Peak height pattern in dichloro-rhodamine and energy transfer dye terminator sequencing

Establishing the pattern in peak heights within local sequence contexts improves the accuracy of base calling and the identification of DNA sequence variations in dye-terminator cycle sequencing. We have systematically examined pairs of sequence-tagged sites (STSs) that vary at only a single nucleotide to determine how base changes influence the peak heights of neighboring bases in sequencing traces generated by two recently commercialized dye-terminator chemistries, the dichloro-rhodamine (dRhodamine) and the energy transfer (BigDye) terminators. For sequencing traces generated with the dRhodamine terminators, the peak height of a particular base in 28 of 64 possible 3-base windows (44%) can be predicted by knowing just one or two bases 5\u27 to the base in question. For those generated with the BigDye terminators, the peak height of a particular base in 23 of 64 possible 3-base windows (36%) can be predicted by knowing the local sequence context. When the peak heights are binned slightly differently, 75% (48 out of 64 cases) of the base peaks generated by both dRhodamine and BigDye terminators fall in the middle half, confirming that the peak patterns of these two new dye terminator chemistries are much more even than those found in the original rhodamine dye terminator sequences

Gastric Fistula in the Chest After Sleeve Gastrectomy: a Systematic Review of Diagnostic and Treatment Options

This study aimed to establish the optimal diagnostic and treatment algorithm for the management of gastric fistula in the chest (GFIC) after sleeve gastrectomy (SG) through a systematic review of published cases. A multi-database search was performed, which produced 1182 results, of which 26 studies were included in this systematic review. The initial presentation included subphrenic collections, leaks, or (recurrent) pneumonia with associated symptoms such as persistent cough, fever, and/or dyspnea. Computed tomography (CT) scan in combination with either upper gastrointestinal (UGI) series or an esophagogastroduodenoscopy (EGD) was used to adequately diagnose the fistulas. Initial treatment was either with clips and/or clips and stents that were placed endoscopically. When unsuccessful in the majority of the cases, the surgical treatment consisted of total gastrectomy and Roux-en-Y esophagojejunostomy in a laparoscopic or open fashion

AmpliTaq DNA polymerase, FS dye-terminator sequencing: Analysis of peak height patterns

Taq DNA polymerases in which the phenylalanine is substituted by a tyrosine at position 667 (Taq F667Y) are members of a new class of DNA polymerases that incorporate chain-terminating dideoxyribonucleoside triphosphates (ddNTPs) much more efficiently than the wild-type Taq DNA polymerase. Improved incorporation of ddNTPs into DNA during cycle sequencing using AmpliTaq DNA polymerase, FS (Taq-FS, a member of the Taq F667Y family), and dye-labeled primers results in nearly uniform peak heights in the sequencing trace. This is not the case when dye-labeled ddNTPs are used in Taq-FS cycle sequencing reactions. While the rate of dye-terminator incorporation is more efficient with Taq-FS, the peak pattern is still highly variable and different from that produced by the wild-type enzyme. We have systematically examined pairs of sequence-tagged sites that vary at only a single nucleotide to determine how base changes influence the peak heights of neighboring bases in sequencing traces generated by the Taq-FS dye-terminator chemistry. In 31 of 64 possible 3-base windows (48%), we find that the peak height of a particular base can be predicted by knowing just one or two bases 5\u27 to the base in question. We have also compared and contrasted the peak patterns produced by the Taq-FS enzyme with those previously identified for the wild-type enzyme. Establishing the patterns in peak heights within local sequence contexts can improve the accuracy of base-calling and the identification of polymorphisms/mutations when using the Taq-FS dye-terminator cycle-sequencing chemistry

Stabilization and Anticancer Enhancing Activity of the Peptide Nisin by Cyclodextrin-Based Nanosponges against Colon and Breast Cancer Cells

The great variability of cancer types demands novel drugs with broad spectrum, this is the case of Nisin, a polycyclic antibacterial peptide that recently has been considered for prevention of cancer cells growth. As an accepted food additive, this drug would be very useful for intestinal cancers, but the peptide nature would make easier its degradation by digestion procedures. For that reason, the aim of present study to investigate the protective effect of two different β-cyclodextrin-based nanosponges (carbonyl diimidazole and pyromellitic dianhydride) and their anti-cancer enhancement effect of Nisin-Z encapsulated with against colon cancer cells (HT-29). To extend its possible use, a comparison with breast (MCF-7) cancer cell was carried out. The physicochemical properties, loading efficiency, and release kinetics of Nisin complex with nanosponges were studied. Then, tricin-SDS-PAGE electrophoresis was used to understand the effect of NSs on stability of Nisin-Z in the presence of gastric peptidase pepsin. In addition, the cytotoxicity and cell membrane damage of Nisin Z were evaluated by using the MTT and LDH assay, which was complemented via Annexin-V/ Propidium Iodide (PI) by using flowcytometry. CD-NS are able to complex Nisin-Z with an encapsulation efficiency around 90%. A protective effect of Nisin-Z complexed with CD-NSs was observed in presence of pepsin. An increase in the percentage of apoptotic cells was observed when the cancer cells were exposed to Nisin Z complexed with nanosponges. Interestingly, Nisin Z free and loaded on PMDA/CDI-NSs is more selectively toxic towards HT-29 cells than MCF-7 cancer cells. These results indicated that nanosponges might be good candidates to protect peptides and deliver drugs against intestinal cancers

Synthesis and patterning of tunable multiscale materials with engineered cells

Many natural biological systems - such as biofilms, shells and skeletal tissues - are able to assemble multifunctional and environmentally responsive multiscale assemblies of living and non-living components. Here, by using inducible genetic circuits and cellular communication circuits to regulate Escherichia coli curli amyloid production, we show that E. coli cells can organize self-assembling amyloid fibrils across multiple length scales, producing amyloid-based materials that are either externally controllable or undergo autonomous patterning. We also interfaced curli fibrils with inorganic materials, such as gold nanoparticles (AuNPs) and quantum dots (QDs), and used these capabilities to create an environmentally responsive biofilm-based electrical switch, produce gold nanowires and nanorods, co-localize AuNPs with CdTe/CdS QDs to modulate QD fluorescence lifetimes, and nucleate the formation of fluorescent ZnS QDs. This work lays a foundation for synthesizing, patterning, and controlling functional composite materials with engineered cells

Splenic Abscess Following Sleeve Gastrectomy: A Systematic Review of Clinical Presentation and Management Methods

BACKGROUND: Splenic abscess is a rare complication following sleeve gastrectomy. METHODS: We performed a systematic review to clarify its clinical significance, presentation, and management. PubMed, Embase, MEDLINE, Google Scholar, and the Cochrane Library were searched up to the 19th of July 2020. A total of 18 patients were included, of which 11 were female and 7 were male. The mean age was 34.1 ± 12.3 years, and the mean body mass index was 45.8 ± 7.6 kg/m2. Type 2 diabetes mellitus was reported in 11.1% of patients and hypertension in 22.2%. Fever was the most common presenting symptom seen in 17 (94.4%) patients, followed by abdominal pain in 10 (55.6%). The mean duration from surgery to presentation was 98.6 ± 132.7 days (range 10–547 days). Computed tomography was used for investigations in 17/18 (94.4%) patients. Seven patients had reported leak, three reported bleeding, and 2 reported pleural effusion. Thirteen patients had unilocular abscess. All patients were treated with antibiotics. Four patients needed total parenteral nutrition, and three were given proton pump inhibitor. In total, 11 patients needed percutaneous drainage as a part of treatment and 11 patients needed total splenectomy and 1 needed partial splenectomy. CONCLUSION: Splenic abscess following sleeve gastrectomy is a rare identity. The etiology of formation of splenic abscess needs further studies. A computed tomography of the abdomen with contrast is the preferred diagnostic tool. There is no gold standard treatment for splenic abscess

Existing and new arrangements of pumped-hydro storage plants

The energy sector is undergoing substantial transition with the integration of variable renewable energy sources, such as wind and solar energy. These sources come with hourly, daily, seasonal and yearly variations; raising the need for short and long-term energy storage technologies to guarantee the smooth and secure supply of electricity. This paper critically reviews the existing types of pumped-hydro storage plants, highlighting the advantages and disadvantages of each configuration. We propose some innovative arrangements for pumped-hydro storage, which increases the possibility to find suitable locations for building large-scale reservoirs for long-term energy and water storage. Some of the proposed arrangements are compared in a case study for the upper Zambezi water basin, which has considerable water storage limitations due to its flat topography and arid climate. Results demonstrate that the proposed combined short and long-term cycles pumped-storage arrangement could be a viable solution for energy storage and reduce the cost for water storage to near zero

Derailment risk and dynamics of railway vehicles in curved tracks: Analysis of the effect of failed fasteners

[EN] The effect of the fastener s failure in a railway track on the dynamic forces produced in the wheel-rail contact is studied using the simulation software VAMPIRE to assess the derailment risk of two different vehicles in two curves with distinct characteristics. First, a 3D-FEM model of a real track is constructed, paying special attention to fasteners, and calibrated with displacement data obtained experimentally during a train passage. This numerical model is subsequently used to determine the track vertical and lateral stiffness. This study evidences that although the track can practically lose its lateral stiffness as a consequence of the failure of 7 consecutive fasteners, the vehicle stability would not be necessarily compromised in the flawed zone. Moreover, the results reveal that the uncompensated acceleration and the distance along which the fasteners are failed play an important role in the dynamic behavior of the vehicle-track system, influencing strongly the risk of derailmentMorales-Ivorra, S.; Real Herráiz, JI.; Hernández Gracia, C.; Montalbán-Domingo, L. (2016). Derailment risk and dynamics of railway vehicles in curved tracks: Analysis of the effect of failed fasteners. Journal of Modern Transportation. 24(1):38-47. doi:10.1007/s40534-015-0093-zS3847241Iwnicki S (2006) Handbook of railway vehicle dynamics.CRC Press, Boca RatónJin XS, Wen ZF, Wang KY, Zhou ZR, Liu QY, Li CH (2006) Three-dimensional train-track model for study of rail corrugation. J Sound Vib 293:830–855Jin X, Wen Z, Xiao X (2007) A numerical method for prediction of curved rail wear. Multibody Sys Dyn 18:531–557Li W, Xiao G, Wen Z, Xiao X, Jin X (2011) Plastic deformation of curved rail at rail weld caused by train-track dynamic interaction. Wear 271:311–318Jin X, Wen Z (2008) Effect of discrete track support by sleepers on rail corrugation at a curved track. J Sound Vib 315:279–300Di Gialleonardo E, Bruni S, True H (2014) Analysis of the nonlinear dynamics of a 2-axle freight wagon in curves. Veh Syst Dyn 52(1):125–141Wang K, Liu P (2012) Lateral stability analysis of heavy-haul vehicle on curved track based on wheel/rail coupled dynamics. J Transp Technol 2:150–157Kurzeck B, Hecht M (2010) Dynamic simulation of friction-induced vibrations in a light railway bogie while curving compared with measurement results. Veh Syst Dyn 48:121–138Chen P, Gao L, Hao J (2007) Simulation study on parameters influencing wheel/rail wear in railway curve. China Railway Science 5Sun Y, Cole C, Boyd P (2011) A numerical method using VAMPIRE modelling for prediction of turnout curve wheel-rail wear. Wear 271(1–2):482–491Brabie D (2007) On derailment-worthiness in railway vehicle design. Analysis of vehicle features influencing derailment processes and consequences, PhD Thesis, Royal Institute of Technology, StockholmMatsumoto A, Sato Y, Ohno H, Shimizu M, Kurihara J, Saitou T, Michitsuji Y, Matsui R, Tanimoto M, Mizuno M (2014) Actual states of wheel/rail contact forces and friction on sharp curves—continuous monitoring from in-service trains and numerical simulations. Wear 314:189–197Wang L, Huang A, Liu G (2013) Analysis on curve negotiation ability of the rail vehicle based on SIMPACK. Adv Mater Res 721:551–555Eom BG, Lee H (2010) Assessment of running safety of railway vehicles using multibody dynamics. Int J Precis Eng Manuf 11(2):315–320Zhou L, Shen Z (2013) Dynamic analysis of a high-speed train operating on a curved track with failed fasteners. J Zhejiang Univ Sci A 14(6):447–458Xiao X, Jin X, Wen Z (2007) Effect of disabled fastening systems and ballast on vehicle derailment. 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Steps towards understanding variation for water and nitrogen uptake and use in Brassica napus

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Mountain Gravity Energy Storage: A new solution for closing the gap between existing short- and long-term storage technologies

The world is undergoing an energy transition with the inclusion of intermittent sources of energy in the grid. These variable renewable energy sources require energy storage solutions to be integrated smoothly over different time steps. In the near future, batteries can provide short-term storage solutions and pumped-hydro storage can provide long-term energy storage with large generation capacities. However, none of these technologies can provide long-term energy storage in grids with small demand. This paper proposes a new storage concept called Mountain Gravity Energy Storage (MGES) that could fill this gap in storage services. MGES systems move sand or gravel from a lower storage site to an upper elevation. The higher the height difference the greater the amount of stored energy in a given installed capacity, as this technology is constrained to the topography of the location. MGES cost varies from 50 to 100 $/MWh of stored energy and 1–2 M$/MW of installed capacity. MGES could be a feasible option for micro-grids, for example, small islands and isolated areas, and power systems where electricity costs are high, demand for energy storage is smaller than 20 MW with monthly or seasonal storage requirements