An investigation of dead-zone pattern matching algorithms

Thesis (MA)--Stellenbosch, 2016.ENGLISH ABSTRACT: Pattern matching allows us to search some text for a word or for a sequence of characters|a popular feature of computer programs such as text editors. Traditionally, three distinct families of pattern matching algorithms exist: the Boyer-Moore (BM) algorithm, the Knuth-Morris-Pratt (KMP) algorithm, and the Rabin-Karp (RK) algorithm. The basic algorithm in all these algorithmic families was developed in the 1970s and 1980s. However a new family of pattern matching algorithms, known as the Dead-Zone (DZ) family of algorithms, has recently been developed. In a previous study, it was theoretically proven that DZ is able to pattern match a text with fewer match attempts than the well- known Horspool algorithm, a derivative of the BM algorithm. The main aim of this study was to provide empirical evidence to determine whether DZ is faster in practice. A benchmark platform was developed to com- pare variants of the DZ algorithm to existing pattern matching algorithms. Initial experiments were performed with four C implementations of the DZ algorithm (two recursive and two iterative implementations). Subsequent to this, DZ variants that make use of di erent shift functions as well as two parallel variants of DZ (implemented with Pthreads and CUDA) were devel- oped. Additionally, the underlying skeleton of the DZ algorithm was tweaked to determine whether the DZ code was optimal. The benchmark results showed that the C implementation of the iterative DZ variants performed favourably. Both iterative algorithms beat traditional pat- tern matching algorithms when searching natural language and genome texts, particularly for short patterns. When di erent shift functions were used, the only time a DZ implementation performed better than an implementation of the traditional algorithm was for a pattern length of 65536 characters. Con- trary to our expectations, the parallel implementation of DZ did not always provide a speedup. In fact, the Pthreaded variants of DZ were slower than the non-threaded DZ implementations, although the CUDA DZ variants were consistently ve times faster than a CPU implementation of Horspool. By us- ing a cache-friendly DZ algorithm, which reduces cache misses by about 20%, the the original DZ can be improved by approximately 5% for relatively short patterns (up to 128 characters with a natural language text). Moreover, a cost of recursion and the impact of information sharing were observed for all DZ variants and have thus been identi ed as intrinsic DZ characteristics. Further research is recommended to determine whether the cache-friendly DZ algorithm should become the standard implementation of the DZ algorithm. In addition, we hope that the development of our benchmark platform has produced a technique that can be used by researchers in future studies to conduct benchmark testsAFRIKAANSE OPSOMMING: Patroonpassing word gebruik om vir 'n reeks opeenvolgende karakters in 'n blok van teks te soek. Dit word breedvoerig programmaties in rekenaarprogramme gebruik, byvoorbeeld in die teksredigeerders. Tradisioneel is daar drie afsonderlike patroonpassingalgoritme families: die Boyer-Moore (BM) familie, Knuth-Morris-Pratt (KMP) familie en Rabin-Karp (RK) familie. Die basisal- goritmes in hierdie algoritmefamilies was reeds in die 1970s en 1980s ontwikkel. Maar, 'n nuwe patroonpassingsalgoritme familie is egter onlangs ontwikkel. Dit staan as die Dooie Gebied (DG) algoritme familie bekend. 'n Vorige studie het bewys dat DG algoritmes in staat is om patroonpassing uit te voer met minder passingpogings as die welbekende Hoorspool algoritme, wat 'n afgeleide algoritme van die BM algoritme is. Die hoofdoel met hierdie studie was om die DG familie van algoritmes empiries te ondersoek. 'n Normtoets platform is ontwikkel om veranderlikes van die DG algoritme met bestaande patroonpassingsalgoritmes te vergelyk. Aanvanklike eksperimente is met vier C implementasies van die DG algoritme uitgevoer. Twee van die implementasies is rekursief en die ander twee is iteratief. Daarna was DG variante ontwikkel wat van verskillende skuif- funksies gebruik gemaak Twee parallelle variante van DG was ook ontwikkel. Een maak gebruik van \Pthreads' en die ander is in CUDA geimplementeer. Verder was die C kode weergawe van die basiese DG algoritme fyn aangepas om vas te stel of die kode optimaal was. Die normtoetsresultate dui aan dat die C-implementasie van die iteratiewe DG variante gunstig presteer bo-oor die tradisionele patroonpassingsalgoritmes. Beide van die iteratiewe algoritmes klop die tradisionele patroonpassingsalgoritmes wanneer daar met relatiewe kort patrone getoets word. Die verrigting van verskeie skuif-funksies was ook geondersoek. Die enigste keer wanneer die DG algoritmes beter presteer het as die tradisionele algoritme, was vir patroonlengtes van 65536 karakters. Teen ons verwagtinge, het die parallelle implementasie nie altyd spoedtoename voorsien nie. Tewens, die \Pthread" variante van DG was stadiger as die nie-gerygde DG implementasies. Die CUDA DG variante was egter telkens vyf keer vinniger as die konvensionele SVE implementasie van Horspool. Die normtoetse het ook aangedui dat die oorspronklike DG kode naby aan optimaal was. Egter, deur 'n kas-vriendelike weergawe te gebruik wat kas oorslane met omtrent 20% verminder, kon die prestasie met naastenby 5% verbeter word vir relatiewe kort patrone (tot by 128 karakters met natuurlike taal teks). Verder was daar vir al die DG variante n rekursiekoste en 'n impak op inligtingdeling waargeneem wat as interne DG kenmerke geidentifiseer is. Verdere navorsing word aanbeveel om vas te stel of die kas-vriendelike DG algoritme die standaard implementasie van die DG algoritme behoort te word. Bykomstiglik, hoop ons dat die ontwikkeling van ons normtoets platform 'n tegniek geproduseer het wat deur navorsers in toekomstige studies gebruik kan word om normtoetse uit te voer

Head-Tail Galaxies: Beacons of High-Density Regions in Clusters

Using radio data at 1.4 GHz from the ATCA we identify five head-tail (HT) galaxies in the central region of the Horologium-Reticulum Supercluster (HRS). Physical parameters of the HT galaxies were determined along with substructure in the HRS to probe the relationship between environment and radio properties. Using a density enhancement technique applied to 582 spectroscopic measurements in the 2 degree x 2 degree region about A3125/A3128, we find all five HT galaxies reside in regions of extremely high density (>100 galaxies/Mpc^3). In fact, the environments surrounding HT galaxies are statistically denser than those environments surrounding non-HT galaxies and among the densest environments in a cluster. Additionally, the HT galaxies are found in regions of enhanced X-ray emission and we show that the enhanced density continues out to substructure groups of 10 members. We propose that it is the high densities that allow ram pressure to bend the HT galaxies as opposed to previously proposed mechanisms relying on exceptionally high peculiar velocities.Comment: 12 pages, 5 figures, accepted in MNRA

Peri-operative red blood cell transfusion in neonates and infants: NEonate and Children audiT of Anaesthesia pRactice IN Europe: A prospective European multicentre observational study

BACKGROUND: Little is known about current clinical practice concerning peri-operative red blood cell transfusion in neonates and small infants. Guidelines suggest transfusions based on haemoglobin thresholds ranging from 8.5 to 12 g dl-1, distinguishing between children from birth to day 7 (week 1), from day 8 to day 14 (week 2) or from day 15 (≥week 3) onwards. OBJECTIVE: To observe peri-operative red blood cell transfusion practice according to guidelines in relation to patient outcome. DESIGN: A multicentre observational study. SETTING: The NEonate-Children sTudy of Anaesthesia pRactice IN Europe (NECTARINE) trial recruited patients up to 60 weeks' postmenstrual age undergoing anaesthesia for surgical or diagnostic procedures from 165 centres in 31 European countries between March 2016 and January 2017. PATIENTS: The data included 5609 patients undergoing 6542 procedures. Inclusion criteria was a peri-operative red blood cell transfusion. MAIN OUTCOME MEASURES: The primary endpoint was the haemoglobin level triggering a transfusion for neonates in week 1, week 2 and week 3. Secondary endpoints were transfusion volumes, 'delta haemoglobin' (preprocedure - transfusion-triggering) and 30-day and 90-day morbidity and mortality. RESULTS: Peri-operative red blood cell transfusions were recorded during 447 procedures (6.9%). The median haemoglobin levels triggering a transfusion were 9.6 [IQR 8.7 to 10.9] g dl-1 for neonates in week 1, 9.6 [7.7 to 10.4] g dl-1 in week 2 and 8.0 [7.3 to 9.0] g dl-1 in week 3. The median transfusion volume was 17.1 [11.1 to 26.4] ml kg-1 with a median delta haemoglobin of 1.8 [0.0 to 3.6] g dl-1. Thirty-day morbidity was 47.8% with an overall mortality of 11.3%. CONCLUSIONS: Results indicate lower transfusion-triggering haemoglobin thresholds in clinical practice than suggested by current guidelines. The high morbidity and mortality of this NECTARINE sub-cohort calls for investigative action and evidence-based guidelines addressing peri-operative red blood cell transfusions strategies. TRIAL REGISTRATION: ClinicalTrials.gov, identifier: NCT02350348

Wie Pflegekräfte im ambulanten Bereich den Einsatz von Telepräsenzsystemen einschätzen

Hintergrund: Technische Assistenzsysteme werden zunehmend als Lösungsansatz diskutiert, um die gesundheitliche Versorgung älterer Menschen zu unterstützen und die Autonomie im Alter möglichst lange aufrecht zu erhalten. Auch Telepräsenzsysteme (TPS) werden im Zuge dessen im Rahmen von Pflegetätigkeiten eingesetzt. Ziel: Die Studie verfolgt das Ziel, zu beschreiben, inwiefern Pflegekräfte TPS für den Einsatz in der ambulanten Pflege als geeignet einschätzen. Methode: In Fokusgruppen (n = 4) in Sachsen-Anhalt wurde im Anschluss an eine Vorstellung eines TPS über Einsatzmöglichkeiten, Probleme und Potenziale in Bezug zur Einsatzfähigkeit in der ambulanten Pflege diskutiert. Die Datenauswertung erfolgte mittels der Dokumentarischen Methode nach Bohnsack, Nentwig-Gesemann & Nohl (2007). Ergebnisse: Das vorgestellte TPS wurde für die praktische Anwendung im ambulanten Bereich aufgrund fehlender Technikkompetenzen aller Beteiligten, nicht ausreichender Funktionalität des Geräts sowie ethischen und Finanzierungsfragen als eher ungeeignet eingeschätzt. Die Möglichkeit, den Kontakt zwischen Pflegebedürftigen und Angehörigen durch das Gerät zu intensivieren, wird als äußerst positiv erachtet. Weitere Einsatzoptionen könnten die schnelle Kontaktaufnahme in Notfallsituationen oder die Betreuung der Medikamenteneinnahme sein. Schlussfolgerung: TPS sind für den Einsatz in der ambulanten Pflege nicht ausgereift. Zur Entfaltung ihres Potenzials wäre die frühzeitige Einbindung von Pflegekräften bei der Entwicklung von Pflegetechnologien entscheidend. Der Erwerb von Technikkompetenzen bereits in der Pflegeausbildung würde Pflegekräften dabei helfen, an diesem Entwicklungsprozess teilzunehmen

Empirically assessing algorithm performance

The timing performance data of ten related algorithms (solving the single keyword pattern matching problem) executing under a wide variety of operating conditions, was gathered and analysed. Using the resulting 15 million items of timing data, various metrics to estimate algorithm performance were computed and compared. An assessment is made of whether and how various changes in the operating environment affect the measurements

Digitalisierungsstrategien auf dem Prüfstand – eine empirische Untersuchung auf Basis der Grounded-Theory-Methodologie an deutschen Hochschulen

Wilde M, Oevel G, Graf-Schlattmann M, Meister DM. Digitalisierungsstrategien auf dem Prüfstand – eine empirische Untersuchung auf Basis der Grounded-Theory-Methodologie an deutschen Hochschulen. In: Hafer J, Mauch M, Schumann M, eds. Teilhabe in der digitalen Bildungswelt. Medien in der Wissenschaft. Vol 75. Münster, New York: Waxmann; 2019: 14-26

Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury

Studying regeneration in the central nervous system (CNS) is hampered by current histological and imaging techniques because they provide only partial information about axonal and glial reactions. Here we developed a tetrahydrofuranbased clearing procedure that renders fixed and unsectioned adult CNS tissue transparent and fully penetrable for optical imaging. In large spinal cord segments, we imaged fluorescently labeled cells by `ultramicroscopy' and two-photon microscopy without the need for histological sectioning. We found that more than a year after injury growth-competent axons regenerated abundantly through the injury site. A few growth-incompetent axons could also regenerate when they bypassed the lesion. Moreover, we accurately determined quantitative changes of glial cells after spinal cord injury. Thus, clearing CNS tissue enables an unambiguous evaluation of axon regeneration and glial reactions. Our clearing procedure also renders other organs transparent, which makes this approach useful for a large number of preclinical paradigms

A center-based, ambulatory care concept for hidradenitis suppurativa improves patient outcomes and is also cost-effective

AbstractBackground Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease affecting approximately 1% of the population. The patient journey through the German health care system leads to high disease burden and substantial treatment costs. The EsmAiL study showed that an innovative, interprofessional, multimodal care-concept reduces disease activity and burden of HS compared to standard care. This paper examines the costs of treating HS in Germany and compares them with those of the innovative care concept implemented in EsmAiL.Methods EsmAiL was a two-arm, multicenter, prospective randomized controlled trial including 553 adults with HS. The study was registered in the German Clinical Trials Registry (DRKS00022135). The control group (CG) remained in standard care, whereas the intervention group (IG) was referred to specialized so-called ‘acne-inversa-centres (AiZ)’ where patients were treated with a structured, interdisciplinary approach. The present paper analyses the treatment costs for a subpopulation based on health insurance cost data from the two largest German health insurers. Quality-Adjusted Life Years (QALY) was assessed based on Dermatology Life Quality Index (DLQI).Results Total annual treatment costs per patient were €3,966.07 in standard care (n = 89) and €3,974.37 in the innovative care (n = 93). The costs per additional QALY amounted to €12,698.72 in the IG. Given the conventional and established threshold of €22,600 to €33,900 per QALY, the innovative treatment in AiZ proved to be cost-effective.Conclusion Treatment costs of HS are substantial and increase with disease severity. The new form of care is cost-effective and is expected to decrease costs in the long run

An Attempt at a Molecular Prediction of Metastasis in Patients with Primary Cutaneous Melanoma

<div><h3>Background</h3><p>Current prognostic clinical and morphological parameters are insufficient to accurately predict metastasis in individual melanoma patients. Several studies have described gene expression signatures to predict survival or metastasis of primary melanoma patients, however the reproducibility among these studies is disappointingly low.</p> <h3>Methodology/Principal Findings</h3><p>We followed extended REMARK/Gould Rothberg criteria to identify gene sets predictive for metastasis in patients with primary cutaneous melanoma. For class comparison, gene expression data from 116 patients with clinical stage I/II (no metastasis) and 72 with III/IV primary melanoma (with metastasis) at time of first diagnosis were used. Significance analysis of microarrays identified the top 50 differentially expressed genes. In an independent data set from a second cohort of 28 primary melanoma patients, these genes were analyzed by multivariate Cox regression analysis and leave-one-out cross validation for association with development of metastatic disease. In a multivariate Cox regression analysis, expression of the genes Ena/vasodilator-stimulated phosphoprotein-like (EVL) and CD24 antigen gave the best predictive value (p = 0.001; p = 0.017, respectively). A multivariate Cox proportional hazards model revealed these genes as a potential independent predictor, which may possibly add (both p = 0.01) to the predictive value of the most important morphological indicator, Breslow depth.</p> <h3>Conclusion/Significance</h3><p>Combination of molecular with morphological information may potentially enable an improved prediction of metastasis in primary melanoma patients. A strength of the gene expression set is the small number of genes, which should allow easy reevaluation in independent data sets and adequately designed clinical trials.</p> </div

Predictive gene expression set of the Cox proportional hazards model as obtained in a forward stepwise regression procedure.

*<p>A shrinkage factor of 0.74 should be applied on the parameter estimates to prevent an overestimation due to the limited number of patients <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049865#pone.0049865-Verweij1" target="_blank">[59]</a>.</p