets are active areas of investigation. The recent finding that increased plasma levels of a protein shed by myeloid cells —soluble Triggering Receptor Expressed on Myeloid cells 2 (sTREM2) —may be a biomarker for NASH has received much interest. We aimed to test sTREM2 as a biomarker for human NASH and investigate the role of sTREM2 in the pathogenesis of NASH. Methods: We conducted studies in both humans (comparing patients with NASH vs. NAFL) and in mice (comparing different mouse models of NASH) involving measurements of TREM2 gene and protein expression levels in the liver as well as circulating sTREM2 levels in plasma. We investigated the pathogenetic role of sTREM2 in hepatic steatosis using primary hepatocytes and bone marrow derived macrophages. Results: RNA sequencing analysis of livers from patients with NASH or NAFL as well as livers from 2 mouse models of NASH revealed elevated TREM2 expression in patients/mice with NASH as compared with NAFL. Plasma levels of sTREM2 were significantly higher in a well-characterized cohort of patients with biopsy-proven NASH versus NAFL (area under receiver-operating curve 0.807). Mechanistic studies revealed that cocultures of primary hepatocytes and macrophages with an impaired ability to shed sTREM2 resulted in reduced hepatocyte lipid droplet formation on palmitate stimulation, an effect that was counteracted by the addition of exogenous sTREM2 chimeric protein. Conversely, exogenous sTREM2 chimeric protein increased lipid droplet formation, triglyceride content, and expression of the lipid transporter CD36 in hepatocytes. Furthermore, inhibition of CD36 markedly attenuated sTREM2-induced lipid droplet formation in mouse primary hepatocytes. Conclusions: Elevated levels of sTREM2 due to TREM2 shedding may directly contribute to the pathogenesis of NAFLD by promoting hepatocyte lipid accumulation, as well as serving as a biomarker for distinguishing patients with NASH versus NAFL. Further investigation of sTREM2 as a clinically useful diagnostic biomarker and of the therapeutic effects of targeting sTREM2 in NASH is warranted.
El Niño, La Niña, and the Southern Oscillation

El Nino-Southern Oscillation, ENSO, is a dominant mode of climate variability affecting the earth. Occurring every 2–7 years, ENSO arises due to air–sea interactions in the tropical Pacific Ocean and is marked by anomalously warm or cool sea-surface temperatures in the central-to-eastern equatorial Pacific. Warm events in the eastern equatorial Pacific are called El Nino events, and cool events are called La Nina events. Climate and weather phenomena associated with ENSO include floods, droughts, heat waves, and tropical cyclones, which can lead to effects on fisheries, agriculture, health, and air quality.
Seasonal variations of the epididymis in donkeys (Equus asinus) with special reference to blood epididymal barrier

The epididymis, a key component of the male reproductive system, controls spermatozoa's maturation, fertility, and storage. The objective of this study is to evaluate the histological, ultrastructural, and immunohistochemical variations in the epididymis of donkeys that occur throughout the year. During the breeding season (spring) and nonbreeding seasons (summer, autumn, and winter), 20 epididymis were collected from adult, clinically healthy donkeys. Compared to non‐breeding seasons, the epididymal duct displayed a more active lining epithelium and more sperm in the lumen during the breeding season. The epithelial height is the lowest and the lumen is the widest during the breeding season. Furthermore, the epididymal epithelium in the tail region exhibits undulations with polyps‐like projections. The epididymal epithelium is composed mainly of the principal, basal, and dark cells. Tight junction between adjacent principal cells is more obvious in the breeding season as compared to the non‐breeding seasons. However, intraepithelial lymphocytes, phagocytic, and other immune cells are more frequent in non‐breeding seasons. β‐catenin, which is a component of the adherent junctions between adjacent PCs, exhibits more immunoreactivity during the spring. On the other hand, iNOS, an indicator of oxidative stress, reacts positively during the summer. Additionally, during non‐breeding seasons, autophagy was detected within the epididymal epithelium which may be linked to stress adaptation. In conclusion, our findings suggest that the histological and ultrastructural characteristics of the epididymal epithelium are more active during spring compared to other seasons of the year.
Gibberellin and the miRNA156-targeted SlSBPs synergistically regulate tomato floral meristem determinacy and ovary patterning.

Many developmental processes associated with fruit development occur at the floral meristem (FM). Age-regulated microRNA156 (miR156) and gibberellins (GA) interact to control flowering time, but their interplay in subsequent stages of reproductive development is poorly understood. Here, we show GA and miR156-targeted SlSBPs interact in tomato FM and ovary patterning. High GA responses or overexpression of miR156 (156OE), which leads to low levels of miR156-silenced SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL/SBP), resulted in enlarged FMs, ovary indeterminacy, and fruits with increased locule number. Conversely, low GA responses reduced indeterminacy and locule number, and overexpression of a miR156-resistant SlSBP15 allele (rSBP15) reduced FM size and locule number. GA responses were partially required for the defects observed in 156OE and rSBP15 fruits. Transcriptome analysis and genetic interactions revealed shared and divergent functions of miR156-targeted SlSBPs, PROCERA/DELLA and the classical WUSCHEL/CLAVATA pathway, which has been previously associated with meristem size and determinacy. Our findings reveal the miR156/SlSBP/GA regulatory module is deployed differently depending on developmental stage and create novel opportunities to fine-tune aspects of fruit development that have been important for tomato domestication.
A Toxicokinetic–Toxicodynamic Modeling Workflow Assessing the Quality of Input Mortality Data

Toxicokinetic–toxicodynamic (TKTD) models simulate organismal uptake and elimination of a substance (TK) and its effects on the organism (TD). The Reduced General Unified Threshold model of Survival (GUTS‐RED) is a TKTD modeling framework that is well established for aquatic risk assessment to simulate effects on survival. The TKTD models are applied in three steps: parameterization based on experimental data (calibration), comparing predictions with independent data (validation), and prediction of endpoints under environmental scenarios. Despite a clear understanding of the sensitivity of GUTS‐RED predictions to the model parameters, the influence of the input data on the quality of GUTS‐RED calibration and validation has not been systematically explored. We analyzed the performance of GUTS‐RED calibration and validation based on a unique, comprehensive data set, covering different types of substances, exposure patterns, and aquatic animal species taxa that are regularly used for risk assessment of plant protection products. We developed a software code to automatically calibrate and validate GUTS‐RED against survival measurements from 59 toxicity tests and to calculate selected model evaluation metrics. To assess whether specific survival data sets were better suited for calibration or validation, we applied a design in which all possible combinations of studies for the same species–substance combination are used for calibration and validation. We found that uncertainty of calibrated parameters was lower when the full range of effects (i.e., from high survival to high mortality) was covered by input data. Increasing the number of toxicity studies used for calibration further decreased parameter uncertainty. Including data from both acute and chronic studies as well as studies under pulsed and constant exposure in model calibrations improved model predictions on different types of validation data. Using our results, we derived a workflow, including recommendations for the sequence of modeling steps from the selection of input data to a final judgment on the suitability of GUTS‐RED for the data set. Environ Toxicol Chem 2024;43:197–210. © 2023 Bayer AG and The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
Possible impact of the Atlantic Multidecadal Oscillation on the South American summer monsoon

The South American summer monsoon (SASM) is the main source of precipitation for the most densely populated and agriculturally productive regions of tropical and subtropical South America. Here we investigate the impact of the Atlantic Multidecadal Oscillation (AMO) on the SASM using ∼4500 yr long proxy records of the discharge variability of the La Plata River Drainage Basin (PRDB), subtropical South America. We measured the stable oxygen composition of planktic foraminifera (related to the extension of the PRDB plume), and Ti intensity in bulk sediment (related to the source of the terrigenous sediments) from a marine sediment core. Spectral and wavelet analyses of our records indicate an oscillation with period of ∼64 yr. We conclude that the observed oscillation reflects variability in the SASM activity associated to the AMO. Sea surface temperature and atmospheric circulation anomalies triggered by the AMO would control the variability in SASM activity.
Beyond The Conceivable? Pondering A City Without Walls In South Africa

In the late apartheid period South African suburbs began to change dramatically in the way they looked and in the way in which they were designed. Essentially, housing was designed with the aim of keeping ‘intruders’ out. This meant a turn toward increasingly high walls, electrified fences and laser beams. Alongside these ‘investments’ and design innovations came a massive growth of the private security industry. A new mentality emerged which focused on the fortification of home and office space. This mentality, at least initially, was strongly supported and bolstered by the private security industry who had a real vested interest in this rush to monitor space and to harden security. Yet, whether or not high walls and electrified fences do in fact reduce experiences of crime victimisation for individual home owners and residents is up for debate. And the private security industry as well as the public police are now suggesting that walls might not provide the security that home owners believe they do. This research is aimed at interrogating whether walls, electric fences, beams and so on really do reduce fear of crime and victimisation, from the perspective of those who do the policing, i.e. the public and private. The aim here is to discover whether policing actors view walls as a help or a hindrance to policing and security governance. The ‘praxis’ goal of this research is, through public engagement, to shift paradigms about walls and security.
Lessons From Nature In Resolving Interface Problems In Design Of Structures And Systems

Design prototypes for the physical and social worlds are found in nature in the domains of fl ora, fauna and the human body. However, in designing and developing structures and systems, learning from the common creative principles in nature is probably more important than borrowing formal patterns and models. Physical structures and systems in development are designed and modifi ed in response to needs that arise at various interfaces concerning societies and individuals. Principles, learned from nature, and adopted as approaches to structural and behavior aspects of design can assist in resolving successfully intrinsic and extrinsic interface problems of interactions in space and time. The signifi cance of the principles of heterogeneity, complexity, adaptability and integration grows with ever-deepening exploration of nature. Their manifestations are found in an endless variety of forms and relationships in the universe. The lessons derived from nature contribute to a general philosophy of engineering design and justify solutions toward innovations and sustainable existence.
Severe Pediatric COVID-19 and Multisystem Inflammatory Syndrome in Children From Wild-type to Population Immunity: A Prospective Multicenter Cohort Study With Real-time Reporting

Background: SARS-CoV-2 variant evolution and increasing immunity altered the impact of pediatric SARS-CoV-2 infection. Public health decision-making relies on accurate and timely reporting of clinical data. Methods: This international hospital-based multicenter, prospective cohort study with real-time reporting was active from March 2020 to December 2022. We evaluated longitudinal incident rates and risk factors for disease severity. Results: We included 564 hospitalized children with acute COVID-19 (n = 375) or multisystem inflammatory syndrome in children (n = 189) from the Netherlands, Curaçao and Surinam. In COVID-19, 134/375 patients (36%) needed supplemental oxygen therapy and 35 (9.3%) required intensive care treatment. Age above 12 years and preexisting pulmonary conditions were predictors for severe COVID-19. During omicron, hospitalized children had milder disease. During population immunity, the incidence rate of pediatric COVID-19 infection declined for older children but was stable for children below 1 year. The incidence rate of multisystem inflammatory syndrome in children was highest during the delta wave and has decreased rapidly since omicron emerged. Real-time reporting of our data impacted national pediatric SARS-CoV-2 vaccination- and booster-policies. Conclusions: Our data supports the notion that similar to adults, prior immunity protects against severe sequelae of SARS-CoV-2 infections in children. Real-time reporting of accurate and high-quality data is feasible and impacts clinical and public health decision-making. The reporting framework of our consortium is readily accessible for future SARS-CoV-2 waves and other emerging infections.
The Corellification of Cephallonian Tourism

ABSTRACT Research suggests that popular media such as literature, television and cinema films can increase visitor numbers to featured destinations. This study investigates the ramifications for the Cephallonian tourism industry, following the success of the novel and subsequent film ‘Captain Corelli's Mandolin’. In situ observations to establish the extent of related commodification discovered neither managed attractions nor significant promotion of the ‘Corelli’ theme. Those Cephallonian residents who participated in a quantitative survey were fully aware of local “CCM” links, with a majority maintaining positive perceptions of tourists despite their increased numbers. This study contributes horizontally to the broad band of literature concerning general perceptions of tourism, whilst vertically advancing existing knowledge in the niche area of film and literary tourism.
Comparative genomics hints at dispensability of multiple essential genes in two Escherichia coli L-form strains

Abstract Despite the critical role of bacterial cell walls in maintaining cell shapes, certain environmental stressors can induce the transition of many bacterial species into a wall-deficient state called L-form. Long-term induced Escherichia coli L-forms lose their rod shape and usually hold significant mutations that affect cell division and growth. Besides this, the genetic background of L-form bacteria is still poorly understood. In the present study, the genomes of two stable L-form strains of E. coli (NC-7 and LWF+) were sequenced and their gene mutation status was determined and compared with their parental strains. Comparative genomic analysis between two L-forms reveals both unique adaptions and common mutated genes, many of which belong to essential gene categories not involved in cell wall biosynthesis, indicating that L-form genetic adaptation impacts crucial metabolic pathways. Missense variants from L-forms and Lenski’s long-term evolution experiment (LTEE) were analyzed in parallel using an optimized DeepSequence pipeline to investigate predicted mutation effects (α) on protein functions. We report that the two L-form strains analyzed display a frequency of 6–10% (0% for LTEE) in mutated essential genes where the missense variants have substantial impact on protein functions (α<0.5). This indicates the emergence of different survival strategies in L-forms through changes in essential genes during adaptions to cell wall deficiency. Collectively, our results shed light on the detailed genetic background of two E. coli L-forms and pave the way for further investigations of the gene functions in L-form bacterial models.
What is a Thrust? What is a Nappe?

Summary The definitions of thrusts and nappes are discussed and the criteria used to define these structures are analysed. A ‘thrust fault’ is defined as a map-scale contraction fault. A ‘thrust nappe’ is an allochthonous tectonic sheet which has moved along a thrust fault. Suggested definitions are also given for, a fold nappe; extension fault; contraction fault; listric normal fault; reverse listric fault; klippe; tectonic slide; ramps and flats; duplex structure; blind thrusts.
Managing salinity in the Indus Basin of Pakistan

Abstract Waterlogging and salinity have plagued irrigated agriculture in the Indus Basin for the past 30–40 years. Approximately 6 million ha (35–40% of total irrigated area) experience these twin problems. As a result, the production potential of the Indus Basin has been reduced by 25%. Over the last 40 years, the Government of Pakistan has adopted engineering, reclamation, and biological measures to address these problems. Part of the engineering solution involved large‐scale Salinity Control and Reclamation Projects (SCARPs) in all four provinces. The program covered 8 million ha and cost approximately US$2 billion. Two big disposal projects were also initiated to solve the drainage disposal problems. To address the saline soil problem, some of the measures tested include leaching of salts by excess irrigation, use of chemicals (such as gypsum and acids), and addition of organic matter and biological measures (such as salt‐tolerant plants, grasses, and shrubs). The success of these initiatives has been limited: 35–40% of irrigated land still suffers from high water tables and moderate to severe salinity. Lack of coordination among federal and provincial governments, research institutes, and national and international organizations; conventional farming and irrigation methods used by farmers; limited attention to reclamation and saline agricultural approaches; and lack of resources are some of the reasons for the low success rate. A more concerted effort that includes a greater focus on saline agriculture, capacity building of farmers, and promotion of local interventions to improve self‐reliance is necessary for the management of salinity in the Indus Basin. A sustainable solution would also require coordination among different provinces and strengthening of federal and provincial government agencies.