Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitochondrial Pathway Is Involved in Advanced Glycation End Products-Induced Apoptosis of Rabbit Annulus Fibrosus Cells

Study Design. Experimental study. Objective. The purposes of this study were to evaluate whether advanced glycation end-products (AGEs) induce annulus fibrosus (AF) cell apoptosis and further to explore the mechanism by which this process occurs. Summary of Background Data. Recent studies revealed that AGEs accumulation is considered an important factor in diabetic intervertebral disc (IVD) degeneration. However, the effect of AGEs on intervertebral disc remains unclear. Methods. AF cells were treated with various concentrations of AGEs for 3 days. Cell viability and cell proliferation were measured by Cell Counting Kit-8 (CCK-8) and 5-ethynyl-2′-deoxyuridine (EdU) incorporation assays, respectively. Cell apoptosis was examined by Annexin V/PI apoptosis detection kit and Hoechst 33342. The expression of apoptosis-related proteins, including Bax, Bcl-2, cytochrome c, caspase-3, and caspase-9, was detected by western blotting. In addition, Bax and Bcl-2 mRNA expression levels were detected by real-time PCR (RT-PCR). Mitochondrial membrane potential (MMP) and intracellular reactive oxygen species (ROS) production of AF cell were examined by 5,5′,6,6′ -Tetrachloro-1,1′,3,3′- tetraethyl-imidacarbocyanine iodide (JC-1) staining and 2′,7′-Dichlorodihydrofluorescein diacetate (DCFH-DA) fluorescent probes, respectively. Results. Our results indicated that AGEs had inhibitory effects on AF cell proliferation and induced AF cell apoptosis. The molecular data showed that AGEs significantly up-regulated Bax expression and inhibited Bcl-2 expression. In addition, AGEs increased the release of cytochrome c into the cytosol and enhanced caspase-9 and caspase-3 activation. Moreover, treatment with AGEs resulted in a decrease in MMP and the accumulation of intracellular ROS in AF cells. The antioxidant N-acetyl-L-cysteine (NAC) significantly reversed AGE-induced MMP decrease and AF cell apoptosis. Conclusion. These results suggested that AGEs induce rabbit AF cell apoptosis and mitochondrial pathway may be involved in AGEs-mediated cell apoptosis, which may provide a theoretical basis for diabetic IVD degeneration. Level of Evidence: N/A
A Hardware Architecture for the Affine-Invariant Extension of SIFT

Affine-invariant extension of scale-invariant feature transform (ASIFT) algorithm requires a large amount of computation and memory access, and consequently, is hard to process in real time. In order to increase the operation speed of ASIFT algorithm, this paper proposes a new hardware architecture for the ASIFT algorithm. In order to reduce the memory access time, the affine transform is modified to allow external memory access in the raster-scan order with a little accuracy drop. In addition, image filtering with skewed kernel is proposed in order to reduce the memory space for image storage. Additional complexity reduction is attempted to reduce the number of simulated viewpoints. As a result, throughput of the affine transform module is increased to 325% and the proposed hardware processes a video graphics array-sized ( $640\times480$ ) video at 20 fps.
Using Sequential Information in Polyphonic Sound Event Detection

To detect the class, and start and end times of sound events in real world recordings is a challenging task. Current computer systems often show relatively high frame-wise accuracy but low event-wise accuracy. In this paper, we attempted to merge the gap by explicitly including sequential information to improve the performance of a state-of-the-art polyphonic sound event detection system. We propose to 1) use delayed predictions of event activities as additional input features that are fed back to the neural network; 2) build N-grams to model the co-occurrence probabilities of different events; 3) use se-quentialloss to train neural networks. Our experiments on a corpus of real world recordings show that the N-grams could smooth the spiky output of a state-of-the-art neural network system, and improve both the frame-wise and the event-wise metrics.
Projection Patterns of Corticofugal Neurons Associated with Vibrissa Movement

Abstract Rodents actively whisk their vibrissae, which, when they come in contact with surrounding objects, enables rodents to gather spatial information about the environment. Cortical motor command of whisking is crucial for the control of vibrissa movement. Using awake and head-fixed rats, we investigated the correlations between axonal projection patterns and firing properties in identified layer 5 neurons in the motor cortex, which are associated with vibrissa movement. We found that cortical neurons that sent axons to the brainstem fired preferentially during large-amplitude vibrissa movements and that corticocallosal neurons exhibited a high firing rate during small vibrissa movements or during a quiet state. The differences between these two corticofugal circuits may be related to the mechanisms of motor-associated information processing.
Parallel Valuation: A Direct Comparison of EQ-5D-3L and EQ-5D-5L Societal Value Sets

Objective. To compare and contrast EQ-5D-5L (5L) and EQ-5D-3L (3L) health state values derived from a common sample. Methods. Data from the 2017 US EQ-5D valuation study were analyzed. Value sets were estimated with random-effects linear regression based on composite time trade-off (cTTO) valuations for 3L and 5L health states with 2 approaches to model specification: main effects only and additional N3/N45 terms. Properties of the descriptive system and value set characteristics were compared by examining distributions of predicted index scores, ceiling effects, and single-level transition values from adjacent corner health states. Mean transition values were calculated for all predicted 3L and 5L health states and plotted against baseline index scores. Results. A total of 1062 respondents were included in the analysis. The observed mean cTTO values for the worst possible 3L and 5L health states were −0.423 and −0.343, respectively. The range of scale was larger with the 3L, compared to the 5L, for both main effects and N term models. Values for the mildest 5L health states (range, 0.857−0.924) were similar to 11111 for the 3L. Parameter estimates for matched dimension levels differed by <|0.07| except for the most severe level of Mobility. For the main effects model, 3L mean transition values were greater for more severe baseline 3L index scores, whereas 5L mean transition values remained constant irrespective of the baseline index score. Conclusions. Compared to the 3L, the 5L exhibited a lower ceiling effect and improved measurement properties. There was a larger range of scale for the 3L compared to 5L; however, this difference was driven by differences in preference for the most severe level of problems in Mobility.
To Retweet or Not to Retweet: Understanding What Features of Cardiovascular Tweets Influence Their Retransmission

Twitter is one of the largest social networking sites (SNSs) in the world, yet little is known about what cardiovascular health related tweets go viral and what characteristics are associated with retransmission. The current study aims to identify a function of the observable characteristics of cardiovascular tweets, including characteristics of the source, content, and style that predict the retransmission of these tweets. We identified a random sample of 1,251 tweets associated with CVD originating from the United States between 2009 and 2015. Automated coding was conducted on the affect values of the tweets as well as the presence/absence of any URL, mention of another user, question mark, exclamation mark, and hashtag. We hand-coded the tweets’ novelty, utility, theme, and source. The count of retweets was positively predicted by message utility, health organization source, and mention of user handle, but negatively predicted by the presence of URL and nonhealth organization source. Regarding theme, compared to the tweets focusing on risk factor, tweets on treatment and management predicted fewer retweets while supportive tweets predicted more retweets. These findings suggest opportunities for harnessing Twitter to better disseminate cardiovascular educational and supportive information on SNSs.
FGFR genes mutation is an independent prognostic factor and associated with lymph node metastasis in squamous non-small cell lung cancer

ABSTRACT Targeting FGFRs is one of the most promising therapeutic strategies in squamous non-small cell lung cancer (SQCC). However, different FGFR genomic aberrations can be associated with distinct biological characteristics that result in different clinical outcomes or therapeutic consequences. Currently, the full spectrum of FGFR gene aberrations and their clinical significance in SQCC have not been comprehensively studied. Here, we used Next-generation sequencing to investigate the presence of FGFR gene mutations in 143 tumors from patients with stage I, II or III SQCC and who had not been treated with chemotherapy or radiotherapy prior to surgery. FGFR gene mutations were identified in 24 cases, resulting in an overall frequency of 16.9%. Among the mutations, 7% (10/143) were somatic mutations, and 9.8% (14/143) germline mutations. FGFR mutations were significantly associated with an increased risk of lymph node metastasis. SQCC patients with a FGFR somatic mutation had shorter OS (overall survival, log rank P = 0.005) and DFS (disease-free survival，log rank P = 0.004) compared with those without an FGFR mutation. The multivariate analysis confirmed that a somatic mutation was an independent poor prognostic factor for OS (HR: 4.26, 95% CI: 1.49–12.16, P = 0.007) and DFS (HR: 3.16, 95% CI: 1.20–8.35, P = 0.020). Our data indicate that FGFR genes mutation is an independent prognostic factor and associated with lymph node metastasis in stage I to III Chinese SQCC patients.
SoK: Shining Light on Shadow Stacks

Control-Flow Hijacking attacks are the dominant attack vector against C/C++ programs. Control-Flow Integrity (CFI) solutions mitigate these attacks on the forward edge, i.e., indirect calls through function pointers and virtual calls. Protecting the backward edge is left to stack canaries, which are easily bypassed through information leaks. Shadow Stacks are a fully precise mechanism for protecting backwards edges, and should be deployed with CFI mitigations. We present a comprehensive analysis of all possible shadow stack mechanisms along three axes: performance, compatibil- ity, and security. For performance comparisons we use SPEC CPU2006, while security and compatibility are qualitatively analyzed. Based on our study, we renew calls for a shadow stack design that leverages a dedicated register, resulting in low performance overhead, and minimal memory overhead, but sacrifices compatibility. We present case studies of our implementation of such a design, Shadesmar, on Phoronix and Apache to demonstrate the feasibility of dedicating a general purpose register to a security monitor on modern architectures, and Shadesmar’s deployability. Our comprehensive analysis, including detailed case studies for our novel design, allows compiler designers and practitioners to select the correct shadow stack design for different usage scenarios. Shadow stacks belong to the class of defense mechanisms that require metadata about the program’s state to enforce their defense policies. Protecting this metadata for deployed mitigations requires in-process isolation of a segment of the virtual address space. Prior work on defenses in this class has relied on information hiding to protect metadata. We show that stronger guarantees are possible by repurposing two new Intel x86 extensions for memory protection (MPX), and page table control (MPK). Building on our isolation efforts with MPX and MPK, we present the design requirements for a dedicated hardware mechanism to support intra-process memory isolation, and discuss how such a mechanism can empower the next wave of highly precise software security mitigations that rely on partially isolated information in a process.
Whisper: read sorting allows robust mapping of DNA sequencing data

MOTIVATION Mapping reads to a reference genome is often the first step in a sequencing data analysis pipeline. The reduction of sequencing costs implies a need for algorithms able to process increasing amounts of generated data in reasonable time. RESULTS We present Whisper, an accurate and high-performant mapping tool, based on the idea of sorting reads and then mapping them against suffix arrays for the reference genome and its reverse complement. Employing task and data parallelism as well as storing temporary data on disk result in superior time efficiency at reasonable memory requirements. Whisper excels at large NGS read collections, in particular Illumina reads with typical WGS coverage. The experiments with real data indicate that our solution works in about 15% of the time needed by the well-known BWA-MEM and Bowtie2 tools at a comparable accuracy, validated in a variant calling pipeline. AVAILABILITY AND IMPLEMENTATION Whisper is available for free from https://github.com/refresh-bio/Whisper or http://sun.aei. polsl.pl/REFRESH/Whisper/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Modelling the Behavior of Lighting Systems Controlled at a Constant Level of Illuminance

The paper deals with the issue of the dimming of lighting systems of the artificial lighting controlled to a constant level of illuminance based on contributions of daylight. It solves the issue of differences, which arise when setting the existing lighting systems without daylight and their subsequent operation in dimming to a constant illuminance level with the presence of daylight. This issue is addressed in the paper by means of modelling the illuminance systems of the artificial lighting and CIE overcast sky producing different illuminance of an outdoor, unscreened surface. The modelling took place based on the contributions of the equally cloudy sky to the interior. The article analyses the influence of the location and reception characteristics of the light sensor on the course of illuminance and the uniformity by solving the interior spaces at various levels of outdoor lighting. Primarily, the simplest types of lighting systems dimmed as a whole based on the input of one illuminance sensor were modelled there.
Preparation of Graphite Oxide Containing Different Oxygen-Containing Functional Groups and the Study of Ammonia Gas Sensitivity

A series of graphite oxide samples were prepared using the modified Hummers method. Flake graphite was used as the raw material and the reaction temperature of the aqueous solution was changed (0 °C, 30 °C, 50 °C, 60 °C, 70 °C, 80 °C, and 100 °C). X-ray diffraction, Fourier-transform infrared spectroscopy, Raman spectral analysis, X-ray photoelectron spectroscopy, and contact angle tests were performed to characterize the structure, chemical bonding, type, and content of oxygen-containing functional groups of the graphite oxide samples. The results showed that the type and content of each oxygen-containing functional group could be controlled by changing the reaction temperature with the addition of water. As the temperature of the system increased, the degree of oxidation of the graphite oxide samples first increased and then decreased. Too high a temperature (100 °C) of the system led to the formation of epoxy groups by the decomposition of some hydroxyl groups in the samples, causing the reduction of oxygen-containing functional groups between the graphite layers, poor hydrophilic properties, and low moisture content. When the system temperature was 50 °C, the interlayer spacing of the graphite oxide samples was at its highest, the graphite was completely oxidized (C/O = 1.85), and the oxygen-containing functional groups were mainly composed of hydroxyl groups (accounting for approximately 28.88% of the total oxygen-containing functional groups). The high content of hydroxyl and carboxyl groups had good hydrophilic ability and showed the highest moisture content. The sample at 50 °C had better sensitivity to ammonia because of its high hydroxyl group and carboxyl group content, with the sample showing an excellent profile when the ammonia concentration was 20–60 ppm.
Occupational Risk Prevention through Smartwatches: Precision and Uncertainty Effects of the Built-In Accelerometer

Wearable technology has had a significant growth in the last years; this is particularly true of smartwatches, due to their potential advantages and ease of use. These smart devices integrate sensors that can be potentially used within industrial settings and for several applications, such as safety, monitoring, and the identification of occupational risks. The accelerometer is one of the main sensors integrated into these devices. However, several studies have identified that sensors integrated into smart devices may present inaccuracies during data acquisition, which may influence the performance of their potential applications. This article presents an analysis from the metrological point of view to characterize the amplitude and frequency response of the integrated accelerometers in three currently available commercial smartwatches, and it also includes an analysis of the uncertainties associated with these measurements by adapting the procedures described in several International Organization for Standardization (ISO) standards. The results show that despite the technical limitations produced by the factory configuration, these devices can be used in various applications related to occupational risk assessment. Opportunities for improvement have also been identified, which will allow us to take advantage of this technology in several innovative applications within industrial settings and, in particular, for occupational health purposes.
CT of Gastric Volvulus: Interobserver Reliability, Radiologists' Accuracy, and Imaging Findings.

OBJECTIVE The objective of this study was to identify CT findings and determine interobserver reliability of surgically proven gastric volvulus. MATERIALS AND METHODS This single-center retrospective study included 30 patients (21 women, nine men; mean age, 73 years old) with surgically proven gastric volvulus who underwent preoperative CT and 31 age- and sex-matched control subjects (21 women, nine men; mean age, 74 years old) with large hiatal hernias who were imaged for reasons other than abdominal pain. Two blinded radiologists reviewed the CT images and recorded findings of organoaxial and mesenteroaxial gastric volvulus and ischemia. Interobserver reliability, reader accuracy, sensitivity, specificity, and likelihood ratios of each CT finding were calculated. RESULTS The radiologists were overall 90% accurate (55/61; six false-negatives per reader) in identifying gastric volvulus. Interobserver agreement was substantial (κ = 0.71) for identifying the presence or absence of gastric volvulus. Agreement for most CT findings of gastric volvulus (11/14, 79%) was excellent (5/14, 36%) or substantial (6/14, 43%); the remaining findings showed moderate agreement (3/14, 21%). The most frequent and sensitive CT findings of volvulus with high positive likelihood ratios were stenosis at the hernia neck (reader 1, sensitivity = 80%, positive likelihood ratio = 26.66; reader 2, sensitivity = 77%, positive likelihood ratio = 12.83) and transition point at the pylorus (reader 1, sensitivity = 80%, positive likelihood ratio = 17; reader 2, sensitivity = 70%, positive likelihood ratio = 15). The presence of perigastric fluid or a pleural effusion were significantly more frequent in patients with ischemia at surgical pathology (p < 0.05 in all comparisons, both radiologists). CONCLUSION In our series, CT showed substantial interobserver agreement and fair accuracy in identifying the presence of gastric volvulus.
Trends, in Diagnosis and Treatment of Polycystic Ovarian Syndrome by Specialty.

OBJECTIVE To identify trends in the diagnostic work- up of polycystic ovarian syndrome (PCOS) performed by specialists in general medicine, endocrinology, and gynecology. STUDY DESIGN Ret- rospective electronic chart review of adolescents and young women whose workup for PCOS was initiated by specialists in endocrinology, general medicine, or gyne- cology. RESULTS Of 530 charts reviewed, 84 patients quali- fied for inclusion. Approximately two-thirds of patients seen by generalists and endocrinologists had lipid test- ing done; no gynecologist in this study ordered lipid tests. Cortisol levels and markers of congenital adrenal hyperplasia were more often ordered for patients seen by endocrinologists than for those seen by generalists or gynecologists. There was no significant difference among specialties in the use of diagnostic criteria for PCOS, including menstrual irregularity, hyperandrogenism, ovarian imaging, or exclusion of other etiologies. Women seen by endocrinologists tended to be prescribed met- formin more often; however, there was no significant difference in the use of hormonal contraceptives, piogli- tazone, and spironolactone among specialties. CONCLUSION Across 3 clinical practice specialties commonly evaluating menstrual irregularity and/or hirsutism in young women, patients were consistently diagnosed with PCOS based on appropriate, clinically- accepted criteria. However, no patients seen by gyne- cologists received lipid test- ing, which is considered an important screening study for cardiovascular disease risk in this population.
The spread of bovine tuberculosis in Canadian shared pastures: Data, model, and simulations

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is a chronic disease typical of cattle. Nonetheless, it can affect many mammals including humans, making it one of the most widespread zoonotic diseases worldwide. In industrialized countries, the main pathways of introduction of bTB into a herd are animal trade and contact with infected wildlife. In addition, for slow-spreading diseases with a long latent period such as bTB, shared seasonal pastures might be a between-herd transmission pathway, indeed farmers might unknowingly send infected animals to the pasture, since clinical signs are rarely evident in early infection. In this study, we developed a dynamic stochastic model to represent the spread of bTB in pastures. This was tailored to Canadian cow-calf herds, as we calibrated the model with data sourced from a recent bTB outbreak in Western Canada. We built a model for a herd with seasonal management, characterized by its partition into a group staying in the main facility and the remaining group(s) moving to summer pastures. We used this model to estimate the time of the first introduction of bTB into the herd. Furthermore, we expanded the model to include herds categorized as high-risk contacts with the index herd, in order to estimate the potential for disease spread on shared pastures. Finally, we explored two control scenarios to be applied to high-risk farms after the outbreak detection. Our results showed that the first introduction likely happened 3 to 5 years prior to the detection of the index herd, and the probability of bTB spreading in pastures was low, but not negligible. Nevertheless, the surveillance system currently in place was effective to detect potential outbreaks.