Miracle-dz/UniFAR-FTUs huggingface dataset:
Homeostatic Proliferation and Gene Regulation in Selective DNA Demethylation Accompanies T Cell

Systemic lupus erythematosus (SLE) is characterized by increased DNA demethylation in T cells, although it is unclear whether this occurs primarily in a subset of SLE T cells. The process driving the DNA demethylation and the consequences on overall gene expression are also poorly understood and whether this represents a secondary consequence of SLE or a primary contributing factor. Lupus-prone lpr mice accumulate large numbers of T cells with age because of a mutation in Fas (CD95). The accumulating T cells include an unusual population of CD4CD8TCR-ab (DN) T cells that arise from CD8 precursors and are also found in human SLE. We have previously observed that T cell accumulation in lpr mice is due to dysregulation of T cell homeostatic proliferation, which parallels an increased expression of numerous genes in the DN subset, including several proinflammatory molecules and checkpoint blockers. We thus determined the DNA methylome in lpr DN T cells compared with their CD8 precursors. Our findings show that DN T cells manifest discrete sites of extensive demethylation throughout the genome, and these sites correspond to the location of a large proportion of the upregulated genes. Thus, dysregulated homeostatic proliferation in lpr mice and consequent epigenetic alterations may be a contributing factor to lupus pathogenesis. ImmunoHorizons, 2020, 4: 679–687.
Ramachandran Sharpening Up ‘ The Science of Art ’ An Interview with Anthony Freeman

Freeman: The article ‘The Science of Art’ by William Hirstein and yourself (Ramachandran and Hirstein, 1999) has proved one of the most stimulating ever published in JCS. Criticisms of it abound, so to focus your response I will put to you questions that summarize the chief points made by our formal commentators [see Journal of Consciousness Studies, 6 (6–7), 1999, and 7 (8–9), 2000] and also pick up other questions that are frequently asked about it. But first I should like to know what motivated you to write the paper — and did you anticipate the reaction it would provoke?
The applications of appropriate renewable energy technologies by the refugees and displaced persons under humanitarian assistance programmes

Sri Lanka is an island country situated south of India which has experienced with a large number of refugees and internally displaced persons especially since 1983 due to natural and human induced disasters and events from time to time. This study explores and describes how the displaced communities were supplied with appropriate renewable energy technologies to meet their energy demands as against the electricity generated from diesel generators or by providing expensive petroleum gases which contribute towards environmental pollution and greenhouse gas emissions while them being comparatively expensive. This study adopted a ‘single longitudinal case study in retrospect’ research approach. As sustainable energy solutions, providing of fuelwood based energy efficient clay cook stoves, solar photovoltaic lighting and water pumping, solar dryers, biogas systems, small wind turbines, and solar-wind hybrids have been introduced to them on an ad hoc basis depending on the interests and priorities of the supporting agencies. The existing national policies do not place an adequate specific attention to the meeting of energy needs of the displaced communities of Sri Lanka.
Effectiveness of IBS in Reducing Foreign Workers in the Malaysian Construction Workforce: A Review

Nowadays, our country have totally depends on foreign workers in construction development especially in site activities. In June 2007, there are 69% (552,000) out of total 800,000 of registered workers is foreign workers according to Construction Industry Development Board (CIDB) Malaysia (CIDB, 2008). Large scale dependency on foreign worker in construction industry was producing a leak in the economy due to the repatriation of the large amount of funds outside Malaysia (CIDB, 2006). These foreign workers are from Indonesia and the Association of Southeast Asian Nations (ASEAN) is unskilled which impact on the productivity and the quality of the construction industry. Today, Industrialized Building System (IBS) is most preferred construction method which replaces the labor-intensive conventional methods. Syarul and Nor (2003) indicate that IBS promotes labor reduction, cleaner and neater sites, easy installation, fast completion, enhancement of quality finished products and flexibility. However, the use of system formwork has very limited impact on the foreign workers reduction and not to replace wet trades at site (IBS Survey, 2010). Therefore, high involvement of foreign workers problem still have to be solved. This paper is intended to review the effectiveness of IBS method on the foreign workers dependency in current Malaysian construction industry. The findings hopefully will give more clearly evidences that relates to the IBS effectiveness in reducing the dependency on foreign workers in construction industry. This in return will provide directions in producing the effective measures that will ensure labor reduction and increase local involvement in IBS construction projects.
Design of Zero Index Metamaterial Lens for Gain Enhancement of the Antenna array

A zero index metamterial layer used for the gain enhancement of the patch antenna array operating in the L band. The slotted double circular ring resonator structure acts as the metamterial for the gain enhancement of the Microstrip patch antenna array. An improved gain, compact size with Near Zero Index (NZI) patch antenna array is designed with enhanced radiation properties. Slotted Double Circular Ring Resonator structure layer is placed above the microstrip patch antenna array. Moreover, it acts as Meta Surface lens. The proposed NZI lens is designed to increase the measured gain in E- and H-plane in operating frequency band (L-band).
SpecTaint: Speculative Taint Analysis for Discovering Spectre Gadgets

—Software patching is a crucial mitigation approach against Spectre-type attacks. It utilizes serialization instructions to disable speculative execution of potential Spectre gadgets in a program. Unfortunately, there are no effective solutions to detect gadgets for Spectre-type attacks. In this paper, we propose a novel Spectre gadget detection technique by enabling dynamic taint analysis on speculative execution paths. To this end, we simulate and explore speculative execution at system level (within a CPU emulator). We have implemented a prototype called SpecTaint to demonstrate the efﬁcacy of our proposed approach. We evaluated SpecTaint on our Spectre Samples Dataset, and compared SpecTaint with existing state-of-the-art Spectre gadget detection approaches on real-world applications. Our experimental results demonstrate that SpecTaint outperforms existing methods with respect to detection precision and recall by large margins, and it also detects new Spectre gadgets in real-world applications such as Caffe and Brotli. Besides, SpecTaint signiﬁcantly reduces the performance overhead after patching the detected gadgets, compared with other approaches.
Complete mitochondrial genome of the marine polychaete, Nereis zonata (Phyllodocida, Nereididae) isolated from the Beaufort Sea

Abstract Here, we present the first whole mitogenome sequence of the marine polychaete, Nereis zonata, isolated from the Beaufort Sea. The mitochondrial genome of N. zonata is 15,757 bp in length and consists of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a non-coding region that is typical of polychaetes. GC content of the N. zonata mitogenome is 37.2%. A maximum-likelihood gene tree based on the N. zonata mitogenome combined with previously published annelid mitogenome data revealed that N. zonata is clustered with Cheilonereis cyclurus, which form a sister group to Nereis sp.
Epithelial cell-turnover ensures robust coordination of tissue growth in Drosophila ribosomal protein mutants

Highly reproducible tissue development is achieved by robust, time-dependent coordination of cell proliferation and cell death. To study the mechanisms underlying robust tissue growth, we analyzed the developmental process of wing imaginal discs in Drosophila Minute mutants, a series of heterozygous mutants for a ribosomal protein gene. Minute animals show significant developmental delay during the larval period but develop into essentially normal flies, suggesting there exists a mechanism ensuring robust tissue growth during abnormally prolonged developmental time. Surprisingly, we found that both cell death and compensatory cell proliferation were dramatically increased in developing wing pouches of Minute animals. Blocking the cell-turnover by inhibiting cell death resulted in morphological defects, indicating the essential role of cell-turnover in Minute wing morphogenesis. Our analyses showed that Minute wing discs elevate Wg expression and JNK-mediated Dilp8 expression that causes developmental delay, both of which are necessary for the induction of cell-turnover. Furthermore, forced increase in Wg expression together with developmental delay caused by ecdysone depletion induced cell-turnover in the wing pouches of non-Minute animals. Our findings suggest a novel paradigm for robust coordination of tissue growth by cell-turnover, which is induced when developmental time axis is distorted.
The complete chloroplast genome of Rhododendron platypodum (Ericaceae): an endemic and endangered species from China

Abstract Rhododendron platypodum Diels (Ericaceae) is a Chinese endemic and endangered species with high ornamental value. Here the complete chloroplast (cp) genome of R. platypodum was assembled and characterized. The cp genome is in a total length of 201,047 bp with the typical quadripartite structure of angiosperms, containing two inverted repeats (IRs) of 44,650 bp separated by a large single-copy (LSC) region of 109,134 bp and a small single-copy (SSC) region of 2613 bp. The whole cp genome of R. platypodum contains 143 genes, including 93 protein-coding genes, 42 transfer RNA genes and 8 ribosomal RNA genes. Phylogenetic analysis based on the coding sequences of cp genome within the Ericaceae family suggests that R. platypodum is closely related to R. delavayi.
The complete chloroplast genome sequence of Vitis vinifera × Vitis labrusca ‘Shenhua’

Abstract Vitis vinifera × Vitis labrusca ‘Shenhua’ is a tetraploid grape, a Franco-american species. This study first published the complete chloroplast genome of Vitis vinifera × Vitis labrusca ‘Shenhua’ was assembled. The chloroplast genome is 160928 bp in length, including a large single copy region (89,148 bp), a small single-copy region (19,072 bp) and a pair of inverted repeats of 26,354 bp. The chloroplast genome encodes 133 genes, comprising 88 CDSs, 37 tRNA genes and 8 rRNA genes. The phylogenetic tree demonstrated that Vitis vinifera × Vitis labrusca ‘Shenhua’ is different from the other 16 varieties.
Conditioned medium from adipose-derived stem cells attenuates ischemia/reperfusion-induced cardiac injury through the microRNA-221/222/PUMA/ETS-1 pathway

Rationale: Cardiovascular diseases, such as myocardial infarction (MI), are the leading causes of death worldwide. Reperfusion therapy is the common standard treatment for MI. However, myocardial ischemia/reperfusion (I/R) causes cardiomyocyte injury, including apoptosis and fibrosis. We aimed to investigate the effects of conditioned medium from adipose-derived stem cells (ADSC-CM) on apoptosis and fibrosis in I/R-treated hearts and hypoxia/reoxygenation (H/R)-treated cardiomyocytes and the underlying mechanisms. Methods: ADSC-CM was collected from ADSCs. The effects of intramuscular injection of ADSC-CM on cardiac function, cardiac apoptosis, and fibrosis examined by echocardiography, Evans blue/TTC staining, TUNEL assay, and Masson's trichrome staining in I/R-treated mice. We also examined the effects of ADSC-CM on apoptosis and fibrosis in H/R-treated H9c2 cells by annexin V/PI flow cytometry, TUNEL assay, and immunocytochemistry. Results: ADSC-CM treatment significantly reduced heart damage and fibrosis of I/R-treated mice and H/R-treated cardiomyocytes. In addition, the expression of apoptosis-related proteins, such as p53 upregulated modulator of apoptosis (PUMA), p-p53 and B-cell lymphoma 2 (BCL2), as well as the fibrosis-related proteins ETS-1, fibronectin and collagen 3, were significantly reduced by ADSC-CM treatment. Moreover, we demonstrated that ADSC-CM contains a large amount of miR-221/222, which can target and regulate PUMA or ETS-1 protein levels. Furthermore, the knockdown of PUMA and ETS-1 decreased the induction of apoptosis and fibrosis, respectively. MiR-221/222 overexpression achieved similar results. We also observed that cardiac I/R markedly increased apoptosis and fibrosis in miR-221/222 knockout (KO) mice, while ADSC-CM decreased these effects. The increased phosphorylation of p38 and NF‐κB not only mediated myocardial apoptosis through the PUMA/p53/BCL2 pathway but also regulated fibrosis through the ETS-1/fibronectin/collagen 3 pathway. Conclusions: Overall, our results show that ADSC-CM attenuates cardiac apoptosis and fibrosis by reducing PUMA and ETS-1 expression, respectively. The protective effect is mediated via the miR-221/222/p38/NF-κB pathway.
Psychological outcomes, knowledge and preferences of pregnant women on first-trimester screening for fetal structural abnormalities: A prospective cohort study

Introduction The primary aim of this study is to investigate the impact of a 13-week anomaly scan on the experienced levels of maternal anxiety and well-being. Secondly, to explore women’s knowledge on the possibilities and limitations of the scan and the preferred timing of screening for structural abnormalities. Material and methods In a prospective-cohort study conducted between 2013–2015, pregnant women in the North-Netherlands underwent a 13-week anomaly scan. Four online-questionnaires (Q1, Q2, Q3 and Q4) were completed before and after the 13- and the 20-week anomaly scans. In total, 1512 women consented to participate in the study and 1118 (74%) completed the questionnaires at Q1, 941 (64%) at Q2, 807 (55%) at Q3 and 535 (37%) at Q4. Psychological outcomes were measured by the state-trait inventory-scale (STAI), the patient’s positive-negative affect (PANAS) and ad-hoc designed questionnaires. Results Nine-nine percent of women wished to be informed as early as possible in pregnancy about the absence/presence of structural abnormalities. In 87% of women levels of knowledge on the goals and limitations of the 13-week anomaly scan were moderate-to-high. In women with a normal 13-week scan result, anxiety levels decreased (P < .001) and well-being increased over time (P < .001). In women with false-positive results (n = 26), anxiety levels initially increased (STAI-Q1: 39.8 vs. STAI-Q2: 48.6, P = 0.025), but later decreased around the 20-week anomaly scan (STAI-Q3: 36.4 vs. STAI-Q4: 34.2, P = 0.36). Conclusions The 13-week scan did not negatively impact the psychological well-being of pregnant women. The small number of women with screen-positive results temporarily experienced higher anxiety after the scan but, in false-positive cases, anxiety levels normalized again when the abnormality was not confirmed at follow-up scans. Finally, most pregnant women have moderate-to-high levels of knowledge and strongly prefer early screening for fetal structural abnormalities.
Noninvasive ventilation in critically ill very old patients with pneumonia: A multicenter retrospective cohort study

Background Very old patients (≥ 80 years-old, VOP) are increasingly admitted to intensive care units (ICUs). Community-acquired pneumonia (CAP) is a common reason for admission and the best strategy of support for respiratory failure in this scenario is not fully known. We evaluated whether noninvasive ventilation (NIV) would be beneficial compared to invasive mechanical ventilation (IMV) regarding hospital mortality. Methods Multicenter cohort study of VOPs admitted with CAP in need of IMV or NIV to 11 Brazilian ICUs from 2009 through 2012. We used logistic regression models to evaluate the association between the initial ventilatory strategy (NIV vs. IMV) and hospital mortality adjusting for confounding factors. We evaluated effect modification with interaction terms in pre-specified sub-groups. Results Of 369 VOPs admitted for CAP with respiratory failure, 232 (63%) received NIV and 137 (37%) received IMV as initial ventilatory strategy. IMV patients were sicker at baseline (median SOFA 8 vs. 4). Hospital mortality was 114/232 (49%) for NIV and 90/137 (66%) for IMV. For the comparison NIV vs. IMV (reference), the crude odds ratio (OR) was 0.50 (95% CI, 0.33–0.78, p = 0.002). This association was largely confounded by antecedent characteristics and non-respiratory SOFA (adjOR = 0.70, 95% CI, 0.41–1.20, p = 0.196). The fully adjusted model, additionally including Pao2/Fio2 ratio, pH and Paco2, yielded an adjOR of 0.81 (95% CI, 0.46–1.41, p = 0.452). There was no strong evidence of effect modification among relevant subgroups, such as Pao2/Fio2 ratio ≤ 150 (p = 0.30), acute respiratory acidosis (p = 0.42) and non-respiratory SOFA ≥ 4 (p = 0.53). Conclusions NIV was not associated with lower hospital mortality when compared to IMV in critically ill VOP admitted with CAP, but there was no strong signal of harm from its use. The main confounders of this association were both the severity of respiratory dysfunction and of extra-respiratory organ failures.
Using prosocial behavior to safeguard mental health and foster emotional well-being during the COVID-19 pandemic: A registered report protocol for a randomized trial

The COVID-19 pandemic, the accompanying lockdown measures, and their possible long-term effects have made mental health a pressing public health concern. Acts that focus on benefiting others—known as prosocial behaviors—offer one promising intervention that is both flexible and low cost. However, neither the range of emotional states prosocial acts impact nor the size of those effects is currently clear, both of which directly influence its attractiveness as a treatment option. Using a large online sample from Canada and the United States, we will examine the effect of a three-week prosocial intervention on two indicators of emotional well-being (happiness and the belief that one’s life is valuable) and mental health (anxiety and depression). Respondents will be randomly assigned to perform prosocial, self-focused, or neutral behaviors each week. Two weeks after the intervention, a final survey will assess whether the intervention has a lasting effect on mental health and emotional well-being. Our results will illuminate whether prosocial interventions are a viable approach to addressing mental health needs during the current COVID-19 pandemic, as well for those who face emotional challenges during normal times.
The complete mitochondrial genome of Rhinolophus affinis himalayanus

Abstract Here we generated the complete mitochondrial genome of one subspecies of R. affinis (R. affinis himalayanus) using next generation sequencing and Sanger sequencing. The length of the complete mitochondrial genome was 16,886 bp, containing 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a non-coding control region. A maximum-likelihood tree based on the 13 concatenated mitochondrial protein-coding genes of 16 Rhinolophus taxon and one outgroup Hipposideros armiger indicates that R. affinis shows a closer relationship with R. sinicus complex than with other taxa.
Characterization of the complete mitochondrial genome of the Dayu yak (Bos grunniens)

Abstract Dayu yak (Bos grunniens) is a long-furred yak breed from the Qinghai-Tibetan Plateau, and is highly adapted to local high-altitude and cold environments. In this study, its mitochondrial genome was characterized via high-throughput sequencing technology. The genome is 16,323 bp long with an AT-biased base composition (61.0% A + T; light strand), and harbors the typical set of 37 mitochondrial genes and a noncoding control region. Its gene arrangement is identical to those of other bovid taxa. Phylogenetic analysis suggests that Dayu yak is most closely related to Maiwa, Niangya, Qinghai Plateau, Xueduo and Yushu yaks.
The complete chloroplast genome of Chenopodium acuminatum Willd. (Amaranthaceae)

Abstract The complete chloroplast genome (plastome) of the Chenopodium acuminatum was assembled and annotated in this study. The complete plastome was composed of circular DNA molecules with a total length of 152,200 bp, comprising a large single-copy region (83,683 bp), a small single-copy region (18,131 bp), and two inverted repeat regions (25,193 bp). GC content of this complete plastome was 37.2%. In total, 113 unique genes were annotated, including 79 protein-coding genes (PCGs), 30 transfer RNAs, and 4 ribosomal RNAs. Phylogenomic analysis showed that C. acuminatum was closely related to C. album.
Overall survival of pancreatic ductal adenocarcinoma is doubled by Aldh7a1 deletion in the KPC mouse

Rationale: The activity of aldehyde dehydrogenase 7A1 (ALDH7A1), an enzyme that catalyzes the lipid peroxidation of fatty aldehydes was found to be upregulated in pancreatic ductal adenocarcinoma (PDAC). ALDH7A1 knockdown significantly reduced tumor formation in PDAC. We raised a question how ALDH7A1 contributes to cancer progression. Methods: To answer the question, the role of ALDH7A1 in energy metabolism was investigated by knocking down and knockdown gene in mouse model, because the role of ALDH7A1 has been reported as a catabolic enzyme catalyzing fatty aldehyde from lipid peroxidation to fatty acid. Oxygen consumption rate (OCR), ATP production, mitochondrial membrane potential, proliferation assay and immunoblotting were performed. In in vivo study, two human PDAC cell lines were used for pre-clinical xenograft model as well as spontaneous PDAC model of KPC mice was also employed for anti-cancer therapeutic effect. Results: ALDH7A1 knockdown significantly reduced tumor formation with reduction of OCR and ATP production, which was inversely correlated with increase of 4-hydroxynonenal. This implies that ALDH7A1 is critical to process fatty aldehydes from lipid peroxidation. Overall survival of PDAC is doubled by cross breeding of KPC (KrasG12D; Trp53R172H; Pdx1-Cre) and Aldh7a1-/- mice. Conclusion: Inhibitions of ALDH7A1 and oxidative phosphorylation using gossypol and phenformin resulted in a regression of tumor formation in xenograft mice model and KPC mice model.