Miracle-dz/UniFAR-FTUs huggingface dataset:
Simian immunodeficiency virus from African green monkeys

Simian immunodeficiency virus (SIV) was isolated from the total peripheral blood mononuclear cell population and the monocyte-macrophage adherent cell population of three seropositive green monkeys originating from Kenya. SIV from these African green monkeys (SIVagm) was isolated and continuously produced with the MOLT-4 clone 8 (M4C18) cell line but not with a variety of other cells including HUT-78, H9, CEM, MT-4, U937, and uncloned MOLT-4 cells. Once isolated, these SIVagm isolates were found to replicate efficiently in M4C18, SupT1, MT-4, U937, and Jurkat-T cells but much less efficiently if at all in HUT-78, H9, CEM, and MOLT-4 cells. The range of CD4+ cells fully permissive for replication of these SIVagm isolates thus differs markedly from that of previous SIV isolates from macaques (SIVmac). These SIVagm isolates had a morphogenesis and morphology like that of human immunodeficiency virus (HIV) and other SIV isolates. Antigens of SIVagm and SIVmac cross-reacted by comparative enzyme-linked immunosorbent assay only with reduced efficiency, and optimal results were obtained when homologous antibody and antigen were used. Western blotting (immunoblotting) of purified preparations of SIVagm isolate 385 (SIVagm385) revealed major viral proteins of 120, 27, and 16 kilodaltons (kDa). The presumed major core protein of 27 kDa cross-reacted antigenically with the corresponding proteins of SIVmac (28 kDa) and HIV-1 (24 kDa) by Western blotting. Hirt supernatant replicative-intermediate DNA prepared from cells freshly infected with SIVagm hybridized to SIVmac and HIV-2 DNA probes. Detection of cross-hybridizing DNA sequences, however, required very low stringency, and the restriction endonuclease fragmentation patterns of SIVagm were not similar to those of SIVmac and HIV-2. The nucleotide sequence of a portion of the pol gene of SIVagm385 revealed amino acid identities of 65% with SIVmac142, 64% with HIV-2ROD, and 56% with HIV-1BRU; SIVagm385 is thus related to but distinct from previously described primate lentiviruses SIVmac, HIV-1, and HIV-2. Precise information on the genetic makeup of these and other SIV isolates will possibly lead to better understanding of the history and evolution of these viruses and may provide insight into the origin of viruses that cause acquired immunodeficiency syndrome in humans.
New treatments in hemophilia: insights for the clinician

Hemophilia has evolved from an often fatal hereditary bleeding disorder to a disorder for which safe and effective treatment is available. However, there are several challenges remaining in the treatment of hemophilia. Prophylaxis to prevent bleeding is costly and requires frequent intravenous injections, which are cumbersome for patients. Venous access is often difficult to achieve, especially in small children where central venous lines may need to be implanted. Development of inhibitory antibodies makes treatment of acute bleeds difficult and prophylaxis in patients with inhibitors must also be better addressed. In order to improve treatment, new products are being developed, some of which are already in clinical trials. There are several approaches to prolonging half-lives such as PEGylation, Fc fusion and albumin fusion. Increased activity has been demonstrated in preclinical trials for factor IX and in a human trial with factor VII where the activity of the molecules has been increased by manipulation of the molecular composition. Additional approaches, including blockage of inhibitors of clotting, are also under investigation. Factor VIII and factor IX gene therapy have become a tangible possibility since phase I data recently have been published. Results are promising and there is hope that in the near future substantial progress will be made, perhaps making hemophilia the first genetic condition to be cured.
Quantum Entanglement Concentration Based on Nonlinear Optics for Quantum Communications

Entanglement concentration is of most importance in long distance quantum communication and quantum computation. It is to distill maximally entangled states from pure partially entangled states based on the local operation and classical communication. In this review, we will mainly describe two kinds of entanglement concentration protocols. One is to concentrate the partially entangled Bell-state, and the other is to concentrate the partially entangled W state. Some protocols are feasible in current experimental conditions and suitable for the optical, electric and quantum-dot and optical microcavity systems.
Binaural sound localization for untrained directions based on a Gaussian mixture model

We propose and evaluate estimation methods for all sound source directions on the horizontal plane based on a Gaussian mixture model (GMM) using binaural signals. An estimation method based on GMM can estimate a sound source direction on which GMM has already been trained; however, it cannot estimate without a model that corresponds to a sound source direction. Three methods with interpolation techniques are investigated. Two generate GMMs for all directions by interpolating an acoustic transfer function or statistical values of GMM, and the other calculates the posterior probability for all directions with a limited number of GMMs. In our experiments, we investigated six interval conditions. From the results, the interpolation methods of an acoustic transfer function and the statistical values of GMM achieve better performance. Although there were 12 trained GMMs for the 30° intervals, the interpolation method of the statistical values of GMMestimated 62.5%accuracy (45/72) with 2.8° estimation error. These results indicate that the proposed method can estimate all sound source directions with a small amount of known information.
Evolving Musical Counterpoint: The Chronopoint Musical Evolution System

Musical counterpoint, a musical technique in which two or more independent melodies are played simultaneously with the goal of creating harmony, has been around since the baroque era. However, to our knowledge computational generation of aesthetically pleasing linear counterpoint based on subjective fitness assessment has not been explored by the evolutionary computation community (although generation using objective fitness has been attempted in quite a few cases). The independence of contrapuntal melodies and the subjective nature of musical aesthetics provide an excellent platform for the application of genetic algorithms. In this paper, a genetic algorithm approach to generating contrapuntal melodies is explained, with a description of the various musical heuristics used and of how variable-length chromosome strings are used to avoid generating "jerky" rhythms and melodic phrases, as well as how subjectivity is incorporated into the algorithm's fitness measures. Next, results from empirical testing of the algorithm are presented, with a focus on how a user's musical sophistication influences their experience. Lastly, further musical and compositional applications of the algorithm are discussed along with planned future work on the algorithm.
Campylobacter in Poultry: Ecology and Potential Interventions

SUMMARY Avian hosts constitute a natural reservoir for thermophilic Campylobacter species, primarily Campylobacter jejuni and Campylobacter coli, and poultry flocks are frequently colonized in the intestinal tract with high numbers of the organisms. Prevalence rates in poultry, especially in slaughter-age broiler flocks, could reach as high as 100% on some farms. Despite the extensive colonization, Campylobacter is essentially a commensal in birds, although limited evidence has implicated the organism as a poultry pathogen. Although Campylobacter is insignificant for poultry health, it is a leading cause of food-borne gastroenteritis in humans worldwide, and contaminated poultry meat is recognized as the main source for human exposure. Therefore, considerable research efforts have been devoted to the development of interventions to diminish Campylobacter contamination in poultry, with the intention to reduce the burden of food-borne illnesses. During the past decade, significant advance has been made in understanding Campylobacter in poultry. This review summarizes the current knowledge with an emphasis on ecology, antibiotic resistance, and potential pre- and postharvest interventions.
Endogenous Nmnat2 Is an Essential Survival Factor for Maintenance of Healthy Axons

We conclude that endogenous Nmnat2 prevents spontaneous degeneration of healthy axons and propose that, when present, the more long-lived, functionally related WldS protein substitutes for Nmnat2 loss after axon injury. Endogenous Nmnat2 represents an exciting new therapeutic target for axonal disorders.
Efficient and Fast Differentiation of Human Neural Stem Cells from Human Embryonic Stem Cells for Cell Therapy

Stem cell-based therapies have been used for repairing damaged brain tissue and helping functional recovery after brain injury. Aberrance neurogenesis is related with brain injury, and multipotential neural stem cells from human embryonic stem (hES) cells provide a great promise for cell replacement therapies. Optimized protocols for neural differentiation are necessary to produce functional human neural stem cells (hNSCs) for cell therapy. However, the qualified procedure is scarce and detailed features of hNSCs originated from hES cells are still unclear. In this study, we developed a method to obtain hNSCs from hES cells, by which we could harvest abundant hNSCs in a relatively short time. Then, we examined the expression of pluripotent and multipotent marker genes through immunostaining and confirmed differentiation potential of the differentiated hNSCs. Furthermore, we analyzed the mitotic activity of these hNSCs. In this report, we provided comprehensive features of hNSCs and delivered the knowledge about how to obtain more high-quality hNSCs from hES cells which may help to accelerate the NSC-based therapies in brain injury treatment.
Landscape moderation of biodiversity patterns and processes ‐ eight hypotheses

Understanding how landscape characteristics affect biodiversity patterns and ecological processes at local and landscape scales is critical for mitigating effects of global environmental change. In this review, we use knowledge gained from human‐modified landscapes to suggest eight hypotheses, which we hope will encourage more systematic research on the role of landscape composition and configuration in determining the structure of ecological communities, ecosystem functioning and services. We organize the eight hypotheses under four overarching themes. Section A: ‘landscape moderation of biodiversity patterns' includes (1) the landscape species pool hypothesis—the size of the landscape‐wide species pool moderates local (alpha) biodiversity, and (2) the dominance of beta diversity hypothesis—landscape‐moderated dissimilarity of local communities determines landscape‐wide biodiversity and overrides negative local effects of habitat fragmentation on biodiversity. Section B: ‘landscape moderation of population dynamics' includes (3) the cross‐habitat spillover hypothesis—landscape‐moderated spillover of energy, resources and organisms across habitats, including between managed and natural ecosystems, influences landscape‐wide community structure and associated processes and (4) the landscape‐moderated concentration and dilution hypothesis—spatial and temporal changes in landscape composition can cause transient concentration or dilution of populations with functional consequences. Section C: ‘landscape moderation of functional trait selection’ includes (5) the landscape‐moderated functional trait selection hypothesis—landscape moderation of species trait selection shapes the functional role and trajectory of community assembly, and (6) the landscape‐moderated insurance hypothesis—landscape complexity provides spatial and temporal insurance, i.e. high resilience and stability of ecological processes in changing environments. Section D: ‘landscape constraints on conservation management' includes (7) the intermediate landscape‐complexity hypothesis—landscape‐moderated effectiveness of local conservation management is highest in structurally simple, rather than in cleared (i.e. extremely simplified) or in complex landscapes, and (8) the landscape‐moderated biodiversity versus ecosystem service management hypothesis—landscape‐moderated biodiversity conservation to optimize functional diversity and related ecosystem services will not protect endangered species. Shifting our research focus from local to landscape‐moderated effects on biodiversity will be critical to developing solutions for future biodiversity and ecosystem service management.
A Novel Functional Interaction between the Sp1-like Protein KLF13 and SREBP-Sp1 Activation Complex Underlies Regulation of Low Density Lipoprotein Receptor Promoter Function*

Cholesterol homeostasis is regulated by a family of transcription factors designated sterol regulatory element-binding proteins (SREBPs). Precise control of SREBP-targeted genes requires additional interactions with co-regulatory transcription factors. In the case of the low density lipoprotein receptor (LDLR), SREBP cooperates with the specificity protein Sp1 to activate the promoter. In this report, we describe a novel pathway in LDLR transcriptional regulation distinct from the SREBP-Sp1 activation complex involving the Sp1-like protein Krueppel-like factor 13 (KLF13). Using a combination of RNA interference, electrophoretic mobility shift, chromatin immunoprecipitation, and reporter assays, deletion, and site-directed mutagenesis, we demonstrated that KLF13 mediates repression in a DNA context-selective manner. KLF13 repression of LDLR promoter activity appears to be needed to keep the receptor silent, a state that can be antagonized by Sp1, SREBP, and inhibitors of histone deacetylase activity. Chromatin immunoprecipitation assay confirmed that KLF13 binds proximal LDLR DNA sequences in vivo and that exogenous oxysterol up-regulates such binding. Together these studies identify a novel regulatory pathway in which gene repression by KLF13 must be overcome by the Sp1-SREBP complex to activate the LDLR promoter. Therefore, these data should replace a pre-existent and more simple paradigm that takes into consideration only the induction of the activator proteins Sp1-SREBP as necessary for LDLR promoter drive without including default repression, such as that by KLF13, of the LDLR gene.
An Ultra Low-Power Body Sensor Network Control Processor with Centralized Node Control

A body sensor network (BSN) system needs ultra-low power consumption to provide a user-friendly small form-factor. This paper presents the dual-mode system architecture to manage 254 nodes in the BSN with low-power consumption. Its instantaneous program execution with external program counter scheme prohibits unnecessary RISC operation and wakes up the RISC from its turn-off state just in 3-clock cycles, the same as reset sequence. The TCAM-based periodic event generator manages 254 periods of each network node with low energy consumption. The implemented test chip consumes 24.2muW average power for 254 nodes management and 4.2-MIPS performance
Complete Genome Sequence of the Anaerobic Perchlorate-Reducing Bacterium Azospira suillum Strain PS

ABSTRACT Azospira suillum strain PS (formally Dechlorosoma suillum strain PS) is a metabolically versatile betaproteobacterium first identified for its ability to grow by dissimilatory reduction of perchlorate and chlorate [denoted (per)chlorate]. Together with Dechloromonas species, these two genera represent the dominant (per)chlorate-reducing bacteria in mesophilic freshwater environments. In addition to (per)chlorate reduction, A. suillum is capable of the anaerobic oxidation of humic substances and is the first anaerobic nitrate-dependent Fe(II) oxidizer outside the Diaphorobacter and Acidovorax genera for which there is a completed genome sequence.
THE EFFECTS OF PYRIDOXINE DEFICIENCY AND OF CALORIC RESTRICTION ON LIPIDS IN THE DEVELOPING RAT BRAIN 1

Abstract— The effects of dietary deficiency of pyridoxine upon the contents of lipids in the brain were determined at several times after birth for three groups of rats. The mothers of the nursing pups were fed one of the following dietary regimes: pyridoxine‐deficient diet ad lib. , pyridoxine‐supplemented diet ad lib. , or pyridoxine‐supplemented diet in restricted amounts. At 7 and 14 days of postnatal age there were no significant differences between supplemented and deficient animals for any of the cerebral lipids studied. At 21 days the content of sphingomyelin in the brains of deficient animals was significantly lower than that in brains from the supplemented or calorically restricted animals in terms of percentage of total lipid and phospholipid phosphorus or tissue weight. On a per brain basis the content of sphingomyelin in the brains of calorically‐restricted rats was significantly lower than in the brains of rats fed the supplemented diet ad lib. The contents of cerebrosides but not of sulphatides or ceramides were also significantly lower in brains of the deficient group than in brains from the other two groups.
CPP2XMI: Reverse Engineering of UML Class, Sequence, and Activity Diagrams from C++ Source Code

In most cases, reverse engineering is used to retrieve missing design documentation from the source code in the form of an abstract (e.g., UML) model. In the context of this work, reverse engineering is used as a part of the verification and validation chain of software systems, where the static structure and the dynamic behavior of a system are derived from the source code and represented in XML Metadata Interchange (XMI) format. The obtained model is further analyzed for such characteristics as soundness and complexity of the system. XMI is a standard that enables us to express objects using Extensible Markup Language (XML). XMI can be used to represent objects from UML model in XML. In this paper, we describe a reverse engineering tool, CPP2XMI, which allows extracting UML class, sequence, and activity diagrams in XMI format from C++ source code, and its position in the toolset for software system analysis
Endometriosis and Infertility

Endometriosis is an estrogen‐dependent disorder defined as the presence of endometrial tissue outside of the uterine cavity. A leading cause of infertility, endometriosis has a prevalence of 0.5–5% in fertile and 25–40% in infertile women. The optimal choice of management for endometriosis‐associated infertility remains obscure. Removal or suppression of endometrial deposits by medical or surgical means constitutes the basis of endometriosis management. Current evidence indicates that suppressive medical treatment of endometriosis does not benefit fertility and should not be used for this indication alone. Surgery is probably efficacious for all stages of the disease. Controlled ovarian hyperstimulation with intrauterine insemination is recommended in early‐stage and surgically corrected endometriosis when pelvic anatomy is normal. In advanced cases, in vitro fertilization is a treatment of choice, and its success may be augmented with prolonged gonadotropin‐releasing hormone analog treatment. Further randomized clinical trials focusing on diverse etiopathogenic mechanisms and therapeutic innovation are necessary to find more conclusive, evidence‐based answers regarding this enigmatic disease.
Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma

Metastatic melanoma patients have a poor prognosis, mainly attributable to the underlying heterogeneity in melanoma driver genes and altered gene expression profiles. These characteristics of melanoma also make the development of drugs and identification of novel drug targets for metastatic melanoma a daunting task. Systems biology offers an alternative approach to re-explore the genes or gene sets that display dysregulated behaviour without being differentially expressed. In this study, we have performed systems biology studies to enhance our knowledge about the conserved property of disease genes or gene sets among mutually exclusive datasets representing melanoma progression. We meta-analysed 642 microarray samples to generate melanoma reconstructed networks representing four different stages of melanoma progression to extract genes with altered molecular circuitry wiring as compared to a normal cellular state. Intriguingly, a majority of the melanoma network-rewired genes are not differentially expressed and the disease genes involved in melanoma progression consistently modulate its activity by rewiring network connections. We found that the shortlisted disease genes in the study show strong and abnormal network connectivity, which enhances with the disease progression. Moreover, the deviated network properties of the disease gene sets allow ranking/prioritization of different enriched, dysregulated and conserved pathway terms in metastatic melanoma, in agreement with previous findings. Our analysis also reveals presence of distinct network hubs in different stages of metastasizing tumor for the same set of pathways in the statistically conserved gene sets. The study results are also presented as a freely available database at http://bioinfo.icgeb. res.in/m3db/. The web-based database resource consists of results from the analysis presented here, integrated with cytoscape web and user-friendly tools for visualization, retrieval and further analysis.
Advanced process modules and architectures for half-terahertz SiGe:C HBTs

The European project DOTFIVE [1] addresses evolutionary scaling of self-aligned selective epitaxial base SiGe:C HBTs, investigates novel SiGe:C HBT architectures, and develops novel process modules to push SiGe BiCMOS towards 500 GHz Fmax and 2.5 ps gate delay. In this paper, scaling issues of SiGe:C HBT technology will be addressed. The limitations of the different commonly used architectures will be described, and measures taken in the project to overcome these limitations will be summarized. Initial results indicate that the objectives of the project can be reached.
Frequency Control in Isolated/Islanded Microgrids Through Voltage Regulation

This paper presents a frequency control mechanism for an isolated/islanded microgrid through voltage regulation. The proposed scheme makes use of the load voltage sensitivity to operating voltages and can be easily adopted for various types of isolated microgrids. The proposed controller offers various advantages, such as allowing the integration of significant levels of intermittent renewable resources in isolated/islanded microgrids without the need for large energy storage systems, providing fast and smooth frequency regulation with no steady-state error, regardless of the generator control mechanism. The controller requires no extra communication infrastructure, and only local voltage and frequency is used as feedback. The performance of the controller is evaluated and validated through various simulation studies in the PSCAD/EMTDC software environment based on a realistic microgrid test system, using small-perturbation stability analysis to demonstrate the positive effect of the proposed controller in system damping.