Miracle-dz/UniFAR-FTUs huggingface dataset:
Determination of Chitin Content in Insects: An Alternate Method Based on Calcofluor Staining

Chitin is an aminopolysaccharide present in yeast cells and arthropod cuticle and is one of the most abundant biopolymers. The conventional methods for the quantitation of chitin content in biological samples are based on its hydrolysis (acid or enzymatic), and the assessment of the byproduct, glucosamine. However, previously described methodologies are time-consuming, laborious, low throughput, and not applicable to insect samples in many cases. Here we describe a new approach to chitin content quantitation based on calcofluor fluorescent brightener staining of samples, followed by microplate fluorescence readings. Calcofluor is a specific chitin stain commonly used for topological localization of the polymer. The protocol was tested in three important disease vector species, namely Lutzomyia longipalpis, Aedes aegypti, and Rhodnius prolixus, and then compared to a classic colorimetric chitin assessment method. Results show that chitin content in the tested insects can vary largely in a range of 8–4600 micrograms of chitin per insect, depending on species, sex, and instar. Comparisons between measurements from the previous protocol and calcofluor method showed statistically significant differences in some samples. However, the difference might be due to interference in the classic method from non-chitin sources of glucosamine and reducing agents. Furthermore, chitinase hydrolysis reduces the total chitin mass estimated between 36 and 74%, consolidating the fluorescent measurements as actual stained chitin in the same extent that was observed with the standard protocol. Therefore, the calcofluor staining method revealed to be a fast and reliable technique for chitin quantitation in homogenized insect samples.
Why Are There so Many Plant Species That Transiently Flush Young Leaves Red in the Tropics?

Delayed greening of young leaves is a ubiquitous and visually striking phenomenon in the tropics. Here, we investigated the potential ecological functions of red coloration patterns in young leaves. To detect any protective function of the red coloration on the young leaves, leaf damage by insect herbivores was recorded in the field. To determine capacity for chemical defense, the concentrations of tannins and anthocyanins were measured in both young and mature leaves. To test the hypothesis that anthocyanins function as photo-protective molecules, chlorophyll content, maximum photochemical efficiency of PSII (F v /Fm ), non-photochemical quenching (NPQ), and effective quantum yield of PSII (ΦPSII ) were measured in the field. Phylogenetic relationships were analyzed to test the relationary significance of the occurrence of redness in young leaves. Compared to the coloration in non-red leaves, young red leaves had significant higher anthocyanins and tannins content and lower herbivore damages. Young, red leaves had the lowest Fv /Fm values, which were significantly lower than those of non-red leaves. NPQ values in young red leaves were comparable to those of other groups. Although young red leaves had high ΦPSII , these values were significantly lower than those of the other three groups. The results suggest that the red coloration of young leaves protects them from insect herbivory primary by chemical defense through high concentrations of tannins and anthocyanins. Additionally, low Fv /Fm values in young red leaves indicate that anthocyanins might not be functioning as light attenuators to compensate for insufficient photo-protection mediated by NPQ. And finally, red coloration in young leaves is predominantly a result of adaptation to heavy herbivory stress but without significant intrinsic phylogenetic relationship of plant species.
Reduction of Onset Delay in Functional Near-Infrared Spectroscopy: Prediction of HbO/HbR Signals

An intrinsic problem when using hemodynamic responses for the brain-machine interface is the slow nature of the physiological process. In this paper, a novel method that estimates the oxyhemoglobin changes caused by neuronal activations is proposed and validated. In monitoring the time responses of blood-oxygen-level-dependent signals with functional near-infrared spectroscopy (fNIRS), the early trajectories of both oxy- and deoxy-hemoglobins in their phase space are scrutinized. Furthermore, to reduce the detection time, a prediction method based upon a kernel-based recursive least squares (KRLS) algorithm is implemented. In validating the proposed approach, the fNIRS signals of finger tapping tasks measured from the left motor cortex are examined. The results show that the KRLS algorithm using the Gaussian kernel yields the best fitting for both ΔHbO (i.e., 87.5%) and ΔHbR (i.e., 85.2%) at q = 15 steps ahead (i.e., 1.63 s ahead at a sampling frequency of 9.19 Hz). This concludes that a neuronal activation can be concluded in about 0.1 s with fNIRS using prediction, which enables an almost real-time practice if combined with EEG.
Comparative Transcriptomics Analysis of the Responses of the Filamentous Fungus Glarea lozoyensis to Different Carbon Sources

The natural product pneumocandin B0 is the precursor of the antifungal drug caspofungin. We found that replacing glucose in the initial fermentation medium with 20 g/L fructose is more conducive to pneumocandin B0 production and biomass accumulation. In order to explore the mechanism of the different metabolic responses to fructose and glucose, we used each as the sole carbon source, and the results showed that fructose increased the total pneumocandin B0 yield and biomass by 54.76 and 13.71%, respectively. Furthermore, we analyzed the differences of gene expression and metabolic pathways between the two different carbon sources by transcriptomic analysis. When fructose was used as the carbon source, genes related to the pentose phosphate pathway (PPP), glycolysis and branched-chain amino acid metabolism were significantly upregulated, resulting in increased intracellular pools of NADPH and acetyl-CoA in Glarea lozoyensis for cell growth and pneumocandin B0 product synthesis. Interestingly, the pneumocandin B0 biosynthetic gene cluster and the genes of the TCA cycle were significantly downregulated, while the FAS genes were significantly upregulated, indicating that more acetyl-CoA was used for fatty acid synthesis. In particular, we found that excessive synthesis of fatty acids caused lipid accumulation, and lipid droplets can sequester lipophilic secondary metabolites such as pneumocandin B0 to reduce cell damage, which may also be an important reason for the observed increase of pneumocandin B0 yield. These results provide new insights into the relationship between pneumocandin B0 biosynthesis and carbon sources in G. lozoyensis. At the same time, this study provides important genomic information for improving pneumocandin B0 production through metabolic engineering strategies in the future.
Identification of Multigene Biomarker for Shrimp White Feces Syndrome by Full-Length Transcriptome Sequencing

The pacific white shrimp, Litopenaeus vannamei, with the largest shrimp industry production in the world, is currently threatened by a severe disease, white feces syndrome (WFS), which cause devastating losses globally, while its causal agents remain largely unknown. Herein, compared to the Control shrimp by metagenomic analysis, we firstly investigated that the altered functions of intestinal microbial community in WFS shrimp were the enrichment of bacterial chemotaxis and flagellar assembly pathways, hinting at a potential role of pathogenic bacteria for growth and development, which might be related to WFS occurrence. Single-molecule real-time (SMRT) sequencing was to further identify the gene structure and gene regulation for more clues in WFS aetiology. Totally 50,049 high quality transcripts were obtained, capturing 39,995 previously mapped and 10,054 newly detected transcripts, which were annotated to 30,554 genes. A total of 158 differentially expressed genes (DEGs) were characterized in WFS shrimp. These DEGs were strongly associated with various immune related genes that regulated the expression of multiple antimicrobial peptides (e.g., antilipopolysaccharide factors, penaeidins, and crustin), which were further experimentally validated using quantitative PCR on transcript level. Collectively, multigene biomarkers were identified to be closely associated with WFS, especially those functional alterations in microbial community and the upregulated immune related gene with antibacterial activities. Our finding not only inspired our cogitation on WFS aetiology from both microbial and host immune response perspectives with combined metagenomic and full-length transcriptome sequencing, but also provided valuable information for enhancing shrimp aquaculture.
Influence of Estrogen on the NSCLC Microenvironment: A Comprehensive Picture and Clinical Implications

Lung cancer mortality represents the leading cause of cancer related deaths in the United States and worldwide. Almost half of these deaths occur in female patients, making lung cancer the most common cause of cancer mortality in women with a higher annual mortality rate than breast, uterine, and ovarian cancers combined. The distinct epidemiological, histological and biological presentation of non-small cell lung cancer (NSCLC) in women combined with extensive preclinical data have demonstrated that the female sex hormone β-estradiol (E2) plays an important role in NSCLC tumorigenesis, prognosis, and treatment response. Estrogen receptors are widely expressed on stromal and immune cells, and estrogen-linked signaling pathways are known to be involved in regulating the response of both the innate and adaptive immune system. Immune evasion has been recognized as a “hallmark” of cancer and immunotherapy has re-defined standard of care treatment for NSCLC. Despite these advancements, the low response rates observed in patients treated with immune checkpoint inhibitors has led to a search for mediators of immunosuppression and ways to augment the action of these agents. We focus on emerging data describing sex differences that modulate immunotherapy efficacy in NSCLC, immunosuppressive properties of E2 that lead to a pro-tumor microenvironment (TME), and the translational potential of altering the immune microenvironment by targeting the estrogen signaling pathway. E2-induced modulation affects multiple cell types within the TME, including cancer-associated fibroblasts, tumor infiltrating myeloid cells, and tumor infiltrating lymphocytes, all of which interplay with lung tumor cells via E2 and estrogen receptor engagement, ultimately shaping the TME that may, in part, be responsible for the sex-based disparities observed in NSCLC. An improved understanding of the role of the estrogen pathway in NSCLC anti-cancer immunity may lead to novel therapeutic approaches for altering the TME to improve the efficacy of immunotherapy agents.
PbGA20ox2 Regulates Fruit Set and Induces Parthenocarpy by Enhancing GA4 Content

Fruit set and development occur following successful fertilization. Parthenocarpy, a valuable trait in some self-incompatible species, produces seedless fruit without fertilization. Gibberellin (GA) is a crucial hormone in fruit-set regulation and development. While investigating the development of parthenocarpy in pear (Pyrus bretschneideri Rehd.), we determined that GA 20-oxidases (GA20ox) may play key roles in seedless pear fruit development. Sequence analysis revealed three PbGA20ox genes: PbGA20ox1, PbGA20ox2, and PbGA20ox3. We analyzed the expression patterns of candidate genes and found that PbGA20ox2 levels significantly changed in pollinated fruits. Tissue-specific expression assays revealed that PbGA20ox2 is highly expressed in young fruit and leaves. Subcellular localization assays showed it was located in the cytoplasm, nucleus, and plasma membrane. Overexpressed PbGA20ox2 tomato plants were taller and had longer hypocotyls and internodes, and the emasculated flowers produced parthenocarpic fruit. In pear, the transient overexpression of PbGA20ox2 promoted fruit development and delayed the drop of nonpollinated fruit. Furthermore, the fruit of PbGA20ox2-overexpressing tomato and transient PbGA20ox2-overexpressing pear had increased GA4 (but not GA3 and GA1) contents. This result provided evidence that PbGA20ox2 was necessary for GA4-dependent pear fruit development. Our study revealed that PbGA20ox2 altered the GA biosynthetic pathway and enhanced GA4 synthesis, thereby promoting fruit set and parthenocarpic fruit development.
Lay Theories About Whether Emotion Helps or Hinders: Assessment and Effects on Emotional Acceptance and Recovery From Distress

This investigation examined how people’s beliefs about the functionality of emotion shape their emotional response and regulatory strategies when encountering distressing events. In Study 1, we present data supporting the reliability and validity of an 8-item instrument, the Help and Hinder Theories about Emotion Measure (HHTEM), designed to assess an individual’s beliefs about the functionality of emotion. Participants who more strongly endorsed a Help Theory reported greater wellbeing, emotional acceptance, and use of reappraisal to regulate emotion. Participants who more strongly endorsed a Hinder Theory reported less wellbeing and more expressive suppression and substance use. In Study 2, we demonstrate that encouraging participants to view emotion as helpful affected their physiological and regulatory response to a distressing event. Participants in the Help Theory condition showed greater physiological reactivity (SCL) during a distressing film than control participants but were more accepting of their emotional response. Shortly after the film, SCL decreased for participants in the Help Theory condition. Compared to control participants, they engaged in less suppression and reported less lingering effect of the film on their mood. Together, these studies suggest that people’s theories about the functionality of emotion influence their reactivity, the strategies they adopt to regulate emotion, and their ability to rebound after distressing events.
Design and Performance Evaluation of a Novel Wearable Parallel Mechanism for Ankle Rehabilitation

Repetitive and intensive physiotherapy is indispensable to patients with ankle disabilities. Increasingly robot-assisted technology has been employed in the treatment to reduce the burden of the therapists and the related costs of the patients. This paper proposes a configuration of a wearable parallel mechanism to supplement the equipment selection for ankle rehabilitation. The kinematic analysis, i.e., the inverse position solution and Jacobian matrices, is elaborated. Several performance indices, including the reachable workspace index, motion isotropy index, force transfer index, and maximum torque index, are developed based on the derived kinematic solution. Moreover, according to the proposed kinematic configuration and wearable design concept, the mechanical structure that contains a basic machine-drive system and a multi-model position/force data collection system is designed in detail. Finally, the results of the performance evaluation indicate that the wearable parallel robot possesses sufficient motion isotropy, high force transfer performance, and large maximum torque performance within a large workspace that can cover all possible range of motion of human ankle complex, and is suitable for ankle rehabilitation.
A Method for Producing Highly Pure Magnetosomes in Large Quantity for Medical Applications Using Magnetospirillum gryphiswaldense MSR-1 Magnetotactic Bacteria Amplified in Minimal Growth Media

We report the synthesis in large quantity of highly pure magnetosomes for medical applications. For that, magnetosomes are produced by MSR-1 Magnetospirillum gryphiswaldense magnetotactic bacteria using minimal growth media devoid of uncharacterized and toxic products prohibited by pharmaceutical regulation, i.e., yeast extract, heavy metals different from iron, and carcinogenic, mutagenic and reprotoxic agents. This method follows two steps, during which bacteria are first pre-amplified without producing magnetosomes and are then fed with an iron source to synthesize magnetosomes, yielding, after 50 h of growth, an equivalent OD565 of ~8 and 10 mg of magnetosomes in iron per liter of growth media. Compared with magnetosomes produced in non-minimal growth media, those particles have lower concentrations in metals other than iron. Very significant reduction or disappearance in magnetosome composition of zinc, manganese, barium, and aluminum are observed. This new synthesis method paves the way towards the production of magnetosomes for medical applications.
Functional Integration and Segregation in Multiplex Brain Networks for Alzheimer's Disease

Growing evidence links impairment of brain functions in Alzheimer's disease (AD) with disruptions of brain functional connectivity. However, whether the AD brain shows similar changes from a dynamic or cross-frequency view remains poorly explored. This paper provides an effective framework to investigate the properties of multiplex brain networks in AD considering inter-frequency and temporal dynamics. Using resting-state EEG signals, two types of multiplex networks were reconstructed separately considering the network interactions between different frequency bands or time points. We further applied multiplex network features to characterize functional integration and segregation of the cross-frequency or time-varying networks. Finally, machine learning methods were employed to evaluate the performance of multiplex-network-based indexes for detection of AD. Results revealed that the brain networks of AD patients are disrupted with reduced segregation particularly in the left occipital area for both cross-frequency and time-varying networks. However, the alteration of integration differs among brain regions and may show an increasing trend in the frontal area of AD brain. By combining the features of integration and segregation in time-varying networks, the best classification performance was achieved with an accuracy of 92.5%. These findings suggest that our multiplex framework can be applied to explore functional integration and segregation of brain networks and characterize the abnormalities of brain function. This may shed new light on the brain network analysis and extend our understanding of brain function in patients with neurological diseases.
Holding space and transitional space: stroke survivors’ lived experience of being on an acute stroke unit. A hermeneutic phenomenological study

Despite substantial reorganisation of stroke unit provision in the United Kingdom, limited qualitative research has explored how stroke survivors experience the acute stroke unit. This hermeneutic phenomenological study used accounts from four stroke survivors who experienced one of two acute stroke units. Through detailed analysis, the acute stroke unit emerged as a meaningful space, in two distinct but interconnected forms. As holding space, the unit was understood to offer protection and safe haven, as the stroke survivors looked to cope and respond to the temporal, bodily, biographical disruption and significant vulnerability brought about by stroke and by being in hospital. Holding was fulfilled by different people (including their fellow stroke survivors) and reflected a human response to human need and existential vulnerability. This space, and the practices within it, functioned to hold them intimately but also at a distance from their prestroke lifeworld. As such, the acute stroke unit holding space was intertwined with how it supported, encouraged or provoked transition. In the transitional space of the acute stroke unit, stroke survivors described how they survived the hospital‐healthcare space, stroke unit and poststroke space. This paper articulates how transition was meaningfully signified through its absence or presence, as they transformed, relinquished or re‐asserted their ‘self’, and in one case, recovered whilst ‘in there’. The findings of this study provide phenomenological insight into stroke survivors’ lived experience, the meaningful holding and transitional contribution of the unit, and how these spatial forms were intertwined. These insights are discussed in relation to the existing evidence base and stroke unit provision.
S100B outperforms clinical decision rules for the identification of intracranial injury on head CT scan after mild traumatic brain injury

ABSTRACT Objective: To compare the classification accuracy of S100B to two clinical decision rules— Canadian CT Head Rule (CCHR) and New Orleans Criteria (NOC)—for predicting traumatic intracranial injuries (ICI) after mild traumatic brain injury (mild TBI). Methods: A secondary analysis of a prospective observational study of mild TBI patients was performed. The diagnostic performance of S100B for predicting ICI on head CT was compared to both the CHRR and NOC. Area under receiver operator characteristic (AUC) curves were used and multivariable analysis was used to create a new decision rule based on a combination of S100B and decision rule-related variables. Results: S100B had the highest negative predictive value (97.3%), positive predictive value (7.21%), specificity (33.6%) and positive likelihood ratio (1.3), and the lowest negative likelihood ratio (0.5). The proportion of mild TBI subjects with potentially avoidable head CT scans was highest using S100B (37.7%). The addition of S100B to both clinical decision rules significantly increased AUC. A novel decision rule adding S100B to three decision rule-related variables significantly improved prediction (p < 0.05). Conclusion: Serum S100B outperformed clinical decision rules for identifying mild TBI patients with ICI. Incorporating clinical variables with S100B maximized ICI prediction, but requires validation in an independent cohort.
The Role of Reasoning and Pragmatics in the Modifier Effect

The modifier effect refers to the fact that the perceived likelihood of a property in a noun category is diminished if the noun is modified. For example, "Pigs live on farms" is rated as more likely than "Dirty pigs live on farms. " The modifier effect has been demonstrated in many studies, but the underlying cognitive mechanisms are still unclear. This paper reports two series of experiments that jointly point to the conclusion that the modifier effect is the result of a superposition of three cognitive mechanisms: (a) probabilistically softened default inheritance, (b) pragmatic implicatures due to Gricean relevance assumptions, and (c) inference based on world knowledge. We present evidence that the pragmatic effects operate largely on an unconscious level and that their influence can be reduced by changing the presentation format of the cognitive task.