Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing Biosynthetic Gene Cluster Diversity of Specialized Metabolites in the Conserved Gut Symbionts of Herbivorous Turtle Ants

Cephalotes are herbivorous ants (>115 species) feeding on low-nitrogen food sources, and they rely on gut symbionts to supplement their diet by recycling nitrogen food waste into amino acids. These conserved gut symbionts, which encompass five bacterial orders, have been studied previously for their primary nitrogen metabolism; however, little is known about their ability to biosynthesize specialized metabolites which can play a role in bacterial interactions between communities living in close proximity in the gut. To evaluate the biosynthetic potential of their gut symbionts, we mine 14 cultured isolate genomes and gut metagenomes across 17 Cephalotes species to explore the biodiversity of biosynthetic gene clusters (BGCs) producing specialized metabolites. The diversity of BGCs across Cephalotes phylogeny was analyzed using sequence similarity networking and BGC phylogenetic reconstruction. Our results reveal that the conserved gut symbionts involved in the nutritional symbiosis possess 80% of all the 233 BGCs retrieved in this work. Furthermore, the phylogenetic analysis of BGCs reveals different patterns of distribution, suggesting different mechanisms of conservation. A siderophore BGC shows high similarity in a single symbiont across different ant host species, whereas a BGC encoding the production of non-ribosomal peptides (NRPs) found different symbionts within a single host species. Additionally, BGCs were abundant in four of the five bacterial orders of conserved symbionts co-occurring in the hindgut. However, one major symbiont localized alone in the midgut lack BGCs. Because the spatial isolation prevents direct interaction with other symbionts, this result supports the idea that BGCs are maintained in bacteria living in close proximity but are dispensable for an alone-living symbiont. These findings together pave the way for studying the mechanisms of BGC conservation and evolution in gut bacterial genomes associated with Cephalotes. This work also provides a genetic background for further study, aiming to characterize bacterial specialized metabolites and to understand their functional role in multipartite mutualisms between conserved gut symbionts and Cephalotes turtle ants.
Regulation of ADAMTS Proteases

A disintegrin and metalloprotease with thrombospondin type I motifs (ADAMTS) proteases are secreted metalloproteinases that play key roles in the formation, homeostasis and remodeling of the extracellular matrix (ECM). The substrate spectrum of ADAMTS proteases can range from individual ECM proteins to entire families of ECM proteins, such as the hyalectans. ADAMTS-mediated substrate cleavage is required for the formation, remodeling and physiological adaptation of the ECM to the needs of individual tissues and organ systems. However, ADAMTS proteases can also be involved in the destruction of tissues, resulting in pathologies such as arthritis. Specifically, ADAMTS4 and ADAMTS5 contribute to irreparable cartilage erosion by degrading aggrecan, which is a major constituent of cartilage. Arthritic joint damage is a major contributor to musculoskeletal morbidity and the most frequent clinical indication for total joint arthroplasty. Due to the high sequence homology of ADAMTS proteases in their catalytically active site, it remains a formidable challenge to design ADAMTS isotype-specific inhibitors that selectively inhibit ADAMTS proteases responsible for tissue destruction without affecting the beneficial functions of other ADAMTS proteases. In vivo, proteolytic activity of ADAMTS proteases is regulated on the transcriptional and posttranslational level. Here, we review the current knowledge of mechanisms that regulate ADAMTS protease activity in tissues including factors that induce ADAMTS gene expression, consequences of posttranslational modifications such as furin processing, the role of endogenous inhibitors and pharmacological approaches to limit ADAMTS protease activity in tissues, which almost exclusively focus on inhibiting the aggrecanase activity of ADAMTS4 and ADAMTS5.
When Depression Breeds Rejection Rather Than Compassion: Disagreeableness, Stigma, and Lack of Empathic Concern Among Support Providers

Past research has shown that the close relationships of depressed individuals are often characterised by rejection rather than compassion. The goal of this research was to broaden interpersonal models of depression by investigating the reports of support providers themselves. Individual differences, including disagreeableness, stigmatic beliefs about depression, and empathic concern were measured. These were examined in relation to reported interpersonal behaviours toward a significant other who was currently depressed. A cross-sectional design was used in an undergraduate (N = 312) and community sample (N = 296). Disagreeable individuals reported less compassionate and more rejecting behaviours toward depressed significant others based on an interpersonal circumplex model of social support. Serial mediation models further indicated that the associations between disagreeableness and rejecting behaviours reported by providers were mediated by stigma and lower empathic concern. The current studies shed light on how the personality, attitudes and emotions of support providers influence the level of compassion expressed toward depressed individuals.
Targeting the Nerve Growth Factor Signaling Impairs the Proliferative and Migratory Phenotype of Triple-Negative Breast Cancer Cells

Triple-negative breast cancer is a heterogeneous disease that still lacks specific therapeutic approaches. The identification of new biomarkers, predictive of the disease’s aggressiveness and pharmacological response, is a challenge for a more tailored approach in the clinical management of patients. Nerve growth factor, initially identified as a key factor for neuronal survival and differentiation, turned out to be a multifaceted molecule with pleiotropic effects in quite divergent cell types, including cancer cells. Many solid tumors exhibit derangements of the nerve growth factor and its receptors, including the tropomyosin receptor kinase A. This receptor is expressed in triple-negative breast cancer, although its role in the pathogenesis and aggressiveness of this disease is still under investigation. We now report that triple-negative breast cancer-derived MDA-MB-231 and MDA-MB-453 cells express appreciable levels of tropomyosin receptor kinase A and release a biologically active nerve growth factor. Activation of tropomyosin receptor kinase by nerve growth factor treatment positively affects the migration, invasion, and proliferation of triple-negative breast cancer cells. An increase in the size of triple-negative breast cancer cell spheroids is also detected. This latter effect might occur through the nerve growth factor-induced release of matrix metalloproteinase 9, which contributes to the reorganization of the extracellular matrix and cell invasiveness. The tropomyosin receptor kinase A inhibitor GW441756 reverses all these responses. Co-immunoprecipitation experiments in both cell lines show that nerve growth factor triggers the assembly of the TrkA/β1-integrin/FAK/Src complex, thereby activating several downstream effectors. GW441756 prevents the complex assembly induced by nerve growth factor as well as the activation of its dependent signaling. Pharmacological inhibition of the tyrosine kinases Src and FAK (focal adhesion kinase), together with the silencing of β1-integrin, shows that the tyrosine kinases impinge on both proliferation and motility, while β1-integrin is needed for motility induced by nerve growth factor in triple-negative breast cancer cells. The present data support the key role of the nerve growth factor/tropomyosin receptor kinase A pathway in triple-negative breast cancer and offer new hints in the diagnostic and therapeutic management of patients.
Bioinformatic Analysis of the Campylobacter jejuni Type VI Secretion System and Effector Prediction

The Type VI Secretion System (T6SS) has important roles relating to bacterial antagonism, subversion of host cells, and niche colonisation. Campylobacter jejuni is one of the leading bacterial causes of human gastroenteritis worldwide and is a commensal coloniser of birds. Although recently discovered, the T6SS biological functions and identities of its effectors are still poorly defined in C. jejuni. Here, we perform a comprehensive bioinformatic analysis of the C. jejuni T6SS by investigating the prevalence and genetic architecture of the T6SS in 513 publicly available genomes using C. jejuni 488 strain as reference. A unique and conserved T6SS cluster associated with the Campylobacter jejuni Integrated Element 3 (CJIE3) was identified in the genomes of 117 strains. Analyses of the T6SS-positive 488 strain against the T6SS-negative C. jejuni RM1221 strain and the T6SS-positive plasmid pCJDM202 carried by C. jejuni WP2-202 strain defined the “T6SS-containing CJIE3” as a pathogenicity island, thus renamed as Campylobacter jejuni Pathogenicity Island-1 (CJPI-1). Analysis of CJPI-1 revealed two canonical VgrG homologues, CJ488_0978 and CJ488_0998, harbouring distinct C-termini in a genetically variable region downstream of the T6SS operon. CJPI-1 was also found to carry a putative DinJ-YafQ Type II toxin-antitoxin (TA) module, conserved across pCJDM202 and the genomic island CJIE3, as well as several open reading frames functionally predicted to encode for nucleases, lipases, and peptidoglycan hydrolases. This comprehensive in silico study provides a framework for experimental characterisation of T6SS-related effectors and TA modules in C. jejuni.
Navigation of Sounding Balloons with Deep Reinforcement Learning

With the availability of high performance miniaturized electronics, sounding balloons have become a viable options to conduct scientific experiments and commercial missions in the stratosphere, acting as a reduced size, low mass, low cost alternative to large zero-pressure or superpressure balloons. This paper explores the use of deep reinforcement learning for controlling a stratospheric sounding balloon to perform station-keeping over a specified area. In particular, we implement the deep Q-network (DQN) algorithm to learn a control policy for the balloon by exploiting different wind directions at different altitudes, reached by dropping ballast or releasing lifting gas. We conduct experiments using a simulation environment and evaluate the performance of the trained DQN model in real historical data. Our results show that the DQN algorithm can effectively learn a control policy that achieves satisfactory station-keeping with a high success rate, outperforming other, more direct control approaches. Our study presents a possible solution for the control of stratospheric sounding balloons in various applications.
Computational modeling of UV photocatalytic reactors: model development, evaluation, and application.

A computational model for simulating the performance of immobilized photocatalytic ultraviolet (UV) reactors used for water treatment was developed, experimentally evaluated, and applied to reactor design optimization. This model integrated hydrodynamics, species mass transport, chemical reaction kinetics, and irradiance distribution within the reactor. Among different hydrodynamic models evaluated against experimental data, the laminar, Abe–Kondoh–Nagano, and Reynolds stress turbulence models showed better performance (errors <5%, 12%, and 20%, respectively) in terms of external mass transfer and surface reaction prediction capabilities at different hydrodynamic conditions. A developed finite-volume-based UV lamp emission model was able to predict, with errors of less than 5%, near- and far-field irradiance measurements. Combining all these models, the integrated computational fluid dynamics (CFD)-based model was able to successfully predict the photocatalytic degradation rate of model pollutants (benzoic acid and 2,4-D) in various configurations of annular reactors and UV lamp sizes, over a wide range of hydrodynamic conditions (350 < Re < 11,000). In addition, the integrated model was used in combination with a Taguchi design of experiments method to perform reactor design optimization. Following this approach, a base case annular reactor design was modified to obtain a 50% more efficient design.
High photosynthesis rate in the selected wild rice is driven by leaf anatomy

48 The importance of increasing photosynthetic efficiency for sustainable crop yield 49 increases to feed the growing world population is well recognized. The natural genetic 50 variation for leaf photosynthesis in crop plants is largely unexploited for increasing genetic 51 yield potential. The genus Oryza , including cultivated rice and wild relatives, offers 52 tremendous genetic variability to explore photosynthetic differences, and underlying 53 biochemical, photochemical, and developmental bases. We quantified leaf photosynthesis 54 and related physiological parameters for six cultivated and three wild rice genotypes, and 55 identified photosynthetically efficient wild rice accessions. Fitting A / C i curves and 56 biochemical analyses showed that the leaf photosynthesis in cultivated rice varieties, IR64 57 and Nipponbare, was limited due to leaf nitrogen content, Rubisco activity, and electron 58 transport rate compared to photosynthetically efficient accessions of wild rice Oryza 59 australiensis and Oryza latifolia . The selected wild rice accessions with high leaf 60 photosynthesis per unit area had striking anatomical features, such as larger mesophyll cells 61 with more chloroplasts, fewer mesophyll cells between two consecutive veins, and higher 62 mesophyll cell and chloroplast surface area exposed to intercellular space. Our results show 63 the existence of desirable variations in Rubisco activity, electron transport rate, and leaf 64 anatomical features in the rice system itself that could be targeted for increasing the 65 photosynthetic efficiency of cultivated rice varieties.
A Critical Study of the Ph4AsPh4B Assumption for Single Ion Thermodynamics in Amphiprotic and Dipolar-Aprotic Solvents; Evaluation of Physical Parameters Relevant to Theoretical Consideration

The paper presents a critical study of the Ph4AsPh4B assumption, as for verification of its plausibility, that the standard free energies of transfer for the electrolyte from water to organic solvents, às„G°, can be divided equally, or almost equally, between the cation and anion. Discussion is made on the basis of a model treating the solvation energy of an ion being a composite of electrostatic and non electrostatic contributions. The physical parameters relevant to theoretical consideration of microscopic ion solvent interactions are carefully evaluated or semiempirically determined. They are the average molecular sizes, considered as effective spherical hard cores, of solvents, the effective charge of the reference ion, the quadrupole moments of some solvent molecules, and other parameters. Based on these data and others from the literature, the electrostatic parts of standard free energies of transfer are calculated, which accounts for interactions between the charges of ions and multiples of solvent molecules. The theoretical calculation shows a reasonable accordance with experiment for 13 solvents under investigation. For discussion, the neutral parts of standard free energies of transfer are replaced by the experimental values obtained with Ph4Ge and Ph4C, which are proved to be, by their sizes and structures, the neutral analogues of the reference cation and anion, respectively. The sums of the electrostatic and neutral contributions are then compared with the corresponding values from experiment and reasonable agreements are observed. The results from the present study corroborate the Ph4AsPh4B assumption, which enables the determination of thermodynamic quantities for single ions, with the reservation that an asymmetric partition, with a constant partition factor for all solvents, is clearly preferred to the equal partition practised in the literature.
PAVER

The massive parallelism present in GPUs comes at the cost of reduced L1 and L2 cache sizes per thread, leading to serious cache contention problems such as thrashing. Hence, the data access locality of an application should be considered during thread scheduling to improve execution time and energy consumption. Recent works have tried to use the locality behavior of regular and structured applications in thread scheduling, but the difficult case of irregular and unstructured parallel applications remains to be explored. We present PAVER, a Priority-Aware Vertex schedulER, which takes a graph-theoretic approach toward thread scheduling. We analyze the cache locality behavior among thread blocks (TBs) through a just-in-time compilation, and represent the problem using a graph representing the TBs and the locality among them. This graph is then partitioned to TB groups that display maximum data sharing, which are then assigned to the same streaming multiprocessor by the locality-aware TB scheduler. Through exhaustive simulation in Fermi, Pascal, and Volta architectures using a number of scheduling techniques, we show that PAVER reduces L2 accesses by 43.3%, 48.5%, and 40.21% and increases the average performance benefit by 29%, 49.1%, and 41.2% for the benchmarks with high inter-TB locality.
Effect of salinity on the growth of petroleum hydrocarbons degrading Bacillus sp . isolated from chronically polluted ship breaking yards

The aim of this paper is to determine the effect of salinity on the growth of some previously known petroleum biodegrading Bacillus sp. under laboratory condition where petroleum hydrocarbons are the sole source of carbon. Bushnell-Hass (BH) mineral salt media consisting of different NaCl concentrations (0.0 to 0.4 mole/liter or ML -1 ) were prepared and supplemented with 2% kerosene/diesel/engine oil. The media were then inoculated with the bacteria namely Bacillus pasteurii, B. badius, B. cirroflagellosus, B. circulans and B. brevis individually. After 7 days of incubation, bacterial growth was determined by measuring the optical density (OD) of the media at 620 nm. We found that salinity has a great impact on the growth of the bacteria under investigation. A NaCl concentration ranging from 0.05 to 0.3 ML -1 was found to have a positive impact on the growth of all 5 Bacillus sp. NaCl concentrations below and above the said range were found to be growth limiting. Interestingly our findings indicate that the maximum growth of a bacterium depends not only on the optimum salinity level but also on the type of petroleum hydrocarbons provided. The findings of this study are important for understanding the impact of salinity on the biodegradation process of petroleum hydrocarbons and for developing optimized application approaches to sweep such pollutants from contaminated sites. © 2014 Elixir All rights reserved. Elixir Bio Technology 68 (2014) 22280-22283 Bio Technology Available online at www.elixirpublishers. com (Elixir International Journal)
The defect structure and transport properties of some high Tc superconductors

The defect structures and transport properties of La2-. xSrxCuO4. 8, Nd2-xCeXCuO4+a, and YBa 2Cu 3-xTix0 6+a were studied by 4-probe DC conductivity and thermoelectric power measurements as functions of temperature, P0 2 and doping concentration. The conductivity and thermoelectric power of La 2CuO 4.8 both follow a P0 2 1/6 dependence at high temperatures, consistent with a defect model which involves equilibration between doubly-ionized oxygen defects and holes. The insensitivity of both properties to temperature implies that the enthalpy of the redox reaction is insignificant. Initially, Sr doping of La2-. xSrxCuO4.8 is compensated by holes which increases the conductivity, up to a maximum at x ~ 0.3. A transition to oxygen vacancy compensation at x ~ 0.3 is evidenced by a decrease in conductivity and an increase in P0 2 dependence. The conductivity also undergoes an apparent metal-insulator transition with x at x 0.9. At large x, a more rapid change of conductivity with temperature at high temperature is attributed to a redox reaction, an interpretation which is supported by a fixed-composition cooling experiment. In LaSrCuO4-8, a p-n transition emerges at high temperatures and low PO2's. Nd 2CuO 4.is an n-type semiconductor. The electron mobility was found not to be thermally activated. At high temperatures the electron density is primarily determined by a reduction reaction. The Ce donor substitution on Nd sites increases the conductivity up to 15% of Ce. At high Ce levels, the charge carriers become degenerate so that the conductivity and thermoelectric power become Po 2 and temperature independent. YBa2Cu3-xTix06+s is metallic below ~ 400 *C. Above that temperature the redox reaction dominates carrier generation. At T = 700 *C in 1OOppm 02, it undergoes a p-n transition. The magnitude of conductivity and its dependence on temperature and P0 2 are nearly independent of Ti concentration up to x = 0.1 and are very similar to the undoped YBa 2Cu 30 6+8, suggesting a large oxygen disorder. Thesis Advisor: Harry L. Tuller Title: Professor of Ceramics and Electronic Materials TABLE OF CONTENTS TITLE PA G E. --------------------------. 1 A B STRA CT. -. ------------------------. 2 TABLE OF CONTENTS. 4 LIST OF FIGURES. 7 LIST OF TABLES. -. 14 ACKNOWLEDGEMENTS. 15
Supplementary material to "Reduced El Niño variability in the mid-Pliocene according to the PlioMIP2 ensemble"

Abstract. The mid-Pliocene warm period (3.264–3.025 Ma) is the most recent geological period during which atmospheric CO2 levels were similar to recent historical values (~400 ppm). Several proxy reconstructions for the mid-Pliocene show highly reduced zonal sea surface temperature (SST) gradients in the tropical Pacific Ocean, indicating an El Niño-like mean state. However, past modelling studies do not show these highly reduced gradients. Efforts to understand mid-Pliocene climate dynamics have led to the Pliocene Model Intercomparison Project (PlioMIP). Results from the first phase (PlioMIP1) showed clear El Niño variability (albeit significantly reduced) and did not show the greatly reduced time-mean zonal SST gradient suggested by some of the proxies. In this work, we study El Niño-Southern Oscillation (ENSO) variability in the PlioMIP2 ensemble, which consists of additional global coupled climate models and updated boundary conditions compared to PlioMIP1. We quantify ENSO amplitude, period, spatial structure and flavour, as well as the tropical Pacific annual mean state in mid-Pliocene and pre-industrial simulations. Results show a reduced ENSO amplitude in the model-ensemble mean (−24 %) with respect to the pre-industrial, with 15 out of 17 individual models showing such a reduction. Furthermore, the spectral power of this variability considerably decreases in the 3–4 year band. The spatial structure of the dominant empirical orthogonal function shows no particular change in the patterns of tropical Pacific variability in the model-ensemble mean, compared to the pre-industrial. Although the time-mean zonal SST gradient in the equatorial Pacific decreases for 14 out of 17 models (0.2 °C reduction in the ensemble mean), there does not seem to be a correlation with the decrease in ENSO amplitude. The models showing the most ‘El Niño-like’ mean state changes show a similar ENSO amplitude as in the pre-industrial reference, while models showing more ‘La Niña-like’ mean state changes generally show a large reduction in ENSO variability. The PlioMIP2 results show a reasonable agreement both with time-mean proxies indicating a reduced zonal SST gradient, as well as reconstructions indicating a reduced, or similar, ENSO variability.