Genome and life-history evolution link bird diversification to the end-Cretaceous mass extinction.

Complex patterns of genome evolution associated with the end-Cretaceous [Cretaceous-Paleogene (K-Pg)] mass extinction limit our understanding of the early evolutionary history of modern birds. Here, we analyzed patterns of avian molecular evolution and identified distinct macroevolutionary regimes across exons, introns, untranslated regions, and mitochondrial genomes. Bird clades originating near the K-Pg boundary exhibited numerous shifts in the mode of molecular evolution, suggesting a burst of genomic heterogeneity at this point in Earth's history. These inferred shifts in substitution patterns were closely related to evolutionary shifts in developmental mode, adult body mass, and patterns of metabolic scaling. Our results suggest that the end-Cretaceous mass extinction triggered integrated patterns of evolution across avian genomes, physiology, and life history near the dawn of the modern bird radiation.

Social impairment in survivors of pediatric brain tumors via reduced social attention and emotion-specific facial expression recognition.

BACKGROUND/OBJECTIVES: Survivors of pediatric brain tumors (SPBT) experience significant social challenges, including fewer friends and greater isolation than peers. Difficulties in face processing and visual social attention have been implicated in these outcomes. This study evaluated facial expression recognition (FER), social attention, and their associations with social impairments in SPBT. METHODS: SPBT (N = 54; ages 7-16) at least 2 years post treatment completed a measure of FER, while parents completed measures of social impairment. A subset (N = 30) completed a social attention assessment that recorded eye gaze patterns while watching videos depicting pairs of children engaged in joint play. Social Prioritization scores were calculated, with higher scores indicating more face looking. Correlations and regression analyses evaluated associations between variables, while a path analysis modeling tool (PROCESS) evaluated the indirect effects of Social Prioritization on social impairments through emotion-specific FER. RESULTS: Poorer recognition of angry and sad facial expressions was significantly correlated with greater social impairment. Social Prioritization was positively correlated with angry FER but no other emotions. Social Prioritization had significant indirect effects on social impairments through angry FER. CONCLUSION: Findings suggest interventions aimed at improving recognition of specific emotions may mitigate social impairments in SPBT. Further, reduced social attention (i.e., diminished face looking) could be a factor in reduced face processing ability, which may result in social impairments. Longitudinal research is needed to elucidate temporal associations between social attention, face processing, and social impairments.

Development of a Novel Fluorescent-Based Lateral Flow Assay for the Detection of Neisseria gonorrhoeae at the Point of Care.

BACKGROUND: Neisseria gonorrhoeae (NG) has acquired significant resistance, primarily due to extensive and unwarranted antibiotic utilization over several decades. This resistance has largely been associated with the syndromic management of sexually transmitted infections, particularly in low- and middle-income countries where affordable point of care tests are unavailable. To address this diagnostic gap, FIND has developed a low-cost lateral flow assay for the detection of NG at the point of care. METHODS: The early performance of the lateral flow assay was evaluated using frozen clinical samples. Limit of detection, inclusivity, and exclusivity studies were performed using well-characterized NG strains, common commensal genital microorganisms, and other Neisseria bacteria. Subsequently, clinical performance was evaluated at 2 sexual health clinics in Birmingham, Alabama. RESULTS: The observed limit of detection with reference NG strains was 5 × 103 CFU/mL. Inclusivity was demonstrated for 31 NG strains. Exclusivity testing showed no cross-reactivity with 28 non-Neisseria and nongonococcal Neisseria species; cross-reactivity was observed with Neisseria meningitidis, Neisseria lactamica, and Neisseria polysaccharea. The lateral flow assay demonstrated clinical sensitivity and specificity of 78.6% and 100% in female vaginal swabs and 100% and 89.7% in male urine, respectively. CONCLUSIONS: FIND has developed a lateral flow assay that aligns with the majority of the World Health Organization Target Product Profile criteria for confirming or excluding NG infection at the point of care. The NG lateral flow assay has now achieved design freeze (final device optimization) and is ready for technology transfer to a manufacturing partner. This test has the potential to support the shift in patient management from a syndromic to an etiological approach.

Design and field evaluation of a lateral flow cassette device for point-of-care bilirubin measurement.

Neonatal jaundice is an important cause of morbidity and mortality worldwide, and neonates born in low and middle-income countries bear a disproportionate burden. We previously developed a low-cost, point-of-care system to measure total serum bilirubin (TSB) in neonates. This device was effective at detecting and monitoring jaundice; however, the disposable strips were difficult to produce at scale. Here, we report a new lateral flow cassette design, called BiliDx, that was produced at scale using traditional manufacturing techniques. We evaluated the performance of BiliDx at sites in Nigeria and Malawi. The lateral flow strip consists of plasma separation membranes, nitrocellulose, and a plastic cassette. We evaluated the performance of the strips and reader at two hospitals located in Nigeria and Malawi compared to reference standard TSB. We also assessed performance for samples with high direct bilirubin (DB) and high hematocrit (HCT). We collected 1,144 samples from 758 neonates (TSB ranged from 0.2 to 45.9 mg/dL). The mean bias of BiliDx measurements in the validation set was +0.75 mg/dL, and 95% limits of agreement were -2.57 to 4.07 mg/dL. The mean bias and limits of agreement were comparable for samples with HCT < 60% and HCT ≥ 60%, and for samples with low and intermediate DB levels; the samples with high DB levels had wider 95% limits of agreement (-4.50 to +3.03 mg/dL). Error grid analysis shows that 96.9% of samples measured with BiliDx would have resulted in the same clinical decision as the reference standard. This performance is comparable to previous results that used a handmade two-dimensional strip. Additionally, error grid analysis shows that all 20 samples with high DB levels would have resulted in the same clinical decision as the reference standard. This evaluation supports the use of BiliDx lateral flow cassettes to provide accurate point-of-care measurements in low-resource settings.

Indigenous peoples and inclusion in clinical and genomic research: Understanding the history and navigating contemporary engagement.

Despite significant improvements in pediatric cancer survival outcomes, there remain glaring disparities in under-represented racial and ethnic groups that warrant mitigation by the scientific and clinical community. To address and work towards eliminating such disparities, the Pacific Pediatric Neuro-Oncology Consortium (PNOC) and Children's Brain Tumor Network (CBTN) established a Diversity, Equity, and Inclusion (DEI) working group in 2020. The DEI working group is dedicated to improving access to care for all pediatric patients with central nervous system (CNS) tumors, broadening diversity within the research community, and providing sustainable data-driven solutions. To this end, the DEI working group aims to coordinate regular educational sessions centered on critical DEI topics in pediatric research and clinical care of pediatric patients, with a focus on pediatric neuro-oncology. In April 2022, the group led a moderated panel of experts on Indigenous Peoples' rights and participation in clinical research activities. The following paper serves to provide the scientific community a perspective on how to prioritize the inclusion of Indigenous Peoples in research with cultural sensitivity and with the intent of improving not only representation, but patient outcomes regardless of patient race, ethnicity, or socioeconomic background.

Risk Factors and Comorbidities Associated with Diabetic Kidney Disease.

INTRODUCTION/OBJECTIVES: Diabetic Kidney Disease (DKD) is the leading cause of end-stage kidney disease. Despite optimal glycemic control and blood pressure management, progression to DKD cannot be halted in some patients. We aimed to find the association of modifiable and non-modifiable risk factors and comorbid conditions in patients with DKD. METHODS: Retrospective medical record review of adult patients with diabetes mellitus (DM) was performed who visited our internal medicine office between January 1, 2020 and December 31, 2020. RESULTS: Among 728 patients with DM, 471 (64.7%) patients had DKD, and 257 (35.3%) patients were without DKD. Among the group of patients with DKD, the majority were in CKD stage G1A2 (34.6%), followed equally by G2A2 and G3aA1 (16.8% each). Mean age of the patients with DKD was significantly greater than the patients without DKD (69.4 years vs 62.2 years; P < .001). For each unit increase in age, there was a 7.8% increase in the odds of DKD (95% CI 5.3-10.4; P < .001). Women had 2.32 times greater odds of DKD (95% CI, 1.41-3.81; P = .001). We found decreased odds of DKD for those who consumed alcohol moderately (OR 0.612, 95% CI 0.377-0.994; P < .05). Significantly higher frequencies of associations of several comorbid medical conditions were seen in patients with DKD compared to the patients without DKD, such as hypertension (91.9% vs 75.6%), hyperlipidemia (86.6% vs 78.2%), coronary artery disease (39.3% vs 16.8%), cerebrovascular accidents (13.4% vs 7.4%), congestive heart failure (12.9% vs 4.1%), carotid artery stenosis (11.3% vs 2.6%), aortic aneurysm (5.4% vs 2.0%), peripheral artery disease (10.8% vs 3.5%), gout (12.4% vs 5.5%), and osteoarthritis (41.4% vs 31.2%). CONCLUSIONS: In patients with diabetes, increasing age, female sex, and lack of moderate alcohol consumption were associated with increased odds of DKD. Higher frequencies of association of hypertension, hyperlipidemia, coronary artery disease, cerebrovascular accidents, congestive heart failure, carotid artery stenosis, aortic aneurysm, peripheral artery disease, gout, and osteoarthritis were also seen in patients with DKD.

How should functional relationships be evaluated using phylogenetic comparative methods? A case study using metabolic rate and body temperature.

Phylogenetic comparative methods are often used to test functional relationships between traits. However, million-year macroevolutionary observational datasets cannot definitively prove causal links between traits-correlation does not equal causation and experimental manipulation over such timescales is impossible. Although this caveat is widely understood, it is less appreciated that different phylogenetic approaches imply different causal assumptions about the functional relationships of traits. To make meaningful inferences, it is critical that our statistical methods make biologically reasonable assumptions. Here we illustrate the importance of causal reasoning in comparative biology by examining a recent study by Avaria-Llautureo et al (2019). that tested for the evolutionary coupling of metabolic rate and body temperature across endotherms and found that these traits were unlinked through evolutionary time and that body temperatures were, on average, higher in the early Cenozoic than they are today. We argue that the causal assumptions embedded into their models made it impossible for them to test the relevant functional and evolutionary hypotheses. We reanalyze their data using more biologically appropriate models and find support for the exact opposite conclusions, corroborating previous evidence from physiology and paleontology. We highlight the vital need for causal thinking, even when experiments are impossible.

Omental patch versus gastric resection for perforated gastric ulcer: Systematic review and meta-analysis for an unresolved debate.

BACKGROUND: Perforated gastric ulcers are surgical emergencies with paucity of data on the preferred treatment modality of resection versus omental patch. We aim to compare outcomes with ulcer repair and gastric resection surgeries in perforated gastric ulcers after systematic review of literature. METHODS: A systematic literature search was performed for publications in PubMed Medline, Embase, and Cochrane Central Register of Controlled Trials. We included all studies which compared ulcer repair vesus gastric resection surgeries for perforated gastric ulcers. We excluded studies which did not separate outcomes gastric and duodenal ulcer perforations. RESULTS: The search included nine single-institution retrospective reviews comparing ulcer repair (449 patients) versus gastric resection surgeries (212 patients). Meta-analysis was restricted to perforated gastric ulcers and excluded perforated duodenal ulcers. The majority of these studies did not control for baseline characteristics, and surgical strategies were often chosen in a non-randomized manner. All of the studies included were at high risk of bias. The overall odds ratio of mortality in ulcer repair surgery compared to gastric resection surgery was 1.79, with 95% CI 0.72 to 4.43 and p-value 0.209. CONCLUSION: In this meta-analysis, there was no difference in mortality between the two surgical groups. The overall equivalence of clinical outcomes suggests that gastric resection is a potentially viable alternative to ulcer repair surgery and should not be considered a secondary strategy. We would recommend a multicenter randomized control trial to evaluate the surgical approach that yields superior outcomes. LEVEL OF EVIDENCE: Systematic review and meta-analysis, level III.

ß-Branched Amino Acids Stabilize Specific Conformations of Cyclic Hexapeptides.

Cyclic peptides (CPs) are a promising class of molecules for drug development, particularly as inhibitors of protein-protein interactions. Predicting low-energy structures and global structural ensembles of individual CPs is critical for the design of bioactive molecules, but these are challenging to predict and difficult to verify experimentally. In our previous work, we used explicit-solvent molecular dynamics simulations with enhanced sampling methods to predict the global structural ensembles of cyclic hexapeptides containing different permutations of glycine, alanine, and valine. One peptide, cyclo-(VVGGVG) or P7, was predicted to be unusually well structured. In this work, we synthesized P7, along with a less well-structured control peptide, cyclo-(VVGVGG) or P6, and characterized their global structural ensembles in water using NMR spectroscopy. The NMR data revealed a structural ensemble similar to the prediction for P7 and showed that P6 was indeed much less well-structured than P7. We then simulated and experimentally characterized the global structural ensembles of several P7 analogs and discovered that ß-branching at one critical position within P7 is important for overall structural stability. The simulations allowed deconvolution of thermodynamic factors that underlie this structural stabilization. Overall, the excellent correlation between simulation and experimental data indicates that our simulation platform will be a promising approach for designing well-structured CPs and also for understanding the complex interactions that control the conformations of constrained peptides and other macrocycles.

Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones.

The threat of viral pandemics demands a comprehensive understanding of evolution at the host-pathogen interface. Here, we show that the accessibility of adaptive mutations in influenza nucleoprotein at fever-like temperatures is mediated by host chaperones. Particularly noteworthy, we observe that the Pro283 nucleoprotein variant, which (1) is conserved across human influenza strains, (2) confers resistance to the Myxovirus resistance protein A (MxA) restriction factor, and (3) critically contributed to adaptation to humans in the 1918 pandemic influenza strain, is rendered unfit by heat shock factor 1 inhibition-mediated host chaperone depletion at febrile temperatures. This fitness loss is due to biophysical defects that chaperones are unavailable to address when heat shock factor 1 is inhibited. Thus, influenza subverts host chaperones to uncouple the biophysically deleterious consequences of viral protein variants from the benefits of immune escape. In summary, host proteostasis plays a central role in shaping influenza adaptation, with implications for the evolution of other viruses, for viral host switching, and for antiviral drug development.

Understanding and designing head-to-tail cyclic peptides.

Cyclic peptides (CPs) are an exciting class of molecules with a variety of applications. However, design strategies for CP therapeutics, for example, are generally limited by a poor understanding of their sequence-structure relationships. This knowledge gap often leads to a trial-and-error approach for designing CPs for a specific purpose, which is both costly and time-consuming. Herein, we describe the current experimental and computational efforts in understanding and designing head-to-tail CPs along with their respective challenges. In addition, we provide several future directions in the field of computational CP design to improve its accuracy, efficiency and applicability. These advances, combined with experimental techniques, shall ultimately provide a better understanding of these interesting molecules and a reliable working platform to rationally design CPs with desired characteristics.

Designing Well-Structured Cyclic Pentapeptides Based on Sequence-Structure Relationships.

Cyclic peptides are a promising class of molecules for unique applications. Unfortunately, cyclic peptide design is severely limited by the difficulty in predicting the conformations they will adopt in solution. In this work, we use explicit-solvent molecular dynamics simulations to design well-structured cyclic peptides by studying their sequence-structure relationships. Critical to our approach is an enhanced sampling method that exploits the essential transitional motions of cyclic peptides to efficiently sample their conformational space. We simulated a range of cyclic pentapeptides from all-glycine to a library of cyclo-(X1X2AAA) peptides to map their conformational space and determine cooperative effects of neighboring residues. By combining the results from all cyclo-(X1X2AAA) peptides, we developed a scoring function to predict the structural preferences for X1-X2 residues within cyclic pentapeptides. Using this scoring function, we designed a cyclic pentapeptide, cyclo-(GNSRV), predicted to be well structured in aqueous solution. Subsequent circular dichroism and NMR spectroscopy revealed that this cyclic pentapeptide is indeed well structured in water, with a nuclear Overhauser effect and J-coupling values consistent with the predicted structure.

Host proteostasis modulates influenza evolution.

Predicting and constraining RNA virus evolution require understanding the molecular factors that define the mutational landscape accessible to these pathogens. RNA viruses typically have high mutation rates, resulting in frequent production of protein variants with compromised biophysical properties. Their evolution is necessarily constrained by the consequent challenge to protein folding and function. We hypothesized that host proteostasis mechanisms may be significant determinants of the fitness of viral protein variants, serving as a critical force shaping viral evolution. Here, we test that hypothesis by propagating influenza in host cells displaying chemically-controlled, divergent proteostasis environments. We find that both the nature of selection on the influenza genome and the accessibility of specific mutational trajectories are significantly impacted by host proteostasis. These findings provide new insights into features of host-pathogen interactions that shape viral evolution, and into the potential design of host proteostasis-targeted antiviral therapeutics that are refractory to resistance.

Predictions for α-Helical Glycopeptide Design from Structural Bioinformatics Analysis.

Glycosylation not only impacts the functions of glycoproteins but can also improve glycoprotein stability and folding efficiency-characteristics that are desirable for protein engineering and therapeutic design. To further elucidate the effects of N-glycosylation on protein structure and to provide principles useful for the rational design of α-helical glycopeptides, we investigate stabilizing protein-sugar interactions in α-helical glycosylation sites using an integrated structural bioinformatics analysis and molecular dynamics simulation approach. We identify two glycan conformations with an Asn χ1 of 180° or 300° that are amenable to α-helical structure in natural α-helical glycosylation sites in the Protein Data Bank. A combination of sterics and favorable intraglycopeptide enthalpy explains the existence of only these two conformations. Furthermore, we catalog all known protein-sugar interactions that utilize these conformational modes. The most common interactions involve either a Glu residue at the -4 position interacting with the GlcNAc whose Asn has χ1 = 300° or a Glu residue at the +4 position interacting with the GlcNAc whose Asn has χ1 = 180°. Via metadynamics simulations of model α-helical glycopeptides with each of these two interactions, we find that both interactions are stabilizing as a result of favorable electrostatic intraglycopeptide interactions. Thus, we suggest that incorporating a Glu at either the -4 or +4 position relative to an N-linked glycan may be a useful strategy for engineering stable α-helical glycoproteins.

Toward accurately modeling N-methylated cyclic peptides.

Cyclic peptides have unique properties and can target protein surfaces specifically and potently. N-Methylation provides a promising way to further optimize the pharmacokinetic and structural profiles of cyclic peptides. The capability to accurately model structures adopted by N-methylated cyclic peptides would facilitate rational design of this interesting and useful class of molecules. We apply molecular dynamics simulations with advanced enhanced sampling methods to efficiently characterize the structural ensembles of N-methylated cyclic peptides, while simultaneously evaluating the overall performance of several simulation force fields. We find that one of the residue-specific force fields, RSFF2, is able to recapitulate experimental structures of the N-methylated cyclic peptide benchmarks tested here when the correct amide isomers are used as initial configurations and enforced during the simulations. Thus, using our simulation approach, it is possible to accurately and efficiently predict the structures of N-methylated cyclic peptides if sufficient information is available to determine the correct amide cis/trans configuration. Moreover, our results suggest that, upon further optimization of RSFF2 to more reliably predict cis/trans isomers, molecular dynamics simulations will be able to de novo predict N-methylated cyclic peptides in the near future, strongly motivating such continued optimization.

Mapping the sequence-structure relationships of simple cyclic hexapeptides.

Cyclic peptides are promising protein-protein interaction modulators with high binding affinities and specificities, as well as enhanced stabilities and oral availabilities over linear analogs. Despite their relatively small size and cyclic architecture, it is currently difficult to predict the favored conformation(s) of most classes of cyclic peptides. An improved understanding of the sequence-structure relationships for cyclic peptides will offer an avenue for the rational design of cyclic peptides as possible therapeutics. In this work, we systematically explored the sequence-structure relationships for two cyclic hexapeptide systems using molecular dynamics simulation techniques. Starting with an all-glycine cyclic hexapeptide, cyclo-G6, we systematically replaced glycine residues with alanines and characterized the structural ensembles of different variants. The same process was repeated with valines to investigate the effects of larger side chains. An analysis of the origin of structure preferences was performed using thermodynamics decomposition and several general observations are reported.

Computational methods to design cyclic peptides.

Cyclic peptides (CPs) are promising modulators of protein-protein interactions (PPIs), but their application remains challenging. It is currently difficult to predict the structures and bioavailability of CPs. The ability to design CPs using computer modeling would greatly facilitate the development of CPs as potent PPI modulators for fundamental studies and as potential therapeutics. Herein, we describe computational methods to generate CP libraries for virtual screening, as well as current efforts to accurately predict the conformations adopted by CPs. These advances are making it possible to envision robust computational design of active CPs. However, unique properties of CPs pose significant challenges associated with sampling CP conformational space and accurately describing CP energetics. These major obstacles to structure prediction likely must be solved before robust design of active CPs can be reliably achieved.

Insights into How Cyclic Peptides Switch Conformations.

Cyclic peptides have recently emerged as promising modulators of protein-protein interactions. However, it is currently highly difficult to predict the structures of cyclic peptides owing to their rugged conformational free energy landscape, which prevents sampling of all thermodynamically relevant conformations. In this article, we first investigate how a relatively flexible cyclic hexapeptide switches conformations. It is found that, although the circular geometry of small cyclic peptides of size 6-8 may require rare, coherent dihedral changes to sample a new conformation, the changes are rather local, involving simultaneous changes of ϕi and ψi or ψi and ϕi+1. The understanding of how these cyclic peptides switch conformations enables the use of metadynamics simulations with reaction coordinates specifically targeting such coupled two-dihedral changes to effectively sample cyclic peptide conformational space.

The laparoscopic Nissen-Hill hybrid: pilot study of a combined antireflux procedure.

BACKGROUND: Laparoscopic antireflux surgery is highly effective in patients with uncomplicated gastroesophageal reflux disease (GERD). However, long-term failure rates in paraesophageal hernia (PEH) and Barrett's metaplasia (BE) are higher and warrant a more durable repair. Outcomes for the laparoscopic Nissen fundoplication (LNF) and Hill repair (LHR) are equivalent, but their anatomic components are different and may complement each other (Aye R Ann Thorac Surg, 2012). We designed and tested the feasibility and safety of an operation that combines the essential components of each repair. METHODS: A prospective, phase II pilot study was performed on patients with symptomatic giant PEH hernias and/or GERD with nondysplastic Barrett's metaplasia. Pre- and postoperative esophagogastroduodenoscopy (EGD), upper gastrointestinal study (UGI), 48-hour pH testing, manometry, and three quality-of-life metrics were obtained. RESULTS: Twenty-four patients were enrolled in the study. Three patients did not complete the planned procedure, leaving 21 patients, including 12 with PEH, 7 with BE, and 2 with both. There were no 30-day or in-hospital mortalities. At a median follow-up of 13 (range 6.4-30.2) months, there were no reoperations or clinical recurrences. Two patients required postoperative dilation for dysphagia, with complete resolution. Mean DeMeester scores improved from 54.3 to 7.5 (p < 0.0036). Mean lower esophageal sphincter pressures (LESP) increased from 8.9 to 21.3 mmHg (p < 0.013). Mean short-term and long-term QOLRAD scores improved from 4.09 at baseline to 6.04 and 6.48 (p < 0.0001). Mean short-term and long-term GERD-HQRL scores improved from 22.9 to 7.5 and 6.9 (p < 0.03). Mean long-term Dysphagia Severity Score Index improved from 33.3 to 40.6 (p < 0.064). CONCLUSIONS: The combination of a Nissen plus Hill hybrid reconstruction of the gastroesophageal junction (GEJ) is technically feasible, safe, and not associated with increased side effects. Short-term clinical results in PEH and BE suggest that this may be an effective repair, supporting the value of further study.

A readout for large arrays of microwave kinetic inductance detectors.

Microwave kinetic inductance detectors (MKIDs) are superconducting detectors capable of counting single photons and measuring their energy in the UV, optical, and near-IR. MKIDs feature intrinsic frequency domain multiplexing (FDM) at microwave frequencies, allowing the construction and readout of large arrays. Due to the microwave FDM, MKIDs do not require the complex cryogenic multiplexing electronics used for similar detectors, such as transition edge sensors, but instead transfer this complexity to room temperature electronics where they present a formidable signal processing challenge. In this paper, we describe the first successful effort to build a readout for a photon counting optical/near-IR astronomical instrument, the ARray Camera for Optical to Near-infrared Spectrophotometry. This readout is based on open source hardware developed by the Collaboration for Astronomy Signal Processing and Electronics Research. Designed principally for radio telescope backends, it is flexible enough to be used for a variety of signal processing applications.