Perception of unfamiliar caregivers during sickness - Using the new caregiver perception task (CgPT) during experimental endotoxemia

Social withdrawal is a well-established part of sickness behavior, but in some contexts sick animals might gain from keeping close instead of keeping away. For instance, sick individuals are more willing to be near known individuals who can provide care and safety (close others) compared to when healthy. Yet, interactions with some strangers might also be beneficial (i.e., healthcare professionals), but it is not known how sickness interplay with social behavior towards such individuals. Here, we assessed if sickness affects perception of caregivers and developed a new task, the Caregiver Perception Task (CgPT). Twenty-six participants conducted the CgPT, once after an injection of lipopolysaccharide (LPS, 0.8 ng/kg body weight, n = 24), and once after an injection of saline (n = 25), one hour and forty-five minutes post-injection. During the task, participants watched short videeo-clips of three types of caregivers: a healthcare professional taking care of a sick individual (HP-c), a healthcare professional not taking care of a sick individual (HP-nc), and a non-healthcare professional taking care of their sick adult child or partner (NHP-c). After each videeo clip, the likability, trustworthiness, professionalism, and willingness to interact with and receive care from the caregiver were rated on visual analogue scales. Results showed that participants injected with saline rated healthcare professionals who did not take care of a sick individual less positively on all aspects compared to healthcare professionals who took care of a sick individual. Moreover, compared to saline, LPS increased the participants' willingness to receive care from healthcare professionals and non-healthcare professionals providing care, but not from healthcare professionals not providing care. Thus, our results indicate that sick individuals may approach unknown individuals with potential to provide care and support.

Clinical correlates of diagnostic certainty in children and youths with Autistic Disorder

BACKGROUND

Clinicians diagnosing autism rely on diagnostic criteria and instruments in combination with an implicit knowledge based on clinical expertise of the specific signs and presentations associated with the condition. This implicit knowledge influences how diagnostic criteria are interpreted, but it cannot be directly observed. Instead, insight into clinicians' understanding of autism can be gained by investigating their diagnostic certainty. Modest correlations between the certainty of an autism diagnosis and symptom load have been previously reported. Here, we investigated the associations of diagnostic certainty with specific items of the ADOS as well as other clinical features including head circumference.

METHODS

Phenotypic data from the Simons Simplex Collection was used to investigate clinical correlates of diagnostic certainty in individuals diagnosed with Autistic Disorder (n = 1511, age 4 to 18 years). Participants were stratified by the ADOS module used to evaluate them. We investigated how diagnostic certainty was associated with total ADOS scores, age, and ADOS module. We calculated the odds-ratios of being diagnosed with the highest possible certainty given the presence or absence of different signs during the ADOS evaluation. Associations between diagnostic certainty and other cognitive and clinical variables were also assessed.

RESULTS

In each ADOS module, some items showed a larger association with diagnostic certainty than others. Head circumference was significantly higher for individuals with the highest certainty rating across all three ADOS modules. In turn, head circumference was positively correlated with some of the ADOS items that were associated with diagnostic certainty, and was negatively correlated with verbal/nonverbal IQ ratio among those assessed with ADOS module 2.

LIMITATIONS

The investigated cohort was heterogeneous, e.g. in terms of age, IQ, language level, and total ADOS score, which could impede the identification of associations that only exist in a subgroup of the population. The variability of the certainty ratings in the sample was low, limiting the power to identify potential associations with other variables. Additionally, the scoring of diagnostic certainty may vary between clinicians.

CONCLUSION

Some ADOS items may better capture the signs that are most associated with clinicians' implicit knowledge of Autistic Disorder. If replicated in future studies, new diagnostic instruments with differentiated weighting of signs may be needed to better reflect this, possibly resulting in better specificity in standardized assessments.

Considerations for study design in the DAHANCA 35 trial of protons versus photons for head and neck cancer

Proton radiotherapy offers a dosimetric advantage compared to photon therapy in sparing normal tissue, but the clinical evidence for toxicity reductions in the treatment of head and neck cancer is limited. The Danish Head and Neck Cancer Group (DAHANCA) has initiated the DAHANCA 35 randomised trial to clarify the value of proton therapy (NCT04607694). The DAHANCA 35 trial is performed in an enriched population of patients selected by an anticipated benefit of proton therapy to reduce the risk of late dysphagia or xerostomia based on normal tissue complication probability (NTCP) modelling. We present our considerations on the trial design and a test of the selection procedure conducted before initiating the randomised study.

From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry

When selecting microbial strains for the production of fermented foods, various microbial phenotypes need to be taken into account to achieve target product characteristics, such as biosafety, flavor, texture, and health-promoting effects. Through continuous advances in sequencing technologies, microbial whole-genome sequences of increasing quality can now be obtained both cheaper and faster, which increases the relevance of genome-based characterization of microbial phenotypes. Prediction of microbial phenotypes from genome sequences makes it possible to quickly screen large strain collections in silico to identify candidates with desirable traits. Several microbial phenotypes relevant to the production of fermented foods can be predicted using knowledge-based approaches, leveraging our existing understanding of the genetic and molecular mechanisms underlying those phenotypes. In the absence of this knowledge, data-driven approaches can be applied to estimate genotype-phenotype relationships based on large experimental datasets. Here, we review computational methods that implement knowledge- and data-driven approaches for phenotype prediction, as well as methods that combine elements from both approaches. Furthermore, we provide examples of how these methods have been applied in industrial biotechnology, with special focus on the fermented food industry.

Unshielded portable optically pumped magnetometer for the remote detection of conductive objects using eddy current measurements

Electrically conductive objects can be detected using the principle of electromagnetic induction, where a primary oscillating magnetic field induces eddy currents in the object, which in turn produce a secondary magnetic field that can be measured with a magnetometer. We have developed a portable radio-frequency optically pumped magnetometer (RF OPM) working in unshielded conditions with sub-pT/Hz magnetic field sensitivity when used for the detection of small oscillating magnetic fields, setting a new benchmark for the sensitivity of a portable RF OPM in unshielded conditions. Using this OPM, we have detected the induced magnetic field from aluminum disks with diameters as small as 1.5 cm and with the disks being ∼25 cm from both the excitation coil and the magnetometer. When used for eddy current detection, our magnetometer achieves a sensitivity of a 2-6 pT/Hz. We have also detected a moving aluminum disk using our RF OPM and analyzed the magnetometer signals, which depend on the position of the disk, illustrating the potential of high sensitivity RF OPMs for remote sensing applications.

Representativeness of autistic samples in studies recruiting through social media

Survey-based research with recruitment through online channels is a convenient way to obtain large samples and has recently been increasingly used in autism research. However, sampling from online channels may be associated with a high risk of sampling bias causing findings not to be generalizable to the autism population. Here we examined autism studies that have sampled on social media for markers of sampling bias. Most samples showed one or more indicators of sampling bias, in the form of reversed sex ratio, higher employment rates, higher education level, lower fraction of individuals with intellectual disability, and later age of diagnosis than would be expected when comparing with for example population study results from published research. Findings from many of the included studies are therefore difficult to generalize to the broader autism population. Suggestions for how research strategies may be adapted to address some of the problems are discussed. LAY SUMMARY: Online surveys offer a convenient way to recruit large numbers of participants for autism research. However, the resulting samples may not fully reflect the autism population. Here we investigated the samples of 36 autism studies that recruited participants online and found that the demographic composition tended to deviate from what has been reported about the autism population in previous research. The results may thus not be generalizable to autism in general.

Abstract 2570: Discovery of potent, selective, and orally available WEE1 inhibitors that demonstrate increased DNA damage and mitosis in tumor cells leading to tumor regression in vivo

WEE1 inhibits the activation of both CDK1 and CDK2 through phosphorylation of Tyr15, allowing DNA damage repair before entering mitosis, thereby regulating the cell cycle in S and G2/M phases. Inhibition of WEE1 could result in premature progression through the G2/M cell cycle checkpoint with unresolved DNA damage, leading to mitotic catastrophe and cell death. Small molecule WEE1 inhibitors, such as AZD1775 and Zn-C3, are currently being evaluated in the clinic and have demonstrated promising efficacy in solid tumors including ovarian, colon, and uterine carcinoma.

By applying Schrödinger’s computational platform including Free Energy Perturbation (FEP) and Protein FEP, we have identified novel, potent, and highly selective WEE1 inhibitors with IC50 values in the low nanomolar range in a biochemical kinase activity assay and cellular target engagement (CDK1 pTyr15) IC50s of 100 - 300 nM in A427 and OVCAR3 cell lines. The compounds also show potent anti-proliferative activity in over 20 breast and ovarian tumor cell lines, including cell lines insensitive to PARP inhibitors. The compounds demonstrate superior kinase selectivity compared to AZD1775 and Zn-C3 in a broad kinase panel with >450 kinases (ScanMAX). In addition, the compounds show desirable ADME properties and PK profiles in preclinical species. Based on in vitro CYP3A4 TDI assay performance (kinact/KI), we have reduced the potential for drug-drug interaction liabilities compared to AZD1775. In the A427 xenograft model, our WEE1 inhibitors demonstrate dose-dependent tumor growth inhibition and tumor regression at high doses. Anti-tumor activity is also demonstrated in additional tumor models, including OVCAR3 and HCC1806 xenograft models. The established PK-PD relationship shows sustained target engagement (pCDK1), increased DNA damage (gH2AX) and mitosis (pHH3). We demonstrate that hematological adverse effects can be mitigated by dosing holidays in xenograft tumor models while maintaining anti-tumor activity. Notably, our compound shows more sustained anti-tumor activity with dosing holidays compared to AZD1775, which we believe is attributable to the prolonged and higher exposure in tumor and plasma with our compound. In the A427 non small-cell lung cancer xenograft model, following 3 dosing holiday cycles at high doses, tumor eradication was maintained after treatment was stopped. In summary, we have identified novel, potent and exquisitely selective WEE1 kinase inhibitors that demonstrate robust anti-tumor activity and sustained target engagement in tumor models. The compound’s anti-tumor effects are maintained with dosing holidays while allowing full recovery of mechanism-based hematological effects.

Citation Format: Shaoxian Sun, Sarah Silvergleid, Aleksey I. Gerasyuto, Jiashi Wang, Robert D. Pelletier, Andrew Placzek, Jennifer L. Knight, Anthony Clark, Hamish Wright, Wu Yin, Jackson Chief Elk, Jeff Bell, Pieter H. Bos, Nicholas A. Boyles, Eric Therrien, Kristian Jensen, Karen Akinsanya. Discovery of potent, selective, and orally available WEE1 inhibitors that demonstrate increased DNA damage and mitosis in tumor cells leading to tumor regression in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2570.

Dose and robustness comparison of nominal, daily and accumulated doses for photon and proton treatment of sinonasal cancer

INTRODUCTION

The aim was to evaluate and compare the dosimetric effect and robustness towards day-to-day anatomical and setup variations in the delivered dose for photon and proton treatments of sinonasal cancer (SNC) patients.

MATERIALS AND METHODS

Photon (VMAT) and proton (IMPT) plans were optimized retrospectively for 24 SNC patients. Synthetic CTs (synCT) were obtained by deforming the planning CT (pCT) to the anatomy of every daily cone-beam CT. Both VMAT and IMPT plans were recalculated on the synCTs. The recalculated daily dose was accumulated over the whole treatment on the pCT. Target coverage and dose to organs and risk (OARs) were evaluated for all patients for the nominal, daily and accumulated dose distribution.

RESULTS

In general, dose to OARs farther away from the target, including brain, chiasm and contralateral optic nerve, was lower for proton plans than photon plans. Whereas, OARs in proximity of the target received a lower dose for photon plans. For proton plans, the target coverage (volume of CTV receiving 95% of prescribed dose), V95%, fell below 99% for 9/24 patients in one or more fractions. For photon plans, 4/24 patients had one or more fractions where V95% fell below 99%. For accumulated doses, V95% was below 99% only in two cases, but above 98% for all patients.

CONCLUSION

Photon and proton treatment have different strengths regarding OAR sparing. The robustness was high for both treatment modalities. Patient selection for either proton or photon radiation therapy of SNC patients should be based on a case-by-case comparison.

Discovery of a Novel Class of d-Amino Acid Oxidase Inhibitors Using the Schrödinger Computational Platform

d-Serine is a coagonist of the N-methyl d-aspartate (NMDA) receptor, a key excitatory neurotransmitter receptor. In the brain, d-serine is synthesized from its l-isomer by serine racemase and is metabolized by the D-amino acid oxidase (DAO, DAAO). Many studies have linked decreased d-serine concentration and/or increased DAO expression and enzyme activity to NMDA dysfunction and schizophrenia. Thus, it is feasible to employ DAO inhibitors for the treatment of schizophrenia and other indications. Powered by the Schrödinger computational modeling platform, we initiated a research program to identify novel DAO inhibitors with the best-in-class properties. The program execution leveraged an hDAO FEP+ model to prospectively predict compound potency. A new class of DAO inhibitors with desirable properties has been discovered from this endeavor. Our modeling technology on this program has not only enhanced the efficiency of structure-activity relationship development but also helped to identify a previously unexplored subpocket for further optimization.

Hybrid high-intensity interval training using functional electrical stimulation leg cycling and arm ski ergometer for people with spinal cord injuries: a feasibility study

Aim

The aim was to assess safety and feasibility of Hybrid High-Intensity Interval Training (HIIT) using Functional Electrical Stimulation (FES) leg cycling and arm ski ergometer in people with Spinal Cord Injuries (SCI).

Method

Eight outpatients (mean age 42.8 years; 7 men) with stable SCI paraplegia (mean 14.5 years since injury) participated in hybrid HIIT (90% peak watts; 4 × 4–min intervals), three times a week (over 8 weeks). Primary outcomes were Adverse Events (AE), participant acceptability, shoulder pain, training intensity (% peak watts), and attendance.

Secondary outcomes were effect on peak oxygen uptake (VO₂peak) during FES hybrid poling, mean watts, self-reported leisure time physical activity, quality of life, and fatigue.

Results

No serious AE occurred; acceptability with the training modality was high, while shoulder pain increased by 9% (SD 95.2). During training, 50% of the participants reached > 90% peak watts during the intervals, three with the legs (FES cycle) and one with the arms (Ski-Erg). Overall, mean training intensity (% peak watts) was 92% (SD 18.9) for legs and 82% (SD 10.3) for arms. Proportion of fulfilled training minutes was 82% (range 36–100%); one participant dropped out after 6 weeks due to back pain. Mean VO₂peak increased by 17% (SD 17.5). Participants reported increased leisure time physical activity and health-related quality of life, besides reduced fatigue.

Conclusion

Hybrid HIIT was safe for people with SCI paraplegia. The majority of the criteria for feasibility were met with acceptable attendance rate, limited drop out, participants enjoyed training, and increased VO₂peak and mean watts. However, the intensity of 90% peak watts was reached by < 60% of the participants despite high RPE ratings during training. The method of measuring and calculating intensity needs to be studied further before a study using this HIIT protocol is undertaken.

Trial registration

Clinicaltrials.gov, NCT04211311, registered 12 December 2019 retrospectively registered

Supplementary Information

The online version contains supplementary material available at 10.1186/s40814-022-00997-2.

Childhood diagnoses in individuals identified as autistics in adulthood

Background

Autism is a developmental condition, where symptoms are expected to occur in childhood, but a significant number of individuals are diagnosed with autism for the first time in adulthood. Here, we examine diagnoses given in childhood among individuals that are diagnosed with autism in adulthood, to investigate whether the late autism diagnosis might be explained by misdiagnosis in childhood or diagnostic overshadowing.

Methods

Through the Danish National Patient Registry, we identified individuals diagnosed with autism in adulthood (N = 2199), as well as a control sample with no records of an autism diagnosis (N = 460,798) and calculated how many had received different psychiatric or neurological diagnoses in childhood.

Results

We found that most childhood diagnoses were overrepresented in those with an adult autism diagnosis, and attention-deficit hyperactivity disorder, affective disorders, anxiety, and stress disorders were the most prevalent childhood conditions in this group. However, 69% of males and 61% of females with adult autism diagnoses were not found to have received any of the investigated diagnoses before 18 years of age, and most childhood diagnoses were given after the age of 12.

Limitations

Milder to moderate cases of psychiatric conditions that have been solely treated by family physicians or school psychologists may not be fully included in our dataset. The study is based on data from the Danish health care system, and further research is needed to assess whether the findings can be generalized to other countries.

Conclusion

A majority of those with an adult autism diagnosis had no records of having received any of the investigated diagnoses in childhood. In these cases, the late autism diagnosis is therefore unlikely to be explained by either misdiagnosis or overshadowing. This result is at odds with the prevailing notion that autistic symptoms tend to diminish with age. Therefore, further research is warranted to examine how and if early signs of autism may have manifested among these individuals, and how similar they are to autistic people diagnosed earlier in their development.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13229-021-00478-y.

Autism comorbidities show elevated female-to-male odds ratios and are associated with the age of first autism diagnosis

OBJECTIVE

To investigate the association between the comorbidity rates in autism and sex, birth year and the age at which autism was first diagnosed and compare the relative impact of each.

METHOD

Using the Danish National Patient Registry, cumulative incidences up to the age of 16 for 11 comorbid conditions (psychosis, affective disorders, anxiety disorders, conduct disorder, eating disorders, obsessive-compulsive disorder, attention-deficit hyperactivity disorder, epilepsy, tic disorders, sleep disorders or intellectual disability) were calculated for individuals with autism (N = 16,126) and non-autism individuals (N = 654,977). Individuals were further stratified based on the age at the first autism diagnoses and comorbid diagnoses up to the age of 16 were compared.

RESULTS

Most comorbidities were significantly associated with birth year and sex. Female/male odds ratios for 8 of 11 comorbid conditions were up to 67% higher than the corresponding odds ratios in the non-autism population, including conditions that are generally more common in males than in females as well as conditions that are more common in females. All comorbidity rates were significantly associated with the age at the first autism diagnosis, which was a stronger predictor than sex and birth year for 8 conditions.

CONCLUSIONS

Comorbidity rates for females exceed what would be expected based on the sex ratios among non-autistic individuals, indicating that the association between autism and comorbidity is stronger in females. Comorbidity rates are also highly dependent on the age at the first autism diagnosis, which may contribute to autism heterogeneity in research and clinical practice.

Abstract 1338: Discovery of novel, potent USP7 inhibitors that upregulate p53 leading to anti-proliferative effects in cancer cells

Introduction: Ubiquitin-specific protease 7 (USP7) is a deubiquitinase that regulates several proteins involved in cell cycle, DNA repair, genomic stability, and epigenetics and has been implicated in cancer progression. A key substrate of USP7 is MDM2, the oncogenic E3 ubiquitin ligase that promotes degradation of the tumor suppressor p53. USP7-mediated stabilization of MDM2 leads to the degradation of p53, preventing cell cycle arrest and the induction of apoptosis and promoting tumor cell growth. In addition to the MDM2-p53 pathway, USP7 regulates a number of other substrates involved in cancer, including PIM2 kinase, MYCN, the DNA methyltransferase DNMT1, and the PTEN tumor suppressor. Consistent with its function promoting oncogenic signaling pathways, genetic and pharmacological inhibition of USP7 has been shown to inhibit growth of a number of tumor cell lines in vitro and in vivo, and this anti-tumor activity is significantly enriched among cells expressing wild type p53. Thus, inhibition of USP7 is a promising therapeutic strategy, especially in cancers carrying wild type p53 that can be reactivated by suppression of MDM2.

Results: We have discovered a new class of potent and selective USP7 inhibitors. These compounds bind to USP7 and prevent deubiquitinase activity in biochemical activity assays with picomolar potency. Our compounds induce accumulation of p53 and exhibit IC50s below 50 nM in cell viability assays in Multiple Myeloma and Acute Myeloid Leukemia (AML) cell lines. In AML cell lines, our USP7 inhibitors strongly synergize with the approved Bcl-2 inhibitor venetoclax. Unlike MDM2 antagonists currently undergoing clinical trials in AML, these USP7 inhibitors do not lead to a significant increase in MDM2 levels, and our compounds result in a more modest induction of p53, both of which could provide significant safety benefits. We have demonstrated differential sensitivity to MDM2 antagonists and our USP7 inhibitors in select cell lines and show that this effect is dependent upon p53 induction. Our compounds are orally bioavailable with a desirable PK profile in mice and induce p53 in tumor cells in CDX mouse models of Multiple Myeloma.

Conclusions: We have identified novel, potent, orally bioavailable USP7 inhibitors that lead to p53 accumulation and cytotoxicity in cancer cells. We demonstrate mechanistic differences between USP7 and MDM2-p53 antagonists, which may lead to a safety advantage. We observe strong synergy between USP7 inhibitors and an approved treatment. Our lead compounds have favorable drug-like properties, promising mouse PK profiles, and can induce p53 accumulation in mouse CDX tumor models. These data demonstrate the therapeutic potential of our USP7 inhibitors and reveal specific opportunities for their use in the treatment of Multiple Myeloma and AML.

Citation Format: Alan Futran, Tao Lu, Katherine Amberg-Johnson, Xiaoxiao Yang, Saidi He, Jeffrey Bell, Sarah Boyce, Markus Dahlgren, Karen Dingley, Liping Fang, Heidi Koldsoe, Zef Konst, Fang-Yu Lin, Robert Pelleltier, Heng Qian, Mats Svensson, Michael Trzoss, Jie Xu, Shuping Xu, Zhaowu Xu, Engin Yapici, Yan Zhang, Li Xing, Takao Suzuki, Xianhai Huang, Jiayi Xu, Hamish Wright, Kristian Jensen, Wayne Tang, Tao Guo, Karen Akinsanya, David Madge. Discovery of novel, potent USP7 inhibitors that upregulate p53 leading to anti-proliferative effects in cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1338.

Abstract 1277: Discovery of novel CDC7 inhibitors that disrupt cell cycle dynamics and show anti-proliferative effects in cancer cells

Introduction: CDC7 is a serine/threonine protein kinase that phosphorylates the MCM2-7 helicase complex, a required step in DNA replication initiation. CDC7 has emerged as an attractive target for cancer treatment because of high expression in a number of tumors (e.g. ovarian, lung, and oral) which is thought to be linked to their proliferative capacity and ability to bypass DNA damage responses. Consistent with this, disruption of CDC7 activity in cancer cells results in delayed DNA replication, mitotic abnormalities and cell death whereas non-transformed, p53 wildtype cells are protected from cytotoxicity due to G1 cell cycle arrest. Due to the low ATP Km of CDC7, very potent inhibitor molecules are required to effectively block CDC7 activity and drive cancer cells into apoptosis. We have identified novel potent and selective CDC7 inhibitors targeting the ATP binding site that are active in biophysical, biochemical and cellular assays as well as in vivo CDX models.

Results: Our lead compounds show potent picomolar (pM) inhibition of CDC7 in a biochemical kinase activity assay, pM affinity in SPR assay and complete inhibition of MCM2 (S53) phosphorylation in COLO205, A427, MV-4-11 and SW48 cancer cell lines. In a broad kinase selectivity panel, the novel inhibitors showed good selectivity for CDC7 kinase. Mechanistic studies show that our CDC7 inhibitors induced apoptosis, disrupted DNA replication and cell cycle dynamics with accumulation of polyploid cells after 48 h of treatment of cancer cells with minimal effects on human fibroblast cell lines. Our compounds have shown potent anti-proliferative and cytotoxic effects in a panel of more than a 100 cancer cell lines of varying origin including COLO205, SW48, A427, MOLM-13, and SUM149. Comparison of CDC7 inhibitors with other oncology drugs in a panel of cancer cell lines revealed a unique mechanism of action. In vivo, our compounds reduced tumor cell MCM2 (S53) phosphorylation in the mouse COLO205 xenograft model and showed strong tumor growth inhibition. We have also examined the effect of CDC7 inhibitors on cancer cell proliferation in combination with other anti-cancer agents, including other DNA damage response (DDR) targeting agents.

Conclusions: We have identified novel potent ATP-competitive CDC7 inhibitors that show target engagement in cells and CDX tumors and have shown strong inhibition of cancer cell proliferation in vitro and tumor growth in vivo. CDC7 inhibitors show promise for use in combination with other targeted therapies for the treatment of cancers of varying origin.

Citation Format: Lyuben Tsvetkov, Adam Levinson, Xianhai Huang, Sayan Mondal, Jeff Bell, Lin Tang, Robert Pelletier, Karen Dingley, Nick Boyles, Jackson Chief Elk, Leah Frye, Alan Futran, Phani Ghanakota, Jeremy Greenwood, George Lai, Sarah Silvergleid, Wu Yin, Hamish Wright, Karen Akinsanya, Wayne Tang, Kristian Jensen. Discovery of novel CDC7 inhibitors that disrupt cell cycle dynamics and show anti-proliferative effects in cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1277.

Gene-Trait Matching and Prevalence of Nisin Tolerance Systems in Lactococus lactis

Lactococcus lactis cheese starter cultures typically contain a mix of many strains and may include variants that produce and/or tolerate the antimicrobial bacteriocin nisin. Nisin is well-established as an effective agent against several undesirable Gram-positive bacteria in cheese and various other foods. In the current study, we have examined the effect of nisin on 710 individual L. lactis strains during milk fermentations. Changes in milk acidification profiles with and without nisin exposure, ranging from unaltered acidification to loss of acidification, could be largely explained by the type(s) and variants of nisin immunity and nisin degradation genes present, but surprisingly, also by genotypic lineage (L. lactis ssp. cremoris vs. ssp. lactis). Importantly, we identify that nisin degradation by NSR is frequent among L. lactis and therefore likely the main mechanism by which dairy-associated L. lactis strains tolerate nisin. Insights from this study on the strain-specific effect of nisin tolerance and degradation during milk acidification is expected to aid in the design of nisin-compatible cheese starter cultures.

Air variability in maxillary sinus during radiotherapy for sinonasal carcinoma

INTRODUCTION

The aim was to characterise patterns and predictability of aeration changes in the ipsilateral maxillary sinus during intensity-modulated radiotherapy (IMRT) for sinonasal cancer (SNC), and in a sample evaluate the dosimetric effects of aeration changes for both photon and proton therapy.

MATERIALS AND METHODS

The study included patients treated with IMRT for SNC in a single institution in 2009-2017. The volume of air in the ipsilateral maxillary sinus was recorded in 1578 daily cone beam computer tomography (CBCT) from 53 patients. Patterns of changing air volumes were categorised as 'stable', increasing', 'decreasing', or 'erratic'. For the prediction analysis, categorisation was performed based both on the entire treatment course and the first five fractions (F1-5). Photon and proton therapy plans were generated for four patients, the one from each category with the largest aeration variation. Synthetic CT images were generated for each CBCT and all plans were recalculated on the daily synthetic CTs.

RESULTS

The absolute volume of air varied considerably during the treatment course, ranging from 0 to 25.9 cm3. Changes within a single participant varied in the range of 0-18.7 cm3. In the categorisation of patterns, most patients had increasing aeration of the sinus. Generally, patterns of aeration could not be predicted from F1-5. Patients categorised as increasing in F1-5 had the best prediction, with 78% predicted correctly as increasing for the entire treatment course. The numeric correlation coefficients for target coverage and air volume were low for 3/4 scenarios (photons 0.03-0.23, protons 0.26-0.48). No straightforward correlation between the dosimetric effect and the volume changes could be detected in the sample test of four patients for neither photon nor proton therapy.

CONCLUSION

The variation of aeration was large and unpredictable. No clear dosimetric consequences of the aeration variation were evident for neither IMRT nor proton therapy for the patients investigated.

Thermographic visualization of facial vasoconstriction is associated with 30-day all-cause mortality in medical patients; prospective observational two-site cohort study

INTRODUCTION

Quick and reliable assessment of acute patients is required for accurate triage. The temperature gradient between core and peripheral temperature could possibly instantly provide information on circulatory status.

METHODS

Adult medical patients, who did not receive supplementary oxygen, attending two emergency departments, had a thermographic image taken on arrival. The association between 30-day mortality and gradients was tested using logistic regression.

RESULTS

726 patients were studied, median age was 64 years and 14 (1.9%) died within 30 days. There was a significant association between mortality and temperature gradient, comparable to vital signs, age, and clinical intuition.

CONCLUSION

Temperature gradient between nose and eye had an acceptable discriminatory power for 30-day all-cause mortality.

Hemoglobin level at stabilization is associated with long-term all-cause mortality in patients with left-sided endocarditis, a POET substudy

Background

Left-sided infectious endocarditis (IE) has a high 1-year mortality. Anemia is a common finding in patients with IE, yet little is known about frequency, severity, and associated outcomes in this setting.

Purpose

To examine the relationship between Hemoglobin (Hgb) level measured at IE stabilization (time of randomization) in the Partial Oral versus intravenous Antibiotic Treatment of Endocarditis (POET) trial - and long-term all-cause mortality.

Methods

In the POET trial, 400 patients with left-sided IE were randomized, after medical and/or surgical stabilization, to conventional antibiotic treatment or partial oral treatment. Only non-surgically treated patients were considered in this study. Patients were divided by quartiles into four groups based on Hgb level at randomization.

Results

We examined 248 patients with non-surgically treated IE. Median time from diagnosis of IE to randomization was 14 days (IQ 12–19). At long-term follow-up (median 3.2 years, IQ 2.18–4.60), 71 patients had died (28.6%). Patients in the lowest quantile (Hgb ≤6.0 mmol) had a HR of 4.17 (95% CI 1.81–9.61, p&lt;0.001) for death compared to patients in the highest quantile (Hgb &gt;7.5 mmol/L). This association remained significant after multivariable adjustment for age, sex, renal disease, C-Reactive Protein, and Prosthetic heart valve (HR 2.69, 95% CI 1.11–6.50); p=0.028).

Conclusion

Low Hemoglobin level at stabilization in patients with IE was associated with an increased risk of long-term mortality. Whether intensified treatment of anemia in patients with IE could improve long-term outcome requires investigation.

Funding Acknowledgement

Type of funding source: Foundation. Main funding source(s): The Danish Heart Foundation, The Capital Regions Research Council

Late toxicity in the brain after radiotherapy for sinonasal cancer: Neurocognitive functioning, MRI of the brain and quality of life

•

Compared with matched normative data, impaired cognitive function was substantial.

•

Several correlations between radiation dose and cognitive impairment were present.

•

Radiation-induced white matter hyperintensities were present in 2/27 participants.

•

One participant displayed radiation-induced necrosis in the temporal lobe.

•

The domains affecting quality of life the most were fatigue and quality of sleep.

Purpose

The aim of the study was to evaluate neurocognitive late effects, structural alterations and associations between cognitive impairment and radiation doses as well as cerebral tissue damage after radiotherapy for sinonasal cancer. Furthermore, the aim was to report quality of life (QoL) and self-reported cognitive capacity.

Materials and methods

Recurrence-free patients previously treated with intensity-modulated radiotherapy with a curative intent were eligible for the study. Study examinations comprised comprehensive neurocognitive testing, MRI of the brain, and self-reported outcomes.

Results

A total of 27 patients were included. Median age was 67 years (range 47–83). The majority of test outcomes were below normative values in any degree, and 37% of the participants had clinically significant neurocognitive impairment when compared with normative data. Correlations between absorbed doses to specific substructures of the brain and neurocognitive outcomes were present for Wechsler’s Adult Intelligence Scale-digit span and Controlled Oral Word Association Test-S. Structural MRI revealed macroscopic abnormalities in three patients; infarction (n = 1), diffuse white matter intensities (n = 2) and necrosis (n = 1). In the analysis of atrophy of cerebral tissue, no correlations were present with neither radiation dose to cerebral substructures nor neurocognitive impairment. The global QoL of the cohort was 75. The most affected outcomes were ‘fatigue’, ‘insomnia’, and ‘drowsiness’. A total of 59% of participants reported significantly impaired quality of sleep. Self-reported cognitive function revealed that ‘memory’ was the most affected cognitive domain. For the domains of ‘memory’ and ‘language’, self-reported functioning was associated with objectively measured neurocognitive outcomes.

Conclusion

Cerebral toxicity after radiotherapy for sinonasal cancer was substantial. Clinically significant cognitive impairment was present in more than one third of the participants, and several dose–response associations were present. Furthermore, the presence of macroscopic radiation sequelae indicated considerable impact of radiotherapy on brain tissue.

Grazing mediates soil microbial activity and litter decomposition in salt marshes

Salt marshes contribute to climate change mitigation because of their great capacity to store organic matter (OM) in soils. Most of the research regarding OM turnover in salt marshes in times of global change focuses on effects of rising temperature and accelerated sea-level rise, while effects of land-use change have gained little attention. The present work investigates the mechanisms by which livestock grazing can affect OM decomposition in salt marsh soils. In a grazing exclusion experiment at the mouth of the Yangtze estuary, China, we assessed soil microbial exo-enzyme activity (EEA) to gain insight into the microbial carbon (C) and nitrogen (N) demand. Additionally, we studied the decomposition of plant litter in soil using the Tea Bag Index (TBI), a widely used standardized litter bag assay to fingerprint soil decomposition dynamics. Based on EEAs, grazing markedly reduced microbial C acquisition, whereas microbial N acquisition was strongly increased. These opposing grazing effects were also evident in the decomposition of standardized plant litter: The decomposition rate constant (k) and the stabilization (S) of litter were not inversely related, as would be expected, but instead both were reduced by livestock grazing. Our data suggest that gazing effects on EEAs and litter decomposition can just partly be explained by grazing-driven soil compaction and resulting lower oxygen availability, which has previously been hypothesized as a main pathway by which grazing can reduce microbial activity in wetland soils. Instead, grazing effects on microbial nutrient demand occurs to be an at least equally important control on soil decomposition processes.

Fungal secretome profile categorization of CAZymes by function and family corresponds to fungal phylogeny and taxonomy: Example Aspergillus and Penicillium

Fungi secrete an array of carbohydrate-active enzymes (CAZymes), reflecting their specialized habitat-related substrate utilization. Despite its importance for fitness, enzyme secretome composition is not used in fungal classification, since an overarching relationship between CAZyme profiles and fungal phylogeny/taxonomy has not been established. For 465 Ascomycota and Basidiomycota genomes, we predicted CAZyme-secretomes, using a new peptide-based annotation method, Conserved-Unique-Peptide-Patterns, enabling functional prediction directly from sequence. We categorized each enzyme according to CAZy-family and predicted molecular function, hereby obtaining a list of "EC-Function;CAZy-Family" observations. These "Function;Family"-based secretome profiles were compared, using a Yule-dissimilarity scoring algorithm, giving equal consideration to the presence and absence of individual observations. Assessment of "Function;Family" enzyme profile relatedness (EPR) across 465 genomes partitioned Ascomycota from Basidiomycota placing Aspergillus and Penicillium among the Ascomycota. Analogously, we calculated CAZyme "Function;Family" profile-similarities among 95 Aspergillus and Penicillium species to form an alignment-free, EPR-based dendrogram. This revealed a stunning congruence between EPR categorization and phylogenetic/taxonomic grouping of the Aspergilli and Penicillia. Our analysis suggests EPR grouping of fungi to be defined both by "shared presence" and "shared absence" of CAZyme "Function;Family" observations. This finding indicates that CAZymes-secretome evolution is an integral part of fungal speciation, supporting integration of cladogenesis and anagenesis.

Four New Species of Paraorygmatobothrium (Eucestoda: Phyllobothriidea) From Sharks of the Gulf of Mexico and the Atlantic Ocean, with Comments on Their Host Specificity

Four new species of Paraorygmatobothrium are described from carcharhinid shark species from the Gulf of Mexico and the U.S. coast of the northwestern Atlantic Ocean. Paraorygmatobothrium bullardi n. sp. is described from Carcharhinus brevipinna as its type host, and from Carcharhinus acronotus and Carcharhinus limbatus. Paraorygmatobothrium campbelli n. sp. is described from Rhizoprionodon terraenovae. Paraorygmatobothrium deburonae n. sp. is described from Carcharhinus isodon as its type host, as well as from C. brevipinna, C. limbatus, and R. terraenovae. Paraorygmatobothrium mattisi n. sp. is described from R. terraenovae as its type host, and from C. brevipinna and C. limbatus. These 4 species differ from other species of Paraorygmatobothrium and from each other in bothridial microthrix shape, and in various combinations of features such as the total length of the worm, apical sucker size, bothridial musculature, proglottid number, testes number, and genital pore position. Difficulty in differentiating these 4 species from one another, and from other species of Paraorygmatobothrium, points to limitations in the use of morphology alone to recognize species diversity in this genus. A phylogenetic analysis of Paraorygmatobothrium and related genera, based on partial (D1-D3) 28S rDNA sequence data, confirms that the genus is not monophyletic. Genetic distances of COI revealed that sequence divergence between species of Paraorygmatobothrium is generally at least an order of magnitude larger than COI divergence within a species. Patterns of host use for 3 of the new species are consistent with previous findings that point to a lack of host specificity in Paraorygmatobothrium.

QuantumATK: an integrated platform of electronic and atomic-scale modelling tools

QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented, the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals. The platform includes a long list of advanced modules, including Green's-function methods for electron transport simulations and surface calculations, first-principles electron-phonon and electron-photon couplings, simulation of atomic-scale heat transport, ion dynamics, spintronics, optical properties of materials, static polarization, and more. Seamless integration of the different simulation engines into a common platform allows for easy combination of different simulation methods into complex workflows. Besides giving a general overview and presenting a number of implementation details not previously published, we also present four different application examples. These are calculations of the phonon-limited mobility of Cu, Ag and Au, electron transport in a gated 2D device, multi-model simulation of lithium ion drift through a battery cathode in an external electric field, and electronic-structure calculations of the composition-dependent band gap of SiGe alloys.

Interactive website for head and neck cancer patients: Adherence and coping program to prevent dysphagia after radiation

INTRODUCTION

Pharyngeal and laryngeal cancers are highly curable; however survivors are at high risk for long-term dysphagia after radiation. To address lack of access to preventive care in community settings, we developed a responsive web-based application to help patients adhere to preventive swallowing exercises and cope with radiation side effects. We conducted an interim study analysis to determine website usage characteristics and to examine the effect size for future trials.

METHODS

Pharyngeal and laryngeal cancer patients were recruited for enrollment by speech language pathologists before primary radiation and introduced to the interactive website. The program (English and Spanish) features tracking logs for preventive exercises, instructional videos, patient stories and search features. Patients' self-reported swallowing function was assessed with the MD Anderson Dysphagia Inventory (MDADI) at baseline and at 6 months. Adherence to preventive exercises was assessed during the 10 week intervention. Number of unique website visits, total duration of website exposure, and rankings of the most popular webpages were calculated. Preliminary regression models were run using adherence and MDADI as outcomes.

RESULTS

Of the 160 enrolled, 96 had 10-week adherence data and 61 had 6-month MDADI data. The average age was 63 (SD = 12.26), 49.4% were from rural counties, 44% had a high school education or lower, and 42% reported annual income of $30,000 or less. The average number of visits was 5.49 (SD = 9.96) and the average total time spent with the website was 41.09 min (SD =88.48). Preliminary analyses indicated that number of unique visits to the website was independently associated with increased adherence to preventive exercises (p = .001-.008).

CONCLUSION

Our website showed significant effects in promoting adherence to swallowing exercises. However, our return visit rate showed that the platform needs improvement in navigability and usability for this older population undergoing challenging treatment in community settings with low resources.

Temporal Changes in Effect Sizes of Studies Comparing Individuals With and Without Autism: A Meta-analysis

Importance

The definition and nature of autism have been highly debated, as exemplified by several revisions of the DSM (DSM-III, DSM-IIIR, DSM-IV, and DSM-5) criteria. There has recently been a move from a categorical view toward a spectrum-based view. These changes have been accompanied by a steady increase in the prevalence of the condition. Changes in the definition of autism that may increase heterogeneity could affect the results of autism research; specifically, a broadening of the population with autism could result in decreasing effect sizes of group comparison studies.

Objective

To examine the correlation between publication year and effect size of autism-control group comparisons across several domains of published autism neurocognitive research.

Data Sources

This meta-analysis investigated 11 meta-analyses obtained through a systematic search of PubMed for meta-analyses published from January 1, 1966, through January 27, 2019, using the search string autism AND (meta-analysis OR meta-analytic). The last search was conducted on January 27, 2019.

Study Selection

Meta-analyses were included if they tested the significance of group differences between individuals with autism and control individuals on a neurocognitive construct. Meta-analyses were only included if the tested group difference was significant and included data with a span of at least 15 years.

Data Extraction and Synthesis

Data were extracted and analyzed according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting guideline using fixed-effects models.

Main Outcomes and Measures

Estimated slope of the correlation between publication year and effect size, controlling for differences in methods, sample size, and study quality.

Results

The 11 meta-analyses included data from a total of 27 723 individuals. Demographic data such as sex and age were not available for the entire data set. Seven different psychological and neurologic constructs were analyzed based on data from these meta-analyses. Downward temporal trends for effect size were found for all constructs (slopes: -0.067 to -0.003), with the trend being significant in 5 of 7 cases: emotion recognition (slope: -0.028 [95% CI, -0.048 to -0.007]), theory of mind (-0.045 [95% CI, -0.066 to -0.024]), planning (-0.067 [95% CI, -0.125 to -0.009]), P3b amplitude (-0.048 [95% CI, -0.093 to -0.004]), and brain size (-0.047 [95% CI, -0.077 to -0.016]). In contrast, 3 analogous constructs in schizophrenia, a condition that is also heterogeneous but with no reported increase in prevalence, did not show a similar trend.

Conclusions and Relevance

The findings suggest that differences between individuals with autism and those without the diagnosis have decreased over time and that possible changes in the definition of autism from a narrowly defined and homogenous population toward an inclusive and heterogeneous population may reduce our capacity to build mechanistic models of the condition.

An opposite pattern of cognitive performance in autistic individuals with and without alexithymia

Oakley, Brewer, Bird, and Catmur (2016) investigated whether the Reading the Minds in the Eyes Test (RMET) measures emotion recognition rather than theory of mind (ToM). To explore this, 19 participants with autism and 23 controls, matched on alexithymia traits, were tested with the RMET, as well as the ToM Movie for Assessment of Social Cognition (MASC). The authors found a significant difference between the two groups on the MASC but not on the RMET, but dividing the groups based on alexithymia resulted in a significantly lower performance on the RMET but not on the MASC for the alexithymia group. Therefore, they conclude that difficulties on the RMET are associated with alexithymia, not autism, while difficulties on the MASC are associated with autism, not alexithymia. Here we investigated what seems to be opposite patterns of performance on the two cognitive tasks within the autism group, which modified the authors' interpretation of their data. This was examined by correlating the alexithymia scores with the RMET and a subscale of the MASC scores, referred to as the cognitive MASC. We found a negative correlation between the alexithymia score and the RMET score while also finding a positive correlation between the alexithymia score and the cognitive MASC score in the autism group. Such an opposite pattern of performance suggests the presence of distinct patterns of ToM difficulties within the autism group. This also indicates that, contrary to what is reported by Oakley et al., there is an association between alexithymia and the MASC within the autism group. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

NTCP model validation method for DAHANCA patient selection of protons versus photons in head and neck cancer radiotherapy

Introduction: Prediction models using logistic regression may perform poorly in external patient cohorts. However, there is a need to standardize and validate models for clinical use. The purpose of this project was to describe a method for validation of external NTCP models used for patient selection in the randomized trial of protons versus photons in head and neck cancer radiotherapy, DAHANCA 35. Material and methods: Organs at risk of 588 patients treated primarily with IMRT in the randomized controlled DAHANCA19 trial were retrospectively contoured according to recent international recommendations. Dose metrics were extracted using MatLab and all clinical parameters were retrieved from the DAHANCA database. The model proposed by Christianen et al. to predict physician-rated dysphagia was validated through the closed testing, where change of the model intercept, slope and individual beta's were tested for significant prediction improvements. Results: Six months prevalence of dysphagia in the validation cohort was 33%. The closed testing procedure for physician-rated dysphagia showed that the Christianen et al. model needed an intercept refitting for the best match for the Danish patients. The intercept update increased the risk of dysphagia for the validation cohort by 7.9 ± 2.5% point. For the raw model performance, the Brier score (mean squared residual) was 0.467, which improved significantly with a new intercept to 0.415. Conclusions: The previously published Dutch dysphagia model needed an intercept update to match the Danish patient cohort. The implementation of a closed testing procedure on the current validation cohort allows quick and efficient validation of external NTCP models for patient selection in the future.

MARSI: metabolite analogues for rational strain improvement

Summary

Metabolite analogues (MAs) mimic the structure of native metabolites, can competitively inhibit their utilization in enzymatic reactions, and are commonly used as selection tools for isolating desirable mutants of industrial microorganisms. Genome-scale metabolic models representing all biochemical reactions in an organism can be used to predict effects of MAs on cellular phenotypes. Here, we present the metabolite analogues for rational strain improvement (MARSI) framework. MARSI provides a rational approach to strain improvement by searching for metabolites as targets instead of genes or reactions. The designs found by MARSI can be implemented by supplying MAs in the culture media, enabling metabolic rewiring without the use of recombinant DNA technologies that cannot always be used due to regulations. To facilitate experimental implementation, MARSI provides tools to identify candidate MAs to a target metabolite from a database of known drugs and analogues.

Availability and implementation

The code is freely available at https://github.com/biosustain/marsi under the Apache License V2. MARSI is implemented in Python.

Supplementary information

Supplementary data are available at Bioinformatics online.

Exercise-based cardiac rehabilitation in patients with reduced left ventricular ejection fraction: The Cardiac Rehabilitation Outcome Study in Heart Failure (CROS-HF): A systematic review and meta-analysis

Background

In heart failure with reduced left ventricular ejection fraction (HFrEF) patients the effects of exercise-based cardiac rehabilitation on top of state-of-the-art pharmacological and device therapy on mortality, hospitalization, exercise capacity and quality-of-life are not well established.

Design

The design of this study involved a structured review and meta-analysis.

Methods

Evaluation of randomised controlled trials of exercise-based cardiac rehabilitation in HFrEF-patients with left ventricular ejection fraction ≤40% of any aetiology with a follow-up of ≥6 months published in 1999 or later.

Results

Out of 12,229 abstracts, 25 randomised controlled trials including 4481 HFrEF-patients were included in the final evaluation. Heterogeneity in study population, study design and exercise-based cardiac rehabilitation-intervention was evident. No significant difference in the effect of exercise-based cardiac rehabilitation on mortality compared to control-group was found (hazard ratio 0.75, 95% confidence interval 0.39–1.41, four studies; 12-months follow-up: relative risk 1.29, 95% confidence interval 0.66–2.49, eight studies; six-months follow-up: relative risk 0.91, 95% confidence interval 0.26–3.16, seven studies). In addition there was no significant difference between the groups with respect to ‘hospitalization-for-any-reason’ (12-months follow-up: relative risk 0.79, 95% confidence interval 0.41–1.53, four studies), or ‘hospitalization-due-to-heart-failure’ (12-months follow-up: relative risk 0.59, 95% confidence interval 0.12–2.91, four studies; six-months follow-up: relative risk 0.84, 95% confidence interval 0.07–9.71, three studies). All studies show improvement of exercise capacity. Participation in exercise-based cardiac rehabilitation significantly improved quality-of-life as evaluated with the Kansas City Cardiomyopathy Questionnaire: (six-months follow-up: mean difference 1.94, 95% confidence interval 0.35–3.56, two studies), but no significant results emerged for quality-of-life measured by the Minnesota Living with Heart Failure Questionnaire (nine-months or more follow-up: mean difference –4.19, 95% confidence interval –10.51–2.12, seven studies; six-months follow-up: mean difference –5.97, 95% confidence interval –16.17–4.23, four studies).

Conclusion

No association between exercise-based cardiac rehabilitation and mortality or hospitalisation could be observed in HFrEF patients but exercise-based cardiac rehabilitation is likely to improve exercise capacity and quality of life.

OptCouple: Joint simulation of gene knockouts, insertions and medium modifications for prediction of growth-coupled strain designs

Biological production of chemicals is an attractive alternative to petrochemical-based production, due to advantages in environmental impact and the spectrum of feasible targets. However, engineering microbial strains to overproduce a compound of interest can be a long, costly and painstaking process. If production can be coupled to cell growth it is possible to use adaptive laboratory evolution to increase the production rate. Strategies for coupling production to growth, however, are often not trivial to find. Here we present OptCouple, a constraint-based modeling algorithm to simultaneously identify combinations of gene knockouts, insertions and medium supplements that lead to growth-coupled production of a target compound. We validated the algorithm by showing that it can find novel strategies that are growth-coupled in silico for a compound that has not been coupled to growth previously, as well as reproduce known growth-coupled strain designs for two different target compounds. Furthermore, we used OptCouple to construct an alternative design with potential for higher production. We provide an efficient and easy-to-use implementation of the OptCouple algorithm in the cameo Python package for computational strain design.

A New Species of Pentaloculum (Cestoda: "Tetraphyllidea") from the Taiwan Saddled Carpetshark, Cirrhoscyllium formosanum (Orectolobiformes: Parascylliidae)

Collection of cestodes from the Taiwan saddled carpetshark, Cirrhoscyllium formosanum, for the first time led to the discovery of Pentaloculum hoi n. sp. This species provided important insights into the identity of the heretofore monotypic Pentaloculum-known previously only from the blind electric ray, Typhlonarke aysoni, in New Zealand. The new species differs from Pentaloculum macrocephalum in testis number, vitelline follicle and cirrus sac configuration, and in that it is hyperapolytic rather than euapolytic. Maximum-likelihood analysis of sequence data generated for the D1-D3 region of the 28S rDNA gene not only confirmed this generic placement but also confirmed the close affinities between both species of Pentaloculum and specimens previously referred to in the literature as new genus 7 n. sp. 1. Examination of limited material of the latter, including that of a second specimen from which partial 28S rDNA sequence data were generated here, led to the realization that new genus 7 n. sp. 1 represents an undescribed species of Pentaloculum, referred to here as Pentaloculum n. sp. 2. All 3 species share bothridia divided into 1 anterior and 2 consecutive pairs of loculi. Given that Pentaloculum n. sp. 2 parasitizes a member of the second and only other genus of parascylliid sharks (i.e., Parascyllium), we predict that the 4 other species of Parascyllium and the 2 other species of Cirrhoscyllium are likely to host other species of Pentaloculum. The factors that might account for the eclectic host associations of Pentaloculum, which include a torpediniform ray and 2 species of orectilobiform sharks, are currently unclear. The compilation of diet data for these elasmobranchs and determination of the final intermediate hosts for these cestodes would be interesting avenues of further investigation given that cestodes are trophically transmitted between their intermediate and definitive hosts. The phylogenetic affinities of Pentaloculum among elasmobranch cestodes remain unresolved.