A window to the world of global insect declines: Moth biodiversity trends are complex and heterogeneous.

Moths are the most taxonomically and ecologically diverse insect taxon for which there exist considerable time-series abundance data. There is an alarming record of decreases in moth abundance and diversity from across Europe, with rates varying markedly among and within regions. Recent reports from Costa Rica reveal steep cross-lineage declines of caterpillars, while other sites (Ecuador and Arizona, reported here) show no or only modest long-term decreases over the past two decades. Rates of decline for dietary and ecological specialists are steeper than those for ecologically generalized taxa. Additional traits commonly associated with elevated risks include large wingspans, small geographic ranges, low dispersal ability, and univoltinism; taxa associated with grasslands, aridlands, and nutrient-poor habitats also appear to be at higher risk. In temperate areas, many moth taxa limited historically by abiotic factors are increasing in abundance and range. We regard the most important continental-scale stressors to include reductions in habitat quality and quantity resulting from land-use change and climate change and, to a lesser extent, atmospheric nitrification and introduced species. Site-specific stressors include pesticide use and light pollution. Our assessment of global macrolepidopteran population trends includes numerous cases of both region-wide and local losses and studies that report no declines. Spatial variation of reported losses suggests that multiple stressors are in play. With the exception of recent reports from Costa Rica, the most severe examples of moth declines are from Northern Hemisphere regions of high human-population density and intensive agriculture.

Precipitation buffers temperature-driven local extinctions of moths at warm range margins.

Species' distributions are moving polewards in response to climate change, and although range expansions of relatively warm-adapted species are widely reported, reports of range retractions in cool-adapted species are less common. Here, we analysed species' distribution shifts for 76 cool-adapted moths in Great Britain using citizen science occurrence records from the National Moth Recording Scheme over a 40-year period. Although we find evidence for trailing edge shifts to higher latitudes, shifts in species' range centroids are oriented towards the north-west, and are more closely correlated with directional changes in total precipitation than average temperature. We also found that species' local extinction risk is higher in areas where temperature is high and precipitation is low, but this risk diminishes as precipitation increases. Adaptation efforts should therefore focus on maintaining or increasing water availability as the climate continues to change.

Optimizing the strain engineering process for industrial-scale production of bio-based molecules.

Biomanufacturing could contribute as much as ${\$}$30 trillion to the global economy by 2030. However, the success of the growing bioeconomy depends on our ability to manufacture high-performing strains in a time- and cost-effective manner. The Design-Build-Test-Learn (DBTL) framework has proven to be an effective strain engineering approach. Significant improvements have been made in genome engineering, genotyping, and phenotyping throughput over the last couple of decades that have greatly accelerated the DBTL cycles. However, to achieve a radical reduction in strain development time and cost, we need to look at the strain engineering process through a lens of optimizing the whole cycle, as opposed to simply increasing throughput at each stage. We propose an approach that integrates all 4 stages of the DBTL cycle and takes advantage of the advances in computational design, high-throughput genome engineering, and phenotyping methods, as well as machine learning tools for making predictions about strain scale-up performance. In this perspective, we discuss the challenges of industrial strain engineering, outline the best approaches to overcoming these challenges, and showcase examples of successful strain engineering projects for production of heterologous proteins, amino acids, and small molecules, as well as improving tolerance, fitness, and de-risking the scale-up of industrial strains.

Population Bottlenecks Strongly Affect the Evolutionary Dynamics of Antibiotic Persistence.

Bacterial persistence is a potential cause of antibiotic therapy failure. Antibiotic-tolerant persisters originate from phenotypic differentiation within a susceptible population, occurring with a frequency that can be altered by mutations. Recent studies have proven that persistence is a highly evolvable trait and, consequently, an important evolutionary strategy of bacterial populations to adapt to high-dose antibiotic therapy. Yet, the factors that govern the evolutionary dynamics of persistence are currently poorly understood. Theoretical studies predict far-reaching effects of bottlenecking on the evolutionary adaption of bacterial populations, but these effects have never been investigated in the context of persistence. Bottlenecking events are frequently encountered by infecting pathogens during host-to-host transmission and antibiotic treatment. In this study, we used a combination of experimental evolution and barcoded knockout libraries to examine how population bottlenecking affects the evolutionary dynamics of persistence. In accordance with existing hypotheses, small bottlenecks were found to restrict the adaptive potential of populations and result in more heterogeneous evolutionary outcomes. Evolutionary trajectories followed in small-bottlenecking regimes additionally suggest that the fitness landscape associated with persistence has a rugged topography, with distinct trajectories toward increased persistence that are accessible to evolving populations. Furthermore, sequencing data of evolved populations and knockout libraries after selection reveal various genes that are potentially involved in persistence, including previously known as well as novel targets. Together, our results do not only provide experimental evidence for evolutionary theories, but also contribute to a better understanding of the environmental and genetic factors that guide bacterial adaptation to antibiotic treatment.

Cabin air quality on non-smoking commercial flights: A review of published data on airborne pollutants.

We reviewed 47 documents published 1967-2019 that reported measurements of volatile organic compounds (VOCs) on commercial aircraft. We compared the measurements with the air quality standards and guidelines for aircraft cabins and in some cases buildings. Average levels of VOCs for which limits exist were lower than the permissible levels except for benzene with average concentration at 5.9 ± 5.5 µg/m3 . Toluene, benzene, ethylbenzene, formaldehyde, acetaldehyde, limonene, nonanal, hexanal, decanal, octanal, acetic acid, acetone, ethanol, butanal, acrolein, isoprene and menthol were the most frequently measured compounds. The concentrations of semi-volatile organic compounds (SVOCs) and other contaminants did not exceed standards and guidelines in buildings except for the average NO2 concentration at 12 ppb. Although the focus was on VOCs, we also retrieved the data on other parameters characterizing cabin environment. Ozone concentration averaged 38 ppb below the upper limit recommended for aircraft. The outdoor air supply rate ranged from 1.7 to 39.5 L/s per person and averaged 6.0 ± 0.8 L/s/p (median 5.8 L/s/p), higher than the minimum level recommended for commercial aircraft. Carbon dioxide concentration averaged 1315 ± 232 ppm, lower than what is permitted in aircraft and close to what is permitted in buildings. Measured temperatures averaged 23.5 ± 0.8°C and were generally within the ranges recommended for avoiding thermal discomfort. Relative humidity averaged 16% ± 5%, lower than what is recommended in buildings.

Capecitabine compared with observation in resected biliary tract cancer (BILCAP): a randomised, controlled, multicentre, phase 3 study.

BACKGROUND: Despite improvements in multidisciplinary management, patients with biliary tract cancer have a poor outcome. Only 20% of patients are eligible for surgical resection with curative intent, with 5-year overall survival of less than 10% for all patients. To our knowledge, no studies have described a benefit of adjuvant therapy. We aimed to determine whether adjuvant capecitabine improved overall survival compared with observation following surgery for biliary tract cancer. METHODS: This randomised, controlled, multicentre, phase 3 study was done across 44 specialist hepatopancreatobiliary centres in the UK. Eligible patients were aged 18 years or older and had histologically confirmed cholangiocarcinoma or muscle-invasive gallbladder cancer who had undergone a macroscopically complete resection (which includes liver resection, pancreatic resection, or, less commonly, both) with curative intent, and an Eastern Cooperative Oncology Group performance status of less than 2. Patients who had not completely recovered from previous surgery or who had previous chemotherapy or radiotherapy for biliary tract cancer were also excluded. Patients were randomly assigned 1:1 to receive oral capecitabine (1250 mg/m2 twice daily on days 1-14 of a 21-day cycle, for eight cycles) or observation commencing within 16 weeks of surgery. Treatment was not masked, and allocation concealment was achieved with a computerised minimisation algorithm that stratified patients by surgical centre, site of disease, resection status, and performance status. The primary outcome was overall survival. As prespecified, analyses were done by intention to treat and per protocol. This study is registered with EudraCT, number 2005-003318-13. FINDINGS: Between March 15, 2006, and Dec 4, 2014, 447 patients were enrolled; 223 patients with biliary tract cancer resected with curative intent were randomly assigned to the capecitabine group and 224 to the observation group. The data cutoff for this analysis was March 6, 2017. The median follow-up for all patients was 60 months (IQR 37-60). In the intention-to-treat analysis, median overall survival was 51·1 months (95% CI 34·6-59·1) in the capecitabine group compared with 36·4 months (29·7-44·5) in the observation group (adjusted hazard ratio [HR] 0·81, 95% CI 0·63-1·04; p=0·097). In a protocol-specified sensitivity analysis, adjusting for minimisation factors and nodal status, grade, and gender, the overall survival HR was 0·71 (95% CI 0·55-0·92; p=0·010). In the prespecified per-protocol analysis (210 patients in the capecitabine group and 220 in the observation group), median overall survival was 53 months (95% CI 40 to not reached) in the capecitabine group and 36 months (30-44) in the observation group (adjusted HR 0·75, 95% CI 0·58-0·97; p=0·028). In the intention-to-treat analysis, median recurrence-free survival was 24·4 months (95% CI 18·6-35·9) in the capecitabine group and 17·5 months (12·0-23·8) in the observation group. In the per-protocol analysis, median recurrence-free survival was 25·9 months (95% CI 19·8-46·3) in the capecitabine group and 17·4 months (12·0-23·7) in the observation group. Adverse events were measured in the capecitabine group only, and of the 213 patients who received at least one cycle, 94 (44%) had at least one grade 3 toxicity, the most frequent of which were hand-foot syndrome in 43 (20%) patients, diarrhoea in 16 (8%) patients, and fatigue in 16 (8%) patients. One (<1%) patient had grade 4 cardiac ischaemia or infarction. Serious adverse events were observed in 47 (21%) of 223 patients in the capecitabine group and 22 (10%) of 224 patients in the observation group. No deaths were deemed to be treatment related. INTERPRETATION: Although this study did not meet its primary endpoint of improving overall survival in the intention-to-treat population, the prespecified sensitivity and per-protocol analyses suggest that capecitabine can improve overall survival in patients with resected biliary tract cancer when used as adjuvant chemotherapy following surgery and could be considered as standard of care. Furthermore, the safety profile is manageable, supporting the use of capecitabine in this setting. FUNDING: Cancer Research UK and Roche.

Using prognostic and predictive clinical features to make personalised survival prediction in advanced hepatocellular carcinoma patients undergoing sorafenib treatment.

BACKGROUND: Sorafenib is the current standard of care for patients with advanced hepatocellular carcinoma (aHCC) and has been shown to improve survival by about 3 months compared to placebo. However, survival varies widely from under three months to over two years. The aim of this study was to build a statistical model that allows personalised survival prediction following sorafenib treatment. METHODS: We had access to 1130 patients undergoing sorafenib treatment for aHCC as part of the control arm for two phase III randomised clinical trials (RCTs). A multivariable model was built that predicts survival based on baseline clinical features. The statistical approach permits both group-level risk stratification and individual-level survival prediction at any given time point. The model was calibrated, and its discrimination assessed through Harrell's c-index and Royston-Sauerbrei's R2D. RESULTS: The variables influencing overall survival were vascular invasion, age, ECOG score, AFP, albumin, creatinine, AST, extra-hepatic spread and aetiology. The model-predicted survival very similar to that observed. The Harrell's c-indices for training and validation sets were 0.72 and 0.70, respectively indicating good prediction. CONCLUSIONS: Our model ('PROSASH') predicts patient survival using baseline clinical features. However, it will require further validation in a routine clinical practice setting.

Ramsey-Bordé Matter-Wave Interferometry for Laser Frequency Stabilization at 10

We demonstrate Ramsey-Bordé (RB) atom interferometry for high performance laser stabilization with fractional frequency instability <2×10^{-16} for timescales between 10 and 1000s. The RB spectroscopy laser interrogates two counterpropagating ^{40}Ca beams on the ^{1}S_{0}-^{3}P_{1} transition at 657 nm, yielding 1.6 kHz linewidth interference fringes. Fluorescence detection of the excited state population is performed on the (4s4p) ^{3}P_{1}-(4p^{2}) ^{3}P_{0} transition at 431 nm. Minimal thermal shielding and no vibration isolation are used. These stability results surpass performance from other thermal atomic or molecular systems by 1 to 2 orders of magnitude, and further improvements look feasible.

C-H Arylation in the Formation of a Complex Pyrrolopyridine, the Commercial Synthesis of the Potent JAK2 Inhibitor, BMS-911543.

The development of an improved short and efficient commercial synthesis of the JAK2 inhibitor, a complex pyrrolopyridine, BMS-911543, is described. During the discovery and development of this synthesis, a Pd-catalyzed C-H functionalization was invented which enabled the rapid union of the key pyrrole and imidazole fragments. The synthesis of this complex, nitrogen-rich heterocycle was accomplished in only six steps (longest linear sequence) from readily available materials.

Understanding the Efficiency of Splenic Hemangiosarcoma Diagnosis Using Monte Carlo Simulations.

Hemangiosarcoma is a common neoplasm of the spleen in older dogs. However, diagnosis is complicated by necrosis and hemorrhage, which can mimic a number of benign processes. Currently, there is no consensus about the number of sections pathologists should examine to rule out hemangiosarcoma. To answer this question, we examined 413 histopathologic sections from 50 cases of canine hemangiosarcoma (mean: 8.1 sections per case; range, 5-14). Each section had the presence or absence of hemangiosarcoma determined by 2 board-certified anatomic pathologists. Then, 100 Monte Carlo simulations were performed, randomly selecting sections from each case 10 000 times and the results averaged. These simulations suggest that examination of 5 sections from a spleen with hemangiosarcoma yields a 95.02% chance of diagnosing hemangiosarcoma, while examination of 10 sections yields a 98.59% chance of diagnosis when hemangiosarcoma is in fact present. The data emphasize the need to submit the entire spleen for histopathologic examination in suspected cases of hemangiosarcoma and suggest that 5 sections obtained by a trained individual are likely sufficient for diagnosis.

Strategy To Prepare 3-Bromo- and 3-Chloropyrazoles.

A general strategy to prepare substituted 3-bromo- and 3-chloropyrazoles is described. The three-step method involves condensation of crotonates or ß-chloro carboxylic acids with hydrazines, followed by halogenation and oxidation. Several condensation and oxidation protocols were developed to enable preparation of a wide variety of 3-halopyrazoles with good to excellent yields and regiocontrol.

Impact of disease stage and aetiology on survival in hepatocellular carcinoma: implications for surveillance.

BACKGROUND: Variation in survival in hepatocellular carcinoma (HCC) has been attributed to different aetiologies or disease stages at presentation. While international guidelines recommend surveillance of high-risk groups to permit early diagnosis and curative treatment, the evidence that surveillance decreases disease-specific mortality is weak. METHODS: We compared HCC survival figures from Japan (n=1174) and Hong Kong (n=1675) over similar time periods (Japan 2000-2013, Hong Kong, China 2003-2014). The former has an intensive national surveillance programme, while the latter has none. We also analysed changes in survival in Japan over a 50-year period including data from before and after institution of a national HCC surveillance programme. RESULTS: In Japan, over 75% of cases are currently detected by surveillance, whereas in Hong Kong <20% of cases are detected presymptomatically. Median survival was 52 months in Japan and 17.8 months in Hong Kong; this survival advantage persisted after allowance for lead-time bias. Sixty-two per cent of Japanese patients had early disease at diagnosis and 63% received curative treatment. The comparable figures for Hong Kong were 31.7% and 44.1%, respectively. These differences could not be accounted for by disease aetiology, and patients in Hong Kong who were detected at an early stage had a similar survival to the analogous patients in Japan. CONCLUSIONS: The variation in survival is largely accounted for by stage at diagnosis, which in turn relates to the intensity of surveillance programmes and the consequent variation in curative therapeutic options.

The dark side of street lighting: impacts on moths and evidence for the disruption of nocturnal pollen transport.

Among drivers of environmental change, artificial light at night is relatively poorly understood, yet is increasing on a global scale. The community-level effects of existing street lights on moths and their biotic interactions have not previously been studied. Using a combination of sampling methods at matched-pairs of lit and unlit sites, we found significant effects of street lighting: moth abundance at ground level was halved at lit sites, species richness was >25% lower, and flight activity at the level of the light was 70% greater. Furthermore, we found that 23% of moths carried pollen of at least 28 plant species and that there was a consequent overall reduction in pollen transport at lit sites. These findings support the disruptive impact of lights on moth activity, which is one proposed mechanism driving moth declines, and suggest that street lighting potentially impacts upon pollination by nocturnal invertebrates. We highlight the importance of considering both direct and cascading impacts of artificial light.

Using citizen science butterfly counts to predict species population trends.

Citizen scientists are increasingly engaged in gathering biodiversity information, but trade-offs are often required between public engagement goals and reliable data collection. We compared population estimates for 18 widespread butterfly species derived from the first 4 years (2011-2014) of a short-duration citizen science project (Big Butterfly Count [BBC]) with those from long-running, standardized monitoring data collected by experienced observers (U.K. Butterfly Monitoring Scheme [UKBMS]). BBC data are gathered during an annual 3-week period, whereas UKBMS sampling takes place over 6 months each year. An initial comparison with UKBMS data restricted to the 3-week BBC period revealed that species population changes were significantly correlated between the 2 sources. The short-duration sampling season rendered BBC counts susceptible to bias caused by interannual phenological variation in the timing of species' flight periods. The BBC counts were positively related to butterfly phenology and sampling effort. Annual estimates of species abundance and population trends predicted from models including BBC data and weather covariates as a proxy for phenology correlated significantly with those derived from UKBMS data. Overall, citizen science data obtained using a simple sampling protocol produced comparable estimates of butterfly species abundance to data collected through standardized monitoring methods. Although caution is urged in extrapolating from this U.K. study of a small number of common, conspicuous insects, we found that mass-participation citizen science can simultaneously contribute to public engagement and biodiversity monitoring. Mass-participation citizen science is not an adequate replacement for standardized biodiversity monitoring but may extend and complement it (e.g., through sampling different land-use types), as well as serving to reconnect an increasingly urban human population with nature.

Directed evolution of an ultrastable carbonic anhydrase for highly efficient carbon capture from flue gas.

Carbonic anhydrase (CA) is one of nature's fastest enzymes and can dramatically improve the economics of carbon capture under demanding environments such as coal-fired power plants. The use of CA to accelerate carbon capture is limited by the enzyme's sensitivity to the harsh process conditions. Using directed evolution, the properties of a ß-class CA from Desulfovibrio vulgaris were dramatically enhanced. Iterative rounds of library design, library generation, and high-throughput screening identified highly stable CA variants that tolerate temperatures of up to 107 °C in the presence of 4.2 M alkaline amine solvent at pH >10.0. This increase in thermostability and alkali tolerance translates to a 4,000,000-fold improvement over the natural enzyme. At pilot scale, the evolved catalyst enhanced the rate of CO2 absorption 25-fold compared with the noncatalyzed reaction.

A retrospective study of ultrasound and FNA cytology investigation of thyroid nodules: working towards combined risk stratification.

The British Thyroid Association recommended in new guidelines on thyroid cancer treatment [Kwak et al. (Korean J Radiol 14:110-117, 2013)] that ultrasound grading of thyroid nodules should be incorporated into MDT management. A retrospective study was carried out to determine that the impact of US grading has had on MDT decision making in practice. The design used in the study is a retrospective review of case notes. The study was carried out in the hub hospital for thyroid cancer in the North west London Cancer network. We included consecutive patients referred to the regional thyroid multidisciplinary meeting between August 2014 and May 2015 for investigation of thyroid nodules. Data were collected on patient demographics, co-morbidity, thy grading, ultrasound grading, surgery, post-operative histology, and radioactive iodine treatment details. Accuracy of cytology and ultrasound in diagnosing malignancy was correlated to definitive histology. 99 patients with thyroid nodules were included in the study. 97% of patients had at least one fine needle aspiration and 75% had ultrasound grading. Thy3f (Bethesda IV) nodules were more likely to be carcinoma if associated with a U4 grade rather than U3 (67 vs 18%, p = 0.028). Ultrasound grading has recently been introduced to the standard practice in investigation of thyroid nodules. Further assessment of the accuracy of ultrasound grading in clinical practice may allow us to risk-stratify thy3a/thy3f (Bethesda III/IV) lesions and personalise treatment.

Long-term impact of liver function on curative therapy for hepatocellular carcinoma: application of the ALBI grade.

BACKGROUND: Application of curative therapy for hepatocellular carcinoma is crucially dependent on underlying liver function. Using the recently described ALBI grade we examined the long-term impact of liver dysfunction on survival of early-stage hepatocellular carcinoma (HCC) patients. METHODS: This cohort study comprised 2559 HCC patients from different geographic regions, all treated with curative intent. We also examined the relation between indocyanine green (ICG) clearance and ALBI score. Survival was measured from the date of treatment to the date of death or last follow-up. RESULTS: The ALBI score correlated well with ICG clearance. Among those undergoing surgical resection, patients with ALBI grade-1 (good liver function) survived approximately twice as long as those with ALBI grade-2 (less good liver function), although more than 90% of these patients were classified as Child-Pugh (C-P) grade A. In the cohort receiving ablative therapies, there was a similar difference in survival between ALBI grade-1 and grade-2. Cox regression analysis confirmed that the ALBI score along with age, gender, aetiology and tumour factors (AFP, tumour size/number and vascular invasion) independently influenced survival in HCC patients receiving curative treatments. CONCLUSIONS: The ALBI score represents a simple approach to the assessment of liver function in patients with HCC. After potentially curative therapy, those with ALBI grade-1 survived approximately twice as long as those with ALBI grade-2. These data suggest that ALBI grade-1 patients are appropriately treated with surgical resection whereas ALBI grade-2 patients may, where the option exists, be more suitable for liver transplantation or the less invasive curative ablative therapies.