Miracle-dz/UniFAR-FTUs huggingface dataset:
Predictors of Early and Late Infarct Growth in DEFUSE 3

Introduction: The goal of this study is to explore the impact of reperfusion and collateral status on infarct growth in the early and late time windows. Materials and Methods: Seventy patients from the DEFUSE 3 trial (Endovascular Therapy Following Imaging Evaluation for Ischemic Stroke) with baseline, 24-h, and late follow-up scans were evaluated. Scans were taken with DWI or CTP at time of enrollment (Baseline), with DWI or CT 24-h after enrollment (24-h), and with DWI or CT 5 days after enrollment (Late). Early infarct growth (between baseline and 24-h scans) and late infarct growth (between 24-h and late scans) was assessed for each patient. The impact of collateral and reperfusion status on infarct growth was assessed in univariate and multivariate regression. Results: The median early infarct growth was 30.3 ml (IQR 16.4–74.5) and the median late infarct growth was 6.7 ml (IQR −3.5–21.6) in the overall sample. Patients with poor collaterals showed greater early infarct growth (Median 58.5 ml; IQR 18.6–125.6) compared to patients with good collaterals (Median 28.4 ml; IQR 15.8–49.3, unadjusted p = 0.04, adjusted p = 0.06) but showed no difference in late infarct growth. In contrast, patients who reperfused showed no reduction in early infarct growth but showed reduced late infarct growth (Median 1.9 ml; IQR −6.1–8.5) compared to patients without reperfusion (Median 11.2 ml; IQR −1.1–27.2, unadjusted p < 0.01, adjusted p = 0.04). Discussion: In the DEFUSE 3 population, poor collaterals predict early infarct growth and absence of reperfusion predicts late infarct growth. These results highlight the need for timely reperfusion therapy, particularly in patients with poor collaterals and indicate that the 24-h timepoint is too early to assess the full impact of reperfusion therapy on infarct growth. Clinical Trial Registration: http://www.clinicaltrials. gov, Unique identifier [NCT02586415].
Edging on Mutational Bias, Induced Natural Selection From Host and Natural Reservoirs Predominates Codon Usage Evolution in Hantaan Virus

The molecular evolutionary dynamics that shape hantaviruses’ evolution are poorly understood even now, besides the contribution of virus-host interaction to their evolution remains an open question. Our study aimed to investigate these two aspects in Hantaan virus (HTNV)—the prototype of hantaviruses and an emerging zoonotic pathogen that infects humans, causing hemorrhagic fever with renal syndrome (HFRS): endemic in Far East Russia, China, and South Korea—via a comprehensive, phylogenetic-dependent codon usage analysis. We found that host- and natural reservoir-induced natural selection is the primary determinant of its biased codon choices, exceeding the mutational bias effect. The phylogenetic analysis of HTNV strains resulted in three distinct clades: South Korean, Russian, and Chinese. An effective number of codon (ENC) analysis showed a slightly biased codon usage in HTNV genomes. Nucleotide composition and RSCU analyses revealed a significant bias toward A/U nucleotides and A/U-ended codons, indicating the potential influence of mutational bias on the codon usage patterns of HTNV. Via ENC-plot, Parity Rule 2 (PR2), and neutrality plot analyses, we would conclude the presence of both mutation pressure and natural selection effect in shaping the codon usage patterns of HTNV; however, natural selection is the dominant factor influencing its codon usage bias. Codon adaptation index (CAI), Relative codon deoptimization index (RCDI), and Similarity Index (SiD) analyses uncovered the intense selection pressure from the host (Human) and natural reservoirs (Striped field mouse and Chinese white-bellied rat) in shaping HTNV biased codon choices. Our study clearly revealed the evolutionary processes in HTNV and the role of virus-host interaction in its evolution. Moreover, it opens the door for a more comprehensive codon usage analysis for all hantaviruses species to determine their molecular evolutionary dynamics and adaptability to several hosts and environments. We believe that our research will help in a better and deep understanding of HTNV evolution that will serve its future basic research and aid live attenuated vaccines design.
Comprehensive Transcriptomic Analysis Reveals the Role of the Immune Checkpoint HLA-G Molecule in Cancers

Human leukocyte antigen G (HLA-G) is known as a novel immune checkpoint molecule in cancer; thus, HLA-G and its receptors might be targets for immune checkpoint blockade in cancer immunotherapy. The aim of this study was to systematically identify the roles of checkpoint HLA-G molecules across various types of cancer. ONCOMINE, GEPIA, CCLE, TRRUST, HAP, PrognoScan, Kaplan-Meier Plotter, cBioPortal, LinkedOmics, STRING, GeneMANIA, DAVID, TIMER, and CIBERSORT were utilized. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. In this study, we comprehensively analysed the heterogeneous expression of HLA-G molecules in various types of cancer and focused on genetic alterations, coexpression patterns, gene interaction networks, HLA-G interactors, and the relationships between HLA-G and pathological stage, prognosis, and tumor-infiltrating immune cells. We first identified that the mRNA expression levels of HLA-G were significantly upregulated in both most tumor tissues and tumor cell lines on the basis of in-depth analysis of RNAseq data. The expression levels of HLA-G were positively associated with those of the other immune checkpoints PD-1 and CTLA-4. Abnormal expression of HLA-G was significantly correlated with the pathological stage of some but not all tumor types. There was a significant difference between the high and low HLA-G expression groups in terms of overall survival (OS) or disease-free survival (DFS). The results showed that HLA-G highly expressed have positive associations with tumor-infiltrating immune cells in the microenvironment in most types of tumors (P<0.05). Additionally, we identified the key transcription factor (TF) targets in the regulation of HLA-G expression, including HIVEP2, MYCN, CIITA, MYC, and IRF1. Multiple mutations (missense, truncating, etc.) and the methylation status of the HLA-G gene may explain the differential expression of HLA-G across different tumors. Functional enrichment analysis showed that HLA-G was primarily related to T cell activation, T cell regulation, and lymphocyte-mediated immunity. The data may provide novel insights for blockade of the HLA-G/ILT axis, which holds potential for the development of more effective antitumour treatments.
Broad-Scale Responses of Harbor Porpoises to Pile-Driving and Vessel Activities During Offshore Windfarm Construction

Offshore windfarm developments are expanding, requiring assessment and mitigation of impacts on protected species. Typically, assessments of impacts on marine mammals have focused on pile-driving, as intense impulsive noise elicits adverse behavioral responses. However, other construction activities such as jacket and turbine installation also change acoustic habitats through increased vessel activity. To date, the contribution of construction-related vessel activity in shaping marine mammal behavioral responses at windfarm construction sites has been overlooked and no guidelines or mitigation measures have been implemented. We compared broad-scale spatio-temporal variation in harbor porpoise occurrence and foraging activity between baseline periods and different construction phases at two Scottish offshore windfarms. Following a Before-After Control-Impact design, arrays of echolocation click detectors (CPODs) were deployed in 25 km by 25 km impact and reference blocks throughout the 2017–2019 construction. Echolocation clicks and buzzes were used to investigate porpoise occurrence and foraging activity, respectively. In parallel, we characterized broadband noise levels using calibrated noise recorders (SoundTraps and SM2Ms) and vessel activities using AIS data integrated with engineering records. Following an impact gradient design, we then quantified the magnitude of porpoise responses in relation to changes in the acoustic environment and vessel activity. Compared to baseline, an 8–17% decline in porpoise occurrence was observed in the impact block during pile-driving and other construction activities. The probability of detecting porpoises and buzzing activity was positively related to the distance from vessel and construction activities, and negatively related to levels of vessel intensity and background noise. Porpoise displacement was observed at up to 12 km from pile-driving activities and up to 4 km from construction vessels. This evidence of broad-scale behavioral responses of harbor porpoises to these different construction activities highlights the importance of assessing and managing all vessel activities at offshore windfarm sites to minimize potential impacts of anthropogenic noise.
Drought and Nitrogen Application Modulate the Morphological and Physiological Responses of Dalbergia odorifera to Different Niche Neighbors

Mixed stands can be more productive if growth facilitation via niche segregation occurs. Dalbergia odorifera T. Chen, a tropical tree species endemic to Hainan Island with great economic values, belongs to the family Leguminosae. However, selecting mixed species with suitable ecological niches to efficiently construct mixed forests of D. odorifera in the context of abiotic stress [drought, nitrogen (N) deposition] remained obscure. In the present study, the target plant D. odorifera was planted with the same species D. odorifera, heterogeneous but the same family Delonix regia and non-Leguminous Family Swietenia mahagoni in the root interaction and isolated models under two watering regimes [100% and 30% field capacity (FC)] and two N applications (application, non-application), respectively. Principle component analysis based on the performances of growth, phenotype, and physiology was performed to identify the main factors affected by the treatments and the most discriminatory effects of water, N level, and species interaction models. Both comprehensive evaluation values and comprehensive index values were calculated to evaluate the influences of different niche neighbors on D. odorifera. Results showed that D. odorifera was benefited from S. mahagoni but inhibited from D. odorifera in all treatments under root system interaction. Drought stress aggravated the inhibitory effects on D. odorifera from D. odorifera. N application stimulated the promoted effects on D. odorifera from S. mahagoni but enhanced competition intensity of D. odorifera from D. regia under the 100% FC condition. N application alleviated the inhibitory effect of drought stress on D. odorifera from D. odorifera and S. mahagoni. Furthermore, the responses of D. odorifera to different niche neighbors were dominated by belowground interaction rather than the negligible aboveground one. Therefore, the feasibility of niche segregation as the criterion for selecting neighbors to construct D. odorifera mixed stands was confirmed. In addition, water level and N application could alter responses of D. odorifera to different niche neighbors under the root system interaction. Appropriate N application could alleviate the inhibitory effect of drought stress on D. odorifera in its mixed forests. A mixture with S. mahagoni under appropriate N application could be the optimal planting model.
The Role of High-Content Complex Dietary Fiber in Medical Nutrition Therapy for Gestational Diabetes Mellitus

Objectives: A controlled open clinical study was conducted to evaluate the role of Ricnoat, a high-content complex dietary fiber powder produced by Zhuhai Aimed Biotechnology Co. Ltd., in medical nutrition therapy (MNT) to treat gestational diabetes mellitus (GDM). The study aimed to investigate glycemic control, lipid control, weight control, and pregnancy outcomes (neonatal weight) in patients with GDM, as well as evaluate the clinical safety of Ricnoat. Methods: A total of 120 patients with GDM who were admitted to three hospitals in Shanghai between January 2019 and January 2020 were enrolled. Ricnoat was used for intervention for patients in the experimental group. Using a χ2 test and t-test, respectively, comparisons were conducted between the measurement data and countable data of the demographics and baseline disease characteristics of the experimental group and control group. Results: Fasting blood glucose, 2-h postprandial blood glucose, glycated hemoglobin, total cholesterol, triglycerides, low-density lipoprotein, maternal gestational weight gain, neonatal weight, serum creatinine, glutamate transaminase, and aspartate aminotransferase were lower in the experimental group than in the control group, whereas high-density lipoprotein was higher in the experimental group than in the control group. Ricnoat intervention resulted in satiety higher than the expected 80% and more common occurrence of type 4 (smooth and soft, like salami or a snake) and type 5 (a soft mass with clear edges) stools. Conclusion: Ricnoat intervention had a significant effect on glycemic control, lipid control, weight control, and pregnancy outcomes (neonatal weight) in patients with GDM by enhancing maternal satiety and improving the stool features of pregnant women. It was also found to be safe for application during pregnancy.
Supporting Spatial Management of Data-Poor, Small-Scale Fisheries With a Bayesian Approach

Marine conservation areas are an important tool for the sustainable management of multispecies, small-scale fisheries. Effective spatial management requires a proper understanding of the spatial distribution of target species and the identification of its environmental drivers. Small-scale fisheries, however, often face scarcity and low-quality of data. In these situations, approaches for the prioritization of conservation areas need to deal with scattered, biased, and short-term information and ideally should quantify data- and model-specific uncertainties for a better understanding of the risks related to management interventions. We used a Bayesian hierarchical species distribution modeling approach on annual landing data of the heavily exploited, small-scale, and data-poor fishery of Chwaka Bay (Zanzibar) in the Western Indian Ocean to understand the distribution of the key target species and identify potential areas for conservation. Few commonalities were found in the set of important habitat and environmental drivers among species, but temperature, depth, and seagrass cover affected the spatial distribution of three of the six analyzed species. A comparison of our results with information from ecological studies suggests that our approach predicts the distribution of the analyzed species reasonably well. Furthermore, the two main common areas of high relative abundance identified in our study have been previously suggested by the local fisher as important areas for spatial conservation. By using short-term, catch per unit of effort data in a Bayesian hierarchical framework, we quantify the associated uncertainties while accounting for spatial dependencies. More importantly, the use of accessible and interpretable tools, such as the here created spatial maps, can frame a better understanding of spatio-temporal management for local fishers. Our approach, thus, supports the operability of spatial management in small-scale fisheries suffering from a general lack of long-term fisheries information and fisheries independent data.
Report of the Largest Chinese Cohort With SLC19A3 Gene Defect and Literature Review

Thiamine metabolism dysfunction syndrome 2 (THMD2) is a rare metabolic disorder caused by SLC19A3 mutations, inherited in autosomal recessive pattern. As a treatable disease, early diagnosis and therapy with vitamin supplementation is important to improve the prognosis. So far, the reported cases were mainly from Saudi Arab regions, and presented with relatively simple clinical course because of the hot spot mutation (T422A). Rare Chinese cases were described until now. In this study, we investigated 18 Chinese THMD2 patients with variable phenotypes, and identified 23 novel SLC19A3 mutations, which expanded the genetic and clinical spectrum of the disorder. Meanwhile, we reviewed all 146 reported patients from different countries. Approximately 2/3 of patients presented with classical BTBGD, while 1/3 of patients manifested as much earlier onset and poor prognosis, including infantile Leigh-like syndrome, infantile spasms, neonatal lactic acidosis and infantile BTBGD. Literature review showed that elevated lactate in blood and CSF, as well as abnormal OXPHOS activities of muscle or skin usually correlated with infantile phenotypes, which indicated poor outcome. Brainstem involvement on MRI was more common in deceased cases. Thiamine supplementation is indispensable in the treatment of THMD2, whereas combination of biotin and thiamine is not superior to thiamine alone. But biotin supplementation does work in some patients. Genotypic-phenotypic correlation remains unclear which needs further investigation, and biallelic truncated mutations usually led to more severe phenotype.
Whole Genome-Based Characterization of Listeria monocytogenes Isolates Recovered From the Food Chain in South Africa

Listeria monocytogenes is an important foodborne pathogen which has the ability to adapt and survive in food and food processing facilities where it can persist for years. In this study, a total of 143 L. monocytogenes isolates in South Africa (SA) were characterized for their strain’s genetic relatedness, virulence profiles, stress tolerance and resistance genes associated with L. monocytogenes. The Core Genome Multilocus Sequence Typing (cgMLST) analysis revealed that the most frequent serogroups were IVb and IIa; Sequence Types (ST) were ST204, ST2, and ST1; and Clonal Complexes (CC) were CC204, CC1, and CC2. Examination of genes involved in adaptation and survival of L. monocytogenes in SA showed that ST1, ST2, ST121, ST204, and ST321 are well adapted in food processing environments due to the significant over-representation of Benzalkonium chloride (BC) resistance genes (bcrABC cassette, ermC, mdrL and Ide), stress tolerance genes (SSI-1 and SSI-2), Prophage (φ) profiles (LP_101, vB LmoS 188, vB_LmoS_293, and B054 phage), plasmids profiles (N1-011A, J1776, and pLM5578) and biofilm formation associated genes. Furthermore, the L. monocytogenes strains that showed hyper-virulent potential were ST1, ST2 and ST204, and hypo-virulent were ST121 and ST321 because of the presence and absence of major virulence factors such as LIPI-1, LIPI-3, LIPI-4 and the internalin gene family members including inlABCEFJ. The information provided in this study revealed that hyper-virulent strains ST1, ST2, and ST204 could present a major public health risk due to their association with meat products and food processing environments in SA.
Potential and Pitfalls of Digital Voice Assistants in Older Adults With and Without Intellectual Disabilities: Relevance of Participatory Design Elements and Ecologically Valid Field Studies

Citation: Schlomann A, Wahl H-W, Zentel P, Heyl V, Knapp L, Opfermann C, Krämer T and Rietz C (2021) Potential and Pitfalls of Digital Voice Assistants in Older Adults With and Without Intellectual Disabilities: Relevance of Participatory Design Elements and Ecologically Valid Field Studies. Front. Psychol. 12:684012. doi: 10.3389/fpsyg.2021. 684012 Potential and Pitfalls of Digital Voice Assistants in Older Adults With and Without Intellectual Disabilities: Relevance of Participatory Design Elements and Ecologically Valid Field Studies
Rapidoxy® 100: A Solvent-Free Pre-treatment for Production of Canolol

RapidOxy® 100 is an automated instrument originally designed for measuring the oxidative stability of both solid and liquid samples. The compact and portable design of RapidOxy® 100, and its built-in pressurized heating chamber, provides a suitable environment for studying processing conditions. The feasibility of using oxygen or an inert atmosphere provides the ideal environment to study the effect of dry heat pre-treatment on canola antioxidants. The current study used RapidOxy® 100 to examine the impact of pressurized dry heat pre-treatment, under nitrogen, on the ultrasonic extraction of phenolic compounds. The effect of different pre-treatment temperature-time combinations of 120, 140, 160, and 180°C for 2, 5, 10, 15, and 20 min on the subsequent extraction of canola phenolic compounds was examined. The major sinapates identified by HPLC were sinapine, sinapic acid, and canolol. The optimum RapidOxy® condition for the maximum recovery of canolol was 160°C for 10 min. RapidOxy® 100 proved to be a novel and versatile instrument for enhancing the extraction of phenolic compounds.
Systems and Circuits Linking Chronic Pain and Circadian Rhythms

Research over the last 20 years regarding the link between circadian rhythms and chronic pain pathology has suggested interconnected mechanisms that are not fully understood. Strong evidence for a bidirectional relationship between circadian function and pain has been revealed through inflammatory and immune studies as well as neuropathic ones. However, one limitation of many of these studies is a focus on only a few molecules or cell types, often within only one region of the brain or spinal cord, rather than systems-level interactions. To address this, our review will examine the circadian system as a whole, from the intracellular genetic machinery that controls its timing mechanism to its input and output circuits, and how chronic pain, whether inflammatory or neuropathic, may mediate or be driven by changes in these processes. We will investigate how rhythms of circadian clock gene expression and behavior, immune cells, cytokines, chemokines, intracellular signaling, and glial cells affect and are affected by chronic pain in animal models and human pathologies. We will also discuss key areas in both circadian rhythms and chronic pain that are sexually dimorphic. Understanding the overlapping mechanisms and complex interplay between pain and circadian mediators, the various nuclei they affect, and how they differ between sexes, will be crucial to move forward in developing treatments for chronic pain and for determining how and when they will achieve their maximum efficacy.
Effect of Aerobic Exercise on White Matter Tract Microstructure in Young and Middle-Aged Healthy Adults

Recent evidence suggests that being physically active can mitigate age-related white matter (WM) changes. In a randomized clinical trial, the effect of 6-month aerobic exercise (AE) or stretching/toning interventions on measures of WM microstructure (WMM) was assessed in a sample of 74 adults aged 20–67 years. Major WM pathways were reconstructed. No significant group-level change in WM tract microstructure following an AE training was observed. Without adjustment for multiple comparisons, an increase in fractional anisotropy (FA) and a decrease in mean diffusivity (MD) of the uncinate fasciculus were observed post-intervention in the AE group in comparison with the stretching group. In the AE group, a significant increase in cardiorespiratory fitness was measured but did not correlate with FA and MD change. The present results of this study are in accordance with similar studies in healthy adults that did not show significant benefit on WMM after participating in an AE program. Clinical Trial Registration: Clinicaltrials.gov identifier, NCT01179958.