Benchmarking atlas-level data integration in single-cell genomics.

Single-cell atlases often include samples that span locations, laboratories and conditions, leading to complex, nested batch effects in data. Thus, joint analysis of atlas datasets requires reliable data integration. To guide integration method choice, we benchmarked 68 method and preprocessing combinations on 85 batches of gene expression, chromatin accessibility and simulation data from 23 publications, altogether representing >1.2 million cells distributed in 13 atlas-level integration tasks. We evaluated methods according to scalability, usability and their ability to remove batch effects while retaining biological variation using 14 evaluation metrics. We show that highly variable gene selection improves the performance of data integration methods, whereas scaling pushes methods to prioritize batch removal over conservation of biological variation. Overall, scANVI, Scanorama, scVI and scGen perform well, particularly on complex integration tasks, while single-cell ATAC-sequencing integration performance is strongly affected by choice of feature space. Our freely available Python module and benchmarking pipeline can identify optimal data integration methods for new data, benchmark new methods and improve method development.

The role of microbial populations in the containment of aromatic hydrocarbons in the subsurface.

A survey of soil gases associated with gasoline stations on the Swan Coastal Plain of Western Australia has shown that 20% leak detectable amounts of petroleum. The fates of volatile hydrocarbons in the vadose zone at one contaminated site, and dissolved hydrocarbons in groundwater at another site were followed in a number of studies which are herein reviewed. Geochemical evidence from a plume of hydrocarbon-contaminated groundwater has shown that sulfate reduction rapidly developed as the terminal electron accepting process. Toluene degradation but not benzene degradation was linked to sulfate reduction. The sulfate-reducing bacteria isolated from the plume represented a new species, Desulfosporosinus meridiei. Strains of the species do not mineralise 14C-toluene in pure culture. The addition of large numbers of cells and sulfate to microcosms did stimulate toluene mineralisation but not benzene mineralisation. Attempts to follow populations of sulfate-reducing bacteria by phospholipid signatures, or Desulfosporosinus meridiei by FISH in the plume were unsuccessful, but fluorescently-labeled polyclonal antibodies were successfully used. In the vadose zone at a different site, volatile hydrocarbons were consumed in the top 0.5 m of the soil profile. The fastest measured rate of mineralisation of 14C-benzene in soils collected from the most active zone (6.5 mg kg(-1) day(-1)) could account for the majority of the flux of hydrocarbon vapourtowards the surface. The studies concluded that intrinsic remediation by subsurface microbial populations in groundwater on the Swan Coastal Plain can control transport of aromatic hydrocarbon contamination, except for the transport of benzene in groundwater. In the vadose zone, intrinsic remediation by the microbial populations in the soil profile can contain the transport of aromatic hydrocarbons, provided the physical transport of gases, in particular oxygen from the atmosphere, is not impeded by structures.

Using polymer mats to biodegrade atrazine in groundwater: laboratory column experiments.

Large-scale column experiments were undertaken to evaluate the potential of in situ polymer mats to deliver oxygen into groundwater to induce biodegradation of the pesticides atrazine, terbutryn and fenamiphos contaminating groundwater in Perth, Western Australia. The polymer mats, composed of woven silicone (dimethylsiloxane) tubes and purged with air, were installed in 2-m-long flow-through soil columns. The polymer mats proved efficient in delivering dissolved oxygen to anaerobic groundwater. Dissolved oxygen concentrations increased from <0.2 mg l(-1) to approximately 4 mg l(-1). Degradation rates of atrazine in oxygenated groundwater were relatively high with a zero-order rate of 240-380 microg l(-1) or a first-order half-life of 0.35 days. Amendment with an additional carbon source showed no significant improvement in biodegradation rates, suggesting that organic carbon was not limiting biodegradation. Atrazine degradation rates estimated in the column experiments were similar to rates determined in laboratory culture experiments, using pure cultures of atrazine-mineralising bacteria. No significant degradation of terbutryn or fenamiphos was observed under the experimental conditions within the time frames of the study. Results from these experiments indicate that remediation of atrazine in a contaminated aquifer may be achievable by delivery of oxygen using an in situ polymer mat system.

The formation of malodorous dimethyl oligosulphides in treated groundwater: the role of biofilms and potential precursors.

Water distributed from the Wanneroo Groundwater Treatment Plant intermittently contains dimethyl trisulphide (DMTS). The compound is responsible for a "swampy odour" in the water. DMTS production from potential precursors was insignificant in the absence of biofilms when compared with DMTS production from precursors in the presence of biofilms in a biofilm reactor. Greatest dimethyl disulphide (DMDS) and DMTS production (> 3000 ng L-1 DMTS) occurred in the reactors when supplied with methane thio-containing compounds, such as methionine, S-methyl cysteine and methyl-3-(methylmercapto)-propionate. Abiotic DMTS production from oligosulphides also occurred through the addition of the methylating agents, methyl iodide or methyl-p-toluene sulphonate. Significant DMTS production also occurred with Wanneroo water that contained added omega-thio-containing compounds such as cysteine (1400 ng L-1 DMTS), and 3-mercaptopropionate (210 ng L-1). Biomethylation, a ubiquitous response by microorganisms for the detoxification of toxic compounds, generated DMDS/TS from biofilm oligosulphides. Biofilms exposed to the toxic compounds selenate or 2,4,6-trichlorophenol methylated oligosulphides in addition to the toxins. Sodium sulphide also stimulated DMTS production. Easily Biodegradable Dissolved Organic Carbon (BDOC) probably contributed indirectly to DMTS production by the biofilms, although whether this was a result of its stimulation of greater microbial activity or consumption of oxygen, or both, remains unresolved. Stagnation of water in the biofilm reactors also increased DMTS production, which was concomitant with depletion of oxygen concentrations in the bulk water. Many processes, such as degradation of methane thio-containing compounds, methylation of sulphides and oligosulphides, and changes in contributions of different metabolic pathways upon depletion of oxygen concentrations upon water stagnation, probably contribute simultaneously to "swampy odour" production in the distribution system.

Antimuscarinic activity of telenzepine on isolated human urinary bladder: no role for M1-muscarinic receptors.

1. The antimuscarinic activity of the selective M1-blocking drug, telenzepine, was investigated on the isolated human urinary bladder, contracted with exogenous muscarinic agonists and with field stimulation. 2. Telenzepine (3 x 10(-8)-10(-5) M) concentration-dependently shifted to the right the dose-response curves of bethanechol, acetylcholine and McN-A343, and partially depressed the electrically-evoked twitch responses. 3. pA2 values of telenzepine against bethanechol and McN-A343 were very close. 4. McN-A343 did not modify twitch responses elicited by field stimulation up to 10(-5) M. 5. The lack of muscarinic M1 receptors in human detrusor muscle is confirmed.

Effect of cimetropium bromide and other antispasmodic compounds on in vitro guinea-pig gallbladder.

The effect of cimetropium bromide, a new antimuscarinic compound, on bethanechol- and electrically-induced contractions was studied on isolated guinea-pig gallbladder. Atropine and two other widely employed antispasmodics (i.e., rociverine and octylonium bromide) were employed as reference compounds. Cimetropium and atropine proved to be competitive antimuscarinics, their pA2 being 7.77 +/- 0.14 and 8.31 +/- 0.14, respectively. On the contrary, rociverine displayed a dual effect being a competitive antagonist at low (up to 10(-5) mol/l) and a mixed one at high (greater than 10(-5) mol/l) concentrations. When tested against bethanechol- and electrically-induced contractions, all the compounds, with the exception of octylonium bromide, showed a concentration-dependent relaxant effect. In both experimental conditions, the potency of cimetropium was of the same order of magnitude as that of atropine and 150-200 times higher than that of rociverine. These data, together with the reported activity on human gallbladder in vivo and the well known involvement of cholinergic system in the control of gallbladder motility, could represent the rationale for the clinical use of cimetropium in the treatment of biliary colics as well as spasms of biliary tree.

Inhibition of caerulein-induced gall bladder emptying by cimetropium bromide in humans.

The effect of cimetropium bromide, a new potent antimuscarinic compound, on caerulein-induced gall bladder emptying in 8 male volunteers was studied by real time ultrasonography. During saline infusion, caerulein (10-40 ng.kg-1.h-1) induced dose-dependent emptying of the gall bladder. There was a significant linear correlation between the dose of the peptide and the reduction in gall bladder size. A continuous infusion of cimetropium bromide (5 mg.h-1) significantly inhibited the contracting effect of caerulein on the human gall bladder, by 74% in response to the lowest dose and by 45% and 22%, respectively, to the two higher doses. The data confirm that the contracting effect of CCK-like peptides on the human gall bladder is at least partly cholinergically mediated, and they demonstrate the relaxing activity of cimetropium previously shown in animals. Provided its antispasmodic activity is also evident in disease, cimetropium should be regarded as a potentially useful agent for the treatment of biliary colic and spasm of the biliary tree.

Antisecretory and antiulcer effect of the H2-receptor antagonist famotidine in the rat: comparison with ranitidine.

1 The effects of the new H2-receptor antagonist famotidine, administered orally, on gastric secretion and emptying as well as on experimentally-induced gastric and duodenal ulcers were studied in the rat. Ranitidine was used as a reference compound. 2 Both compounds inhibited acid secretion in a dose-dependent manner. Calculated ED50 values were 0.80 and 6.84 mg kg-1 for famotidine and ranitidine, respectively. However, the duration of the antisecretory action was the same for both drugs. 3 The effect of the two drugs, administered at equiactive antisecretory doses, on gastric emptying was different. Ranitidine significantly accelerated the emptying rate whereas famotidine had no effect. 4 Famotidine reduced, in a dose-dependent manner, ulcer incidence in stomachs of dimaprit-treated rats and in duodena of cysteamine-treated animals with a potency respectively 2 and 7 times higher than that of ranitidine. 5 Famotidine is therefore an effective antisecretory and untiulcer compound. Its potency, but not its efficacy, is higher than that of ranitidine. Moreover, the duration of the antisecretory action is virtually the same for both drugs.

Inhibition of gastric acid secretion by adenosine receptor stimulation in the rat.

The effects of adenosine and its metabolically stable derivative L-phenylisopropyladenosine (L-PIA), acting mainly on A1 receptors, on gastric acid secretion were studied in the rat. Although inactive by intraduodenal route, subcutaneous adenosine significantly inhibited acid secretion. This inhibition, however, was not dose-dependent. On the contrary, L-PIA was able to decrease dose-dependently acid output by both subcutaneous and intraduodenal route, its ED50 being 0.11 mg/kg subcutaneously and 0.24 mg/kg intraduodenally. The inhibitory effect of L-PIA was reduced by prior administration of theophylline. These results suggest that activation of A1-receptors inhibits acid secretion in the rat.

Action of pirenzepine on the human urinary bladder in vitro.

The novel compound pirenzepine was tested for its antimuscarinic effect on the human urinary bladder "in vitro." Its behavior towards the contractions induced by acetylcholine or bethanechol and towards electrically induced contractions was identical to that of atropine. However, its potency was 100 to 300 times lower than that of atropine. Results obtained with ganglion blocking agents, tetrodotoxin and cooled preparations of urinary bladder seem to indicate the virtually total absence of ganglionic cells. On the other hand they point out the fundamental role of post-synaptic muscarinic M2 receptors as the most important component of the cholinergic system in the bladder. Of course the existence of other transmitters released at the cholinergic nerve endings after electrical field stimulation cannot be excluded on the basis of our experiments.

Effects of rociverine on the human ureter: in vivo and in vitro experimental study.

An in vitro and in vivo study was conducted to verify the effects of rociverine--a new spasmolytic agent--on peristalsis in the human ureter. In vitro (human ureter strips), rociverine exerted a spasmolytic activity both on the baseline motility and on the spasm induced by direct contractants (eledoisin, KCl) or by histamine. It may therefore be concluded that rociverine is a predominantly myotropic spasmolytic. In the in vivo study, conducted in patients with cutaneous ureterostomy, the drug showed a marked inhibitory effect on the amplitude and frequency of the ureteral rhythmic spikes, without affecting the baseline tone.

Histamine receptors in the human ureter.

The occurrence of histamine H1- and H2-receptors in the human ureter was studied by means of relatively selective agonists and antagonists of both kinds of receptors. Isolated preparations of small strips of human ureters removed during surgery were used. Histamine and the H1-agonist 2-aminoethylthiazole contracted the ureter in a dose-dependent fashion whereas the H2-agonists dimaprit and impromidine were ineffective. The H1-antagonist chlorpheniramine shifted to the right the dose-response curves to histamine and to 2-aminoethylthiazole with the kinetics of the competitive antagonism. Conversely the H2-antagonists cimetidine, metiamide and tiotidine potentiated the effect of histamine by a factor of 3 though high concentrations had to be used (25 - 30 micrograms/ml). Both H1 and H2-antagonists were not able to modify the basal tone and/or motility showed by ureteral strips. All the above data suggested that H1-receptors are predominant in the human ureteral muscle and the contraction induced by their stimulation completely mask the effect of the H2-receptors stimulation. Since H2-agonists were ineffective in basal conditions and H2-antagonists potentiated the effect of histamine which is spasmogenic, we may suggest that H2-receptors are less numerous than H1-receptors and their stimulation cause a slight relaxation of the ureteral muscle. This situation is not uncommon in other smooth muscle system (e.g. respiratory system and gastrointestinal tract).

Evidence against the temperature-dependent interconversion of histamine H1- and H2-receptors in the guinea-pig ileum.

1 The possible temperature-dependent interconversion of histamine H1- and H2-receptors in the guinea-pig ileum suggested from previous studies was re-investigated by use of new and selective H2-receptor agonists and antagonists. 2 Chlorpheniramine, and H1-blocker, caused a rightward shift of the cumulative histamine dose-response curve at both 37 degrees C and 12 degrees C. Conversely cimetidine and tiotidine, two H2-receptor blockers, were ineffective at both temperatures. Metiamide behaved as a non competitive antagonist at 12 degrees C but only in very high concentrations. 3 Dimaprit and impromidine, two selective H2-receptor agonists, were inactive at both 37 degrees C and 12 degrees C when given alone, whereas at both temperatures they elicited the already described relaxation of the contractions induced by histamine. 4 Similar results were obtained on the guinea-pig whole ileum and on the longitudinal muscle strip: this indicates a lack of interference of the circular smooth muscle. 5 Our results allow us to conclude that no temperature-dependent interconversion of histamine H1- and H2-receptors occurs in the guinea-pig ileum.

Histamine receptors in the guinea-pig duodenum.

Guinea-pig duodenum contracted by histamine or by acetylcholine was relaxed dose-dependently by a series of H2-receptor selective agonists namely dimaprit, impromidine, clonidine and tolazoline. This relaxation was not neurally mediated since it was not modified by tetrodotoxin nor was it exerted through sympathetic receptors because it was not modified by pretreatment with propranolol or phentolamine. Apparently it was connected with the H2-receptor stimulation more than to peculiarities of the single compounds. However a series of H2-blocker (metiamide, cimetidine, ranitidine or oxmetidine) were unable to counteract the effect of the H2-agonists or the relaxant effect of histamine in the presence of chlorpheniramine. This peculiar situation seems to indicate the existence of anomalous H2-receptors, susceptible to the action of the agonists by not to that of the antagonists.