bluuebunny/crossref_metadata_2025 huggingface dataset:
Inside the Circle
Authors: Noxolo Patricia
Published: May 2022

In a discussion of Jovan Scott Lewis’s Scammer’s Yard: The Crime of Black Repair in Jamaica (2020), the book is considered as ethnography written from “inside the circle” (Sadiya Hartman) of a generation of young Black men brought up in Jamaica. Nonetheless, Lewis shows genuine appreciation of the profound differences between himself and his respondents. However, the response ends by proposing that Lewis needed to widen the circle to include those who died in the terrible violence that was a consequence of the scamming practices that he describes, and that his arguments about Black repair might have been all the more convincing had he been able to do so.
Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream ofnpas4landetv2
Authors: Capon Samuel J. , Uribe Veronica , Dominado Nicole , Ehrlich Ophelia , Smith Kelly A.
Published: May 2022

The endocardium plays important roles in the development and function of the vertebrate heart; however, few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here, we describe the Gt(SAGFF27C); Tg(4xUAS:egfp) line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan-endothelium confirms molecular distinction between these populations and time-course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity, we employed npas4l, etv2 and scl loss-of-function models. Endocardial expression is lost in npas4l mutants, significantly reduced in etv2 mutants and only modestly affected upon scl loss-of-function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression, whereas Bmp inhibition decreased expression. Finally, epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast, overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together, these results describe the differentiation of the endocardium, distinct from vasculature, and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation.
Honey bees respond to multimodal stimuli following the principle of inverse effectiveness
Authors: Gil-Guevara Oswaldo , Bernal Hernan A. , Riveros Andre J.
Published: May 2022

Multisensory integration is assumed to entail benefits for receivers across multiple ecological contexts. However, signal integration effectiveness is constrained by features of the spatiotemporal and intensity domains. How sensory modalities are integrated during tasks facilitated by learning and memory, such as pollination, remains unsolved. Honey bees use olfactory and visual cues during foraging, making them a good model to study the use of multimodal signals. Here, we examined the effect of stimulus intensity on both learning and memory performance of bees trained using unimodal or bimodal stimuli. We measured the performance and the latency response across planned discrete levels of stimulus intensity. We employed the conditioning of the proboscis extension response protocol in honey bees using an electromechanical setup allowing us to control simultaneously and precisely olfactory and visual stimuli at different intensities. Our results show that the bimodal enhancement during learning and memory was higher as the intensity decreased when the separate individual components were least effective. Still, this effect was not detectable for the latency of response. Remarkably, these results support the principle of inverse effectiveness, traditionally studied in vertebrates, predicting that multisensory stimuli are more effectively integrated when the best unisensory response is relatively weak. Thus, we argue that the performance of the bees while using a bimodal stimulus depends on the interaction and intensity of its individual components. We further hold that the inclusion of findings across all levels of analysis enriches the traditional understanding of the mechanics and reliance of complex signals in honey bees.
Development of Visible Light-Driven Hybrid Catalysts Composed of Earth Abundant Metal Ion Modified TiO2 and B12 Complex
Authors: Shichijo Keita , Watanabe Midori , Hisaeda Yoshio , Shimakoshi Hisashi
Published: May 2022

The development of highly-functional visible light-driven hybrid catalysts (B12-Mn+/TiO2) prepared from B12 complexes (B12) derived from natural vitamin B12, earth-abundant metal ions (Mn+), and titanium oxide (TiO2) was reported. The metal ions, such as Cu2+, Ni2+, Fe2+, Zn2+, Mn2+, Al3+, and Mg2+, were modified on the surface of TiO2 (2.4 × 10−5–9.9 × 10−5 mol/g) to obtain effective response to visible light, and the B12 complex was also loaded (6.2 × 10−6–1.1 × 10−5 mol/g) to produce a highly-functional hybrid catalyst. Amide formations from dichlorodiphenyltrichloroethane (DDT) catalyzed by the B12-Mn+/TiO2 proceeded in up to 89% yields in the presence of triethylamine (NEt3) under visible light irradiation (λ ≧ 420 nm) in air at room temperature. These hybrid catalysts could be classified into two groups based on these reactivities, and it was found that the B12-Mg2+/TiO2 showed the most effective catalytic activities of all the prepared samples. The B12-Mg2+/TiO2 also catalyzed the syntheses of fine chemicals, such as N,N-diethyl-3-methylbenzeamide (DEET), and N,N-diethylcyanoformamide, from the corresponding trichloromethyl compounds (FG-CCl3) with about 80% yields.
A review on the application of deep learning for CT reconstruction, bone segmentation and surgical planning in oral and maxillofacial surgery
Authors: Minnema Jordi , Ernst Anne , van Eijnatten Maureen , Pauwels Ruben , Forouzanfar Tymour , Batenburg Kees Joost , Wolff Jan
Published: May 2022

Computer-assisted surgery (CAS) allows clinicians to personalize treatments and surgical interventions and has therefore become an increasingly popular treatment modality in maxillofacial surgery. The current maxillofacial CAS consists of three main steps: (1) CT image reconstruction, (2) bone segmentation, and (3) surgical planning. However, each of these three steps can introduce errors that can heavily affect the treatment outcome. As a consequence, tedious and time-consuming manual post-processing is often necessary to ensure that each step is performed adequately. One way to overcome this issue is by developing and implementing neural networks (NNs) within the maxillofacial CAS workflow. These learning algorithms can be trained to perform specific tasks without the need for explicitly defined rules. In recent years, an extremely large number of novel NN approaches have been proposed for a wide variety of applications, which makes it a difficult task to keep up with all relevant developments. This study therefore aimed to summarize and review all relevant NN approaches applied for CT image reconstruction, bone segmentation, and surgical planning. After full text screening, 76 publications were identified: 32 focusing on CT image reconstruction, 33 focusing on bone segmentation and 11 focusing on surgical planning. Generally, convolutional NNs were most widely used in the identified studies, although the multilayer perceptron was most commonly applied in surgical planning tasks. Moreover, the drawbacks of current approaches and promising research avenues are discussed.
Czy wizja małżeństwa i rodziny papieża Franciszka ujęta w Amoris laetitia może być pastoralną kontynuacją encykliki Pawła VI Humanae vitae?
Authors: Pieja Wiesław
Published: May 2022

Poprawnie zbudowana etyka jest możliwa na fundamencie integralnej antropologii. Antropologia ta zakłada poszanowanie godności osoby ludzkiej. Owa godność w szczególny sposób dotyka małżeństwa i rodziny. Karol Wojtyła wiele razy poruszał zagadnienie godności małżeńskiej. Obecnie, ponownie przypominamy aktualność nauczania Humanae vitae Pawła VI, czyli te podstawowe prawdy dotyczące małżeństwa i rodziny, zrodzenia potomstwa, przekazu wiary, uzupełnione o Amoris laetitia papieża Franciszka. W końcowej wersji artykułu zamieszczamy, zagrożenia wynikające z „wybujałego indywidualizmu” oraz kryzysy przekazane przez papieża Franciszka. Naszym celem było ukazanie aktualnego nauczania Franciszka w adhortacji Amoris laetitia, o małżeństwie, rodzinie i zagrożeniach, jako pastoralnej kontynuacji encykliki Humanae vitae Pawła VI.
Generación de un constructo de narrativa memética desde la incidencia sociodigital
Authors: NAVA LA CORTE FERNANDO
Published: May 2022

En el presente trabajo se exponen las interpretaciones de los usos sociales, significados y reinterpretaciones de una serie de memes y publicaciones de Instagram para reconocer el tratamiento simbólico dado a cada una de ellas y su impacto entre la sociedad contemporánea. Consecutivamente, se estudió la función informativa que desempeñaron sus variadas narrativas en los medios digitales. A partir de la certeza del conocimiento y de las relaciones que intervienen en estas comunicaciones, se pudieron establecer analogías de aplicaciones y procesos que generan propuestas con fines establecidos, en condiciones que responden a las lecturas del universo memético. La aproximación metodológica de análisis de contenido que se plantea es de carácter cualitativo y el trabajo de campo empírico está circunscrito dentro del universo narrativo digital contemporáneo, que permite identificar ensambles y desensambles con los que las personas buscan visibilizar y dar respuesta a sus preocupaciones cotidianas, políticas, académicas o laborales. El trabajo termina con la distinción de cinco narrativas meméticas
First records of road-killed mammals in the state of Sinaloa, México
Authors: Rubio-Rocha Yamel , Gaxiola-Camacho Soila , Morales-García María , Artigas-Gutiérrez Brayan , Sánchez-Ríos Alfredo , Carvajal-Sauceda Fabiola , Espinoza-Evans Gerardo
Published: May 2022

La ausencia de datos sobre el impacto que genera el tráfico vehicular en las poblaciones de animales silvestres motivó la presente investigación, que tuvo como objetivo conocer el número de muertes por atropellamiento de mamíferos en las carreteras de Sinaloa, México.  Los registros de las colisiones se obtuvieron a través de transectos libres en carreteras, registros de la red social Naturalista y reportes ciudadanos.  Se identificaron 11 especies de mamíferos, resaltando algunos en estado de conservación como el jaguar (Panthera onca), el ocelote (Leopardus pardalis) y el tlalcoyote (Taxidea taxus).  Se obtuvieron 45 registros de colisiones en las carreteras de la región centro-sur del estado dentro del periodo de febrero de 2019 a junio de 2021.  Las especies con más accidentes registrados fueron el coatí (Nasua narica), el tlacuache (Didelphis virginiana) y el lince (Lynx rufus).  Este trabajo documenta por primera vez la mortalidad de mamíferos como resultado de las colisiones con el tráfico vehicular y resalta la necesidad de dirigir mayores recursos en esta línea de investigación que emerge ante la necesidad de conservar la fauna silvestre y la integridad de los usuarios de las carreteras
Comparison of road-killed mammals on roads of different types of jurisdictions and traffic volume in Veracruz, México
Authors: Ruíz-Ramírez Lucero , González-Gallina Alberto , Soto Víctor , Pacheco-Figueroa Coral Jazvel , Pech-Canché Juan Manuel
Published: May 2022

Los proyectos viales son un elemento importante de desarrollo humano, pero a la vez representan un riesgo para la fauna silvestre, por lo que el objetivo del trabajo fue determinar el número de mamíferos atropellados en tres tipos de caminos en función de su jurisdicción y flujo vehicular en el norte del estado de Veracruz, México.  Se seleccionaron dos caminos por tipo de jurisdicción (federal, estatal y municipal) en dos tipos de flujo vehicular, alto y bajo, registrando de manera sistemática todos los mamíferos silvestres atropellados y enriqueciendo el inventario con registros no sistemáticos.  Se emplearon pruebas no paramétricas para analizar las diferencias en los atropellamientos de mamíferos en función del tipo de camino y flujo.  Se registraron 49 individuos atropellados pertenecientes a 4 especies y 1 género de mamíferos sin determinar a nivel específico, además de 3 especies por registros incidentales, donde Didelphis marsupialis representa la especie más atropellada.  No se encontraron diferencias significativas en las tasas de atropellamientos en función del tipo de camino, pero sí con relación al flujo vehicular, con mayores registros durante el flujo alto.  Los registros no sistemáticos permitieron enriquecer el inventario de especies atropelladas en la zona, además de incluir el registro de 2 especies de mamíferos bajo alguna categoría de protección.  Las características biológicas de las especies condicionan su grado de afectación por las carreteras; la afluencia vehicular es un factor importante que determina el impacto de las carreteras sobre la fauna silvestre.  Los registros no sistemáticos pueden ayudar a mejorar los inventarios y brindar mejores herramientas para evaluar el efecto de las carreteras sobre la fauna silvestre.
Design and Testing of a Denucleation and Decortication Device for Lychee
Authors: Li Xiang , Lu Enli , Lu Huazhong , Xiao Boyi , Guo Jiaming , Li Pengfei
Published: May 2022

Abstract. An automatic machine for lychee denucleation and decortication was designed to improve lychee processing efficiency and ensure the integrity of the lychee pulp. The main structure and operating parameters of this machine were determined by theoretical analysis and two orthogonal tests. The effects of the denucleation knife diameter, processing speed, and distance during denucleation and decortication were investigated. The denucleation rate, decortication rate, and juice loss rate were evaluated. The results of the processing tests showed that the denucleation rate was 94% when the diameter of the lychee fruit was between 29 and 33 mm, the diameter of the lychee seed was less than 10 mm, the diameter of the denucleation knife was 6 mm, and the processing speed of the denucleation knife was 0.5 m s-1. The decortication rate was 85% when the diameter of the baffle hole was 26 mm and there were eight grooves in the hole, yielding zero distance between the upper end of the decortication rod and the groove during operation. This machine is designed to perform automatic lychee processing, which includes the functions of denucleation, decortication, and lychee pulp separation. The processing speed of the machine is 600 kg d-1. This enhanced output is ten times greater than the output of conventional processing, and significant production costs are saved. Keywords: Decortication, Denucleation, Lychee, Processing, Pulp.
Influence of Subsurface Pipe Perforations on Transient Water Table Response and Steady Soil-Water Flux under Subirrigation
Authors: Gaj Naresh , Madramootoo Chandra A.
Published: May 2022

Highlights

Water table rise was slower under a sparsely perforated pipe as compared to a pipe that was densely perforated.

Response time increased as buried pipe depth decreased for both combinations of perforation characteristics.

Fluxes from buried pipes spaced at 15 m in loamy sand satisfied the water demand for cereal/grain crops (6 mm d-1).

Increasing perforation density on the pipe wall is the most effective way to reduce exit head losses.

Abstract. It is important to consider the water table rise into the unsaturated zone when designing subsurface irrigation systems that consist of buried perforated corrugated pipes. Corrections to pipe spacing equations for head losses due to perforations are based on the entrance resistance, which is derived for buried pipes operating in drainage mode. However, the boundary condition at the soil-pipe interface when operated in subsurface irrigation mode requires the use of the exit resistance to accurately account for perforations in the pipe wall. Simulations of a subsurface irrigation system with four soil textures, three lateral pipe spacings, and three buried depths were carried out, with the numerical model COMSOL, to demonstrate the effects of variable perforation characteristics on the transient water table rise into the unsaturated zone. Soil-water fluxes were also computed for the system when operated under steady-state conditions. The simulated water table rise exceeded or approached a predetermined target water level of 1.65 m above the buried pipes in coarse-textured soils (loamy sands and silt loams) with lateral pipe spacings as large as 10 m. Increasing the number and length of rectangular slots in the pipe wall (densely perforated) can reduce the water table response time to reach the target level by 15 h in a silt loam soil and 25 h in a clay soil. The optimum pipe spacing needed to sustain a soil-water flux of 6 mm d-1 (common to eastern Canada and the U.S. Midwest) can be increased from 15.1 to 16.2 m in loamy sands by using densely perforated pipes. In contrast, increasing perforations in pipes buried in clays and sandy clays will result in pipe spacing increases of less than 0.2 m because these fine-textured soils have lower hydraulic conductivity. This study has demonstrated that variable perforation characteristics can be included in the analysis and design of subsurface drainage systems for improving water management. Keywords: Corrugated perforated pipes, Exit resistance, Head loss, Subirrigation, Unsaturated zone, Water table response.
Discrete Element Method Simulation of Wheat Bulk Density as Affected by Grain Drop Height and Kernel Size Distribution
Authors: Petingco Marvin Carpena , Casada Mark E. , Maghirang Ronaldo G. , Thompson Sidney A. , Turner Aaron P. , McNeill Samuel G. , Montross Michael
Published: May 2022

Highlights

The predicted bulk density of two wheat varieties varied with drop height, similar to the experiments.

The percentage composition of three kernel size fractions in the wheat varieties affected the bulk density.

Accurate particle shape representation simulated the heap profile better but required longer computational time.

The single-sphere model is more practical to use because of its higher accuracy and lower computational cost.

Abstract. Grain bulk density varies widely depending on kernel properties and handling practices. The discrete element method (DEM) can model such behavior at the particle level, including wide-ranging interactions with equipment. The objective of this study was to develop a DEM model to predict wheat bulk density as affected by grain drop height and kernel size distribution. The bulk density of two wheat varieties was measured experimentally for a range of drop heights with a modified test weight per bushel apparatus and was simulated in EDEM v2018.1 using single-sphere and five-sphere particle models that accounted for three kernel size fractions. For both particle models, simulations matched the observed behavior, showing a bulk density increase with increasing drop height and bulk density differences between varieties due to different kernel size fractions. The single-sphere particle model predicted the bulk density with higher accuracy than the five-sphere particle model, while the five-sphere model, which more accurately represented the shape of wheat kernels, allowed better simulation of the heap profile at the cost of longer computation time. These particle models can be used to simulate bulk density of wheat under compaction and to improve prediction models of grain pack factor for wheat. Keywords: Bulk density, DEM, Drop height, Size distribution, Wheat.
The making of irregular migration: post-Brexit immigration policy and risk of labour exploitation
Authors: Åhlberg Meri , Granada Lucila
Published: May 2022

This article highlights the role states have in creating the conditions under which labour exploitation can occur. Specifically, it identifies several immigration policy decisions related to the UK’s exit from the European Union that will likely result in an increase in the number of irregular migrants in the United Kingdom and how this increase, when combined with measures that have progressively restricted the rights and entitlements of various immigration categories, creates an environment conducive to labour exploitation. It presents measures that could help address this problem, including changes to immigration policies and the strengthening of the labour market enforcement system.
Polarization mode dispersion correction in endoscopic polarization-sensitive optical coherence tomography with incoherent polarization input states
Authors: Adams David C. , Majid Adnan , Suter Melissa J.
Published: May 2022

The incorporation of polarization sensitivity into optical coherence tomography (PS-OCT) imaging can greatly enhance utility by allowing differentiation via intrinsic contrast of many types of tissue. In fiber-based OCT systems such as those employing endoscopic imaging probes, however, polarization mode dispersion (PMD) can significantly impact the ability to obtain accurate polarization data unless valuable axial resolution is sacrificed. In this work we present a new technique for compensating for PMD in endoscopic PS-OCT with minimal impact on axial resolution and without requiring mutually coherent polarization inputs, needing only a birefringent structure with known orientation in view (such as the catheter sheath). We then demonstrate the advantages of this technique by comparing it against the current state of the art approach.
Guided-mode resonance sensors: different schemes for different applications
Authors: Maleki Morteza , Mehran Mahdiyeh
Published: May 2022

This work performs a quantitative comparison of different dielectric-based guided-mode resonance (D-GMR) sensors. To this end, diverse D-GMR structures are classified into three different classes, and their sensitivity (S) is compared to each other. For one of these classes in various schemes, the sensitivity is investigated for the TE and TM modes. Moreover, grating height effects are studied for different cases in this category, and analytical sensitivity equations are used as benchmarks. Then, the three classes are compared and, based on the numerical results and analytical equations, various applications are proposed for different structures in the refractive index (RI) of interest. Comparing our results to other recent works, we prove that the proposed classification leads to great sensing performances and the predictions are reliable. A comparison has been performed for methane as a gas sample (with RI of 1.0003) and a hemoglobin solution and toluene as two different analytes (with RIs of 1.33 and 1.4778, respectively). The results show a sensitivity of

S

=

1427.3

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m

/

r
e
f
r
a
c
t
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e

index unit (nm/RIU) for methane with a detection precision of one to a few volume percentages in the air, which can also be calibrated to illuminate the fabrication variation errors. For hemoglobin, a sensitivity of 1073.4 nm/RIU is obtained, with a limit of detection of 116.15 mg/lit for 65-87 g/lit of hemoglobin in water; for the toluene sensor,

S

=

1019.7

n
m

/

R
I
U

is calculated. As a general result, a high figure of merit/sensitivity can be achieved over a wide range of applications, from gases to high RI analytes, using our proposed classifications.
Dissipative pure-quartic soliton fiber laser
Authors: Qian Zi-Chen , Liu Meng , Luo Ai-Ping , Luo Zhi-Chao , Xu Wen-Cheng
Published: May 2022

The evolution of ultrafast laser technology hinges partially on the understanding of the soliton nonlinear dynamics. Recently, the concept of pure-quartic soliton (PQS) that arises from the balance of pure negative fourth-order dispersion (FOD) and nonlinearity was proposed to generate high peak power pulse. Herein, we investigate the generation of dissipative pure-quartic soliton (DPQS) in a fiber laser, which is balanced among the positive FOD, nonlinearity, gain and loss. The DPQS features the shape-preserving propagation despite the asymmetrical temporal profile at higher pulse energy. It is found that the asymmetrical temporal profile of DPQS is resulted from the mismatching of the phase shift profiles caused by self-phase modulation and FOD. Moreover, it is demonstrated that the DPQS possesses a higher energy-scaling ability compared to conventional dissipative soliton, owing to the nonlinear relationship between the pulse energy and pulse duration. These findings demonstrated that the employment of positive FOD could be a promising way for manipulation of optical pulse as well as the improvement of laser performance.
Mode spacing multiplication of optical frequency combs without power loss
Authors: Kageyama Taiki , Hasegawa Taro
Published: May 2022

We demonstrate the mode spacing multiplication of optical frequency combs (OFCs) using interleaving technique. The pulse train of an OFC after interleaving is phase modulated, and phase demodulation is necessary for mode spacing multiplication. This scheme enables mode spacing multiplication without power loss in principle, which is in contrast to the conventional mode filtering technique. During demonstration, the mode spacing of the OFC of a mode-locked Er-doped fiber laser (repetition rate of 97 MHz) is quadrupled by the interleaving process and successive phase demodulation.
Influence of multiphoton resonance excitation on the above-threshold ionization of a hydrogen atom
Authors: Yuan Haiying , Yang Yujun , Guo Fuming , Wang Jun , Cui Zhiwen
Published: May 2022

The photo-electron emission of a hydrogen atom irradiated by an ultraviolet laser pulse is investigated by numerically solving the time-dependent Schrödinger equation in momentum space. A subpeak structure with high intensity is observed in the photo-electron emission spectrum, and the peak of the enhanced structure shifts to a higher energy as the laser intensity increases. Through the strong-field approximation and the analysis of the population of the bound state , it is found that this subpeak structure is generated from the interference between the ionized electrons from the ground state and the ionized electrons from the 2p state after the resonant transition from the ground state to the 2p state. Analyzing the change rule of the photo-electron emission spectrum can further deepen the understanding of the energy change of the dressed bound state for an atom irradiated by an intense laser pulse.
Passive laser power stabilization via an optical spring
Authors: Cullen Torrey , Aronson Scott , Pagano Ron , Trad Nery Marina , Cain Henry , Cripe Jonathon , Cole Garrett D. , Sharifi Safura , Aggarwal Nancy , Willke Benno , Corbitt Thomas
Published: May 2022

Metrology experiments can be limited by the noise produced by the laser involved via small fluctuations in the laser’s power or frequency. Typically, active power stabilization schemes consisting of an in-loop sensor and a feedback control loop are employed. Those schemes are fundamentally limited by shot noise coupling at the in-loop sensor. In this Letter, we propose to use the optical spring effect to passively stabilize the classical power fluctuations of a laser beam. In a proof of principle experiment, we show that the relative power noise of the laser is stabilized from approximately 2 × 10−5 Hz−1/2 to a minimum value of 1.6 × 10−7 Hz−1/2, corresponding to the power noise reduction by a factor of 125. The bandwidth at which stabilization occurs ranges from 400 Hz to 100 kHz. The work reported in this Letter further paves the way for high power laser stability techniques which could be implemented in optomechanical experiments and in gravitational wave detectors.
Chaotic optical communications of 12.5-Gbaud OOK and 10-Gbaud QPSK signals based on mutual injection of semiconductor lasers
Authors: Xiang Shunkai , Yang Min , Wang Jian
Published: May 2022

Chaotic optical communications can provide a high level of security in data transmission. High-speed chaotic optical communications have hardly been implemented so far limited by the bandwidth of chaotic signals and the difficulties of wideband chaos synchronization. Here, we experimentally demonstrate all-optical wideband chaos synchronization and communications based on mutual injection of semiconductor lasers. Both 12.5-Gbaud on–off keying (OOK) signals and 10-Gbaud quadrature phase shift keying (QPSK) signals are successfully encrypted and transmitted over a 10-km and 2-km single-mode fiber (SMF), respectively.
Numerical study on a random plasmonic laser in the metal–insulator–metal structure
Authors: Yao Fengfeng , Pei Yanbo , Hou Chunfeng , Sun Xiudong
Published: May 2022

This Letter proposes a random plasmonic laser in the metal–insulator–metal (MIM) structure, in which the dielectric core with gain is dispersed with circular dielectric nanoscatterers. The numerical results from finite-difference time-domain simulation indicate that scattering by the randomly distributed dielectric nanoscatterers in the MIM waveguide provides feedback to the random laser with surface plasmon. The design bypasses the requirement of a distributed feedback structure for the plasmonic waveguide-based nanolasers, which is challenging and expensive in fabrication. Additionally, the MIM structure makes this type of random laser easily applicable to nanoscale integrated photonic devices and circuits.
Optical isolation via direction-dependent soliton routing in birefringent soft matter
Authors: Calisto Enrique , Smyth Noel F. , Assanto Gaetano
Published: May 2022

We introduce optical isolation based on reorientational solitary waves in nonuniformly oriented uniaxial soft matter, namely nematic liquid crystals. A longitudinally nonsymmetric angular distribution of the optic axis provides the system with direction-dependent routing, resulting in an all-optical diode owing to input-side sensitive steering. Numerical experiments demonstrate the phenomenon and its effectiveness in realistic samples.
Wavelength and bandwidth tunable filter and its application in a dissipative soliton fiber laser
Authors: Wang Chaoran , Li Xingliang , Zhang Shumin , Yan Dan , Li Huijie
Published: May 2022

A wavelength and bandwidth tunable filter and its application in a dissipative soliton (DS) Yb-doped fiber laser are demonstrated. The spectral filter consisting of six cascaded temperature-sensitive long-period fiber gratings is designed and fabricated for the first time, to the best of our knowledge. The corresponding spectral characteristics of the filter are also characterized with temperature. Its 3-dB bandwidth can be adjusted from 4.84 to 11.02 nm, and the center wavelength is continuously adjustable from 1036 to 1045 nm. The sensitivity of the variation of the center wavelength and the linearity of the center wavelength variation are 32 pm/°C and 99.53%, respectively. This home-made spectral filter has two notable features: i) with regard to the tunable spectrum, the 3-dB bandwidth of the spectrum filter can be unchanged; ii) with regard to the spectral tunability, the 3-dB bandwidth of the spectral filter can also be quantitatively changed as needed by changing the heating mode. The home-made spectral filter is used in the DS fiber laser to further realize the continuous adjustment of DS with a tuning accuracy of 0.03 nm by a step size of 1°C. Such a wavelength-tunable DS fiber laser greatly enhances the design flexibility of the coherent anti-Stokes Raman scattering source.
Electric-field-resolved near-infrared microscopy
Authors: Mamaikin Mikhail , Li Yik-Long , Ridente Enrico , Chen Wei Ting , Park Joon-Suh , Zhu Alexander Y. , Capasso Federico , Weidman Matthew , Schultze Martin , Krausz Ferenc , Karpowicz Nicholas
Published: May 2022

Access to the complete spatiotemporal response of matter due to
structured light requires field sampling techniques with
sub-wavelength resolution in time and space. We demonstrate spatially
resolved electro-optic sampling of near-infrared waveforms, providing
a versatile platform for the direct measurement of electric field
dynamics produced by photonic devices and sub-wavelength structures
both in the far and near fields. This approach offers high-resolution,
time- or frequency-resolved imaging by encoding a broadband signal
into a narrowband blueshifted image, lifting the resolution limits
imposed by both chromatic aberration and diffraction. Specifically,
measuring the field of a near-infrared laser with a broadband sampling
laser, we achieve 1.2 µm resolution in space and 2.2 fs resolution in
time. This provides an essential diagnostic for complete
spatiotemporal control of light with metasurface components,
demonstrated via a metalens as well as a meta-axicon that forms
broadband, ultrashort, truncated Bessel beams in the near infrared.
Finally, we demonstrate the electric field dynamics of locally
enhanced hot spots with sub-wavelength dimensions, recording the full
temporal evolution of the electric field at each point in the image
simultaneously. The imaging modality opens a path
toward hyperspectral microscopy with simultaneous sub-wavelength
resolution and wide-field imaging capability.
A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota
Authors: Sommer Alice J. , Peters Annette , Rommel Martina , Cyrys Josef , Grallert Harald , Haller Dirk , Müller Christian L. , Bind Marie-Abèle C.
Published: May 2022

Statistical analysis of microbial genomic data within epidemiological cohort studies holds the promise to assess the influence of environmental exposures on both the host and the host-associated microbiome. However, the observational character of prospective cohort data and the intricate characteristics of microbiome data make it challenging to discover causal associations between environment and microbiome. Here, we introduce a causal inference framework based on the Rubin Causal Model that can help scientists to investigate such environment-host microbiome relationships, to capitalize on existing, possibly powerful, test statistics, and test plausible sharp null hypotheses. Using data from the German KORA cohort study, we illustrate our framework by designing two hypothetical randomized experiments with interventions of (i) air pollution reduction and (ii) smoking prevention. We study the effects of these interventions on the human gut microbiome by testing shifts in microbial diversity, changes in individual microbial abundances, and microbial network wiring between groups of matched subjects via randomization-based inference. In the smoking prevention scenario, we identify a small interconnected group of taxa worth further scrutiny, includingChristensenellaceaeandRuminococcaceaegenera, that have been previously associated with blood metabolite changes. These findings demonstrate that our framework may uncover potentially causal links between environmental exposure and the gut microbiome from observational data. We anticipate the present statistical framework to be a good starting point for further discoveries on the role of the gut microbiome in environmental health.
Multiscale modeling of presynaptic dynamics from molecular to mesoscale
Authors: Garcia Jonathan W. , Bartol Thomas M. , Sejnowski Terrence J.
Published: May 2022

Chemical synapses exhibit a diverse array of internal mechanisms that affect the dynamics of transmission efficacy. Many of these processes, such as release of neurotransmitter and vesicle recycling, depend strongly on activity-dependent influx and accumulation of Ca2+. To model how each of these processes may affect the processing of information in neural circuits, and how their dysfunction may lead to disease states, requires a computationally efficient modelling framework, capable of generating accurate phenomenology without incurring a heavy computational cost per synapse. Constructing a phenomenologically realistic model requires the precise characterization of the timing and probability of neurotransmitter release. Difficulties arise in that functional forms of instantaneous release rate can be difficult to extract from noisy data without running many thousands of trials, and in biophysical synapses, facilitation of per-vesicle release probability is confounded by depletion. To overcome this, we obtained traces of free Ca2+ concentration in response to various action potential stimulus trains from a molecular MCell model of a hippocampal Schaffer collateral axon. Ca2+ sensors were placed at varying distance from a voltage-dependent calcium channel (VDCC) cluster, and Ca2+ was buffered by calbindin. Then, using the calcium traces to drive deterministic state vector models of synaptotagmin 1 and 7 (Syt-1/7), which respectively mediate synchronous and asynchronous release in excitatory hippocampal synapses, we obtained high-resolution profiles of instantaneous release rate, to which we applied functional fits. Synchronous vesicle release occurred predominantly within half a micron of the source of spike-evoked Ca2+ influx, while asynchronous release occurred more consistently at all distances. Both fast and slow mechanisms exhibited multi-exponential release rate curves, whose magnitudes decayed exponentially with distance from the Ca2+ source. Profile parameters facilitate on different time scales according to a single, general facilitation function. These functional descriptions lay the groundwork for efficient mesoscale modelling of vesicular release dynamics.
Noradrenergic deficits contribute to apathy in Parkinson’s disease through the precision of expected outcomes
Authors: Hezemans Frank H. , Wolpe Noham , O’Callaghan Claire , Ye Rong , Rua Catarina , Jones P. Simon , Murley Alexander G. , Holland Negin , Regenthal Ralf , Tsvetanov Kamen A. , Barker Roger A. , Williams-Gray Caroline H. , Robbins Trevor W. , Passamonti Luca , Rowe James B.
Published: May 2022

Apathy is a debilitating feature of many neuropsychiatric diseases, that is typically described as a reduction of goal-directed behaviour. Despite its prevalence and prognostic importance, the mechanisms underlying apathy remain controversial. Degeneration of the locus coeruleus-noradrenaline system is known to contribute to motivational deficits, including apathy. In healthy people, noradrenaline has been implicated in signalling the uncertainty of expectations about the environment. We proposed that noradrenergic deficits contribute to apathy by modulating the relative weighting of prior beliefs about action outcomes. We tested this hypothesis in the clinical context of Parkinson’s disease, given its associations with apathy and noradrenergic dysfunction. Participants with mild-to-moderate Parkinson’s disease (N = 17) completed a randomised double-blind, placebo-controlled, crossover study with 40 mg of the noradrenaline reuptake inhibitor atomoxetine. Prior weighting was inferred from psychophysical analysis of performance in an effort-based visuomotor task, and was confirmed as negatively correlated with apathy. Locus coeruleus integrity was assessed in vivo using magnetisation transfer imaging at ultra-high field 7T. The effect of atomoxetine depended on locus coeruleus integrity: participants with a more degenerate locus coeruleus showed a greater increase in prior weighting on atomoxetine versus placebo. The results indicate a contribution of the noradrenergic system to apathy and potential benefit from noradrenergic treatment of people with Parkinson’s disease, subject to stratification according to locus coeruleus integrity. More broadly, these results reconcile emerging predictive processing accounts of the role of noradrenaline in goal-directed behaviour with the clinical symptom of apathy and its potential pharmacological treatment.
Modelling the acclimation capacity of coral reefs to a warming ocean
Authors: Raharinirina Nomenjanahary Alexia , Acevedo-Trejos Esteban , Merico Agostino
Published: May 2022

The symbiotic relationship between corals and photosynthetic algae is the foundation of coral reef ecosystems. This relationship breaks down, leading to coral death, when sea temperature exceeds the thermal tolerance of the coral-algae complex. While acclimation via phenotypic plasticity at the organismal level is an important mechanism for corals to cope with global warming, community-based shifts in response to acclimating capacities may give valuable indications about the future of corals at a regional scale. Reliable regional-scale predictions, however, are hampered by uncertainties on the speed with which coral communities will be able to acclimate. Here we present a trait-based, acclimation dynamics model, which we use in combination with observational data, to provide a first, crude estimate of the speed of coral acclimation at the community level and to investigate the effects of different global warming scenarios on three iconic reef ecosystems of the tropics: Great Barrier Reef, South East Asia, and Caribbean. The model predicts that coral acclimation may confer some level of protection by delaying the decline of some reefs such as the Great Barrier Reef. However, the current rates of acclimation will not be sufficient to rescue corals from global warming. Based on our estimates of coral acclimation capacities, the model results suggest substantial declines in coral abundances in all three regions, ranging from 12% to 55%, depending on the region and on the climate change scenario considered. Our results highlight the importance and urgency of precise assessments and quantitative estimates, for example through laboratory experiments, of the natural acclimation capacity of corals and of the speed with which corals may be able to acclimate to global warming.
RecombineX: A generalized computational framework for automatic high-throughput gamete genotyping and tetrad-based recombination analysis
Authors: Li Jing , Llorente Bertrand , Liti Gianni , Yue Jia-Xing
Published: May 2022

Meiotic recombination is an essential biological process that ensures faithful chromosome segregation and promotes parental allele shuffling. Tetrad analysis is a powerful approach to quantify the genetic makeups and recombination landscapes of meiotic products. Here we present RecombineX (https://github.com/yjx1217/RecombineX), a generalized computational framework that automates the full workflow of marker identification, gamete genotyping, and tetrad-based recombination profiling based on any organism or genetic background with batch processing capability. Aside from conventional reference-based analysis, RecombineX can also perform analysis based on parental genome assemblies, which facilitates analyzing meiotic recombination landscapes in their native genomic contexts. Additional features such as copy number variation profiling and missing genotype inference further enhance downstream analysis. RecombineX also includes a dedicate module for simulating the genomes and reads of recombinant tetrads, which enables fine-tuned simulation-based hypothesis testing. This simulation module revealed the power and accuracy of RecombineX even when analyzing tetrads with very low sequencing depths (e.g., 1-2X). Tetrad sequencing data from the budding yeast Saccharomyces cerevisiae and green alga Chlamydomonas reinhardtii were further used to demonstrate the accuracy and robustness of RecombineX for organisms with both small and large genomes, manifesting RecombineX as an all-around one stop solution for future tetrad analysis. Interestingly, our re-analysis of the budding yeast tetrad sequencing data with RecombineX and Oxford Nanopore sequencing revealed two unusual structural rearrangement events that were not noticed before, which exemplify the occasional genome instability triggered by meiosis.
A Bayesian model selection approach to mediation analysis
Authors: Crouse Wesley L. , Keele Gregory R. , Gastonguay Madeleine S. , Churchill Gary A. , Valdar William
Published: May 2022

Genetic studies often seek to establish a causal chain of events originating from genetic variation through to molecular and clinical phenotypes. When multiple phenotypes share a common genetic association, one phenotype may act as an intermediate for the genetic effects on the other. Alternatively, the phenotypes may be causally unrelated but share genetic loci. Mediation analysis represents a class of causal inference approaches used to determine which of these scenarios is most plausible. We have developed a general approach to mediation analysis based on Bayesian model selection and have implemented it in an R package, bmediatR. Bayesian model selection provides a flexible framework that can be tailored to different analyses. Our approach can incorporate prior information about the likelihood of models and the strength of causal effects. It can also accommodate multiple genetic variants or multi-state haplotypes. Our approach reports posterior probabilities that can be useful in interpreting uncertainty among competing models. We compared bmediatR with other popular methods, including the Sobel test, Mendelian randomization, and Bayesian network analysis using simulated data. We found that bmediatR performed as well or better than these alternatives in most scenarios. We applied bmediatR to proteome data from Diversity Outbred (DO) mice, a multi-parent population, and demonstrate the power of mediation with multi-state haplotypes. We also applied bmediatR to data from human cell lines to identify transcripts that are mediated through or are expressed independently from local chromatin accessibility. We demonstrate that Bayesian model selection provides a powerful and versatile approach to identify causal relationships in genetic studies using model organism or human data.
Mice lacking the mitochondrial exonuclease MGME1 develop inflammatory kidney disease with glomerular dysfunction
Authors: Milenkovic Dusanka , Sanz-Moreno Adrián , Calzada-Wack Julia , Rathkolb Birgit , Veronica Amarie Oana , Gerlini Raffaele , Aguilar-Pimentel Antonio , Misic Jelena , Simard Marie-Lune , Wolf Eckhard , Fuchs Helmut , Gailus-Durner Valerie , de Angelis Martin Hrabě , Larsson Nils-Göran
Published: May 2022

Mitochondrial DNA (mtDNA) maintenance disorders are caused by mutations in ubiquitously expressed nuclear genes and lead to syndromes with variable disease severity and tissue-specific phenotypes. Loss of function mutations in the gene encoding the mitochondrial genome and maintenance exonuclease 1 (MGME1) result in deletions and depletion of mtDNA leading to adult-onset multisystem mitochondrial disease in humans. To better understand the in vivo function of MGME1 and the associated disease pathophysiology, we characterized a Mgme1 mouse knockout model by extensive phenotyping of ageing knockout animals. We show that loss of MGME1 leads to de novo formation of linear deleted mtDNA fragments that are constantly made and degraded. These findings contradict previous proposal that MGME1 is essential for degradation of linear mtDNA fragments and instead support a model where MGME1 has a critical role in completion of mtDNA replication. We report that Mgme1 knockout mice develop a dramatic phenotype as they age and display progressive weight loss, cataract and retinopathy. Surprisingly, aged animals also develop kidney inflammation, glomerular changes and severe chronic progressive nephropathy, consistent with nephrotic syndrome. These findings link the faulty mtDNA synthesis to severe inflammatory disease and thus show that defective mtDNA replication can trigger an immune response that causes age-associated progressive pathology in the kidney.