Miracle-dz/UniFAR-FTUs huggingface dataset:
Bergera unifolia (Rutaceae), A New Species from Guangxi (China) Based on Morphological and Molecular Data

A new species, Bergera unifolia C.L. Deng & F.J. Mou (Rutaceae, Aurantioideae, Clauseneae) is described and illustrated from Dahua County, Guangxi Province, China, based on morphological characters as well as on nrDNA (ITS) and cpDNA (trnL-F, atpB-rbcL, rbcL, matK, psbH-petB and psbA-trnH) sequences. It is characterised by unifoliate leaves similar to those of Murraya stenocarpa (Murraya sect. Bergera, or Chalcas sect. Bergera) but differs from it by having smaller and thinner subcoriaceous leaflets with irregularly toothed margins. The leaflets resemble those of M. kwangsiensis (Murraya sect. Bergera) in having hairs under the leaflets, oil glands and similar odour. Based on molecular data, B. unifolia is closely related to M. stenocarpa and M. kwangsiensis and thus it is important for resolving the classification of those species within Murraya sect. Bergera that should be formally transferred to Bergera.
Identification of Modal Combinations for Nonlinear Static Analysis of Building Structures

Abstract: An essential requisite in performance‐based seismic design is the estimation of inelastic deformation demands in structural members. An increasingly popular analytical method to establish these demand values is a “pushover” analysis in which a model of the building structure is subjected to an invariant distribution of lateral forces. Although such an approach takes into consideration the redistribution of forces following yielding of sections, it does not incorporate the effects of varying dynamic characteristics during the inelastic response. Simple modal combination schemes are investigated in this article to indirectly account for higher mode effects. Because the modes that contribute to deformations may be different from the modes that contribute to forces, it is necessary to identify unique modal combinations that provide reliable estimates of both force and deformation demands. The proposed procedure is applied to typical moment frame buildings to assess the effectiveness of the methodology. It is shown that the envelope of demands obtained from a series of nonlinear static analysis using the proposed modal‐combination‐based lateral load patterns results in better estimation of inter‐story drift, a critical parameter in seismic evaluation and design.
Communicative Perspectives on Strategic Organization

While in the past, perspectives that focus on language and communication have perhaps not received the attention they deserve in the mainstream literature in strategy and organization, interest in this area has been growing in recent years. The present essay serves to introduce a collection of insightful papers (independently submitted and reviewed, but brought together in this themed issue) that offer an opportunity to reflect on the contributions of a rich variety of research perspectives on communication to research in strategic organization. Building on the seven contributions featured in this issue, we show how communicative perspectives speak to questions of the who, how, what, and what then, of strategy. We then discuss dualisms that underpin research on strategic organization adopting a communicative lens and propose directions for future work that might bridge these divides.
Integrating IoT-sensing and crowdsensing for privacy-preserving parking monitoring

Data sensing and gathering is essential for diverse information-driven services in smart cities. On the one hand, Internet of Things (IoT) sensors can be deployed at certain fixed locations to capture data reliably but suffering from limited sensing coverage. On the other hand, data can be gathered dynamically by crowdsensing contributed from voluntary users but suffering from its unreliability and the lack of incentives for users' contributions. In this paper, we explore an integrated paradigm called "hybrid sensing" that aims to harness both IoT-sensing and crowdsensing in a complementary and privacy-preserving manner. We implemented our hybrid sensing system and conducted some initial empirical evaluations.
Structure and functionality of a multimeric human COQ7:COQ9 complex

Coenzyme Q (CoQ, ubiquinone) is a redox-active lipid essential for core metabolic pathways and antioxidant defense. CoQ is synthesized upon the mitochondrial inner membrane by an ill-defined ‘complex Q’ metabolon. Here we present a structure and functional analyses of a substrate- and NADH-bound oligomeric complex comprised of two complex Q subunits: the hydroxylase COQ7, which performs the penultimate step in CoQ biosynthesis, and the prenyl lipid-binding protein COQ9. We reveal that COQ7 adopts a modified ferritin-like fold with an extended hydrophobic access channel whose substrate binding capacity is enhanced by COQ9. Using molecular dynamics simulations, we further show that two COQ7:COQ9 heterodimers form a curved tetramer that deforms the membrane, potentially opening a pathway for CoQ intermediates to translocate from within the bilayer to the proteins’ lipid-binding sites. Two such tetramers assemble into a soluble octamer, closed like a capsid, with lipids captured within. Together, these observations indicate that COQ7 and COQ9 cooperate to access hydrophobic precursors and coordinate subsequent synthesis steps toward producing mature CoQ.
The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies

The spread of antibiotic resistance genes on plasmids is a threat to human and animal health. Phylogenies of bacteria and their plasmids contain clues regarding the frequency of plasmid transfer events, as well as the co-evolution of plasmids and their hosts. However, whole genome sequencing data from diverse ecological or clinical bacterial samples is rarely used to study plasmid phylogenies and resistance gene transfer. This is partially due to the difficulty to extract plasmids from short-read sequencing data. Here, we use both short- and long-read sequencing data of 24 clinical extended-spectrum β-lactamase producing Escherichia coli to estimate chromosomal and plasmid phylogenies. We compare the impact of different sequencing and assembly methodologies on these phylogenies and on the inference of horizontal gene transfer. We find chromosomal phylogenies can be estimated robustly with all methods, whereas plasmid phylogenies have more variable topology and branch lengths across the methods used. Specifically, hybrid methods that use long reads to resolve short-read assemblies (HybridSPAdes and Unicycler) perform better than those that started from long-reads during assembly graph generation (Canu). In contrast, the inference of plasmid and antibiotic resistance gene transfer using a parsimony-based criterion is mostly robust to the choice of sequencing and assembly method.
Recent Advancements in Serum Albumin-Based Nanovehicles Toward Potential Cancer Diagnosis and Therapy

Recently, drug delivery vehicles based on nanotechnology have significantly attracted the attention of researchers in the field of nanomedicine since they can achieve ideal drug release and biodistribution. Among the various organic or inorganic materials that used to prepare drug delivery vehicles for effective cancer treatment, serum albumin-based nanovehicles have been widely developed and investigated due to their prominent superiorities, including good biocompatibility, high stability, nontoxicity, non-immunogenicity, easy preparation, and functionalization, allowing them to be promising candidates for cancer diagnosis and therapy. This article reviews the recent advances on the applications of serum albumin-based nanovehicles in cancer diagnosis and therapy. We first introduce the essential information of bovine serum albumin (BSA) and human serum albumin (HSA), and discuss their drug loading strategies. We then discuss the different types of serum albumin-based nanovehicles including albumin nanoparticles, surface-functionalized albumin nanoparticles, and albumin nanocomplexes. Moreover, after briefly discussing the application of serum albumin-based nanovehicles used as the nanoprobes in cancer diagnosis, we also describe the serum albumin-based nanovehicle-assisted cancer theranostics, involving gas therapy, chemodynamic therapy (CDT), phototherapy (PTT/PDT), sonodynamic therapy (SDT), and other therapies as well as cancer imaging. Numerous studies cited in our review show that serum albumin-based nanovehicles possess a great potential in cancer diagnostic and therapeutic applications.
Development of Methodology to Investigate the Surface SMALPome of Mammalian Cells

Extraction of membrane proteins from biological membranes has traditionally involved detergents. In the past decade, a new technique has been developed, which uses styrene maleic acid (SMA) copolymers to extract membrane proteins into nanodiscs without the requirement of detergents. SMA nanodiscs are compatible with analytical techniques, such as small-angle scattering, NMR spectroscopy, and DLS, and are therefore an attractive medium for membrane protein characterization. While mass spectrometry has also been reported as a technique compatible with copolymer extraction, most studies have focused on lipidomics, which involves solvent extraction of lipids from nanodiscs prior to mass-spectrometry analysis. In this study, mass spectrometry proteomics was used to investigate whether there are qualitative or quantitative differences in the mammalian plasma membrane proteins extracted with SMA compared to a detergent control. For this, cell surface proteins of 3T3L1 fibroblasts were biotinylated and extracted using either SMA or detergent. Following affinity pull-down of biotinylated proteins with NeutrAvidin beads, samples were analyzed by nanoLC-MS. Here, we report for the first time, a global proteomics protocol for detection of a mammalian cell “SMALPome”, membrane proteins incorporated into SMA nanodiscs. Removal of SMA from samples prior to processing of samples for mass spectrometry was a crucial step in the protocol. The reported surface SMALPome of 3T3L1 fibroblasts consists of 205 integral membrane proteins. It is apparent that the detergent extraction method used is, in general, quantitatively more efficient at extracting proteins from the plasma membrane than SMA extraction. However, samples prepared following detergent extraction contained a greater proportion of proteins that were considered to be “non-specific” than in samples prepared from SMA extracts. Tantalizingly, it was also observed that proteins detected uniquely or highly preferentially in pull-downs from SMA extracts were primarily multi-spanning membrane proteins. These observations hint at qualitative differences between SMA and detergent extraction that are worthy of further investigation.
Humanized Mice as a Valuable Pre-Clinical Model for Cancer Immunotherapy Research

Immunotherapy with checkpoint inhibitors opened new horizons in cancer treatment. Clinical trials for novel immunotherapies or unexplored combination regimens either need years of development or are simply impossible to perform like is the case in cancer patients with limited life expectancy. Thus, the need for preclinical models that rapidly and safely allow for a better understanding of underlying mechanisms, drug kinetics and toxicity leading to the selection of the best regimen to be translated into the clinic, is of high importance. Humanized mice that can bear both human immune system and human tumors, are increasingly used in recent preclinical immunotherapy studies and represent a remarkably unprecedented tool in this field. In this review, we describe, summarize, and discuss the recent advances of humanized mouse models used for cancer immunotherapy research and the challenges faced during their establishment. We also highlight the lack of preclinical studies using this model for radiotherapy-based research and argue that it can be a great asset to understand and answer many open questions around radiation therapy such as its presumed associated “abscopal effect”.
Phenotypic Clustering of Patients With Newly Diagnosed Coronary Artery Disease Using Cardiovascular Magnetic Resonance and Coronary Computed Tomography Angiography

Background: Epidemiological characteristics and prognostic profiles of patients with newly diagnosed coronary artery disease (CAD) are heterogeneous. Therefore, providing individualized cardiovascular (CV) risk stratification and tailored prevention is crucial. Objective: Phenotypic unsupervised clustering integrating clinical, coronary computed tomography angiography (CCTA), and cardiac magnetic resonance (CMR) data were used to unveil pathophysiological differences between subgroups of patients with newly diagnosed CAD. Materials and Methods: Between 2008 and 2020, consecutive patients with newly diagnosed obstructive CAD on CCTA and further referred for vasodilator stress CMR were followed for the occurrence of major adverse cardiovascular events (MACE), defined by cardiovascular death or non-fatal myocardial infarction. For this exploratory work, a cluster analysis was performed on clinical, CCTA, and CMR variables, and associations between phenogroups and outcomes were assessed. Results: Among 2,210 patients who underwent both CCTA and CMR, 2,015 (46% men, mean 70 ± 12 years) completed follow-up [median 6.8 (IQR 5.9–9.2) years], in which 277 experienced a MACE (13.7%). Three mutually exclusive and clinically distinct phenogroups (PG) were identified based upon unsupervised hierarchical clustering of principal components: (PG1) CAD in elderly patients with few traditional risk factors; (PG2) women with metabolic syndrome, calcified plaques on CCTA, and preserved left ventricular ejection fraction (LVEF); (PG3) younger men smokers with proximal non-calcified plaques on CCTA, myocardial scar, and reduced LVEF. Using survival analysis, the occurrence of MACE, cardiovascular mortality, and all-cause mortality (all p < 0.001) differed among the three PG, in which PG3 had the worse prognosis. In each PG, inducible ischemia was associated with MACE [PG1, Hazards Ratio (HR) = 3.09, 95% CI, 1.70–5.62; PG2, HR = 3.62, 95% CI, 2.31–5.7; PG3, HR = 3.55, 95% CI, 2.3–5.49; all p < 0.001]. The study presented some key limitations that may impact generalizability. Conclusions: Cluster analysis of clinical, CCTA, and CMR variables identified three phenogroups of patients with newly diagnosed CAD that were associated with distinct clinical and prognostic profiles. Inducible ischemia assessed by stress CMR remained associated with the occurrence of MACE within each phenogroup. Whether automated unsupervised phenogrouping of CAD patients may improve clinical decision-making should be further explored in prospective studies.
Precise Investigation of the Efficacy of Multicomponent Drugs Against Pneumonia Infected With Influenza Virus

Background: Viral pneumonia is one of the most serious respiratory diseases, and multicomponent traditional Chinese medicines have been applied in the management of infected patients. As a representative TCM, HouYanQing (HYQ) oral liquid shows antiviral activity. However, the unclear mechanisms, as well as the ambiguous clinical effects, limit widespread application of this treatment. Therefore, in this study, a proteomics-based approach was utilized to precisely investigate its efficacy. Methods: Based on the efficacy evaluation of HYQ in a mouse model of pneumonia caused by influenza A virus (H1N1) and the subsequent proteomics analysis, specific signatures regulated by HYQ treatment of viral pneumonia were identified. Results: Experimental verifications indicate that HYQ may show distinctive effects in viral pneumonia patients, such as elevated galectin-3-binding protein and glutathione peroxidase 3 levels. Conclusion: This study provides a precise investigation of the efficacy of a multicomponent drug against viral pneumonia and offers a promising alternative for personalized management of viral pneumonia.
Women With Cerebral Infarction Feature Worse Clinical Profiles at Admission but Comparable Success to Men During Long-Term Inpatient Neurorehabilitation

Objective: Little is known about possible sex and gender differences in post-stroke neurorehabilitation outcomes. We aimed to analyze if functional performance, prevalence and impact of comorbidities at admission, and success of inpatient stroke-neurorehabilitation differ between men and women. Methods: Retrospective cohort analysis of 1,437 men and 907 women with prior cerebral infarction treated at a neurorehabilitation clinic between 2012 and 2017; multiple linear regression was used to examine the influence of sex/gender as well as multiple confounders on health and functional outcomes. The main outcome measures were Barthel index (BI) at admission and its change during 4 weeks inpatient neurorehabilitation. Results: Men had been diagnosed with osteoporosis less frequently than women but more often with type 2 diabetes mellitus, coronary artery or chronic kidney disease (p ≤ 0.01). Although twice as many women presented with pre-stroke depression compared to men, the risk of post-stroke depression detected during rehabilitation was comparable. Men were more likely to have less than 30 days between diagnosis and neurorehabilitation start than women (p < 0.03). At admission, women exhibited less autonomy, a lower BI, a higher pain score and worse 2-min walk test (2′WT) compared to men (p < 0.001). Among males osteoporosis and peripheral artery disease independently predicted BI at admission, in women it was pre-stroke depression, dementia, and arterial fibrillation. During neurorehabilitation, both sexes improved regarding BI, pain and walk tests (p < 0.001). Despite comparable rehabilitation effectiveness, women still had worse functional outcomes than males at discharge. Time after stroke to start of neurorehabilitation and length of the stay but, most strongly, the simple 2′WT at admission, and in women, pain intensity independently predicted post-stroke functional status and recovery. Conclusion: Women presented with worse functional status at admission to neurorehabilitation. Although men and women showed similar rehabilitation effectiveness, women still displayed worse clinical outcome measures and higher levels of pain at discharge. Early access and gender-sensitive, personalized post-stroke care with more focus on different comorbidities and psychosocial factors like pain levels and management, could further improve neurorehabilitation outcomes.
Insilico Functional Analysis of Genome-Wide Dataset From 17,000 Individuals Identifies Candidate Malaria Resistance Genes Enriched in Malaria Pathogenic Pathways

Recent genome-wide association studies (GWASs) of severe malaria have identified several association variants. However, much about the underlying biological functions are yet to be discovered. Here, we systematically predicted plausible candidate genes and pathways from functional analysis of severe malaria resistance GWAS summary statistics (N = 17,000) meta-analysed across 11 populations in malaria endemic regions. We applied positional mapping, expression quantitative trait locus (eQTL), chromatin interaction mapping, and gene-based association analyses to identify candidate severe malaria resistance genes. We further applied rare variant analysis to raw GWAS datasets (N = 11,000) of three malaria endemic populations including Kenya, Malawi, and Gambia and performed various population genetic structures of the identified genes in the three populations and global populations. We performed network and pathway analyses to investigate their shared biological functions. Our functional mapping analysis identified 57 genes located in the known malaria genomic loci, while our gene-based GWAS analysis identified additional 125 genes across the genome. The identified genes were significantly enriched in malaria pathogenic pathways including multiple overlapping pathways in erythrocyte-related functions, blood coagulations, ion channels, adhesion molecules, membrane signalling elements, and neuronal systems. Our population genetic analysis revealed that the minor allele frequencies (MAF) of the single nucleotide polymorphisms (SNPs) residing in the identified genes are generally higher in the three malaria endemic populations compared to global populations. Overall, our results suggest that severe malaria resistance trait is attributed to multiple genes, highlighting the possibility of harnessing new malaria therapeutics that can simultaneously target multiple malaria protective host molecular pathways.
Behavioral Attributes of Social Groups Determine the Strength and Direction of Selection on Neural Investment

The evolution of social systems can place novel selective forces on investment in expensive neural tissue by changing cognitive demands. Previous hypotheses about the impact of sociality on neural investment have received equivocal support when tested across diverse taxonomic groups and social structures. We suggest previous models for social behavior-brain relationships have overlooked important variation in social groups. Social groups vary significantly in structure and function, and the specific attributes of a social group may be more relevant to setting cognitive demands than sociality in general. We have identified intragroup competition, relationship differentiation, information sharing, dominance hierarchies, and task specialization and redundancy as attributes of social behavior which may impact selection for neural investment, and outline how variation in these attributes can result in increased or decreased neural investment with transitions to sociality in different taxa. Finally, we test some of the predictions generated using this framework in a phylogenetic comparison of neural tissue investment in Anelosimus social spiders. Social Anelosimus spiders engage in cooperative prey capture and brood care, which allows for individual redundancy in the completion of these tasks. We hypothesized that in social spider species, the presence of redundancy would reduce selection for individual neural investment relative to subsocial species. We found that social species had significantly decreased investment in the arcuate body, the cognitive center of the spider brain, supporting our predictions. Future comparative tests of brain evolution in social species should account for the special behavioral characteristics that accompany social groups in the subject taxa.
Plasma C-C Chemokine Concentrations in Intermediate Age-Related Macular Degeneration

Purpose: To determine the relationship between plasma concentrations of the C-C chemokines CCL2, CCL3, CCL4, and CCL5 and intermediate age-related macular degeneration (iAMD) patients compared with control inidividuals to further define the inflammatory pathways associated with age-related macular degeneration. Methods: The concentrations of CCL2, CCL3, CCL4, and CCL5 were measured using multiplex assays in plasma collected from 210 patients with iAMD and 102 control individuals with no macular degeneration as defined by multi-modal imaging. Non-inflammatory data included in the analysis were: age, sex, family history of AMD, history of smoking, body mass index, presence of reticular pseudo-drusen and cardiovascular disease. Median concentrations as well as a cutoff value for each chemokine were compared between the two groups. Results: The median concentrations of CCL2 and CCL4 did not differ between control and iAMD groups, however, CCL2 was elevated in iAMD when a cutoff comparison was used (p < 0.05). Median CCL3 and CCL5 concentrations were significantly decreased in the macular degeneration group compared with controls (p < 0.001) as well as when a cutoff value comparison was used. CCL3 and CCL5 were negatively correlated in cases and positively correlated in controls. Conclusions: Plasma CCL3 and CCL5 concentrations were significantly decreased and CCL2 concentrations were increased in patients with iAMD compared with controls, suggesting a role for C-C chemokines in the systemic inflammatory processes associated with disease development.