Miracle-dz/UniFAR-FTUs huggingface dataset:
Taxonomy and biogeography of Molgolaimus Ditlevsen, 1921 (Nematoda: Chromadoria) with reference to the origins of deep sea nematodes

Molgolaimus is a genus of free-living marine nematodes which is found in high densities (10–35% of the total community) up to 2000 m depth. Its occurrence is often associated with organically enriched and recently disturbed areas. Currently, only 16 species have been described, mainly from shallow waters. The present study contributes 17 new species mainly from the Weddell Sea but also from the Pacific Ocean, and provides an illustrated polytomous identification key to species level. The 33 Molgolaimus species described can be identified based on just a few morphometric features: spicule length, body length, anal body diameter, tail length and pharynx length. A first insight into the biogeography of this deep sea genus at species level is presented. A comparison of morphometric characteristics between species suggests that the most similar species co-occur in the same geographical region, rather than within the same bathymetric zones or similar ecosystems separated over long distances. These observations suggest that deep sea nematodes may not have a common origin but might have derived “recently” from shallow water taxa. Therefore, global distribution of nematodes could be explained by means of palaeogeographical events.
Helping Students Understand Assessment

During the last decade, many schools have begun to emphasize formative assessment. As teachers work to develop short-cycle or common assessments and engage in data-driven decision making, they typically remain in the central decision-making role. This approach reflects the underlying assumption that teachers control learning. Although teachers must create the conditions for learning, however, students ultimately decide whether they feel capable of learning and whether they will do the work. Therefore, students are equally important users of formative assessment information. The research tells us why.
Role of man in the development of Holocene vegetation in Central Bohemia

In the subcontinental, semiarid lowland region of Central Bohemia (Czech Republic), continuous human impact acting together with diverse natural environmental conditions resulted in the present extraordinarily complex pattern of vegetation. Three radiocarbon-dated pollen diagrams for the area indicate that this complexity results from past vegetation development. During prehistory, places suitable for settlement (with respect to climate, geology, hydrology, etc.) were colonized and transformed first. This resulted in a diachrony in vegetation development due to human activity starting in the first half of the Holocene. This caused an increase in diversity in the region as plant species persisting from previous periods, along with those associated with different agricultural practices, increased. Local abiotic factors affected not only the chronology of human impact but also its specific effects on the ecosystem. Anthropogenic pressure may have had different effects under different conditions. Human population pressure was the mediator between the abiotic diversity and selectively transformed vegetation suitable for the respective habitats. Differences in the chronology of human impact, mixed oak woodland degradation, and the chronology of beech, silver fir and hornbeam expansion are documented for the different ecological zones of the study area. These differences shed light on the mechanisms resulting in some of the important changes in Holocene vegetation. In the absence of man, the decline in mixed oak woodlands, typical of the Middle Holocene in Central Bohemia, would have been probably much slower and less extensive. Unlike in the uplands and mountains, the expansion in the area of beech, silver fir and hornbeam would have been insignificant. The present vegetation resulted to a large extent from management during High Middle Ages. There is almost no continuity in vegetation from the late prehistory to the present.
Application of YSI 6600 for Cyanobacteria Bloom Early Warning in Taihu Lake

Cyanobacteria density YSI(CBD) and chlorophyll YSI(Chl) were measured by YSI 6600-v2 multi-parameter water quality detector and microscopy.The measurement finding was discussed for early-warning monitoring of cyanobacteria bloom in Taihu Lake.The results indicated that the YSI(CBD) was significantly correlated with YSI(Chl) which suggested that algae community structure was stable,and the YSI(CBD) was non-significantly correlated with YSI(Chl) meant the succession of algae community structure.If ratio of YSI(CBD) to YSI(Chl) dropped sharply,the dominance of blue-green algae in lake water took on a decreasing trend,and conversely the dominance descended.
Microbial Population Diversity of Activated Sludge for Wastewater Treatment

In order to study the microbial diversity of activated sludge(AS) for wastewater treatment,the macro-genomic DNA of the AS was extracted from a wastewater factory in Shanghai.The 16S rDNA of the AS bacteria was amplified using bacteria general primers 27F and 1492R to construct the bacterial 16S rDNA clone library,and analyzed the microbial population of the library.All together 200 bands of high quality sequences were obtained and established a phylogenetic tree.The results showed that the main bacterial population of the AS was the phyla of Proteobacteria(91.9%),Firmicutes(4.6%),Bacteroidetes(2%),Chloroflexi(0.5%),Nitrospirae(1%). Among them Alcaligenes feacalis(55%),Pseudomonas aeruginosa(12.8%),and Stenotrophomonas(12.8%) were noticeably dominant bacterial population,enzyme production capacity of the dominant bacteria showed the ecological restoration function in the AS.
Computational Intelligence, Bioinformatics and Computational Biology: A Brief Overview of Methods, Problems and Perspectives

The paper is an overview of methods of computational intelligence (CI) used in the area of Bioinformatics (BI) for the purpose of advancing the area Computational Biology (CB) and facilitating discoveries from biological data. CI is the area of developing generic intelligent information processing methods and systems with wider applications, one of them being Bioinformatics. CI adopts many principles from Biology, thus offering suitable methods and tools for BI. While CB aims at understanding the biology principles through their computational modeling, BI is aiming at the use and the development of new information methods and systems to enhance the storage, the analysis, modeling, and discovery from biological data. The synergism between the three disciplines, their methodologies, problems, and some current solutions are review in the paper. Some new methods and experimental results are introduced, such as feature and model optimization with genetic algorithms applied on gene expression data.
The molecular landscape of neural differentiation in the developing Drosophila brain revealed by targeted scRNA-seq and a multi-informatic analysis paradigm

The Drosophila type-II neuroblast (NB) lineages present an attractive model to investigate the neural differentiation process. With only 16 stem cells, the type-II NB lineages generate many intermediate neural progenitors (INPs) to rapidly expand the neuron and glia pool, similar to those in the human outer subventricular zone (OSVZ). We performed targeted single-cell mRNA sequencing (scRNA-seq) in 3rd instar larval brains and created MiCV, an scRNA-seq data visualization web tool to integrate results from multiple bioinformatics analyses, display co-expression patterns of multiple genes simultaneously, and retrieve gene function and ortholog annotations. We identified novel markers that label distinct neural subsets using MiCV and subsequently in situ profiled them to recover the spatial information lacking in the scRNA-seq data. These new markers further enabled us to build novel neural developmental trajectories that lead to unique neuronal cell fates. Combining prior knowledge, in silico analyses, and in situ evidence, this multi-informatic investigation describes the molecular landscape of neural differentiation from a single developmental snapshot in Drosophila, and provides an experimental and analytical roadmap for navigating the differentiation process of more complex brains.
IL-6 signalling protects zebrafish larvae during Staphylococcus epidermidis infection in a novel bath immersion model

Host immune responses to Staphylococcus epidermidis, a frequent cause of nosocomial infections, are not well understood. We have established a novel bath immersion model of this infection in zebrafish larvae. S.epidermidis infection activates Tlr-2 signalling pathway by upregulation of tlr-2. Macrophages play a primary role in the host immune response and are involved in clearance of infection in the larvae. There is marked inflammation characterised by heightened NF-κB signalling and elevation of several pro-inflammatory cytokines. Infected larvae show rapid upregulation of il-1b and tnf-a transcripts and relatively slower elevation of il-6 transcription. The IL-6 signalling pathway is additionally subject to amplification by elevation of IL-6 signal transducer (il-6st) levels, which negatively correlates with miRNA dre-miR-142-5p expression. Enhanced IL-6 signalling is protective to the host in this model as inhibition of the signalling pathway resulted in increased mortality upon S.epidermidis infection. Our study describes the host immune responses to S.epidermidis infection, identifies a likely role for miR-142-5p – il-6st interaction in modulating this response and establishes the importance of IL-6 signalling in this infection model.
Histone chaperones and modifiers cooperate to maintain heterochromatin integrity following DNA damage

Heterochromatin is a critical chromatin compartment, whose integrity governs genome stability and cell fate transitions. How heterochromatin features, including higher-order chromatin folding and histone modifications associated with transcriptional silencing, are maintained following a genotoxic stress challenge is unknown. Here, we establish a system for targeting UV damage to pericentric heterochromatin in mammalian cells and for tracking the heterochromatin response to UV in real time. We uncover profound heterochromatin compaction changes during repair, orchestrated by the UV damage sensor DDB2. Importantly, the restoration of heterochromatin folding is uncoupled from the maintenance of heterochromatin-specific histone modifications. We also unveil a central role for the methyltransferase SETDB1 in the maintenance of heterochromatic histone marks after UV, SETDB1 coordinating H3 methylation with new histone deposition by histone H3 chaperones in damaged heterochromatin. Our data thus shed light on fundamental molecular mechanisms safeguarding higher-order chromatin integrity following DNA damage. HIGHLIGHTS The damage sensor DDB2 governs heterochromatin unfolding and refolding after UV Restoration of heterochromatin folding and silencing histone marks are uncoupled The methylase SETDB1 promotes H3K9me3 maintenance in damaged heterochromatin SETDB1 coordinates H3K9me3 with new H3 deposition by histone chaperones
The use of online groups to involve older people in influencing nursing care guidance

The drive to involve service users in policy and practice decisions is occurring on an international basis, yet meaningful involvement is not as commonplace as it should be. There are numerous barriers to meaningful involvement of service users, and groupwork offers a potentially empowering approach to helping service users influence the policy and practice decisions that impact their lives. This paper describes a model of service user involvement based on an online communities of practice approach. Twenty-one older people and carers were recruited to take part in a project aimed at influencing the policy and practice of nursing older people on a national level (Scotland). Participants were taught IT skills and worked as an online group to articulate what they thought constituted good nursing care of older people. Together they produced two statements concerning prevention of depression and ensuring adequate nutrition for older people in care. This paper reports on one aspect of a larger evaluation of the project, namely the role of groupwork in the involving model. Content analysis of the groupwork records highlights the importance of groupwork and mutual aid in achieving group goals. The combination of groupwork, service user involvement, and interactive computer technology has much potential.
Targeting the endolysosomal host-SARS-CoV-2 interface by clinically licensed functional inhibitors of acid sphingomyelinase (FIASMA) including the antidepressant fluoxetine

The Corona Virus Disease 2019 (COVID-19) pandemic caused by the Severe Acute Respiratory Syndrome Related Coronavirus 2 (SARS-CoV-2) is a global health emergency. As only very limited therapeutic options are clinically available, there is an urgent need for the rapid development of safe, effective, and globally available pharmaceuticals that inhibit SARS-CoV-2 entry and ameliorate COVID-19. In this study, we explored the use of small compounds acting on the homeostasis of the endolysosomal host-pathogen interface, to fight SARS-CoV-2 infection. We find that fluoxetine, a widely used antidepressant and a functional inhibitor of acid sphingomyelinase (FIASMA), efficiently inhibited the entry and propagation of SARS-CoV-2 in the cell culture model without cytotoxic effects and also exerted potent antiviral activity against two currently circulating influenza A virus subtypes, an effect which was also observed upon treatment with the FIASMAs amiodarone and imipramine. Mechanistically, fluoxetine induced both impaired endolysosomal acidification and the accumulation of cholesterol within the endosomes. As the FIASMA group consists of a large number of small compounds that are well-tolerated and widely used for a broad range of clinical applications, exploring these licensed pharmaceuticals may offer a variety of promising antivirals for host-directed therapy to counteract enveloped viruses, including SARS-CoV-2 and COVID 19.
Sensemaking, Emotion, and Assessments of an Organizational Change Initiated by Others

Thisstudyfocusesontheinterpretationsandexperiencesofchangerecipients,thosewhocarryoutorganizationalinterventionsinitiatedbyothers.Basedonthewaysnursesexpe-rienced a shared governance initiative implemented in their hospital, the authors investi-gated change recipients’sensemaking about organizational change through their ascribedmeanings, emotional responses, and perceptions of its impacts on them. Survey datademonstrated how nurses subjectively assessed their gains and losses from the changeinitiative.Participationintheinitiativeincreasedtheexperienceofgains,asdidmember-shipinaunitwherechangewasimplemented morefully.Textualanalysisofopen-endedresponsestothesurveyindicatedthatgainswerelinkedwithinterpretationsofthechangeinitiative and pleasant feelings and that there was considerable emotional contagionwithin work units. Such effects are particularly likely in employee empowerment initia-tives as experiences are linked to interpretation and mood among change recipients.
The incidence of induced abortion in Uganda

Contexte: Malgre la restriction de la legislation ougandaise sur l'IVG aux seuls cas ou la vie de la femme est en danger, beaucoup de femmes se font avorter, dans des conditions souvent peu hygieniques. Les etudes de petite envergure laissent entendre que l'avortement a risques represente un serieux probleme de sante en Ouganda. Il n'existe cependant aucune etude nationale quantitative de l'avortement. Methodes: Une etude nationalement representative de 313 etablissements de sante traitant les complications de l'avortement et une enquete aupres de 53 professionnels au courant des conditions de l'IVG en Ouganda ont ete menees en 2003. Les techniques d'estimation indirecte ont ete appliquees aux donnees pour calculer le nombre d'avortements pratiques chaque annee. Les taux et quotients d'IVG et les taux de grossesse non planifiee ont ete calcules pour le pays et ses quatre regions principales. Resultats: On estime a 297.000 le nombre d'avortements provoques chaque annee en Ouganda; pres de 85.000 femmes sont traitees pour cause de complications. L'IVG se pratique a un taux de 54 pour mille femmes âgees de 15 a 49 ans; une grossesse sur cinq se termine ainsi. Le taux d'avortement est superieur a la moyenne dans la region du Centre (62 pour mille), la plus urbaine et la plus economiquement developpee du pays. Il est egalement particulierement eleve dans la region du Nord (70 pour mille). A l'echelle nationale, environ la moitie des grossesses ne sont pas planifiees; 51% des femmes mariees âgees de 15 a 49 ans et 12% de leurs homologues celibataires presentent un besoin non satisfait de contraception efficace. Conclusions: L'avortement non medicalise impose un lourd fardeau aux Ougandaises. Pour reduire les grossesses non planifiees et l'avortement a risques, et pour ameliorer la sante des femmes, un meilleur acces aux services de contraception doit etre assure a toutes les femmes.
SIMULATION OF THE GROUND VIBRATION INDUCED BY TRAIN

The purpose of this study is to make clear the mechanism of the ground vibration induced by trains and to develop a numerical simulation tool which can quantitatively evaluate the effect of wave filtering works. A 3D viscoelastic finite-difference method is used to study the mechanism of the ground vibration induced by train. At first, the special case which the force from train is constant for place is analyzed, because the ground vibration does not happen in this case. So the not-constant force from the train is measured. Finally, a numerical simulation is promoted by using this inhomogeneous force from the train. The result of this numerical simulation qualitatively and quantitatively resembles field ground vibration data. It is recognized that one reason of the generation of the ground vibration is caused by inhomogeneous force from the train. Introduction Running trains generate ground vibration and can require attenuation methods to be engineered to reduce problems for people and structures near the track. In the case of the Shinkansen ‘bullet-trains’ in Japan, their source characteristics have not been investigated in detail. Thus, the transient force from the train onto the tracks is measured by using strain gauges mounted on the wheels, and conducted 3D numerical wavefield simulations employing these sources forces. In the second section, methodology of the 3D finite-difference numerical simulation is outlined. A 3D viscoelastic finite-difference method is used to adjust the attenuation. In the third section, qualitative classification of source characteristics is tested specially. Because on the homogeneous medium, a kind of ideal static line source dose not induce the vibrational response (Dunkin and Corbin, 1970). Finally, a quantitative simulation is promoted. 409 Methodology of the 3D finite-difference numerical simulation With the previously estimated input waveform, the wavefield propagating through an earth model can be calculated by numerical simulation. We use the viscoelastic wave equation (Robertsson et al, 1994) and a 3D Finite Difference method (FD). The grid arrangement of the FD framework is a standard staggered grid. The absorbing boundaries at the sides and bottom are based on Cerjan et al (1985). At the top of the grid (free surface) two boundary conditions are employed. Along the train tracks, the stress is set to zero, as per Levander et al (1988). Elsewhere at the surface, both primary wave velocity Vp and secondary wave velocity Vs are set to zero, known as the vacuum formulation (Graves, 1996). Referring to Blanch et al (1995) and using the Zener model, the attenuation factor Q is dominated by ( ) ( ) 2 0 0 1 0 0 1 / Q I Q I ω ω ω ω ω + = (1) Where, ( ) { } 2 0 0 0 ln 1 / 2 b a I ω ω ω ω ω ⎡ ⎤ = + ⎣ ⎦ , ( ) ( ) 0 0 1 0 2 0 / arctan / 2 1 / b
Generation of a infectious cDNA clone of highly pathogenic porcine reproductive and respiratory syndrome virus HuN4

In this study, a infectious cDNA clone of highly pathogenic porcine reproductive and respiratory syndrome virus (PRRSV) strain HuN4 was generated by cloning of the 6 overlapped RT-PCR fragments into pBlueScript Ⅱ SK(+), designated pHuN4. In addition, sp6 promoter at 5'-terminus and a NotⅠsite in Poly(A) tail at 3'-terminus were introduced into the cDNA of PRRSV for viral RNA transcription in vitro and the pHuN4 linearization, respectively. Furthmore, the A at 14,680 nt was replaced by G (silent mutation) to generate restriction enzyme MluⅠsite as molecular marker for identification of rescued virus. The pHuN4 was linearized and transcribed in vitro, the transcripts were transfected primarily into BHK cells and then Marc145 cells, the virus was successfully rescued from Marc145 cells identified by indirect immofluorescent assay and MluⅠdigestion. The rescued virus showed similar growth curve to its parental virus HuN4 strain. All the piglets infected with the fifth passage of the rescued virus developed clinical signs at 3 day-past-infection and died within 20 days. The results showed that the rescued virus remained similar biological characterizations as its parental virus. The pHuN4 developed in the study by reverse genetic system might provide a platform for further study on pathogenesis mechanism of highly pathogenic PRRSV.
Leray and LANS-$\alpha$ modeling of turbulent mixing

Mathematical regularization of the nonlinear terms in the Navier-Stokes equations is found to provide a systematic approach to deriving subgrid closures for numerical simulations of turbulent flow. By construction, these subgrid closures imply existence and uniqueness of strong solutions to the corresponding modelled system of equations. We will consider the large-eddy interpretation of two such mathematical regularization principles, i.e. Leray and LANS-$\alpha$ regularization. The Leray principle introduces a smoothed transport velocity as part of the regularized convective nonlinearity. The LANS-$\alpha$ principle extends the Leray formulation in a natural way in which a filtered Kelvin circulation theorem, incorporating the smoothed transport velocity, is explicitly satisfied. These regularization principles give rise to implied subgrid closures which are implemented in large eddy simulations of turbulent mixing. Comparison with filtered direct numerical simulation data and with predictions obtained from popular dynamic eddy-viscosity modelling shows that these mathematical regularization models provide considerably more accuracy at a lower computational cost than the dynamic approaches. In particular, the regularization models perform especially well in capturing the flow features characteristic of the smaller resolved scales. Variations in spatial resolution and Reynolds number establish that the Leray model is more robust but also slightly less accurate than the LANS-$\alpha$ model. The LANS-$\alpha$ model retains more of the small-scale variability in the resolved solution. However, this requires a corresponding increase in the required spatial resolution. When using second-order finite volume discretization, the potential accuracy of the implied LANS-$\alpha$ model is found to be realized by using a grid spacing that is not larger than the length scale a that appears in the definition of this model.