bluuebunny/crossref_metadata_2025 huggingface dataset:
Learning entanglement breakdown as a phase transition by confusion
Authors: Gavreev M A , Mastiukova A S , Kiktenko E O , Fedorov A K
Published: July 2022

Quantum technologies require methods for preparing and manipulating entangled multiparticle states. However, the problem of determining whether a given quantum state is entangled or separable is known to be an NP-hard problem in general, and even the task of detecting entanglement breakdown for a given class of quantum states is difficult. In this work, we develop an approach for revealing entanglement breakdown using a machine learning technique, which is known as ‘learning by confusion’. We consider a family of quantum states, which is parameterized such that there is a single critical value dividing states within this family into separate and entangled. We demonstrate the ‘learning by confusion’ scheme allows us to determine the critical value. Specifically, we study the performance of the method for the two-qubit, two-qutrit, and two-ququart entangled state. In addition, we investigate the properties of the local depolarization and the generalized amplitude damping channel in the framework of the confusion scheme. Within our approach and setting the parameterization of special trajectories, we obtain an entanglement-breakdown ‘phase diagram’ of a quantum channel, which indicates regions of entangled (separable) states and the entanglement-breakdown region. Then we extend the way of using the ‘learning by confusion’ scheme for recognizing whether an arbitrary given state is entangled or separable. We show that the developed method provides correct answers for a variety of states, including entangled states with positive partial transpose. We also present a more practical version of the method, which is suitable for studying entanglement breakdown in noisy intermediate-scale quantum devices. We demonstrate its performance using an available cloud-based IBM quantum processor.
Hybrid no-signaling-quantum correlations
Authors: Banacki Michał , Mironowicz Piotr , Ramanathan Ravishankar , Horodecki Paweł
Published: July 2022

Fundamental investigations in non-locality have shown that while the no-signaling principle alone is not sufficient to single out the set of quantum non-local correlations, local quantum mechanics and no-signaling together exactly reproduce the set of quantum correlations in the two-party Bell scenario. Here, we introduce and study an intermediate hybrid no-signaling quantum set of non-local correlations that we term HNSQ in the multi-party Bell scenario where some subsystems are locally quantum while the remaining subsystems are only constrained by the no-signaling principle. Specifically, the set HNSQ is a super-quantum set of correlations derived from no-signaling assemblages by performing quantum measurements on the trusted subsystems. We show that in contrast to the set NS of no-signaling behaviors, there exist extreme points of HNSQ in the tripartite Bell scenario that admit quantum realization. As a tool for optimization over the set HNSQ, we introduce an outer hierarchy of semi-definite programming approximations to the set following an approach put forward by Doherty–Parrilo–Spedalieri. We perform an extensive numerical analysis of the maximal violation of the facet Bell inequalities in the three-party binary input–output scenario and study the corresponding self-testing properties. In contrast to the usual no-signaling correlations, the new set allows for simple security proofs of (one-sided)-device-independent applications against super-quantum adversaries.
Melting of spin ice state and development of fifth order susceptibility with magnetic field in pyrochlore Tb2Sn2O7
Authors: Singh Karan , Ranaut Dheeraj , Sharma G , Mukherjee K
Published: July 2022

Pyrochlores offer an ideal playground to investigate the magnetic ground state of frustrated magnetic systems. In this class of materials, competition between various magnetic interactions remains frustrated and prevents an ordered magnetic state at low temperatures. Tb2Sn2O7 has recently attracted significant attention due to its ordered spin-ice state. Additionally, in such systems, application of external magnetic field might result in exotic magnetic states. Our current investigation on Tb2Sn2O7 reveal the presence of a new phase associated with fifth order susceptibility at low temperatures and high magnetic fields. In this compound, at zero fields, for a stabilized spin-ice state, the singlet–singlet state separated by δ play an imperative role. Under magnetic fields, δ increases and the Zeeman energy associated with the magnetic anisotropy is believed to get enhanced; which can be the key ingredient for evolution of higher-order moments, above 10 kOe, in this compound.
Thermoelectric properties of 2D semiconducting Pt2CO2
Authors: Wei Xiao-Ping , Shen Jing , Du Lan-Lan , Chang Wen-Li , Tao Xiao-Ma
Published: July 2022

Quantum confinement effect in 2D materials leads to the reduction of the degree of freedom of space and the weakening of the correlation between the thermoelectric factors. Only by adjusting a certain physical quantity can optimized the thermoelectric performance. MXenes as a new class of 2D material have attracted widely attention due to their good mechanical and chemical stability, controllable layer thickness, easily functionalized surface and excellent electrical conductivity. In the present paper, using first-principles calculations, we design and study the stability, electronic and thermoelectric properties of 2D monolayer Pt2CO2. Results show that the Pt2CO2 is a new non-magnetic semiconductor, and can bear its own weight, and maintain its free-standing planar structure without substrate support. Futher, the stable calculations indicate that the Pt2CO2 meets thermodynamic, mechanical and dynamic stabilities. Finally, using the Boltzmann transport theory combined with Slack model, we calculate the Seebeck coefficient S, electrical conductivity σ/τ, and the thermal conductivity κ, and then obtain the ZT value from 300 K to 1000 K. It is found that the largest ZT value closes to 1.05 at 1000 K, implying the Pt2CO2 potential application as thermoelectric material.
Optimal design for vibration energy harvesters based on quasi-periodic structures
Authors: Dowlati Shakiba , Kacem Najib , Bouhaddi Noureddine
Published: July 2022

In this paper, the design of large-scale quasi-periodic Vibration Energy Harvesters (VEH) is optimized to enhance the harvested power of an electromagnetic mode localized structure. This work aims to optimize the output power by employing the energy localization phenomenon in a large-scale periodic configuration by introducing the minimum number of perturbations. The harvested power, number and location of perturbations are among the objectives that need to be optimized. A genetic-based mixed-integer optimization algorithm is used to meet the objective functions within a constraint on the system kinetic energy. Numerical simulations for quasi-periodic systems with 20 and 100 Degrees of Freedom (DOF) are performed. It is shown that the ratio of harvested power increases as the number of perturbations rises and it exceeds 80% of the total output power by perturbing almost one-third of the total DOFs. The proposed methodology is a decision-making aid to provide an optimal design in a generalized quasi-periodic VEH in order to reduce the number of harvesting transducers while providing a significantly high amount of harvested power.
PV-reduction of sunset topology with auxiliary vector
Authors: Feng Bo , Li Tingfei
Published: July 2022

The Passarino–Veltman (PV) reduction method has proven to be very useful for the computation of general one-loop integrals. However, not much progress has been made when it is applied to higher loops. Recently, we have improved the PV-reduction method by introducing an auxiliary vector. In this paper, we apply our new method to the simplest two-loop integrals, i.e., the sunset topology. We show how to use differential operators to establish algebraic recursion relations for reduction coefficients. Our algorithm can be easily applied to the reduction of integrals with arbitrary high-rank tensor structures. We demonstrate the efficiency of our algorithm by computing the reduction with the total tensor rank up to four.
Effect of FeNb on microstructure and mechanical properties of Al-Cu-Ni alloy
Authors: Pulisheru Kumara Swamy , Birru Anil Kumar , Dixit Uday Shanker
Published: July 2022

The present research work deals with the investigation of mechanical properties and microstructure evaluation by particulate reinforcement of ferroniobium (FeNb) into Al-5Cu-2Ni alloy. The two-step stir casting method was employed for the fabrication of the material. The metallography study was carried out with optical microscopy (OM), scanning electron microscopy (SEM) with energy-dispersive x-ray spectroscopy (EDS), and x-ray diffraction (XRD). The XRD peaks revealed the presence of the Fe2Nb phase and intermetallic compound phases of Al2Cu and Al3Ni2. However, the Fe2Nb phase is in the form of short sticks uniformly distributed around the intermetallic compound phases. Tensile strength, microhardness and impact strength were evaluated according to ASTM standards. The average tensile strength and Vickers microhardness of the Al-5Cu-2Ni matrix alloy were 179 MPa and 115 HV respectively. By adding 1%, 3% and 5% of FeNb particulate reinforcement into Al-5Cu-2Ni alloy, the tensile strength could be enhanced to 185, 193 and 207 MPa respectively. The corresponding microhardness values were 130, 132 and 151 HV, respectively. Thus, the addition of 5% ferroniobium particulate reinforcement material could significantly enhance the tensile strength and microhardness of the composites. Fractography revealed that fracture mode changes from ductile to brittle with the reinforcement of FeNb particles. The FeNb particles resist the dislocation movement of the intermetallic compound phases in the composites leading to micro-cracks and subsequent brittle fracture.
Effects of Nb microalloying on properties of Zr-Al-Fe-Cu glassy alloy
Authors: Yu De-chuan , Zheng Chong-wei , Qin Qiong , Li Chun-xin , Li Xue-hong , Di Wu  , Qi Yang , Zhang Hai-feng , Wang Yong , Yu Yue
Published: July 2022

The effects of Nb-microalloying on glass forming ability, thermal properties and mechanical properties of (Zr0.6032Cu0.2256Fe0.0995Al0.0717)100-xNbx (x = 0, 1, 2, 3, 4) alloys were investigated. The best glass former was obtained for (Zr0.6032Cu0.2256Fe0.0995Al0.0717)97Nb3, which could be fabricated into full glass with diameter up to 6 mm at least. In addition, the origin of enhancing GFA of ZrAlFeCu amorphous alloy by means of the minor addition of Nb, Gd and Hf, was also discussed from the aspects of clusters and mixing entropy, which might provide a method of understanding the mechanism of enhancing glass-forming ability via microalloying, and choosing minor alloying element with an aim of enhancing glass-forming ability. It was found that the thermal stability reduced as the content of Nb increased along with the supercooled liquid region decreased. Nb-microalloying decease the fracture strength. However, moderate Nb microalloying could enhance the room temperature plastic strain.
Strip detector array (SDA) for beam monitoring in radiotherapy: reconstruction of MLC parameters from multiple projections of flux
Authors: Hoegele W , Zygmanski P
Published: July 2022

Objective. In this paper we propose and investigate a new detector with multiple strip detector arrays (SDA) for monitoring MLC shaped x-ray beams for radiotherapy treatment. Approach. Each SDA measures 1D dose profiles equivalent to dose projections. The goal of such a detector is to determine individual MLC leaf positions as well as the Monitor Units (MU) per MLC segment during radiotherapy. In the present work we investigate an optimal SDA detector configuration and reconstruction algorithm. We determine the accuracy of SDA for different treatment sites (spine, pelvis, retroperitoneum, prostate, brain SRT, SRS, lung and head and neck). We perform a simulation study accounting for different type of MLC leaf positional errors: random MLC leaf, systematic for the whole leaf bank and systematic for an individual leaf. In a similar fashion, we also account for errors in Monitor Units per segment. Main results. We demonstrate that for a broad range of IMRT treatment plans a robust reconstruction of errors is achievable with only 3 projections (3 sets of SDA oriented at at 0°, 45° and 135°). The SDA is capable of capturing both systematic errors in leaf banks and individual leaves as well as random errors sufficient for practical clinical purposes. Significance. These features of the SDA detector makes it suitable for real-time Quality Control of MLC collimated linac output.
Interregional flows of virtual cropland within China
Authors: Wu Hanfei , Liu Ao , Jin Ruochen , Chai Li
Published: July 2022

Cropland is an essential resource for agricultural system and greatly impacts agricultural sustainability. Cropland can be embodied in the goods and transferred among regions. Managing cropland as a virtual resource, similar with virtual water strategy, is an effective measure to achieve sustainability. Therefore, it is of significance for policymakers to understand how virtual cropland transfers in the economic society. This study employed a Multi-Regional Input-Output model with high resolution in the agriculture sectors (nine categories of crops) to examine the interregional flows of virtual cropland within China in 2015. The results show that Heilongjiang, Inner Mongolia, and Jilin contributed the most virtual cropland, while Guangdong, Zhejiang, and Shandong were the largest receivers. The largest flow was from Heilongjiang to Guangdong embodied in cereals. Most of virtual flows were embodied in cereals, followed by sugar crops, other crops, legumes, and vegetables. Heilongjiang, Xinjiang, and Guangxi dominated the virtual outflows embodied in legumes, fruits, and oilseeds, respectively. This study is informative and implicative for policymakers to understand the spatial transfer pattern of virtual cropland, identify the key nodes, and design the effective measures to achieve sustainability.
StabilitySort: assessment of protein stability changes on a genome-wide scale to prioritize potentially pathogenic genetic variation
Authors: Chuah Aaron , Li Sean , Do Andrea , Field Matt , Andrews Dan
Published: July 2022

Missense mutations that change protein stability are strongly associated with human genetic disease. With the recent availability of predicted structures for all human proteins generated using the AlphaFold2 prediction model, genome-wide assessment of the stability effects of genetic variation can, for the first time, be easily performed. This facilitates the interrogation of personal genetic variation for potentially pathogenic effects through the application of stability metrics. Here, we present a novel tool to prioritize variants predicted to cause strong instability in essential proteins. We show that by filtering by ΔΔG values and then prioritizing by StabilitySort Z-scores, we are able to more accurately discriminate pathogenic, protein-destabilizing mutations from population variation, compared with other mutation effect predictors.

Availability and implementation

StabilitySort is available as a web service (https://www.stabilitysort.org), as a data download for integration with other tools (https://www.stabilitysort.org/download) or can be deployed as a standalone system from source code (https://gitlab.com/baaron/StabilitySort).

Supplementary information

Supplementary data are available at Bioinformatics online.
TogoID: an exploratory ID converter to bridge biological datasets
Authors: Ikeda Shuya , Ono Hiromasa , Ohta Tazro , Chiba Hirokazu , Naito Yuki , Moriya Yuki , Kawashima Shuichi , Yamamoto Yasunori , Okamoto Shinobu , Goto Susumu , Katayama Toshiaki
Published: July 2022

Motivation

Understanding life cannot be accomplished without making full use of biological data, which are scattered across databases of diverse categories in life sciences. To connect such data seamlessly, identifier (ID) conversion plays a key role. However, existing ID conversion services have disadvantages, such as covering only a limited range of biological categories of databases, not keeping up with the updates of the original databases and outputs being hard to interpret in the context of biological relations, especially when converting IDs in multiple steps.

Results

TogoID is an ID conversion service implementing unique features with an intuitive web interface and an application programming interface (API) for programmatic access. TogoID currently supports 65 datasets covering various biological categories. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations.

Availability and implementation

The TogoID service is freely available on the TogoID website (https://togoid.dbcls.jp/) and the API is also provided to allow programmatic access. To encourage developers to add new dataset pairs, the system stores the configurations of pairs at the GitHub repository (https://github.com/togoid/togoid-config) and accepts the request of additional pairs.

Supplementary information

Supplementary data are available at Bioinformatics online.
Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments
Authors: Darvish Mitra , Seiler Enrico , Mehringer Svenja , Rahn René , Reinert Knut
Published: July 2022

Motivation

The ever-growing size of sequencing data is a major bottleneck in bioinformatics as the advances of hardware development cannot keep up with the data growth. Therefore, an enormous amount of data is collected but rarely ever reused, because it is nearly impossible to find meaningful experiments in the stream of raw data.

Results

As a solution, we propose Needle, a fast and space-efficient index which can be built for thousands of experiments in <2 h and can estimate the quantification of a transcript in these experiments in seconds, thereby outperforming its competitors. The basic idea of the Needle index is to create multiple interleaved Bloom filters that each store a set of representative k-mers depending on their multiplicity in the raw data. This is then used to quantify the query.

Availability and implementation

https://github.com/seqan/needle.

Supplementary information

Supplementary data are available at Bioinformatics online.
Acidic Cannabinoids Suppress Proinflammatory Cytokine Release by Blocking Store-operated Calcium Entry
Authors: Faouzi Malika , Wakano Clay , Monteilh-Zoller Mahealani K , Neupane Ram P , Starkus John G , Neupane Jayanti Bhandari , Cullen Aaron J , Johnson Brandon E , Fleig Andrea , Penner Reinhold
Published: July 2022

Cannabis sativa has long been known to affect numerous biological activities. Although plant extracts, purified cannabinoids, or synthetic cannabinoid analogs have shown therapeutic potential in pain, inflammation, seizure disorders, appetite stimulation, muscle spasticity, and treatment of nausea/vomiting, the underlying mechanisms of action remain ill-defined. In this study we provide the first comprehensive overview of the effects of whole-plant Cannabis extracts and various pure cannabinoids on store-operated calcium (Ca2+) entry (SOCE) in several different immune cell lines. Store-operated Ca2+ entry is one of the most significant Ca2+ influx mechanisms in immune cells, and it is critical for the activation of T lymphocytes, leading to the release of proinflammatory cytokines and mediating inflammation and T cell proliferation, key mechanisms for maintaining chronic pain. While the two major cannabinoids cannabidiol and trans-Δ9-tetrahydrocannabinol were largely ineffective in inhibiting SOCE, we report for the first time that several minor cannabinoids, mainly the carboxylic acid derivatives and particularly cannabigerolic acid, demonstrated high potency against SOCE by blocking calcium release-activated calcium currents. Moreover, we show that this inhibition of SOCE resulted in a decrease of nuclear factor of activated T-cells activation and Interleukin 2 production in human T lymphocytes. Taken together, these results indicate that cannabinoid-mediated inhibition of a proinflammatory target such as SOCE may at least partially explain the anti-inflammatory and analgesic effects of Cannabis.
Local health systems resilience in managing the COVID-19 pandemic: lessons from Mexico
Authors: Juárez-Ramírez Clara , Reyes-Morales Hortensia , Gutiérrez-Alba Gaudencio , Reartes-Peñafiel Diana L , Flores-Hernández Sergio , Muños-Hernández José Alberto , Escalante-Castañón André , Malo Miguel
Published: July 2022

The concept of resilience was applied to the public health field to investigate the way health systems are impacted by health crises, what conditions allow them to mitigate the blow and how they reorganize once the crisis is over. In 2020, the COVID-19 pandemic caused by the SARS-CoV-2 virus represented a global challenge demanding immediate response to an unprecedented health crisis. Various voices drew attention to the intensity of the crisis in countries with greater inequalities, where the pandemic converged with other social emergencies. We documented the experiences of health personnel who faced the pandemic at the primary care level while simultaneously maintaining the functioning of other areas of medical care. Our results derived from a qualitative study comprising 103 participants from five states of Mexico. We aimed to show through inferential analysis their perspective on what we call ‘the resilience of local health systems’. We observed three stages of experience during the crisis: (a) Preparation (official guidelines received to organize care, training and planning of epidemiological surveillance); (b) Adaptation (performance of community-based prevention activities, infrastructure modifications, telehealth); and (c) Learning (participatory governance with city councils, business sector and organized population). The study suggests that the local health systems analysed benefited from the initiatives of health personnel that in some cases positively exceeded their duties. In terms of the resilience analysis, they were able to handle the impact of the crisis and cope with it. Their transformative capacity came from the strategies implemented to adapt health services by managing institutional resources. Their experience represents a lesson on the strengthening of the essential functions of health systems and shows a way to address successfully the increasingly complex health challenges of the present and future times.
A CROSS-CULTURAL INVESTIGATION OF SELF-COMPASSION IN ADOLESCENTS ACROSS GENDER
Authors: Cheung H N , Ho W S , Chan S W Y , Williams J
Published: July 2022

Background

Self-compassion encourages one to accept oneself, reduce self-criticism and self-judgment, and see one’s shortcomings and setbacks in a balanced view. Adolescent self-compassion is a crucial protective factor against mental illness. It is, however, affected by gender. Given the scarcity of self-compassion scales for adolescents, the current study evaluates the Self-Compassion Scale for Youth (SCS-Y) in a large cross-cultural sample and investigates how the subscales of SCS-Y relate to the dimensions of depressive symptoms across gender.

Subjects and Methods

Through the internet-based Qualtrics, a total of 2881 teenagers aged 12 to 18 years were recruited from Hong Kong (HK), China, and the United Kingdom. A Multiple Indicator Multiple Cause (MIMIC) model was used to evaluate measurement invariance of the SCS-Y, and differential item functioning (DIF) was checked across gender. Upon the establishment of the best model, a multigroup structural equation model (SEM) was built between factors of SCS-Y and Multidimensional depression assessment scale (MDAS) which assesses four dimensions of depressive symptoms (emotional, cognitive, somatic and interpersonal).

Results

The SCS-Y was shown to have good reliability and validity. The MIMIC model produced a good model fit for a hypothetical six-factor model (CFI = 0.980; TLI = 0.974; RMSEA = 0.038) and no item was flagged for DIF across gender. A gender difference was observed between SCS-Y factors and depression dimensions.

Conclusions

The SCS-Y exhibits good psychometric characteristics, including measurement invariance across gender. The study also highlights the gender difference between self-compassion factors and depression dimensions.

Acknowledgements

Supported by a project grant from Hong Kong Metropolitan University Research and Development Scheme (PACRD/R6423).
SUPPRESSOR EFFECT OF FACEBOOK USAGES ON OBSESSIVE BELIEFS
Authors: Lee Soon Li
Published: July 2022

Background

This research aimed to demonstrate a significant suppressor effect between Facebook usages (Facebook intensity and Facebook addiction) on obsessive beliefs (threat, perfectionism, inflated responsibility, control of thoughts).

Subjects and Methods

Participants were 204 university students who completed self-reported measures of Facebook intensity, Facebook addiction, and obsessive beliefs. To examine the significance of the suppressor effect, the conceptual models were analyzed using GSCA Pro.

Results

Results indicated that the suppressor effect was not significant. Facebook intensity, which refers to regular Facebook use, did not significantly predict the facets of obsessive beliefs. Facebook addiction, which represents the maladaptive use of Facebook, significantly predicted these facets.

Conclusions

Results indicated that Facebook intensity did not increase the relationship between Facebook addiction and obsessive beliefs. Facebook addiction increases the saliency of obsessive beliefs, which possibly increases the risk of OCD.

Acknowledgements

This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.
An alert tool to promote lung protective ventilation for possible acute respiratory distress syndrome
Authors: Knighton Andrew J , Kuttler Kathryn G , Ranade-Kharkar Pallavi , Allen Lauren , Throne Taylor , Jacobs Jason R , Carpenter Lori , Winberg Carrie , Johnson Kyle , Shrestha Neer , Ferraro Jeffrey P , Wolfe Doug , Peltan Ithan D , Srivastava Rajendu , Grissom Colin K
Published: July 2022

Objective

Computer-aided decision tools may speed recognition of acute respiratory distress syndrome (ARDS) and promote consistent, timely treatment using lung-protective ventilation (LPV). This study evaluated implementation and service (process) outcomes with deployment and use of a clinical decision support (CDS) synchronous alert tool associated with existing computerized ventilator protocols and targeted patients with possible ARDS not receiving LPV.

Materials and Methods

We performed an explanatory mixed methods study from December 2019 to November 2020 to evaluate CDS alert implementation outcomes across 13 intensive care units (ICU) in an integrated healthcare system with >4000 mechanically ventilated patients annually. We utilized quantitative methods to measure service outcomes including CDS alert tool utilization, accuracy, and implementation effectiveness. Attitudes regarding the appropriateness and acceptability of the CDS tool were assessed via an electronic field survey of physicians and advanced practice providers.

Results

Thirty-eight percent of study encounters had at least one episode of LPV nonadherence. Addition of LPV treatment detection logic prevented an estimated 1812 alert messages (41%) over use of disease detection logic alone. Forty-eight percent of alert recommendations were implemented within 2 h. Alert accuracy was estimated at 63% when compared to gold standard ARDS adjudication, with sensitivity of 85% and positive predictive value of 62%. Fifty-seven percent of survey respondents observed one or more benefits associated with the alert.

Conclusion

Introduction of a CDS alert tool based upon ARDS risk factors and integrated with computerized ventilator protocol instructions increased visibility to gaps in LPV use and promoted increased adherence to LPV.
Outcomes of COVID-19 Vaccination–Related Incidental Axillary Adenopathy in Women Undergoing Breast MRI
Authors: Zuckerman Samantha P , McDonald Elizabeth S , Weinstein Susan P , Birnbaum Julia A , Tobey Jennifer D , Conant Emily F , Edmonds Christine E
Published: July 2022

Objective

To assess the frequency, management, and early outcomes of COVID-19 vaccine–related adenopathy on breast MRI.

Methods

This IRB-exempt retrospective study reviewed patients who underwent breast MRI following COVID-19 vaccine approval in the U.S. from December 14, 2020, to April 11, 2021 (N = 1912) and compared patients who underwent breast MRI the year prior to the pandemic, March 13, 2019, to March 12, 2020 (N = 5342). Study indication, patient age, date of study, date and type of vaccination(s), time difference between study and vaccinations, lymph node–specific and overall management recommendations, and outcomes of additional examinations were recorded. Differences in the final assessment categories between the subjects scanned pre-pandemic and post-vaccine were compared using the Fisher exact test.

Results

Vaccine-related adenopathy was mentioned in 67 breast MRI reports; only 1 in the pre-pandemic group. There were no clinically relevant differences in patient demographics between groups. There was a statistically significant increase in BI-RADS 0 assessments between the pre-pandemic and post-vaccine approval groups—0.8% (45/5342) versus 1.8% (34/1912) (P = 0.001) and BI-RADS 3 assessments—6.5% (348/5342) versus 9.2% (176/1912) (P < 0.0001). Of the 29 patients who underwent additional imaging (range, 2–94 days following MRI) and the 2 patients who underwent biopsy, 47% (31/66), none were found to have malignant adenopathy.

Conclusion

COVID-19 vaccination is associated with transient axillary adenopathy of variable duration. This leads to additional imaging in women undergoing breast MRI, so far with benign outcomes, and this may affect audits of outcomes of MRI.
Recent progress on the activation of the cGAS–STING pathway and its regulation by biomolecular condensation
Authors: Yu Xiaoyu , Zhao Zhen , Jiang Zhengfan
Published: July 2022

The cyclic guanosine monophosphate (GMP)–adenosine monophosphate (AMP) synthetase (cGAS)–stimulator of interferon genes (STING) pathway, comprising the DNA sensor cGAS, the second messenger cyclic GMP–AMP (cGAMP), and the endoplasmic reticulum (ER) adaptor protein STING, detects cytoplasmic double-stranded DNA (dsDNA) to trigger type I-interferon responses for host defense against pathogens. Previous studies defined a model for the allosteric activation of cGAS by DNA-binding, but recent work reveals other layers of mechanisms to regulate cGAS activation such as the phase condensation and metal ions, especially the discovery of Mn2+ as a cGAS activator. Activation of the 2′3′-cGAMP sensor STING requires translocating from the ER to the Golgi apparatus. The sulfated glycosaminoglycans at the Golgi are found to be the second STING ligand promoting STING oligomerization and activation in addition to 2′3′-cGAMP, while surpassed levels of 2′3′-cGAMP induce ER-located STING to form a highly organized ER membranous condensate named STING phase-separator to restrain STING activation. Here, we summarize recent advances in the regulation of cGAS–STING activation and their implications in physiological or pathological conditions, particularly focusing on the emerging complexity of the regulation.
Leaf litter decomposition characteristics and controlling factors across two contrasting forest types
Authors: Zhao Yuan-Yuan , Li Zhuo-Ting , Xu Ting , Lou An-ru
Published: July 2022

Plant leaf litter decomposition provides a source of energy and nutrients in forest ecosystems. In addition to traditional environmental factors, the degradation process of litter is also affected by plant functional traits and litter quality. However, at the community level, it is still unclear whether the relative importance of plant traits and litter quality on the litter decomposition rate is consistent. A year-long mixed leaf litter decomposition experiment in a similar environment was implemented by using the litterbag method in seven typical forest types in Dongling Mountain, Beijing, North China, including six monodominant communities dominated by Juglans mandshurica, Populus cathayana, Betula dahurica, Betula platyphylla, Pinus tabuliformis and Larix gmelinii var. principis-rupprechtii and one codominant community dominated by Fraxinus rhynchophylla, Quercus mongolica and Tilia mongolica. The results showed that there were considerable differences in the litter decomposition rate (k-rate) among the different forest types. The community weighted mean (CWM) traits of green leaves and litter quality explained 35.60% and 9.05% of the k-rate variations, respectively, and the interpretation rate of their interaction was 23.37%, indicating that the CWM traits and their interaction with litter quality are the main factors affecting the k-rate variations. In the recommended daily allowance, leaf nitrogen content, leaf dry matter content, leaf tannin content and specific leaf area were the main factors affecting the k-rate variations. Therefore, we suggest that future studies should focus on the effects of the CWM traits of green leaves on litter decomposition at the community level.
A Rare Etiology for Ascending Paralysis in an Infant
Authors: Abe Keisuke , Casamina Chanel , Ching Natascha , Abe Keith K , Melish Marian , Thompson Karen S , Ahmed Asim A , Purohit Prashant J
Published: July 2022

An 11-month-old male infant with ascending paralysis had an unremarkable initial cerebrospinal fluid (CSF) analysis and imaging. Progressive neurological symptoms resulted in repeated CSF sampling, microscopy, and plasma microbial cell-free DNA next-generation sequencing analysis, that in combination with epidemiology, confirmed the diagnosis.
Measuring the thermal and ionization state of the low-z IGM using likelihood free inference
Authors: Hu Teng , Khaire Vikram , Hennawi Joseph F , Walther Michael , Hiss Hector , Alsing Justin , Oñorbe Jose , Lukic Zarija , Davies Frederick
Published: July 2022

We present a new approach to measure the power-law temperature density relationship $T=T_0 (\rho/ \bar{\rho })^{\gamma -1}$ and the UV background photoionization rate $\Gamma _{{{{\rm H\, {\small I}}}}{}}$ of the intergalactic medium (IGM) based on the Voigt profile decomposition of the Ly α forest into a set of discrete absorption lines with Doppler parameter b and the neutral hydrogen column density $N_{\rm H\, {\small I}}$. Previous work demonstrated that the shape of the $b-N_{{{{\rm H\, {\small I}}}}{}}$ distribution is sensitive to the IGM thermal parameters T0 and γ, whereas our new inference algorithm also takes into account the normalization of the distribution, i.e. the line-density dN/dz, and we demonstrate that precise constraints can also be obtained on $\Gamma _{{{{\rm H\, {\small I}}}}{}}$. We use density-estimation likelihood-free inference (DELFI) to emulate the dependence of the $b-N_{{{{\rm H\, {\small I}}}}{}}$ distribution on IGM parameters trained on an ensemble of 624 nyx hydrodynamical simulations at z = 0.1, which we combine with a Gaussian process emulator of the normalization. To demonstrate the efficacy of this approach, we generate hundreds of realizations of realistic mock HST/COS data sets, each comprising 34 quasar sightlines, and forward model the noise and resolution to match the real data. We use this large ensemble of mocks to extensively test our inference and empirically demonstrate that our posterior distributions are robust. Our analysis shows that by applying our new approach to existing Ly α forest spectra at z ≃ 0.1, one can measure the thermal and ionization state of the IGM with very high precision ($\sigma _{\log T_0} \sim 0.08$ dex, σγ ∼ 0.06, and $\sigma _{\log \Gamma _{{{{\rm H\, {\small I}}}}{}}} \sim 0.07$ dex).
Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation
Authors: Guilbaud Guillaume , Murat Pierre , Wilkes Helen S , Lerner Leticia Koch , Sale Julian E , Krude Torsten
Published: July 2022

Replication of the human genome initiates within broad zones of ∼150 kb. The extent to which firing of individual DNA replication origins within initiation zones is spatially stochastic or localised at defined sites remains a matter of debate. A thorough characterisation of the dynamic activation of origins within initiation zones is hampered by the lack of a high-resolution map of both their position and efficiency. To address this shortcoming, we describe a modification of initiation site sequencing (ini-seq), based on density substitution. Newly replicated DNA is rendered ‘heavy-light’ (HL) by incorporation of BrdUTP while unreplicated DNA remains ‘light-light’ (LL). Replicated HL-DNA is separated from unreplicated LL-DNA by equilibrium density gradient centrifugation, then both fractions are subjected to massive parallel sequencing. This allows precise mapping of 23,905 replication origins simultaneously with an assignment of a replication initiation efficiency score to each. We show that origin firing within early initiation zones is not randomly distributed. Rather, origins are arranged hierarchically with a set of very highly efficient origins marking zone boundaries. We propose that these origins explain much of the early firing activity arising within initiation zones, helping to unify the concept of replication initiation zones with the identification of discrete replication origin sites.
Identification of nucleobase chemical modifications that reduce the hepatotoxicity of gapmer antisense oligonucleotides
Authors: Yoshida Tokuyuki , Morihiro Kunihiko , Naito Yuki , Mikami Atsushi , Kasahara Yuuya , Inoue Takao , Obika Satoshi
Published: July 2022

Currently, gapmer antisense oligonucleotide (ASO) therapeutics are under clinical development for the treatment of various diseases, including previously intractable human disorders; however, they have the potential to induce hepatotoxicity. Although several groups have reported the reduced hepatotoxicity of gapmer ASOs following chemical modifications of sugar residues or internucleotide linkages, only few studies have described nucleobase modifications to reduce hepatotoxicity. In this study, we introduced single or multiple combinations of 17 nucleobase derivatives, including four novel derivatives, into hepatotoxic locked nucleic acid gapmer ASOs and examined their effects on hepatotoxicity. The results demonstrated successful identification of chemical modifications that strongly reduced the hepatotoxicity of gapmer ASOs. This approach expands the ability to design gapmer ASOs with optimal therapeutic profiles.
Short LNA-modified oligonucleotide probes as efficient disruptors of DNA G-quadruplexes
Authors: Chowdhury Souroprobho , Wang Jiayi , Nuccio Sabrina Pia , Mao Hanbin , Di Antonio Marco
Published: July 2022

G-quadruplexes (G4s) are well known non-canonical DNA secondary structures that can form in human cells. Most of the tools available to investigate G4-biology rely on small molecule ligands that stabilise these structures. However, the development of probes that disrupt G4s is equally important to study their biology. In this study, we investigated the disruption of G4s using Locked Nucleic Acids (LNA) as invader probes. We demonstrated that strategic positioning of LNA-modifications within short oligonucleotides (10 nts.) can significantly accelerate the rate of G4-disruption. Single-molecule experiments revealed that short LNA-probes can promote disruption of G4s with mechanical stability sufficient to stall polymerases. We corroborated this using a single-step extension assay, revealing that short LNA-probes can relieve replication dependent polymerase-stalling at G4 sites. We further demonstrated the potential of such LNA-based probes to study G4-biology in cells. By using a dual-luciferase assay, we found that short LNA probes can enhance the expression of c-KIT to levels similar to those observed when the c-KIT promoter is mutated to prevent the formation of the c-KIT1 G4. Collectively, our data suggest a potential use of rationally designed LNA-modified oligonucleotides as an accessible chemical-biology tool for disrupting individual G4s and interrogating their biological functions in cells.
RETRACTED: Changes in Tobacco Dependence and Association With Onset and Progression of Use by Product Type From Wave 1 to Wave 3 of the Population Assessment of Tobacco and Health (PATH) Study
Authors: Strong David R , Pierce John P , White Martha , Stone Matthew D , Abrams David B , Glasser Allison M , Wackowski Olivia A , Cummings K Michael , Hyland Andrew , Taylor Kristie , Edwards Kathryn C , Silveira Marushka L , Kimmel Heather L , Lambert Elizabeth Y , Compton Wilson M , Hull Lynn C , Niaura Raymond
Published: July 2022

Introduction

This study examined trajectories of tobacco dependence (TD) in relation to changes in tobacco product use and explored the effects of product-specific adding, switching, or discontinued use on dependence over time.

Aims and Methods

Data were analyzed from the first three waves of the Population Assessment of Tobacco and Health (PATH) Study, a nationally representative, longitudinal study of adults and youth in the United States. Data included 9556 Wave 1 (2013/2014) adult current established tobacco users who completed all three interviews and had established use at ≥2 assessments. Groups included cigarettes-only users, e-cigarettes-only users, cigars-only users, hookah-only users, any smokeless-only users, cigarette + e-cigarette dual users, and multiple product users. A validated 16-item scale assessed TD across product users.

Results

Wave 1 e-cigarette-only users’ who maintained exclusive e-cigarette use increased levels of TD through Wave 3 as did those who added or switched to another product. Wave 1 multiple product users’ TD decreased across waves. TD for all other Wave 1 user groups remained about the same. For Wave 1 cigarette-only smokers, switching to another product or moving to a pattern of no established use was associated with lower levels of TD than smokers whose use stayed the same. Movement to no established use of any tobacco product was consistently associated with lower TD for all other product users.

Conclusions

Except for Wave 1 e-cigarette-only users, TD among US tobacco product users was stable over time, with daily users less likely to vary from baseline.

Implications

The level of TD among most US tobacco users was stable over the first three waves of the PATH Study and trends in levels of TD were predominantly unrelated to changes in patterns of continued product use. Stable levels of TD suggest a population at persistent risk of health impacts from tobacco. Wave 1 e-cigarette users, including those maintaining exclusive e-cigarette use, experienced increasing levels of TD over time, perhaps because of increases in quantity or frequency of their e-cigarette product use or increasing efficiency of nicotine delivery over time.
What the Senses Cannot ‘Say’
Authors: Morgan Jonathan Brink
Published: July 2022

Some have claimed that there are laws of appearance, i.e. in principle constraints on which types of sensory experiences are possible. Within a representationalist framework, these laws amount to restrictions on what a given experience can represent. I offer an in-depth defence of one such law and explain why prevalent externalist varieties of representationalism have trouble accommodating it. In light of this, I propose a variety of representationalism on which the spatial content of experience is determined by intrinsic features of conscious subjects. I conclude by considering an externalist-friendly reworking of my proposal, but suggest that the success of such a reworking is dubious.
Exploring Family Planning Perspectives Among Men Receiving Medications for Opioid Use Disorder: Implications for Service Development
Authors: Rinehart Deborah J. , Stowell Melanie , Barrett Kaeli , Langland Katie , Thomas-Gale Tara , Al-Tayyib Alia , O’Connell Ryan
Published: July 2022

Objective

Studies have consistently found high rates of unintended pregnancy among women with substance use disorder. While research efforts have begun to focus on understanding needs and providing family planning services for women in treatment, few studies have included men. This has resulted in a gap in the literature regarding men’s reproductive health experiences and family planning desires.

Methodology

Between December 2019 and February 2020, we conducted semistructured qualitative interviews with adult men receiving medications for opioid use disorder at a safety-net healthcare system in Denver, Colorado. Interviews were recorded and analyzed using the Rapid Assessment Process.

Results

Fifteen men participated in an interview. Overall, men described feeling excluded from family planning education and services as well as from decision making with their partners. Participants desired knowledge and resources related to contraceptive methods, partner communication, and parenting. Additional themes included loss of autonomy around pregnancy decisions, the importance of fatherhood, and the importance of addressing family planning during recovery. Participants expressed interest in a family planning intervention but indicated that engaging men on this topic may be challenging.

Conclusions

Our findings suggest that men in treatment desire education and involvement in family planning. Participants endorsed access to a subject expert within the treatment environment, but engagement strategies that underscore topic relevance to men will be critical. Initiating a conversation involving education and service navigation in the treatment setting may be a promising strategy for engaging men in recovery in family planning and improving men’s access to needed services and resources.
“Helping the Helpers”—Making Access to Buprenorphine the New Standard of Care for Physicians in State Monitoring Programs
Authors: Dwarakanath Megana , Klipp Stephanie
Published: July 2022

This commentary argues that the Federation of State Medical Board's (FSMB) recommendations concerning the use of buprenorphine for physicians in their state-affiliated monitoring programs falls short of effectively permitting an evidence-based treatment for opioid use disorder. Although the FSMB acknowledges the benefits of medications for opioid use disorder and recommends that physicians who elect to start on buprenorphine receive treatment safely and privately, the FSMB is opposed to health care professionals practicing while on buprenorphine. Their rationale is based on the notion that physicians are exceptional in their ability to remain in recovery without medications for opioid use disorder and the unsupported assumption that buprenorphine causes significant cognitive impairment. This commentary contends that FSMB policy recommendations should work to destigmatize and indeed support evidence-based treatments for physicians with substance use disorders.