bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative omics approaches to advance rare disease diagnostics
Authors: Smirnov Dmitrii , Konstantinovskiy Nikita , Prokisch Holger 
Published: August 2023

AbstractOver the past decade high‐throughput DNA sequencing approaches, namely whole exome and whole genome sequencing became a standard procedure in Mendelian disease diagnostics. Implementation of these technologies greatly facilitated diagnostics and shifted the analysis paradigm from variant identification to prioritisation and evaluation. The diagnostic rates vary widely depending on the cohort size, heterogeneity and disease and range from around 30% to 50% leaving the majority of patients undiagnosed. Advances in omics technologies and computational analysis provide an opportunity to increase these unfavourable rates by providing evidence for disease‐causing variant validation and prioritisation. This review aims to provide an overview of the current application of several omics technologies including RNA‐sequencing, proteomics, metabolomics and DNA‐methylation profiling for diagnostics of rare genetic diseases in general and inborn errors of metabolism in particular.
SERS evidence of urea‐disordered G‐quadruplex structure
Authors: Petrović Petra , Saftić Dijana Pavlović , Kenđel Adriana , Miljanić Snežana 
Published: August 2023

AbstractStructural changes of the human telomeric d(TTAGGG)4 sequence (Tel24) in the presence of sodium ions and urea were studied using SERS spectroscopy. The SERS spectra indicated that Tel24 (4 × 10−5 mol/l) formed an anti‐parallel G‐quadruplex in a medium containing Na+ ions (100 mmol/l), which was disrupted by the subsequent addition of urea (7.2 mol/l). Intensity ratios of SERS bands originating from breathing vibrations of adenine (~730 cm−1) and guanine (~660 cm−1) rings clearly pointed to the urea‐induced unfolding of G‐quadruplex. In addition, SERS bands assigned to guanine implied the breaking of Hoogsteen hydrogen bonds, most likely due to the bonding of guanine bases with the urea molecules. Considering various experimental conditions applied, the structure‐related SERS response was more pronounced in the silver than in the gold colloid as well as upon NIR (785 nm) rather than Vis (532 nm) laser excitation. The CD spectra of the same colloidal samples supported structural changes of Tel24 obtained by SERS.
The protective effect of Schisandra chinensis (Turcz.) Baill. polysaccharide on DSS‐induced ulcerative colitis in mice via the modulation of gut microbiota and inhibition of NF‐κB activation
Authors: Guo Xiaorong , Liu Lei , Zhao Wenqi , Li Xingyun , Wang Xiaoli , Ning Anhong , Cao Jing , Zhang Wei , Cao Liang , Zhong Mintao 
Published: August 2023

AbstractBACKGROUNDSchisandra chinensis (Turcz.) Baill, a fruit utilized in traditional Chinese medicine (TCM), has a long history of medical application. It has been used to treat diseases of the gastrointestinal tract. Schisandra chinensis (Turcz.) Baill polysaccharide (SACP) is an important biologically active ingredient that has been shown to have a variety of beneficial effects including immune regulation and anti‐oxidative properties. Ulcerative colitis (UC) is a complicated gastrointestinal inflammatory disease. We explore the protective effect of SACP against UC.RESULTSSchisandra chinensis (Turcz.) Baill polysaccharide significantly reduced the disease activity index (DAI) and levels of myeloperoxidase(MPO) and malondialdehyde (MDA) in colonic tissue. It also alleviated weight loss and histopathological damage of mice. The expression of MUC2 and occludin proteins was increased and the barrier function of the colonic mucosa was enhanced by SACP treatment. NF‐κB pathway activation was also inhibited and the production of pro‐inflammatory cytokines was decreased whereas anti‐inflammatory cytokines were increased. 16SrDNA sequencing of fecal flora showed that SACP increased the abundance of Muribaculaceaeunclassified, LachnospiraceaeNK4A136group and reduced the abundance of Bacteroides and Erysipelatoclostridium.CONCLUSIONSchisandra chinensis (Turcz.) Baill polysaccharide can protect against Dextran Sulfate Sodium Salt (DSS)‐induced ulcerative colitis in mice. © 2023 Society of Chemical Industry.
Functional vegetation community responses to soil and topographic factors in the Loess Plateau of China
Authors: Zhang Hengshuo , Zha Tonggang , Yu Yang , Zhang Zhiqiang , Zhang Xiaoxia , Zhang Hongli , Ji Xiaodong 
Published: August 2023

AbstractGiven the developmental program outlined in United Nations Sustainable Development Goal 15 (Life on Land) and the to effectively address the challenge of biodiversity decline while mitigating the adverse effects of climate change, particularly drought, on terrestrial forest ecosystems, a fundamental reorientation of global forest restoration paradigms is warranted. It is imperative to move beyond a narrow emphasis on expanding forest area and instead prioritize the enhancement of biodiversity and functional attributes within these ecosystems. However, the differential response mechanisms of forest ecosystem functional communities and main plant functional types (PFTs) to environmental factors, especially soil and topography, remains unclear, especially at plant level. Here, we divided the functional communities of 93 sites in the study area into seven groups through Two‐way indicator species analysis (TWINSPAN), and studied the different functional communities, namely dynamic succession, species richness, and PFT compositional differences. We also analyzed the various PFTs and functional community response mechanisms to soil and topographic factors using canonical correspondence analysis (CCA). The main results were as follows: (1) With the successional stages of PFTs, vegetation diversity across multiple functional communities inceased, tree and shrub proportions and importance increased, while herbs decreased. (2) From the arid and barren areas (i.e., G2), to the humid and fertile areas (i.e., G6 and G7), various compositional PFT differences, and their responses to soil and topographic factors, were found, namely, xerophytic, annual and biennial species gradually changed to mesophytic, hygrophytic, and perennial species (richness increased 6.94 ~ 27.33%, important value (IV) increased 8.73 ~ 29.45%) for shrubs and herbs. (3) Functional communities in various successional stages display distinct sensitivities to soil and topographic factors, as evidenced by a notable increase in the richness and IV of deciduous broad‐leaved tree species, rendering their communities more responsive to SOC and AS, whereas evergreen coniferous trees (e.g., Pinus tabuliformis Carr.) were sensitive to altitude (AL) and exhibited a tendency to transition from plantations to natural secondary forests predominantly at higher altitudes (above 1200 m). Our findings suggest that site conditions influence scenarios, and that different PFT responses and adjustments to soil and topography factors affect whole functional community dynamic succession processes, which can profoundly impact forest ecosystem function predictions based on PFT changes in the Loess Plateau of China.
Fractional ablative CO2 laser and oral isotretinoin—A prospective randomized controlled split‐face trial comparing concurrent versus delayed laser treatment for acne scars
Authors: Taleb Eyal , Gallo Elisa S. , Salameh Fares , Koren Amir , Shehadeh Waseem , Artzi Ofir 
Published: August 2023

AbstractBackgroundTherapeutic dogma has been to treat acne scars with ablative fractional laser no less than 6 months after isotretinoin (ITN) cessation.ObjectiveTo evaluate the safety and efficacy of fractional ablative CO2 laser (FACL) in patients treated concurrently with ITN.MethodsWe conducted a prospective split‐face randomized control trial in patients treated with FACL concurrently with ITN versus patients treated with FACL 6 months post‐ITN treatment. Patients received 3 monthly sessions of FACL with concurrent ITN treatment on half of the face; the other side of the face received the same FACL treatment regimen 6 months post‐ITN cessation. Patients were followed for adverse effects up to 6 months post‐FACL treatment. Final cosmesis was scored using the Quantitative Global Acne Scarring Grading System (GASGS) by three independent dermatologists.ResultsThe GASGS of the concurrent ITN‐FACL treated side of the face was significantly lower than the side treated with delayed laser therapy (4.7 ± 2.5 vs. 7.7 ± 2.9, respectively, p < 0.001).LimitationsThe laser's settings were standardized, and not adjusted per patient skin type.ConclusionPer our prospective trial, concurrent treatment of FACL ‐ITN is superior to delayed FACL treatment 6 months post‐ITN cessation.Fractional ablative laser treatment is effective in improving acne scars, which persist despite isotretinoin therapy.
Regulation of SELENOF translation by eIF4a3: Possible role in prostate cancer progression
Authors: Bera Soumen , Kadkol Shrinidhi , Hong Lenny K. , Ali Waleed , Brockman John D. , Sverdlov Maria , Brister Eileen , Macais Virgilia , Kajdacsy‐Balla Andre , Valyi‐Nagy Klara , Xu Ziqiao , Kastrati Irida , Liu Li , Diamond Alan M. 
Published: August 2023

AbstractThe levels of the SELENOF selenoprotein are dramatically reduced in prostate cancer compared to adjacent benign tissue and reducing SELENOF in prostate epithelial cells results in the acquisition of features of the transformed phenotype. It was hypothesized that the aberrant increase in the eiF4a3 translation factor, which has an established role in RNA splicing and the regulation of selenoprotein translation, contributes to the lower levels of SELENOF. Using the available databases, eIF4a3 messenger RNA (mRNA) levels are elevated in prostate cancer compared to normal tissue as is the hypomethylation of the corresponding gene. Using a prostate cancer tissue microarray, we established that eiF4a3 levels are higher in prostate cancer tissue. Ectopic expression of eIF4a3 in prostate cancer cells reduced SELENOF levels and attenuated the readthrough of the UGA codon using a specialized reporter construct designed to examine UGA decoding, with the opposite effects observed using eIF4a3 knock‐down constructs. Direct binding of eIF4a3 to the regulatory regions of SELENOF mRNA was established with pull‐down experiments. Lastly, we show that an eIF4a3 inhibitor, eIF4a3‐IN‐2, increases SELENOF levels, UGA readthrough, and reduces binding of eIF4a3 to the SELENOF mRNA 3′‐UTR in exposed cells. These data establish eIF4a3 as a likely prostate cancer oncogene and a regulator of SELENOF translation.
Selection of pricing tactics in a dual‐channel supply chain under demand information asymmetry
Authors: Sun Haining , Cai Jianhu , Jia Lishuang , Hu Xiaoqing 
Published: August 2023

AbstractThis paper explores the differences of three pricing tactics in the dual‐channel supply chain (SC) under demand information asymmetry. The manufacturer holds confidential demand information. According to the decision sequences, three pricing tactics are considered. Specifically, the corresponding signaling games based on the three pricing tactics are analyzed under no information sharing. The results show when the confidential information is shared, the first move of retail pricing brings the positive impact on the SC members. However, under demand information asymmetry, the first move of retail pricing may not always benefit the member based on the signaling games.
Task‐Related Reorganization of Cognitive Network in Parkinson's Disease Using Electrophysiology
Authors: Bar‐On May , Baharav Shaked , Katzir Zoya , Mirelman Anat , Sosnik Ronen , Maidan Inbal 
Published: August 2023

AbstractBackgroundCognitive deficits in Parkinson's disease (PD) patients are well described, however, their underlying neural mechanisms as assessed by electrophysiology are not clear.ObjectivesTo reveal specific neural network alterations during the performance of cognitive tasks in PD patients using electroencephalography (EEG).MethodsNinety participants, 60 PD patients and 30 controls underwent EEG recording while performing a GO/NOGO task. Source localization of 16 regions of interest known to play a pivotal role in GO/NOGO task was performed to assess power density and connectivity within this cognitive network. The connectivity matrices were evaluated using a graph‐theory approach that included measures of cluster‐coefficient, degree, and global‐efficiency. A mixed‐model analysis, corrected for age and levodopa equivalent daily dose was performed to examine neural changes between PD patients and controls.ResultsPD patients performed worse in the GO/NOGO task (P < 0.001). The power density was higher in δ and θ bands, but lower in α and β bands in PD patients compared to controls (interaction group × band: P < 0.001), indicating a general slowness within the network. Patients had more connections within the network (P < 0.034) than controls and these were used for graph‐theory analysis. Differences between groups in graph‐theory measures were found only in cluster‐coefficient, which was higher in PD compared to controls (interaction group × band: P < 0.001).ConclusionsCognitive deficits in PD are underlined by alterations at the brain network level, including higher δ and θ activity, lower α and β activity, increased connectivity, and segregated network organization. These findings may have important implications on future adaptive deep brain stimulation. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
Adverse Events and Subsequent Management Associated With Eustachian Tube Balloon Dilation
Authors: Jeoung Sarah , Man Li‐Xing , Mandych Alexander K. , Schmale Isaac L. 
Published: August 2023

AbstractObjectiveEustachian tube balloon dilation is a minimally invasive technique used to improve persistent Eustachian tube dysfunction. Currently, the US Food and Drug Administration (FDA) has approved the use of balloon dilation devices produced by three manufacturers, but little is known about associated adverse events and subsequent management.Study DesignCase series.SettingFDA Manufacturer and User Facility Device Experience (MAUDE) database.MethodsReports submitted to the FDA using the MAUDE database searched from January 2000 to July 2022 were analyzed for adverse events and management.ResultsA total of 13 adverse events were found in the database. Subcutaneous emphysema (n = 8) was the most common event. Other less frequent events included patulous Eustachian tube (n = 2), vascular dissection (n = 1), nasopharyngeal mucocele (n = 1), and tinnitus (n = 1). A majority of patients who experienced subcutaneous emphysema received antibiotics (n = 5) and were admitted to the hospital (n = 4). The patient with a carotid dissection 7 days postprocedure presented with a stroke and fully recovered after stent placement. There was limited preprocedure information in the MAUDE database. There were 2 patients who did not fully recover after a complication. Three patients underwent corrective surgical interventions. No one company had more associated adverse events reported.ConclusionSubcutaneous emphysema is the most common adverse event after Eustachian tube dilation. Further studies exploring potential balloon dilation adverse events to allow for better patient counseling are warranted.
Prediction of coexisting invasive carcinoma on ductal carcinoma in situ (DCIS) lesions by mass spectrometry imaging
Authors: Chen Hong , Li Xin , Li Fengling , Li Yijie , Chen Fei , Zhang Lu , Ye Feng , Gong Meng , Bu Hong 
Published: August 2023

AbstractDue to limited biopsy samples, ~20% of DCIS lesions confirmed by biopsy are upgraded to invasive ductal carcinoma (IDC) upon surgical resection. Avoiding underestimation of IDC when diagnosing DCIS has become an urgent challenge in an era discouraging overtreatment of DCIS. In this study, the metabolic profiles of 284 fresh frozen breast samples, including tumor tissues and adjacent benign tissues (ABTs) and distant surrounding tissues (DSTs), were analyzed using desorption electrospray ionization‐mass spectrometry (DESI‐MS) imaging. Metabolomics analysis using DESI‐MS data revealed significant differences in metabolite levels, including small‐molecule antioxidants, long‐chain polyunsaturated fatty acids (PUFAs) and phospholipids between pure DCIS and IDC. However, the metabolic profile in DCIS with invasive carcinoma components clearly shifts to be closer to adjacent IDC components. For instance, DCIS with invasive carcinoma components showed lower levels of antioxidants and higher levels of free fatty acids compared to pure DCIS. Furthermore, the accumulation of long‐chain PUFAs and the phosphatidylinositols (PIs) containing PUFA residues may also be associated with the progression of DCIS. These distinctive metabolic characteristics may offer valuable indications for investigating the malignant potential of DCIS. By combining DESI‐MS data with machine learning (ML) methods, various breast lesions were discriminated. Importantly, the pure DCIS components were successfully distinguished from the DCIS components in samples with invasion in postoperative specimens by a Lasso prediction model, achieving an AUC value of 0.851. In addition, pixel‐level prediction based on DESI‐MS data enabled automatic visualization of tissue properties across whole tissue sections. Summarily, DESI‐MS imaging on histopathological sections can provide abundant metabolic information about breast lesions. By analyzing the spatial metabolic characteristics in tissue sections, this technology has the potential to facilitate accurate diagnosis and individualized treatment of DCIS by inferring the presence of IDC components surrounding DCIS lesions. © 2023 The Pathological Society of Great Britain and Ireland.
A (Ba0.94Ca0.06)(Ti0.95Zr0.05)O3 ceramic sheet doping to improve the inverse piezoelectric effect of the poly (vinylidene fluoride‐trifluoroethylene)‐based composite film
Authors: Ping Yufan , Xia Weimin , Zhou Jiahong , Zhang Xiaofang , Li Zhong 
Published: August 2023

AbstractA lead‐free tetragonal‐phase (Ba0.94Ca0.06)(Ti0.95Zr0.05)O3 (BCTZ) micro sheet is prepared by molten‐salt growth method, which exhibits a polarizing behavior of relaxor ferroelectricity and possesses a high dielectric constant (εr) of ~2400. Subsequently, the BCTZ sheet is evenly doped into ferroelectric copolymer P(VDF‐TrFE)55/45 mol% with different mass fractions, and the flexible BCTZ/P(VDF‐TrFE) composite films are prepared using a conventional solution casting process. εr of BCTZ/P(VDF‐TrFE) increases with the mass content of BCTZ, and reaches 23.8 in 20 wt% BCTZ sample. Meanwhile, at a high electrical field of 30 MV/m, the strain and electric field of BCTZ/P(VDF‐TrFE) are in the opposite direction, indicating a negative value of piezoelectric strain coefficient (d33) caused by inverse piezoelectric effect. In addition, d33 of different BCTZ/P(VDF‐TrFE) films are fitted using a strain‐electrical field curve, which firstly increases and then decreases with increases in BCTZ content. As such, a high d33 of −47.3 pC/N is obtained in BCTZ/P(VDF‐TrFE)15/85 wt% film. Thus, this research concerning the inverse piezoelectric effect may provide a reference for designing a piezoelectric composite using in transducers and actuators.
Estimating protein complex model accuracy based on ultrafast shape recognition and deep learning in CASP15
Authors: Liu Jun , Liu Dong , He Guangxing , Zhang Guijun 
Published: August 2023

AbstractThis article reports and analyzes the results of protein complex model accuracy estimation by our methods (DeepUMQA3 and GraphGPSM) in the 15th Critical Assessment of techniques for protein Structure Prediction (CASP15). The new deep learning‐based multimeric complex model accuracy estimation methods are proposed based on the ensemble of three‐level features coupling with deep residual/graph neural networks. For the input multimeric complex model, we describe it from three levels: overall complex features, intra‐monomer features, and inter‐monomer features. We designed an overall ultrafast shape recognition (USR) to characterize the relationship between local residues and the overall complex topology, and an inter‐monomer USR to characterize the relationship between the residues of one monomer and the topology of other monomers. DeepUMQA3 (Group name: GuijunLab‐RocketX) ranked first in the interface residue accuracy estimation of CASP15. The Pearson correlation between the interface residue Local Distance Difference Test (lDDT) predicted by DeepUMQA3 and the real lDDT is 0.570, the only method that exceeds 0.5. Among the top 5 methods, DeepUMQA3 achieved the highest Pearson correlation of lDDT on 25 out of 39 targets. GraphGPSM (Group name: GuijunLab‐PAthreader) has TM‐score Pearson correlations greater than 0.9 on 14 targets, showing a good ability to estimate the overall fold accuracy. The DeepUMQA3 server is available at http://zhanglab-bioinf.com/DeepUMQA/ and the GraphGPSM server is available at http://zhanglab-bioinf.com/GraphGPSM/.
Suspension Concentrate crop protection formulation design and performance for low spray volume and UAS spray application
Authors: Faers Malcolm A , Sato Yoshitaka , Hilz Emilia , Lamprecht Sybille , Dong Jun , Qi Feng , Ratschinski Arno , Peris Gorka , Gaertzen Oliver , Roechling Andreas 
Published: August 2023

AbstractBACKGROUNDUnmanned aerial systems (UAS) are providing interesting disruptive solutions for spray application of crop protection products with very‐low spray volumes (VLV) down to 8 L/ha that offer improved sustainability through reduced water volumes and reduced soil compaction. However, the efficacy of products can be reduced by the significantly lower crop/plant spray coverage and formulation designs that can compensate for this are highly important here.RESULTSSuspension Concentrate (SC) formulations designed for VLV use containing and delivering low dose rates (g/ha) of organosilicone alkoxylate high‐spreading surfactants were found to result in leaf coverage of VLVs comparable to those observed at higher spray volumes. High spreading was observed on textured leaf surfaces containing sub‐micron sized epicuticular wax crystals. Greenhouse fungal disease studies showed enhanced efficacy with these SC formulations compared to standard SC formulations without these additives and maintained the observed increase in efficacy when applied at VLV. Alternatively, SC formulations without high spreading formulants but containing uptake promoting nonionic surfactants showed enhanced cuticle penetration through isolated cuticles at VLV in comparison to higher spray volumes, with coffee‐ring spray deposit microstructures present at VLVs. Similarly, greenhouse studies showed enhanced efficacy that was maintained at VLV relative to SCs without these additives.CONCLUSIONAt VLVs, SC formulations applied at relatively low dose rates (g/ha) of formulants (adjuvants) enhancing spreading on the leaf surface and/or uptake of the active ingredient(s) maintained good spreading, uptake and biological efficacy in greenhouse studies overcoming the coverage limitations of SC formulations without these additives. This result is unexpected considering the low dose rate of adjuvants used. © 2023 Bayer AG. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.