Miracle-dz/UniFAR-FTUs huggingface dataset:
State of the Globe: Yellow Fever is Still Around and Active!

W have conquered space in the 21st century but people are still dying from yellow fever. We know what causes the disease—a virus belonging to the family Flaviviridae. Although an effective vaccine is available, the WHO still estimates an annual occurrence of 200000 yellow fever cases with 30000 related deaths. These statistics are even more alarming when we consider the fact that no disease can be considered as strictly endemic today. Airplanes unwittingly transport infected travelers, vectors, viruses, bacteria, and their disease to all corners of the earth. Mosquitoes can carry the YF virus globally with the present ease in international travel. Americans, Europeans, and especially, Asians are vulnerable as they have the competent vector mosquitoes and nonhuman primates. [1]
High Expression of Antioxidant Proteins in Dendritic Cells

Dendritic cells (DCs) display the unique ability to activate naive T cells and to initiate primary T cell responses revealed in DC-T cell alloreactions. DCs frequently operate under stress conditions. Oxidative stress enhances the production of inflammatory cytokines by DCs. We performed a proteomic analysis to see which major changes occur, at the protein expression level, during DC differentiation and maturation. Comparative two-dimensional gel analysis of the monocyte, immature DC, and mature DC stages was performed. Manganese superoxide dismutase (Mn-SOD) reached 0.7% of the gel-displayed proteins at the mature DC stage. This important amount of Mn-SOD is a primary antioxidant defense system against superoxide radicals, but its product, H2O2, is also deleterious for cells. Peroxiredoxin (Prx) enzymes play an important role in eliminating such peroxide. Prx1 expression level continuously increased during DC differentiation and maturation, whereas Prx6 continuously decreased, and Prx2 peaked at the immature DC stage. As a consequence, DCs were more resistant than monocytes to apoptosis induced by high amounts of oxidized low density lipoproteins containing toxic organic peroxides and hydrogen peroxide. Furthermore DC-stimulated T cells produced high levels of receptor activator of nuclear factor κB ligand, a chemotactic and survival factor for monocytes and DCs. This study provides insights into the original ability of DCs to express very high levels of antioxidant enzymes such as Mn-SOD and Prx1, to detoxify oxidized low density lipoproteins, and to induce high levels of receptor activator of nuclear factor κB ligand by the T cells they activate and further emphasizes the role that DCs might play in atherosclerosis, a pathology recognized as a chronic inflammatory disorder.
Early Appearance of TNF-α and Other Cytokines in Bronchus Associated Lymphoid Tissues (BALT) from Growing Wistar Rats. What is the Role of TNF-α?

Several different cytokines trigger the development of determined cell subsets in BALT of growing Wistar rats. Early appearance (4 days post partum) of γδT cells in BALT has been shown, as well as its role in up-regulating TNF-α production. In the present report, we studied in the BALT: (1) the profile of the cytokines, TNF-α, INF-γ and IL-10 and (2) in TCR γδ+ cells, the existence of a colocalization with TNF-α as well as with INF-γ. All the cytokines studied were observed at an early stage of BALT development by immunohistochemistry and in bronchoalveolar cells (BAL cells) by flow cytometry and western blot. (1) The principal cytokine found at 4 days of age in BALT cells was TNF-α that increases along BALT development. The same behavior was found for cells containing IL-10 and INF-γ. (2) TCR γδ+ cells colocalize mainly with TNF-α as it has been shown by immunohistochemistry in BALT and by flow cytometry when we studied BAL. The early appearance of TNF-α concomitant with TCR γδ+ cell suggests an important role for this cytokine along BALT development. Moreover, mutual regulation between them exists taking part in the immune surveillance and repair of damaged epithelia.
The Candida glabrata sterol scavenging mechanism, mediated by the ATP‐binding cassette transporter Aus1p, is regulated by iron limitation

During disseminated infection by the opportunistic pathogen Candida glabrata, uptake of sterols such as serum cholesterol may play a significant role during pathogenesis. The ATP‐binding cassette transporter Aus1p is thought to function as a sterol importer and in this study, we show that uptake of exogenous sterols occurred under anaerobic conditions in wild‐type cells of C. glabrata but not in AUS1‐deleted mutant (aus1Δ) cells. In aerobic cultures, growth inhibition by fluconazole was prevented in the presence of serum, and AUS1 expression was upregulated. Uptake of sterol by azole treated cells required the presence of serum, and sterol alone did not reverse FLC inhibition of growth. However, if iron availability in the growth medium was limited by addition of the iron chelators ferrozine or apo‐transferrin, growth of wild‐type cells, but not aus1Δ cells, was rescued. In a mouse model of disseminated infection, the C. glabrata aus1Δ strain caused a significantly decreased kidney fungal burden than the wild‐type strain or a strain in which AUS1 was restored. We conclude that sterol uptake in C. glabrata can occur in iron poor environment of host tissues and thus may contribute to C. glabrata pathogenesis.
Face Recognition using Curvelet and ICA

In recent years, many different image features have been used for face recognition. Wavelet Transform is a popular multiresolution analysis tool in image processing and computer vision. Recent researches on multi-scale analysis, especially the curvelet research, provide good opportunity to extract face image features. The transform was designed to represent edges and other singularities along curves much more efficiently than traditional transforms. In this paper we extract image features of facial images from curvelet transform. We then transformed this feature vector into the basis space of PCA and ICA and compared the performance using Euclidean distance measure as classifier. The results show maximum accuracy of 87.50% and 85.00% for curvelet-ICA and curvelet-PCA respectively. Whereas accuracy using PCA and ICA alone was 82.50 and 73% respectively.
Characterization of PID and lead/lag compensators satisfying given H/sub /spl infin// specifications

This note deals with the problem of characterizing a class of second-order three-parameter controllers [including proportional-integral-derivative (PID) and lead/lag compensators] satisfying given H/sub /spl infin// closed-loop specifications. Design characterizations of similar form as in the recent work on PID control, are derived for a larger class of compensators using simple geometric considerations. Specifically it is shown that, given the value of one parameter: i) the region of the plane defined by the other two parameters where the considered H/sub /spl infin// constraint is satisfied, consists of the union of disjoint convex sets whose number can be bounded by means of the pancake-cutting formula, and ii) the closed-loop pole distribution can be related to them. An example illustrates how the method can be applied to design a PID controller in the case of bounded sensitivity.
The Role and Clinical Relevance of Disseminated Tumor Cells in Breast Cancer

Tumor cell dissemination is a common phenomenon observed in most cancers of epithelial origin. One-third of breast cancer patients present with disseminated tumor cells (DTCs) in bone marrow at time of diagnosis; these patients, as well as patients with persistent DTCs, have significantly worse clinical outcome than DTC-negative patients. Since DTC phenotype may differ from the primary tumor with regard to ER and HER2 status, reevaluation of predictive markers on DTCs may optimize treatment choices. In the present review, we report on the clinical relevance of DTC detection in breast cancer.
Novel PAPR Reduction Technique Based On Conventional Partial Transmit Sequence ( PTS )

In this paper, a novel approach combining two well known signal processing techniques with traditional partial transmit sequence (PTS) has been proposed and analyzed. This includes convolutional code (CC) and repeating clipping filtering (RCF) techniques. The main objective is to reduce the peak-to-average power ratio (PAPR) of orthogonal frequency division multiplexed (OFDM) signal. The proposed PAPR method is referred to as convolutional-repeating clipping filtering PTS technique (CRCF_PTS). Simulation results show that our proposed PAPR achieved better power reduction factor as compared to the conventional PTS technique (about 2.3 dB). In addition, the overall bit error rate (BER) of OFDM system has been evaluated with and without our proposed PAPR for different standard channel models (Additive Gaussian Noise and Rayleigh fading channels). The results show that our PAPR technique has insignificant slightly changes in the bit BER in case of fading channel model. Therefore, proposed CRCF_PTS technique is practically feasible for OFDM system with no additional processing time. Index Term-OFDM, PTS, and PAPR reduction techniques
A NOVEL MULTIDICTIONARY BASED TEXT COMPRESSION

The amount of digital contents grows at a faster speed as a result does the demand for communicate them. On the other hand, the amount of storage and bandwidth increases at a slower rate. Thus powerful and efficient compression methods are required. The repetition of words and phrases cause the reordered text much more compressible than the original text. On the whole system is fast and achieves close to the best result on the test files. In this study a novel fast dictionary based text compression technique MBRH (Multidictionary with burrows wheeler transforms, Run length coding and Huffman coding) is proposed for the purpose of obtaining improved performance on various document sizes. MBRH algorithm comprises of two stages, the first stage is concerned with the conversion of input text into dictionary based compression . The second stage deals mainly with reduction of the redundancy in multidictionary based compression by using BWT, RLE and Huffman coding. Bib test files of input size of 111, 261 bytes achieves compression ratio of 0.192, bit rate of 1.538 and high speed using MBRH algorithm. The algorithm has attained a good compression ratio, reduction of bit rate and the increase in execution speed.
Text Classification through Time - Efficient Label Propagation in Time-Based Graphs

One of the fundamental assumptions for machine-learning based text classification systems is that the underlying distribution from which the set of labeled-text is drawn is identical to the distribution from which the text-to-be-labeled is drawn. However, in live news aggregation sites, this assumption is rarely correct. Instead, the events and topics discussed in news stories dramatically change over time. Rather than ignoring this phenomenon, we attempt to explicitly model the transitions of news stories and classifications over time to label stories that may be acquired months after the initial examples are labeled. We test our system, based on efficiently propagating labels in time-based graphs, with recently published news stories collected over an eighty day period. Experiments presented in this paper include the use of training labels from each story within the first several days of gathering stories, to using a single story as a label.
Conformational behavior of DNA-templated CdS inorganic nanowire

We describe the conformational behavior and morphological control of DNA-mineralized CdS nanowires in a bulk solution. The conformational behavior of individual double-stranded DNA in the presence of cadmium ions and stoichiometric mixtures of cadmium ions and sulfide ions was directly visualized by fluorescence microscopy. It was found that in the presence of mixtures of cadmium ions and sulfide ions, DNA molecules exhibit a conformational transition from an elongated coil to a compacted state. Mineralized DNA nanowires possess a significant conformational freedom at a microscale, and flexibility in the micro- and nanodimensions. The density of the inorganic material on the nanowire can be controlled by varying the concentrations and the molar ratio of Na2S to Cd(ClO4)2.
Atg24-assisted mitophagy in the foot cells is necessary for proper asexual differentiation in Magnaporthe oryzae

Macroautophagy-mediated glycogen catabolism is required for asexual differentiation in the blast fungus, Magnaporthe oryzae. However, the function(s) of selective subtypes of autophagy has not been studied therein. Here, we report that mitophagy, selective autophagic delivery of mitochondria to the vacuoles for degradation, occurs during early stages of Magnaporthe conidiation. Specifically, mitophagy was evident in the foot cells while being undetectable in aerial hyphae and/or conidiophores. We show that loss of MoAtg24, a sorting nexin related to yeast Snx4, disrupts mitophagy and consequently leads to highly reduced conidiation, suggesting that mitophagy in the foot cells plays an important role during asexual development in Magnaporthe. Ectopic expression of yeast ScATG32 partially suppressed the conidiation initiation defects associated with MoATG24 deletion. MoAtg24 was neither required for pexophagy nor for macroautophagy, or for MoAtg8 localization per se, but directly associated with and likely recruited mitochondria to the autophagic structures during mitophagy. Lastly, MoAtg24 was also required for oxidative stress response in Magnaporthe.
Electrodeposition and the Optimization of Molybdenum Layer on Nb-Ti-Si Based Ultra-High Alloys from Aqueous Solution

Depositing a molybdenum layer through electrodeposition is a possible and economical way to prepare Mo layer. It could be a new preparation of MoSi2 coating on Nb-Ti-Si based alloys combined with halide pack cementation. In this paper, the effects of pre-coated Re layer on the substrate, pH of the electrolyte, water to acetate ratio and the applied current density on the deposition were investigated and optimized to obtain low oxygen content, adherent molybdenum coating on Nb-Ti-Si based alloys. The surface morphology and cross section were characterized by SEM. The thickness of the deposit is about 6 μm and nodules and cracks were observed on the surface. EDS and EPMA analysis suggested the presence of Mo and its oxides in the deposit; XPS results confirmed the presence of Mo, Mo2O3 and MoO3 in the as-deposited layer. The crystal structure of as-prepared coating was amorphous by the XRD investigation, and the metallic molybdenum was the main existence form of the molybdenum element in the deposit.
A regulatory cascade involving retinoic acid, Cbfa1, and matrix metalloproteinases is coupled to the development of a process of perichondrial invasion and osteogenic differentiation during bone formation

Tissue-remodeling processes are largely mediated by members of the matrix metalloproteinase (MMP) family of endopeptidases whose expression is strictly controlled both spatially and temporally. In this article, we have examined the molecular mechanisms that could contribute to modulate the expression of MMPs like collagenase-3 and MT1-MMP during bone formation. We have found that all-trans retinoic acid (RA), which usually downregulates MMPs, strongly induces collagenase-3 expression in cultures of embryonic metatarsal cartilage rudiments and in chondrocytic cells. This effect is dose and time dependent, requires the de novo synthesis of proteins, and is mediated by RAR-RXR heterodimers. Analysis of the signal transduction mechanisms underlying the upregulating effect of RA on collagenase-3 expression demonstrated that this factor acts through a signaling pathway involving p38 mitogen-activated protein kinase. RA treatment of chondrocytic cells also induces the production of MT1-MMP, a membrane-bound metalloproteinase essential for skeletal formation, which participates in a proteolytic cascade with collagenase-3. The production of these MMPs is concomitant with the development of an RA-induced differentiation program characterized by formation of a mineralized bone matrix, downregulation of chondrocyte markers like type II collagen, and upregulation of osteoblastic markers such as osteocalcin. These effects are attenuated in metatarsal rudiments in which RA induces the invasion of perichondrial osteogenic cells from the perichondrium into the cartilage rudiment. RA treatment also resulted in the upregulation of Cbfa1, a transcription factor responsible for collagenase-3 and osteocalcin induction in osteoblastic cells. The dynamics of Cbfa1, MMPs, and osteocalcin expression is consistent with the fact that these genes could be part of a regulatory cascade initiated by RA and leading to the induction of Cbfa1, which in turn would upregulate the expression of some of their target genes like collagenase-3 and osteocalcin.
Fast Collision Detection Algorithms with Applications to Particle Flow

In this paper, we present efficient algorithms for collision detection of arbitrarily shaped rigid moving objects in a variety of interactive as well as non‐interactive environments. The algorithms primarily consist of two stages. The first stage involves finding candidate objects for possible collisions. The second stage involves detecting exact (within a prespecified tolerance) collision between these candidates. The primary data structure used in the algorithms is an octree. In the first stage, we build an octree for the enclosure containing the objects, which is used to detect possible collisions. Assuming spatial/temporal coherence i.e., that the particles move slowly or that the time sampling is fast enough, the average time complexity of this stage can be shown to be O(n) (excluding the time complexity for a one time octree construction), where n is the number of particles. In the second stage, we build a surface‐octree for each object. If the objects are convex and assuming coherence, the expected time complexity to detect precise (within a prespecified tolerance) collision for each pair is a constant (excluding the time complexity for a one time surface‐octree construction). Therefore, the overall expected time complexity for convex object collision detection is linear with respect to n. For the concave objects, complexity analysis is nontrivial to perform and instead we provide a very practical (almost linear time) algorithm. We apply our algorithms to particle flow simulations by simulating flow density conditions often arising in granular flows.
DeepChrome: deep-learning for predicting gene expression from histone modifications

MOTIVATION Histone modifications are among the most important factors that control gene regulation. Computational methods that predict gene expression from histone modification signals are highly desirable for understanding their combinatorial effects in gene regulation. This knowledge can help in developing 'epigenetic drugs' for diseases like cancer. Previous studies for quantifying the relationship between histone modifications and gene expression levels either failed to capture combinatorial effects or relied on multiple methods that separate predictions and combinatorial analysis. This paper develops a unified discriminative framework using a deep convolutional neural network to classify gene expression using histone modification data as input. Our system, called DeepChrome, allows automatic extraction of complex interactions among important features. To simultaneously visualize the combinatorial interactions among histone modifications, we propose a novel optimization-based technique that generates feature pattern maps from the learnt deep model. This provides an intuitive description of underlying epigenetic mechanisms that regulate genes. RESULTS We show that DeepChrome outperforms state-of-the-art models like Support Vector Machines and Random Forests for gene expression classification task on 56 different cell-types from REMC database. The output of our visualization technique not only validates the previous observations but also allows novel insights about combinatorial interactions among histone modification marks, some of which have recently been observed by experimental studies. AVAILABILITY AND IMPLEMENTATION Codes and results are available at www.deepchrome. org CONTACT yanjun@virginia.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Hepatocellular Carcinoma With Bile Duct Tumor Thrombus

AbstractAlthough hepatocellular carcinoma (HCC) with bile duct tumor thrombus (BDTT) is a rare entity, most patients experience tumor recurrence even after curative resection and the prognosis remains dismal. This study aimed to analyze the clinicopathological risk factors for recurrence and poor outcome after surgical treatment of HCC with BDTT.Clinicopathological data of 37 patients with HCC and BDTT who underwent surgical treatment from July 2005 to June 2012 at the authors’ hospital were reviewed retrospectively. Prognostic factors and potential risk factors for recurrence were assessed by Cox proportional hazard model and binary logistic regression model, respectively.Among the 37 patients, anatomical and nonanatomical liver resection was performed in 26 and 11 patients, respectively. The resection was considered curative in 19 patients and palliative in 18 patients. Also, 21 cases had tumor recurrence after operation and 7 cases of them were reoperated. Multivariate binary logistic regression model revealed that surgical curability was the only independent risk factor associated with postoperative tumor recurrence (P = 0.034). In addition, postoperative overall survival rates at 1, 2, and 3 years were 64.2%, 38.9%, and 24.3%, respectively. Cox multivariate analysis indicated that surgical curability and tumor recurrence were independent prognostic factors for both overall survival and recurrence-free survival (P < 0.05). Although patients with HCC and BDTT had a relatively high rate of early recurrence after surgery, relatively favorable long-term outcome after curative hepatic resection could be achieved. Therefore, extensive and curative surgical treatment should be recommended when complete resection can be achieved and liver functional reserve is satisfactory.
Online Entity Resolution Using an Oracle

Entity resolution (ER) is the task of identifying all records in a database that refer to the same underlying entity. This is an expensive task, and can take a significant amount of money and time; the end-user may want to take decisions during the process, rather than waiting for the task to be completed. We formalize an online version of the entity resolution task, and use an oracle which correctly labels matching and non-matching pairs through queries. In this setting, we design algorithms that seek to maximize progressive recall, and develop a novel analysis framework for prior proposals on entity resolution with an oracle, beyond their worst case guarantees. Finally, we provide both theoretical and experimental analysis of the proposed algorithms.
Survey-Based Analysis of the Proposed Component-Based Development Process

The concept of component-based development (CBD) is widely practiced in software (SW) development. CBD is based on reuse of the existing components with the new ones. The objective of this paper is to propose a novel process model for CBD. Importance of repository has also been discussed. A survey has been conducted to evaluate the proposed model. The results of the survey show that proposed process model can be efficiently implemented for CBD projects.