Fast Exact String Pattern-matching Algorithms Adapted to the Characteristics of the Medical Language

Objective: The authors consider the problem of exact string pattern matching using algorithms that do not require any preprocessing. To choose the most appropriate algorithm, distinctive features of the medical language must be taken into account. The characteristics of medical language are emphasized in this regard, the best algorithm of those reviewed is proposed, and detailed evaluations of time complexity for processing medical texts are provided. Design: The authors first illustrate and discuss the techniques of various string pattern-matching algorithms. Next, the source code and the behavior of representative exact string pattern-matching algorithms are presented in a comprehensive manner to promote their implementation. Detailed explanations of the use of various techniques to improve performance are given. Measurements: Real-time measures of time complexity with English medical texts are presented. They lead to results distinct from those found in the computer science literature, which are typically computed with normally distributed texts. Results: The Boyer-Moore-Horspool algorithm achieves the best overall results when used with medical texts. This algorithm usually performs at least twice as fast as the other algorithms tested. Conclusion: The time performance of exact string pattern matching can be greatly improved if an efficient algorithm is used. Considering the growing amount of text handled in the electronic patient record, it is worth implementing this efficient algorith

Evaluation of a Command-line Parser-based Order Entry Pathway for the Department of Veterans Affairs Electronic Patient Record

Objective: To improve and simplify electronic order entry in an existing electronic patient record, the authors developed an alternative system for entering orders, which is based on a command- interface using robust and simple natural-language techniques. Design: The authors conducted a randomized evaluation of the new entry pathway, measuring time to complete a standard set of orders, and users' satisfaction measured by questionnaire. A group of 16 physician volunteers from the staff of the Department of Veterans Affairs Puget Sound Health Care System-Seattle Division participated in the evaluation. Results: Thirteen of the 16 physicians (81%) were able to enter medical orders more quickly using the natural-language-based entry system than the standard graphical user interface that uses menus and dialogs (mean time spared, 16.06 ± 4.52 minutes; P=0.029). Compared with the graphical user interface, the command--based pathway was perceived as easier to learn (P<0.01), was considered easier to use and faster (P<0.01), and was rated better overall (P<0.05). Conclusion: Physicians found the command- interface easier to learn and faster to use than the usual menu-driven system. The major advantage of the system is that it combines an intuitive graphical user interface with the power and speed of a natural-language analyze

Effects of APETALA2 on embryo, endosperm, and seed coat development determine seed size in Arabidopsis

Arabidopsis APETALA2 (AP2) controls seed mass maternally, with ap2 mutants producing larger seeds than wild type. Here, we show that AP2 influences development of the three major seed compartments: embryo, endosperm, and seed coat. AP2 appears to have a significant effect on endosperm development. ap2 mutant seeds undergo an extended period of rapid endosperm growth early in development relative to wild type. This early expanded growth period in ap2 seeds is associated with delayed endosperm cellularization and overgrowth of the endosperm central vacuole. The subsequent period of moderate endosperm growth is also extended in ap2 seeds largely due to persistent cell divisions at the endosperm periphery. The effect of AP2 on endosperm development is mediated by different mechanisms than parent-of-origin effects on seed size observed in interploidy crosses. Seed coat development is affected; integument cells of ap2 mutants are more elongated than wild type. We conclude that endosperm overgrowth and/or integument cell elongation create a larger postfertilization embryo sac into which the ap2 embryo can grow. Morphological development of the embryo is initially delayed in ap2 compared with wild-type seeds, but ap2 embryos become larger than wild type after the bent-cotyledon stage of development. ap2 embryos are able to fill the enlarged postfertilization embryo sac, because they undergo extended periods of cell proliferation and seed filling. We discuss potential mechanisms by which maternally acting AP2 influences development of the zygotic embryo and endosperm to repress seed size

A comprehensive overview of grain development in Brachypodium distachyon variety Bd21

A detailed and comprehensive understanding of seed reserve accumulation is of great importance for agriculture and crop improvement strategies. This work is part of a research programme aimed at using Brachypodium distachyon as a model plant for cereal grain development and filling. The focus was on the Bd21-3 accession, gathering morphological, cytological, and biochemical data, including protein, lipid, sugars, starch, and cell-wall analyses during grain development. This study highlighted the existence of three main developmental phases in Brachypodium caryopsis and provided an extensive description of Brachypodium grain development. In the first phase, namely morphogenesis, the embryo developed rapidly reaching its final morphology about 18 d after fertilization (DAF). Over the same period the endosperm enlarged, finally to occupy 80% of the grain volume. During the maturation phase, carbohydrates were continuously stored, mainly in the endosperm, switching from sucrose to starch accumulation. Large quantities of β-glucans accumulated in the endosperm with local variations in the deposition pattern. Interestingly, new β-glucans were found in Brachypodium compared with other cereals. Proteins (i.e. globulins and prolamins) were found in large quantities from 15 DAF onwards. These proteins were stored in two different sub-cellular structures which are also found in rice, but are unusual for the Pooideae. During the late stage of development, the grain desiccated while the dry matter remained fairly constant. Brachypodium exhibits some significant differences with domesticated cereals. Beta-glucan accumulates during grain development and this cell wall polysaccharide is the main storage carbohydrate at the expense of starch

Community recommendations on terminology and procedures used in flooding and low oxygen stress research

Apart from playing a key role in important biochemical reactions, molecular oxygen (O2) and its by-products also have crucial signaling roles in shaping plant developmental programs and environmental responses. Even under normal conditions, sharp O2 gradients can occur within the plant when cellular O2 demand exceeds supply, especially in dense organs such as tubers, seeds and fruits. Spatial and temporal variations in O2 concentrations are important cues for plants to modulate development (van Dongen & Licausi, 2015; Considine et al., 2016). Environmental conditions can also expand the low O2 regions within the plant. For example, excessive rainfall can lead to partial or complete plant submergence resulting in O2 deficiency in the root or the entire plant (Voesenek & Bailey-Serres, 2015). Climate change-associated increases in precipitation events have made flooding a major abiotic stress threatening crop production and food sustainability. This increased flooding and associated crop losses highlight the urgency of understanding plant flooding responses and tolerance mechanisms. Timely manifestation of physiological and morphological changes triggering developmental adjustments or flooding survival strategies requires accurate sensing of O2 levels. Despite progress in understanding how plants sense and respond to changes in intracellular O2 concentrations (van Dongen & Licausi, 2015), several questions remain unanswered due to a lack of high resolution tools to accurately and noninvasively monitor (sub)cellular O2 concentrations. In the absence of such tools, it is therefore critical for researchers in the field to be aware of how experimental conditions can influence plant O2 levels, and thus on the importance of accurately reporting specific experimental details. This also requires a consensus on the definition of frequently used terms. At the 15th New Phytologist Workshop on Flooding stress (Voesenek et al., 2016), community members discussed and agreed on unified nomenclature and standard norms for low O2 and flooding stress research. This consensus on terminology and experimental guidelines is presented here. We expect that these norms will facilitate more effective interpretation, comparison and reproducibility of research in this field. We also highlight the current challenges in noninvasively monitoring and measuring O2 concentrations in plant cells, outlining the technologies currently available, their strengths and drawbacks, and their suitability for use in flooding and low O2 research

The effects of siblings on the migration of women in two rural areas of Belgium and the Netherlands, 1829-1940

This study explores the extent to which the presence and activities of siblings shaped the chances of women migrating to rural and urban areas in two rural areas of Belgium and the Netherlands during the second half of the nineteenth and first decades of the twentieth century. Shared-frailty Cox proportional hazard analyses of longitudinal data from historical population registers show that siblings exerted an additive impact on women's migration, independently of temporal and household characteristics. Just how siblings influenced women's migration depended on regional modes of production and on employment opportunities. In the Zeeland region, sisters channelled each other into service positions. In the Pays de Herve, where men and women found industrial work in the Walloon cities, women were as much influenced by their brothers' activities. Evidence is found for two mechanisms explaining the effects of siblings: micro-economic notions of joint-household decision-making and social capital theory

Lack of Evidence for Neonatal Misoprostol Neurodevelopmental Toxicity in C57BL6/J Mice

Misoprostol is a synthetic analogue of prostaglandin E1 that is administered to women at high doses to induce uterine contractions for early pregnancy termination and at low doses to aid in cervical priming during labor. Because of the known teratogenic effects of misoprostol when given during gestation and its effects on axonal growth in vitro, we examined misoprostol for its potential as a neurodevelopmental toxicant when administered to neonatal C57BL6/J mice. Mice were injected subcutaneously (s.c.) with 0.4, 4 or 40 µg/kg misoprostol on postnatal day 7, the approximate developmental stage in mice of human birth, after which neonatal somatic growth, and sensory and motor system development were assessed. These doses were selected to span the range of human exposure used to induce labor. In addition, adult mice underwent a battery of behavioral tests relevant to neurodevelopmental disorders such as autism including tests for anxiety, stereotyped behaviors, social communication and interactions, and learning and memory. No significant effects of exposure were found for any measure of development or behavioral endpoints. In conclusion, the results of the present study in C57BL/6J mice do not provide support for neurodevelopmental toxicity after misoprostol administration approximating human doses and timed to coincide with the developmental stage of human birth

Alignment of the CMS silicon tracker during commissioning with cosmic rays

This is the Pre-print version of the Article. The official published version of the Paper can be accessed from the link below - Copyright @ 2010 IOPThe CMS silicon tracker, consisting of 1440 silicon pixel and 15 148 silicon strip detector modules, has been aligned using more than three million cosmic ray charged particles, with additional information from optical surveys. The positions of the modules were determined with respect to cosmic ray trajectories to an average precision of 3–4 microns RMS in the barrel and 3–14 microns RMS in the endcap in the most sensitive coordinate. The results have been validated by several studies, including laser beam cross-checks, track fit self-consistency, track residuals in overlapping module regions, and track parameter resolution, and are compared with predictions obtained from simulation. Correlated systematic effects have been investigated. The track parameter resolutions obtained with this alignment are close to the design performance.This work is supported by FMSR (Austria); FNRS and FWO (Belgium); CNPq, CAPES, FAPERJ, and FAPESP (Brazil); MES (Bulgaria); CERN; CAS, MoST, and NSFC (China); COLCIENCIAS (Colombia); MSES (Croatia); RPF (Cyprus); Academy of Sciences and NICPB (Estonia); Academy of Finland, ME, and HIP (Finland); CEA and CNRS/IN2P3 (France); BMBF, DFG, and HGF (Germany); GSRT (Greece); OTKA and NKTH (Hungary); DAE and DST (India); IPM (Iran); SFI (Ireland); INFN (Italy); NRF (Korea); LAS (Lithuania); CINVESTAV, CONACYT, SEP, and UASLP-FAI (Mexico); PAEC (Pakistan); SCSR (Poland); FCT (Portugal); JINR (Armenia, Belarus, Georgia, Ukraine, Uzbekistan); MST and MAE (Russia); MSTDS (Serbia); MICINN and CPAN (Spain); Swiss Funding Agencies (Switzerland); NSC (Taipei); TUBITAK and TAEK (Turkey); STFC (United Kingdom); DOE and NSF (USA)

Commissioning and performance of the CMS pixel tracker with cosmic ray muons

This is the Pre-print version of the Article. The official published verion of the Paper can be accessed from the link below - Copyright @ 2010 IOPThe pixel detector of the Compact Muon Solenoid experiment consists of three barrel layers and two disks for each endcap. The detector was installed in summer 2008, commissioned with charge injections, and operated in the 3.8 T magnetic field during cosmic ray data taking. This paper reports on the first running experience and presents results on the pixel tracker performance, which are found to be in line with the design specifications of this detector. The transverse impact parameter resolution measured in a sample of high momentum muons is 18 microns.This work is supported by FMSR (Austria); FNRS and FWO (Belgium); CNPq, CAPES, FAPERJ, and FAPESP (Brazil); MES (Bulgaria); CERN; CAS, MoST, and NSFC (China); COLCIENCIAS (Colombia); MSES (Croatia); RPF (Cyprus); Academy of Sciences and NICPB (Estonia); Academy of Finland, ME, and HIP (Finland); CEA and CNRS/IN2P3 (France); BMBF, DFG, and HGF (Germany); GSRT (Greece); OTKA and NKTH (Hungary); DAE and DST (India); IPM (Iran); SFI (Ireland); INFN (Italy); NRF (Korea); LAS (Lithuania); CINVESTAV, CONACYT, SEP, and UASLP-FAI (Mexico); PAEC (Pakistan); SCSR (Poland); FCT (Portugal); JINR (Armenia, Belarus, Georgia, Ukraine, Uzbekistan); MST and MAE (Russia); MSTDS (Serbia); MICINN and CPAN (Spain); Swiss Funding Agencies (Switzerland); NSC (Taipei); TUBITAK and TAEK (Turkey); STFC (United Kingdom); DOE and NSF (USA)

Performance of the CMS drift-tube chamber local trigger with cosmic rays

The performance of the Local Trigger based on the drift-tube system of the CMS experiment has been studied using muons from cosmic ray events collected during the commissioning of the detector in 2008. The properties of the system are extensively tested and compared with the simulation. The effect of the random arrival time of the cosmic rays on the trigger performance is reported, and the results are compared with the design expectations for proton-proton collisions and with previous measurements obtained with muon beams