bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utilizing a reductionist model to study host-microbe interactions in intestinal inflammation
Authors: Tsou Amy M. , Goettel Jeremy A. , Bao Bin , Biswas Amlan , Kang Yu Hui , Redhu Naresh S. , Peng Kaiyue , Putzel Gregory G. , Saltzman Jeffrey , Kelly Ryan , Gringauz Jordan , Barends Jared , Hatazaki Mai , Frei Sandra M. , Emani Rohini , Huang Ying , Shen Zeli , Fox James G. , Glickman Jonathan N. , Horwitz Bruce H. , Snapper Scott B. 
Published: November 2021

Abstract
Background
The gut microbiome is altered in patients with inflammatory bowel disease, yet how these alterations contribute to intestinal inflammation is poorly understood. Murine models have demonstrated the importance of the microbiome in colitis since colitis fails to develop in many genetically susceptible animal models when re-derived into germ-free environments. We have previously shown that Wiskott-Aldrich syndrome protein (WASP)-deficient mice (Was−/−) develop spontaneous colitis, similar to human patients with loss-of-function mutations in WAS. Furthermore, we showed that the development of colitis in Was−/− mice is Helicobacter dependent. Here, we utilized a reductionist model coupled with multi-omics approaches to study the role of host-microbe interactions in intestinal inflammation.

Results
Was−/− mice colonized with both altered Schaedler flora (ASF) and Helicobacter developed colitis, while those colonized with either ASF or Helicobacter alone did not. In Was−/− mice, Helicobacter relative abundance was positively correlated with fecal lipocalin-2 (LCN2), a marker of intestinal inflammation. In contrast, WT mice colonized with ASF and Helicobacter were free of inflammation and strikingly, Helicobacter relative abundance was negatively correlated with LCN2. In Was−/− colons, bacteria breach the mucus layer, and the mucosal relative abundance of ASF457 Mucispirillum schaedleri was positively correlated with fecal LCN2. Meta-transcriptomic analyses revealed that ASF457 had higher expression of genes predicted to enhance fitness and immunogenicity in Was−/− compared to WT mice. In contrast, ASF519 Parabacteroides goldsteinii’s relative abundance was negatively correlated with LCN2 in Was−/− mice, and transcriptional analyses showed lower expression of genes predicted to facilitate stress adaptation by ASF519 in Was−/−compared to WT mice.

Conclusions
These studies indicate that the effect of a microbe on the immune system can be context dependent, with the same bacteria eliciting a tolerogenic response under homeostatic conditions but promoting inflammation in immune-dysregulated hosts. Furthermore, in inflamed environments, some bacteria up-regulate genes that enhance their fitness and immunogenicity, while other bacteria are less able to adapt and decrease in abundance. These findings highlight the importance of studying host-microbe interactions in different contexts and considering how the transcriptional profile and fitness of bacteria may change in different hosts when developing microbiota-based therapeutics.
Evaluation of POD based surrogate models of fields resulting from nonlinear FEM simulations
Authors: de Gooijer Boukje M. , Havinga Jos , Geijselaers Hubert J. M. , van den Boogaard Anton H. 
Published: November 2021

AbstractSurrogate modelling is a powerful tool to replace computationally expensive nonlinear numerical simulations, with fast representations thereof, for inverse analysis, model-based control or optimization. For some problems, it is required that the surrogate model describes a complete output field. To construct such surrogate models, proper orthogonal decomposition (POD) can be used to reduce the dimensionality of the output data. The accuracy of the surrogate models strongly depends on the (pre)processing actions that are used to prepare the data for the dimensionality reduction. In this work, POD-based surrogate models with Radial Basis Function interpolation are used to model high-dimensional FE data fields. The effect of (pre)processing methods on the accuracy of the result field is systematically investigated. Different existing methods for surrogate model construction are compared with a novel method. Special attention is given to data fields consisting of several physical meanings, e.g. displacement, strain and stress. A distinction is made between the errors due to truncation and due to interpolation of the data. It is found that scaling the data per physical part substantially increases the accuracy of the surrogate model.
Investigating regional excess mortality during 2020 COVID-19 pandemic in selected Latin American countries
Authors: Lima Everton E. C. , Vilela Estevão A. , Peralta Andrés , Rocha Marília , Queiroz Bernardo L. , Gonzaga Marcos R. , Piscoya-Díaz Mario , Martinez-Folgar Kevin , García-Guerrero Víctor M. , Freire Flávio H. M. A. 
Published: November 2021

AbstractIn this paper, we measure the effect of the 2020 COVID-19 pandemic wave at the national and subnational levels in selected Latin American countries that were most affected: Brazil, Chile, Ecuador, Guatemala, Mexico, and Peru. We used publicly available monthly mortality data to measure the impacts of the pandemic using excess mortality for each country and its regions. We compare the mortality, at national and regional levels, in 2020 to the mortality levels of recent trends and provide estimates of the impact of mortality on life expectancy at birth. Our findings indicate that from April 2020 on, mortality exceeded its usual monthly levels in multiple areas of each country. In Mexico and Peru, excess mortality was spreading through many areas by the end of the second half of 2020. To a lesser extent, we observed a similar pattern in Brazil, Chile, and Ecuador. We also found that as the pandemic progressed, excess mortality became more visible in areas with poorer socioeconomic and sanitary conditions. This excess mortality has reduced life expectancy across these countries by 2–10 years. Despite the lack of reliable information on COVID-19 mortality, excess mortality is a useful indicator for measuring the effects of the coronavirus pandemic, especially in the context of Latin American countries, where there is still a lack of good information on causes of death in their vital registration systems.
NeuroAid II (MLC901) and polypharmacy in stroke and the risk of hepatotoxicity: a case report
Authors: Abdul Rashid Anna Misya’il , Md Noh Mohamad Syafeeq Faeez , Yusof Khan Abdul Hanif Khan , Loh Wei Chao , Baharin Janudin , Ibrahim Azliza , Inche Mat Liyana Najwa , Wan Sulaiman Wan Aliaa , Hoo Fan Kee , Hanapiah Fazah Akhtar , Basri Hamidon 
Published: November 2021

Abstract
Background
NeuroAid II (MLC901) is a promising therapy for stroke patients who present outside of therapeutic window for reperfusion therapy. Studies have proven its efficacy in ischemic stroke; however, data of drug safety and combination with other medications especially anticoagulants are heterogenous. We report a possible case of hepatotoxicity induced by NeuroAid II in combination with anticoagulants.

Case presentation
We report an elderly patient who developed symptoms of cardioembolic stroke presented outside of time window for reperfusion therapy. He was started on a regiment of statins, anticoagulation, beta blockers and NeuroAid II. One month later he presented with deranged liver enzymes. Cessation of NeuroAid II resulted in rapid improvement of transaminitis within days.

Conclusions
We wish to highlight the potential harmful effect of administering NeuroAid II with an anticoagulant and the importance of routine follow-up and blood monitoring in the elderly patients with stroke.
Pathophysiological role of major adipokines in Atrial Fibrillation
Authors: Rafaqat Saira , Rafaqat Sana , Rafaqat Simon 
Published: November 2021

Abstract
Background
The adipokines, secreted from adipose tissue or body fats, are also called adipocytokines which are cytokines, cell signaling proteins or cell–cell communication. However, AF is a common cardiac arrhythmia in which the heart beats so fast by abnormal beating and is a serious public health disease associated with increased heart failure, systemic thromboembolism, and death. Adipokines are cardiovascular disease (CVD) mediators or biomarkers that affect the heart as well as blood vessels, by increasing the cardiac contractility and action potential duration, which result in the extent of left ventricular and atrial remodeling.

Main body
Google Scholar, PubMed, and science direct were used to review the literature. Many keywords were used for searching the literature such as Adipokines, Leptin, Apelin, Adiponectin, Omentin-1, Chemerin, CTRP3, TNF-α, IL-6, IL-10, and AF. According to the literature, much more data are available for numerous adipokines, but this review article only has taken few major adipokines which played their major role in Atrial Fibrillation. The review article did not limit the time frame.

Conclusion
In conclusion, adipokines play a significant role in the development and progress of atrial fibrillation. Also, there are major adipokines such as adiponectin, apelin, C1q/TNF-Related Protein 3 (CTRP3), Chemerin, Omentin-1, interleukin-6, Leptin, TNF-α, resistin, and interleukin-10, which played their pathophysiological role in atrial fibrillation by causing cardiac hypertrophy, increasing the cardiac contractility and action potential duration, atrial fibrosis, electrical and structural remodeling of atrial tissue.
Frontal tangential coronal view two-dimensional ultrasonography in assessment of fetal face [mouth and nose] in comparison with four-dimensional ultrasonography
Authors: Elghany Algahlan Hisham A. , Elsemary Mamdouh , Hazem Mohammed 
Published: November 2021

Abstract
Background
The fetal face reflects strictly the development of the fetal brain during its growth. Four-dimensional (4D) examination permits continuous monitoring of the examined parts of fetal face and surface. The final performance of obstetric sonographic images depends upon multiple factors, such as fetal lie, uterine wall, abdominal wall fat, amniotic fluid, and the number of gestations which may limit the optimum performance of (4D) ultrasound. The two-dimensional (2D) ultrasound is the first choice due to its wide availability, low cost, and real-time capabilities. The tangential view obtained by (2D) ultrasound coronal sections through the face showed the nose, nostril, lips, eye, lens, and hard palate.

Results
One hundred and sixty fetuses showed straight forwards obstetric examination by both 2D and 4D examinations with identical final reports. While the total number of fetuses with clear images by 2D frontal tangential coronal examination was 191 cases, only 29 cases failed, whereas 170 cases obtained clear images by 4D examination, and 50 cases failed. Both 2D and 4D ultrasound failed to obtain clear images of 19 cases, while 4D failed for 31 cases, and 2D failed for 10 cases. 2D imaging was found to be significantly better than 4D imaging, with a P value of 0.009.

Conclusion
2D ultrasound using the frontal tangential coronal view is an essential part of the fetal examination and more superior than 4D ultrasound in assessing facial anatomy and anomalies, as well comparable to 4D ultrasound as regards fascial expression.
Modelling the mechanical behaviours of glassy hydrogels
Authors: Chen Baihong , Zhang Xinning , Wu Ziliang , Xiao Rui 
Published: November 2021

Abstract
Our recent works show that poly(methacrylamide-co-methacrylic acid) (P(MAAm-co-MAAc)) hydrogels with moderate water content (50–70 wt%) exhibit similar glass transition behaviours as in dry polymers. In the glassy state, these gels exhibit a modulus of several hundred megapascals and a failure strength of tens of megapascals, which are much higher than other reported tough gels. In this work, we apply a viscoplastic model to describe the temperature-dependent and rate-dependent mechanical behaviours of the P(MAAm-co-MAAc) gels. It is found that the viscoplastic model developed for dry polymers can also describe the stress-strain responses of gels including yielding and strain softening. It can also capture the stress relaxation behaviours. This work confirms that the glass transition in the gels and dry polymers shares a similar physical mechanism. Meanwhile, it indicates the classic viscoelastic/viscoplastic models can be readily applied for this new type of tough gels.
CK1α protects WAVE from degradation to regulate cell shape and motility in the immune response
Authors: Hirschhäuser Alexander , van Cann Marianne , Bogdan Sven 
Published: November 2021

ABSTRACT
The WAVE regulatory complex (WRC) is the main activator of the Arp2/3 complex, promoting lamellipodial protrusions in migrating cells. The WRC is basally inactive but can be activated by Rac1 and phospholipids, and through phosphorylation. However, the in vivo relevance of the phosphorylation of WAVE proteins remains largely unknown. Here, we identified casein kinase I alpha (CK1α) as a regulator of WAVE, thereby controlling cell shape and cell motility in Drosophila macrophages. CK1α binds and phosphorylates WAVE in vitro. Phosphorylation of WAVE by CK1α appears not to be required for activation but, rather, regulates its stability. Pharmacologic inhibition of CK1α promotes ubiquitin-dependent degradation of WAVE. Consistently, loss of Ck1α but not ck2 function phenocopies the depletion of WAVE. Phosphorylation-deficient mutations in the CK1α consensus sequences within the VCA domain of WAVE can neither rescue mutant lethality nor lamellipodium defects. By contrast, phosphomimetic mutations rescue all cellular and developmental defects. Finally, RNAi-mediated suppression of 26S proteasome or E3 ligase complexes substantially rescues lamellipodia defects in CK1α-depleted macrophages. Therefore, we conclude that basal phosphorylation of WAVE by CK1α protects it from premature ubiquitin-dependent degradation, thus promoting WAVE function in vivo.
This article has an associated First Person interview with the first author of the paper.
Value of contrast-enhanced ultrasound in predicting early lymph-node metastasis in oral cancer
Authors: Ding Shiwen , Xiong Ping , Zuo Jiaxin 
Published: November 2021

Objectives: To explore the value of contrast-enhanced ultrasound (CEUS) in predicting early lymph node metastasis in clinically node-negative oral cancer patients. Methods: We recruited 42 patients (a total of 70 lymph nodes) with clinically node-negative oral cancer in the study. All of them received both conventional ultrasound (B-mode and power Doppler) and CEUS before operation and then they were taken for pathological examination to analyze the diagnostic accuracy. And their CEUS data were analyzed qualitatively and quantitatively. Results: The sensitivity and specificity of CEUS in the diagnosis of cervical lymph node metastasis of oral cancer were 82.7 and 82.9%, respectively. The accuracy of conventional ultrasound was only 67.1% while that of CEUS was up to 82.9%. The area under the cure (AUC) of CEUS in detecting lymph node metastasis was 0.828, which was higher than the 0.614 by conventional ultrasound, with statistically significant differences observed (p < 0.05). Most of the metastatic lymph nodes were characterized by inhomogeneous enhancement and the peak intensity (PI) of the metastatic group was lower than that of the non-metastatic group (p < 0.05). Conclusions: Compared with conventional ultrasound, CEUS may have higher clinical value for predicting early lymph node metastasis in clinically node-negative oral cancer patients. And quantitative parameters obtained from CEUS may provide valuable information in the diagnosis of cervical lymph node metastasis.
Isolation and sequencing of three RB49-like bacteriophages infecting O antigen-producing E. coli strains
Authors: Efimov Alexander , Kulikov Eugene , Golomidova Alla , Belalov Ilya , Babenko Vladislav , Letarov Andrey 
Published: November 2021

E. coli strains 4s, F5 and F17, whose O antigens are structurally characterized and shown to effectively shield the cell surface from bacteriophage attack, were used as the hosts to isolate novel RB49-like bacteriophages. Three novel phage isolates were obtained, and their genomes were sequenced and annotated. Despite high overall identity levels of these genomic sequences, the variants of large distal tail fiber subunit, orthologous to the bacteriophage T2 long tail receptor recognition protein gp38, were unique for each phage, suggesting their role in host range determination. The annotated genomes are available via NCBI Genbank, acc. numbers MZ504876-MZ504878.
An Analytic Center Cutting Plane Method to Determine Complete Positivity of a Matrix
Authors: Badenbroek Riley , de Klerk Etienne 
Published: November 2021

We propose an analytic center cutting plane method to determine whether a matrix is completely positive and return a cut that separates it from the completely positive cone if not. This was stated as an open (computational) problem by Berman et al. [Berman A, Dur M, Shaked-Monderer N (2015) Open problems in the theory of completely positive and copositive matrices. Electronic J. Linear Algebra 29(1):46–58]. Our method optimizes over the intersection of a ball and the copositive cone, where membership is determined by solving a mixed-integer linear program suggested by Xia et al. [Xia W, Vera JC, Zuluaga LF (2020) Globally solving nonconvex quadratic programs via linear integer programming techniques. INFORMS J. Comput. 32(1):40–56]. Thus, our algorithm can, more generally, be used to solve any copositive optimization problem, provided one knows the radius of a ball containing an optimal solution. Numerical experiments show that the number of oracle calls (matrix copositivity checks) for our implementation scales well with the matrix size, growing roughly like [Formula: see text] for d × d matrices. The method is implemented in Julia and available at https://github.com/rileybadenbroek/CopositiveAnalyticCenter.jl . Summary of Contribution: Completely positive matrices play an important role in operations research. They allow many NP-hard problems to be formulated as optimization problems over a proper cone, which enables them to benefit from the duality theory of convex programming. We propose an analytic center cutting plane method to determine whether a matrix is completely positive by solving an optimization problem over the copositive cone. In fact, we can use our method to solve any copositive optimization problem, provided we know the radius of a ball containing an optimal solution. We emphasize numerical performance and stability in developing this method. A software implementation in Julia is provided.
Enhancing undergraduate midwifery: using drug and alcohol baby simulators in education
Authors: Khan Humaira , Cescutti-Butler Luisa 
Published: November 2021

Background In the UK, simulation in midwifery education mostly relates to developing clinical skills such as managing obstetric emergencies. However, there is minimal use of neonate simulators in educating student midwives on the impact of teratogens on fetal development. There is also limited research on using neonatal simulators as a creative pedagogical tool in undergraduate midwifery education. Objectives The two main objectives of this study were to ascertain whether students could recognise the physical impact of teratogens in the early postnatal period while interacting with simulators and to explore whether midwifery students understood their role as future midwives when working with pregnant women who may be misusing substances. Methods This qualitative research involved Level 4 student midwives from south England. A taught session on protecting the unborn environment was provided and students were tasked to interact with low fidelity fetal alcohol syndrome simulators and medium fidelity drug affected simulators. Student responses to group activities, such as interacting with the simulators and considering their role as future midwives in educating pregnant women about the impact of teratogens on a fetus and newborn baby, were collected. Results The use of the simulators was a useful pedagogical tool for enhancing student knowledge around teratogenesis and fetal impact. Conclusions Neonatal simulators can be used to engage undergraduate midwifery students and enhance their learning and knowledge.
Introducing a day-case arthroplasty pathway significantly reduces overall length of stay
Authors: Saunders Paul , Smith Nick , Syed Farhan , Selvaraj Thomas , Waite Jon , Young Stephen 
Published: November 2021

Aims Day-case arthroplasty is gaining popularity in Europe. We report outcomes from the first 12 months following implementation of a day-case pathway for unicompartmental knee arthroplasty (UKA) and total hip arthroplasty (THA) in an NHS hospital. Methods A total of 47 total hip arthroplasty (THA) and 24 unicompartmental knee arthroplasty (UKA) patients were selected for the day-case arthroplasty pathway, based on preoperative fitness and agreement to participate. Data were likewise collected for a matched control group (n = 58) who followed the standard pathway three months prior to the implementation of the day-case pathway. We report same-day discharge (SDD) success, reasons for delayed discharge, and patient-reported outcomes. Overall length of stay (LOS) for all lower limb arthroplasty was recorded to determine the wider impact of implementing a day-case pathway. Results Patients on the day-case pathway achieved SDD in 47% (22/47) of THAs and 67% (16/24) of UKAs. The most common reasons for failed SDD were nausea, hypotension, and pain, which were strongly associated with the use of fentanyl in the spinal anaesthetic. Complications and patient-reported outcomes were not significantly different between groups. Following the introduction of the day-case pathway, the mean LOS reduced significantly by 0.7, 0.6, and 0.5 days respectively in THA, UKA, and total knee arthroplasty cases (p < 0.001). Conclusion Day-case pathways are feasible in an NHS set-up with only small changes required. We do not recommend fentanyl in the spinal anaesthetic for day-case patients. An important benefit seen in our unit is the so-called ‘day-case effect’, with a significant reduction in mean LOS seen across all lower limb arthroplasty. Cite this article: Bone Jt Open 2021;2(11):900–908.