Miracle-dz/UniFAR-FTUs huggingface dataset:
Neutralization Of SARS-CoV-2 Variants By A Human Polyclonal Antibody Therapeutic (COVID-HIG, NP-028) With High Neutralizing Titers To SARS-CoV-2

Since the start of the COVID-19 outbreak the World Health Organization (WHO) has classified multiple SARS-CoV-2 Variants-of-Concern and Variants-of-Interest (VOC/VOI) with mutations in their Spike protein that increase transmissibility and/or reduce the effectiveness of vaccines and monoclonal antibody therapeutics. The emergence of these variants represents a significant health risk and highlights the need for additional COVID-19 therapeutics that maintain the ability to neutralize current, as well as future variants. COVID-HIG (NP-028) is a polyclonal Anti-SARS-CoV-2 human Immunoglobulin purified from source human plasma screened for high antibody titers to SARS-CoV-2 antigens. COVID-HIG was previously evaluated in INSIGHT 013 clinical trial [NCT04546581] which was an international, multi-center, adaptive, randomized, double-blind, placebo-controlled trial of the safety, tolerability and efficacy of a single dose infusion (up to 400 mL) of Anti-Coronavirus Hyperimmune Intravenous Immunoglobulin (hIVIG) for the treatment of adult recently hospitalized COVID-19 patients (N=593). COVID-HIG is currently being evaluated for clinical efficacy in a Phase 3 placebo-controlled study INSIGHT 012 (NCT04910269) to compare the safety and efficacy of a single infusion of anti-COVID-19 hyperimmune immunoglobulin (hIVIG) versus placebo among adults with recently diagnosed SARS-CoV-2 infection who do not require hospitalization. In the present study, in-vitro pseudovirus and live virus neutralization assays were used to assess the impact of SARS-CoV-2 variant spike mutations on neutralizing potency of COVID-HIG. These assays are valuable tools for monitoring the potential impact of variant mutations on efficacy of antibody therapeutics as well as vaccines/natural immunity. To date, COVID-HIG (NP-028) has been shown to retain neutralizing potency against 20 full spike protein sequence SARS-CoV-2 pseudovirus variants including all currently classified VOC/VOI (Alpha, Beta, Gamma, Delta/Delta+, Eta, Iota, Kappa, Lambda, Mu as of Sept 2021) as well as 4 live virus variants (Alpha, Beta, Gamma, and Iota).
State Prediction of Slagging on Coal-fired Boilers Based on Fuzzy C-means Clustering and Support Vector Machine

A model of support vector machine(SVM)forecasting system was built up for state prediction of slagging on coal-fired boilers based on fuzzy C-means clustering(FCM)data preprocessing,which takes the softening temperature,alkali-acid ratio,SiO2-Al2O3ratio,percentage of silicon content,dimensionless average furnace temperature and dimensionless diameter of actual tangential flow circle as input variables, and the slagging degree as output variable.Slagging characteristics of 10boilers were evaluated with the optimized model.Results show that the model is able to avoid over-fitting of training sample sets,and it has relatively strong generalization capability.The prediction accuracy with FCM-SVM model used in this experiment is 100%,indicating high prediction accuracy of boiler slagging characteristics.
Quantitative analysis of volatile organic compounds (VOCs) in soil via passive sampling : polyethylene sampler design and optimization

The author hereby grants to MIT permission to reproduce and to distribute publicly paper and electronic copies of this thesis document in whole or in part in any medium now known or hereafter created. ABSTRACT The potential for the release of volatile organic compounds (VOCs) to our natural environment is pervasive. However, the ability to accurately measure and predict VOC soil vapor concentrations is still limited. A polyethylene (PE) quantitative passive sampler using performance reference compounds and deployed via a hand driven probe is proposed as a solution. Additionally, a 1D diffusion mass transfer model was developed in MATLAB to predict the mass uptake into the PE sampler over time. The model was then implemented to investigate the effects of PE size and deployment time on the detection limit of BTEX compounds. Preliminary testing of the deployment probe indicates that a design to secure the PE around the outside of a driven rod must include a protective cover over the PE during insertion. A perforated pipe design is suggested. After deployment and recovery, the PE is extracted into water. The extraction water is then analyzed by direct aqueous injection to GC/FID. The minimum concentration detectable in soil vapors, by this PE passive sampling method, was determined to be the product of the target compound's air-water partitioning coefficient and the analytical detection limit. Assuming a 5 ng/mL analytical detection limit, the minimum soil vapor detection limit for toluene was approximately 1.25 mg/m 3. This limit would be similar for all BTEX compound and is above sub-slab vapor intrusion screening levels for the more toxic compounds such as benzene. This indicates that direct aqueous injection provides insufficient sensitivity and that purge and trap concentrations of VOCs is likely needed. It was also determined that a PE sampler, with dimensions as small as 5"x5/8"x0.0005", could theoretically reach 10 mg/m 3 sensitivity within a 1 h deployment time. This result suggests potential applications of the sampler for rapid and accurate site characterization of BTEX compounds. I would like to thank my Thesis Supervisor Philip Gschwend for providing me with endless hours of guidance, advice, and insight. I am deeply appreciative of his teaching, mentorship, and contagious enthusiasm. I am also grateful for sharing the exploration into this research topic with my classmates jaren Soo and Hanqing Liu. Always willing to discuss their thoughts and findings with me, their individual research helped to propel my …
Distributed Time-Varying Group Formation Tracking for Multiagent Systems With Switching Interaction Topologies via Adaptive Control Protocols

In this article, time-varying group formation (TVGF) tracking problems for general linear multiagent systems (GLMASs) with switching interaction topologies are investigated. Different from previous studies, a novel TVGF tracking approach is proposed, where all agents are divided into three types: the virtual leader, the group leader, and the follower. The virtual leader is designed to assign the trajectory of GLMASs. Subgroups can be interacted with each other by cooperation among group leaders such that the relative configuration between different groups can be adjusted simultaneously. The followers in each group can achieve time-varying subformations. Moreover, under the influence of external disturbances and switching topologies, based on the distributed observer, two different distributed adaptive control protocols are constructed without using any global information such as the eigenvalue of the Laplacian matrix related to the communication topologies, the upper boundness of the leader’s input, and so on. The algorithms to determine parameters of control protocols are also presented. Furthermore, the closed-loop stability of GLMASs is proven by the Lyapunov theory. Finally, numerical simulations are given to verify the effectiveness of theoretical results.
Asian Newsrooms in Transition: A Study of Data Journalism Forms and Functions in Singapore’s State-Mediated Press System

ABSTRACT As more newsrooms practice data journalism in this age of “big data”, discussions on the forms and functions of data journalism continue to be Western-centric, focusing on its ability to conduct investigations, enhance democracy and empower the public. This study focuses on newsrooms in Asia transitioning into greater data journalism practice that may have an abundance of data at their disposal but operate within strictly regulated media environments, to uncover if data journalism takes on different forms and plays different normative roles in the region. Focus is placed on Singapore, a global city in Asia, and interviews with local newsworkers and a two-part content analysis of their “nomination-worthy” data stories and actual data stories produced were conducted. Results indicate a view of improving the audience experience as consumer rather than citizen, and a tendency for data stories on politics to be set beyond one’s own borders. A lower data literacy among newsworkers may also have hindered the complexity and variety of data visualizations used and resulted in extensive reference to “official sources”. To be deemed exceptional, data stories need not play a watchdog role either, or feature investigative elements, but may be informative in less adversarial ways.
The determinants of risk reporting during the period of adoption of Basel II Accord: evidence from the Portuguese commercial banks

PurposeThe purpose of this paper to analyze the risk reporting practices and its determinants of commercial banks during the period of the adoption of the Basel II Accord in Portugal.Design/methodology/approachThe paper conducts a content analysis of the risk and risk management sections included in the management reports and the notes of the annual reports of Portuguese commercial banks, for the years 2007, 2010 and 2013.FindingsFindings show that theoretical frameworks underpinned in agency and legitimacy theories continue to provide valid explanations for risk reporting by Portuguese banks. More specifically, findings indicate that agency costs, public visibility and reputation are crucial drivers of risk reporting. Findings also indicate that younger banks with lower risk management skills use risk reporting either as an informational process or as a channel to manage organizational legitimacy.Research limitations/implicationsThe content analysis does not allow readily for in-depth qualitative inquiry. The coding instrument is subject to coder bias. Information about risk can be provided in sources other than annual reports. Additionally, not all banks disclose information on corporate governance-related variables that could also influence risk reporting.Originality/valueThe current research setting has never been studied hitherto. In this sense, this study seems to be of great relevance given the scarcity of literature on the subject in Portugal.
BlotIt—Optimal alignment of Western blot and qPCR experiments

Biological systems are frequently analyzed by means of mechanistic mathematical models. In order to infer model parameters and provide a useful model that can be employed for systems understanding and hypothesis testing, the model is often calibrated on quantitative, time-resolved data. To do so, it is typically important to compare experimental measurements over broad time ranges and various experimental conditions, e.g. perturbations of the biological system. However, most of the established experimental techniques such as Western blot, or quantitative real-time polymerase chain reaction only provide measurements on a relative scale, since different sample volumes, experimental adjustments or varying development times of a gel lead to systematic shifts in the data. In turn, the number of measurements corresponding to the same scale enabling comparability is limited. Here, we present a new flexible method to align measurement data that obeys different scaling factors. We propose an alignment model to estimate these scaling factors and provide the possibility to adapt this model depending on the measurement technique of interest. In addition, an error model can be specified to adequately weight the different data points and obtain scaling-model based confidence intervals of the finally scaled data points. Our approach is applicable to all sorts of relative measurements and does not need a particular experimental condition that has been measured over all available scales. An implementation of the method is provided with the R package blotIt including refined ways of visualization.
Differential Glycemic Effects of Low- versus High-Glycemic Index Mediterranean-Style Eating Patterns in Adults at Risk for Type 2 Diabetes: The MEDGI-Carb Randomized Controlled Trial

A Mediterranean-style healthy eating pattern (MED-HEP) supports metabolic health, but the utility of including low-glycemic index (GI) foods to minimize postprandial glucose excursions remain unclear. Therefore, we investigated the relative contribution of GI towards improvements in postprandial glycemia and glycemic variability after adopting a MED-HEP. We conducted a randomized, controlled dietary intervention, comparing high- versus low-GI diets in a multi-national (Italy, Sweden, and the United States) sample of adults at risk for type 2 diabetes. For 12 weeks, participants consumed either a low-GI or high-GI MED-HEP. We assessed postprandial plasma glucose and insulin responses to high- or low-GI meals, and daily glycemic variability via continuous glucose monitoring at baseline and post-intervention. One hundred sixty adults (86 females, 74 males; aged 55 ± 11 y, BMI 31 ± 3 kg/m2, mean ± SD) with ≥two metabolic syndrome traits completed the intervention. Postprandial insulin concentrations were greater after the high-GI versus the low-GI test meals at baseline (p = 0.004), but not post-intervention (p = 0.17). Postprandial glucose after the high-GI test meal increased post-intervention, being significantly higher than that after the low-GI test meal (35%, p < 0.001). Average daily glucose concentrations decreased in both groups post-intervention. Indices of 24-h glycemic variability were reduced in the low-GI group as compared to baseline and the high-GI intervention group. These findings suggest that low-GI foods may be an important feature within a MED-HEP.
HDAC5 modulates PD-L1 expression and cancer immunity via p65 deacetylation in pancreatic cancer

Rationale: Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with a dismal 5-year survival less than 10%. Most patients with PDAC exhibit poor response to single-agent immunotherapy. Multimodal therapies targeting mechanisms of resistance to immunotherapy are urgently needed. We found that the class IIa histone deacetylase (HDAC) member, HDAC5 is downregulated in multiple solid tumors and its level were associated with favorable prognosis in PDAC patients. Upregulated genes in patients harboring HDAC5 deletions were enriched in adaptive immune responses and lymphocyte-mediated immunity in The Cancer Genome Atlas (TCGA) pancreatic cancer dataset. Methods: Tissue microarray of pancreatic cancer were used to analysis the correlation between HDAC5 and PD-L1. RNA-seq, transcription factor motif analysis, drug screening and molecular biology assays were performed to identify the mechanism of HDAC5's repression on PD-L1. Allografts of pancreatic cancer in mouse were applied to test the efficiency of HDAC5 inhibition and anti-PD1 co-treatment. Results: HDAC5 regulated PD-L1 expression by directly interacting with NF-κB p65; this interaction was suppressed by p65 phosphorylation at serine-311. Additionally, HDAC5 diminished p65 acetylation at lysine-310, which is essential for the transcriptional activity of p65. Importantly, we demonstrated that HDAC5 silencing or inhibition sensitized PDAC tumors to immune checkpoint blockade (ICB) therapy in syngeneic mouse model and KPC mouse derived PDAC model. Conclusion: Our findings revealed a previously unknown role of HDAC5 in regulating the NF-κB signaling pathway and antitumor immune responses. These findings provide a strong rationale for augment the antitumor effects of ICB in immunotherapy-resistant PDAC by inhibiting HDAC5.
A Review on the Enhancement of Mechanical and Tribological Properties of MCrAlY Coatings Reinforced by Dispersed Micro- and Nano-Particles

The application of metal-matrix composite coatings for protecting and improving the service life of sliding components has demonstrated to have the potentials of meeting the requirements of a diverse range of engineering industries. Recently, a significant body of research has been devoted to study the mechanical and tribological performance of dispersion-strengthened MCrAlY coatings. These coatings belong to a class of emerging wear-resistant materials, offering improved properties and being considered as promising candidates for the protection of engineering structural materials exposed to tribological damage, especially at elevated temperature regimes. This paper attempts to comprehensively review the different reinforcements used in the processing of MCrAlY-based alloys and how they influence the mechanical and tribological properties of the corresponding coatings. Further, the major fabrication techniques together with their benefits and challenges are also reviewed. Discussion on the failure mechanisms of these coatings as well as the main determining factors are also included. In addition, a comprehensive survey of studies and investigations in recent times are summarized and elaborated to further substantiate the review.
Concomitant Gastric Acid Suppressants on the Survival of Patients with Non-Small-Cell Lung Cancer Treated with Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors: A Meta-Analysis

Background The influence of concomitant use of gastric acid suppressants (AS) on survival of patients with non-small-cell lung cancer (NSCLC) treated with epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) is inconsistent according to previous studies. We performed a meta-analysis to evaluate the effect of additional AS in patients with NSCLC taking TKIs. Methods Relevant observational studies were identified by a search of Medline, Embase, and Web of Science databases. Only studies with multivariate analyses were included. A random-effect model was used to combine the results. Results Thirteen retrospective studies with 12259 patients were included. Pooled results showed that concomitant use of AS was associated with worse progression-free survival (PFS, adjusted hazard ratio (HR): 1.57, 95% confidence interval (CI): 1.31 to 1.89, P < 0.001; I2 = 65%) and overall survival (OS, adjusted HR: 1.38, 95% CI: 1.19 to 1.61, P < 0.001; I2 = 70%) in NSCLC patients taking TKIs. Sensitivity analysis limited to studies including NSCLC with EGFR mutation showed consistent results (HR for PFS: 1.53, P=0.003; HR for OS: 1.43, P=0.001). Subgroup analyses indicated that the association between concomitant use of AS and poor survival was not significantly affected by the category of AS used (proton pump inhibitors or histamine type-2 receptor antagonists) or the country of the study (Asian or non-Asian, P for subgroup analysis all >0.05). Conclusions Concomitant use of AS in patients with NSCLC taking TKIs may be associated with poor survival outcomes.
Research on Automatic Extraction Method of Complex Web Page Data

: The Internet presents great deal of helpful info that is sometimes formatted for its users, that makes it laborious to extract relevant knowledge from numerous sources. Therefore, there's a big would like of strong, versatile info Extraction systems that remodel the net pages into program friendly structures like a computer database can become essential. The projected system focuses on info extraction from websites. We tend to cluster the net documents supported the common example structures so the example for every cluster is extracted at the same time. The planet wide net could be a huge and speedily growing supply of helpful info that is employed to publish and access the knowledge on the net. It uses totally different templates with contents for providing quick access for readers. This is often wont to extract info from example websites.
Computer-Aided Assessment of Melanocytic Lesions by Means of a Mitosis Algorithm

An increasing number of pathology laboratories are now fully digitised, using whole slide imaging (WSI) for routine diagnostics. WSI paves the road to use artificial intelligence (AI) that will play an increasing role in computer-aided diagnosis (CAD). In melanocytic skin lesions, the presence of a dermal mitosis may be an important clue for an intermediate or a malignant lesion and may indicate worse prognosis. In this study a mitosis algorithm primarily developed for breast carcinoma is applied to melanocytic skin lesions. This study aimed to assess whether the algorithm could be used in diagnosing melanocytic lesions, and to study the added value in diagnosing melanocytic lesions in a practical setting. WSI’s of a set of hematoxylin and eosin (H&E) stained slides of 99 melanocytic lesions (35 nevi, 4 intermediate melanocytic lesions, and 60 malignant melanomas, including 10 nevoid melanomas), for which a consensus diagnosis was reached by three academic pathologists, were subjected to a mitosis algorithm based on AI. Two academic and six general pathologists specialized in dermatopathology examined the WSI cases two times, first without mitosis annotations and after a washout period of at least 2 months with mitosis annotations based on the algorithm. The algorithm indicated true mitosis in lesional cells, i.e., melanocytes, and non-lesional cells, i.e., mainly keratinocytes and inflammatory cells. A high number of false positive mitosis was indicated as well, comprising melanin pigment, sebaceous glands nuclei, and spindle cell nuclei such as stromal cells and neuroid differentiated melanocytes. All but one pathologist reported more often a dermal mitosis with the mitosis algorithm, which on a regular basis, was incorrectly attributed to mitoses from mainly inflammatory cells. The overall concordance of the pathologists with the consensus diagnosis for all cases excluding nevoid melanoma (n = 89) appeared to be comparable with and without the use of AI (89% vs. 90%). However, the concordance increased by using AI in nevoid melanoma cases (n = 10) (75% vs. 68%). This study showed that in general cases, pathologists perform similarly with the aid of a mitosis algorithm developed primarily for breast cancer. In nevoid melanoma cases, pathologists perform better with the algorithm. From this study, it can be learned that pathologists need to be aware of potential pitfalls using CAD on H&E slides, e.g., misinterpreting dermal mitoses in non-melanotic cells.
Spontaneous and ART-induced large offspring syndrome: similarities and differences in DNA methylome

Large/abnormal offspring syndrome (LOS/AOS) is a congenital overgrowth syndrome reported in ruminants produced by assisted reproduction (ART-LOS) which exhibit global disruption of the epigenome and transcriptome. LOS/AOS shares phenotypes and epigenotypes with the human congenital overgrowth condition Beckwith-Wiedemann syndrome. We have reported that LOS occurs spontaneously (SLOS), however, to date, no study has been conducted to determine if SLOS has the same methylome epimutations as ART-LOS. In this study, we performed whole genome bisulfite sequencing to examine global DNA methylation in SLOS and ART-LOS tissues. We observed unique patterns of global distribution of differentially methylated regions (DMRs) over different genomic contexts, such as promoters, CpG islands and surrounding regions, and repetitive sequences from different treatment groups. In addition, we identified hundreds of LOS-vulnerable DMRs across different cattle breeds when analyzing four idependent LOS experiments together. Specifically, there are 25 highly vulnerable DMRs that could potentially serve as molecular markers for the diagnosis of LOS, including at the promoters of DMRT2 and TBX18, at the imprinted gene bodies of IGF2R, PRDM8, and BLCAP/NNAT, and at multiple CpG islands. We also observed tissue-specific DNA methylation patterns between muscle and blood, and conservation of ART-induced DNA methylation changes between muscle and blood. We conclude that as in ART-LOS, alterations of the epigenome are involved in the etiology of SLOS. In addition, SLOS and ART-LOS share some similarities in methylome epimutations.