Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonadaptive host‐use specificity in tropical armored scale insects

Abstract Most herbivorous insects are diet specialists in spite of the apparent advantages of being a generalist. This conundrum might be explained by fitness trade‐offs on alternative host plants, yet the evidence of such trade‐offs has been elusive. Another hypothesis is that specialization is nonadaptive, evolving through neutral population‐genetic processes and within the bounds of historical constraints. Here, we report on a striking lack of evidence for the adaptiveness of specificity in tropical canopy communities of armored scale insects. We find evidence of pervasive diet specialization, and find that host use is phylogenetically conservative, but also find that more‐specialized species occur on fewer of their potential hosts than do less‐specialized species, and are no more abundant where they do occur. Of course local communities might not reflect regional diversity patterns. But based on our samples, comprising hundreds of species of hosts and armored scale insects at two widely separated sites, more‐specialized species do not appear to outperform more generalist species.
Non-invasive quality determination of spinach under simulated sale conditions and prediction of possible changes.

Chlorophyll fluorescence, especially the optimum quantum yield Fv/Fm, is used to quantify the physiological state of plants, because stress, infections or wilting may lower the optimum quantum yield. The characteristics of chlorophyll fluorescence have attracted our attention for its use to determine the quality of spinach, because the measurement of Fv/ Fm during storage can be performed quickly and non-destructively, delivering information about spinach quality and its sale suitability. Applicability of modern techniques for quick and non-invasive in vivo determination of such parameters as quality and freshness of spinach under simulated sale conditions was tested in our study. In this experiment, application of chlorophyll fluorescence for quantification of quality as well as physical and physiological changes which occur in fresh products was verified. The experiment was conducted on spinach, a product characterized by rapid appearance of postharvest losses. Spinach was harvested as leafy vegetable for direct consumption and stored for 5 days (16 h in a cooling room at 2-4°C, 96-98% relative humidity, followed by 8 h at room temperature: ca 22oC, 65% relative humidity). Variants were represented by different cultivation conditions (fertilizer, leaf application of Previcur, CaCl2 and Cerone). The investigations revealed that fresh mass losses in the postharvest phase could be described by changes of Fv/Fm spinach leaves adapted to darkness by a linear relationship of parameters (r=0.77). The disadvantage of chlorophyll fluorescence measurement was the less precise determination of the critical loss of fresh mass of 3%. Instead, losses of 4 to 5% resulted in a the decrease of optimum quantum yield below the critical value of 0.80, which indicates the occurrence of postharvest stress. Leaf application
Value of adding the apparent diffusion coefficient to capsular contact for the prediction of extracapsular extension in prostate cancer

Objective To determine whether evaluating the mean apparent diffusion coefficient (ADC) together with capsular contact (CC) adds value in the prediction of microscopic extracapsular extension (ECE) of prostate cancer. Materials and Methods Between January 2012 and December 2016, 383 patients underwent multiparametric magnetic resonance imaging (mpMRI) of the prostate. A total of 67 patients were selected for inclusion. Two radiologists (observers 1 and 2), working independently, performed qualitative and quantitative analyses of ECE, macroscopic ECE, and microscopic ECE. A third radiologist assessed the correlation with the clinical data, and two experienced pathologists reviewed all histopathological findings. Results Among the 67 patients, mpMRI showed lesions that were confined to the capsule in 44 (66.7%), had microscopic ECE in 12 (17.9%), and had macroscopic ECE in 11 (16.4%). There were no significant differences, in terms of the diagnostic accuracy, as measured by determining the area under the curve (AUC), of CC on T2-weighted images (CCT2), CC on diffusion-weighted imaging (CCDWI), and the mean ADC for the prediction of microscopic ECE, between observer 1 (AUC of 0.728, 0.691, and 0.675, respectively) and observer 2 (AUC of 0.782, 0.821, and 0.799, respectively). Combining the mean ADC with the CCT2 or CCDWI did not improve the diagnostic accuracy for either observer. There was substantial interobserver agreement for the qualitative evaluation of ECE, as demonstrated by the kappa statistic, which was 0.77 (0.66-0.87). The diagnostic accuracy (AUC) of the qualitative assessment for predicting microscopic ECE was 0.745 for observer 1 and 0.804 for observer 2, and the difference was less than significant. In a multivariate analysis, none of clinical or imaging parameters were found to be associated with ECE. Conclusion For the detection of microscopic ECE on mpMRI, CC appears to have good diagnostic accuracy, especially if the observer has considerable experience. Adding the mean ADC to the CCT2 or CCDWI does not seem to provide any significant improvement in that diagnostic accuracy.
Cell‐Based Therapy for Canavan Disease Using Human iPSC‐Derived NPCs and OPCs

Canavan disease (CD) is a fatal leukodystrophy caused by mutation of the aspartoacylase (ASPA) gene, which leads to deficiency in ASPA activity, accumulation of the substrate N‐acetyl‐L‐aspartate (NAA), demyelination, and spongy degeneration of the brain. There is neither a cure nor a standard treatment for this disease. In this study, human induced pluripotent stem cell (iPSC)‐based cell therapy is developed for CD. A functional ASPA gene is introduced into patient iPSC‐derived neural progenitor cells (iNPCs) or oligodendrocyte progenitor cells (iOPCs) via lentiviral transduction or TALEN‐mediated genetic engineering to generate ASPA iNPC or ASPA iOPC. After stereotactic transplantation into a CD (Nur7) mouse model, the engrafted cells are able to rescue major pathological features of CD, including deficient ASPA activity, elevated NAA levels, extensive vacuolation, defective myelination, and motor function deficits, in a robust and sustainable manner. Moreover, the transplanted mice exhibit much prolonged survival. These genetically engineered patient iPSC‐derived cellular products are promising cell therapies for CD. This study has the potential to bring effective cell therapies, for the first time, to Canavan disease children who have no treatment options. The approach established in this study can also benefit many other children who have deadly genetic diseases that have no cure.
A polycentric network strategy for regional diversification of agriculture: theory and implementation

Widespread and substantial diversification of current agroecosystems appears fundamental to meeting many grand challenges in agriculture. Despite urgent calls for diversification on regional scales, particularly in regions dominated by industrialized, low-diversity agriculture, strategies for diversification on such scales are in early stages of development, conceptually and practically. We outline such a strategy, and its implementation by the Forever Green Partnership, a public-private-NGO coalition in support of agricultural diversification in the U.S. Midwest region. Our strategy supports introduction and scaling of multiple novel crops in a region, which requires development of many interdependent supporting elements, including supportive markets, infrastructure, policy, finance, and R&D. The core of our strategy is development of sustainable supply chains (SSCs) for a set of novel crops. We define SSCs as rudimentary systems of these supporting elements for novel crops, linking on-farm crop production to end-use markets while advancing economic, environmental, and social sustainability criteria that are demanded by stakeholders. SSCs provide a scaffold upon which fully-developed support systems for multiple novel crops can be constructed, thus driving regional diversification. SSCs cannot be “built in a day”; rather they must evolve as production of novel crops expands over time and space, and as new challenges and opportunities emerge. Therefore, regional diversification requires a system to sustain this evolutionary process across time and multiple novel crops. We posit that an effective system can be built from two crucial elements: a process of conscious and concerted cultural evolution, and a polycentric network that organizes and supports that process. We outline this system and its conceptual basis, and its implementation by the Forever Green Partnership, and associated challenges and accomplishments. Three years after its inception, the Partnership has attracted substantial resources, developed a polycentric network, and some elements of the cultural-evolution process are in place. However, node development is uneven across the network, hindering its operation. In addition to advancing strategies for regional-scale diversification, the Partnership is seeking to advance conceptual and practical understanding of sustainability transitions in agriculture, and to explore the potential value of conscious cultural evolution in such transitions.
Silencing of MEF2D by siRNA Loaded Selenium Nanoparticles for Ovarian Cancer Therapy

Background Delivery of therapeutic small interfering RNA (siRNA) via functionalized nanoparticles holds great promise for cancer therapy. However, developing a safe and efficient delivery carrier of siRNA is a challenging issue. Methods RGDfC peptide was used to modify the surface of selenium nanoparticles (SeNPs) to synthesize a biocompatible siRNA delivery vehicle (R-SeNPs), and MEF2D-siRNA was loaded onto R-SeNPs to prepare a functionalized selenium nanoparticle R-Se@MEF2D-siRNA. The chemical properties of R-SeNPs were characterized, and the anticancer efficacy as well as related mechanisms of R-Se@MEF2D-siRNA were further explored. Results R-Se@MEF2D-siRNA was significantly taken up by SKOV3 cells and could enter SKOV3 cells mainly in the clathrin-associated endocytosis way. The result of in vitro siRNA release demonstrated that R-Se@MEF2D-siRNA could release MEF2D-siRNA quicker in a microenvironment simulating a lysosomal environment in tumor cells compared to a normal physiological environment. The results of qRT-PCR assay proved that R-Se@MEF2D-siRNA could effectively silence the expression of the MEF2D gene in SKOV3 cells. R-Se@MEF2D-siRNA remarkably suppressed the proliferation of SKOV3 cells and further triggered its apoptosis. In addition, R-Se@MEF2D-siRNA had the capability to disrupt mitochondrial membrane potential (MMP) in SKOV3 cells and resulted in the overproduction of reactive oxygen species (ROS), indicating that mitochondrial dysfunction and ROS generation played an important role in the apoptosis of SKOV3 cells induced by R-Se@MEF2D-siRNA. In vivo, R-Se@MEF2D-siRNA also exhibited excellent antitumor activity mainly through decreasing tumor cells proliferation and triggering their apoptosis in tumor-bearing nude mice. Conclusion R-Se@MEF2D-siRNA provides an alternative strategy for ovarian cancer treatment in the clinic.
Stock specific high-seas distribution of maturing sockeye salmon in the North Pacific

The stock-specific distribution of maturing and adult salmon in the Northeast (NE) Pacific has been a persistent information gap that has prevented us from determining the ocean conditions experienced by individual stocks. This continues to impede understanding of the role of ocean conditions in stock-specific population dynamics. We assessed scale archives for 17 sockeye salmon (Oncorhynchus nerka) stocks covering the entire North Pacific, from the Columbia River to Kamchatka Peninsula, to define salmon locations during their last growing season before returning to their spawning grounds. We used the relationship between δ13C in salmon scales and sea water temperature to estimate salmon distribution based on correlation strength. Significant correlations were found for 13 of the stocks allowing us to define feeding grounds with confidence. Complementary information from δ15N, historical tagging studies, and connectivity analysis were used to further refine distribution estimates. Based on the estimated distributions of the NE Pacific stocks, we suggest a sequence of steps that could result in salmon marine distributions. This study is a first step toward determining stock-specific distributions of salmon in the NE Pacific, and provides a basis for the application of the approach to other salmon scale archives. This information will improve our ability to relate stock dynamics to ocean conditions, ultimately enabling improved stock management. For example, our estimated distributions of Bristol Bay and NE Pacific stocks demonstrated that they occupy different areas with a number of the former being distributed in the high productivity shelf waters of the Aleutian Islands and Bering Sea. This may explain while these stocks seem to have responded differently to changes in ocean conditions, and the long term trend of increased productivity of Bristol Bay sockeye.
Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction

Abstract Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome‐scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR‐based Sanger sequencing, following the dawn of the second‐generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained.
Novel PI3K/Akt/mTOR signaling inhibitor, W922, prevents colorectal cancer growth via the regulation of autophagy

W922, a novel PI3K/Akt/mTOR pathway inhibitor, exhibits efficient anti-tumor effects on HCT116, MCF-7 and A549 human cancer cells compared with other synthesized compounds. The present study aimed to investigate its anti-tumor effects on colorectal cancer cells. A total, of seven different colorectal cell lines were selected to test the anti-proliferation profile of W922, and HCT116 was found to be the most sensitive cell line to the drug treatment. W922 inhibited HCT116 cell viability and cell proliferation in vitro in concentration- and time-dependent manners. Furthermore, W922 suppressed the tumor growth in a xenograft mouse model and exhibited low toxicity. The proteomic alterations in W922-treated HCT116 cells were found to be associated with cell cycle arrest, negative regulation of signal transduction and lysosome-related processes. W922 caused cell cycle arrest of HCT116 cells in G0-G1 phase, but only triggered slight apoptosis. In addition, the PI3K/Akt/mTOR signaling proteins were dephosphorylated upon W922 treatment. It has been reported that inhibition of mTOR is relevant to autophagy, and the present results also indicated that W922 was involved in autophagy induction. An autophagy inhibitor, chloroquine, was used to co-treat HCT116 cells with W922, and it was identified that the cell cycle arrest was impaired. Moreover, co-treatment of W922 and chloroquine led to a significant population of apoptotic cells, thus providing a promising therapeutic strategy for colorectal cancer.
Cooperative hydrogen-bonding in models of antiparallel β-sheets

We present fully geometrically optimized density functional theory calculations at the B3LYP/D95(d,p) level on antiparallel β-sheet models consisting of two or four strands of two or four glycine residues and artificial nylon-like two- or four-strand models of two glycine residues separated by two methylene groups. Unlike the H-bonds in α-helices and chains of H-bonding amides, the association of polyglycine strands shows little or no H-bond cooperativity. We show that C5 intrastrand H-bonds are either disrupted or enhanced upon formation of interstrand H-bonds, depending upon the H-bonding pattern in the glycine (but not the nylon-like) structures. The apparent relative absence of H-bond cooperativity in β-sheet models of polyglycine derives from the weakening and strengthening of these intrastrand H-bonds. Normal cooperative H-bonding occurs when the nylon-like strands (which cannot form the intrastrand H-bond) form two- and four-strand sheets. The H-bonding interactions are stronger and the H-bonding d.
TEMPERATURE DEPENDENCE ON THE GRATING FORMATION IN PHOTOREFRACTIVE POLYMERIC COMPOSITE

We investigated the dependence of the grating formation on temperature in photorefractive polymeric composite, especially the index contrast of the grating. For photorefractive polymeric materials, temperature is one of the most important factors together with the external electric field, because it is closely related with photogeneration efficiency, carrier mobility, electro-optic coefficient tensor, and so on. The diffraction efficiency of the photorefractive polymeric composite decreased with increasing the temperature, and it could be explained with the magnitude of space-charge field and the electro-optic behavior at various temperatures.
Understanding the biological basis of dyslexia at a neural systems level

Abstract We examined the naming speed performance of 18 typically achieving and 16 dyslexic adults while simultaneously recording eye movements, articulations and fMRI data. Naming speed tasks, which require participants to name a list of letters or objects, have been proposed as a proxy for reading and are thought to recruit similar reading networks in the left hemisphere of the brain as more complex reading tasks. We employed letter and object naming speed tasks, with task manipulations to make the stimuli more or less phonologically and/or visually similar. Compared to typically achieving readers, readers with dyslexia had a poorer behavioural naming speed task performance, longer fixation durations, more regressions and increased activation in areas of the reading network in the left-hemisphere. Whereas increased network activation was positively associated with performance in dyslexics, it was negatively related to performance in typically achieving readers. Readers with dyslexia had greater bilateral activation and recruited additional regions involved with memory, namely the amygdala and hippocampus; in contrast, the typically achieving readers additionally activated the dorsolateral prefrontal cortex. Areas within the reading network were differentially activated by stimulus manipulations to the naming speed tasks. There was less efficient naming speed behavioural performance, longer fixation durations, more regressions and increased neural activity when letter stimuli were both phonologically and visually similar. Discussion focuses on the differences in activation within the reading network, how they are related to behavioural task differences, and how progress in furthering the understanding of the relationship between behavioural performance and brain activity can change the overall trajectories of children with reading difficulties by contributing to both early identification and remediation processes.
A new southern record of the holopelagic annelid Poeobius meseres Heath, 1930 (Flabelligeridae)

Abstract Background The unusual holopelagic annelid Poeobius meseres Heath, 1930 (Flabelligeridae) was first collected from Monterey Bay, California and has been subsequently recorded across the northern Pacific from Japan to the Gulf of California. Rare occurrences in the eastern tropical Pacific have extended as far as 7° S off Peru. New information Using molecular phylogenetic analysis of a newly-collected specimen from the Salas y Gómez Ridge off Chile, we extend the known geographic range of P. meseres southwards by 2040 km. This subtropical specimen showed higher genetic similarity to a specimen from the type locality (< 1.5% pairwise COI distance) than to representatives from the Aleutian Islands and Japan (5-6%), establishing the first genetically-confirmed occurrence of this species in the Southern Hemisphere. The latitudinal range of P. meseres encompasses the sole collection locality, off Ecuador, of Enigma terwielii Betrem, 1925, a pelagic annelid which has been compared to P. meseres, but is indeterminable due to an inadequate description. We therefore suggest that the earlier sole record of E. terwielii may have been an occurrence of what is known now as P. meseres.
Partial restoration of normal intestinal microbiota in morbidly obese women six months after bariatric surgery

We studied the impact of bariatric surgery on the intestinal microbiota of morbidly obese study subjects. A total of 13 morbidly obese women (five of which had type 2 diabetes) and 14 healthy age- and gender-matched controls were recruited and the microbiota composition of fecal samples were determined by using a phylogenetic microarray. Sampling of the patients took place just one month before and 6 months after the operation. Within six months after bariatric surgery, the obese subjects had lost on average a quarter of their weight whereas four of the five of the diabetic subjects were in remission. Bariatric surgery was associated with an increased microbial community richness and Bacteroidetes/Firmicutes ratio. In addition, we observed an increased relative abundance of facultative anaerobes, such as Streptococcus spp. , and a reduction in specific butyrate-producing Firmicutes. The observed postoperative alterations in intestinal microbiota reflect adaptation to the changing conditions in the gastrointestinal tract, such as energy restriction and the inability to process fiber-rich foods after bariatric surgery.
Locally Applied Stem Cell Exosome-Scaffold Attenuates Nerve Injury-Induced Pain in Rats

Purpose Nerve injury-induced pain is difficult to treat. In this study, we developed an alginate scaffold with human umbilical cord mesenchymal stem cell exosomes (EX-SC) to treat nerve injury-induced pain. Materials and Methods The scaffold was prepared and characterized for its physical traits and biocompatibility. In vitro studies of PC12 and HEK293 cells were used to evaluate the neuroprotective and neurotrophic effects of exosomes. Right L5/6 spinal nerve ligation (SNL) was performed in Sprague-Dawley rats to induce mechanical allodynia and thermal hyperalgesia, evaluated by von Frey hair and radiant heat tests. The EX-SC was wrapped around ligated L5/6 spinal nerves for treatment. Western blotting and immunofluorescence staining were used to evaluate neuron/glial activation, cytokines and neurotrophic factor of affected dorsal root ganglion (DRG). Results In cell culture assay, the exosomes induce neurite outgrowth of PC12 cells and protect PC12 and HEK293 cells against formaldehyde acid treatment. On post-ligation day 21, rats receiving EX-SC had significantly higher median (interquartile range) withdrawal threshold and latency [14.1 (13.7–15.5) g, 14.2 (13.7–15.3) s] than saline-SC-treated rats [2.1 (1.7–3.0) g, 2.0 (1.8–2.4) s, P=0.02 and 0.002]. The EX-SC also attenuated SNL-induced up-regulation of c-Fos, GFAP, Iba1, TNF-α and IL-1β, while enhancing the level of IL-10 and GDNF, in the ipsilateral L5/6 DRG. After implantation for 21 days, the EX-SC enhanced the expression of myelin basic protein and IL-10 in injured L5/6 axons. Conclusion We demonstrate the EX-SC possesses antinociceptive, anti-inflammation and pro-neurotrophic effects in the SNL pain model. It could be a promising therapeutic alternative for nerve injury-induced pain.