bluuebunny/crossref_metadata_2025_split huggingface dataset:
‘One-stop-shop’ diagnosis and stage-adapted surgical therapy for small nodules of early stage lung cancer in a hybrid operating room
Authors: Caviezel C , Kostopanagiotou K , Puippe G D , Werner R S , Opitz I 
Published: June 2022

Abstract

Objective
Emergent lung cancer screening programs increased detection of small pulmonary nodules. Anatomical resection in case of early-stage lung cancer with only one intervention becomes increasingly desirable. Current literature lacks procedure data about both diagnosis and subsequent indicated resection. After starting our hybrid operating room program, we reviewed the efficacy of detection, diagnosis and therapy in one-step.

Methods
Undiagnosed pulmonary nodules suspicious of lung cancer, which were not detectable by conventional video-assisted thoracoscopic surgery (VATS) due to localization and size, were scheduled for a hybrid procedure consisting of a cone-beam CT-guided hookwire insertion and C-arm assisted thoracoscopic wedge resection for frozen section. All procedures were analyzed for perioperative outcomes including success rate of image-guided nodule resection and rate of concomitant correct anatomical resection.

Results
Between July 2020 and July 2021, 23 patients with 25 nodules underwent image-guided VATS (iVATS) in the hybrid room. Twenty-two nodules were successfully marked by hookwire, three nodules were detected by ultrasound in one case and palpation in two cases. In 16 patients (70%) wedge resection with frozen section showed malignancy. Five patients with previous history of operated lung cancer received only a diagnostic wedge, as frozen section could not differentiate between primary or metastatic lung cancer. Eleven patients (48%) had early-stage primary lung cancer (8 adenocarcinoma, one typical carcinoid, one small-cell lung cancer and one squamous-cell lung cancer). Ten of them (91%) received a synchronous completion anatomical resection (seven lobectomies, three segmentectomies). In one patient, malignancy was only confirmed in final histology.

Conclusion
One-stop-shop diagnosis and treatment by iVATS with frozen section and concomitant completion anatomical resection in a hybrid operating room for otherwise non-well approachable early stage lung cancer is patient-convenient for the increasingly detected small pulmonary nodules.
The yin and the yang of early classical pathway complement disorders
Authors: Sullivan Kathleen E 
Published: June 2022

Summary
The classical pathway of the complement cascade has been recognized as a key activation arm, partnering with the lectin activation arm and the alternative pathway to cleave C3 and initiate the assembly of the terminal components. While deficiencies of classical pathway components have been recognized since 1966, only recently have gain-of-function variants been described for some of these proteins. Loss-of-function variants in C1, C4, and C2 are most often associated with lupus and systemic infections with encapsulated bacteria. C3 deficiency varies slightly from this phenotypic class with membranoproliferative glomerulonephritis and infection as the dominant phenotypes. The gain-of-function variants recently described for C1r and C1s lead to periodontal Ehlers Danlos syndrome, a surprisingly structural phenotype. Gain-of-function in C3 and C2 are associated with endothelial manifestations including hemolytic uremic syndrome and vasculitis with C2 gain-of-function variants thus far having been reported in patients with a C3 glomerulopathy. This review will discuss the loss-of-function and gain-of-function phenotypes and place them within the larger context of complement deficiencies.
Isolation of an ectoine-producing Sinobaca sp. and identification of genes that are involved in ectoine biosynthesis
Authors: Chen Shan-Yu , Peng Tzu-Chia , Huang Shan-Ze , Chien Chih-Ching 
Published: June 2022

Abstract
A moderate halophilic bacterium that could accumulate ectoine and hydroxyectoine was isolated from soil near a salt mine and was identified as a Sinobaca sp. (designed strain H24) according to 16S rRNA gene sequence analysis. The bacterium grew well in the presence of 1–2 M NaCl, while growth in a medium that contained 2 M NaCl led to higher accumulation of ectoines. The yields of ectoine and hydroxyectoine by Sinobaca sp. H24 reached 11.27 mg/l and 1.34 mg/l, respectively, when cultured in the following medium: NaCl (2 M), peptone (5 g/l), yeast extract (1 g/l), NH4Cl (0.02 M), KH2PO4 (1 M), K2HPO4 (0.1 M), and glycerol (1% w/v). Genes that are involved in ectoine biosynthesis of Sinobaca sp. H24 were also identified, and their sequences were determined by a metagenomics approach. The results demonstrated that Sinobaca sp. H24 possesses ectoine metabolism genes for both ectoine biosynthesis (ectA, ectB, ectC, and ectD) and ectoine degradation (doeA). Genes that are related to ectoine biosynthesis, such as lysC and asd, were also characterized. The identification and characterization results for ectoine/hydroxyectoine biosynthesis genes are in agreement with the physiology of Sinobaca sp. H24 as a potential candidate for ectoine production for industrial applications. This report established for the first time the accumulation of ectoine/hydroxyectoine in Sinobaca sp. and characterized the genes that are involved in ectoine/hydroxyectoine biosynthesis in Sinobaca sp. H24.
Cross-genus inhibitory activity of polyoxins against aflatoxin production by Aspergillus parasiticus and fumonisin production by Fusarium fujikuroi
Authors: Yoshinari Tomoya , Watanabe Maiko , Hara-Kudo Yukiko 
Published: June 2022

Abstract
Co-exposure to aflatoxin and fumonisin is a health concern where corn is a staple food, and a method to prevent co-contamination of these mycotoxins in foods is urgently needed. Polyoxins are chitin synthase inhibitors produced by Streptomyces cacaoi var. asoensis. The aflatoxin production inhibitory activity of a commercially available polyoxin D and four polyoxins purified from polyoxin AL water-soluble powder, an agricultural chemical containing polyoxins, was tested. The five polyoxins dose-dependently inhibited aflatoxin production by Aspergillus parasiticus and the IC50 values of polyoxin A, B, D, K and L were 16, 74, 110, 9 and 280 µmol L−1, respectively. Polyoxins also inhibited fumonisin production by Fusarium fujikuroi, and the IC50 values of polyoxin B, D, K and L were 270, 42, 65 and 62 µmol L−1, respectively. Polyoxins repressed the transcription of genes encoding proteins required for aflatoxin biosynthesis in A. parasiticus and fumonisin biosynthesis in F. fujikuroi. Polyoxin K and D also inhibited conidiation in A. parasiticus and F. fujikuroi, respectively. These results suggest that a mixture of polyoxins may effectively prevent co-contamination of aflatoxin and fumonisin in foods.
Plasmodium falciparumPfRUVBL proteins bind at the TARE region andvargene promoter located in the subtelomeric region
Authors: Saxena Himani , Gupta Ashish 
Published: June 2022

AbstractIn order to survive and establish infection, the Plasmodium parasite employs various strategies to evade the host immune response. The var genes family, a repertoire of 60 genes, expresses parasite-specific protein PfEMP1, a variable surface antigen, on the membrane of infected erythrocytes, and by continuously switching the variants of PfEMP1, help the parasite to avoid detection and destruction by the host immune system during the intra-erythrocytic developmental cycle. Although chromatin modifications are recognised to be a prominent phenomenon in regulation of mono-allelic expression of these var genes, the precise histone codes and molecular players and mechanisms guiding these modifications have yet to be unravelled in depth. In this study, we have functionally characterised RUVBL proteins of Plasmodium falciparum and shown that PfMYST (an essential lysine acetyl transferase) and PfRUVBL protein complex occupy the TARE region and var gene promoter in the ring stage of the parasite. Further, we have demonstrated that the PfMYST/PfRUVBL complex interacts with core histones, H3 and H4. Overall the findings of this study add further information by identifying the potential role of epigenetic regulators, PfMYST and PfRUVBL, in the regulation of monoallelic expression of var genes in the malaria parasite.
Genome-wide transcriptional regulation in Saccharomyces cerevisiae in response to carbon dioxide
Authors: Tan Lin-Rui , Liu Jing-Jing , Deewan Anshu , Lee Jae Won , Xia Peng-Fei , Rao Christopher V , Jin Yong-Su , Wang Shu-Guang 
Published: June 2022

Abstract
Sugar metabolism by Saccharomyces cerevisiae produces ample amounts of CO2 under both aerobic and anaerobic conditions. High solubility of CO2 in fermentation media, contributing to enjoyable sensory properties of sparkling wine and beers by S. cerevisiae, might affect yeast metabolism. To elucidate the overlooked effects of CO2 on yeast metabolism, we examined glucose fermentation by S. cerevisiae under CO2 as compared to N2 and O2 limited conditions. While both CO2 and N2 conditions are considered anaerobic, less glycerol and acetate but more ethanol were produced under CO2 condition. Transcriptomic analysis revealed that significantly decreased mRNA levels of GPP1 coding for glycerol-3-phosphate phosphatase in glycerol synthesis explained the reduced glycerol production under CO2 condition. Besides, transcriptional regulations in signal transduction, carbohydrate synthesis, heme synthesis, membrane and cell wall metabolism, and respiration were detected in response to CO2. Interestingly, signal transduction was uniquely regulated under CO2 condition, where upregulated genes (STE3, MSB2, WSC3, STE12, and TEC1) in the signal sensors and transcriptional factors suggested that MAPK signaling pathway plays a critical role in CO2 sensing and CO2-induced metabolisms in yeast. Our study identifies CO2 as an external stimulus for modulating metabolic activities in yeast and a transcriptional effector for diverse applications.
Predicting Lumber Grade Occurrence and Volume in Sugar Maple and Yellow Birch Logs
Authors: Havreljuk Filip , Achim Alexis , Pothier David 
Published: June 2022

AbstractThe North American temperate deciduous forests are an important source of hardwoods sought after by the appearance wood products industries. The purpose of this study was to model the relationships between log characteristics and sawn board attributes in sugar maple (Acer saccharum Marsh.) and yellow birch (Betula alleghaniensis Britt.). We harvested sixty-four sugar maple and thirty-two yellow birch trees from two locations in southern Quebec, Canada, which were then processed into 189 sawlogs and 2,236 boards. We developed statistical models linking log characteristics to the volume recovery of the various lumber grades and color specifications according to the National Hardwood Lumber Association rules. In both species, board grades were strongly related to log length, position of the log in the stem, and small-end diameter and decay of the log. Color classes were related to small-end diameter of the log and red heartwood diameter of the log at both ends for sugar maple, and to log length, diameter of the log at the small-end, and red heartwood diameter at the large-end of the log for yellow birch. These models outperformed a log classification used in practice for predicting lumber volume recovery from different log grades.
Genetic diversity of Listeria monocytogenes isolates from farm products in Shanghai, China
Authors: Suo Yujuan , Qu Yang , Bai Yalong , Zhou Xiujuan , Lin Ting , Wang Jing , Chen Wanyi , Zhou Changyan 
Published: June 2022

Abstract
Farm products are considered important vehicles for the transmission of Listeria monocytogenes (L. monocytogenes). The typing of L. monocytogenes from farm products contributes to the surveillance and source tracing of the pathogen. In this study, 77 L. monocytogenes strains from seven farm product categories in Shanghai were analyzed by serological typing, multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and whole-genome nucleotide polymorphism (wgSNP). The results showed that the 77 isolates were classified into four serovars (1/2a, 1/2c, 1/2b, and 4b), and of these, 1/2a (n=47) was the most prevalent. Seventeen sequence types (STs) were generated by MLST with two novel STs (ST1402 and ST1403), and 20 of 77 L. monocytogenes isolates had high genetic identity with previously documented outbreak isolates according to the minimum spanning tree from the MLST results. Moreover, 34 PFGE patterns (PF1–PF34) were differentiated, and based on a similarity value higher than 80% by the unweighted pair group method dendrogram, the discriminatory index was relatively low (equal to 0.775). Furthermore, 14 isolates were chosen and further analyzed by wgSNP based on the previous typing results, which demonstrated that wgSNP and MLST yielded mostly consistent typing results but higher resolution than PFGE. In conclusion, 77 L. monocytogenes isolates from farm products collected in nine districts in Shanghai were highly genetically diverse, and 20 of these isolates had high relatedness with previously documented outbreak strains worldwide. The results indicate a possible cross-contamination risk of L. monocytogenes and a potential public health concern resulting from farm products during the supply chain in Shanghai, China.
The First Annotated Genome Assembly of Macrophomina tecta Associated with Charcoal Rot of Sorghum
Authors: Poudel Barsha , Purushotham Neeraj , Jones Ashley , Nasim Jamila , Adorada Dante L. , Sparks Adam H. , Schwessinger Benjamin , Vaghefi Niloofar 
Published: June 2022

Abstract
Charcoal rot is an important soilborne disease caused by a range of Macrophomina species, which affects a broad range of commercially important crops worldwide. Even though Macrophomina species are fungal pathogens of substantial economic importance, their mechanism of pathogenicity and host spectrum are poorly understood. There is an urgent need to better understand the biology, epidemiology, and evolution of Macrophomina species, which, in turn, will aid in improving charcoal rot management strategies. Here, we present the first high-quality genome assembly and annotation of Macrophomina tecta strain BRIP 70781 associated with charcoal rot symptoms on sorghum. Hybrid assembly integrating long reads generated by Oxford Nanopore Technology and short Illumina paired-end reads resulted in 43 contigs with a total assembly size of ∼54 Mb, and an N50 of 3.4 Mb. In total, 12,926 protein-coding genes and 7,036 repeats were predicted. Genome comparisons detected accumulation of DNA transposons in Macrophomina species associated with sorghum. The first reference genome of M. tecta generated in this study will contribute to more comparative and population genomics studies of Macrophomina species.
The German Response to Austria’s Annexation of Cracow in 1846
Authors: Šedivý Miroslav 
Published: June 2022

Abstract
The annexation of the Free City of Cracow by Austria in November 1846 has been regarded by historians as one of the most important international events in the period before the outbreak of revolutions in 1848. The annihilation of an independent state has been seen as a flagrant violation of international law that led to a weakening of Europeans’ faith in the justice of the post-Napoleonic order. Consequently, it is surprising that even as this evaluation has become rooted in historical scholarship, the public response to this affair has scarcely been analysed. The aim of this article is to reveal the impact of the annexation on the broad public in the German Confederation and the decline in people’s trust in justice in international relations. Germans across various political camps primarily perceived the annexation of Cracow not from the perspective of political modernization but in terms of geopolitical security. Their concern was not just with the position of the individual German states in relation to Prussia, Austria, Britain, France and Russia or the position of the entire German Confederation in relation to France, Britain and Russia, but also with their position within the political-legal system of European politics. The ensuing debate on the necessity for external security against threats from other European powers and nations became the most important outcome of this affair in Germany, with an egoistic, power-oriented response to the annexation of Cracow paving the way for conflicts among the Germans, Poles and other nations in 1848.
Imaging subsurface structure over the Xiadian fault using P waves extracted from urban traffic noise
Authors: Song Youngseok , Seol Soon Jee , Byun Joongmoo , Hayashi Koichi , Tan Shunjia 
Published: June 2022

SUMMARY
The imaging of subsurface structures is an essential task in subsurface engineering projects; it provides information regarding the locations of active faults and layer boundaries. Among the methods available for imaging of subsurface structures, the body wave imaging method using urban traffic noise has recently attracted attention because it permits continuous measurement at low cost in urban areas. However, because the urban traffic noise signal used for imaging on the engineering scale has characteristics that differ from the ambient noise used on the crustal scale, the conventional crustal-scale data processing workflow should be modified through systematic data analysis. In this study, traffic noise sources were systematically analysed using field data obtained over the Xiadian fault in Hebei province, China. The traffic noise signals were recorded in various patterns because of diverse incoming directions and show marked amplitude changes depending on time of recording. The overlapping signals originating from opposite directions generate spurious events and noise in the seismic interferometry images; constant processing parameters cannot respond to the large amplitude changes. In this study, to remove surface waves with markedly changing amplitude, we applied actively varying threshold values to each set of traces using the moving average of amplitude changes within the trace. In addition, the signals originating from diverse directions were separated into negative and positive slopes through the f–k filter; the interference generated by overlapping signals was minimized by applying data processing (e.g. median filtering and high amplitude removal) separately to the negative and positive slopes of each simultaneously acquired trace gather. Due to the modified data processing workflow, most spurious events were successfully suppressed in the final stacked image compared with those produced using the conventional data processing workflow, and reflections were imaged more clearly. Fault spatial locations and layer boundary depth variation in the final image obtained by the modified processing workflow were similar to those reported in previous studies.
Simulation of seismic velocity changes in brittle rocks subjected to triaxial stresses using 3-D microstructural models
Authors: Bai Qingsheng , Zhang Cun , Konietzky Heinz , Young R Paul 
Published: June 2022

SUMMARYNumerical simulation of non-linear elastic wave propagation in rocks is indispensable for understanding stress/damage dependence of wave velocity changes and the associated micromechanisms. A numerical microstructural model is presented here to investigate seismic velocity changes due to stress and damage. By introducing pre-existing cracks and considering the valid microstructures in the bonded particle model, the proposed method successfully reproduces velocity changes of experiments on dry Lac du Bonnet granite and dry Darley Dale sandstone in both loading and unloading processes. Velocity increasing results from the closure of pre-existing cracks during loading stages, while the reopen of cracks during the unloading process causes velocity decreasing. Particle velocity vectors are used to illustrate wave propagation in a micromechanical way. P wave wave fronts are observed from the source to travel through the model, and wave intersections are clearly shown in the medium when the tensile wave front meets the compressive wave. The microstructure of the model shows a significant effect on rock mechanical behaviour and velocities and lends credibility to the velocity simulation. The valid microstructure produces realistic mechanical behaviour and velocity changes. Also, it replicates the initial hardening in the axial stress versus the axial strain curve, while invalid microstructures (e.g. cement overlap) underestimate the elastic modulus. The simulations also show that the wave velocities scale with the square root of the corresponding component of the coordination number, which can be used to quantify the mechanisms behind the velocity changes. Direct relations were established between velocity changes and opened crack density, which displays a similar tendency compared with predictions of the effective elastic theory. The microstructural model provides the ability to simulate the macro behaviour of rock under loadings in a more realistic manner and to directly examine the microprocesses underlying velocity changes.
Mutation burden analysis of six common mental disorders in African Americans by whole genome sequencing
Authors: Liu Yichuan , Qu Hui-Qi , Chang Xiao , Qu Jingchun , Mentch Frank D , Nguyen Kenny , Tian Lifeng , Glessner Joseph , Sleiman Patrick M A , Hakonarson Hakon 
Published: June 2022

Abstract
Mental disorders present a global health concern and have limited treatment options. In today’s medical practice, medications such as antidepressants are prescribed not only for depression but also for conditions such as anxiety and attention deficit hyperactivity disorder (ADHD). Therefore, identifying gene targets for specific disorders is important and offers improved precision. In this study, we performed a genetic analysis of six common mental disorders—ADHD, anxiety, depression, delays in mental development, intellectual disabilities (IDs) and speech/language disorder—in the ethnic minority of African Americans (AAs) using whole genome sequencing (WGS). WGS data were generated from blood-derived DNA from 4178 AA individuals, including 1384 patients with the diagnosis of at least one mental disorder. Mutation burden analysis was applied based on rare and deleterious mutations in the AA population between cases and controls, and further analyzed in the context of patients with single mental disorder diagnosis. Certain genes uncovered demonstrated significant P-values in mutation burden analysis. In addition, exclusive recurrences in specific type of disorder were scanned through gene–drug interaction databases to assess for availability of potential medications. We uncovered 15 genes harboring deleterious mutations, including 3-Hydroxy-3-Methylglutaryl-CoA Reductase (HMGCR) and Uronyl 2-Sulfotransferase (UST) for ADHD; Farnesyltransferase, CAAX Box, Beta (FNTB) for anxiety; Xin Actin Binding Repeat Containing 2 (XIRP2), Natriuretic Peptide C (NPPC), Serine/Threonine Kinase 33 (STK33), Pannexin 1 (PANX1) and Neurotensin (NTS) for depression; RUNX Family Transcription Factor 3 (RUNX3), Tachykinin Receptor 1 (TACR1) and NADH:Ubiquinone Oxidoreductase Core Subunit S7 (NDUFS7) for delays in mental development; Hepsin (HPN) for ID and Collagen Type VI Alpha 3 Chain (COL6A3), Damage Specific DNA Binding Protein 1 (DDB1) and NADH:Ubiquinone Oxidoreductase Subunit A11 (NDUFA11) for speech/language disorder. Taken together, we have established critical insights into the development of new precision medicine approaches for mental disorders in AAs.