bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses
Authors: Lui Lauren M. , Nielsen Torben N. 
Published: August 2024

ABSTRACT

Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic and viral genomes. This study focuses on decomposing an estuarine metagenome to obtain a more accurate estimate of microbial diversity. To achieve this, we developed a new bead-based DNA extraction method, a novel bin refinement method, and obtained 150 Gbp of Nanopore sequencing. We estimate that there are ~500 bacterial and archaeal species in our sample and obtained 68 high-quality bins (>90% complete, <5% contamination, ≤5 contigs, contig length of >100 kbp, and all ribosomal and tRNA genes). We also obtained many contigs of picoeukaryotes, environmental DNA of larger eukaryotes such as mammals, and complete mitochondrial and chloroplast genomes and detected ~40,000 viral populations. Our analysis indicates that there are only a few strains that comprise most of the species abundances.

IMPORTANCE
Ocean and estuarine microbiomes play critical roles in global element cycling and ecosystem function. Despite the importance of these microbial communities, many species still have not been cultured in the lab. Environmental sequencing is the primary way the function and population dynamics of these communities can be studied. Long-read sequencing provides an avenue to overcome limitations of short-read technologies to obtain complete microbial genomes but comes with its own technical challenges, such as needed sequencing depth and obtaining high-quality DNA. We present here new sampling and bioinformatics methods to attempt decomposing an estuarine microbiome into its constituent genomes. Our results suggest there are only a few strains that comprise most of the species abundances from viruses to picoeukaryotes, and to fully decompose a metagenome of this diversity requires 1 Tbp of long-read sequencing. We anticipate that as long-read sequencing technologies continue to improve, less sequencing will be needed.
Double subduction controls on long-lived continental tectonics and subcontinental mantle temperatures
Authors: Li Lin-Sen , Capitanio Fabio A. , Cawood Peter A. , Wu Ben-Jun , Zhai Ming-Guo , Wang Xiao-Lei 
Published: August 2024

Abstract
The complexities of convergent margins commonly include the interactions of subduction zones, with many geological records of “double” subduction. Here, we build two-dimensional numerical models to explore the evolution of complex subduction systems by systematically testing single and inward-dipping double subduction beneath a continental upper plate and the impact of continental collision on these systems. When compared to single subduction models, the inward-dipping double subduction shows hindered trench migrations and larger volumes of upwelling mantle enhanced by excess sinking slab mass. Double subduction draws larger volumes of hotter mantle beneath the continent in an area much broader than the marginal basins of single subductions, contributing to subcontinental heating by ~200 °C. As collision jams one margin of a double subduction system, the other margin follows the evolution of migrating single subduction zones, although characterized by persisting higher mantle temperatures and strong upwellings, inherited from the double subduction stage, and large-scale upper plate extension. The modeling outcomes are compared to scaling arguments to test the viability of the mechanism proposed for tectonics of the Cenozoic South China Sea and Neoproterozoic Yangtze Block (southeastern China), where the inward-dipping double subduction provides a context for protracted large-scale continental extension, hotter subcontinental temperatures, and channeled mantle flow not easily reconciled with the dynamics of single subduction zones.
Limits of Laser Cooling of Light Alkali Metals in a Polychromatic Light Field
Authors: Ilenkov R. Ya. , Prudnikov O. N. , Taichenachev A. V. , Yudin V. I. 
Published: August 2024

Abstract
A model was developed for laser cooling of alkali atoms in a polychromatic field, considering the real structure of atomic levels. The model was tested by the example of the 6Li atom. The minimum achievable temperatures of laser cooling of light alkali atoms were studied for different polarizations of the light field components, and the possibility of cooling below the Doppler limit was shown.
Breast phyllodes tumour with epithelioid feature predisposes to malignant transformation
Authors: Shao Mumin , Zhang Lu , Li Xia , Bi Jiaxin , Jiang Xu , Yu Xuewen , Liang Yingying , Xu Hua , Meng Gang , Gong Xiyu 
Published: August 2024

AimsPhyllodes tumours (PTs) are relatively common fibroepithelial tumours comprising epithelial and stromal component. Usually, PTs show a spindle cell morphology with a fibroblast phenotype, while some tumour cells exhibit epithelioid morphological features and sarcomatoid transformation. However, the molecular characteristics of this morphology subset remain unclear. This study aimed to summarise the clinicopathological, morphological and molecular characteristics of seven cases of PT with epithelioid features.MethodsMorphological and clinicopathological characteristics were observed and retrieved. Immunohistochemistry, immunofluorescence and electron microscope were performed on seven cases of epithelioid PT to explore immunophenotypic and ultrastructural characteristics. Transcriptomic and proteomic analyses were conducted to compare differentially expressed genes and proteins between epithelioid PT and classical PT.ResultsPatients with epithelioid PT exhibit a high recurrence rate (42.8%). Morphologically, in addition to having epithelioid cytological features, neoplastic stromal cells exhibit moderate to marked atypia and often exhibit sarcomatoid transformation, similar to the characteristics of borderline PT. Transcriptomic and proteomic analyses demonstrated that epithelioid PTs are distinct from classical PTs in gene expression and protein abundance levels. Immunohistochemical analysis showed that among all differentially expressed proteins, epithelioid PT showed abnormal p16/retinoblastoma expression patterns, similar to those of malignant PT.ConclusionsEpithelioid PT has unique morphological characteristics, biological behaviour and protein expression profile, which meets the diagnostic criteria of borderline PT and is prone to sarcomatoid transformation. It may be a special morphological subgroup of borderline PT and has partial characteristics of malignant PT, which should be taken seriously in pathological diagnosis and clinical management.
Assessing IgG4-related ophthalmic disease and its mimics: a comparison of ACR/EULAR, organ-specific and revised comprehensive diagnostic criteria
Authors: Bakshi Neha , Aggarwal Aditi , Dhawan Shashi , Grover A K , Duggal Lalit , Badwal Sonia , Rao Seema 
Published: August 2024

AimsDiagnosis of IgG4-related ophthalmic disease (IgG4-ROD) rests on the correlation of clinical features, serological testing and histopathology, using internationally accepted diagnostic criteria for objective interpretation; however, several mimickers of IgG4-RD overlap in clinical presentation and histopathology. We assess histopathological features in a series of presumptive IgG4-ROD cases, with emphasis on histopathological mimics and comparison of three IgG4-ROD diagnostic/classification criteria (organ-specific (OS), revised comprehensive diagnostic (RCD) and American College of Rheumatology/European Alliance of Associations for Rheumatology (ACR/EULAR) criteria).MethodsThe histopathology database was screened for cases with clinical/histopathological suspicion of IgG4-ROD. Slides were reviewed, OS, RCD and ACR/EULAR criteria were applied, and the final clinicopathological diagnosis was recorded.Results37 patients (24 females, 13 males; 19–73 years) were diagnosed as either IgG4-ROD (n=18) or non-IgG4-related disease (n=19). Non-IgG4-related disease group showed elevated serum IgG4 (55.5%), fibrosis (100%), dense lymphoplasmacytic inflammation (92.8%), with an increase in tissue IgG4+plasma cells (57.1%) and elevated IgG4:IgG+plasma cell ratio (14.3%). ACR/EULAR missed 50% (9/18, sensitivity—52.8%) of true IgG4-ROD cases, while OS and RCD criteria missed 11.1% (2/18, sensitivity—88.9%) of IgG-ROD cases. ACR/EULAR criteria mislabelled 7.14% (1/14, specificity—90.9%) while OS and RCD criteria wrongly categorised 71.4% (10/14, specificity—47.4%) and 50% (7/14, specificity—63.2%) specific non-IgG4-ROD cases as IgG4-ROD. Storiform fibrosis, obliterative phlebitis, increased IgG4:IgG+plasma cell ratio and elevated serum IgG were statistically significant in distinguishing IgG4-ROD from its mimics.ConclusionACR/EULAR criteria showed high specificity but were cumbersome and sensitivity was low, while RCD and OS criteria showed low specificity. Stringent clinicopathological correlation to exclude mimics is critical in avoiding diagnostic errors in IgG4-ROD.
‘Gout was like the boss’. A qualitative study exploring the impact of gout on employment
Authors: Diaz-Torne Cesar , Pou Maria Antonia , Horne Anne , Gasteiger Chiara , Dalbeth Nicola 
Published: August 2024

ObjectivePrevious research has identified that gout impacts various domains of daily life. However, there have been no qualitative studies focusing on employment. This study aimed to understand the impact of gout on employment.MethodsSemistructured interviews were conducted in Spain and Aotearoa/New Zealand, in people with gout (according to the 2015 American College of Rheumatology/European Alliance of Associations for Rheumatology criteria) who had experienced a gout flare during their employment. The interviews were guided by questions exploring the impact on employment, job changes, disclosure and co-workers’ reactions. Data were analysed thematically.ResultsEighteen participants were interviewed (89% male, mean age 52.9 years). Six themes were identified. The characteristics of the disease (pain intensity, tophi and joints affected) and the job itself (including physical job requirement and workplace flexibility) determined the experience of working with gout. The experiences were divided into physical (from total incapacity to working despite pain), emotional (feeling responsible, embarrassment, guilt and depression) and social (including disclosure responses and financial impact). Gout management strategies including rapid gout flare management and urate-lowering therapy reduced the number of flares and the intensity of pain, and allowed work attendance and participation.ConclusionBoth gout and work characteristics influence the employment experience for people with gout. Effective management of gout led to improved work experiences in all its domains.
Current-Dependent Lithium Metal Microstructure in ‘Anode-Free’ Solid-State Batteries at the Steel|LPSCI Interface
Authors: Becker Juri , Fuchs Till , Richter Felix H. , Janek Jürgen 
Published: August 2024

Further improvement of energy densities of state-of-the-art batteries could be achieved with the utilization of lithium metal anodes.1 Due to the reactivity of the alkali metal, the fabrication process needs to be monitored carefully. To circumvent degradation during storage as well as the handling of lithium metal, reservoir-free cells (RFCs) are investigated.2 Using accessible lithium stored within lithiated cathode materials, the lithium anode is formed in a formation step during the first charging cycle. The electrochemical properties of the electrodeposited lithium film are strongly dependent on its microstructure, and can, for example, influence the resoluble amount of lithium during subsequent cycling.3,4 Until now, the microstructure of electrodeposited lithium and how to control it is elusive.
To observe and characterize the microstructure of electrodeposited lithium at the stainless steel|LPSCl interface, a combination of electrochemical impedance spectroscopy, focused ion beam and scanning electron microscopy as well as electron backscatter diffraction was used. With this setup, the correlation between deposition current density and resulting microstructure of the lithium film was investigated. For higher current densities, a twenty times smaller grain size was observed, while the grain density showed a twelvefold increase, which could have a major influence on the subsequent dissolution of lithium. Furthermore, the microstructural evolution during prolonged lithium deposition was investigated.
1 J. Janek and W. G. Zeier, Nat. Energy, 2016, 1, 16141.
2 M. J. Wang, E. Carmona, A. Gupta, P. Albertus and J. Sakamoto, Nat Commun., 2020, 11, 1–9.
3 S. E. Sandoval and M. T. McDowell, Matter, 2023, 6, 2101–2102.
4 D. K. Singh, T. Fuchs, C. Krempaszky, B. Mogwitz, S. Burkhardt, F. H. Richter and J. Janek, Adv. Funct. Mater., 2023, 33, 2211067.
The Importance of Adhesion in Solid-State Batteries
Authors: Tsai Wan-Yu , Owensby Kyra D'Yana , Sahore Ritu , Browning Katie , Kalnaus Sergiy , Westover Andrew S , Chen Xi Chelsea 
Published: August 2024

Solid-state batteries are one of the key technologies to expedite the electrification of the economy. Compared with traditional liquid electrolytes, solid-state electrolytes are intrinsically safer and can enable high-energy designs by pairing with high-capacity cathodes and lithium metal anodes. However, maintaining the solid/solid contact between electrode and electrolyte during electrochemical cycling is non-trivial and the main challenge for all-solid-state batteries. The common strategy for combatting the contact issue is applying stack pressure, which is a sort of scientific shortcut that masks the real challenges of maintaining good contact between the different electrodes and electrolytes. Improving the adhesion between different battery components is a more effective and commercially viable strategy. We hypothesized that increasing the adhesion between electrode and electrolyte will improve electrode integrity, mitigate contact loss, and increase Coulombic efficiency and cycle life.
There are very few studies on the adhesion of battery materials. This is primarily due to limited techniques to measure adhesion at the nanometer and micrometer scales relevant to the battery operation. In this work, we proposed to use atomic force microscopy (AFM) with customized probes to investigate adhesion between a model solid polymer electrolyte (SPE) consisting of crosslinked poly(ethylene oxide) (xPEO) and lithium bis(trifluoromethanesulfonyl)imide (LiTFSI), and a model cathode active material, LiNi0.6Mn0.2Co0.2O2 (NMC622). We showed that a two-fold increase in polymer stiffness (storage shear modulus, G’) from increasing the crosslinking density, leads to a 40% reduction in the bulk ionic conductivity in the SPE. However, we show evidence that this trade-off relationship between stiffness and ionic conductivity does not significantly impact the battery performance. In drastic contrast, it leads to a decrease in the work of adhesion at the electrolyte|cathode interface, which has a profound impact on the resulting discharge capacity of the battery. How the crosslinking density of the polymer affects the NMC-xPEO adhesion at the microscale and how this affects battery performance remain open questions, which the authors wish to gain insight into from the discussions.
Understanding Electrode-Electrolyte Interfaces in Gel Polymer Electrolytes Using in-Operando Raman Spectroscopy
Authors: Pereira Rhyz , Yim Taber , Dopilka Andrew , Kostecki Robert , Kalra Vibha 
Published: August 2024

Gel polymer electrolytes hold enormous potential for advancing battery performance and technology, promising high energy densities and safe, rechargeable quasi solid-state batteries. GPEs offer higher ionic conductivities than solid electrolytes and enhanced safety in comparison to liquid electrolytes. A particular advantage of these electrolytes has been their ability to create robust electrode electrolyte interfaces that guide uniform deposition and stripping of lithium via their mechanical strength from the polymer and interface species that form during initial cycling.
Herein we report that 1:1 dimethoxyethane (DME) and dioxolane (DOL) with lithium bistrifluoromethanosulfonyl imide (LiTFSI) and lithium nitrate entrapped in Poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) gel polymer electrolytes have shown stability for up to 500 hours in lithium metal symmetric cells at 1 mAh/cm2 and performs at 5mAh/cm2 in dynamic symmetric cell cycling. To understand the fundamental interfacial phenomenon governing lithium deposition and growth in this system in-operando Raman was conducted on an anodeless Cu|PVDF-HFP|Li cell. Copper was sputtered onto the polymer electrolyte before assembly with a thickness of 20nm, providing an optically transparent electrode through which the Raman laser could pass through to detect interfacial species. We observe that PVDF-HFP acted as a chemically stable polymer electrolyte while Raman shifts associated with TFSI anions disappear near the electrode surface. The spectral and electrochemical data allow us to build a model for the growth and evolution of interfaces in an anodeless lithium metal battery cell with a GPE.
Acknowledgement:

This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists, Office of Science Graduate Student Research (SCGSR) program. The SCGSR program is administered by the Oak Ridge Institute for Science and Education for the DOE under contract number DE‐SC0014664.

Figure 1
Microstructure Evolution of Electrodeposited Magnesium on Copper Current Collector during Cycles for Anode-Free Rechargeable Magnesium Battery
Authors: Tsai Wei-Shiang , Wu Ying-Chen , Huang Yu-Shan , Chu Peng-Wei 
Published: August 2024

Rechargeable magnesium (Mg) batteries attract lots of interest owing to their high theoretical volumetric energy density and low cost from the natural abundance of Mg. Additionally, Mg is less prone to dendrite growth during charging, which improves the battery safety. However, rechargeable Mg battery systems suffer from sluggish reaction kinetics on the electrodes and poor cycle life, greatly limiting their practical competitiveness. While most studies of rechargeable Mg batteries focus on the development of electrolytes and their feasibilities, the microstructure evolution of the Mg metal anodes during cycles is not fully unveiled. Furthermore, when using Mg metal as the anode, the excessive Mg may limit the overall energy density of the cells. Recently, anode-free battery systems were introduced to further improve the battery capacity. In this report, we investigated anode-free rechargeable magnesium batteries by electrodepositing Mg on a copper (Cu) current collector in an all phenyl complex (APC) electrolyte. Afterward, the microstructure evolution of the electrodeposited Mg after discharge/charge cycles was studied.
The electrodeposited Mg on the Cu current collector with a current density of 2.25 mA/cm2 and a capacity of 1.5 mAh/cm2 shows a uniform distribution of Mg grains with an average grain size of 1.14 ± 0.06 μm. Subsequent Mg stripping with half the deposited capacity (0.75 mAh/cm2) was conducted at various current densities. Stripping with intermediate current density (0.75 mA/cm2) results in non-uniform discharge holes and possible local exposure of the Cu current collector, which could deteriorate the anode integrity. In contrast, the stripped electrodeposited Mg at relatively large (2.25 mA/cm2) and small (0.25 mA/cm2) discharge current densities show dense and uniform discharged holes on the surface. After prolonged discharge/charge cycles at a relatively large current density (2.25 mA/cm2), the electrodeposited Mg still exhibits a uniform surface morphology. In addition to cycling the electrodeposited Mg, a Mg-sulfur (Mg-S) full cell was also assembled with an anode of electrodeposited Mg on Cu and a sulfur/graphite cathode to explore the potential of anode-free rechargeable Mg-S battery.

Figure 1
On the Correlation of Kramers-Kronig (KK) Analysis and Non-Linear Harmonic Analysis (NHA)
Authors: Katırcı Gökberk , Civan Fazlı Eren , Ülgüt Burak 
Published: August 2024

Primary lithium batteries are known for their elevated volumetric and gravimetric energy densities and production cost efficiency. Within this category, lithium thionyl chloride (Li/SOCl2) batteries exhibit a constant discharge voltage (~3.6 V) and a broad operational temperature range (-50ᵒC to 80ᵒC). Moreover, forming a LiCl passivation layer on the metallic Li anode can extend its shelf-life up to 20 years at optimal storage temperature. These characteristics render lithium thionyl chloride batteries applicable in military and security applications, microcomputers, measurement devices, and medical instruments. Therefore, the characterization of lithium thionyl chloride batteries accurately has the utmost importance. Understanding the critical electrochemical processes that occur inside the battery without damaging or disassembling the cell requires delicate techniques.
EIS has emerged as a non-destructive and in-situ measurement technique with increasing popularity. Essential battery properties can be derived from EIS data. The credibility of EIS data, considering linearity, causality, and stability, can be verified through Kramers-Kronig relations. The obtained spectrum is fitted with an optimal number of Voigt elements (RC components in parallel)[1]. Given the linearity and stability of these individual Voigt elements, the entire spectrum should exhibit linearity if it is Kramers-Kronig compatible[2].
Non-linear harmonic analysis (NHA) is a complementary technique to EIS, wherein the response signal undergoes conversion from the time domain to the frequency domain through Fast Fourier Transformation (FFT). While EIS employs a single-phased pure sinusoidal signal as the input, the response includes a fundamental frequency and harmonics at integer frequencies of this fundamental response signal. NHA can be utilized in the diagnosis of non-linear, non-stationary situations alongside the identification of drift and initial transients.
This study first explains a new EIS measurement method for Li/SOCl2 batteries and Li/SOCl2/SO2Cl2 mixture batteries. The new method describes the solid electrolyte interface (SEI) stability of the batteries and the modifications needed to get KK-compatible results. After that, the equivalent circuit fits applied to the acquired spectra. Essential battery parameters such as solution resistance, charge transfer resistance, and double-layer capacitance were calculated. Kramers-Kronig analysis of the batteries was conducted, and the residuals of the fits were investigated. Subsequently, the NHA of the batteries was examined and compared to the Kramers-Kronig residuals. A correlation between the residuals and NHA of the batteries was extended based on the terms "KK-compatible" and "non-KK-compatible" in comparing KK-residuals and NHA results.
[1] Boukamp, B. A. , Journal of the Electrochemical Society 142.6 (1995): 1885.
[2] Agarwal, et al., Journal of the Electrochemical Society 142.12 (1995): 4159.

Figure 1