Miracle-dz/UniFAR-FTUs huggingface dataset:
Relationship between NaCl- and H2O2-Induced Cytosolic Ca2+ Increases in Response to Stress in Arabidopsis

Salinity is among the environmental factors that affect plant growth and development and constrain agricultural productivity. Salinity stress triggers increases in cytosolic free Ca2+ concentration ([Ca2+]i) via Ca2+ influx across the plasma membrane. Salinity stress, as well as other stresses, induces the production of reactive oxygen species (ROS). It is well established that ROS also triggers increases in [Ca2+]i. However, the relationship and interaction between salinity stress-induced [Ca2+]i increases and ROS-induced [Ca2+]i increases remain poorly understood. Using an aequorin-based Ca2+ imaging assay we have analyzed [Ca2+]i changes in response to NaCl and H2O2 treatments in Arabidopsis thaliana. We found that NaCl and H2O2 together induced larger increases in [Ca2+]i in Arabidopsis seedlings than either NaCl or H2O2 alone, suggesting an additive effect on [Ca2+]i increases. Following a pre-treatment with either NaCl or H2O2, the subsequent elevation of [Ca2+]i in response to a second treatment with either NaCl or H2O2 was significantly reduced. Furthermore, the NaCl pre-treatment suppressed the elevation of [Ca2+]i seen with a second NaCl treatment more than that seen with a second treatment of H2O2. A similar response was seen when the initial treatment was with H2O2; subsequent addition of H2O2 led to less of an increase in [Ca2+]i than did addition of NaCl. These results imply that NaCl-gated Ca2+ channels and H2O2-gated Ca2+ channels may differ, and also suggest that NaCl- and H2O2-evoked [Ca2+]i may reduce the potency of both NaCl and H2O2 in triggering [Ca2+]i increases, highlighting a feedback mechanism. Alternatively, NaCl and H2O2 may activate the same Ca2+ permeable channel, which is expressed in different types of cells and/or activated via different signaling pathways.
Thalamus segmentation based on the local diffusion direction: A group study

Fast and accurate segmentation of deep gray matter regions in the brain is important for clinical applications such as surgical planning for the placement of deep brain stimulation implants. Mapping anatomy from stereotactic atlases to patient data is problematic because of individual differences in subject anatomy that are not accounted for by commonly used atlases. We present a segmentation method for individual subject diffusion tensor MR data that is based on local diffusion information to identify subregions of the thalamus. We show the correspondence of our segmentation results to anatomy by comparison with stereotactic atlas data. Importantly, we verify the consistency of our segmentation by evaluating the method on 63 healthy volunteers. Our method is fast, reliable, and independent of any segmentation before the classification of regions within the thalamus. It should, therefore, be useful in clinical applications. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
Differences in inflammation and acute phase response but similar genotoxicity in mice following pulmonary exposure to graphene oxide and reduced graphene oxide

We investigated toxicity of 2–3 layered >1 μm sized graphene oxide (GO) and reduced graphene oxide (rGO) in mice following single intratracheal exposure with respect to pulmonary inflammation, acute phase response (biomarker for risk of cardiovascular disease) and genotoxicity. In addition, we assessed exposure levels of particulate matter emitted during production of graphene in a clean room and in a normal industrial environment using chemical vapour deposition. Toxicity was evaluated at day 1, 3, 28 and 90 days (18, 54 and 162 μg/mouse), except for GO exposed mice at day 28 and 90 where only the lowest dose was evaluated. GO induced a strong acute inflammatory response together with a pulmonary (Serum-Amyloid A, Saa3) and hepatic (Saa1) acute phase response. rGO induced less acute, but a constant and prolonged inflammation up to day 90. Lung histopathology showed particle agglomerates at day 90 without signs of fibrosis. In addition, DNA damage in BAL cells was observed across time points and doses for both GO and rGO. In conclusion, pulmonary exposure to GO and rGO induced inflammation, acute phase response and genotoxicity but no fibrosis.
Induction of Tumor-specific T Cell Immunity by Anti-DR5 Antibody Therapy

Because tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) preferentially induces apoptosis in tumor cells and plays a critical role in tumor surveillance, its receptor is an attractive target for antibody-mediated tumor therapy. Here we report that a monoclonal antibody (mAb) against the mouse TRAIL receptor, DR5, exhibited potent antitumor effects against TRAIL-sensitive tumor cells in vivo by recruiting Fc receptor–expressing innate immune cells, with no apparent systemic toxicity. Administration of the agonistic anti-DR5 mAb also significantly inhibited experimental and spontaneous tumor metastases. Notably, the anti-DR5 mAb-mediated tumor rejection by innate immune cells efficiently evoked tumor-specific T cell immunity that could also eradicate TRAIL-resistant variants. These results suggested that the antibody-based therapy targeting DR5 is an efficient strategy not only to eliminate TRAIL-sensitive tumor cells, but also to induce tumor-specific T cell memory that affords a long-term protection from tumor recurrence.
Drug Self-Assembly on DNA: Sequence Effects with trans-bis-(4-N-methylpyridiniumyl)diphenyl Porphyrin and Hoechst 33258

Abstract Self assembly in biological systems is increasingly being recognised as an important phenomenon. We have examined two model systems: the cationic meso-substituted free base porphyrin derivative frans-bis-(4-N-methylpyridiniumyl)diphenyl porphyrin (t-H2P) and Hoechst 33258 (Hoechst) both of which were known to assemble on DNA. t-H2P self-assembles in solution under appropriate conditions, whereas Hoechst does not. By varying ionic strength and ligand: DNA mixing ratios, these features together with their different steric constraints have led to quite different DNA binding behaviour. Hoechst on poly[d(A-T)]2 stacks across the major groove, probably after filling its well established monomeric minor groove binding mode. By way of contrast the Hoechst/poly[d(G-C)]2 self-assembled aggregates involve partially intercalated molecules stacking in the major groove. The binding mode adopted by t-H2P with poly[d(A-T)]2 and poly[d(G-C)]2 appears to be kinetically controlled and to be determined by the pre-existence of monomer binding and/or ligand stacks in solution. With poly[d(A-T)]2 the modes adopted both involve displacing the DNA bases to be more parallel than perpendicular to the helix axis. One is probably based on porphyrin intercalation and the other on minor groove binding. Resonance light scattering, linear dichroism, circular dichroism, normal absorption and fluorescence spectroscopies have been used to characterise the self-assembly in these systems.
Alternative Okazaki Fragment Ligation Pathway by DNA Ligase III

Higher eukaryotes have three types of DNA ligases: DNA ligase 1 (Lig1), DNA ligase 3 (Lig3) and DNA ligase 4 (Lig4). While Lig1 and Lig4 are present in all eukaryotes from yeast to human, Lig3 appears sporadically in evolution and is uniformly present only in vertebrates. In the classical, textbook view, Lig1 catalyzes Okazaki-fragment ligation at the DNA replication fork and the ligation steps of long-patch base-excision repair (BER), homologous recombination repair (HRR) and nucleotide excision repair (NER). Lig4 is responsible for DNA ligation at DNA double strand breaks (DSBs) by the classical, DNA-PKcs-dependent pathway of non-homologous end joining (C-NHEJ). Lig3 is implicated in a short-patch base excision repair (BER) pathway, in single strand break repair in the nucleus, and in all ligation requirements of the DNA metabolism in mitochondria. In this scenario, Lig1 and Lig4 feature as the major DNA ligases serving the most essential ligation needs of the cell, while Lig3 serves in the cell nucleus only minor repair roles. Notably, recent systematic studies in the chicken B cell line, DT40, involving constitutive and conditional knockouts of all three DNA ligases individually, as well as of combinations thereof, demonstrate that the current view must be revised. Results demonstrate that Lig1 deficient cells proliferate efficiently. Even Lig1/Lig4 double knockout cells show long-term viability and proliferate actively, demonstrating that, at least in DT40, Lig3 can perform all ligation reactions of the cellular DNA metabolism as sole DNA ligase. Indeed, in the absence of Lig1, Lig3 can efficiently support semi-conservative DNA replication via an alternative Okazaki-fragment ligation pathway. In addition, Lig3 can back up NHEJ in the absence of Lig4, and can support NER and HRR in the absence of Lig1. Supporting observations are available in less elaborate genetic models in mouse cells. Collectively, these observations raise Lig3 from a niche-ligase to a universal DNA ligase, which can potentially substitute or backup the repair and replication functions of all other DNA ligases in the cell nucleus. Thus, the old model of functionally dedicated DNA ligases is now replaced by one in which only Lig4 remains dedicated to C-NHEJ, with Lig1 and Lig3 showing an astounding functional flexibility and interchangeability for practically all nuclear ligation functions. The underlying mechanisms of Lig3 versus Lig1 utilization in DNA repair and replication are expected to be partly different and remain to be elucidated.
Applying Natural Language Generation to Indicative Summarization

The task of creating indicative summaries that help a searcher decide whether to read a particular document is a difficult task. This paper examines the indicative summarization task from a generation perspective, by first analyzing its required content via published guidelines and corpus analysis. We show how these summaries can be factored into a set of document features, and how an implemented content planner uses the topicality document feature to create indicative multidocument query-based summaries.
Reduction of Glucose Metabolic Activity Is More Accurate than Change in Size at Predicting Histopathologic Response to Neoadjuvant Therapy in High-Grade Soft-Tissue Sarcomas

Purpose: Change in tumor size as classified by Response Evaluation Criteria in Solid Tumors poorly correlates with histopathologic response to neoadjuvant therapy in patients with soft-tissue sarcomas. The aim of this study was to prospectively evaluate whether positron emission tomography with 18F-fluorodeoxyglucose (FDG-PET) allows for a more accurate evaluation of histopathologic response. Experimental Design: From January 2005 to January 2007, 42 patients with resectable biopsy-proven high-grade soft-tissue sarcoma underwent a FDG-PET/computed tomography scan before and after neoadjuvant treatment. Relative changes in tumor FDG uptake and size from the baseline to the follow-up scan were calculated, and their accuracy for assessment of histopathologic response was compared by receiver operating characteristic curve analysis. Histopathologic response was defined as ≥95% tumor necrosis. Results: In histopathologic responders (n = 8; 19%), reduction in tumor FDG uptake was significantly greater than in nonresponders (P < 0.001), whereas no significant differences were found for tumor size (P = 0.24). The area under the receiver operating characteristic curve for metabolic changes was 0.93, but only 0.60 for size changes (P = 0.004). Using a 60% decrease in tumor FDG uptake as a threshold resulted in a sensitivity of 100% and a specificity of 71% for assessment of histopathologic response, whereas Response Evaluation Criteria in Solid Tumors showed a sensitivity of 25% and a specificity of 100%. Conclusion: Quantitative FDG-PET was significantly more accurate than size-based criteria at assessing histopathologic response to neoadjuvant therapy. FDG-PET should be considered as a modality to monitor treatment response in patients with high-grade soft-tissue sarcoma.
Biodiesel Production from Waste Frying Oil and Palm Oil Mixtures

Biodiesel is a renewable fuel obtained from biological raw materials as vegetable oils, sugars, micro algae and bacteria among them. Particularly, biodiesel based in virgin materials, such as palm oil and produced via alkali transterification, have become an industrial standard for large scale facilities. However, the cost associated to virgin raw materials constitutes a huge percentage of production costs, and in addition to low petroleum prices, there is a need to reduce production cost without need to make important modifications in both, the plant infrastructure and processing parameters. Therefore, this work is focused in the evaluation of quality of biodiesel obtained from mixtures of palm oil and Waste Frying Oil (WFO) at low proportions. The conditions employed for the synthesis were: alkali transterification (1% w/w KOH) catalyst, molar ratio methanol/mixed oil 6:1 at 65 C was developed. The best obtained yield was 98.69% and conversion of 95.53% for 5% WFO and 95% palm oil. Results reveal that a high amount of methyl esters and physicochemical properties evaluated under ASTM, NTC and EN standards, are comparable with Biodiesel from virgin palm oil. Also, the study demonstrates that it is possible to use WFO at low proportions with palm oil without an appreciable change in this properties compared with biodiesel from pure virgin oil. As a general estimation, potential savings could be of 3.2% in production cost.
Effects of steroid hormones on Neisseria gonorrhoeae

Various steroids were tested for their effects upon gonococcal O2 consumption and glucose catabolism. The ability to inhibit gonococcal O2 uptake appeared to be related to the molecular configuration of the steroid. The presence of lipophilic groups enhanced inhibition, whereas the addition of hydrophilic groups markedly diminished inhibition. Steroid inhibition decreased with an increasing number of polar groups. Glucose catabolism was inhibited by steroid hormones, and the degree of inhibition was influenced by pH and medium composition. Changes in growth medium and pH also resulted in differential steroid inhibition of O2 uptake. Under certain conditions, lactate partially relieved this inhibition. Gonococci that were grown in one environment and shifted to a new environment were inhibited by steroids to the same extent as if they had been originally grown in the new environment. The differential effects of medium and pH upon steroid inhibition may be due to structural rearrangements involving membrane phase transitions or to altered receptor affinity.
Denial of service to same-sex and interracial couples: Evidence from a national survey experiment

Americans’ views on service refusal vary by several factors but not by whether it is for religious or nonreligious reasons. Legislatures and courts are debating whether businesses can deny services to same-sex couples for religious reasons. Yet, little is known about public views on this issue. In a national survey experiment, Americans (n = 2035) responded to an experimental vignette describing a gay or interracial couple refused service. Vignettes varied the reason for refusal (religion/nonreligious) and by business type (individual/corporation). Results confirm greater support of service refusal by the self-employed than by corporations and to gay couples than to interracial couples. However, religious reasons for refusal to gay couples elicit no more support than do nonreligious reasons. In the first national study to experimentally analyze views on service refusal to sexual minorities, we demonstrate that views vary by several factors but not by whether the refusal was for religious reasons.
When does a radiologist's recommendation for follow-up result in high-cost imaging?

PURPOSE To measure the proportion of high-cost imaging generated by a radiologist's recommendation and to identify the imaging findings resulting in follow-up. MATERIALS AND METHODS This retrospective HIPAA-compliant study had institutional review board approval, with waiver of informed consent. A recommended examination was defined as one performed within a single episode of care (defined as fewer than 60 days after the initial imaging) following a radiologist's recommendation in a prior examination report. Chest and abdominal computed tomography (CT), brain and lumbar spine magnetic resonance (MR) imaging, and body positron emission tomography were included for analysis. From a database of all radiology examinations (approximately 200,000) at one institution over a 6-month period, a computerized search identified all high-cost examinations that were preceded by an examination containing a radiologist recommendation. Medical records were reviewed to verify accuracy of the recommending-recommended examination pairs and to determine the reason for the radiologist's recommendation. For proportions, 95% confidence intervals were calculated. RESULTS Overall, 1558 of 29,232 (5.3%) high-cost examinations followed a radiologist's recommendation. Chest CT was the high-cost examination most often resulting from a radiologist's recommendation (878 of 9331, 9.4%), followed by abdominal CT (390 of 10,258, 3.8%) and brain MR imaging (222 of 6436, 3.4%). The examination types with the highest numbers of follow-up examinations were chest radiography (n=431), chest CT (n=410), abdominal CT (n=214), and abdominal ultrasonography (n=120). The most common findings resulting in follow-up were pulmonary nodules or masses (559 of 1558, 35.9%), other pulmonary abnormalities (150 of 1558, 9.6%), adenopathy (103 of 1558, 6.6%), renal lesions (101 of 1558, 6.5%), and negative examination findings (101 of 1558, 6.5%). CONCLUSION Radiologists' recommendations account for only a small proportion of outpatient high-cost imaging examinations. Pulmonary nodule follow-up is the most common cause for radiologist-generated examinations.
RNase H As Gene Modifier, Driver of Evolution and Antiviral Defense

Retroviral infections are ‘mini-symbiotic’ events supplying recipient cells with sequences for viral replication, including the reverse transcriptase (RT) and ribonuclease H (RNase H). These proteins and other viral or cellular sequences can provide novel cellular functions including immune defense mechanisms. Their high error rate renders RT-RNases H drivers of evolutionary innovation. Integrated retroviruses and the related transposable elements (TEs) have existed for at least 150 million years, constitute up to 80% of eukaryotic genomes and are also present in prokaryotes. Endogenous retroviruses regulate host genes, have provided novel genes including the syncytins that mediate maternal-fetal immune tolerance and can be experimentally rendered infectious again. The RT and the RNase H are among the most ancient and abundant protein folds. RNases H may have evolved from ribozymes, related to viroids, early in the RNA world, forming ribosomes, RNA replicases and polymerases. Basic RNA-binding peptides enhance ribozyme catalysis. RT and ribozymes or RNases H are present today in bacterial group II introns, the precedents of TEs. Thousands of unique RTs and RNases H are present in eukaryotes, bacteria, and viruses. These enzymes mediate viral and cellular replication and antiviral defense in eukaryotes and prokaryotes, splicing, R-loop resolvation, DNA repair. RNase H-like activities are also required for the activity of small regulatory RNAs. The retroviral replication components share striking similarities with the RNA-induced silencing complex (RISC), the prokaryotic CRISPR-Cas machinery, eukaryotic V(D)J recombination and interferon systems. Viruses supply antiviral defense tools to cellular organisms. TEs are the evolutionary origin of siRNA and miRNA genes that, through RISC, counteract detrimental activities of TEs and chromosomal instability. Moreover, piRNAs, implicated in transgenerational inheritance, suppress TEs in germ cells. Thus, virtually all known immune defense mechanisms against viruses, phages, TEs, and extracellular pathogens require RNase H-like enzymes. Analogous to the prokaryotic CRISPR-Cas anti-phage defense possibly originating from TEs termed casposons, endogenized retroviruses ERVs and amplified TEs can be regarded as related forms of inheritable immunity in eukaryotes. This survey suggests that RNase H-like activities of retroviruses, TEs, and phages, have built up innate and adaptive immune systems throughout all domains of life.
Calving cycle of the Brunt Ice Shelf, Antarctica, driven by changes in ice shelf geometry

Abstract. Despite the potentially detrimental impact of large-scale calving events on the geometry and ice flow of the Antarctic Ice Sheet, little is known about the processes that drive rift formation prior to calving, or what controls the timing of these events. The Brunt Ice Shelf in East Antarctica presents a rare natural laboratory to study these processes, following the recent formation of two rifts, each now exceeding 50 km in length. Here we use 2 decades of in situ and remote sensing observations, together with numerical modelling, to reveal how slow changes in ice shelf geometry over time caused build-up of mechanical tension far upstream of the ice front, and culminated in rift formation and a significant speed-up of the ice shelf. These internal feedbacks, whereby ice shelves generate the very conditions that lead to their own (partial) disintegration, are currently missing from ice flow models, which severely limits their ability to accurately predict future sea level rise.
Migration of the dinoflagellate Galeacysta etrusca and its implications for the Messinian Salinity Crisis

The First Occurrence of the cysts of the dinoflagellate Galeacysta etrusca is a well-known marker for the final stage of the Messinian Salinity Crisis in the Mediterranean Basin. This taxon originated from the Paratethys in the north and migrated in a stepwise fashion towards the Mediterranean. Using the First Occurrence of this species throughout different Paratethyan basins and the Mediterranean, we here update and revise its migration path. We show that G. etrusca rapidly migrated from the Pannonian Basin into the Dacian, Black Sea and Caspian basins after the Pontian flooding at ~ 6.1 Ma. During the final stage of the Messinian Salinity Crisis (5.37–5.33 Million year ago), G. etrusca simultaneously appeared in the Mediterranean, indicating a single phase of Paratethyan water spilling into the Mediterranean. We propose to reimpose this single brackish water dominated unit/phase at the end of the MSC as the only valid ‘Lago Mare’ event.
Real-time whole body imitation by humanoic robot based on particle filter and dimension reduction by autoencoder

A humanoid robot needs various motions, however, it is difficult to design all motions of the humanoid robot in advance. We proposed to use a particle filter for joint angle estimation for the imitation[1]. The particle-filter-based method provides a reasonable solution for the real-time humanoid robot imitation through observation of human demonstration with a less computational cost. However, the degree of freedom of the humanoid robot is generally high, therefore, the exploration space for the particle filter becomes big. In order to reduce the dimension of the exploration space, we propose to introduce a multi-layer autoencoder that middle layer output represents the posture of the humanoid robot. The autoencoder successfully provides a reasonable posture space of a humanoid robot with a low dimension so that the particle filter needs less number of particles and lower computational cost. The proposed method was evaluated through the experiments using a humanoid robot, Softbank Robotics NAO, and show its validity.