bluuebunny/crossref_metadata_2025 huggingface dataset:
What are we afraid of when we fear for our health? The symptom context of hypochondriacal complaints
Authors: Klasa Katarzyna , Sobański Jerzy , Konop Magdalena , Dembińska Edyta , Mielimąka Michał , Citkowska-Kisielewska Anna , Jęda Patrycja , Pelc Magdalena , Rutkowski Krzysztof
Published: October 2021

Cel pracy

Określenie zbioru objawów, które najczęściej współwystępują ze skargami hipochondrycznymi zgłaszanymi przez pacjentów z zaburzeniami nerwicowymi lub osobowości

Metoda

Przeprowadzono analizy korelacji nieparametrycznych rang Spearmana między zmiennymi kwestionariusza objawowego KO”O” opisującymi symptomy hipochondryczne i pozostałymi objawami zawartymi w kwestionariuszu. W celu zwiększenia rzetelności uzyskanych wyników analizy przeprowadzono niezależnie w dwóch grupach: 3929 pacjentów kwalifikowanych do przyjęcia do oddziału dziennego w latach 1980-2002 (grupa A) i 3190 pacjentów kwalifikowanych w latach 2004-2015 (grupa B).

Wyniki

Dla wyodrębnionych grup pacjentów uzyskano listy współczynników korelacji obrazujące najważniejsze (najsilniejsze) i istotne statystycznie powiązania między pięcioma objawami hipochondrycznymi oraz objawami somatyzacyjnymi ze strony układu mięśniowego, dusznością, objawami ze strony układu krążenia, objawami lękowymi i myślami natrętnymi bez określonej treści

Wnioski

Potwierdzono istnienie wieloaspektowości skarg hipochondrycznych oraz ich powiązań z objawami somatyzacyjnymi o charakterze podobnym do infekcji lub stanu zapalenia. Istotnym objawem wiążącym się z lękiem o własne zdrowie na który warto zwrócić uwagę kliniczną jest również lęk o najbliższych
Dynamic Programming for Response-Adaptive Dose-Finding Clinical Trials
Authors: Nasrollahzadeh Amir Ali , Khademi Amin
Published: October 2021

Identifying the right dose is one of the most important decisions in drug development. Adaptive designs are promoted to conduct dose-finding clinical trials as they are more efficient and ethical compared with static designs. However, current techniques in response-adaptive designs for dose allocation are complex and need significant computational effort, which is a major impediment for implementation in practice. This study proposes a Bayesian nonparametric framework for estimating the dose-response curve, which uses a piecewise linear approximation to the curve by consecutively connecting the expected mean response at each dose. Our extensive numerical results reveal that a first-order Bayesian nonparametric model with a known correlation structure in prior for the expected mean response performs competitively when compared with the standard approach and other more complex models in terms of several relevant metrics and enjoys computational efficiency. Furthermore, structural properties for the optimal learning problem, which seeks to minimize the variance of the target dose, are established under this simple model.

Summary of Contribution: In this work, we propose a methodology to derive efficient patient allocation rules in response-adaptive dose-finding clinical trials, where computational issues are the main concern. We show that our methodologies are competitive with the state-of-the-art methodology in terms of solution quality, are significantly more computationally efficient, and are more robust in terms of the shape of the dose-response curve, among other parameter changes. This research fits in “the intersection of computing and operations research” as it adapts operations research techniques to produce computationally attractive solutions to patient allocation problems in dose-finding clinical trials.
Portfolio Optimization Under Regime Switching and Transaction Costs: Combining Neural Networks and Dynamic Programs
Authors: Li Xiaoyue , Mulvey John M.
Published: October 2021

The contributions of this paper are threefold. First, by combining dynamic programs and neural networks, we provide an efficient numerical method to solve a large multiperiod portfolio allocation problem under regime-switching market and transaction costs. Second, the performance of our combined method is shown to be close to optimal in a stylized case. To our knowledge, this is the first paper to carry out such a comparison. Last, the superiority of the combined method opens up the possibility for more research on financial applications of generic methods, such as neural networks, provided that solutions to simplified subproblems are available via traditional methods.

The research on combining fast starts with neural networks began about four years ago. We observed that Professor Weinan E’s approach for solving systems of differential equations by neural networks had much improved performance when starting close to an optimal solution and could stall if the current iterate was far from an optimal solution. As we all know, this behavior is common with Newton- based algorithms. As a consequence, we discovered that combining a system of differential equations with a feedforward neural network could much improve overall computational performance.

In this paper, we follow a similar direction for dynamic portfolio optimization within a regime-switching market with transaction costs. It investigates how to improve efficiency by combining dynamic programming with a recurrent neural network. Traditional methods face the curse of dimensionality. In contrast, the running time of our combined approach grows approximately linearly with the number of risky assets. It is inspiring to explore the possibilities of combined methods in financial management, believing a careful linkage of existing dynamic optimization algorithms and machine learning will be an active domain going forward.

Relationship of the authors: Professor John M. Mulvey is Xiaoyue Li’s doctoral advisor.
Optimal Portfolio Choice with Estimation Risk: No Risk-Free Asset Case
Authors: Kan Raymond , Wang Xiaolu , Zhou Guofu
Published: October 2021

We propose an optimal combining strategy to mitigate estimation risk for the popular mean-variance portfolio choice problem in the case without a risk-free asset. We find that our strategy performs well in general, and it can be applied to known estimated rules and the resulting new rules outperform the original ones. We further obtain the exact distribution of the out-of-sample returns and explicit expressions of the expected out-of-sample utilities of the combining strategy, providing not only a fast and accurate way of evaluating the performance, but also analytical insights into the portfolio construction.

This paper was accepted by Tyler Shumway, finance.
Technical Note—Capacitated Assortment Optimization: Hardness and Approximation
Authors: Désir Antoine , Goyal Vineet , Zhang Jiawei
Published: October 2021

Assortment optimization is an important problem arising in various applications. In many practical settings, the assortment is subject to a capacity constraint. In “Capacitated Assortment Optimization: Hardness and Approximation,” Désir, Goyal, and Zhang study the capacitated assortment optimization problem. The authors first show that adding a general capacity constraint makes the problem NP-hard even for the simple multinomial logit model. They also show that under the mixture of multinomial logit model, even the unconstrained problem is hard to approximate within any reasonable factor when the number of mixtures is not constant. In view of these hardness results, the authors present near-optimal algorithms for a large class of parametric choice models including the mixture of multinomial logit, Markov chain, nested logit, and d-level nested logit choice models. In fact, their approach extends to a large class of objective functions that depend only on a small number of linear functions.
Social Movements, Collective Identity, and Workplace Allies: The Labeling of Gender Equity Policy Changes
Authors: Wang Cynthia S. , Whitson Jennifer A. , King Brayden G , Ramirez Rachel L.
Published: October 2021

Social movements seek allies as they campaign for social, political, and organizational changes. How do activists gain allies in the targeted institutions they hope to change? Despite recognition of the importance of ally support in theories about institutional change and social movements, these theories are largely silent on the microdynamics of ally mobilization. We examine how the labeling of organizational policies that benefit women influences potential workplace allies’ support for these policies. We theorize that one barrier to mobilizing workplace allies is a misalignment of the labels that activists use to promote new policies and employees’ affiliation with collective identities. We conducted five experiments to test our hypotheses and 26 qualitative interviews to provide illustration of our core concepts. We demonstrate that employees high in feminist identification are more likely to support feminist-labeled (feminist and #MeToo) than unlabeled policies, whereas those low in feminist identification are less likely to support feminist-labeled than unlabeled policies (Studies 1–3). However, we find that participants for whom organizational identification was high (whether measured or manipulated) and feminist identification was low supported organizationally labeled policies more than feminist-labeled polices (Studies 4 and 5). This illustrates that policies whose aims may not align with one collective identity can still garner support by activating another relevant collective identity. Within our studies, we provide evidence that these effects are mediated via feelings of pride in the organization (and not fear or anger), suggesting that positive emotions are a central mechanism in mobilizing workplace allies.

History: This paper has been accepted for the Organization Science Special Issue on Experiments in Organizational Theory.

Supplemental Material: The online appendix is available at https://doi.org/10.1287/orsc.2021.1492 .
ECG of the month
Authors: Regan Martin
Published: October 2021

In this issue's ECG of the month, Martin Regan presents a case of a 71-year-old man with who underwent a 24-hour tape after he presented to his GP with breathlessness and an irregular heart rate.
Global palliative nursing partnerships in the face of COVID-19
Authors: Rosa William E , Downing Julia , Ferrell Betty R , Grant Liz , Matula Samuel T , Pandey Shila , Sey-Sawo Jainaba , Sowe Mansur , Upvall Michele
Published: October 2021

Background:

Mutually respectful and long-term global partnerships are critical to increasing hospice and palliative care access as a key component of universal health coverage. The importance of sustained, transnational palliative care collaboration has become more urgent since the COVID-19 pandemic.

Aim:

To provide an overview of characteristics for successful global palliative nursing partnerships.

Method:

The authors highlight the need to adapt approaches to meet the challenges and demands of COVID-19 in both clinical and academic spaces. Exemplars of thriving global partnerships are provided, alongside palliative nursing considerations and strategies to advance and sustain them.

Conclusion:

The role of nursing to drive and enhance palliative care partnerships, especially with equitable input from low- and middle-income country stakeholders, must be leveraged to advance shared goals and reduce serious health-related suffering around the world.
Iranian nurses' educational needs and competence in palliative cancer care
Authors: Nouhi Esmat , Faramarzpour Vahid , shahrbabaki Parvin Mangolian
Published: October 2021

Aim:

This study was conducted to determine the competence and educational needs of Iranian nurses in the field of palliative cancer care.

Method:

This cross-sectional study was performed on nurses working in oncology departments of hospitals in Kerman, in southeast Iran. The data were collected using nurses' core competence in palliative care inventory and a questionnaire for assessing the educational needs of nurses in the field of palliative cancer care. Pearson correlation coefficient, Independent t-test, ANOVA and Linear regression were used to examine the data.

Results:

210 nurses participated in this study and the response rate was 98.13%. The results showed that the mean score of educational needs in palliative cancer care was 3.6±0.7. The highest average score was observed in the mental and psychological (3.83±0.89) dimensions, and the lowest in the social dimension (3.34±0.84). The mean score of nurses' competence in palliative cancer care was 1.78±0.51. The highest mean score was related to interpersonal skills (2.28±0.74), and the lowest mean score belonged to the use of Edmonton symptoms evaluation (1.10±1.27). There was a low significant and inverse correlation between nurses' competence and their educational needs. (P<0.001, r=- 0.242).

Conclusion:

This study showed that Iranian nurses have the need for palliative cancer care training. Therefore, it is necessary to assign a higher priority to the evaluation of the clinical competence and educational needs of nurses in different healthcare centres.
Luz Marina García Herrera, pionera de la geografía urbana crítica en España
Authors: Díaz-Rodríguez María del Carmen , Armas-Díaz Alejandro , Sabaté-Bel Fernando , Torres-Gutiérrez Francisco José
Published: October 2021

El artículo explora los inicios en España de la geografía urbana crítica y marxista de raíz anglosajona, a partir de las contribuciones pioneras que bajo este enfoque introduce la geógrafa Luz Marina García Herrera (1953-2020). Sus investigaciones sobre periferias urbanas, relaciones de propiedad del suelo y agentes urbanos son hoy un referente obligado en el panorama de la geografía radical española. Este análisis trata de reconstruir un capítulo del pensamiento geográfico, centrando la atención en los trabajos sobre periferias urbanas, objeto destacado de estudio de la geografía urbana crítica, y en las innovadoras aportaciones teóricas y empíricas que sobre tales ámbitos debemos a la profesora García Herrera. Para ello se analizan en profundidad sus dos monografías principales centradas en esta temática; se revisa la producción bibliográfica desde 1970; y se realizan entrevistas a personas del entorno académico y sociopolítico de esta investigadora, prematuramente fallecida, a quien rendimos homenaje desde estas líneas.
Art with Revolution! Political mobilization in artistic practices between 1974 and 1977 in Portugal
Authors: Pratas Cruzeiro Cristina
Published: October 2021

This article analyzes the relationship between Portuguese artists and bodies of power and the popular masses after the Revolution of 25 April 1974 and until 1977.

The analysis of this period in Portugal will consider the dynamics surrounding socially engaged artistic practices integrated in the public space, within its historic and social framework.

The article argues that the Portuguese artistic context under consideration arose from the politicians and artists motivation to bring art and the popular masses closer to the ongoing revolutionary process. In this approach, I identify collaboration as the most frequent attitude used by artists in relation to the political system and population. This approach decreased since 1976, at which time there was an increase in conflict with the political power structures. Regarding the relationship with the population, from that moment on there was also a decrease in the use of collaborative tools and an intensification of transgressive and provocative tools in artisticpractices.

These changes will be articulated in the article based on the country’s objective political and social conditions, and their influence on attitudinal nuances identified in the socially engaged artistic practices under analysis.
Nested nonconcentric microring resonators with high-Q and large fabrication tolerance
Authors: Haldar Raktim , Ummethala Sandeep , Sinha Rajat K. , Varshney Shailendra K.
Published: October 2021

Microring resonators are one of the most sought-after optical components for realizing several on-chip functionalities that include sensing, data routing, new frequency generation, and quantum photonic applications. Many of these applications demand a high quality factor and large notch depth (high extinction ratio), which can be achieved by critical coupling. However, the critical coupling is very sensitive to fabrication accuracies and thermal drift. Geometrical parameters of the resonators are generally swept to attain critical coupling, where a few designs can pass the critical coupling condition criteria. In this work, we propose a methodology to circumvent this vital issue. The proposed technique is based on coupled-resonator systems where two different microrings are embedded into a larger microring, referred to as a nonconcentric nested microring resonator (NN-MRR). The NN-MRR configuration relaxes the requirement of the critical coupling condition by 20% when the strip optical waveguide has either smooth or rough sidewalls. Numerical simulations reveal that, unlike standard MRR, a high

Q

-factor (

>

1

0

5

) and a large transmission notch depth

>

10

d
B

can be maintained irrespective of the rings’ coupling conditions for the nested MRRs. Besides the extra degree of freedom of design provided by the inner rings, the other significant advantage of the proposed NN-MRR is its compactness. We believe that the nested MRR arrangement could be highly efficient for biosensing, nonlinear, and quantum applications within a broad ambient temperature range. We have fabricated the NN-MRRs in a silicon-on-insulator platform through electron beam lithography and experimentally demonstrated the theoretical and numerical findings.
Bidirectional coupling of diamond emitters to optical nanowire: tunable and efficient
Authors: Murmu Satyajit , Kumar Avijit , Jha Rajan
Published: October 2021

Negatively charged nitrogen vacancy (

N
V

−

) centers in diamond are required to be coupled to optical systems for various applications. A slowly varied tapered waveguide displays a near-unity power transfer from an optical fiber to on-chip photonic devices. This physical situation refers to an adiabatic transition of photons from a highly effective confinement mode to a lower effective confinement mode or vice versa. Here, we report tunable bidirectional coupling with enhanced efficiency in a hybrid structure of elliptically faceted (ELFA) diamond nanowire with

N
V

−

centers integrated to optical nanowire. Initiating from diabatic transition to adiabatic transition, corresponding to smaller length to longer wire length, respectively, the coupling efficiency oscillates and asymptotically saturates to a maximum value. Our calculations indicate coupling efficiencies of 85% and 84% for azimuthal and radial dipole configurations for the hybrid structure, respectively. The structure with optimum geometry provides similar coupling efficiency of

∼

81

%

for radial and azimuthal dipole configurations. By excitation of one of few dipoles placed strategically at various locations in the cylindrical region of the diamond nanowire will allow one to tune coupling efficiency in the two directions. Tailored size and tunable bidirectional coupling of ELFA diamond nanowire with enhanced efficiency will enable its wide-field applications including multi-scale quantum photonics devices.
Rapid prototyping of grating magneto-optical traps using a focused ion beam
Authors: Sun Xiao , Rickard William D. A. , Sparkes Ben M. , White Ben R. , Offer Rachel F. , Luiten Andre N. , Ironside Charlie N.
Published: October 2021

We have developed a rapid prototyping approach for creating custom grating magneto-optical traps using a dual-beam system combining a focused ion beam and a scanning electron microscope. With this approach we have created both one- and two-dimensional gratings of up to 400 µm × 400 µm in size with structure features down to 100 nm, periods of 620 nm, adjustable aspect ratios (ridge width : depth ∼ 1 : 0.3 to 1 : 1.4) and sidewall angles up to 71°. The depth and period of these gratings make them suitable for holographic trapping and cooling of neutral ytterbium on the 1S0 → 1P1 399 nm transition. Optical testing of the gratings at this wavelength has demonstrated a total first order diffraction of 90% of the reflected light. This work therefore represents a fast, high resolution, programmable and maskless alternative to current photo and electron beam lithography-based procedures and provides a time efficient process for prototyping of small period, high aspect ratio grating magneto-optical traps and other high resolution structures.
Circular nanocavity substrate-assisted plasmonic tip for its enhancement in nanofocusing and optical trapping
Authors: Lu Fanfan , Zhang Wending , Sun Lixun , Mei Ting , Yuan Xiaocong
Published: October 2021

Plasmonic tip nanofocusing has widely been applied in tip-enhanced Raman spectroscopy, optical trapping, nonlinear optics, and super-resolution imaging due to its capability of high local field enhancement. In this work, a substrate with a circular nanocavity is proposed to enhance the nanofocusing and optical trapping characteristics of the plasmonic tip. Under axial illumination of a tightly focused radial polarized beam, the circular nanohole etched on a metallic substrate can form a nanocavity to induce an interference effect and further enhance the electric field intensity. When a plasmonic tip is placed closely above such a substrate, the electric field intensity of the gap-plasmon mode can further be improved, which is 10 folds stronger than that of the conventional gap-plasmon mode. Further analysis reveals that the enhanced gap-plasmon mode can significantly strengthen the optical force exerted on a nanoparticle and stably trap a 4-nm-diameter dielectric nanoparticle. Our proposed method can improve the performance of tip-enhanced spectroscopy, plasmonic tweezers and extend their applications. We anticipate that our methods allow simultaneously manipulating and characterizing single nanoparticles in-situ.
Attosecond-precision balanced linear-optics timing detector
Authors: Wang Tong , Ren Qun , Şafak Kemal , Kärtner Franz X. , Xin Ming
Published: October 2021

A new timing detection method based on acousto-optic modulation is demonstrated. The timing detector is immune to dispersion effects and the environmental and laser amplitude noise can be well suppressed by a balanced configuration. With 1 mW power per pulse train, the measured timing noise floor is about 1×10−10 fs2/Hz, which is close to the shot noise limit. The integrated timing jitter is 26 as at [1 Hz, 1 MHz]. With 170 fs pulse width and typical detector parameters, the calculated detector’s timing noise floor is more than 5 and 12 orders of magnitude lower than that of a BOC, at 1 mW and 1 µW input power, respectively. This timing detector has a variety of potential applications in ultra-long fiber link stabilization, quantum metrology, weak signal timing control, etc.
Polarization-independent all-dielectric guided-mode resonance filter according to binary grating and slab waveguide dimensions
Authors: Bark Hyeon Sang , Baek In Hyung , Kim Gyeong-Ryul , Jeong Young Uk , Jang Kyu-Ha , Lee Kitae , Jeon Tae-In
Published: October 2021

All-dielectric binary gratings, with and without slab waveguides, are designed to generate polarization-independent guided-mode resonance filters (GMRFs) operating in the THz frequency region using the rigorous coupled-wave analysis (RCWA) method. The filling factor and thickness of the grating were adjusted to have equal resonance frequencies of transverse electric (TE)- and transverse magnetic (TM)-polarized THz beams. The single polarization-independent resonance for a binary grating without a slab waveguide was obtained at 0.459 THz with full width at half maximum (FWHM) values of 8.3 and 8.5 GHz for the TE and TM modes, respectively. Moreover, double-layered polarization-independent resonances for binary gratings with slab waveguides were obtained at 0.369 and 0.442 THz with very high Q-factors of up to 284. This is the first study to propose a polarization-independent GMRF with two resonant frequencies.
Computational polarized Raman microscopy on sub-surface nanostructures with sub-diffraction-limit resolution
Authors: Li Zheng , Persits Nili , Gray Dodd J. , Ram Rajeev J.
Published: October 2021

Raman microscopy with resolution below the diffraction limit is demonstrated on sub-surface nanostructures. Unlike most other modalities for nanoscale measurements, our approach is able to image nanostructures buried several microns below the sample surface while still extracting details about the chemistry, strain, and temperature of the nanostructures. In this work, we demonstrate that combining polarized Raman microscopy adjusted to optimize edge enhancement effects and nanostructure contrast with fast computational deconvolution methods can improve the spatial resolution while preserving the flexibility of Raman microscopy. The cosine transform method demonstrated here enables significant computational speed-up from O(N3) to O(Nlog N) - resulting in computation times that are significantly below the image acquisition time. CMOS poly-Si nanostructures buried below 0.3 − 6 µm of complex dielectrics are used to quantify the performance of the instrument and the algorithm. The relative errors of the feature sizes, the relative chemical concentrations and the fill factors of the deconvoluted images are all approximately 10% compared with the ground truth. For the smallest poly-Si feature of 230 nm, the absolute error is approximately 25 nm.
Spatiotemporal couplings through a nonlinear phase in broadband optical parametric amplification
Authors: Wang Yirui , Wang Jing , Zhou Bingjie , Ma Jingui , Yuan Peng , Qian Liejia
Published: October 2021

Optical parametric chirped-pulse amplification (OPCPA) is prone to undesired spatiotemporal couplings. This Letter studies a family of OPCPA couplings resulting from the nonlinear phase shift induced by frequency-dependent phase mismatch. These OPCPA couplings manifest as pulse-front deformation, transversely varying pulse duration, and spectrally varying wavefront curvature, which are directly linked with the phase–mismatch dispersion terms. The numerical study in this Letter also reveals that the focused signal intensity severely degrades with increasing signal bandwidth and pump depletion.
Transmission of a 56  Gbit/s PAM4 signal with low-resolution DAC and pre-equalization only over 80  km fiber in C-band IM/DD systems for optical interconnects
Authors: Yin Mingzhu , Zou Dongdong , Wang Wei , Li Fan , Li Zhaohui
Published: October 2021

A low-cost intensity modulation and direct detection scheme using a 4-bit digital-to-analog converter for 56 Gbit/s pre-equalized PAM-4 generation at the transmitter and without receiver side post-equalization over 80 km single-mode fiber transmission in a C-band is experimentally demonstrated in this Letter. Pre-equalization includes pre-emphasis for channel response, a modified Gerchberg–Saxton algorithm with five iterations for chromatic dispersion compensation, and a noise shaping technique implemented by a five-tap finite impulse response filter for quantization noise suppression. Enabled by the pre-equalization techniques, the bit error rate of the received signal without post-equalization can reach the hard-decision forward error correction threshold with

−

2

d
B
m

receiver optical power. The experimental results indicate that our proposed scheme is a promising candidate for the standardization of 400 GbE wavelength division multiplexing-based long-haul distance data center interconnects.
Conjugate wavefront encoding: an efficient eyebox extension approach for holographic Maxwellian near-eye display
Authors: Wang Zi , Zhang Xu , Lv Guoqiang , Feng Qibin , Wang Anting , Ming Hai
Published: October 2021

Conventional holographic display suffers from the conjugate light issue. In this Letter, we propose to efficiently extend the eyebox of holographic Maxwellian near-eye display by encoding the conjugate wavefront as the multiplication of plane wave phase with the target image. It is interesting that after being focused by the lens, the generated conjugate viewpoints also present erect virtual images with the same image quality as the signal viewpoints. Multiple plane wave encoding is used for eyebox extension, and, because of the utilization of conjugate light, the effect of eyebox extension is doubled. That is, the space bandwidth of the amplitude-type hologram is fully used. A speckless holographic image is produced in mid-air with high quality within a large depth range. The proposed display is compact and promising for the augmented reality near-eye display. Furthermore, it may inspire better solutions for the conjugate light issue of amplitude-type holography.
Wide spectral range optical characterization of yttrium aluminum garnet (YAG) single crystal by the universal dispersion model
Authors: Franta Daniel , Mureșan Mihai-George
Published: October 2021

Pure YAG single crystal was optically characterized in the wide spectral range (from far IR to vacuum UV) by applying the universal dispersion model. Data obtained from a broad range of characterization instruments and methods was simultaneously processed using least-square method and the result were compared with literature findings. The universal dispersion model describes individual elementary electron and phonon excitations in materials as separate contributions. For the first time recorded, an asymmetric Voigt peak approximation was used for modeling the contribution of one-phonon absorption in crystalline material. The optical constants are presented both graphically and in detailed dispersion parameters sets.
RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family
Authors: Kourelis Jiorgos , Sakai Toshiyuki , Adachi Hiroaki , Kamoun Sophien
Published: October 2021

Reference datasets are critical in computational biology. They help define canonical biological features and are essential for benchmarking studies. Here, we describe a comprehensive reference dataset of experimentally validated plant nucleotide-binding leucine-rich repeat (NLR) immune receptors. RefPlantNLR consists of 481 NLRs from 31 genera belonging to 11 orders of flowering plants. This reference dataset has several applications. We used RefPlantNLR to determine the canonical features of functionally validated plant NLRs and to benchmark 5 NLR annotation tools. This revealed that although NLR annotation tools tend to retrieve the majority of NLRs, they frequently produce domain architectures that are inconsistent with the RefPlantNLR annotation. Guided by this analysis, we developed a new pipeline, NLRtracker, which extracts and annotates NLRs from protein or transcript files based on the core features found in the RefPlantNLR dataset. The RefPlantNLR dataset should also prove useful for guiding comparative analyses of NLRs across the wide spectrum of plant diversity and identifying understudied taxa. We hope that the RefPlantNLR resource will contribute to moving the field beyond a uniform view of NLR structure and function.
Pinging the brain with visual impulses reveals electrically active, not activity-silent, working memories
Authors: Barbosa Joao , Lozano-Soldevilla Diego , Compte Albert
Published: October 2021

Persistently active neurons during mnemonic periods have been regarded as the mechanism underlying working memory maintenance. Alternatively, neuronal networks could instead store memories in fast synaptic changes, thus avoiding the biological cost of maintaining an active code through persistent neuronal firing. Such “activity-silent” codes have been proposed for specific conditions in which memories are maintained in a nonprioritized state, as for unattended but still relevant short-term memories. A hallmark of this “activity-silent” code is that these memories can be reactivated from silent, synaptic traces. Evidence for “activity-silent” working memory storage has come from human electroencephalography (EEG), in particular from the emergence of decodability (EEG reactivations) induced by visual impulses (termed pinging) during otherwise “silent” periods. Here, we reanalyze EEG data from such pinging studies. We find that the originally reported absence of memory decoding reflects weak statistical power, as decoding is possible based on more powered analyses or reanalysis using alpha power instead of raw voltage. This reveals that visual pinging EEG “reactivations” occur in the presence of an electrically active, not silent, code for unattended memories in these data. This crucial change in the evidence provided by this dataset prompts a reinterpretation of the mechanisms of EEG reactivations. We provide 2 possible explanations backed by computational models, and we discuss the relationship with TMS-induced EEG reactivations.
Understanding degraded speech leads to perceptual gating of a brainstem reflex in human listeners
Authors: Hernández-Pérez Heivet , Mikiel-Hunter Jason , McAlpine David , Dhar Sumitrajit , Boothalingam Sriram , Monaghan Jessica J. M. , McMahon Catherine M.
Published: October 2021

The ability to navigate “cocktail party” situations by focusing on sounds of interest over irrelevant, background sounds is often considered in terms of cortical mechanisms. However, subcortical circuits such as the pathway underlying the medial olivocochlear (MOC) reflex modulate the activity of the inner ear itself, supporting the extraction of salient features from auditory scene prior to any cortical processing. To understand the contribution of auditory subcortical nuclei and the cochlea in complex listening tasks, we made physiological recordings along the auditory pathway while listeners engaged in detecting non(sense) words in lists of words. Both naturally spoken and intrinsically noisy, vocoded speech—filtering that mimics processing by a cochlear implant (CI)—significantly activated the MOC reflex, but this was not the case for speech in background noise, which more engaged midbrain and cortical resources. A model of the initial stages of auditory processing reproduced specific effects of each form of speech degradation, providing a rationale for goal-directed gating of the MOC reflex based on enhancing the representation of the energy envelope of the acoustic waveform. Our data reveal the coexistence of 2 strategies in the auditory system that may facilitate speech understanding in situations where the signal is either intrinsically degraded or masked by extrinsic acoustic energy. Whereas intrinsically degraded streams recruit the MOC reflex to improve representation of speech cues peripherally, extrinsically masked streams rely more on higher auditory centres to denoise signals.
How conformity can lead to polarised social behaviour
Authors: Panizza Folco , Vostroknutov Alexander , Coricelli Giorgio
Published: October 2021

Learning social behaviour of others strongly influences one’s own social attitudes. We compare several distinct explanations of this phenomenon, testing their predictions using computational modelling across four experimental conditions. In the experiment, participants chose repeatedly whether to pay for increasing (prosocial) or decreasing (antisocial) the earnings of an unknown other. Halfway through the task, participants predicted the choices of an extremely prosocial or antisocial agent (either a computer, a single participant, or a group of participants). Our analyses indicate that participants polarise their social attitude mainly due to normative expectations. Specifically, most participants conform to presumed demands by the authority (vertical influence), or because they learn that the observed human agents follow the norm very closely (horizontal influence).
Estimating ectopic beat probability with simplified statistical models that account for experimental uncertainty
Authors: Jin Qingchu , Greenstein Joseph L. , Winslow Raimond L.
Published: October 2021

Ectopic beats (EBs) are cellular arrhythmias that can trigger lethal arrhythmias. Simulations using biophysically-detailed cardiac myocyte models can reveal how model parameters influence the probability of these cellular arrhythmias, however such analyses can pose a huge computational burden. Here, we develop a simplified approach in which logistic regression models (LRMs) are used to define a mapping between the parameters of complex cell models and the probability of EBs (P(EB)). As an example, in this study, we build an LRM for P(EB) as a function of the initial value of diastolic cytosolic Ca2+ concentration ([Ca2+]iini), the initial state of sarcoplasmic reticulum (SR) Ca2+ load ([Ca2+]SRini), and kinetic parameters of the inward rectifier K+ current (IK1) and ryanodine receptor (RyR). This approach, which we refer to as arrhythmia sensitivity analysis, allows for evaluation of the relationship between these arrhythmic event probabilities and their associated parameters. This LRM is also used to demonstrate how uncertainties in experimentally measured values determine the uncertainty in P(EB). In a study of the role of [Ca2+]SRini uncertainty, we show a special property of the uncertainty in P(EB), where with increasing [Ca2+]SRini uncertainty, P(EB) uncertainty first increases and then decreases. Lastly, we demonstrate that IK1 suppression, at the level that occurs in heart failure myocytes, increases P(EB).
Translational repression of NMD targets by GIGYF2 and EIF4E2
Authors: Zinshteyn Boris , Sinha Niladri K. , Enam Syed Usman , Koleske Benjamin , Green Rachel
Published: October 2021

Translation of messenger RNAs (mRNAs) with premature termination codons produces truncated proteins with potentially deleterious effects. This is prevented by nonsense-mediated mRNA decay (NMD) of these mRNAs. NMD is triggered by ribosomes terminating upstream of a splice site marked by an exon-junction complex (EJC), but also acts on many mRNAs lacking a splice junction after their termination codon. We developed a genome-wide CRISPR flow cytometry screen to identify regulators of mRNAs with premature termination codons in K562 cells. This screen recovered essentially all core NMD factors and suggested a role for EJC factors in degradation of PTCs without downstream splicing. Among the strongest hits were the translational repressors GIGYF2 and EIF4E2. GIGYF2 and EIF4E2 mediate translational repression but not mRNA decay of a subset of NMD targets and interact with NMD factors genetically and physically. Our results suggest a model wherein recognition of a stop codon as premature can lead to its translational repression through GIGYF2 and EIF4E2.
AKAP13 couples GPCR signaling to mTORC1 inhibition
Authors: Zhang Shihai , Wang Huanyu , Melick Chase H. , Jeong Mi-Hyeon , Curukovic Adna , Tiwary Shweta , Lama-Sherpa Tshering D. , Meng Delong , Servage Kelly A. , James Nicholas G. , Jewell Jenna L.
Published: October 2021

The mammalian target of rapamycin complex 1 (mTORC1) senses multiple stimuli to regulate anabolic and catabolic processes. mTORC1 is typically hyperactivated in multiple human diseases such as cancer and type 2 diabetes. Extensive research has focused on signaling pathways that can activate mTORC1 such as growth factors and amino acids. However, less is known about signaling cues that can directly inhibit mTORC1 activity. Here, we identify A-kinase anchoring protein 13 (AKAP13) as an mTORC1 binding protein, and a crucial regulator of mTORC1 inhibition by G-protein coupled receptor (GPCR) signaling. GPCRs paired to Gαs proteins increase cyclic adenosine 3’5’ monophosphate (cAMP) to activate protein kinase A (PKA). Mechanistically, AKAP13 acts as a scaffold for PKA and mTORC1, where PKA inhibits mTORC1 through the phosphorylation of Raptor on Ser 791. Importantly, AKAP13 mediates mTORC1-induced cell proliferation, cell size, and colony formation. AKAP13 expression correlates with mTORC1 activation and overall lung adenocarcinoma patient survival, as well as lung cancer tumor growth in vivo. Our study identifies AKAP13 as an important player in mTORC1 inhibition by GPCRs, and targeting this pathway may be beneficial for human diseases with hyperactivated mTORC1.
Recommended reporting items for epidemic forecasting and prediction research: The EPIFORGE 2020 guidelines
Authors: Pollett Simon , Johansson Michael A. , Reich Nicholas G. , Brett-Major David , Del Valle Sara Y. , Venkatramanan Srinivasan , Lowe Rachel , Porco Travis , Berry Irina Maljkovic , Deshpande Alina , Kraemer Moritz U. G. , Blazes David L. , Pan-ngum Wirichada , Vespigiani Alessandro , Mate Suzanne E. , Silal Sheetal P. , Kandula Sasikiran , Sippy Rachel , Quandelacy Talia M. , Morgan Jeffrey J. , Ball Jacob , Morton Lindsay C. , Althouse Benjamin M. , Pavlin Julie , van Panhuis Wilbert , Riley Steven , Biggerstaff Matthew , Viboud Cecile , Brady Oliver , Rivers Caitlin
Published: October 2021

Background

The importance of infectious disease epidemic forecasting and prediction research is underscored by decades of communicable disease outbreaks, including COVID-19. Unlike other fields of medical research, such as clinical trials and systematic reviews, no reporting guidelines exist for reporting epidemic forecasting and prediction research despite their utility. We therefore developed the EPIFORGE checklist, a guideline for standardized reporting of epidemic forecasting research.

Methods and findings

We developed this checklist using a best-practice process for development of reporting guidelines, involving a Delphi process and broad consultation with an international panel of infectious disease modelers and model end users. The objectives of these guidelines are to improve the consistency, reproducibility, comparability, and quality of epidemic forecasting reporting. The guidelines are not designed to advise scientists on how to perform epidemic forecasting and prediction research, but rather to serve as a standard for reporting critical methodological details of such studies.

Conclusions

These guidelines have been submitted to the EQUATOR network, in addition to hosting by other dedicated webpages to facilitate feedback and journal endorsement.
Land use and land cover change and its impacts on dengue dynamics in China: A systematic review
Authors: Gao Panjun , Pilot Eva , Rehbock Cassandra , Gontariuk Marie , Doreleijers Simone , Wang Li , Krafft Thomas , Martens Pim , Liu Qiyong
Published: October 2021

Background

Dengue is a prioritized public health concern in China. Because of the larger scale, more frequent and wider spatial distribution, the challenge for dengue prevention and control has increased in recent years. While land use and land cover (LULC) change was suggested to be associated with dengue, relevant research has been quite limited. The “Open Door” policy introduced in 1978 led to significant LULC change in China. This systematic review is the first to review the studies on the impacts of LULC change on dengue dynamics in China. This review aims at identifying the research evidence, research gaps and provide insights for future research.

Methods

A systematic literature review was conducted following the PRISMA protocol. The combinations of search terms on LULC, dengue and its vectors were searched in the databases PubMed, Web of Science, and Baidu Scholar. Research conducted on China published from 1978 to December 2019 and written in English or Chinese was selected for further screening. References listed in articles meeting the inclusion criteria were also reviewed and included if again inclusion criteria were met to minimize the probability of missing relevant research.

Results

28 studies published between 1978 and 2017 were included for the full review. Guangdong Province and southern Taiwan were the major regional foci in the literature. The majority of the reviewed studies observed associations between LULC change factors and dengue incidence and distribution. Conflictive evidence was shown in the studies about the impacts of green space and blue space on dengue in China. Transportation infrastructure and urbanization were repeatedly suggested to be positively associated with dengue incidence and spread. The majority of the studies reviewed considered meteorological and sociodemographic factors when they analyzed the effects of LULC change on dengue. Primary and secondary remote sensing (RS) data were the primary source for LULC variables. In 21 of 28 studies, a geographic information system (GIS) was used to process data of environmental variables and dengue cases and to perform spatial analysis of dengue.

Conclusions

The effects of LULC change on the dynamics of dengue in China varied in different periods and regions. The application of RS and GIS enriches the means and dimensions to explore the relations between LULC change and dengue. Further comprehensive regional research is necessary to assess the influence of LULC change on local dengue transmission to provide practical advice for dengue prevention and control.
Different individual-level responses of great black-backed gulls (Larus marinus) to shifting local prey availability
Authors: Maynard Laurie D. , Gulka Julia , Jenkins Edward , Davoren Gail K.
Published: October 2021

To grow, survive and reproduce under anthropogenic-induced changes, individuals must respond quickly and favourably to the surrounding environment. A species that feeds on a wide variety of prey types (i.e. generalist diet) may be comprised of generalist individuals, specialist individuals that feed on different prey types, or a combination of the two. If individuals within a population respond differently to an environmental change, population-level responses may not be detectable. By tracking foraging movements of great black-backed gulls (Larus marinus), a generalist species, we compared group-level and individual-level responses to an increase in prey biomass (capelin; Mallotus villosus) during the breeding season in coastal Newfoundland, Canada. As hypothesized, shifts in prey availability resulted in significantly different individual responses in foraging behaviour and space use, which was not detectable when data from individuals were combined. Some individuals maintained similar foraging areas, foraging trip characteristics (e.g., trip length, duration) and habitat use with increased capelin availability, while others shifted foraging areas and habitats resulting in either increased or decreased trip characteristics. We show that individual specialization can be non-contextual in some gulls, whereby these individuals continuously use the same feeding strategy despite significant change in prey availability conditions. Findings also indicate high response diversity among individuals to shifting prey conditions that a population- or group-level study would not have detected, emphasizing the importance of examining individual-level strategies for future diet and foraging studies on generalist species.
A new inertial navigation system for guiding implant placement. An in-vitro proof-of-concept study
Authors: Esteve-Pardo G. , Esteve-Colomina L. , Fernández E.
Published: October 2021

The aim of this study was to assess the potential use of a new advanced inertial navigation system for guiding dental implant placement and to compare this approach with standard stereolithographic template guiding. A movement processing unit with a 9-axis absolute orientation sensor was adapted to a surgical handpiece and wired to a computer navigation interface. Sixty implants were placed by 10 operators in 20 jaw models. The 30 implants of the test group were placed in 10 models guided by the new inertial navigation prototype. The 30 implants of the control group were placed in another 10 models using a CAD-CAM template. Both groups were subdivided into experienced and non-experienced operators. Pre- and postoperative computer tomography images were obtained and matched to compare the planned and final implant positions. Four deviation parameters (global, angular, depth, and lateral deviation) were defined and calculated. The primary outcome was the angular deviation between the standard stereolithographic approach and the new inertial navigation system. Results showed no significant differences between both groups, suggesting that surgical navigation based on inertial measurement units (IMUs) could potentially be useful for guiding dental implant placement. However, more studies are still needed to translate this new approach into clinical practice.