Miracle-dz/UniFAR-FTUs huggingface dataset:
Determination of nonligand amino acids critical to [4Fe-4S]2+/+ assembly in ferredoxin maquettes.

The prototype ferredoxin maquette, FdM, is a 16-amino acid peptide which efficiently incorporates a single [4Fe-4S]2+/+ cluster with spectroscopic and electrochemical properties that are typical of natural bacterial ferredoxins. Using this synthetic protein scaffold, we have investigated the role of the nonliganding amino acids in the assembly of the iron-sulfur cluster. In a stepwise fashion, we truncated FdM to a seven-amino acid peptide, FdM-7, which incorporates a cluster spectroscopically identical to FdM but in lower yield, 29% relative to FdM. FdM-7 consists solely of the. CIACGAC. consensus ferredoxin core motif observed in natural protein sequences. Initially, all of the nonliganding amino acids were substituted for either glycine, FdM-7-PolyGly (.CGGCGGC.), or alanine, FdM-7-PolyAla (.CAACAAC.), on the basis of analysis of natural ferredoxin sequences. Both FdM-7-PolyGly and FdM-7-PolyAla incorporated little [4Fe-4S]2+/+ cluster, 6 and 7%, respectively. A systematic study of the incorporation of a single isoleucine into each of the four nonliganding positions indicated that placement either in the second or in the sixth core motif positions,. CIGCGGC. or.CGGCGIC. , restored the iron-sulfur cluster binding capacity of the peptides to the level of FdM-7. Incorporation of an isoleucine into the fifth position,. CGGCIGC. , which in natural ferredoxins is predominantly occupied by a glycine, resulted in a loss of [4Fe-4S] affinity. The substitution of leucine, tryptophan, and arginine into the second core motif position illustrated the stabilization of the [4Fe-4S] cluster by bulky hydrophobic amino acids. Furthermore, the incorporation of a single isoleucine into the second core motif position in a 16-amino acid ferredoxin maquette resulted in a 5-fold increase in the level of [4Fe-4S] cluster binding relative to that of the glycine variant. The protein design rules derived from this study are fully consistent with those derived from natural ferredoxin sequence analysis, suggesting they are applicable to both the de novo design and structure-based redesign of natural proteins.
Jua : Customer Facing System to Improve User Experience in Public Clouds

—Public cloud providers lease virtual machines(VM) on a server to customers. This model makes it easier for cloud providers to manage their infrastructure. However, on the other hand, it presents the customers with difﬁculty in terms of manually selecting the VM instance type. The inherent performance heterogeneity observed in public clouds further leads to the uncertainty of VM performance observed. We propose Jua , a customer facing system that solves the above problems. It consists of two main modules - VM Instance Selector and VM placement Gamer. The former performs the task of choosing the appropriate VM instance type adopting a machine learning methodology and the latter module implements a number of placement gaming strategies to ensure that the customers get the best performance relative to the cost they incur. Initial evaluation of Jua conﬁrms the viability of using a machine learning based approach for the selection of instance type. Finally, we develop a simulator to model and implement the various placement strategies and evaluate the same using a wide variety of synthetic benchmarks. We achieve a maximum performance improvement of 70%.
The Role of Climatic and Density Dependent Factors in Shaping Mosquito Population Dynamics: The Case of Culex pipiens in Northwestern Italy

Culex pipiens mosquito is a species widely spread across Europe and represents a competent vector for many arboviruses such as West Nile virus (WNV), which has been recently circulating in many European countries, causing hundreds of human cases. In order to identify the main determinants of the high heterogeneity in Cx. pipiens abundance observed in Piedmont region (Northwestern Italy) among different seasons, we developed a density-dependent stochastic model that takes explicitly into account the role played by temperature, which affects both developmental and mortality rates of different life stages. The model was calibrated with a Markov chain Monte Carlo approach exploring the likelihood of recorded capture data gathered in the study area from 2000 to 2011; in this way, we disentangled the role played by different seasonal eco-climatic factors in shaping the vector abundance. Illustrative simulations have been performed to forecast likely changes if temperature or density–dependent inputs would change. Our analysis suggests that inter-seasonal differences in the mosquito dynamics are largely driven by different temporal patterns of temperature and seasonal-specific larval carrying capacities. Specifically, high temperatures during early spring hasten the onset of the breeding season and increase population abundance in that period, while, high temperatures during the summer can decrease population size by increasing adult mortality. Higher densities of adult mosquitoes are associated with higher larval carrying capacities, which are positively correlated with spring precipitations. Finally, an increase in larval carrying capacity is expected to proportionally increase adult mosquito abundance.
Identification of the Rabies Virus Alpha/Beta Interferon Antagonist: Phosphoprotein P Interferes with Phosphorylation of Interferon Regulatory Factor 3

ABSTRACT Rabies virus (RV) of the Rhabdoviridae family grows in alpha/beta interferon (IFN)-competent cells, suggesting the existence of viral mechanisms preventing IFN gene expression. We here identify the viral phosphoprotein P as the responsible IFN antagonist. The critical involvement of P was first suggested by the observation that an RV expressing an enhanced green fluorescent protein (eGFP)-P fusion protein (SAD eGFP-P) (S. Finke, K. Brzózka, and K. K. Conzelmann, J. Virol. 78:12333-12343, 2004) was eliminated in IFN-competent HEp-2 cell cultures, in contrast to wild-type (wt) RV or an RV replicon lacking the genes for matrix protein and glycoprotein. SAD eGFP-P induced transcription of the IFN-β gene and expression of the IFN-responsive MxA and STAT-1 genes. Similarly, an RV expressing low levels of P, which was generated by moving the P gene to a promoter-distal gene position (SAD ΔPLP), lost the ability to prevent IFN induction. The analysis of RV mutants lacking expression of truncated P proteins P2, P3, or P4, which are expressed from internal AUG codons of the wt RV P open reading frame, further showed that full-length P is competent in suppressing IFN-β gene expression. In contrast to wt RV, the IFN-inducing SAD ΔPLP caused S386 phosphorylation, dimerization, and transcriptional activity of IFN regulatory factor 3 (IRF-3). Phosphorylation of IRF-3 by TANK-binding kinase-1 expressed from transfected plasmids was abolished in wt RV-infected cells or by cotransfection of P-encoding plasmids. Thus, RV P is necessary and sufficient to prevent a critical IFN response in virus-infected cells by targeting activation of IRF-3 by an upstream kinase.
The eIF3c/NIP1 PCI domain interacts with RNA and RACK1/ASC1 and promotes assembly of translation preinitiation complexes

Several subunits of the multifunctional eukaryotic translation initiation factor 3 (eIF3) contain well-defined domains. Among them is the conserved bipartite PCI domain, typically serving as the principal scaffold for multisubunit 26S proteasome lid, CSN and eIF3 complexes, which constitutes most of the C-terminal region of the c/NIP1 subunit. Interestingly, the c/NIP1-PCI domain is exceptional in that its deletion, despite being lethal, does not affect eIF3 integrity. Here, we show that a short C-terminal truncation and two clustered mutations directly disturbing the PCI domain produce lethal or slow growth phenotypes and significantly reduce amounts of 40S-bound eIF3 and eIF5 in vivo. The extreme C-terminus directly interacts with blades 1–3 of the small ribosomal protein RACK1/ASC1, which is a part of the 40S head, and, consistently, deletion of the ASC1 coding region likewise affects eIF3 association with ribosomes. The PCI domain per se shows strong but unspecific binding to RNA, for the first time implicating this typical protein–protein binding domain in mediating protein–RNA interactions also. Importantly, as our clustered mutations severely reduce RNA binding, we conclude that the c/NIP1 C-terminal region forms an important intermolecular bridge between eIF3 and the 40S head region by contacting RACK1/ASC1 and most probably 18S rRNA.
Chaos Synchronization: a Lagrange Programming Network Approach Running Title - Chaos Synchronization: a Lagrange Programming Network Approach

In this paper we interpret chaos synchronization schemes within the framework of Lagrange programming networks, which form a class of continuous-time optimization methods for solving constrained nonlinear optimization problems. From this study it follows that standard synchronization schemes can be regarded as a Lagrange programming network with soft constraining, where synchronization between state vectors is de ned as a constraint to the dynamical systems. New schemes are proposed then which implement synchronization by hard and soft constraints within Lagrange programming networks. A version is derived which takes into account synchronization errors within the problem formulation. Furthermore Lagrange programming networks for achieving partial and generalized synchronization are given. The methods assume the existence of potential functions for the given systems. The proposed Lagrange programming networks with hard and soft constraining show improved performance on many simulation examples for identical and non-identical chaotic systems. The schemes are illustrated on Chua's circuit, Lorenz attractor and n-scroll circuits.
Establishment and Characterization Epithelioid Hemangioendothelioma Thyroid Tumor of a Malignant from Mouse

A mouse epithelioid hemangioendothelioma (mEHE) cell line, passagable in vivo without TSH stimulation, was established from a thyroid tumor. Before establishment of the cell line, the primary thyroid tumor which was co-transplanted with a TSH-producing pituitary adenoma showed signs of hyperplasia and then transformed during several in vivo transplantable passages. The cell line which was established from an in vitro culture, was deficient in thyroid-specific differentiation function and had characteristics of endothelial cell origin such as vascular cavity formation and factor VIII expression. The cell growth of mEHE/CH1-5 cell lines was independent of TSH but was inhibited by c-AMP and vitamin D3. c-Myc proto-oncogene expression was also suppressed by vitamin D3 treatment. Both serum depletion and heparin treatment induced morphological changes in mEHE/CH 5 from an epithelial cell-like to an endothelial cell-like shape. Immunohistochemical analysis showed that epithelial membrane antigen expression was decreased and factor VIII expression was increased in relation to the morphological changes. In a further in vivo transplantation experiment, the histology of the mEHE/CH5 cell tumor had an angiosarcoma-like structure. These results indicate that this cell line established from a thyroid tumor possesses both epithelial and endothelial characteristics. The mEHE/ CH5 cells might provide a good model for analyzing thyroid tumorigenesis and allow functional characterization of endothelial cells.
A role for SUMOylation in snoRNP biogenesis revealed by quantitative proteomics

A role for SUMOylation in the biogenesis and/or function of Box C/D snoRNPs has been reported, mediated via SUMO2 conjugation to the core snoRNP protein, Nop58. A quantitative proteomics screen, based on SILAC (stable-isotope labeling by amino acids in cell culture) and mass spectrometry using extracts prepared from cultured mammalian cells expressing either 6His-SUMO1 or -SUMO2, revealed that the snoRNP-related proteins Nop58, Nhp2, DKC1 and NOLC1 are amongst the main SUMO-modified proteins in the nucleolus. SUMOylation of Nhp2 and endogenous Nop58 was confirmed using a combination of in vitro and cell-based assays and the modified lysines identified by site-directed mutagenesis. SUMOylation of Nop58 was found to be important for high-affinity Box C/D snoRNA binding and the localisation of newly transcribed snoRNAs to the nucleolus. Here, these findings are reviewed and a model for understanding Nop58 SUMOylation in the context of Box C/D snoRNP biogenesis is presented. Given the essential role of snoRNPs in the modification of pre-ribosomal RNA, this work suggests that SUMO, snoRNPs and ribosome assembly, and thus cellular translation, growth and proliferation, may be linked via novel mechanisms which warrant further investigation.
Central Angiotensin II Stimulation Promotes β Amyloid Production in Sprague Dawley Rats

Background Stress and various stress hormones, including catecholamines and glucocorticoids, have recently been implicated in the pathogenesis of Alzheimer's disease (AD), which represents the greatest unresolved medical challenge in neurology. Angiotensin receptor blockers have shown benefits in AD and prone-to-AD animals. However, the mechanisms responsible for their efficacy remain unknown, and no studies have directly addressed the role of central angiotensin II (Ang II), a fundamental stress hormone, in the pathogenesis of AD. The present study focused on the role of central Ang II in amyloidogenesis, the critical process in AD neuropathology, and aimed to provide direct evidence for the role of this stress hormone in the pathogenesis of AD. Methodology/Principal Findings Increased central Ang II levels during stress response were modeled by intracerebroventricular (ICV) administration of graded doses of Ang II (6 ng/hr low dose, 60 ng/hr medium dose, and 600 ng/hr high dose, all delivered at a rate of 0.25 µl/hr) to male Sprague Dawley rats (280–310 g) via osmotic pumps. After 1 week of continuous Ang II infusion, the stimulation of Ang II type 1 receptors was accompanied by the modulation of amyloid precursor protein, α-, β-and γ-secretase, and increased β amyloid production. These effects could be completely abolished by concomitant ICV infusion of losartan, indicating that central Ang II played a causative role in these alterations. Conclusions/Significance Central Ang II is essential to the stress response, and the results of this study suggest that increased central Ang II levels play an important role in amyloidogenesis during stress, and that central Ang II-directed stress prevention and treatment might represent a novel anti-AD strategy.
The Compressor: concurrent, incremental, and parallel compaction

The widely used Mark-and-Sweep garbage collector has a drawback in that it does not move objects during collection. As a result, large long-running realistic applications, such as Web application servers, frequently face the fragmentation problem. To eliminate fragmentation, a heap compaction is run periodically. However, compaction typically imposes very long undesirable pauses in the application. While efficient concurrent collectors are ubiquitous in production runtime systems (such as JVMs), an efficient non-intrusive compactor is still missing.In this paper we present the Compressor, a novel compaction algorithm that is concurrent, parallel, and incremental. The Compressor compacts the entire heap to a single condensed area, while preserving the objects' order, but reduces pause times significantly, thereby allowing acceptable runs on large heaps. Furthermore, the Compressor is the first compactor that requires only a single heap pass. As such, it is the most efficient compactors known today, even when run in a parallel Stop-the-World manner (i.e., when the program threads are halted). Thus, to the best of our knowledge, the Compressor is the most efficient compactor known today. The Compressor was implemented on a Jikes Research RVM and we provide measurements demonstrating its qualities.
Automatically Recognizing Facial Expressions in the Spatio-Temporal Domain

We developed a computer vision system that automatically recognizes facial action units (AUs) or AU combinations using Hidden Markov Models (HMMs). AUs are defined as visually discriminable muscle movements. The facial expressions are recognized in digitized image sequences of arbitrary length. In this paper, we use two approaches to extract the expression information: (1) facial feature point tracking, which is sensitive to subtle feature motion, in the mouth region, and (2) pixel-wise flow tracking, which includes more motion information, in the forehead and brow regions. In the latter approach, we use principal component analysis (PCA) to compress the data. We accurately recognize 93% of the lower face expressions and 91% of the upper face expressions.
A high-speed algorithm for elliptical object detection

A high-speed method for elliptical object location is proposed. Through the use of the geometric symmetry, it first locates the centers of elliptical objects and classifies the boundary points. Then, each point possible on an elliptical object boundary is used to obtain the remaining three parameters of the elliptical object. Since each boundary point is at most transformed to one point on the parameter space, the proposed method is very fast. Some experimental results are also given to show that the proposed method is better than some existing methods under the consideration of space and storage.
An Adaptive Manifold Learning Algorithm Based on ISOMAP

Manifold learning algorithms, such as ISOMAP, LLE, Laplacian Eigenmaps, LTSA and so on, are designed to map nonlinear high dimensional data into the low dimensional space. The key of their success is to select a suitable neighborhood parameter. However, it is difficult to determine a proper neighborhood size for most of manifold learning methods, in particular for non-uniform data sets. An adaptive manifold learning algorithm based on ISOMAP is presented to solve the problem by combining two methods of building the neighborhoods. In the method, all points within a fixed radius are taken as the neighborhood candidate points. The data point number contained in the neighborhood is constricted to a more proper range by setting a minimum value and a maximum value containing points in the neighborhood. Experiments show that the proposed algorithm is effective for the uniform data sets as well as the non-uniform data sets. Moreover, the difficulty of selecting the neighborhood parameter is greatly degraded.
Robust facial expression recognition based on RPCA and AdaBoost

In this paper, we consider the problem of robust facial expression recognition and propose a novel scheme for facial expression recognition under facial occlusion. There are two main contributions in this work. Firstly, a novel method for facial occlusion detection based on robust principal component analysis (RPCA) and saliency detection performs efficiently to detect facial occlusions. Secondly, a novel method based on occlusion reconstruction and reweighted AdaBoost classification is prosed for facial expression recognition. Experimental results have shown the effectiveness of our proposed method for robust facial expression recognition.
Obesity measures, metabolic profiles, blood pressure and intake of dietary fatty acids in rural women of Asian Indian origin: Santiniketan women study

Objectives: The present cross-sectional study was aimed to investigate obesity measures, metabolic profiles, blood pressure, and intake of dietary fatty acids in rural women of Asian Indian origin. Materials and Methods: A total of 280 healthy rural women aged 25–65 years took part in the study. A random sampling procedure using a local voters′ registration list was followed to select the participants. All participants belonged to the Bengalee population and were inhabitants of the Bolpur-Santiniketan area, West Bengal, India. Anthropometric measures, namely, height, weight, circumferences of waist and hip, skinfolds at biceps, triceps, subscapular, and suprailiac regions, etc., were collected using standard techniques. Body mass index (BMI), percentages of body fat (PBFs), basal metabolic rate (BMR), and intra-abdominal visceral fat (IVF) were measured using an Omron body fat analyzer (Omron Corporation, Tokyo, Japan). Fat mass (FM), fat free mass (FFM), waist–hip ratio (WHR), and sum of four skinfolds (SF4) were also taken into consideration. Blood pressure and metabolic and hormonal profiles were measured using standard techniques. The weekly consumption (frequency) of food stuffs was collected using an already validated food frequency schedule. Results: The result showed that the mean age was 41.52 ± 10.95, BMI 23.07 ± 4.34, PBF 31.76 ± 7.06, BMR 1162.34 ± 139.59, WHR 0.83 ± 0.06, systolic blood pressure 118.84 ± 20.35, diastolic blood pressure 77.77 ± 12.12, total cholesterol 185.61 ± 25.19, triglyceride level 135.82 ± 30.39, high-density lipoprotein 48.13 ± 6.13, low-density lipoprotein 109.90 ± 22.53, fasting blood glucose 90.91 ± 7.98, and insulin 11.98 ± 3.42. The result also shows the mean intake of total protein to be 177.01 ± 47.79, total energy 8321.60 ± 1354.86, total fat 210.36 ± 53.57, total PUFA 82.02 ± 49.73, and total MUFA 94.01 ± 16.38. The percentile distribution of the dietary fat intake revealed that the 10th and 95th percentile values of the total protein intake were 125.3 and 261.5, total energy intake were 7491.6 and 10470.2, total fat intake were 178.8 and 273.5, total PUFA intake were 55.5 and 191.7, and of the total MUFA intake were 86.0 and 126.9, respectively. Conclusion: It seems reasonable to argue that dietary management including dietary guidelines across India is essential to retard the growing incidence of cardiovascular diseases in coming years.
capt2web — An embedded Web-based gateway platform for spatially distributed wireless networks

A novel communication platform is presented, which helps in the monitoring and deployment of distributed wireless networks. Its major part is based on distributed embedded web servers connected to RF-communication heads. The web servers act as distributed communication hubs and exchange data via XML-feeds with web2.0-capable clients. The first implementations are concentrating on the monitoring direction, as this approach eases supervision of spatially distributed wireless networks, and also allows seamless remote monitoring. But it is also capable to feed data frames into the wireless network. The platform already supports protocols like Wireless MBus and EnOcean Radio Protocol (ERP), but is flexible to integrate arbitrary protocols. In addition, this is — to the very best knowledge of the authors — the very first AJAX implementation on a very lean embedded web server.