Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep Eutectic Solvent as Green Solvent in Extraction of Biological Macromolecules: A Review

Greater awareness of environmental sustainability has driven many industries to transition from using synthetic organic solvents to greener solvents in their manufacturing. Deep eutectic solvents (DESs) have emerged as a highly promising category of green solvents with well-demonstrated and wide-ranging applications, including their use as a solvent in extraction of small-molecule bioactive compounds for food and pharmaceutical applications. The use of DES as an extraction solvent of biological macromolecules, on the other hand, has not been as extensively studied. Thereby, the feasibility of employing DES for biomacromolecule extraction has not been well elucidated. To bridge this gap, this review provides an overview of DES with an emphasis on its unique physicochemical properties that make it an attractive green solvent (e.g., non-toxicity, biodegradability, ease of preparation, renewable, tailorable properties). Recent advances in DES extraction of three classes of biomacromolecules—i.e., proteins, carbohydrates, and lipids—were discussed and future research needs were identified. The importance of DES’s properties—particularly its viscosity, polarity, molar ratio of DES components, and water addition—on the DES extraction’s performance were discussed. Not unlike the findings from DES extraction of bioactive small molecules, DES extraction of biomacromolecules was concluded to be generally superior to extraction using synthetic organic solvents.
OsNAC016 regulates plant architecture and drought tolerance by interacting with the kinases GSK2 and SAPK8.

Ideal plant architecture and drought tolerance are important determinants of yield potential in rice (Oryza sativa). Here, we found that OsNAC016, a rice stress-responsive NAC transcription factor, functions as a regulator in the crosslink between BR-mediated plant architecture and ABA-regulated drought responses. The loss-of-function mutant osnac016 exhibited erect leaves and shortened internodes, but OsNAC016-overexpressing plants had opposite phenotypes. Further investigation revealed that OsNAC016 regulated the expression of the brassinosteroid biosynthesis gene D2 by binding to its promoter. Moreover, OsNAC016 interacted with and was phosphorylated by GSK3/SHAGGY-LIKE KINASE2 (GSK2), a negative regulator in the BR pathway. Meanwhile, the mutant osnac016 had improved drought stress tolerance, supported by a decreased water loss rate and enhanced stomatal closure in response to exogenous ABA, but OsNAC016-overexpressing plants showed attenuated drought tolerance and reduced ABA sensitivity. Further, OSMOTIC STRESS/ABA-ACTIVATED PROTEIN KINASE8 (SAPK8) phosphorylated OsNAC016 and reduced its stability. The ubiquitin/26S proteasome system is an important degradation pathway of OsNAC016 via the interaction with PLANT U-BOX PROTEIN43 (OsPUB43) that mediates the ubiquitination of OsNAC016. Notably, RNA-sequencing analysis revealed global roles of OsNAC016 in promoting BR-mediated gene expression and repressing ABA-dependent drought-responsive gene expression, which was confirmed by ChIP-qPCR analysis. Our findings establish that OsNAC016 is positively involved in BR-regulated rice architecture, negatively modulates ABA-mediated drought tolerance, and is regulated by GSK2, SAPK8, and OsPUB43 through post-translational modification. Our data provide insights into how plants balance growth and survival by coordinately regulating the growth-promoting signaling pathway and response under abiotic stresses.
Structural dynamics of receptor recognition and pH-induced dissociation of full-length Clostridioides difficile Toxin B

Clostridioides difficile secretes Toxin B (TcdB) as one of its major virulence factors, which binds to intestinal epithelial and subepithelial receptors, including frizzled proteins and chondroitin sulfate proteoglycan 4 (CSPG4). Here, we present cryo-EM structures of full-length TcdB in complex with the CSPG4 domain 1 fragment (D1401-560) at cytosolic pH and the cysteine-rich domain of frizzled-2 (CRD2) at both cytosolic and acidic pHs. CSPG4 specifically binds to the autoprocessing and delivery domains of TcdB via networks of salt bridges, hydrophobic and aromatic/proline interactions, which are disrupted upon acidification eventually leading to CSPG4 drastically dissociating from TcdB. In contrast, FZD2 moderately dissociates from TcdB under acidic pH, most likely due to its partial unfolding. These results reveal structural dynamics of TcdB during its preentry step upon endosomal acidification, which provide a basis for developing therapeutics against C. difficile infections.
Rapid Identification of Pollen- and Anther-Specific Genes in Response to High-Temperature Stress Based on Transcriptome Profiling Analysis in Cotton

Anther indehiscence and pollen sterility caused by high temperature (HT) stress have become a major problem that decreases the yield of cotton. Pollen- and anther-specific genes play a critical role in the process of male reproduction and the response to HT stress. In order to identify pollen-specific genes that respond to HT stress, a comparative transcriptome profiling analysis was performed in the pollen and anthers of Gossypium hirsutum HT-sensitive Line H05 against other tissue types under normal temperature (NT) conditions, and the analysis of a differentially expressed gene was conducted in the pollen of H05 under NT and HT conditions. In total, we identified 1111 pollen-specific genes (PSGs), 1066 anther-specific genes (ASGs), and 833 pollen differentially expressed genes (DEGs). Moreover, we found that the late stage of anther included more anther- and pollen-specific genes (APSGs). Stress-related cis-regulatory elements (CREs) and hormone-responsive CREs are enriched in the promoters of APSGs, suggesting that APSGs may respond to HT stress. However, 833 pollen DEGs had only 10 common genes with 1111 PSGs, indicating that PSGs are mainly involved in the processes of pollen development and do not respond to HT stress. Promoters of these 10 common genes are enriched for stress-related CREs and MeJA-responsive CREs, suggesting that these 10 common genes are involved in the process of pollen development while responding to HT stress. This study provides a pathway for rapidly identifying cotton pollen-specific genes that respond to HT stress.
A photovoice study on the meaning of life in widows

Abstract This study aimed to picture the experience of the meaning of life in widows by using a photovoice approach with thematic analysis. The participants involved were 10 widows living in West Timor, Indonesia. The results of the thematic analysis show that the meaning of life in widows relates to the following three themes: the spiritual meaning of life, risks of abuses and harassment, and supporting systems for widows. The photovoice approach managed to spark social change and improve community awareness on issues threatening widows' well-being.
SIDS in Saudi Arabia: Reality or Myth?

We conducted a study on sudden infant death syndrome (SIDS) in Saudi Arabia. SIDS affects nearly half of all post-neonatal deaths, particularly in Western countries, and relies on a thorough autopsy for a diagnosis of exclusion. The National Institute of Child Health and Human Development and SIDS International have developed an International Standardized Autopsy Protocol for infant death [1], and involve radio-logical, histological, toxicological, metabolic, molecular and microbiological testing, and internal and external examination. The prevalence and processes related to SIDS in the Middle East and the issue of autopsies, especially in children, is a sensitive issue for Muslim practitioners whose cultural and religious beliefs guide autopsy pro-tocols and influence conditions that permit autopsies. In this environment, the exact causes of infant death remain understudied. We collected data from the Ministry of Health of Saudi Arabia annual report obtained from the ministry’s open-source website [1] inclusively from 2011 to 2020. We found that no autopsies were performed on non-homicide patients. Suspicious autopsies conducted under the criminal code, which are mainly homicide or highly suspicious of homicide, were conducted at forensic medicine centers. No cases of SIDS could be verified. The question arises on how best to identify those cases most likely to represent SIDS in an environment where autopsies are not culturally accepted. The earliest research into infant mortality in Saudi Arabia occurred in the Qatif area and a prevalence rate for SIDS of 6.3% was reported in 1992 [2]. In contrast, in the rural areas of Riyadh, an absence of SIDS was reported but this was based on the mother’s ability to identify the condition [3]. A comprehensive study into factors responsible for SIDS made up of participants of mixed-age groups for 223 sudden-death cases reported that SIDS accounted for 32.2% of all deaths (72 cases). A high frequency was observed in males and infectious diseases were part of the reported cases [4].
Latency Aligning Task-Related Component Analysis Using Wave Propagation for Enhancing SSVEP-Based BCIs

Due to the high robustness to artifacts, steady-state visual evoked potential (SSVEP) has been widely applied to construct high-speed brain-computer interfaces (BCIs). Thus far, many spatial filtering methods have been proposed to enhance the target identification performance for SSVEP-based BCIs, and task-related component analysis (TRCA) is among the most effective ones. In this paper, we further extend TRCA and propose a new method called Latency Aligning TRCA (LA-TRCA), which aligns visual latencies on channels to obtain accurate phase information from task-related signals. Based on the SSVEP wave propagation theory, SSVEP spreads from posterior occipital areas over the cortex with a fixed phase velocity. Via estimation of the phase velocity using phase shifts of channels, the visual latencies on different channels can be determined for inter-channel alignment. TRCA is then applied to aligned data epochs for target recognition. For the validation purpose, the classification performance comparison between the proposed LA-TRCA and TRCA-based expansions were performed on two different SSVEP datasets. The experimental results illustrated that the proposed LA-TRCA method outperformed the other TRCA-based expansions, which thus demonstrated the effectiveness of the proposed approach for enhancing the SSVEP detection performance.
Re‐evaluation of missense variant classifications in NF2

Missense variants in the NF2 gene result in variable NF2 disease presentation. Clinical classification of missense variants often represents a challenge, due to lack of evidence for pathogenicity and function. This study provides a summary of NF2 missense variants, with variant classifications based on currently available evidence. NF2 missense variants were collated from pathology‐associated databases and existing literature. Association for Clinical Genomic Sciences Best Practice Guidelines (2020) were followed in the application of evidence for variant interpretation and classification. The majority of NF2 missense variants remain classified as variants of uncertain significance. However, NF2 missense variants identified in gnomAD occurred at a consistent rate across the gene, while variants compiled from pathology‐associated databases displayed differing rates of variation by exon of NF2. The highest rate of NF2 disease‐associated variants was observed in exon 7, while lower rates were observed toward the C‐terminus of the NF2 protein, merlin. Further phenotypic information associated with variants, alongside variant‐specific functional analysis, is necessary for more definitive variant interpretation. Our data identified differences in frequency of NF2 missense variants by exon between gnomAD population data and NF2 disease‐associated variants, suggesting a potential genotype‐phenotype correlation; further work is necessary to substantiate this.
Postoperative outcomes in surgical patients with obstructive sleep apnoea diagnosed by sleep studies: a meta‐analysis and trial sequential analysis

Identifying surgical patients with obstructive sleep apnoea may assist with anaesthetic management to minimise postoperative complications. Using trial sequential analysis, we evaluated the impact of obstructive sleep apnoea diagnosed by polysomnography or home sleep apnoea testing on postoperative outcomes in surgical patients. Multiple databases were systematically searched. Outcomes included: total postoperative complications, systemic complications (cardiovascular, respiratory, neurological, renal, infectious) and specific complications (atrial fibrillation, myocardial infarction, combined hospital and intensive care unit re‐admission, mortality). The pooled odds ratios of postoperative complications were evaluated by the Mantel–Haenszel method random‐effects model. Meta‐analysis and meta‐regression were conducted, and the GRADE approach was used to evaluate the certainty of evidence. Twenty prospective cohort studies with 3756 patients (2127 obstructive sleep apnoea and 1629 non‐obstructive sleep apnoea) were included (9 in non‐cardiac surgery and 11 in cardiac surgery). Postoperative complications were almost two‐fold higher with obstructive sleep apnoea, OR (95%CI) 1.92 (1.52–2.42), p < 0.001; certainty of evidence, moderate. Obstructive sleep apnoea was associated with a 1.5 times increased risk of postoperative cardiovascular complications, OR (95%CI) 1.56 (1.20–2.02), p = 0.001; certainty of evidence, moderate; an almost two‐fold increase in respiratory complications, OR (95%CI) 1.91 (1.39–2.62), p < 0.001; certainty of evidence, moderate; and hospital and ICU re‐admission, OR (95%CI) 2.25 (1.21–4.19), p = 0.01; certainty of evidence, low. Trial sequential analysis showed adequate information size for postoperative complications. Baseline confounding factors were adjusted by meta‐regression, and the sub‐group analysis did not materially change our results. This increased risk occurred especially in patients in whom obstructive sleep apnoea had been newly diagnosed, emphasising the importance of pre‐operative screening.
Xenogeneic nucleoid-associated EnrR thwarts H-NS silencing of bacterial virulence with unique DNA binding

Abstract Type III and type VI secretion systems (T3/T6SS) are encoded in horizontally acquired genomic islands (GIs) that play crucial roles in evolution and virulence in bacterial pathogens. T3/T6SS expression is subjected to tight control by the host xenogeneic silencer H-NS, but how this mechanism is counteracted remains to be illuminated. Here, we report that xenogeneic nucleoid-associated protein EnrR encoded in a GI is essential for virulence in pathogenic bacteria Edwardsiella and Salmonella. We showed that EnrR plays critical roles in T3/T6SS expression in these bacteria. Various biochemical and genetic analyses demonstrated that EnrR binds and derepresses the promoter of esrB, the critical regulator of T3/T6SS, to promote their expression by competing with H-NS. Additionally, EnrR targets AT-rich regions, globally modulates the expression of ∼363 genes and is involved in various cellular processes. Crystal structures of EnrR in complex with a specific AT-rich palindromic DNA revealed a new DNA-binding mode that involves conserved HTH-mediated interactions with the major groove and contacts of its N-terminal extension to the minor groove in the symmetry-related duplex. Collectively, these data demonstrate that EnrR is a virulence activator that can antagonize H-NS, highlighting a unique mechanism by which bacterial xenogeneic regulators recognize and regulate foreign DNA.
Predator-prey landscapes of large sharks and game fishes in the Florida Keys.

Interspecific interactions can play an essential role in shaping wildlife populations and communities. To date, assessments of interspecific interactions, and more specifically predator-prey dynamics, in aquatic systems over broad spatial and temporal scales (i.e., hundreds of km and multiple years) are rare due to constraints on our abilities to measure effectively at those scales. We applied new methods to identify space use overlap and potential predation risk to Atlantic tarpon (Megalops atlanticus) and permit (Trachinotus falcatus) from two known predators, great hammerhead (Sphyrna mokarran) and bull (Carcharhinus leucas) sharks over a three year period using acoustic telemetry in the coastal region of the Florida Keys (USA). By examining spatial-temporal overlap, as well as the timing and order of arrival at specific locations compared to random chance, we show that potential predation risk from great hammerhead and bull sharks to Atlantic tarpon and permit are heterogeneous across the Florida Keys. Additionally, we found that predator encounter rates with these game fishes are elevated at specific locations and times, including a pre-spawning aggregation site in the case of Atlantic tarpon. Further, using machine learning algorithms, we identify environmental variability in overlap between predators and their potential prey, including location, habitat, time of year, lunar cycle, depth, and water temperature. These predator-prey landscapes provide insights into fundamental ecosystem function and biological conservation, especially in the context of emerging fisheries-related depredation issues in coastal marine ecosystems.
Arrestin Facilitates Rhodopsin Dephosphorylation in Vivo

Deactivation of G-protein-coupled receptors (GPCRs) involves multiple phosphorylations followed by arrestin binding, which uncouples the GPCR from G-protein activation. Some GPCRs, such as rhodopsin, are reused many times. Arrestin dissociation and GPCR dephosphorylation are key steps in the recycling process. In vitro evidence suggests that visual arrestin (ARR1) binding to light-activated, phosphorylated rhodopsin hinders dephosphorylation. Whether ARR1 binding also affects rhodopsin dephosphorylation in vivo is not known. We investigated this using both male and female mice lacking ARR1. Mice were exposed to bright light and placed in darkness for different periods of time, and differently phosphorylated species of rhodopsin were assayed by isoelectric focusing. For WT mice, rhodopsin dephosphorylation was nearly complete by 1 h in darkness. Surprisingly, we observed that, in the Arr1 KO rods, rhodopsin remained phosphorylated even after 3 h. Delayed dephosphorylation in Arr1 KO rods cannot be explained by cell stress induced by persistent signaling, since it is not prevented by the removal of transducin, the visual G-protein, nor can it be explained by downregulation of protein phosphatase 2A, the putative rhodopsin phosphatase. We further show that cone arrestin (ARR4), which binds light-activated, phosphorylated rhodopsin poorly, had little effect in enhancing rhodopsin dephosphorylation, whereas mice expressing binding-competent mutant ARR1-3A showed a similar time course of rhodopsin dephosphorylation as WT. Together, these results reveal a novel role of ARR1 in facilitating rhodopsin dephosphorylation in vivo. SIGNIFICANCE STATEMENT G-protein-coupled receptors (GPCRs) are transmembrane proteins used by cells to receive and respond to a broad range of extracellular signals that include neurotransmitters, hormones, odorants, and light (photons). GPCR signaling is terminated by two sequential steps: phosphorylation and arrestin binding. Both steps must be reversed when GPCRs are recycled and reused. Dephosphorylation, which is required for recycling, is an understudied process. Using rhodopsin as a prototypical GPCR, we discovered that arrestin facilitated rhodopsin dephosphorylation in living mice.
An Investigation into the Design Parameters of Double Layer Space Frame Grids

A parametric study of the various factors affecting the design of double layer space frame grids is presented. This parametric study was conducted with the help of example structures and covered the support arrangement, the grid depth, the grid module and the grid layouts. The intent is to give the designer an idea about the effects of the choice of any of these parameters on the grid's behaviour and design requirements. This information should serve as a means for developing successful preliminary designs and as such reduce the need for many trials before the design is finalised.
Effects of aggressive predilatation, sizing, and postdilatation strategy for coronary bioresorbable vascular scaffolds implantation

Background: The results of the recent Amsterdam Investigator-Initiated Absorb Strategy All-Comers trial showed that the predilatation, sizing, and postdilatation (PSP) technique did not lower the long-term rates of scaffold thrombosis and adverse events. We evaluated the impact of aggressive PSP bioresorbable vascular scaffold (BRS) implantation on the short- and long-term clinical outcomes. Methods: From June 2014 to December 2016, 150 patients with BRS implantation were enrolled and received successful percutaneous coronary intervention (PCI), of whom 104 received aggressive PSP technique (high-pressure predilatation and lesion preparation in addition to the traditional PSP technique). Short- and long-term outcomes were compared. Results: All patients underwent successful PCI and BRS implantation with final Thrombolysis in Myocardial Infarction grade 3 flow. The baseline and procedure characteristics were similar in both groups. Debulking techniques were used in 13 (8.7%) patients. Intracoronary imaging modalities were used in 73 (48.7%) patients. After BRS implantation, no adverse events were observed within 30 days in both groups. During the mean follow-up period of 2.98 ± 0.77 years, 12 (8.0%) patients experienced major adverse cardiovascular events (MACEs), including one cardiovascular death (0.6%), three nonfatal myocardial infarction (2.0 %), and 11 target-vessel revascularization (7.3 %). Multivariate Cox regression analysis showed that aggressive PSP remained an independent protective factor for MACEs. Moreover, the use of intracoronary imaging and rotablation atherectomy was associated with better clinical outcomes. Conclusion: Lesion preparation by aggressive PSP in BRS implantation was associated with better long-term clinical outcomes.
Children of the Revolution: The Impact of 1960s and 1970s Cultural Identification on Baby Boomers’ Views on Retirement

There is widespread speculation that baby boomers will make significant changes to the retirement landscape. Some attribute these changes, at least in part, to countercultural movements this generation pioneered during the sixties and seventies. However, empirical investigation into the long-term impact of countercultural identification in youth is scarce. To address this, our study examines associations between baby boomers’ retirement views and identification with counterculture. Using data from 6024 pre-retired Dutch older workers, we investigate whether greater identification with counterculture is associated with more active retirement views. Our results show that greater identification with counterculture is associated with more active retirement views, even when controlling for potential confounders. Beyond highlighting the diversity of the baby boom generation, these findings support the idea that (counter)cultural identity in youth has an impact across the life course and may therefore have implications for other key questions of life’s third age beyond retirement.