Miracle-dz/UniFAR-FTUs huggingface dataset:
The Genomic Environment of BRAF Mutated and BRAF/PIK3CA Double Mutated Colorectal Cancers

Background: Colorectal cancer represents the most prevalent gastrointestinal malignancy. Prognosis of metastatic disease has improved in recent years with the introduction of effective systemic therapies, but mean survival remains in the range of two to three years. Targeted therapies based on specific molecular alterations in sub-sets of colorectal cancers have the potential of contributing to therapeutic progress. BRAF and PIK3CA are oncogenic kinases commonly mutated in colorectal cancers and can be targeted through small molecule kinase inhibitors. Methods: Clinical and genomic data from two extensive series of colorectal cancers were interrogated to define the molecular characteristics of cancers with BRAF mutations with and without concomitant mutations in PIK3CA. Results: Colorectal cancers that are BRAF and PIK3CA double mutants represent a small minority of about 5% of colorectal cancers in the two examined series of mostly localized disease. They also represent about one third of all BRAF mutated colorectal cancers. Most mutations in BRAF are classic V600E mutations. A high prevalence of MSI and CIMP is observed in BRAF mutated colorectal cancers with or without PIK3CA mutations. Mutations in tumor suppressors FBXW7 and ATM display a higher prevalence in BRAF mutated cancers. The prognosis of BRAF mutated colorectal cancers with or without PIK3CA mutations is not significantly different than counterparts with wild type BRAF. This contrasts with the known adverse prognostic effect of BRAF in metastatic disease and relates to the different prevalence of MSI in mutant BRAF localized versus metastatic colorectal cancers. Conclusions: BRAF mutations are the defining molecular alterations in double mutant BRAF and PIK3CA colorectal cancers as determined by increased MSI and CIMP in BRAF subsets with and without PIK3CA mutations. Moreover, BRAF mutated cancers with and without PIK3CA mutations are characterized by the absence of KRAS mutations and a lower prevalence of APC mutations than BRAF wild type counterparts. Mismatch-repair-associated gene mutations display higher frequencies in BRAF mutated colorectal cancers. Despite the absence of prognosis implications of BRAF mutations in the studied cohorts of mostly localized cancers, such mutations could be prognostic in certain subsets. The presence of mutations in other genes, such as ATM and high MSI status present opportunities for combination therapies.
Extracts of Moringa oleifera and Croton californicus against infections of Vibrio parahaemolyticus (IPNGS16) in juvenile Pacific white shrimp (Penaeus vannamei)

We evaluated the inhibition activity of extracts from two common plants, moringa (Moringa oleifera) and croton (Croton californicus), against Vibrio parahaemolyticus (IPNGS16), which causes acute hepatopancreatic necrosis disease (AHPND). The experiment was developed in three phases. First, extracts were prepared, and phytochemical screening of plants was performed. Second, microbiological tests were applied to calculate the minimum inhibitory concentration (MIC). Finally, two bioassays were performed on juvenile shrimp by administering the extracts (first) in shrimp feed at 24 and 72 h, pre-infection, and the second in feed and directly to the culture water. Based on preliminary results of antimicrobial activity, an extract concentration of 60 mg mL-1 inhibited V. parahaemolyticus (IPNGS16) at a final concentration of approximately 1×106 CFU mL-1. Bioassays were carried out in order to determine the V. parahaemolyticus (IPNGS16) median lethal dose (LC50) for juvenile Penaeus vannamei (0.20 ± 0.05 g); the LC50 was 85×103 CFU mL-1. As a first test, the extracts were added to commercial feed at doses of 20, 40, and 60 mg mL-1. After feeding, the shrimp were infected with V. parahaemolyticus (IPNGS16), and mortality was recorded. For the first infection time (24 h), survival was 46 and 33% with croton and moringa, respectively; for the second infection time (72 h), survival was 16 and 25% with croton and moringa. Application of antibacterial extracts directly to culture water were effective against V. parahaemolyticus (IPNGS16). The best result (94% survival) was obtained with a high dose (3.6 mg mL-1 or 30%) of moringa extracts added directly to culture water. Moringa methanol extracts produce active compounds capable of inhibiting replication of V. parahaemolyticus (IPNGS16) in shrimp aquaculture and reducing shrimp mortality.
Social Inﬂuence Given (Partially) Deliberate Matching: Career Imprints in the Creation of Academic Entrepreneurs 1

Actors and associates often match on a few dimensions that matter most for the relationship at hand. In so doing, they are exposed to unanticipated social in ﬂ uences because counterparts have broader attitudes and preferences than would-be contacts considered when they ﬁ rst chose to pair. The authors label as “ partially deliberate ” social matching that occurs on a small set of attributes, and they present empirical methods for identifying causal social in ﬂ uence effects when relationships follow this generative logic. A data set tracking the training and professional activities of academic biomedical scientists is used to show that young scientists adopt their advisers ’ orientations toward commercial science as evidenced by adviser-to-advisee transmission of patenting behavior. The authors demonstrate this in two-stage models that account for the endogeneity of matching, using both inverse probability of treatment weights and an instrumental variables approach. They also draw on qualitative methods to support a causal interpretation. Overall, they present a theory and a triangu-lation of methods to establish evidence of social in ﬂ uence when tie formation is partially deliberate.
Deciphering the Potential of Pre and Pro-Vitamin D of Mushrooms against Mpro and PLpro Proteases of COVID-19: An In Silico Approach

Vitamin D’s role in combating the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the virus causing COVID-19, has been established in unveiling viable inhibitors of COVID-19. The current study investigated the role of pre and pro-vitamin D bioactives from edible mushrooms against Mpro and PLpro proteases of SARS-CoV-2 by computational experiments. The bioactives of mushrooms, specifically ergosterol (provitamin D2), 7-dehydrocholesterol (provitamin-D3), 22,23-dihydroergocalciferol (provitamin-D4), cholecalciferol (vitamin-D3), and ergocalciferol (vitamin D2) were screened against Mpro and PLpro. Molecular docking analyses of the generated bioactive protease complexes unravelled the differential docking energies, which ranged from −7.5 kcal/mol to −4.5 kcal/mol. Ergosterol exhibited the lowest binding energy (−7.5 kcal/mol) against Mpro and PLpro (−5.9 kcal/mol). The Molecular Mechanics Poisson–Boltzmann Surface Area (MMPBSA) and MD simulation analyses indicated that the generated complexes were stable, thus affirming the putative binding of the bioactives to viral proteases. Considering the pivotal role of vitamin D bioactives, their direct interactions against SARS-CoV-2 proteases highlight the promising role of bioactives present in mushrooms as potent nutraceuticals against COVID-19.
Modeling Colorectal Cancer Progression Reveals Niche-Dependent Clonal Selection

Simple Summary Colorectal cancer (CRC) starts as a localized tumor and becomes a systemic disease with fatal consequences. However, clonal dynamics during progression are not well understood. Here, we present various techniques to model the different stages of CRC progression. Using genetically engineered mouse models (GEMMs) or organoid transplantation, localized tumors as well as liver metastases with characteristic intra-tumor heterogeneity were generated. The optical barcoding of transplanted organoids revealed niche-dependent clonal selection, implying that distinct niche factors control clonal outgrowth. Abstract Colorectal cancer (CRC) is among the deadliest cancers worldwide, with metastasis being the main cause of patient mortality. During CRC progression the complex tumor ecosystem changes in its composition at virtually every stage. However, clonal dynamics and associated niche-dependencies at these stages are unknown. Hence, it is of importance to utilize models that faithfully recapitulate human CRC to define its clonal dynamics. We used an optical barcoding approach in mouse-derived organoids (MDOs) that revealed niche-dependent clonal selection. Our findings highlight that clonal selection is controlled by a site-specific niche, which critically contributes to cancer heterogeneity and has implications for therapeutic intervention.
The use and measurement of communication self-efficacy techniques in a UK undergraduate accounting course

ABSTRACT This research contributes to helping educational establishments across the world develop self-efficacy techniques to improve communication skills within an accounting course design and other disciplines. This paper asks the research question: Does self-efficacy enhances accounting students’ communication ability? Previous research has identified the business community requiring accountants to display high levels of communication ability. However, despite many deliberate pedagogical interventions over the years, communication skills are lacking in graduating accounting students. This paper describes a new approach of deliberate self-efficacy interventions in one UK university’s undergraduate accounting curriculum to improve accounting students’ communication ability. In addition, a self-efficacy framework of Stone and Bailey [(2007). Team conflict self-efficacy and outcome expectancy of business students. Journal of Education for Business, 82(5), 258–266. https://doi.org/10.3200/JOEB.82. 5.258-266. ] is developed to model communication self-efficacy, outcome expectancy and behavioral intentions of the students. The data consists of the results of 131 first-year accounting students, and this paper contributes by helping to pinpoint two self-efficacy techniques to improving students’ communication skills: ‘personal mastery’ and ‘mentor support’.
Graphene Film Growth on Silicon Carbide by Hot Filament Chemical Vapor Deposition

The electrical properties of graphene on dielectric substrates, such as silicon carbide (SiC), have received much attention due to their interesting applications. This work presents a method to grow graphene on a 6H-SiC substrate at a pressure of 35 Torr by using the hot filament chemical vapor deposition (HFCVD) technique. The graphene deposition was conducted in an atmosphere of methane and hydrogen at a temperature of 950 °C. The graphene films were analyzed using Raman spectroscopy, scanning electron microscopy, atomic force microscopy, energy dispersive X-ray, and X-ray photoelectron spectroscopy. Raman mapping and AFM measurements indicated that few-layer and multilayer graphene were deposited from the external carbon source depending on the growth parameter conditions. The compositional analysis confirmed the presence of graphene deposition on SiC substrates and the absence of any metal involved in the growth process.
Improved African Vulture Optimization Algorithm Based on Quasi-Oppositional Differential Evolution Operator

In this study, an improved African vulture optimization algorithm (IAVOA) that combines the African vulture optimization algorithm (AVOA) with both quasi-oppositional learning and differential evolution is proposed to address specific drawbacks of the AVOA, including low population diversity, bad development capability, and unbalanced exploration and development capabilities. The improved algorithm has three parts. First, quasi-oppositional learning is introduced in the population initialization and exploration stages to improve population diversity. Second, a differential evolution operator is introduced in the local search position update of each population to improve exploration capability. Third, adaptive parameters are introduced to the differential evolution operator, thus balancing the algorithm exploration and development. A numerical simulation experiment based on 36 different types of benchmark functions showed that while the IAVOA can enhance the convergence speed and solution accuracy of the basic AVOA and two variants of AVOA, IAVOA outperforms the other 7 swarm intelligence algorithms in the mean and best values of 33 benchmark functions.
Public Acceptance of Autonomous Vehicles in China

Abstract Autonomous vehicles (AVs) have attracted extensive attention worldwide for their huge potential to revolutionize urban cities. The diffusion of AVs in cities will largely depend on public acceptance of AVs. But many studies revealed that people hold a high level of concern about AVs. This study aims to enrich our understanding of public acceptance of AVs in China, both at the explicit level and at the implicit level. We also attempt to enhance people’s positive attitudes toward AVs by Evaluative Conditioning (EC). Study 1 found that participants recognized the benefits of AVs, but were also concerned about them. Moreover, participants showed only moderate trust in AVs. In Study 2, it was observed that participants mainly showed positive implicit attitudes toward AVs and there was no significant correlation between implicit and explicit attitudes toward AVs. In Study 3, EC offered an alternative way to change implicit attitudes. Specifically, implicit attitudes toward AVs were positively increased through EC, whereas explicit attitudes did not change significantly. This research provides several theoretical and practical implications. The findings support the notion that explicit and implicit attitudes involve independent psychological processes, and that implicit attitude can be changed through EC.
A Novel Pathway of Chlorimuron-Ethyl Biodegradation by Chenggangzhangella methanolivorans Strain CHL1 and Its Molecular Mechanisms

Chlorimuron-ethyl is a widely used herbicide in agriculture. However, uncontrolled chlorimuron-ethyl application causes serious environmental problems. Chlorimuron-ethyl can be effectively degraded by microbes, but the underlying molecular mechanisms are not fully understood. In this study, we identified the possible pathways and key genes involved in chlorimuron-ethyl degradation by the Chenggangzhangella methanolivorans strain CHL1, a Methylocystaceae strain with the ability to degrade sulfonylurea herbicides. Using a metabolomics method, eight intermediate degradation products were identified, and three pathways, including a novel pyrimidine-ring-opening pathway, were found to be involved in chlorimuron-ethyl degradation by strain CHL1. Transcriptome sequencing indicated that three genes (atzF, atzD, and cysJ) are involved in chlorimuron-ethyl degradation by strain CHL1. The gene knock-out and complementation techniques allowed for the functions of the three genes to be identified, and the enzymes involved in the different steps of chlorimuron-ethyl degradation pathways were preliminary predicted. The results reveal a previously unreported pathway and the key genes of chlorimuron-ethyl degradation by strain CHL1, which have implications for attempts to enrich the biodegradation mechanism of sulfonylurea herbicides and to construct engineered bacteria in order to remove sulfonylurea herbicide residues from environmental media.
Cannabidiol (CBD) Protects Adipose-Derived Mesenchymal Stem Cells (ASCs) against Endoplasmic Reticulum Stress Development and Its Complications

Background: Recent studies suggested that individuals with metabolic disorders have altered function of adipocytes and adipose stem cell subpopulations, which impairs tissue homeostasis, promoting insulin resistance and diabetes development. The non-psychoactive phytocannabinoid CBD was found to modulate adipose tissue metabolism, however, its exact role in controlling ASCs’ fate is still poorly understood. Objectives: This investigation aimed to elucidate whether pretreatment of ASCs with CBD can protect against ER stress development and maintain the cytophysiological properties of cells. Methods: Human ASCs were cultured under control and adipogenic conditions. Prior to the experiments, cells in the experimental group were pretreated with CBD following the addition of an ER stress inducer—tunicamycin. After the experiments, the cells were subsequently tested for expression of the apoptotic, ER stress, and anti-inflammatory-related genes using RT-qPCR. Oxidative stress was analysed with flow cytometric assays. Results: Cells pretreated with CBD displayed decreased apoptosis and enhanced proliferation rate. Additionally, the expression of pro-inflammatory cytokines and miRNAs was significantly reduced. The obtained results also demonstrated an obvious reduction in intracellular accumulated ROS and NO, as well as mitigated ER stress through the down-regulation of IRE-1, PERK, CHOP, and ATF6 transcripts upon CBD treatment. Conclusion: The presented data provide the evidence that CBD protects ASCs against ER stress development and its complications and, thus, offers new insights for the management of obesity through the regulation of adipose tissue dynamics.
Interferometry with Atoms

Optics and interferometry with matter waves is the art of coherently manipulating the translational motion of particles like neutrons, atoms and molecules. Coherent atom optics is an extension of techniques that were developed for manipulating \emph{internal} quantum states. Applying these ideas to translational motion required the development of techniques to localize atoms and transfer population coherently between distant localities. In this view position and momentum are (continuouse) quantum mechanical degree of freedom analogous to discrete internal quantum states. In our contribution we start with an introduction into matter-wave optics in section 1, discuss coherent atom optics and atom interferometry techniques for molecular beams in section 2 and for trapped atoms in section 3. In section 4 we then describe tools and experiments that allow us to probe the evolution of quantum states of many-body systems by atom interference.
Self-multiplexing textile antenna aided by SIW cavity for wearable applications

ABSTRACT In this paper, a self-multiplexing textile antenna aided by a substrate integrated waveguide (SIW) is designed for wearable applications. The proposed antenna operates at wireless body area network (WBAN) frequencies such as 5, 5.2, 5.5 and 5.8 GHz. Extended unequal half mode substrate integrated waveguide (HMSIW) cavities are utilised for self-multiplexing operations with the open-ended magnetic wall working as the radiator for the proposed textile antenna. All the four unequal HMSIW cavities share the same electric wall which is realised using brass eyelets. The textile antenna is fabricated and the antenna parameters are measured to elucidate the proposed antenna concept. The port isolation has achieved above 33 dB between any ports. The measured gains for the four frequencies are above 5.1 dBi with high efficiency. The proposed multiplexing antenna is designed in 90 × 65 * 0.57 mm3 dimensions and the proposed antenna has exhibited good performance which makes it suitable for integrating with wearable devices and obviating the extra multiplexer circuits.
Biomarkers of Renal and Overall Survival in Patients with Granulomatosis Polyangiitis

Introduction: Granulomatosis with polyangiitis (GPA) is a kind of small blood vessel vasculitis that is characterized by lung and renal involvement with a high mortality rate. This study was aimed to investigate the association of baseline laboratory, demographic, clinical parameters between renal and overall survival in patients with GPA. Methods: Twenty-four patients diagnosed with GPA between 2010 and 2020 from a tertiary hospital were analyzed retrospectively. Baseline hematological and biochemical parameters, C reactive protein (CRP), and antineutrophil cytoplasmic antibodies (ANCA) were also recorded. History of plasmapheresis and acute dialysis were recorded. Primary endpoints were defined as the diagnosis of end-stage kidney disease and mortality. Results: Mean age of patients were 53,00±13,78. Ten (41,7%) of 24 patients were male. Median estimated glomerular filtration (eGFR) rate was 62 ml/min/1,73m2 (22,50-88,75). C-ANCA was positive in 15 (65%) patients. Median proteinuria level was 1,30 gr/day (0,80-2,05). Median CRP level was 14,00 g/dl at baseline (4,58-96,80). Cox regression analysis with the adjusted model by age and gender showed that platelet count, eGFR, proteinuria, and CRP levels were significantly associated with renal survival and hemoglobin levels were also associated with overall survival. Platelet count below 150 103/µL and hemoglobin levels below 12 g/dL showed the worst prognosis in terms of renal and overall survival. Discussion and Conclusion: The platelet count and hemoglobin level could be useful in predicting renal and overall survival at the baseline assessment of patients with granulomatosis polyangiitis.
Transductive Inference with Graphs

We propose a general regularization framework for transductive inference. The given data are thought of as a graph, where the edges encode the pairwise relationships among data. We develop discrete analysis and geometry on graphs, and then naturally adapt the classical regularization in the continuous case to the graph situation. A new and effective algorithm is derived from this general framework, as well as an approach we developed before.
Taxonomic Documentation and Statistical Analysis of Soil Mycoflora of Sanjay Gandhi National Park, Maharashtra, India

Aims: The present paper deals with documentation of diversity and analysis of ecological aspects of soil microfungal flora of Sanjay Gandhi National Park (SGNP). Study Design: The study area was divided into five zones, defined over span of three ranges and 10% peripheral area. Place and Duration of Study: SGNP, Maharashtra, India between September 2016 and September 2020. Methodology: A total of 43 soil samples were collected from 5 zones. Microscopic and molecular methods were used for identification of species. We examine dissimilarity in species composition by pairwise Jaccard Dissimilarity Index. We examine diversity of microfungi using diversity indices of Gini-Simpson’s and Shannon’s, true diversity (Shannon’s effective number of species) and equitability of species with Pielou’s evenness index. Results: The study resulted in a total of 77 isolates of 77 soil fungi obtained from 43 soil samples. A total of 36 species were documented under 15 genera. Aspergillus was dominant genus with 16 species, whereas Aspergillus niger was dominant species representing maximum 12 isolates. Pairwise Jaccard Dissimilarity Index was found to be above 66% in all cases, with only one species common in all the zones. In diversity indices, Gini-Simpson’s was 0.9347, and Shannon’s, was 3.1450. Pielou’s evenness index was 0.8776, causing true diversity, calculated as effective number of species (23), to be less than observed species richness (36). Conclusion: Thus, based on systematics and statistical analysis, it can be concluded that SGNP exhibits rich diversity of soil microfungi.
A 28-/39-GHz Dual-Band CMOS LNA With Shunt-Series Transformer Feedback

This letter presents a concurrent dual-band low-noise amplifier (LNA) operating at 28 and 39 GHz for multiband 5G wireless systems. In order to achieve a wideband input power matching, the LNA adopts a shunt-series feedback structure. Detailed noise analysis of the shunt-series transformer feedback LNA is proposed to guide the noise-optimized design, and a modified input network is proposed to improve the noise matching. The modified method also enhances the transconductance of the input stage, thus suppressing the noise of the subsequent circuit and obtaining a better overall noise figure (NF). Based on this input structure, a dual-band LNA with excellent NF is designed in a 65-nm complimentary metal–oxide–semiconductor (CMOS) process. This dual-band LNA achieves 18.1/18.4-dB gain and 3.1/3.8-dB NF at 28/39 GHz, consuming 10.2 mW from a 1.0-V power supply.