bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinico‐cytopathologic analysis of 574 Pericardial Effusion Specimens: Application of the international system for reporting serous fluid cytopathology (ISRSFC) and long‐term clinical follow‐up
Authors: Song Min Jeong , Jo Uiree , Jeong Ji‐Seon , Cho Kyung‐Ja , Gong Gyungyub , Cho Yong Mee , Song Joon Seon 
Published: November 2021

AbstractIntroductionA pericardial effusion (PE) has a variable etiology and the primary role is diagnosis of metastatic malignancy. We analyzed the PE cytology in a large cohort in accordance with the international system for reporting serous fluid cytopathology (ISRSFC) and evaluated the long‐term patient outcomes.MethodsPE specimens from 2010 to 2014 with an available clinical history, cytologic data, and pericardial biopsy results were collected.ResultsA total of 574 PE specimens were obtained from 486 patients, representing 1.5% (574/38,589) of all body fluid specimens. Three hundred and eighty‐two (66.6%) cases were “negative,” 54 (9.4%) cases were “atypia of undetermined significance,” 10 (1.7%) cases were “suspicious for malignancy,” and 128 (22.3%) cases were “malignancy”. The most common origin for malignant PE was the lung (82.1%), in both men (70.5%) and women (50.6%). Breast cancer (20%) in women and gastric cancer (4.9%) in men were the second most common malignant PE, respectively. The mean interval from the occurrence of malignant PE to death was 10.06 months (range; 0–116.03 months, median 3.5 months), and the 1‐year survival rate was 16.7%. In addition, the 1‐year survival rates after malignant PE onset were 0% for gastric cancer, 13.9% for lung cancer, 19.8% for breast cancer, and 21.1% for the other cancers (p = 0.011).ConclusionOur present study is the first to our knowledge to classify the pericardial fluid from 574 cases in accordance with the recently published ISRSFC, and to present the long‐term outcomes of patients with malignant PE at the same time. Moreover, we report for the first time that it is gastric and not lung cancer patients that have the poorest prognosis after the occurrence of malignant PE.
In Vivo Whole‐Nerve Electrophysiology Setup, Action Potential Recording, and Data Analyses in a Rodent Model
Authors: Zhao Diane , Behzadian Negin , Yeomans David , Anderson T. Anthony 
Published: November 2021

AbstractIn vivo rodent, whole peripheral nerve models are useful for studying the electrical conduction of sensory and motor fibers under normal physiological conditions as well as for assessing neurological outcomes after the application of physical alterations or pharmacological agents to the nervous system. Significant literature has focused on single‐neuron and central nervous system electrophysiology protocol development. However, creation and development of in vivo whole‐nerve electrophysiological recording protocols are sparse in the scientific literature. Here, detailed protocols for designing and building an in vivo whole‐nerve electrophysiology system are described, including straightforward techniques to create working stimulation and recording electrodes that may be adapted to numerous study designs. Further, we include details for rodent anesthesia, surgical dissection (for the sciatic nerve), compound action potential signal optimization, data acquisition, data analyses, and troubleshooting tips. © 2021 Wiley Periodicals LLC.Basic Protocol 1: In vivo electrophysiology system wiring, hardware, and software setupsSupport Protocol 1: Design and 3D printing of electrophysiology base electrodesSupport Protocol 2: Building needle electrodesBasic Protocol 2: Rodent anesthesia and surgery for nerve exposureBasic Protocol 3: Compound action potential recording and troubleshooting using WinWCPBasic Protocol 4: Compound action potential data analysis using WinWCP
A Robust Protocol for CRISPR‐Cas9 Gene Editing in Human Suspension Cell Lines
Authors: Wardyn Joanna D. , Chan Allison S. Y. , Jeyasekharan Anand D. 
Published: November 2021

AbstractThe implementation of clustered regularly interspaced short palindromic repeats (CRISPR)‐Cas9 systems in mammalian cells has sparked an exciting new era in targeted gene editing. CRISPR‐Cas9 technologies allow gene function to be interrogated by gene deletions, mutations, and truncations, and by epitope tagging and promoter activity modulation. Many robust protocols have been published to date on CRISPR‐Cas9 techniques, however, most of these focus on adherent cell lines. Suspension cell lines, typically of hematolymphoid origin, such as Jurkat, Daudi, and TOLEDO, pose unique challenges to the setup of CRISPR experiments. Here, using B cell lymphoma cells as a primary model, we describe a comprehensive protocol for targeted gene manipulations using the CRISPR‐Cas9 system in suspension cells. We also highlight necessary optimization steps to make this approach universal to other suspension cell lines. We first describe a detailed protocol for transient expression of the Cas9 nuclease and guide RNAs. We then suggest workflows for obtaining single‐cell clones and for screening for successful homozygous knockout (KO) clones in suspension lines. This protocol aims to serve as a comprehensive resource to facilitate gene editing experiments for users starting CRISPR‐Cas9 gene editing protocols on suspension cell lines or those looking to optimize their current workflows. © 2021 Wiley Periodicals LLC.Basic Protocol 1: Transient CRISPR Cas9‐gRNA delivery for gene knockout by NeonTM electroporationSupport Protocol 1: Designing and preparing gene‐specific gRNASupport Protocol 2: Preparation of conditioned medium and culture vessels for single‐cell FACSAlternate Protocol 1: Transient CRISPR Cas9‐gRNA delivery for gene knockout by Nepagene electroporatorBasic Protocol 2: FACS and single‐cell clone generationAlternate Protocol 2: Manual cell dilution to obtain single‐cell clonesBasic Protocol 3: Confirming indels status in single‐cell clones by PCR on genomic DNA and Sanger sequencing
A 10‐MHz to 50‐GHz low‐jitter multiphase clock generator for high‐speed oscilloscope in 0.15‐μm GaAs technology
Authors: Wu Tianxiang , Wang Xi , Chen Yong , Ren Junyan , Ma Shunli 
Published: November 2021

AbstractThe data acquisition system is widely used in electronic measuring instruments, for example, the oscilloscope. The development direction of the oscilloscope reflects the research status and development trend of the data acquisition system. Currently, the index of oscilloscopes is progressing toward a high sampling rate, and the performance of the analog‐to‐digital converter (ADC) has become the main bottleneck to improve the sampling rate of the acquisition system. The alternate sampling technology entails multichannel low sampling rate ADCs to achieve high sampling rate data acquisition through parallel sampling and realize data reconstruction through software. The sampling clock is the most important and difficult part of the system. For ADCs with the 100‐GS/s sampling rate and 10‐bit resolution, the jitter of the sampling clock needs to be in sub‐100 fs along with multiple phases. Based on the principle of injection locking, a 150‐GS/s sampling clock is proposed in this paper, which is implemented in a 0.15‐μm GaAs process, and the 50‐GHz locking range is achieved. The measurement results show that the sampling frequency is 150 GS/s, the root mean square (RMS) jitter is 63 fs with the integrated range from 1 kHz to 10 MHz, and the phase noise can meet the sampling requirements of the 10‐bit oscilloscope, which can provide a clocking scheme for small and low‐power ultrahigh‐speed oscilloscope.
The multicellular signalling network of ovarian cancer metastases
Authors: Sommerfeld Leah , Finkernagel Florian , Jansen Julia M. , Wagner Uwe , Nist Andrea , Stiewe Thorsten , Müller‐Brüsselbach Sabine , Sokol Anna M. , Graumann Johannes , Reinartz Silke , Müller Rolf 
Published: November 2021

AbstractBackgroundTranscoelomic spread is the major route of metastasis of ovarian high‐grade serous carcinoma (HGSC) with the omentum as the major metastatic site. Its unique tumour microenvironment with its large populations of adipocytes, mesothelial cells and immune cells establishes an intercellular signaling network that is instrumental for metastatic growth yet poorly understood.MethodsBased on transcriptomic analysis of tumour cells, tumour‐associated immune and stroma cells we defined intercellular signaling pathways for 284 cytokines and growth factors and their cognate receptors after bioinformatic adjustment for contaminating cell types. The significance of individual components of this network was validated by analysing clinical correlations and potentially pro‐metastatic functions, including tumour cell migration, pro‐inflammatory signal transduction and TAM expansion.ResultsThe data show an unexpected prominent role of host cells, and in particular of omental adipocytes, mesothelial cells and fibroblasts (CAF), in sustaining this signaling network. These cells, rather than tumour cells, are the major source of most cytokines and growth factors in the omental microenvironment (n = 176 vs. n = 13). Many of these factors target tumour cells, are linked to metastasis and are associated with a short survival. Likewise, tumour stroma cells play a major role in extracellular‐matrix‐triggered signaling. We have verified the functional significance of our observations for three exemplary instances. We show that the omental microenvironment (i) stimulates tumour cell migration and adhesion via WNT4 which is highly expressed by CAF; (ii) induces pro‐tumourigenic TAM proliferation in conjunction with high CSF1 expression by omental stroma cells and (iii) triggers pro‐inflammatory signaling, at least in part via a HSP70–NF‐κB pathway.ConclusionsThe intercellular signaling network of omental metastases is majorly dependent on factors secreted by immune and stroma cells to provide an environment that supports ovarian HGSC progression. Clinically relevant pathways within this network represent novel options for therapeutic intervention.
A European pilot study in Dravet Syndrome to delineate what really matters for the patients and families
Authors: Chemaly Nicole , Kuchenbuch Mathieu , Teng Théo , Marie Elodie , D'Onofrio Gianluca , Lo Barco Tommaso , Brambilla Isabella , Flege Silke , Hallet Anne‐Sophie , Nabbout Rima 
Published: November 2021

AbstractWe aimed to identify caregivers' opinions on the outcome measures that matter in clinical trials in individuals with Dravet syndrome (DS). We conducted a prospective European multicenter study based on an 11 closed questions survey developed by the French reference center for rare epilepsies and DS patients’ advocacy groups. Items included questions on seizures and daily life outcomes that a clinical trial on a therapy for individuals with DS should target. Statistical analyses were performed to evaluate the impact of the country of residence and of the patients’ age. The survey was answered by 153 caregivers (68%: France, 28%: Germany, and 24%: Italy) off individuals with DS. Individuals with DS included 86 males (mean age of 11.4 [interquartile: 7‐20.4] years). Families ranked as important almost all the items proposed. However, items related to daily life had the highest rank in all three countries compared to items about seizures (P = 0.02). Increase in individuals’ age was associated with a higher age at diagnosis (ρ = 0.26, P = 0.02), and a lower impact of seizure duration (ρ = −0.25, P = 0.005) and on the need of hospital referral (ρ = −0.26, P = 0.005). These data can help tailor patient‐centered outcome measures in future clinical and real‐life trials for DS.
Ten simple rules for reporting machine learning methods implementation and evaluation on biomedical data
Authors: Seghier Mohamed L. 
Published: November 2021

AbstractThere is a huge discrepancy in how researchers implement, evaluate, and report the performance of a machine learning method for classification or segmentation of biomedical data. Poor reporting and inadequate inferences are, however, not unusual to see in current literature. More specifically, vague aims and scope, missing details about the data, ambiguous preprocessing procedures, lack of clarity regarding the method's implementation, poor validation and testing, invalid comparisons between methods, and the absence of a clear rationale for performance metric choices are making it difficult to draw the right conclusions from many studies in the field. This report suggests 10 guidelines and principles that should be followed when reporting the implementation of a method and the evaluation of its performance in order to make the study transparent, interpretable, replicable, and useful. All stages of data processing and method's performance evaluation should be clearly described, and parameters and metric choices must be justified in order to aid readers in appreciating the performance of the method or in comparing it with other relevant methods. We feel that these guidelines are important for clear scientific communication in the field of biomedical data processing.
Thirty years of fruitful collaborations between a physician and mass spectrometrists in diabetes field
Authors: Lapolla Annunziata 
Published: November 2021

AbstractThe nonenzymatic protein glycation and the subsequent formation of advanced glycation end products is a process involved in the long‐term complications of diabetes. In this context the collaboration, in the last 30 years, between my research group, operating in the DPT of Medicine of Padua University, and the mass spectrometric group, operating in CNR of Padua, are described and discussed. The development of new mass spectrometric techniques has allowed investigation more indepth, starting from the applications on small molecules responsible for the browning observed in the interactions between sugars and proteins, and growing up to intact proteins as albumin, immunoglobulin, hemoglobin, and so forth, with the determination of their glycation levels as well as their glycation sites. This study has helped to clarify the role of advanced glycation end products in the pathogenesis of the chronic complications of diabetes. In particular the results obtained in diabetic nephropathy, diabetic cardiovascular disease and in placenta samples of patients affected by gestational diabetes are described in this review.
Flavonoid‐Like Components of Peanut Stem and Leaf Extract Promote Sleep by Decreasing Neuronal Excitability
Authors: Guo Rui , Shi Ai‐min , Deng Lei , Li Lei , Wang Lie‐chen , Oteng Antwi‐Boasiako , Wei Meng‐ping , Zhao Zhi‐hao , Hooiveld Guido , Zhang Chen , Wang Qiang 
Published: November 2021

ScopePeanut stem and leaf (PSL), a traditional Chinese medicine, is widely used as a dietary supplement to improve sleep quality; however, the underlying mechanism is unclear. Here, the study aims to determine whether active compounds in PSL extract exert their effects by mediating neuronal excitability.Methods and ResultsAqueous PSL extract (500 mg kg−1 BW) increases the duration of total sleep (TS), slow wave sleep (SWS) and rapid eye movement sleep (REMS) in BALB/c mice after 7 and 14 continuous days of intragastric administration. Two PSL extract components with flavonoid‐like structures: 4',7‐di‐O‐methylnaringenin (DMN, 61 µg kg−1 BW) and 2’‐O‐methylisoliquiritigenin (MIL, 12 µg kg−1 BW), show similar effects on sleep in BALB/c mice. Moreover, incubation with DMN (50 µM) and MIL (50 µM) acutely reduces voltage‐gated sodium and potassium currents and suppresses the firing of evoked action potential in mouse cortical neurons, indicating the inhibition on neuronal excitability. Meanwhile, RNA‐seq analysis predicts the potential regulation of voltage‐gated channels, which is according with the molecular docking simulation that both MIL and DMN can bind to voltage gated sodium channels 1.2 (Nav1.2).ConclusionsDMN and MIL are the active ingredients of PSL that improve sleep quality, suggesting that PSL promotes sleep by regulating the excitability of neurons.
Isolation of high crystalline nanocellulose from Mimosa pudica plant fibres with potential in packaging applications
Authors: George Tresa Sunitha , Muhammadaly Sainul Abidh , Parambath Kanoth Bipinbal , Joseph Texin , Chemmarickal Dominic Midhun Dominic , George Neena , Balachandrakurupp Venugopal , John Honey 
Published: November 2021

AbstractMimosa pudica Linn (sensitive plant) is a medicinal plant of family Fabaceae. Its stem is a good source of cellulose. This research work reports isolation of cellulose nanocrystals (CNCs) from M. pudica stem fibres by combined chemical and mechanical treatments. Polyvinyl alcohol (PVA)/starch composites were prepared with incorporation of isolated CNC (1, 3 and 5 wt.%) by solution casting method. Addition of CNC in polymer composites improved its mechanical strength and barrier properties. Isolation process of CNC includes alkali treatment, bleaching and acid hydrolysis followed by homogenization. Chemical composition, thermal stability, structure, surface morphology, crystallinity and size of the freeze‐dried nanocellulose were studied carefully. Fourier transform infrared analysis of raw fibre and CNC showed elimination of non‐cellulosic fragments from untreated M. pudica stem fibre. Electron microscopy analysis and dynamic light scattering (DLS) confirmed the isolation of nanocellulose. X‐ray diffraction showed improvement in the crystallinity of obtained nanocellulose. Increase in crystallinity indicates high Young's modulus of isolated nanocellulose which makes them proper reinforcement material in composites. Polymer composites with the addition of 3 wt.% of CNC showed the highest tensile strength and lowest water vapour transmission rate (WVTR), moisture absorption and oxygen transmission rate (OTR). As M. pudica is an abundant natural resource, it can be utilized as an efficient source of nanocellulose for different applications especially as fillers in sustainable polymer composites for packaging.
Adaptive large neighborhood search for mixed integer programming
Authors: Hendel Gregor 
Published: November 2021

AbstractLarge Neighborhood Search (LNS) heuristics are among the most powerful but also most expensive heuristics for mixed integer programs (MIP). Ideally, a solver adaptively concentrates its limited computational budget by learning which LNS heuristics work best for the MIP problem at hand. To this end, this work introduces Adaptive Large Neighborhood Search (ALNS) for MIP, a primal heuristic that acts as a framework for eight popular LNS heuristics such as Local Branching and Relaxation Induced Neighborhood Search (RINS). We distinguish the available LNS heuristics by their individual search spaces, which we call auxiliary problems. The decision which auxiliary problem should be executed is guided by selection strategies for the multi armed bandit problem, a related optimization problem during which suitable actions have to be chosen to maximize a reward function. In this paper, we propose an LNS-specific reward function to learn to distinguish between the available auxiliary problems based on successful calls and failures. A second, algorithmic enhancement is a generic variable fixing prioritization, which ALNS employs to adjust the subproblem complexity as needed. This is particularly useful for some LNS problems which do not fix variables by themselves. The proposed primal heuristic has been implemented within the MIP solver SCIP. An extensive computational study is conducted to compare different LNS strategies within our ALNS framework on a large set of publicly available MIP instances from the MIPLIB and Coral benchmark sets. The results of this simulation are used to calibrate the parameters of the bandit selection strategies. A second computational experiment shows the computational benefits of the proposed ALNS framework within the MIP solver SCIP.
Vulnerability of fishery-based livelihoods to climate variability and change in a tropical island: insights from small-scale fishers in Seychelles
Authors: Etongo Daniel , Arrisol Lyn 
Published: November 2021

AbstractWhile climate shocks and stressors are not unique to developing countries, their impacts are expected to be most acute here due to limitations in the assets and infrastructure required for adaptation. This study assesses the vulnerability of fishery-based livelihoods to the impacts of climate variability and change across two major islands in Seychelles based on 80 household surveys and three shared dialogue workshops (SDWs) with small-scale fishers. Results showed that the percentage of fishers’ households that depend mainly on fisheries as a source of income was 95% and 97% for Mahe and Praslin respectively with alternative income streams along the fishing value chain such as transportation, fish mongers and processor. Fishers on Mahe Island had a dependency ratio index that was slightly higher than those on Praslin. Overall, fishing households on Mahe showed greater vulnerability on socio-demographic profile index compared to their counterparts on Praslin. However, greater livelihood diversification was recorded for householders on Mahe than Praslin as fishers earned income from tourism-related activities such as guest house, car rental, boat ride, and sales of coconuts as mentioned during the SDWs. Fishers on Mahe struggled to find fish for 3 months during the southeast monsoon season compared to 2 months for those on Praslin given that access is granted to fish in the lagoon during this season. More importantly, the voluntary closure of some fishing zones between the months of November to April on Praslin is a sustainability strategy that witnessed an increase in size and number for both rabbit and parrotfish. Further studies are needed in two key areas as follows: the role of subsidies and sustainable fisheries management, and a value-chain approach to vulnerability of small-scale fishers within the fishery sector in Seychelles.
Epidemiology, clinical features, and outcomes of coronavirus disease among children in Al-Madinah, Saudi Arabia
Authors: Alshengeti Amer , Alahmadi Hatem , Barnawi Ashwaq , Alfuraydi Nouf , Alawfi Abdulsalam , Al-Ahmadi Arwa , Sheikh Mohammad , Almaghthawi Amani , Alnakhli Zahera , Rasheed Raghad , Ibrahim Amany , Sobhi Ahmed , Al Shahrani Dayel , Kordy Faisal 
Published: November 2021

Background and Objective:
Coronavirus disease (COVID-19) is milder with favorable outcomes in children than in adults. However, detailed data regarding COVID-19 in children from Saudi Arabia are scarce. This study aimed to describe COVID-19 among children in Al-Madinah, Saudi Arabia.

Methods:
This retrospective observational study included children <14 years old hospitalized with COVID-19 between May 1, 2020 and July 31, 2020. Clinical data, COVID-19 disease severity, and outcomes were collected. The total number of presenting symptoms and signs were computed by counting those recorded upon presentation. The Kruskal-Wallis non-parametric test was used to compare the number of symptoms and signs across all levels of COVID-19 severity.

Result:
Overall, 106 patients met the inclusion criteria; their ages ranged from 2 weeks to 13 years. Most patients were ≤12 months of age (43.4%). Bronchial asthma was the most common comorbidity (9.4%). Among 99 symptomatic patients, fever was the most common symptom (84.8%); seven patients (7%) were diagnosed with febrile seizure. Most COVID-19 cases were mild (84%); one patient (0.94%) was in critical condition and one patient (0.94%) met the Multisystem Inflammatory Syndrome in children criteria. The mean number of symptoms and signs in children with severe or critical COVID-19 was significantly higher than that in children with mild cases or non-severe pneumonia (P < .001). One patient died owing to COVID-19 (0.94%).

Conclusions:
COVID-19 mortality in children is rare; however, while most children exhibit mild disease with favorable outcomes, children with chronic lung disease may be at higher risk for severe disease.