Parallel Measurements Research Articles

Understanding the P-cluster of Vanadium Nitrogenase: an EPR and XAS study of the holo vs. apo forms of the enzyme.

The catalytic moiety of nitrogenases contains two complex metalloclusters: the M-cluster (also called cofactor), where the catalytic reduction of substrates takes place, and the [Fe8S7] P-cluster responsible for electron transfer. Due to discrepancies between crystallography and EPR spectroscopy, the exact structure of the P-cluster in the VFe protein remains a topic of debate. Herein, we use an apo-form of VFe (which retains the P-cluster but lacks the FeVco) to study the VFe P-cluster. SDS-PAGE and NativePAGE showed a heterogeneous composition of the VFe and the apo-VFe samples with presence of α1β2δ2 and α1β2 complexes. The parallel mode EPR measurements of IDS oxidized MoFe, apo-MoFe, and VFe samples reveal a signal at g = 12 associated with the two-electron oxidized state of the P-cluster (P2+) for all three samples, albeit with different intensities. In contrast, no P2+ was observed for IDS oxidized apo-VFe. Additionally, comparisons between apo-MoFe, apo-VFe and the model complex (NBu4)2[Fe4S4(SPh)4] via XAS and EXAFS measurements showed that apo-VFe does not contain a fully formed [Fe8S7] P-cluster, but rather is comprised of fragmented iron-sulfur clusters. Our results point to a possible variation on the structure of the P-cluster in the different forms of the nitrogenase.

Tomography of a Spatially Resolved Single-Atom Detector in the Presence of Shot-to-Shot Number Fluctuations

The tomography of single-particle-resolved detectors is of primary importance for characterizing particle correlations, with applications in quantum metrology, quantum simulation, and quantum computing. However, it is a nontrivial task in practice due to the uncertainties on the statistics of the state impinging on the detector and to the unavoidable presence of noise that affects the measurement but does not originate from the detector. In this work, we address this problem for a three-dimensional single-atom-resolved detector where shot-to-shot atom-number fluctuations are a central issue in performing a quantum detector tomography. We overcome this difficulty by exploiting the parallel measurement of the counting statistics in subvolumes of the detector, from which we evaluate the effect of shot-to-shot fluctuations and perform a local tomography of the detector. In addition, we illustrate the validity of our method from applying it to Gaussian quantum states with different number statistics. Finally, we show that the response of microchannel plate detectors is well described by using a binomial distribution with the detection efficiency as a single parameter. Published by the American Physical Society 2024

Low-overhead quantum computing with the color code

Fault-tolerant quantum computation demands significant resources: large numbers of physical qubits must be checked for errors repeatedly to protect quantum data as logic gates are implemented in the presence of noise. We demonstrate that an approach based on the color code can lead to considerable reductions in the resource overheads compared with conventional methods, while remaining compatible with a two-dimensional layout. We propose a lattice surgery scheme that exploits the rich structure of the color-code phase to perform arbitrary pairs of commuting logical Pauli measurements in parallel while keeping the space cost low. Compared to lattice surgery schemes based on the surface code with the same code distance, and assuming the same amount of time is needed to complete a round of syndrome measurements, our approach yields about a 3× improvement in the space-time overhead, obtained from a combination of a 1.5× improvement in spatial overhead together with a 2× speedup due to the parallelization of commuting logical measurements. Even when taking into account the color code's lower error threshold using current decoders, the overhead is reduced by 10% at a physical error rate of 10−3 and by 50% at 10−4. Published by the American Physical Society 2024

Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning.

mRNA degradation is a central process that affects all gene expression levels, though it remains challenging to predict the stability of a mRNA from its sequence, due to the many coupled interactions that control degradation rate. Here, we carried out massively parallel kinetic decay measurements on over 50,000 bacterial mRNAs, using a learn-by-design approach to develop and validate a predictive sequence-to-function model of mRNA stability. mRNAs were designed to systematically vary translation rates, secondary structures, sequence compositions, G-quadruplexes, i-motifs, and RppH activity, resulting in mRNA half-lives from about 20 seconds to 20 minutes. We combined biophysical models and machine learning to develop steady-state and kinetic decay models of mRNA stability with high accuracy and generalizability, utilizing transcription rate models to identify mRNA isoforms and translation rate models to calculate ribosome protection. Overall, the developed model quantifies the key interactions that collectively control mRNA stability in bacterial operons and predicts how changing mRNA sequence alters mRNA stability, which is important when studying and engineering bacterial genetic systems.

Laser ablation inductively coupled plasma mass spectrometry measurements for high-resolution chemical ice core analyses with a first application to an ice core from Skytrain Ice Rise (Antarctica)

Abstract. Conventional methods of inorganic impurity analysis do not provide high enough depth resolution for many scientific questions in ice core science. In this study, we present a setup of laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) for high-resolution glacier ice impurity analysis to the sub-millimetre scale. This setup enables ice core chemical impurity analysis to a depth resolution of ∼182 µm while consuming only very small amounts of ice. The system performs simultaneous analysis of sodium, magnesium and aluminium incorporated in the ice matrix. In this case study within the framework of the WACSWAIN (WArm Climate Stability of the West Antarctic Ice Sheet in the last INterglacial) project, our method is applied to a selection of samples from the Skytrain ice core (West Antarctica) over a total length of 6.7 m consisting of about 130 single samples. The main goal of this study is to use the new LA-ICP-MS method to extract meaningful climate signals on a depth resolution level beyond the limits of continuous-flow analysis (CFA). A comparison between low-resolution CFA data and the high-resolution LA-ICP-MS data reveals generally good agreement on the decimetre scale. Stacking of parallel laser measurements together with frequency analysis is used to analyse the high-resolution LA-ICP-MS data at millimetre resolution. Spectral analysis reveals that despite effects of impurity accumulation along ice crystal grain boundaries, periodic concentration changes in the Skytrain ice core on the millimetre scale can be identified in ice from 26.8 ka (kiloyears before present, i.e. 1950 CE). These findings open new possibilities for climate data interpretation with respect to fast changes in the last glacial period and beyond, for example within the Beyond EPICA oldest-ice project.

Should We Use Clinician Self-Report to Tailor Implementation Strategies? Predicting Use of Youth CBT with Clinician Self-Report Versus Direct Observation.

Developing tailored implementation strategies to increase the use of evidence-based practice (EBP) requires accurate identification of predictors of their use. However, known difficulties with measuring EBP use complicates interpretation of the extant literature. In this proof-of-concept study, we examined whether the same predictors of use of cognitive behavioral therapy (CBT) are identified when CBT use is measured with clinician self-report compared to direct observation. We examined four candidate predictors of CBT use - clinician participation in an EBP training initiative, years of experience, caseload, and employment status - in a sample of 36 clinicians (64% female; 72% White and 28% Black) from 19 community mental health agencies treating youth in greater Philadelphia. CBT use was captured for 100 unique client sessions (M = 2.8 recorded sessions per clinician) through both clinician self-report and direct observation, using parallel measures. We used three-level (client, clinician, and agency) regression models with random intercepts to estimate the relationship between each predictor variable and CBT use in both measures and compared the magnitude and direction of each model across self-report and direct observation using z-tests. There was no alignment for any of the four candidate predictors between predictive relationships identified by self-report compared to those identified by direct observation. The findings in this study extend literature documenting limitations of using clinician self-report to capture clinician behavior and suggest that even the characteristics that predict higher self-reported CBT use do not align with (and often are discordant with) those that predict directly observed CBT use. This raises questions about the utility of relying on self-reported use to inform implementation strategy design.

Online Optical Axis Parallelism Measurement Method for Continuous Zoom Camera Based on High-Precision Spot Center Positioning Algorithm

Ensuring precise alignment of the optical axis is critical for achieving high-quality imaging in continuous zoom cameras. However, existing methods for measuring optical axis parallelism often lack accuracy and fail to assess parallelism across the entire focal range. This study introduces an online measurement method designed to address these limitations by incorporating two enhancements. First, image processing methodologies enable sub-pixel-level extraction of the spot center, achieved through improved morphological processing and the incorporation of an edge tracing algorithm. Second, measurement software developed using Qt Creator can output real-time data on optical axis parallelism across the full focal range post-measurement. This software features a multi-threaded architecture that facilitates the concurrent execution of image acquisition, data processing, and serial communication. Experimental results derived from simulations and real data indicate that the maximum average error in extracting the center of the spot is 0.13 pixels. The proposed system provides critical data for optical axis calibration during camera adjustment and inspection.

Experimental Sample-Efficient Quantum State Tomography via Parallel Measurements.

Quantum state tomography (QST) via local measurements on reduced density matrices (LQST) is a promising approach but becomes impractical for large systems. To tackle this challenge, we developed an efficient quantum state tomography method inspired by quantum overlapping tomography [Phys. Rev. Lett. 124, 100401 (2020)PRLTAO0031-900710.1103/PhysRevLett.124.100401], which utilizes parallel measurements (PQST). In contrast to LQST, PQST significantly reduces the number of measurements and offers more robustness against shot noise. Experimentally, we demonstrate the feasibility of PQST in a treelike superconducting qubit chip by designing high-efficiency circuits, preparing W states, ground states of Hamiltonians, and random states, and then reconstructing these density matrices using full quantum state tomography (FQST), LQST, and PQST. Our results show that PQST reduces measurement cost, achieving fidelities of 98.68% and 95.07% after measuring 75 and 99 observables for six-qubit and nine-qubit W states, respectively. Furthermore, thereconstruction of the largest density matrix of the 12-qubit W state is achieved with the similarity of 89.23% after just measuring 243 parallel observables, while 3^{12}=531 441 complete observables are needed for FQST. Consequently, PQST will be a useful tool for future tasks such as the reconstruction, characterization, benchmarking, and properties learning of states.

Massively parallel binding assay (MPBA) reveals limited transcription factor binding cooperativity, challenging models of specificity.

DNA-binding domains (DBDs) within transcription factors (TFs) recognize short sequence motifs that are highly abundant in genomes. In vivo, TFs bind only a small subset of motif occurrences, which is often attributed to the cooperative binding of interacting TFs at proximal motifs. However, large-scale testing of this model is still lacking. Here, we describe a novel method allowing parallel measurement of TF binding to thousands of designed sequences within yeast cells and apply it to quantify the binding of dozens of TFs to libraries of regulatory regions containing clusters of binding motifs, systematically mutating all motif combinations. With few exceptions, TF occupancies were well explained by independent binding to individual motifs, with motif cooperation being of only limited effects. Our results challenge the general role of motif combinatorics in directing TF genomic binding and open new avenues for exploring the basis of protein-DNA interactions within cells.

A New Activity Assay Method for Diamine Oxidase Based on Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

Copper-containing diamine oxidases are ubiquitous enzymes that participate in many important biological processes. These processes include the regulation of cell growth and division, programmed cell death, and responses to environmental stressors. Natural substrates include, for example, putrescine, spermidine, and histamine. Enzymatic activity is typically assayed using spectrophotometric, electrochemical, or fluorometric methods. The aim of this study was to develop a method for measuring activity using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry based on the intensity ratio of product to product-plus-substrate signals in the reaction mixtures. For this purpose, an enzyme purified to homogeneity from pea (Pisum sativum) seedlings was used. The method employed α-cyano-4-hydroxycinnamic acid as a matrix with the addition of cetrimonium bromide. Product signal intensities with pure compounds were evaluated in the presence of equal substrate amounts to determine intensity correction factors for data processing calculations. The kinetic parameters kcat and Km for the oxidative deamination of selected substrates were determined. These results were compared to parallel measurements using an established spectrophotometric method, which involved a coupled reaction of horseradish peroxidase and guaiacol, and were discussed in the context of data from the literature and the BRENDA database. It was found that the method provides accurate results that are well comparable with parallel spectrophotometry. This method offers advantages such as low sample consumption, rapid serial measurements, and potential applicability in assays where colored substances interfere with spectrophotometry.

Effect of Difference in Serum Creatinine between Jaffe and Enzymatic Methods in Outpatient Kidney Transplant Recipients.

Background: Deviations in serum creatinine (SCr), due to its determination using a Jaffe or an enzymatic method, have an effect on kidney disease detection and staging. It is not yet clear how large this effect is in kidney transplant recipients (KTRs). SCr measurement differences are of particular importance here to evaluate the graft function. Methods: The results of all parallel SCr measurements (Jaffe and enzymatic method) of adult outpatient KTRs in the same serum sample at the University Hospital Essen (Germany) between January 2020 and October 2023 were evaluated. A Bland-Altman plot with 95% limits of agreement (LoA) was used to assess the difference between the Jaffe and the enzymatic SCr (eSCr). For all patients, we used the CKD-EPI 2009 and EKFC formula, and for patients ≥ 70 years, we also used the BIS1 formula for the determination of eGFR. Results: A total of 12,081 parallel SCr measurements from 1243 KTRs were analyzed, where 61% were male and the median age was 53 years. On average, Jaffe SCr was 0.03 mg/dL higher than eSCr (LoA -0.16; 0.21 mg/dL). On average, the eGFR determined by Jaffe SCr was 1.9 mL/min/1.73 m2 lower than the eGFR determined by eSCr (LoA -9.5; 5.7 mL/min/1.73 m2). The comparison of eGFR between the two SCr methods revealed a different CKD stage in 1589 (13%) of all analyzed measurements, most frequently between G2/G3a (41%) and G3a/G3b (24%). When using the EKFC and BIS1 formulas, there were approximately the same number of measurements leading to a different CKD stage. Conclusions: In more than every tenth SCr determination in outpatient KTRs, the difference between the Jaffe and enzymatic methods had an influence on the assignment to a CKD stage. This effect was comparably pronounced for all eGFR formulas applied.

Quantifying the role of iron recycling by Adélie and Emperor penguins over the austral spring and summer in Prydz Bay

In large areas of the Southern Ocean, iron limits phytoplankton production. Although biologically mediated iron recycling has been studied for the higher trophic-level whales and the lower trophic-level krill, less is known of the numerically abundant seabirds foraging in Antarctic waters. In this study, we estimate the magnitude of iron recycled by two Antarctic breeding seabirds, the Adélie and emperor penguins, across the austral spring and summer in the Prydz Bay region, East Antarctica. Their contribution to iron recycling and associated pathways differs in line with their contrasting life history strategies (summer and winter breeding) and their breeding habitat (land and fast ice). We consider their breeding cycle in relation to their terrestrial activities compared to foraging periods at sea. High iron concentration (~419 mg kg−1) in guano of both penguin species suggests that they are a source of regenerated iron. Breeding emperor penguins supplied an average of 237 μmol iron m−2 day−1 on the fast ice that they breed on that eventually ends in the ocean when the ice melts completely in summer (November–February). During their foraging trips, the adult emperor penguins contribute between 7 × 10−5 and 4 × 10−4 μmol iron m−2 day−1, as their foraging ranges increase over the breeding season. In contrast, breeding Adélie penguins supplied between 254 and 1,243 μmol iron m−2 day−1 whilst at their colony, with a fraction of guano entering the ocean via meltwater flowing into the ocean. The flux decreases to 2 × 10−3 to 6 × 10−2 μmol iron m−2 d−1, whilst they are foraging. Our study finds that penguins redistribute a large flux of iron onto their colonies, which may enter the adjacent water through sea ice melt and facilitated through katabatic winds. Despite their high abundance in Prydz Bay, the contribution of penguins to iron flux during their foraging periods is minor, due to the enormous foraging range being covered. Further research into the bioavailability of iron by marine organisms coupled with parallel measurements of seawater iron concentration and phytoplankton uptake experiments will be invaluable in refining iron budgets in both this region and other hotspots along the Antarctic coast where higher trophic-level animals are abundant.

Varying photosynthetic quotients strongly influence net kelp primary production and seasonal differences increase under warming

Reliable net primary production (NPP) estimations of kelp forests are important to evaluate their C-fixation potential. Photosynthetic oxygen measurements can be converted to C-fixation using photosynthetic quotients (PQs). Although there is a known high variability in PQs, the extent and the consequences for NPP is understudied in kelp species. Thus, the present study aimed (i) to quantify the variability of PQs, (ii) to model NPP and (iii) to assess the impact of warming on both. The kelp, Laminaria hyperborea, was studied near the island of Helgoland (North Sea, Germany) along a depth gradient (2, 4, 6 m below mean low water spring tide) across all four seasons. Blade discs were cultivated during at least 6 days per season under simulated ambient photosynthetic photon flux density (PPFD) and temperature conditions and, in parallel, in a warming scenario (+ 4°C). PQs were calculated from parallel oxygen production and 14C-fixation measurements at saturating PPFD at the end of the incubation period. Seasonal PQs varied between 1.7 and 4.4, with highest values in summer due to increased oxygen production. The warming scenario stimulated C-fixation in most seasons, lowering the PQ in comparison to ambient temperature conditions, while collection depth had no significant effect on PQs. The seasonal PQs were used to model daily NPP rates for kelp standing stock at 4 m depth. These daily NPP rates were compared between temperature treatments and with daily NPP rates based on fixed PQs. The warming scenario had a stimulating effect on daily NPP rates in the high-light season spring. In the low-light season autumn, warming resulted in negative daily NPP rates, as the high respiration rates could not be compensated by gross photosynthesis. Overall, annual NPP rate under warming conditions (347 g C m–2 yr–1) was 14% higher than the annual NPP rate under ambient conditions (303 g C m–2 yr–1). Modelling daily NPP with fixed PQs, which neglects the seasonal variation of the PQs, led to a high overestimation of up to 255%. We, therefore, recommend modelling NPP rates not with a fixed PQ, but with seasonal PQs determined under different temperature scenarios in order to obtain reliable future predictions.

Acoustic and Kinematic Predictors of Intelligibility and Articulatory Precision in Parkinson's Disease.

This study investigated relationships within and between perceptual, acoustic, and kinematic measures in speakers with and without dysarthria due to Parkinson's disease (PD) across different clarity conditions. Additionally, the study assessed the predictive capabilities of selected acoustic and kinematic measures for intelligibility and articulatory precision ratings. Forty participants, comprising 22 with PD and 18 controls, read three phrases aloud using conversational, less clear, and more clear speaking conditions. Acoustic measures and their theoretical kinematic parallel measures (i.e., acoustic and kinematic distance and vowel space area [VSA]; second formant frequency [F2] slope and kinematic speed) were obtained from the diphthong /aɪ/ and selected vowels in the sentences. A total of 368 listeners from crowdsourcing provided ratings for intelligibility and articulatory precision. The research questions were examined using correlations and linear mixed-effects models. Intelligibility and articulatory precision ratings were highly correlated across all speakers. Acoustic and kinematic distance, as well as F2 slope and kinematic speed, showed moderately positive correlations. In contrast, acoustic and kinematic VSA exhibited no correlation. Among all measures, acoustic VSA and kinematic distance were robust predictors of both intelligibility and articulatory precision ratings, but they were stronger predictors of articulatory precision. The findings highlight the importance of measurement selection when examining cross-domain relationships. Additionally, they support the use of behavioral modifications aimed at eliciting larger articulatory gestures to improve intelligibility in individuals with dysarthria due to PD. https://doi.org/10.23641/asha.27011281.

Validation of clinical tumor depth of invasion measure in patients with oral cavity cancer

ObjectivesThe 8th edition of the American Joint Committee on Cancer (AJCC) for head and neck malignancies incorporated depth of invasion (DOI) for oral cavity squamous cell carcinoma (OCSCC). Currently, there is no standardized method to determine clinical DOI (cDOI). We aim to validate radiologic DOI (rDOI) utilizing contrast-enhanced computed tomography (CECT) imaging. Materials and MethodsRadiographic DOI was defined as the coronal measurement of the deepest margin parallel to the expected normal mucosal plane. To establish a valid, accurate and repeatable rDOI, a retrospective cohort at a single institution tertiary hospital underwent preoperative CECT. Radiographic DOI was independently assessed by 2 neuroradiologists. Correlation was determined between rDOI and pDOI. A prospective pilot study of 49 patients with newly diagnosed OCSCC underwent rDOI assessment compared to final pDOI to assess our rDOI method clinical applicability. ResultsNeuroradiologists demonstrated a high degree of predictability between rDOI and pDOI with as great as 90.91% accuracy for readable CECTs. Inter-observer correlations were strong in the retrospective (Session 1: ICC= 0.956; Session 2: ICC= 0.932) and prospective cohorts (Session 1: ICC= 0.859; Session 2: ICC=0.913) illustrating reliability. Intraobserver correlations were also strong (Retrospective Reader 1 ICC=0.968, Reader 2 ICC=0.941; prospective Reader 1 ICC=0.965, Reader 2 ICC=0.800, p<0.001). T1 lesions were immeasurable 25-62.5% of the time. ConclusionsUsing CECT, the coronal measurement of the deepest margin parallel to the expected normal mucosal plane can enhance determination of a reliable cDOI in OCSCC corresponding to pDOI without change in staging for T2 and greater lesions.

A 3D-Printable smartphone accessory for plant leaf chlorophyll measurement

Plant health and nutrition are universally inferred from leaf chlorophyll content. This research developed a 3D-printed accessory which attaches to the ambient light sensor in a smartphone to estimate leaf chlorophyll content in five tropical plant species. It unveils 3D printing files and assembling details to freely built the accessory anywhere. It is made from a 3D-printed body, a lighting circuit and common spare parts to measure a 663 nm LED band transmission through intact plant leaves. This chlorophyll absorbing light band allows to measure its concentration. The device was tested by comparing its readings to the universal spectrophotometric test or by leaf parallel measurements with a standard SPAD 502™ meter, and it performed as well as these universal standard methods. Due to well-studied relationships between chlorophyll concentration and nutritional status of plants, and the ubiquitous presence of other sensors in smartphones today, the independent improvement and adoption of this smartphone-connected system would ease the spread of precision farming and digital agronomy practices throughout the different scales of agriculture.

An unusual triplet population pathway in the Reaction Centre of the Chlorophyll-d binding Photosystem I of A. marina, as revealed by a combination of TR-EPR and ODMR spectroscopies

Photo-induced Chlorophyll (Chl) triplet states in the isolated Photosystem I (PSI) of Acaryochloris marina, that harbours Chl d as its main pigment, were investigated by Optically Detected Magnetic Resonance (ODMR) and Time-Resolved Electron Paramagnetic Resonance (TR-EPR), and as a function of pre-illumination of the sample under reducing redox poising. Fluorescence Detected Magnetic Resonance (FDMR) allowed resolving four Chl d triplet (3Chl d) populations (T1-T4) both in untreated and illuminated samples in the presence of ascorbate and N,N,N′,N′-tetramethyl-p-phenylenediamine (TMPD). The FDMR signals increased following the pre-illumination treatment, particularly for the T3 and T4 populations, which are therefore sensitive to the redox state of PSI cofactors. Microwave-induced Triplet minus Singlet (TmS) spectra were detected in the |D|-|E| resonance window of the T3 and T4 triplets. These showed a broad singlet bleaching centred at 740 nm and also displayed complex spectral structure with several derivative-like features, indicating that both the T3 and T43Chl d populations are associated with the PSI reaction centre (RC) triplet, P3740. Parallel measurements by TR-EPR demonstrated that triplet signals observed under all conditions investigated are dominated by an electron spin polarisation (esp), which is typical of intersystem crossing, differently from what expected for recombination triplet states formed from a radical pair precursor. Moreover, stronger reductant conditions obtained by pre-illumination of the samples in the presence of dithionite and 5-methylphenazinium methyl sulfate (PMS) did not lead to a recombination triplet state esp, but rather to a decrease of the whole signal intensity. The energetics of A. marina PSI and the possible occurrence of distributions of cofactors redox properties are discussed in order to address the unexpected P3740 esp.

Continuity of long-term climate data series after the transition from manual to automatic weather station

In climatology, transitioning from conventional manual weather stations (MWS) to automatic weather stations (AWS) presents challenges in maintaining the homogeneity of long-term data series. At the Skalnaté Pleso Observatory (1778 m a.s.l., High Tatras), manual meteorological measurements have been conducted since 1943 using the same methods and devices at the same location. In 2014, the AWS Physicus was installed to record meteorological data parallelly with manual measurements. This study processed six years of parallel measurements (2017–2022) to derive corrections for AWS monthly atmospheric precipitation totals and maximum (Tmax), minimum (Tmin) and mean air temperatures (Tmean) measured in 2023. Two correction approaches were proposed: monthly regressions (MR) and cumulative distribution functions (CDF), including Generalized Extreme Value (GEV) distribution, normal distribution (GAUSS), and Gamma distribution (GAMMA). Analyses of monthly data revealed an underestimation of precipitation totals in AWS data, with a mean bias error (MBE) of −6.8 mm and a root mean squared error (RMSE) of 20.0 mm. The most suitable correction method was the MR, which decreased MBE to 1.5 mm and RMSE to 11.1 mm. AWS monthly air temperature data were overestimated by 0.1 °C, 0.3 °C, and 0.1 °C for Tmax, Tmin, and Tmean, respectively. For Tmax, correction using the MR and GEV methods reduced the MBE to 0.0 °C and achieved RMSE of 0.1 °C for both. After applying GAUSS, MBE and RMSE decreased to 0.1 °C. The most appropriate correction method for Tmin was the MR resulting in MBE of 0.0 °C and RMSE of 0.3 °C. For Tmean, the MR and GEV methods reduced the MBE to 0.0 °C and the RMSE to 0.1 °C for both methods. These results demonstrate that AWS monthly data, when corrected using the presented methods, have the potential to maintain the continuity of historical climate data series at Skalnaté Pleso.

High-throughput discovery of inhibitory protein fragments with AlphaFold.

Peptides can bind to specific sites on larger proteins and thereby function as inhibitors and regulatory elements. Peptide fragments of larger proteins are particularly attractive for achieving these functions due to their inherent potential to form native-like binding interactions. Recently developed experimental approaches allow for high-throughput measurement of protein fragment inhibitory activity in living cells. However, it has thus far not been possible to predict de novo which of the many possible protein fragments bind to protein targets, let alone act as inhibitors. We have developed a computational method, FragFold, that employs AlphaFold to predict protein fragment binding to full-length proteins in a high-throughput manner. Applying FragFold to thousands of fragments tiling across diverse proteins revealed peaks of predicted binding along each protein sequence. Comparisons with experimental measurements establish that our approach is a sensitive predictor of fragment function: Evaluating inhibitory fragments from known protein-protein interaction interfaces, we find 87% are predicted by FragFold to bind in a native-like mode. Across full protein sequences, 68% of FragFold-predicted binding peaks match experimentally measured inhibitory peaks. Deep mutational scanning experiments support the predicted binding modes and uncover superior inhibitory peptides in high throughput. Further, FragFold is able to predict previously unknown protein binding modes, explaining prior genetic and biochemical data. The success rate of FragFold demonstrates that this computational approach should be broadly applicable for discovering inhibitory protein fragments across proteomes.

Development and Preliminary Validation of Stigma Measures for Care Partners of Persons Who Are d/Deaf or Hard of Hearing.

A great deal of literature documents the significant demands, both physical and psychosocial, that care partners experience when providing care to persons with a range of health conditions. There is, however, far less research available on care partners of adult persons who are d/Deaf or hard of hearing (d/DHH). In response to this gap, the authors developed measures of d/DHH stigma among care partners as part of the work of the Lancet Commission on Hearing Loss' Measures, Models, and Stigma Reduction Subgroup. The measures examined in this article are part of a larger set of parallel measures to enable comparison of stigma measurement across groups. The present study describes the preliminary validation of five stigma scales specifically tailored for use to assess the prevalence and effect of stigma on the care partners of adult people who are d/DHH in the United States. Care partners in this context are defined broadly and can include spouses, partners, adult children, siblings, and friends of persons who are d/DHH. The scales describe the care partner's own assessment of how the person who is d/DHH experiences and perceives stigma as well as the care partner's own internalized, experienced, and perceived stigma as a result of their association with a person who is d/DHH. This latter set of three scales describes secondary stigma, or the stigma a person experiences related to their association with a member of a stigmatized group. Measures were developed through a process that included a literature review, Delphi groups with people who became d/DHH after they developed spoken language, cognitive interviews, and a pretest. An online, self-administered preliminary validation survey was conducted with 151 care partners. Results support the internal reliability of each of the five stigma scales (ordinal α's all greater than 0.9) and that each scale is assessing a single factor. Additional testing is needed to confirm the validity of these measures. After further validation, they can be used to assess the prevalence and effect of stigma on care partners of persons who are d/DHH and to evaluate the success of interventions developed to address stigma and its effects both on the care partner and the person who is d/DHH and receiving the care.