Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of functional cell surface expression by oligomerization and N-linked glycosylation of membrane proteins

ii TABLE OF CONTENTS . iii LIST OF TABLES. vii LIST OF FIGURES. viii LIST OF ABBREVIATIONS.x ACKNOWLEDGEMENTS . xi DEDICATION . xii CO-AUTHORSHIP STATEMENT. xiii
ACNMP: Flexible Skill Formation with Learning from Demonstration and Reinforcement Learning via Representation Sharing

: 1 To equip robots with dexterous skills, an effective approach is to ﬁrst transfer 2 the desired skill via Learning from Demonstration (LfD), then let the robot im-3 prove it by self-exploration via Reinforcement Learning (RL). In this paper, we 4 propose a novel LfD+RL framework, namely Adaptive Conditional Neural Move-5 ment Primitives (ACNMP), that allows efﬁcient policy improvement in novel en-6 vironments and effective skill transfer between different agents. This is achieved 7 through exploiting the latent representation learned by the underlying Conditional 8 Neural Process (CNP) model, and simultaneous training of the model with su-9 pervised learning (SL) for acquiring the demonstrated trajectories and via RL for 10 new trajectory discovery. Through simulation experiments, we show that (i) AC-11 NMP enables the system to extrapolate to situations where pure LfD fails; (ii) 12 Simultaneous training of the system through SL and RL preserves the shape of 13 demonstrations while adapting to novel situations due to the shared representa-14 tions used by both learners; (iii) ACNMP enables sample-efﬁcient RL in extrap-15 olation of reaching tasks compared to the existing approaches; (iv) ACNMPs can 16 be used to implement skill transfer between robots having different morphology, 17 with competitive learning speeds and importantly with less number of assump-18 tions compared to the state-of-the-art approaches. Finally, we show the real-world 19 suitability of ACNMPs through real robot experiments involving obstacle avoid-20 ance and manipulation. 21
Progressive‐Change BACIPS: a flexible approach for environmental impact assessment

The Before‐After Control‐Impact Paired Series (BACIPS) design distinguishes natural spatial and temporal variability from variation induced by an environmental impact (or intervention) of interest. BACIPS is a powerful tool to derive inferences about interventions when classic experimental approaches (e.g. which rely on spatial replicates and random assignment of treatments) are not feasible or desirable. Previously applied BACIPS designs generally assume that effects are sudden, constant and long‐lived: that is, that systems exhibit ‘step‐changes’ in response to interventions. However, complex ecological interactions or gradual interventions may create delayed and/or progressive responses, potentially impeding the reliability of classic (step‐change) analyses. We propose a novel approach, the Progressive‐Change BACIPS, which generalizes and expands the scope of BACIPS analyses. We evaluate the relative performance of this approach using both simulated and real data that exhibit step‐change, linear, asymptotic and sigmoid responses following an intervention. We quantify the statistical power and accuracy of the Progressive‐Change BACIPS under varying initial population densities, intensity of spatial sampling, effect sizes and number of sampling dates After the intervention. We show that Progressive‐Change BACIPS identified the correct model among the set of candidate models under most conditions and led to accurate estimates of the parameters that were used to generate the simulated data. When data were sparse, and the dynamics complex, simpler (more parsimonious) models were favoured over the more complex models that actually generated the simulated data. Application of the Progressive‐Change BACIPS to existing data sets from the literature led to strong support for specific models (over alternatives) and led to more specific inferences than possible under the classic BACIPS approach. The Progressive‐Change BACIPS proposed here is more flexible than the original BACIPS formulation because the data are used to inform the form of the final model, rather than having the form of the model imposed on the data. This leads to better estimates of the effects of environmental impacts and the time‐scales over which they operate. As a result, the Progressive‐Change BACIPS should be applicable to a wide range of studies and should help improve investigation of time‐dependent effects. R code to perform Progressive‐Change BACIPS analysis is provided.
Bumble bee species exhibit divergent responses to urbanisation in a Southern California landscape

1. Bees are ecologically important pollinators that are threatened by disease, habitat degradation, and habitat loss. Bee species that share ecological traits (e.g. body size, diet breadth, and sociality) may often respond similarly to environmental disturbance; however, few studies have examined the extent to which closely related, ecologically similar species exhibit divergent responses to the same forms of disturbance.
Cephalopod‐Inspired High Dynamic Range Mechano‐Imaging in Polymeric Materials

Cephalopods, such as squid, cuttlefish, and octopuses, use an array of responsive absorptive and photonic dermal structures to achieve rapid and reversible color changes for spectacular camouflage and signaling displays. Challenges remain in designing synthetic soft materials with similar multiple and dynamic responsivity for the development of optical sensors for the sensitive detection of mechanical stresses and strains. Here, a high dynamic range mechano‐imaging (HDR‐MI) polymeric material integrating physical and chemical mechanochromism is designed providing a continuous optical read‐out of strain upon mechanical deformation. By combining a colloidal photonic array with a mechanically responsive dye, the material architecture significantly improves the mechanochromic sensitivity, which is moreover readily tuned, and expands the range of detectable strains and stresses at both microscopic and nanoscopic length scales. This multi‐functional material is highlighted by creating detailed HDR mechanographs of membrane deformation and around defects using a low‐cost hyperspectral camera, which is found to be in excellent agreement with the results of finite element simulations. This multi‐scale approach to mechano‐sensing and ‐imaging provides a platform to develop mechanochromic composites with high sensitivity and high dynamic mechanical range.
The Chip ‘n’ Ship: A Prototype Rock Chip Sampling Tool for Use on Microgravity Bodies

In response to NASA’s Micro-g Neutral Buoyancy Experiment Design Teams program challenge, a rock chip sampling device called the Chip ‘n’ Ship was designed, constructed, and tested. It was developed for use on microgravity bodies, primarily asteroids. The device incorporates a commercially-available, unmodified pneumatic hammer mounted inside a section of aluminum housing. It also features three interchangeable collection cartridges, specifically engineered to mitigate cross-contamination between sampling sites. The Chip ‘n’ Ship was subjected to functional testing by the Neutral Buoyancy Laboratory dive team at NASA’s Johnson Space Center in Houston, Texas in August 2015. The Chip ‘n’ Ship chipped a variety of rock samples successfully but could use general improvement to the sample collection mechanism and sealing of the sample inside the collection unit. Design Teams (Micro-g NExT) program as part of their Microgravity University (formerly Reduced Gravity Education Flight Program, or RGEFP) outreach initiative. Micro-g NExT challenges undergraduate students to “design, build, and test” a device or simulant that addressed an “authentic, current space exploration problem” selected by NASA engineers [2]. The program encourages participants to innovate with hands-on engineering design and functional test operations in the simulated microgravity environment of NASA’s Neutral Buoyancy Lab (NBL) facility. Professional NBL divers test all tools that are accepted into the program, under the direction of the student teams via radio communications. Specifically, the Micro-g NExT program W exploring the Moon, astronauts relied solely on hand tools to extract and collect rock chip samples. This process is labor intensive and inefficient, and National Aeronautics and Space Administration (NASA) officials are seeking alternative tool designs to develop a more efficient rock chip sampling process [1]. Such techniques should be established before NASA moves forward in planning and executing missions to asteroids. Due to safety and transportation restrictions, the design of any new tool must minimize risk of harm to the user while not significantly encroaching on mission payload limitations. As part of the search for new ideas and engineering innovation, NASA established the Micro-g Neutral Buoyancy Experiment Brooks, Cantor, Ickowski, Simeonides, Stidham and Vasquez Soto
Retinoic acid signaling in zebrafish fin regeneration

Adult teleosts rebuild amputated fins through a proliferation-dependent process called epimorphic regeneration, in which a blastema of cycling progenitor cells replaces the lost fin tissue. The genetic networks that control formation of blastema cells from formerly quiescent stump tissue and subsequent blastema function are still poorly understood. Here, we investigated the cellular and molecular consequences of genetically interfering with retinoic acid (RA) signaling for the formation of the zebrafish blastema. We show that RA signaling is upregulated within the first few hours after fin amputation in the stump mesenchyme, where it controls Fgf, Wnt/β-catenin and Igf signaling. Genetic inhibition of the RA pathway at this stage blocks blastemal formation by inhibiting cell cycle entry of stump cells and impairs the formation of the basal epidermal layer, a signaling center in the wound epidermis. In the established blastema, RA signaling remains active to ensure the survival of the highly proliferative blastemal population by controlling expression of the anti-apoptotic factor bcl2. In addition, RA signaling maintains blastemal proliferation through the activation of growthstimulatory signals mediated by Fgf and Wnt/β-catenin signaling, as well as by reducing signaling through the growth-inhibitory non-canonical Wnt pathway. The endogenous roles of RA in adult vertebrate appendage regeneration are uncovered here for the first time. They provide a mechanistic framework to understand previous observations in salamanders that link endogenous sources of RA to the regeneration process itself and support the hypothesis that the RA signaling pathway is an essential component of vertebrate tissue regeneration.
Leaf Cellular Automata.

Recently, genetic algorithms and other newly developed search techniques have received a lot of attention, because of their easy to use nature in many engineering problems. They are capable of locating good approximates in extremely large search spaces with a reasonable amount of computational effort. This study is one of a series in which the optimization systems of plants are applied to the field of engineering. Plants have been adapting themselves to severe environmental conditions to survive and reproduce by using many optimization techniques. The leaf cellular automata (LCA) developed in this study are also one of the search algorithms inspired by the mechanisms of the reactions of a leaf. The basic calculation procedure is similar to that of conventional of cellular automata. In order to test the performance of this algorithm, a knapsack problem that is a typical combinational optimization problem was solved by LCA. LCA could be used to obtain a considerably better solution than random walks.
Upregulation of GLE1 and LCP2 Genes in H5N1 Influenza Virus Infected Patients

Previous study showed that the Gle1 RNA export mediator-like (Gle1l) gene and the lymphocyte cytosolic protein 2 (Lcp2) gene were upregulated in response to influenza virus A/Puerto Rico/8/1934 (H1N1) in a mouse mode. To determine whether these two genes were upregulated in humans after influenza A virus infection, nasopharyngeal swabs were collected from eleven patients with flu-like symptoms for viral RNA extraction and PCR amplification. Sequencing analysis revealed that nucleoprotein (NP) gene fragments amplified from nasopharyngeal swabs of four patients shared the highest similarity with the NP gene from avian influenza A (H5N1) virus (A/ goose/Shantou/753/2002). Peripheral blood samples were then collected from four patients for quantitative analysis of GLE1 and LCP2 gene expression. Our results demonstrated that both GLE1 and LCP2 genes were upregulated in H5N1 influenza A virus infected patients, suggesting that upregulation of GLE1 and LCP2 genes may be important for the host defense against influenza A viruses.
Evaluating Changes to Fake Account Verification Systems

Online social networks (OSNs) such as Facebook, Twitter, and LinkedIn give hundreds of millions of individuals around the world the ability to communicate and build communities. However, the extensive user base of OSNs provides considerable opportunity for malicious actors to abuse the system, with fake accounts generating the vast majority of harmful actions and content. Social networks employ sophisticated detection mechanisms based on machine-learning classiﬁers and graph analysis to identify and remediate the actions of fake accounts. Disabling or deleting these detected accounts is not tractable when the number of false positives (i.e., real users disabled) is signiﬁcant in absolute terms. Using challenge-based veriﬁ-cation systems such as CAPTCHAs or phone conﬁrmation as a response for detected fake accounts can enable erroneously detected real users to recover their access, while also making it difﬁcult for attackers to abuse the platform. In order to maintain a veriﬁcation system’s effectiveness over time, it is important to iterate on the system to improve the real user experience and adapt the platform’s response to adversarial actions. However, at present there is no established method to evaluate how effective each iteration is at stopping fake accounts and letting real users through. This paper proposes a method of assessing the effectiveness of experimental iterations for OSN veriﬁcation systems, and presents an evaluation of this method against human-labelled ground truth data using production Facebook data. Our method reduces the volume of necessary human labelled data by 70%, decreases the time necessary for classiﬁcation by 81%, has suitable precision/recall for making decisions in response to experiments, and enables continuous monitoring of the effectiveness of the applied experimental changes.
Non-Strongyloides rhabditida identified in fecal samples – two case reports: lessons learned from morphological and molecular diagnostic approaches

Nematodes in the order Rhabditida, including species of Strongyloides and Pelodera, may be parasites of domestic animals. In this paper, we describe two apparent cases of rhabditid infections, one in a dog and one in a litter of piglets. The dog infection was originally considered likely to be an infection with Strongyloides, based on superficial morphological examination and PCR results without sequencing. However, more careful morphological analysis and inclusion of several molecular analyses, including sequencing, revealed that an infection with Pelodera sp. was more likely, probably Pelodera pseudoteres. Treatment with fenbendazole and selamectin was apparently successful. Similarly, based on both morphological and molecular analyses the apparent piglet infections were considered most likely to be withRhabditis spp. , possibly Rhabditis axei. The detection of larvae of nematodes in the order Rhabditida in fecal samples, particularly from dogs, may easily be considered as being indicative of Strongyloides infection. Given the zoonotic potential of canine Strongyloides, correct diagnosis is important. However, as illustrated by these two cases, careful morphological examination and measurement, supported by full molecular investigations, including sequencing, are essential in order to avoid this misdiagnosis.
Comparison Analysis of Swine Gut Microbiota between Landrace and Yorkshire at Various Growth Stages

In this study, we conducted a next generation sequencing based microbial community analysis to investigate gut microbiota of the two commercially most available swine breeds, Yorkshire and Landrace. Bacterial 16S rRNA gene was amplified from fecal DNA using universal primer sets designed for V4 regions. Our comparison analysis of the gut microbiota of the two breeds suggested that their gut microbiota changed depending on the growth stages, while the difference between the two breeds was insignificant. However, there was a limited number of genera, the abundance of which was found to be different between the breeds. Those included the genus Xylanibacter in the Yorkshire samples, which was previously reported as a fiber digesting bacteria, likely increasing energy harvesting capacity of swine. In addition, others included opportunistic pathogens mostly found in the Yorkshire samples while the Landrace samples had significantly more prevalent Clostridium_IV species that were known to play a key role in systemic immunity of hosts. While microbial community shifts was found to be associated with growth stages, the difference between the two breeds seemed to be insignificant. However, there were several bacterial genera showing differential abundance, which may affect growth of hosts.
Some records of bryozoans from NW Spain

Nous regroupons dans le present travail des observations portant sur douze especes de Bryozoaires Chilostomes, recoltees au nord-ouest de la Peninsule Iberique, dont cinq sont citees pour la premiere fois; la revision d'echantillons de collections confirme la presence de six autres especes, citees precedemment sous des noms differents. Une nouvelle espece, Smittina jordii est decrite. La signalisation d'Escharella praealta elargit sa repartition geographique et bathymetrique. Nous proposons d'elever Bugula neritina sessilis au niveau specifique, en la placant dans le genre Dendrobeania.
Effect of calcium and vitamin D2 fortification on quality characteristics of dahi

Two levels (500 and 600 ppm) of calcium (calcium phosphate and calcium citrate) along with vitamin D2 (600 IU/L) were fortified in milk for dahi preparation. pH, water-holding capacity and syneresis of fortified dahi were not affected significantly (P > 0.05). However, acetaldehyde content decreased and setting time increased upon fortification. Microbial count significantly (P < 0.05) decreased in calcium phosphate-fortified dahi, whereas no difference was observed in calcium citrate-fortified dahi. Firmness and viscosity decreased in calcium phosphate-fortified dahi, whereas it increased in calcium citrate-fortified dahi as compared to control. All dahi samples showed good sensory acceptability.
The Impact of Sedimentation on Cone Yeast Heterogeneity

Studies of yeast obtained postfermentation have largely considered individual cells within the crop to be phenotypically and genotypically similar. However, previous studies have indicated that environmental conditions within the cone of a cylindroconical vessel are variable, suggesting that physiological and potentially genetic heterogeneity may occur. Two 2,000-hL fermentation vessels, pitched in parallel with a lager strain, were cropped using two regimens and yeast fractions obtained at 500-kg intervals. Each yeast fraction was analyzed for factors impacting fermentation performance. In addition, characteristics of the barm beer were investigated. Analysis of yeast postfermentation indicated extensive heterogeneity within the crop, in terms of physiological condition, flocculation potential, cell size, and replicative age. In addition, environmental conditions within the cone were also observed to vary substantially. Gradients in terms of temperature, pH, gravity, and ethanol were all detected within the cone. Although cropping regimens can differ, it is proposed that variation in yeast quality throughout the cone may facilitate selection during cropping. Successively cropping and pitching with a specific portion of the cone may lead to the accumulation of a population comprising cells with inappropriate fermentative characteristics, potentially leading to fermentation inconsistency.
Whole‐tree sap flux in Quercus serrata trees after three levels of partial sapwood removal to simulate Japanese oak wilt

Plant transpiration plays a key role in the hydrological cycle in forested watersheds. Oak trees infested with Japanese oak wilt may show changes in transpiration even if they are still alive. However, to our knowledge, no study has shown changes in transpiration and its threshold for tree weakening. We hypothesized that whole‐tree sap flux would be reduced in surviving oak trunks owing to sapwood dysfunction; however, part of this reduction would be compensated by enhanced sap flux density (Fd) in the remaining functioning sapwood. To test this hypothesis, 25%, 50%, and 75% of sapwood was removed at breast height to simulate xylem dysfunction for nine Quercus serrata trees in a warm‐temperate secondary forest in Japan. Granier probes were used to measure the Fd of the treated and three control trees before and after the treatment. Even though tested trees were still alive until at least the end of the second growing season, external symptoms of weakening were detected in 75% treated trees. Analysis using a linear mixed model showed that whole‐tree sap flux was significantly reduced in all treatments. However, 25% and 50% treated trees showed significant Fd compensation, whereas 75% treated trees showed significantly smaller whole‐tree sap flux than the value expected from the treatment. These results suggest that the threshold of tree weakening lies between 50% and 75% of sapwood removal, above which the Fd compensation cannot be attained. Therefore, whole‐tree sap flux in infested but surviving trees varies with respect to the intensity of sapwood damage.
Ralstonia solanacearum virulence in tomato seedlings inoculated by leaf clipping

Ralstonia solanacearum is a phytopathogenic bacterium that colonizes the xylem vessels of host plants leading to a lethal wilt disease. Although several studies have been undertaken on R. solanacearum virulence using adult host plants, infection studies at the seedling stages of hosts by this pathogen are less common. In a preliminary observation, inoculation of R. solanacearum F1C1 on 6 to 7 day old tomato seedlings by a simple ‘leaf-clip’ strategy resulted in a lethal pathogenic condition in seedlings that eventually killed these seedlings within a week post-inoculation. This prompted testing of the effect of this inoculation technique in seedlings from different cultivars of tomato and similar results were obtained. Colonization and spread of the bacteria throughout the infected seedlings could be demonstrated using a gus marked R. solanacearum F1C1 strain. Ralstonia solanacearum GMI1000 strain was also found to be virulent on tomato seedlings using the same inoculation technique. Independent mutants of the R. solanacearum GMI1000 strain deficient in the important virulence functions hrpB, hrpG, phcA and gspD genes respectively were also found to be non-virulent on tomato seedlings when inoculated by this strategy. The leaf clip strategy for tomato seedling inoculation discussed here has the potential to be a valuable approach with respect to time, space, labour savings and costs. This article is protected by copyright. All rights reserved.