Miracle-dz/UniFAR-FTUs huggingface dataset:
Iron Concentrations in Biofortified Beans and Nonbiofortified Marketplace Varieties in East Africa Are Similar.

BACKGROUND The predominant bean iron (Fe) biofortification approach is to breed for high Fe concentration and assumes the average Fe concentration is 50 μg/g. This approach also assumes that a 40 μg/g increase is sustainable and Fe bioavailability will not decrease to negate the increase in Fe. OBJECTIVE The overall objective was to determine if bean Fe biofortification via breeding for high Fe is producing beans with higher Fe concentration relative to nonbiofortified lines found in the East Africa marketplace. METHODS Seventy-six marketplace samples (East Africa Marketplace Collection; EAMC), and 154 genotypes known to be representative of the marketplace were collected from breeders in the Pan-Africa Bean Research Alliance (designated the East Africa Breeder Collection; EABC). Within the EAMC and EABC were 18 and 35 samples, respectively, that were released as biofortified lines. All samples were measured for Fe concentration. The Caco-2 cell bioassay assessed Fe bioavailability of the EAMC. Biofortified versus nonbiofortified samples were compared by the appropriate t-test or ANOVA. RESULTS The Fe concentration of the 58 nonbiofortified EAMC lines was (mean ± SD [range]) 71 ± 9 μg/g (52-93 μg/g) which did not differ significantly from the 18 biofortified EAMC varieties (71 ± 11 μg/g [55-94 μg/g]). The Fe concentration of the 119 nonbiofortified EABC varieties was 66 ± 7 μg/g (51-90 μg/g) which was significantly different (P < 0.0001) from the 35 EABC biofortified lines (73 ± 9 μg/g [60-91 μg/g]). However, the EABC biofortified lines were not different from the nonbiofortified EAMC samples. In the Caco-2 cell bioassay, biofortified EAMC varieties did not deliver more Fe compared with nonbiofortified EAMC varieties. CONCLUSIONS The assumptions of the high Fe bean biofortification approach are not met in the East African marketplace. Iron concentration and bioavailability measurement indicate the biofortified bean varieties are providing no additional dietary Fe.
Health Impacts from Ambient Particle Exposure in Southern Sweden

A health impact assessment (HIA) is an important tool for making informed decisions regarding the design and evaluation of environmental interventions. In this study, we performed a quantitative HIA for the population of Scania (1,247,993), the southernmost county in Sweden, in 2016. The impact of annual mean concentrations of particulate matter with an aerodynamic diameter <2.5 µm (PM2.5), modeled at their home residences for the year 2011, on mortality, asthma, dementia, autism spectrum disorders, preeclampsia and low birth weight (LBW) was explored. Concentration–response (C-R) functions were taken from epidemiological studies reporting meta-analyses when available, and otherwise from single epidemiological studies. The average level of PM2.5 experienced by the study population was 11.88 µg/m3. The PM2.5 exposure was estimated to cause 9–11% of cases of LBW and 6% of deaths from natural causes. Locally produced PM2.5 alone contributed to 2–9% of the cases of diseases and disorders investigated. Reducing concentrations to a maximum of 10 µg/m3 would, according to our estimations, reduce mortality by 3% and reduce cases of LBW by 2%. Further analyses of separate emission sources’ distinct effects were also presented. Reduction of air pollution levels in the study area would, as expected, have a substantial effect on both mortality and adverse health outcomes. Reductions should be aimed for by local authorities and on national and even international levels.
Genome-Wide Identification and Expression Analysis of the bZIP Transcription Factors in the Mycoparasite Coniothyrium minitans

The basic leucine zipper (bZIP) proteins family is one of the largest and most diverse transcription factors, widely distributed in eukaryotes. However, no information is available regarding the bZIP gene family in Coniothyrium minitans, an important biocontrol agent of the plant pathogen Sclerotinia sclerotiorum. In this study, we identified 34 bZIP genes from the C. minitans genome, which were classified into 8 groups based on their phylogenetic relationships. Intron analysis showed that 28 CmbZIP genes harbored a variable number of introns, and 15 of them shared a feature that intron inserted into the bZIP domain. The intron position in bZIP domain was highly conserved, which was related to recognize the arginine (R) and could be treated as a genomic imprinting. Expression analysis of the CmbZIP genes in response to abiotic stresses indicated that they might play distinct roles in abiotic stress responses. Results showed that 22 CmbZIP genes were upregulated during the later stage of conidial development. Furthermore, transcriptome analysis indicated that CmbZIP genes are involved in different stages of mycoparasitism. Among deletion mutants of four CmbZIPs (CmbZIP07, -09, -13, and -16), only ΔCmbZIP16 mutants significantly reduced its tolerance to the oxidative stress. The other mutants exhibited no significant effects on colony morphology, mycelial growth, conidiation, and mycoparasitism. Taken together, our results suggested that CmbZIP genes play important roles in the abiotic stress responses, conidial development, and mycoparasitism. These results provide comprehensive information of the CmbZIP gene family and lay the foundation for further research on the bZIP gene family regarding their biological functions and evolutionary history.
Lysosomal Storage Disorders Shed Light on Lysosomal Dysfunction in Parkinson’s Disease

The lysosome is a central player in the cell, acting as a clearing house for macromolecular degradation, but also plays a critical role in a variety of additional metabolic and regulatory processes. The lysosome has recently attracted the attention of neurobiologists and neurologists since a number of neurological diseases involve a lysosomal component. Among these is Parkinson’s disease (PD). While heterozygous and homozygous mutations in GBA1 are the highest genetic risk factor for PD, studies performed over the past decade have suggested that lysosomal loss of function is likely involved in PD pathology, since a significant percent of PD patients have a mutation in one or more genes that cause a lysosomal storage disease (LSD). Although the mechanistic connection between the lysosome and PD remains somewhat enigmatic, significant evidence is accumulating that lysosomal dysfunction plays a central role in PD pathophysiology. Thus, lysosomal dysfunction, resulting from mutations in lysosomal genes, may enhance the accumulation of α-synuclein in the brain, which may result in the earlier development of PD.
Development and validation of an integrative methylation signature and nomogram for predicting survival in clear cell renal cell carcinoma

Background Growing evidence has shown that genetic or epigenetic alterations are highly involved in the initiation and progression of renal cell carcinoma (RCC). This study aimed to find prognostic methylation markers in clear cell RCC (ccRCC). Methods In this study, we developed and confirmed an integrated and comprehensive methylation signature by integrating DNA methylation, gene expression, and The Cancer Genome Atlas (TCGA) survival data. First, the methylation signature was found and checked based on data analysis of published datasets. Then, independent predictive factors were selected using the Cox proportional model and incorporated into the nomogram. Finally, the predictive nomogram was derived and validated using a concordance index and calibration plots. Results A series of differentially expressed and methylated genes were identified. After intersection analysis, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, protein-protein interaction (PPI) analysis, and correlation analysis, FCGR1A, F2, and NOD2 were established as a predictive signature. According to the Kaplan-Meier survival analysis, the risk score system based on the predictive signature was able to stratify the patients into high- and low-risk groups with significantly different overall survival. The receiver operating characteristic (ROC) analysis further showed that the predictive signature yielded high sensitivity and specificity in predicting the prognosis outcome of ccRCC patients. Moreover, univariate and multivariate Cox regression analysis confirmed that the three-gene methylation signature was an independent prognostic factor in ccRCC. Finally, a nomogram comprising the predictive signature and several independent variables were constructed and proved to effectively predict ccRCC patient survival. Conclusions The three-gene methylation signature was revealed to be a potential novel and independent adverse predictor of prognosis for ccRCC patients and may serve as a promising marker for treatment management and survival outcome improvement. However, substantial validation experiments are required to characterize the molecular background of the predictive signature.
Use of Porous Implants for the Prosthetic Rehabilitation of Fibula Free Flap Reconstructed Patients.

Vascularized free flaps represent today the gold standard in Maxillo-Facial reconstructive treatment of the upper and lower compromised maxillas.The aim of this study is to perform the advantages and disadvantages of the vascularized fibula free flap and the available rehabilitation options with porous implants.In this study the authors analyzed 45 patients with 211 inserted implants treated and reconstructed with vascularized fibula flaps. The authors compared the use of 103 titanium tapered implants (with micro rough surface) versus 108 tantalum-titanium porous implants to evaluate the bone reabsorption and implant survival. Immediate implant stability, the peri-implant reabsorption, and the survival were evaluated. The follow-up was after 3, 6, 12, and 24 months.The authors found that for the 108 Zimmer TM they had an average bone loss of 1 mm ± 0.2 mm after 1 year of follow-up, compared with the other implants where the average bone loss was 2.27 mm ± 0.4. This study demonstrated that the problems caused by different fibula flaps level, compared with the mandibula or, with adjacent teeth in the maxilla, can be solved using TM porous implants that almost duplicate the fixture surface and guarantees long life prognosis to the authors' prosthetic devices.
Diel scent and nectar rhythms of an African orchid in relation to bimodal activity patterns of hawkmoth pollinators.

BACKGROUND AND AIMS The temporal dimensions of floral adaptation to pollinators are not yet well understood, partly because we lack accurate information on the diel rhythms of flower visitation for many pollinators. We investigated whether diel patterns of pollinator visitation to flowers of the African woodland orchid Bonatea polypodantha are synchronised with rhythms of floral anthesis, scent emission and nectar availability. METHODS Direct observations and motion-activated cameras were used to identify pollinators of B. polypodantha and to document their activity periods. The timing of pollinaria removal from flowers, emission of scent and availability of nectar were also measured. RESULTS We found that B. polypodantha is pollinated exclusively by short-tongued hawkmoths. Pollinaria of the orchid are affixed between the labial palps of the moths and brush over the protruding stigmatic arms. The flowers also receive visits by long-tongued hawkmoths, but these act as nectar thieves. Tracking of pollinaria removal from flowers confirmed that pollination occurs only at night. Camera footage revealed a striking crepuscular pattern of foraging by short-tongued hawkmoths with peaks of activity during the twilight periods at dusk and at dawn. In contrast, long-tongued hawkmoths were found to visit flowers throughout the night. Flowers of B. polypodantha exhibit unimodal peaks of anthesis, scent emission (dominated by nitrogenous aromatics) and nectar availability before or around dusk. CONCLUSIONS Flowers of B. polypodantha are pollinated exclusively by short-tongued hawkmoths which show crepuscular foraging activity at dusk and dawn. Floral phenophases of the orchid are closely synchronised with the peak of pollinator activity at dusk.
The senolytic agent navitoclax inhibits angiotensin II-induced heart failure in mice Navitoclax inhibits heart failure.

Navitoclax, which is a type of senolytic drug, selectively eliminates senescent cells. This study aimed to evaluate the therapeutic potential of navitoclax in treatment of angiotensin II (Ang II)-induced heart failure in mice. Navitoclax or vehicle was administrated in mice with Ang II-induced heart failure. Cardiac function and electrophysiology were assessed before and after administration of navitoclax. Cardiac remodeling, including morphological changes, fibrosis, and inflammatory responses, were analyzed in myocardial tissue. Cellular effects of navitoclax were validated in isolated primary cardiomyocytes and cardiac fibroblasts in vitro. Echocardiography of mice showed that navitoclax improved cardiac dysfunction by improving the left ventricular ejection fraction (vehicle: 45.88±2.19%; navitoclax: 54.70±1.65%, p<0.01). In cardiac electrophysiological testing, navitoclax increased conduction velocity (vehicle: 1.37±0.05 mm/ms; navitoclax: 1.69±0.08 mm/ms, p<0.05) and decreased susceptibility to ventricular tachyarrhythmia induced by programmed electrical stimulation. Histopathological staining, immunofluorescence, and western blotting examinations showed that navitoclax ameliorated Ang II-induced cardiac fibrosis, hypertrophy, and the inflammatory response. Moreover, navitoclax eliminated senescent cells by inducing apoptosis. Therefore, navitoclax improved cardiac function and electrophysiological characteristics via decreasing cardiac fibrosis, hypertrophy, and inflammation in mice with heart failure. Pharmacological clearance of senescent cells may be a potential therapeutic approach in heart failure with reduced ejection fraction.
A portable device with low-power consumption for monitoring mouse vital signs during in vivo photoacoustic imaging and photothermal therapy

Objective: The aim of this study was to monitor the physiological changes and cytotoxic effects of exogenous contrast agents during photoacoustic imaging (PAI) and photothermal therapy (PTT). In this paper, a low-power telemetric device for mouse vital signs monitoring was designed and demonstrated. Approach: The power consumption was optimized through hardware and software co-design with a 17% increased operating time compared with typical operation. To demonstrate the feasibility of the monitoring device, PAI and PTT experiments with chitosan-polypyrrole nanocomposites (CS-PPy NCs) as exogenous contrast agents were conducted. Herein, the physiological variation in groups of mice with different CS-PPy NC concentrations was observed and analyzed. Main results: The experimental results indicated the influence of CS-PPy NCs and anesthesia on mouse vital signs in PAI and PTT. Additionally, the association between core temperature, heart rate, and saturation of peripheral oxygen (SpO2) during PAI and PTT was shown. The strong near-infrared absorbance of exogenous contrast agents could account for the increase in mouse core temperature and tumor temperature in this study. Furthermore, high cross-correlation values between core temperature, heart rate, and SpO2 were demonstrated to explain the fluctuation of mouse vital signs during PAI and PTT. Significance: A design of a vital signs monitoring device, with low power consumption, was introduced in this study. A high cross correlation coefficient of mouse vital signs and the effects of CS-PPy NCs were observed, which explained the mouse physiological variation during the PAI and PTT experiments.
Sulfur dioxide: an endogenous protector against myocardial injury.

Sulfur dioxide (SO2) was previously known as a harmful gas in air pollution. Recently, it was reported that SO2 can be endogenously generated in cardiovascular tissues. Many studies have revealed that endogenous SO2 has important physiological and pathophysiological significance and pharmacological potential. As a novel gasotransmitter, SO2 has important regulatory effects on the heart. It has a dose-dependent negative inotropic effect on cardiac function, in which L-type calcium channels are involved. SO2 can also attenuate myocardial injury caused by various harmful stimuli and play an important role in myocardial ischemia-reperfusion injury as well as the recovery of myocardial hypertrophy. These effects are thought to be linked to its ability to reduce inflammation and as an antioxidant. In addition, SO2 regulates cardiomyocyte apoptosis and autophagy. Therefore, endogenous SO2 plays an important role in maintaining cardiovascular system homeostasis. In the present review, the literature concerning the metabolism of endogenous SO2-, its cardiac toxicological effects and physiological regulatory effects, mechanisms for SO2-mediated myocardial protection and its pharmacological applications are summarized and discussed.
Gaussian Moments as Physically Inspired Molecular Descriptors for Accurate and Scalable Machine Learning Potentials.

Machine learning techniques allow a direct mapping of atomic positions and nuclear charges to the potential energy surface with almost ab-initio accuracy and the computational efficiency of empirical potentials. In this work we propose a machine learning method for constructing high-dimensional potential energy surfaces based on feed-forward neural networks. As input to the neural network we propose an extendable invariant local molecular descriptor constructed from geometric moments. Their formulation via pairwise distance vectors and tensor contractions allows a very efficient implementation on graphical processing units (GPUs). The atomic species is encoded in the molecular descriptor, which allows the restriction to one neural network for the training of all atomic species in the data set. We demonstrate that the accuracy of the developed approach in representing both chemical and configurational spaces is comparable to the one of several established machine learning models. Due to its high accuracy and efficiency, the proposed machine-learned potentials can be used for any further tasks, for example the optimization of molecular geometries, the calculation of rate constants or molecular dynamics.
Basis for the control of soilborne plant pathogens with composts

Environmental problems caused by disposal of organic wastes in landfills and streams or by incineration have forced man to examine alternative procedures. For example, burning of tree bark was a nuisance because of associated air pollution problems. This waste has now been turned into a resource through development of profitable composting processes and efficient energy retrieval systems. S ludges are removed from waste waters at a major cost to taxpayers and industries to reduce pollution of streams. Compo sting is chosen in­ creasingly as the least objectionable treatment process for these wastes; thus sludges provide another type of compost. Finally, with the increase in size of farms, the composting process has become a practical procedure for treatment of manures because it allows storage of a stabilized product until a time of year when its market value is highest. I n China, Japan, and other parts of the Orient, composts have been used in agriculture with beneficial effects for years (58). In the West, however, utilization of composts is a relatively recent phenomenon. During the past two decades several reports have discussed suppressive effects of composts to a variety of soilborne plant pathogens. Most of this literature is on ornamental crops. Only a few diseases of vegetable and field crops are controlled with
Protein Kinase Mζ Synthesis from a Brain mRNA Encoding an Independent Protein Kinase Cζ Catalytic Domain

Protein kinase Mζ (PKMζ) is a newly described form of PKC that is necessary and sufficient for the maintenance of hippocampal long term potentiation (LTP) and the persistence of memory in Drosophila. PKMζ is the independent catalytic domain of the atypical PKCζ isoform and produces long term effects at synapses because it is persistently active, lacking autoinhibition from the regulatory domain of PKCζ. PKM has been thought of as a proteolytic fragment of PKC. Here we report that brain PKMζ is a new PKC isoform, synthesized from a PKMζ mRNA encoding a PKCζ catalytic domain without a regulatory domain. Multiple ζ-specific antisera show that PKMζ is expressed in rat forebrain as the major form of ζ in the near absence of full-length PKCζ. A PKCζ knockout mouse, in which the regulatory domain was disrupted and catalytic domain spared, still expresses brain PKMζ, indicating that this form of PKM is not a PKCζ proteolytic fragment. Furthermore, the distribution of brain PKMζ does not correlate with PKCζ mRNA but instead with an alternate ζ RNA transcript thought incapable of producing protein. In vitro translation of this RNA, however, generates PKMζ of the same molecular weight as that in brain. Metabolic labeling of hippocampal slices shows increased de novo synthesis of PKMζ in LTP. Because PKMζ is a kinase synthesized in an autonomously active form and is necessary and sufficient for maintaining LTP, it serves as an example of a link coupling gene expression directly to synaptic plasticity.
Effect of 3D Printed Spatial Reinforcement on Flexural Characteristics of Conventional Mortar

In their fourth decade of development, additive manufacturing technologies are slowly entering research programs dedicated to building materials. While the majority of research effort is focused on using 3D printing of concrete, the authors propose using the technology for creation of spatial plastic reinforcement. Obviously, the strength properties of a 3D printed polymer are much lower than those of steel. Nevertheless, the unconventional spatial shape of a 3D printed reinforcement can substitute for much of the lower mechanical performance of polymer. Flexural characteristics of a cement mortar prism specimen reinforced by hexagon spatial elements were tested and analyzed in this paper. The hexagonal geometric shape was chosen due to its high rigidness. It was proven that it is possible to efficiently reinforce concrete beams by spatial 3D printed polymer elements. Directions of needed research were pointed and discussed.