Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural and functional characterization of the cytotoxic protein ledodin, an atypical ribosome‐inactivating protein from shiitake mushroom (Lentinula edodes)

We have purified ledodin, a cytotoxic 22‐kDa protein from shiitake mushroom (Lentinula edodes) consisting of a 197 amino acid chain. Ledodin possessed N‐glycosylase activity on the sarcin‐ricin loop of mammalian 28S rRNA and inhibited protein synthesis. However, it was not active against insect, fungal, and bacterial ribosomes. In vitro and in silico studies suggested that ledodin exhibits a catalytic mechanism like that of DNA glycosylases and plant ribosome‐inactivating proteins. Moreover, the sequence and structure of ledodin was not related to any protein of known function, although ledodin‐homologous sequences were found in the genome of several species of fungi, some edible, belonging to different orders of the class Agaricomycetes. Therefore, ledodin could be the first of a new family of enzymes widely distributed among this class of basidiomycetes. The interest of these proteins lies both, in the fact that they can be a toxic agent of some edible mushrooms and in their application in medicine and biotechnology.
Improving growth properties of Corynebacterium glutamicum by implementing an iron‐responsive protocatechuate biosynthesis

Corynebacterium glutamicum experiences a transient iron limitation during growth in minimal medium, which can be compensated by the external supplementation of protocatechuic acid (PCA). Although C. glutamicum is genetically equipped to form PCA from the intermediate 3‐dehydroshikimate catalysed by 3‐dehydroshikimate dehydratase (encoded by qsuB), PCA synthesis is not part of the native iron‐responsive regulon. To obtain a strain with improved iron availability even in the absence of the expensive supplement PCA, we re‐wired the transcriptional regulation of the qsuB gene and modified PCA biosynthesis and degradation. Therefore, we ushered qsuB expression into the iron‐responsive DtxR regulon by replacing the native promoter of the qsuB gene by the promoter PripA and introduced a second copy of the PripA‐qsuB cassette into the genome of C. glutamicum. Reduction of the degradation was achieved by mitigating expression of the pcaG and pcaH genes through a start codon exchange. The final strain C. glutamicum IRON+ showed in the absence of PCA a significantly increased intracellular Fe2+ availability, exhibited improved growth properties on glucose and acetate, retained a wild type‐like biomass yield but did not accumulate PCA in the supernatant. For the cultivation in minimal medium C. glutamicum IRON+ represents a useful platform strain that reveals beneficial growth properties on different carbon sources without affecting the biomass yield and overcomes the need of PCA supplementation.
Correlation-based full-waveform shear wave elastography

Objective. With the ultimate goal of reconstructing 3D elasticity maps from ultrasound particle velocity measurements in a plane, we present in this paper a methodology of inverting for 2D elasticity maps from measurements on a single line. Approach. The inversion approach is based on gradient optimization where the elasticity map is iteratively modified until a good match is obtained between simulated and measured responses. Full-wave simulation is used as the underlying forward model to accurately capture the physics of shear wave propagation and scattering in heterogeneous soft tissue. A key aspect of the proposed inversion approach is a cost functional based on correlation between measured and simulated responses. Main results. We illustrate that the correlation-based functional has better convexity and convergence properties compared to the traditional least-squares functional, and is less sensitive to initial guess, robust against noisy measurements and other errors that are common in ultrasound elastography. Inversion with synthetic data illustrates the effectiveness of the method to characterize homogeneous inclusions as well as elasticity map of the entire region of interest. Significance. The proposed ideas lead to a new framework for shear wave elastography that shows promise in obtaining accurate maps of shear modulus using shear wave elastography data obtained from standard clinical scanners.
Clustered interior phase transition layers for an inhomogeneous Allen-Cahn equationin higher dimensional domains

For a singularly perturbed equation of inhomogeneous Allen-Cahn type with positive potential function in high dimensional general domain, we prove the existence of solutions, at least for some sequence of the positive parameter, which have clustered phase transition layers with mass centered close to a smooth closed stationary and non-degenerate hypersurface. Moreover, the interaction between neighboring layers is governed by a type of Jacobi-Toda system.
Identification of distinct subpopulations of Gli1‐lineage cells in the mouse mandible

The Hedgehog pathway gene Gli1 has been proposed to mark a subpopulation of skeletal stem cells (SSCs) in craniofacial bone. Skeletal stem cells (SSCs) are multi‐potent cells crucial for the development and homeostasis of bone. Recent studies on long bones have suggested that skeletal stem cells in endochondral or intramembranous ossification sites have different differentiation capacities. However, this has not been well‐defined in neural crest derived bones. Generally, the long bones are derived from mesoderm and follow an endochondral ossification model, while most of the cranial bones are neural crest (NC) in origin and follow an intramembranous ossification model. The mandible is unique: It is derived from the neural crest lineage but makes use of both modes of ossification. Early in fetal development, the mandibular body is generated by intramembranous ossification with subsequent endochondral ossification forming the condyle. The identities and properties for SSCs in these two sites remain unknown. Here, we use genetic lineage tracing in mouse to identify cells expressing the Hedgehog responsive gene Gli1, which is thought to mark the tissue resident SSCs. We track the Gli1+ cells, comparing cells within the perichondrium to those in the periosteum covering the mandibular body. In juvenile mice, these have distinct differentiation and proliferative potential. We also assess the presence of Sox10+ cells, thought to mark neural crest stem cells, but find no substantial population associated with the mandibular skeleton, suggesting that Sox10+ cells have limited contribution to maintaining postnatal mandibular bone. All together, our study indicates that the Gli1+ cells display distinct and limited differentiation capacity dependent on their regional associations.
Teams and Complexity: Merging Theories towards a Finite Structure

The process of structuring teams in projects is not being implemented, and practitioners have lost confidence in the process. In order to improve the current status, there is a need for a major rethink, one that will enable the structuring of teams/complex adaptive systems. Therefore, using deductions drawn from research results, regarding the implementation of the process and the effects of complexity, a tentative proposal for a Finite Structural approach is made for setting up and testing the structure of teams. This is done by integrating a number of progressive theories not only from the field of organisation design but also from engineering, physics, and psychology, with theories such as social network theory, actornetwork theory, finite element analysis, complexity, clustering, and cross functional team behaviours. This chapter presents the above and throws the gauntlet for discussion and improvement of the approach that will enable project managers and others to improve the process of structuring of teams. DOI: 10.4018/978-1-4666-2509-9.ch010
PAK1 c.1409 T > a (p. Leu470Gln) de novo variant affects the protein kinase domain, leading to epilepsy, macrocephaly, spastic quadriplegia, and hydrocephalus: Case report and review of the literature

The p‐21‐activated kinase 1 (PAK1) protein, encoded by the PAK1 gene, is an evolutionarily conserved serine/threonine‐protein kinase that regulates key cellular developmental processes. To date, seven de novo PAK1 variants have been reported to cause the Intellectual Developmental Disorder with Macrocephaly, Seizures, and Speech Delay (IDDMSSD). In addition to the namesake features, other common characteristics include structural brain anomalies, delayed development, hypotonia, and dysmorphic features. Here, we report a de novo PAK1 NM_002576. 5: c.1409 T > A variant (p.Leu470Gln) identified by trio genome sequencing (GS) in a 13‐year‐old boy with postnatal macrocephaly, obstructive hydrocephalus, medically refractory epilepsy, spastic quadriplegia, white matter hyperintensities, profound developmental disabilities, and a horseshoe kidney. This is the first recurrently affected residue identified in the protein kinase domain. Combined assessment of the eight pathogenic PAK1 missense variants reveal that the variants cluster in either the protein kinase or autoregulatory domains. Although interpretation of the phenotypic spectrum is limited by the sample size, neuroanatomical alterations were found more often in individuals with PAK1 variants in the autoregulatory domain. In contrast, non‐neurological comorbidities were found more often in individuals with PAK1 variants in the protein kinase domain. Together, these findings expand the clinical spectrum of PAK1‐associated IDDMSSD and reveal potential correlations with the affected protein domains.
Low‐energy helium nozzle beam

A high‐intensity supersonic nozzle beam source is described, whose beam energy can be varied between 2 and 170 meV (helium). Experimental performance and time‐of‐flight measurements on cold helium beams are reported. Condensation in the free jet expansions of helium has been studied by mass spectrometric detection of He+2. A correlation between the maximum speed ratio and the onset of clustering is observed.
How Does Occupational Lifting Affect Ambulatory Blood Pressure, Relative Aerobic Workload and Level of Physical Activity?

Abstract Introduction Occupational physical activity (OPA), including occupational lifting (OL), seems to increase the risk of cardiovascular disease (CVD). Knowledge about the association between OL and risk of CVD is sparse, but repeated OL is assumed to result in prolonged raised blood pressure and heart rate (HR) eventually augmenting the risk of CVD. To disentangle parts of the mechanisms behind the raised 24-hour ambulatory blood pressure measurement (24h-ABPM), by exposure to OL, this study aimed to explore the acute differences in 24h-ABPM, relative aerobic workload (RAW) and OPA across workdays with and without OL, and secondary to assess the feasibility and rater agreement of direct field observations of the frequency and load of occupational lifting. Methods This controlled cross-over study investigates associations between moderate to high OL and 24h-ABPM, RAW in per cent of heart rate reserve (%HRR) and level of OPA. This included 2x24h monitoring of 24h-ABPM (Spacelabs 90217), PA (Axivity) and HR (Actiheart), comprising a workday containing OL and a workday without. The frequency and burden of OL were directly observed in field. The data were time synchronized and processed in the Acti4 software. Differences across workdays with and without OL in 24h-ABPM, RAW and OPA were evaluated using repeated 2 × 2 mixed-models among 60 blue-collar workers in Denmark. Exposure to OL was estimated by direct manual field observation, registering burden and frequency of OL. Interrater reliability tests were performed across 15 participants representing 7 occupational groups. Interclass correlation coefficient (ICC) estimates of total burden lifted and frequency of lifts were calculated, based on a mean-rating (k = 2), absolute-agreement, 2 way mixed-effects model, indicating the raters as fixed effects. Results OL led to non-significant increases in ABPM during work-time (systolic Δ1.79 mmHg, 95%CI −4.49–8.08, diastolic Δ0.43 mmHg, 95%CI −0.80–1.65), and on 24-hours basis (systolic Δ1.96 mmHg, 95%CI −3.80–7.72, diastolic Δ0.53 mmHg, 95%CI −3.12–4.18), significant increases in RAW during work (Δ7.74 %HRR, 95%CI 3.57–11.91) as well as a raised level of OPA (Δ4156.88 steps, 95%CI 1898.83–6414.93, Δ−0.67 hours of sitting time, 95%CI −1.25–0.10, Δ−0.52 hours of standing time, 95%CI −1.03–0.01, Δ0.48 hours of walking time, 95%CI 0.18–0.78). ICC estimates were 0.998 (95% CI 0.995–0.999) for total burden lifted and 0.992 (95% CI 0.975–0.997) for frequency of lift. Discussion OL increased both intensity and volume of OPA among blue-collar workers, which supposedly to contributes to an augmented risk of CVD. Although this study finds hazardous acute effects, further investigations are needed to evaluate the long-term effects of OL on ABPM, HR and volume of OPA, also effects of cumulative exposure to OL would be relevant to investigate. Conclusion OL significantly raised the intensity and volume of OPA. Direct field observation of occupational lifting showed an excellent interrater reliability.
Development of the Pseudomonas syringae pv. morsprunorum Biofilm Monitored in Real Time Using Attenuated Total Reflection Fourier Transform Infrared Measurements in a Flow Cell Chamber

Biofilms of sessile Pseudomonas syringae cells formed on top of plant host's leaves or fruits allow surviving harsh environmental conditions (desiccation) and improve their resistance to antibacterial treatments of crops. A better understanding of these biofilms can help minimize their effect on harvests. In the present study, infrared attenuated total reflection spectroscopy coupled with optical and confocal laser scanning microscopy has been applied for the first time to analyze Pseudomonas syringae pathovar morsprunorum biofilm development in real time. The biofilm development was observed within a spectral window 4000–800 cm−1 under constant flow conditions for 72 h. The kinetics of representative integrated band areas (nucleic acids with polysaccharides at 1141–1006 cm−1, amino acid side chains with free fatty acids at 1420–1380 cm−1, proteins at 1580–1490 cm−1, and lipids with proteins at 2935–2915 cm−1) were analyzed with regard to the observed biofilm structure and the following P. syringae biofilm developmental stages were attributed: The inoculation phase, washing of weakly attached bacteria closely followed by recolonization of the vacated surface, the restructuration phase, and finally the maturation phase.
Changes in frequency of cannabis use among people with HIV during the COVID-19 pandemic: a multi-methods study to explore the underlying reasons for change

ABSTRACT Background: People with HIV (PWH) report higher rates of cannabis use than the general population. It is unclear how cannabis use among PWH has been impacted by the COVID-19 pandemic and the implications for the health and wellbeing of PWH. Objectives: To describe changes in frequency of cannabis use among a sample of PWH during the pandemic, reasons for those changes, and implications of the findings. Methods: The data are cross-sectional and come from questions asked in a follow-up phone survey administered to a prospective cohort of PWH in Florida between May 2020 and March 2021. Participants who used cannabis were asked about changes in their frequency of cannabis use in a quantitative survey and reasons for changes in a qualitative open-ended question. Qualitative data were analyzed using thematic analysis. Results: Among 227 PWH (mean age 50, 50% men, 69% Black/African American, 14% Hispanic/Latino), 13% decreased frequency of cannabis, 11% increased frequency, and 76% reported no change. The most common reasons for increasing frequency of cannabis use were reducing anxiety/stress, trying to relax, coping with grief or reducing symptoms of depression, and reducing boredom during the pandemic. Supply or access issues, health concerns, and having already wanted to reduce cannabis use were common reasons for decreased frequency. Conclusion: Nearly 25% of the sample changed their cannabis use frequency during the pandemic. These findings shed light on the behaviors and motivations of PWH who use cannabis and can inform clinical practice and interventions during public health emergencies and beyond.
Local Minima, Symmetry-breaking, and Model Pruning in Variational Free Energy Minimization

Approximate inference by variational free energy minimization (also known as variational Bayes, or ensemble learning) has maximum likelihood and maximum a posteriori methods as special cases, so we might hope that it can only work better than these standard methods. However, cases have been found in which degrees of freedom are ‘pruned’, perhaps inappropriately. This paper investigates this phenomenon in a toy example. Approximate inference by variational free energy minimization (also known as variational Bayes, or ensemble learning, or learning with noisy weights { see (MacKay 1995) for a review) hasmaximumlikelihoodandmaximum a posteriori methodsasspecialcases,sowemighthope that it can only work better than these standard methods. However, cases have been found in which degrees of freedom are ‘pruned’, perhaps inappropriately. This paper investigates this phenomenon in a toy example. Motivations for VFE: want to incorporate uncertainty about parameters into the modelfltting process. Also worried about the electric monastry { location in parameter space where the likelihooddiverges. Uncertainty is greatest (and singularities in the likelihood more prominent) when there is little data, so VFE is of most interest for small N. ProblemobservedbyZoubinGhahramani(studyingensemblelearningforHMMs(MacKay 1997)): extra degrees of freedom are not used. The model self-prunes. Annoying because we don’t want the pruned model, we want the model we believe in { with lots of parameters, and big error bars on them! Parameter pruning is bad news because we would like predictions to take into accoutn uncertainty. Commentonspontaneouspruning: issometimesviewedasaconvenientautomaticOccam’s razor,but does it behave correctly? Occam efiect should bevery weak for small N.
Structure‐Activity Relationships of a Steroid Family using Quantum Similarity Measures and Topological Quantum Similarity Indices

This work will try to study an application example of quantum similarity measures, in order to determine quantitative relationships between the structure and biological activity for a family of steroids. The studied family is composed of 31 molecules, and the property analyzed is the affinity to the corticosteroid binding globulin receptor. Two methodologies have been chosen to perform QSAR on the mentioned steroid set. Both methodological frameworks are based on quantum similarity measures, the first one is based on the use of similarity indices as molecular descriptors and the second methodology uses quantum similarity topological indices for the same purpose. The use of molecular descriptors, obtained from quantum similarity topological indices constructs, constitutes a new technique developed recently in our laboratory to be used in QSAR in close relationship with the already explored field of quantum similarity measures. Results become comparable to other 3D-QSAR techniques.
Vernalisation and photoperiod responses of diverse wheat genotypes

Abstract Context. Wheat (Triticum aestivum L.) adaptation is highly dependent on crop lifecycle duration, particularly the time at which flowering occurs in a specific environment. Frost, low solar radiation, heat and drought can significantly reduce yield if a crop flowers too early or late. Wheat genotypes have different lifecycle durations determined by plant responses to temperature (thermal time accumulation and vernalisation) and photoperiod. These responses are largely controlled by five phenology genes (two PPD1 and three VRN1 genes). Advances in crop phenology modelling suggest that flowering time under field conditions could be accurately predicted with parameters derived from photoperiod and vernalisation responses obtained in controlled environments. Aims. This study quantified photoperiod and vernalisation responses of 69 Australian wheat genotypes selected for diversity at the PPD1 and VRN1 loci. Methods. Spring and winter genotypes were grown in four controlled environments at a constant temperature of 22°C with photoperiod (17 or 8 h) and vernalisation (0 or 8 weeks) treatments as factors. Key results. Thermal time from coleoptile emergence to flowering in spring genotypes was typically decreased more by long photoperiod than by vernalisation; the opposite was true for winter genotypes. Spring genotypes that were sensitive to vernalisation contained a sensitive allele at the Vrn-A1 locus. Conclusions. There is large diversity in phenological responses of wheat genotypes to photoperiod and vernalisation, including among those with matching multi-locus genotype. Implications. Data from this study will be used to parameterise and test a wheat phenology model in a future study.
A New Theoretical Method for Studying Effects of Microstructure on Effective Thermal Conductivity of Vermicular Graphite Cast Iron

To provide the basis for thermal conductivity regulation of vermicular graphite cast iron (VGI), a new theoretical method consisting of shape interpolation, unit cell model and numerical calculation was proposed. Considering the influence of the graphite anisotropy and interfacial contact thermal conductivity (ICTC), the effective thermal conductivity of a series of unit cell models was calculated by numerical calculation based on finite difference. The effects of microstructure on effective thermal conductivity of VGI were studied by shape interpolation. The experimental results were in good agreement with the calculated ones. The effective thermal conductivity of VGI increases in power function with the decrease in graphite shape parameter, and increases linearly with the increase in graphite volume fraction and thermal conductivity of matrix. When the graphite volume fraction increases by 1%, the thermal conductivity of nodular cast iron increases by about 0.18 W/(m·K), while that of gray cast iron increases by about 3 W/(m·K). The thermal conductivity of cast iron has the same sensitivity to the thermal conductivity of matrix regardless of the graphite shape parameter. The thermal conductivity of matrix increased by 15 W/(m·K) and the thermal conductivity of cast iron increased by about 12 W/(m·K). Moreover, the more the graphite shape deviates from the sphere, the greater the enhancement effect of graphite anisotropy on thermal conductivity than the hindrance effect of interface between graphite and matrix. This work can provide guidance for the development of high thermal conductivity VGI and the study of thermal conductivity of composites containing anisotropic dispersed phase particles with complex shapes.