bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental investigation of environmental interference mitigation and blocked LEDs using a memory-artificial neural network in 3D indoor visible light positioning systems
Authors: Cao Zicai , Cheng Mengfan , Yang Qi , Tang Ming , Liu Deming , Deng Lei
Published: September 2021

Environmental interference and blocked light-emitting diodes (LEDs) often happen in the received signal strength (RSS)-based indoor visible light positioning (VLP) systems, while few solutions to these problems exist. In this paper, we proposed a novel deviation-correction algorithm named memory-artificial neural network (M-ANN) in the 3-dimensional (3D) indoor RSS-VLP system. By memorizing and utilizing the features of signal strength conversion between adjacent test moments, M-ANN can adapt to different test environments in the positioning process. Also, with the help of a designed genetic algorithm (GA) module, M-ANN can efficiently search and retrieve the missing data from an offline simulation database to prevent the VLP outage caused by the blocked LED. The experimental results in a test region of 0.6×0.6×0.8 m3 demonstrate that the proposed M-ANN can significantly mitigate the impact of environmental interference, and it can still maintain relatively high-precision positioning even in the case of blocked LEDs. The average positioning error of 1.04 cm, 2.89 cm, and 3.53 cm is experimentally achieved in the situation of environmental interference, one blocked LED and two blocked LEDs, respectively.
Mie-enhanced photothermal/thermo-optical nonlinearity and applications on all-optical switch and super-resolution imaging [Invited]
Authors: Tang Yu-Lung , Yen Te-Hsin , Nishida Kentaro , Takahara Junichi , Zhang Tianyue , Li Xiangping , Fujita Katsumasa , Chu Shi-Wei
Published: September 2021

Nonlinear optical interactions are of fundamental significance for advanced photonic applications, but usually the nonlinearity magnitude is insufficient. Here we review recent progresses to boost the optical nonlinearity of metal or semiconductor nanostructures via the combination of Mie resonance and coupled photothermal/thermo-optical effects. In plasmonic and silicon nanoparticles, the effective photothermal nonlinear index n2 is enhanced by 103 and 105 times over that of bulk, respectively. The large nonlinearities enable applications of not only all-optical switch, but also super-resolution imaging based on suppression of scattering, saturation (sub-linearity) and reverse saturation (super-linearity).
Dynamic control of photon lifetime for quantum random number generation
Authors: Okawachi Yoshitomo , Kim Bok Young , Zhao Yun , Ji Xingchen , Lipson Michal , Gaeta Alexander L.
Published: September 2021

In a passive cavity geometry, there exists a trade-off between resonant enhancement and response time, which is inherently limited by the cavity photon lifetime. We demonstrate frequency-selective, dynamic control of the photon lifetime using a silicon-nitride coupled-ring resonator. The photon lifetime is tuned by controlling an avoided mode crossing using thermo-optic tuning of the cavity resonance with integrated heaters. Using this effect, we achieve fast turn-on/off of a

χ

(
3
)

degenerate optical parametric oscillator (DOPO) and on-chip true random number generation. Our approach allows us to overcome the

Q

-limited generation rate of a single-ring-based DOPO and offers a path toward the development of a scalable integrated high-quality entropy source for modern cryptographic systems.
Light-induced rotation of dielectric microparticles around an optical nanofiber: publisher’s note
Authors: Tkachenko Georgiy , Toftul Ivan , Esporlas Cindy , Maimaiti Aili , Le Kien Fam , Truong Viet Giang , Chormaic Síle Nic
Published: September 2021

This publisher’s note reports a correction to the funding section of
Optica
7, 59 (2020)OPTIC82334-253610.1364/OPTICA.374441.
Bias-sensitive transparent single-element ultrasound transducers using hot-pressed PMN-PT
Authors: Sobhani Mohammad R. , Latham Katherine , Brown Jeremy , Zemp Roger J.
Published: September 2021

Here we introduce electrostrictive hot-pressed lead magnesium niobate (PMN) with low lead titanate (PT) doping as a candidate transparent transducer material. We fabricate transparent high-frequency single-element transducers and characterize their optical, electrical, and acoustic properties. PMN-PT may offer sensitivity advantages over other transducer materials such as lithium niobate owing to its high electromechanical efficiency and bias-voltage sensitivity. The transparency of the fabricated transducer was measured ∼67% at 532 nm wavelength with a maximum electromechanical coefficient of ∼0.68 with a DC bias level of 100 V. The photoacoustic impulse response showed a center frequency of ∼27.6 MHz with a −6 dB bandwidth of ∼61% at a DC bias level of 40 V. Results demonstrate that the new transparent transducers hold promise for future optical-ultrasonic and photoacoustic imaging applications.
Detail enhancement for infrared images based on Relativity of Gaussian-Adaptive Bilateral Filter
Authors: Feng Xiongwei , Pan Zhongliang
Published: September 2021

Detail enhancement is the key to the display of infrared image. For the infrared image detail enhancement algorithms, it is very important to present a good visual effect for people effectively. A novel algorithm for detail enhancement of infrared images is proposed in this paper. The method is based on the relativity of Gaussian-adaptive bilateral Filter. The algorithm consists of three steps. The first step is to divide the input image into the base layer and the detail layer by the relativity of Gaussian-adaptive bilateral filter. In the second step, the detail layer is multiplied by the proposed weight coefficient, and the base layer is processed by histogram projection. The third step is to combine the detail layer and the base layer processed in the second step and output it to the 8-bit domain display. Compare with other methods, the new algorithm reduces the running time greatly. The experimental results showed that the proposed algorithm improves the contrast of infrared images effectively.
Digitalisierung von Management-Reporting-Prozessen – Ein technologieorientiertes Reifegradmodell zum Einsatz in KMU
Authors: Stoffers Pascal , Karla Jürgen , Kaufmann Jens
Published: September 2021

Der Begriff der Digitalisierung umfasst eine große Bandbreite unterschiedlicher Themen und Aktivitäten. Zur gezielten Entwicklung von Unternehmen ist es daher erforderlich, die eigene Position und entsprechende Verbesserungspotenziale zu (er)kennen und eine erfolgreiche Prozess-Weiterentwicklung zu ermöglichen. Das Controlling eines Unternehmens nimmt als Informationslieferant und Bestandteil der Entscheidungsunterstützung in vielfältiger Hinsicht Einfluss auf bestehende und zu entwickelnde Geschäftsmodelle und ist von der Digitalisierung besonders betroffen, insbesondere hinsichtlich der Planungs- und Reporting-Prozesse.

Zur Unterstützung der Digitalisierung vornehmlich in kleinen und mittleren Unternehmen wird ein Reifegradmodell entwickelt, das sich der beschriebenen Thematik widmet. Eine umfangreiche Vorstudie zeigt, welche existierenden Reifegradmodelle im Bereich der Managementinformation und des Controllings existieren und inwiefern diese noch nicht für die Fragestellung und/oder Anwendung ausreichend sind. Basierend auf der Identifikation von aktuellen, relevanten technologischen Entwicklungen werden Reifegradausprägungen eines neuen Modells erstellt, die die unterschiedlichen Dimensionen der unternehmerischen Tätigkeit einbeziehen.

In diesem Beitrag wird das Modell zur Bestimmung des aktuellen Reifegrads von Unternehmen entwickelt und vorgestellt.
Memes: A motif analysis environment in R using tools from the MEME Suite
Authors: Nystrom Spencer L. , McKay Daniel J.
Published: September 2021

Identification of biopolymer motifs represents a key step in the analysis of biological sequences. The MEME Suite is a widely used toolkit for comprehensive analysis of biopolymer motifs; however, these tools are poorly integrated within popular analysis frameworks like the R/Bioconductor project, creating barriers to their use. Here we present memes, an R package that provides a seamless R interface to a selection of popular MEME Suite tools. memes provides a novel “data aware” interface to these tools, enabling rapid and complex discriminative motif analysis workflows. In addition to interfacing with popular MEME Suite tools, memes leverages existing R/Bioconductor data structures to store the multidimensional data returned by MEME Suite tools for rapid data access and manipulation. Finally, memes provides data visualization capabilities to facilitate communication of results. memes is available as a Bioconductor package at https://bioconductor.org/packages/memes, and the source code can be found at github.com/snystrom/memes.
Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in Down syndrome
Authors: De Toma Ilario , Sierra Cesar , Dierssen Mara
Published: September 2021

Trisomy of human chromosome 21 (HSA21) causes Down syndrome (DS). The trisomy does not simply result in the upregulation of HSA21--encoded genes but also leads to a genome-wide transcriptomic deregulation, which affect differently each tissue and cell type as a result of epigenetic mechanisms and protein-protein interactions.

We performed a meta-analysis integrating the differential expression (DE) analyses of all publicly available transcriptomic datasets, both in human and mouse, comparing trisomic and euploid transcriptomes from different sources. We integrated all these data in a “DS network”.

We found that genome wide deregulation as a consequence of trisomy 21 is not arbitrary, but involves deregulation of specific molecular cascades in which both HSA21 genes and HSA21 interactors are more consistently deregulated compared to other genes. In fact, gene deregulation happens in “clusters”, so that groups from 2 to 13 genes are found consistently deregulated. Most of these events of “co-deregulation” involve genes belonging to the same GO category, and genes associated with the same disease class. The most consistent changes are enriched in interferon related categories and neutrophil activation, reinforcing the concept that DS is an inflammatory disease. Our results also suggest that the impact of the trisomy might diverge in each tissue due to the different gene set deregulation, even though the triplicated genes are the same.

Our original method to integrate transcriptomic data confirmed not only the importance of known genes, such as SOD1, but also detected new ones that could be extremely useful for generating or confirming hypotheses and supporting new putative therapeutic candidates. We created “metaDEA” an R package that uses our method to integrate every kind of transcriptomic data and therefore could be used with other complex disorders, such as cancer. We also created a user-friendly web application to query Ensembl gene IDs and retrieve all the information of their differential expression across the datasets.
Hybrid computational modeling demonstrates the utility of simulating complex cellular networks in type 1 diabetes
Authors: Shi Zhenzhen , Li Yang , Jaberi-Douraki Majid
Published: September 2021

Persistent destruction of pancreatic β-cells in type 1 diabetes (T1D) results from multifaceted pancreatic cellular interactions in various phase progressions. Owing to the inherent heterogeneity of coupled nonlinear systems, computational modeling based on T1D etiology help achieve a systematic understanding of biological processes and T1D health outcomes. The main challenge is to design such a reliable framework to analyze the highly orchestrated biology of T1D based on the knowledge of cellular networks and biological parameters. We constructed a novel hybrid in-silico computational model to unravel T1D onset, progression, and prevention in a non-obese-diabetic mouse model. The computational approach that integrates mathematical modeling, agent-based modeling, and advanced statistical methods allows for modeling key biological parameters and time-dependent spatial networks of cell behaviors. By integrating interactions between multiple cell types, model results captured the individual-specific dynamics of T1D progression and were validated against experimental data for the number of infiltrating CD8+T-cells. Our simulation results uncovered the correlation between five auto-destructive mechanisms identifying a combination of potential therapeutic strategies: the average lifespan of cytotoxic CD8+T-cells in islets; the initial number of apoptotic β-cells; recruitment rate of dendritic-cells (DCs); binding sites on DCs for naïve CD8+T-cells; and time required for DCs movement. Results from therapy-directed simulations further suggest the efficacy of proposed therapeutic strategies depends upon the type and time of administering therapy interventions and the administered amount of therapeutic dose. Our findings show modeling immunogenicity that underlies autoimmune T1D and identifying autoantigens that serve as potential biomarkers are two pressing parameters to predict disease onset and progression.
A model of head direction and landmark coding in complex environments
Authors: Yan Yijia , Burgess Neil , Bicanski Andrej
Published: September 2021

Environmental information is required to stabilize estimates of head direction (HD) based on angular path integration. However, it is unclear how this happens in real-world (visually complex) environments. We present a computational model of how visual feedback can stabilize HD information in environments that contain multiple cues of varying stability and directional specificity. We show how combinations of feature-specific visual inputs can generate a stable unimodal landmark bearing signal, even in the presence of multiple cues and ambiguous directional specificity. This signal is associated with the retrosplenial HD signal (inherited from thalamic HD cells) and conveys feedback to the subcortical HD circuitry. The model predicts neurons with a unimodal encoding of the egocentric orientation of the array of landmarks, rather than any one particular landmark. The relationship between these abstract landmark bearing neurons and head direction cells is reminiscent of the relationship between place cells and grid cells. Their unimodal encoding is formed from visual inputs via a modified version of Oja’s Subspace Algorithm. The rule allows the landmark bearing signal to disconnect from directionally unstable or ephemeral cues, incorporate newly added stable cues, support orientation across many different environments (high memory capacity), and is consistent with recent empirical findings on bidirectional HD firing reported in the retrosplenial cortex. Our account of visual feedback for HD stabilization provides a novel perspective on neural mechanisms of spatial navigation within richer sensory environments, and makes experimentally testable predictions.
A lipoprotein allosterically activates the CwlD amidase during Clostridioides difficile spore formation
Authors: Alves Feliciano Carolina , Eckenroth Brian E. , Diaz Oscar R. , Doublié Sylvie , Shen Aimee
Published: September 2021

Spore-forming pathogens likeClostridioides difficiledepend on germination to initiate infection. During gemination, spores must degrade their cortex layer, which is a thick, protective layer of modified peptidoglycan. Cortex degradation depends on the presence of the spore-specific peptidoglycan modification, muramic-∂-lactam (MAL), which is specifically recognized by cortex lytic enzymes. InC.difficile, MAL production depends on the CwlD amidase and its binding partner, the GerS lipoprotein. To gain insight into how GerS regulates CwlD activity, we solved the crystal structure of the CwlD:GerS complex. In this structure, a GerS homodimer is bound to two CwlD monomers such that the CwlD active sites are exposed. Although CwlD structurally resembles amidase_3 family members, we found that CwlD does not bind Zn2+stably on its own, unlike previously characterized amidase_3 enzymes. Instead, GerS binding to CwlD promotes CwlD binding to Zn2+, which is required for its catalytic mechanism. Thus, in determining the first structure of an amidase bound to its regulator, we reveal stabilization of Zn2+co-factor binding as a novel mechanism for regulating bacterial amidase activity. Our results further suggest that allosteric regulation by binding partners may be a more widespread mode for regulating bacterial amidase activity than previously thought.
Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature
Authors: Achtman Mark , Van den Broeck Frederik , Cooper Kerry K. , Lemey Philippe , Parker Craig T. , Zhou Zhemin ,   the ATCC14028s Study Group
Published: September 2021

Salmonella enterica serovar Typhimurium strain ATCC14028s is commercially available from multiple national type culture collections, and has been widely used since 1960 for quality control of growth media and experiments on fitness (“laboratory evolution”). ATCC14028s has been implicated in multiple cross-contaminations in the laboratory, and has also caused multiple laboratory infections and one known attempt at bioterrorism. According to hierarchical clustering of 3002 core gene sequences, ATCC14028s belongs to HierCC cluster HC20_373 in which most internal branch lengths are only one to three SNPs long. Many natural Typhimurium isolates from humans, domesticated animals and the environment also belong to HC20_373, and their core genomes are almost indistinguishable from those of laboratory strains. These natural isolates have infected humans in Ireland and Taiwan for decades, and are common in the British Isles as well as the Americas. The isolation history of some of the natural isolates confirms the conclusion that they do not represent recent contamination by the laboratory strain, and 10% carry plasmids or bacteriophages which have been acquired in nature by HGT from unrelated bacteria. We propose that ATCC14028s has repeatedly escaped from the laboratory environment into nature via laboratory accidents or infections, but the escaped micro-lineages have only a limited life span. As a result, there is a genetic gap separating HC20_373 from its closest natural relatives due to a divergence between them in the late 19th century followed by repeated extinction events of escaped HC20_373.
RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics
Authors: Choe Donghui , Szubin Richard , Poudel Saugat , Sastry Anand , Song Yoseb , Lee Yongjae , Cho Suhyung , Palsson Bernhard , Cho Byung-Kwan
Published: September 2021

RNA sequencing techniques have enabled the systematic elucidation of gene expression (RNA-Seq), transcription start sites (differential RNA-Seq), transcript 3′ ends (Term-Seq), and post-transcriptional processes (ribosome profiling). The main challenge of transcriptomic studies is to remove ribosomal RNAs (rRNAs), which comprise more than 90% of the total RNA in a cell. Here, we report a low-cost and robust bacterial rRNA depletion method, RiboRid, based on the enzymatic degradation of rRNA by thermostable RNase H. This method implemented experimental considerations to minimize nonspecific degradation of mRNA and is capable of depleting pre-rRNAs that often comprise a large portion of RNA, even after rRNA depletion. We demonstrated the highly efficient removal of rRNA up to a removal efficiency of 99.99% for various transcriptome studies, including RNA-Seq, Term-Seq, and ribosome profiling, with a cost of approximately $10 per sample. This method is expected to be a robust method for large-scale high-throughput bacterial transcriptomic studies.
Grhl3 promotes retention of epidermal cells under endocytic stress to maintain epidermal architecture in zebrafish
Authors: Phatak Mandar , Kulkarni Shruti , Miles Lee B. , Anjum Nazma , Dworkin Sebastian , Sonawane Mahendra
Published: September 2021

Epithelia such as epidermis cover large surfaces and are crucial for survival. Maintenance of tissue homeostasis by balancing cell proliferation, cell size, and cell extrusion ensures epidermal integrity. Although the mechanisms of cell extrusion are better understood, how epithelial cells that round up under developmental or perturbed genetic conditions are reintegrated in the epithelium to maintain homeostasis remains unclear. Here, we performed live imaging in zebrafish embryos to show that epidermal cells that round up due to membrane homeostasis defects in the absence of goosepimples/myosinVb (myoVb) function, are reintegrated into the epithelium. Transcriptome analysis and genetic interaction studies suggest that the transcription factor Grainyhead-like 3 (Grhl3) induces the retention of rounded cells by regulating E-cadherin levels. Moreover, Grhl3 facilitates the survival of MyoVb deficient embryos by regulating cell adhesion, cell retention, and epidermal architecture. Our analyses have unraveled a mechanism of retention of rounded cells and its importance in epithelial homeostasis.
Relative risks of adverse events among older adults receiving opioids versus NSAIDs after hospital discharge: A nationwide cohort study
Authors: Herzig Shoshana J. , Anderson Timothy S. , Jung Yoojin , Ngo Long , Kim Dae H. , McCarthy Ellen P.
Published: September 2021

Background

Although analgesics are initiated on hospital discharge in millions of adults each year, studies quantifying the risks of opioids and nonsteroidal anti-inflammatory drugs (NSAIDs) among older adults during this transition are limited. We sought to determine the incidence and risk of post-discharge adverse events among older adults with an opioid claim in the week after hospital discharge, compared to those with NSAID claims only.

Methods and findings

We performed a retrospective cohort study using a national sample of Medicare beneficiaries age 65 and older, hospitalized in United States hospitals in 2016. We excluded beneficiaries admitted from or discharged to a facility. We derived a propensity score that included over 100 factors potentially related to the choice of analgesic, including demographics, diagnoses, surgeries, and medication coadministrations. Using 3:1 propensity matching, beneficiaries with an opioid claim in the week after hospital discharge (with or without NSAID claims) were matched to beneficiaries with an NSAID claim only. Primary outcomes included death, healthcare utilization (emergency department [ED] visits and rehospitalization), and a composite of known adverse effects of opioids or NSAIDs (fall/fracture, delirium, nausea/vomiting, complications of slowed colonic motility, acute renal failure, and gastritis/duodenitis) within 30 days of discharge. After propensity matching, there were 13,385 beneficiaries in the opioid cohort and 4,677 in the NSAID cohort (mean age: 74 years, 57% female). Beneficiaries receiving opioids had a higher incidence of death (1.8% versus 1.1%; relative risk [RR] 1.7 [1.3 to 2.3], p < 0.001, number needed to harm [NNH] 125), healthcare utilization (19.0% versus 17.4%; RR 1.1 [1.02 to 1.2], p = 0.02, NNH 59), and any potential adverse effect (25.2% versus 21.3%; RR 1.2 [1.1 to 1.3], p < 0.001, NNH 26), compared to those with an NSAID claim only. Specifically, they had higher relative risk of fall/fracture (4.5% versus 3.4%; RR 1.3 [1.1 to 1.6], p = 0.002), nausea/vomiting (9.2% versus 7.3%; RR 1.3 [1.1 to 1.4], p < 0.001), and slowed colonic motility (8.0% versus 6.2%; RR 1.3 [1.1 to 1.4], p < 0.001). Risks of delirium, acute renal failure, and gastritis/duodenitis did not differ between groups. The main limitation of our study is the observational nature of the data and possibility of residual confounding.

Conclusions

Older adults filling an opioid prescription in the week after hospital discharge were at higher risk for mortality and other post-discharge adverse outcomes compared to those filling an NSAID prescription only.
A dengue outbreak in a rural community in Northern Coastal Ecuador: An analysis using unmanned aerial vehicle mapping
Authors: Lee Gwenyth O. , Vasco Luis , Márquez Sully , Zuniga-Moya Julio C. , Van Engen Amanda , Uruchima Jessica , Ponce Patricio , Cevallos William , Trueba Gabriel , Trostle James , Berrocal Veronica J. , Morrison Amy C. , Cevallos Varsovia , Mena Carlos , Coloma Josefina , Eisenberg Joseph N. S.
Published: September 2021

Dengue is recognized as a major health issue in large urban tropical cities but is also observed in rural areas. In these environments, physical characteristics of the landscape and sociodemographic factors may influence vector populations at small geographic scales, while prior immunity to the four dengue virus serotypes affects incidence. In 2019, a rural northwestern Ecuadorian community, only accessible by river, experienced a dengue outbreak. The village is 2–3 hours by boat away from the nearest population center and comprises both Afro-Ecuadorian and Indigenous Chachi households. We used multiple data streams to examine spatial risk factors associated with this outbreak, combining maps collected with an unmanned aerial vehicle (UAV), an entomological survey, a community census, and active surveillance of febrile cases. We mapped visible water containers seen in UAV images and calculated both the green-red vegetation index (GRVI) and household proximity to public spaces like schools and meeting areas. To identify risk factors for symptomatic dengue infection, we used mixed-effect logistic regression models to account for the clustering of symptomatic cases within households. We identified 55 dengue cases (9.5% of the population) from 37 households. Cases peaked in June and continued through October. Rural spatial organization helped to explain disease risk. Afro-Ecuadorian (versus Indigenous) households experience more symptomatic dengue (OR = 3.0, 95%CI: 1.3, 6.9). This association was explained by differences in vegetation (measured by GRVI) near the household (OR: 11.3 95% 0.38, 38.0) and proximity to the football field (OR: 13.9, 95% 4.0, 48.4). The integration of UAV mapping with other data streams adds to our understanding of these dynamics.
Implementation of mass drug administration for neglected tropical diseases in Guinea during the COVID-19 pandemic
Authors: Sakho Fatoumata , Badila Christelly Flore , Dembele Benoit , Diaby Aissatou , Camara Abdoul Karim , Lamah Lamine , Reid Steven D. , Weng Angel , Fuller Brian B. , Sanchez Katherine A. , Kabore Achille , Zhang Yaobi , Weaver Angela
Published: September 2021

Background

Guinea reported its first case of COVID-19 on March 12, 2020. Soon thereafter, a national state of emergency was declared, all land borders were closed, schools were shut down, and public gatherings were limited. Many health activities, including field-based activities targeting neglected tropical diseases (NTDs), were paused. The World Health Organization (WHO) issued updated guidance on the resumption of NTD field-based activities on July 27, 2020. In response, the Guinea Ministry of Health (MoH) and its partners planned and resumed mass drug administration (MDA) in mid-August to September 2020 in 19 health districts.

Methodology/principal findings

A risk-benefit assessment was conducted to identify potential risks associated with the MDA in the COVID-19 context. Following this assessment, a risk mitigation plan with barrier measures was developed to guide MDA implementation. These measures included COVID-19 testing for all national staff leaving Conakry, mask wearing, social distancing of two meters, and hand washing/sanitizing. A checklist was developed and used to monitor compliance to risk mitigation measures. Data on adherence to risk mitigation measures were collected electronically during the MDA. A total of 120 checklists, representing 120 community drug distributor (CDD) teams (two CDDs per team) and 120 households, were completed. Results indicated that washing or disinfecting hands was practiced by 68.3% of CDD teams, compared to 45.0% among households. Face masks to cover the mouth and nose were worn by 79.2% of CDD teams, while this was low among households (23.3%). In 87.5% of households, participants did not touch the dose pole and in 88.3% of CDD teams, CDDs did not touch the hands of the participants while giving the drugs. A large majority of CDD teams (94.2%) and household members (94.2%) were willing to participate in the MDA despite the pandemic. The epidemiological coverage was ≥65% for lymphatic filariasis, onchocerciasis and soil-transmitted helminths in 10 out of 19 HDs and ≥75% for schistosomiasis for school-aged children in 7 out of 11 HDs.

Conclusions/significance

Guinea was one of the first countries in Africa to resume MDA activities during the COVID-19 pandemic without causing an observed increase of transmission. The development of a risk mitigation plan and a method to monitor adherence to barrier measures was critical to this unprecedented effort. The rapid incorporation of COVID-19 barrier measures and their acceptance by CDDs and household members demonstrated both the adaptability of the National NTD Program to respond to emerging issues and the commitment of the MoH to implement NTD programs.
Fine-scale movement patterns and habitat selection of little owls (Athene noctua) from two declining populations
Authors: Mayer Martin , Šálek Martin , Fox Anthony David , Juhl Lindhøj Frej , Jacobsen Lars Bo , Sunde Peter
Published: September 2021

Advances in bio-logging technology for wildlife monitoring have expanded our ability to study space use and behavior of many animal species at increasingly detailed scales. However, such data can be challenging to analyze due to autocorrelation of GPS positions. As a case study, we investigated spatiotemporal movements and habitat selection in the little owl (Athene noctua), a bird species that is declining in central Europe and verges on extinction in Denmark. We equipped 6 Danish food-supplemented little owls and 6 non-supplemented owls in the Czech Republic with high-resolution GPS loggers that recorded one position per minute. Nightly space use, measured as 95% kernel density estimates, of Danish male owls were on average 62 ha (± 64 SD, larger than any found in previous studies) compared to 2 ha (± 1) in females, and to 3 ± 1 ha (males) versus 3 ± 5 ha (females) in the Czech Republic. Foraging Danish male owls moved on average 4-fold further from their nest and at almost double the distance per hour than Czech males. To create availability data for the habitat selection analysis, we accounted for high spatiotemporal autocorrelation of the GPS data by simulating correlated random walks with the same autocorrelation structure as the actual little owl movement trajectories. We found that habitat selection was similar between Danish and Czech owls, with individuals selecting for short vegetation and areas with high structural diversity. Our limited sample size did not allow us to infer patterns on a population level, but nevertheless demonstrates how high-resolution GPS data can help to identify critical habitat requirements to better formulate conservation actions on a local scale.
Leadership styles and employee knowledge sharing: Exploring the mediating role of introjected motivation
Authors: Chaman Seemab , Zulfiqar Sehar , Shaheen Sadia , Saleem Sharjeel
Published: September 2021

Drawing on Social Exchange Theory and Self-Determination Theory, this study examines the impact of three leadership styles (ethical, transformational, and passive avoidant) on employee knowledge sharing. Further, this study explores the mediating effect of introjected motivation in the relationship between three leadership styles and employee knowledge sharing. Using time lag data this study employed a sample of 254 faculty members of public sector universities in Pakistan. Results supported the positive relationship between three styles of leadership and employee knowledge sharing. Moreover, our findings confirmed the mediating role of introjected motivation in the relationship between three leadership styles and employee knowledge sharing. Our study is unique, as it simultaneously examines how various styles of leadership predict introjected motivation and employee knowledge sharing. Implications along with limitations and future research directions are discussed.
Post-interval EEG activity is related to task-goals in temporal discrimination
Authors: Bueno Fernanda Dantas , Cravo André Mascioli
Published: September 2021

Studies investigating the neural mechanisms of time perception often measure brain activity while participants perform a temporal task. However, several of these studies are based exclusively on tasks in which time is relevant, making it hard to dissociate activity related to decisions about time from other task-related patterns. In the present study, human participants performed a temporal or color discrimination task of visual stimuli. Participants were informed which magnitude they would have to judge before or after presenting the two stimuli (S1 and S2) in different blocks. Our behavioral results showed, as expected, that performance was better when participants knew beforehand which magnitude they would judge. Electrophysiological data (EEG) was analysed using Linear Discriminant Contrasts (LDC) and a Representational Similarity Analysis (RSA) approach to investigate whether and when information about time and color was encoded. During the presentation of S1, we did not find consistent differences in EEG activity as a function of the task. On the other hand, during S2, we found that temporal and color information was encoded in a task-relevant manner. Taken together, our results suggest that task goals strongly modulate decision-related information in EEG activity.
Factors affecting duration of SARS-Cov-2 viral shedding in mildly symptomatic patients isolated in a community facility
Authors: Cheng Hui Mei , Zhao Xiahong , Lim Wei Shyann , Tan Beatrice Jia Min , Tey Hong Liang
Published: September 2021

Introduction

Mildly symptomatic cases of Covid-19 in previously-well individuals form the majority of infections and also serve as potent vectors of transmission. The factors affecting the duration of SARS-CoV-2 RNA viral shedding (DVS) in these patients remain largely unknown.

Objectives

To perform a systematic analysis of the clinical, radiologic, laboratory investigations in patients with few comorbidities infected with mild Covid-19 to identify factors associated with the DVS.

Methods

In this retrospective cohort study, patients with mild or asymptomatic Covid-19 were included. Baseline characteristics including age, nationality, comorbidities, concomitant medications, and type of isolation arrangement in the facility (single or in pairs) were collected. Clinical features and radiologic/haematologic findings were also collected. Taking day 28 as the cut-off, 187 patients who had a negative swab result up to day 28 (no prolonged DVS) were compared to 126 patients with a persistently positive result on or after day 28 (prolonged DVS).

Results

Of 964 consecutive patients included, 851 (88.3%) patients were symptomatic. 266 patients had a documented negative RT-PCR assay with a median DVS of 25 days (range: 13 to 96 days; interquartile range (IQR): 22 to 33 days). Patients isolated in pairs were associated with prolonged DVS (OR: 2.7; 95% CI: 1.7 to 4.5; p<0.0001) compared to those isolated individually. Among vital signs, only tachycardia was associated with prolonged DVS (OR: 2.6; 95% CI: 1.0 to 7.1; p = 0.03). Amongst investigations, only a raised CRP was associated with prolonged DVS (OR: 2.7; 95% CI: 1.1 to 6.8; p = 0.02).

Conclusions

In young, mildly symptomatic Covid-19 patients, prolonged DVS was associated with being isolated in pairs compared to individually. In situations where a negative RT-PCR test result is required, retesting in patients who were not isolated individually, or who had baseline tachycardia or a raised CRP, may be delayed to increase the yield of a negative result.
Computerized history-taking improves data quality for clinical decision-making—Comparison of EHR and computer-acquired history data in patients with chest pain
Authors: Zakim David , Brandberg Helge , El Amrani Sami , Hultgren Andreas , Stathakarou Natalia , Nifakos Sokratis , Kahan Thomas , Spaak Jonas , Koch Sabine , Sundberg Carl Johan
Published: September 2021

Patients’ medical histories are the salient dataset for diagnosis. Prior work shows consistently, however, that medical history-taking by physicians generally is incomplete and not accurate. Such findings suggest that methods to improve the completeness and accuracy of medical history data could have clinical value. We address this issue with expert system software to enable automated history-taking by computers interacting directly with patients, i.e. computerized history-taking (CHT). Here we compare the completeness and accuracy of medical history data collected and recorded by physicians in electronic health records (EHR) with data collected by CHT for patients presenting to an emergency room with acute chest pain. Physician history-taking and CHT occurred at the same ED visit for all patients. CHT almost always preceded examination by a physician. Data fields analyzed were relevant to the differential diagnosis of chest pain and comprised information obtainable only by interviewing patients. Measures of data quality were completeness and consistency of negative and positive findings in EHR as compared with CHT datasets. Data significant for the differential of chest pain was missing randomly in all EHRs across all data items analyzed so that the dimensionality of EHR data was limited. CHT files were near complete for all data elements reviewed. Separate from the incompleteness of EHR data, there were frequent factual inconsistencies between EHR and CHT data across all data elements. EHR data did not contain representations of symptoms that were consistent with those reported by patients during CHT.

Trial registration: This study is registered at https://www.clinicaltrials.gov (unique identifier: NCT03439449).
Photosynthetic performance of rocket (Eruca sativa. Mill.) grown under different regimes of light intensity, quality, and photoperiod
Authors: Elmardy Naif Ali , Yousef Ahmed F. , Lin Kui , Zhang Xiwen , Ali Muhammad Moaaz , Lamlom Sobhi F. , Kalaji Hazem M. , Kowalczyk Katarzyna , Xu Yong
Published: September 2021

In recent years, much effort has been devoted to understanding the response of plants to various light sources, largely due to advances in industry light-emitting diodes (LEDs). In this study, the effect of different light modes on rocket (Eruca sativa. Mill.) photosynthetic performance and other physiological traits was evaluated using an orthogonal design based on a combination between light intensity, quality, and photoperiod factors. Some morphological and biochemical parameters and photosynthetic efficiency of the plants were analyzed. Plants grew in a closed chamber where three light intensities (160, 190, and 220 μmol m-2 s-1) provided by LEDs with a combination of different ratios of red, green, and blue (R:G:B- 7:0:3, 3:0:7, and 5:2:3) and three different photoperiods (light/dark -10/14 h, 12/12 h, and 14/10 h) were used and compared with white fluorescent light (control). This experimental setup allowed us to study the effect of 9 light modes (LM) compared to white light. The analyzes performed showed that the highest levels of chlorophyll a, chlorophyll b, and carotenoids occurred under LM4, LM3, and LM1, respectively. Chlorophyll a fluorescence measurement showed that the best effective quantum yield of PSII photochemistry Y(II), non-photochemical quenching (NPQ), photochemical quenching coefficient (qP), and electron transport ratio (ETR) were obtained under LM2. The data showed that the application of R7:G0:B3 light mode with a shorter photoperiod than 14/10 h (light/dark), regardless of the light intensity used, resulted in a significant increase in growth as well as higher photosynthetic capacity of rocket plants. Since, a clear correlation between the studied traits under the applied light modes was not found, more features should be studied in future experiments.
A workflow for the relative quantification of multiple fish species from oceanic water samples using environmental DNA (eDNA) to support large-scale fishery surveys
Authors: Ramón-Laca Ana , Wells Abigail , Park Linda
Published: September 2021

While the number of published marine studies using environmental DNA (eDNA) has increased substantially in recent years, marine fish surveys are still scarce. To examine the potential for eDNA to support marine fisheries monitoring surveys, we optimized an eDNA isolation method, developed a multispecies assay and tested it on eDNA samples collected along the Pacific coast of the United States. Four commercial DNA extraction kits that exploit the capability of the nucleic acids binding a solid phase (two using a silica matrix and two magnetic beads) as well an organic separation method were tested. A species-specific multiplex qPCR assay was developed and tested to simultaneously target Pacific hake (Merluccius productus), Pacific lamprey (Entosphenus tridentatus) and eulachon (Thaleichthys pacificus). The specificity of the assay was tested in silico, in vitro and in natura. Environmental DNA isolation using phenol:chloroform:isoamyl purification with a phase lock was optimized and yielded the highest amount of total and target DNA and was used to extract 46 marine water samples for the detection of the three species of interest. The multiplex qPCR assay used in the quantification process was also optimized to provide convenience and accuracy. Pacific hake was present in 44% of the eDNA samples while the other two species were absent. Here, we present a complete workflow for the simultaneous detection and quantification of multiple marine fish species using eDNA. This workflow supports large-scale at-sea sampling efforts with preservation at ambient temperatures and has demonstrated DNA extraction efficiency and reliability. The multiplex qPCR assay is shown to be sensitive and specific for the purposes of simultaneously monitoring the relative abundance of multiple targeted fish species.
Bacterial community structure of early-stage biofilms is dictated by temporal succession rather than substrate types in the southern coastal seawater of India
Authors: Sushmitha T. J. , Rajeev Meora , Sriyutha Murthy P. , Ganesh S. , Toleti Subba Rao , Karutha Pandian Shunmugiah
Published: September 2021

Bacterial communities colonized on submerged substrata are recognized as a key factor in the formation of complex biofouling phenomenon in the marine environment. Despite massive maritime activities and a large industrial sector in the nearshore of the Laccadive Sea, studies describing pioneer bacterial colonizers and community succession during the early-stage biofilm are scarce. We investigated the biofilm-forming bacterial community succession on three substrata viz. stainless steel, high-density polyethylene, and titanium over 15 days of immersion in the seawater intake area of a power plant, located in the southern coastal region of India. The bacterial community composition of biofilms and peripheral seawater were analyzed by Illumina MiSeq sequenced 16S rRNA gene amplicons. The obtained metataxonomic results indicated a profound influence of temporal succession over substrate type on the early-stage biofilm-forming microbiota. Bacterial communities showed vivid temporal dynamics that involved variations in abundant bacterial groups. The proportion of dominant phyla viz.Proteobacteriadecreased over biofilm succession days, whileBacteroidetesincreased, suggesting their role as initial and late colonizers, respectively. A rapid fluctuation in the proportion of two bacterial orders viz.AlteromonadalesandVibrionaleswere observed throughout the successional stages. LEfSe analysis identified specific bacterial groups at all stages of biofilm development, whereas no substrata type-specific groups were observed. Furthermore, the results of PCoA and UPGMA hierarchical clustering demonstrated that the biofilm-forming community varied considerably from the planktonic community. PhylumProteobacteriapreponderated the biofilm-forming community, while theBacteroidetes,Cyanobacteria, andActinobacteriadominated the planktonic community. Overall, our results refute the common assumption that substrate material has a decisive impact on biofilm formation; rather, it portrayed that the temporal succession overshadowed the influence of the substrate material. Our findings provide a scientific understanding of the factors shaping initial biofilm development in the marine environment and will help in designing efficient site-specific anti-biofouling strategies.
Experimental and mathematical insights on the interactions between poliovirus and a defective interfering genome
Authors: Shirogane Yuta , Rousseau Elsa , Voznica Jakub , Xiao Yinghong , Su Weiheng , Catching Adam , Whitfield Zachary J. , Rouzine Igor M. , Bianco Simone , Andino Raul
Published: September 2021

During replication, RNA viruses accumulate genome alterations, such as mutations and deletions. The interactions between individual variants can determine the fitness of the virus population and, thus, the outcome of infection. To investigate the effects of defective interfering genomes (DI) on wild-type (WT) poliovirus replication, we developed an ordinary differential equation model, which enables exploring the parameter space of the WT and DI competition. We also experimentally examined virus and DI replication kinetics during co-infection, and used these data to infer model parameters. Our model identifies, and our experimental measurements confirm, that the efficiencies of DI genome replication and encapsidation are two most critical parameters determining the outcome of WT replication. However, an equilibrium can be established which enables WT to replicate, albeit to reduced levels.
Comparison of transcriptional profiles of Treponema pallidum during experimental infection of rabbits and in vitro culture: Highly similar, yet different
Authors: De Lay Bridget D. , Cameron Todd A. , De Lay Nicholas R. , Norris Steven J. , Edmondson Diane G.
Published: September 2021

Treponema pallidum ssp. pallidum, the causative agent of syphilis, can now be cultured continuously in vitro utilizing a tissue culture system, and the multiplication rates are similar to those obtained in experimental infection of rabbits. In this study, the RNA transcript profiles of the T. pallidum Nichols during in vitro culture and rabbit infection were compared to examine whether gene expression patterns differed in these two environments. To this end, RNA preparations were converted to cDNA and subjected to RNA-seq using high throughput Illumina sequencing; reverse transcriptase quantitative PCR was also performed on selected genes for validation of results. The transcript profiles in the in vivo and in vitro environments were remarkably similar, exhibiting a high degree of concordance overall. However, transcript levels of 94 genes (9%) out of the 1,063 predicted genes in the T. pallidum genome were significantly different during rabbit infection versus in vitro culture, varying by up to 8-fold in the two environments. Genes that exhibited significantly higher transcript levels during rabbit infection included those encoding multiple ribosomal proteins, several prominent membrane proteins, glycolysis-associated enzymes, replication initiator DnaA, rubredoxin, thioredoxin, two putative regulatory proteins, and proteins associated with solute transport. In vitro cultured T. pallidum had higher transcript levels of DNA repair proteins, cofactor synthesis enzymes, and several hypothetical proteins. The overall concordance of the transcript profiles may indicate that these environments are highly similar in terms of their effects on T. pallidum physiology and growth, and may also reflect a relatively low level of transcriptional regulation in this reduced genome organism.