Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure of Lysophosphatidylglyceryl-Remazolbrilliant Blue (LPG-RBB) from the Surface of Dyed Wheat Starch Granules

ABSTRACT Wheat starch granule surface was covalently stained with Remazolbrilliant blue-R dye (RBB) and then extracted with 1% SDS containing 1% 2-mercaptoethanol (2-ME) at room temperature for 14.5 hr. The extracted blue-staining material (A650) separated into two fractions. Low molecular weight (LMW) material was further purified by Sephadex G-75 size-exclusion chromatography and thin-layer chromatography. Infrared and nuclear magnetic resonance (1H-NMR and 13C-NMR) spectroscopy indicated that the structure of the purified LMW material was 18-O-(6-lysophosphatidylglyceryl)-RBB.
Studies on fouling by the freshwater mussel limnoperna fortunei and the antifouling effects of low energy surfaces

Attachment of the freshwater mussel, Limnoperna fortunei, was tested using non‐treated surfaces, viz. glass, nylon, rubber, silicone and Teflon, together with glass surfaces modified with nine kinds of silane coupling agents. Among the surfaces tested, the mussel avoided attaching to Teflon, silicone, and glass modified with 3‐bromopropyltrimethoxysilane or 3,3,3‐(trifluo‐ropropyl)‐trimethoxysilane. With respect to the relationship between the percentage attachment and the surface free energy (sfe) of the substrates, it was found that attachment was considerably reduced on the substrates which exhibited relatively low sfe, as above. The mean number of secreted byssuses per attaching mussel also decreased with decreasing substrate sfe. Furthermore, when the sfe was divided into the dispersion and polar components, the percentage mussel attachment was related to the polar component. These results suggest that effective antifouling towards L. fortunei is achieved on substrates with a low sfe polar component.
Impacts of the Introduced Round Goby (Apollonia melanostoma) on Dreissenids (Dreissena polymorpha and Dreissena bugensis) and on Macroinvertebrate Community between 2003 and 2006 in the Littoral Zone of Green Bay, Lake Michigan

Abstract We show that the invasion of round gobies (Apollonia melanostoma) in Green Bay, Lake Michigan, has changed the benthic food web in fundamental ways related to their impact on invasive dreissenid mussels. Dreissenid mussels are of specific interest because they are one of the primary dietary items for round gobies. In this study, we collected rocks from each of 10 study sites along approximately 60 km of the eastern shoreline of Green Bay, Lake Michigan, to assess a temporal change in macroinvertebrate abundance related to the northward movement of the round goby invasion front from a point about midway along the shoreline in 2003 to the entire coast in 2006. The pattern of macroinvertebrate abundance in 2003 suggested that round gobies had already caused significant decreases in macroinvertebrate abundances south of the invasion front (interpretation of the data could have been compromised by confounding environmental gradients). In subsequent sampling in 2006 macroinvertebrates were picked off of sampled rocks in the field and underwater transects were videotaped to estimate round goby abundance at each site. Round gobies were collected for stomach analysis to assist in determining which invertebrates would likely be impacted by goby predation. Our results indicated that by 2006, round gobies had become abundant at those sites where they were absent in 2003 and zebra mussels (Dreissena polymorpha), quagga mussels (Dreissena bugensis), isopods, amphipods, trichopterans, and gastropods in the newly invaded sites had significantly decreased at the newly invaded sites.
Protein Hydrolysate from Brewer’s Spent Grain and its Inhibitory Ability of α-Glucosidase

Brewer’s spent grain (BSG) rich in proteins is the main by-products in brewery. BSC proteins were extracted and hydrolyzed by Alcalase. The effects of hydrolysis time, temperature, pH and amount of enzyme added on the peptide yield were investigated. Inhibition of BSG protein hydrolysate against α-glucosidase was evaluated in vitro. BSG protein hydrolysate at 4.0 mg/mL showed the inhibition of 21.42% against α-glucosidase. The BSG protein hydrolysate after ultrafiltration purification exhibited much higher inhibition than that without ultrafiltration purification. The inhibition of BSC protein hydrolysate fraction with molecular weight fraction less than 5 kDa was 56.41%.
Active and repressed biosynthetic gene clusters have spatially distinct chromosome states

Significance Clusters of coexpressed and colocalized biosynthetic pathway genes in plants are a paradigmatic example of the nonrandom organization of the eukaryotic genome and present an ideal opportunity to understand the logic of eukaryote gene cluster regulation. Here, we carry out an in-depth analysis of the chromosomal topology of biosynthetic gene clusters and their positioning in nuclear space. We demonstrate that plant biosynthetic gene clusters reside in highly interactive domains that undergo marked changes in local conformation and nuclear positioning in cluster expressing and nonexpressing organs. As such, metabolic gene clusters rank among the most dynamic regions in the genome of the model species A. thaliana. Our results shed light on the potential mechanisms that constrain coexpression within clusters of genes. While colocalization within a bacterial operon enables coexpression of the constituent genes, the mechanistic logic of clustering of nonhomologous monocistronic genes in eukaryotes is not immediately obvious. Biosynthetic gene clusters that encode pathways for specialized metabolites are an exception to the classical eukaryote rule of random gene location and provide paradigmatic exemplars with which to understand eukaryotic cluster dynamics and regulation. Here, using 3C, Hi-C, and Capture Hi-C (CHi-C) organ-specific chromosome conformation capture techniques along with high-resolution microscopy, we investigate how chromosome topology relates to transcriptional activity of clustered biosynthetic pathway genes in Arabidopsis thaliana. Our analyses reveal that biosynthetic gene clusters are embedded in local hot spots of 3D contacts that segregate cluster regions from the surrounding chromosome environment. The spatial conformation of these cluster-associated domains differs between transcriptionally active and silenced clusters. We further show that silenced clusters associate with heterochromatic chromosomal domains toward the periphery of the nucleus, while transcriptionally active clusters relocate away from the nuclear periphery. Examination of chromosome structure at unrelated clusters in maize, rice, and tomato indicates that integration of clustered pathway genes into distinct topological domains is a common feature in plant genomes. Our results shed light on the potential mechanisms that constrain coexpression within clusters of nonhomologous eukaryotic genes and suggest that gene clustering in the one-dimensional chromosome is accompanied by compartmentalization of the 3D chromosome.
MIPPIE: the mouse integrated protein–protein interaction reference

Abstract Cells operate and react to environmental signals thanks to a complex network of protein–protein interactions (PPIs), the malfunction of which can severely disrupt cellular homeostasis. As a result, mapping and analyzing protein networks are key to advancing our understanding of biological processes and diseases. An invaluable part of these endeavors has been the house mouse (Mus musculus), the mammalian model organism par excellence, which has provided insights into human biology and disorders. The importance of investigating PPI networks in the context of mouse prompted us to develop the Mouse Integrated Protein–Protein Interaction rEference (MIPPIE). MIPPIE inherits a robust infrastructure from HIPPIE, its sister database of human PPIs, allowing for the assembly of reliable networks supported by different evidence sources and high-quality experimental techniques. MIPPIE networks can be further refined with tissue, directionality and effect information through a user-friendly web interface. Moreover, all MIPPIE data and meta-data can be accessed via a REST web service or downloaded as text files, thus facilitating the integration of mouse PPIs into follow-up bioinformatics pipelines.
Landscape Disturbances Impact Affect the Distribution and Abundance of Exotic Grasses in Northern Fescue Prairies

Abstract The presence of landscape disturbances increases the establishment of exotic plants inside natural areas. Here, we examine the effect of human disturbances to prairie landscapes on the distribution and abundance of Kentucky bluegrass and smooth brome, exotic grasses that threaten the integrity of prairie ecosystems throughout the northern Great Plains. Using plant inventory data from Riding Mountain National Park in Manitoba, Canada, we investigated how roads, trails, and the intensity of historic livestock grazing affect the distribution and abundance of exotic grasses. On the basis of our results, both Kentucky bluegrass and smooth brome were more abundant in areas closer to roads. Kentucky bluegrass was also more abundant in areas farther from trails and those historically grazed by cattle. Our research demonstrates that the effect of landscape disturbances on exotic grasses varies between species and suggests that patterns of invasion may reflect different introduction histories. Given our findings, conserving the integrity of northern fescue prairies should account for human disturbances of landscapes and their effects on the proliferation of exotic plants into areas of native prairie. Nomenclature: Smooth brome, Bromus inermis Leyss. BROIN, Kentucky bluegrass, Poa pratensis L. POAPR. Management Implications: Our research demonstrates that human disturbance of prairie landscapes, including roads, trails, and historic livestock grazing, affect the distribution and abundance of Kentucky bluegrass and smooth brome in northern fescue prairies. Conservation managers concerned about the proliferation of these invaders throughout the Great Plains can use distances from roads and grazing history to prioritize their inventory and management. For example, by focusing their attention on road margins, managers may be able to reduce the proliferation of Kentucky bluegrass and smooth brome into adjacent areas of native prairie. Our work also illustrates the persistent effect of historic livestock grazing on the abundance of Kentucky bluegrass and suggests that managers could reduce its proliferation by focusing on source areas located within historic grazing disturbances. Future management of northern fescue prairies will require limiting or restoring human disturbances of prairie landscapes in areas where the conservation of native biodiversity is a management priority.
A Preliminary Study of Spatial Bias in Knn Distance Metrics

A machine learning algorithm for image classiﬁcation exhibits spatial bias if permuting the order of image pixels sig-niﬁcantly alters its classiﬁcation accuracy. In this paper, we explore the spatial bias of a number of different distance metrics for k-nearest-neighbor image classiﬁcation. One distance metric is inspired by the convolutional kernels employed in convolutional neural networks. The other metrics are based on BRIEF descriptors, which generate bit vectors corresponding to images based on comparisons of pixel intensity values. We found that the convolutional distance metric exhibited a strong positive spatial bias, as did one of the BRIEF descriptors. Another BRIEF descriptor exhibited a negative spatial bias, and the remainder exhibited little or no spatial bias. These results lay a foundation for future work that would involve larger numbers of convolutional iterations, potentially synergized with BRIEF-style image preprocessing. The complete implementation of the work in this paper is available online at https://github.com/gjf2a/ﬂairs33.
KV4.3 N-terminal deletion mutant D2-39

Gating transitions in the KV4.3 N-terminal deletion mutant D2-39 were characterized in the absence and presence of KChIP2b. We particularly focused on gating characteristics of macroscopic (open state) versus closed state inactivation (CSI) and recovery. In the absence of KChIP2b D2-39 did not significantly alter the steady-state activation "a4" relationship or general CSI characteristics, but it did slow the kinetics of deactivation, macroscopic inactivation, and macroscopic recovery. Recovery kinetics (for both WT KV4.3 and D2-39) were complicated and displayed sigmoidicity, a process which was enhanced by D2-39. Deletion of the proximal N-terminal domain therefore appeared to specifically slow mechanisms involved in regulating gating transitions occurring after the channel open state(s) had been reached. In the presence of KChIP2b D2-39 recovery kinetics (from both macroscopic and CSI) were accelerated, with an apparent reduction in initial sigmoidicity. Hyperpolarizing shifts in both "a4" and isochronal inactivation "i" were also produced. KChIP2b-mediated remodeling of KV4.3 gating transitions was therefore not obligatorily dependent upon an intact N-terminus. To account for these effects we propose that KChIP2 regulatory domains exist in KV4.3 a subunit regions outside of the proximal N-terminal. In addition to regulating macroscopic inactivation, we also propose that the KV4.3 N-terminus may act as a novel regulator of deactivation-recovery coupling.
Influence of long-term application of manure type and bedding on yield, protein, fiber, and energy value of irrigated feed barley.

Published in Agron. J. 107:121–128 (2015) doi:10.2134/agronj14.0321 Copyright © 2015 by the American Society of Agronomy, 5585 Guilford Road, Madison, WI 53711. All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. ABSTRACT
Estimating the Population Health Impact of Recently Introduced Modified Risk Tobacco Products: A Comparison of Different Approaches

Abstract Introduction Various approaches have been used to estimate the population health impact of introducing a Modified Risk Tobacco Product (MRTP). Aims and Methods We aimed to compare and contrast aspects of models considering effects on mortality that were known to experts attending a meeting on models in 2018. Results Thirteen models are described, some focussing on e-cigarettes, others more general. Most models are cohort-based, comparing results with or without MRTP introduction. They typically start with a population with known smoking habits and then use transition probabilities either to update smoking habits in the “null scenario” or joint smoking and MRTP habits in an “alternative scenario”. The models vary in the tobacco groups and transition probabilities considered. Based on aspects of the tobacco history developed, the models compare mortality risks, and sometimes life-years lost and health costs, between scenarios. Estimating effects on population health depends on frequency of use of the MRTP and smoking, and the extent to which the products expose users to harmful constituents. Strengths and weaknesses of the approaches are summarized. Conclusions Despite methodological differences, most modellers have assumed the increase in risk of mortality from MRTP use, relative to that from cigarette smoking, to be very low and have concluded that MRTP introduction is likely to have a beneficial impact. Further model development, supplemented by preliminary results from well-designed epidemiological studies, should enable more precise prediction of the anticipated effects of MRTP introduction. Implications There is a need to estimate the population health impact of introducing modified risk nicotine-containing products for smokers unwilling or unable to quit. This paper reviews a variety of modeling methodologies proposed to do this, and discusses the implications of the different approaches. It should assist modelers in refining and improving their models, and help toward providing authorities with more reliable estimates.
A Dairy Cow Body Condition Scoring System and Its Relationship to Selected Production Characteristics

Abstract A scoring system with 1 to 5 scale was devised to measure body condition of dairy cows at any point during the lactation cycle. Cows were scored on appearance and palpation of back and hind quarters only. Relationships of body weight, frame size measurements, milk production, and characteristics related to the body condition scoring system were determined. During 18 mo, 28 cows in each of 29 dairy herds were used for body measurements and body condition scores. Data were obtained from each herd at 3-mo intervals. Body weight and frame size measurements could not be correlated with body condition score. Dairy cows of greatest efficiency of milk production showed no significant increase in body condition during lactation, had fewer days open, but had lower persistency of lactation. Dairy cows that increased significantly in body condition during lactation were less efficient producers, had a greater number of days open, and had high body condition scores at the end of lactation. The body condition scoring system is a means of accurately determining body condition of dairy cows, independent of body weight and frame size.
OPERATING FEATURES OF THE AUDION

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Species-Specific, pH-Independent, Standard Redox Potential of Selenocysteine and Selenocysteamine

Microscopic redox equilibrium constants and standard redox potential values were determined to quantify selenolate-diselenide equilibria of biological significance. The highly composite, codependent acid-base and redox equilibria of selenolates could so far be converted into pH-dependent, apparent parameters (equilibrium constants, redox potentials) only. In this work, the selenolate-diselenide redox equilibria of selenocysteamine and selenocysteine against dithiothreitol were analyzed by quantitative nuclear magnetic resonance (NMR) methods to characterize the interfering acid-base and redox equilibria. The directly obtained, pH-dependent, conditional redox equilibrium constants were then decomposed by our method into pH-independent, microscopic constants, which characterize the two-electron redox transitions of selenocysteamine and selenocysteine. The 12 different, species-specific parameter values show close correlation with the respective selenolate basicities, providing a tool to estimate otherwise inaccessible site-specific selenolate-diselenide redox potentials of related moieties in large peptides and proteins.
Sex Differences and Commonalities in the Impact of a Palatable Meal on Thalamic and Insular Connectivity

The neural mechanisms underlying subjective responses to meal ingestion remain incompletely understood. We previously showed in healthy men an increase in thalamocortical, and a decrease in insular-cortical connectivity in response to a palatable meal. As sex is increasingly recognized as an important biological variable, we aimed to evaluate sex differences and commonalities in the impact of a well-liked meal on thalamic and anterior insular connectivity in healthy individuals. Participants (20 women and 20 age-matched men) underwent resting-state magnetic resonance imaging (rsMRI) before and after ingesting a palatable meal. In general, the insula showed extensive postprandial reductions in connectivity with sensorimotor and prefrontal cortices, while the thalamus showed increases in connectivity with insular, frontal, and occipital cortices, in both women and men. However, reductions in insular connectivity were more prominent in men, and were related to changes in meal-related sensations (satiety and digestive well-being) in men only. In contrast, increases in thalamic connectivity were more prominent in women, and were related to changes in satiety and digestive well-being in women only. These results suggest that brain imaging may provide objective and sex-specific biomarkers of the subjective feelings associated with meal ingestion.
Human Menstrual Blood-Derived Mesenchymal Cells Improve Mouse Embryonic Development.

There is a constant need for improving embryo culture conditions in assisted reproduction. One possibility is to use mesenchymal stem/stromal cells derived from menstrual blood (mbMSCs), with an endometrial origin. In this study, we sought to analyze the expansion of mouse embryos in a direct coculture model with mbMSCs. Our results showed that after five passages, mbMSCs presented a spindle-shaped morphology, with surface markers that were comparable with the normal mesenchymal cell phenotype. mbMSCs could differentiate into adipogenic and osteogenic lineages and secrete angiopoetin-2 and hepatocyte growth factor. The coculture experiments employed 103 two-cell-stage embryos that were randomly divided into two groups: control (n = 50), embryos cultured in GV-Blast medium, and cocultured mbMSCs (n = 53), embryos cocultured with GV-Blast and mbMSCs. Typically, two to three embryos were placed in a well with 200 μL of culture medium and observed until developmental day 5. After 5 days, the cocultured group had more embryos in the blastocyst stage (69.8%) when compared with the control group (30%) (p < 0.001). It was also found that nearly 57% of blastocysts in the cocultured group reached the hatching stage, while only 13% achieved this stage in the control group (p < 0.001). Analyses of cultured mbMSCs and growth media, in the presence or absence of an embryo, were also performed. Immunofluorescence detected similar levels of collagen I and III and fibronectin in both mbMSCs and cocultured mbMSCs, and similar amounts of growth factors, VEGF, PDGF-AA, and PDGF-BB, were also observed in the conditioned medium, regardless of embryo presence. The present study describes, for the first time, an easy, noninvasive, and autologous method that could potentially increase blastocyst growth rates during assisted reproductive procedures (i.e., in vitro fertilization). It is proposed that this mbMSC coculture strategy enriches the embryonic microenvironment and promotes embryo development. This technique may complement or replace existing assisted reproduction methods and is directly relevant to the field of personalized medicine. Impact statement The study demonstrates a novel and potentially personalized assisted reproduction approach. The search for alternative and autologous methods provides assisted reproduction patients with a better chance of a successful pregnancy. In this study, mesenchymal cells derived from menstrual blood resembled the outside uterine surface and could potentially be employed for improving embryo outgrowth. Our protocol enriches the embryonic microenvironment and facilitates high-quality single-embryo transfer.