Miracle-dz/UniFAR-FTUs huggingface dataset:
In situ detection of protein interactions for recombinant therapeutic enzymes

Despite their therapeutic potential, many protein drugs remain inaccessible to patients since they are difficult to secrete. Each recombinant protein has unique physicochemical properties and requires different machinery for proper folding, assembly, and post-translational modifications (PTMs). Here we aimed to identify the machinery supporting recombinant protein secretion by measuring the protein-protein interaction (PPI) networks of four different recombinant proteins (SERPINA1, SERPINC1, SERPING1 and SeAP) with various PTMs and structural motifs using the proximity-dependent biotin identification (BioID) method. We identified PPIs associated with specific features of the secreted proteins using a Bayesian statistical model, and found proteins involved in protein folding, disulfide bond formation and N-glycosylation were positively correlated with the corresponding features of the four model proteins. Among others, oxidative folding enzymes showed the strongest association with disulfide bond formation, supporting their critical roles in proper folding and maintaining the ER stability. Knockdown of disulfide-isomerase PDIA4, a measured interactor with significance for SERPINC1 but not SERPINA1, led to the decreased secretion of SERPINC1, which relies on its extensive disulfide bonds, compared to SERPINA1, which has no disulfide bonds. Proximity-dependent labeling successfully identified the transient interactions supporting synthesis of secreted recombinant proteins and refined our understanding of key molecular mechanisms of the secretory pathway during recombinant protein production.
Gamma rhythms and visual information in mouse V1 specifically modulated by somatostatin-positive neurons in reticular thalamus

Visual perception in natural environments depends on the ability to focus on salient stimuli while ignoring distractions. This kind of selective visual attention is associated with gamma activity in the visual cortex. While the nucleus reticularis thalami (nRT) has been implicated in selective attention, its role in modulating visual perception remains unknown. Here we show that somatostatin-(SOM) but not parvalbumin-expressing (PV) neurons in the nRT preferentially project to visual thalamic nuclei. In freely behaving mice, single-unit and field recordings reveal powerful modulation of both visual information transmission and gamma activity in primary visual cortex (V1), as well as in the dorsal lateral geniculate nucleus (dLGN). These findings pinpoint the SOM neurons in nRT as powerful modulators of the visual information encoding accuracy in V1, and represent a novel circuit through which the nRT can influence representation of visual information.
The impact of graph construction scheme and community detection algorithm on the repeatability of community and hub identification in structural brain networks

The human brain is a complex network of volumes of tissue (nodes) that are interconnected by white matter tracts (edges). It can be represented as a graph to allow us to use graph theory to gain insight into normal human development and brain disorders. Most graph theoretical metrics measure either whole-network (global) or node-specific (local) properties of the network. However, a critical question in network neuroscience is how nodes cluster together to form communities, each of which possibly plays a specific functional role. Community partition analysis allows us to investigate the mesoscale organization of the brain. Various algorithms have been proposed in the literature, that allow the identification of such communities, with each algorithm resulting in different communities for the network. Those communities also depend on the method used to weigh the edges of the graphs representing the brain networks. In this work, we use the test-retest data from the Human Connectome Project to compare 32 such community detection algorithms, each paired with 7 graph construction schemes, and assess the reproducibility of the resulting community partitions. The reproducibility of community partition depended heavily on both the graph construction scheme and the community detection algorithm. Hard community detection algorithms, via which each node is assigned to only one community, outperformed soft ones, via which each node can be a part of more than one community. The best reproducibility was observed for the graph construction scheme that combines 9 white matter tract metrics paired with the greedy stability optimization algorithm, with either discrete or continuous Markovian chain. This graph-construction scheme / community detection algorithm pair also gave the highest similarity between representative group community affiliation and individual community affiliation. Connector hubs were better reproduced than provincial hubs.
Histopathologic Changes in a Hypogonadal Male on Exogenous Testosterone Diagnosed With Prostatic Adenocarcinoma: A Case Report

Abstract In the United States, prostatic adenocarcinoma is the most common nonskin cancer and second leading cause of cancer death. Pathologic diagnostics are paramount to guiding treatment but require an awareness that hormonal treatments have the capacity to alter the histological appearance of prostate cancer. This case highlights the importance of accurate diagnostics and grading through a discussion of histological findings in an unusual case of a male patient with hypogonadism on long-term exogenous testosterone who was diagnosed with prostatic adenocarcinoma.
Abundance of Scyphophorus acupunctatus Gyllenhal (Coleoptera: Dryophthoridae) in Agave tequilana Weber (Asparagaceae) Fields of Different Age and Agronomic Management

Abstract. One of the most important pests that affect the blue agave, Agave tequilana is Scyphophorus acupunctatus Gyllenhal which as larvae bore into and make galleries in the plant and also damage plant tissues as adults. In the present study, the abundance of S. acupunctatus was analyzed in plantations of A. tequilana of ages of 2, 3 and 4 years through monthly samples from May to November of 2016 in nine plantations distributed in the municipalities of Tequila, Magdalena and Arandas in the state of Jalisco, Mexico. In each plantation, nine traps were placed with synthetic aggregation pheromone (2-methyl-4-octanone 950 g/L y 2-methyl-4- octanol 5g/L), placed 50 m apart and arranged as follows: three within the A. tequilana plantings, three on the crop edges, and three in adjacent non-cultivated areas, for a total of 81 traps which were checked monthly. The temperature and humidity of each plantation was registered with dataloggers and the precipitation from data from NASA, as well as historical data of these variables were obtained from 1951 to 2016. A total of 4,390 individuals were trapped, consisting of 3,289 females and 1,101 males. We found significant differences among the weevil abundance in A. tequilana plots of different age and agronomic management. There was less abundance of weevils in plantations where no agrochemicals were used and where natural vegetation was allowed within rows suggesting that natural habitat complexity is an important factor in reducing the abundance of the weevil.
INDUCTION OF OOCYTE MATURATION BY DISULFIDE‐REDUCING AGENT IN THE SEA CUCUMBER, STICHOPUS JAPONICUS

1‐Methyladenine (1‐MeAde) is known to be a natural inducer of starfish oocyte maturation. Disulfide‐reducing agents such as dithiothreitol (DTT) and 2, 3‐dimercapto‐1‐propanol (BAL) are known to mimic the action of 1‐MeAde in inducing starfish oocyte maturation. Although 1‐MeAde failed to induce oocyte maturation in sea cucumbers, breakdown of germinal vesicles and subsequent meiotic behaviour of chromosomes were induced by the treatment with DTT in the pronase‐treated oocytes of the sea cucumber, Stichopus japonicus. These findings suggest that reduction of disulfide bonds plays an important role in triggering oocyte maturation in some marine forms such as echinoderms.
A comparison of the Droop and the Monod models of nutrient limited growth applied to natural populations of phytoplankton

The extent of nutrient limitation of phytoplankton in eutrophic Pluβsee was studied by enrichment bioassays and by analysing the cellular stoichiometry of monospecific fractions obtained by size fractionation and density-gradient separation. In this lake silicate and nitrogen, but not phosphorus, at times limit the reproductive rates of phytoplankton. The dependence of nutrient-limited reproductive rates on the cellular content of the limiting nutrient (cell quota) could well be described by the Droop model. Biomass specific minimal cell quotas of nitrogen ranged from 0.014 to 0.061 mol N mol-1 C, minimal cell quotas of silicon ranged from 0.055 to 0.127 mol Si mol-1 C. The cell quotas of the non-limiting nutrients usually increased with the cell quotas of the limiting nutrient. In contrast to the Droop model, the Monod model which relies on ambient concentrations of limiting nutrients was a much poorer predictor of growth rates.
Pheromone‐mediated upwind flight of male gypsy moths, Lymantria dispar, in a forest

Abstract Lymantria dispar L. males flying upwind in a pheromone plume in a forest were video‐recorded at 2.5, 10 and 20 m from the source of pheromone. Males flew slower and steered more across the wind as they approached the source. In concert, their ground speed decreased and track angles increased. In contrast to these changes, their drift angles were fairly constant and the transverse component of image flow, above and/or below the moths eyes, showed almost no change. The inter‐turn duration (time between sequential turns), a temporal aspect of the male flight manoeuvres, showed a consistent but relatively small increase as the distance from the source increased. The flight tracks narrowed as the males approached close (2.5 m) to the source. Because of unpredicted correlations between physical variables (i.e. temperature, wind velocity) and the distance from the source, we used principal components analysis to generate a set of completely independent variables. Greater than 90% of the variability in the data could be explained by four principal factors which corresponded well with known relationships in the flight manoeuvres. All four of these factors showed a significant regression against distance to the source. Although uncontrolled factors such as temperature and wind velocity may have contributed to changes in flight behaviour, recent data indicate that, in addition to concentration, certain temporal and spatial characteristics (i.e. burst period, burst return period) of plumes in wind vary systematically with distance from the source. We propose that L.dispar males might adjust their flight manoeuvres in response to these changes.
Altered geographic and temporal variability in phenology in response to climate change

Aim In response to recent climate warming, numerous studies have reported an earlier onset of spring and, to a lesser degree, a later onset of autumn, both determined from phenological observations. Here, we examine whether these reported changes have affected the synchronization of events on a regional level by examining temporal and spatial variability in phenology. In particular, we study whether years with earlier springs are associated with an altered spatial variability in phenology. Location Germany and the United Kingdom. Methods Plant phenological observations of 35 different phases (events such as flowering and leafing) collected by the German Weather Service (1951–2002) and butterfly phenological records of 29 species collected by the UK Butterfly Monitoring Scheme (1976–2003) are used. In these long-term records, we examine the temporal (year-to-year) variability and the spatial (geographic or between site) variability with particular emphasis on how they vary with time of the year and with earliness or lateness of the phase. Results Early phenological events (i.e. spring) are more variable than later events, both in time and in space, although the pattern is clearer for plants than for butterflies. Confirming previous results, we find a clear relationship between the mean date of spring and summer phases and the degree to which they have become earlier. The spatial variability of spring events is greater in warmer years that have faster plant development. However, late spring and summer events do not show a consistent relationship. Autumn events are somewhat more spatially variable in years characterized by later seasons. Main conclusions This is the first examination of spatial variability of plant and animal phenological events at a multinational scale. Earlier spring events are likely to be associated with increased spatial variability in plants, although this is unlikely to also be true for summer events. If species experience differential changes in geographic variation this may disrupt interactions among them, e.g. in food webs. On the other hand, these may offer advantages for mobile species. Further research on linked species is recommended.
Environmental and genetic factors influence the liveweight of adult Merino and Border Leicester × Merino ewes across multiple sites and years

Variation in liveweight change in the ewe flock during periods of poor nutrition can affect farm profitability through the effects of liveweight loss on potential stocking rate, management interventions including supplementary feeding, and ewe and lamb survival and productivity. There is variation between individual animals in their ability to manage periods of poor nutrition, but the links between liveweight change and breeding values in the adult ewe flock have not been quantified. We analysed 5216 liveweight profiles for 2772 ewes managed over 3 years at eight sites across Australia, to define the relative effects of environment, reproductive performance and breeding values on liveweight change. The range in liveweight loss varied from 1.3 kg to 21.6 kg, and for liveweight gain from 0.4 kg to 28.1 kg. Site and year had the largest influence on liveweight change, which demonstrates that seasonal conditions and management were the most important factors influencing liveweight change. Liveweight loss was influenced by previous and current reproductive performance but these effects were small in comparison to the effects of site and year. There were mixed associations with sire breeding values for growth, fat and muscle depending on site. An increase in sire breeding values for fat by 1 mm was associated with a reduction in liveweight loss by up to 1.3 kg regardless of ewe breed, and this was more evident at sites where ewes lost a greater proportion of their liveweight. While management had the greatest effect on liveweight change, there appears to be scope to use breeding values to select sheep that will lose less weight during periods of poor nutrition in some environments.
Phylogenetic position of Arabis arenicola and generic limits of Aphragmus and Eutrema (Brassicaceae) based on sequences of nuclear ribosomal DNA

Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region of 45 taxa were used to determine the phylogenetic relationship of Arabis arenicola to Arabis, Arabidopsis, Braya, and Eutrema, and that of Eutrema to the purportedly related genera Aphragmus, Lignariella, Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella. Arabis arenicola was originally described as Eutrema in 1830, transferred to Arabis in 1898, and has remained in Arabis to the present, even though it is morphologically more similar to Arabidopsis, Braya, and Eutrema. Sequence data were obtained from representative taxa of Arabis, Arabidopsis, and related Boechera and Catolobus, Braya and Neotorularia, and Eutrema, Aphragmus, Lignariella, Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella. The five Arabis arenicola accessions examined had ITS sequences that were identical to each other and to four Arabidopsis lyrata accessions. In both maximum parsimony and maximum likelihood analyses, Arabis ar.
Effect of NaCl pretreatment on the growth and survival of Listeria monocytogenes at high osmolarity

L. monocytogenes est un pathogene d'origine alimentaire largement repandu dans l'environnement et potentiellement present dans de nombreux aliments frais ou transformes. La capacite de ce microorganisme a tolerer des environnements sales est importante et dans ce contexte la capacite de croissance et de survie en presence de sel a ete etudiee pour sept souches de L. monocytogenes. Il a ete montre dans ce travail que certaines souches peuvent se multiplier dans des milieux contenant jusqu'a 11% de NaCI et que le delai de detection d'une croissance varie selon la concentration en sel et les souches utilisees. La suite de cette etude a ete effectuee sur la souche L028 de L. monocytogenes, une souche de reference bien caracterisee par de nombreux auteurs. Afin d'evaluer l'augmentation de resistance de cette souche au sel, elle a d'abord ete exposee a de faibles concentrations de cet agent avant un traitement a des concentrations plus elevees. Aucune des conditions testees n'a permis d'augmenter la resistance de la souche L028 au sel, qui reste identique quels que soient les pretraitements appliques.
A Smart Surface-Enhanced Resonance Raman Scattering Nanoprobe for Monitoring Cellular Alkaline Phosphatase Activity during Osteogenic Differentiation.

High-efficiency induction of bone marrow mesenchymal stem cells (BMSCs) to osteogenic differentiation in vitro can help to solve a series of bone diseases such as bone injury, fracture repair, and osteoporosis. In order to explore the optimal conditions for different chemical inducers to promote BMSCs differentiation and the possible differentiation mechanisms, we developed a smart nanoprobe that can achieve in situ alkaline phosphatase (ALP) activity detection during osteogenic differentiation in cells. The smart nanoprobe (Au@BCIP) was designed as the surface decoration of gold nanoparticles (AuNPs) with 5-bromo-4-chloro-3-indolyl phosphate (BCIP). The nanoprobe was co-cultured with differentiated BMSCs at different stages to monitor the ALP activity based on an ALP-catalyzed hydrolysis reaction with the BCIP as a substrate. The product can be quickly oxidized by dissolved oxygen to achieve a Raman-active species (5,5'-dibromo-4,4'-dichloro-1H,1H-[2,2'] biindolylidene-3,3'-dione; BCI). The SERS sensitivity has been greatly improved by resonating the excitation wavelength of 632.8 nm. It is a new strategy for tracing bone disease related ALP activity in vivo model with high sensitivity, selectivity, and non-invasion. By using this nanoprobe, osteogenic differentiation of cells under osteogenic supplements was assessed and the p38 MAPK signaling pathway for osteogenic differentiation was experimentally evidenced, which are of significance for understanding BMSCs and regulating their osteogenic differentiation process.
Simultaneous and rapid determination of sesamin and sesamolin in sesame oils using excitation-emission matrix fluorescence coupling with self-weighted alternating trilinear decomposition.

BACKGROUND Sesamin and sesamolin are two typical and major lignans isolated from sesame oil. Various researches have shown the bioactivity, physiological activity and potential health benefits of the two components. In this study, a simultaneous and rapid method for determination of sesamin and sesamolin in sesame oils was proposed. The excitation-emission fluorescence spectra of the oils were obtained after a simple pretreatment method, then the self-weighted alternating trilinear decomposition were adopted to extract the quantitative information from the highly overlapped spectra. RESULTS It was found that reasonable quantification results can be obtained with the limits of detection for the two lignans were 0.05 mg/g and 0.24 mg/g, while limits of quantitation were 0.14 mg/g and 0.74 mg/g, respectively. In addition, the average recoveries for sesamin and sesamolin were 99.05% and 94.97%. CONCLUSION The results indicate that with simple sample pretreatment, the application for combining excitation-emission fluorescence spectra and self-weighted alternating trilinear decomposition can be a useful and sensitive tool for the determination of lignans in sesame oil. This article is protected by copyright. All rights reserved.
Survival Rates of Female Greater Sage-Grouse in Autumn and Winter in Southeastern Oregon

Abstract We estimated survival rates of 135 female greater sage-grouse (Centrocercus urophasianus) on 3 study areas in southeastern Oregon, USA during autumn and winter for 3 years. We used known-fate models in Program MARK to test for differences among study areas and years, investigate the potential influence of weather, and compute estimates of overwinter survival. We found no evidence for differences in survival rates among study areas, which was contrary to our original hypothesis. There also were no declines in survival rates during fall–winter, but survival rates varied among years and time within years. Average survival rate from October through February was 0.456 (SE = 0.062). The coefficient of variation for this estimate was 13.6% indicating good precision in our estimates of survival. We found strong evidence for an effect of weather (i.e., mean daily min. temp, extreme min. temp, snow depth) on bi-weekly survival rates of sage-grouse for 2 of the study areas in one year. Extremely low (<−15° C) temperatures over an 8-week period and accumulation of snow had a negative effect on survival rates during the winter of 1990–1991 on the 2 study areas at the higher (>1,500 m) elevations. In contrast, we found no evidence for an influence of weather on the low-elevation study area or during the winters of 1989–1990 and 1991–1992. Extreme weather during winter can cause lower survival of adult female sage-grouse, so managers should be aware of these potential effects and reduce harvest rates accordingly.