Miracle-dz/UniFAR-FTUs huggingface dataset:
Three-Photon Luminescence of Gold Nanorods Excited by 1040 nm Femtosecond Laser for High Contrast Tissue and In Vivo Imaging

Gold Nanorods (GNRs) with tunable aspect ratios can strongly absorb and scatter light in the NIR region due to their localized surface plasmon resonance (LSPR) property, and have been demonstrated to exhibit strong plasmon enhanced multiphoton luminescence (MPL) with brightness many times stronger than the conventional organic chromophores. In this study, we synthesized GNRs with longitudinal LSPR peak at 1036 nm to match our home-built light source 1040 nm femtosecond laser, which locates in the “optical window” where the tissue absorbs relatively little light. PEGylated GNRs with great biocompatibility were intravenously injected through the tail vein into mice. Excited by 1040 nm laser, the GNRs exhibit bright three-photon luminescence (3PL) signals while circulating in the blood vessels. The use of GNRs as bright contrast agents for 3PL imaging of mouse ear blood vessels in vivo was demonstrated. And GNRs targeted in tissues can be excited by 1040 nm laser and could be clearly visualized with no autofluorescence background. These results indicated that 3PL of GNRs is very promising for deep in vivo bioimaging and assessing the distribution of GNRs in tissues with high contrast.
Taggle: Scalable Visualization of Tabular Data through Aggregation

Visualization of tabular data---for both presentation and exploration purposes---is a well-researched area. Although effective visual presentations of complex tables are supported by various plotting libraries, creating such tables is a tedious process and requires scripting skills. In contrast, interactive table visualizations that are designed for exploration purposes either operate at the level of individual rows, where large parts of the table are accessible only via scrolling, or provide a high-level overview that often lacks context-preserving drill-down capabilities. In this work we present Taggle, a novel visualization technique for exploring and presenting large and complex tables that are composed of individual columns of categorical or numerical data and homogeneous matrices. The key contribution of Taggle is the hierarchical aggregation of data subsets, for which the user can also choose suitable visual representations.The aggregation strategy is complemented by the ability to sort hierarchically such that groups of items can be flexibly defined by combining categorical stratifications and by rich data selection and filtering capabilities. We demonstrate the usefulness of Taggle for interactive analysis and presentation of complex genomics data for the purpose of drug discovery.
Eye Tracking in Infancy Research

The current review offers a unique introduction to the use of corneal reflection eye tracking in infancy research. We provide a detailed description of how to calibrate, collect, and analyze infants' gaze in a series of experimental paradigms, focusing specifically on the analysis of visual tracking, point of gaze, and the latency of gaze shifts (prediction and reactive gaze shifts). The article ends with a critical discussion about the pros and cons of corneal reflection eye tracking.
A 2.4 GHz Power Amplifier With 40% Global Efficiency at ${-}$ 5 dBm Output for Autonomous Wireless Sensor Nodes

Energy scavenged Wireless Sensor Nodes (WSNs) usually require a small output power ( 0 dBm) due to their short-range application and limited power budget. This makes the RF Power Amplifier (PA) design differ from conventional PAs as the output power becomes comparable to the PA driver's power consumption. In this letter, a 2.4 GHz tuned switching PA and driver is proposed with an on-chip duty cycle calibration loop to enhance efficiency. A prototype is fabricated in 40 nm CMOS technology and supports On-Off keying (OOK). Measurements show a global efficiency of 40% when delivering -5 dBm to a 50 Ω load.
Who watches the watchers: Validating the ProB Validation Tool

Over the years, ProB has moved from a tool that complemented proving, to a development environment that is now sometimes used instead of proving for applications, such as exhaustive model checking or data validation. This has led to much more stringent requirements on the integrity of ProB. In this paper we present a summary of our validation efforts for ProB, in particular within the context of the norm EN 50128 and safety critical applications in the railway domain.
Bacterial copper storage proteins

Copper is essential for most organisms as a cofactor for key enzymes involved in fundamental processes such as respiration and photosynthesis. However, copper also has toxic effects in cells, which is why eukaryotes and prokaryotes have evolved mechanisms for safe copper handling. A new family of bacterial proteins uses a Cys-rich four-helix bundle to safely store large quantities of Cu(I). The work leading to the discovery of these proteins, their properties and physiological functions, and how their presence potentially impacts the current views of bacterial copper handling and use are discussed in this review.
β-Ga 2 O 3 solar-blind deep-ultraviolet photodetector based on annealed sapphire substrate

β-Ga 2 O 3 solar-blind deep-ultraviolet photodetectors were fabricated based on as-supplied and annealed c-plane sapphire substrates. It was found the β-Ga 2 O 3 epitaxial film exhibited better crystalline quality, and accordingly the fabricated device performed significantly improved characteristics, for example, higher responsibility (153 AAV), by adopting annealed sapphire substrate. However, the degradations in dark current and response time were also observed on the photodetector based on annealed sapphire substrate, possibly attributed to higher carrier mobility and longer carrier lifetime in β-Ga 2 O 3 epitaxial film respectively.
Structural basis for the glycosyltransferase activity of the Salmonella effector SseK3

The Salmonella-secreted effector SseK3 translocates into host cells, targeting innate immune responses, including NF-κB activation. SseK3 is a glycosyltransferase that transfers an N-acetylglucosamine (GlcNAc) moiety onto the guanidino group of a target arginine, modulating host cell function. However, a lack of structural information has precluded elucidation of the molecular mechanisms in arginine and GlcNAc selection. We report here the crystal structure of SseK3 in its apo form and in complex with hydrolyzed UDP-GlcNAc. SseK3 possesses the typical glycosyltransferase type-A (GT-A)-family fold and the metal-coordinating DXD motif essential for ligand binding and enzymatic activity. Several conserved residues were essential for arginine GlcNAcylation and SseK3-mediated inhibition of NF-κB activation. Isothermal titration calorimetry revealed SseK3's preference for manganese coordination. The pattern of interactions in the substrate-bound SseK3 structure explained the selection of the primary ligand. Structural rearrangement of the C-terminal residues upon ligand binding was crucial for SseK3's catalytic activity, and NMR analysis indicated that SseK3 has limited UDP-GlcNAc hydrolysis activity. The release of free N-acetyl α-d-glucosamine, and the presence of the same molecule in the SseK3 active site, classified it as a retaining glycosyltransferase. A glutamate residue in the active site suggested a double-inversion mechanism for the arginine N-glycosylation reaction. Homology models of SseK1, SseK2, and the Escherichia coli orthologue NleB1 reveal differences in the surface electrostatic charge distribution, possibly accounting for their diverse activities. This first structure of a retaining GT-A arginine N-glycosyltransferase provides an important step toward a better understanding of this enzyme class and their roles as bacterial effectors.
The impact of tumor receptor heterogeneity on the response to anti-angiogenic cancer treatment

Multiple promoters and inhibitors mediate angiogenesis, the formation of new blood vessels, and these factors represent potential targets for impeding vessel growth in tumors. Vascular endothelial growth factor (VEGF) is a potent angiogenic factor targeted in anti-angiogenic cancer therapies. In addition, thrombospondin-1 (TSP1) is a major endogenous inhibitor of angiogenesis, and TSP1 mimetics are being developed as an alternative type of anti-angiogenic agent. The combination of bevacizumab, an anti-VEGF agent, and ABT-510, a TSP1 mimetic, has been tested in clinical trials to treat advanced solid tumors. However, the patients’ responses are highly variable and show disappointing outcomes. To obtain mechanistic insight into the effects of this combination anti-angiogenic therapy, we have constructed a novel whole-body pharmacokinetic model including the VEGF and TSP1 reaction networks. Using this molecular-detailed model, we investigated how the combination anti-angiogenic therapy changes the extracellular angiogenic balance in cancer patients and how the effect of the combination therapy is influenced by tumor receptor expression. Overall, this model complements the clinical administration of combination anti-angiogenic therapy, highlights the role of tumor receptor variability in the heterogeneous responses to anti-angiogenic therapy and identifies the tumor receptor profiles that correlate with a high likelihood of a positive response to combination therapy. In addition, this study provides novel understanding of the VEGF-TSP1 balance in cancer patients at the systems-level and could be further used to optimize combination anti-angiogenic therapy. Financial support The authors acknowledge the support of the US National Science Foundation (CAREER Award 1552065 to S.D.F.) and the American Cancer Society (130432-RSG-17-133-01-CSM to S.D.F.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Deletion of the African Swine Fever Virus Gene DP148R Does Not Reduce Virus Replication in Culture but Reduces Virus Virulence in Pigs and Induces High Levels of Protection against Challenge

ABSTRACT Many of the approximately 165 proteins encoded by the African swine fever virus (ASFV) genome do not have significant similarity to known proteins and have not been studied experimentally. One such protein is DP148R. We showed that the DP148R gene is transcribed at early times postinfection. Deletion of this gene did not reduce virus replication in macrophages, showing that it is not essential for replication in these cells. However, deletion of this gene from a virulent isolate, Benin 97/1, producing the BeninΔDP148R virus, dramatically reduced the virulence of the virus in vivo. All pigs infected with the BeninΔDP148R virus survived infection, showing only transient mild clinical signs soon after immunization. Following challenge with the parental virulent virus, all pigs immunized by the intramuscular route (11/11) and all except one immunized by the intranasal route (5/6) survived. Mild or no clinical signs were observed after challenge. As expected, control nonimmune pigs developed signs of acute African swine fever (ASF). The virus genome and infectious virus were observed soon after immunization, coincident with the onset of clinical signs (∼106 genome copies or 50% tissue culture infective doses/ml). The levels of the virus genome declined over an extended period up to 60 days postimmunization. In contrast, infectious virus was no longer detectable by days 30 to 35. Gamma interferon (IFN-γ) was detected in serum between days 4 and 7 postimmunization, and IFN-γ-producing cells were detected in all pigs analyzed following stimulation of immune lymphocytes with whole virus. ASFV-specific antibodies were first detected from day 10 postimmunization. IMPORTANCE African swine fever (ASF) is endemic in Africa, parts of the Trans Caucasus, the Russian Federation, and several European countries. The lack of a vaccine hinders control. Many of the ASF virus genes lack similarity to known genes and have not been characterized. We have shown that one of these, DP148R, is transcribed early during virus replication in cells and can be deleted from the virus genome without reducing virus replication. The virus with the gene deletion, BeninΔDP148R, caused mild clinical signs in pigs and induced high levels of protection against challenge with the parental virulent virus. Therefore, deletion of this gene can provide a target for the rational development of vaccines.
Behavioral intervention to reduce opioid overdose among high-risk persons with opioid use disorder: A pilot randomized controlled trial

Objective The United States is amidst an opioid epidemic, including synthetic opioids that may result in rapid death, leaving minimal opportunity for bystander rescue. We pilot tested a behavioral intervention to reduce the occurrence of opioid overdose among opioid dependent persons at high-risk for subsequent overdose. Materials and methods We conducted a single-blinded randomized-controlled trial of a repeated dose motivational interviewing intervention (REBOOT) to reduce overdose versus treatment as usual, defined as information and referrals, over 16 months at the San Francisco Department of Public Health from 2014–2016. Participants were 18–65 years of age, had opioid use disorder by Structured Clinical Interview, active opioid use, opioid overdose within 5 years, and prior receipt of naloxone kits. The intervention was administered at months 0, 4, 8, and 12, preceded by the assessment which was also administered at month 16. Dual primary outcomes were any overdose event and number of events, collected by computer-assisted personal interview, as well as any fatal overdose events per vital records. Results A total of 78 persons were screened and 63 enrolled. Mean age was 43 years, 67% were born male, 65% White, 17% African-American, and 14% Latino. Ninety-two percent of visits and 93% of counseling sessions were completed. At baseline, 33.3% of participants had experienced an overdose in the past four months, with a similar mean number of overdoses in both arms (p = 0.95); 29% overdosed during follow-up. By intention-to-treat, participants assigned to REBOOT were less likely to experience any overdose (incidence rate ratio [IRR] 0.62 [95%CI 0.41–0.92, p = 0.019) and experienced fewer overdose events (IRR 0.46, 95%CI 0.24–0.90, p = 0.023), findings that were robust to sensitivity analyses. There were no differences between arms in days of opioid use, substance use treatment, or naloxone carriage. Conclusions REBOOT reduced the occurrence of any opioid overdose and the number of overdoses. Trial registration clinicaltrials.gov NCT02093559
Investigation of Multilayer Subwavelength Metallic-Dielectric Stratified Structures

We investigate dispersion properties of n-layers unit cell metallic-dielectric stratified structures (MDSSs) for the first time to our knowledge. An efficient and flexible numerical method is applied to study optical characteristics of the MDSSs. As an example, we systematically investigate the influences of geometric parameters, operating frequency, and gain material on the dispersion properties of the n-layers unit cell MDSSs in the terahertz regime. The results show that the effective index of the n-layers unit cell MDSSs decreases with the increase of operating frequency. The full-width-half-maximum of the transmittance of the n-layers unit cell MDSSs can be designed wider than that of the binary unit cell MDSSs, which is beneficial for the design of certain optical devices, such as superlenses. Furthermore, the effective index/loss of the proposed structure increases/decreases with the increase of the material gain. Due to the high flexibility of the proposed n-layers unit cell MDSSs, we believe they would have broad applications in the fields of nanophotonics and integrated optoelectronics.
Small Changes in Gene Expression of Targeted Osmoregulatory Genes When Exposing Marine and Freshwater Threespine Stickleback (Gasterosteus aculeatus) to Abrupt Salinity Transfers

Salinity is one of the key factors that affects metabolism, survival and distribution of fish species, as all fish osmoregulate and euryhaline fish maintain osmotic differences between their extracellular fluid and either freshwater or seawater. The threespine stickleback (Gasterosteus aculeatus) is a euryhaline species with populations in both marine and freshwater environments, where the physiological and genomic basis for salinity tolerance adaptation is not fully understood. Therefore, our main objective in this study was to investigate gene expression of three targeted osmoregulatory genes (Na+/K+-ATPase (ATPA13), cystic fibrosis transmembrane regulator (CFTR) and a voltage gated potassium channel gene (KCNH4) and one stress related heat shock protein gene (HSP70)) in gill tissue from marine and freshwater populations when exposed to non-native salinity for periods ranging from five minutes to three weeks. Overall, the targeted genes showed highly plastic expression profiles, in addition the expression of ATP1A3 was slightly higher in saltwater adapted fish and KCNH4 and HSP70 had slightly higher expression in freshwater. As no pronounced changes were observed in the expression profiles of the targeted genes, this indicates that the osmoregulatory apparatuses of both the marine and landlocked freshwater stickleback population have not been environmentally canalized, but are able to respond plastically to abrupt salinity challenges.
Modelling the Transmission Dynamics and Control of Mumps in Mainland China

Mumps is a common childhood viral disease and children have been vaccinated throughout the world since 1967. The incidence of mumps has increased with more than 300,000 young people infected with mumps annually in mainland China since 2005. Therefore, we designed and analyzed long-term mumps surveillance data in an SVEILR (susceptible–vaccinated–exposed–severely infectious–mildly infectious–recovered) dynamic transmission model with optimized parameter values to describe the dynamics of mumps infections in China. There were 18.02% of mumps infected young adults seeking medical advice. The vaccine coverage has been insufficient in China. Young adults with frequent contact and mild infection were identified as a major driver of mumps epidemics. The reproduction number of mumps was determined 4.28 in China. Sensitivity analysis of the basic reproduction number and the endemic equilibrium was conducted to evaluate the effectiveness of mumps control measures. We propose to increase the vaccine coverage and make two doses of MMR (Measles, mumps and rubella) vaccines freely available in China.
Dual extruder 3D-bioprinter for computer designed cardiac structures

A precise location of cells is of high interest for the characterization of cell interaction in in-vitro studies. Bioprinters can be a useful and automatized tool to produce these biological structures with precision. The objective of this study is to develop and validate a low-cost novel dual-extruder 3D bioprinter with enough resolution to study the electrophysiological interaction between different cell types. An open source classical 3D printer was adapted to incorporate two syringe extruders, allowing controlled delivery of hydrogel-cell ink. Four different parameters were studied to adjust precision: the needle lumen (G), the density of the hydrogel (%), the linear velocity of the extruder in the platform (mm/s) and the extrusion velocity (steps of the NEMA 17 extruder motor). Cell viability was tested with alamarBlue test and spatial distribution of cells was studied with fluorescence microscopy. As a result of this study, thin lines of 1.18 mm in width with 85% viability after 24h of printing process were obtained.
Study of Biological Properties of Thin-Film Materials on the Basis of the SIO2–P2O5–СaO System

Thin films were obtained from film-forming solutions by the sol-gel method on the basis of the SiO2-P2O5-СаO system. Thin films were produced on the single-crystal silicon substrates (model substrate) by extraction at a velocity of 5 mm/s following by heat treatment at a temperature of 60°С for 20 minutes and at a temperature of 600°С for 1 hour. During the experiment it was established that film-forming solutions are usable only for 2 to 7 days from the moment of preparation. Using thermal and infra-red – spectroscopic analysis main stages of oxide system formation were retraced. According to data from x-ray phase analysis phases CaClH2PO4∙H2O, Ca(H2PO4)2∙H2O, CaHPO4∙2H2O, Ca2SiO4∙H2O, Ca5(PO4)3Cl. On the supporter’s surface a homogeneous film coating with quite equally spaced crystal-like formations with the diameter of 10-11 microns at the distance of 1-30 microns was formed. Phase composition, surface properties and biological activity of the synthesized materials were investigated. XRD results indicated that after being immersed into the SBF, hydroxylapatite, wollastonite, and chlorapatite were formed on the samples’ surfaces, which was important for practical applications
Seasonality of Fire Weather Strongly Influences Fire Regimes in South Florida Savanna-Grassland Landscapes

Fire seasonality, an important characteristic of fire regimes, commonly is delineated using seasons based on single weather variables (rainfall or temperature). We used nonparametric cluster analyses of a 17-year (1993–2009) data set of weather variables that influence likelihoods and spread of fires (relative humidity, air temperature, solar radiation, wind speed, soil moisture) to explore seasonality of fire in pine savanna-grassland landscapes at the Avon Park Air Force Range in southern Florida. A four-variable, three-season model explained more variation within fire weather variables than models with more seasons. The three-season model also delineated intra-annual timing of fire more accurately than a conventional rainfall-based two-season model. Two seasons coincided roughly with dry and wet seasons based on rainfall. The third season, which we labeled the fire season, occurred between dry and wet seasons and was characterized by fire-promoting conditions present annually: drought, intense solar radiation, low humidity, and warm air temperatures. Fine fuels consisting of variable combinations of pyrogenic pine needles, abundant C4 grasses, and flammable shrubs, coupled with low soil moisture, and lightning ignitions early in the fire season facilitate natural landscape-scale wildfires that burn uplands and across wetlands. We related our three season model to fires with different ignition sources (lightning, military missions, and prescribed fires) over a 13-year period with fire records (1997–2009). Largest wildfires originate from lightning and military ignitions that occur within the early fire season substantially prior to the peak of lightning strikes in the wet season. Prescribed ignitions, in contrast, largely occur outside the fire season. Our delineation of a pronounced fire season provides insight into the extent to which different human-derived fire regimes mimic lightning fire regimes. Delineation of a fire season associated with timing of natural lightning ignitions should be useful as a basis for ecological fire management of humid savanna-grassland landscapes worldwide.