Miracle-dz/UniFAR-FTUs huggingface dataset:
Detected for Ig Class Switching Two New Isotype-Specific Switching Activities

Ig class switch recombination (CSR) occurs by an intrachromosomal deletional process between switch (S) regions in B cells. To facilitate the study of CSR, we derived a new B cell line, 1.B4. B6, which is uniquely capable of (cid:1) 3 (cid:2) 3, (cid:1) 3 (cid:3) , and (cid:1) 3 (cid:4) , but not (cid:1) 3 (cid:2) 1 CSR at its endogenous loci. The 1.B4. B6 cell line was used in combination with plasmid-based isotype-speciﬁc S substrates in transient transfection assays to test for the presence of trans-acting switching activities. The 1.B4. B6 cell line supports (cid:1) 3 (cid:2) 3, but not (cid:1) 3 (cid:2) 1 recombination, on S substrates. In contrast, normal splenic B cells activated with LPS and IL-4 are capable of plasmid-based (cid:1) 3 (cid:2) 1 CSR and demonstrate that this S plasmid is active. Activation-induced deaminase (AID) was used as a marker to identify existing B cell lines as possible candidates for supporting CSR. The M12 and A20 cell lines were identiﬁed as AID positive and, following activation with CD40L and other activators, were found to differentially support (cid:1) 3 (cid:3) and (cid:1) 3 (cid:4) plasmid-based CSR. These studies provide evidence for two new switching activities for (cid:1) 3 (cid:2) 1 and (cid:1) 3 (cid:3) CSR, which are distinct from (cid:1) 3 (cid:2) 3 and (cid:1) 3 (cid:4) switching activities previously described. AID is expressed in all the B cell lines capable of CSR, but cannot account for the isotype speciﬁcity deﬁned by the S plasmid assay. These results are consistent with a model in which isotype-speciﬁc switching factors are either isotype-speciﬁc recombinases or DNA binding proteins with sequence speciﬁcity for S DNA. The Journal of Immunology, 2002, 168: 2835–2846.
Evaluation of the ALMA Prototype Antennas 1

The ALMA North American and European prototype antennas have been evaluated by a variety of measurement systems to quantify the major performance specifications. Nearfield holography was used to set the reflector surfaces to 17 μm RMS. Pointing and fast switching performance was determined with an optical telescope and by millimeter wavelength radiometry, yielding 2 absolute and 0.6 offset pointing accuracies. Path length stability was measured to be . 20 μm over 10 minute time periods using optical measurement devices. Dynamical performance was studied with a set of accelerometers, providing data on wind induced tracking errors and structural deformation. Considering all measurements made during this evaluation, both prototype antennas meet the major ALMA antenna performance specifications.
Evolution of the two-point correlation function in the Zel'dovich approximation

We study the evolution of the mass autocorrelation function by describing the growth of density fluctuations through the Zel'dovich approximation. The results are directly compared with the predictions of the scaling hypothesis for clustering evolution extracted from numerical simulations (Hamilton et al. 1991), as implemented by Jain, Mo & White (1995). We find very good agreement between the correlations on mildly non-linear scales and on completely linear scales. In between these regimes, we note that the density fields evolved through the Zel'dovich approximation show more non-linear features than predicted by the scaling ansatz which is, however, forced to match the linear evolution on scales larger than the simulation box. In any case, the scaling ansatz by Baugh & Gaztanaga (1996), calibrated against large box simulations agrees better with ZA predictions on large scales, keeping good accuracy also on intermediate scales. We show that mode-coupling is able to move the first zero crossing of xi(r) as time goes on. A detailed fit of the time dependence of this shifting is given for a CDM model. The evolution of the cross correlation of the density fluctuation field evaluated at two different times is also studied. The possible implications of the results for the analysis of the observed correlation function of high redshift galaxies are discussed.
Homoplastic evolution of external colouration in Asian stout newts (Pachytriton) inferred from molecular phylogeny

Wu, Y. , Wang, Y. , Jiang, K. , Chen, X. & Hanken, J. (2009). Homoplastic evolution of external colouration in Asian stout newts (Pachytriton) inferred from molecular phylogeny. —Zoologica Scripta, 39, 9–22.
Flow cytometric evaluation of physico-chemical impact on Gram-positive and Gram-negative bacteria

Since heat sensitivity of fruits and vegetables limits the application of thermal inactivation processes, new emerging inactivation technologies have to be established to fulfill the requirements of food safety without affecting the produce quality. The efficiency of inactivation treatments has to be ensured and monitored. Monitoring of inactivation effects is commonly performed using traditional cultivation methods which have the disadvantage of the time span needed to obtain results. The aim of this study was to compare the inactivation effects of peracetic acid (PAA), ozonated water (O3), and cold atmospheric pressure plasma (CAPP) on Gram-positive and Gram-negative bacteria using flow cytometric methods. E. coli cells were completely depolarized after treatment (15 s) with 0.25% PAA at 10°C, and after treatment (10 s) with 3.8 mg l−1 O3 at 12°C. The membrane potential of CAPP treated cells remained almost constant at an operating power of 20 W over a time period of 3 min, and subsequently decreased within 30 s of further treatment. Complete membrane permeabilization was observed after 10 s O3 treatment, but treatment with PAA and CAPP did not completely permeabilize the cells within 2 and 4 min, respectively. Similar results were obtained for esterase activity. O3 inactivates cellular esterase but esterase activity was detected after 4 min CAPP treatment and 2 min PAA treatment. L. innocua cells and P. carotovorum cells were also permeabilized instantaneously by O3 treatment at concentrations of 3.8 ± 1 mg l−1. However, higher membrane permeabilization of L. innocua and P. carotovorum than of E. coli was observed at CAPP treatment of 20 W. The degree of bacterial damage due to the inactivation processes is highly dependent on treatment parameters as well as on treated bacteria. Important information regarding the inactivation mechanisms can be obtained by flow cytometric measurements and this enables the definition of critical process parameters.
OsLEA3-2, an Abiotic Stress Induced Gene of Rice Plays a Key Role in Salt and Drought Tolerance

Late embryogenesis abundant (LEA) proteins are involved in tolerance to drought, cold and high salinity in many different organisms. In this report, a LEA protein producing full-length gene OsLEA3-2 was identified in rice (Oryza sativa) using the Rapid Amplification of cDNA Ends (RACE) method. OsLEA3-2 was found to be only expressed in the embryo and can be induced by abiotic stresses. The coding protein localizes to the nucleus and overexpression of OsLEA3-2 in yeast improved growth performance compared with control under salt- and osmotic-stress conditions. OsLEA3-2 was also inserted into pHB vector and overexpressed in Arabidopsis and rice. The transgenic Arabidopsis seedlings showed better growth on MS media supplemented with 150 mM mannitol or 100 mM NaCl as compared with wild type plants. The transgenic rice also showed significantly stronger growth performance than control under salinity or osmotic stress conditions and were able to recover after 20 days of drought stress. In vitro analysis showed that OsLEA3-2 was able to protect LDH from aggregation on freezing and inactivation on desiccation. These results indicated that OsLEA3-2 plays an important role in tolerance to abiotic stresses.
Multi-pair two-way relay networks: Interference management using lattice codes and amplify and compute relaying

In this paper, we consider lattice codes for inter-pair interference cancellation in a multi-pair two-way relay network (TWRN) with amplify-and-compute relaying. We investigate a new method to separate the desired message from the interference signal by computing only two equations at the users. First, we formulate the sum rate for this lattice code based approach and find that it has better sum rate than the existing beamforming based approaches. Next, we analytically obtain the optimum power allocation coefficient for the users' and the relay's power to maximize the sum rate. We show that for larger number of user pairs, optimum power allocation allows more improvement compared to that for smaller number of user pairs.
Organizing a Global Coordinate System from Local Information on an Amorphous Computer

This paper demonstrates that it is possible to generate a reasonably accurate coordinate system on randomly distributed processors, using only local information and local communication. By coordinate system we imply that each element assigns itself a logical coordinate that maps to its global physical location, starting with no apriori knowledge of position or orientation. The algorithm presented is inspired by biological systems that use chemical gradients to determine the position of cells [12]. Extensive analysis and simulation results are presented. Two key results are: there is a critical minimum average neighborhood size of 15 for good accuracy and there is a fundamental limit on the resolution of any coordinate system determined strictly from local communication. We also demonstrate that using this algorithm, random distributions of processors produce signi cantly better accuracy than regular processor grids such as those used by cellular automata. This has implications for discrete models of biology as well as for building smart sensor arrays. Copyright c Massachusetts Institute of Technology, 1999. This publication can be retrieved from http://www.ai.mit.edu/publications/ This report describes research done at the Arti cial Intelligence Laboratory of the Massachusetts Institute of Technology. Nagpal is advised by Professors G.J. Sussman and H. Abelson. The author is supported in part by DARPA, under contract number N00014-96-1-1228 administered by ONR, and in part by the Lucent GRPW Fellowship Program. Address: radhi@ai.mit.edu, Room 432, 545 Technology Square, Cambridge MA 02139.
Luminosity functions for galaxies and quasars in the Spitzer Wide-area Infrared Extragalactic Legacy Survey

We construct rest-frame luminosity functions (LFs) at 3.6, 4.5, 5.8, 8 and 24 μm over the redshift range 0 < z < 2 for galaxies and 0 < z < 4 for optical quasi-stellar objects (QSOs), using optical and infrared (IR) data from the Spitzer Wide-area Infrared Extragalactic (SWIRE) Survey. The 3.6- and 4.5-μm galaxy LFs show evidence for moderate positive luminosity evolution up to z~ 1.5, consistent with the passive ageing of evolved stellar populations. Their comoving luminosity density was found to evolve passively, gradually increasing out to z~ 0.5–1 but flattening, or even declining, at higher redshift. Conversely, the 24-μm galaxy LF, which is more sensitive to obscured star formation and/or active galactic nuclei (AGN) activity, undergoes strong positive evolution, with the derived IR energy density and star formation rate (SFR) density ∝ (1 +z)^γ with γ= 4.5^(+0.7)_(−0.6) and the majority of this evolution occurring since z~ 1. Optical QSOs, however, show positive luminosity evolution in all bands, out to the highest redshifts (3 < z < 4). Modelling as L^* ∝ (1 +z)^γ gave γ= 1.3^(+0.1)_(−0.1) at 3.6 μm, γ= 1.0^(+0.1)_(−0.1) at 4.5 μm and stronger evolution at the longer wavelengths (5.8, 8 and 24 μm), of γ~ 3. Comparison of the galaxy LFs to predictions from a semi-analytic model based on cold dark matter (CDM) indicates that an initial mass function (IMF) skewed towards higher mass star formation in bursts compared to locally be preferred. As a result, the currently inferred massive SFRs in distant submm sources may require substantial downwards revision.
Performance of wideband CDMA systems supporting multimedia traffic

We evaluate the performance of wideband CDMA cellular systems providing different classes of multimedia traffic and supporting user mobility. A Markovian teletraffic model of the user dynamics is developed. Constraints are imposed in the model which account for the multiple access interference among active users. Results are shown in terms of call blocking probabilities and average number of active connections. The methodology proposed is a useful tool for the design and planning of third generation cellular systems.
The Development of Excitatory Synapses in Cultured Spinal Neurons

Immunohistochemical studies of synapses in the CNS have demonstrated that glutamate receptors (GluRs) are concentrated at postsynaptic sites in vivo and in vitro(Baude et al., 1995). The mechanisms leading to receptor clustering at excitatory synapses are far less understood than those governing acetylcholine receptor accumulation at the neuromuscular junction (Hall and Sanes,1993) or glycine receptor aggregation at central inhibitory synapses (Kirsch et al., 1993). Using cultured rat spinal cord neurons, we demonstrate that clustering of the AMPA receptor subunit GluR1 is among the earliest events in excitatory synapse formation in vitro, coincident with the onset of miniature EPSCs and in many cases preceding presynaptic vesicle accumulation. Postsynaptic receptor clustering is induced in a highly specific and reiterative pattern, independent of receptor activation, by contact with a subset of axons capable of inducing receptor clusters. The subunit composition of AMPA receptor clusters varied significantly between neurons but was invariant within a given neuron. The presence of either GluR2 or GluR3 was common to all receptor clusters. Neither high-affinity glutamate transporters nor NMDA receptors appeared to be concentrated with AMPA receptor subunits at these excitatory synapses.
Transpacific Resonances and Affiliations in Leanne Dunic’s to Love the Coming End and Ruth Ozeki’s the Tale for the Time Being

Abstract This article examines methods of tracing affiliations across transpacific critiques through a reading of Leanne Dunic’s To Love the Coming End and Ruth Ozeki’s The Tale for the Time Being. The article proposes that, rather than reproducing a nation-bound framing of the 2011 earthquake off the Pacific coast of Tōhoku that envisions it as a solely Japanese crisis, Dunic’s and Ozeki’s works explore what it would mean to read the earthquake and its aftermath as a transpacific event. It argues that these works facilitate new relations between national cultures and the global, suggesting that, by narrating the earthquake and recovering its transpacific resonances, both works recover and write transcultural links that are obscured in nation-bound narratives of events. By self-reflexively commenting on this process of creative forms of transpacific intimacy, Dunic’s and Ozeki’s works directly address the potential for literary narratives to implicate individuals from disparate nations in a global, historical, narrative of events
The Option Value of Patent Licenses

Patent valuation is one of the most relevant issues within the studies on the management of intellectual property rights. As firms rely more and more on external sources of innovation, the need for reliable measurements of what is traded becomes essential. Patent valuation is especially challenging primary because of the great uncertainty affecting their returns and for the lack of market-based data. The most recent and promising attempts in this research field have been developed within the real option theory (ROT), which recognizes the effect of uncertainty on patent value, and they have taken advantage of the increasing amount of information available about licenses. The aim of this paper is to propose and empirically test a valuation model of licensed patents based on ROT. According to our model, the initial fee paid by the licensee is considered analogous to the premium she is willing to pay to buy an option to commercialize the licensed patents in the future. A fundamental prediction of ROT is that this option value increases with volatility. In order analyze the relationship between volatility and the initial fee of the license, we assume that volatility is primarily determined by market and technological uncertainty. We analyse 105 patent licenses. The results of our regression model show that both market and technological uncertainty positively affect the initial fee paid for a patent license.
Inertial BSN-Based Characterization and Automatic UPDRS Evaluation of the Gait Task of Parkinsonians

The analysis and assessment of motor tasks, such as gait, can provide important information on the progress of neurological disorders such as Parkinson's disease (PD). In this paper, we design a Boby Sensor Network (BSN)-based system for the characterization of gait in Parkinsonians through the extraction of kinematic features, in both time and frequency domains, embedding information on the status of the PD. The gait features extraction is performed on a set of 34 PD patients using a BSN formed by only three inertial nodes (one on the chest and one per thigh). We investigate also the relationship between the selected kinematic features and the Unified Parkinson's Disease Rating Scale (UPDRS) scores assigned to patients by expert neurologists. This work extends a previously proposed approach to the analysis of leg agility and sit-to-stand tasks and, as such, represents a further step to develop a system for automatic and comprehensive evaluation of different PD motor tasks. A performance analysis of different classification techniques is carried out, showing the feasibility of an automatic (and, eventually, remote) UPDRS scoring system, suitable for tele-health applications in the realm of affective medicine.
Insurance Mandates for Diagnosis and Treatment of Children and Adolescents with Autism and Evaluative Data Sources: A Case Study of Two U.S. States

ACKNOWLEDGEMENTS First, I would like to express my sincere gratitude to my committee chair, Dr. Shanta Dube, for her continuous dedication throughout all stages of this project. Her experience, vision, and academic guidance were decisive to keep me motivated and focused during troubling times. My appreciation also goes to the other outstanding member of my committee, Dr. William Thompson. His collaboration went beyond the Capstone review: Dr. Thompson was a distinctive mentor that pushed me to mature my professional goals. Furthermore, I sincerely thank all the agencies that voluntarily informed this study and were decisive for the quality of its content. Secondly, I must acknowledge the participation of some key protagonists in the construction of my critical thinking in public health, which is reflected in this project. Dr. Daniel Crimmins, for immersing me in the study of questions involving disability, determinant experience for many of my current and future career choices. Dr. Bruce Perry and Dr. Rodney Lyn for so brilliantly introducing me to the policy and structure of the U.S. healthcare systems and collaborating for the consolidation of my study focus as a public health scientist. And Pearly Dhingra for the uninterrupted motivation to keeping fighting for my wildest and most utopic philosophies in public health. Lastly, and most importantly, I would like to dedicate this project and the MPH conclusion to my family and friends. Regardless of the physical distance, my parent's support and inspiration were the principal motivator that kept me moving forward with my objectives. Thank you also to my family, in-laws, and friends in the U.S., that helped me find security and warmth out of my comfort zone. Lastly, I doubted whether I could make it through the challenging and tough times in the past two years without my boyfriend Ben by my side. An unconditional love brought us together and is inspiring a beautiful journey in my career and personal realization. ABSTRACT BACKGROUND: It is recognized among providers, parents and health organizations that the current health care system is unprepared for a rising number of children diagnosed with Autism Spectrum Disorder (ASD) worldwide. Meanwhile, differences in mandated insurance coverage for ASD across the U.S. could drastically impact the diagnosis and treatment strategies chosen by providers and families. PURPOSE OF RESEARCH: The present case study aimed to review and compare policies and programs for children and adolescents with ASD in Pennsylvania (PA) and Georgia (GA), …
A POS Tagger for Code Mixed Indian Social Media Text - ICON-2016 NLP Tools Contest Entry from Surukam

Building Part-of-Speech (POS) taggers for code-mixed Indian languages is a particularly challenging problem in computational linguistics due to a dearth of accurately annotated training corpora. ICON, as part of its NLP tools contest has organized this challenge as a shared task for the second consecutive year to improve the state-of-the-art. This paper describes the POS tagger built at Surukam to predict the coarse-grained and fine-grained POS tags for three language pairs - Bengali-English, Telugu-English and Hindi-English, with the text spanning three popular social media platforms - Facebook, WhatsApp and Twitter. We employed Conditional Random Fields as the sequence tagging algorithm and used a library called sklearn-crfsuite - a thin wrapper around CRFsuite for training our model. Among the features we used include - character n-grams, language information and patterns for emoji, number, punctuation and web-address. Our submissions in the constrained environment,i.e., without making any use of monolingual POS taggers or the like, obtained an overall average F1-score of 76.45%, which is comparable to the 2015 winning score of 76.79%.
Multimedia Transmission over Optic, DSL and PLC Systems

This work presents an analysis based on an multimedia transmission generated on optical fiber backbone and two combined access technologies, PLC (Power Line Communications) and ADSL2+ (Asymmetric Digital Subscriber Line), called of pDSL. This paper points a case study of multimedia traffic using pDSL combination with intention to present measured and simulated results that prove the proposal solution viability.
CRFs-Based Chinese Named Entity Recognition with Improved Tag Set

Chinese Named entity recognition is one of the most important tasks in NLP. The paper mainly describes our work on NER tasks. The paper built up a system under the framework of Conditional Random Fields (CRFs) model. With an improved tag set the system gets an F-value of 93.49 using SIGHAN2007 MSRA corpus.
Double-Layer Magnetic Nanoparticle-Embedded Silica Particles for Efficient Bio-Separation

Superparamagnetic Fe3O4 nanoparticles (NPs) based nanomaterials have been exploited in various biotechnology fields including biomolecule separation. However, slow accumulation of Fe3O4 NPs by magnets may limit broad applications of Fe3O4 NP-based nanomaterials. In this study, we report fabrication of Fe3O4 NPs double-layered silica nanoparticles (DL MNPs) with a silica core and highly packed Fe3O4 NPs layers. The DL MNPs had a superparamagnetic property and efficient accumulation kinetics under an external magnetic field. Moreover, the magnetic field-exposed DL MNPs show quantitative accumulation, whereas Fe3O4 NPs single-layered silica nanoparticles (SL MNPs) and silica-coated Fe3O4 NPs produced a saturated plateau under full recovery of the NPs. DL MNPs are promising nanomaterials with great potential to separate and analyze biomolecules.