bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative and dynamic profiling of human gut core microbiota by real-time PCR
Authors: Yan Ziheng , Hao Tongyu , Yan Yanfeng , Zhao Yanting , Wu Yarong , Tan Yafang , Bi Yujing , Cui Yujun , Yang Ruifu , Zhao Yong 
Published: June 2024

Abstract
The human gut microbiota refers to a diverse community of microorganisms that symbiotically exist in the human intestinal system. Altered microbial communities have been linked to many human pathologies. However, there is a lack of rapid and efficient methods to assess gut microbiota signatures in practice. To address this, we established an appraisal system containing 45 quantitative real-time polymerase chain reaction (qPCR) assays targeting gut core microbes with high prevalence and/or abundance in the population. Through comparative genomic analysis, we selected novel species-specific genetic markers and primers for 31 of the 45 core microbes with no previously reported specific primers or whose primers needed improvement in specificity. We comprehensively evaluated the performance of the qPCR assays and demonstrated that they showed good sensitivity, selectivity, and quantitative linearity for each target. The limit of detection ranged from 0.1 to 1.0 pg/µL for the genomic DNA of these targets. We also demonstrated the high consistency (Pearson’s r = 0.8688, P < 0.0001) between the qPCR method and metagenomics next-generation sequencing (mNGS) method in analyzing the abundance of selected bacteria in 22 human fecal samples. Moreover, we quantified the dynamic changes (over 8 weeks) of these core microbes in 14 individuals using qPCR, and considerable stability was demonstrated in most participants, albeit with significant individual differences. Overall, this study enables the simple and rapid quantification of 45 core microbes in the human gut, providing a promising tool to understand the role of gut core microbiota in human health and disease.

Key points
• A panel of original qPCR assays was developed to quantify human gut core microbes.
• The qPCR assays were evaluated and compared with mNGS using real fecal samples.
• This method was used to dynamically profile the gut core microbiota in individuals.
Partial dominance in branch-price-and-cut algorithms for vehicle routing and scheduling problems with a single-segment tradeoff
Authors: Faldum Stefan , Machate Sarah , Gschwind Timo , Irnich Stefan 
Published: June 2024

AbstractFor many variants of vehicle routing and scheduling problems solved by a branch-price-and-cut (BPC) algorithm, the pricing subproblem is an elementary shortest-path problem with resource constraints (SPPRC) typically solved by a dynamic-programming labeling algorithm. Solving the SPPRC subproblems consumes most of the total BPC computation time. Critical to the performance of the labeling algorithms and thus the BPC algorithm as a whole is the use of effective dominance rules. Classical dominance rules rely on a pairwise comparison of labels and have been used in many labeling algorithms. In contrast, partial dominance describes situations where several labels together are needed to dominate another label, which can then be safely discarded. In this work, we consider SPPRCs, where a linear tradeoff describes the relationship between two resources. We derive a unified partial dominance rule to be used in ad hoc labeling algorithms for solving such SPPRCs as well as insights into its practical implementation. We introduce partial dominance for two important variants of the vehicle routing problem, namely the electric vehicle routing problem with time windows with a partial recharge policy and the split-delivery vehicle routing problem with time windows (SDVRPTW). Computational experiments show the effectiveness of the approach, in particular for the SDVRPTW, leading to an average reduction of 20% of the total BPC computation time, with savings of 30% for the more difficult instances requiring more than 600 s of computation time.
Characterization of induced quasi-two-dimensional transport in n-type InxGa1−xAs1 − yBiy bulk layer
Authors: Aydin Mustafa , Yilmaz Selen Nur , Bork James , Zide Joshua , Erol Ayse , Donmez Omer 
Published: June 2024

AbstractThe temperature-dependent transport properties of n-type InGaAsBi epitaxial alloys with various doping densities are investigated by conducting magnetoresistance (MR) and Hall Effect (HE) measurements. The electronic band structure of the alloys and free electron distribution were calculated using Finite Element Method (FEM). Analysis of the oscillations in the transverse (Hall) resistivity shows that quasi-two-dimensional electron gas (Q-2D) in the bulk InGaAsBi epitaxial layer (three-dimensional, 3D) forms at the sample surface under magnetic field even though there is no formation of the spacial two-dimensional electron gas (2DEG) at the interface between InGaAs and InP:Fe interlayer. The formation of Q-2D in the 3D epitaxial layer was verified by temperature and magnetic field dependence of the resistivity and carrier concentration. Analysis of Shubnikov-de Haas (SdH) oscillations in longitudinal (sample) resistivity reveals that the electron effective mass in InGaAsBi alloys are not affect by Bi incorporation into host InGaAs alloys, which verifies the validity of the Valence Band Anti-Crossing (VBAC) model. The Hall mobility of the nondegenerate samples shows the conventional 3D characteristics while that of the samples is independence of temperature for degenerated samples. The scattering mechanism of the electrons at low temperature is in long-range interaction regime. In addition, the effects of electron density on the transport parameters such as the effective mass, and Fermi level are elucidated considering bandgap nonparabolicity and VBAC interaction in InGaAsBi alloys.
Vaulting further: cranial vault expansion for craniocerebral disproportion without primary craniosynostosis
Authors: Ng Jinggang J. , Saikali Linda M. , Zapatero Zachary D. , Massenburg Benjamin B. , Wu Meagan , Romeo Dominic J. , Heuer Gregory G. , Bartlett Scott P. , Taylor Jesse A. , Swanson Jordan W. , Lang Shih-Shan 
Published: June 2024

Abstract
Purpose
Treatment of subjects with refractory idiopathic intracranial hypertension (IIH) or shunted hydrocephalus with chronic shunt complications is challenging. What is the role for cranial vault expansion, particularly utilizing posterior vault distraction osteogenesis (PVDO), in these cases? This study assesses medium-term efficacy of cranial vault expansion in this unique patient population.

Methods
A retrospective review was conducted of patients who underwent cranial vault expansion from 2008 to 2023 at the Children’s Hospital of Philadelphia. Subjects who did not have a diagnosis of primary craniosynostosis were included in the study. Demographic information, medical history, and perioperative details were collected from medical records. Primary outcomes were the rate of CSF diversion procedures and resolution of presenting signs and symptoms. Secondary outcomes were perioperative and 90-day complications and reoperation requirement.

Results
Among 13 included subjects, nine (69.2%) patients had a primary diagnosis of shunted hydrocephalus and 4 (30.8%) patients had IIH. Twelve (92.3%) subjects underwent posterior vault distraction osteogenesis (PVDO) and one (7.7%) underwent posterior vault remodeling (PVR). All 4 patients with IIH demonstrated symptomatic improvement following PVDO, including resolution of headaches, vomiting, and/or papilledema. Among 9 patients with shunted hydrocephalus, CSF diversion requirement decreased from 2.7 ± 1.6 procedures per year preoperatively to 1.2 ± 1.8 per year following cranial vault expansion (p = 0.030). The mean postoperative follow-up was 4.1 ± 2.1 years and four (30.8%) patients experienced complications within 90 days of surgery, including infection (n = 2), CSF leak (n = 1), and elevated ICP requiring lumbar puncture (n = 1). Four (30.8%) patients underwent repeat cranial vault expansion for recurrence of ICP-related symptoms. At most recent follow-up, 7 of 9 patients with shunted hydrocephalus demonstrated symptomatic improvement.

Conclusion
Cranial vault expansion reduced intracranial hypertension-related symptomology as well as the rate of CSF diversion-related procedures in patients with refractory IIH and shunted hydrocephalus without craniosynostosis, and should be considered in those who have significant shunt morbidity.
CCAAT Promoter element regulates transgenerational expression of the MHC class I gene
Authors: Weissman Jocelyn D. , Kotekar Aparna , Barbash Zohar , Mu Jie , Singer Dinah S. 
Published: June 2024

Abstract Transgenerational gene expression depends on both underlying DNA sequences and epigenetic modifications. The latter, which can result in transmission of variegated gene expression patterns across multiple generations without DNA alterations, has been termed epigenetic inheritance and has been documented in plants, worms, flies and mammals. Whereas transcription factors binding to cognate DNA sequence elements regulate gene expression, the molecular basis for epigenetic inheritance has been linked to histone and DNA modifications and non-coding RNA. Here we report that mutation of the CCAAT box promoter element abrogates NF-Y binding and disrupts the stable transgenerational expression of an MHC class I transgene. Transgenic mice with a mutated CCAAT box in the MHC class I transgene display variegated expression of the transgene among littermates and progeny in multiple independently derived transgenic lines. After 4 generations, CCAAT mutant transgenic lines derived from a single founder stably displayed distinct patterns of expression. Histone modifications and RNA polymerase II binding correlate with expression of CCAAT mutant transgenic lines, whereas DNA methylation and nucleosome occupancy do not. Mutation of the CCAAT box also results in changes to CTCF binding and DNA looping patterns across the transgene that correlate with expression status. These studies identify the CCAAT promoter element as a regulator of stable transgenerational gene expression such that mutation of the CCAAT box results in variegated transgenerational inheritance. Considering that the CCAAT box is present in 30% of eukaryotic promoters, this study provides insights into how fidelity of gene expression patterns is maintained through multiple generations.
A scoping review of the effect of chronic stretch training on sleep quality in people with sleep disorders
Authors: Mohammad Alimoradi , Elham Hosseini , Andreas Konrad 
Published: June 2024

Abstract
Purpose
The widespread and health-detrimental sleep disorders have resulted in stretching exercises being investigated as a non-drug solution for enhanced sleep quality. However, a comprehensive understanding of the impact of stretching exercises on individuals with sleep disorders is lacking.

Methods
This scoping review systematically maps the existing literature and identifies research gaps on the impact of stretching exercises on sleep quality in individuals with sleep disorders.

Results
Sixteen eligible studies were included, where the weighted mean changes indicate a positive trend in sleep quality improvement, ranging from trivial to very large magnitudes. However, concerning the individual study results only 5 out of 16 studies reported significant improvements. Notable enhancements include a small 1.22% overall sleep quality improvement, a large 6.51% reduction in insomnia severity, a large 8.88% increase in sleep efficiency, a moderate 4.36% decrease in sleep onset latency, a large 8.27% decrease in wake after sleep onset, and a very large 14.70% improvement in total sleep time. Trivial changes are noted in sleep duration (0.58%), sleep disturbance reduction (0.07%), and daytime dysfunction reduction (0.19%). Likely mechanisms for the improvement of sleep include autonomic nervous system modulation, muscle tension relief, cortisol regulation, enhanced blood circulation, and psychological benefits such as stress reduction and mood enhancement.

Conclusion
There is little evidence that stretching exercises positively impact sleep quality in individuals with sleep disorders. Additionally, further research is vital for designing optimal protocols, understanding of the long-term effects, and clarification of the mechanisms.
Environmental and ecological factors affecting tick infestation in wild birds of the Americas
Authors: Busi Ana , Martínez-Sánchez Estefani T. , Alvarez-Londoño Johnathan , Rivera-Páez Fredy A. , Ramírez-Chaves Héctor E. , Fontúrbel Francisco E. , Castaño-Villa Gabriel J. 
Published: June 2024

AbstractThe Americas hold the greatest bird diversity worldwide. Likewise, ectoparasite diversity is remarkable, including ticks of the Argasidae and Ixodidae families – commonly associated with birds. Considering that ticks have potential health implications for humans, animals, and ecosystems, we conducted a systematic review to evaluate the effects of bioclimatic, geographic variables, and bird species richness on tick infestation on wild birds across the Americas. We identified 72 articles that met our inclusion criteria and provided data on tick prevalence in wild birds. Using Generalized Additive Models, we assessed the effect of environmental factors, such as habitat type, climatic conditions, bird species richness, and geographic location, on tick infestation. Our findings show that most bird infestation case studies involved immature ticks, such as larvae or nymphs, while adult ticks represented only 13% of case studies. We found birds infested by ticks of the genera Amblyomma (68%), Ixodes (22%), Haemaphysalis (5%), Dermacentor (1%), and Rhipicephalus (0.8%) in twelve countries across the Americas. Our findings revealed that temperature variation and bird species richness were negatively associated with tick infestation, which also varied with geographic location, increasing in mid-latitudes but declining in extreme latitudes. Our results highlight the importance of understanding how environmental and bird community factors influence tick infestation in wild birds across the Americas and the dynamics of tick-borne diseases and their impact on biodiversity.
Coarse Embeddability of Wasserstein Space and the Space of Persistence Diagrams
Authors: Pritchard Neil , Weighill Thomas 
Published: June 2024

AbstractWe prove an equivalence between open questions about the embeddability of the space of persistence diagrams and the space of probability distributions (i.e. Wasserstein space). It is known that for many natural metrics, no coarse embedding of either of these two spaces into Hilbert space exists. Some cases remain open, however. In particular, whether coarse embeddings exist with respect to the p-Wasserstein distance for $$1\le p\le 2$$

1
≤
p
≤
2

remains an open question for the space of persistence diagrams and for Wasserstein space on the plane. In this paper, we show that embeddability for persistence diagrams is equivalent to embeddability for Wasserstein space on $$\mathbb {R}^2$$

R

2

. When $$p > 1$$

p
>
1

, Wasserstein space on $$\mathbb {R}^2$$

R

2

is snowflake universal (an obstruction to embeddability into any Banach space of non-trivial type) if and only if the space of persistence diagrams is snowflake universal.
Applied climatology for heritage
Authors: Brimblecombe Peter , Richards Jenny 
Published: June 2024

AbstractThe protection of heritage from a changing climate has been of increasing interest over the last few decades, which creates a need for a systematic approach to the impacts of climate on tangible and intangible heritage. We present heritage climatology as an applied, interdisciplinary field of science that examines aspects of climate that affect heritage and provides data, statistics, well-tuned climate parameters and projections that can aid interpreting past changes and future management of heritage. It must consider the impact of extreme events, cyclic processes and the gradual accumulation of damage. Climate threats to heritage need to be represented at the appropriate temporal and spatial scales, and transferred using dose–response functions such that they can be interpreted in terms of management decisions yet be resistant to errors from both the representation of the climate threat and its translation into policy.
The first evaluation of the in vitro effects of silver(I)-N-heterocyclic carbene complexes on Encephalitozoon intestinalis and Leishmania major promastigotes
Authors: Ataş Ahmet Duran , Akın-Polat Zübeyda , Gülpınar Derya Gül , Şahin Neslihan 
Published: June 2024

AbstractEncephalitozoon intestinalis is an opportunistic microsporidian parasite that primarily infects immunocompromised individuals, such as those with HIV/AIDS or undergoing organ transplantation. Leishmaniasis is responsible for parasitic infections, particularly in developing countries. The disease has not been effectively controlled due to the lack of an effective vaccine and affordable treatment options. Current treatment options for E. intestinalis infection and leishmaniasis are limited and often associated with adverse side effects. There is no previous study in the literature on the antimicrosporidial activities of Ag(I)-N-heterocyclic carbene compounds. In this study, the in vitro antimicrosporidial activities of previously synthesized Ag(I)-N-heterocyclic carbene complexes were evaluated using E. intestinalis spores cultured in human renal epithelial cell lines (HEK-293). Inhibition of microsporidian replication was determined by spore counting. In addition, the effects of the compounds on Leishmania major promastigotes were assessed by measuring metabolic activity or cell viability using a tetrazolium reaction. Statistical analysis was performed to determine significant differences between treated and control groups. Our results showed that the growth of E. intestinalis and L. major promastigotes was inhibited by the tested compounds in a concentration-dependent manner. A significant decrease in parasite viability was observed at the highest concentrations. These results suggest that the compounds have potential anti-microsporidial and anti-leishmanial activity. Further research is required to elucidate the underlying mechanisms of action and to evaluate the efficacy of the compounds in animal models or clinical trials.
Graphical abstract
Enabling personalized VR experiences: a framework for real-time adaptation and recommendations in VR environments
Authors: Valmorisco Sergio , Raya Laura , Sanchez Alberto 
Published: June 2024

AbstractThe personalization of user experiences through recommendation systems has been extensively explored in Internet applications, but this has yet to be fully addressed in Virtual Reality (VR) environments. The complexity of managing geometric 3D data, computational load, and natural interactions poses significant challenges in real-time adaptation in these immersive experiences. However, tailoring VR environments to individual user needs and interests holds promise for enhancing user experiences. In this paper, we present Virtual Reality Environment Adaptation through Recommendations (VR-EAR), a framework designed to address this challenge. VR-EAR employs customizable object metadata and a hybrid recommendation system modeling implicit user feedback in VR environments. We utilize VR optimization techniques to ensure efficient performance. To evaluate our framework, we designed a virtual store where product locations dynamically adjust based on user interactions. Our results demonstrate the effectiveness of VR-EAR in adapting and personalizing VR environments in real time. domains.
Mechanical and hydraulic properties of unsaturated layered pyroclastic ashes in landslide-prone areas of Campania (Italy)
Authors: Roman Quintero Daniel Camilo , Damiano Emilia , Olivares Lucio , Greco Roberto 
Published: June 2024

AbstractAir-fall pyroclastic soil deposits usually display a loose fabric composed of alternating layers of ashes and pumices. Such deposits, when lying on steep slopes, represent a major geohazard due to the occurrence of landslides. This is the case of the carbonate massifs in Campania (southern Italy), a wide landslide-prone area of approximately 400 km2 covered with pyroclastic soils. In such cohesionless deposits, the additional shear strength provided by soil suction in unsaturated conditions is important for ensuring slope stability and can be jeopardized by soil wetting during rainwater infiltration. This paper provides a comprehensive view of the hydraulic and shear strength characteristics of different layers of pyroclastic deposits at different sites in Campania, revealing a broad view of their similarities and differences. To that end, some datasets from previous studies and novel data are gathered, linking the index properties, the hydraulic behavior of the soils and the contribution of suction to the shear strength of the studied materials. Two types of ashes at different positions within the stratigraphic sequence are identified: ashes interbedded between pumice layers, where landslide failure surfaces usually occur, and altered ashes in contact with the bedrock, which affects water leakage from the overlying soil profile. The former show quite uniform characteristics, and this allowed testing some predictive models for the assessment of the unsaturated shear strength of pyroclastic ashes in the absence of direct measurements. In contrast, the latter may exhibit significantly different behaviors, with great variability in hydraulic and mechanical properties.
Microbiological risk factors, ICU survival, and 1-year survival in hematological patients with pneumonia requiring invasive mechanical ventilation
Authors: Seybold Benjamin , Funk Timo , Dreger Peter , Egerer Gerlinde , Brandt Juliane , Mueller-Tidow Carsten , Giesen Nicola , Merle Uta 
Published: June 2024

Abstract
Purpose
To identify pathogenic microorganisms and microbiological risk factors causing high morbidity and mortality in immunocompromised patients requiring invasive mechanical ventilation due to pneumonia.

Methods
A retrospective single-center study was performed at the intensive care unit (ICU) of the Department of Internal Medicine at Heidelberg University Hospital (Germany) including 246 consecutive patients with hematological malignancies requiring invasive mechanical ventilation due to pneumonia from 08/2004 to 07/2016. Microbiological and radiological data were collected and statistically analyzed for risk factors for ICU and 1-year mortality.

Results
ICU and 1-year mortality were 63.0% (155/246) and 81.0% (196/242), respectively. Pneumonia causing pathogens were identified in 143 (58.1%) patients, multimicrobial infections were present in 51 (20.7%) patients. Fungal, bacterial and viral pathogens were detected in 89 (36.2%), 55 (22.4%) and 41 (16.7%) patients, respectively. Human herpesviruses were concomitantly reactivated in 85 (34.6%) patients. As significant microbiological risk factors for ICU mortality probable invasive Aspergillus disease with positive serum-Galactomannan (odds ratio 3.1 (1.2-8.0), p = 0.021,) and pulmonary Cytomegalovirus reactivation at intubation (odds ratio 5.3 (1.1–26.8), p = 0.043,) were identified. 1-year mortality was not significantly associated with type of infection. Of interest, 19 patients had infections with various respiratory viruses and Aspergillus spp. superinfections and experienced high ICU and 1-year mortality of 78.9% (15/19) and 89.5% (17/19), respectively.

Conclusions
Patients with hematological malignancies requiring invasive mechanical ventilation due to pneumonia showed high ICU and 1-year mortality. Pulmonary Aspergillosis and pulmonary reactivation of Cytomegalovirus at intubation were significantly associated with negative outcome.