The Experimentalist's Guide to Machine Learning for Small Molecule Design

Initially part of the field of artificial intelligence, machine learning (ML) has become a booming research area since branching out into its own field in the 1990s. After three decades of refinement, ML algorithms have accelerated scientific developments across a variety of research topics. The field of small molecule design is no exception, and an increasing number of researchers are applying ML techniques in their pursuit of discovering, generating, and optimizing small molecule compounds. The goal of this review is to provide simple, yet descriptive, explanations of some of the most commonly utilized ML algorithms in the field of small molecule design along with those that are highly applicable to an experimentally focused audience. The algorithms discussed here span across three ML paradigms: supervised learning, unsupervised learning, and ensemble methods. Examples from the published literature will be provided for each algorithm. Some common pitfalls of applying ML to biological and chemical data sets will also be explained, alongside a brief summary of a few more advanced paradigms, including reinforcement learning and semi-supervised learning.

Urban green infrastructure size, quality and proximity and health outcomes in older populations

Background

A city's multi-functional network of green and blue spaces has an important role underpinning the health and wellbeing of its residents. Although evidence of positive links between nature and health is plentiful, little is known about which particular aspects of green and blue spaces are most influential, and how benefits might vary between social groups and age.

Methods

We used a green infrastructure (GI) approach combining a high-resolution spatial dataset of land-cover and function with area-level demographic and socio-economic data. A comprehensive characterisation of the Greater Manchester UK city region was generated. The GI attributes were used in step-wise multi-level regression analyses to test for associations between population chronic morbidity and the functional, physical and spatial components of GI across an urban socio-demographic gradient.

Results

Individual GI attributes were significantly associated with health in all socio-demographic contexts; even when associations between health and overall green cover were non-significant. For areas with having higher proportions of older people ('older neighbourhoods'), associations were found between health and land-cover diversity, informal greenery and patch size in high income areas. In lower income areas, health was predicted by proximity to public parks and recreation land.

Conclusions

A nuanced description of greenspace in terms of quality, cover type, diversity explains more variation in population health than a single metric such as percentage green cover. People in urban neighbourhoods that have older age populations and lower income are disproportionately healthy if their neighbourhoods contain accessible, good quality public greenspace. This has implications for strategies to decrease health inequalities and inform international initiatives, such as the World Health Organisation's Age-Friendly Cities programme.

Key messages

A nuanced description of green and blue space in terms of quality, cover type, diversity explains more variation in population health than a single metric such as percentage green cover. People in urban neighbourhoods that have older age populations and lower income are disproportionately healthy if their neighbourhoods contain accessible, good quality public greenspace.

Response rate to a single dose of vinblastine administered to dogs with treatment-naive multicentric lymphoma

Vincristine is included in vincristine, cyclophosphamide, doxorubicin and prednisone (CHOP) chemotherapy protocols, which are the gold-standard treatment for high-grade canine lymphoma. Vincristine can result in relatively high rates of gastrointestinal toxicity, whereas vinblastine is generally well tolerated and thus may represent an under-utilized and minimally toxic alternative to vincristine. Our objective was to determine the response rate and toxicity associated with a single dose of vinblastine administered to dogs with treatment-naïve, intermediate to large-cell, multicentric lymphoma. Twenty client-owned dogs were enrolled with signed owner consent. A Simon's minimax, phase II, two-stage trial was performed to test the efficacy of vinblastine administered at 2 mg/m² IV followed by a pilot trial of vinblastine at 2.5 mg/m² . No dogs were administered concurrent steroids or other chemotherapy. One out of 14 dogs receiving vinblastine at 2 mg/m² demonstrated a partial response. Three out of five dogs demonstrated a partial response to vinblastine at 2.5 mg/m² . Gastrointestinal toxicity was infrequent and low grade for both groups. The majority of dogs (80%) in the 2.5 mg/m² dosing group developed neutropenia 1-week post administration. Vinblastine was well tolerated but minimally efficacious at a dose of 2 mg/m² IV in dogs with treatment-naive, multicentric lymphoma. Because of poor response rates, treatment at this dose is not recommended. A small subset of dogs administered 2.5 mg/m² had significantly improved response rates (P = 0.04), suggesting that higher doses may have improved efficacy, although further research is indicated to confirm these preliminary findings.

Magnetic Meckel's: an unusual case report of foreign body ingestion

Foreign body ingestion in children is common. Most items pass spontaneously, however rarer cases may result in obstruction and or perforation. Ingestion of multiple magnetic items can be more troublesome, as a consequence of the ability of the items to attract across different sections of bowel, or by coalescing to form a larger foreign body. Very few cases of foreign body ingestion have led to the presentation of a complicated Meckel's diverticulum. We present of a case of an adolescent boy with intestinal obstruction secondary to multiple magnetic foreign body ingestion and sequestration within a Meckel's diverticulum.

Modelling air pollution for epidemiologic research--part II: predicting temporal variation through land use regression

Over recent years land use regression (LUR) has become a frequently used method in air pollution exposure studies, as it can model intra-urban variation in pollutant concentrations at a fine spatial scale. However, very few studies have used the LUR methodology to also model the temporal variation in air pollution exposure. The aim of this study is to estimate annual mean NO(2) and PM(10) concentrations from 1996 to 2008 for Greater Manchester using land use regression models. The results from these models will be used in the Manchester Asthma and Allergy Study (MAAS) birth cohort to determine health effects of air pollution exposure. The Greater Manchester LUR model for 2005 was recalibrated using interpolated and adjusted NO(2) and PM(10) concentrations as dependent variables for 1996-2008. In addition, temporally resolved variables were available for traffic intensity and PM(10) emissions. To validate the resulting LUR models, they were applied to the locations of automatic monitoring stations and the estimated concentrations were compared against measured concentrations. The 2005 LUR models were successfully recalibrated, providing individual models for each year from 1996 to 2008. When applied to the monitoring stations the mean prediction error (MPE) for NO(2) concentrations for all stations and years was -0.8μg/m³ and the root mean squared error (RMSE) was 6.7μg/m³. For PM(10) concentrations the MPE was 0.8μg/m³ and the RMSE was 3.4μg/m³. These results indicate that it is possible to model temporal variation in air pollution through LUR with relatively small prediction errors. It is likely that most previous LUR studies did not include temporal variation, because they were based on short term monitoring campaigns and did not have historic pollution data. The advantage of this study is that it uses data from an air dispersion model, which provided concentrations for 2005 and 2010, and therefore allowed extrapolation over a longer time period.

Modelling air pollution for epidemiologic research--Part I: A novel approach combining land use regression and air dispersion

A common limitation of epidemiological studies on health effects of air pollution is the quality of exposure data available for study participants. Exposure data derived from urban monitoring networks is usually not adequately representative of the spatial variation of pollutants, while personal monitoring campaigns are often not feasible, due to time and cost restrictions. Therefore, many studies now rely on empirical modelling techniques, such as land use regression (LUR), to estimate pollution exposure. However, LUR still requires a quantity of specifically measured data to develop a model, which is usually derived from a dedicated monitoring campaign. A dedicated air dispersion modelling exercise is also possible but is similarly resource and data intensive. This study adopted a novel approach to LUR, which utilised existing data from an air dispersion model rather than monitored data. There are several advantages to such an approach such as a larger number of sites to develop the LUR model compared to monitored data. Furthermore, through this approach the LUR model can be adapted to predict temporal variation as well as spatial variation. The aim of this study was to develop two LUR models for an epidemiologic study based in Greater Manchester by using modelled NO(2) and PM(10) concentrations as dependent variables, and traffic intensity, emissions, land use and physical geography as potential predictor variables. The LUR models were validated through a set aside "validation" dataset and data from monitoring stations. The final models for PM(10) and NO(2) comprised nine and eight predictor variables respectively and had determination coefficients (R²) of 0.71 (PM(10): Adj. R²=0.70, F=54.89, p<0.001, NO(2): Adj. R²=0.70, F=62.04, p<0.001). Validation of the models using the validation data and measured data showed that the R² decreases compared to the final models, except for NO(2) validation in the measured data (validation data: PM(10): R²=0.33, NO(2): R²=0.62; measured data: PM(10): R²=0.56, NO(2): R²=0.86). The validation further showed low mean prediction errors and root mean squared errors for both models.

Serotonin transporter polymorphism, memory and hippocampal volume in the elderly: association and interaction with cortisol

The s allele variant of the serotonin transporter gene (5-HTT) has recently been observed to moderate the relationship of stress to depression and anxiety. To date no study has considered interactive effects of 5-HTT genotype, stress and hypothalamic-pituitary-adrenal (HPA) function on cognition in healthy, older adults, which may reflect developmental, functional or neurodegenerative effects of the serotonin transporter polymorphism. We investigated whether 5-HTT genotype interacts with cumulative life stress and HPA-axis measures of waking and diurnal cortisol slope to impact cognition in 154 non-depressed, older adults. Structural images of hippocampal volume were acquired on a subsample of 56 participants. The 5-HTT s allele was associated with both significantly lower delayed recall and higher waking cortisol levels. Presence of the s allele interacted with higher waking cortisol to negatively impact memory. We also observed a significant interaction of higher waking cortisol and the s allele on lower hippocampal volume. Smaller hippocampi and higher cortisol were associated with lower delayed recall only in s allele carriers. No impact or interactions of cumulative life stress with 5-HTT or cortisol were observed. This is the first investigation to identify an association of the 5-HTT s allele with poorer memory function in older adults. The interactive effects of the s allele and waking cortisol levels on reduced hippocampal volume and lower memory suggest that the negative effect of the serotonin polymorphism on memory is mediated by the HPA axis. Further, given the significant association of the s allele with higher waking cortisol in our investigation, future studies may be needed to evaluate the impact of the serotonin transporter polymorphism on any neuropsychiatric or behavioral outcome which is influenced by HPA axis function in older adults.

A study of the aetiology of pseudopregnancy in the bitch and the effect of cabergoline therapy

Thirty-two permanently pseudopregnant bitches were treated with the anti-prolactin drug cabergoline. They had all been ovariohysterectomised up to five months after their last season, in some cases over two years previously, when most were reported as showing no signs of the condition. The clinical signs were mainly behavioural, the majority being aggressive, and a small number were lactating. The efficiency of the cabergoline therapy was classified by the owners as 'excellent' or 'good' in 50 per cent of the cases, and fair in 36 per cent. The rate of success was markedly better than in similar cases treated with reproductive steroids. In all but one of the bitches, the plasma prolactin concentrations were basal.

Effect and mechanisms of the anti-prolactin drug cabergoline on pseudopregnancy in the bitch

A potent anti-prolactin drug, cabergoline, administered orally for five days, was clinically successful in treating three different clinical manifestations of pseudopregnancy in referred bitches. The clinical conditions treated were categorised as standard pseudopregnant bitches (n = 8), those previously unsuccessfully treated with hormones (n = 10) and those which had behavioural pseudopregnancy following ovariohysterectomy (n = 8). The number of bitches whose owners reported a 'good' response was seven out of eight, six out of 10 and six out of eight, respectively. There were very few side effects in that only one bitch vomited following treatment. The clinical response did not necessarily appear to be related to an alteration in circulating prolactin concentrations, suggesting that the drug may have a direct effect on the tissues as well as in most cases reducing the plasma prolactin concentrations.

Upper eyelid retraction in the absence of other evidence for progressive ophthalmopathy is associated with eye muscle autoantibodies

We have studied 25 clinically euthyroid patients with eyelid lag and retraction referred to thyroid/eye clinic for clinical and orbital imaging evidence of extraocular eye muscle (EM) involvement, evidence of progressive ophthalmopathy and serum antibodies reactive with EM membrane antigens in immunoblotting. Fourteen patients had Graves' hyperthyroidism, 5 had Hashimoto's thyroiditis, and 6 had euthyroid Graves' disease. By carrying out orbital imaging we showed EM abnormalities in 10 of 23 patients (43%). Serum antibodies reactive with EM membrane antigens were detected in 96% of patients. Antibodies reactive with a 64-kDa antigen were detected in 66% of patients, while those reactive with 35-, 55-, and 95-kDa antigens were found in 21, 33, and 25% of patients, respectively. Antibody prevalences compared to normals were significantly different (P < 0.005) only for the 64-kDa protein. The prevalence and the degree of reactivity of 64-kDa antibodies were significantly different in patients with abnormal EM compared to those with normal EM at orbital imaging (P < 0.04 and P < 0.01, respectively). The results of this work suggest that in some patients inflammation of the eyelid muscles may be an isolated feature of ophthalmopathy and remains as the only sign of a "subclinical" eye disease in patients with thyroid autoimmunity.

Relief of subglottic stenosis by anterior cricoid resection: an operation for the difficult case

Anterior cricoid resection is an effective procedure to relieve subglottic stenosis. This is well documented in adults, although reports of the procedure in growing airways are limited. Over an 11-year period, seven pediatric patients underwent anterior cricoid resection for recalcitrant subglottic stenosis. In four patients, the stricture was secondary to prolonged intubation, one developed subglottic stenosis following a high placement of tracheostomy for epiglottitis and another had congenital subglottic stenosis. One child had subglottic stenosis combined with laryngotracheoesophageal cleft and more distally located tracheoesophageal fistula. All patients had failed to respond to previous treatment: dilatations (3 to 20), steroid injection (3 patients), and Evan's tracheoplasty (2 patients). All patients had an excellent result from anterior cricoid resection. The median age of children undergoing anterior cricoid resection was 3 years. There was no mortality. Tracheostomy decannulation was accomplished within 12 weeks following operation in all patients. It was necessary to remove a tracheal granuloma in one patient. Anterior cricoid wedge resection leaving the posterior portion of the cricoid in place is done to avoid recurrent nerve injury. It is a relatively simple and effective procedure. There has been minimal morbidity and no mortality. Follow-up from 1 to 11 years shows no recurrence of stenosis. There has been normal laryngeal and airway growth.

Cerebral specialization in young adults with Down syndrome

Adults with and without Down syndrome performed a rapid unimanual finger-tapping task alone and while sound-shadowing high frequency words. For male subjects, the concurrent speech disrupted right-hand, but not left-hand performance. Females suffered finger-tapping decrements in both hands in the dual-task situation. These results provide no evidence for reverse (right hemisphere) lateralization of speech in individuals with Down syndrome.

Portal vein ultrasonography in the early diagnosis of necrotizing enterocolitis

The nonoperative diagnosis of necrotizing enterocolitis (NEC) is dependent upon the radiographic finding of pneumatosis intestinalis. A significant number of neonates develop clinical signs compatible with NEC but nondiagnostic radiographs. This can result in delayed, inappropriate, or unnecessary therapy. This paper presents experience with portal vein (PV) ultrasonography in the diagnosis of NEC. Since January 1984, 15 newborns with suspected NEC have undergone PV ultrasonography (mean gestation 33 weeks, mean weight 1,705 g). Each had developed abdominal distention with evidence of sepsis. Stool was positive for occult blood in 11. Abdominal radiographs were interpreted as abnormal but nonspecific in 10 neonates, definite pneumatosis in 3, and normal in 2. No infant had portal vein air on plain abdominal radiograph. Occult PV air was detected by ultrasonography in five infants. These included all infants with obvious pneumatosis, a newborn with a nonspecific radiograph and a neonate with a "normal" x-ray. Of the ten infants without PV air on ultrasound, clinical symptoms resolved without specific therapy in seven. Two infants were proven to have nonenteric sepsis, and the remaining newborn developed intestinal necrosis secondary to aortic thrombus. In the five infants with occult PV air on ultrasound, two subsequently required intestinal resection. The remaining three were treated medically for ten days without sequelae. PV ultrasonography has proven to be a helpful adjunct in the early diagnosis of NEC. This diagnostic maneuver, when applied appropriately, may enable early therapy of the infant with NEC and avoid inappropriate or unnecessary therapy in the suspected case.

Sex differences in dual-task interference between speaking and a manual force-production task

12 male and 12 female right-handed adults performed a unimanual force-production task alone and while sound-shadowing high frequency words. The secondary speech task disrupted right-hand performance by men and left-hand performance by women. The implications of these findings for intrahemisphere-interference models of dual-task performance are discussed.

Tuberculosis of the orbit

Two cases of orbital tuberculosis in white Canadians are reported. The two patients did not suffer from pulmonary tuberculosis, the orbital disease was associated with tuberculosis sinusitis in the first case and blood-borne from constrictive tuberculous pericarditis in the second case. Acid-fast bacilli are difficult to detect in the pathological specimens and the diagnosis is usually based on the following: (1) the positive tuberculin skin test; (2) the caseating granulomatous inflammatory lesion on histopathology, which is highly suggestive of active tuberculosis; (3) the positive culture for Mycobacterium tuberculosis if the specimens are obtained early in the course of the disease; and (4) the complete resolution of the disease with the specific antituberculous medications.

Microtubules in immature oocytes of Xenopus laevis

Previous work indicated that immature oocytes of Xenopus were incapable of assembling microtubules but that competence was achieved during maturation. We report here that small numbers of microtubules do exist in immature oocytes. Consistent with this finding, ultrastructural observations indicate that brain microtubules injected into immature oocytes persist in large numbers for at least 30 min. We report that the tubulin dimers of mature and immature oocytes are equally capable of assembling with brain tubulin in vitro. We confirmed previous results that injection of taxol into immature oocytes has no effect when assayed by light microscopy. However, ultrastructural observations suggest that some microtubule assembly is stimulated by taxol. We tested for the ability of immature oocytes to elongate microtubules from ‘seeds’ by injecting deciliated pellicles of Tetrahymena. No elongation was observed either by light or electron microscopic observation. We conclude that the immature oocyte is capable of very limited microtubule assembly and that a marked increase in assembly competence occurs during maturation. Our data suggest that the change in assembly competence during maturation is due to the release, activation or synthesis of a stimulatory co-factor.

Spatial organization of axonal microtubules

Several workers have found that axonal microtubules have a uniform polarity orientation. It is the "+" end of the polymer that is distal to the cell body. The experiments reported here investigate whether this high degree of organization can be accounted for on the basis of structures or mechanisms within the axon. Substantial depolymerization of axonal microtubules was observed in isolated, postganglionic sympathetic nerve fibers of the cat subjected to cold treatment; generally less than 10% of the original number of microtubules/micron 2 remained in cross section. The number of cold stable MTs that remained was not correlated with axonal area and they were also found within Schwann cells. Microtubules were allowed to repolymerize and the polarity orientation of the reassembled microtubules was determined. In fibers from four cats, a majority of reassembled microtubules returned with the original polarity orientation. However, in no case was the polarity orientation as uniform as the original organization. The degree to which the original orientation returned in a fiber was correlated with the number of cold-stable microtubules in the fiber. We suggest that stable microtubule fragments serve as nucleating elements for microtubule assembly and play a role in the spatial organization of neuronal microtubules. The extremely rapid reassembly of microtubules that we observed, returning to near control levels within the first 5 min, supports microtubule elongation from a nucleus. However, in three of four fibers examined this initial assembly was followed by an equally rapid, but transient decline in microtubule number to a value that was significantly different than the initial peak. This observation is difficult to interpret; however, a similar transient peak has been reported upon repolymerization of spindle microtubules after pressure induced depolymerization.