bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum chip design optimization and automation in superconducting coupler architecture
Authors: Li Fei-Yu , Jin Li-Jing 
Published: July 2023

Abstract
Superconducting coupler architecture demonstrates great potential for scalable and high-performance quantum processors, yet how to design efficiently and automatically ‘Qubit–Coupler–Qubit (QCQ)’ of high performance from the layout perspective remains obscure. In this work, this issue is studied for the first time resulting in three key findings. Firstly, we acquire the crucial zero-coupling condition that is only dependent on the geometric design of the layout. Secondly, the upper bound of the qubit–qubit effective coupling is found as

0.0822

ω
l

/

β
s
2

which surprisingly depends only on the artificially pre-decided quantities

ω
l

,

β
s

instead of specific layouts. Thirdly, we propose an optimal layout design procedure to reach the very upper bound, leading to efficient and high-performance layout design. The effectiveness of the procedure has been demonstrated scrupulously using electromagnetic simulation experiments. As a stirring application, we report a state-of-the-art 3202 um long-range and scalable QCQ layout that is especially crucial to quantum error correction. Our work provides practical guides to optimize the performance of the existing coupler architecture, find out novel layouts, and further advance the progress of quantum chip design automation.
Addendum for: “Solar cell parameter accuracy improvement, via refinement of the Co-Content function. Part 2: Discussion on the experimental application” (2022 Eng. Res. Express
4 015020)
Authors: Rangel-Kuoppa Victor Tapio 
Published: July 2023

Abstract
This paper is an addendum to reference (Rangel-Kuoppa 2022 Eng. Res. Express 4 015020), in which the deduction of the five solar cell parameters, through the polynomial fitting of Co-content function

CC

V
,
I

=

∫

0

V

I
−

I

sc

dV

(

I

sc

=
I
(
V
=
0
)

), was reported, as a function of a constant percentage noise (

p

n

) of the maximum measured constant, i.e., I

max
, and the number of measured points per voltage (

P

V

). In this addendum, the extraction of the five solar cell parameters is researched, in the 0 V to open-circuit voltage range, for the illumination case, as a function of

P

V

,

and a p

n
of the

I

sc

.
Two birds with one stone: integrated assessment of coronary physiology and plaque vulnerability from a single angiographic view—a case report
Authors: Fezzi Simone , Huang Jiayue , Wijns William , Tu Shengxian , Ribichini Flavio 
Published: July 2023

Abstract

Background
Physiology-guided coronary revascularization was shown to improve clinical outcomes in multiple patient subsets, whilst in those presenting with acute coronary syndromes, it seems to be associated with an excess of cardiovascular events. One of the major drawbacks in this setting is the potential deferral of non–flow-limiting but ‘vulnerable’ coronary plaques.

Case summary
A 40-year-old patient presented with a myocardial infarction without ST-segment elevation (NSTEMI). At the invasive coronary angiography (ICA) a sub-occlusive stenosis on his left circumflex artery was detected and treated with percutaneous coronary intervention (PCI). The treatment of a concomitant intermediate eccentric focal stenosis on the right coronary artery (RCA) was deferred after a negative pressure wire–based physiological assessment. The patient was re-admitted 9 months later due to a recurrent NSTEMI, and a severe progression of the deferred RCA lesion was found at the ICA. In retrospect, an angiography-based assessment of physiological severity and plaque vulnerability of the non-culprit RCA stenosis by means of Murray’s law–based QFR (μQFR) and radial wall strain (RWS) was performed. At baseline, μQFR value (0.90) corroborated the non-ischaemic findings of wire-based assessment. However, RWS analysis showed a marked hotspot (maximum RWS value 27.7%), indicating the presence of a vulnerable plaque.

Discussion
Radial wall strain is a novel biomechanical deformation index derived from coronary angiography. Segments with high RWS are associated with lipid-rich plaques that are prone to progression and plaque rupture. Therefore, the identification of RWS hotspots might potentially improve the risk stratification of non-culprit lesions and empower secondary prevention strategies.
Chromosome-level reference genomes of two imperiled desert fishes: spikedace (Meda fulgida) and loach minnow (Tiaroga cobitis)
Authors: Alexandre Nicolas M , Cameron Alexander C , Tian David , Chatla Kamalakar , Kolora Sree R R , Whiteman Noah K , Turner Thomas F , Reinthal Peter N 
Published: July 2023

Abstract
North American minnows (Cypriniformes: Leuciscidae) comprise a diverse taxonomic group, but many members, particularly those inhabiting deserts, face elevated extinction risks. Despite conservation concerns, leuciscids remain under sampled for reference assemblies relative to other groups of freshwater fishes. Here, we present 2 chromosome-scale reference genome assemblies spikedace (Meda fulgida) and loach minnow (Tiaroga cobitis) using PacBio, Illumina and Omni-C technologies. The complete assembly for spikedace was 882.1 Mb in total length comprised of 83 scaffolds with N50 = 34.8 Mb, L50 = 11, N75 = 32.3 Mb, and L75 = 18. The complete assembly for loach minnow was 1.3 Gb in total length comprised of 550 scaffolds with N50 = 48.6 Mb, L50 = 13, N75 = 42.3 Mb, and L75 = 20. Completeness assessed via Benchmarking Universal Single-Copy Orthologues (BUSCO) metrics using the Actinopterygii BUSCO database showed ∼97% for spikedace and ∼98% for loach minnow of complete BUSCO proportions. Annotation revealed approximately 32.58 and 29.04% of spikedace and loach minnow total genome lengths to be comprised of protein-coding genes, respectively. Comparative genomic analyses of these endangered and co-distributed fishes revealed widespread structural variants, gene family expansions, and evidence of positive selection in both genomes.
Quantifying the impact of the COVID-19 pandemic on cancer center clinical trial operations
Authors: George Thomas J , Lin Tara L , Adrales Bentz Tricia , Grant Stefan , Houston Collette M , Nashawati Melissa A , Pappu Bhanu , Peck Helen , Zafirovski Alex , Kerstann Kimberly , LoRusso Patricia , Schnatterly Anne , Hofacker Janie , Cameron Kendra , Honeycutt Hailey , Werner Theresa L 
Published: July 2023

Abstract

Background
Oncology clinical trials are complex, and the COVID-19 pandemic caused major disruptions in 2020.

Methods
Using its networking and sharing of best practices, the Association of American Cancer Institutes, comprising 105 cancer centers, solicited a longitudinal series of voluntary surveys from members to assess how clinical trial office operations were affected. The surveys showed that centers were able to keep oncology trials available to patients while maintaining safety. Data were collected regarding interventional clinical trial accruals for the calendar years 2019, 2020, and 2021.

Results
Data demonstrated a sizeable decrease in interventional treatment trial accruals in both 2020 and 2021 compared with prepandemic figures in 2019. No cancer center reported an increase in interventional treatment trial accruals in 2020 compared with 2019, with most centers reporting a moderate decrease. In mid-2022, 15% of respondents reported an increasing trend, 31% reported no significant change, and 54% continued to report a decrease.

Conclusions
The pandemic necessitated rapid adoption of trial operations, with the emergence of several best practices, including remote monitoring, remote consenting, electronic research charts, and work-from-home strategies for staff. The national infrastructure to conduct trials was significantly affected by the pandemic, with noteworthy resiliency, evidenced by improvements in efficiencies and patient-centered care delivery but with residual capacity challenges that will be evident for the foreseeable future.
Ureteral reconstruction with appendiceal interposition graft following resection of retroperitoneal leiomyosarcoma
Authors: Williams Taylor R , Diallo Ismael , Issa Muta , Massarweh Nader N 
Published: July 2023

Abstract
Ureteral defects can be repaired using a variety of different techniques that depend on the length and position of the defect. Here we describe a case where a long, upper-ureteral defect was successfully reconstructed using an appendiceal interposition graft. A 60-year-old female patient underwent resection of a right-sided retroperitoneal leiomyosarcoma that was encasing the entire upper ureter and obstructing the right kidney. The mass was resected en bloc, leaving behind an 11 cm ureteral defect. The defect was successfully reconstructed with an appendiceal interposition graft. Appendiceal interposition grafts are a feasible and effective approach for ureteral reconstruction in adults following oncologic resection. We describe various technical aspects that optimize the success of ureteral reconstruction.
Current and emerging deep-learning methods for the simulation of fluid dynamics
Authors: Lino Mario , Fotiadis Stathi , Bharath Anil A. , Cantwell Chris D. 
Published: July 2023

Over the last decade, deep learning (DL), a branch of machine learning, has experienced rapid progress. Powerful tools for tasks that have been traditionally complex to automate have been developed, such as image synthesis and natural language processing. In the context of simulating fluid dynamics, this has led to a series of novel DL methods for replacing or augmenting conventional numerical solvers. We broadly classify these methods into physics- and data-driven methods. Physics-driven methods, generally, tune a DL model to provide an analytical and differentiable solution to a given fluid dynamics problem by minimizing the residuals of the governing partial differential equations. Data-driven methods provide a fast and approximate solution to any fluid dynamics problem that shares some physical properties with the observations used when tuning the DL model’s parameters. Meanwhile, the symbiosis of numerical solvers and DL has led to promising results in turbulence modelling and accelerating iterative solvers. However, these methods present some challenges. Exclusively data-driven flow simulators often suffer from poor extrapolation, error accumulation in time-dependent simulations, as well as difficulties in training against turbulent flows. Substantial effort is, therefore, being invested into approaches that may improve the current state of the art.
High resolution spatial investigation of intracellular oxygen in muscle cells
Authors: Penjweini Rozhin , Pasut Alessandra , Roarke Branden , Alspaugh Greg , Sackett Dan L. , Knutson Jay R. 
Published: July 2023

ABSTRACTMolecular oxygen (O2) is one of the most functionally relevant metabolites. O2is essential for mito-chondrial aerobic respiration. Changes in O2affect muscle metabolism and play a critical role in the maintenance of skeletal muscle mass, with lack of sufficient O2resulting in detrimental loss of muscle mass and function. How exactly O2is used by muscle cells is less known, mainly due to the lack of tools to address O2dynamics at the cellular level. Here we discuss a new imaging method for the real time quantification of intracellular O2in muscle cells based on a genetically encoded O2-responsive sensor, Myoglobin-mCherry. We show that we can spatially resolve and quantify intracellular O2concentration in single muscle cells and that the spatiotemporal O2gradient measured by the sensor is linked to, and reflects, functional metabolic changes occurring during the process of muscle differentiation.HighlightsReal time quantitation of intracellular oxygen with spatial resolutionIdentification of metabolically active sites in single cellsOxygen metabolism is linked to muscle differentiation
Investigating robust associations between functional connectivity based on graph theory and general intelligence
Authors: Metzen Dorothea , Stammen Christina , Fraenz Christoph , Schlüter Caroline , Johnson Wendy , Güntürkün Onur , DeYoung Colin G. , Genç Erhan 
Published: July 2023

AbstractPrevious research investigating relations between general intelligence and graph-theoretical properties of the brain’s intrinsic functional network has yielded contradictory results. A promising approach to tackle such mixed findings is multi-center analysis. For this study, we analyzed data from four independent data sets (total N > 2000) to identify robust associations amongst samples betweengfactor scores and global as well as node-specific graph metrics. On the global level,gshowed no significant associations with global efficiency in any sample, but significant positive associations with global clustering coefficient and small-world propensity in two samples. On the node-specific level, elastic-net regressions for nodal efficiency and local clustering yielded no brain areas that exhibited consistent associations amongst data sets. Using the areas identified via elastic-net regression in one sample to predictgin other samples was not successful for nodal efficiency and only led to significant predictions between two data sets for local clustering. Thus, using conventional graph theoretical measures based on resting-state imaging did not result in replicable associations between functional connectivity and general intelligence.
Breakthrough infection elicits hypermutated IGHV3-53/3-66 public antibodies with broad and potent neutralizing activity against SARS-CoV-2 variants including BQ and XBB lineages
Authors: Li Ling , Chen Xixian , Wang Zuowei , Li Yunjian , Wang Chen , Jiang Liwei , Zuo Teng 
Published: July 2023

AbstractThe rapid emergence of SARS-CoV-2 variants of concern (VOCs) calls for efforts to study broadly neutralizing antibodies elicited by infection or vaccination so as to inform the development of vaccines and antibody therapeutics with broad protection. Here, we identified two convalescents of breakthrough infection with relatively high neutralizing titers against all tested viruses including BQ and XBB lineages. Among 50 spike-specific monoclonal antibodies (mAbs) cloned from their B cells, the top 6 neutralizing mAbs (KXD01-06) belong to previously defined IGHV3-53/3-66 public antibodies. Although most antibodies in this class are dramatically escaped by VOCs, KXD01-06 exhibit broad neutralizing capacity with the IC50s of KXD01 ranging from 0.011∼0.059μg/ml. Deep mutational scanning reveals that KXD01-06 target highly conserved sites on RBD including D420, Y421, L455, F456, A475 and N487. Genetic and functional analysis further indicates that the extent of somatic hypermutation is critical for the breadth of IGHV3-53/3-66 public antibodies. Overall, we discovered and characterized IGHV3-53/3-66 public antibodies with broad and potent neutralizing activity against SARS-CoV-2, which provides rationale for novel vaccines and antibody therapeutics based on this class of antibodies.
Evolution of spite versus evolution of altruism through a disbandment mechanism
Authors: Kurokawa Shun 
Published: July 2023

AbstractAltruism and spite are costly to the actor; therefore, from the perspective of natural selection, the existence of them is a mysterious phenomenon and require explanation. If altruistic individuals are more likely to be recipients for altruism than non-altruistic individuals, then altruism can be favored by natural selection. Similarly, if spiteful individuals are less likely to be recipients for spite than non-spiteful individuals, then spite can be favored by natural selection. Spite is altruism’s evil twin or ugly sister of altruism. In some mechanisms (e.g. repeated interaction), if altruism is favored by natural selection, then spite is also favored by natural selection. In contrast, there is a situation which facilitates the evolution of altruism but is unlikely to facilitate the evolution of spite. Population structure is one typical example. Here we focus on the mechanism in which individuals choose to keep the interaction or stop the interaction according to the opponent’s behavior. We, by using evolutionary game theory, investigate the evolution of altruism and the evolution of spite under this mechanism. Our model shows that the evolution of spite is less likely than the evolution of altruism. This main result provides a nice intuition for why altruism is more abundant than spite in general in the real world.
Parsing variance by marker type: Testing biogeographic hypotheses and differential contribution of historical processes to population structure in a desert lizard
Authors: Holmes Iris A. , Monagan Ivan V. , Westphal Michael F. , Johnson Paul J. , Davis Rabosky Alison R. 
Published: July 2023

AbstractA fundamental goal of population genetic studies is to identify historical biogeographic patterns and understand the processes that generate them. However, localized demographic events can skew population genetic inference. Assessing populations with multiple types of genetic markers, each with unique mutation rates and responses to changes in population size, can help to identify potentially confounding population‐specific demographic processes. Here, we compared population structure and connectivity inferred from microsatellites and restriction site‐associated DNA loci among 17 populations of an arid‐specialist lizard, the desert night lizard, Xantusia vigilis, in central California to test among historical processes structuring population genetic diversity. We found that both marker types yielded generally concordant insights into population genetic structure including a major phylogenetic break maintained between two populations separated by less than 10 km, suggesting that either marker type could be used to understand generalized demographic patterns across the region for management purposes. However, we also found that the effects of demography on marker discordance could be used to elucidate population histories and distinguish among competing biogeographic hypotheses. Our results suggest that comparisons of within‐population diversity across marker types provide powerful opportunities for leveraging marker discordance, particularly for understanding the creation and maintenance of contact zones among clades.
Asian‐type DEL (RHD*DEL1) with an allo‐anti‐D: A paradoxical observation in a healthy multiparous woman
Authors: Ohto Hitoshi , Ito Shoichi , Srivastava Kshitij , Ogiyama Yoshiko , Uchikawa Makoto , Nollet Kenneth Eric , Flegel Willy Albert 
Published: July 2023

AbstractBackgroundThe DEL phenotype is the D variant expressing the least amounts of D antigen per red cell. Asian‐type DEL (RHD:c:1227G > A) is the most prevalent DEL in East Asia without any anti‐D alloimmunization reported before. We investigated the first observation of an anti‐D in any DEL phenotype, reported in the Japanese language at a 1987 conference, only 3 years after the discovery of DEL.MethodsWe contacted the proband 35 years after the initial report. Standard hemagglutination, adsorption/elution, and flow cytometry tests were performed, as was nucleotide sequencing for the RHD, RHCE, and HLA class I and class II genes.ResultsThe healthy multiparous Japanese woman, a regular blood donor, still had the anti‐D of titer 8 representing an alloantibody by standard serologic methods. Unexpectedly, she carried an Asian‐type DEL without any additional RHD gene variation. All 12 HLA alleles identified were known in the Japanese population. Interestingly, one of her HLA‐DRB1 and a variant of her HLA‐DQB1 alleles had previously been associated with anti‐D immunization.ConclusionWe described an allo‐anti‐D, maintained for more than three decades, in an Asian‐type DEL. The combination of two implicated HLA alleles were rare and could have contributed to the anti‐D immunization. Continued monitoring of anti‐D immunization events in patients with DEL is warranted, and we discuss possible mechanisms for further study. As only this single observation has been recognized in the last 35 years, the current recommendation is affirmed: Individuals with Asian‐type DEL should be treated as Rh D‐positive for transfusion and Rh immune prophylaxis purposes.
Assessing trends and reasons for unsuccessful implant discontinuation in Burkina Faso and Kenya between 2016 and 2020: a cross-sectional study
Authors: Tumlinson Katherine , Senderowicz Leigh , Bullington Brooke W , Chung Stephanie , Goland Emilia , Zimmerman Linnea , Gichangi Peter , Thiongo Mary , Guiella Georges ,   PMA Principal Investigators Group, Karp Celia 
Published: July 2023

ObjectivesContraceptive implant use has grown considerably in the last decade, particularly among women in Burkina Faso and Kenya, where implant use is among the highest globally. We aim to quantify the proportion of current implant users who have unsuccessfully attempted implant removal in Burkina Faso and Kenya and document reasons for and location of unsuccessful removal.MethodsWe use nationally representative data collected between 2016 and 2020 from a cross-section of women of reproductive age in Burkina Faso and Kenya to estimate the prevalence of implant use, proportion of current implant users who unsuccessfully attempted removal and proportion of all removal attempts that have been unsuccessful. We describe reasons for and barriers to removal, including the type of facility where successful and unsuccessful attempts occurred.FindingsThe total number of participants ranged from 3221 (2017) to 6590 (2020) in Burkina Faso and from 5864 (2017) to 9469 (2019) in Kenya. Over a 4 year period, the percentage of current implant users reporting an unsuccessful implant discontinuation declined from 9% (95% CI: 7% to 12%) to 2% (95% CI: 1% to 3%) in Kenya and from 7% (95% CI: 4% to 14%) to 3% (95% CI: 2% to 6%) in Burkina Faso. Common barriers to removal included being counselled against removal by the provider or told to return a different day.ConclusionUnsuccessful implant discontinuation has decreased in recent years. Despite progress, substantial numbers of women desire having their contraceptive implant removed but are unable to do so. Greater attention to health systems barriers preventing implant removal is imperative to protect reproductive autonomy and ensure women can achieve their reproductive goals.