Pacybara: accurate long-read sequencing for barcoded mutagenized allelic libraries

MOTIVATION

Long-read sequencing technologies, an attractive solution for many applications, often suffer from higher error rates. Alignment of multiple reads can improve base-calling accuracy, but some applications, e.g. sequencing mutagenized libraries where multiple distinct clones differ by one or few variants, require the use of barcodes or unique molecular identifiers. Unfortunately, sequencing errors can interfere with correct barcode identification, and a given barcode sequence may be linked to multiple independent clones within a given library.

RESULTS

Here we focus on the target application of sequencing mutagenized libraries in the context of multiplexed assays of variant effects (MAVEs). MAVEs are increasingly used to create comprehensive genotype-phenotype maps that can aid clinical variant interpretation. Many MAVE methods use long-read sequencing of barcoded mutant libraries for accurate association of barcode with genotype. Existing long-read sequencing pipelines do not account for inaccurate sequencing or nonunique barcodes. Here, we describe Pacybara, which handles these issues by clustering long reads based on the similarities of (error-prone) barcodes while also detecting barcodes that have been associated with multiple genotypes. Pacybara also detects recombinant (chimeric) clones and reduces false positive indel calls. In three example applications, we show that Pacybara identifies and correctly resolves these issues.

AVAILABILITY AND IMPLEMENTATION

Pacybara, freely available at https://github.com/rothlab/pacybara, is implemented using R, Python, and bash for Linux. It runs on GNU/Linux HPC clusters via Slurm, PBS, or GridEngine schedulers. A single-machine simplex version is also available.

Pacybara: Accurate long-read sequencing for barcoded mutagenized allelic libraries

Long read sequencing technologies, an attractive solution for many applications, often suffer from higher error rates. Alignment of multiple reads can improve base-calling accuracy, but some applications, e.g. sequencing mutagenized libraries where multiple distinct clones differ by one or few variants, require the use of barcodes or unique molecular identifiers. Unfortunately, sequencing errors can interfere with correct barcode identification, and a given barcode sequence may be linked to multiple independent clones within a given library. Here we focus on the target application of sequencing mutagenized libraries in the context of multiplexed assays of variant effects (MAVEs). MAVEs are increasingly used to create comprehensive genotype-phenotype maps that can aid clinical variant interpretation. Many MAVE methods use long-read sequencing of barcoded mutant libraries for accurate association of barcode with genotype. Existing long-read sequencing pipelines do not account for inaccurate sequencing or non-unique barcodes. Here, we describe Pacybara, which handles these issues by clustering long reads based on the similarities of (error-prone) barcodes while also detecting barcodes that have been associated with multiple genotypes. Pacybara also detects recombinant (chimeric) clones and reduces false positive indel calls. In three example applications, we show that Pacybara identifies and correctly resolves these issues.

Epitaxial Growth of InN Films by Molecular-Beam Epitaxy Using Hydrazoic Acid (HN3) as an Efficient Nitrogen Source

Epitaxial InN films have been successfully grown on c-plane GaN template by gas-source molecular-beam epitaxy with hydrazoic acid (HN3) as an efficient nitrogen source. Results in residual-gas analyzer show that the HN3 is highly dissociated to produce nitrogen radicals and can be controlled in the amounts of active nitrogen species by tuning HN3 pressure. A flat and high-purity InN epifilm has been realized at the temperature near 550 degrees C, and a growth rate of 200 nm/hr is also achieved. Moreover, the epitaxial relationship of the InN(002) on the GaN(002) is reflected in the X-ray diffraction, and the full-width at half-maximum of the InN(002) peak as narrow as 0.05 degrees is related to a high-quality crystallinity. An infrared photoluminescence (PL) emission peak at 0.705 eV and the integrated intensity increasing linearly with excitation power suggest that the observed PL can be attributed to a free-to-bound recombination.

Effects of glutamine-supplemented total parenteral nutrition on cytokine production and T cell population in septic rats

BACKGROUND

This study was designed to investigate the effects of total parenteral nutrition (TPN) enriched with glutamine (GLN) on in vivo cytokine production and cellular immune response in early and late septic stages of rats.

METHODS

Male Wistar rats were divided into 2 experimental groups and received TPN solution at an energy level of 270 kcal/kg body weight. The TPN solutions were isonitrogenous and identical in nutrients composition except for differences in amino acid content. One group received 2% GLN, whereas the other group received glycine (Gly) instead. TPN was maintained for 5 or 6 days according to the sacrifice schedule of the rats. On day 5, sepsis was induced by cecal ligation and puncture (CLP). Respective groups of rats were sacrificed 2, 4, 6, and 24 hours after CLP.

RESULTS

Sepsis resulted in a negative nitrogen balance in both groups, and nitrogen loss was significantly lower in the GLN than the Gly group. Interleukin (IL)-2 and interferon (IFN)-gamma in most of the samples collected at various time points were not detectable in plasma or peritoneal lavage fluid. No differences in plasma IL-6 and TNF-alpha concentrations were observed between the GLN and Gly groups. Also, there were no significant differences in IL-1beta, IL-6, and TNF-alpha concentrations in peritoneal lavage fluid between the 2 groups at various time points. The CD4+/CD8+ ratio was significantly higher in the GLN group than in the Gly group only at 4 hours after CLP, and no difference was observed at 24 hours after CLP.

CONCLUSIONS

TPN preinfused with a GLN-supplemented solution had a beneficial effect in ameliorating the extent of negative nitrogen balance in septic rats. However, parenterally administered GLN did not reduce the production of inflammatory mediators systemically or at the site of injury, and the influence on enhancing cellular immunity was not obvious.

Preserved esophagogastric manometric motility in patients after distal gastrectomy

BACKGROUND/AIMS

A prospective study resolved whether commonly employed distal gastrectomies could influence the esophagogastric manometric measurements and the role of vasoactive intestinal polypeptide in mediating motility after surgery.

METHODOLOGY

Studied groups consisted of 20 patients following radical subtotal gastrectomy for gastric cancer, 20 patients after subtotal gastrectomy for duodenal ulcer and 20 controls. Fasting blood was obtained to measure serum vasoactive intestinal polypeptide levels. A pneumohydraulic infusion system measured esophagogastric motility parameters.

RESULTS

Measured lower esophageal sphincter pressures in subjects of gastric cancer surgery, duodenal ulcer surgery and controls were 15.3 +/- 4.7, 13.1 +/- 5.3 and 12.6 +/- 5.0 mmHg, respectively (NS), while the sphincter lengths were 3.15 +/- 0.81, 3.22 +/- 0.79 and 2.86 +/- 0.85 cm, respectively (NS). In addition, other parameters including lower esophageal body remained unchanged. The serum vasoactive intestinal polypeptide levels of three groups were 24.1 +/- 10.8, 22.5 +/- 9.5 and 21.3 +/- 7.8 pg/ml, respectively (NS).

CONCLUSIONS

Neither gastric cancer nor duodenal ulcer in distal stomach removal can alter the lower esophageal body and LES manometric motilities. Unchanged serum VIP levels after gastric surgery are likely one of the mechanisms preserving esophagogastric integrity.

Alteration of distal esophageal motor functions on different body positions

BACKGROUND/AIMS

This study tried to resolve whether changed body position influences esophageal manometric parameters.

MATERIAL AND METHODS

A pneumohydraulic infusion system was employed to measure esophageal parameters for 32 healthy volunteers. They underwent two consecutive manometries on both supine and sitting positions in a random order. These motility measurements included lower esophageal sphincter pressure, dry/wet swallow induced contractile amplitude and interval of distal esophageal body, and its peristaltic speed.

RESULTS

Sitting position evoked a higher lower esophageal sphincter pressure than the supine measurement (Mean +/- SD: 14.6 +/- 4.0 mmHg vs. 11.9 +/- 4.2 mmHg, p < 0.01). At the distal esophagus, a swallow led to a stronger contractile amplitude and longer interval on supine measurement.

CONCLUSIONS

Recorded peristaltic speeds in various esophageal segments resulted in a difference while this result was mainly due to the different recorded body positions (p < 0.01). Partial esophageal manometric parameters recorded on sitting position are different from the supine measurement. Hence altered body position may modulate some distal esophageal motor functions.

Abnormal thyroid hormone levels in critical nonthyroidal illness

Low levels of thyroid hormone in the absence of clinical hypothyroidism often happen to patients with critical non-thyroidal illnesses (NTI). Low thyroid hormone concentrations in serum do not necessarily mean hypofunction of the thyroid gland; rather it is a helpful adaptation of the human body to the underlying diseases. We collected 133 hospitalized cases of critical NTI and analyzed the incidence of this phenomenon. Fifty-three per cent of the patients had T3 level lower than 60 ng/dl (normal:85-165 ng/dl) and 60% had T4 level lower than 6 ug/dl (normal:6-12 ug/dl). The lowest levels were observed in patients who had sepsis, were aged over 70 or died in this admission. Free T4 and TSH levels were within normal range in most cases. There is a strong negative correlation between the prognosis and the level of T4 in these patients. Those patients with markedly low levels of T3 and T4 should be treated more sophisticatedly.

[The efficacy of sonic and ultrasonic appliances on root canal debridement]

The purpose of this study was to compare the debridement efficacy of hand, sonic (MM-3000), and ultrasonic (Cavi-Endo) appliances, utilizing the same K-type files and a constant flow irrigation system, in the mesial root canals of extracted human mandibular 1st and 2nd molars. Only those roots with a canal curvature of between 10 and 30 degrees, by Schneider's method, were used in this study. The instrumentation time per mesial root canal for each treatment group was also evaluated. Following canal preparation and histological processing, the middle and apical cross-sections were examined to determine the percentage of canal and isthmus cleanliness, and the percentage of planed canal walls in the main canal area. Statistical analysis indicated no significant difference in canal and isthmus cleanliness at the middle and apical levels. All techniques achieved a high level of canal cleanliness. However, step-back hand instrumentation had the greatest percentage of planed canal walls in the main canal area at every portion of the root. Sonic instrumentation, in this study, was significantly faster than hand instrumentation in preparing the root canal system.

Long-term immunogenicity and efficacy of hepatitis B vaccine in infants born to HBeAg-positive HBsAg-carrier mothers

In an attempt to evaluate the long-term immunogenicity and efficacy of plasma-derived hepatitis B vaccine in preventing hepatitis B virus infection, 199 infants born to hepatitis B e antigen-positive hepatitis B surface antigen-carrier mothers were found to be antibody to HBsAg-positive (greater than or equal to 10 mIU per ml) 2 months after the first booster of hepatitis B vaccination at age 1, and their serum HBsAg and anti-HBs were rechecked annually to ages 3 to 5. Of the nine infants whose initial anti-HBs were low (10 to 100 mIU per ml) in concentration, four (44%) were found to be anti-HBs seronegative at age 3, while none of the 127 vaccine responders with high anti-HBs levels (greater than 1,000 mIU per ml) lost their anti-HBs during the 4-year follow-up period. Also, in 63 infants whose initial anti-HBs titers were around 101 to 1,000 mIU per ml, only two lost their anti-HBs at age 4, and another two at age 5, respectively. Whether the vaccine responders lost their anti-HBs or not, no hepatitis B virus infection occurred in these vaccinees during the follow-up period. Thus, in the first 5 years of life, the protective efficacy in the high-risk infants who responded to plasma-derived hepatitis B vaccine was 100%. Because of the diversity of anti-HBs response in individuals, we suggest testing anti-HBs titer in all vaccinated infants after the first booster vaccination in order to calculate the time of next booster before the minimal protective level is reached.

Cockroach hypersensitivity: preliminary study of allergic cockroach asthma in Taiwan

One hundred eight-two atopic patients were skin tested with cockroach antigen. Of these 182 patients, 54.9% gave positive immediate skin reaction by intracutaneous test. Among those atopic patients tested, 57.5% of patients with asthma and 50.7% of patients with allergic rhinitis were sensitive to cockroach extracts. The specific IgE antibody was determined by fluoroallergosorbent test. Of 79 cockroach-positive atopic patients, 39.2% were found to contain IgE antibodies against cockroach. No specific IgE was detected in cockroach-negative atopic and nonatopic subjects. Bronchial provocation test with cockroach antigen was performed on 15 subjects. Immediate asthmatic response was detected in six of nine cockroach-positive subjects with asthma. Two cockroach-negative subjects with asthma and four nonatopic subjects demonstrated no significant decrease in FEV1. The results indicate that cockroach induces antigen-specific IgE-mediated bronchial asthma, and cockroach is one of the major causes of allergic asthma.

The hemodynamic effect of verapamil on portal hypertension in patients with postnecrotic cirrhosis

Wedged hepatic venous pressure, free hepatic venous pressure and cardiac index were measured before and 1 hr after i.v. administration as well as 1 month and 3 months after chronic oral administration of verapamil in 10 patients with HBsAg-positive cirrhosis. The gradient between wedged hepatic venous pressure and free hepatic venous pressure was decreased 14% at 1 hr after i.v. administration of 10 mg verapamil, and the sustained decrease in hepatic venous pressure gradient was also demonstrated in the patients after 1 month, and in six patients after 3 months of continuous oral administration of verapamil. The mean arterial pressure significantly decreased (p less than 0.01) 1 hr after the administration of verapamil. There was no significant change in other hemodynamic values. We conclude that chronic oral administration of verapamil can reduce the hepatic venous pressure gradient in patients with compensated HBsAg-positive cirrhosis and portal hypertension.

Histologic and clinicopathologic features of Chinese patients with HBsAg-positive chronic active hepatitis

Needle biopsies of both the right and left lobes of the liver were performed during peritoneoscopy in 20 male patients with chronic active hepatitis B in Taiwan. Microscopic study of these biopsy specimens led to the recognition of three groups: 1) five patients in whom the lobular architecture was easily recognizable but in whom necrosis and early intralobular fibrosis were present, along with severe chronic inflammation of the portal tracts; 2) seven patients in whom the livers were characterized by early septal formation and a good regenerative response, but few recognizable lobules with normal architecture; and 3) eight patients in whom the disease had progressed to severe fibrosis with septal formation and tiny pseudolobules, indicative of early cirrhosis. The left lobe was the more severely damaged in 16 of the 20 patients.

Immunoprophylaxis of infection with hepatitis B virus in infants born to hepatitis B surface antigen-positive carrier mothers

Infants born to carrier mothers positive for hepatitis B surface antigen (HBsAg) and hepatitis B e antigen (HBeAg) received 5 micrograms of hepatitis B virus (HBV) vaccine on four occasions. Group 1 received vaccine only, group 2 received vaccine plus hepatitis B immune globulin (HBIG) at birth, and group 3 received vaccine plus HBIG at birth and at one month. Infants born to HBeAg-positive mothers (group 4) received a reduced dose of vaccine (2.5 micrograms) on three occasions as well as HBIG at birth. As compared with 78.4% of the control group (infants whose parents refused vaccination) who became chronic HBV carriers at the age of 14 months, the protective efficacy rate of vaccination was 75.3% in group 1,85.5% in group 2,89.7% in group 3, and 87.2% in group 4. HBV vaccine (5 micrograms) was also given to infants born to HBsAg-positive, HBeAg-negative mothers on four on four occasions. The antibody response to HBsAg in vaccine recipients was 12% after the first dose, 44% after the second dose, and 75% and 100% at six months and 1.5 years of age, respectively.

Combined passive and active immunization for interruption of perinatal transmission of hepatitis B virus in Taiwan

We attempted a clinical trial to interrupt transmission of hepatitis B virus (HBV) infection from hepatitis B surface antigen (HBsAg) positive and hepatitis Be antigen (HBsAg) positive mothers to their infants in Taiwan. Screening of 5,595 pregnant women revealed that 856 (15.3%) were HBsAg positive. Three hundred and sixty-one (42.2%) of the HBsAg positive pregnant women were HBeAg positive. Infants born to HBsAg and HBeAg positive mothers were randomized into 3 groups to receive the HBV vaccine alone or combined with hepatitis B immune globulin (HBIG). HGV vaccine was given at 2, 6, and 10 weeks after birth. Group I received HBV vaccine alone while Group II received HBV vaccine in combination with HBIG at birth and group III received HBV vaccine plus HBIG at birth and again at one month old. Group IV constituted the control group when their parents refused vaccination. At 6 months of age, the HBV carrier rate was 23.7% (9/38) in Group I, 11.1% (4/36) in Group II, and 5.3% (2/38) in Group III infants. Compared with 90% of infants who became HBV carriers in the control group (Group IV), the efficacy of HBV vaccination in preventing HBV infection among these high risk infants at the 6th month was 73.7% in Group I, 87.7% in Group II, and 94.1% in Group III. The antibody to HBsAg (anti-HBs) positivity rate in sera of Group I, II, III infants at 6 months of age was 79.0%, 88.9% and 94.7%, respectively. These initial results indicate that combined passive and active immunization is efficacious in interrupting perinatal transmission of HBV infection.

Restoration of multichannel microwave radiometric images

A constrained iterative image restoration method is applied to multichannel diffraction-limited imagery. This method is based on the Gerchberg-Papoulis algorithm utilizing incomplete information and partial constraints. The procedure is described using the orthogonal projection operators which project onto two prescribed subspaces iteratively. Its properties and limitations are presented. The effect of noise was investigated and a better understanding of the performance of the algorithm with noisy data has been achieved. The restoration scheme with the selection of appropriate constraints was applied to a practical problem. The 6.6, 10.7, 18, and 21 GHz satellite images obtained by the scanning multichannel microwave radiometer (SMMR), each having different spatial resolution, were restored to a common, high resolution (that of the 37 GHz channels) to demonstrate the effectiveness of the method. Both simulated data and real data were used in this study. The restored multichannel images may be utilized to retrieve rainfall distributions.

Optical properties of composites of selected shades in white light

Light reflectivity, scattering coefficient, absorption coefficient, infinite optical thickness, and contrast ratio were determined in white light, for seven shades of a conventional composite and five shades of a microfilled composite, from reflection spectrophotometric data using Kubelka's equations. Significant differences among shades were observed for each property. Values of infinite optical thickness ranged from 2.97 to 5.90 mm among the shades studied.

Color of selected shades of composites by reflection spectrophotometry

The colors of seven shades of a conventional composite and five shades of a microfilled composite were measured by reflection spectrophotometry at three thicknesses and for two backgrounds. Intrinsic color was determined from reflectirity data computed from optical properties. As thickness increased, the color approached the intrinsic color. Differences in color among shades were statistically significant.

Optical properties of composites of selected shades

The optical properties of seven shades of a conventional composite and five shades of a microfilled composite were determined from reflection spectrophotometric data with Kubelka's equations. Scattering and absorption coefficients decreased and values of infinite optical thickness increased as wavelength increased from 405 to 700 nm. Reflectivity curves were determined.

Properties of addition-type silicone impression materials

Addition-type silicone impression materials have low dimensional change after setting, low creep, moderately short working time, and are fairly stiff with moderately high resistance to tears after setting.

Effect of H3PO4 concentration on bond strength

Prior to bonding, the enamel surface of the tooth is normally etched using a solution of 37%-50% phosphoric acid (H3PO4) for 60 seconds. The purpose of this study was to evaluate the tensile bond strength, debonding interface distribution and enamel surface detachment of various concentrations of H3PO4 solution, from 2% to 80%, applied for 15 seconds. Statistically significant differences in bond strength were found among the various concentrations tested: concentrations in the 10% to 60% range produced greater bond strengths than both the weaker and stronger concentrations. The weaker the bond strength, the greater the debonding interface between resin and enamel. The greater the bond strength, the greater the debonding interface between the bracket and resin. Enamel detachment occurred as the H3PO4 concentration rose above 30%. To obtain greater bond strength and less enamel detachment, 10%-30% concentrations of phosphoric acid for 15 seconds etching are suggested for clinical bonding.