Efficient synthesis of limonene production in Yarrowia lipolytica by combinatorial engineering strategies.

BACKGROUND: Limonene has a variety of applications in the foods, cosmetics, pharmaceuticals, biomaterials, and biofuels industries. In order to meet the growing demand for sustainable production of limonene at industry scale, it is essential to find an alternative production system to traditional plant extraction. A promising and eco-friendly alternative is the use of microbes as cell factories for the synthesis of limonene. RESULTS: In this study, the oleaginous yeast Yarrowia lipolytica has been engineered to produce D- and L-limonene. Four target genes, l- or d-LS (limonene synthase), HMG (HMG-CoA reductase), ERG20 (geranyl diphosphate synthase), and NDPS1 (neryl diphosphate) were expressed individually or fused together to find the optimal combination for higher limonene production. The strain expressing HMGR and the fusion protein ERG20-LS was the best limonene producer and, therefore, selected for further improvement. By increasing the expression of target genes and optimizing initial OD, 29.4 mg/L of L-limonene and 24.8 mg/L of D-limonene were obtained. We also studied whether peroxisomal compartmentalization of the synthesis pathway was beneficial for limonene production. The introduction of D-LS and ERG20 within the peroxisome improved limonene titers over cytosolic expression. Then, the entire MVA pathway was targeted to the peroxisome to improve precursor supply, which increased D-limonene production to 47.8 mg/L. Finally, through the optimization of fermentation conditions, D-limonene production titer reached 69.3 mg/L. CONCLUSIONS: In this work, Y. lipolytica was successfully engineered to produce limonene. Our results showed that higher production of limonene was achieved when the synthesis pathway was targeted to the peroxisome, which indicates that this organelle can favor the bioproduction of terpenes in yeasts. This study opens new avenues for the efficient synthesis of valuable monoterpenes in Y. lipolytica.

MedT5SQL: a transformers-based large language model for text-to-SQL conversion in the healthcare domain.

Introduction: In response to the increasing prevalence of electronic medical records (EMRs) stored in databases, healthcare staff are encountering difficulties retrieving these records due to their limited technical expertise in database operations. As these records are crucial for delivering appropriate medical care, there is a need for an accessible method for healthcare staff to access EMRs. Methods: To address this, natural language processing (NLP) for Text-to-SQL has emerged as a solution, enabling non-technical users to generate SQL queries using natural language text. This research assesses existing work on Text-to-SQL conversion and proposes the MedT5SQL model specifically designed for EMR retrieval. The proposed model utilizes the Text-to-Text Transfer Transformer (T5) model, a Large Language Model (LLM) commonly used in various text-based NLP tasks. The model is fine-tuned on the MIMICSQL dataset, the first Text-to-SQL dataset for the healthcare domain. Performance evaluation involves benchmarking the MedT5SQL model on two optimizers, varying numbers of training epochs, and using two datasets, MIMICSQL and WikiSQL. Results: For MIMICSQL dataset, the model demonstrates considerable effectiveness in generating question-SQL pairs achieving accuracy of 80.63%, 98.937%, and 90% for exact match accuracy matrix, approximate string-matching, and manual evaluation, respectively. When testing the performance of the model on WikiSQL dataset, the model demonstrates efficiency in generating SQL queries, with an accuracy of 44.2% on WikiSQL and 94.26% for approximate string-matching. Discussion: Results indicate improved performance with increased training epochs. This work highlights the potential of fine-tuned T5 model to convert medical-related questions written in natural language to Structured Query Language (SQL) in healthcare domain, providing a foundation for future research in this area.

Mediating Effects of Self-Efficacy and Illness Perceptions on Mental Health in Men with Localized Prostate Cancer: A Secondary Analysis of the Prostate Cancer Patient Empowerment Program (PC-PEP) Randomized Controlled Trial.

Understanding how interventions reduce psychological distress in patients with prostate cancer is crucial for improving patient care. This study examined the roles of self-efficacy, illness perceptions, and heart rhythm coherence in mediating the effects of the Prostate Cancer Patient Empowerment Program (PC-PEP) on psychological distress compared to standard care. In a randomized controlled trial, 128 patients were assigned to either the PC-PEP intervention or standard care. The PC-PEP, a six-month program emphasizing daily healthy living habits, included relaxation and stress management, diet, exercise, pelvic floor muscle exercises, and strategies to improve relationships and intimacy, with daily activities supported by online resources and live sessions. Participants in the intervention group showed significant improvements in self-efficacy and specific illness perceptions, such as personal control and emotional response, compared to the control group. These factors mediated the relationship between the intervention and its psychological benefits, with self-efficacy accounting for 52% of the reduction in psychological distress. No significant differences in heart rhythm coherence were observed. This study highlights the critical role of self-efficacy and illness perceptions in enhancing psychological health in prostate cancer patients through the PC-PEP. The results underscore this program's effectiveness and the key mechanisms through which it operates. Given the high rates of distress among men undergoing prostate cancer treatments, these findings emphasize the importance of integrating the PC-PEP into clinical practice. The implementation of the PC-PEP in clinical settings can provide a structured approach to reducing psychological distress and improving overall patient well-being.

Patient-reported outcomes and healthcare resource utilization in systemic lupus erythematosus: impact of disease activity.

BACKGROUND: Limited real-world data exists on clinical outcomes in systemic lupus erythematosus (SLE) patients by SLE Disease Activity Index 2000 (SLEDAI-2 K), hereafter, SLEDAI. We aimed to examine the association between SLEDAI score and clinical, patient-reported and economic outcomes in patients with SLE. METHODS: Rheumatologists from the United States of America and Europe provided real-world demographic, clinical, and healthcare resource utilization (HCRU) data for SLE patients. Patients provided self-reported outcome data, capturing their general health status using the EuroQol 5-dimension 3-level questionnaire (EQ-5D-3 L), health-related quality of life using the Functional Assessment of Chronic Illness Therapy (FACIT) and work productivity using the Work Productivity and Activity Impairment questionnaire (WPAI). Low disease activity was defined as SLEDAI score ≤ 4 and ≤ 7.5 mg/day glucocorticoids; patients not meeting these criteria were considered to have "higher" active disease. Data were compared between patients with low and higher disease activity. Logistic regression estimated a propensity score for SLE based on demographic and clinical characteristics. Propensity score matched analyses compared HCRU, patient-reported outcomes, income loss and treatment satisfaction in patients with low disease activity versus higher active disease. RESULTS: Data from 296 physicians reporting on 730 patients (46 low disease activity, 684 higher active disease), and from 377 patients' self-reported questionnaires (24 low disease activity, 353 higher active disease) were analyzed. Flaring in the previous 12 months was 2.6-fold more common among patients with higher versus low active disease. Equation 5D-3 L utility index was 0.79 and 0.88 and FACIT-Fatigue scores were 34.78 and 39.79 in low versus higher active disease patients, respectively, indicating better health and less fatigue, among patients with low versus higher active disease. Absenteeism, presenteeism, overall work impairment, and total activity impairment were 47.0-, 2.0-, 2.6- and 1.5-fold greater in patients with higher versus low disease activity. In the previous 12 months there were 28% more healthcare consultations and 3.4-fold more patients hospitalized in patients with higher versus low disease activity. CONCLUSION: Compared to SLE patients with higher active disease, patients with low disease activity experienced better health status, lower HCRU, less fatigue, and lower work productivity impairment, with work absenteeism being substantially lower in these patients.

Large contribution of in-cloud production of secondary organic aerosol from biomass burning emissions.

Organic compounds released from wildfires and residential biomass burning play a crucial role in shaping the composition of the atmosphere. The solubility and subsequent reactions of these compounds in the aqueous phase of clouds and fog remain poorly understood. Nevertheless, these compounds have the potential to become an important source of secondary organic aerosol (SOA). In this study, we simulated the aqueous SOA (aqSOA) from residential wood burning emissions under atmospherically relevant conditions of gas-liquid phase partitioning, using a wetted-wall flow reactor (WFR). We analyzed and quantified the specific compounds present in these emissions at a molecular level and determined their solubility in clouds. Our findings reveal that while 1% of organic compounds are fully water-soluble, 19% exhibit moderate solubility and can partition into the aqueous phase in a thick cloud. Furthermore, it is found that the aqSOA generated in our laboratory experiments has a substantial fraction being attributed to the formation of oligomers in the aqueous phase. We also determined an aqSOA yield of 20% from residential wood combustion, which surpasses current estimates based on gas-phase oxidation. These results indicate that in-cloud chemistry of organic gases emitted from wood burning can serve as an efficient pathway to produce organic aerosols, thus potentially influencing climate and air quality.

Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity.

Arthropods contribute importantly to ecosystem functioning but remain understudied. This undermines the validity of conservation decisions. Modern methods are now making arthropods easier to study, since arthropods can be mass-trapped, mass-identified, and semi-mass-quantified into 'many-row (observation), many-column (species)' datasets, with homogeneous error, high resolution, and copious environmental-covariate information. These 'novel community datasets' let us efficiently generate information on arthropod species distributions, conservation values, uncertainty, and the magnitude and direction of human impacts. We use a DNA-based method (barcode mapping) to produce an arthropod-community dataset from 121 Malaise-trap samples, and combine it with 29 remote-imagery layers using a deep neural net in a joint species distribution model. With this approach, we generate distribution maps for 76 arthropod species across a 225 km2 temperate-zone forested landscape. We combine the maps to visualize the fine-scale spatial distributions of species richness, community composition, and site irreplaceability. Old-growth forests show distinct community composition and higher species richness, and stream courses have the highest site-irreplaceability values. With this 'sideways biodiversity modelling' method, we demonstrate the feasibility of biodiversity mapping at sufficient spatial resolution to inform local management choices, while also being efficient enough to scale up to thousands of square kilometres. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

Temperature, humidity, and ionisation effect of iodine oxoacid nucleation.

Iodine oxoacids are recognised for their significant contribution to the formation of new particles in marine and polar atmospheres. Nevertheless, to incorporate the iodine oxoacid nucleation mechanism into global simulations, it is essential to comprehend how this mechanism varies under various atmospheric conditions. In this study, we combined measurements from the CLOUD (Cosmic Leaving OUtdoor Droplets) chamber at CERN and simulations with a kinetic model to investigate the impact of temperature, ionisation, and humidity on iodine oxoacid nucleation. Our findings reveal that ion-induced particle formation rates remain largely unaffected by changes in temperature. However, neutral particle formation rates experience a significant increase when the temperature drops from +10 °C to -10 °C. Running the kinetic model with varying ionisation rates demonstrates that the particle formation rate only increases with a higher ionisation rate when the iodic acid concentration exceeds 1.5 × 107 cm-3, a concentration rarely reached in pristine marine atmospheres. Consequently, our simulations suggest that, despite higher ionisation rates, the charged cluster nucleation pathway of iodic acid is unlikely to be enhanced in the upper troposphere by higher ionisation rates. Instead, the neutral nucleation channel is likely to be the dominant channel in that region. Notably, the iodine oxoacid nucleation mechanism remains unaffected by changes in relative humidity from 2% to 80%. However, under unrealistically dry conditions (below 0.008% RH at +10 °C), iodine oxides (I2O4 and I2O5) significantly enhance formation rates. Therefore, we conclude that iodine oxoacid nucleation is the dominant nucleation mechanism for iodine nucleation in the marine and polar boundary layer atmosphere.

Real-Time Identification of Aerosol-Phase Carboxylic Acid Production Using Extractive Electrospray Ionization Mass Spectrometry.

Comprehensive identification of aerosol sources and their constituent organic compounds requires aerosol-phase molecular-level characterization with a high time resolution. While real-time chemical characterization of aerosols is becoming increasingly common, information about functionalization and structure is typically obtained from offline methods. This study presents a method for determining the presence of carboxylic acid functional groups in real time using extractive electrospray ionization mass spectrometry based on measurements of [M - H + 2Na]+ adducts. The method is validated and characterized using standard compounds. A proof-of-concept application to α-pinene secondary organic aerosol (SOA) shows the ability to identify carboxylic acids even in complex mixtures. The real-time capability of the method allows for the observation of the production of carboxylic acids, likely formed in the particle phase on short time scales (<120 min). Our research explains previous findings of carboxylic acids being a significant component of SOA and a quick decrease in peroxide functionalization following SOA formation. We show that the formation of these acids is commensurate with the increase of dimers in the particle phase. Our results imply that SOA is in constant evolution through condensed-phase processes, which lower the volatility of the aerosol components and increase the available condensed mass for SOA growth and, therefore, aerosol mass loading in the atmosphere. Further work could aim to quantify the effect of particle-phase acid formation on the aerosol volatility distributions.

Unsupervised restoration of a complex learned behavior after large-scale neuronal perturbation.

Reliable execution of precise behaviors requires that brain circuits are resilient to variations in neuronal dynamics. Genetic perturbation of the majority of excitatory neurons in HVC, a brain region involved in song production, in adult songbirds with stereotypical songs triggered severe degradation of the song. The song fully recovered within 2 weeks, and substantial improvement occurred even when animals were prevented from singing during the recovery period, indicating that offline mechanisms enable recovery in an unsupervised manner. Song restoration was accompanied by increased excitatory synaptic input to neighboring, unmanipulated neurons in the same brain region. A model inspired by the behavioral and electrophysiological findings suggests that unsupervised single-cell and population-level homeostatic plasticity rules can support the functional restoration after large-scale disruption of networks that implement sequential dynamics. These observations suggest the existence of cellular and systems-level restorative mechanisms that ensure behavioral resilience.

Exogenous Insulin Antibody Syndrome (EIAS) Presenting in an Elderly, Long-Term Patient with Type 1 Diabetes Mellitus that Resolved with Low-Cost Outpatient Therapy with Mycophenolate Mofetil and Regular Insulin by Pump.

Exogenous insulin antibody syndrome (EIAS) has until recently been a rarely described complication of exogenous insulin therapy. EIAS results not only in hyperglycemia, but also in hypoglycemia and occasionally in ketoacidosis (DKA). The incidence of EIAS is increasing probably due to an overall increase in autoimmunity associated with the coronavirus disease 2019 (Covid-19) epidemic resulting in increasing binding of insulin by antibodies. Herein, we describe a case of EIAS occurring in an elderly patient with longstanding type 1 diabetes mellitus (T1DM) who had progressive loss of glycemic control. It responded positively, as we have previously described, to oral mycophenolate mofetil and the use of soluble regular insulin delivered by continuous subcutaneous insulin infusion (CSII). Therefore, EIAS is an increasingly frequent cause of hyperglycemia with and without DKA, and hypoglycemia in subjects with T1DM. Once diagnosed, they can be treated with mycophenolate mofetil and soluble insulin in an outpatient setting, which will decrease the rate of hospitalization and lower the expense of therapy.

Six-Month Prostate Cancer Empowerment Program (PC-PEP) Improves Urinary Function: A Randomized Trial.

Purpose: This is a secondary analysis examining a six-month home-based Prostate Cancer-Patient Empowerment Program (PC-PEP) on patient-reported urinary, bowel, sexual, and hormonal function in men with curative prostate cancer (PC) against standard of care. Methods: In a crossover clinical trial, 128 men scheduled for PC surgery (n = 62) or radiotherapy with/without hormones (n = 66) were randomized to PC-PEP (n = 66) or waitlist-control and received the standard of care for 6 months, and then PC-PEP to the end of the year. PC-PEP included daily emails with video instructions, aerobic and strength training, dietary guidance, stress management, and social support, with an initial PFMT nurse consultation. Over 6 months, participants in the PC-PEP received optional text alerts (up to three times daily) reminding them to follow the PFMT video program, encompassing relaxation, quick-twitch, and endurance exercises; compliance was assessed weekly. Participants completed baseline, 6, and 12-month International Prostate Symptom Score (IPSS) and Expanded Prostate Cancer Index Composite (EPIC) questionnaires. Results: At 6 months, men in the PC-PEP reported improved urinary bother (IPSS, p = 0.004), continence (EPIC, p < 0.001), and irritation/obstruction function (p = 0.008) compared to controls, with sustained urinary continence benefits at 12 months (p = 0.002). Surgery patients in the waitlist-control group had 3.5 (95% CI: 1.2, 10, p = 0.024) times and 2.3 (95% CI: 0.82, 6.7, p = 0.11) times higher odds of moderate to severe urinary problems compared to PC-PEP at 6 and 12 months, respectively. Conclusions: PC-PEP significantly improves lower urinary tract symptoms, affirming its suitability for clinical integration alongside established mental health benefits in men with curative prostate cancer.

Dual quantum spin Hall insulator by density-tuned correlations in TaIrTe4.

The convergence of topology and correlations represents a highly coveted realm in the pursuit of new quantum states of matter1. Introducing electron correlations to a quantum spin Hall (QSH) insulator can lead to the emergence of a fractional topological insulator and other exotic time-reversal-symmetric topological order2-8, not possible in quantum Hall and Chern insulator systems. Here we report a new dual QSH insulator within the intrinsic monolayer crystal of TaIrTe4, arising from the interplay of its single-particle topology and density-tuned electron correlations. At charge neutrality, monolayer TaIrTe4 demonstrates the QSH insulator, manifesting enhanced nonlocal transport and quantized helical edge conductance. After introducing electrons from charge neutrality, TaIrTe4 shows metallic behaviour in only a small range of charge densities but quickly goes into a new insulating state, entirely unexpected on the basis of the single-particle band structure of TaIrTe4. This insulating state could arise from a strong electronic instability near the van Hove singularities, probably leading to a charge density wave (CDW). Remarkably, within this correlated insulating gap, we observe a resurgence of the QSH state. The observation of helical edge conduction in a CDW gap could bridge spin physics and charge orders. The discovery of a dual QSH insulator introduces a new method for creating topological flat minibands through CDW superlattices, which offer a promising platform for exploring time-reversal-symmetric fractional phases and electromagnetism2-4,9,10.

The potential for improved outcomes in the prevention and therapy of diabetic kidney disease through 'stacking' of drugs from different classes.

Aggressive therapy of diabetic kidney disease (DKD) can not only slow the progression of DKD to renal failure but, if utilized at an early enough stage of DKD, can also stabilize and/or reverse the decline in renal function. The currently recognized standard of therapy for DKD is blockade of the renin-angiotensin system with angiotensin-converting enzyme (ACE) inhibitors or angiotensin II receptor blockers (ARBs). However, unless utilized at a very early stage, monotherapy with these drugs in DKD will only prevent or slow the progression of DKD and will neither stabilize nor reverse the progression of DKD to renal decompensation. Recently, the addition of a sodium-glucose cotransporter-2 inhibitor and/or a mineralocorticoid receptor blocker to ACE inhibitors or ARBs has been clearly shown to further decelerate the decline in renal function. The use of glucagon-like peptide-1 (GLP-1) agonists shown promise in decelerating the progression of DKD. Other drugs that may aid in the deceleration the progression of DKD are dipeptidyl peptidase-4 inhibitors, pentoxifylline, statins, and vasodilating beta blockers. Therefore, aggressive therapy with combinations of these drugs (stacking) should improve the preservation of renal function in DKD.

PC-PEP, a Comprehensive Daily Six-Month Home-Based Patient Empowerment Program Leads to Weight Loss in Men with Prostate Cancer: A Secondary Analysis of a Clinical Trial.

Background: The Prostate Cancer-Patient Empowerment Program (PC-PEP) is a six-month daily home-based program shown to improve mental health and urinary function. This secondary analysis explores weight loss in male PC-PEP participants. Methods: In a randomized clinical trial with 128 men undergoing curative prostate cancer (PC) treatment, 66 received 'early' PC-PEP, while 62 were assigned to the 'late' waitlist-control group, receiving 6 months of standard-of-care treatment followed by 6 months of PC-PEP. PC-PEP comprised 182 daily emails with video-based exercise and dietary (predominantly plant-based) education, live online events, and 30 min strength training routines (using body weight and elastic bands). Weight and height data were collected via online surveys (baseline, 6 months, and 12 months) including medical chart reviews. Adherence was tracked weekly. Results: No attrition or adverse events were reported. At 6 months, the early PC-PEP group experienced significant weight loss, averaging 2.7 kg (p < 0.001) compared to the waitlist-control group. Weight loss was noted in the late intervention group of PC-PEP, albeit less pronounced than in the early group. Early PC-PEP surgery patients lost on average 1.4 kg (SE = 0.65) from the trial's start to surgery day. High adherence to exercise and dietary recommendations was noted. Conclusions: PC-PEP led to significant weight loss in men undergoing curative prostate cancer treatment compared to standard-of-care.

Extraction of volatile organic compounds liberated upon filament extrusion by 3D pen and its comparison with a desktop 3D printer using solid-phase microextraction fiber and Arrow.

Desktop 3D printers that operate by the fused deposition modeling (FDM) mechanism are known to release numerous hazardous volatile organic compounds (VOCs) during printing, including some with potential carcinogenic effects. Operating in a similar manner to FDM 3D printers, 3D pens have gained popularity recently from their ability to allow users to effortlessly draw in the air or create various 3D printed shapes while handling the device like a pen. In contrast to numerous modern 3D printers, 3D pens lack their own ventilation systems and are often used in settings with minimum airflow. Their operation makes users more vulnerable to VOC emissions, as the released VOCs are likely to be in the breathing zone. Consequently, monitoring VOCs released during the use of 3D pens is crucial. In this study, VOCs liberated while extruding acrylonitrile butadiene styrene (ABS) filaments from a 3D pen were measured by solid-phase microextraction (SPME) combined with gas chromatography/mass spectrometry (GC/MS). SPME was investigated using the traditional fiber and Arrow geometries with the DVB/Carbon WR/PDMS sorbent while four different brands of ABS filaments-Amazon Basics, Gizmodork, Mynt 3D, and Novamaker-were used with the 3D pen. Heatmap analysis showed differentiation among these brands based on the liberated VOCs. The nozzle temperature and printing speed were found to affect the number and amount of released VOCs. This study goes a step further and presents for the first time a comparison between 3D pen and a desktop 3D printer based on liberated VOCs. Interestingly, the findings reveal that the 3D pen releases a greater number and amount of VOCs compared to the printer. The amounts of liberated VOCs, as indicated by the corresponding chromatographic peak areas, were found to be 1.4 to 62.6 times higher for the 3D pen compared to the 3D printer when using SPME Arrow.

An in-depth analysis on the effects of body composition in patients receiving neoadjuvant chemotherapy for urothelial cell carcinoma.

INTRODUCTION: Neoadjuvant chemotherapy (NAC) is the standard of care for patients undergoing radical cystectomy (RC) for muscle-invasive bladder cancer (MIBC); however, NAC can be associated with significant side effects and morbidity in some patients. NAC may contribute to sarcopenia, obesity, and the combination of the two. Our study examined the effects of NAC on body composition and the association between body composition and adverse events. METHODS: We created a retrospective database of patients with non-metastatic MIBC receiving NAC prior to RC. The change in skeletal muscle index (SMI) and fat mass index (FMI) was calculated using computed tomography (CT) scans done within three months prior to NAC and after the first two cycles. The association between body composition (sarcopenia, obesity, and sarcopenic obesity) and preoperative adverse events was investigated using a multivariable logistic regression. Changes in body composition were calculated using a paired Student's t-test. RESULTS: A total of 70 patients were included in our study. There was a mean decrease in SMI of 2.2±3.2 cm2/m2. Adiposity and FMI were unchanged by NAC. Sarcopenic obesity was found to be associated with adverse events among patients receiving NAC in the multivariable analysis. There was a total of 637 preoperative complications with grades 1-2 and 33 complications with grades 3-5. CONCLUSIONS: Based on our retrospective cohort study, NAC did not affect obesity and FMI, but there was a significant decrease in SMI. Sarcopenic obesity was associated with increased severity of NAC adverse events. As such, the presence of this factor may help predict tolerance of NAC.

Uncovering the dominant contribution of intermediate volatility compounds in secondary organic aerosol formation from biomass-burning emissions.

Organic vapors from biomass burning are a major source of secondary organic aerosols (SOAs). Previous smog chamber studies found that the SOA contributors in biomass-burning emissions are mainly volatile organic compounds (VOCs). While intermediate volatility organic compounds (IVOCs) are efficient SOA precursors and contribute a considerable fraction of biomass-burning emissions, their contribution to SOA formation has not been directly observed. Here, by deploying a newly-developed oxidation flow reactor to study SOA formation from wood burning, we find that IVOCs can contribute ∼70% of the formed SOA, i.e. >2 times more than VOCs. This previously missing SOA fraction is interpreted to be due to the high wall losses of semi-volatile oxidation products of IVOCs in smog chambers. The finding in this study reveals that SOA production from biomass burning is much higher than previously thought, and highlights the urgent need for more research on the IVOCs from biomass burning and potentially other emission sources.