Miracle-dz/UniFAR-FTUs huggingface dataset:
Longitudinal and Vertical Variations of Dissolved Labile Phosphoric Monoesters and Diesters in the Subtropical North Pacific

The labile fraction of dissolved organic phosphorus (DOP) – predominantly consisting of phosphoric esters – is an important microbial P source in the subtropical oligotrophic ocean. However, unlike phosphate, knowledge for labile DOP is still limited due to the scarcity of broad and intensive observations. In this study, we examined the concentrations and size-fractionated hydrolysis rates of labile phosphoric monoesters and diesters along a >10,000 km longitudinal transect in the North Pacific (23°N; upper 200-m layer). Depth-integrated monoesters decreased westward with a maximum difference of fivefold. Vertical profiles of monoesters in the eastern and western basins showed decreasing and increasing trends with depth, respectively. The monoester-depleted shallow layer of the western basin was associated with phosphate depletion and monoesterase activity was predominant in the large size fraction (>0.8 μm), suggesting that monoesters are significant P sources particularly for large microbes. In contrast, diester concentrations were generally lower than monoester concentrations and showed no obvious horizontal or vertical variation in the study area. Despite the unclear distribution pattern of diesters, diesterase activity in the particulate fraction (>0.2 μm) increased in the phosphate-depleted shallow layer of the western basin, suggesting that the targeted diesters in the assay were also important microbial P sources. Diesterase activities in the dissolved fraction (<0.2 μm) were not correlated with ambient phosphate concentrations; however, cell-free diesterase likely played a key role in P cycling, as dissolved diesterase activities were substantially higher than those in the particulate fraction. The horizontal and vertical variability of labile monoesters in the subtropical North Pacific were therefore predominantly regulated by P stress in particularly large microbes, whereas the distributions of labile diesters and diesterase activities were generally independent of microbial P stress, indicating a more complex regulation of diesters to that of monoesters.
In-vitro Characterization of a Hernia Mesh Featuring a Nanostructured Coating

Abdominal hernia repair is a frequently performed surgical procedure worldwide. Currently, the use of polypropylene (PP) surgical meshes for the repair of abdominal hernias constitutes the primary surgical approach, being widely accepted as superior to primary suture repair. Surgical meshes act as a reinforcement for the weakened or damaged tissues and support tissue restoration. However, implanted meshes could suffer from poor integration with the surrounding tissues. In this context, the present study describes the preliminary evaluation of a PCL-Gel-based nanofibrous coating as an element to develop a multicomponent hernia mesh device (meshPCL-Gel) that could overcome this limitation thanks to the presence of a nanostructured biomimetic substrate for enhanced cell attachment and new tissue formation. Through the electrospinning technique, a commercial PP hernia mesh was coated with a nanofibrous membrane from a polycaprolactone (PCL) and gelatin (Gel) blend (PCL-Gel). Resulting PCL-Gel nanofibers were homogeneous and defect-free, with an average diameter of 0.15 ± 0.04 μm. The presence of Gel decreased PCL hydrophobicity, so that membranes average water contact angle dropped from 138.9 ± 1.1° (PCL) to 99.9 ± 21.6°, while it slightly influenced mechanical properties, which remained comparable to those of PCL (E = 15.7 ± 2.7 MPa, σR= 7.7 ± 0.6 εR = 118.8 ± 13.2%). Hydrolytic and enzymatic degradation was conducted on PCL-Gel up to 28 days, with maximum weight losses around 20 and 40%, respectively. The meshPCL-Gel device was obtained with few simple steps, with no influences on the original mechanical properties of the bare mesh, and good stability under physiological conditions. The biocompatibility of meshPCL-Gel was assessed by culturing BJ human fibroblasts on the device, up to 7 days. After 24 h, cells adhered to the nanofibrous substrate, and after 72 h their metabolic activity was about 70% with respect to control cells. The absence of detectable lactate dehydrogenase in the culture medium indicated that no necrosis induction occurred. Hence, the developed nanostructured coating provided the meshPCL-Gel device with chemical and topographical cues similar to the native extracellular matrix ones, that could be exploited for enhancing the biological response and, consequently, mesh integration, in abdominal wall hernia repair.
A Review of Remote Sensing Challenges for Food Security with Respect to Salinity and Drought Threats

Drought and salinity stress are considered to be the two main factors limiting crop productivity. With climate change, these stresses are projected to increase, further exacerbating the risks to global food security. Consequently, to tackle this problem, better agricultural management is required on the basis of improved drought and salinity stress monitoring capabilities. Remote sensing makes it possible to monitor crop health at various spatiotemporal scales and extents. However, remote sensing has not yet been used to monitor both drought and salinity stresses simultaneously. The aim of this paper is to review the current ability of remote sensing to detect the impact of these stresses on vegetation indices (VIs) and crop trait responses. We found that VIs are insufficiently accurate (0.02 ≤ R2 ≤ 0.80) to characterize the crop health under drought and salinity stress. In contrast, we found that plant functional traits have a high potential to monitor the impacts of such stresses on crop health, as they are more in line with the vegetation processes. However, we also found that further investigations are needed to achieve this potential. Specifically, we found that the spectral signals concerning drought and salinity stress were inconsistent for the various crop traits. This inconsistency was present (a) between studies utilizing similar crops and (b) between investigations studying different crops. Moreover, the response signals for joint drought and salinity stress overlapped spectrally, thereby significantly limiting the application of remote sensing to monitor these separately. Therefore, to consistently monitor crop responses to drought and salinity, we need to resolve the current indeterminacy of the relationships between crop traits and spectrum and evaluate multiple traits simultaneously. Using radiative transfer models (RTMs) and multi-sensor frameworks allow monitoring multiple crop traits and may constitute a way forward toward evaluating drought and salinity impacts.
Physiological and Proteomic Insights Into Red and Blue Light-Mediated Enhancement of in vitro Growth in Scrophularia kakudensis—A Potential Medicinal Plant

The current study has determined the effect of red and blue lights on the enhancement of growth, antioxidant property, phytochemical contents, and expression of proteins in Scrophularia kakudensis. In vitro-grown shoot tip explants of S. kakudensis were cultured on the plant growth regulator-free Murashige and Skoog (MS) medium and cultured under the conventional cool white fluorescent lamp (control), blue light-emitting diodes (LED) light, or red LED light. After 4 weeks, growth, stomatal ultrastructure, total phenols and flavonoids, activities of antioxidant enzymes, and protein expressions were determined. Interestingly, blue or red LED treatment increased the shoot length, shoot diameter, root length, and biomass on comparison with the control. In addition, the LED treatments enhanced the contents of phytochemicals in the extracts. The red LED treatment significantly elicited the accumulation of flavonoids in comparison with the control. In accordance with the secondary metabolites, the LED treatments modulated the activities of antioxidant enzymes. Moreover, the proteomic insights using two-dimensional gel electrophoresis system revealed the proteins involved in transcription and translation, carbohydrate mechanism, post-translational modification, and stress responses. Taken together, the incorporation of blue or red LED during in vitro propagation of S. kakudensis can be a beneficial way to increase the plant quality and medicinal values of S. kakudensis.
Detection of Two Different Grapevine Yellows in Vitis vinifera Using Hyperspectral Imaging

Grapevine yellows (GY) are serious phytoplasma-caused diseases affecting viticultural areas worldwide. At present, two principal agents of GY are known to infest grapevines in Germany: Bois noir (BN) and Palatinate grapevine yellows (PGY). Disease management is mostly based on prophylactic measures as there are no curative in-field treatments available. In this context, sensor-based disease detection could be a useful tool for winegrowers. Therefore, hyperspectral imaging (400–2500 nm) was applied to identify phytoplasma-infected greenhouse plants and shoots collected in the field. Disease detection models (Radial-Basis Function Network) have successfully been developed for greenhouse plants of two white grapevine varieties infected with BN and PGY. Differentiation of symptomatic and healthy plants was possible reaching satisfying classification accuracies of up to 96%. However, identification of BN-infected but symptomless vines was difficult and needs further investigation. Regarding shoots collected in the field from different red and white varieties, correct classifications of up to 100% could be reached using a Multi-Layer Perceptron Network for analysis. Thus, hyperspectral imaging seems to be a promising approach for the detection of different GY. Moreover, the 10 most important wavelengths were identified for each disease detection approach, many of which could be found between 400 and 700 nm and in the short-wave infrared region (1585, 2135, and 2300 nm). These wavelengths could be used further to develop multispectral systems.
SurvNet: A Novel Deep Neural Network for Lung Cancer Survival Analysis With Missing Values

Survival analysis is important for guiding further treatment and improving lung cancer prognosis. It is a challenging task because of the poor distinguishability of features and the missing values in practice. A novel multi-task based neural network, SurvNet, is proposed in this paper. The proposed SurvNet model is trained in a multi-task learning framework to jointly learn across three related tasks: input reconstruction, survival classification, and Cox regression. It uses an input reconstruction mechanism cooperating with incomplete-aware reconstruction loss for latent feature learning of incomplete data with missing values. Besides, the SurvNet model introduces a context gating mechanism to bridge the gap between survival classification and Cox regression. A new real-world dataset of 1,137 patients with IB-IIA stage non-small cell lung cancer is collected to evaluate the performance of the SurvNet model. The proposed SurvNet achieves a higher concordance index than the traditional Cox model and Cox-Net. The difference between high-risk and low-risk groups obtained by SurvNet is more significant than that of high-risk and low-risk groups obtained by the other models. Moreover, the SurvNet outperforms the other models even though the input data is randomly cropped and it achieves better generalization performance on the Surveillance, Epidemiology, and End Results Program (SEER) dataset.
Anomalous Behavior of Highly Active Helical Swimmers

Artificially designed self-propelled objects can allow studying active matter phenomena with great detail that is not possible in natural, e.g. biological systems. Here, we show experimental results on helical shaped, magnetically actuated, reciprocal swimmers, where the degree of randomness in the reciprocal sequence plays an important role in determining their effective motility. Here, for the first time we show the results at high activity levels where the degree of randomness is further affected by the presence of the surface, which in turn results in a non-monotonic increase of motility as a function of magnetic drive. It will be interesting to extend these studies to denser systems where the swimmers can interact with each other through hydrodynamic forces.
Clinical Phenotyping and Biomarkers in Spinal and Bulbar Muscular Atrophy

Background: Spinal and bulbar muscular atrophy (SBMA) or Kennedy disease [OMIM: 313200] is a rare X-linked neuromuscular disease. Patients commonly present with muscle cramps, tremors, leg weakness, dysarthria and dysphagia. Methods: We deeply phenotyped and evaluated the possible extent of affected systems in all patients with SBMA in Latvia (n = 5). In addition, neurophysiological studies and blood analyses were used to perform a molecular diagnosis and evaluate biochemical values. We analyzed neurofilament light (NfL) as a possible biomarker. Results: Neurological examination revealed typical SBMA clinical manifestations; all patients had small or large nerve fiber neuropathy. Three of five patients had increased neurofilament light levels. Conclusion: The study confirms the systemic involvement in patients suffering from SBMA. Increased NfL concentration was associated with either peripheral neuropathy or decreased body mass index. The complex phenotype of the disease should be kept in mind, as it could help to diagnose patients with SBMA.
Evaluation of Proteoforms of the Transmembrane Chemokines CXCL16 and CX3CL1, Their Receptors, and Their Processing Metalloproteinases ADAM10 and ADAM17 in Proliferative Diabetic Retinopathy

The transmembrane chemokine pathways CXCL16/CXCR6 and CX3CL1/CX3CR1 are strongly implicated in inflammation and angiogenesis. We investigated the involvement of these chemokine pathways and their processing metalloproteinases ADAM10 and ADAM17 in the pathophysiology of proliferative diabetic retinopathy (PDR). Vitreous samples from 32 PDR and 24 non-diabetic patients, epiretinal membranes from 18 patients with PDR, rat retinas, human retinal Müller glial cells and human retinal microvascular endothelial cells (HRMECs) were studied by enzyme-linked immunosorbent assay, immunohistochemistry and Western blot analysis. In vitro angiogenesis assays were performed and the adherence of leukocytes to CXCL16-stimulated HRMECs was assessed. CXCL16, CX3CL1, ADAM10, ADAM17 and vascular endothelial growth factor (VEGF) levels were significantly increased in vitreous samples from PDR patients. The levels of CXCL16 were 417-fold higher than those of CX3CL1 in PDR vitreous samples. Significant positive correlations were found between the levels of VEGF and the levels of CXCL16, CX3CL1, ADAM10 and ADAM17. Significant positive correlations were detected between the numbers of blood vessels expressing CD31, reflecting the angiogenic activity of PDR epiretinal membranes, and the numbers of blood vessels and stromal cells expressing CXCL16, CXCR6, ADAM10 and ADAM17. CXCL16 induced upregulation of phospho-ERK1/2, p65 subunit of NF-κB and VEGF in cultured Müller cells and tumor necrosis factor-α induced upregulation of soluble CXCL16 and ADAM17 in Müller cells. Treatment of HRMECs with CXCL16 resulted in increased expression of intercellular adhesion molecule-1 (ICAM-1) and increased leukocyte adhesion to HRMECs. CXCL16 induced HRMEC proliferation, formation of sprouts from HRMEC spheroids and phosphorylation of ERK1/2. Intravitreal administration of CXCL16 in normal rats induced significant upregulation of the p65 subunit of NF-κB, VEGF and ICAM-1 in the retina. Our findings suggest that the chemokine axis CXCL16/CXCR6 and the processing metalloproteinases ADAM10 and ADAM17 might serve a role in the initiation and progression of PDR.
Detecting Biophysical Characteristics and Nitrogen Status of Finger Millet at Hyperspectral and Multispectral Resolutions

Finger millet (Eleusine coracana Gaertn L.) is an important grain crop for small farmers in many countries. Reliable estimates of crop parameters, such as crop growth and nitrogen (N) content, through remote sensing techniques can improve in-season management of finger millet. This study investigated the relationships of hyperspectral reflectance with canopy height, green canopy cover, leaf area index (LAI), and N concentrations of finger millet using an optimal waveband selection procedure with partial least square regression (PLSR). Predictive performance of 13 vegetation indices (VIs) computed from the original hyperspectral data as well as synthesized Landsat-8 and Sentinel-2 data were evaluated and compared for estimating various crop parameters with simple linear regression (SLR) and multilinear regression (MLR) models. The optimal wavebands determined by PLSR were mostly concentrated within 1,000–1,100 nm for both LAI and dry biomass but were scattered for other canopy parameters. The SLR statistics resulted in the simple ratio pigment index (SRPI) and red/green index (RGI) performing best when predicting LAI (R2v = 0.53–0.59) and canopy cover (R2v = 0.72–0.76). The blue/green index (BGI1) was strongly related to canopy height (R2v = 0.65–0.78), dry biomass (R2v = 0.42–0.49), and N concentration (R2v = 0.70–0.83) of finger millet, regardless of spectral resolutions. The MLR approach, using four maximum VIs as input variables, improved the prediction accuracy of N concentration by 14% compared to both SLR and waveband selection methods. VIs computed from synthesized Landsat-8 and Sentinel-2 satellite data resulted in similar or greater prediction accuracy than hyperspectral data for various canopy parameters of finger millet, indicating publicly accessible multispectral data could serve as alternative to hyperspectral data for improved crop management decisions via precision agriculture.
Relevance of NADH Dehydrogenase and Alternative Two-Enzyme Systems for Growth of Corynebacterium glutamicum With Glucose, Lactate, and Acetate

The oxidation of NADH with the concomitant reduction of a quinone is a crucial step in the metabolism of respiring cells. In this study, we analyzed the relevance of three different NADH oxidation systems in the actinobacterial model organism Corynebacterium glutamicum by characterizing defined mutants lacking the non-proton-pumping NADH dehydrogenase Ndh (Δndh) and/or one of the alternative NADH-oxidizing enzymes, L-lactate dehydrogenase LdhA (ΔldhA) and malate dehydrogenase Mdh (Δmdh). Together with the menaquinone-dependent L-lactate dehydrogenase LldD and malate:quinone oxidoreductase Mqo, the LdhA-LldD and Mdh-Mqo couples can functionally replace Ndh activity. In glucose minimal medium the Δndh mutant, but not the ΔldhA and Δmdh strains, showed reduced growth and a lowered NAD+/NADH ratio, in line with Ndh being the major enzyme for NADH oxidation. Growth of the double mutants ΔndhΔmdh and ΔndhΔldhA, but not of strain ΔmdhΔldhA, in glucose medium was stronger impaired than that of the Δndh mutant, supporting an active role of the alternative Mdh-Mqo and LdhA-LldD systems in NADH oxidation and menaquinone reduction. In L-lactate minimal medium the Δndh mutant grew better than the wild type, probably due to a higher activity of the menaquinone-dependent L-lactate dehydrogenase LldD. The ΔndhΔmdh mutant failed to grow in L-lactate medium and acetate medium. Growth with L-lactate could be restored by additional deletion of sugR, suggesting that ldhA repression by the transcriptional regulator SugR prevented growth on L-lactate medium. Attempts to construct a ΔndhΔmdhΔldhA triple mutant were not successful, suggesting that Ndh, Mdh and LdhA cannot be replaced by other NADH-oxidizing enzymes in C. glutamicum.
Influence of Magnetic Field Strength on Magnetic Resonance Imaging Radiomics Features in Brain Imaging, an In Vitro and In Vivo Study

Background The development and clinical adoption of quantitative imaging biomarkers (radiomics) has established the need for the identification of parameters altering radiomics reproducibility. The aim of this study was to assess the impact of magnetic field strength on magnetic resonance imaging (MRI) radiomics features in neuroradiology clinical practice. Methods T1 3D SPGR sequence was acquired on two phantoms and 10 healthy volunteers with two clinical MR devices from the same manufacturer using two different magnetic fields (1.5 and 3T). Phantoms varied in terms of gadolinium concentrations and textural heterogeneity. 27 regions of interest were segmented (phantom: 21, volunteers: 6) using the LIFEX software. 34 features were analyzed. Results In the phantom dataset, 10 (67%) out of 15 radiomics features were significantly different when measured at 1.5T or 3T (student’s t-test, p < 0.05). Gray levels resampling, and pixel size also influence part of texture features. These findings were validated in healthy volunteers. Conclusions According to daily used protocols for clinical examinations, radiomic features extracted on 1.5T should not be used interchangeably with 3T when evaluating texture features. Such confounding factor should be adjusted when adapting the results of a study to a different platform, or when designing a multicentric trial.
Modification of the Sensory Profile and Volatile Aroma Compounds of Tomato Fruits by the Scion × Rootstock Interactive Effect

Sensory quality is of increasing importance to consumer decisions in choosing a product, and it is certainly an important factor in repurchasing in terms of meeting the necessary aroma quality and taste properties. To better understand the effects of rootstocks and scions on fruit quality, the sensory profile and volatile aroma composition of the fruits of hydroponically grown tomato plants were evaluated. Experiments were established using the tomato cultivars Clarabella and Estatio as scions during two spring-summer seasons. In both experiments, the scion plants were self-grafted or grafted onto rootstocks of cultivars Arnold, Buffon, Emperador, and Maxifort, with the exception that in experiment 1, the Estatio scion was not grafted onto Buffon. The scions and rootstocks caused differences in observed sensory properties in both experiments. For most of the sensory traits, interaction effects between scion and rootstock were observed. Compared to those obtained from self-grafted Clarabella, the fruits obtained from Clarabella grafted onto Buffon in the first experiment and Clarabella grafted onto Arnold in the second experiment were sweeter by one measurement unit. The contents of seven aldehydes, six alcohols, five terpenes and two ketones were determined. A lower accumulation of total aldehydes, 22–45%, due to lower amounts of pentanal, (E)-2-heptanal and (E,E)-2,4-decadienal, was found in the fruits from plants where Estatio was rootstock compared with the other rootstocks treatments. Clarabella as a rootstock increased (Z)-3-hexenal + (E)-2-hexenal accumulation from 35 to 65%. Grafting Clarabella onto the tested rootstocks led to a change in the composition of volatile compounds, while differences between the combinations with Estatio as a scion were generally not recorded. Fruits from self-grafted Clarabella had higher (Z)-3-hexenal + (E)-2-hexenal concentrations than did fruits from Clarabella grafted onto Arnold (for 54%) and Emperador (for 68%), and in the second experiment, grafting onto all commercial rootstocks reduced (Z)-3-hexenal + (E)-2-hexenal concentrations, from 25 to 74%, compared to those from self-grafted Clarabella. Higher (+)-2-carene and (−)-caryophyllene oxide concentrations were attained in plants in which Clarabella was grafted onto Maxifort (by 56%) and plants in which Estatio was grafted onto Arnold (by 36%) compared to self-grafted plants. This study showed the possibility of altering the composition of volatile aroma compounds and sensory properties of tomato fruits by the use of grafting techniques.