bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating the generation interval from the incidence rate, the optimal quarantine duration and the efficiency of fast switching periodic protocols for COVID-19
Authors: Lippiello Eugenio , Petrillo Giuseppe , de Arcangelis Lucilla 
Published: March 2022

AbstractThe transmissibility of an infectious disease is usually quantified in terms of the reproduction number $$R_t$$

R
t

representing, at a given time, the average number of secondary cases caused by an infected individual. Recent studies have enlightened the central role played by w(z), the distribution of generation times z, namely the time between successive infections in a transmission chain. In standard approaches this quantity is usually substituted by the distribution of serial intervals, which is obtained by contact tracing after measuring the time between onset of symptoms in successive cases. Unfortunately, this substitution can cause important biases in the estimate of $$R_t$$

R
t

. Here we present a novel method which allows us to simultaneously obtain the optimal functional form of w(z) together with the daily evolution of $$R_t$$

R
t

, over the course of an epidemic. The method uses, as unique information, the daily series of incidence rate and thus overcomes biases present in standard approaches. We apply our method to one year of data from COVID-19 officially reported cases in the 21 Italian regions, since the first confirmed case on February 2020. We find that w(z) has mean value $${\overline{z}} \simeq 6$$

z
¯

≃
6

days with a standard deviation $$\sigma \simeq 1$$

σ
≃
1

day, for all Italian regions, and these values are stable even if one considers only the first 10 days of data recording. This indicates that an estimate of the most relevant transmission parameters can be already available in the early stage of a pandemic. We use this information to obtain the optimal quarantine duration and to demonstrate that, in the case of COVID-19, post-lockdown mitigation policies, such as fast periodic switching and/or alternating quarantine, can be very efficient.
Prevalence, intensity and endemicity of intestinal schistosomiasis and soil-transmitted helminthiasis and its associated factors among school-aged children in Southern Ethiopia
Authors: Zerdo Zerihun , Bastiaens Hilde , Anthierens Sibyl , Massebo Fekadu , Masne Matewos , Biresaw Gelila , Shewangizaw Misgun , Tunje Abayneh , Chisha Yilma , Yohannes Tsegaye , Van Geertruyden Jean-Pierre 
Published: March 2022

AbstractPreventive chemotherapy (PC), the main strategy recommended by the World Health Organization to eliminate soil-transmitted helminthiasis (STH) and schistosomiasis (SCH), should be strengthened through identification of the remaining SCH transmission foci and evaluating its impact to get a lesson. This study was aimed to assess the prevalence of STH/SCH infections, the intensity of infections, and factors associated with STH infection among school-aged children (SAC) in Uba Debretsehay and Dara Mallo districts (previously not known to be endemic for SCH) in southern Ethiopia, October to December 2019. Structured interview questionnaire was used to collect household data, anthropometric measurements were taken and stool samples collected from 2079 children were diagnosed using the Kato-Katz technique. Generalize mixed-effects logistic regression models were used to assess the association of STH infections with potential predictors. A P-value less than 0.05 was considered statistically significant. The prevalence ofSchistosoma mansoniin the Dara Mallo district was 34.3% (95%CI 30.9–37.9%). Light, moderate, and heavyS. mansoniinfections were 15.2%, 10.9%, and 8.2% respectively. The overall prevalence of any STH infection was 33.2% with a 95% confidence interval (CI) of 31.1–35.3%. The intensity of infections was light (20.9%, 11.3% & 5.3%), moderate (1.1%, 0.1% & 0.4%) and heavy (0.3%, 0% & 0%) for hookworm, whipworm and roundworms respectively. The overall moderate-to-heavy intensity of infection among the total diagnosed children was 2% (41/2079). STH infection was higher among male SAC with Adjusted Odds Ratio (AOR) of 1.7 (95%CI 1.4–2.1); occupation of the household head other than farmer or housewife (AOR = 0.5; 95%CI 0.3–0.8), middle [AOR = 1.1; 95%CI 1.0–1.3] or high [AOR = 0.7; 95%CI 0.5–0.9] socioeconomic status. Dara Mallo district was moderate endemic forS. mansoni; and it needs sub-district level mapping and initiating a deworming campaign. Both districts remained moderate endemic for STH. Evidence-based strategies supplementing existing interventions with the main focus of the identified factors is important to realize the set targets.
Global gene expression responses of Atlantic salmon skin to Moritella viscosa
Authors: Eslamloo Khalil , Kumar Surendra , Xue Xi , Parrish Kathleen S. , Purcell Sara L. , Fast Mark D. , Rise Matthew L. 
Published: March 2022

AbstractMoritella viscosa is a Gram-negative pathogen that causes large, chronic ulcers, known as winter-ulcer disease, in the skin of several fish species including Atlantic salmon. We used a bath challenge approach to profile the transcriptome responses of M. viscosa-infected Atlantic salmon skin at the lesion (Mv-At) and away from the lesion (Mv-Aw) sites. M. viscosa infection was confirmed through RNA-based qPCR assays. RNA-Seq identified 5212 and 2911 transcripts differentially expressed in the Mv-At compared to no-infection control and Mv-Aw groups, respectively. Also, there were 563 differentially expressed transcripts when comparing the Mv-Aw to control samples. Our results suggest that M. viscosa caused massive and strong, but largely infection site-focused, transcriptome dysregulations in Atlantic salmon skin, and its effects beyond the skin lesion site were comparably subtle. The M. viscosa-induced transcripts of Atlantic salmon were mainly involved in innate and adaptive immune response-related pathways, whereas the suppressed transcripts by this pathogen were largely connected to developmental and cellular processes. As validated by qPCR, M. viscosa dysregulated transcripts encoding receptors, signal transducers, transcription factors and immune effectors playing roles in TLR- and IFN-dependent pathways as well as immunoregulation, antigen presentation and T-cell development. This study broadened the current understanding of molecular pathways underlying M. viscosa-triggered responses of Atlantic salmon, and identified biomarkers that may assist to diagnose and combat this pathogen.
Pigeon egg white protein-based transparent durable hydrogel via monodisperse ionic surfactant-mediated protein condensation
Authors: Zhou Xinlian , Chen Zaozao , Nojima Tatsuya 
Published: March 2022

AbstractThe thermal gelation property of proteins is useful in creating protein-based materials. The gelation of protein solution often proceeds by the random aggregation of denatured proteins, and the protein-based gels are typically brittle or opaque, or both. Improvement in the mechanical and optical properties of protein-based materials are required for them to be practical and functional. This study investigated pigeon egg white, which is semitransparent in its thermally gelled state, as a protein source for creating hydrogel materials. The protein thermal gelation process was initiated from the orderly condensed state of proteins complexed with monodisperse ionic surfactants to suppress random aggregation. The resultant gel showed transparency in the visible light region and was not destroyed at 99% compression under 17.8 MPa compressive stress, 350-fold higher than the compressive fracture strength of typical boiled pigeon egg white. These results showed that durable transparent hydrogels could be fabricated by the rational combination of natural proteins and surfactants.
Risk factors for reoperation after lumbar spine surgery in a 10-year Korean national health insurance service health examinee cohort
Authors: Noh Sung Hyun , Cho Pyung Goo , Kim Keung Nyun , Lee Boeun , Lee Jae Kwang , Kim Sang Hyun 
Published: March 2022

AbstractDegenerative lumbar spine disease is becoming increasingly prevalent in the aging population. Surgical treatment is the standard treatment modality for intractable cases, but the reoperation rate remains high. We conducted this study to longitudinally evaluate the impact of health risk factors on the risk of lumbar spine reoperation in Koreans aged over 40 years. Subjects aged > 40 years who underwent their first lumbar spinal surgery between January 2005 and December 2008 were selected and followed up until 2015. A total of 6300 people were included. The reoperation rate during the 10-year follow-up period was 13.2% (831/6300 patients). The reoperation rate was the highest in patients in their 60 s (15.4%, P < 0.05). The reoperation rates were also significantly higher in men (vs. women: 14.7% vs. 11.7%, P < 0.05), smokers (vs. non-smokers: 15.2% vs. 12.7%, P < 0.05), alcohol drinkers (vs. non-drinkers: 14.7% vs. 12.4%, P < 0.05), and those with a higher Charlson Comorbidity Index (CCI) score (CCI 0, 11.6%; 1–2, 13.2%; and ≥ 3, 15%; P < 0.05). Among patients undergoing lumbar spine surgery, reoperation is performed in 13.2% of patients within 10 years. Male sex, age in the 60 s, alcohol use, smoking, higher Hgb and a high CCI score increased the risk of reoperation after lumbar spine operation.
Coordination patterns reveal online political astroturfing across the world
Authors: Schoch David , Keller Franziska B. , Stier Sebastian , Yang JungHwan 
Published: March 2022

AbstractOnline political astroturfing—hidden information campaigns in which a political actor mimics genuine citizen behavior by incentivizing agents to spread information online—has become prevalent on social media. Such inauthentic information campaigns threaten to undermine the Internet’s promise to more equitable participation in public debates. We argue that the logic of social behavior within the campaign bureaucracy and principal–agent problems lead to detectable activity patterns among the campaign’s social media accounts. Our analysis uses a network-based methodology to identify such coordination patterns in all campaigns contained in the largest publicly available database on astroturfing published by Twitter. On average, 74% of the involved accounts in each campaign engaged in a simple form of coordination that we call co-tweeting and co-retweeting. Comparing the astroturfing accounts to various systematically constructed comparison samples, we show that the same behavior is negligible among the accounts of regular users that the campaigns try to mimic. As its main substantive contribution, the paper demonstrates that online political astroturfing consistently leaves similar traces of coordination, even across diverse political and country contexts and different time periods. The presented methodology is a reliable first step for detecting astroturfing campaigns.
Investigation of sheath properties in a warm plasma with two kappa-distributed electrons and monoenergetic electron beam
Authors: Hatami M. M. 
Published: March 2022

AbstractSheath formation criterion of an electropositive plasma consisting of singly charged positive ions, two kappa-distributed electron species with different effective temperatures and a monoenergetic electron beam is investigated by the Sagdeev potential approach. Using this criterion, effects of electron beam, superthermality of electron species as well as temperature and concentration of positive ions on the sheath properties are studied numerically. It is shown that the temperature of positive ions, concentration and superthermality of electron species and presence of electron beam affect Bohm velocity of positive ions. Also, it is observed that density distribution of the charged particles and sheath thickness increase in the presence of electron beam. In addition, it is found that with increasing the ion temperature, the sheath width and density distribution of the charged particles in the sheath area decrease.
In vitro assessment of the biocompatibility of chemically treated silicone materials with human lens epithelial cells
Authors: Kao Elizabeth C. Y. , Seo Junghee , McCanna David J. , Subbaraman Lakshman N. , Jones Lyndon W. 
Published: March 2022

AbstractCytotoxicity testing is a regulatory requirement for safety testing of new ocular implants. In vitro toxicity tests determine whether toxic chemicals are present on a material surface or leach out of the material matrix. A method of evaluating the cytotoxicity of ocular implants was developed using fluorescent viability dyes. To assess the assay’s sensitivity in detecting toxic substances on biomaterials, zinc diethydithiocarbamate (ZDEC) and benzalkonium chloride (BAK) were deposited on silicone surfaces at different concentrations. Human lens epithelial cells (HLEC) were added to the surface of these treated silicone surfaces and were assessed for viability. The viability of both the adherent and non-adherent cells was determined using confocal microscopy with, annexin V, ethidium homodimer, and calcein. Cell metabolism was also evaluated using resazurin and the release of inflammatory cytokines was quantified using a multiplex Mesoscale Discovery platform. Confocal microscopy was shown to be a sensitive assay for evaluating material toxicity, as significant toxicity (p < 0.05) from ZDEC and BAK-treated surfaces compared to the untreated silicone control was detected. Patterns of cytokine release from cells varied depending on the toxin evaluated and the toxin concentration and did not directly correlate with the reduction in cell metabolic activity measured by alamarBlue.
Educational inequalities in epilepsy mortality in the Baltic countries and Finland in 2000–2015
Authors: Stickley Andrew , Neligan Aidan , Baburin Aleksei , Jasilionis Domantas , Krumins Juris , Martikainen Pekka , Kondo Naoki , Sumiyoshi Tomiki , Shin Jae Il , Oh Hans , Waldman Kyle , Leinsalu Mall 
Published: March 2022

AbstractLittle is known about socioeconomic differences in epilepsy mortality. This study examined educational inequalities in epilepsy mortality in the general population in the Baltic countries and Finland in 2000–2015. Education-specific mortality estimates for individuals aged 30–74 in Estonia, Latvia and Lithuania were obtained from census-linked mortality datasets while data for Finland came from the register-based population and death data file of Statistics Finland. Trends and educational inequalities in epilepsy mortality were assessed using age-standardised mortality rates (ASMRs) per 100,000 person years and age-adjusted mortality rate ratios (RRs) calculated using Poisson regression. ASMRs were higher in men than women in all countries. ASMRs reduced in 2000–2015 among all men and women except for Finnish women. Among men, an inverse educational gradient in epilepsy mortality in 2000–2007 widened in 2008–2015 with ASMRs falling among high and mid educated men in all countries but increasing among low educated men in three countries. An inverse educational gradient in female mortality remained in all countries throughout 2000–2015. Although epilepsy mortality fell in the Baltic countries and Finland (men only) in 2000–2015, this masked a clear inverse educational gradient in mortality that became steeper across the period.
Semi-supervised generative and discriminative adversarial learning for motor imagery-based brain–computer interface
Authors: Ko Wonjun , Jeon Eunjin , Yoon Jee Seok , Suk Heung-Il 
Published: March 2022

AbstractConvolutional neural networks (CNNs), which can recognize structural/configuration patterns in data with different architectures, have been studied for feature extraction. However, challenges remain regarding leveraging advanced deep learning methods in BCIs. We focus on problems of small-sized training samples and interpretability of the learned parameters and leverages a semi-supervised generative and discriminative learning framework that effectively utilizes synthesized samples with real samples to discover class-discriminative features. Our framework learns the distributional characteristics of EEG signals in an embedding space using a generative model. By using artificially generated and real EEG signals, our framework finds class-discriminative spatio-temporal feature representations that help to correctly discriminate input EEG signals. It is noteworthy that the framework facilitates the exploitation of real, unlabeled samples to better uncover the underlying patterns inherent in a user’s EEG signals. To validate our framework, we conducted experiments comparing our method with conventional linear models by utilizing variants of three existing CNN architectures as generator networks and measuring the performance on three public datasets. Our framework exhibited statistically significant improvements over the competing methods. We investigated the learned network via activation pattern maps and visualized generated artificial samples to empirically justify the stability and neurophysiological plausibility of our model.
Gut microbiota analysis of Blenniidae fishes including an algae-eating fish and clear boundary formation among isolated Vibrio strains
Authors: Yoshida Masa-aki , Tanabe Takuma , Akiyoshi Hideo , Kawamukai Makoto 
Published: March 2022

AbstractSome marine fishes are algae-feeding, and the microorganisms in their digestive tracts produce carbohydrate hydrolyzing enzymes such as agarose and fucosidase, which are potentially interesting resource for new functional enzymes. The purpose of this study was to establish a method for identifying and utilizing characteristic bacteria from the intestines of two algae-eating fish species: Andamia tetradactylus, which exclusively eats algae on the rock surface, and stellar rockskipper Entomacrodus stellifer, which feeds on both algae and invertebrates. We tested the species composition of the intestinal bacterial flora and found that Proteobacteria were commonly found both in species as in the common gut communities of marine fish, whereas Spirochaetes and Tenericutes occupied the flora of A. tetradactylus. We then performed anaerobic and aerobic cultures and isolated 34 and 44 strains including 48 strains belonged to Vibrio species from A. tetradactylus and E. stellifer. We observed that some Vibrio strains formed a clear boundary to avoid contacting other strains of bacteria. Whole-genome sequencing of such two Vibrio alginolyticus strains revealed two cyclic chromosomes commonly found in the genome of Vibrio species, and some unique genes encoding alginate lyase, chitinases, and type I-F CRISPR-associated endoribonuclease for the first time in Vibrio alginolyticus.
Post-lockdown changes of age-specific susceptibility and its correlation with adherence to social distancing measures
Authors: Lau Max S. Y. , Liu Carol , Siegler Aaron J. , Sullivan Patrick S. , Waller Lance A. , Shioda Kayoko , Lopman Benjamin A. 
Published: March 2022

AbstractSocial distancing measures are effective in reducing overall community transmission but much remains unknown about how they have impacted finer-scale dynamics. In particular, much is unknown about how changes of contact patterns and other behaviors including adherence to social distancing, induced by these measures, may have impacted finer-scale transmission dynamics among different age groups. In this paper, we build a stochastic age-specific transmission model to systematically characterize the degree and variation of age-specific transmission dynamics, before and after lifting the lockdown in Georgia, USA. We perform Bayesian (missing-)data-augmentation model inference, leveraging reported age-specific case, seroprevalence and mortality data. We estimate that overall population-level transmissibility was reduced to 41.2% with 95% CI [39%, 43.8%] of the pre-lockdown level in about a week of the announcement of the shelter-in-place order. Although it subsequently increased after the lockdown was lifted, it only bounced back to 62% [58%, 67.2%] of the pre-lockdown level after about a month. We also find that during the lockdown susceptibility to infection increases with age. Specifically, relative to the oldest age group (> 65+), susceptibility for the youngest age group (0–17 years) is 0.13 [0.09, 0.18], and it increases to 0.53 [0.49, 0.59] for 18–44 and 0.75 [0.68, 0.82] for 45–64. More importantly, our results reveal clear changes of age-specific susceptibility (defined as average risk of getting infected during an infectious contact incorporating age-dependent behavioral factors) after the lockdown was lifted, with a trend largely consistent with reported age-specific adherence levels to social distancing and preventive measures. Specifically, the older groups (> 45) (with the highest levels of adherence) appear to have the most significant reductions of susceptibility (e.g., post-lockdown susceptibility reduced to 31.6% [29.3%, 34%] of the estimate before lifting the lockdown for the 6+ group). Finally, we find heterogeneity in case reporting among different age groups, with the lowest rate occurring among the 0–17 group (9.7% [6.4%, 19%]). Our results provide a more fundamental understanding of the impacts of stringent lockdown measures, and finer evidence that other social distancing and preventive measures may be effective in reducing SARS-CoV-2 transmission. These results may be exploited to guide more effective implementations of these measures in many current settings (with low vaccination rate globally and emerging variants) and in future potential outbreaks of novel pathogens.
Breed dependent regulatory mechanisms of beneficial and non-beneficial fatty acid profiles in subcutaneous adipose tissue in cattle with divergent feed efficiency
Authors: Zhou Mi , Zhu Zhi , Sun Hui-Zeng , Zhao Ke , Dugan Mike E. R. , Bruce Heather , Fitzsimmons Carolyn , Li Changxi , Guan Le Luo 
Published: March 2022

AbstractThe current study aimed to determine whether breed and feed efficiency affect the molecular mechanisms regulating beneficial and non-beneficial fatty acid profiles in subcutaneous adipose tissue of beef steers. Fatty acid profiling and RNA-Seq based transcriptome analysis were performed on subcutaneous adipose tissues collected from beef steers with three divergent breeds (Angus, ANG, n = 47; Charolais, CHAR, n = 48; Kinsella Composite, KC, n = 48) and different residual feed intake (RFI, a measure of feed efficiency). The comparison of fatty acid profiles showed that KC had higher beneficial FAs compared to the other two breeds. Distinct FA profiles between H-RFIfat and L-RFIfat steers was more obvious for KC steers, where H-RFIfat steers tended to have higher proportion of healthy FAs and lower proportion of the unhealthy FAs. A higher number of differentially expressed (DE) genes were observed for KC steers, whereas ANG and CHAR steers had a lower number of DE genes between H- and L-RFIfat steers. The association analyses of the gene expressions and FA profiles showed that 10 FA metabolism-associated genes together with the one upstream regulator (SREBF1) were associated with the proportion of C18:2n-6, total n-6, PUFA and PUFA/SFA for KC steers but not the other two breeds. Subcutaneous adipose tissue FA profiles and healthy FA index differed in cattle with divergent feed efficiency and such variation was unique for the three examined cattle breeds. Key FA metabolism-associated genes together with SREBF1 which is the upstream regulator of a set of genes involved in lipid metabolism may be of importance for genetic selection of meat with higher healthy FA index in beef cattle.