Towards the biogeography of prokaryotic genes.

Microbial genes encode the majority of the functional repertoire of life on earth. However, despite increasing efforts in metagenomic sequencing of various habitats1-3, little is known about the distribution of genes across the global biosphere, with implications for human and planetary health. Here we constructed a non-redundant gene catalogue of 303 million species-level genes (clustered at 95% nucleotide identity) from 13,174 publicly available metagenomes across 14 major habitats and use it to show that most genes are specific to a single habitat. The small fraction of genes found in multiple habitats is enriched in antibiotic-resistance genes and markers for mobile genetic elements. By further clustering these species-level genes into 32 million protein families, we observed that a small fraction of these families contain the majority of the genes (0.6% of families account for 50% of the genes). The majority of species-level genes and protein families are rare. Furthermore, species-level genes, and in particular the rare ones, show low rates of positive (adaptive) selection, supporting a model in which most genetic variability observed within each protein family is neutral or nearly neutral.

Consistency across multi-omics layers in a drug-perturbed gut microbial community.

Multi-omics analyses are used in microbiome studies to understand molecular changes in microbial communities exposed to different conditions. However, it is not always clear how much each omics data type contributes to our understanding and whether they are concordant with each other. Here, we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers (16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics and metabolomics). We find that all the omics methods with species resolution are highly consistent in estimating relative species abundances. Furthermore, different omics methods complement each other for capturing functional changes. For example, while nearly all the omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control. Metabolomics revealed a decrease in oligosaccharide uptake, likely caused by Bacteroidota depletion. Our study highlights how multi-omics datasets can be utilized to reveal complex molecular responses to external perturbations in microbial communities.

Using an artificial neural network for fast mapping of the oxygen extraction fraction with combined QSM and quantitative BOLD.

PURPOSE: To apply an artificial neural network (ANN) for fast and robust quantification of the oxygen extraction fraction (OEF) from a combined QSM and quantitative BOLD analysis of gradient echo data and to compare the ANN to a traditional quasi-Newton (QN) method for numerical optimization. METHODS: Random combinations of OEF, deoxygenated blood volume ( ν ), R2 , and nonblood magnetic susceptibility ( χnb ) with each parameter following a Gaussian distribution that represented physiological gray matter and white matter values were used to simulate quantitative BOLD signals and QSM values. An ANN was trained with the simulated data with added Gaussian noise. The ANN was applied to multigradient echo brain data of 7 healthy subjects, and the reconstructed parameters and maps were compared to QN results using Student t test and Bland-Altman analysis. RESULTS: Intersubject means and SDs of gray matter were OEF =43.5±0.8 %, R2=13.5±0.3 Hz, ν=3.4±0.1 %, χnb=-25±5 ppb for ANN; and OEF = 43.8±5.2 %, R2=12.2±0.8 Hz, ν=4.2±0.6 %, χnb=-39±7 ppb for QN, with a significant difference ( P<0.05 ) for R2 , ν , and χnb . For white matter, they were OEF = 47.5±1.1 %, R2=17.1±0.4 Hz, ν=2.5±0.2 %, χnb=-38±5 ppb for ANN; and OEF =42.3±5.6 %, R2=16.7±0.7 Hz, ν=2.9±0.3 %, χnb=-45±9 ppb for QN, with a significant difference ( P<0.05 ) for OEF and ν . ANN revealed more gray-white matter contrast but less intersubject variation in OEF than QN. In contrast to QN, the ANN reconstruction did not need an additional sequence for parameter initialization and took approximately 1 s rather than roughly 1 h. CONCLUSION: ANNs allow faster and, with regard to initialization, more robust reconstruction of OEF maps with lower intersubject variation than QN approaches.

Comparison of gradient echo and gradient echo sampling of spin echo sequence for the quantification of the oxygen extraction fraction from a combined quantitative susceptibility mapping and quantitative BOLD (QSM+qBOLD) approach.

PURPOSE: To compare gradient echo (GRE) and gradient echo sampling of spin echo (GESSE) sequences for the quantification of the oxygen extraction fraction (OEF) from combined quantitative BOLD and quantitative susceptibility mapping (QSM) with regard to accuracy, precision and parameter initialization. METHODS: GRE and GESSE data were acquired from 7 healthy volunteers. QSM was applied to the GRE data and used as a regularization for the single-compartment quantitative BOLD fit to the GESSE and GRE data, respectively, to quantify OEF, deoxygenated blood volume (ν), R2 , and non-blood susceptibility (χnb ). Intersubject means within gray and white matter, respectively, were compared between GESSE and GRE (Student's t) and gray-white matter contrast was determined for each sequence separately. A single- and multi-compartment simulation was used to compare reconstruction accuracy. RESULTS: Intersubject means and SDs for gray and white matter were OEF = 32.4 ± 1.6%, ν = 2.9 ± 0.1%, R2 = 14.2 ± 0.5 Hz, χnb = -43 ± 5 ppb for GESSE and OEF = 43.0 ± 5.4%, ν = 3.5 ± 0.4%, R2 = 14.4 ± 0.7 Hz, χnb = -43 ± 8 ppb for GRE with a significant difference (P < 0.05) for OEF and ν. Gray-white matter contrast was significant (P < 0.05) in all parameters for GESSE but only in ν and R2 for GRE. All parameters reconstructed from GESSE had higher accuracy than from GRE in the single- but not multi-compartment simulation. CONCLUSION: GESSE yields higher parameter accuracy in simulated gray matter but produces unphysiological gray-white matter contrast in OEF in vivo. GRE produces uniform OEF maps in vivo and is more efficient, which could facilitate a clinical implementation, but revealed biases in simulation. The appropriate sequence should be chosen depending on application.

Putty Index for Tripoding.

Precise orientation and transfer of the selected path of insertion and removal is a critical step in cast removable partial denture prosthesis design. An easy technique for registering the same is described using addition silicon putty and a used diamond disk.

Microwave Chip-Based Beam Splitter for Low-Energy Guided Electrons.

We present a novel beam splitter for low-energy electrons using a micro-structured guiding potential created above the surface of a planar microwave chip. Beam splitting arises from smoothly transforming the transverse guiding potential for an electron beam from a single-well harmonic confinement into a double well, thereby generating two separated output beams with 5 mm lateral spacing. Efficient beam splitting is observed for electron kinetic energies up to 3 eV, in excellent agreement with particle tracking simulations. We discuss prospects of this novel beam splitter approach for electron-based quantum matter-wave optics experiments.

Probing of optical near-fields by electron Rescattering on the 1 nm scale.

We present a new method of measuring optical near-fields within ~1 nm of a metal surface based on rescattering of photoemitted electrons. With this method, we precisely measure the field enhancement factor for tungsten and gold nanotips as a function of tip radius. The agreement with Maxwell simulations is very good. Further simulations yield a field enhancement map for all materials, which shows that optical near-fields at nanotips are governed by a geometric effect under most conditions, while plasmon resonances play only a minor role. Last, we consider the implications of our results on quantum mechanical effects near the surface of nanostructures and discuss features of quantum plasmonics.

Enhanced cryoprecipitate for skin graft and donor site wound healing in pigs.

Due to similarities in skin characteristics, the authors hypothesise that a pig model would most accurately show the ability of autologous, enhanced cryoprecipitate (eCryo) to improve the wound healing of split-thickness skin grafts (STSGs) and corresponding donor sites. Fifty-two STSGs (5 × 5 cm) were fashioned and treated according to a randomised protocol with an autologous eCryo-treated and a control group. Macroscopic assessment, histological evaluation and cellular composition were completed at days 7, 14, 21 and 28. Thirty-two donor sites were also created and assessed in a similar manner. Histologic analysis showed enhancement of healing over all time points for eCryo-treated donor sites. All other results showed no statistically significant improvement with the use of eCryo. Autologous cryoprecipitate appears to be a safe, inexpensive and easy-to-use alternative to fibrin glue, which carries risks and is, in many cases, prohibitively expensive. Further studies are necessary to evaluate the full potential of eCryo. Interestingly, eCryo application may improve donor site aesthetic appearance. We believe that a pig model most reliably simulates eCryo's behaviour in humans to accurately reflect its future clinical applicability.

Association between iron accumulation in the dorsal striatum and compulsive drinking in alcohol use disorder.

RATIONALE: Brain iron accumulation has been observed in neuropsychiatric disorders and shown to be related to neurodegeneration. OBJECTIVES: In this study, we used quantitative susceptibility mapping (QSM), an emerging MRI technique developed for quantifying tissue magnetic susceptibility, to examine brain iron accumulation in individuals with alcohol use disorder (AUD) and its relation to compulsive drinking. METHODS: Based on our previous projects, QSM was performed as a secondary analysis with gradient echo sequence images, in 186 individuals with AUD and 274 healthy participants. Whole-brain susceptibility values were calculated with morphology-enabled dipole inversion and referenced to the cerebrospinal fluid. Then, the susceptibility maps were compared between AUD individuals and healthy participants. The relationship between drinking patterns and susceptibility was explored. RESULTS: Whole-brain analyses showed that the susceptibility in the dorsal striatum (putamen and caudate) among AUD individuals was higher than healthy participants and was positively related to the Obsessive Compulsive Drinking Scale (OCDS) scores and the amount of drinking in the past three months. CONCLUSIONS: Increased susceptibility suggests higher iron accumulation in the dorsal striatum in AUD. This surrogate for the brain iron level was linearly associated with the compulsive drinking pattern and the recent amount of drinking, which provides us a new clinical perspective in relation to brain iron accumulation, and also might indicate an association of AUD with neuroinflammation as a consequence of brain iron accumulation. The iron accumulation in the striatum is further relevant for functional imaging studies in AUD by potentially producing signal dropout and artefacts in fMRI images.

Nanoscale organization of the endogenous ASC speck.

The NLRP3 inflammasome is a central component of the innate immune system. Its activation leads to formation of the ASC speck, a supramolecular assembly of the inflammasome adaptor protein ASC. Different models, based on ASC overexpression, have been proposed for the structure of the ASC speck. Using dual-color 3D super-resolution imaging (dSTORM and DNA-PAINT), we visualized the ASC speck structure following NLRP3 inflammasome activation using endogenous ASC expression. A complete structure was only obtainable by labeling with both anti-ASC antibodies and nanobodies. The complex varies in diameter between ∼800 and 1000 nm, and is composed of a dense core with emerging filaments. Dual-color confocal fluorescence microscopy indicated that the ASC speck does not colocalize with the microtubule-organizing center at late time points after Nigericin stimulation. From super-resolution images of whole cells, the ASC specks were sorted into a pseudo-time sequence indicating that they become denser but not larger during formation.

Generating few-cycle pulses for nanoscale photoemission easily with an erbium-doped fiber laser.

We demonstrate a simple setup capable of generating four-cycle pulses at a center wavelength of 1700 nm for nanoscale photoemission. Pulses from an amplified erbium-doped fiber laser are spectrally broadened by propagation through a highly non-linear fiber. Subsequently, we exploit dispersion in two different types of glass to compress the pulses. The pulse length is estimated by measuring an interferometric autocorrelation trace and comparing it to a numerical simulation. We demonstrate highly non-linear photoemission of electrons from a nanometric tungsten tip in a hitherto unexplored pulse parameter range.

Rapid electrophoretic deposition of biocompatible graphene coatings for high-performance recording neural electrodes.

The electrical and biological interfacial properties of invasive electrodes have a significant impact on the performance and longevity of neural recordings in the brain. In this study, we demonstrated rapid electrophoretic deposition and electrochemical reduction of graphene oxide (GO) on metal-based neural electrodes. Scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS) and other characterizations confirmed the existence of a uniform and effectively reduced graphene oxide coating. Electrochemically reduced graphene oxide (ErGO) coated Pt/Ir neural electrodes exhibited 15.2-fold increase in charge storage capacity (CSC) and 90% decrease in impedance with only 3.8% increase in electrode diameter. Patch clamp electrophysiology and calcium imaging of primary rat hippocampus neurons cultured on ErGO demonstrated that there was no adverse impact on the functional development of neurons. Immunostaining showed a balanced growth of excitatory and inhibitory neurons, and astrocytes. Acute recordings from the auditory cortex and chronic recordings (19 days) from the somatosensory cortex found ErGO coating improved the performance of neural electrodes in signal-to-noise ratio (SNR) and amplitude of signals. The proposed approach not only provides an in-depth evaluation of the effect of ErGO coating on neural electrodes but also widens the coating methods of commercial neural electrodes.

Hyperbaric oxygenation therapy alleviates chronic constrictive injury-induced neuropathic pain and reduces tumor necrosis factor-alpha production.

BACKGROUND: The development of hyperalgesia and allodynia after chronic constrictive injury (CCI) is associated with significantly increased tumor necrosis factor (TNF)-α and interleukin (IL)-1ß. Theoretically, if the production of TNF-α and/or IL-1ß could be reduced, neuropathic pain syndrome may be alleviated. Recently, a beneficial effect of hyperbaric oxygenation therapy (HBOT) in the treatment of pain disorders has been suggested. Our present study was designed to examine the hypotheses that (1) CCI-induced neuropathic pain may be associated with increased production of TNF-α and IL-1ß, (2) HBOT may alleviate CCI-induced neuropathic pain, and (3) the alleviated neuropathic pain may be associated with reduced production of TNF-α and/or IL-1ß. METHODS: Male rats (weighing 250-300 g) were anesthetized with ketamine and xylazine. The common sciatic nerve was exposed through the biceps femoris. Proximal to the sciatic's trifurcation, 4 ligatures were loosely tied around the nerve. In the sham group, an identical dissection was performed without ligation of the sciatic nerve. Mechanical allodynia and cold allodynia were tested by von Frey filament stimulation and the spread of acetone, respectively. HBO rats (n =18) were exposed to pure oxygen for 1 hour at 2.4 atm once a day. Non-HBO (n =18) and sham rats (n =6) were placed in the HBOT chamber breathing air. TNF-α and IL-1ß in the sciatic nerve were assayed with ELISA. The presence of TNF-α protein in homogenates was verified by Western blot analysis. RESULTS: CCI induced significant cold and mechanical allodynia as measured after CCI on days 4 and 7. The cold allodynia response frequency was significantly lower in HBO rats than in non-HBO rats. The values were 20% ± 1.6% vs 50% ± 4.5% on day 4 and 40% ± 4.6% vs 70% ± 4.5% on day 7 (F =87.42, confidence interval [for the difference between HBO and non-HBO]=29.612 ± 8.781, P < 0.05 for day 4 and day 7). The threshold of mechanical allodynia significantly increased in HBO rats compared with non-HBO rats. The values were 6.20 ± 0.9 vs 4.1 ± 1.0 g on day 4 and 3.8.2 ± 0.5 vs 2.3 ± 0.4 g on day 7 (F =18.8, confidence interval [for the difference between HBO and non-HBO]=1.806 ± 1.171, P < 0.05 for day 4 and day 7). TNF-α content was significantly higher in non-HBO rats than in sham rats on day 4 (17.89 ± 0.83 vs 10.66 ± 1.1 pg/mg protein, P < 0.05) and day 7 (18.97 ± 1.57 vs 9.09 ± 1.5 pg/mg protein, P < 0.05). HBOT significantly reduced TNF-α content to near the level in sham rats, which was 10.94 ± 2.78 and 11.32 ± 2.98 pg/mg protein on day 4 (P < 0.05 versus non-HBO) and 7 (P < 0.05 versus non-HBO), respectively. Western blot analysis confirmed the presence of proteins with molecular weights of 51 kDa in the rat sciatic nerve homogenates. IL-1ß content was also significantly higher in non-HBO rats than in sham rats on day 4 (636 ± 74 vs 256 ± 31 pg/mg protein, P < 0.05) and on day 7 (687 ± 89 vs 288 ± 35 pg/mg protein, P < 0.05). HBOT had no effect on IL-1ß content, which was 671 ± 85 pg/mg protein on day 4 and 672 ± 75 pg/mg protein on day 7 in HBO rats (P =not significant versus non-HBO rats). CONCLUSION: These data show that HBOT alleviates CCI-induced neuropathic pain and inhibits endoneuronal TNF-α production, but not IL-1ß in CCI-induced neuropathic pain. Reduced TNF-α production may, at least in part, contribute to the beneficial effect of HBOT.

Focal Neurologic Deficit After Epidural Catheter Removal Leads to Meningioma Diagnosis.

We present an unusual case of a 60-year-old female who developed subtle, new-onset left upper and lower extremity weakness on day five of perioperative thoracic epidural placement. The onset of a focal neurological deficit after epidural placement usually raises suspicion for the presence of an epidural hematoma, abscess, or traumatic cord lesion. However, in this patient, brain imaging revealed a large, previously undiagnosed intracranial mass. Classically, the risk of mass-related intracranial pressure shifts leading to neurological changes is associated with spinal techniques, including diagnostic lumbar puncture, combined spinal-epidural catheter analgesia, and unintended dural puncture during epidural placement. However, based on this case and our summary of case reports in the literature, we determined that symptom onset associated with an intracranial mass may also arise after apparently uncomplicated epidural placement. Symptom onset in our case series ranged from six hours to ten days and was highly variable depending on tumor location, with reported signs and symptoms including headache, vision changes, focal deficits, or alterations of consciousness. Further studies are required to establish definitive causation between the epidural technique and changes in cerebrospinal fluid pressures leading to symptom onset. Though rare, this is a time-sensitive diagnosis that must be considered for any patient with unexplained neurological findings after neuraxial anesthesia.

The Effect of a 2-Week Pre-clerkship Residency Exploration Program on Specialty Interest and Understanding of Physical Medicine and Rehabilitation.

OBJECTIVE: To assess the effect the Pre-clerkship Residency Exploration Program (PREP) had on student career interest and improving understanding of physical medicine and rehabilitation (PMR). DESIGN: During a 2-week program, students were exposed to a PMR elective, workshop, career presentation, and panel discussion with PMR residents. Interest and understanding were assessed using pre- and postprogram questionnaires. SETTING: PREP was held at a Canadian medical school during the summer between the second and third years of undergraduate medical training. PARTICIPANTS: Second-year medical student participants (N=40) (26 women and 14 men, aged 20 to >30 y) were randomly selected from 74 applicants at a Canadian medical school. INTERVENTIONS: Of the 40 program participants, 20 participated in a PMR elective and specialty-specific workshop. The full cohort of 40 participants participated in the PMR career presentation and PMR resident panel discussion. MAIN OUTCOME MEASURE: Primary outcome measure was an increase in understanding of the PMR specialty. RESULTS: Understanding of the roles and responsibilities of physiatrists increased significantly, with larger trends in those with greater exposure time. After PREP, comfort level in common PMR procedures also significantly increased. Higher exposure time was correlated with an increased top 3 career selection. Student interest in PMR did not significantly change after the program. CONCLUSION: Although no statistically significant effects were found from the 2-week PREP in this population in terms of career choice, benefits were found in the participants comfort with PMR procedures and understanding the roles and responsibilities of physiatrists. A brief exposure as part of a 2-week summer elective is beneficial for career decision planning and may be feasible to implement in medical curricula.

Methyl methacrylate permeability of dental and industrial gloves.

Our study was undertaken to measure the amount and time it took for methyl methacrylate monomer (MMA) to permeate latex, vinyl and industrial neoprene gloves and to compare the results to obtain a rating of the permeability of each of the gloves studied to MMA. The monomer, permeated under static conditions, was measured using a spectrophotometer. Latex and vinyl clinical gloves became permeable to MMA in a very short amount of time. Neoprene industrial gloves remained impervious for 25 minutes. Dentists and dental technicians should be aware of the toxic effects of MMA and understand that clinical gloves do not afford protection from MMA.

12 Tips for taking a Student Led Medical Education Program from Concept to Curriculum.

This article was migrated. The article was marked as recommended. The choice of a future career specialty has always been a stressful decision for medical students. To mitigate this stress and assist students in making more informed career decisions we developed the Pre-clerkship Residency Exploration Program (PREP), a two-week summer elective program that provides students with the opportunity to gain exposure to specialities that traditionally do not receive a lot of attention in medical school. To initiate this student led program we faced many obstacles, suffered many failures, learned a tremendous amount and eventually found success. In this article, we offer 12 tips on how to create a medical education program that is sustainable, effective and receives strong buy-in from faculty and administration. Our tips come from the perspective of students starting their own program but are translatable to anyone interested in taking an innovative idea and seeing it through to fruition.

Esophageal Diameters in Children Correlated to Body Weight.

INTRODUCTION: The development of stenoses after correction of an esophageal atresia or acid and lye burn of the esophagus are well-known problems in pediatric surgery. Currently, stenoses are treated in the majority of cases by repeated balloon dilatations. The diameter of the balloons used is not standardized; standard curves do not exist. The aim of this study was to evaluate the diameter of the esophagus correlated to the body weight of the children as measured in upper gastrointestinal (GI) studies to answer the important question to what extent a stenosis should be dilated. MATERIALS AND METHODS: Within the time period from 2011 through 2016, 60 patients with upper GI studies were selected. Evaluations were blinded to two different examiners. The diameters were measured under maximum contrast filling between the second and third rib (cranial point of measurement) and between the seventh and eighth rib (caudal point of measurement). For both, the anteroposterior and lateral aspect was examined. The diameter was calculated as the arithmetic average of both measurements within one level. The diameters were correlated to the weight of the children. RESULTS: All children (n = 38) within the 3rd to 97th weight percentile were analyzed. Linear correlation and coefficients of 0.67 at the cranial point and 0.70 at the caudal point were found. Mean diameter at the cranial point of measurement was 6.75 mm at the lowest weight (2.6 kg) and 14 mm at 74 kg. Mean weight of these children (standard deviation [SD]) was 25.3 (18.8) kg and median age was 7 years. Within weight groups (0-10 kg; 10-20 kg; 20-35 kg; 35-50 kg; >50 kg), we calculated SD and two side tested critical 95% confidence interval for all measurements (n = 74). CONCLUSION: Although the variation in measurements is considerable, this evaluation gives a reliable hint to which extent esophageal stenoses should be dilated in relation to the body weight. To the best of our knowledge, this is the first investigation to evaluate the diameter of the esophagus in children in relation to the body weight.

Experimental subarachnoid hemorrhage in the rat: influences of nimodipine.

BACKGROUND: Traumatic subarachnoid hemorrhage is a common finding following traumatic brain injury. Clinical studies revealed a positive influence of Nimodipine. However, till now no experimental studies have been performed. The aim of the present study was to determine the influence of early Nimodipine administration on outcome and histological findings in the rat: METHODS: Diffuse brain injury was produced in Sprague-Dawley rats using a brass weight falling from a predetermined height. Traumatic subarachnoidal hemorrhage was produced by administration of heparin before the injury. A total number of 52 animals were divided in 4 groups. FINDINGS: Mortality increased following administration of heparin. Mortality was not reduced following administration of Nimodipine. The histological investigation revealed less cell loss in animals with administration of Nimodipine as well as increased GFAP immunoexpression. CONCLUSIONS: Administration of Heparin results in a marked traumatic subrachnoidal hemorrhage following diffuse traumatic brain injury. Administration of Nimodipine does not reduce overall mortality. However, histological investigations indicate a positive effect of Nimodipine on cell loss.