Miracle-dz/UniFAR-FTUs huggingface dataset:
Title of the paper : Evaluation of the carbon content of aerosols from the burning of biomass in the Brazilian Amazon using thermal , optical and thermal-optical analysis methods

Referee #1: “Additional attention should be paid to the TOT and TOR results (e.g., how large were pyrolysis corrections in each case, how do these values compare to the other methods, were there day/night differences? )” Authors: The pyrolysis (charring) correction in TOT and TOR can be addressed, but for the TOA data this is not possible because of the use of a single wavelength to distinguish OC from EC/BC and because of the absence of measurements of pure EC/BC and pure char, which would be important for determining the charring EC/BC in the sample, as stated by Hadley et al. [2008]. The actual amount of char generated during TOT and TOR should be the same if samples are analyzed under the same atmosphere (i.e., either He, O2, or He/O2) and with the same temperature program. If the instrument/temperature program is the same, we can expect that different TOR and TOT results are due to the optical correction alone. The TOT usually reports higher char (i.e., pyrolytic organic carbon, POC) amounts leading to lower ECa. TOT is more sensitive to char within the filter media than TOR, which only detects char on the filter surface. Within-filter char is often minor in quantity, but absorbs light much more strongly than surface char and native EC (Chow et al., 2004; Chen et al., 2004; Subramanian et al., 2006). This leads to "over-correction" of EC. However, POC could be substantial for smoldering-dominated samples due to production of brown carbon during smoldering combustion (Chen et al., 2010; Chakrabarty et al., 2010). The IMPROVE-TOR and NIOSH-TOT results provide bounds for ECa measurements and the ranges are larger for some samples than others, largely depending on their charring potential. The NIOSH-TOT attributes more of the POC to OC than IMPROVE-TOR, which attributes the POC more to EC. According to the results presented by Szidat et al. [2010], it seems that the extent of charring is smaller in an O2 atmosphere (as was used in our TOA) than in a He atmosphere (as is used for the TOT and TOR instruments). With respect to day/night char differences there are no data available because daytime samples were only measured by TOA (Table 1). However, we expect higher charring for night time samples since the water-soluble material is responsible for the charring, as shown in Figure 3a, and this material is present in higher concentrations in nighttime vs. daytime samples.
cD24 isoform a promotes cell proliferation, migration and invasion and is downregulated by egr1 in hepatocellular carcinoma

of hepatocellular carcinoma (HCC). However, little is known about the expression and function of CD24 isoform a (CD24A) and CD24 isoform b (CD24B) in HCC. Materials and methods: Quantitative real-time polymerase chain reaction (qPCR) and Western blotting were performed to detect CD24 and EGR1 expression in HCC cells and tissue. The function of CD24 in cell proliferation was verified with MTT assays, colony formation assays and tumor xenograft models. Wound healing assays and invasion assays were performed to clarify the function of CD24 in the regulation of cell migration and invasion in HCC. A dual luciferase reporter assay and chromatin immunoprecipitation assay were used to analyze the regulation mechanism of CD24A. Results: CD24A but not CD24B, which was barely detected by qPCR and Western blotting, is significantly upregulated in HCC tissue. Both CD24A and CD24B contribute to HCC cell proliferation, migration and invasion, but CD24A is more effective than CD24B. EGR1 downregulates CD24A and exerts transcription-promoting activity on the CD24A promoter. Furthermore, EGR1 represses HCC cell proliferation via downregulation of CD24A. Conclusion: CD24A is the predominant CD24 isoform in HCC and plays a major role in cell proliferation, migration, and invasion. EGR1 can exert its antitumor effect through transcriptional downregulation of CD24A in HCC.
Original Research Article: Longitudinal Relationships of Depressive Symptoms to Pain Intensity and Functional Disability Among Children with Disease-Related Pain

Objective—To examine the longitudinal relationship between depressive symptoms at study entry (T1) on pain intensity (PI) and functional disability over a 1-year period among children with either sickle cell disease (SCD) or juvenile idiopathic arthritis (JIA). Methods—119 children, ages 8–17 years, completed measures of depression at T1 as well as pain and functional disability at T1, 6-month (T2), and 12-month (T3) follow-ups. Caregivers also rated their child’s pain and disability at each time point. General linear mixed modeling was employed to examine longitudinal relationships between study variables. Results—For children with JIA, T1 pain significantly moderated the effects of T1-depressive symptoms on T2 and T3 pain where T1-depressive symptoms predicted future child-reported pain only when T1 pain was relatively mild. Similarly, T1-depressive symptoms predicted future childreported disability only when initial reports of disability were relatively low. Only family income significantly predicted T2 and T3 pain in children with SCD. Conclusions—Study findings suggest that T1-depressive symptoms play a role in the longitudinal course of pain symptoms in children with JIA but not in children with SCD.
Comparing TMS perturbations to occipital and parietal cortices in concurrent TMS-fMRI studies-Methodological considerations

Neglect and hemianopia are two neuropsychological syndromes that are associated with reduced awareness for visual signals in patients’ contralesional hemifield. They offer the unique possibility to dissociate the contributions of retino-geniculate and retino-colliculo circuitries in visual perception. Yet, insights from patient fMRI studies are limited by heteroge-neity in lesion location and extent, long-term functional reorganization and behavioural compensation after stroke. Transcranial magnetic stimulation (TMS) has therefore been proposed as a complementary method to investigate the effect of transient perturbations on functional brain organization. This concurrent TMS-fMRI study applied TMS perturbation to occipital and parietal cortices with the aim to ‘mimick’ neglect and hemianopia. Based on the challenges and interpretational limitations of our own study we aim to provide tutorial guidance on how future studies should compare TMS to primary sensory and association areas that are governed by distinct computational principles, neural dynamics and functional architecture.
A Methodology for Creating Ontologies for Engineering Design

This paper describes a methodology for developing ontologies for engineering design. The methodology combines a number of methods from social science and computer science, together with taxonomies developed in the field of engineering design. A case study is used throughout the paper focusing upon the use of an ontology for searching, indexing and retrieving of engineering knowledge. An ontology for indexing design knowledge can assist the users to formulate their queries when searching for engineering design knowledge. The root concepts of the ontology were elicited from engineering designers during an empirical research study. These formed individual taxonomies within the ontology and were validated through indexing a set of ninety-two documents. Relationships between concepts are extracted as the ontology is populated with instances. The identified root concepts were found to be complete and sufficient for the purpose of indexing. A thesaurus and an automatic classification are being developed as a result of this evaluation. The methodology employed during the test case is presented in this paper. There are six separate stages, which are presented together with the research methods employed for each stage and the evaluation of each stage. The main contribution of this research is the development of a methodology to allow researchers and industry to create ontologies for their particular purpose and to develop a thesaurus for the terms within the ontology. The methodology is based upon empirical research and hence, focuses upon understanding a user’s domain models as opposed to extracting an ontology from documentation.Copyright © 2005 by ASME
Integration of circadian and phototransduction pathways in the network controlling CAB gene transcription in Arabidopsis (firefly luciferaseyluminescence imagingycircadian rhythmygene expression)

ThetranscriptionofCABgenes,encodingthe chlorophyllayb-binding proteins, is rapidly induced in dark- grown Arabidopsis seedlings following a light pulse. The transientinductionisfollowedbyseveralcyclesofacircadian rhythm. Seedlings transferred to continuous light are known to exhibit a robust circadian rhythm ofCABexpression. The precise waveform of CAB expression in light-dark cycles, however, reflects a regulatory network that integrates infor- mation from photoreceptors, from the circadian clock and possibly from a developmental program. We have used the luciferase reporter system to investigateCABexpression with high time resolution. We demonstrate thatCABexpression in light-grown plants exhibits a transient induction following light onset, similar to the response in dark-grown seedlings. The circadian rhythm modulates the magnitude and the kinetics of the response to light, such that theCABpromoter isnotlightresponsiveduringthesubjectivenight.Asignaling pathway from the circadian oscillator must therefore antag- onize the phototransduction pathways controlling the CAB promoter. We have further demonstrated that the phase of maximalCABexpression is delayed in light-dark cycles with long photoperiods, due to the entrainment of the circadian oscillator. Under short photoperiods, this pattern of entrain- ment ensures that dawn coincides with a phase of high light responsiveness, whereas under long photoperiods, the light response at dawn is reduced.
Hypermethylation of Tumor Suppressor Genes Involved in Critical Regulatory Pathways for Developing a Blood-Based Test in Breast Cancer

Background Aberrant DNA methylation patterns might be used as a biomarker for diagnosis and management of cancer patients. Methods and Findings To achieve a gene panel for developing a breast cancer blood-based test we quantitatively assessed the DNA methylation proportion of 248 CpG sites per sample (total of 31,248 sites in all analyzed samples) on 10 candidate genes (APC, BIN1, BMP6, BRCA1, CST6, ESR-b, GSTP1, P16, P21 and TIMP3). The number of 126 samples consisting of two different cohorts was used (first cohort: plasma samples from breast cancer patients and normal controls; second cohort: triple matched samples including cancerous tissue, matched normal tissue and serum samples). In the first cohort, circulating cell free methylated DNA of the 8 tumor suppressor genes (TSGs) was significantly higher in patients with breast cancer compared to normal controls (P<0.01). In the second cohort containing triple matched samples, seven genes showed concordant hypermethylated profile in tumor tissue and serum samples compared to normal tissue (P<0.05). Using eight genes as a panel to develop a blood-based test for breast cancer, a sensitivity and specificity of more than 90% could be achieved in distinguishing between tumor and normal samples. Conclusions Our study suggests that the selected TSG panel combined with the high-throughput technology might be a useful tool to develop epigenetic based predictive and prognostic biomarker for breast cancer relying on pathologic methylation changes in tumor tissue, as well as in circulation.
New normalized Rortex/vortex identification method

A new vortex identification criterion, named ΩR, is proposed for the normalization of Rortex, using the idea of the Omega method (Ω). ΩR is a normalized function from 0 to 1, which measures the relative rotation strength on the plane perpendicular to the local rotation axis. The advantages of the proposed ΩR method can be summarized as follows: (1) ΩR is from 0 to 1 and can be further used in statistics and correlation analysis as a physical quantity. (2) ΩR can distinguish the rotational vortices from the shear layers, discontinuity structures, and other non-physical structures. (3) ΩR is quite robust and can be always set as 0.52 to capture vortex structures in different cases and at different time steps.A new vortex identification criterion, named ΩR, is proposed for the normalization of Rortex, using the idea of the Omega method (Ω). ΩR is a normalized function from 0 to 1, which measures the relative rotation strength on the plane perpendicular to the local rotation axis. The advantages of the proposed ΩR method can be summarized as follows: (1) ΩR is from 0 to 1 and can be further used in statistics and correlation analysis as a physical quantity. (2) ΩR can distinguish the rotational vortices from the shear layers, discontinuity structures, and other non-physical structures. (3) ΩR is quite robust and can be always set as 0.52 to capture vortex structures in different cases and at different time steps.
Improving Space-Time-Frequency MIMO-OFDM with ICI Self-Cancellation Scheme using Least Square Error Estimator

Channel estimation techniques for Multiple-input Multiple-output Orthogonal Frequency Division Multiplexing (MIMO-OFDM) based on comb type pilot arrangement with least-square error (LSE) estimator was investigated with space-time-frequency (STF) diversity implementation. The frequency offset in OFDM effected its performance. This was mitigated with the implementation of the presented inter-carrier interference selfcancellation (ICI-SC) techniques and different space-time subcarrier mapping. STF block coding in the system exploits the spatial, temporal and frequency diversity to improve performance. Estimated channel was fed into a decoder which combined the STF decoding together with the estimated channel coefficients using LSE estimator for equalization. The performance of the system was compared by measuring the symbol error rate with a PSK-16 and PSK-32. The results show that subcarrier mapping together with ICI-SC were able to increase the system performance. Introduction of channel estimation was also able to estimate the channel coefficient at only 5dB difference with a perfectly known channel.
Crank-Nicolson Schemes for Optimal Control Problems with Evolution Equations

Crank--Nicolson methods are often used for the simulation of initial boundary value problems for parabolic partial differential equations. In this paper we present a family of discretizations for parabolic optimal control problems based on Crank--Nicolson schemes with different time discretizations for state $y$ and adjoint state $p$ so that discretization and optimization commute. One of these methods can also be explained as a Stormer--Verlet scheme in the context of geometric numerical integration of Hamiltonian systems. Two of the schemes may also be obtained as a Galerkin method with quadrature. Further we investigate the schemes for a variable time step size and prove second order convergence for this case if the time step size is chosen with respect to an arbitrary, sufficiently smooth mesh generating function.
Analysis of Antarctic Crustal Motion Using Remote Sensing and GPS Data: Applications to Ice Mass Change Studies

ii Dedication.iv Acknowledgments.v Vita.vii List of Tables.ix List of Figures.x Chapter 1: Paleoshoreline records of glacial isostatic adjustment in the Dry Valleys region, Antarctica.1 Chapter 2: Multisensor analysis of paleoshoreline tilt in the Dry Valleys, Antarctica: applications to ice mass change studies . 36 Chapter 3: GPS and paleoshoreline constraints on glacial isostatic adjustment in Victoria Land, Antarctica.82 References.132
Thinking Positive: Arithmetic Geometry in Characteristic $p$

Renee Bell is a Hans Rademacher Instructor at the University of Pennsylvania. Her email address is rhbell@math.upenn. edu. Julia Hartmann is a professor at the University of Pennsylvania. Her email address is hartmann@math.upenn. edu. Valentijn Karemaker is a postdoctoral research fellow at the University of Pennsylvania. Her email address is vkarem@math.upenn. edu. Padmavathi Srinivasan is a Hale Visiting Assistant Professor at the Georgia Institute of Technology. Her email address is padmavathi.srinivasan @math.gatech. edu. Isabel Vogt is a Massachusetts Institute of Technology graduate student currently visiting Stanford University. Her email address is ivogt@mit.edu. For permission to reprint this article, please contact: reprint-permission@ams.org.
Detecting privacy leaks using corpus-based association rules

Detecting inferences in documents is critical for ensuring privacy when sharing information. In this paper, we propose a refined and practical model of inference detection using a reference corpus. Our model is inspired by association rule mining: inferences are based on word co-occurrences. Using the model and taking the Web as the reference corpus, we can find inferences and measure their strength through web-mining algorithms that leverage search engines such as Google or Yahoo! Our model also includes the important case of private corpora, to model inference detection in enterprise settings in which there is a large private document repository. We find inferences in private corpora by using analogues of our Web-mining algorithms, relying on an index for the corpus rather than a Web search engine. We present results from two experiments. The first experiment demonstrates the performance of our techniques in identifying all the keywords that allow for inference of a particular topic (e.g. "HIV") with confidence above a certain threshold. The second experiment uses the public Enron e-mail dataset. We postulate a sensitive topic and use the Enron corpus and the Web together to find inferences for the topic. These experiments demonstrate that our techniques are practical, and that our model of inference based on word co-occurrence is well-suited to efficient inference detection.
machine E-Mail worm Detection using Data Mining

This work applies data mining techniques to detect e-mail worms. E-mail messages contain a number of different features such as the total number of words in message body/subject, presence/absence of binary attachments, type of attachments, and so on. The goal is to obtain an efficient classification model based on these features. The solution consists of several steps. First, the number of features is reduced using two different approaches: feature-selection and dimension-reduction. This step is necessary to reduce noise and redundancy from the data. The feature-selection technique is called Two-phase Selection (TPS), which is a novel combination of decision tree and greedy selection algorithm. The dimension-reduction is performed by Principal Component Analysis. Second, the reduced data is used to train a classifier. Different classification techniques have been used, such as Support Vector Machine (SVM), Naïve Bayes, and their combination. Finally, the trained classifiers are tested on a dataset containing both known and unknown types of worms. These results have been compared with published results. It is found that the proposed TPS selection along with SVM classification achieves the best accuracy in detecting both known and unknown types of worms.
Let’s All Dance: Enhancing Amateur Dance Motions (Supplementary Material)

In the experiment w/o DTW, the network contains the temporal alignment stage and dance enhancement stage connected as in our approach. The main difference is the absence of the dynamic time warping step, as well as the building and training of the affinity matrix in the temporal alignment stage. Specifically, we build the affinity matrix via the attention mechanism [3] by taking the music features as queries and motion features as keys, and mask out the values far from the diagonal items in the affinity matrix by multiplying with a mask matrix. The affinity matrix is defined as:
A novel asynchronous FPGA architecture design and its performance evaluation

This paper proposes GAPLA: a globally asynchronous locally synchronous programmable logic array architecture. The whole FPGA area is divided into locally synchronous blocks wrapped with asynchronous I/O interfaces. Data communications between synchronous blocks are controlled by 2-phase handshaking signals under bundled-data delay assumption. The size and shape of each locally synchronous block are programmable so that different modules in a design can be effectively implemented. By dividing the FPGA area into smaller blocks, the delays of long interconnect wires, which could easily dominate other delays in conventional FPGAs, only come into picture when there are communications between blocks. Therefore, each block could run at higher speed. The area overhead of adopting the GALS style in GAPLA architecture is estimated to be very small (about 7%). Experimental results show an up to 55% performance improvement compared to the conventional FPGAs.
Optimized geographical routing protocol for inter-vehicle communications

New applications of mobile communications require improved quality and reliability of inter-vehicle communications protocols. Taking in account problems related with absorbing and scattering energy of wireless signals, the presence of "grey zones" in reception, raise the necessity of improving present inter-vehicle communications protocols. We present a reliable hierarchical routing protocol that takes in account those issues. Our protocol is based on geographical routing. It enables point-to-point communications between cars in highway. The protocol is designed for highway travelers but can be used in any mobile ad-hoc network. The highway is divided in virtual cells, which moves as the vehicles moves. The cell members might choose one or two centers that will behave for a certain time interval as base stations. Every node has its geographical position given by Global Positioning System (GPS). In this protocol we take in consideration the presence of high traffic areas, "grey areas", in which receivers experience significant variable and unstable reception over time and failure of transmission between random cell leaders. Our simulation results show that our proposed protocol improves the network utilization compared to existing inter-vehicles protocols. The protocol can be used to implement differentiated mobile services and message prioritization.
Improving human-proceedings interaction: indexing the CHI index

Over the past two years, the CHI conference committee has tried to improve the usability of the conference proceedings through improving the index. Latent Semantic Indexing, a statistically-based retrieval method, was used to analyze the tiles and abstracts of papers and suggest additional relevant keywords not provided by the authors. This poster describes the method for generating the indices and shows how it can be used as a general approach for improving access to paper-based documents.
Graph Regularized Non-negative Matrix Factorization for Data Representation ∗

Recently Non-negative Matrix Factorization (NMF) has received a lot of attentions in information retrieval, computer vision and pattern recognition. NMF aims to find two non-negative matrices whose product can well approximate the original matrix. The sizes of these two matrices are usually smaller than the original matrix. This results in a compressed version of the original data matrix. The solution of NMF yields a natural parts-based representation for the data. When NMF is applied for data representation, a major disadvantage is that it fails to consider the geometric structure in the data. In this paper, we develop a graph based approach for parts-based data representation in order to overcome this limitation. We construct an affinity graph to encode the geometrical information and seek a matrix factorization which respects the graph structure. We demonstrate the success of this novel algorithm by applying it on real world problems.