Miracle-dz/UniFAR-FTUs huggingface dataset:
On the deformability of an empirical fitness landscape by microbial evolution

Significance Fitness landscapes map the relationship between genotype and phenotype, and are a core tool for predicting evolutionary processes from the emergence of resistant pathogens to cancer. The topography of fitness landscapes is determined by the environment. However, populations can also dynamically modify their environment, for instance by releasing metabolites to it, and thus they may potentially deform their own adaptive landscape. Using a combination of genome-scale metabolic simulations and experiments with Escherichia coli strains from the Lenski laboratory Long-Term Evolution Experiment, we systematically and quantitatively characterize the deformability of an empirical fitness landscape. We show that fitness landscapes retain their power to forecast evolution over short mutational distances but environment building may attenuate this capacity over longer adaptive trajectories. A fitness landscape is a map between the genotype and its reproductive success in a given environment. The topography of fitness landscapes largely governs adaptive dynamics, constraining evolutionary trajectories and the predictability of evolution. Theory suggests that this topography can be deformed by mutations that produce substantial changes to the environment. Despite its importance, the deformability of fitness landscapes has not been systematically studied beyond abstract models, and little is known about its reach and consequences in empirical systems. Here we have systematically characterized the deformability of the genome-wide metabolic fitness landscape of the bacterium Escherichia coli. Deformability is quantified by the noncommutativity of epistatic interactions, which we experimentally demonstrate in mutant strains on the path to an evolutionary innovation. Our analysis shows that the deformation of fitness landscapes by metabolic mutations rarely affects evolutionary trajectories in the short range. However, mutations with large environmental effects produce long-range landscape deformations in distant regions of the genotype space that affect the fitness of later descendants. Our results therefore suggest that, even in situations in which mutations have strong environmental effects, fitness landscapes may retain their power to forecast evolution over small mutational distances despite the potential attenuation of that power over longer evolutionary trajectories. Our methods and results provide an avenue for integrating adaptive and eco-evolutionary dynamics with complex genetics and genomics.
Two-wavelength oximetry of tissue microcirculation based on sidestream dark-field imaging

Abstract. Monitoring oxygen saturation (SO2) in microcirculation is effective for understanding disease dynamics. We have developed an SO2 estimation method, sidestream dark-field (SDF) oximetry, based on SDF imaging. SDF imaging is a noninvasive and clinically applicable technique to observe microcirculation. We report the first in vivo experiment observing the changes in SO2 of microcirculation using SDF oximetry. First, heat from the light-emitting diodes used for the SDF imaging might affect hemodynamics in microcirculation, hence, we performed an experiment to evaluate the influence of that on the SDF oximetry. The result suggested that SDF oximetry had enough stability for long-term experiments. Then, to evaluate the sensitivity of SDF oximetry to alterations in the hemodynamics of the microcirculation, we observed the time-lapsed SO2 changes in the dermis microcirculation of rats under hypoxic stimulation. We confirmed that the SO2 estimated by SDF oximetry was in accordance with changes in the fraction of inspired oxygen (FiO2). Thus, SDF oximetry is considered to be able to observe SO2 changes that occur in accordance with alteration of the microcirculation.
The vitellogenin receptor has an essential role in vertical transmission of rice stripe virus during oogenesis in the small brown plant hopper.

BACKGROUND The small brown plant hopper (SBPH), Laodelphax striatellus Fallén, is one of the most destructive pests on rice. This pest transmits rice stripe virus (RSV) both horizontally and vertically, leading to major yield and economic losses in rice production. However, the way that RSV particles enter oocytes of SBPH remains largely unknown. Thus, identification of key factors involved in the interaction between SBPH and RSV in the ovary is crucial. RESULTS Transcriptome of non-viruliferous (NV) or high viruliferous (HV) SBPH ovaries at 24 and 48 h of emergence was sequenced. Differentially expressed genes analysis showed that vitellogenin receptor was significantly highly expressed in the ovary of the HV SBPH strains compared to NV strains. Quantitative real-time polymer chain reaction showed that the vitellogenin receptor in L. striatellus (LsVgR) was highly expressed in the ovaries of female adults and maintained a high level of expression at the early stage of ovary development. By using RNA interference, the expression of LsVgR in the ovaries of the HV strain was significantly decreased by 98.1%. RSV titer was reduced by 60.9% as quantified by viral RNA3 intergenic region and the transcripts of nucleocapsid protein gene (CP) reduced by 46.3%. The numbers of offspring hatched were significantly reduced in dsRNA-treated groups. The transcripts of CP were not affected by silencing LsVgR, whereas the abundance of RNA-dependent RNA polymerase increased by 15-fold in the member of surviving progenies. CONCLUSION Our results suggest that vitellogenin receptor participates in regulating RSV replication during oogenesis. © 2018 Society of Chemical Industry.
Climate-driven declines in arthropod abundance restructure a rainforest food web

Significance Arthropods, invertebrates including insects that have external skeletons, are declining at an alarming rate. While the tropics harbor the majority of arthropod species, little is known about trends in their abundance. We compared arthropod biomass in Puerto Rico’s Luquillo rainforest with data taken during the 1970s and found that biomass had fallen 10 to 60 times. Our analyses revealed synchronous declines in the lizards, frogs, and birds that eat arthropods. Over the past 30 years, forest temperatures have risen 2.0 °C, and our study indicates that climate warming is the driving force behind the collapse of the forest’s food web. If supported by further research, the impact of climate change on tropical ecosystems may be much greater than currently anticipated. A number of studies indicate that tropical arthropods should be particularly vulnerable to climate warming. If these predictions are realized, climate warming may have a more profound impact on the functioning and diversity of tropical forests than currently anticipated. Although arthropods comprise over two-thirds of terrestrial species, information on their abundance and extinction rates in tropical habitats is severely limited. Here we analyze data on arthropod and insectivore abundances taken between 1976 and 2012 at two midelevation habitats in Puerto Rico’s Luquillo rainforest. During this time, mean maximum temperatures have risen by 2.0 °C. Using the same study area and methods employed by Lister in the 1970s, we discovered that the dry weight biomass of arthropods captured in sweep samples had declined 4 to 8 times, and 30 to 60 times in sticky traps. Analysis of long-term data on canopy arthropods and walking sticks taken as part of the Luquillo Long-Term Ecological Research program revealed sustained declines in abundance over two decades, as well as negative regressions of abundance on mean maximum temperatures. We also document parallel decreases in Luquillo’s insectivorous lizards, frogs, and birds. While El Niño/Southern Oscillation influences the abundance of forest arthropods, climate warming is the major driver of reductions in arthropod abundance, indirectly precipitating a bottom-up trophic cascade and consequent collapse of the forest food web.
Comparison of bench-top simulation versus traditional training models in diagnostic arthroscopic skills training.

OBJECTIVES This study aims to compare the efficacy of existing training models for acquisition of arthroscopic skills and to investigate the most effective training method or combination of methods for residents. MATERIALS AND METHODS A total of 100 fifth-year students from medical school (40 males, 60 females; mean age 23.7 years; range, 22 to 33 years) volunteered to participate in the study and were randomly divided into five education groups (E1-5): group E1 (trained on bench-top simulator), group E2 (read surgical technique), group E3 (read surgical technique and watched surgical video), group E4 (watched surgical video only), and group E5 (control group). After completion of the pre-training, each student was individually asked to perform an arthroscopy practice. A checklist containing the tasks to be performed was given to students and students were asked to complete the tasks on the checklist in five minutes. RESULTS In group E1, the mean rate of successful achievement of tasks was significantly higher than other groups in both knee and shoulder arthroscopy models. Rate of each task was statistically similar for groups E2, E3, E4 and E5. In group E1, mean durations for completion of tasks in both arthroscopy models were significantly shorter than other groups. There was no statistically significant difference in terms of gender between those who successfully completed the tasks in both arthroscopy models. CONCLUSION A basic arthroscopic bench-top simulator may be a low-cost and effective training method to increase arthroscopic skill levels in resident training compared to traditional methods.
Evolution and development of the fish jaw skeleton

The evolution of the jaw represents a key innovation in driving the diversification of vertebrate body plans and behavior. The pharyngeal apparatus originated as gill bars separated by slits in chordate ancestors to vertebrates. Later, with the acquisition of neural crest, pharyngeal arches gave rise to branchial basket cartilages in jawless vertebrates (agnathans), and later bone and cartilage of the jaw, jaw support, and gills of jawed vertebrates (gnathostomes). Major events in the evolution of jaw structure from agnathans to gnathostomes include axial regionalization of pharyngeal elements and formation of a jaw joint. Hox genes specify the anterior–posterior identity of arches, and edn1, dlx, hand2, Jag1b‐Notch2 signaling, and Nr2f factors specify dorsal–ventral identity. The formation of a jaw joint, an important step in the transition from an un‐jointed pharynx in agnathans to a hinged jaw in gnathostomes involves interaction between nkx3.2, hand2, and barx1 factors. Major events in jaw patterning between fishes and reptiles include changes to elements of the second pharyngeal arch, including a loss of opercular and branchiostegal ray bones and transformation of the hyomandibula into the stapes. Further changes occurred between reptiles and mammals, including the transformation of the articular and quadrate elements of the jaw joint into the malleus and incus of the middle ear. Fossils of transitional jaw phenotypes can be analyzed from a developmental perspective, and there exists potential to use genetic manipulation techniques in extant taxa to test hypotheses about the evolution of jaw patterning in ancient vertebrates.
RSV infection and respiratory sequelae.

INTRODUCTION The association between respiratory syncytial virus (RSV) infections and long-term respiratory sequelae has long been recognized. It is estimated that individuals with a history of RSV bronchiolitis have 2- to 12-fold higher risk of developing asthma. Although this risk tends to decrease with age, persistent airway obstruction and hyperresponsiveness are observed even 30 years after RSV infection. EVIDENCE ACQUISITION Our data search strategy was designed to address the following questions: What is the epidemiological evidence available on the association between RSV infection and long-term respiratory morbidity? What are the potential pathogenic pathways linking RSV infection to long-term respiratory morbidity? Are there any host genetic backgrounds that can predispose to both severe RSV lower respiratory tract infection and asthma? Are antiviral therapies and RSV prevention measures effective in reducing respiratory morbidities? EVIDENCE SYNTHESIS This article reviews the recent scientific literature on the epidemiological association and pathogenic links between early RSV infection and long-term respiratory morbidities. CONCLUSIONS Nowadays, asthma is increasingly considered a heterogeneous disease, caused by interactions between several host and environmental factors. Understanding the specific causative role of respiratory viruses, and the pathogenic mechanisms through which bronchiolitis predisposes to asthma, is a challenging, but essential starting point for the development of prevention and treatment strategies potentially capable of preserving lung function.
An Fe‐Ni‐Cr embedded atom method potential for austenitic and ferritic systems

Fe‐Ni‐Cr stainless‐steels are important structural materials because of their superior strength and corrosion resistance. Atomistic studies of mechanical properties of stainless‐steels, however, have been limited by the lack of high‐fidelity interatomic potentials. Here using density functional theory as a guide, we have developed a new Fe‐Ni‐Cr embedded atom method potential. We demonstrate that our potential enables stable molecular dynamics simulations of stainless‐steel alloys at high temperatures, accurately reproduces the stacking fault energy—known to strongly influence the mode of plastic deformation (e.g., twinning vs. dislocation glide vs. cross‐slip)—of these alloys over a range of compositions, and gives reasonable elastic constants, energies, and volumes for various compositions. The latter are pertinent for determining short‐range order and solute strengthening effects. Our results suggest that our potential is suitable for studying mechanical properties of austenitic and ferritic stainless‐steels which have vast implementation in the scientific and industrial communities. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.
A Comparison of the Central versus Peripheral Gastrointestinal Prokinetic Activity of Two Novel Ghrelin Mimetics

The gastrointestinal (GI) prokinetic effects of ghrelin occur through direct peripheral effects on ghrelin receptors within the enteric nervous system and via the ghrelin receptor on the vagus nerve, which activate a centrally mediated mechanism. However, the relative contribution of peripheral versus central effects to the overall prokinetic effect of ghrelin agonists requires further investigation. Here, we investigated the central versus peripheral prokinetic effect of ghrelin by using two novel ghrelin agonists: HM01 (N′-[(1S)-1-(2,3-dichloro-4-methoxyphenyl)ethyl]-N-methyl-N-[1,3,3-trimethyl-(4R)-piperidyl]-urea HCL) with high brain penetration compared with HM02 (N′-[(1S)-1-(2,3-dichloro-4-methoxyphenyl)ethyl]-N-hydroxy-N-(1-methyl-4-piperidinyl)-urea), a more peripherally acting ghrelin agonist. The pharmacokinetic profiles of both ghrelin agonists were evaluated after intravenous and oral administration in rats. The efficacy of HM01 and HM02 was assessed in a rat model of postoperative ileus (POI) induced by abdominal surgery and in a rodent defecation assay. Pharmacokinetic results in our models confirmed that HM01, but not HM02, was a brain-penetrant ghrelin agonist. Administration of either HM01 or HM02 reversed the delayed upper and lower gastrointestinal transit induced by abdominal surgery to levels resembling the non-POI controls. In the defecation test, HM01, but not HM02, significantly increased the weight of fecal pellets. Our findings suggest that, in a rodent model of POI, synthetic ghrelin agonists stimulate GI transit through a peripheral site of action. However, in the defecation assay, our data suggest that a ghrelin-mediated mechanism is located at a central site. Taken together, a ghrelin agonist with both central and peripheral prokinetic activity may show therapeutic potential to treat delayed GI transit disorders.
Result Pattern Hiding Searchable Encryption for Conjunctive Queries

The recently proposed Oblivious Cross-Tags (OXT) protocol (CRYPTO 2013) has broken new ground in designing efficient searchable symmetric encryption (SSE) protocol with support for conjunctive keyword search in a single-writer single-reader framework. While the OXT protocol offers high performance by adopting a number of specialised data-structures, it also trades-off security by leaking 'partial' database information to the server. Recent attacks have exploited similar partial information leakage to breach database confidentiality. Consequently, it is an open problem to design SSE protocols that plug such leakages while retaining similar efficiency. In this paper, we propose a new SSE protocol, called Hidden Cross-Tags (HXT), that removes 'Keyword Pair Result Pattern' (KPRP) leakage for conjunctive keyword search. We avoid this leakage by adopting two additional cryptographic primitives - Hidden Vector Encryption (HVE) and probabilistic (Bloom filter) indexing into the HXT protocol. We propose a 'lightweight' HVE scheme that only uses efficient symmetric-key building blocks, and entirely avoids elliptic curve-based operations. At the same time, it affords selective simulation-security against an unbounded number of secret-key queries. Adopting this efficient HVE scheme, the overall practical storage and computational overheads of HXT over OXT are relatively small (no more than 10% for two keywords query, and 21% for six keywords query), while providing a higher level of security.
Fast Multiparty Threshold ECDSA with Fast Trustless Setup

A threshold signature scheme enables distributed signing among n players such that any subgroup of size $t+1$ can sign, whereas any group with t or fewer players cannot. While there exist previous threshold schemes for the ECDSA signature scheme, we are the first protocol that supports multiparty signatures for any $t łeq n$ with an efficient dealerless key generation. Our protocol is faster than previous solutions and significantly reduces the communication complexity as well. We prove our scheme secure against malicious adversaries with a dishonest majority. We implemented our protocol, demonstrating its efficiency and suitability to be deployed in practice.
Survey research on the habitation and biological information of Callipogonrelictus Semenov in Gwangneung forest, Korea and Ussurisky nature reserve, Russia (Coleoptera, Cerambycidae, Prioninae)

Abstract An investigation on the habitation of Callipogonrelictus Semenov, 1899 in Gwangneung forest was carried out, where the Korea National Arboretum is located. In an investigation spanning the last eleven years (2007–2017), 22 emergence holes, nine pupal chambers, six adults, and two larvae of C.relictus were identified. In this study, biological information about habitation of C.relictus is provided by comparing and combining the results of this investigation with a survey conducted in Ussurisky Nature Reserve, Russia, in 2015. The distribution is also reviewed to include the Korean Peninsula and a new location of South Korea is added to the distribution for C.relictus.
Towards a better understanding of AQP4′s role in astrocytic process extension

At the blood–brain–barrier (BBB), blood vessels are surrounded by the endfoot structures formed by astroglial cells. The latter are themselves part of a larger syncytial network of astrocytes connected to each other via a complex web of processes. The water‐permeable channel aquaporin‐4 (AQP4) is expressed at high concentrations at these endfeet, held in place by the dystrophin glycoprotein complex (DGC), a collection of proteins that act as a bridge linking AQP4 to the laminin‐containing basal lamina found in between the blood vessels and the astrocytic endfeet. Although AQP4, supported by the DGC, has well‐established roles in facilitating certain neurological processes, and in mediating the removal of excess water from the brain in certain disease states, relatively few studies have looked at the importance of these components in the regulation of the extension of the processes that are so characteristic of astrocytes. In this Editorial Highlight, we discuss an article by Sato et al., published in this issue of the Journal of Neurochemistry, which attempts to address this question.
The Neuropilin‐1 Ligand, Sema3A, Acts as a Tumor Suppressor in the Pathogenesis of Acute Leukemia

Semaphorin‐3A (Sema3A) and vascular endothelial growth factor (VEGF165) are ligands of neuropilin‐1 (NRP‐1 or CD304) and are related to immunoregulation and tumor angiogenesis, respectively. However, possible interactions between NRP‐1 and Sema3A and VEGF165 in acute leukemia remain unclear, especially whether Sema3A plays a role in acute leukemia. In this study, both of the proportion of regulatory T cells (Tregs) and their expression of NRP‐1 were found to increase in acute leukemia patients compared with healthy controls. In contrast, lower mRNA and plasma levels of Sema3A were detected in the acute leukemia patients. In vitro, the addition of exogenous Sema3A inhibited the expression of NRP‐1 on Tregs and it promoted apoptosis of leukemia cells. However, in the presence of anti‐Sema3A antibody, the effect of rhSema3A on NRP‐1 expression was reversed. These results suggest that Sema3A promotes apoptosis in leukemia cells by inhibiting expression of NRP‐1, and thus, represents a tumor suppressor protein with a role in the pathogenesis of acute leukemia. Consequently, NRP‐1/Sema3A signaling may represent a novel target for the treatment of acute leukemia and should be further studied. Anat Rec, 302:1127–1135, 2019. © 2018 Wiley Periodicals, Inc.
Adverse effects of acrolein, a ubiquitous environmental toxicant, on muscle regeneration and mass

Acrolein is an extremely electrophilic aldehyde. Increased urinary acrolein adducts have been found in type 2 diabetic patients and people with a smoking habit. The increased blood acrolein was shown in patients who received the cancer drug cyclophosphamide. Both diabetes and smoking are risk factors for skeletal muscle wasting or atrophy. Acrolein has been found to induce myotube atrophy in vitro. The in vitro and in vivo effects and mechanisms of acrolein on myogenesis and the in vivo effect of acrolein on muscle wasting still remain unclear.
Grounding Robot Plans from Natural Language Instructions with Incomplete World Knowledge

: Our goal is to enable robots to interpret and execute high-level tasks conveyed using natural language instructions. For example, consider tasking a household robot to, “prepare my breakfast”, “clear the boxes on the table” or “make me a fruit milkshake”. Interpreting such underspeciﬁed instructions requires environmental context and background knowledge about how to accomplish complex tasks. Further, the robot’s workspace knowledge may be incomplete: the environment may only be partially-observed or background knowledge may be missing causing a failure in plan synthesis. We introduce a probabilistic model that utilizes background knowledge to infer latent or missing plan constituents based on semantic co-associations learned from noisy textual corpora of task descriptions. The ability to infer missing plan constituents enables information-seeking actions such as visual exploration or dialogue with the human to acquire new knowledge to ﬁll incomplete plans. Results indicate robust plan inference from under-speciﬁed instructions in partially-known worlds.