Robust and scalable single-molecule protein sequencing with fluorosequencing.

The need to accurately survey proteins and their modifications with ever higher sensitivities, particularly in clinical settings with limited samples, is spurring development of new single molecule proteomics technologies. Fluorosequencing is one such highly parallelized single molecule peptide sequencing platform, based on determining the sequence positions of select amino acid types within peptides to enable their identification and quantification from a reference database. Here, we describe substantial improvements to fluorosequencing, including identifying fluorophores compatible with the sequencing chemistry, mitigating dye-dye interactions through the use of extended polyproline linkers, and developing an end-to-end workflow for sample preparation and sequencing. We demonstrate by fluorosequencing peptides in mixtures and identifying a target neoantigen from a database of decoy MHC peptides, highlighting the potential of the technology for high sensitivity clinical applications.

Local Sn Dipolar-Character Displacements behind the Low Thermal Conductivity in SnSe Thermoelectric.

The local atomic structure of SnSe was characterized across its orthorhombic-to-orthorhombic structural phase transition using x-ray pair distribution function analysis. Substantial Sn displacements with a dipolar character persist in the high-symmetry high-temperature phase, albeit with a symmetry different from that of the ordered displacements below the transition. The analysis implies that the transition is neither order-disorder nor displacive but rather a complex crossover. Robust ferrocoupled SnSe intralayer distortions suggest a ferroelectriclike instability as the driving force. These local symmetry-lowering Sn displacements are likely integral to the ultralow lattice thermal conductivity mechanism in SnSe.

Estimating error rates for single molecule protein sequencing experiments.

The practical application of new single molecule protein sequencing (SMPS) technologies requires accurate estimates of their associated sequencing error rates. Here, we describe the development and application of two distinct parameter estimation methods for analyzing SMPS reads produced by fluorosequencing. A Hidden Markov Model (HMM) based approach, extends whatprot, where we previously used HMMs for SMPS peptide-read matching. This extension offers a principled approach for estimating key parameters for fluorosequencing experiments, including missed amino acid cleavages, dye loss, and peptide detachment. Specifically, we adapted the Baum-Welch algorithm, a standard technique to estimate transition probabilities for an HMM using expectation maximization, but modified here to estimate a small number of parameter values directly rather than estimating every transition probability independently, which should help prevent overfitting. We demonstrate a high degree of accuracy on simulated data, but on experimental datasets, we observed that the model needed to be augmented with an additional error type, N-terminal blocking. This, in combination with data pre-processing, results in reasonable parameterizations of experimental datasets that agree with controlled experimental perturbations. A second independent implementation using a hybrid of DIRECT and Powell's method to reduce the root mean squared error (RMSE) between simulations and the real dataset was also developed. We compare these methods on both simulated and real data, finding that our Baum-Welch based approach outperforms DIRECT and Powell's method by most, but not all, criteria. Although some discrepancies between the results exist, we also find that both approaches provide similar error rate estimates from experimental single molecule fluorosequencing datasets.

Physiological tremor is suppressed and force steadiness is enhanced with increased availability of serotonin regardless of muscle fatigue.

Although there is evidence that 5-HT acts as an excitatory neuromodulator to enhance maximal force generation, it is largely unknown how 5-HT activity influences the ability to sustain a constant force during steady-state contractions. A total of 22 healthy individuals participated in the study, where elbow flexion force was assessed during brief isometric contractions at 10% maximal voluntary contraction (MVC), 60% MVC, MVC, and during a sustained MVC. The selective serotonin reuptake inhibitor, paroxetine, suppressed physiological tremor and increased force steadiness when performing the isometric contractions. In particular, a main effect of drug was detected for peak power of force within the 8-12 Hz range (P = 0.004) and the coefficient of variation (CV) of force (P < 0.001). A second experiment was performed where intermittent isometric elbow flexions (20% MVC sustained for 2 min) were repeatedly performed so that serotonergic effects on physiological tremor and force steadiness could be assessed during the development of fatigue. Main effects of drug were once again detected for peak power of force in the 8-12 Hz range (P = 0.002) and CV of force (P = 0.003), where paroxetine suppressed physiological tremor and increased force steadiness when the elbow flexors were fatigued. The findings of this study suggest that enhanced availability of 5-HT in humans has a profound influence of maintaining constant force during steady-state contractions. The action of 5-HT appears to suppress fluctuations in force regardless of the fatigue state of the muscle.NEW & NOTEWORTHY Converging lines of research indicate that enhanced serotonin availability increases maximal force generation. However, it is largely unknown how serotonin influences the ability to sustain a constant force. We performed two experiments to assess physiological tremor and force steadiness in unfatigued and fatigued muscle when serotonin availability was enhanced in the central nervous system. Enhanced availability of serotonin reduced physiological tremor amplitude and improved steadiness regardless of muscle fatigue.

Kinetic and Computational Analysis of CO Substitution in a Dinuclear Osmium Carbonyl Complex: Intersection between Dissociative and Dissociative-Interchange Mechanisms.

The mechanism for the CO substitution reaction involving the diosmium carbonyl sawhorse complex Os2(µ-O2CH)2(CO)6, which contains an Os-Os single bond, two axial CO ligands, and four equatorial CO ligands, was investigated experimentally and theoretically. Kinetic measurements show 13CO axial substitution proceeding by a dissociative reaction that is first-order in the complex and zero-order in 13CO but with an unexpectedly negative entropy of activation. The corresponding electronic structure calculations yield an enthalpy of activation for axial CO dissociation that is much larger than that determined by the kinetic experiments, but in agreement with the complex's stability with respect to CO loss. Additional calculations yield a dissociative interchange transition state whose free energy, enthalpy, and entropy of activation are in good agreement with those obtained from the kinetic measurements for the apparently dissociative substitution. These results point to an exchange reaction mechanism that is surprisingly close to the poorly understood transition from a dissociative mechanism with a CO-loss intermediate to a dissociative interchange mechanism with a transition state involving both the entering and the leaving COs. The key to explain these findings is provided by the vibrational analysis, which shows very low energy wagging motions for the axial COs. Thus, the incoming CO only displaces the outgoing CO when the complex has an outgoing CO near the wag's turning point. This dissociative interchange mechanism predicted by the calculation explains the unexpected combination of kinetics and stability characteristics. Kinetics reveals that the reaction is first-order in the Os dimer with a negative Eyring entropy, while a stability study shows that the Os dimer's decomposition rate is several orders of magnitude slower than CO exchange.

James Sydney Jackson (1944-2020).

James Sydney Jackson (1944-2020). Jackson had a profound, wholly unique, and enduring impact on the discipline of psychology and a host of other affiliated fields of study. His insistence on seeing Black populations and other peoples of color in full- appreciating their complexities, variabilities, and contrasts- fundamentally altered our approach to the study of race/ethnicity within these scholarly frames. In the Fall of 1971, Jackson assumed his first (and only) academic post in the University of Michigan's Department of Psychology. Jackson held a number of key positions over the years, and served as the 7th director of Michigan's famed Institute for Social Research (ISR) from 2005-2015. In 2014, he was appointed by President Barack Obama to the National Science Board. Jackson was also elected to the National Academy of Medicine, the National Academy of Science, and the American Academy of Arts and Sciences. Jackson's most pivotal contribution to psychology, social science, public health, and other related fields was the legion of impactful scholars he mentored, nurtured, and encouraged throughout his and their academic careers. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

Germline ATM variants predispose to melanoma: a joint analysis across the GenoMEL and MelaNostrum consortia.

PURPOSE: Ataxia-Telangiectasia Mutated (ATM) has been implicated in the risk of several cancers, but establishing a causal relationship is often challenging. Although ATM single-nucleotide polymorphisms have been linked to melanoma, few functional alleles have been identified. Therefore, ATM impact on melanoma predisposition is unclear. METHODS: From 22 American, Australian, and European sites, we collected 2,104 familial, multiple primary (MPM), and sporadic melanoma cases who underwent ATM genotyping via panel, exome, or genome sequencing, and compared the allele frequency (AF) of selected ATM variants classified as loss-of-function (LOF) and variants of uncertain significance (VUS) between this cohort and the gnomAD non-Finnish European (NFE) data set. RESULTS: LOF variants were more represented in our study cohort than in gnomAD NFE, both in all (AF = 0.005 and 0.002, OR = 2.6, 95% CI = 1.56-4.11, p < 0.01), and familial + MPM cases (AF = 0.0054 and 0.002, OR = 2.97, p < 0.01). Similarly, VUS were enriched in all (AF = 0.046 and 0.033, OR = 1.41, 95% CI = 1.6-5.09, p < 0.01) and familial + MPM cases (AF = 0.053 and 0.033, OR = 1.63, p < 0.01). In a case-control comparison of two centers that provided 1,446 controls, LOF and VUS were enriched in familial + MPM cases (p = 0.027, p = 0.018). CONCLUSION: This study, describing the largest multicenter melanoma cohort investigated for ATM germline variants, supports the role of ATM as a melanoma predisposition gene, with LOF variants suggesting a moderate-risk.

Dual Orbital Degeneracy Lifting in a Strongly Correlated Electron System.

The local structure of NaTiSi_{2}O_{6} is examined across its Ti-dimerization orbital-assisted Peierls transition at 210 K. An atomic pair distribution function approach evidences local symmetry breaking preexisting far above the transition. The analysis unravels that, on warming, the dimers evolve into a short range orbital degeneracy lifted (ODL) state of dual orbital character, persisting up to at least 490 K. The ODL state is correlated over the length scale spanning ∼6 sites of the Ti zigzag chains. Results imply that the ODL phenomenology extends to strongly correlated electron systems.

The upgraded Polaris powder diffractometer at the ISIS neutron source.

This paper describes the design and operation of the Polaris time-of-flight powder neutron diffractometer at the ISIS pulsed spallation neutron source, Rutherford Appleton Laboratory, UK. Following a major upgrade to the diffractometer in 2010-2011, its detector provision now comprises five large ZnS scintillator-based banks, covering an angular range of 6° ≤ 2θ ≤ 168°, with only minimal gaps between each bank. These detectors have a substantially increased solid angle coverage (Ω âˆ¼ 5.67 sr) compared to the previous instrument (Ω âˆ¼ 0.82 sr), resulting in increases in count rate of between 2× and 10×, depending on 2θ angle. The benefits arising from the high count rates achieved are illustrated using selected examples of experiments studying small sample volumes and performing rapid, time-resolved investigations. In addition, the enhanced capabilities of the diffractometer in the areas of in situ studies (which are facilitated by the installation of a novel design of radial collimator around the sample position and by a complementary programme of advanced sample environment developments) and in total scattering studies (to probe the nature of short-range atomic correlations within disordered crystalline solids) are demonstrated.

Multifaceted Approach to Enhance Pill-Swallowing Ability in Children and Adults With Barth Syndrome.

IMPORTANCE: People with Barth syndrome (BTHS) present with sensory and motor deficits that affect their ability to swallow medications in solid form. Inability to swallow pills can reduce opportunities for people with BTHS to participate in clinical trial research. OBJECTIVE: To evaluate the effectiveness of a brief, multifaceted pill-swallowing program that used evidence-based training methods. DESIGN: Pretest-posttest with 6-mo follow-up. SETTING: Community setting. PARTICIPANTS: A convenience sample of children, adolescents, and adults with a genetically confirmed diagnosis of BTHS. INTERVENTION: Possible intervention strategies included behavioral approaches (e.g., shaping), adaptive approaches, and positioning approaches. Interventions were tailored to each participant's needs and were carried out by occupational therapy practitioners with advanced training in feeding and eating. OUTCOMES AND MEASURES: Pill-swallowing milestones were ranked on a scale ranging from 0 to 12; participants were scored pretraining, immediately posttraining, and at 6-mo posttraining. RESULTS: Sixteen participants with BTHS, ages 6-34 yr, participated in the training. Fourteen of the 16 participants demonstrated improvement in their pill-swallowing ability. Overall, there was a statistically significant change in pill-swallowing ability from pretraining to posttraining, and these changes were maintained after 6 mo. CONCLUSION: and Relevance: This study suggests that a brief multifaceted training approach, led by trained professionals, may be effective for helping people with sensory and motor deficits learn to swallow pills independently. WHAT THIS ARTICLE ADDS: Very little has been published in the occupational therapy literature describing how to teach the skill of pill swallowing to clients or how to measure progress toward this goal. This study tested the outcomes of a multifaceted approach to pill swallowing that can be conducted by occupational therapy practitioners; a novel measurement approach is also introduced that can be used with clients in clinical practice.

A Fatal Case of Louping-ill in a Dog: Immunolocalization and Full Genome Sequencing of the Virus.

Louping-ill (LI), caused by louping-ill virus (LIV), results in a frequently fatal encephalitis primarily affecting sheep and red grouse (Lagopus lagopus scotica), but it does occur in other species. An adult male Border collie dog was definitively diagnosed with fatal LI and the lesion profile, LIV antigen distribution and full genome sequence of the LIV responsible were investigated to determine if this differed significantly from sheep-derived LIV. No gross lesions were present. The histological lesions were confined to the central nervous system and comprised of lymphocytic perivascular cuffs, glial foci, neuronal necrosis and neuronophagia. Immunolocalization of viral antigen showed small amounts present in neurons only. These histological and immunohistochemical findings were similar to those reported in affected sheep. Compared with published full genome sequences of sheep-derived LIV, only very minor differences were present and phylogenetically the virus clustered individually between a subclade containing Scottish strains, LIV 369/T2 and G and another subclade containing an English isolate LIV A. The LIV isolated from the dog shares a common progenitor with LIV A. These findings suggest there is no canine-specific LIV strain, dogs are susceptible to sheep-associated strains of LI and with the increase in tick prevalence, and therefore exposure to LIV, a safe, effective vaccine for dogs may be required.

A suite-level review of the neutron powder diffraction instruments at Oak Ridge National Laboratory.

The suite of neutron powder diffractometers at Oak Ridge National Laboratory (ORNL) utilizes the distinct characteristics of the Spallation Neutron Source and High Flux Isotope Reactor to enable the measurements of powder samples over an unparalleled regime at a single laboratory. Full refinements over large Q ranges, total scattering methods, fast measurements under changing conditions, and a wide array of sample environments are available. This article provides a brief overview of each powder instrument at ORNL and details the complementarity across the suite. Future directions for the powder suite, including upgrades and new instruments, are also discussed.

Coupling of emergent octahedral rotations to polarization in (K,Na)NbO3 ferroelectrics.

Perovskite potassium sodium niobates, K1-xNaxNbO3, are promising lead-free piezoelectrics. Their dielectric and piezoelectric characteristics peak near x = 0.5, but the reasons for such property enhancement remain unclear. We addressed this uncertainty by analyzing changes in the local and average structures across the x = 0.5 composition, which have been determined using simultaneous Reverse Monte Carlo fitting of neutron and X-ray total-scattering data, potassium EXAFS, and diffuse-scattering patterns in electron diffraction. Within the A-sites, Na cations are found to be strongly off-centered along the polar axis as a result of oversized cube-octahedral cages determined by the larger K ions. These Na displacements promote off-centering of the neighboring Nb ions, so that the Curie temperature and spontaneous polarization remain largely unchanged with increasing x, despite the shrinking octahedral volumes. The enhancement of the properties near x = 0.5 is attributed to an abrupt increase in the magnitude and probability of the short-range ordered octahedral rotations, which resembles the pre-transition behavior. These rotations reduce the bond tension around Na and effectively soften the short Na-O bond along the polar axis - an effect that is proposed to facilitate reorientation of the polarization as external electric field is applied.

Mapping Free-Carriers in Multijunction Silicon Nanowires Using Infrared Near-Field Optical Microscopy.

We report the use of infrared (IR) scattering-type scanning near-field optical microscopy (s-SNOM) as a nondestructive method to map free-carriers in axially modulation-doped silicon nanowires (SiNWs) with nanoscale spatial resolution. Using this technique, we can detect local changes in the electrically active doping concentration based on the infrared free-carrier response in SiNWs grown using the vapor-liquid-solid (VLS) method. We demonstrate that IR s-SNOM is sensitive to both p-type and n-type free-carriers for carrier densities above ∼1 × 1019 cm-3. We also resolve subtle changes in local conductivity properties, which can be correlated with growth conditions and surface effects. The use of s-SNOM is especially valuable in low mobility materials such as boron-doped p-type SiNWs, where optimization of growth has been difficult to achieve due to the lack of information on dopant distribution and junction properties. s-SNOM can be widely employed for the nondestructive characterization of nanostructured material synthesis and local electronic properties without the need for contacts or inert atmosphere.

Kinematic effects of inertia and friction added by a robotic knee exoskeleton after prolonged walking.

The capabilities of robotic gait assistive devices are ever increasing; however, their adoption outside of the lab is still limited. A critical barrier for the functionality of these devices are the still unknown mechanical properties of the human leg during dynamic conditions such as walking. We built a robotic knee exoskeleton to address this problem. Here, we present the effects of our device on the walking pattern of four subjects. We assessed the effects after a short period of acclimation as well as after a 1.5h walking protocol. We found that the knee exoskeleton decreased (towards extension) the peak hip extension and peak knee flexion of the leg with the exoskeleton, while minimally affecting the non-exoskeleton leg. Comparatively smaller changes occurred after prolonged walking. These results suggest that walking patterns attained after a few minutes of acclimation with a knee exoskeleton are stable for at least a couple of hours.

TET2 binds the androgen receptor and loss is associated with prostate cancer.

Genetic alterations associated with prostate cancer (PCa) may be identified by sequencing metastatic tumour genomes to identify molecular markers at this lethal stage of disease. Previously, we characterized somatic alterations in metastatic tumours in the methylcytosine dioxygenase ten-eleven translocation 2 (TET2), which is altered in 5-15% of myeloid, kidney, colon and PCas. Genome-wide association studies previously identified non-coding risk variants associated with PCa and melanoma. We perform fine-mapping of PCa risk across TET2 using genotypes from the PEGASUS case-control cohort and identify six new risk variants in introns 1 and 2. Oligonucleotides containing two risk variants are bound by the transcription factor octamer-binding protein 1 (Oct1/POU2F1) and TET2 and Oct1 expression are positively correlated in prostate tumours. TET2 is expressed in normal prostate tissue and reduced in a subset of tumours from the Cancer Genome Atlas (TCGA). Small interfering RNA-mediated TET2 knockdown (KD) increases LNCaP cell proliferation, migration and wound healing, verifying loss drives a cancer phenotype. Endogenous TET2 bound the androgen receptor (AR) and AR-coactivator proteins in LNCaP cell extracts, and TET2 KD increases prostate-specific antigen (KLK3/PSA) expression. Published data reveal TET2 binding sites and hydroxymethylcytosine proximal to KLK3. A gene co-expression network identified using TCGA prostate tumour RNA-sequencing identifies co-regulated cancer genes associated with 2-oxoglutarate (2-OG) and succinate metabolism, including TET2, lysine demethylase (KDM) KDM6A, BRCA1-associated BAP1, and citric acid cycle enzymes IDH1/2, SDHA/B, and FH. The co-expression signature is conserved across 31 TCGA cancers suggesting a putative role for TET2 as an energy sensor (of 2-OG) that modifies aspects of androgen-AR signalling. Decreased TET2 mRNA expression in TCGA PCa tumours is strongly associated with reduced patient survival, indicating reduced expression in tumours may be an informative biomarker of disease progression and perhaps metastatic disease.

Impostor syndrome and burnout among American medical students: a pilot study.

Objectives: To describe levels of burnout and impostor syndrome (IS) in medical students, and to recognize demographic differences in those experiencing burnout and IS. Methods: Anonymous survey administered online in 2014 that included demographic data, the Maslach Burnout Inventory and an IS screening questionnaire. Main outcome measures were level of burnout, and presence or absence of imposter syndrome. The presence of IS and burnout components were analyzed across age, gender, race, year of training, intention to pursue fellowship training, and greater than one year of work experience outside of medicine using chi-squared tests. The association between burnout and IS was also compared using chi-squared tests. Results: One hundred and thirty-eight students completed the questionnaire. Female gender was significantly associated with IS (χ2(3)=10.6, p=0.004) with more than double the percentage of females displaying IS than their male counterparts (49.4% of females versus 23.7% of males). IS was significantly associated with the burnout components of exhaustion (χ2 (2)=5.9, p=0.045), cynicism (χ2(2)=9.4, p=0.004), emotional exhaustion (χ2(2)=8.0, p=0.018), and depersonalization (χ2 (2)=10.3, p=0.006). The fourth year of medical school was significantly associated with IS (χ2(3)=10.5, p=0.015). Conclusions: Almost a quarter of male medical students and nearly half of female students experience IS and IS was found to be significantly associated with burnout indices. Given the high psychological morbidity of these conditions, this association cannot be ignored. It behooves us to reconsider facets of medical education (i.e. shame-based learning and overall teaching style) and optimize the medical learning environment.

Revisiting the cost of carnivory in mammals.

Predator-prey relationships play a key role in the evolution and ecology of carnivores. An understanding of predator-prey relationships and how this differs across species and environments provides information on how carnivorous strategies have evolved and how they may change in response to environmental change. We aim to determine how mammals overcame the challenges of living within the marine environment; specifically, how this altered predator-prey body mass relationships relative to terrestrial mammals. Using predator and prey mass data collected from the literature, we applied phylogenetic piecewise regressions to investigate the relationship between predator and prey size across carnivorous mammals (51 terrestrial and 56 marine mammals). We demonstrate that carnivorous mammals have four broad dietary groups: small marine carnivores (< 11 000 kg) and small terrestrial carnivores (< 11 kg) feed on prey less than 5 kg and 2 kg, respectively. On average, large marine carnivores (> 11 000 kg) feed on prey equal to 0.01% of the carnivore's body size, compared to 45% or greater in large terrestrial carnivores (> 11 kg). We propose that differences in prey availability, and the relative ease of processing large prey in the terrestrial environment and small prey in marine environment, have led to the evolution of these novel foraging behaviours. Our results provide important insights into the selection pressures that may have been faced by early marine mammals and ultimately led to the evolution of a range of feeding strategies and predatory behaviours.

ASPP2 deficiency causes features of 1q41q42 microdeletion syndrome.

Chromosomal abnormalities are implicated in a substantial number of human developmental syndromes, but for many such disorders little is known about the causative genes. The recently described 1q41q42 microdeletion syndrome is characterized by characteristic dysmorphic features, intellectual disability and brain morphological abnormalities, but the precise genetic basis for these abnormalities remains unknown. Here, our detailed analysis of the genetic abnormalities of 1q41q42 microdeletion cases identified TP53BP2, which encodes apoptosis-stimulating protein of p53 2 (ASPP2), as a candidate gene for brain abnormalities. Consistent with this, Trp53bp2-deficient mice show dilation of lateral ventricles resembling the phenotype of 1q41q42 microdeletion patients. Trp53bp2 deficiency causes 100% neonatal lethality in the C57BL/6 background associated with a high incidence of neural tube defects and a range of developmental abnormalities such as congenital heart defects, coloboma, microphthalmia, urogenital and craniofacial abnormalities. Interestingly, abnormalities show a high degree of overlap with 1q41q42 microdeletion-associated abnormalities. These findings identify TP53BP2 as a strong candidate causative gene for central nervous system (CNS) defects in 1q41q42 microdeletion syndrome, and open new avenues for investigation of the mechanisms underlying CNS abnormalities.