Miracle-dz/UniFAR-FTUs huggingface dataset:
Design strategies for research-based physics activities

Physics education researchers often design activities, then test whether the activities are effective in helping students learn. Many published activities have been described in the physics education literature. However, some instructors may want to create their own activities; these instructors may want to know about how the published activities were designed. To this end, we have interviewed several prominent designers and analyzed their publications as well as an American Association of Physics Teachers’ report on lab design. This paper focuses on a particular set of design philosophies that were important to these designers. “Revisiting cycles,” which address a single question in depth, were a common theme. We also argue that designers’ view of conceptual learning and of “thinking like a physicist” shapes their design plans.
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Given a set P of n locations on which facilities can be placed and an integer k, we want to place k facilities on some locations so that a designated objective function is maximized. The problem is called the kdispersion problem. In this paper we give a simple O(n) time algorithm to solve the max-min version of the k-dispersion problem if P is a set of points on a line. This is the first O(n) time algorithm to solve the max-min kdispersion problem for the set of “unsorted” points on a line. If P is a set of sorted points on a line, and the input is given as an array in which the coordinates of the points are stored in the sorted order, then by slightly modifying the algorithm above one can solve the dispersion problem in time. This is the first sublinear time algorithm to solve the max-min kdispersion problem for the set of sorted points on a line.
Bifurcated Response of a Regional Forest to Drought

Several lines of evidence suggest that forest growth in many regions is declining as a consequence of changing climate. To predict the fate of forests in the future, a quantitative understanding of how the key climate variables (insolation, precipitation and temperature) interact with forests to cause the decline is a pressing need. Here we use a regionally-averaged tree-ring width index (RWIr) to quantify forest growth in the Southwest United States (SWUS). We show that over a period of 90 years, SWUS RWIr bifurcated into forest stands with enhanced (healthy) and reduced (declining) branches when regressed on shortwave-radiation and temperature, respectively. The reduced branch was controlled overwhelmingly by drought as measured with a regionally-averaged precipitationevapotranspiration index (SPEIr). As SPEIr approached -1.6 (previously shown as a tipping-point for SWUS conifer forest growth), RWIr approached zero and in extreme drought years, wide spread tree mortality has been observed. Modeled trends in SPEI based on four IPCC-GHG scenarios predict SWUS SPEIr falling below -1.6 more or less continuously within a few decades. With drought expanding north- and eastward over larger areas, tree mortality may become a semi-continental phenomenon with coniferous forests transitioning to more xeric ecosystems. Our results provide insights into how to differentiate functions of climate impacts on forest growth and how to identify tipping-point control parameters for forest regime transitions.
CTCPI – Convolution Tree Kernel-based Chemical-Protein Interaction Detection

In this paper we introduce a chemical-protein interaction detection system called CTCPI, which uses Convolution Tree Kernel to separate various levels of interaction mechanisms exhibited by chemicals while interacting with proteins/genes. Our system enlists a novel feature engineering method based on Algebraic Invariance to identify and consolidate distinct linguistic features for each class from the candidate sets and use these feature patterns as a screening function for generating the feature tree for SVM-CTK classifier. Our system achieved about 30.92% performance for chemical protein interaction class identification task.
Synthesis of transparent dispersions of aluminium hydroxide nanoparticles

Transparent dispersions of inorganic nanoparticles are attractive materials in many fields. However, a facile method for preparing such dispersions of aluminium hydroxide nanoparticles is yet to be realized. Here, we report a direct reactive method to prepare transparent dispersions of pseudo-boehmite nanoparticles (1 wt%) without any surface modification, and with an average particle size of 80 nm in length and 10 nm in width, as well as excellent optical transparency over 94% in the visible range. Furthermore, transparent dispersions of boehmite nanoparticles (1.5 wt%) were also achieved after an additional hydrothermal treatment. However, the optical transparency of dispersions decreased with the rise of hydrothermal temperature and the shape of particles changed from rhombs to hexagons. In particular, monodisperse hexagonal boehmite nanoplates with an average lateral size of 58 nm and a thickness of 12.5 nm were obtained at a hydrothermal temperature of 220 °C. The selectivity of crystal growth direction was speculated as the possible formation mechanism of these as-prepared aluminium hydroxide nanoparticles. Besides, two values of 19.6 wt% and 14.64 wt% were separately measured for the weight loss of pseudo-boehmite and boehmite nanoparticles after a continuous heating, indicating their potential flame-resistant applications in the fabrication of plastic electronics and optical devices with high transparency.
Evaluation of Dried Blood Spots and Oral Fluids as Alternatives to Serum for Human Papillomavirus Antibody Surveillance

Human papillomavirus (HPV) is the causative agent of cervical and other anogenital cancers. HPV vaccination, primarily targeted at young girls before the age of sexual debut, is starting to demonstrate population-level declines in HPV infection and early disease associated with vaccine-incorporated genotypes. Monitoring young women for vaccine-specific antibody is important for vaccine surveillance and may be useful as an adjunct test within a cervical screening context. We evaluated serum, dried blood spots, and oral fluid as potential samples for such applications and report robust measures of diagnostic accuracy. This is the first time a direct comparison of alternative sample types has been made between vaccinated and unvaccinated women for the detection and quantitation of HPV antibodies. ABSTRACT Human papillomavirus (HPV) vaccination elicits high-titer genotype-specific antibody responses that are associated with a reduced risk of cervical disease caused by vaccine-incorporated genotypes. Our objective was to evaluate dried blood spots (DBSs) and oral mucosal transudate (OMT) as alternative samples to serum to confirm HPV vaccine antibody status. A study was carried out to evaluate the feasibility of detecting HPV16 and HPV18 antibodies in OMT, DBSs, and sera among women who self-reported being unvaccinated or fully vaccinated with the HPV vaccine. Serum had the highest sensitivity (100%) for detection of antibodies against both HPV16 and HPV18 but the lowest specificity, due to the detection of natural infection antibodies in 16% of unvaccinated women. Conversely, DBSs and OMT had lower sensitivity (96% and 82%, respectively) but high specificity (98%). We confirmed that these antibodies were functional (i.e., neutralizing) and that their detection was quantitatively reproducible and well correlated between sample types when normalized to IgG content. DBSs and OMT are appropriate alternative sample types for HPV vaccine surveillance. These alternative sample types warrant consideration for the purposes of cervical screening, diagnosis, and management, but more work will be needed to establish the stringent parameters required for such application. IMPORTANCE Human papillomavirus (HPV) is the causative agent of cervical and other anogenital cancers. HPV vaccination, primarily targeted at young girls before the age of sexual debut, is starting to demonstrate population-level declines in HPV infection and early disease associated with vaccine-incorporated genotypes. Monitoring young women for vaccine-specific antibody is important for vaccine surveillance and may be useful as an adjunct test within a cervical screening context. We evaluated serum, dried blood spots, and oral fluid as potential samples for such applications and report robust measures of diagnostic accuracy. This is the first time a direct comparison of alternative sample types has been made between vaccinated and unvaccinated women for the detection and quantitation of HPV antibodies.
Utilizing postmortem drug concentrations in mechanistic modeling and simulation of cardiac effects: a proof of concept study with methadone

Abstract Methadone-related poisoning has been found to be the leading and increasing cause of death among intoxication cases in several countries. Aside from respiratory depression, methadone is known to cause QT-prolongation, which may lead to sudden cardiac death. Concentrations in heart tissue should be more accurate for estimating cardiotoxic effects. The aim of this study was to investigate whether the effect of methadone on the QT-interval could be simulated and whether the concentrations in heart tissues allowed for better prediction of the Bazett corrected QT-interval (QTcB). A predictive performance study was conducted using the simulation platform Cardiac Safety Simulator to mimic five literature studies using their described study conditions. Both free and total plasma and heart concentrations were investigated using two different in silico models: the O’Hara-Rudy (ORD) model and the 10 Tusscher (TNNP) model. The results showed that the QTcB of methadone was best predicted either with total plasma using the TNNP model or with free plasma using the ORD model. The ORD model was highly sensitive to the total heart concentrations, resulting in overprediction of the QTcB. The TNNP model also overpredicted the QTcB, but to a lesser degree than the ORD model. Furthermore, due to a low baseline QTcB, the ORD model underpredicted the QTcB for both the free plasma and free heart concentrations. In conclusion, it is possible to simulate the cardiac effects of methadone, yet several elements influence the approach uncertainty including but not limited to biophysically details model of cardiac electrophysiology, exposure data, and input parameters.
Co-delivery of gambogenic acid and VEGF-siRNA with anionic liposome and polyethylenimine complexes to HepG2 cells

Abstract Background and objective: The combination of two or more different mechanisms of drugs in the treatment of cancer has become one of the effective methods. The purpose of this study was to successfully prepare a non-viral delivery system that could efficiently co-delivery siRNA and gambogenic acid (GNA) to improve the anti-cancer efficiency in HepG2 cells. Methods: The delivery system was prepared by a two-step method. First, the GNA-anionic liposome took shape by a solvent evaporation method, and then the liposome was bound to the PEI/siRNA complex by electrostatic interaction to form the final carrier system (lipopolyplexes). Agarose gel electrophoresis, MTT, particle size and zeta potential were detected to analyse the lipopolyplexes formation. The transfection efficiency of siRNA was determined by confocal laser scanning microscopy and flow cytometry. Western blotting was used to assess the VEGF protein expression levels of HepG2 cells. The cell apoptosis assay was used to assess the anti-tumour superiority of lipopolyplexes. Results: GNA-PEI/siRNA-liposome (lipopolyplexes) are significantly less cytotoxicity compared to PEI mediated carriers. Simultaneously, the results of flow cytometry and confocal laser scanning microscopy indicated that the lipopolyplexes could successfully carry siRNA into the cytoplasm, and the western-blot result evidence that the delivery system has a potential for VEGF to express down. Also compared with the control group, the results of apoptosis test suggest that the lipopolyplexes can significantly promote cell apoptosis. Conclusion: The delivery system has a potential in the combination of various drugs for cancer therapy in future.
Duty-Related Posttraumatic Stress Symptoms in 911 Telecommunicators: The Roles of Childhood Trauma Exposure and Emotion-Focused Coping

ABSTRACT A history of childhood trauma exposure has been linked to the development of posttraumatic stress symptoms in adulthood following new exposure. Unhealthy coping behaviors that could develop or be utilized in response to early trauma could lend themselves to psychological issues in adulthood. Emotion-focused and problem-focused coping strategies in relation to stressful duty-related situations are examined as indirect pathways through which childhood trauma exposure could be associated with duty-related posttraumatic stress symptoms in 911 telecommunicators (N = 808). Multiple mediation models revealed that 3 of the 4 emotion-focused coping strategies, but not the problem-focused strategies, functioned as significant mediators in the association between childhood exposure and duty-related posttraumatic stress symptoms. Pairwise comparisons showed that self-controlling and escape-avoidance strategies were the strongest pathways of the indirect childhood trauma exposure–posttraumatic stress symptoms association. Implications of results regarding coping in response to new traumatic events in adulthood and potential research and intervention directions are discussed.
The function and regulation of TBX22 in avian frontonasal morphogenesis

The frontonasal mass gives rise to the facial midline and fuses with the maxillary prominence to form the upper lip. Here we focus on the regulation and function of TBX22, a repressor dynamically expressed in the frontonasal mass. Both FGF and Noggin (a BMP antagonist) strongly induce gTBX22, however, each has opposite effects on morphogenesis ‐ Noggin inhibits whereas FGF stimulates growth. To determine whether TBX22 mediates these effects, we used retroviruses to locally increase expression levels. RCAS::hTBX22 decreased proliferation, reduced expression of MSX2 and DLX5 and caused cleft lip. Decreased levels of endogenous gTBX22 were also observed but were not the primary cause of the phenotype as determined in rescue experiments. Our data suggest that genetic or environmental insults such as those affecting the BMP pathway could lead to a gain‐of‐function of TBX22 and predispose an individual to cleft lip. Developmental Dynamics 239:458–473, 2010. © 2009 Wiley‐Liss, Inc.
FlowFields++: Accurate Optical Flow Correspondences Meet Robust Interpolation

Optical Flow algorithms are of high importance for many applications. Recently, the Flow Field algorithm and its modifications have shown remarkable results, as they have been evaluated with top accuracy on different data sets. In our analysis of the algorithm we have found that it produces accurate sparse matches, but there is room for improvement in the interpolation. Thus, we propose in this paper FlowFields++, where we combine the accurate matches of Flow Fields with a robust interpolation. In addition, we propose improved variational optimization as post-processing. Our new algorithm is evaluated on the challenging KITTI and MPI Sintel data sets with public top results on both benchmarks.
Assessing Optimal Flight Parameters for Generating Accurate Multispectral Orthomosaicks by UAV to Support Site-Specific Crop Management

This article describes the technical specifications and configuration of a multirotor unmanned aerial vehicle (UAV) to acquire remote images using a six-band multispectral sensor. Several flight missions were programmed as follows: three flight altitudes (60, 80 and 100 m), two flight modes (stop and cruising modes) and two ground control point (GCP) settings were considered to analyze the influence of these parameters on the spatial resolution and spectral discrimination of multispectral orthomosaicked images obtained using Pix4Dmapper. Moreover, it is also necessary to consider the area to be covered or the flight duration according to any flight mission programmed. The effect of the combination of all these parameters on the spatial resolution and spectral discrimination of the orthomosaicks is presented. Spectral discrimination has been evaluated for a specific agronomical purpose: to use the UAV remote images for the detection of bare soil and vegetation (crop and weeds) for in-season site-specific weed management. These results show that a balance between spatial resolution and spectral discrimination is needed to optimize the mission planning and image processing to achieve every agronomic objective. In this way, users do not have to sacrifice flying at low altitudes to cover the whole area of interest completely.
Obligation and Prohibition Extraction Using Hierarchical RNNs

We consider the task of detecting contractual obligations and prohibitions. We show that a self-attention mechanism improves the performance of a BILSTM classifier, the previous state of the art for this task, by allowing it to focus on indicative tokens. We also introduce a hierarchical BILSTM, which converts each sentence to an embedding, and processes the sentence embeddings to classify each sentence. Apart from being faster to train, the hierarchical BILSTM outperforms the flat one, even when the latter considers surrounding sentences, because the hierarchical model has a broader discourse view.
Logic gates and memory elements design and simulation using PMOS organic transistor

Multi-flngered OTFTs, with staggered top-gate configuration have been fabricated on flexible polyethylene-naphtalate (PEN) substrates (100 μm thick). Inkjet printing technique has been used to setup the silver contacts, while the organic layers and the dielectric fluoropolymer have been deposited by spin-coating. The p-type polymeric semiconductor is a solution processed 6,13-bis(triisopropyl-silyletynyl) pentacene. The semiconductor layer thickness is about 30 nm, while the dielectric fluoropolymer is 400 nm thick. These transistors have been characterized and a DC, and a transient accurate models have been developed and imported in CADENCE. Finally, SPECTRE has been used to simulate model circuits based on such a device. In this work we describe the design of high frequency logic gates and preliminary flip-flops design, exploiting PMOS organic transistor and its expected performances.
Effects of VEGF‐ANG‐1‐PLA nano‐sustained release microspheres on proliferation and differentiation of ADSCs

The improvement of fat graft viability might depend on the presence of multipotent resident adipose derived stem cells (ADSCs) which is the important component of stromal vascular fraction (SVF). Vascular endothelial growth factor (VEGF) and angiogenin‐1 (Ang‐1) are responsible for neovascularization. However, their half‐life is too short to produce a biological effect. We thus investigated whether VEGF‐ANG‐1‐polylactic acid (PLA) microspheres could enhance the angiogenic properties of ADSCs. PLA microspheres containing VEGF and ANG‐1 were prepared by in vitro ultrasonic emulsification and characterized according to their encapsulation efficiency (EE), drug‐loading rate (DL), particle size, and drug release. The systemic toxicity of empty loaded nanospheres (NPs) and the ability of these microspheres to promote the proliferation and differentiation of ADSCs were evaluated. The EE and DL were above 86 and 2.8%, respectively. The drug release was completed after 20 days. Systemic toxicity was verified in ADSCs that received the unloaded NPs. It was observed that ADSCs treated with VEGF‐ANG‐1‐PLA microspheres had an increase in the proliferation and the number of CD31 positive cells. ADSCs proliferation and differentiation toward endothelial cells (ECs) could be enhanced by the addition of VEGF‐ANG‐1‐PLA nano‐sustained release microspheres.
Primary experimental results of the navigation method of multiple autonomous underwater vehicles

We report the first experimental results of the navigation method of multiple Autonomous Underwater Vehicles (AUVs) for wide seafloor surveys proposed by us in our previous reports. The key idea of the proposed method is that moving AUVs estimate their states (horizontal position and heading angle) based on AUVs remaining stationary on the seafloor (landmark AUVs), alternating between these roles to expand the observational coverage. Moving AUVs land on the seafloor and transmit compressed information about their estimated states to the landmark AUVs when they change the roles. Sea trials were carried out using two AUVs to evaluate the performance of this method. One is the AUV Tri-Dog 1 (TD) which can move and estimate the states and the other is a Dummy AUV (DA) which cannot move but can estimate the states. In the experiments, TD and DA alternatively estimated the states. To evaluate the positioning accuracy of the proposed method, the states were recalculated based on sensor data obtained at sea trials in post processing. As a result, positioning errors of the proposed method were estimated to be smaller than dead reckoning. The Errors were found to be about 0.4 m in horizontal position and about 1.5 degree in heading angle. The method demonstrated to be successful in stable positioning with AUVs alternating between the moving role and the landmark role. Future works include the verification of the method using two AUVs in sea environment to realize wide seafloor survey.
Galectin-3 modulates the polarized surface delivery of β1-integrin in epithelial cells

ABSTRACT Epithelial cells require a precise intracellular transport and sorting machinery to establish and maintain their polarized architecture. This machinery includes β-galactoside-binding galectins for targeting of glycoprotein to the apical membrane. Galectin-3 sorts cargo destined for the apical plasma membrane into vesicular carriers. After delivery of cargo to the apical milieu, galectin-3 recycles back into sorting organelles. We analysed the role of galectin-3 in the polarized distribution of β1-integrin in MDCK cells. Integrins are located primarily at the basolateral domain of epithelial cells. We demonstrate that a minor pool of β1-integrin interacts with galectin-3 at the apical plasma membrane. Knockdown of galectin-3 decreases apical delivery of β1-integrin. This loss is restored by supplementation with recombinant galectin-3 and galectin-3 overexpression. Our data suggest that galectin-3 targets newly synthesized β1-integrin to the apical membrane and promotes apical delivery of β1-integrin internalized from the basolateral membrane. In parallel, knockout of galectin-3 results in a reduction in cell proliferation and an impairment in proper cyst development. Our results suggest that galectin-3 modulates the surface distribution of β1-integrin and affects the morphogenesis of polarized cells. Highlighted Article: The lectin galectin-3 redistributes β1-integrins and elevates their apical cell surface delivery to promote accurate tubulocyst formation.
NETWORK STACK OPTIMIZATION IN MAPREDUCE

Recently, improvements in networking hardware have caused traditional assumptions about network bottlenecks to become invalid. In environments with very fast networks such as datacenters, the networking bottleneck has shifted from networking hardware to network processing done in the CPU. One proposed solution to this is kernel bypass networking in which network stacks execute in user-space, avoiding overheads and inefficiencies in the Linux kernel. Tools such as DPDK and mTCP implement kernel bypass and provide application-ready interfaces. This project explores using mTCP and DPDK in MapReduce to analyze the practicality and effect of using kernel bypass in datacenter applications. Performance results weren’t exemplary, mostly due to difficulty integrating the tools. It’s likely that more impressive results could be achieved in the near future with some more work in the area and more mature tools.