Miracle-dz/UniFAR-FTUs huggingface dataset:
On the use of dissolved oxygen isotopologues as biogeochemical tracers in the Pacific Ocean

The isotopic composition of dissolved oxygen offers a family of potentially unique tracers of respiration and transport in the subsurface ocean. Uncertainties in transport parameters and isotopic fractionation factors, however, have limited the strength of the constraints offered by 18O/16O and 17O/16O ratios in dissolved oxygen. In particular, puzzlingly low 17O/16O ratios observed for some low-oxygen samples have been difficult to explain. To improve our understanding of oxygen cycling in the ocean’s interior, we investigated the systematics of oxygen isotopologues in the subsurface Pacific using new data and a 2-D isotopologue-enabled isopycnal reaction-transport model. We measured 18O/16O and 17O/16O ratios, as well as the “clumped” 18O18O isotopologue in the northeast Pacific, and compared the results to previously published data. We find that transport and respiration rates constrained by O2 concentrations in the oligotrophic Pacific yield good measurement-model agreement across all O2 isotopologues only when using a recently reported set of respiratory isotopologue fractionation factors that differ from those most often used for oxygen cycling in the ocean. These fractionation factors imply that an elevated proportion of 17O compared to 18O in dissolved oxygen–i.e., its triple-oxygen isotope composition–does not uniquely reflect gross primary productivity and mixing. For all oxygen isotopologues, transport, respiration, and photosynthesis comprise important parts of their respective budgets. Mechanisms of oxygen removal in the subsurface ocean are discussed. Hosted file supplemental information nepac o2.docx available at https://authorea.com/users/561207/ articles/608816-on-the-use-of-dissolved-oxygen-isotopologues-as-biogeochemical-tracersin-the-pacific-ocean
Biological Control for some Insects by Using Plant Growth Promoting Bacteria in Laboratory and Field Conditions

The cotton leafworm and aphid insects are major pests in Egypt that attack many host plants. Pesticides use can cause different problems in the plant system. So, it is very important to use nature products to be safe as a alternatives to synthetic pesticides. This research aimed to evaluate the efficacy of three bacterial types: Lysinibacillus macroides, Brevundimonas olei and Acinetobacter sp. in laboratory and field conditions throughout two seasons 2021 & 2022. L. macroides and B. olei showed more toxicity and LC50 levels than Acinetobacter sp with > 90 % corrected mortality towards the cotton leafworm and bean aphid after 3 days exposure time under laboratory conditions. Under field conditions, there were two insect pests fall armyworm (Spodoptera frugiperda) and aphid insects (Myzus persica (Sulzer) that investigate pepper plants in Ismallia Governorate. The results also showed a high efficacy of two bacterial strains, L. macroides and B. olei against M. persicae and S. frugiperda with more than 80% and 60% reduction percent respectively. The data stated that, L. macrolides strain was the most effective on suppressing the aphid and fall armyworm insects population. Some bacterial enzymes and biochemical products produced by bacteria used, such as protease, chitinase, catalase, glutathione peroxidase, polyphenol oxidase (PPOs) and HCN. They play a role in insect population reduction in laboratory and field conditions throughout integrated crop management.
A Monoclonal Antibody Produced in Glycoengineered Plants Potently Neutralizes Monkeypox Virus

The 2022 global outbreaks of monkeypox virus (MPXV) and increased human-to-human transmission calls for the urgent development of countermeasures to protect people who cannot benefit from vaccination. Here, we describe the development of glycovariants of 7D11, a neutralizing monoclonal IgG antibody (mAb) directed against the L1 transmembrane protein of the related vaccinia virus, in a plant-based system as a potential therapeutic against the current MPVX outbreak. Our results indicated that 7D11 mAb quickly accumulates to high levels within a week after gene introduction to plants. Plant-produced 7D11 mAb assembled correctly into the tetrameric IgG structure and can be easily purified to homogeneity. 7D11 mAb exhibited a largely homogeneous N-glycosylation profile, with or without plant-specific xylose and fucose residues, depending on the expression host, namely wild-type or glycoengineered plants. Plant-made 7D11 retained specific binding to its antigen and displayed a strong neutralization activity against MPXV, as least as potent as the reported activity against vaccinia virus. Our study highlights the utility of anti-L1 mAbs as MPXV therapeutics, and the use of glycoengineered plants to develop mAb glycovariants for potentially enhancing the efficacy of mAbs to combat ever-emerging/re-emerging viral diseases.
Inhibitory Investigations of Acyl-CoA Derivatives against Human Lipoxygenase Isozymes

Lipid metabolism is a complex process crucial for energy production resulting in high levels of acyl-coenzyme A (acyl-CoA) molecules in the cell. Acyl-CoAs have also been implicated in inflammation, which could be possibly linked to lipoxygenase (LOX) biochemistry by the observation that an acyl-CoA was bound to human platelet 12-lipoxygenase via cryo-EM. Given that LOX isozymes play a pivotal role in inflammation, a more thorough investigation of the inhibitory effects of acyl-CoAs on lipoxygenase isozymes was judged to be warranted. Subsequently, it was determined that C18 acyl-CoA derivatives were the most potent against h12-LOX, human reticulocyte 15-LOX-1 (h15-LOX-1), and human endothelial 15-LOX-2 (h15-LOX-2), while C16 acyl-CoAs were more potent against human 5-LOX. Specifically, oleoyl-CoA (18:1) was most potent against h12-LOX (IC50 = 32 μM) and h15-LOX-2 (IC50 = 0.62 μM), stearoyl-CoA against h15-LOX-1 (IC50 = 4.2 μM), and palmitoleoyl-CoA against h5-LOX (IC50 = 2.0 μM). The inhibition of h15-LOX-2 by oleoyl-CoA was further determined to be allosteric inhibition with a Ki of 82 +/− 70 nM, an α of 3.2 +/− 1, a β of 0.30 +/− 0.07, and a β/α = 0.09. Interestingly, linoleoyl-CoA (18:2) was a weak inhibitor against h5-LOX, h12-LOX, and h15-LOX-1 but a rapid substrate for h15-LOX-1, with comparable kinetic rates to free linoleic acid (kcat = 7.5 +/− 0.4 s−1, kcat/KM = 0.62 +/− 0.1 µM−1s−1). Additionally, it was determined that methylated fatty acids were not substrates but rather weak inhibitors. These findings imply a greater role for acyl-CoAs in the regulation of LOX activity in the cell, either through inhibition of novel oxylipin species or as a novel source of oxylipin-CoAs.
CrossCT: CNN and Transformer cross–teaching for multimodal image cell segmentation

Segmenting microscopy images is a crucial step for quantitatively analyzing biological imaging data. Classical tools for biological image segmentation need to be adjusted to the cell type and image conditions to get decent results. Another limitation is the lack of high-quality labeled data to train alternative methods like Deep Learning since manual labeling is costly and time-consuming. Weakly Supervised Cell Segmentation in Multi-modality High-Resolution Microscopy Images 1 was organized by NeurIPS to solve this problem. The aim of the challenge was to develop a versatile method that can work with high variability, with few labeled images, a lot of unlabeled images, and with no human interaction. We developed CrossCT, a framework based on the cross–teaching between a CNN and a Transformer. The main idea behind this work was to improve the organizers’ baseline methods and use both labeled and unlabeled data. Experiments show that our method outperforms the baseline methods based on a supervised learning approach. We achieved an F1 score of 0.5988 for the Transformer and 0.5626 for the CNN respecting the time limits imposed for inference. The code is available on GitHub
Virtual Water Coolers: A Field Experiment on the Role of Virtual Interactions on Organizational Newcomer Performance

Designing management practices to better onboard organizational newcomers working remotely is a key priority for firms. We report results from a randomized field experiment conducted at a large global firm that estimates the performance effects of different types of virtual interactions for remote summer interns. Findings indicate that virtual water coolers—or videoconference sessions for small groups of interns and a senior manager—may yield higher performance and career outcomes when they facilitate a demographic match between interns and senior managers or occur at regular intervals during the internship. No other virtual interactions, including an asynchronous Q&A discussion forum, an intern-only water cooler, and an intern group project, enhanced job productivity compared to the control condition. An abductive exploration of mechanisms using surveys, machine learning, and an online laboratory study suggests a tradeoff: while the virtual interactions may offer opportunities for newcomer socialization, they also introduce greater constraints on interns’ time. The relative outperformance of the senior manager virtual water cooler with a demographic match can be explained by their potential to foster improved organizational commitment among treated interns, which may have led to their higher job performance and career outcomes.
Representation of Women Among Grand Rounds Speakers at an Academic Health System Early in the COVID-19 Pandemic

Introduction An invitation to speak at grand rounds (GR) is considered an honor and an activity important for academic promotion. The aim of this study was to determine the representation of women among invited speakers at departmental GR and assess the impact of the COVID-19 pandemic on it. Methods We conducted a retrospective descriptive study on gender differences in all GR speakers between January 2019 and June 2021 at an academic health system in Western Massachusetts. We calculated the overall percentage of women presenters and compared it with the percentage of women faculty at our institution and nationally. To evaluate the impact of COVID-19 on this association, we calculated the absolute percentage difference between women and men speakers using the date of March 13, 2020, as the cut-off and conducted a sensitivity analysis using June 15, 2020, as the cut-off. Results During the study period, 46% (276/607) of GR speakers at our institution were women. This percentage reflected the percentage of the women faculty overall at our institution and was similar to women’s representation among faculty nationally. Departments with high percentages of women faculty (Obstetrics and Gynecology, 76%; Pediatrics, 65%) had high percentages of women GR speakers (Obstetrics and Gynecology, 70%; Pediatrics, 51%; Psychiatry, 62%). COVID-19 did not appear to significantly influence gender representation among speakers. Conclusion At our institution, less than half of the GR speakers were women. However, this percentage appears to reflect the overall percentage of women faculty. Potential barriers and opportunities resulting from the COVID-19 pandemic did not appear to impact this finding.
The Extraordinary Case of a Woman with a 30-Year-Long Diffuse Leishmaniasis Cured with One Single Ampoule of Intranasal Pentavalent Antimoniate

Infection with Leishmania amazonensis and L. mexicana may lead to diffuse cutaneous leishmaniasis. The cure is exceptional, especially for the strange case of this lady. Case report: The patient acquired the disease in childhood and remained with lesions for over 30 years, albeit several treatments. She worsened after a pregnancy, developing disseminated lesions. Miltefosine with amphotericin B and pentamidine resulted in remission. Lesions reappeared after one year, accompanied by intra-nasal infiltration of the disease. The nasal spraying of a single ampoule of pentavalent antimoniate resulted in the sustained disappearance of the nasal symptoms and all the cutaneous lesions. After over eight years, she remains disease-free, albeit under renal replacement therapy. The high nasal mucosal antimonial concentration may explain the long-lasting cure via new MHC class I epitope-specific CD8+ cell clones against L. amazonensis present in the nasal mucosa.
Identification of a Gene Signature Predicting (Nano)Particle-Induced Adverse Lung Outcome in Rats

Nanoparticles are extensively used in industrial products or as food additives. However, despite their contribution to improving our quality of life, concerns have been raised regarding their potential impact on occupational and public health. To speed up research assessing nanoparticle-related hazards, this study was undertaken to identify early markers of harmful effects on the lungs. Female Sprague Dawley rats were either exposed to crystalline silica DQ-12 with instillation, or to titanium dioxide P25, carbon black Printex-90, or multi-walled carbon nanotube Mitsui-7 with nose-only inhalation. Tissues were collected at three post-exposure time points to assess short- and long-term effects. All particles induced lung inflammation. Histopathological and biochemical analyses revealed phospholipid accumulation, lipoproteinosis, and interstitial thickening with collagen deposition after exposure to DQ-12. Exposure to the highest dose of Printex-90 and Mitsui-7, but not P25, induced some phospholipid accumulation. Comparable histopathological changes were observed following exposure to P25, Printex-90, and Mitsui-7. Comparison of overall gene expression profiles identified 15 potential early markers of adverse lung outcomes induced by spherical particles. With Mitsui-7, a distinct gene expression signature was observed, suggesting that carbon nanotubes trigger different toxicity mechanisms to spherical particles.
STRAINTS: A THEORY OF FUNCTIONAL CELL TYPES

Neurons in the brain are often finely tuned for specific task variables. Moreover, such disentangled representations are highly sought after in machine learning. Here we mathematically prove that simple biological constraints on neurons, namely nonnegativity and energy efficiency in both activity and weights, promote such sought after disentangled representations by enforcing neurons to become selective for single factors of task variation. We demonstrate these constraints lead to disentanglement in a variety of tasks and architectures, including variational autoencoders. We also use this theory to explain why the brain partitions its cells into distinct cell types such as grid and object-vector cells, and also explain when the brain instead entangles representations in response to entangled task factors. Overall, this work provides a mathematical understanding of why single neurons in the brain often represent single human-interpretable factors, and steps towards an understanding task structure shapes the structure of brain representation.
Detection of Surface Defects of Magnetic Tiles Based on Improved YOLOv5

The typical defect detection algorithm is ineffective due to the contrast between the magnetic tile defect and the various defect features. An improved YOLOv5-based algorithm, for detecting magnetic tile defects with varying defect features, is suggested. The procedure begins by incorporating the CBAM into feature extraction network of YOLOv5. It improves the feature of network learning capabilities for the target region by filtering and weighting the feature vectors in such a way that the processing of network is dominated by the essential target characteristics. A new loss function of detection model is then proposed according to the properties of the magnetic tile picture, and the confidence of prediction box is increased. Data augmentation technologies are introduced to increase the number of data samples. Based on magnetic tile defect datasets, the evaluation results have shown that the precision of the proposed approach is 98.56%, 3.21%, and 7.22% greater than the original YOLOv5 and Faster R-CNN, respectively, all of which demonstrate the effectiveness and accuracy of the proposed method.
Pen+Touch+Midair: Cross-Space Hybrid Bimanual Interaction on Horizontal Surfaces in Virtual Reality

We present and explore a design space for hybrid bimanual pen and touch input extended to midair interaction in desktop-based virtual reality (VR). The investigation focuses on asymmetric interaction patterns combining the pen with the other hand when interacting in the same “space” (either surface or midair), across both spaces, and with cross-space transitions (from surface to midair and vice versa). To show how these interactions and associated gestures can work in context, we create three testbed applications for modelling, volumetric rendering, and terrain editing. A qualitative evaluation with 16 participants provides insights into hand and space preferences for key tasks including object manipulation, navigation, and menu invocation. From the results, design implications are identified for VR systems that combine pen, touch, and midair input, and extensions to other forms of extended reality are discussed.
Deletion of the H240R Gene in African Swine Fever Virus Partially Reduces Virus Virulence in Swine

African swine fever (ASF) is a highly contagious disease that affects wild and domestic swine. Currently, the disease is present as a pandemic affecting pork production in Eurasia and the Caribbean region. The etiological agent of ASF is a large, highly complex structural virus (ASFV) harboring a double-stranded genome encoding for more than 160 proteins whose functions, in most cases, have not been experimentally characterized. We show here that deletion of the ASFV gene H240R from the genome of the highly virulent ASFV-Georgia2010 (ASFV-G) isolate partially decreases virus virulence when experimentally inoculated in domestic swine. ASFV-G-∆H240R, a recombinant virus harboring the deletion of the H240R gene, was produced to evaluate the function of the gene in the development of disease in pigs. While all animals intramuscularly inoculated with 102 HAD50 of ASFV-G developed a fatal form of the disease, forty percent of pigs receiving a similar dose of ASFV-G-∆H240R survived the infection, remaining healthy during the 28-day observational period, and the remaining sixty percent developed a protracted but fatal form of the disease compared to that induced by ASFV-G. Additionally, all animals inoculated with ASFV-G-∆H240R presented protracted viremias with reduced virus titers when compared with those found in animals inoculated with ASFV-G. Animals surviving infection with ASFV-G-∆H240R developed a strong virus-specific antibody response and were protected against the challenge of the virulent parental ASFV-G.
Measuring Fiscal Multipliers in Egypt: Applying the Bucket and SVAR Approaches

Contrary to the Keynesian view, quantifying the fiscal multipliers in Egypt yields small magnitude using empirical and non-empirical approaches. The effectiveness of fiscal policy is analyzed using two approaches. Firstly, the ‘Bucket approach’ deduces the size of fiscal multipliers within the framework of several structural factors that are believed to have a significant effect in determining the size of fiscal multiplier. This represents the first such study that applies the “Bucket approach” in the case of Egypt. Secondly, the Structural Vector Auto-Regression (SVAR) approach is estimated over the period (2005/06 – 2017/18) with quarterly data. This high-frequency data enables identifying the SVAR model through imposing the contemporaneous restrictions. The model includes government expenditures, tax revenues, output and interest rate in real terms. The findings of the ‘Bucket approach’ and SVAR were consistent and confirm a limited Keynesian demand push effect. Government spending proves to be much more effective tool than the tax revenues.
Evaluation of Otolith Shape as an Approach for Stock Discrimination of Sardina pilchardus off the Moroccan Atlantic Coast

1 Laboratory "Water, Biodiversity & climate change ", Department of Biology, Faculty of Sciences, Semlalia, Cadi Ayyad University, Marrakech, P.O. Box2390, 40000, Morocco 2 The Natural History Museum of Marrakech, Research Centre on Biodiversity, Cadi Ayyad University, Bd Allal El Fassi, Marrakech, Morocco 3 Laboratory of Biotechnology & Sustainable Development of Natural Resources. Polydisciplinary Faculty of Beni Mellal, Sultan Moulay Slimane University, Mghila PO Box. 592, Beni Mellal 23000, Morocco 4 Department of Environmental Engineering, Higher School of Technology, Sultan Moulay Slimane University, Khénifra 54000, Morocco 5 Laboratory of Natural Substances & Synthesis and Molecular Dynamics, Faculty of Sciences and Techniques, Moulay ismail University, Errachidia, Morocco 6 Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources, Department of Biology, Faculty of Sciences-Semlalia, Cadi Ayyad University, P.O. Box 2390, 40090 Marrakesh, Morocco Corresponding Author: mnraziz1980@gmail.com
The Relation of Parasitic Infection and Growth States in Pediatric Patients with Irritable Bowel Syndrome

Background: Irritable bowel syndrome (IBS) is a group of diseases of the gastrointestinal tract (GIT) with a heterogeneous pathophysiology and unclear role for intestinal parasitic infections. Objective: The aim of the current study was to detect the relationship of parasitic infection with malnutrition among cases of IBS. Patients and methods: A cross sectional study was conducted and included 120 children in age from 5 to 15 years old attending the outpatient clinics in October 6 University Hospital and Primary Healthcare centers with GIT symptoms suggesting IBS. All cases subjected to medical evaluation, anthropometric assessment and stool analysis. Result: The study revealed that 68/120 (56.7%) of IBS cases had parasitic infection (Group A) with Giardia lamblia stages is the most frequent one (25/68 samples, 36.7% of group A, and 20.8% of total IBS case). IBSdiarrheic type (IBS-D) was the predominant subtypes (54/120, 45%) and associated with parasitic infection (P-value <0.05) that wasn’t observed in other subtypes. The most frequent form of malnutrition according to the Egyptian Z score was overweight (19/120, 15.8%) of IBS cases and no cases with undernutrition or obesity. No significant relation between parasitic infection and malnutrition in IBS (P-value >0.05) for all parameters. Conclusion: Parasitic infection is common among cases of IBS and associated with diarrhea. Overweight is the most frequent form of malnutrition in cases of IBS even in presence of parasitic infection that revealed no association of parasitic infection with undernutrition in cases of IBS.
Glycemic Dysregulation, Inflammation and Disease Outcomes in Patients Hospitalized with COVID-19: Beyond Diabetes and Obesity

Introduction: During the COVID-19 pandemic, diabetes mellitus (DM) and obesity were associated with high rates of morbidity and mortality. The aim of this study was to investigate the relationship between markers of inflammation, disease severity, insulin resistance, hyperglycemia, and outcomes in COVID-19 patients with and without diabetes and obesity. Materials and Methods: Epidemiological, clinical, and laboratory data were collected from the University Hospital of Ioannina COVID-19 Registry and included hospitalized patients from March 2020 to December 2022. The study cohort was divided into three subgroups based on the presence of DM, obesity, or the absence of both. Results: In diabetic patients, elevated CRP, IL-6, TRG/HDL-C ratio, and TyG index, severe pneumonia, and hyperglycemia were associated with extended hospitalization. Increased IL-6, NLR, and decreased PFR were associated with a higher risk of death. In the obese subgroup, lower levels of PFR were associated with longer hospitalization and a higher risk of death, while severe lung disease and hyperglycemia were associated with extended hospitalization. In patients without DM or obesity severe pneumonia, NLR, CRP, IL-6, insulin resistance indices, and hyperglycemia during hospitalization were associated with longer hospitalization. Conclusion: Inflammatory markers and disease severity indices were strongly associated with disease outcomes and hyperglycemia across all subgroups.