bluuebunny/crossref_metadata_2025_split huggingface dataset:
A source of hidden diversity: soil seed bank and aboveground populations of a common herb contain similar levels of genetic variation
Authors: Iberl K. , Poschlod P. , Reisch C. 
Published: September 2023

Abstract
In many landscapes, successful re‐establisment of plant populations depends on the presence of diaspores, either near or directly beneath sites to be restored. The soil seed bank is, therefore, an important part of ecosystem resilience and a vital pillar for regeneration of genetic diversity in many plant populations. However, regeneration from the soil seed bank and the siubsequent restoration can only be considered successful when genetic diversity of restored populations is not eroded nor genetic differentiation inflated.
We compared genetic variation within and among soil seed bank and aboveground populations of Origanum vulgare, to test whether genetically variable populations can be restored from the soil seed bank. We explored levels of genetic diversity within aboveground populations and the corresponding soil seed banks. Furthermore, we assessed the extent to which the soil seed bank differs genetically from the aboveground population.
Levels of genetic diversity were to generally similar in aboveground populations and the corresponding soil seed banks. Only levels of inbreeding were slightly higher in the lower layer of the soil seed bank compared to the aboveground populations, probably because of selection processes acting against homozygotes accumulating in the seed bank. Furthermore, significant genetic differentiation between the aboveground population and the corresponding seed banks was completely absent. Across all sites, genetic differentiation between the soil seed bank was similar to that between aboveground populations, probably due to the absence of severe climate conditions, strong bottlenecks or disturbance events.
Our conclusions support the possibility of successful re‐establishment of healthy, genetically variable plant populations after aboveground destruction or following soil re‐allocation from persistent seed banks.
Treatment of periorbital hyperpigmentation using sublative fractional radiofrequency (SFR)
Authors: Nilforoushzadeh Mohammad Ali , Heidari‐Kharaji Maryam , Fakhim Tannaz , Torkamaniha Elham , Tehrani Sepideh , Delavar Shohreh , Rafiee Shohreh , Nouri Maryam , Najar Nobari Niloufar , Shahverdi Mohammadhasan 
Published: September 2023

AbstractBackgroundPeriorbital hyperpigmentation (POH) is a common cosmetic concern. Numerous techniques of treatment have been assessed with variable results.AimThe purpose of this research is to assess the efficacy of non‐ablative radiofrequency, Sublative fractional Radiofrequency (SFR) on POH treatment.MethodsIn this research study, nine patients with POH and the age range of 25−57 years, were enrolled. The patients were treated by non‐ablative radiofrequency SRF. The outcomes were assessed by biometric assessment. The skin lightness and melanin content of the periorbital skin were assessed by colorimeter and Mexameter. Skin elasticity was assessed by Cutometer. The skin ultrasound imaging system was used to evaluate the diameter and density of the epidermis and dermis. Visioface was used to evaluate the skin color and wrinkles. Also, patient's satisfaction and physician's assessment were assessed.ResultsThe results showed that the lightness and elasticity of the periorbital skin were significantly increased after treatment. Also, the melanin content of the skin was decreased. The denser skin layers were seen in both dermis and epidermis. The Visioface results displayed the reduction in the percent change of the skin color and wrinkle (p < 0.05). Similarly, the physician and patients’ assessment confirmed the outcomes. No serious adverse effect was reported.ConclusionIn conclusion, the SFR technique is an effective and satisfactory therapeutic choice for treatment of POH.
The role of imagination and recollection in the method of phenomenal contrast
Authors: Nourbakhshi Hamid 
Published: September 2023

AbstractThe method of phenomenal contrast (in perception) invokes the phenomenal character of perceptual experience as a means to discover its contents. The method implicitly takes for granted that ‘what it is like’ to have a perceptual experience e is the same as ‘what it is like’ to imagine or recall it; accordingly, in its various proposed implementations, the method treats imaginations and/or recollections as interchangeable with real experiences. The method thus always contrasts a pair of experiences, at least one of which is imagined or remembered rather than occurrent. Surveying all eighteen forms of implementing the method, I argue that in all of the proposed pairings, the substitution of imagination or recollection for perceptual experience in the method, is either inconceivable or impermissible. I identify four reasons why I think imagination cannot be substituted for real experience, and three reasons why recollection cannot be substituted for real experience. If my argument works, there is no form of implementing the method that is useful for discovering the contents of experience, and thus the method is not a well‐functioning tool to study the contents of perception.
Supplemental findings of the 2021 National Blood Collection and Utilization Survey
Authors: Kracalik Ian , Sapiano Mathew R. P. , Wild Robert C. , Chavez Ortiz Joel , Stewart Phylicia , Berger James J. , Basavaraju Sridhar V. , Free Rebecca J. 
Published: September 2023

AbstractBackgroundThe Department of Health and Human Services' National Blood Collection and Utilization Survey (NBCUS) has been conducted biennially since 1997. Data are used to estimate national blood collection and use. Supplemental data from the 2021 NBCUS not presented elsewhere are presented here.MethodsData on survey participation, donor characteristics, blood component cost, transfusion‐associated adverse reactions, and implementation of blood safety measures, including pathogen‐reduction of platelets, during 2021, were analyzed. Comparisons are made to 2019 survey data where available (2013–2019 for survey participation).ResultsDuring 2021, there were 11,507,000 successful blood donations in the United States, a 4.8% increase from 2019. Persons aged 45–64 years accounted for 42% of all successful blood donations. Donations by persons aged 65 years and older increased by 40.7%, while donations among minorities and donors aged <25 years decreased. From 2019 to 2021, the median price hospitals paid per unit of leukoreduced red blood cells, leukoreduced and pathogen‐reduced apheresis platelets, and fresh frozen plasma increased. The largest increase in price per unit of blood component in 2021 was for leukoreduced apheresis platelets, which increased by ~$51. Between 2019 and 2021, the proportion of transfusing facilities reporting use of pathogen‐reduced platelets increased, from 13% to 60%. Transfusion‐related adverse reactions declined slightly between 2019 and 2021, although the rate of transfusion‐transmitted bacterial infections remained unchanged.ConclusionDuring 2021, blood donations increased nationally, although donations from those aged <25 years and minorities declined. The prices hospitals paid for most blood products increased, as did the use of pathogen‐reduced platelets.
The use of oclacitinib compared to azathioprine in the management of canine pemphigus foliaceus: A retrospective analysis
Authors: Hernandez‐Bures Andrea , Bidot Wille A. , Griffin Craig E. , Rosenkrantz Wayne S. 
Published: September 2023

AbstractBackgroundOclacitinib (Apoquel; Zoetis) has been reported to be beneficial for treating immune‐mediated disorders.Hypothesis/ObjectivesThis retrospective study evaluates in which group of dogs [oclacitinib (OC) or azathioprine (AZ)] remission of pemphigus foliaceus (PF) was more effectively achieved with matched induction dosing of glucocorticoids; it further evaluates which group had a higher glucocorticoid‐sparing effect.AnimalsReview of 30 medical records of dogs diagnosed with PF presented to a private practice dermatological service.Materials and MethodsRetrospective analysis of dogs diagnosed with PF and treated with OC or AZ in combination with glucocorticoids.ResultsThere was no significant difference in the ability to induce remission between AZ and OC groups. In the AZ group, 13 of 15 dogs went into some type of remission (partial or complete), compared with 11 of 15 in the OC group. There was no significant difference between the two groups for the glucocorticoid‐sparing effect. The AZ group had an average reduction of 77.9% from the induction glucocorticoid dose, and OC group had an average reduction of 64.4%. One of 15 patients in the AZ group and three of 15 patients in the OC group had a 100% reduction of the glucocorticoid dose.Conclusions and Clinical RelevanceThese results indicate that OC can be considered as a treatment option for canine PF.
Astrocytes in functional recovery following central nervous system injuries
Authors: Alhadidi Qasim M. , Bahader Ghaith A. , Arvola Oiva , Kitchen Philip , Shah Zahoor A. , Salman Mootaz M. 
Published: September 2023

AbstractAstrocytes are increasingly recognised as partaking in complex homeostatic mechanisms critical for regulating neuronal plasticity following central nervous system (CNS) insults. Ischaemic stroke and traumatic brain injury are associated with high rates of disability and mortality. Depending on the context and type of injury, reactive astrocytes respond with diverse morphological, proliferative and functional changes collectively known as astrogliosis, which results in both pathogenic and protective effects. There is a large body of research on the negative consequences of astrogliosis following brain injuries. There is also growing interest in how astrogliosis might in some contexts be protective and help to limit the spread of the injury. However, little is known about how astrocytes contribute to the chronic functional recovery phase following traumatic and ischaemic brain insults. In this review, we explore the protective functions of astrocytes in various aspects of secondary brain injury such as oedema, inflammation and blood–brain barrier dysfunction. We also discuss the current knowledge on astrocyte contribution to tissue regeneration, including angiogenesis, neurogenesis, synaptogenesis, dendrogenesis and axogenesis. Finally, we discuss diverse astrocyte‐related factors that, if selectively targeted, could form the basis of astrocyte‐targeted therapeutic strategies to better address currently untreatable CNS disorders.
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Fluid–Thermal–Structural Analysis of Partial Admission Axial Impulse Turbines With Liquid Jet Impingement Cooling
Authors: Wang Hanwei , Luo Kai , Zhi Ruoyang , Qin Kan 
Published: September 2023

Abstract
Increasing turbine inlet temperature is beneficial to enhance turbine performance. However, this also results in stringent cooling requirements. Unlike turbines in air cycle machines, the partial admission axial impulse turbines for underwater vehicles can utilize the abundant seawater as the cooling medium. In addition, the short blades cannot accommodate the complex cooling channels used in aero-engines, and the alternative way is jet impingement liquid cooling. This paper proposes a fluid–thermal–structural coupling method to investigate the performance of partial admission axial impulse turbines with water-cooling on the rotating wheel front surface. The volume of fluid multiphase model is employed to study the transient gas–liquid interaction, while the Lee model is chosen to model the heat and mass transfer during phase change. Also, a two-way weakly coupling method among fluid, thermal, and structure is utilized to account for fluid–structure interaction. The results show that the temperature distribution at the turbine wheel drops significantly with the jet impingement liquid cooling. The turbine efficiency is also reduced by 3.38% due to the mixing of cooling medium and gas. From stress analysis, the use of water-cooling can minimize turbine damage and ensure stable turbine operation. This study provides insight into the cooling method for partial admission axial impulse turbines for the underwater vehicle.
CO Laser Absorption Measurements During Syngas Combustion at High Pressure
Authors: Cooper Sean P. , Nativel Damien , Mathieu Olivier , Fikri Mustapha , Petersen Eric L. , Schulz Christof 
Published: September 2023

Abstract
Syngas is a desirable fuel for combustion in the Allam-Fetvedt cycle, which involves combustion under supercritical-CO2 conditions. While some work has been conducted in collecting ignition delay times (IDT) at the extreme pressures required by these systems, significant model deficiencies remain. Additionally, considerable barriers in terms of nonideal gas dynamic effects have been shown for these experiments in shock tubes. Further investigation into the fundamental combustion kinetics of H2/CO/CO2 mixtures is required. Time-resolved speciation measurements for target species have been shown to better aid in improving the understanding of underlying chemical kinetics than global ignition delay time measurements. Therefore, laser absorption measurements of CO were measured behind reflected shock waves during combustion of syngas at 5 and 10 bar and temperatures between 1080 and 2100 K. The mixtures investigated utilized H2-to-CO ratios of 1:1 and 1:4, respectively, each at stoichiometric conditions, allowing for discussions of the effect of initial fuel composition. A ratio of fuel to CO2 of 1:2 was also utilized to represent commercially available syngas. The mixtures were diluted in helium and argon (20% He, 76.5% Ar) to minimize thermal effects and to expedite CO thermal relaxation during the experiment. The resulting CO time histories were then compared to modern chemical kinetics mechanisms, and disagreement is seen for this system, which is assumed to be fairly well known. This study elucidates particular chemistry that needs improvement in moving toward a better understanding of syngas combustion at elevated pressures.
Plasmodium falciparum
GCN5 plays a key role in regulating artemisinin resistance-related stress responses
Authors: Lucky Amuza Byaruhanga , Wang Chengqi , Shakri Ahmad Rushdi , Kalamuddin Mohammad , Chim-Ong Anongruk , Li Xiaolian , Miao Jun 
Published: September 2023

ABSTRACT

Plasmodium falciparum
causes the most severe malaria and is exposed to various environmental and physiological stresses in the human host. Given that GCN5 plays a critical role in regulating stress responses in model organisms, we aimed to elucidate PfGCN5’s function in stress responses in
P. falciparum
. The protein level of PfGCN5 was substantially induced under three stress conditions [heat shock, low glucose starvation, and dihydroartemisinin, the active metabolite of artemisinin (ART)]. With a TetR-DOZI conditional knockdown (KD) system, we successfully down-regulated PfGCN5 to ~50% and found that KD parasites became more sensitive to all three stress conditions. Transcriptomic analysis via RNA-seq identified ~1,000 up- and down-regulated genes in the wild-type (WT) and KD parasites under these stress conditions. Importantly, DHA induced transcriptional alteration of many genes involved in many aspects of stress responses, which were heavily shared among the altered genes under heat shock and low glucose conditions, including ART-resistance-related genes such as
K13
and
coronin
. Based on the expression pattern between WT and KD parasites under three stress conditions, ~300–400 genes were identified to be involved in PfGCN5-dependent, general, and stress-condition-specific responses with high levels of overlaps among three stress conditions. Notably, using ring-stage survival assay, we found that KD or inhibition of PfGCN5 could sensitize the ART-resistant parasites to the DHA treatment. All these indicate that PfGCN5 is pivotal in regulating general and ART-resistance-related stress responses in malaria parasites, implicating PfGCN5 as a potential target for malaria intervention.
Evaluation of the QIAstat-Dx Meningitis/Encephalitis Panel, a multiplex PCR platform for the detection of community-acquired meningoencephalitis
Authors: Sundelin Thomas , Bialas Johanna , de Diego Juana , Hermanowski Markus , Leibhan Hendrik , Ponderand Léa , Juanola-Falgarona Marti , Jones Tara , Rey Melisa , Johnson Sarah , Pareja Josep , Caspar Yvan 
Published: September 2023

ABSTRACT

Rapid identification of the causative pathogens of central nervous system infections is essential for providing appropriate management and improving patient outcomes. The performance of QIAstat-Dx Meningitis/Encephalitis (ME) Panel—a multiplex PCR testing platform—in detecting pathogens implicated in meningitis and/or encephalitis was evaluated using BioFire FilmArray ME Panel as a comparator method. This multicenter study analyzed 585 retrospective residual cerebrospinal fluid specimens and 367 contrived specimens. The QIAstat-Dx ME Panel showed positive percent agreement (PPA) values of 100% for
Neisseria meningitidis
,
Streptococcus agalactiae
,
Escherichia coli
K1,
Listeria monocytogenes
, and
Cryptococcus gattii
/
neoformans
on clinical samples compared to the BioFire FilmArray ME Panel. The PPA values observed for
Haemophilus influenzae
and
Streptococcus pneumoniae
were 80% and 88.24%, respectively. Negative percent agreement (NPA) values were >99.0% for each of the six bacterial targets and one fungal target tested with clinical samples. One viral target, herpes simplex virus 1, exhibited a PPA value of 100.0%, while the remaining viral targets—human parechovirus, herpes simplex virus 2, human herpes virus 6, and varicella zoster virus—were >90.0%, with the exception of enterovirus, which had a PPA value of 77.8%. The QIAstat-Dx ME Panel detected five true-positive and four true-negative cases compared to BioFire FilmArray ME Panel. The NPA values for all viral pathogens were >99.0%. Overall, the QIAstat-Dx ME Panel showed comparable performance to the BioFire FilmArray ME Panel as a rapid diagnostic tool for community-acquired meningitis and encephalitis.
Structural and antigenic characterization of the avian adeno-associated virus capsid
Authors: Hsi Jane , Mietzsch Mario , Chipman Paul , Afione Sandra , Zeher Allison , Huang Rick , Chiorini John , McKenna Robert 
Published: September 2023

ABSTRACT
All adeno-associated virus (AAV) vectors currently used in clinical trials or approved gene therapy biologics are based on human or non-human primate AAVs. A major challenge for AAV gene therapy is the high prevalence of circulating neutralizing antibodies (NAbs) in the general population targeting the virus capsids leading to vector inactivation and a loss of treatment efficacy. A strategy to escape detection by NAbs is the utilization of AAVs that do not disseminate in the primate population and exhibit low or no antigenicity. One such example is avian AAV (AAAV), which was first identified in preparations of the Olson strain of quail bronchitis, an avian adenovirus. AAAV shows very low sequence identities (~54–58%) to the AAV serotypes including to the sequences of the structurally diverse AAV4 and AAV5. In this study, the structure of empty and genome-filled AAAV capsids was determined by cryo-electron microscopy (cryo-EM) at 2.5 and 3.1 Å resolution. Furthermore, AAAV was found to utilize galactose for cell attachment, similar to AAV9 and AAVrh.10. Characterization of AAAV’s antigenic properties revealed that 30% of human sera from healthy individuals were capable of neutralizing transduction. This high rate of antigenicity is caused by conserved epitopes around the fivefold channel of the capsid allowing cross-reactivity of NAbs. This was further confirmed by mapping a cross-reactive human anti-AAV9 monoclonal antibody using cryo-EM. This structure-function characterization will be beneficial to further expand the current repertoire of AAV vectors in human gene therapy applications.

Importance
AAVs are extensively studied as promising therapeutic gene delivery vectors. In order to circumvent pre-existing antibodies targeting primate-based AAV capsids, the AAAV capsid was evaluated as an alternative to primate-based therapeutic vectors. Despite the high sequence diversity, the AAAV capsid was found to bind to a common glycan receptor, terminal galactose, which is also utilized by other AAVs already being utilized in gene therapy trials. However, contrary to the initial hypothesis, AAAV was recognized by approximately 30% of human sera tested. Structural and sequence comparisons point to conserved epitopes in the fivefold region of the capsid as the reason determinant for the observed cross-reactivity.
Identification of hidden N4-like viruses and their interactions with hosts
Authors: Zheng Kaiyang , Liang Yantao , Paez-Espino David , Zou Xiao , Gao Chen , Shao Hongbing , Sung Yeong Yik , Mok Wen Jye , Wong Li Lian , Zhang Yu-Zhong , Tian Jiwei , Chen Feng , Jiao Nianzhi , Suttle Curtis A. , He Jianfeng , McMinn Andrew , Wang Min 
Published: September 2023

ABSTRACT
The N4-like viruses, which were recently assigned to the novel viral family Schitoviridae in 2021, belong to a podoviral-like viral lineage and possess conserved genomic characteristics and a unique replication mechanism. Despite their significance, our understanding of N4-like viruses is primarily based on viral isolates. To address this knowledge gap, this study has established a comprehensive N4-like viral data sets comprising 342 high-quality N4-like viruses/proviruses (144 viral isolates, 158 uncultured viruses, and 40 integrated N4-like proviruses). These viruses were classified into 97 subfamilies (89 of which are newly identified), 148 genera (100 of which are newly identified), and 253 species (177 of which are newly identified). The study reveals that N4-like viruses inhibit the polar region, oligotrophic open oceans, and the human gut, where they infect various bacterial lineages, such as Alpha/Beta/Gamma/Epsilon-proteobacteria in the Proteobacteria phylum. Although N4-like viral endogenization appears to be prevalent in Proteobacteria, it has also been observed in Firmicutes. Additionally, the phylogenetic analysis has identified evolutionary divergence within the hallmark genes of N4-like viruses, indicating a complex origin of the different conserved parts of viral genomes. Moreover, 1,101 putative auxiliary metabolic genes (AMGs) were identified in the N4-like viral pan-proteome, which mainly participate in nucleotide and cofactor/vitamin metabolisms. Of these AMGs, 27 were found to be associated with virulence, suggesting their potential involvement in the spread of bacterial pathogenicity.

Importance
The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.