Miracle-dz/UniFAR-FTUs huggingface dataset:
Randomized Study of Long-term (15-17 Years) Outcome After Microfracture Versus Mosaicplasty in Knee Articular Cartilage Defects

Background: Few comparative randomized long-term studies on microfracture versus mosaicplasty have been published, and only 2 studies reported a follow-up of 10 years. Hypothesis/Purpose: The purpose was to compare the clinical outcome of microfracture versus mosaicplasty/osteochondral autograft transfer in symptomatic cartilage lesions. The null hypothesis was that the outcome was not statistically different at any point of time. Study Design: Randomized controlled trial; Level of evidence, 1. Methods: Forty patients with articular cartilage defects were randomized to undergo cartilage repair by either microfracture (n = 20) or mosaicplasty (n = 20). Inclusion criteria were as follows: age 18 to 50 years at the time of surgery, 1 or 2 symptomatic focal full-thickness articular chondral defects on the femoral condyles or trochlea, and size 2 to 6 cm2. The main outcome variable was the Lysholm knee score recorded before the surgery and at 12 months, median 5 years, median 10 years, and minimum 15 years after the surgery. Results: Forty patients were included in the study (28 men, 12 women; median age, 32 years; range, 18-48 years). Defects with a median size of 3.5 cm2 (range, 2-5 cm2) were treated. A significant increase in the Lysholm score was seen for all subjects— from a mean 53 (SD, 16) at baseline to 69 (SD, 21) at the minimum 15-year follow-up (P = .001). The mean Lysholm score was significantly higher in the mosaicplasty group than the microfracture group at 12 months, median 5 years, median 10 years, and minimum 15 years: 77 (SD, 17) versus 61 (SD, 22), respectively (P = .01), at the last follow-up. At all follow-up time points, the difference in mean Lysholm score was clinically significant (>10 points). Conclusion: At short, medium, and long term (minimum 15 years), mosaicplasty results in a better, clinically relevant outcome than microfracture in articular cartilage defects (2-5 cm2) of the distal femur of the knee in patients aged 18 to 50 years.
Assessment of Urinary Deoxynivalenol Biomarkers in UK Children and Adolescents

Deoxynivalenol (DON), the mycotoxin produced mainly by Fusarium graminearum and found in contaminated cereal-based foodstuff, has been consistently detected in body fluids in adults. Available data in children and adolescents are scarce. This study assessed urinary DON concentrations in children aged 3–9 years (n = 40) and adolescents aged 10–17 years (n = 39) in the UK. Morning urine samples were collected over two consecutive days and analysed for free DON (un-metabolised form), DON-glucuronides (DON-GlcA), deepoxy deoxynivalenol (DOM-1), and total DON (sum of free DON, DON-GlcA, and DOM-1). Total DON was detected in the urine of >95% of children and adolescents on both days. Mean total DON concentrations (ng/mg creatinine) were 41.6 and 21.0 for children and adolescents, respectively. The greatest total DON levels were obtained in female children on both days (214 and 219 ng/mg creatinine on days 1 and 2, respectively). Free DON and DON-GlcA were detected in most urine specimens, whereas DOM-1 was not present in any sample. Estimation of dietary DON exposure suggested that 33–63% of children and 5–46% of adolescents exceeded current guidance regarding the maximum provisional tolerable daily intake (PMTDI) for DON. Although moderate mean urinary DON concentrations were shown, the high detection frequency of urinary DON, the maximum biomarker concentrations, and estimated dietary DON exposure are concerning.
Molecular and Microscopic Analysis of Bacteria and Viruses in Exhaled Breath Collected Using a Simple Impaction and Condensing Method

Exhaled breath condensate (EBC) is increasingly being used as a non-invasive method for disease diagnosis and environmental exposure assessment. By using hydrophobic surface, ice, and droplet scavenging, a simple impaction and condensing based collection method is reported here. Human subjects were recruited to exhale toward the device for 1, 2, 3, and 4 min. The exhaled breath quickly formed into tiny droplets on the hydrophobic surface, which were subsequently scavenged into a 10 µL rolling deionized water droplet. The collected EBC was further analyzed using culturing, DNA stain, Scanning Electron Microscope (SEM), polymerase chain reaction (PCR) and colorimetry (VITEK 2) for bacteria and viruses. Experimental data revealed that bacteria and viruses in EBC can be rapidly collected using the method developed here, with an observed efficiency of 100 µL EBC within 1 min. Culturing, DNA stain, SEM, and qPCR methods all detected high bacterial concentrations up to 7000 CFU/m3 in exhaled breath, including both viable and dead cells of various types. Sphingomonas paucimobilis and Kocuria variants were found dominant in EBC samples using VITEK 2 system. SEM images revealed that most bacteria in exhaled breath are detected in the size range of 0.5–1.0 µm, which is able to enable them to remain airborne for a longer time, thus presenting a risk for airborne transmission of potential diseases. Using qPCR, influenza A H3N2 viruses were also detected in one EBC sample. Different from other devices restricted solely to condensation, the developed method can be easily achieved both by impaction and condensation in a laboratory and could impact current practice of EBC collection. Nonetheless, the reported work is a proof-of-concept demonstration, and its performance in non-invasive disease diagnosis such as bacterimia and virus infections needs to be further validated including effects of its influencing matrix.
The Effect of Saffron on Depression among Recovered Consumers of Methamphetamine Living with HIV/AIDS

ABSTRACT Background: From one hand, depression is one of the symptoms that occur after abstinence from methamphetamine. On the other people living with HIV/AIDS are in isolation due to the nature of their illness and depression is one of the most common mental health problems they experience. Objectives: This study was aimed at determining the effectiveness of saffron on reducing depression among recovered consumers of methamphetamine living with HIV/AIDS. Methods: The design of this study was semi-experimental with pre-test, post-test and control (placebo) groups. The statistical population consisted of all recovered consumers of methamphetamine living with HIV/AIDS who were referred to the Positive Club. Fifty-seven (57) recovered consumers of methamphetamine, living with HIV/AIDS, were selected by convenience sampling method. They were randomly assigned to an experimental (saffron) group and a control (placebo) group. The experimental group received 30 ml of saffron per day for 8 weeks, whereas the control (placebo) group received placebo the same way. BDI-II was used in this study as a measurement instrument. ANCOVA models were used for statistical inference. Results: The findings showed that saffron and its ingredients had been effective in reducing depression among this group (P < 0.05). Conclusion: In fact, saffron with its active ingredients (Crusin and Saffranal) by serotonin and dopamine secretion in the brain, help in reducing depression among recovered consumers of methamphetamine living with HIV/AIDS.
Traffic state estimation method with efficient data fusion based on the Aw-Rascle-Zhang model

Higher-order traffic flow models describe the dynamics of non-equilibrium traffic (e.g., capacity drop, traffic oscillation). Therefore, a traffic state estimation (TSE) method based on higher-order models could have notable advantages over conventional method based on an equilibrium (first-order) model. First, they can encompass non-equilibrium traffic phenomena inherent to the nonlinearity of traffic flow. Second, they can directly fuse heterogeneous traffic data, such as flow measured by detectors and speed measured by probe vehicles. These features would be useful for large volumes of data. This article proposes a data-assimilation-based TSE method for capturing non-equilibrium traffic dynamics based on the Aw-Rascle-Zhang model, which is known as a physically-consistent higher-order model but not received as much attention as other models. The proposed method can efficiently and simply fuse heterogeneous data. Additionally, it is computationally efficient because it uses the extended Kalman filter with an analytical derivative. The features of the proposed method were investigated empirically and quantitatively using experimental dataset collected from actual traffic. We investigate the empirical relationship between the accuracy and amount of available data, and compare the proposed method with a conventional TSE method.
Protein instability, haploinsufficiency, and cortical hyper-excitability underlie STXBP1 encephalopathy

De novo heterozygous mutations in STXBP1 cause early infantile epileptic encephalopathy. Kovačević et al. analyse the underlying disease mechanisms in silico, in vitro and in vivo, and show that protein instability, haploinsufficiency and cortical hyperexcitability explain STXBP1-encephalopathy. In addition, they demonstrate the construct, face and predictive validity of Stxbp1+/- mice.
Creatine kinase enzyme level correlates positively with serum creatinine and lean body mass, and is a prognostic factor for survival in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative condition for which there is no single diagnostic test or biomarker. The level of the creatine kinase (CK) enzyme in serum may be mild to moderately elevated in some patients with ALS, the precise cause of which and its behaviour with disease progression is unknown. The aim of this study was to examine the usefulness of monitoring CK serially during the ALS disease trajectory and to determine whether CK levels mirror disease progression.
Are the basal ganglia actually controlling movement or quite the opposite?

In Parkinson’s disease (PD) patients, levels of dopamine in basal ganglia (BG) are lowered, leading to the imbalance in neuronal activity between the direct and indirect pathways, which, in turn, hinder proper movement and walking. However, neither the pathophysiological mechanisms nor the role of the basal ganglia and connecting structures involved in gait and locomotion in PD are well understood. Two new studies from the group of Prof. Kreitzer provide some new insight into these eluding issues. The first study, published in Neuron by Parker and colleagues, carefully examined the changes of the strength of synaptic inputs in a PD mouse model. They performed whole-cell recordings in both direct and indirect medium spiny neurons (MSNs) neurons while optically stimulating sensorimotor cortex or thalamus. They discovered that dopamine loss results in a miscommunication between the thalamus and the BG, producing reduced activation of the direct pathway and slowness and disruption of movements. This was restored by blocking the thalamostriatal terminals using chemo and optogenetic tools. These findings underscore the role of thalamus in PD motor features. However, it should be noted that their results might be difficult to reconcile with data from previous studies where they described cell loss in the thalamus of PD animals or lack of motor benefit after chemical ablation of thalamic projections in parkinsonian monkeys. The second study, published in Cell by Roseberry and colleagues, combined techniques, such as optogenetics, single-cell recording, and virus-based mapping, in mice in order to examine the mechanisms underlying the control of the mesencephalic locomotor region (MLR) by the BG pathways. Interestingly, their results revealed that the direct pathway selectively activated one type of these MLR neurons, the glutamatergic ones, in the brainstem and that these are the ones triggering locomotion, and the indirect pathway inhibits them, stopping movement. Outstandingly, they found that the power of the brainstem neurons could trump BG signals given that they were able to optogenetically control the initiation of movement in the animal regardless of the signal coming from the direct or indirect pathways. Nonetheless, because of the technical complexity of the experiments and the multiple parallel pathways from BG nuclei to the MLR region, cautious relevance should be given to these findings. Together, both articles may give rise to further studies on non-BG regions, perhaps leading to newer therapeutic developments for this major challenge and unmet need in clinical practice.
Anatomy of machine learning algorithm implementations in MPI, Spark, and Flink

With the ever-increasing need to analyze large amounts of data to get useful insights, it is essential to develop complex parallel machine learning algorithms that can scale with data and number of parallel processes. These algorithms need to run on large data sets as well as they need to be executed with minimal time in order to extract useful information in a time-constrained environment. Message passing interface (MPI) is a widely used model for developing such algorithms in high-performance computing paradigm, while Apache Spark and Apache Flink are emerging as big data platforms for large-scale parallel machine learning. Even though these big data frameworks are designed differently, they follow the data flow model for execution and user APIs. Data flow model offers fundamentally different capabilities than the MPI execution model, but the same type of parallelism can be used in applications developed in both models. This article presents three distinct machine learning algorithms implemented in MPI, Spark, and Flink and compares their performance and identifies strengths and weaknesses in each platform.
The Effect of Multispot Laser Panretinal Photocoagulation on Retinal Sensitivity and Driving Eligibility in Patients With Diabetic Retinopathy.

IMPORTANCE Panretinal photocoagulation (PRP) for proliferative diabetic retinopathy (PDR) may lead to peripheral field loss that prevents driving. Anti-vascular endothelial growth factor agents are proposed as treatments for PDR that spare peripheral vision. If multispot lasers cause less visual field loss, continuing to perform PRP may be justified. OBJECTIVE To assess the effect of bilateral multispot laser PRP on retinal sensitivity and driving visual fields in PDR. DESIGN, SETTING, AND PARTICIPANTS This prospective nonrandomized interventional cohort analysis performed at a tertiary referral center included 43 laser-naive patients with PDR that required bilateral PRP. Participants were recruited from June 27, 2012, to October 14, 2013. At baseline and 6-month follow-up, patients underwent detailed static and kinetic perimetry, microperimetry, optical coherence tomography, wide-field color fundus photography, and fluorescein angiography. Quantitative change in retinal sensitivity was assessed by comparing the mean global retinal sensitivity before and after laser treatment and by comparing the modeled hill of vision by deriving a volumetric measure. Final follow-up was completed on May 21, 2014. INTERVENTIONS Multispot laser treatment was applied using standard parameters, until neovascularization regressed or complete retinal coverage was achieved. MAIN OUTCOMES AND MEASURES Participants who passed the Esterman binocular visual field test for driving in the United Kingdom (at least 120° horizontal field with no significant defects within the central 20°) and full-field and macular retinal sensitivity. RESULTS Of the 43 patients (17 men; 26 women; mean [SD] age, 46.6 [13.3] years), 38 (88%) completed the study. Before treatment, 41 of 43 patients (95%) passed the Esterman visual field test for driving; after completion of laser treatment, 35 of 38 patients (92%) passed. The mean (SD) change in retinal sensitivity on static perimetry was -1.4 (3.7) (95% CI, -2.7 to -0.1) dB OD and -2.4 (2.9) (95% CI, -3.4 to -1.4) dB OS. Mean (SD) 4° macular sensitivity decreased by 3.0 (5.2) dB OD and 2.6 (5.4) dB OS. CONCLUSIONS AND RELEVANCE This prospective study investigating the effects of multispot laser PRP on retinal sensitivity demonstrates a high likelihood of retaining eligibility to drive based on adequate visual field. A mild loss of retinal sensitivity was detected at 6 months after completion of laser treatment. Further change to visual fields may have occurred with longer follow-up. This study provides information that might be used to counsel patients requiring PRP and informs the debate regarding the role of anti-vascular endothelial growth factor therapy in patients with PDR who might otherwise receive laser treatment.
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology

Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms.
Genotoxic and mutagenic properties of Ni and NiO nanoparticles investigated by comet assay, γ‐H2AX staining, Hprt mutation assay and ToxTracker reporter cell lines

Nickel (Ni) compounds are classified as carcinogenic to humans but the underlying mechanisms are still poorly understood. Furthermore, effects related to nanoparticles (NPs) of Ni have not been fully elucidated. The aim of this study was to investigate genotoxicity and mutagenicity of Ni and NiO NPs and compare the effect to soluble Ni from NiCl2. We employed different models; i.e., exposure of (1) human bronchial epithelial cells (HBEC) followed by DNA strand break analysis (comet assay and γ‐H2AX staining); (2) six different mouse embryonic stem (mES) reporter cell lines (ToxTracker) that are constructed to exhibit fluorescence upon the induction of various pathways of relevance for (geno)toxicity and cancer; and (3) mES cells followed by mutagenicity testing (Hprt assay). The results showed increased DNA strand breaks (comet assay) for the NiO NPs and at higher doses also for the Ni NPs whereas no effects were observed for Ni ions/complexes from NiCl2. By employing the reporter cell lines, oxidative stress was observed as the main toxic mechanism and protein unfolding occurred at cytotoxic doses for all three Ni‐containing materials. Oxidative stress was also detected in the HBEC cells following NP‐exposure. None of these materials induced the reporter related to direct DNA damage and stalled replication forks. A small but statistically significant increase in Hprt mutations was observed for NiO but only at one dose. We conclude that Ni and NiO NPs show more pronounced (geno)toxic effects compared to Ni ions/complexes, indicating more serious health concerns. Environ. Mol. Mutagen. 59:211–222, 2018. © 2017 The Authors Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society
Enhanced intensity of global tropical cyclones during the mid-Pliocene warm period

Significance To better understand how tropical cyclones (TCs) may respond to future warming, we explore the behavior of TCs during the mid-Pliocene warm period (∼3 Ma), which shares characteristics of projected warmer climate. Our TC-permitting numerical simulations predict enhanced global-average peak TC intensity, longer duration, increased power dissipation, and a poleward migration of the location of peak intensity during the mid-Pliocene, although there are regional differences in the magnitude and statistical power of the climate/TC relationships. Our results share similarities with global TC changes observed during recent global warming and in most future projections and provide a window into the potential TC activity that may be expected in a warmer world. Given the threats that tropical cyclones (TC) pose to people and infrastructure, there is significant interest in how the climatology of these storms may change with climate. The global historical record has been extensively examined, but it is short and plagued with recurring questions about its homogeneity, limiting its effectiveness at assessing how TCs vary with climate. Past warm intervals provide an opportunity to quantify TC behavior in a warmer-than-present world. Here, we use a TC-resolving (∼25 km) global atmospheric model to investigate TC activity during the mid-Pliocene warm period (3.264−3.025 Ma) that shares similarities with projections of future climate. Two experiments, one driven by the reconstructed sea surface temperatures (SSTs) and the other by the SSTs from an ensemble of mid-Pliocene simulations, consistently predict enhanced global-average peak TC intensity during the mid-Pliocene coupled with longer duration, increased power dissipation, and a poleward migration of the location of peak intensity. The simulations are similar to global TC changes observed during recent global warming, as well as those of many future projections, providing a window into the potential TC activity that may be expected in a warmer world. Changes to power dissipation and TC frequency, especially in the Pacific, are sensitive to the different SST patterns, which could affect the viability of the role of TCs as a factor for maintaining a reduced zonal SST gradient during the Pliocene, as recently hypothesized.
Fog-Based Crime-Assistance in Smart IoT Transportation System

Smart transportation safety (STS) envisions improving public safety through a significant paradigm shift for police authority responses on crimes toward a pro-active one. The application of smart surveillance in STS is critical for automatic and accurate identification of events in case of security threats in target environments. Cloud computing reduces costs and high resource consumption of smart surveillance capable STS systems, at the cost of introducing additional latency through far away centralized systems. In this paper, the fog-framework for intelligent public safety in vehicular environment (FISVER) framework applies fog computing in smart video surveillance-based STS to enhance crime assistance in a cost-efficient way. Through fog-FISVER, in-vehicle and fog infrastructures support autonomous and real-time crime detection on public bus services. A fog-FISVER laboratory testbed prototype was created and extensive evaluations in a real testbed were performed. Results show that fog-FISVER delivers outstanding system performance and device survivability behavior over typical STS use cases.