Miracle-dz/UniFAR-FTUs huggingface dataset:
Altered gene activity correlated with long‐term memory formation of conditioned taste aversion in Lymnaea

The pond snail Lymnaea stagnalis is capable of learning conditioned taste aversion (CTA) and then consolidating that learning into long‐term memory (LTM) that persists for at least 1 month. LTM requires de novo protein synthesis and altered gene activity. Changes in gene activity in Lymnaea that are correlated with, much less causative, memory formation have not yet been identified. As a first step toward rectifying this situation, we constructed a cDNA microarray with mRNAs extracted from the central nervous system (CNS) of Lymnaea. We then, using this microarray assay, identified genes whose activity either increased or decreased following CTA memory consolidation. We also identified genes whose expression levels were altered after inhibition of the cyclic AMP response element‐binding protein (CREB) that is hypothesized to be a key transcription factor for CTA memory. We found that the molluscan insulin‐related peptide II (MIP II) was up‐regulated during CTA‐LTM, whereas the gene encoding pedal peptide preprohormone (Pep) was down‐regulated by CREB2 RNA interference. We next examined mRNAs of MIP II and Pep using real‐time RT‐PCR with SYBR Green. The MIP II mRNA level in the CNS of snails exhibiting “good” memory for CTA was confirmed to be significantly higher than that from the CNS of snails exhibiting “poor” memory. In contrast, there was no significant difference in expression levels of the Pep mRNA between “good” and “poor” performers. These data suggest that in Lymnaea MIP II may play a role in the consolidation process that forms LTM following CTA training. © 2006 Wiley‐Liss, Inc.
Peak Panel Reactive Antibody, Cancer, Graft, and Patient Outcomes in Kidney Transplant Recipients

Background High levels of pretransplant panel reactive antibodies (PRA) are known to be associated with detrimental effects on graft outcomes, but the association between pretransplant PRA levels and long-term patient outcomes is unclear. Methods Using the Australian and New Zealand Dialysis and Transplant Registry (ANZDATA), we assessed the risk of rejection, graft failure, mortality and cancer in kidney transplant recipients with varying peak PRA levels. Results In 7,118 kidney transplant recipients between 1997 and 2009, there were a total of 3,171 (44.6%), 3,306 (46.4%), 323 (4.5%), and 318 (4.5%) recipients with peak PRA levels of 0%, 1% to 50%, 51% to 80%, and greater than 80%, respectively. Compared to recipients with 0% peak PRA level, recipients with peak PRA levels greater than 80% were at increased risk of acute rejection (odds ratio, 1.81, 95% confidence interval [95% CI], 1.30–2.35; P < 0.001), death censored graft failure (hazard ratio [HR], 2.06; 95% CI, 1.46–2.91; P < 0.001), all-cause mortality (HR, 1.56; 95% CI, 1.15–2.11; P < 0.001) and cancer (HR, 1.94; 95% CI, 1.26–2.97; P = 0.002) in the adjusted models independent of human leukocyte antigen mismatches and initial immunosuppression. Conclusion Highly sensitized kidney transplant recipients with peak PRA greater than 80% had a greater risk of rejection, graft failure, cancer and death independent of age and time on dialysis. Strategies to reduce transplant waiting time and avoidance of sensitization in all potential transplant candidates are imperative to improve the overall graft and patient survival.
Diastolic isthmus length and 'vertical' isthmus angulation identify patients with difficult catheter ablation of typical atrial flutter: a pre-procedural MRI study.

AIMS Catheter ablation of isthmus-dependent atrial flutter is technically demanding in some patients and extremely simple in others. The intervention targets a defined anatomical structure, the so-called cavotricuspid isthmus (CTI). We sought to characterize CTI anatomy in vivo in patients with difficult and simple catheter ablation of atrial flutter. METHODS AND RESULTS Twenty-six patients were studied. Seven patients with difficult (n = 6) or extremely simple (n = 1) CTI ablation procedures were retrospectively selected from our catheter ablation database. Thereafter, we prospectively studied 19 patients undergoing CTI ablation in our department. We visualized CTI anatomy by ECG- and respiration-gated free precession 1.5 T cardiac magnetic resonance imaging (MRI). Magnetic resonance imaging was analysed for systolic and diastolic CTI length, the angle between the vena cava inferior and CTI, and pouch-like recesses. These parameters were compared between patients with difficult and simple procedures, split by the median number of energy applications. Patients with difficult procedures had a longer diastolic CTI length (diastolic isthmus length 20.3 +/- 1.8 mm) than those with simple procedures (diastolic isthmus length 16.6 +/- 1.7 mm, all data as mean +/- SEM, P < 0.05). Cavotricuspid isthmus angulation with respect to inferior vena cava was closer to 90 degrees in patients with difficult procedures (deviation from 90 degrees: 15 +/- 2 degrees) than those with simple procedures (deviation 23 +/- 4 degrees, P < 0.05). Systolic CTI length was not different between groups (32 +/- 2 mm in both groups, P > 0.2). CONCLUSION Longer diastolic, but not systolic, CTI length and a rectangular angle between CTI and inferior vena cava render CTI catheter ablation difficult. Visualization of isthmus anatomy may help to guide difficult CTI ablation procedures.
Intercellular adhesion molecule (ICAM)-1 and vascular cell adhesion molecule (VCAM)-1 at the early stages of atherosclerosis in a rat model.

BACKGROUND Members of the immunoglobulin superfamily of endothelial adhesion molecules, vascular cell adhesion molecule (VCAM-1) and intercellular cell adhesion molecule (ICAM-1), participate in leukocyte adhesion to the endothelium and play an important role in all stages of atherosclerosis. The aim of the study was to examine the expression of VCAM-1 and ICAM-1 in the aorta of rats at the early stages of atherosclerosis and the correlation with their plasma concentrations. MATERIALS AND METHODS Male rats (n=44), 10 weeks of age, were divided in 4 groups. Groups A and C (n=12) were fed with rich cholesterol diet for 12 and 16 weeks, respectively. Group B (regression group, n=12) was fed for the first 12 weeks with rich cholesterol diet and for another 4 weeks with normal diet. Group D (control group, n=8) was fed with normal diet for 12 weeks. We measured the serum lipid profile, the concentration of soluble ICAM-1 and the immunohistochemical expression of ICAM-1 and VCAM-1 in the endothelium, media and vasa vasorum of the aorta. RESULTS There were significant differences (p<0.05) in the expression of ICAM-1 between group C (maximum time of rich cholesterol diet) and all other groups in the 3 groups of the aorta studied. There was regression of the expression of ICAM-1 in group B and significant differences (p<0.05) between group B and all the other groups, except group D in the expression of ICAM-1. There were no significant differences in the expression of VCAM-1 between any groups. The serum concentration of soluble ICAM-1 positively correlated with the expression of the molecule in the vasa vasorum (r=0.35, p<0.05) and fibroblasts/smooth muscular cells (r=0.34, p<0.05) of the aorta. CONCLUSION A cholesterol diet plays a role in the expression of ICAM-1 but not in that of VCAM-1 in the rat aorta. The expression of ICAM-1 in the aorta regresses after the withdrawal of a cholesterol-rich diet. Soluble ICAM-1 is a reliable measure of ICAM-1 expression in the aorta, vasa vasorum and fibroblasts/smooth muscle cells.
"Developmental Effects of Endocrine-Disrupting Chemicals in Wildlife and Humans" (1993), by Theo Colborn, Frederick S. vom Saal, and Ana M. Soto

"Developmental Effects of Endocrine-Disrupting Chemicals in Wildlife and Humans," was published in 1993 in Environmental Health Perspectives. In the article, the authors present an account of two decades' worth of scientific research that describes the effects of certain pollutants on the health of wildlife, domestic animals, and humans [5], particularly when exposure takes place during embryonic growth. The term endocrine disruptor was coined in the article to describe the chemical pollutants that target the development and function of the endocrine system. Since its publication, "Developmental Effects" has increased research interest in endocrine disruption and has raised awareness among the general public, the scientific community, and government organizations about the effects that some chemicals may have on development and reproduction.
Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs) in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75%) of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR) retrotransposon class of retroelements, with >400 families (>350 newly discovered) contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families) and LINEs (at least 30 families), were observed to contribute 1,991 and ∼35,000 copies, respectively, or a combined ∼1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all) medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to differentially occupy and exploit this genomic diversity.
Neurotrophic effects of neudesin in the central nervous system

Neudesin (neuron-derived neurotrophic factor; NENF) was identified as a neurotrophic factor that is involved in neuronal differentiation and survival. It is abundantly expressed in the central nervous system, and its neurotrophic activity is exerted via the mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3-kinase (PI3K) pathways. Neudesin is also an anorexigenic factor that suppresses food intake in the hypothalamus. It is a member of the membrane-associated progesterone receptor (MAPR) family and shares key structural motifs with the cytochrome b5-like heme/steroid-binding domain. Progesterone receptor membrane component 1 (PGRMC1), the first to be discovered among the MAPR family, binds progesterone to induce “rapid non-genomic effects” in biological responses that are unrelated to the nuclear progesterone receptors (PRs). Hence, neudesin may also be involved in the rapid non-genomic actions of progesterone. In this review, we summarize the identification, structure, and activity of neudesin in the central nervous system, and present an essential overview of the current understanding of its physiological roles and the prospect of elucidating its non-genomic progesterone effects.
Imaging of Lithospheric Structure Beneath Jeju Volcanic Island by Teleseismic Traveltime Tomography

Jeju Island (JI) is an intraplate volcanic field located at the continental margin of Northeast Asia. This volcanic island has been formed by multiple eruptions from the Pleistocene to the Holocene (~3.7 ka), which have yielded hundreds of monogenetic volcanic cones and a central basaltic shield. To understand the volcanic structures and mechanism beneath JI, we deployed 20 broadband temporary seismometers across the island for over two years (October 2013 to November 2015). We investigated the crustal and upper mantle structures in JI for the first time using the gathered data. Through teleseismic traveltime tomography, we obtained images of the lithospheric structure related to the volcanic system. A major finding was the identification of a prominent low‐velocity anomaly (<−0.3 km/s in P wave velocity relative to the surrounding high‐velocity region) beneath the summit of the central shield volcano at greater depths (50–60 km), which separates into low‐velocity zones at shallower depths (10–45 km). Based on previous geological observations, the anomalies were interpreted as a magmatic system, potentially with partial melting. Moreover, relatively high velocity zones were consistently imaged to the north, east, and west of the island, indicating relatively thick lithospheric structures at the southern margin of the continental lithosphere beneath the Korean Peninsula. Based on the geometries of the imaged structures, we suggest that a focused decompressional melting at sublithospheric depths and complex magma interactions within the lithosphere resulted in the characteristics of JI volcanism as intraplate magmatic activities that are isolated in space and confined in time.
Abnormal Immunological Profile and Vaginal Microbiota in Women Prone to Urinary Tract Infections

ABSTRACT The host determinants of susceptibility to recurrent urinary tract infections (UTI) are poorly understood. We investigated whether the susceptibility is associated with abnormalities in the immunological defense and further explored the linkage to vaginal microbiota. For this purpose, we compared vaginal, urine, and blood samples collected during a disease-free period from 22 women with recurrent UTI and from 17 controls. In UTI-prone women, interleukin-12 (IL-12) production in peripheral monocytes and myeloid dendritic cells (DCs) was significantly (P < 0.05) enhanced whether measured in relative numbers of IL-12-producing cells or in mean IL-12 production per cell. In contrast, no T-cell polarization was observed. Interestingly, it seemed that the cytokine production of DCs and monocytes did not translate into T-cell activation in the UTI-prone group in a manner similar to that seen with the controls. In vaginal mucosa, UTI-prone women had a lower concentration of tissue repair-associated vascular endothelial growth factor (VEGF) (P = 0.006) and less often had detectable amounts of the chief monocyte and DC chemoattractant, monocyte chemotactic protein 1 (P = 0.005), than the controls. The microbiota of UTI-prone women was characterized by a diminished lactobacillus morphotype composition, with an abnormally high (>3) mean Nugent score of 4.6 compared to 1.7 for the controls (P = 0.003). Normal lactobacillus composition was associated with increased IL-17 and VEGF concentrations in vaginal mucosa. In conclusion, immunological defects and a persistently aberrant microbiota, a lack of lactobacilli in particular, may contribute to susceptibility to recurrent UTI. Further studies of antigen-presenting-cell function and T-cell activation in recurrent UTI are called for.
QSA influences on isotopic ratio measurements

The quasi-simultaneous arrival (QSA) effect has been tested with the Cameca NanoSIMS 50. The capability of obtaining rather large values of K (ratio of secondary ions ejected per primary ions) has been used to follow the evolution of QSA over a large range of K value by changing the collection efficiency. The amplitude of the effect associated with QSA has been determined and compared to the theoretical value by using silicon and sulfur isotopic ratio measurements. QSA influence on pulse height distribution (PHD) has also been demonstrated. # 2004 Elsevier B.V. All rights reserved.
Drug-target interaction prediction by learning from local information and neighbors

MOTIVATION In silico methods provide efficient ways to predict possible interactions between drugs and targets. Supervised learning approach, bipartite local model (BLM), has recently been shown to be effective in prediction of drug-target interactions. However, for drug-candidate compounds or target-candidate proteins that currently have no known interactions available, its pure 'local' model is not able to be learned and hence BLM may fail to make correct prediction when involving such kind of new candidates. RESULTS We present a simple procedure called neighbor-based interaction-profile inferring (NII) and integrate it into the existing BLM method to handle the new candidate problem. Specifically, the inferred interaction profile is treated as label information and is used for model learning of new candidates. This functionality is particularly important in practice to find targets for new drug-candidate compounds and identify targeting drugs for new target-candidate proteins. Consistent good performance of the new BLM-NII approach has been observed in the experiment for the prediction of interactions between drugs and four categories of target proteins. Especially for nuclear receptors, BLM-NII achieves the most significant improvement as this dataset contains many drugs/targets with no interactions in the cross-validation. This demonstrates the effectiveness of the NII strategy and also shows the great potential of BLM-NII for prediction of compound-protein interactions. CONTACT jpmei@ntu.edu. sg SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
ATP modulates anti-IgE-induced release of histamine from human lung mast cells.

Adenosine 5'-triphosphate (ATP) is released from the cytoplasm under physiologic and pathophysiologic conditions and enters the extracellular space, where it acts on a group of recently cloned cell-surface receptors termed P2-purinoceptors (subtypes P2X and P2Y). We examined the effects of extracellular ATP, uridine triphosphate (UTP), the stable ATP analogues alpha,betamethylene-ATP (alpha,betamATP), beta,gammamethylene-ATP (beta,gammamATP), and 2-methylthio-ATP (2mSATP), and adenosine (10(-6)-10(-3) M) on histamine release from human lung mast cells (HLMC) induced by anti-IgE and the calcium ionophore A23187. None of the nucleotides or adenosine directly induced histamine release. Adenosine exhibited a bimodal effect, enhancing histamine release at 10(-6) to 10(-4) M (P > 0.05, NS) and inhibiting it at 10(-3) M (P < 0.05). ATP (10(-4) M) enhanced anti-IgE-induced histamine release (10.9 +/- 2.7% to 19. 2 +/- 2.9%, n = 20, P < 0.01), but not ionophore A23187-induced histamine release (n = 10). The adenine nucleotides consistently enhanced anti-IgE-induced histamine release; the rank order for this action was: ATP > 2mSATP > alpha,betamATP > beta,gammamATP, suggesting mediation by a P2Y-purinoceptor subtype. The selective P2X purinoceptor antagonist pyridoxalphosphate-6-azophenyl-2', 4'-disulfonic acid failed to influence the effect of ATP, further supporting P2Y-purinoceptor mediation of anti-IgE-induced histamine release. UTP, an agonist at P2Y-purinoceptors, also significantly enhanced anti-IgE-induced histamine release. Application of the reverse transcription-polymerase chain reaction indicated that HLMC constitutively express the messenger RNAs encoding the P2Y1- and P2Y2-purinoceptor subtypes, and not that encoding the P2X7-purinoceptor (i.e., P2Z), a subtype implicated in ATP-induced histamine release in rodent peritoneal mast cells. The data produced in the study suggest that ATP plays an important modulatory role in histamine release from HLMC, and that it may therefore be mechanistically involved in human allergic/asthmatic reactions.
Validation of QuikSCAT wind vectors by dropwindsonde data from DOTSTAR

1 The accuracy of 10-meter wind vectors derived from the QuikSCAT satellite near tropical 2 cyclones is validated against soundings from 457 GPS dropwindsondes deployed by DOTSTAR 3 (Dropwindsonde Observations for Typhoon Surveillance near the Taiwan Region) during 2003-2007. 4 To maximize the database, the surface to 40-m wind speed in the dropwindsondes is averaged and 5 interpolated to the 10-m wind speed by linear regression. After removing rain-flagged data, the 6 root-mean-squared differences between QuikSCAT and dropwindsonde data were 2.6 m s or 18% 7 (wind speed) and 17 (wind direction) based on 896 matching samples. Further analyses also 8 indicate that the QuikSCAT data slightly underestimates the wind speed of medium wind regime 9 (between 10 and 17.2 m s) and possesses some clockwise directional bias in the high wind regime 10 (above 17.2 m s). In summary, this study suggests that the QuikSCAT wind vectors below 11 tropical storm wind strength (17.2 m s) are accurate enough for forecasters to determine the critical 12 wind radius of 34-kt wind, while a new error bound of the QuikSCAT wind estimate in high-wind 13 regimes near tropical cyclones is suggested to be set at about 4 m s. 14
Identifiability of regular and singular multivariate autoregressive models from mixed frequency data

This paper is concerned with identifiability of an underlying high frequency multivariate AR system from mixed frequency observations. Such problems arise for instance in economics when some variables are observed monthly whereas others are observed quarterly. If we have identifiability, the system and noise parameters and thus all second moments of the output process can be estimated consistently from mixed frequency data. Then linear least squares methods for forecasting and interpolating nonobserved output variables can be applied. Two ways for guaranteeing generic identifiability are discussed.
Robust Mpc for Actuator–Fault Tolerance Using Set–Based Passive Fault Detection and Active Fault Isolation

Abstract In this paper, a fault-tolerant control (FTC) scheme is proposed for actuator faults, which is built upon tube-based model predictive control (MPC) as well as set-based fault detection and isolation (FDI). In the class of MPC techniques, tubebased MPC can effectively deal with system constraints and uncertainties with relatively low computational complexity compared with other robust MPC techniques such as min-max MPC. Set-based FDI, generally considering the worst case of uncertainties, can robustly detect and isolate actuator faults. In the proposed FTC scheme, fault detection (FD) is passive by using invariant sets, while fault isolation (FI) is active by means of MPC and tubes. The active FI method proposed in this paper is implemented by making use of the constraint-handling ability of MPC to manipulate the bounds of inputs. After the system has been detected to become faulty, the input-constraint set of the MPC controller is adjusted to actively excite the system for achieving FI guarantees on-line, where an active FI-oriented input set is designed off-line. In this way, the system can be excited in order to obtain more extra system-operating information for FI than passive FI approaches. Overall, the objective of this paper is to propose an actuator MPC scheme with as little as possible of FI conservatism and computational complexity by combining tube-based MPC and set theory within the framework of MPC, respectively. Finally, a case study is used to show the effectiveness of the proposed FTC scheme.