Miracle-dz/UniFAR-FTUs huggingface dataset:
Highly heterogeneous diazotroph communities in the Kuroshio Current and the Tokara Strait, Japan

In this study, we used 454-pyrosequencing to report the highly diverse diazotroph communities in the Kuroshio and its adjacent waters along a transect across the Tokara Strait, Japan. Terrestrial input from the islands resulted in a highly heterogeneous diazotroph community within a relatively small geographic region, which was presumably caused by the remarkably different responses of UCYN-A2, UCYN-C and Trichodesmium to the steep environmental gradient. On the other hand, most major cyanobacterial OTUs found in this study were also detected in an unpublished dataset from the upstream Kuroshio, which suggests transportation of diazotrophs by the Kuroshio in large geographic scale. A significant amount of UCYN-C was found in the Kuroshio and offshore stations, suggesting the importance of this potentially overlooked group in the western North Pacific Ocean (WNPO). Moreover, a novel sublineage of UCYN-B was defined, which was predominant in an oligotrophic water sample; and it was also found to be widely distributed in oceanic waters. In addition, the apparent increase in relative abundance of UCYN-A2 from offshore to near-shore water provides evidence for the earlier and under-debating view that UCYN-A2 prefers coastal conditions. Our report provides new knowledge for understanding the phylogeny and ecology of unicellular cyanobacterial diazotrophs in WNPO.
Epidemiology of Candidemia in Brazil: a Nationwide Sentinel Surveillance of Candidemia in Eleven Medical Centers

ABSTRACT Candidemia studies have documented geographic differences in rates and epidemiology, underscoring the need for surveillance to monitor trends. We conducted prospective candidemia surveillance in Brazil to assess the incidence, species distribution, frequency of antifungal resistance, and risk factors for fluconazole-resistant Candida species. Prospective laboratory-based surveillance was conducted from March 2003 to December 2004 in 11 medical centers located in 9 major Brazilian cities. A case of candidemia was defined as the isolation of Candida spp. from a blood culture. Incidence rates were calculated per 1,000 admissions and 1,000 patient-days. Antifungal susceptibility tests were performed by using the broth microdilution assay, according to the Clinical and Laboratory Standards Institute guidelines. We detected 712 cases, for an overall incidence of 2.49 cases per 1,000 admissions and 0.37 cases per 1,000 patient-days. The 30-day crude mortality was 54%. C. albicans was the most common species (40.9%), followed by C. tropicalis (20.9%) and C. parapsilosis (20.5%). Overall, decreased susceptibility to fluconazole occurred in 33 (5%) of incident isolates, 6 (1%) of which were resistant. There was a linear correlation between fluconazole and voriconazole MICs (r = 0.54 and P < 0.001 [Spearman's rho]). This is the largest multicenter candidemia study conducted in Latin America and shows the substantial morbidity and mortality of candidemia in Brazil. Antifungal resistance was rare, but correlation between fluconazole and voriconazole MICs suggests cross-resistance may occur.
Epidermal Growth Factor as a Candidate for Ex Vivo Expansion of Bone Marrow–Derived Mesenchymal Stem Cells

Bone marrow mesenchymal stem cells (BMMSCs) are pluripotent cells capable of differentiating into several cell types and are thus an attractive cell source for connective tissue engineering. A challenge in such a use is expansion and directed seeding in vitro, requiring proliferation and survival, and directed migration, respectively, prior to functional differentiation. The epidermal growth factor (EGF) receptor (EGFR) is the prototypal growth factor receptor and elicits these responses from a wide variety of stromal, epithelial, and endothelial cells. Ligands for this receptor are appealing for use in tissue engineering because they are relatively resistant to biological extremes and amenable to high‐volume production. Therefore, we determined whether an EGFR ligand, EGF, could be used for ex vivo expansion of BMMSCs. EGF stimulated motility in rat and immortalized human BMMSCs. EGF‐induced proliferation was observed in immortalized human BMMSCs but was not apparent in rat BMMSCs under our experimental conditions. EGF did not, however, rescue either type of BMMSC from apoptosis due to lack of serum. During our examination of key signaling intermediaries, EGF caused robust phosphorylation of extracellular signal‐regulated protein kinase (ERK) and protein kinase B/akt (AKT) but only minimal phosphorylation of EGFR and phospholipase C‐γ in rat BMMSCs, whereas in the human BMMSCs these intermediaries were all strongly activated. EGF also induced robust ERK activation in primary porcine mesenchymal stem cells. EGF pretreatment or cotreatment did not interfere with secondarily induced differentiation of either type of BMMSC into adipogenic or osteogenic lineages. Platelet‐derived growth factor (PDGF) effects were similar to but not additive with those elicited by EGF, with some quantitative differences; however, PDGF did interfere with the differentiation of these BMMSCs. These findings suggest that EGFR ligands could be used for ex vivo expansion and direction of BMMSCs.
Direct visualization at the single-cell level of electrically mediated gene delivery

Electropermeabilization is one of the nonviral methods successfully used to transfer genes into living cells in vitro and in vivo. Although this approach shows promise in the field of gene therapy, very little is known about the basic processes supporting DNA transfer. The present investigation studies this process at the single-cell level by using digitized fluorescence microscopy. Permeabilization is a prerequisite for gene transfer. Its assay by propidium-iodide (PI) penetration shows that it occurs at the sides of the cell membrane facing the two electrodes, whereas fluorescently labeled plasmids only interact with the electropermeabilized side of the cell facing the cathode. The plasmid interaction with the electropermeabilized part of the cell surface results in the formation of localized aggregates. These membrane-associated spots are formed only when pulses with a longer duration than a critical value are applied. These complexes are formed within 1 s after the pulses and cannot be destroyed by pulses of reversed polarities. They remain at the membrane level up to 10 min after pulsing. Although freely accessible to DNA dye (TOTO-1) 1 min after the pulses, they are fully protected when the addition takes place 10 min after. They diffuse in the cytoplasm 30 min after pulses and are present around the nucleus 24 h later.
Bounds on the interchannel interference of OFDM in time-varying impairments

In this article, tight and universal bounds have been derived for the interchannel interference (ICI) of an orthogonal frequency-division multiplexing (OFDM) signal resulting from Doppler spread. The universal bound depends only on the product of the maximum Doppler frequency and the OFDM symbol duration. The tight bound also depends on the variance of the Doppler spectrum. Compared with the exact ICI expressions derived by other researchers, these bounds are easier to evaluate and can provide useful insight.
Distributed and Multi-Threaded Learning of Regression Models

Machine learning and databases are two closely related fields that have played an increasingly central role in the recent years, both in terms of theoretical work and practical applications in our daily lives. Unfortunately, most machine learning systems rely on their own dedicated way of representing and handling data, which makes integration with existing database systems more challenging and also slows down their development. Some of the research conducted at the University of Oxford has been focused on better integrating these two fields, most recently with the development of F, a system capable of learning regression models over factorised joins. F introduces novel ideas on how to perform some common machine learning tasks on databases, and is capable of outperforming popular commercial systems by several orders of magnitude. Nevertheless, F is by design single-threaded and can only run on a single machine, limitations that undermine its scalability. In addition to some extensive re-engineering work on F, the thesis focuses on these threading and distribution aspects, and shows how a state-of-the-art system can still be improved by orders of magnitude and guarantee a high degree of scalability. An endto-end system is presented, capable of loading and parsing database tables, distributing the data around a cluster of machines, sorting it efficiently, launching an optimised and multi-threaded version of F on each machine, and merging the partial results together in order to produce the final result.
Intolerance of Uncertainty and Coping Mechanisms in Nonclinical Young Subjects.

INTRODUCTION We aimed to explore the relationship between intolerance of uncertainty (IU) and coping mechanisms in a nonclinical sample with the same age and educational level. METHODS The Coping Orientations to Problems Experienced (COPE) scale was used to evaluate the coping mechanisms. The IU scale was used to evaluate IU situations. RESULTS We found that the negative impact of uncertainty on the action in female students was greater than males. While female students used more planning, instrumental support, reinterpretation, religion, emotional support, venting, and mental disengagement coping styles, male students used more humor, denial, and alcohol/drug abuse coping styles. Subjects with psychological problems had higher IU scores and used some more coping mechanisms (restraint, acceptance, behavioral disengagement, and alcohol/drug abuse) than the others. CONCLUSION Our results suggest that healthy subjects use different coping styles and respond differently to uncertainty in both genders.
Altered membrane fluidity and lipid raft composition in presenilin‐deficient cells

The pathology of Alzheimer's disease is closely connected with lipid metabolism. Processing of amyloid precursor protein (APP) is sensitive to membrane alterations in levels of cholesterol and gangliosides. As cholesterol and gangliosides are major components of rafts and BACE I and γ‐secretase are supposed to be localized to rafts there might be a yet unknown biological function underlying this connection. Increasing evidence shows a close connection between cholesterol homeostasis and APP processing and Aβ production respectively. We measured membrane fluidity by anisotropy determination, isolated detergent resistant membrane (DRM) fractions from membrane preparations and determined cholesterol content of these fractions by a coupled enzymatic assay. We found membrane fluidity to be changed in mouse embryonic fibroblasts (MEF) PS1/2 ‐/‐ along with altered cholesterol content in DRM fraction of these cells. In addition, total ganglioside levels were enhanced in absence of presenilin (PS).
Three Early Algorithms

Three well-known algorithms, implemented separately within a span of 20 years, demonstrate the use of mathematics developed hundreds of years ago. The algorithms don't have much in common except for two things: they were implemented between 1949 and 1965 during the so-called first generation of computing hardware-and they are good examples of rigorous thinking. First, I explain Bresenham's algorithm and apply it to a fundamental process of computer graphics-drawing a line on a raster screen. Second, although there are several ways to calculate a square root, the square root algorithm is interesting because it takes advantage of hardware design. And, finally, while the calculation of n goes back more than 2,200 years, Machin's algorithm from 1706 is of importance to the history of computing.
Information Technology and Quantitative Management ( ITQM 2013 ) Mining Explainable User Interests from Scalable User Behavior Data

Capturing user interests from big user behavior data is critical for online advertising. Based on the user interests, advertisers can significantly reduce their advertising cost by delivering the most relevant ads for the user. The state-of-the-art user Behavior Targeting (BT) models treat user behaviors as documents, and thus use topic models to extract their interests. A limitation of these methods is that user behaviors are usually described as unexplainable hidden topics, which cannot be directly used to guide online advertising. To this end, we propose in this paper a systematic User Interest Distribution Mining (UIDM for short) Framework to extract explainable user interests from big user behavior data. In the solution, we first use the Probabilistic Latent Semantic Analysis (PLSA) to discover the relationship between users and their behaviors, which can be described as hidden topics. Then, we construct a mapping matrix between the hidden topics and user interests by manually labeling a feature entity matrix. Experiments on real-world data sets demonstrate the performance of the proposed method.
Clinical manifestations of the antiphospholipid syndrome in patients with systemic lupus erythematosus associate more strongly with anti-beta 2-glycoprotein-I than with antiphospholipid antibodies.

OBJECTIVE To investigate antibodies to phospholipid-free beta 2-glycoprotein-I (a beta 2 GP-I) in the serum of patients with systemic lupus erythematosus (SLE). METHODS We studied alpha beta 2 GP-I by Western blot, dot blot, and ELISA in 94 patients with SLE. Twenty-one had antiphospholipid syndrome (APS) by clinical and serological criteria, 33 had neither of these features, 18 had the clinical criteria for APS but no serum antiphospholipid antibodies (aPL). and 22 had positive aPL but no related clinical manifestations. As controls, we also studied 76 normal sera. Sera were also inhibited with cardiolipin micelles and tested for anticardiolipin antibodies (aCL) or a beta GP-I activities. RESULTS Thirty-five of 39 patients with SLE with clinical manifestations of APS has serum a beta 2 GP-I, while only 2 of 55 patients with SLE without such clinical manifestations had them (p = 0.000000001). Sixteen patients with SLE with clinical APS but aPL negative were a beta GP-I positive. All 35 patients with SLE who were a beta 2 GP-I positive had vascular manifestations, but these antibodies were present in only 4 of 55 patients with SLE without vascular manifestations (p = 0.00000001). No patient having either aPL or a beta 2 GP-I had clinical manifestations of APS, whereas all 19 patients positive for both antibodies had clinical APS. The a beta 2 GP-I positive, aPL negative patients with SLE had clinical APS more frequently (16/18) than did a beta GP-I negative, aPL positive patients with SLE (2/24) (p = 0.000000001). The association of clinical manifestations of APS with a beta 2 GP-I was stronger than with aPL. Inhibition studies also indicate that aPL and a beta 2 GP-I are 2 different antigen/antibody systems. CONCLUSIONS Our findings indicate that the so called APS associates strongly with antibodies recognizing phospholipid-free beta 2 GP-I. There are patients' sera that also recognize cardiolipin and/or its cofactor beta 2 GP-I, the latter perhaps by reacting with a neoepitope on this protein that appears after its interaction with cardiolipin. These would be the previously considered (beta 2 GP-I dependent) aCL.
IZIP: In-place zero overhead interconnect protection via PIP redundancy

Modern SRAM based FPGAs (Field Programmable Gate Arrays) are powerful, but due to the soft error sensitivity of the configuration RAM (CRAM), it is difficult to use them in high reliability applications. We present a new technique, called IZIP (In-place Zero-overhead Interconnect Protection) which protects the programmable interconnect point (PIP) with almost zero overhead. We demonstrate IZIP on a commercial FPGA achieving a 7% reduction in the number of critical bits and in the total number of errors in PIPs, without changing the original placement.
6F-2 Extended Insulation Layer Structure for CMUTs

Electrostatic transducers require an electrically insulating structure between their electrodes. In state-of-the-art transducers, such as capacitive (micromachined) ultrasonic transducers (CUTs, CMUTs), this insulating structure is the main limiting factor in terms of device reliability (electrical breakdown, parasitic charging effects) and device performance (thin gap devices with low parasitic capacitance). We present a configuration, based on an extended insulation layer structure, which addresses all of these issues. A deep-trench-oxidation technique is used, that allows the fabrication of a released thermally-grown silicon dioxide structure, which can be more than 30 mum deep extended into the substrate. Preliminary measurement results from a CUT, featuring a back plate with such a deep extended insulation layer structure, are presented. The approach of using an extended insulation layer structure not only can improve the present CUT and CMUT technology in terms of reliability and performance, it also opens the door to high temperature applications of various types of electrostatic transducers.
Sulforaphane can protect lens cells against oxidative stress: implications for cataract prevention.

PURPOSE Protecting the lens against oxidative stress is of great importance in delaying the onset of cataract. Isothiocyanates, such as sulforaphane (SFN), are proposed to provide cytoprotection against oxidative stress. We therefore tested the ability of SFN to perform this role in lens cells and establish its ability to delay the onset of cataract. METHODS The human lens epithelial cell line FHL124 and whole porcine lens culture systems were used. The ApoTox-Glo Triplex Assay was used to assess FHL124 cell survival, cytotoxicity, and apoptosis. The MTS assay was used to assess cell populations. To determine levels of DNA strand breaks, the alkaline comet assay was performed and quantified. Lactate dehydrogenase levels in the medium were evaluated to reflect cell damage/death. To assess level of gene expression, an Illumina whole-genome HT-12 v4 beadchip was used. Protein expression was determined by Western blot and immunocytochemistry. RESULTS Exposures of 30 μM H2O2 to FHL124 cells caused a reduction in cell viability and increased cytotoxicity/apoptosis; these effects were significantly inhibited by 24-hour pretreatment with 1 μM SFN. In addition, 1 μM SFN significantly reduced H2O2-induced DNA strand breaks. When applied to cultured porcine lenses, SFN protected against H2O2-induced opacification. Illumina whole-genome HT-12 v4 beadchip microarray data revealed eight genes upregulated following 24-hour exposure to 1- and 2-μM SFN, which included NQO1 and TXNRD1. This pattern was confirmed at the protein level. Nrf2 translocated to the nucleus in response to 0.5- to 2.0-μM SFN exposure CONCLUSIONS The dietary component SFN demonstrates an ability to protect human lens cells against oxidative stress and thus could potentially delay the onset of cataract.
Quantification of pyrrolizidine alkaloids in North American plants and honey by LC-MS: single laboratory validation

Pyrrolizidine alkaloids (PAs) are a class of naturally occurring compounds produced by many flowering plants around the World. Their presence as contaminants in food systems has become a significant concern in recent years. For example, PAs are often found as contaminants in honey through pollen transfer. A validated method was developed for the quantification of four pyrrolizidine alkaloids and one pyrrolizidine alkaloid N-oxide in plants and honey grown and produced in British Columbia. The method was optimised for extraction efficiency from the plant materials and then subjected to a single-laboratory validation to assess repeatability, accuracy, selectivity, LOD, LOQ and method linearity. The PA content in plants ranged from1.0 to 307.8 µg/g with repeatability precision between 3.8 and 20.8% RSD. HorRat values were within acceptable limits and ranged from 0.62 to 1.63 for plant material and 0.56–1.82 for honey samples. Method accuracy was determined through spike studies with recoveries ranging from 84.6 to 108.2% from the raw material negative control and from 82.1–106.0 % for the pyrrolizidine alkaloids in corn syrup. Based on the findings in this single-laboratory validation, this method is suitable for the quantitation of lycopsamine, senecionine, senecionine N-oxide, heliosupine and echimidine in common comfrey (Symphytum officinale), tansy ragwort (Senecio jacobaea), blueweed (Echium vulgare) and hound’s tongue (Cynoglossum officinale) and for PA quantitation in honey and found that PA contaminants were present at low levels in BC honey.
MammaPrint™ 70-gene signature: another milestone in personalized medical care for breast cancer patients

The MammaPrint™ assay (Agendia BV, The Netherlands) is the first fully commercialized microarray-based multigene assay designed to individualize treatment for patients with breast cancer. MammaPrint, the first assay to be cleared at the 510(k) level by the US FDA’s new in vitro diagnostic multivariate index assay classification, is offered as a prognostic test for women under the age of 61 years with either estrogen receptor-positive or -negative, lymph node-negative breast cancer. Unlike the Oncotype DX™ assay (Genomic Health, CA, USA), this test requires freshly prepared tissues collected into an RNA preservative solution. The 70 genes that comprise the MammaPrint assay are focused primarily on proliferation with additional genes associated with invasion, metastasis, stromal integrity and angiogenesis. The Microarray In Node-negative Disease may Avoid Chemotherapy (MINDACT) trial, sponsored by the European Organization for Research and Treatment of Cancer, involves the assessment of patients in the adjuvant treatment setting by the standard clinicopathologic prognostic factors included on Adjuvant! Online and by the 70-gene MammaPrint assay. The following article will consider the basic biology, technology, ease of clinical use, level of clinical validation and potential clinical utility of this test.
A Phase I Trial of Epstein-Barr Virus Gp350 Vaccine for Children With Chronic Kidney Disease Awaiting Transplantation

Background. Vaccination against Epstein-Barr virus (EBV), inducing an antibody response to the envelope glycoprotein gp350, might protect EBV-negative children with chronic kidney disease from lymphoproliferative disease after transplantation. Methods. A phase I trial recruited children with chronic kidney disease to two successive cohorts given three injections of 12.5 μg (n=6) and 25 μg (n=10) recombinant gp350/alhydrogel vaccine over 6 to 8 weeks. Results. One in each cohort acquired wild EBV before the week 28 evaluation. Both doses were similarly immunogenic, inducing an IgG response in all 13 evaluable patients. Neutralizing antibodies were detected in four recipients (1/4 in the 12.5 μg and 3/9 in the 25 μg cohort). Median time from first vaccination to transplantation was 24 weeks. Immune responses declined rapidly and were unlikely to affect posttransplant events. Discussion. The vaccine was immunogenic but a prolonged vaccine schedule up to time of transplantation or improved adjuvants are required in future trials to reduce posttransplant EBV load and risk of lymphoproliferative disease.