Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantification of brain PET studies

PET pharmacokinetic analysis involves fitting of measured PET data to a PET pharmacokinetic model. The fitted parameters may, however, suffer from bias or be unrealistic, especially in case of noisy data. There are many optimisation algorithms, each having different characteristics. The purpose of the present study was to evaluate (1) the performance of different optimisation algorithms and (2) the effects of using incorrect weighting factors during optimisation in terms of both accuracy and reproducibility of fitted PET pharmacokinetic parameters. In this study, the performance of commonly used optimisation algorithms (i.e. interior-reflective Newton methods) and a simulated annealing (SA) method were evaluated. This SA algorithm, known as basinhopping, was modified for the present application. In addition, optimisation was performed using various weighting factors. Algorithms and effects of using incorrect weighting factors were studied using both simulated and clinical time activity curves (TACs). Input data, taken from [15O]H2O, [11C]Flumazenil and (R)-[11C]PK11195 studies, were used to simulate time activity curves at various variance levels (0 15% COV ). Clinical evaluation was based on studies with the same three tracers. SA was able to produce accurate results without the need for selecting appropriate starting values for (kinetic) parameters, in contrast to the interior-reflective Newton method. The latter gave biased results unless it was modified to allow for a range of starting values for the different parameters. For patient studies, where large variability is expected, both SA and the extended Newton method provided accurate results. Simulations and clinical assessment showed similar results for the evaluation of different weighting models in that small to intermediate mismatches between data variance and weighting factors did not significantly affect the outcome of the fits. Large errors were only observed when the mismatch between weighting model and data variance was large. It is concluded that selection of specific optimisation algorithms and weighting factors can have a large effect on the accuracy and precision of PET pharmacokinetic analysis. Apart from carefully selecting appropriate algorithms and variance models, further improvement in accuracy might be obtained by using noise reducing strategies, such as wavelet filtering, provided that these methods do not introduce significant bias.
Ocean acidification changes the vertical movement of stone crab larvae

Anthropogenic activities are increasing ocean temperature and decreasing ocean pH. Some coastal habitats are experiencing increases in organic runoff, which when coupled with a loss of vegetated coastline can accelerate reductions in seawater pH. Marine larvae that hatch in coastal habitats may not have the ability to respond to elevated temperature and changes in seawater pH. This study examined the response of Florida stone crab (Menippe mercenaria) larvae to elevated temperature (30°C control and 32°C treatment) and CO2-induced reductions in pH (8.05 pH control and 7.80 pH treatment). We determined whether those singular and simultaneous stressors affect larval vertical movement at two developmental stages. Geotactic responses varied between larval stages. The direction and rate of the vertical displacement of larvae were dependent on pH rather than temperature. Stage III larvae swam upwards under ambient pH conditions, but swam downwards at a faster rate under reduced pH. There was no observable change in the directional movement of Stage V larvae. The reversal in orientation by Stage III larvae may limit larval transport in habitats that experience reduced pH and could pose challenges for the northward dispersal of stone crabs as coastal temperatures warm.
The use of extruded finite-element models as a novel alternative to tomography-based models: a case study using early mammal jaws

Finite-element (FE) analysis has been used in palaeobiology to assess the mechanical performance of the jaw. It uses two types of models: tomography-based three-dimensional (3D) models (very accurate, not always accessible) and two-dimensional (2D) models (quick and easy to build, good for broad-scale studies, cannot obtain absolute stress and strain values). Here, we introduce extruded FE models, which provide fairly accurate mechanical performance results, while remaining low-cost, quick and easy to build. These are simplified 3D models built from lateral outlines of a relatively flat jaw and extruded to its average width. There are two types: extruded (flat mediolaterally) and enhanced extruded (accounts for width differences in the ascending ramus). Here, we compare mechanical performance values resulting from four types of FE models (i.e. tomography-based 3D, extruded, enhanced extruded and 2D) in Morganucodon and Kuehneotherium. In terms of absolute values, both types of extruded model perform well in comparison to the tomography-based 3D models, but enhanced extruded models perform better. In terms of overall patterns, all models produce similar results. Extruded FE models constitute a viable alternative to the use of tomography-based 3D models, particularly in relatively flat bones.
Estimation of Grassland Production in Central and Eastern Mongolia from 2006 to 2015 via Remote Sensing

Abstract: Mongolia is an important part of the Belt and Road Initiative “China-Mongolia-Russia Economic Corridor” and a region that has been severely affected by global climate change. Changes in grassland production have had a profound impact on the sustainable development of the region. Our study explored an optimal model for estimating grassland production in Mongolia and discovered its temporal and spatial distributions. Three estimation models were established using a statistical analysis method based on EVI, MSAVI, NDVI, and PsnNet from Moderate Resolution Imaging Spectroradiometer (MODIS) remote sensing data and measured data. A model evaluation and accuracy comparison showed that an exponential model based on MSAVI was the best simulation (model accuracy 78%). This was selected to estimate the grassland production in central and eastern Mongolia from 2006 to 2015. The results show that the grassland production in the study area had a significantly fluctuating trend for the decade study; a slight overall increasing trend was observed. For the first five years, the grassland production decreased slowly, whereas in the latter five years, significant fluctuations were observed. The grassland production (per unit yield) gradually increased from the southwest to northeast. In most provinces of the study area, the production was above 1000 kg ha-1, with the largest production in Hentiy, at 3944.35 kg ha-1. The grassland production (total yield) varied greatly among the provinces, with Kent showing the highest production, 2341.76×104 t. Results also indicate that the trend in grassland production along the China-Mongolia railway was generally consistent with that of the six provinces studied.
Metagenomic Resolution of Functional Diversity in Copper Surface-Associated Marine Biofilms

We used metagenomic sequencing combined with morphological and chemical analyses to investigate microbial taxa and functions related to copper-resistance and microbiologically influenced corrosion in mature copper-associated biofilms in coastal seawater for 44 months. Facultative anaerobic microbes such as Woeseia sp. were found to be the dominant groups on the copper surface. Genes related to stress response and possible heavy metal transport systems, especially RNA polymerase sigma factors (rpoE) and putative ATP-binding cassette (ABC) transport system permease protein (ABC.CD.P) were observed to be highly enriched in copper-associated biofilms, while genes encoding DNA-methyltransferase and RNA polymerase subunit were highly enriched in aluminum-associated biofilms and seawater planktonic cells, respectively. Moreover, copper-associated biofilms harbored abundant copper-resistance genes including cus, cop and pco, as well as abundant genes related to extracellular polymeric substances, indicating the presence of diverse copper-resistance patterns. The proportion of dsr in copper-associated biofilms, key genes related to sulfide production, was as low as that in aluminum biofilm and seawater, which ruled out the possibility of microbial sulfide-induced copper-corrosion under field conditions. These results may fill knowledge gaps about the in situ microbial functions of marine biofilms and their effects on toxic-metal corrosion.
Natural Killer Cell-Derived Exosomal miR-3607-3p Inhibits Pancreatic Cancer Progression by Targeting IL-26

Increasing evidences have suggested that natural killer (NK) cells in the tumor microenvironment are involved in the regulation of cancer development. However, the potential biological roles and regulatory mechanisms of NK cells in pancreatic cancer (PC) remain unclear. Co-culture system of NK cells with PC cells is used to test the ability of cancer cell proliferation, migration and invasion both in vitro and in vivo. And tail vein intravenous transfer was used to test metastasis in vivo. Meanwhile, extracellular vesicles (EVs) were separated and examined. Furthermore, reporter assay and Biotin-RNA pull down assay were performed to verify the interaction between molecules. NK cells can inhibit the malignant transformation of co-cultured PC cells both in vivo and in vitro, which requires miR-3607-3p. miR-3607-3p is found enriched in the EVs of NK cells and transmitted to PC cells, and low level of miR-3607-3p predicts poor prognosis in PC patients. It can also inhibit proliferation, migration and invasion of PC cells in vitro. Importantly, IL-26 is found to be a direct target of miR-3607-3p in PC cells. miR-3607-3p enriched in EVs derived from NK cells can inhibit the malignant transformation of PC probably through directly targeting of IL-26.
Selenium-Enriched Pollen Grains of Olea europaea L.: Ca2+ Signaling and Germination Under Oxidative Stress

Selenium (Se) shows antioxidant properties that can be exploited in plants to combat abiotic stresses caused by reactive oxygen species produced in excess (ROS). Here, we show that the Se-fertilization of olive trees with sodium selenate effectively protects the pollen from oxidative stress. Pollen isolated from plants treated with Se or from untreated controls was incubated in vitro with H2O2 to produce an oxidative challenge. Given the impact of ROS on Ca2+ homeostasis and Ca2+-dependent signaling, cytosolic Ca2+ was measured to monitor cellular perturbations. We found that H2O2 interrupted Ca2+ homeostasis only in untreated pollen, while in samples treated in vitro with sodium selenate or selenium methionine, Ca2+ homeostasis was preserved. Furthermore, germination rates were considerably better maintained in Se-fertilized pollen compared to non-fertilized pollen (30% vs. 15%, respectively) after exposure to 1 mM H2O2. The same was observed with pollen treated in vitro with Se-methionine, which is the organic form of Se, in which part of the fertigated sodium selenate is converted in the plant. Combined, our results show a close correlation between ROS, Ca2+ homeostasis, and pollen fertility and provide clear evidence that Se-fertilization is a potential approach to preserve or improve agricultural productivity.
Brain 5-HT Deficiency Prevents Antidepressant-Like Effects of High-Fat-Diet and Blocks High-Fat-Diet-Induced GSK3β Phosphorylation in the Hippocampus

Obesity is associated with an increased risk of depression and anxiety disorders, but the nature of the relationship(s) between obesity and mental illness remains highly controversial. Some argue that depression and anxiety lead to increased consumption of “comfort foods,” the intake of which reduces negative affect and promotes obesity. In contrast, others have theorized that negative affect results from chronic excessive consumption of highly palatable foods. The brain serotonin (5-HT) system has long been implicated in both the development and treatment of mental illness. Preclinical studies have shown that low brain 5-HT exacerbates depression- and anxiety-like behaviors induced by stress and blocks reductions in depression-like behavior induced by antidepressants, but the effects of brain 5-HT deficiency on responses to high-fat diet (HFD) have not been explored. The current work used genetically modified mice to evaluate the effects of low 5-HT on behavioral and molecular alterations induced by chronic exposure to HFD. Our results reveal that HFD decreases depression-like behavior and increases some anxiety-like behaviors in wild-type (WT) mice. However, genetic brain 5-HT deficiency blocks HFD-induced reductions in forced swim immobility and prevents HFD-induced increases in hippocampal GSK3β phosphorylation despite having no significant effects on HFD-induced changes in body weight or anxiety-like behavior. Together, our results suggest that brain 5-HT deficiency significantly impacts a subset of behavioral and molecular responses to HFD, a finding that could help explain the complex relationships between obesity and mental illness.
Behavioral States Related to Environmental Conditions and Fisheries During Olive Ridley Turtle Migration From Pacific Panama

Sea turtles migrate from breeding grounds to foraging areas through the territorial waters of several countries. Olive ridleys lack clear migratory routes, which makes it a challenge for conservation. This study aimed to evaluate if the migratory behavior of olive ridleys nesting on the Pacific Coast of Panama is correlated to environmental conditions along the migration and to identify common foraging areas. Thirty-four olive ridley turtles were tagged with satellite transmitters along the Pacific coast of Panama and tracked for up to nine months. A Hidden Markov Model was used to identify behavioral states (foraging and migrating) and their correlation to chlorophyll a concentration, sea surface temperature, eddy kinetic energy, and primary productivity. Turtle tracks overlapped with eddies and industrial fishing areas. The probability of foraging rather than migrating was positively correlated to sea surface temperature, productivity and chlorophyll levels and negatively correlated to eddy kinetic energy. Turtles spent an average 30% of their time migrating and 70% foraging. Only 8.4% of the turtle locations occurred within an eddy, and 82.7% of the locations overlapped with previously described industrial fishing areas. Although this sea turtle species seems to migrate freely, without clear migratory corridors, turtles may have preferred foraging destinations that they travel to through different migratory routes, such as the gulfs of Tehuantepec, Fonseca, and Guayaquil. Turtles traveled up to 6,684 km through nine countries, most of them foraging in oceanic waters in Salvador, Costa Rica, and Panama, which highlights the importance of collaborative conservation strategies throughout foraging and nesting areas. The creation of a regional management unit, including Costa Rica, Panama and Colombia, is discussed based on the observed seasonal overlap with the use of multiple fishing gears in coastal and oceanic fishing areas.
Globular Glial Tauopathy Type I Presenting as Atypical Progressive Aphasia, With Comorbid Limbic-Predominant Age-Related TDP-43 Encephalopathy

Globular glial tauopathies (GGTs) have heterogeneous presentations with little available information regarding typical clinical manifestations. We report on a case of atypical primary progressive aphasia (PPA) due to comorbid GGT and limbic transactive response DNA binding protein of 43 kDa (TDP-43) proteinopathy. The initial clinical phenotype was compatible with the nonfluent-agrammatical variant of PPA and early hippocampal amnesia. Progressively, parkinsonism and supranuclear oculomotor impairment occurred, and finally, late mutism with frontal-type dementia, impaired comprehension, and behavioral manifestations developed. The neuropathology was characteristic of GGT type I with vascular changes and comorbid limbic-predominant age-related TDP-43 encephalopathy (LATE). Our findings expand the clinical spectrum of GGTs to include a complex progressive aphasia syndrome. The extraordinary feature, in this case, was the combination of two progressive aphasia subtypes, that is, the early nonfluent-agrammatical variant and the late semantic variant. Our findings also expand the spectrum of neuropathological comorbidities in GGT.
Cerebrospinal fluid flow in children with normal and dilated ventricles studied by MR imaging

Purpose: To quantify the cerebrospinal fluid (CSF) dynamics in the aqueduct of children with normal and dilated ventricles using MR phase-contrast technique. Material and Methods: Eighteen patients (6 months to 17 years of age) with various neurological symptoms underwent routine brain MR imaging and CSF flow measurement in the aqueduct. Nine patients had normal ventricles, 5 had dilated ventricles and 4 had a ventriculoperitoneal shunt. Results: The CSF velocity and flow rates in the aqueduct in patients with normal and dilated ventricles showed marked inter-individual variation and clear overlap. In a patient with tight aqueductal stenosis and increased ventricular pressure, pronounced CSF flow in the aqueduct was measured. Absence of flow in another patient with aqueductal stenosis was detected. Measurable although low flow in the aqueduct in 4 patients with a ventriculoperitoneal shunt was found. Conclusion: Quantitative phase MR flow measurement in the aqueduct demonstrated aqueductal stenosis; these patients had either pronounced flow or no flow in the aqueduct.
Bridging the Vendor-User Gap in Enterprise Cloud Software Development through Data-Driven Requirements Engineering

The shift from on-premise to cloud software has fundamentally changed the interactions between enterprise software vendors and their users. Where user involvement has traditionally been a challenge, increasingly large amounts of user input now allow for data-driven requirements engineering (RE). Research has paid little attention so far to the changes entailed by data-driven RE and addressed neither technical nor empirical perspectives of data-driven RE in enterprise software development. We aim to understand how the increasing availability of large amounts of user input impact RE in enterprise cloud software development. We provide a conceptualization of the newly available user input and how it changes traditional RE. We collect and analyze rich data from multiple product units at a leading enterprise software company and examine the integration of user input into RE; specifically requirements discovery, prioritization, experimentation, and specification. We thereby aim to contribute to non-normative and empirical work on RE.
Predicting Violent Crime with Gang Social Media Postings

Many large cities in the U.S. have a problem with violent crime, some of which is committed by gang affiliates. Those individuals use social media platforms like Twitter to express messages of loss and aggression, which can grow in volume and disseminate quickly, often serving as credible signals to commit an imminent violent crime. These tweets may be useful to law enforcement and community service workers who seek to mitigate violent crime by halting the criminal activity. Thus, this research focuses on exploring the feasibility of automatically ﬁnding criminal signaling of gang members on Twitter and examining the relationship between this signaling and daily crime increase per city. Content and dissemination features from this analysis and other auxiliary predictors are used to train supervised classiﬁers, with the goal of finding criminal signals in the virtual space before actual crimes are committed in the physical space
Walk this Way! Incentive Structures of Different Token Designs for Blockchain-Based Applications

Cryptoeconomics is an emerging research area in the field of blockchain technology aiming at understanding token design mechanisms intended to incentivize certain behaviors. Whereas several blockchain ecosystems have been emerging in recent years, little is known about incentive design in blockchain protocols other than Bitcoin. To address this gap, we use agent-based modeling (ABM) to simulate the effects of different token designs on usage in the context of prediction markets. We find that network tokens (i.e., tokens providing services within a system) provide the largest incentive for individuals to join and become long-term active users. Moreover, we find that investment tokens (i.e., tokens used to passively invest in the issuing entity) provide the smallest incentive compared to network tokens and cryptocurrencies (i.e., means of payment in a blockchain ecosystem). We advance the literature by testing the boundary conditions of different token designs for blockchain-based ecosystems using a novel ABM approach.
Effectiveness of water-saving technologies during early stages of restoration of endemic Opuntia cacti in the Galápagos Islands, Ecuador

Restoration of keystone species is a primary strategy used to combat biodiversity loss and recover ecological services. This is particularly true for oceanic islands, which despite their small land mass, host a large fraction of the planet’s imperiled species. The endemic Opuntia spp. cacti are one example and a major focus for restoration in the Galápagos archipelago, Ecuador. These cacti are keystone species that support much of the unique vertebrate animal community in arid zones, yet human activities have substantially reduced Opuntia populations. Extreme aridity poses an obstacle for quickly restoring Opuntia populations though water-saving technologies may provide a solution. The aim of this study was to evaluate current restoration efforts and the utility of two water-saving technologies as tools for the early stages of restoring Opuntia populations in the Galápagos archipelago. We planted 1,425 seedlings between 2013 and 2018, of which 66% had survived by the end of 2018. Compared with no-technology controls, seedlings planted with Groasis Waterboxx® water-saving technology (polypropylene trays with water reservoir and protective refuge for germinants) had a greater rate of survival in their first two-years of growth on one island (Plaza Sur) and greater growth rate on four islands whereas the “Cocoon” water-saving technology (similar technology but made of biodegradable fiber) did not affect growth and actually reduced seedling survival. Survival and growth rate were also influenced by vegetation zone, elevation, and precipitation in ways largely contingent on island. Overall, our findings suggest that water-saving technologies are not always universally applicable but can substantially increase the survival and growth rate of seedlings in certain conditions, providing in some circumstances a useful tool for improving restoration outcomes for rare plants of arid ecosystems.