bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection
Authors: Mu Andre , McDonald Daniel , Jarmusch Alan K. , Martino Cameron , Brennan Caitriona , Bryant Mackenzie , Humphrey Gregory C. , Toronczak Julia , Schwartz Tara , Nguyen Dominic , Ackermann Gail , D’Onofrio Anthony , Strathdee Steffanie A. , Schooley Robert T. , Dorrestein Pieter C. , Knight Rob , Aslam Saima 
Published: April 2021

Abstract
Background
Infectious bacterial diseases exhibiting increasing resistance to antibiotics are a serious global health issue. Bacteriophage therapy is an anti-microbial alternative to treat patients with serious bacterial infections. However, the impacts to the host microbiome in response to clinical use of phage therapy are not well understood.

Results
Our paper demonstrates a largely unchanged microbiota profile during 4 weeks of phage therapy when added to systemic antibiotics in a single patient with Staphylococcus aureus device infection. Metabolomic analyses suggest potential indirect cascading ecological impacts to the host (skin) microbiome. We did not detect genomes of the three phages used to treat the patient in metagenomic samples taken from saliva, stool, and skin; however, phages were detected using endpoint-PCR in patient serum.

Conclusion
Results from our proof-of-principal study supports the use of bacteriophages as a microbiome-sparing approach to treat bacterial infections.
Novel targetable FGFR2 and FGFR3 alterations in glioblastoma associate with aggressive phenotype and distinct gene expression programs
Authors: Georgescu Maria-Magdalena , Islam Mohammad Zahidul , Li Yan , Traylor James , Nanda Anil 
Published: April 2021

AbstractPrognostic molecular subgrouping of glioblastoma is an ongoing effort and the current classification includes IDH-wild-type and IDH-mutant entities, the latter showing significantly better prognosis. We performed a comparative integrated analysis of the FGFR glioblastoma subgroup consisting of 5 cases from a prospective 101-patient-cohort. FGFR alterations includedFGFR2-TACC2andFGFR2amplifications arising in a multifocal IDH-mutant glioblastoma with unexpected 2.5-month patient survival, novelFGFR3carboxy-terminal duplication andFGFR3-TLN1fusion, and two previously describedFGFR3-TACC3fusions. The FGFR2 tumors showed additional mutations inSERPINE1/PAI-1 andMMP16, as part of extensive extracellular matrix remodeling programs. Whole transcriptomic analysis revealed common proliferation but distinct morphogenetic gene expression programs that correlated with tumor histology. The kinase program revealedEPHA3,LTKandALKreceptor tyrosine kinase overexpression in individual FGFR tumors. Paradoxically, all FGFR-fused glioblastomas shared strong PI3K and MAPK pathway suppression effected bySPRY,DUSPandAKAP12inhibitors, whereas theFGFR2-TACC2tumor elicited also EGFR suppression byERRFI1upregulation. This integrated analysis outlined the proliferation and morphogenetic expression programs in FGFR glioblastoma, and identified four novel, clinically targetable FGFR2 and FGFR3 alterations that confer aggressive phenotype and trigger canonical pathway feedback inhibition, with important therapeutic implications.
Correlative light and electron microscopy suggests that mutant huntingtin dysregulates the endolysosomal pathway in presymptomatic Huntington’s disease
Authors: Zhou Ya , Peskett Thomas R. , Landles Christian , Warner John B. , Sathasivam Kirupa , Smith Edward J. , Chen Shu , Wetzel Ronald , Lashuel Hilal A. , Bates Gillian P. , Saibil Helen R. 
Published: April 2021

AbstractHuntington’s disease (HD) is a late onset, inherited neurodegenerative disorder for which early pathogenic events remain poorly understood. Here we show that mutant exon 1 HTT proteins are recruited to a subset of cytoplasmic aggregates in the cell bodies of neurons in brain sections from presymptomatic HD, but not wild-type, mice. This occurred in a disease stage and polyglutamine-length dependent manner. We successfully adapted a high-resolution correlative light and electron microscopy methodology, originally developed for mammalian and yeast cells, to allow us to correlate light microscopy and electron microscopy images on the same brain section within an accuracy of 100 nm. Using this approach, we identified these recruitment sites as single membrane bound, vesicle-rich endolysosomal organelles, specifically as (1) multivesicular bodies (MVBs), or amphisomes and (2) autolysosomes or residual bodies. The organelles were often found in close-proximity to phagophore-like structures. Immunogold labeling localized mutant HTT to non-fibrillar, electron lucent structures within the lumen of these organelles. In presymptomatic HD, the recruitment organelles were predominantly MVBs/amphisomes, whereas in late-stage HD, there were more autolysosomes or residual bodies. Electron tomograms indicated the fusion of small vesicles with the vacuole within the lumen, suggesting that MVBs develop into residual bodies. We found that markers of MVB-related exocytosis were depleted in presymptomatic mice and throughout the disease course. This suggests that endolysosomal homeostasis has moved away from exocytosis toward lysosome fusion and degradation, in response to the need to clear the chronically aggregating mutant HTT protein, and that this occurs at an early stage in HD pathogenesis.
NaCl-related weathering of stone: the importance of kinetics and salt mixtures in environmental risk assessment
Authors: Godts Sebastiaan , Orr Scott Allan , Desarnaud Julie , Steiger Michael , Wilhelm Katrin , De Clercq Hilde , Cnudde Veerle , De Kock Tim 
Published: April 2021

Abstract
Salt weathering is one of the most important causes of deterioration in the built environment. Two crucial aspects need further investigation to understand the processes and find suitable measures: the impact of different climatic environments and the properties of salt mixture crystallization. We demonstrate the importance of kinetics in quantifying crystallization and dissolution cycles by combining droplet and capillary laboratory experiments with climate data analysis. The results proved that dissolution times for pure NaCl are typically slower than crystallization, while thermodynamic modelling showed a lower RHeq of NaCl (65.5%) in a salt mixture (commonly found in the built heritage) compared to its RHeq as a single salt (75.5%). Following the results, a minimum time of 30 min is considered for dissolution and the two main RHeq thresholds could be applied to climate data analysis. The predicted number of dissolution/crystallization cycles was significantly dependent on the measurement frequency (or equivalent averaging period) of the climatic data. An analysis of corresponding rural and urban climate demonstrated the impact of spatial phenomena (such as the urban heat island) on the predicted frequency cycles. The findings are fundamental to improve appropriate timescale windows that can be applied to climate data and to illustrate a methodology to quantify salt crystallization cycles in realistic environments as a risk assessment procedure. The results are the basis for future work to improve the accuracy of salt risk assessment by including the kinetics of salt mixtures.
Correlation between the cracking pattern of historical structure and soil properties: the case of the church in Kożuchów
Authors: Raszczuk Krzysztof , Karolak Anna 
Published: April 2021

Abstract
The paper presents a diagnosis of damage to heritage structures based on the case of the historic church in Kożuchów. The Church of the Purification of the Blessed Virgin Mary dates back to the thirteenth century and is an important sacral building in south-west Poland. Renovation and strengthening works have been conducted in recent years with the goal of structurally stabilizing the heritage building. The paper includes a short history of the building, as well as a review of contemporary diagnostic methods used in heritage buildings with emphasis on the methods used in the diagnosis of the discussed object. Correct diagnosis of the heritage building is the key to selecting an optimal design solution for supporting and strengthening the building structure. Pre-design analysis was based on a geotechnical assessment of ground conditions, identifying cracking patterns of walls and vaults, preparing a digital model using Heritage—Building Information Modeling technology and performing structural analysis. The main cause of cracking of the walls and vaults of the church is related to uneven subsidence and localized stability loss of the building’s foundations, resulting from differentiated soil and water conditions beneath the building. Based on the research and analysis, final conclusions and proposals for strengthening the structure were presented, including jet-grouting columns, tie rods and Fibre Reinforced Cementitious Matrix systems.
Surface energetics to assess influence of biomass-type and biomass–adsorbent interactions in expanded beds
Authors: Yelemane Vikas , Kangwa Martin , Dsouza Roy N. , Fernández-Lahore Marcelo 
Published: April 2021

AbstractIn integrated bioprocessing applications, expanded bed adsorption (EBA) chromatography presents an opportunity to harvest biomolecules directly from the crude feedstock. However, unfavorable biomass interactions with adsorbent usually leads to fouling, which reduces its protein binding capacity as it alters column hydrodynamics and binding site availability. In this work, a detailed study on biomass adhesion behavior of four different industrially relevant microorganisms on 26 different, most commonly occurring adsorbent surfaces with varying degrees of surface energy and surface charge has been conducted. The results showed the derivation of a relative “stickiness” factor for every microorganism, which further classifies each organism based on their general degree of adhesion to surfaces with respect to one another. The obtained results can help to better understand the effect of biomass homogenization on biomass–adsorbent interactions in EBA. The data of surface energy and charge for the surfaces investigated in this work can be used to calculate the stickiness factor of other microorganisms of interest and may assist in the development of novel adsorbent materials for EBA chromatography.
Energy cost of walking and functional aerobic capacity during moderate intensity exercise in adults with obstructive sleep apnea: a cross-sectional study
Authors: Aldhahi Monira , Puri Shipra , Jain Vivek , E. Herrick Jeffrey 
Published: April 2021

Abstract
Background
Autonomic dysregulation associated with obstructive sleep apnea (OSA) may limit cardiopulmonary responses to exercise, which, in turn, may impair functional aerobic capacity (FAC) and walking economy. We aimed to characterize walking economy and FAC in OSA patients compared with healthy adults (non-OSA) and examine their relationship with OSA severity (apnea-hypopnea index [AHI]).

Methods
A total of 26 adults (OSA, n = 13; non-OSA, n = 13) participated in this cross-sectional study. In this study, the participants with OSA were between the ages of 25 and 60 years, with a body mass index of 25 kg/m2 to 39 kg/m2, and who had undergone a recent third-party sleep study with an AHI of 5 or greater. Participants completed a maximal integrated cardiopulmonary exercise test, three separate exercise bouts of constant work rate (CWR) treadmill test at 85% of anaerobic threshold (AT), and a 10-min walk test (10MWT). Multiple linear regression analysis corrected for weight, age, and BMI were performed to examine the associations.

Results
There were significant differences between OSA and non-OSA participants in VO2peak (29.7 ± 5.6 mL/kg/min vs. 37.5 ± 6.5 mL/kg/min, p = 0.03) and Net VO2 during CWR (12.7 ± 5 vs.19 ± 6 mL/kg/min, p = 0.02). The 10MWT speed and distance were significantly lower in the OSA group (all p < 0.001). The energy cost of walking during submaximal exercise and 10-min walk test was higher among patients with OSA (all p < 0.001). The AHI scores were associated with 10MWT distance (R2 = 0.85, p < 0.001), energy cost of walking (R2 = 87, p < 0.001), and VO2 at anaerobic threshold (R2 = 0.92, p < 0.001).

Conclusions
The findings of this study show that patients with OSA have reduced FAC and a higher energy cost of walking. AHI explained 87% of variance in the energy cost of walking during the 10MWT. The results suggest that individuals with more severe obstructive sleep apnea experience greater impairment in functional performance.
Peripheral blood mononuclear cells (PBMC) microbiome is not affected by colon microbiota in healthy goats
Authors: Peña-Cearra Ainize , Belanche Alejandro , Gonzalez-Lopez Monika , Lavín José Luis , Pascual-Itoiz Miguel Ángel , Jiménez Elisabeth , Rodríguez Héctor , Aransay Ana Mª. , Anguita Juan , Yáñez-Ruiz David R. , Abecia Leticia 
Published: April 2021

Abstract
Background
The knowledge about blood circulating microbiome and its functional relevance in healthy individuals remains limited. An assessment of changes in the circulating microbiome was performed by sequencing peripheral blood mononuclear cells (PBMC) bacterial DNA from goats supplemented or not in early life with rumen liquid transplantation.

Results
Most of the bacterial DNA associated to PBMC was identified predominantly as Proteobacteria (55%) followed by Firmicutes (24%), Bacteroidetes (11%) and Actinobacteria (8%). The predominant genera found in PBMC samples were Pseudomonas, Prevotella, Sphingomonas, Acinetobacter, Corynebacterium and Ruminococcus. Other genera such as Butyrivibrivio, Bifidobacterium, Dorea and Coprococcus were also present in lower proportions. Several species known as blood pathogens or others involved in gut homeostasis such as Faecalibacterium prausnitzii were also identified. However, the PBMC microbiome phylum composition differed from that in the colon of goats (P ≤ 0.001), where Firmicutes was the predominant phylum (83%). Although, rumen liquid administration in early-life altered bacterial community structure and increased Tlr5 expression (P = 0.020) in colon pointing to higher bacterial translocation, less than 8% of OTUs in colon were also observed in PBMCs.

Conclusions
Data suggest that in physiological conditions, PBMC microbiome differs from and is not affected by colon gut microbiota in small ruminants. Although, further studies with larger number of animals and covering other animal tissues are required, results point to a common circulating bacterial profile on mammals being phylum Proteobacteria, and genera Pseudomonas and Prevotella the most abundants. All suggest that PBMC microbiome in healthy ruminants could be implicated in homeostatic condition. This study expands our knowledge about PBMC microbiome contribution to health in farm animals.
Addressing widespread misidentifications of traditional medicinal mushrooms in Sanghuangporus (Basidiomycota) through ITS barcoding and designation of reference sequences
Authors: Shen Shan , Liu Shi-Liang , Jiang Ji-Hang , Zhou Li-Wei 
Published: April 2021

Abstract“Sanghuang” refers to a group of important traditionally-used medicinal mushrooms belonging to the genus Sanghuangporus. In practice, species of Sanghuangporus referred to in medicinal studies and industry are now differentiated mainly by a BLAST search of GenBank with the ITS barcoding region as a query. However, inappropriately labeled ITS sequences of “Sanghuang” in GenBank restrict accurate species identification and, to some extent, the utilization of these species as medicinal resources. We examined all available 271 ITS sequences related to “Sanghuang” in GenBank including 31 newly submitted sequences from this study. Of these sequences, more than half were mislabeled so we have now corrected the corresponding species names. The mislabeled sequences mainly came from strains utilized by non-taxonomists. Based on the analyses of ITS sequences submitted by taxonomists as well as morphological characters, we separate the newly described Sanghuangporus subbaumii from S. baumii and treat S. toxicodendri as a later synonym of S. quercicola. Fourteen species of Sanghuangporus are accepted, with intraspecific distances up to 1.30% (except in S. vaninii, S. weirianus and S. zonatus) and interspecific distances above 1.30% (except between S. alpinus and S. lonicerinus, and S. baumii and S. subbaumii). To stabilize the concept of these 14 species of Sanghuangporus, their taxonomic information and reliable ITS reference sequences are provided. Moreover, ten potential diagnostic sequences are provided for Hyperbranched Rolling Circle Amplification to rapidly confirm three common commercial species, viz. S. baumii, S. sanghuang, and S. vaninii. Our results provide a practical method for ITS barcoding-based species identification of Sanghuangporus and will promote medicinal studies and commercial development from taxonomically correct material.
Validity of MDCT cholangiography in differentiating benign and malignant biliary obstruction
Authors: Alsowey Ahmed M. , Salem Ahmed F. , Amin Mohamed I. 
Published: April 2021

Abstract
Background
MDCT cholangiography can be utilized to identify variant biliary anatomy to guide preoperative planning of biliary surgery, and determine the cause and level of biliary obstruction. Early tumor detection and staging of biliary cancer are key factors for a possible cure by surgical resection. Between December 2019 and October 2020, 69 patients with clinically suspected biliary obstruction were enrolled in the study, subjected to clinical assessment (full history taking and clinical examination) and imaging assessment by MDCT cholangiography. Our findings were correlated to standard reference examinations including operative/ERCP/biopsy and histopathology findings.

Results
The most affected age was between 60 and 70 years old, and males were more affected. The commonest clinical presentation was yellowish discoloration of the skin and sclera followed by biliary colic. Right hypochondrial tenderness was the main clinical finding on clinical examination. Our patients were categorized according to the etiology of biliary obstruction into 7 groups: malignant stricture 52.2% (36 patients), calcular 24.6% (17 patients), iatrogenic 5.8% (4 patients), portahepatis lesions 5.8% (4 patients), benign stricture 4.3% (3 patients), inflammatory 4.3% (3 patients), and congenital 1.4% (1 patient). The malignant group shows dominant mass, moderate biliary obstruction, and arterial and venous enhancement. The overall sensitivity was 94% for malignancy.

Conclusion
MDCT cholangiography is non-invasive, fast, and highly sensitive and specific in the diagnosis of different causes and levels of biliary obstruction and is useful in the characterization of the lesion in cases of malignant obstruction and differentiating it from benign stricture. It can be used as an effective alternative to ERCP or PTC.
Room-Temperature Coalescence of Tri-n-Octylphosphine-Oxide-Capped Cu-Ag Core-Shell Nanoparticles: Effect of Sintering Agent and/or Reducing Agent
Authors: Okada Soichiro , Nakahara Yoshio , Watanabe Mitsuru , Tamai Toshiyuki , Kobayashi Yasuyuki , Yajima Setsuko 
Published: April 2021

Abstract
Metal nanoparticle pastes are useful for nanoinks to form fine conductive patterns in printed electronics. This study reports a novel method for room-temperature coalescence of Cu-Ag core-shell nanoparticles (Cu@Ag NPs), which are expected to have the properties of both migration and oxidation resistance originating from Cu and Ag, respectively. First, oleylamine/oleic-acid capped Cu@Ag NPs were synthesized by the galvanic replacement method. Second, the ligand exchange reaction to tri-n-octylphosphine oxide (TOPO) was carried out on the surface of Cu@Ag NPs. Finally, TOPO-capped Cu@Ag NPs were dipped into methanol containing a sintering agent and/or a reducing agent. When HCl was added as a sintering agent to methanol, the crystallite size of Cu@Ag NPs significantly increased. Furthermore, the almost complete removal of organic compounds and suppression of significant oxidation of Ag and Cu were observed. In consideration of these results, a Cu/Ag conductive thin film was prepared from TOPO-capped Cu@Ag NPs by dipping into methanol containing HCl at room temperature under air atmosphere. Electrical resistivity of the obtained Cu/Ag thin film was (5.1 ± 1.7) × 10−5 Ω m. Microstructural observations and X-ray diffractions of the Cu/Ag thin film revealed that Cu@Ag NPs effectively coalesced at room temperature with slight oxidation.
Prevalence of asymptomatic P. falciparum gametocyte carriage among school children in Mbita, Western Kenya and assessment of the association between gametocyte density, multiplicity of infection and mosquito infection prevalence.
Authors: Touray Abdoulie O. , Mobegi Victor A. , Wamunyokoli Fred , Butungi Hellen , Herren Jeremy K. 
Published: April 2021

Background: Asymptomatic Plasmodium falciparum gametocyte carriers are reservoirs for sustaining transmission in malaria endemic regions. Gametocyte presence in the host peripheral blood is a predictor of capacity to transmit malaria. However, it does not always directly translate to mosquito infectivity. Factors that affect mosquito infectivity include, gametocyte sex-ratio and density, multiplicity of infection (MOI), and host and vector anti-parasite immunity. We assess the prevalence of gametocyte carriage and some of its associated risk factors among asymptomatic schoolchildren in Western Kenya and to further analyse the association between gametocyte density, multiplicity of infection (MOI) and mosquito infection prevalence. Methods: P. falciparum parasite infections were detected by RDT (Rapid Diagnostic Test) and microscopy among schoolchildren (5-15 years old). Blood from 37 microscopy positive gametocyte carriers offered to laboratory reared An. gambiae s.l. mosquitoes. A total of 3395 fully fed mosquitoes were screened for Plasmodium sporozoites by ELISA. P. falciparum was genotyped using 10 polymorphic microsatellite markers. The association between MOI and gametocyte density and mosquito infection prevalence was investigated. Results: A significantly higher prevalence of P. falciparum infection was found in males 31.54% (764/2422) (p-value < 0.001) compared to females 26.72% (657/2459). The microscopic gametocyte prevalence among the study population was 2% (84/4881). Children aged 5-9 years have a higher prevalence of gametocyte carriage (odds ratios = 2.1 [95% CI = 1.3–3.4], P = 0.002) as compared to children aged 10-15 years. After offering gametocyte positive blood to An. gambiae s.l. by membrane feeding assay, our results indicated that 68.1% of the variation in mosquito infection prevalence was accounted for by gametocyte density and MOI (R-SQR. = 0.681, p < 0.001). Conclusions: We observed a higher risk of gametocyte carriage among the younger children (5-9 years). Gametocyte density and MOI significantly predicted mosquito infection prevalence.