Miracle-dz/UniFAR-FTUs huggingface dataset:
Gathering morphological and molecular data for identifying two species of trematodes from the neotropical Vaillant's frog, Lithobates vaillanti (Amphibia: Ranidae) in the highlands of Chiapas, south-eastern Mexico

Abstract Mexico possesses a large diversity of amphibians partly due to its complex topography and transitional position between the Nearctic and Neotropical biogeographical regions. However, its helminth parasite fauna has been relatively poorly studied. Specimens of the Vaillant's frog, Lithobates vaillanti (Brocchi) were sampled in the tropical rain forest of Nahá, in the Chiapas Highlands, and examined for parasites. Two trematode species were collected from their hosts; morphologically, specimens were allocated to the genera Langeronia Caballero and Bravo-Hollis, 1949 and Haematoloechus Looss, 1899, respectively. Individuals were sequenced for two molecular markers (the mitochondrial cytochrome c oxidase gene, and the ribosomal gene 28S), and processed for morphological analyses, including scanning electron microscopy. The new evidence was not enough to accomplish the identification at species level of Langeronia sp. due to the lack of sequence data from the type localities of Langeronia parva Christian, 1970 and Langeronia macrocirra Caballero and Bravo-Hollis, 1949. Likewise, the newly generated data were useful to properly identify the adult specimens of lung flukes as Haematoloechus complexus Seely, 1906.
Itraconazole Repolarizes Tumor-associated Macrophages and Suppresses Cervical Cancer Cell Growth

Background/Aim: Itraconazole (ITZ), an antifungal agent, has been reported to have anti-tumor effects in patients with multiple cancer types. We investigated the involvement of tumor-associated macrophages (TAMs) in its tumor-agnostic mechanism. Materials and Methods: M1 and M2 macrophages were established from human monocyte leukemia cell line (THP-1) and their phenotypes were determined morphologically. Cell membrane antigens and secreted proteins were evaluated by western blots and enzyme-linked immunosorbent assay, respectively. The proteomic profiling of cells was done by liquid chromatography with tandem mass spectrometry and analyzed. Viability of cervical cancer cells (CaSki) was evaluated after addition of the supernatant of M2 macrophages and during co-culture with M2 macrophages, with or without 10−5 M ITZ. Results: Co-culture of M1 macrophages inhibited the proliferation of CaSki cells (p=0.012), while that of M2 macrophages promoted their proliferation (p<0.0001). After treatment of M2 macrophages with ITZ for 24 h, they changed into M1-like shape with decreased expression of cluster of differentiation 163 (CD163) and chemokine ligand 18 (CCL18). The M1-like shape was maintained for 7 weeks of ITZ treatment and reverted to original after ITZ removal. Proteomic analysis of ITZ treated-M2 macrophages also demonstrated M1-like signature including the elevated levels of tumor necrosis factor (TNF)-related proteins. After treatment with ITZ, both the supernatant of the M2 macrophages and the co-culture with M2 macrophages significantly inhibited the proliferation of CaSki cells (each, p<0.0001). Conclusion: ITZ repolarized M2 macrophages to M1 type and suppressed cervical cancer cell growth demonstrating TAM-mediated anti-cancer activity of ITZ.
How Authentic Leadership Shapes Bank Employees' Work Engagement: A Moderated Mediation

In order to explore how authentic leadership shapes banking employees’ work engagement, we conducted a three-wave study among 300 employees from a large bank in northeastern China by measuring their perception of authentic leadership, power distance orientation, identification with supervisor, psychological empowerment and work engagement. The results showed that identification with supervisor and psychological empowerment fully mediate the relationship between authentic leadership and work engagement and that the indirect effect of identification with supervisor is further moderated by employees’ power distance orientation. Specifically, this indirect effect is stronger among employees with high (vs. low) levels of power distance orientation. This study therefore reveals the mechanism and boundary conditions of the effects of authentic leadership on employees' work engagement in the banking industry. Specifically, authentic leadership can promote employees' work engagement through their identification with supervisor and psychological empowerment; among employees with high levels of power orientation, the effect of authentic leadership on their engagement through identification with supervision is more salient. The practical implications were further discussed.
A Combined Model of Lean Manufacturing Tools to Increase Efficiency in a Peruvian Textile Company

In Peru, there are more than 9,000 micro-enterprises focused on the production of garment. Over the last few years, these numbers have remained stable while the number of medium-sized and large companies dedicated to this sector has decreased considerably. This situation is partly attributable to the current situation in the country due to the global pandemic, as well as the low-operational performance of the companies in this sector. However, just as this situation has left a large part of the economy paralyzed, the economic reactivation stimulated by the government represents a great opportunity to re-enter into the textile industry. Consequently, this paper proposes a model to improve the competitiveness of a case belonging to this sector through a model for improving the overall efficiency of the production process of its standard product based on tools oriented to the Lean Manufacturing philosophy, so that by reducing errors and shortening unproductive times, the productivity and competitiveness of the case study is increased. This model aims to focus on error reduction to improve its competitiveness, through a low-cost implementation that can be applied in almost any small manufacturing company. In order to validate this model, a pilot test was carried out using SMED, Poka-Yoke and work standardization tools, which resulted in a 20% reduction in recurring processes and a 21% reduction in set-up times, achieving a production efficiency of 84%.
Research on Long Rental Apartment Market News Monitoring Based on the Structural Topic Model

In recent years, the long rental apartment industry faced many problems, and its development is in trouble. This paper proposes a research framework for monitoring news about the long rental apartment market based on the structural topic model (STM), aiming to clarify the problems faced by the long rental apartment industry and explore the potential causes. First, the structural topic model was used to extract the topics of the long rental apartments news, and these topics were summarized and analyzed to get the focus of the market and the public on the long rental apartment industry and the urgent problems to be solved. Second, the time of news coverage was included as a covariate in STM to observe the focus of news media coverage at different periods. The STM model overcomes the one-sided defects of traditional word frequency statistics methods, improves the accuracy of the topic analysis, and provides beneficial guidance for the long rental apartment industry and relevant government departments to formulate reasonable regulatory policies.
How Connected Are Our Conference Review Boards?

Dense co-authorship network formed by the review board members of a conference may adversely impact the quality and integrity of the review process. In this report, we shed light on the topological characteristics of such networks for three major data management conference venues. Our results show all these venues give rise to dense networks with a large giant component. We advocate to rethink the traditional way review boards are formed to mitigate the emergence of dense networks.
Towards Policy Development of Entrepreneurial Ecosystem: A Review in Indonesia Financial Technology Sector

Finance sector is one of the crucial sectors with high potential growth in Indonesia. However, the sector face challenges because the policies have not been able to cover the headway of the financial technology. Furthermore, the finance sector perceived as lack of interactive cooperation between the stakeholder in the game, which makes its ecosystem less entrepreneurial. This research assesses policy development through a literature review on the entrepreneurial ecosystem of financial technology. Financial technology devises innovation to add more value between consumers and businesses —this study draws attention to the financial technology sector, which has matured compared to other industries. The study deployed a qualitative approach using an entrepreneurial framework by Isenberg, which discussed actors, roles, infrastructure, organizations, and actions that produce an environment that supports entrepreneurs. The results show the player and key roles among regulators’ policies and consumers of financial technology, especially when it relates to the benefit perceived. There are also overlapping related to delivering support for financial technology between regulators, but lack of social performance improvement. Current disruptive technology in finance, such as artificial intelligence, blockchain, cloud computing, and big data, could play vital roles in achieving sustainability. The framework of the entrepreneurial ecosystem is given to provide an understanding of the policy strategy in the financial technology case.
Advances in electrochromic device technology through the exploitation of nanophotonic and nanoplasmonic effects

Abstract Research regarding electrochromic (EC) materials, such materials that change their color upon application of an electrochemical stimulus, has been conducted for centuries. However, most recently, increasing efforts have been put into developing novel solutions to utilize these on-off switching materials in advanced nanoplasmonic and nanophotonic devices. Due to the significant change in dielectric properties of oxides such as WO3, NiO, Mn2O3 and conducting polymers like PEDOT:PSS and PANI, EC materials have transcended beyond simple smart window applications and are now found in plasmonic devices for full-color displays and enhanced modulation transmission and photonic devices with ultra-high on-off ratios and sensing abilities. Advancements in nanophotonic ECDs have further decreased EC switching speed by several orders of magnitude, allowing integration in real-time measurement and lab-on-chip applications. The EC nature of such nanoscale devices promises low energy consumption with low operating voltages paired with bistability and long lifetimes. We summarize these novel approaches to EC device design, lay out the current short comings and draw a path forward for future utilization.
Nanotechnology-based drug delivery for the treatment of CNS disorders

Abstract Approximately 6.8 million people die annually because of problems related to the central nervous system (CNS), and out of them, approximately 1 million people are affected by neurodegenerative diseases that include Alzheimer’s disease, multiple sclerosis, epilepsy, and Parkinson’s disease. CNS problems are a primary concern because of the complexity of the brain. There are various drugs available to treat CNS disorders and overcome problems with toxicity, specificity, and delivery. Barriers like the blood–brain barrier (BBB) are a challenge, as they do not allow therapeutic drugs to cross and reach their target. Researchers have been searching for ways to allow drugs to pass through the BBB and reach the target sites. These problems highlight the need of nanotechnology to alter or manipulate various processes at the cellular level to achieve the desired attributes. Due to their nanosize, nanoparticles are able to pass through the BBB and are an effective alternative to drug administration and other approaches. Nanotechnology has the potential to improve treatment and diagnostic techniques for CNS disorders and facilitate effective drug transfer. With the aid of nanoengineering, drugs could be modified to perform functions like transference across the BBB, altering signaling pathways, targeting specific cells, effective gene transfer, and promoting regeneration and preservation of nerve cells. The involvement of a nanocarrier framework inside the delivery of several neurotherapeutic agents used in the treatment of neurological diseases is reviewed in this study.
Cooperation between physiological defenses and immune resistance produces asymptomatic carriage of a lethal bacterial pathogen

Animals have evolved two defense strategies to survive infections. Antagonistic strategies include mechanisms of immune resistance that operate to sense and kill invading pathogens. Cooperative or physiological defenses mediate host adaptation to the infected state, limiting physiological damage and disease, without killing the pathogen, and have been shown to cause asymptomatic carriage and transmission of lethal pathogens. Here we demonstrate that physiological defenses cooperate with the adaptive immune response to generate long-term asymptomatic carriage of the lethal enteric murine pathogen, Citrobacter rodentium. Asymptomatic carriage of genetically virulent C. rodentium provided immune resistance against subsequent infections. Host immune protection was dependent on systemic antibody responses and pathogen virulence behavior, rather than the recognition of specific virulent factor antigens. Finally, we demonstrate that an avirulent strain of C. rodentium in the field has background mutations in two genes that are important for LPS structure. Our work reveals novel insight into how asymptomatic infections can arise mechanistically with immune resistance, mediating exclusion of phenotypically virulent enteric pathogen to promote asymptomatic carriage.
Cont-ID: Detection of samples cross-contamination in viral metagenomic data

Background High Throughput sequencing (HTS) technologies completed by the bioinformatic analysis of the generated data are becoming an important detection technique for virus diagnostics. They have the potential to replace or complement the current PCR-based methods thanks to their improved inclusivity and analytical sensitivity, as well as their overall good repeatability and reproducibility. Cross-contamination is a well-known phenomenon in molecular diagnostics and corresponds to the exchange of genetic material between samples. Cross-contamination management was a key drawback during the development of PCR-based detection and is now adequately monitored in routine diagnostics. HTS technologies are facing similar difficulties due to their very high analytical sensitivity. As a single viral read could be detected in millions of sequencing reads, it is mandatory to fix a detection threshold that will be influenced by cross-contamination. Cross-contamination monitoring should therefore be a priority when detecting viruses by HTS technologies. Results We present Cont-ID, a bioinformatic tool designed to check for cross-contamination by analysing the relative abundance of virus sequencing reads identified in sequence metagenomic datasets and their duplication between samples. It can be applied when the samples in a sequencing batch have been processed in parallel in the laboratory and with at least one external alien control. Using 273 real datasets, including 68 virus species from different hosts (fruit tree, plant, human) and several library preparation protocols (Ribodepleted total RNA, small RNA and double stranded RNA), we demonstrated that Cont-ID classifies with high accuracy (91%) viral species detection into (true) infection or (cross) contamination. This classification raises confidence in the detection and facilitates the downstream interpretation and confirmation of the results by prioritising the virus detections that should be confirmed. Conclusions Cross-contamination between samples when detecting viruses using HTS can be monitored and highlighted by Cont-ID (provided an alien control is present). Cont-ID is based on a flexible methodology relying on the output of bioinformatics analyses of the sequencing reads and considering the contamination pattern specific to each batch of samples. The Cont-ID method is adaptable so that each laboratory can optimise it before its validation and routine use.
YTHDC2 serves a distinct late role in spermatocytes during germ cell differentiation

Post-transcriptional regulation of gene expression by RNA-binding proteins helps facilitate fast, clean transitions from one cell state to the next during germ cell differentiation. Previously we showed that the RNA helicase YTHDC2 is required for germ cells to properly switch from mitosis to meiosis (Bailey et al., 2017). While YTHDC2 protein is first expressed as male germ cells enter meiosis, when it is needed to shut down the mitotic program, YTHDC2 expression continues to increase and reaches its highest levels later in meiotic prophase, in pachytene spermatocytes. Here we show that YTHDC2 has an additional essential role regulating meiotic progression in late spermatocytes during mouse germ cell differentiation. Inducing conditional knockout of Ythdc2 during the first wave of spermatogenesis, after the germ cells have already initiated meiotic prophase, allowed Ythdc2-deficient germ cells to successfully reach the pachytene stage and properly express many meiotic markers. However, instead of continuing through meiotic prophase and initiating the meiotic divisions, late pachytene spermatocytes failed to transition to the diplotene stage and quickly died. Loss of function of Ythdc2 in spermatocytes resulted in changes in transcript levels for a number of genes, some up-regulated and some down-regulated, compared to control mid-stage spermatocytes. YTHDC2 interacts with different proteins in early and late spermatocytes, with many of the interacting proteins involved in post-transcriptional RNA regulation and present in RNA granules, similar to YTHDC2. Our findings suggest that YTHDC2 facilitates proper progression of germ cells through multiple steps of meiosis, potentially via several mechanisms of post-transcriptional RNA regulation.
Cdc73 protects Notch-induced T-cell leukemia cells from DNA damage and mitochondrial stress

Activated Notch signaling is highly prevalent in T-cell acute lymphoblastic leukemia (T-ALL) but pan-Notch inhibitors were toxic in clinical trials. To find alternative ways to target Notch signals, we investigated Cell division cycle 73 (Cdc73), which is a Notch cofactor and component of transcriptional machinery, a potential target in T-ALL. While we confirmed previous work that CDC73 interacts with NOTCH1, we also found that the interaction in T-ALL was context-dependent and facilitated by the lymphoid transcription factor ETS1. Using mouse models, we showed that Cdc73 is important for Notch-induced T-cell development and T-ALL maintenance. Mechanistically, Cdc73, Ets1, and Notch intersect chromatin at promoters and enhancers to activate oncogenes and genes that are important for DNA repair and oxidative phosphorylation. Consistently, Cdc73 deletion in T-ALL cells induced DNA damage and impaired mitochondrial function. Our data suggests that Cdc73 might promote a gene expression program that was eventually intersected by Notch to mitigate the genotoxic and metabolic stresses of elevated Notch signaling. We also provide mechanistic support for testing inhibitors of DNA repair, oxidative phosphorylation, and transcriptional machinery. Inhibiting pathways like Cdc73 that intersect with Notch at chromatin might constitute a strategy to weaken Notch signals without directly targeting the Notch complex.
AtOM, an ontology model for standardizing use of brain atlases in tools, workflows, and data infrastructures

Brain atlases are important reference resources for accurate anatomical description of neuroscience data. Open access, three-dimensional atlases serve as spatial frameworks for integrating experimental data and defining regions-of-interest in analytic workflows. However, naming conventions, parcellation criteria, area definitions, and underlying mapping methodologies differ considerably between atlases and across atlas versions. This lack of standardization impedes use of atlases in analytic tools and registration of data to different atlases. To establish a machine-readable standard for representing brain atlases, we identified four fundamental atlas elements, defined their relations, and created an ontology model. Here we present our Atlas Ontology Model (AtOM) and exemplify its use by applying it to mouse, rat, and human brain atlases. We propose minimum requirements for FAIR atlases and discuss how AtOM may facilitate atlas interoperability and data integration. AtOM provides a standardized framework for communication and use of brain atlases to create, use, and refer to specific atlas elements and versions. We argue that AtOM will accelerate analysis, sharing, and reuse of neuroscience data.
Novel Pipeline for Large-Scale Comparative Population Genetics

This study determined population genetic structure measures, compared these measures across species with different biological traits; and created efficient, reproducible, reusable programming modules that are publicly available for future research. Cytochrome C Oxidase subunit I gene sequences from Diptera (true fly) species from Greenland and Canada were used as a case study and proof of concept. We hypothesized that population genetic structure measures will be influenced by the biological traits of organisms. Data were pulled from public databases, as well as taxon-specific literature. The R pipeline includes fifteen modules that can be adapted and applied to a diverse set of animal groups, geographic regions, genes, and traits. Habitat, larval diet, geographical distance, latitude, and longitude were all significantly related to population genetic structure in Diptera. Overall, this study has created efficient, reusable bioinformatics modules, as well as provided insight into the factors affecting population genetic structure in Northern fly communities.
Gemini: memory-efficient integration of hundreds of gene networks with high-order pooling

Motivation The exponential growth of genomic sequencing data has created ever-expanding repositories of gene networks. Unsupervised network integration methods are critical to learn informative representations for each gene, which are later used as features for downstream applications. However, these network integration methods must be scalable to account for the increasing number of networks and robust to an uneven distribution of network types within hundreds of gene networks. Results To address these needs, we present Gemini, a novel network integration method that uses memory-efficient high-order pooling to represent and weight each network according to its uniqueness. Gemini then mitigates the uneven distribution through mixing up existing networks to create many new networks. We find that Gemini leads to more than a 10% improvement in F1 score, 14% improvement in micro-AUPRC, and 71% improvement in macro-AURPC for protein function prediction by integrating hundreds of networks from BioGRID, and that Gemini’s performance significantly improves when more networks are added to the input network collection, while the comparison approach’s performance deteriorates. Gemini thereby enables memory-efficient and informative network integration for large gene networks, and can be used to massively integrate and analyze networks in other domains. Availability Gemini can be accessed at: https://github.com/MinxZ/Gemini. Contact addiewc@cs.washington. edu, swang@cs.washington. edu