Miracle-dz/UniFAR-FTUs huggingface dataset:
Early versus Delayed Hepatectomy for Spontaneously Ruptured Hepatocellular Carcinoma: A Systematic Review and Meta-Analysis

Abstract Objective Here, we aimed to compare early hepatectomy (EH) with delayed hepatectomy (DH) as a treatment for spontaneously ruptured hepatocellular carcinoma (HCC). Methods Several databases were systematically searched for eligible studies that compared DH with EH for spontaneously ruptured HCC treatment. Studies that met the inclusion criteria were reviewed systematically, and the reported data were aggregated statistically, using the RevMan v5.3 software. Results Seven studies were included, with a total of 385 patients, comprising of 224 EH cases and 161 DH cases. Compared with the EH group, incidence of intraoperative bleeding [mean difference (MD), 353.93; 95% CI, 230.04-447.83; P < 0.00001], volume of intraoperative blood transfusion (MD, 420.61; 95% CI, 354.40-486.81, P < 0.00001), and 30-day mortality rate (OR, 14.94; 95% CI, 1.76-126.66; P = 0.01) were significantly lower in the DH group. Furthermore, the 1-, 2-, and 3-year survival rates were significantly higher in the DH group [1-year：hazard ratio (HR), 1.76; 95% CI, 1.06-2.94; P = 0.03; 2-year：HR, 1.52; 95% CI, 1.02-2.25; P = 0.04; 3-year: HR, 1.53; 95% CI, 1.06-2.21; P = 0.02]. There was no difference between the groups in the 5-year survival rate (HR, 1.40; 95% CI, 0.92-2.11; P = 0.11). Conclusion For resectable spontaneously ruptured HCC, DH could reduce intraoperative bleeding, intraoperative blood transfusion volume, and 30-day mortality rate and increase the 1-, 2-, and 3-year survival rates, endowing the patients with greater short- and long-term benefits during and following the surgery.
Discriminate suckling in pipistrelle bats is supported by DNA fingerprinting

DNA fingerprints were obtained by using Jeffreys' probes 33.6 and 33.15 with DNA extracted from nine mother‐young pairs of pipistrelle bats Pipistrellus pipistrellns to investigate the feasibility of this technique for determining relatedness in this species. The bats had mated in the wild and gave birth in captivity. All of nine pairs in which infants were found attached showed band‐sharing coefficients higher than those for individuals presumed to be unrelated but run in adjacent lanes of the gels. We therefore conclude that all attached infants were probably true offspring.
ALTERATIONS OF CLUB CELL ACTIVITY IN EPIDERMIS OF COMMON CARP, CYPRINUS CARPIO (ACTINOPTERYGII: CYPRINIFORMES: CYPRINIDAE), DUE TO INFECTION BY ICHTHYOPHTHIRIUS MULTIFILIIS (PROTISTA: CILIOPHORA)

The epidermal tissue of fish is often the primary barrier, to pathogens in the environment (Singh and Mittal 1990, Iger et al. 1994, Buchmann et al. 2004, Rakers et al. 2010, Ottesen et al. 2010). The cell-mediated innate mechanisms of epidermal tissues include specialized cells such as macrophages, granulocytes, natural killer cells, and also physical barriers such as mucous layers and skin epithelial tissue lines (Jones 2001, Aoki et al. 2008). The epidermal club cells of many fishes in the superorder Ostariophysi have evolved primarily as part of the immune system (Chivers et al. 2007, Halbgewachs et al. 2009, Ferrari et al. 2010) but their functional mechanisms, with non-specific and/or specific immunity, have not been explored in detail. The evolution of club cells of ostariophysan fish remains enigmatic and controversial as it has been historically linked to chemical alarm signalling (von Frisch 1941, Smith1992, James et al. 2009). However, Carreau-Green et al. (2008) suggested that club cells do not have an alarm function in fathead minnow, Pimephales promelas Rafinesque, 1820. Such evidence would support the possibility that club cells of fishes may be maintained by natACTA ICHTHYOLOGICA ET PISCATORIA (2011) 41 (3): 185–192 DOI: 10.3750/AIP2011.41. 3.06
Effects of fluorinated porcine hydroxyapatite on lateral ridge augmentation: an experimental study in the canine mandible.

PURPOSE The aim of this study was to evaluate the effects of porcine hydroxyapatite (PHA) and fluorinated porcine hydroxyapatite (FPHA) applied concomitantly with collagen membranes (CMs) on bone regeneration in mandibular lateral ridge defects. MATERIALS AND METHODS Mandibular third premolar to second molar were extracted bilaterally in six male beagle dogs. After 8 weeks of healing, six standardized box-shaped defects were bilaterally created at the buccal aspect of the mandibles and randomly allocated in a split-mouth design to the (i) PHA, (ii) FPHA or (iii) blank group and covered with CMs. After 12 weeks, biopsies of the defects were obtained for micro-computed tomography (micro-CT) evaluation and histological analysis. RESULTS Both FPHA and PHA promoted new bone formation and showed a better ridge width maintenance capacity than the blank control treatment. The micro-CT evaluation showed that the bone volume fraction (BV/TV) in the FPHA group was significantly higher than that in the PHA group. The trabecular number (Tb.N) in the FPHA group was significantly higher than that in the blank group. Histomorphometric analysis revealed a significantly larger area and higher ratio of newly formed bone in the FPHA group than those in the PHA group. The ratio of non-mineralized tissue in the FPHA group was significantly lower than that in the PHA group. No significant difference in the amount of residual materials was found between the FPHA and PHA groups. CONCLUSIONS FPHA achieved better ridge width maintenance and bone regeneration outcomes than PHA as a bone substitute in lateral ridge augmentation.
An internally eGFP‐tagged α‐adaptin is a fully functional and improved fiduciary marker for clathrin‐coated pit dynamics

Clathrin mediated endocytosis (CME) has been extensively studied in living cells by quantitative total internal reflection fluorescence microscopy (TIRFM). Fluorescent protein fusions to subunits of the major coat proteins, clathrin light chains or the heterotetrameric adaptor protein (AP2) complexes, have been used as fiduciary markers of clathrin coated pits (CCPs). However, the functionality of these fusion proteins has not been rigorously compared. Here, we generated stable cells lines overexpressing mRuby‐CLCa and/or μ2‐eGFP, σ2‐eGFP, two markers currently in use, or a novel marker generated by inserting eGFP into the unstructured hinge region of the α subunit (α‐eGFP). Using biochemical and TIRFM‐based assays, we compared the functionality of the AP2 markers. All of the eGFP‐tagged subunits were efficiently incorporated into AP2 and displayed greater accuracy in image‐based CCP analyses than mRuby‐CLCa. However, overexpression of either μ2‐eGFP or σ2‐eGFP impaired transferrin receptor uptake. In addition, μ2‐eGFP reduced the rates of CCP initiation and σ2‐eGFP perturbed AP2 incorporation into CCPs and CCP maturation. In contrast, CME and CCP dynamics were unperturbed in cells overexpressing α‐eGFP. Moreover, α‐eGFP was a more sensitive and accurate marker of CCP dynamics than mRuby‐CLCa. Thus, our work establishes α‐eGFP as a robust, fully functional marker for CME.
Tarsal chemoreception in the polyphagous grasshopper Schistocerca americana: behavioural assays, sensilla distributions and electrophysiology

ABSTRACT Behavioural and electrophysiological responses of Schistocerca americana (Drury) (Orthoptera: Acrididae) to chemical stimulation of the tarsi were investigated. Using restrained insects, differences in leg‐waving behaviour were observed following stimulation by sucrose and nicotine hydrogen tartrate (NHT), compared to control stimulations by water. Furthermore, free‐walking insects were able to detect NHT on leaf surfaces, resulting in leg‐raising to avoid tarsal contact.
Global declines in human‐driven mangrove loss

Global mangrove loss has been attributed primarily to human activity. Anthropogenic loss hotspots across Southeast Asia and around the world have characterized the ecosystem as highly threatened, though natural processes such as erosion can also play a significant role in forest vulnerability. However, the extent of human and natural threats has not been fully quantified at the global scale. Here, using a Random Forest‐based analysis of over one million Landsat images, we present the first 30 m resolution global maps of the drivers of mangrove loss from 2000 to 2016, capturing both human‐driven and natural stressors. We estimate that 62% of global losses between 2000 and 2016 resulted from land‐use change, primarily through conversion to aquaculture and agriculture. Up to 80% of these human‐driven losses occurred within six Southeast Asian nations, reflecting the regional emphasis on enhancing aquaculture for export to support economic development. Both anthropogenic and natural losses declined between 2000 and 2016, though slower declines in natural loss caused an increase in their relative contribution to total global loss area. We attribute the decline in anthropogenic losses to the regionally dependent combination of increased emphasis on conservation efforts and a lack of remaining mangroves viable for conversion. While efforts to restore and protect mangroves appear to be effective over decadal timescales, the emergence of natural drivers of loss presents an immediate challenge for coastal adaptation. We anticipate that our results will inform decision‐making within conservation and restoration initiatives by providing a locally relevant understanding of the causes of mangrove loss.
Nitrogen and phosphorus resorption in a salt marsh in northern Turkey

This study was conducted to investigate foliar nitrogen and phosphorus dynamics, nitrogen and phosphorus resorption, and some leaf traits (i.e. SLA=specific leaf area) in some coastal salt marsh plants located in northern Turkey. The study area is located on the east bank of the Kizilirmak River in the central Black Sea Region. There were statistically significant differences among months (from June to October) in terms of SLA in all species except for Artemisia santonicum. However, no significant differences were found with respect to P in all species. The highest N and P resorption efficiencies were found in Salicornia prostrata, whereas the lowest resorption efficiencies were found in Euphorbia paralias. P resorption proficiency is biochemically complete in all species. N resorption proficiency is biochemically complete except for E. paralias. Additionally, Grime's CSR (C: competitive; S: stress-tolerant; R: ruderal) strategies were also investigated and it was found that all of the species exhibit competitive ruderal strategy.
Using an adoption design to test genetically based differences in risk for child behavior problems in response to home environmental influences

Abstract Differential susceptibility theory (DST) posits that individuals differ in their developmental plasticity: some children are highly responsive to both environmental adversity and support, while others are less affected. According to this theory, “plasticity” genes that confer risk for psychopathology in adverse environments may promote superior functioning in supportive environments. We tested DST using a broad measure of child genetic liability (based on birth parent psychopathology), adoptive home environmental variables (e.g., marital warmth, parenting stress, and internalizing symptoms), and measures of child externalizing problems (n = 337) and social competence (n = 330) in 54-month-old adopted children from the Early Growth and Development Study. This adoption design is useful for examining DST because children are placed at birth or shortly thereafter with nongenetically related adoptive parents, naturally disentangling heritable and postnatal environmental effects. We conducted a series of multivariable regression analyses that included Gene × Environment interaction terms and found little evidence of DST; rather, interactions varied depending on the environmental factor of interest, in both significance and shape. Our mixed findings suggest further investigation of DST is warranted before tailoring screening and intervention recommendations to children based on their genetic liability or “sensitivity. ”
Evaluating the influence of stocking history and barriers to movement on the spatial extent of hybridization between westslope cutthroat trout and rainbow trout

In this study we examine how the stocking of rainbow trout (Oncorhynchus mykiss), as well as the presence of fish movement barriers, influences the probability of introgression with westslope cutthroat trout (Oncorhynchus clarkii lewisi). We measured the level of introgression in cutthroat trout sampled from 32 locations that occurred either above or below fish movement barriers along with the frequency and number of rainbow trout stocked in the watershed over a 43-year period. The occurrence and level of hybridization in cutthroat trout were not related to whether the site was above a movement barrier or not. In contrast, the level of introgression was related to the distance to the nearest stocking location, the number of stocking events within the nearest watershed, and the total number of rainbow trout stocked in that watershed. Our data indicate that westslope cutthroat trout located further from stocking have a lower risk of introgression with rainbow trout, but those isolated above movement barrier.
Quantitative ecology and the brown trout

1. : Introduction: the brown trout and quantitative ecology. 2. : The brown trout, a successful polytypic species. 3. : Case-study: population dynamics of migratory brown trout in Black Brows Beck, 1966-1990. 4. : Growth and energetics of brown trout. 5. : Case-study: growth and production of migratory brown trout in Black Brows Beck, 1966-1990. 6. : Ecological differences between brown trout populations. 7. : Natural selection and genetic differences between brown trout. 8. : Mechanisms responsible for population regulation in young brown trout. 9. : General conclusions. References. Author index. Subject index
Immunity in Caenorhabditis elegans : A Tale of Two Transcription Factors

Immunity in Caenorhabditis elegans: A Tale of Two Transcription Factors by Michael TeKippe Department of Molecular Genetics and Microbiology Duke University Date:_______________________ Approved: ___________________________ Alejandro Aballay, Ph.D., Supervisor ___________________________ Fred Dietrich, Ph.D. ___________________________ John Perfect, M.D. ___________________________ Raphael Valdivia, Ph.D. An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Molecular Genetics and Microbiology in the Graduate School of Duke University 2009
Interactive visualization and analysis of morphological skeletons of brain vasculature networks with VessMorphoVis

Abstract Motivation Accurate morphological models of brain vasculature are key to modeling and simulating cerebral blood flow in realistic vascular networks. This in silico approach is fundamental to revealing the principles of neurovascular coupling. Validating those vascular morphologies entails performing certain visual analysis tasks that cannot be accomplished with generic visualization frameworks. This limitation has a substantial impact on the accuracy of the vascular models employed in the simulation. Results We present VessMorphoVis, an integrated suite of toolboxes for interactive visualization and analysis of vast brain vascular networks represented by morphological graphs segmented originally from imaging or microscopy stacks. Our workflow leverages the outstanding potentials of Blender, aiming to establish an integrated, extensible and domain-specific framework capable of interactive visualization, analysis, repair, high-fidelity meshing and high-quality rendering of vascular morphologies. Based on the initial feedback of the users, we anticipate that our framework will be an essential component in vascular modeling and simulation in the future, filling a gap that is at present largely unfulfilled. Availability and implementation VessMorphoVis is freely available under the GNU public license on Github at https://github.com/BlueBrain/VessMorphoVis. The morphology analysis, visualization, meshing and rendering modules are implemented as an add-on for Blender 2.8 based on its Python API (application programming interface). The add-on functionality is made available to users through an intuitive graphical user interface, as well as through exhaustive configuration files calling the API via a feature-rich command line interface running Blender in background mode. Supplementary information Supplementary data are available at Bioinformatics online.
Applying gene‐editing technology to elucidate the functional consequence of genetic and epigenetic variation in Alzheimer’s disease

Recent studies have highlighted a potential role of genetic and epigenetic variation in the development of Alzheimer’s disease. Application of the CRISPR‐Cas genome‐editing platform has enabled investigation of the functional impact that Alzheimer’s disease‐associated gene mutations have on gene expression. Moreover, recent advances in the technology have led to the generation of CRISPR‐Cas–based tools that allow for high‐throughput interrogation of different risk variants to elucidate the interplay between genomic regulatory features, epigenetic modifications, and chromatin structure. In this review, we examine the various iterations of the CRISPR‐Cas system and their potential application for exploring the complex interactions and disruptions in gene regulatory circuits that contribute to Alzheimer’s disease.
Genetic monitoring of translocated plant populations in practice

Plant translocations allow the restoration of genetic diversity in inbred and depauperate populations and help to prevent the extinction of critically endangered species. However, the successes of plant translocations in restoring genetically viable populations and the possible associated key factors are still insufficiently evaluated. To fill this gap, we carried out a thorough genetic monitoring of three populations of Arnica montana that were created or reinforced by the translocation of plants obtained from seeds of two large natural source populations from southern Belgium. We genotyped nine microsatellite markers and measured fitness quantitative traits over two generations (transplants, F1 seed progeny and newly established F1 juveniles). Two years after translocation, the genetic restoration had been effective, with high genetic diversity and low genetic differentiation across generations, extensive contemporary pollen flow, admixture between seed sources in the F1 generation and recruitment of new individuals from seeds. We detected site, seed source and maternal plant effects on plant fitness. The results also suggest that phenotypic plasticity may favour short‐term individual survival and long‐term adaptive capacity and enhance the evolutionary resilience of the populations to changing environmental conditions. We found no sign of heterosis or outbreeding depression at early life stages in the F1 generation. Our findings emphasize the importance of the translocation design (700 transplants of mixed sources, planted at high density) as well as the preparatory site management for the successful outcome of the translocations, which maximized flowering, random mating, and recruitment from seeds in the first years after translocation.
Mark–recapture on large spatial scale reveals long distance dispersal in the Marsh Fritillary, Euphydryas aurinia

1. Long distance dispersal (LDD), or movements far beyond the occupied habitat borders, maintains the integrity of metapopulations in fragmented landscapes. Recent studies on butterflies increasingly reveal that LDD exists even in species that were long regarded as sedentary. Mark–recapture (MR) studies covering larger study areas typically reveal movements among distant colonies.
Whole blood viscosity and red blood cell adhesion: Potential biomarkers for targeted and curative therapies in sickle cell disease

Sickle cell disease (SCD) is a recessive genetic blood disorder exhibiting abnormal blood rheology. Polymerization of sickle hemoglobin, due to a point mutation in the β‐globin gene of hemoglobin, results in aberrantly adhesive and stiff red blood cells (RBCs). Hemolysis, abnormal RBC adhesion, and abnormal blood rheology together impair endothelial health in people with SCD, which leads to cumulative systemic complications. Here, we describe a microfluidic assay combined with a micro particle image velocimetry technique for the integrated in vitro assessment of whole blood viscosity (WBV) and RBC adhesion. We examined WBV and RBC adhesion to laminin (LN) in microscale flow in whole blood samples from 53 individuals with no hemoglobinopathies (HbAA, N = 10), hemoglobin SC disease (HbSC, N = 14), or homozygous SCD (HbSS, N = 29) with mean WBV of 4.50 cP, 4.08 cP, and 3.73 cP, respectively. We found that WBV correlated with RBC count and hematocrit in subjects with HbSC or HbSS. There was a significant inverse association between WBV and RBC adhesion under both normoxic and physiologically hypoxic (SpO2 of 83%) tests, in which lower WBV associated with higher RBC adhesion to LN in subjects with HbSS. Low WBV has been found by others to associate with endothelial activation. Altered WBV and abnormal RBC adhesion may synergistically contribute to the endothelial damage and cumulative pathophysiology of SCD. These findings suggest that WBV and RBC adhesion may serve as clinically relevant biomarkers and endpoints in assessing emerging targeted and curative therapies in SCD.
Perspectives for Progress in the Assessment of Neuroplasticity with Strength Training.

Including a brief overview of current investigative approaches, the present Perspectives for Progress paper offers an overview of potential future experiments in the field of exercise-related neuroplasticity to strength training. It is proposed that the combination of specific experimental approaches and recently developed techniques holds the potential for unravelling spinal and supraspinal mechanisms involved in the adaptation to strength training.