Miracle-dz/UniFAR-FTUs huggingface dataset:
Differentiating successful and failed molluscan invaders in estuarine ecosystems

ABSTRACT: Despite mounting evidence of invasive species’ impacts on the environment and society,our ability to predict invasion establishment, spread, and impact are inadequate. Efforts to explainand predict invasion outcomes have been limited primarily to terrestrial and freshwater ecosystems.Invasions are also common in coastal marine ecosystems, yet to date predictive marine invasion mod-els are absent. Here we present a model based on biological attributes associated with invasion suc-cess (establishment) of marine molluscs that compares successful and failed invasions from a groupof 93 species introduced to San Francisco Bay (SFB) in association with commercial oyster transfersfrom eastern North America (ca. 1869 to 1940). A multiple logistic regression model correctly classi-fied 83% of successful and 80% of failed invaders according to their source region abundance at thetime of oyster transfers, tolerance of low salinity, and developmental mode. We tested the generalityof the SFB invasion model by applying it to 3 coastal locations (2 in North America and 1 in Europe)that received oyster transfers from the same source and during the same time as SFB. The model cor-rectly predicted 100, 75, and 86% of successful invaders in these locations, indicating that abun-dance, environmental tolerance (ability to withstand low salinity), and developmental mode not onlyexplain patterns of invasion success in SFB, but more importantly, predict invasion success in geo-graphically disparate marine ecosystems. Finally, we demonstrate that the proportion of marine mol-luscs that succeeded in the latter stages of invasion (i.e. that establish self-sustaining populations,spread and become pests) is much greater than has been previously predicted or shown for otheranimals and plants.KEY WORDS: Invasion · Bivalve · Gastropod · Mollusc · Marine · Oyster · Vector · Risk assessment
Nuclear protein import in permeabilized mammalian cells requires soluble cytoplasmic factors

We have developed an in vitro system involving digitonin-permeabilized vertebrate cells to study biochemical events in the transport of macromolecules across the nuclear envelope. While treatment of cultured cells with digitonin permeabilizes the plasma membranes to macromolecules, the nuclear envelopes remain structurally intact and nuclei retain the ability to transport and accumulate proteins containing the SV40 large T antigen nuclear location sequence. Transport requires addition of exogenous cytosol to permeabilized cells, indicating the soluble cytoplasmic factor(s) required for nuclear import are released during digitonin treatment. In this reconstituted import system, a protein containing a nuclear location signal is rapidly accumulated in nuclei, where it reaches a 30-fold concentration compared to the surrounding medium within 30 min. Nuclear import is specific for a functional nuclear location sequence, requires ATP and cytosol, and is temperature dependent. Furthermore, accumulation of the transport substrate within nuclei is completely inhibited by wheat germ agglutinin, which binds to nuclear pore complexes and inhibits transport in vivo. Together, these results indicate that the permeabilized cell system reproduces authentic nuclear protein import. In a preliminary biochemical dissection of the system, we observe that the sulfhydryl alkylating reagent N- ethylmaleimide inactivates both cytosolic factor(s) and also component(s) in the insoluble permeabilized cell fraction required for nuclear protein import. Because this permeabilized cell model is simple, efficient, and works effectively with cells and cytosol fractions prepared from a variety of different vertebrate sources, it will prove powerful for investigating the biochemical pathway of nuclear transport.
Evaluating the landfill leachate quality using leachate pollution index (LPI) and technique for order preference by similarity to an ideal solution (TOPSIS)

Variability and diversity of landfill leachate cause difficulties in assessing the actual degree of threat to the environment and selecting an appropriate method of disposal or treatment. Therefore, quantifying leachate contamination potential is essential in landfill management and could be used to assess the accuracy of landfill operation and its impact on surrounding areas. The aim of this paper was to evaluate the performance of the Technique for Order Preference by Similarity to an Ideal Solution (TOPSIS) method and its suitability in determining leachate pollution potential in comparison to the Leachate Pollution Index (LPI) method. For this purpose, the quality of leachate from the landfill, collected four times a year from 2004 to 2021, was analysed. The following parameters were monitored: pH, EC, Pb, Cu, Zn, Cr, and Hg. On the basis of the measured parameters, the LPI and TOPSIS indexes were calculated. The obtained results indicated that the TOPSIS method is more sensitive and accurate in observing changes in leachate quality. It can be applied to any number of contaminant parameters without restrictions on scope, quantity, or their relative importance. It can also be used to compare the variations in leachate quality over time or to analyse differences in leachate quality among various landfill sites.
Deployment‐Related Military Sexual Trauma Predicts Heavy Drinking and Alcohol Problems Among Male Reserve and National Guard Soldiers

BACKGROUND Military sexual trauma (MST) is associated with a range of deleterious mental and physical health consequences; however, far less attention has been paid to the associations between MST and negative health behaviors, such as substance abuse. This study examined 2 focal research questions: (i) What is the prevalence of experiencing MST during deployment among male Reserve and National Guard soldiers? and (ii) to what extent is the degree of MST exposure during deployment associated with frequent heavy drinking and alcohol problems postdeployment? METHODS Data from male soldiers who had been deployed (N = 248) were drawn from the baseline wave of Operation: SAFETY (Soldiers And Families Excelling Through the Years) an ongoing study examining health among U.S. Army Reserve and National Guard and their partners. Participants were recruited over a 15-month period (Summer 2014 to Fall 2015) from units in New York State. Deployments occurred prior to the baseline wave of the study. Analyses examined the relation between degree of MST exposure during soldiers' most recent deployment and (i) frequent heavy drinking and (ii) alcohol problems, measured at baseline, controlling for posttraumatic stress disorder symptoms and age. RESULTS 17.3% of the male service members reported experiencing MST during their most recent deployment. Further, greater MST exposure was associated with a greater likelihood of engaging in frequent heavy drinking (adjusted risk ratio [aRR] = 1.03, 95% CI [1.01, 1.05]) and experiencing alcohol problems (aRR = 1.03, 95% CI [1.01, 1.06]) at baseline. CONCLUSIONS Findings demonstrate that MST rates are high among male Reserve and National Guard soldiers, and greater MST exposure is associated with an increased likelihood of engaging in frequent heavy drinking and experiencing alcohol problems among a population already at risk for problematic alcohol use.
Effect of NF-κB inhibitors on the chemotherapy-induced apoptosis of the colon cancer cell line HT-29

This study aimed to investigate the impact of the combined use of the nuclear factor-κB (NF-κB) inhibitors pyrrolidine dithiocarbamate (PDTC), bortezomib or SN50, and the chemotherapy agents arsenic acid (As2O3), fluorouracil (5FU), oxaliplatin or paclitaxel on the growth and apoptosis of HT-29 cells. Cell morphology was observed using inverted microscopy, and cell viability and apoptosis were assessed using the MTT assay and flow cytometry, respectively. The activities of NF-κB were analyzed by western blotting and electrophoretic mobility shift assay (EMSA). Cell growth was significantly inhibited by As2O3, oxaliplatin and paclitaxel in a time- and concentration-dependent manner (P<0.05), while 5FU inhibited cell growth in a time-dependent manner only (P<0.05). The growth inhibition rate and apoptosis induction ratio were increased following the combined treatment of the chemotherapy agent and NF-κB inhibitor. The expression of NF-κB p65 was upregulated when cells were treated with a chemotherapy drug, however it was downregulated following combined treatment or treatment with an NF-κB inhibitor alone. In conclusion, an NF-κB inhibitor combined with a chemotherapy drug effectively inhibited cell proliferation, induced cell apoptosis and inhibited NF-κB activity to enhance the chemotherapeutic sensitivity of HT-29 cells.
Unravelling the mishmash: A new phylogeny for the family Empheriidae (Psocodea, Trogiomorpha) with a new genus and species from Cretaceous Charentese amber

The order Psocodea, including barklice, booklice, and parasitic lice, is diverse and widely distributed since the Cretaceous. That is particularly the case for the speciose extinct family Empheriidae (Psocodea, Trogiomorpha, Atropetae), recently fused with the ‘Archaeatropidae’. Understanding the evolution of barklice is dependent in part on studying this family, as its representatives have been found from the Early Cretaceous to the Eocene, surviving the K/Pg extinction event. The phylogenetic relationships of Empheriidae in relation to other families, such as Lepidopsocidae or Psoquillidae, have been extensively debated. However, distinguishing diagnostic characters for the Empheriidae has proven challenging. In this study, we describe the new empheriid Santonipsocus mimeticusgen. et sp. nov. from Cretaceous Charentese amber (France). It is the third empheriid species found in this locality. The new genus is compared with the other genera in the family, and Proprionoglaris guyoti and Proprionoglaris axioperierga are revised based on the type material and new specimens. We explore the phylogeny of Empheriidae, both the relationships with other families and the inner relationships between the genera, through maximum parsimony analysis and Bayesian inference analysis. Our results suggest that Empheriidae may represent a paraphyletic evolutionary grade to the rest of Atropetae. The phylogenetic relationships between genera align with the biogeography of the family and support previous hypotheses. In addition, we discuss the possible biology of the members of the family, shedding light on the evolutionary history of Empheriidae.
Functional Analysis of a Wheat AGPase Plastidial Small Subunit with a Truncated Transit Peptide

ADP-glucose pyrophosphorylase (AGPase), the key enzyme in starch synthesis, consists of two small subunits and two large subunits with cytosolic and plastidial isoforms. In our previous study, a cDNA sequence encoding the plastidial small subunit (TaAGPS1b) of AGPase in grains of bread wheat (Triticum aestivum L.) was isolated and the protein subunit encoded by this gene was characterized as a truncated transit peptide (about 50% shorter than those of other plant AGPS1bs). In the present study, TaAGPS1b was fused with green fluorescent protein (GFP) in rice protoplast cells, and confocal fluorescence microscopy observations revealed that like other AGPS1b containing the normal transit peptide, TaAGPS1b-GFP was localized in chloroplasts. TaAGPS1b was further overexpressed in a Chinese bread wheat cultivar, and the transgenic wheat lines exhibited a significant increase in endosperm AGPase activities, starch contents, and grain weights. These suggested that TaAGPS1b subunit was targeted into plastids by its truncated transit peptide and it could play an important role in starch synthesis in bread wheat grains.
Efficient Production of Lumichrome by Microbacterium sp. Strain TPU 3598

ABSTRACT Lumichrome is a photodegradation product of riboflavin and is available as a photosensitizer and fluorescent dye. To develop new efficient methods of lumichrome production, we isolated bacterial strains with high lumichrome productivity from soil. The strain with highest productivity was identified as Microbacterium sp. strain TPU 3598. Since this strain inductively produced lumichrome when cultivated with riboflavin, we developed two different methods, a cultivation method and a resting cell method, for the production of large amounts of lumichrome using the strain. In the cultivation method, 2.4 g (9.9 mmol) of lumichrome was produced from 3.8 g (10.1 mmol) of riboflavin at the 500-ml scale (98% yield). The strain also produced 4.7 g (19.4 mmol) of lumichrome from 7.6 g (20.2 mmol) of riboflavin (96% yield) by addition of riboflavin during cultivation at the 500-ml scale. In the resting cell method, 20 g of cells (wet weight) in 100 ml of potassium phosphate buffer, pH 7.0, produced 2.4 g of lumichrome from 3.8 g of riboflavin (98% yield). Since the lumichrome production by these methods was carried out in suspension, the resulting lumichrome was easily purified from the cultivation medium or reaction mixture by centrifugation and crystallization. Thus, the biochemical methods we describe here are a significant improvement in terms of simplicity and yield over the existing chemical, photolytic, and other biochemical methods of lumichrome production.
Gene Expression Profiles in Murine Influenza Pneumonia

Background: Many in vitro studies have focused on gene expression in influenza-infected leukocytes, lung tissue or cell lines. However, knowledge of in vivo gene expression in these compartments is limited. Methods: To obtain insight into gene expression profiles during influenza infection, we determined the expression of multiple genes by using a newly developed mouse-specific multiplex ligation-dependent probe amplification assay. Results: The genes involved in inflammation, Toll-like receptor signaling, coagulation, fibrinolysis, cell adhesion, tissue repair and homeostasis were measured in lung tissue, leukocytes in bronchoalveolar lavage fluid and tracheal epithelial cells in mice, before and after intranasal infection with influenza A. Most of the genes investigated were differentially expressed during the course of infection and returned to baseline levels when mice had recovered from the infection. However, expression of several genes remained altered even though mice had completely cleared the virus. Conclusion: These data provide the first information on compartmentalized gene expression profiles in the respiratory tract during influenza.
Knowledge in Quantum Systems (Extended Abstract)

This paper applies to quantum systems a modelling for the logic of knowledge, originally developed for reasoning about distributed systems, but since then applied to game theory, computer security and artificial intelligence. A formal model of quantum message passing systems is developed and the question of how one might define the semantics of a modal operator for knowledge in this model is considered. It is argued that there are at least two plausible semantics, depending on whether the agents are permitted to make use of their quantum state in determining what they know, and on whether one is dealing with single instances of quantum systems, or ensembles. The framework is illustrated using a number of examples from the quantum computing literature, including protocols for quantum key distribution and teleportation.
The TRITON versus PLATO trials: Differences beyond platelet inhibition

Summary Clopidogrel monopoly as an exclusive oral antiplatelet agent used in combination with aspirin or as a monotherapy for treatment or/and prevention of occlusive thrombotic vascular events has been recently challenged. Based on the indirect comparison of TRITON and PLATO trial data, ticagrelor is clearly superior to prasugrel in a population of patients with acute coronary syndrome (ACS) because of absolute mortality reduction, realistic second myocardial infarction (MI) prevention, growing over time vascular outcome benefit, fewer haemorrhagic fatalities, potentially less coronary artery bypass graft (CABG)- related bleeding events, and lack of cancer risks. Despite an unfavourable immediate safety profile, ticagrelor has a lot of room to compensate for agitation, dyspnea, and ventricular pauses, if used in appropriate patients. It will be naïve and wrong to assume that ticagrelor will completely substitute clopidogrel, especially considering higher discontinu-ation rates after ticagrelor, generic competition, and other health economics issues. However, unless the regulatory authorities discover some unexpected serious flaws with PLATO, the ticagrelor will substantially change the present landscape of oral antiplatelet therapy, especially in high-risk patients, diabetics, and those with repeated vascular events including stent thrombosis. In contrast, a too exclusive trial design, a lack of persistent vascular benefit despite issues with event adjudication, growing-over-time bleeding complications, an issue with cancer, and finally an increase in mortality risk among unstable angina and non ST-elevated myocardial infarction will likely prevent a broad prasugrel implementation, unless more reassuring evidence becomes available.
Concomitant Functional Gastrointestinal Symptoms Influence Psychological Status in Korean Migraine Patients

Background/Aims Migraine is frequently accompanied by symptoms consistent with functional gastrointestinal disorders (FGIDs). This study evaluated the prevalence of functional gastrointestinal symptoms and assessed the symptoms' relationship with the concomitant functional symptoms of anxiety, depression, and headache-related disability. Methods This prospective study included 109 patients with migraine who were recruited from a headache clinic at a teaching hospital. The participants completed a self-administered survey that collected information on headache characteristics, functional gastrointestinal symptoms (using Rome III criteria to classify FGID), anxiety, depression, and headache-related disability. Results In total, 71% of patients met the Rome III criteria for at least one FGID. In patients with FGID, irritable bowel syndrome was the most common symptom (40.4%), followed by nausea and vomiting syndrome (24.8%) and functional dyspepsia (23.9%). Depression and anxiety scores were significantly higher in patients meeting the criteria for any FGID. The number of the symptoms consistent with FGID in individual patients correlated positively with depression and anxiety. Conclusions FGID symptoms defined by the Rome III criteria are highly prevalent in migraine. These symptoms correlate with psychological comorbidities, such as depression and anxiety.
Venture Capital's Role in the Formation of a New Technological Ecosystem: Evidence from the Cloud

The diffusion of new information technology (IT) requires the development of an ecosystem of hardware and software producers, users, and other firms. It is widely believed that venture capitalists (VCs) can play a role in the development of such ecosystems. However, empirical research to elaborate on these points is lacking. Focusing on the recent rapid rise of one platform, cloud computing, we assemble a unique dataset to look at the period just before the cloud’s wide acceptance. We find evidence of complementarity between VC financing and the introduction of new products offered over the cloud. Moreover, the complementarity effects are significantly stronger for firms backed by VCs that had rich experience in the IT industry and are significantly weaker for firms that had prior experience developing traditional client/server products. These results provide evidence that supports a role for VC financing in the creation of new technological ecosystems.
The Difficult Case of Crystallization and Structure Solution for the ParC55 Breakage-Reunion Domain of Topoisomerase IV from Streptococcus pneumoniae

Background Streptococcus pneumoniae is the major cause of community-acquired pneumonia and is also associated with bronchitis, meningitis, otitis and sinusitis. The emergence and increasing prevalence of resistance to penicillin and other antibiotics has led to interest in other anti-pneumonococcal drugs such as quinolones that target the enzymes DNA gyrase and topoisomerase IV. During crystallization and in the avenues to finding a method to determine phases for the structure of the ParC55 breakage-reunion domain of topoisomerase IV from Streptococcus pneumoniae, obstacles were faced at each stage of the process. These problems included: majority of the crystals being twinned, either non-diffracting or exhibiting a high mosaic spread. The crystals, which were grown under conditions that favoured diffraction, were difficult to flash-freeze without loosing diffraction. The initial structure solution by molecular replacement failed and the approach proved to be unviable due to the complexity of the problem. In the end the successful structure solution required an in-depth data analysis and a very detailed molecular replacement search. Methodology/Principal Findings Crystal anti-twinning agents have been tested and two different methods of flash freezing have been compared. The fragility of the crystals did not allow the usual method of transferring the crystals into the heavy atom solution. Consequently, it was necessary to co-crystallize in the presence of the heavy atom compound. The multiple isomorphous replacement approach was unsuccessful because the 7 cysteine mutants which were engineered could not be successfully derivatized. Ultimately, molecular replacement was used to solve the structure by sorting through a large number of solutions in space group P1 using CNS. Conclusions/Significance The main objective of this paper is to describe the obstacles which were faced and overcome in order to acquire data sets on such difficult crystals and determine phases for successful structure solution.
IB-DFE Techniques Applied to Multi-Antenna Systems

With the rise of data-hungry mobile services, scientists have struggled to deliver the desired mobile data rates whilst using the limited available bandwidth. As the higher frequencies are yet inaccessible, namely the millimeter wave frequencies (between 60 and 100 GHz), spectral efficiency is becoming the defining factor for future standards. As result of this, MIMO techniques have been gathering interest in the past few years. The basic concept of a MIMO system consists in transmitting different signals through several antennas, using the same frequency band and with at least as many receiving antennas on the receiver. Exploiting the lack of correlation between the multiple channels, it is possible to isolate and detach each received signal at the receiver. While it seems to be a straightforward method to increase the spectral efficiency, as result of multiple signals being squeezed in the same frequency band, the complexity of the signal separation algorithms is awfully high. Additionally, these algorithms fail to separate signals whose power is far inferior than their peers’, imposing limitations to MIMO based systems. This work proposes three independent solutions to improve MIMO uplink communications for single-carrier block-based transmissions with iterative frequency domain equalization (IB-DFE). The first uses magnitude modulation techniques so as to improve the transmitter’s power efficiency. The second employs base station cooperation techniques to improve the user’s performance at cell edges. Lastly, the third solution apply a clusterbased multi-user detection, allowing for an increased number of users to share the same channel without exhausting the computational resources at the receiver.