Machine learning for cell type classification from single nucleus RNA sequencing data

With the advent of single cell/nucleus RNA sequencing (sc/snRNA-seq), the field of cell phenotyping is now a data-driven exercise providing statistical evidence to support cell type/state categorization. However, the task of classifying cells into specific, well-defined categories with the empirical data provided by sc/snRNA-seq remains nontrivial due to the difficulty in determining specific differences between related cell types with close transcriptional similarities, resulting in challenges with matching cell types identified in separate experiments. To investigate possible approaches to overcome these obstacles, we explored the use of supervised machine learning methods-logistic regression, support vector machines, random forests, neural networks, and light gradient boosting machine (LightGBM)-as approaches to classify cell types using snRNA-seq datasets from human brain middle temporal gyrus (MTG) and human kidney. Classification accuracy was evaluated using an F-beta score weighted in favor of precision to account for technical artifacts of gene expression dropout. We examined the impact of hyperparameter optimization and feature selection methods on F-beta score performance. We found that the best performing model for granular cell type classification in both datasets is a multinomial logistic regression classifier and that an effective feature selection step was the most influential factor in optimizing the performance of the machine learning pipelines.

Epidemiological profile and transmission dynamics of COVID-19 in the Philippines

The Philippines confirmed local transmission of COVID-19 on 7 March 2020. We described the characteristics and epidemiological time-to-event distributions for laboratory-confirmed cases in the Philippines recorded up to 29 April 2020 and followed until 22 May 2020. The median age of 8212 cases was 46 years (IQR 32-61), with 46.2% being female and 68.8% living in the National Capital Region. Health care workers represented 24.7% of all detected infections. Mean length of hospitalisation for those who were discharged or died were 16.00 days (95% CI 15.48-16.54) and 7.27 days (95% CI 6.59-8.24). Mean duration of illness was 26.66 days (95% CI 26.06-27.28) and 12.61 days (95% CI 11.88-13.37) for those who recovered or died. Mean serial interval was 6.90 days (95% CI 5.81-8.41). Epidemic doubling time prior to the enhanced community quarantine (ECQ; 11 February and 19 March) was 4.86 days (95% CI 4.67-5.07) and the reproductive number was 2.41 (95% CI 2.33-2.48). During the ECQ (20 March to 9 April), doubling time was 12.97 days (95% CI 12.57-13.39) and the reproductive number was 0.89 (95% CI 0.78-1.02).

Distinct long-term neurocognitive outcomes after equipotent sevoflurane or isoflurane anaesthesia in immature rats

BACKGROUND

Many anaesthetics when given to young animals cause cell death and learning deficits that persist until much later in life. Recent attempts to compare the relative safety or toxicity between different agents have not adequately controlled for the relative dose of anaesthetic given, thereby making direct comparisons difficult.

METHODS

Isoflurane or sevoflurane were given at 1 minimum alveolar concentration (MAC) for 4 h to postnatal day 7 (P7) rat pups. Beginning at P75 these animals underwent fear conditioning and at P83 Morris water maze testing to assess working memory, short-term memory and early long-term memory using delays of 1 min, 1 h, and 4 h.

RESULTS

No difference between groups was seen in fear conditioning experiments. Morris water maze learning was equivalent between groups, and no difference was seen in working memory. Sevoflurane-treated animals had a deficit in early long-term memory, and isoflurane-treated animals had a deficit in both short-term and early long-term memory.

CONCLUSIONS

Both isoflurane and sevoflurane delivered at 1 MAC for 4 h to immature rats caused a deficit in long-term memory. Isoflurane also caused a deficit in short-term memory. Isoflurane might be more detrimental than sevoflurane in very young animals.

Cumulative clinical experience with use of insulin lispro: critical appraisal, role in therapy, and patient considerations

We have now at our disposal the new rapid-acting insulin analogs, of which insulin lispro was the first to become commercially available. While the differences in pharmacokinetic and pharmacodynamic characteristics are indisputable, the clinical benefits attained by these changes have not been as clear. In the present review, we discuss the structure, pharmacology, and landmark studies related to insulin lispro. The clinical characteristics of insulin lispro are compared with those of insulin regular and other insulin analogs in different clinical situations. Also included are the aspects of quality of life and cost-effectiveness that may modify the modern practitioner's decision to adopt one type of insulin over another.

Does induction of plastic change in motor cortex improve leg function after stroke?

Combined peripheral nerve and brain stimulation ("dual stimulation") induces changes in the excitability of normal motor cortex. The authors sought to establish whether dual stimulation would also induce motor cortex plasticity and associated functional improvements in nine stroke patients with chronic stable hemiparesis. Following 4 weeks of daily dual stimulation, improvements were seen in some neurophysiological and functional measures. This technique may offer therapeutic opportunities in some stroke patients.

Increased cortical excitability induced by transcranial DC and peripheral nerve stimulation

This study investigated the effect of short periods of simultaneous weak anodal direct current (DC) stimulation and peripheral ulnar nerve (ES) stimulation on corticospinal excitability. The experiments involved repeated testing of ten normal subjects with four different protocols: (1) No Stimulation; (2) DC only; (3) ES only; (4) DC plus ES. Motor evoked potentials (MEP) were recorded from the First Dorsal Interosseous (FDI); Abductor Digiti Minimi (ADM) and Flexor Carpi Ulnaris (FCU). The baseline MEP amplitude was compared with that obtained immediately after the first set of stimulation, after the second set of stimulation, 15 min post stimulation and 30 min after stimulation. No significant change was seen with the No Stimulation and ES Only protocols. FDI showed a significant change in the DC protocol after the second set of stimulation but the changes were not present 15 or 30 min after. The DC plus ES protocol showed FDI changes that were significant after the second set of stimulation with the elevations persisting when tested 15 and 30 min post intervention. These observations show that a period of anodal DC stimulation preceding a period of ulnar nerve stimulation resulted in significant and persistent elevations in cortical excitability.

Changes in motor cortical excitability induced by paired associative stimulation

OBJECTIVE

Changes in afferent input have been shown to be capable of inducing reorganisations of motor cortex in humans. Using TCMS we examined the efficacy of a new associative afferent stimulation paradigm in inducing motor cortical reorganisation in humans.

METHODS

Using TCMS, stimulus response curves were constructed before and following a 1 h period of associative stimulation of two muscles motor points. The effect of an asynchronous peripheral stimulation paradigm was investigated in a separate series of control experiments.

RESULTS

One hour of associative stimulation of two muscles motor points resulted in a significant increase in the excitability of the corticospinal projection to those stimulated muscles. The increase in excitability peaked 1 h following the stimulation period. This increase in excitability did not generalise to either adjacent or more remote muscles. The control stimulation paradigm produced no significant change in corticospinal excitability.

CONCLUSIONS

These results confirm the importance of associative input for the induction of plasticity in the human motor cortex.

SIGNIFICANCE

The findings reported here further elucidate the role of afferent input in motor cortical reorganisation. These findings have implications for our understanding of the mechanisms of motor learning and may also be relevant to the design of new afferent stimulation therapies.

Femoropopliteal and femorotibial greater saphenous vein "in situ" reconstructions in non selected patients. Life table analysis

594 non selected "in situ" reconstructions were analyzed retrospectively using the life table method. Especially after immediate occlusion the cumulative patency rate is unsatisfactory (33.1% vs 62.3% after 6 years). Patency rates are influenced by the anastomotic site and mainly by run off conditions. The number of patent tibial arteries seems to be the most important determinant. These results prove to be statistically significant.

Male hypogonadism with gynecomastia caused by late-onset deficiency of testicular 17-ketosteroid reductase

BACKGROUND

17-Ketosteroid reductase deficiency results in male pseudohermaphroditism because conversion of the weak androgen androstenedione to the more potent androgen testosterone is impaired. If a late-onset form exists, hypogonadism and gynecomastia caused by decreased testosterone production and increased estrogen production, respectively, would be expected as the major clinical manifestations in men.

METHODS

We studied 48 male subjects, ranging from 14 to 26 years of age, who had idiopathic pubertal gynecomastia. Serum concentrations of gonadal and adrenal steroid hormones were measured before and after the administration of corticotropin and after the combined administration of chorionic gonadotropin and dexamethasone for three days.

RESULTS

We identified three unrelated subjects (ages, 16, 17, and 26 years) with results indicative of a partial deficiency of testicular 17-ketosteroid reductase. The three subjects had gynecomastia as well as decreased libido and impotence. Their mean (+/- SD) base-line serum androstenedione and estrone concentrations were elevated as compared with the levels in the 45 subjects without this enzyme deficiency (androstenedione, 380 +/- 70 vs. 110 +/- 70 ng per deciliter [13 +/- 2 vs. 4 +/- 2 nmol per liter]; estrone, 138 +/- 12 vs. 46 +/- 9 pg per milliliter [511 +/- 44 vs. 170 +/- 33 pmol per liter]). After the administration of chorionic gonadotropin, the mean serum androstenedione concentration in these three subjects was 910 +/- 48 ng per deciliter (32 +/- 2 nmol per liter) and the mean serum estrone concentration was 260 +/- 16 pg per milliliter (962 +/- 59 pmol per liter). The mean serum testosterone concentration at base line was 210 +/- 80 ng per deciliter (7.4 +/- 2.8 nmol per liter) in the 3 subjects, as compared with a value of 410 +/- 12 ng per deciliter (14.4 +/- 0.42 nmol per liter) in the 45 other subjects, and it did not increase in response to the administration of chorionic gonadotropin. The concentrations of androstenedione and estrone in spermatic venous serum were 19 times higher and 73 times higher, respectively, than in normal men. The serum concentrations of follicle-stimulating hormone and luteinizing hormone in these three subjects were inappropriately low, suggesting the presence of hypogonadotropic hypogonadism.

CONCLUSIONS

A late-onset form of testicular 17-ketosteroid reductase deficiency can cause gynecomastia and hypogonadism in men.

Elevated serum estradiol associated with increased androstenedione-testosterone ratio in adolescent males with varicocele and gynecomastia

OBJECTIVE

To investigate the testicular function in adolescents with pubertal gynecomastia associated with varicocele before and after varicocelectomy.

DESIGN AND PATIENTS

We have studied six male adolescents 15 to 19 years of age with bilateral gynecomastia. They were selected among other adolescents with gynecomastia because of the presence of visible varicoceles. All of them had normal physical examination and secondary sexual characteristics. This was prospective study of 3 months' duration. All the patients that were included finished the study.

SETTING

All the patients were evaluated in the Endocrine Clinic of Winthrop-University Hospital, a tertiary care unit.

INTERVENTION

Serum testosterone (T), androstenedione (A), and estradiol (E2) responses to the administration of human chorionic gonadotropin (hCG) 2,000 IU for 3 consecutive days before and 3 months after varicocelectomy were determined.

RESULTS

Varicocelectomy did not cause any significant changes in the basal (pre-hCG) levels of the steroid. However, the increase in T levels achieved with hCG was significantly (P less than 0.005) higher after varicocelectomy (before T, 925 +/- 212 ng%; after T, 1,649 +/- 406 ng%). Simultaneously, the stimulated levels of E2 and A were significantly lower (P less than 0.005) after varicocelectomy (E2, 62 +/- 12 pg/mL; A, 326 ng% +/- 80 ng%) than before (E2, 106 +/- 13 pg/mL; A, 580 ng% +/- 95 ng%).

CONCLUSION

The reciprocal effect on the levels of T and its immediate precursor, A, suggests an impairment of the 17-ketoreductase enzyme activity. The increased levels of E2 after hCG and its normalization after varicocelectomy suggests that varicoceles may play a pathogenetic role in the development of gynecomastia.

Leydig cell function in adolescent boys with varicoceles

The incidence of varicoceles in adolescent boys ranges from 5% to 19.5%. We studied five adolescent boys aged 17 to 20 years with visible left-sided varicoceles. All of them had public hair and testicular volumes between 20 to 25 mL and had achieved stage V of pubertal development. Serum gonadotropin response to the intravenous administration of 100 micrograms of gonadotropin-releasing hormone (GnRH) and testosterone response to the administration of 2,000 IU human chorionic gonadotropin (hCG) daily for 3 days before and 3 months after varicocelectomy were measured. Basal levels of both gonadotropins were in the pubertal range, and there was no significant difference between serum levels before and after varicocelectomy. Both gonadotropins, however, showed increased responses to the administration of GnRH (luteinizing hormone [LH]: basal, 12.0 +/- 5.1 mIU/mL; peak, 105.0 +/- 36.0 mIU/mL; follicle-stimulating hormone [FSH]: basal, 11.6 +/- 4.2 mIU/mL, peak, 60.0 +/- 18.0 mIU/ml) that decreased after varicocelectomy (LH: basal, 14.3 +/- 6.0 mIU/mL; peak, 58.6 +/- 12.0 mIU/mL; FSH: basal, 6.8 +/- 4.6 mIU/mL; peak, 38.0 +/- 8.1 mIU/mL). Serum testosterone response to hCG was also significantly improved by varicocelectomy (testosterone peak: before, 780 +/- 210 ng/dL; after, 1850 +/- 170 ng/dL). Testicular biopsy specimens showed no histologic abnormalities and normal spermatogenesis. Endocrine evaluation in adolescent boys with varicoceles could detect an early Leydig cell dysfunction that could be corrected by varicocelectomy.

Provocation of panic with carbon dioxide inhalation in patients with premenstrual dysphoria

The effects of double breath inhalation of a 35% CO2 mixture in oxygen and placebo air inhalation were compared in 14 women seeking treatment for marked premenstrual dysphoric changes who did not have panic disorder and 12 control women. The first exposure to CO2 inhalation induced a panic attack reaction (severe subjective anxiety with autonomic symptoms) in 9 of 14 women with premenstrual dysphoria but none of the controls. Neither patients nor controls panicked in response to the air inhalation. Control subjects experienced mild anxiety and/or somatic symptoms after CO2 inhalation, but these did not resemble panic attacks and were clearly different from the response of the patient group.

Respiratory physiology and pathological anxiety

There has been comparatively little attention paid to the respiratory derangements in anxiety disorders. Some authorities contend, however, that indices of respiratory function may be the best objective marker of anxiety state. Furthermore, an understanding of the ventilatory status of patients with anxiety disorder has shed light on the basic pathophysiology of abnormal anxiety. For example, it is now clear that patients with a wide variety of anxiety disorders hyperventilate both chronically and acutely. Therefore, we present an explanation of the physiological changes produced by hyperventilation. In order to further study ventilatory physiology in patients with anxiety disorder, our group and others have used the carbon dioxide challenge test. The data from these experiments suggest that patients with panic disorder are hypersensitive to carbon dioxide and that carbon dioxide inhalation induces panic attacks in susceptible patients. Hyperventilation appears to be a secondary, but pathophysiologically important, event in the generation of acute panic. The implications of work in respiratory physiology for clinical management of patients with anxiety disorder are discussed.

CO2 challenge of patients with panic disorder

In an open trial, five of eight panic disorder patients and none of five control subjects panicked after inhalation of two breaths of 35% CO2 and 65% O2; none panicked after placebo. Using 35% CO2 to induce panic is safe, simple, and well tolerated and may provide a valuable laboratory model of panic.

Treatment of surgical infections with a modern quinolone: therapy of soft tissue infections and pneumonia with ofloxacin

A randomized, open, prospective study including 45 patients with either soft tissue infections (29 cases) or pneumonia (15 cases) after surgical intervention and one case having both indications was carried out with ofloxacin. The standard dose was 200 mg ofloxacin b. i. d. In most cases, clinical symptoms, such as fever, rubor, swelling and pain in soft tissue infections, as well as fever, dyspnoea, physical and radiological signs for pneumonia, subsided within two to seven days. Laboratory data (blood analyses, liver enzymes) remained in the normal range. The overall tolerability was good. Bacteriological controls have proven that ofloxacin is able to eradicate a broad range of pathogens, including persister pathogens and also certain bacteria like Clostridium perfringens and Erysipelothrix rhusiopathiae. In our study, Streptococcus faecalis was of intermediate sensitivity in one case and resistant in another. Ofloxacin has proven to be effective in soft tissue infections and pneumonia after surgical intervention.

Enzyme activities of human myocardium: creatine kinase and hexose phosphate isomerase

Creatine kinase (CK) and hexose phosphate isomerase (PHI) activities were determined in 36 samples of human heart muscle obtained from patients during cardiovascular surgery. With one exception, CK activities were higher than any reported so far in the literature (papillary muscle, left ventricle: 2,521 +/- 776 IU/g wet weight at 37 degrees C). PHI Activities, the first time measured, are comparable to those in skeletal muscle (200-400 U/g, higher in papillary muscle than in the right auricle). The activities of both enzymes determined correlate significantly (all samples considered together: r = 0.773; p < 0.001). Results are discussed with respect to their possible clinical interest as well as their significance for myocardial metabolism.

Light filtration during transillumination of the neonate: a method to reduce heat buildup in the skin

Filtration of the light used for transillumination of neonates is employed to reduce heat buildup in the skin during transillumination. Clinical and experimental evaluation of the effects of filtration are presented.