The effects of endurance trainability phenotype, sex, and interval running training on bone collagen synthesis in adult rats.

Bone is influenced by many factors such as genetics and mechanical loading, but the short-term physiological effects of these factors on bone (re)modelling are not well characterised. This study investigated the effects of endurance trainability phenotype, sex, and interval running training (7-week intervention) on bone collagen formation in rats using a deuterium oxide stable isotope tracer method. Bone samples of the femur diaphysis, proximal tibia, mid-shaft tibia, and distal tibia were collected after necropsy from forty-six 9 ± 3-month male and female rats selectively bred for yielding low (LRT) or high (HRT) responses to endurance training. Bone collagen proteins were isolated and hydrolysed, and fractional synthetic rates (FSRs) were determined by the incorporation of deuterium into protein-bound alanine via GC-pyrolysis-IRMS. There was a significant large main effect of phenotype at the femur site (p < 0.001; η2g = 0.473) with HRT rats showing greater bone collagen FSRs than LRT rats. There was a significant large main effect of phenotype (p = 0.008; η2g = 0.178) and a significant large main effect of sex (p = 0.005; η2g = 0.196) at the proximal site of the tibia with HRT rats showing greater bone collagen FSRs than LRT rats, and male rats showing greater bone collagen FSRs compared to female rats. There was a significant large main effect of training at the mid-shaft site of the tibia (p = 0.012; η2g = 0.159), with rats that underwent interval running training having greater bone collagen FSRs than control rats. Similarly, there was a significant large main effect of training at the distal site of the tibia (p = 0.050; η2g = 0.156), with rats in the interval running training group having greater bone collagen FSRs compared to rats in the control group. Collectively, this evidence highlights that bone responses to physiological effects are site-specific, indicating that interval running training has positive effects on bone collagen synthesis at the tibial mid-shaft and distal sites, whilst genetic factors affect bone collagen synthesis at the femur diaphysis (phenotype) and proximal tibia (phenotype and sex) in rats.

Evaluating the Effectiveness of Commercially Available Antiadhesion Tendon Protector Sheets in Tendon Repair Surgery Versus Tendon Repair Surgery Alone: A Preclinical Model Study.

PURPOSE: Adhesion formation is the major complication after tendon repairs that halts functional restoration and causes disability in patients. This study aimed to compare the antiadhesion efficacy of two tendon protector sheets using a previously established turkey flexor tendon model. METHODS: Twenty-four adult Bourbon Red turkeys were randomized into three groups: (1) control, (2) type I collagen-glycosaminoglycan (Collagen-GAG), and (3) hyaluronic acid. In each group, the flexor digitorum profundus tendon of the middle digit was sharply lacerated at the proximal interphalangeal joint level. All operated feet were immobilized until sacrifice 6 weeks after the surgery. After sacrifice, the repaired and normal digits were collected for biomechanical testing, adhesion scores, histological examination, and adhesion-related gene expression analysis. RESULTS: At 42 days after tendon repair, the normalized work of flexion of the repaired digit was the lowest in the Collagen-GAG group. The Collagen-GAG group also had the lowest gross adhesion score, indicating minimal adhesion. The hyaluronic acid group showed lower adhesion scores compared with the control, but the difference was not statistically significant. Microscopically, the Collagen-GAG group had a significantly lower histological adhesion score than the control group. In the Collagen-GAG group, the gene expression levels of WNT3A, WNT5A, and WNT7A were suppressed. CONCLUSIONS: In an avian model of flexor tendon repair, the application of tendon protector sheets reduces peritendinous fibrotic tissue formation histologically. CLINICAL RELEVANCE: There are currently limited commercially available products to reduce postoperative peritendinous adhesions. Further validation is needed to confirm the effectiveness of tendon protector sheets in improving surgical outcomes following tendon repairs.

Proteostasis and metabolic dysfunction in a distinct subset of storage-induced senescent erythrocytes targeted for clearance.

Although refrigerated storage slows the metabolism of volunteer donor RBCs, cellular aging still occurs throughout this in vitro process, which is essential in transfusion medicine. Storage-induced microerythrocytes (SMEs) are morphologically-altered senescent RBCs that accumulate during storage and which are cleared from circulation following transfusion. However, the molecular and cellular alterations that trigger clearance of this RBC subset remain to be identified. Using a staining protocol that sorts long-stored SMEs (i.e., CFSE high ) and morphologically-normal RBCs (CFSE low ), these in vitro aged cells were characterized. Metabolomics analysis identified depletion of energy, lipid-repair, and antioxidant metabolites in CFSE high RBCs. By redox proteomics, irreversible protein oxidation primarily affected CFSE high RBCs. By proteomics, 96 proteins, mostly in the proteostasis family, had relocated to CFSE high RBC membranes. CFSE high RBCs exhibited decreased proteasome activity and deformability; increased phosphatidylserine exposure, osmotic fragility, and endothelial cell adherence; and were cleared from the circulation during human spleen ex vivo perfusion. Conversely, molecular, cellular, and circulatory properties of long-stored CFSE low RBCs resembled those of short-stored RBCs. CFSE high RBCs are morphologically and metabolically altered, have irreversibly oxidized and membrane-relocated proteins, and exhibit decreased proteasome activity. In vitro aging during storage selectively alters metabolism and proteostasis in SMEs, targeting these senescent cells for clearance.

Electrohydraulic musculoskeletal robotic leg for agile, adaptive, yet energy-efficient locomotion.

Robotic locomotion in unstructured terrain demands an agile, adaptive, and energy-efficient architecture. To traverse such terrains, legged robots use rigid electromagnetic motors and sensorized drivetrains to adapt to the environment actively. These systems struggle to compete with animals that excel through their agile and effortless motion in natural environments. We propose a bio-inspired musculoskeletal leg architecture driven by antagonistic pairs of electrohydraulic artificial muscles. Our leg is mounted on a boom arm and can adaptively hop on varying terrain in an energy-efficient yet agile manner. It can also detect obstacles through capacitive self-sensing. The leg performs powerful and agile gait motions beyond 5 Hz and high jumps up to 40 % of the leg height. Our leg's tunable stiffness and inherent adaptability allow it to hop over grass, sand, gravel, pebbles, and large rocks using only open-loop force control. The electrohydraulic leg features a low cost of transport (0.73), and while squatting, it consumes only a fraction of the energy (1.2 %) compared to its conventional electromagnetic counterpart. Its agile, adaptive, and energy-efficient properties would open a roadmap toward a new class of musculoskeletal robots for versatile locomotion and operation in unstructured natural environments.

Discovery and Development of Highly Potent and Orally Bioavailable Nonpeptidic αvß6 Integrin Inhibitors.

A series of 3-aryl((S)-3-fluoropyrrolidin-1-yl)butanoic acids were developed as potent orally bioavailable αvß6 integrin inhibitors. Starting from a zwitterionic peptidomimetic series optimized for inhaled administration, the balancing of potency and passive permeability to achieve suitable oral agents through modification and exploration of aryl substituents and pKa of the central cyclic amine is described. (S)-4-((S)-3-Fluoro-3-(2-(5,6,7,8-tetrahydro-1,8-naphthyridin-2-yl)ethyl)pyrrolidin-1-yl)-3-(3-(2-methoxyethoxy)phenyl)butanoic acid was found to have highly desirable oral pharmacokinetic profiles in rat, dog, and minipig, with low to moderate clearance (26%, 7%, and 18% liver blood flow, respectively), moderate volumes of distribution (3.6, 1.4, and 0.9 L/kg, respectively), high to complete oral bioavailabilities, high αvß6 integrin potency of pIC50 of 8.0, and high solubility in physiological media (>2 mg/mL). Equating to the estimated human dose range of 10-75 mg b.i.d. to achieve 90% αvß6 target engagement at Cmin, it was selected for further investigation as a potential therapeutic agent for the treatment of idiopathic pulmonary fibrosis.

Splam: a deep-learning-based splice site predictor that improves spliced alignments.

The process of splicing messenger RNA to remove introns plays a central role in creating genes and gene variants. We describe Splam, a novel method for predicting splice junctions in DNA using deep residual convolutional neural networks. Unlike previous models, Splam looks at a 400-base-pair window flanking each splice site, reflecting the biological splicing process that relies primarily on signals within this window. Splam also trains on donor and acceptor pairs together, mirroring how the splicing machinery recognizes both ends of each intron. Compared to SpliceAI, Splam is consistently more accurate, achieving 96% accuracy in predicting human splice junctions.

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.

Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.

Use of a PHQ-9 Heat Map to Facilitate Management Decisions in Patients With Depression.

BACKGROUND: Depression is a common concern for patients seeking medical care. The Patient Health Questionnaire-9 (PHQ-9) is a tool used to diagnose and manage depression. Tracking individual symptom scores rather than the sum of multiple symptom scores has been found to be more predictive of depression treatment response. METHODS: The records of 30 patients who had a follow-up visit in primary care were reviewed. We discuss 3 patient scenarios and present their PHQ-9 data as individual symptom scores, in the form of a color-coded heat map. RESULTS: In the cases presented, medication side effects, anxiety, a thyroid disorder, and fibromyalgia were identified as possible influencers of the PHQ-9 survey scores. DSICUSSION: A heat map helped clinicians understand the patient's clinical status in an efficient manner. We encourage the development of a PHQ-9 heat map in electronic medical record systems.

Correlates of improved outcomes in patients with COVID-19 treated in US emergency departments.

BACKGROUND: The COVID-19 pandemic was managed in part by the rapid development of vaccines, diagnostics, and therapeutics including antiviral agents and advances in emergency airway and ventilatory management. The impact of these therapeutic advances on clinically pertinent metrics of emergency care have not been well-studied. METHODS: We abstracted data from emergency department (ED) visits made to 21 US health systems during the first two years of the pandemic, from February 1, 2020 to January 31, 2022. These health systems were participants in the NIH-supported COVID EHR Cohort, in which the University of Wisconsin served as the coordinating site. Limited patient-level data files were submitted monthly. Data elements included demographic and clinical variables, as well as standard measures of ED outcomes including 72-h returns, 72-h returns leading to readmission, and in-hospital mortality. Multivariable models were fitted to identify correlates of each of the dependent variables. A test for trend was used to detect changes in outcomes over time. RESULTS: During the two-year period, 150,357 individuals aged 18 years or older visited the ED. The median age was 45.4 years (IQR 27), 58.1 % were female, 49 % were White, 18.3 % Hispanic/Latino, and 45 % were publicly insured or uninsured. The prevalence of 72-h ED returns, readmissions, and in-hospital mortality significantly declined across the two-year period. SARS-CoV-2 vaccination was associated with reduced ED returns and mortality. Therapeutic agents were associated with increased mortality risk but were likely confounded by unmeasured covariates. CONCLUSIONS: Operational and clinical outcomes of ED-based treatment of individuals with COVID-19 improved in the first two years of the pandemic. This improvement is likely multifactorial and includes the development and deployment of SARS-CoV-2-specific vaccines, therapeutic agents, and improved healthcare delivery in the ED and elsewhere addressing management of airway and ventilatory status, as well as increased innate immunity in the general population.

Complex Bentall Operation: Clinical Pearls to Standardize the Procedure.

BACKGROUND: A straightforward Bentall operation can be performed safely with low mortality, but some challenging cases require a more complex operation. In this manuscript, we will discuss the steps of the Bentall procedure. METHODS: We reviewed specific scenarios such as acute aortic dissection, native valve or prosthetic valve endocarditis, redo Bentall after aortic root replacement, calcified aortic root, and patients with prior coronary artery bypass grafting, mechanical aortic valve replacement, stentless aortic valve replacement, and prior extensive aortic arch repair with proximalization of neck vessels. RESULTS: Variety of techniques were reported regarding reconstruction of aortic annulus (e.g. Dacron graft is everted to create 5 to 6 crimps when sewing a bioprosthesis. The height of the skirt can be adjusted depending on tissue defect) and reimplantation of coronary buttons (Interposition of Dacron graft for coronary button reimplantation [original Cabrol technique], short interposition of Dacron graft is known as Piehler technique, and technique in redo Bentall after prior aortic root replacement). In patients with a history of coronary artery bypass grafting, direct reimplantation of previous vein graft patch to the Dacron graft or interposition of short Dacron graft were introduced. In addition, repair of coronary button in Type A dissection or calcified aortic root were also described. CONCLUSIONS: There are various techniques available in modified Bentall operation. Surgeons should be familiar with the setup, anatomy of aortic root and surrounding structures, ways to treat tissue defect and prepare coronary buttons, and the various bail-out procedures.

Coupling antitoxins and blue/white screening with parAB/resolvase mutation as a strategy for Salmonella spp. plasmid curing.

Despite the dissemination of multidrug resistance plasmids, including those carrying virulence genes in Salmonella spp., efficient plasmid curing tools are lacking. Plasmid partitioning and multimer resolution systems are attractive targets for plasmid cure. However, plasmid curing strategies targeting these systems are often hindered by the host addiction system through a process known as post-segregation killing. Here, we developed vector tools that can mutate the above systems while replenishing short-lived antitoxins. Cloning was performed using Gibson assembly. parAB or resolvase (res) genes on Incompatibility Group (Inc)FIB, IncA/C, IncX4, and plasmids carried by Salmonella species were deleted by first knocking in the N-terminal ß-galactosidase encoding gene (bgaB), followed by in-frame insertion of its C-terminal region using pDG1 and pDG2 vectors, respectively. pDG1 was used as a backbone to develop a vector, designated as pDG-At, expressing 13 antitoxins driven by strong promoters. Plasmid curing was achieved by transforming pDG-At to parAB or res mutants followed by blue-white screening and PCR; however, parAB mutant isolation with this method was low and often non-reproducible. To elucidate whether the prior presence of pDG-At in cells improves viable mutant isolation, we re-constructed pDG-At, designated as pDG-Atπ, using a vector with the R6Kϒ origin of replication with its π-factor required for replication under araBAD promoter. Results showed that pDG-Atπ can replicate in the absence of arabinose but can be cured by growing cells in glucose-rich media. Next, we repeated IncFIB's parAB deletion using pDG1 but in cells carrying pDG-Atπ. Many white colonies were detected on X-Gal-supplemented media but none of them carried the target parA mutation; however, ~80% of the white colonies lost IncFIB plasmid, while the others retained the wild-type plasmid. Similar results were obtained for IncX4 plasmid curing but also found that this method was not reproducible as the white colonies obtained after allelic replacement did not always result in plasmid curing or mutant isolation. This is the first report describing a simple blue/white screening method for plasmid curing that can avoid laborious screening procedures. IMPORTANCE: Plasmids play an important role in bacterial physiology, adaptation, evolution, virulence, and antibiotic resistance. An in-depth study of these roles partly depends on the generation of plasmid-free cells. This study shows that vector tools that target genes required for plasmid stability in the presence of an antitoxin-expressing helper plasmid are a viable approach to cure specific plasmids. Expression of bgaB from target plasmids can greatly facilitate visual detection of plasmid cured colonies avoiding time-consuming screening procedures. This approach can be refined for the development of a universal plasmid curing system that can be used to generate plasmid-free cells in other human bacterial pathogens including Gram positives and Gram negatives.

Exploring the body condition of gray whales (Eschrichtius robustus) through adipocyte analysis during unusual mortality events.

The blubber is the characteristic fatty tissue of most marine mammals; it comprises adipocytes, blood vessels, lymphatics, and abundant collagen and elastic fibers. Containing the reserve of excess and accumulated energy from feeding. Previous studies found that the adipocyte area may change according to the amount of accumulated and expended energy during migration, reproduction, lactation and breeding. This cellular characteristic reflects the energetic status of an individual (i.e., the balance between intake and total energy investment), which can be interpreted as reproductive success and general health. In the present study, we measured the adipocyte area of the gray whales wintering in Laguna San Ignacio, Baja California Sur, Mexico, to evaluate body condition. Adipose tissue was sampled from 116 individuals (31 calves, 22 mothers, and 63 solitary individuals) over a study period of 62 days. Each whale was assigned a priori body condition (good, fair, poor). Histological preparations stained with hematoxylin-eosin were microphotographs used to measure the adipocyte area with the software Adiposoft as a plugin to ImageJ. The adipocyte area of the calves was significantly lower than that of the adults and showed an increase during the study period. The three body condition categories found no differences in the adipocyte area. The adipocyte area analysis applied in the present study appears to be a useful tool in assessing body condition in calves, although it appears to be limited to adults. According to the OneHealth paradigm, environmental health is closely related to the health of the gray whale, which in turn is related to public health and the socioeconomic well-being of local communities that use this species as a resource.

Metagenomic next generation sequencing of plasma RNA for diagnosis of unexplained, acute febrile illness in Uganda.

Metagenomic next generation metagenomic sequencing (mNGS) has proven to be a useful tool in the diagnosis and identification of novel human pathogens and pathogens not identified on routine clinical microbiologic tests. In this study, we applied mNGS to characterize plasma RNA isolated from 42 study participants with unexplained acute febrile illness (AFI) admitted to tertiary referral hospitals in Mubende and Arua, Uganda. Study participants were selected based on clinical criteria suggestive of viral infection (i.e., thrombocytopenia, leukopenia). The study population had a median age of 28 years (IQR:24 to 38.5) and median platelet count of 114 x103 cells/mm3 (IQR:66,500 to 189,800). An average of 25 million 100 bp reads were generated per sample. We identified strong signals from diverse virus, bacteria, fungi, or parasites in 10 (23.8%) of the study participants. These included well recognized pathogens like Helicobacter pylori, human herpes virus-8, Plasmodium falciparum, Neisseria gonorrhoeae, and Rickettsia conorii. We further confirmed Rickettsia conorii infection, the cause of Mediterranean Spotted Fever (MSF), using PCR assays and Sanger sequencing. mNGS was a useful addition for detection of otherwise undetected pathogens and well-recognized non-pathogens. This is the first report to describe the molecular confirmation of a hospitalized case of MSF in sub-Saharan Africa (SSA). Further studies are needed to determine the utility of mNGS for disease surveillance in similar settings.

Part II: superconductivity observed in magnetically separated nanoscale anatase titania at ambient temperature and pressure in an aqueous environment at its point of zero charge.

This is the first work to investigate if and/or how changes in the surface structure/properties affect the charge transfer resistance (R CT) of anatase titania with decreasing particle size. It was accomplished by measuring the R CT (Ω) of same weight anatase titania pellets, with particle sizes ranging from 5.31 nm to 142.61 nm. Measurements were made using Electrochemical Impedance Spectroscopy (EIS) at each material's point of zero charge (PZC). Results demonstrated two regions of R CT. Above an average primary particle diameter of 23.54 nm, R CT remained essentially constant. Below, this diameter the R CT value first increased significantly, then decreased almost linearly toward zero. The projected average primary particle diameter where the materials R CT was projected to reach zero resistance is at a diameter of approximately 4.39 nm. A simple test was then developed to determine if at a small enough particle size the material would be affected by an external magnetic field. It was found that a sample with an average particle diameter of 12.689 nm, formed fine needles/threads of particles in deionized water, perpendicular to the settled powder at the base of the potash tube. This led to the development of a simple magnetic separation method to obtain strongly diamagnetic material from a parent population with an average primary particle diameter of 5.31 nm. A pellet consisting of these magnetically separated particles was then pressed at the same weight and pressure as the prior samples. The pellet's R CT was then measured using EIS under the identical conditions as the prior samples. EIS results of the magnetically separated particles in pellet form, under multiple conditions, resulted in Nyquist plots indicating the material exhibited no detectable R CT (i.e., superconductivity). Correlation of the shift in the materials R CT with known structure/property changes for each sample with decreasing particle size allowed the development of a model explaining: (1) the significant increase in diamagnetic strength of the magnetically separated particles and (2) the mechanism controlling the material's R CT.

Clostridium scindens : an endocrine keystone species in the mammalian gut.

Clostridium scindens is a keystone human gut microbial taxonomic group that, while low in abundance, has a disproportionate effect on bile acid and steroid metabolism in the mammalian gut. Numerous studies indicate that the two most studied strains of C. scindens (i.e., ATCC 35704 and VPI 12708) are important for a myriad of physiological processes in the host. We focus on both historical and current microbiological and molecular biology work on the Hylemon-Björkhem pathway and the steroid-17,20-desmolase pathway that were first discovered in C. scindens. Our most recent analysis now calls into question whether strains currently defined as C. scindens represent two separate taxonomic groups. Future directions include developing genetic tools to further explore the physiological role bile acid and steroid metabolism by strains of C. scindens , and the causal role of these pathways in host physiology and disease.

A first-in-kind MAPK13 inhibitor that can correct stem cell reprogramming and post-injury disease.

The stress kinase MAPK13 (aka p38δ-MAPK) is an attractive entry point for therapeutic intervention because it regulates the structural remodeling that can develop after epithelial barrier injury in the lung and likely other tissue sites. However, a selective, safe, and effective MAPK13 inhibitor is not yet available for experimental or clinical application. Here we identify a first-in-kind MAPK13 inhibitor using structure-based drug design combined with a screening funnel for cell safety and molecular specificity. This inhibitor (designated NuP-4) down-regulates basal-epithelial stem cell reprogramming, structural remodeling, and pathophysiology equivalently to Mapk13 gene-knockout in mouse and mouse organoid models of post-viral lung disease. This therapeutic benefit persists after stopping treatment as a sign of disease modification and attenuates key aspects of inflammation and remodeling as an indication of disease reversal. Similarly, NuP-4 treatment can directly control cytokine-stimulated growth, immune activation, and mucinous differentiation in human basal-cell organoids. The data thereby provide a new tool and potential fix for long-term stem cell reprogramming after viral injury and related conditions that require MAPK13 induction-activation.