Fast Searching in Packed Strings

Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time which is optimal if we can only read one character at the time. However, most strings are stored in a computer in a packed representation with several characters in a single word, giving us the opportunity to read multiple characters simultaneously. In this paper we study the worst-case complexity of string matching on strings given in packed representation. Let $m \leq n$ be the lengths $P$ and $Q$, respectively, and let $\sigma$ denote the size of the alphabet. On a standard unit-cost word-RAM with logarithmic word size we present an algorithm using time O\left(\frac{n}{\log_\sigma n} + m + \occ\right). Here \occ is the number of occurrences of $P$ in $Q$. For $m = o(n)$ this improves the $O(n)$ bound of the Knuth-Morris-Pratt algorithm. Furthermore, if $m = O(n/\log_\sigma n)$ our algorithm is optimal since any algorithm must spend at least \Omega(\frac{(n+m)\log \sigma}{\log n} + \occ) = \Omega(\frac{n}{\log_\sigma n} + \occ) time to read the input and report all occurrences. The result is obtained by a novel automaton construction based on the Knuth-Morris-Pratt algorithm combined with a new compact representation of subautomata allowing an optimal tabulation-based simulation.Comment: To appear in Journal of Discrete Algorithms. Special Issue on CPM 200

Transport and Fate of MethyI Iodide and Its Pest Control in Soils

For fumigants, information on transport and fate, as well as pest control, is needed to develop management practices with the fewest human and environmental health risks while offering sufficient pest control efficacy. For this purpose, a 2-D soil chamber (60 cm wide, 60 cm long, and 6 cm thick) with a surface-mounted flux chamber was designed to determine volatilization, spatial and temporal distribution of soil gas-phase concentration, degradation and organism survivability after methyl iodide (MeI) fumigation. Three types of pests (barnyardgrass seed [Echinochloa crus-galli], citrus nematode [Tylenchulus semipenetrans], and fungi [Fusarium oxysporum]) were used to give a broad spectrum of pest control information. After MeI fumigation at a rate of 56.43 kg ha-1 for 24 hr, about 25.8 % of MeI was emitted into air, 6.8 % remained in the soil, and 43.6% degraded in the soil (based on the residual iodide concentration). The uncertainty in the measured MeI degradation using iodide concentration was thought to contribute to the unrecovered MeI (about 23%). Based on the spatial and temporal distribution of soil gas-phase concentration, the concentration-time index (CT) and its distribution was quantified. The citrus nematodes were effectively eliminated even at low CT values (< 30 µg hr ml-1) but all Fusarium oxysporum survived at the applied rate. The response of barnyardgrass seeds spatially varied with the concentration-time index (CT) values in the 2-D soil chamber. To fully control barnyardgrass seeds, CT of greater than 300 µg hr ml-1 was required. Using this experimental approach, different fumigant emission reduction strategies can be tested and mathematical models can be verified to determine which strategies produce least emission to atmosphere while maintaining sufficient pest control efficacy

Efficient exact pattern-matching in proteomic sequences

This paper proposes a novel algorithm for complete exact pattern-matching focusing the specificities of protein sequences (alphabet of 20 symbols) but, also highly efficient considering larger alphabets. The searching strategy uses large search windows allowing multiple alignments per iteration. A new filtering heuristic, named compatibility rule, contributed decisively to the efficiency improvement. The new algorithm’s performance is, on average, superior in comparison with its best-rated competitors

Medical students' personal experience of high-stakes failure:case studies using interpretative phenomenological analysis

Abstract (provisional): Background Failing a high-stakes assessment at medical school is a major event for those who go through the experience. Students who fail at medical school may be more likely to struggle in professional practice, therefore helping individuals overcome problems and respond appropriately is important. There is little understanding about what factors influence how individuals experience failure or make sense of the failing experience in remediation. The aim of this study was to investigate the complexity surrounding the failure experience from the student’s perspective using interpretative phenomenological analysis (IPA). Methods The accounts of 3 medical students who had failed final re-sit exams, were subjected to in-depth analysis using IPA methodology. IPA was used to analyse each transcript case-by-case allowing the researcher to make sense of the participant’s subjective world. The analysis process allowed the complexity surrounding the failure to be highlighted, alongside a narrative describing how students made sense of the experience. Results The circumstances surrounding students as they approached assessment and experienced failure at finals were a complex interaction between academic problems, personal problems (specifically finance and relationships), strained relationships with friends, family or faculty, and various mental health problems. Each student experienced multi-dimensional issues, each with their own individual combination of problems, but experienced remediation as a one-dimensional intervention with focus only on improving performance in written exams. What these students needed to be included was help with clinical skills, plus social and emotional support. Fear of termination of the their course was a barrier to open communication with staff. Conclusions These students’ experience of failure was complex. The experience of remediation is influenced by the way in which students make sense of failing. Generic remediation programmes may fail to meet the needs of students for whom personal, social and mental health issues are a part of the picture

Approximate string matching with reduced alphabet

Peer reviewe

Customer emotions in service failure and recovery encounters

Emotions play a significant role in the workplace, and considerable attention has been given to the study of employee emotions. Customers also play a central function in organizations, but much less is known about customer emotions. This chapter reviews the growing literature on customer emotions in employee–customer interfaces with a focus on service failure and recovery encounters, where emotions are heightened. It highlights emerging themes and key findings, addresses the measurement, modeling, and management of customer emotions, and identifies future research streams. Attention is given to emotional contagion, relationships between affective and cognitive processes, customer anger, customer rage, and individual differences

Loss-of-function ABCC8 mutations in pulmonary arterial hypertension

Background: In pulmonary arterial hypertension (PAH), pathological changes in pulmonary arterioles progressively raise pulmonary artery pressure and increase pulmonary vascular resistance, leading to right heart failure and high mortality rates. Recently, the first potassium channelopathy in PAH, because of mutations in KCNK3, was identified as a genetic cause and pharmacological target. Methods: Exome sequencing was performed to identify novel genes in a cohort of 99 pediatric and 134 adult-onset group I PAH patients. Novel rare variants in the gene identified were independently identified in a cohort of 680 adult-onset patients. Variants were expressed in COS cells and function assessed by patch-clamp and rubidium flux analysis. Results: We identified a de novo novel heterozygous predicted deleterious missense variant c.G2873A (p.R958H) in ABCC8 in a child with idiopathic PAH. We then evaluated all individuals in the original and a second cohort for rare or novel variants in ABCC8 and identified 11 additional heterozygous predicted damaging ABCC8 variants. ABCC8 encodes SUR1 (sulfonylurea receptor 1)—a regulatory subunit of the ATP-sensitive potassium channel. We observed loss of ATP-sensitive potassium channel function for all ABCC8 variants evaluated and pharmacological rescue of all channel currents in vitro by the SUR1 activator, diazoxide. Conclusions: Novel and rare missense variants in ABCC8 are associated with PAH. Identified ABCC8 mutations decreased ATP-sensitive potassium channel function, which was pharmacologically recovered