Miracle-dz/UniFAR-FTUs huggingface dataset:
Targeted Delivery of Glucan Particle Encapsulated Gallium Nanoparticles Inhibits HIV Growth in Human Macrophages

Glucan particles (GPs) are hollow, porous 3–5 μm microspheres derived from the cell walls of Baker's yeast (Saccharomyces cerevisiae). The 1,3-β-glucan outer shell provides for receptor-mediated uptake by phagocytic cells expressing β-glucan receptors. GPs have been used for macrophage-targeted delivery of a wide range of payloads (DNA, siRNA, protein, small molecules, and nanoparticles) encapsulated inside the hollow GPs or bound to the surface of chemically derivatized GPs. Gallium nanoparticles have been proposed as an inhibitory agent against HIV infection. Here, macrophage targeting of gallium using GPs provides for more efficient delivery of gallium and inhibition of HIV infection in macrophages compared to free gallium nanoparticles.
The pomegranate (Punica granatum L.) genome provides insights into fruit quality and ovule developmental biology

Pomegranate (Punica granatum L.) with an uncertain taxonomic status has an ancient cultivation history, and has become an emerging fruit due to its attractive features such as the bright red appearance and the high abundance of medicinally valuable ellagitannin-based compounds in its peel and aril. However, the absence of genomic resources has restricted further elucidating genetics and evolution of these interesting traits. Here we report a 274-Mb high-quality draft pomegranate genome sequence, which covers approximately 81.5% of the estimated 336 Mb genome, consists of 2,177 scaffolds with an N50 size of 1.7 Mb, and contains 30,903 genes. Phylogenomic analysis supported that pomegranate belongs to the Lythraceae family rather than the monogeneric Punicaceae family, and comparative analyses showed that pomegranate and Eucalyptus grandis shares the paleotetraploidy event. Integrated genomic and transcriptomic analyses provided insights into the molecular mechanisms underlying the biosynthesis of ellagitannin-based compounds, the color formation in both peels and arils during pomegranate fruit development, and the unique ovule development processes that are characteristic of pomegranate. This genome sequence represents the first reference in Lythraceae, providing an important resource to expand our understanding of some unique biological processes and to facilitate both comparative biology studies and crop breeding.
Making Laplacians commute

In this paper, we construct multimodal spectral geometry by finding a pair of closest commuting operators (CCO) to a given pair of Laplacians. The CCOs are jointly diagonalizable and hence have the same eigenbasis. Our construction naturally extends classical data analysis tools based on spectral geometry, such as diffusion maps and spectral clustering. We provide several synthetic and real examples of applications in dimensionality reduction, shape analysis, and clustering, demonstrating that our method better captures the inherent structure of multi-modal data.
Stochastic Information Management in Smart Grid

Rising concerns about the efficiency, reliability, economics, and sustainability in electricity production and distribution have been driving an evolution of the traditional electric power grid toward smart grid. A key enabler of the smart grid is the two-way communications throughout the power system, based on which an advanced information system can make optimal decisions on power system operation. Due to the expected deep penetration of renewable energy sources, energy storage devices, demand side management (DSM) tools, and electric vehicles (EVs) in the future smart grid, there exist significant technical challenges on power system planning and operation. Specifically, efficient stochastic information management schemes should be developed to address the randomness in renewable power generation, buffering effect of energy storage devices, consumer behavior patterns in the context of DSM, and high mobility of EVs. In this paper, we provide a comprehensive literature survey on the stochastic information management schemes for the smart grid. We start this survey with an introduction to the smart grid system architecture and the technical challenges in information management. Various component-level modeling techniques are presented to characterize the sources of randomness in the smart grid. Built upon the component-level models, we further explore the system-level stochastic information management schemes for smart grid planning and operation. Future research directions and open research issues are identified.
Ambient metals, elemental carbon, and wheeze and cough in New York City children through 24 months of age.

RATIONALE The effects of exposure to specific components of ambient fine particulate matter (PM(2.5)), including metals and elemental carbon (EC), have not been fully characterized in young children. OBJECTIVES To compare temporal associations among PM(2.5); individual metal constituents of ambient PM(2.5), including nickel (Ni), vanadium (V), and zinc (Zn); and EC and longitudinal reports of respiratory symptoms through 24 months of age. METHODS Study participants were selected from the Columbia Center for Children's Environmental Health birth cohort recruited in New York City between 1998 and 2006. Respiratory symptom data were collected by questionnaire every 3 months through 24 months of age. Ambient pollutant data were obtained from state-operated stationary monitoring sites located within the study area. For each subject, 3-month average inverse-distance weighted concentrations of Ni, V, Zn, EC, and PM(2.5) were calculated for each symptom-reporting period based on the questionnaire date and the preceding 3 months. Associations between pollutants and symptoms were characterized using generalized additive mixed effects models, adjusting for sex, ethnicity, environmental tobacco smoke exposure, and calendar time. MEASUREMENTS AND MAIN RESULTS Increases in ambient Ni and V concentrations were associated significantly with increased probability of wheeze. Increases in EC were associated significantly with cough during the cold/flu season. Total PM(2.5) was not associated with wheeze or cough. CONCLUSIONS These results suggest that exposure to ambient metals and EC from heating oil and/or traffic at levels characteristic of urban environments may be associated with respiratory symptoms among very young children.
Cidofovir for BK virus-associated hemorrhagic cystitis: a retrospective study.

BACKGROUND BK virus-associated hemorrhagic cystitis (BKV-HC) is a severe complication after allogeneic hematopoietic stem cell transplantation (HSCT), but antiviral treatment for this condition has not been evaluated. METHODS We conducted a retrospective survey on the safety and outcome of cidofovir treatment for patients with BKV-HC in centers affiliated with the European Group for Blood and Marrow Transplantation. RESULTS From 1 April 2004 to 31 December 2007, 62 patients received a diagnosis of BKV-HC after a median interval of 35 days after HSCT (range, 3-577 days). Fifty-seven patients (92%) received intravenous cidofovir, whereas 5 patients received cidofovir intravesically. Complete response (CR) was recorded in 38 (67%) of 57 patients with HC treated with intravenous cidofovir, whereas partial response (PR) was documented in 7 patients (12%). CR was documented in 3 patients and PR in 1 patient with HC treated with intravesical cidofovir. A reduction of 1-3 logs in BKV load was documented in 8 of the 10 patients achieving CR. Mild-to-moderate toxic effects were recorded in 18 of 57 patients who received intravenous cidofovir administration. In a multivariate analysis, the factors significantly associated with response to cidofovir were the stem cell source (P = .01) and the use of total body irradiation (P = .03). After a median follow-up of 287 days, overall survival and total treatment-related mortality rates were 63% and 40% for patients achieving CR, compared with 14% and 72% for patients with PR or no response to cidofovir, respectively (P = .001 and P = .001, respectively). CONCLUSIONS Cidofovir may be a potentially effective therapy for BKV-HC, but evidence supporting its use requires randomized controlled trials.
How was the notochord born?

More than 550 million years ago, chordates originated from a common ancestor shared with nonchordate deuterostomes by developing a novel type of larva, the “tadpole larva. ” The notochord is the supporting organ of the larval tail and the most prominent feature of chordates; indeed, phylum Chordata is named after this organ. In this review, we discuss the molecular mechanisms involved in the formation of the notochord over the course of chordate evolution with a special emphasis on a member of T‐box gene family, Brachyury. Comparison of the decoded genome of a unicellular choanoflagellate with the genomes of sponge and cnidarians suggests that T‐box gene family arose at the time of the evolution of multicellular animals. Gastrulation is a morphogenetic movement that is essential for the formation of two‐ or three‐germ‐layered embryos. Brachyury is transiently expressed in the blastopore (bp) region, where it confers on cells the ability to undergo invagination. This process is involved in the formation of the archenteron in all metazoans. This is a “primary” function of Brachyury. During the evolution of chordates, Brachyury gained an additional expression domain at the dorsal midline region of the bp. In this new expression domain, Brachyury served its “secondary” function, recruiting another set of target genes to form a dorsal axial organ, notochord. The Wnt/β‐catenin, BMP/Nodal, and FGF‐signaling pathways are involved in the transcriptional activation of Brachyury. We discuss the molecular mechanisms of Brachyury secondary function in the context of the dorsal–ventral (D–V) inversion theory and the aboral‐dorsalization hypothesis. Although the scope of this review requires some degree of oversimplification of Brachyury function, it is beneficial to facilitate studies on the notochord formation, a central evolutionary developmental biology problem in the history of metazoan evolution, pointed out first by Alexander Kowalevsky.
Pathogen translocation and histopathological lesions in an experimental model of Salmonella Dublin infection in calves receiving lactic acid bacteria and lactose supplements

The purpose of this study was to evaluate the capacity of a lactic acid bacteria (LAB) inoculum to protect calves with or without lactose supplements against Salmonella Dublin infection by evaluating histopathological lesions and pathogen translocation. Fifteen calves were divided into three groups [control group (C-G), a group inoculated with LAB (LAB-G), and a group inoculated with LAB and given lactose supplements (L-LAB-G)] with five, six, and four animals, respectively. The inoculum, composed of Lactobacillus (L.) casei DSPV 318T, L. salivarius DSPV 315T, and Pediococcus acidilactici DSPV 006T, was administered with milk replacer. The LAB-G and L-LAB-G received a daily dose of 109 CFU/kg body weight of each strain throughout the experiment. Lactose was provided to the L-LAB-G in doses of 100 g/day. Salmonella Dublin (2 × 1010 CFU) was orally administered to all animals on day 11 of the experiment. The microscopic lesion index values in target organs were 83%, 70%, and 64.3% (p < 0.05) for the C-G, LAB-G, and L-LAB-G, respectively. Administration of the probiotic inoculum was not fully effective against infection caused by Salmonella. Although probiotic treatment was unable to delay the arrival of pathogen to target organs, it was evident that the inoculum altered the response of animals against pathogen infection.
The inhibitory effects of alpha-benzene hexachloride on 3'-methyl-4-dimethylaminoazobenzene and DL-ethionine carcinogenesis in rats.

Summary This study was on the inhibitory effects of 0.06% α-benzene hexachloride (α-BHC) on hepatic changes including development of hepatoma in rats induced by 0.06% 3′-methyl-4-dimethylaminoazobenzene (3′-Me-DAB) or 0.25% dl-ethionine. α-BHC inhibited the induction of hepatocellular carcinoma in rats treated with 3′-Me-DAB for 5 months or with ethionine for 4.5 months. α-BHC inhibited the induction of nodular hyperplasia in rats treated with 3′-Me-DAB for 2 months or with dl-ethionine for 4.5 months but did not inhibit the induction of nodular hyperplasia in rats treated with 3′-Me-DAB for 5 months. In addition, α-BHC inhibited the occurrence of oval cell infiltration and caused the increase in liver weight in proportion to body weight in rats treated with 3′-Me-DAB or dl-ethionine for 2 months.
The "Agency" Model of Transactions: Toward an Understanding of Children's Theory of Control.

In this paper, I discuss how children come to disentangle purpose and causation —or psychological and physical descriptions—when explaining the behaviors of “simple-minded intelligent artifacts," as well as the behaviors of people and of things. I argue that very early on, children attempt to build a synthesis between these two kinds of explanations, and that they do so in a similar way when explaining the functioning of people, of objects, and of living and artificial creatures. The most striking characteristic of this synthesis is children's focus on "who" is impacting "whom" (and how), and "who" is impacted by "whom" (and how) in a given transaction. Both people and things are understood in terms of how they control each other's behavior, either through direct or mediated action (A does something to B, or tells or signals something to B, and B acts or signals back accordingly). Such = an "agency" model of transactions requires that the actors at play be animated. It forms the core of what will become a cybernetic view of the world. And like cybernetics, it provides a conceptual framework for explaining control and communication across the range of the living and the inanimate. Young children's tendency to animate objects constitutes a crucial step toward the construction of cybernetic theories. It is by no means a mere sign of cognitive immaturity.
Cell Surface Markers in Colorectal Cancer Prognosis

The classification of colorectal cancers (CRC) is currently based largely on histologically determined tumour characteristics, such as differentiation status and tumour stage, i.e., depth of tumour invasion, involvement of regional lymph nodes and the occurrence of metastatic spread to other organs. These are the conventional prognostic factors for patient survival and often determine the requirement for adjuvant therapy after surgical resection of the primary tumour. However, patients with the same CRC stage can have very different disease-related outcomes. For some, surgical removal of early-stage tumours leads to full recovery, while for others, disease recurrence and metastasis may occur regardless of adjuvant therapy. It is therefore important to understand the molecular processes that lead to disease progression and metastasis and to find more reliable prognostic markers and novel targets for therapy. This review focuses on cell surface proteins that correlate with tumour progression, metastasis and patient outcome, and discusses some of the challenges in finding prognostic protein markers in CRC.
Resident- and Facility-Level Predictors of Quality of Life in Long-Term Care.

PURPOSE OF THE STUDY Although there is substantial research on quality of care in nursing homes (NH), less is known about what contributes to quality of life (QOL) for NH residents. This study assesses multiple domains of QOL and examines facility- and resident-level correlates for different domains. DESIGN AND METHODS Data come from (a) self-reported resident interviews using a multidimensional measure of QOL; (b) resident clinical data from the Minimum Data Set; and (c) facility-level characteristics from Minnesota Department of Human Services. We used factor analysis to confirm domains of QOL, and then employed cross-sectional hierarchical linear modeling to identify significant resident- and facility-level predictors of each domain. RESULTS We examined six unique domains of QOL: environment, personal attention, food, engagement, negative mood, and positive mood. In multilevel models, resident-level characteristics were more reliable correlates of QOL than facility characteristics. Among resident characteristics, gender, age, marital status, activities of daily living, mood disorders, cognitive limitations, and length of stay consistently predicted QOL domains. Among facility characteristics, size, staff hours, quality of care, and percent of residents on Medicaid predicted multiple QOL domains. IMPLICATIONS Examining separate domains rather than a single summary score makes associations with predictors more accurate. Resident characteristics account for the majority of variability in resident QOL. Helping residents maintain functional abilities, and providing an engaging social environment may be particularly important in improving QOL.
Dietary Lignans: Potential Role in Cancer Prevention

Abstract: Recent in vitro, animal, and epidemiological studies suggest that dietary lignans may be chemopreventive, potentially through anti-estrogenic, anti-angiogenic, pro- apoptotic, and anti-oxidant mechanisms. In this article, we review lignan food sources and metabolism, proposed anti-carcinogenic mechanisms, and the evidence for a role of lignans in breast, colon, and prostate cancer prevention from animal and epidemiologic literature. Although a number of in vitro and animal studies support a role for lignan-rich foods and purified lignans in the modulation of cancer events of the breast, prostate, and colon, epidemiological studies, sparse and often retrospective in nature, offer inconsistent findings. The most support for a role of lignans in cancer is observed for premenopausal breast cancer. Additional epidemiological studies that use a prospective design and well-developed food databases and questionnaires are needed to adequately evaluate the role of lignans in cancer prevention.
Myopic choroidal neovascularisation: current concepts and update on clinical management

Choroidal neovascularisation (CNV) is a common vision-threatening complication of myopia and pathological myopia. Despite significant advances in understanding the epidemiology, pathogenesis and natural history of myopic CNV, there is no standard definition of myopic CNV and its relationship to axial length and other myopic degenerative changes. Several treatments are available to ophthalmologists, but with the advent of new therapies there is a need for further consensus and clinical management recommendations. Verteporfin photodynamic therapy has been an established treatment for subfoveal myopic CNV for many years, but this treatment does not restore visual acuity and is associated with long-term chorioretinal atrophy. More recently, clinical trials investigating the efficacy and safety of anti-vascular endothelial growth factor agents in patients with myopic CNV have demonstrated substantial visual acuity gains and quality of life increases compared with photodynamic therapy. These enhanced outcomes provide updated evidence-based clinical management guidelines of myopic CNV, and increase the need for a generally accepted definition for myopic CNV. This review critically summarises the latest myopic CNV literature in the context of clinical experience and recommends a myopic CNV treatment algorithm.
Comparison of Free Energy Surfaces Calculations from Ab Initio Molecular Dynamic Simulations at the Example of Two Transition Metal Catalyzed Reactions

We carried out ab initio molecular dynamic simulations in order to determine the free energy surfaces of two selected reactions including solvents, namely a rearrangement of a ruthenium oxoester in water and a carbon dioxide addition to a palladium complex in carbon dioxide. For the latter reaction we also investigated the gas phase reaction in order to take solvent effects into account. We used two techniques to reconstruct the free energy surfaces: thermodynamic integration and metadynamics. Furthermore, we gave a reasonable error estimation of the computed free energy surface. We calculated a reaction barrier of ΔF = 59.5 ± 8.5 kJ mol−1 for the rearrangement of a ruthenium oxoester in water from thermodynamic integration. For the carbon dioxide addition to the palladium complex in carbon dioxide we found a ΔF = 44.9 ± 3.3 kJ mol−1 from metadynamics simulations with one collective variable. The investigation of the same reactions in the gas phase resulted in ΔF = 24.9 ± 6.7 kJ mol−1 from thermodynamic integration, in ΔF = 26.7 ± 2.3 kJ mol−1 from metadynamics simulations with one collective variable, and in ΔF = 27.1 ± 5.9 kJ mol−1 from metadynamics simulations with two collective variables.
Thermal expression of intersubjectivity offers new possibilities to human–machine and technologically mediated interactions

The evaluation of the psychophysiological state of the interlocutor is an important element of interpersonal relationships and communication. Thermal infrared (IR) imaging has proved to be a reliable tool for non-invasive and contact-less evaluation of vital signs, psychophysiological responses, and emotional states. This technique is quickly spreading in many fields, from psychometrics to social and developmental psychology; and from the touch-less monitoring of vital signs and stress, up to the human–machine interaction. In particular, thermal IR imaging promises to be of use for gathering information about affective states in social situations. This paper presents the state of the art of thermal IR imaging in psychophysiology and in the assessment of affective states. The goal is to provide insights about its potentialities and limits for its use in human–artificial agent interaction in order to contribute to a major issue in the field: the perception by an artificial agent of human psychophysiological and affective states.
Structural Analysis phi92: a Comprehensive Genomic and Explains the Broad Host Range of Phage A Multivalent Adsorption Apparatus

Published Ahead of Print 11 July 2012. 2012, 86(19):10384. DOI: 10.1128/JVI.00801-12. J. Virol. Gerardy-Schahn Stummeyer, Martina Mühlenhoff, Petr G. Leiman and Rita Bethe, Astrid Oberbeck, Valorie D. Bowman, Katharina Browning, Sergey Nazarov, Wolfgang Rabsch, Andrea David Schwarzer, Falk F. R. Buettner, Christopher Structural Analysis phi92: a Comprehensive Genomic and Explains the Broad Host Range of Phage A Multivalent Adsorption Apparatus
Sexually Dimorphic Gene Expression Associated with Growth and Reproduction of Tongue Sole (Cynoglossus semilaevis) Revealed by Brain Transcriptome Analysis

In this study, we performed a comprehensive analysis of the transcriptome of one- and two-year-old male and female brains of Cynoglossus semilaevis by high-throughput Illumina sequencing. A total of 77,066 transcripts, corresponding to 21,475 unigenes, were obtained with a N50 value of 4349 bp. Of these unigenes, 33 genes were found to have significant differential expression and potentially associated with growth, from which 18 genes were down-regulated and 12 genes were up-regulated in two-year-old males, most of these genes had no significant differences in expression among one-year-old males and females and two-year-old females. A similar analysis was conducted to look for genes associated with reproduction; 25 genes were identified, among them, five genes were found to be down regulated and 20 genes up regulated in two-year-old males, again, most of the genes had no significant expression differences among the other three. The performance of up regulated genes in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was significantly different between two-year-old males and females. Males had a high gene expression in genetic information processing, while female’s highly expressed genes were mainly enriched on organismal systems. Our work identified a set of sex-biased genes potentially associated with growth and reproduction that might be the candidate factors affecting sexual dimorphism of tongue sole, laying the foundation to understand the complex process of sex determination of this economic valuable species.