bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation of a MS/MS database for isoquinoline alkaloids and other annonaceous metabolites
Authors: Agnès Salemon Akpa , Okpekon Timothée , Kouadio Yvette Affoué , Jagora Adrien , Bréard Dimitri , Costa Emmanoel V. , da Silva Felipe M. A. , Koolen Hector H. F. , Le Ray-Richomme Anne-Marie , Richomme Pascal , Champy Pierre , Beniddir Mehdi A. , Le Pogam Pierre 
Published: June 2022

AbstractThis data descriptor reports on the upload to a public repository (GNPS) of the IQAMDB, IsoQuinoline and Annonaceous Metabolites Data Base, comprising 320 tandem mass spectra. This project originated from our in-house collection of isoquinolines. The diversity of compounds included in this database was further extended through the contribution of two additional laboratories involved in isoquinoline alkaloids research: University of Angers and University of Manaus. The generated MS/MS data were processed and annotated on an individual basis to promote their straightforward reuse by natural product chemists interested in either the description of new isoquinoline alkaloids or the dereplication of isoquinoline-containing samples. The interest of the current repertoire for dereplication purposes has been validated based on the molecular networking of the well-investigated plant modelAnnona montanaagainst the IQAMDB‐implemented GNPS.
On-chip complex refractive index detection at multiple wavelengths for selective sensing
Authors: El Shamy Raghi S. , Swillam Mohamed A. , Li Xun 
Published: June 2022

AbstractIn this work we propose a method for on-chip detection of the complex refractive index of the sensing medium at multiple wavelengths for selective sensing. For the optical sensor to be selective, i.e. able to determine the substance present in the medium, either surface functionalization or absorption spectroscopy is often used. Surface functionalization is a complex process and is mainly limited to biological media. On the other hand, absorption spectroscopy is not suitable for on-chip sensing with micrometer dimensions as this will result in poor sensitivity, especially when working far from the substance absorption peaks. Here, we detect the dispersion of both the real n and imaginary k parts of the refractive index which are unique for each substance. This is done using a single micro-ring resonator (MRR) that exhibits multiple resonances over the operating wavelength range. The real and imaginary parts of the medium refractive index are determined at each resonance using the resonance wavelength and the absorption coefficient, respectively. In addition, using this technique the concentration composition of a multi-element medium can be determined by solving a system of linear equations that corresponds to the different wavelengths (resonances). We designed a silicon-on-insulator (SOI) ring-resonator operating in the near-infrared region from λ = 1.46 µm to λ = 1.6 µm. The ring exhibits 11 resonances over the 140 nm operating wavelength range where the corresponding medium refractive index is obtained. This design can detect four different substances namely, methanol, ethanol, propanol, and water. An average error of less than 0.0047% and 1.65% in the detection of the real and imaginary parts, respectively were obtained. Finally, the concentration composition of different multi-element media were successfully determined using the least square method with 97.4% detection accuracy.
Usefulness of low tidal volume ventilation strategy for patients with acute respiratory distress syndrome: a systematic review and meta-analysis
Authors: Yamamoto Ryohei , Okazaki Satoru Robert , Fujita Yoshihito , Seki Nozomu , Kokei Yoshufumi , Sekine Shusuke , Wada Soichiro , Norisue Yasuhiro , Narita Chihiro 
Published: June 2022

AbstractThe effects of lower tidal volume ventilation (LTV) were controversial for patients with acute respiratory distress syndrome (ARDS). This systematic review and meta-analysis aimed to evaluate the use of LTV strategy in patients with ARDS. We performed a literature search on MEDLINE, CENTRAL, EMBASE, CINAHL, “Igaku-Chuo-Zasshi”, clinical trial registration sites, and the reference of recent guidelines. We included randomized controlled trials (RCTs) to compare the LTV strategy with the higher tidal volume ventilation (HTV) strategy in patients with ARDS. Two authors independently evaluated the eligibility of studies and extracted the data. The primary outcomes were 28-day mortality. We used the GRADE methodology to assess the certainty of evidence. Among the 19,864 records screened, 13 RCTs that recruited 1874 patients were included in our meta-analysis. When comparing LTV (4–8 ml/kg) versus HTV (> 8 ml/kg), the pooled risk ratio for 28-day mortality was 0.79 (11 studies, 95% confidence interval [CI] 0.66–0.94, I2 = 43%, n = 1795, moderate certainty of evidence). Subgroup-analysis by combined high positive end-expiratory pressure with LTV showed interaction (P = 0.01). Our study indicated that ventilation with LTV was associated with reduced risk of mortality in patients with ARDS when compared with HTV.Trial registration: UMIN-CTR (UMIN000041071).
Label-free multiplex electrochemical immunosensor for early diagnosis of lysosomal storage disorders
Authors: Abdulkarim Haya , Siaj Mohamed 
Published: June 2022

AbstractPompe, Gaucher and Krabbe disease are lysosomal storage disorders (LSDs) which are a group of genetic diseases that causes the accumulation of lipids in tissues and cells. Pompe, Gaucher and Krabbe are characterized by the deficiency of acid α-glucosidase (GAA), β-Glucocerebrosidase (GBA) and galactocerebrosidase (GALC), and treatable if detected in their early stages. Here, we present the fabrication of an electrochemical immunosensor for the multiplexed quantification and simultaneous detection of GAA, GBA and GALC. The sensor was developed by electrodepositing gold nanoparticles (AuNPs) on an array of carbon electrodes, followed by the immobilization of GAA, GBA and GALC specific antibodies via functionalization with cysteamine and glutaraldehyde. The multiplexed immunosensor was able to successfully detect GAA, GBA and GALC at the femtomolar level with respective low detection limits of 0.12 pg/ml, 0.31 pg/ml and 0.18 pg/ml. The immunosensor showed good selectivity, sensitivity and good recovery when spiked in human serum, which confirms its possible applicability in point-of-care testing for the early diagnosis of LSDs.
Forecasting induced seismicity in Oklahoma using machine learning methods
Authors: Qin Yan , Chen Ting , Ma Xiaofei , Chen Xiaowei 
Published: June 2022

AbstractOklahoma earthquakes in the past decade have been mostly associated with wastewater injection. Here we use a machine learning technique—the Random Forest to forecast induced seismicity rate in Oklahoma based on injection-related parameters. We split the data into training (2011.01–2015.05) and test (2015.06–2020.12) periods. The model forecasts seismicity rate during the test period based on input features, including operational parameters (injection rate and pressure), geological information (depth to basement), and modeled pore pressure and poroelastic stress. The results show overall good match with observed seismicity rate (adjusted$$R^2$$R2of 0.75). The model shows that pore pressure rate and poroelastic stressing rates are the two most important features in forecasting. The absolute values of pore pressure and poroelastic stress, and the injection rate itself, are less important than the stressing rates. These findings further emphasize that temporal changes of stressing rates would lead to significant changes in seismicity rates.
High-throughput metabolomics reveals dysregulation of hydrophobic metabolomes in cancer cell lines by Eleusine indica
Authors: Puah Perng Yang , Lee Dexter Jiunn Herng , Puah Soo Huan , Lah Nik Amin Sahid Nik , Ling Yee Soon , Fong Siat Yee 
Published: June 2022

AbstractEleusine indica, which is used in traditional medicine, exhibits antiproliferative activity against several cancer cell lines. However, metabolomic studies to evaluate the metabolite changes induced by E. indica in cancer cells are still lacking. The present study investigated the anticancer effects of a root fraction of E. indica (R-S5-C1-H1) on H1299, MCF-7, and SK-HEP-1 cell lines and analyzed metabolic changes in the treated cancer cells using ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS). Cell metabolic activity assays demonstrated that the cell viability of the three cancer cell lines was significantly reduced following treatment with R-S5-C1-H1, with half-maximal inhibitory concentrations values of 12.95 µg/mL, 15.99 µg/mL, and 13.69 µg/mL at 72 h, respectively. Microscopy analysis using Hoechst 33342 and Annexin V fluorescent dyes revealed that cells treated with R-S5-C1-H1 underwent apoptotic cell death, while chemometric analysis suggested that apoptosis was triggered 48 h after treatment with R-S5-C1-H1. Deconvoluted cellular metabolomics revealed that hydrophobic metabolites were significantly altered, including triacylglycerols, phosphatidylcholine, phosphatidylethanolamine, sphingomyelin, and ceramide, suggesting that apoptosis induction by R-S5-C1-H1 potentially occurred through modulation of phospholipid synthesis and sphingolipid metabolism. These metabolomic profiling results provide new insights into the anticancer mechanisms of E. indica and facilitate the overall understanding of molecular events following therapeutic interventions.
Accuracy of real-time PCR and digital PCR for the monitoring of total HIV DNA under prolonged antiretroviral therapy
Authors: Renault Constance , Bolloré Karine , Pisoni Amandine , Motto-Ros Camille , Van de Perre Philippe , Reynes Jacques , Tuaillon Edouard 
Published: June 2022

AbstractTotal HIV DNA is a standard marker to monitor the HIV reservoir in people living with HIV. We investigated HIV DNA quantification accuracy by a real-time PCR kit (qPCR) and digital PCR (dPCR) method within the same set of primers and probes. Among 48 aviremic patients followed for up to 7 years with qPCR, the mean coefficient of variation of total HIV DNA between two successive measurements was 77% (± 0.42log10 HIVDNA copies/106 PBMC). The total HIV DNA quantified by the two PCR methods has a high correlation (0.99 and 0.83, for 8E5 and PLHIV samples, respectively), but we observed better repeatability and reproducibility of the dPCR compared to the qPCR (CV of 11.9% vs. 24.7% for qPCR, p-value = 0.024). Furthermore, we highlighted a decay of the number of HIV copies in the 8E5 cell line qPCR standard over time (from 0.73 to 0.43 copies per cell), contributing to variations of HIV DNA results in patients whose HIV reservoir should be theoretically stabilized. Our study highlighted that absolute quantification of total HIV DNA by dPCR allows more accurate monitoring of the HIV reservoir than qPCR in patients under prolonged antiretroviral therapy.
Autologous matrix-induced chondrogenesis is effective for focal chondral defects of the knee
Authors: Migliorini Filippo , Maffulli Nicola , Baroncini Alice , Bell Andreas , Hildebrand Frank , Schenker Hanno 
Published: June 2022

AbstractFocal chondral defects of the knee are common and their management is challenging. This study investigated the efficacy and safety of Autologous Matrix-Induced Chondrogenesis (AMIC) for focal chondral defects of the knee. A systematic review and meta-analysis was conducted (according to the 2020 PRISMA statement) to investigate the efficacy of AMIC in improving symptoms and to compare AMIC versus microfracture (MFx). In January 2022, the following databases were accessed: Pubmed, Web of Science, Google Scholar, Embase. No time constrain was used for the search. All the clinical trials investigating AMIC and/or those comparing AMIC versus MFx for focal chondral defects of the knee were accessed. Only studies published in peer reviewed journals were considered. Studies which investigated other locations of the defects rather than knee were not eligible, nor those reporting data form mixed locations. Studies which reported data on revision settings, as well as those investigating efficacy on kissing lesions or multiple locations, were not suitable. The mean difference (MD) and odd ratio (OR) effect measure were used for continuous and binary data, respectively. Data from 18 studies (548 patients) were retrieved with a mean follow-up of 39.9 ± 26.5 months. The mean defect size was 3.2 ± 1.0 cm2. The visual analogue scale (VAS) decreased of − 3.9/10 (95% confidence interval (CI) − 4.0874 to -3.7126), the Tegner Activity Scale increased of + 0.8/10 (95% CI 0.6595 to 0.9405). The Lysholm Knee Scoring System increased of + 28.9/100 (95% CI 26.8716 to 29.1284), as did the International Knee Documentation Committee (IKDC) + 33.6/100 (95% CI 32.5800 to 34.6200). At last follow-up no patient showed signs of hypertrophy. 4.3% (9 of 210) of patients underwent revision procedures. The rate of failure was 3.8% (9 of 236). Compared to MFx, AMIC demonstrated lower VAS score (MD: − 1.01; 95% CI − 1.97 to 0.05), greater IKDC (MD: 11.80; 95% CI 6.65 to 16.94), and lower rate of revision (OR: 0.16; 95% CI 0.06 to 0.44). AMIC is effective for focal chondral defects of the knee. Furthermore, AMIC evidenced greater IKDC, along with a lower value of VAS and rate of revision compared to MFx.
Selective autophagy: adding precision in plant immunity
Authors: Leong Jia Xuan , Langin Gautier , Üstün Suayib 
Published: June 2022

Abstract
Plant immunity is antagonized by pathogenic effectors during interactions with bacteria, viruses or oomycetes. These effectors target core plant processes to promote infection. One such core plant process is autophagy, a conserved proteolytic pathway involved in ensuring cellular homeostasis. It involves the formation of autophagosomes around proteins destined for autophagic degradation. Many cellular components from organelles, aggregates, inactive or misfolded proteins have been found to be degraded via autophagy. Increasing evidence points to a high degree of specificity during the targeting of these components, strengthening the idea of selective autophagy. Selective autophagy receptors bridge the gap between target proteins and the forming autophagosome. To achieve this, the receptors are able to recognize specifically their target proteins in a ubiquitin-dependent or -independent manner, and to bind to ATG8 via canonical or non-canonical ATG8-interacting motifs. Some receptors have also been shown to require oligomerization to achieve their function in autophagic degradation. We summarize the recent advances in the role of selective autophagy in plant immunity and highlight NBR1 as a key player. However, not many selective autophagy receptors, especially those functioning in immunity, have been characterized in plants. We propose an in silico approach to identify novel receptors, by screening the Arabidopsis proteome for proteins containing features theoretically needed for a selective autophagy receptor. To corroborate these data, the transcript levels of these proteins during immune response are also investigated using public databases. We further highlight the novel perspectives and applications introduced by immunity-related selective autophagy studies, demonstrating its importance in research.
Analytical investigations on discrimination of partial discharge defective cable termination among healthy ones with joint sheath‐ground connection
Authors: Babaee Abbas , Shahinfar Kian , Shahrtash Seyed Mohammad 
Published: June 2022

AbstractIndustrial complexes suffer from crosstalk of Partial Discharge (PD) defects in cable terminations connected to the same medium voltage busbars. This phenomenon happens because the sheath‐ground connections of all cables of one switchboard are first fastened together and then connected to ground, which leads to PD pulses being induced from the source termination to others. In this paper, based on mathematical investigations on PD pulse propagation and by introducing an energy‐based index, a simple rule‐based procedure is proposed for discrimination between defective terminations and healthy ones connected to common busbars. The proposed procedure has been verified by simulations even when there exists noise pollution or multiple defects of different strengths.
Activity location recognition from mobile phone data using improved HAC and Bi‐LSTM
Authors: Jiang Haihang , Yang Fei , Su Weijie , Yao Zhenxing , Dai Zhuang 
Published: June 2022

AbstractExisting studies on activity location recognition based on mobile phone data has made great progresses. However, current studies generally assume constant distance threshold when performing activity location clustering, and ignore the influence of base station layout on positioning accuracies of mobile phone data. Given different recognition accuracy requirements, the authors propose two methods to recognise activity locations: (1) An improved hierarchical agglomerative clustering algorithm that integrates a genetic algorithm component to search and dynamically adjust optimal distance thresholds based on base station densities; (2) The recognition method based on Bi‐directional long short‐term memory network that classifies travel statuses of mobile phone traces. Results show that, compared with existing methods, the activity location recognition accuracy of the proposed hierarchical agglomerative clustering algorithm increases by about 5%. The Bi‐directional long short‐term memory network model further outperforms the improved hierarchical agglomerative clustering, especially in the aspect of recognising non‐commuting activity locations. However, the Bi‐directional long short‐term memory network model training requires the users’ actual travel information, so there are certain obstacles in popularising Bi‐directional long short‐term memory network in practice.
The COVID-19 Pandemic Impact on Breast Cancer Diagnosis: A Retrospective Study
Authors: Negrao Erika Marina Solla , Cabello Cesar , Conz Livia , Mauad Edmundo Carvalho , Zeferino Luiz Carlos , Vale Diama Bhadra 
Published: June 2022

Abstract
Objective This study aimed to evaluate the diagnostic profile of breast cancer cases during the coronavirus disease 2019 (COVID-19) pandemic compared with the previous year.
Methods It is a retrospective study of cases diagnosed by a reference service in the public health system of Campinas, SP, Brazil. Two periods were analyzed: March to October 2019 (preCOVID period) and March to October 2020 (COVID-period). All women diagnosed during the periods were included. The Chi-Squared or Fisher exact and Mann-Whitney tests were used.
Results In the preCOVID and COVID periods, breast cancers were diagnosed, respectively, in 115 vs 59 women, and the mean ages at diagnosis were 55 and 57 years (p = 0.339). In the COVID period, the family history of breast cancer was more observed (9.6% vs 29.8%, p < 0.001), cases were more frequently symptomatic (50.4% vs 79.7%, p < 0.001) and had more frequently palpable masses (56.5% vs 79.7%, p = 0.003). In symptomatic women, the mean number of days from symptom to mammography were 233.6 (458.3) in 2019 and 152.1 (151.5) in 2020 (p = 0.871). Among invasive tumors, the proportion of breast cancers in stages I and II was slightly higher in the COVID period, although not significantly (76.7% vs 82.4%, p = 0.428). Also in the COVID period, the frequency of luminal A-like tumors was lower (29.2% vs 11.8%, p = 0.018), of triple-negative tumors was twice as high (10.1% vs 21.6%, p = 0.062), and of estrogen receptor-positive tumors was lower (82.2% vs 66.0%, p = 0.030).
Conclusion During the COVID-19 pandemic, breast cancer diagnoses were reduced. Cases detected were suggestive of a worse prognosis: symptomatic women with palpable masses and more aggressive subtypes. Indolent tumors were those more sensitive to the interruption in screening.
Picosecond optospintronic tunnel junctions
Authors: Wang Luding , Cheng Houyi , Li Pingzhi , van Hees Youri L. W. , Liu Yang , Cao Kaihua , Lavrijsen Reinoud , Lin Xiaoyang , Koopmans Bert , Zhao Weisheng 
Published: June 2022

Significance
Spintronic devices have become promising candidates for next-generation memory architecture. However, state-of-the-art devices, such as perpendicular magnetic tunnel junctions (MTJs), are still fundamentally constrained by a subnanosecond speed limitation, which has remained a long-lasting scientific obstacle in the ultrafast spintronics field. The highlight of our work is the demonstration of an optospintronic tunnel junction, an all-optical MTJ device which emerges as a new category of integrated photonic–spintronic memory. We demonstrate 1) laser-induced deterministic and efficient writing by an all-optical approach and electrical readout by tunnel magnetoresistance, 2) writing speed within 10 ps, demonstrated by femtosecond-resolved measurements, and 3) integration with state-of-the-art MTJ performance and a complementary metal–oxide–semiconductor-compatible fabrication progress.
Prolonged eye‐hand decoupling deficits in young adults with a history of concussion from adolescence
Authors: Phillips Brandon , Adkins Jaxon C. , Jones Briasha D. , Dalecki Marc 
Published: June 2022

ABSTRACTPrevious studies reported that adolescents with a sport‐related concussion history showed prolonged visuomotor deficits during an eye‐hand decoupling task until around 1.5–2 years post‐event. The present study expands this work, examining whether such deficits do or do not emerge when testing individuals in young adulthood, i.e. later post‐event. Twenty‐one non‐athlete college students with sport‐related concussion history from adolescence (CH; M = 21 yrs.; M = 46 months post‐concussion, range 10–90 months) and twenty controls with no history of concussion (NoH; M = 21 yrs.) performed two touchscreen‐based visuomotor tasks. It included a coupled task where eyes and hand moved in similar directions, and decoupled‐task with eyes and hand going to different directions. Movement planning (e.g. reaction time, initial direction error) and execution (e.g. movement time, path length) related variables were analyzed in both groups and conditions. Movement execution measures were similar for both groups and conditions (all p > 0.05). However, movement planning was impaired in the CH participants in the eye‐hand decoupling condition (p < 0.05). CH's initial direction error was larger (i.e. worse spatial movement planning) than in the NoH group. Although movement execution deficits shown in earlier work in youth were not present in young adults, the present results suggest that a sport‐related concussion sustained in adolescence can lead to prolonged deficits with spatial movement planning processes while performing eye‐hand decoupling tasks about four years post‐injury. Further research should investigate whether these deficits continue into adulthood and expand control on time since concussion and number of concussion metrics.Highlights
Young adult college students with a history of a sport‐related concussion from adolescence, tested about four years post‐incident, showed spatial movement preparation deficits during an eye‐hand decoupling visuomotor task.
Eye‐hand reversal decoupling errors also correlated with time since concussion in those with concussion history.
These prolonged eye‐hand decoupling deficits may emerge with ongoing time post‐event, as comparable deficits were absent in previous work where youth were tested sooner post‐injury.
Our current findings point towards long‐lasting performance impairments in young adult non‐athletes after a sport‐related concussion from adolescence.