Linear Approximate Pattern Matching Algorithm

Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can be as an exact or as an approximate (inexact) matching. Exact matching is to search for the pattern without allowing for mismatches (or insertions and deletions) of one or more characters in the pattern), while approximate matching is the opposite. For exact matching, several data structures that can be built in linear time and space are used and in practice nowadays. For approximate matching, the solutions proposed to solve this matching are non-linear and currently impractical. In this paper, we designed and implemented a structure that can be built in linear time and space and solve the approximate matching problem in (O(m + {log_Σ^k}n/{k!} + occ) search costs, where m is the length of the pattern, n is the length of the reference, and k is the number of tolerated mismatches (and insertion and deletions).

Stream Macroinvertebrates and Carbon Cycling in Tangled Food Webs

The annual global loss of organic carbon from terrestrial ecosystems into rivers is similar to the organic carbon stored in soils each year. Dissolved organic matter (DOM) flows through the food web to macroinvertebrates, but little is known about the effect of DOM increase on stream food webs and how much macroinvertebrates may contribute to the regulation of carbon fluxes in rivers. Using a before and after control impact (BACI) experimental design, we increased by 12% (+ 0.52 mg C L−1) the concentration of DOM in a stream for three weeks by adding sucrose, with a distinctive δ13C signature, to simulate a pulse of natural DOM supply from soils. We partitioned the diet of macroinvertebrates from carbon sources according to the green pathway (autotrophs) and detrital pathways (bacteria and terrestrial organic matter). Our flow food web approach based on C fluxes, with bacteria as a key node, showed the dominant contribution of the detrital pathways for macroinvertebrates in the reference stream. DOM addition induced changes in the diets of individual taxa, but did not have any strong effects on the relative overall contribution of the detrital pathways versus the green pathway. Autotrophic uptake of CO2 respired by bacteria was much larger than bacterial C flux to invertebrates (that is, the classic microbial loop) and allowed a significant fraction of natural allochthonous organic carbon to make its way to macroinvertebrates via autotrophs fixing CO2 respired by bacteria. Overall macroinvertebrates did not regulate directly to any great extent the flux of stream DOM towards downstream ecosystems.

Mild impacts do not subsidize aquatic insect communities in an Atlantic Forest stream

Odum’s perturbation theory hypothesizes that toxic pollutants cause damage to ecosystems early in the course of contamination. In contrast, organic pollutants enrich the ecosystem until it exceeds their carrying capacity, an effect known as the subsidy-stress gradient. Understanding this dynamic can improve the efficiency of river restoration programs and bring significant benefits to society by providing ecosystem services that were lost. However, the initial effects of the most common human-induced disturbances in Atlantic Forest streams are not well known, indicating the necessity to evaluate the subsidy-stress gradient in these vulnerable and diverse ecosystems.AimWe evaluated the composition and abundance of the community of aquatic insects from leaf litter of headwater streams in three conditions: a fully forested area (reference stream), a low-intensity urban settlement (urban stream), and a region with small farms dedicated to the cultivation of fruits and vegetables (agricultural stream).MethodsWe used alpha and beta diversity metrics and a specific biotic index to test the subsidy-stress gradient prediction.ResultsThe agricultural stream showed the most degraded ecological condition. The urban stream and the reference stream showed similarity in alpha diversity metrics. According to the biotic index, the streams showed a gradient of environmental quality, with the reference stream showing the best quality and the agricultural stream the worst quality.ConclusionsThe agricultural stream showed a decrease in the environmental quality consistent with the effect predicted by the subsidy-stress gradient due to toxic pollutants’ contribution. However, the low-intensity enrichment of organic matter from the urban settlement causes a disorder in the ecosystem that reduces its environmental quality, contrary to the predicted by the subsidy-stress gradient.

Invertebrate colonization of a newly constructed diversion channel in the Canadian Shield

Construction of artificial channels to divert water is common in a variety of natural resource development projects; however, the length of time required for these stream channels to become productive fish habitat remains an understudied aspect. The creation of a bedrock channel (∼150 m) to drain a third-order boreal lake and its watershed (∼300 ha) offered the unique opportunity to study colonization by comparing habitat and invertebrate metrics with a reference stream. The amount of riparian vegetation on the banks of the diversion channel steadily increased, but remained much lower than the reference stream after 5 years. The channel was quickly colonized by benthic macroinvertebrates, which were of comparable abundance to the reference stream starting in the first year, and thereafter were greater in abundance. Taxa diversity and richness responded more slowly, becoming similar to the reference stream after 3 years. Results from this study suggest that newly created, lake-outlet channels can become productive small stream habitats in a relatively short time period (<5 years) in southern boreal regions.

Survey Inter-Reference Recency Based Page Replacement Policies to Cope with Weak Locality Workloads

Least recently used (LRU) makes bold assumption on recency factor only which made LRU miss behave with weak locality workloads. If the “frequency”, of each page reference is taken into consideration, it will perform better in the case where workload has weak locality. Frequency count leads to serious problem after a long duration of reference stream because it cannot cope with change in locality. Reuse distance or inter reference recency (IRR) of a block is equal to number of distinct pages accessed between recent consecutive or correlated access of that particular block. Many recent variations of LRU use IRR rather than recency such that LRU can be made friendly with weak locality workloads. This papers surveys LRU variants that use IRR to make page replacement decision.

Energy-Efficient Hybrid Spintronic–Straintronic Nonvolatile Reconfigurable Equality Bit Comparator

We propose and analyze a “spintronic/straintronic” reconfigurable equality bit comparator implemented with a nanowire spin valve whose two contacts are two-phase multiferroic nanomagnets and possess bistable magnetization. A reference bit is “written” into a stable magnetization state of one contact and an input bit in that of the other with electrically generated strain. The spin-valve’s resistance is lowered (raised) if the bits match (do not match). Multiple comparators can be interfaced in parallel with a magneto-tunneling junction to determine if an [Formula: see text]-bit input stream matches an [Formula: see text]-bit reference stream bit by bit. The system is robust against thermal noise at room temperature and a 16-bit comparator can operate at [Formula: see text][Formula: see text]MHz while dissipating [Formula: see text][Formula: see text]28[Formula: see text]fJ per cycle. This implementation is more energy-efficient than CMOS-based implementations and the reference bits can be stored in the comparator itself without the need for refresh cycles or the need to fetch them from a remote memory for comparison. That improves reliability, speed and security.

Potential loss and rehabilitation of stream longitudinal connectivity: fish populations in urban streams with culverts

Riverine connectivity is important to the persistence of fish communities, but culverts may impede fish movements to varying degrees and in both directions. Baffles can be installed in culverts to mitigate upstream connectivity loss; however, evaluation of their effectiveness is limited. To examine the potential impacts of culverts and their potential rehabilitation with baffles, we sampled fish populations in 26 streams that contained either (i) nonbaffled culverts or (ii) baffled culverts or (iii) lacked culverts (reference streams) in Metro Vancouver, British Columbia, Canada. Using mixed effects models, we compared fish responses across these three stream types to infer effects at the whole-stream scale (i.e., over both upstream and downstream positions equally), the within-stream scale (i.e., upstream versus downstream of culverts), and the interaction of scales. Densities (n·m−2) of coastrange sculpin (Cottus aleuticus) and prickly sculpin (Cottus asper) were significantly lower in nonbaffled and baffled stream types than in reference stream types, while densities of cutthroat trout (Oncorhynchus clarkii) and rainbow trout (Oncorhynchus mykiss) were significantly lower in reference stream types, indicating whole-stream differences. Using multivariate statistics, we similarly found that fish community compositions were significantly different across stream types. For our various fish responses, we found no interaction between stream type and upstream or downstream position. Further, we found reaches directly downstream of baffled culverts had greater fish biomass and that overall species richness increased with age of baffles. These data suggest that culverts may drive changes in fish populations at whole-stream scales, and restoration of these effects with baffles may take decades.

Effects of remediation on the bacterial community of an acid mine drainage impacted stream

Acid mine drainage (AMD) represents a global threat to water resources, and as such, remediation of AMD-impacted streams is a common practice. During this study, we examined bacterial community structure and environmental conditions in a low-order AMD-impacted stream before, during, and after remediation. Bacterial community structure was examined via polymerase chain reaction amplification of 16S rRNA genes followed by denaturing gradient gel electrophoresis. Also, bacterial abundance and physicochemical data (including metal concentrations) were collected and relationships to bacterial community structure were determined using BIO-ENV analysis. Remediation of the study stream altered environmental conditions, including pH and concentrations of some metals, and consequently, the bacterial community changed. However, remediation did not necessarily restore the stream to conditions found in the unimpacted reference stream; for example, bacterial abundances and concentrations of some elements, such as sulfur, magnesium, and manganese, were different in the remediated stream than in the reference stream. BIO-ENV analysis revealed that changes in pH and iron concentration, associated with remediation, primarily explained temporal alterations in bacterial community structure. Although the sites sampled in the remediated stream were in relatively close proximity to each other, spatial variation in community composition suggests that differences in local environmental conditions may have large impacts on the microbial assemblage.