Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular phylogeny and shell microstructure of Fungiacava eilatensis Goreau et al. 1968, boring into mushroom corals (Scleractinia: Fungiidae), in relation to other mussels (Bivalvia: Mytilidae)

Research on the evolution of the symbiosis between the boring mussel Fungiacava eilatensis (Bivalvia: Mytilidae) and its mushroom coral hosts (Scleractinia: Fungiidae), which requires phylogenetic reconstructions of both the Mytilidae and the Fungiidae, contributes to the understanding of the complexity of coral reef ecosystems. Previously, Fungiacava was regarded as a genus that had descended from Leiosolenus or as belonging to the subfamily Crenellinae, but no phylogenetic support has been obtained for this hypothesis. In the present study, the 18s rRNA sequences of ten mytilid species and the shell microstructures of 12 mytilids were investigated. The phylogenetic position of F. eilatensis is discussed in relation to its associations with its host species. The results of the molecular phylogenetic analysis indicate that F. eilatensis forms a sister group with Leiosolenus simplex, a livecoral-boring species within the Leiosolenus clade. Scanning electron microscope observations indicate that the shell of F. eilatensis is constructed of 3 layers: the outer shell layer with a homogeneous structure, the middle shell layer as a sheet nacreous structure, and the inner shell layer with an irregular simple prism structure. This shell microstructure of F. eilatensis is similar to that of Leiosolenus malaccanus and L. simplex. These findings show that F. eilatensis has descended from a coral-boring Leiosolenus species and that it would be adequate for Fungiacava to be treated as Leiosolenus. However, because of its extraordinary shell shape it has been kept as a separate genus.
Growth differentiation factor 9 gene variants in Sudanese desert sheep ecotypes

Certain variants in the growth differentiation factor 9 ( GDF9 ) gene have major effects on the ovulation rate in sheep. The aim of this study was to analyse GDF9 variability in the Sudanese desert sheep ecotypes Ashgar, Dubasi and Watish, and to test identified variants for association with litter size. For this purpose, ewes of these ecotypes with litter size records for at least two litters were sampled. The complete GDF9 exon 2 was sequenced in a total of 28 ewes. An additional variant in exon 1 (c260G>A) was genotyped by restriction-length polymorphism analysis in 97 ewes. Differences in genotype and allele frequencies of polymorphic positions between two groups differing in litter size (only a single lamb versus more than a single lamb) were tested for significance using Fisher's exact test. GDF9 exon 2 variants c.477G>A and c.721G>A and exon 1 variant c.260G>A were found to be polymorphic in all three sheep ecotypes. Exon 2 variants c.471C>T and c.978 A>G were polymorphic in at least one ecotype. No significant associations were observed between allele and genotype frequencies of identified variants and litter size. This suggests that GDF9 variants influencing ovulation are absent in these Sudanese sheep ecotypes, and therefore cannot be used to increase litter size within this population of sheep. Keywords: Ashgar, Dubasi, fecundity, litter size, ovine fertility, Watish
Bioremediation of Al-Sayyadin Lagoon polluted water using wild and mutant strains of microalgae

In this study, an attempt was made to reduce the pollutants of Al-Sayyadin Lagoon water, which is still the main site of open fishing in Ismailia, Egypt, using the wild and mutant strains of two green microalgae called Chlamydomonas reinhardtii CC1021 and Parachlorella kessleri PC. Four mutant strains were obtained from UV mutagenesis of the two wild types. One mutant strain was from C. reinhardtii CC1021 (CC1021Mut1) and the 3 other strains ((PCMut2, PCMut3 and PCMut4) were from P. kessleri PC. Reduction of nutrients like phosphate, ammonia, chemical oxygen demand (COD), biological oxygen demand (BOD) as well as some heavy metals like Co, Zn by the six microalgal strains was studied. The results obtained showed that the treated wild and mutant strains with mixture of TAP medium and polluted water showed highest growth rate and were more efficient in improving water quality than that treated with polluted water only in phycoremediation. The dose of UV radiation used in this study had no negative impact on the efficiency of bio-remediation potentials of the tested mutant strains but in some results it enhanced their growth rate and removal efficiency. The statistical analysis indicated that there was significant differences (p<0.05) found in bioremediation of water parameters between the selected algae. The wild and mutant strains of P. kessleri had higher efficiency in phycoremediation than the wild and mutant strains of C. reinhardtii CC1021. The mutant algae of P. kessleri PC exhibited significant higher growth rate and removal efficiency than the wild type.
Redundancy effects in the perception and memory of visual objects

Is visual representation of an object affected by whether surrounding objects are identical to it, different from it, or absent? To address this question, we tested perceptual priming, visual short-term, and long-term memory for objects presented in isolation or with other objects. Experiment 1 used a priming procedure, where the prime display contained a single face, four identical faces, or four different faces. Subjects identified the gender of a subsequent probe face that either matched or mismatched with one of the prime faces. Priming was stronger when the prime was four identical faces than when it was a single face or four different faces. Experiments 2 and 3 asked subjects to encode four different objects presented on four displays. Holding memory load constant, visual memory was better when each of the four displays contained four duplicates of a single object, than when each display contained a single object. These results suggest that an object's perceptual and memory representations are enhanced when presented with identical objects, revealing redundancy effects in visual processing.
Tropical to extratropical: Marine environmental changes associated with Superstorm Sandy prior to its landfall

Superstorm Sandy was a massive storm that impacted the U.S. East Coast on 22–31 October 2012, generating large waves, record storm surges, and major damage. The Coupled Ocean‐Atmosphere‐Wave‐Sediment Transport modeling system was applied to hindcast this storm. Sensitivity experiments with increasing complexity of air‐sea‐wave coupling were used to depict characteristics of this immense storm as it underwent tropical to extratropical transition. Regardless of coupling complexity, model‐simulated tracks were all similar to the observations, suggesting the storm track was largely determined by large‐scale synoptic atmospheric circulation, rather than by local processes resolved through model coupling. Analyses of the sea surface temperature, ocean heat content, and upper atmospheric shear parameters showed that as a result of the extratropical transition and despite the storm encountering much cooler shelf water, its intensity and strength were not significantly impacted. Ocean coupling was not as important as originally thought for Sandy.
Distributional semantic Features in russian Verbal metaphor iDentiFication

Our experiment is aimed at evaluating the performance of distributional semantic features in metaphor identification in Russian raw text. We apply two types of distributional features representing similarity between the metaphoric/literal verb and its syntactic or linear context. Our approach is evaluated on a dataset of nine Russian verb context, which is made available to the community. The results show that both sets of similarity features are useful for metaphor identification, and do not replicate each other, as their combination systematically improves the performance for individual verb sense classification, reaching state-of-the-art results for verbal metaphor identification. A combined verb classification demonstrates that the suggested features effectively generalize over metaphoric usage in different verbs, shows that linear coherence features perform as well as the combined feature approach. By analyzing the errors we conclude that syntactic parsing quality is still modest for raw-text metaphor identification in Russian, and discuss properties of semantic models required for high performance.
A Posteriori Human Reliability Analysis of a Train Crash Scenario by the Fuzzy CREAM

In this paper a fuzzy quantification procedure for computing probabilities of operator action failure within the Cognitive Reliability and Error Analysis Method (CREAM) is applied to an actually occurred train crash scenario. The fuzzy version of the CREAM paradigm is shown capable of accounting for: i) the ambiguity in the qualification of the conditions under which the action is performed (Common Performance Conditions, CPCs) and ii) the fact that the effects of such conditions on the human performance reliability may not all be equal. This research work has been carried out within the project Vs (Virthualis, web site: http://www.virthualis.org), FIS5-1999-00250, funded by the European Union
Who is Addressed in this Comment?

User comments have become an essential part of online journalism. However, newsrooms are often overwhelmed by the vast number of diverse comments, for which a manual analysis is barely feasible. Identifying meta-comments that address or mention newsrooms, individual journalists, or moderators and that may call for reactions is particularly critical. In this paper, we present an automated approach to identify and classify meta-comments. We compare comment classification based on manually extracted features with an end-to-end learning approach. We develop, optimize, and evaluate multiple classifiers on a comment dataset of the large German online newsroom SPIEGEL Online and the "One Million Posts" corpus of DER STANDARD, an Austrian newspaper. Both optimized classification approaches achieved encouraging F0.5 values between 76% and 91%. We report on the most significant classification features with the results of a qualitative analysis and discuss how our work contributes to making participation in online journalism more constructive.
Suppression of AMPK/aak-2 by NRF2/SKN-1 down-regulates autophagy during prolonged oxidative stress

NF‐E2‐related factor 2 (NRF2) transcription factor has a fundamental role in cell homeostasis maintenance as one of the master regulators of oxidative and electrophilic stress responses. Previous studies have shown that a regulatory connection exists between NRF2 and autophagy during reactive oxygen species‐generated oxidative stress. The aim of the present study was to investigate how autophagy is turned off during prolonged oxidative stress, to avoid overeating and destruction of essential cellular components. AMPK is a key cellular energy sensor highly conserved in eukaryotic organisms, and it has an essential role in autophagy activation at various stress events. Here the role of human AMPK and its Caenorhabditis elegans counterpart AAK‐2 was explored upon oxidative stress. We investigated the regulatory connection between NRF2 and AMPK during oxidative stress induced by ferf‐butyl hydroperoxide (TBHP) in HEK293T cells and C. elegans. Putative conserved NRF2/protein skinhead‐1 binding sites were found in AMPK/aak‐2 genes by in silico analysis and were later confirmed experimentally by using EMSA. After addition of TBHP, NRF2 and AMPK showed a quick activation; AMPK was later down‐regulated, however, while NRF2 level remained high. Autophagosome formation and Unc‐51‐like autophagy activating kinase 1 phosphorylation were initially stimulated, but they returned to basal values after 4 h of TBHP treatment. The silencing of NRF2 resulted in a constant activation of AMPK leading to hyperactivation of autophagy during oxidative stress. We observed the same effects in C. elegans demonstrating the conservation of this self‐defense mechanism to save cells from hyperactivated autophagy upon prolonged oxidative stress. We conclude that NRF2 negatively regulates autophagy through delayed down‐regulation of the expression of AMPK upon prolonged oxidative stress. This regulatory connection between NRF2 and AMPK may have an important role in understanding how autophagy is regulated in chronic human morbidities characterized by oxidative stress, such as neurodegenerative diseases, certain cancer types, and in metabolic diseases. —Kosztelnik, M. , Kurucz, A. , Papp, D. , Jones, E. , Sigmond, T. , Barna, J., Traka, M. H. , Lorincz, T. , Szarka, A. , Banhegyi, G. , Vellai, T. , Korcsmaros, T. , Kapuy, O. Suppression of AMPK/aak‐2 by NRF2/SKN‐1 down‐regulates autophagy during prolonged oxidative stress. FASEB J. 33, 2372–2387 (2019). www.fasebj. org
Context-Aware End-To-End Relation Extracting from Clinical Texts with Attention-based Bi-Tree-GRU

Extracting clinical entities and their relations from clinical texts is a preliminary task for constructing medical knowledge graph. Existing end-to-end models for extracting entity and relation have limited performance in clinical text because they rarely take both latent syntactic information and the effect of context information into account. Thus, this paper proposed a context-aware end-toend neural model for extracting relations between entities from clinical texts with two level attention. We show that entity-level attention effectively acquires more syntactic information by learning a weighted sum of child word nodes rooted at the target entities. Meanwhile, sub sentence-level attention in an effort to capture the interactions between the target entity pairs and context entity pairs by assigning weights of each context representation within one sentence. Experiments on real-world clinical texts from Shanghai Ruijin Hospital demonstrate that our model significantly gains better performance in the application of clinical texts compared with existing joint models.
Population history of deep-sea vent and seep Provanna snails (Mollusca: Abyssochrysoidea) in the northwestern Pacific

Background Gastropods of the genus Provanna are abundant and widely distributed in deep-sea chemosynthetic environments with seven extant species described in the northwestern Pacific. Methods We investigated the population history and connectivity of five Provanna species in the northwestern Pacific through population genetic analyses using partial sequences of the cytochrome c oxidase subunit I gene. Results We found that P. subglabra, the most abundant and genetically diverse species, is genetically segregated by depth. Among the five species, the three comparatively shallower species (P. lucida, P. kuroshimensis, P. glabra) had a more constant demographic history compared to the deeper species (P. subglabra, P. clathrata). Discussion Environmental differences, especially depth, appears to have a role in the segregation of Provanna snails. The population of P. clathrata in the Irabu Knoll appears to have expanded after P. subglabra population. The remaining three species, P. lucida, P. kuroshimensis, and P. glabra, are only known from a single site each, all of which were shallower than 1,000 m. These data indicate that Provanna gastropods are vertically segregated, and that their population characteristics likely depend on hydrothermal activities.
User Experience Aware Active Queue Management in Cellular Networks

Active queue management plays an important role in the performance of all IP based networks and cellular networks in particular where large buffers are deployed in order to absorb bursts resulting from the dynamic nature of the radio channel. Long standing queues building up in large buffers leads to “Bufferbloat”, degrading the performance especially for delaysensitive applications while small buffers may lower the link utilization. This paper proposes a novel AQM algorithm tailored to cellular networks, mainly by utilizing the Quality of Experience (QoE) metric in order to mitigate Bufferbloat and maintain acceptable levels of performance. Simulation results show the proposed algorithm provides a good balance between drops and delay hence successfully maintains expected levels of service. 
What gives them the right? Legal privilege and waivers of consent for research

Waivers of informed consent for research participation are permitted in the United States under the Common Rule, the Health Insurance Portability and Accountability Act regulations, and the US Food and Drug Administration’s Exception from Informed Consent rule for emergency research. We assess the novel question regarding what legal right researchers have to carry out research procedures on or about another person, be it experimental medical intervention, psychological or social manipulation, or invasion of privacy, without the permission of their subjects. Our analysis frames waivers of consent as a species of presumed consent, and we address the underlying empirical question of whether it is reasonable to believe that subjects from whom no consent is sought would in fact agree, if asked. A scoping review of what is known about participation and refusal rates in United States-based research suggests that a large minority, on average, do not agree to take part in research. Refusal rates vary widely. This suggests that, while researchers may assert the social utility of their studies are high enough to justify waivers, there is reason to suspect that many who would be enrolled under a waiver of consent would not want to be enrolled. We conclude that waivers should be rare and that institutional review boards and researchers must explicitly address study acceptability in the community at large and the target population of their proposed research.
Pepducin-mediated cardioprotection via β-arrestin-biased β2-adrenergic receptor-specific signaling

Reperfusion as a therapeutic intervention for acute myocardial infarction-induced cardiac injury itself induces further cardiomyocyte death. β-arrestin (βarr)-biased β-adrenergic receptor (βAR) activation promotes survival signaling responses in vitro; thus, we hypothesize that this pathway can mitigate cardiomyocyte death at the time of reperfusion to better preserve function. However, a lack of efficacious βarr-biased orthosteric small molecules has prevented investigation into whether this pathway relays protection against ischemic injury in vivo. We recently demonstrated that the pepducin ICL1-9, a small lipidated peptide fragment designed from the first intracellular loop of β2AR, allosterically engaged pro-survival signaling cascades in a βarr-dependent manner in vitro. Thus, in this study we tested whether ICL1-9 relays cardioprotection against ischemia/reperfusion (I/R)-induced injury in vivo. Methods: Wild-type (WT) C57BL/6, β2AR knockout (KO), βarr1KO and βarr2KO mice received intracardiac injections of either ICL1-9 or a scrambled control pepducin (Scr) at the time of ischemia (30 min) followed by reperfusion for either 24 h, to assess infarct size and cardiomyocyte death, or 4 weeks, to monitor the impact of ICL1-9 on long-term cardiac structure and function. Neonatal rat ventricular myocytes (NRVM) were used to assess the impact of ICL1-9 versus Scr pepducin on cardiomyocyte survival and mitochondrial superoxide formation in response to either serum deprivation or hypoxia/reoxygenation (H/R) in vitro and to investigate the associated mechanism(s). Results: Intramyocardial injection of ICL1-9 at the time of I/R reduced infarct size, cardiomyocyte death and improved cardiac function in a β2AR- and βarr-dependent manner, which led to improved contractile function early and less fibrotic remodeling over time. Mechanistically, ICL1-9 attenuated mitochondrial superoxide production and promoted cardiomyocyte survival in a RhoA/ROCK-dependent manner. RhoA activation could be detected in cardiomyocytes and whole heart up to 24 h post-treatment, demonstrating the stability of ICL1-9 effects on βarr-dependent β2AR signaling. Conclusion: Pepducin-based allosteric modulation of βarr-dependent β2AR signaling represents a novel therapeutic approach to reduce reperfusion-induced cardiac injury and relay long-term cardiac remodeling benefits.
Cryo-neutron crystallographic data collection and preliminary refinement of left-handed Z-DNA d(CGCGCG).

Crystals of left-handed Z-DNA [d(CGCGCG)]2 diffract X-rays to beyond 1 Å resolution, feature a small unit cell (∼18 × 31 × 44 Å) and are well hydrated, with around 90 water molecules surrounding the duplex in the asymmetric unit. The duplex shows regular hydration patterns in the narrow minor groove, on the convex surface and around sugar-phosphate backbones. Therefore, Z-DNA offers an ideal case to test the benefits of low-temperature neutron diffraction data collection to potentially determine the donor-acceptor patterns of first- and second-shell water molecules. Nucleic acid fragments pose challenges for neutron crystallography because water molecules are located on the surface rather than inside sequestered spaces such as protein active sites or channels. Water molecules can be expected to display dynamic behavior, particularly in cases where water is not part of an inner shell and directly coordinated to DNA atoms. Thus, nuclear density maps based on room-temperature diffraction data with a resolution of 1.6 Å did not allow an unequivocal determination of the orientations of water molecules. Here, cryo-neutron diffraction data collection for a Z-DNA crystal on the Macromolecular Neutron Diffractometer at the Spallation Neutron Source at Oak Ridge National Laboratory and the outcome of an initial refinement of the structure are reported. A total of 12 diffraction images were recorded with an exposure time of 3.5 h per image, whereby the crystal was static for each diffraction image with a 10° ϕ rotation between images. Initial refinements using these neutron data indicated the positions and orientations of 30 water molecules within the first hydration shell of the DNA molecule. This experiment constitutes a state-of-the-art approach and is the first attempt to our knowledge to determine the low-temperature neutron structure of a DNA crystal.
Heterogeneous Replica for Query on Cassandra

Cassandra is a popular structured storage system with high-performance, scalability and high availability, and is usually used to store data that has some sortable attributes. When deploying and configuring Cassandra, it is important to design a suitable schema of column families for accelerating the target queries. However, one schema is only suitable for a part of queries, and leaves other queries with high latency. In this paper, we propose a new replica mechanism, called heterogeneous replica, to reduce the query latency greatly while ensuring high write throughput and data recovery. With this replica mechanism, different replica has the same dataset while having different serialization on disk. By implementing the heterogeneous replica mechanism on Cassandra, we show that the read performance of Cassandra can be improved by two orders of magnitude with TPC-H data set.
Resolving Digital Staphylococcal Osteomyelitis Using Bacteriophage—A Case Report

Infections involving diabetic foot ulcers (DFU) are a major public health problem and have a substantial negative impact on patient outcomes. Osteomyelitis in an ulcerated foot substantially increases the difficulty of successful treatment. While literature suggests that osteomyelitis in selected patients can sometimes be treated conservatively, with no, or minimal removal of bone, we do not yet have clear treatment guidelines and the standard treatment failure fallback remains amputation. The authors report on the successful treatment, with a long term follow up, of a 63 YO diabetic female with distal phalangeal osteomyelitis using bacteriophage, a form of treatment offering the potential for improved outcomes in this era of escalating antibiotic resistance and the increasingly recognized harms associated with antibiotic therapy.