Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling and Prediction of Rigid Body Motion with Planar Non-Convex Contact

We present a principled method for motion prediction via dynamic simulation for rigid bodies in intermittent contact with each other where the contact region is a planar non-convex contact patch. Such methods are useful in planning and controlling for robotic manipulation. The planar non-convex contact patch can either be a topologically connected set or a disconnected set. Most works in rigid body dynamic simulation assume that the contact between objects is a point contact, which may not be valid in many applications. In this paper, using the convex hull of the contact patch, we build on our recent work on simulating rigid bodies with convex contact patches for simulating motion of objects with planar non-convex contact patches. We formulate a discrete-time mixed complementarity problem to solve the contact detection and integration of the equations of motion simultaneously. We solve for the equivalent contact point (ECP) and contact impulse of each contact patch simultaneously along with the state, i.e., configuration and velocity of the objects. We prove that although we are representing a patch contact by an equivalent point, our model for enforcing non-penetration constraints ensures that there is no artificial penetration between the contacting rigid bodies. We provide empirical evidence to show that our method can seamlessly capture transition among different contact modes like patch contact, multiple or single point contact.
AndroidPropTracker : Mining Lifetime Properties of Android Projects

Android operating system introduces new releases frequently. This fact led to the existence of several Android Application Programming Interfaces (APIs) which is one of the causes of the Android fragmentation phenomenon. As a consequence of fragmentation, many apps became not ready for new Android releases. Aiming at investigation of the readiness of Android apps, we developed a software repository mining tool to understand how ready apps are (and were) for Android releases. The tool tracks the changes of Android projects properties over time, contributing for a deeper analysis through collecting data since the beginning of the projects. It allows researchers to examine when exactly Android properties were changed, how many times they were changed, as well as all their values along time. This mechanism can support researchers to understand the evolution of Android projects and to answer research questions. In addition, developers can use the tool to track their apps evolution and perform comparisons and analysis with other open source apps. The tool can help developers to have a broader view of their apps evolution as well as to analyze competitor apps evolution.
Ventriculoperitoneal shunt complications in an adult population: A comparison of various shunt designs to prevent overdrainage

Background: Overdrainage after cerebrospinal fluid diversion remains a significant morbidity. The hydrostatic, gravitational force in the upright position can aggravate this. Siphon control (SC) mechanisms, as well as programmable and flow regulating devices, were developed to counteract this. However, limited studies have evaluated their safety and efficacy. In this study, direct comparisons of the complication rates between siphon control (SC) and non-SC (NSC), fixed versus programmable, and flow- versus pressure regulating valves are undertaken. Methods: A retrospective chart review was performed over all shunt implantations from January 2011 to December 2016 within the Houston Methodist Hospital system. Complication rates within 6 months of the operative date, including infection, subdural hematoma, malfunction, and any other shunt-related complication, were analyzed via Fisher’s exact test, with P < 0.05 regarded as significant. Subgroup analyses based on diagnoses – normal pressure hydrocephalus (HCP), pseudotumor cerebri, or other HCP – were also performed. Results: The overall shunt-related complication rate in this study was 19%. Overall rates of infection, shunt failure, and readmission within 180 days were 3%, 11%, and 34%, respectively. No difference was seen between SC and NSC groups in any complication rate overall or on subgroup analyses. When comparing fixed versus programmable and flow- versus pressure-regulating valves, the latter in each analysis had significantly lower malfunction and total complication rates. Conclusions: Programmable and pressure regulating devices may lead to lower shunt malfunction and total complication rates. Proper patient selection should guide valve choice. Future prospective studies may further elucidate the difference in complication rates between these various shunt designs.
Financiamiento de redes integradas de servicios de salud

Resumen Los países de América Latina y el Caribe necesitan aumentar sus recursos públicos en salud para ampliar el acceso equitativo y eficiente a la salud. El aumento debe financiar un modelo específico que ha mostrado evidencia de eficacia, como el de redes integradas de servicios de salud (RISS) basadas en atención primaria de salud. La literatura global no ha prestado suficiente atención al financiamiento a las RISS; más bien se ha focalizado en establecimientos y agentes aislados, así como en mecanismos específicos. Sin embargo, en la Región de las Américas su desarrollo es una necesidad desde hace años. Una RISS es un conjunto de organizaciones de salud que ofrece intervenciones y servicios de salud coordinados a una población bajo su cargo y asume la responsabilidad de salud y económica en el logro de mejores resultados de salud. Un sistema de pago a una RISS debe ir dirigido a promover la integralidad de la atención y a fomentar un enfoque centrado en el ciclo de vida de las personas, la articulación y la coordinación de servicios. El presupuesto poblacional ajustado por riesgos se muestra como un mecanismo posible y potente para apoyar el logro de los objetivos. Su desarrollo requiere reconocer que la forma de financiamiento no responderá por sí sola a los desafíos y que se necesita, a la vez, de la planificación y de la gestión sanitarias. Se requiere abordar los desafíos técnicos, políticos e institucionales para tener éxito en este esfuerzo, que a su vez debe estar inserto en el proceso global de transformación de los sistemas de salud hacia la salud universal.
Spatial Nano-Morphology of the Prolamellar Body in Etiolated Arabidopsis thaliana Plants With Disturbed Pigment and Polyprenol Composition

The prolamellar body (PLB) is a periodic bicontinuous membrane structure based on tubular tetrahedral units. PLBs are present in plant etioplasts and, upon illumination, directly transform into the lamellar thylakoid networks within chloroplasts. Efficient tubular-lamellar rearrangement and later formation of the photosynthetically active thylakoid membranes are crucial steps in the development of plant autotrophy. PLB membranes are mainly composed of galactolipids, carotenoids, and protochlorophyllide (Pchlide), the chlorophyll precursor, bound in a complex with NADPH and Pchlide oxidoreductase. Although the PLB structure has been studied for over 50 years, the direct role of particular membrane components in the formation of the PLB paracrystalline network remains elusive. Moreover, despite the numerous literature data regarding the PLB geometry, their reliable comparative analysis is complicated due to variable experimental conditions. Therefore, we performed comprehensive ultrastructural and low-temperature fluorescence analysis of wild type Arabidopsis thaliana (Arabidopsis) seedlings grown in different conditions typical for studies on etiolated seedlings. We established that the addition of sucrose to the growing media significantly affected the size and compactness of the PLB. The etiolation period was also an important factor influencing the PLB structural parameters and the ratio of free to complex-bound Pchlide. Thus, a reliable PLB structural and spectral analysis requires particular attention to the applied experimental conditions. We investigated the influence of the pigment and polyprenol components of the etioplast membranes on the formation of the PLB spatial structure. The PLB 3D structure in several Arabidopsis mutants (ccr1-1, lut5-1, szl1-1npq1-2, aba1-6, pif1, cpt7) with disturbed levels of particular pigments and polyprenols using electron tomography technique was studied. We found that the PLB nano-morphology was mainly affected in the pif1 and aba1-6 mutants. An increased level of Pchlide (pif1) resulted in the substantial shift of the structural balance between outer and inner PLB water channels and overall PLB compactness compared to wild type plants. The decrease in the relative content of β-branch xanthophylls in aba1-6 plants was manifested by local disturbances in the paracrystalline structure of the PLB network. Therefore, proper levels of particular etioplast pigments are essential for the formation of stable and regular PLB structure.
Alfaxalone and Dexmedetomidine as an Alternative to Gas Anesthesia for Micro-CT Lung Imaging in a Bleomycin-Induced Pulmonary Fibrosis Murine Model

Micro-CT imaging could be considered a powerful non-invasive tool for accessing pulmonary fibrosis in mice. However, the choice of the anesthesia protocol plays a fundamental role to obtain robust and reproducible data, avoiding misinterpretations of the results. Inhaled anesthesia is commonly used for micro-CT lung imaging, but sometimes the standardization of the protocol may be challenging for routine activities in drug discovery. In this study we used micro-CT to evaluate the effects of two anesthetic protocols, consisting in Alfaxalone and Dexmedetomidine mixture, as injectable agents, and gaseous isoflurane, on vehicle and bleomycin-treated mice. No significant differences were highlighted between the protocols either for lung aeration degrees by micro-CT or histologic analyses in both the controls and bleomycin-treated groups. Our results support Alfaxalone and Dexmedetomidine mixture as a suitable and safe alternative compared to isoflurane for lung imaging. We also concluded that this injectable mixture may be applied for several imaging technologies and on different mice models.
Fabrication Development of a Large Area Grating for Out of Plane Beam Coupling

We develop a single-layer waveguide surface grating structure to vertically couple near infrared (NIR) light at ~1.55 um wavelength from a large area (~100 um length scale) Si waveguide on a Silicon-On-Insulator (SOI) substrates to free-space for high-power laser applications. Our design approach is based on the optimization of local emission angles and the out-coupling intensities. Simulation results show that a focal spot with a 1/e2 width of 3.82 um can be achieved at the desired focal position, with 33% (-4.81 dB) simulated source to free-space focusing efficiency, while initial measurements show an efficiency of 22% (-6.58 dB).
Mild fever as a catalyst for consumption of the ischaemic penumbra despite endovascular reperfusion

Abstract Cerebrovascular ischaemia is potentiated by hyperthermia, and even mild temperature elevation has proved detrimental to ischaemic brain. Infarction progression following endovascular reperfusion relates to multiple patient-specific and procedural variables; however, the potential influence of mild systemic temperature fluctuations is not fully understood. This study aims to assess the relationship between systemic temperatures in the early aftermath of acute ischaemic stroke and the loss of at-risk penumbral tissues, hypothesizing consumption of the ischaemic penumbra as a function of systemic temperatures, irrespective of reperfusion status. A cross-sectional, retrospective evaluation of a single-institution, prospectively collected endovascular therapy registry was conducted. Patients with anterior circulation, large vessel occlusion acute ischaemic stroke who underwent initial CT perfusion, and in whom at least four-hourly systemic temperatures were recorded beginning from presentation and until the time of final imaging outcome were included. Initial CT perfusion core and penumbra volumes and final MRI infarction volumes were computed. Systemic temperature indices including temperature maxima were recorded, and pre-defined temperature thresholds varying between 37°C and 38°C were examined in unadjusted and adjusted regression models which included glucose, collateral status, reperfusion status, CT perfusion-to-reperfusion delay, general anaesthesia and antipyretic exposure. The primary outcome was the relative consumption of the penumbra, reflecting normalized growth of the at-risk tissue volume ≥10%. The final study population comprised 126 acute ischaemic stroke subjects (mean 63 ± 14.5 years, 63% women). The primary outcome of penumbra consumption ≥10% occurred in 51 (40.1%) subjects. No significant differences in baseline characteristics were present between groups, with the exception of presentation glucose (118 ± 26.6 without versus 143.1 ± 61.6 with penumbra consumption, P = 0.009). Significant differences in the likelihood of penumbra consumption relating to systemic temperature maxima were observed [37°C (interquartile range 36.5 − 37.5°C) without versus 37.5°C (interquartile range 36.8 − 38.2°C) with penumbra consumption, P = 0.001]. An increased likelihood of penumbra consumption was observed for temperature maxima in unadjusted (odds ratio 3.57, 95% confidence interval 1.65 − 7.75; P = 0.001) and adjusted (odds ratio 3.06, 95% confidence interval 1.33 − 7.06; P = 0.009) regression models. Significant differences in median penumbra consumption were present at a pre-defined temperature maxima threshold of 37.5°C [4.8 ml (interquartile range 0 − 11.5 ml) versus 21.1 ml (0 − 44.7 ml) for subjects not reaching or reaching the threshold, respectively, P = 0.007]. Mild fever may promote loss of the ischaemic penumbra irrespective of reperfusion, potentially influencing successful salvage of at-risk tissue volumes following acute ischaemic stroke.
TeaForN: Teacher-Forcing with N-grams

Sequence generation models trained with teacher-forcing suffer from issues related to exposure bias and lack of differentiability across timesteps. Our proposed method, Teacher-Forcing with N-grams (TeaForN), addresses both these problems directly, through the use of a stack of N decoders trained to decode along a secondary time axis that allows model parameter updates based on N prediction steps. TeaForN can be used with a wide class of decoder architectures and requires minimal modifications from a standard teacher-forcing setup. Empirically, we show that TeaForN boosts generation quality on one Machine Translation benchmark, WMT 2014 English-French, and two News Summarization benchmarks, CNN/Dailymail and Gigaword.
Modified Wuzi Yanzong Prescription Inhibited Tau Protein Hyperphosphorylation induced by Aβ_(25-35)-in PC12 Cells

Objective:To investigate the neuroprotective effect of modified Wuzi Yanzong prescription(MWP)on β-amyloid protein(Aβ25-35)-induced tau protein hyperphosphorylation in PC12 cells and the potential mechanism.Method: Control,Aβ25-35 model and sample treatment groups were set in our study. Aβ25-35(30 μmol.L-1)was used to induce tau protein hyperphosphorylation in PC12 cells,and MWP(50-400 mg.L-1) was also simultaneously added.Then,the neuroprotective effects of MWP were investigated.Result: MWP alone did not show any cytotoxicity in PC12 cells.MWP significantly protected PC12 cells from Aβ25-35-induced neurotoxicity,cellviability increased from(70 ± 4.9)% to(98 ± 6.5)%(P 0.01),and apoptosis-related protein(Caspase-3 and PARP) expressions were also effectively inhibited,Caspase-3 and PARP were down-regulated from(378.15 ±34.65)% and(985.12 ± 45.32)% to(127.65 ± 12.65)% and(543.61 ± 39.07)%(P 0.01). In addition,tau protein hyperphosphorylation in PC12 cells was significantly down-regulated,p-tau(in Ser396 site) expression decreased from(130.01 ± 5.83)% to(113.75 ± 6.34)%(P 0.01),and p-tau(in Ser404 site) expression decreased from(150.17 ± 10.28)% to(105.37 ± 4.57)%(P 0.01). The inhibitory effects of MWP on the phosphorylation of glycogen synthase kinase 3β(GSK-3β) at Ser9 site and mitogen-activated protein kinases (MAPK) may explain the potential mechanism.Conclusion: MWP could inhibit Aβ25-35-induced tau protein hyperphosphorylation on PC12 cells,showing a neuroprotective effect in Alzheimer’s disease.
Improved Detection of in vivo Human NK Cell-Mediated Antibody-Dependent Cellular Cytotoxicity Using a Novel NOG-FcγR-Deficient Human IL-15 Transgenic Mouse

We generated an NOD/Shi-scid-IL2Rγnull (NOG) mouse deficient for the Fcer1g and Fcgr2b genes (NOG-FcγR−/− mice), in which monocytes/macrophages do not express activating (FcγRI, III, and IV) or inhibitory (FcγRIIB) Fcγ receptors. Antibody-dependent cellular cytotoxicity (ADCC) by innate immune cells was strongly reduced in this strain. Thus, while the growth of xenogeneic human tumors engrafted in conventional NOG mice was suppressed by innate cells upon specific antibody treatment, such growth inhibition was abrogated in NOG-FcγR−/− mice. Using this novel strain, we further produced NOG-FcγR−/−-mice expressing human IL-15 (NOG-FcγR−/−-hIL-15 Tg). The mice inherited unique features from each strain, i.e., the long-term sustenance of human natural killer (NK) cells, and the elimination of mouse innate cell-mediated ADCC. As a result, segregation of human NK cell-mediated ADCC from mouse cell-mediated ADCC was possible in the NOG-FcγR−/−-hIL-15 Tg mice. Our results suggest that NOG-FcγR−/−-hIL-15 Tg mice are useful for validating the in vivo function of antibody drug candidates.
Modeling the Dynamic Landscape Evolution of a Volcanic Coastal Environment Under Future Climate Trajectories

As anthropogenic forcing continues to rapidly modify worldwide climate, impacts on landscape changes will grow. Olivine weathering is a natural process that sequesters carbon out of the atmosphere, but is now being proposed as a strategy that can be artificially implemented to assist in the mitigation of anthropogenic carbon emissions. We use the landscape evolution model Badlands to identify a region (Tweed Caldera catchment in Eastern Australia) that has the potential for naturally enhanced supply of mafic sediments, known to be a carbon sink, into coastal environments. Although reality is more complex than what can be captured within a model, our models have the ability to unravel and estimate how erosion of volcanic edifices and landscape dynamics will react to future climate change projections. Local climate projections were taken from the Australian government and the IPCC in the form of four alternative pathways. Three additional scenarios were designed, with added contributions from the Antarctic Ice Sheet, to better understand how the landscape/dynamics might be impacted by an increase in sea level rise due to ice sheet tipping points being hit. Three scenarios were run with sea level held constant and precipitation rates increased in order to better understand the role that precipitation and sea level plays in the regional supply of sediment. Changes between scenarios are highly dependent upon the rate and magnitude of climatic change. We estimate the volume of mafic sediment supplied to the erosive environment within the floodplain (ranging from ∼27 to 30 million m3 by 2100 and ∼78–315 million m3 by 2500), the average amount of olivine within the supplied sediment under the most likely scenarios (∼7.6 million m3 by 2100 and ∼30 million m3 by 2500), and the amount of CO2 that is subsequently sequestered (∼53–73 million tons by 2100 and ∼206–284 million tons by 2500). Our approach not only identifies a region that can be further studied in order to evaluate the efficacy and impact of enhanced silicate weathering driven by climate change, but can also help identify other regions that have a natural ability to act as a carbon sink via mafic rock weathering.
Defining trust in IoT environments via distributed remote attestation using blockchain

The constantly growing number of Internet of Things (IoT) devices and their resource-constrained nature makes them particularly vulnerable and increasingly attractive for exploitation by cyber criminals. Current estimates commonly reach the tens of billions for the number of connected 'things'. The heterogeneous capabilities of these devices serve as a motivation for resource sharing among them. However, for effective resource sharing, it is essential that trust be retained in the multitude of pervasive and diverse IoT devices. Remote attestation is a well-known technique used to build such trust. Thus, this paper proposes a blockchain based remote attestation protocol to establish trust between IoT devices. The blockchain offers a secure framework for device registration while the attestation is based on Physical Unclonable Functions (PUF). This combination of technologies results in a tamper resistant scheme with protection against physical and proxy attacks.
The unique features of SARS‐CoV‐2 transmission: Comparison with SARS‐CoV, MERS‐CoV and 2009 H1N1 pandemic influenza virus

From 2002 to 2019, three deadly human coronaviruses (hCoVs), severe acute respiratory syndrome coronavirus (SARS‐CoV), Middle Eastern respiratory syndrome coronavirus (MERS‐CoV) and severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) emerged to produce outbreaks of SARS, MERS and coronavirus disease 2019 (Covid‐19), respectively. All three hCoVs are members of the Betacoronavirus genus in the subfamily Orthocoronavirinae and share many similarities in virology and epidemiology. However, the pattern and scale of Covid‐19 global spread is similar to 2009 pandemic H1N1 influenza (H1N1pdm09), rather than SARS or MERS. Covid‐19 exhibits high viral shedding in the upper respiratory tract at an early stage of infection, and has a high proportion of transmission competent individuals that are pre‐symptomatic, asymptomatic and mildly symptomatic, characteristics seen in H1N1pdm09 but not in SARS or MERS. These two traits of Covid‐19 and H1N1pdm09 result in reduced efficiency in identification of transmission sources by symptomatic screening and play important roles in their ability to spread unchecked to cause pandemics. To overcome these attributes of Covid‐19 in community transmission, identifying the transmission source by testing for virus shedding and interrupting chains of transmission by social distancing and public masking are required.
Performance analysis of indoor localization based on channel state information ranging model

Due to robustness against multi-path effect, channel state information (CSI) of Orthogonal Frequency Division Multiplexing (OFDM) systems is supposed to provide accurate distance measurement for indoor localization. However, we find that the original CSI ranging model is biased, so the model cannot be used to directly derive Cramer-Rao lower bound (CRLB) of positioning error for CSI-ranging based localization scheme. In this paper we first analyze the estimation bias of the original CSI ranging model according to indoor wireless channel model. Then we propose a negative power summation ranging model which can be used as an unbiased ranging model for both Line-Of-Sight (LOS) and Non-LOS scenarios. Subsequently, based on the proposed model, we derive both the CRLB of ranging error and the CRLB of positioning error for CSI-ranging localization scheme. Through simulation we validate the bias of the original ranging model and the approximately zero bias of our proposed ranging model. Through comprehensive experiments in different indoor scenarios, localization errors by different ranging models are compared to the CRLB, meanwhile our proposed ranging model is demonstrated to have better ranging and localization accuracy than the original ranging model.