Miracle-dz/UniFAR-FTUs huggingface dataset:
NEM-Tar: A Probabilistic Graphical Model for Cancer Regulatory Network Inference and Prioritization of Potential Therapeutic Targets From Multi-Omics Data

Targeted therapy has been widely adopted as an effective treatment strategy to battle against cancer. However, cancers are not single disease entities, but comprising multiple molecularly distinct subtypes, and the heterogeneity nature prevents precise selection of patients for optimized therapy. Dissecting cancer subtype-specific signaling pathways is crucial to pinpointing dysregulated genes for the prioritization of novel therapeutic targets. Nested effects models (NEMs) are a group of graphical models that encode subset relations between observed downstream effects under perturbations to upstream signaling genes, providing a prototype for mapping the inner workings of the cell. In this study, we developed NEM-Tar, which extends the original NEMs to predict drug targets by incorporating causal information of (epi)genetic aberrations for signaling pathway inference. An information theory-based score, weighted information gain (WIG), was proposed to assess the impact of signaling genes on a specific downstream biological process of interest. Subsequently, we conducted simulation studies to compare three inference methods and found that the greedy hill-climbing algorithm demonstrated the highest accuracy and robustness to noise. Furthermore, two case studies were conducted using multi-omics data for colorectal cancer (CRC) and gastric cancer (GC) in the TCGA database. Using NEM-Tar, we inferred signaling networks driving the poor-prognosis subtypes of CRC and GC, respectively. Our model prioritized not only potential individual drug targets such as HER2, for which FDA-approved inhibitors are available but also the combinations of multiple targets potentially useful for the design of combination therapies.
Sounds Like Respect. The Impact of Background Music on the Acceptance of Gay Men in Audio-Visual Advertising

Companies increasingly seek to use gay protagonists in audio-visual commercials to attract a new affluent target group. There is also growing demand for the diversity present in society to be reflected in media formats such as advertising. Studies have shown, however, that heterosexual consumers (especially men), who may be part of the company's loyal consumer base, tend to react negatively to gay-themed advertising campaigns. Searching for an instrument to mitigate this unwanted effect, the present study investigated whether carefully selected background music can shape the perceived gender of gay male advertising protagonists. In a 2 × 2 between-subjects online experiment (musical connotation × gender of the participant), 218 heterosexual participants watched a commercial promoting engagement rings that featured gay male protagonists, scored with feminine- or masculine-connoted background music. As expected, women generally reacted more positively than men to the advertising. Men exposed to the masculine-connoted background music rated the promoted brand more positively, and masculine music also enhanced (at least in the short term) these men's acceptance of gay men in general (low and medium effect sizes) more than was the case for feminine background music. Carefully selected background music affecting the perceived gender of gay male advertising protagonists may prevent negative reactions from heterosexual audiences and, therefore, motivate companies to use gay protagonists in television commercials on a more regular basis.
Assessment of the Potential Risk of Rock-Climbing for Cliff Plant Species and Natural Protected Areas of Spain

In recent years, the popularity of rock-climbing has grown tremendously, setting an increasing pressure on cliff habitats. Climbing may be particularly harmful in the Mediterranean biome due to its appropriate environmental conditions for climbing. A few studies have identified the effect of climbing on plant diversity at a small-scale (namely locally or even just in specific climbing areas). However, no studies exist assessing the potential risk of rock-climbing on a broad-scale (e.g., regional or national). The study aims to identify the priority locations and priority cliff plant species in Spain to focus future study efforts. Spain was selected because it is a plant biodiversity hotspot, with a great diversity of endemic and endangered species, and one of the most popular destinations for climbers. We used a geographic information system-based approach to model the spatial concurrence among Spanish climbing areas (and climbing intensity), natural protected areas (NPAs), and distribution of threatened cliff plants (and their IUCN threat category). We found that 53.5% of climbing areas in Spain are located within a NPA, most of them falling into NPAs of medium protection level. We mapped 151 threatened cliff plants, identifying four medium priority Mediterranean locations and eight priority species in which future research efforts should be focused. High-priority study locations are absent in Spain according to our spatial modeling. For the first time on a national scale, this study identifies areas in which climbing represents a potential threat for cliff habitats and threatened plants. These findings contribute to designing field studies on the effects of rock-climbing on Mediterranean cliffs, laying the groundwork for a sustainable, yet challenging, balance between the protection of these unique habitats and rock-climbing.
An Actinobacterium Strain From Soil of Cerrado Promotes Phosphorus Solubilization and Plant Growth in Soybean Plants

The huge biological diversity of the Brazilian Cerrado is an important source of economically interesting microbial agents. The phylum Actinobacteria plays an important role in nutrient cycling, potentially improving their availability to plants. In this study, we isolated an actinobacteria (strain 3AS4) from wheat rhizospheres of crops cultivated in the Cerrado biome. Strain 3AS4 was identified as belonging to the genus Streptomyces and had phosphorus mobilization ability, mineralizing approximately 410 μg ml–1 from phytate, 300 μg ml–1 from calcium phosphate, and 200 μg ml–1 from rock phosphate. The analysis of the actinobacteria crude extract by spectrometric techniques revealed the presence of gluconic and 2-ketogluconic acid, and a greenhouse experiment was carried out to evaluate its plant growth promotion activity in soybean. Soil in its natural condition (with no phosphorus addition), 40 kg ha–1 rock phosphate from Bayovar (RP) added to soil, and triple super phosphate (SPT) added to soil were used. Significant differences in plant height were observed at 6 weeks when the plants were inoculated with the 3AS4 strain. The growth of inoculated plants in natural condition was promoted in 17% compared with the RP and SPT non-inoculated conditions, suggesting that inoculation can enable plants to grow with lower chemical P fertilizers. In the plants that were inoculated with the 3AS4 strain in the RP condition, the plant height increased by approximately 80% and the shoot:root ratio was approximately 30% higher compared to control conditions (non-inoculated plants in natural conditions). 3AS4 has P-solubilizing potential and can be exploited as an inoculant for soybean cultivation. These results suggest that this actinobacterium is a valuable resource for sustainable agriculture and will allow the reduction of phosphate fertilization in the future.
The Role of Antibodies Against the Crude Capsular Extract in the Immune Response of Porcine Alveolar Macrophages to In Vitro Infection of Various Serovars of Glaesserella (Haemophilus) parasuis

In Glässer’s disease outbreaks, Glaesserella (Haemophilus) parasuis has to overcome the non-specific immune system in the lower respiratory tract, the alveolar macrophages. Here we showed that porcine alveolar macrophages (PAMs) were able to recognize and phagocyte G. parasuis with strain-to-strain variability despite the presence of the capsule in virulent (serovar 1, 5, 12) as well in avirulent strains (serovar 6 and 9). The capsule, outer membrane proteins, virulence-associated autotransporters, cytolethal distending toxins and many other proteins have been identified as virulence factors of this bacterium. Therefore, we immunized pigs with the crude capsular extract (cCE) from the virulent G. parasuis CAPM 6475 strain (serovar 5) and evaluated the role of the anti-cCE/post-vaccinal IgG in the immune response of PAMs to in vitro infection with various G. parasuis strains. We demonstrated the specific binding of the antibodies to the cCE by Western-blotting assay and immunoprecipitation as well as the specific binding to the strain CAPM 6475 in transmission electron microscopy. In the cCE, we identified several virulence-associated proteins that were immunoreactive with IgG isolated from sera of immunized pigs. Opsonization of G. parasuis strains by post-vaccinal IgG led to enhanced phagocytosis of G. parasuis by PAMs at the first two hours of infection. Moreover, opsonization increased the oxidative burst and expression/production of both pro- and anti-inflammatory cytokines. The neutralizing effects of these antibodies on the antioxidant mechanisms of G. parasuis may lead to attenuation of its virulence and pathogenicity in vivo. Together with opsonization of bacteria by these antibodies, the host may eliminate G. parasuis in the infection site more efficiently. Based on these results, the crude capsular extract is a vaccine candidate with immunogenic properties.
Comparative Genomics and Transcriptomics of the Extreme Halophyte Puccinellia tenuiflora Provides Insights Into Salinity Tolerance Differentiation Between Halophytes and Glycophytes

Halophytes and glycophytes exhibit clear differences in their tolerance to high levels of salinity. The genetic mechanisms underlying this differentiation, however, remain unclear. To unveil these mechanisms, we surveyed the evolution of salinity-tolerant gene families through comparative genomic analyses between the model halophyte Puccinellia tenuiflora and glycophytic Gramineae plants, and compared their transcriptional and physiological responses to salinity stress. Under salinity stress, the K+ concentration in the root was slightly enhanced in P. tenuiflora, but it was greatly reduced in the glycophytic Gramineae plants, which provided a physiological explanation for differences in salinity tolerance between P. tenuiflora and these glycophytes. Interestingly, several K+ uptake gene families from P. tenuiflora experienced family expansion and positive selection during evolutionary history. This gene family expansion and the elevated expression of K+ uptake genes accelerated K+ accumulation and decreased Na+ toxicity in P. tenuiflora roots under salinity stress. Positively selected P. tenuiflora K+ uptake genes may have evolved new functions that contributed to development of P. tenuiflora salinity tolerance. In addition, the expansion of the gene families involved in pentose phosphate pathway, sucrose biosynthesis, and flavonoid biosynthesis assisted the adaptation of P. tenuiflora to survival under high salinity conditions.
Regulation of Drosophila Long-Term Courtship Memory by Ecdysis Triggering Hormone

Endocrine state is an important determinant of learning and memory in animals. In Drosophila, rejection of male courtship overtures by mated females leads to an aversive response manifested as courtship memory. Here we report that ecdysis triggering hormone (ETH) is an obligatory enabler of long-term courtship memory (LTM). ETH deficiency suppresses LTM, whereas augmented ETH release reduces the minimum training period required for LTM induction. ETH receptor knockdown either in the mushroom body (MB) γ lobe or in octopaminergic dorsal-anterior-lateral (DAL) neurons impairs memory performance, indicating its direct action in these brain areas. Consistent with these findings, brain exposure to ETH mobilizes calcium in MB γ lobe neuropils and DAL neurons. ETH receptor (ETHR) knockdown in the corpus allatum (CA) to create juvenile hormone (JH) deficiency also suppresses LTM, as does knockdown of the JH receptor Met in the MB γ lobe, indicating a convergence of ETH and JH signaling in this region of the brain. Our findings identify endocrine-enabled neural circuit components in the brain that are critical for persistent behavioral changes resulting from aversive social experience.
Water Table Fluctuation in Peatlands Facilitates Fungal Proliferation, Impedes Sphagnum Growth and Accelerates Decomposition

Northern peatlands are substantial carbon sinks because organic matter in peat is highly stable due to the low rate of decomposition. Waterlogged anaerobic conditions induce accumulation of Sphagnum-derived phenolic compounds that inhibit peat organic matter decomposition, a mechanism referred to as the “enzymic latch”. Recent studies have predicted that the water table in northern peatlands may become unstable. We observed that such unstable water table levels can impede the development of Sphagnum mosses. In this study, we determined the effects of low and high frequency water table fluctuation regimes on Sphagnum growth and peat organic matter decomposition, by conducting a year-long mesocosm experiment. In addition, we conducted a molecular analysis to examine changes in abundance of fungal community which may play a key role in the decomposition of organic matter in peatlands. We found that rapid water table fluctuation inhibited the growth of Sphagnum due to fungal infection but stimulated decomposition of organic matter that may dramatically destabilize peatland carbon storage. Increased pH, induced by the fluctuation, may contribute to the enhanced activity of hydrolases in peat. We demonstrated that the water table fluctuation in peatlands impeded Sphagnum growth and accelerates decomposition due to fungal proliferation. Thus, we suggested that understanding the microbial community in the northern peatlands is essential for elucidating the possible changes in carbon cycle of peatland under the changing world.
Seed Biology of Witchgrass (Panicum capillare L.) Ensures Its Success Under Different Environmental Conditions

Witchgrass (Panicum capillare L.) is a summer growing grass weed species and is increasing its prevalence in southern Australia. A better understanding of the seed biology is needed to effectively manage this weed. A series of field and laboratory studies were conducted to determine seed germination factors, field emergence patterns, and soil seedbank longevity. Witchgrass germination was stimulated by light and it germinated better at temperature over 20°C, with 93–100% germination at the two constant temperatures of 20 and 30°C, and the two alternating day/night temperatures of 30/25 and 35/25°C. It is highly tolerant to moisture stress at germination, with 2–7% germination even at −0.48 Mpa. Witchgrass seed lost 47–68% viability after 12 months of burial in the soil, however the seed persisted for more than 4 years if buried at 10 cm in the soil. Witchgrass emergence in southern New South Wales (NSW) commenced in mid spring (early October), with peak emergence of 63–83% in November and then significantly reduced to 16–37% emergence in December. Little emergence (<1%) occurred in the summer months from January to February. These results provide useful information for designing effective management strategies and the optimum timing of control. Climate change could favor the phenological development and the further spread of this weed, which present new challenges for its effective management. Further study is needed to investigate the impact of climate change on the biology, spread, and management of witchgrass.
Association of CD40 Gene Polymorphisms With Systemic Lupus Erythematosus and Rheumatoid Arthritis in a Chinese Han Population

Systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) are complex autoimmune diseases. CD40 participates in inflammatory response, and promotes fibroblast proliferation, leading to occurrence and progression of SLE, RA. This study explores CD40 gene polymorphisms in SLE and RA patients from a Chinese Han population. Two hundred SLE patients, 340 RA patients, and 900 healthy controls were enrolled. Genomic DNA was extracted from peripheral blood, and six polymorphisms of CD40 gene (rs3765456, rs1569723, rs73115010, rs13040307, rs1883832, and rs4810485) were detected by KASP method. Frequencies of rs1569723 genotypes AA, AC, AA+AC were significantly higher in RA patients as compared to those in healthy controls (P = 0.049, P = 0.024, P = 0.022). Frequencies of genotypes CT, CC+CT of rs1883832, and GT, GG+GT of rs4810485 were significantly higher in RA patients as compared to those in healthy controls (P = 0.012, P = 0.018, P = 0.009, P = 0.015). RA patients carrying rs13040307 C allele and rs73115010 T allele showed increased number of swollen joints. Moreover, frequency of allele T of rs13040307 was lower in SLE patients with positive anti-dsDNA and hematuria as compared to that in patients without these parameters (P = 0.038, P = 0.045). There were increased frequencies of genotype TT, allele T for rs13040307 and lower frequencies of genotype TT, allele T for rs73115010 in lupus patients with myositis (all P<0.05). Interestingly, frequencies of rs1569723 A allele, rs4810485 T allele were higher in SLE patients with myositis, and frequencies of rs3765456 A allele, rs1883832 T allele were lower in SLE patients with myositis (All P<0.05). In conclusion, CD40 gene polymorphisms may associate with susceptibility to SLE and RA.
Production of Mass-Separated Erbium-169 Towards the First Preclinical in vitro Investigations

The β−-particle-emitting erbium-169 is a potential radionuclide toward therapy of metastasized cancer diseases. It can be produced in nuclear research reactors, irradiating isotopically-enriched 168Er2O3. This path, however, is not suitable for receptor-targeted radionuclide therapy, where high specific molar activities are required. In this study, an electromagnetic isotope separation technique was applied after neutron irradiation to boost the specific activity by separating 169Er from 168Er targets. The separation efficiency increased up to 0.5% using resonant laser ionization. A subsequent chemical purification process was developed as well as activity standardization of the radionuclidically pure 169Er. The quality of the 169Er product permitted radiolabeling and pre-clinical studies. A preliminary in vitro experiment was accomplished, using a 169Er-PSMA-617, to show the potential of 169Er to reduce tumor cell viability.
Intensified Job Demands and Cognitive Stress Symptoms: The Moderator Role of Individual Characteristics

Intensified job demands (IJDs) originate in the general accelerated pace of society and ever-changing working conditions, which subject workers to increasing workloads and deadlines, constant planning and decision-making about one’s job and career, and the continual learning of new professional knowledge and skills. This study investigated how individual characteristics, namely negative and positive affectivity related to competence demands, and multitasking preference moderate the association between IJDs and cognitive stress symptoms among media workers (n = 833; 69% female, mean age 48 years). The results show that although IJDs were associated with higher cognitive stress symptoms at work, that is, difficulties in concentration, thinking clearly, decision-making, and memory, competence demands-related negative affectivity explained the most variance in cognitive stress symptoms. In addition, IJDs were more strongly associated with cognitive stress symptoms at work in individuals with high competence demand-related negative affectivity, and low multitasking preference (moderation effects). Altogether, the present findings suggest that HR practices or workplace interventions to ease employees’ negative affectivity from increasing competence demands at work could usefully support employees’ effective cognitive functioning when confronted with IJDs.
Delineation of Upper Crustal Structure Beneath the Island of Lombok, Indonesia, Using Ambient Seismic Noise Tomography

We have successfully conducted the first ambient noise tomography on the island of Lombok, Indonesia using local waveform data observed at 20 temporary stations. Ambient noise tomography was used to delineate the seismic velocity structure in the upper crust. The waveform data were recorded from August 3rd to September 9th, 2018, using short-period and broadband sensors. There are 185 Rayleigh waves retrieved from cross-correlating the vertical components of the seismograms. We used frequency-time analysis (FTAN) to acquire the interstation group velocity from the dispersion curves. Group velocity was obtained for the period range of 1 s to 6 s. The group velocity maps were generated using the subspace inversion method and Fast Marching Method (FMM) to trace ray-paths of the surface waves through a heterogeneous medium. To extract the shear wave velocity (Vs) from the Rayleigh wave group velocity maps, we utilize the Neighborhood Algorithm (NA) method. The 2-D tomographic maps provide good resolution in the center and eastern parts of Lombok. The tomograms show prominent features with a low shear velocity that appears up to 4 km depth beneath Rinjani Volcano, Northern Lombok, and Eastern Lombok. We suggest these low velocity anomalies are associated with Quaternary volcanic products, including the Holocene pyroclastic deposits of Samalas Volcano (the ancient Rinjani Volcano) which erupted in 1257. The northeast of Rinjani Volcano is characterized by higher Vs, and we suggest this may be due to the presence of igneous intrusive rock at depth.
A Methodological Review of fNIRS in Driving Research: Relevance to the Future of Autonomous Vehicles

As automobile manufacturers have begun to design, engineer, and test autonomous driving systems of the future, brain imaging with functional near-infrared spectroscopy (fNIRS) can provide unique insights about cognitive processes associated with evolving levels of autonomy implemented in the automobile. Modern fNIRS devices provide a portable, relatively affordable, and robust form of functional neuroimaging that allows researchers to investigate brain function in real-world environments. The trend toward “naturalistic neuroscience” is evident in the growing number of studies that leverage the methodological flexibility of fNIRS, and in doing so, significantly expand the scope of cognitive function that is accessible to observation via functional brain imaging (i.e., from the simulator to on-road scenarios). While more than a decade’s worth of study in this field of fNIRS driving research has led to many interesting findings, the number of studies applying fNIRS during autonomous modes of operation is limited. To support future research that directly addresses this lack in autonomous driving research with fNIRS, we argue that a cogent distillation of the methods used to date will help facilitate and streamline this research of tomorrow. To that end, here we provide a methodological review of the existing fNIRS driving research, with the overarching goal of highlighting the current diversity in methodological approaches. We argue that standardization of these approaches will facilitate greater overlap of methods by researchers from all disciplines, which will, in-turn, allow for meta-analysis of future results. We conclude by providing recommendations for advancing the use of such fNIRS technology in furthering understanding the adoption of safe autonomous vehicle technology.