Miracle-dz/UniFAR-FTUs huggingface dataset:
Distorted Relation between mRNA Copy Number and Corresponding Major Histocompatibility Complex Ligand Density on the Cell Surface*S

The major histocompatibility complex (MHC) presents peptides derived from degraded cellular proteins to T-cells and is thus crucial for triggering specific immune responses against viral infections or cancer. Up to now, there has been no evidence for a correlation between levels of mRNA (the “transcriptome”) and the density of MHC-peptide complexes (the “MHC ligandome”) on cells. Because such dependences are of intrinsic importance for the detailed understanding of translation efficiency and protein turnover and thus for systems biology in general and for tumor immunotherapy in practical application, we quantitatively analyzed the levels of mRNA and corresponding MHC ligand densities in samples of renal cell carcinomas and their autologous normal kidney tissues. Relative quantification was carried out by gene chip analysis and by stable isotope peptide labeling, respectively. In comparing more than 270 pairs of gene expression and corresponding peptide presentation ratios, we demonstrate that there is no clear correlation (r = 0.32) between mRNA levels and corresponding MHC peptide levels in renal cell carcinoma. A significant number of peptides presented predominantly on tumor or normal tissue showed no or only minor changes in mRNA expression levels. In several cases, peptides could even be identified despite the virtual absence of the respective mRNA. Thus we conclude that a majority of epitopes from tumor-associated antigens will not be found in approaches based mainly on mRNA expression studies as mRNA expression reflects a distorted picture of the situation on the cell surface as visible for T-cells.
Resveratrol Prevents the Prohypertrophic Effects of Oxidative Stress on LKB1

Background— Master regulators of protein synthesis such as mammalian target of rapamycin (mTOR) and p70S6 kinase contribute to left ventricular hypertrophy. These prohypertrophic pathways are modulated by a number of kinase cascades, including the hierarchical LKB1/AMP-activated protein kinase (AMPK) energy-sensing pathway. Because oxidative stress inhibits the LKB1/AMPK signaling axis to promote abnormal cell growth in cancer cells, we investigated whether oxidative stress associated with hypertension also results in the inhibition of this kinase circuit to contribute to left ventricular hypertrophy. Methods and Results— In the spontaneously hypertensive rat, a well-established genetic model of hypertension and subsequent cardiac hypertrophy, the development of left ventricular hypertrophy is associated with an increase in the electrophilic lipid peroxidation byproduct 4-hydroxy-2-nonenal (HNE). Using isolated cardiomyocytes, we show that elevated levels of HNE result in the formation of HNE-LKB1 adducts that inhibit LKB1 and subsequent AMPK activity. Consistent with inhibition of the LKB1/AMPK signaling pathway, the mTOR/p70S6 kinase system is activated, which is permissive for cardiac myocyte cell growth. Treatment of cardiomyocytes with resveratrol prevents HNE modification of the LKB1/AMPK signaling axis and blunts the prohypertrophic p70S6 kinase response. Furthermore, administration of resveratrol to spontaneously hypertensive rats results in increased AMPK phosphorylation and activity and reduced left ventricular hypertrophy. Conclusions— Our data identify a molecular mechanism in the cardiomyocyte involving the oxidative stress–derived lipid peroxidation byproduct HNE and the LKB1/AMPK signaling pathway that contributes to the development of left ventricular hypertrophy. We also suggest that resveratrol may be a potential therapy for patients at risk for developing pathological cardiac hypertrophy by preventing this prohypertrophic process.
A potassium transporter of the yeast Schwanniomyces occidentalis homologous to the Kup system of Escherichia coli has a high concentrative capacity.

The yeast Schwanniomyces occidentalis has a high‐affinity K+ uptake system with a high concentrative capacity, which is able to deplete the external K+ to < 0.03 microM. We have cloned the gene HAK1 of S.occidentalis which complements defective K+ uptake by trk1 and trk1 trk2 mutants of Saccharomyces cerevisiae. When HAK1 was expressed in a trk1 trk2 S.cerevisiae mutant, transport affinities for K+ and other alkali cations resembled those of S.occidentalis. The predicted amino acid sequence of the HAK1 protein shows significant homology with the hydrophobic region of the Kup transporter of Escherichia coli. In S.occidentalis HAK1 expresses in K(+)‐limiting conditions. Our data indicate that in K(+)‐starved cells the system encoded by HAK1 is the major K+ transporter of S.occidentalis.
An alternative to push, press, and tap-tap-tap: gesturing on an isometric joystick for mobile phone text entry

A gestural text entry method for mobile is presented. Unlike most mobile phone text entry methods, which rely on repeatedly pressing buttons, our gestural method uses an isometric joystick and the EdgeWrite alphabet to allow users to write by making letter-like "pressure strokes. " In a 15-session study comparing character-level EdgeWrite to Multitap, subjects' speeds were statistically indistinguishable, reaching about 10 WPM. In a second 15-session study comparing word-level EdgeWrite to T9, the same subjects were again statistically indistinguishable, reaching about 16 WPM. Uncorrected errors were low, around 1% or less for each method. In addition, subjective results favored EdgeWrite. Overall, results indicate that our isometric joystick-based method is highly competitive with two commercial keypad-based methods, opening the way for keypad-less designs and text entry on tiny devices. Additional results showed that a joystick on the back could be used at about 70% of the speed of the front, and the front joystick could be used eyes-free at about 80% of the speed of normal use.
Wheel Slip Control of EVs Based on Sliding Mode Technique With Conditional Integrators

This paper presents a new control system, based on field programmable gate array technology, targeting the powertrain control of multi-motor electric vehicles (EVs). The control chip builds around a reusable intellectual property core named propulsion control unit, which features motor control functions with field-orientation methods, and energy loss minimization of induction motors. In order to improve the EV safety, the control system was extended with a wheel slip controller based on the sliding mode framework. The robustness to parametric and modeling uncertainties is the main attraction in this design, thanks to a simple connection that was found between the driving torque request and the model uncertainty. To overcome the chattering issue, which arrives from the discontinuous nature of the sliding control, the conditional integrator approach was employed, enabling a smooth transition to a Proportional+Integral control law, with anti-windup, when the tire slip is close to the setpoint. The controller asymptotic stability and robustness was analytically investigated through the Lyapunov method. Experimental results, obtained with a multi-motor EV prototype under low grip conditions, demonstrate a good slip regulation and robustness to disturbances.
Phosphorylation of FOXP3 by LCK Downregulates MMP9 Expression and Represses Cell Invasion

Forkhead Box P3 (FOXP3) is a member of the forkhead/winged helix family of the transcription factors and plays an important role not only as a master gene in T-regulatory cells, but also as a tumor suppressor. In this study, we identified lymphocyte-specific protein tyrosine kinase (LCK), which correlates with cancer malignancy, as a binding partner of FOXP3. FOXP3 downregulated LCK-induced MMP9, SKP2, and VEGF-A expression. We observed that LCK phosphorylated Tyr-342 of FOXP3 by immunoprecipitation and in vitro kinase assay, and the replacement of Tyr-342 with phenylalanine (Y342F) abolished the ability to suppress MMP9 expression. Although FOXP3 decreased the invasive ability induced by LCK in MCF-7 cells, Y342F mutation in FOXP3 diminished this suppressive effect. Thus we demonstrate for the first time that LCK upregulates FOXP3 by tyrosine phosphorylation, resulting in decreased MMP9, SKP2, and VEGF-A expression, and suppressed cellular invasion. We consider that further clarification of transcriptional mechanism of FOXP3 may facilitate the development of novel therapeutic approaches to suppress cancer malignancy.
Turbulent drag effectiveness and shear stability of xanthan-gum-based graft copolymers

A number of graft copolymers of xanthan gum and polyacrylamide have been synthesized by grafting acrylamide onto xanthan gum using the ceric-ion-initiated solution polymerization technique. The effects of various synthesis parameters such as amount of catalyst, reaction time, and ratio of xanthan and acrylamide on drag reduction effectiveness of the graft copolymers have been studied. The scaling up of grafting reaction has been accomplished in 40-L reactor. The drag reduction effectiveness of the graft copolymers is investigated over a wide range of concentrations and Reynolds numbers. It is shown that the maximum drag reduction obtainable in xanthan gum solutions above 300 ppm can be obtained in solutions of graft copolymers at concentrations of 100–150 ppm. The grafting also improves the shear stability at higher Reynolds numbers. The shear stability of the graft copolymers at constant wall stress has been found to be superior to polyacrylamide and the mixtures of polyacrylamide and xanthan gum. In general, the shear stability of graft copolymers and polyacrylamide is shown to increase with concentration. The drag reduction characteristics and shear stability have been discussed in terms of structural features of the graft copolymers. The drag reduction characteristics of the graft copolymers are found to be similar to those of flexible polymers.
Who Thinks about the Competition? Managerial Ability and Strategic Entry in US Local Telephone Markets

This paper examines how manager and firm characteristics relate to entry decisions in US local telephone markets. To do so, it develops a structural econometric model that allows managers to be heterogeneous in their ability to correctly conjecture competitor behavior. The model adapts Camerer, Ho, and Chong’s (2004) Cognitive Hierarchy model to a real-world setting. We observe the industry in 1998, shortly after the Telecommunications Act of 1996 opened up the market. We find that older firms with older, more experienced managers have higher estimated levels of strategic ability. Managers with degrees in economics or business, and managers with graduate degrees, also have higher estimated levels of strategic ability. We find no evidence that university quality is related to ability. We repeat this exercise using data from 2000, 2002, and 2004. While the core results do not change, the overall level of measured strategic ability increases substantially by 2004. The estimates of strategic ability are also correlated with survival: those firms with lower estimated levels of ability are more likely to exit the industry early.
Underparameterized model of sequence evolution leads to bias in the estimation of diversification rates from molecular phylogenies.

"Las inferencias macroevolucionarias a partir de filogenias moleculares son cada vez mas comunes (ver Harvey et al., 1996; Mooers y Heard, 1997; Pagel, 1999; Barraclough y Nee, 2001). Muchos metodos en los que se invocan filogenias para la inferencia historica asumen que una filogenia molecular es una representacion sin errores de la historia filogenetica subyacente de los taxones incluidos (pero ver Lutzoni et al., 2001; Huelsenbeck et al., 2000; Huelsenbeck y Rannala, 2003 ). Sin embargo, las filogenias moleculares son estimaciones de esta historia basadas en un modelo particular de evolucion; asi, hay algo de Wagner, G. P. 1989b. El origen de los caracteres morfologicos y la base biologica de la homologia. Evolucion 43: 1157-1171. Wagner, G. P. y P. F. Stadler. 2003. Cuasi-independencia, homologia y unidad de tipo: una teoria topologica de caracteres. J. Theor. Biol. 220: 505–527. Wheeler, W. C. 1996. Optimizacion de alineacion: ? El final de la alineacion de multiples secuencias en filogenia? Cladistica 12: 1-10. Wheeler, W. C. y D. S. Gladstein. 1994. MALIGN: Un programa de alineacion de secuencias multiples. J. Hered. 85: 417–418. Wheeler, W. C. y R. L. Honeycutt. 1988. Diferencia de secuencia apareada en ARN ribosomales: implicaciones evolutivas y filogeneticas. Mol. Biol. Evol. 5: 90–96. Wiley, E. O. 1978. "
The reputational and social network benefits of prosociality in an Andean community

Significance Scientists have long debated how group cooperation can be maintained. From many standard evolutionary and economic perspectives, the best decision for an individual is to engage in free riding on the cooperation of others (i.e., share in the benefits but pay no costs). Such free riding, however, reduces the collective benefits of group cooperation and can unravel cooperation. Some propose that this “tragedy of the commons” can be solved if cooperators are compensated with reputational benefits. Our research in an Andean community found that cooperative households have better reputations for various qualities and have larger support networks, with the latter associated with healthier households. This finding supports the argument that positive reputations gained by cooperators can solve the tragedy of the commons. Several theories have emerged to explain how group cooperation (collective action) can arise and be maintained in the face of incentives to engage in free riding. Explanations focusing on reputational benefits and partner choice have particular promise for cases in which punishment is absent or insufficient to deter free riding. In indigenous communities of highland Peru, collective action is pervasive and provides critical benefits. Participation in collective action is unequal across households, but all households share its benefits. Importantly, investment in collective action involves considerable time, energy, and risk. Differential participation in collective action can convey information about qualities of fellow community members that are not easily observable otherwise, such as cooperative intent, knowledge, work ethic, skill, and/or physical vitality. Conveying such information may enhance access to adaptive support networks. Interview and observational data collected in a Peruvian highland community indicate that persons who contributed more to collective action had greater reputations as reliable, hard workers with regard to collective action and also were considered the most respected, influential, and generous people in the community. Additionally, household heads with greater reputations had more social support partners (measured as network indegree centrality), and households with larger support networks experienced fewer illness symptoms.
Organic-soluble chitosan/polyhydroxybutyrate ultrafine fibers as skin regeneration prepared by electrospinning

In the present contribution, the ultrafine fiber membranes of polyhydroxybutyrate (PHB) and organic-soluble chitosan(O-CS) was prepared by electrospinning. The structure and thermal stability were studied by infrared (FTIR) and thermogravimetric analysis (TG). The surface properties of ultrafine fibers were estimated by contact angle measurements using water. The morphology was observed by scanning electron microscopy (SEM). The cytotoxicity assessment with mouse fibroblast cells (L929) was also investigated. Cell culture results showed that it benefits promoting the cell attachment and proliferation. The results showed it could be as tissue engineering for skin regeneration. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
AN INCREASING STELLAR BARYON FRACTION IN BRIGHT GALAXIES AT HIGH REDSHIFT

Recent observations have shown that the characteristic luminosity of the rest-frame ultraviolet (UV) luminosity function does not significantly evolve at 4 < z < 7 and is approximately M UV * ∼ − 21 . > We investigate this apparent non-evolution by examining a sample of 173 bright, MUV < −21 galaxies at z = 4–7, analyzing their stellar populations and host halo masses. Including deep Spitzer/IRAC imaging to constrain the rest-frame optical light, we find that M UV * ? > galaxies at z = 4–7 have similar stellar masses of log(M/M⊙) = 9.6–9.9 and are thus relatively massive for these high redshifts. However, bright galaxies at z = 4–7 are less massive and have younger inferred ages than similarly bright galaxies at z = 2–3, even though the two populations have similar star formation rates and levels of dust attenuation for a fixed dust-attenuation curve. Matching the abundances of these bright z = 4–7 galaxies to halo mass functions from the Bolshoi ΛCDM simulation implies that the typical halo masses in ∼ M UV * ? > galaxies decrease from log(Mh/M⊙) = 11.9 at z = 4 to log(Mh/M⊙) = 11.4 at z = 7. Thus, although we are studying galaxies at a similar stellar mass across multiple redshifts, these galaxies live in lower mass halos at higher redshift. The stellar baryon fraction in ∼ M UV * ? > galaxies in units of the cosmic mean Ωb/Ωm rises from 5.1% at z = 4 to 11.7% at z = 7; this evolution is significant at the ∼3σ level. This rise does not agree with simple expectations of how galaxies grow, and implies that some effect, perhaps a diminishing efficiency of feedback, is allowing a higher fraction of available baryons to be converted into stars at high redshifts.
A Survey of Indoor Localization Systems and Technologies

Indoor localization has recently witnessed an increase in interest, due to the potential wide range of services it can provide by leveraging Internet of Things (IoT), and ubiquitous connectivity. Different techniques, wireless technologies and mechanisms have been proposed in the literature to provide indoor localization services in order to improve the services provided to the users. However, there is a lack of an up-to-date survey paper that incorporates some of the recently proposed accurate and reliable localization systems. In this paper, we aim to provide a detailed survey of different indoor localization techniques, such as angle of arrival (AoA), time of flight (ToF), return time of flight (RTOF), and received signal strength (RSS); based on technologies, such as WiFi, radio frequency identification device (RFID), ultra wideband (UWB), Bluetooth, and systems that have been proposed in the literature. This paper primarily discusses localization and positioning of human users and their devices. We highlight the strengths of the existing systems proposed in the literature. In contrast with the existing surveys, we also evaluate different systems from the perspective of energy efficiency, availability, cost, reception range, latency, scalability, and tracking accuracy. Rather than comparing the technologies or techniques, we compare the localization systems and summarize their working principle. We also discuss remaining challenges to accurate indoor localization.
A relative GAGA principle for families of curves

We prove a relative GAGA principle for families of curves, showing: (i) analytic families of pointed curves whose fibres have finite automorphism groups are algebraizable; and (ii) analytic birational models of Mg,n possessing modular interpretations with the finite automorphism property are algebraizable. This is accomplished by extending some well‐known GAGA results for proper schemes to non‐separated Deligne–Mumford stacks.
The Use of N-Terminal-Pro-BNP in Preterm Infants

The use of natriuretic peptides in the neonatal population is emerging. B-type Natriuretic Peptide (BNP) and N-terminal-Pro-BNP (NTpBNP) are used in the adult population to assess myocardial function and volume loading. Their role in prognosis following cardiac surgery has also been identified. In preterm infants NTpBNP is becoming increasingly recognised as a potential screening tool for patent ductus arteriosus (PDA), and a marker for myocardial performance. In addition, NTpBNP may provide prognostic information in preterm infants and term infants with congenital diaphragmatic hernia (CDH). In this paper, the role of NTpBNP in the preterm population will be discussed.
Testing the Disk Regulation Paradigm with Spitzer Observations. I. Rotation Periods of Pre-Main-Sequence Stars in the IC 348 Cluster

We present 105 stellar rotation periods in the young cluster IC 348, 75 of which are new detections, increasing the total number of known periods in this cluster to 143. The period distribution resembles that seen in the heart of the Orion Nebula cluster by Herbst and colleagues. Stars estimated to be less massive than 0.25 M☉ show a unimodal distribution of fast rotators (P ~ 1-2 days) and a tail of slower rotators, while stars estimated to be more massive than 0.25 M☉ show a bimodal distribution with peaks at ~2 and ~8 days. We combine all published rotation periods in IC 348 with Spitzer mid-IR (3.6, 4.5, 5.8, and 8.0 μm) photometry, an unprecedentedly efficient and reliable disk indicator, in order to test the disk-braking paradigm. We find no evidence that the tail of slow rotators in low-mass stars or the long-period peak in high-mass stars are preferentially populated by objects with disks as might be expected based on the current disk-braking model. We find some indication that the disk fraction decreases significantly for stars with very short periods (P ≲ 1.5 days), which is the only feature of our sample that could potentially be interpreted as evidence for disk braking. It has been proposed that the observational signatures of disk braking might be significantly masked by the intrinsic breadth of the initial period distribution. We argue that more rigorous modeling of angular momentum evolution and a quantitative analysis of the observational data are required before the disk-braking model can be regarded as inconsistent with observations.
Cloudlets: bringing the cloud to the mobile user

Although mobile devices are gaining more and more capabilities (i.e. CPU power, memory, connectivity, .), they still fall short to execute complex rich media and data analysis applications. Offloading to the cloud is not always a solution, because of the high WAN latencies, especially for applications with real-time constraints such as augmented reality. Therefore the cloud has to be moved closer to the mobile user in the form of cloudlets. Instead of moving a complete virtual machine from the cloud to the cloudlet, we propose a more fine grained cloudlet concept that manages applications on a component level. Cloudlets do not have to be fixed infrastructure close to the wireless access point, but can be formed in a dynamic way with any device in the LAN network with available resources. We present a cloudlet architecture together with a prototype implementation, showing the advantages and capabilities for a mobile real-time augmented reality application.
Fast MIR in a Sparse Transform Domain

We consider in this paper sparse audio coding as an alternative to transform audio coding for efficient MIR in the transform domain. We use an existing audio coder based on a sparse representation in a union of MDCT bases, and propose a fast algorithm to compute mid-level representations for beat tracking and chord recognition, respectively an onset detection function and a chromagram. The resulting transform domain system is significantly faster than a comparable state-of-the-art system while obtaining close performance above 8 kbps.