Miracle-dz/UniFAR-FTUs huggingface dataset:
A new Capsicum baccatum accession shows tolerance to wild‐type and resistance‐breaking isolates of Tomato spotted wilt virus

D.E. D. was the recipient of a fellowship FPU from the Spanish Ministry of Education, Culture and Sports. This work was funded in part by INIA projects RTA2008-00010-C03 and RTA2013-00047-C02. We thank E. Lazaro and Dr. C. Armero (Dept. Statistics and Operational Research, University of Valencia) for helpful suggestions on statistics and Drs. N. Duran and J. Guerri (IVIA) for critical reading of the manuscript.
Strategic supply system design – a holistic evaluation of operational and production cost for a biorefinery supply chain

Pioneer cellulosic biorefineries across the United States rely on a conventional feedstock supply system based on one‐year contracts with local growers, who harvest, locally store, and deliver feedstock in low‐density format to the conversion facility. While the conventional system is designed for high biomass yield areas, pilot scale operations have experienced feedstock supply shortages and price volatilities due to reduced harvests and competition from other industries. Regional supply dependency and the inability to actively manage feedstock stability and quality, provide operational risks to the biorefinery, which translate into higher investment risk. The advanced feedstock supply system based on a network of depots can mitigate many of these risks and enable wider supply system benefits. This paper compares the two concepts from a system‐level perspective beyond mere logistic costs. It shows that while processing operations at the depot increase feedstock supply costs initially, they enable wider system benefits including supply risk reduction (leading to lower interest rates on loans), industry scale‐up, conversion yield improvements, and reduced handling equipment and storage costs at the biorefinery. When translating these benefits into cost reductions per liter of gasoline equivalent (LGE), we find that total cost reductions between –$0.46 to –$0.21 per LGE for biochemical and –$0.32 to –$0.12 per LGE for thermochemical conversion pathways are possible. Naturally, these system level benefits will differ between individual actors along the feedstock supply chain. Further research is required with respect to depot sizing, location, and ownership structures. Published 2015. This article is a U.S. Government work and is in the public domain in the USA. Biofuels, Bioproducts and Biorefining published by Society of Industrial Chemistry and John Wiley & Sons Ltd.
Functionality of Protein Isolates from Argentine Anchovy (Engraulis anchoita) Residue Obtained Using pH Shift Processing

The aim of this study was to obtain a protein isolate from Argentine anchovy (Engraulis anchoita) residue produced using the pH shifting process, with acid and alkaline solubilization and isoelectric precipitation of the protein, and evaluate their functional properties. The lowest solubility was obtained at pH 5 where 8.32% and 2.96% were found for acid and alkali respectively. The highest solubility was obtained at extreme pH. The maximum water holding capacity was presented by the alkaline protein isolate at pH 11 (9.63 g H(subscript 2)O/g protein). The oil holding capacity was 4.20mL/g protein, 7.26mL/g of protein for the acid and alkaline protein isolates, respectively. The strain showed higher oil holding capacity in alkaline pH, lower solubility in pH near the protein isoelectric point and a lower capacity to retain water in extreme pH when compared with the acid isolate.
A spatial comparison of common guillemots and sandeels in Scottish waters

The lesser sandeel (Ammodytes marinus) is an important prey of many seabirds and is the subject of the largest single-species fishery in the North Sea. Owing to their dependence on suitable sediment types, the distribution of post-settled sandeels (late 0-group and older age classes) is restricted and constant through time. Consequently, it is possible to compare the presence/absence of post-settled sandeels with the distribution of predators without the requirement for simultaneous collection of data on predator and prey distribution. Post-settled sandeels are an important prey of guillemots (Uria aalge), particularly during the breeding season. This paper examines the extent to which the spatial distribution of guillemots, sandeels, and fisheries overlaps. A recently collated database on the distribution of post-settled sandeels together with data from the European Seabirds at Sea database is used to compare the seasonal distributions of guillemots and sandeels. Spatial analyses were conducted at a single scale using two approaches: a non-parametric test which determines whether the distributions of predator and prey are the same; and generalized additive modelling. These analyses indicate that sandeel distribution is an important influence on guillemot distribution in the breeding season, but is less important during other times of the year. As such, the seasonal changes in association appear to reflect changes in diet and prey availability. Other factors that appeared to be important in influencing guillemot distribution were distance from colony and latitude (colony location). Data on fishery landings per ICES rectangle were used to consider the degree of common utilization of sandeel grounds by fisheries and guillemots in recent years. This comparison indicated that there were some areas important for both guillemots and fisheries, but that most concentrations of guillemots were found in unexploited sandeel areas.
Role of Insoluble Fiber on Gizzard Activity in Layers

SUMMARY Effect of access to wood shavings on gizzard activity was examined for birds fed pelleted wheat and oat diets with or without whole cereal inclusion. Layers on litter floor fed wheat diets with access to coarse wood shavings showed up to 60% higher weight of the gizzard and its content than caged layers fed the same diets without access to wood shavings. No such effect was found by feeding oat diets. Thus, a significant interaction was found, indicating that the appetite for wood shavings may be dependent of fiber level of the diet. Appetite for wood shavings and paper was examined for birds fed wheat and oat diets in 2 other experiments. The intake of wood shavings and paper by birds fed a wheat-based diet was numerically twice as high as in birds fed an oatbased diet. However, the individual variation was remarkably high. Neutral detergent fiber (NDF) concentration in the gizzard of birds fed the oat diet was up to twice (P < 0.05) the fiber concentration in the gizzard of birds fed the wheat diet. Passage of structural fibers through the gizzard and the appetite for feathers in the absence of structural fibers were also studied in an experiment using diets based on rice and casein. Coarse fiber structures were observed to accumulate in the gizzard. In the absence of fiber, birds ate feathers, indicating that birds may eat feathers to compensate for the lack of structural components in the feed.
The relationship of host size to feeding by mosquitoes of the Anopheles gambiae Giles complex (Diptera: Culicidae)

Attention has recently been focussed on the problem of why mosquitoes feed on some people more than others. In this paper, investigations of selective feeding by mosquitoes of the Anopheles gambiae Giles complex conducted in two villages in the Gambia are reported. Fed mosquitoes were collected from the bed nets of 35 groups of people who normally sleep together, for example mothers and infants or two children or two adults. A total of 2339 meals was analysed using haptoglobin or ABO typing to determine from which individual each meal had been obtained. The results showed that the proportion of feeds upon an individual in a group can be associated with the proportion of the total surface area or weight of the group contributed by that individual. The incidence of multiple feeding was between 3 and 6%. The results are discussed in relation to host selection by mosquitoes and their significance for models of malaria epidemiology.
Denoising Diffusion Samplers

Denoising diffusion models are a popular class of generative models providing state-of-the-art results in many domains. One adds gradually noise to data using a diffusion to transform the data distribution into a Gaussian distribution. Samples from the generative model are then obtained by simulating an approximation of the time-reversal of this diffusion initialized by Gaussian samples. Practically, the intractable score terms appearing in the time-reversed process are approximated using score matching techniques. We explore here a similar idea to sample approximately from unnormalized probability density functions and estimate their normalizing constants. We consider a process where the target density diffuses towards a Gaussian. Denoising Diffusion Samplers (DDS) are obtained by approximating the corresponding time-reversal. While score matching is not applicable in this context, we can leverage many of the ideas introduced in generative modeling for Monte Carlo sampling. Existing theoretical results from denoising diffusion models also provide theoretical guarantees for DDS. We discuss the connections between DDS, optimal control and Schr\"odinger bridges and finally demonstrate DDS experimentally on a variety of challenging sampling tasks.
Estimation of genetic parameters using health, fertility and production data from a management recording system for dairy cattle

The Dairy Information System (DAISY) was developed to record fertility and health information for use in research and to help farmers manage their farms. Data from 33 herds recording health and fertility over a 6-year period were used to study genetic relationships of several health, fertility and production traits. There were 10 569 records from 4642 cows of all parities. These were used to estimate genetic parameters for health: mastitis, lameness and somatic cell score (SCS), for fertility: calving interval, days to first service, conception to first service and for production: 305-day milk, butterfat and protein yields. Heritabilities for these traits were also estimated for the first three lactations. (Co)variances were estimated using linear, multitrait restricted maximum likelihood (REML) with an animal model. Mastitis and lameness were treated as all-or-none traits. The incidence of these diseases increased with lactation number, which may lead to variance component estimation problems, as the mean is linked to the variance in binomial distributions. Therefore, a method was used to fix the within-lactation variance to one in all lactations while maintaining the same mean. The heritability for SCS across lactations was 0·15. Heritabilities for other health and fertility traits were low and ranged between 0·013 and 0·047. All genetic correlations with the production traits were antagonistic implying that selection for yield may have led to a deterioration in health and fertility. The genetic correlation between SCS and mastitis was 0·65 indicating that indirect selection for improvements in mastitis may be achieved using somatic cell counts as a selection criterion. The potential use of linear type scores as predictors of the health traits was investigated by regressing health traits on sire predicted transmitting abilities for type. The results indicate that some type traits may be useful as future selection criteria.
Genetic diversity and biogeography of red turpentine beetle Dendroctonus valens in its native and invasive regions

Sequences of 479 bp region of the mitochondrial COI gene were applied to detect population genetic diversity and structure of Dendroctonus valens populations. By comparing the genetic diversity between native and invasive populations, it was shown that the genetic diversity of Chinese populations was obviously lower than that of native populations with both indices of haplotype diversity and Nei's genetic diversity, suggesting genetic bottleneck occurred in the invasive process of D. valens, and was then followed by a relatively quick population buildup. According to phylogenetic analyses of haplotypes, we suggested that the origin of the Chinese population was from California, USA. Phylogenetic and network analysis of native populations of D. valens revealed strong genetic structure at two distinct spatial and temporal scales in North America. The main cause resulting in current biogeographic pattern was supposedly due to recycled glacial events. Meanwhile, a cryptic species might exist in the Mexican and Guatemalan populations.
Forest Seral Stage and Large Woody Debris Abundance in an Allegheny High Plateau Foreststream System

ABSTRACT: Large woody debris (LWD) in the form of standing dead trees and down logs is an important structural and functional component of forest ecosystems and is a key factor linking riparian forests and streams. We examined the influence of forest seral stage (old-growth vs. second-growth forest) on terrestrial (snags and down logs) and in-stream LWD abundance in a riparian forest-stream system in Cook Forest State Park, Pennsylvania. Snag density, but not basal area, was significantly greater in second-growth forest due to elevated mortality of eastern white pine (Pinus strobus L.). Abundance of both terrestrial and in-stream LWD was significantly greater in the old-growth forest-stream system than in second-growth. Eastern hemlock, Tsuga canadensis (L.) Carr. , strongly dominated the volume of both terrestrial and in-stream LWD in the old-growth stand and adjacent stream reaches. Terrestrial and in-stream LWD loadings that we recorded are similar to loadings occurring in forest-stream systems elsewhere in the eastern United States, especially the Appalachian region, suggesting that these values may be useful targets for LWD enhancement projects for Allegheny High Plateau forest-stream systems.
Hemozoin Increases IFN-γ-Inducible Macrophage Nitric Oxide Generation Through Extracellular Signal-Regulated Kinase- and NF-κB-Dependent Pathways 1

NO overproduction has been suggested to contribute to the immunopathology related to malaria infection. Even though a role for some parasite molecules (e.g., GPI) in NO induction has been proposed, the direct contribution of hemozoin (HZ), another parasite metabolite, remains to be established. Therefore, we were interested to determine whether Plasmodium falciparum (Pf) HZ and synthetic HZ, β-hematin, alone or in combination with IFN-γ, were able to induce macrophage (Mφ) NO synthesis. We observed that neither Pf HZ nor synthetic HZ led to NO generation in B10R murine Mφ; however, they significantly increased IFN-γ-mediated inducible NO synthase (iNOS) mRNA and protein expression, and NO production. Next, by investigating the transductional mechanisms involved in this cellular regulation, we established that HZ induces extracellular signal-regulated kinase (ERK)1/2 mitogen-activated protein kinase phosphorylation as well as NF-κB binding to the iNOS promoter, and enhances the IFN-γ-dependent activation of both second messengers. Of interest, cell pretreatment with specific inhibitors against either NF-κB or the ERK1/2 pathway blocked the HZ + IFN-γ-inducible NF-κB activity and significantly reduced the HZ-dependent increase on IFN-γ-mediated iNOS and NO induction. Even though selective inhibition of the Janus kinase 2/STAT1α pathway suppressed NO synthesis in response to HZ + IFN-γ, HZ alone did not activate this signaling pathway and did not have an up-regulating effect on the IFN-γ-induced Janus kinase 2/STAT1α phosphorylation and STAT1α binding to the iNOS promoter. In conclusion, our results suggest that HZ exerts a potent synergistic effect on the IFN-γ-inducible NO generation in Mφ via ERK- and NF-κB-dependent pathways.
Evaluation of plant extracts against Pythium aphanidermatum inciting damping off of Tomato

The efficacy of 17 plant extracts were evaluated in vitro by poisoned food technique against Pythium aphanidermatum. The mycelial growth of test pathogen was effectively inhibited by extracts of Azadirachta indica, Datura stramonium, Parthenium hysterophorus, Diospyros cordifolia, Argemone mexicana, Aloe barbandensis and Ricinus comunis at all concentrations. These extracts were also evaluated by growing tomato seedling in green house condition. Plants extract were found highly effective in reducing pre and post emergence mortality and also resulted in increase seedling vigour and dry matter production of tomato. Among plant extracts, A. indica and R. communis proved most superior as compared to others.
Association of HLA-A24 With Complete β-Cell Destruction in IDDM

A sensitive C-peptide immunoreactivity radioimmunoassay demonstrated the presence of subtle, but definite residual β-cell function in patients with IDDM of long duration. Although HLA antigens are known to influence susceptibility to IDDM, their contribution to the extent of pancreatic β-cell destruction has not yet been examined extensively. We studied the relationship between residual β-cell function and HLA class I and class II antigens in 111 unrelated Japanese IDDM patients. Using the sensitive C-peptide immunoreactivity radioimmunoassay, the presence or absence of residual β-cell function was evaluated by the C-peptide immunoreactivity response to a 100-g oral glucose load. DNA typing for HLA-DQA1 and HLA-DQB1 antigens was performed in addition to serological typing of HLA-A, HLA-B, HLA-C, and HLA-DR antigens. A C-peptide immunoreactivity response > 0.033 nM was regarded as an indication of the presence of residual β-cell function, not the assay error. Surprisingly, 35 of 37 (94.6%) patients without residual β-cell function had HLA-A24, whereas only 39 of 74 (52.7%) patients with residual β-cell function had this antigen (corrected P = 9.795 × 10(–6). Any other HLA antigens, including the DR and DQ loci, showed no difference in the frequency with regard to residual β-cell function. The duration of diabetes was similar between the groups with and without residual β-cell function. The duration of diabetes was similar between the groups with and without residual β-cell function. Even when the patients were stratified according to the duration of diabetes, HLA-A24 was more common in those with early complete loss of β-cell function (duration of diabetes <1 yr) (P = 0.035) and was less common in those with residual β-cell function despite a long duration of diabetes (>10 yr) (P = 0.001). The correlation between HLA-A24 positivity and complete β-cell loss also was confirmed in younger-onset (<30 yr old) and elder-onset (≥30 yr old) groups. The C-peptide immunoreactivity response in patients with HLA-A24 (0.09 ± 0.02 nM, mean ± SE, n = 74) was significantly lower than that in patients without HLA-A24 (0.19 ± 0.03 nM, n = 37, P < 5.0 × 10−5). Further typing of HLA-A24 by one-dimensional isoelectric focusing gel electrophoresis revealed that the isoelectric point of HLA-A24 was identical in charge in 17 of 18 patients and 7 normal control subjects (isoeletric point 6.32, HLA-A24.1). We conclude that a specific HLA class I antigen, HLA-A24, promotes pancreatic p-cell destruction in IDDM patients with other disease-susceptible HLA antigens.
Coalescence of microsomal vesicles from rat liver: a phenomenon occurring in parallel with enhancement of the glycosylation activity during incubation of stripped rough microsomes with GTP

Rough microsomes from rat liver have been subjected to various treatments and incubated afterwards with UDP-N-acetyl-[14C]glucosamine and GDP-mannose in the presence of GTP (0.5 mM), or of other nucleotides. In agreement with earlier results from this laboratory, the preparations previously treated to strip off the ribosomes and incubated in the presence of GTP assembled dolichol-linked oligosaccharides and transferred these oligosaccharides to endogenous protein acceptors much more actively than untreated preparations, or stripped preparations incubated in the absence of GTP. Thin-section and freeze-fracture electron microscopy have revealed that pyrophosphate- treated preparations incubated with GTP are aggregated and contain numerous vesicles as large as 1-4 micrometer, or more. Such large vesicles were not present before incubation and thus were considered to have been formed through coalescence of regular-sized ones. Like glycosylation, the coalescence phenomenon depends upon the removal of ribosomes, because it occurred whether ribosomes had been stripped, at least partly, with pyrophosphate, KCl, or puromycin, but not when rough microsomes had been washed with 0.25 M sucrose or with KCl and MgCl2. Like glycosylation, it also depends on the addition of GTP and was not induced by ATP, UTP, CTP, and nonhydrolysable analogues of GTP. Rough microsomes coalesced, however, when pyrophosphate-treated preparations were incubated with GTP in the absence of nucleotide sugars, or in the presence f tunicamycin, indicating that the coalescence phenomenon does not result from the glycosylation of some membrane constituents.
Effect of growing density on biomass and stem volume growth of downy birch stands on peatland in Western and Northern Finland.

The objective of the study was to ascertain the relationship of thinning intensity of downy birch (Betula pubescens Ehrh.) stands with height, crown, and diameter development as well as pulp- wood,�stemvolume, �andbioma ssincrementusinglong-term �(20−30 �years) �fieldexperiments. � Diametergrowt hofbi rchesi ncreasedwi tht hinningi ntensityduri ngt hefirst �15 �ye arsfromt hinning� in all development phases, though after that it did so only for the youngest stands. The thinning responsewaslow . �Thinningintensityhadnoinfluenceonincreaseinheight. �Intermsofstem � volume with bark, the mortality in unthinned stands during the study period was 30-45 m 3 ha -1 . The mean stem number in unthinned birch thickets fell from 25 000 ha -1 at a dominant height of 7 m to 3000 ha -1 �at �18 �m. �Thestemvolumeincre mentoverthefirst �15 �yearswashighest �(5-6 � m 3 ha -1 a -1 )�ontheverylightlythinnedorunthinnedplots, �butlatertherewasnosignificantdif- ferencebetweeninitialthinningintensities. �Themaximumabove-groundleaflessbiomass �(over � 100 Mg ha -1 ) was achieved on very lightly thinned plots. Also, the total production (including thinning removal) of biomass or stem volume or even the production of pulpwood increased with stand density, with these values being greatest for very lightly thinned or unthinned plots. During 50-yearrotation , �thehighestleaflessabove-groundbiomassproductionwas �2.5 �Mgha -1 a -1 as a meanvaluefromtheexperiments. �Thehighestmeanannualproductionofpulpwood �(d�> �6.5 �cm) � was 3.2 m 3 ha -1 a -1 , and, in practice, no saw timber or veneer timber was produced, because of the small size and low quality of the stems. A thinning in downy birch stands increased slightly thesizeofstemstoberemovedinfuturecuttings, �butwithexceptionforverylightthinningit � decreased the production of biomass and merchantable wood.