Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimizing Stony Coral Tissue Loss Disease (SCTLD) Intervention Treatments on Montastraea cavernosa in an Endemic Zone

Stony coral tissue loss disease (SCTLD) has persisted since 2014 in the Southeast Florida Coral Reef Ecosystem Conservation Area (Coral ECA) where it was first discovered. Most of the highly susceptible corals have perished, leaving Montastraea cavernosa as the most abundant reef-building species with high SCTLD prevalence. Disease interventions (DI) have been conducted throughout Florida’s Coral Reef to save the remaining corals and reduce the disease prevalence with varying degrees of success. The two main treatments were chlorinated (Chl) epoxy and an antibiotic paste. The antibiotic paste was highly effective in the Florida Keys, but its effectiveness in the Coral ECA was questionable. Therefore, we compared the effectiveness of the antibiotic paste and Chl epoxy treatments on M. cavernosa to optimize DI efforts on this species in the Coral ECA. Significant differences were found between the treatment materials and applications related to the proportion of quiesced lesions and corals where antibiotic paste (91.2% success) outperformed Chl epoxy (20% success). By day 351, 50.6% of the antibiotic paste disease-break tissue was fully healed compared to 2.2% of the total Chl epoxy-filled disease-break area. During the study, new lesions occurred on previously treated colonies, as well as colonies not previously treated and new lesion rates varied through time, indicating revisitation is necessary to eliminate disease. Most margin treatments failed within the first 9 days, however, most disease-breaks failed before 44 days. Considering the high treatment success of the antibiotic paste and the conditional variation of new lesion rates, about 1 month is a good practical re-visitation time for retreating failures and any new lesions. DI using antibiotic paste is currently the most effective way to intervene the SCTLD epidemic, but this is only effective as a stopgap measure while the larger causative agents are identified and remediated. Conducting DI at a reef-scape scale is time consuming and requires extensive person-power and resources, making it very expensive. But this expense pales in comparison to the current cost to restore the diversity and live tissue saved with DI. This method also comes with the risk of introducing antibiotics into coral reef environments, which may have unintended outcomes.
Expression of Autophagy-Related Factors LC3A and Beclin 1 and Apoptosis-Related Factors Bcl-2 and BAX in Osteoblasts Treated With Sodium Fluoride

Objective This study aims to analyze the expressions of autophagy-related factors light chain 3 alpha (LC3A) and Beclin 1 and apoptosis-related factors B-cell lymphoma 2 (Bcl-2) and Bcl-2-associated X (BAX) in primary osteoblasts treated with sodium fluoride (NaF). Methods Osteoblasts were extracted from Sprague-Dawley rats and treated with 0, 2.5, 5, and 10 mg/L NaF solutions, followed by 10 mmol/L 3-methyladenine (3-MA) for 24 h. The apoptotic rate was determined by flow cytometry, and the expressions of the autophagy- and apoptosis-related factors were measured by western blotting and real-time quantitative polymerase chain reaction. Results The mRNA expressions of LC3A, Beclin 1, and BAX in the NaF-treated osteoblast group were higher than those in the control group, while the protein expressions of these factors in the NaF-treated group were significantly higher than those in the control group. However, the Bcl-2 protein expression in the NaF-treated osteoblasts was significantly decreased compared to that in the control cells. After the 3-MA treatment, the protein expressions of LC3A, Beclin 1, and Bcl-2 were significantly decreased compared with those of the NaF-treated group, whereas the expression of BAX increased. Moreover, the apoptosis rate was increased after the addition of the 3-MA inhibitor. Conclusion NaF stimulation promoted autophagy and apoptosis of the osteoblasts, suggesting the involvement of fluoride damage in these processes.
Endomembrane-Targeting Plasmodiophora brassicae Effectors Modulate PAMP Triggered Immune Responses in Plants

Plasmodiophora brassicae is a devastating obligate, intracellular, biotrophic pathogen that causes clubroot disease in crucifer plants. Disease progression is regulated by effector proteins secreted by P. brassicae. Twelve P. brassicae putative effectors (PbPEs), expressed at various stages of disease development [0, 2, 5, 7, 14, 21, and 28 days post inoculation (DPI)] in Arabidopsis and localizing to the plant endomembrane system, were studied for their roles in pathogenesis. Of the 12 PbPEs, seven showed an inhibitory effect on programmed cell death (PCD) as triggered by the PCD inducers, PiINF1 (Phytophthora infestans Infestin 1) and PiNPP1 (P. infestans necrosis causing protein). Showing the strongest level of PCD suppression, PbPE15, a member of the 2-oxoglutarate (2OG) and Fe (II)-dependent oxygenase superfamily and with gene expression during later stages of infection, appears to have a role in tumorigenesis as well as defense signaling in plants. PbPE13 produced an enhanced PiINF1-induced PCD response. Transient expression, in Nicotiana benthamiana leaves of these PbPEs minus the signal peptide (SP) (ΔspPbPEGFPs), showed localization to the endomembrane system, targeting the endoplasmic reticulum (ER), Golgi bodies and nucleo-cytoplasm, suggesting roles in manipulating plant cell secretion and vesicle trafficking. ΔspPbPE13GFP localized to plasma membrane (PM) lipid rafts with an association to plasmodesmata, suggesting a role at the cell-to-cell communication junction. Membrane relocalization of ΔspPbPE13GFP, triggered by flagellin N-terminus of Pseudomonas aeruginosa (flg22 – known to elicit a PAMP triggered immune response in plants), supports its involvement in raft-mediated immune signaling. This study is an important step in deciphering P. brassicae effector roles in the disruption of plant immunity to clubroot disease.
Novel Reclassification of Adult Diabetes Is Useful to Distinguish Stages of β-Cell Function Linked to the Risk of Vascular Complications: The DOLCE Study From Northern Ukraine

Background Presently, persons with diabetes are classified as having type 1 (T1D) or type 2 diabetes (T2D) based on clinical diagnosis. However, adult patients exhibit diverse clinical representations and this makes treatment approaches challenging to personalize. A recent Scandinavian study proposed a novel classification of adult diabetes into five clusters based on disease pathophysiology and risk of vascular complications. The current study aimed to characterize new subgroups of adult diabetes using this strategy in a defined population from northern Ukraine. Methods We analyzed 2,140 patients with established diabetes from the DOLCE study (n = 887 with new-onset diabetes and n = 1,253 with long duration). We used the k-means approach to perform clustering analyses using BMI, age at onset of diabetes, HbA1c, insulin secretion (HOMA2-B), and insulin resistance (HOMA2-IR) indices and glutamic acid decarboxylase antibodies (GADA) levels. Risks of macro- (myocardial infarction or stroke) and microvascular [retinopathy, chronic kidney disease (CKD) and neuropathy] complications and associations of genetic variants with specific clusters were studied using logistic regression adjusted for age, sex, and diabetes duration. Results Severe autoimmune diabetes (SAID, 11 and 6%) and severe insulin-deficient diabetes (SIDD, 25 and 14%) clusters were twice as prevalent in patients with long-term as compared to those with new-onset diabetes. Patients with long duration in both SAID and SIDD clusters had highest risks of proliferative retinopathy, and elevated risks of CKD. Long-term insulin-resistant obese diabetes 1 (IROD1) subgroup had elevated risks of CKD, while insulin-resistant obese diabetes 2 (IROD2) cluster exhibited the highest HOMA2-B, lowest HbA1c, and lower prevalence of all microvascular complications as compared to all other clusters. Genetic analyses of IROD2 subgroup identified reduced frequency of the risk alleles in the TCF7L2 gene as compared to all other clusters, cumulatively and individually (p = 0.0001). Conclusion The novel reclassification algorithm of patients with adult diabetes was reproducible in this population from northern Ukraine. It may be beneficial for the patients in the SIDD subgroup to initiate earlier insulin treatment or other anti-diabetic modalities to preserve β-cell function. Long-term diabetes cases with preserved β-cell function and lower risk for microvascular complications represent an interesting subgroup of patients for further investigations of protective mechanisms.
Truck Parking Occupancy Prediction: XGBoost-LSTM Model Fusion

For haul truck drivers it is becoming increasingly difficult to find appropriate parking at the end of a shift. Proper, legal, and safe overnight parking spots are crucial for truck drivers in order for them to be able to comply with Hours of Service regulation, reduce fatigue, and improve road safety. The lack of parking spaces affects the backbone of the economy because 70% of all United States domestic freight shipments (in terms of value) are transported by trucks. Many research projects provide real-time truck parking occupancy information at a given stop. However, truck drivers ultimately need to know whether parking spots will be available at a downstream stop at their expected arrival time. We propose a machine-learning-based model that is capable of accurately predicting occupancy 30, 60, 90, and 120 min ahead. The model is based on the fusion of Extreme Gradient Boosting (XGBoost) and Long Short-Term Memory (LSTM) with the help of a feed-forward neural network. Our results show that prediction of truck parking occupancy can be achieved with small errors. Root mean square error metrics are 2.1, 2.9, 3.5, and 4.1 trucks for the four different horizons, respectively. The unique feature of our proposed model is that it requires only historic occupancy data. Thus, any truck occupancy detection system could also provide forecasts by implementing our model.
Circulating Plasmacytoid and Conventional Dendritic Cells Are Numerically and Functionally Deficient in Patients With Scrub Typhus

Background Dendritic cells (DCs) are specialized antigen-presenting cells known to bridge innate and adaptive immune reactions. However, the relationship between circulating DCs and Orientia tsutsugamushi infection is unclear. Therefore, this study aimed to examine the level and function of plasmacytoid DCs (pDCs) and conventional DCs (cDCs), two subsets of circulating DCs, in scrub typhus patients. Methods The study included 35 scrub typhus patients and 35 healthy controls (HCs). pDC and cDC levels, CD86 and CD274 expression, and cytokine levels were measured using flow cytometry. Results Circulating pDC and cDC levels were found to be significantly reduced in scrub typhus patients, which were correlated with disease severity. The patients displayed increased percentages of CD86+ pDCs, CD274+ pDCs, and CD274+ cDCs in the peripheral blood. The alterations in the levels and surface phenotypes of pDCs and cDCs were recovered in the remission state. In addition, the production of interferon (IFN)-α and tumor necrosis factor (TNF)-α by circulating pDCs, and interleukin (IL)-12 and TNF-α by circulating cDCs was reduced in scrub typhus patients. Interestingly, our in vitro experiments showed that the percentages of CD86+ pDCs, CD274+ pDCs, and CD274+ cDCs were increased in cultures treated with cytokines including IFN-γ, IL-12, and TNF-α. Conclusions This study demonstrates that circulating pDCs and cDCs are numerically deficient and functionally impaired in scrub typhus patients. In addition, alterations in the expression levels of surface phenotypes of pDCs and cDCs could be affected by pro-inflammatory cytokines.
Effects of a Submesoscale Oceanographic Filament on Zooplankton Dynamics in the Arctic Marginal Ice Zone

Submesoscale structures, characterized by intense vertical and horizontal velocities, potentially play a crucial role in oceanographic dynamics and pelagic fluxes. Due to their small spatial scale and short temporal persistence, conditions for in situ measurements are challenging and thus the role of such structures for zooplankton distribution is still unclear. During RV Polarstern expedition PS107 to Arctic Fram Strait in July/August 2017, a submesoscale filament was detected, which initiated an ad hoc oceanographic and biological sampling campaign. To determine zooplankton taxonomic composition, horizontal and vertical distribution, abundance and biomass, vertical MultiNet hauls (depth intervals: 300–200–100–50–10–0 m) were taken at four stations across the filament. Zooplankton data were evaluated in context with the physical-oceanographic observations of the filament to assess submesoscale physical-biological interactions. Our data show that submesoscale features considerably impact zooplankton dynamics. While structuring the pelagial with distinct zooplankton communities in a vertical as well as horizontal dimension, they accumulate abundance and biomass of epipelagic species at the site of convergence. Further, high-velocity jets associated with such dynamics are possibly of major importance for species allocation and biological connectivity, accelerating for instance processes such as the ‘Atlantification’ of the Arctic. Thus, submesoscale features affect the surrounding ecosystem in multiple ways with consequences for higher trophic levels and biogeochemical cycles.
The Effect of Animal Bipedal Posture on Perceived Cuteness, Fear, and Willingness to Protect Them

Human–animal relationships have long been the subject of controversy because they are shaped by several cultural, inter-individual, and evolutionary factors. Understanding these relationships, however, is important to optimize conservation efforts. There is agreement that perceived similarity between animals and humans is associated with more positive attitudes. The human–animal similarity could be caused by phylogenetic closeness. We hypothesized that the bipedal posture of an animal may be perceived as a cue of phenotypic similarity with humans. We examined this topic by comparing perceived cuteness, fear, and willingness to protect animals differing in body posture, body size, and phylogenetic closeness with humans on a sample of N = 349 Slovak participants. We found that the bipedal posture enhanced perceived cuteness, but this effect was most pronounced in small-bodied animals, particularly those with direct eye contact. Phylogenetically close and small-bodied species (e.g., small mammals) received greater conservation support than phylogenetically distant species (e.g., invertebrates). However, anthropomorphic-looking animals received greater conservation support, suggesting that pictures of animals that more closely resemble humans can be used in conservation campaigns.
Representing a Heterogeneous Pharmaceutical Knowledge-Graph with Textual Information

We deal with a heterogeneous pharmaceutical knowledge-graph containing textual information built from several databases. The knowledge graph is a heterogeneous graph that includes a wide variety of concepts and attributes, some of which are provided in the form of textual pieces of information which have not been targeted in the conventional graph completion tasks. To investigate the utility of textual information for knowledge graph completion, we generate embeddings from textual descriptions given to heterogeneous items, such as drugs and proteins, while learning knowledge graph embeddings. We evaluate the obtained graph embeddings on the link prediction task for knowledge graph completion, which can be used for drug discovery and repurposing. We also compare the results with existing methods and discuss the utility of the textual information.
The Predictability Limit of Ocean Mesoscale Eddy Tracks in the Kuroshio Extension Region

In this study, the nonlinear local Lyapunov exponent and nonlinear error growth dynamics are employed to estimate the predictability limit of oceanic mesoscale eddy (OME) tracks quantitatively using three datasets. The results show that the mean predictability limit of OME tracks is about 53 days for cyclonic eddy (CE) and 52 days for anticyclonic eddy (AE) in the Kuroshio Extension (KE). The predictability limit varies spatially. The predictability limit of OME tracks is higher for the eastern region (about 62.5 days) than that for the western part (about 46 days). The CEs (AEs) predictability limit is relatively high in the southern (northern) region. Additionally, the lifetime, amplitude, and radius of OME are closely related to the predictability limit. The long-lived, large-amplitude, and large-sized OMEs tend to be more predictable. The eastern region often generates long-lived and large-size OMEs, thereby obtaining a higher predictability limit of OME tracks. Furthermore, the relationship between the predictability limit and the smoothness of the OME tracks was investigated using a metric to describe the track’s complexation. Usually, OMEs with high predictability limit values often show extender and smoother trajectories. The effects of the surface ocean circulations and the surface winds are also investigated. The strong and energetic currents lead to a short limitation in the west region.
Optimization of chemical cleaning condition for microfiltration process using response surface methodology

AbstractMicrofiltration (MF) processes are used in a variety of separation and concentration applications. Since membrane fouling is inevitable, membranes must be regularly cleaned to remove both organic and inorganic material deposited on the surface and/or into the membrane bulk. Optimization of the cleaning conditions for MF membranes is especially important. If the dose of cleaning chemical or cleaning time is inadequate, the membrane permeability is not recovered. If a dose of the chemical or the time is excess, irreversible damages in membrane properties occur. However, it is difficult to find the optimum conditions for chemical cleaning of MF. In this study, response surface methodology (RSM), a facile tool for optimization, was employed to determine the optimum conditions for chemical cleaning of MF. The Box–Behnken center-united experimental design was used to quantify the effects of respective chemicals (citric acid and sodium hypochlorite) dose and treatment time on fouling control and organic .
Volume Increase of the Dentate Gyrus Induced by Electroconvulsive Therapy Shedding Light on the Clinical Relevance of Plasticity in the Hippocampus

To the Editor: A lthough electroconvulsive therapy (ECT) is more effective than other treatments used for severe major depression, it is associated with a high relapse rate in patients who do not receive continuation or maintenance pharmacotherapy or ECT. In addition, a subset of patients including those with longer duration of depressive episode, nonresponse to adequate medication trials, and comorbid borderline personality disorder may require an increased number of treatments during their index episode to obtain response. In addition, although ECT is safe and efficacious for geriatric depression, older age is associated with increased seizure threshold. Irrespective of when it is used in the treatment cycle, the generation of a generalized tonic-clonic seizure of sufficient duration is necessary for effective treatment. Previous research has demonstrated that up to 5% of patients have a short seizure or no seizure during their index course of ECT despite maximum stimulus intensity. Strategies to augment or maintain seizure duration are thus of ongoing importance. Ketamine has been used as an alternate anesthetic agent for ECT. It has been shown to prolong seizure duration and induce a more intense seizure. Ketamine does not appear to enhance ECT response, and concerns surrounding more extended posttreatment disorientation, restlessness, blood pressure elevations, and recovery times have precluded its widespread adoption. Sheppard Pratt Hospital, Towson, a 259-bed not-for-profit hospital is the flagship inpatient facility of Sheppard Pratt Health System. They have been a high-volume provider of inpatient and outpatient ECT services averaging 3517 treatments annually over the past 5 years. During this time, we have had 9 patients receive ketamine anesthesia after being unable to generate an adequate or even any seizure with the use of other agents. The patients had an average age of 56.1 years (37–78 years), 6 were male and 3 female. Four carried diagnosis of major depression recurrent, 4 had bipolar 1 or 2 diagnoses, and 1 had schizoaffective disorder. All patients received treatment on aThymatron System IV, pulse width of 1.0 milliseconds with titration to maximum stimulus charge of 504 mC. All patients received initial treatment with 1 mg/kg of methohexital with subsequent switch to etomidate for
A reduced model for particle calcination for use in DEM/CFD simulations

We treat the accurate simulation of the calcination reaction in particles, where the particles are large and, thus, the inner-particle processes must be resolved. Because these processes need to be described with coupled partial differential equations that must be solved numerically, the computation times for a single particle are too high for use in simulations that involve many particles. Simulations of this type arise when the Discrete Element Method (DEM) is combined with Computational Fluid Dynamics (CFD) to investigate industrial systems such as quick lime production in lime shaft kilns. We show that, based on proper orthogonal de-composition and Galerkin projection, reduced models can be derived for single particles that provide the same spatial and temporal resolution as the original PDE models at a considerably reduced computational cost. Replacing the finite-volume particle models with the reduced models results in an overall reduction of the reactor simulation time by about 60% for the simple example treated here.
Adsorption of Silver Nanoparticles on Modified Surfaces

Uniform films of silver nanoparticles (Ag NPs) were fabricated by self-assembly on 3-aminopropyltriethoxysilane (APTES) and [3-(2-aminoethyl) aminopropyl] trimethoxysilane (AEAPTES) modified glass slides. A stable Ag NPs suspension was synthesized via the reduction of silver nitrate using sodium citrate. Bulk characteristics of Ag NPs in aqueous solution were carried out by measuring their absorption spectrum, morphology and particle shape using the UV-vis absorption spectroscopy and transmission electron microscopy (TEM), respectively. The average diameter of Ag NPs is about 50 nm. The coverage of adsorbed particles on the modified glasses was measured by scanning electron microscopic imaging (SEM). The SEM images indicate that the Ag NPs films on the glasses are uniform. It is supposed that the adsorption processes are mainly controlled by electrostatic interactions. The adsorption amount of Ag NPs on APTES modified glass slides is much more than the amount on AEAPTES modified glass slides.
Introducing a Framework for Managing Technical Debt Developed by Practitioners

Technical Debt (TD) and the subsequent problems are equally discussed in industry and scientiﬁc papers. In this paper we introduce a framework developed by an IT-unit in industry that tried to tackle these problems. The solution consists of methods to manage and repay technical debt. The goal of the framework is to provide a better overview of the TD items for the mangers of the IT-unit. Additionally, the framework is able to diﬀerentiate between general technical issues and TD as initially described in [1]