Miracle-dz/UniFAR-FTUs huggingface dataset:
Lawrence Berkeley National Laboratory Lawrence Berkeley National Laboratory Title Ceramic capillaries for use in microarray fabrication

We have used ceramic capillary tips generally used in the microelectronics industry for the production of DNA microarrays. The ceramic tips improve the morphology of microarray elements, allow higher element density, and increase printing tip life over the customary slotted stainless steel pins. Ceramic capillaries are less expensive than steel pins and allow printing from 1536-well sample source plates. In this paper, we describe experiments that verify (establish? ) printing performance of these ceramic tips, and hybridization experiments that demonstrate that DNA hybridization is unaffected by the choice of tip material. Reed A. George, page 2 Introduction Over the past several years, the applications of DNA microarray technology have diversified from the initial gene expression studies in yeast (Schena et al. 1995, DeRisi et al. 1997) to include the characterization of human cancer tumor tissues (Perou et al. 2000), high-throughput SNP genotyping (Hacia et al. 1999), and the study of in vivo binding of transcription factor proteins (Ren et al. 2000). Two very different technical approaches to microarray production have enabled this rapid expansion: synthesis of short oligonucleotide probes directly on glass surfaces (in situ synthesis) and the deposition of probes (either PCR products or oligonucleotides) onto glass surfaces using either metal pins or modified ink jet systems (spotted arrays). A low-cost robotic system developed at Stanford University for producing spotted arrays has found application in many laboratories (Schena et al. 1995, Bowtell et al. 1999). This system uses stainless steel printing tips, similar in design to a fountain pen, to aspirate and deposit DNA onto glass microscope slides. Through repeated cycles of sample aspiration, deposition onto a series of slides, and cleaning of the printing tips, high-density microarrays are produced. We have developed a microarray production method that uses cylindrical ceramic capillary tips instead of stainless steel tips. The capillaries are adapted from microelectronics applications, where they are typically used for bonding high-density interconnections (wires less than .001” in diameter) during the assembly of integrated circuit packages. The capillaries are manufactured to very tight tolerances, and are available commercially. Our data demonstrate that the ceramic tips improve the consistency of deposit morphology, resist deformation over long-term use, cost less, and offer the potential for significant improvement in deposit density.
Self-Supervised Learning for Robust Video Indexing

The performance of video analysis and indexing algorithms strongly depends on the type, content and recording characteristics of the analyzed video. Current video indexing approaches often make use of thresholding techniques or supervised learning which requires labeling of possibly large training sets. Furthermore, the application of the same training model or parameters might lead to a suboptimal indexing accuracy for a given video. In this paper, we propose to use a novel self-supervised learning framework for robust video indexing to address this issue. Based on an initial classification result for a given video, the best features are selected by adaboost and are then used to train SVM (support vector machine) classifiers, all on the given video. Finally, a specialized ensemble of classifiers is employed for the given video for decision making. Experimental results show that a state-of-the-art video cut detection approach can be significantly improved by the self-supervised learning approach
The contribution of systemic hypertension to progression of chronic renal failure in the rat remnant kidney: effect of treatment with an angiotensin converting enzyme inhibitor or a calcium inhibitor.

In order to establish if pharmacological treatment of systemic hypertension modifies the course of progressive renal failure, we studied the effects of an angiotensin converting enzyme inhibitor and a calcium antagonist, on the renal structure and function in the remnant kidney model of chronic renal failure in the rat. Progressive renal failure was induced in adult female Sprague Dawley rats (SDR) by surgical removal of the right kidney, and segmental infarction of seven-eighths of the left kidney. Following subtotal nephrectomy, plasma creatinine rose from 65 +/- 16 mumol/l to 173 +/- 19 mumol/l (P less than 0.001) over a period of 6 weeks, systolic blood pressure (SBP) rose from 121 +/- 2 mmHg to 176 +/- 7 mmHg (P less than 0.001) and urinary protein excretion from 0.6 +/- 0.2 to 84 +/- 22 mg/24 h (P less than 0.001). Glomerular mesangial expansion was present after 2 weeks, then progressed, in association with the development of glomerular sclerosis, which became prominent after 6 weeks. Rats were treated with enalapril (5 mg/kg per day) or felodipine (30 mg/kg per day) from 1 week after subtotal nephrectomy, and their course compared with that of untreated rats. Systemic SBP decreased to a similar degree by both drug treatments. Six weeks after surgery, plasma creatinine concentration was lower in the enalapril-treated group (110 +/- 8 mumol/l, P less than 0.05) than in the felodipine-treated group (153 +/- 23 mumol/l). The latter group showed similar plasma creatinine concentrations to those of the untreated rats (173 +/- 19 mumol/l). (ABSTRACT TRUNCATED AT 250 WORDS)
Linking Expression of Fructan Active Enzymes, Cell Wall Invertases and Sucrose Transporters with Fructan Profiles in Growing Taproot of Chicory (Cichorium intybus): Impact of Hormonal and Environmental Cues

In chicory taproot, the inulin-type fructans serve as carbohydrate reserve. Inulin metabolism is mediated by fructan active enzymes (FAZYs): sucrose:sucrose 1-fructosyltransferase (1-SST; fructan synthesis), fructan:fructan-1-fructosyltransferase (1-FFT; fructan synthesis and degradation), and fructan 1-exohydrolases (1-FEH1/2a/2b; fructan degradation). In developing taproot, fructan synthesis is affected by source-to-sink sucrose transport and sink unloading. In the present study, expression of FAZYs, sucrose transporter and CWI isoforms, vacuolar invertase and sucrose synthase was determined in leaf blade, petiole and taproot of young chicory plants (taproot diameter: 2 cm) and compared with taproot fructan profiles for the following scenarios: (i) N-starvation, (ii) abscisic acid (ABA) treatment, (iii) ethylene treatment (via 1-aminoyclopropane-1-carboxylic acid [ACC]), and (iv) cold treatment. Both N-starvation and ABA treatment induced an increase in taproot oligofructans. However, while under N-starvation this increase reflected de novo synthesis, under ABA treatment gene expression profiles indicated a role for both de novo synthesis and degradation of long-chain fructans. Conversely, under ACC and cold treatment oligofructans slightly decreased, correlating with reduced expression of 1-SST and 1-FFT and increased expression of FEHs and VI. Distinct SUT and CWI expression profiles were observed, indicating a functional alignment of SUT and CWI expression with taproot fructan metabolism under different source-sink scenarios.
Signal-dependent noise removal in pointwise shape-adaptive DCT domain with locally adaptive variance

This paper presents a novel effective method for denoising of images corrupted by signal-dependent noise. Denoising is performed by coefficient shrinkage in the shape-adaptive DCT (SA-DCT) transform-domain. The Anisotropic Local Polynomial Approximation (LPA) - Intersection of Confidence Intervals (ICI) technique is used to define the shape of the transform's support in a pointwise adaptive manner. The use of such an adaptive transform support enables both a simpler modelling of the noise in the transform domain and a sparser decomposition of the signal. Consequently, coefficient shrinkage is very effective and the reconstructed estimate's quality is high, in terms of both numerical error-criteria and visual appearance, with sharp detail preservation and clean edges. Simulation experiments demonstrate the superior performance of the proposed algorithm for a wide class of noise models with a signal-dependent variance, including Poissonian (photon-limited imaging), film-grain, and speckle noise.
Long-term effect of preventive therapy for tuberculosis in a cohort of HIV-infected Zambian adults

ObjectiveTo determine the long-term effect of preventive therapy (PT) for tuberculosis on the rates of tuberculosis, mortality and HIV progression. MethodsIn a randomized controlled trial, 1053 HIV-positive Zambian adults received isoniazid (H) for 6 months, rifampicin plus pyrazinamide (RZ) for 3 months, or a placebo. CD4 percentage, neopterin, absolute lymphocyte count and haemoglobin were measured from enrolment (absolute CD4 cell counts from 12 months after enrolment). Because PT reduced the incidence of tuberculosis, eligible placebo subjects were offered H. Here, tuberculosis and mortality rates are compared in the three original arms (intention to treat) using data beyond the end of the trial (average follow-up 3 years; maximum 7 years). ResultsThere were 102 cases of tuberculosis and 281 deaths (rates 3.6 and 9.0/100 person-years, respectively). There was no significant difference between the tuberculosis rates in the H and RZ groups at any time. The effect of H/RZ on tuberculosis diminished over time (P = 0.011) but the cumulative risk of tuberculosis in the first 2.5 years was significantly lower in the H/RZ group than the placebo group (rate ratio 0.55; 95% confidence interval 0.32–0.93;P = 0.028). There was no significant effect of PT on mortality or progression markers. Tuberculosis was associated with an increased mortality (adjusted rate ratio 1.96; 95% confidence interval 1.21–3.18;P = 0.006). ConclusionsBoth PT regimens protect against tuberculosis for at least 2.5 years but appear to have no effect on HIV progression or mortality. These results may be used in cost-effectiveness models of PT.
Defective Th1 and Th2 cytokine synthesis in the T‐T cell presentation model for lack of CD40/CD40 ligand interaction

In this study, T or NK cell clones used as antigen‐presenting cells (T‐ or NK‐APC) were shown to be significantly less efficient than professional APC in inducing Th1 and Th2 cytokines by antigen‐specific T cell clones. This phenomenon was not related to a limited engagement of TCR by T‐APC, since comparable thresholds of TCR down‐regulation were shown when antigen was presented by either T‐APC or professional APC. Rather, the stimulatory T‐APC weakness was due to their inability, because they are CD40−, to provide the appropriate co‐stimuli to responder T cells both indirectly via IL‐12, and partially via direct CD40L triggering on T cells. Indeed, the simultaneous addition of IL‐12 and reagents directly engaging CD40L on responder T cells restored T cell cytokine synthesis when antigen was presented by T‐APC. In addition, either IL‐12 production or blocking of T cell cytokine synthesis by anti‐IL‐12 p75 antibodies was evident only when professional APC were used in our antigen‐specific system. The down‐regulation of cytokine synthesis in the system of T‐T cell presentation could represent a novel mechanism of immune regulation, which may intervene to switch off detrimental Th1‐ or Th2‐mediated responses induced by antigen presentation among activated T cells infiltrating inflamed tissues.
Person tracking in real-world scenarios using statistical methods

This paper presents a novel approach to robust and flexible person tracking using an algorithm that combines two powerful stochastic modeling techniques: pseudo-2D hidden Markov models (P2DHMM) used for capturing the shape of a person within an image frame, and the well-known Kalman-filtering algorithm, that uses the output of the P2DHMM for tracking the person by estimation of a bounding box trajectory indicating the location of the person within the entire video sequence. Both algorithms cooperate together in an optimal way, and with this co-operative feedback, the proposed approach even makes the tracking of people possible in the presence of background motions caused by moving objects or by camera operations as, e.g., panning or zooming. Our results are confirmed by several tracking examples in real scenarios, shown at the end of the paper and provided on the Web server of our institute.
Intellectual capital and distinctive skills in SMEs of the timber industry in Argentina

In the knowledge economy, intellectual capital is increasingly becoming important as a source of core competences. A core competence is obtained by combining internal and external factors of the company by means of the strategy to generate better performance than its competitors. The Argentinian wood SMEs often have specific characteristics and, in particular, a limited intellectual capital. Consequently, it is expected that the process of establishing core competences is different. This paper analyzes the characteristics of that process. The results show how they organize their resources and capabilities to provide their competitiveness. This competitiveness leads to better organizational performance, but does not directly affect economic performance.
Moral distress, autonomy and nurse-physician collaboration among intensive care unit nurses in Italy.

AIM To explore the level of moral distress and potential associations between moral distress indices and (1) nurse-physician collaboration, (2) autonomy, (3) professional satisfaction, (4) intention to resign, and (5) workload among Italian intensive care unit nurses. BACKGROUND Poor nurse-physician collaboration and low autonomy may limit intensive care unit nurses' ability to act on their moral decisions. METHODS A cross-sectional correlational design with a sample of 566 Italian intensive care unit nurses. RESULTS The intensity of moral distress was 57.9 ± 15.6 (mean, standard deviation) (scale range: 0-84) and the frequency of occurrence was 28.4 ± 12.3 (scale range: 0-84). The mean score of the severity of moral distress was 88.0 ± 44 (scale range: 0-336). The severity of moral distress was associated with (1) nurse-physician collaboration and dissatisfaction on care decisions (r = -0.215, P < 0.001); and (2) intention to resign (r = 0.244, P < 0.0001). The frequency of occurrence of moral distress was associated with the intention of nurses to resign (r = -0. 209, P < 0.0001). CONCLUSION Moral distress seems to be associated with the intention to resign, whereas poor nurse-physician collaboration appears to be a pivotal factor accounting for nurses' moral distress. IMPLICATIONS FOR NURSING MANAGEMENT Enhancement of nurse-physician collaboration and nurses' participation in end-of-life decisions seems to be a managerial task that could lead to the alleviation of nurses' moral distress and their retention in the profession.
From Pythagoreans and Weierstrassians to True Infinitesimal Calculus

In teaching infinitesimal calculus we sought to present basic concepts like continuity and convergence by comparing and contrasting various definitions, rather than presenting “the definition” to the students as a monolithic absolute. We hope that our experiences could be useful to other instructors wishing to follow this method of instruction. A poll run at the conclusion of the course indicates that students tend to favor infinitesimal definitions over -δ ones.
Epstein‐Barr virus infection and risk of lymphoma: Immunoblot analysis of antibody responses against EBV‐related proteins in a large series of lymphoma subjects and matched controls

Epstein‐Barr Virus (EBV) is consistently associated with distinct lymphoproliferative malignancies and aberrant EBV antibody patterns are found in most EBV cancer patients. We evaluate the detection of an abnormal reactive serological pattern to EBV (ab_EBV) infection and the risk of lymphoma in a multicentric case–control study. Serum samples were collected at study entry from 1,085 incident lymphoma cases from Spain, France, Germany, Czech Republic, Italy and 1,153 age, sex and country matched controls. EBV immunoglobulin G (IgG) serostatus was evaluated through a peptide‐based ELISA combining immunodominant epitopes of EBNA1 (BKRF1) and VCA‐p18 (BFRF3). Further, immunoblot analysis was performed to evaluate distinct antibody diversity patterns to EBV early antigens (EA), besides EBNA1, VCA‐p18, VCA‐p40 (BdRF1) and Zebra (BZLF1). Patients with chronic active EBV infection and aberrant EBV activity were characterized as having an abnormal reactive pattern (ab_EBV). Ab_EBV was observed in 20.9% of 2,238 included subjects with an increased proportion of cases presenting ab_EBV as compared to the control population (23.9% vs. 18.0% p = 0.001). Ab_EBV positivity was a risk factor for all lymphomas combined (odds ratio [OR] = 1.42, 95% confidence interval [CI]=1.15–1.74), and specifically for chronic lymphocytic leukaemia (OR = 2.96, 95%CI = 2.22–3.95). Lower levels of ab_EBV were observed for follicular lymphoma (OR = 0.38, 95%CI = 0.15–0.98). EBV may be involved in a larger subset of lymphomas among clinically immunocompetent subjects than previously thought, probably explained by an underlying loss of immune control of EBV latent infection. Ab_EBV is a useful tool to explore EBV imbalances preceeding or paralleling possible EBV associated oncogenic events. © 2007 Wiley‐Liss, Inc.
Do public expenditures on health and families relate to alcohol abstaining in adolescents? Multilevel study of adolescents in 24 countries

INTRODUCTION AND AIMS Several European countries have observed an increase in the proportion of adolescents that abstain from drinking alcohol in the last decade. The reasons for this trend remain underexplored. We hypothesised that more generous government expenditures on health services and benefits to families with children relate to a positive trend in abstainers. DESIGN AND METHODS We used data on 15-year-olds in four successive cycles of the World Health Organization Health Behaviour in School-aged Children study (2002 to 2014) in 24 North American and European countries (pooled n = 175 331). Generalised linear mixed-effects models were tested to analyse trends in alcohol abstinence and to investigate whether cross-country differences in these trends relate to public expenditures on health and families with children (in proportion to gross domestic product). RESULTS Overall, we observed an increase in the proportion of abstainers from 21% in 2002 to 35% in 2014. An exception was Greece where abstaining had decreased from 20% to 15%. Similar results were found in boys and girls. The upward trend in abstinence related to larger government expenditures on health and families. DISCUSSIONS AND CONCLUSIONS More generous expenditures on health services and family benefits relate to more adolescents abstaining from alcohol.
Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes

With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa) gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional annotation of those modules. Additionally, the expression patterns of genes across the treatments/conditions of an expression experiment comprise a second form of useful annotation.
A Few AI Challenges Raised while Developing an Architecture for Human-Robot Cooperative Task Achievement

Over the last five years, and while developing an architecture for autonomous service robots in human environments, we have identified several key decisional issues that are to be tackled for a cognitive robot to share space and tasks with a human. We introduce some of them here: situation assessment and mutual modelling, management and exploitation of each agent (human and robot) knowledge in separate cognitive models, natural multi-modal communication, "human-aware" task planning, and human and robot interleaved plan achievement. As a general "take home" message, it appears that explicit knowledge management, both symbolic and geometric, proves to be a successful key while attempting to address these challenges, as it pushes for a different, more semantic way to address the decision-making issue in human-robot interactions.