bluuebunny/crossref_metadata_2025 huggingface dataset:
Lifetime estimation model of vapor cells in atomic magnetometers
Authors: Liu Zhi , Zou Sheng , Yin Kaifeng , Zhou Binquan , Ning Xiaolin , Yuan Heng
Published: April 2022

A lifetime estimation model is proposed by characterizing the consumption of the components inside the atomic vapor cells in this work. The buffer gas leakage and alkali metal consumption in vapor cells will significantly destroy the performance of atomic magnetometers. Combining the light absorption method and aging experiments, the deterioration of helium pressure, rubidium vapor density, and cell wall transmittance were obtained to construct the lifetime estimation model that depends on time, working temperature, and initial contents. Then, the causes and consequences of these deteriorations were analyzed, and the combination of theoretical analysis and experimental data showed that the vapor cell invalidation caused by these factors conforms to the Weibull distribution. In order to establish the relationship between the component consumption and the performance of the magnetometer constituted by this cell, a single-beam magnetometer prototype was designed for sensitivity testing. Experiments have shown that the sensitivity of magnetometer is rapidly deteriorating after operating 600 h under 150 °C, which is mainly related to alkali metal consumption. Additionally, 200 °C is a trade-off aging experimental temperature between the aging efficiency and the stability of the cell. The proposed model can be applied to optimize the lifetime of the vapor cells used not only in magnetometers but also in gyroscopes and atomic clocks.
Electroweak phase transition in the presence of hypermagnetic field and the generation of gravitational waves
Authors: Abedi H , Ahmadvand M , Gousheh S S
Published: April 2022

We investigate the effects of a large-scale background hypermagnetic field on the electroweak phase transition (EWPT). We propose a model in which an effective weak angle varies during the EWPT and upon its use we show that, although for the majority of the parameter space the phase transition is a crossover, there are tiny regions in which the phase transition occurs in two steps and can be first-order. We obtain all of the important quantities characterizing the details of the first-order phase transition, including the latent heat, transition temperature and duration. We then calculate the gravitational wave energy spectrum generated during the first-order part of the EWPT and find that, for strong enough background hypermagnetic fields, these signals can be detected by the Ultimate-DECIGO interferometer.
Laser induced enhanced coupling between photons and squeezed magnons in antiferromagnets
Authors: Henriques J C G , Antão T V C , Peres N M R
Published: April 2022

In this paper we consider a honeycomb antiferromagnet subject to an external laser field. Obtaining a time-independent effective Hamiltonian, we find that the external laser renormalizes the exchange interaction between the in-plane components of the spin-operators, and induces a synthetic Dzyaloshinskii–Moria interaction (DMI) between second neighbors. The former allows the control of the magnon dispersion’s bandwidth and the latter breaks time-reversal symmetry inducing non-reciprocity in momentum space. The eigen-excitations of the system correspond to squeezed magnons whose squeezing parameters depend on the properties of the laser. When studying how these spin excitations couple with cavity photons, we obtain a coupling strength which can be enhanced by an order of magnitude via careful tuning of the laser’s intensity, when compared to the case where the laser is absent. The transmission plots through the cavity are presented, allowing the mapping of the magnons’ dispersion relation.
A phenomenological theory of superconductor diodes
Authors: He James Jun , Tanaka Yukio , Nagaosa Naoto
Published: April 2022

Nonreciprocal responses in noncentrosymmetric systems contain a broad range of phenomena. Especially, non-dissipative and coherent nonreciprocal transport in solids is an important fundamental issue. The recent discovery of superconductor (SC) diodes under external magnetic fields, where the magnitude of the critical current changes as the direction is reversed, significantly boosted this research area. However, a theoretical understanding of such phenomena is lacking. Here, we provide theoretical descriptions of SC diodes with a generalized Ginzburg–Landau method. The theory is applied to Rashba spin–orbit coupled systems, where analytical relations between the nonreciprocal critical currents and the system parameters are achieved. Numerical calculations with mean-field theory are also obtained to study broader parameter regions. These results offer a rather general description and design principles of SC diodes.
Quantitative laser-based x-ray fluorescence and particle-induced x-ray emission
Authors: Boivin Frédéric , Vallières Simon , Fourmaux Sylvain , Payeur Stéphane , Antici Patrizio
Published: April 2022

In this work, we demonstrate the feasibility of quantitative laser-based x-ray fluorescence (XRF) combined with particle-induced x-ray emission (PIXE) (called XPIF for x-ray and particle-induced fluorescence) spectroscopy analysis for elemental composition in solid samples. A multi-hundred TW laser system accelerated protons and produced x-rays that were impinging on solid samples, inducing characteristic line emissions of the elements contained in the material. The x-ray yield obtained from the characteristic emissions for each element can be related to its mass concentration using both the thick PIXE and thick XRF formalism. This is performed by using of an iterative numerical procedure. We tested the validity of our method on three homogeneous metallic materials, stainless steel, bronze and brass. The mass proportions of these samples retrieved by our analysis (XPIF) is within the errors bars compared with a commercial energy dispersive x-ray spectrometer.
Probing the properties of dense nuclear matter with photon conversions at NICA
Authors: Burmasov N , Kryshen E , Ivanishchev D , Kotov D , Malaev M , Riabov V , Ryabov Y
Published: April 2022

Photons serve as valuable probes of the properties of the hot and dense nuclear matter created in collisions of heavy ions. Thermal photon spectra at RHIC and LHC energies indicate that the temperature of the produced medium far exceeds the temperature of the phase transition to the quark-gluon plasma in lattice QCD calculations. Measurements of thermal photon spectra in heavy ion collisions at lower energies at the future NICA collider may help to trace the transition from partonic to hadronic degrees of freedom. In this contribution, feasibility studies on thermal photon measurements using the photon conversion method in the future MPD experiment at NICA will be reviewed. In this work, a possibility to increase photon reconstruction efficiency with a dedicated conversion layer is presented and feasibility to probe the material budget of the experiment with converted photons is discussed.
Two dimensional relativistic electron in a constant magnetic field
Authors: Bentalha Z
Published: April 2022

The (2+1)-dimensional Dirac equation for an electron in a constant magnetic field is considered. Exact solutions of this equation along with the corresponding energy spectrum are derived in a concise form. Among these solutions, we noticed that the lowest Landau level wavefunction corresponds to an anti-electron (an electron with a negative energy). The latter appears because special relativity allows solutions with negative energies. This means that a relativistic electron (matter) in a uniform magnetic field, at the lowest Landau level, is mutated to an anti-electron (anti-matter). This is a good finding for those that are interested in anti-matter applications.
Physical analysis of normally-off ALD Al2O3/GaN MOSFET with different substrates using self-terminating thermal oxidation-assisted wet etching technique
Authors: Huang Cheng-Yu , Wang Jin-Yan , Zhang Bin , Fu Zhen , Liu Fang , Wang Mao-Jun , Li Meng-Jun , Wang Xin , Wang Chen , He Jia-Yin , He Yan-Dong
Published: April 2022

Based on the self-terminating thermal oxidation-assisted wet etching technique, two kinds of enhancement mode Al2O3/GaN MOSFETs (metal–oxide–semiconductor field-effect transistors) separately with sapphire substrate and Si substrate are prepared. It is found that the performance of sapphire substrate device is better than that of silicon substrate. Comparing these two devices, the maximum drain current of sapphire substrate device (401 mA/mm) is 1.76 times that of silicon substrate device (228 mA/mm), and the field-effect mobility (μ
FEmax) of sapphire substrate device (176 cm2/V⋅s) is 1.83 times that of silicon substrate device (96 cm2/V⋅s). The conductive resistance of silicon substrate device is 21.2Ω ⋅mm, while that of sapphire substrate device is only 15.2Ω ⋅mm, which is 61% that of silicon substrate device. The significant difference in performance between sapphire substrate and Si substrate is related to the differences in interface and border trap near Al2O3/GaN interface. Experimental studies show that (i) interface/border trap density in the sapphire substrate device is one order of magnitude lower than in the Si substrate device, (ii) Both the border traps in Al2O3 dielectric near Al2O3/GaN and the interface traps in Al2O3/GaN interface have a significantly effect on device channel mobility, and (iii) the properties of gallium nitride materials on different substrates are different due to wet etching. The research results in this work provide a reference for further optimizing the performances of silicon substrate devices.
Dual-channel tunable near-infrared absorption enhancement with graphene induced by coupled modes of topological interface states
Authors: Su Zeng-Ping , Wei Tong-Tong , Wang Yue-Ke
Published: April 2022

The dual-channel nearly perfect absorption is realized by the coupled modes of topological interface states (TIS) in the near-infrared range. An all-dielectric layered heterostructure composed of photonic crystals (PhC)/graphene/PhC/graphene/PhC on GaAs substrate is proposed to excite the TIS at the interface of adjacent PhC with opposite topological properties. Based on finite element method (FEM) and transfer matrix method (TMM), the dual-channel absorption can be modulated by the periodic number of middle PhC, Fermi level of graphene, and angle of incident light (TE and TM polarizations). Especially, by fine-tuning the Fermi level of graphene around 0.4 eV, the absorption of both channels can be switched rapidly and synchronously. This design is hopefully integrated into silicon-based chips to control light.
Targeted Search for Fast Radio Bursts with Nanshan 26 m Radio Telescope
Authors: Mao Jian-Wei , Yuan Jian-Ping , Wen Zhi-Gang , Li Jian , Wang Na , Wang Pei , Yuen Rai , Wang Yu-Bin , Zhai Nan-Nan , Liu Zhi-Yong , Chen Mao-Zheng , Li Guang-Hui
Published: April 2022

Fast radio bursts (FRBs) are radio transients that are bright and have short duration, with their physical mechanism not being fully understood. We conducted a targeted search for bursts from FRB 20201124A between 2021 June 2 and July 20. High time-resolution data were collected for 104.5 hr using the ROACH2-based digital backend. We introduce the details of our FRB search pipeline which is based on HEIMDALL and FETCH. Testing of the injected mock FRBs search could help us better understand the performance of the pipelines, and improve the search algorithms and classifiers. To study the efficiency of our pipeline, 5000 mock FRBs were injected into the data and searched using the pipeline. The results of the mock FRB search show that our pipeline can recover almost all (≳90%) the injected mock FRBs above a signal-to-noise ratio (S/N) threshold of 15, and the performance is still acceptable (≳80%) for injected S/Ns from 10 to 15. The recovery fraction displays relations with S/N, dispersion measure and pulse width. No bursts were detected from FRB 20201124A in the middle of 2021. The non-detection of FRB 20201124A may be due to its quiet phase window or no emission above the threshold of the Nanshan telescope.
Optimizing the montage for cerebellar transcranial alternating current stimulation (tACS): a combined computational and experimental study
Authors: Sadeghihassanabadi Fatemeh , Misselhorn Jonas , Gerloff Christian , Zittel Simone
Published: April 2022

Objective. The application of cerebellar transcranial alternating current stimulation (tACS) is limited by the absence of commonly agreed montages and also the presence of unpleasant side effects. We aimed to find the most effective cerebellar tACS montage with minimum side effects (skin sensations and phosphenes). Approach. We first simulated cerebellar tACS with five montages (return electrode on forehead, buccinator, jaw, and neck positions, additionally focal montage with high-definition ring electrodes) to compare induced cerebellar current, then stimulated healthy participants and evaluated side effects for different montages and varying stimulation frequencies. Main results. The simulation revealed a descending order of current density in the cerebellum from forehead to buccinator, jaw, neck and ring montage respectively. Montages inducing higher current intensity in the eyeballs during the simulation resulted in stronger and broader phosphenes during tACS sessions. Strong co-stimulation of the brainstem was observed for the neck. Skin sensations did not differ between montages or frequencies. We propose the jaw montage as an optimal choice for maximizing cerebellar stimulation while minimizing unwanted side effects. Significance. These findings contribute to adopting a standard cerebellar tACS protocol. The combination of computational modelling and experimental data offers improved experimental control, safety, effectiveness, and reproducibility to all brain stimulation practices.
Interpretable functional specialization emerges in deep convolutional networks trained on brain signals
Authors: Hammer J , Schirrmeister R T , Hartmann K , Marusic P , Schulze-Bonhage A , Ball T
Published: April 2022

Objective.Functional specialization is fundamental to neural information processing. Here, we study whether and how functional specialization emerges in artificial deep convolutional neural networks (CNNs) during a brain–computer interfacing (BCI) task.Approach.We trained CNNs to predict hand movement speed from intracranial electroencephalography (iEEG) and delineated how units across the different CNN hidden layers learned to represent the iEEG signal.Main results.We show that distinct, functionally interpretable neural populations emerged as a result of the training process. While some units became sensitive to either iEEG amplitude or phase, others showed bimodal behavior with significant sensitivity to both features. Pruning of highly sensitive units resulted in a steep drop of decoding accuracy not observed for pruning of less sensitive units, highlighting the functional relevance of the amplitude- and phase-specialized populations.Significance.We anticipate that emergent functional specialization as uncovered here will become a key concept in research towards interpretable deep learning for neuroscience and BCI applications.
First-passage Brownian functionals with stochastic resetting
Authors: Singh Prashant , Pal Arnab
Published: April 2022

We study the statistical properties of first-passage time functionals of a one dimensional Brownian motion in the presence of stochastic resetting. A first-passage functional is defined as

V
=

∫

0

t

f

Z

[

x

(

τ

)

]

where t
f is the first-passage time of a reset Brownian process x(τ), i.e., the first time the process crosses zero. In here, the particle is reset to x

R
> 0 at a constant rate r starting from x
0 > 0 and we focus on the following functionals: (i) local time

T

l
o
c

=

∫

0

t

f

d
τ
δ

(

x
−

x

R

)

, (ii) residence time

T

r
e
s

=

∫

0

t

f

d
τ
θ

(

x
−

x

R

)

, and (iii) functionals of the form

A

n

=

∫

0

t

f

d
τ

[

x

(

τ

)

]

n

with n > −2. For first two functionals, we analytically derive the exact expressions for the moments and distributions. Interestingly, the residence time moments reach minima at some optimal resetting rates. A similar phenomena is also observed for the moments of the functional A

n
. Finally, we show that the distribution of A

n
for large A

n
decays exponentially as

∼

exp

−

A

n

/

a

n

for all values of n and the corresponding decay length a

n
is also estimated. In particular, exact distribution for the first passage time under resetting (which corresponds to the n = 0 case) is derived and shown to be exponential at large time limit in accordance with the generic observation. This behavioural drift from the underlying process can be understood as a ramification due to the resetting mechanism which curtails the undesired long Brownian first passage trajectories and leads to an accelerated completion. We confirm our results to high precision by numerical simulations.
Apparent heating due to imperfect calorimetric measurements
Authors: Donvil Brecht , Ankerhold Joachim
Published: April 2022

Performing imperfect or noisy measurements on a quantum mechanical system both impacts the measurement outcome and the state of the system after the measurement. In this paper we are concerned with imperfect calorimetric measurements. In calorimetric measurements one typically measures the energy of a thermal environment to extract information about the system. In our setting the measurement is imperfect due to noise directly acting on the detector. Concretely, we consider an additional noise bath such that its energy is measured simultaneously with the calorimeter energy. Under weak coupling assumptions, we derive a hybrid master equation for the state of the system and the detected energy and find that the presence of the noise bath manifests itself by modifying the jump rates of the reduced system dynamics. We study an example of a driven qubit interacting with a resonant boson calorimeter and demonstrate that increasing the additional noise leads to an apparent reduction in the power flowing from qubit to calorimeter and thus to a seemingly detected heating up of the calorimeter.
Dynamical charge inversion of polarization correlation vortex in propagating vector speckle field
Authors: Pandit Himangi J , Kumar Vijay , Singh R P
Published: April 2022

A study on first-order polarization correlation in propagating vector speckle fields is carried out. Vector speckle field, generated by scattering of Poincare beam, is propagated through a spherical and a cylindrical lens. The first-order polarization correlation is experimentally constructed from intensity images of vector speckle fields at various planes before and after the focal plane. We have shown with supporting experimental and simulation results that polarization correlation vortex experiences charge inversion while vector speckle field propagates through a cylindrical lens. The importance of this study relies on the fact that it provides insight into one of the important properties of light, i.e. the phase between the orthogonal polarization components, how it evolves as the optical field propagates through various optical components. This study could find application in optical data processing, imaging, sensing, speckle meteorology, phase unwrapping, optical communication, etc.
Interventions to reduce falls in hospitals: a systematic review and meta-analysis
Authors: Morris Meg E , Webster Kate , Jones Cathy , Hill Anne-Marie , Haines Terry , McPhail Steven , Kiegaldie Debra , Slade Susan , Jazayeri Dana , Heng Hazel , Shorr Ronald , Carey Leeanne , Barker Anna , Cameron Ian
Published: April 2022

Background

Falls remain a common and debilitating problem in hospitals worldwide. The aim of this study was to investigate the effects of falls prevention interventions on falls rates and the risk of falling in hospital.

Design

Systematic review and meta-analysis.

Participants

Hospitalised adults.

Intervention

Prevention methods included staff and patient education, environmental modifications, assistive devices, policies and systems, rehabilitation, medication management and management of cognitive impairment. We evaluated single and multi-factorial approaches.

Outcome measures

Falls rate ratios (rate ratio: RaR) and falls risk, as defined by the odds of being a faller in the intervention compared to control group (odds ratio: OR).

Results

There were 43 studies that satisfied the systematic review criteria and 23 were included in meta-analyses. There was marked heterogeneity in intervention methods and study designs. The only intervention that yielded a significant result in the meta-analysis was education, with a reduction in falls rates (RaR = 0.70 [0.51–0.96], P = 0.03) and the odds of falling (OR = 0.62 [0.47–0.83], P = 0.001). The patient and staff education studies in the meta-analysis were of high quality on the GRADE tool. Individual trials in the systematic review showed evidence for clinician education, some multi-factorial interventions, select rehabilitation therapies, and systems, with low to moderate risk of bias.

Conclusion

Patient and staff education can reduce hospital falls. Multi-factorial interventions had a tendency towards producing a positive impact. Chair alarms, bed alarms, wearable sensors and use of scored risk assessment tools were not associated with significant fall reductions.
Erectile dysfunction predicts mortality in middle-aged and older men independent of their sex steroid status
Authors: Antonio Leen , Wu Frederick C W , Moors Hannes , Matheï Cathy , Huhtaniemi Ilpo T , Rastrelli Giulia , Dejaeger Marian , O’Neill Terence W , Pye Stephen R , Forti Gianni , Maggi Mario , Casanueva Felipe F , Slowikowska-Hilczer Jolanta , Punab Margus , Tournoy Jos , Vanderschueren Dirk ,   the EMAS Study Group, Forti Gianni , Petrone Luisa , Corona Giovanni , Rastrelli Giulia , Maggi (Florence) Mario , Vanderschueren Dirk , Tournoy Jos , Borghs Herman , Antonio (Leuven) Leen , Kula Krzysztof , Slowikowska-Hilczer Jolanta , Walczak-Jedrzejowska (Łódz) Renata , Huhtaniemi (London) Ilpo , Giwercman (Malmö) Aleksander , Wu Frederick , Silman Alan , O’Neill Terence , Finn Joseph , Pye (Manchester) Stephen , Casanueva Felipe , Crujeiras (Santiago) Ana B , Bartfai Gyorgy , Földesi Imre , Fejes (Szeged) Imre , Punab Margus , Korrovitz (Tartu) Paul
Published: April 2022

Background

erectile dysfunction is associated with mortality, whereas the association between low testosterone (T) and higher mortality remains controversial. Sexual dysfunction and low T often coexist, but the relative importance of sexual symptoms versus low T in predicting mortality is not known. We studied the interrelationships between sex steroids and sexual symptoms with all-cause mortality in a large prospective cohort of European men.

Design

survival status was assessed in 1,788 community-dwelling men, aged 40–79, who participated in the European Male Ageing Study (EMAS). Sexual symptoms were evaluated via a validated questionnaire (EMAS-SFQ). Sex steroids were measured by mass spectrometry. Cox proportional hazard models were used to study the association between hormones, sexual symptoms and mortality.

Results

about 420 (25.3%) men died during a mean follow-up of 12.6 ± 3.1 years. Total T levels were similar in both groups, but free T was lower in those who died. Men with three sexual symptoms (erectile dysfunction, reduced morning erections and lower libido) had a higher mortality risk compared with men with none of these symptoms (adjusted hazard ratio (HR) and 95% confidence intervals: 1.75 (1.28–2.40, P = 0.001)). Particularly, erectile dysfunction and poor morning erections, but not lower libido, were associated with increased mortality (HR 1.40 (1.13–1.74, P = 0.002), 1.28 (1.04–1.59, P = 0.023) and 1.12 (0.90–1.39, P = 0.312), respectively). Further adjusting for total T, free T or oestradiol did not influence the observed risk.

Conclusions

sexual symptoms, in particular erectile dysfunction, predict all-cause mortality independently of sex steroids and can be an early warning sign of a poor health status.
Effect of frailty on outcomes of endovascular treatment for acute ischaemic stroke in older patients
Authors: Tan Benjamin Y Q , Ho Jamie S Y , Leow Aloysius S , Chia Magdalene L J , Sia Ching Hui , Koh Ying Ying , Seetharaman Santhosh K , Yang Cunli , Gopinathan Anil , Teoh Hock Luen , Sharma Vijay K , Seet Raymond C S , Chan Bernard P L , Yeo Leonard L L , Tan Li Feng
Published: April 2022

Background

frailty has been shown to be a better predictor of clinical outcomes than age alone across many diseases. Few studies have examined the relationship between frailty, stroke and stroke interventions such as endovascular thrombectomy (EVT).

Objective

we aimed to investigate the impact of frailty measured by clinical frailty scale (CFS) on clinical outcomes after EVT for acute ischemic stroke (AIS) in older patients ≥70 years.

Methods

in this retrospective cohort study, we included all consecutive AIS patients age ≥ 70 years receiving EVT at a single comprehensive stroke centre. Patients with CFS of 1–3 were defined as not frail, and CFS > 3 was defined as frail. The primary outcome was modified Rankin Score (mRS) at 90 days. The secondary outcomes included duration of hospitalisation, in-hospital mortality, carer requirement, successful reperfusion, symptomatic intracranial haemorrhage and haemorrhagic transformation.

Results

a total of 198 patients were included. The mean age was 78.1 years and 52.0% were female. Frail patients were older, more likely to be female, had more co-morbidities. CFS was significantly associated with poor functional outcome after adjustment for age, NIHSS and time to intervention (adjusted odds ratio [aOR] 1.54, 95% confidence interval [CI] 1.04–2.28, P = 0.032). There was trend towards higher mortality rate in frail patients (frail: 18.3%; non-frail: 9.6%; P = 0.080). There were no significant differences in other secondary outcomes except increased carer requirement post discharge in frail patients (frail: 91.6%; non-frail: 72.8%; P = 0.002).

Conclusions

frailty was associated with poorer functional outcome at 90 days post-EVT in patients ≥ 70 years.
Reduced humoral response 3 months following BNT162b2 vaccination in SARS-CoV-2 uninfected residents of long-term care facilities
Authors: Trigueros Macedonia , Pradenas Edwards , Palacín Dolors , Muñoz-López Francisco , Ávila-Nieto Carlos , Trinité Benjamin , Bonet-Simó Josep Maria , Isnard Mar , Moreno Nemesio , Marfil Silvia , Rovirosa Carla , Puig Teresa , Grau Eulàlia , Chamorro Anna , Martinez Ana , Toledo Ruth , Font Marta , Ara Jordi , Carrillo Jorge , Mateu Lourdes , Blanco Julià , Clotet Bonaventura , Prat Nuria , Massanella Marta ,   on behalf of the CoronAVI@S and the KING cohort extension studies, Reyes Carrión S , Salarich Solà N , Vidal A , Alvarez Viñallonga R , Tornero J , Vilamala E , Suarez C , Gonzalo T , Perez L , Sans D , Blancas Loras A , Garcia Archer A , Borràs J , Cervelló S , Llados G , España S , Santos J R , Loste C , López C , Casafont I , Estany C , Rodriguez C , Moreno-Muñoz J , Prats A , Herrero C , Garcia A , Montero M , Tornero P , Gonzalez Palomares N , Grajea A , Ortiz L , Miranda C , Abad E , Figueroa D , Mancera A , Gonzalez Alonso S , Perez M , Esteban L , Ortiz M , Valls L , Ceron L , Baena T , Puig C , Cucurell M , Puig J
Published: April 2022

Background

SARS-CoV-2 vaccination is the most effective strategy to protect older residents of long-term care facilities (LTCF) against severe COVID-19, but primary vaccine responses are less effective in older adults. Here, we characterised the humoral responses of institutionalised seniors 3 months after they had received the mRNA/BNT162b2 vaccine.

Methods

plasma levels of SARS-CoV-2-specific total IgG, IgM and IgA antibodies were measured before and 3 months after vaccination in older residents of LTCF. Neutralisation capacity was assessed in a pseudovirus neutralisation assay against the original WH1 and later B.1.617.2/Delta variants. A group of younger adults was used as a reference group.

Results

three months after vaccination, uninfected older adults presented reduced SARS-CoV-2-specific IgG levels and a significantly lower neutralisation capacity against the WH1 and Delta variants compared with vaccinated uninfected younger individuals. In contrast, COVID-19-recovered older adults showed significantly higher SARS-CoV-2-specific IgG levels after vaccination than their younger counterparts, whereas showing similar neutralisation activity against the WH1 virus and an increased neutralisation capacity against the Delta variant. Although, similarly to younger individuals, previously infected older adults elicit potent cross-reactive immune responses, higher quantities of SARS-CoV-2-specific IgG antibodies are required to reach the same neutralisation levels.

Conclusions

although hybrid immunity seems to be active in previously infected older adults 3 months after mRNA/BNT162b2 vaccination, humoral immune responses are diminished in COVID-19 uninfected but vaccinated older residents of LTCF. These results suggest that a vaccine booster dose should be prioritised for this particularly vulnerable population.
High Counts in Hematologic Malignancies Predict Low Metaphase Yield for Cytogenetic Analysis
Authors: Chacko Mary P , Yuvarani Sugumaran , Kalaiyarasi Jayachandran P , Radhakrishnan Venkatraman , Gowri Mahasampath , Kamath Vandana
Published: April 2022

Objectives

This study examined the impact of various preanalytical variables on metaphase yield in hematologic malignancies.

Methods

Marrow samples from patients with hematologic malignancies that were subjected to cytogenetic analysis were categorized into two groups: one with samples that yielded an adequate number of metaphases, defined as at least 20, and a second with a low number of metaphases (LNM), having fewer than 20 metaphases. Age, sex, bone marrow nucleated cell (MNC) count, and peripheral blood counts (hemoglobin, total WBC count, and platelet count) were analyzed for an association with LNM.

Results

Of 455 samples, 17% (79/455) belonged to the LNM group, including 6% (27/455) that yielded no metaphases. MNCs and WBCs were higher in the LNM group (P < .001 for both). MNCs were higher in LNM groups in both acute myeloid leukemia (P = .008) and acute lymphoblastic leukemia (P = .001). Receiver operating characteristic curves showed moderate prediction of MNC and WBC counts for LNM with areas under the curves of 0.7. Other analyzed parameters showed no significant associations with LNM.

Conclusions

Low metaphase yields occur frequently in hematologic malignancies with high counts. This could reflect biological characteristics of these malignancies that merit further investigation.
Invited Commentary: Conducting and Emulating Trials to Study Effects of Social Interventions
Authors: Rojas-Saunero L Paloma , Labrecque Jeremy A , Swanson Sonja A
Published: April 2022

All else being equal, if we had 1 causal effect we wished to estimate, we would conduct a randomized trial with a protocol that mapped onto that causal question, or we would attempt to emulate that target trial with observational data. However, studying the social determinants of health often means there are not just 1 but several causal contrasts of simultaneous interest and importance, and each of these related but distinct causal questions may have varying degrees of feasibility in conducting trials. With this in mind, we discuss challenges and opportunities that arise when conducting and emulating such trials. We describe designing trials with the simultaneous goals of estimating the intention-to-treat effect, the per-protocol effect, effects of alternative protocols or joint interventions, effects within subgroups, and effects under interference, and we describe ways to make the most of all feasible randomized trials and emulated trials using observational data. Our comments are grounded in the study results of Courtin et al. (Am J Epidemiol. 2022;191(8):1444–1452).
Gallbladder Disease and Risk of Type 2 Diabetes in Postmenopausal Women: A Women’s Health Initiative Study
Authors: Ako Ako Adams , Michael Yvonne L , Robinson Lucy F , Wactawski-Wende Jean , Shadyab Aladdin H , Garcia Lorena , Nriagu Bede N , Saquib Nazmus , Nassir Rami , Liu Simin , Wallace Robert B
Published: April 2022

Studies have suggested that adults with gallbladder disease have increased risk of type 2 diabetes. This prospective cohort study assessed the risk of type 2 diabetes in postmenopausal women with gallbladder disease. Data from women enrolled in the Women’s Health Initiative from 1993 to 2005, aged 50–79 years (mean = 63.2; standard deviation, 7.2), were analyzed. Cox proportional hazards regression models were used to estimate the risk of type 2 diabetes associated with gallbladder disease. There were 8,896 new cases of type 2 diabetes after 1,025,486 person-years of follow-up. Gallbladder disease was significantly associated with type 2 diabetes (hazard ratio = 1.52; 95% confidence interval (CI): 1.38,1.67). The observed risk of type 2 diabetes in women with both gallbladder disease and central obesity was 37% higher than expected (relative excess risk due to interaction = 0.37, 95% CI: 0.11,0.63) on the additive scale. The hazard ratios for type 2 diabetes associated with gallbladder disease were 1.25 (95% CI: 1.19,1.32) and 1.48 (95% CI: 1.34,1.63) in women with and without central obesity, respectively, on the multiplicative scale. Results of this study support further studies to determine whether interventions in older women with gallbladder disease would reduce type 2 diabetes risk, especially among those with central obesity. Future research should examine the pathophysiological basis of the association between gallbladder disease and type 2 diabetes.
Alcohol Addiction: One Entity or Different Entities? A DSM-4-Based Attempt Toward a Geographicization of Alcohol Addiction and Abuse
Authors: Allamani Allaman , Voller Fabio , Bravi Stefano , Pepe Pasquale , Biffino Marco , Buscema Paolo Massimo , Maurelli Guido , Massini Giulia , Einstein S , Manthey Jakob , Rehm Jürgen
Published: April 2022

Aim

To examine whether in Europe perceptions of ‘alcoholism’ differ in a discrete manner according to geographical area.

Method

Secondary analysis of a data set from a European project carried out in 2013–2014 among 1767 patients treated in alcohol addiction units of nine countries/regions across Europe. The experience of all 11 DSM-4 criteria used for diagnosing ‘alcohol dependence’ and ‘alcohol abuse’ were assessed in patient interviews. The analysis was performed through Multiple Correspondence Analysis.

Results

The symptoms of ‘alcohol dependence’ and ‘alcohol abuse’, posited by DSM-IV, were distributed according to three discrete geographical patterns: a macro-area mainly centered on drinking beer and spirit, a culture traditionally oriented toward wine and a mixed intermediate alcoholic beverage situation.

Conclusion

These patterns of perception seem to parallel the diverse drinking cultures of Europe.
Narrative and Personal Identity
Authors: Schroeder Mark
Published: April 2022

In this paper I explore how and why personal identity might be essentially narrative in nature. My topic is the question of personal identity in the strict sense of identity—the question of which person you are, and how that person is extended in space, time, and quality. In this my question appears to contrast with the question of personal identity in the sense sought by teenagers and sufferers of mid-life crises who are trying to ‘find themselves’. But in fact it will be key to my argument that these questions are not distinct and independent. Whereas Parfit was concerned, in his work on personal identity, with how he was extended over time, the teenager who is finding themselves is concerned with how they are extended in quality. Indeed, the core of my argument is that because narrative is the key to understanding how we are extended in quality, and quality is just one more dimension along which we are extended, along with space and time, narrative must also be the clue as to how we are extended in space and time. You, I will argue, are the protagonist in the best story of your life.
Heterogeneity in resource competition covaries with individual variation in long-term social relationships
Authors: Levengood Alexis L , Strickland Kasha , Foroughirad Vivienne , Mann Janet , Cristescu Romane H , Krzyszczyk Ewa , Frère Céline H
Published: April 2022

Resource competition among conspecifics is central to social evolution, as it serves as one of the primary selective pressures of group living. This is because the degree of competition for resources impacts the costs and benefits of social interactions. Despite this, how heterogeneity in resource competition drives variation in the type and quantity of long-term social relationships individuals foster has been overlooked. By measuring male mating competition and female foraging competition in a highly social, long-lived mammal, we demonstrate that individual variation in long-term intrasexual social relationships covaries with preferred habitat and experienced resource competition, and this effect differs based on the sex of the individual. Specifically, greater resource competition resulted in fewer social preferences, but the magnitude of the effect varied by both habitat and sex, whereas for social avoidances, both the directionality and magnitude of the effect of resource competition varied by habitat and sex. Together our work shows how fine-scale variation in individual socioecological niches (i.e., unique physical and social environments) can drive extensive variation in individual social behavior (here long-term relationships) within a population, thereby broadening current theories of social evolution.
GraphTGI: an attention-based graph embedding model for predicting TF-target gene interactions
Authors: Du Zhi-Hua , Wu Yang-Han , Huang Yu-An , Chen Jie , Pan Gui-Qing , Hu Lun , You Zhu-Hong , Li Jian-Qiang
Published: April 2022

Motivation

Interaction between transcription factor (TF) and its target genes establishes the knowledge foundation for biological researches in transcriptional regulation, the number of which is, however, still limited by biological techniques. Existing computational methods relevant to the prediction of TF-target interactions are mostly proposed for predicting binding sites, rather than directly predicting the interactions. To this end, we propose here a graph attention-based autoencoder model to predict TF-target gene interactions using the information of the known TF-target gene interaction network combined with two sequential and chemical gene characters, considering that the unobserved interactions between transcription factors and target genes can be predicted by learning the pattern of the known ones. To the best of our knowledge, the proposed model is the first attempt to solve this problem by learning patterns from the known TF-target gene interaction network.

Results

In this paper, we formulate the prediction task of TF-target gene interactions as a link prediction problem on a complex knowledge graph and propose a deep learning model called GraphTGI, which is composed of a graph attention-based encoder and a bilinear decoder. We evaluated the prediction performance of the proposed method on a real dataset, and the experimental results show that the proposed model yields outstanding performance with an average AUC value of 0.8864 +/- 0.0057 in the 5-fold cross-validation. It is anticipated that the GraphTGI model can effectively and efficiently predict TF-target gene interactions on a large scale.

Availability

Python code and the datasets used in our studies are made available at https://github.com/YanghanWu/GraphTGI
RNMFLP: Predicting circRNA–disease associations based on robust nonnegative matrix factorization and label propagation
Authors: Peng Li , Yang Cheng , Huang Li , Chen Xiang , Fu Xiangzheng , Liu Wei
Published: April 2022

Circular RNAs (circRNAs) are a class of structurally stable endogenous noncoding RNA molecules. Increasing studies indicate that circRNAs play vital roles in human diseases. However, validating disease-related circRNAs in vivo is costly and time-consuming. A reliable and effective computational method to identify circRNA–disease associations deserves further studies. In this study, we propose a computational method called RNMFLP that combines robust nonnegative matrix factorization (RNMF) and label propagation algorithm (LP) to predict circRNA–disease associations. First, to reduce the impact of false negative data, the original circRNA–disease adjacency matrix is updated by matrix multiplication using the integrated circRNA similarity and the disease similarity information. Subsequently, the RNMF algorithm is used to obtain the restricted latent space to capture potential circRNA–disease pairs from the association matrix. Finally, the LP algorithm is utilized to predict more accurate circRNA–disease associations from the integrated circRNA similarity network and integrated disease similarity network, respectively. Fivefold cross-validation of four datasets shows that RNMFLP is superior to the state-of-the-art methods. In addition, case studies on lung cancer, hepatocellular carcinoma and colorectal cancer further demonstrate the reliability of our method to discover disease-related circRNAs.
Balancing the transcriptome: leveraging sample similarity to improve measures of gene specificity
Authors: Bondhus Leroy , Varma Roshni , Hernandez Yenifer , Arboleda Valerie A
Published: April 2022

The spatial and temporal domain of a gene’s expression can range from ubiquitous to highly specific. Quantifying the degree to which this expression is unique to a specific tissue or developmental timepoint can provide insight into the etiology of genetic diseases. However, quantifying specificity remains challenging as measures of specificity are sensitive to similarity between samples in the sample set. For example, in the Gene-Tissue Expression project (GTEx), brain subregions are overrepresented at 13 of 54 (24%) unique tissues sampled. In this dataset, existing specificity measures have a decreased ability to identify genes specific to the brain relative to other organs. To solve this problem, we leverage sample similarity information to weight samples such that overrepresented tissues do not have an outsized effect on specificity estimates. We test this reweighting procedure on 4 measures of specificity, Z-score, Tau, Tsi and Gini, in the GTEx data and in single cell datasets for zebrafish and mouse. For all of these measures, incorporating sample similarity information to weight samples results in greater stability of sets of genes called as specific and decreases the overall variance in the change of specificity estimates as sample sets become more unbalanced. Furthermore, the genes with the largest improvement in their specificity estimate’s stability are those with functions related to the overrepresented sample types. Our results demonstrate that incorporating similarity information improves specificity estimates’ stability to the choice of the sample set used to define the transcriptome, providing more robust and reproducible measures of specificity for downstream analyses.
Predicting miRNA–disease associations via learning multimodal networks and fusing mixed neighborhood information
Authors: Lou Zhengzheng , Cheng Zhaoxu , Li Hui , Teng Zhixia , Liu Yang , Tian Zhen
Published: April 2022

Motivation

In recent years, a large number of biological experiments have strongly shown that miRNAs play an important role in understanding disease pathogenesis. The discovery of miRNA–disease associations is beneficial for disease diagnosis and treatment. Since inferring these associations through biological experiments is time-consuming and expensive, researchers have sought to identify the associations utilizing computational approaches. Graph Convolutional Networks (GCNs), which exhibit excellent performance in link prediction problems, have been successfully used in miRNA–disease association prediction. However, GCNs only consider 1st-order neighborhood information at one layer but fail to capture information from high-order neighbors to learn miRNA and disease representations through information propagation. Therefore, how to aggregate information from high-order neighborhood effectively in an explicit way is still challenging.

Results

To address such a challenge, we propose a novel method called mixed neighborhood information for miRNA–disease association (MINIMDA), which could fuse mixed high-order neighborhood information of miRNAs and diseases in multimodal networks. First, MINIMDA constructs the integrated miRNA similarity network and integrated disease similarity network respectively with their multisource information. Then, the embedding representations of miRNAs and diseases are obtained by fusing mixed high-order neighborhood information from multimodal network which are the integrated miRNA similarity network, integrated disease similarity network and the miRNA–disease association networks. Finally, we concentrate the multimodal embedding representations of miRNAs and diseases and feed them into the multilayer perceptron (MLP) to predict their underlying associations. Extensive experimental results show that MINIMDA is superior to other state-of-the-art methods overall. Moreover, the outstanding performance on case studies for esophageal cancer, colon tumor and lung cancer further demonstrates the effectiveness of MINIMDA.

Availability and implementation

https://github.com/chengxu123/MINIMDA and http://120.79.173.96/
MLGL-MP: a Multi-Label Graph Learning framework enhanced by pathway interdependence for Metabolic Pathway prediction
Authors: Du Bing-Xue , Zhao Peng-Cheng , Zhu Bei , Yiu Siu-Ming , Nyamabo Arnold K , Yu Hui , Shi Jian-Yu
Published: April 2022

Motivation

During lead compound optimization, it is crucial to identify pathways where a drug-like compound is metabolized. Recently, machine learning-based methods have achieved inspiring progress to predict potential metabolic pathways for drug-like compounds. However, they neglect the knowledge that metabolic pathways are dependent on each other. Moreover, they are inadequate to elucidate why compounds participate in specific pathways.

Results

To address these issues, we propose a novel Multi-Label Graph Learning framework of Metabolic Pathway prediction boosted by pathway interdependence, called MLGL-MP, which contains a compound encoder, a pathway encoder and a multi-label predictor. The compound encoder learns compound embedding representations by graph neural networks. After constructing a pathway dependence graph by re-trained word embeddings and pathway co-occurrences, the pathway encoder learns pathway embeddings by graph convolutional networks. Moreover, after adapting the compound embedding space into the pathway embedding space, the multi-label predictor measures the proximity of two spaces to discriminate which pathways a compound participates in. The comparison with state-of-the-art methods on KEGG pathways demonstrates the superiority of our MLGL-MP. Also, the ablation studies reveal how its three components contribute to the model, including the pathway dependence, the adapter between compound embeddings and pathway embeddings, as well as the pre-training strategy. Furthermore, a case study illustrates the interpretability of MLGL-MP by indicating crucial substructures in a compound, which are significantly associated with the attending metabolic pathways. It is anticipated that this work can boost metabolic pathway predictions in drug discovery.

Availability and implementation

The code and data underlying this article are freely available at https://github.com/dubingxue/MLGL-MP.