Miracle-dz/UniFAR-FTUs huggingface dataset:
Fluorometric Quantification of Polyphosphate in Environmental Plankton Samples: Extraction Protocols, Matrix Effects, and Nucleic Acid Interference

ABSTRACT Polyphosphate (polyP) is a ubiquitous biochemical with many cellular functions and comprises an important environmental phosphorus pool. However, methodological challenges have hampered routine quantification of polyP in environmental samples. We tested 15 protocols to extract inorganic polyphosphate from natural marine samples and cultured cyanobacteria for fluorometric quantification with 4′,6-diamidino-2-phenylindole (DAPI) without prior purification. A combination of brief boiling and digestion with proteinase K was superior to all other protocols, including other enzymatic digestions and neutral or alkaline leaches. However, three successive extractions were required to extract all polyP. Standard addition revealed matrix effects that differed between sample types, causing polyP to be over- or underestimated by up to 50% in the samples tested here. Although previous studies judged that the presence of DNA would not complicate fluorometric quantification of polyP with DAPI, we show that RNA can cause significant interference at the wavelengths used to measure polyP. Importantly, treating samples with DNase and RNase before proteinase K digestion reduced fluorescence by up to 57%. We measured particulate polyP along a North Pacific coastal-to-open ocean transect and show that particulate polyP concentrations increased toward the open ocean. While our final method is optimized for marine particulate matter, different environmental sample types may need to be assessed for matrix effects, extraction efficiency, and nucleic acid interference.
Movement Synchrony Forges Social Bonds across Group Divides

Group dynamics play an important role in the social interactions of both children and adults. A large amount of research has shown that merely being allocated to arbitrarily defined groups can evoke disproportionately positive attitudes toward one's in-group and negative attitudes toward out-groups, and that these biases emerge in early childhood. This prompts important empirical questions with far-reaching theoretical and applied significance. How robust are these inter-group biases? Can biases be mitigated by behaviors known to bond individuals and groups together? How can bonds be forged across existing group divides? To explore these questions, we examined the bonding effects of interpersonal synchrony on minimally constructed groups in a controlled experiment. In-group and out-group bonding were assessed using questionnaires administered before and after a task in which groups performed movements either synchronously or non-synchronously in a between-participants design. We also developed an implicit behavioral measure, the Island Game, in which physical proximity was used as an indirect measure of interpersonal closeness. Self-report and behavioral measures showed increased bonding between groups after synchronous movement. Bonding with the out-group was significantly higher in the condition in which movements were performed synchronously than when movements were performed non-synchronously between groups. The findings are discussed in terms of their importance for the developmental social psychology of group dynamics as well as their implications for applied intervention programs.
Ectopic divisions in vascular and ground tissues of Arabidopsis thaliana result in distinct leaf venation defects

Leaf venation patterns vary considerably between species and between leaves within a species. A mechanism based on canalization of auxin transport has been suggested as the means by which plastic yet organized venation patterns are generated. This study assessed the plasticity of Arabidopsis thaliana leaf venation in response to ectopic ground or procambial cell divisions and auxin transport inhibition (ATI). Ectopic ground cell divisions resulted in vascular fragments between major veins, whereas ectopic procambial cell divisions resulted in additional, abnormal vessels along major veins, with more severely perturbed lines forming incomplete secondary and higher-order venation. These responses imply limited vascular plasticity in response to unscheduled cell divisions. Surprisingly, a combination of ectopic ground cell divisions and ATI resulted in massive vascular overgrowth. It is hypothesized that the vascular overproduction in auxin transport-inhibited wild-type leaves is limited by simultaneous differentiation of ground cells into mesophyll cells. Ectopic ground cell divisions may negate this effect by providing undifferentiated ground cells that respond to accumulated auxin by differentiation into vascular cells.
Real-Time Predictions of Reservoir Size and Rebound Time during Antiretroviral Therapy Interruption Trials for HIV

Monitoring the efficacy of novel reservoir-reducing treatments for HIV is challenging. The limited ability to sample and quantify latent infection means that supervised antiretroviral therapy (ART) interruption studies are generally required. Here we introduce a set of mathematical and statistical modeling tools to aid in the design and interpretation of ART-interruption trials. We show how the likely size of the remaining reservoir can be updated in real-time as patients continue off treatment, by combining the output of laboratory assays with insights from models of reservoir dynamics and rebound. We design an optimal schedule for viral load sampling during interruption, whereby the frequency of follow-up can be decreased as patients continue off ART without rebound. While this scheme can minimize costs when the chance of rebound between visits is low, we find that the reservoir will be almost completely reseeded before rebound is detected unless sampling occurs at least every two weeks and the most sensitive viral load assays are used. We use simulated data to predict the clinical trial size needed to estimate treatment effects in the face of highly variable patient outcomes and imperfect reservoir assays. Our findings suggest that large numbers of patients – between 40 and 150 – will be necessary to reliably estimate the reservoir-reducing potential of a new therapy and to compare this across interventions. As an example, we apply these methods to the two “Boston patients”, recipients of allogeneic hematopoietic stem cell transplants who experienced large reductions in latent infection and underwent ART-interruption. We argue that the timing of viral rebound was not particularly surprising given the information available before treatment cessation. Additionally, we show how other clinical data can be used to estimate the relative contribution that remaining HIV+ cells in the recipient versus newly infected cells from the donor made to the residual reservoir that eventually caused rebound. Together, these tools will aid HIV researchers in the evaluating new potentially-curative strategies that target the latent reservoir.
SemEval-2012 Task 3: Spatial Role Labeling

This SemEval2012 shared task is based on a recently introduced spatial annotation scheme called Spatial Role Labeling. The Spatial Role Labeling task concerns the extraction of main components of the spatial semantics from natural language: trajectors, landmarks and spatial indicators. In addition to these major components, the links between them and the general-type of spatial relationships including region, direction and distance are targeted. The annotated dataset contains about 1213 sentences which describe 612 images of the CLEF IAPR TC-12 Image Benchmark. We have one participant system with two runs. The participant's runs are compared to the system in (Kordjamshidi et al., 2011c) which is provided by task organizers.
A High-Throughput Data Mining of Single Nucleotide Polymorphisms in Coffea Species Expressed Sequence Tags Suggests Differential Homeologous Gene Expression in the Allotetraploid Coffea arabica1[W]

Polyploidization constitutes a common mode of evolution in flowering plants. This event provides the raw material for the divergence of function in homeologous genes, leading to phenotypic novelty that can contribute to the success of polyploids in nature or their selection for use in agriculture. Mounting evidence underlined the existence of homeologous expression biases in polyploid genomes; however, strategies to analyze such transcriptome regulation remained scarce. Important factors regarding homeologous expression biases remain to be explored, such as whether this phenomenon influences specific genes, how paralogs are affected by genome doubling, and what is the importance of the variability of homeologous expression bias to genotype differences. This study reports the expressed sequence tag assembly of the allopolyploid Coffea arabica and one of its direct ancestors, Coffea canephora. The assembly was used for the discovery of single nucleotide polymorphisms through the identification of high-quality discrepancies in overlapped expressed sequence tags and for gene expression information indirectly estimated by the transcript redundancy. Sequence diversity profiles were evaluated within C. arabica (Ca) and C. canephora (Cc) and used to deduce the transcript contribution of the Coffea eugenioides (Ce) ancestor. The assignment of the C. arabica haplotypes to the C. canephora (CaCc) or C. eugenioides (CaCe) ancestral genomes allowed us to analyze gene expression contributions of each subgenome in C. arabica. In silico data were validated by the quantitative polymerase chain reaction and allele-specific combination TaqMAMA-based method. The presence of differential expression of C. arabica homeologous genes and its implications in coffee gene expression, ontology, and physiology are discussed.
Chronic interstitial lung disease in children.

OBJECTIVES To describe clinical and diagnostic features and the results of therapeutic conduct in a group of pediatric patients with chronic interstitial lung disease. METHODS A retrospective study of 25 immunocompetent patients, aged 2 months to 17 years, with chronic interstitial lung disease, admitted to the Pediatric Pulmonary Section, Department of Pediatrics, Hospital dos Servidores do Estado, over a 20-year period (1984-2004). A routine protocol for persistent chronic pneumonias was used and the patients with interstitial lung disease were selected. Clinical, laboratory and imaging data were analyzed. RESULTS Twenty-five patients were diagnosed with chronic interstitial lung disease, 13 were aged less than 2 years and 17 were male. Diagnoses were made based on history, physical examination and routine tests in one case, based on more complex tests in three cases and based on the results of invasive tests in 21 cases (20 by lung biopsy and one by bronchoalveolar lavage). Except for one patient with pulmonary lymphangiectasia, the long-term treatment (1 to 7 years) consisted of corticosteroid, in six cases associated with hydroxychloroquine. Four patients required home oxygen therapy. The authors followed the patients in the outpatient department (6 a 8 visits/year). Patient outcome was: good (15); regular, with mild sequelae (4); and poor, with severe sequelae (3). One patient was lost in the follow-up period and two died. CONCLUSIONS Chronic interstitial lung diseases in children are a group of rare pulmonary disorders, but a relevant one because of the possible progression to pulmonary fibrosis. Early diagnosis and a long-term, specialized treatment and follow-up are important for the patient outcome. Pediatricians should be aware of these diseases because in many cases diagnosis and treatment are overlooked.
Combining biomarkers to optimize patient treatment recommendations

Markers that predict treatment effect have the potential to improve patient outcomes. For example, the OncotypeDX® RecurrenceScore® has some ability to predict the benefit of adjuvant chemotherapy over and above hormone therapy for the treatment of estrogen‐receptor‐positive breast cancer, facilitating the provision of chemotherapy to women most likely to benefit from it. Given that the score was originally developed for predicting outcome given hormone therapy alone, it is of interest to develop alternative combinations of the genes comprising the score that are optimized for treatment selection. However, most methodology for combining markers is useful when predicting outcome under a single treatment. We propose a method for combining markers for treatment selection which requires modeling the treatment effect as a function of markers. Multiple models of treatment effect are fit iteratively by upweighting or “boosting” subjects potentially misclassified according to treatment benefit at the previous stage. The boosting approach is compared to existing methods in a simulation study based on the change in expected outcome under marker‐based treatment. The approach improves upon methods in some settings and has comparable performance in others. Our simulation study also provides insights as to the relative merits of the existing methods. Application of the boosting approach to the breast cancer data, using scaled versions of the original markers, produces marker combinations that may have improved performance for treatment selection.
Coordinating Progressive Levels of Simulation Fidelity to Maximize Educational Benefit

Purpose To evaluate the effectiveness of a novel, simulation-based educational model rooted in scaffolding theory that capitalizes on a systematic progressive sequence of simulators that increase in realism (i.e., fidelity) and information content. Method Forty-five medical students were randomly assigned to practice intravenous catheterization using high-fidelity training, low-fidelity training, or progressive training from low to mid to high fidelity. One week later, participants completed a transfer test on a standardized patient simulation. Blinded expert raters assessed participants' global clinical performance, communication, procedure documentation, and technical skills on the transfer test. Participants' management of the resources available during practice was also recorded. Data were analyzed using multivariate analysis of variance. The study was conducted in fall 2008 at the University of Toronto. Results The high-fidelity group scored higher (P < .05) than the low-fidelity group on all measures except procedure documentation. The progressive group scored higher (P < .05) than other groups for documentation and global clinical performance and was equivalent to the high-fidelity group for communication and technical skills. Total practice time was greatest for the progressive group; however, this group required little practice time on the resource-intensive high-fidelity simulator. Conclusions Allowing students to progress in their practice on simulators of increasing fidelity led to superior transfer of a broad range of clinical skills. Further, this progressive group was resource-efficient, as participants concentrated on lower fidelity and lower resource-intensive simulators. It is suggested that clinical training curricula incorporate exposure to multiple simulators to maximize educational benefit and potentially save educator time.
Schedule Analysis of Concurrent Logic programs

A compilation technique is proposed for concurrent logic programs called schedule analysis. Schedule analysis deduces at compile-time a partial schedule for the processes of a program by partitioning the atoms of each clause into threads. Threads are totally ordered sets of atoms whose relative ordering is determined by a scheduler. Threads reduce scheduler activity and permit a wealth of traditional Prolog optimisations to be applied to the program. A framework for schedule analysis is proposed and this defines a procedure for creating threads. A safety result is presented stating the conditions under which the work of the scheduler can be reduced from ordering processes to ordering threads. Schedule analysis has been integrated into a compiler and implementation has suggested that it can play a central role in compilation. Optimisations which follow from schedule analysis include a reduction in scheduling, the removal of synchronisation checks, the simplification of unification, decreased garbage collection and a reduction in argument copying.
Guidelines for data-parallel cycle-stealing in networks of workstations. II. On maximizing guaranteed output

For pt. I see 12th IEEE Intl. Parallel Proc. Symp. , p. 519-23 (1998). We derive efficient guidelines for scheduling data-parallel computations within a draconian mode of cycle-stealing in networks of workstations wherein an interruption by the owner of the "borrowed" workstation kills all jobs currently in progress. We derive both adaptive and non-adaptive scheduling guidelines that maximize, up to low-order additive terms, the amount of work that one is guaranteed to accomplish during a cycle-stealing opportunity, no matter when the opportunity is interrupted-up to a prespecified number of times.
A Genetic Algorithm for Database Query Optimization

Current query optimization techniques are inadequate to support some of the emerging database applications. In this paper, we outline a database query optimization problem and describe the adaptation of a genetic algorithm to the problem. We present a method for encoding arbitrary binary trees as chromosomes and describe several crossover operators for such chromosomes. Preliminary computational comparisons with the current best{known method for query optimization indicate this to be a promising approach. In particular, the output quality and the time needed to produce such solutions is comparable to and in general better than the current method.
Modern concept of biological identification of selenoproteins

Humans possess 25 selenoproteins, approximately half of which are enzymes (selenoenzymes) required for preventing, regulating, or reversing oxidative damage, while others participate in providing calcium metabolism, thyroid hormone maintenance, protein synthesis, cytoskeletal structure etc. This review examines the latest evidences of the biological effects of selenoproteins according to the method of complex analysis of the material. Selenoprotein P promotes insulin resistance in type 2 diabetes, mediates myocardial ischemic-reperfusion injuries and provides protection against disease by reducing chronic oxidative stress. Selenoprotein T is expressed at the endoplasmic reticulum membrane in all cells during development, but is confined to endocrine tissues in adulthood, controls homeostasis of glucose and prevents neurodegeneration by reducing oxidative stress factors. Expression of selenoprotein K is required for efficient Ca2+ flux into melanoma cancer cells, tumour growth and metastasic potential depend on SelK but it suppresses human choriocarcinoma cells. SelK also serves to maintain the normal physiological functions of skeletal muscle. Selenoprotein N deficiency, caused by mutations in the human gene, promotes myopathy characterized by muscle weakness, spinal rigidity, respiratory insufficiency. Sel N participates in normal physiology of skeletal and smooth muscle tissues. Selenoprotein M is located in the endoplasmic reticulum, characterized by high expression in the brain, antioxidative, neuroprotective activity and regulates intracellular Ca2+ levels. Also, the overexpression of SelM was detected in human hepatocellular carcinoma. Selenoprotein S is mentioned as a regulator of ER stress and inflammatory processes. Selenoprotein F controls cell proliferation by the impact on G1period of the cell cycle. Moreover, it is implicated in the pathogenesis of some types of cancer. The Sel F deficiency reduces the migration and invasive ability of the cells. Knockdown of selenoprotein W in rodents leads to increased release of Ca2+, causes oxidative ultramicroscopic injuries of the endoplasmic reticulum and mitochondria ultrastructure, which in turn increases the levels of inflammatory factors. Selenoprotein H is involved in redox regulation, in tumourogenesis. Knockdown of selenoprotein H decreases cellular differentiation and increases proliferation and migration of cells. Selenoproteins U, V, I, O, R are recently identified and their functions are not clearly known. The data analyzed in the review help determine promising directions in the study of the selenoproteins.
Patients’ Perspectives on Physicians’ Roles: Implications for Curricular Reform

Purpose To elucidate the perspectives of patients on the conceptual framework for a new undergraduate medical curriculum organized around the healer and professional roles of the physician (their physicianship), and to illustrate how these perspectives can affect program development. Method In 2006, using an adapted interpretive description design and semistructured interviews, the authors collected data from a sample of 58 patients receiving care in a major academic medical center. Results Three findings were particularly salient. (1) The concepts of the physician as healer and professional, although central to the curriculum, did not resonate strongly with patients. The words professionalism and healer occasionally accrued negative connotations. There was little concordance between the lexicon patients use to describe ideal physician behaviors and a faculty-defined list of core physicianship attributes. (2) The listening skills of physicians were highly valued and seen as an “essentia” of ideal doctoring. (3) Being treated as a number by physicians represented a threat to patients’ personal identity. Conclusions This study found important differences between patients’ and physicians’ perspectives on key curricular concepts. Understanding these differences represents an important resource for program design and development. The findings also suggest avenues for future research on highly topical issues such as professionalism.
A new quadrannulate species of Orobdella (Hirudinida, Arhynchobdellida, Orobdellidae) from western Honshu, Japan

Abstract A new quadrannulate species of Orobdella Oka, 1895, Orobdella naraharaetmagarum sp. n. , from the mountainous region of western Honshu, Japan is described. Orobdella naraharaetmagarum is a small species with a body length of less than 5 cm. Phylogenetic analyses using nuclear 18S rRNA and histone H3, as well as mitochondrial cytochrome c oxidase subunit I, tRNACys, tRNAMet, 12S rRNA, tRNAVal, 16S rRNA, tRNALeu and NADH dehydrogenase subunit 1 markers indicated that the present new species is the sister species of the quadrannulate Orobdella esulcata Nakano, 2010. Furthermore, mitochondrial DNA genealogy within Orobdella naraharaetmagarum demonstrated that this new species is divided into eastern and western lineages.
Imaging of Moving Target with Rotating Parts Based on Hough Transform

The rotation of structures in a target introduces additional frequency modulations on the returned signals and also generates side-bands about the center Doppler frequency of the target. In other words, the body image will be contaminated due to the interference from the rotating parts. In this paper, an imaging method for moving targets with rotating parts is presented. The method is simple to implement and is based on the Hough transform which is widely used in the image processing. Using the Standard Hough Transform and an extended Hough Transform, we put forward a separation method by detecting the straight line and the sinusoid on the spectrogram, respectively. A computer simulation is given to illustrate the effectiveness of the proposed method. KeywordsMicro-Doppler, rotating parts, Hough Transform, moving targets, spectrogram.