DeepCLEM: automated registration for correlative light and electron microscopy using deep learning [version 3; peer review: 1 approved, 2 approved with reservations]

In correlative light and electron microscopy (CLEM), the fluorescent images must be registered to the EM images with high precision. Due to the different contrast of EM and fluorescence images, automated correlation-based alignment is not directly possible, and registration is often done by hand using a fluorescent stain, or semi-automatically with fiducial markers. We introduce “DeepCLEM”, a fully automated CLEM registration workflow. A convolutional neural network predicts the fluorescent signal from the EM images, which is then automatically registered to the experimentally measured chromatin signal from the sample using correlation-based alignment. The complete workflow is available as a Fiji plugin and could in principle be adapted for other imaging modalities as well as for 3D stacks

Simultaneously measuring two ultrashort laser pulses on a single-shot using double-blind frequency-resolved optical gating

We demonstrate a simple self-referenced single-shot method for simultaneously measuring two different arbitrary pulses, which can potentially be complex and also have very different wavelengths. The method is a variation of cross-correlation frequency-resolved optical gating (XFROG) that we call double-blind (DB) FROG. It involves measuring two spectrograms, both of which are obtained simultaneously in a single apparatus. DB FROG retrieves both pulses robustly by using the standard XFROG algorithm, implemented alternately on each of the traces, taking one pulse to be ?known? and solving for the other. We show both numerically and experimentally that DB FROG using a polarization-gating beam geometry works reliably and appears to have no nontrivial ambiguities

Coronary microvascular dysfunction in Takotsubo syndrome: an analysis using angiography-derived index of microcirculatory resistance

BACKGROUND Coronary microvascular dysfunction (CMD) has been proposed as a crucial factor in the pathophysiology of Takotsubo syndrome (TTS). The angiography-derived index of microcirculatory resistance (caIMR) offers an alternative to conventional hyperemic wire-based IMR to assess CMD. We aimed to evaluate CMD's prevalence, transience, and impact on in-hospital outcomes in TTS. METHODS All three coronary arteries of 96 patients with TTS were assessed for their coronary angiography derived Index of microcirculatory Resistance (caIMR) and compared to non-obstructed vessels of matched patients with ST-elevation myocardial infarction. Further, the association between caIMR and the TTS-specific combined in-hospital endpoint of death, cardiac arrest, ventricular arrhythmogenic events and cardiogenic shock was investigated. RESULTS Elevated IMR was present in all TTS patients, with significantly elevated caIMR values in all coronary arteries compared to controls. CaIMR did not differ between apical and midventricular TTS types. CaIMR normalized in TTS patients with follow-up angiographies performed at a median of 28 months (median caIMR at event vs follow-up: LAD 34.8 [29.9-41.1] vs 20.3 [16.0-25.3], p < 0.001; LCX: 38.7 [32.9-50.1] vs 23.7 [19.4-30.5], p < 0.001; RCA: 31.7 [25.0-39.1] vs 19.6 [17.1-24.0], p < 0.001). The extent of caIMR elevation significantly correlated with the combined in-hospital endpoint (p = 0.036). CONCLUSION TTS patients had evidence of elevated caIMR in at least one coronary artery with a trend towards higher LAD caIMR in apical type TTS and normalization after recovery. Furthermore, extent of caIMR elevation was associated with increased risk of in-hospital MACE of TTS patients

American Journal of Potato Research 85 5 367 374 Springer New York, NY

Potatoes are commonly grown in rotation with cereal and forage crops. Storage trials were conducted in Prince Edward Island, Canada from 2002 to 2004 to determine whether isolates of Fusarium spp. obtained from cereals or forages were able to cause disease (dry rot) in stored potato tubers. In each year of study, tubers of the cultivars &#39;Red Norland&#39;, &#39;Yukon Gold&#39; and &#39;Russet Burbank&#39; were wounded and then inoculated with an agar plug containing active mycelium of one of the 30 isolates tested. Following incubation for 5 weeks in a storage facility, tubers were cut longitudinally at the point of inoculation and the depth of necrosis measured. Isolates of F. sambucinum, F. coeruleum and F. avenaceum originating from potato tubers were strongly pathogenic to inoculated potato tubers. Isolates of F. oxysporum f.sp. medicaginis sourced from alfalfa were nonpathogenic to potato tubers, however, isolates of F. avenaceum from alfalfa and clover and F. oxysporum from clover were pathogenic to potatoes. Isolates of F. poae and F. sporotrichioides sourced from cereals were nonpathogenic and weakly pathogenic, respectively, to inoculated tubers. All isolates of F. graminearum (obtained from cereal crops) that were tested were pathogenic to potato tubers. Thus, crops grown in rotation with potatoes may harbour Fusarium spp. that can act as pathogens in subsequent potato crops.CR: *ATL PROV AGR SERV, 1993, ATL PROV AGR SERV CO ABRAMSON D, 1993, CAN J PLANT PATHOL, V15, P147 ALI S, 2005, PLANT DIS, V89, P105, DOI 10.1094/PD-89-0105B BOOTH C, 1971, GENUS FUSARIUM BOTTALICO A, 1998, J PLANT PATHOL, V80, P85 BOURDAGES JV, 2006, CAN J PLANT PATHOL, V28, P419 BURGESS LW, 1981, FUSARIUM DIS BIOL TA, P225 CARTER MR, 2001, SOIL TILL RES, V63, P1 CHELKOWSKI J, 1989, J PHYTOPATHOL, V124, P155 DAAMIREMADI M, 2006, J AGRONOMY, V5, P350 DESJARDINS AE, 1989, J AGR FOOD CHEM, V37, P388 DESJARDINS AE, 1993, PHYTOPATHOLOGY, V83, P164 DESJARDINS AE, 2006, FUSARIUM CHEM GENETI, P268 ELBANNA AA, 1984, APPL ENVIRON MICROB, V47, P1169 GEISER DM, 2004, EUR J PLANT PATHOL, V110, P473 GERLACH W, 1982, MITT BIOL BUNDESANST, V209, P1 HANSON LE, 1996, PHYTOPATHOLOGY, V86, P378 HIDE GA, 1992, PLANT PATHOL, V41, P745 JOFFE AZ, 1986, FUSARIUM SPECIES THE KAWCHUK LM, 1994, AM POTATO J, V71, P185 LEATH KT, 1978, PHYTOPATHOLOGY, V68, P826 MANICI LM, 1994, POTATO RES, V37, P129 MILLERGARVIN JE, 1994, CROP SCI, V34, P1461 NELSON PE, 1983, FUSARIUM SPECIES ILL OCAMB CM, 2007, AM J POTATO RES, V84, P169 PANKHURST CE, 1998, PLANT PATHOL, V47, P749 PARRY DW, 1995, PLANT PATHOL, V44, P207 PASCOE IG, 1990, MYCOTAXON, V37, P121 PEGG GF, 1983, ANN APPL BIOL, V103, P45 PETERS RD, 2001, PLANT DIS, V85, P1030 PLATT HW, 1997, PHYTOPROTECTION, V78, P1 POLLEY RW, 1995, ANN APPL BIOL, V126, P45 ROTKIEWICZ T, 1993, ACTA MICROBIOL POL, V42, P51 SATYAPRASAD K, 1997, POTATO RES, V40, P357 SECOR GA, 2001, COMPENDIUM POTATO DI, P23 SEPPANEN E, 1981, ANN AGR FENN, V20, P156 SIVASITHAMPARAM K, 1993, ADV PLANT PATHOL, V10, P245 SNIJDERS CHA, 1990, NETH J PLANT PATHOL, V96, P187 THANASSOULOPOUL.CC, 1985, POTATO RES, V28, P515 THERON DJ, 1989, PHYTOPHYLACTICA, V21, P175 TIVOLI B, 1981, AGRONOMIE, V1, P787 UPSTONE ME, 1970, PLANT PATHOL, V19, P150 VENTER SL, 1992, PHYTOPATHOLOGY, V82, P858 VENTER SL, 1998, POTATO RES, V41, P289 VENUTO BC, 1995, PLANT DIS, V79, P406 WEIMER JL, 1928, J AGRIC RES, V37, P41

GGDEF domain as spatial on-switch for a phosphodiesterase by interaction with landmark protein HubP

In bacteria, the monopolar localization of enzymes and protein complexes can result in a bimodal distribution of enzyme activity between the dividing cells and heterogeneity of cellular behaviors. In Shewanella putrefaciens, the multidomain hybrid diguanylate cyclase/phosphodiesterase PdeB, which degrades the secondary messenger c-di-GMP, is located at the flagellated cell pole. Here, we show that direct interaction between the inactive diguanylate cyclase (GGDEF) domain of PdeB and the FimV domain of the polar landmark protein HubP is crucial for full function of PdeB as a phosphodiesterase. Thus, the GGDEF domain serves as a spatially controlled on-switch that effectively restricts PdeBs activity to the flagellated cell pole. PdeB regulates abundance and activity of at least two crucial surface-interaction factors, the BpfA surface-adhesion protein and the MSHA type IV pilus. The heterogeneity in c-di-GMP concentrations, generated by differences in abundance and timing of polar appearance of PdeB, orchestrates the population behavior with respect to cell-surface interaction and environmental spreading