Designing algorithms to aid discovery by chemical robots

Recently, automated robotic systems have become very efficient, thanks to improved coupling between sensor systems and algorithms, of which the latter have been gaining significance thanks to the increase in computing power over the past few decades. However, intelligent automated chemistry platforms for discovery orientated tasks need to be able to cope with the unknown, which is a profoundly hard problem. In this Outlook, we describe how recent advances in the design and application of algorithms, coupled with the increased amount of chemical data available, and automation and control systems may allow more productive chemical research and the development of chemical robots able to target discovery. This is shown through examples of workflow and data processing with automation and control, and through the use of both well-used and cutting-edge algorithms illustrated using recent studies in chemistry. Finally, several algorithms are presented in relation to chemical robots and chemical intelligence for knowledge discovery

Universal chemical synthesis and discovery with 'The Chemputer'

There is a growing drive in the chemistry community to exploit rapidly growing robotic technologies along with artificial intelligence-based approaches. Applying this to chemistry requires a holistic approach to chemical synthesis design and execution. Here, we outline a universal approach to this problem beginning with an abstract representation of the practice of chemical synthesis that then informs the programming and automation required for its practical realization. Using this foundation to construct closed-loop robotic chemical search engines, we can generate new discoveries that may be verified, optimized, and repeated entirely automatically. These robots can perform chemical reactions and analyses much faster than can be done manually. As such, this leads to a road map whereby molecules can be discovered, optimized, and made on demand from a digital code

A portable 3D printer system for the diagnosis and treatment of multidrug-resistant bacteria

Summary: Multidrug-resistant bacteria are a major threat to human health, but broad-spectrum antibiotics are losing efficacy. There is a need to screen a given drug against a bacterial infection outside of the laboratory. To address this need, we have designed and built an inexpensive and easy-to-use 3D-printer-based system that allows easily readable quantitative tests for the performance of antibacterial drugs. The platform creates a sterile diagnostic device by using 3D printing, and the device is filled automatically with growth medium, and then antibiotics are sprayed onto the medium by ink-jet technology. The sample for testing can be introduced via a fluid port, and the printer hot bed is used to incubate the device, allowing operation in the field. Combining advantages from various established tests of antibacterial performance, this allows the comparison of a specific antibiotics and bacteria. Also, this system can create and test several antibiotic formulations for therapeutic use, and we demonstrate this potential by investigating a mixture of pathogens that are only killed by a mixture of drugs

SARS-Cov-2 viral and serological screening of staff in 31 European fertility units

Study Question: What is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral presence and seroconversion in staff members in European fertility units prior to recommencement of clinical activity? Summary Answer: A large proportion of fertility clinic staff remain susceptible to SARS-CoV-2 with no evidence of seroconversion, indicating that continued comprehensive risk mitigation strategies are essential. What is Known Already: In response to the coronavirus disease 2019 (COVID-19) pandemic, caused by SARS-CoV-2, routine fertility treatment was temporarily stopped in several European countries. The SARS-CoV-2 prevalence and seroconversion in fertility clinic staff, who are at potentially lower risk than routine healthcare workers, are unknown. Study Design, Size, Duration: This cross-sectional study included 554 staff in 16 European IVF clinics, 13 ultrasound clinics, one diagnostic laboratory and one head office in four European countries (Austria, Denmark, Germany and the UK) between 15 April and 30 June 2020. Participants/Materials, Setting, Methods: There were 554 staff members returning for resumption of clinical activity. Paired nucleic acid amplification tests of oropharyngeal swabs for SARS-CoV-2 and serological testing for SARS-CoV-2 IgG were performed. Main Results and the Role of Chance: Of the 554 staff members tested, 0.19% (95% CI 0.03, 1.10%) had evidence of SARS-CoV-2 as detected by RT-PCR. In contrast, 23 staff members, i.e. 4.15% (95% CI 2.78, 6.15%), had antibodies against SARS-CoV-2, with a wide range of antibody titres. There was no evidence of differences in seroconversion between countries with estimates ranging from 2.78% (95% CI 0.77, 9.58) in Austria to 6.75% (95% CI 4.46, 10.1) for the UK. There was no strong evidence of clustering within the clinics, with 21 of the 30 facilities having no staff members affected (prevalence estimates ranging from 0% to 35%), and one clinic having seven staff members affected (35% (95% CI 18.1%, 56.7%)). The single staff member who tested positive for SARS-CoV-2 virus was in the pre-symptomatic phase and was isolated, with no contacts having evidence of infection on repeat testing. Limitations, Reasons for Caution: This was a cross-sectional study prior to resumption of clinical activity, with repeat testing not undertaken. Wider Implications of the Findings: The low prevalence of seroconversion of fertility clinic staff highlights the need for continued comprehensive risk mitigation strategies and engagement with national endeavours to identify and isolate new cases and their contacts as we embark on the resumption of fertility services. Study Funding/Competing Interest(s): The Fertility Partnership funded the study. S.M.N. reports personal fees from Access Fertility, personal fees from Merck, personal fees from Ferring, grants and personal fees from Roche Diagnostics, personal fees from The Fertility Partnership and personal fees from Modern Fertility, outside the submitted work. T.C. reports personal fees from Merck and personal fees from Ferring, outside the submitted work. G.T. reports personal fees from Merck, personal fees from Ferring and personal fees from Roche Diagnostics, outside the submitted work. S.E. and P.S.G. report no conflicts of interest

Integrated synthesis of nucleotide and nucleosides influenced by amino acids

Research on prebiotic chemistry and the origins of nucleic acids and proteins has traditionally been focussed on only one or the other. However, if nucleotides and amino acids co-existed on the early Earth, their mutual interactions and reactivity should be considered explicitly. Here we set out to investigate nucleotide/nucleoside formation by simple dehydration reactions of constituent building blocks (sugar, phosphate, and nucleobase) in the presence of different amino acids. We demonstrate the simultaneous formation of glycosidic bonds between ribose, purines, and pyrimidines under mild conditions without catalysts or activated reagents, as well as nucleobase exchange, in addition to the simultaneous formation of nucleotide and nucleoside isomers from several nucleobases. Clear differences in the distribution of glycosylation products are observed when glycine is present. This work demonstrates that reaction networks of nucleotides and amino acids should be considered when exploring the emergence of catalytic networks in the context of molecular evolution

Association of epidural analgesia in women in labor with neonatal and childhood outcomes in a population cohort

Importance: Although use of epidural analgesia during labor is safe, detailed information about its association with neonatal and child outcomes is limited. Objective: To investigate the association of labor epidural analgesia with neonatal outcomes and childhood development during the first 1000 days of life. Design, Setting, and Participants: This population-based cohort study used Scottish National Health Service hospital administrative data of all 435 281 singleton live births in Scotland between January 1, 2007, and December 31, 2016, with follow-up over the first 1000 days of life. All 435 281 mother-infant pairs delivering between 24 weeks 0 days and 43 weeks 6 days’ gestation who were in active labor with cephalic presentation and who delivered vaginally or via unplanned cesarean delivery were included. Stillbirths and infants with known congenital anomalies were excluded. Data were analyzed between August 1, 2020, and July 23, 2021. Exposures: Epidural analgesia in labor. Main Outcomes and Measures: Neonatal outcomes included resuscitation, Apgar score less than 7 at 5 minutes, and neonatal unit admission. Childhood development measures (gross and fine motor function, communication, and social functioning) were obtained from standardized national childhood surveillance assessments performed at 2 years. Results: This study included a total of 435 281 live births with cephalic presentation in labor (median gestational age at delivery, 40 weeks [IQR, 39-41 weeks]; 221 153 male infants [50.8%]), of which 94 323 (21.7%) had labor epidural. Epidural analgesia was associated with a reduction in spontaneous vaginal deliveries (confounder-adjusted [Cadj] relative risk [RR], 0.46; 95% CI, 0.42-0.50), an increased risk of neonatal resuscitation (Cadj RR, 1.07; 95% CI, 1.03-1.11), and an increased risk of neonatal unit admission (Cadj RR, 1.14; 95% CI, 1.11-1.17). With additional analysis for mediation by mode of delivery (CMadj), these associations were reversed (CMadj RR, 0.83; 95% CI, 0.79-0.86 for neonatal resuscitation and CMadj RR, 0.94; 95% CI, 0.91-0.97 for neonatal unit admission). Epidural analgesia was associated with a reduced risk of an Apgar score less than 7 at 5 minutes in both confounder and confounder/mediation analyses. Epidural analgesia was associated with a reduced risk of having developmental concern in any domain at 2 years in confounder and confounder/mediation analyses (CMadj RR, 0.96; 95% CI, 0.93-0.98), with specifically fewer concerns regarding communication (CMadj RR, 0.96; 95% CI, 0.93-0.99) and fine motor skills (CMadj RR, 0.89; 95% CI, 0.82-0.97). Conclusions and Relevance: The results of this cohort study suggest that labor epidural analgesia is not independently associated with adverse neonatal or childhood development outcomes. Associations with neonatal resuscitation and admission were likely mediated by mode of delivery

Environmental control programs the emergence of distinct functional ensembles from unconstrained chemical reactions

Many approaches to the origin of life focus on how the molecules found in biology might be made in the absence of biological processes, from the simplest plausible starting materials. Another approach could be to view the emergence of the chemistry of biology as process whereby the environment effectively directs “primordial soups” toward structure, function, and genetic systems over time. This does not require the molecules found in biology today to be made initially, and leads to the hypothesis that environment can direct chemical soups toward order, and eventually living systems. Herein, we show how unconstrained condensation reactions can be steered by changes in the reaction environment, such as order of reactant addition, and addition of salts or minerals. Using omics techniques to survey the resulting chemical ensembles we demonstrate there are distinct, significant, and reproducible differences between the product mixtures. Furthermore, we observe that these differences in composition have consequences, manifested in clearly different structural and functional properties. We demonstrate that simple variations in environmental parameters lead to differentiation of distinct chemical ensembles from both amino acid mixtures and a primordial soup model. We show that the synthetic complexity emerging from such unconstrained reactions is not as intractable as often suggested, when viewed through a chemically agnostic lens. An open approach to complexity can generate compositional, structural, and functional diversity from fixed sets of simple starting materials, suggesting that differentiation of chemical ensembles can occur in the wider environment without the need for biological machinery

Neonatal and early childhood outcomes following maternal anesthesia for cesarean section: a population-based cohort study

Background: The fetus is vulnerable to maternal drug exposure. We determined associations of exposure to spinal, epidural, or general anesthesia on neonatal and childhood development outcomes during the first 1000 days of life. Methods: Population-based study of all singleton, cesarean livebirths of 24+0 to 43+6 weeks gestation between January 2007 and December 2016 in Scotland, stratified by urgency with follow-up to age 2 years. Models were adjusted for: maternal age, weight, ethnicity, socioeconomic status, smoking, drug-use, induction, parity, previous cesarean or abortion, pre-eclampsia, gestation, birth weight, and sex. Results: 140 866 mothers underwent cesarean section (41.2% (57,971/140,866) elective, 58.8% (82,895/140,866) emergency) with general anesthesia used in 3.2% (1877/57,971) elective and 9.8% (8158/82,895) of emergency cases. In elective cases, general anesthesia versus spinal was associated with: neonatal resuscitation (crude event rate 16.2% vs 1.9% (adjusted RR 8.20, 95% CI 7.20 to 9.33), Apgar <7 at 5 min (4.6% vs 0.4% (adjRR 11.44, 95% CI 8.88 to 14.75)), and neonatal admission (8.6% vs 4.9% (adjRR 1.65, 95% CI 1.40 to 1.94)). Associations were similar in emergencies; resuscitation (32.2% vs 12.3% (adjRR 2.40, 95% CI 2.30 to 2.50)), Apgar <7 (12.6% vs 2.8% (adjRR 3.87, 95% CI 3.56 to 4.20), and admission (31.6% vs 19.9% (adjRR 1.20, 95% CI 1.15 to 1.25). There was a weak association between general anesthesia in emergency cases and having ≥1 concern noted in developmental assessment at 2 years (21.0% vs 16.5% (adjRR 1.08, 95% CI 1.01 to 1.16)). Conclusions: General anesthesia for cesarean section, irrespective of urgency, is associated with neonatal resuscitation, low Apgar, and neonatal unit admission. Associations were strongest in non-urgent cases and at term. Further evaluation of long-term outcomes is warranted

Population implications of cessation of IVF during the COVID-19 pandemic

Research question: Discontinuation of IVF cycles has been part of the radical transformation of healthcare provision to enable reallocation of staff and resources to deal with the COVID-19 pandemic. This study sought to estimate the impact of cessation of treatment on individual prognosis and US population live birth rates. Design: Data from 271,438 ovarian stimulation UK IVF cycles was used to model the effect of age as a continuous, yet non-linear, function on cumulative live birth rate. This model was recalibrated to cumulative live birth rates reported for the 135,673 stimulation cycles undertaken in the USA in 2016, with live birth follow-up to October 2018. The effect of a 1-month, 3-month and 6-month shutdown in IVF treatment was calculated as the effect of the equivalent increase in a woman's age, stratified by age group. Results: The average reduction in cumulative live birth rate would be 0.3% (95% confidence interval [CI] 0.3–0.3), 0.8% (95% CI 0.8–0.8) and 1.6% (95% CI 1.6–1.6) for 1-month, 3-month and 6-month shutdowns. This corresponds to a reduction of 369 (95% CI 360–378), 1098 (95% CI 1071–1123) and 2166 (95% CI 2116–2216) live births in the cohort, respectively. Th e greatest contribution to this reduction was from older mothers. Conclusions: The study demonstrated that the discontinuation of fertility treatment for even 1 month in the USA could result in 369 fewer women having a live birth, due to the increase in patients’ age during the shutdown. As a result of reductions in cumulative live birth rate, more cycles may be required to overcome infertility at individual and population levels

Identifying molecules as biosignatures with assembly theory and mass spectrometry

The search for alien life is hard because we do not know what signatures are unique to life. We show why complex molecules found in high abundance are universal biosignatures and demonstrate the first intrinsic experimentally tractable measure of molecular complexity, called the molecular assembly index (MA). To do this we calculate the complexity of several million molecules and validate that their complexity can be experimentally determined by mass spectrometry. This approach allows us to identify molecular biosignatures from a set of diverse samples from around the world, outer space, and the laboratory, demonstrating it is possible to build a life detection experiment based on MA that could be deployed to extraterrestrial locations, and used as a complexity scale to quantify constraints needed to direct prebiotically plausible processes in the laboratory. Such an approach is vital for finding life elsewhere in the universe or creating de-novo life in the lab