Reference-free structural variant detection in microbiomes via long-read co-assembly graphs.

MOTIVATION: The study of bacterial genome dynamics is vital for understanding the mechanisms underlying microbial adaptation, growth, and their impact on host phenotype. Structural variants (SVs), genomic alterations of 50 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to the absence of clear reference genomes and the presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing all metagenomic samples in a series (time or other metric) into a single co-assembly graph. The log fold change in graph coverage between successive samples is then calculated to call SVs that are thriving or declining. RESULTS: We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, particularly as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between successive time and temperature samples, suggesting host advantage. Our approach leverages previous work in assembly graph structural and coverage patterns to provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial gene flux. AVAILABILITY AND IMPLEMENTATION: rhea is open source and available at: https://github.com/treangenlab/rhea.

Sleep Disruption Precedes Forebrain Synaptic Tau Burden and Contributes to Cognitive Decline in a Sex-Dependent Manner in the P301S Tau Transgenic Mouse Model.

Sleep disruption and impaired synaptic processes are common features in neurodegenerative diseases, including Alzheimer's disease (AD). Hyperphosphorylated Tau is known to accumulate at neuronal synapses in AD, contributing to synapse dysfunction. However, it remains unclear how sleep disruption and synapse pathology interact to contribute to cognitive decline. Here, we examined sex-specific onset and consequences of sleep loss in AD/tauopathy model PS19 mice. Using a piezoelectric home-cage monitoring system, we showed PS19 mice exhibited early-onset and progressive hyperarousal, a selective dark-phase sleep disruption, apparent at 3 months in females and 6 months in males. Using the Morris water maze test, we report that chronic sleep disruption (CSD) accelerated the onset of decline of hippocampal spatial memory in PS19 males only. Hyperarousal occurs well in advance of robust forebrain synaptic Tau burden that becomes apparent at 6-9 months. To determine whether a causal link exists between sleep disruption and synaptic Tau hyperphosphorylation, we examined the correlation between sleep behavior and synaptic Tau, or exposed mice to acute or chronic sleep disruption at 6 months. While we confirm that sleep disruption is a driver of Tau hyperphosphorylation in neurons of the locus ceruleus, we were unable to show any causal link between sleep loss and Tau burden in forebrain synapses. Despite the finding that hyperarousal appears earlier in females, female cognition was resilient to the effects of sleep disruption. We conclude sleep disruption interacts with the synaptic Tau burden to accelerate the onset of cognitive decline with greater vulnerability in males.

Repurposing Metformin for the Treatment of Atrial Fibrillation: Current Insights.

Metformin is an orally effective anti-hyperglycemic drug that despite being introduced over 60 years ago is still utilized by an estimated 120 to 150 million people worldwide for the treatment of type 2 diabetes (T2D). Metformin is used off-label for the treatment of polycystic ovary syndrome (PCOS) and for pre-diabetes and weight loss. Metformin is a safe, inexpensive drug with side effects mostly limited to gastrointestinal issues. Prospective clinical data from the United Kingdom Prospective Diabetes Study (UKPDS), completed in 1998, demonstrated that metformin not only has excellent therapeutic efficacy as an anti-diabetes drug but also that good glycemic control reduced the risk of micro- and macro-vascular complications, especially in obese patients and thereby reduced the risk of diabetes-associated cardiovascular disease (CVD). Based on a long history of clinical use and an excellent safety record metformin has been investigated to be repurposed for numerous other diseases including as an anti-aging agent, Alzheimer's disease and other dementias, cancer, COVID-19 and also atrial fibrillation (AF). AF is the most frequently diagnosed cardiac arrythmia and its prevalence is increasing globally as the population ages. The argument for repurposing metformin for AF is based on a combination of retrospective clinical data and in vivo and in vitro pre-clinical laboratory studies. In this review, we critically evaluate the evidence that metformin has cardioprotective actions and assess whether the clinical and pre-clinical evidence support the use of metformin to reduce the risk and treat AF.

MethPhaser: methylation-based long-read haplotype phasing of human genomes.

The assignment of variants across haplotypes, phasing, is crucial for predicting the consequences, interaction, and inheritance of mutations and is a key step in improving our understanding of phenotype and disease. However, phasing is limited by read length and stretches of homozygosity along the genome. To overcome this limitation, we designed MethPhaser, a method that utilizes methylation signals from Oxford Nanopore Technologies to extend Single Nucleotide Variation (SNV)-based phasing. We demonstrate that haplotype-specific methylations extensively exist in Human genomes and the advent of long-read technologies enabled direct report of methylation signals. For ONT R9 and R10 cell line data, we increase the phase length N50 by 78%-151% at a phasing accuracy of 83.4-98.7% To assess the impact of tissue purity and random methylation signals due to inactivation, we also applied MethPhaser on blood samples from 4 patients, still showing improvements over SNV-only phasing. MethPhaser further improves phasing across HLA and multiple other medically relevant genes, improving our understanding of how mutations interact across multiple phenotypes. The concept of MethPhaser can also be extended to non-human diploid genomes. MethPhaser is available at https://github.com/treangenlab/methphaser .

Opening Side of Unilateral Open-Door Laminoplasty Does Not Impact Improvement in Arm Pain or Space Available for the Spinal Cord.

Background/Objectives: There exists limited data guiding open-door laminoplasty. The objective of this study is to determine if open-door laminoplasty affects radiographic decompression or arm pain outcomes. Methods: Adult patients who underwent unilateral open-door laminoplasty cervical myelopathy were included. The side opened was dependent on surgeon discretion. We recorded preoperative side of symptoms, side of radiographic compression, arm pain scores, and canal diameter. Patients with open-side ipsilateral or contralateral to dominant symptoms or compression were compared to determine any effect on arm pain outcomes or spinal canal diameter. If the symptoms were equal bilaterally, patients were neutral. Results: A total of 167 patients were included, with an average age of 64 ± 11 years and average follow-up time of 64.5 ± 72 weeks. The average preoperative arm pain visual analog score (VAS) was 2.13 ± 2.86, and the average arm VAS after 6 months was 1.52 ± 2.68. For dominant symptoms, the ipsilateral, contralateral, and neutral groups had a significant improvement in arm VAS at >6 months postoperatively. For dominant compression, the ipsilateral and contralateral groups had a significant improvement in both arm VASs and canal diameter at >6 months postoperatively. No differences were seen between groups for either. We observed a significant correlation between size of plate and change in canal diameter; however, no differences were noted for arm pain. Conclusions: Laminoplasty may be effective in addressing radicular arm pain by increasing the spinal canal's diameter and space available for the cord. The laterality of open-door laminoplasty did not affect arm pain improvement or canal expansion.

MetaCompass: Reference-guided Assembly of Metagenomes.

Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in a metagenomic context. Here we describe the first effective approach for reference-guided metagenomic assembly that can complement and improve upon de novo metagenomic assembly methods for certain organisms. Such approaches will be increasingly useful as more genomes are sequenced and made publicly available.

Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet.

Taxonomic profiling is a ubiquitous task in the analysis of clinical and environmental microbiomes. The advent of long-read sequencing of microbiomes necessitates the development of new taxonomic profilers tailored to long-read shotgun metagenomic datasets. Here, we introduce Lemur and Magnet, a pair of tools optimized for lightweight and accurate taxonomic profiling from long-read shotgun metagenomic datasets. Lemur is a marker-gene based method that leverages an EM algorithm to reduce false positive calls while preserving true positives; Magnet makes detailed presence/absence calls for bacterial genomes based on whole-genome read mapping. The tools work in sequence: Lemur estimates abundances conservatively, and Magnet operates on the genomes of identified organisms to filter out likely false positive taxa. The result is an increase in precision of as much as 70%, which far exceeds competing methods. By operating only on marker genes, Lemur is a comparatively lightweight software. We demonstrate that it can run in minutes to hours on a laptop with 32 GB of RAM, even for large inputs - a crucial feature given the portability of long-read sequencing machines. Furthermore, the marker gene database used by Lemur is only 4 GB and contains information from over 300,000 RefSeq genomes. The reference is available at https://zenodo.org/records/10802546, and the software is open-source and available at https://github.com/treangenlab/lemur.

Impact of age on comparative outcomes of decompression alone versus fusion for L4 degenerative spondylolisthesis.

PURPOSE: To compare the outcomes of decompression alone and fusion for L4-5 DLS in different age cohorts (< 70 years, ≥ 70 years). METHODS: This retrospective cohort study included patients who underwent minimally invasive decompression or fusion for L4-5 DLS and had a minimum of 1-year follow-up. Outcome measures were: (1) patient-reported outcome measures (PROMs) (Oswestry Disability Index, ODI; Visual Analog Scale back and leg, VAS; 12-Item Short Form Survey Physical Component Score, SF-12 PCS), (2) minimal clinically important difference (MCID), (3) patient acceptable symptom state (PASS), (4) response on the global rating change (GRC) scale, and (5) complication rates. The decompression and fusion groups were compared for outcomes separately in the < 70-year and ≥ 70-year age cohorts. RESULTS: 233 patients were included, out of which 52% were < 70 years. Patients < 70 years showed non-significant improvement in SF-12 PCS and significantly lower MCID achievement rates for VAS back after decompression compared to fusion. Analysis of the ≥ 70-year age cohort showed no significant differences between the decompression and fusion groups in the improvement in PROMs, MCID/PASS achievement rates, and responses on GRC. Patients ≥ 70 years undergoing fusion had significantly higher in-hospital complication rates. When analyzed irrespective of the surgery type, both < 70-year and ≥ 70-year age cohorts showed significant improvement in PROMs with no significant difference. CONCLUSIONS: Patients < 70 years undergoing decompression alone did not show significant improvement in physical function and had significantly less MCID achievement rate for back pain compared to fusion. Patients ≥ 70 years showed no difference in outcomes between decompression alone and fusion.

Prediction of photodynamics of 200 nm excited cyclobutanone with linear response electronic structure and ab initio multiple spawning.

Simulations of photochemical reaction dynamics have been a challenge to the theoretical chemistry community for some time. In an effort to determine the predictive character of current approaches, we predict the results of an upcoming ultrafast diffraction experiment on the photodynamics of cyclobutanone after excitation to the lowest lying Rydberg state (S2). A picosecond of nonadiabatic dynamics is described with ab initio multiple spawning. We use both time dependent density functional theory (TDDFT) and equation-of-motion coupled cluster singles and doubles (EOM-CCSD) theory for the underlying electronic structure theory. We find that the lifetime of the S2 state is more than a picosecond (with both TDDFT and EOM-CCSD). The predicted ultrafast electron diffraction spectrum exhibits numerous structural features, but weak time dependence over the course of the simulations.

Patients May Return to Work Sooner After Laminoplasty: Occupational Outcomes of the Cervical Spondylotic Myelopathy Surgical Trial.

BACKGROUND AND OBJECTIVES: Return-to-work (RTW) is an important outcome for employed patients considering surgery for cervical spondylotic myelopathy (CSM). We conducted a post hoc analysis of patients as-treated in the Cervical Spondylotic Myelopathy Surgical Trial, a prospective, randomized trial comparing surgical approaches for CSM to evaluate factors associated with RTW. METHODS: In the trial, patients were randomized (2:3) to either anterior surgery (anterior cervical decompression/fusion [ACDF]) or posterior surgery (laminoplasty [LP], or posterior cervical decompression/fusion [PCDF], at surgeon's discretion). Work status was recorded at 1, 3, 6, and 12 months postoperatively. For patients working full-time or part-time on enrollment, time to RTW was compared across as-treated surgical groups using discrete-time survival analysis. Multivariate logistic regression was used to assess predictors of RTW. Clinical outcomes were compared using a linear mixed-effects model. RESULTS: A total of 68 (42%) of 163 patients were working preoperatively and were analyzed. In total, 27 patients underwent ACDF, 29 underwent PCDF, and 12 underwent LP. 45 (66%) of 68 patients returned to work by 12 months. Median time to RTW differed by surgical approach (LP = 1 month, ACDF = 3 months, PCDF = 6 months; P = .02). Patients with longer length-of-stay were less likely to be working at 1 month (odds ratio 0.51; 95% CI, 0.29-0.91; P = .022) and 3 months (odds ratio 0.39; 95% CI, 0.16-0.96; P = .04). At 3 months, PCDF was associated with lower Short-Form 36 physical component summary scores than ACDF (estimated mean difference [EMD]: 6.42; 95% CI, 1.4-11.4; P = .007) and LP (EMD: 7.98; 95% CI, 2.7-13.3; P = .003), and higher Neck Disability Index scores than ACDF (EMD: 12.48; 95% CI, 2.3-22.7; P = .01) and LP (EMD: 15.22; 95% CI, 2.3-28.1; P = .014), indicating worse perceived physical functioning and greater disability, respectively. CONCLUSION: Most employed patients returned to work within 1 year. LP patients resumed employment earliest, while PCDF patients returned to work latest, with greater disability at follow-up, suggesting that choice of surgical intervention may influence occupational outcomes.

Conical Intersection Accessibility Dictates Brightness in Red Fluorescent Proteins.

Red fluorescent protein (RFP) variants are highly sought after for in vivo imaging since longer wavelengths improve depth and contrast in fluorescence imaging. However, the lower energy emission wavelength usually correlates with a lower fluorescent quantum yield compared to their green emitting counterparts. To guide the rational design of bright variants, we have theoretically assessed two variants (mScarlet and mRouge) which are reported to have very different brightness. Using an α-CASSCF QM/MM framework (chromophore and all protein residues within 6 Å of it in the QM region, for a total of more than 450 QM atoms), we identify key points on the ground and first excited state potential energy surfaces. The brighter variant mScarlet has a rigid scaffold, and the chromophore stays largely planar on the ground state. The dimmer variant mRouge shows more flexibility and can accommodate a pretwisted chromophore conformation which provides easier access to conical intersections. The main difference between the variants lies in the intersection seam regions, which appear largely inaccessible in mScarlet but partially accessible in mRouge. This observation is mainly related with changes in the cavity charge distribution, the hydrogen-bonding network involving the chromophore and a key ARG/THR mutation (which changes both charge and steric hindrance).

Effect of dimethyl fumarate on mitochondrial metabolism in a pediatric porcine model of asphyxia-induced in-hospital cardiac arrest.

Neurological and cardiac injuries are significant contributors to morbidity and mortality following pediatric in-hospital cardiac arrest (IHCA). Preservation of mitochondrial function may be critical for reducing these injuries. Dimethyl fumarate (DMF) has shown potential to enhance mitochondrial content and reduce oxidative damage. To investigate the efficacy of DMF in mitigating mitochondrial injury in a pediatric porcine model of IHCA, toddler-aged piglets were subjected to asphyxia-induced CA, followed by ventricular fibrillation, high-quality cardiopulmonary resuscitation, and random assignment to receive either DMF (30 mg/kg) or placebo for four days. Sham animals underwent similar anesthesia protocols without CA. After four days, tissues were analyzed for mitochondrial markers. In the brain, untreated CA animals exhibited a reduced expression of proteins of the oxidative phosphorylation system (CI, CIV, CV) and decreased mitochondrial respiration (p < 0.001). Despite alterations in mitochondrial content and morphology in the myocardium, as assessed per transmission electron microscopy, mitochondrial function was unchanged. DMF treatment counteracted 25% of the proteomic changes induced by CA in the brain, and preserved mitochondrial structure in the myocardium. DMF demonstrates a potential therapeutic benefit in preserving mitochondrial integrity following asphyxia-induced IHCA. Further investigation is warranted to fully elucidate DMF's protective mechanisms and optimize its therapeutic application in post-arrest care.

Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater.

Wastewater surveillance for SARS-CoV-2 provides early warnings of emerging variants of concerns and can be used to screen for novel cryptic linked-read mutations, which are co-occurring single nucleotide mutations that are rare, or entirely missing, in existing SARS-CoV-2 databases. While previous approaches have focused on specific regions of the SARS-CoV-2 genome, there is a need for computational tools capable of efficiently tracking cryptic mutations across the entire genome and investigating their potential origin. We present Crykey, a tool for rapidly identifying rare linked-read mutations across the genome of SARS-CoV-2. We evaluated the utility of Crykey on over 3,000 wastewater and over 22,000 clinical samples; our findings are three-fold: i) we identify hundreds of cryptic mutations that cover the entire SARS-CoV-2 genome, ii) we track the presence of these cryptic mutations across multiple wastewater treatment plants and over three years of sampling in Houston, and iii) we find a handful of cryptic mutations in wastewater mirror cryptic mutations in clinical samples and investigate their potential to represent real cryptic lineages. In summary, Crykey enables large-scale detection of cryptic mutations in wastewater that represent potential circulating cryptic lineages, serving as a new computational tool for wastewater surveillance of SARS-CoV-2.

Brain structural and functional abnormalities associated with acute post-traumatic headache: iron deposition and functional connectivity.

BACKGROUND: The purpose of this study was to interrogate brain iron accumulation in participants with acute post-traumatic headache (PTH) due to mild traumatic brain injury (mTBI), and to determine if functional connectivity is affected in areas with iron accumulation. We aimed to examine the correlations between iron accumulation and headache frequency, post-concussion symptom severity, number of mTBIs, and time since most recent TBI. METHODS: Sixty participants with acute PTH and 60 age-matched healthy controls (HC) underwent 3T magnetic resonance imaging including quantitative T2* maps and resting-state functional connectivity imaging. Between group T2* differences were determined using T-tests (p < 0.005, cluster size threshold of 90 voxels). For regions with T2* differences, two analyses were conducted. First, the correlations with clinical variables including headache frequency, number of lifetime mTBIs, time since most recent mTBI, and Sport Concussion Assessment Tool (SCAT) symptom severity scale scores were investigated using linear regression. Second, the functional connectivity of these regions with the rest of the brain was examined (significance of p < 0.05 with family wise error correction for multiple comparisons). RESULTS: The acute PTH group consisted of 60 participants (22 male, 38 female) with average age of 42 ± 14 years. The HC group consisted of 60 age-matched controls (17 male, 43 female, average age of 42 ± 13). PTH participants had lower T2* values compared to HC in the left posterior cingulate and the bilateral cuneus. Stronger functional connectivity was observed between bilateral cuneus and right cerebellar areas in PTH compared to HC. Within the PTH group, linear regression showed negative associations of T2* in the left posterior cingulate with SCAT symptom severity score (p = 0.05) and T2* in the left cuneus with headache frequency (p = 0.04). CONCLUSIONS: Iron accumulation in posterior cingulate and cuneus was observed in those with acute PTH relative to HC; stronger functional connectivity was detected between the bilateral cuneus and the right cerebellum. The correlations of decreased T2* (suggesting higher iron content) with headache frequency and post mTBI symptom severity suggest that the iron accumulation that results from mTBI might reflect the severity of underlying mTBI pathophysiology and associate with post-mTBI symptom severity including PTH.

Functional impairment of chronic migraine with medication overuse: Secondary analysis from the Medication Overuse Treatment Strategy (MOTS) trial.

BACKGROUND: Chronic migraine exerts substantial negative impacts on daily functioning. Efforts to manage impaired functioning may result in medication overuse, which contributes to the worsening profile and chronification of migraine. The Migraine Functional Impact Questionnaire (MFIQ) is a recently developed measure assessing the impact of migraine on physical, social, and emotional function. OBJECTIVE: The objective of this analysis was to assess changes in MFIQ scores following initiation or modification of migraine preventive medication and determine if changes in function are associated with changes in other aspects of migraine burden, such as headache frequency, headache intensity, and symptoms of anxiety and depression. METHODS: This is a secondary analysis of data from the Medication Overuse Treatment Strategy (MOTS) trial, a prospective pragmatic clinical trial that investigated two treatment strategies for those with chronic migraine and medication overuse. Data from both treatment arms were pooled and analyzed using a pre-post design. Prior to and 12 weeks following initiation or modification of migraine preventive medication, participants completed a series of questionnaires that captured migraine characteristics, medication use, migraine-related physical impairment (MFIQ), anxiety (Generalized Anxiety Disorder-7), and depression (Patient Health Questionnaire 9 [PHQ-9]) symptoms. Changes from baseline in all measures were assessed using the paired t-test. Relationships between changes in MFIQ scores and other measures were assessed using linear regression. Multivariable modeling was performed to determine which additional variables contributed to the change in MFIQ beyond that already explained by an individual variable. Model terms were selected by using elastic net regularization. Only those participants who completed the baseline and 12-week MFIQ were included in this analysis. RESULTS: Of the 537 patients, 88.2% were female, and the average age was 45 years (standard deviation 13). The mean frequency of days with moderate-to-severe headache improved 39.2% from 13.5 per 30 days at baseline to 8.1 per 30 days at week 12. The mean MFIQ Usual Activities Global score improved by 15.0 points (on a 100-point scale). All five domains (Usual Activities Global, Usual Activities, Social Function, Emotional Function, Physical Function) of the MFIQ improved by a mean of at least 13.0 points. Changes in PHQ-9 score, followed by changes in headache frequency, had the strongest associations with change in all domains of the MFIQ. CONCLUSIONS: The negative impact of chronic migraine with medication overuse on physical, social, and emotional functioning substantially lessened following initiation or modification of migraine preventive medication. Improved functioning, as measured by the MFIQ, was most strongly associated with reductions in depression scores and headache frequency, highlighting the importance of recognizing and monitoring changes in depressive symptoms, in addition to headache frequency and functional impairment, when evaluating response to preventive medications.

Phase-specific outcmes of arginine or branched-chain amino acids supplementation in low crude protein diets on performance, nutrient digestibility, and expression of tissue protein synthesis and degradation in broiler chickens infected with mixed Eimeria spp.

A 35-d study investigated the impact of dietary supplementation with Arginine (Arg) or branched-chain amino acids (BCAA) of broilers receiving low-protein diets whilst infected with mixed Eimeria species. All birds were given the same starter (d0-10) and finisher (d28-35) diets. The 4 grower diets used were a positive control (PC) with adequate protein (18.5%), a low protein diet (NC;16.5% CP), or the NC supplemented with Arg or BCAA. Supplemental AA was added at 50% above the recommended levels. The treatments were in a 4 × 2 factorial arrangement, with 4 diets, with or without Eimeria inoculation on d14. Birds and feed were weighed after inoculation in phases: prepatent (d14-17), acute (d18-21), recovery (d22-28), and compensatory (d29-35). Ileal digesta, jejunum, and breast tissue were collected on d21, 28, and 35. There was no diet × Eimeria inoculation on growth performance at any phase. Infected birds weighed less and consumed less feed (P < 0.05) in all phases. In the prepatent and acute phases, birds on the Arg diets had higher weight gain (P < 0.05) and lower FCR, similar to PC, when compared to NC and BCAA-fed ones. Infection reduced AA digestibility on d21 and 28 (Met and Cys). However, birds that received supplemental AA had higher digestibility (P < 0.05) of their respective supplemented AA on d 21 only. Infected birds had lower (P < 0.05) BO + AT and higher PEPT1 expression on d21. There was a diet × Eimeria interaction (P = 0.004) on gene expression at d28; 4EBP1 genes were significantly downwardly expressed (P < 0.05) in birds fed Arg diet, irrespective of infection. Infected birds exhibited an upward expression (P < 0.05) of Eef2 on d21 and d28 but experienced a downward expression on d35. Supplemental Arg and BCAA had variable effects on growth performance, apparent ileal AA digestibility, and genes of protein synthesis and degradation, but the effect of Arg on promoting weight gain, irrespective of the Eimeria challenge, was more consistent.

Parsnp 2.0: scalable core-genome alignment for massive microbial datasets.

MOTIVATION: Since 2016, the number of microbial species with available reference genomes in NCBI has more than tripled. Multiple genome alignment, the process of identifying nucleotides across multiple genomes which share a common ancestor, is used as the input to numerous downstream comparative analysis methods. Parsnp is one of the few multiple genome alignment methods able to scale to the current era of genomic data; however, there has been no major release since its initial release in 2014. RESULTS: To address this gap, we developed Parsnp v2, which significantly improves on its original release. Parsnp v2 provides users with more control over executions of the program, allowing Parsnp to be better tailored for different use-cases. We introduce a partitioning option to Parsnp, which allows the input to be broken up into multiple parallel alignment processes which are then combined into a final alignment. The partitioning option can reduce memory usage by over 4× and reduce runtime by over 2×, all while maintaining a precise core-genome alignment. The partitioning workflow is also less susceptible to complications caused by assembly artifacts and minor variation, as alignment anchors only need to be conserved within their partition and not across the entire input set. We highlight the performance on datasets involving thousands of bacterial and viral genomes. AVAILABILITY AND IMPLEMENTATION: Parsnp v2 is available at https://github.com/marbl/parsnp.

Preoperative Physical Therapy is Associated with Decreased Length of Stay and Improved Postoperative Mobility in Patients with Sarcopenia Undergoing Adult Spinal Deformity Surgery.

STUDY DESIGN: Retrospective cohort study. OBJECTIVE: To determine the relationship between preoperative physical therapy (PT) and postoperative mobility, adverse events (AEs), and length of stay (LOS) among patients with low normalized total psoas area (NTPA) undergoing ASD surgery. SUMMARY OF BACKGROUND DATA: Sarcopenia as defined by low NTPA has been shown to predict poor perioperative outcomes following adult spinal deformity (ASD) surgery. However, there is limited evidence correlating the benefits of PT within the sarcopenic patient population. METHODS: NTPA was analyzed at the L3 and L4 mid-vertebral body on preoperative magnetic resonance imaging (MRI). Receiver operating characteristic (ROC) curve analysis was used to determine gender-specific NTPA cut-off values for predicting perioperative AEs. Patients were categorized as having low NTPA if both L3 and L4 NTPA were below these cut-off values. Perioperative outcomes were compared between patients with low NTPA that underwent documented formal PT within 6 months prior to ASD surgery with those that did not. RESULTS: 103 patients (42 males, 61 females) met criteria for low NTPA for inclusion in the study, of which 42 underwent preoperative PT and 61 did not. The preoperative PT group had a shorter LOS (111.2±37.5 vs. 162.1±97.0 h, P<0.001), higher ambulation distances (feet) on postoperative day (POD) 1 (61.7±50.3 vs. 26.1±69.0, P<0.001), POD 2 (113.2±81.8 vs. 62.1±73.1, P=0.003), and POD 3 (126.0±61.2 vs. 91.2±72.6, P=0.029), and lower rates of total AEs (31.0% vs. 54.1%, P=0.003) when excluding anemia requiring transfusion. Multivariable analysis found preoperative PT to be the most significant predictor of decreased LOS (OR 0.32, P=0.013). CONCLUSION: Sarcopenic patients may benefit from formal preoperative PT prior to undergoing ASD surgery to improve early postoperative mobility, decrease AEs, and decrease LOS. LEVEL OF EVIDENCE: 3.

Normoxic Management during Cardiopulmonary Bypass Does Not Reduce Cerebral Mitochondrial Dysfunction in Neonatal Swine.

Optimal oxygen management during pediatric cardiopulmonary bypass (CPB) is unknown. We previously demonstrated an increase in cortical mitochondrial reactive oxygen species and decreased mitochondrial function after CPB using hyperoxic oxygen management. This study investigates whether controlled oxygenation (normoxia) during CPB reduces cortical mitochondrial dysfunction and oxidative injury. Ten neonatal swine underwent three hours of continuous CPB at 34 °C (flow > 100 mL/kg/min) via cervical cannulation targeting a partial pressure of arterial oxygen (PaO2) goal < 150 mmHg (normoxia, n = 5) or >300 mmHg (hyperoxia, n = 5). The animals underwent continuous hemodynamic monitoring and serial arterial blood sampling. Cortical microdialysate was serially sampled to quantify the glycerol concentration (represents neuronal injury) and lactate-to-pyruvate ratio (represents bioenergetic dysfunction). The cortical tissue was analyzed via high-resolution respirometry to quantify mitochondrial oxygen consumption and reactive oxygen species generation, and cortical oxidized protein carbonyl concentrations were quantified to assess for oxidative damage. Serum PaO2 was higher in hyperoxia animals throughout CPB (p < 0.001). There were no differences in cortical glycerol concentration between groups (p > 0.2). The cortical lactate-to-pyruvate ratio was modestly elevated in hyperoxia animals (p < 0.03) but the values were not clinically significant (<30). There were no differences in cortical mitochondrial respiration (p = 0.48), protein carbonyls (p = 0.74), or reactive oxygen species generation (p = 0.93) between groups. Controlled oxygenation during CPB does not significantly affect cortical mitochondrial function or oxidative injury in the acute setting. Further evaluation of the short and long-term effects of oxygen level titration during pediatric CPB on cortical tissue and other at-risk brain regions are needed, especially in the presence of cyanosis.

Potent neutralization by a receptor binding domain monoclonal antibody with broad specificity for SARS-CoV-2 JN.1 and other variants.

SARS-CoV-2 continues to be a public health burden, driven in-part by its continued antigenic diversification and resulting emergence of new variants. While increasing herd immunity, current vaccines, and therapeutics have improved outcomes for some; prophylactic and treatment interventions that are not compromised by viral evolution of the Spike protein are still needed. Using a rationally designed SARS-CoV-2 Receptor Binding Domain (RBD) - ACE2 fusion protein and differential selection process with native Omicron RBD protein, we developed a recombinant human monoclonal antibody (hmAb) from a convalescent individual following SARS-CoV-2 Omicron infection. The resulting hmAb, 1301B7 potently neutralized a wide range of SARS-CoV-2 variants including the original Wuhan and more recent Omicron JN.1 strain, as well as SARS-CoV. Structure determination of the SARS-CoV-2 EG5.1 Spike/1301B7 Fab complex by cryo-electron microscopy at 3.1Å resolution demonstrates 1301B7 contacts the ACE2 binding site of RBD exclusively through its VH1-69 heavy chain, making contacts using CDRs1-3, as well as framework region 3 (FR3). Broad specificity is achieved through 1301B7 binding to many conserved residues of Omicron variants including Y501 and H505. Consistent with its extensive binding epitope, 1301B7 is able to potently diminish viral burden in the upper and lower respiratory tract and protect mice from challenge with Omicron XBB1.5 and Omicron JN.1 viruses. These results suggest 1301B7 has broad potential to prevent or treat clinical SARS-CoV-2 infections and to guide development of RBD-based universal SARS-CoV-2 prophylactic vaccines and therapeutic approaches.