bluuebunny/crossref_metadata_2025 huggingface dataset:
On the Same Page? What Users Benefit from a Desktop View on Mobile Devices
Authors: Fink Lior , Papismedov Daniele
Published: May 2022

The presentation of online content is routinely adapted to the smaller screens of mobile devices by implementing an information architecture (IA) that hierarchically restructures the information being presented to users, in conjunction with layout and size adaptations. Despite the understanding that users of mobile devices are likely to experience lower usability and higher load without such adaptations, a recent trend is to offer these users the ability to opt out of content adaptation and revert to a desktop view. In two experiments in which users are asked to make an online hotel reservation, we show that a desktop view may benefit mobile users by increasing the accuracy of their decisions. From a practical standpoint, the findings suggest that the increasing availability of the option to switch to a desktop view on mobile devices is a positive evolution that should be encouraged, particularly in situations in which users may be highly sensitive to the quality of their decisions. This study addresses the prices that mobile users pay for the convenience of content adaptation, demonstrating that an adaptation technique designed to benefit mobile users may paradoxically impair their ability to make accurate decisions.
Zinc Chloride Ameliorates the Adverse Effects of Silver Nitrates Compared to Silver Nanoparticle in Post-Natal Model of Toxicity.
Authors: Fehaid Alaa , T. Elazab Sara , G. Elhadidy Mona , El Nashar Eman Mohamad , Abdalla Asim Mohammed , Al-Khater Khulood Mohammed , Alghamdi Mansour Abdallah , M. Elalfy Mahmoud
Published: May 2022

Silver nanoparticles have been shown to increase postnatal toxicity in breastfeeding female rats, with negative consequences for their offspring. We wanted to investigate more about the differences in toxicity between silver nitrates and silver nanoparticles, as well as the impact of zinc chloride treatment on the silver nitrates induced toxicity on female albino rats. For 21 days, breastfeeding female albino rats and their puppies were exposed to silver nitrates at dosages of 0, 50, and 100 mg/kg. The results demonstrated that silver nitrates were more hazardous than nano-silver, as evidenced by higher free radical release, increased MDA levels, and decreased antioxidant enzyme levels (SOD). In addition, the silver ions-treated group had higher levels of liver enzymes and creatinine. Zinc chloride treatment, in particular, had a protective impact and mitigated the negative effects of silver nitrates, as seen by the restoration of baseline levels of liver enzyme, creatinine, and antioxidant enzyme. In addition, zinc chloride therapies reduced the harmful effects of silver nitrates on liver and kidney tissues but not lung tissue.
The service-learning methodology as a facilitating tool for
education for sustainable development (ESD)
Authors: González-Sánchez Rocío , Medina-Salgado Sonia , Torrejón-Ramos María , González-Mendes Soraya , Alonso-Muñoz Sara
Published: May 2022

INTRODUCTION. An educational environment that facilitates
student engagement and critical thinking is essential for the
success of Education for Sustainable Development (ESD) according to
the 17 Sustainable Development Goals (SDGs). This requires that the
tools favour learning from a new approach, which involves a social
component and takes into account the students’ soft skills.
METHODOLOGY. The Service-Learning (S-L) for educational proposal
establishes fruitful relationships with society, in which both
parties benefit. This paper proposes the application of the S-L
methodology to achieve a successful implementation of ESD. RESULTS.
In line with Goal 11 (SDGs) ‘Sustainable Cities and Communities’,
this proposal aims for students to contribute to making cities more
inclusive, safe, resilient and sustainable. To this end, a S-L
activity was carried out at the Rey Juan Carlos University with the
participation of 140 students of the subject “Tourist Transport”.
DISCUSSION. This work demonstrates the usefulness of the
Service-Learning methodology in the transmission of values
associated with environmental, social and economic sustainability.
In the activity, the students provide a service of transferring
values to society while improving their communication and teamwork
skills.
Design of a linear field-of-view oblique imaging system with a low
distortion
Authors: Xu Chen , Gong Chen , Wang Yongtian , Song Weitao
Published: May 2022

For conventional ultra-wide-angle or oblique cameras, it is difficult to fully correct
the

f
−

tan

θ

distortion without the scarification
of the edge image performance. In this paper, we propose a linear
field-of-view (FOV) oblique imaging system by varying the entrance
pupil size over the FOV with freeform mirrors, and thus the
diffraction limit around the edge field can be improved. An off-axis
reflective system with conic surfaces has been selected as the initial
system, and a point-by-point surface design method is then applied on
the primary mirror to increase the entrance pupil size for edge fields
in the FOV direction. All surfaces for the system converted to
freeform during the optimization process, and the FOV of the final
design can achieve

+

35

∘

to

+

65

∘

, with a distortion less than 1.1%. It
is possible to achieve a wide-linear FOV over 130° with a low
distortion by the integration of two oblique systems and a central
imaging channel.
Arduino-based, low-cost imaging incubator for extended live cell imaging
Authors: Rossi Vincent M. , Davidson Katherine C. , Moore Lauren E.
Published: May 2022

To image live cells for prolonged periods of time, an Arduino-based, low-cost imaging incubator was constructed. The imaging incubator keeps cells viable by controlling for temperature and

C
O

2

to maintain physiological conditions for cells during imaging. All devices and parts employed in the build were typical maker-type components to minimize the cost of the imaging incubator. The imaging incubator allows for real-time imaging of live cells exposed to any desired perturbation or stimulus. As a proof of the system’s functionality, cells were imaged over 24 h while remaining viable in the imaging incubator.
Undergraduate research–why start so early?: editorial
Authors: Bennett Gisele
Published: May 2022

Editor-in-Chief Gisele Bennett highlights the importance of early
exposure to research.
Light transmission mechanisms in a SMF-capillary fiber-SMF structure and its application to bi-directional liquid level measurement
Authors: Huang Ziyi , Liu Dejun , Wu Qiang , Tian Ke , Zhao Haoyu , Shen Changyu , Farrell Gerald , Semenova Yuliya , Wang Pengfei
Published: May 2022

Capillary fiber (CF) has been extensively investigated in a singlemode fiber (SMF)-CF-SMF (SCS) sensing structure since multiple light guiding mechanisms can be easily excited by simply tuning the air core diameter (cladding diameter) and length of the CF. Understanding the light guiding principles in an SCS structure is essential for improved implementation of a CF based fiber sensor. In this work, light guiding principles in a relatively large air core diameter (≥ 20 µm) and long length of CF (> 1 mm) are investigated theoretically and experimentally. It is found that both multimode interference (MMI) and Anti-Resonant Reflecting Optical Waveguide (ARROW) light guiding mechanisms are excited in the SCS structure in the transmission configuration. However, MMI dips are not observed in the spectrum for the air core diameters of CF smaller than 50 µm in the experiment due to large transmission loss in small air core CFs. Further experimental results demonstrate that a CF with a bigger air core diameter shows a higher sensitivity to curvature, and the highest sensitivity of -16.15 nm/m-1 is achieved when an CF-100 was used. In addition, a SMF-CF-20-CF-30-SMF (SCCS) structure is proposed for high sensitivity bi-direction liquid level measurement for the first time, to the best of our knowledge. Two types of ARROW dips (Dip-20 and Dip-30) are simultaneously excited in transmission, hence both liquid level and liquid flow direction can be detected by tracing the dip strength changes of Dip-20 and Dip-30, respectively.
Dissipative rogue waves generated by multi-soliton explosions in an ultrafast fiber laser
Authors: Luo Min , Zhang Ze-Xian , Liu Meng , Luo Ai-Ping , Xu Wen-Cheng , Luo Zhi-Chao
Published: May 2022

Derived from oceanography, nowadays the investigation of rogue waves (RWs) has been widely spread in various fields, particularly in nonlinear optics. Passively mode-locked fiber laser has been regarded as one of the excellent platforms to investigate the dissipative RWs (DRWs). Here, we report the observation of DRW generation induced by single and multi-soliton explosions in a passively mode-locked fiber laser. It was demonstrated that through the gain-mediated soliton interactions, one soliton could erupt because of the explosion of another soliton in the laser cavity. Meanwhile, the high-amplitude waves, which fulfill the DRWs criteria, could be detected in the multi-soliton explosion states. The DRWs were identified by characterizing the peak intensity statistics of the time-stretched soliton profiles. Particularly, it was found that the ratio between the highest recorded amplitudes and significant wave heights (SWHs) of DRWs induced by multi-soliton explosions is higher than that by single-soliton explosion case. Our findings will further contribute to the understanding of the physical mechanisms of DRWs in the soliton explosion regime.
Simplified numerical modeling for Fano interference-induced asymmetric light reflectance effect using equivalent medium theory
Authors: Chen Binghuan , Lu Weifang , Li Penggang , Yang Xu , Li Jinchai , Huang Kai , Kang Junyong , Zhang Rong
Published: May 2022

Localized surface plasmons exhibit promising capabilities in optoelectronic devices. In most cases, the metal nanoparticle arrays are located on interfaces or inside optical cavities. Fano interferences have been observed and explained via the interference between the waves generated by the localized surface plasmon and dielectric interfaces. Conventionally, these Fano interferences are modeled using the modified Fresnel equation. However, certain issues persist in the fundamental physics or in the numerical calculation process. Here, we adopt the equivalent medium theory (Maxwell-Garnett theory, MGT) to calculate and elucidate Fano interferences in different structures, in the region comprising nanoparticle arrays and dielectrics equivalent to a homogeneous layer of media via the mean field theory. Using this method, the Fano interference can be modeled by mixing different materials, i.e., metals and dielectrics in these cases. Furthermore, a multiple-layered equivalent medium theory is proposed to significantly improve the scalability of this simplified numerical method. In other words, this method can be easily extended to nanoparticles with different shapes, sizes, and materials; in addition, it exhibits robust practicability. Compared with the modified Fresnel equation and finite-difference time-domain methods, this MGT-based method can effectively minimize the calculation process, which is beneficial to the prospective application of plasmon photonics.
High-efficiency topological pumping with discrete supersymmetry transformations
Authors: Viedma David , Queraltó Gerard , Mompart Jordi , Ahufinger Verònica
Published: May 2022

Making use of the isospectrality of Supersymmetry transformations, we propose a general and high-fidelity method to prepare gapped topological modes in discrete systems from a single-site excitation. The method consists of adiabatically connecting two superpartner structures, deforming the input state into the desired mode. We demonstrate the method by pumping topological states of the Su-Schrieffer-Heeger model in an optical waveguide array, where the adiabatic deformation is performed along the propagation direction. We obtain fidelities above F = 0.99 for a wide range of coupling strengths when pumping edge and interface states.
Direct detection of virus-like particles using color images of plasmonic nanostructures
Authors: Li Yi-Ru , Lee Kuang-Li , Chen Kuan-Ming , Lu Yun Cheng , Wu Pin Chieh , Chen Sy-Hann , Lee Jiun-Haw , Wei Pei-Kuen
Published: May 2022

We propose a measurement method for sensitive and label-free detections of virus-like particles (VLPs) using color images of nanoplasmonic sensing chips. The nanoplasmonic chip consists of 5×5 gold nanoslit arrays and the gold surface is modified with specific antibodies for spike protein. The resonant wavelength of the 430-nm-period gold nanoslit arrays underwater environment is about 570 nm which falls between the green and red bands of the color CCD. The captured VLPs by the specific antibodies shift the plasmonic resonance of the gold nanoslits. It results in an increased brightness of green pixels and decreased brightness of red pixels. The image contrast signals of (green - red) / (red + green) show good linearity with the surface particle density. The experimental tests show the image contrast method can detect 100-nm polystyrene particles with a surface density smaller than 2 particles/µm2. We demonstrate the application for direct detection of SARS-CoV-2 VLPs using a simple scanner platform. A detection limit smaller than 1 pg/mL with a detection time less than 30 minutes can be achieved.
Simulation framework for fringe projection profilometry using ray tracing and light transport coefficient measurement
Authors: Zhao Huijie , Liu Chenghao , Jiang Hongzhi , Li Xudong
Published: May 2022

Fringe projection profilometry is widely used in optical metrology, and fringe analysis is important to improve measurement accuracy. However, the fringe images captured by cameras are influenced by many factors, an analytical study of which, to characterize the imaging process, is difficult to perform. We propose a method to accurately simulate the real imaging system in the virtual environment using ray tracing algorithm. The light transport coefficients of the cameras are measured to simulate defocus instead of using Gaussian function. Experimental results show that the proposed method can simulate a physical system in the virtual environment more accurately than the Gaussian function at large defocus condition.
Covariations between pupil diameter and supplementary eye field activity suggest a role in cognitive effort implementation
Authors: Claron Julien , Royo Julie , Arcizet Fabrice , Deffieux Thomas , Tanter Mickael , Pouget Pierre
Published: May 2022

In both human and nonhuman primates (NHP), the medial prefrontal region, defined as the supplementary eye field (SEF), can indirectly influence behavior selection through modulation of the primary selection process in the oculomotor structures. To perform this oculomotor control, SEF integrates multiple cognitive signals such as attention, memory, reward, and error. As changes in pupil responses can assess these cognitive efforts, a better understanding of the precise dynamics by which pupil diameter and medial prefrontal cortex activity interact requires thorough investigations before, during, and after changes in pupil diameter. We tested whether SEF activity is related to pupil dynamics during a mixed pro/antisaccade oculomotor task in 2 macaque monkeys. We used functional ultrasound (fUS) imaging to examine temporal changes in brain activity at the 0.1-s time scale and 0.1-mm spatial resolution concerning behavioral performance and pupil dynamics. By combining the pupil signals and real-time imaging of NHP during cognitive tasks, we were able to infer localized cerebral blood volume (CBV) responses within a restricted part of the dorsomedial prefrontal cortex, referred to as the SEF, an area in which antisaccade preparation activity is also recorded. Inversely, SEF neurovascular activity measured by fUS imaging was found to be a robust predictor of specific variations in pupil diameter over short and long-time scales. Furthermore, we directly manipulated pupil diameter and CBV in the SEF using reward modulations. These results bring a novel understanding of the physiological links between pupil and SEF, but it also raises questions about the role of anterior cingulate cortex (ACC), as CBV variations in the ACC seems to be negligible compared to CBV variations in the SEF.
Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers
Authors: Montaño-Gutierrez Luis Fernando , Moreno Nahuel Manzanaro , Farquhar Iseabail L. , Huo Yu , Bandiera Lucia , Swain Peter S.
Published: May 2022

Responding to change is a fundamental property of life, making time-series data invaluable in biology. For microbes, plate readers are a popular, convenient means to measure growth and also gene expression using fluorescent reporters. Nevertheless, the difficulties of analysing the resulting data can be a bottleneck, particularly when combining measurements from different wells and plates. Here we present omniplate, a Python module that corrects and normalises plate-reader data, estimates growth rates and fluorescence per cell as functions of time, calculates errors, exports in different formats, and enables meta-analysis of multiple plates. The software corrects for autofluorescence, the optical density’s non-linear dependence on the number of cells, and the effects of the media. We use omniplate to measure the Monod relationship for the growth of budding yeast in raffinose, showing that raffinose is a convenient carbon source for controlling growth rates. Using fluorescent tagging, we study yeast’s glucose transport. Our results are consistent with the regulation of the hexose transporter (HXT) genes being approximately bipartite: the medium and high affinity transporters are predominately regulated by both the high affinity glucose sensor Snf3 and the kinase complex SNF1 via the repressors Mth1, Mig1, and Mig2; the low affinity transporters are predominately regulated by the low affinity sensor Rgt2 via the co-repressor Std1. We thus demonstrate that omniplate is a powerful tool for exploiting the advantages offered by time-series data in revealing biological regulation.
Investigating the structural changes due to adenosine methylation of the Kaposi’s sarcoma-associated herpes virus ORF50 transcript
Authors: Röder Konstantin , Barker Amy M. , Whitehouse Adrian , Pasquali Samuela
Published: May 2022

Kaposi’s sarcoma-associated herpes virus (KSHV) is a human oncovirus. KSHV relies on manipulating the host cell N6-methyl adenosine (m6A) RNA modification pathway to enhance virus replication. Methylation within a RNA stem loop of the open reading frame 50 (ORF50) increases transcript stability via the recruitment of the m6A reader, SND1. In this contribution we explore the energy landscapes of the unmethylated and methylated RNA stem loops of ORF50 to investigate the effect of methylation on the structure of the stem loop. We observe a significant shift upon methylation between an open and closed configuration of the top of the stem loop. In the unmethylated stem loop the closed configuration is much lower in energy, and, as a result, exhibits higher occupancy.
Evidence of pandemic fatigue associated with stricter tiered COVID-19 restrictions
Authors: Delussu Federico , Tizzoni Michele , Gauvin Laetitia
Published: May 2022

Despite the availability of effective vaccines against SARS-CoV-2, non-pharmaceutical interventions remain an important part of the effort to reduce viral circulation caused by emerging variants with the capability of evading vaccine-induced immunity. With the aim of striking a balance between effective mitigation and long-term sustainability, several governments worldwide have adopted systems of tiered interventions, of increasing stringency, that are calibrated according to periodic risk assessments. A key challenge remains in quantifying temporal changes in adherence to interventions, which can decrease over time due to pandemic fatigue, under such kind of multilevel strategies. Here, we examine whether there was a reduction in adherence to tiered restrictions that were imposed in Italy from November 2020 through May 2021, and in particular we assess whether temporal trends in adherence depended on the intensity of the restrictions adopted. We analyzed daily changes in movements and in residential time, combining mobility data with the restriction tier enforced in the Italian regions. Through mixed-effects regression models, we identified a general trend of reduction in adherence and an additional effect of faster waning associated with the most stringent tier. We estimated both effects being of the same order of magnitude, suggesting that adherence decreased twice as fast during the strictest tier as in the least stringent one. Our results provide a quantitative measure of behavioral responses to tiered interventions—a metric of pandemic fatigue—that can be integrated into mathematical models to evaluate future epidemic scenarios.
Profile of the in silico secretome of the palm dieback pathogen, Fusarium oxysporum f. sp. albedinis, a fungus that puts natural oases at risk
Authors: Rafiqi Maryam , Jelonek Lukas , Diouf Aliou Moussa , Mbaye AbdouLahat , Rep Martijn , Diarra Alhousseine
Published: May 2022

Understanding biotic changes that occur alongside climate change constitute a research priority of global significance. Here, we address a plant pathogen that poses a serious threat to life on natural oases, where climate change is already taking a toll and severely impacting human subsistence. Fusarium oxysporum f. sp. albedinis is a pathogen that causes dieback disease on date palms, a tree that provides several critical ecosystem services in natural oases; and consequently, of major importance in this vulnerable habitat. Here, we assess the current state of global pathogen spread, we annotate the genome of a sequenced pathogen strain isolated from the native range and we analyse its in silico secretome. The palm dieback pathogen secretes a large arsenal of effector candidates including a variety of toxins, a distinguished profile of secreted in xylem proteins (SIX) as well as an expanded protein family with an N-terminal conserved motif [SG]PC[KR]P that could be involved in interactions with host membranes. Using agrobiodiversity as a strategy to decrease pathogen infectivity, while providing short term resilient solutions, seems to be widely overcome by the pathogen. Hence, the urgent need for future mechanistic research on the palm dieback disease and a better understanding of pathogen genetic diversity.
Plasma MicroRNAs as noninvasive diagnostic biomarkers in patients with Brugada syndrome
Authors: Ikeuchi Yoshihiro , Ochi Hidenori , Motoda Chikaaki , Tokuyama Takehito , Okubo Yousaku , Okamura Sho , Miyauchi Syunsuke , Miyamoto Shogo , Uotani Yukimi , Onohara Yuko , Nakashima Mika , Akiyama Rie , Tahara Hidetoshi , Chayama Kazuaki , Kihara Yasuki , Nakano Yukiko
Published: May 2022

Background

Brugada syndrome (BrS) can be diagnosed by a type 1 BrS tracing in a 12-lead electrocardiogram (ECG). However, there are daily variations in the ECGs of BrS patients, which presents a challenge when diagnosing BrS. Although many susceptibility genes have been identified, the SCN5A gene is reportedly the main causative gene of BrS. However, most patients do not have an evidence of genetic predisposition to develop BrS. In addition, the diagnosis and risk stratification for ventricular fibrillation (VF) in patients with BrS presents some problems. Meanwhile, circulating micro RNAs (miRNAs) have drawn increased attention as potential biomarkers of various diseases. We hypothesize that circulating miRNAs may be potential diagnostic biomarkers for BrS.

Methods

We enrolled 70 Japanese BrS patients and 34 controls for the screening cohort. A total of 2,555 miRNA sequences were detected using the 3D-Gene miRNAs labeling kit and 3D-Gene Human miRNAs Oligo Chip. We compared the expression of the miRNAs between the BrS patients and the controls. We validated whether the miRNA were significantly up- or downregulated in the screening cohort using RT-PCR. We also enrolled 72 Japanese BrS patients and 56 controls to replicate these miRNAs.

Results

Eight miRNAs (hsa-miR-223-3p, hsa-miR-22-3p, hsa-miR-221-3p, hsa-miR-4485-5p, hsa-miR-550a-5p, hsa-miR-423-3p, hsa-miR-23a-3p, and hsa-miR-30d-5p) were downregulated, and one miRNA (hsa-miR-873-3p) was upregulated by more than 3-fold in BrS patients. The multivariate logistic regression analysis determined that hsa-miR-423-3p, hsa-miR-223-3p, and hsa-miR-23a-3p were independently associated with BrS (P < 0.0001). The AUC based on cross validation was 0.871 with a sensitivity and specificity of 83.5% and 81.1%, respectively.

Conclusions

The plasma miRNAs are potential noninvasive biomarkers of BrS, and the constructed logistic model was useful for discriminating BrS.
“I wanna live and not think about the future” what place for advance care planning for people living with severe multiple sclerosis and their families? A qualitative study
Authors: Koffman Jonathan , Penfold Clarissa , Cottrell Laura , Farsides Bobbie , Evans Catherine J. , Burman Rachel , Nicholas Richard , Ashford Stephen , Silber Eli
Published: May 2022

Background

Little is known about how people with multiple sclerosis (MS) and their families comprehend advance care planning (ACP) and its relevance in their lives.

Aim

To explore under what situations, with whom, how, and why do people with MS and their families engage in ACP.

Methods

We conducted a qualitative study comprising interviews with people living with MS and their families followed by an ethical discussion group with five health professionals representing specialties working with people affected by MS and their families. Twenty-seven people with MS and 17 family members were interviewed between June 2019 and March 2020. Interviews and the ethical discussion group were audio-recorded and transcribed verbatim. Data were analysed using the framework approach.

Results

Participants’ narratives focused on three major themes: (i) planning for an uncertain future; (ii) perceived obstacles to engaging in ACP that included uncertainty concerning MS disease progression, negative previous experiences of ACP discussions and prioritising symptom management over future planning; (iii) Preferences for engagement in ACP included a trusting relationship with a health professional and that information then be shared across services. Health professionals’ accounts from the ethical discussion group departed from viewing ACP as a formal document to that of an ongoing process of seeking preferences and values. They voiced similar concerns to people with MS about uncertainty and when to initiate ACP-related discussions. Some shared concerns of their lack of confidence when having these discussions.

Conclusion

These findings support the need for a whole system strategic approach where information about the potential benefits of ACP in all its forms can be shared with people with MS. Moreover, they highlight the need for health professionals to be skilled and trained in engaging in ACP discussions and where information is contemporaneously and seamlessly shared across services.
Cross-reactive antibodies targeting surface-exposed non-structural protein 1 (NS1) of dengue virus-infected cells recognize epitopes on the spaghetti loop of the β-ladder domain
Authors: Kraivong Romchat , Traewachiwiphak Somchoke , Nilchan Napon , Tangthawornchaikul Nattaya , Pornmun Nuntaya , Poraha Ranyikar , Sriruksa Kanokwan , Limpitikul Wannee , Avirutnan Panisadee , Malasit Prida , Puttikhunt Chunya
Published: May 2022

Non-structural protein 1 (NS1) is a glycoprotein component of dengue virus (DENV) that is essential for viral replication, infection and immune evasion. Immunization with NS1 has been shown to elicit antibody-mediated immune responses which protect mice against DENV infections. Here, we obtained peripheral blood mononuclear cells from human subjects with secondary dengue infections, which were used to construct a dengue immune phage library displaying single-chain variable fragments. Phage selective for DENV NS1 were obtained by biopanning. Twenty-one monoclonal antibodies (mAbs) against DENV NS1 were generated from the selected phage and characterized in detail. We found most anti-NS1 mAbs used IGHV1 heavy chain antibody genes. The mAbs were classified into strongly and weakly-reactive groups based on their binding to NS1 expressed in dengue virus 2 (DENV2)-infected cells. Antibody binding experiments with recombinant NS1 proteins revealed that the mAbs recognize conformational epitopes on the β-ladder domain (amino acid residues 178–273) of DENV NS1. Epitope mapping studies on alanine-substituted NS1 proteins identified distinct but overlapping epitopes. Protruding amino acids distributed around the spaghetti loop are required for the binding of the strongly-reactive mAbs, whereas the recognition residues of the weakly-reactive mAbs are likely to be located in inaccessible sites facing toward the cell membrane. This information could guide the design of an NS1 epitope-based vaccine that targets cross-reactive conserved epitopes on cell surface-associated DENV NS1.
Factors influencing the pigment composition and dynamics of photoautotrophic picoplankton in shallow eutrophic lakes
Authors: Tamm Marju , Nõges Tiina , Nõges Peeter , Panksep Kristel , Zingel Priit , Agasild Helen , Freiberg Rene , Hunt Triin , Tõnno Ilmar
Published: May 2022

Photoautotrophic picoplankton (0.2–2 μm) can be a major contributor to primary production and play a significant part in the ecosystem carbon flow. However, the understanding about the dynamics of both eukaryotic and prokaryotic components of picoplankton in shallow eutrophic freshwater environments is still poor. Very few studies in these ecosystems reveal the taxonomic composition of picoeukaryotes. The main objective of this study was to investigate the seasonal dynamics of phototrophic picoplankton with the emphasis on the eukaryote community composition in a large shallow, eutrophic lake of the northern temperate zone (Lake Võrtsjärv). Phytoplankton pigments were employed to determine the taxonomic composition of photoautotrophic picoplankton. We found out that photoautotrophic picoplankton constitutes an important part of the phytoplankton community in Lake Võrtsjärv and its contribution can be highly variable (from ~9.3% to ~39%) in different years. The eukaryotic photoautotrophic picoplankton was dominated by diatoms followed by chrysophytes and other minor groups. Picoeukaryotes were prevailing in low-light conditions and low temperatures as their predominance in the picoplankton community was tightly linked to the presence or absence of ice cover. Ice cover strongly suppressed the growth of picocyanobacteria. Total phosphorus, turbidity and metazooplankton abundance had a clear relationship with photoautotrophic picoplankton chlorophyll a.
The involvement of CYP1A2 in biodegradation of dioxins in pigs
Authors: Swigonska Sylwia , Molcan Tomasz , Nynca Anna , Ciereszko Renata E.
Published: May 2022

2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is one of the most harmful chemicals showing resistance to biodegradation. The majority of TCDD effects is mediated by the aryl hydrocarbon receptor (AhR) pathway. TCDD binding to AhR results in the activation of cytochrome P450 enzymes (CYP1A1, CYP1A2, CYP1B1) involved in dioxin biodegradation. Thegoalof the study was to explore thepotentialroleofCYP1A2in themetabolismof TCDD. We investigated a molecular structure of CYP1A2 and the binding selectivity and affinity between the pig CYP1A2 and: 1/ DiCDD or TCDD (dioxins differing in toxicity and biodegradability) or 2/ their selected metabolites. pCYP1A2 demonstrated higher affinity towards DiCDD and TCDD than other pCYP1 enzymes. All dioxin-pCYP1A2 complexes were found to be stabilized by hydrophobic interactions. The calculated distances between the heme oxygen and the dioxin carbon nearest to the oxygen, reflecting the hydroxylating potential of CYP1A2, were higher than in other pCYP1 enzymes. The distances between the heme iron and the nearest dioxin carbon exceeded 5 Å, a distance sufficient to allow the metabolites to leave the active site. However, the molecular dynamics simulations revealed that two access channels of CYP1A2 were closed upon binding the majority of the examined dioxins. Moreover, the binding of dioxin metabolites did not promote opening of channel S–an exit for hydroxylated products. It appears that the undesired changes in the behavior of access channels prevail over the hydroxylating potential of CYP1A2 towards TCDD and the favorable distances, ultimately trapping the metabolites at the enzyme’s active site.
Solving pickup and drop-off problem using hybrid pointer networks with deep reinforcement learning
Authors: Alharbi Majed G. , Stohy Ahmed , Elhenawy Mohammed , Masoud Mahmoud , Khalifa Hamiden Abd El-Wahed
Published: May 2022

In this study, we propose a general method for tackling the Pickup and Drop-off Problem (PDP) using Hybrid Pointer Networks (HPNs) and Deep Reinforcement Learning (DRL). Our aim is to reduce the overall tour length traveled by an agent while remaining within the truck’s capacity restrictions and adhering to the node-to-node relationship. In such instances, the agent does not allow any drop-off points to be serviced if the truck is empty; conversely, if the vehicle is full, the agent does not allow any products to be picked up from pickup points. In our approach, this challenge is solved using machine learning-based models. Using HPNs as our primary model allows us to gain insight and tackle more complicated node interactions, which simplified our objective to obtaining state-of-art outcomes. Our experimental results demonstrate the effectiveness of the proposed neural network, as we achieve the state-of-art results for this problem as compared with the existing models. We deal with two types of demand patterns in a single type commodity problem. In the first pattern, all demands are assumed to sum up to zero (i.e., we have an equal number of backup and drop-off items). In the second pattern, we have an unequal number of backup and drop-off items, which is close to practical application, such as bike sharing system rebalancing. Our data, models, and code are publicly available at Solving Pickup and Dropoff Problem Using Hybrid Pointer Networks with Deep Reinforcement Learning.
High prevalence of an alpha variant lineage with a premature stop codon in ORF7a in Iraq, winter 2020–2021
Authors: Al-Rashedi Nihad A. M. , Alburkat Hussein , Hadi Abas O. , Munahi Murad G. , Jasim Ali , Hameed Alaa , Oda Basel Saber , Lilo Kareem Moamin , AlObaidi Laith A. H. , Vapalahti Olli , Sironen Tarja , Smura Teemu
Published: May 2022

Since the first reported case of coronavirus disease 2019 (COVID-19) in China, SARS-CoV-2 has been spreading worldwide. Genomic surveillance of SARS-CoV-2 has had a critical role in tracking the emergence, introduction, and spread of new variants, which may affect transmissibility, pathogenicity, and escape from infection or vaccine-induced immunity. As anticipated, the rapid increase in COVID-19 infections in Iraq in February 2021 is due to the introduction of variants of concern during the second wave of the COVID-19 pandemic. To understand the molecular epidemiology of SARS-CoV-2 during the second wave in Iraq (2021), we sequenced 76 complete SARS-CoV-2 genomes using NGS technology and identified genomic mutations and proportions of circulating variants among these. Also, we performed an in silico study to predict the effect of the truncation of NS7a protein (ORF7a) on its function. We detected nine different lineages of SARS-CoV-2. The B.1.1.7 lineage was predominant (80.20%) from February to May 2021, while only one B.1.351 strain was detected. Interestingly, the phylogenetic analysis showed that multiple strains of the B.1.1.7 lineage clustered closely with those from European countries. A notable frequency (43.33%) of stop codon mutation (NS7a Q62stop) was detected among the B.1.1.7 lineage sequences. In silico analysis of NS7a with Q62stop found that this stop codon had no considerable effect on the function of NS7a. This work provides molecular epidemiological insights into the spread variants of SARS-CoV-2 in Iraq, which are most likely imported from Europe.
Leveraging large multi-center cohorts of Alzheimer disease endophenotypes to understand the role of Klotho heterozygosity on disease risk
Authors: Ali Muhammad , Sung Yun Ju , Wang Fengxian , Fernández Maria V. , Morris John C. , Fagan Anne M. , Blennow Kaj , Zetterberg Henrik , Heslegrave Amanda , Johansson Per M. , Svensson Johan , Nellgård Bengt , Lleó Alberto , Alcolea Daniel , Clarimon Jordi , Rami Lorena , Molinuevo José Luis , Suárez-Calvet Marc , Morenas-Rodríguez Estrella , Kleinberger Gernot , Haass Christian , Ewers Michael , Levin Johannes , Farlow Martin R. , Perrin Richard J. ,   on behalf of the Alzheimer’s Disease Neuroimaging Initiative (ADNI),   on behalf of the Dominantly Inherited Alzheimer Network (DIAN), Cruchaga Carlos
Published: May 2022

Two genetic variants in strong linkage disequilibrium (rs9536314 and rs9527025) in the Klotho (KL) gene, encoding a transmembrane protein, implicated in longevity and associated with brain resilience during normal aging, were recently shown to be associated with Alzheimer disease (AD) risk in cognitively normal participants who are APOE ε4 carriers. Specifically, the participants heterozygous for this variant (KL-SVHET+) showed lower risk of developing AD. Furthermore, a neuroprotective effect of KL-VSHET+ has been suggested against amyloid burden for cognitively normal participants, potentially mediated via the regulation of redox pathways. However, inconsistent associations and a smaller sample size of existing studies pose significant hurdles in drawing definitive conclusions. Here, we performed a well-powered association analysis between KL-VSHET+ and five different AD endophenotypes; brain amyloidosis measured by positron emission tomography (PET) scans (n = 5,541) or cerebrospinal fluid Aβ42 levels (CSF; n = 5,093), as well as biomarkers associated with tau pathology: the CSF Tau (n = 5,127), phosphorylated Tau (pTau181; n = 4,778) and inflammation: CSF soluble triggering receptor expressed on myeloid cells 2 (sTREM2; n = 2,123) levels. Our results found nominally significant associations of KL-VSHET+ status with biomarkers for brain amyloidosis (e.g., CSF Aβ positivity; odds ratio [OR] = 0.67 [95% CI, 0.55–0.78], β = 0.72, p = 0.007) and tau pathology (e.g., biomarker positivity for CSF Tau; OR = 0.39 [95% CI, 0.19–0.77], β = -0.94, p = 0.007, and pTau; OR = 0.50 [95% CI, 0.27–0.96], β = -0.68, p = 0.04) in cognitively normal participants, 60–80 years old, who are APOE e4-carriers. Our work supports previous findings, suggesting that the KL-VSHET+ on an APOE ε4 genotype background may modulate Aβ and tau pathology, thereby lowering the intensity of neurodegeneration and incidence of cognitive decline in older controls susceptible to AD.
Correlation between relative afferent pupillary defect and visual field defects on Humphrey automated perimetry: A cross-sectional clinical trial
Authors: Witthayaweerasak Juthamat , Lertjittham Pemika , Aui-aree Nipat
Published: May 2022

Purpose

To evaluate the correlations between relative afferent pupillary defect (RAPD) magnitude, assessed using the clinical plus scale and neutral density filters, and visual field parameters in patients with unilateral or asymmetrical bilateral optic neuropathy or retinopathy.

Methods

Fifty-two patients with RAPD, graded by the swinging flashlight test and neutral density filters, were analyzed in this cross-sectional trial. The RAPD clinical plus scale was divided into grade 1+, initial weak constriction; grade 2+, initial stall then dilatation; grade 3+, immediate dilatation; and grade 4+, fixed amaurotic pupil. Patients with positive RAPD underwent a visual field examination with Humphrey automated perimetry that included visual field index (VFI), mean deviation (MD), and pattern standard deviation (PSD). Spearman’s rank correlation coefficients and linear regression were used to analyze the association between RAPD grades and visual field parameters.

Results

RAPD clinical plus grades were correlated with interocular VFI (r = 0.55, P < 0.001) and MD (r = 0.48, P = 0.004) differences. Average interocular VFI differences were estimated as follows: 16.75 × RAPD plus grade– 7.53. RAPD, graded by neutral density filters, was correlated with VFI (r = 0.59, P < 0.001), MD (r = 0.54, P < 0.001), and PSD (r = 0.34, P = 0.01).

Conclusions

The RAPD plus scale and neutral density filter grading systems were associated with quantitative visual field defect parameters, with VFI showing the strongest association. RAPD clinical grading could substitute more sophisticated central visual field evaluation methods as a low-cost, low-tech, and widely available approach.
A feasibility study to test a novel approach to dietary weight loss with a focus on assisting informed decision making in food selection
Authors: Lee Mindy H. , Applegate Catherine C. , Shaffer Annabelle L. , Emamaddin Abrar , Erdman John W. , Nakamura Manabu T.
Published: May 2022

Obesity is a significant contributor to the development of chronic diseases, some of which can be prevented or reversed by weight loss. However, dietary weight loss programs have shortcomings in the success rate, magnitude, or sustainability of weight loss. The Individualized Diet Improvement Program’s (iDip) objective was to test the feasibility of a novel approach that helps individuals self-select a sustainable diet for weight loss and maintenance instead of providing weight loss products or rigid diet instructions to follow. The iDip study consisted of 22 dietary improvement sessions over 12 months with six months of follow-up. Daily weights were collected, and a chart summarizing progress was provided weekly. Six 24-hour dietary records were collected, and dietary feedback was provided in the form of a protein-fiber plot, in which protein/energy and fiber/energy of foods were plotted two-dimensionally together with a target box specific to weight loss or maintenance. An exit survey was conducted at 12 months. Twelve (nine female, 46.3±3.1 years (mean±SE)) of the initial 14 participants (BMI>28 kg/m2) completed all sessions. Mean percent weight loss (n = 12) at six and 12 months was -4.9%±1.1 (p = 0.001) and -5.4%±1.7 (p = 0.007), respectively. Weight loss varied among individuals at 12 months; top and bottom halves (n = 6 each) achieved -9.7%±1.7 (p = 0.0008) and -1.0%±1.4 weight loss, respectively. The 24-hour records showed a significant increase in protein density from baseline to final (4.1g/100kcal±0.3 vs. 5.7g/100kcal±0.5; p = 0.008). Although mean fiber density showed no significant change from the first month (1.3g/100kcal±0.1), the top half had significantly higher fiber/energy intake than the bottom half group. The survey suggested that all participants valued the program and its self-guided diet approach. In conclusion, half of the participants successfully lost >5% and maintained the lost weight for 12 months without strict diet instructions, showing the feasibility of the informed decision-making approach.
Did you even see that? visual sensory processing of single stimuli under different locomotor loads
Authors: Reiser Julian Elias , Arnau Stefan , Rinkenauer Gerhard , Wascher Edmund
Published: May 2022

Modern living and working environments are more and more interspersed with the concurrent execution of locomotion and sensory processing, most often in the visual domain. Many job profiles involve the presentation of visual information while walking, for example in warehouse logistics work, where a worker has to manage walking to the correct aisle to pick up a package while being presented with visual information over data-glasses concerning the next order. Similar use-cases can be found in manufacturing jobs, for example in car montage assembly lines where next steps are presented via augmented reality headsets while walking at a slow pace. Considering the overall scarcity of cognitive resources available to be deployed to either the cognitive or motor processes, task performance decrements were found when increasing load in either domain. Interestingly, the walking motion also had beneficial effects on peripheral contrast detection and the inhibition of visual stream information. Taking these findings into account, we conducted a study that comprised the detection of single visual targets (Landolt Cs) within a broad range of the visual field (-40° to +40° visual angle) while either standing, walking, or walking with concurrent perturbations. We used questionnaire (NASA-TLX), behavioral (response times and accuracy), and neurophysiological data (ERPs and ERSPs) to quantify the effects of cognitive-motor interference. The study was conducted in a Gait Real-time Analysis Interactive Laboratory (GRAIL), using a 180° projection screen and a swayable and tiltable dual-belt treadmill. Questionnaire and behavioral measures showed common patterns. We found increasing subjective physical workload and behavioral decrements with increasing stimulus eccentricity and motor complexity. Electrophysiological results also indicated decrements in stimulus processing with higher stimulus eccentricity and movement complexity (P3, Theta), but highlighted a beneficial role when walking without perturbations and processing more peripheral stimuli regarding earlier sensory components (N1pc/N2pc, N2). These findings suggest that walking without impediments can enhance the visual processing of peripheral information and therefore help with perceiving non-foveal sensory content. Also, our results could help with re-evaluating previous findings in the context of cognitive-motor interference, as increased motor complexity might not always impede cognitive processing and performance.
Breast cancer incidence and predictions (Monastir, Tunisia: 2002–2030): A registry-based study
Authors: Zemni Imen , Kacem Meriem , Dhouib Wafa , Bennasrallah Cyrine , Hadhri Rim , Abroug Hela , Ben Fredj Manel , Mokni Moncef , Bouanene Ines , Belguith Asma Sriha
Published: May 2022

Introduction

Breast cancer is a major public health problem worldwide. It is the leading cause of cancer deaths in females. In developing countries like Tunisia, the frequency of this cancer is still growing. The aim of this study was to determine the crude and standardized incidence rates, trends and predictions until 2030 of breast cancer incidence rates in a Tunisian governorate.

Methods

This is a descriptive study including all female patients diagnosed with breast cancer in Monastir between 2002 and 2013. The data were collected from the cancer register of the center. Tumors were coded according to the 10th version of international classification of disease (ICD-10). Trends and predictions until 2030 were calculated using Poisson linear regression.

Results

A total of 1028 cases of female breast cancer were recorded. The median age of patients was 49 years (IQR: 41–59 years) with a minimum of 16 years and a maximum of 93 years. The age-standardized incidence rate (ASR) was of 39.12 per 100000 inhabitants. It increased significantly between 2002 and 2013 with APC of 8.4% (95% CI: 4.9; 11.9). Prediction until 2030 showed that ASR would reach 108.77 (95% CI: 57.13–209.10) per 100000 inhabitants.

Conclusion

The incidence and the chronological trends of breast cancer highlighted that this disease is of a serious concern in Tunisia. Strengthening preventive measures is a primary step to restrain its burden.