bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oscillatory- and sector-zoned pyrochlore from carbonatites of the Kerimasi volcano, Gregory rift, Tanzania
Authors: Zaitsev Anatoly N. , Spratt John , Shtukenberg Alexander G. , Zolotarev Andrei A. , Britvin Sergey N. , Petrov Sergey V. , Kuptsova Alina V. , Antonov Anton V. 
Published: December 2020

AbstractThe Quaternary carbonatite–nephelinite Kerimasi volcano is located within the Gregory rift in northern Tanzania. It is composed of nephelinitic and carbonatitic pyroclastic rocks, tuffs, tuff breccias and pyroclastic breccias, which contain blocks of different plutonic (predominantly ijolite) and volcanic (predominantly nephelinite) rocks including carbonatites. The plutonic and volcanic carbonatites both contain calcite as the major mineral with variable amounts of magnetite or magnesioferrite, apatite and forsterite. Carbonatites also contain accessory baddeleyite, kerimasite, pyrochlore and calzirtite. Zr and Nb minerals are rarely observed in rock samples, though they are abundant in eluvial deposits of carbonatite tuff/pyroclastic breccias in the Loluni and Kisete craters. Pyrochlore, ideally (CaNa)Nb2O6F, occurs as octahedral and cubo-octahedral crystals up to 300 μm in size. Compositionally, pyrochlore from Loluni and Kisete differs. The former is enriched in U (up to 19.4 wt.% UO2), light rare earth elements (up to 8.3 wt.% LREE2O3) and Zr (up to 14.4 wt.% ZrO2), and the latter contains elevated Ti (up to 7.3 wt.% TiO2). All the crystals investigated were crystalline, including those with high U content (a= 10.4152(1) Å for Loluni anda= 10.3763(1) Å for Kisete crystals). They have little or no subsolidus alteration nor low-temperature cation exchange (A-site vacancy up to 1.5% of the site), and are suitable for single-crystal X-ray diffraction analysis (R1= 0.0206 and 0.0290; for all independent reflections for Loluni and Kisete crystals, respectively). Observed variations in the pyrochlore composition, particularly Zr content, from the Loluni and Kisete craters suggest crystallisation from compositionally different carbonatitic melts. The majority of pyrochlore crystals studied exhibit exceptionally well-preserved oscillatory- and sometimes sector-type zoning. The preferential incorporation of smaller and higher charged elements into more geometrically constrained sites on the growing surfaces explains the formation of the sector zoning. The oscillatory zoning can be rationalised by considering convectional instabilities of carbonatite magmas during their emplacement.
Paediatric RCC with sarcomatoid variation: a rare entity
Authors: Mahajan Anuj , Adiga Prashanth , Pai Vivek , Raj Keerthi 
Published: December 2020

Abstract
Background
Malignant renal masses in paediatric age group are mostly Wilms’ tumour. RCC is very rare in this age group, papillary variant being the most common. Sarcomatoid variation occurs in 5% of adult RCC, while it is extremely rare in children. No treatment protocol exists in the management of paediatric RCC.

Case presentation
Here, we present a case of 10-year-old female who presented with left flank mass. Radical nephrectomy was done which showed clear cell carcinoma with sarcomatoid variant on histopathological examination.

Conclusion
RCC with sarcomatoid variation can occur in children. However, further studies and long-term follow-up are needed for formulating a treatment protocol and prognostication factors for the same.
Moving forward through the in silico modeling of tuberculosis: a further step with UISS-TB
Authors: Russo Giulia , Sgroi Giuseppe , Parasiliti Palumbo Giuseppe Alessandro , Pennisi Marzio , Juarez Miguel A. , Cardona Pere-Joan , Motta Santo , Walker Kenneth B. , Fichera Epifanio , Viceconti Marco , Pappalardo Francesco 
Published: December 2020

Abstract
Background
In 2018, about 10 million people were found infected by tuberculosis, with approximately 1.2 million deaths worldwide. Despite these numbers have been relatively stable in recent years, tuberculosis is still considered one of the top 10 deadliest diseases worldwide. Over the years, Mycobacterium tuberculosis has developed a form of resistance to first-line tuberculosis treatments, specifically to isoniazid, leading to multi-drug-resistant tuberculosis. In this context, the EU and Indian DBT funded project STriTuVaD—In Silico Trial for Tuberculosis Vaccine Development—is supporting the identification of new interventional strategies against tuberculosis thanks to the use of Universal Immune System Simulator (UISS), a computational framework capable of predicting the immunity induced by specific drugs such as therapeutic vaccines and antibiotics.

Results
Here, we present how UISS accurately simulates tuberculosis dynamics and its interaction within the immune system, and how it predicts the efficacy of the combined action of isoniazid and RUTI vaccine in a specific digital population cohort. Specifically, we simulated two groups of 100 digital patients. The first group was treated with isoniazid only, while the second one was treated with the combination of RUTI vaccine and isoniazid, according to the dosage strategy described in the clinical trial design. UISS-TB shows to be in good agreement with clinical trial results suggesting that RUTI vaccine may favor a partial recover of infected lung tissue.

Conclusions
In silico trials innovations represent a powerful pipeline for the prediction of the effects of specific therapeutic strategies and related clinical outcomes. Here, we present a further step in UISS framework implementation. Specifically, we found that the simulated mechanism of action of RUTI and INH are in good alignment with the results coming from past clinical phase IIa trials.
Utilizing heart rate variability to predict ICU patient outcome in traumatic brain injury
Authors: Zhang Ping , Roberts Tegan , Richards Brent , Haseler Luke J. 
Published: December 2020

Abstract
Background
Prediction of patient outcome in medical intensive care units (ICU) may help for development and investigation of early interventional strategies. Several ICU scoring systems have been developed and are used to predict clinical outcome of ICU patients. These scores are calculated from clinical physiological and biochemical characteristics of patients. Heart rate variability (HRV) is a correlate of cardiac autonomic regulation and has been evident as a marker of poor clinical prognosis. HRV can be measured from the electrocardiogram non-invasively and monitored in real time. HRV has been identified as a promising ‘electronic biomarker’ of disease severity. Traumatic brain injury (TBI) is a subset of critically ill patients admitted to ICU, with significant morbidity and mortality, and often difficult to predict outcomes. Changes of HRV for brain injured patients have been reported in several studies. This study aimed to utilize the continuous HRV collection from admission across the first 24 h in the ICU in severe TBI patients to develop a patient outcome prediction system.

Results
A feature extraction strategy was applied to measure the HRV fluctuation during time. A prediction model was developed based on HRV measures with a genetic algorithm for feature selection. The result (AUC: 0.77) was compared with earlier reported scoring systems (highest AUC: 0.76), encouraging further development and practical application.

Conclusions
The prediction models built with different feature sets indicated that HRV based parameters may help predict brain injury patient outcome better than the previously adopted illness severity scores.
Computational modeling of the immune response in multiple sclerosis using epimod framework
Authors: Pernice Simone , Follia Laura , Maglione Alessandro , Pennisi Marzio , Pappalardo Francesco , Novelli Francesco , Clerico Marinella , Beccuti Marco , Cordero Francesca , Rolla Simona 
Published: December 2020

Abstract
Background
Multiple Sclerosis (MS) represents nowadays in Europe the leading cause of non-traumatic disabilities in young adults, with more than 700,000 EU cases. Although huge strides have been made over the years, MS etiology remains partially unknown. Furthermore, the presence of various endogenous and exogenous factors can greatly influence the immune response of different individuals, making it difficult to study and understand the disease. This becomes more evident in a personalized-fashion when medical doctors have to choose the best therapy for patient well-being. In this optics, the use of stochastic models, capable of taking into consideration all the fluctuations due to unknown factors and individual variability, is highly advisable.

Results
We propose a new model to study the immune response in relapsing remitting MS (RRMS), the most common form of MS that is characterized by alternate episodes of symptom exacerbation (relapses) with periods of disease stability (remission). In this new model, both the peripheral lymph node/blood vessel and the central nervous system are explicitly represented. The model was created and analysed using Epimod, our recently developed general framework for modeling complex biological systems. Then the effectiveness of our model was shown by modeling the complex immunological mechanisms characterizing RRMS during its course and under the DAC administration.

Conclusions
Simulation results have proven the ability of the model to reproduce in silico the immune T cell balance characterizing RRMS course and the DAC effects. Furthermore, they confirmed the importance of a timely intervention on the disease course.
Toward computational modelling on immune system function
Authors: Pappalardo Francesco , Russo Giulia , Reche Pedro A. 
Published: December 2020

AbstractThe 3rd edition of the computational methods for the immune system function workshop has been held in San Diego, CA, in conjunction with the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2019) from November 18 to 21, 2019. The workshop has continued its growing tendency, with a total of 18 accepted papers that have been presented in a full day workshop. Among these, the best 10 papers have been selected and extended for presentation in this special issue. The covered topics range from computer-aided identification of T cell epitopes to the prediction of heart rate variability to prevent brain injuries, from In Silico modeling of Tuberculosis and generation of digital patients to machine learning applied to predict type-2 diabetes risk.
Molecular dynamics of the immune checkpoint programmed cell death protein I, PD-1: conformational changes of the BC-loop upon binding of the ligand PD-L1 and the monoclonal antibody nivolumab
Authors: Roither Bernhard , Oostenbrink Chris , Schreiner Wolfgang 
Published: December 2020

Abstract
Background
The immune checkpoint receptor programmed cell death protein I (PD-1) has been identified as a key target in immunotherapy. PD-1 reduces the risk of autoimmunity by inducing apoptosis in antigen-specific T cells upon interaction with programmed cell death protein ligand I (PD-L1). Various cancer types overexpress PD-L1 to evade the immune system by inducing apoptosis in tumor-specific CD8+ T cells. The clinically used blocking antibody nivolumab binds to PD-1 and inhibits the immunosuppressive interaction with PD-L1. Even though PD-1 is already used as a drug target, the exact mechanism of the receptor is still a matter of debate. For instance, it is hypothesized that the signal transduction is based on an active conformation of PD-1.

Results
Here we present the results of the first molecular dynamics simulations of PD-1 with a complete extracellular domain with a focus on the role of the BC-loop of PD-1 upon binding PD-L1 or nivolumab. We could demonstrate that the BC-loop can form three conformations. Nivolumab binds to the BC-loop according to the conformational selection model whereas PD-L1 induces allosterically a conformational change of the BC-loop.

Conclusion
Due to the structural differences of the BC-loop, a signal transduction based on active conformation cannot be ruled out. These findings will have an impact on drug design and will help to refine immunotherapy blocking antibodies.
Transcriptome analysis reveals modulation of the STAT family in PEDV-infected IPEC-J2 cells
Authors: Hu Zhengzheng , Li Yuchen , Du Heng , Ren Junxiao , Zheng Xianrui , Wei Kejian , Liu Jianfeng 
Published: December 2020

Abstract
Background
Porcine epidemic diarrhea virus (PEDV) is a causative agent of serious viral enteric disease in suckling pigs. Such diseases cause considerable economic losses in the global swine industry. Enhancing our knowledge of PEDV-induced transcriptomic responses in host cells is imperative to understanding the molecular mechanisms involved in the immune response. Here, we analyzed the transcriptomic profile of intestinal porcine epithelial cell line J2 (IPEC-J2) after infection with a classical strain of PEDV to explore the host response.

Results
In total, 854 genes were significantly differentially expressed after PEDV infection, including 716 upregulated and 138 downregulated genes. Functional annotation analysis revealed that the differentially expressed genes were mainly enriched in the influenza A, TNF signaling, inflammatory response, cytokine receptor interaction, and other immune-related pathways. Next, the putative promoter regions of the 854 differentially expressed genes were examined for the presence of transcription factor binding sites using the MEME tool. As a result, 504 sequences (59.02%) were identified as possessing at least one binding site of signal transducer and activator of transcription (STAT), and five STAT transcription factors were significantly induced by PEDV infection. Furthermore, we revealed the regulatory network induced by STAT members in the process of PEDV infection.

Conclusion
Our transcriptomic analysis described the host genetic response to PEDV infection in detail in IPEC-J2 cells, and suggested that STAT transcription factors may serve as key regulators in the response to PEDV infection. These results further our understanding of the pathogenesis of PEDV.
Identification of the neuropeptide precursor genes potentially involved in the larval settlement in the Echiuran worm Urechis unicinctus
Authors: Hou Xitan , Qin Zhenkui , Wei Maokai , Fu Zhong , Liu Ruonan , Lu Li , Bai Shumiao , Ma Yubin , Zhang Zhifeng 
Published: December 2020

Abstract
Background
In marine invertebrate life cycles, which often consist of planktonic larval and benthonic adult stages, settlement of the free-swimming larva to the sea floor in response to environmental cues is a key life cycle transition. Settlement is regulated by a specialized sensory–neurosecretory system, the larval apical organ. The neuroendocrine mechanisms through which the apical organ transduces environmental cues into behavioral responses during settlement are not fully understood yet.

Results
In this study, a total of 54 neuropeptide precursors (pNPs) were identified in the Urechis unicinctus larva and adult transcriptome databases using local BLAST and NpSearch prediction, of which 10 pNPs belonging to the ancient eumetazoa, 24 pNPs belonging to the ancient bilaterian, 3 pNPs belonging to the ancient protostome, 9 pNPs exclusive in lophotrochozoa, 3 pNPs exclusive in annelid, and 5 pNPs only found in U. unicinctus. Furthermore, four pNPs (MIP, FRWamide, FxFamide and FILamide) which may be associated with the settlement and metamorphosis of U. unicinctus larvae were analysed by qRT-PCR. Whole-mount in situ hybridization results showed that all the four pNPs were expressed in the region of the apical organ of the larva, and the positive signals were also detected in the ciliary band and abdomen chaetae. We speculated that these pNPs may regulate the movement of larval cilia and chaeta by sensing external attachment signals.

Conclusions
This study represents the first comprehensive identification of neuropeptides in Echiura, and would contribute to a complete understanding on the roles of various neuropeptides in larval settlement of most marine benthonic invertebrates.
Physiological benefits evaluated by quantitative flow ratio in patients with reduced left ventricular ejection fraction who underwent percutaneous coronary intervention
Authors: Zhong Jiaxin , Chen Qin , Chen Long , Ye Zhen , Chen Huang , Sun Jianmin , Hong Juchang , Ye Mingfang , Yan Yuanming , Chen Lianglong , Luo Yukun 
Published: December 2020

Abstract
Background
To explore the clinical benefits of revascularization in patients with different levels of left ventricular ejection fraction (LVEF) from the perspective of quantitative flow ratio (QFR).

Methods
Patients who underwent successful percutaneous coronary intervention (PCI) and one-year angiographic follow-up were retrospectively screened and computed by QFR analysis. Based on their LVEF, 301 eligible patients were classified into reduced LVEF (≤ 50%, n = 48) and normal LVEF (> 50%, n = 253) groups. Pre-PCI QFR, post-PCI QFR, follow-up QFR, late lumen loss (LLL), LVEF and major adverse cardiovascular and cerebrovascular events (MACCEs) at one year were compared between groups.

Results
The reduced LVEF group had a lower mean pre-PCI QFR than the normal LVEF group (0.67 ± 0.16 vs. 0.73 ± 0.15, p = 0.004), but no significant difference was found in the post-PCI or one-year follow-up QFR. No association was found between LVEF and QFR at pre-PCI or follow-up. The reduced LVEF group had greater increases in QFR (0.27 ± 0.18 vs. 0.22 ± 0.15, p = 0.043) and LVEF (6.05 ± 9.45% vs. − 0.37 ± 8.11%, p < 0.001) than the normal LVEF group. The LLL results showed no difference between the two groups, indicating a similar degree of restenosis. The reduced LVEF group had a higher incidence of MACCEs (14.6% vs. 4.3%, p = 0.016), which was mainly due to the higher risk of heart failure (6.3% vs. 0%, p = 0.004).

Conclusion
Compared to the corresponding normal LVEF patients, patients with reduced LVEF who underwent successful PCI were reported to have greater increases in QFR and LVEF, a similar degree of restenosis, and a higher incidence of MACCEs due to a higher risk of heart failure. It seems that patients with reduced LVEF gain more coronary benefits from successful revascularization from the perspective of flow physiology evaluations.
Development and validation of the peptic ulcer scale under the system of quality of life instruments for chronic diseases based on classical test theory and generalizability theory
Authors: Wan Chonghua , Chen Ying , Gao Li , Zhang Qingqing , Quan Peng , Sun Xiaoyuan 
Published: December 2020

Abstract
Background
Quality of life (QOL) for patients with Peptic ulcer disease (PUD) is of interest worldwide and disease-specific instruments are needed for clinical research and practice. This paper focus on the development and validation of the PUD scale under the system of quality of life instruments for chronic diseases (QLICD-PU) by the modular approach and both classical test theory and Generalizability Theory.

Methods
The QLICD-PU is developed based on programmatic decision-making procedures, including multiple nominal and focus group discussions, in-depth interviews, and quantitative statistical procedures. Based on the data of 153 PUD inpatients, correlation analysis, factor analysis, t-test, and Generalizability Theory analysis (including generalizability study and decision study, ie. G-study and D-study) were used to assess the validity, reliability, and responsiveness of the scale.

Results
When the popular scale health survey short form (SF-36) was used as the standard, correlation and factor analysis confirmed good construct validity and criterion-related validity of QLICD-PU. Except for the social domain (0.62), the internal consistency α of all domains is higher than 0.70. The overall score and the test–retest reliability coefficients (Pearson r and intra-class correlation ICC) in all domains are higher than 0.80 (0.77 in the social domain). After treatments, the overall score and scores of all domains have statistically significant changes (P < 0.01), except for social impact and sexual function scores. The SRM (Standardized response mean) of domain-level scores ranges from 0.34 to 1.03. The G coefficient and reliability index (Ф coefficient) further confirm the reliability of the scale through more accurate variance components and decision-making information about changes in the number of items.

Conclusions
The QLICD-PU can be used as a useful measurement to assess the quality of life of PUD patients with good psychometric characteristics and multiple advantages.
Development of amoebic liver abscess in early pregnancy years after initial amoebic exposure: a case report
Authors: Kaiser Rainer W. J. , Allgeier Julian , Philipp Alexander B. , Mayerle Julia , Rothe Camilla , Wallrauch Claudia , op den Winkel Mark 
Published: December 2020

Abstract
Background
Infection with Entamoeba histolytica and associated complications are relatively rare in developed countries. The overall low prevalence in the Western world as well as the possibly prolonged latency period between infection with the causing pathogen and onset of clinical symptoms may delay diagnosis of and adequate treatment for amoebiasis. Amoebic liver abscess (ALA) is the most common extraintestinal manifestation of invasive amoebiasis. Pregnancy has been described as a risk factor for development of invasive amoebiasis and management of these patients is especially complex.

Case presentation
A 30-year-old Caucasian woman in early pregnancy presented to our emergency department with abdominal pain alongside elevated inflammatory markers and liver function tests. Travel history revealed multiple journeys to tropic and subtropic regions during the past decade and a prolonged episode of intermittently bloody diarrhea during a five month stay in Indonesia seven years prior to admission. Sonographic and magnetic resonance imaging revealed a 5 × 4 cm hepatic abscess. After ultrasound-guided transcutaneous liver drainage, both abscess fluids and blood cultures showed neither bacterial growth nor microscopic signs of parasitic disease. Serological testing confirmed an infection with Entamoeba histolytica, which was treated with metronidazole, followed by eradication therapy with paromomycin. Subsequent clinical, laboratory and imaging follow-up exams showed regression of the ALA. In addition, the pregnancy completed without complications and a healthy baby boy was born 7 months after termination of treatment.

Conclusions
This case of invasive amoebiasis in early pregnancy outside of endemic regions and several years after exposure demonstrates the importance of broad differential diagnostics in the context of liver abscesses. The complex interdisciplinary decisions regarding the choice of imaging techniques as well as interventional and antibiotic therapy in the context of pregnancy are discussed. Furthermore, we present possible explanations for pregnancy as a risk factor for an invasive course of amoebiasis.