Miracle-dz/UniFAR-FTUs huggingface dataset:
Imaging of caspase-3 activation by a novel FRET probe composed of CFP and DsRed

Caspases-3 is a kind of cysteine proteases and plays an important role in cell apoptosis. It has been reported that caspase-3 activation can be real-time detected in living cells by fluorescence resonance energy transfer (FRET) between an enhanced cyan fluorescent protein and enhanced yellow fluorescent protein. However, the large spectral overlap between cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) emission and the highly sensitivity to pH of YFP restricted their detecting sensitivity and reliability. CFP and red fluorescent protein (DsRed) possess superb wavelength separation of donor and acceptor emission spectra and DsRed was insensitive to pH, so the FRET probe composed of CFP and DsRed would be more suitable for imaging caspase-3 activation than the FRET probe composed of CFP and YFP. We constructed a vector that encoded CRS (caspase-3 recognition site) fused with CFP and DsRed (CFP-CRS-DsRed). In CFP-CRS-DsRed expressing tumor cells, FRET from CFP to DsRed could be detected. In the Clinical applications of cancer chemotherapy, cisplatin is one of the most broadly used drugs. It was already confirmed that caspase-3 was activated in HeLa cell treated by cisplatin. When the cells were stimulated with cisplatin, we found that the FRET efficient was remarkably decreased and then disappeared. It indicated that actived caspase-3 cleaved the CFP-CRS-DsRed fusion protein at CRS site. Thus, the FRET probe of CFP-CRS-DsRed could sensitively and reliably monitor caspase-3 activation in living cell. This probe will be highly useful for rapid-screening potential drugs that may target the apoptotic process and for imaging tumors in vivo.
The Long Non-coding RNA NR_045363 Regulates Cardiomyocyte Apoptosis and Cardiac Repair Through Activating P53 Signal Pathway.

Long noncoding RNAs (lncRNAs) can participate in various biological behaviors, including regulating cell differentiation, proliferation and apoptosis. The investigators have previously confirmed that highly conserved lncRNA NR_045363 controls cardiomyocyte (CM) proliferation and cardiac repair. The present study investigates the effects of NR_045363 on CM apoptosis. Seven-day-old mice were subjected to permanent left anterior descending coronary artery ligation (LAD), and the NR_045363 expression was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). The expression of NR_045363 in the MI group significantly exceeded the Sham group during the first week after the operation. The NR_045363 expression was knocked down in primary cultured CMs using a NR_045363-targeting LncRNA Smart silencer, and the apoptosis of CMs was analyzed by Terminal-deoxynucleoitidyl Transferase Mediated Nick End Labeling (TUNEL) and Annexin-V/PI double staining. These present results indicate that the NR_045363 knockdown significantly promoted the apoptosis of CMs. In order to investigate the underlying mechanism, RNA-sequencing (RNA-seq) was performed, and ingenuity pathway analysis (IPA) was used to analyze the RNA-seq results. The RNA-seq data revealed that a total of 2,291 genes were upregulated or downregulated in NR_045363 knockdown CMs, and the IPA analysis indicated that p53 was the upstream regulator. In vivo, the NR_045363 overexpression through the AAV9 system improved the heart function after MI in 7-day-old mice and inhibited the CM apoptosis. These data suggests that NR_045363 is involved in CM apoptosis, and that NR_045363 overexpression exerts positive effects on cardiac repair by alleviating CM apoptosis through the activation of the p53 pathway. This article is protected by copyright. All rights reserved.
Prediction of new thermodynamically stable ZnN2O3 at high pressure.

Pressure has become a useful parameter to prepare novel functional materials. Considering the excellent performance of ZnO and Zn3N2 and the formation of strong Zn-O, Zn-N, and N-O bonds in the known compounds, we explored potential Zn-N-O ternary compounds with interesting properties. With the aid of first-principles swarm-intelligence search calculations, we identified a hitherto unknown ZnN2O3 ternary compound with a symmetry of P21. Its remarkable feature is that N pairs interconnect the distorted Zn-centered decahedrons, in which the Zn atom forms bonds with one N and six O atoms. The compression of ZnO + NO2 + N2 might be an easy way to synthesize ZnN2O3. Electronic property calculations disclose that ZnN2O3 is a wide band gap semiconductor with a gap value of 3.48 eV, which is larger than those of ZnO and Zn3N2. Moreover, the high-pressure phase diagram of Zn-N binary compounds was explored with a wide range of chemical compositions. Two metallic N-rich zinc nitrides (e.g., ZnN2 and ZnN4) are proposed, containing intriguing N2 dimers and zigzag N chains. ZnN2 exhibits superconducting properties, and becomes the first example of superconductor in zinc nitrides. Our current results unravel the unusual stoichiometry of Zn-N-O compounds and provide further insight into the diverse electronic properties of zinc nitrides under high pressure.
Proteomic biomarkers of sleep apnea.

Obstructive sleep apnea (OSA) is characterized by recurrent partial to complete upper airway obstructions during sleep, leading to repetitive arousals and oxygen desaturations. Although many OSA biomarkers have been reported individually, only a small subset have been validated through both cross-sectional and intervention studies. Here, we used a highly multiplexed aptamer array (SomaScan) for proteomic analysis of serum samples from 713 individuals in the Stanford Sleep Cohort, a patient-based registry. Outcome measures derived from overnight polysomnography included Obstructive Apnea Hypopnea Index (OAHI), Central Apnea Index (CAI), 2% Oxygen Desaturation index, mean and minimum oxygen saturation indices during sleep. Additionally, a separate intervention-based cohort of 16 individuals was used to assess proteomic profiles pre- and post-intervention with positive airway pressure. After statistical adjustment for age, age of sample, gender and body mass index, OAHI was associated with 65 proteins, predominantly pathways of complement, coagulation, cytokine signaling, and hemostasis which were upregulated. CAI was associated with two proteins including Roundabout homolog 3 (ROBO3), a protein involved in bilateral synchronization of the pre-Bötzinger complex and cystatin F. Analysis of pre- and post- intervention samples were less revealing as only 2 proteins that were differentially associated with active treatment: Insulin-like growth factor-binding protein3 (IGFBP-3) increased while LEAP1 (Hepicidin) decreased with intervention. An OAHI machine learning classifier (OAHI >=15 vs OAHI<15) trained on SomaScan protein measures alone performed robustly, achieving 76% accuracy in a validation dataset. Multiplex protein assays offer diagnostic potential and provide new insights into the biological basis of sleep disordered breathing.
COLLAGENOUS COLITIS IS ASSOCIATED WITH HLA SIGNATURE AND SHARES GENETIC RISKS WITH OTHER IMMUNE-MEDIATED DISEASES.

BACKGROUND AND AIMS Collagenous colitis (CC) is an inflammatory bowel disorder with unknown etiopatogenesis involving human leukocyte antigen (HLA)-related immune-mediated responses, environmental and genetic risk factors. We carried out an array-based genetic association study in a cohort of CC patients and investigated the common genetic basis between CC and Crohn's disease (CD), ulcerative colitis (UC) and celiac disease. METHODS DNA from 804 CC formalin-fixed, paraffin-embedded tissue samples was genotyped with Illumina Immunochip. Matching genotype data on controls and CD, UC and celiac disease cases were provided by the respective Consortia. A discovery association study followed by meta-analysis with an independent cohort, polygenic risk score (PRS) calculation, and cross-phenotype analyses were performed. Enrichment of regulatory expression quantitative trait loci (eQTLs) among the CC variants was assessed in hemopoietic and intestinal cells. RESULTS Three HLA alleles (HLA-B*08:01, HLA-DRB1*03:01, and HLA-DQB1*02:01), related to the ancestral haplotype 8.1, were significantly associated with increased CC risk. We also identified an independent protective effect of HLA-DRB1*04:01 on CC risk. PRS quantifying the risk across multiple susceptibility loci was strongly associated with CC risk. An enrichment of eQTLs was detected among the CC susceptibility variants in various cell types. The cross-phenotype analysis identified a complex pattern of polygenic pleiotropy between CC and other immune-mediated diseases. CONCLUSION In this largest genetic study of CC to date with histologically confirmed diagnosis, we strongly implicated the HLA locus and proposed potential non-HLA mechanisms in disease pathogenesis. We also detected a shared genetic risk between CC, celiac disease, CD and UC, which supports clinical observations of comorbidity.
A review of the species of Anastatus Motschulsky (Hymenoptera: Chalcidoidea: Eupelmidae) of the Indian subcontinent

The species of Anastatus Motschulsky (Chalcidoidea: Eupelmidae) from the Indian subcontinent are reviewed. A total of 28 species are recognized from the region based on females, including 13 species newly described from India. A key to females of the species is provided and figures illustrating differential features of 15 of the species included. Distribution and host data are provided where known. Anastatus dentatus Narayanan, Subba Rao & Ramachandra Rao, 1960 is newly placed in synonymy with Anastatus ramakrishnai (Mani, 1935).
Comparison of Optimization-Modelling Methods for Metabolites Production in Escherichia coli

Abstract The metabolic network is the reconstruction of the metabolic pathway of an organism that is used to represent the interaction between enzymes and metabolites in genome level. Meanwhile, metabolic engineering is a process that modifies the metabolic network of a cell to increase the production of metabolites. However, the metabolic networks are too complex that cause problem in identifying near-optimal knockout genes/reactions for maximizing the metabolite’s production. Therefore, through constraint-based modelling, various metaheuristic algorithms have been improvised to optimize the desired phenotypes. In this paper, PSOMOMA was compared with CSMOMA and ABCMOMA for maximizing the production of succinic acid in E. coli. Furthermore, the results obtained from PSOMOMA were validated with results from the wet lab experiment.
Birth-weight differences at term are explained by placental dysfunction and not by maternal ethnicity. Study in newborns of first generation immigrants

Abstract Objective The aim of the study was to investigate the influence of ethnicity and cerebroplacental ratio (CPR) on the birth weight (BW) of first generation Indo-Pakistan immigrants’ newborns. Methods This was a retrospective study in a mixed population of 620 term Caucasian and Indo-Pakistan pregnancies, evaluated in two reference hospitals of Spain and Italy. All fetuses underwent a scan and Doppler examination within two weeks of delivery. The influence of fetal gender, ethnicity, GA at delivery, CPR, maternal age, height, weight and parity on BW was evaluated by multivariable regression analysis. Results Newborns of first generation Indo-Pakistan immigrants were smaller than local Caucasian newborns (mean BW mean= 3048 ± 435 g versus 3269 ± 437 g, p < .001). Multivariable regression analysis demonstrated that all studied parameters, but maternal age and ethnicity, were significantly associated with BW. The most important were GA at delivery (partial R 2 = 0.175, p < .001), CPR (partial R 2 = 0.032, p < .001), and fetal gender (partial R 2 = 0,029, p < .001). Conclusions The propensity to a lower BW, explained by placental dysfunction but not by maternal ethnicity is transmitted to newborns of first generation immigrants. Whatever are the factors implied they persist in the new residential setting.
Further Observations on the “Animal Protein Factor”

Summary and Addendum 1. Fermentation products of Streptomyces aureofaciens were found to promote growth in depleted chicks on various diets which were adequately supplied with vitamin B12. 2. Growth responses in chicks on a corn-soybean diet were also produced by crystalline aureomycin hydrochloride and by cultures in which the aureomycin, as measured by antibiotic potency, was destroyed by alkaline hydrolysis. 3. Responses were also obtained with succinylsulfathiazole, streptomycin and 3-nitro-4-hydroxyphenylarsonic acid, but these substances appeared less potent than aureomycin. No responses were obtained with dried whey or dried brewer's yeast. Following the submission of this manuscript, Dr. Paul Gyorgy kindly showed us a manuscript (Gyorgy, P., Stokes, J., Jr., Smith, W. H., and Goldblatt, H., Transactions of Conference on Biological Antioxidants, sponsored by the Macy Foundation, November, 1949) which described a beneficial exerted by aureomycin on growth and the prevention of dietary hepatic necrosis in rats. The assumption was made that aureomycin might act through the suppression of the intestinal flora. The assistance of Vincent Stryeski, Alfred Plattner and Joseph Lang in the care of the animals is gratefully acknowledged.
Effects of rice bran-nonstarch polysaccharides and fiber-degrading enzymes on performance and nutrient digestibility in broiler chicks

This experiment was conducted to study the effect of varying levels (0, 4, and 7%) of total nonstarch polysaccharides (NSP) prepared from defatted rice bran on performance, nutrient digestibility, and energy value of the diet in the 1- to 14-d-old broiler chicks. Two of the 7%-NSP diets were supplemented with LAMINEX XL® (3,080 units xylanase/kg of diet), or LAMINEX XL® plus LAMINEX BG® (366 units β-glucanase/kg of diet). All diets contained 3.00 Mcal of metabolizable energy (MEn)/kg of diet and 22% of crude protein. The results showed that feeding chicks a diet containing up to 7% of NSP had no effects on feed intake, body weight gain, feed : gain ratio, and fat digestibility. However, chicks receiving the 7%-NSP diet showed a greater protein digestibility compared with those receiving the 0%- or the 4%-NSP diet at d 7 (P<0.01) or with those receiving the 0%-NSP at d 14 (P<0.05). Dietary 7%-NSP depressed pancreatic lipase activities at d 14. Although this depressing effect was ameliorated with xylanase or xylanase plus β-glucanase supplementations, the supplemental enzymes did not improve fat digestibility that was adversely affected (P<0.01) by 7% of NSP in the diet on d 14. Xylanase improved protein digestibility of the 7%-NSP diet on d 7 (P<0.05), and xylanase plus β-glucanase also showed an improving effect on d 14 (P<0.05). The supplementation of enzyme did not influence the MEn values of the diet. The results of the present study suggest that at up to 7%, NSP of defatted rice bran possesses no antinutritive effects on nutrient digestibility, but positively influences the MEn value of the diet. The favoring effect of enzymes on protein digestibility did not contribute to the performance of the chicks at early age.
Angiographic analysis of the variation of arterial collaterals in moyamoya and atherosclerosis at a tertiary care center in Saudi Arabia.

OBJECTIVES To evaluate the anatomical variation of arterial collaterals and their prevalence in moyamoya and atherosclerosis. METHODS Data was collected retrospectively from patients (n=46) database who underwent digital subtraction angiography between January 2010 and December 2018 at the Radiology Department, King Fahad Medical City, Riyadh, Saudi Arabia. Demographic details and clinical data of the patients such as age, gender, etiology, clinical presentation, angiographic staging using Suzuki grading for moyamoya cases, variation of arterial collaterals, and their prevalence, treatment and follow up were obtained. RESULTS Four types of collaterals network were observed in atherosclerosis (n=21) and moyamoya (n=25); the leptomeningeal, durocortical, subependymal, inner-interstriatal and intrathalamic networks. More number of collaterals were observed in the moyamoya (n=534) than atherosclerosis (n=40). Leptomeningeal network (n=198, 37.1%) and subependymal network (n=170, 31.8%) were greater than durocortical and inner-interstriatal or intrathalamic in patients with moyamoya. Whereas leptomeningeal network (n=25, 62.5%) and inner-interstriatal or intrathalamic (n=7, 17.5%) were predominant in atherosclerosis. Out of 25 cases of moyamoya, Suzuki grading V was noted in 5 (20%) and grade IV in 13 (52%). CONCLUSION Understanding the dynamics that have evolved in the development of the collaterals and therefore can improve both management and prognosis.
Kidney displaced by giant retroperitoneal liposarcoma in HIV patient

A 56-year-old male with a history of infection of human immunodeficiency virus over ten years, was referred to our center because of intermittent epigastralgia and gradual increase of abdominal girth in the last two months. Physical examination revealed palpable abdominal mass at the right upper quadrant measuring around 20cm. Laboratory examinations of complete blood counts, urine tests, and tumor markers were otherwise normal. CT scan of the abdomen showed a huge fatty mass of 23.3 x 22.9 x 34.5cm with Kidney displaced by giant retroperitoneal liposarcoma in HIV patient _______________________________________________
A 5-nV/√Hz Chopper Negative-R Stabilization Preamplifier for Audio Applications

This paper presents a low-noise and low-power audio preamplifier. The proposed low-noise preamplifier employs a delay-time chopper stabilization (CHS) technique and a negative-R circuit, both in the auxiliary amplifier to cancel the non-idealities of the main amplifier. The proposed technique makes it possible to mitigate the preamplifier 1/f noise and thermal noise and improve its linearity. The low-noise preamplifier is implemented in 65 nm complementary metal-oxide semiconductor (CMOS) technology. The supply voltage is 1.2 V, while the power consumption is 159 µW, and the core area is 192 µm2. The proposed circuit of the preamplifier was fabricated and measured. From the measurement results over a signal bandwidth of 20 kHz, it achieves a signal-to-noise ratio (SNR) of 80 dB, an equivalent-input referred noise of 5 nV/√Hz and a noise efficiency factor (NEF) of 1.9 within the frequency range from 1 Hz to 20 kHz.
Characterisation of Fiber Obtained from Pumpkin (cucumis moschata duch.) Mesocarp Through Enzymatic Treatment

Cell wall-enriched pumpkin (Cucumis moschata Duch.) powder was submitted to enzymatic hydrolysis by cellulase or hemicellulase in order to evaluate the performance of these cell wall-degrading enzymes on that substrate. Different enzyme-substrate ratios were evaluated and the effect exerted by the buffer on cell wall polysaccharides. Cellulase produced the release of pectin macromolecules which include homogalacturonans side chains, the rhamnogalacturonan I core and rhamnogalacturonan II, in conjunction with xylogalacturonans. The content of galacturonic acid in product obtained ranged from 545 to 781 g/kg of fiber. Hemicellulases produced intense pectin hydrolysis leading to fiber-fractions with galacturonic acid contents ranging from 390 to 444 g/kg of fiber and enriched in glucose polymers as the enzyme proportion increased. Few rhamnogalacturonan-I was present.The acidic citrate buffer (pH 5.2) used for allowing enzyme activity could per se remove noncovalent cross-links like ionic bonds. As a consequence, pectin-in-extensin entanglements, pectins joined by Ca2+-bridges through the homogalacturonan side chains, and some pectins that are originally soluble in cold water due to little or no binding to the cell wall, could be removed by this citrate buffer. Enzymatic hydrolysis as well as buffer extraction produced fiber-products with an important thickening effect of aqueous systems. This effect was smaller as the ratio enzyme-substrate was increased and, in general, the fiber fractions isolated produced an in vitro glucose diffusion retardation.
The role of extracellular LRR-extensin (LRX) proteins in cell wall formation

Chimeric LRR-extensin proteins were identified that are involved in cell wall development. The proteins are exported to the extracellular matrix and their structure implies a regulatory and/or signalling function. A summary on the LRX gene family is presented and the possible roles of LRXs during plant development are discussed.
Exploring the Challenges of Developing and Operating Consortium Blockchains: A Case Study

Blockchain and smart contracts are being embraced by more and more industrial practitioners in multiple domains including agriculture, manufacturing, and healthcare. As a distributed, immutable, and partly public ledger, the consortium blockchain demonstrates its potential to enable trustworthy interoperability and collaboration between organizations. However, the mismatch between the unruled software engineering practices and the increased interest of the consortium blockchain technology may pose threats to the quality of systems implemented. To mitigate the possible threats, this study takes the angle of software engineering to systematically understand the challenges and possible solutions in terms of developing and operating a consortium blockchain-based system. For this purpose, we conducted a case study on a typical consortium blockchain-based system and exhaustively collected the data by two rounds in-depth interviews on practitioners of different roles in the case project. Based on the data analysis, eight pairs of challenges and potential solutions were identified, which cover the phases of the development and operation of consortium blockchains. Moreover, we also captured two implications after further analysis of the findings, which worth the special attention of researchers in the near future, i.e. DevOps and microservices for blockchain or smart contracts.
Nutritional reduction of protein and usage of enzyme in the diet of light layers

The objective of this study was to evaluate the reduction of protein, the formulation of diets and supplementation of an enzyme complex for laying hens. The layers were distributed in a completely randomized 2 × 2 × 2 factorial arrangement, with two levels of crude protein reduction (0.0 and 4.0 g/kg), two kinds of diet formulation (without and with reformulation, considering 75 kcal of metabolizable energy) and two enzyme supplementations (without and with enzyme complex supplementation), totalizing 8 treatments of 8 layers each, with 7 replications, in a total of 448 laying hens at 30 weeks of age. After data analysis, it was found that the enzyme complex supplementation in the diet of layers improves performance, promotes a similar egg quality and improves the bone and intestinal health of the layers.
Mechanical stimulation of rumen fill and alimentary behaviour in sheep

The effects of an increase of rumen fill obtained with polystyrene cubes, and able to stimulate mechanically the rumen wall were investigated on alimentary behaviour and reticulo-rumen motility in sheep. The introduction through a rumen cannula of a volume of polystyrene cubes equal to one-quarter of the ruminal pool size depressed the daily intake of both low-quality cocksfoot hay and good-quality lucerne hay ( P P