Constructing suffix arrays in linear time

AbstractThe time complexity of suffix tree construction has been shown to be equivalent to that of sorting: O(n) for a constant-size alphabet or an integer alphabet and O(nlogn) for a general alphabet. However, previous algorithms for constructing suffix arrays have the time complexity of O(nlogn) even for a constant-size alphabet.In this paper we present a linear-time algorithm to construct suffix arrays for integer alphabets, which do not use suffix trees as intermediate data structures during its construction. Since the case of a constant-size alphabet can be subsumed in that of an integer alphabet, our result implies that the time complexity of directly constructing suffix arrays matches that of constructing suffix trees

Transcranial Direct Current Stimulation of motor cortex enhances running performance.

Transcranial direct current stimulation (tDCS) is a technique used to modulate neuronal excitability through non-invasive brain stimulation that can enhance exercise performance. We hypothesize that tDCS would improve submaximal running time to exhaustion (TTE) and delay the increase in the rating of perceived exertion (RPE) over time. We also hypothesize that tDCS would not lead to difference in cardiorespiratory responses. We employed a randomized, single-blinded, and counterbalanced design in which 10 trained men participated. After receiving either 20 min of 1.98 mA anodal tDCS applied over the primary motor cortex (M1) or sham-operated control on separate days, participants completed a constant-load test involving running at a speed equivalent to 80% of their own maximum oxygen consumption (VO2max). During this constant-load test, RPE, heart rate (HR), VO2, pulmonary ventilation (VE), respiratory exchange ratio (RER), and ventilatory threshold (VT) were continuously monitored. TTE was recorded at the end of the test. TTEs were significantly longer in the tDCS than in the sham conditions (21.18 ± 7.13 min; 18.44 ± 6.32 min; p = 0.011). For TTE, no significant differences were found in RPE between conditions at isotime. In addition, no significant differences in HR, VO2, VE, RER, and VT were found during TTE between the two stimulation conditions at any time point. These results indicate that the application of tDCS does not induce a change of the exercise performance-related index; however, it can affect the increase of the exercise duration due to the stimuli in the M1 area

Bioimaging of Nucleolin Aptamer-Containing 5-(N-benzylcarboxyamide)-2′-deoxyuridine More Capable of Specific Binding to Targets in Cancer Cells

Chemically modified nucleotides have been developed and applied into SELEX procedure to find a novel type of aptamers to fit with targets of interest. In this study, we directly performed chemical modification of 5-(N-benzylcarboxyamide)-2′-deoxyuridine (called 5-BzdU) in the AS1411 aptamer, which binds to the nucleolin protein expressed in cancer cells. Forty-seven compounds of AS1411-containing Cy3-labeled 5-BzdU (called Cy3-(5-BzdU)-modified-AS1411) were synthesized by randomly substituting thymidines one to twelve in AS1411 with Cy3-labeled 5-BzdU. Both statistically quantified fluorescence measurements and confocal imaging analysis demonstrated at least three potential compounds of interest: number 12, 29 and 41 that significantly increased the targeting affinity to cancer cells but no significant activity from normal healthy cells. These results suggest that the position and number of substituents in AS1411 are critical parameters to improve the aptamer function. In this study, we demonstrated that chemical modification of the existing aptamers enhanced the binding and targeting affinity to targets of interest without additional SELEX procedures

Efficient Algorithms for Approximate String Matching with Swaps

this paper we include the swap operation that interchanges two adjacent characters into the set of allowable edit operations, and we present an O(t min(m, n))-time algorithm for the extended edit distance problem, where t is the edit distance between the given strings, and an O(kn)-time algorithm for the extended k-differ- ences problem. That is, we add swaps into the set of edit operations without increasing the time complexities of previous algorithms that consider only changes, insertions, and deletions for the edit distance and k-differences problems. # 1999 Academic Press 1. INTRODUCTION Given two strings A[1}}}m] and B[1}}}n] over an alphabet 7, the edit distance between A and<F1

Transcranial Direct Current Stimulation of motor cortex enhances running performance.

Transcranial direct current stimulation (tDCS) is a technique used to modulate neuronal excitability through non-invasive brain stimulation that can enhance exercise performance. We hypothesize that tDCS would improve submaximal running time to exhaustion (TTE) and delay the increase in the rating of perceived exertion (RPE) over time. We also hypothesize that tDCS would not lead to difference in cardiorespiratory responses. We employed a randomized, single-blinded, and counterbalanced design in which 10 trained men participated. After receiving either 20 min of 1.98 mA anodal tDCS applied over the primary motor cortex (M1) or sham-operated control on separate days, participants completed a constant-load test involving running at a speed equivalent to 80% of their own maximum oxygen consumption (VO2max). During this constant-load test, RPE, heart rate (HR), VO2, pulmonary ventilation (VE), respiratory exchange ratio (RER), and ventilatory threshold (VT) were continuously monitored. TTE was recorded at the end of the test. TTEs were significantly longer in the tDCS than in the sham conditions (21.18 ± 7.13 min; 18.44 ± 6.32 min; p = 0.011). For TTE, no significant differences were found in RPE between conditions at isotime. In addition, no significant differences in HR, VO2, VE, RER, and VT were found during TTE between the two stimulation conditions at any time point. These results indicate that the application of tDCS does not induce a change of the exercise performance-related index; however, it can affect the increase of the exercise duration due to the stimuli in the M1 area

Pusan National University

To achieve both the flexibility of software and the performance of hardware, we design a hybrid architecture for a TCP offload engine that is based on hardware/software co-design. In this architecture, the transmission and reception paths of TCP/IP are completely separated with the aid of two general embedded processors to process data transmission and reception simultaneously. We implement this architecture based on an FPGA that has two general embedded processor cores. In the experiments based on the gigabit Ethernet, the hybrid TOE has a minimum latency of 13.5 μs. The CPU utilization is less than 3%, which is at least eighteen times lower than that of the general gigabit Ethernet adapters. The maximum unidirectional bandwidth of the hybrid TOE is 110 MB/s − comparable to that of the general gigabit Ethernet adapters − although the embedded processors operate with a clock speed that is seven times lower than that of the host CPU. By using two embedded processors, the bidirectional bandwidth of the hybrid TOE improves to about 201 MB/s, comparable to that of the general gigabit Ethernet adapters, and a 34 % improvement over an experimental TOE implementation in which only one embedded processor is used