Miracle-dz/UniFAR-FTUs huggingface dataset:
Organic compounds drive growth in phytoplankton taxa from different functional groups

Phytoplankton are usually considered autotrophs by default, but an increasing number of studies shows that many taxa are able to also utilise organic carbon. Acquiring nutrients and energy from different sources might enable an efficient uptake of required substances and provide a strategy to deal with a varying resource availability, especially in highly dynamic ecosystems such as estuaries. In our study we investigated the effects of 31 organic carbon sources on the growth of 17 phytoplankton strains from the Elbe estuary spanning four functional groups. All of our strains were able to make use of at least 1 and up to 26 organic compounds for growth. Pico-sized green algae such as Mychonastes, Choricystis and Chlorella, as well as nano-sized green algae from the genus Monoraphidium in particular were positively affected by a high variety of substances. Reduced light availability, typically appearing in turbid estuaries and similar habitats, resulted in an overall poorer ability to utilise organic substances for growth, indicating that organic carbon acquisition was not primarily a specific strategy to deal with darkness. Our results give further evidence for mixotrophy being an ubiquitous ability of phytoplankton and highlight the importance to consider this trophic strategy in research.
Ocelli: an open-source tool for the visualization of developmental multimodal single-cell data

The recent expansion of single-cell technologies has enabled simultaneous genome-wide measurements of multiple modalities in the same single cell. The potential to jointly profile such modalities as gene expression, chromatin accessibility, protein epitopes, or multiple histone modifications at single-cell resolution represents a compelling opportunity to study developmental processes at multiple layers of gene regulation. Here, we present Ocelli, a lightweight Python package for scalable visualization and exploration of developmental multimodal single-cell data. The core functionality of Ocelli focuses on diffusion-based modeling of developmental processes. Ocelli addresses common tasks in developmental single-cell data analysis, such as visualization of cells on a low-dimensional embedding that preserves the continuity of the developmental progression of cells, identification of rare and transient cell states, integration with trajectory inference algorithms, and imputation of undetected feature counts. Extensive benchmarking shows that Ocelli outperforms existing methods regarding computational time and quality of the reconstructed low-dimensional representation of developmental data.
Vinculin-Arp2/3 Interaction Inhibits Branched Actin Assembly to Control Cell Migration and Cell Cycle Progression

Vinculin is a mechanotransducer that reinforces links between cell adhesions and linear arrays of actin filaments upon myosin-mediated contractility. Both adhesions to the substratum and neighboring cells, however, are initiated within membrane protrusions that originate from Arp2/3-nucleated branched actin networks. Vinculin has been reported to interact with the Arp2/3 complex, but the role of this interaction remains poorly understood. Here we compared the phenotypes of vinculin knock-out (KO) cells with those of knock-in (KI) cells, where the point mutation P878A that impairs the Arp2/3 interaction is introduced in the two vinculin alleles of MCF10A mammary epithelial cells. The interaction of vinculin with Arp2/3 inhibits actin polymerization at membrane protrusions and decreases migration persistence of single cells. In cell monolayers, vinculin recruits Arp2/3 and the vinculin-Arp2/3 interaction participates in cell-cell junction plasticity. Through this interaction, vinculin controls the decision to enter a new cell cycle as a function of cell density.
Bamboozling Interactions: Interspecific associations within mixed-species bird flocks in bamboo in the Eastern Himalaya

Bamboo is one of the most rarely studied habitats in the world, even though it is widespread and supports significant biodiversity wherever it occurs. Several species across taxonomic groups - including birds - are partial to bamboo habitat, with some species being obligate bamboo specialists. Mixed-species bird flocks (hereafter, flocks) are an important and regular feature of tropical and temperate forest bird communities, and have been very well-studied. However, how and why flocks might differ between bamboo and non-bamboo habitats has never been examined. We studied flocks in rainforest and bamboo stands in winter and summer in the Eastern Himalaya, and used network analysis and null models to quantify and compare the composition of flocks and interspecific associations. We found that bamboo and rainforest flocks differed greatly in their composition and interspecific associations, with bamboo flocks being more cohesive, less modular and their species more connected with each other. Further, bamboo flocks were more consistent in their composition across seasons whereas rainforest flocks were highly diverse and variable. Rainforest flocks partially disintegrated in summer, probably due to an increase in the abundance of arthropods. The loss of arthropods in an entire substrate in bamboo in summer and the increase in arthropod abundance in other substrates was probably not sufficient for flocking to cease in bamboo. We discuss species’ roles and the potential costs and benefits for species in flocks in bamboo and rainforest. Our study is one of the few to describe bamboo flocks, and the results highlight the need to conserve bamboo stands to ensure the persistence of these obligate bamboo specialists in the Eastern Himalaya.
Modulation of calcium signaling and metabolic pathways in endothelial cells with magnetic fields

Calcium signaling plays a crucial role in various physiological processes, including muscle contraction, cell division, and neurotransmitter release. Dysregulation of calcium levels and signaling has been linked to a range of pathological conditions such as neurodegenerative disorders, cardiovascular disease, and cancer. Here, we suggest that in the endothelium, calcium ion channel activity and calcium signaling can be modulated by applying either a time-varying or static gradient magnetic field (MF). This modulation is achieved by exerting magnetic forces or torques on either biogenic or non-biogenic magnetic nanoparticles that are bound to endothelial cell membranes. Since calcium signaling in endothelial cells induces neuromodulation and influences blood flow control, treatment with a magnetic field shows promise for regulating neurovascular coupling and treating vascular dysfunctions associated with aging and neurodegenerative disorders. Furthermore, magnetic treatment can enable control over the decoding of Ca signals, ultimately impacting protein synthesis. The ability to modulate calcium wave frequencies using MFsand the MF-controlled decoding of Ca signaling present promising avenues for treating diseases characterized by calcium dysregulation.
Who Moved My Data? a Backup Tracking System for Dynamic Workstation Environments 1.0 Introduction

Periodic data backup is a system administration requirement that has changed as wireless machines have altered the fundamental structure of networks. These changes necessitate a complete rethinking of modern network backup strategies. The approaches of the 1980's and 1990's are no longer sufficient and must be updated. In addition to standard backup programs from vendors, specialized system administration tools are often needed. This paper examines one backup system and the major software components used to implement it. NCSA has developed a Backup Tracking System (BTS) to perform backup operations based on knowledge of the network and when each machine was last successfully backed up. BTS can chronologically list all computers: from those currently attached to the network through those that have ever been attached over the life of the BTS program. BTS also provides information about all backup operations including the time of last attempt, success state, amount backed up, etc. The BTS database also contains the date of the last successful backup for each machine and whether it has at least one VIP user (to be given preferred status during backups) or all non-VIP users. Modern networks of end-user machines are becoming increasingly dynamic and heterogeneous. Operating systems come in various versions of Unix, Windows, or MacOS. Mobile hosts, which may only be available on the network rarely or on an intermittent basis, have become almost as common as desktop workstations. The data on individual hosts can be critical to the success of an organization (for cautionary stories of those who have been victims of data loss without backup see [19]). A wide variety of backup and data integrity techniques exist, and they vary in cost, features, and effectiveness. Mirroring SAN systems are at the very high end. Such systems can provide real-time on and off-site mirroring and versioning of data as it is modified, and can allow quick recovery from both common and catastrophic failures. At the low end, users can individually manage backups to removable media, such as external hard drives, CD-R, or Zip disks. While the techniques available to protect data have increased greatly, the management of such protection has not. Systems such as Amanda [14] expect collections of always-on, always-connected Unix workstations. Later commercial products like IBM's Tivoli Enterprise Management Suite [9] and Legato Systems NetWorker [11] have focused on extending support for the backend archive technology and new host operating systems. Unlike previous systems, …
CARDON RESEARCH PAPERS IN AGRICULTURAL AND RESOURCE ECONOMICS

We provide a review of recent developments in the calculation of standard errors and test statistics for statistical inference. While much of the focus of the last two decades in economics has been on generating unbiased coefficients, recent years has seen a variety of advancements in correcting for non-standard standard errors. We synthesize these recent advances in addressing challenges to conventional inference, like heteroskedasticity, clustering, serial correlation, and testing multiple hypotheses. We also discuss recent advancements in numerical methods, such as the bootstrap, wild bootstrap, and randomization inference. We make three specific recommendations. First, applied economists need to clearly articulate the challenges to statistical inference that are present in data as well as the source of those challenges. Second, modern computing power and statistical software means that applied economists have no excuse for not correctly calculating their standard errors and test statistics. Third, because complicated sampling strategies and research designs make it difficult to work out the correct formula for standard errors and test statistics, we believe that in the applied economics profession it should become standard practice to rely on asymptotic refinements to the distribution of an estimator or test statistic via bootstrapping. Throughout, we reference built-in and user-written Stata commands that allow one to quickly calculate accurate standard errors and relevant test statistics.
Learning Frontier Selection for Navigation in Unseen Structured Environment

Learning end-to-end policy for navigation with a focus on intelligent exploration is a difﬁcult task in robotics. While methods like soft-Q learning and ensembles of policies can demonstrate navigation behaviors in completely observed maps, we currently do not have ways of extending these policies to unexplored or partially explored environments. To this end, we propose a hierarchical formulation to tackle the problem of learning based efﬁcient exploration. We decompose the the task into two sub-problems: selecting the next best goal in the visible space, followed by efﬁciently navigating to this space in the partial map setting. We propose a global policy network that learns the selection of the next best goal(‘frontier’) in the observable space, followed by a local policy that learns low-level navigation conditioned on different goal embeddings in known environments. Our key approach to this decomposition is to enable the independent training of both of these components by creating randomized gridmaps on a large-scale for both subtasks. We demonstrate our approach by training both policies for navigation in the FourRooms environment in gym-minigrid. The ﬁnal combined policy is, therefore, an end-to-end differentiable policy for map exploration. We evaluate the performance of the goal-conditioned local policy and present analysis of sparse reward based the global policy.
Profiling Users in the UNlX OS Environment

This paper presents results obtained by using a method of profiling a user based on the login host, the login time, the command set, and the command set execution time of the profiled user. It is assumed that the user is logging onto a UNIX host on a computer network. The paper concentrates on two areas: short-term and long-term profiling. In short-term profiling the focus is on profiling the user at a given session where user characteristics do not change much. In long-term profiling, the duration of observation is over a much longer period of time. The latter is more challenging because of a phenomenon called concept or profile drift. Profile drift occurs when a user logs onto a host for an extended period of time (over several sessions).
Magnetic Susceptibility Detection of Small Protohistoric Sites in the Raganello Basin, Calabria (Italy)

This paper presents pilot geophysical investigations carried out in 2005–2006 by the Groningen Institute of Archaeology in northern Calabria, Italy. The aim of this work was to find out if and how surface magnetic susceptibility (MS) measurements might be of use to correct significant visibility biases in the results of earlier large‐scale systematic and intensive field‐walking, in particular for unobtrusive rural protohistoric sites. It was found that MS yields encouraging results under specific geopedological conditions, but that a better understanding of post‐depositional site histories and large‐scale geomorphology‐driven MS variations is needed before an effective MS‐based detection protocol in support of large‐scale field‐walking can be developed; follow‐on studies are now being conducted by the authors to this end. Copyright © 2014 John Wiley & Sons, Ltd.
Macrophages in Tumor Microenvironment: From Molecular Aspects to Clinical Applications

: M1 Macrophage cells are a part of the immune system, which are also involved in tumor microenvironment (TME). Specific macrophages are activated by different chemokines like IL-4, IL-13 and IFN-γ and subsequently are able to differentiate into M1 and M2. Moreover, Ms2 are divided into 4 sub-phenotypes: M2a, M2b, M2c and M2d. We have analysed the relationship between macrophages, the role of micro RNAs and their importance in angiogenesis and lymphangiogenesis. Furthermore, we investigated how macrophages interact in the pathogenesis of breast, gastric and colorectal cancer. We reported several studies regarding the involvement of these cells in tumoral angiogenesis and proliferation. This review represents a starting point to better comprehend the molecular and biological steps regarding the involvement of Ms in cancer, focusing the attention on their effects in specific tumors.
A comparison of curve number based methods for runoff estimation from small watersheds in a semi-arid region of India

The performance of five curve number based methods, generally employed for estimation of runoff, viz. National Engineering Handbook (NEH-4), storm event (SE), rank order (RO), lognormal frequency (LF) and s-probability (SP), was evaluated using runoff data recorded from three small watersheds in a semi-arid region of India. The most effective and reliable curve number method for runoff estimation was selected based upon several tests of goodness of fit including coefficient of determination ( R 2 ), index of agreement ( D ), root mean square error (RMSE) and relative bias (RB). The LF method was adjudged as the most promising curve number method for estimating runoff from small watersheds in the semi-arid regions of India. The runoff predicted by the LF method was in close agreement with the observed runoff for all four tests of goodness of fit. Though the performance of the SE, RO and NEH-4 methods was almost comparable to each other, the SP method registered higher deviation from the observed runoff values. From the analysis, it is concluded that the LF method can be successfully employed for estimation of curve number based runoff from small watersheds in the semi-arid regions of India.
Inhibiting the ERK pathway and the TRPM7 ion channel in gastric and bladder cancer cells

Gastric and bladder cancers occur when the cells start to reproduce uncontrollably, starting within the innermost layer of tissue. The transient receptor potential cation subfamily M member 7 (TRPM7) is an ion channel that plays an important role in the survival of both of these cancers. In addition, extracellular regulated kinases (ERKs) contribute to the carcinogenesis of many cancers including gastric cancer. Therefore, the treatments Ginsenoside Rd, NS8593, curcumin, and icariin that have the ability to inhibit TRPM7 and ERK could potentially be used as a treatment for these cancers. We hypothesized that these treatments would decrease proliferation and induce apoptosis by inhibiting TRPM7 and ERK in AGS gastric cancer cells and T24 bladder cancer cells; the data supported the hypothesis. Individually, the overall most effective treatment was NS8593 which reduced the proliferation by 81.1% and increased apoptosis by 38.5% in AGS cells compared to the negative control. Individually, the overall most effective treatment was NS8593 which reduced the proliferation by 88.4% and increased apoptosis by 78.0% in T24 cells compared to the negative control. Using all the treatments in combination was the most effective in reducing proliferation and increasing apoptosis in gastric cancer cells. There was also a correlation between the TRPM7, extracellular regulated kinases (ERKs), proliferation, and apoptosis levels. These results could pose in future more effective treatments for both gastric and cancer on top of other types of cancers that rely on TRPM7 and ERK.
In vivo Antiplasmodial Studies on Trichilia heudelotii Planch ex. Oliver (Meliaceae) Leaf

: The study evaluated the antimalarial activities of the methanolic extract of Trichilia heudelotii leaf in mice, identified the most active partitioned and chromatographic fractions with a view to providing information on the scientific basis of the ethnomedicinal uses of the plant in treatment of malaria. The air-dried leaf of T. heudelotii was milled into powder and extracted with methanol. The median lethal dose (LD 50 ) was determined according to Lorke’s method. The extract was tested against chloroquine-sensitive strain of Plasmodium bergheii bergheii NK-65 at doses of 100–800 mg/kg using the chemosuppressive antimalarial model while distilled water (0.2 mL) and chloroquine (10 mg/kg) were used as the negative and positive controls, respectively. The methanol extract was successively partitioned to obtain n-hexane (THH), dichloromethane (THD), ethylacetate (THE), n-butanol (THB) and aqueous fractions (THA) which were each tested at 50, 100 and 200 mg/kg similarly. The most active THH was successively chromatographed and the most active fractions THH2B and THH3B identified. The percentage chemosuppression and percentage survivor in mice was used as a measure of the antiplasmodial activities of the extract, partitioned and column fractions. The LD 50 of T. heudelotii leaf extract was greater than 5000 mg/kg. It gave the highest chemosuppression of 88.7% at 200mg/kg, the n-hexane partitioned fraction (THH) gave percentage chemosuppression of 66% at 50mg/kg while subsequent column fractions, THH2B and THH3B gave 77 and 74% respectively. The chemosuppressive activities of T. heudelotii leaf was obviously retained during subsequent purification with the fractions demonstrating good% chemosuppression and percentage survivor profile as to contain the antimalarial constituents of the plant. Gas Chromatography-Mass Spectroscopy of THH3B, the most active column fraction suggested 6, 10, 14-trimethyl-2-pentadecanone, methyl palmitate and 11-Octadecenoic acid, methyl ester that were the major compounds identified in the fraction as possible antimalarial compounds in the plant.
The reaction of glass during gamma irradiation in a saturated tuff environment: Part 3, long-term experiments at 1 x 10{sup 4}rad/hour

Savannah River Laboratory 165 type glass was leached with equilibrated J-13 groundwater at 90{degree}C for times up to 182 days. These experiments were performed as part of an effort by the Nevada Nuclear Waste Storage Investigations Project to assess the importance of radiation effects on repository performance and waste glass corrosion. The gamma radiation field used in this work was 1. 0 +- 0.2 x 10{sup 4} rad/h. Glass dissolution is notably incongruent throughout the entire experimental periods and normalized releases follow the sequence Li {ge} Na {ge} B {approx_equal} U {ge} Si. The normalized leach rates of these elements, as well as the measured growth rates of the reaction layers, decreased with time. The only significant variation observed in the abundance of anions is the systematic decrease in NO{sub 3}/sup {minus}//NO{sub 2}/sup {minus}/ ratio from the starting EJ-13 groundwater to the EJ-13 blank experiments to the tuff- and glass-containing experiments. A leaching model that is consistent with the observed solution data and depth profiles is presented. The applicability and limitation of the present results in predicting the actual interactions that may occur in the NNWSI repository are discussed. 35 refs., 30 figs., 12 tabs.