Miracle-dz/UniFAR-FTUs huggingface dataset:
Fluctuating selection and global change: a synthesis and review on disentangling the roles of climate amplitude, predictability and novelty

A formidable challenge for global change biologists is to predict how natural populations will respond to the emergence of conditions not observed at present, termed novel climates. Popular approaches to predict population vulnerability are based on the expected degree of novelty relative to the amplitude of historical climate fluctuations experienced by a population. Here, we argue that predictions focused on amplitude may be inaccurate because they ignore the predictability of environmental fluctuations in driving patterns of evolution and responses to climate change. To address this disconnect, we review major findings of evolutionary theory demonstrating the conditions under which phenotypic plasticity is likely to evolve in natural populations, and how plasticity decreases population vulnerability to novel environments. We outline key criteria that experimental studies should aim for to effectively test theoretical predictions, while controlling for the degree of climate novelty. We show that such targeted tests of evolutionary theory are rare, with marine systems being overall underrepresented in this venture despite exhibiting unique opportunities to test theory. We conclude that with more robust experimental designs that manipulate both the amplitude and predictability of fluctuations, while controlling for the degree of novelty, we may better predict population vulnerability to climate change.
Historical biogeography of a neglected family of armoured harvestmen (Opiliones : Laniatores : Icaleptidae) with the first record and a new genus for tropical Mesoamerica

Abstract. Among Opiliones (Arachnida), there are many taxa either with no familial assignment or erroneously located in their current family. This is the case of Ethobunus pilosus, formerly in Phalangodidae and before this work in Zalmoxidae. To assess the phylogenetic position of this taxon, we started with a revision of the male genitalia; followed by the inclusion of three molecular markers: nuclear 28S and 18S, and mitochondrial protein-encoding cytochrome c oxidase subunit I (COI) from E. pilosus in the previously published phylogenies of the Samooidea + Zalmoxoidea clade. The results revealed that E. pilosus is a derived lineage within the family Icaleptidae, thus it is transferred from Zalmoxidae, and the new name Trypophobica gen. nov. is proposed to accommodate it, with the new combination Trypophobica pilosa comb. nov. With its inclusion in Icaleptidae, and the description of Trypophobica llama sp. nov., the current diagnosis of the family needs updating, and further morphological characters should be considered as putative synapomorphies. In addition, the reconstruction of the ancestral ranges of Icaleptidae suggests a mid-Cretaceous origin c. 104 Ma in South America, with a subsequent colonisation to north Mesoamerica c. 80 Ma.
Traffic Jam Analysis using Multi-Language Twitter Data

The popularity of social media together with the widespread of location-aware devices have let to the explosion of geo-tagged data. As a result, many interesting location-based services were developed. In particular, road traffic jam detection and analyzer service is of great importance to Intelligent Transportation Systems. Current works proposed traffic jam detection from a single language data stream. In this paper, we propose a traffic jam analysis system that uses Multi-language (English, Arabic, and dialect) Twitter data stream. Relevant features are extracted from the stream and used to identify the traffic tweets. Traffic tweet are then classified into the causes of traffic jams. The detected spatio-temporal traffic events are visualized on a dynamic map. The detection and prediction results are validated against ground truth data obtained from the concerned authorities in the UAE.
Information Orientation, Smart Supply Chain Practice and Firm Performance: An Empirical Study

The development of information technology has facilitated supply chain integration and innovation, leading to smart supply chain practice. Exploring how to optimize traditional supply chain practice and build smart supply chain is of great significance for enterprises. The article aims to discover the relationship among information orientation, smart supply chain practice and firm performance. Based on resource-based view, we select the annual reports of manufacturing companies in Shanghai and Shenzhen stock markets, and quantify the level of information orientation and smart supply chain practice using the method of content analysis. The result reveals that both information orientation and smart supply chain practice have a positive impact on firm performance. Accordingly, theoretical and managerial implications are discussed.
Moving From Me to We: Interpersonal Coordination’s Effects on Self-Construal

Abstract We all move in time together throughout our lives, and doing so has been shown to lead to more pro-social attitudes and behaviors towards co-actors. However, little research has investigated how coordinated movement affects how individuals feel about themselves. This mixed-methods study took self-generated qualitative responses of how participants construed their own identities after either coordinated movement or a carefully matched control task. Responses were analysed qualitatively using thematic analyses, and quantitatively using content analysis. Four themes were identified from thematic analysis, and inferential statistical testing showed significant differences in how participants construed their identities post coordination (cf. control). Participants in the coordinated condition generated a higher proportion of interdependent (social) rather than independent (personal) self-construals, driven by differences in broad social structures/constructs rather than close specific social relations. Furthermore, participants in the coordinated condition reported less mental state items, and more sexual/romantic items. These findings may explain how and why coordinated movement leads to prosociality amongst those who take part, by leading individuals to think of themselves and each other in group terms.
A month for the mission: using a sentinel approach to determine the transmission window of digenean cercariae in the subarctic White Sea

Abstract In the digenean life cycle the cercaria ensures an important transmission stage, from the first intermediate host to the second or the definitive host. In regions with pronounced seasonality, this process occurs within a certain interval, the transmission window. In high latitudes, the size of transmission window has previously been determined only by comparing data on seasonal dynamics of infection level in various categories of hosts or extrapolating the results of laboratory experiments on cercarial biology to natural conditions. In this study, we evaluated the dynamics of infection of the second intermediate hosts (mussels Mytilus edulis) with cercariae of two digenean species, Himasthla elongata (Himasthlidae) and Cercaria parvicaudata (Renicolidae), at a littoral site at the White Sea by exposing cages with uninfected mussels during the warm season. This is the first such study in a subarctic sea. Mussel infection was observed from May to mid-September, but its intensity was the greatest only for approximately a month, from some moment after 10 July to mid-August, when water temperature was within the optimal range for cercarial emergence in both studied species (15‒20°C). During this time, the mussels accumulated 66.3 ± 6.2% metacercariae of H. elongata and 79.7 ± 5.3% metacercariae of C. parvicaudata out of the total number accumulated during the experimental period. We suggest that climate warming at high latitudes may prolong the period when the water temperatures are optimal for cercariae emergence, thereby intensifying digenean transmission in coastal ecosystems.
TLR7/8 Agonist and SHP2 Inhibitor Loaded Nanoparticle Enhances Macrophage Immunotherapy Efficacy

Tumor‐associated macrophages (TAMs) are among the most abundant immune cells in the solid tumor microenvironment, making them an attractive target for cancer immunotherapy. However, there are two important challenges. First, tumors repolarize the TAMs predominantly to M2 tumor‐aiding phenotype by secreting various immunosuppressive cytokines. Second, CD47 on cancer cells interacts with signal‐regulating protein a (SIRPa) expressed on macrophages. This crosstalk provides a downregulatory signal in the form of activation of SHP1/2 that inhibits cancer cell phagocytosis. These challenges can be overcome by engineering a nanoparticle that can deliver a rationale combination of immunomodulatory agents to the TAMs that can repolarize the M2 macrophages to M1 phenotype efficiently and concurrently block CD47‐SIRPa interactions by inhibiting SHP2 signaling. A lipid nanoparticle (LNP) system loaded with amphiphilic R848‐cholesterol (TLR7/8 agonist) and SHP099 (SHP2 inhibitor) in a predefined ratio has been designed. In vitro studies show that the LNPs system repolarized to M2 macrophages to M1 phenotype and expressed co‐stimulatory molecules while enhancing phagocytic potential. In vivo efficacy studies in 4T1 tumor‐bearing mice show that LNPs exhibit superior anti‐tumor efficacy than other treatments. Thus, the lipid nanoparticle‐mediated co‐delivery of a rational combination of TLR7/8 agonist and SHP2 inhibitor in the TAMs can enhance macrophage immunotherapy.
Multiple knockout mutants reveal a high redundancy of phytotoxic compounds that determine necrotrophic pathogenesis of Botrytis cinerea

Botrytis cinerea is a major pathogen of more than 1400 plant species. During infection, the kills host cells during infection and spreads through necrotic tissue, which is believed to be supported by induction of programmed plant cell death. To comprehensively evaluate the contributions of most of the currently known plant cell death inducing proteins (CDIPs) and metabolites for necrotrophic infection, an optimized CRISPR/Cas protocol was established which allowed serial marker-free mutagenesis to generate Botrytis mutants lacking up to 12 different CDIPs. Infection analysis revealed a decrease in virulence with increasing numbers of knockouts, and differences in the effects of knockouts on different host plants. The on planta secretomes obtained from these mutants revealed substantial remaining necrotic activity after infiltration into leaves. Our study has addressed for the first time the functional redundancy of virulence factors of a fungal pathogen, and demonstrates that B. cinerea releases a highly redundant cocktail of proteins and metabolites to achieve necrotrophic infection of a wide variety of host plants.
The properties of human disease mutations at protein interfaces

The assembly of proteins into complexes and interactions with other biomolecules are often vital for their biological function. While it is known that mutations at protein interfaces have a high potential to be damaging and cause human genetic disease, there has been relatively little consideration for how this varies between different types of interfaces. Here we investigate the properties of human pathogenic and putatively benign missense variants at homomeric (isologous and heterologous), heteromeric, DNA, RNA and other ligand interfaces, and at different regions with respect to those interfaces. We find that different types of interfaces vary greatly in their propensity to be associated with pathogenic mutations, with homomeric heterologous and DNA interfaces being particularly enriched in disease. We also find that residues that do not directly participate in an interface, but are close in 3D space, also show a significant disease enrichment. Finally, we show that mutations at different types of interfaces tend to have distinct property changes when undergoing amino acid substitutions associated with disease, and that this is linked to substantial variability in their identification by computational variant effect predictors.
Chromosomal rearrangements preserve adaptive divergence in ecological speciation

Despite increasing empirical evidence that chromosomal rearrangements may play an important role in adaptive divergence and speciation, the degree to which divergent genomic regions are associated with chromosomal rearrangements remains unclear. In this study, we provide the first whole-genome analyses of ecological speciation and chromosomal evolution in a Daphnia species complex, using chromosome-scale assemblies and natural-population sequencing of the recently diverged species pair, Daphnia pulicaria and Daphnia pulex, which occupy distinct yet overlapping habitats in North America, and the outgroup species Daphnia obtusa. Our results describe a mixed mode of geographic divergence (isolation with secondary contact) resulting in a heterogeneous landscape of genomic divergence. Large contiguous “continents of divergence” encompass over one third of the genome (36%) and contain nearly all the fixed differences (94%) between the species, while the background genome has been homogenized. Chromosomal rearrangements between species, including inversions and intrachromosomal translocations, are associated with the continents of divergence and capture multiple adaptive alleles in genes and pathways thought to contribute to the species’ phenotypic differences.
The population genetics of collateral resistance and sensitivity

Resistance mutations against one drug can elicit collateral sensitivity against other drugs. Multi-drug treatments exploiting such trade-offs can help slow down the evolution of resistance. However, if mutations with diverse collateral effects are available, a treated population may evolve either collateral sensitivity or collateral resistance. How to design treatments robust to such uncertainty is unclear. We show that many resistance mutations in Escherichia coli against various antibiotics indeed have diverse collateral effects. We propose to characterize such diversity with a joint distribution of fitness effects (JDFE) and develop a theory for describing and predicting collateral evolution based on simple statistics of the JDFE. We show how to robustly rank drug pairs to minimize the risk of collateral resistance and how to estimate JDFEs. In addition to practical applications, these results have implications for our understanding of evolution in variable environments.
Seismic Phase Association Based on the Maximum Likelihood Method

Phase association is a process that links seismic phases triggered at the stations of a seismic network to declare the occurrence of earthquakes. During phase association, a set of phases from different stations is examined to determine the common origin of phases within a specific region, predominantly on the basis of a grid search and the sum of observations. The association of seismic phases in local earthquake monitoring systems or earthquake early warning systems is often disturbed not only by transient noises, but also by large regional or teleseismic events. To mitigate this disturbance, we developed a seismic phase association method, binder_max, which uses the maximum likelihood method to associate seismic phases. The method is based on the framework of binder_ew, the phase associator of Earthworm, but it uses a likelihood distribution of the arrival information instead of stacking arrival information. Applying binder_max to data from seismic networks of South Korea and Ohio, United States, we found a significant improvement in the robustness of the method against large regional or teleseismic events compared to binder_ew. Our results indicate that binder_max can associate seismic phases of local earthquakes to the same degree as binder_ew as well as can avoid many of the false associations that have limited binder_ew.
Absence of CD11a Expression Identifies Embryonic Hematopoietic Stem Cell Precursors via Competitive Neonatal Transplantation Assay

Hematopoietic stem cells (HSCs) are defined by their self-renewal, multipotency, and bone marrow (BM) engraftment abilities. How HSCs emerge during embryonic development remains unclear, but are thought to arise from hemogenic endothelium through an intermediate precursor called “pre-HSCs. ” Pre-HSCs have self-renewal and multipotent activity, but lack BM engraftability. They can be identified functionally by transplantation into neonatal recipients, or by in vitro co-culture with cytokines and stroma followed by transplantation into adult recipients. While pre-HSCs express markers such as Kit and CD144, a precise surface marker identity for pre-HSCs has remained elusive due to the fluctuating expression of common HSC markers during embryonic development. We have previously determined that the lack of CD11a expression distinguishes HSCs in adults as well as multipotent progenitors in the embryo. Here, we use a neonatal transplantation assay to identify pre-HSC populations in the mouse embryo. We establish CD11a as a critical marker for the identification and enrichment of pre-HSCs in day 10.5 and 11.5 mouse embryos. Our proposed pre-HSC population, termed “11a- eKLS” (CD11a- Ter119- CD43+ Kit+ Sca1+ CD144+), contains all in vivo long-term engrafting embryonic progenitors. This population also displays a cell-cycle status expected of embryonic HSC precursors. Furthermore, we identify the neonatal liver as the likely source of signals that can mature pre-HSCs into BM-engraftable HSCs.
Equity Structure, Strategic Investment Psychology, and Performance in China’s Green Economy Context

This study empirically tests the impacts of equity structure on strategic investment psychology in green affairs in R&D vs. Marketing dimensions and company performance. Based on data from Chinese high-tech industry listed companies, the empirical results show that: (1) the largest shareholder’s shareholding ratio has a positive effect on marketing investment psychology and a negative impact on R&D investment psychology, (2) other large shareholders’ shareholding ratio are positive related to R&D investment psychology; (3) R&D investment psychology has a negative effect and marketing investment psychology has a positive influence on the current performance; (4) equity counterbalance is positive related to R&D investment psychology and has a negative effect on the current performance. This study contributes to the literature of corporate governance on sustainability issue by providing a new psychological perspective. The results also provide an important guidance for the corporate governance practice in green economies.
MicroRNA as an Important Target for Anticancer Drug Development

Cancer has become the second greatest cause of death worldwide. Although there are several different classes of anticancer drugs that are available in clinic, some tough issues like side-effects and low efficacy still need to dissolve. Therefore, there remains an urgent need to discover and develop more effective anticancer drugs. MicroRNAs (miRNAs) are a class of small endogenous non-coding RNAs that regulate gene expression by inhibiting mRNA translation or reducing the stability of mRNA. An abnormal miRNA expression profile was found to exist widely in cancer cell, which induces limitless replicative potential and evading apoptosis. MiRNAs function as oncogenes (oncomiRs) or tumor suppressors during tumor development and progression. It was shown that regulation of specific miRNA alterations using miRNA mimics or antagomirs can normalize the gene regulatory network and signaling pathways, and reverse the phenotypes in cancer cells. The miRNA hence provides an attractive target for anticancer drug development. In this review, we will summarize the latest publications on the role of miRNA in anticancer therapeutics and briefly describe the relationship between abnormal miRNAs and tumorigenesis. The potential of miRNA-based therapeutics for anticancer treatment has been critically discussed. And the current strategies in designing miRNA targeting therapeutics are described in detail. Finally, the current challenges and future perspectives of miRNA-based therapy are conferred.
Workplace Relations and Opportunities for Career Development Impact the Retention of Veterinarians in Shelter Medicine

Shelter medicine has grown considerably over recent years with many shelters hiring veterinarians for the first time or expanding their veterinary teams. As a result, there is a dearth of shelter veterinarians and retention has become a key concern for the field. The goal of this study was to describe veterinarians' perceptions of shelter medicine, and their feelings of job satisfaction, loneliness, and professional fulfillment. The sample included 52 shelter veterinarians, 39 previous shelter veterinarians and 130 non-shelter veterinarians (n = 221) who each completed an online survey. Current and previous shelter veterinarians had comparable perceptions regarding the appeal of most shelter medicine duties, although there were differences in the duties they performed within their job. More current shelter veterinarians participated in population management, policy development, administrative duties, and decision-making for individual patients (euthanasia, treatment, and adoptability). Considering other employment attributes, we found previous shelter veterinarians had lower mean rankings than current and non-shelter veterinarians regarding their interactions with administrative staff, ability to be part of a multiple veterinarian team and the availability of mentorship. Loneliness and professional fulfillment were mostly comparable between the groups, although previous shelter veterinarians were more likely to report they felt unhappy (X2 = 16.60, p = 0.02) and left out at work (X2 = 12.43, p = 0.02). Our findings suggest veterinarians who participate in decision-making for patients and shelter management procedures may be more willing to continue working in shelter medicine. Animal shelters should also employ strategies to improve workplace relationships and offer career development opportunities to improve job satisfaction and retention of veterinarians within the field.
Time-Resolved Monitoring of the Oxygen Transfer Rate of Chinese Hamster Ovary Cells Provides Insights Into Culture Behavior in Shake Flasks

Cultivations of mammalian cells are routinely conducted in shake flasks. In contrast to instrumented bioreactors, reliable options for non-invasive, time-resolved monitoring of the culture status in shake flasks are lacking. The Respiration Activity Monitoring Respiration Activity Monitoring System system was used to determine the oxygen transfer rate (OTR) in shake flasks. It was proven that the OTR could be regarded as equal to the oxygen uptake rate as the change of the dissolved oxygen concentration in the liquid phase over time was negligibly small. Thus, monitoring the oxygen transfer rate (OTR) was used to increase the information content from shake flask experiments. The OTR of a Chinese hamster ovary cell line was monitored by applying electrochemical sensors. Glass flasks stoppered with cotton plugs and polycarbonate flasks stoppered with vent-caps were compared in terms of mass transfer characteristics and culture behavior. Similar mass transfer resistances were determined for both sterile closures. The OTR was found to be well reproducible within one experiment (standard deviation <10%). It correlated with changes in cell viability and depletion of carbon sources, thus, giving more profound insights into the cultivation process. Culture behavior in glass and polycarbonate flasks was identical. Monitoring of the OTR was applied to a second culture medium. Media differed in the maximum OTR reached during cultivation and in the time when all carbon sources were depleted. By applying non-invasive, parallelized, time-resolved monitoring of the OTR, the information content and amount of data from shake flask experiments was significantly increased compared to manual sampling and offline analysis. The potential of the technology for early-stage process development was demonstrated.