bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial salivary microbiome associates with asthma among african american children and young adults
Authors: Espuela‐Ortiz Antonio , Lorenzo‐Diaz Fabian , Baez‐Ortega Adrian , Eng Celeste , Hernandez‐Pacheco Natalia , Oh Sam S. , Lenoir Michael , Burchard Esteban G. , Flores Carlos , Pino‐Yanes Maria 
Published: September 2019

AbstractSeveral studies have shown that the airways of asthma patients contain higher diversity of bacteria and are enriched in pathogenic species. However, sampling the airways in children is challenging. Here we aimed to identify differences in the salivary bacterial composition between African Americans children with and without asthma. Saliva samples from 57 asthma cases and 57 healthy controls were analyzed by means of 16S ribosomal RNA amplicon profiling. Measurements of bacterial diversity and genus relative abundance were compared between cases and controls using the nonparametric Wilcoxon test and multivariate regression models. A total of five phyla and a mean of 56 genera were identified. Among them, 15 genera had a relative abundance greater than 1%, being Prevotella, Haemophilus, Streptococcus, and Veillonella the most abundant genera. Differences between cases and controls were found in terms of diversity, as well as in relative abundance for Streptococcus genus (13.0% in cases vs 18.3% in controls; P = .003) and Veillonella genus (11.1% in cases vs 8.0% in controls; P = .002). These differences remained significant after correction for multiple comparisons and when potential confounders were taken into account in logistic regression models. In conclusion, we identified changes in the salivary microbiota associated with asthma among African Americans.
Family history is significantly associated with prostate cancer and its early onset in Chinese population
Authors: Xu Yang , Huang Da , Wu Yishuo , Ye Dingwei , Zhang Ning , Gao Yi , Xu Danfeng , Na Rong , Xu Jianfeng 
Published: September 2019

AbstractBackgroundFamily history (FH) of prostate cancer (PCa) in Chinese population is poorly understood. The objective of this study is to evaluate the association between FH and PCa in a Chinese biopsy cohort.MethodsConsecutive patients who received 10 to 12 core systematic prostate biopsies from April 2013 to October 2018 in three medical centers were enrolled in this study. Demographic information and clinical information were obtained through prebiopsy questionnaire, including cancer FH, age, and total prostate‐specific antigen (tPSA).ResultsOf 2321 patients, 83 (3.6%) were reported a FH of PCa. The positive biopsy rate in these patients was 54.2%, significantly higher than the patients without the family history of PCa (42.6%; relative risk [RR] = 1.27; P =
.024). In patients with positive FH of breast cancer gene (BRCA)‐related cancers (breast, ovarian, and prostate cancer, n = 154), 74 (48.1%) were diagnosed as PCa, higher than those without FH (42.7%; RR = 1.13; P =
.112). Multivariate logistic regression analysis (after adjusting for age and tPSA values) showed that there was 2.1‐fold increased risk of PCa in patients with positive FH of PCa (P =
.005), and 1.6‐fold increased risk in patients with positive FH of BRCA‐related cancers (P =
.019). However, there was no significant association between FH of PCa or BRCA‐related cancer and high‐grade PCa after adjusting age and tPSA level (P =
.404 for PCa, P =
0.991 for BRCA‐related cancers).ConclusionsPatients with positive FH of PCa had 2.1‐fold higher risk of PCa, and patients with positive FH of BRCA‐related cancers had 1.6‐fold higher risk in this biopsy cohort of Chinese population. Patients with positive FH of PCa or BRCA‐related cancers would have earlier age at onset of PCa.
Lys‐Sequencer: An algorithm for de novo sequencing of peptides by paired single residue transposed Lys‐C and Lys‐N digestion coupled with high‐resolution mass spectrometry
Authors: Mao Yuan , Daly Thomas J. , Li Ning 
Published: September 2019

RationaleDatabase‐dependent identification of proteins by mass spectrometry is well established, but has limitations when there are novel proteins, mutations, splice variants, and post‐translational modifications (PTMs) not available in the established reference database. De novo sequencing as a database‐independent approach could address these limitations by deducing peptide sequences directly from experimental tandem mass spectrometry spectra, while concomitantly yielding residue‐by‐residue confidence metrics.MethodsEqual amounts of bovine serum albumin (BSA) sample aliquots were digested separately with Lys‐C and Lys‐N complementary peptidases, separated by reversed‐phase ultra‐high‐performance liquid chromatography (UPLC), and analyzed by collision‐induced dissociation (CID)‐based mass spectrometry on an Orbitrap mass spectrometer. In the Lys‐Sequencer algorithm, matched tandem mass spectra with equal precursor ion mass from complementary digestions were paired, and fragment ion types were identified based on the unique mass relationship between fragment ions extracted from a spectrum pair followed by de novo sequencing of peptides with identification confidence assigned at the residue level.ResultsIn all the matched spectrum pairs, 34 top‐ranked BSA peptides were identified, from which 391 amino acid residues were identified correctly, covering ~67% of the full sequence of BSA (583 residues) with only ~6% (35 residues) exhibiting ambiguity in the sequence order (although amino acid compositions were still correctly assigned). Of note, this approach identified peptide sequences up to 17 amino acids in length without ambiguity, with the exception of the N‐terminal or C‐terminal peptides containing lysine (18‐mer).ConclusionsThe algorithm (“Lys‐Sequencer”) developed in this work achieves high precision for de novo sequencing of peptides. This method facilitates the identification of point mutation and new PTMs in the protein characterization and discovery of new peptides and proteins with varying levels of confidence.
Proteomic characterization of arsenic and cadmium exposure in bladder cells
Authors: Chen Yi‐Ting , Ou Yang Wei‐Ting , Juang Horng‐Heng , Chen Chien‐Lun , Chen Hsiao‐Wei , Tsui Ke‐Hung , Chang Ying‐Hsu , Tsai Cheng‐Han , Hsueh Chuen , Liao Wei‐Chao 
Published: September 2019

RationaleAccumulating evidence has linked prolonged exposure to heavy metals to cancer occurrence in the urinary system. However, the specific biological mechanisms responsible for the association of heavy metals with the unusually high incidence of upper tract urothelial carcinoma in Taiwan are complex and incompletely understood.MethodsTo elucidate the specific biological mechanism and identify molecular indicators of the unusually high association of upper tract urothelial carcinoma with heavy metal exposure, protein expression following the treatment of T24 human bladder carcinoma and RT4 human bladder papilloma cell line models with arsenic (As) and cadmium (Cd) was studied. Proteomic changes in these cell models were integrated with data from a human bladder cancer (BLCA) tissue proteome to identify possible protein indicators of heavy metal exposure.ResultsAfter mass spectrometry based proteomic analysis and verification by Western blotting procedures, we identified 66 proteins that were up‐regulated and 92 proteins that were down‐regulated in RT4 cell extracts after treatment with As or Cd. Some 52 proteins were up‐regulated and 136 proteins were down‐regulated in T24 cell extracts after treatment with Cd. We further confirmed that down‐expression of the PML (promyelocytic leukemia) protein was sustained for at least 75 days after exposure of bladder cells to As. Dysregulation of these cellular proteins by As was associated with three biological pathways. Immunohistochemical analyses of paraffin‐embedded BLCA tissue slides confirmed that PML protein expression was decreased in BLCA tumor cells compared with adjacent noncancerous epithelial cells.ConclusionsThese data suggest that PML may play an important role in the pathogenesis of BLCA and may be an indicator of heavy metal exposure in bladder cells.
Taming the Combinatorial Explosion of the Formose Reaction via Recursion within Mineral Environments
Authors: Colón‐Santos Stephanie , Cooper Geoffrey J. T. , Cronin Leroy 
Published: September 2019

AbstractThe front cover artwork is provided by Naomi B. Johnson, University of Glasgow (UK). The image shows the complexity of the combinatorial explosion in the formose reaction and formamide condensation, becoming refined into distinct products through cycles and the influence of minerals. Read the full text of the Communication at 10.1002/syst.201900014.
Protective effects of trehalose against Mn‐induced α‐synuclein oligomerization in mice: Involvement of oxidative stress and autophagy
Authors: Jing Meng‐Jiao , Liu Kuan , Liu Chang , Yan Dong‐Ying , Ma Zhuo , Wang Can , Deng Yu , Liu Wei , Xu Bin 
Published: September 2019

AbstractOverexposure to manganese (Mn) is widely known to induce alpha‐synuclein (α‐Syn) oligomerization, which has been attributed to the oxidative damage of α‐Syn protein. Trehalose has been shown to induce autophagy and serve as a chemical chaperone, but little information has been reported about its effect on Mn‐induced α‐Syn oligomerization. In this study, we investigate whether trehalose can effectively interfere with Mn‐induced α‐Syn oligomerization, using different concentrations of trehalose (2% and 4% (g/vol [mL])) in a mouse model of manganism. After 6 weeks of exposure to Mn, both oxidative stress and autophagy were activated and resulted in α‐Syn oligomerization and neuronal cell damage in the mouse brain tissue. Our results also revealed that pretreatment with trehalose significantly reduced the oxidative damage to α‐Syn protein and increased autophagy activation. These findings clearly demonstrated that trehalose can relieve Mn‐induced α‐Syn oligomerization and neuronal cell damage through its anti‐oxidative and autophagy‐inducing effects.
Embeddability of pairs of weighted quasi-arithmetic means into a semiflow
Authors: Głazowska Dorota , Jarczyk Justyna , Jarczyk Witold 
Published: September 2019

AbstractWe determine the form of all semiflows of pairs of weighted quasi-arithmetic means, those over positive dyadic numbers as well as the continuous ones. Then the iterability of such pairs is characterized: necessary and sufficient conditions for a given pair of weighted quasi-arithmetic means to be embeddable into a continuous semiflow are given. In particular, it turns out that surprisingly the existence of a square iterative root in the class of such pairs implies the embeddability.
Geophysical Evaluation of Effectiveness of Blasting for Roof Caving During Longwall Mining of Coal Seam
Authors: Wojtecki Łukasz , Konicek Petr , Mendecki Maciej J. , Gołda Iwona , Zuberek Wacław M. 
Published: September 2019

AbstractDeep longwall mining of coal seams is made in the Upper Silesian Coal Basin (USCB) under complicated and mostly unfavourable geological and mining conditions. Usually, it is correlated with rockburst hazard mostly at a high level. One of the geological factors affecting the state of rockburst hazard is the presence of competent rocks in the roof of extracted coal seams, so rock falling behind the longwall face does not occur, and hanging-up of roof rocks remains. The long-lasting absence of caving may lead to an occurrence of high-energy tremor in the vicinity of the longwall face. Roof caving behind the longwall face may be forced by blasting. The column of explosives is then located in blastholes drilled in layers of roof rocks, e.g. sandstones behind the longwall face. In this article, a characterization of tremors initiated by blasts for roof caving during underground extraction of coal seam no. 507 in one of the collieries in the USCB has been made using three independent methods. By the basic seismic effect method, the effectiveness of blasting is evaluated according to the seismic energy of incited tremors and mass of explosives used. According to this method, selected blasts gave extremely good or excellent effect. An inversion of the seismic moment tensor enables determining the processes happening in the source of tremors. In the foci of provoked tremors the slip mechanism dominated or was clearly distinguished. The expected explosion had lesser significance or was not present. By the seismic source parameters analysis, among other things, an estimation of the stress drop in the focus or its size may be determined. The stress drop in the foci of provoked tremors was in the order of 105 Pa and the source radius, according to the Brune’s model, varied from 44.3 to 64.5 m. The results of the three mentioned methods were compared with each other and observations in situ. In all cases the roof falling was forced.
Synthesis, antimicrobial activity, and determination of the lipophilicity of ((cyclohex-3-enylmethylene)hydrazinyl)thiazole derivatives
Authors: Biernasiuk Anna , Kawczyńska Magdalena , Berecka-Rycerz Anna , Rosada Beata , Gumieniczek Anna , Malm Anna , Dzitko Katarzyna , Łączkowski Krzysztof Z. 
Published: September 2019

Abstract
Synthesis and investigation of antimicrobial activity of fifteen novel thiazoles containing cyclohexene moiety are presented. Among the derivatives, compounds 3a–3d, 3f, 3n, and 3o showed very strong activity against the reference Candida spp. strains with MIC = 0.015–3.91 µg/ml. The activity of these compounds is similar and even higher than the activity of nystatin used as positive control. Compounds 3d, 3f, 3n, 3o showed the highest activity with very strong effect towards most of yeasts isolated from clinical materials with MIC = 0.015–7.81 µg/ml. The cytotoxicity studies for the most active compounds showed that Candida spp. growth was inhibited at noncytotoxic concentrations for the mammalian L929 fibroblast. In addition, a good correlation was obtained between lipophilicity of compounds determined using reversed phase thin-layer chromatography and their antifungal activity.
Associations of short stature and components of height with incidence of type 2 diabetes: mediating effects of cardiometabolic risk factors
Authors: Wittenbecher Clemens , Kuxhaus Olga , Boeing Heiner , Stefan Norbert , Schulze Matthias B. 
Published: September 2019

Abstract

Aims/hypothesis
This study aimed to evaluate associations of height as well as components of height (sitting height and leg length) with risk of type 2 diabetes and to explore to what extent associations are explainable by liver fat and cardiometabolic risk markers.

Methods
A case-cohort study within the European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam study comprising 26,437 participants who provided blood samples was designed. We randomly selected a subcohort of 2500 individuals (2029 diabetes-free at baseline and with anamnestic, anthropometrical and metabolic data for analysis). Of the 820 incident diabetes cases identified in the full cohort during 7 years of follow-up, 698 remained for analyses after similar exclusions.

Results
After adjustment for age, potential lifestyle confounders, education and waist circumference, greater height was related to lower diabetes risk (HR per 10 cm, men 0.59 [95% CI 0.47, 0.75] and women 0.67 [0.51, 0.88], respectively). Leg length was related to lower risk among men and women, but only among men if adjusted for total height. Adjustment for liver fat and triacylglycerols, adiponectin and C-reactive protein substantially attenuated associations between height and diabetes risk, particularly among women.

Conclusions/interpretation
We observed inverse associations between height and risk of type 2 diabetes, which was largely related to leg length among men. The inverse associations may be partly driven by lower liver fat content and a more favourable cardiometabolic profile.
On recursive utilities with non-affine aggregator and conditional certainty equivalent
Authors: Balbus Łukasz 
Published: September 2019

Abstract
In this paper, we consider the problem of the existence and the uniqueness of a recursive utility function defined on intertemporal lotteries. The purpose of this paper is to provide the results of the existence and the uniqueness of a recursive utility function. The utility function is obtained as the limit of iterations on a nonlinear operator and is independent on initial starting points, with iterations converging at an exponential rate. We also find the maximum utility and an optimal strategy by means of iterations of the Bellman operator.
The Griffiths bundle is generated by groups
Authors: Goldring Wushi 
Published: September 2019

AbstractFirst the Griffiths line bundle of a$$\mathbf {Q}$$Q-VHS$${\mathscr {V}}$$Vis generalized to a Griffiths character$${{\,\mathrm{grif}\,}}(\mathbf {G}, \mu ,r)$$grif(G,μ,r)associated to any triple$$(\mathbf {G}, \mu , r)$$(G,μ,r), where$$\mathbf {G}$$Gis a connected reductive group over an arbitrary fieldF,$$\mu \in X_*(\mathbf {G})$$μ∈X∗(G)is a cocharacter (over$$\overline{F}$$F¯) and$$r:\mathbf {G}\rightarrow GL(V)$$r:G→GL(V)is anF-representation; the classical bundle studied by Griffiths is recovered by taking$$F=\mathbf {Q}$$F=Q,$$\mathbf {G}$$Gthe Mumford–Tate group of$${\mathscr {V}}$$V,$$r:\mathbf {G}\rightarrow GL(V)$$r:G→GL(V)the tautological representation afforded by a very general fiber and pulling back along the period map the line bundle associated to$${{\,\mathrm{grif}\,}}(\mathbf {G}, \mu , r)$$grif(G,μ,r). The more general setting also gives rise to the Griffiths bundle in the analogous situation in characteristicpgiven by a scheme mapping to a stack of$$\mathbf {G}$$G-Zips. When$$\mathbf {G}$$GisF-simple, we show that, up to positive multiples, the Griffiths character$${{\,\mathrm{grif}\,}}(\mathbf {G},\mu ,r)$$grif(G,μ,r)(and thus also the Griffiths line bundle) is essentially independent ofrwith central kernel, and up to some identifications is given explicitly by$$-\mu $$-μ. As an application, we show that the Griffiths line bundle of a projective$${{\mathbf {G}{\text{- }}{} \mathtt{Zip}}}^{\mu }$$G-Zipμ-scheme is nef.
Undecidability of the word problem for one-relator inverse monoids via right-angled Artin subgroups of one-relator groups
Authors: Gray Robert D. 
Published: September 2019

AbstractWe prove the following results: (1) There is a one-relator inverse monoid$$\mathrm {Inv}\langle A\,|\,w=1 \rangle $$Inv⟨A|w=1⟩with undecidable word problem; and (2) There are one-relator groups with undecidable submonoid membership problem. The second of these results is proved by showing that for any finite forest the associated right-angled Artin group embeds into a one-relator group. Combining this with a result of Lohrey and Steinberg (J Algebra 320(2):728–755, 2008), we use this to prove that there is a one-relator group containing a fixed finitely generated submonoid in which the membership problem is undecidable. To prove (1) a new construction is introduced which uses the one-relator group and submonoid in which membership is undecidable from (2) to construct a one-relator inverse monoid$$\mathrm {Inv}\langle A\,|\,w=1 \rangle $$Inv⟨A|w=1⟩with undecidable word problem. Furthermore, this method allows the construction of anE-unitary one-relator inverse monoid of this form with undecidable word problem. The results in this paper answer a problem originally posed by Margolis et al. (in: Semigroups and their applications, Reidel, Dordrecht, pp. 99–110, 1987).
Ultra-low-dose CT for extremities in an acute setting: initial experience with 203 subjects
Authors: Alagic Zlatan , Bujila Robert , Enocson Anders , Srivastava Subhash , Koskinen Seppo K. 
Published: September 2019

Abstract

Objective
The purpose of this study was to assess if ultra-low-dose CT is a useful clinical alternative to digital radiographs in the evaluation of acute wrist and ankle fractures.

Materials and methods
An ultra-low-dose protocol was designed on a 256-slice multi-detector CT. Patients from the emergency department were evaluated prospectively. After initial digital radiographs, an ultra-low-dose CT was performed. Two readers independently analyzed the images. Also, the radiation dose, examination time, and time to preliminary report was compared between digital radiographs and CT.

Results
In 207 extremities, digital radiography and ultra-low-dose CT detected 73 and 109 fractures, respectively (p < 0.001). The odds ratio for fracture detection with ultra-low-dose CT vs. digital radiography was 2.0 (95% CI, 1.4–3.0). CT detected additional fracture-related findings in 33 cases (15.9%) and confirmed or ruled out suspected fractures in 19 cases (9.2%). The mean effective dose was comparable between ultra-low-dose CT and digital radiography (0.59 ± 0.33 μSv, 95% CI 0.47–0.59 vs. 0.53 ± 0.43 μSv, 95% CI 0.54–0.64). The mean combined examination time plus time to preliminary report was shorter for ultra-low-dose CT compared to digital radiography (7.6 ± 2.5 min, 95% CI 7.1–8.1 vs. 9.8 ± 4.7 min, 95% CI 8.8–10.7) (p = 0.002). The recommended treatment changed in 34 (16.4%) extremities.

Conclusions
Ultra-low-dose CT is a useful alternative to digital radiography for imaging the peripheral skeleton in the acute setting as it detects significantly more fractures and provides additional clinically important information, at a comparable radiation dose. It also provides faster combined examination and reporting times.
CRISPR/Cas9 gene correction of HbH-CS thalassemia-induced pluripotent stem cells
Authors: Yingjun Xie , Yuhuan Xie , Yuchang Chen , Dongzhi Li , Ding Wang , Bing Song , Yi Yang , Dian Lu , Yanting Xue , Zeyu Xiong , Nengqing Liu , Diyu Chen , Xiaofang Sun 
Published: September 2019

Abstract
Haemoglobin (Hb) H-constant spring (CS) alpha thalassaemia (- -/-αCS) is the most common type of nondeletional Hb H disease in southern China. The CRISPR/Cas9-based gene correction of patient-specific induced pluripotent stem cells (iPSCs) and cell transplantation now represent a therapeutic solution for this genetic disease. We designed primers for the target sites using CRISPR/Cas9 to specifically edit the HBA2 gene with an Hb-CS mutation. After applying a correction-specific PCR assay to purify the corrected clones followed by sequencing to confirm the mutation correction, we verified that the purified clones retained full pluripotency and exhibited a normal karyotype. This strategy may be promising in the future, although it is far from representing a solution for the treatment of HbH-CS thalassemia now.
Particle image velocimetry in refractive index fields of combustion flows
Authors: Vanselow Christoph , Stöbener Dirk , Kiefer Johannes , Fischer Andreas 
Published: September 2019

Abstract
Optical measurements inside reacting flows are often disturbed by refractive index fields, e.g., due to the strong density gradients in flames. Although occurring measurement errors due to light refraction are a known problem for certain particle image velocimetry (PIV) applications, only a qualitative analysis of the resulting measurement uncertainty inside flame flows has been carried out to date. As an important step forward, a measurement approach is proposed, which enables a quantification of the resulting measurement uncertainties due to light refraction. As an example, the measurement approach is applied to a premixed propane flame. The uncertainty analysis is based on the determination of occurring particle position errors due to light refraction inside the flame. For three different measurement planes, the velocity field is measured with PIV and the particle position errors are experimentally measured and verified by ray-tracing simulation based on the measured refractive index field, which is determined by the background-oriented Schlieren method. In the examined flow, maximal position errors amount up to 14 μm and yield significant systematic velocity errors of up to 4% and random velocity errors of up to 6%. In contrast to the systematic velocity error, the random velocity error varies significantly for the analyzed measurement planes inside the flame flow.

Graphic abstract