Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies

Although the therapeutic efficacy and commercial success of monoclonal antibodies (mAbs) are tremendous, the design and discovery of new candidates remain a time and cost-intensive endeavor. In this regard, progress in the generation of data describing antigen binding and developability, computational methodology, and artificial intelligence may pave the way for a new era of in silico on-demand immunotherapeutics design and discovery. Here, we argue that the main necessary machine learning (ML) components for an in silico mAb sequence generator are: understanding of the rules of mAb-antigen binding, capacity to modularly combine mAb design parameters, and algorithms for unconstrained parameter-driven in silico mAb sequence synthesis. We review the current progress toward the realization of these necessary components and discuss the challenges that must be overcome to allow the on-demand ML-based discovery and design of fit-for-purpose mAb therapeutic candidates.

Individualized VDJ recombination predisposes the available Ig sequence space

The process of recombination between variable (V), diversity (D), and joining (J) immunoglobulin (Ig) gene segments determines an individual's naive Ig repertoire and, consequently, (auto)antigen recognition. VDJ recombination follows probabilistic rules that can be modeled statistically. So far, it remains unknown whether VDJ recombination rules differ between individuals. If these rules differed, identical (auto)antigen-specific Ig sequences would be generated with individual-specific probabilities, signifying that the available Ig sequence space is individual specific. We devised a sensitivity-tested distance measure that enables inter-individual comparison of VDJ recombination models. We discovered, accounting for several sources of noise as well as allelic variation in Ig sequencing data, that not only unrelated individuals but also human monozygotic twins and even inbred mice possess statistically distinguishable immunoglobulin recombination models. This suggests that, in addition to genetic, there is also nongenetic modulation of VDJ recombination. We demonstrate that population-wide individualized VDJ recombination can result in orders of magnitude of difference in the probability to generate (auto)antigen-specific Ig sequences. Our findings have implications for immune receptor-based individualized medicine approaches relevant to vaccination, infection, and autoimmunity.

Causes of death among Syrian children using verbal autopsy

The causes of death in children under five years were studied using a structured verbal autopsy questionnaire. Possible determinants of death were also investigated. About 44% of deaths were among neonates [below 28 days of age] ; the major causes of death in neonates were prematurity [33%] and birth-related factors [30%]. In infants [1-11 months of age], the leading cause of death was congenital malformations [24%]. Accidents were responsible for one-third of deaths in children aged 1-4 years. Factors that might have contributed to death were investigated. The public health importance of causes of death was evaluated and its implications were discussed

Women’s experiences with labor companionship in public facilities in Arab countries

Background

Childbirth in the Arab region is characterized by over-medicalization and inequities in access to-and provision of care. Hospital practices do not provide choices for women and respond to the convenience of providers rather than women’s needs. Provision of maternity care is reflective of existing social inequities which is manifested through mistreatment and disrespect of women within the health care system. One such example lies in the restriction of birth companions in public facilities in Arab countries despite being practiced in private settings and the strong evidence supporting its implementation globally.

Methods

A phased mixed-methods implementation research study was undertaken in three public hospitals in Lebanon, Egypt and Syria with the aim of developing a tailored labor companionship model and evaluating its implementation. Data presented emanate from the qualitative component of the study. Semi-structured interviews were conducted with women giving birth (n = 59) and their labor companions (n = 57) in three facilities. Thematic analysis was used.

Results

Beyond the introduction of the model into the system, women reported improvements in dimensions of respectful maternity care. Changes made in shared labor rooms improved women’s privacy. The presence of labor companions improved communication between health care providers, women and their families. Women reported feeling “dignified” and “strong” in the presence of companions. There was a “feedback loop” from the facility to the community with word spreading about labor companionship “just like in private hospitals”.

Conclusions

The labor companionship model improved equitable access to dignified and respectful maternity care through better rapport between women and health care providers, preservation of women’s privacy and having access to birth companion of choice. The provision of evidence-based care has potential implications on women’s experiences with the health care system.

Key messages

This labor companionship model ensured positive experiences for women giving birth in public facilities in Arab countries. Women perceived the model as type of care that reduces differential treatment based on social status and enhances respectful maternity care.

Hepatitis B and C in the Syrian Arab Republic: a review

This paper reviews the epidemiology and determinants of hepatitis B and C in the Syrian Arab Republic as well as their treatment and prevention. A systematic search of Medline, PubMed and Index Medicus for the Eastern Mediterranean Region was carried out in addition to a review of grey literature and relevant datasets in the Syrian Arab Republic. Low to low-intermediate levels of endemicity of both infections were noted at the national level. However, striking geographic differences and high prevalence among high-risk groups were noticeable. As a result of data limitations, further research is needed, and a national control strategy to combat hepatitis B and C in the Syrian Arab Republic should be developed, especially during the current conflict.

Involving patients in medical education: ethical issues experienced by Syrian patients

INTRODUCTION

Patients' involvement and their willingness to cooperate in clinical teaching is a vital element of medical education. Clinical teaching at the Faculty of Medicine of Damascus University relies heavily on inpatients at teaching hospitals but also on patients brought to teaching rooms. The purpose of this study was to identify patients' experiences and their attitudes toward the involvement of medical students in clinical consultations within teaching rooms conducted mainly for students' benefit.

METHODS

In-depth interviews were carried out by a sociologist using an interview guide with 14 patients whose clinical cases were presented to a large group of students in the teaching room at Damascus University teaching hospitals. Data analysis involved content analysis.

FINDINGS

Main themes were identified with negative ethical aspects, such as the lack of patient's involvement in decision making and approving to be part of clinical teaching. Risk and benefits were experienced by patients and identified in their experiences. Some felt that they were treated inhumanely and with a lack of dignity. Patients nevertheless felt a responsibility to be part of the teaching process. They expressed their positive attitudes towards involvement in the teaching process to serve medical students as well as the greater community.

DISCUSSION

Findings provide perspectives and insights into the current clinical teaching at Damascus University Faculty of Medicine. The findings highlight the need in our institution to carry out medical education involving patients in a more ethical manner. Medical students and their teachers need more training in the ethical involvement of patients in students' learning process, as well as the need to better regulate patients' involvement in education.

Results of the feasibility test of the Practical Approach to Lung Health in the Syrian Arab Republic

We assessed implementation of the Practical Approach to Lung Health (PAL) in primary care facilities in the Syrian Arab Republic and its short-term impact on respiratory care in patients aged 5+ years. After training on PAL for 76 general practitioners in 75 health centres, referrals and sputum smear examinations for patients increased. The mean number of drugs prescribed per patient decreased by 14.8% and that of antibiotics by 33.3%, while prescriptions for inhaled medications increased. The mean cost of drug prescriptions fell by 26.2%.

Patterns and determinants of maternity care in Damascus

This descriptive study was designed to describe the patterns and determinants of maternity care among Syrian women living in Damascus. All 39 birth registers in 2 large provinces were used to recruit 500 mothers of healthy newborns. Mothers were interviewed in their homes using a semistructured questionnaire. Multivariate analysis of the determinants of the frequency of use of antenatal care showed the following variables were significant: urban residence and visit to antenatal care in the 1st trimester. The significant variables for an early visit to antenatal care were the woman's level of education; being pregnant with the 1st baby; and number of visits to antenatal care. Being young (age < 20 years) also correlated with early timing of the 1st antenatal visit.

Community-based study of unintentional injuries among preschool children in Damascus

To assess injuries among 1125 preschool children in Damascus, and to investigate the risk factors, a retrospective home survey of childhood injuries for a period of 12 months was carried out in 4 areas of residence: agricultural rural, non-agricultural rural, periurban and urban. More than 75% of mothers believed that injuries were preventable. During the year preceding the study, 261 injuries were reported, an incidence of 23%. The most frequent injuries were from falls, 52.0%, and most injuries (73.9%) occurred inside the home. Area of residence was the only independent predictor for the occurrence of childhood injuries.

Gender differences and tuberculosis in the Syrian Arab Republic: patients' attitudes, compliance and outcomes

In a prospective study of gender and TB outcomes, 552 newly diagnosed smear-positive patients throughout the Syrian Arab Republic were interviewed at recruitment [from January 2002 to July 2002] and followed until the end of treatment. Delay in diagnosis was significantly longer among males. Significant differences between males and females were noted in relation to the place they usually use to seek care. Gender did not seem to affect knowledge and attitudes of TB patients. Although the women reported more barriers to seeking care, compliance with treatment tended to be higher and the treatment success rate was significantly higher among females than males. Multivariate analysis showed that male sex was a significant predictor of a negative treatment outcome, after controlling for other significant sociodemographic and health care related variables

Gender differences and tuberculosis in the Syrian Arab Republic: patients' attitudes, compliance and outcomes

In a prospective study of gender and TB outcomes, 552 newly diagnosed smear-positive patients throughout the Syrian Arab Republic were interviewed at recruitment (from January 2002 to July 2002) and followed until the end of treatment. Delay in diagnosis was significantly longer among males. Significant differences between males and females were noted in relation to the place they usually use to seek care. Gender did not seem to affect knowledge and attitudes of TB patients. Although the women reported more barriers to seeking care, compliance with treatment tended to be higher and the treatment success rate was significantly higher among females than males. Multivariate analysis showed that male sex was a significant predictor of a negative treatment outcome, after controlling for other significant sociodemographic and health care related variables.

Cost-effectiveness of different treatment strategies for tuberculosis in Egypt and Syria

SETTING

The National Tuberculosis Programmes in Egypt and Syria.

OBJECTIVES

To calculate the costs and effectiveness of alternative ways of implementing TB control in Egypt and Syria, in order to illustrate the factors influencing the cost-effectiveness of TB treatment in middle-income countries.

DESIGN

We compared the costs and cure rates in Egypt and Syria of the World Health Organization recommended directly observed treatment, short-course (DOTS) strategy and alternative strategies. The study included costs both to the health services and to the patient.

RESULTS

In Egypt and Syria, the cost-effectiveness of DOTS implemented through the primary health care (PHC) system was respectively $258 and $243 per patient cured. This compares to a cost per patient cured of $297 (Egypt) and $693 (Syria) for alternative strategies implemented through specialist clinics. In Egypt, when DOTS is implemented through specialist chest clinics it costs $585 per patient cured. Hospitalisation costs either $1490, $1621 or $1699 per patient cured, depending on treatment delivery in the continuation phase.

CONCLUSION

This study demonstrates that the move towards DOTS integrated at the PHC level has substantially improved the effectiveness of TB treatment in Egypt and Syria, without substantially increasing costs. An analysis of the different costs and effectiveness of the variety of TB treatment strategies has enabled both National Tuberculosis Programmes to expand DOTS and implement it in a way that takes into account limited resources and local health systems.

Reasons for underreporting of notifiable diseases by Syrian paediatricians

We investigated reasons for underreporting of notifiable diseases among Syrian paediatricians. Self-administered questionnaires and self-addressed envelopes were sent to all paediatricians listed in the recent records of the Syrian Medical Association. Of 723 questionnaires, 55 were returned by the post office due to an incorrect address. Only 160 questionnaires [23.9%] were answered. Approximately 50% of paediatricians gave two reasons for underreporting: lack of reporting forms and ignorance of reporting telephone numbers. Nearly 70% indicated that the most important improvements would be the availability of easy reporting forms and a condensed and feasible list of notifiable diseases.

Reasons for underreporting of notifiable diseases by Syrian paediatricians

We investigated reasons for underreporting of notifiable diseases among Syrian paediatricians. Self-administered questionnaires and self-addressed envelopes were sent to all paediatricians listed in the recent records of the Syrian Medical Association. Of 723 questionnaires, 55 were returned by the post office due to an incorrect address. Only 160 questionnaires (23.9%) were answered. Approximately 50% of paediatricians gave two reasons for underreporting: lack of reporting forms and ignorance of reporting telephone numbers. Nearly 70% indicated that the most important improvements would be the availability of easy reporting forms and a condensed and feasible list of notifiable diseases.

Hepatitis E in Damascus, Syria

A hospital-based study of acute hepatitis was conducted in Damascus, Syria, from 1995 to 1998. One hundred ninety-three sera from defined acute hepatitis cases were screened by ELISA for IgM anti-HAV, HBsAg, IgM anti-HBc and anti-HCV. Serum samples negative for all markers indicating recent infection by hepatitis A, B, or C were tested for HEV markers. Overall, 47 cases (24.4%) had no detectable hepatitis markers (non-A-E). HAV infection was detected in 71.2% of all viral hepatitis cases. Acute hepatitis B and C constituted 24 and 1.4% of the cases, respectively. Only five cases of acute hepatitis E were noted. Of 47 patients who had non-A-E hepatitis, fifteen (31.9%) tested positive for IgG anti HEV. This study provides indirect evidence that HEV is very likely to be endemic in Damascus, Syria. It reports for the first time the occurrence of hepatitis E in the country, a health problem that should be investigated further.