Miracle-dz/UniFAR-FTUs huggingface dataset:
Elucidating the Activation Mechanism of AMPK by Direct Pan-Activator PF-739

Adenosine monophosphate-activated protein kinase (AMPK) is a key energy sensor regulating the cell metabolism in response to energy supply and demand. The evolutionary adaptation of AMPK to different tissues is accomplished through the expression of distinct isoforms that can form up to 12 heterotrimeric complexes, which exhibit notable differences in the sensitivity to direct activators. To comprehend the molecular factors of the activation mechanism of AMPK, we have assessed the changes in the structural and dynamical properties of β1- and β2-containing AMPK complexes formed upon binding to the pan-activator PF-739. The analysis revealed the molecular basis of the PF-739-mediated activation of AMPK and enabled us to identify distinctive features that may justify the slightly higher affinity towards the β1−isoform, such as the β1−Asn111 to β2−Asp111 substitution, which seems to be critical for modulating the dynamical sensitivity of β1- and β2 isoforms. The results are valuable in the design of selective activators to improve the tissue specificity of therapeutic treatment.
Speed and Endurance Do Not Trade Off in Phrynosomatid Lizards

Trade-offs are a common focus of study in evolutionary biology and in studies of locomotor physiology and biomechanics. A previous comparative study of 12 species of European lacertid lizards found a statistically significant negative correlation between residual locomotor speed and stamina (controlling for variation in body size), consistent with ideas about trade-offs in performance based on variation in muscle fiber type composition and other subordinate traits. To begin examining the generality of this finding in other groups of squamates, we measured maximal sprint running speed on a high-speed treadmill and endurance at 1.0 km/h (0.28 m/s) in 14 species of North American phrynosomatid lizards, plus a sample of nine additional species to encompass some of the broadscale diversity of lizards. We used both conventional and phylogenetically informed regression analyses to control for some known causes of performance variation (body size, stockiness, body temperature) and then computed residual performance values. We found no evidence for a trade-off between speed and endurance among the 14 phrynosomatids or among the 23 species in the extended data set. Possible explanations for the apparent difference between lacertids and phrynosomatids are discussed.
Modifiable Walking Pattern of a Humanoid Robot by Using Allowable ZMP Variation

In order to handle complex navigational commands, this paper proposes a novel algorithm that can modify a walking period and a step length in both sagittal and lateral planes. By allowing a variation of zero moment point (ZMP) over the convex hull of foot polygon, it is possible to change the center of mass (CM) position and velocity independently throughout the single support phase. This permits a range of dynamic walking motion, which is not achievable using the 3-D linear inverted pendulum mode (3D-LIPM). In addition, the proposed algorithm enables to determine the dynamic feasibility of desired motion via the construction of feasible region, which is explicitly computed from the current CM state with simple ZMP functions. Moreover, adopting the closed-form functions makes it possible to calculate the algorithm in real time. The effectiveness of the proposed algorithm is demonstrated through both computer simulation and experiment on the humanoid robot, HanSaRam-VII, developed at the Robot Intelligence Technology (RIT) laboratory, Korea Advanced Institute of Science and Technology (KAIST).
Bcl-2 Is a Prognostic Marker in Breast Cancer Independently of the Nottingham Prognostic Index

Purpose: Prognostication of breast cancer using clinicopathologic variables, although useful, remains imperfect. Many reports suggest that gene expression profiling can refine the current approach. Alternatively, it has been shown that panels of proteins assessed by immunohistochemistry might also be useful in this regard. We evaluate the prognostic potential of a panel of markers by immunohistochemistry in a large case series to establish if either a single marker or a panel could improve the prognostic power of the Nottingham Prognostic Index (NPI). We validated the results in an independent series. Experimental Design and Results: The expression of 13 biomarkers was evaluated in 930 breast cancers on a tissue microarray. Eight markers [estrogen receptor (ER), progesterone receptor (PR), Bcl-2, cyclin E, p53, MIB-1, cytokeratin 5/6, and HER2] showed a significant association with survival at 10 years on univariate analysis. On multivariate analysis that included these eight markers and the NPI, only the NPI [hazard ratio (HR), 1.35; 95% confidence interval (95% CI), 1.16-1.56; P = 0.0005], ER (HR, 0.59; 95% CI, 0.39-0.88; P = 0.011), and Bcl-2 (HR, 0.68; 95% CI, 0.46-0.99; P = 0.055) were significant. In a subsequent multivariate analysis that included the NPI, ER, and Bcl-2, only Bcl-2 (HR, 0.62; 95% CI, 0.44-0.87; P = 0.006) remained independent of NPI (HR, 1.50; 95% CI, 1.16-1.56; P = 0.004). In addition, Bcl-2, used as a single marker, was more powerful than the use of a panel of markers. Based on these results, an independent series was used to validate the prognostic significance of Bcl-2. ER and PR were also evaluated in this validation series. Bcl-2 (HR, 0.83; 95% CI, 0.71-0.96; P = 0.018) retained prognostic significance independent of the NPI (HR, 2.04; 95% CI, 1.67-2.51; P < 0.001) with an effect that was maximal in the first 5 years. Conclusion: Bcl-2 is an independent predictor of breast cancer outcome and seems to be useful as a prognostic adjunct to the NPI, particularly in the first 5 years after diagnosis.
3,3′-Diindolylmethane inhibits the invasion and metastasis of nasopharyngeal carcinoma cells in vitro and in vivo by regulation of epithelial mesenchymal transition

Nasopharyngeal carcinoma (NPC) is characterized by silent progression and atypical early symptoms. Early metastasis to the neck lymph nodes is common. However, conventional chemoradiotherapy is limited and unable to effectively control cervical lymph node metastasis of NPC. In addition, toxicities caused by chemoradiotherapy often induce damage to normal tissues and organs. Thus, the aim of this study was to investigate the ability of 3,3′-diindolylmethane (DIM) to inhibit the invasion and metastasis of NPC cells in vitro and in vivo. The migration and invasive abilities of the 5–8F human NPC cell line were detected using a Transwell assay. Lymph node metastasis in nude mice was observed following the implantation of xenograft tumors for 8 weeks. In addition, western blot analysis was used to detect the expression levels of epithelial mesenchymal transition (EMT)-associated key proteins in NPC cells treated with DIM in vitro and in vivo. The results demonstrated that DIM effectively inhibited the migration and invasion of NPC cells in vitro and the effect was concentration-dependent. In addition, DIM significantly delayed and reduced the occurrence of lymph node metastasis in the animal model. The expression levels of a number of key proteins associated with EMT were affected by DIM treatment. In the animal model, there were no signs of toxicity in the vital organs, including the heart, liver and kidney, of animals fed a diet containing DIM. Therefore, the results of the present study indicate that DIM affects the expression levels of a number of EMT-associated key proteins and induces the inhibition of invasion and metastasis of NPC cells in vitro and in vivo.
Universally Composable Key-Evolving Signature

The standard digital signature scheme can be easily subject to key exposure problem In order to overcome this problem; a feasible and effective approach is employed by key-evolving signature scheme. In this paper, we study key-evolving signature within the UC framework and propose an appropriate ideal functionality that captures the basic security requirements of key-evolving signature. Then, we present a generic way to transform a key-evolving signature scheme into a real-life protocol. Finally, we show that UC definition of security is equivalent to previous definition of security which is termed as EUF-ACMA security.
The New Keynesian Dsge Model and Alternative Monetary Policy Rules in the Czech Republic

The paper deals with a comparison of alternative monetary policy rules also known as Taylor rules. First, a New Keynesian DSGE model is specifi ed. Results of this model are used as a benchmark. These results are obtained using Bayesian techniques. Bayesian techniques are used for both the estimation and the subsequent model comparison. The main experiment introduces three modifi cations to monetary policy rules. One specifies simple, Svensson and forward-looking monetary policy rules. The estimation is performed on Czech data and the period is from 2000Q1 to 2012Q3. Each specifi cation of the New Keynesian model contains the same observed variables, GDP growth and inflation. The estimation of the benchmark model contains an interesting output as a shock decomposition of both the observed variables. The main finding of this paper is that the parameter estimates of all the modifications of monetary policy rules are almost the same and the log data density looks very similar for all the specified models. On the other hand, a completely opposite conclusion may be derived from the results of the Bayesian comparison of the DSGE models. The key output is that a forward-looking monetary policy rule significantly improves the ability of the New Keynesian DSGE model to fit the observed data.
Aliso: a Journal of Systematic and Evolutionary Botany Recognition of Bromus Richardsonii and B. Ciliatus: Evidence from Morphology, Cytology, and Dna Fingerprinting (poaceae: Bromeae) Recognition of Bromus Richardsonii and B. Ciljatus: Evidence from Morphology, Cytology, and Dna Fingerprinting (poa

Sin ce our goa l was to dete rm ine character istic difference s betwee n Brom us richardsonii a nd B. cilia /us. a d iscr iminate analysis (DA), princ ipal components ana lysis (PC A), mult idimen s ional sca ling (M DS) , bivar iate ana lysis , and an amplified fragm ent len gth polym orphism s (AFL P) ana lys is were und ert ake n o n 93 herbar ium speci mens and 31 field-coll ec ted popul ation s. A cytologi ca l survey of B. cili a tus. B. richa rdsonii , a nd B. mu croglumis confirm previous rep ort s that the first spec ies is dipl oid (2n = 14) and the latter two are tetrapl oid (2 n = 28). All tax a we re co rrec tly c lassi fied in the DA and impo rta nt charac ters fo r each of the species were identified. Bromus rich ardson ii has lemmas with sca ttered hair s on the low er half between the mid nerve and margins [glabrous in B. cilia/US], anthers (1.2) 1.6-2.7 (3.4) mm lon g [(0.9) 1-1.4 (1.6) mm long in B. cilia/us], second glumes (7.8) 8.9-11.3 (13.2) mm lon g [(6.2) 7.1-8.5 (9.5) in B. cilia /us); and basal sheaths with den se, short to medium hairs [gl abr ou s or with lon g hairs in B. cilia /us]. The PCA easily separated B. cilia/US and B. richa rd-sonii into two we ll-de fined groups and MDS mirrored the principal components analysis but displ ayed mor e ove rlap of indivi dua ls between the two groups. The AFLP-derived UPGMA dendrogram se pa-rated 154 ind ividua ls into two d istinct c lusters, one consisting entirely of B. cilia/us individuals and the other co ns isting of B. richa rdso n ii individuals with six individuals of B. mucroglumis embedded within. Our study c lear ly ind icates that there are distinctive morphological, cytological , and ge netic differen ces to distin gui sh B. richa rdso nii and B. ciliarus as separate species. la parte baja entre el nervio medio y las mill-genes [glabra en B. cilia/us ]. 5) en B. ciliatusi ; y vaina basal con pelo den so , corto a medio [glabra 0 con pelo s largos en B. cilia/us). EI PCA separ6 facilrnente a B. cilia/us …
Extraction and Classification of Objects in Multispectral Images

Presented here is an algorithm that partitions a digitized multispectral image into parts that correspond to objects in the scene being sensed. The algorithm partitions an image into successively smaller rectangles and produces a partition that tends to minimize a criterion function. Supervised and unsupervised classification techniques can be applied to partitioned images. This partition-then-classify approach is used to process images sensed from aircraft and the ERTS-1 satellite, and the method is shown to give relatively accurate results in classifying agricultural areas and extracting urban areas.
Multilevel PWM methods at low modulation indices

When utilized at low amplitude modulation indices, existing multilevel carrier-based PWM strategies have no special provisions for this operating region, and several levels of the inverter go unused. This paper proposes some novel multilevel PWM strategies to take advantage of the multiple levels in both a diode-clamped inverter and a cascaded H-bridge inverter by utilizing all of the levels in the inverter even at low modulation indices. Simulation results show what effects the different strategies have on the active device utilization. A prototype 6-level diode-clamped inverter and an 11-level cascaded 11-bridge inverter have been built and controlled with the novel PWM strategies proposed in this paper.
1-Aminocyclopropane-1-Carboxylate Oxidase Induction in Tomato Flower Pedicel Phloem and Abscission Related Processes Are Differentially Sensitive to Ethylene

Ethylene has impact on several physiological plant processes, including abscission, during which plants shed both their vegetative and reproductive organs. Cell separation and programmed cell death are involved in abscission, and these have also been correlated with ethylene action. However, the detailed spatiotemporal pattern of the molecular events during abscission remains unknown. We examined the expression of two tomato ACO genes, LeACO1, and LeACO4 that encode the last enzyme in ethylene biosynthesis, 1-aminocyclopropane-1-carboxylate oxidase (ACO), together with the expression of other abscission-associated genes involved in cell separation and programmed cell death, during a period of 0–12 h after abscission induction in the tomato flower pedicel abscission zone and nearby tissues. In addition, we determined their localization in specific cell layers of the flower pedicel abscission zone and nearby tissues obtained by laser microdissection before and 8 h after abscission induction. The expression of both ACO genes was localized to the vascular tissues in the pedicel. While LeACO4 was more uniformly expressed in all examined cell layers, the main expression site of LeACO1 was in cell layers just outside the abscission zone in its proximal and distal part. We showed that after abscission induction, ACO1 protein was synthesized in phloem companion cells, in which it was localized mainly in the cytoplasm. Samples were additionally treated with 1-methylcyclopropene (1-MCP), a competitive inhibitor of ethylene actions, and analyzed 8 h after abscission induction. Cell-layer-specific changes in gene expression were observed together with the specific localization and ethylene sensitivity of the hallmarks of cell separation and programmed cell death. While treatment with 1-MCP prevented separation of cells through inhibition of the expression of polygalacturonases, which are the key enzymes involved in degradation of the middle lamella, this had less impact on the occurrence of different kinds of membrane vesicles and abscission-related programmed cell death. In the flower pedicel abscission zone, the physical progressions of cell separation and programmed cell death are perpendicular to each other and start in the vascular tissues.
Extraction of representative point from hand contour data based on laser range scanner for hand motion estimation

This paper shows a novel method to extract hand Representative Point (RP) based on 2-dimensional laser range scanner for hand motion estimation on projecting system. Image-projecting Desktop Arm Trainer (IDAT) is a projecting system for hand-eye coordination training, in which a projector displays an exercise screen on the desktop, and a laser range scanner detects trainee's hand motion. To realize multi-user HMI and expand more entertainment functions in IDAT system, an Air Hockey application was developed in which the hand RP requires a high precision. To generate hand RP precisely, we proposed our method in two parts to solve the data error problem and changeable hand contour problem. In part one, a data modifier is proposed and a sub-experiment is carried out to establish a modifying function for correcting sensor original data. In part two, we proposed three RP algorithms and carried out an evaluation experiment to estimate the reliability of three algorithms under different conditions. From the result, we get the most reliable algorithm corresponding to different situations in which the error of hand RP is less than 9.6 mm.
Mucosal B Cells Are Associated with Delayed SIV Acquisition in Vaccinated Female but Not Male Rhesus Macaques Following SIVmac251 Rectal Challenge

Many viral infections, including HIV, exhibit sex-based pathogenic differences. However, few studies have examined vaccine-related sex differences. We compared immunogenicity and protective efficacy of monomeric SIV gp120 with oligomeric SIV gp140 in a pre-clinical rhesus macaque study and explored a subsequent sex bias in vaccine outcome. Each immunization group (16 females, 8 males) was primed twice mucosally with replication-competent Ad-recombinants encoding SIVsmH4 env/rev, SIV239 gag and SIV239 nefΔ1–13 and boosted twice intramuscularly with SIVmac239 monomeric gp120 or oligomeric gp140 in MF59 adjuvant. Controls (7 females, 5 males) received empty Ad and MF59. Up to 9 weekly intrarectal challenges with low-dose SIVmac251 were administered until macaques became infected. We assessed vaccine-induced binding, neutralizing, and non-neutralizing antibodies, Env-specific memory B cells and plasmablasts/plasma cells (PB/PC) in bone marrow and rectal tissue, mucosal Env-specific antibodies, and Env-specific T-cells. Post-challenge, only one macaque (gp140-immunized) remained uninfected. However, SIV acquisition was significantly delayed in vaccinated females but not males, correlated with Env-specific IgA in rectal secretions, rectal Env-specific memory B cells, and PC in rectal tissue. These results extend previous correlations of mucosal antibodies and memory B cells with protective efficacy. The gp140 regimen was more immunogenic, stimulating elevated gp140 and cyclic V2 binding antibodies, ADCC and ADCP activities, bone marrow Env-specific PB/PC, and rectal gp140-specific IgG. However, immunization with gp120, the form of envelope immunogen used in RV144, the only vaccine trial to show some efficacy, provided more significant acquisition delay. Further over 40 weeks of follow-up, no gp120 immunized macaques met euthanasia criteria in contrast to 7 gp140-immunized and 2 control animals. Although males had higher binding antibodies than females, ADCC and ADCP activities were similar. The complex challenge outcomes may reflect differences in IgG subtypes, Fc glycosylation, Fc-R polymorphisms, and/or the microbiome, key areas for future studies. This first demonstration of a sex-difference in SIV vaccine-induced protection emphasizes the need for sex-balancing in vaccine trials. Our results highlight the importance of mucosal immunity and memory B cells at the SIV exposure site for protection.
A Study of Trimethylsilane (3MS) and Tetramethylsilane (4MS) Based α-SiCN:H/α-SiCO:H Diffusion Barrier Films

Amorphous nitrogen-doped silicon carbide (α-SiCN:H) films have been used as a Cu penetration diffusion barrier and interconnect etch stop layer in the below 90-nanometer ultra-large scale integration (ULSI) manufacturing technology. In this study, the etching stop layers were deposited by using trimethylsilane (3MS) or tetramethylsilane (4MS) with ammonia by plasma-enhanced chemical vapor deposition (PECVD) followed by a procedure for tetra-ethoxyl silane (TEOS) oxide. The depth profile of Cu distribution examined by second ion mass spectroscopy (SIMs) showed that 3MS α-SiCN:H exhibited a better barrier performance than the 4MS film, which was revealed by the Cu signal. The FTIR spectra also showed the intensity of Si-CH3 stretch mode in the α-SiCN:H film deposited by 3MS was higher than that deposited by 4MS. A novel multi structure of oxygen-doped silicon carbide (SiC:O) substituted TEOS oxide capped on 4MS α-SiC:N film was also examined. In addition to this, the new multi etch stop layers can be deposited together with the same tool which can thus eliminate the effect of the vacuum break and accompanying environmental contamination.
Association of the Myostatin Gene with Obesity, Abdominal Obesity and Low Lean Body Mass and in Non-Diabetic Asian Indians in North India

Background To determine the association of the A55T and K153R polymorphisms of the Myostatin gene with obesity, abdominal obesity and lean body mass (LBM) in Asian Indians in north India. Materials and Methods A total of 335 subjects (238 men and 97 women) were assessed for anthropometry, % body fat (BF), LBM and biochemical parameters. Associations of Myostatin gene polymorphisms were evaluated with anthropometric, body composition and biochemical parameters. In A55T polymorphism, BMI (p = 0.04), suprailiac skinfold (p = 0.05), total skinfold (p = 0.008), %BF (p = 0.002) and total fat mass (p = 0.003) were highest and % LBM (p = 0.03) and total LBM (Kg) were lowest (p = 0.04) in subjects with Thr/Thr genotype as compared to other genotypes. Association analysis of K153R polymorphism showed that subjects with R/R genotype had significantly higher BMI (p = 0.05), waist circumference (p = 0.04), %BF (p = 0.04) and total fat mass (p = 0.03), and lower %LBM (p = 0.02) and total LBM [(Kg), (p = 0.04)] as compared to other genotypes. Using a multivariate logistic regression model after adjusting for age and sex, subjects with Thr/Thr genotype of A55T showed high risk for high %BF (OR, 3.92, 95% Cl: 2.61–12.41), truncal subcutaneous adiposity (OR, 2.9, 95% Cl: 1.57–6.60)] and low LBM (OR, 0.64, 95% CI: 0.33–0.89) whereas R/R genotype of K153R showed high risk of obesity (BMI; OR, 3.2, 95% CI: 1.2–12.9; %BF, OR, 3.6, 95% CI: 1.04–12.4), abdominal obesity (OR, 2.12, 95% CI: 2.71–14.23) and low LBM (OR, 0.61, 95% CI: 0.29–0.79). Conclusions/Significance We report that variants of Myostatin gene predispose to obesity, abdominal obesity and low lean body mass in Asian Indians in north India.
Highly Coherent Pattern Identification Using Graph-based Clustering

This paper presents an enhanced graph based parameter independent clustering technique. The algorithm produces highly coherent clusters in terms of visual representation and cluster validity measures. The technique finds highly coherent patterns of genes having high biological relevance. The method was tested on four real life datasets and the results compared with those of other similar algorithms in terms of various quality measures and found to be significantly better.