A simple and efficient approach for reducing TCP timeouts due to lack of duplicate acknowledgments in data center networks

The problem of TCP incast in data centers attracts a lot of attention in our research community. TCP incast is a catastrophic throughput collapse that occurs when multiple senders transmitting TCP data simultaneously to a single aggregator. Based on several experiments, researchers found that TCP timeouts are the primary cause of incast problem. Particularly, timeouts due to insufficient duplicate acknowledgments is unavoidable when at least one of the last three segments is lost from the tail of a window. As a result, this type of timeouts should be avoided to improve the goodput of TCP in data center networks. A few attempts have been made to reduce timeouts, but still the problem is not completely solved especially in the case of timeouts due to insufficient duplicate acknowledgments. In this paper, we present an efficient TCP fast retransmission approach, called TCP-EFR, which is capable to reduce TCP timeouts due to lack of duplicate acknowledgments which is caused by the loss of packets from the tail of a window in data center networks. TCP-EFR makes changes in the fast retransmission and recovery algorithm of TCP by using the congestion signal mechanism of DCTCP based on instantaneous queue length. In addition, TCP-EFR controls the sending rate for avoiding the overflow of switch buffer in order to reduce the loss of packets. The results of a series of simulations in single as well as multiple bottleneck topologies using qualnet 4.5 demonstrates that TCP-EFR can significantly reduce the timeouts due to inadequate duplicate acknowledgments and noticeably improves the performance compared to DCTCP, ICTCP and TCP in terms of goodput, accuracy and stability under various network conditions.     

Persistence of Mycobacterium avium subsp. paratuberculosis and Other Zoonotic Pathogens during Simulated Composting, Manure Packing, and Liquid Storage of Dairy Manure

Livestock manures contain numerous microorganisms which can infect humans and/or animals, such as Escherichia coli O157:H7, Listeria monocytogenes, Salmonella spp., and Mycobacterium avium subsp. paratuberculosis (Mycobacterium paratuberculosis). The effects of commonly used manure treatments on the persistence of these pathogens have rarely been compared. The objective of this study was to compare the persistence of artificially inoculated M. paratuberculosis, as well as other naturally occurring pathogens, during the treatment of dairy manure under conditions that simulate three commonly used manure management methods: thermophilic composting at 55°C, manure packing at 25°C (or low-temperature composting), and liquid lagoon storage. Straw and sawdust amendments used for composting and packing were also compared. Manure was obtained from a large Ohio free-stall dairy herd and was inoculated with M. paratuberculosis at 10⁶ CFU/g in the final mixes. For compost and pack treatments, this manure was amended with sawdust or straw to provide an optimal moisture content (60%) for composting for 56 days. To simulate liquid storage, water was added to the manure (to simulate liquid flushing and storage) and the slurry was placed in triplicate covered 4-liter Erlenmeyer flasks, incubated under ambient conditions for 175 days. The treatments were sampled on days 0, 3, 7, 14, 28, and 56 for the detection of pathogens. The persistence of M. paratuberculosis was also assessed by a PCR hybridization assay. After 56 days of composting, from 45 to 60% of the carbon in the compost treatments was converted to CO₂, while no significant change in carbon content was observed in the liquid slurry. Escherichia coli, Salmonella, and Listeria were all detected in the manure and all of the treatments on day 0. After 3 days of composting at 55°C, none of these organisms were detectable. In liquid manure and pack treatments, some of these microorganisms were detectable up to 28 days. M. paratuberculosis was detected by standard culture only on day 0 in all the treatments, but was undetectable in any treatment at 3 and 7 days. On days 14, 28, and 56, M. paratuberculosis was detected in the liquid storage treatment but remained undetectable in the compost and pack treatments. However, M. paratuberculosis DNA was detectable through day 56 in all treatments and up to day 175 in liquid storage treatments. Taken together, the results indicate that high-temperature composting is more effective than pack storage or liquid storage of manure in reducing these pathogens in dairy manure. Therefore, thermophilic composting is recommended for treatment of manures destined for pathogen-sensitive environments such as those for vegetable production, residential gardening, or application to rapidly draining fields.     

Preliminary evidence that American bullfrogs (Rana catesbeiana) are suitable hosts for Escherichia coli O157:H7

We orally inoculated Rana catesbeiana tadpoles (n=23) and metamorphs (n=24) to test their suitability as hosts for Escherichia coli O157:H7. Tadpoles were housed in flowthrough aquaria and did not become infected. Metamorphs were housed in stagnant aquaria, and 54% tested positive through 14 days postinoculation, suggesting that they are suitable hosts for E. coli O157:H7.     

Preliminary Evidence that American Bullfrogs (Rana catesbeiana) Are Suitable Hosts for Escherichia coli O157:H7

We orally inoculated Rana catesbeiana tadpoles (n = 23) and metamorphs (n = 24) to test their suitability as hosts for Escherichia coli O157:H7. Tadpoles were housed in flowthrough aquaria and did not become infected. Metamorphs were housed in stagnant aquaria, and 54% tested positive through 14 days postinoculation, suggesting that they are suitable hosts for E. coli O157:H7.     

Synthesis and conformational behavior of the difluoromethylene linked C-glycoside analog of beta-galactopyranosyl-(1<-->1)-alpha-mannopyranoside

C-Glycosides in which the pseudoglycosidic substituent is a methylene group have been advertised as hydrolytically stable mimetics of their parent O-glycosides. While this substitution assures greater stability, the lower polarity and increased conformational flexibility in the intersaccharide linker brought about by this change may compromise biological mimicry. In this regard, C-glycosides, in which the pseudoanomeric methylene is replaced with a difluoromethylene group, are interesting because the CF2 group is more of an isopolar replacement for oxygen than CH2. In addition, the CF2 residue is expected to instill conformational bias into the intersaccharide torsions. Herein is described the synthesis and conformational behavior of the difluoromethylene linked C-glycoside of beta-D-galactopyranosyl-(1<-->1)-alpha-D-mannopyranoside. The synthesis centers on the formation of the galactose residue via an oxocarbenium ion-enol ether cyclization. Conformational analysis, using a combination of molecular mechanics, dynamics, and NMR spectroscopy, suggests that the difluoro-C-glycoside populates the non-exo-Gal/exo-Man conformer to a major extent (ca 50%), with a minor contribution ( approximately 15%) from the exo-Gal/exo-Man conformer that corresponds to the ground sate of the parent O-glycoside.     

Persistence of Mycobacterium avium subsp. paratuberculosis and other zoonotic pathogens during simulated composting, manure packing, and liquid storage of dairy manure

Livestock manures contain numerous microorganisms which can infect humans and/or animals, such as Escherichia coli O157:H7, Listeria monocytogenes, Salmonella spp., and Mycobacterium avium subsp. paratuberculosis (Mycobacterium paratuberculosis). The effects of commonly used manure treatments on the persistence of these pathogens have rarely been compared. The objective of this study was to compare the persistence of artificially inoculated M. paratuberculosis, as well as other naturally occurring pathogens, during the treatment of dairy manure under conditions that simulate three commonly used manure management methods: thermophilic composting at 55 degrees C, manure packing at 25 degrees C (or low-temperature composting), and liquid lagoon storage. Straw and sawdust amendments used for composting and packing were also compared. Manure was obtained from a large Ohio free-stall dairy herd and was inoculated with M. paratuberculosis at 10(6) CFU/g in the final mixes. For compost and pack treatments, this manure was amended with sawdust or straw to provide an optimal moisture content (60%) for composting for 56 days. To simulate liquid storage, water was added to the manure (to simulate liquid flushing and storage) and the slurry was placed in triplicate covered 4-liter Erlenmeyer flasks, incubated under ambient conditions for 175 days. The treatments were sampled on days 0, 3, 7, 14, 28, and 56 for the detection of pathogens. The persistence of M. paratuberculosis was also assessed by a PCR hybridization assay. After 56 days of composting, from 45 to 60% of the carbon in the compost treatments was converted to CO2, while no significant change in carbon content was observed in the liquid slurry. Escherichia coli, Salmonella, and Listeria were all detected in the manure and all of the treatments on day 0. After 3 days of composting at 55 degrees C, none of these organisms were detectable. In liquid manure and pack treatments, some of these microorganisms were detectable up to 28 days. M. paratuberculosis was detected by standard culture only on day 0 in all the treatments, but was undetectable in any treatment at 3 and 7 days. On days 14, 28, and 56, M. paratuberculosis was detected in the liquid storage treatment but remained undetectable in the compost and pack treatments. However, M. paratuberculosis DNA was detectable through day 56 in all treatments and up to day 175 in liquid storage treatments. Taken together, the results indicate that high-temperature composting is more effective than pack storage or liquid storage of manure in reducing these pathogens in dairy manure. Therefore, thermophilic composting is recommended for treatment of manures destined for pathogen-sensitive environments such as those for vegetable production, residential gardening, or application to rapidly draining fields.     

Antibacterial properties of nine pure metals: a laboratory study using Staphylococcus aureus and Escherichia coli

Bacterial attachment and growth on material surfaces are considered to be the primary steps leading to the formation of biofilm. Biofilms in hospital and food processing settings can result in bacterial infection and food contamination, respectively. Prevention of bacterial attachment, therefore, is considered to be the best strategy for abating these menaces and therefore the development of antibacterial metals becomes important. In this study, nine pure metals, viz. titanium, cobalt, nickel, copper, zinc, zirconium, molybdenum, tin, and lead have been tested for their antibacterial properties against two bacterial strains, Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli. This was accomplished using two assay methods, the film contact method and the shaking flask method. The results show that the antibacterial properties varied significantly with different metals and the effectiveness of metals to resist bacterial attachment varied with the bacterial strain. Among the metals tested, titanium and tin did not exhibit antibacterial properties. TEM images showed that metal accumulation resulted in the disruption of the bacterial cell wall and other cellular components.     

Dynamics of grazing protozoa follow that of microalgae in natural biofilm communities

This study investigates the dynamics of protozoan community in biofilms formed on inert artificial surfaces suspended in various freshwater environments. The results also test the hypothesis that the dynamics of protozoan and microalgal communities in biofilms are interdependent because the latter form one of the major food items of benthic protozoa. Cleaned glass slides were suspended in surface waters at four sampling locations to collect biofilm communities. The glass slides after retrieval were observed under a microscope for diatom and protozoan density and their generic composition. Members of protozoa belonging to phylum Sarcomastigophora dominated the protozoan community followed by phylum Ciliophora in all sampling locations. The variation of protozoan feeding groups showed an initial abundance of autotrophs/holophytes which gave way to heterotrophs, predators, and bacterivores towards the end of the study. The density and generic composition of protozoa varied significantly with the age of biofilm and sampling location. The density variation of protozoa followed that of diatoms in all four sampling locations and this has resulted in a significant positive correlation between diatom and protozoan densities. This suggests the dependency and/or food web connectedness of these two communities in natural biofilms.     

Bacterial attachment to stainless steel welds: Significance of substratum microstructure

AISI Type 304 L stainless steel (SS) is a widely used material in industry due to its strength and resistance to corrosion. However, corrosion on SS is reported largely at welds or adjacent areas. Bacteria were observed to colonize preferentially near welds as a result of surface roughness. In the present study, the influence of another important metal surface condition on bacterial adhesion has been evaluated, i.e. substratum microstructure. Type 304 L SS weld samples were prepared and machined to separate weld metal, the heat affected zone (HAZ) and base metal regions. The coupons were molded in resin so that only the surfaces polished to a 3 p.m finish were exposed to the experimental medium with Pseudomonas sp. isolated from a corrosive environment in Japan. The coupons were exposed for varying durations. The area of bacterial attachment showed significant differences with time of exposure and; the type of coupons. Generally, the weld metal samples showed more attachment whilst the base metal showed the least. The area of attachment was inversely proportional to the average grain size of the three samples. As the bacteria started colonizing, attachment mainly occurred on the grain boundaries of the base metal (after 8h, 84.62% and 15.38% of the total number of bacteria attached in the field of view (FOV) at the grain boundary and matrix, respectively) and on the austenite‐ferrite interface in the weld metal (after 8h, 88.33% and 11.77% of the total number of bacteria attached in the FOV at the boundary and matrix, respectively). The weld area had more grains and hence more grain boundary/ unit area than the base metal, resulting in more bacterial attachment. SEM observations showed this increased attachment of Pseudomonas sp. resulted in the initiation of microbiologically influenced corrosion (MIC) on the weld coupons by 16 d. Therefore, the results provide data to support the fact that substratum microstructure influences bacterial attachment, which in turn leads to corrosion.     

Influence of surface characteristics and microstructure on adhesion of bacterial cells onto a type 304 stainless steel

A study was carried out to understand the influence of the surface characteristics/microstructure of a type 304 stainless steel on bacterial adhesion by exposing solution-annealed, sensitized and air-oxidized stainless steel specimens in a culture of Pseudomonas sp. in dilute nutrient broth. Epifluorescence microscopy of the exposed surfaces revealed that the pattern of adhesion as well as number density of bacterial cells was different depending on the metallurgical condition of the substratum. Among the specimens with different microstructures, the sensitized specimens had the highest bacterial density, followed by the solution annealed and the oxidized specimens. The same trend was shown by the total viable counts on the various surfaces, estimated by a plate count technique. The study assumes significance in the context of the widely reported observation of preferential attack of the welded region during microbiologically influenced corrosion of fabricated components.