bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of microbial signatures between paired faecal and rectal biopsy samples from healthy volunteers using next-generation sequencing and culturomics
Authors: Mukhopadhya Indrani , Martin Jennifer C. , Shaw Sophie , McKinley Aileen J. , Gratz Silvia W. , Scott Karen P. 
Published: October 2022

AbstractBackgroundFaecal samples are frequently used to characterise the gut microbiota in health and disease, yet there is considerable debate about how representative faecal bacterial profiles are of the overall gut community. A particular concern is whether bacterial populations associated with the gut mucosa are properly represented in faecal samples, since these communities are considered critical in the aetiology of gastrointestinal diseases. In this study we compared the profiles of the faecal and mucosal microbiota from ten healthy volunteers using bacterial culturing (culturomics) and next-generation sequencing targeting the 16S ribosomal nucleic acid (rRNA) gene. Paired fresh rectal biopsies and faecal samples were processed under stringent anaerobic conditions to maintain the viability of the bacteria. Four different sample types were analysed: faecal (F), faecal homogenised (FHg), biopsy tissue (B) and biopsy wash (BW) samples. ResultsThere were no significant statistical differences in either bacterial richness or diversity between biopsy washes (BW) and faecal (F) or faecal homogenised (FHg) samples. Principal coordinates analysis of a Bray–Curtis distance matrix generated from sequence variant tables did not show distinct clustering between these samples (PERMANOVA;p = 0.972) but showed strong clustering of samples from individual donors. However, the rectal biopsy tissue (B) samples had a significantly altered bacterial signature with greater abundance of Proteobacteria and Acidobacteria compared to faecal (F) and faecal homogenised (FHg) samples. A total of 528 bacteria encompassing 92 distinct bacterial species were isolated and cultured from a subset of six volunteer samples (biopsy washes and faeces). This included isolation of 22 novel bacterial species. There was significant similarity between the bacterial species grown in anaerobic culture and those identified by 16S rRNA gene sequencing (Spearman correlation; rho = 0.548,p = 0.001).ConclusionThis study showed that the bacterial profiles of paired faecal and rectal biopsy wash samples were very similar, validating the use of faecal samples as a convenient surrogate for rectal biopsy-associated microbiota. Anaerobic bacterial culture results showed similar taxonomic patterns to the amplicon sequence analysis disproving the dogma that culture-based methods do not reflect findings of molecular assessments of gut bacterial composition.
Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota
Authors: Xie Yuan-Guo , Luo Zhen-Hao , Fang Bao-Zhu , Jiao Jian-Yu , Xie Qi-Jun , Cao Xing-Ru , Qu Yan-Ni , Qi Yan-Lin , Rao Yang-Zhi , Li Yu-Xian , Liu Yong-Hong , Li Andrew , Seymour Cale , Palmer Marike , Hedlund Brian P. , Li Wen-Jun , Hua Zheng-Shuang 
Published: October 2022

AbstractBackgroundCandidatusNanohaloarchaeota, an archaeal phylum within the DPANN superphylum, is characterized by limited metabolic capabilities and limited phylogenetic diversity and until recently has been considered to exclusively inhabit hypersaline environments due to an obligate association withHalobacteria. Aside from hypersaline environments,Ca.Nanohaloarchaeota can also have been discovered from deep-subsurface marine sediments.ResultsThree metagenome-assembled genomes (MAGs) representing a new order within theCa.Nanohaloarchaeota were reconstructed from a stratified salt crust and proposed to represent a novel order,Nucleotidisoterales. Genomic features reveal them to be anaerobes capable of catabolizing nucleotides by coupling nucleotide salvage pathways with lower glycolysis to yield free energy. Comparative genomics demonstrated that these and otherCa.Nanohaloarchaeota inhabiting saline habitats use a “salt-in” strategy to maintain osmotic pressure based on the high proportion of acidic amino acids. In contrast, previously describedCa.Nanohaloarchaeota MAGs from geothermal environments were enriched with basic amino acids to counter heat stress. Evolutionary history reconstruction revealed that functional differentiation of energy conservation strategies drove diversification withinCa.Nanohaloarchaeota, further leading to shifts in the catabolic strategy from nucleotide degradation within deeper lineages to polysaccharide degradation within shallow lineages.ConclusionsThis study provides deeper insight into the ecological functions and evolution of the expanded phylumCa.Nanohaloarchaeota and further advances our understanding on the functional and genetic associations between potential symbionts and hosts.
Looking under the skin: multi-scale CT scanning of a peculiarly constructed cornett in the Rijksmuseum
Authors: Dorscheid Jan , Bossema Francien G. , van Duin Paul , Coban Sophia B. , van Liere Robert , Batenburg K. Joost , Di Stefano Giovanni Paolo 
Published: October 2022

Abstract
Covered tightly by a thin leather skin, three early seventeenth-century cornetts from the collection of the Rijksmuseum were examined with the focus on their construction and manufacturing. One cornett of the three unexpectedly turned out to have a peculiar construction and to be made out of two sections of different wood species. The question arose whether this could be original or is the result of an extensive restoration.
As the internal structure is not accessible for analysis and examination, multi-scale Computed Tomography (CT) scanning was employed to identify the exact regions of interest (ROI) and subsequently perform scans at a sufficiently high resolution in those areas. 3D images of the hollow spaces such as the tunnelling structure caused by the common furniture beetle (Anobium punctatum) criss-crossing the wood species could be computed from the 3D x-ray tomography reconstruction. This allowed to place the occurrence of the insect infestation after the joining of the two sections. Fine tool-marks, signs of construction and potential indications of earlier treatments could be visualized. These results were compared with the other two instruments of the same group and cross-referenced to instruments in other collections, in an attempt to answer questions about the instrument’s authenticity and originality. While the unusual construction out of two wood species might be the result of an extensive repair, another possible hypothesis—based on the combination of the results—is that this unique choice of original manufacturing was intentional, possibly to avoid splitting of the wood when inserting the mouthpiece or to counteract undesired vibrations when played.
Machine Learning-Enabled NIR Spectroscopy in Assessing Powder Blend Uniformity: Clear-Up Disparities and Biases Induced by Physical Artefacts
Authors: Muthudoss Prakash , Tewari Ishan , Chi Rayce Lim Rui , Young Kwok Jia , Ann Eddy Yii Chung , Hui Doreen Ng Sean , Khai Ooi Yee , Allada Ravikiran , Rao Manohar , Shahane Saurabh , Das Samir , Babla Irfan , Mhetre Sandeep , Paudel Amrit 
Published: October 2022

AbstractNIR spectroscopy is a non-destructive characterization tool for the blend uniformity (BU) assessment. However, NIR spectra of powder blends often contain overlapping physical and chemical information of the samples. Deconvoluting the information related to chemical properties from that associated with the physical effects is one of the major objectives of this work. We achieve this aim in two ways. Firstly, we identified various sources of variability that might affect the BU results. Secondly, we leverage the machine learning-based sophisticated data analytics processes. To accomplish the aforementioned objectives, calibration samples of amlodipine as an active pharmaceutical ingredient (API) with the concentrations ranging between 67 and 133% w/w (dose ~ 3.6% w/w), in powder blends containing excipients, were prepared using a gravimetric approach and assessed using NIR spectroscopic analysis, followed by HPLC measurements. The bias in NIR results was investigated by employing data quality metrics (DQM) and bias-variance decomposition (BVD). To overcome the bias, the clustered regression (non-parametric and linear) was applied. We assessed the model’s performance by employing the hold-out and k-fold internal cross-validation (CV). NIR-based blend homogeneity with low mean absolute error and an interval estimates of 0.674 (mean) ± 0.218 (standard deviation) w/w was established. Additionally, bootstrapping-based CV was leveraged as part of the NIR method lifecycle management that demonstrated the mean absolute error (MAE) of BU ± 3.5% w/w and BU ± 1.5% w/w for model generalizability and model transferability, respectively. A workflow integrating machine learning to NIR spectral analysis was established and implemented.
Graphical Abstract
Impact of various data learning approaches on NIR spectral data
Effect of Texture and Surface Chemistry on Deagglomeration and Powder Retention in Capsule-Based Dry Powder Inhaler
Authors: Groß Roman , Berkenfeld Kai , Schulte Christoph , Ebert Anselm , Sule Sunita , Sule Ameet , Lamprecht Alf 
Published: October 2022

AbstractPulmonary delivery systems should administer a high dose of the required formulation with the designated dry powder inhaler (DPI) to achieve therapeutic success. While the effects of device geometry and individual components used on powder dispersion are described in literature, potential effects of DPI surface properties on powder retention within the device and deagglomeration have not been adequately studied, but could impact inhalation therapy by modifying the available dose. For this, inner parts of a model DPI were modified by plasma treatment using various processes. Since both the hydrophilic-hydrophobic and structural properties of the surface were altered, conclusions can be drawn for future optimization of devices. The results show that surface topography has a greater influence on powder deposition and deagglomeration than hydrophilic or hydrophobic surface modification. The most important modification was observed with an increased rough surface texture in the mouth piece, resulting in lower powder deposition in this part (from 5 to 1% quantified amount of powder), without any change in powder deagglomeration compared to an untreated device. In summary, increasing the surface roughness of DPI components in the size range of a few nanometers could be an approach for future optimization of DPIs to increase the delivered dose.
Graphical abstract
Three-Dimensional Modeling and Augmented Reality and Virtual Reality Simulation of Fiber Dissection of the Cerebellum and Brainstem
Authors: Gurses Muhammet Enes , Gungor Abuzer , Rahmanov Serdar , Gökalp Elif , Hanalioglu Sahin , Berker Mustafa , Cohen-Gadol Aaron A. , Türe Uğur 
Published: October 2022

BACKGROUND:
Surgeons must understand the complex anatomy of the cerebellum and brainstem and their 3-dimensional (3D) relationships with each other for surgery to be successful. To the best of our knowledge, there have been no fiber dissection studies combined with 3D models, augmented reality (AR), and virtual reality (VR) of the structure of the cerebellum and brainstem. In this study, we created freely accessible AR and VR simulations and 3D models of the cerebellum and brainstem.

OBJECTIVE:
To create 3D models and AR and VR simulations of cadaveric dissections of the human cerebellum and brainstem and to examine the 3D relationships of these structures.

METHODS:
Ten cadaveric cerebellum and brainstem specimens were prepared in accordance with the Klingler's method. The cerebellum and brainstem were dissected under the operating microscope, and 2-dimensional and 3D images were captured at every stage. With a photogrammetry tool (Qlone, EyeCue Vision Technologies, Ltd.), AR and VR simulations and 3D models were created by combining several 2-dimensional pictures.

RESULTS:
For the first time reported in the literature, high-resolution, easily accessible, free 3D models and AR and VR simulations of cerebellum and brainstem dissections were created.

CONCLUSION:
Fiber dissection of the cerebellum-brainstem complex and 3D models with AR and VR simulations are a useful addition to the goal of training neurosurgeons worldwide.
Posterior Quadrant Disconnection Procedure for Intractable Epilepsy: A Case Series of 5 Young Pediatric Patients
Authors: Patel Smruti K. , Gibson Justin L. , Lovha Mykhailo , Leach James L. , Arya Ravindra , Tenney Jeffrey R. , Holland Katherine D. , Aungaroon Gewalin , Greiner Hansel M. , Skoch Jesse , Mangano Francesco T. 
Published: October 2022

BACKGROUND:
Posterior quadrant disconnection (PQD) has been described as a treatment for patients with refractory posterior quadrant subhemispheric epilepsy. Surgical outcomes are difficult to interpret because of limited literature.

OBJECTIVE:
To provide insight regarding the operative technique and postsurgical seizure freedom in young pediatric patients who underwent surgical disconnection for the treatment of posterior quadrant subhemispheric epilepsy at our institution.

METHODS:
The authors retrospectively analyzed a series of 5 patients who underwent PQD between 2019 and 2021. Charts were reviewed for preoperative workup including noninvasive/invasive testing, operative reports, and postoperative follow-up data which included degree of seizure freedom, completion of disconnection, and complications.

RESULTS:
Five patients were included in this series. The median age at seizure onset was 12 months (range 3-24 months), and the median age at surgery was 36 months (range 22-72 months). Histopathology confirmed focal cortical dysplasia in 3 of 5 patients (2 patients with type IB; 1 with type IIID). The average length of follow-up after surgery was 16.8 months (range 12-24 months). All patients underwent complete disconnection of the posterior quadrant without complications. Four of 5 patients (80%) had Engel score of I, while the remaining patient had an Engel score of IIB.

CONCLUSION:
Our early results demonstrate that complete PQD can be successful at providing excellent seizure freedom and functional outcomes in carefully selected young pediatric patients who have concordant seizure semiology, noninvasive/invasive testing, and imaging findings with primary seizure onset zone within the ipsilateral posterior quadrant. Meticulous surgical planning and thorough understanding of the surgical anatomy and technique are critical to achieving complete disconnection.
A desiccation compound as a biofilm- and necrosis-removing agent: a case series
Authors: Cogo Alberto , Bignozzi A Carlo , Hermans Michel HE , Quint Bert J , Snels Johannes Petrus , Schultz Gregory 
Published: October 2022

Objective: A new compound, Debrichem (DEBx Medical BV, the Netherlands), a topical desiccation agent (TDA), is an active gel that contains an acidic species with a potent hygroscopic action. When in contact with microorganisms and necrosis, rapid desiccation and carbonisation of the proteins in these microorganisms, as well as of the extracellular matrix of biofilms and necrosis, occurs. The resulting ‘precipitate’ rapidly dislodges from the wound bed, resulting in a clean wound which granulates, which is a prerequisite for healing by secondary intention. Method: In a retrospective study, a series of mostly large and hard-to-heal lesions of different aetiologies were treated with a one-time application of the TDA, followed by weekly dressing changes. Results: Of the total of 54 lesions included in this case series, 22 were diagnosed as venous leg ulcers (VLUs), 20 as diabetic foot ulcers (DFUs), nine as post-traumatic, hard-to-heal lesions, two as vascular ulcers and one as an ischaemic ulcer. All of the VLUs, 75% of the DFUs and all of the other lesions reached complete granulation. Conclusion: The use of a TDA may contribute to the consistent, fast and easy removal of both biofilms and necrosis, and hence to wound healing.
Relationships Between School Enjoyment, Social Integration, and Achievement at the Beginning of Primary School: Does Family Background Matter?
Authors: Ömeroğulları Melike , Gläser-Zikuda Michaela 
Published: October 2022

<p style="text-align:justify">At the beginning of primary school, young children need to adapt academically, socially, and emotionally to their new school environment. Enjoying going to school and becoming socially integrated are important preconditions for successful learning. However, children from disadvantaged families have fewer resources and receive less support, and such deficits can result in lower attainment, negative emotions, and lower well-being. In recent years, interest in emotions and well-being in school has grown in educational research. However, studies analyzing the affective characteristics of disadvantaged students, especially in primary school, are still scarce. In this study, we analyzed reciprocal relationships between school enjoyment, social integration, and achievement using cross-lagged structural equation modeling (Grades 1 and 2), while controlling for family background and sex. We used data from the National Educational Panel Study in Germany (NEPS; N = 4,986). Results showed positive effects of school enjoyment on achievement and social integration on school enjoyment. Additionally, a better home learning environment had positive effects on school enjoyment and social integration in Grade 1. Effects of socioeconomic and migration background on school enjoyment and social integration were not significant. Our results show no evidence that educationally disadvantaged students are additionally disadvantaged in their school enjoyment or social integration at the beginning of primary school. </p>
Procedure for spotted fever group Rickettsia isolation from limited clinical blood specimens
Authors: Condit Marah E. , Jones Emma , Biggerstaff Brad J. , Kato Cecilia Y. 
Published: October 2022

Background
Current isolation techniques for spotted fever group Rickettsia from clinical samples are laborious and are limited to tissue, blood and blood derivatives with volumes ideally greater than 1 mL. We validated the use of simplified methodologies for spotted fever group Rickettsia culture isolation that overcome sample volume limitations and provide utility in clinical diagnostics and research studies.

Methodology/Principal findings
A modified cell culture method is evaluated for the isolation of Rickettsia ssp. from human diagnostic samples. Culture sampling method, culture platform, and growth phase analysis were evaluated to determine best practices for optimal culture isolation conditions. Rickettsial isolates (R. conorii, R. rickettsii, and R. parkeri) were grown in Vero E6 cells over a course of 5 to 7 days at low inoculum treatments (~40 bacterial copies) to standardize the sampling strategy at a copy number reflective of the bacteremia in acute diagnostic samples. This methodology was verified using small volumes (50 μL) of 25 unprocessed clinical whole blood, plasma, and serum samples from acute samples of patients suspected of having Rocky Mountain Spotted Fever, of which 10 were previously confirmed positive via the PanR8 qPCR assay, 13 had no detectable Rickettsia DNA by the PanR8 qPCR assay, and 2 were not previously tested; these samples resulted in the cultivation of 7 new R. rickettsii isolates.

Conclusions/Significance
We observed that rickettsial isolate growth in culture is reproducibly identified by real-time PCR testing of culture media within 72 hours after inoculation. Additionally, specimen sedimentation prior to isolation to remove red blood cells was found to decrease the amount of total organism available in the inoculum. A small volume culture method was established focusing on comparative qPCR detection rather than bacterial visualization, taking significantly shorter time to detect, and requiring less manipulation compared to traditional clinical isolate culture methods.
Association between breastfeeding, host genetic factors, and calicivirus gastroenteritis in a Nicaraguan birth cohort
Authors: Vielot Nadja Alexandra , François Ruthly , Huseynova Emilya , González Fredman , Reyes Yaoska , Gutierrez Lester , Nordgren Johan , Toval-Ruiz Christian , Vilchez Samuel , Vinjé Jan , Becker-Dreps Sylvia , Bucardo Filemon 
Published: October 2022

Background
Norovirus and sapovirus are important causes of childhood acute gastroenteritis (AGE). Breastfeeding prevents AGE generally; however, it is unknown if breastfeeding prevents AGE caused specifically by norovirus and sapovirus.

Methods
We investigated the association between breastfeeding and norovirus or sapovirus AGE episodes in a birth cohort. Weekly data on breastfeeding and AGE episodes were captured during the first year of life. Stools were collected from children with AGE and tested by RT-qPCR for norovirus and sapovirus. Time-dependent Cox models estimated associations between weekly breastfeeding and time to first norovirus or sapovirus AGE.

Findings
From June 2017 to July 2018, 444 newborns were enrolled in the study. In the first year of life, 69 and 34 children experienced a norovirus and a sapovirus episode, respectively. Exclusive breastfeeding lasted a median of 2 weeks, and any breastfeeding lasted a median of 43 weeks. Breastfeeding in the last week did not prevent norovirus (HR: 1.09, 95% CI: 0.62, 1.92) or sapovirus (HR: 1.00, 95% CI: 0.82, 1.21) AGE in a given week, adjusting for household sanitation, consumption of high-risk foods, and mother’s and child’s histo-blood group phenotypes. Maternal secretor-positive phenotype was protective against norovirus AGE, whereas child’s secretor-positive phenotype was a risk factor for norovirus AGE.

Interpretation
Exclusive breastfeeding in this population was short-lived, and no conclusions could be drawn about its potential to prevent norovirus or sapovirus AGE. Non-exclusive breastfeeding did not prevent norovirus or sapovirus AGE in the first year of life. However, maternal secretor-positive phenotype was associated with a reduced hazard of norovirus AGE.