bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved conditional differential attacks on lightweight hash family QUARK
Authors: Lu Xiaojuan , Li Bohan , Liu Meicheng , Lin Dongdai
Published: June 2022

Nonlinear feedback shift register (NFSR) is one of the most important cryptographic primitives in lightweight cryptography. At ASIACRYPT 2010, Knellwolf et al. proposed conditional differential attack to perform a cryptanalysis on NFSR-based cryptosystems. The main idea of conditional differential attack is to restrain the propagation of the difference and obtain a detectable bias of the difference of the output bit. QUARK is a lightweight hash function family which is designed by Aumasson et al. at CHES 2010. Then the extended version of QUARK was published in Journal of Cryptology 2013. In this paper, we propose an improved conditional differential attack on QUARK. One improvement is that we propose a method to select the input difference. We could obtain a set of good input differences by this method. Another improvement is that we propose an automatic condition imposing algorithm to deal with the complicated conditions efficiently and easily. It is shown that with the improved conditional differential attack on QUARK, we can detect the bias of output difference at a higher round of QUARK. Compared to the current literature, we find a distinguisher of U-QUARK/D-QUARK/S-QUARK/C-QUARK up to 157/171/292/460 rounds with increasing 2/5/33/8 rounds respectively. We have performed the attacks on each instance of QUARK on a 3.30 GHz Intel Core i5 CPU, and all these attacks take practical complexities which have been fully verified by our experiments. As far as we know, all of these results have been the best thus far.
Effect of COVID-19 infection on psychological aspects of pre-schooler children: a cross-sectional study
Authors: Ahmed Gellan K. , Mostafa Sayed , Elbeh Khaled , Gomaa Hamdy M. , Soliman Saeed
Published: June 2022

Background

Coronavirus disease 2019 (COVID-19) had a tremendous effect on individual’s lives worldwide. The pandemic’s significant socioecological impact is one of the many burdens children confront in the current crises. As a result, this study was designed to determine the psychological impacts of the COVID-19 pandemic on preschoolers, particularly the consequences of COVID-19 infection. This study involved 138 children aged 2–5.11 years old who were classified into two groups based on their COVID-19 infection history, which was documented via a PCR test. All participants were assessed by the Socioeconomic Scale and The Children’s Behavior Checklist (CBCL).

Results

COVID-19 infection was found in 21.7% of the children who participated in this study. Furthermore, children with COVID-19 had a higher percentage of clinical rating on the CBCL Profile of DSM-5 scales for affective problems (13.3 vs. 7.4%), anxiety problems (13.3 vs. 9.3%), pervasive developmental problems (20 vs. 13%), and oppositional defiant problems (6.7 vs. 5.6%) than children without COVID-19. Anxiety and somatic problems had a positive correlation with the impact of the COVID-19 pandemic on the lives of children.

Conclusions

Children infected with COVID-19 were more likely to have psychological issues, such as affective disorders, anxiety problems, pervasive developmental problems, and oppositional defiant problems. These psychological issues had a relationship with the impact of the COVID-19 pandemic on the lives of children.
Risk assessment score for adverse pregnancy outcome in systemic lupus erythematosus patients
Authors: Makarm Wafaa K. , Zaghlol Rabab S. , Kotb Lobna I.
Published: June 2022

Background

Systemic lupus is a chronic autoimmune multisystem disease that mainly affects females of childbearing age. SLE still possesses risks during pregnancy that lead to poor maternal and fetal outcomes. The objectives of the study were to identify factors associated with unfavorable pregnancy outcomes and develop a predictive risk score for adverse pregnancy outcomes in patients with SLE.

Results

The main predictive factors associated with adverse pregnancy outcomes among lupus patients in multiple linear regression were an absence of remission for at least 6 months before conception, preexisting lupus nephritis, active disease at conception, C3 hypocomplementemia, and antiphospholipid antibody syndrome. Each predictor is assigned a weighted point score, and the sum of points represents the risk score. The area under the receiver operating characteristic curve (ROC) was 0.948 (95% confidence interval, 0.908–0.988), suggesting that the score had strong discriminatory power for adverse pregnancy outcomes.

Conclusions

In this study, a predictive model with a risk score classification for adverse pregnancy outcomes in SLE patients was developed. This could help rheumatologists identify high-risk pregnant patients for better disease monitoring and management, resulting in better maternal/fetal outcomes.
Effects of curvature on epithelial tissue —Coordinated rotational movement and other spatiotemporal arrangements
Authors: Happel L. , Wenzel D. , Voigt A.
Published: June 2022

Coordinated movements of epithelial tissue are linked with active matter processes. We here consider the influence of curvature on the spatiotemporal arrangements and the shapes of the cells. The cells are represented by a multiphase field model which is defined on the surface of a sphere. Besides the classical solid and liquid phases, which depend on the curvature of the sphere, on mechanical properties of the cells and the strength of activity, we identify a phase of global rotation. This rotation provides a coordinated cellular movement which can be linked to tissue morphogenesis. This investigation on a sphere is a first step to investigate the delicate interplay between topological constraints, geometric properties and collective motion. Besides the rotational state we also analyse positional defects, identify global nematic order and study the associated orientational defects.
Simple and robust analytical model for dipolar resonances in plasmonic particle-substrate systems
Authors: Castro Claudio Silvestre , Bruyant Aurelien , Vincent Rémi
Published: June 2022

We revisit the theory of light-matter interactions induced by a small metallic particle near a planar surface. The resonant features of the coupled system are investigated using an approach that determines the particle permittivity that brings the system to resonance. Analytical results are presented for the case of a spherical particle near a flat substrate and compared to previous results, whereas a general recipe involving Green's function is also given. In contrast to previous work, our analytical results allow the determination of eigenfrequencies in the presence of strong temporal dispersion and include radiative damping. Furthermore, the model can be related to stationary normal modes, thereby providing physical insight and a design tool for surface-enhanced devices and sensing.
Short- and Long-Term Outcomes of Pancreatic Cancer Resection in Elderly Patients: A Nationwide Analysis
Authors: Henry Anne Claire , Schouten Thijs J. , Daamen Lois A. , Walma Marieke S. , Noordzij Peter , Cirkel Geert A. , Los Maartje , Besselink Marc G. , Busch Olivier R. , Bonsing Bert A. , Bosscha Koop , van Dam Ronald M. , Festen Sebastiaan , Groot Koerkamp Bas , van der Harst Erwin , de Hingh Ignace H. J. T. , Kazemier Geert , Liem Mike S. , de Meijer Vincent E. , Nieuwenhuijs Vincent B. , Roos Daphne , Schreinemakers Jennifer M. J. , Stommel Martijn W. J. , Molenaar I. Quintus , van Santvoort Hjalmar C. ,   for the Dutch Pancreatic Cancer Group
Published: June 2022

Background

The number of elderly patients with pancreatic cancer is growing, however clinical data on the short-term outcomes, rate of adjuvant chemotherapy, and survival in these patients are limited and we therefore performed a nationwide analysis.

Methods

Data from the prospective Dutch Pancreatic Cancer Audit were analyzed, including all patients undergoing pancreatic cancer resection between January 2014 and December 2016. Patients were classified into two age groups: <75 and ≥75 years. Major complications (Clavien–Dindo grade 3 or higher), 90-day mortality, rates of adjuvant chemotherapy, and survival were compared between age groups. Factors associated with start of adjuvant chemotherapy and survival were evaluated with logistic regression and multivariable Cox regression analysis.

Results

Of 836 patients, 198 were aged ≥75 years (24%) and 638 were aged <75 years (76%). Median follow-up was 38 months (interquartile range [IQR] 31–47). Major complications (31% vs. 28%; p = 0.43) and 90-day mortality (8% vs. 5%; p = 0.18) did not differ. Adjuvant chemotherapy was started in 37% of patients aged ≥75 years versus 69% of patients aged <75 years (p < 0.001). Median overall survival (OS) was 15 months (95% confidence interval [CI] 14–18) versus 21 months (95% CI 19–24; p < 0.001). Age ≥75 years was not independently associated with OS (hazard ratio 0.96, 95% CI 0.79–1.17; p = 0.71), but was associated with a lower rate of adjuvant chemotherapy (odds ratio 0.27, 95% CI 0.18–0.40; p < 0.001).

Conclusions

The rate of major complications and 90-day mortality after pancreatic resection did not differ between elderly and younger patients; however, elderly patients were less often treated with adjuvant chemotherapy and their OS was shorter.
Self-Assembly of a Zinc Bacteriochlorophyll-d Analog with a Lipophilic Tertiary Amide Group in the 17-Substituent
Authors: Shoji Sunao , Stepanenko Vladimir , Würthner Frank , Tamiaki Hitoshi
Published: June 2022

Self-assembled aggregates of bacteriochlorophyll(BChl)-c/d/e pigments play key roles in major light-harvesting antenna systems of photosynthetic green bacteria. Herein, we report the self-assembly of a lipophilic zinc BChl-d model with an N,N-didodecylamide in the 17-substituent. The present model formed two types of J-aggregates, which formed under kinetic and thermodynamic controls.
Black Economists on Race and Policy: Contributions to Education, Poverty and Mobility, and Public Finance
Authors: Francis Dania V. , Hardy Bradley L. , Jones Damon
Published: June 2022

We explore the contributions of Black economists to research on major economic and social policy problems in the United States. We focus on applications in education, poverty and economic mobility, and public finance to extract common themes and patterns. The major themes that emerge include (i) Black economists’ examination of individual versus structural explanations for economic outcomes, (ii) the role played by race and discrimination, (iii) the endogenous determination of race, and (iv) the nature of objectivity and positionality in economic research. A unifying theme is a willingness of many Black economists to engage critically on economic policy issues, using frameworks both from within as well as outside of mainstream neoclassical economics.(JEL A11, D72, I23, I28, I32, J15, K42)
Species-specific formation of paraspeckles in intestinal epithelium revealed by characterization of NEAT1 in naked mole-rat
Authors: Yamada Akihiro , Toya Hikaru , Tanahashi Mayuko , Kurihara Misuzu , Mito Mari , Iwasaki Shintaro , Kurosaka Satoshi , Takumi Toru , Fox Archa , Kawamura Yoshimi , Miura Kyoko , Nakagawa Shinichi
Published: June 2022

Paraspeckles are mammalian-specific nuclear bodies built on the long noncoding RNA NEAT1_2. The molecular mechanisms of paraspeckle formation have been mainly studied using human or mouse cells, and it is not known if the same molecular components are involved in the formation of paraspeckles in other mammalian species. We thus investigated the expression pattern of NEAT1_2 in naked mole-rats (nNEAT1_2), which exhibit extreme longevity and lower susceptibility to cancer. In the intestine, nNEAT1_2 is widely expressed along the entire intestinal epithelium, which is different from the expression of mNeat1_2 that is restricted to the cells of the distal tip in mice. Notably, the expression of FUS, a FET family RNA binding protein, essential for the formation of paraspeckles both in humans and mice, was absent in the distal part of the intestinal epithelium in naked mole-rats. Instead, mRNAs of other FET family proteins EWSR1 and TAF15 were expressed in the distal region. Exogenous expression of these proteins in Fus-deficient murine embryonic fibroblast cells rescued the formation of paraspeckles. These observations suggest that nNEAT1_2 recruits a different set of RNA binding proteins in a cell type-specific manner during the formation of paraspeckles in different organisms.
Risk factors of developing inflammatory bowel diseases
Authors: Zimna Aleksandra Iwona , Wróblewski Hubert , Chojęta Dariusz , Zygmunt Ewelina , Kozłowska Anna
Published: June 2022

Introduction: The pathogenesis of inflammatory bowel disease (IBD) is still unknown. It is known to be multi-factorial. The world is seeing an ever increasing number of new cases of these diseases. Ulcerative colitis and Crohn's disease are the main representatives of inflammatory bowel diseases.

Aim: The aim of the study was to analyze risk factors for inflammatory bowel diseases.

Materials and methods: The results were obtained on the basis of a questionnaire survey.

Results: 95 people took part in the survey aged 16 to 72 years old. 35.8% were men and 64.2% were women. 78% lives in cites, only 22% are rural residents.  56.4% of them suffer from ulcerative colitis and 43.6% from Crohn's disease. 40.4% of respondents smoked cigarettes in the past, but currently only 12.6% are still struggling with the addiction. Only 4 people declare brushing their teeth after each meal. 18 people confirm the presence of NCDH in their families, 19 suffer from other autoimmune diseases at the same time. 2 people from among the respondents - also celiac disease. One person had Salmonella and Shigella infection.  Conclusions: Due to the mutual cause-effect relationships between genetic predisposition and the influence of environmental factors, it is currently difficult to state which of the above factors plays a decisive role. Environmental factors that play a role in the etiopathogenesis of IBD include, first and foremost, the intestinal bacterial flora, diet, human environment and smoking. There is a clear tendency for the coexistence of autoimmune diseases in the group of patients with NCJ and a predisposition to the disease in the family. There is also a need to educate patients about the benefits of taking probiotics and taking care of proper eating habits. Key words: inflammatory bowel diseases, risk of developing the disease, irresponsible patient
The Façade, the Face, and the Sympathies: Opening the Black Box of Symbolic Capital as a Source of Philanthropic Attractiveness
Authors: Shymko Yuliya , Roulet Thomas J , de Melo Pimentel Bernardo
Published: June 2022

Although most studies on philanthropy have focused on corporate benefactors, limited attention has been given to beneficiaries and their characteristics. The literature thus falls short in explaining how the variance in the perceived value of those characteristics can condition the philanthropic attractiveness of recipients for donors. Drawing from Bourdieu’s concept of symbolic capital and qualitative insights drawn from our empirical context of philanthropy in the field of cultural production in the Russian Federation, we argue that the attractiveness of cultural organizations for potential corporate benefactors depends on a range of determinants, which we classify under the broad umbrellas of respectability and reputability. By using political orientation as a moderator, we show that, although respectability is an indiscriminately attractive part of symbolic capital, reputability, associated with artistic celebrity and renown, can become a deterrent to potential donors when it augments the risk of jeopardizing their relationship with the government. We also demonstrate that a board of trustees, which signals openness to stakeholder involvement, diminishes the returns of reputability for potential donors. We test our hypotheses using original and representative longitudinal data on 449 Russian theaters (2004–2011). Taking an indirect recursive approach to estimate models with high-dimensional fixed effects, we find strong support for our hypotheses across a variety of econometric specifications. Our research offers a unique focus on the beneficiary side of the beneficiary-benefactor relationship, which has both theoretical and practical implications for the literatures on corporate philanthropy, and cultural industries.

Supplemental Material: The online appendices are available at https://doi.org/10.1287/orsc.2022.1603 .
Coordinating roles in the stoma care pathway: practical recommendations from France
Authors: Chaumier Danièle
Published: June 2022

Danièle Chaumier introduces recommendations for hospital discharge and community follow-up after ostomy formation, developed by the Strategic Healthcare Initiative for Easier Life Days (SHIELD)'s committee of multidisciplinary experts
A holistic view of the stoma care pathway in Italy: a nationwide learning survey
Authors: Toma Elena , Torre Filippo La , Barone Filippo , Rovere Marcello , Ercolani Maria Sole , Pocek Paola , Filomeno Lucia , Torre Giuseppe La
Published: June 2022

Background:

The therapeutic care pathway for a patient with a stoma starts with a preoperative diagnosis and the decision to form an ostomy, followed by postoperative education, and it continues for as long as the stoma is in place. Clinical studies in this area are often limited to analysing a specific stage in this process, and less attention has been given to how each stage influences the rest of the pathway.

Aim:

This study aimed to provide a holistic assessment of the entire stoma care pathway, encompassing professional management of emerging complications, as well as the patient's perceptions of care and capacity for self-management, to determine how one management stage might affect another.

Method:

The study consisted of an anonymous questionnaire with 96 items divided into nine sections. It enrolled people with one or more urinary and/or intestinal stoma/s and lasted from September 2017 to December 2019.

Findings:

In the sample of 403 ostomates, 52% were female and 48% male, while 74% had an intestinal stoma, 19% a urinary stoma and 7% both. Of all respondents, 52% presented with peristomal lesions. Pre-operatively, a lack of training (76%), stoma siting (70%) and psychological support (92%) were observed. After discharge, 75% had peristomal lesions, 47% had professional care. At the time of the study, 60% were self-sufficient in ostomy care, 52% had lesions, while 38% were unsatisfied with the device used.

Conclusion:

Detailed discussion is given to peristomal skin care, self-sufficiency, ongoing support and the needs of people with both a urinary and an intestinal stoma. Patient education, psychological support and access to a stoma care specialist all likely affect acceptance and quality of life.
Factors predictive of optimal peristomal skin status in patients with an ostomy: a secondary analysis
Authors: González Eugenia Rodriguez , Zurita Carmen del Pino , Caballero Gemma Arrontes , Rodríguez Araceli Hoyo , Rodríguez Eugenia Zapatero , Blázquez Eduardo García
Published: June 2022

Peristomal skin problems are common in ostomy patients and are connected to decreased quality of life and patient independence, as well as increased treatment costs. This study analysed the factors related to peristomal skin changes in order to better define the clinical profile of patients with optimal peristomal skin status. Secondary analysis of data from a nationwide, cross-sectional, retrospective, multicentre study performed in Spain (Uses and Attitudes in Ostomy) ( Bueno Cruz et al, 2021 ) evaluated clinical data, including demographics, preoperative stoma site marking, type of ostomy, device used, frequency of leakage and scores from the Ostomy Skin Tool (OST) and quality of life (QoL) questionnaires. Risk factors for peristomal skin changes were analysed using multivariate analysis, and a predictive nomogram to anticipate optimal peristomal skin status (defined here as discolouration (D), erosion (E), and tissue overgrowth (T) (DET) score of 0) was developed. Some 871 patients with an ostomy using different commercial devices in Spain were evaluated. Multivariate analysis to predict optimal peristomal skin status revealed leakage frequency, patient age, type of ostomy, preoperative siting and type of baseplate used were independent predictors of peristomal skin status. Optimal peristomal skin care should be a treatment goal for nurse specialists in stomal therapy, and its individual influencing variables should be taken into account by nurses specialising in ostomy care.
Freeform wide-angle camera lens enabling mitigable distortion
Authors: Zhuang Zhenfeng , Parent Jocelyn , Roulet Patrice , Thibault Simon
Published: June 2022

Allowing natural scenes as well as maximizing field of view (FoV) can benefit from the minimization of distortion for the wide-angle camera. The wide-angle camera utilizing freeform surfaces for mitigating distortions, either barrel distortion or pincushion distortion, is therefore of interest. In this paper, the designs of using all-aspherical surfaces and aspherical surfaces combined with freeform surfaces are investigated. To minimize the deviation before and after converting from aspherical surfaces to freeform surfaces, a mathematical conversion scheme is derived. By applying it to the design example, the methodology is shown to be effective in the case of an optical system with a large number of aspherical/freeform surfaces. Additionally, custom freeform analysis tools are developed for quantitative analysis and visualization of the critical characteristics of optical performance, namely, a 2D lateral color field map, 2D relative illumination field map, 2D spot radius field map, and 2D average modulation transfer function (MTF) field map. Compared to classical all-aspherical design, simulation results show that freeform design has the capability to reduce distortion, and other performances such as relative illumination, spot size, and MTF can also be improved, even though there are some compromises on the peripheral FoV. The design approach will have potential important research and application values for lens systems utilized in miniature camera lenses, especially the wide FoV capability.
Interferometric laser imaging for droplet-size measurement in spray
Authors: Ma Yarui , Cui Jiwen , Tan Jiubin
Published: June 2022

An upgraded droplet-size measurement method, based on laser interference particle imaging (IPI) technology, is applied to accomplish high-precision measurement of particle size and spatial distribution of gas–liquid two-phase flow in the atomization field. In this study, an improved morphological-Hough transform interference fringe location algorithm is applied to IPI measurement. The particle size of the standard particle field with a diameter of 24 µm is measured by the upgraded IPI measurement experimentally, whose absolute error and relative error are 0.14 µm and 0.58%, respectively. The atomization field of the 400 µm centrifugal nozzle under different pressures is demonstrated by direct imaging and IPI technology, where the assessment results are evaluated by SMD value and particle size distribution, and the results exhibit good agreement.
Leveraging non-expert crowdsourcing to segment the optic cup and disc of multicolor fundus images
Authors: Zhang Jichang , Zheng Yuanjie , Hou Wanchen , Jiao Wanzhen
Published: June 2022

Multicolor scanning laser imaging (MCI) images have broad application potential in the diagnosis of fundus diseases such as glaucoma. However, the performance level of automatic aided diagnosis systems based on MCI images is limited by the lack of high-quality annotations of numerous images. Producing annotations for vast amounts of MCI images will be a prolonged process if we only employ experts. Therefore, we consider non-expert crowdsourcing, which is an alternative approach to produce useful annotations efficiently and low cost. In this work, we aim to explore the effectiveness of non-expert crowdsourcing on the segmentation of the optic cup (OC) and optic disc (OD), which is an upstream task for glaucoma diagnosis, using MCI images. To this end, desensitized MCI images are independently annotated by four non-expert annotators, constructing a crowdsourcing dataset. To profit from crowdsourcing, we propose a model consisting of coupled regularization network and segmentation network. The regularization network generates learnable pixel-wise confusion matrices (CMs) that reflects preferences of each annotator. During training, the CMs and segmentation network are simultaneously optimized to enable dynamic trade-offs for non-expert annotations and generate reliable predictions. Crowdsourcing learning using our method have an average Mean Intersection Over Union (M) of 91.34%, while the averageMof model trained by expert annotations is 91.72%. In addition, comparative experiments show that in our segmentation task non-expert crowdsourcing can be on a par with the expert who annotates 90% of data. Our work suggests that crowdsourcing in the segmentation of OC and OD using MCI images has the potential to be a substitute to expert annotation, which will accelerate the construction of large datasets to facilitate the application of deep learning in clinical diagnosis using MCI images.
Full-color micro-display by heterogeneous integration of InGaN blue/green dual-wavelength and AlGaInP red LEDs
Authors: Li Peian , Zhang Xu , Qi Longheng , Lau Kei May
Published: June 2022

A full-color micro-display via bonding of a InGaN blue/green dual-wavelength light-emitting diode (LED) array and a AlGaInP red LED array is demonstrated. The micro-display has a 120 µm pixel pitch, and each pixel consists of 40 µm × 120 µm red/green/blue (R/G/B) subpixels. The red LED array was integrated with the blue/green dual-wavelength LED array by Au/In flip-chip bonding to achieve full-color emission. Full-color images presented by the micro-display have high brightness and a wide color gamut. This heterogeneous integration technology using conventional LED materials shows the feasibility of a cost-effective approach for reliable high-performance full-color LED micro-displays in virtual reality (VR) and augmented reality (AR) devices.
Accuracy of analytical expressions for Rayleigh backscattered crosstalk in bidirectional multi-core fiber transmissions
Authors: Hayashi Tetsuya
Published: June 2022

Use of bidirectional multi-core fiber (MCF) transmissions is attractive as it suppresses inter-core crosstalk by propagating the signals in opposite directions between nearest neighboring cores; therefore, signal quality and/or core density is improved compared with unidirectional transmissions where all the signals propagate in the same direction across the cores. In long-haul bidirectional MCF transmissions, Rayleigh backscattering is one of the major causes of inter-core crosstalk (XT). In this paper, we derive approximate expressions for Rayleigh backscattered XT and discuss the accuracy of the approximations. The derived expressions revealed that the reduction from conventional co-propagating XT to backscattered XT depends approximately only on wavelength, refractive index, effective area, the Rayleigh scattering component in propagation loss, and span loss.
Fluorescent wavefront shaping using incoherent iterative phase conjugation
Authors: Aizik Dror , Gkioulekas Ioannis , Levin Anat
Published: June 2022

Wavefront shaping correction makes it possible to image fluorescent
particles deep inside scattering tissue. This requires determining a
correction mask to be placed in both the excitation and emission
paths. Standard approaches select correction masks by optimizing
various image metrics, a process that requires capturing a
prohibitively large number of images. To reduce the acquisition cost,
iterative phase conjugation techniques use the observation that the
desired correction mask is an eigenvector of the tissue transmission
operator. They then determine this eigenvector via optical
implementations of the power iteration method, which require capturing
orders of magnitude fewer images. Existing iterative phase conjugation
techniques assume a linear model for the transmission of light through
tissue, and thus only apply to fully coherent imaging systems. We
extend such techniques to the incoherent case. The fact that light
emitted from different sources sums incoherently violates the linear
model and makes linear transmission operators inapplicable. We show
that, surprisingly, the nonlinearity due to incoherent summation
results in an order-of-magnitude acceleration in the convergence of
the phase conjugation iteration.
Brillouin backaction thermometry for modal temperature control
Authors: Lai Yu-Hung , Yuan Zhiquan , Suh Myoung-Gyun , Lu Yu-Kun , Wang Heming , Vahala Kerry J.
Published: June 2022

Stimulated Brillouin scattering provides optical gain for efficient and narrow-linewidth lasers in high-Q microresonator systems. However, the thermal dependence of the Brillouin process as well as the microresonator frequencies impose strict temperature control requirements for long term frequency-stable operation. Here, we study Brillouin backaction and use it to both measure and phase-sensitively lock modal temperature to a reference temperature defined by the Brillouin phase matching condition. At a specific lasing wavelength, the reference temperature can be precisely set by adjusting the resonator’s free spectral range. This backaction control method is demonstrated in a chip-based Brillouin laser, but can be applied in all Brillouin laser platforms. It offers a new approach for frequency-stable operation of Brillouin lasers in atomic clock, frequency metrology, and gyroscope applications.
A new test suggests hundreds of amino acid polymorphisms in humans are subject to balancing selection
Authors: Soni Vivak , Vos Michiel , Eyre-Walker Adam
Published: June 2022

The role that balancing selection plays in the maintenance of genetic diversity remains unresolved. Here, we introduce a new test, based on the McDonald–Kreitman test, in which the number of polymorphisms that are shared between populations is contrasted to those that are private at selected and neutral sites. We show that this simple test is robust to a variety of demographic changes, and that it can also give a direct estimate of the number of shared polymorphisms that are directly maintained by balancing selection. We apply our method to population genomic data from humans and provide some evidence that hundreds of nonsynonymous polymorphisms are subject to balancing selection.
fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions
Authors: Szulc Natalia A. , Mackiewicz Zuzanna , Bujnicki Janusz M. , Stefaniak Filip
Published: June 2022

Computational methods play a pivotal role in drug discovery and are widely applied in virtual screening, structure optimization, and compound activity profiling. Over the last decades, almost all the attention in medicinal chemistry has been directed to protein-ligand binding, and computational tools have been created with this target in mind. With novel discoveries of functional RNAs and their possible applications, RNAs have gained considerable attention as potential drug targets. However, the availability of bioinformatics tools for nucleic acids is limited. Here, we introduce fingeRNAt—a software tool for detecting non-covalent interactions formed in complexes of nucleic acids with ligands. The program detects nine types of interactions: (i) hydrogen and (ii) halogen bonds, (iii) cation-anion, (iv) pi-cation, (v) pi-anion, (vi) pi-stacking, (vii) inorganic ion-mediated, (viii) water-mediated, and (ix) lipophilic interactions. However, the scope of detected interactions can be easily expanded using a simple plugin system. In addition, detected interactions can be visualized using the associated PyMOL plugin, which facilitates the analysis of medium-throughput molecular complexes. Interactions are also encoded and stored as a bioinformatics-friendly Structural Interaction Fingerprint (SIFt)—a binary string where the respective bit in the fingerprint is set to 1 if a particular interaction is present and to 0 otherwise. This output format, in turn, enables high-throughput analysis of interaction data using data analysis techniques. We present applications of fingeRNAt-generated interaction fingerprints for visual and computational analysis of RNA-ligand complexes, including analysis of interactions formed in experimentally determined RNA-small molecule ligand complexes deposited in the Protein Data Bank. We propose interaction fingerprint-based similarity as an alternative measure to RMSD to recapitulate complexes with similar interactions but different folding. We present an application of interaction fingerprints for the clustering of molecular complexes. This approach can be used to group ligands that form similar binding networks and thus have similar biological properties. The fingeRNAt software is freely available athttps://github.com/n-szulc/fingeRNAt.
Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies
Authors: Lupo Cosimo , Spisak Natanael , Walczak Aleksandra M. , Mora Thierry
Published: June 2022

Affinity maturation is crucial for improving the binding affinity of antibodies to antigens. This process is mainly driven by point substitutions caused by somatic hypermutations of the immunoglobulin gene. It also includes deletions and insertions of genomic material known as indels. While the landscape of point substitutions has been extensively studied, a detailed statistical description of indels is still lacking. Here we present a probabilistic inference tool to learn the statistics of indels from repertoire sequencing data, which overcomes the pitfalls and biases of standard annotation methods. The model includes antibody-specific maturation ages to account for variable mutational loads in the repertoire. After validation on synthetic data, we applied our tool to a large dataset of human immunoglobulin heavy chains. The inferred model allows us to identify universal statistical features of indels in heavy chains. We report distinct insertion and deletion hotspots, and show that the distribution of lengths of indels follows a geometric distribution, which puts constraints on future mechanistic models of the hypermutation process.
Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex
Authors: Djahanschiri Bardya , Di Venanzio Gisela , Distel Jesus S. , Breisch Jennifer , Dieckmann Marius Alfred , Goesmann Alexander , Averhoff Beate , Göttig Stephan , Wilharm Gottfried , Feldman Mario F. , Ebersberger Ingo
Published: June 2022

Nosocomial pathogens of the Acinetobacter calcoaceticus-baumannii (ACB) complex are a cautionary example for the world-wide spread of multi- and pan-drug resistant bacteria. Aiding the urgent demand for novel therapeutic targets, comparative genomics studies between pathogens and their apathogenic relatives shed light on the genetic basis of human-pathogen interaction. Yet, existing studies are limited in taxonomic scope, sensing of the phylogenetic signal, and resolution by largely analyzing genes independent of their organization in functional gene clusters. Here, we explored more than 3,000 Acinetobacter genomes in a phylogenomic framework integrating orthology-based phylogenetic profiling and microsynteny conservation analyses. We delineate gene clusters in the type strain A. baumannii ATCC 19606 whose evolutionary conservation indicates a functional integration of the subsumed genes. These evolutionarily stable gene clusters (ESGCs) reveal metabolic pathways, transcriptional regulators residing next to their targets but also tie together sub-clusters with distinct functions to form higher-order functional modules. We shortlisted 150 ESGCs that either co-emerged with the pathogenic ACB clade or are preferentially found therein. They provide a high-resolution picture of genetic and functional changes that coincide with the manifestation of the pathogenic phenotype in the ACB clade. Key innovations are the remodeling of the regulatory-effector cascade connecting LuxR/LuxI quorum sensing via an intermediate messenger to biofilm formation, the extension of micronutrient scavenging systems, and the increase of metabolic flexibility by exploiting carbon sources that are provided by the human host. We could show experimentally that only members of the ACB clade use kynurenine as a sole carbon and energy source, a substance produced by humans to fine-tune the antimicrobial innate immune response. In summary, this study provides a rich and unbiased set of novel testable hypotheses on how pathogenic Acinetobacter interact with and ultimately infect their human host. It is a comprehensive resource for future research into novel therapeutic strategies.
The extant immunoglobulin superfamily, member 1 gene results from an ancestral gene duplication in eutherian mammals
Authors: Smith Courtney L. , Harrison Paul M. , Bernard Daniel J.
Published: June 2022

Immunoglobulin superfamily, member 1 (IGSF1) is a transmembrane glycoprotein with high expression in the mammalian pituitary gland. Mutations in the IGSF1 gene cause congenital central hypothyroidism in humans. The IGSF1 protein is co-translationally cleaved into N- and C-terminal domains (NTD and CTD), the latter of which is trafficked to the plasma membrane and appears to be the functional portion of the molecule. Though the IGSF1-NTD is retained in the endoplasmic reticulum and has no apparent function, it has a high degree of sequence identity with the IGSF1-CTD and is conserved across mammalian species. Based upon phylogenetic analyses, we propose that the ancestral IGSF1 gene encoded the IGSF1-CTD, which was duplicated and integrated immediately upstream of itself, yielding a larger protein encompassing the IGSF1-NTD and IGSF1-CTD. The selective pressures favoring the initial gene duplication and subsequent retention of a conserved IGSF1-NTD are unresolved.
Sonic irrigation for removal of calcium hydroxide in the apical root canal: A micro-CT and light-coupled tracking analysis
Authors: Moon Wonjoon , Chung Shin Hye , Chang Juhea
Published: June 2022

Objective

This study aimed to evaluate the efficacy of three sonic irrigation systems for removal of calcium hydroxide dressing from the apical root canal.

Materials and methods

A total of 96 single-rooted teeth in three categories of root canal curvatures (straight: 0–5°, moderate: 6–20°, and severe: > 20°) were allocated to four groups: conventional needle irrigation, EndoActivator, EQ-S, and Vibringe. The root canals were instrumented using Protaper NEXT and filled with calcium hydroxide. After removal of calcium hydroxide, the remaining volume of calcium hydroxide was measured by micro-CT analysis. Data were compared among root canal curvatures and irrigation systems using the Kruskal-Wallis test and Mann-Whitney test (p < .05). The oscillating range of each irrigation system was measured using light-coupled motion tracking.

Results

The volumes of calcium hydroxide remaining in the canals with severe curvature were significantly higher than in those of straight curvature (p < .05). In the canals of moderate or severe curvature, EQ-S showed the highest removal percentage, followed by EndoActivator, Vibringe, and needle irrigation (p < .05). Light-coupled tracking showed the largest oscillating range in EQ-S (p < .05).

Conclusions

Sonically activated irrigation systems with a flexible tip can be beneficial for calcium hydroxide intracanal dressing removal in the curved apical canals.
Doctoring from home: Physicians’ perspectives on the advantages of remote care delivery during the COVID-19 pandemic
Authors: DePuccio Matthew J. , Gaughan Alice A. , Shiu-Yee Karen , McAlearney Ann Scheck
Published: June 2022

Background

During the COVID-19 pandemic, stay-at-home orders as well as shortages of personal protective equipment forced primary care physicians (PCPs) to transition rapidly from in-person visits to telehealth. While telehealth expanded extensively in a short period of time, research about the consequences of the shift to remote care is lacking. The objective of this qualitative study was to examine how telehealth benefited PCPs and their patients during the COVID-19 pandemic.

Methods

From July to August 2020, semi-structured interviews were conducted with 20 PCPs associated with a single academic medical center to examine their perspectives about delivering care remotely during the COVID-19 pandemic. All interviews were recorded, transcribed verbatim, coded, and analyzed using deductive thematic analysis.

Results

PCPs identified several benefits of remote care delivery for both physicians and patients. They indicated that (1) patients were reassured that they could receive safe and timely care, (2) remote visits were convenient for patients, (3) patients were comfortable receiving care at home, and (4) video visits enhanced patient- and family-centered care during the COVID-19 pandemic. Participants also noted that (1) telehealth accommodated working from home, (2) physicians were equitably reimbursed for telehealth visits, and that (3) telehealth promoted physician work-life balance.

Conclusions

Our data provides preliminary evidence that PCPs and their patients had positive experiences with remote care during the early months of the COVID-19 pandemic. Physicians identified opportunities by which telehealth could enhance the delivery of patient-centered care by allowing them to see patients’ home environments and to engage family members and caregivers during telehealth visits. More research is needed to understand how to sustain these benefits beyond the global COVID-19 pandemic and ensure patients’ needs are met.
Analysis of the saliva metabolic signature in patients with primary Sjögren’s syndrome
Authors: Li Zhen , Mu Yue , Guo Chunlan , You Xin , Liu Xiaoyan , Li Qian , Sun Wei
Published: June 2022

Background

The saliva metabolome has been applied to explore disease biomarkers. In this study we characterized the metabolic profile of primary Sjögren’s syndrome (pSS) patients and explored metabolomic biomarkers.

Methods

This work presents a liquid chromatography-mass spectrometry-based metabolomic study of the saliva of 32 patients with pSS and 38 age- and sex-matched healthy adults. Potential pSS saliva metabolite biomarkers were explored using test group saliva samples (20 patients with pSS vs. 25 healthy adults) and were then verified by a cross-validation group (12 patients with pSS vs. 13 healthy adults).

Results

Metabolic pathways, including tryptophan metabolism, tyrosine metabolism, carbon fixation, and aspartate and asparagine metabolism, were found to be significantly regulated and related to inflammatory injury, neurological cognitive impairment and the immune response. Phenylalanyl-alanine was discovered to have good predictive ability for pSS, with an area under the curve (AUC) of 0.87 in the testing group (validation group: AUC = 0.75).

Conclusion

Our study shows that salivary metabolomics is a useful strategy for differential analysis and biomarker discovery in pSS.
The relationship between cannabis use and taurine: A MRS and metabolomics study
Authors: Newman Sharlene D. , Schnakenberg Martin Ashley M. , Raymond David , Cheng Hu , Wilson Landon , Barnes Stephen , O’Donnell Brian F.
Published: June 2022

Taurine is an essential amino acid. It has been shown to be neuroprotective including protecting against the neurotoxic effects of glutamate. The goal of the current study was to examine the relationship between CB use and taurine measured in brain using magnetic resonance spectroscopy (MRS), and peripherally from a urine sample. Two experiments are presented. The first is a reanalysis of published data that examined taurine and glutamate in the dorsal anterior cingulate of a CB user group and non-user group using MRS. The second experiment, in a separate CB user group, used metabolomics analysis to measure taurine levels in urine. Because body composition has been associated with the pharmacokinetics of cannabis and taurine levels, a moderation model was examined with body composition included as the covariate. The MRS study found taurine levels were correlated with glutamate in both groups and taurine was correlated with frequency of CB use in the CB user group. The moderation model demonstrated significant effects of CB use and BMI; the interaction was marginally significant with lower BMI individuals showing a positive relationship between CB use and taurine. A similar finding was observed for the urine analysis. Both CB use and weight, as well as the interaction were significant. In this case, individuals with higher weight showed an association between CB use and taurine levels. This study shows the feasibility and potential importance of examining the relationship between taurine and CB use as it may shed light on a mechanism that underlies the neuroprotective effects of CB.
Biochemical analyses demonstrate that Bt maize has no adverse effects on Eisenia fetida
Authors: Wu Fengci , Jiang Zhilei , Wang Baifeng , Yin Junqi , Wang Daming , Song Xinyuan
Published: June 2022

The potential effects of Bt (Bacillus thuringiensis) maize on non-target organisms should be evaluated before such maize is commercially planted. Earthworms play an indispensable role in the soil ecosystem; act as important bio-indicators of soil quality and environmental pollution. Therefore, earthworms are often used as the object to evaluate the non-target effect of Bt maize. To accelerate the commercialization of transgenic maize in China, a 90-day Eisenia fetida feeding experiment was conducted to evaluate the potential effects of Bt maize line, BT799—which was developed by China Agricultural University and contains the Cry1Ac gene—and its non-Bt conventional isoline—Zheng 58—on E. fetida. Our results showed that the Bt maize line had no significant effects on the growth, reproduction, or enzymatic activities of these earthworms. In summary, Bt maize had no toxic effects on E. fetida.
Psychometric properties of the Attitudes and Beliefs about Sleepy Driving Scale in Chinese drivers and its relationships with driving behaviours
Authors: Zhao Chunyue , Sun Long , Zhang Changlu
Published: June 2022

Purpose

The present study aimed to adapt the Attitudes and Beliefs about Sleepy Driving Scale (ABSDS) to a sample of Chinese drivers and to examine its reliability and validity.

Methods

Five hundred and twenty drivers aged 18 to 56 years old were asked to complete the ABSDS and a validated Chinese version of the Prosocial and Aggressive Driving Inventory.

Results

The results showed that the final Chinese version of the ABSDS contained 7 items with satisfactory reliability. Second, significant gender differences were found in attitude towards sleepy driving, with female drivers scoring higher than male drivers. Third, significant correlations between ABSDS score and prosocial and aggressive driving behaviours were found. More importantly, ABSDS score can significantly predict drivers’ prosocial driving behaviours. Moreover, ABSDS score can significantly predict drivers’ violation involvement and accident involvement.

Conclusion

The findings supported the psychometric properties of the Chinese version of the ABSDS and suggested that it can be used to assess drivers’ attitudes and beliefs about sleepy driving in China.