scholarly journals PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1603 ◽  
Author(s):  
Ivan Gregor ◽  
Johannes Dröge ◽  
Melanie Schirmer ◽  
Christopher Quince ◽  
Alice C. McHardy
Keyword(s):  
Error Rates ◽  
The Other ◽  
Marker Genes ◽  
Training Method ◽  
Human Expert ◽  
Training Sequences ◽  
Important Challenge ◽  
Taxonomic Characterization ◽  
Taxonomic Binning

Background.Metagenomics is an approach for characterizing environmental microbial communitiesin situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. This is often achieved by a combination of sequence assembly and binning, where sequences are grouped into ‘bins’ representing taxa of the underlying microbial community. Assignment to low-ranking taxonomic bins is an important challenge for binning methods as is scalability to Gb-sized datasets generated with deep sequencing techniques. One of the best available methods for species bins recovery from deep-branching phyla is the expert-trainedPhyloPythiaSpackage, where a human expert decides on the taxa to incorporate in the model and identifies ‘training’ sequences based on marker genes directly from the sample. Due to the manual effort involved, this approach does not scale to multiple metagenome samples and requires substantial expertise, which researchers who are new to the area do not have.Results.We have developedPhyloPythiaS+, a successor to ourPhyloPythia(S)software. The new (+) component performs the work previously done by the human expert.PhyloPythiaS+also includes a newk-mer counting algorithm, which accelerated the simultaneous counting of 4–6-mers used for taxonomic binning 100-fold and reduced the overall execution time of the software by a factor of three. Our software allows to analyze Gb-sized metagenomes with inexpensive hardware, and to recover species or genera-level bins with low error rates in a fully automated fashion.PhyloPythiaS+was compared toMEGAN,taxator-tk,Krakenand the genericPhyloPythiaSmodel. The results showed thatPhyloPythiaS+performs especially well for samples originating from novel environments in comparison to the other methods.Availability.PhyloPythiaS+in a virtual machine is available for installation under Windows, Unix systems or OS X on:https://github.com/algbioi/ppsp/wiki.

A very rapid in situ Kikuchi technique to determine relative crystal misorientation

1988 ◽  
Vol 46 ◽  
pp. 830-831
Author(s):  
J. I. Bennetch
Keyword(s):  
Electron Beam ◽  
Analytical Techniques ◽  
Superplastic Forming ◽  
The Other ◽  
Kikuchi Pattern ◽  
Kikuchi Line ◽  
Line Analysis

In a recent study of the superplastic forming (SPF) behavior of certain Al-Li-X alloys, the relative misorientation between adjacent (sub)grains proved to be an important parameter. It is well established that the most accurate way to determine misorientation across boundaries is by Kikuchi line analysis. However, the SPF study required the characterization of a large number of (sub)grains in each sample to be statistically meaningful, a very time-consuming task even for comparatively rapid Kikuchi analytical techniques.In order to circumvent this problem, an alternate, even more rapid in-situ Kikuchi technique was devised, eliminating the need for the developing of negatives and any subsequent measurements on photographic plates. All that is required is a double tilt low backlash goniometer capable of tilting ± 45° in one axis and ± 30° in the other axis. The procedure is as follows. While viewing the microscope screen, one merely tilts the specimen until a standard recognizable reference Kikuchi pattern is centered, making sure, at the same time, that the focused electron beam remains on the (sub)grain in question.

scholarly journals Lithium-mediated Ferration of Fluoroarenes

2020 ◽  
Vol 74 (11) ◽  
pp. 866-870
Author(s):  
Lewis C. H. Maddock ◽  
Alan Kennedy ◽  
Eva Hevia
Keyword(s):  
Hydrogen Atom ◽  
Organometallic Chemistry ◽  
Room Temperature ◽  
Structural Elucidation ◽  
Side Reactions ◽  
Metal Base ◽  
Lithium Amide ◽  
Mixed Metal ◽  
Important Challenge

While fluoroaryl fragments are ubiquitous in many pharmaceuticals, the deprotonation of fluoroarenes using organolithium bases constitutes an important challenge in polar organometallic chemistry. This has been widely attributed to the low stability of the in situ generated aryl lithium intermediates that even at –78 °C can undergo unwanted side reactions. Herein, pairing lithium amide LiHMDS (HMDS = N{SiMe3}2) with FeII(HMDS)2 enables the selective deprotonation at room temperature of pentafluorobenzene and 1,3,5-trifluorobenzene via the mixed-metal base [(dioxane)LiFe(HMDS)3] (1) (dioxane = 1,4-dioxane). Structural elucidation of the organometallic intermediates [(dioxane)Li(HMDS)2Fe(ArF)] (ArF = C6F5, 2; 1,3,5-F3-C6H2, 3) prior electrophilic interception demonstrates that these deprotonations are actually ferrations, with Fe occupying the position previously filled by a hydrogen atom. Notwithstanding, the presence of lithium is essential for the reactions to take place as Fe II (HMDS)2 on its own is completely inert towards the metallation of these substrates. Interestingly 2 and 3 are thermally stable and they do not undergo benzyne formation via LiF elimination.

Extensive Enteric Leiomyolysis Due to Cytomegalovirus Enterocolitis in Vertically Acquired Human Immunodeficiency Virus Infection in Infants

2000 ◽  
Vol 3 (6) ◽  
pp. 591-596 ◽  
Author(s):  
Virpi V. Smith ◽  
Amanda J. Williams ◽  
Vas Novelli ◽  
Marian Malone
Keyword(s):  
Human Immunodeficiency Virus ◽  
Vascular Endothelium ◽  
Muscularis Propria ◽  
The Other ◽  
Muscularis Mucosae ◽  
Immunodeficiency Virus ◽  
Acquired Immunodeficiency ◽  
Immunodeficiency Syndrome ◽  
Viral Inclusions

We report two infants with the acquired immunodeficiency syndrome (AIDS) and rectal bleeding due to cytomegalovirus (CMV) ileitis and colitis with minimal focal mucosal ulceration but with extensive leiomyolysis of the muscularis propria. Immunostaining and in situ hybridization for CMV showed numerous viral inclusions in the myocytes of the muscularis propria and vascular endothelium/smooth muscle with only occasional inclusions present in the muscularis mucosae. Colectomy was curative in one patient; in the other the bowel was only examined at postmortem.

Did Ground Cover Change Over Geologic Time?

2000 ◽  
Vol 6 ◽  
pp. 171-182 ◽  
Author(s):  
Ben A. LePage ◽  
Hermann W. Pfefferkorn
Keyword(s):  
Fossil Record ◽  
Ground Cover ◽  
The Other ◽  
Detailed Account ◽  
Geologic Time ◽  
The Past ◽  
Other Hand ◽  
Plant Fossil

When one hears the term “ground cover,” one immediately thinks of “grasses.” This perception is so deep-seated that paleobotanists even have been overheard to proclaim that “there was no ground cover before grasses.” Today grasses are so predominant in many environments that this perception is perpetuated easily. On the other hand, it is difficult to imagine the absence or lack of ground cover prior to the mid-Tertiary. We tested the hypothesis that different forms of ground cover existed in the past against examples from the Recent and the fossil record (Table 1). The Recent data were obtained from a large number of sources including those in the ecological, horticultural, and microbiological literature. Other data were derived from our knowledge of Precambrian life, sedimentology and paleosols, and the plant fossil record, especially in situ floras and fossil “monocultures.” Some of the data are original observations, but many others are from the literature. A detailed account of these results will be presented elsewhere (Pfefferkorn and LePage, in preparation).

Reproductive performance of group-synchronized Merino d'Arles and Romanov crossbred ewes. 1. A note on the effects of lactation on fecundity

1977 ◽  
Vol 24 (1) ◽  
pp. 113-116 ◽  
Author(s):  
F. J. Galindez ◽  
M. Prud'hon ◽  
G. Reboul
Keyword(s):  
Treatment Group ◽  
Reproductive Performance ◽  
The Other ◽  
Fertility Level ◽  
Homogeneous Groups ◽  
Treatment Groups ◽  
Significant Superiority

SUMMARYFifty-six Merino d'Aries and 56 Romanov × Merino crossbred lactating ewes were divided into two treatment groups, one (T1) with a ewe-to-ram ratio of 48: 1 (24 Merino and 24 crossbred) and the other (T2) of 64: 1 (32 Merino and 32 crossbred).Intravaginal sponges with 40 mg FGA (Searle) were inserted in two subgroups at 8-day intervals and withdrawn after 12 and 16 days in situ, in four equal groups at 4-day intervals. A dose of 400 IU pregnant mare's serum gonadotrophin (PMSG) was applied at sponge withdrawal.Fertility after two oestrous cycles was equally satisfactory in both treatments, though it was lower in treatment group T2. This could be due to the significantly low (P<0·01) number of Merino ewes raddled by the T2 ram (0·33 Merino against 0·92 crossbred) suggesting preferential behaviour by the ram in this treatment.Comparisons between breeds show a slight superiority in the fertility of crossbred ewes and a highly significant superiority in prolificacy These results suggest that using the described method, 2% of rams seems more than adequate to mate with progestagen-synchronized ewes with a satisfactory fertility level. It is, however, recommended to use homogeneous groups of ewes.

PHASE TRANSITION IN LAYERED PEROVSKITE LIKE MANGANATE Ca3Mn2O7 UNDER HIGH PRESSURE

2001 ◽  
Vol 15 (18) ◽  
pp. 2491-2497 ◽  
Author(s):  
J. L. ZHU ◽  
L. C. CHEN ◽  
R. C. YU ◽  
F. Y. LI ◽  
J. LIU ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
Diamond Anvil Cell ◽  
The Other ◽  
Layered Perovskite ◽  
X Ray Diffraction ◽  
Two Phase ◽  
X Ray ◽  
Diamond Anvil

In situ high pressure energy dispersive X-ray diffraction measurements on layered perovskite-like manganate Ca 3 Mn 2 O 7 under pressures up to 35 GPa have been performed by using diamond anvil cell with synchrotron radiation. The results show that the structure of layered perovskite-like manganate Ca 3 Mn 2 O 7 is unstable under pressure due to the easy compression of NaCl-type blocks. The structure of Ca 3 Mn 2 O 7 underwent two phase transitions under pressures in the range of 0~35 GPa. One was at about 1.3 GPa with the crystal structure changing from tetragonal to orthorhombic. The other was at about 9.5 GPa with the crystal structure changing from orthorhombic back to another tetragonal.

Approaches to Cyclopropa-Fused Quinones. The Synthesis and Photolysis of Some 4,9-Disubstituted 3,3-Dimethyl-3H-benz[f]indazoles

2003 ◽  
Vol 56 (9) ◽  
pp. 903 ◽  
Author(s):  
Gavin E. Collis ◽  
Dieter Wege
Keyword(s):  
Low Temperature ◽  
Functional Group ◽  
Alkoxy Group ◽  
The Other ◽  
Acetoxy Group

Addition of 2-diazopropane to 1,4-naphthoquinone at low temperature, followed by in situ enolization and acetylation or silylation gave 3,3-dimethyl-1H-benz[f]indazol-4,9-diyl diacetate and 3,3-dimethyl-9-(t-butyl-dimethylsilyloxy)-1H-benz[f]indazol-4-ol, respectively. Functional group manipulation of the latter compound provided a number of other 4,9-disubstituted 3,3-dimethyl-3H-benz[f]indazoles. Irradiation of the diacetate led to clean extrusion of nitrogen to give the naphtho[b]cycloproparene and an alkene. Attempts to elaborate the cycloproparene into the derived cyclopropanaphthoquinone were unsuccessful. Of the other 4,9-disubstituted 3,3-dimethyl-3H-benz[f]indazoles examined, only the compound possessing an acetoxy group at C9 was photoactive, and afforded the expected cycloproparene and alkene. Compounds bearing a hydroxy or alkoxy group at C9 were photochemically inert.

Sporogenesis and septum schizolysis in Dipodascus aggregates

1989 ◽  
Vol 67 (7) ◽  
pp. 2150-2153 ◽  
Author(s):  
A. Tsuneda ◽  
S. Murakami
Keyword(s):  
Electron Microscopy ◽  
Freeze Drying ◽  
The Other ◽  
Cross Wall

Asci, ascospores, and arthroconidia of Dipodascus aggregatus were examined by electron microscopy. Freeze-drying of mature asci caused rupture of the ascal walls and made it possible to observe capsulated ascospores in situ. Two types of septa occurred: (i) one having a remarkably thickened cross wall which protruded to form a circumferential ridge on the hyphae, and (ii) the other without such a bulging ridge. Schizolysis of these septa resulted in the formation of morphologically distinct arthroconidia. The scizolytic process of the ridged septa was demonstrated in detail. There was no evidence to support that the plasmadesmal canals in the septa function as disjunctive pegs in the process of arthroconidial separation.

Relationship between the membrane potential of the contractile vacuole complex and its osmoregulatory activity inParamecium multimicronucleatum

2002 ◽  
Vol 205 (20) ◽  
pp. 3261-3270 ◽  
Author(s):  
Heidi K. Grønlien ◽  
Christian Stock ◽  
Marilynn S. Aihara ◽  
Richard D. Allen ◽  
Yutaka Naitoh
Keyword(s):  
Reference Electrode ◽  
Maximum Level ◽  
The Other ◽  
Contractile Vacuole ◽  
Hypertonic Solution ◽  
Hypotonic Solution ◽  
Atpase Inhibitor ◽  
Filling Phase ◽  
High Level

SUMMARYThe electric potential of the contractile vacuole (CV) of Paramecium multimicronucleatum was measured in situ using microelectrodes,one placed in the CV and the other (reference electrode) in the cytosol of a living cell. The CV potential in a mechanically compressed cell increased in a stepwise manner to a maximal value (approximately 80 mV) early in the fluid-filling phase. This stepwise change was caused by the consecutive reattachment to the CV of the radial arms, where the electrogenic sites are located. The current generated by a single arm was approximately 1.3×10-10 A. When cells adapted to a hypotonic solution were exposed to a hypertonic solution, the rate of fluid segregation, RCVC, in the contractile vacuole complex (CVC) diminished at the same time as immunological labelling for V-ATPase disappeared from the radial arms. When the cells were re-exposed to the previous hypotonic solution, the CV potential, which had presumably dropped to near zero after the cell's exposure to the hypertonic solution, gradually returned to its maximum level. This increase in the CV potential occurred in parallel with the recovery of immunological labelling for V-ATPase in the radial arm and the resumption of RCVC or fluid segregation. Concanamycin B, a potent V-ATPase inhibitor, brought about significant decreases in both the CV potential and RCVC. We confirm that (i) the electrogenic site of the radial arm is situated in the decorated spongiome, and (ii) the V-ATPase in the decorated spongiome is electrogenic and is necessary for fluid segregation in the CVC. The CV potential remained at a constant high level(approximately 80 mV), whereas RCVC varied between cells depending on the osmolarity of the adaptation solution. Moreover, the CV potential did not change even though RCVC increased when cells adapted to one osmolarity were exposed to a lower osmolarity, implying that RCVC is not directly correlated with the number of functional V-ATPase complexes present in the CVC.

Pagetoid Bowen Disease

2000 ◽  
Vol 124 (3) ◽  
pp. 427-430 ◽  
Author(s):  
John D. Williamson ◽  
Maria I. Colome ◽  
Aysegul Sahin ◽  
Alberto G. Ayala ◽  
L. Jeffrey Medeiros
Keyword(s):  
Differential Diagnosis ◽  
Carcinoma In Situ ◽  
Clinical Evidence ◽  
Malignant Neoplasm ◽  
The Other ◽  
Paget Disease ◽  
Melanoma In Situ ◽  
Bowen Disease ◽  
Hmb 45

Abstract Bowen disease is a variant of squamous cell carcinoma in situ. In some cases a pagetoid growth pattern can be observed with cytologically atypical clear cells arranged singly and in nests. The differential diagnosis of pagetoid Bowen disease includes primarily Paget disease and malignant melanoma in situ, as well as other less common entities. Two cases of pagetoid Bowen disease are described, one in a 65-year-old man with a thigh lesion and the other in a 25-year-old man with a lesion in the penile/scrotal region. Neither patient had clinical evidence of an internal malignant neoplasm. In both cases, the neoplastic cells were positive for cytokeratin (CK) 7 and CK 19 and were negative for CK 18, CK 20, carcinoembryonic antigen, GCDFP-15, c-erbB2, S100, and HMB-45. In aggregate, these findings support the diagnosis of pagetoid Bowen disease. Previously, others have shown that CK 7 is an almost invariable marker of Paget disease. Thus, we report these two cases to illustrate that CK 7 can be expressed by pagetoid Bowen disease and should not be a cause of confusion in the differential diagnosis.

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