Evolution at the Origins of Life?

The role of evolutionary theory at the origin of life is an extensively debated topic. The origin and early development of life is usually separated into a prebiotic phase and a protocellular phase, ultimately leading to the Last Universal Common Ancestor. Most likely, the Last Universal Common Ancestor was subject to Darwinian evolution, but the question remains to what extent Darwinian evolution applies to the prebiotic and protocellular phases. In this review, we reflect on the current status of evolutionary theory in origins of life research by bringing together philosophy of science, evolutionary biology, and empirical research in the origins field. We explore the various ways in which evolutionary theory has been extended beyond biology; we look at how these extensions apply to the prebiotic development of (proto)metabolism; and we investigate how the terminology from evolutionary theory is currently being employed in state-of-the-art origins of life research. In doing so, we identify some of the current obstacles to an evolutionary account of the origins of life, as well as open up new avenues of research.

Detection of Circulating Tumor DNA After Stereotactic Ablative Radiotherapy in Patients With Unbiopsied Lung Tumors (SABR-DETECT).

For patients with stage I/IIA non-small-cell lung cancer (NSCLC), surgical resection is the standard treatment. However, some of these patients are not candidates for surgery or refuse a surgical option. Definitive stereotactic ablative radiotherapy (SABR) is a standard approach in these patients. Approximately 15% of patients undergoing SABR for localized NSCLC will experience a recurrence within 2 years. Furthermore, many of these patients are deemed appropriate for SABR without a tissue diagnosis, based on the likelihood of malignancy which can be calculated by validated models. A liquid biopsy, detecting ctDNA, would be useful in early detection of recurrences, and documenting a cancer diagnosis in patients without a biopsy. This is a multi-institutional study enrolling patients with suspected stage I/IIA NSCLC and a pretreatment likelihood of malignancy of ≥60% using the validated models for patients without a tissue diagnosis, in cohort 1 (n = 45). The second cohort will consist of biopsied patients (n = 30-60). SABR will be delivered as per risk-adapted protocol. Plasma will be collected for ctDNA analysis prior to the first fraction of SABR, 24 to 72 hours after first fraction, and at 3, 6, 9, 12, 18, and 24-months. The patients will be followed up with imaging at 3, 6, 9, 12, 18, and 24-months. The primary objective is to assess whether a cancer detection liquid biopsy platform can predict recurrence of NSCLC. The secondary objectives are to assess the impact of SABR on detection rates of ctDNA in patients undergoing SABR and to correlate ctDNA positivity and pretreatment probability of malignancy (NCT05921474).

Open Source Antibiotics: Simple Diarylimidazoles Are Potent against Methicillin-Resistant Staphylococcus aureus.

Antimicrobial resistance (AMR) is widely acknowledged as one of the most serious public health threats facing the world, yet the private sector finds it challenging to generate much-needed medicines. As an alternative discovery approach, a small array of diarylimidazoles was screened against the ESKAPE pathogens, and the results were made publicly available through the Open Source Antibiotics (OSA) consortium (https://github.com/opensourceantibiotics). Of the 18 compounds tested (at 32 µg/mL), 15 showed >90% growth inhibition activity against methicillin-resistant Staphylococcus aureus (MRSA) alone. In the subsequent hit-to-lead optimization of this chemotype, 147 new heterocyclic compounds containing the diarylimidazole and other core motifs were synthesized and tested against MRSA, and their structure-activity relationships were identified. While potent, these compounds have moderate to high intrinsic clearance and some associated toxicity. The best overall balance of parameters was found with OSA_975, a compound with good potency, good solubility, and reduced intrinsic clearance in rat hepatocytes. We have progressed toward the knowledge of the molecular target of these phenotypically active compounds, with proteomic techniques suggesting TGFBR1 is potentially involved in the mechanism of action. Further development of these compounds toward antimicrobial medicines is available to anyone under the licensing terms of the project.

Biochar: An environmentally friendly platform for construction of a SARS-CoV-2 electrochemical immunosensor.

Waste management is a key feature to ensure sustainable consumption and production patterns, and to combat the impacts of climate change. In this scenario, the production of biochar from different biomasses results in environmental and economic advantages. In this study, biochar was produced from sugarcane bagasse pyrolysis, to immobilize biomolecules, in order to assemble an electrochemical immunosensor to detect antibodies against SARS-CoV-2. For this, screen-printed carbon electrodes (SPCE) were modified with a dispersion of biochar and used to immobilize the receptor-binding-domain (RBD) against virus S-protein, through EDC/NHS crosslinking reaction. Under the best set of experimental conditions, negative and positive serum samples responses distinguished based on a cutoff value of 82.3 %, at a 95 % confidence level. The immunosensor showed selective behavior to antibodies against yellow fever and its performance was stable up to 7 days of storage. Therefore, biochar yielded from sugarcane bagasse is an ecofriendly material that can be used as a platform to immobilize biomolecules for construction of electrochemical biosensors.

A Comparison of Hypofractionated and Twice-Daily Thoracic Irradiation in Limited-Stage Small-Cell Lung Cancer: An Overlap-Weighted Analysis.

Despite evidence for the superiority of twice-daily (BID) radiotherapy schedules, their utilization in practice remains logistically challenging. Hypofractionation (HFRT) is a commonly implemented alternative. We aim to compare the outcomes and toxicities in limited-stage small-cell lung cancer (LS-SCLC) patients treated with hypofractionated versus BID schedules. A bi-institutional retrospective cohort review was conducted of LS-SCLC patients treated with BID (45 Gy/30 fractions) or HFRT (40 Gy/15 fractions) schedules from 2007 to 2019. Overlap weighting using propensity scores was performed to balance observed covariates between the two radiotherapy schedule groups. Effect estimates of radiotherapy schedule on overall survival (OS), locoregional recurrence (LRR) risk, thoracic response, any ≥grade 3 (including lung, and esophageal) toxicity were determined using multivariable regression modelling. A total of 173 patients were included in the overlap-weighted analysis, with 110 patients having received BID treatment, and 63 treated by HFRT. The median follow-up was 20.4 months. Multivariable regression modelling did not reveal any significant differences in OS (hazard ratio [HR] 1.67, p = 0.38), LRR risk (HR 1.48, p = 0.38), thoracic response (odds ratio [OR] 0.23, p = 0.21), any ≥grade 3+ toxicity (OR 1.67, p = 0.33), ≥grade 3 pneumonitis (OR 1.14, p = 0.84), or ≥grade 3 esophagitis (OR 1.41, p = 0.62). HFRT, in comparison to BID radiotherapy schedules, does not appear to result in significantly different survival, locoregional control, or toxicity outcomes.

Treatment of hallux valgus by Scarf osteotomy - rates and reasons for recurrence and rates of avascular necrosis: A systematic review.

BACKGROUND: We reviewed the rates of and reasons for hallux valgus (HV) recurrence and the rates of avascular necrosis following Scarf osteotomy. METHODS: We searched the Cochrane Library, PubMed, and Embase databases for studies reporting operative management of HV using Scarf osteotomy. The primary endpoints were reasons for and rates of HV recurrence. The secondary endpoint was the rate of avascular necrosis. RESULTS: We included 15 studies with 946 operations for HV. Seven studies reported no recurrence, six reported recurrence rates of 3.6-11.3%, one reported a recurrence rate of 30%, and one reported a recurrence rate of 78%. Thirteen studies (678 feet) reported other complications from Scarf osteotomy without avascular necrosis. CONCLUSIONS: Although HV recurrence is not uncommon following Scarf osteotomy, patient-related factors, surgical competence, and longer follow-up are more likely to be associated with recurrence. Avascular necrosis is an infrequent complication in HV patients treated using Scarf osteotomy.

How can science be well-ordered in times of crisis? Learning from the SARS-CoV-2 pandemic.

The SARS-CoV-2 pandemic constituted a crisis situation in which science was very far from Kitcher's ideal of well-ordered science. I suggest that this could and should have been different. Kitcher's ideal should play a role in assessing the allocation of research resources in future crisis situations, as it provides a way to balance highly divergent interests and incorporate the common good into decision-making processes on research.

Taxa hold little information about organisms: Some inferential problems in biological systematics.

The taxa that appear in biological classifications are commonly seen as representing information about the traits of their member organisms. This paper examines in what way taxa feature in the storage and retrieval of such information. I will argue that taxa do not actually store much information about the traits of their member organisms. Rather, I want to suggest, taxa should be understood as functioning to localize organisms in the genealogical network of life on Earth. Taxa store information about where organisms are localized in the network, which is important background information when it comes to establishing knowledge about organismal traits, but it is not itself information about these traits. The view of species and higher taxa that is proposed here follows from examining three problems that occur in contemporary biological systematics and are discussed here: the problem of generalization over taxa, the problem of phylogenetic inference, and the problematic nature of the Tree of Life.

Author Correction: Insights into Pasteurellaceae carriage dynamics in the nasal passages of healthy beef calves.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Insights into Pasteurellaceae carriage dynamics in the nasal passages of healthy beef calves.

We investigated three bovine respiratory pathobionts in healthy cattle using qPCR optimised and validated to quantify Histophilus somni, Mannheimia haemolytica and Pasteurella multocida over a wide dynamic range. A longitudinal study was conducted to investigate the carriage and density of these bacteria in the nasal passages of healthy beef calves (N = 60) housed over winter in an experimental farm setting. The three pathobiont species exhibited remarkably different carriage rates and density profiles. At housing, high carriage rates were observed for P. multocida (95%), and H. somni (75%), while fewer calves were positive for M. haemolytica (13%). Carriage rates for all three bacterial species declined over the 75-day study, but not all individuals became colonised despite sharing of environment and airspace. Colonisation patterns ranged from continuous to intermittent and were different among pathobiont species. Interval-censored exponential survival models estimated the median duration of H. somni and P. multocida carriage at 14.8 (CI95%: 10.6-20.9) and 55.5 (CI95%: 43.3-71.3) days respectively, and found higher density P. multocida carriage was associated with slower clearance (p = 0.036). This work offers insights into the dynamics of pathobiont carriage and provides a potential platform for further data collection and modelling studies.

Stereotactic radiotherapy in oligometastatic cancer.

Oligometastatic cancer describes a disease state somewhere between localized and metastatic cancer. Proposed definitions of oligometastatic disease have typically used a cut-off of five or fewer sites of disease. Treatment of oligometastatic disease should have the goal of long-term local control, and in selected cases, disease remission. While several retrospective cohorts argue for surgical excision of limited metastases (metastasectomy) as the preferred treatment option for several clinical indications, limited randomized data exists for treating oligometastases. Alternatively, stereotactic ablative radiotherapy (SABR) is a radiotherapy technique that combines high radiation doses per fraction with precision targeting with the goal of achieving long-term local control of treated sites. Published cohort studies of SABR have demonstrated excellent local control rates of 70-90% in oligometastatic disease, with long-term survival in some series approaching 20-40%. A recent randomized phase 2 clinical trial by Gomez et al. demonstrated significantly improved progression free survival with aggressive consolidative therapy (surgery, radiotherapy ± chemotherapy or SABR) in oli-gometastatic non-small cell lung cancer (NSCLC). As additional randomized controlled trials are ongoing to determine the efficacy of SABR in oligometastatic disease, SABR is increasingly being used within routine clinical practice. This review article aims to sum-marize the history and current paradigm of the oligometastatic state, review recently pub-lished literature of SABR in oligometastatic cancer and discuss ongoing trials and future directions in this context.

Quantifying levels of function between different subgroups of chronic ankle instability.

The purpose of this original investigation was to determine if selected sensorimotor, mechanical, and self-reported measures are different among chronic ankle instability (CAI) subgroups, healthy control participants, and lateral ankle sprain copers (LAS-Copers). Ninety-four participants volunteered and were categorized into perceived ankle instability (PI) alone (n = 13), recurrent ankle sprains (RAS) alone (n = 12), PI in combination with RAS (PI-RAS; n = 25), LAS-Copers (n = 18), and controls (n = 26). Participants completed self-assessed global, regional, and psychological health-related quality-of-life (HRQOL) questionnaires and assessments of sensorimotor function and mechanical joint laxity. One-way ANOVAs were performed with the intention of reducing the number of original outcomes into a smaller number of predictor variables. Discriminant functional analysis was used to establish which specific measures best differentiate between groups. Eight outcome measures from neural excitability, postural control, static postural control, and HRQOL showed a significant differentiation between five groups (Wilk's λ = 0.26, χ232  = 114 45, P < 0.001, canonical correlation = 0.80) and correctly determined only 58.1% of group membership, and the PI-RAS and control groups were the only fit in the proposed model. A different model or other sensorimotor outcomes from more dynamic and complex tasks may be needed for the PI, RAS, and LAS-Coper groups.

Quadriceps neural alterations in anterior cruciate ligament reconstructed patients: A 6-month longitudinal investigation.

The purpose of this investigation was to evaluate differences in quadriceps corticospinal excitability, spinal-reflexive excitability, strength, and voluntary activation before, 2 weeks post and 6 months post-anterior cruciate ligament reconstruction (ACLr). This longitudinal, case-control investigation examined 20 patients scheduled for ACLr (11 females, 9 males; age: 20.9 ± 4.4 years; height:172.4 ± 7.5 cm; weight:76.2 ± 11.8 kg) and 20 healthy controls (11 females, 9 males; age:21.7 ± 3.7 years; height: 173.7 ± 9.9 cm; weight: 76.1 ± 19.7 kg). Maximal voluntary isometric contractions (MVIC), central activation ratio (CAR), normalized Hoffmann spinal reflexes, active motor threshold (AMT), and normalized motor-evoked potential (MEP) amplitudes at 120% of AMT were measured in the quadriceps muscle at the specific time points. ACLr patients demonstrated bilateral reductions in spinal-reflexive excitability compared with controls before surgery (P = 0.02) and 2 weeks post-surgery (P ≤ 0.001). ACLr patients demonstrated higher AMT at 6 months post-surgery (P ≤ 0.001) in both limbs. No MEP differences were detected. Quadriceps MVIC and CAR were lower in both limbs of the ACLr group before surgery and 6 months post-surgery (P ≤ 0.05) compared with controls. Diminished excitability of spinal-reflexive and corticospinal pathways are present at different times following ACLr and occur in combination with clinical deficits in quadriceps strength and activation. Early rehabilitation strategies targeting spinal-reflexive excitability may help improve postoperative outcomes, while later-stage rehabilitation may benefit from therapeutic techniques aimed at improving corticospinal excitability.

Osteoarthritis-related biomarkers following anterior cruciate ligament injury and reconstruction: a systematic review.

OBJECTIVE: There is an increased risk of developing knee osteoarthritis (OA) following anterior cruciate ligament (ACL) injury. Biomarkers may provide diagnostic, prognostic, or burden of disease indicators of OA before radiographic changes become apparent. Unfortunately, there has been no systematic review to clarify which biomarkers may be most informative following injury. Therefore, this review critically investigated existing studies of OA-related biomarkers in ACL-deficient (ACL-D) and reconstructed (ACL-R) patients to summarize the current evidence and identify knowledge gaps. DESIGN: A systematic review of the literature in Web of Science and PubMed databases (1960-June 2014) was performed. All English-language case-control and longitudinal studies assessing OA-related biomarkers in ACL-D and ACL-R patients were considered. Data regarding biomarker changes over time within ACL-D and ACL-R patients as well as differences in ACL-D/ACL-R patients compared with a control group were extracted from pertinent studies. RESULTS: A descriptive summary of 20 included studies was produced. In ACL-D patients compared with controls, synovial fluid biomarkers indicated elevated collagen turnover, while the inflammatory cytokine response was inconclusive. In ACL-R patients, serum concentrations indicated decreased collagen breakdown, but urine concentrations were indicative of greater collagen breakdown when compared to controls. Compared to preoperative values, the overall inflammatory cytokine response measured with synovial fluid biomarkers increased while plasma biomarkers did not change following reconstruction. CONCLUSION: Patients with ACL-D or ACL-R have altered biomarkers indicative of OA. More research with standardized reporting is needed to effectively determine which biomarkers are the most indicative for OA development and progression following ACL injury.

Spatial stochastic modeling of sedimentary formations to assess CO2 storage potential.

Carbon capture and sequestration (CCS) is a technology that provides a near-term solution to reduce anthropogenic CO2 emissions to the atmosphere and reduce our impact on the climate system. Assessments of carbon sequestration resources that have been made for North America using existing methodologies likely underestimate uncertainty and variability in the reservoir parameters. This paper describes a geostatistical model developed to estimate the CO2 storage resource in sedimentary formations. The proposed stochastic model accounts for the spatial distribution of reservoir properties and is implemented in a case study of the Oriskany Formation of the Appalachian sedimentary basin. Results indicate that the CO2 storage resource for the Pennsylvania part of the Oriskany Formation has substantial spatial variation due to heterogeneity of formation properties and basin geology leading to significant uncertainty in the storage assessment. The Oriskany Formation sequestration resource estimate in Pennsylvania calculated with the effective efficiency factor, E=5%, ranges from 0.15 to 1.01 gigatonnes (Gt) with a mean value of 0.52 Gt of CO2 (E=5%). The methodology is generalizable to other sedimentary formations in which site-specific trend analyses and statistical models are developed to estimate the CO2 sequestration storage capacity and its uncertainty. More precise CO2 storage resource estimates will provide better recommendations for government and industry leaders and inform their decisions on which greenhouse gas mitigation measures are best fit for their regions.

The social contagion hypothesis: comment on 'Social contagion theory: examining dynamic social networks and human behavior'.

I reflect on the statistical methods of the Christakis-Fowler studies on network-based contagion of traits by checking the sensitivity of these kinds of results to various alternate specifications and generative mechanisms. Despite the honest efforts of all involved, I remain pessimistic about establishing whether binary health outcomes or product adoptions are contagious if the evidence comes from simultaneously observed data.

Blue emitting gold nanoclusters templated by poly-cytosine DNA at low pH and poly-adenine DNA at neutral pH.

Blue fluorescent gold nanoclusters were prepared in the presence of poly-cytosine DNAs at low pH and poly-adenine at neutral pH using citrate as the reducing agent; various buffer conditions affecting the synthesis have been explored.

How-possibly explanations as genuine explanations and helpful heuristics: A comment on Forber.

Recently, Forber introduced a distinction between two kinds of how-possibly explanation, global and local how-possibly explanation, and argued that both play genuinely explanatory roles in evolutionary biology. In this paper I examine the nature of these two kinds of how-possibly explanations, focusing on the question whether they indeed constitute genuine explanations. I will conclude that one of Forber's kinds of how-possibly explanation may be thought of as a kind of genuine explanation but not as a kind of how-possibly explanation, while the other kind plays a heuristic role and should not be conceived of as a kind of explanation at all.

Isolated hip and ankle fatigue are unlikely risk factors for anterior cruciate ligament injury.

Lower extremity neuromuscular fatigue purportedly increases anterior cruciate ligament (ACL) injury risk through promotion of extreme landing mechanics. However, the impact of fatigue on muscle groups critical to the landing strategy remains unclear. This study examined the effects of isolated hip rotator and triceps surae fatigue on lower extremity landing biomechanics. Sixteen healthy females (18-22 years) reported for testing on two occasions, with one muscle group fatigued per session. Subjects performed three single-leg landings onto a force platform pre- and post-fatigue, defined as an 80% decrease in peak torque in the targeted muscle group. Hip rotator fatigue was induced via alternating concentric contractions and triceps surae fatigue through concentric plantar flexion contractions on an isokinetic dynamometer. Initial contact (IC) kinematics and peak stance (PS) kinetics and kinematics were analyzed pre- and post-fatigue. Hip rotator fatigue increased IC (P=0.05) and PS (P=0.04) hip internal rotation angles. Triceps surae fatigue decreased IC knee flexion (P=0.01) angle. Isolated hip rotator and triceps surae fatigue each produced modifications in lower limb kinematic parameters viewed as risk factors for ACL injury. These modifications, however, do not appear of sufficient magnitude to compromise ligament integrity, suggesting injury via an integrative lower extremity fatigue mechanism is more likely.