Miracle-dz/UniFAR-FTUs huggingface dataset:
Convergence of field survey protocols for SERCON (System for Evaluating Rivers for Conservation) and RHS (River Habitat Survey)

1. SERCON is a technique for assessing the conservation value of rivers in terms of criteria such as naturalness, physical diversity and species richness. Part of the process involves gathering information on the physical features of rivers and their corridors, for which accurate survey data are essential. 2. SERCON has been developed in parallel with River Habitat Survey (RHS), a method for compiling an inventory of physical features and for classifying habitat quality based on surveys of discrete river reaches. 3. A study was carried out to compare SERCON scores derived from RHS data with those obtained from a tailor-made SERCON survey method. RHS surveys were carried out at 118 sites (each 0.5 km in length, one site every 4 km) on five rivers in Scotland. The whole length of each river was also surveyed using the SERCON survey method. Additional data comprising a complete RHS coverage of one river in NW England were used to assess the influence of survey site frequency on SERCON scores. 4. Scores derived from both methods were similar for some of the features evaluated. However, other features were either not recorded at all by RHS, or were recorded in a way that led to inaccurate scoring. A survey strategy of one RHS site every 2 km was found to represent the most cost-effective compromise between the ideal of contiguous survey and the reality of limited time and money. 5. A revised SERCON survey protocol has been devised consisting of a modified RHS together with an ‘inter-reach’ survey for assessing any major changes between survey sites. Further modifications to the way some features are scored in SERCON may be needed later to provide full integration with RHS. © 1998 John Wiley & Sons, Ltd.
Dissecting HSV-1-induced host shut-off at RNA level

Herpes simplex virus 1 (HSV-1) installs a profound host shut-off during lytic infection. The virion host shut-off (vhs) protein plays a key role in this process by efficiently cleaving both host and viral mRNAs in a translation-initiation-dependent manner. Furthermore, the onset of viral DNA replication is accompanied by a rapid decline in transcriptional activity of the host genome. Both mechanisms have tremendous impact on the RNA expression profile of the infected cells. To dissect their relative contributions and elucidate gene-specific host transcriptional responses throughout the first 8h of lytic HSV-1 infection, we here employed RNA-seq of total, newly transcribed (4sU-labelled) and chromatin-associated RNA in wild-type (WT) and Δvhs infection of primary human fibroblasts. Following virus entry, vhs activity rapidly plateaued at an elimination rate of around 30% of cellular mRNAs per hour until 8h p.i. In parallel, host transcriptional activity dropped down to 10-20%. While the combined effects of both phenomena dominated infection-induced changes in total RNA, extensive gene-specific transcriptional regulation was observable in chromatin-associated RNA. This was surprisingly concordant between WT HSV-1 and its Δvhs mutant and at least in parts mediated by the embryonic transcription factor DUX4. Furthermore, both WT and Δvhs infection induced strong transcriptional up-regulation of a small subset of genes. Most of these were either poorly or not at all expressed prior to infection but already primed by H3K4me3 histone marks at their promoters. Most interestingly, analysis of chromatin-associated RNA revealed vhs-nuclease-activity-dependent transcriptional down-regulation of at least 150 cellular genes, in particular of many genes encoding integrin adhesome and extracellular matrix components. This was accompanied by a vhs-dependent reduction in protein levels by 8h p.i. for many of these genes. In summary, our study provides a comprehensive picture of the molecular mechanisms that govern cellular RNA metabolism during the first 8h of lytic HSV-1 infection. Author Summary The HSV-1 virion host shut-off (vhs) protein efficiently cleaves both host and viral mRNAs in a translation-dependent manner. In this study, we model and quantify changes in vhs activity as well as the virus-induced global loss of host transcriptional activity during productive HSV-1 infection. In general, HSV-1-induced alterations in total RNA levels were found to be predominantly shaped by these two global processes rather than gene-specific regulation. In contrast, chromatin-associated RNA depicted gene-specific transcriptional changes. This revealed highly concordant transcriptional changes in WT and Δvhs infection, confirmed DUX4 as a key transcriptional regulator in HSV-1 infection and depicted vhs-dependent, transcriptional down-regulation of the integrin adhesome and extracellular matrix. The latter explained some of the gene-specific effects previously attributed to vhs-mediated mRNA degradation and resulted in a concordant loss in protein levels by 8h p.i. for many of the respective genes.
Forest-fragment quality rather than matrix habitat shapes herbivory on tree recruits in South Africa

Abstract: Forest fragmentation can alter herbivory on tree recruits with possible consequences for regeneration. We assessed effects of forest-fragment quality (tree diversity, vegetation complexity, relative abundance of pioneer trees) and matrix habitat on arthropods and herbivory in KwaZulu-Natal, South Africa. We compared arthropod abundances and herbivory on woody seedlings and saplings among four forest-fragment types differing in size and matrix (large fragments and small fragments surrounded by natural grassland, eucalypt and sugarcane plantations; nplots = 24) using analyses of covariance. We recorded 3385 arthropods and inspected 897 seedlings (71 species) and 876 saplings (91 species). Relative abundance of predators increased with fragment quality; that of herbivores decreased. Herbivory responses to fragment quality varied: seedling herbivory decreased with relative abundance of pioneers and sapling herbivory increased with vegetation complexity. Matrix effects were low with little variation in relative abundance of predators (0.39–0.53) and herbivores (0.22–0.32), proportion of seedling (8.3–11.0%) and sapling herbivory (12.4–14.3%) among the forest-fragment types. These findings indicate that herbivory on tree recruits is mediated by forest-fragment quality rather than matrix habitat. Future studies should evaluate whether contrasting effects of fragment quality on arthropods and herbivory are caused by weak trophic interactions and variable herbivore compositions.
Simulation of the hydrodynamic regime of Jebel Ali Harbor, Dubai, United Arab Emirates

Jebel Ali Harbor in Dubai is one of the largest man-made ports in the world. Due to its bottle-like nature, it is anticipated that little mixing or wave action occurs within the harbor; however, no study has been conducted to investigate the harbor's hydrodynamic regime. In this paper, the circulation pattern in Jebel Ali Harbor is presented. The vertical profile of temperature and salinity shows that the harbor water is fairly well-mixed, justifying the use of a depth-averaged, 2-D model. Modeling the hydrodynamic pattern of Jebel Ali Harbor was carried out using MIKE21 model. Although tide is the main driving force of circulation in the harbor, wind and Coriolis forces were taken into account in the simulation. Simulation results showed that both dead and eddy zones exis. As the harbor receives treated wastewater from several industries located in the area, flushing out of a conservative tracer by the advection-dispersion process was also simulated using MIKE21. Results revealed that the flushing time of a conservative tracer from the harbor varies significantly with the discharge location. Simulated results showed that understanding the hydrodynamic regime of Jebel Ali Harbor is useful for selecting the location and time for discharging tracers into the harbor.
A Toxicologist's Guide to Studying Diagnostic Tests

Diagnostic testing plays an important role in medicine, including in clinical toxicology. In comparison with therapeutics however, until recently, much less focus has been input in this vital area of research and practice. In the absence of stringent and constructive criteria, the quality and interpretability of studies evaluating diagnostic accuracy has been less than optimal. Recently, a group of researchers and clinicians have attempted to outline a checklist intended to provide guidelines for undertaking and reporting studies examining diagnostic accuracy. Also, a tool to assess the quality of diagnostic accuracy studies was developed. The purpose of this review is to inform practitioners and researchers in the field of clinical toxicology on the basic concepts underlying measurements of the accuracy of diagnostic tests, methodological concerns related to design and analysis of studies, the strengths and weaknesses of different measures of accuracy and an overview of the Standards for Reporting Diagnostic Accuracy (STARD statement) and the Quality Assessment of Diagnostic Accuracy Studies (QUADAS) tool. Understanding key concepts in the field of diagnostic testing can not only help improve future studies but also explain why diagnostic tests currently used by clinical toxicologists are not performing well in particular circumstances.
INTEGRA: An Open Tool To Support Graph-Based Change Pattern Analyses In Simulated Football Matches

This paper introduces Interactive Graph Analyzer (INTEGRA), a tool to support the comparison of simulated football matches with real ones, through the analysis of dynamic graphs. Our tool supports coordinated views of temporal graphs, beneﬁting from traditional node-link diagrams and graph visual rhythms, a recently proposed 2D image representation. Our proposal is generic and may be tailored to diﬀerent applications. We demonstrate the use of this tool in compelling case studies related to the comparison of graph-based measurements obtained from three diﬀerent kinds of simulated foot-ball matches and real ones. In particular, we exploit usage scenarios related to how graph measurements evolve over time
A Vegetation History and Quantitative Estimate of Holocene Climate from Chapple Vale, in the Otway Region of Victoria, Australia

A well-dated pollen record from Chapple Vale in the north of the Otway region provides a detailed history of vegetation and environments through the last c. 7000 years. From the commencement of the record, a stand of cool temperate rainforest, dominated by Nothofagus cunninghamii (Hook.) Oerst. , grew on or around the site and was surrounded by eucalypt-dominated tall open forest. Between c. 5200 and 4600 years BP (before present), the rainforest declined and tall open forest predominated. Some time after 4400 years BP there was a major and consistent increase in charcoal values, suggesting an increase in burning, the progressive development of scrub–heath vegetation on site and the replacement of tall open forest vegetation by eucalypt woodland surrounding the site. The fossil evidence for N. cunninghamii on the site and its present restriction to wetter areas and gullies of the Otway Ranges indicate, from the application of the present bioclimatic range of the species, a mean annual temperature and winter temperatures that were c. 1˚C cooler than present, and summer temperatures that were possibly slightly cooler than present, together with a much higher effective precipitation from the commencement of the record until c. 4600 years BP. These climatic estimates are in accord with those derived from a similar study of changing distributions of N. cunninghamii in the Central Highlands of lower mean annual and cooler summer temperatures and higher effective precipitation over this time span. However, for winter, the evidence is equivocal. While the Otway estimates suggest lower temperatures, the Central Highlands findings show slightly higher temperatures. Taking into account additional present-day records for N. cunninghamii, it is likely that the Otway estimates are the most reliable.
Mud, microbes, and macrofauna: seasonal dynamics of the iron biogeochemical cycle in an intertidal mudflat

Microorganisms and burrowing animals exert a pronounced impact on the cycling of redox sensitive metals in coastal sediments. Sedimentary metal cycling is likely controlled by seasonal processes including changes in temperature, animal feeding behavior due to food availability, and availability of organic matter in sediments. We hypothesized that the iron biogeochemical cycle and associated sedimentary microbial community will respond to seasonal changes in a bioturbated intertidal mudflat. In this study, we monitored the spatiotemporal dynamics of porewater and highly reactive solid phase iron with the corresponding prokaryotic and eukaryotic sedimentary microbial communities over one annual cycle from November 2015 to November 2016. Continuous and seasonally variable pools of both porewater Fe(II) and highly reactive iron (FeHR) were observed throughout the season with significant increases of Fe(II) and FeHR in response to increased sediment temperature in summer months. Maximum concentrations of Fe(II) and FeHR were predominantly confined to the upper 5 cm of sediment throughout the season. Iron-oxidizing and -reducing microorganisms were present and stable throughout the season, and exhibited strong depth-dependent stratification likely due to availability of Fe(II) and FeHR pools, respectively. Otherwise, the community was dominated by Deltaproteobacteria, which are involved in sulfur and potentially iron cycling, as well as Gammaproteobacteria and Bacteroidetes. The microbial community was relatively stable throughout the seasonal cycle, but showed strong separation with depth, probably driven by changes in oxygen availability and organic matter. The relative abundance of diatoms revealed a noticeable seasonal signature, which we attribute to spring and fall blooms recorded in the sediments. Macro-, meio, and microfauna were detected throughout the season with some seasonal variations that may influence sedimentary iron transformations by active microbial grazing. The seasonal dynamics of the sedimentary iron cycle are controlled by numerous, interdependent processes, with macrobiota-microbiota relationships and depth stratification comprising primary components. Deciphering these processes in natural ecosystems is essential to understand how they might respond to future environmental perturbations, such as anthropogenic nutrient release to coastal systems.
In vivo CRISPR screening identifies Fli1 as a transcriptional safeguard that restrains effector CD8 T cell differentiation during infection and cancer

Improving effector activity of antigen specific T cells is a major goal in cancer immunotherapy. Despite the identification of several effector T cell (TEFF)-driving transcription factors (TF), the transcriptional coordination of TEFF biology remains poorly understood. We developed an in vivo T cell CRISPR screening platform and identified a novel mechanism restraining TEFF biology through the ETS family TF, Fli1. Genetic deletion of Fli1 enhanced TEFF responses without compromising memory or exhaustion precursors. Fli1 restrained TEFF lineage differentiation by binding to cis-regulatory elements of effector-associated genes. Loss of Fli1 increased chromatin accessibility at ETS:RUNX motifs allowing more efficient Runx3-driven TEFF biology. CD8 T cells lacking Fli1 provided substantially better protection against multiple infections and tumors. These data indicate that Fli1 safeguards the developing CD8 T cell transcriptional landscape from excessive ETS:RUNX-driven TEFF cell differentiation. Moreover, genetic deletion of Fli1 improves TEFF differentiation and protective immunity in infections and cancer.
Staged transcatheter closure of chronic postinfarction ventricular septal defects with the Amplatzer septal occluder

Ventricular septal rupture is a serious complication of myocardial infarction with an extremely poor outcome. There are single reports of transcatheter closure of postmyocardial septal defects and clinical experience is limited. This paper reports on a successful staged transcatheter closure of two chronic postmyocardial defects using the Amplatzer septal occluder in a 52-year-old male.
REGULATION OF THE RAT BB1 RNA DURING NORMAL RAT LUNG DEVELOPMENT

BB1 was recently cloned from the WI-38 human fetal lung cell line. Human BB1 (hBB1) is expressed by multiple tissues, including lung. Because inhibition of BB1 translation using antisense oligodeoxynucleotides resulted in prevention of G1 traversal in cultured cells, we hypothesized that BB1 gene expression would be regulated during lung development with greater expression during periods of active lung growth. To gain insight into the expression of BB1 during lung development, a rat BB1 (rBB1) homologue was cloned and used in Northern hybridization analyses and in situ hybridization histochemistry (ISHH). Northern hybridization analyses of fetal and postnatal rat lung demonstrate that rBB1 RNA abundance is relatively low on fetal days E17 through E19, with a small peak of expression occurring on fetal day E20, then increases at birth with peak expression in adult lung. ISHH correlates with the Northern hybridization data and reveals rBB1 RNA expression throughout lung from E17to E21in both epithelium and mesenchyme. In postnatal lung, more intense expression of BB1 was observed than in fetal lung, localizing BB1 transcripts to proximal and distal airways and mesenchymal cells surrounding airways. Proliferating cell nuclear antigen (PCNA) was identified in lung sections adjacent to those used for ISHH and it was found that BB1 expression was present in PCNA positive cells; however, BB1 expression was not limited to PCNA-positive cells in either the fetal or postnatal periods. This was most apparent in adult (60-day) rat lung where essentially no PCNA positive cells were detected, but intense BB1 expression was detected in airway epithelium and surrounding mesenchyme. These studies demonstrate developmental regulation of BB1 during lung development. The findings are consistent with BB1 action in cell growth-related processes of fetal and early postnatal lung; however, the distribution of BB1 expression in relation to PCNA localization suggests that BB1 participates in cellular functions in addition to cell proliferation.
3D-Stacked Memory For Shared-Memory Multithreaded Workloads

This paper aims to address the issue of CPU-memory intercommunication latency with the help of 3D stacked memory. We propose a 3D-stacked memory configuration, where a DRAM module is mounted on top of the CPU to reduce latency. We have used a comprehensive simulation environment to assure both fabrication feasibility and energy efficiency of the proposed 3D stacked memory modules. We have evaluated our proposed architecture by running PARSEC 2.1, a benchmark suite for shared-memory multithreaded workloads. The results demonstrate an average of 40% improvement over conventional DDR3/4 memory architectures.
Duration of Preoperative Electrocardiographic QRS Complex and the Incidence of Heart Arrest after Aorto Coronary Bypass Surgery

Sudden heart arrest (HA) in the early phase after aorto coronary bypass surgery represents a serious event necessitating resuscitation, and for those who survive usually also an extra stay in the coronary care unit. Since such episodes of heart standstill may be related to conduction defects, a study was conducted to determine whether the duration of the QRS complex on the preoperative ECG is a marker for this morbid event. A cohort of 1011 consecutive patients operated on between 1982 and 1986 and followed to January 1st, 1993 were included in the study. Incidence of lethal or non-lethal HA during the first 4 weeks after surgery was considered as the primary endpoint and total mortality as the secondary endpoint. The incidence of HA was 40/1011 = 4%, with the majority of events (60%) being lethal. Independent risk factors of HA using the multivariate logistic model were previous coronary artery bypass surgery, presence of mitral regurgitation, left ventricular ejection fraction and the intraoperative cross-clamp time of aorta. Adjusting for the effect of confounder variables showed that the gradient effect of QRS complex duration on the endpoint HA was still present (p
An overview of studies on a community of Panamanian figs

Findings from long-term studies of eighteen monoecious fig species and their associated pollinators, parasites, and seed dispersers from a lowland tropical forest community in Panama are summarized. Studies of evolutionary genetics confirm the suggestion from earlier morphological studies that pollinator and non-pollinator wasps, as well as parasitic nematodes, are generally species-specific. Further, phylogenetic reconstructions suggest that these systems are predominated by strict-sense co-evolution among several trophic levels of fig-associated organisms. Studies of population genetics show that fig wasps routinely disperse pollen over surprisingly great distances. Moreover, both the number of individual fig trees constituting a breeding population and the area that they occupy (>100km2) are among the largest for any plant species known. Studies of factors influencing reproductive success of both the figs and their pollinators indicate that, for any given species, many factors (e.g. number and size of pollinators, resource availability, parasite loads) interact in complex but systematic ways to affect the production of seeds and pollinator wasps. Across species, there are repeated patterns of associations among characters such as average number of pollinators per fruit, pollinator sex ratios, nematode virulence, fruit size, fruit colour, physiological properties of the fruit, taxa of associated seed dispersers and degree of synchrony of fruit ripening that imply causal, adaptive linkages and trade-offs among these characters. Collectively, these studies suggest the critical role for comparative work of many species, preferably at many sites, in the understanding of this complex mutualism.
Yuripopoverus africanus gen. et sp. n. from East African copal (Hemiptera: Fulgoromorpha: Ricaniidae)

Yuripopoverus africanus gen. et sp. n. from East African copal (Hemiptera: Fulgoromorpha: Ricaniidae) A new genus and species of the planthopper family Ricaniidae Yuripopoverus africanus gen. et sp. n. is described and illustrated on the basis of an inclusion in East African copal.
Comprehensive taxon sampling reveals unaccounted diversity and morphological plasticity in a group of dimitic polypores (Polyporales, Basidiomycota)

The phylogeny of the poroid and hydnoid genera Antrodiella, Junghuhnia, and Steccherinum (Polyporales, Basidiomycota) was studied utilizing sequences of the gene regions ITS, nLSU, mtSSU, atp6, rpb2, and tef1. Altogether 148 taxa, represented by 549 sequences, were included in analyses. Results show that most species of these genera form a well supported clade in the Polyporales, called Steccherinaceae, along with 12 other hydnoid and poroid genera. Within the Steccherinaceae, generic concepts need to be revised: no fewer than 15 new genera are needed to accommodate existing and new species. At least 16 transitions have taken place between poroid and hydnoid hymenophore types within the Steccherinaceae, and similar plasticity can be seen in microscopic characters. Nevertheless, natural genera revealed in the analysis can mostly be characterized morphologically and, with few exceptions, poroid and hydnoid species belong to separate genera. The genus Steccherinum is shown to contain both hydnoid and poroid species. Species of the former Antrodiella belong to at least 10 genera within the Steccherinaceae.