Miracle-dz/UniFAR-FTUs huggingface dataset:
Heat Stress Modulates Mycelium Growth, Heat Shock Protein Expression, Ganoderic Acid Biosynthesis, and Hyphal Branching of Ganoderma lucidum via Cytosolic Ca2+

ABSTRACT Heat stress (HS) influences the growth and development of organisms. Thus, a comprehensive understanding of how organisms sense HS and respond to it is required. Ganoderma lucidum, a higher basidiomycete with bioactive secondary metabolites, has become a potential model system due to the complete sequencing of its genome, transgenic systems, and reliable reverse genetic tools. In this study, we found that HS inhibited mycelium growth, reduced hyphal branching, and induced the accumulation of ganoderic acid biosynthesis and heat shock proteins (HSPs) in G. lucidum. Our data showed that HS induced a significant increase in cytosolic Ca2+ concentration. Further evidence showed that Ca2+ might be a factor in the HS-mediated regulation of hyphal branching, ganoderic acid (GA) biosynthesis, and the accumulation of HSPs. Our results further showed that the calcium-permeable channel gene (cch)-silenced and phosphoinositide-specific phospholipase gene (plc)-silenced strains reduced the HS-induced increase in HSP expression compared with that observed for the wild type (WT). This study demonstrates that cytosolic Ca2+ participates in heat shock signal transduction and regulates downstream events in filamentous fungi. IMPORTANCE Ganoderma lucidum, a higher basidiomycete with bioactive secondary metabolites, has become a potential model system for evaluating how environmental factors regulate the development and secondary metabolism of basidiomycetes. Heat stress (HS) is an important environmental challenge. In this study, we found that HS inhibited mycelium growth, reduced hyphal branching, and induced HSP expression and ganoderic acid biosynthesis in G. lucidum. Further evidence showed that Ca2+ might be a factor in the HS-mediated regulation of hyphal branching, GA biosynthesis, and the accumulation of HSPs. This study demonstrates that cytosolic Ca2+ participates in heat shock signal transduction and regulates downstream events in filamentous fungi. Our research offers a new way to understand the mechanism underlying the physiological and metabolic responses to other environmental factors in G. lucidum. This research may also provide the basis for heat shock signal transduction studies of other fungi.
Acceptance of Third‐Party Cardiac but not Skin Allografts Induced by Neonatal Exposure to Semi‐Allogeneic Lymphohematopoietic Cells

Neonatal tolerance is exclusively donor‐specific when assessed by skin allograft survival and in vitro alloreactivity assays. In contrast, we reported previously that acceptance of primarily vascularized cardiac allografts was not donor‐specific in C3H/He (C3H, H‐2k) mice treated as neonates with BALB/c‐derived (BALB, H‐2d) lymphohematopoietic cells, but included third‐party C57BL/10 (B10, H‐2b) allografts. The present study examined whether this unusual pattern is limited to heart grafts in this strain combination, and defined the relative importance of the donor cell H‐2d haplotype for third‐party cardiac allograft acceptance. C3H neonates were injected with (C3HxBALB)F1 bone marrow and spleen cells. Tolerance was assessed at age 8–10 weeks by transplantation of heart or skin allografts from several donor strains, and by in vitro assays of proliferation and cytotoxicity. Additionally, cells from H‐2d and H‐2b‐expressing strains on BALB or non‐BALB minor histocompatibility (miH) antigen backgrounds were tested as tolerizing inocula. Prolonged survival of cardiac grafts from all donor strains was observed in neonatally treated mice, whereas skin grafting and in vitro assays demonstrated donor‐specific hyporesponsiveness. Both H‐2d haplotype and non‐H‐2 miH background of graft donor and tolerizing cell donor were important to third‐party cardiac allograft acceptance. These results suggest that the functional alteration in alloreactivity induced by neonatal alloantigen exposure depends partly on method of assessment.
A Cognitive Social Simulation of Tribal Survival Strategies: The Importance of Cognitive and Motivational Factors

When trying to understand social processes and phenomena, it is relevant, and arguably important, to take psychology (cognition, motivation, and so on) of individuals into consideration. Detailed computational models of cognitive agents that incorporate a wide range of psychological functionalities have been developed in cognitive science, while most of the work in social simulation still assumes rudimentary psychological functions within agents. In this work, through simulating survival strategies of tribal societies, the interaction of cognition/ motivation on one hand and social institutions and processes on the other is explored. The results of the simulation demonstrate significant interactions between cognitive-motivational factors and social-environmental factors. For example, we show that there are cognitiveenvironmental dependency, cognitive-motivational dependency, and motivational-environmental dependency, among others. This work points to a more psychologically realistic approach towards social simulation (namely, Cognitive Social Simulation; Sun, 2006), as well as an area of research – exploring the cognitive-motivational-social-environmental interaction (through cognitive social simulation).
The emotional dimension of organisational work when B2B relationships are dissolved

The emotional dimension of organizational work is a vital and yet under-explored area of research. A central feature of work in this area is recognition of the tensions employees face when personal goals come into conflict with managerial or organizational goals. This paper will consider the tensions which boundary spanning staff can face when their belief about how they should enact their role is not accepted by their employer as meeting the firm’s objectives. This paper builds upon the growing research on the ending of business relationships by examining the nature and management of emotions during such periods. The discussion will draw on Fiske’s (1992) Relational Models Theory and its extension into the discussion of ‘taboo trade-offs’.
“God loves me no matter how I am”: a phenomenological analysis of the religious and spiritual experiences of HIV-infected African-American women with depression

ABSTRACT Depression is associated with increased HIV morbidity and mortality, particularly among African-American women (AAW) in the United States. The purpose of this qualitative study was to explore religious practices, spiritual beliefs, and experiences among AAW with co-occurring HIV infection and depression. A transcendental phenomenological study design was used to explore the experiences of AAW's religion and spirituality after an HIV diagnosis and living with depression. The four themes that were identified included: Religious Conflict and Return to Religious Practices; Religious Fortitude Broken and Feeling Judged; Spiritual Connection is More Powerful than Attending Church Services; and Spiritual Healing and Re-Connecting with Spirituality. These findings suggest that the distinction between internal and external manifestations of spirituality is important and that given the current religious climate, interventions that focus on supporting internal spiritual practice may be a more important and effective approach for AAW with co-occurring HIV infection and depression.
Crystal Structure of the Escherichia coli Fic Toxin-Like Protein in Complex with Its Cognate Antitoxin

FIC domain proteins mediate post-translational modifications of target proteins, which typically results in their inactivation. Depending on the conservation of crucial active site residues, the FIC fold serves as structural scaffold for various enzymatic activities, mostly target adenylylation. The founding member of the vast Fic protein family, EcFicT, was identified in Escherichia coli some time ago. The G55R point mutant of EcFicT displays the “filamentation induced by cAMP” (Fic) phenotype at high 3',5'-cyclic adenosine monophosphate (cAMP) concentrations and elevated temperature, but the underlying molecular mechanism and any putative biochemical activity of EcFicT have remained unknown. EcFicT belongs to class I Fic toxin proteins that are encoded together with a small inhibitory protein (antitoxin), named EcFicA in E. coli. Here, we report the crystal structures of two mutant EcFicT/EcFicA complexes (EcFicTG55RA and EcFicTAE28G) both showing close resemblance with the structure of the AMP-transferase VbhT from Bartonella schoenbuchensis in complex with its cognate antitoxin VbhA. However, crucial differences in the active site of EcFicT compared to VbhT and other AMP-transferases rationalize the lack of evidence for adenylylation activity. Comprehensive bioinformatic analysis suggests that EcFicT has evolved from canonical AMP-transferases and has acquired a conserved binding site for a yet to be discovered novel substrate. The G55R mutation has no effect on structure or thermal stability of EcFicT, such that the molecular basis for its associated Fic phenotype remains elusive. We anticipate that this structure will inspire further bioinformatic and experimental analyses in order to characterize the enzymatic activity of EcFicT and help revealing its physiological role.
Speaker gaze increases information coupling between infant and adult brains

Significance During communication, social ostensive signals (like gaze) are exchanged in a temporally contingent manner. Synchronized behavior creates social connectedness within human dyads, and even infants synchronize behaviorally with adults. However, the neural mechanisms that support infant–adult synchronization are unknown. Here, we provide evidence that infants up-regulate neural synchronization with adult partners when offered direct ostensive gaze, as compared with gaze aversion. Gaze therefore brings infant–adult neural activity into mutual alignment, creating a joint-networked state that may facilitate communicative success. Further, infants’ own communicative attempts were positively associated with adults’ neural synchronization to them, indicating mutual regulation of synchronization within infant–adult dyads. Thus, interpersonal neural synchronization may provide a mechanism by which infants construct their own earliest social networks. When infants and adults communicate, they exchange social signals of availability and communicative intention such as eye gaze. Previous research indicates that when communication is successful, close temporal dependencies arise between adult speakers’ and listeners’ neural activity. However, it is not known whether similar neural contingencies exist within adult–infant dyads. Here, we used dual-electroencephalography to assess whether direct gaze increases neural coupling between adults and infants during screen-based and live interactions. In experiment 1 (n = 17), infants viewed videos of an adult who was singing nursery rhymes with (i) direct gaze (looking forward), (ii) indirect gaze (head and eyes averted by 20°), or (iii) direct-oblique gaze (head averted but eyes orientated forward). In experiment 2 (n = 19), infants viewed the same adult in a live context, singing with direct or indirect gaze. Gaze-related changes in adult–infant neural network connectivity were measured using partial directed coherence. Across both experiments, the adult had a significant (Granger) causal influence on infants’ neural activity, which was stronger during direct and direct-oblique gaze relative to indirect gaze. During live interactions, infants also influenced the adult more during direct than indirect gaze. Further, infants vocalized more frequently during live direct gaze, and individual infants who vocalized longer also elicited stronger synchronization from the adult. These results demonstrate that direct gaze strengthens bidirectional adult–infant neural connectivity during communication. Thus, ostensive social signals could act to bring brains into mutual temporal alignment, creating a joint-networked state that is structured to facilitate information transfer during early communication and learning.
Landscape Visibility Analysis And Their Visualisation

Visibility analysis or Viewshed is a common function of almost all GIS systems. The aim of this project is to find out the best solution, to compute viewshed for the Olomouc region and ensure the best way of visualisation of the results. The first step to analyze the visibility is making a high quality Digital Terrain Model, choice of the best interpolation method and subsequent addition of vegetation and man-made structures layer. Visibility calculation is contained in a large number of software applications, but not all are able to compute visibility for a large area, so the choice of software was also very important. Currently there are many ways to transmit the analysis results to the target user. One of them is the use of Google Earth. The project deals with the possibilities of exporting the output from the visibility analysis from ArcGIS system to Google Earth. An important part is to optimize the size of the resulting layer using various methods of generalization so that the resulting layer is sufficiently precise and not too voluminous at the same time. The project also explores the possibilities of enrichment of visualization with multimedia content, which can be for example 3D models of buildings, photos, videos or spherical panoramas as we know from Google Street View, etc. The output of the project is an interactive application that will ensure a simple and visually attractive approach to data that represent the visibility of the most important observation points in the area of interest.
Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics

Macrophages are versatile immune cells that can detect a variety of pathogen-associated molecular patterns through their Toll-like receptors (TLRs). In response to microbial challenge, the TLR-stimulated macrophage undergoes an activation program controlled by a dynamically inducible transcriptional regulatory network. Mapping a complex mammalian transcriptional network poses significant challenges and requires the integration of multiple experimental data types. In this work, we inferred a transcriptional network underlying TLR-stimulated murine macrophage activation. Microarray-based expression profiling and transcription factor binding site motif scanning were used to infer a network of associations between transcription factor genes and clusters of co-expressed target genes. The time-lagged correlation was used to analyze temporal expression data in order to identify potential causal influences in the network. A novel statistical test was developed to assess the significance of the time-lagged correlation. Several associations in the resulting inferred network were validated using targeted ChIP-on-chip experiments. The network incorporates known regulators and gives insight into the transcriptional control of macrophage activation. Our analysis identified a novel regulator (TGIF1) that may have a role in macrophage activation.
Surgery for transposition of great arteries: A historical perspective

The history of surgery for transposition of great arteries (TGA) has paralleled the history of cardiac surgery. In fact, it began before the birth of open heart surgery when the palliative Blalock-Hanlon septectomy was first performed in 1948. The atrial switch, which was an attempt to correct the physiology of transposition, had significant shortcomings. The arterial switch sought to address them. This has emerged as an anatomically as well as physiologically appropriate solution. Today we continue to pursue technical refinements as well as try to expand the indications of the arterial switch. This review traces the various milestones in this perpetual journey.
Clinical efficacy of spironolactone for resistant hypertension: a meta analysis from randomized controlled clinical trials.

OBJECTIVES This study sought to determine the current effectiveness and safety of spironolactone for resistant hypertension. METHODS Pubmed, EMBASE and Cochrane databases were searched to identify studies that used spironolactone as add-on treatment in resistant hypertension patients. The major outcome is reduction of blood pressure. RESULTS Three randomized controlled trials, 5 observational study without control group have been identified. At follow-up review, there was a reduction in mean systolic and diastolic blood pressure (BP) respectively, of -20.56 mmHg (95% confidence interval [CI]: -36.47 to -4.65 mmHg) and -6.04 mm Hg (95% CI: -10.24 to -1.85 mm Hg) in controlled study. In uncontrolled studies, at 6-month follow-up, systolic and diastolic BP were reduced -20.73 mm Hg (95% CI: -25.62 to -15.83 mm Hg) and -8.94 mm Hg (95% CI: -10.82 to -7.05 mm Hg, respectively. CONCLUSION Spironolactone resulted in the reduction of mean BP in patients with resistant hypertension. The sustained efficacy and safety of spironolactone need to further confirm by large randomized controlled trials with long-term follow-up.
UNIMIB@NEEL-IT: Named Entity Recognition and Linking of Italian Tweets

English. This paper describes the framework proposed by the UNIMIB Team for the task of Named Entity Recognition and Linking of Italian tweets (NEEL-IT). The proposed pipeline, which represents an entry level system, is composed of three main steps: (1) Named Entity Recognition using Conditional Random Fields, (2) Named Entity Linking by considering both Supervised and Neural-Network Language models, and (3) NIL clustering by using a graph-based approach.
Effects of high-whey-protein intake and resistance training on renal, bone and metabolic parameters in rats

Consumption of high-protein (HP) diets is postulated to exert a negative influence on bone and renal health. However, no conclusive evidence has been presented related to this issue or to the potential protective action of resistance training on HP-induced systemic effects. We examined the effects of HP diet consumption on food intake, body-weight gain, body composition, and renal, bone and metabolic parameters of rats performing resistance training. A total of ninety-six adult male Wistar rats were randomly distributed in twelve experimental groups (n 8): normal-protein (10 %) or HP (45 %) diets, with or without resistance training, killed for experimental periods of 1, 2 or 3 months. Diets were based on a commercial whey protein hydrolysate. Consumption of HP diets and resistance training significantly affected food intake, body weight and body composition, as well as the plasma levels of total cholesterol, HDL-cholesterol and TAG. The buffering action of resistance training on such diet-induced alterations was especially evident in the levels of plasma TAG. Consumption of HP diets led to a considerable increase in kidney weight, urinary volume and acidity, as well as in the urinary excretion of Ca, with a parallel reduction in the urinary excretion of citrate (P < 0·05). No apparent deleterious effect on bone mineral content was found. In conclusion, consumption of HP diets caused alterations in renal health status and some metabolic parameters, but did not seem to affect bone status. Resistance training had a protective action against alterations of renal health status and some metabolic parameters such as plasma TAG.
Direct geolocation of stationary wideband radio signal based on time delays and Doppler shifts

Contrary to the suboptimal (two-step) geolocation procedures, we propose a maximum likelihood estimation for the position of a stationary transmitter which its delayed and Doppler shifted signal is observed by moving receivers. The position is estimated based on the same data used in common methods. However, it is performed in a single step by maximizing a cost function that depends on the unknown position only.
Towards Contextual Experimentation: Creating a Faculty Learning Community to Cultivate Writing-to-Learn Practices

Abstract In order to explore ways to integrate new pedagogical practices, five faculty members created an informal faculty learning community focused on writing-to-learn practices, an inquiry and process-based writing pedagogy. The faculty members learned the writing-to-learn practices together, periodically met to discuss how they implemented the practices, and reflected on each other’s instructional methods in the contexts of their own experiences. The faculty members engaged in a self-study in order to understand how the collaborative nature of the learning community helped them to learn and use the new teaching practices. After participating in a series of workshops together, they shared written reflections about their experiences of employing the practices in their own classrooms. The findings of this study reveal that participation in a faculty learning community provided an engaging and effective way to learn and make use of new pedagogical practices. Participants gained practical adaptive strategies from each other, felt supported in their experimentation with the new practices, and analyzed more deeply the ways in which the new practices could be integrated into their teaching. The authors describe how an informal faculty learning community can be an effective tool for faculty to research, learn, and analyze the learning of specific pedagogical practices.
CodeTimeline: Storytelling with versioning data

Working with a software system typically requires knowledge of the system's history, however this knowledge is often only tribal memory of the development team. In past user studies we have observed that when being presented with collaboration views and word clouds from the system's history engineers start sharing memories linked to those visualizations. In this paper we propose an approach based on a storytelling visualization, which is designed to entice engineers to share and document their tribal memory. Sticky notes can be used to share memories of a system's lifetime events, such as past design rationales but also more casual memories like pictures from after-work beer or a hackathon. We present an early-stage prototype implementation and include two design studies created using that prototype.