Miracle-dz/UniFAR-FTUs huggingface dataset:
In Vitro and In Vivo Evaluation of a Folate-Targeted Copolymeric Submicrohydrogel Based on N-Isopropylacrylamide as 5-Fluorouracil Delivery System

Folate-targeted poly((p-nitrophenyl acrylate)-co-(N-isopropylacrylamide)) nanohydrogel (F-SubMG) was loaded with 5-fluorouracil (5-FU) to obtain low (16.3 ± 1.9 μg 5-FU/mg F-SubMG) and high (46.8 ± 3.8 μg 5-FU/mg F-SubMG) load 5-FU-loaded F-SubMGs. The complete in vitro drug release took place in 8 h. The cytotoxicity of unloaded F-SubMGs in MCF7 and HeLa cells was low; although it increased for high F-SubMG concentration. The administration of 10 μM 5-FU by 5-FU-loaded F-SubMGs was effective on both cellular types. Cell uptake of F-SubMGs took place in both cell types, but it was higher in HeLa cells because they are folate receptor positive. After subcutaneous administration (28 mg 5-FU/kg b.w.) in Wistar rats, F-SubMGs were detected at the site of injection under the skin. Histological studies indicated that the
SZTAKI @ ImageCLEF 2009

Our approach to the ImageCLEF 2009 tasks is based on image segmentation, SIFT keypoints and Okapi BM25 based text retrieval. We use feature vectors to describe the visual content of an image segment, a keypoint or the entire image. The features include color histograms, a shape descriptor as well as a 2D Fourier transform of a segment and an orientation histogram of detected keypoints. We trained a Gaussian Mixture Model (GMM) to cluster the feature vectors extracted from the image segments and keypoints independently. The normalized Fisher gradient vector computed from GMM of SIFT descriptors is a well known technique to represent an image with only one vector. Novel to our method is the combination of Fisher vectors for keypoints with those of the image segments to improve classification accuracy. We introduced training and correlation based combining methods to further improve classification quality.
A Theoretical Validation of the Substrate Depletion Approach to Determining Kinetic Parameters

The substrate depletion approach is an increasingly popular alternative to the traditional method (observing product formation) of determining the kinetic parameters (KM and Vmax) of an enzyme. Obach and Reed-Hagen (Drug Metab Dispos 30:831–837, 2002) used an empirical relationship between substrate depletion rate constants and initial substrate concentration to determine kinetic parameters for a number of cytochrome P450-catalyzed reactions. We present a proof that this relationship can be derived from the Michaelis-Menten equation and, therefore, that kinetic parameters obtained by the substrate depletion approach are equivalent and comparable to those obtained by the traditional product formation approach. Analysis of a simulated data set produced similar kinetic parameters regardless of which approach was used, confirming the theoretical result.
Characterizing of Four Common BCR-ABL Kinase Domain Mutations (T315I, Y253H, M351T and E255K) in Iranian Chronic Myelogenous Leukemia Patients With Imatinib Resistance

Background: Chronic myelogenous leukemia (CML) is a kind of hematopoietic stem-cell cancer. A significant number of CML patients who do not achieve an acceptable response to therapy, show acquired resistance against Imatinib. One of the most considerable causes of resistance against Imatinib as the first line of therapy, are BCR-ABL kinase domain mutations. Objectives: One of the most considerable causes of resistance against Imatinib as the first line of therapy, are BCR-ABL kinase domain mutations. Patients and Methods: The study was performed on 39 CML patients with Imatinib resistance. Basic hematologic parameters in blood samples were checked to identify hematologic response. To identify molecular response, BCR-ABL/ABL ratio was assessed by Real-time PCR. The ABL kinase domain amplification was performed by PCR. Restriction fragment length polymorphism (RFLP) was performed to detect four common mutations (T315I, Y253H, E255K and M351T). Finally the results were approved by direct sequencing. Results: In this study, the Y253H mutation, detected by RFLP method and confirmed by direct sequencing, was the prevalent ABL kinase domain mutation in these 39 CML patients. The G250E, V379I and L384M mutations were found in three different cases with failure molecular response. CML patients with these four ABL kinase domain mutations cannot achieve major molecular response (MMR). In addition, complete hematologic response (CHR) was observed only in the V379I mutated case and not in other mutated patients. Conclusions: Identification of ABL kinase domain mutations may be used as a proper and useful method for improving therapeutic strategies, avoiding delay in treatment and excessive expenditure in CML patients with Imatinib resistance.
MULTIFOCAL ELECTRORETINOGRAPHY IN THE ASSESSMENT OF EYES WITH CENTRAL RETINAL VEIN OCCLUSION

Data suggest that the multifocal electroretinography (mfERG) may have a role in the assessment of patients with central retinal vein occlusion (CRVO). To explore the mfERG responses in patients with CRVO. mfERG responses were recorded at 61 discrete retinal locations from both eyes of 25 patients diagnosed with retinal vein occlusions within 3 weeks of onset. The latencies and amplitudes of average responses of 5 eccentric rings from 0 to 26 degrees relative to fixation, and grouped central and peripheral rings of involved eyes were compared with values obtained from 13 normal fellow eyes of these subjects. The mfERG responses obtained from eyes with CRVO were significantly different from those derived from the fellow eye, especially when the rings are grouped as central and peripheral. mfERG is a new, safe, non-invasive, and quick investigative tool to assess retinal function. Our results suggest that mfERG could be a useful electrophysiologic test in clinical evaluation and determination of the severity of underlying ischemia in patients with retinal vein occlusion. Further studies are needed to evaluate its role as a prognostic method to determine which eyes are prone to serious complications. This is the first report of mfERG results in Iran.
De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties

Sugarcane is an important crop and a major source of sugar and alcohol. In this study, we performed de novo assembly and transcriptome annotation for six sugarcane genotypes involved in bi-parental crosses. The de novo assembly of the sugarcane transcriptome was performed using short reads generated using the Illumina RNA-Seq platform. We produced more than 400 million reads, which were assembled into 72,269 unigenes. Based on a similarity search, the unigenes showed significant similarity to more than 28,788 sorghum proteins, including a set of 5,272 unigenes that are not present in the public sugarcane EST databases; many of these unigenes are likely putative undescribed sugarcane genes. From this collection of unigenes, a large number of molecular markers were identified, including 5,106 simple sequence repeats (SSRs) and 708,125 single-nucleotide polymorphisms (SNPs). This new dataset will be a useful resource for future genetic and genomic studies in this species.
STRUCTURED THALAMOCORTICAL CONNECTIVITY REVEALED BY RANDOM WALKS ON COMPLEX NETWORKS

The segregated regions of the mammalian cerebral cortex and thalamus form an extensive and complex network, whose structure and function are still only incompletely understood. The present article describes an application of the concepts of complex networks and random walks that allows the identification of non-random, highly structured features of thalamocortical connections, and their potential effects on dynamic interactions between cortical areas in the cat brain. Utilizing large-scale anatomical data sets of this thalamocortical system, we investigate uniform random walks in such a network by considering the steady state eigenvector of the respective stochastic matrix. It is shown that thalamocortical connections are organized in such a way as to guarantee strong correlation between the outdegree and occupancy rate (a stochastic measure potentially related to activation) of each cortical area. Possible organizational principles underlying this effect are identified and discussed. The relationship between the topology of structural connection patterns and cortical dynamics currently represents a significant challenge to brain theory. Numerous neuroanatomical studies have revealed that the pathways of the mammalian thalamocortical system exhibit specific patterns ranging in scale from interconnections linking whole brain regions to intra-areal patterns of connections between cell populations or individual cortical neurons. Comprehensive descriptions of large-scale anatomical patterns of cortical connectivity have been collated for several mammalian species (e.g. [1, 2]). Quantitative analysis has revealed that these patterns are neither completely regular nor completely random [3], but exhibit specific attributes, such as short path lengths combined with high clustering [4, 5], short wiring and distinctive hierarchical features [6]. The current article proposes a novel macroscopic approach to studying neuronal dynamics in cortical maps based on concepts from random walks (e.g. [7, 8]) and complex networks (e.g. [9, 10, 11]). Specifically, we examine the interactions between cortex and thalamus in the mammalian central nervous system. The cerebral cortex consists of a network of interconnected functionally specialized regions, each of which maintains reciprocal connections with a specific set of thalamic nuclei. These nuclei relay cortical inputs and outputs, and are thought to play a role in coordinating cortical interactions. The thalamocortical architecture is represented in terms of a complex network, obtained by assigning a node to each cortical region and thalamic nucleus (nodes) and
Model-free visual servoing on complex images based on 3D reconstruction

We present a way to achieve positioning tasks by model-free visual servoing in the case of planar and motionless objects whose shape is unknown. Emphasize is made on the algorithm of 3D reconstruction which allows to synthesize easily the control law. More precisely, the reconstruction phase is based on the measurement of the 2D displacements in a region of interest and on the measurement of the camera velocity. However, we will show that the proposed algorithm is robust with respect to inaccurate values of this velocity. 2D displacements rather than 2D motions are used to remove the assumption that the acquisition rate has to be high. In addition, a particular attention is paid to the complex case of large displacements to access high camera velocities. Once the parameters of the plane are sufficiently stable, a visual servoing scheme is used to control the orientation of the camera with respect to the object and to ensure that it remains in the camera field of view for any desired orientation. The 3D reconstruction phase is maintained active during the servoing to improve the accuracy of the parameters and, consequently, to obtain a small positioning error. Experimental results validate the proposed approach.
Design and Implementation of a Peer-to-Peer Text Retrieval System

We introduce the design and implementation of a peer-to-peer text retrieval and search prototype system called P-Terse in this paper. Compared with existing P2P systems, P-Terse has three novel features: 1) The text content of the shared documents is searchable, which is a natural yet useful extension to file name matching based search provided by existing systems. 2) The system is open for extensions, including more effective retrieval models, more efficient implementation, more supported file formats, and interfaces for integrating with other systems. 3) Our search and query processing techniques are implemented in the system. These techniques are designed for achieving high efficiency and scalability. The presentation of the system includes the design strategies of the system, the research results that are implemented, and the engineering aspects of the system. We also discuss the on-going research and development work related to P-Terse.
Approaches And Experiences In Multicore Software Engineering : bzip 2 Refactoring Sayan Bhattacharyya

In this report, I explore some of the challenges involved with software engineering for multicore architectures. I discuss some background research, including three standard software engineering approaches for application parallelization. I also discuss some related work that has been done based on earlier eforts to parallelize large sequential applications for multicore platforms. I then focus on my efort to parallelize bzip2, the open source compression application. In particular, the focus is on the key issues that I faced, such as the problems with removing data dependencies in the sequential code that hinder the process of parallelism, the challenge of synchronising several parallel threads of execution and other issues. These challenges were non-trivial and I took a signifcant amount of time to refactor the application and fx the bugs that I detected during testing. I discuss the reasons for choosing the approach that I chose, including the choice of the design and the Application Programming Interfaces (API) that I used for implementing parallelism. I also discuss the application profling that I did on the sequential application. This was one of the key tasks that helped me understand and re-factor the design. I also report and discuss the results obtained from the various tests that I conducted. It was found that the choice of the design resulted in an application whose performance gain over the sequential version of bzip2 improves with the number of threads of execution, although the rate of improvement slows down beyond a certain number of threads.
Distinct Roles for the Kainate Receptor Subunits GluR5 and GluR6 in Kainate-Induced Hippocampal Gamma Oscillations

Kainate receptors (KARs) play an important role in synaptic physiology, plasticity, and pathological phenomena such as epilepsy. However, the physiological implications for neuronal networks of the distinct expression patterns of KAR subunits are unknown. Using KAR knock-out mice, we show that subunits glutamate receptor (GluR) 5 and GluR6 play distinct roles in kainate-induced gamma oscillations and epileptiform burst activity. Ablation of GluR5 leads to a higher susceptibility of the network to the oscillogenic and epileptogenic effects of kainate, whereas lack of GluR6 prevents kainate-induced gamma oscillations or epileptiform bursts. Based on experimental and simulated neuronal network data as well as the consequences of GluR5 and GluR6 expression for cellular and synaptic physiology, we propose that the functional interplay of GluR5-containing KARs on axons of interneurons and GluR6-containing KARs in the somatodendritic region of both interneurons and pyramidal cells underlie the oscillogenic and epileptogenic effects of kainate.
A Statistical Analysis of Asian Americans and the Affirmative Action Hiring of Law School Faculty

Law schools have long implemented affirmative action faculty hiring practices to remedy past discrimination, increase diversity, and provide role models for students of color. However, there is a growing sense among the relatively few Asian American law faculty that Asian Americans are not included in affirmative action hiring efforts. The author compares the hiring rates of Asian American, African American, Latino, and white law faculty candidates to test the hypothesis that Asian Americans are not included in affirmative action hiring programs. The author concludes that the pattern of law faculty hiring is consistent with affirmative action policies which exclude Asian Americans.
Outcome of TCF3-PBX1 positive pediatric acute lymphoblastic leukemia patients in Japan: a collaborative study of Japan Association of Childhood Leukemia Study (JACLS) and Children's Cancer and Leukemia Study Group (CCLSG)

This study reviewed the clinical characteristics of 112 pediatric B‐cell precursor acute lymphoblastic leukemia (BCP‐ALL) patients with TCF3‐PBX1 fusion treated according to the Japan Association of Childhood Leukemia Study (JACLS) ALL02 protocol (n = 82) and Children's Cancer and Leukemia Study Group (CCLSG) ALL 2004 protocol (n = 30). The 3‐year event‐free survival (EFS) and overall survival (OS) rates were 85.4 ± 3.9% and 89.0 ± 3.5% in JACLS cohort, and the 5‐year EFS and OS were 82.8 ± 7.0% and 86.3 ± 6.4% in CCLSG cohort, respectively, which are comparable to those reported in western countries. Conventional prognostic factors such as age at onset, initial white blood cell count, and National Cancer Institute risk have also no impact on OS in both cohorts. Surprisingly, the pattern of relapse in JACLS cohort, 9 of 82 patients, was unique: eight of nine patients relapsed during the maintenance phase and one patient had primary induction failure. However, bone marrow status and assessment of minimal residual disease on days 15 and 33 did not identify those patients. Interestingly, the two patients with IKZF1 deletion eventually relapsed in JACLS cohort, as did one patient in CCLSG cohort. International collaborative study of larger cohort is warranted to clarify the impact of the IKZF1 deletion on the poor outcome of TCF3‐PBX1 positive BCP‐ALL.
Online and Global Network Optimization: Towards the Next-Generation of Routing Platforms

The computation power of SDN controllers fosters the development of a new generation of control plane that uses compute-intensive operations to automate and optimize the network configuration across layers. From now on, cutting-edge optimization and machine learning algorithms can be used to control networks in real-time. This formidable opportunity transforms the way routing systems should be conceived and designed. This paper presents a candidate architecture for the next generation of routing platforms built on three main pillars for admission control, re-routing and monitoring that would have not been possible in legacy control planes.
The Guanine Nucleotide Exchange Factor Tiam1 Affects Neuronal Morphology; Opposing Roles for the Small GTPases Rac and Rho

The invasion-inducing T-lymphoma invasion and metastasis 1 (Tiam1) protein functions as a guanine nucleotide exchange factor (GEF) for the small GTPase Rac1. Differentiation-dependent expression of Tiam1 in the developing brain suggests a role for this GEF and its effector Rac1 in the control of neuronal morphology. Here we show that overexpression of Tiam1 induces cell spreading and affects neurite outgrowth in N1E-115 neuroblastoma cells. These effects are Rac-dependent and strongly promoted by laminin. Overexpression of Tiam1 recruits the α6β1 integrin, a laminin receptor, to specific adhesive contacts at the cell periphery, which are different from focal contacts. Cells overexpressing Tiam1 no longer respond to lysophosphatidic acid– induced neurite retraction and cell rounding, processes mediated by Rho, suggesting that Tiam1-induced activation of Rac antagonizes Rho signaling. This inhibition can be overcome by coexpression of constitutively active RhoA, which may indicate that regulation occurs at the level of Rho or upstream. Conversely, neurite formation induced by Tiam1 or Rac1 is further promoted by inactivating Rho. These results demonstrate that Rac- and Rho-mediated pathways oppose each other during neurite formation and that a balance between these pathways determines neuronal morphology. Furthermore, our data underscore the potential role of Tiam1 as a specific regulator of Rac during neurite formation and illustrate the importance of reciprocal interactions between the cytoskeleton and the extracellular matrix during this process.
Communal Constructivism: Students constructing learning for as well as with others.

We believe there is a need for an expanded definition of social constructivism that takes into account the synergy between the more recent advances in information technology which are increasing our potential for communication and the ability to store a variety of data types and advances in virtual learning environments. In particular we are still at an early stage in trying to construct knowledge as to how to teach and learn effectively with ICTs. What we argue for is a communal constructivism where students and teachers are not simply engaged in developing their own information but actively involved in creating knowledge that will benefit other students. In this model students will not simply pass through a course like water through a sieve but instead leave their own imprint in the development of the course, their school or university, and ideally the discipline.
Interactions between location and task affect the spatial and directional firing of hippocampal neurons

When rats forage for randomly dispersed food in a high walled cylinder the firing of their hippocampal “place” cells exhibits little dependence on the direction faced by the rat. On radial arm mazes and similar tasks, place cells are strongly directionally selective within their fields. These tasks differ in several respects, including the visual environment, configuration of the traversable space, motor behavior (e.g., linear and angular velocities), and behavioral context (e.g., presence of specific, consistent goal locations within the environment). The contributions of these factors to spatial and directional tuning of hippocampal neurons was systematically examined in rats performing several tasks in either an enriched or a sparse visual environment, and on different apparati. Place fields were more spatially and directionally selective on a radial maze than on an open, circular platform, regardless of the visual environment. On the platform, fields were more directional when the rat searched for food at fixed locations, in a stereotypic and directed manner, than when the food was scattered randomly. Thus, it seems that place fields are more directional when the animal is planning or following a route between points of special significance. This might be related to the spatial focus of the rat's attention (e.g., a particular reference point). Changing the behavioral task was also accompanied by a change in firing location in about one-third of the cells. Thus, hippocampal neuronal activity appears to encode a complex interaction between locations, their significance and the behaviors the rat is called upon to execute.
Tying rotations of covariance matrices via riemannian subspace clustering

The use of full covariance matrices in acoustic modeling is getting popular, but its huge computational burden in likelihood calculation is a major issue. Semi-tied covariance matrices are commonly used to speed-up the computation, where global or phone-based tying of transforms, or “rotations”, is usually used. However, such tyings are heuristic, and not necessarily optimal. In this paper, we propose a Riemannian-geometric approach to optimally tying rotations of covariance matrices. We first introduce a tangent space of the Riemannian manifold of covariance matrices, which has an excellent distance for measuring dissimilarity between covariance matrices. We then show that covariance matrices having the same rotation to each other lie on the same subspace in the tangent space. Exploiting this property, we fit subspaces to samples (covariances) in the tangent space for finding out clusters of samples that have similar rotations, and tie them together. By doing so, an optimal tying that minimizes the sum of “distortions” of covariance matrices can be found. Experimental results on the Wall Street Journal corpus show a superior performance of the proposed tying over the conventional ones.