bluuebunny/crossref_metadata_2025 huggingface dataset:
CONTROL AND REGULATION OF THE ACTIVITIES OF REGIONAL UNIVERSITIES
Authors: Burceva Kseniya
Published: January 2021

The article explores the problematic issues of the development of the organization of external and internal control of the activities of universities on the basis of a historical approach to the analysis of the experience of the Soviet school and modern principles. The existing system of training and employment of graduates is not always ideal. The study identified clear problems that do not correspond to the needs of the labor market and trained personnel, including in individual regions, which indicates the need to improve the interaction between universities and employers. The systematization of forms of state regulation in the field of higher education made it possible to clearly imagine the directions of external control turned more to regulating the interaction of the three main groups of stakeholders (stakeholders) of the university: state authorities, students and employers. Research was carried out in order to substantiate the logical model of interaction of university stakeholders, which allows controlling their activities. In the developed model, the main unit regulating and monitoring the interaction of stakeholders is the National Council under the President of the Russian Federation. The interaction of the university and the National Council will make it possible to implement the requirements for the qualifications of graduates in the educational process of their training that meet the modern and future requirements of the labor market. It is proposed by the state authorities to determine indicators for monitoring the effectiveness (effectiveness) of state targeted programs for the employment of university graduates, and the educational institution itself to establish target values of control indicators that need preliminary monitoring. It was recommended that the strategic goals of the regional university be balanced in four aspects of activity (business processes of educational activities and resources, relations with stakeholders, finance, research activities), harmonized not only among themselves, but also in a space-time representation. It is proposed to monitor the implementation of tasks for each aspect of the activity on the basis of developed and presented actual and target values of control indicators of regional universities
El (Im)posible Rango Crítico-Decolonial en la Dialéctica Negativa de Adorno.
Authors: Fallas-Vargas Fabrizio
Published: January 2021

The current paper addresses the need to respond critically to the theoretical challenges that arise from the matrix of decolonial thinking and its relation to Theodor W. Adorno’s negative dialectics. Methodologically, a conceptual framework has been developed to establish the possible communicating vessels between the different elaborations on decolonial thinking and Adorno’s theoretical production. Bearing in mind the Castro-Gómez critique of Foucault, this approach disassociates itself from the idea that a thinker is Eurocentric on the mere basis of the locus of enunciation. This work posits that it is perfectly feasible to find an analytical exercise that allows a closer approach to Adorno’s thinking. This implies a paradoxical double movement in the analysis. One is the critical study of the Adornian approach or negative dialectic from decolonial criticism, and the other is determining the possibility of tracing plexuses of concrete interpenetration between both theoretical universes.
Are Postcolonial Narratives useful in Al-Andalus Archaeology?.
Authors: García-Contreras Guillermo
Published: January 2021

Archaeological investigations of al-Andalus has become increasingly important in medieval studies, but it has traditionally been left out of the research agenda of European medieval archaeology. This is due to its exoticism and not fitting in well with the construction of a European identity and Spanish national history based on Christian expansion and the “Reconquest” process. At the same time, due to the geographical location and geopolitical position of the Iberian Peninsula within the “West”, scholars working on Islamic archaeology have dedicated less attention to al-Andalus than to other territories. Several factors pose a challenge for current research: the possibility of confrontation with feudal societies; the increasing importance given to technological transfer all along al-Andalus; religious, economic and institutional differences within Christian territories; the importance given in recent years to the identity construction of alterity; and the strong impact that the Andalusi period had on the creation of current landscapes, especially due to irrigated agriculture. This paper tries to reflect on and analyze the historiographical marginality of al-Andalus in both European medieval archaeology and Islamic archaeology. The aim is to understand how we have built an international narrative of the marginality of a territory that is theoretically outside Europe and outside the environment in which classical Islam developed, based mainly on literature produced in English on this matter. In short, this paper poses the question of whether postcolonial theory is a valid category of analysis for al-Andalus.
Descolonización del Conocimiento y Pensamiento Andaluz Descolonial.
Authors: García-Fernández Javier
Published: January 2021

The aim of this contribution is to recapitulate the scenario of Andalusian studies and Andalusian intellectual traditions from the early tradition of social sciences to Andalusian decolonial theory. The methodology used is a comprehensive review of all the currents of Andalusian critical thinking of the last two centuries to connect Andalusian critical theory with the theoretical proposals of the decolonial shift. It is concluded that Andalusian decolonial thinking is the legacy of the Andalusian intellectual tradition of the last two centuries.
Dwa kryzysy i rewolucja: wydarzenia 2004 i 2014 r. na Ukrainie w perspektywie porównawczej
Authors: Macijewśkyj Jurij
Published: January 2021

Two Crises and a Revolution: 2004 and 2014 Events in Ukraine in Comparative Perspective
Why has V. Yanukovych been long able to survive while L. Kuchma failed? This paper seeks to locate the factors leading to the quick downfall of the Kuchma’s regime in Ukraine in 2004 in comparison to the extended regime survival in 2014. Drawing on the political science theories of dynamics of hybrid regimes and revolution, the author advances two theses: first, the mass mobilization is necessary but not a sufficient condition for the collapse of an autocrat. Comparing the two crisis episodes of 2004 and 2014 in Ukraine by using ten indicators, the author argues that the regime’s organizational capacity initially was higher than both Western democratic pressure and “people’s power”. Only after the third violent attempt to disperse Maidan had failed, the “power vertical” collapsed what led to the creation of a new parliamentary majority and effective loss of power by the incumbent. Second, unlike the crisis of 2004 the crisis of 2014 has not been resolved through the compromise and turned into a revolution. Applying eleven, analytically defined, attributes of the revolution to the Orange events of 2004 resulted only in three matches, while in 2014 there are already seven matches (breakdown of the state, international pressure, economic decline, conflict between elites, mass mobilization, “multiple sovereignty” and violence) and two others (the change of regime and the change of social structure) is theoretically possible. The presence of these attributes suggests that in 2014 Ukraine had a political, but could hardly have a social revolution.
Uczestnictwo polityczne obywateli Ukrainy: wymiar wyborczy, protestacyjny i dyskursywny
Authors: Rotar Natalia
Published: January 2021

Political participation of Ukrainian citizens: electoral, protest, discursive measure
A complex research of the particularities of the Ukrainian citizens’ participation in the cyclic political processes of transformational period has been provided. Logic of electoral cycles in Ukraine is being examined in the context of formation of the three dynamic models of citizens’ participation – electoral, discursive and protest. It has been proved that citizens’ usage of the protest model of political participation has multiple-factor determination, in which the fulfilment of the institutionalization of system opposition is the dominating element. It has been grounded that the most effective model of citizens’ influence on political system is discursive model of political participation, which is able to guarantee system equilibrium in the structure of political system. The main features and mechanisms of formation of the dialogue form of Ukrainian citizens’ political participation have been scrutinized. Perspectives of expansion of the range of political participation by means of the citizens using electronic devices of interaction with authorities, which are given to them by the resources of e-democracy, have been analyzed.
Parallelizing Subgradient Methods for the Lagrangian Dual in Stochastic Mixed-Integer Programming
Authors: Lim Cong Han , Linderoth Jeffrey T. , Luedtke James R. , Wright Stephen J.
Published: January 2021

The dual decomposition of stochastic mixed-integer programs can be solved by the projected subgradient algorithm. We show how to make this algorithm more amenable to parallelization in a master-worker model by describing two approaches, which can be combined in a natural way. The first approach partitions the scenarios into batches and makes separate use of subgradient information for each batch. The second approach drops the requirement that evaluation of function and subgradient information is synchronized across the scenarios. We provide convergence analysis of both methods. We also evaluate their performance on two families of problems from SIPLIB on a single server with 32 single-core worker processes, demonstrating that when the number of workers is high relative to the number of scenarios, these two approaches (and their synthesis) can significantly reduce running time.
First-Order Methods for Constrained Convex Programming Based on Linearized Augmented Lagrangian Function
Authors: Xu Yangyang
Published: January 2021

First-order methods (FOMs) have been popularly used for solving large-scale problems. However, many existing works only consider unconstrained problems or those with simple constraint. In this paper, we develop two FOMs for constrained convex programs, where the constraint set is represented by affine equations and smooth nonlinear inequalities. Both methods are based on the classical augmented Lagrangian function. They update the multipliers in the same way as the augmented Lagrangian method (ALM) but use different primal updates. The first method, at each iteration, performs a single proximal gradient step to the primal variable, and the second method is a block update version of the first one. For the first method, we establish its global iterate convergence and global sublinear and local linear convergence, and for the second method, we show a global sublinear convergence result in expectation. Numerical experiments are carried out on the basis pursuit denoising, convex quadratically constrained quadratic programs, and the Neyman-Pearson classification problem to show the empirical performance of the proposed methods. Their numerical behaviors closely match the established theoretical results.
EFFECT OF ORGANIZATION COMMITMENT, WORK MOTIVATION AND WORK DISCIPLINE ON EMPLOYEE PERFORMANCE (Study at. PT. PLN (Persero) P3b Sumatera UPT Padang)
Authors: Amri Andi , Ramadhi Ramadhi , Ramdani Zulmi
Published: January 2021

Employees are an essential asset for the organization to advance and develop the organization to be more productive. This situation may achieve when employees in the organization have optimal performance. Many factors positively affect the performance of employees in the organization. This study aims to determine how much influence organizational commitment, work motivation and work discipline have on employee performance in PT. PLN (Persero) P3b Sumatera UPT Padang. Respondents who were involved in the study were 60 people who were selected using the saturated sample technique. The results showed that both partially and simultaneously, organizational commitment, work motivation, and work discipline had a significant and positive effect on employee performance. The coefficient of determination of the tested variables is .636. It shows that the percentage contribution of the variable organizational commitment, work motivation and work discipline to employee performance is 64.6%. In comparison, the remaining 35.4%  determined by other variables not analyzed in this study's model. Thus, this study shows that the three tested variables must be an essential consideration for the organization to obtain optimal employee performance.
Development and evaluation of a color-image-based visual roughness measurement method with illumination robustness
Authors: Zhao Xinjia , Yi Huaian , Chen Yonglun , Shu Aihua
Published: January 2021

At present, the application of machine vision methods for roughness measurement in production sites is limited by its adaptability to illumination variations during the measurement. In this study, a machine vision method for roughness measurement with robustness to illumination is proposed so as to explore the functions of its color image indices in improving the mathematical expression of the vector of three primary colors. Besides, virtual images of different-roughness surfaces were analyzed, the effects of the samples’ surface texture orientations on measurement indices were discussed, and the singular value ratio was derived as an index for evaluating roughness. The experimental results showed that the samples’ index values remained unchanged when the illumination was increased for both vertical and horizontal surface textures, indicating that the proposed method has strong robustness to illumination. In addition, the experimental results were verified by a support vector machine (SVM)-based method using 10 different-roughness test samples, with the verification range of 0.127–2.245 µm. It was found that the measurement accuracy reached 90%, suggesting that the proposed method is reasonable and feasible, and shows certain potential to be applied in engineering.
Highly efficient SiO2 trapezoidal grating-based thin-film solar cell
Authors: Aly Asmaa Mohamed A. , Hussein Mohamed , Yahia Ashraf , Hameed Mohamed Farhat O. , Obayya S. S. A.
Published: January 2021

A crystalline silicon thin-film solar cell (c-Si TFSC) with a trapezoidal grating is newly introduced and analyzed. The three-dimensional (3D) finite-difference time-domain (FDTD) method is employed to optimize the geometrical parameters of the trapezoidal grating and hence maximize the light absorption. The proposed trapezoidal grating TFSC offers an optical ultimate efficiency (

η

) of 32.3%, with an enhancement of 81% relative to the conventional TFSC. The light absorption enhancement within wavelength range (300–1100 nm) is based on the diffraction grating, which supports Bloch modes through the suggested solar cell. The electrical characteristics of the proposed design are also studied using the finite-element method. The cell doping concentration, junction thickness, and recombination process are also investigated to further enhance the power conversion efficiency (PCE). The reported design offers a short circuit current density

J

s
c

of

24.8

m
A

/

c
m

2

and PCE of 12.5% with an improvement of 83% over the conventional TFSC.
Color-detuning-dynamics-based quantum sensing with dressed states driving
Authors: Zhang Hao , Qin Guo-Qing , Song Xue-Ke , Long Gui-Lu
Published: January 2021

Exploring quantum technology to precisely measure physical quantities is a meaningful task for practical scientific researches. Here, we propose a novel quantum sensing model based on color detuning dynamics with dressed states driving (DSD) in stimulated Raman adiabatic passage. The model is valid for sensing different physical quantities, such as magnetic field, mass, rotation and so on. For different sensors, the used systems can range from macroscopic scale, e.g. optomechanical systems, to microscopic nanoscale, e.g. solid spin systems. The dynamics of color detuning of DSD passage indicates the sensitivity of sensors can be enhanced by tuning system with more adiabatic or accelerated processes in different color detuning regimes. To show application examples, we apply our approach to build optomechanical mass sensor and solid spin magnetometer with practical parameters.
Computationally image-corrected dual-comb microscopy with a free-running single-cavity dual-comb fiber laser
Authors: Mizuno Takahiko , Nakajima Yoshiaki , Hata Yuya , Tsuda Takuya , Asahara Akifumi , Kato Takashi , Minamikawa Takeo , Yasui Takeshi , Minoshima Kaoru
Published: January 2021

Dual-comb microscopy (DCM), an interesting imaging modality based on the optical-frequency-comb (OFC) mode and image pixel one-to-one correspondence, benefits from scan-less full-field imaging and simultaneous confocal amplitude and phase imaging. However, the two fully frequency-stabilized OFC sources requirement hampers DCM practicality due to the complexity and costs. Here, a bidirectional single-cavity dual-comb fiber laser (SCDCFL) is adopted as a DCM low-complexity OFC source. Although the residual timing jitter in the SCDCFL blurs the image of a static object acquired by DCM, computational image correction significantly suppresses the image blur. Nanometer-order step surface profilometry with a 14.0 nm uncertainty highlights the computationally image-corrected DCM effectiveness. We further discuss a possibility to expand the computational image correction to a dynamic object and demonstrate its preliminary experiment. The proposed method enhances the DCM generality and practicality due to low-complexity OFC source.
Tunable spatiotemporal mode-locked fiber laser at 1.55 μm
Authors: Ma Ze-Long , Long Jin-Gan , Lin Wei , Hong Wei-Yi , Cui Hu , Luo Zhi-Chao , Xu Wen-Cheng , Likhachev Mikhail E. , Aleshkina Svetlana S. , Mashinsky Valery M. , Yashkov Mikhail V. , Luo Ai-Ping
Published: January 2021

We report the spatiotemporal mode-locked multimode fiber laser operating at 1.55 µm based on semiconductor saturable absorber mirrors with the mode-locking threshold as low as 104 mW. Benefiting from the multimode interference filtering effect introduced in the laser cavity not only the central wavelength can be continuously tuned from 1557 nm to 1567 nm, but also the number of the output pulses can be adjusted from 1 to 4 by simply adjusting the polarization controllers. This work provides a new platform for exploring the dynamic characteristics of spatiotemporal mode-locked pulses at negative dispersion regime. Moreover, this kind of tunable laser has potential applications in fields of all-optical signal processing, fiber sensing and information coding.
High-efficient coupler for thin-film lithium niobate waveguide devices
Authors: Hu Changran , Pan An , Li Tingan , Wang Xuanhao , Liu Yuheng , Tao Shiqi , Zeng Cheng , Xia Jinsong
Published: January 2021

Lithium niobate (LN) devices have been widely used in optical communication and nonlinear optics due to its attractive optical properties. The emergence of the thin-film lithium niobate on insulator (LNOI) improves performances of LN-based devices greatly. However, a high-efficient fiber-chip optical coupler is still necessary for the LNOI-based devices for practical applications. In this paper, we demonstrate a highly efficient and polarization-independent edge coupler based on LNOI. The coupler, fabricated by a standard semiconductor process, shows a low fiber-chip coupling loss of 0.54 dB/0.59 dB per facet at 1550 nm for TE/TM light, respectively, when coupled with an ultra-high numerical aperture fiber (UHNAF) of which the mode field diameter is about 3.2 μm. The coupling loss is lower than 1dB/facet for both TE and TM light in the wavelength range of 1527 nm to 1630 nm. A relatively large tolerance for optical misalignment is also proved, due to the coupler’s large mode spot size up to 3.2 μm. The coupler shows a promising stability in high optical power and temperature variation.
Accurate spectroscopy with sCMOS cameras at ultra-low intensities of light
Authors: Matsiaka Oleksii , Plakhotnik Taras
Published: January 2021

Modern image detectors with exceptionally low readout noise of about one electron (

e

−

) per pixel allow for applications with ultra-low levels of light intensity. In this Letter, we report a property of scientific CMOS detectors that makes accurate spectroscopy at ultra-low levels of illumination depending on a thorough calibration procedure. Our results reveal that pixel sensitivity to light may have significant nonlinearity at accumulation levels smaller than

50

e

−

per pixel. The sensitivity decreases by a factor of

∼

0.7

at an accumulation level of

∼

1

e

−

per pixel and photon detection rate of about 170 Hz. We demonstrate that the nature of this nonlinearity might be quite complicated: the photoelectric response of a pixel depends on both the number of accumulated electrons and the detection count rate (at rates larger than 250 Hz).
Optical storage of Ince–Gaussian modes in warm atomic vapor
Authors: Yu Ya , Chen Yun , Wang Chengyuan , Wang Jinwen , Sun Zhaochen , Cao Mingtao , Gao Hong , Li Fuli
Published: January 2021

We report on the optical storage of Ince–Gaussian modes in a warm rubidium vapor cell based on electromagnetically induced transparency protocol, and we also qualitatively analyze how atomic diffusion affects the retrieved beams after storage. Ince–Gaussian modes possess very complex and abundant spatial structures and form a complete infinite-dimensional Hilbert space. Successfully storing such modes could open up possibilities for fundamental high-dimensional optical communication experiments.
1  kW, 10  mJ, 120  fs coherently combined fiber CPA laser system
Authors: Stark Henning , Buldt Joachim , Müller Michael , Klenke Arno , Limpert Jens
Published: January 2021

An ultrafast fiber chirped-pulse amplification laser system based on a coherent combination of 16 ytterbium-doped rod-type amplifiers is presented. It generates 10 mJ pulse energy at 1 kW average power and 120 fs pulse duration. A partially helium-protected, two-staged chirped-pulse amplification grating compressor is implemented to maintain the close to diffraction-limited beam quality by avoiding nonlinear absorption in air.
High-throughput screening of a high-Q mid-infrared Tamm emitter by material informatics
Authors: Xi Wang , Liu Yida , Song Jinlin , Hu Run , Luo Xiaobing
Published: January 2021

Narrowband mid-infrared emitters, quantified by the

Q

-factor, have garnered a lot of attention due to their emerging applications from chemical and biosensing to efficient thermal utilization. Previous studies reported high

Q

-factor emitters within several selected wavelengths, still lacking a large database of emitter structures with very high

Q

-factors. In this Letter, we utilized the Monte Carlo Tree Search (MCTS) algorithm under the framework of material informatics to optimize the Tamm emitters at the infrared range (from 3 to 10 µm) for achieving a high

Q

-factor and high emissivity simultaneously, providing a large database of high and sharp emission peaks in the infrared. Through the MCTS algorithm, the structure with a

Q

-factor of 508 and an emissivity peak of 0.92 at 4.225 µm is obtained, far surpassing the previous results, and the underlying mechanism is discussed by electric field simulations. The high

Q

-factor emitters in the database show good monochromatism and high emissivity, accelerating the selection of proper perfect emitters for desired wavelengths. This Letter also paves a feasible avenue for the emitter and absorber design with ultrahigh monochromatism.
Electro-optic reconfigurable two-mode (de)multiplexer on thin-film lithium niobate
Authors: Zhang Mengruo , Chen Kaixin , Wang Mengke , Wu Jieyun , Chiang Kin Seng
Published: January 2021

We propose and demonstrate a compact electro-optic reconfigurable two-mode (de)multiplexer using the configuration of cascaded Mach–Zehnder interferometers formed on thin-film X-cut lithium niobate on silica. Our fabricated device, which is 9.5-mm long, can spatially switch between the two transverse-electric modes with an efficiency higher than 98% from 1530–1560 nm and beyond at an applied voltage of 6.5 V. The switching speed is faster than 30 ns. Our proposed mode switch could find applications in fiber-based and on-chip mode-division-multiplexing systems.
Multi-pass quartz-enhanced photoacoustic spectroscopy-based trace gas sensing
Authors: Qiao Shunda , Ma Yufei , Patimisco Pietro , Sampaolo Angelo , He Ying , Lang Ziting , Tittel Frank K. , Spagnolo Vincenzo
Published: January 2021

A multi-pass quartz-enhanced photoacoustic spectroscopy (MP-QEPAS)-based trace gas sensor is reported. In MP-QEPAS, a multi-pass laser beam pattern through the prong spacing of a quartz tuning fork (QTF) is obtained by means of two right-angle prisms. A large QTF with the prong length of 17 mm and prong spacing of 0.8 mm was employed to increase the passage of multi-pass time and ease the alignment of the beam reflection pattern through the QTF. This multi-pass configuration allows the laser beam to pass through the QTF prong spacing six times. Water vapor (

H

2

O

) was chosen as target gas to investigate the performance of the MP-QEPAS sensor. Compared to a conventional QEPAS measurement, the MP-QEPAS technique provided an enhancement of signal level of

∼

3.2

times.
Neural signatures of syntactic variation in speech planning
Authors: Sauppe Sebastian , Choudhary Kamal K. , Giroud Nathalie , Blasi Damián E. , Norcliffe Elisabeth , Bhattamishra Shikha , Gulati Mahima , Egurtzegi Aitor , Bornkessel-Schlesewsky Ina , Meyer Martin , Bickel Balthasar
Published: January 2021

Planning to speak is a challenge for the brain, and the challenge varies between and within languages. Yet, little is known about how neural processes react to these variable challenges beyond the planning of individual words. Here, we examine how fundamental differences in syntax shape the time course of sentence planning. Most languages treat alike (i.e., align with each other) the 2 uses of a word like “gardener” in “the gardener crouched” and in “the gardener planted trees.” A minority keeps these formally distinct by adding special marking in 1 case, and some languages display both aligned and nonaligned expressions. Exploiting such a contrast in Hindi, we used electroencephalography (EEG) and eye tracking to suggest that this difference is associated with distinct patterns of neural processing and gaze behavior during early planning stages, preceding phonological word form preparation. Planning sentences with aligned expressions induces larger synchronization in the theta frequency band, suggesting higher working memory engagement, and more visual attention to agents than planning nonaligned sentences, suggesting delayed commitment to the relational details of the event. Furthermore, plain, unmarked expressions are associated with larger desynchronization in the alpha band than expressions with special markers, suggesting more engagement in information processing to keep overlapping structures distinct during planning. Our findings contrast with the observation that the form of aligned expressions is simpler, and they suggest that the global preference for alignment is driven not by its neurophysiological effect on sentence planning but by other sources, possibly by aspects of production flexibility and fluency or by sentence comprehension. This challenges current theories on how production and comprehension may affect the evolution and distribution of syntactic variants in the world’s languages.
Dysregulation of excitatory neural firing replicates physiological and functional changes in aging visual cortex
Authors: Talyansky Seth , Brinkman Braden A. W.
Published: January 2021

The mammalian visual system has been the focus of countless experimental and theoretical studies designed to elucidate principles of neural computation and sensory coding. Most theoretical work has focused on networks intended to reflect developing or mature neural circuitry, in both health and disease. Few computational studies have attempted to model changes that occur in neural circuitry as an organism ages non-pathologically. In this work we contribute to closing this gap, studying how physiological changes correlated with advanced age impact the computational performance of a spiking network model of primary visual cortex (V1). Our results demonstrate that deterioration of homeostatic regulation of excitatory firing, coupled with long-term synaptic plasticity, is a sufficient mechanism to reproduce features of observed physiological and functional changes in neural activity data, specifically declines in inhibition and in selectivity to oriented stimuli. This suggests a potential causality between dysregulation of neuron firing and age-induced changes in brain physiology and functional performance. While this does not rule out deeper underlying causes or other mechanisms that could give rise to these changes, our approach opens new avenues for exploring these underlying mechanisms in greater depth and making predictions for future experiments.
mbkmeans: Fast clustering for single cell data using mini-batch k-means
Authors: Hicks Stephanie C. , Liu Ruoxi , Ni Yuwei , Purdom Elizabeth , Risso Davide
Published: January 2021

Single-cell RNA-Sequencing (scRNA-seq) is the most widely used high-throughput technology to measure genome-wide gene expression at the single-cell level. One of the most common analyses of scRNA-seq data detects distinct subpopulations of cells through the use of unsupervised clustering algorithms. However, recent advances in scRNA-seq technologies result in current datasets ranging from thousands to millions of cells. Popular clustering algorithms, such ask-means, typically require the data to be loaded entirely into memory and therefore can be slow or impossible to run with large datasets. To address this problem, we developed thembkmeansR/Bioconductor package, an open-source implementation of the mini-batchk-means algorithm. Our package allows for on-disk data representations, such as the common HDF5 file format widely used for single-cell data, that do not require all the data to be loaded into memory at one time. We demonstrate the performance of thembkmeanspackage using large datasets, including one with 1.3 million cells. We also highlight and compare the computing performance ofmbkmeansagainst the standard implementation ofk-means and other popular single-cell clustering methods. Our software package is available in Bioconductor athttps://bioconductor.org/packages/mbkmeans.
Sparse deep predictive coding captures contour integration capabilities of the early visual system
Authors: Boutin Victor , Franciosini Angelo , Chavane Frederic , Ruffier Franck , Perrinet Laurent
Published: January 2021

Both neurophysiological and psychophysical experiments have pointed out the crucial role of recurrent and feedback connections to process context-dependent information in the early visual cortex. While numerous models have accounted for feedback effects at either neural or representational level, none of them were able to bind those two levels of analysis. Is it possible to describe feedback effects at both levels using the same model? We answer this question by combining Predictive Coding (PC) and Sparse Coding (SC) into a hierarchical and convolutional framework applied to realistic problems. In the Sparse Deep Predictive Coding (SDPC) model, the SC component models the internal recurrent processing within each layer, and the PC component describes the interactions between layers using feedforward and feedback connections. Here, we train a 2-layered SDPC on two different databases of images, and we interpret it as a model of the early visual system (V1 & V2). We first demonstrate that once the training has converged, SDPC exhibits oriented and localized receptive fields in V1 and more complex features in V2. Second, we analyze the effects of feedback on the neural organization beyond the classical receptive field of V1 neurons using interaction maps. These maps are similar to association fields and reflect the Gestalt principle of good continuation. We demonstrate that feedback signals reorganize interaction maps and modulate neural activity to promote contour integration. Third, we demonstrate at the representational level that the SDPC feedback connections are able to overcome noise in input images. Therefore, the SDPC captures the association field principle at the neural level which results in a better reconstruction of blurred images at the representational level.
Catalytic promiscuity in the RNA World may have aided the evolution of prebiotic metabolism
Authors: Vörös Dániel , Könnyű Balázs , Czárán Tamás
Published: January 2021

The Metabolically Coupled Replicator System (MCRS) model of early chemical evolution offers a plausible and efficient mechanism for the self-assembly and the maintenance of prebiotic RNA replicator communities, the likely predecessors of all life forms on Earth. The MCRS can keep different replicator species together due to their mandatory metabolic cooperation and limited mobility on mineral surfaces, catalysing reaction steps of a coherent reaction network that produces their own monomers from externally supplied compounds. The complexity of the MCRS chemical engine can be increased by assuming that each replicator species may catalyse more than a single reaction of metabolism, with different catalytic activities of the same RNA sequence being in a trade-off relation: one catalytic activity of a promiscuous ribozyme can increase only at the expense of the others on the same RNA strand. Using extensive spatially explicit computer simulations we have studied the possibility and the conditions of evolving ribozyme promiscuity in an initial community of single-activity replicators attached to a 2D surface, assuming an additional trade-off between replicability and catalytic activity. We conclude that our promiscuous replicators evolve under weak catalytic trade-off, relatively strong activity/replicability trade-off and low surface mobility of the replicators and the metabolites they produce, whereas catalytic specialists benefit from very strong catalytic trade-off, weak activity/replicability trade-off and high mobility. We argue that the combination of conditions for evolving promiscuity are more probable to occur for surface-bound RNA replicators, suggesting that catalytic promiscuity may have been a significant factor in the diversification of prebiotic metabolic reaction networks.
A protease protection assay for the detection of internalized alpha-synuclein pre-formed fibrils
Authors: Jarvela Timothy S. , Chaplot Kriti , Lindberg Iris
Published: January 2021

Alpha-synuclein pre-formed fibrils (PFFs) represent a promising model system for the study of cellular processes underlying cell-to-cell transmission of alpha-synuclein proteopathic aggregates. However, the ability to differentiate the fate of internalized PFFs from those which remain in the extracellular environment remains limited due to the propensity for PFFs to adhere to the cell surface. Removal of PFFs requires repeated washing and/or specific quenching of extracellular fluorescent PFF signals. In this paper we present a new method for analyzing the fate of internalized alpha-synuclein. We inserted a tobacco etch virus (TEV) protease cleavage site between alpha-synuclein and green fluorescent protein and subjected cells to brief treatment with TEV protease after incubation with tagged PFFs. As the TEV protease is highly specific, non-toxic, and active under physiological conditions, protection from TEV cleavage can be used to distinguish internalized PFFs from those which remain attached to the cell surface. Using this experimental paradigm, downstream intracellular events can be analyzed via live or fixed cell microscopy as well as by Western blotting. We suggest that this method will be useful for understanding the fate of PFFs after endocytosis under various experimental manipulations.
Temporal development and neutralising potential of antibodies against SARS-CoV-2 in hospitalised COVID-19 patients: An observational cohort study
Authors: Murrell Isa , Forde Donall , Zelek Wioleta , Tyson Linda , Chichester Lisa , Palmer Nicki , Jones Rachel , Morgan B. Paul , Moore Catherine
Published: January 2021

Antibody responses are important in the control of viral respiratory infection in the human host. What is not clear for SARS-CoV-2 is how rapidly this response occurs, or when antibodies with protective capability evolve. Hence, defining the events of SARS-CoV-2 seroconversion and the time frame for the development of antibodies with protective potential may help to explain the different clinical presentations of COVID-19. Furthermore, accurate descriptions of seroconversion are needed to inform the best use of serological assays for diagnostic testing and serosurveillance studies. Here, we describe the humoral responses in a cohort of hospitalised COVID-19 patients (n = 19) shortly following the onset of symptoms. Commercial and ‘in-house’ serological assays were used to measure IgG antibodies against different SARS-CoV-2 structural antigens–Spike (S) S1 sub-unit and Nucleocapsid protein (NP)–and to assess the potential for virus neutralisation mediated specifically by inhibition of binding between the viral attachment protein (S protein) and cognate receptor (ACE-2). Antibody response kinetics varied amongst the cohort, with patients seroconverting within 1 week, between 1–2 weeks, or after 2 weeks, following symptom onset. Anti-NP IgG responses were generally detected earlier, but reached maximum levels slower, than anti-S1 IgG responses. The earliest IgG antibodies produced by all patients included those that recognised the S protein receptor-binding domain (RBD) and were capable of inhibiting binding to ACE-2. These data revealed events and patterns of SARS-CoV-2 seroconversion that may be important predictors of the outcome of infection and guide the delivery of clinical services in the COVID-19 response.
The association of body mass index with functional dyspepsia is independent of psychological morbidity: A cross-sectional study
Authors: Beh Keng Hau , Chuah Kee Huat , Rappek Nurul Azmi Mahamad , Mahadeva Sanjiv
Published: January 2021

Background and aim

The association between body mass index (BMI) and functional gastrointestinal disorders (FGIDs) has been inconsistent. We aimed to explore the association of BMI with FGIDs in a primary care setting to provide more data in this area.

Methods

A cross-sectional study of consecutive Asian adults attending a primary healthcare setting was conducted. This study was conducted in 2 phases: The association between BMI and common FGIDs (functional diarrhea/FD, irritable bowel syndrome/IBS, functional diarrhea and functional constipation/FC) was studied initially. The influence of anxiety and depression on BMI and FGIDs was additionally explored in phase 2.

Results

A total of 1002 subjects (median age 32 years, 65.4% females, 90.7% Malay ethnicity, 73.2% higher than secondary level education) were recruited between August 2019 to January 2020. The majority of subjects were obese (39.2%), and had central obesity (51.7%), while 6.1% had metabolic syndrome. The prevalence of FD, IBS, functional diarrhea and FC were 7.5% (n = 75), 4.0% (n = 40), 1.2% (n = 12) and 10.5% (n = 105) respectively, based on the Rome III criteria. Among individual FGIDs, FD subjects had more underweight adults (BMI<18.5kg/m2) compared to controls (13.3% vs 3.5%, P = 0.002) and being underweight remained as an independent association with FD [OR = 3.648 (95%CI 1.494–8.905), P = 0.004] at multi-variate analysis. There were no independent associations between BMI and other FGIDs. When psychological morbidity was additionally explored, anxiety (OR 2.032; 95%CI = 1.034–3.991, p = 0.040), but not depression, and a BMI<18.5kg/m2 (OR 3.231; 95%CI = 1.066–9.796, p = 0.038) were found to be independently associated with FD.

Conclusions

FD, but not other FGIDs, is associated with being underweight. This association is independent of the presence of anxiety.
Measuring femoral neck loads in healthy young and older adults during stair ascent and descent
Authors: Deng Chen , Gillette Jason C. , Derrick Timothy R.
Published: January 2021

Understanding the hip loading environment for daily activities is useful for hip fracture prevention, rehabilitation, and the design of osteogenic exercises. Seventeen older adults (50–70 yrs) and twenty young adults (18–30 yrs) were recruited. A rigid body model combined with a musculoskeletal model was used to estimate lower extremity loading. An elliptical cross-section model of the femoral neck was used to estimate femoral neck stress during stair ascent and descent. Two peaks were identified in the stress curves, corresponding to the peaks in the vertical ground reaction force. During stair ascent, significantly higher tension on the superior femoral neck was found for the young group at peak 1 (young: 13.5±6.1 MPa, older: 4.2±6.5 MPa, p<0.001). Also during stair ascent, significantly higher compression on the posterior femoral neck was found for the older group at peak 2 (young: -11.4±4.9 MPa, old: -18.1±8.6 MPa, p = 0.006). No significant difference was found for stair descent. Components of stress (muscle vs. reaction forces; axial forces vs. bending moments) were also examined for each trial of stair ascent and descent. The stresses and their components provided loading magnitude and locations of higher stress on the femoral neck during stair ascent and descent. Understanding femoral neck stresses may be used to help prevent hip fractures, reduce pain, improve rehabilitation, and design osteogenic exercises.
Seroprevalence of hepatitis E virus antibodies in adults and children from upstate New York: A cross-sectional study
Authors: Kmush Brittany L. , Lu Amelia M. , Spillane Taylor , Hruska Bryce , Gump Brooks B. , Bendinskas Kestutis G.
Published: January 2021

Hepatitis E virus (HEV) is a major cause of viral hepatitis around the world, especially in developing countries. Recently, HEV has also been recognized as important cause of hepatitis in Europe and Japan, however, there is a paucity of clinical data from the United States. The overall seroprevalence of HEV antibodies is around 10% in the United States, but considerable variation is seen based on geographic location, year, and assay used. In this study, 63 adults and 417 children from New York State were tested for anti-HEV IgG antibodies using the commercially available Wantai IgG assay. The overall seroprevalence of HEV antibodies among adult participants was 9.52% (95% CI: 3.58–19.59%). Positive adults tended to be older than HEV negative adults, all positive adults were female. Only 3 (0.7%, 95% CI:: 0.15–2.09%) of the children were positive, all positive children were male. These results are consistent with global and United States trends in HEV seroprevalence.
Assessing reflective functioning in prospective adoptive parents
Authors: Malcorps Saskia , Vliegen Nicole , Nijssens Liesbet , Tang Eileen , Casalin Sara , Slade Arietta , Luyten Patrick
Published: January 2021

The capacity for reflective functioning (RF) or mentalizing of adoptive parents is hypothesized to play an important role in fostering socio-emotional development in adopted children. This paper reports on the development and preliminary validation of the Adoption Expectations Interview (AEI), a semi-structured interview to assess RF in prospective adoptive parents. The AEI was developed based on the Pregnancy Interview, Parent Development Interview, and Working Model of the Child Interview, three interviews that have been used to assess RF in biological parents, to capture RF before child arrival in prospective adoptive parents. In a sample of 96 prospective adoptive parents, the Reflective Functioning Scale, as applied to the AEI (AEI-RFS) showed good reliability, with strong correlations between the different demand items, high internal consistency, and good to excellent inter-rater reliability. A principal component analysis yielded one component, suggesting that the items measured a unidimensional factor. Preliminary evidence for the construct validity of the AEI-RFS was demonstrated by significant associations between the AEI-RFS and well-validated measures of mentalizing, attachment dimensions, and interpersonal functioning.
Effect of partial hysterectomy on the neurons of the paracervical ganglion (PCG) of the pig
Authors: Podlasz Piotr , Wasowicz Krzysztof
Published: January 2021

Autonomic neurons innervating uterine horn is probably the only nerve cell population capable of periodical physiological degeneration and regeneration. One of the main sources of innervation of the uterus is paracervical ganglion (PCG). PCG is a unique structure of the autonomic nervous system. It contains components of both the sympathetic and parasympathetic nervous system. The present study examines the response of neurons of PCG innervating uterine horn to axotomy caused by partial hysterectomy in the domestic pig animal model. The study was performed using a neuronal retrograde tracing and double immunofluorescent staining for tyrosine hydroxylase (TH), dopamine beta-hydroxylase (DβH), choline acetyltransferase (ChAT), vesicular acetylcholine transporter (VAChT), neuronal nictric oxide synthase (nNOS), galanin, neuropeptide Y (NPY), vasoactive intestinal peptide (VIP), pituitary adenylate cyclase-activating peptide (PACAP), somatostatin and substance P (SP). Our study showed that virtually all neurons of the porcine PCG innervating uterine horn are adrenergic and we did not confirm that PCG is the source of cholinergic fibers innervating uterine horn of the pig. After axotomy there was a decrease in expression of catecholamine-synthesizing enzymes (TH, DβH) and a strong increase in the galanin expression. The increase of the number of NPY-IR neurons in the ganglia after axotomy was observed. There were no changes in the expression of other studied substances in the PCG neurons innervating the uterine horn, what was often found in rodents studies. This indicates that neurons can respond to damage in a species-specific way.
Transcriptomic profiling of susceptible and resistant flax seedlings after Fusarium oxysporum lini infection
Authors: Boba Aleksandra , Kostyn Kamil , Kozak Bartosz , Zalewski Iwan , Szopa Jan , Kulma Anna
Published: January 2021

In this study transcriptome was analyzed on two fibrous varieties of flax: the susceptible Regina and the resistant Nike. The experiment was carried out on 2-week-old seedlings, because in this phase of development flax is the most susceptible to infection. We analyzed the whole seedlings, which allowed us to recognize the systemic response of the plants to the infection. We decided to analyze two time points: 24h and 48h, because our goal was to learn the mechanisms activated in the initial stages of infection, these points were selected based on the previous analysis of chitinase gene expression, whose increase in time ofFusarium oxysporumlini infection has been repeatedly confirmed both in the case of flax and other plant species. The results show that although qualitatively the responses of the two varieties are similar, it is the degree of the response that plays the role in the differences of their resistance toF.oxysporum.