Miracle-dz/UniFAR-FTUs huggingface dataset:
Limitations of recellularized biological scaffolds for human transplantation

A shortage of donor organs for transplantation and the dependence of the recipients on immunosuppressive therapy have motivated researchers to consider alternative regenerative approaches. The answer may reside in acellular scaffolds generated from cadaveric human and animal tissues. Acellular scaffolds are expected to preserve the architectural and mechanical properties of the original organ, permitting cell attachment, growth, and differentiation. Although theoretically, the use of acellular scaffolds for transplantation should pose no threat to the recipient's immune system, experimental data have revealed significant immune responses to allogeneic and xenogeneic transplanted scaffolds. Herein, we review the various factors of the scaffold that could trigger an inflammatory and/or immune response, thereby compromising its use for human transplant therapy. In addition, we provide an overview of the major cell types that have been considered for recellularization of the scaffold and their potential contribution to triggering an immune response.
Haptic Feedback in a simulated representation of a highway in Automotive User Interfaces

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from permissions@acm.org. CHI’18, April 21–April 26, 2018, Montréal, Canada. Copyright © 2018 ACM ISBN DOI string from ACM form confirmation Abstract Optimized interfaces should ease the take-over of partially automated vehicles by providing information about the current traffic situation. Intelligent transportation systems provide vehicles and drivers with information that exceed the individual vehicle’s perception range and might facilitate driver take-overs. The concept of this paper is based on the Providentia system, which combines vehicle and infrastructure perception to provide participants with a multiple kilometer far-reaching view. A visual representation in 3D of the highway and the traffic is modeled in which haptic feedback with Ultrahaptics is given when interacting with the in the air projected visual representation. Within this experience interface of Providentia additionally an augmented reality windshield display is simulated to visualize work documents. To interact with the AR windshield display, haptic feedback is given while editing work documents. Haptic feedback thus improves the performance of the driver when working or interacting with the simulated hologram within the vehicle.
Analyzing the relationship between Altmetric score and literature citations in the Implantology literature.

BACKGROUND The influence of research has long been studied using citations and impact factors (IFs). Electronic media is changing how people interact with the scientific literature. There are few investigations into these trends. PURPOSE To explore whether Altmetrics correlate with traditional bibliometrics in the Implantology literature. MATERIALS AND METHODS Five Implantology journals with the highest IF and the 10 most highly-cited articles within those journals from 2013 to 2016 were reviewed. Altmetric score, citation count, and media "mentions" were recorded. Comparisons were conducted between Altmetric score, citations, and IF by performing Pearson correlation coefficients and descriptive statistics. Twitter accounts were studied and compared to other metrics. RESULTS Analysis revealed no correlation between citations and Altmetrics (r = .096,P = .506) or IF and Altmetrics (r = .111,P = .443) in 2013. Altmetrics were also not significantly correlated with citations (r = 0.148,P = .305) or IF (r = .145,P = .315) in 2016. Total Altmetric scores were nine times higher in 2016 compared to 2013, with news outlets and Twitter seeing large increases in mentions. Twitter was the top medium receiving mentions across the two cohorts. CONCLUSIONS Compared to other fields, Implantology articles received lower Altmetric scores, noting an area of improvement. Altmetrics at this time are insufficient to replace traditional bibliometrics, but may provide helpful real-time information concerning article dissemination.
Major–Minor Long Short-Term Memory for Word-Level Language Model

Language model (LM) plays an important role in natural language processing (NLP) systems, such as machine translation, speech recognition, learning token embeddings, natural language generation, and text classification. Recently, the multilayer long short-term memory (LSTM) models have been demonstrated to achieve promising performance on word-level language modeling. For each LSTM layer, larger hidden size usually means more diverse semantic features, which enables the LM to perform better. However, we have observed that when a certain LSTM layer reaches a sufficiently large scale, the promotion of overall effect will slow down, as its hidden size increases. In this article, we analyze that an important factor leading to this phenomenon is the high correlation between the newly extended hidden states and the original hidden states, which hinders diverse feature expression of the LSTM. As a result, when the scale is large enough, simply lengthening the LSTM hidden states will cost tremendous extra parameters but has little effect. We propose a simple yet effective improvement on each LSTM layer consisting of a large-scale Major LSTM and a small-scale Minor LSTM to break the high correlation between the two parts of hidden states, which we call Major–Minor LSTMs (MMLSTMs). In experiments, we demonstrate the LM with MMLSTMs surpasses the existing state-of-the-art model on Penn Treebank (PTB) and WikiText-2 (WT2) data sets and outperforms the baseline by 3.3 points in perplexity on WikiText-103 data set without increasing model parameter counts.
Squalene lipotoxicity in a lipid droplet‐less yeast mutant is linked to plasma membrane dysfunction

Squalene is a naturally occurring triterpene with wide industrial applications. Due to limited natural resources, production of this valuable lipid in yeast is of high commercial relevance. Typically low levels of squalene in yeast can be significantly increased by specific cultivation conditions or genetic modifications. Under normal conditions, excess squalene is stored in lipid droplets (LD), while in a Saccharomyces cerevisiae mutant unable to form LD it is distributed to cellular membranes. We present here the evidence that squalene accumulation in this LD‐less mutant treated with squalene monooxygenase inhibitor terbinafine induces growth defects and loss of viability. We show that plasma membrane malfunction is involved in squalene toxicity. We have found that subinhibitory concentrations of terbinafine increased the sensitivity of LD‐less mutant to several membrane‐active substances. Furthermore, squalene accumulation in terbinafine‐treated LD‐less cells disturbed the maintenance of membrane potential and increased plasma membrane permeability to rhodamine 6G. LD‐less cells treated with terbinafine showed also high sensitivity to osmotic stress. To confirm the causal relationship between squalene accumulation, loss of viability and impaired plasma membrane functions we treated LD‐less cells simultaneously with terbinafine and squalene synthase inhibitor zaragozic acid. Reduction of squalene levels by zaragozic acid improved cell growth and viability and decreased plasma membrane permeability to rhodamine 6G in terbinafine‐treated LD‐less cells. Our results support the hypothesis that plasma membrane malfunction is involved in the mechanisms of squalene lipotoxicity in yeast cells with defective lipid storage.
Automatic Detection of Pain from Facial Expressions: A Survey

Pain sensation is essential for survival, since it draws attention to physical threat to the body. Pain assessment is usually done through self-reports. However, self-assessment of pain is not available in the case of noncommunicative patients, and therefore, observer reports should be relied upon. Observer reports of pain could be prone to errors due to subjective biases of observers. Moreover, continuous monitoring by humans is impractical. Therefore, automatic pain detection technology could be deployed to assist human caregivers and complement their service, thereby improving the quality of pain management, especially for noncommunicative patients. Facial expressions are a reliable indicator of pain, and are used in all observer-based pain assessment tools. Following the advancements in automatic facial expression analysis, computer vision researchers have tried to use this technology for developing approaches for automatically detecting pain from facial expressions. This paper surveys the literature published in this field over the past decade, categorizes it, and identifies future research directions. The survey covers the pain datasets used in the reviewed literature, the learning tasks targeted by the approaches, the features extracted from images and image sequences to represent pain-related information, and finally, the machine learning methods used.
Maternal dietary inflammatory potential and quality are associated with offspring asthma risk over 10-year follow-up: the Lifeways Cross-Generation Cohort Study.

BACKGROUND Asthma is the most common childhood chronic health condition. Maternal antenatal diet has been associated with offspring asthma risk, but studies investigating maternal whole diet quality and inflammatory potential with long-term offspring follow-up (>5 y) are rare. OBJECTIVES We aimed to elucidate these associations in a prospective cohort study in Ireland. METHODS Early pregnancy diets were assessed using a validated FFQ from which energy-adjusted Dietary Inflammatory Index (E-DII) and Healthy Eating Index (HEI)-2015 scores were computed. Doctor-diagnosed offspring asthma status (general practitioner or parent reports) for the first 10 y of life was collected at 3-y, 5-y, and 9-y follow-up. A total of 862 mother-child pairs with information on maternal diet and ≥1 offspring asthma data points were included. The longitudinal associations between maternal E-DII and HEI scores and offspring asthma status were assessed using generalized estimating equations. RESULTS Cumulative offspring asthma incidence was 21% over the 10-y period. In the main models, adjusted for maternal lifestyle and sociodemographic factors, a higher E-DII score, indicating a more proinflammatory diet, was associated with higher risk of offspring asthma (OR: 1.35; 95% CI: 1.10, 1.65; per 1-SD score increment), whereas a higher HEI-2015 score, indicating better dietary quality, was associated with lower risk (OR: 0.77; 95% CI: 0.64, 0.93) (both P < 0.01). Results persisted with further adjustment for childhood factors (e.g., breastfeeding, diet, and childcare attendance) and parental asthma history. Similar associations were observed when E-DII and HEI-2015 scores were modeled in quartiles (both P-trend < 0.05). Associations for HEI-2015 were attenuated after adjustment for E-DII, suggesting the importance of anti-inflammatory pathways. CONCLUSIONS Our results suggest that a proinflammatory and low-quality diet during pregnancy is associated with a higher risk of offspring asthma. Pending confirmation from other studies, optimizing these aspects of maternal diet can be a promising strategy for reducing childhood asthma risk. This prospective observational study was registered at the ISRCTN Registry as ISRCTN16537904.
Blocks in Tricarboxylic Acid Cycle of Salmonella enterica Cause Global Perturbation of Carbon Storage, Motility, and Host-Pathogen Interaction

We performed perturbation analyses of the tricarboxylic acid cycle of the gastrointestinal pathogen Salmonella enterica serovar Typhimurium. The defect of fumarase activity led to accumulation of fumarate but also resulted in a global alteration of carbon fluxes, leading to increased storage of glycogen. Gross alterations were observed in proteome and metabolome compositions of fumarase-deficient Salmonella. In turn, these changes were linked to aberrant motility patterns of the mutant strain and resulted in highly increased phagocytic uptake by macrophages. Our findings indicate that basic cellular functions and specific virulence functions in Salmonella critically depend on the proper function of the primary metabolism. ABSTRACT The tricarboxylic acid (TCA) cycle is a central metabolic hub in most cells. Virulence functions of bacterial pathogens such as facultative intracellular Salmonella enterica serovar Typhimurium (S. Typhimurium) are closely connected to cellular metabolism. During systematic analyses of mutant strains with defects in the TCA cycle, a strain deficient in all fumarase isoforms (ΔfumABC) elicited a unique metabolic profile. Alongside fumarate, S. Typhimurium ΔfumABC accumulates intermediates of the glycolysis and pentose phosphate pathway. Analyses by metabolomics and proteomics revealed that fumarate accumulation redirects carbon fluxes toward glycogen synthesis due to high (p)ppGpp levels. In addition, we observed reduced abundance of CheY, leading to altered motility and increased phagocytosis of S. Typhimurium by macrophages. Deletion of glycogen synthase restored normal carbon fluxes and phagocytosis and partially restored levels of CheY. We propose that utilization of accumulated fumarate as carbon source induces a status similar to exponential- to stationary-growth-phase transition by switching from preferred carbon sources to fumarate, which increases (p)ppGpp levels and thereby glycogen synthesis. Thus, we observed a new form of interplay between metabolism of S. Typhimurium and cellular functions and virulence. IMPORTANCE We performed perturbation analyses of the tricarboxylic acid cycle of the gastrointestinal pathogen Salmonella enterica serovar Typhimurium. The defect of fumarase activity led to accumulation of fumarate but also resulted in a global alteration of carbon fluxes, leading to increased storage of glycogen. Gross alterations were observed in proteome and metabolome compositions of fumarase-deficient Salmonella. In turn, these changes were linked to aberrant motility patterns of the mutant strain and resulted in highly increased phagocytic uptake by macrophages. Our findings indicate that basic cellular functions and specific virulence functions in Salmonella critically depend on the proper function of the primary metabolism.
Comparative profiling of skeletal muscle models reveals heterogeneity of transcriptome and metabolism

Rat L6, mouse C2C12, and primary human skeletal muscle cells (HSMCs) are commonly used to study biological processes in skeletal muscle, and experimental data on these models are abundant. However, consistently matched experimental data are scarce, and comparisons between the different cell types and adult tissue are problematic. We hypothesized that metabolic differences between these cellular models may be reflected at the mRNA level. Publicly available data sets were used to profile mRNA levels in myotubes and skeletal muscle tissues. L6, C2C12, and HSMC myotubes were assessed for proliferation, glucose uptake, glycogen synthesis, mitochondrial activity, and substrate oxidation, as well as the response to in vitro contraction. Transcriptomic profiling revealed that mRNA of genes coding for actin and myosin was enriched in C2C12, whereas L6 myotubes had the highest levels of genes encoding glucose transporters and the five complexes of the mitochondrial electron transport chain. Consistently, insulin-stimulated glucose uptake and oxidative capacity were greatest in L6 myotubes. Insulin-induced glycogen synthesis was highest in HSMCs, but C2C12 myotubes had higher baseline glucose oxidation. All models responded to electrical pulse stimulation-induced glucose uptake and gene expression but in a slightly different manner. Our analysis reveals a great degree of heterogeneity in the transcriptomic and metabolic profiles of L6, C2C12, or primary human myotubes. Based on these distinct signatures, we provide recommendations for the appropriate use of these models depending on scientific hypotheses and biological relevance.
Cilia-driven asymmetric Hedgehog signalling determines the amphioxus left-right axis by controlling Dand5 expression

ABSTRACT Cilia rotation-driven nodal flow is crucial for the left-right (L-R) break in symmetry in most vertebrates. However, the mechanism by which the flow signal is translated to asymmetric gene expression has been insufficiently addressed. Here, we show that Hedgehog (Hh) signalling is asymmetrically activated (L<R) in the region in which initial asymmetric Dand5 expression is detected. Upregulation of Hh signalling on the left side of wild-type embryos induces ectopic Dand5 expression on the left side, and the unilateral recovery of Hh signalling in Hh homozygous mutants induces Dand5 expression in the Hh signal recovery side. Immunofluorescence analysis results revealed that Hh fusion protein is asymmetrically enriched in the anterior-right paraxial mesoderm at the early neurula stage. Inhibiting embryonic cilia motility using methylcellulose (MC) blocks Hh protein enrichment on the right hand side and randomizes Dand5 expression and organ positioning along the L-R axis. These findings present a model showing that cilia movement is crucial for the symmetry breaks in amphioxus through asymmetric Hh protein transport. The resultant asymmetric Hh signalling provides a clue into the induction of asymmetric Dand5 expression. This article has an associated ‘The people behind the papers’ interview. Highlighted Article: Cilia movement and its induced asymmetric Hh signalling are the two key regulators for the establishment of amphioxus left-right asymmetry, likely representing an evolutionarily conserved mechanism in deuterostomes.
The evolution of spherical cell shape; progress and perspective

Bacterial cell shape is a key trait governing the extracellular and intracellular factors of bacterial life. Rod-like cell shape appears to be original which implies that the cell wall, division, and rod-like shape came together in ancient bacteria and that the myriad of shapes observed in extant bacteria have evolved from this ancestral shape. In order to understand its evolution, we must first understand how this trait is actively maintained through the construction and maintenance of the peptidoglycan cell wall. The proteins that are primarily responsible for cell shape are therefore the elements of the bacterial cytoskeleton, principally FtsZ, MreB, and the penicillin-binding proteins. MreB is particularly relevant in the transition between rod-like and spherical cell shape as it is often (but not always) lost early in the process. Here we will highlight what is known of this particular transition in cell shape and how it affects fitness before giving a brief perspective on what will be required in order to progress the field of cell shape evolution from a purely mechanistic discipline to one that has the perspective to both propose and to test reasonable hypotheses regarding the ecological drivers of cell shape change.
IMPACT OF THE BEAM DYNAMICS SIMULATION FOR THE CONCEPT OF IFMIF ACCELERATOR

The control of the beam loss during the acceleration is a major concern about the deuteron linac design for the International Fusion Materials Irradiation Facility (IFMIF). The baseline design for an accelerator module employs the 175 MHz cw RFQ with 8-MeV, 125-mA output beam, and eight 175 MHz separated DTL tanks to provide 32-, 36-, and 40-MeV beams. A newly developed beam dynamics simulation code for high current linac based on the PIC method can be applied to confirm the accuracy of the design codes such as PARMTEQ, especially in the end regions of the RFQ. The effect of the fluctuation of the incident conditions and the RF control error to the final beam loss and the resulting loss of availability are also discussed.
Statistical and Nature-inspired Metaheuristics Analysis on Flexirubin Production

Nowadays, demand for natural pigments has increased dramatically due to the awareness of the toxicity of some synthetic pigments. Because of the high cost of growth medium for natural pigment production, various studies have been carried out to explore medium which are less costly, such as agricultural waste. This study highlight on the application of firefly algorithm (FA) and bat algorithm (BA) in optimizing yellowish-orange pigment production (flexirubin) from the agricultural waste material. At present, response surface methodology (RSM) is the most preferred statistical method in optimizing pigment production. However, in the last two decades, nature-inspired metaheuristics approach has been used extensively in the fermentation process and have continually improve the efficiency in the optimization problem especially in pigment production. This study compared the analytics studies of RSM, FA and BA in the estimation of fermentation parameters (Lactose, Ltryptophan, and KH2PO4) in flexirubin production from Chryseobacterium artocarpi CECT8497T. All models provided similar quality predictions for the above three independent variables in term of flexirubin production with bat algorithm showing more accurate in estimation, with the coefficient value of 98.87% compare to RSM 98.20% and FA 98.38%.
The Experiences of Pre-service Science Teachers in Educational Content Development Using Web 2.0 Tools

The present study aimed to improve the experiences of pre-service science teachers in content development using Web 2.0 tools and to determine the effects of these experiences on their self-efficacy beliefs in content development via Web 2.0 tools. The present study was conducted with a mixed design that included empirical and phenomenological methods. Forty-two pre-service science teachers participated in the study. During the implementation, pre-service teachers developed content using Web 2.0 tools such as Kahoot, Quizizz, Powtoon, Emaze, MindMeister and Toondoo and shared the content with the class using Edmodo. “Self-Efficacy Belief Scale on Fast Content Development via Web 2.0” was used as pre- and post-tests. Findings demonstrated that pre-service teachers’ self-efficacy beliefs and all sub-dimensions of content development via Web 2.0 tools improved as a result of the implementation. The views of them were grouped under seven themes; prejudice, satisfaction, awareness, fun, infrastructure problems, language problems and tool problems. Additionally, when the mean of item responses were examined, it was seen that the highest one was about preparing worksheet self-efficacy belief. Furthermore, it was determined that pre-service teachers were happy to participate in the implementation, recognized ways to integrate technology in their fields, and had fun while developing content.