Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of surrogate markers of impending death in the galactosamine-sensitized murine model of bacterial endotoxemia.

BACKGROUND AND PURPOSE When evaluating vaccines for efficacy against gram-negative endotoxemia, the challenge has historically required death of a large percentage of test subjects. We attempted to identify surrogate markers of impending death to allow for early euthanasia without interfering with experimental data collection. METHODS Galactosamine-sensitized mice (n = 140) were inoculated intraperitoneally with various dosages of endotoxin, and development of clinical signs of disease--body temperature, body weight, hunched posture, ruffled coat, inability to ambulate, and loss of consciousness--was evaluated. RESULTS Wide fluctuations in body temperature (+/- 4 degrees C) were observed in survivors and nonsurvivors. Posture, coat, and body weight were not accurate predictors of death. Only inability to ambulate, with a positive predictive value of 100% (11 of 11), accurately predicted death in the experimental mice of this study. CONCLUSION Using this surrogate marker, loss of ability to ambulate, 11 of 13 mice that developed this sign could have been euthanized early, preventing anywhere from 2 to 22 h of potential distress prior to death.
FPGA-based CNN inference accelerator synthesized from multi-threaded C software

A deep-learning inference accelerator is synthesized from a C-language software program parallelized with Pthreads. The software implementation uses the well-known producer/consumer model with parallel threads interconnected by FIFO queues. The LegUp high-level synthesis (HLS) [1] tool synthesizes threads into parallel FPGA hardware, translating software parallelism into spatial parallelism. A complete system is generated where convolution, pooling and padding are realized in the synthesized accelerator, with remaining tasks executing on an embedded ARM processor. The accelerator incorporates reduced precision, and a novel approach for zero-weight-skipping in convolution. On a mid-sized Intel Arria 10 SoC FPGA, peak performance on VGG-16 is 138 effective GOPS.
Delay testing for non-robust untestable circuits

Recently published results have shown that, for many circuits, only a small percentage of path delay faults is robust testable. Among the robust untestable faults, a significant percentage of them is not non-robust testable either. In this paper, we take a closer look at the properties of these non-robust untestable faults with the goal of determining whether and how these faults should be tested. <<ETX>>
On the Synthesis of Finite-State Machines from Samples of Their Behavior

The Nerode realization technique for synthesizing finite-state machines from their associated right-invariant equivalence relations is modified to give a method for synthesizing machines from finite subsets of their input-output behavior. The synthesis procedure includes a parameter that one may adjust to obtain machines that represent the desired behavior with varying degrees of accuracy and that consequently have varying complexities. We discuss some of the uses of the method, including an application to a sequential learning problem.
Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails.

Department of Biochemistry and Biophysics, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina 27599-7295, USA; Howard Hughes Medical Institute, Division of Nucleic Acids Enzymology, Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
The design and implementation of a log-structured file system

This paper presents a new technique for disk storage management called a log-structured file system. A log-structured file system writes all modifications to disk sequentially in a log-like structure, thereby speeding up both file writing and crash recovery. The log is the only structure on disk; it contains indexing information so that files can be read back from the log efficiently. In order to maintain large free areas on disk for fast writing, we divide the log into segments and use a segment cleaner to compress the live information from heavily fragmented segments. We present a series of simulations that demonstrate the efficiency of a simple cleaning policy based on cost and benefit. We have implemented a prototype log-structured file system called Sprite LFS; it outperforms current Unix file systems by an order of magnitude for small-file writes while matching or exceeding Unix performance for reads and large writes. Even when the overhead for cleaning is included, Sprite LFS can use 70% of the disk bandwidth for writing, whereas Unix file systems typically can use only 5--10%.
Inhibitory effect of adenine nucleotides and anti‐allergic drugs on phosphorylation of phosphatidylinositol in rat mast cell granules

Rat mast cell granules were obtained by sonication of highly purified rat mast cells and isolated in a Percoll gradient. Phosphorylation of endogenous phosphatidylinositol in rat mast cell granules, which is catalyzed by phosphatidylinositol kinase in the granules, was assayed by measuring the incorporation of 32P from [γ32P]ATP into phosphatidylinositol 4‐phosphate. Lipids were isolated with methanol/chloroform/HCl and were separated by thin‐layer chromatography on oxalic acid impregnated silica gel plates. Phosphatidylinositol 4‐phosphate areas were identified by staining with iodine, scraped and measured for 32P radioactivity. The phosphorylation reaction was inhibited by 50–500 μM adenosine, ADP and 500 μM AMP in a concentration‐dependent manner. Among several antiallergic drugs investigated, 100±1000 μM theophylline and 10±100 μM azelastine inhibited the phosphorylation reaction, but disodium cromoglycate and ketotifen had littel effect.
Molecular basis of the redox regulation of SUMO proteases: a protective mechanism of intermolecular disulfide linkage against irreversible sulfhydryl oxidation

Sumoylation has emerged as an indispensable post‐translational modification that modulates the functions of a broad spectrum of proteins. Recent studies have demonstrated that reactive oxygen species influence the equilibrium of sumoylation‐desumoylation. We show herein that H2O2 induces formation of an intermolecular disulfide linkage of human SUMO protease SENP1 via the active‐site Cys 603 and a unique residue Cys 613. Such reversible modification confers a higher recovery of enzyme activity, which is also observed in yeast Ulp1, but not in human SENP2, suggesting its protective role against irreversible sulfhydryl oxidation. In vivo formation of a disulfide‐linked dimer of SENP1 is also detected in cultured cells in response to oxidative stress. The modifications are further elucidated by the crystal structures of Ulp1 with the catalytic cysteine oxidized to sulfenic, sulfinic, and sulfonic acids. Our findings suggest that, in addition to SUMO conjugating enzymes, SUMO proteases may act as redox sensors and effectors modulating the des‐umoylation pathway and specific cellular responses to oxidative stress. — Xu, Z. , Lam, L. S. M. , Lam, L. H. , Chau, S. F. , Ng, T. B. , Au, S. W. N. Molecular basis of the redox regulation of SUMO proteases: a protective mechanism of intermolecular disulfide linkage against irreversible sulfhydryl oxidation. FASEB J. 22, 127–137 (2008)
DigiNorthern, digital expression analysis of query genes based on ESTs

DigiNorthern (DN) is a web-based tool for virtually displaying expression profiles of query genes based on EST sequences. Two utilities are available: DN1 takes one query gene and quantitatively display its expression levels in tissues/organs that express the gene with comparison between normal and neoplastic status of each tissue; DN2 takes two sequences as query genes and compares their expression profiles side by side.
Modeling embryo survival affected by sediment deposition into salmonid spawning gravels: Application to flushing flow prescriptions

This paper presents a framework for predicting embryo survival in salmonid spawning gravels as a function of sediment deposition. This framework integrates three quantitative relationships modeling the variations of substrate permeability with sediment deposition, apparent velocity with substrate permeability, and embryo survival rate with apparent velocity. The model allows evaluation of the impacts of sediment deposition on embryo survival. The relative sensitivity of embryo survival to three selected environmental factors is investigated. The model results indicate that embryo survival is most sensitive to the composition of fine sediments (or sediment‐gravel size ratio). The maximum influences of the hydraulic pressure head and the length of intragravel flow path are ∼60 and 35% of the value influenced by size ratio. The proposed model is applied to determine the timing of flushing flows. The results suggest that the interval between flushing flows should be reduced when higher levels of embryo survival are prescribed or higher near‐bed sediment concentrations are imposed.
Factors that influence the success of a KM-program in a small-sized airport

Purpose – This paper aims to investigate the nature of what is referred to as the Knowledge Management Engineering & Maintenance Program, which is based on practices that influence the dissemination of knowledge in a structured and sustained manner within a small-sized airport. The air transport system has undergone important changes, particularly in the development of new knowledge management (KM) approaches. In practice, however, results have been mixed. Some programs have been successful, but implementation failures are common and the intended users are frequently reluctant to use such management structures. A possible explanation for efficiency and effectiveness gaps of services provided by these knowledge structures may relate to the advantages and disadvantages of the knowledge processes that airports highlight as a result of their differential structural properties. Design/methodology/approach – Using data collected from the Engineering & Maintenance Department at a Spanish Airport, this work has e.
A Multi-Modal System ICANDO: Intellectual Computer AssistaNt for Disabled Operators

The paper describes a multi-modal system ICANDO (an Intellectual Computer AssistaNt for Disabled Operators) developed by Speech Informatics Group of SPIIRAS and intended for assistance to the persons without hands or with disabilities of their hands or arms in human-computer interaction. This system combines the modules for automatic speech recognition and head tracking in one multi-modal system. The developed system was applied for hands-free work with Graphical User Interface of MS Windows in such tasks as Internet communication and work with text documents. The architecture of the system, the methods for recognition and tracking, information fusion and synchronization, experimental conditions and the obtained results are described in the paper.
Comparison of prevalence of periodontal disease in women with polycystic ovary syndrome and healthy controls

Background: Polycystic ovary syndrome (PCOS) is the most common endocrine disorder among women of reproductive age, affecting 4-18% of them. Previous studies also showed that periodontal diseases are associated with different components of the metabolic syndrome. The aim of this study is to determine the association between PCOS and periodontal diseases. Materials and Methods: A total of 196 women (98 with PCOS and 98 healthy controls) were enrolled. PCOS diagnosis was confirmed by history, clinical signs, physical examination, laboratory parameters, and ultrasound studies. Both cases and controls were examined by the same periodontist. Periodontal parameters including bleeding on probing (BOP), probing depth, clinical attachment loss (CAL), plaque index, and tooth loss were investigated in all participants. Pregnant women, smokers, individuals with a history of malignancy or osteoporosis, and those taking prophylactic antibiotics for dental procedures or receiving periodontal treatment during the 6-month period before examination were excluded. Data were analyzed using t-test, Chi-square test, and linear regression. Statistical significance was set at P < 0.05. Results: CAL and sites with BOP were significantly higher in women with PCOS (P < 0.05). However, no significant difference was observed in the tooth loss rate between PCOS and non-PCOS participants (P = 0.384). Conclusion: The prevalence of periodontal disease seems to be higher in women with PCOS. This may be related to the role of chronic systemic inflammation in the pathophysiology of both PCOS and periodontal diseases.
Pulsatile desynchronizing delayed feedback for closed-loop deep brain stimulation

High-frequency (HF) deep brain stimulation (DBS) is the gold standard for the treatment of medically refractory movement disorders like Parkinson’s disease, essential tremor, and dystonia, with a significant potential for application to other neurological diseases. The standard setup of HF DBS utilizes an open-loop stimulation protocol, where a permanent HF electrical pulse train is administered to the brain target areas irrespectively of the ongoing neuronal dynamics. Recent experimental and clinical studies demonstrate that a closed-loop, adaptive DBS might be superior to the open-loop setup. We here combine the notion of the adaptive high-frequency stimulation approach, that aims at delivering stimulation adapted to the extent of appropriately detected biomarkers, with specifically desynchronizing stimulation protocols. To this end, we extend the delayed feedback stimulation methods, which are intrinsically closed-loop techniques and specifically designed to desynchronize abnormal neuronal synchronization, to pulsatile electrical brain stimulation. We show that permanent pulsatile high-frequency stimulation subjected to an amplitude modulation by linear or nonlinear delayed feedback methods can effectively and robustly desynchronize a STN-GPe network of model neurons and suggest this approach for desynchronizing closed-loop DBS.
On improvement of accuracy of optimal voltage sag monitoring programmes

Selection of monitor locations is a key part of power systems voltage sag characterization utilizing limited monitoring data. In this paper, a technique of determining the optimal locations of monitors is proposed. It calculates the overall sag estimation accuracy to identify the best buses for sag monitoring. The technique can also be implemented to determine the sequence of monitor placement of already configured optimal monitoring programmes and to assess the effectiveness of sub-optimal monitor arrangements. The optimal monitoring scheme for a 295-bus generic distribution system (GDS) is determined using the proposed technique and its performance compared against monitoring schemes obtained with existing methods.
Helicobacter pylori arginase mutant colonizes arginase II knockout mice.

AIM To investigate the role of host and bacterial arginases in the colonization of mice by Helicobacter pylori (H. pylori). METHODS H. pylori produces a very powerful urease that hydrolyzes urea to carbon dioxide and ammonium, which neutralizes acid. Urease is absolutely essential to H. pylori pathogenesis; therefore, the urea substrate must be in ample supply for urease to work efficiently. The urea substrate is most likely provided by arginase activity, which hydrolyzes L-arginine to L-ornithine and urea. Previous work has demonstrated that H. pylori arginase is surprisingly not required for colonization of wild-type mice. Hence, another in vivo source of the critical urea substrate must exist. We hypothesized that the urea source was provided by host arginase II, since this enzyme is expressed in the stomach, and H. pylori has previously been shown to induce the expression of murine gastric arginase II. To test this hypothesis, wild-type and arginase (rocF) mutant H. pylori strain SS1 were inoculated into arginase II knockout mice. RESULTS Surprisingly, both the wild-type and rocF mutant bacteria still colonized arginase II knockout mice. Moreover, feeding arginase II knockout mice the host arginase inhibitor S-(2-boronoethyl)-L-cysteine (BEC), while inhibiting > 50% of the host arginase I activity in several tissues, did not block the ability of the rocF mutant H. pylori to colonize. In contrast, BEC poorly inhibited H. pylori arginase activity. CONCLUSION The in vivo source for the essential urea utilized by H. pylori urease is neither bacterial arginase nor host arginase II; instead, either residual host arginase I or agmatinase is probably responsible.
Retrospective Registration of PET and MR Brain Images: An Algorithm and Its Stereotactic Validation

Objective We present a validation study of an algorithm for retrospective registration of PET and MR brain images. Materials and Methods This algorithm involves two steps. In the first step, the two volumes are reformatted by aligning their interhemispheric fissure planes (midsagittal plane). In the second step, the corresponding planes parallel to the midsagittal plane are further aligned in the reformatted volumes to produce a 3D rigid body registration of the two original volumes. It is an efficient algorithm because both steps are performed in 2D spaces, and in each step only a small number of landmarks are required. A user-friendly system has been implemented to facilitate easy and fast processing of registration and reformatting of image volumes. The accuracy of this algorithm is validated using clinical scans of neurosurgical patients with a stereotaxic frame attached to their skull. The frame-based stereotaxic system provides an effective method for transforming image coordinates from different image volumes into a common coordinate system. This common coordinate system is used for assessing the spatial correspondence of each pixel in the registered image volumes. Validation using the stereotaxic image volumes enables objective estimation of retrospective registration accuracy. Results Analysis of 11 MR/PET image pairs indicates that our registration method not only is efficient but also provides adequate accuracy for most clinical evaluation of PET studies. Conclusion We have implemented and validated an efficient algorithm for retrospective registration of PET and MR brain images.
Reduction of Nonspecific Background Staining in the Fluorescent Treponemal Antibody-Absorption Test

The nonspecific background fluorescence which occurs with the fluorescent treponemal antibody-absorption test for syphilis was found to result from a reaction between serum-treated Treponema pallidum organisms and the conjugated antihuman γ-globulin. It was also shown that β-lipoprotein and albumin were the important contributing factors in human serum. Various dilutions of 2.5% trypsin in phosphate-buffered saline specifically reduced background fluorescence under proper test conditions. By employing a trypsin digestion method, a semiautomated procedure utilizing a visual readout has been postulated as feasible.
The Impact of Data Quality Information on Decision Making: An Exploratory Analysis

This paper describes an experiment that explores the consequences of providing information regarding the quality of data used in decision making. The subjects in the study were given three types of information about the data's quality: none, two-point ordinal, and interval scale. This information was made available to the subjects, along with the actual data. Two decision strategies were explored: conjunctive and weighted linear additive. Two decision environments were used: a simple environment and a relatively complex environment. Various combinations of these factors were employed to explore several issues. These include complacency, consensus, and consistency. The paper provides preliminary insights into which type of data-quality information is most effective and the circumstances in which data-quality information is most effective. Such knowledge would be of value to those responsible for designing databases that support decision-makers. Overall, we find that in a situation where subjects are confronted with clearly differentiated alternatives, the inclusion of data-quality information impacted the selection of the preferred alternative while maintaining group consensus.
Nucleotide sequence analysis of enteropathogenic Escherichia coli (EPEC) adherence factor probe and development of PCR for rapid detection of EPEC harboring virulence plasmids

The 1-kb BamHI-SalI fragment from plasmid pMAR2 termed the enteropathogenic Escherichia coli (EPEC) adherence factor (EAF) probe was cloned in pUC19 and pK18. The nucleotide sequence of this fragment was determined, and a set of primers was designed to amplify a 397-bp region associated with pMAR2 by PCR. An analysis of the whole EAF sequence with database libraries indicated no significant homology to any known genes. However, between bases 701 and 787 of the fragment, an 82.8% homology between the EAF and the insertion sequence IS630 of Shigella sonnei exists. The results of PCR with primers of the EAF sequence demonstrated that all of the 151 EAF probe-positive EPEC strains with localized adherence to HEp-2 cells yielded positive EAF PCR results. In contrast, none of the 277 EAF probe-negative strains reacted to the EAF PCR. In addition, the PCR assay was successfully used to generate vector-free digoxigenin-labeled EAF fragments that gave valid results in colony blot hybridization assays. The EAF PCR appears to be a specific and efficient method for the detection of EPEC strains carrying the EAF plasmids.
ESPACE: Accelerating Convolutional Neural Networks via Eliminating Spatial and Channel Redundancy

Recent years have witnessed an extensive popularity of convolutional neural networks (CNNs) in various computer vision and artificial intelligence applications. However, the performance gains have come at a cost of substantially intensive computation complexity, which prohibits its usage inresource-limited applications like mobile or embedded devices. While increasing attention has been paid to the acceleration of internal network structure, the redundancy of visual input is rarely considered. In this paper, we make the first attempt of reducing spatial and channel redundancy directly from the visual input for CNNs acceleration. The proposed method, termed ESPACE (Elimination of SPAtial and Channel rEdundancy), works by the following three steps: First, the 3D channel redundancy of convolutional layers is reduced by a set of low-rank approximation of convolutional filters. Second, a novel mask based selective processing scheme is proposed, which further speedups the convolution operations via skipping unsalient spatial locations of the visual input. Third, the accelerated network is fine-tuned using the training data via back-propagation. The proposed method is evaluated on ImageNet 2012 with implementations on two widely adopted CNNs, i.e. AlexNet and GoogLeNet. In comparison to several recent methods of CNN acceleration, the proposed scheme has demonstrated new state-of-the-art acceleration performance by a factor of 5.48* and 4.12* speedup on AlexNet and GoogLeNet, respectively, with a minimal decrease in classification accuracy.