bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Single Bounded Input Control Synchronization Criterion for a Category of Hyperchaotic and Chaotic Systems in Presence of Uncertainties
Authors: Pallav  , Handa Himesh , Sharma B. B. 
Published: October 2023

Abstract
Dynamical systems that have a chaotic underlying structure have a sensitive dependency on the initial conditions and the values of their parameters. In this piece of work, a straightforward method for solving the synchronization issue in master–slave arrangement for a category of chaotic or hyperchaotic systems, in which perturbations are present in the parameters of the response system, is discussed. The desired control signal is bounded by the initial state when the controller is activated. There is just one control input that is used, and it is derived from Lyapunov's concept of stability. In general, it is tricky to synchronize hyperchaotic or chaotic systems with single controller, and the work turns out to be significantly more complex when the parameters of the slave system are perturbed. The feedback controller using single input that has been constructed makes certain that the state variables of the response system are in synchronization with the state variables that correspond to them in the drive system. In order to attain the desired level of synchronization, the required conditions that must be satisfied to do so have been identified utilizing Lyapunov's stability analysis in a simple manner. In addition, numerical illustrations have been provided in order to support and confirm the theoretical findings of the paper.
A Fully Implicit Enthalpy-Porosity Model for Phase-Change
Authors: de Lemos Marcelo J. S. , Hodierne Anatole J. U. 
Published: October 2023

Abstract
This article proposes a new formulation for a phase change model based on the enthalpy-porosity idea. A general one-energy equation model (1EEM) is extended to deal with the melting and solidification of pure substances and alloys. Before melting and after solidification, solid material is seen as a porous media with low porosity and very small permeability. During phase change, thermal equilibrium in the mushy zone is assumed. Viscous and form drag in the volume-averaged momentum equation are reduced as the temperature rises above the melting point. In the energy equation, latent heat is treated implicitly in the accumulation term instead of explicitly as in most works in the literature. Liquid fraction for the entire field is updated after a new temperature field is calculated. Thermophysical properties are updated with the new liquid fraction field. Governing equations are discretized according to the control-volume method. Algebraic equation sets are relaxed with the Simple Method. Inner iterations make use of the Strong Implicit Procedure. Preliminary results indicate good agreement with the literature for pure substances.
Neo-Natal Castration Leads to Subtle Differences in Porcine Anterior Cruciate Ligament Morphology and Function in Adolescence
Authors: Thompson Jacob D. , Howe Danielle , Griffith Emily H. , Fisher Matthew B. 
Published: October 2023

Abstract
Female adolescent athletes are at a higher risk of tearing their anterior cruciate ligament (ACL) than male counterparts. While most work related to hormones has focused on the effects of estrogen to understand the increased risk of ACL injury, there are other understudied factors, including testosterone. The purpose of this study was to determine how surgical castration in the male porcine model influences ACL size and function across skeletal growth. Thirty-six male Yorkshire crossbreed pigs were raised to 3 (juvenile), 4.5 (early adolescent), and 6 months (adolescent) of age. Animals were either castrated (barrows) within 2 weeks after birth or were left intact (boars). Posteuthanasia, joint and ACL size were assessed via MRI, and biomechanics were assessed via a robotic testing system. Joint size increased throughout age, yet barrows had smaller joints than boars. ACL cross-sectional area (CSA), length, volume, and in situ stiffness increased with age, as did the percent contribution of the ACL anteromedial (AM) bundle to resisting loads. Boar ACL, AM bundle, and PL bundle volumes were 19%, 25%, and 15% larger than barrows across ages. However, ACL CSA, in situ stiffness, and bundle contribution were similar between boars and barrows. The barrows had smaller temporal increases in AM bundle function than boars, but these data were highly variable. Early and sustained loss in testosterone leads to subtle differences in ACL morphology but may not influence measures associated with increased injury risk, such as CSA or bundle forces in response to applied loads.
Pulsed Red and Blue Photobiomodulation for the Treatment of Thigh Contusions and Soft Tissue Injury: A Randomized Controlled Trial
Authors: Wells Aaron , Rigby Justin , Castel Chris , Castel Dawn 
Published: October 2023

Context: Contusion and soft tissue injuries are common in sports. Photobiomodultion, light and laser therapy, is an effective aid to increase healing rates and improve function after various injury mechanisms. However, it is unclear how well photobiomodulation improves function after a contusion soft tissue injury. This study aimed to determine the effects of a pulsed red and blue photobiomodulation light patch on muscle function following a human thigh contusion injury. Design: Single-blinded randomized control trial design. Methods: We enrolled 46 healthy participants. Participants completed 5 visits on consecutive days. On the first visit, participants completed a baseline isokinetic quadriceps strength testing protocol at 60°/s and 180°/s. On the second visit, participants were struck in the rectus femoris of the anterior thigh with a tennis ball from a serving machine. Immediately following, participants were treated for 30 minutes with an active or placebo photobiomodulation patch (CareWear light patch system, CareWear Corp). Following the treatment, participants completed the same isokinetic quadriceps strength testing protocol. Participants completed the treatment and isokinetic quadriceps strength test during the following daily visits. We normalized the data by calculating the percent change from baseline. We used a mixed model analysis of covariance, with sex as a covariate, to determine the difference between treatment groups throughout the acute recovery process. Results: We found the active photobiomodulation treatment significantly increased over the placebo group, quadriceps peak torque during the 180°/s test (P = .030), and average power during both the 60°/s (P = .041) and 180°/s (P ≤ .001) assessments. The mean peak torque and average power of 180°/s, at day 4, exceeded the baseline levels by 8.9% and 16.8%, respectively. Conclusions: The red and blue photobiomodulation light patch improved muscle strength and power during the acute healing phase of a human thigh contusion injury model.
Accumulated metagenomic studies reveal recent migration, whole genome evolution, and undiscovered diversity of orthomyxoviruses
Authors: Dudas Gytis , Batson Joshua 
Published: October 2023

ABSTRACT

Metagenomic studies have uncovered many novel viruses by looking beyond hosts of public health or economic interest. However, the resulting viral genomes are often incomplete, and analyses largely characterize the distribution of viruses over their dynamics. Here, we integrate accumulated data from metagenomic studies to reveal geographic and evolutionary dynamics in a case study of
Orthomyxoviridae
, the RNA virus family that includes influenza virus. First, we use sequences of the orthomyxovirid Wǔhàn mosquito virus 6 to track the migrations of its host. We then look at orthomyxovirus genome evolution, finding gene gain and loss across members of the family, especially in the surface proteins responsible for cell and host tropism. We find that the surface protein of Wǔhàn mosquito virus 6 exhibits accelerated non-synonymous evolution suggestive of antigenic evolution, i.e., vertebrate infection, and belongs to a wider quaranjavirid group bearing highly diverged surface proteins. Finally, we quantify the progress of orthomyxovirus discovery and forecast that many diverged
Orthomyxoviridae
members remain to be found. We argue that continued metagenomic studies will be fruitful for understanding the dynamics, evolution, ecology of viruses, and their hosts, regardless of whether novel viruses are identified or not, as long as study designs allowing for the resolution of complete viral genomes are employed.

IMPORTANCE

The number of known virus species has increased dramatically through metagenomic studies, which search genetic material sampled from a host for non-host genes. Here, we focus on an important viral family that includes influenza viruses, the
Orthomyxoviridae
, with over 100 recently discovered viruses infecting hosts from humans to fish. We find that one virus called Wǔhàn mosquito virus 6, discovered in mosquitoes in China, has spread across the globe very recently. Surface proteins used to enter cells show signs of rapid evolution in Wǔhàn mosquito virus 6 and its relatives which suggests an ability to infect vertebrate animals. We compute the rate at which new orthomyxovirus species discovered add evolutionary history to the tree of life, predict that many viruses remain to be discovered, and discuss what appropriately designed future studies can teach us about how diseases cross between continents and species.
A hybridization target enrichment approach for pathogen genomics
Authors: Sundararaman Balaji , Sylvester Matthew D. , Kozyreva Varvara K. , Berrada Zenda L. , Corbett-Detig Russell B. , Green Richard E. 
Published: October 2023

ABSTRACT

Genomic epidemiology uses pathogens’ whole-genome sequences to understand and manage the spread of infectious diseases. Whole-genome data can be used to monitor outbreaks and cluster formation, identify cross-community transmissions, and characterize drug resistance and immune evasion. Typically, bacteria are cultured from clinical samples to obtain DNA for sequencing to generate whole-genome data. However, culture-independent diagnostic methods are utilized for some fastidious bacteria for better diagnostic yield and rapid pathogen genomics. Whole-genome enrichment (WGE) using targeted DNA sequencing enables direct sequencing of clinical samples without having to culture pathogens. However, the cost of capture probes (“baits”) limits the utility of this method for large-scale genomic epidemiology. We developed a cost-effective method named
C
ircular
N
ucleic acid
E
nrichment
R
eagent
s
ynthesis (CNERs) to generate whole-genome enrichment probes. We demonstrated the method by producing probes for
Mycobacterium tuberculosis
, which we used to enrich
M. tuberculosis
DNA that had been spiked at concentrations as low as 0.01% and 100 genome copies against a human DNA background to 1,225-fold and 4,636-fold. Furthermore, we enriched DNA from different
M. tuberculosis
lineages and
M. bovis
and demonstrated the utility of the WGE-CNERs data for lineage identification and drug-resistance characterization using an established pipeline. The CNERs method for whole-genome enrichment will be a valuable tool for the genomic epidemiology of emerging and difficult-to-grow pathogens.

IMPORTANCE
Emerging infectious diseases require continuous pathogen monitoring. Rapid clinical diagnosis by nucleic acid amplification is limited to a small number of targets and may miss target detection due to new mutations in clinical isolates. Whole-genome sequencing (WGS) identifies genome-wide variations that may be used to determine a pathogen’s drug resistance patterns and phylogenetically characterize isolates to track disease origin and transmission. WGS is typically performed using DNA isolated from cultured clinical isolates. Culturing clinical specimens increases turn-around time and may not be possible for fastidious bacteria. To overcome some of these limitations, direct sequencing of clinical specimens has been attempted using expensive capture probes to enrich the entire genomes of target pathogens. We present a method to produce a cost-effective, time-efficient, and large-scale synthesis of probes for whole-genome enrichment. We envision that our method can be used for direct clinical sequencing of a wide range of microbial pathogens for genomic epidemiology.
Tetravalent SARS-CoV-2 S1 subunit protein vaccination elicits robust humoral and cellular immune responses in SIV-infected rhesus macaque controllers
Authors: Khan Muhammad S. , Kim Eun , Le Hingrat Quentin , Kleinman Adam , Ferrari Alessandro , Sammartino Jose C. , Percivalle Elena , Xu Cuiling , Huang Shaohua , Kenniston Thomas W. , Cassaniti Irene , Baldanti Fausto , Pandrea Ivona , Gambotto Andrea , Apetrei Cristian 
Published: October 2023

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic has highlighted the need for safe and effective vaccines to be rapidly developed and distributed worldwide, especially considering the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Protein subunit vaccines have emerged as a promising approach due to their proven safety record and ability to elicit robust immune responses. In this study, we evaluated the immunogenicity and efficacy of an adjuvanted tetravalent S1 subunit protein COVID-19 vaccine candidate composed of the Wuhan, B.1.1.7 variant, B.1.351 variant, and P.1 variant spike proteins in a nonhuman primate model with controlled SIVsab infection. The vaccine candidate induced both humoral and cellular immune responses, with T and B cell responses mainly peaking post boost immunization. The vaccine also elicited neutralizing and cross-reactive antibodies, angiotensin-converting enzyme 2 (ACE2)-blocking antibodies, and T cell responses, including spike-specific CD4
+
T cells. Importantly, the vaccine candidate was able to generate Omicron variant spike-binding and ACE2-blocking antibodies without specifically vaccinating with Omicron, suggesting potential broad protection against emerging variants. The tetravalent composition of the vaccine candidate has significant implications for COVID-19 vaccine development and implementation, providing broad antibody responses against numerous SARS-CoV-2 variants.

IMPORTANCE
The study provides important insights into the immunogenicity and efficacy of a tetravalent protein subunit vaccine candidate against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The vaccine induced both humoral and cellular immune responses in nonhuman primates with controlled SIVagm infection and was able to generate Omicron variant-specific antibodies without specifically vaccinating with Omicron. These findings suggest that the tetravalent composition of the vaccine candidate could provide broad protection against multiple SARS-CoV-2 variants while minimizing the risk of immune escape and the emergence of new variants. Additionally, the use of rhesus macaques with controlled SIVsab infection may better represent vaccine immunogenicity in humans with chronic viral diseases, highlighting the importance of preclinical animal models in vaccine development. Overall, the study provides valuable information for the development and implementation of coronavirus disease 2019 vaccines, particularly for achieving global vaccine equity and addressing emerging variants.
Genome sequence of
Streptomyces
BM cluster phage Frankenweenie
Authors: Cleary Katherine E. , Pelagalli Charles , Cassford Marly , Berry Nathan , Aguas Elizabeth , Kim Brandon , deCarvalho Tagide , Jacobs-Sera Deborah , Caruso Steven M. , Cornely Kathleen 
Published: October 2023

ABSTRACT

Frankenweenie is a newly isolated bacteriophage that infects
Streptomyces scabiei
RL-34. Frankenweenie was discovered in Gaithersburg, MD, and has 366 genes comprising a 200,048-bp genome. Frankenweenie is grouped in cluster BM and is predicted to possess a unique tailspike protein that potentially widens its host range.
Manipulating
Agaricus bisporus
developmental patterns by passaging microbial communities in complex substrates
Authors: Vieira Fabricio Rocha , Di Tomassi Isako , O'Connor Eoin , Bull Carolee T. , Pecchia John A. , Hockett Kevin L. 
Published: October 2023

ABSTRACT

There is growing interest in microbiome-based management approaches for plant and animal health and sustainable agricultural practices. To our knowledge, there are no descriptions of
Agaricus bisporus
mushroom developmental patterns using such an approach. Here, we utilized substrate passaging to select for devomes (developmental microbiomes) in either compost or casing material that resulted in earlier developing (best performing experimental units with a higher number of primordia at day 10 of cultivation) mushrooms compared to unpassaged controls. Passaged casing showed earlier pinning (fruiting body formation), while passaged compost delayed fruiting body formation. Despite changes in pin emergence for passaged substrates and higher mushroom yield in the passaged casing’s first harvest, the total mushroom yield in 24 days of crop cycle did not change significantly. The bacterial communities were distinct between compost and casing materials, but in both microenvironments, the alpha diversity tended to increase and stabilize over time in standard and passaged substrates. Community composition within compost and casing microenvironments tended to be more homogenous after colonization of the fungus. Passaging of casing increased the bacterial alpha diversity and shifted community composition. Such changes were not observed in passaged compost. Some bacterial taxa were enriched or depleted by passaging, e.g.,
Pseudomonas
spp. (hypothesized as a stimulus to
A. bisporus
fructification) were depleted in passaged compost and casing. Overall, this work presents an experimental approach to manipulate compost and casing microbial communities with the potential to be combined with currently employed cultivation strategies toward a more sustainable mushroom cultivation system.

IMPORTANCE

Agaricus bisporus
is an economically important edible mushroom and manipulating its developmental patterns is crucial for maximizing yield and quality. One of the potential strategies for achieving such a goal is passaging microbial communities in compost or casing. The current study demonstrated that passaging substrates develop enriched microbial communities, and after a few passages, certain levels of changes in mushroom developmental patterns (the timing of fruiting bodies formation) were observed as well as shifts in the bacterial communities. Overall, a better understanding of the complex interactions between microorganisms present in the cultivation system may help farmers and researchers to develop more efficient and sustainable cultivation practices that can both benefit the environment and human health.
Finding of an Unusually Colored Sporocyst of the Genus Leucochloridium in a Succinea putris Snail
Authors: Usmanova R. R. , Prokhorova E. E. 
Published: October 2023

Abstract—
A Leucochloridium sp. Carus, 1835 sporocyst with a mature colored broodsac was found in a Succinea putris L., 1758 snail in the Boksitogorsk district of Leningrad Region (Russia). The pigmentation of the sporocyst’s broodsac was different from those of other Leucochloridium Carus, 1835 species previously described for Europe. The obtained sporocyst is most similar by the coloration of its broodsac to the trematodes of the same genus from Japan. The genotyping of the investigated sporocyst by the rDNA gene fragments (complete ITS1, ITS2, 5.8S and partial 18S and 28S sequences) was conducted. Genetic distances between the obtained sporocyst and the previously described species of the genus Leucochloridium were higher than intraspecific ones in the most cases. These data and the data of morphological analysis imply that the investigated sporocyst belongs to a separate species of the Leucochloridium genus, previously not described in the European region.
Highly Aggressive Invasive Race Group PstS2 in Russian Populations of the Wheat Yellow Rust Pathogen
Authors: Shaydayuk E. L. , Gultyaeva E. I. 
Published: October 2023

Abstract
The expansion of the area of harmfulness of the wheat yellow rust pathogen (Puccinia striiformis) (Pst) has be observed all over the world in the 2000s. This is due to the emergence of new highly aggressive invasive groups of races PstS1 and PstS2, adopted to the high temperatures, and also as a result of virulence mutations of regional pathogen populations. SCAR-markers were developed for identification of invasive races, and pathogen collections from many countries were studied. In these studies in first in Russia, the analysis of regional populations of P. striiformis for the presence of invasive races PstS1 and PstS2 was carried out. Single pustule isolates were obtained from urediosamples collected from common and durum wheat, triticale and wild grasses in seven regions of the Russian Federation (North Caucasian, Northwestern, Central Black Earth, Lower Volga, Middle Volga, Volga–Vyatka, West Siberian) in 2019–2020. In total 82 isolates were studied. Using SCAR markers, three genotypes were identified in the studied collection of P. striiformis, and one of which belongs to the invasive group PstS2. The other two genotypes had a different origin (other). Isolates of PstS2 group were received from pathogen population samples collected in the Russian Northwest in 2020. Virulence analysis revealed two phenotypes among them: PstS2_R1 (3 isolates) and PstS2_R2 (1 isolate). According to information from the Global Rust Reference Center (http://www.wheatrust.org/), the main characteristic of isolates from invasive PstS2 group is virulence to wheat lines with resistance genes Yr2, Yr6, Yr7, Yr8, Yr9, and Yr25. The Russian R1 phenotype PstS2 was also characterized by virulence to these genes, as well as to Yr1, Yr32, and YrSp. The PstS2_R2 phenotype differed from PstS2_R1 for avirulence to Yr25 and virulence to Yr3 and Yr4. The main difference of Russian PstS2 isolates with detected in other countries is virulence to wheat lines with genes Yr4, Yr32, and YrSp. The first detection of invasive races in the Northwest of Russia indicates the relevance of annual monitoring of regional populations of P. striiformis.