Miracle-dz/UniFAR-FTUs huggingface dataset:
TIP47 Associates with Lipid Droplets*

Most mammalian cells package neutral lipids into droplets that are surrounded by a monolayer of phospholipids and a specific set of proteins including the adipose differentiation-related protein (ADRP; also called adipophilin), which is found in a wide array of cell types, and the perilipins, which are restricted to adipocytes and steroidogenic cells. TIP47 was initially identified in a yeast two-hybrid screen for proteins that interact with the cytoplasmic tail of the mannose 6-phosphate receptor, yet its sequence is highly similar to the lipid droplet protein, ADRP, and more distantly related to perilipins. Hence, we hypothesized that TIP47 might be associated with lipid droplets. In HeLa cells grown in standard low lipid-containing culture media, immunofluorescence microscopy revealed that the cells had few lipid droplets; however, TIP47 and ADRP were found on the surfaces of the small lipid droplets present. When the cells were grown in media supplemented with physiological levels of fatty acids, the amount of neutral lipid stored in lipid droplets increased dramatically, as did the staining of TIP47 and ADRP surrounding these droplets. TIP47 was found primarily in the cytosolic fractions of HeLa cells and murine MA10 Leydig cells grown in low lipid-containing culture medium, while ADRP was undetectable in these fractionated cell homogenates. When HeLa and MA10 Leydig cells were lipid-loaded, significant levels of ADRP were found in the floating lipid droplet fractions and TIP47 levels remained constant, but the distribution of a significant portion of TIP47 shifted from the cytosolic fractions to the lipid droplet fractions. Thus, we conclude that TIP47 associates with nascent lipid droplets and can be classified as a lipid droplet-associated protein.
Making SPARQL query formulation more intuitive

The increasing volume of RDF data available on the Web has motivated people to try querying them. To this end, the SPARQL query language is the recommended standard to be used. However, writing SPARQL queries is not commonly considered as an easy task since it requires knowledge about RDF triple patterns and other concepts. To help matters, we present LData, an approach which provides users with a more intuitive interface for building their data requirements in terms of triples. LData is based on two issues: (i) providing users with the semantics underlying a given RDF dataset, and (ii) allowing the building of triples, which are mapped to patterns used to generate a SPARQL query. In this work, we describe LData contributions and present some accomplished results.
Quality-structure index: A new metric to measure scientific journal influence

An innovative model to measure the influence among scientific journals is developed in this study. This model is based on the path analysis of a journal citation network, and its output is a journal influence matrix that describes the directed influence among all journals. Based on this model, an index of journals' overall influence, the quality-structure index (QSI), is derived. Journal ranking based on QSI has the advantage of accounting for both intrinsic journal quality and the structural position of a journal in a citation network. The QSI also integrates the characteristics of two prevailing streams of journal-assessment measures: those based on bibliometric statistics to approximate intrinsic journal quality, such as the Journal Impact Factor, and those using a journal's structural position based on the PageRank-type of algorithm, such as the Eigenfactor score. Empirical results support our finding that the new index is significantly closer to scholars' subjective perception of journal influence than are the two aforementioned measures. In addition, the journal influence matrix offers a new way to measure two-way influences between any two academic journals, hence establishing a theoretical basis for future scientometrics studies to investigate the knowledge flow within and across research disciplines. © 2011 Wiley Periodicals, Inc.
Proteinuria and epithelial-to-mesenchymal transition: the role of complement.

The extent of injury to the tubulointerstitial compartment has been recognized for several decades as closely linked to declining renal function in glomerular diseases. In addition to secondary inflammatory injury and ischemia as mechanisms of injury in the tubulointerstitium downstream from diseased glomeruli, proteinuria itself is now recognized as a pathogenic factor and an independent risk factor for the progression of kidney disease.1–3 Reduction of proteinuria is now a major therapeutic goal in reducing risk for renal progression.4 Current strategies to reduce proteinuria are largely focused on treatment of the underlying glomerular disease and by alteration of glomerular hemodynamics and filtration. With improved understanding of basic mechanisms of proteinuria-induced injury, however, more refined and proximate strategies based on molecular pathogenesis of proteinuria-induced tubulointerstitial injury may be possible. The damaging effects of proteinuria on the renal tubulointerstitial compartment involve a variety of mechanisms.5 These include tubular cell toxicity, when the lysosomal capacity to degrade …
Fair Scheduling in Internet Routers

Input buffered switch architecture has become attractive for implementing high performance routers and expanding use of the Internet sees an increasing need for quality of service. It is challenging to provide a scheduling technique that is both highly efficient and fair in resource allocation. In this paper, we first introduce an iterative fair scheduling (IFS) scheme for input buffered switches that supports fair bandwidth distribution among the flows and achieves asymptotically 100 percent throughput. The IFS is evaluated both under synthetic workload and with Web traces from the Internet. Compared to the commonly used synthetic input, our simulation results reveal significant difference in performance when the real network traffic is employed. We then consider fair scheduling under various buffer management mechanisms and analyze their impact on the fairness in bandwidth allocation. Our studies indicate that early packet discard in anticipation of congestion is necessary and per-flow based buffering is effective for protecting benign users from being adversely affected by misbehaving traffic. Buffer allocation according to bandwidth reservation is especially helpful when the input traffic is highly bursty.
A perching mechanism for flying robots using a fibre-based adhesive

Robots capable of hover flight in constrained indoor environments have many applications, however their range is constrained by the high energetic cost of airborne locomotion. Perching allows flying robots to scan their environment without the need to remain aloft. This paper presents the design of a mechanism that allows indoor flying robots to attach to vertical surfaces. To date, solutions that enable flying robot with perching capabilities either require high precision control of the dynamics of the robot, or a mechanism robust to high energy impacts. In this article, we propose a perching mechanism comprising a compliant deployable pad and a passive self-alignment system, that does not require any active control during the attachment procedure. More specifically, a perching mechanism using fibre-based dry adhesives was implemented on a 300 g flying platform. An adhesive pad was first modeled and optimized in shape for maximum attachment force at the low pre-load forces inherent to hovering platforms. It was then mounted on a deployable mechanism that stays within the structure of the robot during flight and can be deployed when a perching manoeuvre is initiated. Finally, the perching mechanism is integrated onto a real flying robot and successful perching manoeuvres are demonstrated as a proof of concept.
GPS/INS integration for GF-IMU of twelve mono-axial accelerometers configurations

In this paper we present an integration scheme and performance analysis for the integration of a gyro-free inertial measurement unit (GF-IMU) with a GPS receiver. The GF-IMU is composed of twelve separate mono-axial accelerometers. Using such a GF-IMU produces a vector, which we call the angular information vector that consists of 3D angular acceleration terms and six quadratic terms of angular velocities. Traditional GPS/INS integration using error state space model has been modified to fit this special IMU. Simulation results are presented.
Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies

The evolution of enzymes affects how well a species can adapt to new environmental conditions. During enzyme evolution, certain aspects of molecular function are conserved while other aspects can vary. Aspects of function that are more difficult to change or that need to be reused in multiple contexts are often conserved, while those that vary may indicate functions that are more easily changed or that are no longer required. In analogy to the study of conservation patterns in enzyme sequences and structures, we have examined the patterns of conservation and variation in enzyme function by analyzing graph isomorphisms among enzyme substrates of a large number of enzyme superfamilies. This systematic analysis of substrate substructures establishes the conservation patterns that typify individual superfamilies. Specifically, we determined the chemical substructures that are conserved among all known substrates of a superfamily and the substructures that are reacting in these substrates and then examined the relationship between the two. Across the 42 superfamilies that were analyzed, substantial variation was found in how much of the conserved substructure is reacting, suggesting that superfamilies may not be easily grouped into discrete and separable categories. Instead, our results suggest that many superfamilies may need to be treated individually for analyses of evolution, function prediction, and guiding enzyme engineering strategies. Annotating superfamilies with these conserved and reacting substructure patterns provides information that is orthogonal to information provided by studies of conservation in superfamily sequences and structures, thereby improving the precision with which we can predict the functions of enzymes of unknown function and direct studies in enzyme engineering. Because the method is automated, it is suitable for large-scale characterization and comparison of fundamental functional capabilities of both characterized and uncharacterized enzyme superfamilies.
Gamma Interferon Plays a Crucial Early Antiviral Role in Protection against West Nile Virus Infection

ABSTRACT West Nile virus (WNV) causes a severe central nervous system (CNS) infection in humans, primarily in the elderly and immunocompromised. Prior studies have established an essential protective role of several innate immune response elements, including alpha/beta interferon (IFN-α/β), immunoglobulin M, γδ T cells, and complement against WNV infection. In this study, we demonstrate that a lack of IFN-γ production or signaling results in increased vulnerability to lethal WNV infection by a subcutaneous route in mice, with a rise in mortality from 30% (wild-type mice) to 90% (IFN-γ−/− or IFN-γR−/− mice) and a decrease in the average survival time. This survival pattern in IFN-γ−/− and IFN-γR−/− mice correlated with higher viremia and greater viral replication in lymphoid tissues. The increase in peripheral infection led to early CNS seeding since infectious WNV was detected several days earlier in the brains and spinal cords of IFN-γ−/− or IFN-γR−/− mice. Bone marrow reconstitution experiments showed that γδ T cells require IFN-γ to limit dissemination by WNV. Moreover, treatment of primary dendritic cells with IFN-γ reduced WNV production by 130-fold. Collectively, our experiments suggest that the dominant protective role of IFN-γ against WNV is antiviral in nature, occurs in peripheral lymphoid tissues, and prevents viral dissemination to the CNS.
Gene regulation in the magnocellular hypothalamo-neurohypophysial system.

The hypothalamo-neurohypophysial system (HNS) is the major peptidergic neurosecretory system through which the brain controls peripheral physiology. The hormones vasopressin and oxytocin released from the HNS at the neurohypophysis serve homeostatic functions of water balance and reproduction. From a physiological viewpoint, the core question on the HNS has always been, "How is the rate of hormone production controlled? " Despite a clear description of the physiology, anatomy, cell biology, and biochemistry of the HNS gained over the last 100 years, this question has remained largely unanswered. However, recently, significant progress has been made through studies of gene identity and gene expression in the magnocellular neurons (MCNs) that constitute the HNS. These are keys to mechanisms and events that exist in the HNS. This review is an inventory of what we know about genes expressed in the HNS, about the regulation of their expression in response to physiological stimuli, and about their function. Genes relevant to the central question include receptors and signal transduction components that receive and process the message that the organism is in demand of a neurohypophysial hormone. The key players in gene regulatory events, the transcription factors, deserve special attention. They do not only control rates of hormone production at the level of the gene, but also determine the molecular make-up of the cell essential for appropriate development and physiological functioning. Finally, the HNS neurons are equipped with a machinery to produce and secrete hormones in a regulated manner. With the availability of several gene transfer approaches applicable to the HNS, it is anticipated that new insights will be obtained on how the HNS is able to respond to the physiological demands for its hormones.
Teaching Experiments and Programming for Machine Learning

A temperature regulating control unit and method of making the same are provided, the unit comprising a RTD temperature sensor, a unit for applying electrical signals to the sensor, and a microcomputer for receiving digital signals from the sensor in relation to the temperature being sensed by the sensor, the unit for applying electrical signals to the sensor applying a varying voltage to the sensor.
The effects of age and dietary restriction on the tissue-specific metabolome of Drosophila

Dietary restriction (DR) is a robust intervention that extends lifespan and slows the onset of age‐related diseases in diverse organisms. While significant progress has been made in attempts to uncover the genetic mechanisms of DR, there are few studies on the effects of DR on the metabolome. In recent years, metabolomic profiling has emerged as a powerful technology to understand the molecular causes and consequences of natural aging and disease‐associated phenotypes. Here, we use high‐resolution mass spectroscopy and novel computational approaches to examine changes in the metabolome from the head, thorax, abdomen, and whole body at multiple ages in Drosophila fed either a nutrient‐rich ad libitum (AL) or nutrient‐restricted (DR) diet. Multivariate analysis clearly separates the metabolome by diet in different tissues and different ages. DR significantly altered the metabolome and, in particular, slowed age‐related changes in the metabolome. Interestingly, we observed interacting metabolites whose correlation coefficients, but not mean levels, differed significantly between AL and DR. The number and magnitude of positively correlated metabolites was greater under a DR diet. Furthermore, there was a decrease in positive metabolite correlations as flies aged on an AL diet. Conversely, DR enhanced these correlations with age. Metabolic set enrichment analysis identified several known (e.g., amino acid and NAD metabolism) and novel metabolic pathways that may affect how DR effects aging. Our results suggest that network structure of metabolites is altered upon DR and may play an important role in preventing the decline of homeostasis with age.
16th IHIW: Population Global Distribution of Killer Immunoglobulin‐like Receptor (KIR) and Ligands

In the last fifteen years, published reports have described KIR gene‐content frequency distributions in more than 120 populations worldwide. However, there have been limited studies examining these data in aggregate to detect overall patterns of variation at regional and global levels. Here, we present a summary of the collection of KIR gene‐content data for 105 worldwide populations collected as part of the 15th and 16th International Histocompatibility and Immunogenetics Workshops, and preliminary results for data analysis.
Handwritten address recognition with open vocabulary using character n-grams

In this paper a recognition system, based on tied-mixture hidden Markov models, for handwritten address words is described, which makes use of a language model that consists of backoff character n-grams. For a dictionary-based recognition system it is essential that the structure of the address (name, street, city) is known. If the single parts of the address cannot be categorized, the used vocabulary is unknown and thus unlimited. The performance of this open vocabulary recognition using n-grams is compared to the use of dictionaries of different sizes. Especially, the confidence of recognition results and the possibility of a useful post-processing are significant advantages of language models.
The role and interaction of imprinted genes in human fetal growth

Identifying the genetic input for fetal growth will help to understand common, serious complications of pregnancy such as fetal growth restriction. Genomic imprinting is an epigenetic process that silences one parental allele, resulting in monoallelic expression. Imprinted genes are important in mammalian fetal growth and development. Evidence has emerged showing that genes that are paternally expressed promote fetal growth, whereas maternally expressed genes suppress growth. We have assessed whether the expression levels of key imprinted genes correlate with fetal growth parameters during pregnancy, either early in gestation, using chorionic villus samples (CVS), or in term placenta. We have found that the expression of paternally expressing insulin-like growth factor 2 (IGF2), its receptor IGF2R, and the IGF2/IGF1R ratio in CVS tissues significantly correlate with crown–rump length and birthweight, whereas term placenta expression shows no correlation. For the maternally expressing pleckstrin homology-like domain family A, member 2 (PHLDA2), there is no correlation early in pregnancy in CVS but a highly significant negative relationship in term placenta. Analysis of the control of imprinted expression of PHLDA2 gave rise to a maternally and compounded grand-maternally controlled genetic effect with a birthweight increase of 93/155 g, respectively, when one copy of the PHLDA2 promoter variant is inherited. Expression of the growth factor receptor-bound protein 10 (GRB10) in term placenta is significantly negatively correlated with head circumference. Analysis of the paternally expressing delta-like 1 homologue (DLK1) shows that the paternal transmission of type 1 diabetes protective G allele of rs941576 single nucleotide polymorphism (SNP) results in significantly reduced birth weight (−132 g). In conclusion, we have found that the expression of key imprinted genes show a strong correlation with fetal growth and that for both genetic and genomics data analyses, it is important not to overlook parent-of-origin effects.
Enhanced Expression of Janus Kinase–Signal Transducer and Activator of Transcription Pathway Members in Human Diabetic Nephropathy

OBJECTIVE—Glomerular mesangial expansion and podocyte loss are important early features of diabetic nephropathy, whereas tubulointerstitial injury and fibrosis are critical for progression of diabetic nephropathy to kidney failure. Therefore, we analyzed the expression of genes in glomeruli and tubulointerstitium in kidney biopsies from diabetic nephropathy patients to identify pathways that may be activated in humans but not in murine models of diabetic nephropathy that fail to progress to glomerulosclerosis, tubulointerstitial fibrosis, and kidney failure. RESEARCH DESIGN AND METHODS—Kidney biopsies were obtained from 74 patients (control subjects, early and progressive type 2 diabetic nephropathy). Glomerular and tubulointerstitial mRNAs were microarrayed, followed by bioinformatics analyses. Gene expression changes were confirmed by real-time RT-PCR and immunohistological staining. Samples from db/db C57BLKS and streptozotocin-induced DBA/2J mice, commonly studied murine models of diabetic nephropathy, were analyzed. RESULTS—In human glomeruli and tubulointerstitial samples, the Janus kinase (Jak)-signal transducer and activator of transcription (Stat) pathway was highly and significantly regulated. Jak-1, -2, and -3 as well as Stat-1 and -3 were expressed at higher levels in patients with diabetic nephropathy than in control subjects. The estimated glomerular filtration rate significantly correlated with tubulointerstitial Jak-1, -2, and -3 and Stat-1 expression (R2 = 0.30–0.44). Immunohistochemistry found strong Jak-2 staining in glomerular and tubulointerstitial compartments in diabetic nephropathy compared with control subjects. In contrast, there was little or no increase in expression of Jak/Stat genes in the db/db C57BLKS or diabetic DBA/2J mice. CONCLUSIONS—These data suggest a direct relationship between tubulointerstitial Jak/Stat expression and progression of kidney failure in patients with type 2 diabetic nephropathy and distinguish progressive human diabetic nephropathy from nonprogressive murine diabetic nephropathy.
Target-Specific Encoding of Response Inhibition: Increased Contribution of AMPA to NMDA Receptors at Excitatory Synapses in the Prefrontal Cortex

Impulse control suppresses actions that are inappropriate in one context, but may be beneficial in others. The medial prefrontal cortex (mPFC) mediates this process by providing a top-down signal to inhibit competing responses, although the mechanism by which the mPFC acquires this ability is unknown. To that end, we examined synaptic changes in the mPFC associated with learning to inhibit an incorrect response. Rats were trained in a simple response inhibition task to withhold responding until a signal was presented. We then measured synaptic plasticity of excitatory synapses in the mPFC, using whole-cell patch-clamp recordings, in brain slices prepared from trained rats. Response inhibition training significantly increased the relative contribution of AMPA receptors to the overall EPSC in prelimbic, but not infralimbic, neurons of the mPFC. This potentiation of synaptic transmission closely paralleled the acquisition and extinction of response inhibition. Using a retrograde fluorescent tracer, we observed that these plastic changes were selective for efferents projecting to the ventral striatum, but not the dorsal striatum or amygdala. Therefore, we suggest that response inhibition is encoded by a selective strengthening of a subset of corticostriatal projections, uncovering a synaptic mechanism of impulse control. This information could be exploited in therapeutic interventions for disorders of impulse control, such as addiction, attention deficit–hyperactivity disorder, and schizophrenia.
Tariffying auctions

A strategy to convert quotas to tariffs is to auction the quota rights and use the realized auction prices as guides to setting tariffs. In the 1980s, New Zealand employed auctions to allocate quota licenses. We analyze the relationship between tariff-equivalents and auction prices for auctions with resale. Using panel data from New Zealand’s quota license auctions, we estimate the expected value of the tariff equivalent. We exploit data from secondary market prices to test the model’s predictions. The predictions fail, suggesting either that auction prices may understate or that aftermarket prices overstate the true tariff equivalent.