Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of the Barley Malt Rootlet Proteome

Barley seeds are one of the main ingredients of the malting industry for brewing beer. The barley rootlets that are separated from the kilned seeds at the end of the malting process and used as animal feed are one of the byproducts of this industry. In this study, the proteome of rootlets derived from two stages of the malting process, germination and kilning, from a popular malting barley variety were analyzed. A label-free shotgun proteomics strategy was used to identify more than 800 proteins from the barley rootlets. A high coverage and high confidence Gene Ontology annotations of the barley genome was used to facilitate the functional annotation of the proteins that were identified in the rootlets. An analysis of these proteins using Kellogg Encyclopedia of Genes and Genomes (KEGG) and Plant Reactome databases indicated the enrichment of pathways associated with phytohormones, protein biosynthesis, secondary metabolism, and antioxidants. Increased levels of jasmonic acid and auxin in the rootlets further supported the in silico analysis. As a rich source of proteins and amino acids use of these by-products of the malting industry for animal feed is validated. This study also indicates rootlets as a potential source of naturally occurring phenylpropanoids and antioxidants that can be further exploited in the development of functional foods.
Comparative de novo transcriptomics and untargeted metabolomic analyses elucidate complicated mechanisms regulating celery (Apium graveolens L.) responses to selenium stimuli

Presently, concern regarding the effects of selenium (Se) on the environment and organisms worldwide is increasing. Too much Se in the soil is harmful to plants. In this study, Illumina RNA sequencing and the untargeted metabolome of control and Se-treated celery seedlings were analyzed. In total, 297,911,046 clean reads were obtained and assembled into 150,218 transcripts (50,876 unigenes). A total of 36,287 unigenes were annotated using different databases. Additionally, 8,907 differentially expressed genes, including 5,319 up- and 3,588 downregulated genes, were identified between mock and Se-treated plants. “Phenylpropanoid biosynthesis” was the most enriched KEGG pathway. A total of 24 sulfur and selenocompound metabolic unigenes were differentially expressed. Furthermore, 1,774 metabolites and 237 significant differentially accumulated metabolites were identified using the untargeted metabolomic approach. We conducted correlation analyses of enriched KEGG pathways of differentially expressed genes and accumulated metabolites. Our findings suggested that candidate genes and metabolites involved in important biological pathways may regulate Se tolerance in celery. The results increase our understanding of the molecular mechanism responsible for celery’s adaptation to Se stress.
Glycan biomarkers for Alzheimer disease correlate with T‐tau and P‐tau in cerebrospinal fluid in subjective cognitive impairment

Alzheimer disease (AD) is a devastating disease and a global health problem, and current treatments are only symptomatic. A wealth of clinical studies support that the disease starts to develop decades before the first symptoms appear, emphasizing the importance of studying early changes for improving early diagnosis and guiding toward novel treatment strategies. Protein glycosylation is altered in AD but it remains to be clarified why these alterations occur and how they affect the disease development. Here, we used a glycomics approach to search for alterations in protein glycosylation in cerebrospinal fluid (CSF) in AD compared with nondemented controls. Using both matrix‐assisted laser desorption ionization‐time of flight and liquid chromatography–electrospray mass spectrometry, we observed an increase in N‐glycans carrying bisecting N‐acetylglucosamine in AD. Based on those findings, we designed an enzyme‐linked multiwell plate assay to quantify N‐glycans binding to the lectin Phaseolus vulgaris Erythroagglutinin (PHA‐E), which is specific for N‐glycans containing bisecting N‐acetylglucosamine. Using this assay, we found a similar increase in CSF in AD compared with controls. Further analysis of CSF from 242 patients with subjective cognitive impairment (SCI), mild cognitive impairment (MCI), or AD dementia revealed significantly increased binding to PHA‐E in MCI and AD compared to SCI. Interestingly, PHA‐E binding correlated with CSF levels of phosphorylated tau and total tau and this correlation was most prominent in the SCI group (R = 0.53–0.54). This study supports a link between N‐glycosylation, neurodegeneration, and tau pathology in AD and suggests that glycan biomarkers have potential to identify SCI cases at risk of developing AD.
Weak Fragment Crystallizable (Fc) Domain Interactions Drive the Dynamic Assembly of IgG Oligomers upon Antigen Recognition.

Activation of membrane receptors through clustering is a common mechanism found in various biological systems. Spatial proximity of receptors may be transduced across the membrane to initiate signalling pathways, or alternatively be recognized by peripheral proteins or immune cells to trigger external effector functions. Here we show how specific Immunoglobulin G (IgG) binding induces clustering of monomeric target molecules in lipid membranes through Fc-Fc interactions. We visualize and characterize the dynamic IgG oligomerization process and the molecular interactions involved using high-speed atomic force microscopy, single molecule force spectroscopy, and quartz crystal microbalance experiments. We found that the Fc-Fc interaction strength is precisely tuned to be weak enough to prevent IgG oligomerization in solution at physiological titers, but enabling IgG oligomerization when Fabs additionally bind to their cognate surface epitopes- a mechanism that ultimately targets IgG mediated effector functions such as classical complement activation to antigenic membranes.
How to inform at‐risk relatives? Attitudes of 1379 Dutch patients, relatives, and members of the general population

The uptake of predictive DNA testing in families with a hereditary disease is <50%. Current practice often relies on the proband to inform relatives about the possibility of predictive DNA testing, but not all relatives are informed adequately. To enable informed decision‐making concerning predictive DNA testing, the approach used to inform at‐risk relatives needs to be optimized. This study investigated the preferences of patients, relatives, and the general population from the Netherlands on how to inform relatives at risk of autosomal dominant diseases. Online surveys were sent to people with autosomal dominant neuro‐, onco‐, or cardiogenetic diseases and their relatives via patient organizations (n = 379), and to members of the general population via a commercial panel (n = 1,000). Attitudes of the patient and population samples generally corresponded. A majority believed that initially only first‐degree relatives should be informed, following the principles of a cascade screening approach. Most participants also thought that probands and healthcare professionals (HCPs) should be involved in informing relatives, and a large proportion believed that HCPs should contact relatives directly in cases where patients are unwilling to inform, both for untreatable and treatable conditions. Participants from the patient sample were of the opinion that HCPs should actively offer support. Our findings show that both patients and HCPs should be involved in informing at‐risk relatives of autosomal dominant diseases and suggest that relatives' ‘right to know’ was considered a dominant issue by the majority of participants. Further research is needed on how to increase proactive support in informing of at‐risk relatives.
A Convolutional Neural Network for Compound Micro-Expression Recognition

Human beings are particularly inclined to express real emotions through micro-expressions with subtle amplitude and short duration. Though people regularly recognize many distinct emotions, for the most part, research studies have been limited to six basic categories: happiness, surprise, sadness, anger, fear, and disgust. Like normal expressions (i.e., macro-expressions), most current research into micro-expression recognition focuses on these six basic emotions. This paper describes an important group of micro-expressions, which we call compound emotion categories. Compound micro-expressions are constructed by combining two basic micro-expressions but reflect more complex mental states and more abundant human facial emotions. In this study, we firstly synthesized a Compound Micro-expression Database (CMED) based on existing spontaneous micro-expression datasets. These subtle feature of micro-expression makes it difficult to observe its motion track and characteristics. Consequently, there are many challenges and limitations to synthetic compound micro-expression images. The proposed method firstly implemented Eulerian Video Magnification (EVM) method to enhance facial motion features of basic micro-expressions for generating compound images. The consistent and differential facial muscle articulations (typically referred to as action units) associated with each emotion category have been labeled to become the foundation of generating compound micro-expression. Secondly, we extracted the apex frames of CMED by 3D Fast Fourier Transform (3D-FFT). Moreover, the proposed method calculated the optical flow information between the onset frame and apex frame to produce an optical flow feature map. Finally, we designed a shallow network to extract high-level features of these optical flow maps. In this study, we synthesized four existing databases of spontaneous micro-expressions (CASME I, CASME II, CAS(ME)2, SAMM) to generate the CMED and test the validity of our network. Therefore, the deep network framework designed in this study can well recognize the emotional information of basic micro-expressions and compound micro-expressions.
Intraindividual Consistency Between Auditory and Visual Multistability

We compared perceptual multistability across modalities, using a visual plaid pattern (composed of two transparently overlaid drifting gratings) and auditory streaming (elicited by a repeating “ABA_” tone sequence). Both stimuli can be perceived as integrated (one plaid pattern, one stream comprising “A” and “B” tones) or segregated (two individual gratings, two tone streams). In the segregated case, either stream or grating can be perceived in the foreground. We queried auditory and visual perception with these three response options. We found that perceptual dominance of the integrated states was correlated across modalities: Participants who were more likely to perceive the plaid were also more likely to perceive the integrated auditory stream. When presenting both stimuli simultaneously and querying the auditory percept, eye-movement data showed that perceiving auditory and visual integration is related on a moment-by-moment basis. This suggests that in part common mechanisms underlie multistability in visual and auditory perception.
Expression of Arabidopsis Hexokinase in Tobacco Guard Cells Increases Water-Use Efficiency and Confers Tolerance to Drought and Salt Stress

Abiotic stresses such as drought and saline water impose major limitations on plant growth. Modulation of stomatal behavior may help plants cope with such stresses by reducing both water loss and salt uptake. Hexokinase (HXK) is a sugar-phosphorylating enzyme involved in guard cells’ sugar-sensing, mediating stomatal closure and coordinating photosynthesis with transpiration. We generated transgenic tobacco lines expressing the Arabidopsis hexokinase1 (AtHXK1) under the guard cell-specific promoter KST1 and examined those plants using growth room and greenhouse experiments. The expression of AtHXK1 in tobacco guard cells reduced stomatal conductance and transpiration by about 25% with no negative effects on photosynthesis or growth, leading to increased water-use efficiency. In addition, these plants exhibited tolerance to drought and salt stress due to their lower transpiration rate, indicating that improved stomatal function has the potential to improve plant performance under stress conditions.
Molecular Characterization of Embryonic Stem Cell-Derived Cardiac Neural Crest-Like Cells Revealed a Spatiotemporal Expression of an Mlc-3 Isoform

Background and Objectives Pluripotent embryonic stem (ES) cells represent a perfect model system for the investigation of early developmental processes. Besides their differentiation into derivatives of the three primary germ layers, they can also be differentiated into derivatives of the ‘fourth’ germ layer, the neural crest (NC). Due to its multipotency, extensive migration and outstanding capacity to generate a remarkable number of different cell types, the NC plays a key role in early developmental processes. Cardiac neural crest (CNC) cells are a subpopulation of the NC, which are of crucial importance for precise cardiovascular and pharyngeal glands’ development. CNC-associated malformations are rare, but always severe and life-threatening. Appropriate cell models could help to unravel underlying pathomechanisms and to develop new therapeutic options for relevant heart malformations. Methods Murine ES cells were differentiated according to a mesodermal-lineage promoting protocol. Expression profiles of ES cell-derived progeny at various differentiation stages were investigated on transcript and protein level. Results Comparative expression profiling of murine ES cell multilineage progeny versus undifferentiated ES cells confirmed differentiation into known cell derivatives of the three primary germ layers and provided evidence that ES cells have the capacity to differentiate into NC/CNC-like cells. Applying the NC/CNC cell-specific marker, 4E9R, an unambiguous identification of ES cell-derived NC/CNC-like cells was achieved. Conclusions Our findings will facilitate the establishment of an ES cell-derived CNC cell model for the investigation of molecular pathways during cardiac development in health and disease.
Nickel Poisoning of a Cracking Catalyst Unravelled by Single Particle X-ray Fluorescence-Diffraction-Absorption Tomography.

Ni contamination from crude oil in the Fluid Catalytic Cracking (FCC) process is one of the primary sources of catalyst deactivation, thereby promoting dehydrogenation-hydrogenation and speeding up coke growth. Herein, single particle X-ray fluorescence, diffraction and absorption (µXRF-µXRD-µXAS) tomography has been used in combination with confocal fluorescence microscopy (CFM) after thiophene staining to spatially resolve Ni interaction with catalyst components and investigate zeolite degradation, including the processes of dealumination and Brønsted acid sites distribution changes. The comparison between a Ni-lean particle, exposed to hydrotreated feedstock, and a Ni-rich one, exposed to non-hydrotreated feedstock, revealed a preferential interaction of Ni, found in co-localization with Fe, with the γ-Al2O3 matrix, leading to the formation of spinel-type hotspots. Although both particles show similar surface zeolite degradation, the Ni-rich particle displayed higher dealumination and a clear Brønsted acidity drop.
Modeling beta‐sheet peptide‐protein interactions: Rosetta FlexPepDock in CAPRI rounds 38‐45

Peptide‐protein docking is challenging due to the considerable conformational freedom of the peptide. CAPRI rounds 38‐45 included two peptide‐protein interactions, both characterized by a peptide forming an additional beta strand of a beta sheet in the receptor. Using the Rosetta FlexPepDock peptide docking protocol we generated top‐performing, high‐accuracy models for targets 134 and 135, involving an interaction between a peptide derived from L‐MAG with DLC8. In addition, we were able to generate the only medium‐accuracy models for a particularly challenging target, T121. In contrast to the classical peptide‐mediated interaction, in which receptor side chains contact both peptide backbone and side chains, beta‐sheet complementation involves a major contribution to binding by hydrogen bonds between main chain atoms. To establish how binding affinity and specificity are established in this special class of peptide‐protein interactions, we extracted PeptiDBeta, a benchmark of solved structures of different protein domains that are bound by peptides via beta‐sheet complementation, and tested our protocol for global peptide‐docking PIPER‐FlexPepDock on this dataset. We find that the beta‐strand part of the peptide is sufficient to generate approximate and even high resolution models of many interactions, but inclusion of adjacent motif residues often provides additional information necessary to achieve high resolution model quality.
The sociomateriality of expertise: An exploratory study of trauma surgeons

The importance of knowledge workers and expertise continues to accelerate for both organizations and for economies. In addition, experts are increasingly being tasked with contributing to challenges that span their particular domain of expertise. A contemporary example is the U.S. healthcare industry where physicians are increasingly being asked to serve as active partners with healthcare administrators to solve complex challenges such as rising costs, outcome-based reimbursements, and quality of care. Unfortunately, research has shown that individuals who are highly skilled in one domain (e.g., physicians) are rarely are able to transfer that expertise to other domains. This dissertation used qualitative methods to explore an alternate conceptualization of expertise and how this might influence the contribution of experts across domains. The findings from this study suggest that expertise emerges from the dynamic relationships occurring between the social and the material aspects of a situated environment. Therefore, in addition to the knowledge that is resident within an individual, knowing and expertise is also distributed across the various social and material relationships within the specific environment. The main contribution of this research is to expand the standard conceptualization of expertise, which is based on cognitive and socio-cognitive assumptions. This study does not deny the validity of cognitive assumptions about knowledge and expertise but argues that these assumptions do not go far enough in conceptualizing expertise. This research indicates that a sociomaterial conceptualization of expertise allows for a more nuanced understanding into the various constitutive aspects of expertise and in particular a greater sensitivity to the relationship among the aspects. Degree Type Dissertation Degree Name Doctor of Education (EdD) Graduate Group Education First Advisor Sharon M. Ravitch
Endocannabinoid 2-arachidonoylglycerol is elevated in the coronary circulation during acute coronary syndrome

Objectives The endocannabinoid system modulates coronary circulatory function and atherogenesis. The two major endocannabinoids (eCB), 2-arachidonoylglycerol (2-AG) and N-arachidonoylethanolamide (AEA), are increased in venous blood from patients with coronary artery disease (CAD). However, given their short half-life and their autocrine/paracrine mechanism of action, eCB levels in venous blood samples might not reflect arterial or coronary eCB concentrations. The aim of this cross-sectional study was to identify the local concentration profile of eCB and to detect whether and how this concentration profile changes in CAD and NSTEMI versus patients without CAD. Methods and results 83 patients undergoing coronary angiography were included in this study. Patients were divided into three groups based on their definite diagnosis of a) no CAD, b) stable CAD, or c) non-ST-segment elevation myocardial infarction (NSTEMI). Blood was drawn from the arterial sheath and the aorta in all patients and additionally distal to the culprit coronary lesion in CAD- and NSTEMI patients. 2-AG levels varied significantly between patient groups and between the sites of blood extraction. The lowest levels were detected in patients without CAD; the highest 2-AG concentrations were detected in NSTEMI patients and in the coronary arteries. Peripheral 2-AG levels were significantly higher in NSTEMI patients (107.4 ± 28.4 pmol/ml) than in CAD- (17.4 ± 5.4 pmol/ml; p < 0.001), or no-CAD patients (23.9 ± 7.1 pmol/ml; p < 0.001). Moreover, coronary 2-AG levels were significantly higher in NSTEMI patients than in CAD patients (369.3 ± 57.2 pmol/ml vs. 240.1 ± 25.3 pmol/ml; p = 0.024). Conclusions 2-AG showed significant variability in arterial blood samples drawn from distinct locations. Possibly, lesional macrophages synthesise 2-AG locally, which thereby contributes to endothelial dysfunction and local inflammation.
Characteristics of a Nationwide Voluntary Antibiotic Resistance Awareness Campaign in India; Future Paths and Pointers for Resource Limited Settings/Low and Middle Income Countries

Antibiotic resistance has reached alarming proportions globally, prompting the World Health Organization to advise nations to take up antibiotic awareness campaigns. Several campaigns have been taken up worldwide, mostly by governments. The government of India asked manufacturers to append a ‘redline’ to packages of antibiotics as identification marks and conducted a campaign to inform the general public about it and appropriate antibiotic use. We investigated whether an antibiotic resistance awareness campaign could be organized voluntarily in India and determined the characteristics of the voluntarily organized campaign by administering a questionnaire to the coordinators, who participated in organizing the voluntary campaign India. The campaign characteristics were: multiple electro–physical pedagogical and participatory techniques were used, 49 physical events were organized in various parts of India that included lectures, posters, booklet/pamphlet distribution, audio and video messages, competitions, and mass contact rallies along with broadcast of messages in 11 local languages using community radio stations (CRS) spread all over India. The median values for campaign events were: expenditure—3000 Indian Rupees/day (US$~47), time for planning—1 day, program spread—4 days, program time—4 h, direct and indirect reach of the message—respectively 250 and 500 persons/event. A 2 min play entitled ‘Take antibiotics as prescribed by the doctor’ was broadcast 10 times/day for 5 days on CRS with listener reach of ~5 million persons. More than 85%ofcoordinators thought that the campaign created adequate awareness about appropriate antibiotic use and antibiotic resistance. The voluntary campaign has implications for resource limited settings/low and middle income countries.
Uncontrolled trial of specialized, multi‐component care for individuals with first‐episode psychosis: Effects on motivation orientations

Deficits in motivation are present early in the course of psychotic disorders. However, growing data have highlighted important heterogeneity in motivation among individuals with psychosis, suggesting that this variable may not be a unitary concept. Outside of the psychosis literature, research on self‐determination theory has identified three motivational orientations that guide the initiation and regulation of behaviour: autonomous, controlled and impersonal. Thus, our study goal is to investigate the longitudinal course of motivational orientations among individuals participating in a specialized clinical service for individuals with first‐episode psychosis (ie, coordinated specialty care: CSC).