bluuebunny/crossref_metadata_2025_split huggingface dataset:
Derbylite and graeserite from the Monte Arsiccio mine, Apuan Alps, Tuscany, Italy: occurrence and crystal-chemistry
Authors: Biagioni Cristian , Bonaccorsi Elena , Perchiazzi Natale , Hålenius Ulf , Zaccarini Federica 
Published: September 2020

AbstractNew occurrences of derbylite, Fex2+Fe3+4–2xTi4+3+xSb3+O13(OH), and graeserite, Fex2+Fe3+4–2xTi4+3+xAs3+O13(OH), have been identified in the Monte Arsiccio mine, Apuan Alps, Tuscany, Italy. Derbylite occurs as prismatic to acicular black crystals in carbonate veins. Iron and Ti are replaced by V (up to 0.29 atoms per formula unit, apfu) and minor Cr (up to 0.04 apfu). Mössbauer spectroscopy confirmed the occurrence of Fe2+ (up to 0.73 apfu), along with Fe3+. The Sb/(As+Sb) atomic ratio ranges between 0.73 and 0.82. Minor Ba and Pb (up to 0.04 apfu) substitute. Derbylite is monoclinic, space group P21/m, with unit-cell parameters a = 7.1690(3), b = 14.3515(7), c = 4.9867(2) Å, β = 104.820(3)° and V = 495.99(4) Å3. The crystal structure was refined to R1 = 0.0352 for 1955 reflections with Fo > 4σ(Fo). Graeserite occurs as prismatic to tabular black crystals, usually twinned, in carbonate veins or as porphyroblasts in schist. Graeserite in the first kind of assemblage is V rich (up to 0.66 apfu), and V poor in the second kind (0.03 apfu). Along with minor Cr (up to 0.06 apfu), this element replaces Fe and Ti. The occurrence of Fe2+ (up to 0.68 apfu) is confirmed by Mössbauer spectroscopy. Arsenic is dominant over Sb and detectable amounts of Ba and Pb have been measured (up to 0.27 apfu). Graeserite is monoclinic, space group C2/m, with unit-cell parameters for two samples: a = 5.0225(7), b = 14.3114(18), c = 7.1743(9) Å, β = 104.878(3)°, V = 498.39(11) Å3; and a = 5.0275(4), b = 14.2668(11), c = 7.1663(5) Å, β = 105.123(4)° and V = 496.21(7) Å3. The crystal structures were refined to R1 = 0.0399 and 0.0237 for 428 and 1081 reflections with Fo > 4σ(Fo), respectively. Derbylite and graeserite are homeotypic. They share the same tunnel structure, characterised by an octahedral framework and cuboctahedral cavities, hosting (As/Sb)O3 groups and (Ba/Pb) atoms.
Energetics of the distribution of cell wall in wood based on an eigenvalue analysis
Authors: Tsutsumi Harusa , Haga Hirokazu , Fujimoto Takaaki 
Published: September 2020

AbstractWood is a highly heterogeneous material characterized by a number of properties that vary significantly among samples. Even in woods of the same density, substantial differences in properties show up depending on the distribution pattern of their cell walls. With the aim of deep understanding of the wood variation, we examine this pattern from the physical perspectives using samples of the same density but with significantly different shrinkages. The power spectrum, which represents the regularity of the occurrence of cell walls or lumen, was obtained through Fourier transform processing of micrographs of the transverse sections of wood samples. The set of eigenvalues calculated from the variance–covariance matrix comprising the spectra is identified with a Hamiltonian representing the energy eigenstate of the wood. The cell wall distribution can then be analyzed from within thermodynamics and statistical mechanics. The eigenvalues from the images of latewood were widely distributed compared with those from earlywood. The first eigenvalue is equivalent to the Helmholtz free energy, and thus the high-shrinkage samples showed large Helmholtz free energy because of the high presence of latewood. The Shannon entropy calculated from the probability associated with each energy eigenstate was larger in images of earlywood than latewood. That is, low-shrinkage samples have a more homogeneous structure than high-shrinkage samples. These results were strongly consistent with observations from micrographs and previous knowledge of the physical properties of woods. The physical approaches proposed in this study is independent of the origin of the data and therefore has a wide application.
Prevalence and factors associated with timely initiation of breastfeeding in Kilimanjaro region, northern Tanzania: a cross-sectional study
Authors: Kiwango Frank , Mboya Innocent B. , John Beatrice , Hashim Tamara , Msuya Sia E. , Mgongo Melina 
Published: September 2020

Abstract
Background
The World Health Organization (WHO) recommends early initiation of breastfeeding within 1 h as it confers many benefits to the child and prevents neonatal mortality. This study aimed to determine the prevalence and factors associated with timely initiation of breastfeeding in the Kilimanjaro region, northern Tanzania.

Methods
We analyzed secondary data for 866 participants from a population-based cross-sectional study conducted in April 2016 among mothers with children aged less than 5 years in three districts; Rombo, Same, and Moshi Municipal council in Kilimanjaro region, northern Tanzania. A multistage sampling selected study participants and interviewed using a questionnaire. The generalized linear model, with Poisson family and log-link function was used to estimate the prevalence ratios (PR) and 95% confidence intervals (CI) for factors associated with timely initiation of breastfeeding.

Results
The prevalence of timely initiation of breastfeeding was 71.1%. The vast majority of mothers (90.7%) gave colostrum, and less than a tenth (6.4%) gave pre-lacteal feed to their children. Adjusted for other factors, not giving children prelacteal feeds remained was significantly associated with a higher prevalence of timely initiation of breastfeeding (PR: 2.22, 95%CI 1.38, 3.56, p = 0.001). There was no significant association between other characteristics and the likelihood of timely initiation of breastfeeding in this study.

Conclusion
The prevalence of timely initiation of breastfeeding in the Kilimanjaro region was higher than the national estimate. The practice of not giving infants prelacteal feeds increased the likelihood of timely initiation of breastfeeding. There is a need to encourage mothers on the significance of recommended ANC visits and early initiation of breastfeeding to their infants to improve the practice.
Comprehensive profiling of immune-related genes in soft tissue sarcoma patients
Authors: Hu Chuan , Chen Bo , Huang Zhangheng , Liu Chuan , Ye Lin , Wang Cailin , Tong Yuexin , Yang Jiaxin , Zhao Chengliang 
Published: September 2020

Abstract
Background
Immune-related genes (IRGs) have been confirmed to have an important role in tumorigenesis and tumor microenvironment formation. Nevertheless, a systematic analysis of IRGs and their clinical significance in soft tissue sarcoma (STS) patients is lacking.

Methods
Gene expression files from The Cancer Genome Atlas (TCGA) database and Genotype-Tissue Expression (GTEx) were used to select differentially expressed genes (DEGs). Differentially expressed immune-related genes (DEIRGs) were determined by matching the DEG and ImmPort gene sets, which were evaluated by functional enrichment analysis. Unsupervised clustering of the identified DEIRGs was conducted, and associations with prognosis, the tumor microenvironment (TME), immune checkpoints, and immune cells were analyzed simultaneously. Two prognostic signatures, one for overall survival (OS) and one for progression free survival (PFS), were established and validated in an independent set. Finally, two transcription factor (TF)-IRG regulatory networks were constructed, and a crucial regulatory axis was validated.

Results
In total, 364 DEIRGs and four clusters were identified. OS, TME scores, five immune checkpoints, and 12 types of immune cells were found to be significantly different among the four clusters. The two prognostic signatures incorporating 20 DEIRGs showed favorable discrimination and were successfully validated. Two nomograms combining signature and clinical variables were generated. The C-indexes were 0.879 (95%CI 0.832 ~ 0.926) and 0.825 (95%CI 0.776 ~ 0.874) for the OS and PFS signatures, respectively. Finally, TF-IRG regulatory networks were established, and the MYH11-ADM regulatory axis was verified in three independent datasets.

Conclusion
This comprehensive analysis of the IRG landscape in soft tissue sarcoma revealed novel IRGs related to carcinogenesis and the immune microenvironment. These findings have implications for prognosis and therapeutic responses, which reveal novel potential prognostic biomarkers, promote precision medicine, and provide potential novel targets for immunotherapy.
Determinants of non-recovery in physical health-related quality of life one year after cardiac surgery: a prospective single Centre observational study
Authors: Rijnhart-de Jong Hilda , Haenen Jo , Bol Raap Goris , Jekel Lilian , Vossenberg Tessel , Bondarenko Olga , Boerma Christiaan 
Published: September 2020

Abstract
Background
Recent studies show that substantial percentage of patients experienced worsening of health related quality of life (HRQoL) 1 year after cardiac surgery. The aim of this study is to identify risk factors that interfere with improvement of HRQoL.

Methods
From December 2015 till July 2017 a prospective single centre observational study was carried out in 1920 patients participated who underwent non-salvage cardiac surgery. All patients were requested to complete a Short Form 36 (SF-36) questionnaire before and 1 year after surgery. Primary aim of the study was to identify risk factors for non-recovery in the physical domain of the SF-36 in all cardiac surgery patients. Secondary aim was to identify identical risk factors in patients with isolated coronary artery bypass grafting.

Results
After cardiac surgery, the questionnaires for physical and mental health were completed by respectively 803 and 807 patients. Median age was 69[62–75] years, and 77% was male. In comparison to the preoperative status, 176 patients (21.9%) did not display an improvement in the SF-36 physical domain score 1 year after cardiac surgery. In a multivariate analysis independent risk factors for non-recovery in the SF-36 physical domain were baseline SF36 physical domain score (OR 0.954[0.942–0.965], P < 0.001), diabetes (OR 0.437 [0.265–0.720], P 0.001), female sex (OR 0.492 [0.307–0.789], P 0.003), post-operative infection (OR 0.240 [0.109–0.525], P < 0.001) and PCI within 1 year (OR 0.113 [0.036–0.349], P < 0.001) For isolated CABG, 23.2% of patients did not display an improvement in the physical domain score and risk factors appeared to be identical.

Conclusions
Twenty two percent of all cardiac surgery patients did not show an improvement in the physical domain score of the HRQoL between the preoperative period and 1 year after surgery. Independent risk factors for non-recovery after cardiac surgery were baseline SF-36 physical domain score, diabetes, female sex, any postoperative infection and the need for PCI in the first year. Further research is needed to tailor the patient selection procedure prior to surgery and potentially modify risk factors in the perioperative process.

Trial registration
Due to type of study not applicable. https://www.ccmo.nl/metcs/erkende-metcs/regionale-toetsingscommissie-patientgebonden-onderzoek.
Finding semantic patterns in omics data using concept rule learning with an ontology-based refinement operator
Authors: Malinka František , železný Filip , Kléma Jiří 
Published: September 2020

AbstractBackgroundIdentification of non-trivial and meaningful patterns in omics data is one of the most important biological tasks. The patterns help to better understand biological systems and interpret experimental outcomes. A well-established method serving to explain such biological data is Gene Set Enrichment Analysis. However, this type of analysis is restricted to a specific type of evaluation. Abstracting from details, the analyst provides a sorted list of genes and ontological annotations of the individual genes; the method outputs a subset of ontological terms enriched in the gene list. Here, in contrary to enrichment analysis, we introduce a new tool/framework that allows for the induction of more complex patterns of 2-dimensional binary omics data. This extension allows to discover and describe semantically coherent biclusters.ResultsWe present a new rapid method called sem1R that reveals interpretable hidden rules in omics data. These rules capture semantic differences between two classes: a target class as a collection of positive examples and a non-target class containing negative examples. The method is inspired by the CN2 rule learner and introduces a new refinement operator that exploits prior knowledge in the form of ontologies. In our work this knowledge serves to create accurate and interpretable rules. The novel refinement operator uses two reduction procedures: Redundant Generalization and Redundant Non-potential, both of which help to dramatically prune the rule space and consequently, speed-up the entire process of rule induction in comparison with the traditional refinement operator as is presented in CN2.ConclusionsEfficiency and effectivity of the novel refinement operator were tested on three real different gene expression datasets. Concretely, the Dresden Ovary Dataset, DISC, and m2816 were employed. The experiments show that the ontology-based refinement operator speeds-up the pattern induction drastically. The algorithm is written in C++ and is published as an R package available athttp://github.com/fmalinka/sem1r.
Open-chest versus closed-chest cardiopulmonary resuscitation in trauma patients with signs of life upon hospital arrival: a retrospective multicenter study
Authors: Endo Akira , Kojima Mitsuaki , Hong Zhi-Jie , Otomo Yasuhiro , Coimbra Raul 
Published: September 2020

Abstract
Background
The effectiveness and indications of open-chest cardiopulmonary resuscitation (OCCPR) have been still debatable. Although current guidelines state that the presence of signs of life (SOL) is an indication for OCCPR, scientific evidence corroborating this recommendation has been scarce. This study aimed to compare the effectiveness of OCCPR to closed-chest cardiopulmonary resuscitation (CCCPR) in severe trauma patients with SOL upon arrival at the emergency department (ED).

Methods
A retrospective cohort study analyzing data from the Trauma Quality Improvement Program (TQIP) database, a nationwide trauma registry in the USA, between 2010 and 2016 was conducted. Severe trauma patients who had SOL upon arrival at the hospital and received cardiopulmonary resuscitation within the first 6 h of ED admission were identified. Survival to hospital discharge was evaluated using logistic regression analysis, instrumental variable analysis, and propensity score matching analysis adjusting for potential confounders.

Results
A total of 2682 patients (OCCPR 1032; CCCPR 1650) were evaluated; of those 157 patients (15.2%) in the OCCPR group and 193 patients (11.7%) in the CCCPR group survived. OCCPR was significantly associated with higher survival to hospital discharge in both the logistic regression analysis (adjusted odds ratio [95% confidence interval] = 1.99 [1.42–2.79], p <  0.001) and the instrumental variable analysis (adjusted odds ratio [95% confidence interval] = 1.16 [1.02–1.31], p = 0.021). In the propensity score matching analysis, 531 matched pairs were generated, and the OCCPR group still showed significantly higher survival at hospital discharge (89 patients [16.8%] in the OCCPR group vs 58 patients [10.9%] in the CCCPR group; odds ratio [95% confidence interval] = 1.66 [1.13–2.42], p = 0.009).

Conclusions
Compared to CCCPR, OCCPR was associated with significantly higher survival at hospital discharge in severe trauma patients with SOL upon ED arrival. Further studies to confirm these results and to assess long-term neurologic outcomes are needed.
Analyses of the expression, immunohistochemical properties and serodiagnostic potential of Schistosoma japonicum peroxiredoxin-4
Authors: Dang-Trinh Minh-Anh , Angeles Jose Ma. M. , Moendeg Kharleezelle J. , Macalanda Adrian Miki C. , Nguyen Thu-Thuy , Higuchi Luna , Nakagun Shotaro , Kirinoki Masashi , Chigusa Yuichi , Goto Yasuyuki , Kawazu Shin-ichiro 
Published: September 2020

Abstract
Background
Schistosoma japonicum, which inhabits the mesenteric vein of the mammalian hosts for about 20 to 30 years, is subjected to the oxidative stresses from the host defense mechanism during their intra-mammalian stages. To counteract this host immune attack, the parasite utilizes their antioxidant system for survival inside the host. Peroxiredoxins (Prxs), thiol-specific antioxidant proteins, play an essential role for protecting the parasite against oxidative stress by reducing hydrogen peroxide to water. Only three types of 2-Cys Prxs have been previously characterized in S. japonicum whereas a fourth Prx has been identified for Schistosoma mansoni as Prx-4. A sequence coding homologous to this gene in the S. japonicum database was identified, characterized and expressed as recombinant SjPrx-4 protein (rSjPrx-4). Furthermore, rSjPrx-4 was evaluated in this study for its diagnostic potentials in detecting S. japonicum infection in humans.

Results
The gene found in the parasite genome contained 2 active-site cysteines with conserved sequences in the predicted amino acid (AA) sequence and showed 75% identity with that of the previously characterized Prx (TPx-1) of S. japonicum. The gene was expressed in different stages of schistosome life-cycle with highest transcription level in the adult male. The gene was cloned into a plasmid vector and then transfected into Escherichia coli for expression of rSjPrx-4. Anti-rSjPrx-4 mouse sera recognized native SjPrx-4 in egg and adult worm lysate by western blotting. The result of a mixed function oxidation assay in which rSjPrx-4 prevented the nicking of DNA from hydroxyl radicals confirmed its antioxidant activity. Subsequently, immunolocalization analysis showed the localization of SjPrx-4 inside the egg, on the tegument and in the parenchyma of the adult worm. Enzyme-linked immunosorbent assay results showed that rSjPrx-4 has 83.3% sensitivity and 87.8% specificity. Its diagnostic potential was further evaluated in combination with recombinant SjTPx-1 protein, yielding an improved sensitivity and specificity of 90% and 92.7%, respectively.

Conclusions
These results suggest that SjPrx-4 plays a role as an antioxidant dealing with oxidative stresses of S. japonicum, and its diagnostic potential improved by coupling it with SjTPx-1 is a proof for developing a serological test with better diagnostic performance for human schistosomiasis.
Association of IL-10 and TNF-α polymorphisms with risk and aggressiveness of hepatocellular carcinoma in patients with HCV-related cirrhosis
Authors: Saleh Ahmed , Saed Ahmed M. , Mansour Mostafa 
Published: September 2020

Abstract
Background
Hepatitis C virus (HCV) infection is a significant risk factor for cirrhosis and hepatocellular carcinoma (HCC) that carry a high mortality. The study aims to investigate the effect of tumour necrosis factor (TNF)-α and interleukin (IL)-10 polymorphisms on risk and pattern of HCC in patients with HCV-related cirrhosis.

Results
The mean age of the HCC group was 56.21 ± 4.62 years and 54.27 ± 7.63 years for the cirrhotic group. The GG genotype of TNF-ɑ and TT genotype of IL-10 showed a higher incidence of HCC in comparison to the cirrhotic group with P = 0.01 and 0.004. On the calculation of the aggressiveness index (AgI), the TT haplotype was significantly associated with more aggressive tumours in contrast to the other haplotypes with P < 0.001. There is a significant association of portal vein thrombosis, ascites and high AgI with the GG haplotype in contrast to the other haplotypes with P = 0.002, 0.029 and < 0.001, respectively, as regards TNF-α. High AgI (C) was associated with the TT haplotype of IL-10 and GG haplotype of TNF-ɑ.

Conclusion
Our data bring an essential association of IL-10 and TNF polymorphism with the occurrence of HCC in patients with HCV-related liver cirrhosis. The GG haplotype of TNF-ɑ and TT/AT haplotype of IL-10 are associated with the more aggressive pattern of HCC, so those patients must be treated as early as possible.
Research Committee Update
Authors: Popovici Alexander Mihai 
Published: September 2020

Recently I gave each of my five kids a copy of a book that I had been delighted to read, The Curmudgeon's Guide to Getting Ahead by Charles Murray. I identified with the curmudgeon, hence the title of this column. Murray's book had its origins in postings the author made on the internal website of the American Enterprise Institute where he works, with tips for entry-level staff and interns such as: Excise the word “like” from your spoken English. Don't suck up, meaning don't excessively flatter supervisors. Make strong language count.
Effect of trunk control training on plantar pressure in patients with lumbar disc herniation
Authors: Battesha Hanan Hosny M , Elhak Reda Kotb Abd Elrazik Gad 
Published: September 2020

Background/aims Chronic spinal disc disease leads to disorders in postural movement coordination. An incorrect asymmetrical movement pattern for lower limb loading impairs proprioception and deteriorates postural stability. The aim of this study was to investigate the effect of trunk control training on the redistribution of plantar pressure to reduce the risk of posture sway while standing in patients with sciatica resulting from a herniated lumbar disc. Methods This study included 30 male and female patients with sciatica resulting from lumbar disc herniation, their ages ranged from 45–60 years. The patients were randomly assigned to two equal groups. The study group received posture stability training by using the Biodex Balance System in addition to a selected physical therapy programme. The control group received the selected physical therapy programme only. Results: The results revealed that in the study group, there was a significant increase of plantar pressure at the right and the left centre of heel, while there was a significant decrease of plantar pressure at the right and the left forefoot post treatment. In the control group, there was no significant difference in plantar pressure at the right and the left centre of the heel and forefoot post treatment. Conclusions: Trunk control training, in addition to the selected physical therapy programme, was more effective than only using the selected physical therapy programme to redistribute foot plantar pressure, which can reduce posture sway for patients with sciatica resulting from a herniated lumbar disc.