Miracle-dz/UniFAR-FTUs huggingface dataset:
Primary endothelial cell–specific regulation of hypoxia‐inducible factor (HIF)‐1 and HIF‐2 and their target gene expression profiles during hypoxia

During hypoxia, a cellular adaptive response activates hypoxia‐inducible factors (HIFs; HIF‐1 and HIF‐2) that respond to low tissue‐oxygen levels and induce the expression of a number of genes that promote angiogenesis, energy metabolism, and cell survival. HIF‐1 and HIF‐2 regulate endothelial cell (EC) adaptation by activating genesignaling cascades that promote endothelial migration, growth, and differentiation. An HIF‐1 to HIF‐2 transition or switch governs this process from acute to prolonged hypoxia. In the present study, we evaluated the mechanisms governing the HIF switch in 10 different primary human ECs from different vascular beds during the early stages of hypoxia. The studies demonstrate that the switch from HIF‐1 to HIF‐2 constitutes a universal mechanism of cellular adaptation to hypoxic stress and that HIF1A and HIF2A mRNA stability differences contribute to HIF switch. Furthermore, using 4 genome‐wide mRNA expression arrays of HUVECs during normoxia and after 2, 8, and 16 h of hypoxia, we show using bioinformatics analyses that, although a number of genes appeared to be regulated exclusively by HIF‐1 or HIF‐2, the largest number of genes appeared to be regulated by both. —Bartoszewski, R. , Moszynska, A. , Serocki, M. , Cabaj, A. , Polten, A. , Ochocka, R. , Dell'Italia, L. , Bartoszewska, S. , Króliczewski, J., Dabrowski, M. , Collawn, J. F. Primary endothelial cell–specific regulation of hypoxia‐inducible factor (HIF)‐1 and HIF‐2 and their target gene expression profiles during hypoxia. FASEB J. 33, 7929–7941 (2019). www.fasebj. org
Measuring researcher independence using bibliometric data: A proposal for a new performance indicator

Bibliometric indicators are increasingly used at the individual level – as is exemplified by the popularity of the H-index and many other publication and citation based indicators used in evaluation. The issue isn’t whether these indicators can be considered useful, as they do provide a description of a researcher’s oeuvre. However, at the same time, they are not enough to assess the quality of a researcher and his/her oeuvre: Quality has more dimensions than productivity and impact alone. In this paper, we argue that independence is an equally important characteristic that however lacks validated indicators for measuring it at the individual level. We propose two indicators to measure different dimensions of independence: one assessing whether a researcher has developed an own collaboration network, and another assessing the level of thematic independence. We illustrate how these indicators distinguish between researchers that are equally productive and have similar impact. The independence indicator is a step forward in evaluating individual scholarly quality: in cases where citations and publications do not distinguish, the indicators for independence may do.
Are managers susceptible to framing effects? An experimental study of professional judgment of performance metrics

Abstract Evidence suggests that citizens evaluate government performance differently when equivalent performance information is presented with either a positive or negative framing—but do experienced public managers also suffer from this framing effect? To address this question, we conducted an experiment with 191 public service professionals in the U.S. in which we experimentally varied the framing of performance information about customer satisfaction, job satisfaction and goal achievement for various federal government agencies. Our findings show that public service professionals—just like ordinary citizens—are susceptible to framing effects. Specifically, they tend to evaluate federal agency performance more negatively when percentages of “job dissatisfaction” and “targets not met” were presented, as opposed to logically equivalent percentages of “job satisfaction” and “targets met. ” The pattern is the same for “customer dissatisfaction” versus “customer satisfaction” rates, although the results are not statistically significant. These findings provide a deeper understanding about the use of government performance information, as well as how such information is comprehended and perhaps misunderstood by decision makers.
Resveratrol Anti-Obesity Effects: Rapid Inhibition of Adipocyte Glucose Utilization

Studies in animal models of diabetes and obesity have shown that resveratrol mitigates complications of metabolic diseases, beyond those resulting from oxidative stress. Furthermore, results obtained with cultured preadipocytes have also revealed that prolonged resveratrol treatment impairs adipogenesis. Considering the role of adipocytes in the hypertrophy of fat stores, and keeping in mind that insulin is the main trigger of excessive energy storage during post-prandial periods, the present study aimed to investigate how short-term effects of resveratrol can limit glucose disposal in a gut-adipose tissue axis. We found that resveratrol exhibits a more potent inhibitory capacity towards α-glucosidase than pancreatic lipase activity. Resveratrol also rapidly blunts glucose transport in mature fat cells by counteracting the effect of insulin and insulin-like lipogenic agents. Within two hours, resveratrol also inhibited the incorporation of glucose into lipids of adipocytes, which was unaffected by membrane cholesterol depletion. Moreover, the comparison between adipocytes with invalidated semicarbazide-sensitive amine oxidase activity and their control, or between resveratrol and several inhibitors, did not indicate that the recently described interaction of resveratrol with amine oxidases was involved in its antilipogenic effect. Caffeine and piceatannol, previously said to interact with glucose carriers, also inhibit lipogenesis in adipocytes, whereas other antioxidant phytochemicals do not reproduce such an antilipogenic effect. This study highlights the diverse first steps by which resveratrol impairs excessive fat accumulation, indicating that this natural molecule and its derivatives deserve further studies to develop their potential anti-obesity properties.
Pliocene uplift of the Massif Central (France) constrained by the palaeoelevation quantified from the pollen record of sediments preserved along the Cantal Stratovolcano (Murat area)

The French Massif Central is a key basement relief. This region experienced an intense period of alkaline volcanism, beginning with the Cantal Stratovolcano at 11 Ma and ending at 3 Ma. To quantify the palaeoelevation of the Cantal Stratovolcano and to replace it in the frame of the uplift history of the Massif Central, we first reconstructed the vegetation and climate based on a pollen analysis of the Murat diatomites, which were deposited in a maar lake. The vegetation was organized in three different belts: a Glyptostrobus swamp around the lake; a mixed forest; and, at higher altitudes, a conifer forest. The climate estimated using the climatic amplitude method indicates temperatures between 11.4 and 17°C. Using these estimates and comparison with contemporaneous sites, we infer a palaeoelevation for Murat between 710 and 930 m a.s. l. This site was therefore uplifted by 130 to perhaps 350 m during the Early Pliocene, leading to a reorganization of the drainage pattern and the capture of rivers flowing from the northern edge of the Massif Central towards the Atlantic Ocean. Our study confirms that the Cantal Stratovolcano was a high volcano (>2500 m) before its progressive dismantling during glacial episodes in the Pleistocene.
Dual RNAseq of human leprosy lesions identifies bacterial determinants linked to host immune response

To understand how the interaction between an intracellular bacterium and the host immune system contributes to outcome at the site of infection, we studied leprosy, a disease that forms a clinical spectrum, in which progressive infection by the intracellular bacterium Mycobacterium leprae is characterized by the production of type | IFNs and antibody production. We performed dual RNAseq on patient lesions, identifying a continuum of distinct bacterial states that are linked to the host immune response. The bacterial burden, represented by the fraction of bacterial transcripts, correlates with a host type | IFN gene signature, known to inhibit antimicrobial responses. Second, the bacterial transcriptional activity, defined by the bacterial mRNA/rRNA ratio, links bacterial heat shock proteins with the BAFF-BCMA host antibody response pathway. Our findings provide a platform for interrogation of host and pathogen transcriptomes at the site of infection, allowing insight into mechanisms of inflammation in human disease.
Prevalence of Campylobacter spp. in Poultry in Three Spanish Farms, A Slaughterhouse and A Further Processing Plant

The present study was conducted to investigate the prevalence of Campylobacter spp. in a selection of poultry flocks and the corresponding broiler carcasses as well as the possible impact of contamination during slaughter and processing. Samples of the same flock at different ages in three farms (A, B and C) were taken for the determination of Campylobacter spp. The same broiler flocks were examined at different stages of one slaughterhouse and at a further processing plant. The slaughterhouse environment and processing equipment were sampled. Campylobacter spp. was not detected in 7 and 14-day-old broilers in any of the three farms studied. However, Campylobacter spp. was detected in 35 and 42-day-old broilers at two farms (Farm A and B). This pathogen was detected in both dirty and clean transport crates, in scalding water, and on the defeathering machine and the working table at the end of the working day, but not at the beginning. After defeathering, Campylobacter spp. was detected in all of the sampled carcasses. Campylobacter spp. was detected in all of the carcasses and the poultry meat portion samples from Farm C, although it was not detected at the farm level. This suggests that Campylobacter spp. infected flocks may be a source of these bacteria in the corresponding carcasses, but a cross-contamination during the transportation and slaughter process is also very important.
A two-dimensional conceptual framework for understanding mental well-being

The complex nature of mental well-being is reflected in the great diversity of variables thought to represent aspects of mental flourishing. Discovering the underlying structure of mental well-being is important for a full understanding of this complex construct. Using data from 3 countries (the United States, Japan, and Iran), we performed multi-dimensional scaling to analyze the representation of 9 hedonic and eudaimonic well-being variables in a 2-dimensional psychological space. The analyses revealed 2 interpretable underlying dimensions across cultures and gender groups. The first dimension—eudaimonic well-being versus hedonic well-being—is well-known to well-being researchers. The second dimension—existential relatedness versus Epicurean independence—has not been recognized before. Existential relatedness is the characteristic of being meaningfully interconnected with things other than oneself, and is mainly based on the variables positive relations with others, personal growth, purpose in life, and life satisfaction. Epicurean independence is the characteristic of being relatively free of painful experiences and not feeling the need to have ones’ views accepted by anyone but oneself. Epicurean independence is mainly based on the variables autonomy and absence of negative affect. We explain these dimensions in detail and discuss the implications for well-being research and policy.
Updates on Approaches for Studying Atherosclerosis.

Atherosclerosis is initiated and propagated over decades with no overt clinical symptoms. The complexity and chronicity of its pathophysiological process have been a major challenge to fully define molecular mechanisms and explore more effective therapeutic targets. This Recent Highlights series summarizes ATVB articles published in 2017 and 2018 on the traditional animal model systems and new approaches that have become powerful tools for studying pathogenesis and mechanisms of atherosclerosis.
Validation of Neutrophil Count as An Algorithm-Based Predictive Factor of Progression-Free Survival in Patients with Metastatic Soft Tissue Sarcomas Treated with Trabectedin

Introduction: Based on a mathematical model of trabectedin-induced neutropenia, we assessed the predictive value of absolute neutrophil count (ANC) on progression-free survival (PFS) in an independent validation cohort of patients treated with trabectedin. Methods: We collected data from 87 patients in two expert centers who received at least two cycles of trabectedin for soft tissue sarcomas (STS) treatment. Correlations between ANC, patients’ characteristics, and survival were assessed, and a multivariate model including tumor grade, performance status, ANC, and hemoglobin level was developed. Results: Therapeutic ANC ≥ 7.5 G/L level was associated with shorter PFS: 3.22 months (95% confidence interval (CI), 1.57–4.87) in patients with ANC ≥ 7.5 G/L vs. 5.78 months (95% CI, 3.95–7.61) in patients with ANC < 7.5 G/L (p = 0.009). Age, primary localization, lung metastases, dose reduction, hemoglobin, and albumin rates were also associated with PFS. In multivariate analysis, ANC ≥ 7.5 G/L was independently associated with poor PFS and overall survival. Conclusion: We validated increased pre-therapeutic ANC as a predictive factor of short PFS in patients starting trabectedin for STS. ANC appears to have an impact on survival rates and may be used as a decision-making tool for personalizing second-line strategies in patients with metastatic STS.
Data augmentation on spontaneous Indonesian automatic speech recognition using statistical machine translation

Language model plays an important role in decoding process of the automatic speech recognition. The accuracy of spontaneous speech recognition is still very low compared to dictated speech of the Indonesian automatic speech recognition. It is due to the lack of the number of spontaneous data. Collecting spontaneous data is also difficult to do, so one of the candidate solutions is to augment data from existing spontaneous data. In this research, experiments are conducted on language models to improve the accuracy of spontaneous Indonesian speech recognition by conducting data augmentation. Data augmentation in this research is done by using statistical machine translation named ‘Moses’. Language modeling technique used here is n-gram. GMM-HMM is used for acoustic modeling. First, spontaneous text corpus is added to the text corpus, then the data augmentation is conducted. When the language model is formed from the addition of a spontaneous text corpus, there is an increase in accuracy of 3.59% relative to the baseline. When data augmentation is done on language model there is an increase in accuracy of 2.74% relative to the baseline. However, this decrease is considered not significant compared to the effort required in collecting spontaneous data manually.
Placenta Transcriptome Profiling in Intrauterine Growth Restriction (IUGR)

Intrauterine growth restriction (IUGR) is a serious pathological complication associated with compromised fetal development during pregnancy. The aim of the study was to broaden knowledge about the transcriptomic complexity of the human placenta by identifying genes potentially involved in IUGR pathophysiology. RNA-Seq data were used to profile protein-coding genes, detect alternative splicing events (AS), single nucleotide variant (SNV) calling, and RNA editing sites prediction in IUGR-affected placental transcriptome. The applied methodology enabled detection of 37,501 transcriptionally active regions and the selection of 28 differentially-expressed genes (DEGs), among them 10 were upregulated and 18 downregulated in IUGR-affected placentas. Functional enrichment annotation indicated that most of the DEGs were implicated in the processes of inflammation and immune disorders related to IUGR and preeclampsia. Additionally, we revealed that some genes (S100A13, GPR126, CTRP1, and TFPI) involved in the alternation of splicing events were mainly implicated in angiogenic-related processes. Significant SNVs were overlapped with 6533 transcripts and assigned to 2386 coding sequence (CDS), 1528 introns, 345 5’ untranslated region (UTR), 1260 3’UTR, 918 non-coding RNA (ncRNA), and 10 intergenic regions. Within CDS regions, 543 missense substitutions with functional effects were recognized. Two known mutations (rs4575, synonymous; rs3817, on the downstream region) were detected within the range of AS and DEG candidates: PA28β and PINLYP, respectively. Novel genes that are dysregulated in IUGR were detected in the current research. Investigating genes underlying the IUGR is crucial for identification of mechanisms regulating placental development during a complicated pregnancy.
First-principles study of order-disorder transitions in multicomponent solid-solution alloys

In this review, we will focus on the recent development of the order-disorder transition in metallic materials. The past decades have witnessed fast development in the first-principles methodologies and their applications to ordering transitions in multi-component alloys, particularly the high-entropy alloys. The driving force for the proceedings comes from (i) the advance of algorithms and increasingly cheaper hardware, and also (ii) the great passion to model alloys with increasing number of components. The review starts with a brief introduction of the history for the ordering transitions. More detailed scientific proceedings prior to the 1970s had been well summarized in Krivoglaz and Smirnov (1965 The Theory of Order-Disorder in Alloys (New York: Elsevier)) and Stoloff and Davies (1968 Prog. Mater. Sci. 13 1–84). In the second part, the methods to study the ordering transitions, primarily on the theoretic methods are introduced. These will include (i) KKR-CPA method and supercell methods for energetic calculations; and (ii) thermodynamic and statistical methods to compute the transition temperatures. The third part will focus on representative applications in alloys, including our own work and many others. This part supplies the primary information of this review to the readers. The fourth part will summarize the connections between ordering transitions and broader physical properties (e.g. the mechanical properties). In the last part, some concluding remarks and perspectives will be given.
Short channel monolayer MoS2 field-effect transistors defined by SiOx nanofins down to 20 nm

Layered semiconductors such as transition metal dichalcogenides (TMDs) with proper bandgaps complement the zero-bandgap drawback of graphene, demonstrating great potential for post-silicon complementary metal-oxide-semiconductor technology. Among the TMD family, molybdenum disulfide (MoS2) is highly attractive for its atomically thin body, large bandgap and decent mechanical and chemical stability. However, current nanofabrication techniques hardly satisfy the requirements of short channel and convenient preparation simultaneously. Here, we demonstrate a simple and effective approach to fabricate short channel chemical vapor deposition (CVD) monolayer MoS2 field-effect transistors (FET) with channel length down to 20 nm. Electron-beam lithography based on high-resolution negative-tone hydrogen silsesquioxane electron resists were applied to create 20 nm wide SiOx lines, defining the short channel length. The 20 nm MoS2 FET displays ON-sate current in excess of 100 μA μm−1. The corresponding current ON/OFF ratio at room temperature reaches 105. We carefully studied the short channel effect of as-fabricated MoS2 FETs. Combining with the large-scale growth of CVD method, our results will pave a way for short channel device applications based on atomically thin two-dimensional semiconductors.
Calculation of the optimal number of redundant elements of power systems using the Lagrange multipliers method and information theory

The article analyzes the applicability of information theory tools in solving problems of analysis of functioning engineering networks. This applicability is justified by the laws of distribution of random variables. There is a need to develop methods for determining the number of redundant elements. A method for calculating the optimal number of redundant elements of an engineering network based on the method of Lagrange multipliers taking into account the measure of information uncertainty is proposed. At the end of the article, an example of calculating the number of redundant elements that should be added to the system to increase the system reliability level to the required value is shown.
Automatic Morphology Control of Liquid Metal using a Combined Electrochemical and Feedback Control Approach

Gallium-based liquid metal alloys have been attracting attention from both industry and academia as soft, deformable, reconfigurable and multifunctional materials in microfluidic, electronic and electromagnetic devices. Although various technologies have been explored to control the morphology of liquid metals, there is still a lack of methods that can achieve precise morphological control over a free-standing liquid metal droplet without the use of mechanical confinement. Electrochemical manipulation can be relatively easy to apply to liquid metals, but there is a need for techniques that can enable automatic and precise control. Here, we investigate the use of an electrochemical technique combined with a feedback control system to automatically and precisely control the morphology of a free-standing liquid metal droplet in a sodium hydroxide solution. We establish a proof-of-concept platform controlled by a microcontroller to demonstrate the reconfiguration of a liquid metal droplet to desired patterns. We expect that this method will be further developed to realize future reconfigurable liquid metal-enabled soft robots.
A nomogram for predicting recurrence after complete resection for thymic epithelial tumors based on the TNM classification: A multi‐institutional retrospective analysis

This study aimed to compare the predictive ability between the Masaoka‐Koga (M‐K) staging system and the 8th TNM staging system for the recurrence of thymic epithelial tumors (TETs). In addition, a nomogram was developed on the basis of the proposed TNM classification to predict individual recurrence rate.