Miracle-dz/UniFAR-FTUs huggingface dataset:
Shotgun label‐free proteomic analysis for identification of proteins in HaCaT human skin keratinocytes regulated by the administration of collagen from soft‐shelled turtle

Abstract Soft‐shelled turtles (Pelodiscus sinensis) are widely distributed in some Asian countries, and we previously reported that soft‐shelled turtle tissue could be a useful material for collagen. In the present study, we performed shotgun liquid chromatography (LC)/mass spectrometry (MS)‐based global proteomic analysis of collagen‐administered human keratinocytes to examine the functional effects of collagen from soft‐shelled turtle on human skin. Using a semiquantitative method based on spectral counting, we were able to successfully identify 187 proteins with expression levels that were changed more than twofold by the administration of collagen from soft‐shelled turtle. Based on Gene Ontology analysis, the functions of these proteins closely correlated with cell–cell adhesion. In addition, epithelial–mesenchymal transition was induced by the administration of collagen from soft‐shelled turtle through the down‐regulation of E‐cadherin expression. Moreover, collagen‐administered keratinocytes significantly facilitated wound healing compared with nontreated cells in an in vitro scratch wound healing assay. These findings suggest that collagen from soft‐shelled turtle provides significant benefits for skin wound healing and may be a useful material for pharmaceuticals and medical care products. © 2017 The Authors Journal of Biomedical Materials Research Part B: Applied Biomaterials Published by Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 2403–2413, 2018.
Smart Home Networking: Lessons from Combining Wireless and Powerline Networking

Integrating the power grid technology with renewable power generation technologies, Demand Response (DR) programs enabled by the Advanced Metering Infrastructure (AMI) were introduced into the power grid in the interest of both utilities and residents. They help to achieve load balance and increase the grid reliability by encouraging residents to reduce their power usage during peak load periods in return for incentives. To automate this process, appliances, in-house sensors, and the AMI controller need to be networked together. In this paper, we compare mainstream network technologies applicable to home appliance control and propose a solution combining Power Line Communication (PLC) with wireless communication in smart homes for the purpose of energy saving. We extended NS-2, a popular network simulator, to model such combined network scenarios. Using a number of different routing strategies, we then model and evaluate the network performance of DR programs in smart homes in such a combined network.
Correctness results for on-line robust principal components analysis

This work studies two interrelated problems online robust PCA (RPCA) and online lowrank matrix completion (MC). In recent work by Candès et al., RPCA has been defined as a problem of separating a low-rank matrix (true data), L := [`1, `2, . `t, . , `tmax ] and a sparse matrix (outliers), S := [x1, x2, . xt, . , xtmax ] from their sum, M := L + S. Our work uses this definition of RPCA. An important application where both these problems occur is in video analytics in trying to separate sparse foregrounds (e.g., moving objects) and slowly changing backgrounds. While there has been a large amount of recent work on both developing and analyzing batch RPCA and batch MC algorithms, the online problem is largely open. In this work, we develop a practical modification of our recently proposed algorithm to solve both the online RPCA and online MC problems. The main contribution of this work is that we obtain correctness results for the proposed algorithms under mild assumptions. The assumptions that we need are: (a) a good estimate of the initial subspace is available (easy to obtain using a short sequence of background-only frames in video surveillance); (b) the `t’s obey a ‘slow subspace change’ assumption; (c) the basis vectors for the subspace from which `t is generated are dense (nonsparse); (d) the support of xt changes by at least a certain amount at least every so often; and (e) algorithm parameters are appropriately set.
A Third-Order Sliding-Mode Controller for a Stepper Motor

This paper deals with the robust control problem of a stepper motor subject to parameter uncertainties and load torque perturbation. The developed algorithm is based on third-order sliding-mode control such that a desired angular motor position is accurately tracked. The proposed scheme requires the measurement or the estimation of the motor speed and acceleration for feedback. To avoid the use of tachometers and accelerometers which add cost and energy consumption, a robust second-order sliding-mode observer is presented. Experimental results illustrate the performance and the advantages of the proposed controller.
Get5 Carboxyl-terminal Domain Is a Novel Dimerization Motif That Tethers an Extended Get4/Get5 Complex*

Background: The Get4/Get5 protein complex is a homodimer mediated by the Get5 carboxyl domain. Results: The Get5 homodimerization motif forms a structurally conserved helical domain allowing Get4/Get5 to adopt an extended solution conformation. Conclusion: Get5 homodimerization is mediated by a 35-residue sequence stabilized by a few conserved hydrophobic interactions. Significance: The Get5 carboxyl domain contains a novel example of a stable dimerization motif. Tail-anchored trans-membrane proteins are targeted to membranes post-translationally. The proteins Get4 and Get5 form an obligate complex that catalyzes the transfer of tail-anchored proteins destined to the endoplasmic reticulum from Sgt2 to the cytosolic targeting factor Get3. Get5 forms a homodimer mediated by its carboxyl domain. We show here that a conserved motif exists within the carboxyl domain. A high resolution crystal structure and solution NMR structures of this motif reveal a novel and stable helical dimerization domain. We additionally determined a solution NMR structure of a divergent fungal homolog, and comparison of these structures allows annotation of specific stabilizing interactions. Using solution x-ray scattering and the structures of all folded domains, we present a model of the full-length Get4/Get5 complex.
Mutation-based testing of concurrent programs

Mutation-based software testing is a powerful technique for testing software systems. It requires executing many slightly different versions of the same program to evaluate the quality of the test cases used to test the program. Mutation-based testing has been applied to sequential software; however, problems are encountered when it is applied to concurrent programs. These problems are a product of the nondeterminism inherent in the executions of concurrent programs. In this paper, we describe a general approach to testing and debugging concurrent programs, called deterministic execution testing and debugging. We then describe a combination of deterministic execution testing and mutation-based testing, called deterministic execution mutation testing (DEMT), and illustrate the DEMT approach with an example. <<ETX>>
Harvesting Low Ambient RF-Sources for Autonomous Measurement Systems

This paper presents a concept for rectifying low ambient radiation sources to supply autonomous measurement systems like microsystems. Among an analytic computation and nonlinear simulation of the rectifier circuit with ADS (Advanced Design System), the circuit was built and the efficiency factor of the RF-Harvesting system was measured. A radiation source with the power of 1 muWatt (-30 dBm) and an impedance of 50 Ohm at 300 MHz was used. By well matching of the impedance and a resonance circuit transformation with a high quality factor in front of a Schottky-Diode a passive charge pump with the factor of 25 was realized.
Kinetic Analysis of the Interaction of Actin-depolymerizing Factor (ADF)/Cofilin with G- and F-Actins

The thermodynamics and kinetics of actin interaction with Arabidopsis thalianaactin-depolymerizing factor (ADF)1, human ADF, and S6D mutant ADF1 protein mimicking phosphorylated (inactive) ADF are examined comparatively. ADFs interact with ADP·G-actin in rapid equilibrium (k + = 155 μm −1·s−1 andk − = 16 s−1 at 4 °C under physiological ionic conditions). The kinetics of interaction of plant and human ADFs with F-actin are slower and exhibit kinetic cooperativity, consistent with a scheme in which the initial binding of ADF to two adjacent subunits of the filament nucleates a structural change that propagates along the filament, allowing faster binding of ADF in a “zipper” mode. ADF binds in a non-cooperative faster process to gelsolin-capped filaments or to subtilisin-cleaved F-actin, which are structurally different from standard filaments (Orlova, A., Prochniewicz, E., and Egelman, E. H. (1995) J. Mol. Biol. 245, 598–607). In contrast, the binding of phalloidin to F-actin cooperatively inhibits its interaction with ADF. The ADF-facilitated nucleation of ADP·actin self-assembly indicates that ADF stabilizes lateral interactions in the filament. Plant and human ADFs cause only partial depolymerization of F-actin at pH 8, consistent with identical functions in enhancing F-actin dynamics. Phosphorylation does not affect ADF activity per se, but decreases its affinity for actin by 20-fold.
Study on K-anonymity Models of Sharing Medical Information

Today's globally networked society places great demand on sharing of information. Chinese Medical industry is undergoing a drastic Informationization process while privacy concerns arise. This paper discusses the threatening due to information share in medical industry, especially in a well-informatinized society. We first thoroughly describe the present situation of China Medical informatization level and explain the necessity of cross-organizational information share. The specific problem called linking attack is illustrated. We also formulated a corresponding anonymity model and exemplified the Generalization and Suppression techniques it utilizes to preserve privacy. Then we give an overview of present research areas and classical algorithms. Next, more detailed attacking conditions and the characteristic of medical information are taking into consideration. We formulated a Modified Entropy 1-diversity model which was an extension of the basic k-anonymity. Finally, we look forward to possible future researches.
The effects of divided attention on speech motor, verbal fluency, and manual task performance.

PURPOSE The goal of this study was to evaluate aspects of the functional distance hypothesis, which predicts that tasks regulated by brain networks in closer anatomic proximity will interfere more with each other than tasks controlled by spatially distant regions. Speech, verbal fluency, and manual motor tasks were examined to ascertain whether right-handed activity would interfere more with speech and language performance because of the presumed greater demands on the left hemisphere. METHOD Twenty young adults completed a speech task (repeating a sentence), a verbal fluency task (listing words beginning with the same letter), and right- and left-handed motor tasks (placing pegs and washers in a pegboard) in isolation and concurrently. RESULTS Speech kinematic data showed that during concurrent performance of manual tasks, lip displacement and peak velocity decreased, whereas sound pressure level increased. Spatiotemporal variability increased when the nondominant hand was used for a motor task. Manual motor scores significantly decreased when concurrently performed with the verbal fluency task but not with sentence repetition. CONCLUSION These findings suggest that the control of concurrent tasks may be more complex than is predicted by the functional distance hypothesis.
Assessment of Clinical Impact in the Application of Chang Attenuation Correction to Lung Ventilation/Perfusion SPECT

The presence of a highly nonuniform distribution of attenuating tissues in the thorax may lead to attenuation artifacts and inaccuracies in reconstructed lung ventilation/perfusion SPECT images. The Chang algorithm is an easily applicable and accessible method of attenuation correction. The advantages inherent in the technique prompted us to evaluate the effect of using Chang attenuation correction on the quality of lung SPECT images and the clinical impact on interpretation. Methods: Lung scintigraphy started with planar and SPECT ventilation scans using 81mKr. A few minutes after the ventilation scintigraphy, planar and SPECT perfusion studies using 99mTc-macroaggregated albumin were performed. The Chang algorithm was applied for attenuation correction. Afterward, standard SPECT processing was performed on the images, leading to images in the horizontal, coronal, and sagittal planes. The same studies were also processed to the same planes without application of attenuation correction. Finally, all scintigraphic images were reviewed by 2 nuclear medicine academic clinicians, and a final diagnosis was reached by consensus, categorizing the studies into 3 groups—normal, low/intermediate, and high probability—for pulmonary embolism. Results: The study included 45 patients (16 men and 29 women) with a mean age of 50.0 y. Between the 2 noncorrected and attenuation-corrected readings, 16 diagnoses remained the same. However, after attenuation correction, 13 patients were moved to lower categories (i.e., from high probability to normal or low/intermediate probability or from low/intermediate probability to normal) and 16 patients were moved to higher categories (i.e., from low/intermediate probability to high probability or from normal to low/intermediate or high probability). The difference between noncorrected and attenuation-corrected readings was statistically significant (P < 0.01). Conclusion: After attenuation correction, subjective image quality and sharpness improved, leading in some cases to increased confidence on the part of the readers. The Chang attenuation correction method may have the potential to be considered as an alternative approach toward attenuation correction in those situations in which the additional radiation burden of CT is not acceptable.
Feline calicivirus as a model system for heat inactivation studies of small round structured viruses in shellfish

Commercial heat treatment procedures for molluscan shellfish are based on data obtained for the inactivation of hepatitis A virus (HAV) in cockles. However, the most frequently reported illness associated with consumption of bivalve molluscs is gastroenteritis caused by small round structured viruses (SRSVs) of the Norwalk group. Conditions for inactivation of SRSVs are unknown. In this study a feline calicivirus was used as a model for the SRSV group and conditions for its heat inactivation determined. Experiments showed that feline calicivirus is more readily inactivated in shellfish than HAV, and confirmed that current heating recommendations to the UK shellfish industry are adequate. A reverse transcription polymerase chain reaction (RT-PCR) assay for the detection of calicivirus in shellfish was developed and results compared with isolation in cell culture. The RT-PCR detected virus in some samples that failed to yield virus on culture. This has important implications if molecular virology techniques are to be used in the design and monitoring of shellfish treatment procedures and for routine testing of food samples.
Reassociation method based on top trading cycles for WLANs: Mechanism design approach

This paper proposes the flexible reassociation control scheme for wireless local area networks (WLANs) based on mechanism design theory. The notion of general preference in the theory enables us to formulate users' various kinds of preference (based on such as high throughput and/or low latency). The proposed scheme is guaranteed to provide a unique allocation of access points (APs) to STAs in each step with individual rationality and Pareto-optimality, so that no STA gets associated with a less preferable AP, and no allocation exists which is more preferable to all STAs. In addition, the iterative algorithm is adopted so that the proposed scheme is applicable to the case where each AP associates multiple STAs, while the original algorithm in the theory is not applicable to the case. The remarkable idea is that each AP trades a STA that has the poorest communication quality in some sense among STAs associated with the AP. Simulation results confirm the proposed scheme keeps the individual rationality and performs the throughput improvement with fairness.
Microcapsules formulated in the enteric coating copolymer Eudragit L100 as delivery systems for oral vaccination against infections by gastrointestinal nematode parasites

Microcapsules using the copolymer of methacrylic acid (Eudragit L100) were formulated for oral delivery of vaccines against the enteral/parenteral nematode parasite Trichinella spiralis. Antigenic preparations from first stage larvae (L1) of T. spiralis were microencapsulated in Eudragit L100. The microcapsules prepared by the spray drying method were resistant to acid pH, although the antigen was rapidly released under neutral and basic environmental conditions. The native protein conformation and biological activity was preserved in the microcapsules, as assessed by SDS-PAGE and ELISA. When administered to NIH mice, the antigen loaded microcapsules protected against infection by T. spiralis at both the intestinal and muscular levels, the worm burden diminishing by 45.58 and 53.33%, respectively. Furthermore, following administration of the microparticles an increase of the serum IgG1 response, a marker for the Th2 type response, was evident. These results indicate that microcapsules formulated with anionic biocompatible polymers such as Eudragit may be useful for oral vaccination against nematode infections.
Incidence and patterns of late recurrences in colon cancer patients

Long‐term recurrences of colon cancer raised questions about the possible benefit of prolonging the recommended active 5‐year surveillance. The aim of this study was to determine, for the first time, the incidence and patterns of late 10‐year recurrence following curative resection of colon cancer. Data were obtained from two French digestive cancer registries. A total of 3,622 patients under 85 years resected for cure for colon cancer diagnosed between 1985 and 2000 were included. Information regarding recurrences was actively collected. Cumulative failure rates at 10 years were estimated using Kaplan–Meier estimates corrected by cause‐specific hazards, and multivariable analysis was performed using a model for the subdistribution of a competing risk proposed by Fine and Gray. The overall cumulative recurrence rate between 5 and 10 years after initial surgery was 2.9% for local recurrence and 4.3% for distant metastasis. Among men with no recurrence 5 years after diagnosis of colon cancer, 1 in 12 developed a recurrence between 5 and 10 years, and the corresponding cumulative rate was 7.8%. The frequency was 1 in 19 for women, corresponding to a cumulative rate of 5.2%. In the multivariate analysis, non‐emergency diagnostic feature, female sex and age under 75 were associated with a lower risk of recurrence. Stage at diagnosis was not a predictor of late recurrence. Late recurrence after colon cancer resection with curative intent can occur. A regular clinical follow‐up is necessary to detect early signs of possible recurrence.
Effects of the inverter parameters on the eddy current losses in induction motor fed by PWM inverter

Pulse width modulation (PWM) inverters are widely applied to control motors. It will often increase the eddy current losses in the motors. In this paper, the authors deal with the effects of eddy current losses with amplitude modulation and switching frequency in an induction motor fed by PWM Inverter. The method is employed by a time-stepping finite element analysis (FEA). The FEA model of motor is coupled to an inverter circuit model, in order to analyze the effects of the inverter parameters on the eddy current losses.
Twenty-year follow-up of a randomized study comparing breast-conserving surgery with radical mastectomy for early breast cancer.

BACKGROUND We conducted 20 years of follow-up of women enrolled in a randomized trial to compare the efficacy of radical (Halsted) mastectomy with that of breast-conserving surgery. METHODS From 1973 to 1980, 701 women with breast cancers measuring no more than 2 cm in diameter were randomly assigned to undergo radical mastectomy (349 patients) or breast-conserving surgery (quadrantectomy) followed by radiotherapy to the ipsilateral mammary tissue (352 patients). After 1976, patients in both groups who had positive axillary nodes also received adjuvant chemotherapy with cyclophosphamide, methotrexate, and fluorouracil. RESULTS Thirty women in the group that underwent breast-conserving therapy had a recurrence of tumor in the same breast, whereas eight women in the radical-mastectomy group had local recurrences (P<0.001). The crude cumulative incidence of these events was 8.8 percent and 2.3 percent, respectively, after 20 years. In contrast, there was no significant difference between the two groups in the rates of contralateral-breast carcinomas, distant metastases, or second primary cancers. After a median follow-up of 20 years, the rate of death from all causes was 41.7 percent in the group that underwent breast-conserving surgery and 41.2 percent in the radical-mastectomy group (P=1.0). The respective rates of death from breast cancer were 26.1 percent and 24.3 percent (P=0.8). CONCLUSIONS The long-term survival rate among women who undergo breast-conserving surgery is the same as that among women who undergo radical mastectomy. Breast-conserving surgery is therefore the treatment of choice for women with relatively small breast cancers.
Evidence That Silencing of the HPRT Promoter by DNA Methylation Is Mediated by Critical CpG Sites*

The strong correlation between promoter hypermethylation and gene silencing suggests that promoter methylation represses transcription. To identify methylation sites that may be critical for maintaining repression of the human HPRT gene, we treated human/hamster hybrid cells containing an inactive human X chromosome with the DNA demethylating agent 5-azadeoxycytidine (5aCdr), and we then examined the high resolution methylation pattern of theHPRT promoter in single cell-derived lines. Reactivation ofHPRT correlated with complete promoter demethylation. In contrast, the 61 5aCdr-treated clones that failed to reactivateHPRT exhibited sporadic promoter demethylation. However, three specific CpG sites remained methylated in all unreactivated clones, suggesting these sites may be critical for maintaining transcriptional silencing of the HPRT gene. Re-treatment of partially demethylated (and unreactivated) clones with a second round of 5aCdr did not increase the frequency of HPRTreactivation. This is consistent with mechanisms of methylation-mediated repression requiring methylation at specific critical sites and argues against models invoking overall levels or a threshold of promoter methylation. Treatment of cells with the histone deacetylase inhibitor, trichostatin A, failed to reactivateHPRT on the inactive X chromosome, even when the promoter was partially demethylated by 5aCdr treatment, suggesting that transcriptional repression by DNA methylation is unlikely to depend upon a trichostatin A-sensitive histone deacetylase.