bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of the New Small Wheel Micromegas sectors for the phase 1 upgrade of the muon forward spectrometer of the ATLAS experiment at CERN
Authors: Mancini G
Published: March 2023

The ATLAS experiment is currently upgrading the first muon station in the high-rapidity region with the New Small Wheels (NSW), based on large-size resistive Micromegas (MM) technology and small-strip Thin Gap Chambers (sTGC). The NSW system is going to be installed in the ATLAS underground cavern during the LHC long shutdown 2 (2021) to enter in operation for Run3 (starting in the first months of 2022). 128 Micromegas quadruplets, each composed by four measurement layers two to three square meters in size, are needed to build the two New Small Wheels, covering a total active area of about 1280 m2. The construction of all MM modules, carried out in France, Germany, Italy, Russia and Greece, is completed. Their mechanical integration into sectors, the installation of on-detector services and electronics, for the first NSW is also completed, along with all validation and acceptance tests. The preparation of the second NSW is very well advanced. The advanced status of the project, in view of the imminent installation of the two NSW in ATLAS by the fall of 2021 will be reported. Micromegas detector construction and integration into sectors is presented, together with results obtained with cosmic rays data during the validation tests and the impressive steps of the wheel assembly completion.
A-optimal active learning
Authors: Boesen Tue , Haber Eldad
Published: March 2023

In this work we discuss the problem of active learning. We present an approach that is based on A-optimal experimental design of ill-posed problems and show how one can optimally label a data set by partially probing it, and use it to train a deep network. We present two approaches that make different assumptions on the data set. The first is based on a Bayesian interpretation of the semi-supervised learning problem with the graph Laplacian that is used for the prior distribution and the second is based on a frequentist approach, that updates the estimation of the bias term based on the recovery of the labels. We demonstrate that this approach can be highly efficient for estimating labels and training a deep network.
An accurate operational matrix method based on Lagrange polynomials for solving fractional-order pantograph delay and Riccati differential equations
Authors: Kumar Saurabh , Gupta Vikas , Kumar Ajay , Gómez-Aguilar J F
Published: March 2023

This paper introduces the fractional-order Lagrange polynomials approach to solve initial value problems for pantograph delay and Riccati differential equations involving fractional-order derivatives. The fractional derivative is determined as per the idea of Caputo. First, operational matrices of fractional integration with fractional-order Lagrange polynomials have been constructed using the Laplace transform. Then, we use these operational matrices and the collocation method to convert the given initial value problem to a system of algebraic equations. Subsequently, we use Newton’s iterative approach to solve the resultant system of algebraic equations. Error estimates for the function approximation also have been discussed. Finally, some numerical examples supported the theoretical findings by demonstrating the applicability and accuracy of the proposed strategy.
Ion acoustic solitons collision in spin-polarized relativistic quantum plasma
Authors: Gul Nabi , Zain Kanwal , Ahmad Rashid
Published: March 2023

The dynamics of electrostatic ion acoustic solitons collision in relativistic magnetized spin-polarized plasma is studied using a Magnetized Relativistic Quantum Hydrodynamics model. The plasmas components are relativistic degenerate electron with spin-up (n

e↑) and spin-down (n

e↓) concentrations, and relativistic inertial classical ions. In two-dimensional plasma geometry, a homogeneous external magnetic field is provided along the z-direction, i.e.

B
=

B

0

z

ˆ

. The extended Poincare Lighthill Kuo (PLK) approach is used to calculate the Kortewegde Vries equations for oppositely moving ion-acoustic solitons. Before and after collision, their trajectories and associated phase shifts are computed. Only negative polarity pulses of ion acoustic solitons are observed in our stated relativistic magnetized plasma. The spin density popularization ratio κ is shown to have a significant impact on the phase shifts of colliding solitons. It is found that when κ increases, one soliton's phase shift increases while the other soliton's phase shift decreases. The relativistic effects are also analyzed numerically and found that the phase shift of colliding ions acoustic solitons grows as the relativistic component rises from weakly to ultra-relativistic. It is observed that the phase shift of both solitons is to be dependent on their phase velocity with each other. Our research is noteworthy in that it focuses on, the astrophysical systems such as white dwarf, neutron star and pulsar.
P-bifurcation phenomena of the non-smooth modified rayleigh-duffing oscillator under the combined action of harmonic excitation and noise perturbation
Authors: Ma Shichao , Wang Liang , Zhang Jinxiu , Jia Wantao
Published: March 2023

In this paper, the stochastic dynamics of a modified Rayleigh-Duffing oscillator with Coulomb frictional damping and elastic impact is investigated under combined harmonic and noise excitations. On the premise of retaining the non-smooth properties, a non-smooth steady-state probability density response numerical calculation method is introduced by taking advantage of Markov process. Utilizing this method, the stochastic P-bifurcation phenomena of oscillators without and with externally excitation are discussed in detail by inscribing changes in the topology of the steady-state probability density function. It is displayed that certain nonlinear damping coefficient and external excitation amplitude change the structure of the response, and that both the friction coefficient and the elastic coefficient of the contact surface induce stochastic P-bifurcation phenomena in systems without and with harmonic excitation, respectively. This study reveals the effect of non-smooth factors on the stability of the Rayleigh-Duffing oscillator.
Supercool subtleties of cosmological phase transitions
Authors: Athron Peter , Balázs Csaba , Morris Lachlan
Published: March 2023

We investigate rarely explored details of supercooled cosmological first-order phase transitions at the electroweak scale, which may lead to strong gravitational wave signals or explain the cosmic baryon asymmetry. The nucleation temperature is often used in phase transition analyses, and is defined through the nucleation condition: on average one bubble has nucleated per Hubble volume. We argue that the nucleation temperature is neither a fundamental nor essential quantity in phase transition analysis. We illustrate scenarios where a transition can complete without satisfying the nucleation condition, and conversely where the nucleation condition is satisfied but the transition does not complete. We also find that simple nucleation heuristics, which are defined to approximate the nucleation temperature, break down for strong supercooling. Thus, studies that rely on the nucleation temperature — approximated or otherwise — may misclassify the completion of a transition. Further, we find that the nucleation temperature decouples from the progress of the transition for strong supercooling. We advocate use of the percolation temperature as a reference temperature for gravitational wave production, because the percolation temperature is directly connected to transition progress and the collision of bubbles. Finally, we provide model-independent bounds on the bubble wall velocity that allow one to predict whether a transition completes based only on knowledge of the bounce action curve. We apply our methods to find empirical bounds on the bubble wall velocity for which the physical volume of the false vacuum decreases during the transition. We verify the accuracy of our predictions using benchmarks from a high temperature expansion of the Standard Model and from the real scalar singlet model.
Synchronization–desynchronization transitions in networks of circle maps with sinusoidal coupling
Authors: Zhai Yun , Xiao Jinghua , Zheng Zhigang
Published: March 2023

Coupled phase oscillators are adopted as powerful platforms in studying synchrony behaviors emerged in various systems with rhythmic dynamics. Much attention has been focused on coupled time-continuous oscillators described by differential equations. In this paper, we study the synchronization dynamics of networks of coupled circle maps as the discrete version of the Kuramoto model. Despite of its simplicity in mathematical form, it is found that discreteness may induce many interesting synchronization behaviors. Multiple synchronization and desynchronization transitions of both phases and frequencies are found with varying the coupling among circle-map oscillators. The mechanisms of these transitions are interpreted in terms of the mean-field approach, where collective bifurcation cascades are revealed for coupled circle-map oscillators.
A C-shaped miniaturized coil for transcranial magnetic stimulation in rodents
Authors: Jiang Wenxuan , Isenhart Robert , Liu Charles Y , Song Dong
Published: March 2023

Objective. Transcranial magnetic stimulation (TMS) is a non-invasive technique widely used for neuromodulation. Animal models are essential for investigating the underlying mechanisms of TMS. However, the lack of miniaturized coils hinders the TMS studies in small animals, since most commercial coils are designed for humans and thus incapable of focal stimulation in small animals. Furthermore, it is difficult to perform electrophysiological recordings at the TMS focal point using conventional coils. Approach. We designed, fabricated, and tested a novel miniaturized TMS coil (4-by-7 mm) that consisted of a C-shaped iron powder core and insulated copper wires (30 turns). The resulting magnetic and electric fields were characterized with experimental measurements and finite element modeling. The efficacy of this coil in neuromodulation was validated with electrophysiological recordings of single-unit activities (SUAs), somatosensory evoked potentials (SSEPs), and motor evoked potentials (MEPs) in rats (n = 32) following repetitive TMS (rTMS; 3 min, 10 Hz). Main results. This coil could generate a maximum magnetic field of 460 mT and an electric field of 7.2 V m−1 in the rat brain according to our simulations. With subthreshold rTMS focally delivered over the sensorimotor cortex, mean firing rates of primary somatosensory and motor cortical neurons significantly increased (154

±

5% and 160

±

9% from the baseline level, respectively); MEP and SSEP amplitude significantly increased (136

±

9%) and decreased (74

±

4%), respectively. Significance. This miniaturized C-shaped coil enabled focal TMS and concurrent electrophysiological recording/stimulation at the TMS focal point. It provided a useful tool to investigate the neural responses and underlying mechanisms of TMS in small animal models. Using this paradigm, we for the first time observed distinct modulatory effects on SUAs, SSEPs, and MEPs with the same rTMS protocol in anesthetized rats. These results suggested that multiple neurobiological mechanisms in the sensorimotor pathways were differentially modulated by rTMS.
An active dose-measuring device for X-rays generated by ultra-short, ultra-intense laser pulses
Authors: Wang Fengdie , Wang Zhonghai , Wu Yuchi , Wang Shaoyi , Yan Yonghong , Yu Minghai , Zhang Xiaohui , Wen Jiaxing , Tan Fang , Yang Yue , Zhang Jie , Zhou Rong , Yang Chaowen
Published: March 2023

Ultra-short, ultra-intense laser pulses can create extreme
physical conditions for a wide range of applications in atomic and
molecular physics, materials chemistry, and inertial-confinement
fusion. However, laser-matter interactions can be accompanied by
significant X-ray emission that introduces radiation risks to the
nearby environment and personnel. It is usually to monitor the
radiation dose during in high-intensity laser-target interactions
with optically stimulated luminescence and thermo-luminescence
devices. However, these passive methods cannot measure the radiation
dose in real time, while most active dosimeters cannot accurately
measure pulsed radiation doses. Here, transient pulse X-ray
radiation doses are converted by CdWO4 crystals into slow
signals. Because the crystals have a 14-μs luminescence decay
time, they can absorb sub-nanosecond X-ray pulses and release the
energy at a 100-μs rate, thus reducing the linear-response
pressure of subsequent devices. A pulse detector based on a
CdWO4 crystal, a phototube, and a custom signal-processing
circuit was developed. Experiments were performed at the 45-TW
femtosecond laser facility of the Laser Fusion Research Center. The
detector deviation was less than ±20% relative to that of an
ionization-chamber detector. This initially verified its feasibility
for real-time pulsed X-ray radiation detection.
The Natural Robotics Contest: crowdsourced biomimetic design
Authors: Siddall Robert , Zufferey Raphael , Armanini Sophie , Zhang Ketao , Sareh Sina , Sergeev Elisavetha
Published: March 2023

Biomimetic and bioinspired design is not only a potent resource for roboticists looking to develop robust engineering systems or understand the natural world. It is also a uniquely accessible entry point into science and technology. Every person on Earth constantly interacts with nature, and most people have an intuitive sense of animal and plant behaviour, even without realizing it. The Natural Robotics Contest is novel piece of science communication that takes advantage of this intuition, and creates an opportunity for anyone with an interest in nature or robotics to submit their idea and have it turned into a real engineering system. In this paper we will discuss the competition’s submissions, which show how the public thinks of nature as well as the problems people see as most pressing for engineers to solve. We will then show our design process from the winning submitted concept sketch through to functioning robot, to offer a case study in biomimetic robot design. The winning design is a robotic fish which uses gill structures to filter out microplastics. This was fabricated into an open source robot with a novel 3D printed gill design. By presenting the competition and the winning entry we hope to foster further interest in nature-inspired design, and increase the interplay between nature and engineering in the minds of readers.
Federal incentives for community-level climate adaptation: an evaluation of FEMA’s Community Rating System
Authors: Gourevitch Jesse D , Pinter Nicholas
Published: March 2023

In response to growing threats of climate change, the US federal government is increasingly supporting community-level investments in resilience to natural hazards. As such federal programs become more widespread, evaluating their efficiency and equity is essential. The Community Rating System (CRS), which is part of the National Flood Insurance Program (NFIP), is a promising example of a federal policy designed to reduce flood losses by providing financial incentives for local climate adaptation. In exchange for community engagement in a range of risk communication and risk reduction activities, CRS provides discounts on NFIP premiums ranging from 5% to 45%. Using national-scale NFIP claims, policies, and CRS data between 1998 and 2020, we assess the program, asking whether it has been effective in reducing flood losses, how it can be improved, and what lessons it holds for similar programs. We find that participation in CRS is associated with reduced flood damage, with the percent reduction in claims roughly proportional to NFIP premium discounts. Among CRS activities, those related to ‘Flood Damage Reduction’ are most effective in reducing flood losses and are associated with a 20%–30% decrease in NFIP claims. Between 1998 and 2020, cumulative damage reductions attributable to CRS were $11.4 billion; over the same period, cumulative NFIP premium discounts were $12.1 billion. This close match is an endorsement of CRS historically and supports its future continuation. To improve the efficiency and equity of CRS, we recommend that Federal Emergency Management Agency: (a) reexamine the surcharge levied on NFIP premiums that cross-subsidizes premium discounts, and (b) allocate greater resources towards supporting participation among smaller, under-resourced communities. In general, CRS serves as an effective model for other federal market-based programs seeking to stimulate community-level investment in climate resilience.
Are we ready for ocean acidification? A framework for assessing and advancing policy readiness
Authors: Albright Rebecca , Hansson Lina , Cooley Sarah R , Gattuso Jean-Pierre , Marshall Paul , Marshall Nadine , Fletcher Stephen , Haraldsson Gunnar , Hoegh-Guldberg Ove
Published: March 2023

Effective climate policy that addresses carbon dioxide emissions is essential to minimizing and addressing the impacts of ocean acidification (OA). Here we present a framework to assess the readiness of OA policy, using coral reefs as a focal system. Six dimensions encompass comprehensive preparation by ecosystems and societies for the impacts of OA and other anthropogenic hazards: (1) climate protection measures, (2) OA literacy, (3) area-based management, (4) research and development, (5) adaptive capacity of dependent sectors, and (6) policy coherence. We define standardized indicators, identify leading countries, and evaluate the case study of Australia, the country with the largest coral reef system. The framework provides a rubric for a government unit to self- assess strengths and weaknesses in policy preparedness and to prioritize future endeavors.
Newton’s identities and positivity of trace class integral operators
Authors: Homa G , Balka R , Bernád J Z , Károly M , Csordás A
Published: March 2023

We provide a countable set of conditions based on elementary symmetric polynomials that are necessary and sufficient for a trace class integral operator to be positive semidefinite, which is an important cornerstone for quantum theory in phase-space representation. We also present a new, efficiently computable algorithm based on Newton’s identities. Our test of positivity is much more sensitive than the ones given by the linear entropy and Robertson-Schrödinger’s uncertainty relations; our first condition is equivalent to the non-negativity of the linear entropy.
Alcohol Consumption and Mental Health during the COVID-19 Pandemic
Authors: Yue Yihua , Wang Siyi , Smith Ella , Goyal Divya , Zhu Kexin , Zhang Zuo-Feng , Smith Beth , Niu Zhongzheng , Lei Lijian , Freudenheim Jo L , Cao Ying , Mu Lina
Published: March 2023

Aims

To examine the association between alcohol consumption and mental health during the COVID-19 pandemic.

Methods

An anonymous online survey was distributed among US adults during May–August 2020 through social networks and ResearchMatch. We collected information on demographic, lifestyles and mental health symptoms including anxiety, depression, stress and post-traumatic stress disorder. Logistic regression models were used to examine the cross-sectional association between alcohol consumption and mental health symptoms. We also examined effect modification by race, age, gender, social support, financial insecurity and quarantine status.

Results

The analytical sample consists of 3623 adults. Stable drinking habits and regular drinking behaviors were found to co-exist with better mental health status. Participants who increased their alcohol use had higher odds of developing mental health disorders than those who maintained their pre-pandemic drinking habits. Additionally, participants who engaged in binge drinking during the pandemic had higher odds of depression and stress than those who did not. The associations regarding increased drinking and binge drinking in relation to adverse mental health outcomes were stronger among females, racial minorities, and individuals with financial concerns, poor social support and restricted quarantine status than their counterparts.

Conclusions

During the early stage of the COVID-19 pandemic, increased alcohol use and binge drinking are cross-sectionally associated with higher odds of mental health disorders, which highlighted the need for targeted intervention to address the mental health needs of individuals who have engaged in these behaviors, especially among females, minorities, those with insecurities or with restricted quarantine status.
Guidelines for Optimal Patient Outcomes Using Calcium Hydroxylapatite for Jawline Contour
Authors: Moradi Amir , Green Jeremy B , Kwok Gideon P , Nichols Kim , Rivkin Alexander
Published: March 2023

Background

Calcium hydroxylapatite (CaHA(+); Radiesse(+) [Merz North America, Inc., Raleigh, NC]) is the first FDA-approved injectable filler for subdermal and/or supraperiosteal injection to improve moderate-to-severe loss of jawline contour. CaHA has been recognized in the past for its ability to provide contour and support overlying tissues and utilized for jawline augmentation well before this recent indication; however, with recent FDA approval of CaHA(+) for jawline contour improvement, it is important that clinicians are aware of best practices for patient selection, treatment planning and injection, as well as safety considerations and postprocedure care.

Objectives

To provide guidance on best practices for patient assessment and on-label use of CaHA(+) for jawline rejuvenation and augmentation.

Methods

As part of a 2-h roundtable discussion, 5 clinicians with expertise in both the use of CaHA(+) and jawline treatment discussed patient selection, CaHA(+) injection technique, and important safety measures, with the purpose of developing guidance to support optimal clinical use.

Results

The most common applications of CaHA(+) in the jawline are rejuvenation of the prejowl sulcus, recontouring the jawline, and providing definition to the gonial angle. Improving the gonial angle is of particular interest as it is a procedure sought by patients of all genders and ages. Variations in technique are discussed and case studies are presented.

Conclusions

Jawline augmentation is a procedure with wide-ranging appeal for a diverse array of patients. CaHA(+) is an ideal filler for jawline augmentation due to its rheologic properties (high G′) and ability to achieve defined contours and angles. Appropriate injection technique permits effective treatment and outcomes associated with high patient satisfaction.

Level of Evidence: 5
iATMEcell: identification of abnormal tumor microenvironment cells to predict the clinical outcomes in cancer based on cell–cell crosstalk network
Authors: Sheng Yuqi , Wu Jiashuo , Li Xiangmei , Qiu Jiayue , Li Ji , Ge Qinyu , Cheng Liang , Han Junwei
Published: March 2023

Interactions between Tumor microenvironment (TME) cells shape the unique growth environment, sustaining tumor growth and causing the immune escape of tumor cells. Nonetheless, no studies have reported a systematic analysis of cellular interactions in the identification of cancer-related TME cells. Here, we proposed a novel network-based computational method, named as iATMEcell, to identify the abnormal TME cells associated with the biological outcome of interest based on a cell–cell crosstalk network. In the method, iATMEcell first manually collected TME cell types from multiple published studies and obtained their corresponding gene signatures. Then, a weighted cell–cell crosstalk network was constructed in the context of a specific cancer bulk tissue transcriptome data, where the weight between cells reflects both their biological function similarity and the transcriptional dysregulated activities of gene signatures shared by them. Finally, it used a network propagation algorithm to identify significantly dysregulated TME cells. Using the cancer genome atlas (TCGA) Bladder Urothelial Carcinoma training set and two independent validation sets, we illustrated that iATMEcell could identify significant abnormal cells associated with patient survival and immunotherapy response. iATMEcell was further applied to a pan-cancer analysis, which revealed that four common abnormal immune cells play important roles in the patient prognosis across multiple cancer types. Collectively, we demonstrated that iATMEcell could identify potentially abnormal TME cells based on a cell–cell crosstalk network, which provided a new insight into understanding the effect of TME cells in cancer. iATMEcell is developed as an R package, which is freely available on GitHub (https://github.com/hanjunwei-lab/iATMEcell).
Altered functional dynamics gradient in schizophrenia with cigarette smoking
Authors: Chen Yanchi
Published: March 2023

Schizophrenia is associated with a high prevalence of cigarette smoking. Neural dynamics are spatially structured and shaped by both microscale molecular and macroscale functional architectures, which are disturbed in the diseased brain. The neural mechanism underlying the schizophrenia-nicotine dependence comorbidity remains unknown. In this study, we aimed to test whether there is an interaction between schizophrenia and smoking in brain neural dynamics, and how the main effect of the 2 factors related to the molecular architecture. Functional magnetic resonance imaging data were obtained from 4 groups: schizophrenia and healthy controls with/without smoking. We identified 2 dynamics gradients combined with over 5,000 statistical features of the brain region's time series. The interaction effect was found in the high-order functional network, and the main effect of schizophrenia was in the bilateral orbitofrontal cortices. Moreover, the disease- and smoking-related alteration in brain pattern was associated with spatial distribution of serotonin, cannabinoid, and glutamate. Collectively, these findings supported the self-medication hypothesis in schizophrenia-nicotine dependence with a neural intrinsic dynamics perspective.
A brain-wide genome-wide association study of candidate quantitative trait loci associated with structural and functional phenotypes of pain sensitivity
Authors: Zhang Li , Pan Yiwen , Huang Gan , Liang Zhen , Li Linling , Zhang Min , Zhang Zhiguo
Published: March 2023

Individual pain sensitivity is modulated by the brain’s structural and functional features, but its heritability remains unclear. This paper conducted a brain-wide genome-wide association study (GWAS) to explore the genetic bases of neuroimage phenotypes of pain sensitivity. In total, 432 normal participants were divided into high and low pain sensitivity groups according to the laser quantitative test threshold. Then, the brain’s gray matter density (GMD) features correlated with pain sensitivity were identified. Next, GWAS was performed on each GMD phenotype using quality-controlled genotypes. Based on the heatmap and hierarchical clustering results, the right insula was identified for further refined analysis in terms of subregions GMD and resting-state functional connectivity (rs-FC) phenotypes. The results indicate that the right insula GMD in the high sensitivity group is significantly lower than that in the low sensitivity group. Also, the TT/TC group at locus rs187974 has lower right insula GMD than the CC group. Further, loci at gene CYP2D6 may lead to a variation of rs-FC between the right insula and left putamen. In conclusion, our study suggests that the right insula and multiple candidate loci may be importantly involved in pain sensitivity modulation, which may guide the future development of precision pain therapeutics.
Impact of Treatment on Long-Term Survival of Patients With Mycobacterium avium Complex Pulmonary Disease
Authors: Kim Joong-Yub , Choi Yunhee , Park JiWon , Goo Jin Mo , Kim Taek Soo , Seong Moon-Woo , Kwak Nakwon , Yim Jae-Joon
Published: March 2023

Background

Whether antimicrobial treatment improves long-term survival in patients with Mycobacterium avium complex pulmonary disease (MAC-PD) is unclear.

Methods

We analyzed survival in patients aged ≥18 years who were treated for MAC-PD at a tertiary referral center in South Korea between 1 January 2009 and 31 December 2020. Treatment exposure was divided into 4 time intervals: <6, ≥6 to <12, ≥12 to <18, and ≥18 months. Time-varying multivariable Cox proportional hazards models were used to calculate the all-cause mortality risk in each time interval. The model was adjusted for major clinical factors related to mortality including age, sex, body mass index, presence of cavities, erythrocyte sedimentation rate, positive acid-fast bacilli (AFB) smear, clarithromycin resistance, and comorbid conditions.

Results

A total of 486 patients treated for MAC-PD were included in the analysis. A significant inverse correlation was observed between mortality and duration of treatment (P for trend = .007). Long-term treatment (≥18 months) was significantly associated with reduced mortality (adjusted hazard ratio, 0.32 [95% confidence interval, .15–.71]). In subgroup analyses, patients with cavitary lesions (adjusted hazard ratio, 0.17 [95% confidence interval, .05–.57]) or positive AFB smears (0.13 [.02–.84]) at baseline maintained this significant inverse relationship between treatment duration and mortality.

Conclusions

Long-term antimicrobial treatment should be actively considered in patients with progressive MAC-PD, especially in the presence of cavities or positive AFB smears indicative of high mycobacterial burden.
Crisis and the welfare state: the role of public employment services for job placement and the Danish flexicurity system during COVID-19
Authors: Schmidt Torben Dall , Mitze Timo
Published: March 2023

Denmark is a Nordic welfare state with local government autonomy in public service provision related to workfare policies. We use a policy experiment that re-opened on-site public employment services after the first COVID-19 lockdown in a spatially staggered manner to provide evidence on the effect of public employment services on job placement during a crisis. Early re-opening of on-site public employment services is associated with a better local labour market performance. It particularly benefits low-skilled unemployed and rural areas with specific sector mixes and demographic structures, why workfare-oriented welfare state arrangements remain important to counter social and regional imbalances.
Prediction of heart transplant rejection from routine pathology slides with self-supervised deep learning
Authors: Seraphin Tobias Paul , Luedde Mark , Roderburg Christoph , van Treeck Marko , Scheider Pascal , Buelow Roman D , Boor Peter , Loosen Sven H , Provaznik Zdenek , Mendelsohn Daniel , Berisha Filip , Magnussen Christina , Westermann Dirk , Luedde Tom , Brochhausen Christoph , Sossalla Samuel , Kather Jakob Nikolas
Published: March 2023

Aims

One of the most important complications of heart transplantation is organ rejection, which is diagnosed on endomyocardial biopsies by pathologists. Computer-based systems could assist in the diagnostic process and potentially improve reproducibility. Here, we evaluated the feasibility of using deep learning in predicting the degree of cellular rejection from pathology slides as defined by the International Society for Heart and Lung Transplantation (ISHLT) grading system.

Methods and results

We collected 1079 histopathology slides from 325 patients from three transplant centres in Germany. We trained an attention-based deep neural network to predict rejection in the primary cohort and evaluated its performance using cross-validation and by deploying it to three cohorts. For binary prediction (rejection yes/no), the mean area under the receiver operating curve (AUROC) was 0.849 in the cross-validated experiment and 0.734, 0.729, and 0.716 in external validation cohorts. For a prediction of the ISHLT grade (0R, 1R, 2/3R), AUROCs were 0.835, 0.633, and 0.905 in the cross-validated experiment and 0.764, 0.597, and 0.913; 0.631, 0.633, and 0.682; and 0.722, 0.601, and 0.805 in the validation cohorts, respectively. The predictions of the artificial intelligence model were interpretable by human experts and highlighted plausible morphological patterns.

Conclusion

We conclude that artificial intelligence can detect patterns of cellular transplant rejection in routine pathology, even when trained on small cohorts.
Agl28 and Agl29 are key components of aHalobacterium salinarum N-glycosylation pathway
Authors: Vershinin Zlata , Zaretsky Marianna , Guan Ziqiang , Eichler Jerry
Published: March 2023

Although Halobacterim salinarum provided the first example of N-glycosylation outside the Eukarya, only recently has attention focused on delineating the pathway responsible for the assembly of the N-linked tetrasaccharide decorating selected proteins in this haloarchaeon. In the present report, the roles of VNG1053G and VNG1054G, two proteins encoded by genes clustered together with a set of genes demonstrated to encode N-glycosylation pathway components, were considered. Relying on both bioinformatics and gene deletion and subsequent mass spectrometry analysis of known N-glycosylated proteins, VNG1053G was determined to be the glycosyltransferase responsible for addition of the linking glucose, while VNG1054G was deemed to be the flippase that translocates the lipid-bound tetrasaccharide across the plasma membrane to face the cell exterior, or to contribute to such activity. As observed with Hbt. salinarum lacking other components of the N-glycosylation machinery, both cell growth and motility were compromised in the absence of VNG1053G or VNG1054G. Thus, given their demonstrated roles in Hbt. salinarum N-glycosylation, VNG1053G and VNG1054G were re-annotated as Agl28 and Agl29, according to the nomenclature used to define archaeal N-glycosylation pathway components.
Current trends and future perspective of probiotic yeasts research in Indonesia
Authors: Astuti Rika Indri , Prastya Muhammad Eka , Wulan Rahayu , Anam Khairul , Meryandini Anja
Published: March 2023

Indonesia is a mega biodiversity country with various local wisdom, including the enormous variety of fermented foods and beverages. Indonesian researchers have conducted an intensive study to understand the diversity of microbes on those fermented products, one of which shows probiotic properties. Compared to that lactic acid bacteria, the study on probiotic yeasts is less explored. Probiotic yeast isolates are commonly isolated from traditional Indonesian fermented products. Saccharomyces, Pichia, and Candida are among Indonesia’s most popular genera of probiotic yeasts, primarily applied in poultry and human health. The exploration of functional probiotic characteristics, such as antimicrobial, antifungal, antioxidant, and immunomodulator, has been widely reported from these local probiotic yeast strains. In vivo studies in a model organism such as mice conclude the prospective functional probiotic characteristics of the yeast isolates. Employment of current technology, such as omics, is essential in elucidating those functional properties. Advanced research and development of probiotic yeasts in Indonesia are gaining significant attention currently. For instance, probiotic yeasts-mediated fermentation in the production of kefir and kombucha are among the trend with promising economic value. The future trends of probiotic yeasts research in Indonesia are discussed in this review to give valuable sight into the application of indigenous probiotic yeasts in various fields.
From multiallele fish to nonstandard environments, how ZFIN assigns phenotypes, human disease models, and gene expression annotations to genes
Authors: Bradford Yvonne M , Van Slyke Ceri E , Howe Douglas G , Fashena David , Frazer Ken , Martin Ryan , Paddock Holly , Pich Christian , Ramachandran Sridhar , Ruzicka Leyla , Singer Amy , Taylor Ryan , Tseng Wei-Chia , Westerfield Monte
Published: March 2023

Danio rerio is a model organism used to investigate vertebrate development. Manipulation of the zebrafish genome and resultant gene products by mutation or targeted knockdown has made the zebrafish a good system for investigating gene function, providing a resource to investigate genetic contributors to phenotype and human disease. Phenotypic outcomes can be the result of gene mutation, targeted knockdown of gene products, manipulation of experimental conditions, or any combination thereof. Zebrafish have been used in various genetic and chemical screens to identify genetic and environmental contributors to phenotype and disease outcomes. The Zebrafish Information Network (ZFIN, zfin.org) is the central repository for genetic, genomic, and phenotypic data that result from research using D. rerio. Here we describe how ZFIN annotates phenotype, expression, and disease model data across various experimental designs, how we computationally determine wild-type gene expression, the phenotypic gene, and how these results allow us to propagate gene expression, phenotype, and disease model data to the correct gene, or gene related entity.
Relationship between normalized permeability and resistivity index in hydrate-bearing sediments: fractal model and numerical simulation
Authors: Tian Haitao , Liu Lele , Zhu Linqi , Ge Xinmin , Ding Pinbo , Cai Jianchao
Published: March 2023

Permeability is a critical factor in evaluating the fluid flow capacity and production performance of natural gas hydrate reservoirs. The similarity of electrical conduction and hydraulic flow makes it possible to predict reservoir permeability using electrical data. Clarifying the relationship between the permeability and resistivity of sediments with different hydrate growth habits contributes to the efficient exploration and development of natural gas hydrate resources. In this work, normalized permeability and the resistivity index models for grain-coating (GC) and pore-filling (PF) hydrates are developed based on the fractal geometry theory, forming a new relationship between normalized permeability and resistivity index. The empirical exponent is determined by fractal dimension. Meanwhile, we selected five sets of 3-D computed tomography (CT) images of quartz sand with different particle sizes, GC and PF hydrate digital rocks are constructed using random simulation methods. The numerical simulation of permeability and resistivity index is carried out, based on the pore microstructure images, the box counting method was used to calculate the fractal dimension and analyse the relationship between pore space and transport paths. Furthermore, the pore radius, throat radius and pore connection number are extracted through the pore network method to study the evolution of pore space. The results show that the tortuosity fractal dimension is a critical parameter in the relationship between normalized permeability and resistivity index. The proposed analytical expressions are validated by laboratory and well log data, and the exponent ranges cover existing hydrate permeability–resistivity index data. The models provide the possibility to predict the normalized permeability of hydrate reservoirs based on electrical data alone.
Exploring food environment interventions for diet-related outcomes using a food sovereignty framework: a systematic review
Authors: Lofton Saria , Simonovich Shannon D , Buscemi Joanna , Grant Alexis , O’Donnell Alexander , Nwafor Gilliane , Reid Madeline
Published: March 2023

Building local food systems through a food sovereignty lens, harnessing the right of people to control their own food systems, may enhance healthy food access and increase the consumption of fruits and vegetables in local communities. While research to date has described the outcomes of various multilevel, multicomponent food systems interventions, no known literature reviews to date have systematically examined food system interventions and dietary and health outcomes through the context of a food sovereignty lens. Utilization of a food sovereignty framework allows for the incorporation of key food systems and community-based concepts in the food environment literature. The purpose of this systematic review was to describe and summarize the efficacy of community-based local food system interventions, using the food sovereignty framework, for both pediatric and adult populations and their impact on health behaviors and physiological outcomes. We searched for peer-reviewed articles using Scopus, PubMed, PsychInfo and CINAHL databases and identified 11 articles that met the inclusion criteria for this study. Seven studies found that food systems interventions had a significant positive effect on improving health outcomes, three had null findings and one had null or negative results. Two studies utilized a community-based participatory approach. The most successful interventions involved community-based engagement involving multiple aspects of the food system and involving both children and adults for maximum impact. Our results inform how community-based food systems interventions can be guided by food sovereignty principles to improve health outcomes, such as body weight and fruit and vegetable intake, for both pediatric and adult populations.
The Quran and the Sword
Authors: Auriol Emmanuelle , Platteau Jean-Philippe , Verdier Thierry
Published: March 2023

This paper elucidates the willingness of an autocrat to push through institutional reforms in a context where traditional authorities represented by religious clerics are averse to them and where the military control the means of repression and can potentially stage a coup. We show that although the autocrat always wants to co-opt the military, this is not necessarily true of the clerics. Exclusive co-option of the military obtains where the loyalty of the autocrat’s army is strong while the organizational strength of religious movements is rather low. Radical institutional reforms can then be implemented. Empirically, the dominant regime in contemporary Muslim countries is the regime of double co-option where the autocrat resorts to a double-edged tactic: pleasing the official clerics by slowing the pace of reforms and ensuring the loyalty of the military so as to put down clerics-led rebellions.
A high-quality reference genome for the critically endangered Aeolian wall lizard, Podarcis raffonei
Authors: Gabrielli Maëva , Benazzo Andrea , Biello Roberto , Ancona Lorena , Fuselli Silvia , Iannucci Alessio , Balacco Jennifer , Mountcastle Jacqueline , Tracey Alan , Ficetola Gentile Francesco , Salvi Daniele , Sollitto Marco , Fedrigo Olivier , Formenti Giulio , Jarvis Erich D , Gerdol Marco , Ciofi Claudio , Trucchi Emiliano , Bertorelle Giorgio
Published: March 2023

The Aeolian wall lizard, Podarcis raffonei, is an endangered species endemic to the Aeolian archipelago, Italy, where it is present only in 3 tiny islets and a narrow promontory of a larger island. Because of the extremely limited area of occupancy, severe population fragmentation and observed decline, it has been classified as Critically Endangered by the International Union for the Conservation of Nature (IUCN). Using Pacific Biosciences (PacBio) High Fidelity (HiFi) long-read sequencing, Bionano optical mapping and Arima chromatin conformation capture sequencing (Hi-C), we produced a high-quality, chromosome-scale reference genome for the Aeolian wall lizard, including Z and W sexual chromosomes. The final assembly spans 1.51 Gb across 28 scaffolds with a contig N50 of 61.4 Mb, a scaffold N50 of 93.6 Mb, and a BUSCO completeness score of 97.3%. This genome constitutes a valuable resource for the species to guide potential conservation efforts and more generally for the squamate reptiles that are underrepresented in terms of available high-quality genomic resources.
Detection and estimation of the cosmic dipole with the einstein telescope and cosmic explorer
Authors: Mastrogiovanni S , Bonvin C , Cusin G , Foffa S
Published: March 2023

One of the open issues of the standard cosmological model is the value of the cosmic dipole measured from the Cosmic Microwave Background (CMB), as well as from the number count of quasars and radio sources. These measurements are currently in tension, with the number count dipole being 2–5 times larger than expected from CMB measurements. This discrepancy has been pointed out as a possible indication that the cosmological principle is not valid. In this paper, we explore the possibility of detecting and estimating the cosmic dipole with gravitational waves (GWs) from compact binary mergers detected by the future next-generation detectors Einstein Telescope and Cosmic Explorer. We model the expected signal and show that for binary black holes, the dipole amplitude in the number count of detections is independent of the characteristics of the population and provides a systematic-free tool to estimate the observer velocity. We introduce techniques to detect the cosmic dipole from number counting of GW detections and estimate its significance. We show that a GW dipole consistent with the amplitude of the dipole in radio galaxies would be detectable with >3σ significance with a few years of observation (106 GW detections) and estimated with a 16 per cent precision, while a GW dipole consistent with the CMB one would require at least 107 GW events for a confident detection. We also demonstrate that a total number Ntot of GW detections would be able to detect a dipole with amplitude $v_o/c \simeq 1/\sqrt{N_{\rm tot}}$.
Sarecycline inhibits protein translation inCutibacterium acnes70S ribosome using a two-site mechanism
Authors: Lomakin Ivan B , Devarkar Swapnil C , Patel Shivali , Grada Ayman , Bunick Christopher G
Published: March 2023

Acne vulgaris is a chronic disfiguring skin disease affecting ∼1 billion people worldwide, often having persistent negative effects on physical and mental health. The Gram-positive anaerobe, Cutibacterium acnes is implicated in acne pathogenesis and is, therefore, a main target for antibiotic-based acne therapy. We determined a 2.8-Å resolution structure of the 70S ribosome of Cutibacterium acnes by cryogenic electron microscopy and discovered that sarecycline, a narrow-spectrum antibiotic against Cutibacterium acnes, may inhibit two active sites of this bacterium's ribosome in contrast to the one site detected previously on the model ribosome of Thermus thermophilus. Apart from the canonical binding site at the mRNA decoding center, the second binding site for sarecycline exists at the nascent peptide exit tunnel, reminiscent of the macrolides class of antibiotics. The structure also revealed Cutibacterium acnes-specific features of the ribosomal RNA and proteins. Unlike the ribosome of the Gram-negative bacterium Escherichia coli, Cutibacterium acnes ribosome has two additional proteins, bS22 and bL37, which are also present in the ribosomes of Mycobacterium smegmatis and Mycobacterium tuberculosis. We show that bS22 and bL37 have antimicrobial properties and may be involved in maintaining the healthy homeostasis of the human skin microbiome.