Integration of single cell data by disentangled representation learning

Recent developments of single cell RNA-sequencing technologies lead to the exponential growth of single cell sequencing datasets across different conditions. Combining these datasets helps to better understand cellular identity and function. However, it is challenging to integrate different datasets from different laboratories or technologies due to batch effect, which are interspersed with biological variances. To overcome this problem, we have proposed Single Cell Integration by Disentangled Representation Learning (SCIDRL), a domain adaption-based method, to learn low-dimensional representations invariant to batch effect. This method can efficiently remove batch effect while retaining cell type purity. We applied it to thirteen diverse simulated and real datasets. Benchmark results show that SCIDRL outperforms other methods in most cases and exhibits excellent performances in two common situations: (i) effective integration of batch-shared rare cell types and preservation of batch-specific rare cell types; (ii) reliable integration of datasets with different cell compositions. This demonstrates SCIDRL will offer a valuable tool for researchers to decode the enigma of cell heterogeneity.     

Hematoporphyrin diethers--V. Plasma protein binding and photosensitizing efficiency

1. Binding of added hematoporphyrin (HP) ethers to human plasma proteins and lipoproteins has been investigated by ultracentrifugation. 2. The binding to low density lipoproteins (LDL) has been discussed in terms of photosensitized tumor growth delay of tumors and HPLC-retention time, i.e. degree of polarity. 3. The LDL-binding data show a uniform relationship to sensitizing efficiency and degree of polarity, the only exception being HP-diamyl ether. No such uniform relationship exists for less related dyes, such as HP, tetraphenylporphyrin tetrasulfonate and HP-dimethyl ether.     

Linear Relations between Carbon Dioxide Concentration and Rate of Development Towards Flowering in Sorghum, Cowpea and Soyabean

Negative linear relations were detected (P < 0·005)between the rate of progress from sowing to panicle initiationand CO₂ concentration (210-720 µmol CO₂ mol^-1 air) fortwo genotypes of sorghum [Sorghum bicolor (L.) Moench]. Relationsbetween CO₂ concentration and the rate of progress from sowingto first flowering were also negative in soyabean [Glycine max(L.) Merrill] (P < 0·025), but positive in cowpea[Vigna unguiculata (L.) Walp.] (P < 0·025), albeitthat in both grain legumes sensitivity was much less than insorghum. Thus CO₂ elevation does not delay flowering in allshort-day species. The considerable effect of CO₂ concentrationon times to panicle initiation resulted in large differencesamong the sorghum plants at this developmental stage; with increasein CO₂ concentration, plants were taller with slightly moreleaves and more pronounced apical extension. At the same timeafter sowing however, sorghum plants were heavier (P < 0·05)at 210 than at 360 µmol CO₂ mol^-1 air. In contrast, relationsbetween the dry masses of the soyabean and cowpea plants andCO₂ concentration were positive and curvilinear (P < 0·05).It is suggested that the impact of global environmental changecould be severe for sorghum production in the semi-arid tropics.Copyright1995, 1999 Academic Press Sorghum bicolor (L.) Moench., sorghum, Glycine max (L.) Merrill, soyabean, Vigna unguiculata (L.) Walp., cowpea, development, flowering, CO₂, dry matter accumulation, environmental change     

Molecular dynamics simulation of a synthetic ion channel.

A molecular dynamics simulation has been performed on a synthetic membrane-spanning ion channel, consisting of four alpha-helical peptides, each of which is composed of the amino acids leucine (L) and serine (S), with the sequence Ac-(LSLLLSL)3-CONH2. This four-helix bundle has been shown experimentally to act as a proton-conducting channel in a membrane environment. In the present simulation, the channel was initially assembled as a parallel bundle in the octane portion of a phase-separated water/octane system, which provided a membrane-mimetic environment. An explicit reversible multiple-time-step integrator was used to generate a dynamical trajectory, a few nanoseconds in duration for this composite system on a parallel computer, under ambient conditions. After more than 1 ns, the four helices were found to adopt an associated dimer state with twofold symmetry, which evolved into a coiled-coil tetrameric structure with a left-handed twist. In the coiled-coil state, the polar serine side chains interact to form a layered structure with the core of the bundle filled with H2O. The dipoles of these H2O molecules tended to align opposite the net dipole of the peptide bundle. The calculated dipole relaxation function of the pore H2O molecules exhibits two reorientation times. One is approximately 3.2 ps, and the other is approximately 100 times longer. The diffusion coefficient of the pore H2O is about one-third of the bulk H2O value. The total dipole moment and the inertia tensor of the peptide bundle have been calculated and reveal slow (300 ps) collective oscillatory motions. Our results, which are based on a simple united atom force-field model, suggest that the function of this synthetic ion channel is likely inextricably coupled to its dynamical behavior.     

The effect of body weight on the degree of blood velocity profile skewness in the aortic annulus in domestic pigs

We investigated the blood velocity profile in the aortic annulus (AA) in two groups of domestic pigs using epicardial Doppler echocardiography. The velocity profile skewness in terms of max/mean TVI (the ratio of maximal to cross-sectional mean time-velocity integral along the diameter) was 1.107 +/- 0.01 in the small pigs (n = 10; body weight: 24.6 +/- 0.8 kg) and 1.216 +/- 0.026 in the large pigs (n = 8; body weight: 50.6 +/- 2.5 kg) (P = 0.002). The velocity profile in the AA is more skewed in large animals than in small animals and the skewness in the larger animals is similar to that in normal adult humans. This study shows the importance of choosing animals of sufficient size if flow method investigations are to be performed. This is particularly important for ultrasound Doppler investigations based on a limited sample of velocities across the flow channel.     

Oral vaccination of mice with adenoviral vectors is not impaired by preexisting immunity to the vaccine carrier

Adenovirus vectors with E1 deleted of the human serotype 5 (AdHu5) and the chimpanzee serotype 68 (AdC68) expressing the glycoprotein of the Evelyn Rokiniki Abelseth strain of rabies virus were tested upon oral application for induction of systemic and mucosal transgene product-specific antibody responses in mice. Both vectors induced systemic and mucosal antibodies to rabies virus, including virus-neutralizing antibodies and protection against a severe intracerebral challenge with a mouse-adapted strain of rabies virus. Pre-existing immunity of AdHu5 virus, which dampens induction of transgene product-specific immunity elicited by AdHu5 vectors given systemically did not impair the response induced by oral vaccination. Oral priming-boosting regimens with either heterologous or homologous adenoviral vectors used sequentially increased both mucosal and systemic antibody titers to rabies virus [corrected]     

Use of online-dual-column extraction in conjunction with chiral liquid chromatography tandem mass spectrometry for determination of terbutaline enantiomers in human plasma

An online sample extraction chiral bioanalytical method was developed and validated for the quantification of terbutaline, a beta2-selective adrenoceptor agonist, spiked into human plasma by using two extraction columns and a chiral stationary phase (CSP) in conjunction with liquid chromatography tandem mass spectrometry (LC-MS/MS). In this method, two Oasis HLB extraction columns were used in parallel for plasma sample purification and a Chirobiotic T CSP was used for enantiomeric separation. Atmospheric pressure chemical ionization MS/MS was employed in multiple reaction monitoring mode for the detection and quantification. Subsequent to the addition of an internal standard solution, the plasma samples were directly injected onto the system for extraction and analysis. This method allowed the use of one of the extraction columns for purification while the other was being equilibrated. Hence, the time required for reconditioning the extraction columns did not contribute to the total analysis time per sample, which resulted in a shorter run time and higher throughput. A lower limit of quantification of 1.0 ng/mL was achieved using only 50 microliter of human plasma. The method was validated with a dynamic range of 1.0-200 ng/mL. The intra- and interday precision was no more than 11% CV and the assay accuracy was between 94-106%.     

Inheritance and expression of the cry1Ab gene in Bt ( Bacillus thuringiensis) transgenic rice

The inheritance and expression patterns of the cry1Ab gene were studied in the progenies derived from different Bt (Bacillus thuringiensis) transgenic japonica rice lines under field conditions. Both Mendelian and distorted segregation ratios were observed in some selfed and crossed F₂ populations. Crosses between japonica intra-subspecies had no significant effect on the segregation ratios of the cry1Ab gene, but crossing between japonica and indica inter-subspecies led to distorted segregation of the cry1Ab gene in the F₂ population. Field-release experiments indicated that the cry1Ab gene was stably transmitted in an intact manner via successive sexual generations, and the concentration of the Cry1Ab protein was kept quantitatively stable up to the R₆ generation. The cry1Ab gene, driven by the maize ubiquitin promoter, displayed certain kinds of spatial and temporal expression patterns under field conditions. The content of the Cry1Ab protein varied in different tissues of the main stems, the primary tillers and the secondary tillers. Higher levels of the Cry1Ab protein were found in the stems, leaves and leaf sheaths than in the roots, while the lowest level was detected in grains at the maturation stage. The content of the Cry1Ab protein in the leaves peaked at the booting stage and was lowest at the heading stage. Furthermore, the Cry1Ab content of cry1Ab expression in different tissues of transgenic rice varied individually with temperature. Received: 17 April 2001 / Accepted: 7 May 2001     

Temporary increase in chromosome breakage in an infant prenatally exposed to lead

Summary An infant exposed to high levels of lead in utero was found to have increased numbers of cells with chromosome breaks in blood samples obtained at 6 weeks and 3 months of life. Later samples did not show significant abnormality. Physical and neurological examinations of the patient up to 18 months of age gave results within normal limits.