bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multiparametric fluorescence assay for screening aptamer–protein interactions based on microbeads
Authors: Schmidt Carsten , Kammel Anne , Tanner Julian A. , Kinghorn Andrew B. , Khan Muhammad Moman , Lehmann Werner , Menger Marcus , Schedler Uwe , Schierack Peter , Rödiger Stefan 
Published: February 2022

AbstractFor improving aptamer-ligand binding we have developed a screening system that defines optimal binding buffer composition. Using multiplex assays, one buffer system is needed which guarantees the specific binding of all aptamers. We investigated nine peer-reviewed DNA aptamers. Non-specific binding of aptamers is an obstacle. To address this, we investigated 16 proteins as specificity controls bound covalently to encoded microbeads in a multiplex assay. Increasing the NaCl concentration decreased the binding for all aptamers. Changing pH values by one unit higher or lower did not influence the aptamer binding significantly. However, pH < 5 led to non-specific binding for all aptamers. The PfLDH-aptamer selected in the absence of divalent cations exhibited doubling of its binding signal by the addition of Ca2+ and Mg2+. We confirmed Ca2+ and Mg2+ dependency of the aptamers for streptavidin and thrombin by observing a 90% and 50% binding decrease, respectively. We also achieved a doubling of binding for the streptavidin aptamer when replacing Ca2+ and Mg2+ by Mn2+. A buffer suitable for all aptamers can have considerable variations in pH or ionic strength, but divalent cations (Ca2+, Mg2+, Mn2+) are essential.
Heteroscedastic sparse Gaussian process regression-based stochastic material model for plastic structural analysis
Authors: Chen Baixi , Shen Luming , Zhang Hao 
Published: February 2022

AbstractDescribing the material flow stress and the associated uncertainty is essential for the plastic stochastic structural analysis. In this context, a data-driven approach-heteroscedastic sparse Gaussian process regression (HSGPR) with enhanced efficiency is introduced to model the material flow stress. Different from other machine learning approaches, e.g. artificial neural network (ANN), which only estimate the deterministic flow stress, the HSGPR model can capture the flow stress and its uncertainty simultaneously from the dataset. For validating the proposed model, the experimental data of the Al 6061 alloy is used here. Without setting a priori assumption on the mathematical expression, the proposed HSGPR-based flow stress model can produce a better prediction of the experimental stress data than the ANN model, the conventional GPR model, and Johnson Cook model at elevated temperatures. After the HSGPR-based flow stress model is implemented into finite element analysis, two numerical examples with synthetic material properties are performed to demonstrate the model’s capability in stochastic plastic structural analysis. The results have shown that with sufficient data, the distribution of the structural load carrying capacity at elevated temperatures and the variation of load–displacement curves during the loading and unloading processes can be accurately predicted by the HSGPR-based flow stress model.
Histopathology and surgical outcome of symptomatic treatment-related changes after gamma knife radiosurgery in patients with brain metastases
Authors: Kim Jeong-Hwa , Choi Jung-Won , Kong Doo-Sik , Seol Ho Jun , Nam Do-Hyun , Ryu Jae-Wook , Kim Sung-Tae , Suh Yeon-Lim , Lee Jung-Il 
Published: February 2022

AbstractA late-onset treatment-related changes (TRCs), which represent radiographic radiation necrosis (RN), frequently occur after stereotactic radiosurgery (SRS) for brain metastases and often need surgical treatment. This study aimed to validate the true pathology and investigate clinical implication of surgically resected TRCs on advanced magnetic resonance imaging (MRI). Retrospective analyses of 86 patients who underwent surgical resection after radiosurgery of brain metastases were performed. Fifty-four patients displayed TRCs on preoperative MRI, comprising pure RN in 19 patients (TRC-RN group) and mixed viable tumor cells in 35 patients (TRC-PD group). Thirty-two patients revealed the consistent diagnosis of progressive disease in both MRI and histopathology (PD–PD group). The TRC-PD group showed larger prescription isodose volume (9.4 cm3) than the TRC-RN (4.06 cm3, p = 0.014) group and a shorter time interval from SRS to preoperative MRI diagnosis (median 4.07 months) than the PD–PD group (median 8.77 months, p = 0.004). Progression-free survival was significantly different among the three groups (p < 0.001), but not between TRC-RN and TRC-PD (post hoc test, p = 1.00), while no difference was observed in overall survival (p = 0.067). Brain metastases featured as TRCs after SRS frequently contained viable tumor cells. However, this histologic heterogeneity had a minor impact on benign local prognosis of TRCs after surgical resection.
Tumor cell enrichment by tissue suspension enables detection of mutations with low variant allele frequency and estimation of germline mutations
Authors: Hatakeyama Keiichi , Muramatsu Koji , Nagashima Takeshi , Kawanishi Yuichi , Fukumura Ryutaro , Ohshima Keiichi , Shimoda Yuji , Kenmotsu Hirotsugu , Mochizuki Tohru , Urakami Kenichi , Akiyama Yasuto , Sugino Takashi , Yamaguchi Ken 
Published: February 2022

AbstractTargeted sequencing offers an opportunity to select specific drugs for cancer patients based on alterations in their genome. However, accurate sequencing cannot be performed in cancers harboring diffuse tumor cells because of low tumor content. We performed tumor cell enrichment using tissue suspension of formalin-fixed, paraffin-embedded (FFPE) tissue sections with low tumor cell content. The enriched fractions were used to efficiently identify mutations by sequencing a target panel of cancer-related genes. Tumor-enriched and residual fractions were isolated from FFPE tissue sections of intestinal and diffuse gastric cancers harboring diffuse tumor cells and DNA of suitable quality was isolated for next-generation sequencing. Sequencing of a target panel of cancer-related genes using the tumor-enriched fraction increased the number of detectable mutations and variant allele frequency. Furthermore, mutation analysis of DNA isolated from tumor-enriched and residual fractions allowed us to estimate germline mutations without a blood reference. This approach of tumor cell enrichment will not only enhance the success rate of target panel sequencing, but can also improve the accuracy of detection of somatic mutations in archived specimens.
Mechanoporation enables rapid and efficient radiolabeling of stem cells for PET imaging
Authors: Jung Kyung Oh , Theruvath Ashok Joseph , Nejadnik Hossein , Liu Anna , Xing Lei , Sulchek Todd , Daldrup-Link Heike E. , Pratx Guillem 
Published: February 2022

AbstractRegenerative medicine uses the patient own stem cells to regenerate damaged tissues. Molecular imaging techniques are commonly used to image the transplanted cells, either right after surgery or at a later time. However, few techniques are fast or straightforward enough to label cells intraoperatively. Adipose tissue-derived stem cells (ADSCs) were harvested from knee joints of minipigs. The cells were labeled with PET contrast agent by flowing mechanoporation using a microfluidic device. While flowing through a series of microchannels, cells are compressed repeatedly by micro-ridges, which open transient pores in their membranes and induce convective transport, intended to facilitate the transport of 68Ga-labeled and lipid-coated mesoporous nanoparticles (MSNs) into the cells. This process enables cells to be labeled in a matter of seconds. Cells labeled with this approach were then implanted into cartilage defects, and the implant was imaged using positron emission tomography (PET) post-surgery. The microfluidic device can efficiently label millions of cells with 68Ga-labeled MSNs in as little as 15 min. The method achieved labeling efficiency greater than 5 Bq/cell on average, comparable to 30 min-long passive co-incubation with 68Ga-MSNs, but with improved biocompatibility due to the reduced exposure to ionizing radiation. Labeling time could also be accelerated by increasing throughput through more parallel channels. Finally, as a proof of concept, ADSCs were labeled with 68Ga-MSNs and quantitatively assessed using clinical PET/MR in a mock transplant operation in pig knee joints. MSN-assisted mechanoporation is a rapid, effective and straightforward approach to label cells with 68Ga. Given its high efficiency, this labeling method can be used to track small cells populations without significant effects on viability. The system is applicable to a variety of cell tracking studies for cancer therapy, regenerative therapy, and immunotherapy.
Mutations in the stator protein PomA affect switching of rotational direction in bacterial flagellar motor
Authors: Terashima Hiroyuki , Hori Kiyoshiro , Ihara Kunio , Homma Michio , Kojima Seiji 
Published: February 2022

AbstractThe flagellar motor rotates bi-directionally in counter-clockwise (CCW) and clockwise (CW) directions. The motor consists of a stator and a rotor. Recent structural studies have revealed that the stator is composed of a pentameric ring of A subunits and a dimer axis of B subunits. Highly conserved charged and neighboring residues of the A subunit interacts with the rotor, generating torque through a gear-like mechanism. The rotational direction is controlled by chemotaxis signaling transmitted to the rotor, with less evidence for the stator being involved. In this study, we report novel mutations that affect the switching of the rotational direction at the putative interaction site of the stator to generate rotational force. Our results highlight an aspect of flagellar motor function that appropriate switching of the interaction states between the stator and rotor is critical for controlling the rotational direction.
High-precision micro-displacement sensor based on tunnel magneto-resistance effect
Authors: Wang Xuhu , Li Wang , Jin Li , Gong Meimei , Wang Junqiang , Zhong Yujie , Ruan Yi , Guo Chunhong , Xin Chenguang , Li Mengwei 
Published: February 2022

AbstractA high-precision micro-displacement sensor based on tunnel magneto-resistance effect is reported.We designed and simulated magnetic characteristics of the sensor, and employed chip-level Au-In bonding to implement low-temperature assembly of the TMR devices. We employed the subdivision interpolation technique to enhance the resolution by translating the sine-cosine outputs of a TMR sensor into an output that varies linearly with the displacement. Simultaneously, using the multi-bridge circuit method to suppress external magnetic and geomagnetic interference. Experimental result shows that the micro-displacement sensor has a resolution of 800 nm, accuracy of 0.14$$\%$$
%
and a full-scale range of up to millimeter level. This work enables a high-performance displacement sensor, and provides a significant guide for the design of a micro-displacement sensor in practical applications.
Macromolecular protein crystallisation with biotemplate of live cells
Authors: Sun Mubai , Yang Huaiyu , Miao Xinyu , Wang Weixian , Wang Jinghui 
Published: February 2022

AbstractMacromolecular protein crystallisation was one of the potential tools to accelerate the biomanufacturing of biopharmaceuticals. In this work, it was the first time to investigate the roles of biotemplates, Saccharomyces cerevisiae live cells, in the crystallisation processes of lysozyme, with different concentrations from 20 to 2.5 mg/mL lysozyme and different concentrations from 0 to 5.0 × 107 (cfu/mL) Saccharomyces cerevisiae cells, during a period of 96 h. During the crystallisation period, the nucleation possibility in droplets, crystal numbers, and cell growth and cell density were observed and analysed. The results indicated the strong interaction between the lysozyme molecules and the cell wall of the S. cerevisiae, proved by the crystallization of lysozyme with fluorescent labels. The biotemplates demonstrated positive influence or negative influence on the nucleation, i.e. shorter or longer induction time, dependent on the concentrations of the lysozyme and the S. cerevisiae cells, and ratios between them. In the biomanufacturing process, target proteins were various cells were commonly mixed with various cells, and this work provides novel insights of new design and application of live cells as biotemplates for purification of macromolecules.
Thermal imaging reveals audience-dependent effects during cooperation and competition in wild chimpanzees
Authors: de Vevey Marion , Bouchard Alice , Soldati Adrian , Zuberbühler Klaus 
Published: February 2022

AbstractAccessing animal minds has remained a challenge since the beginnings of modern science. Here, we used a little-tried method, functional infrared thermal imaging, with wild chimpanzees during common social interactions. After removing confounds, we found that chimpanzees involved in competitive events had lower nose skin temperatures whereas those involved in cooperative events had higher temperatures, the latter more so in high- than low-ranking males. Temperatures associated with grooming were akin to those of cooperative events, except when males interacted with a non-reciprocating alpha male. In addition, we found multiple audience effects. Notably, the alpha male’s presence reduced positive effects associated with cooperation, whereas female presence buffered negative effects associated with competition. Copulation was perceived as competitive, especially during furtive mating when other males were absent. Overall, patterns suggest that chimpanzees categorise ordinary social events as cooperative or competitive and that these perceptions are moderated by specific audiences.
Screening methods for enzyme-mediated alcohol oxidation
Authors: Contente Martina L. , Marzuoli Irene , Iding Hans , Wetzl Dennis , Puentener Kurt , Hanlon Steven P. , Paradisi Francesca 
Published: February 2022

AbstractAlcohol oxidation for the generation of carbonyl groups, is an essential reaction for the preparation of fine chemicals. Although a number of chemical procedures have been reported, biocatalysis is a promising alternative for more sustainable and selective processes. To speed up the discovery of novel (bio)catalysts for industrial applications, efficient screening approaches need to be established. Here, we report on an enzyme-mediated alcohol oxidation screening platform to rapidly detect the activities and selectivities of three classes of biocatalysts; ketoreductases (KREDs), alcohol oxidases (AlcOXs) and laccase-mediator systems (LMSs) with diverse substrates.
Explaining the differences of gait patterns between high and low-mileage runners with machine learning
Authors: Xu Datao , Quan Wenjing , Zhou Huiyu , Sun Dong , Baker Julien S. , Gu Yaodong 
Published: February 2022

AbstractRunning gait patterns have implications for revealing the causes of injuries between higher-mileage runners and low-mileage runners. However, there is limited research on the possible relationships between running gait patterns and weekly running mileages. In recent years, machine learning algorithms have been used for pattern recognition and classification of gait features to emphasize the uniqueness of gait patterns. However, they all have a representative problem of being a black box that often lacks the interpretability of the predicted results of the classifier. Therefore, this study was conducted using a Deep Neural Network (DNN) model and Layer-wise Relevance Propagation (LRP) technology to investigate the differences in running gait patterns between higher-mileage runners and low-mileage runners. It was found that the ankle and knee provide considerable information to recognize gait features, especially in the sagittal and transverse planes. This may be the reason why high-mileage and low-mileage runners have different injury patterns due to their different gait patterns. The early stages of stance are very important in gait pattern recognition because the pattern contains effective information related to gait. The findings of the study noted that LRP completes a feasible interpretation of the predicted results of the model, thus providing more interesting insights and more effective information for analyzing gait patterns.
The impact of nutritional status on health-related quality of life in hemodialysis patients
Authors: Visiedo Lucia , Rey Laura , Rivas Francisco , López Francisca , Tortajada Begoña , Giménez Rafael , Abilés Jimena 
Published: February 2022

AbstractMalnutrition is frequent in hemodialysis (HD) patients. Nutritional deficiencies may negatively impact quality of life (QOL). This study examines the utility of the Malnutrition-Inflammation Score (MIS) in detecting nutritional risk (NR) and assesses the correlation between nutritional status and QOL in dialysis patients upon starting a nutritional intervention program (NIP). One hundred and twenty patients were included in this cross-sectional study. The MIS was used to detect NR and the Kidney Disease Quality of Life (KDQOL-SF) instrument version 1.2 was used to assess QOL. 62% of patients were found to be at NR (MIS > 5). Nutritional status was significantly correlated with all generic QOL sub-scales. On a multiple linear regression analysis, malnutrition showed the highest level of explanation in the Kidney Disease Summary Component which explained 28.9% of the variance; the Physical Component Summary which explained 33% of the variance; and the Mental Component Summary which explained 21.5% of the variance. Malnutrition was found to be the most significant predictor of impaired scores on the KDQOL-SF. The use of MIS to identify patients at NR and a nutritional assessment to detect malnutrition in its early stages are important given the effects a NIP can have on improving QOL in HD patients.
Gini's mean difference and the long-term prognostic value of nodal quanta classes after pre-operative chemotherapy in advanced breast cancer
Authors: Vinh-Hung Vincent , Van Parijs Hilde , Gorobets Olena , Fontaine Christel , Nguyen Nam P. , Keam Bhumsuk , Nguyen Dung Minh , De Ridder Mark 
Published: February 2022

AbstractGini's mean difference (GMD, mean absolute difference between any two distinct quantities) of the restricted mean survival times (RMSTs, expectation of life at a given time limit) has been proposed as a new metric where higher GMD indicates better prognostic value. GMD is applied to the RMSTs at 25 years time-horizon to evaluate the long-term overall survival of women with breast cancer who received neoadjuvant chemotherapy, comparing a classification based on the number (pN) versus a classification based on the ratio (LNRc) of positive nodes found at axillary surgery. A total of 233 patients treated in 1980–2009 with documented number of positive nodes (npos) and number of nodes examined (ntot) were identified. The numbers were categorized into pN0, npos = 0; pN1, npos = [1,3]; pN2, npos = [4,9]; pN3, npos ≥ 10. The ratios npnx = npos/ntot were categorized into Lnr0, npnx = 0; Lnr1, npnx = (0,0.20]; Lnr2, npnx = (0.20,0.65]; Lnr3, npnx > 0.65. The GMD for pN-classification was 5.5 (standard error: ± 0.9) years, not much improved over a simple node-negative vs. node-positive that showed a GMD of 5.0 (± 1.4) years. The GMD for LNRc-classification was larger, 6.7 (± 0.8) years. Among other conventional metrics, Cox-model LNRc's c-index was 0.668 vs. pN's c = 0.641, indicating commensurate superiority of LNRc-classification. The usability of GMD-RMSTs warrants further investigation.
Geometric-phase-based shearing interferometry for broadband vortex state decoding
Authors: Lyu Ziyao , Wang Changshun 
Published: February 2022

AbstractGiven that spin and orbital angular momenta of photons have been widely investigated in optical communication and information processing systems, efficient decoding of optical vortex states using a single element is highly anticipated. In this work, a wavelength-independent holographic scheme has been proposed for total angular momentum sorting of both scalar and vector vortex states with a stationary broadband geometric-phase waveplate by means of reference-free shearing interferometry. The entangled spin and orbital angular momentum modes can be distinguished simultaneously based on the spin–orbit optical Hall effect in order to realize single-shot vortex detection. The viability of our scheme has also been demonstrated experimentally.
A deeper look at carrier proteome effects for single-cell proteomics
Authors: Ye Zilu , Batth Tanveer S. , Rüther Patrick , Olsen Jesper V. 
Published: February 2022

AbstractMultiplexing approaches using tandem mass tags with a carrier proteome to boost sensitivity have advanced single cell proteomics by mass spectrometry (SCoPE-MS). Here, we probe the carrier proteome effects in single cell proteomics with mixed species TMTpro-labeled samples. We demonstrate that carrier proteomes, while increasing overall identifications, dictate which proteins are identified. We show that quantitative precision and signal intensity are limited at high carrier levels, hindering the recognition of regulated proteins. Guidelines for optimized mass spectrometry acquisition parameters and best practices for fold-change or protein copy number-based comparisons are provided.
BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies
Authors: Chandrakumar Induja , Gauthier Nick P. G. , Nelson Cassidy , Bonsall Michael B. , Locher Kerstin , Charles Marthe , MacDonald Clayton , Krajden Mel , Manges Amee R. , Chorlton Samuel D. 
Published: February 2022

AbstractA large gap remains between sequencing a microbial community and characterizing all of the organisms inside of it. Here we develop a novel method to taxonomically bin metagenomic assemblies through alignment of contigs against a reference database. We show that this workflow, BugSplit, bins metagenome-assembled contigs to species with a 33% absolute improvement in F1-score when compared to alternative tools. We perform nanopore mNGS on patients with COVID-19, and using a reference database predating COVID-19, demonstrate that BugSplit’s taxonomic binning enables sensitive and specific detection of a novel coronavirus not possible with other approaches. When applied to nanopore mNGS data from cases ofKlebsiella pneumoniaeandNeisseria gonorrhoeaeinfection, BugSplit’s taxonomic binning accurately separates pathogen sequences from those of the host and microbiota, and unlocks the possibility of sequence typing, in silico serotyping, and antimicrobial resistance prediction of each organism within a sample. BugSplit is available athttps://bugseq.com/academic.
Long-lived period-doubled edge modes of interacting and disorder-free Floquet spin chains
Authors: Yates Daniel J. , Abanov Alexander G. , Mitra Aditi 
Published: February 2022

AbstractFloquet spin chains have been a venue for understanding topological states of matter that are qualitatively different from their static counterparts by, for example, hosting π edge modes that show stable period-doubled dynamics. However the stability of these edge modes to interactions has traditionally required the system to be many-body localized in order to suppress heating. In contrast, here we show that even in the absence of disorder, and in the presence of bulk heating, π edge modes are long lived. Their lifetime is extracted from exact diagonalization and is found to be non-perturbative in the interaction strength. A tunneling estimate for the lifetime is obtained by mapping the stroboscopic time-evolution to dynamics of a single particle in Krylov subspace. In this subspace, the π edge mode manifests as the quasi-stable edge mode of an inhomogeneous Su-Schrieffer-Heeger model whose dimerization vanishes in the bulk of the Krylov chain.