Miracle-dz/UniFAR-FTUs huggingface dataset:
The 3D hype: Evaluating the potential of real 3D visualization in geo-related applications

The use of 3D visualization technologies has increased rapidly in many applied fields, including geovisualization, and has been researched from many different perspectives. However, the findings for the benefits of 3D visualization, especially in stereoscopic 3D forms, remain inconclusive and disputed. Stereoscopic “real” 3D visualization was proposed as encouraging the visual perception of shapes and volume of displayed content yet criticised as problematic and limited in a number of ways, particularly in visual discomfort and increased response time in tasks. In order to assess the potential of real 3D visualization for geo-applications, 91 participants were engaged in this study to work with digital terrain models in different 3D settings. The researchers examined the effectivity of stereoscopic real 3D visualization compared to monoscopic 3D (or pseudo 3D) visualization under static and interactive conditions and applied three tasks with experimental stimuli representing different geo-related phenomena, i.e. objects in the terrain, flat areas marked in the terrain and terrain elevation profiles. The authors explored the significant effects of real 3D visualization and interactivity factors in terms of response time and correctness. Researchers observed that the option to interact (t = -10.849, p < 0.001) with a virtual terrain and its depiction with real 3D visualization (t = 4.64, p < 0.001) extended the participants’ response times. Counterintuitively, the data demonstrated that the static condition increased response correctness (z = 5.38, p < 0.001). Regarding detailed analysis of data, an interactivity factor was proposed as a potential substitute for real 3D visualization in 3D geographical tasks.
Metabolic Inflammation and Insulin Resistance in Obesity

Supplemental Digital Content is available in the text. Obesity is becoming an epidemic in the United States and worldwide and increases risk for many diseases, particularly insulin resistance, type 2 diabetes mellitus, and cardiovascular disease. The mechanisms linking obesity with these diseases remain incompletely understood. Over the past 2 to 3 decades, it has been recognized that in obesity, inflammation, with increased accumulation and inflammatory polarization of immune cells, takes place in various tissues, including adipose tissue, skeletal muscle, liver, gut, pancreatic islet, and brain and may contribute to obesity-linked metabolic dysfunctions, leading to insulin resistance and type 2 diabetes mellitus. Therapies targeting inflammation have shed light on certain obesity-linked diseases, including type 2 diabetes mellitus and atherosclerotic cardiovascular disease, but remain to be tested further and confirmed in clinical trials. This review focuses on inflammation in adipose tissue and its potential role in insulin resistance associated with obesity.
Temporal variation in freshwater viral and bacterial community composition

Viruses has a relatively recently been discovered in high abundances in aquatic systems. Their possible importance has therefore been largely overlooked. In aquatic food webs there should be large differences in carbon and nutrient fluxes depending on whether the main cause of bacterial mortality is viral infection or grazing, where lysis following viral infection should result in a release of organic carbon and nutrients from the lysed bacteria and hence not reach higher trophic levels. Recent research on aquatic viruses has mainly focused on marine environments and the number of studies on freshwater viral ecology is limited. Hence, there is a need for more studies on the importance and functioning of viruses in freshwater systems.The aims of this thesis were to explore the functioning and diversity of viruses that infects bacteria (phages) in freshwater systems. To effectively address this I conducted two experiments and three field studies in 23 lakes in different parts of Sweden. The results show that viral infection and subsequent lysis of the host cell can partly explain the formation of non-nucleoid-containing bacteria and further that viruses can respond to increases in phosphorus concentrations without any net increase in bacterial abundance. Generally, a larger part of bacterial production in lakes were grazed by flagellates than lysed by viruses, but a larger fraction of the total bacterial mortality can be attributed to viruses in hypolimnion compared to in epilimnion. Further, the largest impact of phages on bacterial production may be in humic lakes, which have a relatively high frequency of visibly infected bacterial cells, but low flagellate abundance. Community composition of bacteria and viruses were only weakly coupled in the studied systems. The most important factors for predicting viral community composition were temperature and concentrations of dissolved organic carbon, total phosphorus and soluble reactive phosphorus. The viral community composition changed over the season and temperate phages could be detected by incubations with mitomycin C showing that a large fraction of the viruses detected appeared to be temperate phages. The most important environmental factor co-varying with viral community composition was again concentrations of total phosphorus.To summarize, bacteriophages, as a bacterial mortality factor, are important in freshwater microbial food webs and phosphorus supply has a potential central function in the regulation of the importance of bacteriophages and additionally for viral diversity.
Predictors of mortality in hospitalized COVID‐19 patients: A systematic review and meta‐analysis

Mortality rates of coronavirus disease‐2019 (COVID‐19) continue to rise across the world. Information regarding the predictors of mortality in patients with COVID‐19 remains scarce. Herein, we performed a systematic review of published articles, from 1 January to 24 April 2020, to evaluate the risk factors associated with mortality in COVID‐19. Two investigators independently searched the articles and collected the data, in accordance with PRISMA guidelines. We looked for associations between mortality and patient characteristics, comorbidities, and laboratory abnormalities. A total of 14 studies documenting the outcomes of 4659 patients were included. The presence of comorbidities such as hypertension (odds ratio [OR], 2.5; 95% confidence interval [CI], 2.1‐3.1; P < .00001), coronary heart disease (OR, 3.8; 95% CI, 2.1‐6.9; P < .00001), and diabetes (OR, 2.0; 95% CI, 1.7‐2.3; P < .00001) were associated with significantly higher risk of death amongst patients with COVID‐19. Those who died, compared with those who survived, differed on multiple biomarkers on admission including elevated levels of cardiac troponin (+44.2 ng/L, 95% CI, 19.0‐69.4; P = .0006); C‐reactive protein (+66.3 µg/mL, 95% CI, 46.7‐85.9; P < .00001); interleukin‐6 (+4.6 ng/mL, 95% CI, 3.6‐5.6; P < .00001); D‐dimer (+4.6 µg/mL, 95% CI, 2.8‐6.4; P < .00001); creatinine (+15.3 µmol/L, 95% CI, 6.2‐24.3; P = .001); and alanine transaminase (+5.7 U/L, 95% CI, 2.6‐8.8; P = .0003); as well as decreased levels of albumin (−3.7 g/L, 95% CI, −5.3 to −2.1; P < .00001). Individuals with underlying cardiometabolic disease and that present with evidence for acute inflammation and end‐organ damage are at higher risk of mortality due to COVID‐19 infection and should be managed with greater intensity.
Frequency Spectral Evaluation about Hemoglobin Kinetics of Pedal Circulation Attend to Laminar Layer with Near Infrared Spectroscopy in Sound Horse

This study observed the fluctuation of total hemoglobin (tHb) and reduced hemoglobin (dHb) concentrations as a direct reflection of hemodynamics under the hoof wall with near infrared spectroscopy (NIRS). NIRS observation of the laminar layer under the pigmented hoof walls was performed without sedation or invasion on five clinically normal horses. NIRS indexes relating to the concentration change of tHb (tHbindex) and dHb (dHbindex) in tissue were recorded at 2 Hz and evaluated over 0.004 Hz in spectral power. Each NIRS index fluctuated spontaneously and continuously from 0.01 Hz to 0.05 Hz. Over 10 times difference of total power was shown in fluctuations of each NIRS index. Nevertheless, a significant positive correlation was observed betveen NIRS indexes. In the geometrical distribution of the power spectra from 0.0078 Hz to 0.5 Hz, the sub-hand power of the dHbindex dominated the tHbindex in sub-bands with central frequencies of 0.011 Hz and 0.022 Hz. This was interpreted as characteristic of the hemoglobin oxidation-reduction (redox) fluctuation common to forelegs of both sides. NIRS observation based on the second time scale and adapted by spectral analysis was able to evaluate qualitatively the characteristics of spontaneous kinetics of hemoglobin redox regardless of a lack of quantity, suggesting the ability to provide virginal vital signs under hooves.
Psychometrics of the Gratitude Questionnaire-6 in African-Americans at Risk for Cardiovascular Disease

Psychometrics of the Gratitude Questionnaire-6, which measures dispositional gratitude, was originally estimated in healthy college students. The purpose of this study was to examine the scales’ factor structure, convergent/divergent validity, and reliability among 298 AA adults at risk for CVD in the community. Analyses were performed using bivariate correlations, exploratory factor analysis, and confirmatory factor analysis. The scale demonstrated acceptable estimates for internal consistency (Cronbach’s α = 0.729). Our exploratory factor analysis results yielded a one-factor structure consistent with the original instrument, and the confirmatory factor analysis model was a good fit. Convergent/divergent validity was supported by the association with positive affect (coefficient = 0.482, 95% CI = [0.379, 0.573], spiritual well-being (coefficient = 0.608, 95% CI = [0.519, 0.685], and depressive symptoms (coefficient = −0.378, 95% CI = [−0.475, −0.277]. Findings supported the scale’s reliability and convergent/divergent validity among AAs at risk for CVD.
The attenuation of elastic tissue in the aorta of the baboon, Papio doguera

A histological study was made of the quantitative distribution of elastic elements in the aorta of the baboon, Papio doguera. Materials were obtained in East Africa from freshly sacrificed animals as well as from domestic stock, and represented all age groups from a fetus near term to 28 years. Verhoeff's elastic tissue stained sections were prepared from 4 zones from the arch to the bifurcation.
The reliability of whitefish (Coregonus lavaretus (L.)) age determination - differences between methods and between readers

— Age determinations of whitefish (Coregonus lavaretus (L.)) were compared in two different tests. In the first test, the readers determined the age of each individual from one calcified structure (scale, otolith, or opercular bone) at a time. The samples from three populations, 50 specimens in each, were mixed so that the readers did not know which population each calcified structure was from. A sample of known-age whitefish was used in the second age determination test, where information such as time of catch, length, weight, and sex was available to the readers. In each of the 50 envelopes the reader got scale impressions and two otoliths, one of which had been burned and ground. In the first test, the precision of the readers was low both between readers and between different structures. In the samples of slow-growing populations, the determinations made from the otoliths showed older ages than the determinations from the scales. In the second age determination test the results were better; 73-90% (average 82%) of the determinations were correct. The use of two calcified structures and the knowledge of the material were considered to improve the accuracy. Age determination bias may occur that affects the age distribution: even though 80% of the fish were aged correctly, an exceptionally strong or weak year class could remain unidentified. The estimation of growth rate seemed less sensitive to incorrect age determination than age distribution.
Distinctive binding properties of human monoclonal LGI1 autoantibodies determine pathogenic mechanisms

See Zekeridou and Pittock (doi:10.1093/brain/awaa153) for a scientific commentary on this article. Ramberger et al. generate patient-derived monoclonal antibodies against LGI1 and describe their epitopes and sequences, plus their pathogenic potential in vitro and in vivo. They find that binding characteristics of these antibodies inform the molecular mechanisms and relative pathogenicity within polyclonal specificities.
Transfer Learning: Making Retrosynthetic Predictions Based on a Small Chemical Reaction Dataset Scale to a New Level

Effective computational prediction of complex or novel molecule syntheses can greatly help organic and medicinal chemistry. Retrosynthetic analysis is a method employed by chemists to predict synthetic routes to target compounds. The target compounds are incrementally converted into simpler compounds until the starting compounds are commercially available. However, predictions based on small chemical datasets often result in low accuracy due to an insufficient number of samples. To address this limitation, we introduced transfer learning to retrosynthetic analysis. Transfer learning is a machine learning approach that trains a model on one task and then applies the model to a related but different task; this approach can be used to solve the limitation of few data. The unclassified USPTO-380K large dataset was first applied to models for pretraining so that they gain a basic theoretical knowledge of chemistry, such as the chirality of compounds, reaction types and the SMILES form of chemical structure of compounds. The USPTO-380K and the USPTO-50K (which was also used by Liu et al.) were originally derived from Lowe’s patent mining work. Liu et al. further processed these data and divided the reaction examples into 10 categories, but we did not. Subsequently, the acquired skills were transferred to be used on the classified USPTO-50K small dataset for continuous training and retrosynthetic reaction tests, and the pretrained accuracy data were simultaneously compared with the accuracy of results from models without pretraining. The transfer learning concept was combined with the sequence-to-sequence (seq2seq) or Transformer model for prediction and verification. The seq2seq and Transformer models, both of which are based on an encoder-decoder architecture, were originally constructed for language translation missions. The two algorithms translate SMILES form of structures of reactants to SMILES form of products, also taking into account other relevant chemical information (chirality, reaction types and conditions). The results demonstrated that the accuracy of the retrosynthetic analysis by the seq2seq and Transformer models after pretraining was significantly improved. The top-1 accuracy (which is the accuracy rate of the first prediction matching the actual result) of the Transformer-transfer-learning model increased from 52.4% to 60.7% with greatly improved prediction power. The model’s top-20 prediction accuracy (which is the accuracy rate of the top 20 categories containing actual results) was 88.9%, which represents fairly good prediction in retrosynthetic analysis. In summary, this study proves that transferring learning between models working with different chemical datasets is feasible. The introduction of transfer learning to a model significantly improved prediction accuracy and, especially, assisted in small dataset based reaction prediction and retrosynthetic analysis.
Biomechanical Cues Direct Valvulogenesis

The vertebrate embryonic heart initially forms with two chambers, a ventricle and an atrium, separated by the atrioventricular junction. Localized genetic and biomechanical information guides the development of valves, which function to ensure unidirectional blood flow. If the valve development process goes awry, pathology associated with congenital valve defects can ensue. Congenital valve defects (CVD) are estimated to affect 1–2% of the population and can often require a lifetime of treatment. Despite significant clinical interest, molecular genetic mechanisms that direct valve development remain incompletely elucidated. Cells in the developing valve must contend with a dynamic hemodynamic environment. A growing body of research supports the idea that cells in the valve are highly sensitive to biomechanical forces, which cue changes in gene expression required for normal development or for maintenance of the adult valve. This review will focus on mechanotransductive pathways involved in valve development across model species. We highlight current knowledge regarding how cells sense physical forces associated with blood flow and pressure in the forming heart, and summarize how these changes are transduced into genetic and developmental responses. Lastly, we provide perspectives on how altered biomechanical cues may lead to CVD pathogenesis.
Severe Acute Lung Injury Related to COVID‐19 Infection: A Review and the Possible Role for Escin

Acute lung injury (ALI) represents the most severe form of the viral infection sustained by coronavirus disease 2019 (COVID‐19). Today, it is a pandemic infection, and even if several compounds are used as curative or supportive treatment, there is not a definitive treatment. In particular, antiviral treatment used for the treatment of several viral infections (eg, hepatitis C, HIV, Ebola, severe acute respiratory syndrome–coronavirus) are today used with a mild or moderate effect on the lung injury. In fact, ALI seems to be related to the inflammatory burst and release of proinflammatory mediators that induce intra‐alveolar fibrin accumulation that reduces the gas exchange. Therefore, an add‐on therapy with drugs able to reduce inflammation, edema, and cell activation has been proposed as well as a treatment with interferon, corticosteroids or monoclonal antibodies (eg, tocilizumab). In this article reviewing literature data related to the use of escin, an agent having potent anti‐inflammatory and anti‐viral effects in lung injury, we suggest that it could represent a therapeutic opportunity as add‐on therapy in ALI related to COVID‐19 infection.
Can small rare prey be chemically defended? the case for marine larvae

Marine larvae are consumed by a wide variety of generalist fishes and particle-feeding invertebrates, but larvae of any particular species probably constitute a small and variable portion of the diet for these consumers. Because virtually all consumers can ingest small quantities of noxious compounds with minimal detrimental effects, it is uncertain that toxic chemicals in larvae could be consumed in quantities sufficient to select for predator recognition and avoidance. Despite this, chemically defended larvae do occur. We show that, at low doses, secondary metabolites (the didemnins) from adults and larvae of the Caribbean tunicate Trididenmum solidum induced vomiting in fish, resulting in rapid learned aversion to the dedemnin-defended food. The particle-feeding anemone Aiptasia pallida did not learn to avoid the chemically defended food. When anemones ingested the chemical equivalent of 15 larvae/d, representing <2% of the mass of their total daily diet, the didemnins in the {open_quotes}larvae{close_quotes} significantly reduced: (1) growth of adults by 82%, (2) combined growth of adults and daughter clones by 76%, (3) production of daughter clones by 44%, and (4) average mass of individual daughter clones by 41%. At higher water temperatures, anemones cloned more rapidly. Significant differences in the number of daughter clones produced betweenmore » treatment and control anemones occurred after only 4 d at seawater temperatures of 27{degrees}-29{degrees}C vs. 32 d at seawater temperatures of 18{degrees}-21{degrees}C. Consumption of even very small quantities of secondary metabolites can decrease consumer fitness substantially and select for predators that recognize and avoid chemically defended larvae, as do many consumers that co-occur with Trididemnum solidum larvae. This is the first rigorous demonstration that consumption of marine secondary metabolites can decrease consumer fitness when ingested at ecologically realistic doses. 59 refs., 5 figs., 3 tabs. « less
Climate change cannot be entirely responsible for soil carbon loss observed in England and Wales, 1978–2003

We present results from modelling studies, which suggest that, at most, only about 10–20% of recently observed soil carbon losses in England and Wales could possibly be attributable to climate warming. Further, we present reasons why the actual losses of SOC from organic soils in England and Wales might be lower than those reported.
Cannabinoid type 2 receptors inhibit GABAA receptor-mediated currents in cerebellar Purkinje cells of juvenile mice

Signaling through the endocannabinoid system is critical to proper functioning of the cerebellar circuit. However, most studies have focused on signaling through cannabinoid type 1 (CB1) receptors, while relatively little is known about signaling through type 2 (CB2) receptors. We show that functional CB2 receptors are expressed in Purkinje cells using a combination of immunohistochemistry and patch-clamp electrophysiology in juvenile mice. Pharmacological activation of CB2 receptors significantly reduces inhibitory synaptic responses and currents mediated by photolytic uncaging of RuBi-GABA in Purkinje cells. CB2 receptor activation does not change the paired-pulse ratio of inhibitory responses and its effects are blocked by inclusion of GDP-β-S in the internal solution, indicating a postsynaptic mechanism of action. However, CB2 receptors do not contribute to depolarization induced suppression of inhibition (DSI), indicating they are not activated by endocannabinoids synthesized and released from Purkinje cells using this protocol. This work demonstrates that CB2 receptors inhibit postsynaptic GABAA receptors by a postsynaptic mechanism in Purkinje cells. This represents a novel mechanism by which CB2 receptors may modulate neuronal and circuit function in the central nervous system.