bluuebunny/crossref_metadata_2025_split huggingface dataset:
Line scan-based rapid magnetic resonance imaging of repetitive motion
Authors: Lee Hankyeol , Lee Jeongtaek , Park Jang-Yeon , Lee Seung-Kyun 
Published: February 2021

AbstractTwo-dimensional (2D) line scan-based dynamic magnetic resonance imaging (MRI) is examined as a means to capture the interior of objects under repetitive motion with high spatiotemporal resolutions. The method was demonstrated in a 9.4-T animal MRI scanner where line-by-line segmented k-space acquisition enabled recording movements of an agarose phantom and quail eggs in different conditions—raw and cooked. A custom MR-compatible actuator which utilized the Lorentz force on its wire loops in the scanner’s main magnetic field effectively induced the required periodic movements of the objects inside the magnet. The line-by-line k-space segmentation was achieved by acquiring a single k-space line for every frame in a motion period before acquisition of another line with a different phase-encode gradient in the succeeding motion period. The reconstructed time-course images accurately represented the objects’ displacements with temporal resolutions up to 5.5 ms. The proposed method can drastically increase the temporal resolution of MRI for imaging rapid periodic motion of objects while preserving adequate spatial resolution for internal details when their movements are driven by a reliable motion-inducing mechanism.
Distinct chemical blends produced by different reproductive castes in the subterranean termite Reticulitermes flavipes
Authors: Eyer Pierre-André , Salin Jared , Helms Anjel M. , Vargo Edward L. 
Published: February 2021

AbstractThe production of royal pheromones by reproductives (queens and kings) enables social insect colonies to allocate individuals into reproductive and non-reproductive roles. In many termite species, nestmates can develop into neotenics when the primary king or queen dies, which then inhibit the production of additional reproductives. This suggests that primary reproductives and neotenics produce royal pheromones. The cuticular hydrocarbon heneicosane was identified as a royal pheromone inReticulitermes flavipesneotenics. Here, we investigated the presence of this and other cuticular hydrocarbons in primary reproductives and neotenics of this species, and the ontogeny of their production in primary reproductives. Our results revealed that heneicosane was produced by most neotenics, raising the question of whether reproductive status may trigger its production. Neotenics produced six additional cuticular hydrocarbons absent from workers and nymphs. Remarkably, heneicosane and four of these compounds were absent in primary reproductives, and the other two compounds were present in lower quantities. Neotenics therefore have a distinct ‘royal’ blend from primary reproductives, and potentially over-signal their reproductive status. Our results suggest that primary reproductives and neotenics may face different social pressures. Future studies of these pressures should provide a more complete understanding of the mechanisms underlying social regulation in termites.
Long lifetime of bialkali photocathodes operating in high gradient superconducting radio frequency gun
Authors: Wang E. , Litvinenko V. N. , Pinayev I. , Gaowei M. , Skaritka J. , Belomestnykh S. , Ben-Zvi I. , Brutus J. C. , Jing Y. , Biswas J. , Ma J. , Narayan G. , Petrushina I. , Rahman O. , Xin T. , Rao T. , Severino F. , Shih K. , Smith K. , Wang G. , Wu Y. 
Published: February 2021

AbstractHigh brightness, high charge electron beams are critical for a number of advanced accelerator applications. The initial emittance of the electron beam, which is determined by the mean transverse energy (MTE) and laser spot size, is one of the most important parameters determining the beam quality. The bialkali photocathodes illuminated by a visible laser have the advantages of high quantum efficiency (QE) and low MTE. Furthermore, Superconducting Radio Frequency (SRF) guns can operate in the continuous wave (CW) mode at high accelerating gradients, e.g. with significant reduction of the laser spot size at the photocathode. Combining the bialkali photocathode with the SRF gun enables generation of high charge, high brightness, and possibly high average current electron beams. However, integrating the high QE semiconductor photocathode into the SRF guns has been challenging. In this article, we report on the development of bialkali photocathodes for successful operation in the SRF gun with months-long lifetime while delivering CW beams with nano-coulomb charge per bunch. This achievement opens a new era for high charge, high brightness CW electron beams.
Combined unsupervised-supervised machine learning for phenotyping complex diseases with its application to obstructive sleep apnea
Authors: Ma Eun-Yeol , Kim Jeong-Whun , Lee Youngmin , Cho Sung-Woo , Kim Heeyoung , Kim Jae Kyoung 
Published: February 2021

AbstractUnsupervised clustering models have been widely used for multimetric phenotyping of complex and heterogeneous diseases such as diabetes and obstructive sleep apnea (OSA) to more precisely characterize the disease beyond simplistic conventional diagnosis standards. However, the number of clusters and key phenotypic features have been subjectively selected, reducing the reliability of the phenotyping results. Here, to minimize such subjective decisions for highly confident phenotyping, we develop a multimetric phenotyping framework by combining supervised and unsupervised machine learning. This clusters 2277 OSA patients to six phenotypes based on their multidimensional polysomnography (PSG) data. Importantly, these new phenotypes show statistically different comorbidity development for OSA-related cardio-neuro-metabolic diseases, unlike the conventional single-metric apnea–hypopnea index-based phenotypes. Furthermore, the key features of highly comorbid phenotypes were identified through supervised learning rather than subjective choice. These results can also be used to automatically phenotype new patients and predict their comorbidity risks solely based on their PSG data. The phenotyping framework based on the combination of unsupervised and supervised machine learning methods can also be applied to other complex, heterogeneous diseases for phenotyping patients and identifying important features for high-risk phenotypes.
Notch signaling drives development of Barrett’s metaplasia from Dclk1-positive epithelial tuft cells in the murine gastric mucosa
Authors: Kunze Bettina , Middelhoff Moritz , Maurer H. Carlo , Agibalova Tatiana , Anand Akanksha , Bührer Anne-Marie , Fang Hsin-Yu , Baumeister Theresa , Steiger Katja , Strangmann Julia , Schmid Roland M. , Wang Timothy C. , Quante Michael 
Published: February 2021

AbstractBarrett’s esophagus (BE) is a precursor to esophageal adenocarcinoma (EAC), but its cellular origin and mechanism of neoplastic progression remain unresolved. Notch signaling, which plays a key role in regulating intestinal stem cell maintenance, has been implicated in a number of cancers. The kinase Dclk1 labels epithelial post-mitotic tuft cells at the squamo-columnar junction (SCJ), and has also been proposed to contribute to epithelial tumor growth. Here, we find that genetic activation of intracellular Notch signaling in epithelial Dclk1-positive tuft cells resulted in the accelerated development of metaplasia and dysplasia in a mouse model of BE (pL2.Dclk1.N2IC mice). In contrast, genetic ablation of Notch receptor 2 in Dclk1-positive cells delayed BE progression (pL2.Dclk1.N2fl mice), and led to increased secretory cell differentiation. The accelerated BE progression in pL2.Dclk1.N2IC mice correlated with changes to the transcriptomic landscape, most notably for the activation of oncogenic, proliferative pathways in BE tissues, in contrast to upregulated Wnt signalling in pL2.Dclk1.N2fl mice. Collectively, our data show that Notch activation in Dclk1-positive tuft cells in the gastric cardia can contribute to BE development.
Evaluation of the QUANTUM BLUE sCAL rapid test as a point of care tool to identify patients with peritonsillar abscess
Authors: Stahl Lea-Sophie , Roth Johannes , Rudack Claudia , McNally Annika , Weber Jakob , Vogl Thomas , Spiekermann Christoph 
Published: February 2021

AbstractS100A8/A9 (Calprotectin) serves as a biomarker for various inflammatory diseases, such as for peritonsillar abscess (PTA). Recently, the PTA score was developed for reliable PTA identification. It uses a combination of characteristic clinical symptoms and elevated calprotectin levels in serum and saliva to determine this score. Although well-established point-of-care tests (POCT) to determine serum or faecal calprotectin levels exist, a reliable and rapid tool to analyse salivary calprotectin has not yet been described. In this study, we analysed the potential of the QUANTUM BLUE sCAL Test (QBT, BÜHLMANN Laboratories AG, Switzerland) to determine S100A8/A9 levels during outpatient management. These QBT measurements are combined with other clinical factors to determine the PTA score. Significantly higher calprotectin levels were determined by QBT in patients with PTA compared to healthy controls. The receiver operating characteristic (ROC) curves for the QBT revealed cut-off values of 2940 ng/ml (sensitivity = 0.88, specificity = 0.78) in serum and 5310 ng/ml (sensitivity = 0.80, specificity = 0.50) in saliva. By adding the QBT results to determine PTA values, a ROC analysis provided a statistical cut-off score of 2.5 points to identify the existence of a PTA with a sensitivity of 100% and a specificity of 89.3%. The QUANTUM BLUE sCAL Test (QBT) is an appropriate POCT to determine serum and salivary calprotectin levels. Thus, PTA scores can be determined within a short time frame by applying the QBT during outpatient management.
Congener-specific partition properties of chlorinated paraffins evaluated with COSMOtherm and gas chromatographic retention indices
Authors: Hammer Jort , Matsukami Hidenori , Endo Satoshi 
Published: February 2021

AbstractChlorinated Paraffins (CPs) are high volume production chemicals and have been found in various organisms including humans and in environmental samples from remote regions. It is thus of great importance to understand the physical–chemical properties of CPs. In this study, gas chromatographic (GC) retention indexes (RIs) of 25 CP congeners were measured on various polar and nonpolar columns to investigate the relationships between the molecular structure and the partition properties. Retention measurements show that analytical standards of individual CPs often contain several stereoisomers. RI values show that chlorination pattern have a large influence on the polarity of CPs. Single Cl substitutions (–CHCl–, –CH2Cl) generally increase polarity of CPs. However, many consecutive –CHCl– units (e.g., 1,2,3,4,5,6-C11Cl6) increase polarity less than expected from the total number of –CHCl– units. Polyparameter linear free energy relationship descriptors show that polarity difference between CP congeners can be explained by the H-bond donating properties of CPs. RI values of CP congeners were predicted using the quantum chemically based prediction tool COSMOthermX. Predicted RI values correlate well with the experimental data (R2, 0.975–0.995), indicating that COSMOthermX can be used to accurately predict the retention of CP congeners on GC columns.
Equivalent SARS-CoV-2 viral loads by PCR between nasopharyngeal swab and saliva in symptomatic patients
Authors: Yokota Isao , Hattori Takeshi , Shane Peter Y. , Konno Satoshi , Nagasaka Atsushi , Takeyabu Kimihiro , Fujisawa Shinichi , Nishida Mutsumi , Teshima Takanori 
Published: February 2021

AbstractEmerging evidences have shown the utility of saliva for the detection of SARS-CoV-2 by PCR as alternative to nasopharyngeal swab (NPS). However, conflicting results have been reported regarding viral loads between NPS and saliva. We conducted a study to compare the viral loads between NPS and saliva in 42 COVID-19 patients. Viral loads were estimated by the cycle threshold (Ct) values. SARS-CoV-2 was detected in 34 (81%) using NPS with median Ct value of 27.4, and 38 (90%) using saliva with median Ct value of 28.9 (P = 0.79). Kendall’s W was 0.82, showing a high degree of agreement, indicating equivalent viral loads in NPS and saliva. After symptom onset, the Ct values of both NPS and saliva continued to increase over time, with no substantial difference. Self-collected saliva has a detection sensitivity comparable to that of NPS and is a useful diagnostic tool with mitigating uncomfortable process and the risk of aerosol transmission to healthcare workers.
Formulation of a reactive oxygen producing calcium sulphate cement as an anti-bacterial hard tissue scaffold
Authors: Hall Thomas J. , Hughes Erik A. B. , Sajjad Hamzah , Kuehne Sarah A. , Grant Melissa M. , Grover Liam M. , Cox Sophie C. 
Published: February 2021

AbstractProphylactic antibiotic bone cements are extensively used in orthopaedics. However, the development of antimicrobial resistance to antibiotics, demonstrates a need to find alternative treatments. Herein, an antimicrobial honey (SurgihoneyRO-SHRO) has been successfully incorporated into a calcium sulphate (CS) based cement to produce a hard tissue scaffold with the ability to inhibit bacterial growth. Antimicrobial properties elicited from SHRO are predominantly owed to the water-initiated production of reactive oxygen species (ROS). As an alternative to initially loading CS cement with SHRO, in order to prevent premature activation, SHRO was added into the already developing cement matrix, locking available water into the CS crystal structure before SHRO addition. Promisingly, this methodology produced > 2.5 times (715.0 ± 147.3 μM/mL/g) more ROS over 24 h and exhibited a compressive strength (32.2 ± 5.8 MPa) comparable to trabecular bone after 3 weeks of immersion. In-vitro the SHRO loaded CS scaffolds were shown to inhibit growth of clinically relevant organisms, Staphylococcus aureus and Pseudomonas aeruginosa, with comparable potency to equivalent doses of gentamicin. Encouragingly, formulations did not inhibit wound healing or induce an inflammatory response from osteoblasts. Overall this study highlights the prophylactic potential of CS-SHRO cements as an alternative to traditional antibiotics.
Identification of microalgae cultured in Bold’s Basal medium from freshwater samples, from a high-rise city
Authors: Lloyd Charmaine , Tan Kai Heng , Lim Kar Leong , Valu Vimala Gana , Fun Sarah Mei Ying , Chye Teng Rong , Mak Hui Min , Sim Wei Xiong , Musa Sarah  Liyana , Ng Joscelyn Jun Quan , Bte Nordin Nazurah Syazana , Bte Md Aidzil Nurhazlyn , Eng Zephyr Yu Wen , Manickavasagam Punithavathy , New Jen Yan 
Published: February 2021

AbstractThis study aimed at exploring microalgal heterogeneity from fresh water samples collected from inland water bodies in the heavily built city of Singapore. Culturable pure isolates (n = 94) were subject to an in-house microalgal DNA extraction method and LSU rDNA sequencing. Isolates were analysed for their predominance and distribution. A total of 17 different algal genera were identified (H = 2.8, EH = 0.6), of which Scenedesmus spp. and Chlorella spp. constituted 27.5% and 21.3% of isolates respectively, followed by Micractinium spp. (18.8%) and Chlamydomonas spp. (12.5%). We also report 16 new microalgal strains from this region. The data is important from an ecological and biotechnological perspective.
Intraoperative ureter identification with a novel fluorescent catheter
Authors: Barberio Manuel , Al-Taher Mahdi , Felli Eric , Ashoka Anila Hoskere , Marescaux Jacques , Klymchenko Andrey , Diana Michele 
Published: February 2021

AbstractIatrogenic ureteral injuries (IUI) occur in 0.5–1.3% of cases during abdominal surgery. If not recognized intraoperatively, IUI increase morbidity/mortality. A universally accepted method to prevent IUI is lacking. Near-infrared fluorescent imaging (NIRF), penetrating deeper than normal light within the tissue, might be useful, therefore ureter visualization combining NIRF with special dyes (i.e. IRDye 800BK) is promising. Aim of this work is to evaluate the detection of ureters using stents coated with a novel biocompatible fluorescent material (NICE: near-infrared coating of equipment), during laparoscopy. female pigs underwent placement of NICE-coated stents (NS). NIRF was performed, and fluorescence intensity (FI) was computed. Successively, 0.15 mg/kg of IRDye 800BK was administered intravenously, and FI was computed at different timepoints. Ureter visualization using NS only was further assessed in a human cadaver. Both methods allowed in vivo ureter visualization, with equal FI. However, NS were constantly visible whereas IRDye 800BK allowed visualization exclusively during the ureteral peristaltic phases. In the human cadaver, NS provided excellent ureter visualization in its natural anatomical position. NS provided continuous ureteral visualization with similar FI as the IRDye 800BK, which exclusively allowed intermittent visualization, dependent on ureteral peristalsis. NS might prove useful to visualize ureters intraoperatively, potentially preventing IUI.
Universal probabilistic programming offers a powerful approach to statistical phylogenetics
Authors: Ronquist Fredrik , Kudlicka Jan , Senderov Viktor , Borgström Johannes , Lartillot Nicolas , Lundén Daniel , Murray Lawrence , Schön Thomas B. , Broman David 
Published: February 2021

AbstractStatistical phylogenetic analysis currently relies on complex, dedicated software packages, making it difficult for evolutionary biologists to explore new models and inference strategies. Recent years have seen more generic solutions based on probabilistic graphical models, but this formalism can only partly express phylogenetic problems. Here, we show that universal probabilistic programming languages (PPLs) solve the expressivity problem, while still supporting automated generation of efficient inference algorithms. To prove the latter point, we develop automated generation of sequential Monte Carlo (SMC) algorithms for PPL descriptions of arbitrary biological diversification (birth-death) models. SMC is a new inference strategy for these problems, supporting both parameter inference and efficient estimation of Bayes factors that are used in model testing. We take advantage of this in automatically generating SMC algorithms for several recent diversification models that have been difficult or impossible to tackle previously. Finally, applying these algorithms to 40 bird phylogenies, we show that models with slowing diversification, constant turnover and many small shifts generally explain the data best. Our work opens up several related problem domains to PPL approaches, and shows that few hurdles remain before these techniques can be effectively applied to the full range of phylogenetic models.
Limited window for donation of convalescent plasma with high live-virus neutralizing antibody titers for COVID-19 immunotherapy
Authors: Gontu Abhinay , Srinivasan Sreenidhi , Salazar Eric , Nair Meera Surendran , Nissly Ruth H. , Greenawalt Denver , Bird Ian M. , Herzog Catherine M. , Ferrari Matthew J. , Poojary Indira , Katani Robab , Lindner Scott E. , Minns Allen M. , Rossi Randall , Christensen Paul A. , Castillo Brian , Chen Jian , Eagar Todd N. , Yi Xin , Zhao Picheng , Leveque Christopher , Olsen Randall J. , Bernard David W. , Gollihar Jimmy , Kuchipudi Suresh V. , Musser James M. , Kapur Vivek 
Published: February 2021

AbstractMillions of individuals who have recovered from SARS-CoV-2 infection may be eligible to participate in convalescent plasma donor programs, yet the optimal window for donating high neutralizing titer convalescent plasma for COVID-19 immunotherapy remains unknown. Here we studied the response trajectories of antibodies directed to the SARS-CoV-2 surface spike glycoprotein and in vitro SARS-CoV-2 live virus neutralizing titers (VN) in 175 convalescent donors longitudinally sampled for up to 142 days post onset of symptoms (DPO). We observed robust IgM, IgG, and viral neutralization responses to SARS-CoV-2 that persist, in the aggregate, for at least 100 DPO. However, there is a notable decline in VN titers ≥160 for convalescent plasma therapy, starting 60 DPO. The results also show that individuals 30 years of age or younger have significantly lower VN, IgG and IgM antibody titers than those in the older age groups; and individuals with greater disease severity also have significantly higher IgM and IgG antibody titers. Taken together, these findings define the optimal window for donating convalescent plasma useful for immunotherapy of COVID-19 patients and reveal important predictors of an ideal plasma donor.
The SARS-CoV-2 induced targeted amino acid profiling in patients at hospitalized and convalescent stage
Authors: Wu Junfang , Zhao Mingming , Li Chenze , Zhang Yuxuan , Wang Dao Wen 
Published: February 2021

Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced an ongoing global health crisis. Here we utilized a combination of targeted amino acids (AAs) and clinical biochemical profiling to analyze the plasma of coronavirus disease 2019 (COVID-19) subjects at the hospitalization stage and 1-month post-infection convalescent stage, respectively, to investigate the systematic injury during COVID-19 disease progress. We found the virus-induced inflammatory status and reduced liver synthesis capacity in hospitalized patients, which manifested with increased branched-chain AAs (BCAAs), aromatic AAs (AAAs), one-carbon related metabolites, and decreased methionine. Most of these disturbances during infection recover except for the increased levels of medium-chain acylcarnitines (ACs) in the convalescent subjects, implying the existence of incomplete fatty acids oxidation during recovery periods. Our results suggested that the imbalance of the AA profiling in COVID-19 patients. The majority of disturbed AAs recovered in 1 month. The incomplete fatty acid oxidation products suggested it might take longer time for convalescent patients to get complete recovery.
Event‐triggered control of singularly perturbed linear system with DoS attacks
Authors: Ren Xiang , Hao Fei 
Published: February 2021

AbstractThis paper presents the event‐triggered control problem of linear singularly perturbed systems in the presence of denial‐of‐service attacks. To save the communication and computing resources, event‐triggered mechanisms in two transmission channels are used to guarantee the ultimately bounded stability of the closed‐loop system. Absolute event‐triggering conditions are proposed in the sensor and the controller nodes, where the controller node utilises only the state of the slow model of the singularly perturbed system. Positive lower bounds of inter‐event times are given to eliminate Zeno behaviour in the presence and absence of DoS attacks. Finally, two examples are provided to illustrate the efficiency and feasibility of the obtained results.
Analysis of Ill‐conditioning of hybrid state estimators in the presence of PMU measurements
Authors: Mallik Sanjeeb Kumar , Chakrabarti Saikat , Singh Sri Niwas 
Published: February 2021

AbstractIt has been observed by the practicing engineers that the inclusion of measurements from phasor measurement units (PMUs), current measurements in particular, into the conventional state estimators (SEs), may deteriorate the numerical performance of the SEs in terms of convergence and accuracy. This paper analyzes the reason for such possible ill‐conditioning of the hybrid SEs that use both conventional and PMU measurements. It presents simplified analytical approaches to identify what causes such ill‐conditioning when PMU measurements are used. The condition number of SE gain matrix may vary depending on the number of the PMUs and its placement in the network. It has been identified that the large difference in weights that are allocated to the traditional measurements and PMU measurements is the main reason of the ill‐conditioning of the hybrid SEs.