Miracle-dz/UniFAR-FTUs huggingface dataset:
VirusTaxo: Taxonomic classification of virus genome using multi-class hierarchical classification by k-mer enrichment

Taxonomic classification of viruses is a multi-class hierarchical classification problem, as taxonomic ranks (e.g., order, family and genus) of viruses are hierarchically structured and have multiple classes in each rank. Classification of biological sequences which are hierarchically structured with multiple classes is challenging. Here we developed a machine learning architecture, VirusTaxo, using a multi-class hierarchical classification by k-mer enrichment. VirusTaxo classifies DNA and RNA viruses to their taxonomic ranks using genome sequence. To assign taxonomic ranks, VirusTaxo extracts k-mers from genome sequence and creates bag-of-k-mers for each class in a rank. VirusTaxo uses a top-down hierarchical classification approach and accurately assigns the order, family and genus of a virus from the genome sequence. The average accuracies of VirusTaxo for DNA viruses are 99% (order), 98% (family) and 95% (genus) and for RNA viruses 97% (order), 96% (family) and 82% (genus). VirusTaxo can be used to detect taxonomy of novel viruses using full length genome or contig sequences. Availability Online version of VirusTaxo is available at https://omics-lab.com/virustaxo/.
Gated recurrence enables simple and accurate sequence prediction in stochastic, changing, and structured environments

From decision making to perception to language, predicting what is coming next is crucial. It is also challenging in stochastic, changing, and structured environments; yet the brain makes accurate predictions in many situations. What computational architecture could enable this feat? Bayesian inference makes optimal predictions but is prohibitively difficult to compute. Here, we show that a specific recurrent neural network architecture enables simple and accurate solutions in several environments. To this end, a set of three mechanisms suffices: gating, lateral connections, and recurrent weight tuning. Like the human brain, such networks develop internal representations of their changing environment (including estimates of the environment’s latent variables and the precision of these estimates), leverage multiple levels of latent structure, and adapt their effective learning rate to changes without changing their connection weights. Being ubiquitous in the brain, gated recurrence could therefore serve as a generic building block to predict in real-life environments.
Symbiont-conferred immunity interacts with the effects of parasitoid genotype and intraguild predation to shape pea aphid immunity in a clone-specific fashion

Host-parasite interactions represent complex co-evolving systems in which genetic variation within a species can significantly affect selective pressure on traits in the other (for example via inter-species indirect genetic effects). While often viewed as a two-species interaction between host and parasite species, some systems are more complex due to the involvement of symbionts in the host that influence its immunity, enemies of the host, and the parasite through intraguild predation. However, it remains unclear what the joint effects of intraguild predation, defensive endosymbiosis, within-species genetic variation and indirect genetic effects on host immunity are. We have addressed this question in an important agricultural pest system, the pea aphid Acyrthosiphon pisum, which shows significant intraspecific variability in immunity to the parasitoid wasp Aphidius ervi due to immunity conferring endosymbiotic bacteria. In a complex experiment involving a quantitative genetic design of the parasitoid, two ecologically different aphid lineages and the aphid lion Chrysoperla carnea as an intraguild predator, we demonstrate that aphid immunity is affected by intraspecific genetic variation in the parasitoid and the aphid, as well as by associated differences in the defensive endosymbiont communities. Using 16s rRNA sequencing, we identified secondary symbionts that differed between the lineages. We further show that aphid lineages differ in their altruistic behaviour once parasitised whereby infested aphids move away from the clonal colony to facilitate predation. The outcome of these complex between-species interactions not only shape important host-parasite systems but have also implications for understanding the evolution of multitrophic interactions, and aphid biocontrol.
A multisensory circuit for gating intense aversive experiences

The ventral hippocampus (vHPC) is critical for both learned and innate fear, but how discrete projections control different types of fear is poorly understood. Here, we report a novel excitatory circuit from a subpopulation of the ventral hippocampus CA1 subfield (vCA1) to the inhibitory peri-paraventricular nucleus of the hypothalamus (pPVN) which then routes to the periaqueductal grey (PAG). We find that vCA1→pPVN projections modulate both learned and innate fear. Fiber photometric calcium recordings reveal that activity in vCA1→pPVN projections increases during the first moments of exposure to an unconditioned threat. Chemogenetic or optogenetic silencing of vCA1→pPVN cell bodies or vCA1→pPVN axon terminals in the pPVN enhances the initial magnitude of both active and passive unconditioned defensive responses, irrespective of the sensory modalities engaged by a particular innate threat. Moreover, silencing produces a dramatic impact on learned fear without affecting milder anxiety-like behaviors. We also show that vCA1→pPVN projections monosynaptically route to the PAG, a key brain region that orchestrates the fear response. Surprisingly, optogenetic silencing of vCA1 terminals in the pPVN titrates the level of c-Fos neural activity in the PAG differently for learned versus innate threats. Together, our results show how a novel vCA1→pPVN circuit modulates neuronal activity in the PAG to regulate both learned and innate fear. These findings have implications for how initial trauma processing may influence maladaptive defensive behaviors across fear and trauma-related disorders. One Sentence Summary A multisensory gate for high intensity aversive experiences.
Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea

Background Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases the enzymes cannot be isofunctional. Here, we examine a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We list 50 of those cases, each with detailed background information so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Material. Conclusions Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet unexpected functions.
Parallel contextual array insertion deletion P systems and Siromoney matrix grammars

James et al. have introduced a variant of P systems called parallel contextual array insertion deletion P system and studied some of its properties. The family of array languages generated by this variant of PCAIDPS includes families of array languages like recognisable picture languages (REC) and context-sensitive matrix languages . In this paper we show that another interesting family of Siromoney matrix languages is included in the family of array languages generated by PCAIDPS with two membranes. GRAPHICAL ABSTRACT
Swarm-based painting of an area cluttered with obstacles

ABSTRACT This article studies the problem of painting of a rectangular region cluttered with horizontal obstacles, by a swarm of mobile robots. Initially, the robots are deployed randomly within the target area. From the initial configuration, the robots are assembled on the left boundary of the region. Upon assembling on the left boundary, the robots first explore the entire area collectively to make a virtual partition of it and then collectively paint the target region in a subsequent phase. The proposed algorithm assumes that robots work in look–compute–move model. The robots follow a completely distributed algorithm to paint the region. The robots are either synchronous or semi-synchronous. The outcome of the proposed algorithm is a complete painting of an area without any repetition and collision. GRAPHICAL ABSTRACT
Improving the performance of governmental venture capital firms: Reforms at Shenzhen Capital Group

ABSTRACT This paper documents how Shenzhen Capital Group (SCG) tackled agency problems faced by governmental venture-capital firms (GVCs) by adopting an expansion strategy and undertaking a series of reforms in its compensation scheme and decision-making process. Empirical results show that after SCG’s reforms, portfolio companies funded by SCG or a SCG-led syndicate were more likely to achieve successful exits through IPO or M&A than those financed by other GVCs. This paper provides evidence and a live example of how GVCs can effectively mitigate agency problems to achieve better performance.
Anti-aging additives: proposed evaluation process based on literature review

Asphalt binder ageing alters its chemical and physical properties in a manner to make it brittle and more susceptible to thermal and fatigue cracking. The ageing rate of asphalt binders depends on a combination of different factors related to their chemical composition, environmental conditions and mix design. In order to prevent ageing, anti-ageing additives are used. The selection of the optimal additive should follow an iterative process. The additive choice is made concerning each case studied. Then, the selected modified asphalt binder is short-term aged by RTFOT and long-term aged by PAV and ultraviolet (UV) weathering. Rheology performance parameters are measured by DSR and BBR before and after ageing. Consequently, ageing indices are calculated to evaluate the appropriateness of the additive. The paper discusses several findings on the rheological level accordingly to the literature. Finally, a process is proposed to harmonise the research and the engineering practices in studying anti-ageing additives effects on asphalt binders.
Resilience-promoting policies and contexts for children of color in the United States: Existing research and future priorities

Abstract The health status of children in the United States varies by racial and ethnic, shaped by an interrelated set of systems that disadvantage children of color in the United States. In this article, we argue for a broad view of resilience, in both research and policy, that views resilience not just as a property of individuals but also as a characteristic of social contexts and policies. Accordingly, we describe the empirical evidence for policies and contexts as factors that can improve health among children and families that are deprived of equal opportunities and resources due to structural racism. We discuss the evidence and opportunities for policies and interventions across a variety of societal systems, including programs to promote economic and food security, early education, health care, and the neighborhood and community context. Based on this evidence and other research on racism and resilience, we conclude by outlining some directions for future research.
Evaluation of an open-source machine-learning tool to quantify bone marrow plasma cells

Aims The objective of this study was to develop and validate an open-source digital pathology tool, QuPath, to automatically quantify CD138-positive bone marrow plasma cells (BMPCs). Methods We analysed CD138-scanned slides in QuPath. In the initial training phase, manual positive and negative cell counts were performed in representative areas of 10 bone marrow biopsies. Values from the manual counts were used to fine-tune parameters to detect BMPCs, using the positive cell detection and neural network (NN) classifier functions. In the testing phase, whole-slide images in an additional 40 cases were analysed. Output from the NN classifier was compared with two pathologist’s estimates of BMPC percentage. Results The training set included manual counts ranging from 2403 to 17 287 cells per slide, with a median BMPC percentage of 13% (range: 3.1%–80.7%). In the testing phase, the quantification of plasma cells by image analysis correlated well with manual counting, particularly when restricted to BMPC percentages of <30% (Pearson’s r=0.96, p<0.001). Concordance between the NN classifier and the pathologist whole-slide estimates was similarly good, with an intraclass correlation of 0.83 and a weighted kappa for the NN classifier of 0.80 with the first rater and 0.90 with the second rater. This was similar to the weighted kappa between the two human raters (0.81). Conclusions This represents a validated digital pathology tool to assist in automatically and reliably counting BMPC percentage on CD138-stained slides with an acceptable error rate.
Turbulent mixing and trajectories of jets in a supersonic cross-flow with different injectants

Abstract We investigate flow fields and trajectories of sonic jets in a supersonic cross-flow with different injectant properties. The cross-flow is held at a fixed condition with Mach number 1.71, static temperature $\sim$375 K and static pressure $\sim$76 kPa. Jet conditions cover momentum flux ratios $J$ from 1 to 6, molecular weights from $\sim$4 to 44 g mol$^{-1}$ and specific heat ratios from $\sim$1.24 to 1.66. Mie-scattering images are used to study turbulent mixing and trajectory development. Qualitative trends suggest that, at $J=4\text {--}6$, the convective Mach number concept applies as discussed in previous literature. At lower $J$, however, trends for changing molecular weights seem to reverse and the boundary layer might influence turbulent mixing. Analytically estimated jet velocities suggest the suppression of hydrodynamic instabilities changes at different rates for different injectants, as $J$ increases. A newly developed, semi-empirical jet trajectory scaling explicitly considers the momentum flux ratio, boundary layer effects and the existence of the jet bow shock. For validation, this scaling is applied to our trajectory data and those of existing literature, extending the covered parameter space. Quantifying the degree of trajectory correlation shows the scaling is specifically relevant at $J \leq 6$ in this study, where the boundary layer and bow shock influence are important. On the other hand, at higher $J$ and for thin boundary layers, the momentum flux ratio plays a more dominant role. The results in this study can guide the design of injection systems for supersonic applications and improve prediction of jet trajectories.
Structures and Electronic Properties of Organic Self-Assembled Monolayers Characterized by STM and XPS

One of the most important scientific challenges for the next decades is to build and to control devices at the nanometer scale. These nano-devices promise to have many applications in physics, chemistry and medicine. For example the nano-devices may be used to go further in the miniaturization of electronic compounds in order to improve the processors efficiency and perfor- mances. A judicious manner to create nano-devices is to take advantage of inter-molecular interac- tions in order to obtain self-assembled structures using a small numbers of molecules ("bottom-up" approach). The objective of this thesis was to create new organic self-assembled monolayers (SAMs), and to investigate their structures and electronic properties. Scanning tunneling microscopy (STM) was used to determine molecular organization with an atomic resolution. It was observed that the molecular skeleton and substituents used are key parameters driving the molecular self-assembly. Additionally we have showed that a post-annealing of the sample can be used not only to change the structure of a perylene-based film as it is usually expected but also to modify its electronic states. Photoemission-based techniques combined with synchrotron radiation facilities were used to access to the chemical and electronic properties of SAMs. A strong modification of the line- shape and energy positions of the electronic states of SAMs with the molecular film thickness was observed. In the same way core-hole-clock spectroscopy shows that the charge transfer dynamics at the PTCDI/Au(111) interface is strongly affected by the film thickness.
Choleretic and cholagogic effects of anti-cholelithiatic plants

A large number of people suffer from gall stone worldwide and this problem is now being increased significantly due to the malnutrition, changes in living style, lack of exercise and conditions i.e. industrialization. Medicinal plants are used from centuries due to their cultural acceptability, efficacy, safety and fewer side effects as compared to modern synthetic medicines. The aim of this review is to gather the information of the plants utilized in various parts and societies of the world against gallstones. The information provided is not only useful for common people but also for the scientific community for further phytochemical, toxicological and pharmacological studies which may lead to discovery of new, more effective and safer medicines for gallstones.
Green epoxidation of cyclooctene with molecular oxygen over an ecofriendly heterogeneous polyoxometalate-gold catalyst Au/BW11/Al2O3

An ecofriendly heterogeneous polyoxometalate (POM)-gold catalyst Au/BW11/Al2O3 was synthesized and used for solvent-free epoxidation of cyclooctene under mild reaction conditions using molecular oxygen as an oxidant and t-butyl hydroperoxide (TBHP) as an initiator. The catalyst was characterized by Fourier transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDX), X-ray diffraction (XRD), induced coupled plasma optical emission spectrometry (ICP-OES), and Brunauer-Emmett-Teller (BET). The catalyst showed good conversion and high selectivity without use of solvents or environmentally harmful oxidants. Moreover, the catalyst is recyclable up to three cycles with no significant loss in selectivity towards epoxide. 概 要目 的环氧化物是多种有机合成反应的重要中间体, 也可作为环氧树脂、染料和表面活性剂的原料。 传统的环氧化存在催化剂分离难、氧化剂成本高和过程含有溶剂等缺点。 本文旨在探讨纳米金和多金属氧酸盐负载非均相催化剂用于无溶剂条件下环辛烯环氧化的反应条件对催化性能的影响。 创新点1. 把纳米金颗粒和多金属氧酸盐(即BW11)结合并负载在固体载体上制备出了一种新型复合催化剂材料; 2. 采用分子氧作为氧化剂而不是传统的有机酸或者过氧酸; 3. 在温和条件下可获得良好的转化率和较高的环氧化物选择性; 4. 催化反应体系未使用有机溶剂; 5. 催化剂稳定并可循环使用。 方 法1. 根据文献中所述方法制备BW11; 2. 采用标准沉积沉淀法合成Au/Al2O3; 3. 采用湿式浸渍法制备催化剂Au/BW11/Al2O3; 4. 环辛烯环氧化使用叔丁基过氧化氢(TBHP)作为引发剂, 氧气作为氧化剂, 在高压反应釜中进行反应; 5. 采用扫描电镜和X 射线衍射等对催化剂进行表征。 结论1. 提高焙烧温度可改善催化反应性能; 2. 随着催化剂量增加到0. 2 g, 转化率也随之增加(图8); 3. 反应的最佳温度为80 °C(表1); 4. 随着反应时间的增加直到24 h, 转化率逐渐增加, 环氧化物选择性也增加到约87%(图9); 5. 催化剂可适用于多种氧化剂(表2); 6. 无溶剂下转化率和选择性相对较大(表3); 7. 催化剂可以有效活化分子氧和环辛烯; 8. 催化剂可以再生, 在使用三次后, 其活性损失不大。
Comparative evaluation of isoflurane and sevoflurane in avian patients

Background and Aim: Literature comparing the use of isoflurane and sevoflurane inhalation anesthetic agents in birds is scarce. This study aimed to evaluate the comparison of isoflurane and sevoflurane during induction, maintenance, and recovery of anesthesia in avian patients. Materials and Methods: In this study, 24 injured avian patients (n=24) were selected randomly and divided into four groups during kite flying festival. In the present study, isoflurane and sevoflurane were used as induction and maintenance anesthetic agents, with and without butorphanol tartrate premedication agent in all the birds. Different physiological parameters were evaluated, namely, cloacal temperature (°F), heart rate (beats/min), respiratory rate (breaths/min), and SpO2 (%) were recorded at 0, 10, 20 min, and at recovery time. The quality of anesthesia was assessed on the basis of induction time, quality of induction, production of analgesia, muscle relaxation, body reflexes, recovery time, quality of recovery, sitting, standing, and complete recovery time (CRT). Results: The mean±standard error value of induction time was 230.00±32.55, 280.00±25.29, 180.00±21.90, and 260.00±36.87 s, respectively, in Groups I, II, III, and IV. The feather plucking, pharyngeal, and toe pinching reflexes were noticed, when the birds were passing through the light plane of anesthesia during induction. Comparison of cloacal temperature at the time of recovery between Group-I versus Group-III revealed a significant difference (p<0.05). Comparison of mean respiratory rates at the time of recovery between Group-II versus Group-IV revealed a significant difference (p<0.05). Excellent quality of recovery was observed in all the groups of anesthetic protocols. Sitting, standing, and CRT were observed shortest in avian patients maintained with sevoflurane as compared to isoflurane. Conclusion: The quality of induction of anesthesia was rapid in avian patients when induced with sevoflurane as compared to isoflurane. Rapid onset of induction and recovery of anesthesia were found with sevoflurane followed by isoflurane. Induction and maintenance of anesthesia in avian patients with sevoflurane resulted in the lowest time required for sitting, standing, and CRT.
Testicular tissue cryopreservation and culture as a tool for the conservation of wild mammals

Cryopreservation of the testicular tissue is a promising tool for assisted reproduction, allowing the storage of fragments containing a large number of germ cells in various stages of development, including undifferentiated spermatogonia that can be cultured, guaranteeing the unlimited production of spermatozoa. In this review, technical aspects related to the processing and applicability of testicular tissue cryopreservation and culture in wild mammals are discussed, highlighting their challenges and perspectives.
Internet uses for health information seeking

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Internet uses for health information seeking Emilie Renahy, Pierre Chauvin