The impact of package selection and versioning on single-cell RNA-seq analysis

Standard single-cell RNA-sequencing analysis (scRNA-seq) workflows consist of converting raw read data into cell-gene count matrices through sequence alignment, followed by analyses including filtering, highly variable gene selection, dimensionality reduction, clustering, and differential expression analysis. Seurat and Scanpy are the most widely-used packages implementing such workflows, and are generally thought to implement individual steps similarly. We investigate in detail the algorithms and methods underlying Seurat and Scanpy and find that there are, in fact, considerable differences in the outputs of Seurat and Scanpy. The extent of differences between the programs is approximately equivalent to the variability that would be introduced in benchmarking scRNA-seq datasets by sequencing less than 5% of the reads or analyzing less than 20% of the cell population. Additionally, distinct versions of Seurat and Scanpy can produce very different results, especially during parts of differential expression analysis. Our analysis highlights the need for users of scRNA-seq to carefully assess the tools on which they rely, and the importance of developers of scientific software to prioritize transparency, consistency, and reproducibility for their tools.

kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq

The term "RNA-seq" refers to a collection of assays based on sequencing experiments that involve quantifying RNA species from bulk tissue, from single cells, or from single nuclei. The kallisto, bustools, and kb-python programs are free, open-source software tools for performing this analysis that together can produce gene expression quantification from raw sequencing reads. The quantifications can be individualized for multiple cells, multiple samples, or both. Additionally, these tools allow gene expression values to be classified as originating from nascent RNA species or mature RNA species, making this workflow amenable to both cell-based and nucleus-based assays. This protocol describes in detail how to use kallisto and bustools in conjunction with a wrapper, kb-python, to preprocess RNA-seq data.

Voyager: exploratory single-cell genomics data analysis with geospatial statistics

Exploratory spatial data analysis (ESDA) can be a powerful approach to understanding single-cell genomics datasets, but it is not yet part of standard data analysis workflows. In particular, geospatial analyses, which have been developed and refined for decades, have yet to be fully adapted and applied to spatial single-cell analysis. We introduce the Voyager platform, which systematically brings the geospatial ESDA tradition to (spatial) -omics, with local, bivariate, and multivariate spatial methods not yet commonly applied to spatial -omics, united by a uniform user interface. Using Voyager, we showcase biological insights that can be derived with its methods, such as biologically relevant negative spatial autocorrelation. Underlying Voyager is the SpatialFeatureExperiment data structure, which combines Simple Feature with SingleCellExperiment and AnnData to represent and operate on geometries bundled with gene expression data. Voyager has comprehensive tutorials demonstrating ESDA built on GitHub Actions to ensure reproducibility and scalability, using data from popular commercial technologies. Voyager is implemented in both R/Bioconductor and Python/PyPI, and features compatibility tests to ensure that both implementations return consistent results.

Metabolic profiles in adults with autism spectrum disorder and intellectual disabilities

INTRODUCTION

Low levels of blood cholesterol have been found in some children with autism spectrum disorders (ASD). Psychotropic medications, commonly used by people with ASD and people with intellectual disabilities (ID) are frequently associated with altered metabolic profiles.

PURPOSE

We aimed to compare metabolic features of adults with ASD or ID with those of a community-based population.

SUBJECTS AND METHODS

Data on blood fasting glucose (FBG), lipid profile, liver enzyme profile, TSH, BMI, medications and diagnoses of 80 adults with ASD, 77 adults with ID and 828 control adults were drawn from medical charts/database. Candidates that used glucose or lipid lowering medications were not included.

RESULTS

Total-cholesterol levels of people with ASD and ID were significantly lower than those of the controls (168.3 ± 32.78, 168.2 ± 32.91, 185.4 ± 40.49 mg/dL, respectively, P<0.001) but after adjusting for gender, age and BMI and using Bonferroni correction, the significance was lost. Compared to controls, ASD and ID had significantly lower FBG (by -14.45 ± 1.81, -14.58 ± 1.54 mg/dl, respectively; P<0.001 for both) and liver enzymes, despite using psychotropic medications.

DISCUSSION AND CONCLUSION

In contrast to other psychiatric patients receiving similar medications, people with ASD and ID have unaltered lipid profiles and lower glucose and liver enzyme levels compared to a community-based population.

A comprehensive analysis of deletions, multiplications, and copy number variations in PARK2

OBJECTIVES

To perform a comprehensive population genetic study of PARK2. PARK2 mutations are associated with juvenile parkinsonism, Alzheimer disease, cancer, leprosy, and diabetes mellitus, yet ironically, there has been no comprehensive study of PARK2 in control subjects; and to resolve controversial association of PARK2 heterozygous mutations with Parkinson disease (PD) in a well-powered study.

METHODS

We studied 1,686 control subjects (mean age 66.1 ± 13.1 years) and 2,091 patients with PD (mean onset age 58.3 ± 12.1 years). We tested for PARK2 deletions/multiplications/copy number variations (CNV) using semiquantitative PCR and multiplex ligation-dependent probe amplification, and validated the mutations by real-time quantitative PCR. Subjects were tested for point mutations previously. Association with PD was tested as PARK2 main effect, and in combination with known PD risk factors: SNCA, MAPT, APOE, smoking, and coffee intake.

RESULTS

A total of 0.95% of control subjects and 0.86% of patients carried a heterozygous CNV mutation. CNV mutations found in 16 control subjects were all in exons 1-4, sparing exons that encode functionally critical protein domains. Thirteen patients had 2 CNV mutations, 5 had 1 CNV and 1 point mutation, and 18 had 1 CNV mutation. Mutations found in patients spanned exons 2-9. In whites, having 1 CNV was not associated with increased risk (odds ratio 1.05, p = 0.89) or earlier onset of PD (64.7 ± 8.6 heterozygous vs 58.5 ± 11.8 normal).

CONCLUSIONS

This comprehensive population genetic study in control subjects fills the void for a PARK2 reference dataset. There is no compelling evidence for association of heterozygous PARK2 mutations, by themselves or in combination with known risk factors, with PD.

Serotonin: a review

5-Hydroxytryptamine, or serotonin, is a biogenic amine most noted for its role as a neurotransmitter. Manipulation of serotonin in animal models was used as a tool for studying its role in humans. Through such research serotonin has been shown to modulate gastrointestinal motility, peripheral vascular tone, cerebral vascular tone, and platelet function and has been implicated in the pathophysiology of mood disorders, emesis, migraine, irritable bowel syndrome (IBS), and pulmonary and systemic hypertension. The knowledge gained is being directly applied back to animals in research on drugs that manipulate the serotonergic system in dogs and cats. Increasing use and availability of drugs that manipulate the serotonergic system has created a circumstance through which a novel toxicity was discovered in both humans and animals. Serotonin Syndrome describes the clinical picture seen in humans and animals with serotonin toxicity. This paper provides a review the physiology of serotonin and its involvement in the pathophysiologic mechanisms of various conditions, including the Serotonin Syndrome.

Intravenous Rh immune globulin prevents alloimmunization in D- granulocyte recipients but obscures the detection of an allo-anti-K

Rh immune globulin (RhIG) has been used to prevent alloimmunization in D(-) recipients of apheresis platelet transfusions from D(+) donors that may contain up to 5 mL of D(+) red blood cells (RBCs). Granulocyte concentrates contain approximately 30 mL of RBCs and it has been necessary to give D(-) recipients granulocyte transfusions from D(+) donors. Intravenous RhIG has not yet been demonstrated to be effective in preventing D alloimmunization with granulocyte transfusions. Four D(-) recipients received multiple D(+) granulocyte transfusions from D(+) donors and multiple injections of intravenous RhIG at a standard dose of 600 microg for each D(+) transfusion. Two D(-) males with chronic granulomatous disease were given 32 and 13 daily granulocyte transfusions, 18 and 2 of which, respectively, were D(+). After the first dose of intravenous RhIG, both patients exhibited circulating anti-D that was undetectable 3 to 4 years later. Two patients with severe aplastic anemia were given 5 and 14 granulocyte transfusions, 4 and 7 of which, respectively, were D(+). Both patients died before the effectiveness of RhIG could be assessed. In one of these patients the indirect and direct antiglobulin tests became positive after the first dose of intravenous RhIG, which required that subsequent granulocyte transfusions from D(+) donors be crossmatched by immediate spin (IS) testing only. A delayed hemolytic reaction attributed to allo-anti-K occurred after granulocytes from a K(+) donor were given to this patient. These results suggest that intravenous RhIG can be used to prevent alloimmunization to D in D(-) patients receiving large quantities of RBCs from D(+) granulocyte transfusions. However, anti-D and other passive antibodies from RhIG prohibit the use of the antiglobulin crossmatch with antigen-positive granulocyte donor samples. It may be important to frequently collect new samples to screen for newly formed allo-antibodies when IS crossmatches are used in place of the antiglobulin crossmatch.

Esophageal motility dysfunction in cats: a study of 44 cases

A retrospective study evaluated cases of feline esophageal dysfunction. Cats identified had contrast esophagrams performed during a six-year period. Of 56 cases undergoing esophagography, 51 had complete records available for review. Forty-four cases were felt to be abnormal and were included in the study. Cases were analyzed for signalment, presenting complaints, and identifiable causes of abnormal esophageal motility. Response to treatment and case outcome were also reviewed. The signalment of the cases varied widely, especially in age. The occurrence of esophageal motility dysfunction was low, comprising only 0.05% of all feline cases seen in a six-year period. Forty-three percent of cases were considered idiopathic, and 57% were congenital or diagnosed with conditions known to cause esophageal motility dysfunction. The causative disease states included myasthenia gravis, mediastinal masses, vascular ring anomalies, dysautonomia, and esophageal stricture. Seventy-eight percent of those treated with medical therapy (i.e., combinations of sucralfate, H2 receptor antagonists, and either metoclopramide or cisapride) showed clinical improvement.

Polymerase chain reaction for the diagnosis of HIV infection in adults. A meta-analysis with recommendations for clinical practice and study design

PURPOSE

To do a meta-analysis of studies that have evaluated the sensitivity and specificity of polymerase chain reaction (PCR) assay for the diagnosis of human immunodeficiency virus (HIV) infection in adults. Evaluating the performance of PCR is difficult because in certain clinical situations, the sensitivity or specificity of PCR may exceed those of the current reference standard tests (enzyme immunoassay followed by confirmatory Western blot analysis). Therefore, an additional goal was to develop recommendations for 1) the design of future evaluative studies of PCR and 2) the use of PCR in persons with suspected HIV infection.

DATA SOURCES

Studies published between 1988 and 1994 that were identified in a search of 17 computer databases, including MEDLINE, and abstracts identified from conference proceedings.

STUDY SELECTION

Studies were included if DNA amplification by PCR was done on peripheral blood mononuclear cells from adults. Ninety-six studies met the inclusion criteria.

DATA EXTRACTION

Data were extracted independently by two reviewers. Study design was assessed independently by two investigators blinded to study results.

RESULTS

Reported sensitivities for PCR range from 10% to 100%, and specificities range from 40% to 100%. A summary receiver-operating characteristic curve based on all 96 studies has a maximum joint sensitivity and specificity (upper left point on the curve, where sensitivity equals specificity) of 97.0% to 98.1%. If the threshold value that defines a positive PCR result is chosen so that sensitivity is higher than 98.1%, specificity will decrease to less than 98.1%. Conversely, if the threshold value that defines a positive PCR result is chosen so that specificity is greater than 98.1%, sensitivity will decrease to less than 98.1%. If sensitivity and specificity are chosen to be equal, the corresponding false-positive rate is 1.9% to 3.0%. At the maximum joint sensitivity and specificity, the positive predictive value of PCR ranges from 34% to 85% as the prevalence of HIV increases from 1.0% to 10%. We identified seven areas in which study design could be modified to 1) reduce susceptibility to bias in estimates of the sensitivity and specificity of PCR and 2) to increase the generalizability of the study results. These modifications will also help to overcome methodologic problems created by the lack of a reference standard test.

CONCLUSIONS

The PCR assay is not sufficiently accurate to be used for the diagnosis of HIV infection without confirmation. Use of PCR for the diagnosis of HIV in adults should be limited to situations in which antibody tests are known to be insufficient. Future studies of PCR performance should be sufficiently large and should use adequate reference standard tests and standardized methods for the performance of PCR. Specimens should be evaluated by persons blinded to clinical status and to the results of other diagnostic tests for HIV infection.

Specificity of high-resolution CT findings in pulmonary asbestosis: do patients scanned for other indications have similar findings?

OBJECTIVE

High-resolution CT findings in patients with asbestosis include subpleural curvilinear densities, subpleural density in dependent portions of the lung, parenchymal bands, thickened septal lines, and honeycomb lung. Our objective was to examine the prevalence of these CT findings in a random group of patients scanned for a variety of clinical reasons not specifically related to occupational exposure.

MATERIALS AND METHODS

One hundred sixty-eight CT studies of the thorax were performed at six levels in 168 patients examined for a variety of clinical indications. The scans were evaluated by two radiologists for the presence of subpleural curvilinear densities, subpleural density in dependent locations, parenchymal bands, thickened septal lines, and honeycomb lung.

RESULTS

CT scans of 11 patients showed pleural plaques suggesting previous exposure to asbestos. Among the 157 studies showing no evidence of pleural plaques, CT scans showed subpleural curvilinear densities in dependent areas in 32 (20%); subpleural curvilinear densities in nondependent areas in 19 (12%); parenchymal bands in 47 (30%); thickened septal lines in dependent areas in 93 (59%), and septal lines in nondependent areas in 67 (43%); subpleural density in dependent areas in 66 (42%); and honeycomb lung in five (3%).

CONCLUSION

Subpleural curvilinear densities, subpleural density in dependent locations, parenchymal bands, and thickened septal lines occur as isolated and as combined CT findings in patients with a variety of underlying diseases or conditions unrelated to asbestosis and by themselves are nonspecific findings. Their occurrence, even in patients with CT evidence of pleural plaques, does not necessarily indicate the presence of asbestosis.

Importance of monitoring calcium & calcium related properties in carrier detection for Duchenne muscular dystrophy

Calcium and calcium dependent enzymes viz., calcium ATPase, protein kinase C and calcium activated neutral protease (milli CANP mCANP) were studied in the erythrocytes, platelets and lymphocytes of obligate carriers, in order to assess the usefulness of these indices for detection of carriers for Duchenne muscular dystrophy (DMD). With the exception of mCANP and lymphocyte calcium ATPase, other calcium dependent enzyme activities showed considerable overlap between carriers and control. Since the increase in the level of platelet mCANP was found in all affected boys (no false negatives) and obligate carriers, and patients with other myopathic conditions and some neurogenic causes did not show high platelet mCANP activity, this parameter could be considered as a good phenotypic index. Unlike SCK, the platelet mCANP of carriers did not overlap that of controls, hence tests are to be carried out to verify its usefulness as an index of carrier state in mutations other than DNA deletion since testing of non-deletion is both costly and has practical limitations.

Using the patient's history to estimate the probability of coronary artery disease: a comparison of primary care and referral practices

PURPOSE

According to probability theory, the interpretation of new information should depend on the prior probability of disease. We asked if this principle applies to interpreting the history in patients with chest pain. We compared the prevalence of coronary artery disease (CAD) in patients who had similar histories but who came from populations with different disease prevalence.

PATIENTS AND METHODS

We studied two high-disease-prevalence populations (patients referred for coronary arteriography) and two low-disease-prevalence populations (patients from primary care practices). We used clinical characteristics of one arteriography population to develop a logistic rule for estimating the probability of coronary artery narrowing. The number of clinical findings determined the logistic score, which was proportional to the prevalence of CAD.

RESULTS

The prevalence of CAD was much lower in the primary care population than in the arteriography population, even when patients with similar logistic scores, and thus similar clinical histories, were compared.

CONCLUSION

A clinician must take account of the overall prevalence of disease in the clinical setting when using the patient's history to estimate the probability of disease. Failure to observe this caution may lead to errors in test selection and interpretation.

Calcium activated neutral protease in blood cells from patients & carriers of Duchenne muscular dystrophy

As blood cells such as platelets, lymphocytes and erythrocytes from patients with Duchenne muscular dystrophy show evidence of membrane alterations and elevation of intra-cellular calcium, one of the calcium related changes i.e., the activity of calcium activated neutral protease (CANP) was monitored and found to be elevated in erythrocytes, lymphocytes and platelets. As similar changes were observed in platelets of carriers of this disease, CANP in platelets may serve as a useful index for carrier detection.

The effect of dexamethasone on chronic pulmonary oxygen toxicity in infant mice

The effect of dexamethasone (0.1, 1, and 5 mg/kg/d given subcutaneously from d 14-18) was tested in infant mice continuously exposed from birth to either humidified air or 80% oxygen. Dexamethasone significantly decreased lung wet wt (p less than 0.01), lung water (p less than 0.021), lung dry wt, protein, and DNA (p less than 0.001) in both air- and oxygen-exposed animals. Dexamethasone, however, had no effect on lung compliance measured after animals were killed on d 18. It also had no effect on the increase in the blood-air barrier thickness or decrease in the blood-air exchange surface area seen in the 80% oxygen-exposed mice. Dexamethasone decreased thymus gland wt (p less than 0.001), body wt gain (p less than 0.001), brain wt (p less than 0.001), and lung lymphocytes (p less than 0.05) in both air- and oxygen-exposed animals. The effect of 1 mg/kg and 5 mg/kg of the drug could not be differentiated. During the 4 d of drug administration, one air- and one oxygen-exposed animal died; both received 5 mg/kg/d of dexamethasone; microscopic and culture evidence of infection was not found. If dexamethasone causes similar effects in human infants with bronchopulmonary dysplasia, it should be used with great caution even for short-term clinical management.

Calcium-activated neutral protease and its endogenous inhibitor in tissues of dystrophic and normal mice

Calcium-activated neutral protease (milli-CANP) and its endogenous inhibitor are elevated in muscle tissues, primarily the skeletal muscle and heart, of dystrophic mice (C57BL/6J dy/dy) as compared to the control strain (C57BL/10J). Tissues showing relative increase of CANP also show significant loss of enzymes such as CK, LDH in comparison to plasma, where these enzymes register a significant increase. PK is lost minimally from these tissues, probably showing a "sparing effect." Absence of any significant change in CANP activity in the liver points to a specific role of CANP in the dystrophic process. In the skeletal muscle the endogenous CANP inhibitor registers a concomitant increase with CANP without altering the enzyme/inhibitor ratio.

Calcium-activated neutral protease from muscle and platelets of Duchenne muscular dystrophy cases

Calcium-activated neutral protease (CANP) has been purified from its endogenous inhibitor and its activity is monitored in the muscle of Duchenne Muscular Dystrophy (DMD) patients. The specific activity of the enzyme is found to be significantly higher as compared to normal. CANP from platelets of DMD patients is significantly higher as compared to activities in other myopathies and controls. Platelet CANP, therefore, may prove to be an index of pathological condition in DMD, since other myopathies do not show such a significant change.

Complications of rigid anterior chamber implants

Despite accurate lens sizing, 100 eyes with rigid anterior chamber implants showed a high incidence of lens-related trauma postoperatively: pigment dispersion (pseudoguttata), angle recession, peripheral anterior synechiae, iris erosion/atrophy, iris holes from stretching, angle fibrosis, haptic tip erosion into sclera and iris, neovascularization of peripheral iris and angle, lens rotation through iridectomy and into ciliary body, lens tilting with corneal endothelial touch, high refractive cylinder with long intraocular lenses, pigment proliferation onto iris surface, partial slippage of the intraocular lens into vitreous following intracapsular procedure, and pupillary-block glaucoma. Vision results were good. Glaucoma and cystoid macular edema rates were low. Bullous keratopathy and retinal detachment didn't occur. High endothelial cell loss was associated with those lenses that "propellered" and those that tilted and touched endothelium. The adverse findings may be static or may represent a continuing process of tissue damage.

Statistical consulting in clinical research: the two-way street

Clinical research often rests on statistical interpretation of numerical data. Thus, effective collaboration between clinician and statistician can have central importance. Interaction in the planning phases of a project can identify tractable scientific and statistical problems that will need attention and can help avoid intractable ones. The central need is for clear, broad, specific two-way communication on scientific issues and research roles.

Postoperative trigeminal neuralgia--case report

A case report is presented of a postoperative patient who experienced severe, paroxysmal, neuralgic pains in and about his eye. He was successfully treated with diphenylhydantoin. The literature concerning the rationale for this therapy is reviewed.

Continuing medical education before audit

Patient-care-assessment systems have failed to demonstrate efficiency in detecting continuing education needs or in influencing clinical practice. We believe that one of the weaknesses in retrospective audit systems is their tendency to result in the ratification of criteria which match past practices rather than criteria which incorporate new, science-based information. This is in spite of the fact that for many years guidelines for medical audit processes have encouraged physicians to develop science-based criteria. This study was undertaken to determine whether continuing education programs preceding patient care audits can induce physicians to choose criteria beyond their own experience. A highly significant difference was found between audit criteria developed after education programs and those which were developed without such programs. The results indicate that educational efforts can have a striking effect on the criteria ratified by audit committees.

Astigmatism and the Flieringa ring

Routine use of a Flieringa ring in conjunction with a large corneal section for intracapsular or extracapsular surgery facilitates more accurate wound closure and can significantly decrease the amount of postoperative astigmatism.

Capsulotomy technique in the presence of an anterior chamber lens

A modified Sato technique has proved to be a highly successful and atraumatic method of posterior capsulotomy in the presence of an anterior chamber lens. The lens remains undisturbed and iris-ciliary body, vitreous-retinal traction is avoided.

Corneal dellen following cataract extraction with lens implantation

Two cases of dellen following cataract extraction with implant insertion are described. Etiology may be based upon deprivation of nervous and vascular supplies, and possibly related to large corneal sections. Conservative therapy was found to be sufficient in restoring the corneal integrity.

Intraocular pressures and visual fields following pseudophakos implantation

9 of 636 pseudophakos patients developed post-operative intraocular pressure elevations. All were treated successfully, 5 medically and 4 surgically. No permanent glaucomas resulted. Goldmann perimetry on 210 representative patients showed no glaucomatous or peripheral defects.

Kelman anterior chamber lens: a preliminary report

The Kelman anterior chamber lens is thin and lightweight. Its design is unique for introduction through a small limbal incision following phacoemulsification or as a secondary implant. It can be used easily in conjunction with intracapsular or extra-capsular surgery. The postoperative course is quiet and short, and the patient has rapid visual rehabilitation with a comfortable eye.