bluuebunny/crossref_metadata_2025 huggingface dataset:
(Semi)automated approaches to data extraction for systematic reviews and meta-analyses in social sciences: A living review protocol
Authors: Legate Amanda , Nimon Kim
Published: September 2022

Background: An abundance of rapidly accumulating scientific evidence presents novel opportunities for researchers and practitioners alike, yet such advantages are often overshadowed by resource demands associated with finding and aggregating a continually expanding body of scientific information. Across social science disciplines, the use of automation technologies for timely and accurate knowledge synthesis can enhance research translation value, better inform key policy development, and expand the current understanding of human interactions, organizations, and systems. Ongoing developments surrounding automation are highly concentrated in research for evidence-based medicine with limited evidence surrounding tools and techniques applied outside of the clinical research community. Our objective is to conduct a living systematic review of automated data extraction techniques supporting systematic reviews and meta-analyses in the social sciences. The aim of this study is to extend the automation knowledge base by synthesizing current trends in the application of extraction technologies of key data elements of interest for social scientists.

Methods: The proposed study is a living systematic review employing a partial replication framework based on extant literature surrounding automation of data extraction for systematic reviews and meta-analyses. Protocol development, base review, and updates follow PRISMA standards for reporting systematic reviews. This protocol is preregistered in OSF: (Semi)Automated Approaches to Data Extraction for Systematic Reviews and Meta-Analyses in Social Sciences: A Living Review Protocol on August 14, 2022.

Conclusions: Anticipated outcomes of this study include: (a) generate insights supporting advancement in transferring existing reliable methods to social science research; (b) provide a foundation for protocol development leading to enhancement of comparability and benchmarking standards across disciplines; and (c) uncover exigencies that spur continued value-adding innovation and interdisciplinary collaboration for the benefit of the collective systematic review community.
Job characteristics of a Malaysian bank’s anti-money laundering system and its employees’ job satisfaction
Authors: Kannan Rathimala , Reddiar Yonesh , Ramakrishnan Kannan , Eastaff Marrynal S , Ramesh Shobana
Published: September 2022

Background: Banks and financial institutions are vulnerable to money laundering (ML) as a result of crime proceeds infiltrating banks in the form of significant cash deposits. Improved financial crime compliance processes and systems enable anti-ML (AML) analysts to devote considerable time and effort to case investigation and process quality work, thereby lowering financial risks by reporting suspicious activity in a timely and effective manner. This study uses Job Characteristics Theory (JCT) to evaluate the AML system through the job satisfaction and motivation of its users. The purpose of this study is to determine how satisfied AML personnel are with their jobs and how motivated they are to work with the system.

Methods: This cross-sectional study used JCT to investigate the important elements impacting employee satisfaction with the AML system. The five core dimensions of the job characteristics were measured using a job diagnostic survey. The respondents were employees working in the AML department of a Malaysian bank, and the sample group was chosen using a purposive sampling approach. A total of 100 acceptable replies were gathered and analysed using various statistical approaches. A motivating potential score was generated for each employee based on five main job characteristics.

Results: Findings revealed that five core job characteristics, namely, skill diversity, task identity, task importance, autonomy and feedback, positively influence the AML system employees’ job satisfaction. However, skill variety and autonomy are found to be low, which are reflected in the poor motivating potential score.

Conclusion: This study examined the characteristics of the AML system and its users’ job satisfaction. Findings revealed that task significance is the most widely recognised characteristic, followed by feedback and task identity. However, there is a lack of skill variety and autonomy, which must be addressed to improve employee satisfaction with the AML system.
Risk of lowering mortality from the improvement of inflammatory markers and disease progression among moderate, severe, and critical COVID-19 patients using anticoagulant : a cross-sectional study from two second referral hospitals in Surabaya, Indonesia
Authors: Romadhon Pradana Zaky , Bintoro Siprianus Ugroseno Yudho , Suryantoro Satriyo Dwi , Asmarawati Tri Pudy , Nur Rosyid Alfian , Savitri Merlyna , Amrita Putu Niken Ayu , Diansyah Muhammad Noor , Prayoga Ami Ashariati , Windradi Choirina , Mahdi Bagus Aulia , Widiyastuti Krisnina Nurul , Novendrianto Dwiki , Agustin Esthiningrum Dewi , Alkaff Firas Farisi , Prahasanti Kartika , Dewanto Didi Darmahadi
Published: September 2022

Background: To date, coronavirus diseases 2019 (COVID-19) has no definitive treatment. Thrombosis and hypercoagulation may occur in the advanced stage. Further study on how to use anticoagulants is still required to promote the best prognosis.

Methods: A cross-sectional study of 110 moderate, 140 severe, and 81 critical patients receiving unfractioned heparin (UFH), low-molecular-weight heparin (LMWH), and fondaparinux was conducted. Data were collected from March 15th to August 31st 2020 at Universitas Airlangga and Husada Utama Hospital. A comparative study of white blood cell (WBC), neutrophils, lymphocytes, neutrophil-lymphocyte ratio (NLR), c-reactive protein (CRP), procalcitonin (PCT), D-dimer, all-cause mortality rate, length of stay, and days of death among three severities of COVID-19 was done. Univariate and multivariate analysis were used to determine the correlation between inflammatory state after anti-coagulant with patients’ mortality.

Results: Two deaths occurred in moderate cases, 36 deaths in severe cases, and 70 deaths in critical cases on ventilators. On day 13, moderate and severe groups showed decreased WBC, neutrophils, NLR, CRP, and D-dimer (p < 0.05). NLR, CRP, and D-dimer (p<0.05) in critically ill and ventilated patients decreased. Day-13 evaluation revealed 32.73% decrease of inflammatory markers in moderate group; 32.86% in severe patients; and 16.05% in critically ill, ventilated patients. A significant correlation between day 13 inflammatory status with mortality was seen in moderate and critical cases with a ventilator (r=0.337; p< 0.05 and r=0.25; p 0.05). Inflammatory profile on day 6 (adjusted odds ratio [aOR] = 2.36; p < 0.05) and day 13 ([aOR] = 4.15; p < 0.05) was associated with patients’ mortality.

Conclusions: Anticoagulants in COVID-19 patients lower inflammation markers. Evaluating inflammatory status is essential to predict the mortality. Inflammatory markers on day 13, based on the severity of COVID-19 and comorbidities, were associated with mortality in moderate and critical cases.
Concept maps as a novel assessment tool in medical education
Authors: LOIZOU STELLA , Nicolaou Nicoletta , Pincus Bridget Anne , Papageorgiou Alexia , McCrorie Peter
Published: September 2022

Background: Concept Maps (CMs) have been used in a Problem-Based Learning (PBL) setting as  complementary tools to current educational techniques for enhancing medical student knowledge and critical thinking. We conducted a pilot study that used CMs in a PBL-setting to introduce a measure from the field of graph theory and investigate its usefulness as a means of CM quantitative quality assessment.

Methods: Participants were first-year medical students with no or minor prior CM experience. All participants completed questionnaires (demographic information and assessment of learning style) to establish a baseline measure against which the change in clinical and critical thinking was assessed. They were asked to prepare CMs for three PBL cases, and following the submission of the CMs they completed semi-structured critical and clinical thinking questionnaires. A clinical expert also created corresponding “benchmark” CMs for comparison. Qualitative (Wordclouds) and quantitative (graph theory) analysis provided a summary of the key concepts and quantified the CM quality respectively, compared to the “benchmark” CMs.

Results: It was  found that graph-theoretical measures (graph density, modularity) were suitable for distinguishing between CMs that captured more in-depth knowledge, compared to CMs that contained simpler associations. Questionnaires also revealed that CMs helped students recall information, organize material in a concise manner, prepare better for their PBL session and provided a good revision tool.

Conclusions: We have shown that a graph-theoretical approach to quantitative CM assessment is feasible using measures such as graph density and modularity.
The housing environment of participants in the Avon Longitudinal Study of Parents and Children (ALSPAC): a resource for studies of influences on health
Authors: Ellis Genette , Iles-Caven Yasmin , Northstone Kate , Golding Jean
Published: September 2022

Background: Early life environmental health exposures related to housing can have a significant impact on an individual’s physical and mental health and physical development. Housing exposures can fall into two main areas – a representation of social circumstances and physical conditions.  

Methods: During pregnancy and post-delivery, self-completion questionnaires concerning the housing environment were administered until the study offspring were aged 18 to the ALSPAC (Avon Longitudinal Study of Parents & Children) study mothers and their partners. Data collected included types of housing, housing tenure, numbers of rooms in the home, whether shared or sole use of kitchen and indoor flushing toilet, household moves, Council Tax band, difficulties in affording rent/mortgage and becoming homeless. Here we also describe the historic development of housing in the Bristol and surrounding Avon areas.  

Results: Data collected included the tenure (e.g., owned/rented) of the home, its size (indexed by the number of rooms), the presence of over-crowding (measured by the number of residents per room), presence of amenities, and frequency of household moves. This information was collected on over 13,000 women during pregnancy >8000 at age 10 and >4000 at 18 years. Council Tax bands were asked at 10 and 18 years.  

Conclusions: This is the first of two Data Notes on the housing type and housing circumstances of the families enrolled in ALSPAC. A second Data Note will detail their internal housing conditions. The data provides an excellent resource for researchers when considering the influences of housing on physical and mental health and development.
Evaluation of competitiveness power of fishing and aquaculture industry in Turkey
Authors: Yıldırım Çağatay , Türkten Hatice , Ceyhan Vedat
Published: September 2022

There has been a significant lack of data on product and input markets, aquaculture consumption characteristics, production, distribution and marketing issues, and supply and value chain in Turkish fishing and aquaculture sectors. Therefore, the study examined the competitiveness of the Turkish aquaculture industry. Time series data belonging the time period of 1976-2020 gathered from Food and Agriculture Organization (FAO), World Trade Organization and Turkish Statistical Institute (TURKSTAT) were used in the study. In the research, the competitiveness of the Turkish fishing and aquaculture sector has been explored by using the Balassa index, total factor productivity and production costs. The research results show that the fisheries in Turkey are small-scale, technological level are insufficient and there are financial problems. Based on the revealed comparative advantage (RCA) values of the world and EU, which are 0.65 and 1.86, respectively, Turkey 's has competitive power over EU countries, while the reverse is the case for the world. Although fisheries supply chain has been established in Turkey, the value chain has not yet been fully established and activated. The study suggests increasing the efficiency in aquaculture production, having a strong interaction with the market during the production phase, having a high awareness of the price trends and consumer needs throughout the supply chain, using modern production and distribution technologies, and developing effective extension/education activities to reach the desired point in the Turkish aquaculture sector. Quality standards should be at the international level to increase export opportunities and competitiveness of Turkish aquaculture sector.
Practical Guidance for Writing Multiple-Choice Test Questions in Introductory Analytics Courses
Authors: Stevens Scott P. , Palocsay Susan W. , Novoa Luis J.
Published: September 2022

Test writing is a fundamental component of teaching. With increasing pressure to teach larger groups of students, conduct formal assessment of learning outcomes, and offer online and hybrid classes, there is a need for alternatives to constructed response problem-solving test questions. We believe that appropriate use of multiple-choice (MC) questions can alleviate some of these pressures. However, the results will only be acceptable to dedicated faculty if these questions are well written and effective in measuring student learning. In this article, we propose a structured framework consisting of six design principles that serve as a guide for writing MC items that promote higher-order thinking through the use of scenario-based and multistep problems. Then we demonstrate how to apply these principles to develop high-quality test questions in MC format for introductory analytics courses in statistics or operations research/management science.
Modeling and Solving Line Planning with Mode Choice
Authors: Hartleb Johann , Schmidt Marie , Huisman Dennis , Friedrich Markus
Published: September 2022

We present a mixed-integer linear program (MILP) for line planning with mode and route choice. In contrast to existing approaches, the mode and route decisions of passengers are modeled depending on the line plan and commercial solvers can be applied to solve the corresponding MILP. The model aims at finding line plans that maximize the profit for the railway operator while estimating the corresponding passenger demand with aggregate choice models. Hence, the resulting line plans are not only profitable for operators but also attractive to passengers. By suitable preprocessing we are able to apply any aggregate choice model for mode choices using linear constraints. We provide and test means to improve the computational performance. Our experiments on the Intercity network of the Randstad, a metropolitan area in the Netherlands, show that models which assume a fixed passenger assignment to modes cannot attract the passenger numbers they were designed for and therefore lead to inferior profit compared with our new model.

Supplemental Material: The online appendices are available at https://doi.org/10.1287/trsc.2022.1171 .
Longitudinal Trim and Stability Analysis of Generic Air-Breathing Hypersonic Vehicle using Bifurcation Method
Authors: SINGH Ritesh , PRAKASH Om , JOSHI Sudhir , JEPPU Yogananda
Published: September 2022

The Air-breathing Hypersonic Vehicle (AHV) can meet the futuristic goals of rapid global travel, to Low-Earth Orbit and into space in near-term decades. This paper presents the study of the trim and stability characteristics of the 3DOF longitudinal model of the generic AHV. Longitudinal 3DOF AHV simulation is developed with the aerodynamic model for trim analysis considering the complete flight envelope for Mach number from M=0 to 24. Dynamic model simulation of the 3DOF AHV is performed for the trim conditions and stability of the AHV flight for the complete envelope. Bifurcation Analysis is implemented with the longitudinal 3DOF AHV model for trim analysis and stability for the complete AHV flight envelope.
Type-II PPRKTP optical parametric oscillators in the 2  µm spectral range
Authors: Liu Yaqun , Mølster Kjell Martin , Zukauskas Andrius , Lee Cherrie S. J. , Pasiskevicius Valdas
Published: September 2022

We experimentally explored the design parameter space for periodically
poled

R
b

:

K
T
i
O
P
O

4

(PPRKTP) structures in type-II
optical parametric oscillators (OPOs) pumped at 1.064 µm and
operating in the 1.8–2.5 µm range. This study identifies a set
of Sellmeier expansions and thermooptic coefficients that can be used
to accurately design the type-II PPRKTP structures in this spectral
range. The performance of this OPO regime is investigated by employing
different periodicities of PPRKTP, and the effective nonlinear
coefficient is determined. Output at the mJ level with a bandwidth of
better than 10 MHz is readily generated without optical damage.
The temperature tuning rate of about 8 GHz/K of the central OPO
frequency is substantially lower than in similar periodically poled
lithium niobate devices and can be exploited for precise frequency
tuning and easier thermal stabilization. The stimulated backward
polariton scattering in the OPO cavities is also investigated and
discussed.
Comparison of SNR gain between quantum illumination radar and classical radar
Authors: Wei Rongyu , Li Jun , Wang Weihao , Meng Songhao , Zhang Baoshan , Guo Qinghua
Published: September 2022

It has been proved that quantum illumination (QI) radar has the quantum advantages in error-probability exponent. However, the error-probability exponent is not a recognized figure of merit in the radar literature, nor does it correspond in a straightforward manner to any such figure of merit. Signal to noise ratio (SNR) gain is an important criterion in radar theory. While, the theoretical analysis of quantum enhancement in SNR gain of QI radar has not been reported. In this paper, we compare the physical fundamental of matched filter (MF), which can achieve the optimal SNR gain under white noise in classical radar theory, and phase conjugation (PC) receiver. Furthermore, the quantum enhancement of SNR gain in QI radar is studied. It is shown that QI radar with practical receivers can achieve about 3dB quantum advantage in SNR gain. In addition, in the case of extremely weak signal, it can potentially achieve tens of dB enhancement in SNR gain compared with the MF based classical radar.
Detections of the position-vectors of the multi targets located in a circular space based on an asymmetric coupling semiconductor lasers network
Authors: Zhong Dongzhou , Deng Wanan , Zhao Keke , Hu Yalan , Hou Peng , Zhang Jinbo
Published: September 2022

We present a novel scheme for the detections of the position-vectors of the multi targets distributed in a circular space using multi channels of the probe chaotic waves emitted by the asymmetric coupling semiconductor lasers network (ACSLN), where these probe waves possess the attractive features of the time-space uncorrelation and wide bandwidth. Using these features, the accurate measurement for the position-vectors of the multi targets can be achieved by correlating the multi channels of the probe waves with their corresponding reference waves. The further research results show that the detections for the position-vectors of the multi targets possess very low relative errors that are no more than 0.22%. The ranging-resolutions for the multi targets located in a circular space can be achieved as high as 3 mm by optimizing some key parameters, such as injection current and injection strength. In addition, the ranging-resolutions exhibit excellent strong anti-noise performance even when the signal-to-noise ratio and relative noise intensity appear obvious enhancement. The detections for the position-vectors of the multi targets based on the ACSLN offers interesting perspectives for the potential applications in the driverless cars and the object tracking system with omnidirectional vision.
Adjustable enhanced Goos-Hänchen shift in a magneto-optic photonic crystal waveguide
Authors: Huang Yuhao , Tang Gangchao , Chen Jianfeng , Li Zhi-Yuan , Liang Wenyao
Published: September 2022

We have presented adjustable enhanced Goos-Hänchen (GH) shift in a magneto-optical photonic crystal (MOPC) waveguide. The waveguide consists of a top layer of ferrite rods and a lower MOPC with opposite biased dc external magnetic fields (EMFs), and it supports both odd-like and even-like modes simultaneously. The simulation results show the odd-like mode can cause an enhanced negative GH shift, while the even-like mode can result in an enhanced positive GH shift. The physical reason for such negative and positive GH shifts is attributed to the efficient mode coupling and propagation behaviors of the electromagnetic (EM) wave in the waveguide. Furthermore, we have realized the switchable negative/positive GH shift by altering the direction combination of the EMFs. In addition, the magnitudes of both GH shifts can be adjusted by changing the strength of EMF or the width of the waveguide. These results provide new ways to control the transmission behaviors of EM wave and hold promise in applications such as detections, optical switches, and sensors.
Wavefront shaping for forward scattering
Authors: Mastiani Bahareh , Osnabrugge Gerwin , Vellekoop Ivo M.
Published: September 2022

Aberrations and scattering limit the ability of optical microscopy to penetrate deep tissues. Adaptive optics (AO) is a very effective technique to correct for smooth aberrations. Wavefront shaping (WFS) techniques, on the other hand, compensate both scattering and aberrations and have guaranteed convergence even for finding high-dimensional corrections. However, if it is known in advance that the required corrections should be smooth, WFS is suboptimal because it does not use this a priori information. Here, we combine the best of AO and WFS by introducing a WFS method that takes into account the smoothness of the required correction. Our method is numerically stable and robust against noise, and it can find the corrections for multiple targets simultaneously. We experimentally confirmed that this method outperforms existing WFS techniques, especially in forward scattering samples.
Phase-locked terahertz quantum cascade laser array integrated with a Talbot cavity
Authors: Xu Yunfei , Sun Yongqiang , Li Weijiang , Ma Yu , Zhuo Ning , Liu Junqi , Zhang Jinchuan , Zhai Shenqiang , Liu Shuman , Wang Lijun , Liu Fengqi
Published: September 2022

Increasing the power of a quantum cascade laser by widening laser ridges will lead to the degradation of the beam quality because of the operation of high-order transverse modes. We report on a phase-locked array scheme of terahertz quantum cascade laser (THz QCL) utilizing Talbot effect. By adjusting the absorbing boundary width of each ridge in the array, stable operation of the fundamental supermode is realized. A five-element array shows 4 times power amplification than that of a single ridge device. Due to the large power amplification efficiency, stable mode selection, and simple fabricating process, the phase-locked array scheme is very promising to further improve the performance of THz QCL.
Collinear double-pulse laser-induced breakdown spectroscopy based Cd profiling in the soil
Authors: Ren Jie , Yang Zihan , Zhao Yanru , Yu Keqiang
Published: September 2022

Cadmium (Cd) can migrate in the soil and is readily absorbed by crops. High Cd accumulated in grains poses a huge threat to human health by inhibiting the function of the kidney system. Thus, it is crucial to reveal the content of soil Cd in vertical-depth series using a fast, real-time, and reliable method. For this purpose, laser-induced breakdown spectroscopy (LIBS) combined with multivariate chemometrics was developed to analyze Cd content in the soil with vertical-depth series. Soil samples spiked with different levels of Cd were prepared, and LIBS spectra were obtained by single-pulse LIBS (SP-LIBS) and collinear double-pulse LIBS (CDP-LIBS) with wavelengths of 532 nm and 1064 nm. With appropriate parameters, CDP-LIBS showed better performance in detecting Cd than SP-LIBS. Partial least squares regression (PLSR), genetic algorithm (GA)-optimized back propagation artificial neural network (BP-ANN), and particle swarm optimization (PSO)-optimized least squares-support vector machine (LS-SVM) were tested for quantitative analysis of the spectra after median absolute deviation (MAD), multiple scattering correction (MSC), wavelet transform (WT), spectral averaging, and normalization. PSO-optimized LS-SVM yielded an ideal result, with a coefficient of determination (R2, 0.999) and root mean square error (RMSE, 0.359 mg/Kg) in the prediction dataset. Finally, CDP-LIBS coupled with PSO-optimized LS-SVM was employed to analyze soil Cd content in vertical-depth series to reveal the migration pattern of Cd. Our results indicated that soil Cd had a significant positive relationship with the inverse of soil depth. However, Cd was mainly concentrated in 0-20 cm and rarely leached below 45 cm in the soil. This study suggests that LIBS and its enhancement techniques provide a reliable method for revealing the content of soil Cd in vertical-depth series.
Low amplified spontaneous emission threshold from 2-thiophenemethylammonium quasi-2D perovskites via phase engineering
Authors: Qin Chaochao , Zhang Shichen , Zhou Zhongpo , Han Tao , Song Jian , Ma Shuhong , Jia Guangrui , Jiao ZhaoYong , Zhu Zunlue , Chen Xumin , Jiang Yuhai
Published: September 2022

Quasi-2D Ruddlesden-Popper perovskites attract great attention as an optical gain media in lasing applications due to their excellent optoelectronic properties. Herein, a novel quasi-2D Ruddlesden-Popper perovskite based on 2-thiophenemethylammonium (ThMA) is synthesized by a facile solution-processed method. In addition, an anti-solvent treatment method is proposed to tune the phase distribution, and preferential orientation of quasi-2D (ThMA)2Cs
n
-1Pb
n
Br3n+1 thin films. The large-n-dominated narrow domain distribution improves the energy transfer efficiency from small-n to large-n phases. Also, the highly oriented nanocrystals facilitate the efficient Förster energy transfer, beneficial for the carrier population transfer. Furthermore, a green amplified spontaneous emission with a low threshold of 13.92 µJ/cm2 is obtained and a single-mode vertical-cavity laser with an 0.4 nm linewidth emission is fabricated. These findings provide insights into the design of the domain distribution to realize low-threshold multicolor continuous-wave or electrically driven quasi-2D perovskites laser.
High-efficiency simplification method of irregular FOV for accelerating the imaging process in the Risley-Prism system
Authors: Wang Pengfei , Huang Duanhao , Ren He , Huang Feng
Published: September 2022

The Risley-Prism system, which has advantages in large FOV (field of view), high resolution and flexible imaging, faces limitations in image processing speed due to the non-convex characteristics of the FOV. Here, we proposed a simplified FOV model using inscribed rectangle and its property in area size, equivalent resolution and dynamic characteristics are studied, shows high consistency with original FOV. The simulation and experimental results show that the simplified FOV can reduce the calculation time of the total area of multi sub-FOVs from 3500 ms to 7.4 ms, and the image distortion correction time can also be reduced by 88.9%∼96.9%.
Digital aberration correction enhances field of view in visible-light optical coherence microscopy
Authors: Glandorf Lukas , Marchand Paul-James , Lasser Theo , Razansky Daniel
Published: September 2022

In optical coherence microscopy, optical aberrations commonly result in astigmatism-dominated wavefront errors in the peripheral regions of the optical objective, primarily elongating the microscope’s point-spread function along the radial direction in the vicinity of the focal plane. We report on enhanced-field-of-view optical coherence microscopy through computational aberration correction in the visible-light range. An isotropic spatial resolution of 2.5 µm was achieved over an enhanced lateral field of view spanning 1.3 mm × 1.6 mm, as experimentally verified in a micro-bead phantom and further demonstrated in ex vivo tissue samples. The extended field of view achieved by the digital aberration correction facilitates the use of low-cost systems by averting the need for high-quality objectives.
Defect-mediated carrier dynamics and third-order nonlinear optical response of WS2 quantum dots
Authors: Karmakar Riyanka , Mandal Dipendranath , Shrivastava Megha , Adarsh K. V.
Published: September 2022

In this Letter, we report the third-order absorptive and refractive nonlinear optical response of highly luminescent WS2 quantum dots (QDs) in the off-resonant femtosecond and nanosecond pulses, which is beneficial for optical limiting and quantum information processing. For 800 nm femtosecond excitation, QDs show two-photon absorption (β =  (107 ± 2)×10−3 cm/GW) with positive nonlinearity originating from bound carriers. This picture changes significantly for 532 nm nanosecond excitation, where it shows reverse saturable absorption with negative nonlinearity primarily originating from the sequential absorption of two single photons through the shallow defects, creating free carriers. Our results provide a promising route toward low-dimensional optoelectronic devices.
Nonlinear post-compression in multi-pass cells in the mid-IR region using bulk materials
Authors: Carlson D. , Tanksalvala M. , Morrill D. , Roman J. San , Jarque E. Conejero , Kapteyn H. C. , Murnane M. M. , Hemmer M.
Published: September 2022

We numerically investigate the regime of nonlinear pulse compression at
mid-IR wavelengths in a multi-pass cell (MPC) containing a dielectric
plate. This post-compression setup allows for ionization-free spectral
broadening and self-compression while mitigating self-focusing
effects. We find that self-compression occurs for a wide range of MPC
and pulse parameters and derive scaling rules that enable its
optimization. We also reveal the solitonic dynamics of the pulse
propagation in the MPC and its limitations and show that
spatiotemporal/spectral couplings can be mitigated for appropriately
chosen parameters. In addition, we reveal the formation of spectral
features akin to quasi-phase matched degenerate four-wave mixing.
Finally, we present two case studies of self-compression at 3-μm and
6-μm wavelengths using pulse parameters compatible with driving
high-field physics experiments. The simulations presented in this
paper set a framework for future experimental work using few-cycle
pulses at mid-IR wavelengths.
DAC/ADC-free 4 × 12.9 Gbit/s 65,536-level quantum noise stream cipher secure optical WDM transmission based on delta-sigma modulation
Authors: Luo Hanwen , Zhong Linsheng , Dai Xiaoxiao , Cheng Mengfan , Yang Qi , Deng Lei , Liu Deming
Published: September 2022

We propose and experimentally study a novel, to the best of our knowledge, quantum noise stream cipher (QNSC) secure transmission scheme based on the delta-sigma modulation (DSM) technique. The cooperation of the QNSC and DSM mechanisms makes it possible to transmit an ultrahigh-order encrypted signal in the non-return-to-zero (NRZ) on-off keying (OOK) format. The delivery of the NRZ OOK waveform over the fiber link allows us to send and receive signals using digital ports, instead of high-speed and high-resolution digital-to-analog converters (DACs) and analog-to-digital converters (ADCs) in conventional QNSC systems. Meanwhile, clock synchronization can be achieved by using a simple clock data recovery algorithm. The extra clock signal transmission link in conventional QNSC systems is no longer needed. The proposed scheme is also compatible with wavelength division multiplexing (WDM) systems. In this work, 4 × 12.9 Gbit/s plaintext is encrypted to a 65,536-level QNSC signal and then transmitted over a 10-km standard single-mode fiber. The transmitter and receiver are established by commercial 100G QSFP28 optical modules with clock data recovery. This proposed scheme can be easily deployed in commercial systems due to its minimalist implementation architecture and relatively low hardware cost.
Hierarchical-dependent cluster synchronization in directed networks with semiconductor lasers
Authors: Zhang Liyue , Pan Wei , Yan Lianshan , Luo Bin , Zou Xihua , Li Songsui
Published: September 2022

Cluster synchronization in complex networks with mutually coupled semiconductor lasers (SLs) has recently been extensively studied. However, most of the previous works on cluster synchronization patterns have concentrated on undirected networks. Here, we numerically study the complete cluster synchronization patterns in directed networks composed of SLs, and demonstrate that the values of the SLs parameter and network parameter play a prominent role on the formation and stability of cluster synchronization patterns. Moreover, it is shown that there is a hierarchical dependency between the synchronization stability of different clusters in directed networks. The stability of one cluster can be affected by another cluster, but not vice versa. Without loss of generality, the results are validated in another SLs network with more complex topology.
Quasi-distributed fiber-optic acoustic sensor based on a low coherence light source: publisher’s note
Authors: Deng Yuanpeng , Liu Qingwen , Zhao Shuangxiang , Luo Yimin , He Zuyuan
Published: September 2022

This publisher’s note contains a correction to Opt. Lett.
47, 3780 (2022)10.1364/OL.464020.
Helix-shaped tractor and repulsor beams enabling bidirectional optical transport of particles en masse
Authors: Rodrigo José A. , Martínez-Matos Óscar , Alieva Tatiana
Published: September 2022

Three-dimensional programmable transport of micro/nano-particles can be straightforwardly achieved by using optical forces arising from intensity and phase gradients of a structured laser beam. Repulsor and tractor beams based on such forces and shaped in the form of a curved trajectory allow for downstream and upstream (against light propagation) transportation of particles along the beams, respectively. By using both types of beams, bidirectional transport has been demonstrated on the example of a circular helix beam just by tuning its phase gradient. Specifically, the transport of a single particle along a loop of the helix has been reported. However, the design and generation of helix-shaped beams is a complex problem that has not been completely addressed, which makes their practical application challenging. Moreover, there is no evidence of simultaneous transport of multiple particles along the helix trajectory, which is a crucial requisite in practice. Here, we address these challenges by introducing a theoretical background for designing helix beams of any axial extension, shape, and phase gradient that takes into account the experimental limitations of the optical system required for their generation. We have found that only certain phase gradients prescribed along the helix beam are possible. Based on these findings, we have experimentally demonstrated, for the first time, helix-shaped repulsor and tractor beams enabling programmable bidirectional optical transport of particles en masse. This is direct evidence of the essential functional robustness of helix beams arising from their self-reconstructing character. These achievements provide new insight into the behavior of helix-shaped beams, and the proven technique makes their implementation easier for optical transport of particles as well as for other light–matter interaction applications.
Plasma metabolome predicts trained immunity responses after antituberculosis BCG vaccination
Authors: Koeken Valerie A. C. M. , Qi Cancan , Mourits Vera P. , de Bree L. Charlotte J. , Moorlag Simone J. C. F. M. , Sonawane Vidhisha , Lemmers Heidi , Dijkstra Helga , Joosten Leo A. B. , van Laarhoven Arjan , Xu Cheng-Jian , van Crevel Reinout , Netea Mihai G. , Li Yang
Published: September 2022

The antituberculosis vaccine Bacillus Calmette–Guérin (BCG) induces nonspecific protection against heterologous infections, at least partly through induction of innate immune memory (trained immunity). The amplitude of the response to BCG is variable, but the factors that influence this response are poorly understood. Metabolites, either released by cells or absorbed from the gut, are known to influence immune responses, but whether they impact BCG responses is not known. We vaccinated 325 healthy individuals with BCG, and collected blood before, 2 weeks and 3 months after vaccination, to assess the influence of circulating metabolites on the immune responses induced by BCG. Circulating metabolite concentrations after BCG vaccination were found to have a more pronounced impact on trained immunity responses, such as the increase in IL-1β and TNF-α production upon Staphylococcus aureus stimulation, than on specific adaptive immune memory, assessed as IFN-γ production in response to Mycobacterium tuberculosis. Circulating metabolites at baseline were able to predict trained immunity responses at 3 months after vaccination and enrichment analysis based on the metabolites positively associated with trained immunity revealed enrichment of the tricarboxylic acid (TCA) cycle and glutamine metabolism, both of which were previously found to be important for trained immunity. Several new metabolic pathways that influence trained immunity were identified, among which taurine metabolism associated with BCG-induced trained immunity, a finding validated in functional experiments. In conclusion, circulating metabolites are important factors influencing BCG-induced trained immunity in humans. Modulation of metabolic pathways may be a novel strategy to improve vaccine and trained immunity responses.
Blind spots on western blots: Assessment of common problems in western blot figures and methods reporting with recommendations to improve them
Authors: Kroon Cristina , Breuer Larissa , Jones Lydia , An Jeehye , Akan Ayça , Mohamed Ali Elkhansa Ahmed , Busch Felix , Fislage Marinus , Ghosh Biswajit , Hellrigel-Holderbaum Max , Kazezian Vartan , Koppold Alina , Moreira Restrepo Cesar Alberto , Riedel Nico , Scherschinski Lea , Urrutia Gonzalez Fernando Raúl , Weissgerber Tracey L.
Published: September 2022

Western blotting is a standard laboratory method used to detect proteins and assess their expression levels. Unfortunately, poor western blot image display practices and a lack of detailed methods reporting can limit a reader’s ability to evaluate or reproduce western blot results. While several groups have studied the prevalence of image manipulation or provided recommendations for improving western blotting, data on the prevalence of common publication practices are scarce. We systematically examined 551 articles published in the top 25% of journals in neurosciences (n = 151) and cell biology (n = 400) that contained western blot images, focusing on practices that may omit important information. Our data show that most published western blots are cropped and blot source data are not made available to readers in the supplement. Publishing blots with visible molecular weight markers is rare, and many blots additionally lack molecular weight labels. Western blot methods sections often lack information on the amount of protein loaded on the gel, blocking steps, and antibody labeling protocol. Important antibody identifiers like company or supplier, catalog number, or RRID were omitted frequently for primary antibodies and regularly for secondary antibodies. We present detailed descriptions and visual examples to help scientists, peer reviewers, and editors to publish more informative western blot figures and methods. Additional resources include a toolbox to help scientists produce more reproducible western blot data, teaching slides in English and Spanish, and an antibody reporting template.
TAMC: A deep-learning approach to predict motif-centric transcriptional factor binding activity based on ATAC-seq profile
Authors: Yang Tianqi , Henao Ricardo
Published: September 2022

Determining transcriptional factor binding sites (TFBSs) is critical for understanding the molecular mechanisms regulating gene expression in different biological conditions. Biological assays designed to directly mapping TFBSs require large sample size and intensive resources. As an alternative, ATAC-seq assay is simple to conduct and provides genomic cleavage profiles that contain rich information for imputing TFBSs indirectly. Previous footprint-based tools are inheritably limited by the accuracy of their bias correction algorithms and the efficiency of their feature extraction models. Here we introduce TAMC (Transcriptional factor binding prediction fromATAC-seq profile atMotif-predicted binding sites usingConvolutional neural networks), a deep-learning approach for predicting motif-centric TF binding activity from paired-end ATAC-seq data. TAMC does not require bias correction during signal processing. By leveraging a one-dimensional convolutional neural network (1D-CNN) model, TAMC make predictions based on both footprint and non-footprint features at binding sites for each TF and outperforms existing footprinting tools in TFBS prediction particularly for ATAC-seq data with limited sequencing depth.
Digital twin predicting diet response before and after long-term fasting
Authors: Silfvergren Oscar , Simonsson Christian , Ekstedt Mattias , Lundberg Peter , Gennemark Peter , Cedersund Gunnar
Published: September 2022

Today, there is great interest in diets proposing new combinations of macronutrient compositions and fasting schedules. Unfortunately, there is little consensus regarding the impact of these different diets, since available studies measure different sets of variables in different populations, thus only providing partial, non-connected insights. We lack an approach for integrating all such partial insights into a useful and interconnected big picture. Herein, we present such an integrating tool. The tool uses a novel mathematical model that describes mechanisms regulating diet response and fasting metabolic fluxes, both for organ-organ crosstalk, and inside the liver. The tool can mechanistically explain and integrate data from several clinical studies, and correctly predict new independent data, including data from a new study. Using this model, we can predict non-measured variables,e.g. hepatic glycogen and gluconeogenesis, in response to fasting and different diets. Furthermore, we exemplify how such metabolic responses can be successfully adapted to a specific individual’s sex, weight, height, as well as to the individual’s historical data on metabolite dynamics. This tool enables an offline digital twin technology.
A quantitative modelling approach for DNA repair on a population scale
Authors: Zeitler Leo , Denby Wilkes Cyril , Goldar Arach , Soutourina Julie
Published: September 2022

The great advances of sequencing technologies allow the in vivo measurement of nuclear processes—such as DNA repair after UV exposure—over entire cell populations. However, data sets usually contain only a few samples over several hours, missing possibly important information in between time points. We developed a data-driven approach to analyse CPD repair kinetics over time in Saccharomyces cerevisiae. In contrast to other studies that consider sequencing signals as an average behaviour, we understand them as the superposition of signals from independent cells. By motivating repair as a stochastic process, we derive a minimal model for which the parameters can be conveniently estimated. We correlate repair parameters to a variety of genomic features that are assumed to influence repair, including transcription rate and nucleosome density. The clearest link was found for the transcription unit length, which has been unreported for budding yeast to our knowledge. The framework hence allows a comprehensive analysis of nuclear processes on a population scale.
RNA velocity unraveled
Authors: Gorin Gennady , Fang Meichen , Chari Tara , Pachter Lior
Published: September 2022

We perform a thorough analysis of RNA velocity methods, with a view towards understanding the suitability of the various assumptions underlying popular implementations. In addition to providing a self-contained exposition of the underlying mathematics, we undertake simulations and perform controlled experiments on biological datasets to assess workflow sensitivity to parameter choices and underlying biology. Finally, we argue for a more rigorous approach to RNA velocity, and present a framework for Markovian analysis that points to directions for improvement and mitigation of current problems.
Thalamic regulation of frontal interactions in human cognitive flexibility
Authors: Hummos Ali , Wang Bin A. , Drammis Sabrina , Halassa Michael M. , Pleger Burkhard
Published: September 2022

Interactions across frontal cortex are critical for cognition. Animal studies suggest a role for mediodorsal thalamus (MD) in these interactions, but the computations performed and direct relevance to human decision making are unclear. Here, inspired by animal work, we extended a neural model of an executive frontal-MD network and trained it on a human decision-making task for which neuroimaging data were collected. Using a biologically-plausible learning rule, we found that the model MD thalamus compressed its cortical inputs (dorsolateral prefrontal cortex, dlPFC) underlying stimulus-response representations. Through direct feedback to dlPFC, this thalamic operation efficiently partitioned cortical activity patterns and enhanced task switching across different contingencies. To account for interactions with other frontal regions, we expanded the model to compute higher-order strategy signals outside dlPFC, and found that the MD offered a more efficient route for such signals to switch dlPFC activity patterns. Human fMRI data provided evidence that the MD engaged in feedback to dlPFC, and had a role in routing orbitofrontal cortex inputs when subjects switched behavioral strategy. Collectively, our findings contribute to the emerging evidence for thalamic regulation of frontal interactions in the human brain.