Survey of Machine Learning Techniques in Drug Discovery

Background:

Drug discovery, which is the process of discovering new candidate medications, is very important for pharmaceutical industries. At its current stage, discovering new drugs is still a very expensive and time-consuming process, requiring Phases I, II and III for clinical trials. Recently, machine learning techniques in Artificial Intelligence (AI), especially the deep learning techniques which allow a computational model to generate multiple layers, have been widely applied and achieved state-of-the-art performance in different fields, such as speech recognition, image classification, bioinformatics, etc. One very important application of these AI techniques is in the field of drug discovery.

Methods:

We did a large-scale literature search on existing scientific websites (e.g, ScienceDirect, Arxiv) and startup companies to understand current status of machine learning techniques in drug discovery.

Results:

Our experiments demonstrated that there are different patterns in machine learning fields and drug discovery fields. For example, keywords like prediction, brain, discovery, and treatment are usually in drug discovery fields. Also, the total number of papers published in drug discovery fields with machine learning techniques is increasing every year.

Conclusion:

The main focus of this survey is to understand the current status of machine learning techniques in the drug discovery field within both academic and industrial settings, and discuss its potential future applications. Several interesting patterns for machine learning techniques in drug discovery fields are discussed in this survey.

Evaluation of complications and feasibility of indwelling epidural catheter use for post-operative pain control in dogs in the home environment

AIMS

The objective of this study was to describe the use of indwelling epidural catheters post-operatively in dogs in a home environment, and to report associated complications.

METHODS

Dogs undergoing surgical procedures of the hind limb (n=83) were included in the study and were administered 0.05 or 0.10 mg/kg epidural morphine via an indwelling epidural catheter every 6 hours. Data compiled relating to catheter placement included time of placement, ease of placement and problems encountered, number of attempts of placement, and individual placing the catheter. A client questionnaire was provided to evaluate side effects, complications, pain, and ease of use of the epidural catheter system after discharge from the hospital and catheter removal at home. Side effects were compared between the dogs receiving 0.05 or 0.1 mg/kg epidural morphine.

RESULTS

The most common patient complication was abnormal urination patterns (32/82, 39%); specifically dribbling urine where laying, emptying the entire bladder where laying, not urinating for extended periods of time, and taking a longer time to pass urine were reported. There were no significant differences in the number or types of side effects reported in either dosing group. The most common technical issues reported by owners were difficulty getting the needle into the injection port (10/81, 12%) and removing the adhesive covering keeping the epidural catheter system in place (19/78, 24%). There were no reports of inflammation or discharge at the catheter site in any of the dogs. Of the respondents surveyed, 76/79 (97%) found the epidural catheter system easy to use at home in the post-operative period.

CONCLUSIONS

Indwelling epidural catheters are a feasible method of administration of post-operative analgesia in the immediate post-operative period in the home environment and were associated with only a few minor complications in this population.

Protein kinase cδ deficiency causes mendelian systemic lupus erythematosus with B cell-defective apoptosis and hyperproliferation

OBJECTIVE

Systemic lupus erythematosus (SLE) is a prototype autoimmune disease that is assumed to occur via a complex interplay of environmental and genetic factors. Rare causes of monogenic SLE have been described, providing unique insights into fundamental mechanisms of immune tolerance. The aim of this study was to identify the cause of an autosomal-recessive form of SLE.

METHODS

We studied 3 siblings with juvenile-onset SLE from 1 consanguineous kindred and used next-generation sequencing to identify mutations in the disease-associated gene. We performed extensive biochemical, immunologic, and functional assays to assess the impact of the identified mutations on B cell biology.

RESULTS

We identified a homozygous missense mutation in PRKCD, encoding protein kinase δ (PKCδ), in all 3 affected siblings. Mutation of PRKCD resulted in reduced expression and activity of the encoded protein PKCδ (involved in the deletion of autoreactive B cells), leading to resistance to B cell receptor- and calcium-dependent apoptosis and increased B cell proliferation. Thus, as for mice deficient in PKCδ, which exhibit an SLE phenotype and B cell expansion, we observed an increased number of immature B cells in the affected family members and a developmental shift toward naive B cells with an immature phenotype.

CONCLUSION

Our findings indicate that PKCδ is crucial in regulating B cell tolerance and preventing self-reactivity in humans, and that PKCδ deficiency represents a novel genetic defect of apoptosis leading to SLE.

A launch vector for the production of vaccine antigens in plants

Historically, most vaccines have been based on killed or live-attenuated infectious agents. Although very successful at immunizing populations against disease, both approaches raise safety concerns and often have limited production capacity. This has resulted in increased emphasis on the development of subunit vaccines. Several recombinant systems have been considered for subunit vaccine manufacture, including plants, which offer advantages both in cost and in scale of production. We have developed a plant expression system utilizing a 'launch vector', which combines the advantageous features of standard agrobacterial binary plasmids and plant viral vectors, to achieve high-level target antigen expression in plants. As an additional feature, to aid in target expression, stability and purification, we have engineered a thermostable carrier molecule to which antigens are fused. We have applied this launch vector/carrier system to engineer and express target antigens from various pathogens, including, influenza A/Vietnam/04 (H5N1) virus.

Effects of disruption of epiphyseal vasculature on the proximal femoral growth plate

BACKGROUND

Proximal femoral growth disturbance is a major complication associated with ischemic osteonecrotic conditions, such as Legg-Calvè-Perthes disease. The extent of ischemic damage and the mechanisms by which ischemic injury to the growing femoral head produces growth disturbance of the proximal femoral growth plate remain unclear. The purpose of this study was to investigate the effects of disruption of the epiphyseal vasculature on the morphology and function of the proximal femoral growth plate in a porcine model.

METHODS

Ischemic osteonecrosis of the femoral head was surgically induced in sixty-five piglets by placing a ligature tightly around the femoral neck. Radiographic, histological, micro-computed tomographic, cellular viability, hypoxia marker, and cellular proliferation studies were performed.

RESULTS

Disruption of the epiphyseal vasculature did not lead to diffuse growth plate damage in the majority of the ischemic femoral heads. One of the twelve femoral heads analyzed at four weeks and six of the twenty-six femoral heads analyzed at eight weeks had severe disruption of the growth plate that precluded histological assessment of the growth plate zones. In the remaining animals, the proximal part of the femur continued to elongate following induction of ischemia, albeit at a slower rate than on the normal side. Histologically, normal developmental thinning of the growth plate was seen to be absent on the ischemic side. Severe hypoxia and cellular death were limited to the area of the growth plate bordering on the infarcted osseous epiphysis. Normal chondrocytic organization and continued proliferation were observed in the proliferative zone of the growth plate.

CONCLUSIONS

In our porcine model, the proximal femoral growth plate was not diffusely damaged following disruption of the epiphyseal vasculature in the majority of the ischemic femoral heads. The majority of the growth plates remained viable and were able to function despite total disruption of the epiphyseal vasculature. These findings suggest that the source of nutrition for the proximal femoral growth plate is not solely the epiphyseal vasculature as has been traditionally believed.

Hospital doctors' assessment of baseline spirometry

Baseline spirometry is useful in diagnosing and managing pulmonary disease. In a questionnaire survey of 100 hospital doctors in two hospitals in the Mersey region, their views and ability to interpret baseline spirometry was assessed. Of the 70 doctors who responded, 65% felt they could accurately interpret baseline spirometry. However, only 12% accurately interpreted all five vitalographs in the questionnaire. The majority (72%) felt they had not had adequate teaching in interpretation of spirometry, and 63% would prefer a report from a respiratory technician. These result suggest that improvement needs to be made in interpretation of baseline spirometry.

Protein binding and serum bactericidal activities of vancomycin and teicoplanin

In a randomized crossover study, the protein binding and serum bactericidal activities (SBAs) of vancomycin and teicoplanin against Staphylococcus aureus and Streptococcus pyogenes were investigated in six healthy volunteers. Total concentrations in serum 1 h postadministration of vancomycin and teicoplanin were 25.5 +/- 2.7 and 10.8 +/- 8.9 mg/liter, respectively; mean free concentrations were 14.6 +/- 2.0 and 0.6 +/- 0.9 mg/liter, respectively. Protein binding for vancomycin was 36.9% +/- 2.87%, and that for teicoplanin was 97.4% +/- 2.6%. SBA determined in pooled human serum at 1 h against S. aureus ranged from 1:8 to 1:32 for both vancomycin and teicoplanin. Against S. pyogenes SBA at 1 h ranged from 1:16 to 1:128 for vancomycin and 1:256 to 1:2,048 for teicoplanin. In vitro kill curve studies showed that vancomycin is slowly bactericidal and that teicoplanin is bacteriostatic. Despite having less in vitro cidal activity against the study isolates and having low or unrecordable levels of free drug in serum, teicoplanin demonstrated a similar or better SBA than vancomycin. SBA was more closely related to the total drug level (r = 0.77 for S. aureus and r = 0.79 for S. pyogenes) than the free level of teicoplanin (r = 0.59 for S. aureus and r = 0.56 for S. pyogenes). The high level of protein binding of teicoplanin did not seem to impair its antibacterial activity as measured by its SBA.

CT appearances of rounded atelectasis

Five patients examined with CT had lesions fulfilling criteria for a diagnosis of rounded atelectasis (RA) and these were managed without biopsy. In three patients unsuspected contralateral lesions were identified as RA variants, and one of these was biopsied at thoracotomy and proved to be benign. All patients remain well at 6-22 months follow-up. We concur with recent reports that there is a spectrum of CT appearances of RA and that even atypical lesions seldom need further investigation. We also suggest that the appearances of some atypical lesions add support for the fibrosing theory of pathogenesis of RA.

Applications of multidimensional computer graphics in medical systems

Multidimensional computer graphics are demonstrated in two medical systems applications in this paper. First, multidimensional computer graphics are utilized for descriptive purposes to show the differences among 10 physician specialty groups for multivariate data available at admission to medical school. Second, multidimensional computer graphics are demonstrated as a method that can be used for screening school applicants. The novel method utilized to represent multivariate data requires the plotting of a face. Each feature of a face--for example, face height or ear diameter-can be utilized to represent a different dimension of multivariate data. Each face then represents a vector whose elements are the mean values of multiple variables, or it represents a multivariate observation.