bluuebunny/crossref_metadata_2025_split huggingface dataset:
LCLS-II-HE Cryomodule Production Status at Fermilab
Authors: Kaluzny J , Arkan T , Bice D , Blowers J , Checchin M , Grimm C , Hartsell B , Martinello M , Nicol T , Posen S , Premo K 
Published: June 2022

Abstract
The Linac Coherent Light Source (LCLS) is an X-ray science facility at SLAC National Accelerator Laboratory. The LCLS-II project (an upgrade to LCLS) is in its final stages, and the LCLS-II-HE (High Energy) project is another upgrade to the facility enabling higher energy operation. An electron beam is accelerated using superconducting radio frequency (SRF) cavities built into cryomodules. It is planned to build twenty-five modules total for the LCLS-II-HE project. Fourteen of these modules are planned to be assembled and tested at Fermilab. Procurements for production modules have been awarded, and parts are arriving. The design of the LCLS-II-HE modules is similar to the module design used in LCLS-II. The major cryomodule design change from LCLS-II is the nominal gradient required per cavity, increasing from 16 to 21 MV/m. The additional gradient yields additional heat loads. The first LCLS-II-HE cryomodule, referred to as the verification cryomodule (vCM), was assembled using parts from an LCLS-II module with new SRF cavities. The assembly is complete, and this module is currently being tested at Fermilab. The vCM cavities perform well, exceeding the required gradient and quality factor specifications. The first article module assembly is planned to start later in 2021. The status of the production as well as some of the design and assembly changes will be presented.
Microwave Characterization of Gamma Ray Irradiated Thin Film Embedded and Non-embedded Nb Resonators
Authors: Yelamanchili Bhargav , Gupta Vaibhav , Zou Simin , Christiansen Robert , Cichon Max C. , Sellers John A. , Park Minseo , Mahjouri-Samani Masoud , Tuckerman David B. , Hamilton Michael C. 
Published: June 2022

Abstract
Gamma radiation effects on superconducting microwave transmission line structures, which may find use in future radiation challenging environments, such as satellites or accelerators have been investigated. Two versions of weakly coupled through-type Nb microstrip transmission line resonator material stack-ups were explored. In one version, the Nb signal trace was encapsulated with 20 µm of HD-4110 and in the other version the top Nb was not encapsulated. Exposure of the resonators to gamma radiation was performed for 28 days at room temperature in a sealed vacuum chamber using Co-60 as the gamma radiation source. The quality factors of the resonators were extracted at various cryogenic temperatures below the critical temperature of Nb and resonant frequencies up to 20 GHz. A large dose of gamma radiation used in this work showed a small change in the Nb superconducting properties.
Genetically encodable fluorescent protein markers in advanced optical imaging
Authors: Nienhaus Karin , Nienhaus Gerd Ulrich 
Published: June 2022

AbstractOptical fluorescence microscopy plays a pivotal role in the exploration of biological structure and dynamics, especially on live specimens. Progress in the field relies, on the one hand, on technical advances in imaging and data processing and, on the other hand, on progress in fluorescent marker technologies. Among these, genetically encodable fluorescent proteins (FPs) are invaluable tools, as they allow facile labeling of live cells, tissues or organisms, as these produce the FP markers all by themselves after introduction of a suitable gene. Here we cover FP markers from the GFP family of proteins as well as tetrapyrrole-binding proteins, which further complement the FP toolbox in important ways. A broad range of FP variants have been endowed, by using protein engineering, with photophysical properties that are essential for specific fluorescence microscopy techniques, notably those offering nanoscale image resolution. We briefly introduce various advanced imaging methods and show how they utilize the distinct properties of the FP markers in exciting imaging applications, with the aim to guide researchers toward the design of powerful imaging experiments that are optimally suited to address their biological questions.
Open-top light-sheet imaging of CLEAR emulsion for high-throughput loss-free analysis of massive fluorescent droplets
Authors: Jiang Wen , Chen Longbiao , Wang Jie , Shao Xinyang , Jiang Mengcheng , Chen Zitian , Wang Jianbing , Huang Yanyi , Fei Peng 
Published: June 2022

Abstract
Digital droplet PCR (ddPCR) is classified as the third-generation PCR technology that enables absolute quantitative detection of nucleic acid molecules and has become an increasingly powerful tool for clinic diagnosis. We previously established a CLEAR-dPCR technique based on the combination of CLEAR droplets generated by micro-centrifuge-based microtubule arrays (MiCA) and insitu 3D readout by light-sheet fluorescence imaging. This CLEAR-dPCR technique attains very high readout speed and dynamic range. Meanwhile, it is free from sample loss and contamination, showing its advantages over commercial d-PCR technologies. However, a conventional orthogonal light-sheet imaging setup in CLEAR d-PCR cannot image multiple centrifuge tubes, thereby limiting its widespread application to large-scale, high-speed dd-PCR assays. Herein, we propose an in-parallel 3D dd-PCR readout technique based on an open-top light-sheet microscopy setup. This approach can continuously scan multiple centrifuge tubes which contain CLEAR emulsions with highly diverse concentrations, and thus further boost the scale and throughput of our 3D dd-PCR technique.
Diverse densest ternary sphere packings
Authors: Koshoji Ryotaro , Ozaki Taisuke 
Published: June 2022

Abstract
The exploration of the densest structures of multi-sized hard spheres under periodic boundary conditions is a fundamental problem in mathematics and a wide variety of sciences including materials science. We present our exhaustive computational exploration of the densest ternary sphere packings (DTSPs) for 451 radius ratios and 436 compositions on top of our previous study [Koshoji and Ozaki, Phys. Rev. E 104, 024 101 (2021)]. The unbiased exploration by a random structure searching method discovers diverse 22 putative DTSPs, and thereby 60 putative DTSPs are identified in total including the 38 DTSPs discussed by the previous study. Some of the discovered DTSPs are well-ordered, for example, the medium spheres in the (9-7-3) structure are placed in a straight line with comprising the unit cell, and the DTSP has the

Pm

3

¯

m

symmetry if the structural distortion is corrected. At a considerable number of radius ratios, the highest packing fractions are achieved by the phase separations consisting of only the FCC and/or the putative densest binary sphere packings (DBSPs) for all compositions. The trend is becoming more evident as the small and medium spheres are getting larger, which suggests either the binary packings are actually the densest packings or that the dense ternary packings have unit cells larger than those in this study. On the other hand, the number of the DTSPs increase as the particle size of small spheres gets small. The structural diversity indicates that many unknown DTSPs may hide in a very narrow range of radius ratio where the size of small spheres is smaller due to the competition with respect to the packing fractions of many structural candidates. Finally, we discuss the correspondence of the DTSPs with real crystals based on the space group. Our study suggests that the diverse structures of DTSPs can be effectively used as structural prototypes for searching ternary, quaternary, and quinary crystal structures.
Spectroscopic investigation of tau protein conformational changes by static magnetic field exposure
Authors: Darwish Saqer M , Darwish Imtiaz M 
Published: June 2022

Abstract
Electromagnetic fields taint the molecular environment of proteins and induce changes in the central nervous system. This research applied Fourier transform infrared spectroscopic analysis to investigate the effects of static magnetic fields on tau protein in neurological disorders. It explores the conformational changes of tau protein and highlights its’ potential application as a pathological biomarker for early detection and therapeutic interventions. The results indicate that tau protein is susceptible to magnetic field exposure in the amide B, fingerprint, and amide regions (IV-VI). Changes in peak positions and band intensities were identified and delineated as the outcome effect of magnetic forces on molecular vibrations. Magnetic forces may affect the microtubule structure of the tau protein, leading to protein aggregation. These results indicate the potential application of FTIR spectroscopy for the early detection and classification of degenerative diseases through spectrum analysis. Different magnetic fields can be used as spontaneous therapeutic procedures to induce changes in the molecular environment of proteins.
Taguchi’s design optimization for finishing of plane surface with diamond-based sintered magnetic abrasives
Authors: Gill Jagdeep Singh , Singh Palwinder , Singh Lakhvir 
Published: June 2022

Abstract
The magnetic field-assisted abrasive finishing parameters used in this study were the distance of the workpiece from the magnetic pole (D), amount of sintered magnetic abrasives (A), speed of rotation of the pole (R), grain size of the abrasive particles (S) and feed to the workpiece (F). The surface roughness percentage change (SRPC) and material removal rate (MRR) of the plane surface workpiece of aluminum are the response quantities. An orthogonal L16 array of the Taguchi method was constructed and is used in this study to analyze the influence of finishing parameters on the surface roughness percentage change of the workpiece. The analysis of variance (ANOVA) showed the extent to which finishing parameters are important. The experimental results showed that for SRPC, the best combination of levels for the given control factors is the distance of the workpiece from the magnetic pole (D) = 4 mm, the amount of sintered magnetic abrasive (A) = 16 g, the speed of rotation of the pole (R) = 600 rpm, the grain size of the abrasive particles (S) = 175 μm and the feed rate of the workpiece (F) = 1.5 m min−1. For MRR, the best combination of levels for the given control factors is the distance of the workpiece from the magnetic pole (D) = 4 mm, the amount of sintered magnetic abrasive (A) = 16 g, the speed of rotation of the pole (R) = 400 rpm, the grain size of the abrasive particles (S) = 175 μm and the feed rate of the workpiece (F) = 6.0 m min−1. The surface profiles and microscopic images of polished and unpolished workpieces show that the magnetic field-assisted abrasive finishing process is very effective in finishing aluminum surfaces.
MSRCall: a multi-scale deep neural network to basecall Oxford Nanopore sequences
Authors: Yeh Yang-Ming , Lu Yi-Chang 
Published: June 2022

AbstractMotivationMinION, a third-generation sequencer from Oxford Nanopore Technologies, is a portable device that can provide long-nucleotide read data in real-time. It primarily aims to deduce the makeup of nucleotide sequences from the ionic current signals generated when passing DNA/RNA fragments through nanopores charged with a voltage difference. To determine nucleotides from measured signals, a translation process known as basecalling is required. However, compared to NGS basecallers, the calling accuracy of MinION still needs to be improved.ResultsIn this work, a simple but powerful neural network architecture called multi-scale recurrent caller (MSRCall) is proposed. MSRCall comprises a multi-scale structure, recurrent layers, a fusion block and a connectionist temporal classification decoder. To better identify both short-and long-range dependencies, the recurrent layer is redesigned to capture various time-scale features with a multi-scale structure. The results show that MSRCall outperforms other basecallers in terms of both read and consensus accuracies.Availability and implementationMSRCall is available at: https://github.com/d05943006/MSRCall.Supplementary informationSupplementary data are available at Bioinformatics online.
Actions of WNT family member 5A to regulate characteristics of development of the bovine preimplantation embryo
Authors: Jeensuk Surawich , Ortega M Sofia , Saleem Muhammad , Hawryluk Briana , Scheffler Tracy L , Hansen Peter J 
Published: June 2022

Abstract
WNT signaling is important for regulation of embryonic development. The most abundant WNT gene expressed in the bovine endometrium during the preimplantation period is WNT5A. One objective was to determine whether WNT5A regulates competence of the bovine preimplantation embryo to become a blastocyst and alters the number of cells in the inner cell mass and trophectoderm. A second objective was to delineate features of the cell-signaling mechanisms involved in WNT5A actions. WNT5A caused a concentration-dependent increase in the proportion of embryos developing to the blastocyst stage and in the number of inner cell mass cells in the resultant blastocysts. A concentration of 200 ng/mL was most effective, and a higher concentration of 400 ng/mL was not stimulatory. Bovine serum albumin in culture reduced the magnitude of effects of WNT5A on development to the blastocyst stage. WNT5A affected expression of 173 genes at the morula stage; all were upregulated by WNT5A. Many of the upregulated genes were associated with cell signaling. Actions of WNT5A on development to the blastocyst stage were suppressed by a Rho-associated coiled-coil kinase (ROCK) signaling inhibitor, suggesting that WNT5A acts through Ras homology gene family member A (RhoA)/ROCK signaling. Other experiments indicated that actions of WNT5A are independent of the canonical β-catenin signaling pathway and RAC1/c-Jun N-terminal kinase (JNK) signaling. This is the first report outlining the actions of WNT5A to alter the development of the mammalian embryo. These findings provide insights into how embryokines regulate maternal–embryonic communication.
Polyfunctional Antigen Specific CD4+ T cell Responses in Patients With Human Immunodeficiency Virus/AIDS and Histoplasmosis Immune Reconstitution Inflammatory Syndrome
Authors: Manion Maura , Boulougoura Afroditi , Naqvi Nuha , Lage Silvia Lucena , Richards Elizabeth , Grivas Christopher , Laidlaw Elizabeth , Kuriakose Safia , Ortega-Villa Ana M , Tadros Saber , Roby Gregg , Rupert Adam , Galindo France , Anderson Megan , Pau Alice , Deepe George , Sheikh Virginia , Sereti Irini 
Published: June 2022

Abstract
In the combination antiretroviral era, there are limited data regarding the pathogenesis of histoplasmosis immune reconstitution inflammatory syndrome (IRIS) in people with human immunodeficiency virus (HIV). We immunologically characterized 10 cases of histoplasmosis, 4 of whom developed histoplasmosis IRIS. CD4+ T cells in histoplasmosis IRIS demonstrated a significant polyfunctional cytokine response to histoplasma antigen.
Increased Mortality Among Persons With Symptomatic Coronavirus Disease 2019 (COVID-19) During the Period of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) B.1.617.2 (Delta Variant) Predominance: Alaska, November 2020–October 2021
Authors: Mooring Eric Q , Newell Katherine , Castrodale Louisa , Tompkins Megan , Frank Morgan , McLaughlin Joseph 
Published: June 2022

Abstract
We compared the mortality risk in Alaska among persons with symptomatic coronavirus disease 2019 (COVID-19) during the period the Delta variant was predominant to the risk among those with symptomatic COVID-19 before Delta predominance. The Delta period was associated with 2.43-fold higher odds of death. Unvaccinated persons were 4.49 times more likely to die than fully vaccinated persons.
Analysing region of attraction of load balancing on complex network
Authors: Zou Mengbang , Guo Weisi 
Published: June 2022

Abstract
Many complex engineering systems network together functional elements to balance demand spikes but suffer from stability issues due to cascades. The research challenge is to prove the stability conditions for any arbitrarily large and dynamic network topology with any complex balancing function. Most current analyses linearize the system around fixed equilibrium solutions. This approach is insufficient for dynamic networks with multiple equilibria, for example, with different initial conditions or perturbations. Region of attraction (ROA) estimation is needed in order to ensure that the desirable equilibria are reached. This is challenging because a networked system of non-linear dynamics requires compression to obtain a tractable ROA analysis. Here, we employ master stability-inspired method to reveal that the extreme eigenvalues of the Laplacian are explicitly linked to the ROA. This novel relationship between the ROA and the largest eigenvalue in turn provides a pathway to augmenting the network structure to improve stability. We demonstrate using a case study on how the network with multiple equilibria can be optimized to ensure stability.
‘To settle a governement without somthing of Monarchy in it’: Bulstrode Whitelocke’s Memoirs and the Reinvention of the Interregnum
Authors: Fitzgibbons Jonathan 
Published: June 2022

Abstract
The memoirs of the parliamentarian lawyer and MP Bulstrode Whitelocke are invaluable as a primary source for historians wishing to understand the political history of the 1640s and 1650s. Yet, despite broad recognition of the contentious nature of this material, surprisingly little has been done to establish the accuracy of Whitelocke’s account or to probe the motives behind the writing of his post-Restoration reflections. By focusing on Whitelocke’s recollections of two famous encounters with Oliver Cromwell in 1651 and 1652, this article demonstrates that there is much in the detail of those accounts that fails to convince in the light of what is known of events and the author’s activities from evidence beyond his memoirs. Rather, it seems that the accounts of these meetings were fabricated in order to obfuscate Whitelocke’s activities during the Interregnum period and to propagate a series of narratives that served the author’s purposes as he sought political rehabilitation after the Restoration of 1660. By failing to recognise the memory games at play in Whitelocke’s work, historians have unwittingly embedded many of those same narratives in their accounts of the period, not least concerning the durability of the regime established in 1649 and Cromwell’s kingly ambitions.
Impact of society and national guidelines on patient selection for lung cancer surgery in the United Kingdom
Authors: Pons Aina , De Sousa Paulo , Proli Chiara , Booth Sarah A , Palmares Abigail , Leung Maria , Alshammari Abdullah , Vlastos Dimitrios , Raubenheimer Hilgardt , Devbhandari Mohan , Patel Anant , Lim Eric 
Published: June 2022

Abstract

OBJECTIVES
We sought to evaluate the impact of different national clinical guidelines (with consistent and conflicting recommendations) on clinician’s practice in the UK.

METHODS
In this cohort study, we analysed data from National Lung Cancer Audit comprising all patients diagnosed with lung cancer between 2008 and 2013 within England and Wales for consistent (British Thoracic Society and National Institute of Clinical Excellence) recommendations for lower/more permissive lung function but opposing stage (N2) selection parameters for surgery.

RESULTS
From 2008 to 2013, data from 167 192 patients with primary lung cancers were included. The proportion of patients undergoing surgery for lung cancer increased from 9.5% to 20.5% in 2013 (P &lt; 0.001) as the number of general thoracic surgeons in the UK increased from 40 to 81 in the corresponding timeframe. Mean forced expiratory volume in 1 s of surgical patients increased from 76% (22) to 81% (22) in 2013 (P &lt; 0.001). Of the patients undergoing surgery, the proportion of patients with N2 disease across the 6-year interval was broadly consistent between 8% and 11% without any evidence of trend (P = 0.125).

CONCLUSIONS
Within 3 years of new clinical guideline recommendations, we did not observe any overall change suggesting greater selection for surgery on lower levels of lung function. When presented with conflicting recommendation, no observable change in selection was noted on surgery for N2 disease. The observed increase in surgical resection rates is more likely due to greater access to surgery (by increasing number of surgeons) rather than any impact of guideline recommendations.
Antibiotic tolerance in environmentally stressedBacillus subtilis: physical barriers and induction of a viable but nonculturable state
Authors: Morawska Luiza P , Kuipers Oscar P 
Published: June 2022

AbstractBacterial communities exposed to rapid changes in their habitat encounter different forms of stress. Fluctuating conditions of the microenvironment drive microorganisms to develop several stress responses to sustain growth and division, like altering gene expression and changing the cell's physiology. It is commonly known that these protection systems may give rise to differently adapted subpopulations and indirectly impact bacterial susceptibility to antimicrobials. This study focuses on the adaptation of a soil-dwelling bacterium, Bacillus subtilis, to sudden osmotic changes, including transient and sustained osmotic upshift. Here, we demonstrate that physiological changes caused by pre-exposure to osmotic stress facilitate B. subtilis' entry into a quiescent state, helping them survive when exposed to a lethal antibiotic concentration. We show that the adaptation to transient osmotic upshift with 0.6 M NaCl causes decreased metabolic rates and lowered antibiotic-mediated ROS production when cells were exposed to the aminoglycoside antibiotic kanamycin. Using a microfluidic platform combined with time-lapse microscopy, we followed the uptake of fluorescently labelled kanamycin and examined the metabolic activity of differently preadapted populations at a single-cell level. The microfluidics data revealed that under the conditions tested, B. subtilis escapes from the bactericidal activity of kanamycin by entering into a nongrowing dormant state. Combining single-cell studies and population-wide analysis of differently preadapted cultures, we demonstrate that kanamycin-tolerant B. subtilis cells are entrapped in a viable but nonculturable (VBNC) state.