gebhart/patrepeval huggingface dataset:
Comparison of supervised classification methods for protein profiling in cancer diagnosis. (2007)

A key challenge in clinical proteomics of cancer is the identification of biomarkers that could allow detection, diagnosis and prognosis of the diseases. Recent advances in mass spectrometry and proteomic instrumentations offer unique chance to rapidly identify these markers. These advances pose considerable challenges, similar to those created by microarray-based investigation, for the discovery of pattern of markers from high-dimensional data, specific to each pathologic state (e.g. normal vs cancer). We propose a three-step strategy to select important markers from high-dimensional mass spectrometry data using surface enhanced laser desorption/ionization (SELDI) technology. The first two steps are the selection of the most discriminating biomarkers with a construction of different classifiers. Finally, we compare and validate their performance and robustness using different supervised classification methods such as Support Vector Machine, Linear Discriminant Analysis, Quadratic Discriminant Analysis, Neural Networks, Classification Trees and Boosting Trees. We show that the proposed method is suitable for analysing high-throughput proteomics data and that the combination of logistic regression and Linear Discriminant Analysis outperform other methods tested.
Translating Genomics for Precision Cancer Medicine (2014)

The Human Genome Project not only provided the essential reference map for the human genome but also stimulated the development of technology and analytic tools to process massive quantities of genomic data. As a result of this project, new technologies for DNA sequencing have improved in efficiency and cost by more than a millionfold over the past decade, and these technologies can now be routinely applied at a cost of less than $5,000 per genome. Although the application of these technologies in cancer genomics research has continued to contribute to basic discoveries, opportunities for translating them for individual patients have also emerged. This is especially important in clinical cancer research, where genetic alterations in a patient's tumor may be matched to molecularly targeted therapies. In this review, we discuss the integration of cancer genomics and clinical oncology and the opportunity to deliver precision cancer medicine.
Design of a lightweight, tethered, torque-controlled knee exoskeleton (2017)

Lower-limb exoskeletons show promise for improving gait rehabilitation for those with chronic gait abnormalities due to injury, stroke or other illness. We designed and built a tethered knee exoskeleton with a strong lightweight frame and comfortable, four-point contact with the leg. The device is structurally compliant in select directions, instrumented to measure joint angle and applied torque, and is lightweight (0.76 kg). The exoskeleton is actuated by two off-board motors. Closed loop torque control is achieved using classical proportional feedback control with damping injection in conjunction with iterative learning. We tested torque measurement accuracy and found root mean squared (RMS) error of 0.8 Nm with a max load of 62.2 Nm. Bandwidth was measured to be phase limited at 45 Hz when tested on a rigid test stand and 23 Hz when tested on a person's leg. During bandwidth tests peak extension torques were measured up to 50 Nm. Torque tracking was tested during walking on a treadmill at 1.25 m/s with peak flexion torques of 30 Nm. RMS torque tracking error averaged over a hundred steps was 0.91 Nm. We intend to use this knee exoskeleton to investigate robotic assistance strategies to improve gait rehabilitation and enhance human athletic ability.
Multiresponse Optimization of Stochastic WSN Deployment Using Response Surface Methodology and Desirability Functions (2010)

Due to reliance on stochastic deployment, delivery of large-scale WSN presents a major problem in the application of wireless sensor networks (WSN) technology. When deployed in a stochastic manner, the WSN has the utmost challenge of guaranteeing acceptable operational efficiency upon deployment. The research presented in this paper evaluates application of the response surface methodology (RSM) and desirability functions for analysis and optimization of stochastic WSN deployments based on multiple efficiency metrics. Through case studies, the approach is proven successful in modeling individual efficiency metrics, and in providing a way for analyzing deployments, based on numerous efficiency metrics. Additionally, the approach may be used to quantify the effects of optimizing partial efficiency metrics on the overall deployment efficiency.
G Alpha-q/11 Protein Plays a Key Role in Insulin-Induced Glucose Transport in 3T3-L1 Adipocytes (1999)

We evaluated the role of the G alpha-q (Galphaq) subunit of heterotrimeric G proteins in the insulin signaling pathway leading to GLUT4 translocation. We inhibited endogenous Galphaq function by single cell microinjection of anti-Galphaq/11 antibody or RGS2 protein (a GAP protein for Galphaq), followed by immunostaining to assess GLUT4 translocation in 3T3-L1 adipocytes. Galphaq/11 antibody and RGS2 inhibited insulin-induced GLUT4 translocation by 60 or 75%, respectively, indicating that activated Galphaq is important for insulin-induced glucose transport. We then assessed the effect of overexpressing wild-type Galphaq (WT-Galphaq) or a constitutively active Galphaq mutant (Q209L-Galphaq) by using an adenovirus expression vector. In the basal state, Q209L-Galphaq expression stimulated 2-deoxy-D-glucose uptake and GLUT4 translocation to 70% of the maximal insulin effect. This effect of Q209L-Galphaq was inhibited by wortmannin, suggesting that it is phosphatidylinositol 3-kinase (PI3-kinase) dependent. We further show that Q209L-Galphaq stimulates PI3-kinase activity in p110alpha and p110gamma immunoprecipitates by 3- and 8-fold, respectively, whereas insulin stimulates this activity mostly in p110alpha by 10-fold. Nevertheless, only microinjection of anti-p110alpha (and not p110gamma) antibody inhibited both insulin- and Q209L-Galphaq-induced GLUT4 translocation, suggesting that the metabolic effects induced by Q209L-Galphaq are dependent on the p110alpha subunit of PI3-kinase. In summary, (i) Galphaq appears to play a necessary role in insulin-stimulated glucose transport, (ii) Galphaq action in the insulin signaling pathway is upstream of and dependent upon PI3-kinase, and (iii) Galphaq can transmit signals from the insulin receptor to the p110alpha subunit of PI3-kinase, which leads to GLUT4 translocation.
OPTIMIZATION OF TRANSPORTATION NETWORKS DURING URBAN FLOODING1 (2000)

ABSTRACT: In this paper a numerical model for flood propagation in urban areas is proposed. It has been applied to evaluate flooding hydraulic characteristics in terms of potential flood elevations, depths, and inundated areas. Furthermore, the algorithm efficiency and the consequent reduced computation time allow the use of the hydraulic model as a part of a more complex system for civil protection actions, planning, and management. During flood events, the transportation network plays a main role both in rescuing people when they are more vulnerable and in moving people and materials from and toward affected areas. The reduced efficiency of this transportation network is evaluated based on a least‐flood‐risk path‐finding algorithm. The results of a case study concerning the northern part of the city of Rome, show that the numerical model for unsteady flow in open channel networks achieves the proposed aims. It has proven to be able to describe the flood hydraulic characteristics and to be suitable for real‐time flood emergency management in urban areas.
Oral manganese as an MRI contrast agent for the detection of nociceptive activity (2011)

The ability of divalent manganese to enter neurons via calcium channels makes manganese an excellent MRI contrast agent for the imaging of nociception, the afferent neuronal encoding of pain perception. There is growing evidence that nociceptive neurons possess increased expression and activity of calcium channels, which would allow for the selective accumulation of manganese at these sites. In this study, we show that oral manganese chloride leads to increased enhancement of peripheral nerves involved in nociception on T(1)-weighted MRI. Oral rather than intravenous administration was chosen for its potentially better safety profile, making it a better candidate for clinical translation with important applications, such as pain diagnosis, therapy and research. The spared nerve injury (SNI) model of neuropathic pain was used for the purposes of this study. SNI rats were given, sequentially, increasing amounts of manganese chloride (lowest, 2.29 mg/100 g weight; highest, 20.6 mg/100 g weight) with alanine and vitamin D(3) by oral gavage. Compared with controls, SNI rats demonstrated increased signal-to-background ratios on T(1)-weighted fast spin echo MRI, which was confirmed by and correlated strongly with spectrometry measurements of nerve manganese concentration. We also found the difference between SNI and control rats to be greater at 48 h than at 24 h after dosing, indicating increased manganese retention in addition to increased manganese uptake in nociceptive nerves. This study demonstrates that oral manganese is a viable method for the imaging of nerves associated with increased nociceptive activity.
Multimedia streaming via TCP (2004)

TCP is widely used in commercial media streaming systems, with recent measurement studies indicating that a significant fraction of Internet streaming media is currently delivered over HTTP/TCP. These observations motivate us to develop analytic performance models to systematically investigate the performance of TCP for both live and stored media streaming. We validate our models via <i>ns</i> simulations and experiments conducted over the Internet. Our models provide guidelines indicating the circumstances under which TCP streaming leads to satisfactory performance, showing, for example, that TCP generally provides good streaming performance when the achievable TCP throughput is roughly twice the media bitrate, with only a few seconds of startup delay.
Management of Aromatase Inhibitor-Associated Bone Loss (AIBL) in postmenopausal women with hormone sensitive breast cancer : Joint position statement of the IOF, CABS, ECTS, IEG, ESCEO, IMS, and SIOG (2017)

BACKGROUND: Several guidelines have been reported for bone-directed treatment in women with early breast cancer (EBC) for averting fractures, particularly during aromatase inhibitor (AI) therapy. Recently, a number of studies on additional fracture related risk factors, new treatment options as well as real world studies demonstrating a much higher fracture rate than suggested by randomized clinical controlled trials (RCTs). Therefore, this updated algorithm was developed to better assess fracture risk and direct treatment as a position statement of several interdisciplinary cancer and bone societies involved in the management of AI-associated bone loss (AIBL). PATIENTS AND METHODS: A systematic literature review identified recent advances in the management of AIBL. Results with individual agents were assessed based on trial design, size, follow-up, and safety. RESULTS: Several fracture related risk factors in patients with EBC were identified. Although, the FRAX algorithm includes fracture risk factors (RF) in addition to BMD, it does not seem to adequately address the effects of AIBL. Several antiresorptive agents can prevent and treat AIBL. However, concerns regarding compliance and long-term safety remain. Overall, the evidence for fracture prevention is strongest for denosumab 60 mg s.c. every 6 months. Additionally, recent studies as well as an individual patient data meta-analysis of all available randomized trial data support additional anticancer benefits from adjuvant bisphosphonate treatment in postmenopausal women with a 34% relative risk reduction in bone metastasis and 17% relative risk decrease in breast cancer mortality that needs to be taken into account when advising on management of AIBL. CONCLUSIONS: In all patients initiating AI treatment, fracture risk should be assessed and recommendation with regard to exercise and calcium/vitamin D supplementation given. Bone-directed therapy should be given to all patients with a T-score&lt;-2.0 or with a T-score of &lt;-1.5 SD with one additional RF, or with ≥2 risk factors (without BMD) for the duration of AI treatment. Patients with T-score&gt;-1.5 SD and no risk factors should be managed based on BMD loss during the first year and the local guidelines for postmenopausal osteoporosis. Compliance should be regularly assessed as well as BMD on treatment after 12 - 24 months. Furthermore, because of the decreased incidence of bone recurrence and breast cancer specific mortality, adjuvant bisphosphonates are recommended for all postmenopausal women at significant risk of disease recurrence.
Spurious long-range entanglement and replica correlation length (2016)

Topological entanglement entropy has been regarded as a smoking-gun signature of topological order in two dimensions, capturing the total quantum dimension of the topological particle content. An extrapolation method on cylinders has been used frequently to measure the topological entanglement entropy. Here, we show that a class of short-range entangled 2D states, when put on an infinite cylinder of circumference $L$, exhibits the entanglement R\'enyi entropy of any integer index $\ensuremath{\alpha}\ensuremath{\ge}2$ that obeys ${S}_{\ensuremath{\alpha}}=aL\ensuremath{-}\ensuremath{\gamma}$, where $a,\ensuremath{\gamma}&gt;0$. Under the extrapolation method, the subleading term $\ensuremath{\gamma}$ would be identified as the topological entanglement entropy, which is spurious. A nonzero $\ensuremath{\gamma}$ is always present if the 2D state reduces to a certain symmetry-protected topological 1D state, upon disentangling spins that are far from the entanglement cut. The internal symmetry that stabilizes $\ensuremath{\gamma}&gt;0$ is not necessarily a symmetry of the 2D state, but should be present after the disentangling reduction. If the symmetry is absent, $\ensuremath{\gamma}$ decays exponentially in $L$ with a characteristic length, termed as a replica correlation length, which can be arbitrarily large compared to the two-point correlation length of the 2D state. We propose a simple numerical procedure to measure the replica correlation length through replica correlation functions. We also calculate the replica correlation functions for representative wave functions of Abelian discrete gauge theories and the double semion theory in 2D, to show that they decay abruptly to zero. This supports a conjecture that the replica correlation length being small implies that the subleading term from the extrapolation method determines the total quantum dimension.
T cell ontogeny. Organ location of maturing populations as defined by surface antigen markers is similar in neonates and adults. (1981)

Earlier studies have suggested that splenic T cell populations in nursling mice (less than 18 d of age) have Lyt cell surface antigens that identify them as less mature than their adult counterparts. Studies presented here, however, demonstrate that the expression of the Thy-1, Lyt-1, Lyt-2, and Lyt-3 T cell antigens is virtually identical in 14-d-old and adult T cell populations even though at 14 d, T cells constitute less than 10% of the total spleen cell population. Because the expression of these antigens on the immature (cortical) thymocyte population differs substantially from their expression on peripheral T cells, the maturity of splenic T cells as judged by these criteria is similar in nurslings and adults. Very few cells in the neonatal thymus 4 h after birth correspond, in terms of antigen expression, to the more mature (medullary) thymocyte population of adults, but such cells develop rapidly during the first few days of life. They are present, therefore, sufficiently early to serve as the immediate source of peripheral T cells, as they apparently do in the adult. This then suggests that the locations for the major T cell maturational events are established within the first 2 wk of life of the mouse and maintained as such thereafter. The use of monoclonal antibodies and quantitative immunofluorescence analysis in our studies probably explains the differences between our findings and those reported previously, which relied on cytotoxic depletion by alloantisera and complement to estimate the frequencies of cells carrying the Lyt differentiation antigens in nurslings.
Integration von Nanodrahtarrays in Mikrosysteme für die Gasflusssensorik (2010)

Nanodrähte sind durch ihr großes Oberflächen/Volumen-Verhältnis von hier etwa 1,6·10^7 m²/m³ ein interessantes Untersuchungsobjekt zur Minimierung der Ansprechzeit von Mikrogasflusssensoren. Diese Arbeit beschreibt die Modellierung von Nanodrahtarrays in Gasflüssen. Sie geht auf Temperatursprünge von 1 K bei Gasflüssen &lt; 1 m/s ein. Die Simulationsergebnisse legen nahe, dass bei Nanodrahtarrays Zeitkonstanten von &lt; 10^-3 s und bei einzelnen Nanodrähten um mehr als drei Größenordnungen kleinere Zeitkonstanten möglich sind. Weiterhin beschreibt diese Arbeit einen Prozessablauf zur Integration von Nanodrahtarrays in ein Mikrosystem zur Gasflussanalyse. Die Bündelung von drei Nanodrahtarrays ist experimentell realisiert und vereinfacht die Handhabung bei der Montage. Sie ermöglicht eine beidseitige Kontaktierung der Nanodrahtarrays mit einer planaren Mikrostruktur.
Optimal and Scalable Caching for 5G Using Reinforcement Learning of Space-Time Popularities (2017)

Small basestations (SBs) equipped with caching units have potential to handle the unprecedented demand growth in heterogeneous networks. Through low-rate, backhaul connections with the backbone, SBs can prefetch popular files during off-peak traffic hours, and service them to the edge at peak periods. To intelligently prefetch, each SB must learn what and when to cache, while taking into account SB memory limitations, the massive number of available contents, the unknown popularity profiles, as well as the space-time popularity dynamics of user file requests. In this paper, local and global Markov processes model user requests, and a reinforcement learning (RL) framework is put forth for finding the optimal caching policy when the transition probabilities involved are unknown. Joint consideration of global and local popularity demands along with cache-refreshing costs allow for a simple, yet practical asynchronous caching approach. The novel RL-based caching relies on a Q-learning algorithm to implement the optimal policy in an online fashion, thus, enabling the cache control unit at the SB to learn, track, and possibly adapt to the underlying dynamics. To endow the algorithm with scalability, a linear function approximation of the proposed Q-learning scheme is introduced, offering faster convergence as well as reduced complexity and memory requirements. Numerical tests corroborate the merits of the proposed approach in various realistic settings.
Morphological, optical, and Raman characteristics of ZnO nanoflakes prepared via a sol–gel method (2011)

Abstract Two‐dimensional (2D) ZnO nanoflakes were grown on thin aluminum layer, deposited on silicon substrate, using a sol–gel method. The surface morphologies of ZnO nanoflakes at different precursor concentrations were studied using scanning electron microscopy (SEM). Combined studies of SEM, photoluminescence (PL), and Raman spectroscopy suggested that nanorods started to grow along with nanoflakes at a precursor concentration of 0.05 M and the density of the nanorods significantly increased when the concentration was raised to 0.075 M. Both the UV‐luminescence and Raman spectra were intensified and redshifted with the increment of precursor concentration. Spectral intensification suggests improvement in crystal qualities and better optical properties of the fabricated ZnO nanostructures. The structural defects at lower levels of precursor were probably due to the hypoxic environment, whereas, the redshift of PL and Raman spectra was due to the local heating of ZnO nanocrystals.
Algebraic Decomposition for Probing Security. (2016)

The probing security model is very popular to prove the side-channel security of cryp- tographic implementations protected by masking. A common approach to secure nonlinear functions in this model is to represent them as polynomials over a binary eld and to secure their nonlinear multiplications thanks to a method introduced by Ishai, Sahai and Wagner at Crypto 2003. Several schemes based on this approach have been published, leading to the recent proposal of Coron, Roy and Vivek which is currently the best known method when no particular assumption is made on the algebraic structure of the function. In the present paper, we revisit this idea by trading nonlinear mul- tiplications for low-degree functions. Specically, we introduce an algebraic decomposition approach in which a nonlinear function is represented as a sequence of functions with low algebraic degrees. We therefore focus on the probing-secure evaluation of such low-degree functions and we introduce three novel methods to tackle this particular issue. The paper concludes with a comparative analysis of the proposals, which shows that our algebraic decomposition method outperforms the method of Coron, Roy and Vivek in several realistic contexts.
The ubiquitin-editing enzyme A20 controls NK cell homeostasis through regulation of mTOR activity and TNF (2019)

The ubiquitin-editing enzyme A20 is a well-known regulator of immune cell function and homeostasis. In addition, A20 protects cells from death in an ill-defined manner. While most studies focus on its role in the TNF-receptor complex, we here identify a novel component in the A20-mediated decision between life and death. Loss of A20 in NK cells led to spontaneous NK cell death and severe NK cell lymphopenia. The few remaining NK cells showed an immature, hyperactivated phenotype, hallmarked by the basal release of cytokines and cytotoxic molecules. NK-A20<sup>-/-</sup> cells were hypersensitive to TNF-induced cell death and could be rescued, at least partially, by a combined deficiency with TNF. Unexpectedly, rapamycin, a well-established inhibitor of mTOR, also strongly protected NK-A20<sup>-/-</sup> cells from death, and further studies revealed that A20 restricts mTOR activation in NK cells. This study therefore maps A20 as a crucial regulator of mTOR signaling and underscores the need for a tightly balanced mTOR pathway in NK cell homeostasis.
Cellular neuron and large wireless neural network (2006)

A new approach to neural networks is proposed, based on wireless interconnects (synapses) and cellular neurons, both software and hardware; with the capacity of 10<sup>10</sup> neurons, almost fully connected. The core of the system is <i>Spatio-Temporal-Variant</i> (STV) kernel and <i>cellular axon</i> with <i>synaptic plasticity</i> variable in time and space. The novel large neural network hardware is based on two established wireless technologies: RF-cellular and IR-wireless.
Building Human Capital to Meet the Demands in Well Intervention (2006)

Abstract The pace of activity, maturing profiles, incoming workforce expectations, and increasingly focused requirements on the industry’s well intervention needs, is demanding a new approach to building human capital. Today’s challenge is to build the required expertise in a fraction of the time previously available. This paper will provide an overview of current and future skill requirements to determine the most effective way to develop those skills, and a review of on-going programs to develop the required skill levels. Additionally, a review will be completed on the current learning tools as well as the integration of those tools in a comprehensive and accelerated development program.