Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Complexity of Resting State Spiking Activity in Monkey Motor Cortex

Resting state has been established as a classical paradigm of brain activity studies, mostly based on large scale measurements such as fMRI or M/EEG. This term typically refers to a behavioral state characterized by the absence of any task or stimuli. The corresponding neuronal activity is often called idle or ongoing. Numerous modeling studies on spiking neural networks claim to mimic such idle states, but compare their results to task- or stimulus-driven experiments, which might lead to misleading conclusions. To provide a proper basis for comparing physiological and simulated network dynamics, we characterize simultaneously recorded single neurons’ spiking activity in monkey motor cortex and show the differences from spontaneous and task-induced movement conditions. The resting state shows a higher dimensionality, reduced firing rates and less balance between population level excitation and inhibition than behavior-related states. Additionally, our results stress the importance of distinguishing between rest with eyes open and closed.
Macrophage inflammatory state influences susceptibility to lysosomal damage

Macrophages possess mechanisms for reinforcing the integrity of their endolysosomal membranes against damage. This property, termed inducible renitence, was previously reported for macrophages stimulated with LPS, peptidoglycan, IFN-γ, or TNF-α. Here, we expanded the macrophage subtypes examined to include populations with well-defined functional roles in vivo: classically activated macrophages (CA-Mφ), alternatively activated macrophages (AA-Mφ), and regulatory macrophages (Reg-Mφ). We determined that renitence is a property of CA-Mφ and Reg-Mφ, but not of AA-Mφ. Furthermore, LPS-activated macrophages possess features of both CA-Mφ and Reg-Mφ, based on their cytokine secretion profiles. As the generation of these three classes of renitent macrophages required exposure to LPS, a Toll-like receptor (TLR) ligand, we assessed whether TLR stimulation generally induced renitence. Stimulation of TLRs 2/1, 3, and 4 induced renitence, whereas stimulation of TLRs 7/8 and 9 induced modest levels of lysosomal damage protection. Renitence induced by TLR stimulation required the signaling adaptors MyD88 and TRIF. Surprisingly, the specific signaling adaptor usage requirements for some TLRs differed from those established for canonical TLR signaling. Of note, renitence induced by LPS, a TLR4 ligand, required signaling through TRIF but not MyD88. Consistent with this pattern, the type I IFN response, which is triggered by LPS stimulation through a TRIF-dependent, MyD88-independent pathway, contributed to renitence. A biologically relevant type I IFN trigger in macrophages, murine norovirus-1 (MNV-1) infection, also induced renitence. This work establishes the concept that susceptibility to lysosomal damage within macrophages varies according to inflammatory state and depends on the type I IFN response. Summary sentence Macrophages of distinct polarization states exhibit varying degrees of susceptibility to lysosomal damage reflecting their functional roles in host defense and immune regulation
An Efficient Gene Excision System in Maize

Use of the morphogenic genes Baby Boom (Bbm) and Wuschel2 (Wus2), along with new ternary constructs, has increased the genotype range and the type of explants that can be used for maize transformation. In addition, altering the ectopic expression pattern for Bbm/Wus2 has resulted in rapid maize transformation methods that are faster and applicable to a broader range of inbreds. However, expression of Bbm/Wus2 can compromise the quality of regenerated plants, leading to sterility. We reasoned excising morphogenic genes after transformation but before regeneration would increase production of fertile T0 plants. We developed a method that uses an inducible site-specific recombinase (Cre) to excise morphogenic genes. The use of developmentally regulated promoters, such as Ole, Glb1, End2 and Ltp2, to drive Cre enabled excision of morphogenic genes in early embryo development and produced excised events at a rate of 25%-100%. A different strategy utilizing an excision-activated selectable marker produced excised events at a rate of 53.3%-68.4%; however, the transformation frequency was lower (12.9%-49.9%). The use of inducible heat shock promoters (e.g. Hsp17.7, Hsp26) to express Cre, along with improvements in tissue culture conditions and construct design, resulted in high frequencies of T0 transformation (29%-69%), excision (50%-97%), usable quality events (3.6%-14%), and few escapes (non-transgenic; 14%-17%) in three elite maize inbreds. Transgenic events produced by this method are free of morphogenic and marker genes.
Novel mutations in the γ-crystallin genes cause autosomal dominant congenital cataracts

Cataract is an opacification of the eye lens that frequently results in visual impairment or blindness during infancy and early childhood.1 An estimated 200 000 children are blind with bilateral cataract world wide and 20 000-40 000 children with developmental cataract are born each year.2 In the developed nations of Europe and Northern America, national surveillance or cross sectional studies suggest a prevalence of 1-4 cases per 10 000 children.3–6 In southern India the prevalence is higher, at approximately 6.5 cases per 10 000 children7 and bilateral childhood cataract accounts for about 12% of all ocular disorders registered.8 The lens is a unique tissue as it is separated from the surrounding fluids by the lens capsule and there is life long persistence of its cells and their proteins. The β- and γ-crystallins were biochemically characterised as major lens proteins by Morner9 over a century ago. They belong to a superfamily of proteins, which were considered for a long time to be present only in the lens. However, it has recently been reported that β- and γ-crystallin mRNA and protein are also present in other tissues, in particular in the retina, brain, and testis.10–12 The common signature of all β- and γ-crystallins is the so called Greek key motif. Crystallography has shown that each of the β- and γ-crystallins is composed of two domains, each built up by two Greek key motifs. It is widely accepted that β/γ-crystallins evolved in two duplication steps from an ancestral gene coding for a protein folded like a Greek key. The γ-crystallin encoding genes ( Cryg / CRYG genes) in all mammals consist of three exons: the first one codes only for three amino acids, and the subsequent two are responsible for two Greek key motifs each. …
Population structure, seed loads and flowering phenology in three common (Melaleuca styphelioides, M. thymifolia, M. nodosa) and one rare (M. deanei) Melaleuca (Myrtaceae) species of the Sydney region

Melaleuca deanei F.Muell. is listed under state and national protection legislation occurring as small, disjunct populations restricted to the Central Coast botanical district of New South Wales. This paper reports on the population structure, reproductive output and phenology of large and small field populations of M. deanei, compared with three common congeneric species in the area, namely, Melaleuca nodosa (Sol. ex Gaertn.) Sm. , Melaleuca thymifolia Sm. and Melaleuca styphelioides Sm. Both M. deanei and M. styphelioides had few seedlings per population at the sites studied. Results indicated that seedling recruitment is rare and would appear to require specific conditions. In addition, M. deanei had a low incidence of flowering within the small populations, significantly fewer fruiting plants per population and significantly lower numbers of viable seeds per square metre, most likely compounding its limited recruitment. Flowering, when it occurred in M. deanei, was from mid to late October through to late November–early December with increased flowering in response to fire and along road edges. Further study is needed to determine reproductive success at the individual-plant level, the breeding system and recruitment requirements of these species.
Mixed cropping with maize combined with moderate UV-B radiations lead to enhanced flavonoid production and root growth in faba bean

Abstract Flavonoids have recently been proposed to function as developmental regulators and/or signaling molecules under biotic or abiotic stress. The aim of this study was to determine the composition and concentration of fiavonoid aglycones (kaempferol, luteolin, and quercetin) in faba bean shoots and roots, as affected by interspecific root interactions with maize and moderate UV-B radiation. Independent of the UV-B treatment, interspecific root interactions with maize enhanced the concentration of both quercetin and luteolin in the faba bean shoots and roots by 50 and 97.8%, respectively, and improved the root length by 14.6%. In addition, moderate UV-B radiation facilitated a systematic increase of both aglycones in both shoots and roots without affecting plant growth. To our knowledge, this report is the first work documenting the response of faba bean flavonoids to interspecific root interactions with maize and moderate UV-B radiation, and it provides a new perspective for understanding interspecific interactions.
The growth history of anadromous white-spotted charr in northern Japan : a comparison between river and sea life

Anadromous white-spotted charr Salvelinus leucomaenis in a natural river in northern Japan migrated to the sea mainly at age 3+ years. Sea-run charr grew faster than parr, particularly as first time migrants. Sea-run charr repeated seaward migration up to three times; the observed maximum age was 5+ years old. The likelihood ratio test identified significant differences in asymptotic size and individual growth variability between parr and sea-run charr. Sea-run charr had an asymptotic size (L∞) twice as large as parr, while the growth parameter (K) was similar between sea-run and parr. Growth variability was higher for parr than for sea-run charr.
Correlations of red (Cervus elaphus) and roe (Capreolus capreolus) deer densities in Scottish forests with environmental variables

The relationship between densities of red and roe deer and a range of environmental variables were investigated. The aim was to assess which factor, or combination of factors, was most associated with, and hence potentially responsible for, variations in densities of deer. Twenty plantation forests throughout Scotland were used as study sites and estimates of deer densities within them were based on dung-group counts. Using ratios of cull records and local information, 10 forests were selected which were expected to give a wide range of deer densities to aid the correlation exercise. The other 10 were selected randomly from within the geographic range of both species and without expectation of density: this allowed deer densities to be used as predictors of each other in the analyses without any bias that selection on the basis of ratio may have introduced. The variables used in analyses included forest habitat structure, climate, vegetation composition, soil type, culling pressure, and the density of other deer species. Red deer densities were positively correlated with mean daily temperature (P<0.05) throughout the year and mean daily snow depth (P<0.05) for October through to March, but negatively correlated with mean daily windspeed (P<0.05) for the quarter April to June. Roe deer density was negatively correlated with mean daily rainfall (P<0.05) throughout the year. Red deer density was negatively correlated (P<0.05) with an index of culling pressure, but roe deer density was uncorrelated with this parameter. The actual influence of culling pressure on red deer population density is unclear. Proportions of structural habitats within forests (defined by tree age classes and growth form) were uncorrelated with deer densities, but were secondary predictors of deer density in regression analyses: red deer density was predicted by the proportion of open-thicket (trees aged 15-28 years), and roe deer density by the proportion of restocked areas (0-8 years) and pre-thicket (9-14 years). Stepwise multiple regression analyses suggested that high red deer density has an important negative influence on roe deer density (P<0.05), but that the reverse did not hold. Possible mechanisms by which significantly correlated variables may influence deer densities are discussed. It is suggested that the differential variation of red and roe deer densities across Scotland may be a result of different climatic adaptations and, possibly, an interspecific influence of red deer on roe deer.
Comparative Study of Activity and Heat Stability of Limit Dextrinase in 16 Barley Cultivars

ABSTRACT We conducted a comprehensive study of 15 cultivars of Chinese barley and one cultivar of European barley to examine and compare the activity and heat stability of limit dextrinase (LD) among them. Our results revealed that the enzymatic activity of LD drops dramatically at incubation temperatures >65°C, indicating that 65°C is the point of incubation temperature sensitivity for this enzyme. Compared with the European barley cultivar Triumph, the levels of enzymatic activity and heat stability of LD in most Chinese barley cultivars included in this study were low, except for Jipi 2 and 92001, which were nearly equal to Triumph. We also found that the activity and heat stability of LD were strongly influenced by the genotype and growth environment of the cultivar, which suggests that genetic manipulation and optimal cultivation conditions may be useful in producing high-quality barley for the brewing industry.
THE INCIDENCE, DEVELOPMENT, AND EXPERIMENTAL TRANSMISSION OF PNEUMOSTRONGYLUS TENUIS DOUGHERTY (METASTRONGYLOIDEA: PROTOSTRONGYLIDAE) OF THE MENINGES OF THE WHITE-TAILED DEER (ODOCOILEUS VIRGINIANUS BOREALIS) IN ONTARIO

Pneumostrongylus tenuis was found throughout the year in the cranium of 41% of 172 adult deer examined in Algonquin Park. Incidence was higher in summer (46%) than winter (24%). Two fawns were infected (October and March). Worms also occurred on the spinal dura mater and in veins of the dura. Thus, incidence of infection was higher than indicated by examinations of craniums. Larvae developed in species of Discus, Zonitoides, Deroceras, Triodopsis, Stenotrema, and Lymnea sp. Four fawns were infected experimentally. Fourth- and fifth-stage larvae were found in the brain and spinal cord of one fawn examined at 25 days. Fifth stages were found in the tissue and between the meninges of the spinal cord of a fawn examined at 40 days. Subadults were found on the spinal and cerebral dura mater of a fawn autopsied at 50 days. The final fawn passed larvae 91 days after exposure. At 115 days after exposure, mature worms were found on or in the cerebral dura; two were found in the intercavernous sinus. The inflamed du.
Changes in organic chemical components of needle litter during decomposition. Long-term decomposition in a Scots pine forest. I

The decomposition and organic chemical changes in Scots pine (Pinus silvestris) needle litter were studied for a period of 5 years and until 75% weight loss was reached in field incubation. The changes in components such as various groups of lipophilic extractives, low-molecular carbohydrates, cyclitols, phenolic glycosides, polysaccarides, and lignin were followed. There was a great drop of sugars, steryl esters, and triglycerides during the 1st year of decomposition. Some isoprenoid alcohols, sterols, and some acids belonged to the most stable of the soluble components. Of the solid residue the arabinans decomposed rapidly, the cellulose decomposed somewhat faster than the hemicelluloses as a group, and the lignin decomposed rather slowly (about 48% in 5 years).
Isolation and Restriction Mapping of a Spiroplasma Plasmid

A plasmid, pIJ2000, of approximately 7·8; kilobase pairs (kb) and with a base composition of 22·4; mol % (G + C) has been isolated from the non-helical Spiroplasma citri strain ASP-1. pIJ2000 was the only covalently-closed circular DNA molecule detected in cleared lysates of high passage cultures of strain ASP-1 following CsC1/ethidium bromide equilibrium buoyant density centrifugation. A primary isolate of strain ASP-1 contained two additional plasmids of approximately 35·4; kb and 14·8; kb. pIJ2000 contained single sites for the restriction endonucleases Bg/II, HaeIII, Hin dIII and XhoI and three sites for MboI.
Comparative morphology of the venom gland and reservoir in opiine and alysiine braconid wasps (Insecta, Hymenoptera, Braconidae)

Detailed venom reservoir and venom gland intima morphology was investigated in representatives of 178 species and 76 genera of Braconidae belonging to the subfamilies Opiinae (23 genera and 69 species) and Alysiinae (36 genera and 67 species of Alysiini, and 17 genera and 42 species of Dacnusini). The presence of an unsculptured sack–like expansion of the anterior end of the reservoir suggests a relationship between some members of the alysiine tribe Dacnusini, viz. Exotela and Chorebus, and the genera Oenonogaster and Glyphogaster, both of which are currently placed in the Alysiini. The same feature also suggests that Exotela, Chorebus, Oenonogaster and Glyphogaster may be derived from the Opiinae separately from other Alysiinae. Other dacnusines examined are indicated as forming a monophyletic taxon on the basis of their reduced and narrow reservoirs. An anterior insertion of the venom glands on to the reservoir generally supports the Phaenocarpa group of alysiine genera, with some modification, whereas the presence of a discrete, narrow posterior extension of the reservoir represents a synapomorphy for members of the Aspilota group of alysiine genera. The phylogenetic inferences from this venom apparatus study are discussed in the light of the biology of the taxa concerned. Twenty‐one new combinations are made in the Opiinae and seven in the Alysiinae.
Polymer-assisted intratumoral delivery of ethanol: Preclinical investigation of safety and efficacy in a murine breast cancer model

Focal tumor ablation with ethanol could provide benefits in low-resource settings because of its low overall cost, minimal imaging technology requirements, and acceptable clinical outcomes. Unfortunately, ethanol ablation is not commonly utilized because of a lack of predictability of the ablation zone, caused by inefficient retention of ethanol at the injection site. To create a predictable zone of ablation, we have developed a polymer-assisted ablation method using ethyl cellulose (EC) mixed with ethanol. EC is ethanol-soluble and water-insoluble, allowing for EC-ethanol to be injected as a liquid and precipitate into a solid, occluding the leakage of ethanol upon contact with tissue. The aims of this study were to compare the 1) safety, 2) release kinetics, 3) spatial distribution, 4) necrotic volume, and 5) overall survival of EC-ethanol to conventional ethanol ablation in a murine breast tumor model. Non-target tissue damage was monitored through localized adverse events recording, ethanol release kinetics with Raman spectroscopy, injectate distribution with in vivo imaging, target-tissue necrosis with NADH-diaphorase staining, and overall survival by proxy of tumor growth. EC-ethanol exhibited decreased localized adverse events, a slowing of the release rate of ethanol, more compact injection zones, 5-fold increase in target-tissue necrosis, and longer overall survival rates compared to the same volume of pure ethanol. A single 150 µL dose of 6% EC-ethanol achieved a similar survival probability rates to six daily 50 µL doses of pure ethanol used to simulate a slow-release of ethanol over 6 days. Taken together, these results demonstrate that EC-ethanol is safer and more effective than ethanol alone for ablating tumors. Graphical Abstract The inclusion of ethylcellulose limits extra-tumoral leakage of ethanol and increases the target-tissue ablation.
Impact of Minimum Dissolved Oxygen Concentration on Grow-Out Performance of Blue Catfish with Comparison to Channel Catfish

Abstract Feed intake, the feed conversion ratio (FCR), and the production of blue catfish Ictalurus furcatus and channel catfish I. punctatus were examined in 1-acre ponds maintained at either a high or low minimum dissolved oxygen (DO) concentration (mean values of 4.29 and 2.54 ppm [55% and 32% air saturation], respectively). Two additional studies were conducted examining only blue catfish in 0.25-acre ponds maintained at either a high (mean values of 4.43 and 4.46 ppm [56% and 55% air saturation] in the two studies) or low (mean values of 1.41 and 1.64 ppm [18% and 20% air saturation]) minimum DO concentration. Blue and channel catfish exhibited similar feed intake (13,432 versus 13,063 lb/acre), growth (1.40 versus 1.49 lb/fish), gross production (6,662 versus 6,663 lb/acre), and net production (5,935 versus 5,813 lb/acre) in the high-DO treatments in the 1-acre ponds. Within the low-DO treatment, feed intake was not significantly different (13,555 versus 12,398 lb/acre for blue and channel catfish, .
Water Quality Assessment of Streams Using a Qualitative Collection Method for Benthic Macroinvertebrates

A standardized qualitative sampling technique was developed and tested for shallow streams in North Carolina. This method emphasizes multihabitat collections and the use of both coarse- and fine-mesh samplers. All samples are picked in the field, a process facilitated by field-preservation of some samples. The qualitative method was found to be more rapid than a semi-quantitative technique (kick nets), yet produced a greater number of taxa per site. Different taxa richness criteria were developed for each ecoregion to assign water quality classifications, and these values were shown to be related to more conventional physical/chemical measurements. This method has potential as a rapid, inexpensive biomonitoring tool.