Miracle-dz/UniFAR-FTUs huggingface dataset:
Quality assessment of the results obtained by multivariate curve resolution analysis of multiple runs of gasoline blending processes

This work presents a quality assessment study of the results obtained by multivariate curve resolution of multiple runs of gasoline blending processes. This evaluation is performed by noise propagation studies using resampling methods and by calculation of feasible bands due to rotational ambiguities. Results showed that combination of matrix augmentation and use of constraints strategies during alternating least squares optimization minimize both rotational ambiguities and error propagation effects in the resolved solutions. The proposed approach is tested for simulated and experimental data sets obtained in the study of blending processes of gasolines monitored by NIR spectroscopy. Copyright © 2006 John Wiley & Sons, Ltd.
Medical Masks Versus N95 Respirators for Preventing COVID-19 Among Health Care Workers

It is uncertain if medical masks offer similar protection against COVID-19 compared with N95 respirators. This randomized trial, which enrolled participants in Canada, Israel, Pakistan, and Egypt, aimed to determine whether medical masks are noninferior to N95 respirators to prevent COVID-19 in health care workers providing routine care.
IMPRoVED: Integrated Method to Predict PostRouting setup Violations in Early Design Stages

The detail routing process is by far the most time consuming during the physical design flow. Routing starts with an estimation of timing slacks and aims to meet the timing specifications at signoff. In this paper, we propose an improved method to predict the net delays using RandomForestRegressor and thereby predict critical paths early on at the placement stage. Quick timing prediction is also essential in making time-sensitive edits to stepping of the chip based on post-Si feedback. The proposed algorithm is based on five novel features, namely, targeted feature selection, introduction of a one-hot encoding scheme, an outlier identification method, post-route buffer-bloat prediction, and post-route cell sizing prediction. Experimental results on academic benchmarks and industry circuits, both on advanced 10nm process node show that the proposed algorithm has led to significant improvements in accurately predicting timing slacks when compared with state of the art. The proposed algorithm predicts slack within 0.598% of signoff results, whereas the state of art results are erroneous by an average of 53.33% for the same metric. Overall time savings of 44.1% is seen when compared to running the traditional flow, and savings of 90% is seen for obtaining the timing results.
Comparing Norm-Based and Role-Based Strategies for Robot Communication of Role-Grounded Moral Norms

Because robots are perceived as moral agents, they must behave in accordance with human systems of morality. This responsibility is especially acute for language-capable robots because moral communication is a method for building moral ecosystems. Language capable robots must not only make sure that what they say adheres to moral norms; they must also actively engage in moral communication to regulate and encourage human compliance with those norms. In this work, we describe four experiments (total N=316) across which we systematically evaluate two different moral communication strategies that robots could use to influence human behavior: a norm-based strategy grounded in deontological ethics, and a role-based strategy grounded in role ethics. Specifically, we assess the effectiveness of robots that use these two strategies to encourage human compliance with norms grounded in expectations of behavior associated with certain social roles. Our results suggest two major findings, demonstrating the importance of moral reflection and moral practice for effective moral communication: First, opportunities for reflection on ethical principles may increase the efficacy of robots’ role-based moral language; and second, following robots’ moral language with opportunities for moral practice may facilitate role-based moral cultivation.
Accidents and injuries in workers of iron and steel industry in West Bengal, India: Prevalence and associated risk factors

ABSTRACT This study estimates the prevalence and risk factors of accidents and injuries among iron and steel industry workers. A cross-sectional study (N = 505) was conducted from November 2019 to March 2020 in the Indian Iron and Steel Company (IISCO), Burnpur, West Bengal, India. The result shows that about 28% of workers experienced accidents and injuries in the last 12 months. The most frequent injuries reported were cuts from sharp objects (37.32%), followed by fractures and dislocation (30.28%) and burns (19.01%), upper head injury (23.24%) and arm/shoulder injury (14.08%). Non-technical education (adjusted odds ratio [AOR]: 2.52), higher exposure in risky and polluted areas (AOR: 2.85), alcohol consumption (AOR: 2.47), poor occupational health and safety knowledge (AOR: 0.65) were significantly associated with work-related injuries. Occupational health and safety knowledge and usage of safety measures must be propagated and monitored to curb accidents and injuries among iron and steel industry workers in India.
Electron acceleration during guide field magnetic reconnection

Particle-in-cell simulations of the guide field intermittent magnetic reconnection are performed to study electron acceleration and pitch angle distributions. During the growing stage of reconnection, the power-law distribution function for the high-energy electrons and the pitch angle distributions of the low-energy electrons are obtained and compare favorably with observations by the Wind spacecraft. Direct evidence is found for the secondary acceleration during the later reconnection stage. A correlation between the generation of energetic electrons and the induced reconnection electric field is found. Energetic electrons are accelerated first around the X line, and then in the region outside the diffusion region, when the reconnection electric field has a bipolar structure. The physical mechanisms of these accelerations are discussed. The in-plane electrostatic field that traps the low-energy electrons and causes the anisotropic pitch angle distributions has been observed.
Separating the control of moving and holding still in post-stroke arm paresis

Moving and holding still have been posited to be under separate control regimes for both eye and arm movements. The paretic arm after stroke is notable for abnormalities both at rest and during movement, thus it provides an opportunity to address the relationships between control of reaching, stopping, and stabilizing. In this study, we asked whether independence of these behaviors is preserved in arm paresis. To address this question, we quantified resting postural abnormalities in stroke patients by measuring their biases in force production as they held their hand still in various locations in a planar workspace, and then assessed the influence of these resting force biases on active reaching in the same workspace. We found that patients had marked resting postural force biases at each location, even for the case when arm support was provided. However, these biases did not manifest during any phase of arm-supported planar reaching movements: not during initial acceleration, not to mid-trajectory perturbations, and not during deceleration to a stop. Resting force biases only appeared to switch on after a movement had fully stopped. These findings in stroke suggest that moving and holding still are functionally separable modes of control. At the same time, we found that patients’ resting postural force biases mirrored characteristics of abnormal synergies active during movement: they markedly decreased when arm support was provided; they were higher in more distal positions which require breaking out of flexion; and they scaled with the Fugl-Meyer score for the upper extremity (a measure of intrusion of abnormal synergies during active movement). These three shared features suggest a common mechanism for resting postural biases and abnormal synergies, which appears to be a contradiction given the functional separation of moving and holding still observed in the same patients. To resolve this apparent paradox, we propose a model that predicts a breakdown in the functional separation between reaching and holding still when patients move in the absence of weight support. Thus, the model posits that synergies are the behavioral manifestation of a spillover of posture into movement. Mapping these functional systems onto anatomical and physiological details of lesioned substrate after stroke may provide implementation-level insight into how normal arm motor control is assembled.
A 3D genome atlas of genetic variants and their pathological effects

The spatial architecture of the genome can be categorized into distinct layers. Each layer plays a critical role in transcriptional regulation and/or genomic integrity. Alterations at any level of the 3D genome can lead to an unwanted cascade of molecular events, which may ultimately drive the manifestation of disease. However, a comprehensive atlas of the mutations and structural genetic defects that affect genome organization has yet to be compiled. Moreover, we lack a centralized resource for interpretating the pathological effects of such genetic mutations. Therefore, we curated from the literature all the pathological alterations from the chromosome level on down to single nucleotide polymorphisms (SNPs) in order to investigate these diverse genetic mutations. Using a two-phase scoring algorithm, 3DFunc, we scored the transcriptomic causality of all variants in the context of 3D genome architecture from 20 cancer and 15 normal tissues. Further, 3DFunc can identify pathological variant-gene pairs in non-oncological diseases. Finally, we constructed a web-based database, 3DGeOD (https://www.csuligroup.com/3DGeOD/home), to provide all the curated variants, genomic disruptions, as well as the scoring results derived from 3DFunc. In summary, our study constructed a 3D genome atlas of genetic variants and will serve as a valuable resource for mining the putative pathological effects of any genetic mutation.
Analysis of rotating laminated cylindrical shells by different thin shell theories

Abstract The natural frequencies of the forward and backward modes of thin rotating laminated cylindrical shells are determined by using four common thin shell theories, namely Donnell’s, Flugge’s, Love’s and Sanders’. The objective is to present a unified analysis, formulated with the use of tracers so that it can be reduced to any of the four shell theories by giving appropriate values to the tracers. For simplicity, results are presented only for the case of simply supported-simply supported boundary conditions, which can be satisfied by expressing the displacement fields in terms of the products of sine and cosine functions. Numerical results presented are the non-dimensional frequency parameters of the forward and backward travelling modes for rotating cylindrical shells and the non-dimensional frequency parameters for non-rotating cylindrical shells. The present analysis is verified by comparing the numerical results with those in the literature and very good agreement is obtained.
A lysosomal lipid transport pathway that enables cell survival under choline limitation

Lysosomes degrade macromolecules and recycle their nutrient content to support cell function and survival over a broad range of metabolic conditions. Yet, the machineries involved in lysosomal recycling of many essential nutrients remain to be discovered, with a notable example being choline, an essential metabolite liberated in large quantities within the lysosome via the degradation of choline-containing lipids. To identify critical lysosomal choline transport pathways, we engineered metabolic dependency on lysosome-derived choline in pancreatic cancer cells. We then exploited this dependency to perform an endolysosome-focused CRISPR-Cas9 negative selection screen for genes mediating lysosomal choline recycling. Our screen identified the orphan lysosomal transmembrane protein SPNS1, whose loss leads to neurodegeneration-like disease in animal models, as critical for cell survival under free choline limitation. We find that SPNS1 loss leads to massive accumulation of lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE) within the lysosome. Mechanistically, we revealed that SPNS1 is required for the efflux of LPC species from the lysosome to enable their reesterification into choline-containing phospholipids in the cytosol. Using cell-based lipid uptake assays, we determine that SPNS1 functions as a proton gradient-dependent transporter of LPC. Collectively, our work defines a novel lysosomal phospholipid salvage pathway that is required for cell survival under conditions of choline limitation, and more broadly, provides a robust platform to deorphan lysosomal gene functions.
Evaluating restriction enzyme selection for genome reduction in conservation genomics

Conservation genomic studies in non-model organisms generally rely on genome reduction techniques based on restriction enzymes to identify population structure as well as candidate loci for local adaptation. These reduced libraries ensure a high density of SNP loci and high coverage for accurate genotyping. Despite the fraction of the genome that is sequenced is expected to be randomly located, the reduction of the genome might depend on the recognition site of the restriction enzyme used. Here, we evaluate the distribution and functional composition of loci obtained after Genotyping-by-sequencing (GBS) genome reduction with two widely used restriction enzymes (EcoT22I and ApeKI). To do so, we compared data from two endemic fish species (Symphodus ocellatus and Symphodus tinca, EcoT22I enzyme) and two ecosystem engineer sea urchins (Paracentrotus lividus and Arbacia lixula, ApeKI enzyme). In brief, we mapped the sequenced loci to the phylogenetically closest reference genome available (Labrus bergylta for fish and Strongylocentrotus purpuratus for sea urchins), classified them as exonic, intronic, and intergenic, and studied their functionality by using GO terms. We detected an enrichment towards exonic or intergenic regions depending on the restriction enzyme used, and we did not detect differences between total loci and candidate loci for adaptation. Despite most GO terms being shared between species, the analysis of their abundance showed differences between taxonomic groups, which may be attributed to differences of the targeted loci. Our results highlight the importance of restriction enzyme selection and the need for high-quality annotated genomes in conservation genomic studies.
Identification of novel natural product inhibitors of BRD4 using high throughput virtual screening and MD simulation

Bromodomains are evolutionarily conserved structural motifs that recognize acetylated lysine residues on histone tails. They play a crucial role in shaping chromatin architecture and regulating gene expression in various biological processes. Mutations in bromodomains containing proteins leads to multiple human diseases, which makes them attractive target for therapeutic intervention. Extensive studies have been done on BRD4 as a target for several cancers, such as Acute Myeloid Leukemia (AML) and Burkitt Lymphoma. Several potential inhibitors have been identified against the BRD4 bromodomain. However, most of these inhibitors have drawbacks such as nonspecificity and toxicity, decreasing their appeal and necessitating the search for novel non-toxic inhibitors. This study aims to address this need by virtually screening natural compounds from the NPASS database against the Kac binding site of BRD4-BD1 using high throughput molecular docking followed by similarity clustering, pharmacokinetic screening, MD simulation, and MM-PBSA binding free energy calculations. Using this approach, we identified five natural product inhibitors having a similar or better binding affinity to the BRD4 bromodomain compared to JQ1 (previously reported inhibitor of BRD4). Further systematic analysis of these inhibitors resulted in the top three hits: NPC268484 (Palodesangren-B), NPC295021 (Candidine), and NPC313112 (Buxifoliadine-D). Collectively, our in silico results identified some promising natural products that have the potential to act as potent BRD4-BD1 inhibitors and can be considered for further validation through future in vitro and in vivo studies.
Modeling Plots of Narrative Texts as Temporal Graphs

The paper outlines a formal model of plot (and syuzhet) for narrative texts. The basic unit are scenes and the motif repertoire instantiated in the scene. The motif repertoire consists of three sets of (closely related) elements: character stereotypes, types of verbal actions and action types. It is assumed that the motif repertoire is highly dependent on the corpus which is analyzed, in our case a corpus of romance and horror novels published as pulp 昀椀ction. The resulting information is represented in a temporal graph which in turn is used to compute relevant information on the scenes and characters. Scenes are also characterized by their valence and their arousal value. A second representation which o昀昀ers with a topic model of the direct speech and the narrative text a simple proxy for the types of verbal actions and the action types is also created. To assess the ability of these information structures to indicate changes in the temporal structures three evaluation methods are used based on arti昀椀cial data. We can con昀椀rm that a very abstract representation of the plot is able to do so, but contrary to our expectations the more information-rich model which makes use of the topic model is not better in doing so. The main contribution of this paper is its attempt to integrate di昀昀erent research proposals into one integral model. We o昀昀er a descriptive framework and a proposal for the formal model of plot, which makes it possible to identify research problems and align existing approaches.
Localization for uniform algebras generated by smooth functions on two‐manifolds

Conditions are given under which a uniform algebra on a two‐manifold must contain all continuous functions. In particular, it is shown that, if A is a uniform algebra generated by smooth functions on a compact smooth two‐manifold M such that the maximal ideal space of A is M, and every continuous function on M is locally a uniform limit of functions in A, then A = C(M). This gives an affirmative answer to a special case of a question from the Proceedings of the Symposium on Function Algebras held at Tulane University in 1965. It is also shown that, on every smooth manifold of dimension at least four, there exists a uniform algebra that is nonlocal. Additional related results are also established.
Strain dependent resistance in chemical vapor deposition grown graphene

The strain dependence of conductance of monolayer graphene has been studied experimentally here. The results illustrate the notable transitions: the slight increase, the dramatic decrease, and the sudden dropping of the conductance by gradually increasing the uniaxial strain. The graphene conductance behaves reversibly by tuning of the elastic tensile strain up to 4.5%, while it fails to recover after the plastic deformation at 5%. The change in conductance due to strain is surprisingly high, which indicates the potential applications in electromechanical devices.
Transcriptional programs controlling lineages specification of mandibular epithelium during tooth initiation

Tooth development starts with formation of the dental lamina, a localized thickening of the maxillary and mandibular epithelium, at specific location of oral cavity. How this dental lamina is specified within the continuous naïve maxillary and mandibular epithelium, remains as a critical and unresolved question. To identify potential genes and transcriptional regulatory networks that controlling dental lamina formation, we utilized single-cell Multiome-seq and Laser Microdissection coupled RNA-seq to profile gene expression and open chromatin of mandibular epithelium during tooth initiation. We comprehensively identified transcription factors (TFs) and signaling pathways that are differentially expressed among different domains (including dental lamina) along dorsal-ventral axis of mandibular epithelium. Specifically, we found Sox2 and Tfap2a/Tfap2b forming two complementary domains along the dorsal-ventral axis of mandibular epithelium. Furthermore, dental lamina specific or enriched TFs such as Pitx1, Pitx2 and Zfp536 are presented around the interface of Sox2 and Tfap2a/Tfap2b. We also identified correlation between signaling pathways and domain specific TFs. Through computational analysis of single-cell Multiome-seq dataset, we identified potential key/driver TFs and core transcriptional regulatory networks (TRNs) for lineages (oral, dental, skin) specification during tooth initiation. Our computational analysis also reveals a potential cross repression interactions between different groups of TFs (i.e. Pitx1/Pitx2 and Tfap2a/Tfap2b) that might be essential for dental lamina specification.
Inhibitory effect of lactobacilli supernatants on biofilm and filamentation of C. albicans, C. tropicalis, and C. parapsilosis

Probiotic Lactobacillus strains had been investigated for the potential to protect against infection caused by the major fungal pathogen of human, Candida albicans. Besides antifungal activity, lactobacilli demonstrated a promising inhibitory effect on biofilm formation and filamentation of C. albicans. On the other hand, two commonly isolated non-albicans Candida species, C. tropicalis and C. parapsilosis, have similar characteristics in filamentation and biofilm formation with C. albicans. However, there is scant information of the effect of lactobacilli on the two species. In this study, biofilm inhibitory effects of L. rhamnosus ATCC 53103, L. plantarum ATCC 8014, and L. acidophilus ATCC 4356 were tested on the reference strain C. albicans SC5314 and six bloodstream isolated clinical strains, two each of C. albicans, C. tropicalis, and C. parapsilosis. Cell-free culture supernatants (CFSs) of L. rhamnosus and L. plantarum significantly inhibited in vitro biofilm growth of C. albicans and C. tropicalis. L. acidophilus, conversely, had little effect on C. albicans and C. tropicalis but was more effective on inhibiting C. parapsilosis biofilms. Neutralized L. rhamnosus CFS at pH 7 retained the inhibitory effect, suggesting that exometabolites other than lactic acid produced by the Lactobacillus strain might be accounted for the effect. Furthermore, we evaluated the inhibitory effects of L. rhamnosus and L. plantarum CFSs on the filamentation of C. albicans and C. tropicalis strains. Significantly less Candida filaments were observed after co-incubating with CFSs under hyphae-inducing conditions. Expressions of six biofilm-related genes (ALS1, ALS3, BCR1, EFG1, TEC1, and UME6 in C. albicans and corresponding orthologs in C. tropicalis) in biofilms co-incubated with CFSs were analyzed using quantitative real-time PCR. When compared to untreated control, the expressions of ALS1, ALS3, EFG1, and TEC1 genes were downregulated in C. albicans biofilm. In C. tropicalis biofilms, ALS3 and UME6 were downregulated while TEC1 was upregulated. Taken together, the L. rhamnosus and L. plantarum strains demonstrated an inhibitory effect, which is likely mediated by the metabolites secreted into culture medium, on filamentation and biofilm formation of C. albicans and C. tropicalis. Our finding suggested an alternative to antifungals for controlling Candida biofilm.