Miracle-dz/UniFAR-FTUs huggingface dataset:
Satellite SST-Based Coral Disease Outbreak Predictions for the Hawaiian Archipelago

Predicting wildlife disease risk is essential for effective monitoring and management, especially for geographically expansive ecosystems such as coral reefs in the Hawaiian archipelago. Warming ocean temperature has increased coral disease outbreaks contributing to declines in coral cover worldwide. In this study we investigated seasonal effects of thermal stress on the prevalence of the three most widespread coral diseases in Hawai’i: Montipora white syndrome, Porites growth anomalies and Porites tissue loss syndrome. To predict outbreak likelihood we compared disease prevalence from surveys conducted between 2004 and 2015 from 18 Hawaiian Islands and atolls with biotic (e.g., coral density) and abiotic (satellite-derived sea surface temperature metrics) variables using boosted regression trees. To date, the only coral disease forecast models available were developed for Acropora white syndrome on the Great Barrier Reef (GBR). Given the complexities of disease etiology, differences in host demography and environmental conditions across reef regions, it is important to refine and adapt such models for different diseases and geographic regions of interest. Similar to the Acropora white syndrome models, anomalously warm conditions were important for predicting Montipora white syndrome, possibly due to a relationship between thermal stress and a compromised host immune system. However, coral density and winter conditions were the most important predictors of all three coral diseases in this study, enabling development of a forecasting system that can predict regions of elevated disease risk up to six months before an expected outbreak. Our research indicates satellite-derived systems for forecasting disease outbreaks can be appropriately adapted from the GBR tools and applied for a variety of diseases in a new region. These models can be used to enhance management capacity to prepare for and respond to emerging coral diseases throughout Hawai’i and can be modified for other diseases and regions around the world.
Monophonic Distance in Graphs

For any two vertices u and v in a connected graph G, a u – v path is a monophonic path if it contains no chords, and the monophonic distance dm(u, v) from u to v is defined as the length of a longest u – v monophonic path in G. A u – v monophonic path of length dm(u, v) is called a u – v monophonic. The monophonic eccentricity em(v) of a vertex v in G is the maximum monophonic distance from v to a vertex of G. The monophonic radius radm G of G is the minimum monophonic eccentricity among the vertices of G, while the monophonic diameter diamm G of G is the maximum monophonic eccentricity among the vertices of G. It is shown that radm G ≤ diamm G for every connected graph G and that every pair a, b of positive integers with a ≤ b is realizable as the monophonic radius and monophonic diameter of some connected graph. Also, for any three positive integers a, b and c with 3 ≤ a ≤ b ≤ c, there is a connected graph G such that rad G = a, radm G = b and radDG = c; and for any three positive integers a, b and c with 5 ≤ a ≤ b ≤ c, there is a connected graph G such that diam G = a, diamm G = b and diamD G = c, where rad G, diam G, radDG and diamD G denote the radius, diameter, detour radius and detour diameter, respectively. The monophonic center of G is the subgraph induced by the vertices of G having monophonic eccentricity radm G and it is shown that every graph is the monophonic center of some connected graph and also that the monophonic center Cm(G) of every connected graph G is a subgraph of some block of G.
Survey for Placental Disease and Reproductive Pathogens in the Endangered Hawaiian Monk Seal (Neomonachus schauinslandi)

Abstract: There is considerable temporal and spatial variability in the reproductive rates of Hawaiian monk seals (HMS; Neomonachus schauinslandi). Poor reproductive performance limits the recovery of this endangered species; however, causal factors are not fully understood. There is serologic evidence that HMS are exposed to pathogens that can impact reproductive success, but the prevalence of placental infections in HMS has not been evaluated. Placental tissues (n=50), including tissues from 25% of known HMS births, were opportunistically collected in 2011 from six Northwestern Hawaiian Islands and three main Hawaiian Islands. Reproductive histories of the sampled females were representative of the breeding population, as determined through comparisons in age of primiparity and mature reproductive rate. Placental tissues were examined histologically and screened by PCR for Coxiella burnetii, Brucella spp. , Chlamydia spp. , Leptospira spp. , herpesviruses, and Toxoplasma gondii. There was no histologic evidence of placental pathology, and molecular analyses were negative. These negative results can be used to estimate pathogen prevalence in the nonsampled population. For an approximate population size of 1,300 HMS, we can estimate with 99% confidence that the prevalence of each pathogen tested is 9% or less. This is low relative to other pinnipeds and indicates that factors other than reproductive pathology, such as resource limitation, may drive variability in HMS reproductive rates. Further investigation into the cumulative impacts of resource limitation and other stressors on HMS reproduction is warranted.
A Three-Zone Distance Protection Scheme Capable to Cope With the Impact of UPFC

To improve the power transfer capability and reliability of the power grid, the unified power flow controller (UPFC) project has been put into operation in the western Nanjing power grid. Based on the practical project, the influence of UPFC on the distance protection is analyzed. To cope with that, the novel three-zone distance protection scheme is put forward. The zone 2 and zone 3 of the novel three-zone distance protection scheme are the same with those of conventional distance protection; however, the novel distance protection zone 1 is based on the parameter model of transmission line. According to the average value and fluctuation degree of the fault distance calculation results, the proposed distance protection zone 1 can effectively distinguish between the internal faults and external faults. More importantly, the proposed distance protection zone 1 can realize effective cooperation with the conventional distance protection zone 2 and zone 3, to construct a complete three-zone distance protection scheme and guarantee the correct operation of the novel three-zone distance protection scheme. The simulation cases in the PSCAD/EMTDC software environment verifies that the proposed three-zone distance protection has excellent performance, and would not be affected by the operational mode and control parameters of UPFC.
Appropriate methods to combine forward and reverse free-energy perturbation averages

We consider the accuracy of several methods for combining forward and reverse free-energy perturbation averages for two systems (labeled 0 and 1). The practice of direct averaging of these measurements is argued as not reliable. Instead, methods are considered of the form β(A1−A0)=−ln[〈w(u)exp(−βu/2)〉0/〈w(u)exp(+βu/2)〉1], where A is the free energy, β=1/kT is the reciprocal temperature, u=U1−U0 is the difference in configurational energy, w(u) is a weighting function, and the angle brackets indicate an ensemble average performed on the system indicated by the subscript. Choices are considered in which w(u)=1 and 1/cosh[(u−C)/2]; the latter being Bennett’s method where C is a parameter that can be selected arbitrarily, and may be used to optimize the precision of the calculation. We examine the methods in several applications: calculation of the pressure of a square-well fluid by perturbing the volume, the chemical potential of a high-density Lennard-Jones system, and the chemical potential of a model for .
DNA Ligase IV and Artemis Act Cooperatively to Suppress Homologous Recombination in Human Cells: Implications for DNA Double-Strand Break Repair

Nonhomologous end-joining (NHEJ) and homologous recombination (HR) are two major pathways for repairing DNA double-strand breaks (DSBs); however, their respective roles in human somatic cells remain to be elucidated. Here we show using a series of human gene-knockout cell lines that NHEJ repairs nearly all of the topoisomerase II- and low-dose radiation-induced DNA damage, while it negatively affects survival of cells harbouring replication-associated DSBs. Intriguingly, we find that loss of DNA ligase IV, a critical NHEJ ligase, and Artemis, an NHEJ factor with endonuclease activity, independently contribute to increased resistance to replication-associated DSBs. We also show that loss of Artemis alleviates hypersensitivity of DNA ligase IV-null cells to low-dose radiation- and topoisomerase II-induced DSBs. Finally, we demonstrate that Artemis-null human cells display increased gene-targeting efficiencies, particularly in the absence of DNA ligase IV. Collectively, these data suggest that DNA ligase IV and Artemis act cooperatively to promote NHEJ, thereby suppressing HR. Our results point to the possibility that HR can only operate on accidental DSBs when NHEJ is missing or abortive, and Artemis may be involved in pathway switching from incomplete NHEJ to HR.
Electron Transfer

Information about electron-transfer reactions of dissolved organic matter (DOM) is lacking. We determined electron acceptor and donor capacities (EAC and EDC) of a peat humic acid and an untreated peat DOM by electrochemical reduction and reduction with metallic Zn and H2S (EAC), and by oxidation with complexed ferric iron (EDC) at pH 6.5. DOC concentrations (10-100 mg L-1) and pH values (4.58) were varied in selected experiments. EAC reached up to 6.2 mequiv‚(g C)-1 and EDC reached up to 1.52 mequiv‚ (g C)-1. EDC decreased with pH and conversion of chelated to colloidal iron, and the electron-transfer capacity (ETC) was controlled by the redox potential Eh of the reactant (ETC ) 1.016‚Eh 0.138; R 2 ) 0.87; p ) 0.05). The kinetics could be adequately described by pseudo firstorder rate laws, one or two DOM pools, and time constants ranging from 2.1 × 10-3 d-1 to 1.9 × 10-2 d-1 for the fast pool. Reactions were completed after 24-160 h depending on the redox couple applied. The results indicate that DOM may act as a redox buffer over electrochemical potentials ranging from -0.9 to +1.0 V.
Utility of Environmental DNA for Monitoring Rare and Indicator Macroinvertebrate Species

Abstract: Accurate knowledge of the distribution of rare, indicator, or invasive species is required for conservation and management decisions. However, species monitoring done with conventional methods may have limitations, such as being laborious in terms of cost and time, and often requires invasive sampling of specimens. Environmental DNA (eDNA) has been identified as a molecular tool that could overcome these limitations, particularly in aquatic systems. Detection of rare and invasive amphibians and fish in lake and river systems has been effective, but few studies have targeted macroinvertebrates in aquatic systems. We expanded eDNA techniques to a broad taxonomic array of macroinvertebrate species in river and lake systems. We were able to detect 5 of 6 species (Ancylus fluviatilis, Asellus aquaticus, Baetis buceratus, Crangonyx pseudogracilis, and Gammarus pulex) with an eDNA method in parallel to the conventional kicknet-sampling method commonly applied in aquatic habitats. Our eDNA method showed medium to very high consistency with the data from kicknet-sampling and was able to detect both indicator and nonnative macroinvertebrates. Furthermore, our primers detected target DNA in concentrations down to 10-5 ng/µL of total extracted tissue DNA in the absence of background eDNA in the reaction. We demonstrate that an eDNA surveillance method based on standard PCR can deliver biomonitoring data across a wide taxonomic range of macroinvertebrate species (Gastropoda, Isopoda, Ephemeroptera, and Amphipoda) in riverine habitats and may offer the possibility to deliver data on a more refined time scale than conventional methods when focusing on single or few target species. Such information based on nondestructive sampling may allow rapid management decisions and actions.
Eigenfunction Expansions Associated with Second-order Differential Equations for Hilbert Space-valued Functions

where for each r € HO, oo) A(r) is an operator in a Hilbert space H and & acts on ^-valued functions on fO, co). Restricting the domain of <£ appropriately, we can regard 3? as an operator in f) = £2 (0, °° ; H}. Our purpose is to develop an eigenfunction expansion theory associated with the differential operator <£. If dim H=l, i.e. jfiT=C, then & is an ordinary second-order differential operator and A(r) is simply an operator of multiplication by a function g(r). For real-valued g(r) a rather complete eigenfunction expansion theory has been worked out by Weyl ^10], Stone Q8j, Titchmarsh Q9j, Kodaira £4], Q5] and others. But when H is an infinite-dimensional Hilbert space, it seems that no complete theory, comparable with the one for ordinary differential operators, has been presented. Rofe-Beketov Q7] considers the case where A(f) is a bounded selfadjoint operator-valued function on QO, oo) which is continuous in the uniform operator topology. He shows that there exist a non-negative definite, bounded opera tor -valued, interval function p(/), /CR? and a bounded operator-valued function a)(r, ^) on Q03 oo)5 satisfying
Who Profits from Patents? Rent-Sharing at Innovative Firms

This article analyzes how patent-induced shocks to labor productivity propagate into worker compensation using a new linkage of U.S. patent applications to U.S. business and worker tax records. We infer the causal effects of patent allowances by comparing firms whose patent applications were initially allowed to those whose patent applications were initially rejected. To identify patents that are ex ante valuable, we extrapolate the excess stock return estimates of Kogan et al. (2017) to the full set of accepted and rejected patent applications based on predetermined firm and patent application characteristics. An initial allowance of an ex ante valuable patent generates substantial increases in firm productivity and worker compensation. By contrast, initial allowances of lower ex ante value patents yield no detectable effects on firm outcomes. Patent allowances lead firms to increase employment, but entry wages and workforce composition are insensitive to patent decisions. On average, workers capture roughly 30 cents of every dollar of patent-induced surplus in higher earnings. This share is roughly twice as high among workers present since the year of application. These earnings effects are concentrated among men and workers in the top half of the earnings distribution and are paired with corresponding improvements in worker retention among these groups. We interpret these earnings responses as reflecting the capture of economic rents by senior workers, who are most costly for innovative firms to replace.
Finding multiple global optima exploiting differential evolution's niching capability

Handling multimodal functions is a very important and challenging task in evolutionary computation community, since most of the real-world applications exhibit highly multi-modal landscapes. Motivated by the dynamics and the proximity characteristics of Differential Evolution's mutation strategies tending to distribute the individuals of the population to the vicinity of the problem's minima, we introduce two new Differential Evolution mutation strategies. The new mutation strategies incorporate spatial information about the neighborhood of each potential solution and exhibit a niching formation, without incorporating any additional parameter. Experimental results on eight well known multimodal functions and comparisons with some state-of-the-art algorithms indicate that the proposed mutation strategies are competitive and very promising, since they are able to reliably locate and maintain many global optima throughout the evolution process.
Antimicrobial resistance and virulence genes of non-typhoidal Salmonella isolates in The Gambia and Senegal.

INTRODUCTION The prevalence of virulence genes in non-typhoidal Salmonella (NTS) and its association with commonly used antibiotics in West Africa is unknown. METHODOLOGY We tested 185 NTS isolates from children, animals, and food products for the presence of twelve virulence genes by PCR. Ten of the virulence genes tested belonged to the five Salmonella pathogenicity islands implicated in its pathogenesis. RESULTS Ten of twelve virulence genes except sopE and pefA were present in at least 70% of the isolates tested; sopE and pefA were observed in 33% and 44% of the isolates, respectively. The most prevalent gene was invA (99.5%), which is an invasion gene conserved within the Salmonella enterica. pipD and sopB genes, which were associated with serovar Enteritidis, were detected in 92.4% and 94.1% of isolates respectively. S. Istanbul and S. Javiana, which were isolated from chicken-serving restaurants, carried all the virulence genes of the five pathogenicity islands. There was significant association between sopB, sitC, orfLC, pipD and pefA virulence genes and resistance to commonly used antibiotics in Senegal and The Gambia, namely amoxicillin, ticarcillin, trimethoprim plus sulfamethoxazole, tetracycline, trimethoprim, spectinomycin, streptomycin, sulfonamides and nitrofurantoin. CONCLUSIONS This study shows that virulence genes are present in NTS strains isolated from various sources. The significant association between some virulence genes and antibiotic resistance may have important implications with regard to the spread and persistence of resistance and virulence genes in Salmonella and to the prudent use of antimicrobial agents in humans and animals in West Africa.
XRD RESIDUAL STRESS MEASUREMENTS ON ALLOY 600 PRESSURIZER HEATER SLEEVE MOCKUPS

Alloy 600 penetrations in several pressurized water reactors have experienced primary water stress corrosion cracking near the partial penetration Jwelds between the Alloy 600 and the cladding on the inside diameter of the components. The microstructure and tensile properties indicated that the Alloy 600 was susceptible to primary water stress corrosion cracking (PWSCC) providing that a high tensile stress (applied + residual) was present. The residual stress distributions at the inside diameter surface and at different depths below the surface were measured in two Alloy 600 heater sleeve mockups. Surface residual stresses ranged from 340 to 690 MPa. For the most part, the residual stresses decreased with increasing depth below the surface. For the heater sleeve mockups, the percent cold work (i.e. true plastic strain) and yield strength as a function of depth were determined. As a result of pre-reaming and welding the heater sleeves, the amount of plastic strain and yield strength increased to a nominal depth of 0.025 cm. The true plastic strain and yield strength decreased with increasing depth below the surface.
ERCC 1 expression in patients with colorectal cancer : a pilot study

Aim: Excision repair cross complementation group 1 (ERCC1) has a key role in enhanced DNA damage repair caused by oxaliplatin-based therapy and may lead to resistance of these platinum drugs in colorectal cancer (CRC) patients. Hence, the present preliminary study aimed to explore the role of ERCC1 C/T polymorphism at codon 118 as well as its immunoreactivity in patients with primary CRC. Methods: ERCC1 polymorphism was studied using PCR-RFLP and ERCC1 protein expression was examined by immunohistochemistry in 50 CRC patients. Results: ERCC1 codon 118 C/T polymorphism analysis reported the predominance of C/T (52%) genotype as compared to C/C (38%) and T/T (10%) genotypes. Furthermore, 72% of patients showed positive ERCC1 protein expression. Significant correlation was not observed between clinicopathological parameters and ERCC1 polymorphism, while ERCC1 protein expression significantly correlated only with tumor site (colon vs. rectum) (P = 0.046). Further, the present study failed to demonstrate the role of ERCC1 C118T polymorphism or protein expression as useful prognostic markers in CRC patients. Conclusion: ERCC1-positive protein expression may be a useful marker for rectal cancer patients. However, further evaluation in a larger set of CRC patients is required to better understand the role of ERCC1.
Comparison of NF-RO and RO-NF for the Treatment of Mature Landfill Leachates: A Guide for Landfill Operators †

Reverse osmosis (RO) and nanofiltration (NF) are among the state-of-the-art technologies for treating landfill leachates. Due to the complexity and variance in the composition of leachates, numerous combinations of multiple technologies are used for their treatment. One process chain for the treatment of raw leachate is RO followed by further concentration of RO-retentate using NF (RO-NF scheme). The aptness of this process train used by some landfill sites around the world (usually with the aim of volume reduction so as to re-inject the concentrate into the landfill) is questionable. This study investigated two schemes RO-NF and NF-RO (nanofiltration of raw leachate followed by reverse osmosis of NF permeate) to identify their merits/demerits. Experiments were conducted in bench scale using commercial membranes: DOW Filmtec NF270 and SW30HR. Filtration trials were performed at different pressures to compare the water and solute transports in the individual stages of the two schemes. Based on the water fluxes and compositions of retentates and permeates; osmotic pressures, energy demands, and other possible operational advantages were discussed. NF-RO offers some advantages and flexibility for leachate treatment besides being energy efficient compared to RO-NF, wherein osmotic pressure steadily increases during operation in turn increasing operation and maintenance costs.
The direct thrombin inhibitors (argatroban, bivalirudin and lepirudin) and the indirect Xa-inhibitor (danaparoid) increase fibrin network porosity and thus facilitate fibrinolysis

Summary The present study aimed to assess whether the fibrin network structure is modified by the direct thrombin-inhibitors lepirudin, argatroban or bivalirudin and by the indirect Xa-inhibitor danaparoid. Using an in vitro assay that imitates the physiological process of coagulation from thrombin generation to fibrin formation, we examined a normal plasma pool spiked with one of the inhibitors. At concentrations considered to be the plasma levels observed during therapy, almost no influence was detected for lepirudin despite clear-cut effects on “clotting time”. However, argatroban, bivalirudin and danaparoid increased the fibrin gel permeability (Ks) to a similar extent. At concentrations higher than the “therapeutic” levels, the dose-response curve in the Ks assay became very steep for lepirudin while those were shallow for the others. In parallel with the drug-induced increases of Ks, larger network pores in 3D-microscopic images and significant shortenings in “clot lysis time” induced by addition of rtPA were observed. Recombinant factor VIII (rFVIII) added to danaparoid-treated samples profoundly counteracted the increase of Ks but had only a slight or no effect on the other drugs. Thus, in vitro, argatroban, bivalirudin and danaparoid have comparable anticoagulating effects, rendering the fibrin network more permeable and less resistant to fibrinolysis. For lepirudin, the steep dose-response curve supports previous clinical findings, i.e. this thrombin inhibitor has a narrow therapeutic window. Furthermore, our data suggest that the haemostatic agent, rFVIII, might be effective in treatment of bleeding complications induced by danaparoid.