TopoRoot+: computing whorl and soil line traits of field-excavated maize roots from CT imaging.

BACKGROUND: The use of 3D imaging techniques, such as X-ray CT, in root phenotyping has become more widespread in recent years. However, due to the complexity of the root structure, analyzing the resulting 3D volumes to obtain detailed architectural root traits remains a challenging computational problem. When it comes to image-based phenotyping of excavated maize root crowns, two types of root features that are notably missing from existing methods are the whorls and soil line. Whorls refer to the distinct areas located at the base of each stem node from which roots sprout in a circular pattern (Liu S, Barrow CS, Hanlon M, Lynch JP, Bucksch A. Dirt/3D: 3D root phenotyping for field-grown maize (zea mays). Plant Physiol. 2021;187(2):739-57. https://doi.org/10.1093/plphys/kiab311 .). The soil line is where the root stem meets the ground. Knowledge of these features would give biologists deeper insights into the root system architecture (RSA) and the below- and above-ground root properties. RESULTS: We developed TopoRoot+, a computational pipeline that produces architectural traits from 3D X-ray CT volumes of excavated maize root crowns. Building upon the TopoRoot software (Zeng D, Li M, Jiang N, Ju Y, Schreiber H, Chambers E, et al. Toporoot: A method for computing hierarchy and fine-grained traits of maize roots from 3D imaging. Plant Methods. 2021;17(1). https://doi.org/10.1186/s13007-021-00829-z .) for computing fine-grained root traits, TopoRoot + adds the capability to detect whorls, identify nodal roots at each whorl, and compute the soil line location. The new algorithms in TopoRoot + offer an additional set of fine-grained traits beyond those provided by TopoRoot. The addition includes internode distances, root traits at every hierarchy level associated with a whorl, and root traits specific to above or below the ground. TopoRoot + is validated on a diverse collection of field-grown maize root crowns consisting of nine genotypes and spanning across three years. TopoRoot + runs in minutes for a typical volume size of [Formula: see text] on a desktop workstation. Our software and test dataset are freely distributed on Github. CONCLUSIONS: TopoRoot + advances the state-of-the-art in image-based phenotyping of excavated maize root crowns by offering more detailed architectural traits related to whorls and soil lines. The efficiency of TopoRoot + makes it well-suited for high-throughput image-based root phenotyping.

Clinical outcomes with cardiac resynchronization therapy in patients with Cardiac Sarcoidosis: A systematic review and proportional meta-analysis.

BACKGROUND: Cardiac sarcoidosis (CS) is an inflammatory condition that can present with heart failure (HF). Cardiac resynchronization therapy (CRT) is known to improve clinical outcomes for patients with left bundle branch block in the general HF population. However, data about the outcomes of CRT in CS is limited. METHODS: A systematic literature search was conducted using PubMed/Medline, Embase, and the Cochrane Library from inception to February 2024 to identify studies that reported clinical outcomes following the use of CRT in patients with CS. Data for outcomes was extracted, pooled, and analyzed. OpenMetaAnalyst was used for pooling untransformed proportions along with the corresponding 95 % confidence intervals (CIs). RESULTS: Five studies with a total of 176 CS patients who received CRT were included. The pooled incidence for all-cause mortality was 7.6 % (95 % CI: -3 % to 18 %), for HF-related hospitalizations 23.2 % (95 % CI: 2 % to 43 %), and for major adverse cerebral and cardiovascular events 27 % (95 % CI: 8 % to 45 %) after a mean follow-up of 60.1 (±48.7) months. The pooled left ventricular ejection fraction (LVEF) was 34.28 % (95 % CI: 29.88 % to 38.68 %) demonstrating an improvement of 3.75 % in LVEF from baseline LVEF of 30.58 % (95 % CI: 24.68 % to 36.48 %). The mean New York Heart Association (NYHA) functional class was 2.16 (95 % CI: 1.47 to 2.84) after CRT as compared to the baseline mean NYHA of 2.58 (95 % CI: 2.29 to 2.86). CONCLUSION: Although improvements were observed in LVEF and mean NYHA, mortality was high in CS patients with CRT.

Risk Factors of Acute Ischemic Stroke and Mortality Among Adults With Endocardial Fibroelastosis.

OBJECTIVES: Endocardial fibroelastosis (EFE) is a rare form of restrictive cardiomyopathy associated with high morbidity and mortality. The literature is sparse on information pertaining to risk stratification. Thus, we sought to highlight the risk factors of acute ischemic stroke (AIS) and mortality in adults with EFE. METHODS: The National Inpatient Sample (NIS) database was queried from 2001 to 2020 using the International Classification of Diseases 9th Revision (ICD-9) and 10th Revision (ICD-10) codes for adult patients with EFE. Factors associated with AIS and mortality were identified. RESULTS: In all, 18495 cases of EFE fit the inclusion criteria, of which 2370 (12.82%) had AIS. The mean ages for patients with and without AIS were 62.37 and 54.24, respectively. Multivariate regression suggested greater odds of AIS in patients with hypertension (aOR 2.329, P<0.01), dyslipidemia (aOR: 1.566, P<0.01), peripheral vascular disease (PVD) (aOR: 1.736, P<0.01), alcohol abuse (aOR: 1.817, P<0.01), age >60 y (aOR: 1.646, P<0.01), females (vs. males, aOR: 1.238, P<0.01), and smokers (aOR: 1.697, P<0.01). Patients with cirrhosis (aOR: 0.174, P<0.01), CKD (aOR: 0.369, P<0.01), COPD (aOR: 0.402, P<0.01), atrial fibrillation (aOR: 0.542, P<0.01) had lower odds of AIS. 3.1% of EFE patients with AIS died. Diabetes (aOR: 11.665, P<0.01) and COPD (aOR: 3.201, P=0.017) were associated with the greatest odds of all-cause mortality. Dyslipidemia (aOR: 0.387, P=0.010) and females (vs. males, aOR: 0.432, P=0.012) had reduced odds of all-cause mortality. CONCLUSION: Several risk factors are associated with AIS in EFE, while diabetes, COPD, and being male are associated with mortality in EFE.

'Conga lines' of Ediacaran fronds: insights into the reproductive biology of early metazoans.

Late Ediacaran strata from Newfoundland, Canada (~574-560 Ma) document near-census palaeocommunities of some of the earliest metazoans. Such preservation enables reproductive strategies to be inferred from the spatial distribution of populations of fossilized benthic organisms, previously revealing the existence of both propagule and stoloniferous reproductive modes among Ediacaran frondose taxa. Here, we describe 'conga lines': linear arrangements of more than three closely spaced fossil specimens. We calculate probabilistic models of point maps of 13 fossil-bearing bedding surfaces and show that four surfaces contain conga lines that are not the result of chance alignments. We then test whether these features could result from passive pelagic propagules settling in the lee of an existing frond, using computational fluid dynamics and discrete phase modelling. Under Ediacaran palaeoenvironmental conditions, preferential leeside settlement at the spatial scale of the conga lines is unlikely. We therefore conclude that these features are novel and do not reflect previously described reproductive strategies employed by Ediacaran organisms, suggesting the use of mixed reproductive strategies in the earliest animals. Such strategies enabled Ediacaran frondose taxa to act as reproductive generalists and may be an important facet of early metazoan evolution.

Nonidealities in CO2 Electroreduction Mechanisms Revealed by Automation-Assisted Kinetic Analysis.

In electrocatalysis, mechanistic analysis of reaction rate data often relies on the linearization of relatively simple rate equations; this is the basis for typical Tafel and reactant order dependence analyses. However, for more complex reaction phenomena, such as surface coverage effects or mixed control, these common linearization strategies will yield incomplete or uninterpretable results. Cohesive kinetic analysis, which is often used in thermocatalysis and involves quantitative model fitting for data collected over a wide range of reaction conditions, requires more data but also provides a more robust strategy for interrogating reaction mechanisms. In this work, we report a robotic system that improves the experimental workflow for collecting electrochemical rate data by automating sequential testing of up to 10 electrochemical cells, where each cell can have a different electrode, electrolyte, gas-phase reactant composition, and applied voltage. We used this system to investigate the mechanism of carbon dioxide electroreduction to carbon monoxide at several immobilized metal tetrapyrroles. Specifically, at cobalt phthalocyanine (CoPc), cobalt tetraphenylporphyrin (CoTPP), and iron phthalocyanine (FePc), we see signatures of complex reaction mechanisms, where observed bicarbonate and CO2 order dependences change with applied potential. We illustrate how phenomena such as electrolyte poisoning and potential-dependent degrees of rate control can explain the observed kinetic behaviors. Our mechanistic analysis suggests that CoPc and CoTPP share a similar reaction mechanism, akin to one previously proposed, whereas the mechanism for FePc likely involves a species later in the catalytic cycle as the most abundant reactive intermediate. Our study illustrates that complex reaction mechanisms that are not amenable to common Tafel and order dependence analyses may be quite prevalent across this class of immobilized metal tetrapyrrole electrocatalysts.

A late-Ediacaran crown-group sponge animal.

Sponges are the most basal metazoan phylum1 and may have played important roles in modulating the redox architecture of Neoproterozoic oceans2. Although molecular clocks predict that sponges diverged in the Neoproterozoic era3,4, their fossils have not been unequivocally demonstrated before the Cambrian period5-8, possibly because Precambrian sponges were aspiculate and non-biomineralized9. Here we describe a late-Ediacaran fossil, Helicolocellus cantori gen. et sp. nov., from the Dengying Formation (around 551-539 million years ago) of South China. This fossil is reconstructed as a large, stemmed benthic organism with a goblet-shaped body more than 0.4 m in height, with a body wall consisting of at least three orders of nested grids defined by quadrate fields, resembling a Cantor dust fractal pattern. The resulting lattice is interpreted as an organic skeleton comprising orthogonally arranged cruciform elements, architecturally similar to some hexactinellid sponges, although the latter are built with biomineralized spicules. A Bayesian phylogenetic analysis resolves H. cantori as a crown-group sponge related to the Hexactinellida. H. cantori confirms that sponges diverged and existed in the Precambrian as non-biomineralizing animals with an organic skeleton. Considering that siliceous biomineralization may have evolved independently among sponge classes10-13, we question the validity of biomineralized spicules as a necessary criterion for the identification of Precambrian sponge fossils.

Comparing outcomes of an 'early' versus 'late' diagnosis of cardiac sarcoidosis following a baseline presentation of high-grade atrioventricular block.

BACKGROUND: There is a paucity of evidence on impact of a delay in Cardiac Sarcoidosis (CS) diagnosis after high-grade atrioventricular-block (AVB) and this study aims to fill this void. METHODS: Consecutive CS patients (n = 77) with high grade AVB referred to one specialist hospital in London between February 2007 to February 2023 were retrospectively reviewed. The median time from AVB to diagnosing CS (112 days) was used to define the Early (n = 38) and Late (n = 39) cohorts. The primary endpoint was a composite of all-cause mortality, cardiac transplantation, ventricular arrhythmic events or heart failure hospitalisation. Secondary endpoints included difference in maintenance prednisolone dose, need for cardiac device upgrade and device complications. RESULTS: The mean age of the cohort was 54.4 (±10.6) years of whom 64 % were male and 81 % Caucasian. After a mean follow up of 54.9 (±45.3) months, the primary endpoint was reached by more patients from the Late cohort (16/39 vs. 6/38, p = 0.02; multivariable HR 6.9; 95 %CI 1.5-32.2, p = 0.01). Early Group were more likely to have received an Implantable Cardioverter Defibrillator or Cardiac Resynchronisation Therapy-defibrillator as index device after AVB (19/38 vs. 6/39; p < 0.01) and had fewer device upgrades (19/38 vs. 30/39, p = 0.01) and a trend towards fewer device complications (1 vs. 5, p = 0.20). The maintenance dose of prednisolone was significantly higher in Late Group [20.7(±9.7) mg vs. 15.3(±7.9) mg, p = 0.02]. CONCLUSION: A late diagnosis of CS was associated with more adverse events, a greater probability of needing a device upgrade and required higher maintenance steroid dose.

Characterisation and management of expected and unexpected urgent findings from positron emission tomography with 18F-fluorodeoxyglucose integrated with computed tomography in cardiovascular disease.

BACKGROUND: Cardiac 18F-fluorodeoxyglucose (FDG)-PET-CT plays an important role in the assessment of cardiovascular diseases. Effective management of urgent scan findings facilitates optimal patient care. METHODS: We characterised the management of urgent, expected and unexpected findings in patients referred for cardiac [18F]fluorodeoxyglucose integrated with computed tomography (FDG-PET-CT) at the Royal Brompton Hospital (United Kingdom). Urgent findings are escalated by the reporting physicians/radiologists raising RadAlert notifications to the referring clinician. We characterised the indications and time to management (TTM) between the RadAlert and the resulting management. As controls, we characterised the TTM of 33 urgent findings identified before the RadAlert system was implemented. RESULTS: Of the 1497 consecutive FDG-PET-CT scans screened (April 2021 to February 2023), 93 RadAlerts were suitable for analysis (TTM 7 days [interquartile range: 2-14]). Expected urgent findings included active cardiac sarcoidosis (56%; TTM 8 days [5-18]), heart transplant rejection (12%; 6 ± 4 days), infective endocarditis (9%; 2 days [1-12]), cardiac device infections (5%; 1 day [0-2]), acute myocarditis (2%; 5 and 14 days) and epicardial mass (1%; 1 day). TTM did not differ significantly between indications (P = 0.06). RadAlert cases had significantly shorter TTM than controls without RadAlert, P = 0.001. After the RadAlerts, 81% of patients had clinical reviews, and 55% had escalation of medical/surgical therapies. Unexpected findings (total N = 45; median TTM 6 days [1-10]) included malignancies (N = 3), infections (N = 2), pneumothorax (N = 1), benign diagnosis (N = 30), unclear diagnosis (N = 5) and 4 findings disappeared on repeat imaging. CONCLUSIONS: Cardiac FDG-PET-CT identifies expected and unexpected findings in a range of cardiovascular diseases. Serious, unexpected findings are rare and can be effectively escalated by the RadAlert system.

Sarcoidosis Associated Pulmonary Hypertension.

In patients with sarcoidosis, the development of pulmonary hypertension is associated with significant morbidity and mortality. The global prevalence of sarcoidosis-associated pulmonary hypertension (SAPH) reportedly ranges between 2.9% and 20% of sarcoidosis patients. Multiple factors may contribute to the development of SAPH, including advanced parenchymal lung disease, severe systolic and/or diastolic left ventricular dysfunction, veno-occlusive or thromboembolic disease, as well as extrinsic factors such as pulmonary vascular compression from enlarged lymph nodes, anemia, and liver disease. Early diagnosis of SAPH is important but rarely achieved primarily due to insufficiently accurate screening strategies, which rely entirely on non-invasive tests and clinical assessment. The definitive diagnosis of SAPH requires right heart catheterization (RHC), with transthoracic echocardiography as the recommended gatekeeper to RHC according to current guidelines. A 6-min walk test (6MWT) had the greatest prognostic value in SAPH patients based on recent registry outcomes, while advanced lung disease determined using a reduced DLCO (<35% predicted) was associated with reduced transplant-free survival in pre-capillary SAPH. Clinical management involves the identification and treatment of the underlying mechanism. Pulmonary vasodilators are useful in several scenarios, especially when a pulmonary vascular phenotype predominates. End-stage SAPH may warrant consideration for lung transplantation, which remains a high-risk option. Multi-centered randomized controlled trials are required to develop existing therapies further and improve the prognosis of SAPH patients.

Naturalistic food categories are driven by subjective estimates rather than objective measures of food qualities.

Food-related studies often categorize foods using criteria such as fat and sugar content (e.g., high-fat, high-sugar foods; low-fat, low-sugar foods), and use these categorizations for further analyses. While these criteria are relevant to nutritional health, it is unclear whether they agree with the ways in which we typically group foods. Do these objective categories correspond to our subjective sense? To address this question, we recruited a group of 487 online participants to perform a triplet comparison task involving implicit object similarity judgements on images of 36 foods, which varied in their levels of fat and sugar. We also acquired subjective ratings of other food properties from another set of 369 online participants. Data from the online triplet task was used to generate a similarity matrix of these 36 foods. Principal Components Analysis (PCA) of this matrix identified that the strongest determinant of food similarity (the first PC) was most highly related to participants' judgements of how processed the foods were, while the second component was most related to estimates of sugar and fat content. K-means clustering analysis revealed five emergent food groupings along these PC axes: sweets, fats, starches, fruits, and vegetables. Our results suggest that naturalistic categorizations of food are driven primarily by knowledge of the origin of foods (i.e., grown or manufactured), rather than by their sensory or macronutrient properties. These differences should be considered and explored when developing methods for scientific food studies.

Retromuscular drain output at removal does not influence adverse outcome rate in open ventral hernia repairs.

BACKGROUND: Retromuscular drains are commonly placed during retromuscular hernia repair (RHR) to decrease postoperative wound complications and help mesh in-growth. Drains are traditionally removed when output is low but the relationship between drain output at the time of removal and postoperative complications has yet to be delineated. This study aimed to investigate outcomes of RHR patients with drain removal at either high or low output volume. METHODS: An institutional review board-approved retrospective chart review evaluated adult patients undergoing open RHR with retromuscular drain placement between 2013 and 2022 at a single academic medical center. Patients were stratified into low output drainage (LOD, < 50 mL/day) or high output drainage (HOD, ≥ 50 mL/day) groups based on volume on the day of drain removal. RESULTS: We identified 336 patients meeting inclusion criteria: 58% LOD (n = 195) and 42% HOD (n = 141). Demographics and risk factors pertaining to hernia complexity were similar between cohorts. Low-drain output at the time of removal was associated with a significantly longer drain duration (6.3 ± 4.5 vs. 4.4 ± 1.6 days, p < 0.001) and postoperative hospital stay (5.9 ± 3.6 vs. 4.8 ± 2.8 days, p < 0.001). With a 97% 30-day follow-up, incidence of surgical site occurrence (SSO) was not statistically different between groups (29.2% LOD, 26.2% HOD, p = 0.63). Surgical site infection and SSO requiring procedural intervention was also not statistically significant between cohort. At 1-year follow-up, hernia recurrence rates were the same between groups (4.2% LOD, 1.4% HOD, p = 0.25). CONCLUSION: Following open ventral hernia repair with retromuscular mesh placement, the rate of postoperative wound complications was not statistically different based on volume of drain output day of removal. These results suggest that removing drains earlier despite higher output is safe and has no effect on short- or long-term hernia outcomes.

Vascular persistence following precision micropuncture.

OBJECTIVE: The success of engineered tissues continues to be limited by time to vascularization and perfusion. Recently, we described a simple microsurgical approach, termed micropuncture (MP), which could be used to rapidly vascularize an adjacently placed scaffold from the recipient macrovasculature. Here we studied the long-term persistence of the MP-induced microvasculature. METHODS: Segmental 60 µm diameter MPs were created in the recipient rat femoral artery and vein followed by coverage with a simple Type 1 collagen scaffold. The recipient vasculature and scaffold were then wrapped en bloc with a silicone sheet to isolate intrinsic vascularization. Scaffolds were harvested at 28 days post-implantation for detailed analysis, including using a novel artificial intelligence (AI) approach. RESULTS: MP scaffolds demonstrated a sustained increase of vascular density compared to internal non-MP control scaffolds (p < 0.05) secondary to increases in both vessel diameters (p < 0.05) and branch counts (p < 0.05). MP scaffolds also demonstrated statistically significant increases in red blood cell (RBC) perfused lumens. CONCLUSIONS: This study further highlights that the intrinsic MP-induced vasculature continues to persist long-term. Its combination of rapid and stable angiogenesis represents a novel surgical platform for engineered scaffold and graft perfusion.

Engineering the Polymer-MOF Interface in Microporous Composites to Address Complex Mixture Separations.

Poor interfacial compatibility remains a pressing challenge in the fabrication of high-performance polymer-MOF composites. In response, introducing compatible chemistries such as a carboxylic acid moiety has emerged as a compelling strategy to increase polymer-MOF interactions. In this work, we leveraged compatible functionalities in UiO-66-NH2 and a carboxylic acid-functionalized PIM-1 to fabricate mixed-matrix membranes (MMMs) with improved separation performance compared to PIM-1-based MMMs in industrially relevant conditions. Under pure-gas conditions, PIM-COOH-based MMMs retained selectivity with increasing MOF loading and showed increased permeability due to increased diffusion. The composites were further investigated under industrially relevant conditions, including CO2/N2, CO2/CH4, and H2S/CO2/CH4 mixtures, to elucidate the effects of competitive sorption and plasticization. Incorporation of UiO-66-NH2 in PIM-COOH and PIM-1 mitigated the effects of CO2- and H2S-induced plasticization typically observed in linear polymers. In CO2-based binary mixed-gas tests, all samples showed similar performance as that in pure-gas tests, with minimal competitive sorption contributions associated with the amine functional groups of the MOF. In ternary mixed-gas tests, improved plasticization resistance and interfacial compatibility resulted in PIM-COOH-based MMMs having the highest H2S/CH4 and CO2/CH4 selectivity combinations among the films tested in this study. These findings demonstrate that selecting MOFs and polymers with compatible functional groups is a useful strategy in developing high-performing microporous MMMs that require stability under complex and industrially relevant conditions.

Characterisation of Ferritin-Lymphocyte Ratio in COVID-19.

Introduction: The ferritin-lymphocyte ratio (FLR) is a novel inflammatory biomarker for the assessment of acute COVID-19 patients. However, the prognostic value of FLR for predicting adverse clinical outcomes in COVID-19 remains unclear, which hinders its clinical translation. Methods: We characterised the prognostic value of FLR in COVID-19 patients, as compared to established inflammatory markers. Results: In 217 study patients (69 years [IQR: 55-82]; 60% males), FLR was weakly correlated with CRP (R = 0.108, p = 0.115) and white cell count (R = -0.144; p = 0.034). On ROC analysis, an FLR cut-off of 286 achieved a sensitivity of 86% and a specificity of 30% for predicting inpatient mortality (AUC 0.60, 95% CI: 0.53-0.67). The negative predictive values of FLR for ruling out mortality, non-invasive ventilation requirement and critical illness (intubation and/or ICU admission) were 86%, 85% and 93%, respectively. FLR performed similarly to CRP (AUC 0.60 vs. 0.64; p = 0.375) for predicting mortality, but worse than CRP for predicting non-fatal outcomes (all p < 0.05). On Kaplan-Meier analysis, COVID-19 patients with FLR values > 286 had worse inpatient survival than patients with FLR ≤ 286, p = 0.041. Conclusions: FLR has prognostic value in COVID-19 patients, and appears unrelated to other inflammatory markers such as CRP and WCC. FLR exhibits high sensitivity and negative predictive values for adverse clinical outcomes in COVID-19, and may be a good "rule-out" test. Further work is needed to improve the sensitivity of FLR and validate its role in prospective studies for guiding clinical management.

Low CRB-65 Scores Effectively Rule out Adverse Clinical Outcomes in COVID-19 Irrespective of Chest Radiographic Abnormalities.

Background: CRB-65 (Confusion; Respiratory rate ≥ 30/min; Blood pressure ≤ 90/60 mmHg; age ≥ 65 years) is a risk score for prognosticating patients with COVID-19 pneumonia. However, a significant proportion of COVID-19 patients have normal chest X-rays (CXRs). The influence of CXR abnormalities on the prognostic value of CRB-65 is unknown, limiting its wider applicability. Methods: We assessed the influence of CXR abnormalities on the prognostic value of CRB-65 in COVID-19. Results: In 589 study patients (71 years (IQR: 57-83); 57% males), 186 (32%) had normal CXRs. On ROC analysis, CRB-65 performed similarly in patients with normal vs. abnormal CXRs for predicting inpatient mortality (AUC 0.67 ± 0.05 vs. 0.69 ± 0.03). In patients with normal CXRs, a CRB-65 of 0 ruled out mortality, NIV requirement and critical illness (intubation and/or ICU admission) with negative predictive values (NPVs) of 94%, 98% and 99%, respectively. In patients with abnormal CXRs, a CRB-65 of 0 ruled out the same endpoints with NPVs of 91%, 83% and 86%, respectively. Patients with low CRB-65 scores had better inpatient survival than patients with high CRB-65 scores, irrespective of CXR abnormalities (all p < 0.05). Conclusions: CRB-65, CXR and CRP are independent predictors of mortality in COVID-19. Adding CXR findings (dichotomised to either normal or abnormal) to CRB-65 does not improve its prognostic accuracy. A low CRB-65 score of 0 may be a good rule-out test for adverse clinical outcomes in COVID-19 patients with normal or abnormal CXRs, which deserves prospective validation.

A temporal analysis and response to nitrate availability of 3D root system architecture in diverse pennycress (Thlaspi arvense L.) accessions.

Introduction: Roots have a central role in plant resource capture and are the interface between the plant and the soil that affect multiple ecosystem processes. Field pennycress (Thlaspi arvense L.) is a diploid annual cover crop species that has potential utility for reducing soil erosion and nutrient losses; and has rich seeds (30-35% oil) amenable to biofuel production and as a protein animal feed. The objective of this research was to (1) precisely characterize root system architecture and development, (2) understand plastic responses of pennycress roots to nitrate nutrition, (3) and determine genotypic variance available in root development and nitrate plasticity. Methods: Using a root imaging and analysis pipeline, the 4D architecture of the pennycress root system was characterized under four nitrate regimes, ranging from zero to high nitrate concentrations. These measurements were taken at four time points (days 5, 9, 13, and 17 after sowing). Results: Significant nitrate condition response and genotype interactions were identified for many root traits, with the greatest impact observed on lateral root traits. In trace nitrate conditions, a greater lateral root count, length, density, and a steeper lateral root angle was observed compared to high nitrate conditions. Additionally, genotype-by-nitrate condition interaction was observed for root width, width:depth ratio, mean lateral root length, and lateral root density. Discussion: These findings illustrate root trait variance among pennycress accessions. These traits could serve as targets for breeding programs aimed at developing improved cover crops that are responsive to nitrate, leading to enhanced productivity, resilience, and ecosystem service.

Comparison of Lymphocyte-CRP Ratio to Conventional Inflammatory Markers for Predicting Clinical Outcomes in COVID-19.

Background: In COVID-19 patients, lymphocyte-CRP ratio (LCR) is a promising biomarker for predicting adverse clinical outcomes. How well LCR performs compared to conventional inflammatory markers for prognosticating COVID-19 patients remains unclear, which hinders the clinical translation of this novel biomarker. Methods: In a cohort of COVID-19 inpatients, we characterised the clinical applicability of LCR by comparing its prognostic value against conventional inflammatory markers for predicting inpatient mortality and a composite of mortality, invasive/non-invasive ventilation and intensive care unit admissions. Results: Of the 413 COVID-19 patients, 100 (24%) patients suffered inpatient mortality. On Receiver Operating Characteristics analysis, LCR performed similarly to CRP for predicting mortality (AUC 0.74 vs. 0.71, p = 0.049) and the composite endpoint (AUC 0.76 vs. 0.76, p = 0.812). LCR outperformed lymphocyte counts (AUC 0.74 vs. 0.66, p = 0.002), platelet counts (AUC 0.74 vs. 0.61, p = 0.003) and white cell counts (AUC 0.74 vs. 0.54, p < 0.001) for predicting mortality. On Kaplan-Meier analysis, patients with a low LCR (below a 58 cut-off) had worse inpatient survival than patients with other LCR values (p < 0.001). Conclusion: LCR appears comparable to CRP, but outperformed other inflammatory markers, for prognosticating COVID-19 patients. Further studies are required to improve the diagnostic value of LCR to facilitate clinical translation.

Quick and affordable DNA cloning by reconstitution of Seamless Ligation Cloning Extract using defined factors.

The cloning of DNA fragments to plasmid vectors is at the heart of molecular biology. Recent developments have led to various methods utilizing homologous recombination of homology arms. Among them, Seamless Ligation Cloning Extract (SLiCE) is an affordable alternative solution that uses simple Escherichia coli lysates. However, the underlying molecular mechanisms remain unclear and the reconstitution of the extract by defined factors has not yet been reported. We herein show that the key factor in SLiCE is Exonuclease III (ExoIII), a double-strand (ds) DNA-dependent 3'-5' exonuclease, encoded by XthA. SLiCE prepared from the xthAΔ strain is devoid of recombination activity, whereas purified ExoIII alone is sufficient to assemble two blunt-ended dsDNA fragments with homology arms. In contrast to SLiCE, ExoIII is unable to digest (or assemble) fragments with 3' protruding ends; however, the addition of single-strand DNA-targeting Exonuclease T overcomes this issue. Through the combination of commercially available enzymes under optimized conditions, we achieved the efficient, reproducible, and affordable cocktail, "XE cocktail," for seamless DNA cloning. By reducing the cost and time required for DNA cloning, researchers will devote more resources to advanced studies and the careful validation of their own findings.