Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitochondrial Mutations in Adenoid Cystic Carcinoma of the Salivary Glands

Background The MitoChip v2.0 resequencing array is an array-based technique allowing for accurate and complete sequencing of the mitochondrial genome. No studies have investigated mitochondrial mutation in salivary gland adenoid cystic carcinomas. Methodology The entire mitochondrial genome of 22 salivary gland adenoid cystic carcinomas (ACC) of salivary glands and matched leukocyte DNA was sequenced to determine the frequency and distribution of mitochondrial mutations in ACC tumors. Principal Findings Seventeen of 22 ACCs (77%) carried mitochondrial mutations, ranging in number from 1 to 37 mutations. A disproportionate number of mutations occurred in the D-loop. Twelve of 17 tumors (70.6%) carried mutations resulting in amino acid changes of translated proteins. Nine of 17 tumors (52.9%) with a mutation carried an amino acid changing mutation in the nicotinamide adenine dinucleotide dehydrogenase (NADH) complex. Conclusions/Significance Mitochondrial mutation is frequent in salivary ACCs. The high incidence of amino acid changing mutations implicates alterations in aerobic respiration in ACC carcinogenesis. D-loop mutations are of unclear significance, but may be associated with alterations in transcription or replication.
RETAIN: An Interpretable Predictive Model for Healthcare using Reverse Time Attention Mechanism

Accuracy and interpretability are two dominant features of successful predictive models. Typically, a choice must be made in favor of complex black box models such as recurrent neural networks (RNN) for accuracy versus less accurate but more interpretable traditional models such as logistic regression. This tradeoff poses challenges in medicine where both accuracy and interpretability are important. We addressed this challenge by developing the REverse Time AttentIoN model (RETAIN) for application to Electronic Health Records (EHR) data. RETAIN achieves high accuracy while remaining clinically interpretable and is based on a two-level neural attention model that detects influential past visits and significant clinical variables within those visits (e.g. key diagnoses). RETAIN mimics physician practice by attending the EHR data in a reverse time order so that recent clinical visits are likely to receive higher attention. RETAIN was tested on a large health system EHR dataset with 14 million visits completed by 263K patients over an 8 year period and demonstrated predictive accuracy and computational scalability comparable to state-of-the-art methods such as RNN, and ease of interpretability comparable to traditional models.
An Improved Data Representation for Smoking Detection with Wearable Respiration Sensors

This paper proposes a peak-based representation for smoking detection from RIP data as a more robust alternative to the existing segmentation-based representation. The rational for preferring this approach in the presence of noise is that there is much less uncertainty about the location of the peaks in the RIP data than there is about the location of segmentation boundaries. To implement this approach, we first run a peak detection algorithm on the RIP waveform data to extract the peaks (maximum inhalation) and valleys (maximum exhalation) from the input time series. We then extract feature vectors analogous to those used in the segmentation case [1], but defined using relative locations and amplitudes of peaks and valleys. We associate puff (positive) and non-puff (negative) labels with peaks, and learn a classification model to predict the peak labels given the associated feature vectors.
Connecting Phrase based Statistical Machine Translation Adaptation

Although more additional corpora are now available for Statistical Machine Translation (SMT), only the ones which belong to the same or similar domains of the original corpus can indeed enhance SMT performance directly. A series of SMT adaptation methods have been proposed to select these similar-domain data, and most of them focus on sentence selection. In comparison, phrase is a smaller and more fine grained unit for data selection, therefore we propose a straightforward and efficient connecting phrase based adaptation method, which is applied to both bilingual phrase pair and monolingual n-gram adaptation. The proposed method is evaluated on IWSLT/NIST data sets, and the results show that phrase based SMT performances are significantly improved (up to +1.6 in comparison with phrase based SMT baseline system and +0.9 in comparison with existing methods).
Climbing the smalltalk mountain

Part of the promise of object-oriented software technology - and much of the fascination with objected-orientedness -- stems from its psychological implications. Thinking in terms of objects sending and responding to messages is supposed to be more "natural" than thinking of various data structures being operated on by generic procedures. Programming by using or specializing existent objects and their methods is supposed to make code reuse accessible even to beginners.
Mining specifications of malicious behavior

Malware detectors require a specification of maliciousbehavior. Typically, these specifications are manually constructedby investigating known malware. We present an automatic technique to overcome this laborious manual process. Our technique derives such a specification by comparing the execution behavior of a known malware against the execution behaviors of a set of benign programs. In other words, we mine the malicious behavior present in a known malware that is not present in a set of benign programs. The output of our algorithm can be used by malware detectors to detect malware variants. Since our algorithm provides a succinct description of malicious behavior present in a malware, it can also be used by security analysts for understanding the malware. We have implemented a prototype based on our algorithm and tested it on several malware programs. Experimental results obtained from our prototype indicate that our algorithm is effective in extracting malicious behaviors that can be used to detect malware variants
A New Record of Pseudallescheria boydii Isolated from Crop Field Soil in Korea

Abstract Pseudallescheria boydii KNU13-2 was isolated from crop field soil and identified by analysis of internal transcribed spacer regions of rDNA and morphological characteristics. In the literature, P. boydii has been mentioned as a human pathogen. This is the first record of P. boydii isolated from crop field soil in Korea.
MediaBrain: Annotating Videos based on Brain-Computer Interaction

Adding notes to time segments on a video timeline makes it easier to search, find, and playback important segments of the video. Various approaches have been explored to annotate videos (semi) automatically to summarize videos. In this research we investigate the feasibility of implicitly annotating videos based on brain signals retrieved from a Brain-Computer Interface (BCI) headset. The signals provided by the BCI can reveal different information such as brain activities, facial expressions, or the level of users’ excitement. This information correlates with scenes the users watch in a video. Thus, it can be used for annotating a video and automatically generating a summary. To achieve the goal, an annotation tool called MediaBrain is developed and a user study is conducted. The result reveals that it is possible to annotate a video and select a set of highlights based on the excitement information.
Small inductive safe invariants

Computing minimal (or even just small) certificates is a central problem in automated reasoning and, in particular, in automated formal verification. For example, Minimal Unsatisfiable Subsets (MUSes) have a wide range of applications in verification ranging from abstraction and generalization to vacuity detection and more. In this paper, we study the problem of computing minimal certificates for safety properties. In this setting, a certificate is a set of clauses Inυ such that each clause contains initial states, and their conjunction is safe (no bad states) and inductive. A certificate is minimal, if no subset of Inυ is safe and inductive. We propose a two-tiered approach for computing a Minimal Safe Inductive Subset (MSIS) of Inv. The first tier is two efficient approximation algorithms that under-and over-approximate MSIS, respectively. The second tier is an optimized reduction from MSIS to a sequence of computations of Maximal Inductive Subsets (MIS). We evaluate our approach on the HWMCC benchmarks and certificates produced by our variant of IC3. We show that our approach is several orders of magnitude more effective than the naive reduction of MSIS to MIS.
Partitioning Effects during Terminal Carbon and Electron Flow in Sediments of a Low-Salinity Meltwater Pond near Bratina Island, McMurdo Ice Shelf, Antarctica

ABSTRACT A study of anaerobic sediments below cyanobacterial mats of a low-salinity meltwater pond called Orange Pond on the McMurdo Ice Shelf at temperatures simulating those in the summer season (<5°C) revealed that both sulfate reduction and methane production were important terminal anaerobic processes. Addition of [2-14C]acetate to sediment samples resulted in the passage of label mainly to CO2. Acetate addition (0 to 27 mM) had little effect on methanogenesis (a 1.1-fold increase), and while the rate of acetate dissimilation was greater than the rate of methane production (6.4 nmol cm−3 h−1compared to 2.5 to 6 nmol cm−3 h−1), the portion of methane production attributed to acetate cleavage was <2%. Substantial increases in the methane production rate were observed with H2 (2.4-fold), and H2 uptake was totally accounted for by methane production under physiological conditions. Formate also stimulated methane production (twofold), presumably through H2 release mediated through hydrogen lyase. Addition of sulfate up to 50-fold the natural levels in the sediment (interstitial concentration, ∼0.3 mM) did not substantially inhibit methanogenesis, but the process was inhibited by 50-fold chloride (36 mM). No net rate of methane oxidation was observed when sediments were incubated anaerobically, and denitrification rates were substantially lower than rates for sulfate reduction and methanogenesis. The results indicate that carbon flow from acetate is coupled mainly to sulfate reduction and that methane is largely generated from H2 and CO2 where chloride, but not sulfate, has a modulating role. Rates of methanogenesis at in situ temperatures were four- to fivefold less than maximal rates found at 20°C.
Visual odometry for the Autonomous City Explorer

The goal of the autonomous city explorer (ACE) is to navigate autonomously, efficiently and safely in an unpredictable and unstructured urban environment. To achieve this aim, an accurate localization is one of the preconditions. Due to the characteristics of our navigation environment, an elaborated visual odometry system is proposed to estimate the current position and orientation of the ACE platform. The existing algorithms of optical flow computation are experimentally evaluated and compared. The method based on pyramidal Lucas-Kanade algorithm with high-speed performance is selected. Based on the optical flow in 2D images, the camera ego-motion is estimated using image Jacobian matrix and least squares method. The kinematic model is set up to map the camera ego-motion to the robot motion. To eliminate systematic errors, a novel system calibration approach is proposed. Finally the odometry system is evaluated in experiments.
Atlantic Warming Since the Little Ice Age

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Elevated C-reactive protein in atherosclerosis--chicken or egg?

One of the most debated topics in cardiovascular medicine is whether C-reactive protein (CRP), a component of the acute-phase response, is a causal factor in the pathogenesis of atherosclerosis.1,2 If it is, the implications could be far-reaching and include new approaches for the prevention and treatment of myocardial infarction and stroke.3 Support for a role of CRP in the pathogenesis of atherosclerosis comes largely from epidemiologic studies that have consistently observed an association between elevated plasma CRP levels and cardiovascular events.1,4,5 The statistical strength of such associations is at least as robust as that of established risk .
Linear Transformations for Randomness Extraction

Information-efficient approaches for extracting ran- domness from imperfect sources have been extensively studied, but simpler and faster ones are required in the high-speed ap- plications of random number generation. In this paper, we focus on linear constructions, namely, applying linear transformation for randomness extraction. We show that linear transformations based on sparse random matrices are asymptotically optimal to extract randomness from independent sources and bit-fixi ng sources, and they are efficient (may not be optimal) to extrac t randomness from hidden Markov sources. Further study demon- strates the flexibility of such constructions on source mode ls as well as their excellent information-preserving capabilities. Since linear transformations based on sparse random matrices are computationally fast and can be easy to implement using hardware like FPGAs, they are very attractive in the high-speed applications. In addition, we explore explicit constructi ons of transformation matrices. We show that the generator matrices of primitive BCH codes are good choices, but linear transformations based on such matrices require more computational time due to their high densities.
Comparative Assessment of Biological and Fisheries Productivity of Caspian Sturgeons Species

Based on the model describing the dynamics of the number of generations of fish during the life cycle, the influence of growth and maturity on the biological and commercial productivity of conditional populations of Caspian sturgeon, formed from 1.0 million specimens of yearlings, was studied. On the biomass of conditional sturgeon populations, their gross output and catch are influenced by the length of yearlings, the size and age of maturity, the periodicity of spawning, the rate of linear and weight growth of individuals, and the degree of stocks catching. The highest yield of biomass and catch, obtained from 1 million yearlings, is observed in Beluga ( Huso huso ) , then Ship Sturgeon ( Acipenser nudiventris ), Russian sturgeon ( Acipenser gueldenstaedtii ), Stellate Sturgeon ( Acipenser stellatus ) and sterlet ( Acipenser ruthenus ).
Local polynomial regression for symmetric positive definite matrices

Summary. Local polynomial regression has received extensive attention for the non‐parametric estimation of regression functions when both the response and the covariate are in Euclidean space. However, little has been done when the response is in a Riemannian manifold. We develop an intrinsic local polynomial regression estimate for the analysis of symmetric positive definite matrices as responses that lie in a Riemannian manifold with covariate in Euclidean space. The primary motivation and application of the methodology proposed is in computer vision and medical imaging. We examine two commonly used metrics, including the trace metric and the log‐Euclidean metric on the space of symmetric positive definite matrices. For each metric, we develop a cross‐validation bandwidth selection method, derive the asymptotic bias, variance and normality of the intrinsic local constant and local linear estimators, and compare their asymptotic mean‐square errors. Simulation studies are further used to compare the estimators under the two metrics and to examine their finite sample performance. We use our method to detect diagnostic differences between diffusion tensors along fibre tracts in a study of human immunodeficiency virus.
Perceptual and physical space of vowel sounds.

Experiments were carried out to investigate the correlation between the perceptual and physical space of 11 vowel sounds. The signals were single periods out of the constant vowel part of normally spoken words of the type h (vowel) t, generated continuously by computer. Pitch, loudness, onset, and duration were equalized. These signals were presented to 15 subjects in a triadic‐comparison procedure, resulting in a cumulative similarity matrix. Multidimensional scaling (Kruskal) of this matrix resulted in a three‐dimensional perceptual space with 1.6% stress. The signals were also analyzed physically with 13‐oct band filters. Principal‐components analysis of the decibel values per frequency band indicated that three dimensions accounted for 81.7% of the total variance. Matching the perceptual and the physical configurations to maximal congruence yielded an excellent result with correlation coefficients of 0.992, 0.971, and 0.742 along the corresponding dimensions. The formant frequencies and levels were co.
PDS: An I/O-Efficient Scaling Scheme for Parity Declustered Data Layout

Parity declustering is widely deployed in erasure coded storage systems so as to provide fast recovery and high data availability. However, to perform scaling on such RAIDs, it is necessary to preserve the parity declustered data layout so as to guarantee the RAID performance after scaling. Unfortunately, existing scaling algorithms fail to achieve this goal so they can not be applied for scaling RAIDs which have deployed parity declustering. To address this challenge, we develop an efficient scaling algorithm called PDS (Parity Declustering Scaling). In particular, we first employ an auxiliary Balanced Incomplete Block Design (BIBD) to define the data migrations during scaling so as to preserve parity declustered data layout, and then define the addressing algorithm in the scaled system based on the migrations. We provide theoretical proofs to show that PDS preserves the parity declustered data layout, which is the basis for scaling RAIDs with parity declustering, and also theoretically prove that PDS achieves the even distribution of data/parity blocks after scaling and requires only the minimal data migrations. To show the performance of PDS, we implement it in MD in Linux Kernel, and conduct experiments with real-world traces. Results show PDS can reduce 89.70% of data migration time and 24.44% of user response time during scaling on average, compared with the round-robin scheme.
Cardiomyocyte Death Induced by Myocardial Ischemia and Reperfusion: Measurement With Recombinant Human Annexin-V in a Mouse Model

IntroductionPhosphatidylserine (PS) externalization is regarded as one of the earliest hallmarks of cells undergoing programmed cell death. We studied the use of labeled human recombinant annexin-V, a protein selectively binding to PS, to detect cardiomyocyte death in an in vivo mouse model of cardiac ischemia and reperfusion (I/R). Methods and ResultsI/R was induced in mouse hearts by ligation and subsequent release of a suture around the left anterior descending coronary artery. Annexin-V (25 mg/kg) fused to a marker molecule was injected intra-arterially 30 minutes before euthanasia. After 15 minutes of ischemia followed by 30 minutes of reperfusion, 1.4±1.2% (mean±SD) of the cardiomyocytes in the area at risk were annexin-V positive (n=6). This increased to 11.4±1.9% after 15 minutes of ischemia followed by 90 minutes of reperfusion (n=7) and to 20.2±3.3% after 30 minutes of ischemia followed by 90 minutes of reperfusion (n=7). In control mice, including those injected with annexin-V at the binding site of PS, no annexin-V–positive cells were observed. DNA gel electrophoresis showed typical laddering starting after 15 minutes of ischemia followed by 30 minutes of reperfusion, suggesting activation of the cell death program. Intervention in the cell death program by pretreatment with a novel Na+-H+ exchange inhibitor substantially decreased annexin-V–positive cardiomyocytes from 20.2% to 2.2% in mice after 30 minutes of ischemia followed by 90 minutes of reperfusion. ConclusionsThese data suggest that labeled annexin-V is useful for in situ detection of cell death in an in vivo model of I/R in the heart and for the evaluation of cell death–blocking strategies.
Lock Your Robot: A Review of Locking Devices in Robotics

Locking devices are widely used in robotics, for instance to lock springs and joints or to reconfigure robots. This review article classifies the locking devices currently described in the literature and performs a comparative study. Designers can therefore better determine which locking device best matches the needs of their application. The locking devices are divided into three main categories based on different locking principles: 1) mechanical locking, 2) friction-based locking, and 3) singularity locking. Different locking devices in each category can be passive or active. Based on an extensive literature survey, this article summarizes the findings by comparing different locking devices on a set of properties of an ideal locking device.